Multiple sequence alignment - TraesCS4B01G330100

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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 TraesCS4B01G330100 chr4B 100.000 4218 0 0 1 4218 621188275 621192492 0.000000e+00 7790.0
1 TraesCS4B01G330100 chr4B 93.806 2018 84 13 1365 3379 621279395 621281374 0.000000e+00 2996.0
2 TraesCS4B01G330100 chr4B 84.176 1504 215 17 1742 3233 620967275 620965783 0.000000e+00 1437.0
3 TraesCS4B01G330100 chr4B 86.786 280 28 7 1309 1585 620967953 620967680 1.910000e-78 303.0
4 TraesCS4B01G330100 chr4B 88.293 205 24 0 1382 1586 620971579 620971375 3.260000e-61 246.0
5 TraesCS4B01G330100 chr4B 94.286 70 2 2 4150 4217 398759396 398759327 5.770000e-19 106.0
6 TraesCS4B01G330100 chr4B 86.585 82 7 4 5 84 563438996 563438917 2.090000e-13 87.9
7 TraesCS4B01G330100 chr4B 100.000 28 0 0 3377 3404 621281492 621281519 8.000000e-03 52.8
8 TraesCS4B01G330100 chr4D 92.380 2454 117 26 870 3282 486624104 486621680 0.000000e+00 3432.0
9 TraesCS4B01G330100 chr4D 85.693 678 61 17 207 873 486625093 486624441 0.000000e+00 682.0
10 TraesCS4B01G330100 chr5A 95.811 1695 59 3 1709 3403 667067541 667069223 0.000000e+00 2726.0
11 TraesCS4B01G330100 chr5A 94.787 1688 70 9 1598 3282 666874242 666872570 0.000000e+00 2614.0
12 TraesCS4B01G330100 chr5A 84.404 1494 209 15 1744 3225 666825175 666823694 0.000000e+00 1447.0
13 TraesCS4B01G330100 chr5A 88.557 769 46 23 871 1611 667066756 667067510 0.000000e+00 894.0
14 TraesCS4B01G330100 chr5A 88.315 445 38 6 439 873 667065918 667066358 4.830000e-144 521.0
15 TraesCS4B01G330100 chr5A 88.757 338 34 4 55 392 667065344 667065677 1.090000e-110 411.0
16 TraesCS4B01G330100 chr5A 82.105 380 50 17 1215 1585 666826185 666825815 4.100000e-80 309.0
17 TraesCS4B01G330100 chr5A 86.307 241 33 0 1346 1586 666844084 666843844 3.230000e-66 263.0
18 TraesCS4B01G330100 chr5A 96.639 119 4 0 1472 1590 666876504 666876386 9.250000e-47 198.0
19 TraesCS4B01G330100 chr5A 85.405 185 14 5 1297 1479 666886615 666886442 3.350000e-41 180.0
20 TraesCS4B01G330100 chr5A 88.750 80 7 2 4138 4215 177542709 177542630 3.470000e-16 97.1
21 TraesCS4B01G330100 chr3D 90.026 772 31 23 3412 4158 355626763 355626013 0.000000e+00 957.0
22 TraesCS4B01G330100 chr3D 95.312 64 3 0 1 64 181454495 181454558 7.460000e-18 102.0
23 TraesCS4B01G330100 chr3A 89.754 771 41 19 3412 4158 474431675 474430919 0.000000e+00 952.0
24 TraesCS4B01G330100 chr3A 94.366 71 4 0 3455 3525 50537211 50537141 4.460000e-20 110.0
25 TraesCS4B01G330100 chr3A 87.356 87 7 4 4132 4215 519974360 519974275 3.470000e-16 97.1
26 TraesCS4B01G330100 chr3B 88.312 770 43 23 3412 4158 456550140 456549395 0.000000e+00 880.0
27 TraesCS4B01G330100 chr3B 85.070 643 84 9 3523 4156 367476932 367477571 0.000000e+00 645.0
