Multiple sequence alignment - TraesCS7A01G496300

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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 TraesCS7A01G496300 chr7A 100.000 2249 0 0 1 2249 686157648 686155400 0.000000e+00 4154
1 TraesCS7A01G496300 chr7D 92.024 1354 64 20 912 2249 593370395 593369070 0.000000e+00 1862
2 TraesCS7A01G496300 chr7D 91.129 372 17 10 54 410 593371219 593370849 7.220000e-135 490
3 TraesCS7A01G496300 chr7D 89.558 249 14 8 627 869 593370712 593370470 2.810000e-79 305
4 TraesCS7A01G496300 chr7B 84.455 1486 106 53 1 1429 667478605 667480022 0.000000e+00 1349
5 TraesCS7A01G496300 chr7B 93.174 879 33 14 1388 2249 667480060 667480928 0.000000e+00 1266
6 TraesCS7A01G496300 chr6D 90.251 359 35 0 968 1326 111062154 111062512 9.400000e-129 470
7 TraesCS7A01G496300 chr6D 81.853 518 70 17 1740 2248 111063032 111063534 4.470000e-112 414
8 TraesCS7A01G496300 chr6D 94.203 207 12 0 184 390 111061848 111062054 1.300000e-82 316
9 TraesCS7A01G496300 chr6B 89.972 359 36 0 968 1326 200008688 200009046 4.370000e-127 464
10 TraesCS7A01G496300 chr6B 93.720 207 13 0 184 390 200008393 200008599 6.030000e-81 311
11 TraesCS7A01G496300 chr6B 89.573 211 19 3 186 394 528285888 528286097 4.760000e-67 265
12 TraesCS7A01G496300 chr6A 89.972 359 36 0 968 1326 135561310 135561668 4.370000e-127 464
13 TraesCS7A01G496300 chr6A 82.308 520 64 22 1740 2248 135562238 135562740 2.060000e-115 425
14 TraesCS7A01G496300 chr6A 94.175 206 12 0 185 390 135561010 135561215 4.660000e-82 315
15 TraesCS7A01G496300 chr6A 88.995 209 20 3 185 391 492283913 492284120 2.870000e-64 255


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 TraesCS7A01G496300 chr7A 686155400 686157648 2248 True 4154.000000 4154 100.000000 1 2249 1 chr7A.!!$R1 2248
1 TraesCS7A01G496300 chr7D 593369070 593371219 2149 True 885.666667 1862 90.903667 54 2249 3 chr7D.!!$R1 2195
2 TraesCS7A01G496300 chr7B 667478605 667480928 2323 False 1307.500000 1349 88.814500 1 2249 2 chr7B.!!$F1 2248
3 TraesCS7A01G496300 chr6D 111061848 111063534 1686 False 400.000000 470 88.769000 184 2248 3 chr6D.!!$F1 2064
4 TraesCS7A01G496300 chr6B 200008393 200009046 653 False 387.500000 464 91.846000 184 1326 2 chr6B.!!$F2 1142
5 TraesCS7A01G496300 chr6A 135561010 135562740 1730 False 401.333333 464 88.818333 185 2248 3 chr6A.!!$F2 2063

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
