Multiple sequence alignment - TraesCS4D01G306000

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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 TraesCS4D01G306000 chr4D 100.000 4181 0 0 1 4181 474436532 474440712 0.000000e+00 7721.0
1 TraesCS4D01G306000 chr4D 100.000 1678 0 0 4422 6099 474440953 474442630 0.000000e+00 3099.0
2 TraesCS4D01G306000 chr4D 100.000 73 0 0 6480 6552 474443011 474443083 1.150000e-27 135.0
3 TraesCS4D01G306000 chr4A 94.728 2902 92 17 860 3742 681715955 681713096 0.000000e+00 4455.0
4 TraesCS4D01G306000 chr4A 91.484 1644 97 19 4458 6070 681712478 681710847 0.000000e+00 2220.0
5 TraesCS4D01G306000 chr4A 89.803 608 40 18 1 606 681717063 681716476 0.000000e+00 760.0
6 TraesCS4D01G306000 chr4A 99.091 220 1 1 3962 4181 681712704 681712486 1.710000e-105 394.0
7 TraesCS4D01G306000 chr4A 93.578 218 6 2 3724 3934 681712917 681712701 1.060000e-82 318.0
8 TraesCS4D01G306000 chr4B 92.417 2611 104 30 1 2560 597974323 597976890 0.000000e+00 3639.0
9 TraesCS4D01G306000 chr4B 98.157 1628 20 6 2559 4181 597977149 597978771 0.000000e+00 2832.0
10 TraesCS4D01G306000 chr4B 95.774 1680 49 11 4434 6099 597979044 597980715 0.000000e+00 2689.0
11 TraesCS4D01G306000 chr4B 93.151 73 4 1 6480 6552 597987469 597987398 8.990000e-19 106.0
12 TraesCS4D01G306000 chr1A 97.959 49 1 0 411 459 251334848 251334800 1.170000e-12 86.1
13 TraesCS4D01G306000 chr6A 100.000 28 0 0 1997 2024 127604191 127604218 1.200000e-02 52.8


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 TraesCS4D01G306000 chr4D 474436532 474443083 6551 False 3651.666667 7721 100.000000 1 6552 3 chr4D.!!$F1 6551
1 TraesCS4D01G306000 chr4A 681710847 681717063 6216 True 1629.400000 4455 93.736800 1 6070 5 chr4A.!!$R1 6069
2 TraesCS4D01G306000 chr4B 597974323 597980715 6392 False 3053.333333 3639 95.449333 1 6099 3 chr4B.!!$F1 6098

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
338 353 0.029300 CTCGCACACAACCAAACAGG 59.971 55.000 0.00 0.0 45.67 4.00 F
1236 1592 0.310543 TTGTTCATGTCCGTGCTTGC 59.689 50.000 0.00 0.0 0.00 4.01 F
1494 1866 0.390340 GCGGAGACAATGCTCACTCA 60.390 55.000 6.92 0.0 36.62 3.41 F
2257 2629 0.530650 CGCGCCTCAGTTCCATGTAT 60.531 55.000 0.00 0.0 0.00 2.29 F
2756 3394 0.959553 TCTCGACTGTGTTCCCACTC 59.040 55.000 0.00 0.0 42.34 3.51 F
2757 3395 0.962489 CTCGACTGTGTTCCCACTCT 59.038 55.000 0.00 0.0 42.34 3.24 F
3934 4781 2.787866 CTCTCCCCTCCCCCTGAA 59.212 66.667 0.00 0.0 0.00 3.02 F
5214 6091 0.600057 CAACTCTCTTTTGCAGGGCC 59.400 55.000 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1704 1.415659 CAAATTGTTCAAGGGGGCACA 59.584 47.619 0.00 0.0 0.00 4.57 R
2434 2812 3.131478 GCATCCGGAAACCGTGGG 61.131 66.667 9.01 0.0 46.80 4.61 R
3093 3735 4.202233 TGAAGCAAATGAATCAGTTGGCAA 60.202 37.500 22.30 0.0 39.40 4.52 R
3934 4781 2.159179 AGTGGGGCTTGTTTCAGTTT 57.841 45.000 0.00 0.0 0.00 2.66 R
