Multiple sequence alignment - TraesCS7A01G418200

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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 TraesCS7A01G418200 chr7A 100.000 3765 0 0 1 3765 609548041 609551805 0.000000e+00 6953
1 TraesCS7A01G418200 chr7A 87.747 2326 246 27 549 2859 610433524 610435825 0.000000e+00 2680
2 TraesCS7A01G418200 chr7A 84.091 220 25 7 775 992 610432356 610432567 1.770000e-48 204
3 TraesCS7A01G418200 chr7B 92.617 3332 194 24 450 3765 568487896 568491191 0.000000e+00 4743
4 TraesCS7A01G418200 chr7B 89.944 2307 201 22 562 2859 568645606 568647890 0.000000e+00 2946
5 TraesCS7A01G418200 chr7B 93.478 92 5 1 361 452 568487627 568487717 6.560000e-28 135
6 TraesCS7A01G418200 chr7D 87.167 2252 242 27 619 2859 530103031 530105246 0.000000e+00 2514
7 TraesCS7A01G418200 chr7D 97.975 642 13 0 10 651 530024279 530024920 0.000000e+00 1114
8 TraesCS7A01G418200 chr7D 83.270 263 9 12 225 452 530102697 530102959 3.810000e-50 209


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 TraesCS7A01G418200 chr7A 609548041 609551805 3764 False 6953.0 6953 100.0000 1 3765 1 chr7A.!!$F1 3764
1 TraesCS7A01G418200 chr7A 610432356 610435825 3469 False 1442.0 2680 85.9190 549 2859 2 chr7A.!!$F2 2310
2 TraesCS7A01G418200 chr7B 568645606 568647890 2284 False 2946.0 2946 89.9440 562 2859 1 chr7B.!!$F1 2297
3 TraesCS7A01G418200 chr7B 568487627 568491191 3564 False 2439.0 4743 93.0475 361 3765 2 chr7B.!!$F2 3404
4 TraesCS7A01G418200 chr7D 530102697 530105246 2549 False 1361.5 2514 85.2185 225 2859 2 chr7D.!!$F2 2634
5 TraesCS7A01G418200 chr7D 530024279 530024920 641 False 1114.0 1114 97.9750 10 651 1 chr7D.!!$F1 641

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
155 156 0.817654 CACTCACCGCCTCATCTACA 59.182 55.0 0.00 0.00 0.00 2.74 F
1643 2268 0.252881 TGGTTCCTGGAGAGGCTCAT 60.253 55.0 18.26 1.35 39.57 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 2270 0.251354 TGCCACAGCTCCTTCATCTC 59.749 55.0 0.0 0.0 40.80 2.75 R
2814 3457 0.802607 GGCAGTACACTAGCGACAGC 60.803 60.0 0.0 0.0 45.58 4.40 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
155 156 0.817654 CACTCACCGCCTCATCTACA 59.182 55.000 0.00 0.00 0.00 2.74
158 159 2.298610 CTCACCGCCTCATCTACACTA 58.701 52.381 0.00 0.00 0.00 2.74
658 1280 9.874205 CTAGGATCAGAGGATTAAATTGATCTC 57.126 37.037 11.25 3.98 42.24 2.75
724 1346 4.342378 GCACCAGTATGAGACCTATCTTGA 59.658 45.833 0.00 0.00 39.69 3.02
728 1350 5.506483 CCAGTATGAGACCTATCTTGACACG 60.506 48.000 0.00 0.00 39.69 4.49
731 1353 3.632333 TGAGACCTATCTTGACACGGAT 58.368 45.455 0.00 0.00 34.34 4.18
