Multiple sequence alignment - TraesCS2A01G548800

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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 TraesCS2A01G548800 chr2A 100.000 3591 0 0 1 3591 756164566 756168156 0.000000e+00 6632.0
1 TraesCS2A01G548800 chr2A 75.448 1617 360 33 984 2581 718366520 718364922 0.000000e+00 752.0
2 TraesCS2A01G548800 chr7A 91.145 2846 222 15 746 3584 126873051 126875873 0.000000e+00 3832.0
3 TraesCS2A01G548800 chr7A 94.173 738 43 0 1 738 126872218 126872955 0.000000e+00 1125.0
4 TraesCS2A01G548800 chr7A 92.926 311 21 1 3281 3591 126901856 126902165 5.470000e-123 451.0
5 TraesCS2A01G548800 chr4A 88.936 2856 278 27 746 3591 544618539 544615712 0.000000e+00 3489.0
6 TraesCS2A01G548800 chr4A 93.443 732 48 0 7 738 544619369 544618638 0.000000e+00 1086.0
7 TraesCS2A01G548800 chr4A 81.705 645 96 13 7 633 625245309 625244669 5.310000e-143 518.0
8 TraesCS2A01G548800 chr2B 85.127 1338 169 19 746 2058 61027862 61026530 0.000000e+00 1341.0
9 TraesCS2A01G548800 chr2B 87.688 731 90 0 9 739 61028690 61027960 0.000000e+00 852.0
10 TraesCS2A01G548800 chr2B 85.487 565 61 8 2099 2663 61026535 61025992 1.450000e-158 569.0
11 TraesCS2A01G548800 chr5B 74.923 1623 359 38 984 2581 522076449 522078048 0.000000e+00 699.0
12 TraesCS2A01G548800 chr5B 76.364 495 112 5 243 735 44052880 44053371 9.890000e-66 261.0
13 TraesCS2A01G548800 chr5B 78.431 357 75 2 383 738 70087944 70087589 7.750000e-57 231.0
14 TraesCS2A01G548800 chr1D 82.897 649 84 16 7 635 479711156 479711797 3.130000e-155 558.0
15 TraesCS2A01G548800 chr1D 74.684 158 37 3 2063 2218 19772338 19772494 2.310000e-07 67.6
16 TraesCS2A01G548800 chr3B 78.571 476 102 0 263 738 745710008 745710483 7.480000e-82 315.0
17 TraesCS2A01G548800 chr6B 77.311 357 74 6 380 735 415030657 415031007 1.690000e-48 204.0
18 TraesCS2A01G548800 chr6B 73.700 327 78 7 1131 1453 10408246 10407924 1.750000e-23 121.0
19 TraesCS2A01G548800 chr6B 73.476 328 77 10 1131 1453 10473283 10472961 8.150000e-22 115.0
20 TraesCS2A01G548800 chr6B 73.394 327 79 8 1131 1453 10538670 10538348 8.150000e-22 115.0


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 TraesCS2A01G548800 chr2A 756164566 756168156 3590 False 6632.000000 6632 100.000000 1 3591 1 chr2A.!!$F1 3590
1 TraesCS2A01G548800 chr2A 718364922 718366520 1598 True 752.000000 752 75.448000 984 2581 1 chr2A.!!$R1 1597
2 TraesCS2A01G548800 chr7A 126872218 126875873 3655 False 2478.500000 3832 92.659000 1 3584 2 chr7A.!!$F2 3583
3 TraesCS2A01G548800 chr4A 544615712 544619369 3657 True 2287.500000 3489 91.189500 7 3591 2 chr4A.!!$R2 3584
4 TraesCS2A01G548800 chr4A 625244669 625245309 640 True 518.000000 518 81.705000 7 633 1 chr4A.!!$R1 626
5 TraesCS2A01G548800 chr2B 61025992 61028690 2698 True 920.666667 1341 86.100667 9 2663 3 chr2B.!!$R1 2654
