Multiple sequence alignment - TraesCS4B01G322400

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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 TraesCS4B01G322400 chr4B 100.000 3542 0 0 1 3542 613146133 613142592 0.000000e+00 6541
1 TraesCS4B01G322400 chr4B 86.257 553 37 14 2999 3542 189084774 189084252 6.640000e-157 564
2 TraesCS4B01G322400 chr4B 84.477 554 45 8 2999 3542 87820148 87819626 3.150000e-140 508
3 TraesCS4B01G322400 chr4B 83.173 208 30 4 1 204 134927935 134927729 6.040000e-43 185
4 TraesCS4B01G322400 chr4B 93.827 81 4 1 202 281 28406855 28406935 1.730000e-23 121
5 TraesCS4B01G322400 chr6D 95.123 3342 75 34 2 3300 457751366 457754662 0.000000e+00 5188
6 TraesCS4B01G322400 chr6D 80.508 590 98 12 1823 2405 473294438 473295017 1.510000e-118 436
7 TraesCS4B01G322400 chr6D 83.264 478 63 10 1823 2293 473414724 473414257 1.180000e-114 424
8 TraesCS4B01G322400 chr6D 97.268 183 5 0 3360 3542 457757459 457757641 9.550000e-81 311
9 TraesCS4B01G322400 chr6D 82.182 275 30 9 1232 1502 473415002 473414743 5.950000e-53 219
10 TraesCS4B01G322400 chr6D 82.083 240 26 9 3035 3269 435936168 435936395 4.670000e-44 189
11 TraesCS4B01G322400 chr6D 83.178 214 26 5 1 204 402412361 402412574 1.680000e-43 187
12 TraesCS4B01G322400 chr6B 76.790 1327 227 47 1109 2405 718879799 718878524 0.000000e+00 669
13 TraesCS4B01G322400 chr6B 76.699 1339 231 46 1097 2405 718901982 718903269 0.000000e+00 669
14 TraesCS4B01G322400 chr6B 85.641 195 22 5 15 204 234676060 234676253 2.160000e-47 200
15 TraesCS4B01G322400 chr5A 85.897 546 38 14 3003 3539 593346755 593347270 2.400000e-151 545
16 TraesCS4B01G322400 chr5B 85.455 550 38 12 3003 3542 112834367 112833850 5.200000e-148 534
17 TraesCS4B01G322400 chr5B 83.705 448 32 11 3000 3437 113098237 113098653 5.550000e-103 385
18 TraesCS4B01G322400 chr5B 92.857 84 3 3 199 281 696437608 696437527 6.210000e-23 119
19 TraesCS4B01G322400 chr7A 84.686 542 58 16 3003 3542 116511819 116511301 5.240000e-143 518
20 TraesCS4B01G322400 chr7A 86.567 201 24 3 3003 3202 594701604 594701406 5.950000e-53 219
21 TraesCS4B01G322400 chr3A 84.672 548 43 12 3005 3542 647488328 647488844 3.150000e-140 508
22 TraesCS4B01G322400 chr3A 82.841 542 62 19 3003 3540 71786447 71786961 1.160000e-124 457
23 TraesCS4B01G322400 chr3A 73.480 773 127 43 1016 1770 692330073 692330785 1.660000e-53 220
24 TraesCS4B01G322400 chr3A 85.572 201 26 3 3003 3202 20390913 20390715 1.290000e-49 207
25 TraesCS4B01G322400 chr3A 83.178 214 26 5 1 204 738233107 738232894 1.680000e-43 187
26 TraesCS4B01G322400 chr3A 75.325 462 67 16 1316 1776 692326202 692326617 1.010000e-40 178
27 TraesCS4B01G322400 chr1A 84.000 550 47 11 3003 3542 290212423 290212941 1.140000e-134 490
