Multiple sequence alignment - TraesCS2D01G505200

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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 TraesCS2D01G505200 chr2D 100.000 4487 0 0 1 4487 599291052 599286566 0.000000e+00 8287.0
1 TraesCS2D01G505200 chr2D 85.782 422 35 15 3544 3957 309581990 309581586 1.490000e-114 424.0
2 TraesCS2D01G505200 chr2D 76.812 414 51 20 2620 3020 595445423 595445042 1.650000e-44 191.0
3 TraesCS2D01G505200 chr2D 96.610 59 2 0 3538 3596 398350124 398350182 1.030000e-16 99.0
4 TraesCS2D01G505200 chr2D 98.113 53 1 0 3544 3596 585712819 585712767 4.780000e-15 93.5
5 TraesCS2D01G505200 chr2B 93.346 3246 109 34 346 3521 728755123 728751915 0.000000e+00 4698.0
6 TraesCS2D01G505200 chr2B 86.800 250 14 4 1 248 728755375 728755143 1.240000e-65 261.0
7 TraesCS2D01G505200 chr2B 78.261 138 26 3 4319 4454 705533861 705533996 8.000000e-13 86.1
8 TraesCS2D01G505200 chr2A 94.120 3112 111 33 458 3521 733394397 733391310 0.000000e+00 4667.0
9 TraesCS2D01G505200 chr2A 88.535 314 14 9 1 308 733394736 733394439 1.190000e-95 361.0
10 TraesCS2D01G505200 chrUn 85.635 2346 264 38 1170 3480 313597446 313595139 0.000000e+00 2398.0
11 TraesCS2D01G505200 chrUn 86.506 415 33 12 3544 3953 132137178 132136782 6.890000e-118 435.0
12 TraesCS2D01G505200 chr6B 85.635 2346 264 38 1170 3480 707424531 707426838 0.000000e+00 2398.0
13 TraesCS2D01G505200 chr6B 85.635 2346 264 38 1170 3480 707764222 707766529 0.000000e+00 2398.0
14 TraesCS2D01G505200 chr6B 86.657 667 55 18 3544 4185 599396529 599395872 0.000000e+00 708.0
15 TraesCS2D01G505200 chr7A 78.374 2386 394 90 1152 3446 563877158 563874804 0.000000e+00 1435.0
16 TraesCS2D01G505200 chr7A 80.174 1034 161 25 1152 2172 564244151 564243149 0.000000e+00 734.0
17 TraesCS2D01G505200 chr7D 78.276 2366 398 80 1152 3429 498477873 498475536 0.000000e+00 1415.0
18 TraesCS2D01G505200 chr7D 88.646 916 63 30 3572 4456 539821477 539822382 0.000000e+00 1077.0
19 TraesCS2D01G505200 chr7D 83.391 289 38 8 4202 4487 539822228 539822509 4.450000e-65 259.0
20 TraesCS2D01G505200 chr7B 79.081 2089 351 62 1152 3179 526717679 526715616 0.000000e+00 1358.0
21 TraesCS2D01G505200 chr5A 87.649 753 59 28 3542 4285 689166879 689166152 0.000000e+00 845.0
22 TraesCS2D01G505200 chr6D 86.213 602 48 18 3695 4273 400446926 400446337 1.770000e-173 619.0
23 TraesCS2D01G505200 chr6D 86.957 414 30 13 3546 3953 288457454 288457059 1.150000e-120 444.0
24 TraesCS2D01G505200 chr6D 88.235 170 12 6 3544 3711 400447110 400446947 3.540000e-46 196.0
25 TraesCS2D01G505200 chr6D 81.343 134 18 7 3543 3673 84302261 84302390 7.940000e-18 102.0
26 TraesCS2D01G505200 chr1D 82.128 470 37 15 3544 3995 424135532 424135972 4.270000e-95 359.0
