Multiple sequence alignment - TraesCS3A01G050700

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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 TraesCS3A01G050700 chr3A 100.000 3419 0 0 1 3419 26873369 26869951 0.000000e+00 6314.0
1 TraesCS3A01G050700 chr3A 90.481 1954 120 23 866 2761 26828514 26830459 0.000000e+00 2518.0
2 TraesCS3A01G050700 chr3A 81.510 768 106 17 8 759 26827656 26828403 1.760000e-167 599.0
3 TraesCS3A01G050700 chr3A 97.758 223 5 0 2761 2983 26830530 26830752 5.350000e-103 385.0
4 TraesCS3A01G050700 chr3A 94.561 239 9 3 2975 3213 26831373 26831607 1.940000e-97 366.0
5 TraesCS3A01G050700 chr3A 100.000 58 0 0 3299 3356 26831692 26831749 1.300000e-19 108.0
6 TraesCS3A01G050700 chr3A 91.071 56 5 0 2179 2234 95891687 95891742 3.660000e-10 76.8
7 TraesCS3A01G050700 chr3D 90.291 2719 189 43 1 2666 19303373 19300677 0.000000e+00 3489.0
8 TraesCS3A01G050700 chr3D 85.080 2118 225 49 318 2397 19286613 19288677 0.000000e+00 2076.0
9 TraesCS3A01G050700 chr3D 88.942 832 73 12 7 824 19308828 19308002 0.000000e+00 1009.0
10 TraesCS3A01G050700 chr3D 86.667 465 23 17 2922 3356 19300224 19299769 2.390000e-131 479.0
11 TraesCS3A01G050700 chr3D 100.000 38 0 0 851 888 19308003 19307966 1.700000e-08 71.3
12 TraesCS3A01G050700 chr3B 89.088 2841 206 48 1 2761 31069214 31066398 0.000000e+00 3434.0
13 TraesCS3A01G050700 chr3B 88.856 1714 133 24 874 2555 31058339 31060026 0.000000e+00 2054.0
14 TraesCS3A01G050700 chr3B 90.330 455 37 5 2761 3210 31066327 31065875 1.060000e-164 590.0
15 TraesCS3A01G050700 chr3B 100.000 58 0 0 3299 3356 31065786 31065729 1.300000e-19 108.0
16 TraesCS3A01G050700 chr2A 90.229 481 41 5 1263 1739 28200528 28200050 1.040000e-174 623.0
17 TraesCS3A01G050700 chr2A 89.952 209 20 1 1531 1739 690320635 690320428 5.620000e-68 268.0
18 TraesCS3A01G050700 chr2A 76.190 126 29 1 303 428 154131139 154131015 7.920000e-07 65.8
19 TraesCS3A01G050700 chr6B 77.273 528 77 27 1445 1967 163653715 163653226 1.560000e-68 270.0
20 TraesCS3A01G050700 chr2D 95.152 165 8 0 1410 1574 613336810 613336646 9.410000e-66 261.0
21 TraesCS3A01G050700 chr2D 78.689 122 22 3 301 422 304662719 304662836 1.020000e-10 78.7
22 TraesCS3A01G050700 chr1A 92.121 165 13 0 1410 1574 497924740 497924576 2.050000e-57 233.0
23 TraesCS3A01G050700 chr1A 90.698 43 3 1 22 64 243619351 243619392 4.770000e-04 56.5
24 TraesCS3A01G050700 chr7B 89.444 180 14 3 1410 1587 635886512 635886688 4.440000e-54 222.0
25 TraesCS3A01G050700 chr5D 82.955 88 12 3 318 404 529259133 529259218 3.660000e-10 76.8
26 TraesCS3A01G050700 chr5A 100.000 33 0 0 36 68 41166271 41166239 1.020000e-05 62.1
27 TraesCS3A01G050700 chr1B 92.308 39 2 1 26 64 270321356 270321319 2.000000e-03 54.7


