Multiple sequence alignment - TraesCS3D01G353300

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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 TraesCS3D01G353300 chr3D 100.000 5640 0 0 808 6447 464045897 464040258 0.000000e+00 10416
1 TraesCS3D01G353300 chr3D 100.000 419 0 0 1 419 464046704 464046286 0.000000e+00 774
2 TraesCS3D01G353300 chr3A 94.014 2623 85 18 3517 6126 607058262 607055699 0.000000e+00 3908
3 TraesCS3D01G353300 chr3A 90.291 2678 162 48 808 3433 607061226 607058595 0.000000e+00 3415
4 TraesCS3D01G353300 chr3A 94.186 344 19 1 6105 6447 607055679 607055336 2.060000e-144 523
5 TraesCS3D01G353300 chr3A 85.253 434 22 25 1 419 607061641 607061235 6.020000e-110 409
6 TraesCS3D01G353300 chr3B 97.385 1759 35 6 2624 4381 617411873 617410125 0.000000e+00 2983
7 TraesCS3D01G353300 chr3B 93.393 1786 75 15 4374 6125 617410099 617408323 0.000000e+00 2604
8 TraesCS3D01G353300 chr3B 89.757 1318 80 22 808 2075 617413953 617412641 0.000000e+00 1635
9 TraesCS3D01G353300 chr3B 91.065 526 34 6 2099 2623 617412645 617412132 0.000000e+00 699
10 TraesCS3D01G353300 chr3B 96.831 284 8 1 6118 6400 617408288 617408005 2.100000e-129 473
11 TraesCS3D01G353300 chr3B 86.170 376 7 10 59 413 617414314 617413963 1.320000e-96 364
12 TraesCS3D01G353300 chr3B 95.238 84 3 1 6364 6447 617408007 617407925 1.460000e-26 132
13 TraesCS3D01G353300 chr1A 84.332 217 34 0 3744 3960 481925221 481925437 5.060000e-51 213
14 TraesCS3D01G353300 chr1A 82.540 189 29 4 4387 4572 481929082 481929269 5.170000e-36 163
15 TraesCS3D01G353300 chr1A 93.750 80 4 1 2762 2840 481923826 481923905 1.140000e-22 119
16 TraesCS3D01G353300 chr1D 82.805 221 37 1 3740 3960 381307915 381308134 5.100000e-46 196
17 TraesCS3D01G353300 chr1D 82.540 189 29 4 4387 4572 381310485 381310672 5.170000e-36 163
18 TraesCS3D01G353300 chr1D 92.857 84 5 1 2765 2847 381306401 381306484 3.160000e-23 121
19 TraesCS3D01G353300 chr1B 81.951 205 37 0 4076 4280 511447630 511447834 2.390000e-39 174
20 TraesCS3D01G353300 chr1B 81.188 202 32 6 4387 4584 511447917 511448116 2.410000e-34 158
21 TraesCS3D01G353300 chr1B 94.737 76 4 0 2765 2840 511443955 511444030 1.140000e-22 119


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 TraesCS3D01G353300 chr3D 464040258 464046704 6446 True 5595.00 10416 100.000000 1 6447 2 chr3D.!!$R1 6446
1 TraesCS3D01G353300 chr3A 607055336 607061641 6305 True 2063.75 3908 90.936000 1 6447 4 chr3A.!!$R1 6446
2 TraesCS3D01G353300 chr3B 617407925 617414314 6389 True 1270.00 2983 92.834143 59 6447 7 chr3B.!!$R1 6388

