Multiple sequence alignment - TraesCS4A01G204300

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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 TraesCS4A01G204300 chr4A 100.000 5548 0 0 1 5548 495795296 495800843 0.000000e+00 10246.0
1 TraesCS4A01G204300 chr4B 94.099 3745 148 34 1836 5548 118291197 118294900 0.000000e+00 5624.0
2 TraesCS4A01G204300 chr4B 95.254 1791 65 11 59 1834 118289439 118291224 0.000000e+00 2819.0
3 TraesCS4A01G204300 chr4D 96.065 2287 63 19 3279 5548 83278910 83281186 0.000000e+00 3699.0
4 TraesCS4A01G204300 chr4D 96.292 1915 56 11 59 1967 83275224 83277129 0.000000e+00 3129.0
5 TraesCS4A01G204300 chr4D 97.182 887 19 3 2396 3282 83277628 83278508 0.000000e+00 1495.0
6 TraesCS4A01G204300 chr4D 95.729 398 17 0 1997 2394 83277123 83277520 4.690000e-180 641.0
7 TraesCS4A01G204300 chr1A 94.595 74 4 0 1 74 321876408 321876335 1.260000e-21 115.0
8 TraesCS4A01G204300 chr1A 96.875 64 2 0 1 64 12370912 12370849 2.110000e-19 108.0
9 TraesCS4A01G204300 chr6B 98.387 62 1 0 1 62 169224584 169224645 5.880000e-20 110.0
10 TraesCS4A01G204300 chr6A 95.652 69 2 1 1 69 469259646 469259713 5.880000e-20 110.0
11 TraesCS4A01G204300 chr6A 94.286 70 4 0 1 70 190598762 190598831 2.110000e-19 108.0
12 TraesCS4A01G204300 chr2D 98.387 62 1 0 1 62 67702605 67702666 5.880000e-20 110.0
13 TraesCS4A01G204300 chr2D 100.000 28 0 0 4116 4143 381301138 381301165 1.000000e-02 52.8
14 TraesCS4A01G204300 chr7D 96.875 64 2 0 1 64 379324177 379324240 2.110000e-19 108.0
15 TraesCS4A01G204300 chr7D 90.698 43 4 0 4115 4157 536135402 536135360 2.160000e-04 58.4
16 TraesCS4A01G204300 chr2B 96.875 64 2 0 1 64 439892797 439892860 2.110000e-19 108.0
17 TraesCS4A01G204300 chr5D 95.455 66 3 0 1 66 531504882 531504817 7.600000e-19 106.0
18 TraesCS4A01G204300 chr6D 94.915 59 3 0 4179 4237 456669717 456669659 5.920000e-15 93.5
19 TraesCS4A01G204300 chr2A 96.875 32 0 1 4116 4146 762156230 762156261 1.000000e-02 52.8


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 TraesCS4A01G204300 chr4A 495795296 495800843 5547 False 10246.0 10246 100.0000 1 5548 1 chr4A.!!$F1 5547
1 TraesCS4A01G204300 chr4B 118289439 118294900 5461 False 4221.5 5624 94.6765 59 5548 2 chr4B.!!$F1 5489
2 TraesCS4A01G204300 chr4D 83275224 83281186 5962 False 2241.0 3699 96.3170 59 5548 4 chr4D.!!$F1 5489

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
107 108 0.248990 TTGCGCTCCTTTGCACAAAG 60.249 50.000 9.73 14.79 45.47 2.77 F
109 110 0.591170 GCGCTCCTTTGCACAAAGTA 59.409 50.000 18.96 5.46 44.66 2.24 F
736 743 1.019278 CGTCCAATTGACACCCTCCG 61.019 60.000 7.12 0.00 44.71 4.63 F
