Multiple sequence alignment - TraesCS6B01G442200

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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 TraesCS6B01G442200 chr6B 100.000 3222 0 0 1 3222 705884467 705887688 0.000000e+00 5951
1 TraesCS6B01G442200 chr6B 91.650 1509 99 18 1666 3160 705616408 705617903 0.000000e+00 2063
2 TraesCS6B01G442200 chr6B 90.651 1337 110 9 1650 2977 705562766 705564096 0.000000e+00 1762
3 TraesCS6B01G442200 chr6B 88.339 1415 158 5 1650 3062 705862019 705863428 0.000000e+00 1692
4 TraesCS6B01G442200 chr6B 91.702 1181 94 4 1666 2845 706339782 706340959 0.000000e+00 1635
5 TraesCS6B01G442200 chr6B 91.363 1181 98 4 1666 2845 706511720 706512897 0.000000e+00 1613
6 TraesCS6B01G442200 chr6B 87.337 995 88 20 443 1407 705614912 705615898 0.000000e+00 1105
7 TraesCS6B01G442200 chr6B 84.183 961 93 32 698 1631 706510668 706511596 0.000000e+00 878
8 TraesCS6B01G442200 chr6B 85.429 851 81 25 586 1407 705561327 705562163 0.000000e+00 845
9 TraesCS6B01G442200 chr6B 87.022 601 46 14 698 1293 706338311 706338884 0.000000e+00 649
10 TraesCS6B01G442200 chr6B 90.938 320 29 0 972 1291 705860823 705861142 6.390000e-117 431
11 TraesCS6B01G442200 chr6B 90.129 233 22 1 1400 1632 705616051 705616282 5.220000e-78 302
12 TraesCS6B01G442200 chr6B 81.818 187 7 17 3036 3199 705564095 705564277 7.250000e-27 132
13 TraesCS6B01G442200 chr6B 91.489 94 7 1 1532 1625 705562600 705562692 9.380000e-26 128
14 TraesCS6B01G442200 chr6D 90.292 1576 117 25 1656 3199 462863909 462865480 0.000000e+00 2030
15 TraesCS6B01G442200 chr6D 86.915 833 71 23 599 1407 462862027 462862845 0.000000e+00 900
16 TraesCS6B01G442200 chr6D 87.209 172 19 2 1400 1569 462862952 462863122 3.280000e-45 193
17 TraesCS6B01G442200 chr6D 95.385 65 2 1 1570 1634 462863540 462863603 5.690000e-18 102
18 TraesCS6B01G442200 chr6A 91.265 1431 79 18 1 1407 609789230 609790638 0.000000e+00 1908
19 TraesCS6B01G442200 chr6A 91.048 1307 106 8 1650 2951 609791051 609792351 0.000000e+00 1755
20 TraesCS6B01G442200 chr6A 89.523 1279 109 11 1670 2927 609729697 609730971 0.000000e+00 1596
21 TraesCS6B01G442200 chr6A 85.244 820 77 28 618 1407 609728400 609729205 0.000000e+00 804
22 TraesCS6B01G442200 chr6A 88.235 238 21 5 1398 1631 609790704 609790938 8.800000e-71 278
