Multiple sequence alignment - TraesCS2B01G027100

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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 TraesCS2B01G027100 chr2B 100.000 3482 0 0 1 3482 12913567 12917048 0.000000e+00 6431
1 TraesCS2B01G027100 chr2B 96.629 2670 83 5 814 3482 11559746 11557083 0.000000e+00 4425
2 TraesCS2B01G027100 chr2B 94.866 1753 71 10 817 2554 11573864 11572116 0.000000e+00 2721
3 TraesCS2B01G027100 chr2B 95.565 248 11 0 570 817 11560024 11559777 7.000000e-107 398
4 TraesCS2B01G027100 chr2B 83.086 337 44 6 225 549 11577499 11577164 9.450000e-76 294
5 TraesCS2B01G027100 chr2B 85.811 148 14 6 673 817 11574041 11573898 2.160000e-32 150
6 TraesCS2B01G027100 chr2A 91.748 2266 126 23 817 3040 8627227 8629473 0.000000e+00 3092
7 TraesCS2B01G027100 chr2A 82.409 1461 228 12 978 2431 7727378 7728816 0.000000e+00 1247
8 TraesCS2B01G027100 chr2A 80.658 1551 250 26 999 2535 9944092 9945606 0.000000e+00 1157
9 TraesCS2B01G027100 chr2A 82.069 145 19 6 673 817 8627056 8627193 2.200000e-22 117
10 TraesCS2B01G027100 chr2D 87.786 2227 214 34 839 3040 9277335 9279528 0.000000e+00 2553
11 TraesCS2B01G027100 chr2D 92.607 1772 97 9 817 2586 9371354 9373093 0.000000e+00 2516
12 TraesCS2B01G027100 chr2D 88.515 1576 158 12 978 2540 9502197 9503762 0.000000e+00 1886
13 TraesCS2B01G027100 chr2D 82.526 1568 235 20 978 2530 8686448 8687991 0.000000e+00 1341
14 TraesCS2B01G027100 chr2D 82.595 1534 232 15 974 2494 8659771 8661282 0.000000e+00 1321
15 TraesCS2B01G027100 chr2D 86.652 442 58 1 3041 3482 4451872 4451432 4.040000e-134 488
16 TraesCS2B01G027100 chr2D 87.200 250 26 5 570 817 9371075 9371320 2.650000e-71 279
17 TraesCS2B01G027100 chr2D 84.980 253 27 7 570 818 9277006 9277251 2.680000e-61 246
18 TraesCS2B01G027100 chr2D 84.422 199 22 5 817 1012 9502012 9502204 1.650000e-43 187
19 TraesCS2B01G027100 chr2D 84.393 173 17 6 653 817 9501410 9501580 1.000000e-35 161
20 TraesCS2B01G027100 chrUn 83.369 1401 208 15 1140 2530 273231384 273229999 0.000000e+00 1273
21 TraesCS2B01G027100 chrUn 83.369 1401 208 15 1140 2530 292878468 292879853 0.000000e+00 1273
22 TraesCS2B01G027100 chr5A 86.878 442 56 2 3041 3482 111614632 111615071 8.680000e-136 494
23 TraesCS2B01G027100 chr5A 86.878 442 56 2 3041 3482 222606321 222606760 8.680000e-136 494
24 TraesCS2B01G027100 chr6A 86.652 442 58 1 3041 3482 423317933 423317493 4.040000e-134 488
25 TraesCS2B01G027100 chr4A 86.652 442 58 1 3041 3482 164877785 164877345 4.040000e-134 488
26 TraesCS2B01G027100 chr4A 86.652 442 58 1 3041 3482 459853227 459852787 4.040000e-134 488
27 TraesCS2B01G027100 chr3A 86.652 442 58 1 3041 3482 264952561 264952121 4.040000e-134 488