748 1370 6.959361 ACACGGATATATGCATTTGTTTCTC 58.041 36.000 3.54 0.00 0.00 2.87
749 1371 6.542005 ACACGGATATATGCATTTGTTTCTCA 59.458 34.615 3.54 0.00 0.00 3.27
851 1475 6.962116 CCGTATCAGTAGATATGTTGTCGATC 59.038 42.308 0.00 0.00 40.58 3.69
868 1492 5.810587 TGTCGATCCAATAGCTTTTGTCTAC 59.189 40.000 14.65 9.59 0.00 2.59
900 1524 2.380064 TTGCATGTTCACCCCTTCTT 57.620 45.000 0.00 0.00 0.00 2.52
932 1556 1.747355 CCTACTTCCTTGCCATTGCTG 59.253 52.381 0.00 0.00 38.71 4.41
943 1567 1.135689 GCCATTGCTGTACTTGGTTCG 60.136 52.381 0.00 0.00 33.53 3.95
995 1620 1.623811 TGACTTCAGCCCTCCTTACAC 59.376 52.381 0.00 0.00 0.00 2.90
997 1622 3.097614 GACTTCAGCCCTCCTTACACTA 58.902 50.000 0.00 0.00 0.00 2.74
1092 1717 3.364366 GCTCTCAAATTGTGGTCTTGACG 60.364 47.826 0.00 0.00 0.00 4.35
1096 1721 1.967319 AATTGTGGTCTTGACGCTGT 58.033 45.000 0.00 0.00 0.00 4.40
1134 1759 4.457257 GGGGAGATCTTTGTTTCACTCTTG 59.543 45.833 0.00 0.00 0.00 3.02
1181 1806 3.616956 AGACATGCAAGATCTTCCGAA 57.383 42.857 4.57 0.00 0.00 4.30
1182 1807 4.148128 AGACATGCAAGATCTTCCGAAT 57.852 40.909 4.57 0.00 0.00 3.34
1203 1828 0.537188 TGAAGATCAGCTCGGTTCCC 59.463 55.000 0.00 0.00 0.00 3.97
1226 1851 4.551990 CGTCGAGCTTGAAGAGATAGACTC 60.552 50.000 11.14 0.00 42.13 3.36
1235 1860 2.846039 GAGATAGACTCGGCGAACAA 57.154 50.000 12.13 0.00 35.84 2.83
1246 1871 2.023461 CGAACAACGCGGCACAAA 59.977 55.556 12.47 0.00 34.51 2.83
1257 1882 1.511850 CGGCACAAAGTGATGAGTCA 58.488 50.000 0.00 0.00 35.23 3.41
1321 1946 4.390129 ACAGAGTTGAAGAGGAGTAGGA 57.610 45.455 0.00 0.00 0.00 2.94
1418 2043 8.437360 TTTCTGTATATAACTCATGTGCCAAG 57.563 34.615 0.00 0.00 0.00 3.61
1634 2259 3.012502 AGACTACTGGTATGGTTCCTGGA 59.987 47.826 0.00 0.00 0.00 3.86
1643 2268 0.252881 TGGTTCCTGGAGAGGCTCAT 60.253 55.000 18.26 1.35 39.57 2.90
1645 2270 1.691434 GGTTCCTGGAGAGGCTCATAG 59.309 57.143 18.26 11.05 39.57 2.23
1648 2273 2.139382 TCCTGGAGAGGCTCATAGAGA 58.861 52.381 18.26 4.89 39.57 3.10
1660 2285 3.321682 GCTCATAGAGATGAAGGAGCTGT 59.678 47.826 0.00 0.00 41.62 4.40
1769 2394 0.254178 CTTGTAGCAGCTGGGGTCAT 59.746 55.000 17.12 0.00 0.00 3.06
1791 2416 1.308047 TGTTCTGCGCTGTTGATTGT 58.692 45.000 9.73 0.00 0.00 2.71
1848 2473 5.766670 TCAGAAGACTGTCAATGCATTCTTT 59.233 36.000 9.53 0.00 43.81 2.52
1862 2487 4.771577 TGCATTCTTTATGGTGGTGAATGT 59.228 37.500 13.23 0.00 43.20 2.71
1896 2521 3.614092 GGAGAATTCCATTGACTGCTCA 58.386 45.455 0.65 0.00 43.45 4.26
1905 2530 3.332034 CATTGACTGCTCACTCATGTCA 58.668 45.455 0.00 0.00 36.10 3.58
1908 2533 0.322975 ACTGCTCACTCATGTCACCC 59.677 55.000 0.00 0.00 0.00 4.61
1924 2549 3.098377 TCACCCGCCATTGTAGTACTAA 58.902 45.455 3.61 0.00 0.00 2.24
