Multiple sequence alignment - TraesCS1D01G407800

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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 TraesCS1D01G407800 chr1D 100.000 3140 0 0 1 3140 470546394 470543255 0.000000e+00 5799.0
1 TraesCS1D01G407800 chr1D 84.177 790 113 8 990 1771 470532212 470531427 0.000000e+00 756.0
2 TraesCS1D01G407800 chr1D 78.669 1097 199 15 952 2047 470537269 470536207 0.000000e+00 697.0
3 TraesCS1D01G407800 chr1D 76.652 227 50 2 1583 1806 458872829 458873055 4.250000e-24 122.0
4 TraesCS1D01G407800 chr1D 75.714 210 30 7 1682 1888 470523705 470523514 5.580000e-13 86.1
5 TraesCS1D01G407800 chr1A 93.223 2597 115 28 564 3140 564141312 564138757 0.000000e+00 3764.0
6 TraesCS1D01G407800 chr1A 83.156 659 75 24 858 1499 564118922 564118283 1.260000e-158 569.0
7 TraesCS1D01G407800 chr1A 75.607 906 173 29 995 1893 564261562 564262426 3.770000e-109 405.0
8 TraesCS1D01G407800 chr1A 82.468 308 37 12 45 350 564141723 564141431 1.450000e-63 254.0
9 TraesCS1D01G407800 chr1B 95.441 2303 75 14 855 3140 653835178 653837467 0.000000e+00 3644.0
10 TraesCS1D01G407800 chr1B 80.814 1449 188 42 805 2236 653527637 653526262 0.000000e+00 1053.0
11 TraesCS1D01G407800 chr1B 78.268 1201 211 26 973 2142 653314036 653312855 0.000000e+00 726.0
12 TraesCS1D01G407800 chr1B 77.348 1033 199 21 995 2024 653794939 653793939 2.100000e-161 579.0
13 TraesCS1D01G407800 chr1B 85.366 328 29 14 533 858 653834349 653834659 3.910000e-84 322.0
14 TraesCS1D01G407800 chr1B 83.094 278 46 1 1874 2150 653689974 653689697 5.200000e-63 252.0
15 TraesCS1D01G407800 chr1B 84.444 270 17 12 204 471 653832315 653832561 3.130000e-60 243.0
16 TraesCS1D01G407800 chr1B 91.111 45 1 3 823 865 653834709 653834752 1.220000e-04 58.4
17 TraesCS1D01G407800 chr6A 87.705 122 15 0 1586 1707 17946781 17946660 3.260000e-30 143.0
18 TraesCS1D01G407800 chr7A 77.612 134 29 1 1571 1703 712466982 712466849 2.600000e-11 80.5


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 TraesCS1D01G407800 chr1D 470543255 470546394 3139 True 5799.00 5799 100.0000 1 3140 1 chr1D.!!$R2 3139
1 TraesCS1D01G407800 chr1D 470531427 470537269 5842 True 726.50 756 81.4230 952 2047 2 chr1D.!!$R3 1095
2 TraesCS1D01G407800 chr1A 564138757 564141723 2966 True 2009.00 3764 87.8455 45 3140 2 chr1A.!!$R2 3095
3 TraesCS1D01G407800 chr1A 564118283 564118922 639 True 569.00 569 83.1560 858 1499 1 chr1A.!!$R1 641
4 TraesCS1D01G407800 chr1A 564261562 564262426 864 False 405.00 405 75.6070 995 1893 1 chr1A.!!$F1 898
5 TraesCS1D01G407800 chr1B 653832315 653837467 5152 False 1066.85 3644 89.0905 204 3140 4 chr1B.!!$F1 2936
6 TraesCS1D01G407800 chr1B 653526262 653527637 1375 True 1053.00 1053 80.8140 805 2236 1 chr1B.!!$R2 1431
7 TraesCS1D01G407800 chr1B 653312855 653314036 1181 True 726.00 726 78.2680 973 2142 1 chr1B.!!$R1 1169
