Multiple sequence alignment - TraesCS2A01G414000

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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 TraesCS2A01G414000 chr2A 100.000 5205 0 0 1 5205 671270910 671276114 0.000000e+00 9612
1 TraesCS2A01G414000 chr2B 94.264 4655 169 42 585 5203 622473258 622477850 0.000000e+00 7027
2 TraesCS2A01G414000 chr2B 84.843 574 59 15 1 548 622472686 622473257 2.120000e-153 553
3 TraesCS2A01G414000 chr2D 92.459 4469 208 55 208 4610 525302191 525297786 0.000000e+00 6266
4 TraesCS2A01G414000 chr2D 91.064 470 20 9 4737 5203 525297774 525297324 2.660000e-172 616
5 TraesCS2A01G414000 chr2D 88.496 226 11 6 1 212 525407308 525407084 5.170000e-65 259


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 TraesCS2A01G414000 chr2A 671270910 671276114 5204 False 9612 9612 100.0000 1 5205 1 chr2A.!!$F1 5204
1 TraesCS2A01G414000 chr2B 622472686 622477850 5164 False 3790 7027 89.5535 1 5203 2 chr2B.!!$F1 5202
2 TraesCS2A01G414000 chr2D 525297324 525302191 4867 True 3441 6266 91.7615 208 5203 2 chr2D.!!$R2 4995

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
754 785 0.179119 GATGCAGCCCAGTTCATTGC 60.179 55.0 0.00 0.0 35.42 3.56 F
1665 1719 0.171455 ACTCGATCAGTCAAGTCCGC 59.829 55.0 0.00 0.0 0.00 5.54 F
2290 2344 0.249826 ACAAGCGCATTTGTTTGGGG 60.250 50.0 11.47 0.0 38.05 4.96 F
3509 3596 0.253327 ATGGCGGGGAAGAAACTCTC 59.747 55.0 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1798 1.171308 CCGGTAGAACTGTTCTCCGA 58.829 55.0 35.77 19.3 45.17 4.55 R
3497 3584 0.108089 GAGGCCGGAGAGTTTCTTCC 60.108 60.0 5.05 0.0 0.00 3.46 R
3552 3639 0.627451 AGATCATCCCCAGCAAGCAA 59.373 50.0 0.00 0.0 0.00 3.91 R
4946 5041 0.031994 AAAGCCAACATCGGTGCAAC 59.968 50.0 0.00 0.0 0.00 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.333258 GCACGTGCACAAAGACTTCTC 60.333 52.381 34.52 0.00 41.59 2.87
60 61 1.226717 GTCAGAGCGGCTTCGGTAG 60.227 63.158 2.97 0.00 45.16 3.18
62 63 3.148279 AGAGCGGCTTCGGTAGGG 61.148 66.667 2.97 0.00 45.16 3.53
65 66 4.222847 GCGGCTTCGGTAGGGGAG 62.223 72.222 0.00 0.00 0.00 4.30
76 77 5.070823 TCGGTAGGGGAGTAATGAGTAAT 57.929 43.478 0.00 0.00 0.00 1.89
77 78 6.204852 TCGGTAGGGGAGTAATGAGTAATA 57.795 41.667 0.00 0.00 0.00 0.98
87 88 8.989980 GGGAGTAATGAGTAATAACAATAGCAC 58.010 37.037 0.00 0.00 0.00 4.40
116 121 2.494870 GTTCTGGTGGTAGTGGTCGTAT 59.505 50.000 0.00 0.00 0.00 3.06
125 130 5.180868 GTGGTAGTGGTCGTATATAGTCCAG 59.819 48.000 2.03 0.00 0.00 3.86
132 137 6.208994 GTGGTCGTATATAGTCCAGGAATCTT 59.791 42.308 0.00 0.00 0.00 2.40
170 179 5.700402 ATAGGGTGCTTTGTACTTCTGAT 57.300 39.130 0.00 0.00 0.00 2.90
177 186 6.426937 GGTGCTTTGTACTTCTGATGAACTTA 59.573 38.462 0.00 0.00 0.00 2.24
180 189 9.719355 TGCTTTGTACTTCTGATGAACTTATAA 57.281 29.630 0.00 0.00 0.00 0.98
233 248 5.414765 CCTCACCTTTTAAATTTACCGAGCT 59.585 40.000 0.00 0.00 0.00 4.09
258 273 6.649155 TGATATAGCTAAGGCAGTTGTTTGA 58.351 36.000 0.00 0.00 41.70 2.69
344 359 4.455533 GTGCTTTGATGGTCATGAGTGTAA 59.544 41.667 0.00 0.00 0.00 2.41
