Multiple sequence alignment - TraesCS4A01G043700

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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 TraesCS4A01G043700 chr4A 100.000 5413 0 0 1 5413 36385185 36390597 0.000000e+00 9997
1 TraesCS4A01G043700 chr4A 95.062 162 8 0 3262 3423 137966979 137967140 6.960000e-64 255
2 TraesCS4A01G043700 chr4A 95.062 162 8 0 3262 3423 137972830 137972669 6.960000e-64 255
3 TraesCS4A01G043700 chr4D 93.678 3923 142 39 1522 5413 435008652 435012499 0.000000e+00 5773
4 TraesCS4A01G043700 chr4D 94.886 880 26 5 1 872 435006058 435006926 0.000000e+00 1358
5 TraesCS4A01G043700 chr4D 92.125 546 27 10 920 1455 435006928 435007467 0.000000e+00 756
6 TraesCS4A01G043700 chr4D 95.266 169 8 0 3259 3427 34661524 34661692 8.940000e-68 268
7 TraesCS4A01G043700 chr4D 94.030 67 4 0 1448 1514 435008544 435008610 9.590000e-18 102
8 TraesCS4A01G043700 chr4B 92.653 1538 77 21 1 1514 535079832 535081357 0.000000e+00 2182
9 TraesCS4A01G043700 chr4B 96.546 1274 39 5 2351 3622 535082218 535083488 0.000000e+00 2104
10 TraesCS4A01G043700 chr4B 90.233 901 56 15 3616 4510 535084305 535085179 0.000000e+00 1147
11 TraesCS4A01G043700 chr4B 91.347 809 50 9 1522 2322 535081425 535082221 0.000000e+00 1088
12 TraesCS4A01G043700 chr4B 96.552 406 14 0 5008 5413 535085595 535086000 0.000000e+00 673
13 TraesCS4A01G043700 chr4B 81.498 454 23 16 4549 4976 535085178 535085596 3.150000e-82 316
14 TraesCS4A01G043700 chr5D 95.152 165 8 0 3259 3423 529218163 529218327 1.500000e-65 261
15 TraesCS4A01G043700 chr6B 94.545 165 9 0 3259 3423 226361515 226361679 6.960000e-64 255
16 TraesCS4A01G043700 chr2B 93.902 164 10 0 3261 3424 608226724 608226887 1.160000e-61 248
17 TraesCS4A01G043700 chr7D 92.814 167 12 0 3262 3428 454079408 454079242 5.420000e-60 243


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 TraesCS4A01G043700 chr4A 36385185 36390597 5412 False 9997.000000 9997 100.00000 1 5413 1 chr4A.!!$F1 5412
1 TraesCS4A01G043700 chr4D 435006058 435012499 6441 False 1997.250000 5773 93.67975 1 5413 4 chr4D.!!$F2 5412
2 TraesCS4A01G043700 chr4B 535079832 535086000 6168 False 1251.666667 2182 91.47150 1 5413 6 chr4B.!!$F1 5412

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
947 962 0.034896 TTCTCTCCCGAGCCAAACAC 59.965 55.000 0.00 0.00 37.19 3.32 F
1204 1228 0.609681 ATTTTCGGGCCGTGGCTTTA 60.610 50.000 27.32 0.36 41.60 1.85 F
1925 3102 1.202076 GCTAAAAGATGCACTGGTCGC 60.202 52.381 0.00 0.00 0.00 5.19 F
2537 3722 0.316841 TGCAACGAAAAGGATTGGCC 59.683 50.000 0.00 0.00 0.00 5.36 F
3011 4196 1.060729 TGGTAGCAGCAAACCCTGTA 58.939 50.000 13.05 0.00 34.69 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 3500 1.069906 CAGCTTCACAGTAACCAACGC 60.070 52.381 0.00 0.00 0.00 4.84 R