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 TraesCS3A01G050700 chr3A 26869951 26873369 3418 True 6314.000000 6314 100.000000 1 3419 1 chr3A.!!$R1 3418
1 TraesCS3A01G050700 chr3A 26827656 26831749 4093 False 795.200000 2518 92.862000 8 3356 5 chr3A.!!$F2 3348
2 TraesCS3A01G050700 chr3D 19286613 19288677 2064 False 2076.000000 2076 85.080000 318 2397 1 chr3D.!!$F1 2079
3 TraesCS3A01G050700 chr3D 19299769 19303373 3604 True 1984.000000 3489 88.479000 1 3356 2 chr3D.!!$R1 3355
4 TraesCS3A01G050700 chr3D 19307966 19308828 862 True 540.150000 1009 94.471000 7 888 2 chr3D.!!$R2 881
5 TraesCS3A01G050700 chr3B 31058339 31060026 1687 False 2054.000000 2054 88.856000 874 2555 1 chr3B.!!$F1 1681
6 TraesCS3A01G050700 chr3B 31065729 31069214 3485 True 1377.333333 3434 93.139333 1 3356 3 chr3B.!!$R1 3355

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
444 460 2.159435 GGAGCAACACGAACACAAACTT 60.159 45.455 0.00 0.00 0.00 2.66 F
1215 1351 0.104620 AGTACCACCTGGACCTGGTT 60.105 55.000 19.89 9.84 41.28 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1568 0.528470 GAGTCCTTCTCGTGGTCCAG 59.472 60.0 0.0 0.0 33.25 3.86 R
2466 2636 0.966875 TTCAGGATGCCATGCACCAC 60.967 55.0 0.0 0.0 43.04 4.16 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
200 203 6.728089 TTATAGCCCATTGCAATTCATTGA 57.272 33.333 9.83 0.00 44.83 2.57
201 204 5.818678 ATAGCCCATTGCAATTCATTGAT 57.181 34.783 9.83 0.00 44.83 2.57
250 253 5.769484 TGGAAACGTAGCCATTGTTTAAA 57.231 34.783 5.28 0.00 36.06 1.52
252 255 5.299782 TGGAAACGTAGCCATTGTTTAAACT 59.700 36.000 18.72 0.64 36.06 2.66
253 256 6.183360 TGGAAACGTAGCCATTGTTTAAACTT 60.183 34.615 18.72 4.43 36.06 2.66
254 257 6.143278 GGAAACGTAGCCATTGTTTAAACTTG 59.857 38.462 18.72 15.05 36.06 3.16
255 258 6.380095 AACGTAGCCATTGTTTAAACTTGA 57.620 33.333 18.72 6.08 0.00 3.02
257 260 7.675962 ACGTAGCCATTGTTTAAACTTGATA 57.324 32.000 18.72 9.89 0.00 2.15
258 261 7.748847 ACGTAGCCATTGTTTAAACTTGATAG 58.251 34.615 18.72 5.69 0.00 2.08
259 262 7.604927 ACGTAGCCATTGTTTAAACTTGATAGA 59.395 33.333 18.72 0.00 0.00 1.98
266 270 9.740239 CATTGTTTAAACTTGATAGATGATGGG 57.260 33.333 18.72 0.00 0.00 4.00
393 403 8.537728 AGCAACAAAAATTATATCCAGATCCA 57.462 30.769 0.00 0.00 0.00 3.41
406 416 6.865834 ATCCAGATCCATAGAATACCTGAC 57.134 41.667 0.00 0.00 0.00 3.51
407 417 5.715921 TCCAGATCCATAGAATACCTGACA 58.284 41.667 0.00 0.00 0.00 3.58
408 418 6.143206 TCCAGATCCATAGAATACCTGACAA 58.857 40.000 0.00 0.00 0.00 3.18
431 447 3.676049 CGACTATAAGCACTGGAGCAACA 60.676 47.826 0.00 0.00 36.85 3.33
444 460 2.159435 GGAGCAACACGAACACAAACTT 60.159 45.455 0.00 0.00 0.00 2.66
458 474 9.710979 CGAACACAAACTTAAAGTTCATCTAAA 57.289 29.630 0.00 0.00 37.47 1.85