1925 2550 3.707611 TCACCCGCCATTGTAGTACTAAT 59.292 43.478 3.61 0.00 0.00 1.73
1926 2551 4.894705 TCACCCGCCATTGTAGTACTAATA 59.105 41.667 3.61 0.00 0.00 0.98
1932 2557 7.606456 CCCGCCATTGTAGTACTAATATTCATT 59.394 37.037 3.61 0.00 0.00 2.57
1960 2585 5.490159 TGATGTAAGTTGATGACTGCATGA 58.510 37.500 0.00 0.00 39.00 3.07
2032 2661 9.646427 AGTACTTACTTGCTTTAGAATCTCAAG 57.354 33.333 7.59 7.59 39.79 3.02
2035 2664 9.377312 ACTTACTTGCTTTAGAATCTCAAGATC 57.623 33.333 13.99 0.00 37.96 2.75
2055 2684 5.415701 AGATCCATGTGCGACAATTTACTTT 59.584 36.000 0.00 0.00 0.00 2.66
2079 2708 3.010027 TGGTCTCAGGTATTTGCCATCAA 59.990 43.478 0.00 0.00 0.00 2.57
2082 2711 4.458989 GTCTCAGGTATTTGCCATCAACAA 59.541 41.667 0.00 0.00 30.75 2.83
2088 2717 4.447389 GGTATTTGCCATCAACAACAACAC 59.553 41.667 0.00 0.00 30.75 3.32
2091 2720 4.991153 TTGCCATCAACAACAACACTTA 57.009 36.364 0.00 0.00 0.00 2.24
2138 2767 0.721718 CCGATGAGAACACGAAAGGC 59.278 55.000 0.00 0.00 0.00 4.35
2141 2770 2.159787 CGATGAGAACACGAAAGGCAAG 60.160 50.000 0.00 0.00 0.00 4.01
2142 2771 2.613026 TGAGAACACGAAAGGCAAGA 57.387 45.000 0.00 0.00 0.00 3.02
2143 2772 2.483876 TGAGAACACGAAAGGCAAGAG 58.516 47.619 0.00 0.00 0.00 2.85
2171 2800 0.534203 GAGGGTCGTTGGTGCAGAAA 60.534 55.000 0.00 0.00 0.00 2.52
2180 2809 3.140623 GTTGGTGCAGAAATTGGCATTT 58.859 40.909 3.43 0.00 42.75 2.32
2186 2815 3.181457 TGCAGAAATTGGCATTTTCACCA 60.181 39.130 27.20 21.48 35.90 4.17
2211 2840 3.730662 CGGGTTTAATGCGATCTTTGTGG 60.731 47.826 0.00 0.00 0.00 4.17
2258 2887 1.625818 AGGCTCAGAAACGATCCACTT 59.374 47.619 0.00 0.00 0.00 3.16
2267 2896 5.926542 CAGAAACGATCCACTTAACTTCTCA 59.073 40.000 0.00 0.00 0.00 3.27
2285 2914 8.273780 ACTTCTCAACCTTGAACATGATATTC 57.726 34.615 0.00 0.00 36.64 1.75
2304 2933 1.691976 TCGAGGTCATCAGGTGTGTTT 59.308 47.619 0.00 0.00 0.00 2.83
2345 2978 7.920151 TGAAATATTTCATTATTCTGCCGGTTG 59.080 33.333 23.86 0.00 41.88 3.77
2366 2999 4.214310 TGGCAAAGATGGAGAAAAGACAA 58.786 39.130 0.00 0.00 0.00 3.18
2369 3002 4.978580 GCAAAGATGGAGAAAAGACAACAC 59.021 41.667 0.00 0.00 0.00 3.32
2379 3012 4.398044 AGAAAAGACAACACGACAATGGTT 59.602 37.500 0.00 0.00 0.00 3.67
2391 3024 5.294306 CACGACAATGGTTGCATAGACTAAT 59.706 40.000 0.00 0.00 31.02 1.73
2476 3109 5.411361 TGTTTGCAAGAGCTAAACACGATAT 59.589 36.000 7.49 0.00 41.86 1.63
2477 3110 6.592220 TGTTTGCAAGAGCTAAACACGATATA 59.408 34.615 7.49 0.00 41.86 0.86
2479 3112 5.902681 TGCAAGAGCTAAACACGATATACT 58.097 37.500 0.00 0.00 42.74 2.12
2480 3113 7.034685 TGCAAGAGCTAAACACGATATACTA 57.965 36.000 0.00 0.00 42.74 1.82
2481 3114 7.485810 TGCAAGAGCTAAACACGATATACTAA 58.514 34.615 0.00 0.00 42.74 2.24
