Multiple sequence alignment - TraesCS1B01G462400

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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 TraesCS1B01G462400 chr1B 100.000 3516 0 0 1 3516 674810714 674807199 0.000000e+00 6493
1 TraesCS1B01G462400 chr1B 95.946 74 1 1 2860 2933 520094214 520094285 6.170000e-23 119
2 TraesCS1B01G462400 chr1D 90.731 3571 203 51 4 3509 484555267 484551760 0.000000e+00 4643
3 TraesCS1B01G462400 chr1D 85.146 377 29 10 3145 3509 408519904 408520265 9.280000e-96 361
4 TraesCS1B01G462400 chr1D 89.947 189 16 1 2099 2284 484443743 484443555 1.260000e-59 241
5 TraesCS1B01G462400 chr1A 91.035 2878 172 37 4 2847 581870587 581867762 0.000000e+00 3807
6 TraesCS1B01G462400 chr1A 87.218 266 16 10 3219 3472 581866677 581866418 1.600000e-73 287
7 TraesCS1B01G462400 chr1A 80.170 353 37 19 2863 3205 581867425 581867096 2.110000e-57 233
8 TraesCS1B01G462400 chr6B 83.354 799 126 6 1728 2524 403188793 403188000 0.000000e+00 732
9 TraesCS1B01G462400 chr6A 82.228 799 121 11 1728 2524 362714618 362713839 0.000000e+00 669
10 TraesCS1B01G462400 chr4D 85.488 379 28 10 3143 3509 486438297 486437934 1.540000e-98 370
11 TraesCS1B01G462400 chr3D 85.224 379 29 10 3143 3509 54772701 54772338 7.170000e-97 364
12 TraesCS1B01G462400 chr2D 85.294 374 28 10 3148 3509 144463005 144462647 9.280000e-96 361
13 TraesCS1B01G462400 chr2D 85.146 377 29 10 3145 3509 288989539 288989900 9.280000e-96 361
14 TraesCS1B01G462400 chr5D 84.014 294 26 9 3140 3421 214062960 214063244 2.690000e-66 263
15 TraesCS1B01G462400 chr7A 94.595 74 2 1 2860 2933 141090409 141090480 2.870000e-21 113
16 TraesCS1B01G462400 chr7A 94.595 74 2 1 2860 2933 141361697 141361768 2.870000e-21 113
17 TraesCS1B01G462400 chr4A 94.595 74 2 1 2860 2933 588685149 588685220 2.870000e-21 113
18 TraesCS1B01G462400 chr7B 91.892 74 3 2 2860 2933 516295012 516295082 2.230000e-17 100


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 TraesCS1B01G462400 chr1B 674807199 674810714 3515 True 6493.000000 6493 100.000 1 3516 1 chr1B.!!$R1 3515
1 TraesCS1B01G462400 chr1D 484551760 484555267 3507 True 4643.000000 4643 90.731 4 3509 1 chr1D.!!$R2 3505
2 TraesCS1B01G462400 chr1A 581866418 581870587 4169 True 1442.333333 3807 86.141 4 3472 3 chr1A.!!$R1 3468
3 TraesCS1B01G462400 chr6B 403188000 403188793 793 True 732.000000 732 83.354 1728 2524 1 chr6B.!!$R1 796
4 TraesCS1B01G462400 chr6A 362713839 362714618 779 True 669.000000 669 82.228 1728 2524 1 chr6A.!!$R1 796

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
856 877 0.030908 GGCGAGACTAAGACCGGATG 59.969 60.0 9.46 0.0 0.0 3.51 F
857 878 0.595310 GCGAGACTAAGACCGGATGC 60.595 60.0 9.46 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1778 1.019673 CTCCACCATCTGCAATTCCG 58.98 55.000 0.0 0.0 0.00 4.30 R
2791 2831 1.139853 CCGAGCTAAAAGAGGGAGCAT 59.86 52.381 0.0 0.0 38.73 3.79 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
38 39 0.042188 CATAACGCAGGCCGAAATCG 60.042 55.000 0.00 0.00 41.02 3.34
77 79 2.441164 TCTCCCTCCGCTCAGAGC 60.441 66.667 12.94 12.94 38.02 4.09