2537 3722 1.335872 GCCCAAGAACAATCAACCACG 60.336 52.381 0.00 0.00 0.00 4.94 R
3814 5827 0.171903 GTGGCACCATCACTGATTGC 59.828 55.000 6.29 7.04 33.02 3.56 R
4083 6099 0.740868 TAGATGCGCTTGACAGCCAC 60.741 55.000 9.73 0.00 44.06 5.01 R
4496 6516 1.135972 ACGAAGCAAGCAAGCAATACG 60.136 47.619 3.19 0.00 36.85 3.06 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 0.895100 GCAGCAGGATGACCAAACCA 60.895 55.000 0.00 0.00 39.69 3.67
104 105 1.262683 GCAGAGAGCAAACACACAGTC 59.737 52.381 0.00 0.00 44.79 3.51
139 143 1.181098 ACCACAGGCAAGCAACATCC 61.181 55.000 0.00 0.00 0.00 3.51
151 155 0.667184 CAACATCCCCGCAAAACAGC 60.667 55.000 0.00 0.00 0.00 4.40
587 597 1.080705 CTCGCCGGTTCTTTCTCGT 60.081 57.895 1.90 0.00 0.00 4.18
602 615 0.546122 CTCGTGAATGGGGATTGGGA 59.454 55.000 0.00 0.00 0.00 4.37
761 776 3.429080 GAGCGCTCTCTGGCCTCTG 62.429 68.421 29.88 0.00 36.42 3.35
777 792 3.925630 CTGCGGTGGAATGGGCTGT 62.926 63.158 0.00 0.00 0.00 4.40
820 835 2.113139 CCACAGCCCAACTTCCGT 59.887 61.111 0.00 0.00 0.00 4.69
821 836 2.260869 CCACAGCCCAACTTCCGTG 61.261 63.158 0.00 0.00 0.00 4.94
822 837 2.113139 ACAGCCCAACTTCCGTGG 59.887 61.111 0.00 0.00 0.00 4.94
823 838 2.113139 CAGCCCAACTTCCGTGGT 59.887 61.111 0.00 0.00 0.00 4.16
824 839 1.966451 CAGCCCAACTTCCGTGGTC 60.966 63.158 0.00 0.00 0.00 4.02
827 842 0.893727 GCCCAACTTCCGTGGTCATT 60.894 55.000 0.00 0.00 0.00 2.57
828 843 1.616159 CCCAACTTCCGTGGTCATTT 58.384 50.000 0.00 0.00 0.00 2.32
864 879 0.825840 GCCCAGCCCAACTGTGTTAA 60.826 55.000 0.00 0.00 45.68 2.01
873 888 2.227194 CAACTGTGTTAAGGGACCCAC 58.773 52.381 14.60 2.48 0.00 4.61
874 889 0.395312 ACTGTGTTAAGGGACCCACG 59.605 55.000 14.60 1.23 0.00 4.94
876 891 2.030958 GTGTTAAGGGACCCACGCG 61.031 63.158 14.60 3.53 36.53 6.01
877 892 3.122971 GTTAAGGGACCCACGCGC 61.123 66.667 14.60 0.00 36.53 6.86
878 893 3.627952 TTAAGGGACCCACGCGCA 61.628 61.111 14.60 0.00 36.53 6.09
879 894 3.599285 TTAAGGGACCCACGCGCAG 62.599 63.158 14.60 2.42 36.53 5.18
892 907 1.731257 GCGCAGAGAGGCTATACGC 60.731 63.158 0.30 7.71 36.12 4.42
897 912 2.203509 AGAGGCTATACGCGGGCT 60.204 61.111 12.47 10.37 40.44 5.19
911 926 2.254471 GGGCTCCACCGAAGTTTTC 58.746 57.895 0.00 0.00 40.62 2.29
912 927 0.250770 GGGCTCCACCGAAGTTTTCT 60.251 55.000 0.00 0.00 40.62 2.52
913 928 1.157585 GGCTCCACCGAAGTTTTCTC 58.842 55.000 0.00 0.00 0.00 2.87
914 929 1.542547 GGCTCCACCGAAGTTTTCTCA 60.543 52.381 0.00 0.00 0.00 3.27
915 930 1.801178 GCTCCACCGAAGTTTTCTCAG 59.199 52.381 0.00 0.00 0.00 3.35
916 931 2.417719 CTCCACCGAAGTTTTCTCAGG 58.582 52.381 0.00 0.00 34.21 3.86
917 932 1.071699 TCCACCGAAGTTTTCTCAGGG 59.928 52.381 0.00 0.00 32.95 4.45
918 933 1.523758 CACCGAAGTTTTCTCAGGGG 58.476 55.000 0.00 0.00 32.95 4.79
