Multiple sequence alignment - TraesCS2A01G281800

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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 TraesCS2A01G281800 chr2A 100.000 2969 0 0 1 2969 471002622 471005590 0.000000e+00 5483
1 TraesCS2A01G281800 chr2B 88.317 1806 90 33 1235 2969 419320577 419322332 0.000000e+00 2054
2 TraesCS2A01G281800 chr2B 88.136 767 44 25 511 1243 419319793 419320546 0.000000e+00 869
3 TraesCS2A01G281800 chr2B 94.299 421 17 3 78 497 419317718 419318132 3.230000e-179 638
4 TraesCS2A01G281800 chr2B 96.774 62 2 0 1 62 419317670 419317731 1.460000e-18 104
5 TraesCS2A01G281800 chr2D 87.314 1009 60 15 1235 2192 352903572 352904563 0.000000e+00 1092
6 TraesCS2A01G281800 chr2D 93.454 718 29 5 2254 2969 352904584 352905285 0.000000e+00 1050
7 TraesCS2A01G281800 chr2D 84.936 624 37 18 664 1243 352902931 352903541 1.980000e-161 579


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 TraesCS2A01G281800 chr2A 471002622 471005590 2968 False 5483.00 5483 100.0000 1 2969 1 chr2A.!!$F1 2968
1 TraesCS2A01G281800 chr2B 419317670 419322332 4662 False 916.25 2054 91.8815 1 2969 4 chr2B.!!$F1 2968
2 TraesCS2A01G281800 chr2D 352902931 352905285 2354 False 907.00 1092 88.5680 664 2969 3 chr2D.!!$F1 2305

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
801 2468 0.030101 CACGGTGAAATTGCGTGGTT 59.970 50.0 0.74 0.0 0.0 3.67 F
1346 3084 0.107654 GCTATGGGACGAGTTGCCTT 60.108 55.0 0.00 0.0 36.4 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 3424 0.455815 TGGATGACGATGAGGACGTG 59.544 55.0 0.0 0.0 43.97 4.49 R
2574 4384 1.442526 GCGCTTGATCCACCTCCATG 61.443 60.0 0.0 0.0 0.00 3.66 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
22 23 4.000988 AGTAGCTTGTGGTCGGTAATTTG 58.999 43.478 0.00 0.00 0.00 2.32
24 25 4.010667 AGCTTGTGGTCGGTAATTTGTA 57.989 40.909 0.00 0.00 0.00 2.41
49 50 3.691342 CTGCCGTCAGGTTCCCGA 61.691 66.667 0.00 0.00 40.50 5.14
50 51 3.649277 CTGCCGTCAGGTTCCCGAG 62.649 68.421 0.00 0.00 40.50 4.63
52 53 3.691342 CCGTCAGGTTCCCGAGCA 61.691 66.667 0.00 0.00 0.00 4.26
53 54 2.432628 CGTCAGGTTCCCGAGCAC 60.433 66.667 0.00 0.00 0.00 4.40
54 55 2.047179 GTCAGGTTCCCGAGCACC 60.047 66.667 0.00 0.00 0.00 5.01
55 56 2.203788 TCAGGTTCCCGAGCACCT 60.204 61.111 0.00 0.00 44.88 4.00
56 57 2.266055 CAGGTTCCCGAGCACCTC 59.734 66.667 0.00 0.00 41.86 3.85
57 58 2.120718 AGGTTCCCGAGCACCTCT 59.879 61.111 0.00 0.00 39.37 3.69
