Multiple sequence alignment - TraesCS7A01G145400

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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 TraesCS7A01G145400 chr7A 100.000 5438 0 0 1 5438 96571842 96566405 0.000000e+00 10043.0
1 TraesCS7A01G145400 chr7A 85.178 1518 197 27 1980 3486 698679382 698677882 0.000000e+00 1531.0
2 TraesCS7A01G145400 chr7A 85.417 336 41 7 3498 3829 698677753 698677422 5.220000e-90 342.0
3 TraesCS7A01G145400 chr7A 84.138 145 21 2 4082 4225 698677266 698677123 7.340000e-29 139.0
4 TraesCS7A01G145400 chr7D 96.269 3752 71 31 785 4486 93792246 93788514 0.000000e+00 6089.0
5 TraesCS7A01G145400 chr7D 84.732 1513 199 30 1987 3486 606636159 606637652 0.000000e+00 1485.0
6 TraesCS7A01G145400 chr7D 88.049 820 56 21 1 794 93807320 93806517 0.000000e+00 933.0
7 TraesCS7A01G145400 chr7D 86.618 553 68 5 1435 1984 606635501 606636050 1.680000e-169 606.0
8 TraesCS7A01G145400 chr7D 83.776 339 41 12 3498 3829 606637774 606638105 5.290000e-80 309.0
9 TraesCS7A01G145400 chr7D 92.373 118 6 1 5320 5437 93788518 93788404 1.210000e-36 165.0
10 TraesCS7A01G145400 chr7D 82.278 158 24 4 4070 4225 606638249 606638404 3.420000e-27 134.0
11 TraesCS7A01G145400 chr7B 94.530 3967 118 47 603 4486 47004415 47000465 0.000000e+00 6032.0
12 TraesCS7A01G145400 chr7B 85.129 1513 197 26 1985 3486 690754917 690753422 0.000000e+00 1522.0
13 TraesCS7A01G145400 chr7B 85.980 592 63 16 8 584 47005214 47004628 2.780000e-172 616.0
14 TraesCS7A01G145400 chr7B 84.661 339 38 12 3498 3829 690753285 690752954 5.250000e-85 326.0
15 TraesCS7A01G145400 chr7B 84.354 147 20 3 4090 4234 690752790 690752645 2.040000e-29 141.0
16 TraesCS7A01G145400 chr7B 91.398 93 4 2 5320 5412 47000469 47000381 2.060000e-24 124.0
17 TraesCS7A01G145400 chr7B 89.157 83 4 3 5322 5404 701408254 701408177 1.250000e-16 99.0
18 TraesCS7A01G145400 chr6A 90.858 2144 182 14 1350 3486 591440013 591437877 0.000000e+00 2861.0
19 TraesCS7A01G145400 chr6A 89.853 611 17 14 4717 5325 589181327 589180760 0.000000e+00 743.0
20 TraesCS7A01G145400 chr6A 87.052 363 45 2 3485 3846 591437777 591437416 5.070000e-110 409.0
21 TraesCS7A01G145400 chr6A 97.447 235 6 0 4483 4717 589181761 589181527 8.480000e-108 401.0
22 TraesCS7A01G145400 chr6A 79.931 289 46 8 3950 4226 591437337 591437049 9.240000e-48 202.0
23 TraesCS7A01G145400 chr6A 78.201 289 51 8 3950 4226 591436320 591436032 2.010000e-39 174.0
24 TraesCS7A01G145400 chr6A 85.075 67 9 1 4717 4783 589181400 589181335 3.520000e-07 67.6
25 TraesCS7A01G145400 chr6A 85.075 67 9 1 4717 4783 589181473 589181408 3.520000e-07 67.6
26 TraesCS7A01G145400 chr6D 90.498 2168 190 16 1327 3486 443849968 443847809 0.000000e+00 2848.0
