Multiple sequence alignment - TraesCS7A01G342000

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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 TraesCS7A01G342000 chr7A 100.000 3331 0 0 659 3989 501973896 501977226 0.000000e+00 6152.0
1 TraesCS7A01G342000 chr7A 100.000 494 0 0 1 494 501973238 501973731 0.000000e+00 913.0
2 TraesCS7A01G342000 chr7D 93.828 3354 153 20 679 3989 430929144 430925802 0.000000e+00 4998.0
3 TraesCS7A01G342000 chr7B 93.758 3092 134 25 926 3989 448344780 448341720 0.000000e+00 4586.0
4 TraesCS7A01G342000 chr7B 90.317 568 35 5 1822 2388 623463257 623463805 0.000000e+00 726.0
5 TraesCS7A01G342000 chr7B 95.979 373 14 1 2712 3083 623471443 623471071 4.410000e-169 604.0
6 TraesCS7A01G342000 chr7B 95.926 270 11 0 2119 2388 623265392 623265661 4.730000e-119 438.0
7 TraesCS7A01G342000 chr7B 91.941 273 20 2 1822 2093 623264912 623265183 8.090000e-102 381.0
8 TraesCS7A01G342000 chr7B 84.169 379 51 5 20 397 448345765 448345395 3.790000e-95 359.0
9 TraesCS7A01G342000 chr7B 95.928 221 8 1 2864 3083 623266487 623266267 1.360000e-94 357.0
10 TraesCS7A01G342000 chr7B 92.063 252 18 1 2379 2628 623470221 623470472 1.760000e-93 353.0
11 TraesCS7A01G342000 chr7B 95.541 157 7 0 2712 2868 623267973 623267817 6.620000e-63 252.0
12 TraesCS7A01G342000 chr1B 94.595 814 37 1 1822 2628 122922065 122922878 0.000000e+00 1253.0
13 TraesCS7A01G342000 chr1B 95.467 375 14 2 2712 3083 122923854 122923480 2.650000e-166 595.0
14 TraesCS7A01G342000 chr2B 71.803 610 112 54 1349 1928 791471278 791471857 7.000000e-23 119.0
15 TraesCS7A01G342000 chr2D 75.342 219 38 14 1718 1928 644375174 644374964 1.530000e-14 91.6
16 TraesCS7A01G342000 chr2A 75.000 220 37 16 1718 1928 769501509 769501299 7.100000e-13 86.1


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 TraesCS7A01G342000 chr7A 501973238 501977226 3988 False 3532.5 6152 100.0000 1 3989 2 chr7A.!!$F1 3988
1 TraesCS7A01G342000 chr7D 430925802 430929144 3342 True 4998.0 4998 93.8280 679 3989 1 chr7D.!!$R1 3310
2 TraesCS7A01G342000 chr7B 448341720 448345765 4045 True 2472.5 4586 88.9635 20 3989 2 chr7B.!!$R2 3969
3 TraesCS7A01G342000 chr7B 623463257 623463805 548 False 726.0 726 90.3170 1822 2388 1 chr7B.!!$F1 566
4 TraesCS7A01G342000 chr7B 623264912 623265661 749 False 409.5 438 93.9335 1822 2388 2 chr7B.!!$F3 566
5 TraesCS7A01G342000 chr7B 623266267 623267973 1706 True 304.5 357 95.7345 2712 3083 2 chr7B.!!$R3 371
6 TraesCS7A01G342000 chr1B 122922065 122922878 813 False 1253.0 1253 94.5950 1822 2628 1 chr1B.!!$F1 806

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
820 894 0.107643 TGTGTGAGGTGATTGCGGAA 59.892 50.0 0.00 0.0 0.00 4.30 F
1189 1297 0.243907 CGACGAGTCTTCACCACCAT 59.756 55.0 1.56 0.0 0.00 3.55 F
2241 2550 0.390472 CCAACTTCCTCGAGGCTGTC 60.390 60.0 27.39 0.0 34.44 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 2920 0.371645 GCGCGAAGGAACTGATGAAG 59.628 55.000 12.1 0.0 40.86 3.02 R
2685 3001 1.987855 CCGGGACAGGAAGTAGCCA 60.988 63.158 0.0 0.0 0.00 4.75 R
3781 5465 0.318762 GCTCAAGGAGAACGACAGGT 59.681 55.000 0.0 0.0 0.00 4.00 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