58 59 2.266055 GGTTCCCGAGCACCTCTG 59.734 66.667 0.00 0.00 0.00 3.35
59 60 2.584391 GGTTCCCGAGCACCTCTGT 61.584 63.158 0.00 0.00 0.00 3.41
60 61 1.371558 GTTCCCGAGCACCTCTGTT 59.628 57.895 0.00 0.00 0.00 3.16
61 62 0.250338 GTTCCCGAGCACCTCTGTTT 60.250 55.000 0.00 0.00 0.00 2.83
62 63 0.472471 TTCCCGAGCACCTCTGTTTT 59.528 50.000 0.00 0.00 0.00 2.43
63 64 0.472471 TCCCGAGCACCTCTGTTTTT 59.528 50.000 0.00 0.00 0.00 1.94
106 107 6.267928 ACCTCTGTTTCTGCTCTAACTAAAGA 59.732 38.462 0.00 0.00 0.00 2.52
214 215 8.442632 CTTATGAAGCACATTCTCCTTGATTA 57.557 34.615 2.03 0.00 40.07 1.75
223 224 7.912250 GCACATTCTCCTTGATTATACAAAGTG 59.088 37.037 0.00 0.00 0.00 3.16
238 239 3.558418 ACAAAGTGTTTCTCGCGTATGTT 59.442 39.130 5.77 0.00 0.00 2.71
298 299 0.482446 TGGGGTTTCACCTGCTGAAT 59.518 50.000 0.00 0.00 38.74 2.57
303 304 2.827921 GGTTTCACCTGCTGAATCCAAT 59.172 45.455 8.63 0.00 43.98 3.16
314 315 6.271488 TGCTGAATCCAATTCTAACCAAAG 57.729 37.500 1.76 0.00 39.96 2.77
334 335 1.344763 GTACAGGCACAGAGACCAAGT 59.655 52.381 0.00 0.00 0.00 3.16
366 367 5.701750 TGCATGCAACAATTTTAATGAAGCT 59.298 32.000 20.30 0.00 0.00 3.74
367 368 6.872547 TGCATGCAACAATTTTAATGAAGCTA 59.127 30.769 20.30 0.00 0.00 3.32
373 374 9.584839 GCAACAATTTTAATGAAGCTACTTTTG 57.415 29.630 0.00 0.00 0.00 2.44
408 409 0.036875 AACGAAGAAGAAGCAGGGGG 59.963 55.000 0.00 0.00 0.00 5.40
429 431 0.921347 CGAAAGGTAATCCAGCGTCG 59.079 55.000 0.00 0.00 35.89 5.12
443 445 2.594654 CAGCGTCGTTTAGCTACAGAAG 59.405 50.000 0.00 0.00 42.52 2.85
445 447 3.128938 AGCGTCGTTTAGCTACAGAAGAT 59.871 43.478 0.00 0.00 42.60 2.40
446 448 4.334759 AGCGTCGTTTAGCTACAGAAGATA 59.665 41.667 0.00 0.00 42.60 1.98
447 449 4.671516 GCGTCGTTTAGCTACAGAAGATAG 59.328 45.833 0.00 0.00 0.00 2.08
448 450 5.206299 CGTCGTTTAGCTACAGAAGATAGG 58.794 45.833 0.00 0.00 0.00 2.57
449 451 5.521544 GTCGTTTAGCTACAGAAGATAGGG 58.478 45.833 0.00 0.00 0.00 3.53
501 511 3.370672 CAGTTCAAACAAACAAACAGCCC 59.629 43.478 0.00 0.00 0.00 5.19
539 2188 2.101415 ACAAGCTCACAAAGAAAAGCCC 59.899 45.455 0.00 0.00 35.32 5.19
540 2189 2.071778 AGCTCACAAAGAAAAGCCCA 57.928 45.000 0.00 0.00 35.32 5.36
541 2190 1.959282 AGCTCACAAAGAAAAGCCCAG 59.041 47.619 0.00 0.00 35.32 4.45
545 2194 2.693074 TCACAAAGAAAAGCCCAGAACC 59.307 45.455 0.00 0.00 0.00 3.62
576 2225 2.539081 GGGGGAGCTTGAACCCACT 61.539 63.158 10.25 0.00 45.53 4.00
582 2231 0.109342 AGCTTGAACCCACTGACCAG 59.891 55.000 0.00 0.00 0.00 4.00
623 2272 7.399523 CAAATTAGCAATAGGTTACGTCAGTC 58.600 38.462 0.00 0.00 0.00 3.51