23 TraesCS6B01G442200 chr6A 87.083 240 21 6 1400 1631 609729343 609729580 2.470000e-66 263


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 TraesCS6B01G442200 chr6B 705884467 705887688 3221 False 5951.000000 5951 100.000000 1 3222 1 chr6B.!!$F1 3221
1 TraesCS6B01G442200 chr6B 706510668 706512897 2229 False 1245.500000 1613 87.773000 698 2845 2 chr6B.!!$F6 2147
2 TraesCS6B01G442200 chr6B 705614912 705617903 2991 False 1156.666667 2063 89.705333 443 3160 3 chr6B.!!$F3 2717
3 TraesCS6B01G442200 chr6B 706338311 706340959 2648 False 1142.000000 1635 89.362000 698 2845 2 chr6B.!!$F5 2147
4 TraesCS6B01G442200 chr6B 705860823 705863428 2605 False 1061.500000 1692 89.638500 972 3062 2 chr6B.!!$F4 2090
5 TraesCS6B01G442200 chr6B 705561327 705564277 2950 False 716.750000 1762 87.346750 586 3199 4 chr6B.!!$F2 2613
6 TraesCS6B01G442200 chr6D 462862027 462865480 3453 False 806.250000 2030 89.950250 599 3199 4 chr6D.!!$F1 2600
7 TraesCS6B01G442200 chr6A 609789230 609792351 3121 False 1313.666667 1908 90.182667 1 2951 3 chr6A.!!$F2 2950
8 TraesCS6B01G442200 chr6A 609728400 609730971 2571 False 887.666667 1596 87.283333 618 2927 3 chr6A.!!$F1 2309

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
21 22 0.107945 GAGGAAACAGATGAGCGGCT 60.108 55.0 0.0 0.0 0.00 5.52 F
1111 1144 0.033504 GTGGAGCTTCAAGGACGACA 59.966 55.0 0.0 0.0 0.00 4.35 F
1264 1297 1.005340 GCTCGATGAGTTCCAAGCTG 58.995 55.0 0.0 0.0 31.39 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1264 1297 0.321122 CTGGAGGCTGGTTCACTGTC 60.321 60.0 0.00 0.0 0.0 3.51 R
2008 4063 0.963962 CATTGAAGGCCAGTTGTGCT 59.036 50.0 5.01 0.0 0.0 4.40 R
2818 4879 0.989890 GTAGTAACTCACCTTGCGCG 59.010 55.0 0.00 0.0 0.0 6.86 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
18 19 3.721625 TCGAGGAAACAGATGAGCG 57.278 52.632 0.00 0.00 0.00 5.03
21 22 0.107945 GAGGAAACAGATGAGCGGCT 60.108 55.000 0.00 0.00 0.00 5.52
23 24 1.372087 GGAAACAGATGAGCGGCTGG 61.372 60.000 7.50 0.00 36.47 4.85
29 30 2.687200 ATGAGCGGCTGGGGTACA 60.687 61.111 7.50 0.00 0.00 2.90
58 59 2.300152 CTCTACACCTGGAAGCAAGTCA 59.700 50.000 0.00 0.00 0.00 3.41
61 66 1.064758 ACACCTGGAAGCAAGTCAACA 60.065 47.619 0.00 0.00 0.00 3.33
66 71 2.421424 CTGGAAGCAAGTCAACATAGCC 59.579 50.000 0.00 0.00 0.00 3.93
83 88 2.109126 CCGCAGGTAAGCCTCTTGC 61.109 63.158 0.00 0.00 44.97 4.01
87 92 2.269241 GGTAAGCCTCTTGCCGCT 59.731 61.111 0.00 0.00 42.71 5.52
