Multiple sequence alignment - TraesCS1A01G270000

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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 TraesCS1A01G270000 chr1A 100.000 4014 0 0 1 4014 464090072 464086059 0.000000e+00 7413.0
1 TraesCS1A01G270000 chr1A 95.745 47 2 0 500 546 125990021 125989975 4.300000e-10 76.8
2 TraesCS1A01G270000 chr2A 98.449 1096 17 0 2919 4014 188903727 188902632 0.000000e+00 1930.0
3 TraesCS1A01G270000 chr2A 89.610 231 24 0 3305 3535 498841165 498840935 1.090000e-75 294.0
4 TraesCS1A01G270000 chr2A 93.750 144 8 1 2935 3077 276393097 276392954 8.740000e-52 215.0
5 TraesCS1A01G270000 chr2A 93.056 144 9 1 2935 3077 610237463 610237606 4.070000e-50 209.0
6 TraesCS1A01G270000 chr1D 94.577 1254 54 5 1579 2826 365196708 365195463 0.000000e+00 1927.0
7 TraesCS1A01G270000 chr1D 94.912 963 42 4 583 1541 365198161 365197202 0.000000e+00 1500.0
8 TraesCS1A01G270000 chr1D 87.649 502 59 1 46 544 476459313 476459814 7.480000e-162 580.0
9 TraesCS1A01G270000 chr1D 84.560 557 65 12 3 544 387055227 387054677 2.120000e-147 532.0
10 TraesCS1A01G270000 chr4B 98.888 1079 9 2 2935 4013 211497902 211498977 0.000000e+00 1923.0
11 TraesCS1A01G270000 chr4B 93.103 145 8 2 2935 3077 347544281 347544425 1.130000e-50 211.0
12 TraesCS1A01G270000 chr1B 93.779 1286 53 9 1579 2849 488643821 488642548 0.000000e+00 1906.0
13 TraesCS1A01G270000 chr1B 94.100 1000 52 5 544 1541 488645297 488644303 0.000000e+00 1513.0
14 TraesCS1A01G270000 chr2B 87.623 711 84 4 3257 3967 687885442 687884736 0.000000e+00 822.0
15 TraesCS1A01G270000 chr2B 80.761 447 58 18 3102 3537 52916456 52916885 1.390000e-84 324.0
16 TraesCS1A01G270000 chr2B 90.043 231 23 0 3305 3535 437382256 437382026 2.340000e-77 300.0
17 TraesCS1A01G270000 chr2B 86.854 213 16 6 3326 3537 91333808 91334009 1.120000e-55 228.0
18 TraesCS1A01G270000 chr2B 87.500 64 5 2 483 544 743908299 743908237 2.000000e-08 71.3
19 TraesCS1A01G270000 chr7D 85.949 548 64 5 3 546 159709628 159710166 1.250000e-159 573.0
20 TraesCS1A01G270000 chr7D 86.139 505 64 6 46 546 37874089 37874591 1.270000e-149 540.0
21 TraesCS1A01G270000 chr7D 81.911 586 57 19 3 553 582092375 582092946 2.200000e-122 449.0
22 TraesCS1A01G270000 chr6D 87.935 489 52 4 3 491 56836784 56836303 1.620000e-158 569.0
23 TraesCS1A01G270000 chr5A 86.137 541 51 9 3 521 608853870 608854408 2.710000e-156 562.0
24 TraesCS1A01G270000 chr3D 85.158 539 68 4 3 535 398411419 398410887 3.530000e-150 542.0
25 TraesCS1A01G270000 chr3D 83.966 580 62 15 3 553 514850032 514849455 9.880000e-146 527.0
26 TraesCS1A01G270000 chr3D 87.179 195 19 5 3102 3291 66246895 66247088 2.430000e-52 217.0
27 TraesCS1A01G270000 chr5D 84.000 550 74 10 3 546 528136783 528137324 2.140000e-142 516.0
28 TraesCS1A01G270000 chr5D 76.119 469 91 17 1019 1472 412464898 412465360 4.040000e-55 226.0
