Multiple sequence alignment - TraesCS5A01G214700

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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 TraesCS5A01G214700 chr5A 100.000 3647 0 0 1 3647 429995557 429999203 0.000000e+00 6735.0
1 TraesCS5A01G214700 chr5A 96.629 1068 21 10 1665 2721 430042548 430041485 0.000000e+00 1759.0
2 TraesCS5A01G214700 chr5A 91.523 814 61 7 442 1252 430043684 430042876 0.000000e+00 1114.0
3 TraesCS5A01G214700 chr5A 78.165 632 115 14 538 1158 419829199 419829818 7.390000e-102 381.0
4 TraesCS5A01G214700 chr5A 85.672 335 30 11 1300 1623 430042876 430042549 1.620000e-88 337.0
5 TraesCS5A01G214700 chr5A 96.721 61 2 0 465 525 429995935 429995995 6.440000e-18 102.0
6 TraesCS5A01G214700 chr5A 96.721 61 2 0 379 439 429996021 429996081 6.440000e-18 102.0
7 TraesCS5A01G214700 chr5D 91.299 1655 82 24 1300 2917 326404177 326402548 0.000000e+00 2202.0
8 TraesCS5A01G214700 chr5D 91.411 1269 83 16 1 1252 326405436 326404177 0.000000e+00 1716.0
9 TraesCS5A01G214700 chr5D 94.933 1046 35 6 1688 2725 326383639 326384674 0.000000e+00 1622.0
10 TraesCS5A01G214700 chr5D 93.445 839 52 3 438 1274 326382208 326383045 0.000000e+00 1242.0
11 TraesCS5A01G214700 chr5D 92.256 297 19 4 1321 1614 326383044 326383339 5.630000e-113 418.0
12 TraesCS5A01G214700 chr5D 90.871 241 18 4 2976 3216 121073082 121073318 1.630000e-83 320.0
13 TraesCS5A01G214700 chr5D 91.803 61 5 0 379 439 326382237 326382297 6.490000e-13 86.1
14 TraesCS5A01G214700 chr5D 93.333 45 3 0 1616 1660 326383595 326383639 2.350000e-07 67.6
15 TraesCS5A01G214700 chr5B 95.223 1298 37 10 1635 2917 378904365 378903078 0.000000e+00 2030.0
16 TraesCS5A01G214700 chr5B 92.937 1246 70 6 363 1595 378905605 378904365 0.000000e+00 1797.0
17 TraesCS5A01G214700 chr5B 93.975 1112 41 16 1627 2725 378852293 378853391 0.000000e+00 1659.0
18 TraesCS5A01G214700 chr5B 90.315 857 74 7 438 1288 378851170 378852023 0.000000e+00 1114.0
19 TraesCS5A01G214700 chr5B 84.924 922 122 14 1689 2600 375224032 375224946 0.000000e+00 917.0
20 TraesCS5A01G214700 chr5B 80.507 631 112 7 538 1158 375223262 375223891 1.190000e-129 473.0
21 TraesCS5A01G214700 chr5B 88.152 211 11 7 1379 1575 378852068 378852278 4.710000e-59 239.0
22 TraesCS5A01G214700 chr5B 74.899 247 44 12 1 235 107856027 107856267 3.000000e-16 97.1
23 TraesCS5A01G214700 chr5B 91.837 49 4 0 1 49 491438929 491438881 6.530000e-08 69.4
24 TraesCS5A01G214700 chr5B 91.837 49 3 1 1 49 700378333 700378286 2.350000e-07 67.6
25 TraesCS5A01G214700 chr2A 94.675 676 26 2 2981 3647 68861047 68860373 0.000000e+00 1040.0