2483 3116 8.267367 GCAAGAGCTAAACACGATATACTAAAC 58.733 37.037 0.00 0.00 37.91 2.01
2484 3117 9.517609 CAAGAGCTAAACACGATATACTAAACT 57.482 33.333 0.00 0.00 0.00 2.66
2572 3215 0.887247 TGTTTTGCAGCGCATATGGT 59.113 45.000 11.47 0.00 38.76 3.55
2678 3321 1.728323 TTCTGGATGGTGGAGTGACA 58.272 50.000 0.00 0.00 0.00 3.58
2679 3322 1.728323 TCTGGATGGTGGAGTGACAA 58.272 50.000 0.00 0.00 0.00 3.18
2751 3394 1.394618 GCAATGGCCACGGGTAAATA 58.605 50.000 8.16 0.00 0.00 1.40
2806 3449 5.359194 TTGGAAAGGCAAATGTACCAAAA 57.641 34.783 0.00 0.00 33.86 2.44
2836 3479 0.802607 GTCGCTAGTGTACTGCCTGC 60.803 60.000 2.66 0.00 0.00 4.85
2870 3513 9.516314 GGTTTCTAATTGGATTATAGTTTGTGC 57.484 33.333 0.00 0.00 0.00 4.57
2898 3541 2.042104 CTTGCAAAGGACAAGCTTCG 57.958 50.000 0.00 0.00 41.27 3.79
2902 3545 1.335051 GCAAAGGACAAGCTTCGGTTC 60.335 52.381 0.00 0.00 0.00 3.62
2908 3551 1.374947 CAAGCTTCGGTTCCCCTGA 59.625 57.895 0.00 0.00 0.00 3.86
2910 3553 0.253327 AAGCTTCGGTTCCCCTGATC 59.747 55.000 0.00 0.00 0.00 2.92
2923 3566 2.686915 CCCCTGATCAAGTCATCTTTGC 59.313 50.000 0.00 0.00 35.97 3.68
2929 3572 5.716094 TGATCAAGTCATCTTTGCATTTGG 58.284 37.500 0.00 0.00 0.00 3.28
2964 3607 5.886960 AGGTATCAATGCAACTGAAGAAC 57.113 39.130 6.00 5.44 0.00 3.01
3016 3659 1.002659 TGTAACCACATGAGTTCCCCG 59.997 52.381 0.00 0.00 0.00 5.73
3017 3660 0.035820 TAACCACATGAGTTCCCCGC 60.036 55.000 0.00 0.00 0.00 6.13
3018 3661 2.063015 AACCACATGAGTTCCCCGCA 62.063 55.000 0.00 0.00 0.00 5.69
3019 3662 1.303236 CCACATGAGTTCCCCGCAA 60.303 57.895 0.00 0.00 0.00 4.85
3020 3663 0.680921 CCACATGAGTTCCCCGCAAT 60.681 55.000 0.00 0.00 0.00 3.56
3021 3664 1.176527 CACATGAGTTCCCCGCAATT 58.823 50.000 0.00 0.00 0.00 2.32
3022 3665 1.135315 CACATGAGTTCCCCGCAATTG 60.135 52.381 0.00 0.00 0.00 2.32
3027 3670 0.975887 AGTTCCCCGCAATTGCAATT 59.024 45.000 28.77 18.99 42.21 2.32
3138 3781 0.671251 CTTTACCGCTTTGGCACCAA 59.329 50.000 0.00 0.00 43.94 3.67
3175 3818 8.443160 ACGAAATGATAGTGTTGTTTATCACTG 58.557 33.333 7.88 0.00 43.46 3.66
3254 3897 7.798596 TTCAAAGCCTAAAATTTGCATTCAA 57.201 28.000 0.00 0.00 36.55 2.69
3267 3910 3.715628 GCATTCAAATAATGCCTCGGT 57.284 42.857 10.83 0.00 45.31 4.69
3290 3933 7.094975 CGGTATATTTGTTGAGGTCTTTGAACA 60.095 37.037 0.00 0.00 0.00 3.18
3368 4011 1.073284 TGGAAACCCAGCTAACAGGTC 59.927 52.381 0.00 0.00 32.00 3.85
3391 4034 7.115095 GGTCTGAGTTATACGCTAATGCTTAAG 59.885 40.741 0.00 0.00 36.97 1.85
3430 4073 7.667043 ATTTGAAGAAATAACTCTACACGCA 57.333 32.000 0.00 0.00 29.49 5.24
3453 4096 2.467880 TCACTTAAGGCCAGTAGGGAG 58.532 52.381 5.01 0.00 40.01 4.30
