Multiple sequence alignment - TraesCS3B01G314400

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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 TraesCS3B01G314400 chr3B 100.000 2738 0 0 1 2738 505286733 505289470 0.000000e+00 5057
1 TraesCS3B01G314400 chr3B 85.135 148 21 1 1550 1697 505287875 505288021 1.700000e-32 150
2 TraesCS3B01G314400 chr3B 85.135 148 21 1 1143 1289 505288282 505288429 1.700000e-32 150
3 TraesCS3B01G314400 chr3D 92.737 1611 96 10 96 1703 388449630 388451222 0.000000e+00 2307
4 TraesCS3B01G314400 chr3D 88.972 934 52 17 1147 2052 388450747 388451657 0.000000e+00 1107
5 TraesCS3B01G314400 chr3D 92.662 477 23 9 2269 2738 388451750 388452221 0.000000e+00 676
6 TraesCS3B01G314400 chr3D 78.514 498 75 15 1216 1703 388450678 388451153 5.730000e-77 298
7 TraesCS3B01G314400 chr3D 81.991 211 22 12 2531 2737 554693034 554692836 6.070000e-37 165
8 TraesCS3B01G314400 chr3D 85.135 148 21 1 1550 1697 388450674 388450820 1.700000e-32 150
9 TraesCS3B01G314400 chr3D 85.135 148 21 1 1143 1289 388451138 388451285 1.700000e-32 150
10 TraesCS3B01G314400 chr3A 94.674 1333 60 7 110 1432 509547896 509549227 0.000000e+00 2058
11 TraesCS3B01G314400 chr3A 92.813 807 26 7 1429 2204 509549601 509550406 0.000000e+00 1140
12 TraesCS3B01G314400 chr3A 92.674 546 27 7 2200 2738 509550463 509551002 0.000000e+00 774
13 TraesCS3B01G314400 chr3A 79.787 282 37 9 1159 1427 509549601 509549875 1.290000e-43 187
14 TraesCS3B01G314400 chr7D 88.314 599 67 2 407 1005 629598677 629599272 0.000000e+00 715
15 TraesCS3B01G314400 chr6B 83.680 674 95 7 413 1074 9478976 9478306 2.990000e-174 621
16 TraesCS3B01G314400 chr6B 81.324 680 90 12 407 1074 11110840 11111494 4.040000e-143 518
17 TraesCS3B01G314400 chr7A 86.154 585 61 11 502 1070 725613201 725613781 5.010000e-172 614
18 TraesCS3B01G314400 chr7A 90.476 105 10 0 407 511 725612416 725612520 3.680000e-29 139


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 TraesCS3B01G314400 chr3B 505286733 505289470 2737 False 1785.666667 5057 90.0900 1 2738 3 chr3B.!!$F1 2737
1 TraesCS3B01G314400 chr3D 388449630 388452221 2591 False 781.333333 2307 87.1925 96 2738 6 chr3D.!!$F1 2642
2 TraesCS3B01G314400 chr3A 509547896 509551002 3106 False 1039.750000 2058 89.9870 110 2738 4 chr3A.!!$F1 2628
3 TraesCS3B01G314400 chr7D 629598677 629599272 595 False 715.000000 715 88.3140 407 1005 1 chr7D.!!$F1 598
4 TraesCS3B01G314400 chr6B 9478306 9478976 670 True 621.000000 621 83.6800 413 1074 1 chr6B.!!$R1 661
5 TraesCS3B01G314400 chr6B 11110840 11111494 654 False 518.000000 518 81.3240 407 1074 1 chr6B.!!$F1 667
