Multiple sequence alignment - TraesCS1A01G204900

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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 TraesCS1A01G204900 chr1A 100.000 3950 0 0 1 3950 367010434 367006485 0.000000e+00 7295.0
1 TraesCS1A01G204900 chr1B 93.864 3406 150 24 556 3947 395963796 395960436 0.000000e+00 5077.0
2 TraesCS1A01G204900 chr1B 94.728 2257 94 10 724 2978 399195601 399197834 0.000000e+00 3485.0
3 TraesCS1A01G204900 chr1B 88.153 287 24 5 3 280 395967598 395967313 2.270000e-87 333.0
4 TraesCS1A01G204900 chr1D 96.311 2440 72 4 817 3249 294210217 294207789 0.000000e+00 3991.0
5 TraesCS1A01G204900 chr1D 91.435 467 25 3 3252 3716 294204612 294204159 9.320000e-176 627.0
6 TraesCS1A01G204900 chr1D 89.011 273 14 9 555 819 294214454 294214190 1.370000e-84 324.0
7 TraesCS1A01G204900 chr1D 85.870 276 18 7 3 275 294219353 294219096 1.400000e-69 274.0
8 TraesCS1A01G204900 chr5A 90.099 101 10 0 433 533 595905524 595905424 8.910000e-27 132.0
9 TraesCS1A01G204900 chr5A 87.273 110 14 0 437 546 401512480 401512371 4.140000e-25 126.0
10 TraesCS1A01G204900 chr7A 90.625 96 9 0 438 533 109827068 109826973 1.150000e-25 128.0
11 TraesCS1A01G204900 chr7A 89.000 100 10 1 435 533 654201030 654201129 5.360000e-24 122.0
12 TraesCS1A01G204900 chrUn 89.000 100 11 0 434 533 30689424 30689325 1.490000e-24 124.0
13 TraesCS1A01G204900 chr2A 87.619 105 12 1 428 531 55074900 55075004 1.930000e-23 121.0
14 TraesCS1A01G204900 chr2A 90.000 90 9 0 438 527 194551858 194551947 2.490000e-22 117.0
15 TraesCS1A01G204900 chr3A 88.119 101 10 2 428 527 380910340 380910439 6.930000e-23 119.0
16 TraesCS1A01G204900 chr3A 90.110 91 9 0 437 527 515915038 515915128 6.930000e-23 119.0
17 TraesCS1A01G204900 chr5B 85.246 61 8 1 290 350 558380988 558381047 1.190000e-05 62.1


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 TraesCS1A01G204900 chr1A 367006485 367010434 3949 True 7295.000000 7295 100.000000 1 3950 1 chr1A.!!$R1 3949
1 TraesCS1A01G204900 chr1B 399195601 399197834 2233 False 3485.000000 3485 94.728000 724 2978 1 chr1B.!!$F1 2254
2 TraesCS1A01G204900 chr1B 395960436 395967598 7162 True 2705.000000 5077 91.008500 3 3947 2 chr1B.!!$R1 3944
3 TraesCS1A01G204900 chr1D 294204159 294214454 10295 True 1647.333333 3991 92.252333 555 3716 3 chr1D.!!$R2 3161

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
179 186 0.037303 ATGCTGTCCTTGTGTCCTGG 59.963 55.0 0.00 0.0 0.00 4.45 F
229 236 0.108804 TGAGCCATCCGACTTCGAAC 60.109 55.0 0.00 0.0 43.02 3.95 F
399 3321 0.237235 TTTGCCATCTTCGCGTCAAC 59.763 50.0 5.77 0.0 0.00 3.18 F
819 8053 0.676782 GAGTGACCCCCGAAACCATG 60.677 60.0 0.00 0.0 0.00 3.66 F
1451 8685 0.764890 TTGCCAACTGTGCTCCTACT 59.235 50.0 0.00 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 8515 0.111061 AGGTTGTCATGGCTTCTGCA 59.889 50.000 0.00 0.00 41.91 4.41 R
1287 8521 0.478072 TGGTGAAGGTTGTCATGGCT 59.522 50.000 0.00 0.00 0.00 4.75 R
1712 8946 0.885596 TTACCCCAAACTGGAACGCG 60.886 55.000 3.53 3.53 40.96 6.01 R
