Multiple sequence alignment - TraesCS7B01G028300

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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 TraesCS7B01G028300 chr7B 100.000 7973 0 0 1 7973 26778296 26770324 0.000000e+00 14724.0
1 TraesCS7B01G028300 chr7B 97.143 35 1 0 3271 3305 26774953 26774919 8.640000e-05 60.2
2 TraesCS7B01G028300 chr7B 97.143 35 1 0 3344 3378 26775026 26774992 8.640000e-05 60.2
3 TraesCS7B01G028300 chr7D 96.955 6995 151 31 1017 7973 79565314 79558344 0.000000e+00 11681.0
4 TraesCS7B01G028300 chr7D 90.283 1060 33 10 1 1017 79566464 79565432 0.000000e+00 1323.0
5 TraesCS7B01G028300 chr7D 97.143 35 1 0 3344 3378 79563056 79563022 8.640000e-05 60.2
6 TraesCS7B01G028300 chr7D 100.000 29 0 0 3277 3305 79562977 79562949 4.000000e-03 54.7
7 TraesCS7B01G028300 chr7A 96.145 7004 197 38 1017 7973 82224758 82217781 0.000000e+00 11370.0
8 TraesCS7B01G028300 chr7A 92.955 582 15 10 1 582 82226052 82225497 0.000000e+00 824.0
9 TraesCS7B01G028300 chr7A 92.483 439 17 3 595 1017 82225315 82224877 1.470000e-171 614.0
10 TraesCS7B01G028300 chr7A 89.937 159 13 3 2 160 13841855 13842010 1.360000e-47 202.0
11 TraesCS7B01G028300 chr7A 94.805 77 4 0 554 630 82225376 82225300 3.910000e-23 121.0
12 TraesCS7B01G028300 chr7A 93.506 77 5 0 554 630 82225437 82225361 1.820000e-21 115.0
13 TraesCS7B01G028300 chr7A 81.720 93 15 2 539 630 82225472 82225381 8.580000e-10 76.8
14 TraesCS7B01G028300 chr7A 97.143 35 1 0 3271 3305 82222416 82222382 8.640000e-05 60.2
15 TraesCS7B01G028300 chr7A 97.143 35 1 0 3344 3378 82222489 82222455 8.640000e-05 60.2
16 TraesCS7B01G028300 chr1B 76.907 957 141 45 5445 6378 142719074 142719973 3.370000e-128 470.0
17 TraesCS7B01G028300 chr4B 71.990 839 172 45 5561 6374 159625743 159624943 1.060000e-43 189.0
18 TraesCS7B01G028300 chr4A 71.685 837 175 44 5561 6374 425992327 425991530 8.220000e-40 176.0
19 TraesCS7B01G028300 chr4D 71.599 838 177 46 5561 6374 134133518 134134318 1.060000e-38 172.0
20 TraesCS7B01G028300 chr3A 84.783 92 11 1 6298 6389 750435882 750435794 1.100000e-13 89.8
21 TraesCS7B01G028300 chr5D 88.235 68 5 1 7624 7688 526136087 526136020 2.390000e-10 78.7
22 TraesCS7B01G028300 chr5A 86.486 74 7 1 7624 7694 653301071 653300998 2.390000e-10 78.7
23 TraesCS7B01G028300 chr5B 86.301 73 3 2 7623 7688 661234986 661234914 1.110000e-08 73.1


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 TraesCS7B01G028300 chr7B 26770324 26778296 7972 True 4948.133333 14724 98.095333 1 7973 3 chr7B.!!$R1 7972
1 TraesCS7B01G028300 chr7D 79558344 79566464 8120 True 3279.725000 11681 96.095250 1 7973 4 chr7D.!!$R1 7972
2 TraesCS7B01G028300 chr7A 82217781 82226052 8271 True 1655.150000 11370 93.237500 1 7973 8 chr7A.!!$R1 7972
