Multiple sequence alignment - TraesCS2A01G269300

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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 TraesCS2A01G269300 chr2A 100.000 4079 0 0 1 4079 434614614 434610536 0.000000e+00 7533.0
1 TraesCS2A01G269300 chr2B 93.062 2551 105 28 668 3178 397456795 397454277 0.000000e+00 3664.0
2 TraesCS2A01G269300 chr2B 91.724 145 5 3 3279 3422 397454184 397454046 1.160000e-45 195.0
3 TraesCS2A01G269300 chr2D 92.385 2285 72 41 1185 3441 328372809 328370599 0.000000e+00 3162.0
4 TraesCS2A01G269300 chr2D 95.303 511 15 4 668 1177 328373383 328372881 0.000000e+00 802.0
5 TraesCS2A01G269300 chr6A 97.605 668 16 0 1 668 553931060 553931727 0.000000e+00 1146.0
6 TraesCS2A01G269300 chr7B 91.149 644 51 5 3439 4079 531916189 531915549 0.000000e+00 869.0
7 TraesCS2A01G269300 chr7B 89.767 645 51 8 3440 4079 332169954 332169320 0.000000e+00 811.0
8 TraesCS2A01G269300 chr7B 89.744 468 44 3 3475 3940 531904709 531905174 2.710000e-166 595.0
9 TraesCS2A01G269300 chr7B 90.741 108 6 2 3972 4077 69849233 69849128 1.530000e-29 141.0
10 TraesCS2A01G269300 chr7B 92.308 78 5 1 591 668 238108878 238108954 4.310000e-20 110.0
11 TraesCS2A01G269300 chr6B 93.640 566 21 5 1 566 652710121 652710671 0.000000e+00 832.0
12 TraesCS2A01G269300 chr6B 79.218 563 75 12 41 591 127367454 127367986 1.800000e-93 353.0
13 TraesCS2A01G269300 chr6B 92.308 117 8 1 562 677 652733514 652733630 9.070000e-37 165.0
14 TraesCS2A01G269300 chr6B 91.667 108 7 1 3972 4077 548948291 548948184 9.130000e-32 148.0
15 TraesCS2A01G269300 chr6B 91.667 108 7 1 3972 4077 549028803 549028696 9.130000e-32 148.0
16 TraesCS2A01G269300 chr4A 88.700 646 51 11 3437 4079 654900428 654901054 0.000000e+00 769.0
17 TraesCS2A01G269300 chr4A 82.324 611 80 15 1 609 589083286 589083870 4.710000e-139 505.0
18 TraesCS2A01G269300 chr4B 83.655 673 80 16 1 668 23841525 23840878 1.250000e-169 606.0
19 TraesCS2A01G269300 chr7D 84.536 582 80 6 3499 4077 272266372 272266946 5.920000e-158 568.0
20 TraesCS2A01G269300 chr7D 80.412 679 85 19 8 668 51453895 51454543 1.330000e-129 473.0
21 TraesCS2A01G269300 chr7D 91.096 146 11 1 3934 4077 110890313 110890168 3.220000e-46 196.0
22 TraesCS2A01G269300 chr7D 81.529 157 19 7 3445 3600 463035328 463035475 1.990000e-23 121.0
23 TraesCS2A01G269300 chr3D 80.495 687 88 17 8 678 95951891 95951235 6.130000e-133 484.0
24 TraesCS2A01G269300 chr1B 79.466 599 73 24 1 579 572206373 572206941 2.980000e-101 379.0
25 TraesCS2A01G269300 chr1B 82.353 153 25 2 3437 3588 646746059 646746210 9.200000e-27 132.0