27 TraesCS7A01G145400 chr6D 87.569 362 43 2 3485 3845 443847722 443847362 8.420000e-113 418.0
28 TraesCS7A01G145400 chr6D 81.315 289 42 8 3950 4226 443847283 443846995 1.970000e-54 224.0
29 TraesCS7A01G145400 chr6B 90.443 2166 195 12 1327 3486 668250628 668248469 0.000000e+00 2843.0
30 TraesCS7A01G145400 chr6B 87.017 362 45 2 3485 3845 668248352 668247992 1.820000e-109 407.0
31 TraesCS7A01G145400 chr6B 79.791 287 46 8 3952 4226 668247903 668247617 1.190000e-46 198.0
32 TraesCS7A01G145400 chr1D 83.232 1801 259 38 1435 3209 349794640 349792857 0.000000e+00 1613.0
33 TraesCS7A01G145400 chr1D 83.636 110 18 0 5215 5324 334043724 334043615 2.680000e-18 104.0
34 TraesCS7A01G145400 chr1D 100.000 28 0 0 3875 3902 372431939 372431912 1.000000e-02 52.8
35 TraesCS7A01G145400 chr1A 82.935 1799 268 34 1435 3209 450096396 450094613 0.000000e+00 1585.0
36 TraesCS7A01G145400 chr1B 82.843 1801 266 38 1435 3209 471763388 471761605 0.000000e+00 1574.0
37 TraesCS7A01G145400 chr3B 93.257 608 18 3 4717 5324 55096130 55095546 0.000000e+00 874.0
38 TraesCS7A01G145400 chr3B 95.726 234 10 0 4484 4717 55096417 55096184 1.430000e-100 377.0
39 TraesCS7A01G145400 chr3B 83.478 115 17 2 5211 5324 768510040 768510153 7.450000e-19 106.0
40 TraesCS7A01G145400 chr3B 89.286 84 5 2 5322 5404 429973600 429973520 9.640000e-18 102.0
41 TraesCS7A01G145400 chr4B 80.284 563 93 12 2661 3208 586467286 586466727 5.070000e-110 409.0
42 TraesCS7A01G145400 chr4B 87.500 88 6 3 5322 5409 447451783 447451701 4.480000e-16 97.1
43 TraesCS7A01G145400 chr2A 88.073 218 19 4 5112 5325 758758565 758758351 9.040000e-63 252.0
44 TraesCS7A01G145400 chr5A 84.400 250 31 5 5073 5318 6847418 6847663 7.040000e-59 239.0
45 TraesCS7A01G145400 chr3A 85.167 209 25 3 5114 5318 80497574 80497780 5.520000e-50 209.0
46 TraesCS7A01G145400 chr3A 88.050 159 16 3 5142 5300 464236354 464236509 9.300000e-43 185.0
47 TraesCS7A01G145400 chr4A 81.746 126 21 2 5200 5324 481093129 481093253 2.680000e-18 104.0
48 TraesCS7A01G145400 chr5B 90.123 81 5 1 5322 5402 373668147 373668224 9.640000e-18 102.0
49 TraesCS7A01G145400 chr5B 86.022 93 9 3 5322 5413 21154081 21153992 4.480000e-16 97.1
50 TraesCS7A01G145400 chr5B 96.970 33 1 0 3870 3902 490421630 490421598 7.610000e-04 56.5
51 TraesCS7A01G145400 chrUn 89.157 83 4 3 5322 5404 36436902 36436979 1.250000e-16 99.0
52 TraesCS7A01G145400 chr2B 89.024 82 6 2 5322 5403 742080791 742080869 1.250000e-16 99.0


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 TraesCS7A01G145400 chr7A 96566405 96571842 5437 True 10043.000000 10043 100.000000 1 5438 1 chr7A.!!$R1 5437
1 TraesCS7A01G145400 chr7A 698677123 698679382 2259 True 670.666667 1531 84.911000 1980 4225 3 chr7A.!!$R2 2245