3480 4123 6.034898 CCAGAGTCAAAACAAACACACAAATC 59.965 38.462 0.00 0.00 0.00 2.17
3494 4137 5.106038 ACACACAAATCATGCAAGTGGATAG 60.106 40.000 0.00 0.00 35.27 2.08
3501 4144 5.144692 TCATGCAAGTGGATAGAGCTATC 57.855 43.478 8.64 8.64 40.83 2.08
3511 4154 5.048643 GTGGATAGAGCTATCGAGTTTGCTA 60.049 44.000 10.47 0.00 42.10 3.49
3523 4166 3.006247 GAGTTTGCTAAGCCTTCTCTGG 58.994 50.000 0.00 0.00 0.00 3.86
3533 4176 4.706842 AGCCTTCTCTGGTGTCTTTTTA 57.293 40.909 0.00 0.00 0.00 1.52
3592 4235 4.865365 ACAATTACTCTGTTTAGCTCGAGC 59.135 41.667 30.01 30.01 42.49 5.03
3667 4310 1.178276 CTAAGAGCAGTCCCAGTCGT 58.822 55.000 0.00 0.00 0.00 4.34
3693 4336 3.922240 CCTTAGCACATGCATGTTTCAAC 59.078 43.478 29.48 15.81 45.16 3.18
3725 4368 8.934023 AGATGTTTTAACAAGGAAAGGTATCA 57.066 30.769 0.00 0.00 43.03 2.15
3741 4384 8.655935 AAAGGTATCAACTCCATGATTTTCTT 57.344 30.769 0.00 0.00 40.44 2.52
3749 4392 9.830975 TCAACTCCATGATTTTCTTTATATCGA 57.169 29.630 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 3.936453 GGCGGTGAGTGATTATTTGTACA 59.064 43.478 0.00 0.00 0.00 2.90
155 156 1.812571 CATTTGCCGGTTGAGCTTAGT 59.187 47.619 1.90 0.00 0.00 2.24
158 159 1.290009 GCATTTGCCGGTTGAGCTT 59.710 52.632 1.90 0.00 34.31 3.74
232 233 4.479796 AGATTGGGAATCTGGGATCAAAGA 59.520 41.667 0.00 0.00 46.16 2.52
658 1280 3.824133 TCATTGGCTTGATACCATGAGG 58.176 45.455 0.00 0.00 36.96 3.86
724 1346 6.542005 TGAGAAACAAATGCATATATCCGTGT 59.458 34.615 0.00 0.00 0.00 4.49
728 1350 7.934457 AGTGTGAGAAACAAATGCATATATCC 58.066 34.615 0.00 0.00 41.57 2.59
731 1353 7.920160 TGAGTGTGAGAAACAAATGCATATA 57.080 32.000 0.00 0.00 41.57 0.86
748 1370 3.811497 CCATGGTGCTATGTATGAGTGTG 59.189 47.826 2.57 0.00 0.00 3.82
749 1371 3.181451 CCCATGGTGCTATGTATGAGTGT 60.181 47.826 11.73 0.00 0.00 3.55
825 1449 5.761726 TCGACAACATATCTACTGATACGGT 59.238 40.000 0.00 0.00 37.92 4.83
851 1475 6.128007 ACAAATCGGTAGACAAAAGCTATTGG 60.128 38.462 0.00 0.00 34.56 3.16
900 1524 3.791320 AGGAAGTAGGACAGTTGGATCA 58.209 45.455 0.00 0.00 0.00 2.92
932 1556 2.298163 TCAAGAGGACCGAACCAAGTAC 59.702 50.000 0.00 0.00 0.00 2.73
943 1567 2.479566 TTCAGCACATCAAGAGGACC 57.520 50.000 0.00 0.00 0.00 4.46
997 1622 9.125026 AGAAGAAGTTGACAAGAATAACATGTT 57.875 29.630 16.68 16.68 30.32 2.71
1021 1646 3.239449 TGAGGCCAGAAACTGTTAGAGA 58.761 45.455 5.01 0.00 0.00 3.10
1092 1717 2.012673 CCTCCTACAAGCATGAACAGC 58.987 52.381 0.00 0.00 0.00 4.40
1096 1721 1.839994 CTCCCCTCCTACAAGCATGAA 59.160 52.381 0.00 0.00 0.00 2.57
1134 1759 0.833287 TCACTCTAAGCATGAGGCCC 59.167 55.000 0.00 0.00 46.50 5.80
1181 1806 2.419297 GGAACCGAGCTGATCTTCACAT 60.419 50.000 0.00 0.00 0.00 3.21