859 916 0.234884 GTTCACTCGCCTTCCAAACG 59.765 55.0 0.0 0.0 0.0 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2716 2.183046 GTGTCAGAGCTCTCCCGC 59.817 66.667 14.96 10.06 0.0 6.13 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
24 25 1.478510 ACCACTCGCTCACCTAATCAG 59.521 52.381 0.00 0.00 0.00 2.90
28 29 2.621055 ACTCGCTCACCTAATCAGCTAG 59.379 50.000 0.00 0.00 33.33 3.42
75 76 2.860293 GTGCCGTCCACGTCATTG 59.140 61.111 0.00 0.00 37.74 2.82
100 101 1.373497 CTGAGCGGTGACCAGACAC 60.373 63.158 1.11 0.00 39.70 3.67
112 116 3.299977 AGACACGGCGGCACTGTA 61.300 61.111 13.24 0.00 35.54 2.74
114 118 4.675029 ACACGGCGGCACTGTACC 62.675 66.667 13.24 0.00 35.54 3.34
140 144 4.720649 TTGGTTGGACATTTTGTTCGAA 57.279 36.364 0.00 0.00 0.00 3.71
157 161 7.621832 TGTTCGAAAAATGAATAAGCTTGTG 57.378 32.000 9.86 0.00 0.00 3.33
159 163 7.378461 TGTTCGAAAAATGAATAAGCTTGTGTC 59.622 33.333 9.86 4.09 0.00 3.67
161 165 7.077605 TCGAAAAATGAATAAGCTTGTGTCTG 58.922 34.615 9.86 0.00 0.00 3.51
163 167 7.591057 CGAAAAATGAATAAGCTTGTGTCTGAA 59.409 33.333 9.86 0.00 0.00 3.02
395 405 4.752879 CCCGTACCCCTGCACACG 62.753 72.222 0.00 0.00 0.00 4.49
411 426 1.675483 ACACGCATTGCAAAACAGAGA 59.325 42.857 1.71 0.00 0.00 3.10
420 435 5.874895 TTGCAAAACAGAGAGATCATCAG 57.125 39.130 0.00 0.00 0.00 2.90
422 437 3.065095 GCAAAACAGAGAGATCATCAGCC 59.935 47.826 0.00 0.00 0.00 4.85
423 438 3.557228 AAACAGAGAGATCATCAGCCC 57.443 47.619 0.00 0.00 0.00 5.19
425 440 0.686224 CAGAGAGATCATCAGCCCCC 59.314 60.000 0.00 0.00 0.00 5.40
445 465 1.069090 GGTCACCACGTTCTGCTGA 59.931 57.895 0.00 0.00 0.00 4.26
447 467 1.299850 TCACCACGTTCTGCTGACG 60.300 57.895 11.78 11.78 0.00 4.35
459 479 1.284297 TGCTGACGATCAACACGCTG 61.284 55.000 0.00 0.00 0.00 5.18
460 480 1.284982 GCTGACGATCAACACGCTGT 61.285 55.000 0.00 0.00 0.00 4.40
468 488 4.212425 ACGATCAACACGCTGTAATTTCAA 59.788 37.500 0.00 0.00 0.00 2.69
469 489 4.549599 CGATCAACACGCTGTAATTTCAAC 59.450 41.667 0.00 0.00 0.00 3.18
472 492 1.533731 ACACGCTGTAATTTCAACCCG 59.466 47.619 0.00 0.00 0.00 5.28
475 495 2.073816 CGCTGTAATTTCAACCCGAGT 58.926 47.619 0.00 0.00 0.00 4.18
476 496 2.159707 CGCTGTAATTTCAACCCGAGTG 60.160 50.000 0.00 0.00 0.00 3.51
479 499 4.873827 GCTGTAATTTCAACCCGAGTGATA 59.126 41.667 0.00 0.00 0.00 2.15
481 501 6.704493 GCTGTAATTTCAACCCGAGTGATATA 59.296 38.462 0.00 0.00 0.00 0.86
482 502 7.387948 GCTGTAATTTCAACCCGAGTGATATAT 59.612 37.037 0.00 0.00 0.00 0.86