28 TraesCS4B01G322400 chr1A 86.567 201 24 3 3003 3202 36596802 36596604 5.950000e-53 219
29 TraesCS4B01G322400 chr1D 81.200 500 63 23 15 492 363617310 363617800 1.200000e-99 374
30 TraesCS4B01G322400 chr1D 89.862 217 17 5 283 496 199563280 199563066 1.250000e-69 274
31 TraesCS4B01G322400 chr1D 89.401 217 19 4 280 494 37967007 37967221 1.620000e-68 270
32 TraesCS4B01G322400 chr6A 77.778 630 90 24 1331 1954 616606387 616606972 3.390000e-90 342
33 TraesCS4B01G322400 chr6A 79.229 467 75 10 1950 2405 616612214 616612669 4.440000e-79 305
34 TraesCS4B01G322400 chr7D 91.324 219 16 3 280 496 32647208 32646991 2.670000e-76 296
35 TraesCS4B01G322400 chr7D 89.862 217 19 3 280 494 260696744 260696529 3.480000e-70 276
36 TraesCS4B01G322400 chr7D 83.486 218 22 9 1 204 17772569 17772352 1.300000e-44 191
37 TraesCS4B01G322400 chr3D 88.525 244 25 3 254 495 547518853 547518611 3.460000e-75 292
38 TraesCS4B01G322400 chr3D 93.827 81 3 2 203 283 536333171 536333249 1.730000e-23 121
39 TraesCS4B01G322400 chr3D 92.405 79 3 1 203 281 459467377 459467452 3.740000e-20 110
40 TraesCS4B01G322400 chr2D 89.862 217 19 3 280 494 54123297 54123082 3.480000e-70 276
41 TraesCS4B01G322400 chr2D 85.789 190 25 2 3003 3191 619590865 619590677 2.160000e-47 200
42 TraesCS4B01G322400 chr2D 87.629 97 5 4 191 281 310223561 310223466 4.840000e-19 106
43 TraesCS4B01G322400 chr4D 89.498 219 15 8 280 494 134664641 134664427 1.620000e-68 270
44 TraesCS4B01G322400 chr2B 86.765 204 24 3 3000 3202 64864914 64865115 1.280000e-54 224
45 TraesCS4B01G322400 chr2B 87.709 179 14 8 33 204 720679 720502 6.000000e-48 202
46 TraesCS4B01G322400 chr2B 91.566 83 5 2 203 284 674033401 674033320 2.890000e-21 113
47 TraesCS4B01G322400 chr5D 83.412 211 26 6 1 204 558062163 558061955 1.680000e-43 187
48 TraesCS4B01G322400 chr5D 83.256 215 22 10 1 204 460063052 460062841 6.040000e-43 185
49 TraesCS4B01G322400 chr4A 83.178 214 25 6 1 204 3052316 3052104 6.040000e-43 185
50 TraesCS4B01G322400 chr7B 84.375 192 24 3 3000 3191 23060742 23060927 2.170000e-42 183
51 TraesCS4B01G322400 chr2A 90.698 86 4 1 200 281 166854865 166854950 1.040000e-20 111
52 TraesCS4B01G322400 chr1B 90.588 85 7 1 203 287 654631661 654631578 1.040000e-20 111


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 TraesCS4B01G322400 chr4B 613142592 613146133 3541 True 6541.0 6541 100.0000 1 3542 1 chr4B.!!$R4 3541
1 TraesCS4B01G322400 chr4B 189084252 189084774 522 True 564.0 564 86.2570 2999 3542 1 chr4B.!!$R3 543
2 TraesCS4B01G322400 chr4B 87819626 87820148 522 True 508.0 508 84.4770 2999 3542 1 chr4B.!!$R1 543