27 TraesCS2D01G505200 chr1D 86.095 338 23 12 3629 3957 94047558 94047236 4.300000e-90 342.0
28 TraesCS2D01G505200 chr4B 76.573 286 53 9 2873 3153 455756670 455756946 1.300000e-30 145.0
29 TraesCS2D01G505200 chr5B 78.367 245 31 17 2920 3156 656501 656271 6.050000e-29 139.0
30 TraesCS2D01G505200 chr4D 76.224 286 54 9 2873 3153 370674901 370675177 6.050000e-29 139.0
31 TraesCS2D01G505200 chr3D 93.617 47 3 0 3112 3158 175402116 175402162 2.240000e-08 71.3
32 TraesCS2D01G505200 chr3A 93.617 47 3 0 3112 3158 215472508 215472554 2.240000e-08 71.3
33 TraesCS2D01G505200 chr5D 97.500 40 1 0 3112 3151 106520204 106520165 8.050000e-08 69.4
34 TraesCS2D01G505200 chr3B 91.489 47 4 0 3112 3158 254769058 254769104 1.040000e-06 65.8


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 TraesCS2D01G505200 chr2D 599286566 599291052 4486 True 8287.0 8287 100.0000 1 4487 1 chr2D.!!$R4 4486
1 TraesCS2D01G505200 chr2B 728751915 728755375 3460 True 2479.5 4698 90.0730 1 3521 2 chr2B.!!$R1 3520
2 TraesCS2D01G505200 chr2A 733391310 733394736 3426 True 2514.0 4667 91.3275 1 3521 2 chr2A.!!$R1 3520
3 TraesCS2D01G505200 chrUn 313595139 313597446 2307 True 2398.0 2398 85.6350 1170 3480 1 chrUn.!!$R2 2310
4 TraesCS2D01G505200 chr6B 707424531 707426838 2307 False 2398.0 2398 85.6350 1170 3480 1 chr6B.!!$F1 2310
5 TraesCS2D01G505200 chr6B 707764222 707766529 2307 False 2398.0 2398 85.6350 1170 3480 1 chr6B.!!$F2 2310
6 TraesCS2D01G505200 chr6B 599395872 599396529 657 True 708.0 708 86.6570 3544 4185 1 chr6B.!!$R1 641
7 TraesCS2D01G505200 chr7A 563874804 563877158 2354 True 1435.0 1435 78.3740 1152 3446 1 chr7A.!!$R1 2294
8 TraesCS2D01G505200 chr7A 564243149 564244151 1002 True 734.0 734 80.1740 1152 2172 1 chr7A.!!$R2 1020
9 TraesCS2D01G505200 chr7D 498475536 498477873 2337 True 1415.0 1415 78.2760 1152 3429 1 chr7D.!!$R1 2277
10 TraesCS2D01G505200 chr7D 539821477 539822509 1032 False 668.0 1077 86.0185 3572 4487 2 chr7D.!!$F1 915
11 TraesCS2D01G505200 chr7B 526715616 526717679 2063 True 1358.0 1358 79.0810 1152 3179 1 chr7B.!!$R1 2027
12 TraesCS2D01G505200 chr5A 689166152 689166879 727 True 845.0 845 87.6490 3542 4285 1 chr5A.!!$R1 743
13 TraesCS2D01G505200 chr6D 400446337 400447110 773 True 407.5 619 87.2240 3544 4273 2 chr6D.!!$R2 729

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
813 871 0.036164 CGTGTCTCCCCCAACATCAA 59.964 55.000 0.0 0.00 0.00 2.57 F
971 1055 0.036765 GGACATTCCCGTAGCACACA 60.037 55.000 0.0 0.00 0.00 3.72 F
984 1068 1.210478 AGCACACAACACTTGGAGAGT 59.790 47.619 0.0 0.00 39.89 3.24 F