26 TraesCS2A01G269300 chrUn 78.523 596 86 19 8 591 8821013 8821578 1.800000e-93 353.0
27 TraesCS2A01G269300 chrUn 91.667 108 7 1 3972 4077 426294590 426294483 9.130000e-32 148.0
28 TraesCS2A01G269300 chr3B 79.669 423 58 17 182 591 826364617 826364210 3.100000e-71 279.0
29 TraesCS2A01G269300 chr3B 91.358 81 7 0 590 670 803575745 803575825 1.200000e-20 111.0
30 TraesCS2A01G269300 chr5D 87.124 233 30 0 436 668 507770541 507770309 8.690000e-67 265.0
31 TraesCS2A01G269300 chr5D 81.325 166 23 7 3439 3600 44500275 44500436 1.190000e-25 128.0
32 TraesCS2A01G269300 chr7A 89.583 144 13 1 3936 4077 116018524 116018381 9.010000e-42 182.0
33 TraesCS2A01G269300 chr5B 83.333 150 22 3 3437 3586 692995537 692995683 7.110000e-28 135.0
34 TraesCS2A01G269300 chr5B 96.000 50 2 0 620 669 223993913 223993864 9.400000e-12 82.4
35 TraesCS2A01G269300 chr5A 94.737 38 2 0 631 668 494222697 494222660 4.400000e-05 60.2


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 TraesCS2A01G269300 chr2A 434610536 434614614 4078 True 7533.0 7533 100.000 1 4079 1 chr2A.!!$R1 4078
1 TraesCS2A01G269300 chr2B 397454046 397456795 2749 True 1929.5 3664 92.393 668 3422 2 chr2B.!!$R1 2754
2 TraesCS2A01G269300 chr2D 328370599 328373383 2784 True 1982.0 3162 93.844 668 3441 2 chr2D.!!$R1 2773
3 TraesCS2A01G269300 chr6A 553931060 553931727 667 False 1146.0 1146 97.605 1 668 1 chr6A.!!$F1 667
4 TraesCS2A01G269300 chr7B 531915549 531916189 640 True 869.0 869 91.149 3439 4079 1 chr7B.!!$R3 640
5 TraesCS2A01G269300 chr7B 332169320 332169954 634 True 811.0 811 89.767 3440 4079 1 chr7B.!!$R2 639
6 TraesCS2A01G269300 chr6B 652710121 652710671 550 False 832.0 832 93.640 1 566 1 chr6B.!!$F2 565
7 TraesCS2A01G269300 chr6B 127367454 127367986 532 False 353.0 353 79.218 41 591 1 chr6B.!!$F1 550
8 TraesCS2A01G269300 chr4A 654900428 654901054 626 False 769.0 769 88.700 3437 4079 1 chr4A.!!$F2 642
9 TraesCS2A01G269300 chr4A 589083286 589083870 584 False 505.0 505 82.324 1 609 1 chr4A.!!$F1 608
10 TraesCS2A01G269300 chr4B 23840878 23841525 647 True 606.0 606 83.655 1 668 1 chr4B.!!$R1 667
11 TraesCS2A01G269300 chr7D 272266372 272266946 574 False 568.0 568 84.536 3499 4077 1 chr7D.!!$F2 578
12 TraesCS2A01G269300 chr7D 51453895 51454543 648 False 473.0 473 80.412 8 668 1 chr7D.!!$F1 660
13 TraesCS2A01G269300 chr3D 95951235 95951891 656 True 484.0 484 80.495 8 678 1 chr3D.!!$R1 670
14 TraesCS2A01G269300 chr1B 572206373 572206941 568 False 379.0 379 79.466 1 579 1 chr1B.!!$F1 578
15 TraesCS2A01G269300 chrUn 8821013 8821578 565 False 353.0 353 78.523 8 591 1 chrUn.!!$F1 583

