Multiple sequence alignment - TraesCS7D01G483500

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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 TraesCS7D01G483500 chr7D 100.000 2249 0 0 1 2249 593371306 593369058 0.000000e+00 4154
1 TraesCS7D01G483500 chr7A 92.094 1366 64 20 912 2249 686156737 686155388 0.000000e+00 1884
2 TraesCS7D01G483500 chr7A 91.129 372 17 10 88 458 686157595 686157239 7.220000e-135 490
3 TraesCS7D01G483500 chr7A 89.558 249 14 8 595 837 686157022 686156780 2.810000e-79 305
4 TraesCS7D01G483500 chr7B 92.290 882 40 16 1382 2249 667480073 667480940 0.000000e+00 1227
5 TraesCS7D01G483500 chr7B 89.630 974 58 20 451 1410 667479078 667480022 0.000000e+00 1199
6 TraesCS7D01G483500 chr7B 95.726 234 7 2 227 458 667478749 667478981 7.580000e-100 374
7 TraesCS7D01G483500 chr6D 91.389 360 29 2 968 1326 111062154 111062512 2.010000e-135 492
8 TraesCS7D01G483500 chr6D 82.386 528 71 16 1728 2247 111063032 111063545 7.370000e-120 440
9 TraesCS7D01G483500 chr6D 94.175 206 12 0 229 434 111061849 111062054 4.660000e-82 315
10 TraesCS7D01G483500 chr6D 89.151 212 20 3 229 438 351137575 351137365 6.160000e-66 261
11 TraesCS7D01G483500 chr6B 91.111 360 30 2 968 1326 200008688 200009046 9.340000e-134 486
12 TraesCS7D01G483500 chr6B 82.197 528 72 17 1728 2247 200009608 200010121 3.430000e-118 435
13 TraesCS7D01G483500 chr6B 93.689 206 13 0 229 434 200008394 200008599 2.170000e-80 309
14 TraesCS7D01G483500 chr6B 89.573 211 19 3 230 438 528285888 528286097 4.760000e-67 265
15 TraesCS7D01G483500 chr6A 91.111 360 30 2 968 1326 135561310 135561668 9.340000e-134 486
16 TraesCS7D01G483500 chr6A 82.264 530 68 21 1728 2247 135562238 135562751 3.430000e-118 435
17 TraesCS7D01G483500 chr6A 94.175 206 12 0 229 434 135561010 135561215 4.660000e-82 315
18 TraesCS7D01G483500 chr6A 88.479 217 21 4 221 435 492283906 492284120 2.220000e-65 259
19 TraesCS7D01G483500 chr2B 73.945 403 75 22 1732 2127 144433352 144433731 3.900000e-28 135
20 TraesCS7D01G483500 chr2A 73.125 480 86 29 1732 2197 90596451 90596901 5.040000e-27 132
21 TraesCS7D01G483500 chr2D 73.267 404 79 23 1732 2128 92920526 92920907 1.090000e-23 121


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 TraesCS7D01G483500 chr7D 593369058 593371306 2248 True 4154.000000 4154 100.000000 1 2249 1 chr7D.!!$R1 2248
1 TraesCS7D01G483500 chr7A 686155388 686157595 2207 True 893.000000 1884 90.927000 88 2249 3 chr7A.!!$R1 2161
2 TraesCS7D01G483500 chr7B 667478749 667480940 2191 False 933.333333 1227 92.548667 227 2249 3 chr7B.!!$F1 2022
3 TraesCS7D01G483500 chr6D 111061849 111063545 1696 False 415.666667 492 89.316667 229 2247 3 chr6D.!!$F1 2018
4 TraesCS7D01G483500 chr6B 200008394 200010121 1727 False 410.000000 486 88.999000 229 2247 3 chr6B.!!$F2 2018
5 TraesCS7D01G483500 chr6A 135561010 135562751 1741 False 412.000000 486 89.183333 229 2247 3 chr6A.!!$F2 2018

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