90 95 0.460311 GTAAGCCTCTTGCCGCTAGA 59.540 55.000 4.43 4.43 42.71 2.43
98 103 0.674895 CTTGCCGCTAGAAGCCACTT 60.675 55.000 0.00 0.00 38.18 3.16
99 104 0.611200 TTGCCGCTAGAAGCCACTTA 59.389 50.000 0.00 0.00 38.18 2.24
126 131 1.561076 CTTGACTCCATGGGTCCATCA 59.439 52.381 22.90 13.04 33.90 3.07
181 186 9.569122 TGCCTAATTTAGTAATAATTGAGACCC 57.431 33.333 2.88 0.00 0.00 4.46
182 187 9.794719 GCCTAATTTAGTAATAATTGAGACCCT 57.205 33.333 2.88 0.00 0.00 4.34
198 203 1.228510 CCTCCCCTTCTGCCATTCC 59.771 63.158 0.00 0.00 0.00 3.01
250 255 6.945938 ACTAACAAGCGAGACTATCATAGT 57.054 37.500 0.00 0.00 42.86 2.12
260 265 6.237595 GCGAGACTATCATAGTGTGTGTTTTC 60.238 42.308 0.70 0.00 39.59 2.29
337 344 4.173256 GGTATTGAATTTTCCAAGGTGCG 58.827 43.478 0.00 0.00 0.00 5.34
338 345 2.810439 TTGAATTTTCCAAGGTGCGG 57.190 45.000 0.00 0.00 0.00 5.69
363 370 5.336690 GGCAGAAGATTGCTAATTTGGTCAA 60.337 40.000 0.00 0.00 43.57 3.18
390 397 4.697352 GCCTTGCAGAAGATACAGAAAAGA 59.303 41.667 0.00 0.00 0.00 2.52
397 404 6.257630 GCAGAAGATACAGAAAAGATGAGTCC 59.742 42.308 0.00 0.00 0.00 3.85
398 405 7.326454 CAGAAGATACAGAAAAGATGAGTCCA 58.674 38.462 0.00 0.00 0.00 4.02
462 469 8.043710 CCTGACTAAGTGATCCTACAAATCTTT 58.956 37.037 0.00 0.00 0.00 2.52
464 471 8.593679 TGACTAAGTGATCCTACAAATCTTTCA 58.406 33.333 0.00 0.00 0.00 2.69
470 477 8.954350 AGTGATCCTACAAATCTTTCAATTCTG 58.046 33.333 0.00 0.00 0.00 3.02
580 587 4.952460 TGTTAATTAGATAGTCCACCGGC 58.048 43.478 0.00 0.00 0.00 6.13
584 591 1.766494 TAGATAGTCCACCGGCGAAA 58.234 50.000 9.30 0.00 0.00 3.46
589 596 1.120530 AGTCCACCGGCGAAATCTAT 58.879 50.000 9.30 0.00 0.00 1.98
593 600 2.431419 TCCACCGGCGAAATCTATAACA 59.569 45.455 9.30 0.00 0.00 2.41
595 602 3.247648 CCACCGGCGAAATCTATAACAAG 59.752 47.826 9.30 0.00 0.00 3.16
653 660 0.110056 CAGACCAAAGCACGCATCAC 60.110 55.000 0.00 0.00 0.00 3.06
785 799 2.091885 TCTTTTCTTGACCCTTGCCTGT 60.092 45.455 0.00 0.00 0.00 4.00
924 946 5.437289 TGAGTTGGTAACTGCTTCATTTG 57.563 39.130 0.00 0.00 43.03 2.32
992 1025 4.522722 AGAGAAAAGGTACGGTGAAGAG 57.477 45.455 0.00 0.00 0.00 2.85
1084 1117 2.186903 CCATTGGGGACGAGGTCG 59.813 66.667 0.00 0.00 46.33 4.79
1086 1119 3.000819 ATTGGGGACGAGGTCGCA 61.001 61.111 13.66 0.00 45.38 5.10
1090 1123 2.264794 GGGACGAGGTCGCAATGT 59.735 61.111 7.80 0.00 43.51 2.71