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
138 148 0.109342 AAGCAGTCCACCAGTCCAAG 59.891 55.000 0.00 0.00 0.00 3.61 F
948 1001 1.376466 GCAAAGCTCCCTCTGACCA 59.624 57.895 0.00 0.00 0.00 4.02 F
1499 1594 1.004277 GGTGACGAGCGAGTTCTGTG 61.004 60.000 0.00 0.00 0.00 3.66 F
1547 1642 1.079796 TGGGTGGTTGGATCATTGGA 58.920 50.000 0.00 0.00 0.00 3.53 F
1606 1701 1.454201 TGTCGTTTTGTGCTTGTGGA 58.546 45.000 0.00 0.00 0.00 4.02 F
2598 2735 0.674534 GCCCTGGTATGAGTCCTACG 59.325 60.000 0.00 0.00 0.00 3.51 F
3554 4240 0.896923 TGTTTCATGCATGGGCCTTC 59.103 50.000 25.97 11.37 40.13 3.46 F
4434 5154 0.040958 CTTGCTGTGTCTTTGACGGC 60.041 55.000 0.00 0.00 44.61 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1512 0.597377 CAAACGCAAACTTCCAGCCC 60.597 55.000 0.00 0.0 0.00 5.19 R
1910 2022 1.795768 AGCCAATATGTGATACCGCG 58.204 50.000 0.00 0.0 0.00 6.46 R
2503 2640 3.052745 GTGCAGAAAAACAAAGCTAGGC 58.947 45.455 0.00 0.0 0.00 3.93 R
2596 2733 4.092816 CGTTTTGCAACTGTAACTTTCGT 58.907 39.130 0.00 0.0 0.00 3.85 R
2606 2744 4.209452 AGTACATGTCGTTTTGCAACTG 57.791 40.909 0.00 0.0 0.00 3.16 R
3960 4646 3.371898 GCTGCAATAACCAAATTGGCTTC 59.628 43.478 12.67 0.0 42.67 3.86 R
4888 5608 0.668535 AAACCTTGAACGGAGCAAGC 59.331 50.000 8.19 0.0 41.00 4.01 R
6392 7193 2.181954 AAGCAGCAAGAGGACTGAAG 57.818 50.000 0.00 0.0 35.90 3.02 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
47 48 0.884704 GTCGTGGAGAGGCAAGCAAA 60.885 55.000 0.00 0.00 0.00 3.68
48 49 0.603707 TCGTGGAGAGGCAAGCAAAG 60.604 55.000 0.00 0.00 0.00 2.77
49 50 1.583477 GTGGAGAGGCAAGCAAAGC 59.417 57.895 0.00 0.00 0.00 3.51
53 54 0.243095 GAGAGGCAAGCAAAGCAAGG 59.757 55.000 0.00 0.00 0.00 3.61
54 55 1.373873 GAGGCAAGCAAAGCAAGGC 60.374 57.895 0.00 0.00 0.00 4.35
55 56 2.091102 GAGGCAAGCAAAGCAAGGCA 62.091 55.000 9.19 0.00 33.99 4.75
138 148 0.109342 AAGCAGTCCACCAGTCCAAG 59.891 55.000 0.00 0.00 0.00 3.61
186 196 3.021695 ACTTCGACGTCATTCTATCCCA 58.978 45.455 17.16 0.00 0.00 4.37
198 208 2.738213 CTATCCCATCCCGTGCTGCC 62.738 65.000 0.00 0.00 0.00 4.85
287 306 4.778143 CCGCTTCCCTTCCCACGG 62.778 72.222 0.00 0.00 0.00 4.94
288 307 3.702048 CGCTTCCCTTCCCACGGA 61.702 66.667 0.00 0.00 0.00 4.69
329 348 3.406764 CTCACTCCAAAACCTCTCTTGG 58.593 50.000 0.00 0.00 43.00 3.61
945 977 1.681666 CTGGCAAAGCTCCCTCTGA 59.318 57.895 0.00 0.00 0.00 3.27
948 1001 1.376466 GCAAAGCTCCCTCTGACCA 59.624 57.895 0.00 0.00 0.00 4.02
959 1012 2.997315 CTGACCACAGCCCCGAGA 60.997 66.667 0.00 0.00 37.33 4.04
1422 1498 4.135153 CTCCCCTGCTCGTCCGTG 62.135 72.222 0.00 0.00 0.00 4.94