26 TraesCS5A01G214700 chr2A 83.607 915 137 12 1688 2600 680549048 680548145 0.000000e+00 846.0
27 TraesCS5A01G214700 chr2A 92.143 280 20 2 2985 3264 18291706 18291983 9.490000e-106 394.0
28 TraesCS5A01G214700 chr2D 84.590 915 128 12 1688 2600 538598418 538597515 0.000000e+00 896.0
29 TraesCS5A01G214700 chr2D 79.621 633 118 3 536 1158 538599246 538598615 9.290000e-121 444.0
30 TraesCS5A01G214700 chr2D 90.083 242 24 0 2979 3220 520037876 520037635 7.600000e-82 315.0
31 TraesCS5A01G214700 chr2D 74.694 245 48 7 1 234 648132106 648132347 3.000000e-16 97.1
32 TraesCS5A01G214700 chr2D 79.070 129 16 2 1 118 19585335 19585463 1.090000e-10 78.7
33 TraesCS5A01G214700 chr2B 83.716 915 136 12 1688 2600 641194304 641193401 0.000000e+00 852.0
34 TraesCS5A01G214700 chr2B 87.406 667 54 16 2983 3632 93105131 93104478 0.000000e+00 739.0
35 TraesCS5A01G214700 chr2B 78.169 142 26 5 60 197 236842830 236842690 6.490000e-13 86.1
36 TraesCS5A01G214700 chr1A 92.933 283 17 3 2983 3264 113255455 113255175 3.390000e-110 409.0
37 TraesCS5A01G214700 chr1A 83.784 74 11 1 66 139 380296226 380296154 6.530000e-08 69.4
38 TraesCS5A01G214700 chr1B 90.975 277 21 4 2980 3255 1823843 1824116 1.600000e-98 370.0
39 TraesCS5A01G214700 chr6B 86.034 358 28 16 2984 3319 718594601 718594958 7.440000e-97 364.0
40 TraesCS5A01G214700 chr6B 94.268 157 9 0 3318 3474 21317807 21317963 1.310000e-59 241.0
41 TraesCS5A01G214700 chr7D 90.756 238 22 0 2983 3220 631380638 631380875 5.880000e-83 318.0
42 TraesCS5A01G214700 chr6A 89.503 181 18 1 3464 3644 12959217 12959396 1.020000e-55 228.0
43 TraesCS5A01G214700 chr6A 92.357 157 12 0 3318 3474 12958932 12959088 1.320000e-54 224.0
44 TraesCS5A01G214700 chr6A 86.207 58 8 0 1 58 1815432 1815375 3.040000e-06 63.9
45 TraesCS5A01G214700 chr6D 90.446 157 15 0 3318 3474 11709557 11709713 1.330000e-49 207.0
46 TraesCS5A01G214700 chr3B 87.898 157 19 0 3318 3474 40542408 40542564 6.220000e-43 185.0
47 TraesCS5A01G214700 chr3D 78.836 189 38 2 1 189 583012027 583012213 3.820000e-25 126.0
48 TraesCS5A01G214700 chr4A 85.047 107 16 0 1 107 714538313 714538207 3.850000e-20 110.0
49 TraesCS5A01G214700 chr4D 81.679 131 17 2 1 124 142361500 142361370 6.440000e-18 102.0


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 TraesCS5A01G214700 chr5A 429995557 429999203 3646 False 2313.00 6735 97.814000 1 3647 3 chr5A.!!$F2 3646
1 TraesCS5A01G214700 chr5A 430041485 430043684 2199 True 1070.00 1759 91.274667 442 2721 3 chr5A.!!$R1 2279
2 TraesCS5A01G214700 chr5A 419829199 419829818 619 False 381.00 381 78.165000 538 1158 1 chr5A.!!$F1 620
3 TraesCS5A01G214700 chr5D 326402548 326405436 2888 True 1959.00 2202 91.355000 1 2917 2 chr5D.!!$R1 2916