1111 1144 0.033504 GTGGAGCTTCAAGGACGACA 59.966 55.000 0.00 0.00 0.00 4.35
1182 1215 1.527433 CTGAGAGGCGGTCTGTCACA 61.527 60.000 5.22 0.00 40.34 3.58
1264 1297 1.005340 GCTCGATGAGTTCCAAGCTG 58.995 55.000 0.00 0.00 31.39 4.24
1297 1751 2.106511 GCCTCCAGAAAGGTATATGCCA 59.893 50.000 12.79 0.00 38.79 4.92
1306 1760 7.445121 CAGAAAGGTATATGCCATGTCTTCTA 58.555 38.462 12.79 0.00 0.00 2.10
1316 2027 5.363101 TGCCATGTCTTCTATCAATCAGTC 58.637 41.667 0.00 0.00 0.00 3.51
1354 2072 6.303839 TCCTAGTATGGAGTTTGTTGCTTTT 58.696 36.000 0.00 0.00 0.00 2.27
1358 2084 6.639563 AGTATGGAGTTTGTTGCTTTTGTTT 58.360 32.000 0.00 0.00 0.00 2.83
1414 2303 8.090214 CCATAAAACCATGTTCATCTGAAAGTT 58.910 33.333 0.00 0.00 35.58 2.66
1420 2309 6.082338 CCATGTTCATCTGAAAGTTCTTTCG 58.918 40.000 16.91 12.76 35.58 3.46
1569 2748 1.298859 CTGGCCGTGAAACTAGGTGC 61.299 60.000 0.00 0.00 31.75 5.01
1570 2749 2.038837 GGCCGTGAAACTAGGTGCC 61.039 63.158 0.00 0.00 31.75 5.01
1634 3236 6.366315 ACATCTGTGCAAAAGTTTTACGTA 57.634 33.333 0.00 0.00 0.00 3.57
1635 3237 6.196571 ACATCTGTGCAAAAGTTTTACGTAC 58.803 36.000 0.00 0.66 0.00 3.67
1637 3239 5.802064 TCTGTGCAAAAGTTTTACGTACAG 58.198 37.500 21.03 21.03 37.56 2.74
1638 3240 5.581479 TCTGTGCAAAAGTTTTACGTACAGA 59.419 36.000 23.56 23.56 40.07 3.41
1640 3242 7.438757 TCTGTGCAAAAGTTTTACGTACAGATA 59.561 33.333 23.56 11.70 38.84 1.98
1641 3243 8.090250 TGTGCAAAAGTTTTACGTACAGATAT 57.910 30.769 0.00 0.00 0.00 1.63
1757 3806 6.302269 ACCATGGCTTATAAGATGAAGAAGG 58.698 40.000 16.85 8.27 0.00 3.46
1762 3811 5.994668 GGCTTATAAGATGAAGAAGGTGAGG 59.005 44.000 16.85 0.00 0.00 3.86
1797 3846 4.371624 AGATCAGAGAGGATCACGAGAT 57.628 45.455 0.00 0.00 44.89 2.75
1817 3866 7.752239 ACGAGATTTTCAAATTCACACATGATC 59.248 33.333 0.00 0.00 33.85 2.92
1824 3873 5.769162 TCAAATTCACACATGATCACTCCAA 59.231 36.000 0.00 0.00 33.85 3.53
1852 3901 1.242076 ATGTGCAGCAGTTTCCTGAC 58.758 50.000 0.00 0.00 41.50 3.51
1877 3926 2.738135 GGGAAACAACGTCAAATGTGG 58.262 47.619 0.00 0.00 0.00 4.17
1927 3976 4.080638 AGAGACAGGATGAATGTCCTTTCC 60.081 45.833 5.68 0.00 46.45 3.13
1936 3985 6.603201 GGATGAATGTCCTTTCCTTGTTATCA 59.397 38.462 0.00 0.00 35.32 2.15
1959 4014 7.195646 TCAAGCAACAACAACAAAGAAGATAG 58.804 34.615 0.00 0.00 0.00 2.08
2008 4063 5.013704 TGGAGGCATAGGAAAGACAACTTTA 59.986 40.000 0.00 0.00 44.97 1.85