4640 5511 4.102996 TCATGCAGGTAAGATGGCAGATAA 59.897 41.667 0.00 0.0 39.95 1.75 R
4690 5561 5.048504 ACTGCACATGTAAATTTCTCCACAG 60.049 40.000 0.00 0.0 0.00 3.66 R
5225 6102 0.835276 CATCTCTGTGGGCATCTCCA 59.165 55.000 0.00 0.0 36.21 3.86 R
6487 7384 3.456644 TCCAAGTGTTTCTTCCCTACACA 59.543 43.478 0.00 0.0 43.46 3.72 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
131 146 4.030452 GCAGCACCCAAGCACGTC 62.030 66.667 0.00 0.00 36.85 4.34
133 148 2.186160 CAGCACCCAAGCACGTCAA 61.186 57.895 0.00 0.00 36.85 3.18
161 176 4.736126 AGGACAGAAACAAAAACCCTTG 57.264 40.909 0.00 0.00 0.00 3.61
164 179 4.441792 GACAGAAACAAAAACCCTTGCAT 58.558 39.130 0.00 0.00 0.00 3.96
223 238 3.931190 GAAACCATTCCCGGCCGGT 62.931 63.158 40.52 22.26 0.00 5.28
227 242 2.124320 CATTCCCGGCCGGTGATT 60.124 61.111 40.52 27.87 0.00 2.57
264 279 4.007644 CTGCTCACCTGTCGGGCA 62.008 66.667 0.00 0.00 39.10 5.36
319 334 1.846648 CGTGTCAGCGAACTGTGAC 59.153 57.895 0.00 0.00 44.77 3.67
338 353 0.029300 CTCGCACACAACCAAACAGG 59.971 55.000 0.00 0.00 45.67 4.00
346 361 1.152631 AACCAAACAGGAACCCCCG 60.153 57.895 0.00 0.00 41.22 5.73
349 364 3.503839 AAACAGGAACCCCCGGCA 61.504 61.111 0.00 0.00 40.87 5.69
379 399 4.144727 GGAGCGGAGAGGGAGGGA 62.145 72.222 0.00 0.00 0.00 4.20
474 502 3.752167 GACGGAGGGAGGGAGGGA 61.752 72.222 0.00 0.00 0.00 4.20
475 503 3.742248 GACGGAGGGAGGGAGGGAG 62.742 73.684 0.00 0.00 0.00 4.30
476 504 4.548513 CGGAGGGAGGGAGGGAGG 62.549 77.778 0.00 0.00 0.00 4.30
477 505 4.890306 GGAGGGAGGGAGGGAGGC 62.890 77.778 0.00 0.00 0.00 4.70
482 510 3.151022 GAGGGAGGGAGGCGACTG 61.151 72.222 0.00 0.00 44.43 3.51
483 511 3.966930 GAGGGAGGGAGGCGACTGT 62.967 68.421 0.00 0.00 44.43 3.55
492 520 1.646189 GAGGCGACTGTTTGGATCTC 58.354 55.000 0.00 0.00 44.43 2.75
494 522 1.710339 GCGACTGTTTGGATCTCGC 59.290 57.895 7.38 7.38 42.51 5.03
498 526 2.435938 TGTTTGGATCTCGCGGGC 60.436 61.111 6.13 0.00 0.00 6.13
511 539 4.504916 CGGGCGGTCTCTCTGCTG 62.505 72.222 0.00 0.00 46.74 4.41
512 540 4.154347 GGGCGGTCTCTCTGCTGG 62.154 72.222 0.00 0.00 46.74 4.85
514 542 3.071206 GCGGTCTCTCTGCTGGGA 61.071 66.667 0.00 0.00 44.39 4.37
518 546 2.063378 GTCTCTCTGCTGGGAGGGG 61.063 68.421 19.29 0.00 34.76 4.79
520 548 3.615811 TCTCTGCTGGGAGGGGGT 61.616 66.667 0.00 0.00 34.39 4.95
521 549 3.406200 CTCTGCTGGGAGGGGGTG 61.406 72.222 0.00 0.00 0.00 4.61
525 553 4.741239 GCTGGGAGGGGGTGAGGA 62.741 72.222 0.00 0.00 0.00 3.71
694 724 1.407851 CGGAGGGGTTTAGGGTTTAGC 60.408 57.143 0.00 0.00 0.00 3.09
784 814 2.363018 GGGCTTTGGGAGGAAGGC 60.363 66.667 2.22 2.22 45.77 4.35
786 816 2.363018 GCTTTGGGAGGAAGGCCC 60.363 66.667 0.00 0.00 46.22 5.80
846 876 0.710588 GGGGAGTGAGGGGGAAAAAT 59.289 55.000 0.00 0.00 0.00 1.82
1020 1368 0.473117 TGGGGTTCCTCGAGGACTTT 60.473 55.000 33.75 0.00 45.39 2.66
1086 1439 1.669999 TAACCTAACCCTCGCCGCTC 61.670 60.000 0.00 0.00 0.00 5.03
1206 1559 3.998672 TCCAACGCCTCCACGGTC 61.999 66.667 0.00 0.00 37.37 4.79