47 48 0.035439 CCGCCAACCACTCACCTAAT 60.035 55.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 2233 0.417437 TCACTCCCCTTCCATCTCCA 59.583 55.0 0.0 0.0 0.0 3.86 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
17 18 2.805546 TCACGAGCTACCGATGCC 59.194 61.111 1.33 0.00 0.00 4.40
18 19 2.655364 CACGAGCTACCGATGCCG 60.655 66.667 1.33 0.00 0.00 5.69
29 30 4.971125 GATGCCGGCCTAGTCGCC 62.971 72.222 26.77 0.00 46.13 5.54
37 38 4.077184 CCTAGTCGCCGCCAACCA 62.077 66.667 0.00 0.00 0.00 3.67
38 39 2.813908 CTAGTCGCCGCCAACCAC 60.814 66.667 0.00 0.00 0.00 4.16
39 40 3.296709 CTAGTCGCCGCCAACCACT 62.297 63.158 0.00 0.00 0.00 4.00
40 41 3.291101 TAGTCGCCGCCAACCACTC 62.291 63.158 0.00 0.00 0.00 3.51
41 42 4.980805 GTCGCCGCCAACCACTCA 62.981 66.667 0.00 0.00 0.00 3.41
42 43 4.980805 TCGCCGCCAACCACTCAC 62.981 66.667 0.00 0.00 0.00 3.51
44 45 4.643387 GCCGCCAACCACTCACCT 62.643 66.667 0.00 0.00 0.00 4.00
45 46 3.065306 CCGCCAACCACTCACCTA 58.935 61.111 0.00 0.00 0.00 3.08
46 47 1.373435 CCGCCAACCACTCACCTAA 59.627 57.895 0.00 0.00 0.00 2.69
47 48 0.035439 CCGCCAACCACTCACCTAAT 60.035 55.000 0.00 0.00 0.00 1.73
48 49 1.369625 CGCCAACCACTCACCTAATC 58.630 55.000 0.00 0.00 0.00 1.75
49 50 1.338674 CGCCAACCACTCACCTAATCA 60.339 52.381 0.00 0.00 0.00 2.57
50 51 2.790433 GCCAACCACTCACCTAATCAA 58.210 47.619 0.00 0.00 0.00 2.57
51 52 2.488153 GCCAACCACTCACCTAATCAAC 59.512 50.000 0.00 0.00 0.00 3.18
52 53 3.810743 GCCAACCACTCACCTAATCAACT 60.811 47.826 0.00 0.00 0.00 3.16
53 54 3.753272 CCAACCACTCACCTAATCAACTG 59.247 47.826 0.00 0.00 0.00 3.16
54 55 3.703001 ACCACTCACCTAATCAACTGG 57.297 47.619 0.00 0.00 0.00 4.00
55 56 2.290323 ACCACTCACCTAATCAACTGGC 60.290 50.000 0.00 0.00 0.00 4.85
56 57 2.359900 CACTCACCTAATCAACTGGCC 58.640 52.381 0.00 0.00 0.00 5.36
57 58 1.985159 ACTCACCTAATCAACTGGCCA 59.015 47.619 4.71 4.71 0.00 5.36
58 59 2.578021 ACTCACCTAATCAACTGGCCAT 59.422 45.455 5.51 0.00 0.00 4.40
59 60 2.947652 CTCACCTAATCAACTGGCCATG 59.052 50.000 5.51 1.93 0.00 3.66
60 61 2.026641 CACCTAATCAACTGGCCATGG 58.973 52.381 5.51 7.63 0.00 3.66
61 62 1.922447 ACCTAATCAACTGGCCATGGA 59.078 47.619 18.40 4.50 0.00 3.41
62 63 2.311542 ACCTAATCAACTGGCCATGGAA 59.688 45.455 18.40 0.87 0.00 3.53
63 64 2.689983 CCTAATCAACTGGCCATGGAAC 59.310 50.000 18.40 8.04 0.00 3.62
75 76 3.636820 TGGAACAGTGGGTCACGT 58.363 55.556 0.00 0.00 39.64 4.49
76 77 2.823587 TGGAACAGTGGGTCACGTA 58.176 52.632 0.00 0.00 39.64 3.57
77 78 0.677288 TGGAACAGTGGGTCACGTAG 59.323 55.000 0.00 0.00 39.64 3.51
78 79 0.037605 GGAACAGTGGGTCACGTAGG 60.038 60.000 0.00 0.00 39.64 3.18
79 80 0.037605 GAACAGTGGGTCACGTAGGG 60.038 60.000 0.00 0.00 39.64 3.53
80 81 0.470456 AACAGTGGGTCACGTAGGGA 60.470 55.000 0.00 0.00 39.64 4.20
81 82 0.898789 ACAGTGGGTCACGTAGGGAG 60.899 60.000 0.00 0.00 39.64 4.30
82 83 1.305046 AGTGGGTCACGTAGGGAGG 60.305 63.158 0.00 0.00 39.64 4.30
83 84 2.038329 TGGGTCACGTAGGGAGGG 59.962 66.667 0.00 0.00 0.00 4.30