8 TraesCS1D01G407800 chr1B 653793939 653794939 1000 True 579.00 579 77.3480 995 2024 1 chr1B.!!$R4 1029

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
20 21 0.033228 GATGATCCAGTCGGCCAGAG 59.967 60.0 2.24 0.0 0.00 3.35 F
22 23 0.033503 TGATCCAGTCGGCCAGAGTA 60.034 55.0 2.24 0.0 0.00 2.59 F
424 439 0.250252 TCAAGCGTTGGAGATGCACA 60.250 50.0 0.00 0.0 42.96 4.57 F
665 2407 0.536724 GGAATTTTCATGGGCCGCTT 59.463 50.0 0.00 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 9153 0.105778 CTCTTTCCGCCTCCATCTCC 59.894 60.000 0.00 0.0 0.00 3.71 R
1848 9258 1.601759 AAGCAAGTGACGCAGCCAT 60.602 52.632 0.53 0.0 0.00 4.40 R
2094 9504 0.756294 TGAGCTGGTTCAGAACGGAA 59.244 50.000 7.22 0.0 32.44 4.30 R
2142 9552 2.035961 GAGGACACTGTTACAGCAGACA 59.964 50.000 12.80 0.0 39.62 3.41 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
17 18 4.380986 AGATGATCCAGTCGGCCA 57.619 55.556 2.24 0.00 0.00 5.36
18 19 2.131405 AGATGATCCAGTCGGCCAG 58.869 57.895 2.24 0.00 0.00 4.85
19 20 0.397675 AGATGATCCAGTCGGCCAGA 60.398 55.000 2.24 0.00 0.00 3.86
20 21 0.033228 GATGATCCAGTCGGCCAGAG 59.967 60.000 2.24 0.00 0.00 3.35
21 22 0.689080 ATGATCCAGTCGGCCAGAGT 60.689 55.000 2.24 0.76 0.00 3.24
22 23 0.033503 TGATCCAGTCGGCCAGAGTA 60.034 55.000 2.24 0.00 0.00 2.59
23 24 0.671251 GATCCAGTCGGCCAGAGTAG 59.329 60.000 2.24 0.00 0.00 2.57
24 25 0.757188 ATCCAGTCGGCCAGAGTAGG 60.757 60.000 2.24 8.62 0.00 3.18
25 26 1.682684 CCAGTCGGCCAGAGTAGGT 60.683 63.158 2.24 0.00 0.00 3.08
26 27 1.513158 CAGTCGGCCAGAGTAGGTG 59.487 63.158 2.24 0.00 0.00 4.00
27 28 2.184579 GTCGGCCAGAGTAGGTGC 59.815 66.667 2.24 0.00 0.00 5.01
28 29 2.037367 TCGGCCAGAGTAGGTGCT 59.963 61.111 2.24 0.00 0.00 4.40
29 30 2.052690 TCGGCCAGAGTAGGTGCTC 61.053 63.158 2.24 0.00 35.82 4.26
30 31 2.496817 GGCCAGAGTAGGTGCTCG 59.503 66.667 0.00 0.00 40.26 5.03
31 32 2.202810 GCCAGAGTAGGTGCTCGC 60.203 66.667 0.00 0.00 40.26 5.03
32 33 2.496817 CCAGAGTAGGTGCTCGCC 59.503 66.667 0.00 0.00 40.26 5.54
33 34 2.055042 CCAGAGTAGGTGCTCGCCT 61.055 63.158 7.21 7.21 40.26 5.52
34 35 1.435515 CAGAGTAGGTGCTCGCCTC 59.564 63.158 5.10 0.00 40.26 4.70
35 36 1.755008 AGAGTAGGTGCTCGCCTCC 60.755 63.158 5.10 0.00 40.26 4.30
36 37 2.760385 AGTAGGTGCTCGCCTCCC 60.760 66.667 5.10 0.00 39.94 4.30
37 38 2.760385 GTAGGTGCTCGCCTCCCT 60.760 66.667 5.10 0.00 39.94 4.20
38 39 2.038975 TAGGTGCTCGCCTCCCTT 59.961 61.111 5.10 0.00 39.94 3.95
39 40 1.612442 TAGGTGCTCGCCTCCCTTT 60.612 57.895 5.10 0.00 39.94 3.11
40 41 1.899437 TAGGTGCTCGCCTCCCTTTG 61.899 60.000 5.10 0.00 39.94 2.77
41 42 2.347490 GTGCTCGCCTCCCTTTGA 59.653 61.111 0.00 0.00 0.00 2.69
42 43 1.743252 GTGCTCGCCTCCCTTTGAG 60.743 63.158 0.00 0.00 41.07 3.02
50 51 2.564471 CTCCCTTTGAGGCAGCTTG 58.436 57.895 0.00 0.00 37.45 4.01
51 52 1.593296 CTCCCTTTGAGGCAGCTTGC 61.593 60.000 0.00 0.00 44.08 4.01
100 101 9.696917 AAGCCAATCTTATTTTTAGTTGACTTG 57.303 29.630 0.00 0.00 32.10 3.16