1226 1582 4.177026 GTCTCTAGATGCGTTGTTCATGT 58.823 43.478 0.00 0.00 0.00 3.21
1236 1592 0.310543 TTGTTCATGTCCGTGCTTGC 59.689 50.000 0.00 0.00 0.00 4.01
1249 1605 4.389576 CTTGCGGCGTGCCAACTC 62.390 66.667 12.06 0.00 45.60 3.01
1268 1624 6.430451 CAACTCAACCTGTTCATGACTAAAC 58.570 40.000 0.00 0.00 0.00 2.01
1278 1634 4.835284 TCATGACTAAACCTATGTGCCA 57.165 40.909 0.00 0.00 0.00 4.92
1346 1704 4.846779 ATAAATGGATAATTTGGCGCGT 57.153 36.364 8.43 0.00 38.93 6.01
1494 1866 0.390340 GCGGAGACAATGCTCACTCA 60.390 55.000 6.92 0.00 36.62 3.41
1668 2040 4.841813 TCATGAGTGACCCTACCTTTTGTA 59.158 41.667 0.00 0.00 0.00 2.41
1990 2362 7.549256 CATGCATACATATGGAACATGCTTGC 61.549 42.308 22.92 14.42 41.94 4.01
2257 2629 0.530650 CGCGCCTCAGTTCCATGTAT 60.531 55.000 0.00 0.00 0.00 2.29
2434 2812 8.454106 GTGATGTATCATTACCCATGAATTAGC 58.546 37.037 0.00 0.00 45.45 3.09
2594 3232 5.049886 GGAGGTGAAACGAACGATTAGTTTT 60.050 40.000 0.14 0.00 44.35 2.43
2595 3233 5.744490 AGGTGAAACGAACGATTAGTTTTG 58.256 37.500 0.14 0.00 44.35 2.44
2756 3394 0.959553 TCTCGACTGTGTTCCCACTC 59.040 55.000 0.00 0.00 42.34 3.51
2757 3395 0.962489 CTCGACTGTGTTCCCACTCT 59.038 55.000 0.00 0.00 42.34 3.24
2831 3473 3.634397 TTGGACATGGGAGAGTGATTC 57.366 47.619 0.00 0.00 0.00 2.52
2847 3489 9.092876 GAGAGTGATTCTTTTGTAATCGAAGAT 57.907 33.333 0.00 0.00 37.59 2.40
3093 3735 7.564660 TCTGAATTCCCTATTGTATTTTGCCAT 59.435 33.333 2.27 0.00 0.00 4.40
3612 4254 8.425703 ACTCCCTCTGCTTTTCTTTAGATATAC 58.574 37.037 0.00 0.00 0.00 1.47
3934 4781 2.787866 CTCTCCCCTCCCCCTGAA 59.212 66.667 0.00 0.00 0.00 3.02
4764 5635 4.961622 GTCGCATGACATTGCTCG 57.038 55.556 0.00 0.00 44.82 5.03
4984 5855 1.609208 GAACAGAAAAGGAGGCAGCA 58.391 50.000 0.00 0.00 0.00 4.41
5065 5942 1.555533 GGTGCTGGTAGCTTAAGGTCT 59.444 52.381 11.11 0.00 42.97 3.85
5159 6036 5.808042 TTTGCATCTGAGTAGAATCAAGC 57.192 39.130 0.00 0.00 36.32 4.01
5176 6053 3.056678 TCAAGCACCAAGGCATTTGTATG 60.057 43.478 0.00 0.00 34.87 2.39
5214 6091 0.600057 CAACTCTCTTTTGCAGGGCC 59.400 55.000 0.00 0.00 0.00 5.80
5248 6125 3.411114 ATGCCCACAGAGATGCCCG 62.411 63.158 0.00 0.00 0.00 6.13
5253 6130 1.296392 CACAGAGATGCCCGTGGAA 59.704 57.895 0.00 0.00 0.00 3.53
5301 6178 3.431922 GTCGATCCTAATGAACCGACA 57.568 47.619 0.00 0.00 43.78 4.35
5402 6279 1.554160 CACATGTCCTTCCTGAGCTCT 59.446 52.381 16.19 0.00 0.00 4.09
5428 6313 0.728129 GGTTTTAAAGCGCGCTGGTC 60.728 55.000 37.24 20.30 0.00 4.02
5563 6448 2.616510 GGGCAGGTGAGATACATATGGC 60.617 54.545 7.80 0.00 39.65 4.40
5609 6494 2.552743 GGTCATCCGTGATCGTCTGATA 59.447 50.000 0.00 0.00 36.60 2.15
5612 6497 2.047002 TCCGTGATCGTCTGATACCA 57.953 50.000 0.00 0.00 34.09 3.25
5857 6746 2.411547 GCTATGTATGCGCATCGAAACC 60.412 50.000 29.11 9.13 0.00 3.27
5919 6808 3.399330 GCTACTTCCAAGCTGTGTTACA 58.601 45.455 0.00 0.00 37.01 2.41
6025 6921 8.480501 TCATATACACCTACCAAAACTTCCTAC 58.519 37.037 0.00 0.00 0.00 3.18