1182 1807 1.066858 GGAACCGAGCTGATCTTCACA 60.067 52.381 0.00 0.00 0.00 3.58
1203 1828 3.311322 AGTCTATCTCTTCAAGCTCGACG 59.689 47.826 0.00 0.00 0.00 5.12
1235 1860 1.568612 CTCATCACTTTGTGCCGCGT 61.569 55.000 4.92 0.00 32.98 6.01
1238 1863 1.511850 TGACTCATCACTTTGTGCCG 58.488 50.000 0.00 0.00 32.98 5.69
1321 1946 5.423015 CACATATCCTAAGCACTTGACAGT 58.577 41.667 0.00 0.00 0.00 3.55
1418 2043 1.827789 TTCAGTGGGGCACTTGCAC 60.828 57.895 3.15 0.00 42.59 4.57
1634 2259 4.410099 CTCCTTCATCTCTATGAGCCTCT 58.590 47.826 0.00 0.00 42.97 3.69
1643 2268 1.759445 GCCACAGCTCCTTCATCTCTA 59.241 52.381 0.00 0.00 35.50 2.43
1645 2270 0.251354 TGCCACAGCTCCTTCATCTC 59.749 55.000 0.00 0.00 40.80 2.75
1648 2273 0.330604 ATGTGCCACAGCTCCTTCAT 59.669 50.000 3.00 0.00 40.80 2.57
1660 2285 1.355381 AGGGTTCTTGATCATGTGCCA 59.645 47.619 18.22 0.00 0.00 4.92
1769 2394 1.812235 ATCAACAGCGCAGAACATCA 58.188 45.000 11.47 0.00 0.00 3.07
1791 2416 5.324409 AGCCCATCAAACACTGAAGAATTA 58.676 37.500 0.00 0.00 37.67 1.40
1848 2473 1.632920 TGCCTCACATTCACCACCATA 59.367 47.619 0.00 0.00 0.00 2.74
1862 2487 0.252881 ATTCTCCCCTGAGTGCCTCA 60.253 55.000 5.03 5.03 39.75 3.86
1896 2521 0.677731 CAATGGCGGGTGACATGAGT 60.678 55.000 0.00 0.00 45.50 3.41
1905 2530 6.042322 TGAATATTAGTACTACAATGGCGGGT 59.958 38.462 0.91 0.00 0.00 5.28
1908 2533 8.988934 ACAATGAATATTAGTACTACAATGGCG 58.011 33.333 0.91 0.00 0.00 5.69
1926 2551 9.181061 TCATCAACTTACATCATGACAATGAAT 57.819 29.630 0.00 0.00 45.81 2.57
1932 2557 5.352293 GCAGTCATCAACTTACATCATGACA 59.648 40.000 0.00 0.00 43.88 3.58
1948 2573 4.959596 AATGAAGTGTCATGCAGTCATC 57.040 40.909 12.51 4.44 44.02 2.92
2007 2636 9.640963 TCTTGAGATTCTAAAGCAAGTAAGTAC 57.359 33.333 5.96 0.00 37.71 2.73
2022 2651 3.133542 TCGCACATGGATCTTGAGATTCT 59.866 43.478 0.00 0.00 34.37 2.40
2032 2661 4.882671 AGTAAATTGTCGCACATGGATC 57.117 40.909 0.00 0.00 0.00 3.36
2035 2664 5.107530 CCAAAAAGTAAATTGTCGCACATGG 60.108 40.000 0.00 0.00 0.00 3.66
2055 2684 3.517296 TGGCAAATACCTGAGACCAAA 57.483 42.857 0.00 0.00 0.00 3.28
2079 2708 2.291024 TGGGTGGTGTAAGTGTTGTTGT 60.291 45.455 0.00 0.00 0.00 3.32
2082 2711 2.810870 TTGGGTGGTGTAAGTGTTGT 57.189 45.000 0.00 0.00 0.00 3.32
2110 2739 3.495377 CGTGTTCTCATCGGTGGTTTTAA 59.505 43.478 0.00 0.00 0.00 1.52
2138 2767 1.206849 GACCCTCTCTTGCCTCTCTTG 59.793 57.143 0.00 0.00 0.00 3.02
2141 2770 0.968393 ACGACCCTCTCTTGCCTCTC 60.968 60.000 0.00 0.00 0.00 3.20
2142 2771 0.543174 AACGACCCTCTCTTGCCTCT 60.543 55.000 0.00 0.00 0.00 3.69
2143 2772 0.390472 CAACGACCCTCTCTTGCCTC 60.390 60.000 0.00 0.00 0.00 4.70
2171 2800 1.545582 CCGAGTGGTGAAAATGCCAAT 59.454 47.619 0.00 0.00 36.41 3.16
