Multiple sequence alignment - TraesCS2B01G316600

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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 TraesCS2B01G316600 chr2B 100.000 3647 0 0 1 3647 451889275 451892921 0.000000e+00 6735.0
1 TraesCS2B01G316600 chr2B 94.286 35 2 0 2704 2738 162542173 162542139 2.000000e-03 54.7
2 TraesCS2B01G316600 chr2A 89.823 2771 154 57 1 2699 516023480 516026194 0.000000e+00 3437.0
3 TraesCS2B01G316600 chr2A 90.793 782 59 4 2866 3645 516026752 516027522 0.000000e+00 1033.0
4 TraesCS2B01G316600 chr2A 90.476 105 8 2 2691 2793 516026379 516026483 1.770000e-28 137.0
5 TraesCS2B01G316600 chr2D 93.754 1473 65 13 1733 3198 380577853 380579305 0.000000e+00 2185.0
6 TraesCS2B01G316600 chr2D 90.102 879 49 24 405 1249 380576474 380577348 0.000000e+00 1107.0
7 TraesCS2B01G316600 chr2D 90.657 396 26 8 1320 1710 380577392 380577781 1.940000e-142 516.0
8 TraesCS2B01G316600 chr2D 83.455 411 34 6 1 394 380575898 380576291 5.790000e-93 351.0
9 TraesCS2B01G316600 chr2D 88.612 281 29 2 3179 3457 380579644 380579923 4.510000e-89 339.0
10 TraesCS2B01G316600 chr2D 80.000 170 23 6 97 265 436066291 436066450 8.280000e-22 115.0
11 TraesCS2B01G316600 chr4A 86.763 1171 100 23 1527 2661 35151509 35152660 0.000000e+00 1253.0
12 TraesCS2B01G316600 chr4D 86.729 1168 103 23 1527 2663 433699906 433701052 0.000000e+00 1251.0
13 TraesCS2B01G316600 chr4D 94.574 129 7 0 1366 1494 433699694 433699822 2.220000e-47 200.0
14 TraesCS2B01G316600 chr4B 85.824 1171 108 26 1527 2661 532255836 532256984 0.000000e+00 1190.0
15 TraesCS2B01G316600 chr1D 80.928 194 33 4 99 289 4989512 4989320 2.270000e-32 150.0
16 TraesCS2B01G316600 chr1A 79.412 204 39 3 99 300 4688902 4689104 1.370000e-29 141.0
17 TraesCS2B01G316600 chrUn 96.970 33 0 1 2514 2546 241922805 241922836 2.000000e-03 54.7
18 TraesCS2B01G316600 chr7B 96.970 33 0 1 2514 2546 654493528 654493497 2.000000e-03 54.7
19 TraesCS2B01G316600 chr7B 96.970 33 0 1 2514 2546 654507667 654507636 2.000000e-03 54.7
20 TraesCS2B01G316600 chr7B 96.970 33 0 1 2514 2546 654697193 654697162 2.000000e-03 54.7


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 TraesCS2B01G316600 chr2B 451889275 451892921 3646 False 6735.000000 6735 100.0000 1 3647 1 chr2B.!!$F1 3646
1 TraesCS2B01G316600 chr2A 516023480 516027522 4042 False 1535.666667 3437 90.3640 1 3645 3 chr2A.!!$F1 3644
2 TraesCS2B01G316600 chr2D 380575898 380579923 4025 False 899.600000 2185 89.3160 1 3457 5 chr2D.!!$F2 3456
3 TraesCS2B01G316600 chr4A 35151509 35152660 1151 False 1253.000000 1253 86.7630 1527 2661 1 chr4A.!!$F1 1134
4 TraesCS2B01G316600 chr4D 433699694 433701052 1358 False 725.500000 1251 90.6515 1366 2663 2 chr4D.!!$F1 1297
5 TraesCS2B01G316600 chr4B 532255836 532256984 1148 False 1190.000000 1190 85.8240 1527 2661 1 chr4B.!!$F1 1134

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