483 503 8.601845 TGTAATTTCAACCCGAGTGATATATG 57.398 34.615 0.00 0.00 0.00 1.78
484 504 8.208224 TGTAATTTCAACCCGAGTGATATATGT 58.792 33.333 0.00 0.00 0.00 2.29
486 506 7.730364 ATTTCAACCCGAGTGATATATGTTC 57.270 36.000 0.00 0.00 0.00 3.18
487 507 5.862678 TCAACCCGAGTGATATATGTTCA 57.137 39.130 0.00 0.00 0.00 3.18
488 508 5.842907 TCAACCCGAGTGATATATGTTCAG 58.157 41.667 0.00 0.00 0.00 3.02
489 509 5.362717 TCAACCCGAGTGATATATGTTCAGT 59.637 40.000 0.00 0.00 0.00 3.41
516 540 8.846943 TTAAGTAAAGAAGATTCAGACATGCA 57.153 30.769 0.00 0.00 0.00 3.96
529 554 2.950309 AGACATGCAAGATCAATCCTGC 59.050 45.455 6.63 6.63 42.96 4.85
545 570 1.069924 CTGCTGAGAGCGACTTGTCG 61.070 60.000 17.53 17.53 46.26 4.35
549 574 1.512310 GAGAGCGACTTGTCGACCG 60.512 63.158 24.65 10.34 34.64 4.79
550 575 2.504244 GAGCGACTTGTCGACCGG 60.504 66.667 24.65 0.00 34.64 5.28
554 579 1.615107 GCGACTTGTCGACCGGAAAG 61.615 60.000 24.65 12.16 34.64 2.62
555 580 0.318445 CGACTTGTCGACCGGAAAGT 60.318 55.000 16.32 16.32 35.62 2.66
556 581 1.416373 GACTTGTCGACCGGAAAGTC 58.584 55.000 22.86 22.86 41.08 3.01
557 582 1.000496 GACTTGTCGACCGGAAAGTCT 60.000 52.381 26.85 7.43 43.28 3.24
558 583 1.269621 ACTTGTCGACCGGAAAGTCTG 60.270 52.381 9.46 0.00 34.46 3.51
559 584 1.000607 CTTGTCGACCGGAAAGTCTGA 60.001 52.381 9.46 0.00 34.46 3.27
560 585 0.313043 TGTCGACCGGAAAGTCTGAC 59.687 55.000 9.46 8.01 39.04 3.51
566 591 0.949105 CCGGAAAGTCTGACGGTTGG 60.949 60.000 0.00 0.00 41.34 3.77
567 592 1.566018 CGGAAAGTCTGACGGTTGGC 61.566 60.000 1.52 0.00 0.00 4.52
569 594 1.566018 GAAAGTCTGACGGTTGGCGG 61.566 60.000 1.52 0.00 0.00 6.13
570 595 2.319890 AAAGTCTGACGGTTGGCGGT 62.320 55.000 1.52 0.00 0.00 5.68
571 596 2.280592 GTCTGACGGTTGGCGGTT 60.281 61.111 0.00 0.00 0.00 4.44
572 597 2.280524 TCTGACGGTTGGCGGTTG 60.281 61.111 0.00 0.00 0.00 3.77
573 598 3.353836 CTGACGGTTGGCGGTTGG 61.354 66.667 0.00 0.00 0.00 3.77
583 608 3.772619 GGCGGTTGGCACTATAGAA 57.227 52.632 6.78 0.00 46.16 2.10
584 609 2.032680 GGCGGTTGGCACTATAGAAA 57.967 50.000 6.78 0.00 46.16 2.52
585 610 1.940613 GGCGGTTGGCACTATAGAAAG 59.059 52.381 6.78 0.00 46.16 2.62
591 618 4.094442 GGTTGGCACTATAGAAAGGAAACG 59.906 45.833 6.78 0.00 0.00 3.60
601 628 2.087462 AAAGGAAACGCTGGCTTGCC 62.087 55.000 4.43 4.43 0.00 4.52
656 700 2.171940 GTGCGCTCGCTTCAGTTG 59.828 61.111 9.73 0.00 42.51 3.16
660 704 1.448540 CGCTCGCTTCAGTTGGGAT 60.449 57.895 0.00 0.00 0.00 3.85