2438 9689 2.667481 CGCTTGCCACACAATTAAATGG 59.333 45.455 0.00 0.00 37.72 3.16 R
3400 13828 2.148446 TGGGCTAGCTGAATTTGCAT 57.852 45.000 15.72 0.00 0.00 3.96 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
114 115 0.747852 GGGTTCATCTCGTCTCTCCC 59.252 60.000 0.00 0.00 0.00 4.30
135 136 3.406361 GATGCGGCGCGATCGATT 61.406 61.111 28.09 10.71 38.10 3.34
138 139 3.925238 GCGGCGCGATCGATTGTT 61.925 61.111 21.57 0.00 38.10 2.83
147 148 2.537625 GCGATCGATTGTTTCCTCTCTG 59.462 50.000 21.57 0.00 0.00 3.35
149 150 4.177026 CGATCGATTGTTTCCTCTCTGTT 58.823 43.478 10.26 0.00 0.00 3.16
165 166 7.655236 CTCTCTGTTTATGAGGAATATGCTG 57.345 40.000 0.00 0.00 32.78 4.41
166 167 7.129457 TCTCTGTTTATGAGGAATATGCTGT 57.871 36.000 0.00 0.00 32.78 4.40
168 169 6.291377 TCTGTTTATGAGGAATATGCTGTCC 58.709 40.000 0.00 0.00 0.00 4.02
179 186 0.037303 ATGCTGTCCTTGTGTCCTGG 59.963 55.000 0.00 0.00 0.00 4.45
193 200 8.977412 CCTTGTGTCCTGGGTATTTATTATTTT 58.023 33.333 0.00 0.00 0.00 1.82
229 236 0.108804 TGAGCCATCCGACTTCGAAC 60.109 55.000 0.00 0.00 43.02 3.95
238 245 1.693467 CGACTTCGAACACAATCGGA 58.307 50.000 0.00 0.00 42.92 4.55
246 256 2.090041 CGAACACAATCGGAACTACGTG 59.910 50.000 0.00 0.00 39.12 4.49
249 259 1.390123 CACAATCGGAACTACGTGCAG 59.610 52.381 0.00 0.00 34.94 4.41
280 290 4.680979 GTGTACGTACACGAACATGTTTC 58.319 43.478 35.43 14.37 45.87 2.78
282 292 5.624900 GTGTACGTACACGAACATGTTTCTA 59.375 40.000 35.43 5.23 45.87 2.10
283 293 6.142161 GTGTACGTACACGAACATGTTTCTAA 59.858 38.462 35.43 4.86 45.87 2.10
284 294 6.862608 TGTACGTACACGAACATGTTTCTAAT 59.137 34.615 24.10 0.84 43.02 1.73
286 296 5.921976 ACGTACACGAACATGTTTCTAATCA 59.078 36.000 13.36 0.00 43.02 2.57
291 1755 4.759693 ACGAACATGTTTCTAATCAGGCAA 59.240 37.500 13.36 0.00 0.00 4.52
301 1765 9.421806 TGTTTCTAATCAGGCAAATTATGTTTG 57.578 29.630 0.00 2.12 0.00 2.93
303 1767 9.638239 TTTCTAATCAGGCAAATTATGTTTGTC 57.362 29.630 2.77 2.77 34.47 3.18
306 1770 5.295431 TCAGGCAAATTATGTTTGTCGAG 57.705 39.130 0.00 4.28 38.88 4.04
308 1772 5.122239 TCAGGCAAATTATGTTTGTCGAGAG 59.878 40.000 0.00 0.68 38.88 3.20
311 1775 5.106712 GGCAAATTATGTTTGTCGAGAGTGA 60.107 40.000 0.00 0.00 0.00 3.41
312 1776 5.790495 GCAAATTATGTTTGTCGAGAGTGAC 59.210 40.000 0.00 0.00 39.37 3.67
324 1788 6.277605 TGTCGAGAGTGACAAGTTTAATTGA 58.722 36.000 0.00 0.00 45.40 2.57
325 1789 6.929049 TGTCGAGAGTGACAAGTTTAATTGAT 59.071 34.615 0.00 0.00 45.40 2.57
328 1792 7.655732 TCGAGAGTGACAAGTTTAATTGATGAA 59.344 33.333 0.00 0.00 34.20 2.57
329 1793 8.446273 CGAGAGTGACAAGTTTAATTGATGAAT 58.554 33.333 0.00 0.00 34.20 2.57
369 3291 5.125100 TCTTTGCCAAAAGAATGTGCTAG 57.875 39.130 0.00 0.00 46.91 3.42
373 3295 3.888323 TGCCAAAAGAATGTGCTAGTCAA 59.112 39.130 0.00 0.00 0.00 3.18
375 3297 4.261572 GCCAAAAGAATGTGCTAGTCAACA 60.262 41.667 0.00 0.00 0.00 3.33
376 3298 5.565439 GCCAAAAGAATGTGCTAGTCAACAT 60.565 40.000 0.00 0.00 0.00 2.71
383 3305 9.630098 AAGAATGTGCTAGTCAACATAAATTTG 57.370 29.630 0.00 0.00 0.00 2.32