28 TraesCS2B01G027100 chr3A 86.758 438 57 1 3041 3478 375018217 375017781 1.450000e-133 486


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 TraesCS2B01G027100 chr2B 12913567 12917048 3481 False 6431.000000 6431 100.000000 1 3482 1 chr2B.!!$F1 3481
1 TraesCS2B01G027100 chr2B 11557083 11560024 2941 True 2411.500000 4425 96.097000 570 3482 2 chr2B.!!$R1 2912
2 TraesCS2B01G027100 chr2B 11572116 11577499 5383 True 1055.000000 2721 87.921000 225 2554 3 chr2B.!!$R2 2329
3 TraesCS2B01G027100 chr2A 8627056 8629473 2417 False 1604.500000 3092 86.908500 673 3040 2 chr2A.!!$F3 2367
4 TraesCS2B01G027100 chr2A 7727378 7728816 1438 False 1247.000000 1247 82.409000 978 2431 1 chr2A.!!$F1 1453
5 TraesCS2B01G027100 chr2A 9944092 9945606 1514 False 1157.000000 1157 80.658000 999 2535 1 chr2A.!!$F2 1536
6 TraesCS2B01G027100 chr2D 9277006 9279528 2522 False 1399.500000 2553 86.383000 570 3040 2 chr2D.!!$F3 2470
7 TraesCS2B01G027100 chr2D 9371075 9373093 2018 False 1397.500000 2516 89.903500 570 2586 2 chr2D.!!$F4 2016
8 TraesCS2B01G027100 chr2D 8686448 8687991 1543 False 1341.000000 1341 82.526000 978 2530 1 chr2D.!!$F2 1552
9 TraesCS2B01G027100 chr2D 8659771 8661282 1511 False 1321.000000 1321 82.595000 974 2494 1 chr2D.!!$F1 1520
10 TraesCS2B01G027100 chr2D 9501410 9503762 2352 False 744.666667 1886 85.776667 653 2540 3 chr2D.!!$F5 1887
11 TraesCS2B01G027100 chrUn 273229999 273231384 1385 True 1273.000000 1273 83.369000 1140 2530 1 chrUn.!!$R1 1390
12 TraesCS2B01G027100 chrUn 292878468 292879853 1385 False 1273.000000 1273 83.369000 1140 2530 1 chrUn.!!$F1 1390

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
359 372 0.525668 CCGACGGAGAAATCGTGGAG 60.526 60.0 8.64 0.0 41.22 3.86 F
439 452 0.974010 CATGGCCAGCCTGGTGAAAT 60.974 55.0 13.05 0.0 40.46 2.17 F
1739 5280 0.609406 GGAGACAGCCTTTTGGGGAC 60.609 60.0 0.00 0.0 40.82 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 5280 1.379044 GCCCTCCCATCACCAAGTG 60.379 63.158 0.0 0.0 34.45 3.16 R
2076 5624 3.066380 TCTCAACACATCCGTGAACATG 58.934 45.455 0.0 0.0 46.80 3.21 R
3368 6958 0.108585 TGGACACACAAGGAAGGAGC 59.891 55.000 0.0 0.0 0.00 4.70 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
31 32 6.869421 AAAAACATGTCTTGAAACTGTTCG 57.131 33.333 0.00 0.00 36.46 3.95
32 33 5.811399 AAACATGTCTTGAAACTGTTCGA 57.189 34.783 0.00 0.00 36.46 3.71
33 34 5.811399 AACATGTCTTGAAACTGTTCGAA 57.189 34.783 0.00 0.00 36.46 3.71
34 35 5.811399 ACATGTCTTGAAACTGTTCGAAA 57.189 34.783 0.00 0.00 36.46 3.46
35 36 6.377327 ACATGTCTTGAAACTGTTCGAAAT 57.623 33.333 0.00 0.00 36.46 2.17
36 37 7.490962 ACATGTCTTGAAACTGTTCGAAATA 57.509 32.000 0.00 0.00 36.46 1.40