6039 6936 3.886505 ACTTCCTACCGATGTTTGCAAAA 59.113 39.130 14.67 5.00 0.00 2.44
6501 7398 5.382664 AAAGGACTTGTGTAGGGAAGAAA 57.617 39.130 0.00 0.00 0.00 2.52
6502 7399 4.353383 AGGACTTGTGTAGGGAAGAAAC 57.647 45.455 0.00 0.00 0.00 2.78
6503 7400 3.714798 AGGACTTGTGTAGGGAAGAAACA 59.285 43.478 0.00 0.00 0.00 2.83
6504 7401 3.813724 GGACTTGTGTAGGGAAGAAACAC 59.186 47.826 0.00 0.00 43.00 3.32
6505 7402 4.444449 GGACTTGTGTAGGGAAGAAACACT 60.444 45.833 6.41 0.00 43.09 3.55
6506 7403 5.112129 ACTTGTGTAGGGAAGAAACACTT 57.888 39.130 6.41 0.00 43.09 3.16
6507 7404 4.881850 ACTTGTGTAGGGAAGAAACACTTG 59.118 41.667 6.41 2.45 43.09 3.16
6508 7405 3.815809 TGTGTAGGGAAGAAACACTTGG 58.184 45.455 6.41 0.00 43.09 3.61
6509 7406 3.456644 TGTGTAGGGAAGAAACACTTGGA 59.543 43.478 6.41 0.00 43.09 3.53
6510 7407 4.080243 TGTGTAGGGAAGAAACACTTGGAA 60.080 41.667 6.41 0.00 43.09 3.53
6511 7408 5.070685 GTGTAGGGAAGAAACACTTGGAAT 58.929 41.667 0.00 0.00 40.25 3.01
6512 7409 5.535030 GTGTAGGGAAGAAACACTTGGAATT 59.465 40.000 0.00 0.00 40.25 2.17
6513 7410 5.768164 TGTAGGGAAGAAACACTTGGAATTC 59.232 40.000 0.00 0.00 39.13 2.17
6514 7411 4.803452 AGGGAAGAAACACTTGGAATTCA 58.197 39.130 7.93 0.00 39.13 2.57
6515 7412 5.208121 AGGGAAGAAACACTTGGAATTCAA 58.792 37.500 7.93 0.00 39.13 2.69
6516 7413 5.660864 AGGGAAGAAACACTTGGAATTCAAA 59.339 36.000 7.93 0.69 39.13 2.69
6517 7414 6.327365 AGGGAAGAAACACTTGGAATTCAAAT 59.673 34.615 7.93 0.00 39.13 2.32
6518 7415 6.992123 GGGAAGAAACACTTGGAATTCAAATT 59.008 34.615 7.93 0.00 39.13 1.82
6519 7416 7.171508 GGGAAGAAACACTTGGAATTCAAATTC 59.828 37.037 7.93 6.88 40.26 2.17
6520 7417 7.928167 GGAAGAAACACTTGGAATTCAAATTCT 59.072 33.333 7.93 5.65 40.52 2.40
6521 7418 8.877808 AAGAAACACTTGGAATTCAAATTCTC 57.122 30.769 7.93 6.32 43.33 2.87
6522 7419 7.436933 AGAAACACTTGGAATTCAAATTCTCC 58.563 34.615 7.93 1.87 43.33 3.71
6523 7420 6.729690 AACACTTGGAATTCAAATTCTCCA 57.270 33.333 7.93 4.22 43.33 3.86
6524 7421 6.729690 ACACTTGGAATTCAAATTCTCCAA 57.270 33.333 7.93 10.64 43.33 3.53
6525 7422 7.123355 ACACTTGGAATTCAAATTCTCCAAA 57.877 32.000 7.93 5.05 43.33 3.28
6526 7423 7.738847 ACACTTGGAATTCAAATTCTCCAAAT 58.261 30.769 7.93 1.09 43.33 2.32
6527 7424 8.212995 ACACTTGGAATTCAAATTCTCCAAATT 58.787 29.630 7.93 1.64 43.33 1.82
6528 7425 9.059260 CACTTGGAATTCAAATTCTCCAAATTT 57.941 29.630 7.93 0.00 43.33 1.82
6529 7426 9.276590 ACTTGGAATTCAAATTCTCCAAATTTC 57.723 29.630 7.93 0.00 43.33 2.17
6530 7427 8.620116 TTGGAATTCAAATTCTCCAAATTTCC 57.380 30.769 7.93 0.00 43.33 3.13
6531 7428 7.976712 TGGAATTCAAATTCTCCAAATTTCCT 58.023 30.769 7.93 0.00 43.33 3.36
6532 7429 8.439172 TGGAATTCAAATTCTCCAAATTTCCTT 58.561 29.630 7.93 0.00 43.33 3.36
6533 7430 9.288576 GGAATTCAAATTCTCCAAATTTCCTTT 57.711 29.630 7.93 0.00 43.33 3.11
6535 7432 9.850198 AATTCAAATTCTCCAAATTTCCTTTGA 57.150 25.926 0.00 0.00 45.96 2.69
