Multiple sequence alignment - TraesCS1D01G438700

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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 TraesCS1D01G438700 chr1D 100.000 6129 0 0 1 6129 485480862 485474734 0.000000e+00 11319.0
1 TraesCS1D01G438700 chr1D 81.144 2238 276 71 471 2632 485440832 485438665 0.000000e+00 1661.0
2 TraesCS1D01G438700 chr1D 78.732 1467 220 54 3433 4868 485437939 485436534 0.000000e+00 896.0
3 TraesCS1D01G438700 chr1D 81.818 220 30 7 5048 5264 485436530 485436318 6.310000e-40 176.0
4 TraesCS1D01G438700 chr1D 93.269 104 7 0 3321 3424 485477506 485477403 2.960000e-33 154.0
5 TraesCS1D01G438700 chr1D 93.269 104 7 0 3357 3460 485477542 485477439 2.960000e-33 154.0
6 TraesCS1D01G438700 chr1A 95.275 5460 161 35 587 6010 582661320 582655922 0.000000e+00 8564.0
7 TraesCS1D01G438700 chr1A 81.978 2214 273 74 471 2633 582652782 582650644 0.000000e+00 1762.0
8 TraesCS1D01G438700 chr1A 76.220 2254 379 108 2675 4868 582650574 582648418 0.000000e+00 1048.0
9 TraesCS1D01G438700 chr1A 90.847 590 33 5 1 582 582661938 582661362 0.000000e+00 771.0
10 TraesCS1D01G438700 chr1A 90.826 109 7 2 3319 3424 582658548 582658440 6.400000e-30 143.0
11 TraesCS1D01G438700 chr1A 91.667 96 8 0 2861 2956 315265577 315265482 3.850000e-27 134.0
12 TraesCS1D01G438700 chr1A 91.429 70 5 1 3322 3390 582658507 582658438 1.820000e-15 95.3
13 TraesCS1D01G438700 chr1B 94.015 2807 107 29 672 3424 675767788 675764989 0.000000e+00 4196.0
14 TraesCS1D01G438700 chr1B 92.495 2212 89 25 3357 5535 675765092 675762925 0.000000e+00 3094.0
15 TraesCS1D01G438700 chr1B 91.453 585 32 4 5554 6129 675762935 675762360 0.000000e+00 787.0
16 TraesCS1D01G438700 chr1B 77.214 1242 195 43 3433 4656 675743621 675742450 0.000000e+00 645.0
17 TraesCS1D01G438700 chr1B 81.250 480 71 15 2141 2607 675744854 675744381 2.700000e-98 370.0
18 TraesCS1D01G438700 chr1B 74.861 541 64 31 97 583 675768433 675767911 4.880000e-41 180.0
19 TraesCS1D01G438700 chr1B 81.364 220 31 7 5048 5264 675742249 675742037 2.940000e-38 171.0
20 TraesCS1D01G438700 chr1B 91.753 97 7 1 2861 2956 4036446 4036350 3.850000e-27 134.0
21 TraesCS1D01G438700 chr1B 91.667 96 8 0 2861 2956 161324683 161324778 3.850000e-27 134.0
22 TraesCS1D01G438700 chr1B 92.857 70 5 0 3321 3390 675765056 675764987 1.090000e-17 102.0
23 TraesCS1D01G438700 chr3A 89.357 855 74 9 621 1468 38508180 38507336 0.000000e+00 1059.0
