Multiple sequence alignment - TraesCS6A01G155600

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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 TraesCS6A01G155600 chr6A 100.000 4722 0 0 1 4722 144516737 144521458 0.000000e+00 8720.0
1 TraesCS6A01G155600 chr6D 95.358 4265 137 23 459 4676 116334212 116338462 0.000000e+00 6722.0
2 TraesCS6A01G155600 chr6D 93.176 381 19 5 90 468 116333801 116334176 1.920000e-153 553.0
3 TraesCS6A01G155600 chr6B 94.984 4167 142 26 600 4722 206006975 206011118 0.000000e+00 6475.0
4 TraesCS6A01G155600 chr6B 93.939 297 14 3 90 385 206006406 206006699 3.350000e-121 446.0
5 TraesCS6A01G155600 chr6B 83.600 250 14 12 369 604 206006713 206006949 4.790000e-50 209.0
6 TraesCS6A01G155600 chr6B 93.333 90 6 0 1 90 88780891 88780980 2.960000e-27 134.0
7 TraesCS6A01G155600 chr2D 95.506 89 3 1 1 89 375017623 375017536 1.770000e-29 141.0
8 TraesCS6A01G155600 chr3A 94.382 89 5 0 1 89 391883956 391884044 2.290000e-28 137.0
9 TraesCS6A01G155600 chr3A 92.553 94 6 1 1 93 22847403 22847310 2.960000e-27 134.0
10 TraesCS6A01G155600 chr1A 94.382 89 5 0 1 89 540890174 540890262 2.290000e-28 137.0
11 TraesCS6A01G155600 chr7D 94.382 89 4 1 1 89 379774557 379774644 8.240000e-28 135.0
12 TraesCS6A01G155600 chr7D 93.333 90 5 1 1 90 123591769 123591681 1.070000e-26 132.0
13 TraesCS6A01G155600 chr7A 94.382 89 4 1 1 89 432154591 432154504 8.240000e-28 135.0
14 TraesCS6A01G155600 chr1B 90.625 96 9 0 1 96 297001785 297001690 1.380000e-25 128.0
15 TraesCS6A01G155600 chr4B 90.741 54 5 0 1404 1457 643282167 643282220 6.550000e-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 TraesCS6A01G155600 chr6A 144516737 144521458 4721 False 8720.000000 8720 100.000 1 4722 1 chr6A.!!$F1 4721
1 TraesCS6A01G155600 chr6D 116333801 116338462 4661 False 3637.500000 6722 94.267 90 4676 2 chr6D.!!$F1 4586
2 TraesCS6A01G155600 chr6B 206006406 206011118 4712 False 2376.666667 6475 90.841 90 4722 3 chr6B.!!$F2 4632

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
82 83 0.249322 GCAGTTAGCGGCGAATAGGA 60.249 55.0 12.98 0.0 0.0 2.94 F
578 672 1.082117 CACTACGCATCCAACCCGAC 61.082 60.0 0.00 0.0 0.0 4.79 F
1257 1419 0.533491 CATCCTTGCCCCATGTGTTG 59.467 55.0 0.00 0.0 0.0 3.33 F
2187 2349 1.247567 ACGGGTCTTTGGCTCAAATG 58.752 50.0 1.56 0.0 32.7 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1402 0.251297 TCTCAACACATGGGGCAAGG 60.251 55.000 0.0 0.0 0.00 3.61 R
1607 1769 1.231221 TCGGGACAAAAATGACACCG 58.769 50.000 0.0 0.0 41.06 4.94 R
2605 2768 1.732259 CGGACAACAATCAGTAGGTGC 59.268 52.381 0.0 0.0 0.00 5.01 R