947 962 0.034896 TTCTCTCCCGAGCCAAACAC 59.965 55.000 0.00 0.00 37.19 3.32
1109 1133 2.169330 GTAACTCCACTTCCTCCGAGT 58.831 52.381 0.00 0.00 37.17 4.18
1117 1141 2.753452 CACTTCCTCCGAGTGCTAGTTA 59.247 50.000 0.00 0.00 38.20 2.24
1135 1159 4.390264 AGTTAGTTTCCAGTCCAAAGAGC 58.610 43.478 0.00 0.00 0.00 4.09
1204 1228 0.609681 ATTTTCGGGCCGTGGCTTTA 60.610 50.000 27.32 0.36 41.60 1.85
1241 1265 2.863739 TCACTCGTGTTTAGCTGATCG 58.136 47.619 0.00 0.00 0.00 3.69
1269 1293 3.732212 TGCGGAGAGGATGAAATGTATG 58.268 45.455 0.00 0.00 0.00 2.39
1295 1319 4.097135 TCAGTTGAAGTTGCGAATTTGGAA 59.903 37.500 0.00 0.00 0.00 3.53
1297 1321 4.803613 AGTTGAAGTTGCGAATTTGGAAAC 59.196 37.500 0.55 0.00 0.00 2.78
1298 1322 4.377839 TGAAGTTGCGAATTTGGAAACA 57.622 36.364 0.55 0.77 39.83 2.83
1299 1323 4.942852 TGAAGTTGCGAATTTGGAAACAT 58.057 34.783 0.55 0.00 42.32 2.71
1302 1326 7.151308 TGAAGTTGCGAATTTGGAAACATATT 58.849 30.769 0.55 0.00 43.42 1.28
1414 1448 2.889512 ACAAATTCCCTGGAACTTCCC 58.110 47.619 5.30 0.00 36.91 3.97
1514 2631 6.211515 AGACGAAAATATACCGCTCGTAAAT 58.788 36.000 0.00 0.00 42.39 1.40
1517 2634 6.476380 ACGAAAATATACCGCTCGTAAATTGA 59.524 34.615 0.00 0.00 40.69 2.57
1518 2635 7.001922 CGAAAATATACCGCTCGTAAATTGAG 58.998 38.462 0.00 0.00 36.53 3.02
1612 2789 7.204496 ACGAGTAGCTCATAAACTATAGTGG 57.796 40.000 6.06 0.00 0.00 4.00
1633 2810 5.006358 GTGGTACTACTTATTGGATGCAACG 59.994 44.000 0.12 0.00 0.00 4.10
1634 2811 5.114081 GGTACTACTTATTGGATGCAACGT 58.886 41.667 0.12 2.81 0.00 3.99
1646 2823 3.985279 GGATGCAACGTCGCAGTTATATA 59.015 43.478 7.47 0.00 46.99 0.86
1858 3035 4.633126 TCTTATGCTGCTCATTTGACAGTC 59.367 41.667 0.00 0.00 36.63 3.51
1925 3102 1.202076 GCTAAAAGATGCACTGGTCGC 60.202 52.381 0.00 0.00 0.00 5.19
2123 3300 8.618677 CATCAAGCTGATTCTTCTATGCTTTTA 58.381 33.333 0.00 0.00 38.48 1.52
2197 3374 2.070861 GCAGGAGTTGCGAGTTACG 58.929 57.895 0.00 0.00 44.09 3.18
2229 3406 3.751698 GGTGGTGTTGTTCTCAGGTAATC 59.248 47.826 0.00 0.00 0.00 1.75
2230 3407 3.751698 GTGGTGTTGTTCTCAGGTAATCC 59.248 47.826 0.00 0.00 0.00 3.01
2233 3410 5.010282 GGTGTTGTTCTCAGGTAATCCATT 58.990 41.667 0.00 0.00 35.89 3.16
2264 3449 6.020372 GCGAATCATCTGAAACTCTTTGAAG 58.980 40.000 0.00 0.00 0.00 3.02
2274 3459 8.398665 TCTGAAACTCTTTGAAGCTTAGTTTTC 58.601 33.333 19.99 15.91 39.72 2.29
2300 3485 9.137459 CTGATTTCTCTCAGTTAGGTTATCCTA 57.863 37.037 0.00 0.00 40.11 2.94
2383 3568 7.741785 TCTCTCAGTTTGGTAATCCTGTAAAA 58.258 34.615 0.00 0.00 34.23 1.52
2384 3569 7.660208 TCTCTCAGTTTGGTAATCCTGTAAAAC 59.340 37.037 0.00 0.00 34.23 2.43
2537 3722 0.316841 TGCAACGAAAAGGATTGGCC 59.683 50.000 0.00 0.00 0.00 5.36
2724 3909 4.183865 GCATGAACTACACATAGCAGACA 58.816 43.478 0.00 0.00 30.75 3.41