507 526 6.873076 TGGCTTTCTGGCATTTTAAATTAGTG 59.127 34.615 0.00 0.00 46.76 2.74
508 527 6.873605 GGCTTTCTGGCATTTTAAATTAGTGT 59.126 34.615 0.00 0.00 41.37 3.55
510 529 7.598493 GCTTTCTGGCATTTTAAATTAGTGTGA 59.402 33.333 0.00 0.00 0.00 3.58
511 530 9.643693 CTTTCTGGCATTTTAAATTAGTGTGAT 57.356 29.630 0.00 0.00 0.00 3.06
512 531 9.995003 TTTCTGGCATTTTAAATTAGTGTGATT 57.005 25.926 0.00 0.00 0.00 2.57
562 601 6.568869 AGATTAGAGCAATCCGTAGCATATC 58.431 40.000 0.00 0.00 43.63 1.63
573 612 3.191581 CCGTAGCATATCCTGTACTGGAG 59.808 52.174 23.78 13.29 39.78 3.86
592 631 2.216046 AGTGCTGGATATGCGTCAATG 58.784 47.619 0.00 0.00 0.00 2.82
663 705 2.874086 ACTTTTGGGTGTACGTAGCAAC 59.126 45.455 0.00 0.00 0.00 4.17
809 864 4.261994 GCTCCAGTTTTGGCACTAAATCAA 60.262 41.667 0.00 0.00 44.63 2.57
824 879 7.486232 GCACTAAATCAATTTTTACTCAGAGCC 59.514 37.037 0.00 0.00 0.00 4.70
936 1007 6.762661 CACAAATCCAAGAAAACCAACAAGAT 59.237 34.615 0.00 0.00 0.00 2.40
1004 1122 2.831333 CAAGAGGTAGCTAGCCATGTG 58.169 52.381 19.06 8.86 0.00 3.21
1021 1139 0.618968 GTGTCCCTCCCCTGATCTGT 60.619 60.000 0.00 0.00 0.00 3.41
1111 1231 2.896168 TCGTCGGTGAGTTTCTTGTTT 58.104 42.857 0.00 0.00 0.00 2.83
1128 1248 6.855836 TCTTGTTTCATCACTTTATCCATGC 58.144 36.000 0.00 0.00 0.00 4.06
1143 1263 2.275380 ATGCCGGAAAGGTGTTGGC 61.275 57.895 5.05 0.00 45.91 4.52
1163 1299 1.603456 TTCGTTGGAAGAATGCTGCA 58.397 45.000 4.13 4.13 0.00 4.41
1168 1304 3.365820 CGTTGGAAGAATGCTGCAATTTC 59.634 43.478 6.36 7.18 0.00 2.17
1169 1305 4.563061 GTTGGAAGAATGCTGCAATTTCT 58.437 39.130 6.36 9.63 0.00 2.52
1170 1306 4.182693 TGGAAGAATGCTGCAATTTCTG 57.817 40.909 16.70 0.00 30.41 3.02
1171 1307 3.827876 TGGAAGAATGCTGCAATTTCTGA 59.172 39.130 16.70 4.56 30.41 3.27
1172 1308 4.171754 GGAAGAATGCTGCAATTTCTGAC 58.828 43.478 16.70 13.71 30.41 3.51
1173 1309 3.482722 AGAATGCTGCAATTTCTGACG 57.517 42.857 15.59 0.00 0.00 4.35
1174 1310 2.816087 AGAATGCTGCAATTTCTGACGT 59.184 40.909 15.59 0.00 0.00 4.34
1175 1311 3.254166 AGAATGCTGCAATTTCTGACGTT 59.746 39.130 15.59 0.00 0.00 3.99
1176 1312 3.648339 ATGCTGCAATTTCTGACGTTT 57.352 38.095 6.36 0.00 0.00 3.60
1177 1313 2.998772 TGCTGCAATTTCTGACGTTTC 58.001 42.857 0.00 0.00 0.00 2.78
1181 1317 4.549458 CTGCAATTTCTGACGTTTCCATT 58.451 39.130 0.00 0.00 0.00 3.16
1215 1351 0.104620 AGTACCACCTGGACCTGGTT 60.105 55.000 19.89 9.84 41.28 3.67
1305 1441 4.155733 CCCATCCACGGCGTGCTA 62.156 66.667 33.15 23.12 31.34 3.49
1968 2110 1.214305 TGGCATACCAGGGGAAGCTT 61.214 55.000 0.00 0.00 42.67 3.74
2046 2194 0.819259 AAGTGGAGAAGCAGCGCAAA 60.819 50.000 11.47 0.00 0.00 3.68
2049 2197 0.034756 TGGAGAAGCAGCGCAAAGTA 59.965 50.000 11.47 0.00 0.00 2.24