357 372 3.441101 TGAGTGTAATGGTACCTCAGCT 58.559 45.455 14.36 3.86 34.91 4.24
366 381 1.413227 GGTACCTCAGCTACCAGGGAT 60.413 57.143 4.06 0.00 34.74 3.85
380 395 2.619074 CCAGGGATCAAACCTCAGGTTC 60.619 54.545 10.34 0.00 46.20 3.62
381 396 2.040278 CAGGGATCAAACCTCAGGTTCA 59.960 50.000 10.34 0.00 46.20 3.18
385 400 2.260844 TCAAACCTCAGGTTCAGCTG 57.739 50.000 10.34 7.63 46.20 4.24
393 408 1.160137 CAGGTTCAGCTGCTTGGTAC 58.840 55.000 9.47 0.00 0.00 3.34
455 476 3.120105 TCGATAGCGAGGCACCTG 58.880 61.111 0.00 0.00 42.51 4.00
457 478 1.589993 CGATAGCGAGGCACCTGTG 60.590 63.158 0.00 0.00 40.82 3.66
489 510 1.818642 GTCTCAAGACATGCCAGCTT 58.181 50.000 5.28 0.00 44.18 3.74
491 512 3.338249 GTCTCAAGACATGCCAGCTTAA 58.662 45.455 5.28 0.00 44.18 1.85
496 517 3.920231 AGACATGCCAGCTTAATCTCA 57.080 42.857 0.00 0.00 0.00 3.27
499 520 1.600957 CATGCCAGCTTAATCTCACGG 59.399 52.381 0.00 0.00 0.00 4.94
508 533 4.767928 AGCTTAATCTCACGGAGGTATAGG 59.232 45.833 1.76 0.00 0.00 2.57
514 539 5.837770 TCTCACGGAGGTATAGGAATAGA 57.162 43.478 1.76 0.00 0.00 1.98
515 540 6.390048 TCTCACGGAGGTATAGGAATAGAT 57.610 41.667 1.76 0.00 0.00 1.98
527 552 3.674997 AGGAATAGATTGTGCGTGTGTT 58.325 40.909 0.00 0.00 0.00 3.32
541 566 2.798499 CGTGTGTTCGTTCAGAGAAGGT 60.798 50.000 0.00 0.00 0.00 3.50
557 582 5.353678 AGAGAAGGTAGTGTATGTACGTGTC 59.646 44.000 0.00 0.00 0.00 3.67
581 606 3.636043 CGTTTGCTCGTGGCGTGT 61.636 61.111 0.00 0.00 45.43 4.49
583 608 1.063488 GTTTGCTCGTGGCGTGTTT 59.937 52.632 0.00 0.00 45.43 2.83
584 609 0.928451 GTTTGCTCGTGGCGTGTTTC 60.928 55.000 0.00 0.00 45.43 2.78
586 611 1.495584 TTGCTCGTGGCGTGTTTCTC 61.496 55.000 0.00 0.00 45.43 2.87
589 620 0.934496 CTCGTGGCGTGTTTCTCAAA 59.066 50.000 0.00 0.00 0.00 2.69
618 649 1.883084 GGCCGTCACAGAATAGCGG 60.883 63.158 0.00 0.00 44.60 5.52
645 676 9.980780 ACGCCACAAAATAATAATAAAATTTGC 57.019 25.926 0.00 0.00 32.49 3.68
705 736 2.159382 AGAAAGTTGGGCCAACATACG 58.841 47.619 41.66 0.00 45.66 3.06
722 753 1.250840 ACGGCCCATCCAGAAAAAGC 61.251 55.000 0.00 0.00 34.01 3.51
738 769 6.862090 CAGAAAAAGCAGGAAAGAAGAAGATG 59.138 38.462 0.00 0.00 0.00 2.90
754 785 0.179119 GATGCAGCCCAGTTCATTGC 60.179 55.000 0.00 0.00 35.42 3.56
776 807 4.102649 CGTTGTTCCACCTTTTCTGTTTC 58.897 43.478 0.00 0.00 0.00 2.78
787 819 5.161358 CCTTTTCTGTTTCGGCCTTTAATC 58.839 41.667 0.00 0.00 0.00 1.75
974 1006 1.305219 GCATGCTGGTTTCTGCCGTA 61.305 55.000 11.37 0.00 37.08 4.02
1107 1139 2.284331 TTCCTGGGCACGGCTCTA 60.284 61.111 0.00 0.00 0.00 2.43
1220 1252 3.068024 GTGACTGATTGAAACTTTGGCCA 59.932 43.478 0.00 0.00 0.00 5.36
1341 1376 0.179045 ATTCAGTACCGATGGCTGCC 60.179 55.000 12.87 12.87 0.00 4.85
1361 1396 2.698797 CCCCTGTCACATCGTAACCTAT 59.301 50.000 0.00 0.00 0.00 2.57
1367 1402 8.145767 CCCTGTCACATCGTAACCTATAAATAA 58.854 37.037 0.00 0.00 0.00 1.40
1393 1428 3.881220 ACTGAAGGAACCGAGTGAAAAA 58.119 40.909 0.00 0.00 0.00 1.94
1421 1473 4.083003 CGCCATTTTCCTTGTAAACTAGCA 60.083 41.667 0.00 0.00 0.00 3.49