631 2280 0.973423 GTTACGTCAGTCGCGAAGTC 59.027 55.000 12.06 3.50 44.19 3.01
657 2307 1.548719 CGACCAAGTCCCAGACATACA 59.451 52.381 0.00 0.00 34.60 2.29
662 2312 4.827284 ACCAAGTCCCAGACATACAAAAAG 59.173 41.667 0.00 0.00 34.60 2.27
664 2314 5.534654 CCAAGTCCCAGACATACAAAAAGAA 59.465 40.000 0.00 0.00 34.60 2.52
665 2315 6.040391 CCAAGTCCCAGACATACAAAAAGAAA 59.960 38.462 0.00 0.00 34.60 2.52
734 2384 5.661458 TCAACGGAGAGTTAATTGAGGATC 58.339 41.667 0.00 0.00 42.02 3.36
753 2409 1.060713 CACGGTGTGATCTTGACGTC 58.939 55.000 9.11 9.11 35.23 4.34
758 2414 2.408704 GGTGTGATCTTGACGTCTTTCG 59.591 50.000 17.92 2.53 46.00 3.46
801 2468 0.030101 CACGGTGAAATTGCGTGGTT 59.970 50.000 0.74 0.00 0.00 3.67
823 2490 1.827399 TTTCCGAGTGGGTCTCAGCC 61.827 60.000 0.00 0.00 42.88 4.85
831 2498 0.108585 TGGGTCTCAGCCAAGTTGTC 59.891 55.000 1.45 0.00 43.74 3.18
863 2537 1.538204 GCAGGACTCGTTTCTGACACA 60.538 52.381 0.00 0.00 0.00 3.72
936 2625 3.170362 CCTTGGCCCTTGTCCTCA 58.830 61.111 0.00 0.00 0.00 3.86
947 2636 4.570663 GTCCTCATCGTCGGCCGG 62.571 72.222 27.83 10.69 37.11 6.13
965 2654 3.414700 CCGTCAAGCTCGTGTGCC 61.415 66.667 0.00 0.00 0.00 5.01
1002 2701 3.303725 CGTTGGGCCATAATAACGTCATG 60.304 47.826 17.31 0.00 40.50 3.07
1030 2729 0.533755 CATCCTGGAACCAGCCGATC 60.534 60.000 14.66 0.00 42.35 3.69
1033 2732 3.406595 CTGGAACCAGCCGATCCCC 62.407 68.421 7.95 0.00 37.24 4.81
1045 2744 1.745489 GATCCCCTGCGTGTGGAAC 60.745 63.158 0.00 0.00 37.35 3.62
1135 2834 2.045634 GCAGCCAGGTGATGCTCA 60.046 61.111 0.04 0.00 35.12 4.26
1136 2835 2.404995 GCAGCCAGGTGATGCTCAC 61.405 63.158 0.04 7.52 46.23 3.51
1295 3033 7.099764 AGGAATGTTAGATCTGTACACACTTG 58.900 38.462 5.18 0.00 0.00 3.16
1305 3043 2.962697 TACACACTTGCGCGCACTCA 62.963 55.000 36.72 19.56 0.00 3.41
1346 3084 0.107654 GCTATGGGACGAGTTGCCTT 60.108 55.000 0.00 0.00 36.40 4.35
1353 3091 2.664851 CGAGTTGCCTTGCCGTCA 60.665 61.111 0.00 0.00 0.00 4.35
1384 3149 1.227205 GGTGATGCGGCTGAGAGAG 60.227 63.158 0.00 0.00 0.00 3.20
1404 3169 3.490759 GATGCTCGTGTGGGCGTG 61.491 66.667 0.00 0.00 0.00 5.34
1419 3184 2.350514 GTGGCTGAGGCTGCTTCT 59.649 61.111 13.13 0.00 38.73 2.85
1425 3193 4.087892 GAGGCTGCTTCTGCGGGA 62.088 66.667 4.32 0.00 45.30 5.14
1444 3212 5.220989 GCGGGAAAAGATATCAGGGTTTTAC 60.221 44.000 5.32 3.80 0.00 2.01
1508 3297 0.600255 GACAACACGGTCAGTCTGGG 60.600 60.000 0.00 0.00 37.73 4.45
1574 3363 5.697067 AGAAACGGATCTACACTCTCCTAT 58.303 41.667 0.00 0.00 0.00 2.57