18 19 3.662290 GTGATAGTGGGTTGGGCAA 57.338 52.632 0.00 0.00 0.00 4.52
23 24 0.183014 TAGTGGGTTGGGCAACGAAA 59.817 50.000 0.00 0.00 42.02 3.46
27 28 0.391228 GGGTTGGGCAACGAAAATGT 59.609 50.000 0.00 0.00 42.02 2.71
28 29 1.604438 GGGTTGGGCAACGAAAATGTC 60.604 52.381 0.00 0.00 42.02 3.06
112 114 6.525629 CCTATAGGTAGACCCATGAGTTTTG 58.474 44.000 10.96 0.00 36.42 2.44
114 116 2.092323 GGTAGACCCATGAGTTTTGCC 58.908 52.381 0.00 0.00 0.00 4.52
123 125 4.202080 CCCATGAGTTTTGCCACATCTATG 60.202 45.833 0.00 0.00 0.00 2.23
128 130 6.422333 TGAGTTTTGCCACATCTATGGATAA 58.578 36.000 0.00 0.00 43.02 1.75
136 138 7.688343 TGCCACATCTATGGATAAATCATACA 58.312 34.615 0.00 0.00 43.02 2.29
155 157 8.755696 TCATACAAAATTAAAGTTGCATGACC 57.244 30.769 10.94 0.00 34.22 4.02
160 162 7.385752 ACAAAATTAAAGTTGCATGACCAGATG 59.614 33.333 0.00 0.00 0.00 2.90
164 166 1.108776 GTTGCATGACCAGATGGCAT 58.891 50.000 0.00 0.00 39.32 4.40
183 185 5.130145 TGGCATATTATTGTTGGAAAAGGGG 59.870 40.000 0.00 0.00 0.00 4.79
186 188 6.098266 GCATATTATTGTTGGAAAAGGGGAGT 59.902 38.462 0.00 0.00 0.00 3.85
205 207 0.251297 TGGAAGTGAGCCCACAATGG 60.251 55.000 0.00 0.00 45.54 3.16
217 219 2.503356 CCCACAATGGAACTCTAGAGCT 59.497 50.000 19.97 7.64 40.96 4.09
230 232 7.450323 GGAACTCTAGAGCTATTAATGAGAGGT 59.550 40.741 19.97 3.12 34.55 3.85
238 240 6.143915 AGCTATTAATGAGAGGTTAGTGGGA 58.856 40.000 0.00 0.00 0.00 4.37
245 247 4.906618 TGAGAGGTTAGTGGGAATTTGAC 58.093 43.478 0.00 0.00 0.00 3.18
246 248 4.597507 TGAGAGGTTAGTGGGAATTTGACT 59.402 41.667 0.00 0.00 0.00 3.41
256 258 5.826208 AGTGGGAATTTGACTCGTAAGTTTT 59.174 36.000 0.00 0.00 35.28 2.43
260 262 5.844396 GGAATTTGACTCGTAAGTTTTCACG 59.156 40.000 0.00 0.00 35.28 4.35
262 264 5.379757 TTTGACTCGTAAGTTTTCACGTC 57.620 39.130 0.00 0.00 39.18 4.34
298 300 4.584743 CCTTAGGTTTAGCCCCATTCAATC 59.415 45.833 0.00 0.00 38.26 2.67
305 307 1.025041 GCCCCATTCAATCTTCGTCC 58.975 55.000 0.00 0.00 0.00 4.79
306 308 1.680338 CCCCATTCAATCTTCGTCCC 58.320 55.000 0.00 0.00 0.00 4.46
307 309 1.680338 CCCATTCAATCTTCGTCCCC 58.320 55.000 0.00 0.00 0.00 4.81
308 310 1.064758 CCCATTCAATCTTCGTCCCCA 60.065 52.381 0.00 0.00 0.00 4.96
323 325 2.029020 GTCCCCATTGCACCTCTTTTTC 60.029 50.000 0.00 0.00 0.00 2.29
324 326 1.276138 CCCCATTGCACCTCTTTTTCC 59.724 52.381 0.00 0.00 0.00 3.13
325 327 1.276138 CCCATTGCACCTCTTTTTCCC 59.724 52.381 0.00 0.00 0.00 3.97
339 341 5.525199 TCTTTTTCCCGTTTGCTAAATGTC 58.475 37.500 0.00 0.00 0.00 3.06
345 347 2.552315 CCGTTTGCTAAATGTCAGGTGT 59.448 45.455 0.00 0.00 0.00 4.16
347 349 3.498397 CGTTTGCTAAATGTCAGGTGTCT 59.502 43.478 0.00 0.00 0.00 3.41
348 350 4.611355 CGTTTGCTAAATGTCAGGTGTCTG 60.611 45.833 0.00 0.00 42.21 3.51
362 364 4.827284 CAGGTGTCTGAACATTTTTAGGGT 59.173 41.667 0.00 0.00 43.49 4.34
366 368 5.298276 GTGTCTGAACATTTTTAGGGTGTCA 59.702 40.000 0.00 0.00 37.81 3.58
370 372 5.441500 TGAACATTTTTAGGGTGTCAGTCA 58.558 37.500 0.00 0.00 0.00 3.41
375 377 7.433680 ACATTTTTAGGGTGTCAGTCAATTTC 58.566 34.615 0.00 0.00 0.00 2.17
378 380 2.508526 AGGGTGTCAGTCAATTTCTGC 58.491 47.619 3.34 0.00 33.48 4.26
380 382 2.887152 GGGTGTCAGTCAATTTCTGCTT 59.113 45.455 3.34 0.00 33.48 3.91
383 385 5.351458 GGTGTCAGTCAATTTCTGCTTTTT 58.649 37.500 3.34 0.00 33.48 1.94