1287 1294 1.275471 CGTCGAGCGACTCTTTTGCA 61.275 55.000 19.23 0.00 44.77 4.08 F
1963 1977 1.402613 TGGCACATTTGATCATGCTCG 59.597 47.619 16.39 0.00 38.18 5.03 F
2907 3035 1.004745 GGACTTCTGCTCCCCATCAAA 59.995 52.381 0.00 0.00 0.00 2.69 F
3586 4127 1.631405 AAGTTGCAGCATGGCCTTAA 58.369 45.000 3.32 0.00 35.86 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1374 1381 1.567357 TGGCATAGTACTCCTGCACA 58.433 50.000 23.99 18.17 37.64 4.57 R
1524 1531 2.551721 GGCATGTTCATGATCCCTCGAT 60.552 50.000 15.74 0.00 0.00 3.59 R
2549 2671 2.092807 TCTGAGCATATTGCCTGCAAGA 60.093 45.455 10.64 6.17 46.52 3.02 R
2602 2724 2.334977 TGGACTTTACCCTCAAGCTCA 58.665 47.619 0.00 0.00 0.00 4.26 R
3586 4127 0.696501 AAGGTCCCAAACGTGCCTAT 59.303 50.000 0.00 0.00 0.00 2.57 R
4148 4690 1.602311 ACAGTTACGACTCCACGACT 58.398 50.000 0.00 0.00 32.54 4.18 R
5267 5847 1.608717 ATTCGCCCTCGTGAAGCTCT 61.609 55.000 0.00 0.00 41.62 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
36 37 9.167311 AGTTTTAGATACATCCATTTCTGTGAC 57.833 33.333 0.00 0.00 0.00 3.67
37 38 7.770801 TTTAGATACATCCATTTCTGTGACG 57.229 36.000 0.00 0.00 0.00 4.35
38 39 5.598416 AGATACATCCATTTCTGTGACGA 57.402 39.130 0.00 0.00 0.00 4.20
39 40 5.595885 AGATACATCCATTTCTGTGACGAG 58.404 41.667 0.00 0.00 0.00 4.18
40 41 3.685139 ACATCCATTTCTGTGACGAGT 57.315 42.857 0.00 0.00 0.00 4.18
41 42 4.801330 ACATCCATTTCTGTGACGAGTA 57.199 40.909 0.00 0.00 0.00 2.59
42 43 5.147330 ACATCCATTTCTGTGACGAGTAA 57.853 39.130 0.00 0.00 0.00 2.24
43 44 5.734720 ACATCCATTTCTGTGACGAGTAAT 58.265 37.500 0.00 0.00 0.00 1.89
44 45 6.173339 ACATCCATTTCTGTGACGAGTAATT 58.827 36.000 0.00 0.00 0.00 1.40
45 46 6.655003 ACATCCATTTCTGTGACGAGTAATTT 59.345 34.615 0.00 0.00 0.00 1.82
46 47 7.822334 ACATCCATTTCTGTGACGAGTAATTTA 59.178 33.333 0.00 0.00 0.00 1.40
47 48 7.827819 TCCATTTCTGTGACGAGTAATTTAG 57.172 36.000 0.00 0.00 0.00 1.85
48 49 7.608153 TCCATTTCTGTGACGAGTAATTTAGA 58.392 34.615 0.00 0.00 0.00 2.10
49 50 8.092068 TCCATTTCTGTGACGAGTAATTTAGAA 58.908 33.333 0.00 0.00 0.00 2.10
50 51 8.169268 CCATTTCTGTGACGAGTAATTTAGAAC 58.831 37.037 0.00 0.00 0.00 3.01
51 52 6.922980 TTCTGTGACGAGTAATTTAGAACG 57.077 37.500 0.00 0.00 0.00 3.95
52 53 5.396484 TCTGTGACGAGTAATTTAGAACGG 58.604 41.667 0.00 0.00 0.00 4.44
53 54 5.181811 TCTGTGACGAGTAATTTAGAACGGA 59.818 40.000 0.00 0.00 0.00 4.69
54 55 5.396484 TGTGACGAGTAATTTAGAACGGAG 58.604 41.667 0.00 0.00 0.00 4.63
55 56 4.797349 GTGACGAGTAATTTAGAACGGAGG 59.203 45.833 0.00 0.00 0.00 4.30
56 57 4.142315 TGACGAGTAATTTAGAACGGAGGG 60.142 45.833 0.00 0.00 0.00 4.30
