Multiple sequence alignment - TraesCS6A01G158100

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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 TraesCS6A01G158100 chr6A 100.000 2626 0 0 1 2626 148247581 148250206 0.000000e+00 4850.0
1 TraesCS6A01G158100 chr6A 100.000 1574 0 0 2962 4535 148250542 148252115 0.000000e+00 2907.0
2 TraesCS6A01G158100 chr6A 79.412 578 44 34 1304 1843 41083110 41083650 5.620000e-89 339.0
3 TraesCS6A01G158100 chr6A 85.496 131 17 2 1018 1147 5358370 5358499 7.910000e-28 135.0
4 TraesCS6A01G158100 chr6D 92.631 2592 81 39 29 2586 119994612 119997127 0.000000e+00 3627.0
5 TraesCS6A01G158100 chr6D 94.694 1583 57 9 2971 4535 119997173 119998746 0.000000e+00 2433.0
6 TraesCS6A01G158100 chr6B 94.123 1140 45 11 2962 4097 212968689 212967568 0.000000e+00 1714.0
7 TraesCS6A01G158100 chr6B 87.508 1537 84 50 1 1470 212971203 212969708 0.000000e+00 1676.0
8 TraesCS6A01G158100 chr6B 90.339 973 45 14 1660 2618 212969628 212968691 0.000000e+00 1230.0
9 TraesCS6A01G158100 chr6B 92.982 456 26 3 4085 4535 212967267 212966813 0.000000e+00 660.0
10 TraesCS6A01G158100 chr7B 78.976 371 46 14 1676 2038 13705950 13706296 1.640000e-54 224.0
11 TraesCS6A01G158100 chr5A 79.331 329 24 13 1304 1614 680359693 680359995 1.670000e-44 191.0
12 TraesCS6A01G158100 chr5A 80.769 182 33 2 995 1175 587423246 587423066 1.700000e-29 141.0
13 TraesCS6A01G158100 chr5D 78.869 336 26 16 1304 1621 152770595 152770903 7.750000e-43 185.0
14 TraesCS6A01G158100 chr5D 81.868 182 31 2 995 1175 467184284 467184104 7.860000e-33 152.0
15 TraesCS6A01G158100 chr5B 81.868 182 31 2 995 1175 573815909 573815729 7.860000e-33 152.0
16 TraesCS6A01G158100 chr5B 88.136 59 4 3 4011 4067 281107192 281107249 2.930000e-07 67.6
17 TraesCS6A01G158100 chr5B 84.286 70 7 4 4010 4077 638355329 638355396 1.050000e-06 65.8
18 TraesCS6A01G158100 chr2B 81.183 186 31 4 995 1178 180059842 180059659 3.660000e-31 147.0
19 TraesCS6A01G158100 chr2B 87.037 54 7 0 4011 4064 651175556 651175609 1.360000e-05 62.1
20 TraesCS6A01G158100 chr1D 83.439 157 26 0 4301 4457 467040574 467040730 3.660000e-31 147.0
21 TraesCS6A01G158100 chr3B 84.459 148 22 1 4310 4457 730381702 730381556 1.310000e-30 145.0
22 TraesCS6A01G158100 chr3B 83.784 148 24 0 4310 4457 677993370 677993223 1.700000e-29 141.0
23 TraesCS6A01G158100 chr3B 83.108 148 24 1 4310 4457 730399613 730399467 2.850000e-27 134.0
24 TraesCS6A01G158100 chr3B 82.432 148 25 1 4310 4457 730417726 730417580 1.320000e-25 128.0
25 TraesCS6A01G158100 chr7D 83.439 157 23 2 4298 4454 540430465 540430618 4.730000e-30 143.0
26 TraesCS6A01G158100 chr4D 83.784 148 24 0 4310 4457 444518637 444518490 1.700000e-29 141.0