4 TraesCS5A01G214700 chr5D 326382208 326384674 2466 False 687.14 1622 93.154000 379 2725 5 chr5D.!!$F2 2346
5 TraesCS5A01G214700 chr5B 378903078 378905605 2527 True 1913.50 2030 94.080000 363 2917 2 chr5B.!!$R3 2554
6 TraesCS5A01G214700 chr5B 378851170 378853391 2221 False 1004.00 1659 90.814000 438 2725 3 chr5B.!!$F3 2287
7 TraesCS5A01G214700 chr5B 375223262 375224946 1684 False 695.00 917 82.715500 538 2600 2 chr5B.!!$F2 2062
8 TraesCS5A01G214700 chr2A 68860373 68861047 674 True 1040.00 1040 94.675000 2981 3647 1 chr2A.!!$R1 666
9 TraesCS5A01G214700 chr2A 680548145 680549048 903 True 846.00 846 83.607000 1688 2600 1 chr2A.!!$R2 912
10 TraesCS5A01G214700 chr2D 538597515 538599246 1731 True 670.00 896 82.105500 536 2600 2 chr2D.!!$R2 2064
11 TraesCS5A01G214700 chr2B 641193401 641194304 903 True 852.00 852 83.716000 1688 2600 1 chr2B.!!$R3 912
12 TraesCS5A01G214700 chr2B 93104478 93105131 653 True 739.00 739 87.406000 2983 3632 1 chr2B.!!$R1 649

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
735 762 1.153289 GCACATCCTGCGTCCTGAT 60.153 57.895 0.0 0.0 35.72 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 3097 1.301244 AGCACCACAACGAGCTCAG 60.301 57.895 15.4 9.21 30.05 3.35 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
59 71 5.481473 ACAATTTGCTGTTCTGACCCAATAT 59.519 36.000 0.00 0.00 0.00 1.28
60 72 6.014327 ACAATTTGCTGTTCTGACCCAATATT 60.014 34.615 0.00 0.00 0.00 1.28
62 74 6.418057 TTTGCTGTTCTGACCCAATATTTT 57.582 33.333 0.00 0.00 0.00 1.82
72 84 7.153985 TCTGACCCAATATTTTTCTTTTGCTG 58.846 34.615 0.00 0.00 0.00 4.41
118 130 3.636764 AGCTGAAATTTTGAACGGACCTT 59.363 39.130 0.00 0.00 0.00 3.50
120 132 5.476945 AGCTGAAATTTTGAACGGACCTTAT 59.523 36.000 0.00 0.00 0.00 1.73
201 215 7.737972 TTCTTTGAATTTACTGTTCATCGGA 57.262 32.000 0.00 0.00 35.68 4.55
215 229 4.096732 TCATCGGATGCATATGAGTACG 57.903 45.455 13.15 6.48 0.00 3.67
216 230 3.119495 TCATCGGATGCATATGAGTACGG 60.119 47.826 13.15 0.00 0.00 4.02
220 234 2.289694 GGATGCATATGAGTACGGGCTT 60.290 50.000 6.97 0.00 0.00 4.35
222 236 4.383118 GGATGCATATGAGTACGGGCTTAT 60.383 45.833 6.97 0.00 0.00 1.73
292 307 4.439449 CGATGCTTTGATAGAGACGTCTTC 59.561 45.833 21.08 13.99 33.84 2.87
299 314 6.819397 TTGATAGAGACGTCTTCAAAGAGA 57.181 37.500 22.64 6.00 35.32 3.10
360 376 7.581476 TGTCGACCATCTTTTACATTTTCTTC 58.419 34.615 14.12 0.00 0.00 2.87
735 762 1.153289 GCACATCCTGCGTCCTGAT 60.153 57.895 0.00 0.00 35.72 2.90
1056 1083 2.052690 GCGGTCCAGCTCCTCTGTA 61.053 63.158 0.00 0.00 41.25 2.74
1220 1247 6.704289 ATTCATGGTGATGTGTAAATGAGG 57.296 37.500 0.00 0.00 0.00 3.86
