Multiple sequence alignment - TraesCS3D01G485900

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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 TraesCS3D01G485900 chr3D 100.000 2970 0 0 471 3440 582127368 582130337 0.000000e+00 5485.0
1 TraesCS3D01G485900 chr3D 84.391 583 69 15 2742 3317 582030097 582029530 1.400000e-153 553.0
2 TraesCS3D01G485900 chr3D 100.000 74 0 0 1 74 582126898 582126971 1.660000e-28 137.0
3 TraesCS3D01G485900 chr3B 88.734 3018 170 62 533 3428 779368745 779365776 0.000000e+00 3533.0
4 TraesCS3D01G485900 chr3B 81.463 205 15 8 471 655 779370874 779370673 2.770000e-31 147.0
5 TraesCS3D01G485900 chr5D 84.975 406 32 18 1295 1680 301123606 301123210 5.390000e-103 385.0
6 TraesCS3D01G485900 chr5D 76.829 164 20 4 1114 1277 301123751 301123606 3.680000e-10 76.8
7 TraesCS3D01G485900 chr7B 82.368 380 33 14 1331 1680 89036 88661 2.010000e-77 300.0
8 TraesCS3D01G485900 chr7B 80.460 261 24 17 915 1152 110177 109921 1.270000e-39 174.0


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 TraesCS3D01G485900 chr3D 582126898 582130337 3439 False 2811.0 5485 100.0000 1 3440 2 chr3D.!!$F1 3439
1 TraesCS3D01G485900 chr3D 582029530 582030097 567 True 553.0 553 84.3910 2742 3317 1 chr3D.!!$R1 575
2 TraesCS3D01G485900 chr3B 779365776 779370874 5098 True 1840.0 3533 85.0985 471 3428 2 chr3B.!!$R1 2957
3 TraesCS3D01G485900 chr5D 301123210 301123751 541 True 230.9 385 80.9020 1114 1680 2 chr5D.!!$R1 566

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
600 604 0.111253 CCTCAACAAAGCCCCAGAGT 59.889 55.0 0.0 0.0 0.0 3.24 F
605 609 0.326264 ACAAAGCCCCAGAGTAGCAG 59.674 55.0 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 4294 0.037303 CCTGGACATGGTCAGCTTGT 59.963 55.0 10.82 0.0 33.68 3.16 R
2539 4713 0.179171 AGTACAGATTCGACACCGCG 60.179 55.0 0.00 0.0 35.37 6.46 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
48 49 6.570672 TTCAAGATGAACTACGTACAGAGT 57.429 37.500 0.00 0.00 30.26 3.24
49 50 5.939457 TCAAGATGAACTACGTACAGAGTG 58.061 41.667 0.00 0.00 0.00 3.51
50 51 5.704053 TCAAGATGAACTACGTACAGAGTGA 59.296 40.000 0.00 0.00 0.00 3.41
51 52 5.548706 AGATGAACTACGTACAGAGTGAC 57.451 43.478 0.00 0.00 0.00 3.67
52 53 3.800929 TGAACTACGTACAGAGTGACG 57.199 47.619 0.00 0.00 44.57 4.35
68 69 2.847725 ACGTGAGTGCACAAACACA 58.152 47.368 27.65 15.38 46.97 3.72
69 70 1.378531 ACGTGAGTGCACAAACACAT 58.621 45.000 27.65 18.04 46.97 3.21
70 71 1.742831 ACGTGAGTGCACAAACACATT 59.257 42.857 27.65 17.71 46.97 2.71
71 72 2.939756 ACGTGAGTGCACAAACACATTA 59.060 40.909 27.65 2.44 46.97 1.90
72 73 3.375610 ACGTGAGTGCACAAACACATTAA 59.624 39.130 27.65 0.00 46.97 1.40
73 74 3.723764 CGTGAGTGCACAAACACATTAAC 59.276 43.478 27.65 8.59 45.41 2.01
490 494 1.708341 ATGCTGTTTGCCTTGGAACT 58.292 45.000 0.00 0.00 42.00 3.01
496 500 4.557496 GCTGTTTGCCTTGGAACTTAAGAG 60.557 45.833 10.09 0.00 35.15 2.85
499 503 5.241506 TGTTTGCCTTGGAACTTAAGAGATG 59.758 40.000 10.09 0.00 0.00 2.90
519 523 2.714250 TGGTCTCCAAAACCCACTATGT 59.286 45.455 0.00 0.00 35.84 2.29
520 524 3.081804 GGTCTCCAAAACCCACTATGTG 58.918 50.000 0.00 0.00 0.00 3.21
531 535 5.968676 ACCCACTATGTGCTTATCCTAAA 57.031 39.130 0.00 0.00 31.34 1.85
532 536 6.321821 ACCCACTATGTGCTTATCCTAAAA 57.678 37.500 0.00 0.00 31.34 1.52