2745 3930 8.926710 CAGACAAGTAAGATGGTTAACTAGTTG 58.073 37.037 18.56 10.74 0.00 3.16
2855 4040 4.460948 AACTTTGGCATGCTTTCATAGG 57.539 40.909 18.92 3.49 0.00 2.57
3011 4196 1.060729 TGGTAGCAGCAAACCCTGTA 58.939 50.000 13.05 0.00 34.69 2.74
3188 4375 5.489792 ACTTCTAGGCTTTTGAGATGTGA 57.510 39.130 0.00 0.00 0.00 3.58
3219 4406 3.242712 GGCATTTTGTTGTTGACGAACTG 59.757 43.478 0.00 0.00 36.11 3.16
3272 4459 6.349243 TCAGTTAAATTGTACTTCCTCCGA 57.651 37.500 0.00 0.00 0.00 4.55
3373 4561 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3384 4572 1.497991 CGTATGTAGTCCGCATTGGG 58.502 55.000 0.00 0.00 38.76 4.12
3401 4589 6.558909 GCATTGGGATCTCTAAAAAGACTTG 58.441 40.000 0.00 0.00 0.00 3.16
3463 4651 2.866156 ACATATCCAGCGTGTGAATTCG 59.134 45.455 0.04 0.00 0.00 3.34
3465 4653 1.078709 ATCCAGCGTGTGAATTCGTG 58.921 50.000 0.04 0.00 0.00 4.35
3614 4802 4.989168 CACTTAACAGGTCAGTCCACTAAC 59.011 45.833 0.00 0.00 39.02 2.34
3745 5758 2.610232 GCAAGACGCAAAACCCAATGAT 60.610 45.455 0.00 0.00 41.79 2.45
3749 5762 3.069443 AGACGCAAAACCCAATGATTGTT 59.931 39.130 4.27 0.00 0.00 2.83
3750 5763 4.279671 AGACGCAAAACCCAATGATTGTTA 59.720 37.500 4.27 0.00 0.00 2.41
3751 5764 4.555262 ACGCAAAACCCAATGATTGTTAG 58.445 39.130 4.27 0.00 0.00 2.34
3790 5803 9.807649 GAAGCAAATTAATTTCTGGTCATACAT 57.192 29.630 10.53 0.00 0.00 2.29
3810 5823 4.080919 ACATGCTAACTGCTGACCTAATCA 60.081 41.667 0.00 0.00 43.37 2.57
3814 5827 5.163509 TGCTAACTGCTGACCTAATCACTAG 60.164 44.000 0.00 0.00 43.37 2.57
3859 5872 3.382546 AGGGCACTTTGCTGCATATTTAG 59.617 43.478 1.84 0.00 44.28 1.85
3917 5930 6.039270 GCAATACCCAAATTGTGCACTATCTA 59.961 38.462 19.41 0.00 38.78 1.98
3939 5952 3.844211 ACCCTTCACATTAACTAGCCTGA 59.156 43.478 0.00 0.00 0.00 3.86
4001 6016 3.636764 AGGTCAGGTTTTCACACCATTTC 59.363 43.478 0.00 0.00 39.62 2.17
4083 6099 3.859961 AGATAATCAACGTGCAGAACTCG 59.140 43.478 0.00 0.00 40.98 4.18
4163 6180 7.400599 TTGCATCTCAGAGCATTAGAATTTT 57.599 32.000 0.00 0.00 40.94 1.82
4165 6182 6.183360 TGCATCTCAGAGCATTAGAATTTTGG 60.183 38.462 0.00 0.00 35.51 3.28
4166 6183 5.824904 TCTCAGAGCATTAGAATTTTGGC 57.175 39.130 0.00 0.00 0.00 4.52
4167 6184 5.255687 TCTCAGAGCATTAGAATTTTGGCA 58.744 37.500 0.00 0.00 0.00 4.92
4192 6209 8.533965 CAAAAATCTATCCATACGCAAATTGTG 58.466 33.333 4.83 4.83 0.00 3.33
4231 6248 6.199908 TGCGGACATTGATTTTACTTTTGTTG 59.800 34.615 0.00 0.00 0.00 3.33
4364 6384 3.219052 CTTAGCGAGGACGAAGAAAGT 57.781 47.619 0.00 0.00 42.66 2.66
4401 6421 4.360951 ACTGAAAACGAAGGGATTACCA 57.639 40.909 0.00 0.00 43.89 3.25
4428 6448 5.006165 GCAAAATGATGTTTGTTTGTCCGAA 59.994 36.000 0.00 0.00 40.06 4.30
4431 6451 5.703978 ATGATGTTTGTTTGTCCGAATCA 57.296 34.783 0.00 0.00 0.00 2.57
4496 6516 8.988064 TGAAAACAATCTATCTCTGTACACTC 57.012 34.615 0.00 0.00 0.00 3.51