2 TraesCS7A01G145400 chr7D 93788404 93792246 3842 True 3127.000000 6089 94.321000 785 5437 2 chr7D.!!$R2 4652
3 TraesCS7A01G145400 chr7D 93806517 93807320 803 True 933.000000 933 88.049000 1 794 1 chr7D.!!$R1 793
4 TraesCS7A01G145400 chr7D 606635501 606638404 2903 False 633.500000 1485 84.351000 1435 4225 4 chr7D.!!$F1 2790
5 TraesCS7A01G145400 chr7B 47000381 47005214 4833 True 2257.333333 6032 90.636000 8 5412 3 chr7B.!!$R2 5404
6 TraesCS7A01G145400 chr7B 690752645 690754917 2272 True 663.000000 1522 84.714667 1985 4234 3 chr7B.!!$R3 2249
7 TraesCS7A01G145400 chr6A 591436032 591440013 3981 True 911.500000 2861 84.010500 1350 4226 4 chr6A.!!$R2 2876
8 TraesCS7A01G145400 chr6A 589180760 589181761 1001 True 319.800000 743 89.362500 4483 5325 4 chr6A.!!$R1 842
9 TraesCS7A01G145400 chr6D 443846995 443849968 2973 True 1163.333333 2848 86.460667 1327 4226 3 chr6D.!!$R1 2899
10 TraesCS7A01G145400 chr6B 668247617 668250628 3011 True 1149.333333 2843 85.750333 1327 4226 3 chr6B.!!$R1 2899
11 TraesCS7A01G145400 chr1D 349792857 349794640 1783 True 1613.000000 1613 83.232000 1435 3209 1 chr1D.!!$R2 1774
12 TraesCS7A01G145400 chr1A 450094613 450096396 1783 True 1585.000000 1585 82.935000 1435 3209 1 chr1A.!!$R1 1774
13 TraesCS7A01G145400 chr1B 471761605 471763388 1783 True 1574.000000 1574 82.843000 1435 3209 1 chr1B.!!$R1 1774
14 TraesCS7A01G145400 chr3B 55095546 55096417 871 True 625.500000 874 94.491500 4484 5324 2 chr3B.!!$R2 840
15 TraesCS7A01G145400 chr4B 586466727 586467286 559 True 409.000000 409 80.284000 2661 3208 1 chr4B.!!$R2 547

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
289 292 0.115745 AAGGGGGTTCGTGGTAGAGA 59.884 55.000 0.0 0.0 0.00 3.10 F
669 883 0.388649 CTCGTCCCACGGAAGAAGTG 60.389 60.000 0.0 0.0 39.48 3.16 F
1278 1537 0.320374 TTGATCCGCCTTCACGTCTT 59.680 50.000 0.0 0.0 0.00 3.01 F
2629 3003 1.299850 CATCGCCTCATACGCCGAA 60.300 57.895 0.0 0.0 33.10 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1472 1.078426 AATGGCGACGAAGGAAGGG 60.078 57.895 0.00 0.0 0.00 3.95 R
2296 2664 1.479709 CCTCGATGAGGGTCTTGTCT 58.520 55.000 4.89 0.0 45.43 3.41 R
3851 4504 2.343387 GGCGTGCATTTGGGCTTT 59.657 55.556 0.00 0.0 34.04 3.51 R
4964 5958 0.170561 TCTAGCTTCCTCGTCGCAAC 59.829 55.000 0.00 0.0 0.00 4.17 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
25 26 2.483877 GCAGTGTTGGAATGAATGTCGA 59.516 45.455 0.00 0.00 0.00 4.20
102 103 2.549926 TCCATGACGGTGATTTGATCG 58.450 47.619 0.00 0.00 35.57 3.69
130 132 4.218578 CAGCGAGCGCCTCTCCAT 62.219 66.667 11.66 0.00 43.17 3.41
141 143 4.147449 TCTCCATGAGGTGCGCCG 62.147 66.667 11.42 0.00 40.50 6.46
171 174 4.908601 TCAGAAAGGCTCTCAATACCAA 57.091 40.909 0.00 0.00 29.07 3.67