1427 1479 6.870971 TTTCCTTGTAAACTAGCAAATCGT 57.129 33.333 0.00 0.00 0.00 3.73
1431 1483 8.556213 TCCTTGTAAACTAGCAAATCGTAAAT 57.444 30.769 0.00 0.00 0.00 1.40
1444 1498 7.810759 AGCAAATCGTAAATTTTAATTGTCGGT 59.189 29.630 0.00 3.76 0.00 4.69
1463 1517 7.211573 TGTCGGTTTGAAAGATTACTAAGTCA 58.788 34.615 0.00 0.00 0.00 3.41
1533 1587 7.064371 GCATTCTCGATTGATATTGCTCTATGT 59.936 37.037 7.58 0.00 29.79 2.29
1561 1615 1.967319 ATGTGCAGGTTCGAAACACT 58.033 45.000 16.95 4.17 32.49 3.55
1606 1660 9.975218 AAATCAAGGTATTCCAACTTGTACTAT 57.025 29.630 2.26 0.00 41.64 2.12
1665 1719 0.171455 ACTCGATCAGTCAAGTCCGC 59.829 55.000 0.00 0.00 0.00 5.54
1666 1720 0.526524 CTCGATCAGTCAAGTCCGCC 60.527 60.000 0.00 0.00 0.00 6.13
1669 1723 1.613630 ATCAGTCAAGTCCGCCCCT 60.614 57.895 0.00 0.00 0.00 4.79
1680 1734 2.908351 AGTCCGCCCCTTTTAAACTAGA 59.092 45.455 0.00 0.00 0.00 2.43
1695 1749 3.138205 ACTAGATTGTGAAGAGCGACG 57.862 47.619 0.00 0.00 0.00 5.12
1723 1777 8.697507 ATTTACAATCTTGAGGTTTCTCTGTT 57.302 30.769 0.00 0.00 40.58 3.16
1744 1798 2.556144 TCATCTTTCAGCTGCTGTGT 57.444 45.000 27.24 8.93 32.61 3.72
2026 2080 5.163530 TGGCATATTCTATGGTTGTTTGCTG 60.164 40.000 0.00 0.00 0.00 4.41
2053 2107 4.220821 ACAGGTACTTGTCCTCATACTGTG 59.779 45.833 4.53 0.00 34.60 3.66
2164 2218 8.700051 AGGATCCCTTATGAAGTTATGATATCG 58.300 37.037 8.55 0.00 0.00 2.92
2282 2336 2.035832 AGTAAGCCAAACAAGCGCATTT 59.964 40.909 11.47 4.09 34.64 2.32
2289 2343 1.580815 AACAAGCGCATTTGTTTGGG 58.419 45.000 18.81 0.00 46.18 4.12
2290 2344 0.249826 ACAAGCGCATTTGTTTGGGG 60.250 50.000 11.47 0.00 38.05 4.96
2305 2359 4.469227 TGTTTGGGGCTTGTTGCATATTAT 59.531 37.500 0.00 0.00 45.15 1.28
2404 2458 8.547967 AGTTATTTCATTTCGCAGTCTTTCTA 57.452 30.769 0.00 0.00 0.00 2.10
2464 2522 5.112220 TCATCTGCTTTAGTGCAAAGTTG 57.888 39.130 0.00 0.00 44.73 3.16
2504 2562 8.322906 TGAACATCTGGTTGTCTAATTACTTG 57.677 34.615 0.00 0.00 40.63 3.16
2649 2707 5.586339 CGATATGTGAGTCATCTGTTCTGT 58.414 41.667 0.00 0.00 37.91 3.41
2651 2709 6.533012 CGATATGTGAGTCATCTGTTCTGTTT 59.467 38.462 0.00 0.00 37.91 2.83
2652 2710 7.063898 CGATATGTGAGTCATCTGTTCTGTTTT 59.936 37.037 0.00 0.00 37.91 2.43
2699 2757 6.147000 GCTACATTTTCCTATTAGCTCAGCTC 59.853 42.308 0.00 0.00 40.44 4.09
2729 2787 2.559840 CAGGCTTTGCAGCTCACG 59.440 61.111 0.00 0.00 46.44 4.35
2750 2808 3.301835 CGAAGTTTGATTATCGGCTCACG 60.302 47.826 0.00 0.00 46.11 4.35
2901 2959 3.449377 TGTCGCCATTCACTTGAGGTATA 59.551 43.478 0.00 0.00 0.00 1.47
2909 2967 6.498651 CCATTCACTTGAGGTATAGTCCCTAT 59.501 42.308 0.00 0.00 30.60 2.57
3259 3323 7.039784 TGTTGAGTATGATTTCCCCAAAAGAAG 60.040 37.037 0.00 0.00 0.00 2.85
3349 3436 7.680442 TGGTGTCGAAATGATTTTAGATTGA 57.320 32.000 0.00 0.00 30.64 2.57
3497 3584 3.981071 TCTGGAGAAATATATGGCGGG 57.019 47.619 0.00 0.00 0.00 6.13
3509 3596 0.253327 ATGGCGGGGAAGAAACTCTC 59.747 55.000 0.00 0.00 0.00 3.20
3552 3639 3.714798 TCCAAACTTCTACACCAAGGAGT 59.285 43.478 0.00 0.00 36.86 3.85
3686 3773 1.678970 GGCCAAGGTGTTAGCTGGG 60.679 63.158 0.00 0.00 39.82 4.45
