Multiple sequence alignment - TraesCS7D01G218100

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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 TraesCS7D01G218100 chr7D 100.000 5762 0 0 1 5762 178703920 178698159 0.000000e+00 10641.0
1 TraesCS7D01G218100 chr7D 89.201 463 44 6 531 989 179125763 179125303 1.800000e-159 573.0
2 TraesCS7D01G218100 chr7D 87.069 464 46 8 531 989 178942742 178942288 3.980000e-141 512.0
3 TraesCS7D01G218100 chr7D 83.206 262 25 9 556 798 178994023 178993762 7.510000e-54 222.0
4 TraesCS7D01G218100 chr7D 90.164 61 6 0 3206 3266 178700652 178700592 4.790000e-11 80.5
5 TraesCS7D01G218100 chr7D 90.164 61 6 0 3269 3329 178700715 178700655 4.790000e-11 80.5
6 TraesCS7D01G218100 chr7D 83.750 80 5 6 177 252 179126120 179126045 1.040000e-07 69.4
7 TraesCS7D01G218100 chr7A 96.937 2873 80 4 2325 5193 182720342 182717474 0.000000e+00 4811.0
8 TraesCS7D01G218100 chr7A 93.609 1956 92 7 593 2534 182722141 182720205 0.000000e+00 2889.0
9 TraesCS7D01G218100 chr7A 91.079 482 29 6 58 526 182723000 182722520 1.750000e-179 640.0
10 TraesCS7D01G218100 chr7A 87.397 484 27 14 5284 5738 182717448 182716970 5.110000e-145 525.0
11 TraesCS7D01G218100 chr7A 87.192 406 46 4 589 993 183485260 183484860 1.890000e-124 457.0
12 TraesCS7D01G218100 chr7A 86.441 413 39 8 580 989 182860108 182859710 2.470000e-118 436.0
13 TraesCS7D01G218100 chr7A 92.199 282 21 1 708 989 183657929 183657649 1.160000e-106 398.0
14 TraesCS7D01G218100 chr7A 93.443 61 4 0 531 591 182722447 182722387 2.210000e-14 91.6
15 TraesCS7D01G218100 chr7A 91.071 56 5 0 3213 3268 182719391 182719336 6.190000e-10 76.8
16 TraesCS7D01G218100 chr7B 93.403 3077 149 22 80 3121 144709016 144705959 0.000000e+00 4508.0
17 TraesCS7D01G218100 chr7B 96.665 2459 61 7 3104 5547 144705943 144703491 0.000000e+00 4067.0
18 TraesCS7D01G218100 chr7B 89.507 467 37 10 531 989 145057650 145057188 1.080000e-161 580.0
19 TraesCS7D01G218100 chr7B 86.481 466 50 10 531 989 144815436 144814977 3.100000e-137 499.0
20 TraesCS7D01G218100 chr7B 85.650 223 19 7 589 798 145032601 145032379 7.510000e-54 222.0
21 TraesCS7D01G218100 chr7B 87.778 180 10 9 5572 5740 144703370 144703192 3.520000e-47 200.0
22 TraesCS7D01G218100 chr7B 91.803 61 5 0 3269 3329 144705841 144705781 1.030000e-12 86.1
23 TraesCS7D01G218100 chr7B 90.164 61 6 0 3206 3266 144705778 144705718 4.790000e-11 80.5


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 TraesCS7D01G218100 chr7D 178698159 178703920 5761 True 3600.666667 10641 93.442667 1 5762 3 chr7D.!!$R3 5761
1 TraesCS7D01G218100 chr7D 179125303 179126120 817 True 321.200000 573 86.475500 177 989 2 chr7D.!!$R4 812
2 TraesCS7D01G218100 chr7A 182716970 182723000 6030 True 1505.566667 4811 92.256000 58 5738 6 chr7A.!!$R4 5680
3 TraesCS7D01G218100 chr7B 144703192 144709016 5824 True 1788.320000 4508 91.962600 80 5740 5 chr7B.!!$R4 5660

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
26 27 0.027848 GAGCTGACCGTACTAGCGAC 59.972 60.000 0.00 0.0 42.10 5.19 F
907 1260 0.103026 TCGGCTCTTCGACATGGATG 59.897 55.000 0.00 0.0 33.92 3.51 F
