Multiple sequence alignment - TraesCS7D01G365400

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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 TraesCS7D01G365400 chr7D 100.000 4769 0 0 1 4769 471927657 471932425 0.000000e+00 8807.0
1 TraesCS7D01G365400 chr7D 84.034 119 17 2 418 535 211631355 211631472 3.900000e-21 113.0
2 TraesCS7D01G365400 chr7D 89.655 58 4 1 1322 1377 538578631 538578688 6.620000e-09 73.1
3 TraesCS7D01G365400 chr7B 95.762 4672 145 24 133 4769 495754564 495759217 0.000000e+00 7481.0
4 TraesCS7D01G365400 chr7A 89.050 4137 267 91 734 4764 524643853 524639797 0.000000e+00 4959.0
5 TraesCS7D01G365400 chr7A 82.752 516 79 9 133 639 524644530 524644016 7.280000e-123 451.0
6 TraesCS7D01G365400 chr7A 96.610 59 2 0 2732 2790 112776916 112776974 1.090000e-16 99.0
7 TraesCS7D01G365400 chr7A 96.610 59 2 0 2732 2790 112786310 112786252 1.090000e-16 99.0
8 TraesCS7D01G365400 chr6A 98.529 136 2 0 1 136 489683044 489682909 1.710000e-59 241.0
9 TraesCS7D01G365400 chr5D 98.529 136 2 0 1 136 533680818 533680953 1.710000e-59 241.0
10 TraesCS7D01G365400 chr5D 78.000 200 41 2 417 614 371678111 371678309 6.480000e-24 122.0
11 TraesCS7D01G365400 chr5D 74.779 226 39 8 152 360 434424897 434424673 8.500000e-13 86.1
12 TraesCS7D01G365400 chr4D 98.529 136 2 0 1 136 75836492 75836627 1.710000e-59 241.0
13 TraesCS7D01G365400 chr4D 98.529 136 2 0 1 136 212886921 212886786 1.710000e-59 241.0
14 TraesCS7D01G365400 chr4D 91.304 69 6 0 2732 2800 15316066 15316134 1.410000e-15 95.3
15 TraesCS7D01G365400 chr3D 98.529 136 2 0 1 136 161072812 161072947 1.710000e-59 241.0
16 TraesCS7D01G365400 chr3D 98.529 136 2 0 1 136 182610311 182610176 1.710000e-59 241.0
17 TraesCS7D01G365400 chr3D 98.529 136 2 0 1 136 207375275 207375140 1.710000e-59 241.0
18 TraesCS7D01G365400 chr3D 98.529 136 2 0 1 136 357043654 357043519 1.710000e-59 241.0
19 TraesCS7D01G365400 chr3D 95.652 46 1 1 502 547 103350261 103350305 6.620000e-09 73.1
20 TraesCS7D01G365400 chr1A 98.529 136 2 0 1 136 419055700 419055835 1.710000e-59 241.0
21 TraesCS7D01G365400 chr5A 78.857 175 35 2 428 600 474761302 474761476 3.020000e-22 117.0
22 TraesCS7D01G365400 chr5A 93.846 65 4 0 2734 2798 55159008 55159072 1.090000e-16 99.0
23 TraesCS7D01G365400 chr1D 96.721 61 2 0 2732 2792 332956490 332956430 8.440000e-18 102.0