2052 2200 2.162408 GGAGAAGCAGCGCAAAGTAATT 59.838 45.455 11.47 0.00 0.00 1.40
2184 2332 3.923864 TCCAACACGGCGCTGAGT 61.924 61.111 25.98 19.66 33.14 3.41
2391 2539 2.048222 CTCGACGCCAAGCTCCAA 60.048 61.111 0.00 0.00 0.00 3.53
2463 2633 5.105063 GCTTGCTTGGTTCATAAGAAATCC 58.895 41.667 0.00 0.00 35.08 3.01
2469 2639 6.588719 TTGGTTCATAAGAAATCCAAGTGG 57.411 37.500 0.10 0.00 35.90 4.00
2493 2663 6.154445 GTGCATGGCATCCTGAATTAATTAG 58.846 40.000 0.00 0.00 41.91 1.73
2792 3047 8.944029 ACAATATGTTTCTTCTGATGTTCTCTG 58.056 33.333 0.00 0.00 0.00 3.35
2817 3117 9.407380 TGTGCTACCTTGACAATTGATAAATAT 57.593 29.630 13.59 0.00 0.00 1.28
2983 3455 1.063616 CATCTGCATGACGCCAGAAAG 59.936 52.381 0.00 0.00 41.33 2.62
3144 4251 2.013286 AAATGCACGAACGAACGAAC 57.987 45.000 11.97 5.07 37.03 3.95
3145 4252 0.111442 AATGCACGAACGAACGAACG 60.111 50.000 11.97 8.41 37.03 3.95
3146 4253 0.935831 ATGCACGAACGAACGAACGA 60.936 50.000 18.31 3.82 37.03 3.85
3266 4405 2.124942 GGTGCAGCCCAGAGTAGC 60.125 66.667 4.03 0.00 0.00 3.58
3280 4419 0.608640 AGTAGCGTAGGCAGCACTTT 59.391 50.000 10.48 0.00 43.41 2.66
3281 4420 1.822990 AGTAGCGTAGGCAGCACTTTA 59.177 47.619 10.48 0.00 43.41 1.85
3284 4423 2.711542 AGCGTAGGCAGCACTTTATTT 58.288 42.857 10.48 0.00 43.41 1.40
3285 4424 3.081804 AGCGTAGGCAGCACTTTATTTT 58.918 40.909 10.48 0.00 43.41 1.82
3286 4425 3.127030 AGCGTAGGCAGCACTTTATTTTC 59.873 43.478 10.48 0.00 43.41 2.29
3356 4495 2.696125 ATGGGAATGGGCCGGACT 60.696 61.111 7.57 0.00 0.00 3.85
3357 4496 2.965716 GATGGGAATGGGCCGGACTG 62.966 65.000 7.57 0.00 0.00 3.51
3358 4497 4.506255 GGGAATGGGCCGGACTGG 62.506 72.222 7.57 0.00 42.50 4.00
3367 4506 4.609098 CCGGACTGGCCTCTCTAT 57.391 61.111 3.32 0.00 0.00 1.98
3368 4507 2.827715 CCGGACTGGCCTCTCTATT 58.172 57.895 3.32 0.00 0.00 1.73
3369 4508 0.676736 CCGGACTGGCCTCTCTATTC 59.323 60.000 3.32 0.00 0.00 1.75
3370 4509 1.698506 CGGACTGGCCTCTCTATTCT 58.301 55.000 3.32 0.00 0.00 2.40
3371 4510 1.611491 CGGACTGGCCTCTCTATTCTC 59.389 57.143 3.32 0.00 0.00 2.87
3372 4511 2.751479 CGGACTGGCCTCTCTATTCTCT 60.751 54.545 3.32 0.00 0.00 3.10
3373 4512 3.304829 GGACTGGCCTCTCTATTCTCTT 58.695 50.000 3.32 0.00 0.00 2.85
3374 4513 3.069443 GGACTGGCCTCTCTATTCTCTTG 59.931 52.174 3.32 0.00 0.00 3.02
3375 4514 3.957497 GACTGGCCTCTCTATTCTCTTGA 59.043 47.826 3.32 0.00 0.00 3.02
3376 4515 3.960102 ACTGGCCTCTCTATTCTCTTGAG 59.040 47.826 3.32 0.00 0.00 3.02
3377 4516 3.303938 TGGCCTCTCTATTCTCTTGAGG 58.696 50.000 3.32 0.00 45.05 3.86
3378 4517 2.632512 GGCCTCTCTATTCTCTTGAGGG 59.367 54.545 0.00 0.00 43.15 4.30
3379 4518 3.571590 GCCTCTCTATTCTCTTGAGGGA 58.428 50.000 9.05 0.00 43.15 4.20
3380 4519 4.159557 GCCTCTCTATTCTCTTGAGGGAT 58.840 47.826 9.05 0.00 43.15 3.85