3809 3978 2.864343 ACACGTACTTTGACAACAGCTC 59.136 45.455 0.0 0.0 0.00 4.09 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
18 19 2.350738 AAACCACTCAAATGGGCCG 58.649 52.632 0.00 0.00 44.81 6.13
19 20 1.184970 AAACCACTCAAATGGGCCGG 61.185 55.000 0.00 0.00 44.81 6.13
20 21 3.451894 CCACTCAAATGGGCCGGC 61.452 66.667 21.18 21.18 35.95 6.13
21 22 3.451894 CACTCAAATGGGCCGGCC 61.452 66.667 38.57 38.57 0.00 6.13
33 34 4.722700 CCGGCCCAGGGTGAGTTG 62.723 72.222 7.55 0.00 0.00 3.16
34 35 3.953775 CGGCCCAGGGTGAGTTGT 61.954 66.667 7.55 0.00 0.00 3.32
35 36 2.282462 GGCCCAGGGTGAGTTGTG 60.282 66.667 7.55 0.00 0.00 3.33
36 37 2.985847 GCCCAGGGTGAGTTGTGC 60.986 66.667 7.55 0.00 0.00 4.57
37 38 2.282462 CCCAGGGTGAGTTGTGCC 60.282 66.667 0.00 0.00 0.00 5.01
38 39 2.282462 CCAGGGTGAGTTGTGCCC 60.282 66.667 0.00 0.00 42.64 5.36
41 42 2.515901 GGGTGAGTTGTGCCCTGT 59.484 61.111 0.00 0.00 39.31 4.00
42 43 1.898574 GGGTGAGTTGTGCCCTGTG 60.899 63.158 0.00 0.00 39.31 3.66
43 44 1.152963 GGTGAGTTGTGCCCTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
44 45 1.447317 GGTGAGTTGTGCCCTGTGTG 61.447 60.000 0.00 0.00 0.00 3.82
45 46 0.463654 GTGAGTTGTGCCCTGTGTGA 60.464 55.000 0.00 0.00 0.00 3.58
46 47 0.254462 TGAGTTGTGCCCTGTGTGAA 59.746 50.000 0.00 0.00 0.00 3.18
47 48 0.947244 GAGTTGTGCCCTGTGTGAAG 59.053 55.000 0.00 0.00 0.00 3.02
48 49 1.103398 AGTTGTGCCCTGTGTGAAGC 61.103 55.000 0.00 0.00 0.00 3.86
49 50 2.186160 TTGTGCCCTGTGTGAAGCG 61.186 57.895 0.00 0.00 0.00 4.68
50 51 3.357079 GTGCCCTGTGTGAAGCGG 61.357 66.667 0.00 0.00 0.00 5.52
53 54 4.680237 CCCTGTGTGAAGCGGCGA 62.680 66.667 12.98 0.00 0.00 5.54
54 55 3.414700 CCTGTGTGAAGCGGCGAC 61.415 66.667 12.98 1.23 0.00 5.19
55 56 2.356313 CTGTGTGAAGCGGCGACT 60.356 61.111 12.98 4.18 0.00 4.18
56 57 1.080772 CTGTGTGAAGCGGCGACTA 60.081 57.895 12.98 0.00 0.00 2.59
57 58 1.344942 CTGTGTGAAGCGGCGACTAC 61.345 60.000 12.98 3.92 0.00 2.73
58 59 1.080705 GTGTGAAGCGGCGACTACT 60.081 57.895 12.98 0.00 0.00 2.57
59 60 0.666577 GTGTGAAGCGGCGACTACTT 60.667 55.000 12.98 3.67 0.00 2.24
60 61 0.666274 TGTGAAGCGGCGACTACTTG 60.666 55.000 12.98 0.00 0.00 3.16
61 62 1.736645 TGAAGCGGCGACTACTTGC 60.737 57.895 12.98 0.00 0.00 4.01
67 68 2.432628 GCGACTACTTGCCGCAGT 60.433 61.111 0.00 0.00 46.67 4.40
68 69 2.027625 GCGACTACTTGCCGCAGTT 61.028 57.895 0.00 0.00 46.67 3.16
69 70 0.734942 GCGACTACTTGCCGCAGTTA 60.735 55.000 0.00 0.00 46.67 2.24
70 71 1.269166 CGACTACTTGCCGCAGTTAG 58.731 55.000 8.21 8.21 0.00 2.34
71 72 1.000145 GACTACTTGCCGCAGTTAGC 59.000 55.000 9.28 0.00 40.87 3.09