534 538 6.772716 ACCCACTATGTGCTTATCCTAAAATG 59.227 38.462 0.00 0.00 31.34 2.32
535 539 6.998074 CCCACTATGTGCTTATCCTAAAATGA 59.002 38.462 0.00 0.00 31.34 2.57
550 554 6.045106 TCCTAAAATGAGTTACCATATCCCCC 59.955 42.308 0.00 0.00 0.00 5.40
569 573 3.308188 CCCCGGAAAAGTGAAACCTCTAT 60.308 47.826 0.73 0.00 37.80 1.98
574 578 5.935789 CGGAAAAGTGAAACCTCTATTACCA 59.064 40.000 0.00 0.00 37.80 3.25
593 597 3.826729 ACCATAAGAACCTCAACAAAGCC 59.173 43.478 0.00 0.00 0.00 4.35
600 604 0.111253 CCTCAACAAAGCCCCAGAGT 59.889 55.000 0.00 0.00 0.00 3.24
605 609 0.326264 ACAAAGCCCCAGAGTAGCAG 59.674 55.000 0.00 0.00 0.00 4.24
608 612 1.908340 AAGCCCCAGAGTAGCAGCAG 61.908 60.000 0.00 0.00 0.00 4.24
610 614 2.663075 CCCCAGAGTAGCAGCAGCA 61.663 63.158 3.17 0.00 45.49 4.41
612 616 1.023513 CCCAGAGTAGCAGCAGCAAC 61.024 60.000 3.17 0.00 45.49 4.17
672 2782 3.204827 GTGGGGCAGCATAGCACG 61.205 66.667 0.00 0.00 39.34 5.34
695 2805 4.704833 CAGGACCCACGCCCACAG 62.705 72.222 0.00 0.00 0.00 3.66
711 2826 2.035961 CCACAGAGGATATACACCACCG 59.964 54.545 0.00 0.00 41.22 4.94
719 2834 2.246761 TATACACCACCGCCAGCACC 62.247 60.000 0.00 0.00 0.00 5.01
727 2842 4.087892 CGCCAGCACCAGCCTACT 62.088 66.667 0.00 0.00 43.56 2.57
728 2843 2.437359 GCCAGCACCAGCCTACTG 60.437 66.667 0.00 0.00 43.56 2.74
729 2844 3.072476 CCAGCACCAGCCTACTGT 58.928 61.111 0.00 0.00 42.81 3.55
734 2849 1.905512 CACCAGCCTACTGTACCCC 59.094 63.158 0.00 0.00 42.81 4.95
768 2883 0.589729 CGGGCATTCAAAATCTCGCG 60.590 55.000 0.00 0.00 0.00 5.87
794 2909 0.756294 CCAACCCCAAGAACCCAAAC 59.244 55.000 0.00 0.00 0.00 2.93
806 2921 1.080839 CCCAAACCCAAACGCATCG 60.081 57.895 0.00 0.00 0.00 3.84
862 2977 2.606275 GACGGAATCGAATCCAGCC 58.394 57.895 19.38 3.95 39.61 4.85
910 3028 4.751600 GCAATCAAAACCTTCCTTTCCTTG 59.248 41.667 0.00 0.00 0.00 3.61
931 3049 2.321263 CTGTCTGCCGCCAGGATCAT 62.321 60.000 0.00 0.00 41.02 2.45
932 3050 1.596477 GTCTGCCGCCAGGATCATC 60.596 63.158 0.00 0.00 41.02 2.92
934 3052 1.890979 CTGCCGCCAGGATCATCAC 60.891 63.158 0.00 0.00 41.02 3.06
935 3053 2.190313 GCCGCCAGGATCATCACA 59.810 61.111 0.00 0.00 41.02 3.58
936 3054 1.890979 GCCGCCAGGATCATCACAG 60.891 63.158 0.00 0.00 41.02 3.66
964 3082 0.392998 CAACCCCGATCTCCACCTTG 60.393 60.000 0.00 0.00 0.00 3.61
978 3096 2.546584 CCACCTTGCTTTCCTTTCTTGC 60.547 50.000 0.00 0.00 0.00 4.01
979 3097 1.688735 ACCTTGCTTTCCTTTCTTGCC 59.311 47.619 0.00 0.00 0.00 4.52
980 3098 1.001293 CCTTGCTTTCCTTTCTTGCCC 59.999 52.381 0.00 0.00 0.00 5.36
1110 3240 3.845259 GACCCCGGCTACATGCGA 61.845 66.667 0.00 0.00 44.05 5.10
1161 3291 3.869272 GAGGTTGCATCTGCGGCG 61.869 66.667 0.51 0.51 45.83 6.46
1215 3345 4.577677 TTGCTGACCAAGGCGGCA 62.578 61.111 13.08 0.00 45.24 5.69
1266 3396 4.154347 CAGACCTGCTCCTCCGCC 62.154 72.222 0.00 0.00 0.00 6.13
1273 3403 4.168291 GCTCCTCCGCCCAGAAGG 62.168 72.222 0.00 0.00 39.47 3.46
1495 3646 3.119096 GCAAAGGAGACGACGGGC 61.119 66.667 0.00 0.00 0.00 6.13
1754 3926 2.811317 CGGACGCAAGGAGCAGAC 60.811 66.667 0.00 0.00 46.13 3.51
1762 3934 1.805869 CAAGGAGCAGACTGGTCAAG 58.194 55.000 30.15 17.80 45.96 3.02
1764 3936 1.949799 AGGAGCAGACTGGTCAAGAT 58.050 50.000 30.15 13.97 45.96 2.40
1768 3940 2.495270 GAGCAGACTGGTCAAGATGAGA 59.505 50.000 25.95 0.00 43.79 3.27