3381 4520 4.220602 GCCTCTCTATTCTCTTGAGGGATC 59.779 50.000 9.05 0.00 43.15 3.36
3382 4521 5.392995 CCTCTCTATTCTCTTGAGGGATCA 58.607 45.833 0.00 0.00 40.25 2.92
3383 4522 6.018469 CCTCTCTATTCTCTTGAGGGATCAT 58.982 44.000 0.00 0.00 40.25 2.45
3384 4523 6.071221 CCTCTCTATTCTCTTGAGGGATCATG 60.071 46.154 0.00 0.00 40.25 3.07
3385 4524 5.779260 TCTCTATTCTCTTGAGGGATCATGG 59.221 44.000 0.00 0.00 0.00 3.66
3386 4525 5.720162 TCTATTCTCTTGAGGGATCATGGA 58.280 41.667 0.00 0.00 0.00 3.41
3387 4526 4.978438 ATTCTCTTGAGGGATCATGGAG 57.022 45.455 0.00 0.00 0.00 3.86
3388 4527 2.045524 TCTCTTGAGGGATCATGGAGC 58.954 52.381 0.00 0.00 0.00 4.70
3389 4528 1.767088 CTCTTGAGGGATCATGGAGCA 59.233 52.381 0.00 0.00 0.00 4.26
3390 4529 2.372504 CTCTTGAGGGATCATGGAGCAT 59.627 50.000 0.00 0.00 0.00 3.79
3391 4530 2.781757 TCTTGAGGGATCATGGAGCATT 59.218 45.455 0.00 0.00 0.00 3.56
3392 4531 2.651382 TGAGGGATCATGGAGCATTG 57.349 50.000 0.00 0.00 0.00 2.82
3393 4532 1.144298 TGAGGGATCATGGAGCATTGG 59.856 52.381 0.00 0.00 0.00 3.16
3394 4533 1.422781 GAGGGATCATGGAGCATTGGA 59.577 52.381 0.00 0.00 0.00 3.53
3395 4534 1.854939 AGGGATCATGGAGCATTGGAA 59.145 47.619 0.00 0.00 0.00 3.53
3396 4535 1.959282 GGGATCATGGAGCATTGGAAC 59.041 52.381 0.00 0.00 0.00 3.62
3397 4536 1.959282 GGATCATGGAGCATTGGAACC 59.041 52.381 0.00 0.00 0.00 3.62
3398 4537 1.605710 GATCATGGAGCATTGGAACCG 59.394 52.381 0.00 0.00 0.00 4.44
3399 4538 0.394216 TCATGGAGCATTGGAACCGG 60.394 55.000 0.00 0.00 0.00 5.28
3400 4539 1.754234 ATGGAGCATTGGAACCGGC 60.754 57.895 0.00 0.00 0.00 6.13
3401 4540 3.140814 GGAGCATTGGAACCGGCC 61.141 66.667 0.00 0.00 0.00 6.13
3402 4541 3.140814 GAGCATTGGAACCGGCCC 61.141 66.667 0.00 3.39 0.00 5.80
3403 4542 3.936772 GAGCATTGGAACCGGCCCA 62.937 63.158 11.76 11.76 0.00 5.36
3404 4543 2.994417 GCATTGGAACCGGCCCAA 60.994 61.111 25.37 25.37 46.48 4.12
3408 4547 2.080201 TTGGAACCGGCCCAATAGT 58.920 52.632 21.11 0.00 38.64 2.12
3409 4548 0.034863 TTGGAACCGGCCCAATAGTC 60.035 55.000 21.11 0.00 38.64 2.59
3410 4549 1.153025 GGAACCGGCCCAATAGTCC 60.153 63.158 0.00 0.00 0.00 3.85
3411 4550 1.605453 GAACCGGCCCAATAGTCCA 59.395 57.895 0.00 0.00 0.00 4.02
3412 4551 0.182775 GAACCGGCCCAATAGTCCAT 59.817 55.000 0.00 0.00 0.00 3.41
3413 4552 0.182775 AACCGGCCCAATAGTCCATC 59.817 55.000 0.00 0.00 0.00 3.51
3414 4553 1.073199 CCGGCCCAATAGTCCATCC 59.927 63.158 0.00 0.00 0.00 3.51
3415 4554 1.705002 CCGGCCCAATAGTCCATCCA 61.705 60.000 0.00 0.00 0.00 3.41
3416 4555 0.182537 CGGCCCAATAGTCCATCCAA 59.817 55.000 0.00 0.00 0.00 3.53
3417 4556 1.692411 GGCCCAATAGTCCATCCAAC 58.308 55.000 0.00 0.00 0.00 3.77
3418 4557 1.215423 GGCCCAATAGTCCATCCAACT 59.785 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 80 2.492881 CTGCATGTGATTTACCTGCCAA 59.507 45.455 6.42 0.00 46.49 4.52