81 82 2.226269 GCAGTTAGCGGCGAATAGG 58.774 57.895 12.98 0.00 0.00 2.57
82 83 0.249322 GCAGTTAGCGGCGAATAGGA 60.249 55.000 12.98 0.00 0.00 2.94
83 84 1.805120 GCAGTTAGCGGCGAATAGGAA 60.805 52.381 12.98 0.00 0.00 3.36
84 85 2.546778 CAGTTAGCGGCGAATAGGAAA 58.453 47.619 12.98 0.00 0.00 3.13
85 86 3.131396 CAGTTAGCGGCGAATAGGAAAT 58.869 45.455 12.98 0.00 0.00 2.17
86 87 3.560068 CAGTTAGCGGCGAATAGGAAATT 59.440 43.478 12.98 0.00 0.00 1.82
87 88 3.808174 AGTTAGCGGCGAATAGGAAATTC 59.192 43.478 12.98 0.00 0.00 2.17
88 89 1.594331 AGCGGCGAATAGGAAATTCC 58.406 50.000 12.98 3.29 36.58 3.01
109 110 2.975799 GAAGGACGGCCAAACGCA 60.976 61.111 11.69 0.00 40.31 5.24
195 196 9.593134 CCGGAATTATTATTTTTGTTTCCATGA 57.407 29.630 0.00 0.00 32.53 3.07
215 217 7.062839 TCCATGACTTTTTGACTTTTTGTTTCG 59.937 33.333 0.00 0.00 0.00 3.46
220 222 5.462034 TTTTGACTTTTTGTTTCGCATGG 57.538 34.783 0.00 0.00 0.00 3.66
227 229 4.582701 TTTTGTTTCGCATGGATGAGTT 57.417 36.364 0.00 0.00 0.00 3.01
334 339 4.314522 TCCCATGGATTGCTTTTCTACA 57.685 40.909 15.22 0.00 0.00 2.74
411 447 9.007901 ACTAGTACTTGTATTCTTCGTGTAGTT 57.992 33.333 8.27 0.00 0.00 2.24
457 503 1.891150 TCTCCGTGTTGTTCTAGTCCC 59.109 52.381 0.00 0.00 0.00 4.46
481 571 4.740822 GCGTCACCATGGCCCCTT 62.741 66.667 13.04 0.00 0.00 3.95
483 573 2.440599 GTCACCATGGCCCCTTGT 59.559 61.111 13.04 0.00 0.00 3.16
572 666 1.404449 CCCGTTACACTACGCATCCAA 60.404 52.381 0.00 0.00 40.10 3.53
578 672 1.082117 CACTACGCATCCAACCCGAC 61.082 60.000 0.00 0.00 0.00 4.79
621 746 8.853077 TCAATCAATCAAGCTTAGAAAAGAGA 57.147 30.769 0.00 0.00 34.37 3.10
626 751 5.290493 TCAAGCTTAGAAAAGAGACACCA 57.710 39.130 0.00 0.00 34.37 4.17
632 757 3.778954 AGAAAAGAGACACCAAGGAGG 57.221 47.619 0.00 0.00 45.67 4.30
779 904 2.612251 CCCTCTCCCTCTCCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
781 906 2.018086 CCTCTCCCTCTCCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
801 929 3.244457 CCTCCTTTCCTTGTAACCTTCGT 60.244 47.826 0.00 0.00 0.00 3.85
859 988 3.415087 AGGCCAGCAGACCATCCC 61.415 66.667 5.01 0.00 0.00 3.85
1160 1320 2.802816 TCGCTTTTTCTCTCTGCAAGTC 59.197 45.455 0.00 0.00 33.76 3.01
1161 1321 2.096019 CGCTTTTTCTCTCTGCAAGTCC 60.096 50.000 0.00 0.00 33.76 3.85
1241 1402 2.223203 CGTGGAAAGCTTGCTCATCATC 60.223 50.000 3.95 0.00 0.00 2.92
1257 1419 0.533491 CATCCTTGCCCCATGTGTTG 59.467 55.000 0.00 0.00 0.00 3.33
1316 1478 3.067106 GAGCTTCGACTCATCAACCAAA 58.933 45.455 0.00 0.00 36.65 3.28
1398 1560 7.924412 ACTTGCTGCCAAATTTATTCATATCTG 59.076 33.333 0.00 0.00 0.00 2.90