6 TraesCS2A01G548800 chr5B 522076449 522078048 1599 False 699.000000 699 74.923000 984 2581 1 chr5B.!!$F2 1597
7 TraesCS2A01G548800 chr1D 479711156 479711797 641 False 558.000000 558 82.897000 7 635 1 chr1D.!!$F2 628

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
765 876 0.110486 AGGGGTTTTGATGCGTGACT 59.890 50.0 0.0 0.0 0.0 3.41 F
1995 2152 0.178533 AAACGGTGGACAAAGGACGA 59.821 50.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 2318 0.239347 GCGCTGCACTTTGAATCACT 59.761 50.0 0.0 0.0 0.00 3.41 R
2801 2958 0.109342 CCACCAAGCACAGAGGTTCT 59.891 55.0 0.0 0.0 35.33 3.01 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
47 48 6.636454 ACAACCTATATTCTTGGGAAGTCA 57.364 37.500 0.00 0.00 34.70 3.41
73 74 8.487028 AGTTTCGGAATAAGATATGGAAAGAGT 58.513 33.333 0.00 0.00 0.00 3.24
139 140 2.236146 TGGTTGCTCGGTGAGTTCATAT 59.764 45.455 0.00 0.00 31.39 1.78
143 144 5.324697 GTTGCTCGGTGAGTTCATATTTTC 58.675 41.667 0.00 0.00 31.39 2.29
152 153 6.747280 GGTGAGTTCATATTTTCATTCCAACG 59.253 38.462 0.00 0.00 0.00 4.10
153 154 7.305474 GTGAGTTCATATTTTCATTCCAACGT 58.695 34.615 0.00 0.00 0.00 3.99
196 216 3.059884 TGTGTGAGCAAGATTTCGTCTC 58.940 45.455 0.00 0.00 35.67 3.36
214 234 0.251634 TCGGACATGGTGCAATGCTA 59.748 50.000 6.82 0.00 0.00 3.49
216 236 1.064505 CGGACATGGTGCAATGCTAAG 59.935 52.381 6.82 0.00 0.00 2.18
250 270 2.123511 TTTGTGGTGTGCAGGGGG 60.124 61.111 0.00 0.00 0.00 5.40
300 320 0.826715 GATGTGAGTGCCCTGCTCTA 59.173 55.000 0.00 0.00 32.35 2.43
329 349 1.840630 CTGCGTGCATCGGACAACAA 61.841 55.000 10.02 0.00 40.26 2.83
346 366 5.925509 ACAACAACTGGTACATAACAGAGT 58.074 37.500 10.93 6.07 38.20 3.24
427 447 6.512415 GCCTTCTCATAAGCACATTGATGTAC 60.512 42.308 0.00 0.00 39.39 2.90
609 629 2.742053 CGATGTCCGGAAAACACTTCAT 59.258 45.455 5.23 1.96 33.91 2.57
638 658 0.179000 GACATCCAGGCCAACGATCT 59.821 55.000 5.01 0.00 0.00 2.75
694 714 6.150140 AGACAACAAGATTAGAAACCTCATGC 59.850 38.462 0.00 0.00 0.00 4.06
739 759 6.154203 TGCAATACAAATTCTTTGGTGACA 57.846 33.333 4.77 0.00 44.81 3.58
741 761 7.215789 TGCAATACAAATTCTTTGGTGACATT 58.784 30.769 4.77 0.00 44.81 2.71
742 762 7.384660 TGCAATACAAATTCTTTGGTGACATTC 59.615 33.333 4.77 0.00 44.81 2.67
743 763 7.410728 GCAATACAAATTCTTTGGTGACATTCG 60.411 37.037 4.77 0.00 44.81 3.34
744 764 5.766150 ACAAATTCTTTGGTGACATTCGA 57.234 34.783 4.77 0.00 44.81 3.71
765 876 0.110486 AGGGGTTTTGATGCGTGACT 59.890 50.000 0.00 0.00 0.00 3.41
863 975 1.921346 AGGTATTGGGTGGCGGTGA 60.921 57.895 0.00 0.00 0.00 4.02
880 992 5.800438 GGCGGTGAGAAAATTATTTGTTCTC 59.200 40.000 10.73 10.73 44.93 2.87
892 1004 9.918630 AAATTATTTGTTCTCATCCTTGTCAAG 57.081 29.630 5.53 5.53 0.00 3.02
911 1023 5.800438 GTCAAGTTGGACAGTTTTCTTGAAC 59.200 40.000 2.34 0.00 41.38 3.18
912 1024 5.475220 TCAAGTTGGACAGTTTTCTTGAACA 59.525 36.000 2.34 0.00 38.42 3.18