24 TraesCS1D01G438700 chr3A 96.610 59 2 0 343 401 38510149 38510091 1.410000e-16 99.0
25 TraesCS1D01G438700 chr7A 88.772 855 76 12 621 1468 643528308 643527467 0.000000e+00 1029.0
26 TraesCS1D01G438700 chr7A 85.401 137 17 3 343 477 643528498 643528363 8.280000e-29 139.0
27 TraesCS1D01G438700 chr5A 88.668 856 77 11 621 1468 565026993 565027836 0.000000e+00 1026.0
28 TraesCS1D01G438700 chr5A 86.131 137 16 3 343 477 565026803 565026938 1.780000e-30 145.0
29 TraesCS1D01G438700 chr5D 81.889 1027 151 21 1039 2046 540004688 540005698 0.000000e+00 833.0
30 TraesCS1D01G438700 chr5B 82.341 991 143 16 1072 2046 255899110 255898136 0.000000e+00 832.0
31 TraesCS1D01G438700 chr6A 80.059 1013 155 27 1040 2030 72845955 72844968 0.000000e+00 708.0
32 TraesCS1D01G438700 chr6A 92.708 96 7 0 2861 2956 426256712 426256617 8.280000e-29 139.0
33 TraesCS1D01G438700 chr4B 80.061 988 136 32 1072 2046 166564841 166563902 0.000000e+00 676.0
34 TraesCS1D01G438700 chr7B 92.708 96 6 1 2861 2956 425378658 425378752 2.980000e-28 137.0
35 TraesCS1D01G438700 chrUn 91.667 96 8 0 2861 2956 303636816 303636721 3.850000e-27 134.0
36 TraesCS1D01G438700 chrUn 91.667 96 8 0 2861 2956 417910145 417910050 3.850000e-27 134.0


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 TraesCS1D01G438700 chr1D 485474734 485480862 6128 True 3875.666667 11319 95.512667 1 6129 3 chr1D.!!$R2 6128
1 TraesCS1D01G438700 chr1D 485436318 485440832 4514 True 911.000000 1661 80.564667 471 5264 3 chr1D.!!$R1 4793
2 TraesCS1D01G438700 chr1A 582648418 582661938 13520 True 2063.883333 8564 87.762500 1 6010 6 chr1A.!!$R2 6009
3 TraesCS1D01G438700 chr1B 675762360 675768433 6073 True 1671.800000 4196 89.136200 97 6129 5 chr1B.!!$R3 6032
4 TraesCS1D01G438700 chr1B 675742037 675744854 2817 True 395.333333 645 79.942667 2141 5264 3 chr1B.!!$R2 3123
5 TraesCS1D01G438700 chr3A 38507336 38510149 2813 True 579.000000 1059 92.983500 343 1468 2 chr3A.!!$R1 1125
6 TraesCS1D01G438700 chr7A 643527467 643528498 1031 True 584.000000 1029 87.086500 343 1468 2 chr7A.!!$R1 1125
7 TraesCS1D01G438700 chr5A 565026803 565027836 1033 False 585.500000 1026 87.399500 343 1468 2 chr5A.!!$F1 1125
8 TraesCS1D01G438700 chr5D 540004688 540005698 1010 False 833.000000 833 81.889000 1039 2046 1 chr5D.!!$F1 1007
9 TraesCS1D01G438700 chr5B 255898136 255899110 974 True 832.000000 832 82.341000 1072 2046 1 chr5B.!!$R1 974
