Multiple sequence alignment - TraesCS1D01G121300

Loading Multiple Alignment...

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 TraesCS1D01G121300 chr1D 100.000 3566 0 0 1 3566 121236225 121239790 0.000000e+00 6586.0
1 TraesCS1D01G121300 chr1D 78.879 232 39 9 3301 3527 487198135 487197909 7.980000e-32 148.0
2 TraesCS1D01G121300 chr1B 95.447 2416 76 15 412 2798 184193728 184196138 0.000000e+00 3821.0
3 TraesCS1D01G121300 chr1B 91.429 140 11 1 65 203 184193336 184193475 1.310000e-44 191.0
4 TraesCS1D01G121300 chr1B 95.789 95 4 0 607 701 376074230 376074324 1.710000e-33 154.0
5 TraesCS1D01G121300 chr1B 92.784 97 7 0 318 414 184193564 184193660 1.330000e-29 141.0
6 TraesCS1D01G121300 chr1B 89.231 65 6 1 108 171 211317046 211316982 2.950000e-11 80.5
7 TraesCS1D01G121300 chr1B 90.323 62 5 1 110 171 470989950 470989890 2.950000e-11 80.5
8 TraesCS1D01G121300 chr1A 93.707 2495 92 16 446 2913 132795288 132797744 0.000000e+00 3677.0
9 TraesCS1D01G121300 chr1A 86.517 178 11 7 72 245 132795113 132795281 2.190000e-42 183.0
10 TraesCS1D01G121300 chr1A 95.745 94 2 2 611 704 490796265 490796174 2.220000e-32 150.0
11 TraesCS1D01G121300 chr1A 95.699 93 2 2 619 710 256826579 256826488 7.980000e-32 148.0
12 TraesCS1D01G121300 chr1A 92.857 98 7 0 607 704 349361914 349362011 3.710000e-30 143.0
13 TraesCS1D01G121300 chr1A 96.226 53 1 1 449 500 132795228 132795280 6.340000e-13 86.1
14 TraesCS1D01G121300 chr1A 97.727 44 1 0 3523 3566 132797746 132797789 3.820000e-10 76.8
15 TraesCS1D01G121300 chr6A 83.555 602 62 25 2930 3511 272121783 272122367 2.440000e-146 529.0
16 TraesCS1D01G121300 chr6A 86.408 206 16 3 2726 2931 272121522 272121715 7.750000e-52 215.0
17 TraesCS1D01G121300 chr6A 90.361 83 5 2 92 172 327429216 327429297 4.870000e-19 106.0
18 TraesCS1D01G121300 chr6A 85.526 76 9 2 173 246 485349470 485349395 1.060000e-10 78.7
19 TraesCS1D01G121300 chr6D 84.074 540 55 16 2930 3456 209917514 209918035 3.200000e-135 492.0
20 TraesCS1D01G121300 chr6D 85.644 202 17 3 2726 2927 209917253 209917442 6.040000e-48 202.0
21 TraesCS1D01G121300 chr6B 82.687 387 35 16 2928 3309 399738123 399738482 7.430000e-82 315.0
22 TraesCS1D01G121300 chr6B 85.507 207 16 8 2725 2931 399737865 399738057 1.680000e-48 204.0
23 TraesCS1D01G121300 chrUn 92.079 202 15 1 242 443 46202503 46202303 2.100000e-72 283.0
24 TraesCS1D01G121300 chr5D 90.404 198 16 3 254 448 287300588 287300391 1.270000e-64 257.0
25 TraesCS1D01G121300 chr5D 81.860 215 35 4 3312 3522 540230779 540230565 1.020000e-40 178.0
26 TraesCS1D01G121300 chr4A 89.447 199 20 1 251 448 229496234 229496432 2.130000e-62 250.0
27 TraesCS1D01G121300 chr4A 81.132 212 33 6 3318 3524 321899366 321899575 2.850000e-36 163.0
28 TraesCS1D01G121300 chr4A 80.365 219 39 4 3309 3524 368567342 368567559 2.850000e-36 163.0
29 TraesCS1D01G121300 chr4A 91.000 100 9 0 254 353 684658673 684658574 6.210000e-28 135.0
30 TraesCS1D01G121300 chr2D 83.784 185 27 2 3341 3522 332335317 332335133 4.730000e-39 172.0
31 TraesCS1D01G121300 chr2D 80.569 211 30 10 3328 3531 618309908 618309702 6.170000e-33 152.0