101 102 9.077885 AGCCAATCTTATTTTTAGTTGACTTGA 57.922 29.630 0.00 0.00 0.00 3.02
102 103 9.691362 GCCAATCTTATTTTTAGTTGACTTGAA 57.309 29.630 0.00 0.00 0.00 2.69
121 122 5.530519 TGAATGTAAGCAGTCTTTTAGCG 57.469 39.130 0.00 0.00 40.08 4.26
126 127 0.396811 AGCAGTCTTTTAGCGGTGGT 59.603 50.000 0.00 0.00 0.00 4.16
132 133 2.812011 GTCTTTTAGCGGTGGTTGTCAT 59.188 45.455 0.00 0.00 0.00 3.06
144 145 5.588648 CGGTGGTTGTCATATAGGTGATTTT 59.411 40.000 0.00 0.00 0.00 1.82
172 173 9.455847 ACTAAAAACTATAACTATTAGACGCGG 57.544 33.333 12.47 0.00 0.00 6.46
214 215 1.825090 ATGAAGCAAGCGAACCATCA 58.175 45.000 0.00 0.00 0.00 3.07
250 251 3.198068 CATGTTCCGGGTTAGAGTGATG 58.802 50.000 0.00 0.00 0.00 3.07
260 261 6.821665 CCGGGTTAGAGTGATGAAAAGAATTA 59.178 38.462 0.00 0.00 0.00 1.40
274 275 7.217200 TGAAAAGAATTAGGGATGGTCTATCG 58.783 38.462 0.00 0.00 36.62 2.92
275 276 6.996180 AAAGAATTAGGGATGGTCTATCGA 57.004 37.500 0.00 0.00 36.62 3.59
276 277 5.986501 AGAATTAGGGATGGTCTATCGAC 57.013 43.478 0.00 0.00 36.62 4.20
277 278 5.646215 AGAATTAGGGATGGTCTATCGACT 58.354 41.667 0.00 0.00 40.10 4.18
278 279 6.791371 AGAATTAGGGATGGTCTATCGACTA 58.209 40.000 0.00 0.00 40.10 2.59
279 280 6.887545 AGAATTAGGGATGGTCTATCGACTAG 59.112 42.308 0.00 0.00 40.10 2.57
280 281 5.579753 TTAGGGATGGTCTATCGACTAGT 57.420 43.478 0.00 0.00 40.10 2.57
281 282 6.692849 TTAGGGATGGTCTATCGACTAGTA 57.307 41.667 0.00 0.00 40.10 1.82
282 283 5.782677 AGGGATGGTCTATCGACTAGTAT 57.217 43.478 0.00 0.00 40.10 2.12
283 284 6.142259 AGGGATGGTCTATCGACTAGTATT 57.858 41.667 0.00 0.00 40.10 1.89
284 285 6.553857 AGGGATGGTCTATCGACTAGTATTT 58.446 40.000 0.00 0.00 40.10 1.40
292 306 8.524487 GGTCTATCGACTAGTATTTGGATTGAT 58.476 37.037 0.00 0.00 40.10 2.57
326 341 6.936279 TCGAGAGATTTTAGTTTGAGACCAT 58.064 36.000 0.00 0.00 33.31 3.55
328 343 7.878127 TCGAGAGATTTTAGTTTGAGACCATTT 59.122 33.333 0.00 0.00 33.31 2.32
331 346 9.136323 AGAGATTTTAGTTTGAGACCATTTTGT 57.864 29.630 0.00 0.00 0.00 2.83
340 355 5.273674 TGAGACCATTTTGTGCAAAATCA 57.726 34.783 17.04 11.45 43.38 2.57
384 399 9.860898 AGTCTGTGATTTAATTTAATTTGCTCC 57.139 29.630 0.00 0.00 0.00 4.70
411 426 2.079158 AGGACATGTGATGTTCAAGCG 58.921 47.619 1.15 0.00 45.03 4.68
422 437 0.874390 GTTCAAGCGTTGGAGATGCA 59.126 50.000 0.00 0.00 42.96 3.96
423 438 0.874390 TTCAAGCGTTGGAGATGCAC 59.126 50.000 0.00 0.00 42.96 4.57
424 439 0.250252 TCAAGCGTTGGAGATGCACA 60.250 50.000 0.00 0.00 42.96 4.57
425 440 0.806868 CAAGCGTTGGAGATGCACAT 59.193 50.000 0.00 0.00 42.96 3.21
426 441 0.806868 AAGCGTTGGAGATGCACATG 59.193 50.000 0.00 0.00 42.96 3.21
427 442 1.028330 AGCGTTGGAGATGCACATGG 61.028 55.000 0.00 0.00 42.96 3.66
428 443 1.308069 GCGTTGGAGATGCACATGGT 61.308 55.000 0.00 0.00 40.14 3.55
429 444 2.011548 GCGTTGGAGATGCACATGGTA 61.012 52.381 0.00 0.00 40.14 3.25
430 445 1.665679 CGTTGGAGATGCACATGGTAC 59.334 52.381 0.00 0.00 0.00 3.34