28 TraesCS4B01G330100 chr3B 95.588 68 1 2 4148 4215 639068067 639068132 1.600000e-19 108.0
29 TraesCS4B01G330100 chr6A 79.362 1129 192 28 2081 3184 31369043 31367931 0.000000e+00 756.0
30 TraesCS4B01G330100 chr6A 83.465 127 19 2 1745 1870 31369403 31369278 2.660000e-22 117.0
31 TraesCS4B01G330100 chrUn 78.133 1125 213 24 2081 3184 103934273 103933161 0.000000e+00 684.0
32 TraesCS4B01G330100 chrUn 79.006 181 34 4 1745 1923 103934627 103934449 2.060000e-23 121.0
33 TraesCS4B01G330100 chrUn 95.312 64 3 0 1 64 67388578 67388641 7.460000e-18 102.0
34 TraesCS4B01G330100 chr6B 85.714 637 76 12 3523 4151 680133272 680132643 0.000000e+00 658.0
35 TraesCS4B01G330100 chr6B 93.056 72 4 1 4147 4218 659790015 659789945 2.070000e-18 104.0
36 TraesCS4B01G330100 chr1D 84.938 644 82 14 3523 4158 199670974 199670338 4.600000e-179 638.0
37 TraesCS4B01G330100 chr1D 93.939 66 4 0 1 66 321504860 321504925 2.680000e-17 100.0
38 TraesCS4B01G330100 chr1B 85.110 638 80 12 3524 4153 655060239 655060869 4.600000e-179 638.0
39 TraesCS4B01G330100 chr1B 82.278 79 13 1 1762 1840 52347333 52347410 2.720000e-07 67.6
40 TraesCS4B01G330100 chr6D 84.520 646 80 16 3523 4158 443752652 443752017 4.630000e-174 621.0
41 TraesCS4B01G330100 chr6D 96.825 63 1 1 1 63 15493359 15493298 2.070000e-18 104.0
42 TraesCS4B01G330100 chr6D 94.286 70 1 3 4149 4218 124586120 124586054 2.070000e-18 104.0
43 TraesCS4B01G330100 chr2D 84.544 647 78 18 3523 4158 495103430 495102795 4.630000e-174 621.0
44 TraesCS4B01G330100 chr2D 96.875 64 2 0 4155 4218 328942667 328942604 1.600000e-19 108.0
45 TraesCS4B01G330100 chr7B 86.087 115 13 3 3413 3527 725189197 725189308 2.060000e-23 121.0
46 TraesCS4B01G330100 chr7B 90.789 76 5 2 4142 4217 390865330 390865257 2.680000e-17 100.0
47 TraesCS4B01G330100 chr7D 94.030 67 4 0 1 67 423396568 423396634 7.460000e-18 102.0
48 TraesCS4B01G330100 chr7D 91.781 73 5 1 3455 3527 21098042 21097971 2.680000e-17 100.0
49 TraesCS4B01G330100 chr7D 89.157 83 6 2 4137 4217 22815077 22815158 2.680000e-17 100.0
50 TraesCS4B01G330100 chr7A 95.238 63 3 0 3 65 612400536 612400598 2.680000e-17 100.0
51 TraesCS4B01G330100 chr4A 93.939 66 4 0 1 66 485504809 485504874 2.680000e-17 100.0
52 TraesCS4B01G330100 chr2B 93.939 66 3 1 1 66 542994339 542994403 9.650000e-17 99.0
53 TraesCS4B01G330100 chr5B 90.541 74 6 1 3455 3528 605316896 605316824 3.470000e-16 97.1
54 TraesCS4B01G330100 chr2A 89.041 73 7 1 3455 3527 170067664 170067735 5.810000e-14 89.8
55 TraesCS4B01G330100 chr1A 89.041 73 7 1 3455 3527 63007262 63007191 5.810000e-14 89.8


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 TraesCS4B01G330100 chr4B 621188275 621192492 4217 False 7790.0 7790 100.000000 1 4218 1 chr4B.!!$F1 4217