2724 2880 1.979855 TCAACCACATGAACCTGGTG 58.020 50.000 0.0 2.48 40.06 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 2880 0.463620 AGCAGAAGCCGAAGATCCTC 59.536 55.000 0.0 0.0 43.56 3.71 R
2778 2934 2.284258 AGCGAGCCCTTCTCCACT 60.284 61.111 0.0 0.0 38.62 4.00 R
2886 3042 4.015406 TGGTGCAGGTACGCCAGG 62.015 66.667 0.0 0.0 45.14 4.45 R
3644 3837 0.672401 GGAGGGCGTTCGTGATTTCA 60.672 55.000 0.0 0.0 0.00 2.69 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
53 55 4.240096 GTTGATTGCCTTTCTGATTGGTG 58.760 43.478 0.00 0.00 0.00 4.17
100 103 2.602211 CTCTATCAAACAGTGCGCTCAG 59.398 50.000 9.73 4.28 0.00 3.35
133 136 6.147328 CCCATAGTTTAAGACTTATAAGCGGC 59.853 42.308 12.54 2.76 39.86 6.53
248 252 5.048643 TGTTCTCCGTTTGTTTGACTTTGAA 60.049 36.000 0.00 0.00 0.00 2.69
249 253 5.828299 TCTCCGTTTGTTTGACTTTGAAT 57.172 34.783 0.00 0.00 0.00 2.57
250 254 5.816919 TCTCCGTTTGTTTGACTTTGAATC 58.183 37.500 0.00 0.00 0.00 2.52
253 257 5.008217 TCCGTTTGTTTGACTTTGAATCGAT 59.992 36.000 0.00 0.00 0.00 3.59
255 259 5.386323 CGTTTGTTTGACTTTGAATCGATGC 60.386 40.000 0.00 0.00 0.00 3.91
256 260 5.437289 TTGTTTGACTTTGAATCGATGCT 57.563 34.783 4.68 0.00 0.00 3.79
257 261 4.786507 TGTTTGACTTTGAATCGATGCTG 58.213 39.130 4.68 0.00 0.00 4.41
258 262 3.476295 TTGACTTTGAATCGATGCTGC 57.524 42.857 4.68 0.00 0.00 5.25
299 308 3.885777 GCTAGTAGCGTTACGTCGT 57.114 52.632 6.36 2.21 34.88 4.34
305 314 0.721154 TAGCGTTACGTCGTCATCGT 59.279 50.000 0.00 0.00 43.86 3.73
306 315 0.110056 AGCGTTACGTCGTCATCGTT 60.110 50.000 0.00 0.69 41.72 3.85
307 316 0.704551 GCGTTACGTCGTCATCGTTT 59.295 50.000 0.00 0.00 41.72 3.60
308 317 1.265590 GCGTTACGTCGTCATCGTTTC 60.266 52.381 0.00 0.00 41.72 2.78
309 318 1.971284 CGTTACGTCGTCATCGTTTCA 59.029 47.619 0.00 0.00 41.72 2.69
310 319 2.591148 CGTTACGTCGTCATCGTTTCAT 59.409 45.455 0.00 0.00 41.72 2.57
311 320 3.536934 CGTTACGTCGTCATCGTTTCATG 60.537 47.826 0.00 0.00 41.72 3.07
312 321 2.060326 ACGTCGTCATCGTTTCATGT 57.940 45.000 0.00 0.00 38.38 3.21
313 322 2.400399 ACGTCGTCATCGTTTCATGTT 58.600 42.857 0.00 0.00 38.38 2.71
314 323 2.798283 ACGTCGTCATCGTTTCATGTTT 59.202 40.909 0.00 0.00 38.38 2.83
315 324 3.982701 ACGTCGTCATCGTTTCATGTTTA 59.017 39.130 0.00 0.00 38.38 2.01
316 325 4.089493 ACGTCGTCATCGTTTCATGTTTAG 59.911 41.667 0.00 0.00 38.38 1.85
317 326 4.322539 CGTCGTCATCGTTTCATGTTTAGA 59.677 41.667 0.00 0.00 38.33 2.10
318 327 5.004440 CGTCGTCATCGTTTCATGTTTAGAT 59.996 40.000 0.00 0.00 38.33 1.98
319 328 6.178507 GTCGTCATCGTTTCATGTTTAGATG 58.821 40.000 13.62 13.62 37.43 2.90
320 329 4.957967 CGTCATCGTTTCATGTTTAGATGC 59.042 41.667 14.44 10.68 36.41 3.91
321 330 5.445806 CGTCATCGTTTCATGTTTAGATGCA 60.446 40.000 14.44 0.00 36.41 3.96
322 331 6.314018 GTCATCGTTTCATGTTTAGATGCAA 58.686 36.000 14.44 2.40 36.41 4.08