6536 7433 9.850198 ATTCAAATTCTCCAAATTTCCTTTGAA 57.150 25.926 8.89 8.89 45.96 2.69
6537 7434 9.678260 TTCAAATTCTCCAAATTTCCTTTGAAA 57.322 25.926 0.00 0.00 45.96 2.69
6538 7435 9.678260 TCAAATTCTCCAAATTTCCTTTGAAAA 57.322 25.926 0.00 0.00 45.96 2.29
6544 7441 9.981114 TCTCCAAATTTCCTTTGAAAATCTTAC 57.019 29.630 0.00 0.00 45.96 2.34
6545 7442 9.762933 CTCCAAATTTCCTTTGAAAATCTTACA 57.237 29.630 0.00 0.00 45.96 2.41
6546 7443 9.762933 TCCAAATTTCCTTTGAAAATCTTACAG 57.237 29.630 0.00 0.00 45.96 2.74
6547 7444 9.546428 CCAAATTTCCTTTGAAAATCTTACAGT 57.454 29.630 0.00 0.00 45.96 3.55
6549 7446 9.764363 AAATTTCCTTTGAAAATCTTACAGTCC 57.236 29.630 0.00 0.00 43.37 3.85
6550 7447 7.889873 TTTCCTTTGAAAATCTTACAGTCCA 57.110 32.000 0.00 0.00 37.53 4.02
6551 7448 7.889873 TTCCTTTGAAAATCTTACAGTCCAA 57.110 32.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 146 4.433186 TTGTTTCTGTCCTTGTGTGTTG 57.567 40.909 0.00 0.00 0.00 3.33
133 148 5.227152 GTTTTTGTTTCTGTCCTTGTGTGT 58.773 37.500 0.00 0.00 0.00 3.72
223 238 2.354729 CTGGTTCCCCGCCAATCA 59.645 61.111 0.00 0.00 35.32 2.57
232 247 0.329596 AGCAGATTGTCCTGGTTCCC 59.670 55.000 0.00 0.00 41.58 3.97
319 334 0.029300 CCTGTTTGGTTGTGTGCGAG 59.971 55.000 0.00 0.00 0.00 5.03
330 345 2.282887 CCGGGGGTTCCTGTTTGG 60.283 66.667 0.00 0.00 37.74 3.28
367 387 1.541672 CCTCTCTCCCTCCCTCTCC 59.458 68.421 0.00 0.00 0.00 3.71
469 497 1.376037 CCAAACAGTCGCCTCCCTC 60.376 63.158 0.00 0.00 0.00 4.30
470 498 1.201429 ATCCAAACAGTCGCCTCCCT 61.201 55.000 0.00 0.00 0.00 4.20
473 501 1.646189 GAGATCCAAACAGTCGCCTC 58.354 55.000 0.00 0.00 0.00 4.70
474 502 0.108615 CGAGATCCAAACAGTCGCCT 60.109 55.000 0.00 0.00 0.00 5.52
475 503 2.373938 CGAGATCCAAACAGTCGCC 58.626 57.895 0.00 0.00 0.00 5.54
477 505 1.413767 CCGCGAGATCCAAACAGTCG 61.414 60.000 8.23 0.00 0.00 4.18
478 506 1.084370 CCCGCGAGATCCAAACAGTC 61.084 60.000 8.23 0.00 0.00 3.51
479 507 1.079127 CCCGCGAGATCCAAACAGT 60.079 57.895 8.23 0.00 0.00 3.55
480 508 2.464459 GCCCGCGAGATCCAAACAG 61.464 63.158 8.23 0.00 0.00 3.16
481 509 2.435938 GCCCGCGAGATCCAAACA 60.436 61.111 8.23 0.00 0.00 2.83
482 510 3.564027 CGCCCGCGAGATCCAAAC 61.564 66.667 8.23 0.00 42.83 2.93
483 511 4.830765 CCGCCCGCGAGATCCAAA 62.831 66.667 8.23 0.00 42.83 3.28
494 522 4.504916 CAGCAGAGAGACCGCCCG 62.505 72.222 0.00 0.00 0.00 6.13
498 526 2.422231 CCTCCCAGCAGAGAGACCG 61.422 68.421 0.38 0.00 35.82 4.79
506 534 3.406200 CTCACCCCCTCCCAGCAG 61.406 72.222 0.00 0.00 0.00 4.24
508 536 4.741239 TCCTCACCCCCTCCCAGC 62.741 72.222 0.00 0.00 0.00 4.85
509 537 2.074948 CATCCTCACCCCCTCCCAG 61.075 68.421 0.00 0.00 0.00 4.45
510 538 2.042762 CATCCTCACCCCCTCCCA 59.957 66.667 0.00 0.00 0.00 4.37
511 539 2.774351 CCATCCTCACCCCCTCCC 60.774 72.222 0.00 0.00 0.00 4.30
512 540 1.768077 CTCCATCCTCACCCCCTCC 60.768 68.421 0.00 0.00 0.00 4.30
514 542 2.374342 CCTCCATCCTCACCCCCT 59.626 66.667 0.00 0.00 0.00 4.79
518 546 4.554036 GCCGCCTCCATCCTCACC 62.554 72.222 0.00 0.00 0.00 4.02
