Multiple sequence alignment - TraesCS2D01G408000

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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 TraesCS2D01G408000 chr2D 100.000 4539 0 0 1 4539 523024159 523028697 0.000000e+00 8383
1 TraesCS2D01G408000 chr2D 84.416 154 22 2 1800 1953 43249896 43250047 2.830000e-32 150
2 TraesCS2D01G408000 chr2D 90.566 106 9 1 638 742 79056174 79056279 6.120000e-29 139
3 TraesCS2D01G408000 chr2A 92.750 3145 162 33 790 3906 668239167 668242273 0.000000e+00 4484
4 TraesCS2D01G408000 chr2A 93.262 653 24 9 3895 4539 668242310 668242950 0.000000e+00 944
5 TraesCS2D01G408000 chr2B 92.898 2253 101 20 744 2972 616930844 616933061 0.000000e+00 3219
6 TraesCS2D01G408000 chr2B 92.061 718 37 14 2970 3679 616933184 616933889 0.000000e+00 992
7 TraesCS2D01G408000 chr2B 87.771 875 49 19 3678 4539 616933969 616934798 0.000000e+00 970
8 TraesCS2D01G408000 chr2B 90.080 746 61 7 1 742 616930036 616930772 0.000000e+00 955
9 TraesCS2D01G408000 chr4A 86.364 154 19 2 1800 1953 176616785 176616936 2.810000e-37 167
10 TraesCS2D01G408000 chr1D 86.897 145 13 5 1809 1953 22039360 22039222 1.690000e-34 158
11 TraesCS2D01G408000 chr1D 86.842 114 14 1 630 742 246649980 246650093 4.770000e-25 126
12 TraesCS2D01G408000 chr1B 78.151 238 47 4 366 601 330554346 330554112 3.660000e-31 147
13 TraesCS2D01G408000 chrUn 89.623 106 10 1 638 742 50619984 50619879 2.850000e-27 134
14 TraesCS2D01G408000 chr3D 89.720 107 8 2 638 742 76231000 76231105 2.850000e-27 134
15 TraesCS2D01G408000 chr3B 89.524 105 10 1 638 742 383704473 383704370 1.020000e-26 132
16 TraesCS2D01G408000 chr7D 89.423 104 9 1 638 739 454079084 454079187 3.690000e-26 130
17 TraesCS2D01G408000 chr7D 81.818 154 26 2 371 522 25058276 25058123 1.330000e-25 128
18 TraesCS2D01G408000 chr6B 86.179 123 14 3 623 742 537553831 537553953 3.690000e-26 130
19 TraesCS2D01G408000 chr6D 88.679 106 11 1 638 742 48675904 48676009 1.330000e-25 128


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 TraesCS2D01G408000 chr2D 523024159 523028697 4538 False 8383 8383 100.0000 1 4539 1 chr2D.!!$F3 4538
1 TraesCS2D01G408000 chr2A 668239167 668242950 3783 False 2714 4484 93.0060 790 4539 2 chr2A.!!$F1 3749
2 TraesCS2D01G408000 chr2B 616930036 616934798 4762 False 1534 3219 90.7025 1 4539 4 chr2B.!!$F1 4538

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
51 52 0.250684 TTGTGGTGTCATCCATGCGT 60.251 50.000 0.00 0.0 39.81 5.24 F
626 637 0.317160 TCCTTGTACTGCCGTGACAG 59.683 55.000 0.00 0.0 43.59 3.51 F
938 1022 0.533032 CACGTCCCTCTTCCTCCTTC 59.467 60.000 0.00 0.0 0.00 3.46 F
1572 1676 1.403679 TGCGCTTGTTTTGTGTTAGCT 59.596 42.857 9.73 0.0 0.00 3.32 F
2865 2984 1.041726 CGCAACATTTTGAACGTCCG 58.958 50.000 0.00 0.0 34.24 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1665 1770 3.244033 CTGCAAGTAACTGCTAGCTCT 57.756 47.619 17.23 2.62 43.07 4.09 R
2080 2193 0.029834 AGCAGCTCGCAAAGTTTGTG 59.970 50.000 20.74 20.74 46.13 3.33 R
