Multiple sequence alignment - TraesCS3D01G174700

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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 TraesCS3D01G174700 chr3D 100.000 4113 0 0 1 4113 156260190 156256078 0.000000e+00 7596.0
1 TraesCS3D01G174700 chr3A 95.211 2464 76 18 1688 4113 175958751 175956292 0.000000e+00 3858.0
2 TraesCS3D01G174700 chr3A 95.450 1011 43 3 154 1163 176018372 176017364 0.000000e+00 1609.0
3 TraesCS3D01G174700 chr3A 96.992 532 16 0 1159 1690 175959487 175958956 0.000000e+00 894.0
4 TraesCS3D01G174700 chr3A 99.371 159 1 0 1 159 176022791 176022633 5.200000e-74 289.0
5 TraesCS3D01G174700 chr7D 92.766 1258 71 12 958 2204 510458642 510457394 0.000000e+00 1801.0
6 TraesCS3D01G174700 chr7D 89.765 850 56 10 90 917 510459477 510458637 0.000000e+00 1059.0
7 TraesCS3D01G174700 chr7D 79.637 717 95 20 3363 4036 510455417 510454709 6.230000e-128 468.0
8 TraesCS3D01G174700 chr7D 95.539 269 10 1 2214 2482 510456138 510455872 2.940000e-116 429.0
9 TraesCS3D01G174700 chr7D 81.573 445 44 18 2913 3352 510455868 510455457 2.370000e-87 333.0
10 TraesCS3D01G174700 chr7B 92.460 1260 73 13 958 2204 538873964 538872714 0.000000e+00 1781.0
11 TraesCS3D01G174700 chr7B 89.765 850 56 11 90 917 538874799 538873959 0.000000e+00 1059.0
12 TraesCS3D01G174700 chr7B 93.214 280 16 2 2214 2493 538870365 538870089 3.830000e-110 409.0
13 TraesCS3D01G174700 chr7B 81.364 440 48 19 2914 3352 538870093 538869687 1.100000e-85 327.0
14 TraesCS3D01G174700 chr7A 92.448 1258 73 14 958 2204 581353247 581352001 0.000000e+00 1777.0
15 TraesCS3D01G174700 chr7A 89.517 849 59 10 90 917 581354081 581353242 0.000000e+00 1048.0
16 TraesCS3D01G174700 chr7A 93.885 278 14 2 2214 2491 581350644 581350370 2.290000e-112 416.0
17 TraesCS3D01G174700 chr7A 80.909 440 50 14 2914 3352 581350372 581349966 2.390000e-82 316.0
18 TraesCS3D01G174700 chr3B 95.745 329 14 0 3785 4113 225184157 225184485 7.830000e-147 531.0
19 TraesCS3D01G174700 chr3B 97.710 131 3 0 3658 3788 225183946 225184076 4.140000e-55 226.0
20 TraesCS3D01G174700 chr3B 98.148 54 1 0 3610 3663 225180837 225180890 1.220000e-15 95.3


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 TraesCS3D01G174700 chr3D 156256078 156260190 4112 True 7596.00 7596 100.00000 1 4113 1 chr3D.!!$R1 4112
1 TraesCS3D01G174700 chr3A 175956292 175959487 3195 True 2376.00 3858 96.10150 1159 4113 2 chr3A.!!$R3 2954
2 TraesCS3D01G174700 chr3A 176017364 176018372 1008 True 1609.00 1609 95.45000 154 1163 1 chr3A.!!$R1 1009