24 TraesCS7D01G365400 chr1D 92.424 66 5 0 2732 2797 415425000 415424935 1.410000e-15 95.3
25 TraesCS7D01G365400 chr5B 96.610 59 2 0 2732 2790 567789516 567789574 1.090000e-16 99.0
26 TraesCS7D01G365400 chr3B 93.750 64 4 0 2732 2795 781397825 781397888 3.930000e-16 97.1
27 TraesCS7D01G365400 chr6B 78.289 152 27 5 2793 2940 136119664 136119515 5.080000e-15 93.5
28 TraesCS7D01G365400 chr6D 73.401 297 56 15 2793 3083 62504364 62504085 6.570000e-14 89.8
29 TraesCS7D01G365400 chr2D 89.655 58 4 1 1322 1377 166478080 166478137 6.620000e-09 73.1


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 TraesCS7D01G365400 chr7D 471927657 471932425 4768 False 8807 8807 100.000 1 4769 1 chr7D.!!$F2 4768
1 TraesCS7D01G365400 chr7B 495754564 495759217 4653 False 7481 7481 95.762 133 4769 1 chr7B.!!$F1 4636
2 TraesCS7D01G365400 chr7A 524639797 524644530 4733 True 2705 4959 85.901 133 4764 2 chr7A.!!$R2 4631

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
268 272 0.396435 TTTCTGCCTCGTCCACACAT 59.604 50.000 0.00 0.00 0.00 3.21 F
1449 1571 0.166597 ACATTGATTGTGCGTGCTCG 59.833 50.000 3.31 3.31 37.11 5.03 F
1946 2070 1.067213 GCTCGACTTTCTGGCTCTTCT 60.067 52.381 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2212 1.737838 TCGAATTGCTGGTGATGGAC 58.262 50.0 0.00 0.0 0.0 4.02 R
2458 2582 0.110238 TTCGCTGCAATTCACTTCGC 60.110 50.0 0.00 0.0 0.0 4.70 R
3771 3936 2.923426 TTCTCCAGCGCCGCCAATAG 62.923 60.0 4.98 0.0 0.0 1.73 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
24 25 6.831769 CACAGTGTTTTGTCTATGTATCCAC 58.168 40.000 0.00 0.00 0.00 4.02
25 26 6.426633 CACAGTGTTTTGTCTATGTATCCACA 59.573 38.462 0.00 0.00 39.52 4.17
26 27 6.426937 ACAGTGTTTTGTCTATGTATCCACAC 59.573 38.462 0.00 0.00 37.54 3.82
27 28 6.426633 CAGTGTTTTGTCTATGTATCCACACA 59.573 38.462 0.00 0.00 37.54 3.72
28 29 7.119699 CAGTGTTTTGTCTATGTATCCACACAT 59.880 37.037 0.00 0.00 41.88 3.21
29 30 7.119699 AGTGTTTTGTCTATGTATCCACACATG 59.880 37.037 0.00 0.00 39.46 3.21
30 31 6.939730 TGTTTTGTCTATGTATCCACACATGT 59.060 34.615 0.00 0.00 39.46 3.21
31 32 6.983474 TTTGTCTATGTATCCACACATGTG 57.017 37.500 24.25 24.25 45.23 3.21
32 33 5.675684 TGTCTATGTATCCACACATGTGT 57.324 39.130 25.76 25.76 46.17 3.72
33 34 5.660460 TGTCTATGTATCCACACATGTGTC 58.340 41.667 28.38 16.98 42.83 3.67
34 35 5.186797 TGTCTATGTATCCACACATGTGTCA 59.813 40.000 28.38 21.85 42.83 3.58
35 36 6.106003 GTCTATGTATCCACACATGTGTCAA 58.894 40.000 28.38 18.92 42.83 3.18