3 TraesCS7B01G028300 chr1B 142719074 142719973 899 False 470.000000 470 76.907000 5445 6378 1 chr1B.!!$F1 933

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
774 949 0.250234 ATCAGTGACCGTCCATGTGG 59.750 55.000 0.00 0.00 0.00 4.17 F
1110 1415 0.962356 ACCTGCTGCCAGATTTTCCG 60.962 55.000 0.00 0.00 41.77 4.30 F
1413 1718 1.202927 AGCTGAGGGCAAAGCAAAGTA 60.203 47.619 7.84 0.00 44.79 2.24 F
2271 2594 1.316651 GCATCCTGGATCTCCTTTGC 58.683 55.000 6.13 3.15 36.82 3.68 F
3381 3705 2.457366 ACCTAAGACAACTCTTGCCG 57.543 50.000 0.00 0.00 37.32 5.69 F
3584 3909 0.107410 TTCCGGCGCTTGGTAATGAT 60.107 50.000 16.85 0.00 0.00 2.45 F
4913 5251 1.139058 ACGAAAGCACTGAAGGTGTCT 59.861 47.619 0.00 0.00 46.86 3.41 F
5745 6090 1.785041 GCTCTTGTGTGCGCTTTCCA 61.785 55.000 9.73 0.00 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2451 2.435372 ACTCCCTGCACAACAAAGAA 57.565 45.000 0.00 0.00 0.00 2.52 R
2544 2867 2.872245 GCACAGCAAGTTCAGACTAACA 59.128 45.455 0.00 0.00 34.21 2.41 R
3381 3705 1.943340 GTGAATTCAGAATCCTCCGGC 59.057 52.381 8.80 0.00 0.00 6.13 R
3584 3909 1.214424 GAGTTAATAAGGGCCTGGGCA 59.786 52.381 22.68 1.36 44.11 5.36 R
4913 5251 1.005097 TCGCTAGATATAGGGGCGGAA 59.995 52.381 11.09 0.00 44.88 4.30 R
5022 5360 5.619981 GCAATAACATTCGACAGAAGGCTTT 60.620 40.000 0.00 0.00 41.42 3.51 R
6430 6790 0.743345 AATTCGGCTTCGGCAGTACC 60.743 55.000 0.00 0.00 43.96 3.34 R
7313 7683 0.029567 GATCGCCCGACACTACAGAG 59.970 60.000 0.00 0.00 0.00 3.35 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
43 44 5.013495 TGACTCATTGGTTCTCCATTCTCTT 59.987 40.000 0.00 0.00 43.91 2.85
44 45 5.251764 ACTCATTGGTTCTCCATTCTCTTG 58.748 41.667 0.00 0.00 43.91 3.02
45 46 5.013495 ACTCATTGGTTCTCCATTCTCTTGA 59.987 40.000 0.00 0.00 43.91 3.02
84 85 3.003480 ACTCCATTTTAGAGCTCGTTGC 58.997 45.455 8.37 0.00 43.29 4.17
273 274 6.361748 GTCTTGATGATTGCAGTTCAGTTTTC 59.638 38.462 7.40 1.81 0.00 2.29
283 284 4.616835 GCAGTTCAGTTTTCTAGGCATTGG 60.617 45.833 0.00 0.00 0.00 3.16
285 286 5.010012 CAGTTCAGTTTTCTAGGCATTGGTT 59.990 40.000 0.00 0.00 0.00 3.67
286 287 5.598417 AGTTCAGTTTTCTAGGCATTGGTTT 59.402 36.000 0.00 0.00 0.00 3.27
287 288 5.452078 TCAGTTTTCTAGGCATTGGTTTG 57.548 39.130 0.00 0.00 0.00 2.93
288 289 4.892934 TCAGTTTTCTAGGCATTGGTTTGT 59.107 37.500 0.00 0.00 0.00 2.83
290 291 5.691754 CAGTTTTCTAGGCATTGGTTTGTTC 59.308 40.000 0.00 0.00 0.00 3.18
291 292 5.598417 AGTTTTCTAGGCATTGGTTTGTTCT 59.402 36.000 0.00 0.00 0.00 3.01
292 293 6.098266 AGTTTTCTAGGCATTGGTTTGTTCTT 59.902 34.615 0.00 0.00 0.00 2.52
293 294 6.478512 TTTCTAGGCATTGGTTTGTTCTTT 57.521 33.333 0.00 0.00 0.00 2.52
294 295 5.452078 TCTAGGCATTGGTTTGTTCTTTG 57.548 39.130 0.00 0.00 0.00 2.77
296 297 4.058721 AGGCATTGGTTTGTTCTTTGTC 57.941 40.909 0.00 0.00 0.00 3.18