851 1082 0.248458 GGTGTTGTTGTTGCAGGACG 60.248 55.0 0.0 0.0 0.0 4.79 F
1642 1975 0.537188 AATCCACCTTCATCGTCGCT 59.463 50.0 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2842 0.109643 CACCACCATGCATGTTGTCG 60.110 55.0 24.58 11.79 0.0 4.35 R
3306 4500 0.033920 TGATTGCTGCGACACACTCT 59.966 50.0 0.00 0.00 0.0 3.24 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
54 55 6.701841 ACATACACAAGATGATAATCGTGGTC 59.298 38.462 10.37 0.00 34.97 4.02
65 66 1.379916 TCGTGGTCGAGAGGGGTAA 59.620 57.895 0.00 0.00 41.35 2.85
126 143 4.810491 ACACAAACCACATTCAAGCATTTC 59.190 37.500 0.00 0.00 0.00 2.17
174 192 4.452825 CAGAGCTCCAATGATCAACTGAT 58.547 43.478 10.93 0.00 37.51 2.90
175 193 4.273724 CAGAGCTCCAATGATCAACTGATG 59.726 45.833 10.93 0.00 34.37 3.07
377 395 9.255304 GCATAGTAGATAGAAGAAAACAGAAGG 57.745 37.037 0.00 0.00 0.00 3.46
378 396 9.255304 CATAGTAGATAGAAGAAAACAGAAGGC 57.745 37.037 0.00 0.00 0.00 4.35
381 399 8.379331 AGTAGATAGAAGAAAACAGAAGGCTTT 58.621 33.333 0.00 0.00 0.00 3.51
415 605 1.935873 CCACATTATGGCGAGTCTGTG 59.064 52.381 0.00 0.64 43.24 3.66
420 610 3.394674 TTATGGCGAGTCTGTGTTTGA 57.605 42.857 0.00 0.00 0.00 2.69
427 617 4.740695 GGCGAGTCTGTGTTTGAGTATATC 59.259 45.833 0.00 0.00 0.00 1.63
449 645 5.954757 TCCCCTTGTAACCTTCAAAACATA 58.045 37.500 0.00 0.00 0.00 2.29
451 647 6.492087 TCCCCTTGTAACCTTCAAAACATAAG 59.508 38.462 0.00 0.00 0.00 1.73
452 648 6.156519 CCCTTGTAACCTTCAAAACATAAGC 58.843 40.000 0.00 0.00 0.00 3.09
479 680 5.801531 TCATATACGTTATGGAGGTTGCT 57.198 39.130 13.93 0.00 0.00 3.91
493 694 5.546110 TGGAGGTTGCTTATATGGCATAGTA 59.454 40.000 13.39 0.00 39.54 1.82
546 747 1.760029 TGCGTATATGGCAGAGTTCCA 59.240 47.619 0.00 0.00 35.04 3.53
559 760 4.919754 GCAGAGTTCCACATGTCAAAATTC 59.080 41.667 0.00 0.00 0.00 2.17
679 880 2.665537 CTCTGTTCTTGCTTGCTACGAG 59.334 50.000 0.00 0.00 0.00 4.18
767 977 1.442520 CCGGTTCGTGCAGCATTTG 60.443 57.895 0.00 0.00 0.00 2.32
781 991 2.114056 GCATTTGTGTGCGCTATGATG 58.886 47.619 9.73 6.81 35.10 3.07
785 995 2.314323 TGTGTGCGCTATGATGTGAT 57.686 45.000 9.73 0.00 0.00 3.06
803 1013 0.250467 ATGTCAGCTTGTCACCGCTT 60.250 50.000 0.00 0.00 33.45 4.68
851 1082 0.248458 GGTGTTGTTGTTGCAGGACG 60.248 55.000 0.00 0.00 0.00 4.79
880 1111 1.135859 CAAGAAAGTGCGCTTGGCTAG 60.136 52.381 14.36 0.00 44.05 3.42
933 1177 4.514781 TGTGTAGTACATTCTCGTGCTT 57.485 40.909 6.21 0.00 33.58 3.91
947 1191 4.505217 GCTTGTCGGACGCATGCG 62.505 66.667 36.79 36.79 46.03 4.73
991 1239 3.705043 ACATATCGTCCACGTAAGGTC 57.295 47.619 0.00 0.00 46.39 3.85
1214 1463 1.291132 GAGAGGTGCGTGCCTTAATC 58.709 55.000 1.64 0.00 39.34 1.75
1292 1541 2.158842 GCCTCACAAGATAGCCAGTGAT 60.159 50.000 3.92 0.00 39.92 3.06
1307 1556 4.818642 CCAGTGATGAGTGGAGCATATAG 58.181 47.826 0.00 0.00 44.73 1.31
1335 1597 3.086282 AGAACGTGGTCAACCTTTGTTT 58.914 40.909 0.10 0.00 36.82 2.83
1336 1598 3.128068 AGAACGTGGTCAACCTTTGTTTC 59.872 43.478 0.10 0.00 36.82 2.78