36 37 6.256539 GTCTATGTATCCACACATGTGTCAAG 59.743 42.308 28.38 19.10 42.83 3.02
37 38 4.350368 TGTATCCACACATGTGTCAAGT 57.650 40.909 28.38 16.28 42.83 3.16
38 39 4.713553 TGTATCCACACATGTGTCAAGTT 58.286 39.130 28.38 16.24 42.83 2.66
39 40 5.129634 TGTATCCACACATGTGTCAAGTTT 58.870 37.500 28.38 12.40 42.83 2.66
40 41 4.836125 ATCCACACATGTGTCAAGTTTC 57.164 40.909 28.38 0.00 42.83 2.78
41 42 2.948979 TCCACACATGTGTCAAGTTTCC 59.051 45.455 28.38 0.00 42.83 3.13
42 43 2.286950 CCACACATGTGTCAAGTTTCCG 60.287 50.000 28.38 13.57 42.83 4.30
43 44 1.946768 ACACATGTGTCAAGTTTCCGG 59.053 47.619 25.76 0.00 40.24 5.14
44 45 1.946768 CACATGTGTCAAGTTTCCGGT 59.053 47.619 18.03 0.00 0.00 5.28
45 46 2.357637 CACATGTGTCAAGTTTCCGGTT 59.642 45.455 18.03 0.00 0.00 4.44
46 47 3.562141 CACATGTGTCAAGTTTCCGGTTA 59.438 43.478 18.03 0.00 0.00 2.85
47 48 4.035792 CACATGTGTCAAGTTTCCGGTTAA 59.964 41.667 18.03 0.00 0.00 2.01
48 49 4.825085 ACATGTGTCAAGTTTCCGGTTAAT 59.175 37.500 0.00 0.00 0.00 1.40
49 50 5.998981 ACATGTGTCAAGTTTCCGGTTAATA 59.001 36.000 0.00 0.00 0.00 0.98
50 51 5.927954 TGTGTCAAGTTTCCGGTTAATAC 57.072 39.130 0.00 0.00 0.00 1.89
51 52 5.366460 TGTGTCAAGTTTCCGGTTAATACA 58.634 37.500 0.00 0.00 0.00 2.29
52 53 5.821470 TGTGTCAAGTTTCCGGTTAATACAA 59.179 36.000 0.00 0.00 0.00 2.41
53 54 6.487331 TGTGTCAAGTTTCCGGTTAATACAAT 59.513 34.615 0.00 0.00 0.00 2.71
54 55 7.013464 TGTGTCAAGTTTCCGGTTAATACAATT 59.987 33.333 0.00 0.00 0.00 2.32
55 56 7.536281 GTGTCAAGTTTCCGGTTAATACAATTC 59.464 37.037 0.00 0.00 0.00 2.17
56 57 7.446013 TGTCAAGTTTCCGGTTAATACAATTCT 59.554 33.333 0.00 0.00 0.00 2.40
57 58 8.938906 GTCAAGTTTCCGGTTAATACAATTCTA 58.061 33.333 0.00 0.00 0.00 2.10
58 59 9.158233 TCAAGTTTCCGGTTAATACAATTCTAG 57.842 33.333 0.00 0.00 0.00 2.43
59 60 7.549615 AGTTTCCGGTTAATACAATTCTAGC 57.450 36.000 0.00 0.00 0.00 3.42
60 61 7.107542 AGTTTCCGGTTAATACAATTCTAGCA 58.892 34.615 0.00 0.00 0.00 3.49
61 62 7.773690 AGTTTCCGGTTAATACAATTCTAGCAT 59.226 33.333 0.00 0.00 0.00 3.79
62 63 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
63 64 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
64 65 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
65 66 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
66 67 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
126 127 7.881775 AACAACTTTATTATTGCCTCTAGGG 57.118 36.000 0.00 0.00 35.18 3.53