78 80 3.535962 CTCCCTCCGCTCAGAGCC 61.536 72.222 17.16 0.00 38.18 4.70
82 84 3.898509 CTCCGCTCAGAGCCCGAG 61.899 72.222 17.16 16.60 38.18 4.63
232 245 1.074850 TGGTGAGTGGTGAGACCCA 60.075 57.895 0.00 0.00 37.50 4.51
263 276 1.763545 GTAACCTCCCCAGATCCAGTC 59.236 57.143 0.00 0.00 0.00 3.51
264 277 0.621862 AACCTCCCCAGATCCAGTCC 60.622 60.000 0.00 0.00 0.00 3.85
265 278 1.768077 CCTCCCCAGATCCAGTCCC 60.768 68.421 0.00 0.00 0.00 4.46
266 279 1.768077 CTCCCCAGATCCAGTCCCC 60.768 68.421 0.00 0.00 0.00 4.81
267 280 2.774351 CCCCAGATCCAGTCCCCC 60.774 72.222 0.00 0.00 0.00 5.40
270 283 3.083349 CAGATCCAGTCCCCCGCA 61.083 66.667 0.00 0.00 0.00 5.69
365 378 0.383231 CGACGCCGTTAGGGTTCTAT 59.617 55.000 0.00 0.00 42.70 1.98
409 422 0.760945 TCCTTAGAGCTAGCTGGCCC 60.761 60.000 24.99 7.03 0.00 5.80
499 516 2.766400 CGCCAGACTCGAGGGAGAC 61.766 68.421 18.41 2.13 43.27 3.36
551 568 4.718774 TCTTGGTCAGAAATCTAGGATGCT 59.281 41.667 0.00 0.00 0.00 3.79
603 620 1.071471 GTGTGGTGTGGTCCTCCAG 59.929 63.158 0.00 0.00 45.24 3.86
608 625 0.693049 GGTGTGGTCCTCCAGTTCAT 59.307 55.000 0.00 0.00 45.24 2.57
625 642 1.277842 TCATTCATGTACACGCCACCT 59.722 47.619 0.00 0.00 0.00 4.00
636 653 0.034059 ACGCCACCTTCAGACTTGAG 59.966 55.000 0.00 0.00 34.15 3.02
668 685 1.377987 GCCCGTGTTATCTGCCCAA 60.378 57.895 0.00 0.00 0.00 4.12
700 717 2.290641 TGGGCCGTGTAATTCAGTTCAT 60.291 45.455 0.00 0.00 0.00 2.57
705 722 4.406069 CCGTGTAATTCAGTTCATTGCAG 58.594 43.478 0.00 0.00 28.26 4.41
746 763 5.888161 CAGAGCATAATCTTGTTTTACCCCT 59.112 40.000 0.00 0.00 0.00 4.79
747 764 5.888161 AGAGCATAATCTTGTTTTACCCCTG 59.112 40.000 0.00 0.00 0.00 4.45
748 765 5.580022 AGCATAATCTTGTTTTACCCCTGT 58.420 37.500 0.00 0.00 0.00 4.00
749 766 5.418840 AGCATAATCTTGTTTTACCCCTGTG 59.581 40.000 0.00 0.00 0.00 3.66
750 767 5.417580 GCATAATCTTGTTTTACCCCTGTGA 59.582 40.000 0.00 0.00 0.00 3.58
751 768 6.071616 GCATAATCTTGTTTTACCCCTGTGAA 60.072 38.462 0.00 0.00 0.00 3.18
752 769 7.363793 GCATAATCTTGTTTTACCCCTGTGAAT 60.364 37.037 0.00 0.00 0.00 2.57
789 807 3.840468 CATATTGCTGTTGCTGCTGAAA 58.160 40.909 0.00 0.00 40.48 2.69
850 871 3.795623 TTGTATGGGCGAGACTAAGAC 57.204 47.619 0.00 0.00 0.00 3.01
856 877 0.030908 GGCGAGACTAAGACCGGATG 59.969 60.000 9.46 0.00 0.00 3.51
857 878 0.595310 GCGAGACTAAGACCGGATGC 60.595 60.000 9.46 0.00 0.00 3.91
858 879 0.738975 CGAGACTAAGACCGGATGCA 59.261 55.000 9.46 0.00 0.00 3.96
859 880 1.268794 CGAGACTAAGACCGGATGCAG 60.269 57.143 9.46 1.99 0.00 4.41
860 881 2.025155 GAGACTAAGACCGGATGCAGA 58.975 52.381 9.46 0.00 0.00 4.26
861 882 2.625790 GAGACTAAGACCGGATGCAGAT 59.374 50.000 9.46 0.00 0.00 2.90
862 883 2.625790 AGACTAAGACCGGATGCAGATC 59.374 50.000 9.46 0.00 0.00 2.75
863 884 1.338337 ACTAAGACCGGATGCAGATCG 59.662 52.381 9.46 0.00 0.00 3.69
865 886 1.043116 AAGACCGGATGCAGATCGGA 61.043 55.000 25.16 0.00 45.96 4.55
866 887 0.829602 AGACCGGATGCAGATCGGAT 60.830 55.000 25.16 13.87 45.96 4.18
877 898 1.079750 GATCGGATAGCGGCCTTCC 60.080 63.158 0.00 8.38 0.00 3.46
992 1014 1.273606 TGTCTGTCTAGGTCAAGCTGC 59.726 52.381 0.00 0.00 0.00 5.25