29 TraesCS1A01G270000 chr7A 82.966 499 55 22 3049 3535 264335303 264334823 1.330000e-114 424.0
30 TraesCS1A01G270000 chr7A 83.041 342 39 10 2979 3301 673299272 673299613 3.920000e-75 292.0
31 TraesCS1A01G270000 chr7A 94.483 145 6 2 2935 3077 191565826 191565682 5.220000e-54 222.0
32 TraesCS1A01G270000 chr7A 93.103 145 8 2 2935 3077 13393606 13393750 1.130000e-50 211.0
33 TraesCS1A01G270000 chr6A 85.309 388 36 11 2938 3308 602928958 602928575 8.140000e-102 381.0
34 TraesCS1A01G270000 chr6A 87.083 240 25 4 3035 3268 585229596 585229357 2.380000e-67 267.0
35 TraesCS1A01G270000 chr6A 87.678 211 15 6 3326 3535 602928520 602928320 6.710000e-58 235.0
36 TraesCS1A01G270000 chr6A 80.000 245 30 13 3214 3441 617204937 617204695 3.210000e-36 163.0
37 TraesCS1A01G270000 chr2D 89.610 231 24 0 3305 3535 368525552 368525322 1.090000e-75 294.0
38 TraesCS1A01G270000 chr2D 87.952 83 9 1 3 84 482678747 482678665 3.300000e-16 97.1
39 TraesCS1A01G270000 chr7B 87.234 235 23 5 3035 3264 649223003 649223235 1.110000e-65 261.0
40 TraesCS1A01G270000 chr3B 87.892 223 22 3 3087 3306 749767459 749767679 1.430000e-64 257.0
41 TraesCS1A01G270000 chr3B 94.483 145 6 2 2935 3077 430932257 430932113 5.220000e-54 222.0
42 TraesCS1A01G270000 chr3B 86.190 210 18 6 3326 3535 749767736 749767934 2.430000e-52 217.0
43 TraesCS1A01G270000 chr5B 76.282 468 92 16 1019 1472 496828221 496828683 8.680000e-57 231.0
44 TraesCS1A01G270000 chr5B 95.349 129 6 0 2935 3063 454645019 454645147 5.260000e-49 206.0


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 TraesCS1A01G270000 chr1A 464086059 464090072 4013 True 7413.0 7413 100.0000 1 4014 1 chr1A.!!$R2 4013
1 TraesCS1A01G270000 chr2A 188902632 188903727 1095 True 1930.0 1930 98.4490 2919 4014 1 chr2A.!!$R1 1095
2 TraesCS1A01G270000 chr1D 365195463 365198161 2698 True 1713.5 1927 94.7445 583 2826 2 chr1D.!!$R2 2243
3 TraesCS1A01G270000 chr1D 476459313 476459814 501 False 580.0 580 87.6490 46 544 1 chr1D.!!$F1 498
4 TraesCS1A01G270000 chr1D 387054677 387055227 550 True 532.0 532 84.5600 3 544 1 chr1D.!!$R1 541
5 TraesCS1A01G270000 chr4B 211497902 211498977 1075 False 1923.0 1923 98.8880 2935 4013 1 chr4B.!!$F1 1078
6 TraesCS1A01G270000 chr1B 488642548 488645297 2749 True 1709.5 1906 93.9395 544 2849 2 chr1B.!!$R1 2305
7 TraesCS1A01G270000 chr2B 687884736 687885442 706 True 822.0 822 87.6230 3257 3967 1 chr2B.!!$R2 710
8 TraesCS1A01G270000 chr7D 159709628 159710166 538 False 573.0 573 85.9490 3 546 1 chr7D.!!$F2 543
9 TraesCS1A01G270000 chr7D 37874089 37874591 502 False 540.0 540 86.1390 46 546 1 chr7D.!!$F1 500
10 TraesCS1A01G270000 chr7D 582092375 582092946 571 False 449.0 449 81.9110 3 553 1 chr7D.!!$F3 550
11 TraesCS1A01G270000 chr5A 608853870 608854408 538 False 562.0 562 86.1370 3 521 1 chr5A.!!$F1 518
12 TraesCS1A01G270000 chr3D 398410887 398411419 532 True 542.0 542 85.1580 3 535 1 chr3D.!!$R1 532