84 85 2.361771 GGGTCACGTAGGGAGGGA 59.638 66.667 0.00 0.00 0.00 4.20
85 86 1.757340 GGGTCACGTAGGGAGGGAG 60.757 68.421 0.00 0.00 0.00 4.30
86 87 1.305623 GGTCACGTAGGGAGGGAGA 59.694 63.158 0.00 0.00 0.00 3.71
97 98 2.362503 AGGGAGATCGTCGTGCCA 60.363 61.111 0.00 0.00 0.00 4.92
103 104 1.153647 GATCGTCGTGCCATCCACA 60.154 57.895 0.00 0.00 44.91 4.17
106 107 2.516589 CGTCGTGCCATCCACATCG 61.517 63.158 0.00 0.00 44.91 3.84
107 108 1.447838 GTCGTGCCATCCACATCGT 60.448 57.895 0.00 0.00 44.91 3.73
135 136 1.593787 CTGAGCGGTGACCAGACAT 59.406 57.895 1.11 0.00 0.00 3.06
146 147 3.661745 CCAGACATGGCGGTAGTAC 57.338 57.895 0.00 0.00 40.52 2.73
147 148 1.112113 CCAGACATGGCGGTAGTACT 58.888 55.000 0.00 0.00 40.52 2.73
148 149 1.202417 CCAGACATGGCGGTAGTACTG 60.202 57.143 5.39 4.63 40.52 2.74
149 150 1.476891 CAGACATGGCGGTAGTACTGT 59.523 52.381 5.39 1.59 0.00 3.55
150 151 1.476891 AGACATGGCGGTAGTACTGTG 59.523 52.381 5.39 4.12 0.00 3.66
151 152 0.108329 ACATGGCGGTAGTACTGTGC 60.108 55.000 5.39 6.46 0.00 4.57
152 153 0.175760 CATGGCGGTAGTACTGTGCT 59.824 55.000 5.39 3.41 0.00 4.40
153 154 0.175760 ATGGCGGTAGTACTGTGCTG 59.824 55.000 5.39 2.18 0.00 4.41
161 162 3.304458 GGTAGTACTGTGCTGTTTTTGGC 60.304 47.826 5.39 0.00 0.00 4.52
178 179 1.879380 TGGCTGGACATTTTGTTCGAG 59.121 47.619 0.00 0.00 0.00 4.04
189 190 9.405587 GGACATTTTGTTCGAGAAATGAATAAA 57.594 29.630 24.98 4.15 42.85 1.40
191 192 9.191995 ACATTTTGTTCGAGAAATGAATAAACC 57.808 29.630 24.98 0.00 42.85 3.27
195 196 7.504924 TGTTCGAGAAATGAATAAACCTGTT 57.495 32.000 0.00 0.00 0.00 3.16
197 198 8.410141 TGTTCGAGAAATGAATAAACCTGTTTT 58.590 29.630 0.00 0.00 34.23 2.43
198 199 9.887406 GTTCGAGAAATGAATAAACCTGTTTTA 57.113 29.630 0.00 0.00 34.08 1.52
199 200 9.887406 TTCGAGAAATGAATAAACCTGTTTTAC 57.113 29.630 0.00 0.00 32.29 2.01
201 202 9.840427 CGAGAAATGAATAAACCTGTTTTACAT 57.160 29.630 0.00 2.82 32.29 2.29
207 208 9.927668 ATGAATAAACCTGTTTTACATTGGAAG 57.072 29.630 0.00 0.00 32.29 3.46
439 440 3.632080 CCCGTACCCCTGCACACA 61.632 66.667 0.00 0.00 0.00 3.72
440 441 2.047274 CCGTACCCCTGCACACAG 60.047 66.667 0.00 0.00 44.05 3.66
449 555 2.638719 TGCACACAGACGCATTGC 59.361 55.556 0.00 0.00 31.95 3.56
470 576 1.165270 AAAAAGATTCAGACGGCCGG 58.835 50.000 31.76 12.37 0.00 6.13
475 581 3.151958 ATTCAGACGGCCGGGATCG 62.152 63.158 31.76 12.97 0.00 3.69
497 603 2.375766 CGTGGTGAGAGCGACTTGC 61.376 63.158 0.00 0.00 46.98 4.01
513 619 1.069049 CTTGCCCACCCAAAAAGTCTG 59.931 52.381 0.00 0.00 0.00 3.51
514 620 0.260230 TGCCCACCCAAAAAGTCTGA 59.740 50.000 0.00 0.00 0.00 3.27
515 621 1.133199 TGCCCACCCAAAAAGTCTGAT 60.133 47.619 0.00 0.00 0.00 2.90
520 627 4.144297 CCACCCAAAAAGTCTGATGAGAA 58.856 43.478 0.00 0.00 0.00 2.87
535 642 1.677576 TGAGAAGCAGTTTGTTGGCAG 59.322 47.619 0.00 0.00 0.00 4.85
539 646 1.143620 GCAGTTTGTTGGCAGCCAA 59.856 52.632 23.88 23.88 41.69 4.52
556 663 0.875474 CAACAAAACCCTGGCTTGCG 60.875 55.000 0.00 0.00 0.00 4.85
589 700 3.640407 CCGCCGGGATGGGATCAT 61.640 66.667 2.18 0.00 38.63 2.45