1290 1321 8.243426 ACCAAGTAATTAACTGTGTGCATTATG 58.757 33.333 0.00 0.00 38.88 1.90
1292 1323 9.624697 CAAGTAATTAACTGTGTGCATTATGTT 57.375 29.630 0.00 0.00 38.88 2.71
1336 1367 8.520351 CATTATCTACATGAATGGCAATGTCAT 58.480 33.333 6.57 6.26 32.17 3.06
1415 1460 3.695830 GTGGAACTTGTCTACCCATGA 57.304 47.619 0.00 0.00 31.66 3.07
1451 1496 4.493618 TCAACAACCCCATTATTTTCCCA 58.506 39.130 0.00 0.00 0.00 4.37
1513 1583 3.898123 AGACCGATAGCAACAGGACATAT 59.102 43.478 0.00 0.00 0.00 1.78
1562 1634 8.560576 AGAACGATGATACTTGTTTTGTTTTG 57.439 30.769 0.00 0.00 0.00 2.44
1625 1954 5.978919 TCTCAAAGCACATGAATTGTTGTTC 59.021 36.000 0.00 0.00 36.00 3.18
1628 1957 7.487484 TCAAAGCACATGAATTGTTGTTCTAA 58.513 30.769 0.00 0.00 36.00 2.10
1681 2014 1.981256 TTCAGTGCAGGGAAGGAAAC 58.019 50.000 0.00 0.00 0.00 2.78
1685 2018 0.961753 GTGCAGGGAAGGAAACCAAG 59.038 55.000 0.00 0.00 0.00 3.61
1714 2081 0.603975 GAGTGAAAGCCTTGACGCCT 60.604 55.000 0.00 0.00 0.00 5.52
2530 2906 2.267961 GGGAGGTTGTACTGGCGG 59.732 66.667 0.00 0.00 0.00 6.13
2531 2907 2.436115 GGAGGTTGTACTGGCGGC 60.436 66.667 0.00 0.00 0.00 6.53
2532 2908 2.813908 GAGGTTGTACTGGCGGCG 60.814 66.667 0.51 0.51 0.00 6.46
2533 2909 4.388499 AGGTTGTACTGGCGGCGG 62.388 66.667 17.49 17.49 0.00 6.13
2678 3073 2.670934 GTGGCTGTGGCTGAGTGG 60.671 66.667 0.00 0.00 38.73 4.00
2837 3233 2.801111 GGAAAACTTGACGAGGACACTC 59.199 50.000 0.00 0.00 40.44 3.51
2882 3278 4.210746 GGAAAACGTGGTGAGAGTTTACTC 59.789 45.833 1.59 1.59 43.17 2.59
2917 3313 4.097437 CAGACTTCACTATAGGCGGTGTAA 59.903 45.833 4.43 0.00 35.26 2.41
2918 3314 4.894114 AGACTTCACTATAGGCGGTGTAAT 59.106 41.667 4.43 0.00 35.26 1.89
2919 3315 5.363005 AGACTTCACTATAGGCGGTGTAATT 59.637 40.000 4.43 0.00 35.26 1.40
2920 3316 5.985911 ACTTCACTATAGGCGGTGTAATTT 58.014 37.500 4.43 0.00 35.26 1.82
2921 3317 7.069085 AGACTTCACTATAGGCGGTGTAATTTA 59.931 37.037 4.43 0.00 35.26 1.40
2922 3318 7.208080 ACTTCACTATAGGCGGTGTAATTTAG 58.792 38.462 4.43 0.00 35.26 1.85
2923 3319 5.535333 TCACTATAGGCGGTGTAATTTAGC 58.465 41.667 4.43 0.00 35.26 3.09
2924 3320 5.069383 TCACTATAGGCGGTGTAATTTAGCA 59.931 40.000 4.43 0.00 35.26 3.49
2925 3321 5.756347 CACTATAGGCGGTGTAATTTAGCAA 59.244 40.000 4.43 0.00 0.00 3.91
2926 3322 5.756833 ACTATAGGCGGTGTAATTTAGCAAC 59.243 40.000 4.43 0.00 0.00 4.17
2927 3323 3.067684 AGGCGGTGTAATTTAGCAACT 57.932 42.857 0.00 0.00 0.00 3.16
2928 3324 4.210724 AGGCGGTGTAATTTAGCAACTA 57.789 40.909 0.00 0.00 0.00 2.24
2929 3325 4.581868 AGGCGGTGTAATTTAGCAACTAA 58.418 39.130 0.00 0.00 0.00 2.24
2930 3326 5.005094 AGGCGGTGTAATTTAGCAACTAAA 58.995 37.500 2.51 2.51 39.73 1.85