323 332 6.968904 GTCATCGTTTCATGTTTAGATGCAAT 59.031 34.615 14.44 0.00 36.41 3.56
324 333 7.485913 GTCATCGTTTCATGTTTAGATGCAATT 59.514 33.333 14.44 0.00 36.41 2.32
325 334 8.672815 TCATCGTTTCATGTTTAGATGCAATTA 58.327 29.630 14.44 0.00 36.41 1.40
326 335 9.454585 CATCGTTTCATGTTTAGATGCAATTAT 57.545 29.630 0.00 0.00 30.84 1.28
340 349 7.614494 AGATGCAATTATATTAAATGCCCACC 58.386 34.615 0.00 0.00 0.00 4.61
341 350 6.737720 TGCAATTATATTAAATGCCCACCA 57.262 33.333 5.19 0.00 0.00 4.17
342 351 6.757237 TGCAATTATATTAAATGCCCACCAG 58.243 36.000 5.19 0.00 0.00 4.00
343 352 6.326064 TGCAATTATATTAAATGCCCACCAGT 59.674 34.615 5.19 0.00 0.00 4.00
344 353 6.868339 GCAATTATATTAAATGCCCACCAGTC 59.132 38.462 0.00 0.00 0.00 3.51
358 367 5.745227 CCCACCAGTCAATATCTTAGTGTT 58.255 41.667 0.00 0.00 0.00 3.32
385 394 5.945155 TGCGATTGGTGAGGTAAAATAAAC 58.055 37.500 0.00 0.00 0.00 2.01
420 429 3.620488 TCCAATCAACATAACTCTGGGC 58.380 45.455 0.00 0.00 0.00 5.36
424 433 3.719268 TCAACATAACTCTGGGCACAT 57.281 42.857 0.00 0.00 0.00 3.21
426 435 5.372343 TCAACATAACTCTGGGCACATAT 57.628 39.130 0.00 0.00 0.00 1.78
427 436 5.754782 TCAACATAACTCTGGGCACATATT 58.245 37.500 0.00 0.00 0.00 1.28
428 437 6.186957 TCAACATAACTCTGGGCACATATTT 58.813 36.000 0.00 0.00 0.00 1.40
429 438 6.663093 TCAACATAACTCTGGGCACATATTTT 59.337 34.615 0.00 0.00 0.00 1.82
430 439 7.178274 TCAACATAACTCTGGGCACATATTTTT 59.822 33.333 0.00 0.00 0.00 1.94
478 505 5.507315 CCAAGTTATGGTTCTGTGGTTTGAC 60.507 44.000 0.00 0.00 44.85 3.18
485 514 3.624410 GGTTCTGTGGTTTGACGTTTACT 59.376 43.478 0.00 0.00 0.00 2.24
582 625 4.961438 ATGCTGAGGGTTTGACAAAAAT 57.039 36.364 1.27 0.00 0.00 1.82
609 654 5.122869 CAGTCCACTAATCCACAAGTCAATG 59.877 44.000 0.00 0.00 0.00 2.82
612 657 5.013079 TCCACTAATCCACAAGTCAATGACT 59.987 40.000 10.56 10.56 45.64 3.41
615 663 6.596888 CACTAATCCACAAGTCAATGACTCAT 59.403 38.462 17.02 4.96 42.59 2.90
616 664 7.765819 CACTAATCCACAAGTCAATGACTCATA 59.234 37.037 17.02 1.71 42.59 2.15
617 665 8.489489 ACTAATCCACAAGTCAATGACTCATAT 58.511 33.333 17.02 0.00 42.59 1.78
618 666 9.987272 CTAATCCACAAGTCAATGACTCATATA 57.013 33.333 17.02 3.47 42.59 0.86
619 667 8.668510 AATCCACAAGTCAATGACTCATATAC 57.331 34.615 17.02 0.00 42.59 1.47
620 668 7.181569 TCCACAAGTCAATGACTCATATACA 57.818 36.000 17.02 0.00 42.59 2.29
621 669 7.041721 TCCACAAGTCAATGACTCATATACAC 58.958 38.462 17.02 0.00 42.59 2.90
622 670 6.818142 CCACAAGTCAATGACTCATATACACA 59.182 38.462 17.02 0.00 42.59 3.72
623 671 7.334171 CCACAAGTCAATGACTCATATACACAA 59.666 37.037 17.02 0.00 42.59 3.33
624 672 8.171196 CACAAGTCAATGACTCATATACACAAC 58.829 37.037 17.02 0.00 42.59 3.32
625 673 8.097038 ACAAGTCAATGACTCATATACACAACT 58.903 33.333 17.02 0.00 42.59 3.16