37 38 7.352739 ACATGTCTTGAAACTGTTCGAAATAC 58.647 34.615 0.00 0.00 36.46 1.89
38 39 6.912203 TGTCTTGAAACTGTTCGAAATACA 57.088 33.333 0.00 0.00 36.46 2.29
39 40 6.711579 TGTCTTGAAACTGTTCGAAATACAC 58.288 36.000 0.00 0.00 36.46 2.90
40 41 6.314152 TGTCTTGAAACTGTTCGAAATACACA 59.686 34.615 0.00 0.00 36.46 3.72
41 42 6.846283 GTCTTGAAACTGTTCGAAATACACAG 59.154 38.462 11.68 11.68 43.12 3.66
53 54 9.712359 GTTCGAAATACACAGTAATATTTTCCC 57.288 33.333 0.00 0.00 32.42 3.97
54 55 9.451002 TTCGAAATACACAGTAATATTTTCCCA 57.549 29.630 0.00 0.00 32.42 4.37
55 56 9.621629 TCGAAATACACAGTAATATTTTCCCAT 57.378 29.630 0.00 0.00 32.42 4.00
56 57 9.663904 CGAAATACACAGTAATATTTTCCCATG 57.336 33.333 0.00 0.00 32.42 3.66
199 200 9.744468 AACTCACACACATAATTAACCTTTTTC 57.256 29.630 0.00 0.00 0.00 2.29
200 201 8.908903 ACTCACACACATAATTAACCTTTTTCA 58.091 29.630 0.00 0.00 0.00 2.69
201 202 9.912634 CTCACACACATAATTAACCTTTTTCAT 57.087 29.630 0.00 0.00 0.00 2.57
202 203 9.906660 TCACACACATAATTAACCTTTTTCATC 57.093 29.630 0.00 0.00 0.00 2.92
203 204 9.139174 CACACACATAATTAACCTTTTTCATCC 57.861 33.333 0.00 0.00 0.00 3.51
204 205 9.088987 ACACACATAATTAACCTTTTTCATCCT 57.911 29.630 0.00 0.00 0.00 3.24
320 321 2.260434 CCGGACGACCACAACGAT 59.740 61.111 0.00 0.00 35.59 3.73
326 327 0.601558 ACGACCACAACGATGCTAGT 59.398 50.000 0.00 0.00 34.70 2.57
328 329 2.159421 ACGACCACAACGATGCTAGTAG 60.159 50.000 0.00 0.00 34.70 2.57
332 333 0.815734 ACAACGATGCTAGTAGGCGT 59.184 50.000 5.85 5.85 36.68 5.68
353 366 0.806492 GGCTCACCGACGGAGAAATC 60.806 60.000 23.38 9.79 34.24 2.17
358 371 1.246056 ACCGACGGAGAAATCGTGGA 61.246 55.000 23.38 0.00 41.22 4.02
359 372 0.525668 CCGACGGAGAAATCGTGGAG 60.526 60.000 8.64 0.00 41.22 3.86
362 375 1.993370 GACGGAGAAATCGTGGAGTTG 59.007 52.381 0.00 0.00 41.22 3.16
365 378 1.464997 GGAGAAATCGTGGAGTTGTGC 59.535 52.381 0.00 0.00 0.00 4.57
374 387 2.551270 GAGTTGTGCGCCGAGTTG 59.449 61.111 4.18 0.00 0.00 3.16
375 388 2.954753 GAGTTGTGCGCCGAGTTGG 61.955 63.158 4.18 0.00 42.50 3.77
386 399 2.358737 GAGTTGGTCGGGTGCAGG 60.359 66.667 0.00 0.00 0.00 4.85
387 400 3.901797 GAGTTGGTCGGGTGCAGGG 62.902 68.421 0.00 0.00 0.00 4.45
388 401 3.948719 GTTGGTCGGGTGCAGGGA 61.949 66.667 0.00 0.00 0.00 4.20
389 402 3.948719 TTGGTCGGGTGCAGGGAC 61.949 66.667 0.00 0.00 0.00 4.46
400 413 2.280552 GCAGGGACGGGTACAGTGA 61.281 63.158 0.00 0.00 36.51 3.41
402 415 1.608627 AGGGACGGGTACAGTGACC 60.609 63.158 0.00 0.00 36.51 4.02
417 430 3.011517 ACCCCGGAGCTGCAGAAT 61.012 61.111 20.43 4.39 0.00 2.40
426 439 1.811359 GAGCTGCAGAATATCATGGCC 59.189 52.381 20.43 0.00 0.00 5.36
428 441 1.540267 GCTGCAGAATATCATGGCCAG 59.460 52.381 20.43 3.43 0.00 4.85
439 452 0.974010 CATGGCCAGCCTGGTGAAAT 60.974 55.000 13.05 0.00 40.46 2.17