1519 1681 2.543777 TCTGGCGTGAGTTAGCTTTT 57.456 45.000 0.00 0.00 0.00 2.27
1572 1734 2.101249 ACCTCACAAATGGTTGCACTTG 59.899 45.455 0.00 0.00 38.39 3.16
1607 1769 5.205565 GTCATTTCGGTGTTTCTTCTTGTC 58.794 41.667 0.00 0.00 0.00 3.18
1673 1835 8.025445 GCTTCAAATAAGGTATGCTGAATATGG 58.975 37.037 0.00 0.00 0.00 2.74
1679 1841 5.786121 AGGTATGCTGAATATGGCCTATT 57.214 39.130 3.32 5.72 32.56 1.73
1692 1854 3.620488 TGGCCTATTCTGATTCAACCAC 58.380 45.455 3.32 0.00 0.00 4.16
1846 2008 5.092554 TCAACGATATCTAAAACCTGCCA 57.907 39.130 0.34 0.00 0.00 4.92
1898 2060 5.243954 TGCATGCTTCTATAGGTCTAATCGT 59.756 40.000 20.33 0.00 0.00 3.73
1933 2095 6.315393 ACAGTAAAAACCACTAGGCATTATCG 59.685 38.462 0.00 0.00 39.06 2.92
1941 2103 4.560128 CACTAGGCATTATCGTGTAGCAT 58.440 43.478 0.00 0.00 0.00 3.79
1957 2119 3.683365 AGCATAGTGTGTGATGTGTCA 57.317 42.857 0.00 0.00 0.00 3.58
2079 2241 7.385267 TGAAGCAGCCAATTTTTGTGTATTAT 58.615 30.769 0.00 0.00 0.00 1.28
2127 2289 1.352352 AGGAGGTATGCACTGTGCTTT 59.648 47.619 30.43 20.70 45.31 3.51
2128 2290 1.470098 GGAGGTATGCACTGTGCTTTG 59.530 52.381 30.43 0.00 45.31 2.77
2187 2349 1.247567 ACGGGTCTTTGGCTCAAATG 58.752 50.000 1.56 0.00 32.70 2.32
2371 2533 3.920197 TGGACTAAAATCTGGAAAGGGGA 59.080 43.478 0.00 0.00 0.00 4.81
2373 2535 4.705507 GGACTAAAATCTGGAAAGGGGAAC 59.294 45.833 0.00 0.00 0.00 3.62
2560 2723 2.825086 CAACTAATGTTGCGTAGGCC 57.175 50.000 4.72 0.00 45.57 5.19
2605 2768 4.528596 AGTGCCTATAGCCACTACTAATGG 59.471 45.833 14.45 0.00 42.71 3.16
2686 2849 7.710475 TGCAATTTTAGCAGTTAAAGCTCTTTT 59.290 29.630 6.92 0.00 42.32 2.27
2943 3106 4.156922 CCTTCCAACACAACACTAACAACA 59.843 41.667 0.00 0.00 0.00 3.33
2948 3111 6.768381 TCCAACACAACACTAACAACATATCA 59.232 34.615 0.00 0.00 0.00 2.15
3093 3256 4.994217 CGGTATGCTTTTGGGTTTCAATTT 59.006 37.500 0.00 0.00 34.98 1.82
3099 3262 5.115480 GCTTTTGGGTTTCAATTTCACTCA 58.885 37.500 0.00 0.00 34.98 3.41
3245 3408 3.784338 TGTTCTTTGAGCAGCCAAAAAG 58.216 40.909 9.48 7.73 35.83 2.27
3376 3539 9.046296 CATTCAGAAAACTGTATGGTAGGATAC 57.954 37.037 0.00 0.00 42.04 2.24
3377 3540 6.802608 TCAGAAAACTGTATGGTAGGATACG 58.197 40.000 0.00 0.00 44.28 3.06
3630 3793 6.806739 TCTCGTATGCCGATCATATTAAGTTG 59.193 38.462 0.00 0.00 46.23 3.16
3631 3794 6.452242 TCGTATGCCGATCATATTAAGTTGT 58.548 36.000 0.00 0.00 41.60 3.32
3632 3795 6.926826 TCGTATGCCGATCATATTAAGTTGTT 59.073 34.615 0.00 0.00 41.60 2.83
3935 4107 5.542616 AAATTGCATTCTCGAGAGTGAAG 57.457 39.130 34.25 14.33 45.39 3.02
4012 4184 5.126061 GGTGCATTCTGTTATTCCACTTGAT 59.874 40.000 0.00 0.00 0.00 2.57
4013 4185 6.032094 GTGCATTCTGTTATTCCACTTGATG 58.968 40.000 0.00 0.00 0.00 3.07