6 TraesCS3B01G314400 chr7A 725612416 725613781 1365 False 376.500000 614 88.3150 407 1070 2 chr7A.!!$F1 663

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
395 403 0.031585 CGAACGTGAACAGACCTGGA 59.968 55.0 0.0 0.0 34.19 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 2942 0.401738 TTGACCCTTCTCCCTGCTTG 59.598 55.0 0.0 0.0 0.0 4.01 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
17 18 4.364817 CGTGCCGGGTTAAGTTGA 57.635 55.556 2.18 0.00 0.00 3.18
18 19 2.159181 CGTGCCGGGTTAAGTTGAG 58.841 57.895 2.18 0.00 0.00 3.02
19 20 1.873863 GTGCCGGGTTAAGTTGAGC 59.126 57.895 2.18 0.00 0.00 4.26
20 21 1.302993 TGCCGGGTTAAGTTGAGCC 60.303 57.895 2.18 5.82 0.00 4.70
21 22 1.302993 GCCGGGTTAAGTTGAGCCA 60.303 57.895 15.34 0.00 34.35 4.75
22 23 1.305930 GCCGGGTTAAGTTGAGCCAG 61.306 60.000 15.34 5.78 34.35 4.85
23 24 1.305930 CCGGGTTAAGTTGAGCCAGC 61.306 60.000 15.34 0.00 34.35 4.85
24 25 1.305930 CGGGTTAAGTTGAGCCAGCC 61.306 60.000 15.34 0.00 34.35 4.85
25 26 0.038310 GGGTTAAGTTGAGCCAGCCT 59.962 55.000 10.78 0.00 34.82 4.58
26 27 1.454201 GGTTAAGTTGAGCCAGCCTC 58.546 55.000 0.00 0.00 41.15 4.70
33 34 3.995526 TGAGCCAGCCTCATAATCG 57.004 52.632 0.00 0.00 45.44 3.34
34 35 1.413118 TGAGCCAGCCTCATAATCGA 58.587 50.000 0.00 0.00 45.44 3.59
35 36 1.762370 TGAGCCAGCCTCATAATCGAA 59.238 47.619 0.00 0.00 45.44 3.71
36 37 2.224137 TGAGCCAGCCTCATAATCGAAG 60.224 50.000 0.00 0.00 45.44 3.79
37 38 0.871057 GCCAGCCTCATAATCGAAGC 59.129 55.000 0.00 0.00 0.00 3.86
38 39 1.811558 GCCAGCCTCATAATCGAAGCA 60.812 52.381 0.00 0.00 0.00 3.91
39 40 2.775890 CCAGCCTCATAATCGAAGCAT 58.224 47.619 0.00 0.00 0.00 3.79
40 41 3.144506 CCAGCCTCATAATCGAAGCATT 58.855 45.455 0.00 0.00 0.00 3.56
41 42 3.058432 CCAGCCTCATAATCGAAGCATTG 60.058 47.826 0.00 0.00 0.00 2.82
42 43 3.811497 CAGCCTCATAATCGAAGCATTGA 59.189 43.478 0.00 0.00 0.00 2.57
43 44 3.812053 AGCCTCATAATCGAAGCATTGAC 59.188 43.478 0.00 0.00 0.00 3.18
44 45 3.363378 GCCTCATAATCGAAGCATTGACG 60.363 47.826 0.00 0.00 0.00 4.35
45 46 4.051237 CCTCATAATCGAAGCATTGACGA 58.949 43.478 0.00 0.00 40.18 4.20
46 47 4.687948 CCTCATAATCGAAGCATTGACGAT 59.312 41.667 0.00 0.00 46.26 3.73
47 48 5.164012 CCTCATAATCGAAGCATTGACGATC 60.164 44.000 0.00 0.00 44.13 3.69
48 49 4.382754 TCATAATCGAAGCATTGACGATCG 59.617 41.667 14.88 14.88 44.13 3.69
49 50 2.492019 ATCGAAGCATTGACGATCGA 57.508 45.000 24.34 0.00 45.29 3.59
50 51 2.271821 TCGAAGCATTGACGATCGAA 57.728 45.000 24.34 6.94 39.33 3.71
51 52 2.185262 TCGAAGCATTGACGATCGAAG 58.815 47.619 24.34 7.34 39.33 3.79
52 53 1.920574 CGAAGCATTGACGATCGAAGT 59.079 47.619 24.34 0.00 35.65 3.01