142 143 0.846693 AGGGCATATTTCCGAAGCCT 59.153 50.000 8.55 0.00 44.60 4.58
224 227 3.003480 CCAAATCTCTTGAAGACGTCCC 58.997 50.000 13.01 5.21 36.65 4.46
256 260 3.755905 CTCTTCCTTTCCTCTTTTCTGCC 59.244 47.826 0.00 0.00 0.00 4.85
268 272 0.396435 TTTCTGCCTCGTCCACACAT 59.604 50.000 0.00 0.00 0.00 3.21
270 274 1.485124 TCTGCCTCGTCCACACATAT 58.515 50.000 0.00 0.00 0.00 1.78
309 314 0.891449 CATACCCAACCCACAACGCA 60.891 55.000 0.00 0.00 0.00 5.24
377 382 3.469863 AAGTTCGCTGGCACCGGAA 62.470 57.895 9.46 0.00 0.00 4.30
436 441 4.238385 CGTCTCGCGGAACAAGAA 57.762 55.556 6.13 0.00 36.85 2.52
500 505 2.787994 GAGATCAACTGGGGCATATGG 58.212 52.381 4.56 0.00 0.00 2.74
506 514 2.689983 CAACTGGGGCATATGGAACTTC 59.310 50.000 4.56 0.00 0.00 3.01
662 774 1.012086 AGAGCGCTGTCGACGTATAA 58.988 50.000 18.48 0.00 38.10 0.98
687 799 3.128589 GGACGGATTTGCAAAATGCTCTA 59.871 43.478 17.19 0.00 45.31 2.43
712 824 4.647424 ATTCCGAAAAGAAAACTGTGCA 57.353 36.364 0.00 0.00 0.00 4.57
715 827 3.115554 CCGAAAAGAAAACTGTGCAAGG 58.884 45.455 0.00 0.00 0.00 3.61
774 886 1.672356 CTGGGCCTCGAAACCTGTG 60.672 63.158 4.53 0.00 0.00 3.66
844 956 2.063015 AATTCAGTCACGGTGCCCCA 62.063 55.000 2.51 0.00 0.00 4.96
938 1053 1.106285 AAATCGAGCAAAGCCATCCC 58.894 50.000 0.00 0.00 0.00 3.85
1411 1533 2.368821 TAATTGACCCCCGACCCCG 61.369 63.158 0.00 0.00 0.00 5.73
1422 1544 2.033194 CGACCCCGGCTCTGTTTTC 61.033 63.158 0.00 0.00 0.00 2.29
1449 1571 0.166597 ACATTGATTGTGCGTGCTCG 59.833 50.000 3.31 3.31 37.11 5.03
1507 1629 5.659525 TGAGATTGGCAATTCATTGGATTCT 59.340 36.000 14.93 3.19 38.21 2.40
1526 1648 7.121168 TGGATTCTATGAGAATTTGTGTGAACC 59.879 37.037 3.34 0.00 44.41 3.62
1598 1721 8.440021 CAAGTATTGTTTGATAGCTTGTGTTC 57.560 34.615 0.00 0.00 42.34 3.18
1693 1816 4.666655 CGTTTGCAGATTTGTCTCTTACGG 60.667 45.833 0.00 0.00 0.00 4.02
1736 1859 4.606961 TCTTCCGTTTGCAATCTTGTTTC 58.393 39.130 0.00 0.00 0.00 2.78
1946 2070 1.067213 GCTCGACTTTCTGGCTCTTCT 60.067 52.381 0.00 0.00 0.00 2.85
2023 2147 4.576463 GCAACGATCTCCACATTTATTCCT 59.424 41.667 0.00 0.00 0.00 3.36
2088 2212 9.850628 TTATCTTTCTGCTCAAAATTCTCAATG 57.149 29.630 0.00 0.00 0.00 2.82
2148 2272 2.227194 CAGTTTCTTAGCAACCGGGTT 58.773 47.619 6.59 6.59 0.00 4.11
2458 2582 6.439636 TTCCATATTATCCTCTTGACTGGG 57.560 41.667 0.00 0.00 0.00 4.45
2547 2671 6.759497 AAAACTCATACTGAGGTATTTGCC 57.241 37.500 8.85 0.00 45.11 4.52