4512 6532 1.466167 CACTCGTATTGCTTGCTTGCT 59.534 47.619 3.47 0.00 0.00 3.91
4520 6540 1.304254 TGCTTGCTTGCTTCGTGTAA 58.696 45.000 3.47 0.00 0.00 2.41
4525 6545 3.100658 TGCTTGCTTCGTGTAACAGTA 57.899 42.857 0.00 0.00 35.74 2.74
4526 6546 3.057019 TGCTTGCTTCGTGTAACAGTAG 58.943 45.455 0.00 0.00 35.74 2.57
4588 6614 7.902387 TGTAAGTGTAAACTGTAAACACACA 57.098 32.000 20.79 15.90 44.68 3.72
4590 6616 7.603404 TGTAAGTGTAAACTGTAAACACACACT 59.397 33.333 20.79 12.65 45.08 3.55
4653 6689 3.951037 TGTTCCCATTATTGTTCCATCCG 59.049 43.478 0.00 0.00 0.00 4.18
4672 6708 6.128282 CCATCCGTATATTAACCAATGAGCAC 60.128 42.308 0.00 0.00 0.00 4.40
4673 6709 6.169557 TCCGTATATTAACCAATGAGCACT 57.830 37.500 0.00 0.00 0.00 4.40
4674 6710 6.220930 TCCGTATATTAACCAATGAGCACTC 58.779 40.000 0.00 0.00 0.00 3.51
4734 6776 1.134965 GTAGTTGATCAGCACGAGCCT 60.135 52.381 12.41 0.00 43.56 4.58
4738 6780 1.114627 TGATCAGCACGAGCCTGTAT 58.885 50.000 0.00 0.00 43.56 2.29
4742 6784 2.031870 TCAGCACGAGCCTGTATGTAT 58.968 47.619 0.00 0.00 43.56 2.29
4743 6785 2.034685 TCAGCACGAGCCTGTATGTATC 59.965 50.000 0.00 0.00 43.56 2.24
4744 6786 1.341531 AGCACGAGCCTGTATGTATCC 59.658 52.381 0.00 0.00 43.56 2.59
4746 6788 2.608261 GCACGAGCCTGTATGTATCCTC 60.608 54.545 0.00 0.00 33.58 3.71
4747 6789 2.623416 CACGAGCCTGTATGTATCCTCA 59.377 50.000 0.00 0.00 0.00 3.86
4748 6790 2.623889 ACGAGCCTGTATGTATCCTCAC 59.376 50.000 0.00 0.00 0.00 3.51
4803 6863 2.018137 CGAACGTGCGTGCGTATG 59.982 61.111 16.04 0.62 45.00 2.39
4822 6882 6.257423 CGTATGCATGAATGAGTAAGCAAAA 58.743 36.000 10.16 0.00 35.45 2.44
4824 6884 7.044510 CGTATGCATGAATGAGTAAGCAAAAAG 60.045 37.037 10.16 0.00 35.45 2.27
5032 7092 4.351938 TCGGCGAACACGTCCCAG 62.352 66.667 7.35 0.00 0.00 4.45
5035 7095 2.432628 GCGAACACGTCCCAGGAG 60.433 66.667 0.00 0.00 0.00 3.69
5248 7308 2.617274 GCCGTTGAAGCAGGTGGTC 61.617 63.158 0.00 0.00 0.00 4.02
5308 7368 3.518998 TAGAGCAGCTCGTCGGGC 61.519 66.667 16.99 9.70 35.36 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 0.535780 TGGTGCTCTGCCTGAAACTG 60.536 55.000 0.00 0.00 0.00 3.16
151 155 1.630244 CTTCAGAGGCTGCGGTTTCG 61.630 60.000 0.00 0.00 39.81 3.46
155 159 4.400961 GGCTTCAGAGGCTGCGGT 62.401 66.667 4.26 0.00 44.59 5.68
507 514 2.508891 CCGCACGCTGATCGAGAAC 61.509 63.158 0.00 0.00 41.67 3.01
581 591 1.064758 CCCAATCCCCATTCACGAGAA 60.065 52.381 0.00 0.00 38.31 2.87
587 597 0.254059 TCCCTCCCAATCCCCATTCA 60.254 55.000 0.00 0.00 0.00 2.57
602 615 0.690077 CCTAGCTAAACCCCGTCCCT 60.690 60.000 0.00 0.00 0.00 4.20
702 715 3.220999 CTGGACCGTCGAAGGCACA 62.221 63.158 17.91 14.81 33.69 4.57
748 761 3.073735 ACCGCAGAGGCCAGAGAG 61.074 66.667 5.01 0.00 46.52 3.20
761 776 1.819632 CTACAGCCCATTCCACCGC 60.820 63.158 0.00 0.00 0.00 5.68