53 54 3.105937 CGAAGCATTGACGATCGAAGTA 58.894 45.455 24.34 4.26 35.65 2.24
54 55 3.061797 CGAAGCATTGACGATCGAAGTAC 60.062 47.826 24.34 6.41 35.65 2.73
55 56 3.784701 AGCATTGACGATCGAAGTACT 57.215 42.857 24.34 8.70 0.00 2.73
56 57 4.111375 AGCATTGACGATCGAAGTACTT 57.889 40.909 24.34 8.13 0.00 2.24
57 58 4.495422 AGCATTGACGATCGAAGTACTTT 58.505 39.130 24.34 0.00 0.00 2.66
58 59 4.929808 AGCATTGACGATCGAAGTACTTTT 59.070 37.500 24.34 0.00 0.00 2.27
59 60 5.408604 AGCATTGACGATCGAAGTACTTTTT 59.591 36.000 24.34 0.00 0.00 1.94
60 61 6.588756 AGCATTGACGATCGAAGTACTTTTTA 59.411 34.615 24.34 0.00 0.00 1.52
61 62 6.677411 GCATTGACGATCGAAGTACTTTTTAC 59.323 38.462 24.34 2.15 0.00 2.01
62 63 7.620600 GCATTGACGATCGAAGTACTTTTTACA 60.621 37.037 24.34 2.25 0.00 2.41
63 64 7.878477 TTGACGATCGAAGTACTTTTTACAT 57.122 32.000 24.34 0.00 0.00 2.29
64 65 7.502177 TGACGATCGAAGTACTTTTTACATC 57.498 36.000 24.34 3.12 0.00 3.06
65 66 7.085746 TGACGATCGAAGTACTTTTTACATCA 58.914 34.615 24.34 5.96 0.00 3.07
66 67 7.758076 TGACGATCGAAGTACTTTTTACATCAT 59.242 33.333 24.34 0.00 0.00 2.45
67 68 8.475331 ACGATCGAAGTACTTTTTACATCATT 57.525 30.769 24.34 0.00 0.00 2.57
68 69 9.577110 ACGATCGAAGTACTTTTTACATCATTA 57.423 29.630 24.34 0.00 0.00 1.90
106 107 5.699458 TGATCATGAAGTCGATCAATGATGG 59.301 40.000 15.96 0.00 43.78 3.51
111 112 7.552330 TCATGAAGTCGATCAATGATGGTAAAA 59.448 33.333 0.00 0.00 32.06 1.52
112 113 7.307493 TGAAGTCGATCAATGATGGTAAAAG 57.693 36.000 0.00 0.00 0.00 2.27
135 136 8.667592 AAGAGAGGTAAATAAGTACCAGTCTT 57.332 34.615 10.32 10.32 45.27 3.01
184 185 2.032681 AAACAGCCCTCACTCCGC 59.967 61.111 0.00 0.00 0.00 5.54
272 273 6.038985 CAGGATGCAAGATACCATATACTCG 58.961 44.000 0.00 0.00 0.00 4.18
275 276 7.561722 AGGATGCAAGATACCATATACTCGTAT 59.438 37.037 0.00 0.00 0.00 3.06
361 369 3.565905 AATAGCAAAGCACTGAACTGC 57.434 42.857 0.00 0.00 37.44 4.40
383 391 0.160182 GGTGCTTACGAACGAACGTG 59.840 55.000 17.91 6.90 46.02 4.49
385 393 1.518102 GTGCTTACGAACGAACGTGAA 59.482 47.619 17.91 9.69 46.02 3.18
386 394 1.518102 TGCTTACGAACGAACGTGAAC 59.482 47.619 17.91 8.82 46.02 3.18
387 395 1.518102 GCTTACGAACGAACGTGAACA 59.482 47.619 17.91 0.14 46.02 3.18
388 396 2.408110 GCTTACGAACGAACGTGAACAG 60.408 50.000 17.91 11.05 46.02 3.16
389 397 2.753989 TACGAACGAACGTGAACAGA 57.246 45.000 17.91 0.00 46.02 3.41
392 400 1.849097 GAACGAACGTGAACAGACCT 58.151 50.000 0.00 0.00 0.00 3.85
395 403 0.031585 CGAACGTGAACAGACCTGGA 59.968 55.000 0.00 0.00 34.19 3.86
823 1523 1.671742 GCACGACTTCTTCTCCCCA 59.328 57.895 0.00 0.00 0.00 4.96
827 1527 1.978580 ACGACTTCTTCTCCCCATTGT 59.021 47.619 0.00 0.00 0.00 2.71