385 3307 5.708948 TGTGCTAGTCAACATAAATTTGCC 58.291 37.500 0.00 0.00 0.00 4.52
387 3309 6.071447 TGTGCTAGTCAACATAAATTTGCCAT 60.071 34.615 0.00 0.00 0.00 4.40
388 3310 6.473455 GTGCTAGTCAACATAAATTTGCCATC 59.527 38.462 0.00 0.00 0.00 3.51
390 3312 7.093814 TGCTAGTCAACATAAATTTGCCATCTT 60.094 33.333 0.00 0.00 0.00 2.40
391 3313 7.433425 GCTAGTCAACATAAATTTGCCATCTTC 59.567 37.037 0.00 0.00 0.00 2.87
392 3314 6.324819 AGTCAACATAAATTTGCCATCTTCG 58.675 36.000 0.00 0.00 0.00 3.79
393 3315 5.004726 GTCAACATAAATTTGCCATCTTCGC 59.995 40.000 0.00 0.00 0.00 4.70
396 3318 2.262572 AAATTTGCCATCTTCGCGTC 57.737 45.000 5.77 0.00 0.00 5.19
397 3319 1.164411 AATTTGCCATCTTCGCGTCA 58.836 45.000 5.77 0.00 0.00 4.35
398 3320 1.164411 ATTTGCCATCTTCGCGTCAA 58.836 45.000 5.77 0.00 0.00 3.18
399 3321 0.237235 TTTGCCATCTTCGCGTCAAC 59.763 50.000 5.77 0.00 0.00 3.18
400 3322 0.882484 TTGCCATCTTCGCGTCAACA 60.882 50.000 5.77 0.00 0.00 3.33
402 3324 1.286501 GCCATCTTCGCGTCAACATA 58.713 50.000 5.77 0.00 0.00 2.29
403 3325 1.663643 GCCATCTTCGCGTCAACATAA 59.336 47.619 5.77 0.00 0.00 1.90
406 3328 4.730613 GCCATCTTCGCGTCAACATAAAAT 60.731 41.667 5.77 0.00 0.00 1.82
407 3329 5.331902 CCATCTTCGCGTCAACATAAAATT 58.668 37.500 5.77 0.00 0.00 1.82
408 3330 5.799936 CCATCTTCGCGTCAACATAAAATTT 59.200 36.000 5.77 0.00 0.00 1.82
409 3331 6.307800 CCATCTTCGCGTCAACATAAAATTTT 59.692 34.615 5.77 8.75 0.00 1.82
410 3332 6.904954 TCTTCGCGTCAACATAAAATTTTC 57.095 33.333 6.72 0.00 0.00 2.29
412 3334 7.081349 TCTTCGCGTCAACATAAAATTTTCAT 58.919 30.769 6.72 0.00 0.00 2.57
413 3335 6.609907 TCGCGTCAACATAAAATTTTCATG 57.390 33.333 6.72 11.54 0.00 3.07
445 3482 8.958043 CAATACTCTTTTGAACTACAGTTTTGC 58.042 33.333 0.00 0.00 38.56 3.68
446 3483 6.759497 ACTCTTTTGAACTACAGTTTTGCT 57.241 33.333 0.00 0.00 38.56 3.91
450 3581 9.226345 CTCTTTTGAACTACAGTTTTGCTAAAG 57.774 33.333 0.00 3.79 38.56 1.85
451 3582 7.700656 TCTTTTGAACTACAGTTTTGCTAAAGC 59.299 33.333 0.00 0.00 38.56 3.51
455 3586 6.039270 TGAACTACAGTTTTGCTAAAGCACAT 59.961 34.615 3.66 0.00 44.18 3.21
457 3588 7.520614 GAACTACAGTTTTGCTAAAGCACATCT 60.521 37.037 3.66 0.02 44.18 2.90
466 3597 5.793026 GCTAAAGCACATCTAGATATGCC 57.207 43.478 28.11 11.97 41.89 4.40
471 3602 7.918536 AAAGCACATCTAGATATGCCATAAG 57.081 36.000 28.11 5.94 41.89 1.73
472 3603 5.426504 AGCACATCTAGATATGCCATAAGC 58.573 41.667 28.11 5.82 41.89 3.09
483 3614 2.589798 GCCATAAGCATTGCACATGT 57.410 45.000 11.91 0.00 42.97 3.21
486 3617 4.046462 GCCATAAGCATTGCACATGTAAG 58.954 43.478 11.91 2.91 42.97 2.34
487 3618 4.440525 GCCATAAGCATTGCACATGTAAGT 60.441 41.667 11.91 0.00 42.97 2.24
489 3620 3.855689 AAGCATTGCACATGTAAGTCC 57.144 42.857 11.91 0.00 0.00 3.85
490 3621 3.077484 AGCATTGCACATGTAAGTCCT 57.923 42.857 11.91 0.00 0.00 3.85
491 3622 4.220693 AGCATTGCACATGTAAGTCCTA 57.779 40.909 11.91 0.00 0.00 2.94
492 3623 4.785301 AGCATTGCACATGTAAGTCCTAT 58.215 39.130 11.91 0.00 0.00 2.57
494 3625 6.537355 AGCATTGCACATGTAAGTCCTATAT 58.463 36.000 11.91 0.00 0.00 0.86