32 TraesCS1D01G121300 chr3B 83.243 185 28 2 3341 3522 812616894 812616710 2.200000e-37 167.0
33 TraesCS1D01G121300 chr3B 87.692 65 8 0 378 442 794989120 794989056 3.820000e-10 76.8
34 TraesCS1D01G121300 chr4D 96.739 92 2 1 614 704 6267158 6267067 6.170000e-33 152.0
35 TraesCS1D01G121300 chr2A 95.789 95 2 2 611 704 42482112 42482205 6.170000e-33 152.0
36 TraesCS1D01G121300 chr4B 93.939 99 3 3 608 704 631578851 631578948 2.870000e-31 147.0
37 TraesCS1D01G121300 chr2B 77.586 116 22 3 2724 2837 69202627 69202514 2.300000e-07 67.6


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 TraesCS1D01G121300 chr1D 121236225 121239790 3565 False 6586.000000 6586 100.00000 1 3566 1 chr1D.!!$F1 3565
1 TraesCS1D01G121300 chr1B 184193336 184196138 2802 False 1384.333333 3821 93.22000 65 2798 3 chr1B.!!$F2 2733
2 TraesCS1D01G121300 chr1A 132795113 132797789 2676 False 1005.725000 3677 93.54425 72 3566 4 chr1A.!!$F2 3494
3 TraesCS1D01G121300 chr6A 272121522 272122367 845 False 372.000000 529 84.98150 2726 3511 2 chr6A.!!$F2 785
4 TraesCS1D01G121300 chr6D 209917253 209918035 782 False 347.000000 492 84.85900 2726 3456 2 chr6D.!!$F1 730
5 TraesCS1D01G121300 chr6B 399737865 399738482 617 False 259.500000 315 84.09700 2725 3309 2 chr6B.!!$F1 584

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
908 1003 0.458543 CGTGAATCTCACCACTCCCG 60.459 60.000 1.34 0.0 44.2 5.14 F
1615 1717 2.691771 GCTGACCTCGACTCGCTGA 61.692 63.158 0.00 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2420 2522 1.447838 GCGGCGATCTTGAGGTTGA 60.448 57.895 12.98 0.0 0.00 3.18 R
3262 3469 0.100325 TGGCTGTTTGCAACAACTCG 59.900 50.000 0.00 0.0 45.15 4.18 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
29 30 9.929180 ATTCAAAAGCCTAAAATCTCTTAAACC 57.071 29.630 0.00 0.00 0.00 3.27
30 31 8.472007 TCAAAAGCCTAAAATCTCTTAAACCA 57.528 30.769 0.00 0.00 0.00 3.67
31 32 8.919145 TCAAAAGCCTAAAATCTCTTAAACCAA 58.081 29.630 0.00 0.00 0.00 3.67
32 33 9.710900 CAAAAGCCTAAAATCTCTTAAACCAAT 57.289 29.630 0.00 0.00 0.00 3.16
34 35 9.929180 AAAGCCTAAAATCTCTTAAACCAATTC 57.071 29.630 0.00 0.00 0.00 2.17
35 36 8.067751 AGCCTAAAATCTCTTAAACCAATTCC 57.932 34.615 0.00 0.00 0.00 3.01
36 37 7.895962 AGCCTAAAATCTCTTAAACCAATTCCT 59.104 33.333 0.00 0.00 0.00 3.36
37 38 8.191446 GCCTAAAATCTCTTAAACCAATTCCTC 58.809 37.037 0.00 0.00 0.00 3.71
38 39 8.687242 CCTAAAATCTCTTAAACCAATTCCTCC 58.313 37.037 0.00 0.00 0.00 4.30
39 40 7.482169 AAAATCTCTTAAACCAATTCCTCCC 57.518 36.000 0.00 0.00 0.00 4.30
40 41 5.796502 ATCTCTTAAACCAATTCCTCCCA 57.203 39.130 0.00 0.00 0.00 4.37
41 42 5.796502 TCTCTTAAACCAATTCCTCCCAT 57.203 39.130 0.00 0.00 0.00 4.00
42 43 6.901615 TCTCTTAAACCAATTCCTCCCATA 57.098 37.500 0.00 0.00 0.00 2.74
43 44 7.465900 TCTCTTAAACCAATTCCTCCCATAT 57.534 36.000 0.00 0.00 0.00 1.78
44 45 7.882755 TCTCTTAAACCAATTCCTCCCATATT 58.117 34.615 0.00 0.00 0.00 1.28
45 46 8.343787 TCTCTTAAACCAATTCCTCCCATATTT 58.656 33.333 0.00 0.00 0.00 1.40
46 47 8.909423 TCTTAAACCAATTCCTCCCATATTTT 57.091 30.769 0.00 0.00 0.00 1.82
47 48 9.332713 TCTTAAACCAATTCCTCCCATATTTTT 57.667 29.630 0.00 0.00 0.00 1.94