945 1667 0.613853 TCGGAGGAGAACGGAATGGT 60.614 55.000 0.00 0.00 0.00 3.55
985 1707 2.997897 AACTTCTCTCCGGCGCCT 60.998 61.111 26.68 0.00 0.00 5.52
1074 1811 4.760047 GCTGGGGTCGTCGTGCAT 62.760 66.667 0.00 0.00 0.00 3.96
1087 1824 1.738099 GTGCATCTGCGTCTCCGTT 60.738 57.895 0.00 0.00 45.83 4.44
1102 1839 1.413368 CGTTGCGGCGTAGTTGTAC 59.587 57.895 9.37 0.00 0.00 2.90
1331 2068 2.247267 GTTTCACGTTCACGCCGG 59.753 61.111 0.00 0.00 44.43 6.13
1420 2214 2.107041 CTACTCCAACCGTGGTGCCA 62.107 60.000 0.00 0.00 46.11 4.92
1462 2633 4.634703 ACATTGACGCCCACGCCA 62.635 61.111 0.00 0.00 45.53 5.69
1735 2906 2.994995 TCGACATGGACACCGCCT 60.995 61.111 0.00 0.00 0.00 5.52
1743 2914 4.148825 GACACCGCCTGAGCCGAT 62.149 66.667 0.00 0.00 34.57 4.18
1759 2930 2.358247 ATGTTCACCGACGTGCCC 60.358 61.111 0.00 0.00 40.04 5.36
1774 2945 4.722700 CCCCCGGCTGTGGACAAG 62.723 72.222 0.00 0.00 0.00 3.16
1776 2947 4.641645 CCCGGCTGTGGACAAGCA 62.642 66.667 0.00 0.00 0.00 3.91
1872 3057 0.179051 GAGAGAGGGAGCTTGGCATG 60.179 60.000 0.00 0.00 0.00 4.06
1875 3060 2.943265 AGGGAGCTTGGCATGGGT 60.943 61.111 2.33 0.00 0.00 4.51
1951 3142 0.174617 TACCGACGCAATCTGCATGA 59.825 50.000 0.00 0.00 45.36 3.07
1964 3155 7.383029 CGCAATCTGCATGAAAATTATATGGTT 59.617 33.333 0.00 0.00 45.36 3.67
1986 3177 6.238703 GGTTAGTCTCTACGGAGTATTTGAGG 60.239 46.154 0.00 0.00 44.56 3.86
2059 3260 5.880887 TGATAGTGTACTGTCACTCTCGAAT 59.119 40.000 13.56 4.96 45.79 3.34
2062 3263 4.393680 AGTGTACTGTCACTCTCGAATCTC 59.606 45.833 6.96 0.00 44.07 2.75
2194 3397 6.246540 GCTTTTGATTTTCACGTAATCGACTC 59.753 38.462 5.35 0.00 40.62 3.36
2195 3398 5.773239 TTGATTTTCACGTAATCGACTCC 57.227 39.130 5.35 0.00 40.62 3.85
2198 3401 5.575606 TGATTTTCACGTAATCGACTCCTTC 59.424 40.000 5.35 0.00 40.62 3.46
2214 3478 6.422776 ACTCCTTCGCACACTATTATTTTG 57.577 37.500 0.00 0.00 0.00 2.44
2259 3523 8.682128 AACACCATTTTATACGCTGTAAATTG 57.318 30.769 0.00 0.00 0.00 2.32
2269 3533 4.932146 ACGCTGTAAATTGGCATAAATCC 58.068 39.130 0.00 0.00 0.00 3.01
2364 3644 7.399191 TGGAACTAGCTAGGAAGAACAATAGAA 59.601 37.037 24.35 0.00 0.00 2.10
2388 3668 0.386838 GCAATATGCCTCCCACAAGC 59.613 55.000 0.00 0.00 37.42 4.01
2391 3674 0.184451 ATATGCCTCCCACAAGCAGG 59.816 55.000 0.00 0.00 40.40 4.85
2411 3694 5.479027 GCAGGGTAGGGAAAATTAAGAACAA 59.521 40.000 0.00 0.00 0.00 2.83
2414 3697 8.593679 CAGGGTAGGGAAAATTAAGAACAAAAT 58.406 33.333 0.00 0.00 0.00 1.82
2439 3724 1.696884 TCTACATGCAGGTGTGTTGGA 59.303 47.619 15.48 2.25 33.62 3.53
2440 3725 2.079158 CTACATGCAGGTGTGTTGGAG 58.921 52.381 15.48 0.00 33.62 3.86