626 674 8.939929 CAAGTCAATGACTCATATACACAACTT 58.060 33.333 17.02 0.00 42.59 2.66
627 675 8.484641 AGTCAATGACTCATATACACAACTTG 57.515 34.615 10.56 0.00 38.71 3.16
628 676 8.097038 AGTCAATGACTCATATACACAACTTGT 58.903 33.333 10.56 0.00 38.71 3.16
629 677 9.366216 GTCAATGACTCATATACACAACTTGTA 57.634 33.333 6.07 0.00 45.03 2.41
630 678 9.936759 TCAATGACTCATATACACAACTTGTAA 57.063 29.630 0.00 0.00 44.11 2.41
670 718 1.148310 CGGCGGCTATACAAATGGAG 58.852 55.000 7.61 0.00 0.00 3.86
676 724 4.389077 GCGGCTATACAAATGGAGATACAC 59.611 45.833 0.00 0.00 0.00 2.90
730 779 2.782925 TCCCAATATGCAGGGCTTCTTA 59.217 45.455 3.82 0.00 45.07 2.10
813 871 0.036164 CGTGTCTCCCCCAACATCAA 59.964 55.000 0.00 0.00 0.00 2.57
836 894 2.751436 AGCCGCCAACAATCGCAT 60.751 55.556 0.00 0.00 0.00 4.73
891 949 1.153309 TCGCAGCACCCATGATGAG 60.153 57.895 0.00 0.00 45.46 2.90
971 1055 0.036765 GGACATTCCCGTAGCACACA 60.037 55.000 0.00 0.00 0.00 3.72
980 1064 1.577468 CGTAGCACACAACACTTGGA 58.423 50.000 0.00 0.00 34.12 3.53
984 1068 1.210478 AGCACACAACACTTGGAGAGT 59.790 47.619 0.00 0.00 39.89 3.24
1058 1142 2.363795 TTGGATCGCCCTCTCGGT 60.364 61.111 0.00 0.00 35.38 4.69
1219 1309 3.419759 CCACCAACGCCTACACGC 61.420 66.667 0.00 0.00 36.19 5.34
2373 2520 3.446570 GCCGGCAGCAAGCTCAAT 61.447 61.111 24.80 0.00 44.79 2.57
2694 2850 4.778415 CGGTCGGACCTCAGCGTG 62.778 72.222 23.86 3.71 35.66 5.34
2724 2880 1.979855 TCAACCACATGAACCTGGTG 58.020 50.000 0.00 2.48 40.06 4.17
2778 2934 3.592070 CTCCTCGTCTCGGAGCAA 58.408 61.111 0.00 0.00 41.39 3.91
2813 2969 2.815647 CGACAAGGCCCTCTTCGC 60.816 66.667 0.00 0.00 32.41 4.70
3521 3713 3.182967 CTGACGATTAGCACCTGAGAAC 58.817 50.000 0.00 0.00 0.00 3.01
3522 3714 2.094182 TGACGATTAGCACCTGAGAACC 60.094 50.000 0.00 0.00 0.00 3.62
3523 3715 1.207329 ACGATTAGCACCTGAGAACCC 59.793 52.381 0.00 0.00 0.00 4.11
3524 3716 1.473434 CGATTAGCACCTGAGAACCCC 60.473 57.143 0.00 0.00 0.00 4.95
3525 3717 1.840635 GATTAGCACCTGAGAACCCCT 59.159 52.381 0.00 0.00 0.00 4.79
3526 3718 1.742308 TTAGCACCTGAGAACCCCTT 58.258 50.000 0.00 0.00 0.00 3.95
3527 3719 2.634639 TAGCACCTGAGAACCCCTTA 57.365 50.000 0.00 0.00 0.00 2.69
3528 3720 1.742308 AGCACCTGAGAACCCCTTAA 58.258 50.000 0.00 0.00 0.00 1.85
3529 3721 2.062636 AGCACCTGAGAACCCCTTAAA 58.937 47.619 0.00 0.00 0.00 1.52
3530 3722 2.445525 AGCACCTGAGAACCCCTTAAAA 59.554 45.455 0.00 0.00 0.00 1.52
3531 3723 3.117284 AGCACCTGAGAACCCCTTAAAAA 60.117 43.478 0.00 0.00 0.00 1.94
3644 3837 0.033405 TCGTTCGGGAGGAGAGGATT 60.033 55.000 0.00 0.00 0.00 3.01
3676 3869 4.208097 CCTCCCCAGGCCCCCTAT 62.208 72.222 0.00 0.00 30.98 2.57
3752 3986 5.876651 AAGAAGAAGCCCAGATTGTTTTT 57.123 34.783 0.00 0.00 0.00 1.94