1583 3372 5.590818 TCTACACTCTCCTATGGTTCCTTT 58.409 41.667 0.00 0.00 0.00 3.11
1610 3399 1.078759 CACATCTCTTCGTCGGCACC 61.079 60.000 0.00 0.00 0.00 5.01
1629 3418 2.247437 GCAGGACAATCCGATCGGC 61.247 63.158 29.62 14.55 42.75 5.54
1635 3424 1.005630 CAATCCGATCGGCTCCTCC 60.006 63.158 29.62 0.00 34.68 4.30
1659 3448 1.114627 CCTCATCGTCATCCACCTCA 58.885 55.000 0.00 0.00 0.00 3.86
1684 3473 4.072088 GCGACACAAACGGCGAGG 62.072 66.667 16.62 4.60 0.00 4.63
1696 3485 2.264124 GGCGAGGGCGATATCTACA 58.736 57.895 0.34 0.00 41.24 2.74
1774 3563 0.757188 CAGGTATCTCGGGCAGGAGT 60.757 60.000 4.96 0.00 35.52 3.85
1855 3644 1.107114 GAGATTCTCCCTGCGTCTCA 58.893 55.000 1.97 0.00 36.28 3.27
1956 3751 1.948635 GCACCGCAATGCAAAACGT 60.949 52.632 5.91 0.00 45.39 3.99
2006 3801 3.988517 GGATTACTGGTATGCGTTAGCTC 59.011 47.826 0.00 0.00 45.42 4.09
2011 3806 3.181485 ACTGGTATGCGTTAGCTCTTCTC 60.181 47.826 0.00 0.00 45.42 2.87
2031 3826 2.158623 TCTTCTTGGCCAAAAGCAGAGA 60.159 45.455 20.91 8.40 46.50 3.10
2037 3832 1.538047 GCCAAAAGCAGAGACATCCA 58.462 50.000 0.00 0.00 42.97 3.41
2064 3859 1.822506 AACTAGCGAGCCCTTTTTCC 58.177 50.000 0.00 0.00 0.00 3.13
2095 3898 5.152804 GTGAGCTTGATTCTGCTTTTCTTC 58.847 41.667 6.28 0.00 39.91 2.87
2096 3899 5.048852 GTGAGCTTGATTCTGCTTTTCTTCT 60.049 40.000 6.28 0.00 39.91 2.85
2097 3900 5.533903 TGAGCTTGATTCTGCTTTTCTTCTT 59.466 36.000 6.28 0.00 39.91 2.52
2101 3904 6.750963 GCTTGATTCTGCTTTTCTTCTTATGG 59.249 38.462 0.00 0.00 0.00 2.74
2131 3934 5.403166 TGAACTGTATGTTAGTACGTGTTGC 59.597 40.000 0.00 0.00 39.30 4.17
2152 3955 3.474600 CGTTCTACTCTCGGGGATTAGA 58.525 50.000 1.14 1.14 35.38 2.10
2251 4054 2.584791 GTGTTACATTTCGGCTTGCTG 58.415 47.619 0.00 0.00 0.00 4.41
2380 4188 8.975439 CATAATGATTAAAGTACCACGTAGGAC 58.025 37.037 10.46 0.00 41.22 3.85
2482 4292 1.518903 GCATGGGCCTCCGATTAAGC 61.519 60.000 4.53 0.00 35.24 3.09
2540 4350 4.155826 GGCGCCATTGCATACTTATGAATA 59.844 41.667 24.80 0.00 37.32 1.75
2562 4372 5.520748 AAATAAATCACTGGACTGGAGGT 57.479 39.130 0.00 0.00 0.00 3.85
2574 4384 2.103941 GACTGGAGGTGGATCTGATTCC 59.896 54.545 0.00 0.00 36.24 3.01
2625 4435 2.732412 TCTCGCAGAACCTCTTGAAG 57.268 50.000 0.00 0.00 34.09 3.02
2737 4547 2.787866 CCTCCCCCTCCTTCTCCA 59.212 66.667 0.00 0.00 0.00 3.86
2793 4603 2.081212 GTTCACCAGCTCGTCGTCG 61.081 63.158 0.00 0.00 38.55 5.12
2808 4618 1.864862 GTCGTCGTCGTCTTCCTCA 59.135 57.895 1.33 0.00 38.33 3.86