4054 4227 7.255730 AAGTTTTCTTAGAGCATTCTTGCATGT 60.256 33.333 0.33 0.00 44.05 3.21
4110 4287 9.305925 CTGCAATATACGCTGATAAGATAATCA 57.694 33.333 0.00 0.00 34.72 2.57
4194 4374 9.838339 ATGACTAAAATAGGACATCAAACTAGG 57.162 33.333 0.00 0.00 0.00 3.02
4221 4401 4.450419 ACAACTTCAGAAATCAGCTCTTCG 59.550 41.667 0.00 0.00 0.00 3.79
4257 4437 5.758296 TGGTCAGTAGAATGTTTTGACTGTC 59.242 40.000 0.00 0.00 38.87 3.51
4471 4651 5.683681 TGCAATGGAATATAGACAAGCTGA 58.316 37.500 0.00 0.00 0.00 4.26
4478 4658 8.985315 TGGAATATAGACAAGCTGATTGAATT 57.015 30.769 13.20 4.13 41.83 2.17
4551 4731 3.795688 AGGGCCATGAATATTCATCGT 57.204 42.857 24.94 14.30 45.62 3.73
4715 4895 1.073025 TCTGCAAGACGGGCAACAT 59.927 52.632 0.00 0.00 38.67 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.184970 CCGGCCCATTTGAGTGGTTT 61.185 55.000 0.00 0.00 37.57 3.27
1 2 1.606313 CCGGCCCATTTGAGTGGTT 60.606 57.895 0.00 0.00 37.57 3.67
2 3 2.035626 CCGGCCCATTTGAGTGGT 59.964 61.111 0.00 0.00 37.57 4.16
3 4 3.451894 GCCGGCCCATTTGAGTGG 61.452 66.667 18.11 0.00 39.05 4.00
4 5 3.451894 GGCCGGCCCATTTGAGTG 61.452 66.667 36.64 0.00 0.00 3.51
16 17 4.722700 CAACTCACCCTGGGCCGG 62.723 72.222 14.08 5.01 0.00 6.13
17 18 3.953775 ACAACTCACCCTGGGCCG 61.954 66.667 14.08 4.27 0.00 6.13
18 19 2.282462 CACAACTCACCCTGGGCC 60.282 66.667 14.08 0.00 0.00 5.80
19 20 2.985847 GCACAACTCACCCTGGGC 60.986 66.667 14.08 0.00 34.23 5.36
20 21 2.282462 GGCACAACTCACCCTGGG 60.282 66.667 12.28 12.28 0.00 4.45
21 22 2.282462 GGGCACAACTCACCCTGG 60.282 66.667 0.00 0.00 40.75 4.45
24 25 1.898574 CACAGGGCACAACTCACCC 60.899 63.158 0.00 0.00 44.62 4.61
25 26 1.152963 ACACAGGGCACAACTCACC 60.153 57.895 0.00 0.00 0.00 4.02
26 27 0.463654 TCACACAGGGCACAACTCAC 60.464 55.000 0.00 0.00 0.00 3.51
27 28 0.254462 TTCACACAGGGCACAACTCA 59.746 50.000 0.00 0.00 0.00 3.41
28 29 0.947244 CTTCACACAGGGCACAACTC 59.053 55.000 0.00 0.00 0.00 3.01
29 30 1.103398 GCTTCACACAGGGCACAACT 61.103 55.000 0.00 0.00 0.00 3.16
30 31 1.360192 GCTTCACACAGGGCACAAC 59.640 57.895 0.00 0.00 0.00 3.32
31 32 2.186160 CGCTTCACACAGGGCACAA 61.186 57.895 0.00 0.00 0.00 3.33
32 33 2.591429 CGCTTCACACAGGGCACA 60.591 61.111 0.00 0.00 0.00 4.57
33 34 3.357079 CCGCTTCACACAGGGCAC 61.357 66.667 0.00 0.00 0.00 5.01
36 37 4.680237 TCGCCGCTTCACACAGGG 62.680 66.667 0.00 0.00 0.00 4.45
37 38 2.486636 TAGTCGCCGCTTCACACAGG 62.487 60.000 0.00 0.00 0.00 4.00
38 39 1.080772 TAGTCGCCGCTTCACACAG 60.081 57.895 0.00 0.00 0.00 3.66
39 40 1.372499 GTAGTCGCCGCTTCACACA 60.372 57.895 0.00 0.00 0.00 3.72