1771 3943 3.095332 CAGACTGGTCAAGATGAGAGGA 58.905 50.000 3.51 0.00 0.00 3.71
1825 3997 2.607134 AGGACTCTGCTGCCTGCT 60.607 61.111 0.00 0.00 43.37 4.24
1826 3998 2.436292 GGACTCTGCTGCCTGCTG 60.436 66.667 0.00 0.00 43.37 4.41
1842 4014 2.364647 CTGCTGCAGGTCTGATATCTCA 59.635 50.000 21.71 0.00 0.00 3.27
1859 4031 0.906756 TCAGAGGAGCTGGGTCCAAG 60.907 60.000 19.10 9.42 44.98 3.61
1864 4036 0.470341 GGAGCTGGGTCCAAGATACC 59.530 60.000 13.19 0.00 36.51 2.73
1867 4039 1.561542 AGCTGGGTCCAAGATACCAAG 59.438 52.381 0.00 0.00 40.56 3.61
1869 4041 0.623723 TGGGTCCAAGATACCAAGGC 59.376 55.000 0.00 0.00 38.87 4.35
1870 4042 0.623723 GGGTCCAAGATACCAAGGCA 59.376 55.000 0.00 0.00 38.87 4.75
1871 4043 1.005450 GGGTCCAAGATACCAAGGCAA 59.995 52.381 0.00 0.00 38.87 4.52
1874 4046 2.749621 GTCCAAGATACCAAGGCAACAG 59.250 50.000 0.00 0.00 41.41 3.16
1909 4081 6.150140 AGGTGAAATTTCTCTTCCTGAAATCG 59.850 38.462 18.64 0.00 41.54 3.34
1910 4082 5.797434 GTGAAATTTCTCTTCCTGAAATCGC 59.203 40.000 18.64 0.00 41.54 4.58
1943 4115 3.243501 CCAGTTTCAGTTTCCACCACATG 60.244 47.826 0.00 0.00 0.00 3.21
1970 4144 4.036734 TGAATTCCAGAAACAACTGCTGAC 59.963 41.667 2.27 0.00 36.67 3.51
2014 4188 4.817063 CAGATTGCGGCGGCGTTG 62.817 66.667 32.35 18.08 44.10 4.10
2016 4190 4.811761 GATTGCGGCGGCGTTGTC 62.812 66.667 32.35 21.89 44.10 3.18
2026 4200 2.853914 GCGTTGTCGGCTCTTCAC 59.146 61.111 0.00 0.00 37.56 3.18
2031 4205 0.756294 TTGTCGGCTCTTCACTGGAA 59.244 50.000 0.00 0.00 0.00 3.53
2079 4253 4.565236 GCATTTGGTGGGATGAATTTCCAA 60.565 41.667 0.00 0.00 37.53 3.53
2088 4262 3.069158 GGATGAATTTCCAAGATGCAGGG 59.931 47.826 0.00 0.00 35.72 4.45
2145 4319 2.182827 CTGACCATGTCCAGGAGAAGA 58.817 52.381 0.00 0.00 0.00 2.87
2148 4322 2.303022 GACCATGTCCAGGAGAAGAACA 59.697 50.000 0.00 0.00 0.00 3.18
2151 4325 2.103153 TGTCCAGGAGAAGAACACCT 57.897 50.000 0.00 0.00 40.09 4.00
2210 4384 0.250166 CCGAACTTTCTTCCGGTGGT 60.250 55.000 0.00 0.00 37.40 4.16
2229 4403 1.146930 GCCTGATCCGGATGCTGAA 59.853 57.895 24.82 0.80 0.00 3.02
2238 4412 1.200020 CCGGATGCTGAAAAGGTTGAC 59.800 52.381 0.00 0.00 0.00 3.18
2301 4475 2.802816 GTGGATGGTCGATTATGCACTC 59.197 50.000 21.03 4.59 40.91 3.51
2382 4556 1.815408 GCCTTTGAGACTGTTCTGCCA 60.815 52.381 0.00 0.00 29.47 4.92
2385 4559 0.249868 TTGAGACTGTTCTGCCACCG 60.250 55.000 0.00 0.00 29.47 4.94
2391 4565 2.047179 GTTCTGCCACCGGTCCTC 60.047 66.667 2.59 0.00 0.00 3.71
2435 4609 2.169144 AGAAAAGCTTTGCCTGCAACTT 59.831 40.909 13.54 3.16 35.46 2.66
2455 4629 9.662947 GCAACTTATAGGTTTTAGAGGTAAGAA 57.337 33.333 0.00 0.00 0.00 2.52
2464 4638 5.934402 TTTAGAGGTAAGAACAGCTAGGG 57.066 43.478 0.00 0.00 0.00 3.53
2467 4641 2.838813 GAGGTAAGAACAGCTAGGGGTT 59.161 50.000 0.00 0.00 0.00 4.11
2469 4643 4.432316 AGGTAAGAACAGCTAGGGGTTAA 58.568 43.478 0.00 0.00 0.00 2.01
2479 4653 5.656859 ACAGCTAGGGGTTAAAATCATTTCC 59.343 40.000 0.00 0.00 0.00 3.13
2500 4674 6.239217 TCCAGTAGTAGAATGCATTCATGT 57.761 37.500 34.59 22.24 39.23 3.21
2501 4675 6.051074 TCCAGTAGTAGAATGCATTCATGTG 58.949 40.000 34.59 22.57 39.23 3.21
2525 4699 4.386652 GCACAAATTGTTGGTATGCTGAAG 59.613 41.667 0.00 0.00 39.22 3.02
2538 4712 5.008415 GGTATGCTGAAGATTTCACTCATGG 59.992 44.000 0.00 0.00 35.46 3.66
2539 4713 2.751259 TGCTGAAGATTTCACTCATGGC 59.249 45.455 0.00 0.00 35.46 4.40