13 TraesCS1A01G270000 chr3D 514849455 514850032 577 True 527.0 527 83.9660 3 553 1 chr3D.!!$R2 550
14 TraesCS1A01G270000 chr5D 528136783 528137324 541 False 516.0 516 84.0000 3 546 1 chr5D.!!$F2 543
15 TraesCS1A01G270000 chr6A 602928320 602928958 638 True 308.0 381 86.4935 2938 3535 2 chr6A.!!$R3 597

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
829 913 0.110056 CAATTCGCTGTGACACTGCC 60.110 55.0 25.95 12.43 39.5 4.85 F
1419 1505 0.036294 GTGGAGGAGTTACTGTGCCC 60.036 60.0 0.00 0.00 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2522 0.803768 CGGTCACCAGCTCGAAGATG 60.804 60.0 0.0 0.0 33.89 2.90 R
3089 3669 0.957362 GAGGCAGGCAATGGATAAGC 59.043 55.0 0.0 0.0 0.00 3.09 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
97 138 1.152652 GAGGAGGAGGATGAGCCGA 60.153 63.158 0.00 0.00 43.43 5.54
122 163 3.399181 GGATGTGGGGGACGCTGA 61.399 66.667 0.00 0.00 43.80 4.26
145 186 2.586792 GGGATCTGCAGGCGAAGT 59.413 61.111 15.13 0.00 0.00 3.01
181 224 2.045242 CCCTCCGGTCAGAGTCGA 60.045 66.667 0.00 0.00 31.53 4.20
252 296 1.144936 GGAGGAGGCGGAGATGTTG 59.855 63.158 0.00 0.00 0.00 3.33
350 398 4.873129 CGTCGTGGGCATCTCCGG 62.873 72.222 0.00 0.00 34.94 5.14
369 431 1.297664 GCGACGAAGAGTAGCTAGGA 58.702 55.000 0.00 0.00 46.07 2.94
389 451 8.031864 GCTAGGATAGTACGTAGATGTAGTACA 58.968 40.741 5.24 5.24 41.93 2.90
438 502 9.784531 GTATGGATCTAGGAGATGAAATTTGAA 57.215 33.333 0.00 0.00 34.53 2.69
443 507 7.856145 TCTAGGAGATGAAATTTGAAAGAGC 57.144 36.000 0.00 0.00 0.00 4.09
449 513 5.420104 AGATGAAATTTGAAAGAGCCGGATT 59.580 36.000 5.05 0.00 0.00 3.01
521 603 1.880646 CGTTTGAGGGGTCGGATTTGT 60.881 52.381 0.00 0.00 0.00 2.83
528 610 2.004733 GGGGTCGGATTTGTAAAGTCG 58.995 52.381 0.00 0.00 32.71 4.18
539 621 5.664294 TTTGTAAAGTCGGGCTGTAGATA 57.336 39.130 0.00 0.00 0.00 1.98
554 636 6.041069 GGCTGTAGATACTCTAAGACCAACAT 59.959 42.308 0.00 0.00 29.58 2.71
607 689 4.720649 TCCTACGTGAGAGAAGAAATGG 57.279 45.455 0.00 0.00 0.00 3.16
614 696 4.376413 CGTGAGAGAAGAAATGGTTTGACG 60.376 45.833 0.00 0.00 0.00 4.35
620 702 2.841215 AGAAATGGTTTGACGAACGGA 58.159 42.857 0.00 0.00 39.22 4.69
635 717 2.644992 GGAAAAGGGCACAGTGCG 59.355 61.111 19.42 0.00 46.21 5.34
822 906 3.874392 TGAGATCTCAATTCGCTGTGA 57.126 42.857 23.17 0.00 36.53 3.58
823 907 3.515630 TGAGATCTCAATTCGCTGTGAC 58.484 45.455 23.17 0.00 36.53 3.67
829 913 0.110056 CAATTCGCTGTGACACTGCC 60.110 55.000 25.95 12.43 39.50 4.85
888 972 4.950479 AGCATAGCTGTGTCAGGC 57.050 55.556 12.41 0.00 37.57 4.85
901 985 2.901840 CAGGCAGCCGTTGTGTGT 60.902 61.111 5.55 0.00 0.00 3.72
922 1006 6.717540 TGTGTAGTAATTACCAAGTTGGCAAT 59.282 34.615 22.25 17.71 42.67 3.56
923 1007 7.027161 GTGTAGTAATTACCAAGTTGGCAATG 58.973 38.462 22.25 0.00 42.67 2.82
944 1028 2.094906 GTGTGTCCTGCATGTACTACGA 60.095 50.000 0.00 0.00 0.00 3.43