1696 2064 0.034863 GGTGCAGAAAACCCGGGATA 60.035 55.000 32.02 0.0 0.00 2.59 F
2485 2925 2.498807 TGATTCTCAGAGGATTCGCG 57.501 50.000 0.00 0.0 0.00 5.87 F
3853 4326 1.457643 AGCCACCCAGAGCGCTATA 60.458 57.895 11.50 0.0 0.00 1.31 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1261 1629 0.107831 AACACCGCCAGAAGTAGCAA 59.892 50.000 0.0 0.0 0.00 3.91 R
1967 2335 0.534877 AGAGGTCGCATTGCAACACA 60.535 50.000 0.0 0.0 0.00 3.72 R
2697 3137 1.241165 TTGCAGCATGTTCACTCTGG 58.759 50.000 0.0 0.0 39.31 3.86 R
4129 4602 1.073548 GCAACCGACCCCTTAACCA 59.926 57.895 0.0 0.0 0.00 3.67 R
5738 6336 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.0 0.0 0.00 3.82 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
23 24 1.355916 CGGAGCTGACCGTACTAGC 59.644 63.158 5.70 0.00 46.70 3.42
24 25 1.355916 GGAGCTGACCGTACTAGCG 59.644 63.158 0.00 0.00 42.10 4.26
25 26 1.094073 GGAGCTGACCGTACTAGCGA 61.094 60.000 0.00 0.00 42.10 4.93
26 27 0.027848 GAGCTGACCGTACTAGCGAC 59.972 60.000 0.00 0.00 42.10 5.19
27 28 0.392729 AGCTGACCGTACTAGCGACT 60.393 55.000 0.00 0.00 42.10 4.18
28 29 0.248134 GCTGACCGTACTAGCGACTG 60.248 60.000 0.00 0.00 0.00 3.51
29 30 0.248134 CTGACCGTACTAGCGACTGC 60.248 60.000 0.00 0.00 43.24 4.40
30 31 0.956902 TGACCGTACTAGCGACTGCA 60.957 55.000 0.00 0.00 46.23 4.41
31 32 0.522915 GACCGTACTAGCGACTGCAC 60.523 60.000 0.00 0.00 46.23 4.57
32 33 1.226603 CCGTACTAGCGACTGCACC 60.227 63.158 0.00 0.00 46.23 5.01
33 34 1.504900 CGTACTAGCGACTGCACCA 59.495 57.895 0.00 0.00 46.23 4.17
34 35 0.523546 CGTACTAGCGACTGCACCAG 60.524 60.000 0.00 0.00 46.23 4.00
36 37 0.526211 TACTAGCGACTGCACCAGTG 59.474 55.000 2.12 0.00 45.44 3.66
48 49 1.363744 CACCAGTGCTGTTAGCTAGC 58.636 55.000 6.62 6.62 42.97 3.42
49 50 1.066573 CACCAGTGCTGTTAGCTAGCT 60.067 52.381 23.12 23.12 42.97 3.32
50 51 2.166459 CACCAGTGCTGTTAGCTAGCTA 59.834 50.000 20.67 20.67 42.97 3.32
51 52 2.428890 ACCAGTGCTGTTAGCTAGCTAG 59.571 50.000 23.03 16.84 42.97 3.42
60 61 2.255856 GCTAGCTAGCTACCGCGG 59.744 66.667 33.71 26.86 45.62 6.46
71 72 1.379710 TACCGCGGCCAGTACCTAA 60.380 57.895 28.58 0.00 0.00 2.69
73 74 2.574929 CGCGGCCAGTACCTAACA 59.425 61.111 2.24 0.00 0.00 2.41
163 171 2.240612 CTGCACGCCGGAGCTAAAAC 62.241 60.000 5.05 0.00 36.60 2.43
318 330 3.406361 GTCGTGTGCCAGTCAGCG 61.406 66.667 0.00 0.00 34.65 5.18
348 361 1.300233 CTCTCCGCTTACCATCGCC 60.300 63.158 0.00 0.00 0.00 5.54
401 419 1.761198 CCAGGTACCCTACTGGCTAAC 59.239 57.143 8.74 0.00 46.78 2.34
404 422 2.586368 AGGTACCCTACTGGCTAACTCT 59.414 50.000 8.74 0.00 37.83 3.24
526 548 5.955959 TGGTGTATTAGGCTCTCTTCTAACA 59.044 40.000 0.00 0.00 0.00 2.41
527 549 6.096987 TGGTGTATTAGGCTCTCTTCTAACAG 59.903 42.308 0.00 0.00 0.00 3.16
573 668 7.202066 GGTCCAACTCCAACCTAATAAGCTATA 60.202 40.741 0.00 0.00 0.00 1.31
596 938 4.841422 AGATGATAGCCTGATACATTGCC 58.159 43.478 0.00 0.00 0.00 4.52
605 947 0.818040 GATACATTGCCGTGGGGTCC 60.818 60.000 0.00 0.00 34.97 4.46
607 949 2.191786 TACATTGCCGTGGGGTCCTG 62.192 60.000 0.00 0.00 34.97 3.86
677 1019 2.799126 TTTGTTCACTGTCCACACCT 57.201 45.000 0.00 0.00 0.00 4.00
697 1049 3.374058 CCTCCGTTCACACCATTATTGAC 59.626 47.826 0.00 0.00 0.00 3.18