2865 2984 0.593128 AACACACTTCGCATTCCAGC 59.407 50.000 0.00 0.00 0.00 4.85 R
2874 2993 0.732571 ACCAACTGCAACACACTTCG 59.267 50.000 0.00 0.00 0.00 3.79 R
3750 4084 0.105039 CTCGTAGAACCCCATGAGGC 59.895 60.000 0.00 0.00 34.09 4.70 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
21 22 0.834612 AACTGACTTCGACAACCCCA 59.165 50.000 0.00 0.00 0.00 4.96
42 43 1.255882 GCCCATTGATTGTGGTGTCA 58.744 50.000 0.00 0.00 34.87 3.58
51 52 0.250684 TTGTGGTGTCATCCATGCGT 60.251 50.000 0.00 0.00 39.81 5.24
133 134 1.134818 TCGATGACGGGATTTGTCCAG 60.135 52.381 0.00 0.00 40.21 3.86
140 141 1.139058 CGGGATTTGTCCAGTAGGAGG 59.861 57.143 0.00 0.00 46.92 4.30
144 145 3.370633 GGATTTGTCCAGTAGGAGGGTTC 60.371 52.174 0.00 0.00 46.92 3.62
160 161 2.152016 GGTTCTGCTCCGTTTTTAGCT 58.848 47.619 0.00 0.00 39.53 3.32
161 162 3.332034 GGTTCTGCTCCGTTTTTAGCTA 58.668 45.455 0.00 0.00 39.53 3.32
168 169 4.521256 TGCTCCGTTTTTAGCTATGGTTTT 59.479 37.500 0.00 0.00 39.53 2.43
192 193 1.680207 GGTCGACTAGGGTATGTGTCC 59.320 57.143 16.46 0.00 0.00 4.02
197 198 3.066900 CGACTAGGGTATGTGTCCTTCTG 59.933 52.174 0.00 0.00 34.75 3.02
211 212 1.649664 CTTCTGAGGAAGGCGATGTG 58.350 55.000 0.00 0.00 43.68 3.21
244 245 7.501892 GCTCCTTGAAGATGAAATAAGATCCTT 59.498 37.037 0.00 0.00 0.00 3.36
246 247 7.995488 TCCTTGAAGATGAAATAAGATCCTTCC 59.005 37.037 0.00 0.00 0.00 3.46
284 285 2.352001 CGCGTCTACCATCGTCGG 60.352 66.667 0.00 0.00 0.00 4.79
318 319 2.032799 GGTGTGTTTGTTGCGAATCTCA 59.967 45.455 0.00 0.00 0.00 3.27
319 320 3.304659 GGTGTGTTTGTTGCGAATCTCAT 60.305 43.478 0.00 0.00 0.00 2.90
342 343 1.679153 GATTTGGTTGGTGTTGGTCGT 59.321 47.619 0.00 0.00 0.00 4.34
348 349 2.030628 GGTTGGTGTTGGTCGTTAATGG 60.031 50.000 0.00 0.00 0.00 3.16
362 363 3.377172 CGTTAATGGAACTTGGTGGATCC 59.623 47.826 4.20 4.20 35.74 3.36
363 364 4.340617 GTTAATGGAACTTGGTGGATCCA 58.659 43.478 11.44 11.44 45.42 3.41
364 365 6.881805 CGTTAATGGAACTTGGTGGATCCAG 61.882 48.000 16.81 5.86 44.63 3.86
399 400 7.758076 CGTATGTCTACAGTTTGTATCCTTTCA 59.242 37.037 0.00 0.00 31.66 2.69
403 404 8.375506 TGTCTACAGTTTGTATCCTTTCAATCT 58.624 33.333 0.00 0.00 31.66 2.40
467 468 2.872732 TCTATGGGGCCTTAGTAGACG 58.127 52.381 0.84 0.00 0.00 4.18
473 474 1.408340 GGGCCTTAGTAGACGACTTCC 59.592 57.143 0.84 0.00 39.81 3.46
475 476 1.065251 GCCTTAGTAGACGACTTCCCG 59.935 57.143 0.00 0.00 39.81 5.14
493 494 2.413765 CCCGACTGTGTACTACGACAAG 60.414 54.545 0.00 0.00 0.00 3.16
510 511 0.396556 AAGTTTTGGTTGGCTCCGGT 60.397 50.000 0.00 0.00 0.00 5.28
516 517 2.283529 GGTTGGCTCCGGTGAGAGA 61.284 63.158 7.92 0.00 41.42 3.10
525 526 1.604378 CGGTGAGAGAGGGGCAATT 59.396 57.895 0.00 0.00 0.00 2.32
548 549 1.091771 ATGGCGCATCTTCAACTCGG 61.092 55.000 10.83 0.00 0.00 4.63
567 568 5.217978 TCGGTCCAGTGTTTATAGTTGTT 57.782 39.130 0.00 0.00 0.00 2.83
593 594 4.712476 AGATGGTCTATGAACTTGGATGC 58.288 43.478 0.00 0.00 0.00 3.91
619 630 4.846779 TTTTCATGTTCCTTGTACTGCC 57.153 40.909 0.00 0.00 0.00 4.85