2544 4718 1.369091 GATTTCACTCATGGCGCGGT 61.369 55.000 8.83 0.00 0.00 5.68
2554 4728 3.554692 GGCGCGGTGTCGAATCTG 61.555 66.667 8.83 0.00 39.00 2.90
2594 4768 0.917533 AGCTGGAGCAGATGATGGTT 59.082 50.000 0.65 0.00 45.16 3.67
2596 4770 2.709934 AGCTGGAGCAGATGATGGTTAT 59.290 45.455 0.65 0.00 45.16 1.89
2623 4797 1.148310 CTAACTTGGTGGTCACTGCG 58.852 55.000 0.93 0.00 0.00 5.18
2654 4828 4.742649 AGACCTGCTCGGCGAGGA 62.743 66.667 35.03 32.07 35.61 3.71
2734 4911 1.755008 GCTAGGGGTCTCGCTCACT 60.755 63.158 0.00 0.00 37.38 3.41
2736 4913 0.394488 CTAGGGGTCTCGCTCACTGA 60.394 60.000 0.00 0.00 37.38 3.41
2806 4988 5.428496 TGTGCTCATGCTGATATTTTAGC 57.572 39.130 0.00 0.00 40.48 3.09
2812 4994 6.471976 TCATGCTGATATTTTAGCGATGAC 57.528 37.500 9.23 0.00 42.74 3.06
2813 4995 5.990996 TCATGCTGATATTTTAGCGATGACA 59.009 36.000 9.23 0.00 42.74 3.58
2824 5006 5.545658 TTAGCGATGACAAAAATGAGACC 57.454 39.130 0.00 0.00 0.00 3.85
2934 5116 4.125703 GTCTCAGGAATCATGTGTGATCC 58.874 47.826 0.00 0.00 44.20 3.36
2948 5130 4.156922 TGTGTGATCCTTTCGTGTTTGTTT 59.843 37.500 0.00 0.00 0.00 2.83
2963 5145 5.750067 GTGTTTGTTTGCATTCTCTGTGATT 59.250 36.000 0.00 0.00 0.00 2.57
3056 5238 9.769093 CCTATTTGCAATGTGTTAAGTAGTAAC 57.231 33.333 0.00 0.00 42.24 2.50
3065 5253 8.828688 ATGTGTTAAGTAGTAACTCCAGAAAC 57.171 34.615 0.00 0.00 42.36 2.78
3089 5279 9.691362 AACACAATAAGCAATTAAAACACCTAG 57.309 29.630 0.00 0.00 0.00 3.02
3090 5280 8.856103 ACACAATAAGCAATTAAAACACCTAGT 58.144 29.630 0.00 0.00 0.00 2.57
3210 5400 1.375523 GACCTGCTGGGGTGTAACG 60.376 63.158 14.82 0.00 40.06 3.18
3222 5412 1.732259 GGTGTAACGATGCAGAACAGG 59.268 52.381 0.00 0.00 38.12 4.00
3223 5413 1.128692 GTGTAACGATGCAGAACAGGC 59.871 52.381 0.00 0.00 0.00 4.85
3224 5414 0.370273 GTAACGATGCAGAACAGGCG 59.630 55.000 0.00 0.00 36.43 5.52
3225 5415 0.037697 TAACGATGCAGAACAGGCGT 60.038 50.000 0.00 0.00 42.74 5.68
3279 5469 8.627208 AGAGACAGCAGAAGAATTTTCAAATA 57.373 30.769 0.00 0.00 0.00 1.40
3326 5523 2.352503 GTGCGCACCAGAAAATCATT 57.647 45.000 30.12 0.00 0.00 2.57
3356 5553 7.712639 TGGCAAACAAATAAACAAGATTTAGCA 59.287 29.630 0.00 0.00 0.00 3.49
3358 5555 7.735586 GCAAACAAATAAACAAGATTTAGCACG 59.264 33.333 0.00 0.00 0.00 5.34
3359 5556 6.927933 ACAAATAAACAAGATTTAGCACGC 57.072 33.333 0.00 0.00 0.00 5.34
3360 5557 5.861787 ACAAATAAACAAGATTTAGCACGCC 59.138 36.000 0.00 0.00 0.00 5.68
3361 5558 5.897377 AATAAACAAGATTTAGCACGCCT 57.103 34.783 0.00 0.00 0.00 5.52
3362 5559 3.559238 AAACAAGATTTAGCACGCCTG 57.441 42.857 0.00 0.00 0.00 4.85
3406 5603 5.001232 TCTCAGGTACAACCAAAACATAGC 58.999 41.667 0.00 0.00 41.95 2.97
3413 5610 2.215942 ACCAAAACATAGCCCCAGAC 57.784 50.000 0.00 0.00 0.00 3.51
3428 5625 3.355378 CCCAGACAAATGGCACTGAATA 58.645 45.455 5.48 0.00 39.17 1.75
3429 5626 3.379372 CCCAGACAAATGGCACTGAATAG 59.621 47.826 5.48 0.00 39.17 1.73
3430 5627 4.264253 CCAGACAAATGGCACTGAATAGA 58.736 43.478 5.48 0.00 32.48 1.98
3431 5628 4.701651 CCAGACAAATGGCACTGAATAGAA 59.298 41.667 5.48 0.00 32.48 2.10
3432 5629 5.183713 CCAGACAAATGGCACTGAATAGAAA 59.816 40.000 5.48 0.00 32.48 2.52
3433 5630 6.088824 CAGACAAATGGCACTGAATAGAAAC 58.911 40.000 5.48 0.00 32.90 2.78
3434 5631 5.769662 AGACAAATGGCACTGAATAGAAACA 59.230 36.000 5.48 0.00 0.00 2.83