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
700 727 0.105039 GAGAATCGGCGGGAAGTGAT 59.895 55.0 7.21 0.00 0.0 3.06 F
1260 1357 1.160989 TTTGGCGATTGCGTACATGT 58.839 45.0 2.69 2.69 44.1 3.21 F
2736 2873 0.691332 TGGTGTTAACGTGGCCCATA 59.309 50.0 0.00 0.00 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2003 0.975887 GGATGCCCTGAGAGAGATCC 59.024 60.000 0.00 0.0 0.00 3.36 R
3030 3167 0.331954 TGAGAGGCCCGTAGACTCTT 59.668 55.000 9.29 0.0 41.38 2.85 R
3790 3961 1.454539 CGAAGGAGGTTTGGGGTGT 59.545 57.895 0.00 0.0 0.00 4.16 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.027751 GGCGTCTATGGTCGGAGC 59.972 66.667 0.00 0.00 0.00 4.70
57 58 1.272769 AGCGGAAGAGTTAGTGACCAC 59.727 52.381 0.00 0.00 0.00 4.16
130 131 0.771755 AACTTCCGCTTCCCCTTTCT 59.228 50.000 0.00 0.00 0.00 2.52
350 366 2.592512 AGAGGAGGAATAGAAGGTGGGA 59.407 50.000 0.00 0.00 0.00 4.37
452 469 1.507140 TCCCGTGATTTATGCCTCCT 58.493 50.000 0.00 0.00 0.00 3.69
582 602 9.651913 ATTTGATTACCAAAAATGAAAGCGTAT 57.348 25.926 0.00 0.00 46.64 3.06
642 669 1.413077 CGTAAGAGGGGAGATGGAACC 59.587 57.143 0.00 0.00 43.02 3.62
700 727 0.105039 GAGAATCGGCGGGAAGTGAT 59.895 55.000 7.21 0.00 0.00 3.06
901 930 1.286354 TGCGTCGAAAATGACCCGAC 61.286 55.000 0.00 0.00 46.27 4.79
912 941 1.666872 GACCCGACCGTTCCAACTG 60.667 63.158 0.00 0.00 0.00 3.16
965 995 6.487960 AGAATGTAGATTTCACGTCGACTAG 58.512 40.000 14.70 5.87 0.00 2.57
1053 1083 1.340017 TGCATCCTTAGCCTGTTGGTC 60.340 52.381 0.00 0.00 35.27 4.02
1183 1271 5.958955 AGGAACACACGGTACTAATTACTC 58.041 41.667 0.00 0.00 0.00 2.59
1246 1343 4.965119 ACTGACGGAAGATTAATTTGGC 57.035 40.909 0.00 0.00 0.00 4.52
1248 1345 3.601435 TGACGGAAGATTAATTTGGCGA 58.399 40.909 0.00 0.00 0.00 5.54
1260 1357 1.160989 TTTGGCGATTGCGTACATGT 58.839 45.000 2.69 2.69 44.10 3.21
1312 1409 2.880879 GCAGCGAATCACGAGCGA 60.881 61.111 0.00 0.00 45.77 4.93
1317 1414 2.506217 GAATCACGAGCGACCGCA 60.506 61.111 16.97 0.00 44.88 5.69
1392 1489 4.716784 ACGGCCTCATGATGGTATACATAT 59.283 41.667 0.00 0.00 40.72 1.78
1394 1491 6.040955 ACGGCCTCATGATGGTATACATATAG 59.959 42.308 0.00 0.00 40.72 1.31
1396 1493 7.522889 CGGCCTCATGATGGTATACATATAGAG 60.523 44.444 0.00 4.67 40.72 2.43
1472 1580 6.035866 GCAAGTGATGACATTTGTTTTGTTGA 59.964 34.615 0.00 0.00 42.82 3.18
1476 1589 8.605746 AGTGATGACATTTGTTTTGTTGAAATG 58.394 29.630 0.00 0.00 41.07 2.32
1656 1769 4.979197 GCACGTACATCCTCTCATTAGAAG 59.021 45.833 0.00 0.00 0.00 2.85
1694 1807 8.029522 TGCACTCTCTTCTTTGTTGTACTATAG 58.970 37.037 0.00 0.00 0.00 1.31
1695 1808 8.030106 GCACTCTCTTCTTTGTTGTACTATAGT 58.970 37.037 10.87 10.87 0.00 2.12