3 TraesCS3D01G174700 chr7D 510454709 510459477 4768 True 818.00 1801 87.85600 90 4036 5 chr7D.!!$R1 3946
4 TraesCS3D01G174700 chr7B 538869687 538874799 5112 True 894.00 1781 89.20075 90 3352 4 chr7B.!!$R1 3262
5 TraesCS3D01G174700 chr7A 581349966 581354081 4115 True 889.25 1777 89.18975 90 3352 4 chr7A.!!$R1 3262
6 TraesCS3D01G174700 chr3B 225180837 225184485 3648 False 284.10 531 97.20100 3610 4113 3 chr3B.!!$F1 503

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
19 20 0.460987 CGAGTCAGAATGGGTGAGCC 60.461 60.000 0.00 0.0 36.16 4.70 F
1131 1156 1.135333 GACGTTGGACTCCCTCTCATC 59.865 57.143 0.00 0.0 0.00 2.92 F
1678 1703 0.811915 ACGAAGGGTCTCATCGACAG 59.188 55.000 4.02 0.0 44.68 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1521 0.953471 TTCGCGTTCCAGTTCCATGG 60.953 55.000 4.97 4.97 42.11 3.66 R
2815 5644 2.176889 ACTGGTTACCATAGTGAGCGT 58.823 47.619 3.88 0.00 32.96 5.07 R
3563 6429 0.103572 GCCCAGTTATGCATGCCAAG 59.896 55.000 16.68 0.00 0.00 3.61 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 3.056628 CGAGTCAGAATGGGTGAGC 57.943 57.895 0.00 0.00 36.16 4.26
19 20 0.460987 CGAGTCAGAATGGGTGAGCC 60.461 60.000 0.00 0.00 36.16 4.70
33 34 4.157849 GGTGAGCCCTTATTTAGCTTCT 57.842 45.455 0.00 0.00 36.87 2.85
34 35 5.291905 GGTGAGCCCTTATTTAGCTTCTA 57.708 43.478 0.00 0.00 36.87 2.10
35 36 5.681639 GGTGAGCCCTTATTTAGCTTCTAA 58.318 41.667 0.00 0.00 36.87 2.10
36 37 5.527951 GGTGAGCCCTTATTTAGCTTCTAAC 59.472 44.000 0.00 0.00 36.87 2.34
37 38 5.527951 GTGAGCCCTTATTTAGCTTCTAACC 59.472 44.000 0.00 0.00 36.87 2.85
38 39 5.050126 AGCCCTTATTTAGCTTCTAACCC 57.950 43.478 0.00 0.00 31.27 4.11
39 40 4.477213 AGCCCTTATTTAGCTTCTAACCCA 59.523 41.667 0.00 0.00 31.27 4.51
40 41 5.134509 AGCCCTTATTTAGCTTCTAACCCAT 59.865 40.000 0.00 0.00 31.27 4.00
41 42 5.473846 GCCCTTATTTAGCTTCTAACCCATC 59.526 44.000 0.00 0.00 0.00 3.51
42 43 6.691749 GCCCTTATTTAGCTTCTAACCCATCT 60.692 42.308 0.00 0.00 0.00 2.90
43 44 6.937465 CCCTTATTTAGCTTCTAACCCATCTC 59.063 42.308 0.00 0.00 0.00 2.75
44 45 6.937465 CCTTATTTAGCTTCTAACCCATCTCC 59.063 42.308 0.00 0.00 0.00 3.71
45 46 4.772886 TTTAGCTTCTAACCCATCTCCC 57.227 45.455 0.00 0.00 0.00 4.30
46 47 2.270434 AGCTTCTAACCCATCTCCCA 57.730 50.000 0.00 0.00 0.00 4.37
47 48 2.122768 AGCTTCTAACCCATCTCCCAG 58.877 52.381 0.00 0.00 0.00 4.45
48 49 2.119495 GCTTCTAACCCATCTCCCAGA 58.881 52.381 0.00 0.00 0.00 3.86
49 50 2.708325 GCTTCTAACCCATCTCCCAGAT 59.292 50.000 0.00 0.00 34.74 2.90
50 51 3.137360 GCTTCTAACCCATCTCCCAGATT 59.863 47.826 0.00 0.00 31.32 2.40
51 52 4.385754 GCTTCTAACCCATCTCCCAGATTT 60.386 45.833 0.00 0.00 31.32 2.17