947 1060 7.219535 GTCATTGATCAATTCATACTTGTGCAC 59.780 37.037 18.41 10.75 33.34 4.57
1043 1157 7.490657 AAACTTATCCTGATACAGTACACCA 57.509 36.000 0.00 0.00 0.00 4.17
1099 1213 2.288961 AACGCTAGGACCATTGTACG 57.711 50.000 0.00 0.00 0.00 3.67
1181 1295 1.005215 AGAGTTTGAATCAGCCTGGGG 59.995 52.381 0.00 0.00 0.00 4.96
1298 1412 6.348050 GGTGTTTTCTGTGCAAAAATGACAAA 60.348 34.615 0.00 0.00 0.00 2.83
1368 1482 1.038681 CAGCCAGCCCAATGCATGTA 61.039 55.000 0.00 0.00 44.83 2.29
1384 1498 4.049186 GCATGTATTCGTCCGACAATACT 58.951 43.478 21.49 12.36 36.71 2.12
1393 1507 3.739300 CGTCCGACAATACTTGAAACTGT 59.261 43.478 0.00 0.00 0.00 3.55
1451 1565 8.354426 GGAGAAGAGGACTATGATTGTAAGTAC 58.646 40.741 0.00 0.00 0.00 2.73
1524 1671 6.092807 GGGATTTACTGGATGCGATTCTTATC 59.907 42.308 0.00 0.00 0.00 1.75
1527 1674 8.764524 ATTTACTGGATGCGATTCTTATCTAC 57.235 34.615 0.00 0.00 0.00 2.59
1680 1827 7.326063 GCATACAATGTTACTGAAGTGGAAAAC 59.674 37.037 0.00 0.00 0.00 2.43
1685 1832 7.765695 ATGTTACTGAAGTGGAAAACATGAT 57.234 32.000 0.00 0.00 36.49 2.45
1750 1897 4.713814 AGTGGAGCAGAGTTGAATATGAGA 59.286 41.667 0.00 0.00 0.00 3.27
1770 1917 6.884832 TGAGATTACCATTAACGAGGACAAT 58.115 36.000 0.00 0.00 0.00 2.71
1801 1948 3.660111 GCGAGTGCGGCCAGTTTT 61.660 61.111 2.24 0.00 38.16 2.43
1813 1960 0.536460 CCAGTTTTAGCACACGGGGT 60.536 55.000 0.00 0.00 0.00 4.95
1859 2007 6.959311 CGAGTAAACTGCCATAAAACATGTAC 59.041 38.462 0.00 0.00 0.00 2.90
1863 2011 3.687698 ACTGCCATAAAACATGTACCGTC 59.312 43.478 0.00 0.00 0.00 4.79
1930 2087 2.485814 GTGGTTTTCTCTCATGCAGGTC 59.514 50.000 0.00 0.00 0.00 3.85
1975 2132 3.317430 AGATCCCTAAATACCACGTCGTC 59.683 47.826 0.00 0.00 0.00 4.20
1995 2152 0.178533 AAACGGTGGACAAAGGACGA 59.821 50.000 0.00 0.00 0.00 4.20
2024 2181 4.230041 ACATACTACCAGGTCACCTAGTCT 59.770 45.833 0.00 0.00 29.64 3.24
2035 2192 4.453751 GTCACCTAGTCTAGTACCAGAGG 58.546 52.174 6.15 0.00 0.00 3.69
2111 2268 0.460109 CATGGAAGTCGTGCGGATGA 60.460 55.000 0.00 0.00 0.00 2.92
2161 2318 2.228582 CGTCAATGTTGCCCTTGATTCA 59.771 45.455 0.00 0.00 34.18 2.57
2170 2327 3.765381 TGCCCTTGATTCAGTGATTCAA 58.235 40.909 22.62 22.62 33.09 2.69
2248 2405 1.012086 CAACGGCTGATGTCAGGATG 58.988 55.000 11.66 0.00 43.94 3.51
2345 2502 2.270257 GCCATGCAGTGCCTCACAA 61.270 57.895 13.72 0.00 36.74 3.33
2412 2569 0.179018 AAGGCGCCATATGAAGGACC 60.179 55.000 31.54 0.00 0.00 4.46
2505 2662 1.475034 GGATATGCCGAAGAAGCCACA 60.475 52.381 0.00 0.00 0.00 4.17
2515 2672 1.676967 GAAGCCACAGAAGCCTGGG 60.677 63.158 0.00 0.00 44.60 4.45
2672 2829 2.696989 ACATGATCTGTGCCGAATCA 57.303 45.000 0.00 0.00 36.48 2.57
2716 2873 2.202690 TGTGCTTATCGTCCGGCG 60.203 61.111 11.37 11.37 43.01 6.46
2729 2886 1.869132 GTCCGGCGAACTTGTTTACTT 59.131 47.619 9.30 0.00 0.00 2.24
2743 2900 3.799963 TGTTTACTTCTGTACGTGCTGTG 59.200 43.478 4.97 5.20 0.00 3.66