2931 3327 5.090757 GGCGGTGTAATTTAGCAACTAAAC 58.909 41.667 2.08 0.00 38.51 2.01
2932 3328 5.335035 GGCGGTGTAATTTAGCAACTAAACA 60.335 40.000 2.08 0.00 38.51 2.83
2933 3329 6.319399 GCGGTGTAATTTAGCAACTAAACAT 58.681 36.000 2.08 0.00 38.51 2.71
2934 3330 6.250527 GCGGTGTAATTTAGCAACTAAACATG 59.749 38.462 2.08 0.00 38.51 3.21
2935 3331 6.250527 CGGTGTAATTTAGCAACTAAACATGC 59.749 38.462 2.08 0.00 38.51 4.06
2936 3332 6.250527 GGTGTAATTTAGCAACTAAACATGCG 59.749 38.462 2.08 0.00 38.51 4.73
2937 3333 7.018826 GTGTAATTTAGCAACTAAACATGCGA 58.981 34.615 2.08 0.00 38.51 5.10
2938 3334 7.696453 GTGTAATTTAGCAACTAAACATGCGAT 59.304 33.333 2.08 0.00 38.51 4.58
2939 3335 7.696035 TGTAATTTAGCAACTAAACATGCGATG 59.304 33.333 2.08 0.00 38.51 3.84
2940 3336 2.549633 AGCAACTAAACATGCGATGC 57.450 45.000 0.00 0.00 0.00 3.91
2941 3337 1.811965 AGCAACTAAACATGCGATGCA 59.188 42.857 0.00 0.00 44.86 3.96
2942 3338 1.913403 GCAACTAAACATGCGATGCAC 59.087 47.619 0.00 0.00 43.04 4.57
2943 3339 2.168384 CAACTAAACATGCGATGCACG 58.832 47.619 0.00 0.00 43.04 5.34
2944 3340 1.438651 ACTAAACATGCGATGCACGT 58.561 45.000 9.76 0.00 43.04 4.49
2945 3341 2.612604 ACTAAACATGCGATGCACGTA 58.387 42.857 9.76 6.30 43.04 3.57
2947 3343 4.364860 ACTAAACATGCGATGCACGTATA 58.635 39.130 10.67 0.52 44.63 1.47
2948 3344 4.988540 ACTAAACATGCGATGCACGTATAT 59.011 37.500 10.67 0.00 44.63 0.86
2949 3345 6.153756 ACTAAACATGCGATGCACGTATATA 58.846 36.000 10.67 5.86 44.63 0.86
2950 3346 6.811665 ACTAAACATGCGATGCACGTATATAT 59.188 34.615 10.67 0.00 44.63 0.86
2951 3347 6.480524 AAACATGCGATGCACGTATATATT 57.519 33.333 10.67 5.27 44.63 1.28
2952 3348 6.480524 AACATGCGATGCACGTATATATTT 57.519 33.333 10.67 2.58 44.63 1.40
2953 3349 7.589574 AACATGCGATGCACGTATATATTTA 57.410 32.000 10.67 0.00 44.63 1.40
2954 3350 6.989437 ACATGCGATGCACGTATATATTTAC 58.011 36.000 10.67 0.00 44.63 2.01
2955 3351 6.811665 ACATGCGATGCACGTATATATTTACT 59.188 34.615 10.67 0.00 44.63 2.24
2956 3352 7.330946 ACATGCGATGCACGTATATATTTACTT 59.669 33.333 10.67 0.00 44.63 2.24
2957 3353 7.646446 TGCGATGCACGTATATATTTACTTT 57.354 32.000 9.76 0.00 44.60 2.66
2958 3354 8.078959 TGCGATGCACGTATATATTTACTTTT 57.921 30.769 9.76 0.00 44.60 2.27
2959 3355 9.194271 TGCGATGCACGTATATATTTACTTTTA 57.806 29.630 9.76 0.00 44.60 1.52
2960 3356 9.671521 GCGATGCACGTATATATTTACTTTTAG 57.328 33.333 9.76 0.00 44.60 1.85
2961 3357 9.671521 CGATGCACGTATATATTTACTTTTAGC 57.328 33.333 0.00 0.00 37.22 3.09
2964 3360 9.537192 TGCACGTATATATTTACTTTTAGCTGT 57.463 29.630 0.00 0.00 0.00 4.40
2965 3361 9.793245 GCACGTATATATTTACTTTTAGCTGTG 57.207 33.333 0.00 0.00 0.00 3.66