40 41 0.666577 AAGTAGTCGCCGCTTCACAC 60.667 55.000 0.00 0.00 0.00 3.82
41 42 0.666274 CAAGTAGTCGCCGCTTCACA 60.666 55.000 0.00 0.00 0.00 3.58
42 43 1.956620 GCAAGTAGTCGCCGCTTCAC 61.957 60.000 0.00 0.00 0.00 3.18
43 44 1.736645 GCAAGTAGTCGCCGCTTCA 60.737 57.895 0.00 0.00 0.00 3.02
44 45 2.453638 GGCAAGTAGTCGCCGCTTC 61.454 63.158 0.00 0.00 38.82 3.86
45 46 2.434359 GGCAAGTAGTCGCCGCTT 60.434 61.111 0.00 0.00 38.82 4.68
52 53 1.000145 GCTAACTGCGGCAAGTAGTC 59.000 55.000 16.55 8.72 45.18 2.59
63 64 0.249322 TCCTATTCGCCGCTAACTGC 60.249 55.000 0.00 0.00 38.57 4.40
64 65 2.218953 TTCCTATTCGCCGCTAACTG 57.781 50.000 0.00 0.00 0.00 3.16
65 66 2.973694 TTTCCTATTCGCCGCTAACT 57.026 45.000 0.00 0.00 0.00 2.24
66 67 3.059120 GGAATTTCCTATTCGCCGCTAAC 60.059 47.826 8.25 0.00 32.53 2.34
67 68 3.135994 GGAATTTCCTATTCGCCGCTAA 58.864 45.455 8.25 0.00 32.53 3.09
68 69 2.762745 GGAATTTCCTATTCGCCGCTA 58.237 47.619 8.25 0.00 32.53 4.26
69 70 1.594331 GGAATTTCCTATTCGCCGCT 58.406 50.000 8.25 0.00 32.53 5.52
70 71 0.234884 CGGAATTTCCTATTCGCCGC 59.765 55.000 13.45 0.00 33.30 6.53
71 72 1.525619 GTCGGAATTTCCTATTCGCCG 59.474 52.381 13.45 0.00 33.30 6.46
72 73 1.525619 CGTCGGAATTTCCTATTCGCC 59.474 52.381 13.45 0.00 33.30 5.54
73 74 2.466846 TCGTCGGAATTTCCTATTCGC 58.533 47.619 13.45 0.00 33.30 4.70
74 75 3.489785 CCTTCGTCGGAATTTCCTATTCG 59.510 47.826 13.45 11.45 33.30 3.34
75 76 4.507021 GTCCTTCGTCGGAATTTCCTATTC 59.493 45.833 13.45 0.00 34.20 1.75
76 77 4.439968 GTCCTTCGTCGGAATTTCCTATT 58.560 43.478 13.45 0.00 34.20 1.73
77 78 3.490419 CGTCCTTCGTCGGAATTTCCTAT 60.490 47.826 13.45 0.00 34.20 2.57
78 79 2.159338 CGTCCTTCGTCGGAATTTCCTA 60.159 50.000 13.45 0.00 34.20 2.94
79 80 1.403780 CGTCCTTCGTCGGAATTTCCT 60.404 52.381 13.45 0.00 34.20 3.36
80 81 0.997196 CGTCCTTCGTCGGAATTTCC 59.003 55.000 5.28 5.28 34.20 3.13
88 89 2.356553 TTTGGCCGTCCTTCGTCG 60.357 61.111 0.00 0.00 37.94 5.12
100 101 1.008538 CTGGAGTGTTGCGTTTGGC 60.009 57.895 0.00 0.00 43.96 4.52
109 110 1.664965 GCGAGCGTTCTGGAGTGTT 60.665 57.895 0.00 0.00 0.00 3.32
195 196 6.402011 CCATGCGAAACAAAAAGTCAAAAAGT 60.402 34.615 0.00 0.00 0.00 2.66
334 339 8.270030 ACGGTATTATTCTTAAAAGTTAGGGCT 58.730 33.333 0.00 0.00 0.00 5.19
457 503 0.790207 GCCATGGTGACGCGTATATG 59.210 55.000 13.97 14.02 0.00 1.78
481 571 2.036604 TGTGTGCTTCGTGGATCTTACA 59.963 45.455 0.00 0.00 0.00 2.41
483 573 2.930887 GCTGTGTGCTTCGTGGATCTTA 60.931 50.000 0.00 0.00 38.95 2.10
572 666 1.698067 TTCTGGTTTTCGGGTCGGGT 61.698 55.000 0.00 0.00 0.00 5.28
578 672 2.235016 TGATGGTTTCTGGTTTTCGGG 58.765 47.619 0.00 0.00 0.00 5.14