495 3626 6.652481 AGCATTGCACATGTAAGTCCTATATC 59.348 38.462 11.91 0.00 0.00 1.63
496 3627 6.427853 GCATTGCACATGTAAGTCCTATATCA 59.572 38.462 3.15 0.00 0.00 2.15
498 3629 9.006839 CATTGCACATGTAAGTCCTATATCATT 57.993 33.333 0.00 0.00 0.00 2.57
537 3668 9.616156 AGATTGATATGGATATCTTCTTCATGC 57.384 33.333 2.05 0.00 39.82 4.06
539 3670 9.976776 ATTGATATGGATATCTTCTTCATGCTT 57.023 29.630 2.05 0.00 39.82 3.91
545 3676 9.803507 ATGGATATCTTCTTCATGCTTAATTCA 57.196 29.630 2.05 0.00 0.00 2.57
546 3677 9.631257 TGGATATCTTCTTCATGCTTAATTCAA 57.369 29.630 2.05 0.00 0.00 2.69
573 3824 1.485066 GGCCCTTTGAACTATCTCCGA 59.515 52.381 0.00 0.00 0.00 4.55
574 3825 2.552031 GCCCTTTGAACTATCTCCGAC 58.448 52.381 0.00 0.00 0.00 4.79
575 3826 2.810650 CCCTTTGAACTATCTCCGACG 58.189 52.381 0.00 0.00 0.00 5.12
576 3827 2.426024 CCCTTTGAACTATCTCCGACGA 59.574 50.000 0.00 0.00 0.00 4.20
590 3841 4.755629 TCTCCGACGATATAGGAACAGAAG 59.244 45.833 0.00 0.00 30.65 2.85
599 3850 6.360947 CGATATAGGAACAGAAGAACATCGTG 59.639 42.308 0.00 0.00 0.00 4.35
639 3892 3.198872 GCTGGAAAATTAGGAGTCCTCG 58.801 50.000 17.09 0.00 34.61 4.63
672 3925 1.378124 CCTCCGACTCCTCTTCCGTC 61.378 65.000 0.00 0.00 0.00 4.79
681 3938 4.317488 ACTCCTCTTCCGTCGATAGTATC 58.683 47.826 0.00 0.00 37.40 2.24
819 8053 0.676782 GAGTGACCCCCGAAACCATG 60.677 60.000 0.00 0.00 0.00 3.66
987 8221 2.978010 GTTCACCGGCACCACCTG 60.978 66.667 0.00 0.00 35.61 4.00
1119 8353 1.472878 TGTCTCTGGCACGATACAGTC 59.527 52.381 0.00 0.00 36.17 3.51
1134 8368 1.990614 AGTCTTCCCCGCTTCCTCC 60.991 63.158 0.00 0.00 0.00 4.30
1280 8514 1.402984 CGTGTCCTACCTGAGCAGAAC 60.403 57.143 0.00 0.00 0.00 3.01
1281 8515 1.896465 GTGTCCTACCTGAGCAGAACT 59.104 52.381 0.00 0.00 0.00 3.01
1282 8516 1.895798 TGTCCTACCTGAGCAGAACTG 59.104 52.381 0.00 0.00 0.00 3.16
1294 8528 1.817357 CAGAACTGCAGAAGCCATGA 58.183 50.000 23.35 0.00 41.13 3.07
1339 8573 4.496507 GCTTGTTGACAGAGAAGGTGTTTC 60.497 45.833 0.00 0.00 35.97 2.78
1424 8658 1.078848 AGCTCGCGAGGCTCAATTT 60.079 52.632 35.10 9.61 33.31 1.82
1451 8685 0.764890 TTGCCAACTGTGCTCCTACT 59.235 50.000 0.00 0.00 0.00 2.57
1454 8688 1.941668 GCCAACTGTGCTCCTACTGAC 60.942 57.143 0.00 0.00 0.00 3.51
1506 8740 5.420739 GGTCACCCATTAGCTTTTGGATTAA 59.579 40.000 14.51 0.00 34.81 1.40
1553 8787 6.530913 TCATCGCTTATAGTGCTTGAATTC 57.469 37.500 0.00 0.00 0.00 2.17
1700 8934 3.250040 GCCTTGGTATAGTAAACATGGCG 59.750 47.826 0.00 0.00 41.97 5.69
1712 8946 1.160137 ACATGGCGCTCAAGAAACTC 58.840 50.000 7.64 0.00 0.00 3.01
1756 8990 1.132453 GCTGATTCCCGTTTGCCTAAC 59.868 52.381 0.00 0.00 0.00 2.34
2438 9689 8.702438 CATGAATGGTGTTTTGTTTAGATCAAC 58.298 33.333 0.00 0.00 0.00 3.18
2473 9724 1.461897 GCAAGCGCATTTTGCTGAAAT 59.538 42.857 21.55 0.00 45.64 2.17
2824 10078 7.335171 CAGAGTTTGATGTTCCACTGATTGATA 59.665 37.037 0.00 0.00 0.00 2.15
2850 10104 8.976986 ATTACATTTTCTTTGAGCTTGATCAC 57.023 30.769 0.00 0.00 0.00 3.06
2962 10216 5.195940 ACATGCCTTGAGCTGTGTTATTAT 58.804 37.500 0.00 0.00 44.23 1.28
3023 10277 7.759433 CACTAACTTAGGCATTTTAATTGGTGG 59.241 37.037 0.88 0.00 0.00 4.61