1342 1604 6.037098 CGTGGTCAACCTTTGTTTCATTTTA 58.963 36.000 0.10 0.00 36.82 1.52
1343 1605 6.020201 CGTGGTCAACCTTTGTTTCATTTTAC 60.020 38.462 0.10 0.00 36.82 2.01
1344 1606 7.039270 GTGGTCAACCTTTGTTTCATTTTACT 58.961 34.615 0.10 0.00 36.82 2.24
1345 1607 8.192110 GTGGTCAACCTTTGTTTCATTTTACTA 58.808 33.333 0.10 0.00 36.82 1.82
1476 1741 1.081892 CCTCTTTGACGACCATGCTG 58.918 55.000 0.00 0.00 0.00 4.41
1518 1789 5.154222 GTGTTTTGTTCTTTGATCGATCCC 58.846 41.667 22.31 0.00 0.00 3.85
1519 1790 4.824537 TGTTTTGTTCTTTGATCGATCCCA 59.175 37.500 22.31 6.62 0.00 4.37
1520 1791 5.476599 TGTTTTGTTCTTTGATCGATCCCAT 59.523 36.000 22.31 0.00 0.00 4.00
1521 1792 5.818136 TTTGTTCTTTGATCGATCCCATC 57.182 39.130 22.31 8.75 0.00 3.51
1522 1793 3.808728 TGTTCTTTGATCGATCCCATCC 58.191 45.455 22.31 6.98 0.00 3.51
1555 1888 5.711976 CAGAATCACCATTAACCAGAACCTT 59.288 40.000 0.00 0.00 0.00 3.50
1642 1975 0.537188 AATCCACCTTCATCGTCGCT 59.463 50.000 0.00 0.00 0.00 4.93
1645 1978 2.578786 TCCACCTTCATCGTCGCTATA 58.421 47.619 0.00 0.00 0.00 1.31
1721 2065 7.790027 TCTTTCTGGATACTACGTACTAGTCT 58.210 38.462 0.00 0.98 36.95 3.24
1722 2066 8.263640 TCTTTCTGGATACTACGTACTAGTCTT 58.736 37.037 0.00 0.00 36.95 3.01
1764 2164 3.303938 ACATACAGGATGGAGACTCTGG 58.696 50.000 1.74 0.00 43.62 3.86
2162 2562 2.829458 AGGCTCTACTCGTCGGCC 60.829 66.667 0.00 0.00 42.74 6.13
2238 2643 4.466828 CCACGTTTCTCATGTTGTTGATC 58.533 43.478 0.00 0.00 0.00 2.92
2239 2644 4.214119 CCACGTTTCTCATGTTGTTGATCT 59.786 41.667 0.00 0.00 0.00 2.75
2350 2755 1.254026 TGTTCGGACCTCTCATCGTT 58.746 50.000 0.00 0.00 0.00 3.85
2434 2842 2.749621 CCCTGTTTAACTCACATGCCTC 59.250 50.000 0.00 0.00 0.00 4.70
2437 2845 3.064207 TGTTTAACTCACATGCCTCGAC 58.936 45.455 0.00 0.00 0.00 4.20
2591 3020 0.237235 GATGCGCCGAAACTTGTTGA 59.763 50.000 4.18 0.00 0.00 3.18
2605 3034 3.364889 TTGTTGATCAAGACGACGAGT 57.635 42.857 8.80 0.00 0.00 4.18
2611 3040 2.027625 CAAGACGACGAGTTGGGCC 61.028 63.158 0.00 0.00 0.00 5.80
2629 3058 2.936032 AGGGGTCCCTTCCACAGC 60.936 66.667 8.15 0.00 45.70 4.40
2650 3079 3.625764 GCCTAACGGTGAAGCATAATCAA 59.374 43.478 0.00 0.00 0.00 2.57
2702 3324 8.181904 TGCCAGTCAAGATTTTCTTTATTTCT 57.818 30.769 0.00 0.00 33.78 2.52
2731 3364 1.202359 GCAAAAGTTTTGCCTCGTCCA 60.202 47.619 33.57 0.00 39.38 4.02
2732 3365 2.459934 CAAAAGTTTTGCCTCGTCCAC 58.540 47.619 15.06 0.00 0.00 4.02
2733 3366 2.052782 AAAGTTTTGCCTCGTCCACT 57.947 45.000 0.00 0.00 0.00 4.00
2734 3367 2.922740 AAGTTTTGCCTCGTCCACTA 57.077 45.000 0.00 0.00 0.00 2.74
2735 3368 2.922740 AGTTTTGCCTCGTCCACTAA 57.077 45.000 0.00 0.00 0.00 2.24
2736 3369 3.418684 AGTTTTGCCTCGTCCACTAAT 57.581 42.857 0.00 0.00 0.00 1.73
2737 3370 3.751518 AGTTTTGCCTCGTCCACTAATT 58.248 40.909 0.00 0.00 0.00 1.40
2738 3371 3.502211 AGTTTTGCCTCGTCCACTAATTG 59.498 43.478 0.00 0.00 0.00 2.32