1049 1071 0.902531 CAGAAGGCGGGGAGAGTTAA 59.097 55.000 0.00 0.00 0.00 2.01
1069 1091 2.697644 ATGCCCAGGGAGAAGGGG 60.698 66.667 10.89 0.00 45.58 4.79
1101 1123 1.001406 CTTGTCGCAGGAGGAGTTCTT 59.999 52.381 0.00 0.00 0.00 2.52
1102 1124 0.603569 TGTCGCAGGAGGAGTTCTTC 59.396 55.000 0.00 0.00 0.00 2.87
1110 1132 1.899142 GGAGGAGTTCTTCTGAGCACT 59.101 52.381 0.00 0.00 31.80 4.40
1113 1135 3.238597 AGGAGTTCTTCTGAGCACTCTT 58.761 45.455 6.26 0.00 43.17 2.85
1116 1138 4.502259 GGAGTTCTTCTGAGCACTCTTTCA 60.502 45.833 6.26 0.00 43.17 2.69
1123 1145 3.831333 TCTGAGCACTCTTTCAGTCAGAT 59.169 43.478 0.00 0.00 41.21 2.90
1143 1165 1.042003 TTGGGTGCAAGCTGAAGCAA 61.042 50.000 9.94 0.00 43.20 3.91
1155 1177 4.726416 AGCTGAAGCAAATGTTTGATACG 58.274 39.130 9.53 0.00 45.16 3.06
1170 1192 7.021196 TGTTTGATACGAAGAAGCAAAATAGC 58.979 34.615 0.00 0.00 31.19 2.97
1173 1195 3.831715 ACGAAGAAGCAAAATAGCACC 57.168 42.857 0.00 0.00 36.85 5.01
1192 1214 1.688942 CCTCCAGAGGTCTGATGCTCT 60.689 57.143 8.64 0.00 46.59 4.09
1201 1223 2.097142 GGTCTGATGCTCTCATTTGCAC 59.903 50.000 0.00 0.00 42.26 4.57
1204 1226 3.439129 TCTGATGCTCTCATTTGCACTTG 59.561 43.478 0.00 0.00 42.26 3.16
1214 1236 7.421530 TCTCATTTGCACTTGTAGTTCTAAC 57.578 36.000 0.00 0.00 0.00 2.34
1230 1252 4.743057 TCTAACTGCAGTCATATGTGCT 57.257 40.909 21.95 3.19 40.54 4.40
1273 1295 3.731089 TGAATTTGCAGCCAAAAGAAGG 58.269 40.909 0.00 0.00 43.58 3.46
1309 1331 3.341823 ACTACACTCGAATCTGTACCGT 58.658 45.455 0.00 0.00 0.00 4.83
1461 1483 6.986817 CAGCTGGCATAGTAAATACAGTAACT 59.013 38.462 5.57 0.00 0.00 2.24
1492 1516 9.898152 TGATGTCATTAACTGTCATTACCATTA 57.102 29.630 0.00 0.00 34.38 1.90
1561 1585 3.397482 CATGAGTACTAGCCATGAAGCC 58.603 50.000 14.82 0.00 39.86 4.35
1571 1595 6.633856 ACTAGCCATGAAGCCAAAAATTAAG 58.366 36.000 0.00 0.00 0.00 1.85
1577 1601 4.376146 TGAAGCCAAAAATTAAGCCACAC 58.624 39.130 0.00 0.00 0.00 3.82
1613 1637 7.730358 GCTGACACAGTGGCTATATAGCGAA 62.730 48.000 24.80 14.92 40.83 4.70
1636 1660 6.783892 ATTTCGCATTGTTAAATTGCACTT 57.216 29.167 0.00 0.00 0.00 3.16
1638 1662 7.700322 TTTCGCATTGTTAAATTGCACTTTA 57.300 28.000 5.23 5.23 0.00 1.85
1639 1663 6.683090 TCGCATTGTTAAATTGCACTTTAC 57.317 33.333 8.61 5.73 0.00 2.01
1640 1664 6.209361 TCGCATTGTTAAATTGCACTTTACA 58.791 32.000 8.61 7.85 0.00 2.41
1641 1665 6.143118 TCGCATTGTTAAATTGCACTTTACAC 59.857 34.615 8.61 10.35 0.00 2.90
1643 1667 6.347321 GCATTGTTAAATTGCACTTTACACCC 60.347 38.462 8.61 0.00 0.00 4.61
1644 1668 6.472686 TTGTTAAATTGCACTTTACACCCT 57.527 33.333 8.61 0.00 0.00 4.34
1645 1669 6.472686 TGTTAAATTGCACTTTACACCCTT 57.527 33.333 8.61 0.00 0.00 3.95
1646 1670 6.276847 TGTTAAATTGCACTTTACACCCTTG 58.723 36.000 8.61 0.00 0.00 3.61
1647 1671 6.096987 TGTTAAATTGCACTTTACACCCTTGA 59.903 34.615 8.61 0.00 0.00 3.02
1648 1672 4.853924 AATTGCACTTTACACCCTTGAG 57.146 40.909 0.00 0.00 0.00 3.02
1649 1673 2.270352 TGCACTTTACACCCTTGAGG 57.730 50.000 0.00 0.00 43.78 3.86
1681 1705 2.329379 CTAACACTGGACGCTGTCTTC 58.671 52.381 8.26 0.00 32.47 2.87
1753 1778 3.726291 AACTGTTGGTTGTTATGTGCC 57.274 42.857 0.00 0.00 36.70 5.01