81 82 1.777878 TGGTCCCAAGCTTAACTTCCA 59.222 47.619 0.00 2.06 36.04 3.53
90 91 7.939039 TCCCAAGCTTAACTTCCAATCATATAG 59.061 37.037 0.00 0.00 36.04 1.31
171 173 3.505386 AGCACACCCCATATTTCAACAA 58.495 40.909 0.00 0.00 0.00 2.83
176 178 4.160252 ACACCCCATATTTCAACAAGATGC 59.840 41.667 0.00 0.00 0.00 3.91
212 214 3.449632 ACGTGTGGGTTTGTAATTTTGC 58.550 40.909 0.00 0.00 0.00 3.68
229 233 9.090692 GTAATTTTGCTAAGAATGAATGCACAT 57.909 29.630 0.00 0.00 33.13 3.21
285 289 7.989416 ACGGGAAGACAAACTTTATTAATCA 57.011 32.000 0.00 0.00 39.13 2.57
286 290 8.575649 ACGGGAAGACAAACTTTATTAATCAT 57.424 30.769 0.00 0.00 39.13 2.45
287 291 9.675464 ACGGGAAGACAAACTTTATTAATCATA 57.325 29.630 0.00 0.00 39.13 2.15
304 308 8.771920 TTAATCATATGACCGTTACATCATCC 57.228 34.615 7.78 0.00 36.87 3.51
305 309 5.799827 TCATATGACCGTTACATCATCCA 57.200 39.130 0.00 0.00 36.87 3.41
306 310 5.538118 TCATATGACCGTTACATCATCCAC 58.462 41.667 0.00 0.00 36.87 4.02
307 311 5.304357 TCATATGACCGTTACATCATCCACT 59.696 40.000 0.00 0.00 36.87 4.00
308 312 6.492087 TCATATGACCGTTACATCATCCACTA 59.508 38.462 0.00 0.00 36.87 2.74
313 317 4.222145 ACCGTTACATCATCCACTAACAGT 59.778 41.667 0.00 0.00 0.00 3.55
314 318 5.175859 CCGTTACATCATCCACTAACAGTT 58.824 41.667 0.00 0.00 0.00 3.16
316 320 6.148811 CCGTTACATCATCCACTAACAGTTTT 59.851 38.462 0.00 0.00 0.00 2.43
327 331 6.987992 TCCACTAACAGTTTTACGATGAACTT 59.012 34.615 0.00 0.00 34.04 2.66
336 340 1.521681 CGATGAACTTCGGAGGGGC 60.522 63.158 0.00 0.00 35.50 5.80
342 346 0.625849 AACTTCGGAGGGGCATCAAT 59.374 50.000 0.00 0.00 0.00 2.57
353 357 4.106324 AGGGGCATCAATCCAAAAAGATT 58.894 39.130 0.00 0.00 36.92 2.40
382 386 2.307768 TCACGTCCCCATCTAGCTAAG 58.692 52.381 0.00 0.00 0.00 2.18
407 411 7.118971 AGTCATGAGCTACAAAATTTGACTCTC 59.881 37.037 13.19 13.68 38.60 3.20
409 413 8.314021 TCATGAGCTACAAAATTTGACTCTCTA 58.686 33.333 13.19 6.60 33.26 2.43
414 418 9.944376 AGCTACAAAATTTGACTCTCTAATACA 57.056 29.630 13.19 0.00 0.00 2.29
418 422 9.846248 ACAAAATTTGACTCTCTAATACAATGC 57.154 29.630 13.19 0.00 0.00 3.56
422 426 9.453572 AATTTGACTCTCTAATACAATGCTCAA 57.546 29.630 0.00 0.00 0.00 3.02
423 427 7.834068 TTGACTCTCTAATACAATGCTCAAC 57.166 36.000 0.00 0.00 0.00 3.18
424 428 6.935167 TGACTCTCTAATACAATGCTCAACA 58.065 36.000 0.00 0.00 0.00 3.33
430 503 6.701340 TCTAATACAATGCTCAACAGTCACT 58.299 36.000 0.00 0.00 0.00 3.41
433 506 4.558538 ACAATGCTCAACAGTCACTTTC 57.441 40.909 0.00 0.00 0.00 2.62
458 531 6.492087 CCCAAAATCTAGAAAGTGTGGGTTTA 59.508 38.462 16.61 0.00 39.74 2.01
868 963 1.137675 TCCATCTCACATCAGCCGAAG 59.862 52.381 0.00 0.00 0.00 3.79
889 984 2.040544 CCAGGCCCACACAATCGTC 61.041 63.158 0.00 0.00 0.00 4.20
908 1003 0.458543 CGTGAATCTCACCACTCCCG 60.459 60.000 1.34 0.00 44.20 5.14
939 1038 6.941218 GTAACAAGTGCCAGTTACTACTAC 57.059 41.667 7.90 0.00 44.04 2.73
941 1040 5.135508 ACAAGTGCCAGTTACTACTACTG 57.864 43.478 0.00 0.00 42.06 2.74
1062 1164 2.841988 GAGATCCTCCTGGCCGCT 60.842 66.667 0.00 0.00 0.00 5.52
1504 1606 4.704833 GGCTCCTGCTGCCGTTCA 62.705 66.667 0.00 0.00 41.03 3.18
1615 1717 2.691771 GCTGACCTCGACTCGCTGA 61.692 63.158 0.00 0.00 0.00 4.26
2420 2522 2.988839 GCAAGGACCTGGGGCTCAT 61.989 63.158 0.00 0.00 0.00 2.90