521 549 4.292178 CTCGCCGCCTCCATCCTC 62.292 72.222 0.00 0.00 0.00 3.71
650 678 3.767131 GGATGGATCCTTCTAGAGCTACC 59.233 52.174 23.02 4.44 43.73 3.18
762 792 1.128809 TTCCTCCCAAAGCCCACGTA 61.129 55.000 0.00 0.00 0.00 3.57
824 854 3.618855 TTCCCCCTCACTCCCCTCG 62.619 68.421 0.00 0.00 0.00 4.63
828 858 3.463704 AGATATTTTTCCCCCTCACTCCC 59.536 47.826 0.00 0.00 0.00 4.30
830 860 3.885901 GCAGATATTTTTCCCCCTCACTC 59.114 47.826 0.00 0.00 0.00 3.51
831 861 3.269381 TGCAGATATTTTTCCCCCTCACT 59.731 43.478 0.00 0.00 0.00 3.41
832 862 3.631250 TGCAGATATTTTTCCCCCTCAC 58.369 45.455 0.00 0.00 0.00 3.51
833 863 3.527253 TCTGCAGATATTTTTCCCCCTCA 59.473 43.478 13.74 0.00 0.00 3.86
834 864 4.170468 TCTGCAGATATTTTTCCCCCTC 57.830 45.455 13.74 0.00 0.00 4.30
835 865 4.017130 ACTTCTGCAGATATTTTTCCCCCT 60.017 41.667 19.04 0.00 0.00 4.79
836 866 4.098501 CACTTCTGCAGATATTTTTCCCCC 59.901 45.833 19.04 0.00 0.00 5.40
846 876 1.688735 CGATCCCCACTTCTGCAGATA 59.311 52.381 19.04 7.79 0.00 1.98
1020 1368 2.587247 GGAGCACTCACTGGCCTGA 61.587 63.158 17.64 5.48 0.00 3.86
1206 1559 3.553511 GGACATGAACAACGCATCTAGAG 59.446 47.826 0.00 0.00 0.00 2.43
1236 1592 4.025401 GGTTGAGTTGGCACGCCG 62.025 66.667 3.13 0.00 39.42 6.46
1249 1605 6.655003 ACATAGGTTTAGTCATGAACAGGTTG 59.345 38.462 0.00 0.00 0.00 3.77
1268 1624 7.609146 ATGAATAATCAGTACATGGCACATAGG 59.391 37.037 0.00 0.00 40.99 2.57
1304 1662 3.976793 ACATCAGCAACACTTCAACAG 57.023 42.857 0.00 0.00 0.00 3.16
1346 1704 1.415659 CAAATTGTTCAAGGGGGCACA 59.584 47.619 0.00 0.00 0.00 4.57
1549 1921 5.776744 ACACGTAAGGAAACTAATCGTTCT 58.223 37.500 0.00 0.00 42.68 3.01
2434 2812 3.131478 GCATCCGGAAACCGTGGG 61.131 66.667 9.01 0.00 46.80 4.61
2756 3394 6.653273 TCGATAAGTGCAAAGAAAGATGAG 57.347 37.500 0.00 0.00 0.00 2.90
2757 3395 6.037500 CCATCGATAAGTGCAAAGAAAGATGA 59.962 38.462 16.82 0.00 35.20 2.92
2831 3473 6.595716 AGAACCTCCATCTTCGATTACAAAAG 59.404 38.462 0.00 0.00 0.00 2.27
2847 3489 6.886178 ACTAATTTAAGGCTAGAACCTCCA 57.114 37.500 0.00 0.00 39.93 3.86
2912 3554 7.086376 GCAGAAATACATCACAGTGACAAATT 58.914 34.615 5.05 3.02 0.00 1.82
2913 3555 6.207221 TGCAGAAATACATCACAGTGACAAAT 59.793 34.615 5.05 0.00 0.00 2.32
2917 3559 4.452114 TGTGCAGAAATACATCACAGTGAC 59.548 41.667 5.05 0.00 33.33 3.67
3093 3735 4.202233 TGAAGCAAATGAATCAGTTGGCAA 60.202 37.500 22.30 0.00 39.40 4.52
3612 4254 4.881850 AGTTGACTGAACACACCCTAAAAG 59.118 41.667 0.00 0.00 36.98 2.27
3828 4667 7.979444 ACACTTATTGCAACAACATACTAGT 57.021 32.000 0.00 0.00 0.00 2.57
3934 4781 2.159179 AGTGGGGCTTGTTTCAGTTT 57.841 45.000 0.00 0.00 0.00 2.66
4427 5274 9.403583 ACTTTCCTATTCTTTCACACAAACTAA 57.596 29.630 0.00 0.00 0.00 2.24
4428 5275 8.836413 CACTTTCCTATTCTTTCACACAAACTA 58.164 33.333 0.00 0.00 0.00 2.24
4429 5276 7.201821 CCACTTTCCTATTCTTTCACACAAACT 60.202 37.037 0.00 0.00 0.00 2.66
4430 5277 6.918022 CCACTTTCCTATTCTTTCACACAAAC 59.082 38.462 0.00 0.00 0.00 2.93