2028 2053 1.070758 GTTGAGACAGCACCTCAGGAA 59.929 52.381 0.00 0.00 41.16 3.36
2215 2240 0.806868 ATCATTGTGTGGCAGAAGCG 59.193 50.000 0.00 0.00 43.41 4.68
2332 2357 3.797039 TGAGCTGCACTGTATTGGTATC 58.203 45.455 1.02 0.00 0.00 2.24
2407 2432 2.293122 CGAGCTGAAGGAGGTGATAGAG 59.707 54.545 0.00 0.00 30.42 2.43
2534 2559 3.367646 AGGATCTACTCGACAACCTCA 57.632 47.619 0.00 0.00 0.00 3.86
2539 2564 2.998670 TCTACTCGACAACCTCACTACG 59.001 50.000 0.00 0.00 0.00 3.51
2540 2565 0.879765 ACTCGACAACCTCACTACGG 59.120 55.000 0.00 0.00 0.00 4.02
2591 2622 2.217750 TGGTGTTGTCAAGGATTCACG 58.782 47.619 0.00 0.00 0.00 4.35
2688 2719 2.024414 GTCCTTGGTTGCTCAGTGTTT 58.976 47.619 0.00 0.00 0.00 2.83
2791 2831 1.011968 GCAGGCGTGATCGTGTTACA 61.012 55.000 11.29 0.00 39.49 2.41
2795 2835 0.999406 GCGTGATCGTGTTACATGCT 59.001 50.000 0.00 0.00 41.47 3.79
2832 2872 2.033602 GGTTTAGGCCAGTGCGGT 59.966 61.111 5.01 0.00 38.85 5.68
2833 2873 2.038837 GGTTTAGGCCAGTGCGGTC 61.039 63.158 5.01 0.00 41.10 4.79
2881 3242 5.403466 CAGTAAAATGGCTTTGTTTCTCTGC 59.597 40.000 0.00 0.00 0.00 4.26
2889 3250 3.363178 CTTTGTTTCTCTGCGTGTTTCC 58.637 45.455 0.00 0.00 0.00 3.13
2898 3259 1.169661 TGCGTGTTTCCGATGCCTTT 61.170 50.000 0.00 0.00 0.00 3.11
2904 3265 3.489416 GTGTTTCCGATGCCTTTTGTTTC 59.511 43.478 0.00 0.00 0.00 2.78
2934 3295 5.561725 GCAGTTCAGTTCACTCCAGAAAATC 60.562 44.000 0.00 0.00 0.00 2.17
2938 3299 5.551233 TCAGTTCACTCCAGAAAATCGATT 58.449 37.500 4.39 4.39 0.00 3.34
2939 3300 5.997746 TCAGTTCACTCCAGAAAATCGATTT 59.002 36.000 17.60 17.60 0.00 2.17
2943 3304 8.669243 AGTTCACTCCAGAAAATCGATTTATTC 58.331 33.333 22.99 17.26 0.00 1.75
2951 3312 5.357878 AGAAAATCGATTTATTCAGCAGCCA 59.642 36.000 22.99 0.00 0.00 4.75
2957 3318 4.905866 CGATTTATTCAGCAGCCAATAACG 59.094 41.667 6.63 5.40 0.00 3.18
2972 3333 5.901552 CCAATAACGAATGGGCTTAATGTT 58.098 37.500 0.00 0.00 32.87 2.71
2981 3342 5.852282 ATGGGCTTAATGTTTATGGACAC 57.148 39.130 0.00 0.00 31.30 3.67
2986 3347 5.127031 GGCTTAATGTTTATGGACACCACAT 59.873 40.000 0.00 0.00 35.80 3.21
2993 3354 5.221945 TGTTTATGGACACCACATCCTGTAA 60.222 40.000 0.00 0.00 35.80 2.41
2996 3357 2.642311 TGGACACCACATCCTGTAACAT 59.358 45.455 0.00 0.00 37.13 2.71
2999 3360 3.686016 ACACCACATCCTGTAACATTCC 58.314 45.455 0.00 0.00 0.00 3.01
3001 3362 4.263905 ACACCACATCCTGTAACATTCCAT 60.264 41.667 0.00 0.00 0.00 3.41
3003 3364 4.949856 ACCACATCCTGTAACATTCCATTC 59.050 41.667 0.00 0.00 0.00 2.67
3006 3367 6.356556 CACATCCTGTAACATTCCATTCCTA 58.643 40.000 0.00 0.00 0.00 2.94
3017 3390 8.413309 AACATTCCATTCCTATGTATCCATTG 57.587 34.615 0.00 0.00 32.51 2.82
3050 3424 2.440946 AGGCCCAAACCTTTCTTGC 58.559 52.632 0.00 0.00 36.28 4.01
3065 3439 7.624549 ACCTTTCTTGCTACAATCTGATTAGA 58.375 34.615 1.98 0.00 37.35 2.10
3092 3468 6.938507 TGTAACTAACGAGTACCCATGAATT 58.061 36.000 0.00 0.00 33.58 2.17
3098 3476 9.139734 ACTAACGAGTACCCATGAATTAGATAA 57.860 33.333 0.00 0.00 32.65 1.75
3103 3481 6.534634 AGTACCCATGAATTAGATAACTGCC 58.465 40.000 0.00 0.00 0.00 4.85
3141 3519 8.988064 TCATCACTGAAGAGTTTGTATTCTAC 57.012 34.615 0.00 0.00 0.00 2.59