1812 1925 1.226491 GCAGTACGCGTACGACCAT 60.226 57.895 35.87 20.61 43.93 3.55
1816 1929 1.199789 AGTACGCGTACGACCATTCAA 59.800 47.619 35.87 4.74 43.93 2.69
1882 1995 9.575783 GTCACAAAACAAAACAAAATAGGAGTA 57.424 29.630 0.00 0.00 0.00 2.59
1890 2003 7.228706 ACAAAACAAAATAGGAGTACTCACCAG 59.771 37.037 23.91 9.24 0.00 4.00
1936 2050 6.116126 AGTAGATTAAGAAACCTGTGGCATC 58.884 40.000 0.00 0.00 0.00 3.91
1998 2112 2.633657 GACCAGCAACAGCACGTG 59.366 61.111 12.28 12.28 0.00 4.49
2114 2228 4.750098 CGCCGAGGTAATTATGTTTGATCT 59.250 41.667 0.00 0.00 0.00 2.75
2124 2238 9.261180 GTAATTATGTTTGATCTGATTCCGAGA 57.739 33.333 0.00 0.00 0.00 4.04
2139 2253 3.621558 TCCGAGAGTATCACATCACACT 58.378 45.455 0.00 0.00 37.82 3.55
2140 2254 3.628032 TCCGAGAGTATCACATCACACTC 59.372 47.826 0.00 0.00 37.82 3.51
2141 2255 3.378427 CCGAGAGTATCACATCACACTCA 59.622 47.826 3.67 0.00 39.90 3.41
2142 2256 4.346970 CGAGAGTATCACATCACACTCAC 58.653 47.826 3.67 0.00 39.90 3.51
2143 2257 4.142600 CGAGAGTATCACATCACACTCACA 60.143 45.833 3.67 0.00 39.90 3.58
2144 2258 5.065704 AGAGTATCACATCACACTCACAC 57.934 43.478 3.67 0.00 39.90 3.82
2145 2259 3.838120 AGTATCACATCACACTCACACG 58.162 45.455 0.00 0.00 0.00 4.49
2147 2261 2.134201 TCACATCACACTCACACGAC 57.866 50.000 0.00 0.00 0.00 4.34
2148 2262 1.407258 TCACATCACACTCACACGACA 59.593 47.619 0.00 0.00 0.00 4.35
2149 2263 2.035832 TCACATCACACTCACACGACAT 59.964 45.455 0.00 0.00 0.00 3.06
2150 2264 2.156310 CACATCACACTCACACGACATG 59.844 50.000 0.00 0.00 0.00 3.21
2189 2303 1.251251 GTTTGTGATGGCAGGCTCTT 58.749 50.000 0.00 0.00 0.00 2.85
2242 2366 4.286707 ACAGGGTAATTTAAGCATTCCCC 58.713 43.478 0.00 0.00 33.32 4.81
2262 2386 5.251468 TCCCCATTCATTCTCTTCTTCTGAA 59.749 40.000 0.00 0.00 0.00 3.02
2263 2387 5.948162 CCCCATTCATTCTCTTCTTCTGAAA 59.052 40.000 0.00 0.00 30.39 2.69
2270 2394 8.023050 TCATTCTCTTCTTCTGAAATTTCGTC 57.977 34.615 13.34 0.00 0.00 4.20
2278 2402 7.083875 TCTTCTGAAATTTCGTCTGTTTTGT 57.916 32.000 13.34 0.00 0.00 2.83
2310 2440 2.158900 ACGATGGCTGGGAACTAATGAG 60.159 50.000 0.00 0.00 0.00 2.90
2311 2441 2.103094 CGATGGCTGGGAACTAATGAGA 59.897 50.000 0.00 0.00 0.00 3.27
2321 2451 7.613801 GCTGGGAACTAATGAGAGATCTCTATA 59.386 40.741 25.18 17.07 43.25 1.31
2470 2603 1.352156 CTGGTCGGCGTACTGAAAGC 61.352 60.000 6.85 0.00 37.60 3.51
2534 2667 1.190643 CCTCTGTCCAGACCTTCCTC 58.809 60.000 0.00 0.00 33.22 3.71
2594 2727 4.518970 GTCCATTTGGCTCAAAGTGAGTAA 59.481 41.667 7.08 1.14 45.94 2.24
2620 2753 9.125026 AGCTCTATCTCTTTTCAGTTTCAAAAA 57.875 29.630 0.00 0.00 0.00 1.94