297 298 3.706086 AGGCATTGGTTTGTTCTTTGTCT 59.294 39.130 0.00 0.00 0.00 3.41
298 299 4.162131 AGGCATTGGTTTGTTCTTTGTCTT 59.838 37.500 0.00 0.00 0.00 3.01
299 300 4.507756 GGCATTGGTTTGTTCTTTGTCTTC 59.492 41.667 0.00 0.00 0.00 2.87
300 301 4.507756 GCATTGGTTTGTTCTTTGTCTTCC 59.492 41.667 0.00 0.00 0.00 3.46
301 302 5.682212 GCATTGGTTTGTTCTTTGTCTTCCT 60.682 40.000 0.00 0.00 0.00 3.36
302 303 4.981806 TGGTTTGTTCTTTGTCTTCCTG 57.018 40.909 0.00 0.00 0.00 3.86
303 304 4.340617 TGGTTTGTTCTTTGTCTTCCTGT 58.659 39.130 0.00 0.00 0.00 4.00
304 305 4.157656 TGGTTTGTTCTTTGTCTTCCTGTG 59.842 41.667 0.00 0.00 0.00 3.66
305 306 4.105486 GTTTGTTCTTTGTCTTCCTGTGC 58.895 43.478 0.00 0.00 0.00 4.57
306 307 1.939934 TGTTCTTTGTCTTCCTGTGCG 59.060 47.619 0.00 0.00 0.00 5.34
307 308 1.940613 GTTCTTTGTCTTCCTGTGCGT 59.059 47.619 0.00 0.00 0.00 5.24
308 309 1.865865 TCTTTGTCTTCCTGTGCGTC 58.134 50.000 0.00 0.00 0.00 5.19
309 310 1.138069 TCTTTGTCTTCCTGTGCGTCA 59.862 47.619 0.00 0.00 0.00 4.35
310 311 2.146342 CTTTGTCTTCCTGTGCGTCAT 58.854 47.619 0.00 0.00 0.00 3.06
311 312 1.511850 TTGTCTTCCTGTGCGTCATG 58.488 50.000 0.00 0.00 0.00 3.07
312 313 0.392706 TGTCTTCCTGTGCGTCATGT 59.607 50.000 0.00 0.00 0.00 3.21
313 314 1.616374 TGTCTTCCTGTGCGTCATGTA 59.384 47.619 0.00 0.00 0.00 2.29
314 315 2.036604 TGTCTTCCTGTGCGTCATGTAA 59.963 45.455 0.00 0.00 0.00 2.41
315 316 3.064207 GTCTTCCTGTGCGTCATGTAAA 58.936 45.455 0.00 0.00 0.00 2.01
316 317 3.496884 GTCTTCCTGTGCGTCATGTAAAA 59.503 43.478 0.00 0.00 0.00 1.52
317 318 4.024387 GTCTTCCTGTGCGTCATGTAAAAA 60.024 41.667 0.00 0.00 0.00 1.94
397 398 4.960469 ACCATCATGCCTGATTCAGAATTT 59.040 37.500 15.36 0.00 40.20 1.82
454 455 6.695278 TCAACTCGTGGTGAAATGAAAATTTC 59.305 34.615 2.05 0.00 40.10 2.17
468 469 9.481340 AAATGAAAATTTCCTTAGCTTGAAGAC 57.519 29.630 3.00 0.00 0.00 3.01
508 509 1.439679 CAGGCCGTTTTGTCTAGTCC 58.560 55.000 0.00 0.00 0.00 3.85
589 739 6.237384 GCATTACAGAAATGTGAATTTCAGCG 60.237 38.462 12.35 4.59 45.78 5.18
643 813 7.550551 TGTGAAATGCATTGGTTTGTTCTTAAA 59.449 29.630 13.82 0.00 0.00 1.52
647 817 6.841443 TGCATTGGTTTGTTCTTAAATGTG 57.159 33.333 0.00 0.00 0.00 3.21
648 818 6.577103 TGCATTGGTTTGTTCTTAAATGTGA 58.423 32.000 0.00 0.00 0.00 3.58
740 915 3.987547 ACGATCACTATCTGATTGCAGG 58.012 45.455 0.00 0.00 42.73 4.85
774 949 0.250234 ATCAGTGACCGTCCATGTGG 59.750 55.000 0.00 0.00 0.00 4.17
780 955 1.206132 TGACCGTCCATGTGGTATCAC 59.794 52.381 0.00 0.00 43.87 3.06
969 1155 5.046159 TGGGTTCATGTAAATCGTAGGAACT 60.046 40.000 0.00 0.00 46.37 3.01
1110 1415 0.962356 ACCTGCTGCCAGATTTTCCG 60.962 55.000 0.00 0.00 41.77 4.30
1116 1421 2.222027 CTGCCAGATTTTCCGGTATCC 58.778 52.381 0.00 0.00 0.00 2.59
1163 1468 5.207354 TCTCTGTATCAGCTGGAGAGAATT 58.793 41.667 22.56 0.00 36.97 2.17
1413 1718 1.202927 AGCTGAGGGCAAAGCAAAGTA 60.203 47.619 7.84 0.00 44.79 2.24