973 1059 4.780021 ACCTCTCCCAAGTGCATATATAGG 59.220 45.833 0.00 0.00 0.00 2.57
1004 1090 3.938112 GAACGCTCGAAGCAGTGT 58.062 55.556 7.47 0.00 42.58 3.55
1009 1095 1.215014 CGCTCGAAGCAGTGTGACAA 61.215 55.000 7.47 0.00 42.58 3.18
1010 1096 0.937304 GCTCGAAGCAGTGTGACAAA 59.063 50.000 0.00 0.00 41.89 2.83
1013 1099 2.609459 CTCGAAGCAGTGTGACAAAGTT 59.391 45.455 0.00 0.00 0.00 2.66
1162 1248 1.011352 GCGCTACTACGAGACGGTC 60.011 63.158 0.00 0.00 34.06 4.79
1168 1254 1.094073 ACTACGAGACGGTCATCGGG 61.094 60.000 23.66 19.28 43.12 5.14
1408 1494 1.218316 GTACCCTTGCGTGGAGGAG 59.782 63.158 2.93 0.00 36.33 3.69
1419 1505 0.036294 GTGGAGGAGTTACTGTGCCC 60.036 60.000 0.00 0.00 0.00 5.36
1535 1621 6.455647 GGGAATTCGTTCTTTTTCAGGAAAT 58.544 36.000 0.00 0.00 0.00 2.17
1541 1627 5.754406 TCGTTCTTTTTCAGGAAATGTACGA 59.246 36.000 14.33 14.33 44.65 3.43
1542 1628 6.071463 CGTTCTTTTTCAGGAAATGTACGAG 58.929 40.000 11.63 0.00 42.90 4.18
1545 1631 7.647907 TCTTTTTCAGGAAATGTACGAGTAC 57.352 36.000 6.46 6.46 36.63 2.73
1546 1632 6.364165 TCTTTTTCAGGAAATGTACGAGTACG 59.636 38.462 8.62 0.00 45.75 3.67
1550 1923 3.850273 CAGGAAATGTACGAGTACGACAC 59.150 47.826 8.62 1.80 42.66 3.67
1577 1950 5.967088 TCTAAGTTGCTAGCTCTAGTTTGG 58.033 41.667 17.23 4.49 35.65 3.28
1599 2144 9.613428 TTTGGTAATCTTGAATCATTATCGACT 57.387 29.630 0.00 0.00 0.00 4.18
1786 2331 4.270084 TGCTAACATCACGCAGCTTATTAC 59.730 41.667 0.00 0.00 35.05 1.89
1787 2332 4.318831 GCTAACATCACGCAGCTTATTACC 60.319 45.833 0.00 0.00 0.00 2.85
1788 2333 3.260475 ACATCACGCAGCTTATTACCA 57.740 42.857 0.00 0.00 0.00 3.25
1789 2334 2.936498 ACATCACGCAGCTTATTACCAC 59.064 45.455 0.00 0.00 0.00 4.16
1790 2335 2.018542 TCACGCAGCTTATTACCACC 57.981 50.000 0.00 0.00 0.00 4.61
1791 2336 1.014352 CACGCAGCTTATTACCACCC 58.986 55.000 0.00 0.00 0.00 4.61
1878 2426 3.077556 ATGCTCTCGGTTCCGCCT 61.078 61.111 6.35 0.00 34.25 5.52
1937 2485 3.775654 GGTGTCAGCCCTCCGAGG 61.776 72.222 7.56 7.56 34.30 4.63
2124 2672 1.909975 GTGGGGGTACTACGGCAAT 59.090 57.895 0.00 0.00 0.00 3.56
2322 2870 1.139734 CGAGGTGTCGGATGTGAGG 59.860 63.158 0.00 0.00 42.87 3.86
2406 2954 0.618458 CCGGGGATCTCACTTCCAAA 59.382 55.000 0.00 0.00 34.77 3.28
2599 3150 5.700832 TGCATATCATCGAGGTATTGAAACC 59.299 40.000 0.00 0.00 40.06 3.27
2653 3206 6.575162 AGATCAACGGCATTAATTATTCCC 57.425 37.500 0.00 0.00 0.00 3.97
2669 3222 1.375908 CCCGTGGTCCATGTCACAG 60.376 63.158 10.28 0.00 33.83 3.66
2680 3233 4.453478 GTCCATGTCACAGGCACATATATG 59.547 45.833 11.29 11.29 32.48 1.78
2706 3259 8.626526 GTGTATGTTCCCGTCCATTAATTTAAT 58.373 33.333 0.00 0.00 0.00 1.40
2707 3260 9.191479 TGTATGTTCCCGTCCATTAATTTAATT 57.809 29.630 0.00 0.00 0.00 1.40
2709 3262 8.940768 ATGTTCCCGTCCATTAATTTAATTTG 57.059 30.769 0.00 0.00 0.00 2.32
2710 3263 8.123639 TGTTCCCGTCCATTAATTTAATTTGA 57.876 30.769 0.00 0.00 0.00 2.69
2725 3278 6.900568 TTAATTTGAAGTTTGGTTGTGCAG 57.099 33.333 0.00 0.00 0.00 4.41