698 1050 2.997303 TCCGTTCACACCATTATTGACG 59.003 45.455 0.00 0.00 0.00 4.35
699 1051 2.475519 CCGTTCACACCATTATTGACGC 60.476 50.000 0.00 0.00 0.00 5.19
700 1052 2.475519 CGTTCACACCATTATTGACGCC 60.476 50.000 0.00 0.00 0.00 5.68
701 1053 1.364721 TCACACCATTATTGACGCCG 58.635 50.000 0.00 0.00 0.00 6.46
702 1054 0.376852 CACACCATTATTGACGCCGG 59.623 55.000 0.00 0.00 0.00 6.13
703 1055 0.250793 ACACCATTATTGACGCCGGA 59.749 50.000 5.05 0.00 0.00 5.14
704 1056 1.339247 ACACCATTATTGACGCCGGAA 60.339 47.619 5.05 0.00 0.00 4.30
705 1057 1.330521 CACCATTATTGACGCCGGAAG 59.669 52.381 5.05 0.00 0.00 3.46
706 1058 1.208535 ACCATTATTGACGCCGGAAGA 59.791 47.619 5.05 0.00 0.00 2.87
769 1121 4.498520 GCAGCAGCCGTCGCTCTA 62.499 66.667 0.00 0.00 43.95 2.43
907 1260 0.103026 TCGGCTCTTCGACATGGATG 59.897 55.000 0.00 0.00 33.92 3.51
939 1293 3.816523 CAGTGCCAATTTTCTGCCATTTT 59.183 39.130 0.00 0.00 0.00 1.82
989 1345 2.158986 CCTGATCTGGGTACAAGCTCAG 60.159 54.545 16.17 16.17 0.00 3.35
1034 1390 2.360852 ACACATGCAGCCTCAGCC 60.361 61.111 0.00 0.00 41.25 4.85
1261 1629 0.107654 GTGGAGGCTGCGGAAGTATT 60.108 55.000 0.35 0.00 0.00 1.89
1296 1664 2.517402 TTGGCCGTTGGTGTCACC 60.517 61.111 15.64 15.64 39.22 4.02
1379 1747 2.667470 CGATCCTCTCCTCCCACTTAA 58.333 52.381 0.00 0.00 0.00 1.85
1458 1826 6.788598 TCTCTAGTCTTGATCATCTTGCTT 57.211 37.500 0.00 0.00 0.00 3.91
1518 1886 3.059325 GCTCGATGCAGTTTACCATGATC 60.059 47.826 0.00 0.00 42.31 2.92
1568 1936 4.379243 CGCGGGGAGTTGCAGAGT 62.379 66.667 0.00 0.00 0.00 3.24
1582 1950 3.774734 TGCAGAGTACTAAGGTCTTCCA 58.225 45.455 0.00 0.00 35.89 3.53
1625 1993 3.234386 GTTCTGTTTTCGCCTATGTTGC 58.766 45.455 0.00 0.00 0.00 4.17
1644 2012 3.006940 TGCGGTTCATATCCTGTTGTTC 58.993 45.455 0.00 0.00 0.00 3.18
1652 2020 4.474651 TCATATCCTGTTGTTCATGAGGGT 59.525 41.667 0.00 0.00 0.00 4.34
1696 2064 0.034863 GGTGCAGAAAACCCGGGATA 60.035 55.000 32.02 0.00 0.00 2.59
1836 2204 5.002464 AGTTCATATTGATGCTTGCAACC 57.998 39.130 0.00 0.00 32.62 3.77
1962 2330 4.818546 CACAATCTCCTCCGCTTCAATATT 59.181 41.667 0.00 0.00 0.00 1.28
1967 2335 5.684704 TCTCCTCCGCTTCAATATTTTCAT 58.315 37.500 0.00 0.00 0.00 2.57
2084 2452 4.214327 TGTGTGCGTCGTGGCTGA 62.214 61.111 0.00 0.00 0.00 4.26
2175 2543 7.066284 GTGATACTCATAATTGCTGTGGTTCTT 59.934 37.037 0.00 0.00 0.00 2.52
2196 2564 8.439286 GTTCTTATCTGTGTTCTGATTCTTGTC 58.561 37.037 0.00 0.00 34.79 3.18
2240 2608 4.759205 GGTGTGGGTGGATGGGGC 62.759 72.222 0.00 0.00 0.00 5.80
2272 2640 3.047796 GCACTTGACAAAATGCTGAGTG 58.952 45.455 14.13 6.17 36.88 3.51
2336 2704 7.228108 CCAGCAATGTACATATTGTCAGAGAAT 59.772 37.037 9.21 0.00 39.62 2.40
2444 2884 2.566952 GAGCTTGACTCTCAGAGAGC 57.433 55.000 25.20 18.12 46.12 4.09
2479 2919 3.580022 TGCAGAACTTGATTCTCAGAGGA 59.420 43.478 0.00 0.00 44.99 3.71
2485 2925 2.498807 TGATTCTCAGAGGATTCGCG 57.501 50.000 0.00 0.00 0.00 5.87
2510 2950 5.129155 AGCAAGATACAGAGCTTGATTCTCT 59.871 40.000 7.10 0.00 44.94 3.10
2520 2960 5.046448 AGAGCTTGATTCTCTGACAACTCAT 60.046 40.000 0.00 0.00 39.29 2.90
2558 2998 4.442733 GCATGTAGTTCGAGATACAGAAGC 59.557 45.833 14.63 13.82 35.49 3.86