2861 4671 0.185901 CTCTCCTCCTCCTCCTCCTG 59.814 65.000 0.00 0.00 0.00 3.86
2862 4672 1.457455 CTCCTCCTCCTCCTCCTGC 60.457 68.421 0.00 0.00 0.00 4.85
2863 4673 1.938596 TCCTCCTCCTCCTCCTGCT 60.939 63.158 0.00 0.00 0.00 4.24
2864 4674 1.457455 CCTCCTCCTCCTCCTGCTC 60.457 68.421 0.00 0.00 0.00 4.26
2865 4675 1.309347 CTCCTCCTCCTCCTGCTCA 59.691 63.158 0.00 0.00 0.00 4.26
2866 4676 0.105555 CTCCTCCTCCTCCTGCTCAT 60.106 60.000 0.00 0.00 0.00 2.90
2867 4677 0.105760 TCCTCCTCCTCCTGCTCATC 60.106 60.000 0.00 0.00 0.00 2.92
2868 4678 1.462731 CCTCCTCCTCCTGCTCATCG 61.463 65.000 0.00 0.00 0.00 3.84
2869 4679 1.456518 TCCTCCTCCTGCTCATCGG 60.457 63.158 0.00 0.00 0.00 4.18
2934 4744 0.108186 TGTAGAGCACGATGGCCTTG 60.108 55.000 3.32 0.00 0.00 3.61
2938 4748 1.926511 GAGCACGATGGCCTTGTTGG 61.927 60.000 3.32 0.00 39.35 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.017559 CTGACGGCAGCTACCCCTAC 62.018 65.000 4.70 0.00 34.95 3.18
24 25 3.077556 CTGACGGCAGCTACCCCT 61.078 66.667 4.70 0.00 34.95 4.79
64 65 0.885196 GGTGCTCATACCCGCAAAAA 59.115 50.000 0.00 0.00 37.97 1.94
65 66 0.037590 AGGTGCTCATACCCGCAAAA 59.962 50.000 0.00 0.00 41.83 2.44
66 67 0.392461 GAGGTGCTCATACCCGCAAA 60.392 55.000 0.00 0.00 41.83 3.68
67 68 1.220749 GAGGTGCTCATACCCGCAA 59.779 57.895 0.00 0.00 41.83 4.85
68 69 1.685765 AGAGGTGCTCATACCCGCA 60.686 57.895 0.00 0.00 41.83 5.69
69 70 1.227380 CAGAGGTGCTCATACCCGC 60.227 63.158 0.00 0.00 41.83 6.13
70 71 0.537188 AACAGAGGTGCTCATACCCG 59.463 55.000 0.00 0.00 41.83 5.28
71 72 2.237392 AGAAACAGAGGTGCTCATACCC 59.763 50.000 0.00 0.00 41.83 3.69
72 73 3.265791 CAGAAACAGAGGTGCTCATACC 58.734 50.000 0.00 0.00 41.17 2.73
73 74 2.675348 GCAGAAACAGAGGTGCTCATAC 59.325 50.000 0.00 0.00 32.06 2.39
74 75 2.568956 AGCAGAAACAGAGGTGCTCATA 59.431 45.455 0.00 0.00 42.67 2.15
75 76 1.350351 AGCAGAAACAGAGGTGCTCAT 59.650 47.619 0.00 0.00 42.67 2.90
76 77 0.761187 AGCAGAAACAGAGGTGCTCA 59.239 50.000 0.00 0.00 42.67 4.26
106 107 4.096081 GCTATGAAAACAATCAGCTCTGCT 59.904 41.667 0.00 0.00 40.77 4.24
151 152 5.852827 TCAGATCTGAACATACACACACAA 58.147 37.500 23.17 0.00 36.53 3.33
152 153 5.467035 TCAGATCTGAACATACACACACA 57.533 39.130 23.17 0.00 36.53 3.72
153 154 6.974932 AATCAGATCTGAACATACACACAC 57.025 37.500 28.40 0.00 43.58 3.82
154 155 7.445096 ACAAAATCAGATCTGAACATACACACA 59.555 33.333 28.40 2.08 43.58 3.72
209 210 5.636121 ACGCGAGAAACACTTTGTATAATCA 59.364 36.000 15.93 0.00 0.00 2.57