2548 2672 5.700402 AACTCATACTGAGGTATTTGCCT 57.300 39.130 8.85 0.00 43.79 4.75
2549 2673 5.431765 AACTCATACTGAGGTATTTGCCTG 58.568 41.667 8.85 0.00 43.79 4.85
2550 2674 3.808728 TCATACTGAGGTATTTGCCTGC 58.191 45.455 0.00 0.00 39.34 4.85
2551 2675 3.455910 TCATACTGAGGTATTTGCCTGCT 59.544 43.478 0.00 0.00 39.34 4.24
2552 2676 2.119801 ACTGAGGTATTTGCCTGCTG 57.880 50.000 0.00 0.00 39.34 4.41
2787 2920 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
3365 3501 6.374333 GTGGATCATTTTGAAGTTAGGCTGTA 59.626 38.462 0.00 0.00 0.00 2.74
3366 3502 7.067494 GTGGATCATTTTGAAGTTAGGCTGTAT 59.933 37.037 0.00 0.00 0.00 2.29
3499 3641 1.263484 CTTGTGCTTGTGCTCTCACTG 59.737 52.381 0.00 0.00 43.49 3.66
3530 3674 8.764287 CAAAAGGAAAGTACAGGCATTAAAAAG 58.236 33.333 0.00 0.00 0.00 2.27
3771 3936 7.615582 TCCAATGTACTTCATCAGTTGATTC 57.384 36.000 0.00 0.00 36.88 2.52
3841 4014 1.762370 CCATTTTTATGGCCCCACTCC 59.238 52.381 0.00 0.00 34.56 3.85
3969 4172 1.610038 TGCTCAGAAGTGCATGGTTTG 59.390 47.619 0.00 0.00 39.15 2.93
3981 4184 0.463620 ATGGTTTGTGTGTTGTGCCC 59.536 50.000 0.00 0.00 0.00 5.36
4127 4332 3.684103 CTGAAAGTGCCAAACGTTGTA 57.316 42.857 0.00 0.00 29.98 2.41
4138 4343 5.106869 TGCCAAACGTTGTATATTCAGACAC 60.107 40.000 0.00 0.00 0.00 3.67
4222 4437 5.221422 ACAATAATGGGTTTGTGTTGTCAGG 60.221 40.000 0.00 0.00 34.87 3.86
4236 4451 1.342496 TGTCAGGACAGTCTCAGCAAG 59.658 52.381 0.00 0.00 36.21 4.01
4245 4460 2.042464 AGTCTCAGCAAGTTGTCCTCA 58.958 47.619 4.48 0.00 0.00 3.86
4445 4669 4.126437 GTTACAAAACCTTGCATTGCCTT 58.874 39.130 6.12 0.00 35.84 4.35
4446 4670 3.280197 ACAAAACCTTGCATTGCCTTT 57.720 38.095 6.12 0.00 35.84 3.11
4447 4671 3.205338 ACAAAACCTTGCATTGCCTTTC 58.795 40.909 6.12 0.00 35.84 2.62
4448 4672 3.118298 ACAAAACCTTGCATTGCCTTTCT 60.118 39.130 6.12 0.00 35.84 2.52
4550 4778 1.220206 CTCCATGCTCTTGACGGCT 59.780 57.895 0.00 0.00 0.00 5.52
4551 4779 0.809241 CTCCATGCTCTTGACGGCTC 60.809 60.000 0.00 0.00 0.00 4.70
4586 4820 4.771356 TCGGCGCCGTCTTCTTCG 62.771 66.667 44.16 19.18 40.74 3.79
4610 4844 4.399395 TCTTGCTGCGAGGCCCTG 62.399 66.667 16.59 0.00 0.00 4.45
4621 4858 3.056328 GGCCCTGGAACGTGAAGC 61.056 66.667 0.00 0.00 0.00 3.86
4765 5002 0.398318 GCCCTGTCCTGTGAGAAGTT 59.602 55.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.946768 ACCGGAAACTTGACACATGTG 59.053 47.619 24.25 24.25 0.00 3.21