384 386 5.460091 GGTGTCAGTCAATTTCTGCTTTTTC 59.540 40.000 3.34 0.00 33.48 2.29
385 387 6.035843 GTGTCAGTCAATTTCTGCTTTTTCA 58.964 36.000 3.34 0.00 33.48 2.69
395 397 1.608590 CTGCTTTTTCAGAGGCCGAAA 59.391 47.619 0.00 0.00 36.19 3.46
397 399 1.667177 GCTTTTTCAGAGGCCGAAAGC 60.667 52.381 17.29 17.29 43.40 3.51
398 400 1.608590 CTTTTTCAGAGGCCGAAAGCA 59.391 47.619 0.00 0.00 46.50 3.91
400 402 0.108585 TTTCAGAGGCCGAAAGCAGT 59.891 50.000 0.00 0.00 46.50 4.40
402 404 1.004560 CAGAGGCCGAAAGCAGTGA 60.005 57.895 0.00 0.00 46.50 3.41
403 405 1.004440 AGAGGCCGAAAGCAGTGAC 60.004 57.895 0.00 0.00 46.50 3.67
404 406 2.357517 AGGCCGAAAGCAGTGACG 60.358 61.111 0.00 0.00 46.50 4.35
405 407 2.357034 GGCCGAAAGCAGTGACGA 60.357 61.111 0.00 0.00 46.50 4.20
406 408 2.383527 GGCCGAAAGCAGTGACGAG 61.384 63.158 0.00 0.00 46.50 4.18
407 409 1.372997 GCCGAAAGCAGTGACGAGA 60.373 57.895 0.00 0.00 42.97 4.04
425 447 4.208686 GTCGACCCTAGCAGGCCG 62.209 72.222 3.51 0.00 32.73 6.13
433 455 1.005037 CTAGCAGGCCGTGTTGTGA 60.005 57.895 0.00 0.00 0.00 3.58
436 458 2.477176 GCAGGCCGTGTTGTGAACA 61.477 57.895 0.00 0.00 39.52 3.18
440 462 1.299089 GCCGTGTTGTGAACAAGCC 60.299 57.895 0.00 0.00 44.16 4.35
441 463 1.010125 CCGTGTTGTGAACAAGCCG 60.010 57.895 0.00 2.26 44.16 5.52
442 464 1.433053 CCGTGTTGTGAACAAGCCGA 61.433 55.000 13.17 0.00 44.16 5.54
443 465 0.375454 CGTGTTGTGAACAAGCCGAA 59.625 50.000 8.09 0.00 44.16 4.30
444 466 1.594518 CGTGTTGTGAACAAGCCGAAG 60.595 52.381 8.09 0.00 44.16 3.79
445 467 0.380378 TGTTGTGAACAAGCCGAAGC 59.620 50.000 0.00 0.00 38.72 3.86
446 468 0.317854 GTTGTGAACAAGCCGAAGCC 60.318 55.000 0.00 0.00 41.25 4.35
447 469 1.781025 TTGTGAACAAGCCGAAGCCG 61.781 55.000 0.00 0.00 41.25 5.52
481 503 2.338500 GAAGCGACTCCGAAACTTGAT 58.662 47.619 0.00 0.00 38.22 2.57
482 504 1.714794 AGCGACTCCGAAACTTGATG 58.285 50.000 0.00 0.00 38.22 3.07
485 507 1.087501 GACTCCGAAACTTGATGGGC 58.912 55.000 0.00 0.00 0.00 5.36
487 509 0.673644 CTCCGAAACTTGATGGGCGT 60.674 55.000 0.00 0.00 0.00 5.68
488 510 0.953471 TCCGAAACTTGATGGGCGTG 60.953 55.000 0.00 0.00 0.00 5.34
490 512 1.883021 GAAACTTGATGGGCGTGGG 59.117 57.895 0.00 0.00 0.00 4.61
700 773 4.228567 TGAGGCCGCGTGTGACAA 62.229 61.111 4.92 0.00 0.00 3.18
740 814 1.691219 GGGGGATCCAAGCAGTTGA 59.309 57.895 15.23 0.00 35.46 3.18
795 869 7.777440 AGAAGAAAGAAAGGTTGAAGATGAACT 59.223 33.333 0.00 0.00 0.00 3.01
796 870 7.269477 AGAAAGAAAGGTTGAAGATGAACTG 57.731 36.000 0.00 0.00 0.00 3.16
797 871 6.830838 AGAAAGAAAGGTTGAAGATGAACTGT 59.169 34.615 0.00 0.00 0.00 3.55
798 872 6.382869 AAGAAAGGTTGAAGATGAACTGTG 57.617 37.500 0.00 0.00 0.00 3.66
799 873 5.440610 AGAAAGGTTGAAGATGAACTGTGT 58.559 37.500 0.00 0.00 0.00 3.72
800 874 5.529060 AGAAAGGTTGAAGATGAACTGTGTC 59.471 40.000 0.00 0.00 0.00 3.67
801 875 4.696479 AGGTTGAAGATGAACTGTGTCT 57.304 40.909 0.00 0.00 0.00 3.41
820 894 0.107643 TGTGTGAGGTGATTGCGGAA 59.892 50.000 0.00 0.00 0.00 4.30
829 903 2.083774 GTGATTGCGGAAGTTGGATGA 58.916 47.619 0.00 0.00 0.00 2.92
841 915 4.268687 GGATGATGATCCGACGGC 57.731 61.111 9.66 0.00 39.04 5.68
843 917 1.367471 GATGATGATCCGACGGCCA 59.633 57.895 9.66 10.14 0.00 5.36