2719 2852 8.108551 AGAAAGAGATGAAACAAGATTTCTGG 57.891 34.615 0.00 0.00 35.17 3.86
2732 2869 1.310904 TTTCTGGTGTTAACGTGGCC 58.689 50.000 0.00 0.00 0.00 5.36
2736 2873 0.691332 TGGTGTTAACGTGGCCCATA 59.309 50.000 0.00 0.00 0.00 2.74
2752 2889 4.202212 GGCCCATATAATTTGACCCAACAC 60.202 45.833 0.00 0.00 0.00 3.32
2787 2924 5.709164 AGGTATAATCGCCAAGTACGACTAT 59.291 40.000 0.00 0.00 43.23 2.12
2820 2957 3.176708 CGACAACATCAAGTACTACGGG 58.823 50.000 0.00 0.00 0.00 5.28
3030 3167 2.282180 GCTGGGAACGCCAAGGAA 60.282 61.111 0.00 0.00 35.57 3.36
3080 3217 0.036010 AGGCTCCAGGACAAATGACG 60.036 55.000 0.00 0.00 0.00 4.35
3155 3293 7.633789 AGGAGTGGTCATACTTGTAAATCATT 58.366 34.615 0.00 0.00 0.00 2.57
3222 3386 8.792633 AGAAACGACAGAAATTATTTTCCATGA 58.207 29.630 0.00 0.00 41.86 3.07
3224 3388 8.915871 AACGACAGAAATTATTTTCCATGATG 57.084 30.769 0.00 2.01 41.86 3.07
3234 3398 1.026182 TTCCATGATGTCGCAGTGGC 61.026 55.000 0.00 0.00 0.00 5.01
3235 3399 1.746239 CCATGATGTCGCAGTGGCA 60.746 57.895 0.00 0.00 41.24 4.92
3236 3400 1.426621 CATGATGTCGCAGTGGCAC 59.573 57.895 10.29 10.29 41.24 5.01
3237 3401 1.746615 ATGATGTCGCAGTGGCACC 60.747 57.895 15.27 0.00 41.24 5.01
3238 3402 2.358615 GATGTCGCAGTGGCACCA 60.359 61.111 15.27 4.88 41.24 4.17
3239 3403 1.746615 GATGTCGCAGTGGCACCAT 60.747 57.895 15.27 10.04 41.24 3.55
3275 3439 5.815740 GCTCCCTTAGAAAATGATACGTGAA 59.184 40.000 0.00 0.00 0.00 3.18
3315 3479 4.376146 GACTCTGCAACTTGAGAAGAGTT 58.624 43.478 16.92 7.15 45.74 3.01
3391 3556 8.670804 CATACTTTGCTTTTCATCAAGAGAAG 57.329 34.615 0.00 0.00 40.47 2.85
3392 3557 6.949352 ACTTTGCTTTTCATCAAGAGAAGA 57.051 33.333 0.00 0.00 40.05 2.87
3395 3560 5.791367 TGCTTTTCATCAAGAGAAGATCG 57.209 39.130 0.00 0.00 40.05 3.69
3455 3620 8.775527 GCAGGCTAAATCTTTATCTTTACCTAC 58.224 37.037 0.00 0.00 0.00 3.18
3476 3641 9.749340 ACCTACTAATAAACCAACTATTGCTTT 57.251 29.630 0.00 0.00 0.00 3.51
3516 3683 3.181480 GCGATTTTGCATAAAAGCCCCTA 60.181 43.478 8.13 0.00 38.59 3.53
3526 3693 3.382083 AAAAGCCCCTATGTTTCCGAT 57.618 42.857 0.00 0.00 0.00 4.18
3539 3706 1.670791 TTCCGATAAATCAACCCGCC 58.329 50.000 0.00 0.00 0.00 6.13
3561 3728 5.124936 GCCGTCCTATTTTAACTGGTCAATT 59.875 40.000 0.00 0.00 0.00 2.32
3601 3768 2.676748 ACAAAAAGGTCCCTGCATTCA 58.323 42.857 0.00 0.00 0.00 2.57
3652 3820 5.797934 TGAGTGCTAAACAAAGAAAAACACG 59.202 36.000 0.00 0.00 0.00 4.49
3660 3828 0.814457 AAGAAAAACACGCAGGCACA 59.186 45.000 0.00 0.00 0.00 4.57
3769 3940 4.731853 TCCGCCACCTCCCCATCA 62.732 66.667 0.00 0.00 0.00 3.07
3790 3961 1.676678 CCTCCAATCTTCTCGGGCGA 61.677 60.000 0.00 0.00 0.00 5.54
3811 3982 0.838987 ACCCCAAACCTCCTTCGCTA 60.839 55.000 0.00 0.00 0.00 4.26