620 631 2.093306 TCATGTTCCTTGTACTGCCG 57.907 50.000 0.00 0.00 0.00 5.69
621 632 1.346395 TCATGTTCCTTGTACTGCCGT 59.654 47.619 0.00 0.00 0.00 5.68
622 633 1.464608 CATGTTCCTTGTACTGCCGTG 59.535 52.381 0.00 0.00 0.00 4.94
623 634 0.753867 TGTTCCTTGTACTGCCGTGA 59.246 50.000 0.00 0.00 0.00 4.35
624 635 1.145803 GTTCCTTGTACTGCCGTGAC 58.854 55.000 0.00 0.00 0.00 3.67
625 636 0.753867 TTCCTTGTACTGCCGTGACA 59.246 50.000 0.00 0.00 0.00 3.58
626 637 0.317160 TCCTTGTACTGCCGTGACAG 59.683 55.000 0.00 0.00 43.59 3.51
640 651 4.443394 GCCGTGACAGTTATAATACTTCCG 59.557 45.833 0.00 0.00 0.00 4.30
641 652 5.585390 CCGTGACAGTTATAATACTTCCGT 58.415 41.667 0.00 0.00 0.00 4.69
649 660 9.444600 ACAGTTATAATACTTCCGTTCACAAAT 57.555 29.630 0.00 0.00 0.00 2.32
700 712 6.998258 GGATGTATACATACGCGTTTTAGT 57.002 37.500 20.78 13.69 36.57 2.24
701 713 6.804232 GGATGTATACATACGCGTTTTAGTG 58.196 40.000 20.78 11.62 36.57 2.74
702 714 6.129009 GGATGTATACATACGCGTTTTAGTGG 60.129 42.308 20.78 0.00 36.57 4.00
764 846 2.951642 TGTTTCTCTTTTCAGTGGCTGG 59.048 45.455 0.00 0.00 31.51 4.85
923 1005 3.677648 CCGTTCTCCGTCCCACGT 61.678 66.667 0.00 0.00 40.58 4.49
936 1020 1.305381 CCACGTCCCTCTTCCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
938 1022 0.533032 CACGTCCCTCTTCCTCCTTC 59.467 60.000 0.00 0.00 0.00 3.46
1120 1215 4.284234 AGAAGAAGAAGAGCAAGAAGAGCT 59.716 41.667 0.00 0.00 46.82 4.09
1367 1462 2.917701 TAATGTTGTTCGGCATGCTG 57.082 45.000 21.02 21.02 0.00 4.41
1403 1498 3.435601 GCTGTAGATTCCATGGACCCAAT 60.436 47.826 15.91 4.92 0.00 3.16
1431 1535 2.435805 GGATGATGTAGCTCCTGTGGAA 59.564 50.000 0.00 0.00 0.00 3.53
1464 1568 3.619979 GCAGATTAGTGCTAGTTGGTGGT 60.620 47.826 0.00 0.00 40.54 4.16
1471 1575 2.806244 GTGCTAGTTGGTGGTTGTAGTG 59.194 50.000 0.00 0.00 0.00 2.74
1486 1590 4.260139 TGTAGTGGAAATACAGCGACAA 57.740 40.909 0.00 0.00 43.12 3.18
1572 1676 1.403679 TGCGCTTGTTTTGTGTTAGCT 59.596 42.857 9.73 0.00 0.00 3.32
1607 1711 6.456501 ACTACCATAGAAACTCACAAGTCAC 58.543 40.000 0.00 0.00 33.48 3.67
1619 1723 5.822519 ACTCACAAGTCACAACATACAACAT 59.177 36.000 0.00 0.00 0.00 2.71
1633 1737 6.966021 ACATACAACATCACAACACTTAACC 58.034 36.000 0.00 0.00 0.00 2.85
1645 1750 5.163794 ACAACACTTAACCTGAGAACAAACG 60.164 40.000 0.00 0.00 0.00 3.60
1653 1758 3.560068 ACCTGAGAACAAACGTTCATCAC 59.440 43.478 0.00 0.01 44.40 3.06
1665 1770 9.161629 ACAAACGTTCATCACTGATTATATGAA 57.838 29.630 0.00 0.00 36.32 2.57
1671 1776 9.920133 GTTCATCACTGATTATATGAAGAGCTA 57.080 33.333 0.00 0.00 38.61 3.32
1678 1783 9.083422 ACTGATTATATGAAGAGCTAGCAGTTA 57.917 33.333 18.83 0.00 0.00 2.24
1807 1920 3.448093 TCACCATATGCAAGGTTTCCA 57.552 42.857 6.15 0.00 35.52 3.53
1919 2032 2.648059 CTGACAAAGGTGATGGGGATC 58.352 52.381 0.00 0.00 0.00 3.36
2025 2138 9.006839 TCATCCATTCATGTTATGCTTAGATTC 57.993 33.333 0.00 0.00 0.00 2.52
2027 2140 7.520798 TCCATTCATGTTATGCTTAGATTCCT 58.479 34.615 0.00 0.00 0.00 3.36
2028 2141 8.659527 TCCATTCATGTTATGCTTAGATTCCTA 58.340 33.333 0.00 0.00 0.00 2.94