590 701 2.359107 CGCCGGGATGGGATCATG 60.359 66.667 2.18 0.00 38.63 3.07
591 702 2.034687 GCCGGGATGGGATCATGG 59.965 66.667 2.18 0.00 38.63 3.66
592 703 2.034687 CCGGGATGGGATCATGGC 59.965 66.667 0.00 0.00 32.98 4.40
593 704 2.034687 CGGGATGGGATCATGGCC 59.965 66.667 0.00 0.00 32.98 5.36
692 813 4.383602 CCCAAAAGCACGACGCCG 62.384 66.667 0.00 0.00 44.04 6.46
712 834 3.983420 ATGCCACCCACCCACCAG 61.983 66.667 0.00 0.00 0.00 4.00
791 917 1.666209 CCGATGCCCCAACAACCATC 61.666 60.000 0.00 0.00 0.00 3.51
797 923 2.023788 GCCCCAACAACCATCGATGAT 61.024 52.381 26.86 6.74 0.00 2.45
876 1004 2.291346 TGTACCTAGGCTAGTGCAGTGA 60.291 50.000 19.68 0.63 41.91 3.41
886 1014 4.544047 TGCAGTGACTGGCGTGCA 62.544 61.111 15.24 6.27 43.50 4.57
900 1028 0.573987 CGTGCATGACGCTATGACAG 59.426 55.000 0.00 0.00 42.21 3.51
901 1029 0.933097 GTGCATGACGCTATGACAGG 59.067 55.000 0.00 0.00 43.06 4.00
902 1030 0.179076 TGCATGACGCTATGACAGGG 60.179 55.000 0.00 0.00 43.06 4.45
903 1031 0.104855 GCATGACGCTATGACAGGGA 59.895 55.000 0.00 0.00 39.56 4.20
904 1032 1.270518 GCATGACGCTATGACAGGGAT 60.271 52.381 0.00 0.00 39.56 3.85
905 1033 2.029020 GCATGACGCTATGACAGGGATA 60.029 50.000 0.00 0.00 39.56 2.59
906 1034 3.554960 GCATGACGCTATGACAGGGATAA 60.555 47.826 0.00 0.00 39.56 1.75
907 1035 3.728076 TGACGCTATGACAGGGATAAC 57.272 47.619 0.00 0.00 39.56 1.89
908 1036 3.296854 TGACGCTATGACAGGGATAACT 58.703 45.455 0.00 0.00 39.56 2.24
927 1055 4.708726 ACTAAGCAAGCAATCATTGGAC 57.291 40.909 0.00 0.00 0.00 4.02
947 1075 3.589988 ACATGGATTCGAAGTGTGAGAC 58.410 45.455 3.35 0.00 0.00 3.36
949 1077 1.967779 TGGATTCGAAGTGTGAGACCA 59.032 47.619 3.35 0.70 0.00 4.02
956 1084 3.311110 GTGTGAGACCAGGGCCGA 61.311 66.667 0.00 0.00 0.00 5.54
972 1100 2.809601 GATGCGCGACGAACCTGT 60.810 61.111 12.10 0.00 0.00 4.00
1287 1415 2.355126 CACAGCAGCACGTCGTCT 60.355 61.111 0.00 0.00 0.00 4.18
1445 1722 2.908015 GCTGATTGGCGGGTCCTA 59.092 61.111 0.00 0.00 35.26 2.94
1681 2230 1.099879 CCAGCTAGTGGCAATGGAGC 61.100 60.000 1.43 1.54 44.79 4.70
1682 2231 0.393402 CAGCTAGTGGCAATGGAGCA 60.393 55.000 11.74 0.00 44.79 4.26
1683 2232 0.329261 AGCTAGTGGCAATGGAGCAA 59.671 50.000 11.74 0.00 44.79 3.91
1684 2233 1.064166 AGCTAGTGGCAATGGAGCAAT 60.064 47.619 11.74 0.00 44.79 3.56
1685 2234 1.066605 GCTAGTGGCAATGGAGCAATG 59.933 52.381 1.43 0.00 41.35 2.82
1686 2235 1.679680 CTAGTGGCAATGGAGCAATGG 59.320 52.381 0.00 0.00 35.83 3.16
1687 2236 0.040058 AGTGGCAATGGAGCAATGGA 59.960 50.000 0.00 0.00 35.83 3.41
1688 2237 0.458669 GTGGCAATGGAGCAATGGAG 59.541 55.000 0.00 0.00 35.83 3.86
1689 2238 0.332293 TGGCAATGGAGCAATGGAGA 59.668 50.000 0.00 0.00 35.83 3.71
1691 2240 1.340248 GGCAATGGAGCAATGGAGATG 59.660 52.381 0.00 0.00 35.83 2.90
1693 2242 2.940158 CAATGGAGCAATGGAGATGGA 58.060 47.619 0.00 0.00 0.00 3.41
1694 2243 3.293337 CAATGGAGCAATGGAGATGGAA 58.707 45.455 0.00 0.00 0.00 3.53
1698 2247 0.554792 AGCAATGGAGATGGAAGGGG 59.445 55.000 0.00 0.00 0.00 4.79