4431 5278 6.460953 GCCACTTTCCTATTCTTTCACACAAA 60.461 38.462 0.00 0.00 0.00 2.83
4432 5279 5.009610 GCCACTTTCCTATTCTTTCACACAA 59.990 40.000 0.00 0.00 0.00 3.33
4640 5511 4.102996 TCATGCAGGTAAGATGGCAGATAA 59.897 41.667 0.00 0.00 39.95 1.75
4690 5561 5.048504 ACTGCACATGTAAATTTCTCCACAG 60.049 40.000 0.00 0.00 0.00 3.66
4764 5635 1.609208 ATGCACAACTCAGGAACACC 58.391 50.000 0.00 0.00 0.00 4.16
5065 5942 2.437895 GCAGGATCAGCAGCTGCA 60.438 61.111 38.24 21.24 45.16 4.41
5159 6036 5.138125 AGAAACATACAAATGCCTTGGTG 57.862 39.130 0.00 0.00 39.56 4.17
5176 6053 5.821204 AGTTGTGCTGTTACAATGAGAAAC 58.179 37.500 0.00 0.00 42.02 2.78
5225 6102 0.835276 CATCTCTGTGGGCATCTCCA 59.165 55.000 0.00 0.00 36.21 3.86
5248 6125 3.760580 ATCTATAGCTGGCTGTTCCAC 57.239 47.619 5.25 0.00 40.72 4.02
5253 6130 6.429385 GCAATTCTAAATCTATAGCTGGCTGT 59.571 38.462 5.25 0.96 0.00 4.40
5402 6279 1.846541 GCGCTTTAAAACCAAGCACA 58.153 45.000 0.00 0.00 46.01 4.57
5563 6448 1.202698 GCATACCTCCTAGCACAAGGG 60.203 57.143 0.50 0.00 37.24 3.95
5633 6518 4.493547 TCAACAGTTGCTTTCCAAACAAG 58.506 39.130 8.58 0.00 34.68 3.16
5638 6523 4.734398 ACATTCAACAGTTGCTTTCCAA 57.266 36.364 8.58 0.00 0.00 3.53
5857 6746 2.973945 GGCACCTACTGAACTAGGTTG 58.026 52.381 0.00 0.00 43.58 3.77
5901 6790 5.852282 AAAATGTAACACAGCTTGGAAGT 57.148 34.783 0.00 0.00 0.00 3.01
5927 6816 3.120130 AGCGTTCTCGAGCATATAGTAGC 60.120 47.826 7.81 3.06 39.71 3.58
5928 6817 4.152580 TGAGCGTTCTCGAGCATATAGTAG 59.847 45.833 7.81 0.00 42.26 2.57
5929 6818 4.062991 TGAGCGTTCTCGAGCATATAGTA 58.937 43.478 7.81 0.00 42.26 1.82
5930 6819 2.879026 TGAGCGTTCTCGAGCATATAGT 59.121 45.455 7.81 0.00 42.26 2.12
5933 6822 1.678627 ACTGAGCGTTCTCGAGCATAT 59.321 47.619 7.81 0.00 42.26 1.78
5937 6826 0.727970 TAGACTGAGCGTTCTCGAGC 59.272 55.000 7.81 0.00 42.26 5.03
5938 6827 2.869801 AGATAGACTGAGCGTTCTCGAG 59.130 50.000 5.93 5.93 42.26 4.04
5941 6830 4.356289 GGAAAGATAGACTGAGCGTTCTC 58.644 47.826 0.00 0.00 39.78 2.87
5942 6831 3.181495 CGGAAAGATAGACTGAGCGTTCT 60.181 47.826 0.00 0.00 0.00 3.01
6025 6921 8.255665 CAAAATTTTAGTTTTGCAAACATCGG 57.744 30.769 12.39 0.00 40.79 4.18
6070 6967 8.514330 TGTACTGATTCAAACCAGTTTAACTT 57.486 30.769 0.00 0.00 42.86 2.66
6479 7376 5.131067 GTTTCTTCCCTACACAAGTCCTTT 58.869 41.667 0.00 0.00 0.00 3.11
6480 7377 4.165372 TGTTTCTTCCCTACACAAGTCCTT 59.835 41.667 0.00 0.00 0.00 3.36
6481 7378 3.714798 TGTTTCTTCCCTACACAAGTCCT 59.285 43.478 0.00 0.00 0.00 3.85
6482 7379 3.813724 GTGTTTCTTCCCTACACAAGTCC 59.186 47.826 0.00 0.00 41.30 3.85
6483 7380 4.704965 AGTGTTTCTTCCCTACACAAGTC 58.295 43.478 0.00 0.00 43.46 3.01
6484 7381 4.772886 AGTGTTTCTTCCCTACACAAGT 57.227 40.909 0.00 0.00 43.46 3.16
6485 7382 4.275936 CCAAGTGTTTCTTCCCTACACAAG 59.724 45.833 0.00 0.00 43.46 3.16
6486 7383 4.080243 TCCAAGTGTTTCTTCCCTACACAA 60.080 41.667 0.00 0.00 43.46 3.33