3181 10435 3.945285 GTGAAGACAACTTTGAAGGTCCA 59.055 43.478 0.00 0.00 36.39 4.02
3197 10451 5.881923 AGGTCCAACTACAAACTAGTTCA 57.118 39.130 8.95 0.00 35.76 3.18
3296 13724 3.898482 AGTTTTGTTAGTGGTCTTGGCT 58.102 40.909 0.00 0.00 0.00 4.75
3400 13828 3.815809 CACTATTTATGGAGGGGCGAAA 58.184 45.455 0.00 0.00 0.00 3.46
3439 13867 7.130775 AGCCCAACTCTAGGTAGATTTACTTA 58.869 38.462 0.00 0.00 0.00 2.24
3442 13870 7.140048 CCAACTCTAGGTAGATTTACTTAGCG 58.860 42.308 7.48 4.81 38.61 4.26
3448 13876 8.910944 TCTAGGTAGATTTACTTAGCGAAATGT 58.089 33.333 7.48 0.00 38.61 2.71
3518 13946 8.537728 TGTTGAAGGCTATGGATGAAATAATT 57.462 30.769 0.00 0.00 0.00 1.40
3529 13957 7.333528 TGGATGAAATAATTAAGTGTCAGCC 57.666 36.000 13.94 13.94 40.98 4.85
3567 13995 6.745116 CATGTCTTCATGCATCATTATGGTT 58.255 36.000 0.00 0.00 43.66 3.67
3615 14043 4.851843 TGAAGCTCCATCTCATTCATTGT 58.148 39.130 0.00 0.00 0.00 2.71
3623 14051 4.201980 CCATCTCATTCATTGTGCGTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
3626 14054 4.330894 TCTCATTCATTGTGCGTTCATCTC 59.669 41.667 0.00 0.00 0.00 2.75
3681 14113 3.907474 TCAACACTCCCTTCTTGTCCATA 59.093 43.478 0.00 0.00 0.00 2.74
3696 14128 3.785887 TGTCCATACTAGGCCCTTCATTT 59.214 43.478 0.00 0.00 0.00 2.32
3741 14173 7.816513 TGAAATTTTCACAACAACATGTTCTCA 59.183 29.630 8.48 0.00 34.81 3.27
3757 14189 6.325993 TGTTCTCATGAATATTCCCCAGAA 57.674 37.500 12.90 12.74 34.40 3.02
3761 14193 7.152942 TCTCATGAATATTCCCCAGAAATGA 57.847 36.000 12.90 11.36 35.09 2.57
3808 14240 2.364002 GTGGAAGCTCTAGTGAGGGATC 59.636 54.545 0.00 0.00 40.53 3.36
3812 14244 1.133199 AGCTCTAGTGAGGGATCCAGG 60.133 57.143 15.23 0.00 40.53 4.45
3814 14246 2.158445 GCTCTAGTGAGGGATCCAGGTA 60.158 54.545 15.23 0.00 40.53 3.08
3817 14249 2.877154 AGTGAGGGATCCAGGTATGT 57.123 50.000 15.23 0.00 0.00 2.29
3833 14265 6.405065 CCAGGTATGTGTGGATCTTGAAAATG 60.405 42.308 0.00 0.00 35.67 2.32
3849 14281 4.462483 TGAAAATGAATAGTTGTGGAGGCC 59.538 41.667 0.00 0.00 0.00 5.19
3866 14298 0.519961 GCCGTGGGTGTAACAATCAC 59.480 55.000 0.00 0.00 39.98 3.06
3880 14312 4.199432 ACAATCACTGAGATGTCCTGAC 57.801 45.455 0.00 0.00 36.96 3.51
3888 14320 2.632996 TGAGATGTCCTGACCGAAAACT 59.367 45.455 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.133730 AGGTACTCATCCGTCTCCCTC 60.134 57.143 0.00 0.00 0.00 4.30
1 2 0.927767 AGGTACTCATCCGTCTCCCT 59.072 55.000 0.00 0.00 0.00 4.20
127 128 3.775202 ACAGAGAGGAAACAATCGATCG 58.225 45.455 9.36 9.36 0.00 3.69
147 148 6.543831 ACAAGGACAGCATATTCCTCATAAAC 59.456 38.462 0.00 0.00 41.72 2.01
149 150 6.057533 CACAAGGACAGCATATTCCTCATAA 58.942 40.000 0.00 0.00 41.72 1.90
162 163 1.302832 CCCAGGACACAAGGACAGC 60.303 63.158 0.00 0.00 0.00 4.40
163 164 1.348064 TACCCAGGACACAAGGACAG 58.652 55.000 0.00 0.00 0.00 3.51
164 165 2.038863 ATACCCAGGACACAAGGACA 57.961 50.000 0.00 0.00 0.00 4.02
165 166 3.434940 AAATACCCAGGACACAAGGAC 57.565 47.619 0.00 0.00 0.00 3.85
166 167 5.789574 AATAAATACCCAGGACACAAGGA 57.210 39.130 0.00 0.00 0.00 3.36