3754 3988 5.143369 AGAAGAAGCCCAGATTGTTTTTCT 58.857 37.500 0.00 0.00 0.00 2.52
3958 4225 6.112927 TCCTAAGAAAAAGCATGGCAAAAT 57.887 33.333 0.00 0.00 0.00 1.82
3987 4254 9.213799 TCAAAAATACCATGGCAAAAAGTAATC 57.786 29.630 13.04 0.00 0.00 1.75
3991 4258 2.836981 CCATGGCAAAAAGTAATCCCCA 59.163 45.455 0.00 0.00 0.00 4.96
4302 4617 4.976116 GCCATGCCGACTTATGTAAATTTC 59.024 41.667 0.00 0.00 0.00 2.17
4308 4623 5.298276 GCCGACTTATGTAAATTTCCCATGA 59.702 40.000 11.57 4.93 0.00 3.07
4312 4627 8.240682 CGACTTATGTAAATTTCCCATGACAAA 58.759 33.333 11.57 0.00 0.00 2.83
4333 4695 9.598517 GACAAAATAAGATAAATTTGCCATGGA 57.401 29.630 18.40 0.00 36.48 3.41
4381 4768 3.789224 CGATTTAGGTAAAATTGCCGTGC 59.211 43.478 0.00 0.00 37.93 5.34
4389 4776 4.691216 GGTAAAATTGCCGTGCCATTTAAA 59.309 37.500 7.87 0.00 33.73 1.52
4400 4787 5.163903 CCGTGCCATTTAAAGTAAATTTGCC 60.164 40.000 0.00 0.00 36.29 4.52
4429 4816 8.230112 GCAAAAAGAATTAAAAATTGCCATGG 57.770 30.769 7.63 7.63 36.57 3.66
4448 4835 8.672214 GCCATGGCAATAAAAGTTAAAAATTG 57.328 30.769 32.08 0.00 41.49 2.32
4455 4842 7.273164 GCAATAAAAGTTAAAAATTGCCATGGC 59.727 33.333 30.54 30.54 44.11 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 5.471456 CCTTGAACATAGATAGATTGTGCCC 59.529 44.000 0.00 0.00 0.00 5.36
65 67 8.134202 TGTTTGATAGAGACCTTGAACATAGA 57.866 34.615 0.00 0.00 0.00 1.98
106 109 7.929785 CCGCTTATAAGTCTTAAACTATGGGAA 59.070 37.037 13.91 0.00 37.17 3.97
133 136 5.390567 GCCGGGAATTTAAGAAGCGTATATG 60.391 44.000 2.18 0.00 0.00 1.78
138 141 1.092348 GCCGGGAATTTAAGAAGCGT 58.908 50.000 2.18 0.00 0.00 5.07
248 252 0.812811 AATGTCGCAGCAGCATCGAT 60.813 50.000 11.39 0.00 42.27 3.59
249 253 1.423721 GAATGTCGCAGCAGCATCGA 61.424 55.000 0.82 5.08 42.27 3.59
250 254 1.011463 GAATGTCGCAGCAGCATCG 60.011 57.895 0.82 0.00 42.27 3.84
253 257 2.028420 AATAGAATGTCGCAGCAGCA 57.972 45.000 0.82 0.00 42.27 4.41
255 259 4.556135 CACAAAAATAGAATGTCGCAGCAG 59.444 41.667 0.00 0.00 0.00 4.24
256 260 4.023279 ACACAAAAATAGAATGTCGCAGCA 60.023 37.500 0.00 0.00 0.00 4.41
257 261 4.475944 ACACAAAAATAGAATGTCGCAGC 58.524 39.130 0.00 0.00 0.00 5.25
291 300 3.567530 ACATGAAACGATGACGACGTAA 58.432 40.909 0.00 0.00 43.16 3.18
298 307 5.868257 TGCATCTAAACATGAAACGATGAC 58.132 37.500 17.45 11.78 32.21 3.06
299 308 6.493449 TTGCATCTAAACATGAAACGATGA 57.507 33.333 17.45 6.20 32.21 2.92
314 323 8.748412 GGTGGGCATTTAATATAATTGCATCTA 58.252 33.333 14.99 0.00 0.00 1.98
315 324 7.235193 TGGTGGGCATTTAATATAATTGCATCT 59.765 33.333 14.99 0.00 0.00 2.90
316 325 7.385267 TGGTGGGCATTTAATATAATTGCATC 58.615 34.615 14.99 9.31 0.00 3.91
317 326 7.016465 ACTGGTGGGCATTTAATATAATTGCAT 59.984 33.333 14.99 0.00 0.00 3.96