2976 3372 9.997482 TTTACTTTTAGCTGTGTTTTTGTCTAG 57.003 29.630 0.00 0.00 0.00 2.43
2977 3373 7.027778 ACTTTTAGCTGTGTTTTTGTCTAGG 57.972 36.000 0.00 0.00 0.00 3.02
2978 3374 6.826741 ACTTTTAGCTGTGTTTTTGTCTAGGA 59.173 34.615 0.00 0.00 0.00 2.94
2979 3375 7.338449 ACTTTTAGCTGTGTTTTTGTCTAGGAA 59.662 33.333 0.00 0.00 0.00 3.36
2992 3388 5.825593 TGTCTAGGAAAGGAGTCAATTGT 57.174 39.130 5.13 0.00 0.00 2.71
3017 3413 0.538516 ACCACCACATTTGCGGCTAA 60.539 50.000 0.00 0.00 0.00 3.09
3067 3463 3.963665 TCATTGCAGAAAACACCGAAAG 58.036 40.909 0.00 0.00 0.00 2.62
3091 3487 5.554822 TCTGTTAAGTCGTTGCAAAAAGT 57.445 34.783 0.00 0.00 0.00 2.66
3112 3508 1.242076 CTGATCGGATGATTTGGCCC 58.758 55.000 0.00 0.00 34.09 5.80
3118 3514 1.953686 CGGATGATTTGGCCCGTTTAT 59.046 47.619 0.00 0.00 37.40 1.40
3141 3537 1.780919 ACTTTCTTACAAGTGGGGCCT 59.219 47.619 0.84 0.00 35.57 5.19
3315 3720 1.074926 GGCCTCATCCTCCTCCTCA 60.075 63.158 0.00 0.00 0.00 3.86
3404 3809 2.756283 CCTCCGCCTCGACTCCTT 60.756 66.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.881920 ACAGCAAATTGTTTCACATACCC 58.118 39.130 0.00 0.00 0.00 3.69
28 29 5.750067 GTCAGAACAGCAAATTGTTTCACAT 59.250 36.000 0.00 0.00 41.15 3.21
38 39 6.610075 AAATATTGGGTCAGAACAGCAAAT 57.390 33.333 0.00 0.00 0.00 2.32
59 71 5.822519 TGAGTAGCTCTCAGCAAAAGAAAAA 59.177 36.000 10.62 0.00 46.77 1.94
60 72 5.368145 TGAGTAGCTCTCAGCAAAAGAAAA 58.632 37.500 10.62 0.00 46.77 2.29
62 74 4.607293 TGAGTAGCTCTCAGCAAAAGAA 57.393 40.909 10.62 0.00 46.77 2.52
72 84 5.299028 TCATCTGAACATCTGAGTAGCTCTC 59.701 44.000 0.00 0.00 43.03 3.20
92 104 4.853743 GTCCGTTCAAAATTTCAGCTCATC 59.146 41.667 0.00 0.00 0.00 2.92
107 119 1.621317 TCTGTGCATAAGGTCCGTTCA 59.379 47.619 0.00 0.00 0.00 3.18
108 120 2.380084 TCTGTGCATAAGGTCCGTTC 57.620 50.000 0.00 0.00 0.00 3.95
110 122 1.676014 GCTTCTGTGCATAAGGTCCGT 60.676 52.381 0.00 0.00 0.00 4.69
111 123 1.009829 GCTTCTGTGCATAAGGTCCG 58.990 55.000 0.00 0.00 0.00 4.79
199 213 1.276421 AGCCCGTACTCATATGCATCC 59.724 52.381 0.19 0.00 0.00 3.51
201 215 4.826274 ATAAGCCCGTACTCATATGCAT 57.174 40.909 3.79 3.79 0.00 3.96
215 229 7.451566 AGGTTGTGAATATCCATTTATAAGCCC 59.548 37.037 0.00 0.00 32.94 5.19
216 230 8.409358 AGGTTGTGAATATCCATTTATAAGCC 57.591 34.615 0.00 0.00 32.94 4.35
222 236 9.249053 TGCTTTTAGGTTGTGAATATCCATTTA 57.751 29.630 0.00 0.00 0.00 1.40
272 287 4.783764 TGAAGACGTCTCTATCAAAGCA 57.216 40.909 20.33 3.59 0.00 3.91
735 762 2.519771 ATGAGCTGCTTCCATTTGGA 57.480 45.000 2.53 0.00 43.73 3.53
989 1016 0.251341 AAAGGACATGCCGAGCCTTT 60.251 50.000 0.00 0.00 43.80 3.11
1056 1083 2.359230 GAGGTGCTCGCCAAAGCT 60.359 61.111 2.02 0.00 42.94 3.74