145 148 9.686683 CTAATATGCTAGCCCATTATTTACCTT 57.313 33.333 13.29 0.00 0.00 3.50
175 178 7.563020 TCAATGAATTGCAATGGGCTATAAAA 58.437 30.769 13.82 0.00 45.15 1.52
235 238 9.722056 CATCTATCAAGTTTAAACAATGGCTAC 57.278 33.333 20.06 0.00 0.00 3.58
250 253 2.374504 CAGCCCCCATCATCTATCAAGT 59.625 50.000 0.00 0.00 0.00 3.16
252 255 2.641321 CTCAGCCCCCATCATCTATCAA 59.359 50.000 0.00 0.00 0.00 2.57
253 256 2.263545 CTCAGCCCCCATCATCTATCA 58.736 52.381 0.00 0.00 0.00 2.15
254 257 2.264455 ACTCAGCCCCCATCATCTATC 58.736 52.381 0.00 0.00 0.00 2.08
255 258 2.429933 ACTCAGCCCCCATCATCTAT 57.570 50.000 0.00 0.00 0.00 1.98
257 260 1.221523 TCTACTCAGCCCCCATCATCT 59.778 52.381 0.00 0.00 0.00 2.90
258 261 1.622811 CTCTACTCAGCCCCCATCATC 59.377 57.143 0.00 0.00 0.00 2.92
259 262 1.727062 CTCTACTCAGCCCCCATCAT 58.273 55.000 0.00 0.00 0.00 2.45
266 270 0.250513 CACCAACCTCTACTCAGCCC 59.749 60.000 0.00 0.00 0.00 5.19
382 392 7.478721 TGTCAGGTATTCTATGGATCTGGATA 58.521 38.462 0.00 0.00 0.00 2.59
393 403 8.298140 GCTTATAGTCGTTGTCAGGTATTCTAT 58.702 37.037 0.00 0.00 0.00 1.98
399 409 4.703575 AGTGCTTATAGTCGTTGTCAGGTA 59.296 41.667 0.00 0.00 0.00 3.08
404 414 4.106029 TCCAGTGCTTATAGTCGTTGTC 57.894 45.455 0.00 0.00 0.00 3.18
405 415 3.676324 GCTCCAGTGCTTATAGTCGTTGT 60.676 47.826 0.00 0.00 0.00 3.32
406 416 2.860735 GCTCCAGTGCTTATAGTCGTTG 59.139 50.000 0.00 0.00 0.00 4.10
407 417 2.496070 TGCTCCAGTGCTTATAGTCGTT 59.504 45.455 0.00 0.00 0.00 3.85
408 418 2.100197 TGCTCCAGTGCTTATAGTCGT 58.900 47.619 0.00 0.00 0.00 4.34
431 447 7.316544 AGATGAACTTTAAGTTTGTGTTCGT 57.683 32.000 11.88 0.00 38.80 3.85
444 460 9.174166 GGCTCTATTTGGTTTAGATGAACTTTA 57.826 33.333 0.00 0.00 0.00 1.85
458 474 3.826729 GTCAACTTTGGGCTCTATTTGGT 59.173 43.478 0.00 0.00 0.00 3.67
503 519 4.979335 TCCCACAATGACAAATCACACTA 58.021 39.130 0.00 0.00 37.79 2.74
507 526 5.183713 TCTTCATCCCACAATGACAAATCAC 59.816 40.000 0.00 0.00 37.79 3.06
508 527 5.183713 GTCTTCATCCCACAATGACAAATCA 59.816 40.000 0.00 0.00 39.83 2.57
510 529 5.184479 CAGTCTTCATCCCACAATGACAAAT 59.816 40.000 0.00 0.00 35.44 2.32
511 530 4.520111 CAGTCTTCATCCCACAATGACAAA 59.480 41.667 0.00 0.00 35.44 2.83
512 531 4.074259 CAGTCTTCATCCCACAATGACAA 58.926 43.478 0.00 0.00 35.44 3.18
562 601 1.198713 ATCCAGCACTCCAGTACAGG 58.801 55.000 0.00 0.00 0.00 4.00
573 612 2.032549 GTCATTGACGCATATCCAGCAC 60.033 50.000 0.13 0.00 0.00 4.40
809 864 5.441718 TCATCCTGGCTCTGAGTAAAAAT 57.558 39.130 6.53 0.00 0.00 1.82
824 879 6.204301 AGCAATCTTATCACGAAATCATCCTG 59.796 38.462 0.00 0.00 0.00 3.86
936 1007 0.174845 GATCAATGGTCGGTCGGTGA 59.825 55.000 0.00 0.00 0.00 4.02
1004 1122 1.051556 GGACAGATCAGGGGAGGGAC 61.052 65.000 0.00 0.00 0.00 4.46