661 705 1.699656 CGCTCGCTTCAGTTGGGATG 61.700 60.000 0.00 0.00 0.00 3.51
662 706 0.391661 GCTCGCTTCAGTTGGGATGA 60.392 55.000 0.00 0.00 0.00 2.92
663 707 1.945819 GCTCGCTTCAGTTGGGATGAA 60.946 52.381 0.00 0.00 35.45 2.57
836 893 5.413499 CCCAACAACCATTGATGATCTTTC 58.587 41.667 0.83 0.00 35.70 2.62
858 915 0.591659 GGTTCACTCGCCTTCCAAAC 59.408 55.000 0.00 0.00 0.00 2.93
859 916 0.234884 GTTCACTCGCCTTCCAAACG 59.765 55.000 0.00 0.00 0.00 3.60
869 927 1.737793 CCTTCCAAACGCTCCATACAC 59.262 52.381 0.00 0.00 0.00 2.90
871 929 2.380084 TCCAAACGCTCCATACACTC 57.620 50.000 0.00 0.00 0.00 3.51
873 931 1.732259 CCAAACGCTCCATACACTCAC 59.268 52.381 0.00 0.00 0.00 3.51
874 932 1.732259 CAAACGCTCCATACACTCACC 59.268 52.381 0.00 0.00 0.00 4.02
876 960 2.139323 ACGCTCCATACACTCACCTA 57.861 50.000 0.00 0.00 0.00 3.08
878 964 2.025155 CGCTCCATACACTCACCTACT 58.975 52.381 0.00 0.00 0.00 2.57
881 967 3.952323 GCTCCATACACTCACCTACTGTA 59.048 47.826 0.00 0.00 0.00 2.74
886 972 3.156288 ACACTCACCTACTGTAGCTGA 57.844 47.619 9.35 10.46 0.00 4.26
892 978 0.811915 CCTACTGTAGCTGACGTGCT 59.188 55.000 9.35 5.65 46.11 4.40
895 981 0.946221 ACTGTAGCTGACGTGCTTGC 60.946 55.000 5.64 1.20 43.74 4.01
901 987 1.227999 GCTGACGTGCTTGCCACTAA 61.228 55.000 0.00 0.00 42.42 2.24
904 990 1.001974 TGACGTGCTTGCCACTAAGAT 59.998 47.619 0.00 0.00 42.42 2.40
906 992 3.259064 GACGTGCTTGCCACTAAGATAA 58.741 45.455 0.00 0.00 42.42 1.75
907 993 3.871594 GACGTGCTTGCCACTAAGATAAT 59.128 43.478 0.00 0.00 42.42 1.28
908 994 3.871594 ACGTGCTTGCCACTAAGATAATC 59.128 43.478 0.00 0.00 42.42 1.75
909 995 3.060272 CGTGCTTGCCACTAAGATAATCG 60.060 47.826 0.00 0.00 42.42 3.34
910 996 2.872245 TGCTTGCCACTAAGATAATCGC 59.128 45.455 0.00 0.00 0.00 4.58
942 1034 4.756642 TCATTGGATATGGATTCGAAGTGC 59.243 41.667 3.35 0.00 0.00 4.40
1284 1376 4.889856 ACGCACAGCAGCACGTCA 62.890 61.111 0.00 0.00 32.37 4.35
1286 1378 2.949106 GCACAGCAGCACGTCATT 59.051 55.556 0.00 0.00 0.00 2.57
1289 1381 2.029288 ACAGCAGCACGTCATTCGG 61.029 57.895 0.00 0.00 44.69 4.30
1338 1442 2.896854 ACCTGCACGCACACACAG 60.897 61.111 0.00 0.00 0.00 3.66
1339 1443 2.896854 CCTGCACGCACACACAGT 60.897 61.111 0.00 0.00 0.00 3.55
1340 1444 2.628106 CTGCACGCACACACAGTC 59.372 61.111 0.00 0.00 0.00 3.51
1341 1445 2.125350 TGCACGCACACACAGTCA 60.125 55.556 0.00 0.00 0.00 3.41
1342 1446 1.704387 CTGCACGCACACACAGTCAA 61.704 55.000 0.00 0.00 0.00 3.18