27 TraesCS6A01G158100 chr2D 80.645 186 32 4 995 1178 126149546 126149363 1.700000e-29 141.0
28 TraesCS6A01G158100 chr2A 80.000 185 33 4 996 1178 132876429 132876247 2.850000e-27 134.0
29 TraesCS6A01G158100 chr7A 90.741 54 5 0 4012 4065 641076638 641076691 6.290000e-09 73.1
30 TraesCS6A01G158100 chr1A 86.441 59 5 3 4011 4068 100425416 100425472 1.360000e-05 62.1
31 TraesCS6A01G158100 chr4B 85.455 55 8 0 4010 4064 60642791 60642845 1.760000e-04 58.4


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 TraesCS6A01G158100 chr6A 148247581 148252115 4534 False 3878.5 4850 100.0000 1 4535 2 chr6A.!!$F3 4534
1 TraesCS6A01G158100 chr6A 41083110 41083650 540 False 339.0 339 79.4120 1304 1843 1 chr6A.!!$F2 539
2 TraesCS6A01G158100 chr6D 119994612 119998746 4134 False 3030.0 3627 93.6625 29 4535 2 chr6D.!!$F1 4506
3 TraesCS6A01G158100 chr6B 212966813 212971203 4390 True 1320.0 1714 91.2380 1 4535 4 chr6B.!!$R1 4534

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
253 259 0.036022 AGCCAGAGAAGCAACCACTC 59.964 55.0 0.00 0.00 0.0 3.51 F
933 992 0.323908 AGACGGGAGAGAGACCAAGG 60.324 60.0 0.00 0.00 0.0 3.61 F
1235 1313 0.926155 CTTCATCGATCTGCCACGTG 59.074 55.0 9.08 9.08 0.0 4.49 F
2623 2798 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.0 0.00 0.00 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1472 2.116366 CGATGACGTGCATATTCGACA 58.884 47.619 0.00 1.89 37.34 4.35 R
2269 2431 1.152839 GGAGAGGGAGGAGAGGTCG 60.153 68.421 0.00 0.00 0.00 4.79 R
3039 3214 0.541392 AGATTACCATGCGGCACAGA 59.459 50.000 4.03 0.00 34.57 3.41 R
4016 4194 1.017387 CCAAGCGTATGCCTTTCCTC 58.983 55.000 2.51 0.00 44.31 3.71 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
22 23 1.001624 GCCCAAATCGCAAATTCAGC 58.998 50.000 0.00 0.00 0.00 4.26
24 25 1.270971 CCAAATCGCAAATTCAGCCG 58.729 50.000 0.00 0.00 0.00 5.52
38 39 3.936372 TCAGCCGACTTACATATAGCC 57.064 47.619 0.00 0.00 0.00 3.93
43 44 3.125316 GCCGACTTACATATAGCCATTGC 59.875 47.826 0.00 0.00 37.95 3.56
59 62 0.038709 TTGCGGGCAAATGTAACAGC 60.039 50.000 3.16 0.00 32.44 4.40
89 92 8.559536 ACTTTATGCATGGTAGTCAATTAATCG 58.440 33.333 10.16 0.00 0.00 3.34
97 100 5.105269 TGGTAGTCAATTAATCGTGTAGGCA 60.105 40.000 0.00 0.00 0.00 4.75
139 142 6.488006 GCTAATCAGAAGCAATTATGAAGGGA 59.512 38.462 0.00 0.00 39.83 4.20
199 204 5.276440 ACCTCTTCTATATATGGAGGGCAG 58.724 45.833 20.31 8.89 45.44 4.85
253 259 0.036022 AGCCAGAGAAGCAACCACTC 59.964 55.000 0.00 0.00 0.00 3.51
317 323 4.463891 CACCACCAAAAAGAAGCAGGATAT 59.536 41.667 0.00 0.00 0.00 1.63
318 324 5.652014 CACCACCAAAAAGAAGCAGGATATA 59.348 40.000 0.00 0.00 0.00 0.86