318 327 6.326064 ACTGGTGGGCATTTAATATAATTGCA 59.674 34.615 14.99 0.00 0.00 4.08
319 328 6.758254 ACTGGTGGGCATTTAATATAATTGC 58.242 36.000 7.94 7.94 0.00 3.56
320 329 7.950512 TGACTGGTGGGCATTTAATATAATTG 58.049 34.615 0.00 0.00 0.00 2.32
321 330 8.546083 TTGACTGGTGGGCATTTAATATAATT 57.454 30.769 0.00 0.00 30.17 1.40
322 331 8.725606 ATTGACTGGTGGGCATTTAATATAAT 57.274 30.769 0.00 0.00 30.17 1.28
323 332 9.821240 ATATTGACTGGTGGGCATTTAATATAA 57.179 29.630 0.00 0.00 30.17 0.98
324 333 9.461312 GATATTGACTGGTGGGCATTTAATATA 57.539 33.333 0.00 0.00 30.17 0.86
325 334 8.172741 AGATATTGACTGGTGGGCATTTAATAT 58.827 33.333 0.00 0.00 30.17 1.28
326 335 7.526041 AGATATTGACTGGTGGGCATTTAATA 58.474 34.615 0.00 0.00 30.17 0.98
327 336 6.376248 AGATATTGACTGGTGGGCATTTAAT 58.624 36.000 0.00 0.00 30.17 1.40
328 337 5.765510 AGATATTGACTGGTGGGCATTTAA 58.234 37.500 0.00 0.00 30.17 1.52
329 338 5.387113 AGATATTGACTGGTGGGCATTTA 57.613 39.130 0.00 0.00 30.17 1.40
330 339 4.255510 AGATATTGACTGGTGGGCATTT 57.744 40.909 0.00 0.00 30.17 2.32
331 340 3.959495 AGATATTGACTGGTGGGCATT 57.041 42.857 0.00 0.00 30.17 3.56
332 341 3.959495 AAGATATTGACTGGTGGGCAT 57.041 42.857 0.00 0.00 30.17 4.40
333 342 3.780294 ACTAAGATATTGACTGGTGGGCA 59.220 43.478 0.00 0.00 0.00 5.36
334 343 4.130118 CACTAAGATATTGACTGGTGGGC 58.870 47.826 0.00 0.00 0.00 5.36
335 344 5.359194 ACACTAAGATATTGACTGGTGGG 57.641 43.478 0.00 0.00 0.00 4.61
336 345 7.687941 AAAACACTAAGATATTGACTGGTGG 57.312 36.000 0.00 0.00 0.00 4.61
358 367 4.920640 TTTACCTCACCAATCGCAAAAA 57.079 36.364 0.00 0.00 0.00 1.94
478 505 1.779569 AGGCACGAGAACAGTAAACG 58.220 50.000 0.00 0.00 0.00 3.60
485 514 3.325870 CATTAGTCAAGGCACGAGAACA 58.674 45.455 0.00 0.00 0.00 3.18
543 572 4.811024 CAGCATAAGGAAGAATTAGACGCA 59.189 41.667 0.00 0.00 0.00 5.24
582 625 3.650942 ACTTGTGGATTAGTGGACTGGAA 59.349 43.478 0.00 0.00 0.00 3.53
623 671 7.477945 AGCCTATGTACTACAACTTACAAGT 57.522 36.000 0.00 0.00 42.04 3.16
624 672 8.136165 CCTAGCCTATGTACTACAACTTACAAG 58.864 40.741 0.00 0.00 32.07 3.16
625 673 7.417116 GCCTAGCCTATGTACTACAACTTACAA 60.417 40.741 0.00 0.00 32.07 2.41
626 674 6.040166 GCCTAGCCTATGTACTACAACTTACA 59.960 42.308 0.00 0.00 32.83 2.41
627 675 6.445475 GCCTAGCCTATGTACTACAACTTAC 58.555 44.000 0.00 0.00 0.00 2.34
628 676 5.240183 CGCCTAGCCTATGTACTACAACTTA 59.760 44.000 0.00 0.00 0.00 2.24
629 677 4.037684 CGCCTAGCCTATGTACTACAACTT 59.962 45.833 0.00 0.00 0.00 2.66
630 678 3.568853 CGCCTAGCCTATGTACTACAACT 59.431 47.826 0.00 0.00 0.00 3.16
631 679 3.305199 CCGCCTAGCCTATGTACTACAAC 60.305 52.174 0.00 0.00 0.00 3.32
670 718 1.662309 CGAGTATGTCCGCCGTGTATC 60.662 57.143 0.00 0.00 0.00 2.24
676 724 0.457166 TTGAACGAGTATGTCCGCCG 60.457 55.000 0.00 0.00 0.00 6.46