6487 7384 3.456644 TCCAAGTGTTTCTTCCCTACACA 59.543 43.478 0.00 0.00 43.46 3.72
6488 7385 4.081322 TCCAAGTGTTTCTTCCCTACAC 57.919 45.455 0.00 0.00 41.82 2.90
6489 7386 4.781775 TTCCAAGTGTTTCTTCCCTACA 57.218 40.909 0.00 0.00 33.63 2.74
6490 7387 5.768164 TGAATTCCAAGTGTTTCTTCCCTAC 59.232 40.000 2.27 0.00 33.63 3.18
6491 7388 5.947663 TGAATTCCAAGTGTTTCTTCCCTA 58.052 37.500 2.27 0.00 33.63 3.53
6492 7389 4.803452 TGAATTCCAAGTGTTTCTTCCCT 58.197 39.130 2.27 0.00 33.63 4.20
6493 7390 5.529581 TTGAATTCCAAGTGTTTCTTCCC 57.470 39.130 2.27 0.00 33.63 3.97
6494 7391 7.928167 AGAATTTGAATTCCAAGTGTTTCTTCC 59.072 33.333 11.72 0.00 44.55 3.46
6495 7392 8.877808 AGAATTTGAATTCCAAGTGTTTCTTC 57.122 30.769 11.72 0.00 44.55 2.87
6496 7393 7.928167 GGAGAATTTGAATTCCAAGTGTTTCTT 59.072 33.333 11.72 0.00 44.55 2.52
6497 7394 7.069826 TGGAGAATTTGAATTCCAAGTGTTTCT 59.930 33.333 11.72 4.51 44.55 2.52
6498 7395 7.209475 TGGAGAATTTGAATTCCAAGTGTTTC 58.791 34.615 11.72 0.00 44.55 2.78
6499 7396 7.123355 TGGAGAATTTGAATTCCAAGTGTTT 57.877 32.000 11.72 0.00 44.55 2.83
6500 7397 6.729690 TGGAGAATTTGAATTCCAAGTGTT 57.270 33.333 11.72 0.00 44.55 3.32
6501 7398 6.729690 TTGGAGAATTTGAATTCCAAGTGT 57.270 33.333 11.72 0.00 44.55 3.55
6502 7399 8.611654 AATTTGGAGAATTTGAATTCCAAGTG 57.388 30.769 11.72 0.00 44.55 3.16
6503 7400 9.276590 GAAATTTGGAGAATTTGAATTCCAAGT 57.723 29.630 11.72 0.00 44.55 3.16
6504 7401 8.724229 GGAAATTTGGAGAATTTGAATTCCAAG 58.276 33.333 11.72 0.00 44.55 3.61
6505 7402 8.439172 AGGAAATTTGGAGAATTTGAATTCCAA 58.561 29.630 11.72 8.71 44.55 3.53
6506 7403 7.976712 AGGAAATTTGGAGAATTTGAATTCCA 58.023 30.769 11.72 3.53 44.55 3.53
6507 7404 8.853077 AAGGAAATTTGGAGAATTTGAATTCC 57.147 30.769 11.72 0.00 44.55 3.01
6509 7406 9.850198 TCAAAGGAAATTTGGAGAATTTGAATT 57.150 25.926 0.00 0.00 46.93 2.17
6510 7407 9.850198 TTCAAAGGAAATTTGGAGAATTTGAAT 57.150 25.926 0.00 0.00 46.93 2.57
6511 7408 9.678260 TTTCAAAGGAAATTTGGAGAATTTGAA 57.322 25.926 0.00 6.56 46.93 2.69
6512 7409 9.678260 TTTTCAAAGGAAATTTGGAGAATTTGA 57.322 25.926 0.00 0.92 46.93 2.69
6518 7415 9.981114 GTAAGATTTTCAAAGGAAATTTGGAGA 57.019 29.630 0.00 0.00 46.93 3.71
6519 7416 9.762933 TGTAAGATTTTCAAAGGAAATTTGGAG 57.237 29.630 0.00 0.00 46.93 3.86
6520 7417 9.762933 CTGTAAGATTTTCAAAGGAAATTTGGA 57.237 29.630 0.00 0.00 42.40 3.53
6521 7418 9.546428 ACTGTAAGATTTTCAAAGGAAATTTGG 57.454 29.630 0.00 0.00 42.64 3.28
6523 7420 9.764363 GGACTGTAAGATTTTCAAAGGAAATTT 57.236 29.630 0.00 0.00 39.14 1.82
6524 7421 8.923270 TGGACTGTAAGATTTTCAAAGGAAATT 58.077 29.630 0.00 0.00 39.14 1.82
6525 7422 8.477419 TGGACTGTAAGATTTTCAAAGGAAAT 57.523 30.769 0.00 0.00 39.14 2.17
6526 7423 7.889873 TGGACTGTAAGATTTTCAAAGGAAA 57.110 32.000 0.00 0.00 38.20 3.13
6527 7424 7.889873 TTGGACTGTAAGATTTTCAAAGGAA 57.110 32.000 0.00 0.00 37.43 3.36


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

AutoCloner maintained by Alex Coulton.