25 26 2.341846 ACCGGAAACTTGACACATGT 57.658 45.000 9.46 0.00 0.00 3.21
26 27 4.822036 TTAACCGGAAACTTGACACATG 57.178 40.909 9.46 0.00 0.00 3.21
27 28 5.998981 TGTATTAACCGGAAACTTGACACAT 59.001 36.000 9.46 0.00 0.00 3.21
28 29 5.366460 TGTATTAACCGGAAACTTGACACA 58.634 37.500 9.46 0.00 0.00 3.72
29 30 5.927954 TGTATTAACCGGAAACTTGACAC 57.072 39.130 9.46 0.00 0.00 3.67
30 31 7.446013 AGAATTGTATTAACCGGAAACTTGACA 59.554 33.333 9.46 0.00 0.00 3.58
31 32 7.813645 AGAATTGTATTAACCGGAAACTTGAC 58.186 34.615 9.46 0.00 0.00 3.18
32 33 7.989416 AGAATTGTATTAACCGGAAACTTGA 57.011 32.000 9.46 0.00 0.00 3.02
33 34 7.908601 GCTAGAATTGTATTAACCGGAAACTTG 59.091 37.037 9.46 0.00 0.00 3.16
34 35 7.608761 TGCTAGAATTGTATTAACCGGAAACTT 59.391 33.333 9.46 0.00 0.00 2.66
35 36 7.107542 TGCTAGAATTGTATTAACCGGAAACT 58.892 34.615 9.46 0.00 0.00 2.66
36 37 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
37 38 7.771361 TCATGCTAGAATTGTATTAACCGGAAA 59.229 33.333 9.46 1.61 0.00 3.13
38 39 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
39 40 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
40 41 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
100 101 9.574516 CCCTAGAGGCAATAATAAAGTTGTTAT 57.425 33.333 0.00 0.00 0.00 1.89
101 102 8.974060 CCCTAGAGGCAATAATAAAGTTGTTA 57.026 34.615 0.00 0.00 0.00 2.41
102 103 7.881775 CCCTAGAGGCAATAATAAAGTTGTT 57.118 36.000 0.00 0.00 0.00 2.83
118 119 3.866449 GCTTCGGAAATATGCCCTAGAGG 60.866 52.174 0.00 0.00 39.47 3.69
119 120 3.330267 GCTTCGGAAATATGCCCTAGAG 58.670 50.000 0.00 0.00 0.00 2.43
120 121 2.038557 GGCTTCGGAAATATGCCCTAGA 59.961 50.000 7.33 0.00 37.81 2.43
121 122 2.039084 AGGCTTCGGAAATATGCCCTAG 59.961 50.000 13.33 0.00 44.19 3.02
122 123 2.038557 GAGGCTTCGGAAATATGCCCTA 59.961 50.000 13.33 0.00 44.19 3.53
123 124 0.846693 AGGCTTCGGAAATATGCCCT 59.153 50.000 13.33 1.55 44.19 5.19
124 125 1.239347 GAGGCTTCGGAAATATGCCC 58.761 55.000 13.33 4.12 44.19 5.36
125 126 1.967319 TGAGGCTTCGGAAATATGCC 58.033 50.000 9.94 9.94 43.52 4.40
126 127 4.370364 TTTTGAGGCTTCGGAAATATGC 57.630 40.909 0.00 0.00 0.00 3.14
127 128 5.894807 ACATTTTGAGGCTTCGGAAATATG 58.105 37.500 8.86 3.97 0.00 1.78
128 129 7.823745 ATACATTTTGAGGCTTCGGAAATAT 57.176 32.000 8.86 2.82 0.00 1.28
129 130 8.783093 CATATACATTTTGAGGCTTCGGAAATA 58.217 33.333 8.86 0.00 0.00 1.40
130 131 7.255590 CCATATACATTTTGAGGCTTCGGAAAT 60.256 37.037 4.74 4.74 0.00 2.17