1699 2248 0.552848 GCAATGGAGATGGAAGGGGA 59.447 55.000 0.00 0.00 0.00 4.81
1700 2249 1.478288 GCAATGGAGATGGAAGGGGAG 60.478 57.143 0.00 0.00 0.00 4.30
1701 2250 1.849039 CAATGGAGATGGAAGGGGAGT 59.151 52.381 0.00 0.00 0.00 3.85
1702 2251 1.516110 ATGGAGATGGAAGGGGAGTG 58.484 55.000 0.00 0.00 0.00 3.51
1703 2252 0.417437 TGGAGATGGAAGGGGAGTGA 59.583 55.000 0.00 0.00 0.00 3.41
1704 2253 1.127343 GGAGATGGAAGGGGAGTGAG 58.873 60.000 0.00 0.00 0.00 3.51
1705 2254 1.343478 GGAGATGGAAGGGGAGTGAGA 60.343 57.143 0.00 0.00 0.00 3.27
1706 2255 2.472029 GAGATGGAAGGGGAGTGAGAA 58.528 52.381 0.00 0.00 0.00 2.87
1759 2308 4.056125 CTGGTGACGAGGCTGCGA 62.056 66.667 12.16 0.00 34.83 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.805546 GGCATCGGTAGCTCGTGA 59.194 61.111 0.00 0.00 0.00 4.35
1 2 2.655364 CGGCATCGGTAGCTCGTG 60.655 66.667 0.00 0.00 0.00 4.35
20 21 4.077184 TGGTTGGCGGCGACTAGG 62.077 66.667 26.64 0.00 0.00 3.02
21 22 2.813908 GTGGTTGGCGGCGACTAG 60.814 66.667 26.64 0.00 0.00 2.57
22 23 3.291101 GAGTGGTTGGCGGCGACTA 62.291 63.158 26.64 19.81 0.00 2.59
23 24 4.681978 GAGTGGTTGGCGGCGACT 62.682 66.667 26.64 14.77 0.00 4.18
24 25 4.980805 TGAGTGGTTGGCGGCGAC 62.981 66.667 20.72 20.72 0.00 5.19
25 26 4.980805 GTGAGTGGTTGGCGGCGA 62.981 66.667 12.98 0.00 0.00 5.54
27 28 2.741486 TTAGGTGAGTGGTTGGCGGC 62.741 60.000 0.00 0.00 0.00 6.53
28 29 0.035439 ATTAGGTGAGTGGTTGGCGG 60.035 55.000 0.00 0.00 0.00 6.13
29 30 1.338674 TGATTAGGTGAGTGGTTGGCG 60.339 52.381 0.00 0.00 0.00 5.69
30 31 2.488153 GTTGATTAGGTGAGTGGTTGGC 59.512 50.000 0.00 0.00 0.00 4.52
31 32 3.753272 CAGTTGATTAGGTGAGTGGTTGG 59.247 47.826 0.00 0.00 0.00 3.77
32 33 3.753272 CCAGTTGATTAGGTGAGTGGTTG 59.247 47.826 0.00 0.00 0.00 3.77
33 34 3.810743 GCCAGTTGATTAGGTGAGTGGTT 60.811 47.826 0.00 0.00 35.50 3.67
34 35 2.290323 GCCAGTTGATTAGGTGAGTGGT 60.290 50.000 0.00 0.00 35.50 4.16
35 36 2.359900 GCCAGTTGATTAGGTGAGTGG 58.640 52.381 0.00 0.00 36.02 4.00
36 37 2.290260 TGGCCAGTTGATTAGGTGAGTG 60.290 50.000 0.00 0.00 0.00 3.51
37 38 1.985159 TGGCCAGTTGATTAGGTGAGT 59.015 47.619 0.00 0.00 0.00 3.41
38 39 2.787473 TGGCCAGTTGATTAGGTGAG 57.213 50.000 0.00 0.00 0.00 3.51
39 40 2.357050 CCATGGCCAGTTGATTAGGTGA 60.357 50.000 13.05 0.00 0.00 4.02
40 41 2.026641 CCATGGCCAGTTGATTAGGTG 58.973 52.381 13.05 0.00 0.00 4.00
41 42 1.922447 TCCATGGCCAGTTGATTAGGT 59.078 47.619 13.05 0.00 0.00 3.08
42 43 2.689983 GTTCCATGGCCAGTTGATTAGG 59.310 50.000 13.05 2.82 0.00 2.69
43 44 3.355378 TGTTCCATGGCCAGTTGATTAG 58.645 45.455 13.05 0.00 0.00 1.73
44 45 3.245229 ACTGTTCCATGGCCAGTTGATTA 60.245 43.478 23.61 0.00 36.03 1.75
45 46 2.173519 CTGTTCCATGGCCAGTTGATT 58.826 47.619 13.05 0.00 0.00 2.57
46 47 1.076024 ACTGTTCCATGGCCAGTTGAT 59.924 47.619 23.61 8.13 36.03 2.57
47 48 0.478072 ACTGTTCCATGGCCAGTTGA 59.522 50.000 23.61 4.34 36.03 3.18
48 49 0.599558 CACTGTTCCATGGCCAGTTG 59.400 55.000 25.62 19.02 37.34 3.16
49 50 0.540365 CCACTGTTCCATGGCCAGTT 60.540 55.000 25.62 13.77 37.34 3.16