2029 2142 9.458727 CCATTCATGTTATGCTTAGATTCCTAT 57.541 33.333 0.00 0.00 0.00 2.57
2050 2163 7.658982 TCCTATAGATGTGATTTCTTCATGTGC 59.341 37.037 0.00 0.00 36.54 4.57
2080 2193 2.372690 CGATACGTATGCAGGCGGC 61.373 63.158 13.97 0.00 45.13 6.53
2185 2298 3.203040 CCAAGGTATTCCACAGGATTCCT 59.797 47.826 0.00 0.00 35.89 3.36
2189 2302 4.292306 AGGTATTCCACAGGATTCCTTGTT 59.708 41.667 1.28 0.00 35.89 2.83
2205 2318 3.944015 CCTTGTTCCCTCTCATGAATCAC 59.056 47.826 0.00 0.00 0.00 3.06
2242 2355 7.907214 ACTACCGATATAAGGCATTGAAATC 57.093 36.000 0.00 0.00 0.00 2.17
2502 2621 7.520451 AAGTATCTGTTTCAAGGGGTTTTAC 57.480 36.000 0.00 0.00 0.00 2.01
2504 2623 3.888583 TCTGTTTCAAGGGGTTTTACGT 58.111 40.909 0.00 0.00 0.00 3.57
2595 2714 7.653647 TGACTTTCTGTTGTTACTTTTGTTGT 58.346 30.769 0.00 0.00 0.00 3.32
2607 2726 7.808856 TGTTACTTTTGTTGTTGTTAACACTCC 59.191 33.333 8.07 0.00 41.97 3.85
2630 2749 7.318141 TCCTCTACCTTGATTACGTTTAGTTG 58.682 38.462 0.00 0.00 0.00 3.16
2636 2755 8.385898 ACCTTGATTACGTTTAGTTGATTCAA 57.614 30.769 0.00 0.00 0.00 2.69
2644 2763 5.934625 ACGTTTAGTTGATTCAATCTCTGCT 59.065 36.000 1.78 0.00 0.00 4.24
2725 2844 2.294074 GGTGAAGTTACACACTTGGCA 58.706 47.619 10.98 0.00 46.53 4.92
2744 2863 4.260194 GGCATTGCCCGAACAAAC 57.740 55.556 17.28 0.00 44.06 2.93
2787 2906 4.594970 TCGGTGGATGATGGTAAACAAAT 58.405 39.130 0.00 0.00 0.00 2.32
2830 2949 4.881920 ACCAACCTTTGCAATATCACAAC 58.118 39.130 0.00 0.00 0.00 3.32
2865 2984 1.041726 CGCAACATTTTGAACGTCCG 58.958 50.000 0.00 0.00 34.24 4.79
2874 2993 1.573829 TTGAACGTCCGCTGGAATGC 61.574 55.000 0.00 0.00 31.38 3.56
2942 3062 5.988561 GCCATCATTTAAAGTTTCACACCAA 59.011 36.000 0.00 0.00 0.00 3.67
3109 3356 1.499949 CCGCGGTGTTGTATTGTGG 59.500 57.895 19.50 0.00 0.00 4.17
3189 3436 1.870901 GACTAACTGTACGGGCGCG 60.871 63.158 22.69 22.69 0.00 6.86
3193 3441 2.265073 TAACTGTACGGGCGCGGTAC 62.265 60.000 27.52 24.94 39.51 3.34
3202 3450 1.514553 GGCGCGGTACCTTACTCTT 59.485 57.895 8.83 0.00 0.00 2.85
3294 3544 2.160417 GCTGGTAGTTGTGCAGTTCATC 59.840 50.000 0.00 0.00 0.00 2.92
3327 3577 5.902981 TCGTGTTTACTTGTTTATTTGTCGC 59.097 36.000 0.00 0.00 0.00 5.19
3331 3581 6.689241 TGTTTACTTGTTTATTTGTCGCTGTG 59.311 34.615 0.00 0.00 0.00 3.66
3332 3582 4.893424 ACTTGTTTATTTGTCGCTGTGT 57.107 36.364 0.00 0.00 0.00 3.72
3336 3586 6.689669 ACTTGTTTATTTGTCGCTGTGTTTAC 59.310 34.615 0.00 0.00 0.00 2.01
3469 3722 0.600057 AAGCAAAGCAACCTAGCAGC 59.400 50.000 0.00 0.00 36.85 5.25
3480 3733 1.299014 CTAGCAGCGGCGAGAAGAG 60.299 63.158 12.98 0.00 44.53 2.85
3482 3735 2.490217 GCAGCGGCGAGAAGAGTA 59.510 61.111 12.98 0.00 0.00 2.59
3655 3908 7.168972 GCAATGAGAATGTATCTGTCTACACTC 59.831 40.741 0.00 0.00 38.96 3.51
3693 4027 9.224267 AGATGTCATATAATTTGAAATCTCCGG 57.776 33.333 5.73 0.00 42.09 5.14
3695 4029 8.746052 TGTCATATAATTTGAAATCTCCGGTT 57.254 30.769 0.00 0.00 0.00 4.44
3698 4032 9.184523 TCATATAATTTGAAATCTCCGGTTGTT 57.815 29.630 0.00 0.00 0.00 2.83