3982 4073 3.071479 GAGAACTATTCGCCCAAACACA 58.929 45.455 0.00 0.00 34.02 3.72
4196 4287 8.154649 ACAAACTCGAAACTTGTTATCTCAAT 57.845 30.769 1.65 0.00 28.99 2.57
4243 4334 2.511218 AGATCAATTGAGCCTGGCCTTA 59.489 45.455 19.65 0.26 0.00 2.69
4389 4480 5.402270 GTGACAAACAATTTGCATACTGTCC 59.598 40.000 1.23 0.00 44.39 4.02
4565 4656 9.230122 TGATTGTAATGTGTACATGAATGACTT 57.770 29.630 0.00 0.00 36.56 3.01
4630 4721 6.143496 GCTTACCTGTAGCTTGTTTCTTTTC 58.857 40.000 0.00 0.00 0.00 2.29
4638 4729 2.034685 GCTTGTTTCTTTTCGCCCTCTT 59.965 45.455 0.00 0.00 0.00 2.85
4639 4730 3.490933 GCTTGTTTCTTTTCGCCCTCTTT 60.491 43.478 0.00 0.00 0.00 2.52
4640 4731 3.982576 TGTTTCTTTTCGCCCTCTTTC 57.017 42.857 0.00 0.00 0.00 2.62
4641 4732 3.551846 TGTTTCTTTTCGCCCTCTTTCT 58.448 40.909 0.00 0.00 0.00 2.52
4642 4733 3.951680 TGTTTCTTTTCGCCCTCTTTCTT 59.048 39.130 0.00 0.00 0.00 2.52
4643 4734 4.401202 TGTTTCTTTTCGCCCTCTTTCTTT 59.599 37.500 0.00 0.00 0.00 2.52
4644 4735 4.830826 TTCTTTTCGCCCTCTTTCTTTC 57.169 40.909 0.00 0.00 0.00 2.62
4645 4736 4.086706 TCTTTTCGCCCTCTTTCTTTCT 57.913 40.909 0.00 0.00 0.00 2.52
4646 4737 5.223449 TCTTTTCGCCCTCTTTCTTTCTA 57.777 39.130 0.00 0.00 0.00 2.10
4647 4738 5.805728 TCTTTTCGCCCTCTTTCTTTCTAT 58.194 37.500 0.00 0.00 0.00 1.98
4648 4739 5.875359 TCTTTTCGCCCTCTTTCTTTCTATC 59.125 40.000 0.00 0.00 0.00 2.08
4649 4740 5.422214 TTTCGCCCTCTTTCTTTCTATCT 57.578 39.130 0.00 0.00 0.00 1.98
4650 4741 5.422214 TTCGCCCTCTTTCTTTCTATCTT 57.578 39.130 0.00 0.00 0.00 2.40
4651 4742 4.759782 TCGCCCTCTTTCTTTCTATCTTG 58.240 43.478 0.00 0.00 0.00 3.02
4652 4743 3.873952 CGCCCTCTTTCTTTCTATCTTGG 59.126 47.826 0.00 0.00 0.00 3.61
4653 4744 4.203226 GCCCTCTTTCTTTCTATCTTGGG 58.797 47.826 0.00 0.00 0.00 4.12
4654 4745 4.080299 GCCCTCTTTCTTTCTATCTTGGGA 60.080 45.833 0.00 0.00 33.14 4.37
4655 4746 5.679601 CCCTCTTTCTTTCTATCTTGGGAG 58.320 45.833 0.00 0.00 33.14 4.30
4656 4747 5.426833 CCCTCTTTCTTTCTATCTTGGGAGA 59.573 44.000 0.00 0.00 36.09 3.71
4657 4748 6.407979 CCCTCTTTCTTTCTATCTTGGGAGAG 60.408 46.154 0.00 0.00 34.85 3.20
4658 4749 6.156083 CCTCTTTCTTTCTATCTTGGGAGAGT 59.844 42.308 0.00 0.00 34.85 3.24
4659 4750 7.343316 CCTCTTTCTTTCTATCTTGGGAGAGTA 59.657 40.741 0.00 0.00 34.85 2.59
4660 4751 8.299990 TCTTTCTTTCTATCTTGGGAGAGTAG 57.700 38.462 0.00 0.00 34.85 2.57
4661 4752 7.896496 TCTTTCTTTCTATCTTGGGAGAGTAGT 59.104 37.037 0.00 0.00 34.85 2.73
4662 4753 8.437274 TTTCTTTCTATCTTGGGAGAGTAGTT 57.563 34.615 0.00 0.00 34.85 2.24
4663 4754 8.437274 TTCTTTCTATCTTGGGAGAGTAGTTT 57.563 34.615 0.00 0.00 34.85 2.66
4664 4755 7.841956 TCTTTCTATCTTGGGAGAGTAGTTTG 58.158 38.462 0.00 0.00 34.85 2.93
4692 4785 1.737793 GACGGGGTGTGCTCTTAATTG 59.262 52.381 0.00 0.00 0.00 2.32
4750 4843 0.250510 TGTGTGTGTGTGTGTGTGGT 60.251 50.000 0.00 0.00 0.00 4.16
4931 5026 6.404513 GCAACTCTAATACTCTGTCGTAAGGT 60.405 42.308 0.00 0.00 38.47 3.50
4932 5027 6.680874 ACTCTAATACTCTGTCGTAAGGTG 57.319 41.667 0.00 0.00 38.47 4.00
4941 5036 1.226745 TCGTAAGGTGCGTATGCCG 60.227 57.895 4.05 0.00 38.15 5.69