50 51 1.075482 CCACTGTTCCATGGCCAGT 59.925 57.895 23.61 23.61 39.93 4.00
51 52 1.679977 CCCACTGTTCCATGGCCAG 60.680 63.158 22.57 22.57 34.37 4.85
52 53 2.424842 GACCCACTGTTCCATGGCCA 62.425 60.000 8.56 8.56 34.37 5.36
53 54 1.678970 GACCCACTGTTCCATGGCC 60.679 63.158 6.96 0.00 34.37 5.36
54 55 1.074775 TGACCCACTGTTCCATGGC 59.925 57.895 6.96 0.00 34.37 4.40
55 56 0.955428 CGTGACCCACTGTTCCATGG 60.955 60.000 4.97 4.97 35.59 3.66
56 57 0.250295 ACGTGACCCACTGTTCCATG 60.250 55.000 0.00 0.00 31.34 3.66
57 58 1.275291 CTACGTGACCCACTGTTCCAT 59.725 52.381 0.00 0.00 31.34 3.41
58 59 0.677288 CTACGTGACCCACTGTTCCA 59.323 55.000 0.00 0.00 31.34 3.53
59 60 0.037605 CCTACGTGACCCACTGTTCC 60.038 60.000 0.00 0.00 31.34 3.62
60 61 0.037605 CCCTACGTGACCCACTGTTC 60.038 60.000 0.00 0.00 31.34 3.18
61 62 0.470456 TCCCTACGTGACCCACTGTT 60.470 55.000 0.00 0.00 31.34 3.16
62 63 0.898789 CTCCCTACGTGACCCACTGT 60.899 60.000 0.00 0.00 31.34 3.55
63 64 1.605058 CCTCCCTACGTGACCCACTG 61.605 65.000 0.00 0.00 31.34 3.66
64 65 1.305046 CCTCCCTACGTGACCCACT 60.305 63.158 0.00 0.00 31.34 4.00
65 66 2.356780 CCCTCCCTACGTGACCCAC 61.357 68.421 0.00 0.00 0.00 4.61
66 67 2.038329 CCCTCCCTACGTGACCCA 59.962 66.667 0.00 0.00 0.00 4.51
67 68 1.757340 CTCCCTCCCTACGTGACCC 60.757 68.421 0.00 0.00 0.00 4.46
68 69 0.106116 ATCTCCCTCCCTACGTGACC 60.106 60.000 0.00 0.00 0.00 4.02
69 70 1.320507 GATCTCCCTCCCTACGTGAC 58.679 60.000 0.00 0.00 0.00 3.67
70 71 0.179026 CGATCTCCCTCCCTACGTGA 60.179 60.000 0.00 0.00 0.00 4.35
71 72 0.465824 ACGATCTCCCTCCCTACGTG 60.466 60.000 0.00 0.00 0.00 4.49
72 73 0.179023 GACGATCTCCCTCCCTACGT 60.179 60.000 0.00 0.00 35.31 3.57
73 74 1.229315 CGACGATCTCCCTCCCTACG 61.229 65.000 0.00 0.00 0.00 3.51
74 75 0.179023 ACGACGATCTCCCTCCCTAC 60.179 60.000 0.00 0.00 0.00 3.18
75 76 0.179026 CACGACGATCTCCCTCCCTA 60.179 60.000 0.00 0.00 0.00 3.53
76 77 1.454111 CACGACGATCTCCCTCCCT 60.454 63.158 0.00 0.00 0.00 4.20
77 78 3.121019 CACGACGATCTCCCTCCC 58.879 66.667 0.00 0.00 0.00 4.30
78 79 2.413765 GCACGACGATCTCCCTCC 59.586 66.667 0.00 0.00 0.00 4.30
79 80 1.739338 ATGGCACGACGATCTCCCTC 61.739 60.000 0.00 0.00 0.00 4.30
80 81 1.739338 GATGGCACGACGATCTCCCT 61.739 60.000 0.00 0.00 31.22 4.20
81 82 1.300233 GATGGCACGACGATCTCCC 60.300 63.158 0.00 0.00 31.22 4.30
82 83 1.300233 GGATGGCACGACGATCTCC 60.300 63.158 0.00 0.00 34.17 3.71
83 84 0.872021 GTGGATGGCACGACGATCTC 60.872 60.000 0.00 0.00 34.17 2.75
84 85 1.141881 GTGGATGGCACGACGATCT 59.858 57.895 0.00 0.00 34.17 2.75
85 86 0.530650 ATGTGGATGGCACGACGATC 60.531 55.000 0.00 0.00 33.00 3.69
86 87 0.530650 GATGTGGATGGCACGACGAT 60.531 55.000 0.00 0.00 0.00 3.73
97 98 1.453155 GAGTGGCAAACGATGTGGAT 58.547 50.000 0.00 0.00 0.00 3.41
103 104 0.674895 GCTCAGGAGTGGCAAACGAT 60.675 55.000 0.00 0.00 0.00 3.73
106 107 3.257933 CGCTCAGGAGTGGCAAAC 58.742 61.111 1.92 0.00 35.41 2.93
135 136 1.183030 ACAGCACAGTACTACCGCCA 61.183 55.000 0.00 0.00 0.00 5.69