2441 3726 0.473755 ACATGCAGGTGTGTTGGAGA 59.526 50.000 1.71 0.00 0.00 3.71
2575 3861 4.680349 CTGACGACAGCTCGCTAG 57.320 61.111 1.13 0.00 44.33 3.42
2577 3863 2.278271 GACGACAGCTCGCTAGGC 60.278 66.667 0.00 0.00 44.33 3.93
2660 3947 7.166307 CACGAACGTCGATATTTATAGAACCAA 59.834 37.037 13.06 0.00 43.74 3.67
2728 4015 3.162666 TCGATCTATTAACTGCCCCGAT 58.837 45.455 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.583495 GGCTCAACTTAACCCGGCAC 61.583 60.000 0.00 0.00 0.00 5.01
2 3 1.302993 GGCTCAACTTAACCCGGCA 60.303 57.895 0.00 0.00 0.00 5.69
5 6 1.305930 GGCTGGCTCAACTTAACCCG 61.306 60.000 0.00 0.00 0.00 5.28
7 8 1.271379 TGAGGCTGGCTCAACTTAACC 60.271 52.381 28.92 2.76 0.00 2.85
8 9 2.185004 TGAGGCTGGCTCAACTTAAC 57.815 50.000 28.92 3.49 0.00 2.01
9 10 4.568072 TTATGAGGCTGGCTCAACTTAA 57.432 40.909 33.27 24.24 34.26 1.85
10 11 4.708177 GATTATGAGGCTGGCTCAACTTA 58.292 43.478 33.27 20.42 34.26 2.24
11 12 3.549794 GATTATGAGGCTGGCTCAACTT 58.450 45.455 33.27 21.39 34.26 2.66
12 13 2.484417 CGATTATGAGGCTGGCTCAACT 60.484 50.000 33.27 22.05 34.26 3.16
13 14 1.869767 CGATTATGAGGCTGGCTCAAC 59.130 52.381 33.27 22.75 34.26 3.18
14 15 1.762370 TCGATTATGAGGCTGGCTCAA 59.238 47.619 33.27 20.81 34.26 3.02
15 16 1.413118 TCGATTATGAGGCTGGCTCA 58.587 50.000 32.08 32.08 35.13 4.26
16 17 2.411904 CTTCGATTATGAGGCTGGCTC 58.588 52.381 22.95 22.95 0.00 4.70
17 18 1.542108 GCTTCGATTATGAGGCTGGCT 60.542 52.381 2.24 2.24 37.91 4.75
18 19 0.871057 GCTTCGATTATGAGGCTGGC 59.129 55.000 0.00 0.00 37.91 4.85
19 20 2.245159 TGCTTCGATTATGAGGCTGG 57.755 50.000 0.00 0.00 41.18 4.85
20 21 3.811497 TCAATGCTTCGATTATGAGGCTG 59.189 43.478 0.00 0.00 41.18 4.85
21 22 3.812053 GTCAATGCTTCGATTATGAGGCT 59.188 43.478 0.00 0.00 41.18 4.58
22 23 3.363378 CGTCAATGCTTCGATTATGAGGC 60.363 47.826 0.00 0.00 41.00 4.70
23 24 4.051237 TCGTCAATGCTTCGATTATGAGG 58.949 43.478 0.00 0.00 0.00 3.86
24 25 5.442519 CGATCGTCAATGCTTCGATTATGAG 60.443 44.000 7.03 0.00 42.91 2.90
25 26 4.382754 CGATCGTCAATGCTTCGATTATGA 59.617 41.667 7.03 0.00 42.91 2.15
26 27 4.382754 TCGATCGTCAATGCTTCGATTATG 59.617 41.667 15.94 4.35 42.91 1.90
27 28 4.546570 TCGATCGTCAATGCTTCGATTAT 58.453 39.130 15.94 0.00 42.91 1.28
28 29 3.959943 TCGATCGTCAATGCTTCGATTA 58.040 40.909 15.94 0.00 42.91 1.75
29 30 2.809446 TCGATCGTCAATGCTTCGATT 58.191 42.857 15.94 0.00 42.91 3.34
30 31 2.492019 TCGATCGTCAATGCTTCGAT 57.508 45.000 15.94 7.28 44.98 3.59
31 32 2.185262 CTTCGATCGTCAATGCTTCGA 58.815 47.619 15.94 0.00 37.08 3.71
32 33 1.920574 ACTTCGATCGTCAATGCTTCG 59.079 47.619 15.94 0.00 0.00 3.79
33 34 4.106197 AGTACTTCGATCGTCAATGCTTC 58.894 43.478 15.94 0.00 0.00 3.86
