Multiple sequence alignment - TraesCS7A01G178200

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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 TraesCS7A01G178200 chr7A 100.000 2960 0 0 1 2960 131871073 131868114 0.000000e+00 5467.0
1 TraesCS7A01G178200 chr7A 88.618 123 13 1 2359 2481 13798313 13798434 6.610000e-32 148.0
2 TraesCS7A01G178200 chr7D 93.860 2280 86 17 706 2960 133321248 133318998 0.000000e+00 3386.0
3 TraesCS7A01G178200 chr7D 76.000 375 61 20 1559 1929 133665186 133664837 1.820000e-37 167.0
4 TraesCS7A01G178200 chr7B 94.547 1522 46 19 666 2184 94608785 94607298 0.000000e+00 2316.0
5 TraesCS7A01G178200 chr7B 81.287 668 97 15 6 669 94609497 94608854 1.570000e-142 516.0
6 TraesCS7A01G178200 chr6A 79.535 215 38 5 8 217 574229445 574229232 6.610000e-32 148.0
7 TraesCS7A01G178200 chr1B 88.983 118 13 0 2360 2477 616892864 616892747 2.380000e-31 147.0
8 TraesCS7A01G178200 chr1B 86.777 121 15 1 2361 2481 332136160 332136279 1.850000e-27 134.0
9 TraesCS7A01G178200 chr1B 84.553 123 15 3 8 128 431030472 431030592 5.180000e-23 119.0
10 TraesCS7A01G178200 chr1B 83.117 77 13 0 440 516 249629867 249629791 1.470000e-08 71.3
11 TraesCS7A01G178200 chr5D 87.097 124 15 1 2359 2482 120890708 120890830 3.980000e-29 139.0
12 TraesCS7A01G178200 chr1D 87.500 120 14 1 2359 2477 42284725 42284844 1.430000e-28 137.0
13 TraesCS7A01G178200 chr3A 87.288 118 15 0 2361 2478 712958937 712959054 5.150000e-28 135.0
14 TraesCS7A01G178200 chr2D 86.290 124 17 0 2356 2479 233327336 233327213 5.150000e-28 135.0
15 TraesCS7A01G178200 chr4B 85.156 128 18 1 2357 2484 357908333 357908207 2.390000e-26 130.0
16 TraesCS7A01G178200 chr5B 81.538 130 21 2 1 128 458579000 458578872 1.450000e-18 104.0
17 TraesCS7A01G178200 chr3B 88.608 79 9 0 438 516 317624006 317623928 2.430000e-16 97.1
18 TraesCS7A01G178200 chr2A 100.000 28 0 0 455 482 29384500 29384527 5.000000e-03 52.8


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 TraesCS7A01G178200 chr7A 131868114 131871073 2959 True 5467 5467 100.000 1 2960 1 chr7A.!!$R1 2959
1 TraesCS7A01G178200 chr7D 133318998 133321248 2250 True 3386 3386 93.860 706 2960 1 chr7D.!!$R1 2254
2 TraesCS7A01G178200 chr7B 94607298 94609497 2199 True 1416 2316 87.917 6 2184 2 chr7B.!!$R1 2178

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
620 639 0.24912 CCACTTCTGCACCGATGGTA 59.751 55.0 0.0 0.0 32.11 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2082 0.10212 GAGAGTGCGAGACCATCCAG 59.898 60.0 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