1290 1321 8.970691 ATAATGCACACAGTTGATAGAAAAAC 57.029 30.769 0.00 0.00 0.00 2.43
1292 1323 8.565896 AGATAATGCACACAGTTGATAGAAAA 57.434 30.769 0.00 0.00 0.00 2.29
1296 1327 8.493547 CATGTAGATAATGCACACAGTTGATAG 58.506 37.037 0.00 0.00 0.00 2.08
1336 1367 3.511146 GGCAACTCCCTCAAATTCAATCA 59.489 43.478 0.00 0.00 0.00 2.57
1410 1441 0.397941 ATAGGCACGTCCCATCATGG 59.602 55.000 0.00 0.00 37.25 3.66
1415 1460 0.908910 TGTTGATAGGCACGTCCCAT 59.091 50.000 0.00 0.00 34.51 4.00
1562 1634 1.467734 CTGAATCAGTTGCCTGCACTC 59.532 52.381 1.31 0.00 38.66 3.51
1575 1647 5.547465 AGGTTCGTACACAAATCTGAATCA 58.453 37.500 0.00 0.00 0.00 2.57
1578 1650 6.015688 AGACTAGGTTCGTACACAAATCTGAA 60.016 38.462 0.00 0.00 0.00 3.02
1580 1652 5.710984 AGACTAGGTTCGTACACAAATCTG 58.289 41.667 0.00 0.00 0.00 2.90
1581 1653 5.475909 TGAGACTAGGTTCGTACACAAATCT 59.524 40.000 0.00 0.00 0.00 2.40
1582 1654 5.706916 TGAGACTAGGTTCGTACACAAATC 58.293 41.667 0.00 0.00 0.00 2.17
1625 1954 3.845781 TTATCCCCTGCTTGCTCTTAG 57.154 47.619 0.00 0.00 0.00 2.18
1628 1957 1.635487 TGTTTATCCCCTGCTTGCTCT 59.365 47.619 0.00 0.00 0.00 4.09
1714 2081 2.700371 TGAGGTCAAGCTCAACAGAGAA 59.300 45.455 9.34 0.00 0.00 2.87
2636 3027 4.864334 CAGCTGATCACCCGGCCC 62.864 72.222 8.42 0.00 39.18 5.80
2702 3097 1.301244 AGCACCACAACGAGCTCAG 60.301 57.895 15.40 9.21 30.05 3.35
2734 3129 1.736032 GCCATCTATAAGTAGGCCGCG 60.736 57.143 0.00 0.00 39.42 6.46
2837 3233 1.078709 ACGAAATGGACGTCAGCATG 58.921 50.000 18.91 4.69 39.87 4.06
2882 3278 1.155042 GAAGTCTGTTGCTGAGCAGG 58.845 55.000 7.39 2.50 40.61 4.85
2917 3313 5.036737 GCATCGCATGTTTAGTTGCTAAAT 58.963 37.500 4.88 0.00 38.07 1.40
2918 3314 4.083057 TGCATCGCATGTTTAGTTGCTAAA 60.083 37.500 0.00 0.00 36.71 1.85
2919 3315 3.438434 TGCATCGCATGTTTAGTTGCTAA 59.562 39.130 0.00 0.00 36.71 3.09
2920 3316 3.006247 TGCATCGCATGTTTAGTTGCTA 58.994 40.909 0.00 0.00 36.71 3.49
2921 3317 1.811965 TGCATCGCATGTTTAGTTGCT 59.188 42.857 0.00 0.00 36.71 3.91
2922 3318 1.913403 GTGCATCGCATGTTTAGTTGC 59.087 47.619 0.00 2.22 41.91 4.17
2923 3319 2.168384 CGTGCATCGCATGTTTAGTTG 58.832 47.619 0.00 0.00 41.91 3.16
2924 3320 2.525750 CGTGCATCGCATGTTTAGTT 57.474 45.000 0.00 0.00 41.91 2.24
2932 3328 7.827819 AAGTAAATATATACGTGCATCGCAT 57.172 32.000 0.00 4.58 41.91 4.73
2933 3329 7.646446 AAAGTAAATATATACGTGCATCGCA 57.354 32.000 0.00 0.00 44.19 5.10
2934 3330 9.671521 CTAAAAGTAAATATATACGTGCATCGC 57.328 33.333 0.00 0.00 44.19 4.58
2935 3331 9.671521 GCTAAAAGTAAATATATACGTGCATCG 57.328 33.333 0.00 7.07 46.00 3.84
2938 3334 9.537192 ACAGCTAAAAGTAAATATATACGTGCA 57.463 29.630 0.00 0.00 0.00 4.57
2939 3335 9.793245 CACAGCTAAAAGTAAATATATACGTGC 57.207 33.333 0.00 0.00 0.00 5.34