3815 3986 1.630148 CAAACCTCCTTCGCTACTCG 58.370 55.000 0.00 0.00 40.15 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.268899 ACGTGGTCACTAACTCTTCCG 59.731 52.381 0.00 0.00 0.00 4.30
57 58 0.469917 ACCCAATGGCCTCATCTACG 59.530 55.000 3.32 0.00 32.24 3.51
130 131 2.125147 GCATGCTAGCCGTCACCA 60.125 61.111 13.29 0.00 0.00 4.17
350 366 1.915078 CTCCCATTCGTGGAGCCCTT 61.915 60.000 0.00 0.00 42.75 3.95
582 602 3.691342 CCTCGTGCGACCCCTTCA 61.691 66.667 0.00 0.00 0.00 3.02
691 718 3.758300 CGTGCATTTTACATCACTTCCC 58.242 45.455 0.00 0.00 0.00 3.97
901 930 5.935789 TCTTCTTTTATACCAGTTGGAACGG 59.064 40.000 4.92 0.00 38.94 4.44
912 941 5.012768 TCCCCGATCCATCTTCTTTTATACC 59.987 44.000 0.00 0.00 0.00 2.73
965 995 2.304751 TTTTCTTCTACCGATCGGCC 57.695 50.000 33.62 0.00 39.32 6.13
993 1023 3.708890 TGTTAATCTGGCCATACGTACG 58.291 45.455 15.01 15.01 0.00 3.67
994 1024 5.526111 ACATTGTTAATCTGGCCATACGTAC 59.474 40.000 5.51 2.99 0.00 3.67
995 1025 5.525745 CACATTGTTAATCTGGCCATACGTA 59.474 40.000 5.51 0.00 0.00 3.57
996 1026 4.335315 CACATTGTTAATCTGGCCATACGT 59.665 41.667 5.51 0.00 0.00 3.57
1053 1083 4.101790 GCCCCAACGCACATCACG 62.102 66.667 0.00 0.00 0.00 4.35
1084 1114 3.217017 CGATTCCTCCGGAGCCGA 61.217 66.667 26.87 16.03 42.83 5.54
1183 1271 3.118454 CACGCGCCTGGTTACTGG 61.118 66.667 5.73 0.00 38.63 4.00
1246 1343 2.534349 GTCACCTACATGTACGCAATCG 59.466 50.000 0.08 0.00 42.43 3.34
1248 1345 2.164827 TCGTCACCTACATGTACGCAAT 59.835 45.455 12.19 0.00 33.75 3.56
1260 1357 1.246056 CCGTCTTGGGTCGTCACCTA 61.246 60.000 0.00 0.00 43.22 3.08
1343 1440 2.852075 AGGACCGGCACTTTCCCA 60.852 61.111 0.00 0.00 0.00 4.37
1392 1489 6.742109 ACAGTTGCTTTTTCGTAGTACTCTA 58.258 36.000 0.00 0.00 0.00 2.43
1394 1491 5.902051 ACAGTTGCTTTTTCGTAGTACTC 57.098 39.130 0.00 0.00 0.00 2.59
1396 1493 5.006941 TCCAACAGTTGCTTTTTCGTAGTAC 59.993 40.000 7.88 0.00 0.00 2.73
1403 1511 7.713764 ATTAACATCCAACAGTTGCTTTTTC 57.286 32.000 7.88 0.00 0.00 2.29
1472 1580 0.394352 GTCATCCCGTCCTGCCATTT 60.394 55.000 0.00 0.00 0.00 2.32
1476 1589 1.524621 CATGTCATCCCGTCCTGCC 60.525 63.158 0.00 0.00 0.00 4.85
1703 1816 9.929180 GTTCTCATCCAGCATTAGTATTACATA 57.071 33.333 0.00 0.00 0.00 2.29
1704 1817 7.880195 GGTTCTCATCCAGCATTAGTATTACAT 59.120 37.037 0.00 0.00 0.00 2.29
1705 1818 7.217200 GGTTCTCATCCAGCATTAGTATTACA 58.783 38.462 0.00 0.00 0.00 2.41
1706 1819 6.651225 GGGTTCTCATCCAGCATTAGTATTAC 59.349 42.308 0.00 0.00 0.00 1.89
1812 1925 1.174712 GCACCTTCTGCTGGCTTGAA 61.175 55.000 0.00 0.00 43.33 2.69
1877 1990 3.117663 AGAGAGATCCTGGTGAGTACTCC 60.118 52.174 20.11 11.08 0.00 3.85