201 204 4.511826 GCAACCTAACAATATTCCTCTCGG 59.488 45.833 0.00 0.00 0.00 4.63
207 210 8.168725 ACCTAACAATATTCCTCTCGGTCTATA 58.831 37.037 0.00 0.00 0.00 1.31
209 212 9.843334 CTAACAATATTCCTCTCGGTCTATAAC 57.157 37.037 0.00 0.00 0.00 1.89
210 213 7.229581 ACAATATTCCTCTCGGTCTATAACC 57.770 40.000 0.00 0.00 45.45 2.85
216 219 2.548904 CTCTCGGTCTATAACCCTCACG 59.451 54.545 0.00 0.00 46.27 4.35
247 250 6.650427 TCGACTAGCAATAGTGGATTACAT 57.350 37.500 0.00 0.00 31.39 2.29
249 252 7.497595 TCGACTAGCAATAGTGGATTACATTT 58.502 34.615 0.00 0.00 31.39 2.32
251 254 8.064222 CGACTAGCAATAGTGGATTACATTTTG 58.936 37.037 0.00 0.00 0.00 2.44
281 284 1.073098 ATTGAGGAAAGGGGGTTCGT 58.927 50.000 0.00 0.00 0.00 3.85
289 292 0.115745 AAGGGGGTTCGTGGTAGAGA 59.884 55.000 0.00 0.00 0.00 3.10
300 303 3.005472 TCGTGGTAGAGAAAGAACAGGTG 59.995 47.826 0.00 0.00 0.00 4.00
326 332 2.579201 CGGGATTCGTGCTCCACT 59.421 61.111 3.73 0.00 34.24 4.00
348 355 3.284449 GCCCTTCACGCAAACGGT 61.284 61.111 0.00 0.00 46.04 4.83
411 418 1.187087 CTAGACTCTTCGGTTGGGCT 58.813 55.000 0.00 0.00 0.00 5.19
415 422 4.697756 TCTTCGGTTGGGCTGGCG 62.698 66.667 0.00 0.00 0.00 5.69
482 489 1.678728 CGTGGGGTATGCATGTCAGTT 60.679 52.381 10.16 0.00 0.00 3.16
542 556 2.591571 TTGCACGATGATGAGAGAGG 57.408 50.000 0.00 0.00 0.00 3.69
551 571 4.141846 CGATGATGAGAGAGGGGAAGAAAA 60.142 45.833 0.00 0.00 0.00 2.29
570 590 2.403252 AAGATAAGCAGACCGTTGGG 57.597 50.000 0.00 0.00 40.11 4.12
598 629 5.853282 CCAATCGAGTGTCAACTGAAATTTC 59.147 40.000 12.41 11.41 36.52 2.17
631 844 3.399330 TCTTTTCAGTTGACCGATCCAC 58.601 45.455 0.00 0.00 0.00 4.02
635 848 0.608130 CAGTTGACCGATCCACAGGA 59.392 55.000 0.00 0.00 35.55 3.86
665 879 0.601558 CTTTCTCGTCCCACGGAAGA 59.398 55.000 0.00 0.00 42.81 2.87
666 880 1.000506 CTTTCTCGTCCCACGGAAGAA 59.999 52.381 0.00 0.00 39.48 2.52
667 881 0.601558 TTCTCGTCCCACGGAAGAAG 59.398 55.000 0.00 0.00 39.48 2.85
669 883 0.388649 CTCGTCCCACGGAAGAAGTG 60.389 60.000 0.00 0.00 39.48 3.16
673 887 1.124780 TCCCACGGAAGAAGTGAACA 58.875 50.000 0.00 0.00 41.83 3.18
674 888 1.202604 TCCCACGGAAGAAGTGAACAC 60.203 52.381 0.00 0.00 41.83 3.32
676 890 0.859232 CACGGAAGAAGTGAACACCG 59.141 55.000 0.00 0.00 41.83 4.94
710 927 1.676438 GACACGCGCGAAATTCGGTA 61.676 55.000 39.36 0.00 40.84 4.02
771 989 3.248029 CAGGAAGCTGCACGACAC 58.752 61.111 1.02 0.00 0.00 3.67
1242 1472 0.450983 CGTCGACCTGGTAAGTCCTC 59.549 60.000 10.58 0.00 37.07 3.71
1252 1482 1.481363 GGTAAGTCCTCCCTTCCTTCG 59.519 57.143 0.00 0.00 0.00 3.79
1254 1484 1.268066 AAGTCCTCCCTTCCTTCGTC 58.732 55.000 0.00 0.00 0.00 4.20
1255 1485 0.966370 AGTCCTCCCTTCCTTCGTCG 60.966 60.000 0.00 0.00 0.00 5.12
1278 1537 0.320374 TTGATCCGCCTTCACGTCTT 59.680 50.000 0.00 0.00 0.00 3.01