1 TraesCS4B01G330100 chr4B 621279395 621281519 2124 False 1524.4 2996 96.903000 1365 3404 2 chr4B.!!$F2 2039
2 TraesCS4B01G330100 chr4B 620965783 620971579 5796 True 662.0 1437 86.418333 1309 3233 3 chr4B.!!$R3 1924
3 TraesCS4B01G330100 chr4D 486621680 486625093 3413 True 2057.0 3432 89.036500 207 3282 2 chr4D.!!$R1 3075
4 TraesCS4B01G330100 chr5A 666872570 666876504 3934 True 1406.0 2614 95.713000 1472 3282 2 chr5A.!!$R5 1810
5 TraesCS4B01G330100 chr5A 667065344 667069223 3879 False 1138.0 2726 90.360000 55 3403 4 chr5A.!!$F1 3348
6 TraesCS4B01G330100 chr5A 666823694 666826185 2491 True 878.0 1447 83.254500 1215 3225 2 chr5A.!!$R4 2010
7 TraesCS4B01G330100 chr3D 355626013 355626763 750 True 957.0 957 90.026000 3412 4158 1 chr3D.!!$R1 746
8 TraesCS4B01G330100 chr3A 474430919 474431675 756 True 952.0 952 89.754000 3412 4158 1 chr3A.!!$R2 746
9 TraesCS4B01G330100 chr3B 456549395 456550140 745 True 880.0 880 88.312000 3412 4158 1 chr3B.!!$R1 746
10 TraesCS4B01G330100 chr3B 367476932 367477571 639 False 645.0 645 85.070000 3523 4156 1 chr3B.!!$F1 633
11 TraesCS4B01G330100 chr6A 31367931 31369403 1472 True 436.5 756 81.413500 1745 3184 2 chr6A.!!$R1 1439
12 TraesCS4B01G330100 chrUn 103933161 103934627 1466 True 402.5 684 78.569500 1745 3184 2 chrUn.!!$R1 1439
13 TraesCS4B01G330100 chr6B 680132643 680133272 629 True 658.0 658 85.714000 3523 4151 1 chr6B.!!$R2 628
14 TraesCS4B01G330100 chr1D 199670338 199670974 636 True 638.0 638 84.938000 3523 4158 1 chr1D.!!$R1 635
15 TraesCS4B01G330100 chr1B 655060239 655060869 630 False 638.0 638 85.110000 3524 4153 1 chr1B.!!$F2 629
16 TraesCS4B01G330100 chr6D 443752017 443752652 635 True 621.0 621 84.520000 3523 4158 1 chr6D.!!$R3 635
17 TraesCS4B01G330100 chr2D 495102795 495103430 635 True 621.0 621 84.544000 3523 4158 1 chr2D.!!$R2 635

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
694 889 0.180406 GGTACATGATTCTGCCCGGT 59.820 55.000 0.00 0.00 0.00 5.28 F
994 1610 0.894835 TGTTATCCAGAGAGCGTGCA 59.105 50.000 0.00 0.00 0.00 4.57 F
1334 3653 1.077858 CCTTCTTCTCCAGCCTGGC 60.078 63.158 11.65 11.65 37.47 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 6856 0.176910 TGTTGAACGTGCAGAGGACA 59.823 50.0 0.00 0.00 0.00 4.02 R
1943 6983 0.965866 TTGGACTCAGAGTCGGCGAT 60.966 55.0 21.98 1.58 45.96 4.58 R
3282 8382 0.763035 ACTGAAACGGGGTGCTAGTT 59.237 50.0 0.00 0.00 0.00 2.24 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
68 69 3.285484 GGAGACGTATCACCTACCTCAA 58.715 50.000 12.92 0.00 33.05 3.02
103 104 6.489603 TGATGTCACCACCATAATAACCTTT 58.510 36.000 0.00 0.00 0.00 3.11
104 105 7.634718 TGATGTCACCACCATAATAACCTTTA 58.365 34.615 0.00 0.00 0.00 1.85
108 109 7.057894 GTCACCACCATAATAACCTTTATCCA 58.942 38.462 0.00 0.00 0.00 3.41