10 TraesCS1D01G438700 chr6A 72844968 72845955 987 True 708.000000 708 80.059000 1040 2030 1 chr6A.!!$R1 990
11 TraesCS1D01G438700 chr4B 166563902 166564841 939 True 676.000000 676 80.061000 1072 2046 1 chr4B.!!$R1 974

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
277 287 1.866601 GCAGTGGGTTTTCATGTTTGC 59.133 47.619 0.0 0.0 0.00 3.68 F
609 2501 1.884579 AGCGACCGTGAGTCTTCTAAA 59.115 47.619 0.0 0.0 43.91 1.85 F
2220 4195 1.659098 GTTACGGAGAATTGCCTCACG 59.341 52.381 0.0 0.0 34.94 4.35 F
2659 4655 3.885901 GCTATCAGGGAGAATGGTTTTCC 59.114 47.826 0.0 0.0 41.14 3.13 F
3503 5602 2.665008 TATCCGCTGCATGTGCCTCC 62.665 60.000 0.0 0.0 41.18 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 4195 1.115467 TCTTCCTCATCCTCTTCGGC 58.885 55.000 0.0 0.0 0.0 5.54 R
2495 4481 3.452264 CCATCCCAGATACAGAACAGACA 59.548 47.826 0.0 0.0 0.0 3.41 R
3446 5545 1.643880 TGTGCATGTCTGTATCAGCG 58.356 50.000 0.0 0.0 0.0 5.18 R
3644 5743 1.753073 GCAGGCAAAGCATCAGGTATT 59.247 47.619 0.0 0.0 0.0 1.89 R
5276 7422 1.006102 AGTTTCCGTCACTGCTCCG 60.006 57.895 0.0 0.0 0.0 4.63 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
117 118 2.743718 CCGGCAGTGGAGTCTGTT 59.256 61.111 0.00 0.00 37.70 3.16
168 169 4.077184 CCGCAGGCCCGTCTGTTA 62.077 66.667 0.00 0.00 46.14 2.41
194 195 3.471244 CTCGGATCGCTCACCCGAC 62.471 68.421 0.00 0.00 46.17 4.79
198 199 2.833582 ATCGCTCACCCGACGGAT 60.834 61.111 17.49 0.00 40.40 4.18
243 244 2.948720 GCGGCAGCCCCTATCCTAG 61.949 68.421 5.63 0.00 37.42 3.02
277 287 1.866601 GCAGTGGGTTTTCATGTTTGC 59.133 47.619 0.00 0.00 0.00 3.68
322 335 3.196463 TCTCTGGAGATTCGTAGACGAC 58.804 50.000 3.85 0.00 39.29 4.34
323 336 3.369157 TCTCTGGAGATTCGTAGACGACA 60.369 47.826 3.85 0.00 39.29 4.35
369 407 8.099364 TGCTTAATTAGAGGTTCTTGTTTCTG 57.901 34.615 0.00 0.00 0.00 3.02
402 443 3.047093 GTGCGTGTTGGTTAATGGAAAC 58.953 45.455 0.00 0.00 0.00 2.78
405 446 4.214545 TGCGTGTTGGTTAATGGAAACTAG 59.785 41.667 0.00 0.00 0.00 2.57
407 2227 4.379082 CGTGTTGGTTAATGGAAACTAGGC 60.379 45.833 0.00 0.00 0.00 3.93
429 2249 2.061028 GTTGCACATTTTAGCACTGCC 58.939 47.619 0.00 0.00 41.05 4.85
560 2404 2.408991 CGATCTGCGTGTCGATTAATGC 60.409 50.000 0.00 0.00 40.11 3.56
609 2501 1.884579 AGCGACCGTGAGTCTTCTAAA 59.115 47.619 0.00 0.00 43.91 1.85
613 2505 2.853003 GACCGTGAGTCTTCTAAATCGC 59.147 50.000 0.00 0.00 42.69 4.58
657 2553 5.014202 GTGGGAATTTAGGTTTTGGCTAGA 58.986 41.667 0.00 0.00 0.00 2.43
744 2660 5.395682 TTTATGTACTGTCTACGCCACTT 57.604 39.130 0.00 0.00 0.00 3.16