52 53 5.372373 CTTCTAACCCATCTCCCAGATTTC 58.628 45.833 0.00 0.00 31.32 2.17
53 54 4.370776 TCTAACCCATCTCCCAGATTTCA 58.629 43.478 0.00 0.00 31.32 2.69
54 55 4.977739 TCTAACCCATCTCCCAGATTTCAT 59.022 41.667 0.00 0.00 31.32 2.57
55 56 3.872459 ACCCATCTCCCAGATTTCATC 57.128 47.619 0.00 0.00 31.32 2.92
56 57 2.105477 ACCCATCTCCCAGATTTCATCG 59.895 50.000 0.00 0.00 31.32 3.84
57 58 2.149578 CCATCTCCCAGATTTCATCGC 58.850 52.381 0.00 0.00 31.32 4.58
58 59 2.486013 CCATCTCCCAGATTTCATCGCA 60.486 50.000 0.00 0.00 31.32 5.10
59 60 2.315925 TCTCCCAGATTTCATCGCAC 57.684 50.000 0.00 0.00 0.00 5.34
60 61 1.833630 TCTCCCAGATTTCATCGCACT 59.166 47.619 0.00 0.00 0.00 4.40
61 62 2.237143 TCTCCCAGATTTCATCGCACTT 59.763 45.455 0.00 0.00 0.00 3.16
62 63 3.450817 TCTCCCAGATTTCATCGCACTTA 59.549 43.478 0.00 0.00 0.00 2.24
63 64 4.081142 TCTCCCAGATTTCATCGCACTTAA 60.081 41.667 0.00 0.00 0.00 1.85
64 65 4.780815 TCCCAGATTTCATCGCACTTAAT 58.219 39.130 0.00 0.00 0.00 1.40
65 66 5.192927 TCCCAGATTTCATCGCACTTAATT 58.807 37.500 0.00 0.00 0.00 1.40
66 67 6.353323 TCCCAGATTTCATCGCACTTAATTA 58.647 36.000 0.00 0.00 0.00 1.40
67 68 6.998074 TCCCAGATTTCATCGCACTTAATTAT 59.002 34.615 0.00 0.00 0.00 1.28
68 69 7.502226 TCCCAGATTTCATCGCACTTAATTATT 59.498 33.333 0.00 0.00 0.00 1.40
69 70 8.137437 CCCAGATTTCATCGCACTTAATTATTT 58.863 33.333 0.00 0.00 0.00 1.40
70 71 9.520204 CCAGATTTCATCGCACTTAATTATTTT 57.480 29.630 0.00 0.00 0.00 1.82
94 95 9.439500 TTTTTATCCTATGGTAGTGTGTTGTAC 57.561 33.333 0.00 0.00 0.00 2.90
97 98 4.397103 TCCTATGGTAGTGTGTTGTACGAG 59.603 45.833 0.00 0.00 0.00 4.18
114 115 7.821595 TGTACGAGTTGTCCATAGTTATTTG 57.178 36.000 0.00 0.00 0.00 2.32
147 148 4.384056 ACAAGGACATATCAGTATGCAGC 58.616 43.478 0.00 0.00 41.15 5.25
162 163 2.703416 TGCAGCAGATCTGTAGTTTGG 58.297 47.619 23.38 7.17 44.66 3.28
241 242 6.468956 CAGCGAATGGTATTTTTCATGTACAC 59.531 38.462 0.00 0.00 0.00 2.90
433 435 7.310609 CCTCATACAACCCTTCCAAATCAAATT 60.311 37.037 0.00 0.00 0.00 1.82
435 437 7.454380 TCATACAACCCTTCCAAATCAAATTCT 59.546 33.333 0.00 0.00 0.00 2.40
488 491 5.410924 CACTCCTTATCATCACGTCTTTCA 58.589 41.667 0.00 0.00 0.00 2.69
490 493 5.869888 ACTCCTTATCATCACGTCTTTCAAC 59.130 40.000 0.00 0.00 0.00 3.18
534 537 4.660938 AGCGCCCCACTTTCCCAC 62.661 66.667 2.29 0.00 0.00 4.61
657 660 5.527214 TGCGATATTCACAAGGAAATACCAG 59.473 40.000 0.00 0.00 39.39 4.00
807 821 5.246429 GGACCTCTCTTCAGTTCTCCTTAAA 59.754 44.000 0.00 0.00 0.00 1.52
808 822 6.239629 GGACCTCTCTTCAGTTCTCCTTAAAA 60.240 42.308 0.00 0.00 0.00 1.52
809 823 7.138054 ACCTCTCTTCAGTTCTCCTTAAAAA 57.862 36.000 0.00 0.00 0.00 1.94