2739 3372 2.851263 TTGCCTCGTCCACTAATTGT 57.149 45.000 0.00 0.00 0.00 2.71
2740 3373 2.380084 TGCCTCGTCCACTAATTGTC 57.620 50.000 0.00 0.00 0.00 3.18
2741 3374 1.066430 TGCCTCGTCCACTAATTGTCC 60.066 52.381 0.00 0.00 0.00 4.02
2746 3379 4.099573 CCTCGTCCACTAATTGTCCACTAT 59.900 45.833 0.00 0.00 0.00 2.12
2862 3664 3.569701 ACAGGATCATCCAACAAACACAC 59.430 43.478 6.42 0.00 39.61 3.82
2909 3740 3.569277 TGGGTCACAACATCACAAATGAG 59.431 43.478 0.00 0.00 38.57 2.90
2918 3749 3.156293 CATCACAAATGAGACCCCAACA 58.844 45.455 0.00 0.00 38.57 3.33
2927 3758 0.178843 AGACCCCAACACCCCACTAT 60.179 55.000 0.00 0.00 0.00 2.12
2960 3791 7.494625 AGAAGAATCTAACGACAAAGACAACAA 59.505 33.333 0.00 0.00 32.88 2.83
2975 3806 1.462283 CAACAACCACATCTCAGCTCG 59.538 52.381 0.00 0.00 0.00 5.03
3014 3847 1.945394 CTGTATCATGGAAGCACCTGC 59.055 52.381 0.00 0.00 39.86 4.85
3068 3901 7.646922 CCATTGCACTTGCTAAATATCTTCTTC 59.353 37.037 2.33 0.00 42.66 2.87
3072 3905 6.292596 GCACTTGCTAAATATCTTCTTCGGAG 60.293 42.308 0.00 0.00 38.21 4.63
3096 3929 0.103572 GATTTAGGGTGAGCGCCGTA 59.896 55.000 2.29 0.00 0.00 4.02
3100 3933 1.252904 TAGGGTGAGCGCCGTACTTT 61.253 55.000 2.29 0.00 0.00 2.66
3112 3945 2.065512 CCGTACTTTTTGCATTTGCCC 58.934 47.619 0.00 0.00 41.18 5.36
3113 3946 1.718711 CGTACTTTTTGCATTTGCCCG 59.281 47.619 0.00 0.00 41.18 6.13
3114 3947 2.749776 GTACTTTTTGCATTTGCCCGT 58.250 42.857 0.00 0.00 41.18 5.28
3115 3948 1.580815 ACTTTTTGCATTTGCCCGTG 58.419 45.000 0.00 0.00 41.18 4.94
3116 3949 0.867086 CTTTTTGCATTTGCCCGTGG 59.133 50.000 0.00 0.00 41.18 4.94
3117 3950 0.465705 TTTTTGCATTTGCCCGTGGA 59.534 45.000 0.00 0.00 41.18 4.02
3118 3951 0.683973 TTTTGCATTTGCCCGTGGAT 59.316 45.000 0.00 0.00 41.18 3.41
3119 3952 0.037512 TTTGCATTTGCCCGTGGATG 60.038 50.000 0.00 0.00 41.18 3.51
3152 3985 4.564782 TCTGCTTCAAGAGACATCCATT 57.435 40.909 0.00 0.00 0.00 3.16
3206 4400 7.287005 AGTTAGGTATACGACAAATCAGATGGA 59.713 37.037 0.00 0.00 0.00 3.41
3217 4411 6.005823 ACAAATCAGATGGAGAACATGTCAA 58.994 36.000 0.00 0.00 40.72 3.18
3222 4416 4.575236 CAGATGGAGAACATGTCAATGAGG 59.425 45.833 0.00 0.00 40.72 3.86
3238 4432 2.667199 GGTTACGCACCGGCACTT 60.667 61.111 0.00 0.00 41.24 3.16
3239 4433 2.255881 GGTTACGCACCGGCACTTT 61.256 57.895 0.00 0.00 41.24 2.66
3240 4434 0.950071 GGTTACGCACCGGCACTTTA 60.950 55.000 0.00 0.00 41.24 1.85
3306 4500 4.406648 ACTATTTGCATGATGGACTCGA 57.593 40.909 0.00 0.00 0.00 4.04
3315 4511 1.813178 TGATGGACTCGAGAGTGTGTC 59.187 52.381 21.68 5.48 42.66 3.67
3330 4526 1.151668 GTGTCGCAGCAATCAAGAGT 58.848 50.000 0.00 0.00 0.00 3.24
3334 4530 1.066929 TCGCAGCAATCAAGAGTAGCA 60.067 47.619 0.00 0.00 0.00 3.49
3335 4531 1.061711 CGCAGCAATCAAGAGTAGCAC 59.938 52.381 0.00 0.00 0.00 4.40
3336 4532 1.399791 GCAGCAATCAAGAGTAGCACC 59.600 52.381 0.00 0.00 0.00 5.01
3347 4545 1.686052 GAGTAGCACCCTCCTCATCAG 59.314 57.143 0.00 0.00 0.00 2.90
3384 4582 4.072839 GGTTCTAGAAAAGGTGAAGTGGG 58.927 47.826 6.78 0.00 0.00 4.61