4944 5039 0.738412 GTAAGGTGCGTATGCCGTGT 60.738 55.000 4.05 0.00 41.78 4.49
4945 5040 0.037139 TAAGGTGCGTATGCCGTGTT 60.037 50.000 4.05 0.00 41.78 3.32
4946 5041 1.573829 AAGGTGCGTATGCCGTGTTG 61.574 55.000 4.05 0.00 41.78 3.33
4953 5048 0.386731 GTATGCCGTGTTGTTGCACC 60.387 55.000 0.00 0.00 37.92 5.01
4959 5054 0.028770 CGTGTTGTTGCACCGATGTT 59.971 50.000 0.00 0.00 36.08 2.71
5062 5159 3.056322 GCAAGCACCCAATTCTTCATTCT 60.056 43.478 0.00 0.00 0.00 2.40
5086 5183 9.967346 TCTTTAGGATCGAATTACTTCTACATG 57.033 33.333 0.00 0.00 0.00 3.21
5102 5201 5.376625 TCTACATGGTTTCTGTTGCTTTCT 58.623 37.500 0.00 0.00 0.00 2.52
5103 5202 6.530120 TCTACATGGTTTCTGTTGCTTTCTA 58.470 36.000 0.00 0.00 0.00 2.10
5104 5203 5.695851 ACATGGTTTCTGTTGCTTTCTAG 57.304 39.130 0.00 0.00 0.00 2.43
5128 5227 8.133024 AGTACATGATTCTTCTTCAGAGAACT 57.867 34.615 0.00 0.00 36.99 3.01
5150 5249 7.657023 ACTTAAGTGACCCCTATAAGTACTG 57.343 40.000 7.48 0.00 35.62 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.071239 CGAGAAGTCTTTGTGCACGTG 60.071 52.381 12.28 12.28 0.00 4.49
25 26 3.806591 ACCTTGTCGGTGACATACG 57.193 52.632 0.00 0.00 46.80 3.06
49 50 1.039233 TTACTCCCCTACCGAAGCCG 61.039 60.000 0.00 0.00 0.00 5.52
60 61 8.154856 TGCTATTGTTATTACTCATTACTCCCC 58.845 37.037 0.00 0.00 0.00 4.81
62 63 8.700644 CGTGCTATTGTTATTACTCATTACTCC 58.299 37.037 0.00 0.00 0.00 3.85
65 66 8.205948 CGACGTGCTATTGTTATTACTCATTAC 58.794 37.037 0.00 0.00 0.00 1.89
102 107 5.308976 TGGACTATATACGACCACTACCA 57.691 43.478 0.00 0.00 0.00 3.25
150 155 3.327757 TCATCAGAAGTACAAAGCACCCT 59.672 43.478 0.00 0.00 0.00 4.34
233 248 7.109501 TCAAACAACTGCCTTAGCTATATCAA 58.890 34.615 0.00 0.00 40.80 2.57
247 262 2.410730 AGCGTACGTATCAAACAACTGC 59.589 45.455 17.90 0.00 0.00 4.40
248 263 5.944049 ATAGCGTACGTATCAAACAACTG 57.056 39.130 17.90 0.00 0.00 3.16
258 273 3.181497 ACACAACCGAATAGCGTACGTAT 60.181 43.478 17.90 10.38 38.67 3.06
318 333 1.814394 TCATGACCATCAAAGCACAGC 59.186 47.619 0.00 0.00 0.00 4.40
334 349 4.122776 GCTGAGGTACCATTACACTCATG 58.877 47.826 15.94 3.05 36.11 3.07
357 372 2.196595 CCTGAGGTTTGATCCCTGGTA 58.803 52.381 0.00 0.00 30.60 3.25
366 381 1.815408 GCAGCTGAACCTGAGGTTTGA 60.815 52.381 19.33 7.56 46.95 2.69
380 395 2.988010 TATGAGGTACCAAGCAGCTG 57.012 50.000 15.94 10.11 0.00 4.24
381 396 3.370953 CCTTTATGAGGTACCAAGCAGCT 60.371 47.826 15.94 0.00 40.95 4.24
385 400 3.809905 CCTCCTTTATGAGGTACCAAGC 58.190 50.000 15.94 3.47 45.76 4.01
437 458 1.299468 CAGGTGCCTCGCTATCGAC 60.299 63.158 0.00 0.00 40.21 4.20
452 473 0.036952 ACTGACGAAGCCATCACAGG 60.037 55.000 0.00 0.00 36.82 4.00
455 476 1.067565 TGAGACTGACGAAGCCATCAC 60.068 52.381 0.00 0.00 0.00 3.06
457 478 2.094494 TCTTGAGACTGACGAAGCCATC 60.094 50.000 0.00 0.00 0.00 3.51
480 501 1.486310 TCCGTGAGATTAAGCTGGCAT 59.514 47.619 0.00 0.00 0.00 4.40
483 504 1.482593 ACCTCCGTGAGATTAAGCTGG 59.517 52.381 0.00 0.00 0.00 4.85
485 506 4.767928 CCTATACCTCCGTGAGATTAAGCT 59.232 45.833 0.00 0.00 0.00 3.74