319 325 6.322201 CACCACCAAAAAGAAGCAGGATATAT 59.678 38.462 0.00 0.00 0.00 0.86
320 326 7.502226 CACCACCAAAAAGAAGCAGGATATATA 59.498 37.037 0.00 0.00 0.00 0.86
363 372 2.596851 GCCAGTCAAGAGGGCCAGA 61.597 63.158 6.18 0.00 41.90 3.86
364 373 1.601171 CCAGTCAAGAGGGCCAGAG 59.399 63.158 6.18 0.00 0.00 3.35
375 384 1.774856 AGGGCCAGAGTTAACAACTGT 59.225 47.619 22.12 8.81 43.03 3.55
383 392 4.814234 CAGAGTTAACAACTGTTACTGCCA 59.186 41.667 18.37 0.00 43.03 4.92
384 393 4.814771 AGAGTTAACAACTGTTACTGCCAC 59.185 41.667 8.61 0.00 43.03 5.01
396 408 1.544724 ACTGCCACGCATTTACCATT 58.455 45.000 0.00 0.00 38.13 3.16
397 409 2.717390 ACTGCCACGCATTTACCATTA 58.283 42.857 0.00 0.00 38.13 1.90
398 410 2.422127 ACTGCCACGCATTTACCATTAC 59.578 45.455 0.00 0.00 38.13 1.89
652 681 3.315749 GTCTCTCCGTTCTTATGATCCGT 59.684 47.826 0.00 0.00 0.00 4.69
710 739 9.489084 AATTTAGTGAAAAATTCCACTTTAGCC 57.511 29.630 11.62 0.00 42.86 3.93
752 781 5.309323 TCTTTGGTTCCTCGCAAATTATG 57.691 39.130 0.00 0.00 0.00 1.90
753 782 5.007034 TCTTTGGTTCCTCGCAAATTATGA 58.993 37.500 0.00 0.00 0.00 2.15
838 897 2.349886 GTGTTGTTCGATCAGATCCAGC 59.650 50.000 4.73 0.64 0.00 4.85
840 899 3.447229 TGTTGTTCGATCAGATCCAGCTA 59.553 43.478 4.73 0.00 0.00 3.32
849 908 5.009110 CGATCAGATCCAGCTAGTTTGACTA 59.991 44.000 4.73 0.00 0.00 2.59
900 959 3.249080 ACGATTAACCCACGTTGTTCTTG 59.751 43.478 3.63 1.31 36.91 3.02
928 987 1.806568 CAGCAGACGGGAGAGAGAC 59.193 63.158 0.00 0.00 0.00 3.36
930 989 1.679305 GCAGACGGGAGAGAGACCA 60.679 63.158 0.00 0.00 0.00 4.02
932 991 0.814457 CAGACGGGAGAGAGACCAAG 59.186 60.000 0.00 0.00 0.00 3.61
933 992 0.323908 AGACGGGAGAGAGACCAAGG 60.324 60.000 0.00 0.00 0.00 3.61
934 993 1.305381 ACGGGAGAGAGACCAAGGG 60.305 63.158 0.00 0.00 0.00 3.95
935 994 2.060980 CGGGAGAGAGACCAAGGGG 61.061 68.421 0.00 0.00 41.29 4.79
936 995 2.371259 GGGAGAGAGACCAAGGGGC 61.371 68.421 0.00 0.00 37.90 5.80
937 996 2.371259 GGAGAGAGACCAAGGGGCC 61.371 68.421 0.00 0.00 37.90 5.80
1235 1313 0.926155 CTTCATCGATCTGCCACGTG 59.074 55.000 9.08 9.08 0.00 4.49
1300 1378 7.549488 AGCAGCTCGTTAGTATATGTTTCTTTT 59.451 33.333 0.00 0.00 0.00 2.27
1301 1379 8.814235 GCAGCTCGTTAGTATATGTTTCTTTTA 58.186 33.333 0.00 0.00 0.00 1.52
1469 1564 2.781923 TGCTAATCTGTCAGCAAAGCA 58.218 42.857 14.90 14.90 44.49 3.91
1470 1565 2.485426 TGCTAATCTGTCAGCAAAGCAC 59.515 45.455 14.90 0.00 44.49 4.40
1471 1566 2.485426 GCTAATCTGTCAGCAAAGCACA 59.515 45.455 12.53 0.00 37.73 4.57
1472 1567 3.669023 GCTAATCTGTCAGCAAAGCACAC 60.669 47.826 12.53 0.00 37.73 3.82
1542 1659 6.088824 ACAGATCGATGCTGAATTTTTGTTC 58.911 36.000 23.11 0.00 36.86 3.18
1543 1660 6.088173 CAGATCGATGCTGAATTTTTGTTCA 58.912 36.000 0.54 0.00 35.39 3.18