2638 3078 5.896106 ACTGGAGATGTGAGATCTGTATCAA 59.104 40.000 0.00 0.00 34.28 2.57
2697 3137 4.923871 ACAACACTACGTCAATCTCATGAC 59.076 41.667 0.00 0.00 44.96 3.06
2864 3304 8.475639 TGACAGTAGAAATTCTATCCAAGGTAC 58.524 37.037 5.96 0.00 30.76 3.34
2960 3400 2.306219 TGGGATGTGAATTACCCGACAA 59.694 45.455 0.00 0.00 44.70 3.18
3588 4061 5.716228 TGCATATGTTCCTCTCCATGTTTTT 59.284 36.000 4.29 0.00 0.00 1.94
3591 4064 7.148086 GCATATGTTCCTCTCCATGTTTTTGTA 60.148 37.037 4.29 0.00 0.00 2.41
3853 4326 1.457643 AGCCACCCAGAGCGCTATA 60.458 57.895 11.50 0.00 0.00 1.31
3921 4394 6.072508 TGGCTGTCATCATTCTTCTTGTTAAC 60.073 38.462 0.00 0.00 0.00 2.01
3960 4433 3.331150 TGGAATCAAGTCGTACGCAATT 58.669 40.909 11.24 5.36 0.00 2.32
4129 4602 1.492176 CATTAGATGGGCCACTGACCT 59.508 52.381 9.28 3.84 0.00 3.85
4150 4623 3.256824 TTAAGGGGTCGGTTGCGGG 62.257 63.158 0.00 0.00 0.00 6.13
4237 4710 1.635817 TAATGCTCAGGGGTCAGGCC 61.636 60.000 0.00 0.00 0.00 5.19
4256 4729 2.505819 GCCCCCTTATCAGTGAGAAGAA 59.494 50.000 25.51 4.56 33.30 2.52
4556 5029 5.190528 ACTTCATCATGATACTGGACCTGTT 59.809 40.000 8.15 0.00 0.00 3.16
4743 5216 3.117452 GCTGGAGCCTAGCCATGCT 62.117 63.158 0.00 0.00 41.42 3.79
4775 5248 2.609459 CAGCATGATACCGAACCTGAAC 59.391 50.000 0.00 0.00 39.69 3.18
4934 5408 2.812658 TGACAGAGATCTTCAGGCTGA 58.187 47.619 14.43 14.43 0.00 4.26
4984 5458 5.615925 AGTTTGTCCTCACCTATGGTATC 57.384 43.478 0.00 0.00 32.11 2.24
5012 5486 0.691078 GGCTGGATGTAGAGGTGGGA 60.691 60.000 0.00 0.00 0.00 4.37
5154 5636 5.791666 TGGCATTTTTGCATGATCAGTTTA 58.208 33.333 0.09 0.00 36.33 2.01
5245 5727 4.282957 TGTCTGCATCAAATAAGGGCAAAA 59.717 37.500 0.00 0.00 33.58 2.44
5266 5748 7.565789 GCAAAAAGCTGAATTTCGTTTGAGTAG 60.566 37.037 0.00 0.00 41.15 2.57
5273 5755 5.525745 TGAATTTCGTTTGAGTAGTTGCTGA 59.474 36.000 0.00 0.00 0.00 4.26
5349 5832 3.325293 TTAGCCTGCTGAGACAGAAAG 57.675 47.619 0.97 0.00 40.25 2.62
5484 5975 3.403038 AGGCTATTTCAGACACACACAC 58.597 45.455 0.00 0.00 32.94 3.82
5485 5976 3.138304 GGCTATTTCAGACACACACACA 58.862 45.455 0.00 0.00 29.64 3.72
5492 5983 3.574614 TCAGACACACACACATGATACG 58.425 45.455 0.00 0.00 0.00 3.06
5522 6013 9.877178 CCAGGTACAACTATGATTCCTATAATC 57.123 37.037 0.00 0.00 0.00 1.75
5607 6194 5.661458 AGTAAAGGATCACAACTATGTCGG 58.339 41.667 0.00 0.00 37.82 4.79
5655 6244 7.174946 CACTACTTATTCTGAGATCTCTCCTCC 59.825 44.444 22.95 0.00 42.20 4.30
5668 6257 1.760613 TCTCCTCCGTTGTTGTTCAGT 59.239 47.619 0.00 0.00 0.00 3.41
5678 6269 4.403453 GTTGTTGTTCAGTGTTCAGTGAC 58.597 43.478 9.48 6.57 0.00 3.67
5679 6270 3.669536 TGTTGTTCAGTGTTCAGTGACA 58.330 40.909 9.48 8.60 0.00 3.58
5706 6297 5.805728 TGTCTTTTTCTTCTCCAGGATACC 58.194 41.667 0.00 0.00 37.17 2.73
5709 6307 3.914426 TTTCTTCTCCAGGATACCAGC 57.086 47.619 0.00 0.00 37.17 4.85
5715 6313 1.139853 CTCCAGGATACCAGCACCTTC 59.860 57.143 0.00 0.00 37.17 3.46
5738 6336 0.661020 GGGCTAACACACACACACAC 59.339 55.000 0.00 0.00 0.00 3.82
5739 6337 1.374560 GGCTAACACACACACACACA 58.625 50.000 0.00 0.00 0.00 3.72
5740 6338 1.063469 GGCTAACACACACACACACAC 59.937 52.381 0.00 0.00 0.00 3.82