3435 5632 6.017400 ACAAATGGCACTGAATAGAAACAG 57.983 37.500 5.48 0.00 39.65 3.16
3436 5633 4.708726 AATGGCACTGAATAGAAACAGC 57.291 40.909 0.00 0.00 37.61 4.40
3437 5634 3.138884 TGGCACTGAATAGAAACAGCA 57.861 42.857 0.00 0.00 37.61 4.41
3438 5635 3.485394 TGGCACTGAATAGAAACAGCAA 58.515 40.909 0.00 0.00 37.61 3.91
3439 5636 3.503363 TGGCACTGAATAGAAACAGCAAG 59.497 43.478 0.00 0.00 37.61 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.206048 TCACTCTGTACGTAGTTCATCTTGAA 59.794 38.462 0.00 0.00 37.78 2.69
26 27 5.704053 TCACTCTGTACGTAGTTCATCTTGA 59.296 40.000 0.00 0.00 37.78 3.02
27 28 5.795939 GTCACTCTGTACGTAGTTCATCTTG 59.204 44.000 0.00 0.00 37.78 3.02
28 29 5.390673 CGTCACTCTGTACGTAGTTCATCTT 60.391 44.000 0.00 0.00 37.78 2.40
29 30 4.093115 CGTCACTCTGTACGTAGTTCATCT 59.907 45.833 0.00 0.00 37.78 2.90
30 31 4.332788 CGTCACTCTGTACGTAGTTCATC 58.667 47.826 0.00 0.00 37.78 2.92
31 32 4.337985 CGTCACTCTGTACGTAGTTCAT 57.662 45.455 0.00 0.00 37.78 2.57
32 33 3.800929 CGTCACTCTGTACGTAGTTCA 57.199 47.619 0.00 0.00 37.78 3.18
39 40 1.951792 CACTCACGTCACTCTGTACG 58.048 55.000 0.00 0.00 44.47 3.67
40 41 1.001706 TGCACTCACGTCACTCTGTAC 60.002 52.381 0.00 0.00 0.00 2.90
41 42 1.001706 GTGCACTCACGTCACTCTGTA 60.002 52.381 10.32 0.00 32.98 2.74
42 43 0.249073 GTGCACTCACGTCACTCTGT 60.249 55.000 10.32 0.00 32.98 3.41
43 44 0.249031 TGTGCACTCACGTCACTCTG 60.249 55.000 19.41 0.00 46.01 3.35
44 45 0.459899 TTGTGCACTCACGTCACTCT 59.540 50.000 19.41 0.00 46.01 3.24
45 46 1.004927 GTTTGTGCACTCACGTCACTC 60.005 52.381 19.41 0.00 46.01 3.51
46 47 1.006832 GTTTGTGCACTCACGTCACT 58.993 50.000 19.41 0.00 46.01 3.41
47 48 0.724549 TGTTTGTGCACTCACGTCAC 59.275 50.000 19.41 4.75 46.01 3.67
48 49 0.724549 GTGTTTGTGCACTCACGTCA 59.275 50.000 19.41 6.07 46.01 4.35
49 50 0.724549 TGTGTTTGTGCACTCACGTC 59.275 50.000 19.41 11.45 46.01 4.34
50 51 1.378531 ATGTGTTTGTGCACTCACGT 58.621 45.000 19.41 20.12 46.01 4.49
51 52 2.473530 AATGTGTTTGTGCACTCACG 57.526 45.000 19.41 0.00 46.01 4.35
473 474 3.317993 TCTTAAGTTCCAAGGCAAACAGC 59.682 43.478 1.63 0.00 44.65 4.40
476 477 5.335976 CCATCTCTTAAGTTCCAAGGCAAAC 60.336 44.000 1.63 0.00 0.00 2.93
486 490 6.149640 GGTTTTGGAGACCATCTCTTAAGTTC 59.850 42.308 1.63 0.00 42.95 3.01
490 494 4.352595 TGGGTTTTGGAGACCATCTCTTAA 59.647 41.667 5.84 0.15 42.95 1.85
496 500 2.586648 AGTGGGTTTTGGAGACCATC 57.413 50.000 0.00 0.00 38.98 3.51
499 503 3.081804 CACATAGTGGGTTTTGGAGACC 58.918 50.000 0.00 0.00 36.41 3.85
531 535 2.642807 CCGGGGGATATGGTAACTCATT 59.357 50.000 0.00 0.00 37.61 2.57
532 536 2.158066 TCCGGGGGATATGGTAACTCAT 60.158 50.000 0.00 0.00 37.61 2.90
534 538 2.019807 TCCGGGGGATATGGTAACTC 57.980 55.000 0.00 0.00 37.61 3.01
535 539 2.500269 TTCCGGGGGATATGGTAACT 57.500 50.000 0.00 0.00 37.61 2.24
550 554 5.935789 TGGTAATAGAGGTTTCACTTTTCCG 59.064 40.000 0.00 0.00 0.00 4.30
569 573 5.475564 GGCTTTGTTGAGGTTCTTATGGTAA 59.524 40.000 0.00 0.00 0.00 2.85
574 578 3.181423 TGGGGCTTTGTTGAGGTTCTTAT 60.181 43.478 0.00 0.00 0.00 1.73
578 582 0.961753 CTGGGGCTTTGTTGAGGTTC 59.038 55.000 0.00 0.00 0.00 3.62
593 597 1.023513 GTTGCTGCTGCTACTCTGGG 61.024 60.000 19.71 0.00 40.73 4.45
600 604 1.178534 GGGTTTGGTTGCTGCTGCTA 61.179 55.000 17.00 6.36 40.48 3.49