621 746 5.538813 GGTTCTAATTTTTCCTCCTTGGTGT 59.461 40.000 0.00 0.00 37.07 4.16
626 751 8.173412 AGAAGATGGTTCTAATTTTTCCTCCTT 58.827 33.333 0.00 0.00 0.00 3.36
632 757 7.606349 AGCCAAGAAGATGGTTCTAATTTTTC 58.394 34.615 0.00 0.00 42.75 2.29
668 793 4.115199 GCGACCAATGGGGAGGCT 62.115 66.667 3.55 0.00 41.15 4.58
779 904 3.244457 ACGAAGGTTACAAGGAAAGGAGG 60.244 47.826 0.00 0.00 0.00 4.30
781 906 5.305128 TCTTACGAAGGTTACAAGGAAAGGA 59.695 40.000 0.00 0.00 0.00 3.36
801 929 1.079127 GCTGCCGCTGTTCCTCTTA 60.079 57.895 0.00 0.00 0.00 2.10
923 1082 4.520846 GCCGACAGCCGAAATGCG 62.521 66.667 0.00 0.00 41.76 4.73
998 1157 3.554692 CGTCGCCGCTGTTCATCC 61.555 66.667 0.00 0.00 0.00 3.51
1160 1320 5.359009 ACTTCACAGGATTGCATCTTATTGG 59.641 40.000 0.00 0.00 0.00 3.16
1161 1321 6.446781 ACTTCACAGGATTGCATCTTATTG 57.553 37.500 0.00 0.00 0.00 1.90
1180 1340 8.182227 GCCAAGTGAGTAACCATATTAAACTTC 58.818 37.037 0.00 0.00 0.00 3.01
1186 1346 6.509656 CGTAGCCAAGTGAGTAACCATATTA 58.490 40.000 0.00 0.00 0.00 0.98
1221 1381 2.098770 GGATGATGAGCAAGCTTTCCAC 59.901 50.000 0.00 0.00 0.00 4.02
1241 1402 0.251297 TCTCAACACATGGGGCAAGG 60.251 55.000 0.00 0.00 0.00 3.61
1257 1419 6.538945 AAGGAAGTCAACTCTCCTATTCTC 57.461 41.667 11.69 0.00 0.00 2.87
1316 1478 2.607499 TGTGGTTTTGGATTGCAGGAT 58.393 42.857 0.00 0.00 0.00 3.24
1398 1560 3.062774 GGAATCTGCTTACACGAAAGAGC 59.937 47.826 0.00 0.00 35.74 4.09
1459 1621 4.586306 ACCTACCCATTTTGGAGTAAGG 57.414 45.455 0.00 0.00 40.96 2.69
1523 1685 9.781425 AGGTGATCCTACATATGATCTCTTTAT 57.219 33.333 10.38 0.00 43.12 1.40
1526 1688 7.178274 GTGAGGTGATCCTACATATGATCTCTT 59.822 40.741 10.38 0.00 45.24 2.85
1544 1706 1.774254 ACCATTTGTGAGGTGAGGTGA 59.226 47.619 0.00 0.00 36.60 4.02
1572 1734 3.190535 ACCGAAATGACCTGCATAAACAC 59.809 43.478 0.00 0.00 35.78 3.32
1607 1769 1.231221 TCGGGACAAAAATGACACCG 58.769 50.000 0.00 0.00 41.06 4.94
1673 1835 8.671921 CATATATGTGGTTGAATCAGAATAGGC 58.328 37.037 4.43 0.00 0.00 3.93
1679 1841 7.931407 GGTGTACATATATGTGGTTGAATCAGA 59.069 37.037 25.48 0.96 41.89 3.27
1701 1863 5.061179 ACGTTAGCTAACAAAAGATGGTGT 58.939 37.500 30.63 16.22 35.99 4.16
1846 2008 4.042187 AGCTCATTACCTTGAGTGTCCTTT 59.958 41.667 3.65 0.00 44.10 3.11
1856 2018 3.273434 TGCAGCTAAGCTCATTACCTTG 58.727 45.455 0.00 0.00 36.40 3.61
1898 2060 3.706594 TGGTTTTTACTGTGCCATTCCAA 59.293 39.130 0.00 0.00 0.00 3.53
1922 2084 5.243060 ACACTATGCTACACGATAATGCCTA 59.757 40.000 0.00 0.00 0.00 3.93
1933 2095 4.245660 ACACATCACACACTATGCTACAC 58.754 43.478 0.00 0.00 0.00 2.90