1510 1815 9.623350 CAAAAATGTTTGTTTGAATCACCTTTT 57.377 25.926 0.00 0.00 39.49 2.27
1513 1818 8.791327 AATGTTTGTTTGAATCACCTTTTCTT 57.209 26.923 0.00 0.00 0.00 2.52
1643 1948 8.314021 GTTCATCAGAAGTTTATGGGGAATTTT 58.686 33.333 0.00 0.00 33.63 1.82
1933 2238 9.956720 GTTATCCATGAGTTTCCATTTCAATAG 57.043 33.333 0.00 0.00 0.00 1.73
2044 2349 4.003648 CAGATGTACCAAGGTTCCAGAAC 58.996 47.826 0.00 1.77 40.45 3.01
2191 2496 7.775729 AGGGTAAAGTATATTGGCCCAATTAT 58.224 34.615 15.41 8.65 35.54 1.28
2216 2521 6.590234 AAACCTCCCTTTCACACATTTATC 57.410 37.500 0.00 0.00 0.00 1.75
2271 2594 1.316651 GCATCCTGGATCTCCTTTGC 58.683 55.000 6.13 3.15 36.82 3.68
2390 2713 5.888691 TGTAAATTTGGCTTATTCGCAGA 57.111 34.783 0.00 0.00 0.00 4.26
2393 2716 2.779755 TTTGGCTTATTCGCAGAGGA 57.220 45.000 0.00 0.00 38.43 3.71
2483 2806 4.365514 TGGAGTTAGATTTGACAAGCCA 57.634 40.909 0.00 0.00 0.00 4.75
2608 2931 6.433716 CCTACTGATGCTCTTCTGATCTGATA 59.566 42.308 2.84 0.00 0.00 2.15
2675 2998 6.314896 CCCAAGCTCTTCTAGTGATAAACAAG 59.685 42.308 0.00 0.00 0.00 3.16
3381 3705 2.457366 ACCTAAGACAACTCTTGCCG 57.543 50.000 0.00 0.00 37.32 5.69
3584 3909 0.107410 TTCCGGCGCTTGGTAATGAT 60.107 50.000 16.85 0.00 0.00 2.45
3836 4161 9.197306 GGTTTTATCTGGTTTCCCATATAAACT 57.803 33.333 10.20 0.00 43.73 2.66
3951 4276 8.023021 TGCAGATGGTACTTTGTCTAATCTAT 57.977 34.615 0.00 0.00 0.00 1.98
3999 4324 7.094248 ACAAAGCACAGCTATCATATTTGAACA 60.094 33.333 12.46 0.00 38.25 3.18
4148 4475 2.959516 TGTAGCAGTGTTTGATCGAGG 58.040 47.619 0.00 0.00 0.00 4.63
4339 4670 9.066892 GTAGTATTCCCTTGCAATCAATCAATA 57.933 33.333 0.00 0.00 0.00 1.90
4528 4864 7.372451 TGTTGAAGAATTACCAATTACGGAG 57.628 36.000 0.00 0.00 0.00 4.63
4555 4891 6.868622 ACTACTGACTCATGATGGTAAGTTC 58.131 40.000 9.74 0.00 30.56 3.01
4556 4892 6.665680 ACTACTGACTCATGATGGTAAGTTCT 59.334 38.462 9.74 0.00 30.56 3.01
4557 4893 7.834681 ACTACTGACTCATGATGGTAAGTTCTA 59.165 37.037 9.74 0.00 30.56 2.10
4559 4895 8.768501 ACTGACTCATGATGGTAAGTTCTATA 57.231 34.615 0.00 0.00 0.00 1.31
4560 4896 8.855110 ACTGACTCATGATGGTAAGTTCTATAG 58.145 37.037 0.00 0.00 0.00 1.31
4561 4897 8.996651 TGACTCATGATGGTAAGTTCTATAGA 57.003 34.615 0.00 0.00 0.00 1.98
4563 4899 8.768501 ACTCATGATGGTAAGTTCTATAGACA 57.231 34.615 0.67 0.00 0.00 3.41
4564 4900 9.373450 ACTCATGATGGTAAGTTCTATAGACAT 57.627 33.333 0.67 1.44 0.00 3.06
4565 4901 9.636879 CTCATGATGGTAAGTTCTATAGACATG 57.363 37.037 0.67 9.42 33.86 3.21
4567 4903 9.770097 CATGATGGTAAGTTCTATAGACATGTT 57.230 33.333 0.67 0.00 0.00 2.71
4568 4904 9.770097 ATGATGGTAAGTTCTATAGACATGTTG 57.230 33.333 0.67 0.00 0.00 3.33
4750 5088 9.152595 GTACTTCCAACAGAAAGGTAAATAGAG 57.847 37.037 0.00 0.00 32.88 2.43
4894 5232 2.555199 CATGGCCAGTAGTAGCTCAAC 58.445 52.381 13.05 0.00 0.00 3.18