5741 6339 1.735018 GCTAACACACACACACACACA 59.265 47.619 0.00 0.00 0.00 3.72
5742 6340 2.475519 GCTAACACACACACACACACAC 60.476 50.000 0.00 0.00 0.00 3.82
5743 6341 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
5744 6342 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5745 6343 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5746 6344 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5747 6345 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5748 6346 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5749 6347 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5750 6348 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5751 6349 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5752 6350 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5753 6351 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5754 6352 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5755 6353 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
5756 6354 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
5757 6355 0.179227 CACACACACACACACACACG 60.179 55.000 0.00 0.00 0.00 4.49
5758 6356 1.225991 CACACACACACACACACGC 60.226 57.895 0.00 0.00 0.00 5.34
5759 6357 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
5760 6358 3.860125 ACACACACACACACGCGC 61.860 61.111 5.73 0.00 0.00 6.86
5761 6359 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.094073 TCGCTAGTACGGTCAGCTCC 61.094 60.000 9.19 0.00 33.03 4.70
7 8 0.027848 GTCGCTAGTACGGTCAGCTC 59.972 60.000 9.19 1.59 33.03 4.09
8 9 0.392729 AGTCGCTAGTACGGTCAGCT 60.393 55.000 9.19 0.00 33.03 4.24
9 10 0.248134 CAGTCGCTAGTACGGTCAGC 60.248 60.000 0.00 0.00 0.00 4.26
10 11 0.248134 GCAGTCGCTAGTACGGTCAG 60.248 60.000 0.00 0.00 34.30 3.51
11 12 0.956902 TGCAGTCGCTAGTACGGTCA 60.957 55.000 0.00 0.00 39.64 4.02
12 13 0.522915 GTGCAGTCGCTAGTACGGTC 60.523 60.000 0.00 0.00 39.64 4.79
13 14 1.505353 GTGCAGTCGCTAGTACGGT 59.495 57.895 0.00 0.00 39.64 4.83
14 15 1.226603 GGTGCAGTCGCTAGTACGG 60.227 63.158 0.00 0.00 39.64 4.02
15 16 0.523546 CTGGTGCAGTCGCTAGTACG 60.524 60.000 0.00 0.00 39.64 3.67
16 17 0.526662 ACTGGTGCAGTCGCTAGTAC 59.473 55.000 0.00 0.00 41.21 2.73
17 18 0.526211 CACTGGTGCAGTCGCTAGTA 59.474 55.000 0.00 0.00 43.43 1.82
18 19 1.290324 CACTGGTGCAGTCGCTAGT 59.710 57.895 0.00 0.00 43.43 2.57
19 20 4.175599 CACTGGTGCAGTCGCTAG 57.824 61.111 0.00 0.00 43.43 3.42
29 30 1.066573 AGCTAGCTAACAGCACTGGTG 60.067 52.381 17.69 6.69 45.56 4.17
30 31 1.270907 AGCTAGCTAACAGCACTGGT 58.729 50.000 17.69 0.00 45.56 4.00
31 32 2.801342 GCTAGCTAGCTAACAGCACTGG 60.801 54.545 33.71 13.36 45.56 4.00
32 33 2.468831 GCTAGCTAGCTAACAGCACTG 58.531 52.381 33.71 13.97 45.56 3.66
33 34 2.880963 GCTAGCTAGCTAACAGCACT 57.119 50.000 33.71 3.17 45.56 4.40
44 45 2.255856 GCCGCGGTAGCTAGCTAG 59.744 66.667 28.70 16.84 42.32 3.42
45 46 3.292936 GGCCGCGGTAGCTAGCTA 61.293 66.667 28.70 20.67 42.32 3.32
47 48 4.951963 CTGGCCGCGGTAGCTAGC 62.952 72.222 28.70 13.03 42.32 3.42
48 49 2.191513 TACTGGCCGCGGTAGCTAG 61.192 63.158 28.70 21.16 43.81 3.42
49 50 2.124193 TACTGGCCGCGGTAGCTA 60.124 61.111 28.70 15.81 42.32 3.32