109 110 7.012989 GTCACCACCATAATAACCTTTATCCAC 59.987 40.741 0.00 0.00 0.00 4.02
111 112 7.013274 CACCACCATAATAACCTTTATCCACAG 59.987 40.741 0.00 0.00 0.00 3.66
112 113 7.092174 ACCACCATAATAACCTTTATCCACAGA 60.092 37.037 0.00 0.00 0.00 3.41
113 114 7.228706 CCACCATAATAACCTTTATCCACAGAC 59.771 40.741 0.00 0.00 0.00 3.51
114 115 6.990349 ACCATAATAACCTTTATCCACAGACG 59.010 38.462 0.00 0.00 0.00 4.18
115 116 6.073222 CCATAATAACCTTTATCCACAGACGC 60.073 42.308 0.00 0.00 0.00 5.19
158 159 3.181475 ACGAGTGAGTGACAACAACATCT 60.181 43.478 0.00 0.00 0.00 2.90
168 169 5.009610 GTGACAACAACATCTAAACCACCAT 59.990 40.000 0.00 0.00 0.00 3.55
173 174 5.497474 ACAACATCTAAACCACCATAGTCC 58.503 41.667 0.00 0.00 0.00 3.85
177 178 5.013704 ACATCTAAACCACCATAGTCCACAA 59.986 40.000 0.00 0.00 0.00 3.33
179 180 6.134535 TCTAAACCACCATAGTCCACAAAT 57.865 37.500 0.00 0.00 0.00 2.32
343 344 2.159382 CGGTATTGAAGCCACAACCTT 58.841 47.619 0.00 0.00 32.50 3.50
376 377 3.506455 TCACTCTCGGAAGAAGTTGGTAG 59.494 47.826 0.00 0.00 41.32 3.18
399 400 2.426023 GCAGGGTCCAACACGAGT 59.574 61.111 0.00 0.00 0.00 4.18
412 414 1.606889 ACGAGTGAGGGACCTCCAC 60.607 63.158 15.40 12.76 42.09 4.02
430 432 3.677963 CAGAATGTTGCCCCCTCTT 57.322 52.632 0.00 0.00 0.00 2.85
431 433 1.180029 CAGAATGTTGCCCCCTCTTG 58.820 55.000 0.00 0.00 0.00 3.02
461 656 1.244019 ATGAAGCTTGGGCAACGGAC 61.244 55.000 2.10 0.00 41.70 4.79
466 661 2.892334 CTTGGGCAACGGACACACG 61.892 63.158 0.00 0.00 40.31 4.49
534 729 5.596845 GAAAACACTTCCAACATGCCTAAA 58.403 37.500 0.00 0.00 0.00 1.85
609 804 3.429822 GCACGTCAACTAGGGTAGCATTA 60.430 47.826 0.00 0.00 0.00 1.90
694 889 0.180406 GGTACATGATTCTGCCCGGT 59.820 55.000 0.00 0.00 0.00 5.28
755 951 1.402720 CCGGATTGGTTGTGTGCAATC 60.403 52.381 0.00 0.00 36.92 2.67
779 975 2.036862 ACGGTGACCTTTGGAGAGTTAC 59.963 50.000 0.00 0.00 0.00 2.50
785 981 2.038164 ACCTTTGGAGAGTTACCGGAAC 59.962 50.000 9.46 8.67 38.44 3.62
873 1078 5.278758 CCATCGTTGGTGGTTTGAATTAGTT 60.279 40.000 4.23 0.00 38.30 2.24
874 1079 6.072397 CCATCGTTGGTGGTTTGAATTAGTTA 60.072 38.462 4.23 0.00 38.30 2.24
990 1606 3.325870 TGTTGTTGTTATCCAGAGAGCG 58.674 45.455 0.00 0.00 0.00 5.03
991 1607 3.244078 TGTTGTTGTTATCCAGAGAGCGT 60.244 43.478 0.00 0.00 0.00 5.07
993 1609 1.661112 GTTGTTATCCAGAGAGCGTGC 59.339 52.381 0.00 0.00 0.00 5.34
994 1610 0.894835 TGTTATCCAGAGAGCGTGCA 59.105 50.000 0.00 0.00 0.00 4.57
1075 1704 3.407698 TCACTCTCACTCTCACTCTCAC 58.592 50.000 0.00 0.00 0.00 3.51
1269 1908 2.342354 GCGCGCGTTTACTTCTTTACTA 59.658 45.455 32.35 0.00 0.00 1.82
1334 3653 1.077858 CCTTCTTCTCCAGCCTGGC 60.078 63.158 11.65 11.65 37.47 4.85
1362 3687 1.330655 GCGAGGATCAGGAGGTGGAA 61.331 60.000 0.00 0.00 33.17 3.53
1597 3922 3.383505 CGTGGTGAGTATGGATGGAACTA 59.616 47.826 0.00 0.00 0.00 2.24