2542 2644 0.733150 GAACGGCCTCATGGTTAAGC 59.267 55.000 0.00 0.00 35.27 3.09
2556 2658 3.650942 TGGTTAAGCTCAAGAGAAGGGAA 59.349 43.478 6.19 0.00 0.00 3.97
2558 2660 4.263112 GGTTAAGCTCAAGAGAAGGGAAGT 60.263 45.833 0.32 0.00 0.00 3.01
2580 2682 5.357314 AGTGGCTTGATGAAGATGAATGAAG 59.643 40.000 0.00 0.00 0.00 3.02
2593 2695 3.738982 TGAATGAAGTCAGGCTTTTCGA 58.261 40.909 0.00 0.00 37.59 3.71
2705 2807 8.593492 TGTTTGTCGATCTGGATTTATCATAG 57.407 34.615 0.00 0.00 0.00 2.23
2981 3176 1.927174 GCTCAGCAACACGGTGTATAG 59.073 52.381 15.11 8.87 43.83 1.31
2982 3177 2.674177 GCTCAGCAACACGGTGTATAGT 60.674 50.000 15.11 0.00 43.83 2.12
2983 3178 3.428452 GCTCAGCAACACGGTGTATAGTA 60.428 47.826 15.11 0.08 43.83 1.82
2984 3179 4.352039 CTCAGCAACACGGTGTATAGTAG 58.648 47.826 15.11 6.36 43.83 2.57
3003 3198 1.718757 GGCGTCTTGATCACCATGGC 61.719 60.000 13.04 0.00 0.00 4.40
3004 3199 1.718757 GCGTCTTGATCACCATGGCC 61.719 60.000 13.04 0.00 0.00 5.36
3068 3263 5.300286 GGTCACTTCCTTCCAATAATCCATG 59.700 44.000 0.00 0.00 0.00 3.66
3073 3271 6.389869 ACTTCCTTCCAATAATCCATGGTCTA 59.610 38.462 12.58 4.81 37.94 2.59
3096 3294 1.022735 CTTAGAGTAGCTTCCGCCGA 58.977 55.000 0.00 0.00 36.60 5.54
3098 3296 1.434622 TAGAGTAGCTTCCGCCGACG 61.435 60.000 0.00 0.00 36.60 5.12
3099 3297 3.048941 GAGTAGCTTCCGCCGACGT 62.049 63.158 0.00 0.00 37.70 4.34
3100 3298 2.879462 GTAGCTTCCGCCGACGTG 60.879 66.667 0.00 0.00 37.70 4.49
3119 3317 1.679898 GTGGCCAGGCAAGAGTACT 59.320 57.895 15.19 0.00 0.00 2.73
3126 3324 0.461961 AGGCAAGAGTACTGATCGGC 59.538 55.000 0.00 0.00 0.00 5.54
3129 3327 0.179137 CAAGAGTACTGATCGGCGCA 60.179 55.000 10.83 0.00 0.00 6.09
3130 3328 0.101399 AAGAGTACTGATCGGCGCAG 59.899 55.000 10.83 5.07 39.26 5.18
3196 3403 2.466846 GAGAAGAAGAAGAGGGAGGCT 58.533 52.381 0.00 0.00 0.00 4.58
3203 3410 1.203364 AGAAGAGGGAGGCTCCTTTGA 60.203 52.381 31.39 0.00 37.25 2.69
3213 3420 1.005340 GCTCCTTTGATCTCGCTGTG 58.995 55.000 0.00 0.00 0.00 3.66
3217 3424 0.994995 CTTTGATCTCGCTGTGGTCG 59.005 55.000 0.00 0.00 0.00 4.79
3290 3497 1.536766 TGCAAACAGCCATCGAAGAAG 59.463 47.619 0.00 0.00 42.00 2.85
3292 3499 2.421424 GCAAACAGCCATCGAAGAAGAT 59.579 45.455 0.00 0.00 37.41 2.40
3295 3502 5.391950 GCAAACAGCCATCGAAGAAGATAAA 60.392 40.000 0.00 0.00 37.41 1.40
3296 3503 5.803020 AACAGCCATCGAAGAAGATAAAC 57.197 39.130 0.00 0.00 43.58 2.01
3297 3504 3.865745 ACAGCCATCGAAGAAGATAAACG 59.134 43.478 0.00 0.00 43.58 3.60
3299 3506 3.865745 AGCCATCGAAGAAGATAAACGTG 59.134 43.478 0.00 0.00 43.58 4.49
3316 3523 2.131067 TGGACGTGTGACCAGCTCA 61.131 57.895 0.00 0.00 34.93 4.26
3317 3524 1.293498 GGACGTGTGACCAGCTCAT 59.707 57.895 0.00 0.00 0.00 2.90
3397 3607 8.971073 CAGAGAATACTTTGGTTTTGGGAATAT 58.029 33.333 0.00 0.00 0.00 1.28
3406 3616 9.423061 CTTTGGTTTTGGGAATATTCTAGTTTG 57.577 33.333 14.95 0.00 0.00 2.93
3517 3729 9.474920 TTTGAAAATACTTTGCTATCAAACAGG 57.525 29.630 0.00 0.00 37.28 4.00
3518 3730 7.601856 TGAAAATACTTTGCTATCAAACAGGG 58.398 34.615 0.00 0.00 37.28 4.45
3519 3731 5.582689 AATACTTTGCTATCAAACAGGGC 57.417 39.130 0.00 0.00 37.28 5.19