777 792 0.611200 TTTAGCAGGCCGCAGTTCTA 59.389 50.000 19.30 4.01 46.13 2.10
820 835 0.391927 CGGGCCTACGAAAATGACCA 60.392 55.000 0.84 0.00 35.47 4.02
821 836 0.108041 TCGGGCCTACGAAAATGACC 60.108 55.000 0.84 0.00 40.34 4.02
822 837 1.004595 GTCGGGCCTACGAAAATGAC 58.995 55.000 0.84 0.00 45.38 3.06
823 838 0.108041 GGTCGGGCCTACGAAAATGA 60.108 55.000 0.84 0.00 45.38 2.57
824 839 1.093496 GGGTCGGGCCTACGAAAATG 61.093 60.000 0.84 0.00 45.38 2.32
827 842 3.393106 GGGGTCGGGCCTACGAAA 61.393 66.667 0.84 0.00 45.38 3.46
855 870 0.395312 CGTGGGTCCCTTAACACAGT 59.605 55.000 10.00 0.00 31.97 3.55
858 873 2.030958 CGCGTGGGTCCCTTAACAC 61.031 63.158 10.00 0.00 0.00 3.32
873 888 1.441182 CGTATAGCCTCTCTGCGCG 60.441 63.158 0.00 0.00 36.02 6.86
874 889 1.731257 GCGTATAGCCTCTCTGCGC 60.731 63.158 0.00 0.00 40.81 6.09
876 891 1.081108 CCGCGTATAGCCTCTCTGC 60.081 63.158 4.92 0.00 44.76 4.26
877 892 1.581954 CCCGCGTATAGCCTCTCTG 59.418 63.158 4.92 0.00 44.76 3.35
878 893 2.269529 GCCCGCGTATAGCCTCTCT 61.270 63.158 4.92 0.00 44.76 3.10
879 894 2.202703 GAGCCCGCGTATAGCCTCTC 62.203 65.000 4.92 0.00 44.76 3.20
897 912 1.071699 CCCTGAGAAAACTTCGGTGGA 59.928 52.381 0.00 0.00 34.02 4.02
908 923 2.606587 GCCCTGAGCCCCTGAGAAA 61.607 63.158 0.00 0.00 34.35 2.52
911 926 2.549169 GAAAGCCCTGAGCCCCTGAG 62.549 65.000 0.00 0.00 45.47 3.35
912 927 2.532715 AAAGCCCTGAGCCCCTGA 60.533 61.111 0.00 0.00 45.47 3.86
913 928 2.044551 GAAAGCCCTGAGCCCCTG 60.045 66.667 0.00 0.00 45.47 4.45
914 929 2.204213 AGAAAGCCCTGAGCCCCT 60.204 61.111 0.00 0.00 45.47 4.79
915 930 2.264120 GAGAGAAAGCCCTGAGCCCC 62.264 65.000 0.00 0.00 45.47 5.80
916 931 1.223211 GAGAGAAAGCCCTGAGCCC 59.777 63.158 0.00 0.00 45.47 5.19
917 932 1.223211 GGAGAGAAAGCCCTGAGCC 59.777 63.158 0.00 0.00 45.47 4.70
918 933 1.223211 GGGAGAGAAAGCCCTGAGC 59.777 63.158 0.00 0.00 41.31 4.26
1109 1133 4.967084 TTGGACTGGAAACTAACTAGCA 57.033 40.909 0.00 0.00 0.00 3.49
1117 1141 2.708325 AGAGCTCTTTGGACTGGAAACT 59.292 45.455 11.45 0.00 0.00 2.66
1135 1159 3.381272 CAGAGACCTAGAGAAAGGCAGAG 59.619 52.174 0.00 0.00 40.62 3.35
1204 1228 4.082679 CGAGTGAAACCTAGTCTAACTGCT 60.083 45.833 0.00 0.00 37.80 4.24
1241 1265 0.879400 CATCCTCTCCGCATCACTGC 60.879 60.000 0.00 0.00 45.31 4.40
1414 1448 2.699954 AGAGCTGTCCATAAACAACCG 58.300 47.619 0.00 0.00 0.00 4.44
1441 1475 7.545265 GCAATTTGTCAATCATAAGCCTGTTTA 59.455 33.333 0.00 0.00 0.00 2.01
1444 1478 5.186409 AGCAATTTGTCAATCATAAGCCTGT 59.814 36.000 0.00 0.00 0.00 4.00
1445 1479 5.657474 AGCAATTTGTCAATCATAAGCCTG 58.343 37.500 0.00 0.00 0.00 4.85
1446 1480 5.927281 AGCAATTTGTCAATCATAAGCCT 57.073 34.783 0.00 0.00 0.00 4.58
1514 2631 2.041485 TGGAATTCAGGTGGCATCTCAA 59.959 45.455 7.93 0.00 0.00 3.02