786 2702 7.225931 GTGTATAGGAATAGAAATGCGGAACAA 59.774 37.037 0.00 0.00 0.00 2.83
863 2786 5.471556 TGCCATCAATTGACACATTTTCT 57.528 34.783 11.07 0.00 0.00 2.52
948 2874 4.452455 CAGTGAAAGTAAATGGCGTCTTCT 59.548 41.667 0.00 0.00 0.00 2.85
1396 3326 7.593825 ACAGAAACCAATAGATTTTCTTTCCG 58.406 34.615 0.00 0.00 37.46 4.30
1612 3569 7.894708 AGGTACTTACTAGTTCTTCAGAAACC 58.105 38.462 0.00 4.40 31.72 3.27
1626 3583 9.846248 TTCTTCAGAAACCGTATACTAAGTAAC 57.154 33.333 0.56 0.00 0.00 2.50
1787 3749 7.996098 CCTAAAGGTACCTTTTTCTCATCAA 57.004 36.000 37.89 19.63 42.93 2.57
1795 3757 5.324409 ACCTTTTTCTCATCAAGTGGCATA 58.676 37.500 0.00 0.00 0.00 3.14
1808 3770 9.590451 CATCAAGTGGCATAATTCAGTTTATTT 57.410 29.630 0.00 0.00 0.00 1.40
2220 4195 1.659098 GTTACGGAGAATTGCCTCACG 59.341 52.381 0.00 0.00 34.94 4.35
2495 4481 7.266400 GGAGGTCTATTCTCAACGATACTTTT 58.734 38.462 0.00 0.00 33.18 2.27
2498 4484 7.760340 AGGTCTATTCTCAACGATACTTTTGTC 59.240 37.037 0.00 0.00 0.00 3.18
2620 4611 6.208644 GCTAATTTGTTTTGCTCTTCAGTCA 58.791 36.000 0.00 0.00 33.88 3.41
2657 4653 4.228210 TCAGCTATCAGGGAGAATGGTTTT 59.772 41.667 0.00 0.00 0.00 2.43
2658 4654 4.578105 CAGCTATCAGGGAGAATGGTTTTC 59.422 45.833 0.00 0.00 0.00 2.29
2659 4655 3.885901 GCTATCAGGGAGAATGGTTTTCC 59.114 47.826 0.00 0.00 41.14 3.13
2852 4904 7.385894 AGGATGAGCCTCTTTATTCAGTTAT 57.614 36.000 0.00 0.00 46.97 1.89
2853 4905 8.497910 AGGATGAGCCTCTTTATTCAGTTATA 57.502 34.615 0.00 0.00 46.97 0.98
2855 4907 9.732130 GGATGAGCCTCTTTATTCAGTTATAAT 57.268 33.333 0.00 0.00 0.00 1.28
3349 5445 6.293845 GCTGGAGATAAAAATGCTGATACAGG 60.294 42.308 0.00 0.00 31.21 4.00
3355 5451 5.410355 AAAAATGCTGATACAGGCATGTT 57.590 34.783 10.25 0.00 46.70 2.71
3446 5545 4.982916 ACGTCGAATGCTGGAGATAAATAC 59.017 41.667 0.00 0.00 0.00 1.89
3503 5602 2.665008 TATCCGCTGCATGTGCCTCC 62.665 60.000 0.00 0.00 41.18 4.30
3644 5743 5.702670 CACCAGCAAAGATTTTCTCAGTAGA 59.297 40.000 0.00 0.00 0.00 2.59
3856 5977 6.291648 TCTAATGACTTGAGCTCTTCACAT 57.708 37.500 16.19 12.25 34.94 3.21
3921 6045 3.758554 CCCGAACCAGAAATCATTGAGTT 59.241 43.478 0.00 0.00 0.00 3.01
4603 6743 3.858247 ACCGAGTTATCAAGCAGGTAAC 58.142 45.455 4.65 4.65 0.00 2.50
4703 6846 5.690865 AGTTGACACTGGAAAAAGTATCCA 58.309 37.500 0.00 0.00 44.58 3.41
4750 6894 2.362397 TCGTCTCAGATACTTGGGCATC 59.638 50.000 0.00 0.00 0.00 3.91
4880 7024 1.880027 CTACCCAAACCTGTGTTCAGC 59.120 52.381 0.00 0.00 40.09 4.26