605 609 2.524148 AGGGGGTTTGGTTGCTGC 60.524 61.111 0.00 0.00 0.00 5.25
608 612 0.608130 GATTGAGGGGGTTTGGTTGC 59.392 55.000 0.00 0.00 0.00 4.17
610 614 0.863956 TGGATTGAGGGGGTTTGGTT 59.136 50.000 0.00 0.00 0.00 3.67
612 616 1.560505 CTTGGATTGAGGGGGTTTGG 58.439 55.000 0.00 0.00 0.00 3.28
655 676 3.204827 CGTGCTATGCTGCCCCAC 61.205 66.667 0.00 0.00 0.00 4.61
656 677 4.488136 CCGTGCTATGCTGCCCCA 62.488 66.667 0.00 0.00 0.00 4.96
659 680 3.880846 GTGCCGTGCTATGCTGCC 61.881 66.667 0.00 0.00 0.00 4.85
661 682 1.974249 CTGTGTGCCGTGCTATGCTG 61.974 60.000 0.00 0.00 0.00 4.41
666 2776 2.342279 GTCCTGTGTGCCGTGCTA 59.658 61.111 0.00 0.00 0.00 3.49
691 2801 2.545952 GCGGTGGTGTATATCCTCTGTG 60.546 54.545 8.53 0.00 0.00 3.66
692 2802 1.687123 GCGGTGGTGTATATCCTCTGT 59.313 52.381 8.53 0.00 0.00 3.41
695 2805 1.000955 CTGGCGGTGGTGTATATCCTC 59.999 57.143 0.00 0.00 0.00 3.71
711 2826 1.899437 TACAGTAGGCTGGTGCTGGC 61.899 60.000 0.00 0.00 46.62 4.85
721 2836 2.186125 GTGCGGGGTACAGTAGGC 59.814 66.667 0.00 0.00 0.00 3.93
722 2837 2.493030 CGTGCGGGGTACAGTAGG 59.507 66.667 0.00 0.00 0.00 3.18
723 2838 2.202703 GCGTGCGGGGTACAGTAG 60.203 66.667 0.00 0.00 0.00 2.57
724 2839 4.118995 CGCGTGCGGGGTACAGTA 62.119 66.667 6.30 0.00 35.56 2.74
768 2883 1.432023 TTCTTGGGGTTGGGGAGGTC 61.432 60.000 0.00 0.00 0.00 3.85
794 2909 1.721487 GTGGATCGATGCGTTTGGG 59.279 57.895 12.54 0.00 0.00 4.12
860 2975 4.179579 GCAAAGATGGCGACGGGC 62.180 66.667 0.00 0.00 42.51 6.13
873 2991 4.634703 TTGCGGCGAGAGGGCAAA 62.635 61.111 12.98 0.00 43.06 3.68
931 3049 2.112297 GTTGGTTCGGGGCTGTGA 59.888 61.111 0.00 0.00 0.00 3.58
932 3050 2.983592 GGTTGGTTCGGGGCTGTG 60.984 66.667 0.00 0.00 0.00 3.66
952 3070 2.797177 AGGAAAGCAAGGTGGAGATC 57.203 50.000 0.00 0.00 0.00 2.75
964 3082 1.080501 GCGGGCAAGAAAGGAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
1101 3231 1.878522 GCTGGTCGGTCGCATGTAG 60.879 63.158 0.00 0.00 0.00 2.74
1108 3238 4.803426 GGAGCTGCTGGTCGGTCG 62.803 72.222 7.01 0.00 41.26 4.79
1195 3325 2.972505 CGCCTTGGTCAGCAACGT 60.973 61.111 0.00 0.00 0.00 3.99
1198 3328 4.577677 TGCCGCCTTGGTCAGCAA 62.578 61.111 0.00 0.00 41.21 3.91
1254 3384 3.382803 CTTCTGGGCGGAGGAGCAG 62.383 68.421 0.00 0.00 39.27 4.24
1398 3531 0.179089 CCGTCTTGATGAGGCTCCTG 60.179 60.000 12.86 0.00 0.00 3.86
1402 3535 1.260538 TGCTCCGTCTTGATGAGGCT 61.261 55.000 0.00 0.00 0.00 4.58
1477 3628 2.809601 CCCGTCGTCTCCTTTGCG 60.810 66.667 0.00 0.00 0.00 4.85
1495 3646 2.125912 CGCCACCTGGACGAAGAG 60.126 66.667 0.00 0.00 37.05 2.85
1623 3786 2.732016 CACTTGTCCGTCGTCCCA 59.268 61.111 0.00 0.00 0.00 4.37
1710 3882 3.894947 GAGGGAGAGCTCGCCGTC 61.895 72.222 33.48 33.48 41.85 4.79
1726 3898 4.816984 GCGTCCGGGAGAGGGAGA 62.817 72.222 0.00 0.00 33.31 3.71
1754 3926 2.419851 GCCTTCCTCTCATCTTGACCAG 60.420 54.545 0.00 0.00 0.00 4.00
1762 3934 2.421248 CCCAAGAAGCCTTCCTCTCATC 60.421 54.545 0.00 0.00 0.00 2.92
1764 3936 0.987294 CCCAAGAAGCCTTCCTCTCA 59.013 55.000 0.00 0.00 0.00 3.27
1768 3940 0.836400 TCGACCCAAGAAGCCTTCCT 60.836 55.000 0.00 0.00 0.00 3.36
1771 3943 0.984230 TGATCGACCCAAGAAGCCTT 59.016 50.000 0.00 0.00 0.00 4.35
1825 3997 3.117360 TCCTCTGAGATATCAGACCTGCA 60.117 47.826 15.98 0.00 41.34 4.41
1826 3998 3.495331 TCCTCTGAGATATCAGACCTGC 58.505 50.000 15.98 0.00 41.34 4.85