2186 2815 2.981859 AGATCGCATTAAACCCGAGT 57.018 45.000 0.00 0.00 34.21 4.18
2194 2823 5.391523 GCAACTACCACAAAGATCGCATTAA 60.392 40.000 0.00 0.00 0.00 1.40
2198 2827 1.804151 GCAACTACCACAAAGATCGCA 59.196 47.619 0.00 0.00 0.00 5.10
2199 2828 1.130561 GGCAACTACCACAAAGATCGC 59.869 52.381 0.00 0.00 0.00 4.58
2258 2887 9.739276 AATATCATGTTCAAGGTTGAGAAGTTA 57.261 29.630 0.00 0.00 38.61 2.24
2267 2896 5.745227 ACCTCGAATATCATGTTCAAGGTT 58.255 37.500 0.92 0.00 39.37 3.50
2285 2914 2.169832 AAACACACCTGATGACCTCG 57.830 50.000 0.00 0.00 0.00 4.63
2345 2978 4.037923 TGTTGTCTTTTCTCCATCTTTGCC 59.962 41.667 0.00 0.00 0.00 4.52
2366 2999 2.742053 GTCTATGCAACCATTGTCGTGT 59.258 45.455 0.00 0.00 32.85 4.49
2369 3002 5.277490 CCATTAGTCTATGCAACCATTGTCG 60.277 44.000 0.00 0.00 32.85 4.35
2379 3012 7.735917 ACTGCTATTTACCATTAGTCTATGCA 58.264 34.615 0.00 0.00 0.00 3.96
2391 3024 2.789213 TGCTGCAACTGCTATTTACCA 58.211 42.857 0.00 0.00 42.66 3.25
2476 3109 9.578576 TGTGTCCTAAGAGAGTTTAGTTTAGTA 57.421 33.333 0.00 0.00 0.00 1.82
2477 3110 8.474710 TGTGTCCTAAGAGAGTTTAGTTTAGT 57.525 34.615 0.00 0.00 0.00 2.24
2480 3113 9.628500 ATTTTGTGTCCTAAGAGAGTTTAGTTT 57.372 29.630 0.00 0.00 0.00 2.66
2481 3114 9.274206 GATTTTGTGTCCTAAGAGAGTTTAGTT 57.726 33.333 0.00 0.00 0.00 2.24
2485 3118 9.274206 GTTAGATTTTGTGTCCTAAGAGAGTTT 57.726 33.333 0.00 0.00 0.00 2.66
2486 3119 8.652290 AGTTAGATTTTGTGTCCTAAGAGAGTT 58.348 33.333 0.00 0.00 0.00 3.01
2487 3120 8.196378 AGTTAGATTTTGTGTCCTAAGAGAGT 57.804 34.615 0.00 0.00 0.00 3.24
2488 3121 7.486551 CGAGTTAGATTTTGTGTCCTAAGAGAG 59.513 40.741 0.00 0.00 0.00 3.20
2489 3122 7.039923 ACGAGTTAGATTTTGTGTCCTAAGAGA 60.040 37.037 0.00 0.00 0.00 3.10
2490 3123 7.062371 CACGAGTTAGATTTTGTGTCCTAAGAG 59.938 40.741 0.00 0.00 0.00 2.85
2491 3124 6.866770 CACGAGTTAGATTTTGTGTCCTAAGA 59.133 38.462 0.00 0.00 0.00 2.10
2492 3125 6.866770 TCACGAGTTAGATTTTGTGTCCTAAG 59.133 38.462 0.00 0.00 31.88 2.18
2493 3126 6.751157 TCACGAGTTAGATTTTGTGTCCTAA 58.249 36.000 0.00 0.00 31.88 2.69
2572 3215 4.584638 ACCAGTGGATAAACCTGCATTA 57.415 40.909 18.40 0.00 39.86 1.90
2678 3321 6.098266 ACCAAGATTAGCACAAACTTTCCTTT 59.902 34.615 0.00 0.00 0.00 3.11
2679 3322 5.598417 ACCAAGATTAGCACAAACTTTCCTT 59.402 36.000 0.00 0.00 0.00 3.36
2728 3371 3.814268 CCCGTGGCCATTGCGAAG 61.814 66.667 9.72 0.00 38.85 3.79
2735 3378 1.133915 CCAGTATTTACCCGTGGCCAT 60.134 52.381 9.72 0.00 0.00 4.40
2751 3394 5.186198 GCCACTTGTATCATACTTTCCAGT 58.814 41.667 0.00 0.00 36.99 4.00
2814 3457 0.802607 GGCAGTACACTAGCGACAGC 60.803 60.000 0.00 0.00 45.58 4.40