3184 3567 9.388506 CTTCATTCCTGTGACAATCTTAACTAT 57.611 33.333 0.00 0.00 0.00 2.12
3185 3568 8.722480 TCATTCCTGTGACAATCTTAACTATG 57.278 34.615 0.00 0.00 0.00 2.23
3186 3569 8.321353 TCATTCCTGTGACAATCTTAACTATGT 58.679 33.333 0.00 0.00 0.00 2.29
3237 4037 1.529948 ATGTGGCAGCAGCACTTGT 60.530 52.632 2.65 0.00 44.61 3.16
3238 4038 1.802337 ATGTGGCAGCAGCACTTGTG 61.802 55.000 2.65 0.00 44.61 3.33
3240 4040 4.353437 GGCAGCAGCACTTGTGGC 62.353 66.667 2.65 0.00 44.61 5.01
3258 4060 2.519063 TGTGGCTTGTGCACTGGG 60.519 61.111 19.41 8.99 41.91 4.45
3292 4099 6.263344 CAAAATATGGCACTTGATCACTGAG 58.737 40.000 0.00 0.00 0.00 3.35
3303 4110 0.901124 ATCACTGAGTCCTCCTGTGC 59.099 55.000 10.67 0.00 34.97 4.57
3306 4113 0.470833 ACTGAGTCCTCCTGTGCTGT 60.471 55.000 0.00 0.00 0.00 4.40
3383 4196 0.750546 TGGGCATGCAGAGAAGATGC 60.751 55.000 21.36 0.00 44.11 3.91
3385 4198 3.097461 GCATGCAGAGAAGATGCCT 57.903 52.632 14.21 0.00 43.18 4.75
3386 4199 0.663688 GCATGCAGAGAAGATGCCTG 59.336 55.000 14.21 0.00 43.18 4.85
3420 4233 1.257055 GCAGAGCTGGACCTCACTCT 61.257 60.000 0.00 5.87 40.07 3.24
3422 4235 0.324275 AGAGCTGGACCTCACTCTCC 60.324 60.000 0.00 0.00 34.42 3.71
3423 4236 0.324275 GAGCTGGACCTCACTCTCCT 60.324 60.000 0.00 0.00 0.00 3.69
3426 4239 0.040351 CTGGACCTCACTCTCCTCCA 59.960 60.000 0.00 0.00 0.00 3.86
3428 4241 1.930204 TGGACCTCACTCTCCTCCATA 59.070 52.381 0.00 0.00 0.00 2.74
3464 4280 2.755103 GTCCACCATCATGGGAAGAAAC 59.245 50.000 9.04 0.00 43.37 2.78
3477 4293 2.158971 GGAAGAAACAAGGCCAAGCAAA 60.159 45.455 5.01 0.00 0.00 3.68
3487 4303 1.650314 GCCAAGCAAAATGCCCATGC 61.650 55.000 0.00 0.00 46.52 4.06
3491 4307 3.236604 GCAAAATGCCCATGCTGTT 57.763 47.368 0.00 0.00 37.42 3.16
3500 4316 1.080772 CCATGCTGTTGCTGCAGTG 60.081 57.895 16.64 2.48 41.22 3.66
3502 4318 2.197605 ATGCTGTTGCTGCAGTGCA 61.198 52.632 18.58 18.58 41.22 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 79 3.775654 GTGGAGTGAGGGCTCGGG 61.776 72.222 0.00 0.00 36.41 5.14
78 80 3.775654 GGTGGAGTGAGGGCTCGG 61.776 72.222 0.00 0.00 36.41 4.63
79 81 2.583441 TTGGTGGAGTGAGGGCTCG 61.583 63.158 0.00 0.00 36.41 5.03
80 82 1.003233 GTTGGTGGAGTGAGGGCTC 60.003 63.158 0.00 0.00 34.89 4.70
81 83 1.462238 AGTTGGTGGAGTGAGGGCT 60.462 57.895 0.00 0.00 0.00 5.19
82 84 1.003233 GAGTTGGTGGAGTGAGGGC 60.003 63.158 0.00 0.00 0.00 5.19
93 95 2.743718 CACCTGGCGAGAGTTGGT 59.256 61.111 0.00 0.00 0.00 3.67
187 189 3.117171 GCAGCTGCTCCGTCAGTG 61.117 66.667 31.33 0.00 38.21 3.66
188 190 4.385405 GGCAGCTGCTCCGTCAGT 62.385 66.667 35.82 0.00 41.70 3.41
212 225 1.122019 GGGTCTCACCACTCACCAGT 61.122 60.000 0.00 0.00 41.02 4.00
232 245 2.042230 AGGTTACGGGGCGAGGAT 60.042 61.111 0.00 0.00 0.00 3.24
270 283 4.948080 AACCGGACGGGACCTGGT 62.948 66.667 9.46 0.00 39.97 4.00
283 296 1.674322 AGTCGGCCATTTCCAACCG 60.674 57.895 2.24 0.00 46.97 4.44
286 299 1.462616 CATCAGTCGGCCATTTCCAA 58.537 50.000 2.24 0.00 0.00 3.53
343 356 3.286915 AACCCTAACGGCGTCGACC 62.287 63.158 20.03 2.55 40.11 4.79
382 395 3.067461 AGCTAGCTCTAAGGACAATCACG 59.933 47.826 12.68 0.00 0.00 4.35
409 422 0.648958 GAGAAATAAACGACGGCGGG 59.351 55.000 18.49 5.08 43.17 6.13