57 58 4.019174 ACGAGTAATTTAGAACGGAGGGA 58.981 43.478 0.00 0.00 0.00 4.20
58 59 4.097589 ACGAGTAATTTAGAACGGAGGGAG 59.902 45.833 0.00 0.00 0.00 4.30
59 60 4.097589 CGAGTAATTTAGAACGGAGGGAGT 59.902 45.833 0.00 0.00 0.00 3.85
60 61 5.297776 CGAGTAATTTAGAACGGAGGGAGTA 59.702 44.000 0.00 0.00 0.00 2.59
61 62 6.513066 CGAGTAATTTAGAACGGAGGGAGTAG 60.513 46.154 0.00 0.00 0.00 2.57
62 63 6.430007 AGTAATTTAGAACGGAGGGAGTAGA 58.570 40.000 0.00 0.00 0.00 2.59
63 64 6.894103 AGTAATTTAGAACGGAGGGAGTAGAA 59.106 38.462 0.00 0.00 0.00 2.10
83 84 3.528597 ACCTTATCTGAGTTTCTCCGC 57.471 47.619 0.00 0.00 0.00 5.54
104 105 0.388659 ATTTTGCGCTCCTTTGCACA 59.611 45.000 9.73 0.00 41.57 4.57
107 108 0.248990 TTGCGCTCCTTTGCACAAAG 60.249 50.000 9.73 14.79 45.47 2.77
109 110 0.591170 GCGCTCCTTTGCACAAAGTA 59.409 50.000 18.96 5.46 44.66 2.24
114 115 4.670221 CGCTCCTTTGCACAAAGTATTCTC 60.670 45.833 18.96 4.50 44.66 2.87
119 120 3.134574 TGCACAAAGTATTCTCGGGTT 57.865 42.857 0.00 0.00 0.00 4.11
120 121 2.811431 TGCACAAAGTATTCTCGGGTTG 59.189 45.455 0.00 0.00 0.00 3.77
121 122 2.812011 GCACAAAGTATTCTCGGGTTGT 59.188 45.455 0.00 0.00 0.00 3.32
122 123 3.364964 GCACAAAGTATTCTCGGGTTGTG 60.365 47.826 9.23 9.23 45.38 3.33
134 135 1.817740 CGGGTTGTGAACTTGGGTCAT 60.818 52.381 0.00 0.00 0.00 3.06
136 137 2.817844 GGGTTGTGAACTTGGGTCATAC 59.182 50.000 0.00 0.00 0.00 2.39
142 143 4.407621 TGTGAACTTGGGTCATACGGATAT 59.592 41.667 0.00 0.00 0.00 1.63
143 144 5.599242 TGTGAACTTGGGTCATACGGATATA 59.401 40.000 0.00 0.00 0.00 0.86
145 146 7.159372 GTGAACTTGGGTCATACGGATATAAT 58.841 38.462 0.00 0.00 0.00 1.28
146 147 8.308931 GTGAACTTGGGTCATACGGATATAATA 58.691 37.037 0.00 0.00 0.00 0.98
147 148 8.528643 TGAACTTGGGTCATACGGATATAATAG 58.471 37.037 0.00 0.00 0.00 1.73
148 149 7.419711 ACTTGGGTCATACGGATATAATAGG 57.580 40.000 0.00 0.00 0.00 2.57
149 150 5.864418 TGGGTCATACGGATATAATAGGC 57.136 43.478 0.00 0.00 0.00 3.93
180 183 9.737844 AAAATGGGTCACATAAATAAGCAAAAT 57.262 25.926 0.00 0.00 39.40 1.82
545 552 1.679032 GGATTAGTGCGAGGCTTTGGT 60.679 52.381 0.00 0.00 0.00 3.67
580 587 3.703127 GGGGCGGTCGGAAGAGTT 61.703 66.667 0.00 0.00 43.49 3.01
608 615 3.778718 CGAATTGGTGAGTATTTTTCGCG 59.221 43.478 0.00 0.00 0.00 5.87
630 637 4.249661 GGTTTTGGTTGTTTCTTTCTGCA 58.750 39.130 0.00 0.00 0.00 4.41
631 638 4.329801 GGTTTTGGTTGTTTCTTTCTGCAG 59.670 41.667 7.63 7.63 0.00 4.41
635 642 3.130340 TGGTTGTTTCTTTCTGCAGTTCC 59.870 43.478 14.67 3.61 0.00 3.62
730 737 3.966218 CGTTTTCTTCGTCCAATTGACAC 59.034 43.478 7.12 2.18 44.71 3.67
736 743 1.019278 CGTCCAATTGACACCCTCCG 61.019 60.000 7.12 0.00 44.71 4.63