2019 4074 2.618709 AGACAACTTTAGCACAACTGGC 59.381 45.455 0.00 0.00 0.00 4.85
2057 4112 9.481340 CTCAGTTCAAAGATTATAATCATCGGA 57.519 33.333 24.00 14.01 37.89 4.55
2155 4210 6.139671 AGGAAGCCAGAATCTAGATACAAGA 58.860 40.000 5.46 0.00 0.00 3.02
2192 4247 5.320549 ACGCCTTAAAGATCTACTTCGAA 57.679 39.130 0.00 0.00 37.93 3.71
2195 4250 7.486647 ACGCCTTAAAGATCTACTTCGAAATA 58.513 34.615 0.00 0.00 37.93 1.40
2270 4325 6.711277 ACTGGATCAACTCAAGCTTATGTTA 58.289 36.000 13.57 5.97 0.00 2.41
2396 4457 6.124340 TGACATGTGCTGGAGAATAATCAAT 58.876 36.000 1.15 0.00 0.00 2.57
2405 4466 8.355169 TGCTGGAGAATAATCAATCAAAATAGC 58.645 33.333 0.00 0.00 0.00 2.97
2645 4706 7.669722 ACTTTGACACCATATTTGAGGTTATGT 59.330 33.333 0.00 0.00 35.52 2.29
2783 4844 2.159099 TGGCGAGAAGTATGTTAGGCAG 60.159 50.000 0.00 0.00 0.00 4.85
2818 4879 7.935338 TGTCTTTTCTTCAGCATTCAAAATC 57.065 32.000 0.00 0.00 0.00 2.17
2845 4921 5.720202 CAAGGTGAGTTACTACAGCATACA 58.280 41.667 13.31 0.00 37.04 2.29
2956 5036 5.682943 TGTTCACAGTTTGGTACATTAGC 57.317 39.130 0.00 0.00 39.30 3.09
2987 5067 4.394439 TGTTTTGCCCTTAGTGGAAAAC 57.606 40.909 15.02 15.02 36.73 2.43
3009 5089 4.460382 ACAAAGCACTCAAGATATTGGTGG 59.540 41.667 17.59 8.10 0.00 4.61
3030 5114 5.597182 GTGGACCAGATTATACTCCACACTA 59.403 44.000 9.73 0.00 43.83 2.74
3034 5118 8.211629 GGACCAGATTATACTCCACACTATTTT 58.788 37.037 0.00 0.00 0.00 1.82
3077 5162 3.397618 TGGGGAAACATATATGGACCTGG 59.602 47.826 16.96 0.00 0.00 4.45
3081 5166 4.202461 GGAAACATATATGGACCTGGCTCA 60.202 45.833 16.96 0.00 0.00 4.26
3082 5167 5.515534 GGAAACATATATGGACCTGGCTCAT 60.516 44.000 16.96 0.32 0.00 2.90
3090 5175 2.108075 TGGACCTGGCTCATCAAGAAAA 59.892 45.455 0.00 0.00 0.00 2.29
3163 5266 5.237996 CCATTTGGATCACTGCACATAGTAG 59.762 44.000 0.00 0.00 37.39 2.57
3175 5278 7.806690 ACTGCACATAGTAGTGTATTTTGTTG 58.193 34.615 0.00 0.00 41.94 3.33
3199 5302 8.679344 TGGGCTTATCAAATCCAGTCTATATA 57.321 34.615 0.00 0.00 0.00 0.86
3200 5303 9.284131 TGGGCTTATCAAATCCAGTCTATATAT 57.716 33.333 0.00 0.00 0.00 0.86
3206 5309 8.814038 ATCAAATCCAGTCTATATATTTGGCC 57.186 34.615 0.00 0.00 37.85 5.36
3207 5310 7.754624 TCAAATCCAGTCTATATATTTGGCCA 58.245 34.615 0.00 0.00 37.85 5.36
3208 5311 8.224025 TCAAATCCAGTCTATATATTTGGCCAA 58.776 33.333 16.05 16.05 37.85 4.52
3209 5312 8.859090 CAAATCCAGTCTATATATTTGGCCAAA 58.141 33.333 32.12 32.12 35.10 3.28