1131 1156 1.135333 GACGTTGGACTCCCTCTCATC 59.865 57.143 0.00 0.00 0.00 2.92
1248 1273 3.307621 GCCATGGGACCAACATTGATTTT 60.308 43.478 15.13 0.00 0.00 1.82
1249 1274 4.255301 CCATGGGACCAACATTGATTTTG 58.745 43.478 2.85 0.00 0.00 2.44
1282 1307 2.410517 GCACATTCAATGTTTTGCAGCG 60.411 45.455 0.00 0.00 42.70 5.18
1514 1539 1.375396 CCATGGAACTGGAACGCGA 60.375 57.895 15.93 0.00 38.69 5.87
1546 1571 9.852091 TCTAGAAGTAAAAGACCGAGTTTAATC 57.148 33.333 0.00 0.00 0.00 1.75
1547 1572 9.857957 CTAGAAGTAAAAGACCGAGTTTAATCT 57.142 33.333 0.00 0.00 0.00 2.40
1678 1703 0.811915 ACGAAGGGTCTCATCGACAG 59.188 55.000 4.02 0.00 44.68 3.51
1970 2244 8.519526 CAAGGTTATGTTTGATGGTTTAGCTAA 58.480 33.333 0.86 0.86 0.00 3.09
2284 5100 3.469008 TGTGATCCAACGTTGACTCTT 57.531 42.857 29.35 8.78 0.00 2.85
2299 5115 5.545063 TGACTCTTTGATCAGGTACACAA 57.455 39.130 0.00 0.00 0.00 3.33
2476 5292 3.322254 AGGTATGGGACGTGATGATCTTC 59.678 47.826 0.00 1.67 0.00 2.87
2515 5331 9.787435 TTGTTTACTATTACTCTTTCCATGTGT 57.213 29.630 0.00 0.00 0.00 3.72
2543 5359 7.642194 TGTGTTTATCGCAAGTTAGTCAAAAAG 59.358 33.333 0.00 0.00 39.48 2.27
2560 5376 9.308000 AGTCAAAAAGTCAAAATGATATACCCA 57.692 29.630 0.00 0.00 0.00 4.51
2563 5379 8.531146 CAAAAAGTCAAAATGATATACCCACCT 58.469 33.333 0.00 0.00 0.00 4.00
2565 5381 8.664669 AAAGTCAAAATGATATACCCACCTTT 57.335 30.769 0.00 0.00 0.00 3.11
2603 5419 3.243002 GCTGCATTTGGCTATTCAGTCTC 60.243 47.826 0.00 0.00 45.15 3.36
2622 5438 3.057104 TCTCCAACGAGCGATTTTGACTA 60.057 43.478 0.00 0.00 35.94 2.59
2760 5582 5.373222 AGGGGCCAAAATTTTAAAACAGAC 58.627 37.500 4.39 0.00 0.00 3.51
2765 5587 6.421405 GCCAAAATTTTAAAACAGACTGCAG 58.579 36.000 13.48 13.48 0.00 4.41
2815 5644 8.106462 TGGACAATACCTCTGAACATTTCAATA 58.894 33.333 0.00 0.00 39.58 1.90
2818 5647 4.946784 ACCTCTGAACATTTCAATACGC 57.053 40.909 0.00 0.00 39.58 4.42
2845 5674 6.710744 CACTATGGTAACCAGTTTCTTGAGTT 59.289 38.462 0.00 0.00 36.75 3.01
2862 5691 7.885297 TCTTGAGTTAACATTGCTTTGCTTAT 58.115 30.769 8.61 0.00 0.00 1.73
2893 5722 6.616260 GCAATTTTGGCAAAAGTATTGACTCG 60.616 38.462 28.41 15.85 33.58 4.18
2935 5764 2.699954 TCTAGTTTGTTGCTGCTAGCC 58.300 47.619 13.29 0.00 41.51 3.93
3041 5870 5.329399 TCCCAATAACAGTTTATGCACCTT 58.671 37.500 0.00 0.00 0.00 3.50
3083 5912 5.419155 ACTCATGGAAGAAACGACAGATCTA 59.581 40.000 0.00 0.00 0.00 1.98
3086 5915 3.754850 TGGAAGAAACGACAGATCTACGA 59.245 43.478 22.24 1.42 0.00 3.43
3168 5997 3.640029 TCTTACCTGTCGTCTCACCTTTT 59.360 43.478 0.00 0.00 0.00 2.27
3248 6077 6.588204 ACAATGTCAAGGTAGTTGTTCACTA 58.412 36.000 0.00 0.00 36.88 2.74