2744 2901 3.994204 TTACTTCTGTACGTGCTGTGA 57.006 42.857 4.97 0.00 0.00 3.58
2745 2902 2.423926 ACTTCTGTACGTGCTGTGAG 57.576 50.000 4.97 9.52 0.00 3.51
2746 2903 1.954382 ACTTCTGTACGTGCTGTGAGA 59.046 47.619 17.19 5.75 0.00 3.27
2765 2922 7.642669 TGTGAGAAGAAAACTGAAATTGCTAG 58.357 34.615 0.00 0.00 0.00 3.42
2799 2956 9.944376 AACATTAAGAATAAGTAGCTGAGTTGA 57.056 29.630 0.00 0.00 0.00 3.18
2800 2957 9.593134 ACATTAAGAATAAGTAGCTGAGTTGAG 57.407 33.333 0.00 0.00 0.00 3.02
2801 2958 9.809096 CATTAAGAATAAGTAGCTGAGTTGAGA 57.191 33.333 0.00 0.00 0.00 3.27
2803 2960 7.710676 AAGAATAAGTAGCTGAGTTGAGAGA 57.289 36.000 0.00 0.00 0.00 3.10
2804 2961 7.710676 AGAATAAGTAGCTGAGTTGAGAGAA 57.289 36.000 0.00 0.00 0.00 2.87
2805 2962 7.543756 AGAATAAGTAGCTGAGTTGAGAGAAC 58.456 38.462 0.00 0.00 0.00 3.01
2806 2963 4.529109 AAGTAGCTGAGTTGAGAGAACC 57.471 45.455 0.00 0.00 0.00 3.62
2807 2964 3.773560 AGTAGCTGAGTTGAGAGAACCT 58.226 45.455 0.00 0.00 0.00 3.50
2808 2965 3.761752 AGTAGCTGAGTTGAGAGAACCTC 59.238 47.826 0.00 0.00 42.30 3.85
2809 2966 2.888212 AGCTGAGTTGAGAGAACCTCT 58.112 47.619 0.00 0.00 44.28 3.69
2810 2967 2.562298 AGCTGAGTTGAGAGAACCTCTG 59.438 50.000 0.64 0.00 41.35 3.35
2811 2968 2.298729 GCTGAGTTGAGAGAACCTCTGT 59.701 50.000 0.64 0.00 41.35 3.41
2812 2969 3.860378 GCTGAGTTGAGAGAACCTCTGTG 60.860 52.174 0.64 0.00 41.35 3.66
2813 2970 2.036475 TGAGTTGAGAGAACCTCTGTGC 59.964 50.000 0.64 0.00 41.35 4.57
2819 2976 1.071385 AGAGAACCTCTGTGCTTGGTG 59.929 52.381 0.00 0.00 39.62 4.17
2823 2980 1.669115 CCTCTGTGCTTGGTGGTCG 60.669 63.158 0.00 0.00 0.00 4.79
2865 3022 0.319900 CTTCCAGTGGGTGACGACAG 60.320 60.000 9.92 0.00 42.21 3.51
2868 3025 0.321671 CCAGTGGGTGACGACAGAAT 59.678 55.000 0.00 0.00 42.21 2.40
2879 3036 0.321564 CGACAGAATTGGTGGCCTGA 60.322 55.000 3.32 0.00 0.00 3.86
2882 3039 2.424956 GACAGAATTGGTGGCCTGAATC 59.575 50.000 3.32 0.00 0.00 2.52
2883 3040 1.753073 CAGAATTGGTGGCCTGAATCC 59.247 52.381 3.32 0.00 0.00 3.01
2885 3042 0.039618 AATTGGTGGCCTGAATCCGT 59.960 50.000 3.32 0.00 0.00 4.69
2901 3058 2.553086 TCCGTTTACGACTTGTTTGCT 58.447 42.857 3.46 0.00 43.02 3.91
2903 3060 3.033185 CCGTTTACGACTTGTTTGCTTG 58.967 45.455 3.46 0.00 43.02 4.01
2904 3061 3.242478 CCGTTTACGACTTGTTTGCTTGA 60.242 43.478 3.46 0.00 43.02 3.02
2909 3066 1.326245 CGACTTGTTTGCTTGACGACA 59.674 47.619 0.00 0.00 0.00 4.35
2910 3067 2.032894 CGACTTGTTTGCTTGACGACAT 60.033 45.455 0.00 0.00 0.00 3.06
2911 3068 3.291585 GACTTGTTTGCTTGACGACATG 58.708 45.455 0.00 0.00 0.00 3.21
2951 3111 0.542467 TAGTTCTGGCCGTACCCACA 60.542 55.000 0.00 0.00 37.83 4.17
2952 3112 1.198759 AGTTCTGGCCGTACCCACAT 61.199 55.000 0.00 0.00 37.83 3.21
2992 3152 2.459555 ACCATATGCAGGAAAAGGGG 57.540 50.000 0.00 0.00 0.00 4.79
3046 3206 4.357279 AGGCCAAGGCTGAGGTGC 62.357 66.667 5.01 0.00 41.60 5.01
3067 3227 2.315925 ACACTTCAGACACACCACTG 57.684 50.000 0.00 0.00 35.72 3.66