1894 2156 3.123620 GTGAAGCAGGGCGAGCTG 61.124 66.667 0.00 0.00 42.53 4.24
2113 2481 1.734477 CGACAACCTCCTCGTGCTG 60.734 63.158 0.00 0.00 0.00 4.41
2629 3003 1.299850 CATCGCCTCATACGCCGAA 60.300 57.895 0.00 0.00 33.10 4.30
3859 4512 0.968405 CAAGCTAAGCCAAAGCCCAA 59.032 50.000 0.00 0.00 41.02 4.12
3860 4513 1.344114 CAAGCTAAGCCAAAGCCCAAA 59.656 47.619 0.00 0.00 41.02 3.28
3906 4582 3.244976 GCCATTGTTGTTGATTCCTTCG 58.755 45.455 0.00 0.00 0.00 3.79
3907 4583 3.305335 GCCATTGTTGTTGATTCCTTCGT 60.305 43.478 0.00 0.00 0.00 3.85
3908 4584 4.475944 CCATTGTTGTTGATTCCTTCGTC 58.524 43.478 0.00 0.00 0.00 4.20
4227 4923 3.732471 GCAGAACTACACCGTCTGATCTC 60.732 52.174 4.14 0.00 0.00 2.75
4306 5098 2.366533 TCAGCGGGAAGAGTACTACAG 58.633 52.381 0.00 0.00 0.00 2.74
4375 5169 3.753272 GCATAGGTTTTCTTGTGCTCTCA 59.247 43.478 0.00 0.00 34.86 3.27
4378 5172 4.843220 AGGTTTTCTTGTGCTCTCAATG 57.157 40.909 0.00 0.00 0.00 2.82
4379 5173 4.464008 AGGTTTTCTTGTGCTCTCAATGA 58.536 39.130 0.00 0.00 0.00 2.57
4380 5174 4.276926 AGGTTTTCTTGTGCTCTCAATGAC 59.723 41.667 0.00 0.00 0.00 3.06
4382 5176 5.278660 GGTTTTCTTGTGCTCTCAATGACAT 60.279 40.000 0.00 0.00 0.00 3.06
4383 5177 6.211515 GTTTTCTTGTGCTCTCAATGACATT 58.788 36.000 0.00 0.00 0.00 2.71
4384 5178 7.362662 GTTTTCTTGTGCTCTCAATGACATTA 58.637 34.615 0.00 0.00 0.00 1.90
4386 5180 6.915544 TCTTGTGCTCTCAATGACATTATC 57.084 37.500 0.00 0.00 0.00 1.75
4474 5268 3.576118 TCTTGCTTCTCTCACTGCTACTT 59.424 43.478 0.00 0.00 0.00 2.24
4475 5269 4.039730 TCTTGCTTCTCTCACTGCTACTTT 59.960 41.667 0.00 0.00 0.00 2.66
4477 5271 3.258228 GCTTCTCTCACTGCTACTTTCC 58.742 50.000 0.00 0.00 0.00 3.13
4479 5273 3.176924 TCTCTCACTGCTACTTTCCCT 57.823 47.619 0.00 0.00 0.00 4.20
4480 5274 3.093057 TCTCTCACTGCTACTTTCCCTC 58.907 50.000 0.00 0.00 0.00 4.30
4481 5275 2.167487 CTCTCACTGCTACTTTCCCTCC 59.833 54.545 0.00 0.00 0.00 4.30
4537 5331 0.991920 GGGATCTCCACAAACCAGGA 59.008 55.000 0.00 0.00 37.91 3.86
4767 5761 3.388497 AGTCATGCAGGACTGAGGA 57.612 52.632 31.46 0.00 46.02 3.71
4875 5869 0.533755 GAATCATGCAGGACGGAGGG 60.534 60.000 1.71 0.00 0.00 4.30
4964 5958 2.520982 TCGCCTAGGACGGATGGG 60.521 66.667 14.75 0.00 0.00 4.00
4965 5959 2.838225 CGCCTAGGACGGATGGGT 60.838 66.667 14.75 0.00 0.00 4.51
4980 5974 2.048127 GGTTGCGACGAGGAAGCT 60.048 61.111 0.00 0.00 43.86 3.74
4987 5981 1.448922 CGACGAGGAAGCTAGAGGGG 61.449 65.000 0.00 0.00 0.00 4.79
4988 5982 0.106619 GACGAGGAAGCTAGAGGGGA 60.107 60.000 0.00 0.00 0.00 4.81
4989 5983 0.396001 ACGAGGAAGCTAGAGGGGAC 60.396 60.000 0.00 0.00 0.00 4.46
4990 5984 1.448922 CGAGGAAGCTAGAGGGGACG 61.449 65.000 0.00 0.00 0.00 4.79
4991 5985 1.740332 GAGGAAGCTAGAGGGGACGC 61.740 65.000 0.00 0.00 0.00 5.19