1111 1231 2.437651 TCCGGCATGGATAAAGTGATGA 59.562 45.455 0.00 0.00 43.74 2.92
1128 1248 1.852067 CGAAGCCAACACCTTTCCGG 61.852 60.000 0.00 0.00 39.35 5.14
1135 1255 0.310854 CTTCCAACGAAGCCAACACC 59.689 55.000 0.00 0.00 39.21 4.16
1143 1263 1.536766 TGCAGCATTCTTCCAACGAAG 59.463 47.619 0.00 0.00 45.96 3.79
1162 1298 6.621737 CATCAATGGAAACGTCAGAAATTG 57.378 37.500 0.00 0.00 0.00 2.32
1181 1317 1.131638 GTACTCCCCTGCATCCATCA 58.868 55.000 0.00 0.00 0.00 3.07
1380 1519 4.527583 GCCTCGAGCTGCTCCTGG 62.528 72.222 22.97 23.08 38.99 4.45
1425 1564 2.525629 TTCTCGTGGTCCAGGGCA 60.526 61.111 11.60 0.00 0.00 5.36
1429 1568 0.528470 GAGTCCTTCTCGTGGTCCAG 59.472 60.000 0.00 0.00 33.25 3.86
1782 1924 2.278857 CCTTCGATCAGGCCGTCG 60.279 66.667 18.27 18.27 39.11 5.12
1815 1957 3.945304 CTCGCCGGGGTTGTACACC 62.945 68.421 19.13 0.02 46.46 4.16
1817 1959 3.697747 CCTCGCCGGGGTTGTACA 61.698 66.667 19.13 0.00 0.00 2.90
2046 2194 1.153429 GACGCTCCGCCCAATTACT 60.153 57.895 0.00 0.00 0.00 2.24
2049 2197 2.125106 GAGACGCTCCGCCCAATT 60.125 61.111 0.00 0.00 0.00 2.32
2131 2279 4.324991 GGCGTCAAGGTCCCCGTT 62.325 66.667 0.00 0.00 0.00 4.44
2158 2306 2.738521 CGTGTTGGACGCCAGGAG 60.739 66.667 0.00 0.00 42.21 3.69
2169 2317 2.967076 ACACTCAGCGCCGTGTTG 60.967 61.111 18.38 4.71 41.24 3.33
2184 2332 2.357881 CGCTTCTCCTGCTGCACA 60.358 61.111 0.00 0.00 0.00 4.57
2292 2440 2.598045 CGACATCTTCGCCATGAGG 58.402 57.895 0.00 0.00 41.87 3.86
2463 2633 0.968901 AGGATGCCATGCACCACTTG 60.969 55.000 0.00 0.00 43.04 3.16
2466 2636 0.966875 TTCAGGATGCCATGCACCAC 60.967 55.000 0.00 0.00 43.04 4.16
2469 2639 4.595762 ATTAATTCAGGATGCCATGCAC 57.404 40.909 0.00 0.00 43.04 4.57
2493 2663 1.739466 ACATGCATCAACATCACGGTC 59.261 47.619 0.00 0.00 0.00 4.79
2773 3028 4.754114 AGCACAGAGAACATCAGAAGAAAC 59.246 41.667 0.00 0.00 0.00 2.78
2983 3455 3.552890 CCAAAAACTTTGCTACTGCTCCC 60.553 47.826 0.00 0.00 40.48 4.30
3261 4400 0.608640 AAAGTGCTGCCTACGCTACT 59.391 50.000 0.00 0.00 35.36 2.57
3266 4405 4.946784 AGAAAATAAAGTGCTGCCTACG 57.053 40.909 0.00 0.00 0.00 3.51
3280 4419 6.039493 TGCCTACGTTTTGGTCAAAGAAAATA 59.961 34.615 0.00 0.00 0.00 1.40
3281 4420 5.163499 TGCCTACGTTTTGGTCAAAGAAAAT 60.163 36.000 0.00 0.00 0.00 1.82
3284 4423 3.280295 TGCCTACGTTTTGGTCAAAGAA 58.720 40.909 0.00 0.00 0.00 2.52
3285 4424 2.875933 CTGCCTACGTTTTGGTCAAAGA 59.124 45.455 0.00 0.00 0.00 2.52
3286 4425 2.604614 GCTGCCTACGTTTTGGTCAAAG 60.605 50.000 0.00 0.00 0.00 2.77
3356 4495 3.303938 CCTCAAGAGAATAGAGAGGCCA 58.696 50.000 5.01 0.00 39.39 5.36
3357 4496 2.632512 CCCTCAAGAGAATAGAGAGGCC 59.367 54.545 0.00 0.00 43.51 5.19
3358 4497 3.571590 TCCCTCAAGAGAATAGAGAGGC 58.428 50.000 0.00 0.00 43.51 4.70