33 34 7.189087 ACCAATATAAAATGTCTGAAAGGGGT 58.811 34.615 0.00 0.00 0.00 4.95
35 36 8.850156 CCAATATAAAATGTCTGAAAGGGGTAG 58.150 37.037 0.00 0.00 0.00 3.18
47 48 8.437575 GTCTGAAAGGGGTAGATCCAATTATTA 58.562 37.037 0.00 0.00 38.11 0.98
53 54 5.123936 GGGTAGATCCAATTATTATCGGCC 58.876 45.833 0.00 0.00 38.11 6.13
60 61 7.616935 AGATCCAATTATTATCGGCCATCAAAT 59.383 33.333 2.24 0.00 0.00 2.32
67 70 6.845758 ATTATCGGCCATCAAATCATGAAT 57.154 33.333 2.24 0.00 42.54 2.57
72 75 4.262292 CGGCCATCAAATCATGAATCCAAT 60.262 41.667 2.24 0.00 42.54 3.16
74 77 5.221561 GGCCATCAAATCATGAATCCAATGA 60.222 40.000 0.00 0.00 42.54 2.57
87 90 8.997323 CATGAATCCAATGACCTAGATTACTTC 58.003 37.037 0.00 0.00 0.00 3.01
91 94 8.915057 ATCCAATGACCTAGATTACTTCAATG 57.085 34.615 0.00 0.00 0.00 2.82
92 95 7.282585 TCCAATGACCTAGATTACTTCAATGG 58.717 38.462 0.00 0.00 38.23 3.16
97 100 5.675538 ACCTAGATTACTTCAATGGTGAGC 58.324 41.667 0.00 0.00 34.49 4.26
98 101 5.189736 ACCTAGATTACTTCAATGGTGAGCA 59.810 40.000 0.00 0.00 34.49 4.26
99 102 5.525378 CCTAGATTACTTCAATGGTGAGCAC 59.475 44.000 0.00 0.00 34.49 4.40
103 106 2.775890 ACTTCAATGGTGAGCACTCAG 58.224 47.619 0.00 0.00 40.75 3.35
221 225 8.958119 TGCAATTAATTTCCTCTCTAATACGT 57.042 30.769 0.00 0.00 0.00 3.57
240 244 5.734855 ACGTATTACAACATGGATTCAGC 57.265 39.130 0.00 0.00 0.00 4.26
245 249 3.052455 ACAACATGGATTCAGCGTACA 57.948 42.857 0.00 0.00 0.00 2.90
255 259 4.034048 GGATTCAGCGTACACATTTACTGG 59.966 45.833 0.00 0.00 0.00 4.00
257 261 3.997762 TCAGCGTACACATTTACTGGTT 58.002 40.909 0.00 0.00 0.00 3.67
262 266 7.276218 TCAGCGTACACATTTACTGGTTAATAC 59.724 37.037 0.00 0.00 0.00 1.89
263 267 6.254157 AGCGTACACATTTACTGGTTAATACG 59.746 38.462 0.00 0.00 0.00 3.06
279 283 6.207221 GGTTAATACGAAAAGACCCAAAAGGA 59.793 38.462 0.00 0.00 39.89 3.36
297 301 1.829222 GGACGGATCCAGTTAACCTCA 59.171 52.381 13.41 0.00 45.47 3.86
307 311 5.826643 TCCAGTTAACCTCAGCCATAAAAT 58.173 37.500 0.88 0.00 0.00 1.82
322 326 7.980662 CAGCCATAAAATCATTACAATCCAACA 59.019 33.333 0.00 0.00 0.00 3.33
347 351 4.887655 TCTAGATTGCTCGAATGGTGAGTA 59.112 41.667 0.00 0.00 35.85 2.59
366 370 9.056005 GGTGAGTATTCAACATATTTAGCATGA 57.944 33.333 0.00 0.00 40.88 3.07
414 418 9.941664 CAACCTCTATGCTAATCACAAAATTAG 57.058 33.333 0.00 0.00 40.63 1.73
415 419 9.686683 AACCTCTATGCTAATCACAAAATTAGT 57.313 29.630 5.75 0.00 40.08 2.24
453 457 8.903570 TTGTGAGTAAATTAACGCATAATTGG 57.096 30.769 7.36 0.00 42.15 3.16
463 467 8.161425 AATTAACGCATAATTGGTATCCTACCT 58.839 33.333 5.03 0.00 41.57 3.08
493 497 3.886505 ACGTGCAATTAACCTTCTTCCAA 59.113 39.130 0.00 0.00 0.00 3.53