131 132 6.039270 CCATATACATTTTGAGGCTTCGGAAA 59.961 38.462 0.00 0.00 0.00 3.13
142 143 4.656575 TCCTCGTCCCCATATACATTTTGA 59.343 41.667 0.00 0.00 0.00 2.69
198 201 2.675348 GTCTTCAAGAGATTTGGCTCGG 59.325 50.000 0.00 0.00 39.87 4.63
224 227 0.543749 AAAGGAAGAGGGCAGATCGG 59.456 55.000 0.00 0.00 0.00 4.18
256 260 2.138320 GATGGCATATGTGTGGACGAG 58.862 52.381 0.00 0.00 0.00 4.18
268 272 0.318441 GGCAGAGCTACGATGGCATA 59.682 55.000 0.00 0.00 39.18 3.14
270 274 2.501128 GGCAGAGCTACGATGGCA 59.499 61.111 8.73 0.00 39.18 4.92
309 314 3.637273 GTTGGGCCTCCGGTGACT 61.637 66.667 4.53 0.00 35.24 3.41
436 441 0.944311 AATCGACAACACGCTTCGCT 60.944 50.000 0.00 0.00 32.70 4.93
450 455 5.106752 TGTCGATGCATTTCAAGAAAATCGA 60.107 36.000 19.03 19.03 41.37 3.59
489 494 2.204463 TGAGAAGTTCCATATGCCCCA 58.796 47.619 0.00 0.00 0.00 4.96
500 505 8.709386 TGCTCTACAAGATTATTGAGAAGTTC 57.291 34.615 0.00 0.00 0.00 3.01
506 514 8.933807 CCACATATGCTCTACAAGATTATTGAG 58.066 37.037 1.58 0.00 0.00 3.02
643 652 1.003759 CTTATACGTCGACAGCGCTCT 60.004 52.381 17.16 0.00 37.46 4.09
646 655 1.386961 CTCTTATACGTCGACAGCGC 58.613 55.000 17.16 0.00 37.46 5.92
662 774 2.094545 GCATTTTGCAAATCCGTCCTCT 60.095 45.455 13.65 0.00 44.26 3.69
687 799 5.290885 GCACAGTTTTCTTTTCGGAATTGTT 59.709 36.000 0.00 0.00 0.00 2.83
712 824 5.693769 TCTCAATAATTCCTTCGTCCCTT 57.306 39.130 0.00 0.00 0.00 3.95
1007 1123 1.810532 GCGAGAACGAGGAGGATGT 59.189 57.895 0.00 0.00 42.66 3.06
1404 1526 2.032071 AAAACAGAGCCGGGGTCG 59.968 61.111 19.66 16.33 35.00 4.79
1411 1533 3.596214 TGTAATCGGAGAAAACAGAGCC 58.404 45.455 0.00 0.00 43.58 4.70
1422 1544 3.309682 ACGCACAATCAATGTAATCGGAG 59.690 43.478 0.00 0.00 41.46 4.63
1449 1571 5.560953 GCCAATAACAGCGACTGATTAATCC 60.561 44.000 12.90 0.00 35.18 3.01
1507 1629 7.888021 AGTTATGGGTTCACACAAATTCTCATA 59.112 33.333 0.00 0.00 30.29 2.15
1526 1648 9.449719 ACTCACAAATTCTTAAGGTAGTTATGG 57.550 33.333 1.85 0.00 0.00 2.74
1693 1816 6.690194 AGAAATGTGATTATGCTGTCCTTC 57.310 37.500 0.00 0.00 0.00 3.46
1736 1859 1.747355 GATGTTCATGCCCTTCAGGTG 59.253 52.381 0.00 0.00 38.26 4.00
2023 2147 3.496870 GGGTGGCTCTGAAGAAGAAAAGA 60.497 47.826 0.00 0.00 33.37 2.52
2088 2212 1.737838 TCGAATTGCTGGTGATGGAC 58.262 50.000 0.00 0.00 0.00 4.02
2148 2272 2.320681 AGGTTCTACAGCCCACACTA 57.679 50.000 0.00 0.00 0.00 2.74
2458 2582 0.110238 TTCGCTGCAATTCACTTCGC 60.110 50.000 0.00 0.00 0.00 4.70