214 215 4.927425 ACATACGCGAGAAACACTTTGTAT 59.073 37.500 15.93 0.00 0.00 2.29
223 224 3.060138 TGTTGTCAACATACGCGAGAAAC 60.060 43.478 15.93 4.58 36.25 2.78
238 239 4.575180 TGCTGGTGCATGTTGTCA 57.425 50.000 0.00 0.00 45.31 3.58
298 299 5.007682 GCCTGTACTTTGGTTAGAATTGGA 58.992 41.667 0.00 0.00 0.00 3.53
303 304 4.101898 TCTGTGCCTGTACTTTGGTTAGAA 59.898 41.667 0.00 0.00 0.00 2.10
314 315 1.344763 ACTTGGTCTCTGTGCCTGTAC 59.655 52.381 0.00 0.00 0.00 2.90
334 335 0.177373 TTGTTGCATGCACAAGCCAA 59.823 45.000 22.58 14.72 41.13 4.52
366 367 9.337091 CGTTTCTTCTTCTTTTTGTCAAAAGTA 57.663 29.630 10.50 1.34 46.35 2.24
367 368 8.079809 TCGTTTCTTCTTCTTTTTGTCAAAAGT 58.920 29.630 10.50 0.00 46.35 2.66
373 374 8.175716 TCTTCTTCGTTTCTTCTTCTTTTTGTC 58.824 33.333 0.00 0.00 0.00 3.18
408 409 0.743345 ACGCTGGATTACCTTTCGCC 60.743 55.000 0.00 0.00 37.04 5.54
409 410 0.651031 GACGCTGGATTACCTTTCGC 59.349 55.000 0.00 0.00 37.04 4.70
420 422 0.883153 TGTAGCTAAACGACGCTGGA 59.117 50.000 0.00 0.00 37.05 3.86
429 431 8.563123 AAAAACCCTATCTTCTGTAGCTAAAC 57.437 34.615 0.00 0.00 0.00 2.01
443 445 5.016831 ACCCAGACAATGAAAAACCCTATC 58.983 41.667 0.00 0.00 0.00 2.08
445 447 4.148838 CACCCAGACAATGAAAAACCCTA 58.851 43.478 0.00 0.00 0.00 3.53
446 448 2.965147 CACCCAGACAATGAAAAACCCT 59.035 45.455 0.00 0.00 0.00 4.34
447 449 2.698274 ACACCCAGACAATGAAAAACCC 59.302 45.455 0.00 0.00 0.00 4.11
448 450 3.492482 CCACACCCAGACAATGAAAAACC 60.492 47.826 0.00 0.00 0.00 3.27
449 451 3.132111 ACCACACCCAGACAATGAAAAAC 59.868 43.478 0.00 0.00 0.00 2.43
514 524 5.122239 GGCTTTTCTTTGTGAGCTTGTTTTT 59.878 36.000 0.00 0.00 35.53 1.94
523 2172 3.243535 GGTTCTGGGCTTTTCTTTGTGAG 60.244 47.826 0.00 0.00 0.00 3.51
539 2188 2.034124 CCATTATGGGCTTGGGTTCTG 58.966 52.381 2.72 0.00 32.67 3.02
540 2189 2.459555 CCATTATGGGCTTGGGTTCT 57.540 50.000 2.72 0.00 32.67 3.01
564 2213 0.890996 CCTGGTCAGTGGGTTCAAGC 60.891 60.000 0.00 0.00 0.00 4.01
576 2225 0.821711 CCGTTTTGCTTCCCTGGTCA 60.822 55.000 0.00 0.00 0.00 4.02
582 2231 2.034048 TTTGGCCCGTTTTGCTTCCC 62.034 55.000 0.00 0.00 0.00 3.97
623 2272 1.512310 GGTCGACTGAGACTTCGCG 60.512 63.158 16.46 0.00 40.76 5.87
631 2280 0.244994 CTGGGACTTGGTCGACTGAG 59.755 60.000 16.46 15.22 32.65 3.35
699 2349 4.002982 CTCTCCGTTGATGTGATTTCCAA 58.997 43.478 0.00 0.00 0.00 3.53
700 2350 3.007940 ACTCTCCGTTGATGTGATTTCCA 59.992 43.478 0.00 0.00 0.00 3.53
701 2351 3.600388 ACTCTCCGTTGATGTGATTTCC 58.400 45.455 0.00 0.00 0.00 3.13