486 499 3.260483 GAGATCAGCGCTGCCGTG 61.260 66.667 32.44 10.18 36.67 4.94
519 532 3.519930 GAGGTCGGCGAGGAGGTC 61.520 72.222 11.20 0.00 0.00 3.85
543 556 5.364157 CCTTGGTAAGCTAGAGTACCTCAAT 59.636 44.000 18.19 0.00 40.48 2.57
545 558 4.099573 TGGTAAGCTAGAGTACCTCAATGC 59.900 45.833 18.19 0.00 40.48 3.56
549 562 3.131933 AGCTAGAGTACCTCAATGCTGTG 59.868 47.826 0.00 0.00 33.86 3.66
550 563 3.739519 GCTAGAGTACCTCAATGCTGTGG 60.740 52.174 0.00 0.00 41.24 4.17
555 568 1.830279 ACCTCAATGCTGTGGTCATG 58.170 50.000 0.00 0.00 44.39 3.07
557 570 2.224843 ACCTCAATGCTGTGGTCATGAA 60.225 45.455 0.00 0.00 44.39 2.57
558 571 2.422479 CCTCAATGCTGTGGTCATGAAG 59.578 50.000 0.00 0.00 32.48 3.02
559 572 2.422479 CTCAATGCTGTGGTCATGAAGG 59.578 50.000 0.00 0.00 0.00 3.46
560 573 2.040145 TCAATGCTGTGGTCATGAAGGA 59.960 45.455 0.00 0.00 0.00 3.36
561 574 2.821378 CAATGCTGTGGTCATGAAGGAA 59.179 45.455 0.00 0.00 0.00 3.36
562 575 1.896220 TGCTGTGGTCATGAAGGAAC 58.104 50.000 0.00 0.00 0.00 3.62
563 576 1.168714 GCTGTGGTCATGAAGGAACC 58.831 55.000 0.00 0.00 0.00 3.62
565 578 2.862541 CTGTGGTCATGAAGGAACCAA 58.137 47.619 4.87 0.00 31.71 3.67
566 579 3.221771 CTGTGGTCATGAAGGAACCAAA 58.778 45.455 4.87 0.00 31.71 3.28
567 580 3.636300 CTGTGGTCATGAAGGAACCAAAA 59.364 43.478 4.87 0.00 31.71 2.44
568 581 3.636300 TGTGGTCATGAAGGAACCAAAAG 59.364 43.478 4.87 0.00 31.71 2.27
664 3695 1.210155 GCGCGATGCTTTTCCACTT 59.790 52.632 12.10 0.00 41.73 3.16
715 3748 4.182693 TCCCACGTGTGTAGAATGTAAG 57.817 45.455 15.65 0.00 0.00 2.34
808 3847 7.679783 TGGACCTACCATGAATATAACAGATG 58.320 38.462 0.00 0.00 44.64 2.90
1739 5280 0.609406 GGAGACAGCCTTTTGGGGAC 60.609 60.000 0.00 0.00 40.82 4.46
2076 5624 5.247340 CAAATTTCACTTGTCGCAACAAAC 58.753 37.500 0.00 0.00 44.53 2.93
2200 5752 0.814457 GAACCCAACCATGCGCATAA 59.186 50.000 24.84 0.00 0.00 1.90
2270 5822 9.765795 ACTAAGCATGAAACCTTATAGTGATAC 57.234 33.333 0.00 0.00 0.00 2.24
2297 5849 5.244402 TGTCAATCAAGACAGAATTGCCAAT 59.756 36.000 0.00 0.00 43.18 3.16
2308 5860 5.697633 ACAGAATTGCCAATTGTGACATTTC 59.302 36.000 27.91 10.91 42.84 2.17
2450 6002 3.200825 ACATATCAAAGTAGTGCCCTGCT 59.799 43.478 0.00 0.00 34.83 4.24
2657 6230 2.993899 CTGTTGACACCGTGGTATTCTC 59.006 50.000 3.03 0.00 0.00 2.87
2682 6255 6.001460 AGTGAAGAAAATACAATTCGGACCA 58.999 36.000 0.00 0.00 32.04 4.02
2754 6329 8.402472 ACGAATGACATTTCTTTGTGAAACTTA 58.598 29.630 1.39 0.00 46.08 2.24
2915 6503 4.758688 ACTTCACATCATGCGTAGAATGA 58.241 39.130 5.17 0.00 38.37 2.57
3052 6642 4.475345 ACTATTCAGTGGTAGGCTAGAGG 58.525 47.826 0.00 0.00 32.25 3.69
3083 6673 5.702670 CCATAAGATATCGCAACCAACTCAT 59.297 40.000 0.00 0.00 0.00 2.90