844 918 0.249868 GATGATGATCCGACGGCCAA 60.250 55.000 9.66 0.00 0.00 4.52
890 966 3.572255 TGTTTTCACAAATAGGTGCTCCC 59.428 43.478 0.00 0.00 38.66 4.30
1030 1138 3.342377 TTCACCAACTTGTGACTGACA 57.658 42.857 0.00 0.00 44.55 3.58
1035 1143 0.546122 AACTTGTGACTGACAGGCCA 59.454 50.000 5.01 0.18 35.01 5.36
1136 1244 3.050339 CACCACAATGGCCACCAC 58.950 61.111 8.16 0.00 42.67 4.16
1189 1297 0.243907 CGACGAGTCTTCACCACCAT 59.756 55.000 1.56 0.00 0.00 3.55
1191 1299 1.546476 GACGAGTCTTCACCACCATCT 59.454 52.381 0.00 0.00 0.00 2.90
1218 1326 2.011349 CATGTACGAGCTAGCCGCG 61.011 63.158 21.63 21.63 45.59 6.46
1410 1518 1.875813 CACGCTGCTCGACATCCTC 60.876 63.158 5.98 0.00 41.67 3.71
1536 1644 3.108289 CTGTCGCTGCTCACCGTG 61.108 66.667 0.00 0.00 0.00 4.94
1743 1851 3.474570 GGGGTGCTCCTGCTCGAT 61.475 66.667 4.53 0.00 40.48 3.59
1887 1995 2.892425 GCCGTGGATTCGCTCCTG 60.892 66.667 5.59 0.00 45.21 3.86
2057 2165 2.221299 CCCCTGAACCCAAGTCGGA 61.221 63.158 0.00 0.00 36.56 4.55
2058 2166 1.758592 CCCTGAACCCAAGTCGGAA 59.241 57.895 0.00 0.00 36.56 4.30
2077 2185 4.389374 GGAACAAGATCTCACAACCAAGA 58.611 43.478 0.00 0.00 0.00 3.02
2166 2475 1.941975 TCGCGGATACATGAGTTCGTA 59.058 47.619 6.13 0.00 0.00 3.43
2241 2550 0.390472 CCAACTTCCTCGAGGCTGTC 60.390 60.000 27.39 0.00 34.44 3.51
2472 2781 0.750850 CGATGGTGTTCCTCCCGTAT 59.249 55.000 0.00 0.00 34.23 3.06
2604 2920 2.035442 GGCCAACTCCTTCGTGCTC 61.035 63.158 0.00 0.00 0.00 4.26
2685 3001 1.562783 CCGGGTTCTTCCTCTTCTCT 58.437 55.000 0.00 0.00 36.25 3.10
2700 3016 1.853963 TCTCTGGCTACTTCCTGTCC 58.146 55.000 0.00 0.00 0.00 4.02
3009 4659 4.999311 TGACCATTGATCGATCCATGAATC 59.001 41.667 30.94 26.47 33.19 2.52
3021 4671 2.034878 CCATGAATCTCGTCTCCTCCA 58.965 52.381 0.00 0.00 0.00 3.86
3100 4759 1.351430 GCTTCGTGCATGCGACAGTA 61.351 55.000 14.09 0.00 40.85 2.74
3153 4812 5.064325 CAGAGTGGTTAACCGGTAATTAAGC 59.936 44.000 19.65 13.59 39.41 3.09
3260 4919 8.837788 TTCTCTACATGCCATTGATTATACTG 57.162 34.615 0.00 0.00 0.00 2.74
3261 4920 8.193953 TCTCTACATGCCATTGATTATACTGA 57.806 34.615 0.00 0.00 0.00 3.41
3262 4921 8.819845 TCTCTACATGCCATTGATTATACTGAT 58.180 33.333 0.00 0.00 0.00 2.90
3330 5010 7.663081 GGCATGTGAGGAATTCTCTAATGATAA 59.337 37.037 5.23 0.00 42.86 1.75
3435 5115 2.994186 ATTTTGAATGCCTGGCCATC 57.006 45.000 17.53 14.53 0.00 3.51
3498 5179 3.146104 ACCTGGTCATTTGAAGTCCTG 57.854 47.619 0.00 0.00 0.00 3.86
3516 5197 7.365497 AGTCCTGGTCATCTTTTCAAATTTT 57.635 32.000 0.00 0.00 0.00 1.82
3568 5250 5.647658 TCCAACATCGCTTCATACAATCTTT 59.352 36.000 0.00 0.00 0.00 2.52
3627 5309 5.771469 TGTGCAATTTCAGTACTCCAATTG 58.229 37.500 21.88 21.88 38.91 2.32
3683 5366 6.949352 AGGTTATGATATTTCAGCCAACAG 57.051 37.500 8.97 0.00 34.73 3.16
3691 5374 8.347004 TGATATTTCAGCCAACAGACAATTAA 57.653 30.769 0.00 0.00 0.00 1.40
3775 5459 1.974265 TGACCACTGATCGGCAAAAA 58.026 45.000 0.00 0.00 0.00 1.94
3797 5481 2.751166 ATCACCTGTCGTTCTCCTTG 57.249 50.000 0.00 0.00 0.00 3.61
3811 5495 2.360483 TCTCCTTGAGCGCTTCTCTATG 59.640 50.000 13.26 0.00 42.38 2.23
3885 5573 6.314120 AGCCATTATACATTTATCCAAGGCA 58.686 36.000 0.00 0.00 39.60 4.75
3888 5576 7.309990 GCCATTATACATTTATCCAAGGCATGT 60.310 37.037 0.00 0.00 37.23 3.21