498 502 7.759433 CGTGCAATTAACCTTCTTCCAAATATT 59.241 33.333 0.00 0.00 0.00 1.28
505 509 6.190954 ACCTTCTTCCAAATATTAACGTGC 57.809 37.500 0.00 0.00 0.00 5.34
506 510 5.708230 ACCTTCTTCCAAATATTAACGTGCA 59.292 36.000 0.00 0.00 0.00 4.57
507 511 6.377146 ACCTTCTTCCAAATATTAACGTGCAT 59.623 34.615 0.00 0.00 0.00 3.96
508 512 7.093945 ACCTTCTTCCAAATATTAACGTGCATT 60.094 33.333 0.00 0.00 0.00 3.56
509 513 7.432252 CCTTCTTCCAAATATTAACGTGCATTC 59.568 37.037 0.00 0.00 0.00 2.67
510 514 6.791303 TCTTCCAAATATTAACGTGCATTCC 58.209 36.000 0.00 0.00 0.00 3.01
511 515 6.375736 TCTTCCAAATATTAACGTGCATTCCA 59.624 34.615 0.00 0.00 0.00 3.53
512 516 5.885881 TCCAAATATTAACGTGCATTCCAC 58.114 37.500 0.00 0.00 41.15 4.02
600 619 7.271223 GCATTGCATGTACTAGTAACAACAAAG 59.729 37.037 3.61 11.21 33.46 2.77
607 626 6.480981 TGTACTAGTAACAACAAAGCCACTTC 59.519 38.462 3.61 0.00 0.00 3.01
618 637 2.401766 GCCACTTCTGCACCGATGG 61.402 63.158 0.00 0.00 0.00 3.51
619 638 1.003355 CCACTTCTGCACCGATGGT 60.003 57.895 0.00 0.00 35.62 3.55
620 639 0.249120 CCACTTCTGCACCGATGGTA 59.751 55.000 0.00 0.00 32.11 3.25
621 640 1.645034 CACTTCTGCACCGATGGTAG 58.355 55.000 0.00 0.00 32.11 3.18
622 641 1.066858 CACTTCTGCACCGATGGTAGT 60.067 52.381 0.00 0.00 32.11 2.73
623 642 2.165641 CACTTCTGCACCGATGGTAGTA 59.834 50.000 0.00 0.00 32.11 1.82
634 653 6.150641 GCACCGATGGTAGTAGTATATCTCAA 59.849 42.308 0.00 0.00 32.11 3.02
644 663 7.455641 AGTAGTATATCTCAATCCACCTTCG 57.544 40.000 0.00 0.00 0.00 3.79
651 670 2.675348 CTCAATCCACCTTCGAAAGCTC 59.325 50.000 0.00 0.00 0.00 4.09
660 679 3.927142 ACCTTCGAAAGCTCGTAAATCAG 59.073 43.478 0.00 0.00 45.62 2.90
662 681 2.954316 TCGAAAGCTCGTAAATCAGCA 58.046 42.857 0.00 0.00 45.62 4.41
686 777 1.833860 AAATTGTTGCGGACACGTTG 58.166 45.000 0.00 0.00 43.45 4.10
688 779 1.098712 ATTGTTGCGGACACGTTGGT 61.099 50.000 0.00 0.00 43.45 3.67
716 807 1.026718 GGCACAGACATTCCCCGAAG 61.027 60.000 0.00 0.00 0.00 3.79
900 992 3.797184 GCAGACCCTGATAGATCGACAAC 60.797 52.174 0.00 0.00 32.44 3.32
911 1003 1.590238 GATCGACAACCTCATCAAGCG 59.410 52.381 0.00 0.00 0.00 4.68
930 1022 0.317603 GCACACAAGTCAGCAAGCAG 60.318 55.000 0.00 0.00 0.00 4.24
931 1023 0.317603 CACACAAGTCAGCAAGCAGC 60.318 55.000 0.00 0.00 46.19 5.25
948 1047 2.607892 GCCAAGCACACCACGAGTC 61.608 63.158 0.00 0.00 0.00 3.36
949 1048 1.227527 CCAAGCACACCACGAGTCA 60.228 57.895 0.00 0.00 0.00 3.41
950 1049 1.498865 CCAAGCACACCACGAGTCAC 61.499 60.000 0.00 0.00 0.00 3.67
951 1050 0.809636 CAAGCACACCACGAGTCACA 60.810 55.000 0.00 0.00 0.00 3.58