1941 2103 7.170828 GTGAATTAACTGACACATCACACACTA 59.829 37.037 0.00 0.00 36.58 2.74
2079 2241 8.593679 TGATTCTGGTAGAAGTTATTCAACTGA 58.406 33.333 0.00 0.00 44.41 3.41
2127 2289 3.897141 TGACATATTGGTAACCTCGCA 57.103 42.857 0.00 0.00 0.00 5.10
2128 2290 4.873827 TCTTTGACATATTGGTAACCTCGC 59.126 41.667 0.00 0.00 0.00 5.03
2187 2349 1.748493 TGGAGCAAAAACTGGACACAC 59.252 47.619 0.00 0.00 0.00 3.82
2254 2416 9.632638 ACTATCCATTTGTGAGCTAACATTATT 57.367 29.630 4.25 0.00 0.00 1.40
2264 2426 6.016860 TGCATAATCACTATCCATTTGTGAGC 60.017 38.462 0.00 0.00 42.81 4.26
2412 2575 5.893897 AGCAATTTCCAGCAAAACAAAAA 57.106 30.435 0.00 0.00 0.00 1.94
2526 2689 8.650143 AACATTAGTTGGAAAGTGGACATAAT 57.350 30.769 0.00 0.00 36.39 1.28
2560 2723 5.359009 ACTTCTTCATGCAATTATGTGGGAG 59.641 40.000 0.00 0.00 0.00 4.30
2605 2768 1.732259 CGGACAACAATCAGTAGGTGC 59.268 52.381 0.00 0.00 0.00 5.01
2943 3106 7.014134 AGAGATGTCTGTCTTGTCGATTGATAT 59.986 37.037 0.00 0.00 0.00 1.63
2948 3111 5.167121 CAAGAGATGTCTGTCTTGTCGATT 58.833 41.667 0.00 0.00 44.02 3.34
2981 3144 2.965147 ACTTCCAAATTTGTGGTCCCTG 59.035 45.455 16.73 0.00 39.88 4.45
3222 3385 5.509501 CCTTTTTGGCTGCTCAAAGAACATA 60.510 40.000 15.57 1.84 37.82 2.29
3224 3387 3.430651 CCTTTTTGGCTGCTCAAAGAACA 60.431 43.478 15.57 2.63 37.82 3.18
3245 3408 3.096092 TCAGGGGCACAAAATGTTATCC 58.904 45.455 0.00 0.00 0.00 2.59
3376 3539 4.970003 GTCATTTTCTTTGAGGTCAACACG 59.030 41.667 0.00 0.00 35.28 4.49
3377 3540 5.743872 GTGTCATTTTCTTTGAGGTCAACAC 59.256 40.000 0.00 0.00 35.28 3.32
3613 3776 7.227461 CGATGTAACAACTTAATATGATCGGC 58.773 38.462 0.00 0.00 0.00 5.54
3809 3978 2.864343 ACACGTACTTTGACAACAGCTC 59.136 45.455 0.00 0.00 0.00 4.09
3935 4107 5.668471 TGAAGATCAGTCCACAGATTCATC 58.332 41.667 0.00 0.00 0.00 2.92
4061 4234 8.510505 GCAGATCATTATTCTTTATGGAGTTCC 58.489 37.037 0.00 0.00 0.00 3.62
4062 4235 9.060347 TGCAGATCATTATTCTTTATGGAGTTC 57.940 33.333 0.00 0.00 0.00 3.01
4110 4287 9.920946 AACATATGTATCTTGTAACCCTTCAAT 57.079 29.630 9.21 0.00 0.00 2.57
4194 4374 2.352127 GCTGATTTCTGAAGTTGTGCCC 60.352 50.000 0.00 0.00 0.00 5.36
4221 4401 5.416271 TCTACTGACCAGTAACCATTTCC 57.584 43.478 10.65 0.00 42.72 3.13
4257 4437 3.195825 ACTCCGAGTAATGTGAAGAAGGG 59.804 47.826 0.00 0.00 0.00 3.95
4428 4608 5.233988 TGCAAATTCCCTTTTGTTTATCCG 58.766 37.500 0.00 0.00 38.55 4.18
4551 4731 9.621629 TCAAACTGAAAACTCATAGAAGGTTTA 57.378 29.630 0.00 0.00 36.32 2.01
4565 4745 4.305989 TCCAGCATGTCAAACTGAAAAC 57.694 40.909 6.97 0.00 33.10 2.43


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

AutoCloner maintained by Alex Coulton.