1470 1565 2.097925 GCGTTTGCGATCAAAGTGTTTG 60.098 45.455 0.00 0.00 42.31 2.93
1499 1594 1.004277 GGTGACGAGCGAGTTCTGTG 61.004 60.000 0.00 0.00 0.00 3.66
1503 1598 1.400846 GACGAGCGAGTTCTGTGGATA 59.599 52.381 0.00 0.00 0.00 2.59
1509 1604 2.873133 GAGTTCTGTGGATACTCGGG 57.127 55.000 0.00 0.00 37.07 5.14
1514 1609 1.822990 TCTGTGGATACTCGGGTTGTC 59.177 52.381 0.00 0.00 37.07 3.18
1527 1622 3.672447 TTGTCGTAGGTGCGGCGA 61.672 61.111 12.98 0.00 39.62 5.54
1546 1641 2.034124 GATGGGTGGTTGGATCATTGG 58.966 52.381 0.00 0.00 0.00 3.16
1547 1642 1.079796 TGGGTGGTTGGATCATTGGA 58.920 50.000 0.00 0.00 0.00 3.53
1548 1643 1.645391 TGGGTGGTTGGATCATTGGAT 59.355 47.619 0.00 0.00 36.13 3.41
1606 1701 1.454201 TGTCGTTTTGTGCTTGTGGA 58.546 45.000 0.00 0.00 0.00 4.02
1638 1733 5.957796 GTGTATACTCGTTTGCTTTATGTGC 59.042 40.000 4.17 0.00 0.00 4.57
1733 1837 6.039382 GTGGAAATTTATGTGAGGGTGGATAC 59.961 42.308 0.00 0.00 0.00 2.24
1781 1892 7.173907 CACCTGTTGAAACATACTTCAGATTCT 59.826 37.037 0.00 0.00 38.41 2.40
1782 1893 8.375506 ACCTGTTGAAACATACTTCAGATTCTA 58.624 33.333 0.00 0.00 38.41 2.10
1788 1899 5.832539 ACATACTTCAGATTCTATGGGGG 57.167 43.478 0.00 0.00 0.00 5.40
1800 1911 7.029390 AGATTCTATGGGGGCCTAGTATTTTA 58.971 38.462 0.84 0.00 0.00 1.52
1801 1912 6.443995 TTCTATGGGGGCCTAGTATTTTAC 57.556 41.667 0.84 0.00 0.00 2.01
1802 1913 5.734078 TCTATGGGGGCCTAGTATTTTACT 58.266 41.667 0.84 0.00 42.68 2.24
1803 1914 4.995624 ATGGGGGCCTAGTATTTTACTC 57.004 45.455 0.84 0.00 40.14 2.59
1804 1915 2.701951 TGGGGGCCTAGTATTTTACTCG 59.298 50.000 0.84 0.00 40.14 4.18
1814 1926 5.838531 AGTATTTTACTCGACTGGGAGAG 57.161 43.478 5.21 0.84 40.16 3.20
1815 1927 5.507637 AGTATTTTACTCGACTGGGAGAGA 58.492 41.667 5.21 0.00 37.87 3.10
1831 1943 4.407296 GGGAGAGAATGTGTATCTTGGTCT 59.593 45.833 0.00 0.00 0.00 3.85
1844 1956 9.202273 GTGTATCTTGGTCTGAATCAGATAATC 57.798 37.037 16.68 3.17 42.73 1.75
1846 1958 6.471233 TCTTGGTCTGAATCAGATAATCGT 57.529 37.500 16.68 0.00 42.73 3.73
1852 1964 6.018669 GGTCTGAATCAGATAATCGTGGTTTC 60.019 42.308 16.68 0.00 42.73 2.78
1869 1981 7.227711 TCGTGGTTTCAGAATTTGTCAGATTAA 59.772 33.333 0.00 0.00 0.00 1.40
1893 2005 3.354085 GCTTCAAGCAATAGCATGTGCG 61.354 50.000 3.89 0.00 45.62 5.34
1910 2022 6.074888 GCATGTGCGGAAATGTTGTAAATATC 60.075 38.462 9.01 0.00 0.00 1.63
1927 2043 6.662414 AAATATCGCGGTATCACATATTGG 57.338 37.500 13.18 0.00 0.00 3.16
1928 2044 1.790755 TCGCGGTATCACATATTGGC 58.209 50.000 6.13 0.00 0.00 4.52
1966 2094 7.122650 CCAATGTAAACTATCCATCCAACAGTT 59.877 37.037 0.00 0.00 0.00 3.16
2055 2183 2.578021 ACATGGTTAGGAGCATCTGGTT 59.422 45.455 0.00 0.00 41.82 3.67