434 449 3.317406 TGGAGATGCACATGGTACCTAT 58.683 45.455 14.36 2.13 0.00 2.57
471 486 4.969196 CGGCCGATGCGCACCTAT 62.969 66.667 24.07 0.00 38.85 2.57
472 487 2.591715 GGCCGATGCGCACCTATT 60.592 61.111 14.90 0.00 38.85 1.73
475 490 1.156736 GCCGATGCGCACCTATTTAT 58.843 50.000 14.90 0.00 0.00 1.40
482 531 1.148310 CGCACCTATTTATCAGCCGG 58.852 55.000 0.00 0.00 0.00 6.13
543 2284 5.187967 AGGTGAGAAGAATTTATCAGTCGGT 59.812 40.000 0.00 0.00 35.37 4.69
566 2307 3.687212 TGAGTGTGAGCGTTCTTCAAAAA 59.313 39.130 0.00 0.00 0.00 1.94
619 2360 1.329913 CCCTAACAATTGGGCCAGCC 61.330 60.000 6.23 0.00 36.61 4.85
620 2361 0.614415 CCTAACAATTGGGCCAGCCA 60.614 55.000 6.23 0.00 37.98 4.75
621 2362 0.819582 CTAACAATTGGGCCAGCCAG 59.180 55.000 6.23 0.70 37.98 4.85
622 2363 1.257055 TAACAATTGGGCCAGCCAGC 61.257 55.000 6.23 0.00 37.98 4.85
623 2364 4.137872 CAATTGGGCCAGCCAGCG 62.138 66.667 6.23 0.00 37.98 5.18
665 2407 0.536724 GGAATTTTCATGGGCCGCTT 59.463 50.000 0.00 0.00 0.00 4.68
667 2409 0.536724 AATTTTCATGGGCCGCTTCC 59.463 50.000 0.00 0.00 0.00 3.46
691 2439 3.949113 CCGTTTCTAACCTAGCTCTCTCT 59.051 47.826 0.00 0.00 0.00 3.10
692 2440 4.035909 CCGTTTCTAACCTAGCTCTCTCTC 59.964 50.000 0.00 0.00 0.00 3.20
698 2446 1.287739 ACCTAGCTCTCTCTCCTGCTT 59.712 52.381 0.00 0.00 37.02 3.91
703 2451 2.008045 GCTCTCTCTCCTGCTTTGCTG 61.008 57.143 0.00 0.00 0.00 4.41
708 2456 2.282674 TCCTGCTTTGCTGGCCAG 60.283 61.111 29.34 29.34 45.32 4.85
709 2457 2.599578 CCTGCTTTGCTGGCCAGT 60.600 61.111 32.81 0.00 40.48 4.00
710 2458 2.633509 CCTGCTTTGCTGGCCAGTC 61.634 63.158 32.81 24.35 40.48 3.51
711 2459 2.974489 CTGCTTTGCTGGCCAGTCG 61.974 63.158 32.81 19.03 0.00 4.18
712 2460 4.410743 GCTTTGCTGGCCAGTCGC 62.411 66.667 32.81 24.02 0.00 5.19
757 2505 2.897350 GCCAAATCCCTCGCCTCG 60.897 66.667 0.00 0.00 0.00 4.63
758 2506 2.897350 CCAAATCCCTCGCCTCGC 60.897 66.667 0.00 0.00 0.00 5.03
802 2575 3.691342 CGCCGACCACTTCCCAGA 61.691 66.667 0.00 0.00 0.00 3.86
856 2687 4.436998 GCCGTCGACCACTCCCTG 62.437 72.222 10.58 0.00 0.00 4.45
1306 8652 1.973281 CAGGATGTTGCACGGCCTT 60.973 57.895 0.00 0.00 0.00 4.35
1359 8705 3.603532 TGAGGTTAGCAAGCAAGATCAG 58.396 45.455 0.00 0.00 0.00 2.90
1452 8808 2.998493 AGGCGAGGACCTTGAGAAT 58.002 52.632 13.45 0.00 36.28 2.40
1791 9153 2.654749 TCTACACTGACTTGATGCCG 57.345 50.000 0.00 0.00 0.00 5.69
1848 9258 1.267121 GTGGAGCTGAGGAGGTTACA 58.733 55.000 0.00 0.00 0.00 2.41
1924 9334 1.728971 CGATGTGTGAAGAGAGGTTGC 59.271 52.381 0.00 0.00 0.00 4.17
1965 9375 3.499737 GTGTCGGCCATCCTTGCG 61.500 66.667 2.24 0.00 0.00 4.85
2142 9552 5.598416 AGCTTGCTTCCAAAGTTTAGTTT 57.402 34.783 0.00 0.00 0.00 2.66
2170 9580 1.628846 GTAACAGTGTCCTCATGGGGT 59.371 52.381 12.53 0.00 35.33 4.95
2179 9589 2.509964 GTCCTCATGGGGTTTCTGGTAT 59.490 50.000 12.53 0.00 35.33 2.73
2316 9726 3.368248 ACATACTCCGTACCTTGGCTTA 58.632 45.455 0.00 0.00 0.00 3.09