1343 1447 1.301677 TGCACGCACACACAGTCAAA 61.302 50.000 0.00 0.00 0.00 2.69
1344 1448 0.179176 GCACGCACACACAGTCAAAA 60.179 50.000 0.00 0.00 0.00 2.44
1345 1449 1.730772 GCACGCACACACAGTCAAAAA 60.731 47.619 0.00 0.00 0.00 1.94
1393 1509 7.754027 TGTTCAGCAAATTTGAAACATTTTTGG 59.246 29.630 22.31 0.00 36.41 3.28
1394 1510 6.793349 TCAGCAAATTTGAAACATTTTTGGG 58.207 32.000 22.31 0.00 0.00 4.12
1413 1605 1.401018 GGTCGGCGAAGTTTGAATTGG 60.401 52.381 12.92 0.00 0.00 3.16
1414 1606 0.878416 TCGGCGAAGTTTGAATTGGG 59.122 50.000 7.35 0.00 0.00 4.12
1489 1710 4.789075 CACGTCGGCCCGTCGAAT 62.789 66.667 28.12 4.88 40.28 3.34
1490 1711 4.487412 ACGTCGGCCCGTCGAATC 62.487 66.667 28.12 0.00 40.28 2.52
1601 2081 3.051392 GCGCGTGATGGGGAAAAGG 62.051 63.158 8.43 0.00 0.00 3.11
1605 2085 0.802494 CGTGATGGGGAAAAGGAACG 59.198 55.000 0.00 0.00 0.00 3.95
1611 2091 1.673337 GGGAAAAGGAACGTCCCGG 60.673 63.158 0.00 0.00 41.70 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.452474 CACTGTTCCATGACTAGCTAGC 58.548 50.000 20.91 6.62 0.00 3.42
28 29 3.118629 TGATCCACTGTTCCATGACTAGC 60.119 47.826 0.00 0.00 0.00 3.42
61 62 2.358125 TGGCAATGACGTGGACGG 60.358 61.111 0.00 0.00 44.95 4.79
62 63 1.626654 GAGTGGCAATGACGTGGACG 61.627 60.000 0.00 0.00 46.33 4.79
63 64 1.298859 GGAGTGGCAATGACGTGGAC 61.299 60.000 0.00 0.00 0.00 4.02
64 65 1.003839 GGAGTGGCAATGACGTGGA 60.004 57.895 0.00 0.00 0.00 4.02
65 66 1.003355 AGGAGTGGCAATGACGTGG 60.003 57.895 0.00 0.00 0.00 4.94
66 67 0.320683 TCAGGAGTGGCAATGACGTG 60.321 55.000 0.00 0.00 0.00 4.49
67 68 0.036952 CTCAGGAGTGGCAATGACGT 60.037 55.000 0.00 0.00 0.00 4.34
68 69 1.364626 GCTCAGGAGTGGCAATGACG 61.365 60.000 0.00 0.00 0.00 4.35
69 70 1.364626 CGCTCAGGAGTGGCAATGAC 61.365 60.000 0.00 0.00 35.41 3.06
70 71 1.078918 CGCTCAGGAGTGGCAATGA 60.079 57.895 0.00 0.00 35.41 2.57
71 72 3.494378 CGCTCAGGAGTGGCAATG 58.506 61.111 0.00 0.00 35.41 2.82
112 116 5.504853 ACAAAATGTCCAACCAAAAATGGT 58.495 33.333 0.00 0.00 45.55 3.55
114 118 6.036517 TCGAACAAAATGTCCAACCAAAAATG 59.963 34.615 0.00 0.00 0.00 2.32
140 144 8.362639 ACATTCAGACACAAGCTTATTCATTTT 58.637 29.630 0.00 0.00 0.00 1.82
151 155 0.727122 GCGCACATTCAGACACAAGC 60.727 55.000 0.30 0.00 0.00 4.01
153 157 1.569003 CGCGCACATTCAGACACAA 59.431 52.632 8.75 0.00 0.00 3.33
178 188 5.043903 CCAGATCATGAAAGGTACTGTACG 58.956 45.833 11.52 0.00 40.86 3.67
181 191 5.248640 CAACCAGATCATGAAAGGTACTGT 58.751 41.667 14.98 0.67 40.86 3.55