3 TraesCS4B01G322400 chr6D 457751366 457757641 6275 False 2749.5 5188 96.1955 2 3542 2 chr6D.!!$F4 3540
4 TraesCS4B01G322400 chr6D 473294438 473295017 579 False 436.0 436 80.5080 1823 2405 1 chr6D.!!$F3 582
5 TraesCS4B01G322400 chr6D 473414257 473415002 745 True 321.5 424 82.7230 1232 2293 2 chr6D.!!$R1 1061
6 TraesCS4B01G322400 chr6B 718878524 718879799 1275 True 669.0 669 76.7900 1109 2405 1 chr6B.!!$R1 1296
7 TraesCS4B01G322400 chr6B 718901982 718903269 1287 False 669.0 669 76.6990 1097 2405 1 chr6B.!!$F2 1308
8 TraesCS4B01G322400 chr5A 593346755 593347270 515 False 545.0 545 85.8970 3003 3539 1 chr5A.!!$F1 536
9 TraesCS4B01G322400 chr5B 112833850 112834367 517 True 534.0 534 85.4550 3003 3542 1 chr5B.!!$R1 539
10 TraesCS4B01G322400 chr7A 116511301 116511819 518 True 518.0 518 84.6860 3003 3542 1 chr7A.!!$R1 539
11 TraesCS4B01G322400 chr3A 647488328 647488844 516 False 508.0 508 84.6720 3005 3542 1 chr3A.!!$F2 537
12 TraesCS4B01G322400 chr3A 71786447 71786961 514 False 457.0 457 82.8410 3003 3540 1 chr3A.!!$F1 537
13 TraesCS4B01G322400 chr1A 290212423 290212941 518 False 490.0 490 84.0000 3003 3542 1 chr1A.!!$F1 539
14 TraesCS4B01G322400 chr6A 616606387 616606972 585 False 342.0 342 77.7780 1331 1954 1 chr6A.!!$F1 623

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
64 65 0.102300 GACAGGCACGGTTTTGCTTT 59.898 50.0 0.00 0.0 42.56 3.51 F
119 120 0.320421 CGTGCCTCTTTCGGAAAGGA 60.320 55.0 25.66 14.0 39.01 3.36 F
347 348 0.584396 GATTGTGACGCACGGTTTGA 59.416 50.0 5.69 0.0 37.14 2.69 F
1309 1372 0.803740 CCAAGAGCAAGAGCAAGAGC 59.196 55.0 0.00 0.0 45.49 4.09 F
1310 1373 1.520494 CAAGAGCAAGAGCAAGAGCA 58.480 50.0 0.00 0.0 45.49 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1310 1373 0.547954 GGGGTTGTCCTCCTCCTCTT 60.548 60.000 0.00 0.00 35.33 2.85 R
1311 1374 1.081277 GGGGTTGTCCTCCTCCTCT 59.919 63.158 0.00 0.00 35.33 3.69 R
1312 1375 0.547954 AAGGGGTTGTCCTCCTCCTC 60.548 60.000 0.00 0.00 35.80 3.71 R
2356 2453 0.035534 TGGGTTGGATCGTCATGTGG 60.036 55.000 0.00 0.00 0.00 4.17 R
2794 2891 0.466189 AACCAAGGCGGCATAGATGG 60.466 55.000 13.08 13.33 39.03 3.51 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
63 64 1.733526 GACAGGCACGGTTTTGCTT 59.266 52.632 0.00 0.00 42.56 3.91
64 65 0.102300 GACAGGCACGGTTTTGCTTT 59.898 50.000 0.00 0.00 42.56 3.51
72 73 0.991770 CGGTTTTGCTTTGCGAGTCG 60.992 55.000 8.54 8.54 0.00 4.18
119 120 0.320421 CGTGCCTCTTTCGGAAAGGA 60.320 55.000 25.66 14.00 39.01 3.36
216 217 1.547449 GGTATCTACTCCCTCCGTCCC 60.547 61.905 0.00 0.00 0.00 4.46
268 269 7.889469 ACTTTGTACTAGACACTTATTTCGGA 58.111 34.615 0.00 0.00 37.96 4.55
301 302 2.989840 AGTTTTGAAGATCTCGACGCAG 59.010 45.455 0.00 0.00 0.00 5.18