4898 7042 4.331968 TCAGCCATCAAAACGTAATCCTT 58.668 39.130 0.00 0.00 0.00 3.36
4929 7073 7.425224 TTGTTTCATTTTCTTTCTAACCCCA 57.575 32.000 0.00 0.00 0.00 4.96
5022 7166 3.364621 GCATGTGTTTTATGCCTTGTTCG 59.635 43.478 0.00 0.00 43.88 3.95
5045 7189 5.105554 CGGTTTCCCAACAATCCATCAAATA 60.106 40.000 0.00 0.00 34.15 1.40
5276 7422 1.405391 GCTTGGAGTTCCTCTCAGCTC 60.405 57.143 0.00 0.00 44.40 4.09
5288 7434 2.505777 CAGCTCGGAGCAGTGACG 60.506 66.667 29.88 8.62 45.56 4.35
5479 7632 3.195661 GGTAAGCCCAGATAACTGTTCG 58.804 50.000 0.00 0.00 42.05 3.95
5504 7657 6.211515 GTTCTAATCCCATGCAATTGATGTC 58.788 40.000 10.34 0.00 0.00 3.06
5510 7663 5.421277 TCCCATGCAATTGATGTCATTTTC 58.579 37.500 10.34 0.00 0.00 2.29
5619 7773 5.606761 TGTATACCTCCTACCCTCCTTTTT 58.393 41.667 0.00 0.00 0.00 1.94
5668 7822 4.922692 TGTTGCTTGTTTTCAGTTGTTCTG 59.077 37.500 0.00 0.00 44.85 3.02
5669 7823 4.782019 TGCTTGTTTTCAGTTGTTCTGT 57.218 36.364 0.00 0.00 43.97 3.41
5670 7824 5.132897 TGCTTGTTTTCAGTTGTTCTGTT 57.867 34.783 0.00 0.00 43.97 3.16
5671 7825 5.537188 TGCTTGTTTTCAGTTGTTCTGTTT 58.463 33.333 0.00 0.00 43.97 2.83
5672 7826 5.633182 TGCTTGTTTTCAGTTGTTCTGTTTC 59.367 36.000 0.00 0.00 43.97 2.78
5673 7827 5.062183 GCTTGTTTTCAGTTGTTCTGTTTCC 59.938 40.000 0.00 0.00 43.97 3.13
5674 7828 5.975693 TGTTTTCAGTTGTTCTGTTTCCT 57.024 34.783 0.00 0.00 43.97 3.36
5675 7829 6.339587 TGTTTTCAGTTGTTCTGTTTCCTT 57.660 33.333 0.00 0.00 43.97 3.36
5676 7830 6.754193 TGTTTTCAGTTGTTCTGTTTCCTTT 58.246 32.000 0.00 0.00 43.97 3.11
5677 7831 7.213678 TGTTTTCAGTTGTTCTGTTTCCTTTT 58.786 30.769 0.00 0.00 43.97 2.27
5678 7832 7.713073 TGTTTTCAGTTGTTCTGTTTCCTTTTT 59.287 29.630 0.00 0.00 43.97 1.94
5679 7833 7.883229 TTTCAGTTGTTCTGTTTCCTTTTTC 57.117 32.000 0.00 0.00 43.97 2.29
5680 7834 6.582677 TCAGTTGTTCTGTTTCCTTTTTCA 57.417 33.333 0.00 0.00 43.97 2.69
5681 7835 6.386654 TCAGTTGTTCTGTTTCCTTTTTCAC 58.613 36.000 0.00 0.00 43.97 3.18
5682 7836 5.286082 CAGTTGTTCTGTTTCCTTTTTCACG 59.714 40.000 0.00 0.00 39.17 4.35
5683 7837 3.765026 TGTTCTGTTTCCTTTTTCACGC 58.235 40.909 0.00 0.00 0.00 5.34
5684 7838 3.191581 TGTTCTGTTTCCTTTTTCACGCA 59.808 39.130 0.00 0.00 0.00 5.24
5748 7912 7.863375 CCGTTTGAATTTGTAGGTTGTTATTCA 59.137 33.333 0.00 0.00 32.07 2.57
5915 8091 4.483476 ACAGTTTTTAACCTGACGATGC 57.517 40.909 0.00 0.00 0.00 3.91
5959 8149 3.053320 GGGAGGGGTTTCTTGATCTTGAT 60.053 47.826 0.00 0.00 0.00 2.57