2063 2191 2.306805 AGGAGCATCTGGTTGAACATGA 59.693 45.455 0.00 0.00 33.73 3.07
2081 2210 7.438160 TGAACATGACTTTCATATTAGTAGCGG 59.562 37.037 0.00 0.00 34.28 5.52
2127 2264 7.433708 TTCAAGTGTATGAAACCTGTGTATG 57.566 36.000 0.00 0.00 36.42 2.39
2167 2304 5.823045 ACTCCTAAGGACTTGTTTTTCAGTG 59.177 40.000 0.00 0.00 0.00 3.66
2168 2305 5.996644 TCCTAAGGACTTGTTTTTCAGTGA 58.003 37.500 0.00 0.00 0.00 3.41
2199 2336 9.612066 TCATGTTCATGTTGTATGCTATAAGAA 57.388 29.630 11.73 0.00 0.00 2.52
2265 2402 5.790593 TCCGCCACATTCTATTACCTATTC 58.209 41.667 0.00 0.00 0.00 1.75
2447 2584 8.675504 ACTTCTGAATATTTCTCTGCATTTCTG 58.324 33.333 0.00 0.00 0.00 3.02
2449 2586 8.975663 TCTGAATATTTCTCTGCATTTCTGAT 57.024 30.769 0.00 0.00 0.00 2.90
2505 2642 4.628766 GGCTTGATGAATTTCAAAGAAGCC 59.371 41.667 26.83 26.83 42.96 4.35
2508 2645 6.750963 GCTTGATGAATTTCAAAGAAGCCTAG 59.249 38.462 19.69 0.00 35.31 3.02
2596 2733 2.561209 TTGCCCTGGTATGAGTCCTA 57.439 50.000 0.00 0.00 0.00 2.94
2598 2735 0.674534 GCCCTGGTATGAGTCCTACG 59.325 60.000 0.00 0.00 0.00 3.51
2606 2744 6.199937 TGGTATGAGTCCTACGAAAGTTAC 57.800 41.667 0.00 0.00 46.40 2.50
2620 2758 4.201558 CGAAAGTTACAGTTGCAAAACGAC 59.798 41.667 0.00 0.00 0.00 4.34
2660 3057 3.495331 ACAATTTGGCCACAGTGTATGA 58.505 40.909 22.55 0.00 0.00 2.15
2987 3384 1.864029 GCTGGTTTTCTGAACGCAACC 60.864 52.381 13.19 13.19 39.41 3.77
3078 3475 8.467963 TGCATCATGTTGATTGTAATCCTTAT 57.532 30.769 7.98 0.00 34.28 1.73
3554 4240 0.896923 TGTTTCATGCATGGGCCTTC 59.103 50.000 25.97 11.37 40.13 3.46
3603 4289 7.413328 GGTTCTGGCAATTCTGAAAAATAATGC 60.413 37.037 0.00 0.00 0.00 3.56
3960 4646 6.382869 AGTTGATTGAAGAAAGGTGAGTTG 57.617 37.500 0.00 0.00 0.00 3.16
4310 4997 5.938438 AAGACTGTTCTTCATTCTTCTGC 57.062 39.130 0.00 0.00 40.43 4.26
4311 4998 4.965814 AGACTGTTCTTCATTCTTCTGCA 58.034 39.130 0.00 0.00 33.24 4.41
4434 5154 0.040958 CTTGCTGTGTCTTTGACGGC 60.041 55.000 0.00 0.00 44.61 5.68
4599 5319 7.617225 AGTATGTAATGTTGGTGTTACTGCTA 58.383 34.615 0.00 0.00 33.17 3.49
4612 5332 6.438763 GTGTTACTGCTACAAAAGATGCTTT 58.561 36.000 0.00 0.00 0.00 3.51
4677 5397 3.533606 TCTAGTCTGATTTCAGCAGCC 57.466 47.619 2.60 0.00 43.46 4.85
4888 5608 5.357314 AGAAACATTGGCATCAGATGAAGAG 59.643 40.000 15.12 2.12 0.00 2.85
4933 5653 5.495640 AGGAATTGGAGCTCTAAAGTCTTG 58.504 41.667 17.05 0.00 0.00 3.02
4934 5654 4.095632 GGAATTGGAGCTCTAAAGTCTTGC 59.904 45.833 17.05 8.00 0.00 4.01
5028 5748 4.084013 GCTATTGACTACAGCGTTTGTGTT 60.084 41.667 5.17 0.00 41.10 3.32
5200 5920 3.088532 GTTATTGTGGTTCATGGCCAGA 58.911 45.455 13.05 6.16 36.57 3.86