2793 3350 7.673180 ACATTTGGATCAATTCTTTGTGTGAT 58.327 30.769 0.00 0.00 34.32 3.06
2830 3387 2.787601 TCGTGTTTCTACGAGCTGTT 57.212 45.000 0.00 0.00 46.94 3.16
2849 3414 8.239038 AGCTGTTATGAAGCATACTCTACTTA 57.761 34.615 0.00 0.00 43.37 2.24
2850 3415 8.865090 AGCTGTTATGAAGCATACTCTACTTAT 58.135 33.333 0.00 0.00 43.37 1.73
2851 3416 9.134734 GCTGTTATGAAGCATACTCTACTTATC 57.865 37.037 0.00 0.00 40.52 1.75
2866 3431 9.830186 ACTCTACTTATCTCTATCTCTCTCTCT 57.170 37.037 0.00 0.00 0.00 3.10
2870 3435 8.964533 ACTTATCTCTATCTCTCTCTCTCTCT 57.035 38.462 0.00 0.00 0.00 3.10
2871 3436 9.030452 ACTTATCTCTATCTCTCTCTCTCTCTC 57.970 40.741 0.00 0.00 0.00 3.20
2872 3437 9.253832 CTTATCTCTATCTCTCTCTCTCTCTCT 57.746 40.741 0.00 0.00 0.00 3.10
2873 3438 7.716799 ATCTCTATCTCTCTCTCTCTCTCTC 57.283 44.000 0.00 0.00 0.00 3.20
2874 3439 6.857848 TCTCTATCTCTCTCTCTCTCTCTCT 58.142 44.000 0.00 0.00 0.00 3.10
2875 3440 6.945435 TCTCTATCTCTCTCTCTCTCTCTCTC 59.055 46.154 0.00 0.00 0.00 3.20
2876 3441 6.857848 TCTATCTCTCTCTCTCTCTCTCTCT 58.142 44.000 0.00 0.00 0.00 3.10
2877 3442 6.945435 TCTATCTCTCTCTCTCTCTCTCTCTC 59.055 46.154 0.00 0.00 0.00 3.20
2878 3443 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2879 3444 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2880 3445 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2881 3446 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2882 3447 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2883 3448 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2884 3449 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2885 3450 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2886 3451 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2887 3452 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2888 3453 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2889 3454 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
2890 3455 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
2891 3456 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
2892 3457 8.619281 TCTCTCTCTCTCTCTCTCTCTCTATAT 58.381 40.741 0.00 0.00 0.00 0.86
2893 3458 9.913310 CTCTCTCTCTCTCTCTCTCTCTATATA 57.087 40.741 0.00 0.00 0.00 0.86
3089 3669 4.704833 CACTGGCCACCTCCACCG 62.705 72.222 0.00 0.00 31.74 4.94
3652 4273 7.343057 TCAGAAGAAAATAGAGATGTCAGCCTA 59.657 37.037 0.00 0.00 0.00 3.93
3693 4314 1.484240 CCAGCTAGGAGGAGAAACAGG 59.516 57.143 0.00 0.00 41.22 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 138 1.308216 CCCCCACATCCTCCTCCTT 60.308 63.158 0.00 0.00 0.00 3.36
122 163 3.461773 CCTGCAGATCCCCGTCGT 61.462 66.667 17.39 0.00 0.00 4.34
252 296 0.034059 CGACCTCATCCATGTAGGCC 59.966 60.000 0.00 0.00 37.29 5.19
341 389 2.956964 CTTCGTCGCCGGAGATGC 60.957 66.667 21.37 4.13 42.67 3.91
350 398 1.297664 TCCTAGCTACTCTTCGTCGC 58.702 55.000 0.00 0.00 34.74 5.19