1544 1661 6.750501 CAGATCGATGCTGAATTTTTGTTCAT 59.249 34.615 0.54 0.00 37.47 2.57
1877 2029 4.216687 CGCCAACAATTAGACCCTGTTTTA 59.783 41.667 0.00 0.00 30.99 1.52
1932 2084 1.227645 GATGCCGCTAGCCATCACA 60.228 57.895 21.99 9.75 42.71 3.58
2066 2228 4.960469 AGGAGATTAACCACGATCAGGTAA 59.040 41.667 7.22 0.00 38.76 2.85
2070 2232 5.873164 AGATTAACCACGATCAGGTAAACAC 59.127 40.000 7.22 0.64 38.76 3.32
2071 2233 3.478857 AACCACGATCAGGTAAACACA 57.521 42.857 7.22 0.00 38.76 3.72
2072 2234 3.478857 ACCACGATCAGGTAAACACAA 57.521 42.857 5.08 0.00 37.67 3.33
2073 2235 3.399330 ACCACGATCAGGTAAACACAAG 58.601 45.455 5.08 0.00 37.67 3.16
2074 2236 2.159627 CCACGATCAGGTAAACACAAGC 59.840 50.000 0.00 0.00 0.00 4.01
2075 2237 2.805671 CACGATCAGGTAAACACAAGCA 59.194 45.455 0.00 0.00 0.00 3.91
2076 2238 2.806244 ACGATCAGGTAAACACAAGCAC 59.194 45.455 0.00 0.00 0.00 4.40
2077 2239 2.805671 CGATCAGGTAAACACAAGCACA 59.194 45.455 0.00 0.00 0.00 4.57
2078 2240 3.249799 CGATCAGGTAAACACAAGCACAA 59.750 43.478 0.00 0.00 0.00 3.33
2102 2264 9.341899 CAACCAAAAATCACTTATTACTACTGC 57.658 33.333 0.00 0.00 0.00 4.40
2126 2288 7.068593 TGCTAGTAATTAATTTGCCTGCATTCT 59.931 33.333 5.91 0.00 0.00 2.40
2269 2431 4.487412 CGGAGGTACACGGGCGAC 62.487 72.222 0.00 0.00 0.00 5.19
2371 2533 0.958822 AGGTAAAAAGGGCAACGCAG 59.041 50.000 0.00 0.00 37.60 5.18
2401 2563 9.668497 AGGATATGAACTGGTTACTTTTACTTC 57.332 33.333 0.00 0.00 0.00 3.01
2422 2584 3.260632 TCCTTGCAGCACATGAACTACTA 59.739 43.478 0.00 0.00 0.00 1.82
2457 2619 3.270877 AGTTCCATCGTCCATTTACTGC 58.729 45.455 0.00 0.00 0.00 4.40
2480 2642 5.935789 GCACTAATTACCCGGCTAATTCATA 59.064 40.000 16.33 1.51 30.53 2.15
2482 2644 7.414098 GCACTAATTACCCGGCTAATTCATATG 60.414 40.741 16.33 11.91 30.53 1.78
2577 2744 9.901724 CGCAAGGTATATAACGAATTATCAATC 57.098 33.333 0.00 0.00 32.98 2.67
2603 2778 4.453478 TCATTTCGCATCTGCTATTGATCC 59.547 41.667 0.09 0.00 39.32 3.36
2609 2784 2.602257 TCTGCTATTGATCCGGTGTG 57.398 50.000 0.00 0.00 0.00 3.82
2611 2786 1.935873 CTGCTATTGATCCGGTGTGTG 59.064 52.381 0.00 0.00 0.00 3.82
2618 2793 0.531974 GATCCGGTGTGTGTGTGTGT 60.532 55.000 0.00 0.00 0.00 3.72
2619 2794 0.813610 ATCCGGTGTGTGTGTGTGTG 60.814 55.000 0.00 0.00 0.00 3.82
2620 2795 1.743623 CCGGTGTGTGTGTGTGTGT 60.744 57.895 0.00 0.00 0.00 3.72
2621 2796 1.423450 CGGTGTGTGTGTGTGTGTG 59.577 57.895 0.00 0.00 0.00 3.82
2622 2797 1.295357 CGGTGTGTGTGTGTGTGTGT 61.295 55.000 0.00 0.00 0.00 3.72
2623 2798 0.167908 GGTGTGTGTGTGTGTGTGTG 59.832 55.000 0.00 0.00 0.00 3.82
2624 2799 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2625 2800 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