419 432 3.961408 AGGGAGCTAGCTCGAGAAATAAA 59.039 43.478 32.78 0.00 43.59 1.40
420 433 3.567397 AGGGAGCTAGCTCGAGAAATAA 58.433 45.455 32.78 0.00 43.59 1.40
421 434 3.150767 GAGGGAGCTAGCTCGAGAAATA 58.849 50.000 32.78 4.44 43.59 1.40
422 435 1.960689 GAGGGAGCTAGCTCGAGAAAT 59.039 52.381 32.78 17.35 43.59 2.17
460 477 2.202797 CGGGATCTCACTGCCACG 60.203 66.667 0.00 0.00 0.00 4.94
563 580 5.008019 CACATGTACAAATGCATCCTAGGTC 59.992 44.000 9.08 0.05 0.00 3.85
603 620 2.159572 GGTGGCGTGTACATGAATGAAC 60.160 50.000 19.38 8.07 0.00 3.18
608 625 1.070914 TGAAGGTGGCGTGTACATGAA 59.929 47.619 19.38 3.06 0.00 2.57
636 653 3.512516 GGGCATCTCGCTTGGCAC 61.513 66.667 0.00 0.00 41.14 5.01
668 685 0.606401 CACGGCCCAAGTGAGTGAAT 60.606 55.000 3.33 0.00 41.83 2.57
683 700 4.406069 CTGCAATGAACTGAATTACACGG 58.594 43.478 0.00 0.00 0.00 4.94
732 749 5.068460 CACAATTCACAGGGGTAAAACAAGA 59.932 40.000 0.00 0.00 0.00 3.02
746 763 6.527057 TGCAAATATGGATCACAATTCACA 57.473 33.333 0.00 0.00 0.00 3.58
747 764 9.701098 AATATGCAAATATGGATCACAATTCAC 57.299 29.630 0.00 0.00 38.66 3.18
748 765 9.699703 CAATATGCAAATATGGATCACAATTCA 57.300 29.630 0.00 0.00 38.66 2.57
749 766 8.653338 GCAATATGCAAATATGGATCACAATTC 58.347 33.333 0.00 0.00 44.26 2.17
750 767 8.542497 GCAATATGCAAATATGGATCACAATT 57.458 30.769 0.00 0.00 44.26 2.32
789 807 2.681848 GACAAGATTATGCTGCTGCTGT 59.318 45.455 17.00 10.28 40.48 4.40
850 871 0.459237 GCTATCCGATCTGCATCCGG 60.459 60.000 13.35 13.35 44.22 5.14
856 877 2.433318 GGCCGCTATCCGATCTGC 60.433 66.667 0.00 0.00 40.02 4.26
857 878 0.389166 GAAGGCCGCTATCCGATCTG 60.389 60.000 0.00 0.00 40.02 2.90
858 879 1.536943 GGAAGGCCGCTATCCGATCT 61.537 60.000 0.00 0.00 40.02 2.75
859 880 1.079750 GGAAGGCCGCTATCCGATC 60.080 63.158 0.00 0.00 40.02 3.69
860 881 2.584391 GGGAAGGCCGCTATCCGAT 61.584 63.158 11.99 0.00 40.02 4.18
861 882 3.231736 GGGAAGGCCGCTATCCGA 61.232 66.667 11.99 0.00 40.02 4.55
862 883 3.546543 TGGGAAGGCCGCTATCCG 61.547 66.667 11.99 0.00 33.90 4.18
863 884 1.984288 AAGTGGGAAGGCCGCTATCC 61.984 60.000 10.41 10.41 33.83 2.59
864 885 0.533085 GAAGTGGGAAGGCCGCTATC 60.533 60.000 0.00 0.00 33.83 2.08
865 886 1.527370 GAAGTGGGAAGGCCGCTAT 59.473 57.895 0.00 0.00 33.83 2.97
866 887 2.666098 GGAAGTGGGAAGGCCGCTA 61.666 63.158 0.00 0.00 33.83 4.26
877 898 6.208644 CACACAAATACAGAAAAGGAAGTGG 58.791 40.000 0.00 0.00 0.00 4.00
1016 1038 1.009829 CTTCTGCACGCTCCCATTAC 58.990 55.000 0.00 0.00 0.00 1.89
1049 1071 2.311854 CCTTCTCCCTGGGCATGGT 61.312 63.158 8.22 0.00 0.00 3.55
1069 1091 2.383527 CGACAAGAACCCAGCTCGC 61.384 63.158 0.00 0.00 0.00 5.03
1101 1123 3.225940 TCTGACTGAAAGAGTGCTCAGA 58.774 45.455 6.10 0.00 41.38 3.27
1102 1124 3.657015 TCTGACTGAAAGAGTGCTCAG 57.343 47.619 1.82 0.00 43.90 3.35
1104 1126 4.153835 CCAAATCTGACTGAAAGAGTGCTC 59.846 45.833 0.00 0.00 37.43 4.26
1110 1132 3.149196 GCACCCAAATCTGACTGAAAGA 58.851 45.455 0.00 0.00 37.43 2.52
1113 1135 2.655090 TGCACCCAAATCTGACTGAA 57.345 45.000 0.00 0.00 0.00 3.02
1116 1138 1.202976 AGCTTGCACCCAAATCTGACT 60.203 47.619 0.00 0.00 0.00 3.41