5960 8150 4.203226 GGAGGGGTTTCTTGATCTTGATC 58.797 47.826 3.82 3.82 0.00 2.92
5961 8151 4.080072 GGAGGGGTTTCTTGATCTTGATCT 60.080 45.833 11.31 0.00 0.00 2.75
5962 8152 5.504853 GAGGGGTTTCTTGATCTTGATCTT 58.495 41.667 11.31 0.00 0.00 2.40
5963 8153 5.259632 AGGGGTTTCTTGATCTTGATCTTG 58.740 41.667 11.31 5.09 0.00 3.02
5964 8154 5.014544 AGGGGTTTCTTGATCTTGATCTTGA 59.985 40.000 11.31 6.98 0.00 3.02
5979 8169 7.449395 TCTTGATCTTGAACCATCATGAACTTT 59.551 33.333 0.00 0.00 41.44 2.66
5984 8174 7.230747 TCTTGAACCATCATGAACTTTCCTTA 58.769 34.615 0.00 0.00 36.95 2.69
5987 8177 6.434028 TGAACCATCATGAACTTTCCTTAAGG 59.566 38.462 15.98 15.98 38.23 2.69
5990 8180 6.011981 ACCATCATGAACTTTCCTTAAGGGTA 60.012 38.462 21.53 7.38 38.23 3.69
5997 8187 6.271391 TGAACTTTCCTTAAGGGTACATCTCA 59.729 38.462 21.53 12.21 38.23 3.27
6001 8191 6.636454 TTCCTTAAGGGTACATCTCATTGT 57.364 37.500 21.53 0.00 36.25 2.71
6018 8216 4.937620 TCATTGTAGTTCTTGACCATGAGC 59.062 41.667 0.00 0.00 0.00 4.26
6046 15349 4.156455 TCCTCATCCATAGAACCTTTGC 57.844 45.455 0.00 0.00 0.00 3.68
6053 15356 5.105567 TCCATAGAACCTTTGCGGATTTA 57.894 39.130 0.00 0.00 36.31 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 1.056700 AGCACCCAACAGACTCCACT 61.057 55.000 0.00 0.00 0.00 4.00
155 156 2.643551 CAATCAATAACAGACGGGCCT 58.356 47.619 0.84 0.00 0.00 5.19
168 169 1.202568 TGAGCGATCCGAGCAATCAAT 60.203 47.619 0.00 0.00 37.01 2.57
198 199 1.570347 AATTAACCAACGCGCTCGCA 61.570 50.000 5.73 0.00 42.06 5.10
238 239 3.723172 CGCCGTACGTAGCTAGGA 58.277 61.111 19.82 1.38 36.87 2.94
277 287 4.605640 TGGAAAAGGCAAAGAGGAATTG 57.394 40.909 0.00 0.00 0.00 2.32
314 327 5.800941 GCATATATAGGCACTTGTCGTCTAC 59.199 44.000 14.26 0.00 41.75 2.59
322 335 3.012518 GGCAGGCATATATAGGCACTTG 58.987 50.000 20.04 15.01 41.75 3.16
323 336 2.915604 AGGCAGGCATATATAGGCACTT 59.084 45.455 20.04 3.80 41.75 3.16
429 2249 3.440173 CCACCCAAGCAAGTTGTATACAG 59.560 47.826 5.56 0.00 33.87 2.74
582 2426 1.134560 GACTCACGGTCGCTAGGAATT 59.865 52.381 0.00 0.00 35.07 2.17
584 2428 2.177950 GACTCACGGTCGCTAGGAA 58.822 57.895 0.00 0.00 35.07 3.36
585 2429 3.900855 GACTCACGGTCGCTAGGA 58.099 61.111 0.00 0.00 35.07 2.94
613 2505 1.024271 AAATCAATGCCCACGATCGG 58.976 50.000 20.98 8.32 0.00 4.18
657 2553 9.410556 GACAGAACTGTAAAATAAAATGTGCAT 57.589 29.630 7.46 0.00 45.05 3.96
679 2576 3.433709 CTGACTTGCGACTATCTGACAG 58.566 50.000 0.00 0.00 0.00 3.51
691 2588 3.125146 TGCTATTTGTAAGCTGACTTGCG 59.875 43.478 2.06 0.00 41.02 4.85