730 779 6.681729 TGGTCAAGGTATTTTCAGACTAGT 57.318 37.500 0.00 0.00 0.00 2.57
813 871 2.158561 GATTGTTGGCGGCTGGCTTT 62.159 55.000 21.03 0.13 42.94 3.51
891 949 0.668535 GGTGACAAGTTGGTTCTGGC 59.331 55.000 7.96 0.00 0.00 4.85
931 1015 3.241059 CTCGTACGTGCAGCTCGC 61.241 66.667 16.05 0.83 42.89 5.03
980 1064 1.004440 GCGTTTGCTCCTCCACTCT 60.004 57.895 0.00 0.00 38.39 3.24
984 1068 1.675310 CATGGCGTTTGCTCCTCCA 60.675 57.895 0.00 0.00 42.25 3.86
1013 1097 1.657751 GGCGAGCATGAGGAAAACCC 61.658 60.000 0.00 0.00 0.00 4.11
1017 1101 1.377202 GGTGGCGAGCATGAGGAAA 60.377 57.895 0.00 0.00 0.00 3.13
1219 1309 1.811266 CCGTGAACCAGATGGCGAG 60.811 63.158 0.00 0.00 39.32 5.03
1727 1820 3.158537 TTGAGGTTGTCGCTGGCGA 62.159 57.895 13.78 13.78 46.87 5.54
1915 2020 2.663520 CAGCCCGTACGTGCACAA 60.664 61.111 24.29 0.42 0.00 3.33
2373 2520 5.415077 CAGGAAGGAGTAGAAGTAGACGAAA 59.585 44.000 0.00 0.00 0.00 3.46
2694 2850 1.887707 GTGGTTGATCCGGCCGATC 60.888 63.158 30.73 25.63 46.70 3.69
2724 2880 0.463620 AGCAGAAGCCGAAGATCCTC 59.536 55.000 0.00 0.00 43.56 3.71
2778 2934 2.284258 AGCGAGCCCTTCTCCACT 60.284 61.111 0.00 0.00 38.62 4.00
2886 3042 4.015406 TGGTGCAGGTACGCCAGG 62.015 66.667 0.00 0.00 45.14 4.45
3529 3721 5.001874 GGAGTTATCGACTTCAGGGTTTTT 58.998 41.667 0.00 0.00 39.19 1.94
3530 3722 4.565028 GGGAGTTATCGACTTCAGGGTTTT 60.565 45.833 0.00 0.00 39.19 2.43
3531 3723 3.055312 GGGAGTTATCGACTTCAGGGTTT 60.055 47.826 0.00 0.00 39.19 3.27
3532 3724 2.500504 GGGAGTTATCGACTTCAGGGTT 59.499 50.000 0.00 0.00 39.19 4.11
3533 3725 2.108970 GGGAGTTATCGACTTCAGGGT 58.891 52.381 0.00 0.00 39.19 4.34
3534 3726 1.067212 CGGGAGTTATCGACTTCAGGG 59.933 57.143 0.00 0.00 39.19 4.45
3535 3727 2.022195 TCGGGAGTTATCGACTTCAGG 58.978 52.381 0.00 0.00 39.19 3.86
3644 3837 0.672401 GGAGGGCGTTCGTGATTTCA 60.672 55.000 0.00 0.00 0.00 2.69
3727 3959 6.976934 AAACAATCTGGGCTTCTTCTTTTA 57.023 33.333 0.00 0.00 0.00 1.52
3987 4254 7.420002 CGATTATTATTGTATGCATCATGGGG 58.580 38.462 0.19 0.00 0.00 4.96
3991 4258 7.628769 TGGCGATTATTATTGTATGCATCAT 57.371 32.000 0.19 0.00 0.00 2.45
4285 4600 6.317642 TGTCATGGGAAATTTACATAAGTCGG 59.682 38.462 2.10 0.00 0.00 4.79
4302 4617 8.829612 GGCAAATTTATCTTATTTTGTCATGGG 58.170 33.333 0.00 0.00 34.63 4.00
4308 4623 9.956640 TTCCATGGCAAATTTATCTTATTTTGT 57.043 25.926 6.96 0.00 32.88 2.83
4381 4768 6.784176 GCCATGGCAAATTTACTTTAAATGG 58.216 36.000 32.08 0.00 38.45 3.16
4429 4816 7.273164 GCCATGGCAATTTTTAACTTTTATTGC 59.727 33.333 32.08 0.00 46.28 3.56
4448 4835 9.127006 CAAATTAACTTTTTATTTTGCCATGGC 57.873 29.630 30.54 30.54 34.34 4.40


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

AutoCloner maintained by Alex Coulton.