952 1051 0.530650 AAGCACACCACGAGTCACAG 60.531 55.000 0.00 0.00 0.00 3.66
953 1052 2.598632 GCACACCACGAGTCACAGC 61.599 63.158 0.00 0.00 0.00 4.40
954 1053 1.956170 CACACCACGAGTCACAGCC 60.956 63.158 0.00 0.00 0.00 4.85
955 1054 2.421314 CACCACGAGTCACAGCCA 59.579 61.111 0.00 0.00 0.00 4.75
956 1055 1.665916 CACCACGAGTCACAGCCAG 60.666 63.158 0.00 0.00 0.00 4.85
957 1056 2.134287 ACCACGAGTCACAGCCAGT 61.134 57.895 0.00 0.00 0.00 4.00
958 1057 1.373497 CCACGAGTCACAGCCAGTC 60.373 63.158 0.00 0.00 0.00 3.51
959 1058 1.363807 CACGAGTCACAGCCAGTCA 59.636 57.895 0.00 0.00 0.00 3.41
960 1059 0.665670 CACGAGTCACAGCCAGTCAG 60.666 60.000 0.00 0.00 0.00 3.51
961 1060 1.735920 CGAGTCACAGCCAGTCAGC 60.736 63.158 0.00 0.00 0.00 4.26
987 1086 1.272781 CAGAACCAGCTCGATCGTTC 58.727 55.000 15.94 10.19 35.84 3.95
996 1098 1.203928 CTCGATCGTTCATCCTGCAC 58.796 55.000 15.94 0.00 0.00 4.57
1057 1159 1.380515 TGCCTCTTCTCCCTCCTCG 60.381 63.158 0.00 0.00 0.00 4.63
1059 1161 1.388837 GCCTCTTCTCCCTCCTCGTC 61.389 65.000 0.00 0.00 0.00 4.20
1737 1839 2.046604 GTGACCAACCCCTACGGC 60.047 66.667 0.00 0.00 33.26 5.68
1764 1866 5.578615 GGTACTACCAGGGCAATGATGCA 62.579 52.174 0.00 0.00 45.92 3.96
1980 2082 3.365265 CCGTGGGAGCAGGCAAAC 61.365 66.667 0.00 0.00 0.00 2.93
1999 2101 0.102120 CTGGATGGTCTCGCACTCTC 59.898 60.000 0.00 0.00 0.00 3.20
2122 2224 1.202475 ACCCGTTGCAATGTGTTTTCC 60.202 47.619 17.19 0.00 0.00 3.13
2214 2317 4.383850 TCCATGCATGTTTATTTTCGGG 57.616 40.909 24.58 5.48 0.00 5.14
2217 2320 2.808919 TGCATGTTTATTTTCGGGGGA 58.191 42.857 0.00 0.00 0.00 4.81
2224 2327 2.710096 TATTTTCGGGGGAGCTTCTG 57.290 50.000 0.00 0.00 0.00 3.02
2241 2344 0.877071 CTGGACACACTGGATGTTGC 59.123 55.000 0.00 0.00 40.64 4.17
2332 2454 7.087639 AGGAAGAAGACGATCGATATGATTTC 58.912 38.462 24.34 14.63 37.47 2.17
2452 2574 6.393990 GTCTAGATACATTCATTCCTGCGAT 58.606 40.000 0.00 0.00 0.00 4.58
2455 2577 8.585018 TCTAGATACATTCATTCCTGCGATAAA 58.415 33.333 0.00 0.00 0.00 1.40
2463 2585 8.918658 CATTCATTCCTGCGATAAATAATTTGG 58.081 33.333 0.00 0.00 0.00 3.28
2464 2586 7.815840 TCATTCCTGCGATAAATAATTTGGA 57.184 32.000 0.00 0.00 0.00 3.53
2467 2589 6.055231 TCCTGCGATAAATAATTTGGAACG 57.945 37.500 0.00 0.00 0.00 3.95
2468 2590 5.818336 TCCTGCGATAAATAATTTGGAACGA 59.182 36.000 0.00 0.00 0.00 3.85
2517 2639 7.148340 CCTCTGTGTTGTCTATGATTTTCCTTC 60.148 40.741 0.00 0.00 0.00 3.46
2564 2686 2.366533 AGCATTGGATTCAGCTGACTG 58.633 47.619 18.03 8.36 45.95 3.51
2582 2704 5.348986 TGACTGATCCTTAGTTAATCGCAC 58.651 41.667 0.00 0.00 0.00 5.34
2587 2709 4.913335 TCCTTAGTTAATCGCACGATCT 57.087 40.909 5.94 2.25 33.08 2.75