1842 4014 0.043940 ATCTTGGACCCAGCTCCTCT 59.956 55.000 0.00 0.00 0.00 3.69
1859 4031 2.094675 ACATGCTGTTGCCTTGGTATC 58.905 47.619 0.00 0.00 38.71 2.24
1864 4036 3.366679 CCTTTAGACATGCTGTTGCCTTG 60.367 47.826 0.00 0.00 38.71 3.61
1867 4039 2.095059 CACCTTTAGACATGCTGTTGCC 60.095 50.000 0.00 0.00 38.71 4.52
1869 4041 5.437289 TTTCACCTTTAGACATGCTGTTG 57.563 39.130 0.00 0.00 0.00 3.33
1870 4042 6.655078 AATTTCACCTTTAGACATGCTGTT 57.345 33.333 0.00 0.00 0.00 3.16
1871 4043 6.491403 AGAAATTTCACCTTTAGACATGCTGT 59.509 34.615 19.99 0.00 0.00 4.40
1874 4046 7.150783 AGAGAAATTTCACCTTTAGACATGC 57.849 36.000 19.99 0.00 0.00 4.06
1889 4061 6.015940 ACAAGCGATTTCAGGAAGAGAAATTT 60.016 34.615 0.00 0.00 43.60 1.82
1909 4081 4.998788 ACTGAAACTGGAAAGAAACAAGC 58.001 39.130 0.00 0.00 0.00 4.01
1910 4082 6.531594 GGAAACTGAAACTGGAAAGAAACAAG 59.468 38.462 0.00 0.00 0.00 3.16
1963 4135 4.717629 TTCGCCGACGGTCAGCAG 62.718 66.667 16.73 8.96 40.63 4.24
1966 4138 1.736645 ATTGTTCGCCGACGGTCAG 60.737 57.895 16.73 7.75 40.63 3.51
1970 4144 2.776072 GACATTGTTCGCCGACGG 59.224 61.111 10.29 10.29 40.63 4.79
2008 4182 2.357034 TGAAGAGCCGACAACGCC 60.357 61.111 0.00 0.00 38.29 5.68
2013 4187 0.976641 ATTCCAGTGAAGAGCCGACA 59.023 50.000 0.00 0.00 33.05 4.35
2014 4188 1.646189 GATTCCAGTGAAGAGCCGAC 58.354 55.000 0.00 0.00 33.05 4.79
2015 4189 0.537188 GGATTCCAGTGAAGAGCCGA 59.463 55.000 0.00 0.00 33.05 5.54
2016 4190 0.539051 AGGATTCCAGTGAAGAGCCG 59.461 55.000 5.29 0.00 33.05 5.52
2017 4191 1.556911 TGAGGATTCCAGTGAAGAGCC 59.443 52.381 5.29 0.00 33.05 4.70
2018 4192 3.340814 TTGAGGATTCCAGTGAAGAGC 57.659 47.619 5.29 0.00 33.05 4.09
2079 4253 2.195139 GCATCAGCCCCTGCATCT 59.805 61.111 0.00 0.00 41.13 2.90
2120 4294 0.037303 CCTGGACATGGTCAGCTTGT 59.963 55.000 10.82 0.00 33.68 3.16
2145 4319 1.686110 CTCCCCGCCTCTAGGTGTT 60.686 63.158 8.68 0.00 43.97 3.32
2151 4325 2.123425 ATTCGCTCCCCGCCTCTA 60.123 61.111 0.00 0.00 36.73 2.43
2193 4367 0.591659 GCACCACCGGAAGAAAGTTC 59.408 55.000 9.46 0.00 0.00 3.01
2210 4384 1.625417 TTCAGCATCCGGATCAGGCA 61.625 55.000 22.94 4.91 0.00 4.75
2238 4412 0.249784 CGGTCATCTGATGCCTGAGG 60.250 60.000 20.87 0.00 0.00 3.86
2301 4475 0.393077 ACTTGTTCACTGTCCTCCGG 59.607 55.000 0.00 0.00 0.00 5.14
2310 4484 1.101049 CACGGGCCAACTTGTTCACT 61.101 55.000 4.39 0.00 0.00 3.41
2385 4559 1.139947 CTTCTTCTCGCCGAGGACC 59.860 63.158 15.08 0.00 0.00 4.46
2391 4565 1.514443 GTCGGACTTCTTCTCGCCG 60.514 63.158 0.00 0.00 43.11 6.46
2400 4574 2.096860 GCTTTTCTTGTCGTCGGACTTC 60.097 50.000 6.57 0.00 43.79 3.01
2435 4609 8.605325 AGCTGTTCTTACCTCTAAAACCTATA 57.395 34.615 0.00 0.00 0.00 1.31
2455 4629 5.656859 GGAAATGATTTTAACCCCTAGCTGT 59.343 40.000 0.00 0.00 0.00 4.40
2467 4641 9.679661 TGCATTCTACTACTGGAAATGATTTTA 57.320 29.630 0.00 0.00 0.00 1.52
2469 4643 8.757982 ATGCATTCTACTACTGGAAATGATTT 57.242 30.769 0.00 0.00 0.00 2.17
2479 4653 5.277683 GCCACATGAATGCATTCTACTACTG 60.278 44.000 33.23 22.64 37.67 2.74
2491 4665 3.068560 ACAATTTGTGCCACATGAATGC 58.931 40.909 0.00 0.00 0.00 3.56
2500 4674 2.632028 AGCATACCAACAATTTGTGCCA 59.368 40.909 2.13 0.00 34.35 4.92
2501 4675 2.995258 CAGCATACCAACAATTTGTGCC 59.005 45.455 2.13 0.00 34.35 5.01