1517 2634 3.393426 AATGGAATTCAGGTGGCATCT 57.607 42.857 7.93 0.00 0.00 2.90
1576 2753 6.519679 TGAGCTACTCGTATTAAACTCCAA 57.480 37.500 0.00 0.00 32.35 3.53
1577 2754 6.710597 ATGAGCTACTCGTATTAAACTCCA 57.289 37.500 0.00 0.00 32.35 3.86
1590 2767 9.287373 AGTACCACTATAGTTTATGAGCTACTC 57.713 37.037 1.56 0.00 0.00 2.59
1594 2771 9.643735 AAGTAGTACCACTATAGTTTATGAGCT 57.356 33.333 1.56 0.00 32.65 4.09
1607 2784 7.270047 GTTGCATCCAATAAGTAGTACCACTA 58.730 38.462 0.00 0.00 32.75 2.74
1608 2785 5.950544 TGCATCCAATAAGTAGTACCACT 57.049 39.130 0.00 0.00 0.00 4.00
1609 2786 5.006358 CGTTGCATCCAATAAGTAGTACCAC 59.994 44.000 0.00 0.00 32.75 4.16
1612 2789 5.051907 CGACGTTGCATCCAATAAGTAGTAC 60.052 44.000 0.00 0.00 32.75 2.73
1623 2800 0.319986 TAACTGCGACGTTGCATCCA 60.320 50.000 29.86 14.97 45.26 3.41
1628 2805 5.133707 TGTTTATATAACTGCGACGTTGC 57.866 39.130 21.27 21.27 0.00 4.17
1633 2810 6.074463 GCCTACACTGTTTATATAACTGCGAC 60.074 42.308 0.00 0.00 0.00 5.19
1634 2811 5.981315 GCCTACACTGTTTATATAACTGCGA 59.019 40.000 0.00 0.00 0.00 5.10
1646 2823 0.602905 GACCGCAGCCTACACTGTTT 60.603 55.000 0.00 0.00 39.96 2.83
1925 3102 3.243975 ACAGCCCAAATCTTGAAAGCTTG 60.244 43.478 0.00 0.00 31.84 4.01
2197 3374 3.535280 ACAACACCACCAAAACCATTC 57.465 42.857 0.00 0.00 0.00 2.67
2229 3406 7.838771 TTCAGATGATTCGCATATCTAATGG 57.161 36.000 0.00 0.00 37.34 3.16
2230 3407 8.933807 AGTTTCAGATGATTCGCATATCTAATG 58.066 33.333 0.00 0.00 37.34 1.90
2233 3410 7.890515 AGAGTTTCAGATGATTCGCATATCTA 58.109 34.615 0.00 0.00 37.34 1.98
2274 3459 8.017418 AGGATAACCTAACTGAGAGAAATCAG 57.983 38.462 2.28 2.28 46.95 2.90
2300 3485 9.662947 AGTAACCAACGCTTTAGAAACTTATAT 57.337 29.630 0.00 0.00 0.00 0.86
2310 3495 4.610680 GCTTCACAGTAACCAACGCTTTAG 60.611 45.833 0.00 0.00 0.00 1.85
2315 3500 1.069906 CAGCTTCACAGTAACCAACGC 60.070 52.381 0.00 0.00 0.00 4.84
2537 3722 1.335872 GCCCAAGAACAATCAACCACG 60.336 52.381 0.00 0.00 0.00 4.94
2868 4053 4.409718 TTTGGTTAAAGGGAAACAAGGC 57.590 40.909 0.00 0.00 37.32 4.35
3188 4375 3.949132 ACAACAAAATGCCCAAAACTGT 58.051 36.364 0.00 0.00 0.00 3.55
3373 4561 2.910688 TTAGAGATCCCAATGCGGAC 57.089 50.000 0.00 0.00 36.56 4.79
3401 4589 4.280425 CCTACTCCCTCCGTTCCTAAATAC 59.720 50.000 0.00 0.00 0.00 1.89
3463 4651 4.473477 AACTAGCACTATCCTGAACCAC 57.527 45.455 0.00 0.00 0.00 4.16
3465 4653 7.988028 AGAAAATAACTAGCACTATCCTGAACC 59.012 37.037 0.00 0.00 0.00 3.62
3625 4813 9.733556 AACTTCATTACAAACCTACATGTGATA 57.266 29.630 9.11 0.00 0.00 2.15
3627 4815 8.458573 AAACTTCATTACAAACCTACATGTGA 57.541 30.769 9.11 0.00 0.00 3.58
3628 4816 9.825972 CTAAACTTCATTACAAACCTACATGTG 57.174 33.333 9.11 0.00 0.00 3.21
3629 4817 9.787435 TCTAAACTTCATTACAAACCTACATGT 57.213 29.630 2.69 2.69 0.00 3.21