859 866 6.892310 AGAAGAACACAAGCAAAATTGTTC 57.108 33.333 5.38 5.38 45.42 3.18
872 879 3.559238 AATTGTTCTGTCATGCCGTTC 57.441 42.857 0.00 0.00 0.00 3.95
1287 1294 1.275471 CGTCGAGCGACTCTTTTGCA 61.275 55.000 19.23 0.00 44.77 4.08
1415 1422 1.690219 CCAAGCTCATACGGGAGGCT 61.690 60.000 0.00 0.00 35.41 4.58
1524 1531 4.624364 CACGGGCCACTGAGTGCA 62.624 66.667 7.16 0.00 31.34 4.57
1963 1977 1.402613 TGGCACATTTGATCATGCTCG 59.597 47.619 16.39 0.00 38.18 5.03
2014 2028 1.410153 GGGCTGCCAAATGAATCGAAT 59.590 47.619 22.05 0.00 0.00 3.34
2171 2185 1.683385 CCGATGCTCACACCTGATAGA 59.317 52.381 0.00 0.00 0.00 1.98
2177 2191 6.072452 CGATGCTCACACCTGATAGAATAGTA 60.072 42.308 0.00 0.00 0.00 1.82
2432 2552 7.806180 ACTTAAGGCACTATGGTTTATCAGAT 58.194 34.615 7.53 0.00 38.49 2.90
2590 2712 3.121544 GAGGTCTCGTGTTCGAAAACTT 58.878 45.455 16.24 0.00 45.61 2.66
2602 2724 7.519002 GTGTTCGAAAACTTCAGTATATTGCT 58.481 34.615 11.37 0.00 36.30 3.91
2644 2766 5.121105 CAATCATTACAGGTGAGCTCATCA 58.879 41.667 28.21 8.51 34.79 3.07
2907 3035 1.004745 GGACTTCTGCTCCCCATCAAA 59.995 52.381 0.00 0.00 0.00 2.69
2908 3036 2.555227 GGACTTCTGCTCCCCATCAAAA 60.555 50.000 0.00 0.00 0.00 2.44
2909 3037 3.157087 GACTTCTGCTCCCCATCAAAAA 58.843 45.455 0.00 0.00 0.00 1.94
2910 3038 3.160269 ACTTCTGCTCCCCATCAAAAAG 58.840 45.455 0.00 0.00 0.00 2.27
3034 3162 7.924358 ATACTTTTTAAAAGAAGGTTGGGGT 57.076 32.000 22.31 1.39 0.00 4.95
3066 3194 3.322541 TCTGTGACGTTAATGAGGACCAA 59.677 43.478 0.58 0.00 0.00 3.67
3213 3347 8.324306 AGATGGTGTTCAAATTCTGAAGAGATA 58.676 33.333 0.00 0.00 44.83 1.98
3249 3383 6.751514 ACACTATACTGTCTTCTCAGTGAG 57.248 41.667 14.36 14.36 46.36 3.51
3377 3916 5.723672 TTCTGGAGAGATGTCTTTACGTT 57.276 39.130 0.00 0.00 30.97 3.99
3488 4029 3.767278 ACTCAAACGGCGACTACTATTC 58.233 45.455 16.62 0.00 0.00 1.75
3586 4127 1.631405 AAGTTGCAGCATGGCCTTAA 58.369 45.000 3.32 0.00 35.86 1.85
3658 4199 9.442047 AGTCCATAGTTCTTTGATAAGTTCTTG 57.558 33.333 0.00 0.00 32.98 3.02
3728 4269 8.263950 CGCTGAAATTCTAAATGCACAAATATG 58.736 33.333 0.00 0.00 0.00 1.78
3758 4299 6.683974 TGATATTTCAAGTTAGGCTTCTGC 57.316 37.500 0.00 0.00 34.69 4.26
4100 4642 4.516698 ACGAACATCTTCTGCACAAGATTT 59.483 37.500 13.85 11.51 40.52 2.17
4114 4656 5.179182 GCACAAGATTTGGTTTAATTGGGTG 59.821 40.000 0.00 0.00 34.12 4.61
4133 4675 3.243068 GGTGCACTGTTTTTGAGTCGAAT 60.243 43.478 17.98 0.00 0.00 3.34
4145 4687 3.891786 GTCGAATGACTAGTCGCGA 57.108 52.632 22.95 22.95 43.47 5.87
4147 4689 1.062294 GTCGAATGACTAGTCGCGACT 59.938 52.381 40.17 40.17 43.47 4.18
4148 4690 2.283617 GTCGAATGACTAGTCGCGACTA 59.716 50.000 38.33 38.33 43.47 2.59