50 51 3.834799 GTACTGGCCGCGGTAGCT 61.835 66.667 28.70 16.70 42.32 3.32
51 52 4.886121 GGTACTGGCCGCGGTAGC 62.886 72.222 28.70 16.68 40.74 3.58
52 53 1.386525 TTAGGTACTGGCCGCGGTAG 61.387 60.000 28.70 25.88 41.52 3.18
53 54 1.379710 TTAGGTACTGGCCGCGGTA 60.380 57.895 28.70 15.56 41.52 4.02
54 55 2.681064 TTAGGTACTGGCCGCGGT 60.681 61.111 28.70 9.45 41.52 5.68
55 56 2.202837 GTTAGGTACTGGCCGCGG 60.203 66.667 24.05 24.05 41.52 6.46
56 57 1.079681 TTGTTAGGTACTGGCCGCG 60.080 57.895 0.00 0.00 41.52 6.46
57 58 1.356527 CGTTGTTAGGTACTGGCCGC 61.357 60.000 0.00 0.00 41.52 6.53
58 59 0.738412 CCGTTGTTAGGTACTGGCCG 60.738 60.000 0.00 0.00 41.52 6.13
59 60 1.022982 GCCGTTGTTAGGTACTGGCC 61.023 60.000 0.00 0.00 41.52 5.36
60 61 0.320946 TGCCGTTGTTAGGTACTGGC 60.321 55.000 0.00 0.00 41.52 4.85
71 72 0.887387 ATTAACTGCCGTGCCGTTGT 60.887 50.000 13.19 3.10 36.70 3.32
73 74 1.582610 CCATTAACTGCCGTGCCGTT 61.583 55.000 9.72 9.72 39.18 4.44
125 132 3.414700 CACTGTTCCGTGGAGCGC 61.415 66.667 0.00 0.00 39.71 5.92
144 151 2.032634 TTTTAGCTCCGGCGTGCAG 61.033 57.895 20.70 8.77 44.37 4.41
204 212 2.182030 GGCGAAGTCACCTCCGAG 59.818 66.667 0.00 0.00 0.00 4.63
318 330 1.004918 CGGAGAGGGTGTGTTGACC 60.005 63.158 0.00 0.00 34.96 4.02
348 361 3.125829 CAGTGAAATGGAATCTGTGGACG 59.874 47.826 0.00 0.00 0.00 4.79
401 419 5.885230 TGGAACACATGAATAAGCAAGAG 57.115 39.130 0.00 0.00 0.00 2.85
404 422 5.069648 TGGTTTGGAACACATGAATAAGCAA 59.930 36.000 0.00 0.00 39.29 3.91
526 548 3.535561 CCAGTCATATCAAGAAACGGCT 58.464 45.455 0.00 0.00 0.00 5.52
527 549 2.614057 CCCAGTCATATCAAGAAACGGC 59.386 50.000 0.00 0.00 0.00 5.68
529 551 3.871594 GGACCCAGTCATATCAAGAAACG 59.128 47.826 0.00 0.00 33.68 3.60
573 668 5.251764 GGCAATGTATCAGGCTATCATCTT 58.748 41.667 0.00 0.00 0.00 2.40
596 938 2.976494 AAACAAGGCAGGACCCCACG 62.976 60.000 0.00 0.00 40.58 4.94
605 947 4.391405 ACAAAGGAAAGAAACAAGGCAG 57.609 40.909 0.00 0.00 0.00 4.85
607 949 6.816640 AGTTAAACAAAGGAAAGAAACAAGGC 59.183 34.615 0.00 0.00 0.00 4.35
677 1019 2.997303 CGTCAATAATGGTGTGAACGGA 59.003 45.455 0.00 0.00 0.00 4.69
700 1052 0.671251 AAGATAGCCGAGCTCTTCCG 59.329 55.000 12.85 0.00 40.44 4.30
701 1053 2.101582 TCAAAGATAGCCGAGCTCTTCC 59.898 50.000 12.85 0.00 40.44 3.46
702 1054 3.444703 TCAAAGATAGCCGAGCTCTTC 57.555 47.619 12.85 2.96 40.44 2.87
703 1055 3.791245 CTTCAAAGATAGCCGAGCTCTT 58.209 45.455 12.85 0.00 40.44 2.85
704 1056 2.482839 GCTTCAAAGATAGCCGAGCTCT 60.483 50.000 12.85 0.00 40.44 4.09
705 1057 1.864082 GCTTCAAAGATAGCCGAGCTC 59.136 52.381 2.73 2.73 40.44 4.09
706 1058 1.208052 TGCTTCAAAGATAGCCGAGCT 59.792 47.619 3.87 3.87 43.41 4.09
769 1121 1.339055 TGCGGCTTTGAGCTTGTATCT 60.339 47.619 0.00 0.00 41.99 1.98
907 1260 3.874392 AATTGGCACTGGAACTTATGC 57.126 42.857 0.00 0.00 37.35 3.14
939 1293 3.687698 GGTAAGATTAACTGCAAGCGGAA 59.312 43.478 8.05 0.00 37.60 4.30
989 1345 1.880675 CCTCAATCATGGCATGAGCTC 59.119 52.381 31.39 6.82 43.53 4.09
1154 1510 1.502640 GCCTCGATATCCTCCGTCG 59.497 63.158 0.00 0.00 36.75 5.12
1261 1629 0.107831 AACACCGCCAGAAGTAGCAA 59.892 50.000 0.00 0.00 0.00 3.91