3902 5590 6.098124 TCCAAGGCATGTATTTTAATCCCAAG 59.902 38.462 0.00 0.00 0.00 3.61
3906 5594 5.507315 GGCATGTATTTTAATCCCAAGACGG 60.507 44.000 0.00 0.00 0.00 4.79
3907 5595 5.067283 GCATGTATTTTAATCCCAAGACGGT 59.933 40.000 0.00 0.00 0.00 4.83
3912 5600 4.914177 TTTAATCCCAAGACGGTAACCT 57.086 40.909 0.00 0.00 0.00 3.50
3919 5607 0.689055 AAGACGGTAACCTTGACCCC 59.311 55.000 0.00 0.00 32.95 4.95
3920 5608 1.079612 GACGGTAACCTTGACCCCG 60.080 63.158 0.00 0.00 44.06 5.73
3923 5611 1.606885 CGGTAACCTTGACCCCGCTA 61.607 60.000 0.00 0.00 32.95 4.26
3963 5656 3.570550 GGAGACGCTATATGGTGAACTCT 59.429 47.826 20.28 9.77 0.00 3.24
3982 5675 1.815003 CTTCTCAACCAATCACAGCCC 59.185 52.381 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.173913 GTTGCCCAACCCACTATCAC 58.826 55.000 0.00 0.00 35.36 3.06
1 2 0.322098 CGTTGCCCAACCCACTATCA 60.322 55.000 5.64 0.00 38.03 2.15
2 3 0.035820 TCGTTGCCCAACCCACTATC 60.036 55.000 5.64 0.00 38.03 2.08
3 4 0.402504 TTCGTTGCCCAACCCACTAT 59.597 50.000 5.64 0.00 38.03 2.12
4 5 0.183014 TTTCGTTGCCCAACCCACTA 59.817 50.000 5.64 0.00 38.03 2.74
5 6 0.684805 TTTTCGTTGCCCAACCCACT 60.685 50.000 5.64 0.00 38.03 4.00
6 7 0.391228 ATTTTCGTTGCCCAACCCAC 59.609 50.000 5.64 0.00 38.03 4.61
7 8 0.390860 CATTTTCGTTGCCCAACCCA 59.609 50.000 5.64 0.00 38.03 4.51
8 9 0.391228 ACATTTTCGTTGCCCAACCC 59.609 50.000 5.64 0.00 38.03 4.11
9 10 1.604438 GGACATTTTCGTTGCCCAACC 60.604 52.381 5.64 0.00 38.03 3.77
10 11 1.778334 GGACATTTTCGTTGCCCAAC 58.222 50.000 1.12 1.12 37.92 3.77
11 12 0.312416 CGGACATTTTCGTTGCCCAA 59.688 50.000 0.00 0.00 0.00 4.12
12 13 0.535328 TCGGACATTTTCGTTGCCCA 60.535 50.000 0.00 0.00 0.00 5.36
13 14 0.168128 CTCGGACATTTTCGTTGCCC 59.832 55.000 0.00 0.00 0.00 5.36
14 15 1.153353 TCTCGGACATTTTCGTTGCC 58.847 50.000 0.00 0.00 0.00 4.52
15 16 2.961522 TTCTCGGACATTTTCGTTGC 57.038 45.000 0.00 0.00 0.00 4.17
16 17 4.725556 TCTTTCTCGGACATTTTCGTTG 57.274 40.909 0.00 0.00 0.00 4.10
17 18 5.744666 TTTCTTTCTCGGACATTTTCGTT 57.255 34.783 0.00 0.00 0.00 3.85
18 19 5.744666 TTTTCTTTCTCGGACATTTTCGT 57.255 34.783 0.00 0.00 0.00 3.85
94 96 2.092323 GGCAAAACTCATGGGTCTACC 58.908 52.381 0.00 0.00 40.81 3.18
95 97 2.488153 GTGGCAAAACTCATGGGTCTAC 59.512 50.000 0.00 0.00 0.00 2.59
107 109 7.715657 TGATTTATCCATAGATGTGGCAAAAC 58.284 34.615 0.00 0.00 39.19 2.43
112 114 8.565896 TTGTATGATTTATCCATAGATGTGGC 57.434 34.615 0.00 0.00 39.19 5.01
136 138 6.875195 CCATCTGGTCATGCAACTTTAATTTT 59.125 34.615 0.00 0.00 0.00 1.82
155 157 7.654520 CCTTTTCCAACAATAATATGCCATCTG 59.345 37.037 0.00 0.00 0.00 2.90
160 162 5.365314 TCCCCTTTTCCAACAATAATATGCC 59.635 40.000 0.00 0.00 0.00 4.40
164 166 5.955355 CCACTCCCCTTTTCCAACAATAATA 59.045 40.000 0.00 0.00 0.00 0.98
186 188 0.251297 CCATTGTGGGCTCACTTCCA 60.251 55.000 19.48 0.00 43.94 3.53
203 205 7.450014 CCTCTCATTAATAGCTCTAGAGTTCCA 59.550 40.741 20.75 1.49 0.00 3.53
205 207 8.404107 ACCTCTCATTAATAGCTCTAGAGTTC 57.596 38.462 20.75 5.48 0.00 3.01
217 219 9.627123 CAAATTCCCACTAACCTCTCATTAATA 57.373 33.333 0.00 0.00 0.00 0.98
230 232 6.105397 ACTTACGAGTCAAATTCCCACTAA 57.895 37.500 0.00 0.00 0.00 2.24
238 240 6.257193 AGACGTGAAAACTTACGAGTCAAATT 59.743 34.615 0.00 0.00 42.54 1.82