34 35 4.111375 AGTACTTCGATCGTCAATGCTT 57.889 40.909 15.94 0.00 0.00 3.91
35 36 3.784701 AGTACTTCGATCGTCAATGCT 57.215 42.857 15.94 5.69 0.00 3.79
36 37 4.842139 AAAGTACTTCGATCGTCAATGC 57.158 40.909 15.94 3.45 0.00 3.56
37 38 7.726079 TGTAAAAAGTACTTCGATCGTCAATG 58.274 34.615 15.94 0.83 0.00 2.82
38 39 7.878477 TGTAAAAAGTACTTCGATCGTCAAT 57.122 32.000 15.94 2.21 0.00 2.57
39 40 7.595875 TGATGTAAAAAGTACTTCGATCGTCAA 59.404 33.333 15.94 1.72 0.00 3.18
40 41 7.085746 TGATGTAAAAAGTACTTCGATCGTCA 58.914 34.615 15.94 13.22 0.00 4.35
41 42 7.502177 TGATGTAAAAAGTACTTCGATCGTC 57.498 36.000 15.94 11.10 0.00 4.20
42 43 8.475331 AATGATGTAAAAAGTACTTCGATCGT 57.525 30.769 15.94 5.18 0.00 3.73
57 58 9.752961 CATCAATGCTTGGATTAATGATGTAAA 57.247 29.630 0.00 0.00 38.42 2.01
58 59 9.134055 TCATCAATGCTTGGATTAATGATGTAA 57.866 29.630 11.31 0.00 41.91 2.41
59 60 8.694581 TCATCAATGCTTGGATTAATGATGTA 57.305 30.769 11.31 0.00 41.91 2.29
60 61 7.591421 TCATCAATGCTTGGATTAATGATGT 57.409 32.000 11.31 0.00 41.91 3.06
61 62 8.303876 TGATCATCAATGCTTGGATTAATGATG 58.696 33.333 15.17 11.50 42.35 3.07
62 63 8.417273 TGATCATCAATGCTTGGATTAATGAT 57.583 30.769 11.58 11.58 34.35 2.45
63 64 7.826918 TGATCATCAATGCTTGGATTAATGA 57.173 32.000 3.72 3.72 0.00 2.57
64 65 8.303876 TCATGATCATCAATGCTTGGATTAATG 58.696 33.333 4.86 0.00 0.00 1.90
65 66 8.417273 TCATGATCATCAATGCTTGGATTAAT 57.583 30.769 4.86 0.00 0.00 1.40
66 67 7.826918 TCATGATCATCAATGCTTGGATTAA 57.173 32.000 4.86 0.00 0.00 1.40
67 68 7.504574 ACTTCATGATCATCAATGCTTGGATTA 59.495 33.333 4.86 0.00 0.00 1.75
68 69 6.323996 ACTTCATGATCATCAATGCTTGGATT 59.676 34.615 4.86 0.00 0.00 3.01
69 70 5.833667 ACTTCATGATCATCAATGCTTGGAT 59.166 36.000 4.86 0.00 0.00 3.41
70 71 5.198207 ACTTCATGATCATCAATGCTTGGA 58.802 37.500 4.86 0.00 0.00 3.53
71 72 5.515797 ACTTCATGATCATCAATGCTTGG 57.484 39.130 4.86 0.00 0.00 3.61
72 73 5.007332 TCGACTTCATGATCATCAATGCTTG 59.993 40.000 4.86 0.00 0.00 4.01
73 74 5.121105 TCGACTTCATGATCATCAATGCTT 58.879 37.500 4.86 0.00 0.00 3.91
74 75 4.700700 TCGACTTCATGATCATCAATGCT 58.299 39.130 4.86 0.00 0.00 3.79
75 76 5.178809 TGATCGACTTCATGATCATCAATGC 59.821 40.000 4.86 0.00 44.41 3.56
76 77 6.780706 TGATCGACTTCATGATCATCAATG 57.219 37.500 4.86 0.00 44.41 2.82
82 83 5.699458 CCATCATTGATCGACTTCATGATCA 59.301 40.000 0.00 0.00 46.79 2.92
83 84 5.699915 ACCATCATTGATCGACTTCATGATC 59.300 40.000 0.00 0.00 41.08 2.92
84 85 5.618236 ACCATCATTGATCGACTTCATGAT 58.382 37.500 0.00 0.00 30.68 2.45
85 86 5.027293 ACCATCATTGATCGACTTCATGA 57.973 39.130 0.00 0.00 0.00 3.07