434 496 3.253188 CACTTTGAATCCGGCTCTTTCAA 59.747 43.478 13.94 13.94 37.53 2.69
438 502 1.826385 CCACTTTGAATCCGGCTCTT 58.174 50.000 0.00 0.00 0.00 2.85
443 507 1.755179 ATGAGCCACTTTGAATCCGG 58.245 50.000 0.00 0.00 0.00 5.14
449 513 1.888512 GCCTCAAATGAGCCACTTTGA 59.111 47.619 4.87 5.41 40.75 2.69
472 536 1.069765 CCGCGGGCACTGATTAGAT 59.930 57.895 20.10 0.00 36.31 1.98
473 537 2.499205 CCGCGGGCACTGATTAGA 59.501 61.111 20.10 0.00 36.31 2.10
558 640 0.178947 AGAACCGGCCCCATTTTCAA 60.179 50.000 0.00 0.00 0.00 2.69
567 649 0.958876 AAATGAACGAGAACCGGCCC 60.959 55.000 0.00 0.00 43.93 5.80
607 689 1.598676 GCCCTTTTCCGTTCGTCAAAC 60.599 52.381 0.00 0.00 34.31 2.93
614 696 0.310854 CACTGTGCCCTTTTCCGTTC 59.689 55.000 0.00 0.00 0.00 3.95
620 702 1.898574 CTCCGCACTGTGCCCTTTT 60.899 57.895 25.61 0.00 41.12 2.27
635 717 1.374758 CGGCACTTCAGGACACTCC 60.375 63.158 0.00 0.00 36.58 3.85
829 913 1.200474 CTACGTACATCAGTGCCGCG 61.200 60.000 0.00 0.00 0.00 6.46
841 925 7.432252 AGTTGTAAAGTTGTGTGTACTACGTAC 59.568 37.037 0.00 0.00 37.57 3.67
887 971 1.504359 TTACTACACACAACGGCTGC 58.496 50.000 0.00 0.00 0.00 5.25
888 972 4.092383 GGTAATTACTACACACAACGGCTG 59.908 45.833 15.05 0.00 31.45 4.85
922 1006 2.352323 CGTAGTACATGCAGGACACACA 60.352 50.000 4.84 0.00 0.00 3.72
923 1007 2.094906 TCGTAGTACATGCAGGACACAC 60.095 50.000 4.84 3.46 0.00 3.82
944 1028 1.065126 GCACTTGGGAGAGGTAGCAAT 60.065 52.381 0.00 0.00 0.00 3.56
973 1059 0.179258 GCGTTCGTGTTTCGGATGTC 60.179 55.000 0.00 0.00 36.51 3.06
1004 1090 1.098712 GTGGGGTGCGAACTTTGTCA 61.099 55.000 0.00 0.00 0.00 3.58
1009 1095 2.203294 GGTGTGGGGTGCGAACTT 60.203 61.111 0.00 0.00 0.00 2.66
1010 1096 2.559922 TTTGGTGTGGGGTGCGAACT 62.560 55.000 0.00 0.00 0.00 3.01
1013 1099 2.203280 CTTTGGTGTGGGGTGCGA 60.203 61.111 0.00 0.00 0.00 5.10
1102 1188 2.286523 CGACAGGGCCTTGGTCTCT 61.287 63.158 20.34 0.00 0.00 3.10
1168 1254 2.127232 GCGTTGCTGCGGAAGAAC 60.127 61.111 0.00 0.00 0.00 3.01
1408 1494 4.278956 CCGACAGGGCACAGTAAC 57.721 61.111 0.00 0.00 0.00 2.50
1419 1505 4.742201 CCCTGGTGTCGCCGACAG 62.742 72.222 21.90 9.15 43.57 3.51
1535 1621 6.758416 ACTTAGATATGTGTCGTACTCGTACA 59.242 38.462 7.86 0.00 38.57 2.90
1541 1627 6.452494 AGCAACTTAGATATGTGTCGTACT 57.548 37.500 0.00 0.00 0.00 2.73
1542 1628 6.360148 GCTAGCAACTTAGATATGTGTCGTAC 59.640 42.308 10.63 0.00 0.00 3.67
1545 1631 5.524284 AGCTAGCAACTTAGATATGTGTCG 58.476 41.667 18.83 0.00 0.00 4.35
1546 1632 6.744112 AGAGCTAGCAACTTAGATATGTGTC 58.256 40.000 18.83 0.00 0.00 3.67
1550 1923 9.190858 CAAACTAGAGCTAGCAACTTAGATATG 57.809 37.037 18.83 9.86 36.66 1.78
1577 1950 8.551205 TGCAAGTCGATAATGATTCAAGATTAC 58.449 33.333 0.00 0.00 0.00 1.89
1599 2144 3.268603 CGTGTCACCTGCGTGCAA 61.269 61.111 0.00 0.00 40.04 4.08
1790 2335 1.687840 TACAGTCGGGTGATGGGGG 60.688 63.158 0.00 0.00 0.00 5.40
1791 2336 1.520666 GTACAGTCGGGTGATGGGG 59.479 63.158 0.00 0.00 0.00 4.96