4913 5251 1.139058 ACGAAAGCACTGAAGGTGTCT 59.861 47.619 0.00 0.00 46.86 3.41
5022 5360 5.163311 TGGTCACAGAGAATGAGTTTGAGAA 60.163 40.000 0.00 0.00 0.00 2.87
5345 5683 4.614555 TTTGCTCACCAATATAACTGCG 57.385 40.909 0.00 0.00 32.49 5.18
5659 6004 5.655532 AGAATCAGGTGCAAGCTTTATGAAT 59.344 36.000 0.00 0.00 46.63 2.57
5745 6090 1.785041 GCTCTTGTGTGCGCTTTCCA 61.785 55.000 9.73 0.00 0.00 3.53
5853 6198 3.206964 GGCAAGTAAACTATCTCCTGCC 58.793 50.000 5.70 5.70 0.00 4.85
6164 6519 2.233431 GCAGGTAGCATCTATCTCCCTG 59.767 54.545 0.00 0.00 44.79 4.45
6178 6534 7.355101 TCTATCTCCCTGTACTACTTGACAAT 58.645 38.462 0.00 0.00 0.00 2.71
6186 6542 6.369065 CCTGTACTACTTGACAATTCTTGGTC 59.631 42.308 0.00 0.00 34.12 4.02
6300 6660 4.899352 AGCTGATACTGTCCAAAGAAGT 57.101 40.909 0.00 0.00 0.00 3.01
6439 6799 0.378257 GCAATGACATGGTACTGCCG 59.622 55.000 0.00 0.00 41.21 5.69
6565 6925 6.703607 GTGTGAATAGAGATCAACATACAGGG 59.296 42.308 0.00 0.00 0.00 4.45
6585 6950 0.515127 AACACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49
6589 6954 2.021243 CACACACACACACGCACG 59.979 61.111 0.00 0.00 0.00 5.34
6595 6960 3.858989 CACACACGCACGCACACA 61.859 61.111 0.00 0.00 0.00 3.72
6596 6961 3.860125 ACACACGCACGCACACAC 61.860 61.111 0.00 0.00 0.00 3.82
6597 6962 4.918060 CACACGCACGCACACACG 62.918 66.667 0.00 0.00 39.50 4.49
6660 7028 2.541999 GGAGAAGAGTCTGGCGATAACG 60.542 54.545 0.00 0.00 37.06 3.18
6675 7043 2.170012 TAACGGAAGGTAGGCCTGAT 57.830 50.000 17.99 0.00 46.33 2.90
6750 7118 1.689243 CGGCCCATGATCAGGTGAGA 61.689 60.000 6.62 0.00 0.00 3.27
7099 7469 1.038130 CCTCCGACACTCCCACCTAG 61.038 65.000 0.00 0.00 0.00 3.02
7126 7496 6.831976 AGGTATCTAGGTTGATGATTTGGAC 58.168 40.000 0.00 0.00 0.00 4.02
7131 7501 2.649312 AGGTTGATGATTTGGACCCAGA 59.351 45.455 0.00 0.00 0.00 3.86
7133 7503 4.026052 GGTTGATGATTTGGACCCAGATT 58.974 43.478 0.00 0.00 0.00 2.40
7169 7539 3.181465 GGCGATCTGGATCTGTTCCTTTA 60.181 47.826 8.65 0.00 45.68 1.85
7192 7562 4.105377 AGCTATGGATAGGCCTTGTCAAAT 59.895 41.667 12.58 10.06 37.63 2.32
7193 7563 4.829492 GCTATGGATAGGCCTTGTCAAATT 59.171 41.667 12.58 0.00 37.63 1.82
7333 7703 0.678684 TCTGTAGTGTCGGGCGATCA 60.679 55.000 0.00 0.00 0.00 2.92
7574 7944 5.989477 TGTGCAATTATACCTTGAGTAGCT 58.011 37.500 0.00 0.00 33.42 3.32
7653 8023 9.814899 ACATCTACAGAATCAATCAGTAAAGAG 57.185 33.333 0.00 0.00 30.63 2.85
7747 8118 1.068472 ACTAGCTCGGTGAGACAAACG 60.068 52.381 0.00 0.00 0.00 3.60
7751 8122 1.935300 GCTCGGTGAGACAAACGTGAT 60.935 52.381 0.00 0.00 0.00 3.06
7760 8131 0.533491 ACAAACGTGATAGCGGCCTA 59.467 50.000 0.00 0.00 35.98 3.93
7779 8150 4.284234 GCCTATAAAATGGCATTGGGTCAT 59.716 41.667 14.47 5.64 45.82 3.06
7792 8163 4.478206 TTGGGTCATTTTTGCAGAAACA 57.522 36.364 4.29 0.00 0.00 2.83