3520 3732 2.171003 ACTTTGCTATCAAACAGGGCC 58.829 47.619 0.00 0.00 37.28 5.80
3521 3733 2.225117 ACTTTGCTATCAAACAGGGCCT 60.225 45.455 0.00 0.00 37.28 5.19
3533 3745 4.524802 AACAGGGCCTAATTGATGATGA 57.475 40.909 5.28 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.929180 GGTTTAAGAGATTTTAGGCTTTTGAAT 57.071 29.630 0.00 0.00 0.00 2.57
4 5 8.919145 TGGTTTAAGAGATTTTAGGCTTTTGAA 58.081 29.630 0.00 0.00 0.00 2.69
5 6 8.472007 TGGTTTAAGAGATTTTAGGCTTTTGA 57.528 30.769 0.00 0.00 0.00 2.69
6 7 9.710900 ATTGGTTTAAGAGATTTTAGGCTTTTG 57.289 29.630 0.00 0.00 0.00 2.44
8 9 9.929180 GAATTGGTTTAAGAGATTTTAGGCTTT 57.071 29.630 0.00 0.00 0.00 3.51
9 10 8.531982 GGAATTGGTTTAAGAGATTTTAGGCTT 58.468 33.333 0.00 0.00 0.00 4.35
10 11 7.895962 AGGAATTGGTTTAAGAGATTTTAGGCT 59.104 33.333 0.00 0.00 0.00 4.58
11 12 8.067751 AGGAATTGGTTTAAGAGATTTTAGGC 57.932 34.615 0.00 0.00 0.00 3.93
12 13 8.687242 GGAGGAATTGGTTTAAGAGATTTTAGG 58.313 37.037 0.00 0.00 0.00 2.69
13 14 8.687242 GGGAGGAATTGGTTTAAGAGATTTTAG 58.313 37.037 0.00 0.00 0.00 1.85
14 15 8.174085 TGGGAGGAATTGGTTTAAGAGATTTTA 58.826 33.333 0.00 0.00 0.00 1.52
15 16 7.016296 TGGGAGGAATTGGTTTAAGAGATTTT 58.984 34.615 0.00 0.00 0.00 1.82
16 17 6.561294 TGGGAGGAATTGGTTTAAGAGATTT 58.439 36.000 0.00 0.00 0.00 2.17
17 18 6.152638 TGGGAGGAATTGGTTTAAGAGATT 57.847 37.500 0.00 0.00 0.00 2.40
18 19 5.796502 TGGGAGGAATTGGTTTAAGAGAT 57.203 39.130 0.00 0.00 0.00 2.75
19 20 5.796502 ATGGGAGGAATTGGTTTAAGAGA 57.203 39.130 0.00 0.00 0.00 3.10
20 21 8.539117 AAATATGGGAGGAATTGGTTTAAGAG 57.461 34.615 0.00 0.00 0.00 2.85
21 22 8.909423 AAAATATGGGAGGAATTGGTTTAAGA 57.091 30.769 0.00 0.00 0.00 2.10
44 45 4.836175 GGGACCATCTCCTAAAACCAAAAA 59.164 41.667 0.00 0.00 39.39 1.94
45 46 4.140900 TGGGACCATCTCCTAAAACCAAAA 60.141 41.667 0.00 0.00 39.39 2.44
46 47 3.399644 TGGGACCATCTCCTAAAACCAAA 59.600 43.478 0.00 0.00 39.39 3.28
47 48 2.990284 TGGGACCATCTCCTAAAACCAA 59.010 45.455 0.00 0.00 39.39 3.67
48 49 2.638325 TGGGACCATCTCCTAAAACCA 58.362 47.619 0.00 0.00 39.39 3.67
49 50 3.621558 CTTGGGACCATCTCCTAAAACC 58.378 50.000 0.00 0.00 38.97 3.27
50 51 3.017442 GCTTGGGACCATCTCCTAAAAC 58.983 50.000 0.00 0.00 38.97 2.43
51 52 2.919602 AGCTTGGGACCATCTCCTAAAA 59.080 45.455 0.00 0.00 38.97 1.52
52 53 2.562296 AGCTTGGGACCATCTCCTAAA 58.438 47.619 0.00 0.00 38.97 1.85
53 54 2.270434 AGCTTGGGACCATCTCCTAA 57.730 50.000 0.00 0.00 39.39 2.69
54 55 2.270434 AAGCTTGGGACCATCTCCTA 57.730 50.000 0.00 0.00 39.39 2.94
55 56 2.239907 GTTAAGCTTGGGACCATCTCCT 59.760 50.000 9.86 0.00 39.39 3.69
56 57 2.239907 AGTTAAGCTTGGGACCATCTCC 59.760 50.000 9.86 0.00 38.55 3.71
57 58 3.636153 AGTTAAGCTTGGGACCATCTC 57.364 47.619 9.86 0.00 0.00 2.75
58 59 3.308473 GGAAGTTAAGCTTGGGACCATCT 60.308 47.826 9.86 0.00 37.59 2.90
59 60 3.017442 GGAAGTTAAGCTTGGGACCATC 58.983 50.000 9.86 6.73 37.59 3.51
60 61 2.378547 TGGAAGTTAAGCTTGGGACCAT 59.621 45.455 9.86 0.00 37.59 3.55
61 62 1.777878 TGGAAGTTAAGCTTGGGACCA 59.222 47.619 9.86 9.39 37.59 4.02
62 63 2.579410 TGGAAGTTAAGCTTGGGACC 57.421 50.000 9.86 6.87 37.59 4.46
63 64 4.079253 TGATTGGAAGTTAAGCTTGGGAC 58.921 43.478 9.86 5.30 37.59 4.46