3398 4596 3.965258 TGGGCGCCCAAGTCATGT 61.965 61.111 45.50 0.00 44.12 3.21
3416 4614 1.270839 TGTCTGAGGGCACAAACTAGC 60.271 52.381 0.00 0.00 0.00 3.42
3476 4674 2.439507 CCAGGAGTAGGTGCCAACATAT 59.560 50.000 0.00 0.00 0.00 1.78
3489 4687 2.355197 CAACATATTGGTCACCGCAGA 58.645 47.619 0.00 0.00 31.63 4.26
3501 4699 1.667724 CACCGCAGATTCATCAACCTC 59.332 52.381 0.00 0.00 0.00 3.85
3522 4720 3.383505 TCAGATACTACCGACACAATGGG 59.616 47.826 0.00 0.00 0.00 4.00
3528 4726 1.746615 CCGACACAATGGGCTCAGG 60.747 63.158 0.00 0.00 0.00 3.86
3530 4728 2.360350 ACACAATGGGCTCAGGCG 60.360 61.111 0.00 0.00 39.81 5.52
3531 4729 2.360350 CACAATGGGCTCAGGCGT 60.360 61.111 0.00 0.00 39.81 5.68
3541 4739 1.668294 CTCAGGCGTCTCCAGTTGT 59.332 57.895 0.00 0.00 37.29 3.32
3542 4740 0.668706 CTCAGGCGTCTCCAGTTGTG 60.669 60.000 0.00 0.00 37.29 3.33
3546 4744 1.595382 GCGTCTCCAGTTGTGCACT 60.595 57.895 19.41 0.00 35.35 4.40
3550 4748 1.599542 GTCTCCAGTTGTGCACTTGAC 59.400 52.381 19.41 13.65 30.92 3.18
3554 4752 1.600957 CCAGTTGTGCACTTGACAGAG 59.399 52.381 19.41 8.14 30.92 3.35
3563 4761 3.054875 TGCACTTGACAGAGGCTAATCAT 60.055 43.478 0.00 0.00 0.00 2.45
3571 4769 3.181471 ACAGAGGCTAATCATGTTCCTCG 60.181 47.826 12.23 10.61 45.90 4.63
3575 4773 1.258982 GCTAATCATGTTCCTCGCACG 59.741 52.381 0.00 0.00 0.00 5.34
3586 4784 1.875813 CTCGCACGAGGTCATCAGC 60.876 63.158 12.17 0.00 38.51 4.26
3611 4809 2.637382 TCAACCTTCATGTGCTCCACTA 59.363 45.455 0.00 0.00 35.11 2.74
3629 4827 2.202946 GCAGAGGCGAAGTAGGGC 60.203 66.667 0.00 0.00 0.00 5.19
3645 4843 2.592574 GCGCATGCATAGCTCCCA 60.593 61.111 19.57 0.00 42.15 4.37
3646 4844 2.188829 GCGCATGCATAGCTCCCAA 61.189 57.895 19.57 0.00 42.15 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 8.367911 ACCACGATTATCATCTTGTGTATGTAT 58.632 33.333 0.00 0.00 28.52 2.29
28 29 7.722363 ACCACGATTATCATCTTGTGTATGTA 58.278 34.615 0.00 0.00 28.52 2.29
29 30 6.582636 ACCACGATTATCATCTTGTGTATGT 58.417 36.000 0.00 0.00 28.52 2.29
30 31 6.129088 CGACCACGATTATCATCTTGTGTATG 60.129 42.308 0.00 0.00 42.66 2.39
31 32 5.920840 CGACCACGATTATCATCTTGTGTAT 59.079 40.000 0.00 0.00 42.66 2.29
54 55 1.153349 GCTTGGCTTACCCCTCTCG 60.153 63.158 0.00 0.00 33.59 4.04
62 63 1.037579 GGTCATGGGGCTTGGCTTAC 61.038 60.000 0.00 0.00 0.00 2.34
65 66 0.995675 ATAGGTCATGGGGCTTGGCT 60.996 55.000 0.00 0.00 0.00 4.75
126 143 4.386867 TCAATCTTTAGGTACGCCTCAG 57.613 45.455 0.00 0.00 45.64 3.35
174 192 6.556116 TCAATGATACTCAATGAGATCCTCCA 59.444 38.462 18.20 6.19 31.87 3.86
175 193 6.873076 GTCAATGATACTCAATGAGATCCTCC 59.127 42.308 18.20 0.80 37.01 4.30
267 285 5.848406 TCAACACAACAAATAATCCAACCC 58.152 37.500 0.00 0.00 0.00 4.11
406 596 5.282510 GGGATATACTCAAACACAGACTCG 58.717 45.833 0.00 0.00 0.00 4.18
409 599 5.615925 AGGGGATATACTCAAACACAGAC 57.384 43.478 0.00 0.00 0.00 3.51
415 605 6.896883 AGGTTACAAGGGGATATACTCAAAC 58.103 40.000 0.00 0.00 0.00 2.93