3318 6148 1.064357 GTTCGTTCTTTTGGGTCGCAA 59.936 47.619 0.00 0.00 0.00 4.85
3389 6248 4.579340 CCTCCTAGTTCTAGCGTTCACATA 59.421 45.833 1.68 0.00 0.00 2.29
3431 6294 5.566032 CGACTATGTTCAAACCACCTCTGTA 60.566 44.000 0.00 0.00 0.00 2.74
3447 6310 6.199154 CACCTCTGTATTAGTTTATCGCTGTG 59.801 42.308 0.00 0.00 0.00 3.66
3496 6359 6.010850 ACTGTCTTGTATCTTACCTCAGACA 58.989 40.000 0.00 0.00 37.12 3.41
3535 6398 8.856153 TGCTGTTATTTGAAAATCAGTACCTA 57.144 30.769 0.00 0.00 0.00 3.08
3563 6429 4.038162 CCTTGGGTGAGTACTATCTGTAGC 59.962 50.000 0.00 0.00 0.00 3.58
3689 9618 5.363562 TTCTGTCTGATGCATAGGTCATT 57.636 39.130 0.00 0.00 0.00 2.57
3789 9807 1.141858 TGGCGCATCCAATGTATACCA 59.858 47.619 10.83 0.00 43.21 3.25
3888 9931 3.485947 TCTTGCGTGTAATTCCATTGC 57.514 42.857 0.00 0.00 0.00 3.56
3913 9956 6.662865 TTGTGGAAACCATACATGATTGTT 57.337 33.333 0.00 0.00 37.28 2.83
3914 9957 6.662865 TGTGGAAACCATACATGATTGTTT 57.337 33.333 0.00 3.48 37.28 2.83
3980 10031 2.886523 AGAGCTGCAGTAATTTTGCACA 59.113 40.909 16.64 0.00 45.89 4.57
4050 10101 1.136690 TACTTGCTTGTTCAGTCGCG 58.863 50.000 0.00 0.00 0.00 5.87
4108 10160 1.609072 GTCAGGCCTTTGTCCAGAAAC 59.391 52.381 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.460987 GGCTCACCCATTCTGACTCG 60.461 60.000 0.00 0.00 0.00 4.18
1 2 3.467776 GGCTCACCCATTCTGACTC 57.532 57.895 0.00 0.00 0.00 3.36
12 13 4.157849 AGAAGCTAAATAAGGGCTCACC 57.842 45.455 0.00 0.00 35.06 4.02
13 14 5.527951 GGTTAGAAGCTAAATAAGGGCTCAC 59.472 44.000 0.00 0.00 35.06 3.51
14 15 5.397559 GGGTTAGAAGCTAAATAAGGGCTCA 60.398 44.000 0.00 0.00 35.06 4.26
15 16 5.064558 GGGTTAGAAGCTAAATAAGGGCTC 58.935 45.833 0.00 0.00 35.06 4.70
16 17 4.477213 TGGGTTAGAAGCTAAATAAGGGCT 59.523 41.667 0.00 0.00 37.99 5.19
17 18 4.788679 TGGGTTAGAAGCTAAATAAGGGC 58.211 43.478 0.00 0.00 0.00 5.19
18 19 6.842676 AGATGGGTTAGAAGCTAAATAAGGG 58.157 40.000 0.00 0.00 0.00 3.95
19 20 6.937465 GGAGATGGGTTAGAAGCTAAATAAGG 59.063 42.308 0.00 0.00 0.00 2.69
20 21 6.937465 GGGAGATGGGTTAGAAGCTAAATAAG 59.063 42.308 0.00 0.00 0.00 1.73
21 22 6.388689 TGGGAGATGGGTTAGAAGCTAAATAA 59.611 38.462 0.00 0.00 0.00 1.40
22 23 5.908831 TGGGAGATGGGTTAGAAGCTAAATA 59.091 40.000 0.00 0.00 0.00 1.40
23 24 4.726825 TGGGAGATGGGTTAGAAGCTAAAT 59.273 41.667 0.00 0.00 0.00 1.40
24 25 4.108570 TGGGAGATGGGTTAGAAGCTAAA 58.891 43.478 0.00 0.00 0.00 1.85
25 26 3.711704 CTGGGAGATGGGTTAGAAGCTAA 59.288 47.826 0.00 0.00 0.00 3.09
26 27 3.052109 TCTGGGAGATGGGTTAGAAGCTA 60.052 47.826 0.00 0.00 0.00 3.32
27 28 2.122768 CTGGGAGATGGGTTAGAAGCT 58.877 52.381 0.00 0.00 0.00 3.74