90 91 4.456911 CCCATGTATGGTATCATGACAAGC 59.543 45.833 9.87 0.00 46.65 4.01
127 128 7.147915 TGCTTTAGGCCCATCTAACAATTTTAG 60.148 37.037 0.00 2.70 40.92 1.85
171 173 2.053618 GCCACGATCTAGGGCATCT 58.946 57.895 12.59 0.00 46.92 2.90
212 214 7.537715 TGTAAACCATGTGCATTCATTCTTAG 58.462 34.615 0.00 0.00 0.00 2.18
259 263 9.504708 TGATTAATAAAGTTTGTCTTCCCGTAA 57.495 29.630 0.00 0.00 35.02 3.18
260 264 9.675464 ATGATTAATAAAGTTTGTCTTCCCGTA 57.325 29.630 0.00 0.00 35.02 4.02
279 283 8.371699 TGGATGATGTAACGGTCATATGATTAA 58.628 33.333 9.02 0.00 35.33 1.40
281 285 6.650807 GTGGATGATGTAACGGTCATATGATT 59.349 38.462 9.02 1.94 35.33 2.57
282 286 6.014242 AGTGGATGATGTAACGGTCATATGAT 60.014 38.462 9.02 0.00 35.33 2.45
283 287 5.304357 AGTGGATGATGTAACGGTCATATGA 59.696 40.000 0.00 0.00 35.33 2.15
284 288 5.541845 AGTGGATGATGTAACGGTCATATG 58.458 41.667 0.00 0.00 35.33 1.78
285 289 5.808366 AGTGGATGATGTAACGGTCATAT 57.192 39.130 0.00 0.00 35.33 1.78
286 290 6.097129 TGTTAGTGGATGATGTAACGGTCATA 59.903 38.462 0.00 0.00 35.33 2.15
287 291 5.105106 TGTTAGTGGATGATGTAACGGTCAT 60.105 40.000 0.00 0.00 37.76 3.06
288 292 4.221041 TGTTAGTGGATGATGTAACGGTCA 59.779 41.667 0.00 0.00 0.00 4.02
289 293 4.751060 TGTTAGTGGATGATGTAACGGTC 58.249 43.478 0.00 0.00 0.00 4.79
290 294 4.222145 ACTGTTAGTGGATGATGTAACGGT 59.778 41.667 0.00 0.00 39.21 4.83
291 295 4.755411 ACTGTTAGTGGATGATGTAACGG 58.245 43.478 0.00 0.00 37.64 4.44
292 296 6.721571 AAACTGTTAGTGGATGATGTAACG 57.278 37.500 0.00 0.00 0.00 3.18
293 297 8.166706 CGTAAAACTGTTAGTGGATGATGTAAC 58.833 37.037 0.00 0.00 0.00 2.50
294 298 8.089597 TCGTAAAACTGTTAGTGGATGATGTAA 58.910 33.333 0.00 0.00 0.00 2.41
295 299 7.604549 TCGTAAAACTGTTAGTGGATGATGTA 58.395 34.615 0.00 0.00 0.00 2.29
296 300 6.460781 TCGTAAAACTGTTAGTGGATGATGT 58.539 36.000 0.00 0.00 0.00 3.06
297 301 6.961359 TCGTAAAACTGTTAGTGGATGATG 57.039 37.500 0.00 0.00 0.00 3.07
298 302 7.327975 TCATCGTAAAACTGTTAGTGGATGAT 58.672 34.615 16.47 6.25 34.52 2.45
299 303 6.693466 TCATCGTAAAACTGTTAGTGGATGA 58.307 36.000 16.47 16.47 36.40 2.92
300 304 6.961359 TCATCGTAAAACTGTTAGTGGATG 57.039 37.500 13.71 13.71 0.00 3.51
301 305 7.159372 AGTTCATCGTAAAACTGTTAGTGGAT 58.841 34.615 0.00 0.00 34.52 3.41
302 306 6.518493 AGTTCATCGTAAAACTGTTAGTGGA 58.482 36.000 0.00 0.00 34.52 4.02
303 307 6.780706 AGTTCATCGTAAAACTGTTAGTGG 57.219 37.500 0.00 0.00 34.52 4.00
304 308 7.001922 CGAAGTTCATCGTAAAACTGTTAGTG 58.998 38.462 3.32 0.00 35.93 2.74
305 309 6.145048 CCGAAGTTCATCGTAAAACTGTTAGT 59.855 38.462 3.32 0.00 41.16 2.24
306 310 6.364165 TCCGAAGTTCATCGTAAAACTGTTAG 59.636 38.462 3.32 0.00 41.16 2.34
307 311 6.215121 TCCGAAGTTCATCGTAAAACTGTTA 58.785 36.000 3.32 0.00 41.16 2.41
308 312 5.051816 TCCGAAGTTCATCGTAAAACTGTT 58.948 37.500 3.32 0.00 41.16 3.16
313 317 3.592059 CCCTCCGAAGTTCATCGTAAAA 58.408 45.455 3.32 0.00 41.16 1.52
314 318 2.093869 CCCCTCCGAAGTTCATCGTAAA 60.094 50.000 3.32 0.00 41.16 2.01
316 320 1.108776 CCCCTCCGAAGTTCATCGTA 58.891 55.000 3.32 0.00 41.16 3.43
327 331 1.278302 TTGGATTGATGCCCCTCCGA 61.278 55.000 0.00 0.00 0.00 4.55
342 346 9.405587 GACGTGATAAAAATCAATCTTTTTGGA 57.594 29.630 0.00 0.00 38.44 3.53