182 192 4.095483 GCAACCAGATCATGAAAGGTACTG 59.905 45.833 14.98 12.20 40.86 2.74
395 405 4.430137 TGATCTCTCTGTTTTGCAATGC 57.570 40.909 0.00 0.00 0.00 3.56
422 437 4.692475 GAACGTGGTGACCGGGGG 62.692 72.222 6.32 0.00 0.00 5.40
423 438 3.622826 AGAACGTGGTGACCGGGG 61.623 66.667 6.32 0.00 0.00 5.73
425 440 3.041940 GCAGAACGTGGTGACCGG 61.042 66.667 0.00 0.00 0.00 5.28
426 441 2.029073 AGCAGAACGTGGTGACCG 59.971 61.111 0.00 0.00 34.82 4.79
445 465 3.743911 TGAAATTACAGCGTGTTGATCGT 59.256 39.130 0.00 0.00 0.00 3.73
447 467 4.851558 GGTTGAAATTACAGCGTGTTGATC 59.148 41.667 0.00 0.00 0.00 2.92
459 479 8.603242 ACATATATCACTCGGGTTGAAATTAC 57.397 34.615 0.00 0.00 0.00 1.89
460 480 9.268268 GAACATATATCACTCGGGTTGAAATTA 57.732 33.333 0.00 0.00 0.00 1.40
468 488 5.871396 AACTGAACATATATCACTCGGGT 57.129 39.130 0.00 0.00 0.00 5.28
469 489 8.657074 TTAAAACTGAACATATATCACTCGGG 57.343 34.615 0.00 0.00 0.00 5.14
500 524 6.432607 TTGATCTTGCATGTCTGAATCTTC 57.567 37.500 0.00 0.00 0.00 2.87
516 540 2.483363 CGCTCTCAGCAGGATTGATCTT 60.483 50.000 0.00 0.00 42.58 2.40
545 570 4.573162 CCGTCAGACTTTCCGGTC 57.427 61.111 0.00 0.00 35.78 4.79
549 574 1.566018 CGCCAACCGTCAGACTTTCC 61.566 60.000 0.00 0.00 0.00 3.13
550 575 1.566018 CCGCCAACCGTCAGACTTTC 61.566 60.000 0.00 0.00 34.38 2.62
554 579 2.280592 AACCGCCAACCGTCAGAC 60.281 61.111 0.00 0.00 34.38 3.51
555 580 2.280524 CAACCGCCAACCGTCAGA 60.281 61.111 0.00 0.00 34.38 3.27
556 581 3.353836 CCAACCGCCAACCGTCAG 61.354 66.667 0.00 0.00 34.38 3.51
562 587 1.014352 CTATAGTGCCAACCGCCAAC 58.986 55.000 0.00 0.00 36.24 3.77
563 588 0.906066 TCTATAGTGCCAACCGCCAA 59.094 50.000 0.00 0.00 36.24 4.52
564 589 0.906066 TTCTATAGTGCCAACCGCCA 59.094 50.000 0.00 0.00 36.24 5.69
566 591 1.940613 CCTTTCTATAGTGCCAACCGC 59.059 52.381 0.00 0.00 38.31 5.68
567 592 3.536956 TCCTTTCTATAGTGCCAACCG 57.463 47.619 0.00 0.00 0.00 4.44
569 594 4.436986 GCGTTTCCTTTCTATAGTGCCAAC 60.437 45.833 0.00 0.00 0.00 3.77
570 595 3.687698 GCGTTTCCTTTCTATAGTGCCAA 59.312 43.478 0.00 0.00 0.00 4.52
571 596 3.055385 AGCGTTTCCTTTCTATAGTGCCA 60.055 43.478 0.00 0.00 0.00 4.92
572 597 3.309954 CAGCGTTTCCTTTCTATAGTGCC 59.690 47.826 0.00 0.00 0.00 5.01
573 598 3.309954 CCAGCGTTTCCTTTCTATAGTGC 59.690 47.826 0.00 0.00 0.00 4.40
574 599 3.309954 GCCAGCGTTTCCTTTCTATAGTG 59.690 47.826 0.00 0.00 0.00 2.74
575 600 3.197983 AGCCAGCGTTTCCTTTCTATAGT 59.802 43.478 0.00 0.00 0.00 2.12