489 510 7.925622 TCTATTCCTATACCTCCGTGAGATTA 58.074 38.462 2.84 0.00 0.00 1.75
491 512 6.390048 TCTATTCCTATACCTCCGTGAGAT 57.610 41.667 2.84 0.00 0.00 2.75
496 517 5.047235 GCACAATCTATTCCTATACCTCCGT 60.047 44.000 0.00 0.00 0.00 4.69
499 520 5.864474 CACGCACAATCTATTCCTATACCTC 59.136 44.000 0.00 0.00 0.00 3.85
508 533 3.122948 ACGAACACACGCACAATCTATTC 59.877 43.478 0.00 0.00 36.70 1.75
514 539 1.003972 CTGAACGAACACACGCACAAT 60.004 47.619 0.00 0.00 36.70 2.71
515 540 0.371989 CTGAACGAACACACGCACAA 59.628 50.000 0.00 0.00 36.70 3.33
527 552 5.008331 ACATACACTACCTTCTCTGAACGA 58.992 41.667 0.00 0.00 0.00 3.85
541 566 4.142752 GCTCACAGACACGTACATACACTA 60.143 45.833 0.00 0.00 0.00 2.74
572 597 2.181426 TTTTTGAGAAACACGCCACG 57.819 45.000 0.00 0.00 0.00 4.94
589 620 1.084289 GTGACGGCCGCTAATCTTTT 58.916 50.000 28.58 0.57 0.00 2.27
666 697 1.184322 TTTGTGGCCTACGGTCCGTA 61.184 55.000 22.45 22.45 41.54 4.02
705 736 0.533951 CTGCTTTTTCTGGATGGGCC 59.466 55.000 0.00 0.00 37.10 5.80
722 753 2.422832 GGCTGCATCTTCTTCTTTCCTG 59.577 50.000 0.50 0.00 0.00 3.86
738 769 2.146073 AACGCAATGAACTGGGCTGC 62.146 55.000 0.00 0.00 32.71 5.25
776 807 0.462047 AGGCAGACGATTAAAGGCCG 60.462 55.000 0.00 0.00 45.79 6.13
974 1006 1.905512 GGTTATCAGGTCGTGCCCT 59.094 57.895 0.00 0.00 38.26 5.19
1107 1139 2.225963 CGATACGAAGCCTAGGACGAAT 59.774 50.000 23.08 9.78 0.00 3.34
1255 1290 2.761392 AACCGCGTAAACCAAAACTC 57.239 45.000 4.92 0.00 0.00 3.01
1341 1376 5.524971 TTATAGGTTACGATGTGACAGGG 57.475 43.478 0.00 0.00 0.00 4.45
1361 1396 7.499895 ACTCGGTTCCTTCAGTTTGTTTATTTA 59.500 33.333 0.00 0.00 0.00 1.40
1367 1402 2.943033 CACTCGGTTCCTTCAGTTTGTT 59.057 45.455 0.00 0.00 0.00 2.83
1369 1404 2.833794 TCACTCGGTTCCTTCAGTTTG 58.166 47.619 0.00 0.00 0.00 2.93
1393 1428 2.568623 ACAAGGAAAATGGCGAGAGT 57.431 45.000 0.00 0.00 0.00 3.24
1402 1454 7.882179 ACGATTTGCTAGTTTACAAGGAAAAT 58.118 30.769 0.00 0.00 36.75 1.82
1442 1494 9.880064 GAAAGTGACTTAGTAATCTTTCAAACC 57.120 33.333 20.31 4.99 39.86 3.27
1463 1517 3.290710 ACACATGAACAGGCAAGAAAGT 58.709 40.909 0.00 0.00 0.00 2.66
1533 1587 2.419673 CGAACCTGCACATTATGAGCAA 59.580 45.455 17.05 3.37 42.97 3.91
1561 1615 7.730672 TGATTTCCAAATATCAATGGGTTCA 57.269 32.000 3.18 2.43 37.31 3.18
1606 1660 3.473647 CTCCTCCCGCTGCATCCA 61.474 66.667 0.00 0.00 0.00 3.41
1665 1719 7.362142 GCTCTTCACAATCTAGTTTAAAAGGGG 60.362 40.741 0.00 0.00 0.00 4.79
1666 1720 7.530863 GCTCTTCACAATCTAGTTTAAAAGGG 58.469 38.462 0.00 0.00 0.00 3.95
1669 1723 7.358931 CGTCGCTCTTCACAATCTAGTTTAAAA 60.359 37.037 0.00 0.00 0.00 1.52
1680 1734 4.749245 AAATTTCGTCGCTCTTCACAAT 57.251 36.364 0.00 0.00 0.00 2.71
1695 1749 9.617975 CAGAGAAACCTCAAGATTGTAAATTTC 57.382 33.333 0.00 0.00 33.16 2.17
1744 1798 1.171308 CCGGTAGAACTGTTCTCCGA 58.829 55.000 35.77 19.30 45.17 4.55
2026 2080 1.618837 TGAGGACAAGTACCTGTGAGC 59.381 52.381 0.78 0.00 37.93 4.26
2053 2107 4.475944 AGAATTCGCTGCAAATAACACAC 58.524 39.130 0.00 0.00 0.00 3.82
2282 2336 1.709578 TATGCAACAAGCCCCAAACA 58.290 45.000 0.00 0.00 44.83 2.83