1616 6081 4.129737 CGTCACGCTCCCATCCGT 62.130 66.667 0.00 0.00 38.35 4.69
1618 6083 3.458163 TCACGCTCCCATCCGTCC 61.458 66.667 0.00 0.00 35.17 4.79
1619 6084 4.873129 CACGCTCCCATCCGTCCG 62.873 72.222 0.00 0.00 35.17 4.79
1622 6087 3.782443 GCTCCCATCCGTCCGGTT 61.782 66.667 0.00 0.00 36.47 4.44
1623 6088 2.987125 CTCCCATCCGTCCGGTTT 59.013 61.111 0.00 0.00 36.47 3.27
1624 6089 1.449601 CTCCCATCCGTCCGGTTTG 60.450 63.158 0.00 5.21 36.47 2.93
1625 6090 3.131478 CCCATCCGTCCGGTTTGC 61.131 66.667 0.00 0.00 36.47 3.68
1639 6105 1.669115 TTTGCTGTCGCTCTCTGCC 60.669 57.895 0.00 0.00 38.78 4.85
1707 6217 7.816513 TCAGAGTGAAAAATAGTCAGAGTGATG 59.183 37.037 0.00 0.00 0.00 3.07
1714 6224 9.092876 GAAAAATAGTCAGAGTGATGGTAAGAG 57.907 37.037 0.00 0.00 0.00 2.85
1774 6814 4.379243 CTCAGCCCGAACGTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
1916 6956 2.043852 TCGAGTCCAGCCTCCTCC 60.044 66.667 0.00 0.00 0.00 4.30
2070 7146 0.528684 ATAAAGAGCGCTCCGTCTGC 60.529 55.000 32.94 7.95 0.00 4.26
2275 7351 3.899981 CTGCAACGGCTGGCACCTA 62.900 63.158 1.08 0.00 41.91 3.08
2818 7906 4.269523 GGGTGGCTGCACACTGGA 62.270 66.667 16.88 0.00 41.09 3.86
3257 8357 8.900511 AAAATGATGTGACATGTCGATTAAAG 57.099 30.769 20.54 0.00 0.00 1.85
3258 8358 5.469373 TGATGTGACATGTCGATTAAAGC 57.531 39.130 20.54 2.01 0.00 3.51
3262 8362 4.627035 TGTGACATGTCGATTAAAGCTGAG 59.373 41.667 20.54 0.00 0.00 3.35
3278 8378 2.819608 GCTGAGGCCATTCAGTTGTTAA 59.180 45.455 20.00 0.00 45.07 2.01
3279 8379 3.366374 GCTGAGGCCATTCAGTTGTTAAC 60.366 47.826 20.00 0.00 45.07 2.01
3280 8380 4.074970 CTGAGGCCATTCAGTTGTTAACT 58.925 43.478 12.79 0.00 44.06 2.24
3281 8381 5.235850 TGAGGCCATTCAGTTGTTAACTA 57.764 39.130 5.01 0.00 40.46 2.24
3282 8382 5.626142 TGAGGCCATTCAGTTGTTAACTAA 58.374 37.500 5.01 0.00 40.46 2.24
3404 8629 6.199154 ACGATAGCTAAATGTCAATCGACTTG 59.801 38.462 15.93 0.00 41.10 3.16
3405 8630 4.606457 AGCTAAATGTCAATCGACTTGC 57.394 40.909 0.00 0.00 43.06 4.01
3406 8631 3.375299 AGCTAAATGTCAATCGACTTGCC 59.625 43.478 0.00 0.00 43.06 4.52
3407 8632 3.375299 GCTAAATGTCAATCGACTTGCCT 59.625 43.478 0.00 0.00 43.06 4.75
3408 8633 4.142600 GCTAAATGTCAATCGACTTGCCTT 60.143 41.667 0.00 0.00 43.06 4.35
3409 8634 5.064707 GCTAAATGTCAATCGACTTGCCTTA 59.935 40.000 0.00 0.00 43.06 2.69
3410 8635 5.957842 AAATGTCAATCGACTTGCCTTAA 57.042 34.783 0.00 0.00 43.06 1.85
3540 8766 9.883142 ACCAGACATGAAAATTTTAAAAACAGA 57.117 25.926 4.44 0.00 0.00 3.41
3723 8957 3.658351 ATTTCAATAGCGTTCACGAGC 57.342 42.857 2.87 0.00 43.02 5.03
3726 8960 3.497297 TCAATAGCGTTCACGAGCTTA 57.503 42.857 2.87 0.00 44.15 3.09
4167 9454 4.686257 GCGCGCGCATGATACGTC 62.686 66.667 46.11 15.61 41.49 4.34
4168 9455 3.024609 CGCGCGCATGATACGTCT 61.025 61.111 32.61 0.00 0.00 4.18
4169 9456 2.840016 GCGCGCATGATACGTCTC 59.160 61.111 29.10 0.00 0.00 3.36