5233 5980 6.400568 ACTTTTTCACTATGCATGATTTGGG 58.599 36.000 10.16 0.00 0.00 4.12
5429 6180 6.033966 CCAAATAAATCAGAACGCCCTAAAC 58.966 40.000 0.00 0.00 0.00 2.01
5464 6215 0.330604 AGCATCTGCCATGACTGGTT 59.669 50.000 0.00 0.00 45.10 3.67
5465 6216 1.180029 GCATCTGCCATGACTGGTTT 58.820 50.000 0.00 0.00 45.10 3.27
5466 6217 1.135199 GCATCTGCCATGACTGGTTTG 60.135 52.381 0.00 0.00 45.10 2.93
5467 6218 2.439409 CATCTGCCATGACTGGTTTGA 58.561 47.619 0.00 0.00 45.10 2.69
5468 6219 2.189594 TCTGCCATGACTGGTTTGAG 57.810 50.000 0.00 0.00 45.10 3.02
5548 6299 0.240945 CTGGTGGTGTGATTTTCCGC 59.759 55.000 0.00 0.00 0.00 5.54
5622 6373 3.334583 TTGTAGAGACATGTTCAGGCC 57.665 47.619 0.00 0.00 34.86 5.19
5662 6413 0.253610 TGGGGCTAACAATACACCGG 59.746 55.000 0.00 0.00 0.00 5.28
5769 6523 4.502259 CCTTGTACATTGCTAGGCTAGGAG 60.502 50.000 22.40 11.64 0.00 3.69
5861 6615 7.284261 TCGATGATTTTATTCTAATGTGCCCAA 59.716 33.333 0.00 0.00 0.00 4.12
5866 6620 8.647143 ATTTTATTCTAATGTGCCCAATTTCG 57.353 30.769 0.00 0.00 0.00 3.46
5914 6668 2.166254 CCAATGTGGGGTAGATTTGCAC 59.834 50.000 0.00 0.00 32.67 4.57
5969 6725 1.280746 CTTGTTGGCACTGCACTCG 59.719 57.895 2.82 0.00 0.00 4.18
6031 6788 5.591067 ACCAAAAGGTGAAATTCTGTCGTTA 59.409 36.000 0.00 0.00 0.00 3.18
6392 7193 6.091034 GGAAGACGAGACCTCATAAAGAAAAC 59.909 42.308 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.477975 CCTCTCCACGACCGCGAC 62.478 72.222 8.23 0.00 41.64 5.19
25 26 4.373116 TTGCCTCTCCACGACCGC 62.373 66.667 0.00 0.00 0.00 5.68
33 34 0.243095 CTTGCTTTGCTTGCCTCTCC 59.757 55.000 0.00 0.00 0.00 3.71
34 35 0.243095 CCTTGCTTTGCTTGCCTCTC 59.757 55.000 0.00 0.00 0.00 3.20
35 36 1.813728 GCCTTGCTTTGCTTGCCTCT 61.814 55.000 0.00 0.00 0.00 3.69
36 37 1.373873 GCCTTGCTTTGCTTGCCTC 60.374 57.895 0.00 0.00 0.00 4.70
41 42 2.608752 CGATCTTTGCCTTGCTTTGCTT 60.609 45.455 0.00 0.00 0.00 3.91
47 48 0.242017 GTTGCGATCTTTGCCTTGCT 59.758 50.000 0.00 0.00 0.00 3.91
48 49 1.067199 CGTTGCGATCTTTGCCTTGC 61.067 55.000 0.00 0.00 0.00 4.01
49 50 0.238289 ACGTTGCGATCTTTGCCTTG 59.762 50.000 0.00 0.00 0.00 3.61
53 54 2.860735 AGAGATACGTTGCGATCTTTGC 59.139 45.455 0.00 0.00 32.47 3.68
54 55 3.487574 GGAGAGATACGTTGCGATCTTTG 59.512 47.826 0.00 0.00 32.47 2.77
55 56 3.707793 GGAGAGATACGTTGCGATCTTT 58.292 45.455 0.00 0.00 32.47 2.52
138 148 1.856265 CTCTGAGGTTTGTTGCGGGC 61.856 60.000 0.00 0.00 0.00 6.13
274 293 3.315949 CCGTCCGTGGGAAGGGAA 61.316 66.667 8.55 0.00 45.43 3.97
287 306 3.507009 CCCGTCTCCGTCTCCGTC 61.507 72.222 0.00 0.00 0.00 4.79
329 348 3.564027 CTCGGGCGCGTTGGAATC 61.564 66.667 23.19 0.00 0.00 2.52