245 247 4.534168 TCTCAGACGTGAAAACTTACGAG 58.466 43.478 0.00 0.00 42.54 4.18
246 248 4.556942 TCTCAGACGTGAAAACTTACGA 57.443 40.909 0.00 0.00 42.54 3.43
256 258 4.931661 AGGTAAGTTTTCTCAGACGTGA 57.068 40.909 0.00 0.00 0.00 4.35
260 262 9.205719 CTAAACCTAAGGTAAGTTTTCTCAGAC 57.794 37.037 0.00 0.00 33.12 3.51
262 264 7.119407 GGCTAAACCTAAGGTAAGTTTTCTCAG 59.881 40.741 0.00 0.00 33.12 3.35
274 276 2.923629 TGAATGGGGCTAAACCTAAGGT 59.076 45.455 0.00 0.00 39.10 3.50
298 300 1.002134 AGGTGCAATGGGGACGAAG 60.002 57.895 0.00 0.00 39.01 3.79
305 307 1.276138 GGGAAAAAGAGGTGCAATGGG 59.724 52.381 0.00 0.00 0.00 4.00
306 308 1.067635 CGGGAAAAAGAGGTGCAATGG 60.068 52.381 0.00 0.00 0.00 3.16
307 309 1.613437 ACGGGAAAAAGAGGTGCAATG 59.387 47.619 0.00 0.00 0.00 2.82
308 310 1.995376 ACGGGAAAAAGAGGTGCAAT 58.005 45.000 0.00 0.00 0.00 3.56
323 325 2.095263 CACCTGACATTTAGCAAACGGG 60.095 50.000 0.00 0.00 0.00 5.28
324 326 2.552315 ACACCTGACATTTAGCAAACGG 59.448 45.455 0.00 0.00 0.00 4.44
325 327 3.498397 AGACACCTGACATTTAGCAAACG 59.502 43.478 0.00 0.00 0.00 3.60
339 341 4.827284 ACCCTAAAAATGTTCAGACACCTG 59.173 41.667 0.00 0.00 38.91 4.00
345 347 5.690865 ACTGACACCCTAAAAATGTTCAGA 58.309 37.500 0.00 0.00 31.58 3.27
347 349 5.441500 TGACTGACACCCTAAAAATGTTCA 58.558 37.500 0.00 0.00 0.00 3.18
348 350 6.385649 TTGACTGACACCCTAAAAATGTTC 57.614 37.500 0.00 0.00 0.00 3.18
351 353 7.596248 CAGAAATTGACTGACACCCTAAAAATG 59.404 37.037 6.98 0.00 37.54 2.32
362 364 6.095300 TCTGAAAAAGCAGAAATTGACTGACA 59.905 34.615 14.46 5.69 41.65 3.58
366 368 5.508657 GCCTCTGAAAAAGCAGAAATTGACT 60.509 40.000 0.00 0.00 43.75 3.41
370 372 3.305608 CGGCCTCTGAAAAAGCAGAAATT 60.306 43.478 0.00 0.00 43.75 1.82
375 377 1.238439 TTCGGCCTCTGAAAAAGCAG 58.762 50.000 0.00 0.00 37.24 4.24
378 380 1.608590 TGCTTTCGGCCTCTGAAAAAG 59.391 47.619 0.00 2.52 40.92 2.27
380 382 1.238439 CTGCTTTCGGCCTCTGAAAA 58.762 50.000 0.00 0.00 40.92 2.29
383 385 1.004560 CACTGCTTTCGGCCTCTGA 60.005 57.895 0.00 0.00 40.92 3.27
384 386 1.004560 TCACTGCTTTCGGCCTCTG 60.005 57.895 0.00 0.00 40.92 3.35
385 387 1.004440 GTCACTGCTTTCGGCCTCT 60.004 57.895 0.00 0.00 40.92 3.69
395 397 1.579084 GGTCGACTCTCGTCACTGCT 61.579 60.000 16.46 0.00 41.35 4.24
397 399 0.956410 AGGGTCGACTCTCGTCACTG 60.956 60.000 13.55 0.00 39.94 3.66
398 400 0.612229 TAGGGTCGACTCTCGTCACT 59.388 55.000 24.04 0.00 43.45 3.41
400 402 0.743701 GCTAGGGTCGACTCTCGTCA 60.744 60.000 24.04 2.81 41.35 4.35
402 404 0.745128 CTGCTAGGGTCGACTCTCGT 60.745 60.000 24.04 5.96 41.35 4.18
403 405 1.440938 CCTGCTAGGGTCGACTCTCG 61.441 65.000 24.04 17.68 42.10 4.04
404 406 1.730451 GCCTGCTAGGGTCGACTCTC 61.730 65.000 24.04 9.44 35.37 3.20
405 407 1.755008 GCCTGCTAGGGTCGACTCT 60.755 63.158 23.79 23.79 35.37 3.24
406 408 2.787567 GGCCTGCTAGGGTCGACTC 61.788 68.421 16.46 12.41 35.37 3.36
407 409 2.760385 GGCCTGCTAGGGTCGACT 60.760 66.667 16.46 0.00 35.37 4.18
417 439 2.186826 GTTCACAACACGGCCTGCT 61.187 57.895 0.00 0.00 0.00 4.24
425 447 1.859998 GCTTCGGCTTGTTCACAACAC 60.860 52.381 0.00 0.00 41.97 3.32
447 469 2.280186 CTTCCGCCGGCTATCACC 60.280 66.667 26.68 0.00 0.00 4.02