4170 9457 2.649257 GCGCGCATGATACGTCTCC 61.649 63.158 29.10 0.00 0.00 3.71
4171 9458 1.299089 CGCGCATGATACGTCTCCA 60.299 57.895 8.75 0.00 0.00 3.86
4172 9459 0.869880 CGCGCATGATACGTCTCCAA 60.870 55.000 8.75 0.00 0.00 3.53
4173 9460 1.502231 GCGCATGATACGTCTCCAAT 58.498 50.000 0.30 0.00 0.00 3.16
4174 9461 1.193203 GCGCATGATACGTCTCCAATG 59.807 52.381 0.30 0.00 0.00 2.82
4175 9462 2.473816 CGCATGATACGTCTCCAATGT 58.526 47.619 0.00 0.00 0.00 2.71
4176 9463 3.638484 CGCATGATACGTCTCCAATGTA 58.362 45.455 0.00 0.00 33.91 2.29
4177 9464 4.237724 CGCATGATACGTCTCCAATGTAT 58.762 43.478 0.00 0.00 41.77 2.29
4178 9465 4.686091 CGCATGATACGTCTCCAATGTATT 59.314 41.667 0.00 0.00 39.66 1.89
4179 9466 5.177511 CGCATGATACGTCTCCAATGTATTT 59.822 40.000 0.00 0.00 39.66 1.40
4180 9467 6.364976 CGCATGATACGTCTCCAATGTATTTA 59.635 38.462 0.00 0.00 39.66 1.40
4181 9468 7.063426 CGCATGATACGTCTCCAATGTATTTAT 59.937 37.037 0.00 0.00 39.66 1.40
4182 9469 9.366216 GCATGATACGTCTCCAATGTATTTATA 57.634 33.333 0.00 0.00 39.66 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.022406 AGGTAGGTGATACGTCTCCAAC 58.978 50.000 0.00 0.00 39.86 3.77
45 46 3.285484 GAGGTAGGTGATACGTCTCCAA 58.715 50.000 0.00 0.00 43.10 3.53
46 47 2.240414 TGAGGTAGGTGATACGTCTCCA 59.760 50.000 0.00 0.00 45.46 3.86
47 48 2.928334 TGAGGTAGGTGATACGTCTCC 58.072 52.381 0.00 0.00 45.46 3.71
48 49 6.039047 TGTTATTGAGGTAGGTGATACGTCTC 59.961 42.308 0.00 0.00 45.46 3.36
49 50 5.889853 TGTTATTGAGGTAGGTGATACGTCT 59.110 40.000 0.00 0.00 45.46 4.18
50 51 6.140303 TGTTATTGAGGTAGGTGATACGTC 57.860 41.667 0.00 1.77 45.45 4.34
52 53 8.433421 AAAATGTTATTGAGGTAGGTGATACG 57.567 34.615 0.00 0.00 34.99 3.06
80 81 8.691661 ATAAAGGTTATTATGGTGGTGACATC 57.308 34.615 0.00 0.00 46.14 3.06
81 82 7.724061 GGATAAAGGTTATTATGGTGGTGACAT 59.276 37.037 0.00 0.00 46.14 3.06
82 83 7.057894 GGATAAAGGTTATTATGGTGGTGACA 58.942 38.462 0.00 0.00 38.70 3.58
86 87 6.975949 TGTGGATAAAGGTTATTATGGTGGT 58.024 36.000 0.00 0.00 0.00 4.16
92 93 5.995897 GGCGTCTGTGGATAAAGGTTATTAT 59.004 40.000 0.00 0.00 0.00 1.28
93 94 5.362263 GGCGTCTGTGGATAAAGGTTATTA 58.638 41.667 0.00 0.00 0.00 0.98
103 104 2.030551 CTAGCGGCGTCTGTGGATA 58.969 57.895 9.37 0.00 0.00 2.59
104 105 2.808315 CTAGCGGCGTCTGTGGAT 59.192 61.111 9.37 0.00 0.00 3.41
109 110 2.363711 TATTGGGCTAGCGGCGTCTG 62.364 60.000 9.37 0.00 42.94 3.51
111 112 1.664965 CTATTGGGCTAGCGGCGTC 60.665 63.158 9.37 0.13 42.94 5.19
112 113 2.365095 GACTATTGGGCTAGCGGCGT 62.365 60.000 9.37 0.00 42.94 5.68
113 114 1.664965 GACTATTGGGCTAGCGGCG 60.665 63.158 9.00 0.51 42.94 6.46
114 115 0.880718 GTGACTATTGGGCTAGCGGC 60.881 60.000 9.00 0.00 40.90 6.53
115 116 0.464036 TGTGACTATTGGGCTAGCGG 59.536 55.000 9.00 0.00 0.00 5.52