2327 9737 2.310052 ACCTTGGCTTAAGCAATCTCCT 59.690 45.455 27.83 1.97 44.36 3.69
2353 9763 2.888834 TCGATCATGCGATCCTGAAA 57.111 45.000 0.00 0.00 44.55 2.69
2377 9787 3.362040 CCAGGCCTGGTGAAAATGA 57.638 52.632 39.52 0.00 45.53 2.57
2394 9804 4.695217 AATGAAACAGTGTGAACGTGTT 57.305 36.364 0.00 0.00 35.93 3.32
2666 10076 1.765314 GGAGGTAGATGAGCACCATGT 59.235 52.381 0.00 0.00 36.40 3.21
2673 10083 2.508716 AGATGAGCACCATGTTGGAGAT 59.491 45.455 0.00 0.00 40.96 2.75
2727 10137 4.787280 CCTGCGGGTCCTCTCCCT 62.787 72.222 2.29 0.00 44.95 4.20
2758 10168 1.664321 GGTCGATGTAGACGGTGGCT 61.664 60.000 0.00 0.00 41.81 4.75
2779 10189 1.983119 CTCCCACCACACACACCACT 61.983 60.000 0.00 0.00 0.00 4.00
2966 10376 4.483476 AGTTGCATTTTACACGACCTTC 57.517 40.909 0.00 0.00 0.00 3.46
3102 10512 5.540719 ACATCCTCCTAGTCCTAGCAATTAC 59.459 44.000 0.00 0.00 31.95 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.397675 TCTGGCCGACTGGATCATCT 60.398 55.000 0.00 0.00 37.49 2.90
1 2 0.033228 CTCTGGCCGACTGGATCATC 59.967 60.000 0.00 0.00 37.49 2.92
2 3 0.689080 ACTCTGGCCGACTGGATCAT 60.689 55.000 0.00 0.00 37.49 2.45
3 4 0.033503 TACTCTGGCCGACTGGATCA 60.034 55.000 0.00 0.00 37.49 2.92
4 5 0.671251 CTACTCTGGCCGACTGGATC 59.329 60.000 0.00 0.00 37.49 3.36
5 6 0.757188 CCTACTCTGGCCGACTGGAT 60.757 60.000 0.00 0.00 37.49 3.41
6 7 1.379977 CCTACTCTGGCCGACTGGA 60.380 63.158 0.00 0.00 37.49 3.86
8 9 1.513158 CACCTACTCTGGCCGACTG 59.487 63.158 0.00 0.00 0.00 3.51
9 10 2.352032 GCACCTACTCTGGCCGACT 61.352 63.158 0.00 0.00 0.00 4.18
10 11 2.184579 GCACCTACTCTGGCCGAC 59.815 66.667 0.00 0.00 0.00 4.79
11 12 2.037367 AGCACCTACTCTGGCCGA 59.963 61.111 0.00 0.00 0.00 5.54
12 13 2.496817 GAGCACCTACTCTGGCCG 59.503 66.667 0.00 0.00 33.69 6.13
13 14 2.496817 CGAGCACCTACTCTGGCC 59.503 66.667 0.00 0.00 34.35 5.36
14 15 2.202810 GCGAGCACCTACTCTGGC 60.203 66.667 0.00 0.00 34.35 4.85
15 16 2.010582 GAGGCGAGCACCTACTCTGG 62.011 65.000 0.00 0.00 41.32 3.86
16 17 1.435515 GAGGCGAGCACCTACTCTG 59.564 63.158 0.00 0.00 41.32 3.35
17 18 1.755008 GGAGGCGAGCACCTACTCT 60.755 63.158 0.00 0.00 41.32 3.24
18 19 2.787567 GGGAGGCGAGCACCTACTC 61.788 68.421 3.01 0.00 40.93 2.59
19 20 2.760385 GGGAGGCGAGCACCTACT 60.760 66.667 3.01 0.00 40.93 2.57
20 21 1.900545 AAAGGGAGGCGAGCACCTAC 61.901 60.000 5.82 0.00 41.32 3.18
21 22 1.612442 AAAGGGAGGCGAGCACCTA 60.612 57.895 5.82 0.00 41.32 3.08
22 23 2.930562 AAAGGGAGGCGAGCACCT 60.931 61.111 9.51 5.28 45.04 4.00
23 24 2.747855 CAAAGGGAGGCGAGCACC 60.748 66.667 0.00 0.00 0.00 5.01
24 25 1.743252 CTCAAAGGGAGGCGAGCAC 60.743 63.158 0.00 0.00 40.13 4.40
25 26 2.665000 CTCAAAGGGAGGCGAGCA 59.335 61.111 0.00 0.00 40.13 4.26
33 34 1.604593 GCAAGCTGCCTCAAAGGGA 60.605 57.895 0.00 0.00 37.42 4.20
34 35 1.466025 TTGCAAGCTGCCTCAAAGGG 61.466 55.000 0.00 0.00 44.23 3.95
35 36 0.390124 TTTGCAAGCTGCCTCAAAGG 59.610 50.000 0.00 0.00 44.23 3.11