2305 2359 5.359756 AGCATGCACTCGATAAATACAGAA 58.640 37.500 21.98 0.00 0.00 3.02
2322 2376 8.394121 GGATAGAAGCAATAAATAGTAGCATGC 58.606 37.037 10.51 10.51 0.00 4.06
2373 2427 4.732784 TGCGAAATGAAATAACTTCTGCC 58.267 39.130 0.00 0.00 34.86 4.85
2374 2428 5.393962 ACTGCGAAATGAAATAACTTCTGC 58.606 37.500 0.00 0.00 34.86 4.26
2464 2522 2.139917 TGTTCAGGTTATCACACACGC 58.860 47.619 0.00 0.00 0.00 5.34
2617 2675 7.972832 CAGATGACTCACATATCGCTATAATGT 59.027 37.037 0.00 0.00 39.56 2.71
2699 2757 4.379374 CAAAGCCTGCAAAATTTTCGAG 57.621 40.909 0.00 0.00 0.00 4.04
2726 2784 3.616821 TGAGCCGATAATCAAACTTCGTG 59.383 43.478 0.00 0.00 0.00 4.35
2729 2787 3.863424 TCGTGAGCCGATAATCAAACTTC 59.137 43.478 0.00 0.00 41.60 3.01
2750 2808 7.704271 TCTGCAATTCTTCATCAAGATCATTC 58.296 34.615 0.00 0.00 38.50 2.67
2909 2967 8.219546 TCAGCGAAATGTTCATAAATTCCATA 57.780 30.769 0.00 0.00 0.00 2.74
3050 3108 2.817258 CCACCGTTTCCTAATTTCAGCA 59.183 45.455 0.00 0.00 0.00 4.41
3177 3235 4.749598 CCCAACAAAGAGCCAACAATAAAC 59.250 41.667 0.00 0.00 0.00 2.01
3259 3323 4.871993 AATCATCATCTCAAACAGCGTC 57.128 40.909 0.00 0.00 0.00 5.19
3295 3359 7.396418 ACCAAAATCCAATCACTGCAAATATT 58.604 30.769 0.00 0.00 0.00 1.28
3349 3436 5.121811 CACTCAAGTCCTGCTAGCAATAAT 58.878 41.667 19.86 5.98 0.00 1.28
3355 3442 0.248843 AGCACTCAAGTCCTGCTAGC 59.751 55.000 8.10 8.10 33.70 3.42
3386 3473 7.366191 GGAGTTAATGGACATTTTCCCCTAGTA 60.366 40.741 2.53 0.00 45.17 1.82
3416 3503 4.484236 CTCGCAGCATTAAACCAATTTCA 58.516 39.130 0.00 0.00 0.00 2.69
3497 3584 0.108089 GAGGCCGGAGAGTTTCTTCC 60.108 60.000 5.05 0.00 0.00 3.46
3552 3639 0.627451 AGATCATCCCCAGCAAGCAA 59.373 50.000 0.00 0.00 0.00 3.91
4196 4287 8.094548 TCCAAGAATTCTCGTTTTCTATCTCAA 58.905 33.333 8.78 0.00 32.05 3.02
4201 4292 8.260818 TGATCTCCAAGAATTCTCGTTTTCTAT 58.739 33.333 8.78 0.00 32.05 1.98
4206 4297 7.391554 TCAATTGATCTCCAAGAATTCTCGTTT 59.608 33.333 8.78 0.00 38.31 3.60
4243 4334 7.330262 CCAAATATGTACTTTCCCTTTGCATT 58.670 34.615 0.00 0.00 0.00 3.56
4365 4456 5.402270 GGACAGTATGCAAATTGTTTGTCAC 59.598 40.000 14.18 1.34 42.53 3.67
4389 4480 9.517609 ACATATTAACAGAACTAAACTAGAGCG 57.482 33.333 0.00 0.00 0.00 5.03
4565 4656 2.535012 TGTAATTGACAGCACACCGA 57.465 45.000 0.00 0.00 32.86 4.69
4630 4721 3.873952 CCAAGATAGAAAGAAAGAGGGCG 59.126 47.826 0.00 0.00 0.00 6.13
4638 4729 8.314751 CAAACTACTCTCCCAAGATAGAAAGAA 58.685 37.037 0.00 0.00 0.00 2.52
4639 4730 7.455008 ACAAACTACTCTCCCAAGATAGAAAGA 59.545 37.037 0.00 0.00 0.00 2.52
4640 4731 7.616313 ACAAACTACTCTCCCAAGATAGAAAG 58.384 38.462 0.00 0.00 0.00 2.62
4641 4732 7.554959 ACAAACTACTCTCCCAAGATAGAAA 57.445 36.000 0.00 0.00 0.00 2.52
4642 4733 7.455008 AGAACAAACTACTCTCCCAAGATAGAA 59.545 37.037 0.00 0.00 0.00 2.10
4643 4734 6.954684 AGAACAAACTACTCTCCCAAGATAGA 59.045 38.462 0.00 0.00 0.00 1.98
4644 4735 7.176589 AGAACAAACTACTCTCCCAAGATAG 57.823 40.000 0.00 0.00 0.00 2.08
4645 4736 7.455008 AGAAGAACAAACTACTCTCCCAAGATA 59.545 37.037 0.00 0.00 0.00 1.98