28 29 2.119495 TCTGGGAGATGGGTTAGAAGC 58.881 52.381 0.00 0.00 0.00 3.86
29 30 5.104360 TGAAATCTGGGAGATGGGTTAGAAG 60.104 44.000 0.00 0.00 34.65 2.85
30 31 4.788075 TGAAATCTGGGAGATGGGTTAGAA 59.212 41.667 0.00 0.00 34.65 2.10
31 32 4.370776 TGAAATCTGGGAGATGGGTTAGA 58.629 43.478 0.00 0.00 34.65 2.10
32 33 4.778213 TGAAATCTGGGAGATGGGTTAG 57.222 45.455 0.00 0.00 34.65 2.34
33 34 4.202357 CGATGAAATCTGGGAGATGGGTTA 60.202 45.833 0.00 0.00 42.58 2.85
34 35 3.434167 CGATGAAATCTGGGAGATGGGTT 60.434 47.826 0.00 0.00 42.58 4.11
35 36 2.105477 CGATGAAATCTGGGAGATGGGT 59.895 50.000 0.00 0.00 42.58 4.51
36 37 2.775890 CGATGAAATCTGGGAGATGGG 58.224 52.381 0.00 0.00 42.58 4.00
37 38 2.149578 GCGATGAAATCTGGGAGATGG 58.850 52.381 0.00 0.00 42.58 3.51
38 39 2.547211 GTGCGATGAAATCTGGGAGATG 59.453 50.000 0.00 0.00 42.58 2.90
39 40 2.437281 AGTGCGATGAAATCTGGGAGAT 59.563 45.455 0.00 0.00 42.58 2.75
40 41 1.833630 AGTGCGATGAAATCTGGGAGA 59.166 47.619 0.00 0.00 42.58 3.71
41 42 2.322355 AGTGCGATGAAATCTGGGAG 57.678 50.000 0.00 0.00 42.58 4.30
42 43 2.787473 AAGTGCGATGAAATCTGGGA 57.213 45.000 0.00 0.00 42.58 4.37
43 44 5.505173 AATTAAGTGCGATGAAATCTGGG 57.495 39.130 0.00 0.00 42.58 4.45
44 45 9.520204 AAAATAATTAAGTGCGATGAAATCTGG 57.480 29.630 0.00 0.00 42.58 3.86
68 69 9.439500 GTACAACACACTACCATAGGATAAAAA 57.561 33.333 0.00 0.00 0.00 1.94
69 70 7.760794 CGTACAACACACTACCATAGGATAAAA 59.239 37.037 0.00 0.00 0.00 1.52
70 71 7.122501 TCGTACAACACACTACCATAGGATAAA 59.877 37.037 0.00 0.00 0.00 1.40
71 72 6.602803 TCGTACAACACACTACCATAGGATAA 59.397 38.462 0.00 0.00 0.00 1.75
72 73 6.121590 TCGTACAACACACTACCATAGGATA 58.878 40.000 0.00 0.00 0.00 2.59
73 74 4.951715 TCGTACAACACACTACCATAGGAT 59.048 41.667 0.00 0.00 0.00 3.24
74 75 4.334552 TCGTACAACACACTACCATAGGA 58.665 43.478 0.00 0.00 0.00 2.94
75 76 4.157289 ACTCGTACAACACACTACCATAGG 59.843 45.833 0.00 0.00 0.00 2.57
76 77 5.306532 ACTCGTACAACACACTACCATAG 57.693 43.478 0.00 0.00 0.00 2.23
77 78 5.009911 ACAACTCGTACAACACACTACCATA 59.990 40.000 0.00 0.00 0.00 2.74
78 79 4.202182 ACAACTCGTACAACACACTACCAT 60.202 41.667 0.00 0.00 0.00 3.55
79 80 3.130869 ACAACTCGTACAACACACTACCA 59.869 43.478 0.00 0.00 0.00 3.25
80 81 3.709987 ACAACTCGTACAACACACTACC 58.290 45.455 0.00 0.00 0.00 3.18
81 82 3.732721 GGACAACTCGTACAACACACTAC 59.267 47.826 0.00 0.00 0.00 2.73
82 83 3.380954 TGGACAACTCGTACAACACACTA 59.619 43.478 0.00 0.00 34.62 2.74
83 84 2.166870 TGGACAACTCGTACAACACACT 59.833 45.455 0.00 0.00 34.62 3.55
84 85 2.542597 TGGACAACTCGTACAACACAC 58.457 47.619 0.00 0.00 34.62 3.82