3210 5313 9.432982 AAATCCAGTCTATATATTTGGCCAAAA 57.567 29.630 33.43 22.10 33.56 2.44
3211 5314 8.641498 ATCCAGTCTATATATTTGGCCAAAAG 57.359 34.615 33.43 24.56 33.56 2.27
3212 5315 7.811282 TCCAGTCTATATATTTGGCCAAAAGA 58.189 34.615 33.43 26.30 33.56 2.52
3213 5316 8.278639 TCCAGTCTATATATTTGGCCAAAAGAA 58.721 33.333 33.43 21.74 33.56 2.52
3214 5317 9.082313 CCAGTCTATATATTTGGCCAAAAGAAT 57.918 33.333 33.43 25.34 33.56 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.434843 TACCCCAGCCGCTCATCTG 61.435 63.158 0.00 0.00 0.00 2.90
21 22 0.178903 AGAGAGGCTGTTGTACCCCA 60.179 55.000 0.00 0.00 0.00 4.96
23 24 2.094130 GTGTAGAGAGGCTGTTGTACCC 60.094 54.545 0.00 0.00 0.00 3.69
29 30 1.203187 TCCAGGTGTAGAGAGGCTGTT 60.203 52.381 0.00 0.00 0.00 3.16
58 59 0.463833 GGCTTACCTGCGGCTATGTT 60.464 55.000 0.00 0.00 0.00 2.71
79 84 0.674895 AAGTGGCTTCTAGCGGCAAG 60.675 55.000 1.45 0.00 43.62 4.01
80 85 0.611200 TAAGTGGCTTCTAGCGGCAA 59.389 50.000 1.45 0.00 43.62 4.52
81 86 0.830648 ATAAGTGGCTTCTAGCGGCA 59.169 50.000 1.45 6.57 43.62 5.69
83 88 3.798202 AGAAATAAGTGGCTTCTAGCGG 58.202 45.455 0.00 0.00 43.62 5.52
87 92 6.213600 AGTCAAGGAGAAATAAGTGGCTTCTA 59.786 38.462 0.00 0.00 29.59 2.10
90 95 5.248380 AGTCAAGGAGAAATAAGTGGCTT 57.752 39.130 0.00 0.00 0.00 4.35
98 103 4.111577 ACCCATGGAGTCAAGGAGAAATA 58.888 43.478 15.22 0.00 33.85 1.40
99 104 2.922283 ACCCATGGAGTCAAGGAGAAAT 59.078 45.455 15.22 0.00 33.85 2.17
126 131 7.170965 CCACATAGATATTTACAGAGGCCATT 58.829 38.462 5.01 0.00 0.00 3.16
170 175 3.115390 CAGAAGGGGAGGGTCTCAATTA 58.885 50.000 0.00 0.00 31.08 1.40
180 185 1.228510 GGAATGGCAGAAGGGGAGG 59.771 63.158 0.00 0.00 0.00 4.30
181 186 0.106819 CAGGAATGGCAGAAGGGGAG 60.107 60.000 0.00 0.00 0.00 4.30
182 187 0.846427 ACAGGAATGGCAGAAGGGGA 60.846 55.000 0.00 0.00 0.00 4.81
183 188 0.394899 GACAGGAATGGCAGAAGGGG 60.395 60.000 0.00 0.00 0.00 4.79
184 189 0.622665 AGACAGGAATGGCAGAAGGG 59.377 55.000 0.00 0.00 0.00 3.95
185 190 1.407989 GGAGACAGGAATGGCAGAAGG 60.408 57.143 0.00 0.00 0.00 3.46
198 203 9.474920 GATTGAAGATATCTACAAAGGAGACAG 57.525 37.037 5.46 0.00 0.00 3.51
250 255 6.339587 AGGAACAAAAAGAGAAAACACACA 57.660 33.333 0.00 0.00 0.00 3.72
337 344 3.181472 CCAAATTAGCAATCTTCTGCCCC 60.181 47.826 0.00 0.00 43.73 5.80
338 345 3.448660 ACCAAATTAGCAATCTTCTGCCC 59.551 43.478 0.00 0.00 43.73 5.36