2547 2671 4.690184 TTTGATACATGAGTTGCAGCAG 57.310 40.909 2.55 0.00 0.00 4.24
2548 2672 4.701171 TCATTTGATACATGAGTTGCAGCA 59.299 37.500 2.55 0.00 0.00 4.41
2549 2673 5.032863 GTCATTTGATACATGAGTTGCAGC 58.967 41.667 0.00 0.00 31.11 5.25
2550 2674 6.432607 AGTCATTTGATACATGAGTTGCAG 57.567 37.500 0.00 0.00 31.34 4.41
2551 2675 7.989170 AGATAGTCATTTGATACATGAGTTGCA 59.011 33.333 0.00 0.00 36.08 4.08
2552 2676 8.375608 AGATAGTCATTTGATACATGAGTTGC 57.624 34.615 0.00 0.00 36.08 4.17
2921 3055 6.902974 AGGGGATTTATTATTTTGAACCAGCT 59.097 34.615 0.00 0.00 0.00 4.24
3335 3471 7.094377 GCCTAACTTCAAAATGATCCACTAACA 60.094 37.037 0.00 0.00 0.00 2.41
3365 3501 5.187967 ACTCAAAGTCGGAGAAAGATGGTAT 59.812 40.000 0.00 0.00 39.69 2.73
3366 3502 4.527038 ACTCAAAGTCGGAGAAAGATGGTA 59.473 41.667 0.00 0.00 39.69 3.25
3408 3550 5.123805 AGACTGTACGACCTCTCTTTTTC 57.876 43.478 0.00 0.00 0.00 2.29
3499 3641 4.577283 TGCCTGTACTTTCCTTTTGTGTAC 59.423 41.667 0.00 0.00 35.43 2.90
3771 3936 2.923426 TTCTCCAGCGCCGCCAATAG 62.923 60.000 4.98 0.00 0.00 1.73
3841 4014 3.120041 CCGCCAACTTAAACAACTTTGG 58.880 45.455 0.00 0.00 39.86 3.28
3969 4172 1.961277 CCTCTCGGGCACAACACAC 60.961 63.158 0.00 0.00 0.00 3.82
3981 4184 4.392921 ACTTGTATCACCAATCCTCTCG 57.607 45.455 0.00 0.00 0.00 4.04
4001 4204 5.106752 ACAACTTGTGGTGCAATTTTTGAAC 60.107 36.000 0.00 0.00 38.55 3.18
4127 4332 7.182817 TGGTTAGTTAGCAGTGTCTGAATAT 57.817 36.000 0.66 0.00 32.44 1.28
4138 4343 6.801539 TTCAGACATTTGGTTAGTTAGCAG 57.198 37.500 0.00 0.00 35.32 4.24
4222 4437 2.139118 GGACAACTTGCTGAGACTGTC 58.861 52.381 0.00 0.00 39.19 3.51
4236 4451 2.611518 CTCGGTGATTCTGAGGACAAC 58.388 52.381 0.00 0.00 43.70 3.32
4245 4460 2.103771 ACTGCATATGCTCGGTGATTCT 59.896 45.455 27.13 0.00 42.66 2.40
4319 4539 5.931146 CAGTAGAGATTTCTGCAACTGAAGT 59.069 40.000 8.35 0.00 38.78 3.01
4575 4803 3.402058 AGACGATAACGAAGAAGACGG 57.598 47.619 0.00 0.00 42.66 4.79
4576 4804 3.001954 GCAAGACGATAACGAAGAAGACG 60.002 47.826 0.00 0.00 42.66 4.18
4586 4820 0.924090 CCTCGCAGCAAGACGATAAC 59.076 55.000 0.00 0.00 37.72 1.89
4587 4821 0.806102 GCCTCGCAGCAAGACGATAA 60.806 55.000 0.00 0.00 37.72 1.75
4610 4844 1.065358 TCGATTTCGCTTCACGTTCC 58.935 50.000 0.00 0.00 44.19 3.62
4621 4858 1.624323 GAGCCGTTCGTCGATTTCG 59.376 57.895 0.00 2.02 42.86 3.46


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

AutoCloner maintained by Alex Coulton.