3039 3214 8.954350 CATATCTTGGAAGATCAGAACAGTTTT 58.046 33.333 5.14 0.00 44.30 2.43
3058 3233 0.541392 TCTGTGCCGCATGGTAATCT 59.459 50.000 0.00 0.00 37.67 2.40
3061 3236 3.141398 CTGTGCCGCATGGTAATCTATT 58.859 45.455 0.00 0.00 37.67 1.73
3099 3274 3.641437 TGGGAAATTTCTGTTGAAGCG 57.359 42.857 17.42 0.00 33.28 4.68
3101 3276 3.634448 TGGGAAATTTCTGTTGAAGCGAA 59.366 39.130 17.42 0.00 33.28 4.70
3102 3277 4.229876 GGGAAATTTCTGTTGAAGCGAAG 58.770 43.478 17.42 0.00 33.28 3.79
3448 3626 0.102481 TAAGAATCAGCCGACCGAGC 59.898 55.000 0.00 0.00 0.00 5.03
3493 3671 1.667724 CAATTCAGTCACGGCCAGATC 59.332 52.381 2.24 0.00 0.00 2.75
3494 3672 0.179000 ATTCAGTCACGGCCAGATCC 59.821 55.000 2.24 0.00 0.00 3.36
3543 3721 6.839124 AACATTGTTGGCAGAGATTTGATA 57.161 33.333 0.15 0.00 0.00 2.15
3601 3779 4.903649 TGAGCTCTCTGGATTCATGGATTA 59.096 41.667 16.19 0.00 0.00 1.75
3602 3780 5.546887 TGAGCTCTCTGGATTCATGGATTAT 59.453 40.000 16.19 0.00 0.00 1.28
3603 3781 6.044054 TGAGCTCTCTGGATTCATGGATTATT 59.956 38.462 16.19 0.00 0.00 1.40
3604 3782 6.850234 AGCTCTCTGGATTCATGGATTATTT 58.150 36.000 0.00 0.00 0.00 1.40
3757 3935 7.119116 TGTTCTTTCATCATGTTGCGTACTTAT 59.881 33.333 0.00 0.00 0.00 1.73
3758 3936 8.600625 GTTCTTTCATCATGTTGCGTACTTATA 58.399 33.333 0.00 0.00 0.00 0.98
4000 4178 1.834263 ACTTTGACTAGCTAGGCCCAG 59.166 52.381 24.08 20.09 0.00 4.45
4005 4183 0.635009 ACTAGCTAGGCCCAGTGGTA 59.365 55.000 24.35 0.00 0.00 3.25
4035 4213 1.017387 GAGGAAAGGCATACGCTTGG 58.983 55.000 0.00 0.00 38.60 3.61
4140 4641 4.705507 AGTACGGAGATACACAACATCACT 59.294 41.667 0.00 0.00 0.00 3.41
4151 4652 2.297033 ACAACATCACTGCCAAACATCC 59.703 45.455 0.00 0.00 0.00 3.51
4193 4694 1.204704 CGACATGAAGCACCACCTAGA 59.795 52.381 0.00 0.00 0.00 2.43
4195 4696 1.977854 ACATGAAGCACCACCTAGACA 59.022 47.619 0.00 0.00 0.00 3.41
4238 4739 4.533222 GATCGAAGACAACTAGCTAGCTC 58.467 47.826 23.26 12.31 42.51 4.09
4257 4758 1.766143 CGGACCTGCTGCGAAATAGC 61.766 60.000 0.00 0.00 41.49 2.97
4282 4788 1.928706 GCCCGAATTTTGCCGCACTA 61.929 55.000 0.00 0.00 0.00 2.74
4334 4840 6.352222 CCTTAGTCAATAATCTCCACCACTGT 60.352 42.308 0.00 0.00 0.00 3.55
4469 4976 7.093988 CCAATCCAGAACATGTGTTTGGTAATA 60.094 37.037 17.96 4.93 38.56 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.001624 GCTGAATTTGCGATTTGGGC 58.998 50.000 0.00 0.00 0.00 5.36
22 23 3.367932 CGCAATGGCTATATGTAAGTCGG 59.632 47.826 0.00 0.00 38.10 4.79
24 25 3.684788 CCCGCAATGGCTATATGTAAGTC 59.315 47.826 0.00 0.00 38.10 3.01
38 39 2.261345 CTGTTACATTTGCCCGCAATG 58.739 47.619 2.42 6.62 35.70 2.82
43 44 1.745232 TAGGCTGTTACATTTGCCCG 58.255 50.000 9.98 0.00 45.94 6.13
59 62 7.807977 ATTGACTACCATGCATAAAGTTAGG 57.192 36.000 0.00 0.00 0.00 2.69