3098 6688 6.173339 ACCAACTCATAGTTCTAACACATGG 58.827 40.000 0.00 0.00 36.03 3.66
3120 6710 2.594303 CAAGCTTCCACGCACCCA 60.594 61.111 0.00 0.00 0.00 4.51
3156 6746 5.546499 AGTTCTTTGGTTATACTCCAGTCCA 59.454 40.000 0.00 0.00 36.28 4.02
3171 6761 3.433314 CCAGTCCATCAGATCCCTCTTTG 60.433 52.174 0.00 0.00 0.00 2.77
3173 6763 2.092753 GTCCATCAGATCCCTCTTTGCA 60.093 50.000 0.00 0.00 0.00 4.08
3182 6772 1.203237 TCCCTCTTTGCAGACTCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
3183 6773 1.206849 CCCTCTTTGCAGACTCCTCTC 59.793 57.143 0.00 0.00 0.00 3.20
3191 6781 2.233186 TGCAGACTCCTCTCATGTCAAG 59.767 50.000 0.00 0.00 33.56 3.02
3194 6784 4.493547 CAGACTCCTCTCATGTCAAGTTC 58.506 47.826 0.00 0.00 33.56 3.01
3195 6785 3.192422 AGACTCCTCTCATGTCAAGTTCG 59.808 47.826 0.00 0.00 33.56 3.95
3224 6814 3.555956 CCCGACCTTTCTTGACATTATCG 59.444 47.826 0.00 0.00 0.00 2.92
3231 6821 3.969117 TCTTGACATTATCGGCAATGC 57.031 42.857 0.00 0.00 39.13 3.56
3232 6822 2.618241 TCTTGACATTATCGGCAATGCC 59.382 45.455 15.52 15.52 46.75 4.40
3271 6861 3.555967 CCGCTTCTGGAGGCCTAT 58.444 61.111 4.42 0.00 0.00 2.57
3275 6865 1.051812 GCTTCTGGAGGCCTATGCTA 58.948 55.000 4.42 0.00 37.74 3.49
3280 6870 5.746065 GCTTCTGGAGGCCTATGCTAAATAA 60.746 44.000 4.42 0.00 37.74 1.40
3322 6912 0.478072 TTGGGCAAGCTTCTCTCCAA 59.522 50.000 12.53 12.53 32.60 3.53
3327 6917 1.677217 GCAAGCTTCTCTCCAATCGGT 60.677 52.381 0.00 0.00 0.00 4.69
3338 6928 1.029947 CCAATCGGTGCTACCCCAAC 61.030 60.000 0.00 0.00 33.75 3.77
3353 6943 6.377712 GCTACCCCAACTCTATCTCGTATATT 59.622 42.308 0.00 0.00 0.00 1.28
3368 6958 5.758924 TCGTATATTGTCATTCTGGACTCG 58.241 41.667 0.00 0.00 38.61 4.18
3402 6992 3.220110 GTGTCCATGCATCCATCTCAAT 58.780 45.455 0.00 0.00 0.00 2.57
3406 6996 4.014406 TCCATGCATCCATCTCAATATGC 58.986 43.478 0.00 0.00 43.92 3.14
3437 7027 5.335269 CCGGCACAATTAACTGTTGAACATA 60.335 40.000 0.00 0.00 0.00 2.29
3439 7029 6.806249 CGGCACAATTAACTGTTGAACATAAT 59.194 34.615 0.00 0.00 0.00 1.28
3441 7031 7.411804 GGCACAATTAACTGTTGAACATAATGC 60.412 37.037 0.00 3.32 0.00 3.56
3466 7056 1.595382 GTCAGCCAACACTCAGCGT 60.595 57.895 0.00 0.00 0.00 5.07
3478 7068 4.816392 ACACTCAGCGTCATACAACATTA 58.184 39.130 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.616947 TCGAACAGTTTCAAGACATGTTTTT 58.383 32.000 0.00 0.00 34.41 1.94
9 10 6.189677 TCGAACAGTTTCAAGACATGTTTT 57.810 33.333 0.00 0.00 34.41 2.43
10 11 5.811399 TCGAACAGTTTCAAGACATGTTT 57.189 34.783 0.00 0.00 34.41 2.83
11 12 5.811399 TTCGAACAGTTTCAAGACATGTT 57.189 34.783 0.00 0.00 36.83 2.71
12 13 5.811399 TTTCGAACAGTTTCAAGACATGT 57.189 34.783 0.00 0.00 0.00 3.21
13 14 7.321271 GTGTATTTCGAACAGTTTCAAGACATG 59.679 37.037 0.00 0.00 0.00 3.21