1878 1991 4.134563 GAGAGAGATCCTGGTGAGTACTC 58.865 52.174 16.32 16.32 0.00 2.59
1879 1992 3.525609 TGAGAGAGATCCTGGTGAGTACT 59.474 47.826 0.00 0.00 0.00 2.73
1882 1995 2.358090 CCTGAGAGAGATCCTGGTGAGT 60.358 54.545 0.00 0.00 0.00 3.41
1890 2003 0.975887 GGATGCCCTGAGAGAGATCC 59.024 60.000 0.00 0.00 0.00 3.36
1936 2050 1.302431 TCCCCTGCATTCACACACG 60.302 57.895 0.00 0.00 0.00 4.49
2114 2228 4.644685 TGTGATGTGATACTCTCGGAATCA 59.355 41.667 0.00 0.00 0.00 2.57
2124 2238 3.506067 TCGTGTGAGTGTGATGTGATACT 59.494 43.478 0.00 0.00 0.00 2.12
2139 2253 7.589587 GTGTTATTTTTGATTCATGTCGTGTGA 59.410 33.333 0.00 0.00 0.00 3.58
2140 2254 7.591057 AGTGTTATTTTTGATTCATGTCGTGTG 59.409 33.333 0.00 0.00 0.00 3.82
2141 2255 7.648142 AGTGTTATTTTTGATTCATGTCGTGT 58.352 30.769 0.00 0.00 0.00 4.49
2142 2256 7.802720 TGAGTGTTATTTTTGATTCATGTCGTG 59.197 33.333 0.00 0.00 0.00 4.35
2143 2257 7.870826 TGAGTGTTATTTTTGATTCATGTCGT 58.129 30.769 0.00 0.00 0.00 4.34
2144 2258 8.791605 CATGAGTGTTATTTTTGATTCATGTCG 58.208 33.333 0.00 0.00 37.16 4.35
2145 2259 9.630098 ACATGAGTGTTATTTTTGATTCATGTC 57.370 29.630 0.00 0.00 46.32 3.06
2174 2288 2.012673 CAGTAAAGAGCCTGCCATCAC 58.987 52.381 0.00 0.00 0.00 3.06
2189 2303 2.103094 CTCATCGATTCCCAGCCAGTAA 59.897 50.000 0.00 0.00 0.00 2.24
2242 2366 9.275231 CGAAATTTCAGAAGAAGAGAATGAATG 57.725 33.333 17.99 0.00 34.71 2.67
2262 2386 7.696453 CAGTTGAGTTACAAAACAGACGAAATT 59.304 33.333 0.00 0.00 40.36 1.82
2263 2387 7.065324 TCAGTTGAGTTACAAAACAGACGAAAT 59.935 33.333 0.00 0.00 40.36 2.17
2270 2394 5.712217 TCGTCAGTTGAGTTACAAAACAG 57.288 39.130 3.67 0.00 40.36 3.16
2278 2402 2.353704 CCAGCCATCGTCAGTTGAGTTA 60.354 50.000 0.00 0.00 0.00 2.24
2310 2440 5.627499 CAGCAGTCCTGTATAGAGATCTC 57.373 47.826 15.29 15.29 36.79 2.75
2594 2727 8.682936 TTTTGAAACTGAAAAGAGATAGAGCT 57.317 30.769 0.00 0.00 0.00 4.09
2667 2800 4.062677 TCTTTCCTTCTTTTTCGACGGA 57.937 40.909 0.00 0.00 30.37 4.69
2682 2815 9.457110 GTTTCATCTCTTTCTTTCTTTCTTTCC 57.543 33.333 0.00 0.00 0.00 3.13
2719 2852 5.761165 AATTATATGGGCCACGTTAACAC 57.239 39.130 9.28 0.00 0.00 3.32
2732 2869 7.285172 TGATCAGTGTTGGGTCAAATTATATGG 59.715 37.037 0.00 0.00 0.00 2.74
2736 2873 6.484288 TCTGATCAGTGTTGGGTCAAATTAT 58.516 36.000 21.92 0.00 0.00 1.28
2752 2889 5.047731 TGGCGATTATACCTCTTCTGATCAG 60.048 44.000 17.07 17.07 0.00 2.90
3030 3167 0.331954 TGAGAGGCCCGTAGACTCTT 59.668 55.000 9.29 0.00 41.38 2.85
3080 3217 1.005394 AATCACGTCGTGGGTCCAC 60.005 57.895 24.33 9.96 43.01 4.02
3112 3249 8.160106 ACCACTCCTATCCTAAATGAATGAATC 58.840 37.037 0.00 0.00 0.00 2.52