3074 3234 1.453015 GACACACCACTGCCCACAA 60.453 57.895 0.00 0.00 0.00 3.33
3076 3236 1.453745 CACACCACTGCCCACAACT 60.454 57.895 0.00 0.00 0.00 3.16
3185 3345 1.668419 GCATAATGCGTTCCTCCACT 58.332 50.000 0.00 0.00 31.71 4.00
3192 3352 3.410631 TGCGTTCCTCCACTTGATTAA 57.589 42.857 0.00 0.00 0.00 1.40
3196 3356 3.877508 CGTTCCTCCACTTGATTAATCCC 59.122 47.826 12.90 0.00 0.00 3.85
3208 3368 3.134081 TGATTAATCCCGTGAGTTCCTCC 59.866 47.826 12.90 0.00 0.00 4.30
3215 3375 2.622436 CCGTGAGTTCCTCCAATCTTC 58.378 52.381 0.00 0.00 0.00 2.87
3224 3384 6.788218 AGTTCCTCCAATCTTCTTCTGAAAT 58.212 36.000 0.00 0.00 0.00 2.17
3225 3385 7.237255 AGTTCCTCCAATCTTCTTCTGAAATT 58.763 34.615 0.00 0.00 0.00 1.82
3226 3386 7.176340 AGTTCCTCCAATCTTCTTCTGAAATTG 59.824 37.037 5.83 5.83 0.00 2.32
3236 3398 7.428020 TCTTCTTCTGAAATTGGTTTGTGATG 58.572 34.615 0.00 0.00 0.00 3.07
3239 3401 7.874940 TCTTCTGAAATTGGTTTGTGATGTAG 58.125 34.615 0.00 0.00 0.00 2.74
3254 3416 1.869774 TGTAGGCATATGCTTCAGCG 58.130 50.000 26.12 0.00 45.83 5.18
3256 3418 0.758734 TAGGCATATGCTTCAGCGGT 59.241 50.000 26.12 4.97 45.83 5.68
3262 3424 1.153597 TATGCTTCAGCGGTGCATCG 61.154 55.000 16.79 16.79 44.91 3.84
3274 3436 2.632377 GGTGCATCGATTTCTGAAGGA 58.368 47.619 0.00 0.00 0.00 3.36
3280 3442 4.379813 GCATCGATTTCTGAAGGAAGCAAA 60.380 41.667 0.00 0.00 35.16 3.68
3283 3445 6.331369 TCGATTTCTGAAGGAAGCAAAAAT 57.669 33.333 0.00 0.00 35.16 1.82
3286 3448 6.307318 CGATTTCTGAAGGAAGCAAAAATCTG 59.693 38.462 0.00 0.00 35.16 2.90
3311 3473 2.424956 GTTGCAACCTTCATCTCCATCC 59.575 50.000 19.15 0.00 0.00 3.51
3386 3548 0.978146 AGGTCGGGAATGGAGAGGTG 60.978 60.000 0.00 0.00 0.00 4.00
3410 3572 6.480651 TGAGCATTTCGAACTGTACAAAACTA 59.519 34.615 15.83 0.00 0.00 2.24
3416 3578 3.656618 GAACTGTACAAAACTATCGCGC 58.343 45.455 0.00 0.00 0.00 6.86
3443 3605 3.054802 AGCTGAACCTTACCTCAATCCAG 60.055 47.826 0.00 0.00 0.00 3.86
3452 3614 5.508153 CCTTACCTCAATCCAGTCTGATACG 60.508 48.000 0.00 0.00 0.00 3.06
3464 3626 4.272748 CAGTCTGATACGGTTATGTCTCGA 59.727 45.833 0.00 0.00 0.00 4.04
3576 3738 2.355818 GGAAGAAGGGTTTGGCGACTAT 60.356 50.000 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.959030 TGTAGAAGTCATATGCCTCGCT 59.041 45.455 0.00 0.00 0.00 4.93
47 48 8.487028 ACTCTTTCCATATCTTATTCCGAAACT 58.513 33.333 0.00 0.00 0.00 2.66
73 74 0.963856 TCCGCTCGGCTTTGAGTCTA 60.964 55.000 2.96 0.00 38.28 2.59
82 83 2.737376 GTTTTCGTCCGCTCGGCT 60.737 61.111 2.96 0.00 34.68 5.52
196 216 1.064505 CTTAGCATTGCACCATGTCCG 59.935 52.381 11.91 0.00 0.00 4.79
214 234 4.949856 ACAAAGGAAGACATGTCAACACTT 59.050 37.500 27.02 20.06 0.00 3.16
216 236 4.498009 CCACAAAGGAAGACATGTCAACAC 60.498 45.833 27.02 13.92 41.22 3.32
250 270 4.392138 CCTACTGTTTTCGGATTCAGGTTC 59.608 45.833 0.00 0.00 32.92 3.62
279 299 0.826715 GAGCAGGGCACTCACATCTA 59.173 55.000 0.00 0.00 34.18 1.98