193 200 2.418197 GCTCAGCCCGTATACACAAAGA 60.418 50.000 3.32 0.00 0.00 2.52
194 201 1.933853 GCTCAGCCCGTATACACAAAG 59.066 52.381 3.32 0.00 0.00 2.77
197 204 1.820581 GGCTCAGCCCGTATACACA 59.179 57.895 3.37 0.00 44.06 3.72
198 205 4.752514 GGCTCAGCCCGTATACAC 57.247 61.111 3.37 0.00 44.06 2.90
222 229 3.059044 CGTAGTTCCGATTGTGTTCGAAG 59.941 47.826 0.00 0.00 41.62 3.79
229 236 1.390123 CTGCACGTAGTTCCGATTGTG 59.610 52.381 0.00 0.00 41.61 3.33
238 245 1.068417 TTCCGCACTGCACGTAGTT 59.932 52.632 1.11 0.00 41.61 2.24
246 256 2.851104 GTACACGTTCCGCACTGC 59.149 61.111 0.00 0.00 0.00 4.40
260 270 6.674005 TTAGAAACATGTTCGTGTACGTAC 57.326 37.500 18.90 18.90 39.56 3.67
263 273 6.384178 TGATTAGAAACATGTTCGTGTACG 57.616 37.500 12.39 0.00 41.45 3.67
266 276 4.154195 GCCTGATTAGAAACATGTTCGTGT 59.846 41.667 12.39 0.00 0.00 4.49
276 286 9.423061 ACAAACATAATTTGCCTGATTAGAAAC 57.577 29.630 0.00 0.00 32.93 2.78
280 290 7.471721 TCGACAAACATAATTTGCCTGATTAG 58.528 34.615 0.00 0.00 32.93 1.73
282 292 6.150976 TCTCGACAAACATAATTTGCCTGATT 59.849 34.615 0.00 0.00 32.93 2.57
283 293 5.647658 TCTCGACAAACATAATTTGCCTGAT 59.352 36.000 0.00 0.00 32.93 2.90
284 294 5.000591 TCTCGACAAACATAATTTGCCTGA 58.999 37.500 0.00 0.00 32.93 3.86
286 296 5.003804 ACTCTCGACAAACATAATTTGCCT 58.996 37.500 0.00 0.00 32.93 4.75
301 1765 6.764877 TCAATTAAACTTGTCACTCTCGAC 57.235 37.500 0.00 0.00 36.40 4.20
303 1767 7.351414 TCATCAATTAAACTTGTCACTCTCG 57.649 36.000 0.00 0.00 0.00 4.04
348 2632 4.874970 ACTAGCACATTCTTTTGGCAAAG 58.125 39.130 13.04 7.78 40.91 2.77
349 2633 4.340666 TGACTAGCACATTCTTTTGGCAAA 59.659 37.500 8.93 8.93 0.00 3.68
350 2634 3.888323 TGACTAGCACATTCTTTTGGCAA 59.112 39.130 0.00 0.00 0.00 4.52
357 3279 9.630098 CAAATTTATGTTGACTAGCACATTCTT 57.370 29.630 7.82 0.00 0.00 2.52
358 3280 7.756722 GCAAATTTATGTTGACTAGCACATTCT 59.243 33.333 7.82 0.00 0.00 2.40
359 3281 7.009540 GGCAAATTTATGTTGACTAGCACATTC 59.990 37.037 7.82 0.00 30.83 2.67
365 3287 6.799512 AGATGGCAAATTTATGTTGACTAGC 58.200 36.000 0.00 0.00 34.88 3.42
366 3288 7.641411 CGAAGATGGCAAATTTATGTTGACTAG 59.359 37.037 0.00 0.00 34.88 2.57
367 3289 7.471721 CGAAGATGGCAAATTTATGTTGACTA 58.528 34.615 0.00 0.00 34.88 2.59
369 3291 5.004726 GCGAAGATGGCAAATTTATGTTGAC 59.995 40.000 0.00 0.00 34.35 3.18
373 3295 3.128589 ACGCGAAGATGGCAAATTTATGT 59.871 39.130 15.93 0.00 0.00 2.29
375 3297 3.376859 TGACGCGAAGATGGCAAATTTAT 59.623 39.130 15.93 0.00 0.00 1.40
376 3298 2.744741 TGACGCGAAGATGGCAAATTTA 59.255 40.909 15.93 0.00 0.00 1.40
381 3303 0.882484 TGTTGACGCGAAGATGGCAA 60.882 50.000 15.93 2.29 30.13 4.52
383 3305 1.286501 TATGTTGACGCGAAGATGGC 58.713 50.000 15.93 0.00 0.00 4.40
385 3307 6.853279 AAATTTTATGTTGACGCGAAGATG 57.147 33.333 15.93 0.00 0.00 2.90
387 3309 6.431278 TGAAAATTTTATGTTGACGCGAAGA 58.569 32.000 15.93 0.00 0.00 2.87
388 3310 6.667981 TGAAAATTTTATGTTGACGCGAAG 57.332 33.333 15.93 0.00 0.00 3.79
390 3312 6.374578 TCATGAAAATTTTATGTTGACGCGA 58.625 32.000 15.93 0.00 0.00 5.87