734 2384 1.060713 GACGTCAAGATCACACCGTG 58.939 55.000 11.55 0.00 34.45 4.94
823 2490 0.993251 TCGCGTACGTCGACAACTTG 60.993 55.000 23.88 7.96 42.86 3.16
831 2498 4.156622 TCCTGCTCGCGTACGTCG 62.157 66.667 17.90 19.60 41.18 5.12
854 2521 4.946772 TGTTCCAGTTTCATTGTGTCAGAA 59.053 37.500 0.00 0.00 0.00 3.02
855 2522 4.335315 GTGTTCCAGTTTCATTGTGTCAGA 59.665 41.667 0.00 0.00 0.00 3.27
947 2636 4.077188 GCACACGAGCTTGACGGC 62.077 66.667 8.31 3.88 34.93 5.68
948 2637 3.414700 GGCACACGAGCTTGACGG 61.415 66.667 8.31 0.00 34.93 4.79
997 2696 2.163010 CCAGGATGTGCTTCAACATGAC 59.837 50.000 0.00 0.00 40.87 3.06
1002 2701 1.541588 GGTTCCAGGATGTGCTTCAAC 59.458 52.381 0.00 0.00 0.00 3.18
1030 2729 2.203280 TTGTTCCACACGCAGGGG 60.203 61.111 0.00 0.00 0.00 4.79
1033 2732 0.583438 CTGACTTGTTCCACACGCAG 59.417 55.000 0.00 0.00 0.00 5.18
1045 2744 3.123620 GAGGGCGCTGCTGACTTG 61.124 66.667 8.56 0.00 0.00 3.16
1219 2918 1.066858 GTCCGATCCGATATGTGCCAT 60.067 52.381 0.00 0.00 0.00 4.40
1220 2919 0.317160 GTCCGATCCGATATGTGCCA 59.683 55.000 0.00 0.00 0.00 4.92
1305 3043 1.630878 ACTTCTCCCCTTTCAAGCGAT 59.369 47.619 0.00 0.00 0.00 4.58
1311 3049 2.038863 TAGCCACTTCTCCCCTTTCA 57.961 50.000 0.00 0.00 0.00 2.69
1362 3100 4.794439 TCAGCCGCATCACCGACG 62.794 66.667 0.00 0.00 0.00 5.12
1373 3111 1.108727 AGCATCCTCTCTCTCAGCCG 61.109 60.000 0.00 0.00 0.00 5.52
1384 3149 2.512515 GCCCACACGAGCATCCTC 60.513 66.667 0.00 0.00 34.66 3.71
1404 3169 3.132801 GCAGAAGCAGCCTCAGCC 61.133 66.667 0.00 0.00 41.25 4.85
1419 3184 1.843851 ACCCTGATATCTTTTCCCGCA 59.156 47.619 3.98 0.00 0.00 5.69
1508 3297 1.217244 CTTGCCCCTGCTTTGATGC 59.783 57.895 0.00 0.00 38.71 3.91
1583 3372 1.697432 ACGAAGAGATGTGTTCCCCAA 59.303 47.619 0.00 0.00 0.00 4.12
1610 3399 1.951130 CCGATCGGATTGTCCTGCG 60.951 63.158 30.62 0.00 37.50 5.18
1629 3418 1.032657 ACGATGAGGACGTGGAGGAG 61.033 60.000 0.00 0.00 42.37 3.69
1635 3424 0.455815 TGGATGACGATGAGGACGTG 59.544 55.000 0.00 0.00 43.97 4.49
1684 3473 5.646577 ACTCCTATGTTGTAGATATCGCC 57.353 43.478 0.00 0.00 0.00 5.54
1690 3479 3.741388 GCCGCAACTCCTATGTTGTAGAT 60.741 47.826 8.78 0.00 46.33 1.98
1696 3485 1.026718 GCTGCCGCAACTCCTATGTT 61.027 55.000 0.00 0.00 35.78 2.71
1774 3563 1.213296 GGCCTCTGTTCCCTATTGGA 58.787 55.000 0.00 0.00 43.18 3.53
1855 3644 2.270205 CATTGCCTCCTGCTCGGT 59.730 61.111 0.00 0.00 42.00 4.69
1887 3676 3.068691 TCCTTGGCGAGGGAGACG 61.069 66.667 20.82 0.00 46.31 4.18
1891 3680 1.198094 TTGATGTCCTTGGCGAGGGA 61.198 55.000 20.82 8.33 46.31 4.20