3222 3386 1.746615 GATGGTGCCACTGCGACAT 60.747 57.895 0.00 0.00 41.78 3.06
3224 3388 2.358615 TGATGGTGCCACTGCGAC 60.359 61.111 0.00 0.00 41.78 5.19
3234 3398 1.893808 GCCGGCTATGGTGATGGTG 60.894 63.158 22.15 0.00 0.00 4.17
3235 3399 2.044806 GAGCCGGCTATGGTGATGGT 62.045 60.000 32.97 1.35 0.00 3.55
3236 3400 1.302033 GAGCCGGCTATGGTGATGG 60.302 63.158 32.97 0.00 0.00 3.51
3237 3401 1.302033 GGAGCCGGCTATGGTGATG 60.302 63.158 32.97 0.00 0.00 3.07
3238 3402 2.520536 GGGAGCCGGCTATGGTGAT 61.521 63.158 32.97 4.00 0.00 3.06
3239 3403 3.161450 GGGAGCCGGCTATGGTGA 61.161 66.667 32.97 0.00 0.00 4.02
3275 3439 4.463186 AGAGTCCAGTATTCAGTTTACGCT 59.537 41.667 0.00 0.00 0.00 5.07
3286 3450 4.284490 TCTCAAGTTGCAGAGTCCAGTATT 59.716 41.667 0.00 0.00 33.63 1.89
3315 3479 5.885352 CCACCACATTTTGTATCCAGATGTA 59.115 40.000 0.00 0.00 31.76 2.29
3328 3492 3.922171 TTTCAAAGGCCACCACATTTT 57.078 38.095 5.01 0.00 0.00 1.82
3388 3553 3.808095 GCTTATGCTGATTGCGATCTTC 58.192 45.455 15.08 7.18 46.63 2.87
3389 3554 3.892918 GCTTATGCTGATTGCGATCTT 57.107 42.857 15.08 0.87 46.63 2.40
3424 3589 2.200373 AAAGATTTAGCCTGCCACGT 57.800 45.000 0.00 0.00 0.00 4.49
3463 3628 3.365969 GGACGACCAAAAGCAATAGTTGG 60.366 47.826 0.00 0.16 46.05 3.77
3464 3629 3.666902 CGGACGACCAAAAGCAATAGTTG 60.667 47.826 4.48 0.00 35.59 3.16
3467 3632 2.073816 ACGGACGACCAAAAGCAATAG 58.926 47.619 4.48 0.00 35.59 1.73
3469 3634 0.872388 GACGGACGACCAAAAGCAAT 59.128 50.000 4.48 0.00 35.59 3.56
3470 3635 1.492319 CGACGGACGACCAAAAGCAA 61.492 55.000 4.48 0.00 45.77 3.91
3471 3636 1.952133 CGACGGACGACCAAAAGCA 60.952 57.895 4.48 0.00 45.77 3.91
3473 3638 1.602877 CGACGACGGACGACCAAAAG 61.603 60.000 6.90 0.00 45.77 2.27
3476 3641 4.688419 GCGACGACGGACGACCAA 62.688 66.667 17.81 0.00 45.77 3.67
3494 3659 1.933181 GGGGCTTTTATGCAAAATCGC 59.067 47.619 0.00 0.00 33.27 4.58
3495 3660 3.525268 AGGGGCTTTTATGCAAAATCG 57.475 42.857 0.00 0.00 33.27 3.34
3516 3683 3.066203 GCGGGTTGATTTATCGGAAACAT 59.934 43.478 0.00 0.00 0.00 2.71
3526 3693 1.193323 TAGGACGGCGGGTTGATTTA 58.807 50.000 13.24 0.00 0.00 1.40
3539 3706 7.372451 TCAATTGACCAGTTAAAATAGGACG 57.628 36.000 3.38 0.00 0.00 4.79
3601 3768 8.726870 AGTAGCACCACGTGTAAAATAATAAT 57.273 30.769 15.65 0.00 35.75 1.28
3735 3906 2.906354 CGGATGGTCGGAGAAAAAGAT 58.094 47.619 0.00 0.00 39.69 2.40
3740 3911 2.287274 TGGCGGATGGTCGGAGAAA 61.287 57.895 0.00 0.00 39.69 2.52
3769 3940 1.977293 GCCCGAGAAGATTGGAGGCT 61.977 60.000 0.00 0.00 33.64 4.58
3790 3961 1.454539 CGAAGGAGGTTTGGGGTGT 59.545 57.895 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.