85 86 2.963548 TGGACAACTCGTACAACACA 57.036 45.000 0.00 0.00 34.62 3.72
86 87 4.553323 ACTATGGACAACTCGTACAACAC 58.447 43.478 0.00 0.00 43.49 3.32
87 88 4.859304 ACTATGGACAACTCGTACAACA 57.141 40.909 0.00 0.00 43.49 3.33
88 89 7.823149 AATAACTATGGACAACTCGTACAAC 57.177 36.000 0.00 0.00 43.49 3.32
114 115 9.614792 ACTGATATGTCCTTGTTTAAGTAATCC 57.385 33.333 0.00 0.00 31.80 3.01
147 148 7.874940 TGACAAAATTCCAAACTACAGATCTG 58.125 34.615 21.37 21.37 0.00 2.90
190 191 2.838202 ACATTTCAGATCCTACCACGGT 59.162 45.455 0.00 0.00 0.00 4.83
454 457 2.273370 TAAGGAGTGCGTCGATGTTC 57.727 50.000 6.48 2.32 0.00 3.18
488 491 6.183360 CCTGAGAATACAATGCTTCATTCGTT 60.183 38.462 0.15 0.00 31.05 3.85
490 493 5.277683 CCCTGAGAATACAATGCTTCATTCG 60.278 44.000 0.15 0.00 31.05 3.34
534 537 7.094677 TGACAATCGAGGAATTGCATTATATGG 60.095 37.037 0.00 0.00 39.72 2.74
808 822 8.922931 AATAAGCCCAGTCAATTTGAATTTTT 57.077 26.923 0.00 0.00 0.00 1.94
809 823 7.607607 GGAATAAGCCCAGTCAATTTGAATTTT 59.392 33.333 0.00 0.00 0.00 1.82
859 882 5.652891 GGAGACCTGACTAATGTAAGTCTCA 59.347 44.000 16.47 0.00 45.12 3.27
1017 1042 2.896039 AGCTTCCTTAGAGGTGACACT 58.104 47.619 5.39 0.00 36.53 3.55
1131 1156 2.360801 AGACGGTTCAACATGTTTTGGG 59.639 45.455 8.77 0.00 0.00 4.12
1248 1273 7.660112 ACATTGAATGTGCAACTAAGAATTCA 58.340 30.769 10.45 0.00 43.01 2.57
1249 1274 8.524870 AACATTGAATGTGCAACTAAGAATTC 57.475 30.769 12.09 0.00 44.07 2.17
1282 1307 4.762289 TCTTCCTCTCATAAAGCCTTCC 57.238 45.455 0.00 0.00 0.00 3.46
1317 1342 6.765036 ACGAAGCATGACTTGATCATCTATTT 59.235 34.615 0.00 0.00 45.52 1.40
1334 1359 3.476552 TCTTTGGTGAGAAACGAAGCAT 58.523 40.909 0.00 0.00 0.00 3.79
1472 1497 2.664402 AAGTGAGTGCTCCACCAATT 57.336 45.000 0.00 0.00 34.49 2.32
1496 1521 0.953471 TTCGCGTTCCAGTTCCATGG 60.953 55.000 4.97 4.97 42.11 3.66
1514 1539 7.177041 ACTCGGTCTTTTACTTCTAGACATCTT 59.823 37.037 0.00 0.00 39.98 2.40
1672 1697 5.670792 AATGATACCTTGGTTACTGTCGA 57.329 39.130 0.00 0.00 0.00 4.20
1678 1703 5.576774 GCTGCAAAAATGATACCTTGGTTAC 59.423 40.000 0.00 0.00 0.00 2.50
1878 2128 3.728864 GCGATGTGGCATTAACACTTGAG 60.729 47.826 0.00 0.00 39.52 3.02
1970 2244 4.219392 TCTGATCATGGAGATACCCCTT 57.781 45.455 0.00 0.00 37.00 3.95
2284 5100 6.635755 TGATATTCGTTGTGTACCTGATCAA 58.364 36.000 0.00 0.00 0.00 2.57
2299 5115 5.643348 TCTGCAACAACTTCATGATATTCGT 59.357 36.000 0.00 0.00 0.00 3.85
2476 5292 9.968743 GTAATAGTAAACAAAAATCGACTCCAG 57.031 33.333 0.00 0.00 0.00 3.86
2515 5331 7.892778 TTGACTAACTTGCGATAAACACATA 57.107 32.000 0.00 0.00 0.00 2.29
2543 5359 9.965824 CATAAAAGGTGGGTATATCATTTTGAC 57.034 33.333 0.00 0.00 0.00 3.18