3711 4045 2.069273 CGGTTGTTCATCAGTCCTCAC 58.931 52.381 0.00 0.00 0.00 3.51
3716 4050 3.154710 TGTTCATCAGTCCTCACTACGT 58.845 45.455 0.00 0.00 0.00 3.57
3737 4071 7.266922 ACGTTATGGTTACACAGAATTTGTT 57.733 32.000 0.00 0.00 38.16 2.83
3745 4079 9.733556 TGGTTACACAGAATTTGTTATATGACT 57.266 29.630 0.00 0.00 38.16 3.41
3751 4085 9.669353 CACAGAATTTGTTATATGACTTATGGC 57.331 33.333 0.00 0.00 38.16 4.40
3752 4086 8.850156 ACAGAATTTGTTATATGACTTATGGCC 58.150 33.333 0.00 0.00 36.31 5.36
3976 4374 3.257561 CATGGCTCTCGCGAACGG 61.258 66.667 11.33 4.17 40.63 4.44
3977 4375 3.449227 ATGGCTCTCGCGAACGGA 61.449 61.111 11.33 2.88 40.63 4.69
3978 4376 3.701604 ATGGCTCTCGCGAACGGAC 62.702 63.158 11.33 5.86 40.63 4.79
4023 4421 1.539124 AACCGCCCCTCTTCTTCCT 60.539 57.895 0.00 0.00 0.00 3.36
4024 4422 1.554583 AACCGCCCCTCTTCTTCCTC 61.555 60.000 0.00 0.00 0.00 3.71
4025 4423 2.736826 CCGCCCCTCTTCTTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
4044 4442 2.102161 CCTAAAACGGCGGCATGC 59.898 61.111 13.24 9.90 45.38 4.06
4249 4647 4.570663 GGCCCTGGATCGACGACG 62.571 72.222 0.00 0.00 41.26 5.12
4302 4702 6.182627 TGATTGTTGATAATGAGGTGCTCTT 58.817 36.000 0.00 0.00 0.00 2.85
4310 4710 1.679139 TGAGGTGCTCTTGTTGTTGG 58.321 50.000 0.00 0.00 0.00 3.77
4320 4720 3.321497 TCTTGTTGTTGGTGTTGTTTGC 58.679 40.909 0.00 0.00 0.00 3.68
4329 4729 0.498095 GTGTTGTTTGCGTGATTGCG 59.502 50.000 0.00 0.00 37.81 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.393077 CTGGGGTTGTCGAAGTCAGT 59.607 55.000 0.00 0.00 0.00 3.41
15 16 0.618393 CAATCAATGGGCCTGGGGTT 60.618 55.000 4.53 0.00 0.00 4.11
18 19 1.332144 CCACAATCAATGGGCCTGGG 61.332 60.000 4.53 0.00 33.18 4.45
21 22 0.114954 ACACCACAATCAATGGGCCT 59.885 50.000 4.53 0.00 41.97 5.19
27 28 3.131577 GCATGGATGACACCACAATCAAT 59.868 43.478 0.00 0.00 43.03 2.57
51 52 0.691078 GACCATAGCCTCCTCCACCA 60.691 60.000 0.00 0.00 0.00 4.17
53 54 1.043673 ACGACCATAGCCTCCTCCAC 61.044 60.000 0.00 0.00 0.00 4.02
133 134 0.971447 ACGGAGCAGAACCCTCCTAC 60.971 60.000 5.96 0.00 45.37 3.18
140 141 2.152016 AGCTAAAAACGGAGCAGAACC 58.848 47.619 0.00 0.00 41.36 3.62
144 145 3.270877 ACCATAGCTAAAAACGGAGCAG 58.729 45.455 0.00 0.00 41.36 4.24
160 161 4.081309 CCCTAGTCGACCTCAAAAACCATA 60.081 45.833 13.01 0.00 0.00 2.74
161 162 3.307480 CCCTAGTCGACCTCAAAAACCAT 60.307 47.826 13.01 0.00 0.00 3.55
168 169 3.021695 CACATACCCTAGTCGACCTCAA 58.978 50.000 13.01 0.00 0.00 3.02
197 198 2.650813 ATCGCCACATCGCCTTCCTC 62.651 60.000 0.00 0.00 0.00 3.71
211 212 0.179034 ATCTTCAAGGAGCCATCGCC 60.179 55.000 0.00 0.00 34.57 5.54
266 267 3.017314 CGACGATGGTAGACGCGC 61.017 66.667 5.73 0.00 0.00 6.86
304 305 2.488204 TCCCATGAGATTCGCAACAA 57.512 45.000 0.00 0.00 0.00 2.83
318 319 1.977129 CCAACACCAACCAAATCCCAT 59.023 47.619 0.00 0.00 0.00 4.00
319 320 1.343478 ACCAACACCAACCAAATCCCA 60.343 47.619 0.00 0.00 0.00 4.37
342 343 4.666412 TGGATCCACCAAGTTCCATTAA 57.334 40.909 11.44 0.00 46.75 1.40
362 363 4.966249 TGTAGACATACGAACGAAGACTG 58.034 43.478 0.14 0.00 34.39 3.51