86 87 6.849588 TTACCATCATTGATCGACTTCATG 57.150 37.500 0.00 0.00 0.00 3.07
87 88 7.770433 TCTTTTACCATCATTGATCGACTTCAT 59.230 33.333 0.00 0.00 0.00 2.57
88 89 7.102993 TCTTTTACCATCATTGATCGACTTCA 58.897 34.615 0.00 0.00 0.00 3.02
89 90 7.492669 TCTCTTTTACCATCATTGATCGACTTC 59.507 37.037 0.00 0.00 0.00 3.01
90 91 7.331026 TCTCTTTTACCATCATTGATCGACTT 58.669 34.615 0.00 0.00 0.00 3.01
91 92 6.878317 TCTCTTTTACCATCATTGATCGACT 58.122 36.000 0.00 0.00 0.00 4.18
92 93 6.201806 CCTCTCTTTTACCATCATTGATCGAC 59.798 42.308 0.00 0.00 0.00 4.20
93 94 6.127054 ACCTCTCTTTTACCATCATTGATCGA 60.127 38.462 0.00 0.00 0.00 3.59
94 95 6.051717 ACCTCTCTTTTACCATCATTGATCG 58.948 40.000 0.00 0.00 0.00 3.69
111 112 8.667592 AAAGACTGGTACTTATTTACCTCTCT 57.332 34.615 0.00 0.00 42.03 3.10
112 113 9.722184 AAAAAGACTGGTACTTATTTACCTCTC 57.278 33.333 0.00 0.00 42.03 3.20
176 177 2.031012 CCAGCTTGTGCGGAGTGA 59.969 61.111 0.00 0.00 45.42 3.41
184 185 1.709147 GCCAGTATCGCCAGCTTGTG 61.709 60.000 0.00 0.00 0.00 3.33
272 273 4.319622 CGCTGCTGTGTCCTACTACTATAC 60.320 50.000 0.00 0.00 0.00 1.47
275 276 2.014857 CGCTGCTGTGTCCTACTACTA 58.985 52.381 0.00 0.00 0.00 1.82
361 369 1.201769 CGTTCGTTCGTAAGCACCATG 60.202 52.381 0.00 0.00 37.18 3.66
382 390 3.557898 GCTGAAGAATCCAGGTCTGTTCA 60.558 47.826 0.00 3.99 32.51 3.18
383 391 3.006247 GCTGAAGAATCCAGGTCTGTTC 58.994 50.000 0.00 0.00 32.51 3.18
385 393 1.280421 GGCTGAAGAATCCAGGTCTGT 59.720 52.381 0.00 0.00 32.51 3.41
386 394 1.741732 CGGCTGAAGAATCCAGGTCTG 60.742 57.143 0.00 0.00 32.51 3.51
387 395 0.539051 CGGCTGAAGAATCCAGGTCT 59.461 55.000 0.00 0.00 32.51 3.85
388 396 1.092345 GCGGCTGAAGAATCCAGGTC 61.092 60.000 0.00 0.00 32.51 3.85
389 397 1.078143 GCGGCTGAAGAATCCAGGT 60.078 57.895 0.00 0.00 32.51 4.00
392 400 1.746615 GCAGCGGCTGAAGAATCCA 60.747 57.895 32.72 0.00 36.96 3.41
395 403 2.821366 CCGCAGCGGCTGAAGAAT 60.821 61.111 32.72 0.00 41.17 2.40
940 1662 3.665675 GAGCGAGGCCGACACCATT 62.666 63.158 0.00 0.00 38.22 3.16
1087 1824 0.244178 TCATGTACAACTACGCCGCA 59.756 50.000 0.00 0.00 0.00 5.69
1102 1839 1.126846 GTCAACGTCTCGCCTTTCATG 59.873 52.381 0.00 0.00 0.00 3.07
1237 1974 1.006102 CGGAGTCAACGTCAAGCCT 60.006 57.895 0.00 0.00 0.00 4.58
1315 2052 3.641986 GCCGGCGTGAACGTGAAA 61.642 61.111 12.58 0.00 42.22 2.69
1735 2906 1.080093 GTCGGTGAACATCGGCTCA 60.080 57.895 4.80 0.00 36.47 4.26
1759 2930 4.641645 TGCTTGTCCACAGCCGGG 62.642 66.667 2.18 0.00 0.00 5.73
1771 2942 0.401738 TTGACCCTTCTCCCTGCTTG 59.598 55.000 0.00 0.00 0.00 4.01
1773 2944 0.622665 CATTGACCCTTCTCCCTGCT 59.377 55.000 0.00 0.00 0.00 4.24
1774 2945 1.034292 GCATTGACCCTTCTCCCTGC 61.034 60.000 0.00 0.00 0.00 4.85