420 610 7.519347 TTTGAAGGTTACAAGGGGATATACT 57.481 36.000 0.00 0.00 0.00 2.12
427 617 6.658188 TTATGTTTTGAAGGTTACAAGGGG 57.342 37.500 0.00 0.00 0.00 4.79
449 645 3.994392 CCATAACGTATATGAAGCGGCTT 59.006 43.478 16.36 16.36 0.00 4.35
451 647 3.581755 TCCATAACGTATATGAAGCGGC 58.418 45.455 15.10 0.00 0.00 6.53
452 648 4.174009 CCTCCATAACGTATATGAAGCGG 58.826 47.826 15.10 8.47 0.00 5.52
479 680 9.035890 ACATACAAGAGCTACTATGCCATATAA 57.964 33.333 0.00 0.00 0.00 0.98
493 694 3.503748 GGCAAGACAAACATACAAGAGCT 59.496 43.478 0.00 0.00 0.00 4.09
546 747 4.261741 GGTGAGTGCAGAATTTTGACATGT 60.262 41.667 0.00 0.00 0.00 3.21
559 760 3.635331 CAAGTCAAAATGGTGAGTGCAG 58.365 45.455 0.00 0.00 31.41 4.41
758 963 0.179156 ATAGCGCACACAAATGCTGC 60.179 50.000 11.47 0.00 43.80 5.25
764 969 2.421619 TCACATCATAGCGCACACAAA 58.578 42.857 11.47 0.00 0.00 2.83
767 977 1.935873 ACATCACATCATAGCGCACAC 59.064 47.619 11.47 0.00 0.00 3.82
781 991 0.792640 CGGTGACAAGCTGACATCAC 59.207 55.000 10.08 10.08 40.62 3.06
785 995 0.880278 GAAGCGGTGACAAGCTGACA 60.880 55.000 5.61 0.00 43.78 3.58
803 1013 4.068280 TACGTGCACGGACAGAGA 57.932 55.556 39.21 14.89 44.95 3.10
851 1082 1.487482 GCACTTTCTTGTTTTCGGGC 58.513 50.000 0.00 0.00 0.00 6.13
880 1111 1.395826 ATCTGTCCTCCTAGCGGTGC 61.396 60.000 0.00 0.00 0.00 5.01
883 1114 5.297278 GTGTATATATCTGTCCTCCTAGCGG 59.703 48.000 0.00 0.00 0.00 5.52
918 1162 1.654105 CCGACAAGCACGAGAATGTAC 59.346 52.381 0.00 0.00 0.00 2.90
919 1163 1.542472 TCCGACAAGCACGAGAATGTA 59.458 47.619 0.00 0.00 0.00 2.29
920 1164 0.317160 TCCGACAAGCACGAGAATGT 59.683 50.000 0.00 0.00 0.00 2.71
921 1165 0.716108 GTCCGACAAGCACGAGAATG 59.284 55.000 0.00 0.00 0.00 2.67
922 1166 0.732880 CGTCCGACAAGCACGAGAAT 60.733 55.000 0.00 0.00 35.49 2.40
924 1168 2.254350 CGTCCGACAAGCACGAGA 59.746 61.111 0.00 0.00 35.49 4.04
947 1191 2.223386 CGAGCTCAGGAACTACTAGCAC 60.223 54.545 15.40 0.00 39.41 4.40
991 1239 0.322975 CCGATCCCCATGCTCCTTAG 59.677 60.000 0.00 0.00 0.00 2.18
1143 1391 0.739462 CGCCGAACATGAGCCTGTAA 60.739 55.000 0.00 0.00 0.00 2.41
1292 1541 2.630098 GGCAGACTATATGCTCCACTCA 59.370 50.000 0.00 0.00 43.35 3.41
1307 1556 0.531974 TTGACCACGTTCTGGCAGAC 60.532 55.000 18.55 11.52 45.32 3.51
1335 1597 3.861113 CGCGTTAGCCAGTAGTAAAATGA 59.139 43.478 0.00 0.00 41.18 2.57
1336 1598 3.000925 CCGCGTTAGCCAGTAGTAAAATG 59.999 47.826 4.92 0.00 41.18 2.32
1342 1604 2.183555 GCCGCGTTAGCCAGTAGT 59.816 61.111 4.92 0.00 41.18 2.73
1343 1605 1.878522 CAGCCGCGTTAGCCAGTAG 60.879 63.158 4.92 0.00 41.18 2.57
1344 1606 2.183300 CAGCCGCGTTAGCCAGTA 59.817 61.111 4.92 0.00 41.18 2.74
1345 1607 3.934391 GACAGCCGCGTTAGCCAGT 62.934 63.158 4.92 3.22 41.18 4.00
1368 1630 4.099120 CGTTTCTTCCTAGAGATCACACG 58.901 47.826 0.00 0.00 0.00 4.49
1476 1741 1.615392 ACAAAGTCCAGAGCATTTGCC 59.385 47.619 0.00 0.00 43.38 4.52
1518 1789 4.158949 TGGTGATTCTGCATTTCTTGGATG 59.841 41.667 0.00 0.00 0.00 3.51