4167 4709 1.602311 AGTCGTGGAGTCGTAACTGT 58.398 50.000 0.00 0.00 35.28 3.55
4201 4769 0.531974 TGCAGGGTCGACTTGTCAAC 60.532 55.000 16.46 0.00 0.00 3.18
4213 4781 1.000955 CTTGTCAACAGTCGCTACCCT 59.999 52.381 0.00 0.00 0.00 4.34
4218 4786 3.130693 GTCAACAGTCGCTACCCTAGAAT 59.869 47.826 0.00 0.00 0.00 2.40
4481 5052 1.331756 CTTGACTCGCAGTTTGCAAGT 59.668 47.619 0.00 0.00 44.37 3.16
4659 5230 2.022754 GCATCAGGAAAGGAGCAGCAT 61.023 52.381 0.00 0.00 0.00 3.79
4905 5476 6.119536 TGTGGTCTTGTTTCTCTATGTTGTT 58.880 36.000 0.00 0.00 0.00 2.83
4918 5489 7.532571 TCTCTATGTTGTTTTCTTCATGCATG 58.467 34.615 21.07 21.07 0.00 4.06
5121 5692 3.732721 GCAACTTCACTGTGAAATTCTGC 59.267 43.478 22.25 21.07 35.73 4.26
5184 5755 9.050601 GTGAGTAGATTTATCTCATTTGGGAAG 57.949 37.037 0.00 0.00 39.77 3.46
5230 5801 3.311871 CAGTATGGCTGTGCTTCTGATTC 59.688 47.826 0.00 0.00 40.27 2.52
5412 5994 4.501198 CGTTGTTGCCACGATTTAAACTTT 59.499 37.500 0.00 0.00 0.00 2.66
5413 5995 5.681982 CGTTGTTGCCACGATTTAAACTTTA 59.318 36.000 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.167311 GTCACAGAAATGGATGTATCTAAAACT 57.833 33.333 0.00 0.00 0.00 2.66
11 12 8.116753 CGTCACAGAAATGGATGTATCTAAAAC 58.883 37.037 0.00 0.00 0.00 2.43
12 13 8.038351 TCGTCACAGAAATGGATGTATCTAAAA 58.962 33.333 0.00 0.00 0.00 1.52
13 14 7.552459 TCGTCACAGAAATGGATGTATCTAAA 58.448 34.615 0.00 0.00 0.00 1.85
14 15 7.107639 TCGTCACAGAAATGGATGTATCTAA 57.892 36.000 0.00 0.00 0.00 2.10
15 16 6.321435 ACTCGTCACAGAAATGGATGTATCTA 59.679 38.462 0.00 0.00 0.00 1.98
16 17 5.127845 ACTCGTCACAGAAATGGATGTATCT 59.872 40.000 0.00 0.00 0.00 1.98
17 18 5.352284 ACTCGTCACAGAAATGGATGTATC 58.648 41.667 0.00 0.00 0.00 2.24
18 19 5.344743 ACTCGTCACAGAAATGGATGTAT 57.655 39.130 0.00 0.00 0.00 2.29
19 20 4.801330 ACTCGTCACAGAAATGGATGTA 57.199 40.909 0.00 0.00 0.00 2.29
20 21 3.685139 ACTCGTCACAGAAATGGATGT 57.315 42.857 0.00 0.00 0.00 3.06
21 22 6.668541 AATTACTCGTCACAGAAATGGATG 57.331 37.500 0.00 0.00 0.00 3.51
22 23 8.258007 TCTAAATTACTCGTCACAGAAATGGAT 58.742 33.333 0.00 0.00 0.00 3.41
23 24 7.608153 TCTAAATTACTCGTCACAGAAATGGA 58.392 34.615 0.00 0.00 0.00 3.41
24 25 7.827819 TCTAAATTACTCGTCACAGAAATGG 57.172 36.000 0.00 0.00 0.00 3.16
25 26 7.893236 CGTTCTAAATTACTCGTCACAGAAATG 59.107 37.037 0.00 0.00 0.00 2.32
26 27 7.063074 CCGTTCTAAATTACTCGTCACAGAAAT 59.937 37.037 0.00 0.00 0.00 2.17
27 28 6.364165 CCGTTCTAAATTACTCGTCACAGAAA 59.636 38.462 0.00 0.00 0.00 2.52
28 29 5.860182 CCGTTCTAAATTACTCGTCACAGAA 59.140 40.000 0.00 0.00 0.00 3.02
29 30 5.181811 TCCGTTCTAAATTACTCGTCACAGA 59.818 40.000 0.00 0.00 0.00 3.41