1296 1664 1.098050 GGCTCAACCCAGCATTGTAG 58.902 55.000 0.00 0.00 41.65 2.74
1359 1727 2.366640 TAAGTGGGAGGAGAGGATCG 57.633 55.000 0.00 0.00 42.67 3.69
1379 1747 2.470821 CTTCGTATCGCCGGAAGAATT 58.529 47.619 5.05 0.00 0.00 2.17
1458 1826 1.379977 CGCCACTCCCCTACTCAGA 60.380 63.158 0.00 0.00 0.00 3.27
1518 1886 4.197750 CCATGAGACTGAAAAGATCCAGG 58.802 47.826 0.00 0.00 34.85 4.45
1582 1950 5.509498 ACAGACCAGCACCAATATGTAAAT 58.491 37.500 0.00 0.00 0.00 1.40
1625 1993 4.875536 TCATGAACAACAGGATATGAACCG 59.124 41.667 0.00 0.00 34.30 4.44
1644 2012 1.407437 GGCTGTGGAACTACCCTCATG 60.407 57.143 0.00 0.00 38.04 3.07
1652 2020 4.339872 TCTTTTAACGGCTGTGGAACTA 57.660 40.909 0.00 0.00 38.04 2.24
1696 2064 6.543089 TGCGTTTCAGCTTCTTCAGAATGAT 61.543 40.000 0.00 0.00 41.12 2.45
1836 2204 5.359756 TGGTATGTGATAGTAGCAGCAAAG 58.640 41.667 0.00 0.00 0.00 2.77
1962 2330 2.392821 GTCGCATTGCAACACATGAAA 58.607 42.857 0.00 0.00 0.00 2.69
1967 2335 0.534877 AGAGGTCGCATTGCAACACA 60.535 50.000 0.00 0.00 0.00 3.72
2084 2452 1.229359 CCAATGAGCCCCAGCAGAT 59.771 57.895 0.00 0.00 43.56 2.90
2175 2543 8.724229 CAAATGACAAGAATCAGAACACAGATA 58.276 33.333 0.00 0.00 30.46 1.98
2272 2640 3.346631 CTTGCCCCAATGACAGCGC 62.347 63.158 0.00 0.00 0.00 5.92
2323 2691 5.101648 TGATGGTGCATTCTCTGACAATA 57.898 39.130 0.00 0.00 0.00 1.90
2336 2704 2.502947 AGCTCTGTATCTTGATGGTGCA 59.497 45.455 0.00 0.00 0.00 4.57
2443 2883 1.025113 TCTGCATCTTGCTGCTGAGC 61.025 55.000 0.00 0.00 45.31 4.26
2444 2884 1.130749 GTTCTGCATCTTGCTGCTGAG 59.869 52.381 0.00 0.00 46.39 3.35
2479 2919 2.736978 CTCTGTATCTTGCTCGCGAAT 58.263 47.619 11.33 2.35 0.00 3.34
2485 2925 5.358922 AGAATCAAGCTCTGTATCTTGCTC 58.641 41.667 0.00 0.00 39.47 4.26
2510 2950 2.556144 AGCTTGCTGATGAGTTGTCA 57.444 45.000 0.00 0.00 37.02 3.58
2558 2998 4.715896 CAAATTCGACATGACACCTTCTG 58.284 43.478 0.00 0.00 0.00 3.02
2601 3041 7.397221 TCACATCTCCAGTTGATACAAGATTT 58.603 34.615 0.00 0.00 0.00 2.17
2638 3078 3.202818 TCCATGCTATCCAAATCACTGGT 59.797 43.478 0.00 0.00 37.74 4.00
2697 3137 1.241165 TTGCAGCATGTTCACTCTGG 58.759 50.000 0.00 0.00 39.31 3.86
2845 3285 7.985752 CGGTAAAGTACCTTGGATAGAATTTCT 59.014 37.037 4.03 4.03 46.81 2.52
2864 3304 1.635663 CGAGCCCTGCAACGGTAAAG 61.636 60.000 1.67 0.00 0.00 1.85
2960 3400 1.426251 TTCTGTGCTGTCCCCATGGT 61.426 55.000 11.73 0.00 0.00 3.55
3588 4061 7.293828 TCAACCATCCATTATGCCTAAATACA 58.706 34.615 0.00 0.00 33.92 2.29
3591 4064 7.345392 ACTTTCAACCATCCATTATGCCTAAAT 59.655 33.333 0.00 0.00 33.92 1.40
3853 4326 4.624452 GGCGTTCGAGTAGTAGAAAACATT 59.376 41.667 0.00 0.00 0.00 2.71
3921 4394 2.440627 TCCATCCTCACATGATTCCCTG 59.559 50.000 0.00 0.00 0.00 4.45
3978 4451 2.860971 AGGAGGCCCAGCAAACCT 60.861 61.111 0.00 0.00 36.19 3.50
4129 4602 1.073548 GCAACCGACCCCTTAACCA 59.926 57.895 0.00 0.00 0.00 3.67
4150 4623 5.536161 AGTCAGGCTCTAGATGAAGAATCTC 59.464 44.000 0.00 0.00 42.27 2.75
4237 4710 4.033709 TCCTTCTTCTCACTGATAAGGGG 58.966 47.826 4.75 7.25 38.10 4.79
4256 4729 6.987403 AGTACTTCTGTCTCTTCTTTTCCT 57.013 37.500 0.00 0.00 0.00 3.36
4556 5029 2.744166 GCATAAGCTGTCATCAGAGCCA 60.744 50.000 0.00 0.00 43.76 4.75