2525 4699 1.353103 CCGCGCCATGAGTGAAATC 59.647 57.895 0.00 0.00 0.00 2.17
2538 4712 1.515519 TACAGATTCGACACCGCGC 60.516 57.895 0.00 0.00 35.37 6.86
2539 4713 0.179171 AGTACAGATTCGACACCGCG 60.179 55.000 0.00 0.00 35.37 6.46
2594 4768 3.658705 ACCACCAAGTTAGAACCCCAATA 59.341 43.478 0.00 0.00 0.00 1.90
2596 4770 1.854280 ACCACCAAGTTAGAACCCCAA 59.146 47.619 0.00 0.00 0.00 4.12
2623 4797 2.615912 GCAGGTCTCTGGCACAAATATC 59.384 50.000 0.00 0.00 41.19 1.63
2654 4828 0.752054 GCTGGTGAGCAGCTCTCTAT 59.248 55.000 27.49 0.00 45.46 1.98
2724 4901 0.607762 AGCTGACTCAGTGAGCGAGA 60.608 55.000 20.31 0.72 46.70 4.04
2734 4911 3.255888 CACTACACTAACCAGCTGACTCA 59.744 47.826 17.39 0.00 0.00 3.41
2736 4913 2.563179 CCACTACACTAACCAGCTGACT 59.437 50.000 17.39 3.79 0.00 3.41
2806 4988 3.189080 TGCAGGTCTCATTTTTGTCATCG 59.811 43.478 0.00 0.00 0.00 3.84
2812 4994 4.053295 CCAGTTTGCAGGTCTCATTTTTG 58.947 43.478 0.00 0.00 0.00 2.44
2813 4995 3.493176 GCCAGTTTGCAGGTCTCATTTTT 60.493 43.478 0.00 0.00 0.00 1.94
2824 5006 5.063180 TGAATATTCTTGCCAGTTTGCAG 57.937 39.130 16.24 0.00 43.21 4.41
2917 5099 4.194640 CGAAAGGATCACACATGATTCCT 58.805 43.478 0.00 0.29 46.01 3.36
2934 5116 5.036737 AGAGAATGCAAACAAACACGAAAG 58.963 37.500 0.00 0.00 0.00 2.62
2948 5130 6.993902 TGCTGATTATAATCACAGAGAATGCA 59.006 34.615 21.67 21.53 40.32 3.96
2963 5145 6.489603 TGGAACTTCCCTTTTGCTGATTATA 58.510 36.000 5.30 0.00 35.03 0.98
3056 5238 9.474920 TTTTAATTGCTTATTGTGTTTCTGGAG 57.525 29.630 0.00 0.00 0.00 3.86
3089 5279 3.786635 AGTCTCAGCAATCATCGGTTAC 58.213 45.455 0.00 0.00 0.00 2.50
3090 5280 3.701542 AGAGTCTCAGCAATCATCGGTTA 59.298 43.478 1.94 0.00 0.00 2.85
3091 5281 2.499289 AGAGTCTCAGCAATCATCGGTT 59.501 45.455 1.94 0.00 0.00 4.44
3092 5282 2.106566 AGAGTCTCAGCAATCATCGGT 58.893 47.619 1.94 0.00 0.00 4.69
3093 5283 2.886862 AGAGTCTCAGCAATCATCGG 57.113 50.000 1.94 0.00 0.00 4.18
3094 5284 4.566545 AGTAGAGTCTCAGCAATCATCG 57.433 45.455 0.00 0.00 0.00 3.84
3210 5400 2.482374 GCACGCCTGTTCTGCATC 59.518 61.111 0.00 0.00 0.00 3.91
3222 5412 2.350091 GCATTCGATCACGCACGC 60.350 61.111 0.00 0.00 39.58 5.34
3223 5413 1.765161 ATGGCATTCGATCACGCACG 61.765 55.000 0.00 0.00 39.58 5.34
3224 5414 0.316442 CATGGCATTCGATCACGCAC 60.316 55.000 0.00 0.00 39.58 5.34
3225 5415 0.744057 ACATGGCATTCGATCACGCA 60.744 50.000 0.00 0.00 39.58 5.24
3279 5469 4.021102 ACTCTGGACCAAATTGTCGAAT 57.979 40.909 0.00 0.00 36.07 3.34
3317 5508 6.616774 TTTGTTTGCCAGGAAATGATTTTC 57.383 33.333 0.00 0.00 40.48 2.29
3326 5523 6.227298 TCTTGTTTATTTGTTTGCCAGGAA 57.773 33.333 0.00 0.00 0.00 3.36
3356 5553 2.928396 AAGTACCAGGCCAGGCGT 60.928 61.111 15.37 2.04 0.00 5.68
3358 5555 0.393132 GAAGAAGTACCAGGCCAGGC 60.393 60.000 15.37 1.26 0.00 4.85
3359 5556 0.984230 TGAAGAAGTACCAGGCCAGG 59.016 55.000 13.67 13.67 0.00 4.45
3360 5557 3.274288 GAATGAAGAAGTACCAGGCCAG 58.726 50.000 5.01 0.00 0.00 4.85
3361 5558 2.642311 TGAATGAAGAAGTACCAGGCCA 59.358 45.455 5.01 0.00 0.00 5.36
3362 5559 3.350219 TGAATGAAGAAGTACCAGGCC 57.650 47.619 0.00 0.00 0.00 5.19
3406 5603 0.251297 TCAGTGCCATTTGTCTGGGG 60.251 55.000 0.00 0.00 36.75 4.96
3413 5610 4.860907 GCTGTTTCTATTCAGTGCCATTTG 59.139 41.667 0.00 0.00 34.57 2.32


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

AutoCloner maintained by Alex Coulton.