1878 2426 1.078918 CTTGGCGACCATGCTCTGA 60.079 57.895 0.00 0.00 31.53 3.27
1974 2522 0.803768 CGGTCACCAGCTCGAAGATG 60.804 60.000 0.00 0.00 33.89 2.90
2294 2842 1.068472 CCGACACCTCGTATATCCTGC 60.068 57.143 0.00 0.00 38.32 4.85
2322 2870 2.358247 ACGTTCACCGCCATCCAC 60.358 61.111 0.00 0.00 41.42 4.02
2406 2954 1.410517 CACATGTGATCGCTCCCTAGT 59.589 52.381 21.64 0.00 0.00 2.57
2599 3150 5.297776 CCTTCCAATAGCAATAGTTGGTGAG 59.702 44.000 4.78 3.82 42.32 3.51
2653 3206 2.034879 GCCTGTGACATGGACCACG 61.035 63.158 0.00 0.00 36.15 4.94
2680 3233 6.445357 AAATTAATGGACGGGAACATACAC 57.555 37.500 0.00 0.00 0.00 2.90
2706 3259 3.006323 ACACTGCACAACCAAACTTCAAA 59.994 39.130 0.00 0.00 0.00 2.69
2707 3260 2.560542 ACACTGCACAACCAAACTTCAA 59.439 40.909 0.00 0.00 0.00 2.69
2708 3261 2.166829 ACACTGCACAACCAAACTTCA 58.833 42.857 0.00 0.00 0.00 3.02
2709 3262 2.939460 ACACTGCACAACCAAACTTC 57.061 45.000 0.00 0.00 0.00 3.01
2710 3263 3.352648 ACTACACTGCACAACCAAACTT 58.647 40.909 0.00 0.00 0.00 2.66
2751 3304 6.262944 TCCAAATGTAGGATGAATTGAATCGG 59.737 38.462 0.00 0.00 0.00 4.18
2767 3320 8.175925 TCACACAAAGAATTGATCCAAATGTA 57.824 30.769 0.00 0.00 38.94 2.29
2793 3350 7.504924 AACACGAAGACTAAAATTCATGGAA 57.495 32.000 0.00 0.00 0.00 3.53
2849 3414 7.477864 AGAGAGAGAGAGAGAGAGATAGAGAT 58.522 42.308 0.00 0.00 0.00 2.75
2850 3415 6.857848 AGAGAGAGAGAGAGAGAGATAGAGA 58.142 44.000 0.00 0.00 0.00 3.10
2851 3416 6.947733 AGAGAGAGAGAGAGAGAGAGATAGAG 59.052 46.154 0.00 0.00 0.00 2.43
2852 3417 6.857848 AGAGAGAGAGAGAGAGAGAGATAGA 58.142 44.000 0.00 0.00 0.00 1.98
2853 3418 6.947733 AGAGAGAGAGAGAGAGAGAGAGATAG 59.052 46.154 0.00 0.00 0.00 2.08
2854 3419 6.857848 AGAGAGAGAGAGAGAGAGAGAGATA 58.142 44.000 0.00 0.00 0.00 1.98
2855 3420 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
2856 3421 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2857 3422 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2858 3423 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2859 3424 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2860 3425 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2861 3426 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2862 3427 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2863 3428 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2864 3429 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2865 3430 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2866 3431 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2867 3432 8.821686 ATATAGAGAGAGAGAGAGAGAGAGAG 57.178 42.308 0.00 0.00 0.00 3.20
2929 3494 8.798748 GCGATCGCTGGTTTATTAGTATATAT 57.201 34.615 31.94 0.00 38.26 0.86
3089 3669 0.957362 GAGGCAGGCAATGGATAAGC 59.043 55.000 0.00 0.00 0.00 3.09
3652 4273 1.446016 ACCCCTTTCTGTTAGGCTGT 58.554 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.