390 397 7.293828 TCTGTATCTTCTCTGTATGGACTCAT 58.706 38.462 0.00 0.00 37.40 2.90
397 404 8.681806 TCAACTTCTCTGTATCTTCTCTGTATG 58.318 37.037 0.00 0.00 0.00 2.39
398 405 8.815565 TCAACTTCTCTGTATCTTCTCTGTAT 57.184 34.615 0.00 0.00 0.00 2.29
524 531 0.967380 CACAGTTGCCTTCATCCCCC 60.967 60.000 0.00 0.00 0.00 5.40
593 600 9.762933 GCTCATTGAAGACTATCTAATTCTCTT 57.237 33.333 0.00 0.00 0.00 2.85
595 602 9.410556 GAGCTCATTGAAGACTATCTAATTCTC 57.589 37.037 9.40 0.00 0.00 2.87
785 799 4.096682 ACACGTTAGCTTTAACTTTGCCAA 59.903 37.500 0.00 0.00 0.00 4.52
924 946 1.797025 GAACACAGCCTGAGTACCAC 58.203 55.000 0.00 0.00 0.00 4.16
992 1025 4.481870 CATGCGCCATGTTGTTCC 57.518 55.556 4.18 0.00 37.12 3.62
1077 1110 0.948623 TCCACAACATTGCGACCTCG 60.949 55.000 0.00 0.00 43.27 4.63
1084 1117 2.608752 CCTTGAAGCTCCACAACATTGC 60.609 50.000 0.00 0.00 0.00 3.56
1086 1119 2.887152 GTCCTTGAAGCTCCACAACATT 59.113 45.455 0.00 0.00 0.00 2.71
1090 1123 0.756294 TCGTCCTTGAAGCTCCACAA 59.244 50.000 0.00 0.00 0.00 3.33
1111 1144 4.581309 ATGTGTCCTTCATGTCCTTGAT 57.419 40.909 0.00 0.00 0.00 2.57
1182 1215 1.071471 CAACCGCACCAACTCCTCT 59.929 57.895 0.00 0.00 0.00 3.69
1264 1297 0.321122 CTGGAGGCTGGTTCACTGTC 60.321 60.000 0.00 0.00 0.00 3.51
1297 1751 9.956640 AAGAAAAGACTGATTGATAGAAGACAT 57.043 29.630 0.00 0.00 0.00 3.06
1326 2037 7.806180 AGCAACAAACTCCATACTAGGAATAT 58.194 34.615 0.00 0.00 37.20 1.28
1331 2042 6.016276 ACAAAAGCAACAAACTCCATACTAGG 60.016 38.462 0.00 0.00 0.00 3.02
1338 2056 9.606631 ATTATTAAACAAAAGCAACAAACTCCA 57.393 25.926 0.00 0.00 0.00 3.86
1391 2118 8.463930 AGAACTTTCAGATGAACATGGTTTTA 57.536 30.769 0.00 0.00 33.13 1.52
1414 2303 6.662414 CACCAGTTGCTTATATTCGAAAGA 57.338 37.500 0.00 0.00 39.20 2.52
1494 2384 4.392138 CCTCTTGTAAACCCATCGTTCTTC 59.608 45.833 0.00 0.00 31.78 2.87
1508 2409 6.886178 AAGTAGGCTAAATCCCTCTTGTAA 57.114 37.500 0.00 0.00 33.88 2.41
1667 3716 9.793252 CATCTATGAAGGAATTTTAACAAGTGG 57.207 33.333 0.00 0.00 0.00 4.00
1676 3725 8.843308 TTCCCAATCATCTATGAAGGAATTTT 57.157 30.769 14.00 0.00 40.69 1.82
1757 3806 1.194781 TTCCTCAGCTGACCCCTCAC 61.195 60.000 13.74 0.00 0.00 3.51
1762 3811 1.138661 CTGATCTTCCTCAGCTGACCC 59.861 57.143 13.74 0.00 36.53 4.46
1782 3831 6.917217 ATTTGAAAATCTCGTGATCCTCTC 57.083 37.500 0.00 0.00 31.51 3.20
1797 3846 7.147312 GGAGTGATCATGTGTGAATTTGAAAA 58.853 34.615 0.00 0.00 38.01 2.29