158 159 5.475220 CACATTTGTGGACTATGGTGGTTTA 59.525 40.000 2.69 0.00 42.10 2.01
173 174 1.006337 CCAACCGCCCACATTTGTG 60.006 57.895 3.67 3.67 45.23 3.33
177 178 2.990967 CAGCCAACCGCCCACATT 60.991 61.111 0.00 0.00 38.78 2.71
204 205 3.480470 CCATGACACCCTCACCATTATC 58.520 50.000 0.00 0.00 0.00 1.75
205 206 2.175499 CCCATGACACCCTCACCATTAT 59.825 50.000 0.00 0.00 0.00 1.28
280 281 0.626382 GCTAGGGAGCCCTTTTTCCT 59.374 55.000 14.33 0.00 45.70 3.36
281 282 3.192799 GCTAGGGAGCCCTTTTTCC 57.807 57.895 14.33 0.00 45.70 3.13
331 332 2.812011 GTCATCGTTAAGGTTGTGGCTT 59.188 45.455 6.22 0.00 0.00 4.35
343 344 3.340928 TCCGAGAGTGAAGTCATCGTTA 58.659 45.455 3.04 0.00 0.00 3.18
376 377 2.985847 GTTGGACCCTGCCTGTGC 60.986 66.667 0.00 0.00 38.26 4.57
399 400 1.279496 CATTCTGTGGAGGTCCCTCA 58.721 55.000 15.01 0.00 44.40 3.86
412 414 1.180029 CAAGAGGGGGCAACATTCTG 58.820 55.000 0.00 0.00 39.74 3.02
426 428 6.992063 AGCTTCATTGGTTATACACAAGAG 57.008 37.500 0.00 0.00 0.00 2.85
427 429 6.150976 CCAAGCTTCATTGGTTATACACAAGA 59.849 38.462 0.00 0.00 44.01 3.02
430 432 5.895636 CCAAGCTTCATTGGTTATACACA 57.104 39.130 0.00 0.00 44.01 3.72
456 651 3.533105 TGCTGGTCGTGTGTCCGT 61.533 61.111 0.00 0.00 0.00 4.69
461 656 3.036084 GGTCGTGCTGGTCGTGTG 61.036 66.667 0.00 0.00 0.00 3.82
466 661 2.100879 AACTCCAGGTCGTGCTGGTC 62.101 60.000 0.00 0.00 41.28 4.02
508 703 2.043411 CATGTTGGAAGTGTTTTCGCG 58.957 47.619 0.00 0.00 35.20 5.87
534 729 2.604914 CGCATTGAGCTTCGATACTGTT 59.395 45.455 0.00 0.00 42.61 3.16
628 823 3.407967 TTCATCACCTCCCCCGCC 61.408 66.667 0.00 0.00 0.00 6.13
629 824 2.124695 GTTCATCACCTCCCCCGC 60.125 66.667 0.00 0.00 0.00 6.13
630 825 1.221840 CAGTTCATCACCTCCCCCG 59.778 63.158 0.00 0.00 0.00 5.73
669 864 3.206150 GGCAGAATCATGTACCGACAAT 58.794 45.455 0.00 0.00 39.59 2.71
694 889 3.332034 TCGGTCATATCGCTCGATTCTA 58.668 45.455 10.18 0.00 36.17 2.10
700 896 1.399572 CAGTTCGGTCATATCGCTCG 58.600 55.000 0.00 0.00 0.00 5.03
755 951 2.280524 TCCAAAGGTCACCGTGCG 60.281 61.111 0.00 0.00 0.00 5.34
779 975 3.192922 GGGATCGTTGCGTTCCGG 61.193 66.667 0.00 0.00 43.98 5.14
793 989 4.853142 CCAGATCGTCCCCGGGGA 62.853 72.222 39.67 39.67 42.90 4.81
896 1512 3.851403 GCTACGGAAATACGTACACGAAA 59.149 43.478 9.04 0.00 46.58 3.46
899 1515 2.784505 TGCTACGGAAATACGTACACG 58.215 47.619 0.00 2.92 46.58 4.49
909 1525 1.160946 TTGCGTGCTTGCTACGGAAA 61.161 50.000 16.40 6.21 46.19 3.13
993 1609 2.223876 ACAACCAACTTGCATCAAGCTG 60.224 45.455 6.49 4.98 44.43 4.24
994 1610 2.034124 ACAACCAACTTGCATCAAGCT 58.966 42.857 6.49 0.00 44.43 3.74
997 1613 2.223782 GCAGACAACCAACTTGCATCAA 60.224 45.455 0.00 0.00 32.41 2.57
1075 1704 4.175489 GCTGCTGCTCATGGCGTG 62.175 66.667 8.53 0.00 45.43 5.34
1102 1741 5.864418 TGGGTTATTAGTCTACGAAGCAT 57.136 39.130 0.00 0.00 0.00 3.79