4992 5986 1.758906 GGAAGCTAGAGGGGACGCT 60.759 63.158 0.00 0.00 45.08 5.07
5044 6038 1.478631 GGGGAAAGCATGAAGGGAAG 58.521 55.000 0.00 0.00 0.00 3.46
5070 6064 1.895707 GCAGCCGGATGGAGGATTG 60.896 63.158 23.25 0.00 37.49 2.67
5188 6250 6.057321 TCTACGGACCTGGTTTATTGATTT 57.943 37.500 0.00 0.00 0.00 2.17
5189 6251 6.478129 TCTACGGACCTGGTTTATTGATTTT 58.522 36.000 0.00 0.00 0.00 1.82
5276 6540 7.596749 TTCCTAGAAATCAGCTAAAAACTCG 57.403 36.000 0.00 0.00 0.00 4.18
5328 6592 3.701532 TCCAAACAACGCCTAAACAAG 57.298 42.857 0.00 0.00 0.00 3.16
5337 6601 6.461640 ACAACGCCTAAACAAGTATAAGAGT 58.538 36.000 0.00 0.00 0.00 3.24
5347 6611 8.827177 AAACAAGTATAAGAGTGTTTCGATCA 57.173 30.769 0.00 0.00 39.38 2.92
5348 6612 7.813852 ACAAGTATAAGAGTGTTTCGATCAC 57.186 36.000 11.63 11.63 36.22 3.06
5412 6677 3.778629 GGAGGGGGTACTATGAAAACTGA 59.221 47.826 0.00 0.00 0.00 3.41
5437 6702 3.737559 TGCACCTCCTACATCCAAAAT 57.262 42.857 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 3.084579 CTCGCTGACATCGCCAAC 58.915 61.111 0.00 0.00 0.00 3.77
141 143 1.153147 GCCTTTCTGATCCCGTCCC 60.153 63.158 0.00 0.00 0.00 4.46
144 146 0.827368 GAGAGCCTTTCTGATCCCGT 59.173 55.000 0.00 0.00 35.87 5.28
171 174 6.891908 AGGAATATTGTTAGGTTGCTCACATT 59.108 34.615 0.00 0.00 0.00 2.71
201 204 1.402968 TCGCACGTGAGGGTTATAGAC 59.597 52.381 22.23 0.00 36.38 2.59
207 210 1.289109 CGAATTCGCACGTGAGGGTT 61.289 55.000 22.23 14.29 36.38 4.11
209 212 1.445410 TCGAATTCGCACGTGAGGG 60.445 57.895 22.90 7.59 39.60 4.30
210 213 0.732880 AGTCGAATTCGCACGTGAGG 60.733 55.000 22.90 10.42 39.60 3.86
216 219 3.797256 ACTATTGCTAGTCGAATTCGCAC 59.203 43.478 22.90 19.56 32.56 5.34
247 250 5.697473 TCCTCAATTCATGTAACGCAAAA 57.303 34.783 0.00 0.00 0.00 2.44
249 252 5.335583 CCTTTCCTCAATTCATGTAACGCAA 60.336 40.000 0.00 0.00 0.00 4.85
251 254 4.438744 CCCTTTCCTCAATTCATGTAACGC 60.439 45.833 0.00 0.00 0.00 4.84
281 284 2.038557 GCCACCTGTTCTTTCTCTACCA 59.961 50.000 0.00 0.00 0.00 3.25
289 292 2.597510 GGCGGCCACCTGTTCTTT 60.598 61.111 15.62 0.00 0.00 2.52
313 319 0.745845 GCATCCAGTGGAGCACGAAT 60.746 55.000 18.69 0.00 39.64 3.34
320 326 0.393537 GTGAAGGGCATCCAGTGGAG 60.394 60.000 18.69 10.76 34.05 3.86
326 332 1.228398 TTTGCGTGAAGGGCATCCA 60.228 52.632 0.00 0.00 40.62 3.41
348 355 1.361543 AGCTCACCTACTTACCCCTGA 59.638 52.381 0.00 0.00 0.00 3.86
448 455 1.082104 CCACGAAAAGGCAAGTCGC 60.082 57.895 0.00 0.00 38.33 5.19
460 467 0.615850 TGACATGCATACCCCACGAA 59.384 50.000 0.00 0.00 0.00 3.85
494 501 0.477597 ATTCACCCTCCAGTTCCCCA 60.478 55.000 0.00 0.00 0.00 4.96
497 504 4.010349 CAGTTAATTCACCCTCCAGTTCC 58.990 47.826 0.00 0.00 0.00 3.62
542 556 4.095036 CGGTCTGCTTATCTTTTTCTTCCC 59.905 45.833 0.00 0.00 0.00 3.97
551 571 1.628846 ACCCAACGGTCTGCTTATCTT 59.371 47.619 0.00 0.00 38.28 2.40