7878 8249 0.180406 ACCGAGTCATGGGGCATAAC 59.820 55.000 0.00 0.00 0.00 1.89
7891 8262 6.212840 TGGGGCATAACTATAATGGACAAT 57.787 37.500 0.00 0.00 0.00 2.71
7930 8301 2.503920 AGACGTATACATGTTCGGGC 57.496 50.000 2.30 4.57 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 6.040842 TGGAGTCATGACGATAATCTTGATCA 59.959 38.462 19.85 0.00 35.80 2.92
44 45 6.450545 TGGAGTCATGACGATAATCTTGATC 58.549 40.000 19.85 7.39 35.80 2.92
45 46 6.410942 TGGAGTCATGACGATAATCTTGAT 57.589 37.500 19.85 0.00 35.80 2.57
84 85 1.021390 AGAAACAGAGCATTCGCCCG 61.021 55.000 0.00 0.00 39.83 6.13
218 219 8.080417 GGGAAATCTTGTAACTTGGTCTAAAAC 58.920 37.037 0.00 0.00 0.00 2.43
273 274 5.010012 AGACAAAGAACAAACCAATGCCTAG 59.990 40.000 0.00 0.00 0.00 3.02
283 284 4.105486 GCACAGGAAGACAAAGAACAAAC 58.895 43.478 0.00 0.00 0.00 2.93
285 286 2.354510 CGCACAGGAAGACAAAGAACAA 59.645 45.455 0.00 0.00 0.00 2.83
286 287 1.939934 CGCACAGGAAGACAAAGAACA 59.060 47.619 0.00 0.00 0.00 3.18
287 288 1.940613 ACGCACAGGAAGACAAAGAAC 59.059 47.619 0.00 0.00 0.00 3.01
288 289 2.210116 GACGCACAGGAAGACAAAGAA 58.790 47.619 0.00 0.00 0.00 2.52
290 291 1.581934 TGACGCACAGGAAGACAAAG 58.418 50.000 0.00 0.00 0.00 2.77
291 292 1.872952 CATGACGCACAGGAAGACAAA 59.127 47.619 0.00 0.00 31.40 2.83
292 293 1.202639 ACATGACGCACAGGAAGACAA 60.203 47.619 0.00 0.00 34.19 3.18
293 294 0.392706 ACATGACGCACAGGAAGACA 59.607 50.000 0.00 0.00 34.19 3.41
294 295 2.363788 TACATGACGCACAGGAAGAC 57.636 50.000 0.00 0.00 34.19 3.01
296 297 4.481930 TTTTTACATGACGCACAGGAAG 57.518 40.909 0.00 0.00 34.19 3.46
314 315 6.596106 ACTTTTAACACCCGCAAGAAATTTTT 59.404 30.769 0.00 0.00 43.02 1.94
315 316 6.110033 ACTTTTAACACCCGCAAGAAATTTT 58.890 32.000 0.00 0.00 43.02 1.82
316 317 5.666462 ACTTTTAACACCCGCAAGAAATTT 58.334 33.333 0.00 0.00 43.02 1.82
317 318 5.270893 ACTTTTAACACCCGCAAGAAATT 57.729 34.783 0.00 0.00 43.02 1.82
318 319 4.929819 ACTTTTAACACCCGCAAGAAAT 57.070 36.364 0.00 0.00 43.02 2.17
397 398 2.775384 ACCTTTCTGTGAGTGGTTGGTA 59.225 45.455 0.00 0.00 0.00 3.25
454 455 3.406764 AGTTGCAGTCTTCAAGCTAAGG 58.593 45.455 0.00 0.00 0.00 2.69
508 509 5.111293 AGGTGTTGAGAACAAAATTTGCAG 58.889 37.500 5.52 0.00 44.16 4.41
556 584 6.085573 TCACATTTCTGTAATGCATTTCACG 58.914 36.000 18.75 12.10 46.21 4.35
643 813 7.472334 AATAAAGAAGGAATGCACTTCACAT 57.528 32.000 15.56 5.92 45.18 3.21
647 817 9.890352 GATGATAATAAAGAAGGAATGCACTTC 57.110 33.333 7.32 7.32 43.56 3.01
648 818 9.638176 AGATGATAATAAAGAAGGAATGCACTT 57.362 29.630 0.00 0.00 0.00 3.16
740 915 3.902881 ACTGATGGTGAGATGAGGAAC 57.097 47.619 0.00 0.00 0.00 3.62
774 949 3.797256 AGTCGCGCTATTGAAAGTGATAC 59.203 43.478 5.56 0.00 0.00 2.24
780 955 3.121194 GCATAGAGTCGCGCTATTGAAAG 60.121 47.826 5.56 0.00 0.00 2.62
953 1139 6.816640 CCTTGATGAAGTTCCTACGATTTACA 59.183 38.462 0.00 0.00 0.00 2.41