312 313 1.011968 TCGACGCAGGAAATCCAACG 61.012 55.000 11.21 11.21 40.80 4.10
347 348 0.584396 GATTGTGACGCACGGTTTGA 59.416 50.000 5.69 0.00 37.14 2.69
358 359 5.172934 ACGCACGGTTTGAGAGATAAAATA 58.827 37.500 0.00 0.00 0.00 1.40
437 438 2.429571 GCATGTGCGCCACTTGTG 60.430 61.111 4.18 5.74 40.25 3.33
439 440 2.112928 ATGTGCGCCACTTGTGGA 59.887 55.556 22.52 2.44 35.11 4.02
441 442 0.895100 ATGTGCGCCACTTGTGGAAT 60.895 50.000 22.52 5.51 35.11 3.01
444 445 3.039202 GCGCCACTTGTGGAATCCG 62.039 63.158 22.52 16.26 0.00 4.18
468 469 2.627699 GGGTTGGACTGATCTTTGCAAA 59.372 45.455 12.14 12.14 0.00 3.68
488 489 7.903145 TGCAAAGAGTACTCCTTAATTAGTGA 58.097 34.615 19.38 0.00 0.00 3.41
513 514 3.093574 CGAGTTATGAAAGCGCATGTTG 58.906 45.455 11.47 0.00 0.00 3.33
571 573 7.149307 ACTTTAAAATGGTTGATTAACGTGGG 58.851 34.615 0.00 0.00 37.69 4.61
610 612 5.700373 ACGTTAGTTACCAAAGCCGAATTAA 59.300 36.000 0.00 0.00 0.00 1.40
674 676 3.027412 CGCTAGCTAGGGATATGGATGT 58.973 50.000 28.87 0.00 38.40 3.06
714 730 6.697641 GGGGGATATGGATGAGTAAACTTA 57.302 41.667 0.00 0.00 0.00 2.24
754 770 4.067944 GGGGGATATGGATGAGTAGTCT 57.932 50.000 0.00 0.00 0.00 3.24
762 778 5.543507 ATGGATGAGTAGTCTGATTCCAC 57.456 43.478 11.68 0.00 0.00 4.02
775 791 4.646492 TCTGATTCCACGATCTGATCTGAA 59.354 41.667 15.16 13.93 31.59 3.02
927 943 1.484240 AGGAAAGAAGCCCTCGATCAG 59.516 52.381 0.00 0.00 0.00 2.90
928 944 1.482593 GGAAAGAAGCCCTCGATCAGA 59.517 52.381 0.00 0.00 0.00 3.27
929 945 2.103941 GGAAAGAAGCCCTCGATCAGAT 59.896 50.000 0.00 0.00 0.00 2.90
930 946 3.389221 GAAAGAAGCCCTCGATCAGATC 58.611 50.000 0.00 0.00 0.00 2.75
985 1030 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
986 1031 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
987 1032 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
988 1033 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
989 1034 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
990 1035 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
991 1036 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
992 1037 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
993 1038 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
994 1039 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
995 1040 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
996 1041 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
1041 1086 2.035442 GTTCGAGGCCTCCTTGTGC 61.035 63.158 27.20 7.81 36.45 4.57
1307 1370 2.224606 CAACCAAGAGCAAGAGCAAGA 58.775 47.619 0.00 0.00 45.49 3.02
1309 1372 0.803740 CCAAGAGCAAGAGCAAGAGC 59.196 55.000 0.00 0.00 45.49 4.09
1310 1373 1.520494 CAAGAGCAAGAGCAAGAGCA 58.480 50.000 0.00 0.00 45.49 4.26
1311 1374 1.878088 CAAGAGCAAGAGCAAGAGCAA 59.122 47.619 0.00 0.00 45.49 3.91