353 357 5.110814 AGATGGGGACGTGATAAAAATCA 57.889 39.130 0.00 0.00 0.00 2.57
382 386 7.118971 AGAGAGTCAAATTTTGTAGCTCATGAC 59.881 37.037 21.00 0.00 36.95 3.06
407 411 6.974932 AGTGACTGTTGAGCATTGTATTAG 57.025 37.500 0.00 0.00 0.00 1.73
409 413 6.294176 GGAAAGTGACTGTTGAGCATTGTATT 60.294 38.462 0.00 0.00 0.00 1.89
414 418 2.887152 GGGAAAGTGACTGTTGAGCATT 59.113 45.455 0.00 0.00 0.00 3.56
415 419 2.158623 TGGGAAAGTGACTGTTGAGCAT 60.159 45.455 0.00 0.00 0.00 3.79
416 420 1.211703 TGGGAAAGTGACTGTTGAGCA 59.788 47.619 0.00 0.00 0.00 4.26
417 421 1.967319 TGGGAAAGTGACTGTTGAGC 58.033 50.000 0.00 0.00 0.00 4.26
418 422 4.981806 TTTTGGGAAAGTGACTGTTGAG 57.018 40.909 0.00 0.00 0.00 3.02
419 423 5.200483 AGATTTTGGGAAAGTGACTGTTGA 58.800 37.500 0.00 0.00 0.00 3.18
422 426 6.187727 TCTAGATTTTGGGAAAGTGACTGT 57.812 37.500 0.00 0.00 0.00 3.55
423 427 7.510549 TTTCTAGATTTTGGGAAAGTGACTG 57.489 36.000 0.00 0.00 0.00 3.51
424 428 7.751768 CTTTCTAGATTTTGGGAAAGTGACT 57.248 36.000 0.00 0.00 39.50 3.41
430 503 5.538433 CCCACACTTTCTAGATTTTGGGAAA 59.462 40.000 15.55 0.00 34.99 3.13
433 506 4.407365 ACCCACACTTTCTAGATTTTGGG 58.593 43.478 17.66 17.66 38.71 4.12
458 531 9.656040 TGTGCATTCATTCTTAAGCAAAATTAT 57.344 25.926 0.00 0.00 33.37 1.28
500 575 7.369551 ACAAAGGTATTCCAGACCGATATAA 57.630 36.000 0.00 0.00 42.21 0.98
511 586 6.928492 GCATTCTTTTGAACAAAGGTATTCCA 59.072 34.615 8.72 0.00 41.77 3.53
594 669 6.405538 TCCTGCTCATTTTCAAACAACTTTT 58.594 32.000 0.00 0.00 0.00 2.27
611 686 1.673665 CCACTGGTGCTTCCTGCTC 60.674 63.158 0.00 0.00 43.37 4.26
613 688 1.968540 GACCACTGGTGCTTCCTGC 60.969 63.158 5.10 0.00 35.25 4.85
616 691 0.977395 ACTAGACCACTGGTGCTTCC 59.023 55.000 5.10 0.00 36.51 3.46
706 783 0.528901 CTCCAACCGTGTCGTGTTCA 60.529 55.000 0.00 0.00 0.00 3.18
709 786 2.279918 GCTCCAACCGTGTCGTGT 60.280 61.111 0.00 0.00 0.00 4.49
716 793 1.048601 TTTCTCTGAGCTCCAACCGT 58.951 50.000 12.15 0.00 0.00 4.83
868 963 1.678970 GATTGTGTGGGCCTGGGAC 60.679 63.158 4.53 0.00 0.00 4.46
908 1003 0.881796 GGCACTTGTTACTTCCCTGC 59.118 55.000 0.00 0.00 0.00 4.85
916 1011 6.585322 CAGTAGTAGTAACTGGCACTTGTTAC 59.415 42.308 16.29 16.29 43.40 2.50
939 1038 6.419116 CCGACAGTTAATGTACTGATGATCAG 59.581 42.308 20.24 20.24 46.72 2.90
941 1040 5.175856 GCCGACAGTTAATGTACTGATGATC 59.824 44.000 12.90 0.00 46.72 2.92
1062 1164 0.325110 CCAGGGAGAGGAAGCAGAGA 60.325 60.000 0.00 0.00 0.00 3.10
1495 1597 2.390599 CGTGGTCCATGAACGGCAG 61.391 63.158 4.96 0.00 33.77 4.85
1599 1701 2.333417 GGTCAGCGAGTCGAGGTCA 61.333 63.158 18.61 0.00 0.00 4.02
1881 1983 3.728373 GTCATGGCGGGGTCCCTT 61.728 66.667 8.15 0.00 0.00 3.95
2079 2181 3.177883 GTCGAACACGACCGGTTTA 57.822 52.632 9.42 0.00 46.91 2.01
2420 2522 1.447838 GCGGCGATCTTGAGGTTGA 60.448 57.895 12.98 0.00 0.00 3.18
2542 2644 1.627834 AGCCACTTCCCTTCTCTTGAG 59.372 52.381 0.00 0.00 0.00 3.02
2556 2658 4.851843 TCATTCATCTTCATCAAGCCACT 58.148 39.130 0.00 0.00 0.00 4.00
2558 2660 5.258841 ACTTCATTCATCTTCATCAAGCCA 58.741 37.500 0.00 0.00 0.00 4.75
2580 2682 4.274459 AGAATATGCATCGAAAAGCCTGAC 59.726 41.667 0.19 0.00 0.00 3.51