89 92 1.873698 TTTCTTGTCGGTGCCTACAC 58.126 50.000 0.00 0.00 46.66 2.90
97 100 5.763204 TGATTAGCTTTCTTTTCTTGTCGGT 59.237 36.000 0.00 0.00 0.00 4.69
139 142 1.668151 GACGCGCAAACCCTTCTCT 60.668 57.895 5.73 0.00 0.00 3.10
275 281 0.726118 GTTTCTTTCTTGCGCGGCTC 60.726 55.000 8.83 0.00 0.00 4.70
317 323 0.890542 ACGTACGATGGCCGGCTATA 60.891 55.000 26.69 13.21 43.93 1.31
318 324 1.741327 AACGTACGATGGCCGGCTAT 61.741 55.000 26.96 26.96 43.93 2.97
319 325 1.100463 TAACGTACGATGGCCGGCTA 61.100 55.000 28.56 23.38 43.93 3.93
320 326 1.741327 ATAACGTACGATGGCCGGCT 61.741 55.000 28.56 7.30 43.93 5.52
363 372 3.558418 CGTGGCAGTAACAGTTGTTAACT 59.442 43.478 7.22 4.41 41.58 2.24
364 373 3.847105 GCGTGGCAGTAACAGTTGTTAAC 60.847 47.826 6.31 0.00 41.58 2.01
375 384 2.186532 TGGTAAATGCGTGGCAGTAA 57.813 45.000 0.00 0.00 43.65 2.24
383 392 6.857956 TGCAAAATAGTAATGGTAAATGCGT 58.142 32.000 0.00 0.00 33.00 5.24
384 393 7.567409 GCATGCAAAATAGTAATGGTAAATGCG 60.567 37.037 14.21 0.00 33.00 4.73
430 444 0.396060 GATCTCCTCACATCCTGCCC 59.604 60.000 0.00 0.00 0.00 5.36
481 503 1.132643 GAGTGAGGTAGTGTACTGGCG 59.867 57.143 0.00 0.00 0.00 5.69
482 504 2.424246 GAGAGTGAGGTAGTGTACTGGC 59.576 54.545 0.00 0.00 0.00 4.85
483 505 3.018149 GGAGAGTGAGGTAGTGTACTGG 58.982 54.545 0.00 0.00 0.00 4.00
652 681 2.362375 GGGGCATTCTTTCCGGCA 60.362 61.111 0.00 0.00 0.00 5.69
710 739 0.757188 ACTAGGAGGTGGATGCTCCG 60.757 60.000 0.00 0.00 40.17 4.63
720 749 3.583526 GAGGAACCAAAGAACTAGGAGGT 59.416 47.826 0.00 0.00 0.00 3.85
752 781 2.894387 GCCGGATGCAGCACTCTC 60.894 66.667 5.05 0.00 40.77 3.20
753 782 4.479993 GGCCGGATGCAGCACTCT 62.480 66.667 5.05 0.00 43.89 3.24
838 897 6.200665 GCTCTCTGATGCATTAGTCAAACTAG 59.799 42.308 17.19 6.57 31.47 2.57
840 899 4.874966 GCTCTCTGATGCATTAGTCAAACT 59.125 41.667 17.19 0.00 0.00 2.66
849 908 0.814410 CTGGCGCTCTCTGATGCATT 60.814 55.000 7.64 0.00 0.00 3.56
889 948 2.862512 CAGCAACAACAAGAACAACGT 58.137 42.857 0.00 0.00 0.00 3.99
1235 1313 5.465724 TCCAAAGTAGTCGAAAGAAAGAAGC 59.534 40.000 0.00 0.00 45.01 3.86
1300 1378 3.689872 AGAAGACCCCATGCTAGAGTA 57.310 47.619 0.00 0.00 0.00 2.59
1301 1379 2.559381 AGAAGACCCCATGCTAGAGT 57.441 50.000 0.00 0.00 0.00 3.24
1302 1380 2.630580 GGTAGAAGACCCCATGCTAGAG 59.369 54.545 0.00 0.00 43.25 2.43
1340 1424 4.401519 CCACTCTCCCTAAACAGATCGTAA 59.598 45.833 0.00 0.00 0.00 3.18
1341 1425 3.952323 CCACTCTCCCTAAACAGATCGTA 59.048 47.826 0.00 0.00 0.00 3.43
1342 1426 2.761208 CCACTCTCCCTAAACAGATCGT 59.239 50.000 0.00 0.00 0.00 3.73
1381 1469 4.491763 CGATGACGTGCATATTCGACAAAA 60.492 41.667 0.00 0.00 37.34 2.44
1382 1470 3.000177 CGATGACGTGCATATTCGACAAA 60.000 43.478 0.00 0.00 37.34 2.83