363 364 4.694509 ACTGTAGACATACGAACGAAGACT 59.305 41.667 0.14 0.00 34.39 3.24
364 365 4.967437 ACTGTAGACATACGAACGAAGAC 58.033 43.478 0.14 0.00 34.39 3.01
365 366 5.618056 AACTGTAGACATACGAACGAAGA 57.382 39.130 0.14 0.00 34.39 2.87
366 367 5.628193 ACAAACTGTAGACATACGAACGAAG 59.372 40.000 0.14 0.00 34.39 3.79
367 368 5.522456 ACAAACTGTAGACATACGAACGAA 58.478 37.500 0.14 0.00 34.39 3.85
368 369 5.112220 ACAAACTGTAGACATACGAACGA 57.888 39.130 0.14 0.00 34.39 3.85
399 400 6.568462 CGTGCCAATGAAAAGAAGTGTAGATT 60.568 38.462 0.00 0.00 0.00 2.40
403 404 3.252215 CCGTGCCAATGAAAAGAAGTGTA 59.748 43.478 0.00 0.00 0.00 2.90
434 435 2.364632 CCCATAGAACCAACGCATCAA 58.635 47.619 0.00 0.00 0.00 2.57
467 468 2.159599 CGTAGTACACAGTCGGGAAGTC 60.160 54.545 0.38 0.00 0.00 3.01
473 474 2.225019 ACTTGTCGTAGTACACAGTCGG 59.775 50.000 0.38 0.62 0.00 4.79
475 476 5.051240 CCAAAACTTGTCGTAGTACACAGTC 60.051 44.000 0.38 0.00 0.00 3.51
493 494 1.104577 TCACCGGAGCCAACCAAAAC 61.105 55.000 9.46 0.00 0.00 2.43
510 511 3.073503 CCATCATAATTGCCCCTCTCTCA 59.926 47.826 0.00 0.00 0.00 3.27
516 517 1.181098 GCGCCATCATAATTGCCCCT 61.181 55.000 0.00 0.00 0.00 4.79
525 526 3.133691 GAGTTGAAGATGCGCCATCATA 58.866 45.455 17.94 0.00 42.72 2.15
548 549 8.997621 TCTATCAACAACTATAAACACTGGAC 57.002 34.615 0.00 0.00 0.00 4.02
567 568 7.674120 CATCCAAGTTCATAGACCATCTATCA 58.326 38.462 0.00 0.00 37.58 2.15
602 613 1.464608 CACGGCAGTACAAGGAACATG 59.535 52.381 0.00 0.00 0.00 3.21
666 677 8.160342 GCGTATGTATACATCCGATACAAAAAG 58.840 37.037 28.50 9.82 41.76 2.27
670 682 5.106594 ACGCGTATGTATACATCCGATACAA 60.107 40.000 28.50 5.90 41.76 2.41
673 685 5.550232 AACGCGTATGTATACATCCGATA 57.450 39.130 28.50 7.93 37.81 2.92
677 689 6.129009 CCACTAAAACGCGTATGTATACATCC 60.129 42.308 21.49 9.97 37.76 3.51
690 702 2.223294 TGAACAAACCCACTAAAACGCG 60.223 45.455 3.53 3.53 0.00 6.01
691 703 3.110358 GTGAACAAACCCACTAAAACGC 58.890 45.455 0.00 0.00 0.00 4.84
692 704 4.095185 TGAGTGAACAAACCCACTAAAACG 59.905 41.667 0.00 0.00 43.02 3.60
693 705 5.570234 TGAGTGAACAAACCCACTAAAAC 57.430 39.130 0.00 0.00 43.02 2.43
697 709 5.441500 TGAAATGAGTGAACAAACCCACTA 58.558 37.500 0.00 0.00 43.02 2.74
698 710 4.277476 TGAAATGAGTGAACAAACCCACT 58.723 39.130 0.00 0.00 45.37 4.00
699 711 4.097892 ACTGAAATGAGTGAACAAACCCAC 59.902 41.667 0.00 0.00 0.00 4.61
700 712 4.277476 ACTGAAATGAGTGAACAAACCCA 58.723 39.130 0.00 0.00 0.00 4.51
701 713 4.261614 GGACTGAAATGAGTGAACAAACCC 60.262 45.833 0.00 0.00 0.00 4.11
702 714 4.338118 TGGACTGAAATGAGTGAACAAACC 59.662 41.667 0.00 0.00 0.00 3.27
738 750 5.127682 AGCCACTGAAAAGAGAAACAACAAT 59.872 36.000 0.00 0.00 0.00 2.71
742 754 3.381272 CCAGCCACTGAAAAGAGAAACAA 59.619 43.478 0.00 0.00 32.44 2.83
923 1005 1.396594 GGGGAAGGAGGAAGAGGGA 59.603 63.158 0.00 0.00 0.00 4.20
1120 1215 3.632145 GCCTTCTTCACCTTCTTGAACAA 59.368 43.478 0.00 0.00 32.02 2.83
1403 1498 3.906218 AGGAGCTACATCATCCAATGCTA 59.094 43.478 0.00 0.00 35.45 3.49