3810 5823 2.636830 GCACCATCACTGATTGCTAGT 58.363 47.619 8.03 0.00 31.81 2.57
3814 5827 0.171903 GTGGCACCATCACTGATTGC 59.828 55.000 6.29 7.04 33.02 3.56
3859 5872 8.844244 ACTAAGATGATTGAATGCTGGATAAAC 58.156 33.333 0.00 0.00 0.00 2.01
3917 5930 3.844211 TCAGGCTAGTTAATGTGAAGGGT 59.156 43.478 0.00 0.00 0.00 4.34
4001 6016 3.897239 TCCCTGCACATTATTACAAGGG 58.103 45.455 0.00 0.00 35.51 3.95
4083 6099 0.740868 TAGATGCGCTTGACAGCCAC 60.741 55.000 9.73 0.00 44.06 5.01
4101 6117 6.036300 CGTTTACAGGTGACTTTGAAACACTA 59.964 38.462 0.00 0.00 40.21 2.74
4163 6180 4.203226 TGCGTATGGATAGATTTTTGCCA 58.797 39.130 0.00 0.00 0.00 4.92
4165 6182 7.222611 ACAATTTGCGTATGGATAGATTTTTGC 59.777 33.333 0.00 0.00 0.00 3.68
4166 6183 8.533965 CACAATTTGCGTATGGATAGATTTTTG 58.466 33.333 0.00 0.00 0.00 2.44
4167 6184 7.222611 GCACAATTTGCGTATGGATAGATTTTT 59.777 33.333 0.00 0.00 42.79 1.94
4192 6209 1.666189 GTCCGCAGAACCAATCTTAGC 59.334 52.381 0.00 0.00 35.73 3.09
4231 6248 3.244976 GCCACTGTGATGCACAAATAAC 58.755 45.455 9.86 0.00 44.08 1.89
4364 6384 6.403200 CGTTTTCAGTTTCACTTTCCTCTTCA 60.403 38.462 0.00 0.00 0.00 3.02
4401 6421 5.220567 GGACAAACAAACATCATTTTGCGTT 60.221 36.000 0.00 0.00 39.67 4.84
4428 6448 7.865820 TCAAGAGACCTGGATCTTATTTTGAT 58.134 34.615 15.22 0.00 34.04 2.57
4431 6451 6.216456 ACCTCAAGAGACCTGGATCTTATTTT 59.784 38.462 15.22 2.98 34.04 1.82
4496 6516 1.135972 ACGAAGCAAGCAAGCAATACG 60.136 47.619 3.19 0.00 36.85 3.06
4512 6532 9.701098 AGAAAAATACATCTACTGTTACACGAA 57.299 29.630 0.00 0.00 39.39 3.85
4520 6540 9.014297 CCCTGAAAAGAAAAATACATCTACTGT 57.986 33.333 0.00 0.00 42.13 3.55
4525 6545 8.462016 CGAATCCCTGAAAAGAAAAATACATCT 58.538 33.333 0.00 0.00 0.00 2.90
4526 6546 8.244113 ACGAATCCCTGAAAAGAAAAATACATC 58.756 33.333 0.00 0.00 0.00 3.06
4542 6563 5.010719 ACATATACTGGTACACGAATCCCTG 59.989 44.000 0.00 0.00 0.00 4.45
4588 6614 3.797184 GCACTCGTGTTCTCAAAGAGAGT 60.797 47.826 0.00 0.00 44.98 3.24
4590 6616 2.743938 GCACTCGTGTTCTCAAAGAGA 58.256 47.619 0.00 0.00 36.86 3.10
4649 6677 6.769512 AGTGCTCATTGGTTAATATACGGAT 58.230 36.000 0.00 0.00 0.00 4.18
4734 6776 4.673320 CGTTGACACGTGAGGATACATACA 60.673 45.833 25.01 3.55 41.84 2.29
4738 6780 2.341318 CGTTGACACGTGAGGATACA 57.659 50.000 25.01 9.08 41.84 2.29
4763 6823 2.223409 ACAATAACGCTGCGAGATACGA 60.223 45.455 30.47 5.45 45.77 3.43
4803 6863 5.346822 CACCTTTTTGCTTACTCATTCATGC 59.653 40.000 0.00 0.00 0.00 4.06
4861 6921 3.379445 GCCTGAACCCTCCGTCGA 61.379 66.667 0.00 0.00 0.00 4.20
4874 6934 2.435586 CACCAGCTTCCTCGCCTG 60.436 66.667 0.00 0.00 0.00 4.85
4917 6977 2.359975 CCTTCAACAGCCGGGACC 60.360 66.667 2.18 0.00 0.00 4.46
5392 7452 1.065928 GTCCATCTACGAGGTGCCG 59.934 63.158 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.