300 320 3.437795 GCACGCAGCAGCCTGATT 61.438 61.111 4.33 0.00 44.79 2.57
329 349 5.008811 GCTCGATACTCTGTTATGTACCAGT 59.991 44.000 0.00 0.00 0.00 4.00
346 366 1.170442 TGGTTGTGACTCGCTCGATA 58.830 50.000 0.00 0.00 0.00 2.92
427 447 5.389859 TGCTTTATCAAATCCTTGGTGTG 57.610 39.130 0.00 0.00 33.01 3.82
609 629 1.179152 CCTGGATGTCAGCAAATGCA 58.821 50.000 8.28 0.00 45.16 3.96
694 714 3.589881 GCTGCTGCCATTAGCCCG 61.590 66.667 3.85 0.00 43.02 6.13
739 759 1.818674 GCATCAAAACCCCTGTCGAAT 59.181 47.619 0.00 0.00 0.00 3.34
741 761 0.953471 CGCATCAAAACCCCTGTCGA 60.953 55.000 0.00 0.00 0.00 4.20
742 762 1.234615 ACGCATCAAAACCCCTGTCG 61.235 55.000 0.00 0.00 0.00 4.35
743 763 0.240945 CACGCATCAAAACCCCTGTC 59.759 55.000 0.00 0.00 0.00 3.51
744 764 0.179004 TCACGCATCAAAACCCCTGT 60.179 50.000 0.00 0.00 0.00 4.00
765 876 5.171476 CCATTCGAAGCTCTCTTCTTGTTA 58.829 41.667 3.35 0.00 45.01 2.41
855 966 5.242838 AGAACAAATAATTTTCTCACCGCCA 59.757 36.000 0.00 0.00 0.00 5.69
880 992 3.480470 ACTGTCCAACTTGACAAGGATG 58.520 45.455 19.16 15.94 44.19 3.51
892 1004 7.414814 TTTTTGTTCAAGAAAACTGTCCAAC 57.585 32.000 0.00 0.00 0.00 3.77
939 1052 2.074576 CAGACATCTCAGGTGCACAAG 58.925 52.381 20.43 12.61 0.00 3.16
947 1060 5.199024 AGATTCGAATCAGACATCTCAGG 57.801 43.478 33.42 0.00 37.89 3.86
1181 1295 2.085320 TGTACTTGTCGAGGAGAGCTC 58.915 52.381 5.27 5.27 0.00 4.09
1298 1412 1.674057 CTCTCGCTCCTTTGGGTGT 59.326 57.895 0.00 0.00 0.00 4.16
1384 1498 6.074516 CGTTCTCGATCAAACTACAGTTTCAA 60.075 38.462 4.38 0.00 41.65 2.69
1393 1507 2.159476 CGTCCCGTTCTCGATCAAACTA 60.159 50.000 0.00 0.00 39.71 2.24
1451 1565 4.577693 AGCATAGTGTGTATGGCAAGAATG 59.422 41.667 0.00 0.00 0.00 2.67
1685 1832 4.141824 TGTTGTGAGTGGTGATGTACTTCA 60.142 41.667 7.33 7.33 0.00 3.02
1750 1897 7.931578 TTGAATTGTCCTCGTTAATGGTAAT 57.068 32.000 0.00 0.00 0.00 1.89
1770 1917 2.093625 GCACTCGCACGTGAATATTGAA 59.906 45.455 22.23 0.00 37.06 2.69
1801 1948 2.031919 CAGCAACCCCGTGTGCTA 59.968 61.111 0.00 0.00 35.68 3.49
1836 1983 6.128117 CGGTACATGTTTTATGGCAGTTTACT 60.128 38.462 2.30 0.00 0.00 2.24
1859 2007 8.087982 ACTGCATACATTTTTATATCAGACGG 57.912 34.615 0.00 0.00 0.00 4.79
1975 2132 0.306533 CGTCCTTTGTCCACCGTTTG 59.693 55.000 0.00 0.00 0.00 2.93
1995 2152 4.466726 GGTGACCTGGTAGTATGTCTCTTT 59.533 45.833 0.00 0.00 0.00 2.52
2024 2181 4.422057 TGTGAATTGTCCCTCTGGTACTA 58.578 43.478 0.00 0.00 0.00 1.82
2035 2192 3.498397 ACGACATGTTCTGTGAATTGTCC 59.502 43.478 0.00 0.00 38.54 4.02
2080 2237 3.372206 CGACTTCCATGGCTTTGAAGTAG 59.628 47.826 16.55 13.66 46.37 2.57
2148 2305 3.765381 TGAATCACTGAATCAAGGGCAA 58.235 40.909 0.00 0.00 0.00 4.52
2161 2318 0.239347 GCGCTGCACTTTGAATCACT 59.761 50.000 0.00 0.00 0.00 3.41
2170 2327 3.982241 GCCAAAGGCGCTGCACTT 61.982 61.111 7.64 0.00 39.62 3.16