1312 1375 1.810959 AGAGCAAGAGCAAGAGCAAG 58.189 50.000 0.00 0.00 45.49 4.01
1717 1802 4.584743 GTCTCTTTCCAACCAAGGTGATTT 59.415 41.667 0.00 0.00 0.00 2.17
2148 2236 2.156343 GAGCCATACTCCATTCCGAC 57.844 55.000 0.00 0.00 39.75 4.79
2356 2453 0.540923 ATTCTCTGCAGACAGGGCTC 59.459 55.000 13.74 0.00 44.77 4.70
2410 2507 4.446371 CCTCACCAAATATCTCACCTCAC 58.554 47.826 0.00 0.00 0.00 3.51
2427 2524 3.525537 CTCACACGATATTGCCAACTCT 58.474 45.455 0.00 0.00 0.00 3.24
2563 2660 8.737168 TTGATTAATACAGCAGAGTAGCATTT 57.263 30.769 0.00 0.00 36.85 2.32
2564 2661 9.830975 TTGATTAATACAGCAGAGTAGCATTTA 57.169 29.630 0.00 0.00 36.85 1.40
2565 2662 9.261180 TGATTAATACAGCAGAGTAGCATTTAC 57.739 33.333 0.00 0.00 36.85 2.01
2566 2663 9.482627 GATTAATACAGCAGAGTAGCATTTACT 57.517 33.333 0.00 0.00 36.85 2.24
2567 2664 8.648557 TTAATACAGCAGAGTAGCATTTACTG 57.351 34.615 0.00 0.00 36.85 2.74
2568 2665 4.543590 ACAGCAGAGTAGCATTTACTGT 57.456 40.909 0.00 0.00 36.85 3.55
2569 2666 5.661056 ACAGCAGAGTAGCATTTACTGTA 57.339 39.130 0.00 0.00 35.49 2.74
2570 2667 5.411781 ACAGCAGAGTAGCATTTACTGTAC 58.588 41.667 0.00 0.00 35.49 2.90
2571 2668 5.186021 ACAGCAGAGTAGCATTTACTGTACT 59.814 40.000 0.00 0.00 35.49 2.73
2572 2669 5.518128 CAGCAGAGTAGCATTTACTGTACTG 59.482 44.000 0.00 0.00 36.85 2.74
2600 2697 7.673082 ACTGTACTGTACCTACCTTGAATAAGT 59.327 37.037 14.91 4.57 31.80 2.24
2601 2698 9.182214 CTGTACTGTACCTACCTTGAATAAGTA 57.818 37.037 14.91 0.00 31.80 2.24
2602 2699 9.532494 TGTACTGTACCTACCTTGAATAAGTAA 57.468 33.333 14.91 0.00 31.80 2.24
2696 2793 1.160329 AGTTCTGGCACAAGCACGAC 61.160 55.000 0.00 0.00 44.61 4.34
3096 3193 6.097696 ACACAATAAGCTGGTTTTTAGGTTGT 59.902 34.615 0.00 0.00 36.62 3.32
3177 3285 6.267471 ACCTGTTGTGATCCAATACAAACAAT 59.733 34.615 0.00 0.00 38.40 2.71
3267 3384 9.932207 AACTGATCAATATTCAAGCAATTTCAA 57.068 25.926 0.00 0.00 0.00 2.69
3334 5039 4.858850 TCATGCCAATAGAACAGACCAAT 58.141 39.130 0.00 0.00 0.00 3.16
3349 5055 9.994432 GAACAGACCAATGAAACTGATTAATAG 57.006 33.333 0.00 0.00 0.00 1.73
3486 6364 5.873164 AGCCGTTAGTTTTAATCTTGACGAT 59.127 36.000 10.81 0.00 0.00 3.73
3509 6387 1.464608 CGATCAACAAACTGATGGCGT 59.535 47.619 0.00 0.00 36.15 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.628005 TCGTTAACGATAGGCACGG 57.372 52.632 26.00 0.00 44.22 4.94
47 48 1.489881 GCAAAGCAAAACCGTGCCTG 61.490 55.000 0.00 0.00 46.14 4.85
126 127 2.035237 AAACCGAACTGGGAGCACGA 62.035 55.000 0.00 0.00 44.64 4.35
128 129 1.029681 AAAAACCGAACTGGGAGCAC 58.970 50.000 0.00 0.00 44.64 4.40
172 173 7.976734 ACCATGTTGATAAGTTTTGACGAAAAA 59.023 29.630 0.00 0.00 35.35 1.94
173 174 7.484975 ACCATGTTGATAAGTTTTGACGAAAA 58.515 30.769 0.00 0.00 0.00 2.29