1906 3695 0.909610 TCGGCCTCCTCCAACTTGAT 60.910 55.000 0.00 0.00 0.00 2.57
1940 3735 1.369930 CGACGTTTTGCATTGCGGT 60.370 52.632 3.84 0.00 0.00 5.68
1956 3751 1.642215 GATCAGCTAGCGTCGTCGA 59.358 57.895 9.55 0.00 39.71 4.20
1964 3759 1.131504 CGTAGGATCGGATCAGCTAGC 59.868 57.143 18.99 6.62 0.00 3.42
2006 3801 2.624838 TGCTTTTGGCCAAGAAGAGAAG 59.375 45.455 29.20 23.99 40.92 2.85
2011 3806 2.030451 GTCTCTGCTTTTGGCCAAGAAG 60.030 50.000 24.46 24.46 40.92 2.85
2031 3826 5.290493 TCGCTAGTTTTATGGATGGATGT 57.710 39.130 0.00 0.00 0.00 3.06
2037 3832 2.706190 AGGGCTCGCTAGTTTTATGGAT 59.294 45.455 0.00 0.00 0.00 3.41
2064 3859 4.672024 GCAGAATCAAGCTCACATGACAAG 60.672 45.833 0.00 0.00 0.00 3.16
2095 3898 4.637534 ACATACAGTTCAAGCAGCCATAAG 59.362 41.667 0.00 0.00 0.00 1.73
2096 3899 4.588899 ACATACAGTTCAAGCAGCCATAA 58.411 39.130 0.00 0.00 0.00 1.90
2097 3900 4.220693 ACATACAGTTCAAGCAGCCATA 57.779 40.909 0.00 0.00 0.00 2.74
2101 3904 5.220228 CGTACTAACATACAGTTCAAGCAGC 60.220 44.000 0.00 0.00 41.64 5.25
2131 3934 3.474600 TCTAATCCCCGAGAGTAGAACG 58.525 50.000 9.28 0.00 46.38 3.95
2136 3939 6.839657 AGATTTTCTTCTAATCCCCGAGAGTA 59.160 38.462 0.00 0.00 33.45 2.59
2251 4054 9.922305 GAAGCAAATAAATAGACGGCATATATC 57.078 33.333 0.00 0.00 0.00 1.63
2355 4163 8.921205 AGTCCTACGTGGTACTTTAATCATTAT 58.079 33.333 0.00 0.00 37.07 1.28
2380 4188 1.694696 GGGGATGCCAAGGTCTACTAG 59.305 57.143 5.30 0.00 0.00 2.57
2437 4245 4.773323 AAAGAAGGAAAAGATGAAGCCG 57.227 40.909 0.00 0.00 0.00 5.52
2482 4292 7.227512 CACTCCTTAAGCCAGGATTATGTTTAG 59.772 40.741 0.00 1.55 42.42 1.85
2540 4350 5.256474 CACCTCCAGTCCAGTGATTTATTT 58.744 41.667 0.00 0.00 31.79 1.40
2574 4384 1.442526 GCGCTTGATCCACCTCCATG 61.443 60.000 0.00 0.00 0.00 3.66
2576 4386 2.244117 GAGCGCTTGATCCACCTCCA 62.244 60.000 13.26 0.00 0.00 3.86
2625 4435 4.492955 CTGCAGAAGCTCGAGTCC 57.507 61.111 15.13 3.57 42.74 3.85
2750 4560 2.388232 GGGTCGGTGATTGACGTGC 61.388 63.158 0.00 0.00 37.22 5.34
2793 4603 4.436653 CGTGAGGAAGACGACGAC 57.563 61.111 0.00 0.00 39.21 4.34
2808 4618 4.280494 ACGCACTCGCTGTTCCGT 62.280 61.111 0.00 0.00 39.84 4.69
2877 4687 4.838486 GAGCGCGACGTGGAGGAG 62.838 72.222 12.10 0.00 0.00 3.69
2934 4744 4.072088 CAAGACGACGGCGCCAAC 62.072 66.667 28.98 18.23 42.48 3.77
2938 4748 4.072088 CCAACAAGACGACGGCGC 62.072 66.667 12.58 3.05 42.48 6.53


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

AutoCloner maintained by Alex Coulton.