14 15 7.011950 TGTGTATTTCGAACAGTTTCAAGACAT 59.988 33.333 0.00 0.00 0.00 3.06
15 16 6.314152 TGTGTATTTCGAACAGTTTCAAGACA 59.686 34.615 0.00 0.00 0.00 3.41
16 17 6.711579 TGTGTATTTCGAACAGTTTCAAGAC 58.288 36.000 0.00 0.00 0.00 3.01
17 18 6.912203 TGTGTATTTCGAACAGTTTCAAGA 57.088 33.333 0.00 0.00 0.00 3.02
27 28 9.712359 GGGAAAATATTACTGTGTATTTCGAAC 57.288 33.333 0.00 0.00 31.26 3.95
28 29 9.451002 TGGGAAAATATTACTGTGTATTTCGAA 57.549 29.630 0.00 0.00 31.26 3.71
29 30 9.621629 ATGGGAAAATATTACTGTGTATTTCGA 57.378 29.630 11.09 0.00 31.26 3.71
30 31 9.663904 CATGGGAAAATATTACTGTGTATTTCG 57.336 33.333 11.09 0.00 31.26 3.46
173 174 9.744468 GAAAAAGGTTAATTATGTGTGTGAGTT 57.256 29.630 0.00 0.00 0.00 3.01
174 175 8.908903 TGAAAAAGGTTAATTATGTGTGTGAGT 58.091 29.630 0.00 0.00 0.00 3.41
175 176 9.912634 ATGAAAAAGGTTAATTATGTGTGTGAG 57.087 29.630 0.00 0.00 0.00 3.51
176 177 9.906660 GATGAAAAAGGTTAATTATGTGTGTGA 57.093 29.630 0.00 0.00 0.00 3.58
177 178 9.139174 GGATGAAAAAGGTTAATTATGTGTGTG 57.861 33.333 0.00 0.00 0.00 3.82
178 179 9.088987 AGGATGAAAAAGGTTAATTATGTGTGT 57.911 29.630 0.00 0.00 0.00 3.72
205 206 8.514594 CGTGGATGCAGGAACATATTAATTATT 58.485 33.333 0.00 0.00 0.00 1.40
206 207 7.362056 GCGTGGATGCAGGAACATATTAATTAT 60.362 37.037 11.38 0.00 34.15 1.28
207 208 6.072728 GCGTGGATGCAGGAACATATTAATTA 60.073 38.462 11.38 0.00 34.15 1.40
208 209 5.278463 GCGTGGATGCAGGAACATATTAATT 60.278 40.000 11.38 0.00 34.15 1.40
209 210 4.216257 GCGTGGATGCAGGAACATATTAAT 59.784 41.667 11.38 0.00 34.15 1.40
210 211 3.563808 GCGTGGATGCAGGAACATATTAA 59.436 43.478 11.38 0.00 34.15 1.40
211 212 3.138304 GCGTGGATGCAGGAACATATTA 58.862 45.455 11.38 0.00 34.15 0.98
212 213 1.949525 GCGTGGATGCAGGAACATATT 59.050 47.619 11.38 0.00 34.15 1.28
213 214 1.597742 GCGTGGATGCAGGAACATAT 58.402 50.000 11.38 0.00 34.15 1.78
214 215 0.463654 GGCGTGGATGCAGGAACATA 60.464 55.000 11.38 0.00 36.28 2.29
215 216 1.750399 GGCGTGGATGCAGGAACAT 60.750 57.895 11.38 0.00 36.28 2.71
216 217 2.359850 GGCGTGGATGCAGGAACA 60.360 61.111 11.38 0.00 36.28 3.18
217 218 3.134127 GGGCGTGGATGCAGGAAC 61.134 66.667 11.38 2.53 36.28 3.62
218 219 4.776322 CGGGCGTGGATGCAGGAA 62.776 66.667 11.38 0.00 36.28 3.36
267 268 2.202388 CGTGTCGACATACGCCGT 60.202 61.111 23.12 0.00 42.26 5.68
278 279 1.583967 GAGGTCGATGAGCGTGTCG 60.584 63.158 0.00 1.99 41.80 4.35
320 321 0.106868 TGAGCCTACGCCTACTAGCA 60.107 55.000 0.00 0.00 34.57 3.49
326 327 2.117156 GTCGGTGAGCCTACGCCTA 61.117 63.158 0.00 0.00 38.18 3.93
328 329 4.849329 CGTCGGTGAGCCTACGCC 62.849 72.222 0.00 0.00 44.82 5.68
332 333 0.609957 TTTCTCCGTCGGTGAGCCTA 60.610 55.000 15.09 0.00 0.00 3.93
337 338 0.109458 CACGATTTCTCCGTCGGTGA 60.109 55.000 11.88 11.89 41.87 4.02