448 470 2.967615 GCTTCCGCCGGCTATCAC 60.968 66.667 26.68 7.42 0.00 3.06
449 471 4.585526 CGCTTCCGCCGGCTATCA 62.586 66.667 26.68 4.46 0.00 2.15
658 680 1.166129 GCCGCGACCATCTCTATAGA 58.834 55.000 8.23 1.69 35.80 1.98
664 703 4.933064 CCTCGCCGCGACCATCTC 62.933 72.222 12.39 0.00 0.00 2.75
683 756 4.228567 TTGTCACACGCGGCCTCA 62.229 61.111 12.47 0.00 0.00 3.86
695 768 1.005037 CAGCTAGTGGGCGTTGTCA 60.005 57.895 0.00 0.00 37.29 3.58
735 809 3.953775 CACCCACCCGCCTCAACT 61.954 66.667 0.00 0.00 0.00 3.16
795 869 2.837498 CAATCACCTCACACAGACACA 58.163 47.619 0.00 0.00 0.00 3.72
796 870 1.532868 GCAATCACCTCACACAGACAC 59.467 52.381 0.00 0.00 0.00 3.67
797 871 1.873486 CGCAATCACCTCACACAGACA 60.873 52.381 0.00 0.00 0.00 3.41
798 872 0.792640 CGCAATCACCTCACACAGAC 59.207 55.000 0.00 0.00 0.00 3.51
799 873 0.320683 CCGCAATCACCTCACACAGA 60.321 55.000 0.00 0.00 0.00 3.41
800 874 0.320683 TCCGCAATCACCTCACACAG 60.321 55.000 0.00 0.00 0.00 3.66
801 875 0.107643 TTCCGCAATCACCTCACACA 59.892 50.000 0.00 0.00 0.00 3.72
829 903 3.257935 TTTTTGGCCGTCGGATCAT 57.742 47.368 17.49 0.00 0.00 2.45
859 935 6.825721 ACCTATTTGTGAAAACAAATTTGGCA 59.174 30.769 21.74 11.22 44.96 4.92
884 960 7.873719 TTTCTGAAAAATAATATCGGGAGCA 57.126 32.000 0.00 0.00 0.00 4.26
890 966 8.755018 GGGTGCAATTTCTGAAAAATAATATCG 58.245 33.333 6.95 0.00 0.00 2.92
1136 1244 0.738389 GGTGACAGTTGTGGTGGTTG 59.262 55.000 0.00 0.00 0.00 3.77
1189 1297 5.836821 AGCTCGTACATGACATTCTTAGA 57.163 39.130 0.00 0.00 0.00 2.10
1191 1299 5.507482 GGCTAGCTCGTACATGACATTCTTA 60.507 44.000 15.72 0.00 0.00 2.10
1218 1326 0.028505 TCGCGTAGTAGATGTTCCGC 59.971 55.000 5.77 0.00 37.91 5.54
1224 1332 0.660595 CCGGCTTCGCGTAGTAGATG 60.661 60.000 14.43 0.60 0.00 2.90
1300 1408 2.475466 GGATGTACTCGGGCGTCGA 61.475 63.158 0.00 3.32 46.77 4.20
1311 1419 1.585521 CACGTCGCGGAGGATGTAC 60.586 63.158 6.13 0.00 34.50 2.90
1536 1644 1.737008 GAAGGTGAACGTCTCGGCC 60.737 63.158 0.00 0.00 0.00 6.13
1904 2012 4.988716 AGCCGTGGTGGAGGACGA 62.989 66.667 0.00 0.00 42.00 4.20
2057 2165 4.780815 TGTCTTGGTTGTGAGATCTTGTT 58.219 39.130 0.00 0.00 0.00 2.83
2058 2166 4.422073 TGTCTTGGTTGTGAGATCTTGT 57.578 40.909 0.00 0.00 0.00 3.16
2166 2475 2.218603 CACGCCCTTTTGTACAGAACT 58.781 47.619 0.00 0.00 0.00 3.01
2304 2613 1.448717 GAAGAGCCCCAGTCGCTTC 60.449 63.158 0.00 0.00 36.48 3.86
2391 2700 1.352056 CGTCTCAGCGAGCACGATA 59.648 57.895 8.01 0.00 42.66 2.92
2604 2920 0.371645 GCGCGAAGGAACTGATGAAG 59.628 55.000 12.10 0.00 40.86 3.02
2685 3001 1.987855 CCGGGACAGGAAGTAGCCA 60.988 63.158 0.00 0.00 0.00 4.75
3009 4659 4.200874 AGTGTAGTAATGGAGGAGACGAG 58.799 47.826 0.00 0.00 0.00 4.18
3100 4759 3.219281 ACTTTGACATTGGCGTACCTTT 58.781 40.909 0.00 0.00 36.63 3.11
3153 4812 9.696917 TGTTCACAATATACATCAGTATAGCAG 57.303 33.333 0.00 0.00 44.16 4.24
3188 4847 7.984422 TCCATGCATACATTTATGTAGAAGG 57.016 36.000 0.00 6.18 45.46 3.46
3257 4916 6.304624 TCTATACTATCGACCAACCATCAGT 58.695 40.000 0.00 0.00 0.00 3.41
3258 4917 6.127869 CCTCTATACTATCGACCAACCATCAG 60.128 46.154 0.00 0.00 0.00 2.90
3259 4918 5.710567 CCTCTATACTATCGACCAACCATCA 59.289 44.000 0.00 0.00 0.00 3.07
3260 4919 5.125739 CCCTCTATACTATCGACCAACCATC 59.874 48.000 0.00 0.00 0.00 3.51