1817 3866 5.677091 GCTGCACATTAATTAGGTTGGAGTG 60.677 44.000 0.00 0.00 0.00 3.51
1824 3873 5.105756 GGAAACTGCTGCACATTAATTAGGT 60.106 40.000 0.00 0.00 0.00 3.08
1852 3901 1.096386 TTGACGTTGTTTCCCGTGGG 61.096 55.000 0.00 0.00 37.44 4.61
1877 3926 6.041409 TCTCTCCCTATGATGAGTGATTCAAC 59.959 42.308 0.00 0.00 39.77 3.18
1936 3985 5.979517 GCTATCTTCTTTGTTGTTGTTGCTT 59.020 36.000 0.00 0.00 0.00 3.91
1938 3987 5.173854 GTGCTATCTTCTTTGTTGTTGTTGC 59.826 40.000 0.00 0.00 0.00 4.17
2008 4063 0.963962 CATTGAAGGCCAGTTGTGCT 59.036 50.000 5.01 0.00 0.00 4.40
2107 4162 8.272173 CCTTTCCCCAGTACTTGAGAAATTATA 58.728 37.037 4.44 0.00 32.23 0.98
2155 4210 1.623811 AGGCGTTGGTCTATCAACTGT 59.376 47.619 4.70 0.00 43.36 3.55
2270 4325 6.944862 AGACTTTCATCTTGGAGCTTACATTT 59.055 34.615 0.00 0.00 0.00 2.32
2396 4457 6.112734 TCTAGATTCAAAGCCGCTATTTTGA 58.887 36.000 2.46 2.46 40.46 2.69
2405 4466 3.170791 TCAGCTCTAGATTCAAAGCCG 57.829 47.619 0.00 0.00 35.32 5.52
2783 4844 4.827284 TGAAGAAAAGACATCCCAAGGAAC 59.173 41.667 0.00 0.00 34.34 3.62
2818 4879 0.989890 GTAGTAACTCACCTTGCGCG 59.010 55.000 0.00 0.00 0.00 6.86
2894 4970 2.570135 TGCACAGTAACTGTTGCATGA 58.430 42.857 11.16 0.00 42.59 3.07
2938 5018 3.417101 TGGGCTAATGTACCAAACTGTG 58.583 45.455 0.00 0.00 0.00 3.66
2955 5035 2.965147 AGGGCAAAACATATACATGGGC 59.035 45.455 0.00 0.00 36.39 5.36
2956 5036 5.833131 ACTAAGGGCAAAACATATACATGGG 59.167 40.000 0.00 0.00 36.39 4.00
2987 5067 4.701651 TCCACCAATATCTTGAGTGCTTTG 59.298 41.667 6.82 0.00 34.70 2.77
3009 5089 9.262358 GAAAATAGTGTGGAGTATAATCTGGTC 57.738 37.037 0.00 0.00 0.00 4.02
3030 5114 7.442062 CACACTTGGGCAATTTTTAGAGAAAAT 59.558 33.333 0.00 0.00 34.54 1.82
3034 5118 4.280677 CCACACTTGGGCAATTTTTAGAGA 59.719 41.667 0.00 0.00 39.57 3.10
3062 5147 4.170449 TGATGAGCCAGGTCCATATATGT 58.830 43.478 11.73 0.00 0.00 2.29
3096 5181 2.979678 ACTACAACAGGATGGACAAGGT 59.020 45.455 0.00 0.00 43.62 3.50
3097 5182 3.703001 ACTACAACAGGATGGACAAGG 57.297 47.619 0.00 0.00 43.62 3.61
3098 5183 5.411669 GGTAAACTACAACAGGATGGACAAG 59.588 44.000 0.00 0.00 43.62 3.16
3099 5184 5.310451 GGTAAACTACAACAGGATGGACAA 58.690 41.667 0.00 0.00 43.62 3.18
3163 5266 7.277760 GGATTTGATAAGCCCAACAAAATACAC 59.722 37.037 0.00 0.00 36.19 2.90


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

AutoCloner maintained by Alex Coulton.