886 918 1.459455 CCGATCGGGTCTGAGCTGAT 61.459 60.000 26.38 26.38 43.73 2.90
937 969 2.607750 GGGCTGTGGTCAGAGGGA 60.608 66.667 0.00 0.00 43.76 4.20
939 971 4.087892 CGGGGCTGTGGTCAGAGG 62.088 72.222 0.00 0.00 43.76 3.69
995 1048 2.741985 CGTGGTGCTGCATCGGAA 60.742 61.111 5.27 0.00 0.00 4.30
1400 1476 4.787280 ACGAGCAGGGGAGGGGAG 62.787 72.222 0.00 0.00 0.00 4.30
1405 1481 4.135153 CACGGACGAGCAGGGGAG 62.135 72.222 0.00 0.00 0.00 4.30
1430 1506 1.228675 AAACTTCCAGCCCAGCAGG 60.229 57.895 0.00 0.00 36.52 4.85
1431 1507 1.962144 CAAACTTCCAGCCCAGCAG 59.038 57.895 0.00 0.00 0.00 4.24
1432 1508 2.202395 GCAAACTTCCAGCCCAGCA 61.202 57.895 0.00 0.00 0.00 4.41
1433 1509 2.653115 GCAAACTTCCAGCCCAGC 59.347 61.111 0.00 0.00 0.00 4.85
1434 1510 1.455383 AACGCAAACTTCCAGCCCAG 61.455 55.000 0.00 0.00 0.00 4.45
1435 1511 1.040339 AAACGCAAACTTCCAGCCCA 61.040 50.000 0.00 0.00 0.00 5.36
1436 1512 0.597377 CAAACGCAAACTTCCAGCCC 60.597 55.000 0.00 0.00 0.00 5.19
1437 1513 1.215014 GCAAACGCAAACTTCCAGCC 61.215 55.000 0.00 0.00 0.00 4.85
1438 1514 1.539776 CGCAAACGCAAACTTCCAGC 61.540 55.000 0.00 0.00 0.00 4.85
1470 1565 2.027625 CTCGTCACCCAAACCGAGC 61.028 63.158 0.00 0.00 40.12 5.03
1475 1570 0.878961 AACTCGCTCGTCACCCAAAC 60.879 55.000 0.00 0.00 0.00 2.93
1499 1594 1.336125 CCTACGACAACCCGAGTATCC 59.664 57.143 0.00 0.00 0.00 2.59
1503 1598 1.962144 CACCTACGACAACCCGAGT 59.038 57.895 0.00 0.00 0.00 4.18
1509 1604 3.475774 CGCCGCACCTACGACAAC 61.476 66.667 0.00 0.00 34.06 3.32
1527 1622 1.645391 TCCAATGATCCAACCACCCAT 59.355 47.619 0.00 0.00 0.00 4.00
1606 1701 4.304110 CAAACGAGTATACACACCACTGT 58.696 43.478 5.50 0.00 0.00 3.55
1638 1733 1.005037 TGTCCTAACCAGCACGCAG 60.005 57.895 0.00 0.00 0.00 5.18
1716 1820 3.045634 CCTGGTATCCACCCTCACATAA 58.954 50.000 0.00 0.00 45.11 1.90
1733 1837 1.923356 ACACCATTAGTTTGCCCTGG 58.077 50.000 0.00 0.00 0.00 4.45
1759 1863 9.166173 CCATAGAATCTGAAGTATGTTTCAACA 57.834 33.333 0.00 0.00 44.06 3.33
1781 1892 4.529377 CGAGTAAAATACTAGGCCCCCATA 59.471 45.833 0.00 0.00 39.59 2.74
1782 1893 3.326880 CGAGTAAAATACTAGGCCCCCAT 59.673 47.826 0.00 0.00 39.59 4.00
1788 1899 4.340381 TCCCAGTCGAGTAAAATACTAGGC 59.660 45.833 0.00 0.00 39.59 3.93
1800 1911 1.821753 CACATTCTCTCCCAGTCGAGT 59.178 52.381 0.00 0.00 0.00 4.18
1801 1912 1.821753 ACACATTCTCTCCCAGTCGAG 59.178 52.381 0.00 0.00 0.00 4.04
1802 1913 1.924731 ACACATTCTCTCCCAGTCGA 58.075 50.000 0.00 0.00 0.00 4.20
1803 1914 3.634448 AGATACACATTCTCTCCCAGTCG 59.366 47.826 0.00 0.00 0.00 4.18
1804 1915 5.355596 CAAGATACACATTCTCTCCCAGTC 58.644 45.833 0.00 0.00 0.00 3.51