3261 4920 5.017490 CCCTCTATACTATCGACCAACCAT 58.983 45.833 0.00 0.00 0.00 3.55
3262 4921 4.105217 TCCCTCTATACTATCGACCAACCA 59.895 45.833 0.00 0.00 0.00 3.67
3295 4975 1.699083 TCCTCACATGCCACTGAAGAA 59.301 47.619 0.00 0.00 0.00 2.52
3330 5010 2.969821 TCAAGCCAGTACCCACAAAT 57.030 45.000 0.00 0.00 0.00 2.32
3416 5096 1.137479 CGATGGCCAGGCATTCAAAAT 59.863 47.619 15.19 0.00 0.00 1.82
3435 5115 1.392168 TCGAATGCTTAAAAGACGGCG 59.608 47.619 4.80 4.80 0.00 6.46
3498 5179 8.606040 TTGATCCAAAATTTGAAAAGATGACC 57.394 30.769 7.37 0.00 0.00 4.02
3516 5197 3.834938 TGCATGGCAATATCTTGATCCA 58.165 40.909 0.00 0.00 34.76 3.41
3568 5250 8.743085 ACTGTACGTGGTTATAATTCTCTAGA 57.257 34.615 0.00 0.00 0.00 2.43
3579 5261 5.993441 ACTTTAGCAAACTGTACGTGGTTAT 59.007 36.000 0.00 0.00 0.00 1.89
3586 5268 3.966218 GCACAACTTTAGCAAACTGTACG 59.034 43.478 0.00 0.00 0.00 3.67
3627 5309 9.303537 CTTAAGATTAGACAACAGTTAGCCTAC 57.696 37.037 0.00 0.00 0.00 3.18
3669 5351 7.517614 TGTTAATTGTCTGTTGGCTGAAATA 57.482 32.000 0.00 0.00 0.00 1.40
3748 5432 3.057596 GCCGATCAGTGGTCAAATCAAAA 60.058 43.478 3.88 0.00 0.00 2.44
3775 5459 3.771577 AGGAGAACGACAGGTGATTTT 57.228 42.857 0.00 0.00 0.00 1.82
3776 5460 3.071023 TCAAGGAGAACGACAGGTGATTT 59.929 43.478 0.00 0.00 0.00 2.17
3777 5461 2.632996 TCAAGGAGAACGACAGGTGATT 59.367 45.455 0.00 0.00 0.00 2.57
3779 5463 1.613925 CTCAAGGAGAACGACAGGTGA 59.386 52.381 0.00 0.00 0.00 4.02
3780 5464 1.937108 GCTCAAGGAGAACGACAGGTG 60.937 57.143 0.00 0.00 0.00 4.00
3781 5465 0.318762 GCTCAAGGAGAACGACAGGT 59.681 55.000 0.00 0.00 0.00 4.00
3782 5466 0.734253 CGCTCAAGGAGAACGACAGG 60.734 60.000 0.00 0.00 38.04 4.00
3785 5469 0.667792 AAGCGCTCAAGGAGAACGAC 60.668 55.000 12.06 0.00 38.04 4.34
3787 5471 0.389166 AGAAGCGCTCAAGGAGAACG 60.389 55.000 12.06 0.00 38.80 3.95
3788 5472 1.067213 AGAGAAGCGCTCAAGGAGAAC 60.067 52.381 12.06 0.00 46.45 3.01
3797 5481 4.757799 TCTATCACATAGAGAAGCGCTC 57.242 45.455 12.06 4.30 44.29 5.03
3839 5527 8.285163 TGGCTATACCATGATCAGATAGATAGT 58.715 37.037 15.61 2.96 46.36 2.12
3840 5528 8.703378 TGGCTATACCATGATCAGATAGATAG 57.297 38.462 15.61 12.25 46.36 2.08
3885 5573 7.283807 GGTTACCGTCTTGGGATTAAAATACAT 59.716 37.037 0.00 0.00 44.64 2.29
3888 5576 6.961042 AGGTTACCGTCTTGGGATTAAAATA 58.039 36.000 0.00 0.00 44.64 1.40
3902 5590 1.079612 CGGGGTCAAGGTTACCGTC 60.080 63.158 0.00 0.00 39.70 4.79
3906 5594 0.461516 GCTAGCGGGGTCAAGGTTAC 60.462 60.000 0.00 0.00 0.00 2.50
3907 5595 0.905809 TGCTAGCGGGGTCAAGGTTA 60.906 55.000 10.77 0.00 0.00 2.85
3912 5600 0.321298 GACTTTGCTAGCGGGGTCAA 60.321 55.000 20.93 4.32 0.00 3.18
3919 5607 3.482598 CGTCAGAAATGACTTTGCTAGCG 60.483 47.826 10.77 0.00 36.71 4.26
3920 5608 3.181516 CCGTCAGAAATGACTTTGCTAGC 60.182 47.826 8.10 8.10 36.71 3.42
3923 5611 3.070018 CTCCGTCAGAAATGACTTTGCT 58.930 45.455 6.80 0.00 36.71 3.91
3945 5638 4.645136 TGAGAAGAGTTCACCATATAGCGT 59.355 41.667 0.00 0.00 0.00 5.07
3952 5645 4.437682 TTGGTTGAGAAGAGTTCACCAT 57.562 40.909 0.00 0.00 30.99 3.55
3958 5651 3.817647 GCTGTGATTGGTTGAGAAGAGTT 59.182 43.478 0.00 0.00 0.00 3.01
3963 5656 1.881925 CGGGCTGTGATTGGTTGAGAA 60.882 52.381 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.