2197 2354 0.462759 CCTCGAAAGCCAGTCCATCC 60.463 60.000 0.00 0.00 0.00 3.51
2345 2502 1.178276 CCTCTACGCTTCTCTGGTGT 58.822 55.000 0.00 0.00 0.00 4.16
2412 2569 3.675698 GCAGAACCTTGTTCTCTTACTCG 59.324 47.826 6.51 0.00 0.00 4.18
2505 2662 2.014010 TTTGCATTTCCCAGGCTTCT 57.986 45.000 0.00 0.00 0.00 2.85
2665 2822 3.184379 CACAGCGGTATACAATGATTCGG 59.816 47.826 5.01 0.00 0.00 4.30
2666 2823 3.362986 GCACAGCGGTATACAATGATTCG 60.363 47.826 5.01 0.00 0.00 3.34
2672 2829 2.483714 CCTCAGCACAGCGGTATACAAT 60.484 50.000 5.01 0.00 0.00 2.71
2716 2873 5.233689 AGCACGTACAGAAGTAAACAAGTTC 59.766 40.000 0.00 0.00 37.74 3.01
2729 2886 2.227194 TCTTCTCACAGCACGTACAGA 58.773 47.619 0.00 0.00 0.00 3.41
2743 2900 7.080724 CCACTAGCAATTTCAGTTTTCTTCTC 58.919 38.462 0.00 0.00 0.00 2.87
2744 2901 6.515696 GCCACTAGCAATTTCAGTTTTCTTCT 60.516 38.462 0.00 0.00 42.97 2.85
2745 2902 5.631096 GCCACTAGCAATTTCAGTTTTCTTC 59.369 40.000 0.00 0.00 42.97 2.87
2746 2903 5.532557 GCCACTAGCAATTTCAGTTTTCTT 58.467 37.500 0.00 0.00 42.97 2.52
2765 2922 8.336080 GCTACTTATTCTTAATGTTACAGCCAC 58.664 37.037 0.00 0.00 0.00 5.01
2789 2946 2.562298 CAGAGGTTCTCTCAACTCAGCT 59.438 50.000 0.00 0.00 44.81 4.24
2796 2953 2.224378 CCAAGCACAGAGGTTCTCTCAA 60.224 50.000 0.00 0.00 44.81 3.02
2797 2954 1.345741 CCAAGCACAGAGGTTCTCTCA 59.654 52.381 0.00 0.00 44.81 3.27
2798 2955 1.346068 ACCAAGCACAGAGGTTCTCTC 59.654 52.381 0.00 0.00 38.99 3.20
2799 2956 1.071385 CACCAAGCACAGAGGTTCTCT 59.929 52.381 0.00 0.00 42.11 3.10
2800 2957 1.517242 CACCAAGCACAGAGGTTCTC 58.483 55.000 0.00 0.00 35.33 2.87
2801 2958 0.109342 CCACCAAGCACAGAGGTTCT 59.891 55.000 0.00 0.00 35.33 3.01
2802 2959 0.179018 ACCACCAAGCACAGAGGTTC 60.179 55.000 0.00 0.00 35.33 3.62
2803 2960 0.179018 GACCACCAAGCACAGAGGTT 60.179 55.000 0.00 0.00 38.79 3.50
2804 2961 1.451936 GACCACCAAGCACAGAGGT 59.548 57.895 0.00 0.00 35.65 3.85
2805 2962 1.669115 CGACCACCAAGCACAGAGG 60.669 63.158 0.00 0.00 0.00 3.69
2806 2963 1.669115 CCGACCACCAAGCACAGAG 60.669 63.158 0.00 0.00 0.00 3.35
2807 2964 2.425592 CCGACCACCAAGCACAGA 59.574 61.111 0.00 0.00 0.00 3.41
2808 2965 2.111043 ACCGACCACCAAGCACAG 59.889 61.111 0.00 0.00 0.00 3.66
2809 2966 2.203139 CACCGACCACCAAGCACA 60.203 61.111 0.00 0.00 0.00 4.57
2810 2967 2.203153 ACACCGACCACCAAGCAC 60.203 61.111 0.00 0.00 0.00 4.40
2811 2968 2.050836 ATGACACCGACCACCAAGCA 62.051 55.000 0.00 0.00 0.00 3.91
2812 2969 1.302511 ATGACACCGACCACCAAGC 60.303 57.895 0.00 0.00 0.00 4.01
2813 2970 1.577328 GCATGACACCGACCACCAAG 61.577 60.000 0.00 0.00 0.00 3.61
2819 2976 1.647346 TTATTCGCATGACACCGACC 58.353 50.000 0.00 0.00 32.60 4.79
2823 2980 4.500477 GCAAAGATTTATTCGCATGACACC 59.500 41.667 0.00 0.00 0.00 4.16
2865 3022 0.740737 CGGATTCAGGCCACCAATTC 59.259 55.000 5.01 0.00 0.00 2.17
2868 3025 0.178975 AAACGGATTCAGGCCACCAA 60.179 50.000 5.01 0.00 0.00 3.67