30 31 5.396484 TCCGTTCTAAATTACTCGTCACAG 58.604 41.667 0.00 0.00 0.00 3.66
31 32 5.375417 TCCGTTCTAAATTACTCGTCACA 57.625 39.130 0.00 0.00 0.00 3.58
32 33 4.797349 CCTCCGTTCTAAATTACTCGTCAC 59.203 45.833 0.00 0.00 0.00 3.67
33 34 4.142315 CCCTCCGTTCTAAATTACTCGTCA 60.142 45.833 0.00 0.00 0.00 4.35
34 35 4.096984 TCCCTCCGTTCTAAATTACTCGTC 59.903 45.833 0.00 0.00 0.00 4.20
35 36 4.019174 TCCCTCCGTTCTAAATTACTCGT 58.981 43.478 0.00 0.00 0.00 4.18
36 37 4.097589 ACTCCCTCCGTTCTAAATTACTCG 59.902 45.833 0.00 0.00 0.00 4.18
37 38 5.595257 ACTCCCTCCGTTCTAAATTACTC 57.405 43.478 0.00 0.00 0.00 2.59
38 39 6.430007 TCTACTCCCTCCGTTCTAAATTACT 58.570 40.000 0.00 0.00 0.00 2.24
39 40 6.705863 TCTACTCCCTCCGTTCTAAATTAC 57.294 41.667 0.00 0.00 0.00 1.89
40 41 6.097412 GGTTCTACTCCCTCCGTTCTAAATTA 59.903 42.308 0.00 0.00 0.00 1.40
41 42 5.105023 GGTTCTACTCCCTCCGTTCTAAATT 60.105 44.000 0.00 0.00 0.00 1.82
42 43 4.405036 GGTTCTACTCCCTCCGTTCTAAAT 59.595 45.833 0.00 0.00 0.00 1.40
43 44 3.766051 GGTTCTACTCCCTCCGTTCTAAA 59.234 47.826 0.00 0.00 0.00 1.85
44 45 3.011032 AGGTTCTACTCCCTCCGTTCTAA 59.989 47.826 0.00 0.00 0.00 2.10
45 46 2.579860 AGGTTCTACTCCCTCCGTTCTA 59.420 50.000 0.00 0.00 0.00 2.10
46 47 1.358445 AGGTTCTACTCCCTCCGTTCT 59.642 52.381 0.00 0.00 0.00 3.01
47 48 1.849977 AGGTTCTACTCCCTCCGTTC 58.150 55.000 0.00 0.00 0.00 3.95
48 49 2.322339 AAGGTTCTACTCCCTCCGTT 57.678 50.000 0.00 0.00 0.00 4.44
49 50 3.204831 AGATAAGGTTCTACTCCCTCCGT 59.795 47.826 0.00 0.00 0.00 4.69
50 51 3.570550 CAGATAAGGTTCTACTCCCTCCG 59.429 52.174 0.00 0.00 0.00 4.63
51 52 4.805744 TCAGATAAGGTTCTACTCCCTCC 58.194 47.826 0.00 0.00 0.00 4.30
52 53 5.451354 ACTCAGATAAGGTTCTACTCCCTC 58.549 45.833 0.00 0.00 0.00 4.30
53 54 5.475398 ACTCAGATAAGGTTCTACTCCCT 57.525 43.478 0.00 0.00 0.00 4.20
54 55 6.547930 AAACTCAGATAAGGTTCTACTCCC 57.452 41.667 0.00 0.00 0.00 4.30
61 62 3.866327 GCGGAGAAACTCAGATAAGGTTC 59.134 47.826 0.00 0.00 42.25 3.62
62 63 3.260884 TGCGGAGAAACTCAGATAAGGTT 59.739 43.478 0.00 0.00 31.08 3.50
63 64 2.832129 TGCGGAGAAACTCAGATAAGGT 59.168 45.455 0.00 0.00 31.08 3.50
83 84 1.192980 GTGCAAAGGAGCGCAAAATTG 59.807 47.619 11.47 10.82 44.15 2.32
104 105 4.969484 AGTTCACAACCCGAGAATACTTT 58.031 39.130 0.00 0.00 0.00 2.66
107 108 3.435671 CCAAGTTCACAACCCGAGAATAC 59.564 47.826 0.00 0.00 0.00 1.89
109 110 2.504367 CCAAGTTCACAACCCGAGAAT 58.496 47.619 0.00 0.00 0.00 2.40
114 115 0.464735 TGACCCAAGTTCACAACCCG 60.465 55.000 0.00 0.00 0.00 5.28
119 120 1.972075 TCCGTATGACCCAAGTTCACA 59.028 47.619 0.00 0.00 0.00 3.58
120 121 2.754946 TCCGTATGACCCAAGTTCAC 57.245 50.000 0.00 0.00 0.00 3.18