174 175 7.033530 ACCATGTTGATAAGTTTTGACGAAA 57.966 32.000 0.00 0.00 0.00 3.46
186 187 6.497259 GGAGGGAGTAGATACCATGTTGATAA 59.503 42.308 0.00 0.00 31.98 1.75
216 217 8.988934 TGTACTAAGCTTGAGACACTTATTTTG 58.011 33.333 9.86 0.00 0.00 2.44
264 265 0.038744 AACTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
268 269 3.644738 TCTTCAAAACTACTCCCTCCGTT 59.355 43.478 0.00 0.00 0.00 4.44
301 302 1.401018 CGCTTTCACCGTTGGATTTCC 60.401 52.381 0.00 0.00 0.00 3.13
312 313 2.293399 ACAATCTCAAACCGCTTTCACC 59.707 45.455 0.00 0.00 0.00 4.02
468 469 9.186837 TCGAAATCACTAATTAAGGAGTACTCT 57.813 33.333 21.88 6.36 0.00 3.24
482 483 6.455113 GCGCTTTCATAACTCGAAATCACTAA 60.455 38.462 0.00 0.00 32.21 2.24
488 489 4.094887 ACATGCGCTTTCATAACTCGAAAT 59.905 37.500 9.73 0.00 32.21 2.17
610 612 2.440796 CGGAACATGCATGGGCCT 60.441 61.111 29.41 11.64 40.13 5.19
692 708 9.588096 AAAATAAGTTTACTCATCCATATCCCC 57.412 33.333 0.00 0.00 0.00 4.81
754 770 4.686972 GTTCAGATCAGATCGTGGAATCA 58.313 43.478 14.40 0.00 0.00 2.57
762 778 2.860735 GGTTTCCGTTCAGATCAGATCG 59.139 50.000 10.63 10.63 0.00 3.69
846 862 3.118371 GGTTGGTTCCTATTCCGACTCAT 60.118 47.826 0.00 0.00 38.00 2.90
941 957 3.248446 TTCCTTCCTTGGTCGCGGG 62.248 63.158 6.13 0.00 0.00 6.13
942 958 1.741770 CTTCCTTCCTTGGTCGCGG 60.742 63.158 6.13 0.00 0.00 6.46
943 959 1.741770 CCTTCCTTCCTTGGTCGCG 60.742 63.158 0.00 0.00 0.00 5.87
944 960 0.036306 TTCCTTCCTTCCTTGGTCGC 59.964 55.000 0.00 0.00 0.00 5.19
985 1030 4.679372 CGGTCTCATCTTCTTCCTTCCTTC 60.679 50.000 0.00 0.00 0.00 3.46
986 1031 3.196685 CGGTCTCATCTTCTTCCTTCCTT 59.803 47.826 0.00 0.00 0.00 3.36
987 1032 2.763448 CGGTCTCATCTTCTTCCTTCCT 59.237 50.000 0.00 0.00 0.00 3.36
988 1033 2.761208 TCGGTCTCATCTTCTTCCTTCC 59.239 50.000 0.00 0.00 0.00 3.46
989 1034 3.736740 GCTCGGTCTCATCTTCTTCCTTC 60.737 52.174 0.00 0.00 0.00 3.46
990 1035 2.167487 GCTCGGTCTCATCTTCTTCCTT 59.833 50.000 0.00 0.00 0.00 3.36
991 1036 1.754226 GCTCGGTCTCATCTTCTTCCT 59.246 52.381 0.00 0.00 0.00 3.36
992 1037 1.478510 TGCTCGGTCTCATCTTCTTCC 59.521 52.381 0.00 0.00 0.00 3.46
993 1038 2.949451 TGCTCGGTCTCATCTTCTTC 57.051 50.000 0.00 0.00 0.00 2.87
994 1039 2.158986 CCATGCTCGGTCTCATCTTCTT 60.159 50.000 0.00 0.00 0.00 2.52
995 1040 1.411977 CCATGCTCGGTCTCATCTTCT 59.588 52.381 0.00 0.00 0.00 2.85
996 1041 1.410517 TCCATGCTCGGTCTCATCTTC 59.589 52.381 0.00 0.00 0.00 2.87
1307 1370 0.980423 GTTGTCCTCCTCCTCTTGCT 59.020 55.000 0.00 0.00 0.00 3.91
1309 1372 0.615850 GGGTTGTCCTCCTCCTCTTG 59.384 60.000 0.00 0.00 0.00 3.02
1310 1373 0.547954 GGGGTTGTCCTCCTCCTCTT 60.548 60.000 0.00 0.00 35.33 2.85
1311 1374 1.081277 GGGGTTGTCCTCCTCCTCT 59.919 63.158 0.00 0.00 35.33 3.69