1383 1471 2.533942 CGATGACGTGCATATTCGACAA 59.466 45.455 0.00 0.00 37.34 3.18
1384 1472 2.116366 CGATGACGTGCATATTCGACA 58.884 47.619 0.00 1.89 37.34 4.35
1397 1487 2.225068 AATCCAGGCTTACGATGACG 57.775 50.000 0.00 0.00 45.75 4.35
1472 1567 4.183865 TCTCGGAATAAGAACACAGCATG 58.816 43.478 0.00 0.00 46.00 4.06
1542 1659 3.785521 GCGTGTACATGCATGTTGTTATG 59.214 43.478 35.45 22.94 42.66 1.90
1543 1660 3.485051 CGCGTGTACATGCATGTTGTTAT 60.485 43.478 35.45 13.74 43.26 1.89
1544 1661 2.159774 CGCGTGTACATGCATGTTGTTA 60.160 45.455 35.45 16.55 43.26 2.41
1635 1768 5.927954 TGGATTCACTACAAAACCGTAAC 57.072 39.130 0.00 0.00 0.00 2.50
1756 1894 7.001099 TGAACAGGTTTAGTTAGGAACTAGG 57.999 40.000 0.00 0.00 44.25 3.02
1757 1895 7.668492 ACTGAACAGGTTTAGTTAGGAACTAG 58.332 38.462 3.99 0.00 44.22 2.57
1758 1896 7.288389 TGACTGAACAGGTTTAGTTAGGAACTA 59.712 37.037 10.40 0.00 42.81 2.24
1759 1897 6.099269 TGACTGAACAGGTTTAGTTAGGAACT 59.901 38.462 10.40 0.00 45.40 3.01
1760 1898 6.285990 TGACTGAACAGGTTTAGTTAGGAAC 58.714 40.000 10.40 0.00 39.15 3.62
1761 1899 6.488769 TGACTGAACAGGTTTAGTTAGGAA 57.511 37.500 10.40 0.00 39.15 3.36
1762 1900 6.681729 ATGACTGAACAGGTTTAGTTAGGA 57.318 37.500 10.40 0.00 39.15 2.94
1975 2127 5.416013 CCTCAAGCTACATCATCGGATAGTA 59.584 44.000 0.00 0.00 30.87 1.82
2066 2228 4.391523 GTGATTTTTGGTTGTGCTTGTGTT 59.608 37.500 0.00 0.00 0.00 3.32
2070 2232 7.481275 AATAAGTGATTTTTGGTTGTGCTTG 57.519 32.000 0.00 0.00 0.00 4.01
2071 2233 8.421002 AGTAATAAGTGATTTTTGGTTGTGCTT 58.579 29.630 0.00 0.00 0.00 3.91
2072 2234 7.951591 AGTAATAAGTGATTTTTGGTTGTGCT 58.048 30.769 0.00 0.00 0.00 4.40
2073 2235 9.124807 GTAGTAATAAGTGATTTTTGGTTGTGC 57.875 33.333 0.00 0.00 0.00 4.57
2076 2238 9.341899 GCAGTAGTAATAAGTGATTTTTGGTTG 57.658 33.333 0.00 0.00 0.00 3.77
2077 2239 9.297037 AGCAGTAGTAATAAGTGATTTTTGGTT 57.703 29.630 0.00 0.00 0.00 3.67
2078 2240 8.863872 AGCAGTAGTAATAAGTGATTTTTGGT 57.136 30.769 0.00 0.00 0.00 3.67
2102 2264 8.792831 CAGAATGCAGGCAAATTAATTACTAG 57.207 34.615 0.01 0.00 0.00 2.57
2126 2288 3.058983 CGCAGTCAGTTTGTAGATTTGCA 60.059 43.478 0.00 0.00 31.63 4.08
2130 2292 2.480419 GTGCGCAGTCAGTTTGTAGATT 59.520 45.455 12.22 0.00 0.00 2.40
2269 2431 1.152839 GGAGAGGGAGGAGAGGTCG 60.153 68.421 0.00 0.00 0.00 4.79
2401 2563 2.430465 AGTAGTTCATGTGCTGCAAGG 58.570 47.619 2.77 0.00 0.00 3.61
2447 2609 4.274950 CCGGGTAATTAGTGCAGTAAATGG 59.725 45.833 17.61 9.47 0.00 3.16
2448 2610 4.261031 GCCGGGTAATTAGTGCAGTAAATG 60.261 45.833 17.61 4.88 0.00 2.32
2457 2619 7.606456 ACATATGAATTAGCCGGGTAATTAGTG 59.394 37.037 38.24 32.37 33.60 2.74
2480 2642 1.871039 GAACACGGCAGTAACACACAT 59.129 47.619 0.00 0.00 0.00 3.21