2898 3541 3.054065 AAGATGACTTGATCAGGGGAACC 60.054 47.826 9.90 0.00 44.76 3.62
2902 3545 2.686915 GCAAAGATGACTTGATCAGGGG 59.313 50.000 9.90 0.68 41.91 4.79
2908 3551 4.501071 GCCAAATGCAAAGATGACTTGAT 58.499 39.130 0.00 0.00 40.77 2.57
2923 3566 3.446161 ACCTTGATGATGACTGCCAAATG 59.554 43.478 0.00 0.00 0.00 2.32
2929 3572 5.562307 GCATTGATACCTTGATGATGACTGC 60.562 44.000 0.00 0.00 0.00 4.40
2941 3584 6.006449 AGTTCTTCAGTTGCATTGATACCTT 58.994 36.000 2.65 0.00 0.00 3.50
2964 3607 2.708051 ACACATCAACAGATGGCTCAG 58.292 47.619 9.93 0.00 42.71 3.35
3018 3661 5.627499 TCTCTTTCGCTACAATTGCAATT 57.373 34.783 18.99 18.99 0.00 2.32
3019 3662 5.627499 TTCTCTTTCGCTACAATTGCAAT 57.373 34.783 5.99 5.99 0.00 3.56
3020 3663 5.431420 TTTCTCTTTCGCTACAATTGCAA 57.569 34.783 5.05 0.00 0.00 4.08
3021 3664 4.613622 GCTTTCTCTTTCGCTACAATTGCA 60.614 41.667 5.05 0.00 0.00 4.08
3022 3665 3.848582 GCTTTCTCTTTCGCTACAATTGC 59.151 43.478 5.05 0.00 0.00 3.56
3027 3670 6.985188 ATATTTGCTTTCTCTTTCGCTACA 57.015 33.333 0.00 0.00 0.00 2.74
3123 3766 1.326951 AAACTTGGTGCCAAAGCGGT 61.327 50.000 5.10 0.00 44.31 5.68
3138 3781 9.871238 AACACTATCATTTCGTGTCTATAAACT 57.129 29.630 0.00 0.00 40.68 2.66
3166 3809 8.311109 TGAACTTCTATGTAGCACAGTGATAAA 58.689 33.333 4.15 0.00 0.00 1.40
3167 3810 7.836842 TGAACTTCTATGTAGCACAGTGATAA 58.163 34.615 4.15 0.00 0.00 1.75
3175 3818 5.967088 TCTCCTTGAACTTCTATGTAGCAC 58.033 41.667 0.00 0.00 0.00 4.40
3254 3897 7.174946 CCTCAACAAATATACCGAGGCATTATT 59.825 37.037 0.00 0.00 34.13 1.40
3267 3910 8.783093 CACTGTTCAAAGACCTCAACAAATATA 58.217 33.333 0.00 0.00 0.00 0.86
3430 4073 3.041946 CCCTACTGGCCTTAAGTGATCT 58.958 50.000 3.32 0.00 0.00 2.75
3453 4096 2.165437 TGTGTTTGTTTTGACTCTGGCC 59.835 45.455 0.00 0.00 0.00 5.36
3480 4123 3.925299 CGATAGCTCTATCCACTTGCATG 59.075 47.826 10.38 0.00 38.91 4.06
3494 4137 2.797719 GGCTTAGCAAACTCGATAGCTC 59.202 50.000 6.53 0.00 38.47 4.09
3501 4144 2.670414 CAGAGAAGGCTTAGCAAACTCG 59.330 50.000 6.53 4.46 31.76 4.18
3511 4154 3.584733 AAAAGACACCAGAGAAGGCTT 57.415 42.857 0.00 0.00 0.00 4.35
3546 4189 9.952030 TTGTTACTGTTATGAAGATGGTAATGA 57.048 29.630 0.00 0.00 0.00 2.57
3551 4194 9.959721 AGTAATTGTTACTGTTATGAAGATGGT 57.040 29.630 1.81 0.00 44.43 3.55
3561 4204 9.991906 AGCTAAACAGAGTAATTGTTACTGTTA 57.008 29.630 16.31 1.42 46.37 2.41
3592 4235 3.949313 GGCGTTGCTCGACTAAAAG 57.051 52.632 6.11 0.00 45.28 2.27
3682 4325 3.631145 TCTCTTGCAGTTGAAACATGC 57.369 42.857 0.00 9.34 40.40 4.06
3693 4336 6.317789 TCCTTGTTAAAACATCTCTTGCAG 57.682 37.500 0.00 0.00 38.95 4.41


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

AutoCloner maintained by Alex Coulton.