2879 3036 3.562557 AGCAAACAAGTCGTAAACGGATT 59.437 39.130 2.24 0.00 40.29 3.01
2882 3039 3.033185 CAAGCAAACAAGTCGTAAACGG 58.967 45.455 2.24 0.00 40.29 4.44
2883 3040 3.717404 GTCAAGCAAACAAGTCGTAAACG 59.283 43.478 0.00 0.00 41.45 3.60
2885 3042 3.617706 TCGTCAAGCAAACAAGTCGTAAA 59.382 39.130 0.00 0.00 0.00 2.01
2901 3058 1.553195 CGTTGCGTCCATGTCGTCAA 61.553 55.000 8.80 9.79 0.00 3.18
2903 3060 1.554042 AACGTTGCGTCCATGTCGTC 61.554 55.000 0.00 3.43 39.99 4.20
2904 3061 0.318869 TAACGTTGCGTCCATGTCGT 60.319 50.000 11.99 0.00 39.99 4.34
2926 3086 0.245539 TACGGCCAGAACTAGCACAC 59.754 55.000 2.24 0.00 0.00 3.82
2931 3091 0.175073 GTGGGTACGGCCAGAACTAG 59.825 60.000 2.24 0.00 39.65 2.57
2935 3095 1.502690 ATATGTGGGTACGGCCAGAA 58.497 50.000 2.24 0.00 39.65 3.02
2937 3097 1.140052 TGAATATGTGGGTACGGCCAG 59.860 52.381 2.24 0.00 39.65 4.85
3046 3206 3.384668 CAGTGGTGTGTCTGAAGTGTAG 58.615 50.000 0.00 0.00 34.02 2.74
3067 3227 1.305201 TTTCGAACTGAGTTGTGGGC 58.695 50.000 0.90 0.00 0.00 5.36
3074 3234 6.142320 GCGATTTGAAATTTTTCGAACTGAGT 59.858 34.615 0.00 0.00 41.83 3.41
3076 3236 5.401079 GGCGATTTGAAATTTTTCGAACTGA 59.599 36.000 0.00 0.00 41.83 3.41
3125 3285 1.405821 ACTACTTCCCGATTCAGCGAG 59.594 52.381 0.00 0.00 0.00 5.03
3185 3345 4.837093 AGGAACTCACGGGATTAATCAA 57.163 40.909 17.07 0.00 0.00 2.57
3208 3368 7.922278 TCACAAACCAATTTCAGAAGAAGATTG 59.078 33.333 0.00 0.00 35.01 2.67
3215 3375 7.086376 CCTACATCACAAACCAATTTCAGAAG 58.914 38.462 0.00 0.00 0.00 2.85
3224 3384 4.097741 GCATATGCCTACATCACAAACCAA 59.902 41.667 17.26 0.00 37.74 3.67
3225 3385 3.631686 GCATATGCCTACATCACAAACCA 59.368 43.478 17.26 0.00 37.74 3.67
3226 3386 3.885297 AGCATATGCCTACATCACAAACC 59.115 43.478 23.96 0.00 43.38 3.27
3236 3398 1.151668 CCGCTGAAGCATATGCCTAC 58.848 55.000 23.96 15.25 43.38 3.18
3239 3401 1.650912 CACCGCTGAAGCATATGCC 59.349 57.895 23.96 10.41 43.38 4.40
3254 3416 2.632377 TCCTTCAGAAATCGATGCACC 58.368 47.619 0.00 0.00 0.00 5.01
3256 3418 2.679837 GCTTCCTTCAGAAATCGATGCA 59.320 45.455 0.00 0.00 32.88 3.96
3262 3424 6.090493 GCAGATTTTTGCTTCCTTCAGAAATC 59.910 38.462 9.55 9.55 41.48 2.17
3286 3448 2.352127 GGAGATGAAGGTTGCAACAAGC 60.352 50.000 29.55 17.71 45.96 4.01
3296 3458 1.056700 CCCGGGATGGAGATGAAGGT 61.057 60.000 18.48 0.00 42.00 3.50
3358 3520 0.905357 ATTCCCGACCTCCAACTCAG 59.095 55.000 0.00 0.00 0.00 3.35
3386 3548 5.748592 AGTTTTGTACAGTTCGAAATGCTC 58.251 37.500 24.26 17.18 0.00 4.26
3416 3578 2.300152 TGAGGTAAGGTTCAGCTGTCTG 59.700 50.000 14.67 0.00 41.67 3.51
3443 3605 4.808077 TCGAGACATAACCGTATCAGAC 57.192 45.455 0.00 0.00 0.00 3.51
3452 3614 5.285651 CCTGAAGAGAATCGAGACATAACC 58.714 45.833 0.00 0.00 42.67 2.85
3464 3626 0.827368 GACCTCGCCCTGAAGAGAAT 59.173 55.000 0.00 0.00 36.65 2.40


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

AutoCloner maintained by Alex Coulton.