1123 1145 1.042003 TGCTTCAGCTTGCACCCAAA 61.042 50.000 0.00 0.00 42.66 3.28
1143 1165 9.559958 CTATTTTGCTTCTTCGTATCAAACATT 57.440 29.630 0.00 0.00 0.00 2.71
1155 1177 3.758554 TGGAGGTGCTATTTTGCTTCTTC 59.241 43.478 0.00 0.00 0.00 2.87
1173 1195 1.682854 GAGAGCATCAGACCTCTGGAG 59.317 57.143 7.08 0.00 43.91 3.86
1192 1214 6.293407 GCAGTTAGAACTACAAGTGCAAATGA 60.293 38.462 6.97 0.00 45.98 2.57
1201 1223 7.761704 ACATATGACTGCAGTTAGAACTACAAG 59.238 37.037 22.65 8.44 37.08 3.16
1204 1226 6.019479 GCACATATGACTGCAGTTAGAACTAC 60.019 42.308 22.65 5.86 37.08 2.73
1214 1236 2.608090 CAGACAGCACATATGACTGCAG 59.392 50.000 22.21 13.48 34.61 4.41
1248 1270 4.562082 TCTTTTGGCTGCAAATTCAGATG 58.438 39.130 0.50 0.00 36.19 2.90
1273 1295 4.606457 GTGTAGTTCACAAGATCCATGC 57.394 45.455 0.00 0.00 45.51 4.06
1297 1319 6.662414 TCATCATCAAAACGGTACAGATTC 57.338 37.500 0.00 0.00 0.00 2.52
1309 1331 7.599621 CAGTAGCAATTGGTTTCATCATCAAAA 59.400 33.333 16.43 0.00 0.00 2.44
1446 1468 9.640963 GACATCAACTGAGTTACTGTATTTACT 57.359 33.333 10.69 0.00 0.00 2.24
1518 1542 4.887071 TGGATTATGTTCAAGGTATGGCAC 59.113 41.667 0.00 0.00 0.00 5.01
1520 1544 5.769662 TCATGGATTATGTTCAAGGTATGGC 59.230 40.000 0.00 0.00 38.01 4.40
1577 1601 1.081892 GTGTCAGCATACTGCCAGTG 58.918 55.000 7.83 0.00 46.52 3.66
1589 1613 3.321497 GCTATATAGCCACTGTGTCAGC 58.679 50.000 22.02 3.26 43.39 4.26
1596 1620 5.441700 CGAAATTCGCTATATAGCCACTG 57.558 43.478 25.48 13.64 46.34 3.66
1613 1637 6.783892 AAGTGCAATTTAACAATGCGAAAT 57.216 29.167 0.00 0.00 0.00 2.17
1617 1641 6.288419 GTGTAAAGTGCAATTTAACAATGCG 58.712 36.000 19.88 0.00 0.00 4.73
1636 1660 1.073284 GTCAAGGCCTCAAGGGTGTAA 59.927 52.381 5.23 0.00 37.43 2.41
1638 1662 1.062488 AGTCAAGGCCTCAAGGGTGT 61.062 55.000 5.23 0.00 37.43 4.16
1639 1663 0.607489 CAGTCAAGGCCTCAAGGGTG 60.607 60.000 5.23 0.00 37.43 4.61
1640 1664 1.763770 CAGTCAAGGCCTCAAGGGT 59.236 57.895 5.23 0.00 37.43 4.34
1641 1665 1.001641 CCAGTCAAGGCCTCAAGGG 60.002 63.158 5.23 0.05 35.18 3.95
1643 1667 1.676967 GCCCAGTCAAGGCCTCAAG 60.677 63.158 5.23 0.00 45.16 3.02
1644 1668 2.436109 GCCCAGTCAAGGCCTCAA 59.564 61.111 5.23 0.00 45.16 3.02
1696 1720 5.808030 GCCTTTTTGCAACAACTGTTAAGTA 59.192 36.000 0.00 0.00 34.77 2.24
1753 1778 1.019673 CTCCACCATCTGCAATTCCG 58.980 55.000 0.00 0.00 0.00 4.30
2028 2053 6.890979 TCTCTATGATCATCTCATCACGTT 57.109 37.500 12.53 0.00 43.70 3.99
2047 2072 2.435069 AGCTATCTGTGCTTGCATCTCT 59.565 45.455 0.00 0.00 37.52 3.10
2332 2357 1.226435 CTCGCCGTTCCTCTTCTCG 60.226 63.158 0.00 0.00 0.00 4.04
2534 2559 1.838077 AGCCCTAGCAAATTCCGTAGT 59.162 47.619 0.00 0.00 43.56 2.73
2539 2564 3.298686 ACCTTAGCCCTAGCAAATTCC 57.701 47.619 0.00 0.00 43.56 3.01
2540 2565 3.815962 GCTACCTTAGCCCTAGCAAATTC 59.184 47.826 0.00 0.00 45.95 2.17
2591 2622 1.463528 CGTGCGACGAAATCTTTTCCC 60.464 52.381 0.00 0.00 46.05 3.97
2791 2831 1.139853 CCGAGCTAAAAGAGGGAGCAT 59.860 52.381 0.00 0.00 38.73 3.79
2795 2835 1.255667 ACGCCGAGCTAAAAGAGGGA 61.256 55.000 0.00 0.00 0.00 4.20
2856 2896 5.922544 CAGAGAAACAAAGCCATTTTACTGG 59.077 40.000 0.00 0.00 39.45 4.00
2857 2897 5.403466 GCAGAGAAACAAAGCCATTTTACTG 59.597 40.000 0.00 0.00 0.00 2.74