36 37 2.132762 CTTTTGCAAGCTGCCTCAAAG 58.867 47.619 0.00 0.00 44.23 2.77
37 38 2.228138 CTTTTGCAAGCTGCCTCAAA 57.772 45.000 0.00 1.78 44.23 2.69
38 39 3.972107 CTTTTGCAAGCTGCCTCAA 57.028 47.368 0.00 0.00 44.23 3.02
74 75 9.696917 CAAGTCAACTAAAAATAAGATTGGCTT 57.303 29.630 0.00 0.00 41.36 4.35
85 86 9.683069 CTGCTTACATTCAAGTCAACTAAAAAT 57.317 29.630 0.00 0.00 0.00 1.82
87 88 8.220755 ACTGCTTACATTCAAGTCAACTAAAA 57.779 30.769 0.00 0.00 0.00 1.52
88 89 7.715249 AGACTGCTTACATTCAAGTCAACTAAA 59.285 33.333 4.16 0.00 0.00 1.85
89 90 7.217200 AGACTGCTTACATTCAAGTCAACTAA 58.783 34.615 4.16 0.00 0.00 2.24
90 91 6.759272 AGACTGCTTACATTCAAGTCAACTA 58.241 36.000 4.16 0.00 0.00 2.24
91 92 5.615289 AGACTGCTTACATTCAAGTCAACT 58.385 37.500 4.16 0.00 0.00 3.16
92 93 5.931441 AGACTGCTTACATTCAAGTCAAC 57.069 39.130 4.16 0.00 0.00 3.18
93 94 6.942532 AAAGACTGCTTACATTCAAGTCAA 57.057 33.333 4.16 0.00 32.98 3.18
94 95 6.942532 AAAAGACTGCTTACATTCAAGTCA 57.057 33.333 4.16 0.00 32.98 3.41
95 96 7.018235 GCTAAAAGACTGCTTACATTCAAGTC 58.982 38.462 0.00 0.00 32.98 3.01
97 98 6.017933 CGCTAAAAGACTGCTTACATTCAAG 58.982 40.000 0.00 0.00 32.98 3.02
98 99 5.106712 CCGCTAAAAGACTGCTTACATTCAA 60.107 40.000 0.00 0.00 32.98 2.69
99 100 4.391830 CCGCTAAAAGACTGCTTACATTCA 59.608 41.667 0.00 0.00 32.98 2.57
100 101 4.392138 ACCGCTAAAAGACTGCTTACATTC 59.608 41.667 0.00 0.00 32.98 2.67
101 102 4.154195 CACCGCTAAAAGACTGCTTACATT 59.846 41.667 0.00 0.00 32.98 2.71
102 103 3.684788 CACCGCTAAAAGACTGCTTACAT 59.315 43.478 0.00 0.00 32.98 2.29
103 104 3.064207 CACCGCTAAAAGACTGCTTACA 58.936 45.455 0.00 0.00 32.98 2.41
104 105 2.415512 CCACCGCTAAAAGACTGCTTAC 59.584 50.000 0.00 0.00 32.98 2.34
105 106 2.038033 ACCACCGCTAAAAGACTGCTTA 59.962 45.455 0.00 0.00 32.98 3.09
108 109 1.069227 CAACCACCGCTAAAAGACTGC 60.069 52.381 0.00 0.00 0.00 4.40
109 110 2.218603 ACAACCACCGCTAAAAGACTG 58.781 47.619 0.00 0.00 0.00 3.51
121 122 6.601613 TGAAAATCACCTATATGACAACCACC 59.398 38.462 0.00 0.00 0.00 4.61
155 156 4.452114 TCGAAGCCGCGTCTAATAGTTATA 59.548 41.667 4.92 0.00 35.37 0.98
156 157 3.251729 TCGAAGCCGCGTCTAATAGTTAT 59.748 43.478 4.92 0.00 35.37 1.89
157 158 2.613595 TCGAAGCCGCGTCTAATAGTTA 59.386 45.455 4.92 0.00 35.37 2.24
158 159 1.402968 TCGAAGCCGCGTCTAATAGTT 59.597 47.619 4.92 0.00 35.37 2.24
165 166 2.627737 AAGAGTCGAAGCCGCGTCT 61.628 57.895 4.92 0.00 35.37 4.18
171 172 6.670077 AATTAGATTTCAAGAGTCGAAGCC 57.330 37.500 0.00 0.00 0.00 4.35
172 173 9.035607 TCATAATTAGATTTCAAGAGTCGAAGC 57.964 33.333 0.00 0.00 0.00 3.86
229 230 3.118775 TCATCACTCTAACCCGGAACATG 60.119 47.826 0.73 0.00 0.00 3.21
235 236 4.202245 TCTTTTCATCACTCTAACCCGG 57.798 45.455 0.00 0.00 0.00 5.73
238 239 8.047310 TCCCTAATTCTTTTCATCACTCTAACC 58.953 37.037 0.00 0.00 0.00 2.85
250 251 7.442656 TCGATAGACCATCCCTAATTCTTTTC 58.557 38.462 0.00 0.00 42.67 2.29
278 279 9.698309 CGATAGTCACTTATCAATCCAAATACT 57.302 33.333 0.00 0.00 31.70 2.12