1312 1375 0.547954 AAGGGGTTGTCCTCCTCCTC 60.548 60.000 0.00 0.00 35.80 3.71
1805 1890 4.625800 CGGAGCCTCCTTCTTTGG 57.374 61.111 9.52 0.00 33.30 3.28
2148 2236 2.028112 TCCTCTTGTTCCAATCAGGTCG 60.028 50.000 0.00 0.00 39.02 4.79
2356 2453 0.035534 TGGGTTGGATCGTCATGTGG 60.036 55.000 0.00 0.00 0.00 4.17
2410 2507 5.755375 ACTTATCAGAGTTGGCAATATCGTG 59.245 40.000 1.92 6.00 0.00 4.35
2427 2524 3.322541 TCCCTGACGTGTTCAACTTATCA 59.677 43.478 0.00 0.00 32.21 2.15
2563 2660 7.009179 AGGTACAGTACAGTACAGTACAGTA 57.991 40.000 31.71 23.32 46.90 2.74
2564 2661 5.874093 AGGTACAGTACAGTACAGTACAGT 58.126 41.667 31.71 24.16 46.90 3.55
2565 2662 6.314896 GGTAGGTACAGTACAGTACAGTACAG 59.685 46.154 31.71 20.59 46.90 2.74
2566 2663 6.013379 AGGTAGGTACAGTACAGTACAGTACA 60.013 42.308 31.71 18.85 46.90 2.90
2567 2664 6.410540 AGGTAGGTACAGTACAGTACAGTAC 58.589 44.000 26.92 26.92 45.40 2.73
2568 2665 6.627087 AGGTAGGTACAGTACAGTACAGTA 57.373 41.667 24.58 12.11 44.76 2.74
2569 2666 5.511386 AGGTAGGTACAGTACAGTACAGT 57.489 43.478 24.58 13.11 44.76 3.55
2570 2667 5.942236 TCAAGGTAGGTACAGTACAGTACAG 59.058 44.000 24.58 7.52 44.76 2.74
2571 2668 5.879763 TCAAGGTAGGTACAGTACAGTACA 58.120 41.667 24.58 7.50 44.76 2.90
2572 2669 6.824305 TTCAAGGTAGGTACAGTACAGTAC 57.176 41.667 17.67 17.67 42.78 2.73
2600 2697 7.147966 TGCTATCTGAACGAATGTTACTCCTTA 60.148 37.037 0.00 0.00 38.78 2.69
2601 2698 6.043411 GCTATCTGAACGAATGTTACTCCTT 58.957 40.000 0.00 0.00 38.78 3.36
2602 2699 5.127194 TGCTATCTGAACGAATGTTACTCCT 59.873 40.000 0.00 0.00 38.78 3.69
2603 2700 5.348986 TGCTATCTGAACGAATGTTACTCC 58.651 41.667 0.00 0.00 38.78 3.85
2696 2793 7.726079 CATAGTTGCACAAGTTGAAATGAATG 58.274 34.615 10.54 0.00 0.00 2.67
2794 2891 0.466189 AACCAAGGCGGCATAGATGG 60.466 55.000 13.08 13.33 39.03 3.51
3096 3193 6.324254 GTCTTTATTAGGGCCAGTCTTAGAGA 59.676 42.308 6.18 0.00 0.00 3.10
3177 3285 5.394443 GCTGATTGAAATGGCCACAAAGATA 60.394 40.000 8.16 0.00 0.00 1.98
3307 3424 7.062322 TGGTCTGTTCTATTGGCATGAAATAT 58.938 34.615 0.00 0.00 0.00 1.28
3308 3425 6.422333 TGGTCTGTTCTATTGGCATGAAATA 58.578 36.000 0.00 0.00 0.00 1.40
3309 3426 5.263599 TGGTCTGTTCTATTGGCATGAAAT 58.736 37.500 0.00 0.00 0.00 2.17
3310 3427 4.661222 TGGTCTGTTCTATTGGCATGAAA 58.339 39.130 0.00 0.00 0.00 2.69
3334 5039 8.389779 TGTTGCTTGTCTATTAATCAGTTTCA 57.610 30.769 0.00 0.00 0.00 2.69
3349 5055 1.559831 GCACCTGTTTGTTGCTTGTC 58.440 50.000 0.00 0.00 0.00 3.18
3439 6317 2.650322 CTTGCCGGGCCTCTTATTTAA 58.350 47.619 17.97 0.00 0.00 1.52
3486 6364 2.483877 GCCATCAGTTTGTTGATCGTCA 59.516 45.455 0.00 0.00 35.67 4.35
3509 6387 4.593956 TGTGTTGATGGCATGGTGTTATA 58.406 39.130 3.81 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.