969 1155 1.133513 AGTTGTGGTGCCCTTGATGAA 60.134 47.619 0.00 0.00 0.00 2.57
1110 1415 5.985530 GCTTCATTGCCATTTAAAGGATACC 59.014 40.000 0.46 0.00 37.17 2.73
1116 1421 3.912708 GCGCTTCATTGCCATTTAAAG 57.087 42.857 0.00 0.00 0.00 1.85
1163 1468 5.401531 AAAGTTTGAGATACGCTCTGGTA 57.598 39.130 0.00 0.00 44.27 3.25
1171 1476 7.843490 TCCATCCTTAAAAGTTTGAGATACG 57.157 36.000 0.00 0.00 0.00 3.06
1413 1718 6.152831 GCACCAAAAGTATACAGAAAAGGGAT 59.847 38.462 5.50 0.00 0.00 3.85
1547 1852 4.633126 TGCTCTTTGTATTCTCACTGCATC 59.367 41.667 0.00 0.00 0.00 3.91
1643 1948 4.245660 CAGAATTCGCTGGTTTAGAGACA 58.754 43.478 0.00 0.00 34.80 3.41
1933 2238 7.083875 TGCTTAGTTACTATGTTTGGATTGC 57.916 36.000 7.05 0.00 0.00 3.56
2044 2349 3.564511 CAAAAGTTACACCATTGAGCGG 58.435 45.455 0.00 0.00 0.00 5.52
2048 2353 6.155393 ACCTTTTCCAAAAGTTACACCATTGA 59.845 34.615 10.24 0.00 42.92 2.57
2146 2451 2.435372 ACTCCCTGCACAACAAAGAA 57.565 45.000 0.00 0.00 0.00 2.52
2191 2496 7.177744 GGATAAATGTGTGAAAGGGAGGTTTTA 59.822 37.037 0.00 0.00 0.00 1.52
2216 2521 4.157656 TCAAAGTGAAACAGAAACCTGTGG 59.842 41.667 0.00 0.00 43.60 4.17
2271 2594 7.439056 ACAAATATGACCAAAAAGCACAAAGAG 59.561 33.333 0.00 0.00 0.00 2.85
2483 2806 4.207165 CAAGATCATTACCACCCGGAATT 58.793 43.478 0.73 0.00 35.59 2.17
2544 2867 2.872245 GCACAGCAAGTTCAGACTAACA 59.128 45.455 0.00 0.00 34.21 2.41
2608 2931 9.071276 AGAGAAATGTCAAACAGTTAATCACAT 57.929 29.630 0.00 0.00 36.45 3.21
2675 2998 7.263496 ACCTGATTTAACTCGTCTATACCAAC 58.737 38.462 0.00 0.00 0.00 3.77
3381 3705 1.943340 GTGAATTCAGAATCCTCCGGC 59.057 52.381 8.80 0.00 0.00 6.13
3584 3909 1.214424 GAGTTAATAAGGGCCTGGGCA 59.786 52.381 22.68 1.36 44.11 5.36
3643 3968 3.179443 ACATTCTACACCATGCCTACG 57.821 47.619 0.00 0.00 0.00 3.51
3836 4161 6.065976 TCTCTATTCAAAGAAATGGAGCCA 57.934 37.500 5.43 0.00 41.48 4.75
3884 4209 4.799564 TTTTTGAATATGTCACCAGGGC 57.200 40.909 0.00 0.00 35.39 5.19
3999 4324 7.383300 GCTTTCAGCATCAAGTCTTATTTGTTT 59.617 33.333 0.00 0.00 41.89 2.83
4148 4475 8.992073 AGAAATGAAACCATGCAATTAAGTTTC 58.008 29.630 16.84 16.84 44.09 2.78
4528 4864 2.099921 ACCATCATGAGTCAGTAGTCGC 59.900 50.000 0.09 0.00 0.00 5.19
4555 4891 5.987953 CCATGACTGACCAACATGTCTATAG 59.012 44.000 0.00 0.00 39.47 1.31
4556 4892 5.660864 TCCATGACTGACCAACATGTCTATA 59.339 40.000 0.00 0.00 39.47 1.31
4557 4893 4.471025 TCCATGACTGACCAACATGTCTAT 59.529 41.667 0.00 0.00 39.47 1.98
4559 4895 2.639347 TCCATGACTGACCAACATGTCT 59.361 45.455 0.00 0.00 39.47 3.41
4560 4896 2.744202 GTCCATGACTGACCAACATGTC 59.256 50.000 0.00 0.00 39.47 3.06
4561 4897 2.783135 GTCCATGACTGACCAACATGT 58.217 47.619 0.00 0.00 39.47 3.21
4750 5088 8.509690 TGTAATACTCGTAGGACATTAGCATAC 58.490 37.037 0.00 0.00 0.00 2.39