2560 5376 9.586732 TGCAGCTTATATAATTCCATAAAAGGT 57.413 29.630 0.00 0.00 0.00 3.50
2603 5419 5.712217 TTATAGTCAAAATCGCTCGTTGG 57.288 39.130 0.00 0.00 0.00 3.77
2710 5526 5.775686 ACGTGTAAAAGTACTGAGCATACA 58.224 37.500 0.00 0.00 0.00 2.29
2716 5532 6.976925 CCCCTAATACGTGTAAAAGTACTGAG 59.023 42.308 0.00 0.00 0.00 3.35
2781 5603 6.867519 TCAGAGGTATTGTCCAGAAATACA 57.132 37.500 8.19 0.00 40.67 2.29
2815 5644 2.176889 ACTGGTTACCATAGTGAGCGT 58.823 47.619 3.88 0.00 32.96 5.07
2818 5647 6.464222 TCAAGAAACTGGTTACCATAGTGAG 58.536 40.000 3.88 0.00 30.82 3.51
2845 5674 7.374272 TGCTAAACATAAGCAAAGCAATGTTA 58.626 30.769 17.29 5.37 46.57 2.41
2862 5691 8.341173 CAATACTTTTGCCAAAATTGCTAAACA 58.659 29.630 2.58 0.00 31.83 2.83
2935 5764 3.999663 GAGACCAGAATTGACCACTCAAG 59.000 47.826 0.00 0.00 39.83 3.02
3041 5870 2.470196 GTAGCTCGTCTACGCATTGA 57.530 50.000 0.00 0.00 38.40 2.57
3083 5912 6.231211 AGTTGAACAGATTTCCAACTATCGT 58.769 36.000 0.00 0.00 44.93 3.73
3086 5915 7.939039 TCAAGAGTTGAACAGATTTCCAACTAT 59.061 33.333 0.00 0.00 46.21 2.12
3156 5985 3.377172 ACAGTTTTGGAAAAGGTGAGACG 59.623 43.478 0.00 0.00 0.00 4.18
3168 5997 3.011566 TCAGGAAGCAACAGTTTTGGA 57.988 42.857 0.00 0.00 0.00 3.53
3248 6077 5.360144 TGCTCGCTTAAGAACTATTCCTAGT 59.640 40.000 6.67 0.00 39.97 2.57
3318 6148 7.806180 AGCTATACACCAACCAGAAGATAAAT 58.194 34.615 0.00 0.00 0.00 1.40
3389 6248 5.878406 AGTCGGACCAGAGATAAAATCAT 57.122 39.130 4.14 0.00 0.00 2.45
3431 6294 3.800506 GCGTACCACAGCGATAAACTAAT 59.199 43.478 0.00 0.00 0.00 1.73
3447 6310 6.868622 AGGATATTCAGATTATCTGCGTACC 58.131 40.000 16.72 14.44 43.95 3.34
3474 6337 5.773176 TGTGTCTGAGGTAAGATACAAGACA 59.227 40.000 12.20 12.20 42.96 3.41
3496 6359 1.033746 ACAGCAGCAGCAACTTGTGT 61.034 50.000 3.17 0.00 45.49 3.72
3535 6398 0.178941 AGTACTCACCCAAGGTCCGT 60.179 55.000 0.00 0.00 31.02 4.69
3563 6429 0.103572 GCCCAGTTATGCATGCCAAG 59.896 55.000 16.68 0.00 0.00 3.61
3689 9618 4.039245 CAGTTCCTGTTCTGTTCTCTGGTA 59.961 45.833 0.00 0.00 0.00 3.25
3789 9807 7.096551 CCAAAAATTCAGTCCATCGGTAAAAT 58.903 34.615 0.00 0.00 0.00 1.82
3853 9871 7.476540 ACACGCAAGATATCCCAAGTATATA 57.523 36.000 0.00 0.00 43.62 0.86
3888 9931 6.690530 ACAATCATGTATGGTTTCCACAAAG 58.309 36.000 0.00 0.00 38.24 2.77
3913 9956 2.889606 TAGCCCGGACAGCAAGCAA 61.890 57.895 0.73 0.00 0.00 3.91
3914 9957 3.318384 TAGCCCGGACAGCAAGCA 61.318 61.111 0.73 0.00 0.00 3.91
3980 10031 4.019174 CCACAAGTAAATGGAAGCCATCT 58.981 43.478 0.00 0.00 44.40 2.90


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

AutoCloner maintained by Alex Coulton.