2746 2869 7.853299 TCTTGCACCAACAGGTTAATATACTA 58.147 34.615 0.00 0.00 31.84 1.82
2981 3176 2.205074 CATGGTGATCAAGACGCCTAC 58.795 52.381 0.00 0.00 38.55 3.18
2982 3177 1.138859 CCATGGTGATCAAGACGCCTA 59.861 52.381 2.57 0.00 38.55 3.93
2983 3178 0.107508 CCATGGTGATCAAGACGCCT 60.108 55.000 2.57 0.00 38.55 5.52
2984 3179 1.718757 GCCATGGTGATCAAGACGCC 61.719 60.000 14.67 0.00 38.27 5.68
3046 3241 5.044179 ACCATGGATTATTGGAAGGAAGTGA 60.044 40.000 21.47 0.00 0.00 3.41
3096 3294 4.954970 CTTGCCTGGCCACCACGT 62.955 66.667 17.53 0.00 0.00 4.49
3098 3296 2.124507 TACTCTTGCCTGGCCACCAC 62.125 60.000 17.53 0.00 0.00 4.16
3099 3297 1.845664 TACTCTTGCCTGGCCACCA 60.846 57.895 17.53 0.00 0.00 4.17
3100 3298 1.377333 GTACTCTTGCCTGGCCACC 60.377 63.158 17.53 0.00 0.00 4.61
3131 3329 3.123620 GACTTCTGCGGCTGCTGG 61.124 66.667 22.51 13.62 43.34 4.85
3132 3330 1.909141 CTTGACTTCTGCGGCTGCTG 61.909 60.000 20.27 18.90 43.34 4.41
3133 3331 1.670406 CTTGACTTCTGCGGCTGCT 60.670 57.895 20.27 0.00 43.34 4.24
3134 3332 2.684843 CCTTGACTTCTGCGGCTGC 61.685 63.158 11.65 11.65 43.20 5.25
3135 3333 2.684843 GCCTTGACTTCTGCGGCTG 61.685 63.158 0.00 0.00 37.76 4.85
3136 3334 2.359230 GCCTTGACTTCTGCGGCT 60.359 61.111 0.00 0.00 37.76 5.52
3196 3403 0.976641 ACCACAGCGAGATCAAAGGA 59.023 50.000 0.00 0.00 0.00 3.36
3203 3410 1.977009 TGGACGACCACAGCGAGAT 60.977 57.895 1.37 0.00 41.77 2.75
3217 3424 2.338500 GAGATGTTTCTGTCGGTGGAC 58.662 52.381 0.00 0.00 43.71 4.02
3227 3434 0.984230 TTGCCTCCGGAGATGTTTCT 59.016 50.000 33.39 0.00 33.88 2.52
3230 3437 1.202533 CGTATTGCCTCCGGAGATGTT 60.203 52.381 33.39 16.37 0.00 2.71
3262 3469 0.100325 TGGCTGTTTGCAACAACTCG 59.900 50.000 0.00 0.00 45.15 4.18
3296 3503 3.036084 GCTGGTCACACGTCCACG 61.036 66.667 0.00 0.00 46.33 4.94
3297 3504 1.664965 GAGCTGGTCACACGTCCAC 60.665 63.158 1.28 0.00 0.00 4.02
3299 3506 0.320771 AATGAGCTGGTCACACGTCC 60.321 55.000 12.27 0.00 38.28 4.79
3366 3576 7.447238 CCCAAAACCAAAGTATTCTCTGTCTAA 59.553 37.037 0.00 0.00 0.00 2.10
3367 3577 6.940298 CCCAAAACCAAAGTATTCTCTGTCTA 59.060 38.462 0.00 0.00 0.00 2.59
3369 3579 5.768164 TCCCAAAACCAAAGTATTCTCTGTC 59.232 40.000 0.00 0.00 0.00 3.51
3371 3581 6.648879 TTCCCAAAACCAAAGTATTCTCTG 57.351 37.500 0.00 0.00 0.00 3.35
3406 3616 8.519526 TGGTCACCAATAAAAACTGTGATATTC 58.480 33.333 0.00 0.00 38.14 1.75
3413 3623 6.287589 TGTTTGGTCACCAATAAAAACTGT 57.712 33.333 10.97 0.00 43.55 3.55
3511 3723 4.870636 TCATCATCAATTAGGCCCTGTTT 58.129 39.130 0.00 0.00 0.00 2.83
3512 3724 4.524802 TCATCATCAATTAGGCCCTGTT 57.475 40.909 0.00 0.00 0.00 3.16
3513 3725 4.467769 CTTCATCATCAATTAGGCCCTGT 58.532 43.478 0.00 0.00 0.00 4.00
3514 3726 3.825014 CCTTCATCATCAATTAGGCCCTG 59.175 47.826 0.00 0.00 0.00 4.45
3515 3727 3.753193 GCCTTCATCATCAATTAGGCCCT 60.753 47.826 0.00 0.00 41.74 5.19
3516 3728 2.560105 GCCTTCATCATCAATTAGGCCC 59.440 50.000 0.00 0.00 41.74 5.80
3517 3729 3.930634 GCCTTCATCATCAATTAGGCC 57.069 47.619 0.00 0.00 41.74 5.19
3518 3730 5.555017 TCTAGCCTTCATCATCAATTAGGC 58.445 41.667 0.00 0.00 46.57 3.93
3519 3731 8.632906 AAATCTAGCCTTCATCATCAATTAGG 57.367 34.615 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.