391 3313 6.609907 TCATGAAAATTTTATGTTGACGCG 57.390 33.333 3.53 3.53 0.00 6.01
392 3314 9.643652 TTTTTCATGAAAATTTTATGTTGACGC 57.356 25.926 29.13 0.00 39.69 5.19
421 3458 8.451908 AGCAAAACTGTAGTTCAAAAGAGTAT 57.548 30.769 0.00 0.00 37.25 2.12
427 3464 7.749539 GCTTTAGCAAAACTGTAGTTCAAAA 57.250 32.000 0.00 0.00 41.59 2.44
466 3597 5.066893 AGGACTTACATGTGCAATGCTTATG 59.933 40.000 9.11 16.46 0.00 1.90
471 3602 6.427853 TGATATAGGACTTACATGTGCAATGC 59.572 38.462 9.11 0.00 0.00 3.56
472 3603 7.967890 TGATATAGGACTTACATGTGCAATG 57.032 36.000 9.11 0.00 0.00 2.82
511 3642 9.616156 GCATGAAGAAGATATCCATATCAATCT 57.384 33.333 0.00 8.50 41.21 2.40
513 3644 9.976776 AAGCATGAAGAAGATATCCATATCAAT 57.023 29.630 0.00 0.00 41.21 2.57
519 3650 9.803507 TGAATTAAGCATGAAGAAGATATCCAT 57.196 29.630 0.00 0.00 0.00 3.41
537 3668 5.859205 AAGGGCCTATTGCTTGAATTAAG 57.141 39.130 6.41 0.00 40.92 1.85
539 3670 5.268387 TCAAAGGGCCTATTGCTTGAATTA 58.732 37.500 6.41 0.00 40.92 1.40
540 3671 4.095946 TCAAAGGGCCTATTGCTTGAATT 58.904 39.130 6.41 0.00 40.92 2.17
541 3672 3.711863 TCAAAGGGCCTATTGCTTGAAT 58.288 40.909 6.41 0.00 40.92 2.57
542 3673 3.168035 TCAAAGGGCCTATTGCTTGAA 57.832 42.857 6.41 0.00 40.92 2.69
543 3674 2.825532 GTTCAAAGGGCCTATTGCTTGA 59.174 45.455 6.41 10.28 40.92 3.02
544 3675 2.827921 AGTTCAAAGGGCCTATTGCTTG 59.172 45.455 6.41 7.62 40.92 4.01
545 3676 3.175438 AGTTCAAAGGGCCTATTGCTT 57.825 42.857 6.41 0.00 40.92 3.91
546 3677 2.907458 AGTTCAAAGGGCCTATTGCT 57.093 45.000 6.41 4.84 40.92 3.91
548 3679 5.066593 GGAGATAGTTCAAAGGGCCTATTG 58.933 45.833 6.41 13.84 0.00 1.90
549 3680 4.202367 CGGAGATAGTTCAAAGGGCCTATT 60.202 45.833 6.41 0.08 0.00 1.73
550 3681 3.325135 CGGAGATAGTTCAAAGGGCCTAT 59.675 47.826 6.41 0.00 0.00 2.57
551 3682 2.698797 CGGAGATAGTTCAAAGGGCCTA 59.301 50.000 6.41 0.00 0.00 3.93
552 3683 1.486726 CGGAGATAGTTCAAAGGGCCT 59.513 52.381 0.00 0.00 0.00 5.19
553 3684 1.485066 TCGGAGATAGTTCAAAGGGCC 59.515 52.381 0.00 0.00 0.00 5.80
558 3809 6.938596 TCCTATATCGTCGGAGATAGTTCAAA 59.061 38.462 5.37 0.00 41.02 2.69
573 3824 6.039493 ACGATGTTCTTCTGTTCCTATATCGT 59.961 38.462 0.00 0.00 41.10 3.73
574 3825 6.360947 CACGATGTTCTTCTGTTCCTATATCG 59.639 42.308 0.00 0.00 39.43 2.92
575 3826 7.426410 TCACGATGTTCTTCTGTTCCTATATC 58.574 38.462 0.00 0.00 0.00 1.63
576 3827 7.348080 TCACGATGTTCTTCTGTTCCTATAT 57.652 36.000 0.00 0.00 0.00 0.86
590 3841 4.329801 TGTATTGCACAGATCACGATGTTC 59.670 41.667 0.00 0.00 31.89 3.18
599 3850 1.397693 GCGCGATGTATTGCACAGATC 60.398 52.381 12.10 0.00 41.51 2.75
639 3892 1.644786 CGGAGGGACAATTCGGTTGC 61.645 60.000 2.05 0.00 41.69 4.17
819 8053 0.107165 GGCCAAGGGTCACATAGTCC 60.107 60.000 0.00 0.00 0.00 3.85
1119 8353 2.586792 CTGGAGGAAGCGGGGAAG 59.413 66.667 0.00 0.00 0.00 3.46
1134 8368 0.676151 GCTGAAGAACCTCCTGGCTG 60.676 60.000 0.00 0.00 36.63 4.85
1280 8514 0.524862 GGTTGTCATGGCTTCTGCAG 59.475 55.000 7.63 7.63 41.91 4.41
1281 8515 0.111061 AGGTTGTCATGGCTTCTGCA 59.889 50.000 0.00 0.00 41.91 4.41
1282 8516 1.200948 GAAGGTTGTCATGGCTTCTGC 59.799 52.381 0.00 0.00 38.76 4.26