1519 1790 4.346730 TGGTGATTCTGCATTTCTTGGAT 58.653 39.130 0.00 0.00 0.00 3.41
1520 1791 3.765381 TGGTGATTCTGCATTTCTTGGA 58.235 40.909 0.00 0.00 0.00 3.53
1521 1792 4.730949 ATGGTGATTCTGCATTTCTTGG 57.269 40.909 0.00 0.00 0.00 3.61
1522 1793 6.532657 GGTTAATGGTGATTCTGCATTTCTTG 59.467 38.462 0.00 0.00 0.00 3.02
1555 1888 2.951269 CTTGATGGCAAGCACCAGA 58.049 52.632 0.00 0.00 44.41 3.86
1711 2055 3.087031 TCCAAGTGGGAAGACTAGTACG 58.913 50.000 0.00 0.00 44.80 3.67
1722 2066 3.320610 TGTTCCATTTTCCAAGTGGGA 57.679 42.857 0.00 0.00 46.61 4.37
1943 2343 4.208686 AACGAGCCGAGGATCCGC 62.209 66.667 5.98 5.59 39.71 5.54
2162 2562 1.660575 CCGCCTGATTACCGCGTAG 60.661 63.158 4.92 0.00 44.29 3.51
2272 2677 3.854669 ATGAGCGGGAAGGCGGAG 61.855 66.667 0.00 0.00 38.18 4.63
2350 2755 1.443702 CATGACCGCGACGAAGACA 60.444 57.895 8.23 0.00 0.00 3.41
2412 2817 1.818674 GGCATGTGAGTTAAACAGGGG 59.181 52.381 0.00 0.00 30.25 4.79
2434 2842 0.109643 CACCACCATGCATGTTGTCG 60.110 55.000 24.58 11.79 0.00 4.35
2437 2845 1.068125 CAGACACCACCATGCATGTTG 60.068 52.381 24.58 20.69 0.00 3.33
2591 3020 0.389948 GCCCAACTCGTCGTCTTGAT 60.390 55.000 6.31 0.00 0.00 2.57
2629 3058 5.220854 CCTTTGATTATGCTTCACCGTTAGG 60.221 44.000 0.00 0.00 45.13 2.69
2650 3079 6.823689 AGTGTACGCATGATCTTATTTTCCTT 59.176 34.615 9.48 0.00 0.00 3.36
2736 3369 8.349983 GCAACTCTCTTTTTAAATAGTGGACAA 58.650 33.333 5.69 0.00 0.00 3.18
2737 3370 7.719633 AGCAACTCTCTTTTTAAATAGTGGACA 59.280 33.333 5.69 0.00 0.00 4.02
2738 3371 8.100508 AGCAACTCTCTTTTTAAATAGTGGAC 57.899 34.615 5.69 0.00 0.00 4.02
2739 3372 7.117812 CGAGCAACTCTCTTTTTAAATAGTGGA 59.882 37.037 5.69 5.27 39.70 4.02
2740 3373 7.117812 TCGAGCAACTCTCTTTTTAAATAGTGG 59.882 37.037 5.69 1.83 39.70 4.00
2741 3374 8.018677 TCGAGCAACTCTCTTTTTAAATAGTG 57.981 34.615 5.69 4.00 39.70 2.74
2862 3664 9.170734 CAAGTGTATGGATGATTCTATATTGGG 57.829 37.037 0.00 0.00 29.31 4.12
2909 3740 1.587066 TATAGTGGGGTGTTGGGGTC 58.413 55.000 0.00 0.00 0.00 4.46
2918 3749 8.625467 AGATTCTTCTAAAGTTATAGTGGGGT 57.375 34.615 0.00 0.00 0.00 4.95
2960 3791 1.670949 ATCGCGAGCTGAGATGTGGT 61.671 55.000 16.66 0.00 35.62 4.16
2975 3806 2.346847 CAGTTGTCTAGACTGCAATCGC 59.653 50.000 23.01 5.27 38.20 4.58
3014 3847 2.353579 GGGTGACGATAATGGGAAAACG 59.646 50.000 0.00 0.00 0.00 3.60
3068 3901 4.120589 GCTCACCCTAAATCTAAACTCCG 58.879 47.826 0.00 0.00 0.00 4.63
3072 3905 2.612672 GGCGCTCACCCTAAATCTAAAC 59.387 50.000 7.64 0.00 0.00 2.01
3096 3929 1.580815 CACGGGCAAATGCAAAAAGT 58.419 45.000 7.80 0.00 44.36 2.66
3100 3933 0.037512 CATCCACGGGCAAATGCAAA 60.038 50.000 7.80 0.00 44.36 3.68
3112 3945 3.576356 GGCATCCACGCATCCACG 61.576 66.667 0.00 0.00 39.50 4.94
3113 3946 1.718757 GAAGGCATCCACGCATCCAC 61.719 60.000 0.00 0.00 0.00 4.02
3114 3947 1.451927 GAAGGCATCCACGCATCCA 60.452 57.895 0.00 0.00 0.00 3.41
3115 3948 1.153086 AGAAGGCATCCACGCATCC 60.153 57.895 0.00 0.00 0.00 3.51