141 142 3.563808 CAGCCAAAAACAGCACAGTACTA 59.436 43.478 0.00 0.00 0.00 1.82
143 144 2.543653 CCAGCCAAAAACAGCACAGTAC 60.544 50.000 0.00 0.00 0.00 2.73
145 146 0.461135 CCAGCCAAAAACAGCACAGT 59.539 50.000 0.00 0.00 0.00 3.55
146 147 0.746063 TCCAGCCAAAAACAGCACAG 59.254 50.000 0.00 0.00 0.00 3.66
147 148 0.459489 GTCCAGCCAAAAACAGCACA 59.541 50.000 0.00 0.00 0.00 4.57
148 149 0.459489 TGTCCAGCCAAAAACAGCAC 59.541 50.000 0.00 0.00 0.00 4.40
149 150 1.412079 ATGTCCAGCCAAAAACAGCA 58.588 45.000 0.00 0.00 0.00 4.41
150 151 2.531522 AATGTCCAGCCAAAAACAGC 57.468 45.000 0.00 0.00 0.00 4.40
151 152 4.190772 ACAAAATGTCCAGCCAAAAACAG 58.809 39.130 0.00 0.00 0.00 3.16
152 153 4.213564 ACAAAATGTCCAGCCAAAAACA 57.786 36.364 0.00 0.00 0.00 2.83
153 154 4.260172 CGAACAAAATGTCCAGCCAAAAAC 60.260 41.667 0.00 0.00 0.00 2.43
161 162 6.000891 TCATTTCTCGAACAAAATGTCCAG 57.999 37.500 19.10 3.27 41.47 3.86
189 190 4.202111 GCACACTTCCAATGTAAAACAGGT 60.202 41.667 0.00 0.00 0.00 4.00
191 192 3.974401 CGCACACTTCCAATGTAAAACAG 59.026 43.478 0.00 0.00 0.00 3.16
195 196 1.069568 CGCGCACACTTCCAATGTAAA 60.070 47.619 8.75 0.00 0.00 2.01
197 198 1.906994 GCGCGCACACTTCCAATGTA 61.907 55.000 29.10 0.00 0.00 2.29
198 199 2.945984 CGCGCACACTTCCAATGT 59.054 55.556 8.75 0.00 0.00 2.71
199 200 2.502510 GCGCGCACACTTCCAATG 60.503 61.111 29.10 0.00 0.00 2.82
222 223 4.494484 CAGATCATGAAAGGTACGTGACA 58.506 43.478 0.00 0.00 36.35 3.58
225 226 3.861840 ACCAGATCATGAAAGGTACGTG 58.138 45.455 13.53 0.00 0.00 4.49
410 411 2.125961 GTACGGGATGACGGAGGCT 61.126 63.158 0.00 0.00 38.39 4.58
470 576 0.312416 CTCTCACCACGGATCGATCC 59.688 60.000 31.04 31.04 43.65 3.36
475 581 1.226717 GTCGCTCTCACCACGGATC 60.227 63.158 0.00 0.00 0.00 3.36
497 603 2.821969 CTCATCAGACTTTTTGGGTGGG 59.178 50.000 0.00 0.00 0.00 4.61
513 619 2.294233 TGCCAACAAACTGCTTCTCATC 59.706 45.455 0.00 0.00 0.00 2.92
514 620 2.295349 CTGCCAACAAACTGCTTCTCAT 59.705 45.455 0.00 0.00 0.00 2.90
515 621 1.677576 CTGCCAACAAACTGCTTCTCA 59.322 47.619 0.00 0.00 0.00 3.27
520 627 1.329171 TTGGCTGCCAACAAACTGCT 61.329 50.000 29.24 0.00 38.75 4.24
539 646 2.498056 CCGCAAGCCAGGGTTTTGT 61.498 57.895 0.00 0.00 0.00 2.83
588 699 3.432335 CCACCCCCATGAGGCCAT 61.432 66.667 5.01 0.00 0.00 4.40
592 703 4.802051 CACGCCACCCCCATGAGG 62.802 72.222 0.00 0.00 0.00 3.86
712 834 2.383527 CGAGCCAAGGTCGCAGTTC 61.384 63.158 3.05 0.00 45.89 3.01
745 867 1.215423 GATTGGGATGGGTTGGCTAGT 59.785 52.381 0.00 0.00 0.00 2.57
791 917 5.445142 CGAGTGAACCTCAAAAGAATCATCG 60.445 44.000 0.00 0.00 40.48 3.84
797 923 2.218603 GGCGAGTGAACCTCAAAAGAA 58.781 47.619 0.00 0.00 40.48 2.52
849 975 4.164796 TGCACTAGCCTAGGTACAGTAGTA 59.835 45.833 11.31 3.90 41.13 1.82
886 1014 3.898123 AGTTATCCCTGTCATAGCGTCAT 59.102 43.478 0.00 0.00 0.00 3.06
891 1019 5.215252 TGCTTAGTTATCCCTGTCATAGC 57.785 43.478 0.00 0.00 0.00 2.97
895 1023 3.263170 TGCTTGCTTAGTTATCCCTGTCA 59.737 43.478 0.00 0.00 0.00 3.58
898 1026 4.883585 TGATTGCTTGCTTAGTTATCCCTG 59.116 41.667 0.00 0.00 0.00 4.45