2590 2712 6.103997 TCCTTAGTTAATCGCACGATCTTTT 58.896 36.000 5.94 0.00 33.08 2.27
2597 2719 2.412870 TCGCACGATCTTTTGTCATGT 58.587 42.857 0.00 0.00 0.00 3.21
2699 2822 6.392625 TTCAACATAATTTTGAACACGGGA 57.607 33.333 2.69 0.00 37.91 5.14
2700 2823 5.764131 TCAACATAATTTTGAACACGGGAC 58.236 37.500 2.69 0.00 29.89 4.46
2702 2825 3.189702 ACATAATTTTGAACACGGGACCG 59.810 43.478 9.56 9.56 46.03 4.79
2738 2861 7.762159 TCAGAACAATGTTTAAAGTTCCCAAAC 59.238 33.333 0.00 0.00 40.82 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.627123 CTTTCAGACATTTTATATTGGTAGGGA 57.373 33.333 0.00 0.00 0.00 4.20
4 5 8.850156 CCTTTCAGACATTTTATATTGGTAGGG 58.150 37.037 0.00 0.00 0.00 3.53
20 21 3.199442 TGGATCTACCCCTTTCAGACA 57.801 47.619 0.00 0.00 38.00 3.41
22 23 7.465900 AATAATTGGATCTACCCCTTTCAGA 57.534 36.000 0.00 0.00 38.00 3.27
25 26 7.553044 CCGATAATAATTGGATCTACCCCTTTC 59.447 40.741 0.00 0.00 38.82 2.62
28 29 5.104485 GCCGATAATAATTGGATCTACCCCT 60.104 44.000 0.00 0.00 38.82 4.79
33 34 7.194112 TGATGGCCGATAATAATTGGATCTA 57.806 36.000 0.00 0.00 38.82 1.98
35 36 6.757897 TTGATGGCCGATAATAATTGGATC 57.242 37.500 0.00 0.00 38.82 3.36
47 48 3.508793 GGATTCATGATTTGATGGCCGAT 59.491 43.478 0.00 0.00 33.34 4.18
53 54 7.050970 AGGTCATTGGATTCATGATTTGATG 57.949 36.000 0.00 0.00 33.34 3.07
60 61 8.267620 AGTAATCTAGGTCATTGGATTCATGA 57.732 34.615 0.00 0.00 31.89 3.07
67 70 7.092444 ACCATTGAAGTAATCTAGGTCATTGGA 60.092 37.037 15.89 0.00 40.04 3.53
72 75 6.630413 GCTCACCATTGAAGTAATCTAGGTCA 60.630 42.308 0.00 0.00 0.00 4.02
74 77 5.189736 TGCTCACCATTGAAGTAATCTAGGT 59.810 40.000 0.00 0.00 0.00 3.08
83 86 2.775890 CTGAGTGCTCACCATTGAAGT 58.224 47.619 0.00 0.00 35.46 3.01
87 90 1.132453 CATGCTGAGTGCTCACCATTG 59.868 52.381 7.14 1.87 43.37 2.82
91 94 1.242076 AAACATGCTGAGTGCTCACC 58.758 50.000 0.00 0.00 43.37 4.02
92 95 2.159599 GCTAAACATGCTGAGTGCTCAC 60.160 50.000 0.00 0.00 43.37 3.51
195 199 9.561069 ACGTATTAGAGAGGAAATTAATTGCAT 57.439 29.630 8.47 0.15 0.00 3.96
219 223 4.270084 ACGCTGAATCCATGTTGTAATACG 59.730 41.667 0.00 0.00 0.00 3.06
220 224 5.734855 ACGCTGAATCCATGTTGTAATAC 57.265 39.130 0.00 0.00 0.00 1.89
221 225 6.256975 GTGTACGCTGAATCCATGTTGTAATA 59.743 38.462 0.00 0.00 0.00 0.98
222 226 5.064707 GTGTACGCTGAATCCATGTTGTAAT 59.935 40.000 0.00 0.00 0.00 1.89
223 227 4.390603 GTGTACGCTGAATCCATGTTGTAA 59.609 41.667 0.00 0.00 0.00 2.41
224 228 3.930229 GTGTACGCTGAATCCATGTTGTA 59.070 43.478 0.00 0.00 0.00 2.41
225 229 2.742053 GTGTACGCTGAATCCATGTTGT 59.258 45.455 0.00 0.00 0.00 3.32