4646 4737 6.271159 AGAAGAACAAACTACTCTCCCAAGAT 59.729 38.462 0.00 0.00 0.00 2.40
4647 4738 5.602978 AGAAGAACAAACTACTCTCCCAAGA 59.397 40.000 0.00 0.00 0.00 3.02
4648 4739 5.698545 CAGAAGAACAAACTACTCTCCCAAG 59.301 44.000 0.00 0.00 0.00 3.61
4649 4740 5.365605 TCAGAAGAACAAACTACTCTCCCAA 59.634 40.000 0.00 0.00 0.00 4.12
4650 4741 4.899457 TCAGAAGAACAAACTACTCTCCCA 59.101 41.667 0.00 0.00 0.00 4.37
4651 4742 5.231702 GTCAGAAGAACAAACTACTCTCCC 58.768 45.833 0.00 0.00 0.00 4.30
4652 4743 4.918583 CGTCAGAAGAACAAACTACTCTCC 59.081 45.833 0.00 0.00 0.00 3.71
4653 4744 4.918583 CCGTCAGAAGAACAAACTACTCTC 59.081 45.833 0.00 0.00 0.00 3.20
4654 4745 4.262079 CCCGTCAGAAGAACAAACTACTCT 60.262 45.833 0.00 0.00 0.00 3.24
4655 4746 3.988517 CCCGTCAGAAGAACAAACTACTC 59.011 47.826 0.00 0.00 0.00 2.59
4656 4747 3.244112 CCCCGTCAGAAGAACAAACTACT 60.244 47.826 0.00 0.00 0.00 2.57
4657 4748 3.064931 CCCCGTCAGAAGAACAAACTAC 58.935 50.000 0.00 0.00 0.00 2.73
4658 4749 2.701951 ACCCCGTCAGAAGAACAAACTA 59.298 45.455 0.00 0.00 0.00 2.24
4659 4750 1.489230 ACCCCGTCAGAAGAACAAACT 59.511 47.619 0.00 0.00 0.00 2.66
4660 4751 1.602377 CACCCCGTCAGAAGAACAAAC 59.398 52.381 0.00 0.00 0.00 2.93
4661 4752 1.210967 ACACCCCGTCAGAAGAACAAA 59.789 47.619 0.00 0.00 0.00 2.83
4662 4753 0.834612 ACACCCCGTCAGAAGAACAA 59.165 50.000 0.00 0.00 0.00 2.83
4663 4754 0.105964 CACACCCCGTCAGAAGAACA 59.894 55.000 0.00 0.00 0.00 3.18
4664 4755 1.228657 GCACACCCCGTCAGAAGAAC 61.229 60.000 0.00 0.00 0.00 3.01
4692 4785 3.741476 CGGTTGCCCAAGCTCAGC 61.741 66.667 8.36 0.00 40.80 4.26
4730 4823 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
4731 4824 0.250510 ACCACACACACACACACACA 60.251 50.000 0.00 0.00 0.00 3.72
4732 4825 1.663643 CTACCACACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
4773 4866 6.039270 GCCTTGTTGCATTACCAGACAATATA 59.961 38.462 0.00 0.00 30.73 0.86
4774 4867 5.163519 GCCTTGTTGCATTACCAGACAATAT 60.164 40.000 0.00 0.00 30.73 1.28
4941 5036 1.476074 CAACATCGGTGCAACAACAC 58.524 50.000 0.98 0.00 39.98 3.32
4944 5039 1.106351 AGCCAACATCGGTGCAACAA 61.106 50.000 0.98 0.00 39.98 2.83
4945 5040 1.106351 AAGCCAACATCGGTGCAACA 61.106 50.000 0.98 0.00 39.98 3.33
4946 5041 0.031994 AAAGCCAACATCGGTGCAAC 59.968 50.000 0.00 0.00 0.00 4.17
4953 5048 5.399301 CAGTTTTCTAACAAAGCCAACATCG 59.601 40.000 0.00 0.00 36.70 3.84
4959 5054 5.827797 AGACATCAGTTTTCTAACAAAGCCA 59.172 36.000 0.00 0.00 36.70 4.75
5045 5142 7.467811 CGATCCTAAAGAATGAAGAATTGGGTG 60.468 40.741 0.00 0.00 0.00 4.61
5062 5159 8.701895 ACCATGTAGAAGTAATTCGATCCTAAA 58.298 33.333 0.00 0.00 0.00 1.85
5086 5183 6.426937 TCATGTACTAGAAAGCAACAGAAACC 59.573 38.462 0.00 0.00 0.00 3.27
5102 5201 9.249053 AGTTCTCTGAAGAAGAATCATGTACTA 57.751 33.333 0.00 0.00 42.14 1.82
5103 5202 8.133024 AGTTCTCTGAAGAAGAATCATGTACT 57.867 34.615 0.00 0.00 42.14 2.73
5104 5203 8.770438 AAGTTCTCTGAAGAAGAATCATGTAC 57.230 34.615 0.00 0.00 42.14 2.90
5128 5227 7.416731 ACTCAGTACTTATAGGGGTCACTTAA 58.583 38.462 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.