3359 4498 5.392995 TGATCCCTCAAGAGAATAGAGAGG 58.607 45.833 0.00 0.00 44.26 3.69
3360 4499 6.071221 CCATGATCCCTCAAGAGAATAGAGAG 60.071 46.154 0.00 0.00 34.37 3.20
3361 4500 5.779260 CCATGATCCCTCAAGAGAATAGAGA 59.221 44.000 0.00 0.00 34.37 3.10
3362 4501 5.779260 TCCATGATCCCTCAAGAGAATAGAG 59.221 44.000 0.00 0.00 34.37 2.43
3363 4502 5.720162 TCCATGATCCCTCAAGAGAATAGA 58.280 41.667 0.00 0.00 34.37 1.98
3364 4503 5.569227 GCTCCATGATCCCTCAAGAGAATAG 60.569 48.000 0.00 0.00 37.75 1.73
3365 4504 4.285517 GCTCCATGATCCCTCAAGAGAATA 59.714 45.833 0.00 0.00 37.75 1.75
3366 4505 3.072768 GCTCCATGATCCCTCAAGAGAAT 59.927 47.826 0.00 0.00 37.75 2.40
3367 4506 2.437281 GCTCCATGATCCCTCAAGAGAA 59.563 50.000 0.00 0.00 37.75 2.87
3368 4507 2.045524 GCTCCATGATCCCTCAAGAGA 58.954 52.381 0.00 0.00 37.75 3.10
3369 4508 1.767088 TGCTCCATGATCCCTCAAGAG 59.233 52.381 0.00 0.00 38.21 2.85
3370 4509 1.883678 TGCTCCATGATCCCTCAAGA 58.116 50.000 0.00 0.00 34.37 3.02
3371 4510 2.885266 CAATGCTCCATGATCCCTCAAG 59.115 50.000 0.00 0.00 34.37 3.02
3372 4511 2.423803 CCAATGCTCCATGATCCCTCAA 60.424 50.000 0.00 0.00 34.37 3.02
3373 4512 1.144298 CCAATGCTCCATGATCCCTCA 59.856 52.381 0.00 0.00 35.41 3.86
3374 4513 1.422781 TCCAATGCTCCATGATCCCTC 59.577 52.381 0.00 0.00 0.00 4.30
3375 4514 1.526315 TCCAATGCTCCATGATCCCT 58.474 50.000 0.00 0.00 0.00 4.20
3376 4515 1.959282 GTTCCAATGCTCCATGATCCC 59.041 52.381 0.00 0.00 0.00 3.85
3377 4516 1.959282 GGTTCCAATGCTCCATGATCC 59.041 52.381 0.00 0.00 0.00 3.36
3378 4517 1.605710 CGGTTCCAATGCTCCATGATC 59.394 52.381 0.00 0.00 0.00 2.92
3379 4518 1.683943 CGGTTCCAATGCTCCATGAT 58.316 50.000 0.00 0.00 0.00 2.45
3380 4519 0.394216 CCGGTTCCAATGCTCCATGA 60.394 55.000 0.00 0.00 0.00 3.07
3381 4520 2.008268 GCCGGTTCCAATGCTCCATG 62.008 60.000 1.90 0.00 0.00 3.66
3382 4521 1.754234 GCCGGTTCCAATGCTCCAT 60.754 57.895 1.90 0.00 0.00 3.41
3383 4522 2.361104 GCCGGTTCCAATGCTCCA 60.361 61.111 1.90 0.00 0.00 3.86
3384 4523 3.140814 GGCCGGTTCCAATGCTCC 61.141 66.667 1.90 0.00 0.00 4.70
3385 4524 3.140814 GGGCCGGTTCCAATGCTC 61.141 66.667 1.90 0.00 0.00 4.26
3386 4525 3.521765 TTGGGCCGGTTCCAATGCT 62.522 57.895 21.95 0.00 39.15 3.79
3387 4526 2.994417 TTGGGCCGGTTCCAATGC 60.994 61.111 21.95 0.00 39.15 3.56
3390 4529 0.034863 GACTATTGGGCCGGTTCCAA 60.035 55.000 25.89 25.89 46.78 3.53
3391 4530 1.605453 GACTATTGGGCCGGTTCCA 59.395 57.895 13.50 13.50 0.00 3.53
3392 4531 1.153025 GGACTATTGGGCCGGTTCC 60.153 63.158 1.90 6.13 30.75 3.62
3393 4532 4.553668 GGACTATTGGGCCGGTTC 57.446 61.111 1.90 0.00 30.75 3.62
3398 4537 1.215423 AGTTGGATGGACTATTGGGCC 59.785 52.381 0.00 0.00 45.52 5.80
3399 4538 2.736670 AGTTGGATGGACTATTGGGC 57.263 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.