226 230 2.741517 TGTGTACGCTGAATCCATGTTG 59.258 45.455 8.10 0.00 0.00 3.33
237 241 5.849357 TTAACCAGTAAATGTGTACGCTG 57.151 39.130 8.10 0.00 0.00 5.18
238 242 6.254157 CGTATTAACCAGTAAATGTGTACGCT 59.746 38.462 8.10 0.00 0.00 5.07
240 244 7.739022 TCGTATTAACCAGTAAATGTGTACG 57.261 36.000 0.00 0.00 0.00 3.67
245 249 8.724229 GGTCTTTTCGTATTAACCAGTAAATGT 58.276 33.333 0.00 0.00 0.00 2.71
255 259 7.080099 GTCCTTTTGGGTCTTTTCGTATTAAC 58.920 38.462 0.00 0.00 40.87 2.01
257 261 5.409214 CGTCCTTTTGGGTCTTTTCGTATTA 59.591 40.000 0.00 0.00 40.87 0.98
262 266 1.265905 CCGTCCTTTTGGGTCTTTTCG 59.734 52.381 0.00 0.00 40.87 3.46
263 267 2.578786 TCCGTCCTTTTGGGTCTTTTC 58.421 47.619 0.00 0.00 40.87 2.29
279 283 1.207329 GCTGAGGTTAACTGGATCCGT 59.793 52.381 7.39 5.31 0.00 4.69
288 292 8.682710 TGTAATGATTTTATGGCTGAGGTTAAC 58.317 33.333 0.00 0.00 0.00 2.01
293 297 7.014518 TGGATTGTAATGATTTTATGGCTGAGG 59.985 37.037 0.00 0.00 0.00 3.86
295 299 7.894753 TGGATTGTAATGATTTTATGGCTGA 57.105 32.000 0.00 0.00 0.00 4.26
297 301 8.076910 TGTTGGATTGTAATGATTTTATGGCT 57.923 30.769 0.00 0.00 0.00 4.75
322 326 5.163364 ACTCACCATTCGAGCAATCTAGATT 60.163 40.000 12.37 12.37 33.58 2.40
327 331 4.679373 ATACTCACCATTCGAGCAATCT 57.321 40.909 0.00 0.00 33.58 2.40
332 336 3.932710 TGTTGAATACTCACCATTCGAGC 59.067 43.478 0.00 0.00 35.55 5.03
336 340 9.884465 GCTAAATATGTTGAATACTCACCATTC 57.116 33.333 0.00 0.00 36.26 2.67
338 342 8.978874 TGCTAAATATGTTGAATACTCACCAT 57.021 30.769 0.00 0.00 38.21 3.55
385 389 9.851686 ATTTTGTGATTAGCATAGAGGTTGATA 57.148 29.630 0.00 0.00 0.00 2.15
432 436 9.821662 GGATACCAATTATGCGTTAATTTACTC 57.178 33.333 2.60 0.00 38.23 2.59
453 457 9.649167 ATTGCACGTTTATATTAGGTAGGATAC 57.351 33.333 0.00 0.00 42.04 2.24
469 473 4.339814 TGGAAGAAGGTTAATTGCACGTTT 59.660 37.500 0.00 0.00 0.00 3.60
480 484 7.390996 TGCACGTTAATATTTGGAAGAAGGTTA 59.609 33.333 0.00 0.00 0.00 2.85
484 488 7.432252 GGAATGCACGTTAATATTTGGAAGAAG 59.568 37.037 0.00 0.00 0.00 2.85
502 506 2.139917 TGAACACTACGTGGAATGCAC 58.860 47.619 5.70 0.00 37.94 4.57
503 507 2.535012 TGAACACTACGTGGAATGCA 57.465 45.000 5.70 0.00 37.94 3.96
504 508 3.496884 TCTTTGAACACTACGTGGAATGC 59.503 43.478 5.70 0.00 37.94 3.56
505 509 5.666969 TTCTTTGAACACTACGTGGAATG 57.333 39.130 5.70 0.00 37.94 2.67
506 510 6.687081 TTTTCTTTGAACACTACGTGGAAT 57.313 33.333 5.70 0.00 37.94 3.01
507 511 6.497785 TTTTTCTTTGAACACTACGTGGAA 57.502 33.333 5.70 0.00 37.94 3.53
587 606 4.274950 GCAGAAGTGGCTTTGTTGTTACTA 59.725 41.667 0.00 0.00 0.00 1.82
600 619 2.401766 CCATCGGTGCAGAAGTGGC 61.402 63.158 0.00 0.00 0.00 5.01