338 339 1.076533 CCACGATTTCTCCGTCGGTG 61.077 60.000 11.88 9.31 41.87 4.94
339 340 1.214589 CCACGATTTCTCCGTCGGT 59.785 57.895 11.88 0.00 41.87 4.69
358 371 2.972505 CCAACTCGGCGCACAACT 60.973 61.111 10.83 0.00 0.00 3.16
359 372 3.236618 GACCAACTCGGCGCACAAC 62.237 63.158 10.83 0.00 39.03 3.32
380 393 2.264794 CTGTACCCGTCCCTGCAC 59.735 66.667 0.00 0.00 0.00 4.57
381 394 2.203728 ACTGTACCCGTCCCTGCA 60.204 61.111 0.00 0.00 0.00 4.41
382 395 2.264794 CACTGTACCCGTCCCTGC 59.735 66.667 0.00 0.00 0.00 4.85
383 396 1.590147 GTCACTGTACCCGTCCCTG 59.410 63.158 0.00 0.00 0.00 4.45
384 397 1.608627 GGTCACTGTACCCGTCCCT 60.609 63.158 0.00 0.00 33.02 4.20
391 404 3.015312 GCTCCGGGGTCACTGTACC 62.015 68.421 1.62 0.00 38.94 3.34
392 405 1.982938 AGCTCCGGGGTCACTGTAC 60.983 63.158 1.62 0.00 0.00 2.90
393 406 1.982395 CAGCTCCGGGGTCACTGTA 60.982 63.158 1.62 0.00 0.00 2.74
400 413 1.056700 ATATTCTGCAGCTCCGGGGT 61.057 55.000 9.47 0.00 0.00 4.95
402 415 0.394192 TGATATTCTGCAGCTCCGGG 59.606 55.000 9.47 0.00 0.00 5.73
403 416 2.074576 CATGATATTCTGCAGCTCCGG 58.925 52.381 9.47 0.00 0.00 5.14
415 428 0.855598 ACCAGGCTGGCCATGATATT 59.144 50.000 33.04 7.63 42.67 1.28
417 430 0.987613 TCACCAGGCTGGCCATGATA 60.988 55.000 33.04 6.69 42.67 2.15
426 439 1.607178 TGGGCATTTCACCAGGCTG 60.607 57.895 7.75 7.75 31.92 4.85
428 441 1.907807 TGTGGGCATTTCACCAGGC 60.908 57.895 0.00 0.00 37.45 4.85
439 452 1.604308 CCTCTTGCATGTGTGGGCA 60.604 57.895 0.00 0.00 38.46 5.36
543 556 1.545428 GGTTCCTTCATGACCACAGCA 60.545 52.381 0.00 0.00 33.61 4.41
545 558 2.566833 TGGTTCCTTCATGACCACAG 57.433 50.000 0.00 0.00 38.47 3.66
549 562 3.057245 GCTCTTTTGGTTCCTTCATGACC 60.057 47.826 0.00 0.00 0.00 4.02
550 563 3.569701 TGCTCTTTTGGTTCCTTCATGAC 59.430 43.478 0.00 0.00 0.00 3.06
551 564 3.831323 TGCTCTTTTGGTTCCTTCATGA 58.169 40.909 0.00 0.00 0.00 3.07
555 568 3.157087 TCCATGCTCTTTTGGTTCCTTC 58.843 45.455 0.00 0.00 34.48 3.46
557 570 2.800250 CTCCATGCTCTTTTGGTTCCT 58.200 47.619 0.00 0.00 34.48 3.36
558 571 1.203287 GCTCCATGCTCTTTTGGTTCC 59.797 52.381 0.00 0.00 38.95 3.62
559 572 2.643933 GCTCCATGCTCTTTTGGTTC 57.356 50.000 0.00 0.00 38.95 3.62
563 576 8.538492 GAGAATCACAGCTCCATGCTCTTTTG 62.538 46.154 0.00 0.00 43.03 2.44
565 578 5.162305 GAGAATCACAGCTCCATGCTCTTT 61.162 45.833 0.00 0.00 43.03 2.52
566 579 3.682155 GAGAATCACAGCTCCATGCTCTT 60.682 47.826 0.00 0.00 43.03 2.85
567 580 2.158928 GAGAATCACAGCTCCATGCTCT 60.159 50.000 0.00 0.00 43.03 4.09
568 581 2.211806 GAGAATCACAGCTCCATGCTC 58.788 52.381 0.00 0.00 43.03 4.26
583 2983 1.144057 GCCCGGTGATGACGAGAAT 59.856 57.895 0.00 0.00 0.00 2.40
618 3585 6.258727 GTCATCGTCAAGGAAATGATATGTGT 59.741 38.462 0.00 0.00 32.10 3.72