2482 2644 1.578583 AGAACACGGCAGTAACACAC 58.421 50.000 0.00 0.00 0.00 3.82
2577 2744 4.584327 GCAGATGCGAAATGAGCG 57.416 55.556 0.00 0.00 37.44 5.03
2603 2778 1.295357 ACACACACACACACACACCG 61.295 55.000 0.00 0.00 0.00 4.94
3005 3180 5.131642 TGATCTTCCAAGATATGCTCCTGTT 59.868 40.000 1.66 0.00 45.39 3.16
3039 3214 0.541392 AGATTACCATGCGGCACAGA 59.459 50.000 4.03 0.00 34.57 3.41
3058 3233 7.764617 TCCCATTGATTAAGGCAGGATTAATA 58.235 34.615 0.00 0.00 33.94 0.98
3061 3236 5.661503 TCCCATTGATTAAGGCAGGATTA 57.338 39.130 0.00 0.00 0.00 1.75
3075 3250 5.540911 GCTTCAACAGAAATTTCCCATTGA 58.459 37.500 14.61 16.94 0.00 2.57
3103 3278 2.898181 TTTACACGTGCATGCAGATG 57.102 45.000 23.41 23.37 0.00 2.90
3104 3279 4.439305 AAATTTACACGTGCATGCAGAT 57.561 36.364 23.41 9.50 0.00 2.90
3105 3280 3.913548 AAATTTACACGTGCATGCAGA 57.086 38.095 23.41 0.00 0.00 4.26
3106 3281 7.643371 TCATTATAAATTTACACGTGCATGCAG 59.357 33.333 23.41 17.33 0.00 4.41
3111 3289 9.847706 ACAAATCATTATAAATTTACACGTGCA 57.152 25.926 17.22 0.00 0.00 4.57
3448 3626 1.080366 GTGGGTGCATGCATGTGTG 60.080 57.895 25.64 4.46 0.00 3.82
3601 3779 6.595716 CACCGTGATCTTCTTCTTCCTAAAAT 59.404 38.462 0.00 0.00 0.00 1.82
3602 3780 5.932303 CACCGTGATCTTCTTCTTCCTAAAA 59.068 40.000 0.00 0.00 0.00 1.52
3603 3781 5.479306 CACCGTGATCTTCTTCTTCCTAAA 58.521 41.667 0.00 0.00 0.00 1.85
3604 3782 4.081642 CCACCGTGATCTTCTTCTTCCTAA 60.082 45.833 0.00 0.00 0.00 2.69
3757 3935 7.038302 ACCAGGCAATTGTATATAGCTAGCTTA 60.038 37.037 24.88 14.92 0.00 3.09
3758 3936 6.176183 CCAGGCAATTGTATATAGCTAGCTT 58.824 40.000 24.88 13.16 0.00 3.74
3927 4105 2.565046 CCAATGCAACAATTTGGGGT 57.435 45.000 7.96 0.00 36.96 4.95
4016 4194 1.017387 CCAAGCGTATGCCTTTCCTC 58.983 55.000 2.51 0.00 44.31 3.71
4057 4246 3.319689 TGTGTGGTTTCGATGTACTCTGA 59.680 43.478 0.00 0.00 0.00 3.27
4092 4593 4.803908 TGCGTGTGGTTGTGGCCA 62.804 61.111 0.00 0.00 35.93 5.36
4140 4641 1.502990 CGTGTCGTGGATGTTTGGCA 61.503 55.000 0.00 0.00 0.00 4.92
4193 4694 4.020128 CCTCCTTTTGCTCTAGGTAGTTGT 60.020 45.833 0.00 0.00 33.15 3.32
4195 4696 4.426704 TCCTCCTTTTGCTCTAGGTAGTT 58.573 43.478 0.00 0.00 33.15 2.24
4238 4739 1.766143 GCTATTTCGCAGCAGGTCCG 61.766 60.000 0.00 0.00 38.93 4.79
4257 4758 1.153842 GCAAAATTCGGGCTTCGGG 60.154 57.895 0.75 0.00 39.77 5.14
4282 4788 1.079819 CATGGTGCGTTCGACCTCT 60.080 57.895 12.23 2.06 34.26 3.69
4363 4869 1.705186 TCTTCCCTGCTAAGCCTGTTT 59.295 47.619 0.00 0.00 0.00 2.83
4372 4879 4.263199 CCATTGAGCATATCTTCCCTGCTA 60.263 45.833 0.00 0.00 45.79 3.49
4469 4976 4.751431 GCATCTGGCCTTTCTGGT 57.249 55.556 3.32 0.00 38.35 4.00


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

AutoCloner maintained by Alex Coulton.