607 626 5.648526 AGATATACTACTACCATCGGTGCAG 59.351 44.000 0.00 0.00 36.19 4.41
618 637 8.452534 CGAAGGTGGATTGAGATATACTACTAC 58.547 40.741 0.00 0.00 0.00 2.73
619 638 8.380867 TCGAAGGTGGATTGAGATATACTACTA 58.619 37.037 0.00 0.00 0.00 1.82
620 639 7.232188 TCGAAGGTGGATTGAGATATACTACT 58.768 38.462 0.00 0.00 0.00 2.57
621 640 7.450124 TCGAAGGTGGATTGAGATATACTAC 57.550 40.000 0.00 0.00 0.00 2.73
622 641 8.473358 TTTCGAAGGTGGATTGAGATATACTA 57.527 34.615 0.00 0.00 0.00 1.82
623 642 6.978674 TTCGAAGGTGGATTGAGATATACT 57.021 37.500 0.00 0.00 0.00 2.12
634 653 0.608640 ACGAGCTTTCGAAGGTGGAT 59.391 50.000 9.20 0.00 39.77 3.41
644 663 5.283060 TCTTTGCTGATTTACGAGCTTTC 57.717 39.130 0.00 0.00 36.11 2.62
651 670 6.787043 GCAACAATTTTCTTTGCTGATTTACG 59.213 34.615 0.00 0.00 41.98 3.18
660 679 2.863137 TGTCCGCAACAATTTTCTTTGC 59.137 40.909 0.00 0.00 41.85 3.68
662 681 3.112580 CGTGTCCGCAACAATTTTCTTT 58.887 40.909 0.00 0.00 40.31 2.52
688 779 1.064003 ATGTCTGTGCCACTTGGGTA 58.936 50.000 0.00 0.00 39.65 3.69
716 807 2.289820 GGTTCTGGGTTTGAGTTCGTTC 59.710 50.000 0.00 0.00 0.00 3.95
873 965 2.445845 TATCAGGGTCTGCCGGGG 60.446 66.667 2.18 0.00 34.97 5.73
877 969 1.271102 GTCGATCTATCAGGGTCTGCC 59.729 57.143 0.00 0.00 0.00 4.85
900 992 0.167470 CTTGTGTGCGCTTGATGAGG 59.833 55.000 9.73 0.00 0.00 3.86
911 1003 0.317603 CTGCTTGCTGACTTGTGTGC 60.318 55.000 0.00 0.00 0.00 4.57
930 1022 2.591715 ACTCGTGGTGTGCTTGGC 60.592 61.111 0.00 0.00 0.00 4.52
931 1023 1.227527 TGACTCGTGGTGTGCTTGG 60.228 57.895 0.00 0.00 0.00 3.61
932 1024 0.809636 TGTGACTCGTGGTGTGCTTG 60.810 55.000 0.00 0.00 0.00 4.01
933 1025 0.530650 CTGTGACTCGTGGTGTGCTT 60.531 55.000 0.00 0.00 0.00 3.91
934 1026 1.068083 CTGTGACTCGTGGTGTGCT 59.932 57.895 0.00 0.00 0.00 4.40
935 1027 2.598632 GCTGTGACTCGTGGTGTGC 61.599 63.158 0.00 0.00 0.00 4.57
936 1028 1.956170 GGCTGTGACTCGTGGTGTG 60.956 63.158 0.00 0.00 0.00 3.82
937 1029 2.369257 CTGGCTGTGACTCGTGGTGT 62.369 60.000 0.00 0.00 0.00 4.16
948 1047 1.964891 CTGTGGCTGACTGGCTGTG 60.965 63.158 0.29 0.00 42.34 3.66
949 1048 2.429058 CTGTGGCTGACTGGCTGT 59.571 61.111 7.41 0.00 42.34 4.40
950 1049 3.054503 GCTGTGGCTGACTGGCTG 61.055 66.667 7.41 0.00 42.34 4.85
951 1050 4.341783 GGCTGTGGCTGACTGGCT 62.342 66.667 7.41 0.00 43.40 4.75
952 1051 4.648626 TGGCTGTGGCTGACTGGC 62.649 66.667 11.03 11.03 45.95 4.85
953 1052 2.359602 CTGGCTGTGGCTGACTGG 60.360 66.667 0.00 0.00 38.73 4.00
954 1053 1.071987 TTCTGGCTGTGGCTGACTG 59.928 57.895 0.68 0.00 36.02 3.51
955 1054 1.072159 GTTCTGGCTGTGGCTGACT 59.928 57.895 0.68 0.00 36.02 3.41