4762 5235 1.619827 ACATTCCGTTCAGGTTCGGTA 59.380 47.619 3.64 0.00 45.88 4.02
4767 5240 6.659242 AGATATTCAAACATTCCGTTCAGGTT 59.341 34.615 0.00 0.00 41.99 3.50
4775 5248 8.125448 GGAGAAGAAAGATATTCAAACATTCCG 58.875 37.037 0.00 0.00 0.00 4.30
4912 5386 3.132467 TCAGCCTGAAGATCTCTGTCATG 59.868 47.826 0.00 0.00 0.00 3.07
4934 5408 7.014422 CGTCTTAACTAAGGGGATACTTCATCT 59.986 40.741 0.00 0.00 32.74 2.90
4966 5440 3.588210 TCGATACCATAGGTGAGGACA 57.412 47.619 0.00 0.00 36.19 4.02
4967 5441 3.890147 ACTTCGATACCATAGGTGAGGAC 59.110 47.826 0.00 0.00 36.19 3.85
4968 5442 4.180377 ACTTCGATACCATAGGTGAGGA 57.820 45.455 0.00 0.00 36.19 3.71
4984 5458 2.628178 TCTACATCCAGCCCATACTTCG 59.372 50.000 0.00 0.00 0.00 3.79
5012 5486 5.590259 AGACAAAACACAACTCTAAGCATGT 59.410 36.000 0.00 0.00 0.00 3.21
5176 5658 6.252995 ACTACTCCAAATGCCAAAATAAGGA 58.747 36.000 0.00 0.00 0.00 3.36
5245 5727 6.430451 CAACTACTCAAACGAAATTCAGCTT 58.570 36.000 0.00 0.00 0.00 3.74
5273 5755 4.487714 TTGGTTCAAGAGACACTGAAGT 57.512 40.909 0.00 0.00 0.00 3.01
5308 5790 7.598493 GGCTAATGAAAACAGATAAAGCAACAA 59.402 33.333 0.00 0.00 0.00 2.83
5318 5800 4.592942 TCAGCAGGCTAATGAAAACAGAT 58.407 39.130 0.00 0.00 0.00 2.90
5320 5802 4.005650 TCTCAGCAGGCTAATGAAAACAG 58.994 43.478 0.00 0.00 0.00 3.16
5322 5804 3.753272 TGTCTCAGCAGGCTAATGAAAAC 59.247 43.478 0.00 4.95 0.00 2.43
5326 5809 2.460669 TCTGTCTCAGCAGGCTAATGA 58.539 47.619 0.00 0.00 37.12 2.57
5349 5832 1.694696 AGACAGAACACCCCTCAACTC 59.305 52.381 0.00 0.00 0.00 3.01
5484 5975 2.899976 TGTACCTGGCAACGTATCATG 58.100 47.619 0.00 0.00 42.51 3.07
5485 5976 3.267483 GTTGTACCTGGCAACGTATCAT 58.733 45.455 0.00 0.00 37.15 2.45
5492 5983 4.335594 GGAATCATAGTTGTACCTGGCAAC 59.664 45.833 8.59 8.59 44.57 4.17
5522 6013 8.848474 ATAATTGAGAATGATACCCGTAAAGG 57.152 34.615 0.00 0.00 40.63 3.11
5655 6244 3.124466 TCACTGAACACTGAACAACAACG 59.876 43.478 0.00 0.00 0.00 4.10
5678 6269 6.467677 TCCTGGAGAAGAAAAAGACATACTG 58.532 40.000 0.00 0.00 0.00 2.74
5679 6270 6.688073 TCCTGGAGAAGAAAAAGACATACT 57.312 37.500 0.00 0.00 0.00 2.12
5685 6276 5.571658 GCTGGTATCCTGGAGAAGAAAAAGA 60.572 44.000 1.52 0.00 0.00 2.52
5687 6278 4.042809 TGCTGGTATCCTGGAGAAGAAAAA 59.957 41.667 1.52 0.00 0.00 1.94
5697 6288 1.134280 CAGAAGGTGCTGGTATCCTGG 60.134 57.143 0.00 0.00 32.26 4.45
5706 6297 0.615331 TTAGCCCTCAGAAGGTGCTG 59.385 55.000 14.09 0.00 44.25 4.41
5709 6307 1.347707 TGTGTTAGCCCTCAGAAGGTG 59.652 52.381 0.00 0.00 41.59 4.00
5715 6313 1.202639 TGTGTGTGTGTTAGCCCTCAG 60.203 52.381 0.00 0.00 0.00 3.35
5738 6336 0.179227 CGTGTGTGTGTGTGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
5739 6337 1.906994 GCGTGTGTGTGTGTGTGTGT 61.907 55.000 0.00 0.00 0.00 3.72
5740 6338 1.225991 GCGTGTGTGTGTGTGTGTG 60.226 57.895 0.00 0.00 0.00 3.82
5741 6339 2.735677 CGCGTGTGTGTGTGTGTGT 61.736 57.895 0.00 0.00 0.00 3.72
5742 6340 2.021243 CGCGTGTGTGTGTGTGTG 59.979 61.111 0.00 0.00 0.00 3.82
5743 6341 3.860125 GCGCGTGTGTGTGTGTGT 61.860 61.111 8.43 0.00 0.00 3.72
5744 6342 4.918060 CGCGCGTGTGTGTGTGTG 62.918 66.667 24.19 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.