570 590 3.807622 TCAGTTGACACTCGATTGGAAAC 59.192 43.478 7.74 10.37 0.00 2.78
575 595 6.662616 AGAAATTTCAGTTGACACTCGATTG 58.337 36.000 19.99 0.55 0.00 2.67
577 597 6.483307 TCAAGAAATTTCAGTTGACACTCGAT 59.517 34.615 19.99 0.00 0.00 3.59
578 598 5.815222 TCAAGAAATTTCAGTTGACACTCGA 59.185 36.000 19.99 0.00 0.00 4.04
579 599 6.048073 TCAAGAAATTTCAGTTGACACTCG 57.952 37.500 19.99 0.00 0.00 4.18
580 600 8.862550 AAATCAAGAAATTTCAGTTGACACTC 57.137 30.769 19.45 0.00 31.94 3.51
615 828 0.608130 CCTGTGGATCGGTCAACTGA 59.392 55.000 11.43 0.00 30.89 3.41
631 844 1.974236 AGAAAGTGACCTCCTGTCCTG 59.026 52.381 0.00 0.00 43.78 3.86
635 848 1.614413 GACGAGAAAGTGACCTCCTGT 59.386 52.381 0.00 0.00 0.00 4.00
665 879 1.228154 GAAGGGGCGGTGTTCACTT 60.228 57.895 2.98 0.00 0.00 3.16
666 880 2.430367 GAAGGGGCGGTGTTCACT 59.570 61.111 2.98 0.00 0.00 3.41
667 881 3.047877 CGAAGGGGCGGTGTTCAC 61.048 66.667 0.00 0.00 0.00 3.18
669 883 2.281276 AACGAAGGGGCGGTGTTC 60.281 61.111 0.00 0.00 35.12 3.18
710 927 0.035317 TTGGTCTGCGACATCTTGCT 59.965 50.000 10.14 0.00 33.68 3.91
909 1131 2.777972 CGGGCATGAGGGTTGCATG 61.778 63.158 0.00 0.00 44.52 4.06
910 1132 2.440796 CGGGCATGAGGGTTGCAT 60.441 61.111 0.00 0.00 41.95 3.96
991 1213 1.450312 CGTGGGAATGGTGAGAGCC 60.450 63.158 0.00 0.00 0.00 4.70
992 1214 1.450312 CCGTGGGAATGGTGAGAGC 60.450 63.158 0.00 0.00 0.00 4.09
996 1218 0.252057 TCTCTCCGTGGGAATGGTGA 60.252 55.000 0.00 0.00 0.00 4.02
998 1220 0.978146 CCTCTCTCCGTGGGAATGGT 60.978 60.000 0.00 0.00 0.00 3.55
999 1221 0.687757 TCCTCTCTCCGTGGGAATGG 60.688 60.000 0.00 0.00 0.00 3.16
1242 1472 1.078426 AATGGCGACGAAGGAAGGG 60.078 57.895 0.00 0.00 0.00 3.95
1252 1482 1.776034 GAAGGCGGATCAATGGCGAC 61.776 60.000 0.00 0.00 35.52 5.19
1254 1484 1.819208 TGAAGGCGGATCAATGGCG 60.819 57.895 0.00 0.00 35.52 5.69
1255 1485 1.729881 GTGAAGGCGGATCAATGGC 59.270 57.895 0.00 0.00 0.00 4.40
1278 1537 3.505293 TCAAATCAATCCAATGCACACGA 59.495 39.130 0.00 0.00 0.00 4.35
1927 2189 4.103103 GCCGCCTTGCCGAAGAAC 62.103 66.667 0.00 0.00 0.00 3.01
2296 2664 1.479709 CCTCGATGAGGGTCTTGTCT 58.520 55.000 4.89 0.00 45.43 3.41
3851 4504 2.343387 GGCGTGCATTTGGGCTTT 59.657 55.556 0.00 0.00 34.04 3.51
3906 4582 2.028020 ACTGGGACGAAATGGAGAAGAC 60.028 50.000 0.00 0.00 0.00 3.01
3907 4583 2.028112 CACTGGGACGAAATGGAGAAGA 60.028 50.000 0.00 0.00 0.00 2.87
3908 4584 2.028112 TCACTGGGACGAAATGGAGAAG 60.028 50.000 0.00 0.00 0.00 2.85
4065 4746 0.392327 GAGAGCTCCTCCTTGTTGCC 60.392 60.000 10.93 0.00 35.87 4.52
4227 4923 1.522355 ACCGGAGCAGCAATCGATG 60.522 57.895 9.46 0.00 0.00 3.84
4270 5049 0.667993 CTGAAACCCACGCAACACAT 59.332 50.000 0.00 0.00 0.00 3.21
4283 5066 2.745515 AGTACTCTTCCCGCTGAAAC 57.254 50.000 0.00 0.00 31.06 2.78