1775 2946 0.622665 AGCATTGACCCTTCTCCCTG 59.377 55.000 0.00 0.00 0.00 4.45
1776 2947 1.376649 AAGCATTGACCCTTCTCCCT 58.623 50.000 0.00 0.00 0.00 4.20
1830 3010 7.824289 TCTCAACTCCTAAACAATCAAGGTATG 59.176 37.037 0.00 0.00 0.00 2.39
1872 3057 0.890996 CTGCTCTTCCCAACACACCC 60.891 60.000 0.00 0.00 0.00 4.61
1875 3060 1.131638 AGTCTGCTCTTCCCAACACA 58.868 50.000 0.00 0.00 0.00 3.72
1964 3155 5.999044 ACCTCAAATACTCCGTAGAGACTA 58.001 41.667 0.00 0.00 43.39 2.59
1968 3159 5.299531 TGATGACCTCAAATACTCCGTAGAG 59.700 44.000 0.00 0.00 46.36 2.43
1986 3177 5.530519 TCAAAGTGTTAATCGCTGATGAC 57.469 39.130 0.00 0.00 36.95 3.06
2059 3260 3.319405 GTGATAGAGCAAAGGGATCGAGA 59.681 47.826 0.00 0.00 36.90 4.04
2062 3263 2.398498 CGTGATAGAGCAAAGGGATCG 58.602 52.381 0.00 0.00 36.90 3.69
2155 3358 8.579682 AAAATCAAAAGCTTTATGTGTGAGAC 57.420 30.769 13.10 0.00 0.00 3.36
2157 3360 8.482429 GTGAAAATCAAAAGCTTTATGTGTGAG 58.518 33.333 13.10 0.00 0.00 3.51
2194 3397 4.202010 CCCCAAAATAATAGTGTGCGAAGG 60.202 45.833 0.00 0.00 0.00 3.46
2195 3398 4.398044 ACCCCAAAATAATAGTGTGCGAAG 59.602 41.667 0.00 0.00 0.00 3.79
2198 3401 6.262273 AGAATACCCCAAAATAATAGTGTGCG 59.738 38.462 0.00 0.00 0.00 5.34
2214 3478 6.095021 GGTGTTTACATGAAGAAGAATACCCC 59.905 42.308 0.00 0.00 0.00 4.95
2249 3513 5.535753 AGGGATTTATGCCAATTTACAGC 57.464 39.130 3.01 0.00 41.29 4.40
2269 3533 8.143835 TCTGAAAAAGGAAAAGAAAAGCATAGG 58.856 33.333 0.00 0.00 0.00 2.57
2277 3541 8.352942 GCTCTACATCTGAAAAAGGAAAAGAAA 58.647 33.333 0.00 0.00 0.00 2.52
2364 3644 1.133976 GTGGGAGGCATATTGCTCTGT 60.134 52.381 0.00 0.00 44.28 3.41
2388 3668 7.533289 TTTGTTCTTAATTTTCCCTACCCTG 57.467 36.000 0.00 0.00 0.00 4.45
2391 3674 9.419297 GTGATTTTGTTCTTAATTTTCCCTACC 57.581 33.333 0.00 0.00 0.00 3.18
2411 3694 4.397103 CACACCTGCATGTAGATGTGATTT 59.603 41.667 28.92 4.60 39.83 2.17
2414 3697 2.302733 ACACACCTGCATGTAGATGTGA 59.697 45.455 36.30 0.00 39.83 3.58
2439 3724 7.880195 CCGTCCCTAATTTATTCATCATCTTCT 59.120 37.037 0.00 0.00 0.00 2.85
2440 3725 7.878127 TCCGTCCCTAATTTATTCATCATCTTC 59.122 37.037 0.00 0.00 0.00 2.87
2441 3726 7.745717 TCCGTCCCTAATTTATTCATCATCTT 58.254 34.615 0.00 0.00 0.00 2.40
2573 3859 2.035193 GTGAGCAGATCATCTTCGCCTA 59.965 50.000 0.00 0.00 40.92 3.93
2575 3861 1.202510 AGTGAGCAGATCATCTTCGCC 60.203 52.381 0.00 0.00 40.92 5.54
2577 3863 2.864946 CCAAGTGAGCAGATCATCTTCG 59.135 50.000 0.00 0.00 40.92 3.79
2580 3866 3.518705 AGTTCCAAGTGAGCAGATCATCT 59.481 43.478 0.00 0.00 40.92 2.90
2660 3947 4.228666 ACCACCTACATCTACTCTCTGACT 59.771 45.833 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.