1431 1535 6.192970 AGCACTAATCTGCTATAAACCCAT 57.807 37.500 0.00 0.00 46.03 4.00
1464 1568 4.260139 TGTCGCTGTATTTCCACTACAA 57.740 40.909 0.00 0.00 0.00 2.41
1471 1575 4.742438 TCACTTTTGTCGCTGTATTTCC 57.258 40.909 0.00 0.00 0.00 3.13
1486 1590 7.015584 AGGCTAAAGGAAAATCAACATCACTTT 59.984 33.333 0.00 0.00 0.00 2.66
1607 1711 7.378461 GGTTAAGTGTTGTGATGTTGTATGTTG 59.622 37.037 0.00 0.00 0.00 3.33
1619 1723 5.092554 TGTTCTCAGGTTAAGTGTTGTGA 57.907 39.130 0.00 0.00 0.00 3.58
1645 1750 8.830201 AGCTCTTCATATAATCAGTGATGAAC 57.170 34.615 6.34 0.00 34.27 3.18
1653 1758 9.352784 GTAACTGCTAGCTCTTCATATAATCAG 57.647 37.037 17.23 1.78 0.00 2.90
1665 1770 3.244033 CTGCAAGTAACTGCTAGCTCT 57.756 47.619 17.23 2.62 43.07 4.09
1765 1878 8.739972 GGTGAAATCAGACATTAAACCAACTAT 58.260 33.333 0.00 0.00 0.00 2.12
1919 2032 7.335422 ACCACAGTTATAGCAGAATTTCTTCAG 59.665 37.037 0.00 0.00 33.56 3.02
2025 2138 7.660617 AGCACATGAAGAAATCACATCTATAGG 59.339 37.037 0.00 0.00 41.93 2.57
2027 2140 8.969260 AAGCACATGAAGAAATCACATCTATA 57.031 30.769 0.00 0.00 41.93 1.31
2028 2141 7.876936 AAGCACATGAAGAAATCACATCTAT 57.123 32.000 0.00 0.00 41.93 1.98
2029 2142 8.668353 GTTAAGCACATGAAGAAATCACATCTA 58.332 33.333 0.00 0.00 41.93 1.98
2050 2163 8.373256 CCTGCATACGTATCGAATAATGTTAAG 58.627 37.037 4.74 0.00 0.00 1.85
2057 2170 3.239254 CGCCTGCATACGTATCGAATAA 58.761 45.455 4.74 0.00 0.00 1.40
2080 2193 0.029834 AGCAGCTCGCAAAGTTTGTG 59.970 50.000 20.74 20.74 46.13 3.33
2185 2298 3.260632 TCGTGATTCATGAGAGGGAACAA 59.739 43.478 4.42 0.00 0.00 2.83
2189 2302 2.166459 GTGTCGTGATTCATGAGAGGGA 59.834 50.000 8.84 0.00 29.40 4.20
2205 2318 4.871993 ATCGGTAGTAGTAGTTGTGTCG 57.128 45.455 0.00 0.00 0.00 4.35
2483 2601 3.888583 ACGTAAAACCCCTTGAAACAGA 58.111 40.909 0.00 0.00 0.00 3.41
2555 2674 7.875971 ACAGAAAGTCAAAGCTATAAACAAGG 58.124 34.615 0.00 0.00 0.00 3.61
2595 2714 6.681729 ATCAAGGTAGAGGAGTGTTAACAA 57.318 37.500 10.51 0.00 0.00 2.83
2607 2726 8.928270 ATCAACTAAACGTAATCAAGGTAGAG 57.072 34.615 0.00 0.00 0.00 2.43
2671 2790 5.650703 ACAGCAACCACCCTAACATTAATAC 59.349 40.000 0.00 0.00 0.00 1.89
2744 2863 1.659098 GGATTCGAAGTACTGTTGCCG 59.341 52.381 3.35 0.00 0.00 5.69
2830 2949 3.467043 GCGAATGCATGCATGGTAG 57.533 52.632 32.79 22.88 42.15 3.18
2865 2984 0.593128 AACACACTTCGCATTCCAGC 59.407 50.000 0.00 0.00 0.00 4.85
2874 2993 0.732571 ACCAACTGCAACACACTTCG 59.267 50.000 0.00 0.00 0.00 3.79
3109 3356 1.065126 ACCTATCCAAAGCCTCTGCAC 60.065 52.381 0.00 0.00 41.13 4.57
3189 3436 9.668497 ATTAGATTTTGTCAAGAGTAAGGTACC 57.332 33.333 2.73 2.73 0.00 3.34
3294 3544 5.418310 ACAAGTAAACACGAATTCCTGTG 57.582 39.130 10.32 10.56 41.81 3.66
3331 3581 9.503399 CCCTCCATATTCATACCTAAAGTAAAC 57.497 37.037 0.00 0.00 33.70 2.01
3332 3582 9.455144 TCCCTCCATATTCATACCTAAAGTAAA 57.545 33.333 0.00 0.00 33.70 2.01
3336 3586 7.456269 AGTCTCCCTCCATATTCATACCTAAAG 59.544 40.741 0.00 0.00 0.00 1.85
3446 3699 4.619160 GCTGCTAGGTTGCTTTGCTTTAAT 60.619 41.667 0.00 0.00 0.00 1.40