279 280 9.692749 TCGATAGTCACTTATCAATCCAAATAC 57.307 33.333 0.00 0.00 31.70 1.89
280 281 9.914131 CTCGATAGTCACTTATCAATCCAAATA 57.086 33.333 0.00 0.00 31.70 1.40
281 282 8.642432 TCTCGATAGTCACTTATCAATCCAAAT 58.358 33.333 0.00 0.00 31.70 2.32
282 283 8.007405 TCTCGATAGTCACTTATCAATCCAAA 57.993 34.615 0.00 0.00 31.70 3.28
283 284 7.502561 TCTCTCGATAGTCACTTATCAATCCAA 59.497 37.037 0.00 0.00 31.70 3.53
284 285 6.998673 TCTCTCGATAGTCACTTATCAATCCA 59.001 38.462 0.00 0.00 31.70 3.41
326 341 4.161189 TGGGTTCTCTGATTTTGCACAAAA 59.839 37.500 10.70 10.70 43.48 2.44
328 343 3.068024 GTGGGTTCTCTGATTTTGCACAA 59.932 43.478 0.00 0.00 0.00 3.33
331 346 2.158475 AGGTGGGTTCTCTGATTTTGCA 60.158 45.455 0.00 0.00 0.00 4.08
340 355 3.108376 GACTAATCCAGGTGGGTTCTCT 58.892 50.000 0.00 0.00 39.66 3.10
381 396 1.012086 CACATGTCCTTGATGCGGAG 58.988 55.000 0.00 0.00 0.00 4.63
384 399 2.750301 CATCACATGTCCTTGATGCG 57.250 50.000 10.14 0.00 41.93 4.73
411 426 2.017049 GGTACCATGTGCATCTCCAAC 58.983 52.381 7.15 0.00 0.00 3.77
422 437 3.572642 TCGACATCCATAGGTACCATGT 58.427 45.455 15.94 14.33 0.00 3.21
423 438 4.021104 ACATCGACATCCATAGGTACCATG 60.021 45.833 15.94 14.80 0.00 3.66
424 439 4.160329 ACATCGACATCCATAGGTACCAT 58.840 43.478 15.94 2.71 0.00 3.55
425 440 3.572642 ACATCGACATCCATAGGTACCA 58.427 45.455 15.94 0.00 0.00 3.25
426 441 4.602340 AACATCGACATCCATAGGTACC 57.398 45.455 2.73 2.73 0.00 3.34
427 442 6.920817 TGATAACATCGACATCCATAGGTAC 58.079 40.000 0.00 0.00 0.00 3.34
428 443 6.719829 ACTGATAACATCGACATCCATAGGTA 59.280 38.462 0.00 0.00 0.00 3.08
429 444 5.540337 ACTGATAACATCGACATCCATAGGT 59.460 40.000 0.00 0.00 0.00 3.08
430 445 6.030548 ACTGATAACATCGACATCCATAGG 57.969 41.667 0.00 0.00 0.00 2.57
434 449 3.243401 CCGACTGATAACATCGACATCCA 60.243 47.826 0.00 0.00 38.10 3.41
513 562 9.354673 ACTGATAAATTCTTCTCACCTCAAAAA 57.645 29.630 0.00 0.00 0.00 1.94
514 563 8.924511 ACTGATAAATTCTTCTCACCTCAAAA 57.075 30.769 0.00 0.00 0.00 2.44
517 566 6.333416 CGACTGATAAATTCTTCTCACCTCA 58.667 40.000 0.00 0.00 0.00 3.86
518 567 5.751028 CCGACTGATAAATTCTTCTCACCTC 59.249 44.000 0.00 0.00 0.00 3.85
519 568 5.187967 ACCGACTGATAAATTCTTCTCACCT 59.812 40.000 0.00 0.00 0.00 4.00
520 569 5.420409 ACCGACTGATAAATTCTTCTCACC 58.580 41.667 0.00 0.00 0.00 4.02
521 570 6.590292 TCAACCGACTGATAAATTCTTCTCAC 59.410 38.462 0.00 0.00 0.00 3.51
522 571 6.697395 TCAACCGACTGATAAATTCTTCTCA 58.303 36.000 0.00 0.00 0.00 3.27
523 572 6.814146 ACTCAACCGACTGATAAATTCTTCTC 59.186 38.462 0.00 0.00 0.00 2.87
524 573 6.591834 CACTCAACCGACTGATAAATTCTTCT 59.408 38.462 0.00 0.00 0.00 2.85
525 574 6.369065 ACACTCAACCGACTGATAAATTCTTC 59.631 38.462 0.00 0.00 0.00 2.87
526 575 6.147821 CACACTCAACCGACTGATAAATTCTT 59.852 38.462 0.00 0.00 0.00 2.52
528 577 5.637810 TCACACTCAACCGACTGATAAATTC 59.362 40.000 0.00 0.00 0.00 2.17
529 578 5.547465 TCACACTCAACCGACTGATAAATT 58.453 37.500 0.00 0.00 0.00 1.82