4306 5098 1.893801 AGACAGGTATACCGGCATAGC 59.106 52.381 20.50 14.87 42.08 2.97
4378 5172 9.587772 ACACACTTGTATTACAGAGATAATGTC 57.412 33.333 10.84 0.00 32.60 3.06
4379 5173 9.371136 CACACACTTGTATTACAGAGATAATGT 57.629 33.333 10.84 0.00 33.30 2.71
4380 5174 8.820933 CCACACACTTGTATTACAGAGATAATG 58.179 37.037 10.84 3.16 33.30 1.90
4382 5176 7.179516 TCCCACACACTTGTATTACAGAGATAA 59.820 37.037 10.84 0.00 33.30 1.75
4383 5177 6.666113 TCCCACACACTTGTATTACAGAGATA 59.334 38.462 10.84 0.00 33.30 1.98
4384 5178 5.483937 TCCCACACACTTGTATTACAGAGAT 59.516 40.000 10.84 0.68 33.30 2.75
4386 5180 5.147330 TCCCACACACTTGTATTACAGAG 57.853 43.478 0.00 1.53 33.30 3.35
4424 5218 5.296780 TGGTGACAAGAGAGACAAAATGTTC 59.703 40.000 0.00 0.00 37.44 3.18
4474 5268 0.838987 ACAACGCCTTAGGGAGGGAA 60.839 55.000 0.00 0.00 46.40 3.97
4475 5269 0.838987 AACAACGCCTTAGGGAGGGA 60.839 55.000 0.00 0.00 46.40 4.20
4479 5273 0.766131 TCCAAACAACGCCTTAGGGA 59.234 50.000 0.00 0.00 33.58 4.20
4480 5274 1.834188 ATCCAAACAACGCCTTAGGG 58.166 50.000 0.00 0.00 0.00 3.53
4481 5275 3.621715 GTCTATCCAAACAACGCCTTAGG 59.378 47.826 0.00 0.00 0.00 2.69
4537 5331 6.497437 AGATTTTAGTTTGTTACGCCGTTTT 58.503 32.000 0.00 0.00 0.00 2.43
4672 5466 1.792006 GCTGGGATCCGGTTTATACG 58.208 55.000 5.45 0.00 31.34 3.06
4674 5468 1.416243 ACGCTGGGATCCGGTTTATA 58.584 50.000 5.45 0.00 31.34 0.98
4794 5788 0.177604 CTTGCTCTGCTCCCGAGATT 59.822 55.000 0.00 0.00 0.00 2.40
4853 5847 1.153369 CCGTCCTGCATGATTCGGT 60.153 57.895 11.36 0.00 34.38 4.69
4875 5869 3.665675 AACTGCCCTCATCGCGTCC 62.666 63.158 5.77 0.00 0.00 4.79
4964 5958 0.170561 TCTAGCTTCCTCGTCGCAAC 59.829 55.000 0.00 0.00 0.00 4.17
4965 5959 0.452184 CTCTAGCTTCCTCGTCGCAA 59.548 55.000 0.00 0.00 0.00 4.85
4980 5974 2.486907 GCTACTTCTAGCGTCCCCTCTA 60.487 54.545 0.00 0.00 36.26 2.43
4987 5981 1.359475 CCGGGCTACTTCTAGCGTC 59.641 63.158 0.00 0.00 45.82 5.19
4988 5982 2.125961 CCCGGGCTACTTCTAGCGT 61.126 63.158 8.08 0.00 45.82 5.07
4989 5983 2.728817 CCCGGGCTACTTCTAGCG 59.271 66.667 8.08 0.00 45.82 4.26
4990 5984 2.422165 GCCCGGGCTACTTCTAGC 59.578 66.667 38.76 7.31 44.34 3.42
4991 5985 2.857744 CGGCCCGGGCTACTTCTAG 61.858 68.421 42.70 20.07 41.60 2.43
4992 5986 2.836360 CGGCCCGGGCTACTTCTA 60.836 66.667 42.70 0.00 41.60 2.10
5070 6064 0.459585 TCCAAACTCGGCAGCGTATC 60.460 55.000 0.00 0.00 0.00 2.24
5328 6592 9.649024 GTAGTAGTGATCGAAACACTCTTATAC 57.351 37.037 24.56 18.43 45.58 1.47
5381 6645 2.906568 AGTACCCCCTCCGTAAAGAAA 58.093 47.619 0.00 0.00 0.00 2.52
5412 6677 3.384168 TGGATGTAGGAGGTGCATTAGT 58.616 45.455 0.00 0.00 30.44 2.24


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

AutoCloner maintained by Alex Coulton.