4913 5251 1.005097 TCGCTAGATATAGGGGCGGAA 59.995 52.381 11.09 0.00 44.88 4.30
5022 5360 5.619981 GCAATAACATTCGACAGAAGGCTTT 60.620 40.000 0.00 0.00 41.42 3.51
5745 6090 7.615757 AGAAAAATATACCAGCTTTAACAGGCT 59.384 33.333 0.00 0.00 39.60 4.58
5763 6108 9.284594 CACTGAAAACAAGACGAAAGAAAAATA 57.715 29.630 0.00 0.00 0.00 1.40
6164 6519 6.590677 GGAGACCAAGAATTGTCAAGTAGTAC 59.409 42.308 0.00 0.00 46.99 2.73
6178 6534 4.357325 AGAGCTAATGAGGAGACCAAGAA 58.643 43.478 0.00 0.00 0.00 2.52
6186 6542 5.406649 CGCCTAATAAGAGCTAATGAGGAG 58.593 45.833 9.80 4.09 0.00 3.69
6300 6660 4.025040 AGATTCACATCTTCTGCCAACA 57.975 40.909 0.00 0.00 36.18 3.33
6430 6790 0.743345 AATTCGGCTTCGGCAGTACC 60.743 55.000 0.00 0.00 43.96 3.34
6439 6799 3.274288 AGGTCAATGAGAATTCGGCTTC 58.726 45.455 0.00 0.00 0.00 3.86
6565 6925 1.463363 CGTGTGTGTGTGTGTGTGTTC 60.463 52.381 0.00 0.00 0.00 3.18
6597 6962 2.200170 GAATTCAGCCACACCGGTGC 62.200 60.000 34.26 20.87 43.88 5.01
6598 6963 0.888736 TGAATTCAGCCACACCGGTG 60.889 55.000 32.83 32.83 44.85 4.94
6750 7118 8.872845 CAAGTTTTCAAGTAAAGTGCTTTGATT 58.127 29.630 7.38 0.17 34.23 2.57
6762 7130 4.727507 TTGCCAGCAAGTTTTCAAGTAA 57.272 36.364 0.00 0.00 0.00 2.24
6763 7131 4.935352 ATTGCCAGCAAGTTTTCAAGTA 57.065 36.364 11.21 0.00 39.47 2.24
6764 7132 3.825143 ATTGCCAGCAAGTTTTCAAGT 57.175 38.095 11.21 0.00 39.47 3.16
6765 7133 4.240096 CCTATTGCCAGCAAGTTTTCAAG 58.760 43.478 11.21 0.46 39.47 3.02
6934 7304 0.519077 GCCTGTTCTTTGCTCTTCCG 59.481 55.000 0.00 0.00 0.00 4.30
7016 7386 3.300388 TGTTCTCTCCAGGGCAGTATAG 58.700 50.000 0.00 0.00 0.00 1.31
7099 7469 6.876257 CCAAATCATCAACCTAGATACCTAGC 59.124 42.308 0.00 0.00 40.78 3.42
7126 7496 2.932614 CGTAAGAAGCTGTCAATCTGGG 59.067 50.000 0.00 0.00 43.02 4.45
7131 7501 1.067142 TCGCCGTAAGAAGCTGTCAAT 60.067 47.619 0.00 0.00 43.02 2.57
7133 7503 0.530744 ATCGCCGTAAGAAGCTGTCA 59.469 50.000 0.00 0.00 43.02 3.58
7169 7539 2.694397 TGACAAGGCCTATCCATAGCT 58.306 47.619 5.16 0.00 37.29 3.32
7192 7562 6.054941 GGCATCCCTTTTCTTTTTCTTTCAA 58.945 36.000 0.00 0.00 0.00 2.69
7193 7563 5.366477 AGGCATCCCTTTTCTTTTTCTTTCA 59.634 36.000 0.00 0.00 38.74 2.69
7313 7683 0.029567 GATCGCCCGACACTACAGAG 59.970 60.000 0.00 0.00 0.00 3.35
7333 7703 7.218228 TGCACAATGAATACAAGAATGAACT 57.782 32.000 0.00 0.00 0.00 3.01
7483 7853 3.019564 GCTCAGATGTTACCTTGGCAAT 58.980 45.455 0.00 0.00 0.00 3.56
7599 7969 5.767269 TCGAAAGCTGAAATAATTGCAACA 58.233 33.333 0.00 0.00 0.00 3.33
7747 8118 3.127030 GCCATTTTATAGGCCGCTATCAC 59.873 47.826 0.00 0.00 45.18 3.06
7760 8131 6.127675 GCAAAAATGACCCAATGCCATTTTAT 60.128 34.615 14.54 7.18 44.72 1.40
7860 8231 0.469917 AGTTATGCCCCATGACTCGG 59.530 55.000 0.00 0.00 36.21 4.63


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

AutoCloner maintained by Alex Coulton.