2950 3346 9.997482 CTAGACAAAAACACAGCTAAAAGTAAA 57.003 29.630 0.00 0.00 0.00 2.01
2951 3347 8.617809 CCTAGACAAAAACACAGCTAAAAGTAA 58.382 33.333 0.00 0.00 0.00 2.24
2952 3348 7.988599 TCCTAGACAAAAACACAGCTAAAAGTA 59.011 33.333 0.00 0.00 0.00 2.24
2953 3349 6.826741 TCCTAGACAAAAACACAGCTAAAAGT 59.173 34.615 0.00 0.00 0.00 2.66
2954 3350 7.259290 TCCTAGACAAAAACACAGCTAAAAG 57.741 36.000 0.00 0.00 0.00 2.27
2955 3351 7.633193 TTCCTAGACAAAAACACAGCTAAAA 57.367 32.000 0.00 0.00 0.00 1.52
2956 3352 7.201785 CCTTTCCTAGACAAAAACACAGCTAAA 60.202 37.037 0.00 0.00 0.00 1.85
2957 3353 6.262273 CCTTTCCTAGACAAAAACACAGCTAA 59.738 38.462 0.00 0.00 0.00 3.09
2958 3354 5.763204 CCTTTCCTAGACAAAAACACAGCTA 59.237 40.000 0.00 0.00 0.00 3.32
2959 3355 4.580580 CCTTTCCTAGACAAAAACACAGCT 59.419 41.667 0.00 0.00 0.00 4.24
2960 3356 4.578928 TCCTTTCCTAGACAAAAACACAGC 59.421 41.667 0.00 0.00 0.00 4.40
2961 3357 5.823045 ACTCCTTTCCTAGACAAAAACACAG 59.177 40.000 0.00 0.00 0.00 3.66
2962 3358 5.751586 ACTCCTTTCCTAGACAAAAACACA 58.248 37.500 0.00 0.00 0.00 3.72
2963 3359 5.820947 TGACTCCTTTCCTAGACAAAAACAC 59.179 40.000 0.00 0.00 0.00 3.32
2964 3360 5.996644 TGACTCCTTTCCTAGACAAAAACA 58.003 37.500 0.00 0.00 0.00 2.83
2965 3361 6.937436 TTGACTCCTTTCCTAGACAAAAAC 57.063 37.500 0.00 0.00 0.00 2.43
2966 3362 7.559897 ACAATTGACTCCTTTCCTAGACAAAAA 59.440 33.333 13.59 0.00 32.65 1.94
2967 3363 7.060421 ACAATTGACTCCTTTCCTAGACAAAA 58.940 34.615 13.59 0.00 32.65 2.44
2968 3364 6.601332 ACAATTGACTCCTTTCCTAGACAAA 58.399 36.000 13.59 0.00 32.65 2.83
2969 3365 6.187727 ACAATTGACTCCTTTCCTAGACAA 57.812 37.500 13.59 0.00 33.24 3.18
2970 3366 5.825593 ACAATTGACTCCTTTCCTAGACA 57.174 39.130 13.59 0.00 0.00 3.41
2971 3367 8.617290 TTTTACAATTGACTCCTTTCCTAGAC 57.383 34.615 13.59 0.00 0.00 2.59
3017 3413 1.480545 GTTGGTGGTTTCCTGCAAACT 59.519 47.619 0.12 0.00 43.63 2.66
3067 3463 6.199393 ACTTTTTGCAACGACTTAACAGATC 58.801 36.000 0.00 0.00 0.00 2.75
3091 3487 2.224523 GGGCCAAATCATCCGATCAGTA 60.225 50.000 4.39 0.00 0.00 2.74
3141 3537 6.299805 AGCTATGTCAACTCCTTACAATCA 57.700 37.500 0.00 0.00 0.00 2.57
3180 3576 6.833933 GCTTTTGATTTTTAGATCTAGGGGGA 59.166 38.462 2.02 0.00 0.00 4.81
3181 3577 6.607198 TGCTTTTGATTTTTAGATCTAGGGGG 59.393 38.462 2.02 0.00 0.00 5.40
3404 3809 1.455773 ATCCAGGAGCGGATCGTCA 60.456 57.895 0.00 0.00 42.36 4.35
3439 3844 4.954970 CAAGCGGGCACAGTGGGT 62.955 66.667 1.84 0.00 0.00 4.51
3519 3933 1.079819 CAGCGTGTCGTCCCAGAAT 60.080 57.895 0.00 0.00 0.00 2.40
3587 4001 1.453379 CTCTTCCTAGACGCCCGGA 60.453 63.158 0.73 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.