3116 3949 2.020131 CAGAAGGCATCCACGCATC 58.980 57.895 0.00 0.00 0.00 3.91
3117 3950 2.117156 GCAGAAGGCATCCACGCAT 61.117 57.895 0.00 0.00 43.97 4.73
3118 3951 2.747460 GCAGAAGGCATCCACGCA 60.747 61.111 0.00 0.00 43.97 5.24
3206 4400 3.684788 GCGTAACCTCATTGACATGTTCT 59.315 43.478 0.00 0.00 0.00 3.01
3222 4416 0.441145 CTAAAGTGCCGGTGCGTAAC 59.559 55.000 1.90 0.00 41.78 2.50
3238 4432 4.013728 GGGTGATATGTTGTTGTGGCTAA 58.986 43.478 0.00 0.00 0.00 3.09
3239 4433 3.009584 TGGGTGATATGTTGTTGTGGCTA 59.990 43.478 0.00 0.00 0.00 3.93
3240 4434 2.224992 TGGGTGATATGTTGTTGTGGCT 60.225 45.455 0.00 0.00 0.00 4.75
3287 4481 4.100035 ACTCTCGAGTCCATCATGCAAATA 59.900 41.667 13.13 0.00 36.92 1.40
3290 4484 1.827344 ACTCTCGAGTCCATCATGCAA 59.173 47.619 13.13 0.00 36.92 4.08
3306 4500 0.033920 TGATTGCTGCGACACACTCT 59.966 50.000 0.00 0.00 0.00 3.24
3315 4511 1.061711 GTGCTACTCTTGATTGCTGCG 59.938 52.381 0.00 0.00 0.00 5.18
3330 4526 1.395045 CGCTGATGAGGAGGGTGCTA 61.395 60.000 0.00 0.00 0.00 3.49
3334 4530 2.060980 GGTCGCTGATGAGGAGGGT 61.061 63.158 0.00 0.00 0.00 4.34
3335 4531 2.818132 GGTCGCTGATGAGGAGGG 59.182 66.667 0.00 0.00 0.00 4.30
3336 4532 2.415010 CGGTCGCTGATGAGGAGG 59.585 66.667 0.00 0.00 0.00 4.30
3384 4582 1.364626 CTCAGACATGACTTGGGCGC 61.365 60.000 0.00 0.00 0.00 6.53
3398 4596 0.324943 GGCTAGTTTGTGCCCTCAGA 59.675 55.000 0.00 0.00 43.11 3.27
3476 4674 1.003003 TGATGAATCTGCGGTGACCAA 59.997 47.619 1.11 0.00 0.00 3.67
3482 4680 1.278985 TGAGGTTGATGAATCTGCGGT 59.721 47.619 0.00 0.00 0.00 5.68
3489 4687 5.833667 TCGGTAGTATCTGAGGTTGATGAAT 59.166 40.000 0.00 0.00 0.00 2.57
3501 4699 3.717707 CCCATTGTGTCGGTAGTATCTG 58.282 50.000 0.00 0.00 0.00 2.90
3522 4720 1.739562 CAACTGGAGACGCCTGAGC 60.740 63.158 9.08 0.00 38.83 4.26
3528 4726 1.160329 AAGTGCACAACTGGAGACGC 61.160 55.000 21.04 0.00 39.81 5.19
3530 4728 1.599542 GTCAAGTGCACAACTGGAGAC 59.400 52.381 21.04 11.30 39.67 3.36
3531 4729 1.209261 TGTCAAGTGCACAACTGGAGA 59.791 47.619 21.04 4.40 39.67 3.71
3541 4739 2.302733 TGATTAGCCTCTGTCAAGTGCA 59.697 45.455 0.00 0.00 0.00 4.57
3542 4740 2.977914 TGATTAGCCTCTGTCAAGTGC 58.022 47.619 0.00 0.00 0.00 4.40
3546 4744 4.225942 AGGAACATGATTAGCCTCTGTCAA 59.774 41.667 0.00 0.00 0.00 3.18
3550 4748 3.388308 CGAGGAACATGATTAGCCTCTG 58.612 50.000 0.00 1.71 42.27 3.35
3554 4752 1.599542 GTGCGAGGAACATGATTAGCC 59.400 52.381 0.00 0.00 0.00 3.93
3571 4769 1.875813 CTCGCTGATGACCTCGTGC 60.876 63.158 0.00 0.00 0.00 5.34
3575 4773 1.634702 GTTGACTCGCTGATGACCTC 58.365 55.000 0.00 0.00 0.00 3.85
3586 4784 1.728971 GAGCACATGAAGGTTGACTCG 59.271 52.381 0.00 0.00 0.00 4.18
3611 4809 2.726351 GCCCTACTTCGCCTCTGCT 61.726 63.158 0.00 0.00 34.43 4.24
3629 4827 4.146058 TTGGGAGCTATGCATGCG 57.854 55.556 14.09 1.07 35.28 4.73


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

AutoCloner maintained by Alex Coulton.