1184 1823 2.140717 GATTAGAATAACGGTGGCGGG 58.859 52.381 0.00 0.00 0.00 6.13
1312 1960 1.481772 CAGGCTGGAGAAGAAGGAGAG 59.518 57.143 6.61 0.00 0.00 3.20
1313 1961 1.566211 CAGGCTGGAGAAGAAGGAGA 58.434 55.000 6.61 0.00 0.00 3.71
1314 3633 0.540923 CCAGGCTGGAGAAGAAGGAG 59.459 60.000 29.96 0.00 40.96 3.69
1334 3653 2.037620 CTGATCCTCGCCCCTTCCAG 62.038 65.000 0.00 0.00 0.00 3.86
1346 3665 0.327000 CCCTTCCACCTCCTGATCCT 60.327 60.000 0.00 0.00 0.00 3.24
1362 3687 4.101448 GCGTCCATGTCCAGCCCT 62.101 66.667 0.00 0.00 0.00 5.19
1597 3922 3.771160 GGATGGGAGCGTGACGGT 61.771 66.667 10.29 10.29 41.33 4.83
1639 6105 3.050619 CAGAGAGCAAGCAAAGCAAAAG 58.949 45.455 0.00 0.00 0.00 2.27
1774 6814 1.805539 GTGCAGCTCGTACATCGCA 60.806 57.895 0.00 0.00 39.67 5.10
1816 6856 0.176910 TGTTGAACGTGCAGAGGACA 59.823 50.000 0.00 0.00 0.00 4.02
1943 6983 0.965866 TTGGACTCAGAGTCGGCGAT 60.966 55.000 21.98 1.58 45.96 4.58
1954 6994 4.680237 CTGGCGGCGTTGGACTCA 62.680 66.667 9.37 0.00 0.00 3.41
1981 7021 1.012086 CGTCCGAGATGGTTACGAGA 58.988 55.000 0.00 0.00 39.63 4.04
2037 7104 3.633065 GCTCTTTATCAGACCCTCGTAGT 59.367 47.826 0.00 0.00 0.00 2.73
2038 7105 3.304123 CGCTCTTTATCAGACCCTCGTAG 60.304 52.174 0.00 0.00 0.00 3.51
2039 7106 2.617308 CGCTCTTTATCAGACCCTCGTA 59.383 50.000 0.00 0.00 0.00 3.43
2040 7107 1.405821 CGCTCTTTATCAGACCCTCGT 59.594 52.381 0.00 0.00 0.00 4.18
2041 7108 1.866063 GCGCTCTTTATCAGACCCTCG 60.866 57.143 0.00 0.00 0.00 4.63
2042 7109 1.410882 AGCGCTCTTTATCAGACCCTC 59.589 52.381 2.64 0.00 0.00 4.30
2070 7146 2.686816 GGCCACCGGATGTCAAACG 61.687 63.158 9.46 0.00 0.00 3.60
2498 7586 3.157252 GCCGAGCTCCTCCATCCA 61.157 66.667 8.47 0.00 0.00 3.41
3257 8357 1.251251 AACAACTGAATGGCCTCAGC 58.749 50.000 19.31 0.68 45.72 4.26
3258 8358 4.074970 AGTTAACAACTGAATGGCCTCAG 58.925 43.478 18.11 18.11 46.94 3.35
3262 8362 6.327279 AGTTTAGTTAACAACTGAATGGCC 57.673 37.500 8.61 0.00 42.84 5.36
3278 8378 2.369532 TGAAACGGGGTGCTAGTTTAGT 59.630 45.455 0.00 0.00 38.09 2.24
3279 8379 3.000727 CTGAAACGGGGTGCTAGTTTAG 58.999 50.000 0.00 0.00 38.09 1.85
3280 8380 2.369532 ACTGAAACGGGGTGCTAGTTTA 59.630 45.455 0.00 0.00 38.09 2.01
3281 8381 1.142262 ACTGAAACGGGGTGCTAGTTT 59.858 47.619 0.00 0.00 40.32 2.66
3282 8382 0.763035 ACTGAAACGGGGTGCTAGTT 59.237 50.000 0.00 0.00 0.00 2.24
3540 8766 7.769272 TTTGCTCAGATTTCGAAATTTGTTT 57.231 28.000 29.75 9.73 33.59 2.83
3702 8936 3.684788 AGCTCGTGAACGCTATTGAAATT 59.315 39.130 0.00 0.00 39.60 1.82
3872 9110 5.176223 CACAAACACTCTTTTGCATGATTCC 59.824 40.000 0.00 0.00 39.67 3.01
3876 9114 4.717233 ACACAAACACTCTTTTGCATGA 57.283 36.364 0.00 0.00 39.67 3.07
4039 9292 9.710979 ATGTACATTTATAACGCACACATAAAC 57.289 29.630 1.41 0.00 29.50 2.01


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

AutoCloner maintained by Alex Coulton.