3447 3700 3.305335 GCTGCTAGGTTGCTTTGCTTTAA 60.305 43.478 0.00 0.00 0.00 1.52
3448 3701 2.228822 GCTGCTAGGTTGCTTTGCTTTA 59.771 45.455 0.00 0.00 0.00 1.85
3469 3722 1.226717 GCTGGTACTCTTCTCGCCG 60.227 63.158 0.00 0.00 0.00 6.46
3480 3733 4.134563 TCCTTTTGACTTTGAGCTGGTAC 58.865 43.478 0.00 0.00 0.00 3.34
3482 3735 3.297134 TCCTTTTGACTTTGAGCTGGT 57.703 42.857 0.00 0.00 0.00 4.00
3655 3908 7.728847 TTATATGACATCTTTCCAACATCGG 57.271 36.000 0.00 0.00 0.00 4.18
3688 4022 1.276421 AGGACTGATGAACAACCGGAG 59.724 52.381 9.46 1.96 32.92 4.63
3691 4025 2.069273 GTGAGGACTGATGAACAACCG 58.931 52.381 0.00 0.00 32.92 4.44
3693 4027 3.921021 CGTAGTGAGGACTGATGAACAAC 59.079 47.826 0.00 0.00 33.21 3.32
3695 4029 3.154710 ACGTAGTGAGGACTGATGAACA 58.845 45.455 0.00 0.00 42.51 3.18
3698 4032 4.338400 CCATAACGTAGTGAGGACTGATGA 59.662 45.833 0.00 0.00 45.00 2.92
3711 4045 8.025243 ACAAATTCTGTGTAACCATAACGTAG 57.975 34.615 0.00 0.00 36.69 3.51
3737 4071 4.474651 CCCCATGAGGCCATAAGTCATATA 59.525 45.833 5.01 0.00 29.64 0.86
3742 4076 0.846693 ACCCCATGAGGCCATAAGTC 59.153 55.000 5.01 0.00 0.00 3.01
3744 4078 1.496429 AGAACCCCATGAGGCCATAAG 59.504 52.381 5.01 0.00 0.00 1.73
3745 4079 1.607225 AGAACCCCATGAGGCCATAA 58.393 50.000 5.01 0.00 0.00 1.90
3746 4080 2.054799 GTAGAACCCCATGAGGCCATA 58.945 52.381 5.01 0.00 0.00 2.74
3747 4081 0.846693 GTAGAACCCCATGAGGCCAT 59.153 55.000 5.01 0.00 0.00 4.40
3748 4082 1.622607 CGTAGAACCCCATGAGGCCA 61.623 60.000 5.01 0.00 0.00 5.36
3749 4083 1.146263 CGTAGAACCCCATGAGGCC 59.854 63.158 0.00 0.00 0.00 5.19
3750 4084 0.105039 CTCGTAGAACCCCATGAGGC 59.895 60.000 0.00 0.00 34.09 4.70
3751 4085 0.105039 GCTCGTAGAACCCCATGAGG 59.895 60.000 0.00 0.00 34.09 3.86
3752 4086 0.249073 CGCTCGTAGAACCCCATGAG 60.249 60.000 0.00 0.00 34.09 2.90
3788 4122 1.219646 CAAACCAACAATGCAGCCAC 58.780 50.000 0.00 0.00 0.00 5.01
3795 4129 4.554586 CGAATCGATGACAAACCAACAATG 59.445 41.667 0.00 0.00 0.00 2.82
3859 4193 8.785946 AGCACAGCAGCATTTTTATTTTATTTT 58.214 25.926 0.00 0.00 36.85 1.82
3860 4194 8.231837 CAGCACAGCAGCATTTTTATTTTATTT 58.768 29.630 0.00 0.00 36.85 1.40
3861 4195 7.388500 ACAGCACAGCAGCATTTTTATTTTATT 59.612 29.630 0.00 0.00 36.85 1.40
3862 4196 6.875195 ACAGCACAGCAGCATTTTTATTTTAT 59.125 30.769 0.00 0.00 36.85 1.40
3868 4202 2.350676 CGACAGCACAGCAGCATTTTTA 60.351 45.455 0.00 0.00 36.85 1.52
4025 4423 1.721487 CATGCCGCCGTTTTAGGAG 59.279 57.895 0.00 0.00 0.00 3.69
4045 4443 1.830847 ATCGCATGCATGGTGCCAT 60.831 52.632 27.34 6.94 44.23 4.40
4046 4444 2.440613 ATCGCATGCATGGTGCCA 60.441 55.556 27.34 4.55 44.23 4.92
4047 4445 2.027024 CATCGCATGCATGGTGCC 59.973 61.111 27.34 10.17 44.23 5.01
4302 4702 1.000163 ACGCAAACAACACCAACAACA 60.000 42.857 0.00 0.00 0.00 3.33
4310 4710 0.498095 CGCAATCACGCAAACAACAC 59.502 50.000 0.00 0.00 0.00 3.32
4329 4729 3.093278 CCGAGTTCGCCTTGCATC 58.907 61.111 0.00 0.00 38.18 3.91


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

AutoCloner maintained by Alex Coulton.