744 2660 6.663523 TCCTATACACAGAGAACATCTTGTGA 59.336 38.462 19.75 10.38 37.53 3.58
863 2786 3.023119 ACAACACCTGCTCATCACAAAA 58.977 40.909 0.00 0.00 0.00 2.44
948 2874 3.754530 TCGTCGCCGGCTTCATCA 61.755 61.111 26.68 0.00 33.95 3.07
957 2883 0.868602 ATCCGTAATTGTCGTCGCCG 60.869 55.000 0.00 0.00 0.00 6.46
1779 3741 5.748402 ACTGAATTATGCCACTTGATGAGA 58.252 37.500 0.00 0.00 0.00 3.27
1780 3742 6.446781 AACTGAATTATGCCACTTGATGAG 57.553 37.500 0.00 0.00 0.00 2.90
1781 3743 6.839124 AAACTGAATTATGCCACTTGATGA 57.161 33.333 0.00 0.00 0.00 2.92
1782 3744 9.590451 AAATAAACTGAATTATGCCACTTGATG 57.410 29.630 0.00 0.00 0.00 3.07
1784 3746 9.421806 CAAAATAAACTGAATTATGCCACTTGA 57.578 29.630 0.00 0.00 0.00 3.02
1787 3749 9.423061 GTTCAAAATAAACTGAATTATGCCACT 57.577 29.630 0.00 0.00 34.26 4.00
1881 3847 2.048127 GGATACCATCCGAGCGGC 60.048 66.667 3.59 0.00 40.13 6.53
2220 4195 1.115467 TCTTCCTCATCCTCTTCGGC 58.885 55.000 0.00 0.00 0.00 5.54
2495 4481 3.452264 CCATCCCAGATACAGAACAGACA 59.548 47.826 0.00 0.00 0.00 3.41
2498 4484 4.760530 TTCCATCCCAGATACAGAACAG 57.239 45.455 0.00 0.00 0.00 3.16
2620 4611 7.604164 CCCTGATAGCTGAACGAATATAACAAT 59.396 37.037 0.00 0.00 0.00 2.71
2657 4653 5.831103 AGAAGAAAAAGGGCATTATGAGGA 58.169 37.500 0.00 0.00 0.00 3.71
2658 4654 6.535963 AAGAAGAAAAAGGGCATTATGAGG 57.464 37.500 0.00 0.00 0.00 3.86
2659 4655 8.193438 CCTTAAGAAGAAAAAGGGCATTATGAG 58.807 37.037 3.36 0.00 36.85 2.90
3255 5351 6.623767 GCTGAAAGGGAGACATGTATGAAAAC 60.624 42.308 0.00 0.00 0.00 2.43
3349 5445 4.906065 TTATCTCCAGCATTCAACATGC 57.094 40.909 0.00 0.00 44.85 4.06
3355 5451 6.536447 TCAGCATATTTATCTCCAGCATTCA 58.464 36.000 0.00 0.00 0.00 2.57
3446 5545 1.643880 TGTGCATGTCTGTATCAGCG 58.356 50.000 0.00 0.00 0.00 5.18
3503 5602 2.662006 TCATCACCTGCTTCTCTTCG 57.338 50.000 0.00 0.00 0.00 3.79
3644 5743 1.753073 GCAGGCAAAGCATCAGGTATT 59.247 47.619 0.00 0.00 0.00 1.89
3741 5851 9.566432 CCTGGATACTAAGCAAATTCTTCTAAT 57.434 33.333 0.00 0.00 37.61 1.73
3832 5953 6.291648 TGTGAAGAGCTCAAGTCATTAGAT 57.708 37.500 17.77 0.00 35.22 1.98
3838 5959 4.251268 CATCATGTGAAGAGCTCAAGTCA 58.749 43.478 17.77 13.17 35.22 3.41
3856 5977 2.079170 TGTCTTGGCCAAAACCATCA 57.921 45.000 19.23 9.15 40.13 3.07
3921 6045 2.570365 GCACCAAGCATGACATCCA 58.430 52.632 0.00 0.00 44.79 3.41
4703 6846 5.564550 AGTTGACACTGCTTATCCATTTCT 58.435 37.500 0.00 0.00 0.00 2.52