121 122 6.734502 TTATATCCGTATGACCCAAGTTCA 57.265 37.500 0.00 0.00 0.00 3.18
122 123 7.980099 CCTATTATATCCGTATGACCCAAGTTC 59.020 40.741 0.00 0.00 0.00 3.01
180 183 1.588674 CAAGGTGTGCCTACGTCAAA 58.411 50.000 0.00 0.00 46.33 2.69
317 320 2.998772 TGCAGAAACTTTGATGAACGC 58.001 42.857 0.00 0.00 0.00 4.84
402 405 7.363031 AGAAATTGTATAGTACTGAGGGGAGA 58.637 38.462 5.39 0.00 0.00 3.71
545 552 2.117206 ACCCCAGATTTGCCGCAA 59.883 55.556 0.38 0.38 0.00 4.85
580 587 2.173758 TACTCACCAATTCGGCCGCA 62.174 55.000 23.51 11.40 39.03 5.69
608 615 4.249661 TGCAGAAAGAAACAACCAAAACC 58.750 39.130 0.00 0.00 0.00 3.27
630 637 3.570212 AAGGCCGCACCAGGAACT 61.570 61.111 0.00 0.00 43.14 3.01
631 638 3.365265 CAAGGCCGCACCAGGAAC 61.365 66.667 0.00 0.00 43.14 3.62
635 642 4.711949 AGAGCAAGGCCGCACCAG 62.712 66.667 5.37 0.00 43.14 4.00
736 743 0.108041 TCCGCATAAAGGACCGAACC 60.108 55.000 0.00 0.00 31.86 3.62
872 879 1.336440 CTCTACCCACAGATCTCAGCG 59.664 57.143 0.00 0.00 0.00 5.18
1287 1294 2.733593 GCGCTTCCGTCGAACAGT 60.734 61.111 0.00 0.00 36.67 3.55
1374 1381 1.567357 TGGCATAGTACTCCTGCACA 58.433 50.000 23.99 18.17 37.64 4.57
1524 1531 2.551721 GGCATGTTCATGATCCCTCGAT 60.552 50.000 15.74 0.00 0.00 3.59
1963 1977 2.674380 CCTTGCTCCACCACTGGC 60.674 66.667 0.00 0.00 37.49 4.85
2014 2028 9.661954 TGGGCCCTCATTAATATTGTTAAAATA 57.338 29.630 25.70 0.00 0.00 1.40
2238 2252 8.304202 TGTTGTTTTACATTTATGTTGCCATC 57.696 30.769 0.02 0.00 41.97 3.51
2239 2253 8.845413 ATGTTGTTTTACATTTATGTTGCCAT 57.155 26.923 0.02 0.00 41.97 4.40
2538 2660 2.961741 TGCCTGCAAGAAATGTTGGTAA 59.038 40.909 0.00 0.00 34.07 2.85
2549 2671 2.092807 TCTGAGCATATTGCCTGCAAGA 60.093 45.455 10.64 6.17 46.52 3.02
2590 2712 4.202295 CCCTCAAGCTCAGCAATATACTGA 60.202 45.833 0.00 7.84 41.78 3.41
2602 2724 2.334977 TGGACTTTACCCTCAAGCTCA 58.665 47.619 0.00 0.00 0.00 4.26
2880 3008 3.269381 TGGGGAGCAGAAGTCCAAAATAT 59.731 43.478 0.00 0.00 35.57 1.28
3034 3162 6.757478 TCATTAACGTCACAGAAAGTACAACA 59.243 34.615 0.00 0.00 0.00 3.33
3249 3383 4.811557 GCATGTACCCATCACTTAGACTTC 59.188 45.833 0.00 0.00 0.00 3.01
3399 3938 4.431416 TCAGCCTAAAGTTCAACCAGAA 57.569 40.909 0.00 0.00 0.00 3.02
3488 4029 8.263940 TCATTAGGTCTTTGAAGGATAAAACG 57.736 34.615 0.00 0.00 0.00 3.60
3586 4127 0.696501 AAGGTCCCAAACGTGCCTAT 59.303 50.000 0.00 0.00 0.00 2.57
3652 4193 6.741992 TGACACATGATATGTTCCAAGAAC 57.258 37.500 0.00 0.47 42.70 3.01
3658 4199 5.125356 TGTCCATGACACATGATATGTTCC 58.875 41.667 12.46 0.00 42.70 3.62
3700 4241 4.722194 TGTGCATTTAGAATTTCAGCGAC 58.278 39.130 0.00 0.00 0.00 5.19
3773 4314 8.862085 TGAATGGACACATGCATTATATGAATT 58.138 29.630 0.00 0.00 45.94 2.17