664 3695 5.640158 TGGTTTCTTTCCAGAGGAACTTA 57.360 39.130 0.00 0.00 41.87 2.24
715 3748 0.179194 CGTCTTTCGTCGGACTCCTC 60.179 60.000 6.57 0.00 34.52 3.71
1638 5179 4.188462 CAACCAAAGTTTTCTTCCCAACC 58.812 43.478 0.00 0.00 39.48 3.77
1739 5280 1.379044 GCCCTCCCATCACCAAGTG 60.379 63.158 0.00 0.00 34.45 3.16
2076 5624 3.066380 TCTCAACACATCCGTGAACATG 58.934 45.455 0.00 0.00 46.80 3.21
2270 5822 6.094464 TGGCAATTCTGTCTTGATTGACATAG 59.906 38.462 0.00 0.00 44.66 2.23
2286 5838 4.925054 CGAAATGTCACAATTGGCAATTCT 59.075 37.500 22.02 8.74 42.71 2.40
2297 5849 6.711194 TGTTATAAGTTCCCGAAATGTCACAA 59.289 34.615 0.00 0.00 0.00 3.33
2308 5860 6.040616 ACACTAGGATCTGTTATAAGTTCCCG 59.959 42.308 0.00 0.00 36.92 5.14
2338 5890 5.986501 ATTAGAGTGAAGTCTCCTTTCGT 57.013 39.130 0.00 0.00 35.28 3.85
2450 6002 0.040646 TCCTTGTCGCTTCCTCCCTA 59.959 55.000 0.00 0.00 0.00 3.53
2657 6230 6.072728 TGGTCCGAATTGTATTTTCTTCACTG 60.073 38.462 0.00 0.00 0.00 3.66
2915 6503 3.076785 TGGGGGTATCAAACTTGGTCAAT 59.923 43.478 0.00 0.00 0.00 2.57
3052 6642 6.204688 TGGTTGCGATATCTTATGGATTTCAC 59.795 38.462 0.34 0.00 33.80 3.18
3083 6673 5.181245 GCTTGCTTTCCATGTGTTAGAACTA 59.819 40.000 0.00 0.00 0.00 2.24
3098 6688 0.661483 GTGCGTGGAAGCTTGCTTTC 60.661 55.000 19.34 7.98 38.13 2.62
3120 6710 3.010584 ACCAAAGAACTAGGCATGGACAT 59.989 43.478 13.11 0.00 0.00 3.06
3156 6746 3.113824 AGTCTGCAAAGAGGGATCTGAT 58.886 45.455 0.00 0.00 0.00 2.90
3171 6761 2.233431 ACTTGACATGAGAGGAGTCTGC 59.767 50.000 0.00 0.00 30.97 4.26
3173 6763 3.192422 CGAACTTGACATGAGAGGAGTCT 59.808 47.826 0.00 0.00 34.86 3.24
3182 6772 2.232941 GGGTAGACCGAACTTGACATGA 59.767 50.000 0.00 0.00 36.71 3.07
3183 6773 2.618053 GGGTAGACCGAACTTGACATG 58.382 52.381 0.00 0.00 36.71 3.21
3210 6800 3.066621 GGCATTGCCGATAATGTCAAGAA 59.933 43.478 12.82 0.00 41.19 2.52
3254 6844 1.070445 CATAGGCCTCCAGAAGCGG 59.930 63.158 9.68 0.00 0.00 5.52
3275 6865 4.706962 GTCTGAGATGGTTTGGGCTTATTT 59.293 41.667 0.00 0.00 0.00 1.40
3280 6870 1.067295 TGTCTGAGATGGTTTGGGCT 58.933 50.000 0.00 0.00 0.00 5.19
3322 6912 0.617820 AGAGTTGGGGTAGCACCGAT 60.618 55.000 0.00 0.00 39.83 4.18
3327 6917 2.307768 CGAGATAGAGTTGGGGTAGCA 58.692 52.381 0.00 0.00 0.00 3.49
3338 6928 8.951243 TCCAGAATGACAATATACGAGATAGAG 58.049 37.037 0.00 0.00 39.69 2.43
3353 6943 0.532573 GGAGCGAGTCCAGAATGACA 59.467 55.000 0.00 0.00 46.10 3.58
3368 6958 0.108585 TGGACACACAAGGAAGGAGC 59.891 55.000 0.00 0.00 0.00 4.70
3402 6992 2.280119 GTGCCGGAGATGCGCATA 60.280 61.111 25.40 2.04 39.02 3.14
3406 6996 1.013596 TTAATTGTGCCGGAGATGCG 58.986 50.000 5.05 0.00 0.00 4.73
3441 7031 2.300152 TGAGTGTTGGCTGACTAGAAGG 59.700 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.