900 1028 6.211515 CAATGATTGCTTGCTTAGTTATCCC 58.788 40.000 0.00 0.00 0.00 3.85
901 1029 6.039717 TCCAATGATTGCTTGCTTAGTTATCC 59.960 38.462 0.00 0.00 0.00 2.59
902 1030 6.914757 GTCCAATGATTGCTTGCTTAGTTATC 59.085 38.462 0.00 0.00 0.00 1.75
903 1031 6.377996 TGTCCAATGATTGCTTGCTTAGTTAT 59.622 34.615 0.00 0.00 0.00 1.89
904 1032 5.709631 TGTCCAATGATTGCTTGCTTAGTTA 59.290 36.000 0.00 0.00 0.00 2.24
905 1033 4.523943 TGTCCAATGATTGCTTGCTTAGTT 59.476 37.500 0.00 0.00 0.00 2.24
906 1034 4.081406 TGTCCAATGATTGCTTGCTTAGT 58.919 39.130 0.00 0.00 0.00 2.24
907 1035 4.707030 TGTCCAATGATTGCTTGCTTAG 57.293 40.909 0.00 0.00 0.00 2.18
908 1036 4.142116 CCATGTCCAATGATTGCTTGCTTA 60.142 41.667 0.00 0.00 0.00 3.09
927 1055 2.932614 GGTCTCACACTTCGAATCCATG 59.067 50.000 0.00 0.00 0.00 3.66
956 1084 2.809601 GACAGGTTCGTCGCGCAT 60.810 61.111 8.75 0.00 0.00 4.73
1284 1412 2.061740 ACTTGTACTTCGGCGAAGAC 57.938 50.000 45.12 35.83 41.71 3.01
1287 1415 1.411394 CGAACTTGTACTTCGGCGAA 58.589 50.000 22.33 22.33 37.46 4.70
1384 1553 6.019961 GCACGATCACATTTTTCAGTTCAAAA 60.020 34.615 0.00 0.00 0.00 2.44
1391 1638 2.904319 CACGCACGATCACATTTTTCAG 59.096 45.455 0.00 0.00 0.00 3.02
1558 2104 2.040544 CCTTTTCCCATCACGCGCT 61.041 57.895 5.73 0.00 0.00 5.92
1667 2216 1.284491 TCCATTGCTCCATTGCCACTA 59.716 47.619 0.00 0.00 0.00 2.74
1681 2230 1.849039 ACTCCCCTTCCATCTCCATTG 59.151 52.381 0.00 0.00 0.00 2.82
1682 2231 1.849039 CACTCCCCTTCCATCTCCATT 59.151 52.381 0.00 0.00 0.00 3.16
1683 2232 1.010046 TCACTCCCCTTCCATCTCCAT 59.990 52.381 0.00 0.00 0.00 3.41
1684 2233 0.417437 TCACTCCCCTTCCATCTCCA 59.583 55.000 0.00 0.00 0.00 3.86
1685 2234 1.127343 CTCACTCCCCTTCCATCTCC 58.873 60.000 0.00 0.00 0.00 3.71
1686 2235 2.166907 TCTCACTCCCCTTCCATCTC 57.833 55.000 0.00 0.00 0.00 2.75
1687 2236 2.649742 TTCTCACTCCCCTTCCATCT 57.350 50.000 0.00 0.00 0.00 2.90
1688 2237 2.573915 ACTTTCTCACTCCCCTTCCATC 59.426 50.000 0.00 0.00 0.00 3.51
1689 2238 2.307098 CACTTTCTCACTCCCCTTCCAT 59.693 50.000 0.00 0.00 0.00 3.41
1691 2240 1.978580 TCACTTTCTCACTCCCCTTCC 59.021 52.381 0.00 0.00 0.00 3.46
1693 2242 1.349357 GCTCACTTTCTCACTCCCCTT 59.651 52.381 0.00 0.00 0.00 3.95
1694 2243 0.980423 GCTCACTTTCTCACTCCCCT 59.020 55.000 0.00 0.00 0.00 4.79
1698 2247 2.930455 GCCTCAGCTCACTTTCTCACTC 60.930 54.545 0.00 0.00 35.50 3.51
1699 2248 1.001860 GCCTCAGCTCACTTTCTCACT 59.998 52.381 0.00 0.00 35.50 3.41
1700 2249 1.437625 GCCTCAGCTCACTTTCTCAC 58.562 55.000 0.00 0.00 35.50 3.51
1701 2250 3.923354 GCCTCAGCTCACTTTCTCA 57.077 52.632 0.00 0.00 35.50 3.27
1759 2308 2.124570 GGCGTCATGCTCACCCAT 60.125 61.111 0.00 0.00 45.43 4.00
2015 2585 4.554036 GATCCACCGCCAGGCCTC 62.554 72.222 0.00 0.00 42.76 4.70
2017 2587 4.554036 GAGATCCACCGCCAGGCC 62.554 72.222 5.63 0.00 42.76 5.19
2199 2769 4.253257 CCTACGCGGAGGTCGAGC 62.253 72.222 30.13 6.48 42.41 5.03


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

AutoCloner maintained by Alex Coulton.