3783 4324 5.918426 TGTATTTGAATGGACACATGCAT 57.082 34.783 0.00 0.00 42.23 3.96
3803 4344 4.020218 ACAACCACTAGCATGTGACTATGT 60.020 41.667 10.13 6.85 40.12 2.29
3940 4482 3.818180 CCTAAGGCAGCAATCTCTCAAT 58.182 45.455 0.00 0.00 0.00 2.57
3985 4527 3.290948 TCTACAACTGGTGTTTGCCTT 57.709 42.857 2.56 0.00 41.98 4.35
4100 4642 2.672098 ACAGTGCACCCAATTAAACCA 58.328 42.857 14.63 0.00 0.00 3.67
4114 4656 3.968724 GTCATTCGACTCAAAAACAGTGC 59.031 43.478 0.00 0.00 39.22 4.40
4144 4686 2.999355 AGTTACGACTCCACGACTAGTC 59.001 50.000 13.18 13.18 39.00 2.59
4145 4687 2.740981 CAGTTACGACTCCACGACTAGT 59.259 50.000 0.00 0.00 32.54 2.57
4147 4689 2.771089 ACAGTTACGACTCCACGACTA 58.229 47.619 0.00 0.00 32.54 2.59
4148 4690 1.602311 ACAGTTACGACTCCACGACT 58.398 50.000 0.00 0.00 32.54 4.18
4149 4691 3.486584 CTTACAGTTACGACTCCACGAC 58.513 50.000 0.00 0.00 32.54 4.34
4150 4692 2.485426 CCTTACAGTTACGACTCCACGA 59.515 50.000 0.00 0.00 32.54 4.35
4151 4693 2.227388 ACCTTACAGTTACGACTCCACG 59.773 50.000 0.00 0.00 32.54 4.94
4154 4696 4.022503 AGTTGACCTTACAGTTACGACTCC 60.023 45.833 0.00 0.00 32.54 3.85
4167 4709 2.224523 CCCTGCAGTTGAGTTGACCTTA 60.225 50.000 13.81 0.00 0.00 2.69
4201 4769 2.952978 AGTCATTCTAGGGTAGCGACTG 59.047 50.000 0.00 0.00 32.25 3.51
4213 4781 2.884827 TCGAGTCGACGAGTCATTCTA 58.115 47.619 27.39 8.51 37.37 2.10
4218 4786 2.483106 AGATTTTCGAGTCGACGAGTCA 59.517 45.455 27.39 14.70 43.04 3.41
4308 4876 8.526147 CAGTCAGACCATTCCATTTTTCTTAAT 58.474 33.333 0.00 0.00 0.00 1.40
4659 5230 4.892934 GTGATAGGGGCACAATTCCAAATA 59.107 41.667 0.00 0.00 36.31 1.40
4905 5476 5.887598 ACTATGGCTAACATGCATGAAGAAA 59.112 36.000 32.75 18.49 40.82 2.52
4918 5489 3.209410 AGCAATGCAGACTATGGCTAAC 58.791 45.455 8.35 0.00 33.11 2.34
5121 5692 2.290367 TGAAACGAGATGGCACAACTTG 59.710 45.455 0.00 0.00 43.03 3.16
5184 5755 7.802738 TGGCGTGCAAAATATACAAGTATATC 58.197 34.615 11.90 2.70 37.66 1.63
5186 5757 6.764085 ACTGGCGTGCAAAATATACAAGTATA 59.236 34.615 2.68 2.68 33.09 1.47
5187 5758 5.588648 ACTGGCGTGCAAAATATACAAGTAT 59.411 36.000 0.00 0.00 0.00 2.12
5192 5763 4.274705 CCATACTGGCGTGCAAAATATACA 59.725 41.667 0.00 0.00 0.00 2.29
5224 5795 7.010738 ACTCACATTTTGCAAAGTTTGAATCAG 59.989 33.333 19.85 12.84 0.00 2.90
5225 5796 6.817641 ACTCACATTTTGCAAAGTTTGAATCA 59.182 30.769 19.85 5.10 0.00 2.57
5230 5801 6.884096 TGTACTCACATTTTGCAAAGTTTG 57.116 33.333 12.41 12.77 0.00 2.93
5267 5847 1.608717 ATTCGCCCTCGTGAAGCTCT 61.609 55.000 0.00 0.00 41.62 4.09
5331 5911 8.637196 AAGGTTTCTTCGATTTTTCTTCCTAT 57.363 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.