2858 2898 5.532557 GCAGAGAAACAAAGCCATTTTACT 58.467 37.500 0.00 0.00 0.00 2.24
2859 2899 4.382754 CGCAGAGAAACAAAGCCATTTTAC 59.617 41.667 0.00 0.00 0.00 2.01
2860 2900 4.037446 ACGCAGAGAAACAAAGCCATTTTA 59.963 37.500 0.00 0.00 0.00 1.52
2881 3242 1.001815 ACAAAAGGCATCGGAAACACG 60.002 47.619 0.00 0.00 0.00 4.49
2904 3265 2.291741 GAGTGAACTGAACTGCCTTTGG 59.708 50.000 0.00 0.00 0.00 3.28
2934 3295 4.905866 CGTTATTGGCTGCTGAATAAATCG 59.094 41.667 14.63 12.28 0.00 3.34
2938 3299 5.221028 CCATTCGTTATTGGCTGCTGAATAA 60.221 40.000 0.00 6.47 0.00 1.40
2939 3300 4.275689 CCATTCGTTATTGGCTGCTGAATA 59.724 41.667 0.00 0.25 0.00 1.75
2943 3304 1.066002 CCCATTCGTTATTGGCTGCTG 59.934 52.381 0.00 0.00 0.00 4.41
2951 3312 8.141268 CCATAAACATTAAGCCCATTCGTTATT 58.859 33.333 0.00 0.00 0.00 1.40
2957 3318 6.273071 GTGTCCATAAACATTAAGCCCATTC 58.727 40.000 0.00 0.00 0.00 2.67
2967 3328 4.706476 CAGGATGTGGTGTCCATAAACATT 59.294 41.667 0.00 0.00 38.25 2.71
2986 3347 6.575244 ACATAGGAATGGAATGTTACAGGA 57.425 37.500 0.00 0.00 37.43 3.86
3017 3390 1.546029 GGGCCTTGTGTTTGGAATCTC 59.454 52.381 0.84 0.00 0.00 2.75
3065 3439 5.477984 TCATGGGTACTCGTTAGTTACAAGT 59.522 40.000 0.00 0.00 37.15 3.16
3076 3452 7.434492 CAGTTATCTAATTCATGGGTACTCGT 58.566 38.462 0.00 0.00 0.00 4.18
3077 3453 6.366332 GCAGTTATCTAATTCATGGGTACTCG 59.634 42.308 0.00 0.00 0.00 4.18
3088 3464 4.820284 GCACCAGGCAGTTATCTAATTC 57.180 45.455 0.00 0.00 43.97 2.17
3103 3481 1.884579 AGTGATGAAGCAAAGCACCAG 59.115 47.619 0.00 0.00 0.00 4.00
3141 3519 8.960591 AGGAATGAAGGAAACATTACTACATTG 58.039 33.333 0.00 0.00 44.14 2.82
3184 3567 1.879380 GCAGGACAACAGCATACAACA 59.121 47.619 0.00 0.00 0.00 3.33
3185 3568 1.200020 GGCAGGACAACAGCATACAAC 59.800 52.381 0.00 0.00 0.00 3.32
3186 3569 1.202867 TGGCAGGACAACAGCATACAA 60.203 47.619 0.00 0.00 0.00 2.41
3237 4037 3.218470 GTGCACAAGCCACAGCCA 61.218 61.111 13.17 0.00 41.25 4.75
3238 4038 2.908940 AGTGCACAAGCCACAGCC 60.909 61.111 21.04 0.00 41.25 4.85
3240 4040 2.558286 CCCAGTGCACAAGCCACAG 61.558 63.158 21.04 0.00 41.13 3.66
3292 4099 1.670406 CTGCACAGCACAGGAGGAC 60.670 63.158 0.00 0.00 33.79 3.85
3383 4196 0.959553 GCTTGGCCATCATCATCAGG 59.040 55.000 6.09 0.00 0.00 3.86
3384 4197 1.609072 CTGCTTGGCCATCATCATCAG 59.391 52.381 6.09 0.00 0.00 2.90
3385 4198 1.213430 TCTGCTTGGCCATCATCATCA 59.787 47.619 6.09 0.00 0.00 3.07
3386 4199 1.880675 CTCTGCTTGGCCATCATCATC 59.119 52.381 6.09 0.00 0.00 2.92
3420 4233 2.246469 GAGCAGAGCAGATATGGAGGA 58.754 52.381 0.00 0.00 0.00 3.71
3422 4235 1.969208 TGGAGCAGAGCAGATATGGAG 59.031 52.381 0.00 0.00 0.00 3.86
3423 4236 1.969208 CTGGAGCAGAGCAGATATGGA 59.031 52.381 0.00 0.00 32.44 3.41
3426 4239 1.969923 GGACTGGAGCAGAGCAGATAT 59.030 52.381 0.00 0.00 35.18 1.63
3428 4241 0.616964 TGGACTGGAGCAGAGCAGAT 60.617 55.000 0.00 0.00 35.18 2.90
3464 4280 2.547026 GGCATTTTGCTTGGCCTTG 58.453 52.632 3.32 0.00 44.28 3.61
3477 4293 1.594833 CAGCAACAGCATGGGCATT 59.405 52.632 0.00 0.00 43.62 3.56


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

AutoCloner maintained by Alex Coulton.