1283 8517 2.227388 GTGAAGGTTGTCATGGCTTCTG 59.773 50.000 0.00 0.00 0.00 3.02
1284 8518 2.508526 GTGAAGGTTGTCATGGCTTCT 58.491 47.619 0.00 0.00 0.00 2.85
1285 8519 1.541588 GGTGAAGGTTGTCATGGCTTC 59.458 52.381 0.00 0.00 0.00 3.86
1286 8520 1.133513 TGGTGAAGGTTGTCATGGCTT 60.134 47.619 0.00 0.00 0.00 4.35
1287 8521 0.478072 TGGTGAAGGTTGTCATGGCT 59.522 50.000 0.00 0.00 0.00 4.75
1294 8528 2.268076 GCGGCATGGTGAAGGTTGT 61.268 57.895 0.00 0.00 0.00 3.32
1435 8669 1.670087 CGTCAGTAGGAGCACAGTTGG 60.670 57.143 0.00 0.00 0.00 3.77
1506 8740 2.738213 CTTTGCGGCCTCAGGTCAGT 62.738 60.000 0.00 0.00 0.00 3.41
1553 8787 1.021202 TGGAAACAACCAGCTTGACG 58.979 50.000 0.00 0.00 37.44 4.35
1605 8839 1.961180 GCTCCTTGGCTTAGGCTCGA 61.961 60.000 7.43 0.00 38.73 4.04
1712 8946 0.885596 TTACCCCAAACTGGAACGCG 60.886 55.000 3.53 3.53 40.96 6.01
1756 8990 7.264947 AGGAAAACCAAAATATAAATCAGCCG 58.735 34.615 0.00 0.00 0.00 5.52
2066 9307 8.834465 GCAAGTGTAATATGAGAATTCAGTCAT 58.166 33.333 8.44 11.26 36.61 3.06
2309 9560 5.105635 CGGGGCTATCATATAAACCGAACTA 60.106 44.000 0.00 0.00 42.42 2.24
2438 9689 2.667481 CGCTTGCCACACAATTAAATGG 59.333 45.455 0.00 0.00 37.72 3.16
2824 10078 9.415544 GTGATCAAGCTCAAAGAAAATGTAATT 57.584 29.630 0.00 0.00 38.98 1.40
2850 10104 3.644861 GGTTGTAACCTCAGGGTGG 57.355 57.895 6.54 0.00 46.67 4.61
3296 13724 5.456548 TCATGTACTTGTCCAACGACTAA 57.543 39.130 8.46 0.00 39.94 2.24
3400 13828 2.148446 TGGGCTAGCTGAATTTGCAT 57.852 45.000 15.72 0.00 0.00 3.96
3413 13841 6.680540 AGTAAATCTACCTAGAGTTGGGCTA 58.319 40.000 5.48 0.00 40.39 3.93
3518 13946 6.374333 GGATCAAATAAACAGGCTGACACTTA 59.626 38.462 23.66 12.59 0.00 2.24
3529 13957 8.851960 CATGAAGACATGGATCAAATAAACAG 57.148 34.615 0.00 0.00 46.95 3.16
3556 13984 7.177216 TCAAGACTTTGAAGCAACCATAATGAT 59.823 33.333 0.00 0.00 40.26 2.45
3615 14043 0.109272 GACGGACTGAGATGAACGCA 60.109 55.000 0.00 0.00 0.00 5.24
3623 14051 1.339247 GGAGACTGAGACGGACTGAGA 60.339 57.143 0.78 0.00 34.09 3.27
3626 14054 1.133982 CATGGAGACTGAGACGGACTG 59.866 57.143 0.00 0.00 0.00 3.51
3681 14113 0.618458 TCGCAAATGAAGGGCCTAGT 59.382 50.000 6.41 0.00 0.00 2.57
3696 14128 8.437360 AATTTCATATGTTCATACTTCTCGCA 57.563 30.769 1.90 0.00 0.00 5.10
3808 14240 3.912496 TCAAGATCCACACATACCTGG 57.088 47.619 0.00 0.00 0.00 4.45
3812 14244 9.941664 CTATTCATTTTCAAGATCCACACATAC 57.058 33.333 0.00 0.00 0.00 2.39
3814 14246 8.585471 ACTATTCATTTTCAAGATCCACACAT 57.415 30.769 0.00 0.00 0.00 3.21
3817 14249 8.298854 CACAACTATTCATTTTCAAGATCCACA 58.701 33.333 0.00 0.00 0.00 4.17
3833 14265 1.369625 CACGGCCTCCACAACTATTC 58.630 55.000 0.00 0.00 0.00 1.75
3849 14281 2.736721 CTCAGTGATTGTTACACCCACG 59.263 50.000 9.53 6.36 38.82 4.94
3866 14298 2.996621 GTTTTCGGTCAGGACATCTCAG 59.003 50.000 1.41 0.00 0.00 3.35
3880 14312 3.447944 ACTTAGCTAGGAGGAGTTTTCGG 59.552 47.826 10.24 0.00 0.00 4.30
3888 14320 6.437755 TGTATTGGTTACTTAGCTAGGAGGA 58.562 40.000 10.24 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.