1814 1926 7.044181 TCTGATTCAGACCAAGATACACATTC 58.956 38.462 12.38 0.00 35.39 2.67
1815 1927 6.950842 TCTGATTCAGACCAAGATACACATT 58.049 36.000 12.38 0.00 35.39 2.71
1831 1943 6.639563 TCTGAAACCACGATTATCTGATTCA 58.360 36.000 0.00 0.00 0.00 2.57
1844 1956 4.811555 TCTGACAAATTCTGAAACCACG 57.188 40.909 0.00 0.00 29.68 4.94
1846 1958 8.352201 CAGTTAATCTGACAAATTCTGAAACCA 58.648 33.333 0.00 0.00 46.27 3.67
1852 1964 7.587629 TGAAGCAGTTAATCTGACAAATTCTG 58.412 34.615 8.63 0.00 46.27 3.02
1893 2005 5.164606 ACCGCGATATTTACAACATTTCC 57.835 39.130 8.23 0.00 0.00 3.13
1910 2022 1.795768 AGCCAATATGTGATACCGCG 58.204 50.000 0.00 0.00 0.00 6.46
2055 2183 7.438160 CCGCTACTAATATGAAAGTCATGTTCA 59.562 37.037 3.82 0.25 38.75 3.18
2063 2191 6.924060 GTCATCACCGCTACTAATATGAAAGT 59.076 38.462 0.00 0.00 0.00 2.66
2167 2304 6.204301 AGCATACAACATGAACATGAGCTATC 59.796 38.462 19.56 5.16 41.20 2.08
2168 2305 6.060136 AGCATACAACATGAACATGAGCTAT 58.940 36.000 19.56 8.62 41.20 2.97
2243 2380 4.625742 CGAATAGGTAATAGAATGTGGCGG 59.374 45.833 0.00 0.00 0.00 6.13
2245 2382 5.989777 ACACGAATAGGTAATAGAATGTGGC 59.010 40.000 0.00 0.00 0.00 5.01
2246 2383 7.434492 AGACACGAATAGGTAATAGAATGTGG 58.566 38.462 0.00 0.00 0.00 4.17
2247 2384 8.353684 AGAGACACGAATAGGTAATAGAATGTG 58.646 37.037 0.00 0.00 0.00 3.21
2248 2385 8.466617 AGAGACACGAATAGGTAATAGAATGT 57.533 34.615 0.00 0.00 0.00 2.71
2265 2402 8.683550 TGTATGTGAACTAAATAAGAGACACG 57.316 34.615 0.00 0.00 32.92 4.49
2449 2586 9.599866 CAGTAGAATGATACCAGTACATGAAAA 57.400 33.333 0.00 0.00 0.00 2.29
2503 2640 3.052745 GTGCAGAAAAACAAAGCTAGGC 58.947 45.455 0.00 0.00 0.00 3.93
2505 2642 6.833342 AAATGTGCAGAAAAACAAAGCTAG 57.167 33.333 0.00 0.00 0.00 3.42
2508 2645 6.343226 TGTAAATGTGCAGAAAAACAAAGC 57.657 33.333 0.00 0.00 0.00 3.51
2571 2708 4.210331 GACTCATACCAGGGCAATCAAAT 58.790 43.478 0.00 0.00 0.00 2.32
2596 2733 4.092816 CGTTTTGCAACTGTAACTTTCGT 58.907 39.130 0.00 0.00 0.00 3.85
2598 2735 5.090083 TGTCGTTTTGCAACTGTAACTTTC 58.910 37.500 0.00 0.00 0.00 2.62
2606 2744 4.209452 AGTACATGTCGTTTTGCAACTG 57.791 40.909 0.00 0.00 0.00 3.16
2987 3384 7.039363 TGGTAGTGAAAATTTGGGATTACAAGG 60.039 37.037 0.00 0.00 0.00 3.61
3078 3475 4.661222 TGAAAACCCAGTAGCATCATCAA 58.339 39.130 0.00 0.00 0.00 2.57
3554 4240 5.064452 CCTTGAAGTTCTGCATAGCTAACAG 59.936 44.000 17.09 17.09 31.25 3.16
3603 4289 7.641411 CCTGAGATTTACATTTTATGAACAGCG 59.359 37.037 0.00 0.00 0.00 5.18
3960 4646 3.371898 GCTGCAATAACCAAATTGGCTTC 59.628 43.478 12.67 0.00 42.67 3.86
4302 4989 5.219343 TCAGACAGAAGAATGCAGAAGAA 57.781 39.130 0.00 0.00 0.00 2.52