4750 6894 7.654520 CCAAAACAGCAGGATTATCAATTATGG 59.345 37.037 0.00 0.00 0.00 2.74
4880 7024 6.851609 TGATCAAAGGATTACGTTTTGATGG 58.148 36.000 23.08 0.00 32.67 3.51
4929 7073 5.819379 CAGCATCTAACATGTAACATGAGGT 59.181 40.000 0.00 0.00 0.00 3.85
5045 7189 8.651589 TCCTCTTGATCATACTTCGGTAATAT 57.348 34.615 0.00 0.00 33.79 1.28
5276 7422 1.006102 AGTTTCCGTCACTGCTCCG 60.006 57.895 0.00 0.00 0.00 4.63
5288 7434 7.339466 AGGTATAACATTCAACCATGAGTTTCC 59.661 37.037 0.00 0.00 36.18 3.13
5385 7536 9.110502 GGGATTCAAGTAGTTCCTTATAACAAG 57.889 37.037 0.00 0.00 0.00 3.16
5436 7589 9.606631 TTACCAAAGCACATTAAGATTTTTGTT 57.393 25.926 0.00 0.00 0.00 2.83
5437 7590 9.260002 CTTACCAAAGCACATTAAGATTTTTGT 57.740 29.630 0.00 0.00 0.00 2.83
5465 7618 5.753921 GGATTAGAACCGAACAGTTATCTGG 59.246 44.000 5.80 0.00 45.14 3.86
5475 7628 2.639065 TGCATGGGATTAGAACCGAAC 58.361 47.619 0.00 0.00 0.00 3.95
5479 7632 5.069516 ACATCAATTGCATGGGATTAGAACC 59.930 40.000 16.89 0.00 0.00 3.62
5723 7887 8.789881 TGAATAACAACCTACAAATTCAAACG 57.210 30.769 0.00 0.00 32.14 3.60
5795 7959 4.894784 AGCGAGAACTCAAAATAACCTGA 58.105 39.130 2.78 0.00 0.00 3.86
5915 8091 1.000955 GACTATACCCAGCGACCATGG 59.999 57.143 11.19 11.19 37.58 3.66
5959 8149 5.634118 AGGAAAGTTCATGATGGTTCAAGA 58.366 37.500 0.00 0.00 34.96 3.02
5960 8150 5.972107 AGGAAAGTTCATGATGGTTCAAG 57.028 39.130 0.00 0.00 34.96 3.02
5961 8151 7.039784 CCTTAAGGAAAGTTCATGATGGTTCAA 60.040 37.037 17.21 0.00 37.39 2.69
5962 8152 6.434028 CCTTAAGGAAAGTTCATGATGGTTCA 59.566 38.462 17.21 0.00 37.39 3.18
5963 8153 6.127619 CCCTTAAGGAAAGTTCATGATGGTTC 60.128 42.308 23.74 0.27 38.24 3.62
5964 8154 5.716703 CCCTTAAGGAAAGTTCATGATGGTT 59.283 40.000 23.74 0.00 38.24 3.67
5979 8169 6.901300 ACTACAATGAGATGTACCCTTAAGGA 59.099 38.462 23.74 2.75 35.54 3.36
5984 8174 6.875972 AGAACTACAATGAGATGTACCCTT 57.124 37.500 0.00 0.00 34.75 3.95
5987 8177 6.535508 GGTCAAGAACTACAATGAGATGTACC 59.464 42.308 0.00 0.00 34.75 3.34
5990 8180 6.114187 TGGTCAAGAACTACAATGAGATGT 57.886 37.500 0.00 0.00 37.32 3.06
5997 8187 4.265073 GGCTCATGGTCAAGAACTACAAT 58.735 43.478 0.00 0.00 0.00 2.71
6001 8191 2.265367 TGGGCTCATGGTCAAGAACTA 58.735 47.619 0.00 0.00 0.00 2.24
6018 8216 4.455606 GTTCTATGGATGAGGAACTTGGG 58.544 47.826 0.00 0.00 41.55 4.12
6053 15356 7.013083 GTGCACCTATCAAGATCTCAAATGAAT 59.987 37.037 5.22 0.00 0.00 2.57
6097 15400 1.134098 CACCCACCTCAAGTCAAGTGT 60.134 52.381 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.