956 1055 1.968540 GGTTCTGGCTGTGGCTGAC 60.969 63.158 0.68 0.00 36.02 3.51
957 1056 2.401699 CTGGTTCTGGCTGTGGCTGA 62.402 60.000 0.00 0.00 38.73 4.26
958 1057 1.970114 CTGGTTCTGGCTGTGGCTG 60.970 63.158 0.00 0.00 38.73 4.85
959 1058 2.433446 CTGGTTCTGGCTGTGGCT 59.567 61.111 0.00 0.00 38.73 4.75
960 1059 3.368571 GCTGGTTCTGGCTGTGGC 61.369 66.667 0.00 0.00 37.82 5.01
961 1060 1.673665 GAGCTGGTTCTGGCTGTGG 60.674 63.158 0.00 0.00 39.05 4.17
987 1086 3.214123 CCCATGGCGTGCAGGATG 61.214 66.667 11.29 5.87 40.87 3.51
1155 1257 2.571216 CGTGAGGTTCCCCGTGAGT 61.571 63.158 0.00 0.00 35.12 3.41
1737 1839 2.779033 GCCCTGGTAGTACCCGTCG 61.779 68.421 16.91 4.09 37.50 5.12
1932 2034 3.406361 GTCCTGCACTGCGACGTG 61.406 66.667 0.00 0.00 37.94 4.49
1953 2055 3.352338 CTCCCACGGCGTCTACACC 62.352 68.421 10.85 0.00 0.00 4.16
1980 2082 0.102120 GAGAGTGCGAGACCATCCAG 59.898 60.000 0.00 0.00 0.00 3.86
1999 2101 1.664017 CTCCGGATCTCATGCAGCG 60.664 63.158 3.57 0.00 0.00 5.18
2122 2224 2.015736 ATACAACCTCTGCTGCTTCG 57.984 50.000 0.00 0.00 0.00 3.79
2214 2317 0.321122 CAGTGTGTCCAGAAGCTCCC 60.321 60.000 0.00 0.00 0.00 4.30
2217 2320 1.002888 CATCCAGTGTGTCCAGAAGCT 59.997 52.381 0.00 0.00 0.00 3.74
2224 2327 0.877071 CAGCAACATCCAGTGTGTCC 59.123 55.000 0.00 0.00 41.14 4.02
2241 2344 5.105797 TGGATTTTTACAATAGCACCAGCAG 60.106 40.000 0.00 0.00 45.49 4.24
2353 2475 2.729882 CAGACGAAGGGAGTACAAAACG 59.270 50.000 0.00 0.00 0.00 3.60
2427 2549 4.618912 CGCAGGAATGAATGTATCTAGACG 59.381 45.833 0.00 0.00 0.00 4.18
2437 2559 8.918658 CCAAATTATTTATCGCAGGAATGAATG 58.081 33.333 0.00 0.00 0.00 2.67
2445 2567 6.055231 TCGTTCCAAATTATTTATCGCAGG 57.945 37.500 0.00 0.00 0.00 4.85
2452 2574 9.333724 GATACTCCCTTCGTTCCAAATTATTTA 57.666 33.333 0.00 0.00 0.00 1.40
2455 2577 6.895782 TGATACTCCCTTCGTTCCAAATTAT 58.104 36.000 0.00 0.00 0.00 1.28
2463 2585 4.081586 AGGACTTTGATACTCCCTTCGTTC 60.082 45.833 0.00 0.00 0.00 3.95
2464 2586 3.838903 AGGACTTTGATACTCCCTTCGTT 59.161 43.478 0.00 0.00 0.00 3.85
2467 2589 4.409718 GGAGGACTTTGATACTCCCTTC 57.590 50.000 0.00 0.00 42.87 3.46
2544 2666 2.366533 CAGTCAGCTGAATCCAATGCT 58.633 47.619 20.19 5.63 45.28 3.79
2564 2686 5.462405 AGATCGTGCGATTAACTAAGGATC 58.538 41.667 8.54 0.00 34.60 3.36
2582 2704 9.986833 TGTTCATAATTACATGACAAAAGATCG 57.013 29.630 0.00 0.00 34.69 3.69
2699 2822 8.710835 AACATTGTTCTGAATTTTAAAACGGT 57.289 26.923 1.97 0.00 0.00 4.83
2917 3040 3.768215 CCTCTAGAAGTTTCCTAACCCGT 59.232 47.826 0.00 0.00 34.71 5.28


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

AutoCloner maintained by Alex Coulton.