4303 4990 4.879197 TCAGACAGAAGAATGCAGAAGA 57.121 40.909 0.00 0.00 0.00 2.87
4304 4991 6.497785 AATTCAGACAGAAGAATGCAGAAG 57.502 37.500 0.00 0.00 40.15 2.85
4305 4992 6.487668 TGAAATTCAGACAGAAGAATGCAGAA 59.512 34.615 0.00 0.00 40.15 3.02
4306 4993 5.999600 TGAAATTCAGACAGAAGAATGCAGA 59.000 36.000 0.00 0.00 40.15 4.26
4307 4994 6.250344 TGAAATTCAGACAGAAGAATGCAG 57.750 37.500 0.00 0.00 40.15 4.41
4308 4995 6.829229 ATGAAATTCAGACAGAAGAATGCA 57.171 33.333 1.10 0.00 40.15 3.96
4309 4996 7.597743 ACAAATGAAATTCAGACAGAAGAATGC 59.402 33.333 1.10 0.00 40.15 3.56
4310 4997 8.912658 CACAAATGAAATTCAGACAGAAGAATG 58.087 33.333 1.10 0.00 40.15 2.67
4311 4998 8.853126 TCACAAATGAAATTCAGACAGAAGAAT 58.147 29.630 1.10 0.00 40.15 2.40
4599 5319 9.985730 TCATGAAATTTCTAAAGCATCTTTTGT 57.014 25.926 18.64 0.00 0.00 2.83
4677 5397 6.638873 TGTAACAAAAATAATCAGCACCAACG 59.361 34.615 0.00 0.00 0.00 4.10
4691 5411 9.691362 GGACATGTAAATGACTGTAACAAAAAT 57.309 29.630 0.00 0.00 0.00 1.82
4721 5441 8.670135 CATTAATCCAACCTAAACAACATACGA 58.330 33.333 0.00 0.00 0.00 3.43
4888 5608 0.668535 AAACCTTGAACGGAGCAAGC 59.331 50.000 8.19 0.00 41.00 4.01
4933 5653 6.310197 CAGCATACTTCAAAGTTCAGTAAGC 58.690 40.000 0.00 8.13 40.37 3.09
4934 5654 6.148480 AGCAGCATACTTCAAAGTTCAGTAAG 59.852 38.462 0.00 0.00 40.37 2.34
5028 5748 4.866508 AGTCACGAAAACCTCACTATGA 57.133 40.909 0.00 0.00 0.00 2.15
5070 5790 6.418101 TCTTCTATGACCAAGAAGGAAATGG 58.582 40.000 11.73 0.00 46.55 3.16
5220 5940 8.425237 TGTATTTATGATCCCAAATCATGCAT 57.575 30.769 10.09 0.00 38.98 3.96
5464 6215 5.488262 TGAATCAGGATCAGTCAACTCAA 57.512 39.130 0.00 0.00 0.00 3.02
5465 6216 5.688814 ATGAATCAGGATCAGTCAACTCA 57.311 39.130 0.00 0.00 0.00 3.41
5466 6217 6.998968 AAATGAATCAGGATCAGTCAACTC 57.001 37.500 0.00 0.00 0.00 3.01
5467 6218 6.152323 CCAAAATGAATCAGGATCAGTCAACT 59.848 38.462 0.00 0.00 0.00 3.16
5468 6219 6.327934 CCAAAATGAATCAGGATCAGTCAAC 58.672 40.000 0.00 0.00 0.00 3.18
5548 6299 4.636435 AACGGGGGTGCTTGACGG 62.636 66.667 0.00 0.00 0.00 4.79
5622 6373 6.239120 CCCCAGAATTAGCCTACATCAAAATG 60.239 42.308 0.00 0.00 38.93 2.32
5861 6615 8.956426 TCCAAAGAAAAGATATTACAGCGAAAT 58.044 29.630 0.00 0.00 0.00 2.17
5914 6668 2.819477 CCCTCAGGGCTCAGACTAG 58.181 63.158 0.00 0.00 35.35 2.57
6031 6788 4.402155 TGTTTCCAACATGAGACAAAAGCT 59.598 37.500 0.00 0.00 36.25 3.74
6056 6813 5.883685 ATTGCTCAGACAATCTCCAGATA 57.116 39.130 0.00 0.00 35.31 1.98
6392 7193 2.181954 AAGCAGCAAGAGGACTGAAG 57.818 50.000 0.00 0.00 35.90 3.02


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

AutoCloner maintained by Alex Coulton.