530 579 5.147330 TCACACTCAACCGACTGATAAAT 57.853 39.130 0.00 0.00 0.00 1.40
531 580 4.556233 CTCACACTCAACCGACTGATAAA 58.444 43.478 0.00 0.00 0.00 1.40
543 2284 2.595124 TGAAGAACGCTCACACTCAA 57.405 45.000 0.00 0.00 0.00 3.02
619 2360 2.335712 GGCTGAAAAGGTCCCGCTG 61.336 63.158 0.00 0.00 0.00 5.18
620 2361 2.034221 GGCTGAAAAGGTCCCGCT 59.966 61.111 0.00 0.00 0.00 5.52
621 2362 3.062466 GGGCTGAAAAGGTCCCGC 61.062 66.667 0.00 0.00 0.00 6.13
622 2363 1.971695 GTGGGCTGAAAAGGTCCCG 60.972 63.158 0.00 0.00 41.65 5.14
623 2364 1.606601 GGTGGGCTGAAAAGGTCCC 60.607 63.158 0.00 0.00 39.22 4.46
628 2369 4.404654 GCGCGGTGGGCTGAAAAG 62.405 66.667 8.83 0.00 40.44 2.27
646 2388 0.536724 AAGCGGCCCATGAAAATTCC 59.463 50.000 0.00 0.00 0.00 3.01
665 2407 1.197812 GCTAGGTTAGAAACGGGGGA 58.802 55.000 0.00 0.00 0.00 4.81
667 2409 2.101082 GAGAGCTAGGTTAGAAACGGGG 59.899 54.545 0.00 0.00 0.00 5.73
670 2412 4.035909 GGAGAGAGAGCTAGGTTAGAAACG 59.964 50.000 0.00 0.00 0.00 3.60
691 2439 2.282674 CTGGCCAGCAAAGCAGGA 60.283 61.111 22.33 0.00 37.40 3.86
692 2440 2.599578 ACTGGCCAGCAAAGCAGG 60.600 61.111 33.06 7.01 38.28 4.85
708 2456 3.554692 CGGTGCGAGAATGGCGAC 61.555 66.667 0.00 0.00 45.68 5.19
1073 8407 1.953017 CTGGAGCCGGAGTAGATCG 59.047 63.158 5.05 0.00 0.00 3.69
1112 8449 2.501723 ACCACAAGCAGGTGATAGTAGG 59.498 50.000 9.11 0.00 41.32 3.18
1306 8652 2.957402 AACTGGAGATGCACCTTCAA 57.043 45.000 0.00 0.00 0.00 2.69
1359 8705 0.740149 TGATTGCACGGATGAATGCC 59.260 50.000 0.00 0.00 41.33 4.40
1452 8808 2.609427 CATCCTTGAGATGCTCCGAA 57.391 50.000 0.00 0.00 45.76 4.30
1791 9153 0.105778 CTCTTTCCGCCTCCATCTCC 59.894 60.000 0.00 0.00 0.00 3.71
1848 9258 1.601759 AAGCAAGTGACGCAGCCAT 60.602 52.632 0.53 0.00 0.00 4.40
1924 9334 3.806380 AGCTCAAATCTATGTGCTCCAG 58.194 45.455 0.00 0.00 44.37 3.86
2094 9504 0.756294 TGAGCTGGTTCAGAACGGAA 59.244 50.000 7.22 0.00 32.44 4.30
2142 9552 2.035961 GAGGACACTGTTACAGCAGACA 59.964 50.000 12.80 0.00 39.62 3.41
2170 9580 6.499106 TGATCCTCTTATGCATACCAGAAA 57.501 37.500 5.74 0.00 0.00 2.52
2179 9589 6.016860 GCACATATGTTTGATCCTCTTATGCA 60.017 38.462 5.37 0.00 0.00 3.96
2316 9726 3.942829 TCGATCAACAAGGAGATTGCTT 58.057 40.909 0.00 0.00 43.15 3.91
2377 9787 3.500680 ACAGAAACACGTTCACACTGTTT 59.499 39.130 0.00 2.87 38.86 2.83
2394 9804 7.392953 CAGGATCACATAGCTAGATAGACAGAA 59.607 40.741 0.00 0.00 0.00 3.02
2666 10076 2.191400 CCTCACCTCCAAGATCTCCAA 58.809 52.381 0.00 0.00 0.00 3.53
2673 10083 2.366469 GTGCTCCTCACCTCCAAGA 58.634 57.895 0.00 0.00 39.79 3.02
2727 10137 2.176045 ACATCGACCTCCACACATACA 58.824 47.619 0.00 0.00 0.00 2.29
2758 10168 0.691413 TGGTGTGTGTGGTGGGAGTA 60.691 55.000 0.00 0.00 0.00 2.59
2779 10189 1.907739 GCACTGGCTGATGGGAGTA 59.092 57.895 0.00 0.00 36.96 2.59
3102 10512 5.940470 AGTCCCAAAACTAACAAGCTAGATG 59.060 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.