576 601 3.798202 AGCCAGCGTTTCCTTTCTATAG 58.202 45.455 0.00 0.00 0.00 1.31
578 603 2.749621 CAAGCCAGCGTTTCCTTTCTAT 59.250 45.455 0.00 0.00 0.00 1.98
579 604 2.151202 CAAGCCAGCGTTTCCTTTCTA 58.849 47.619 0.00 0.00 0.00 2.10
580 605 0.954452 CAAGCCAGCGTTTCCTTTCT 59.046 50.000 0.00 0.00 0.00 2.52
581 606 0.664466 GCAAGCCAGCGTTTCCTTTC 60.664 55.000 0.00 0.00 0.00 2.62
583 608 2.564721 GGCAAGCCAGCGTTTCCTT 61.565 57.895 6.14 0.00 35.81 3.36
584 609 2.985847 GGCAAGCCAGCGTTTCCT 60.986 61.111 6.14 0.00 35.81 3.36
585 610 4.404654 CGGCAAGCCAGCGTTTCC 62.405 66.667 12.19 0.00 35.37 3.13
656 700 0.744771 GACGGCTTCACCTTCATCCC 60.745 60.000 0.00 0.00 36.69 3.85
661 705 0.036388 TCCATGACGGCTTCACCTTC 60.036 55.000 0.00 0.00 36.92 3.46
662 706 0.036010 CTCCATGACGGCTTCACCTT 60.036 55.000 0.00 0.00 36.92 3.50
663 707 1.599047 CTCCATGACGGCTTCACCT 59.401 57.895 0.00 0.00 36.92 4.00
664 708 2.109126 GCTCCATGACGGCTTCACC 61.109 63.158 0.00 0.00 36.92 4.02
665 709 2.456119 CGCTCCATGACGGCTTCAC 61.456 63.158 0.00 0.00 36.92 3.18
666 710 1.600511 TACGCTCCATGACGGCTTCA 61.601 55.000 0.00 0.00 39.11 3.02
677 721 0.988832 ATCCCAACCTTTACGCTCCA 59.011 50.000 0.00 0.00 0.00 3.86
787 839 2.595754 GAGGCGATTGGGATGGGC 60.596 66.667 0.00 0.00 36.91 5.36
851 908 2.037902 TGAGTGTATGGAGCGTTTGGAA 59.962 45.455 0.00 0.00 0.00 3.53
858 915 2.025155 AGTAGGTGAGTGTATGGAGCG 58.975 52.381 0.00 0.00 0.00 5.03
859 916 2.761208 ACAGTAGGTGAGTGTATGGAGC 59.239 50.000 0.00 0.00 40.11 4.70
873 931 0.811915 AGCACGTCAGCTACAGTAGG 59.188 55.000 9.74 0.00 44.50 3.18
874 932 2.254459 CAAGCACGTCAGCTACAGTAG 58.746 52.381 2.85 2.85 45.89 2.57
876 960 0.946221 GCAAGCACGTCAGCTACAGT 60.946 55.000 0.23 0.00 45.89 3.55
878 964 1.667830 GGCAAGCACGTCAGCTACA 60.668 57.895 0.23 0.00 45.89 2.74
886 972 3.328382 TTATCTTAGTGGCAAGCACGT 57.672 42.857 0.00 0.00 0.00 4.49
892 978 1.864711 GCGCGATTATCTTAGTGGCAA 59.135 47.619 12.10 0.00 0.00 4.52
895 981 2.096713 GCTTGCGCGATTATCTTAGTGG 60.097 50.000 12.10 0.00 0.00 4.00
901 987 2.212652 TGATTGCTTGCGCGATTATCT 58.787 42.857 12.10 0.00 40.37 1.98
904 990 2.541383 CCAATGATTGCTTGCGCGATTA 60.541 45.455 12.10 0.00 40.37 1.75
906 992 0.248743 CCAATGATTGCTTGCGCGAT 60.249 50.000 12.10 0.00 42.99 4.58
907 993 1.137194 CCAATGATTGCTTGCGCGA 59.863 52.632 12.10 0.00 39.65 5.87
908 994 0.248743 ATCCAATGATTGCTTGCGCG 60.249 50.000 0.00 0.00 39.65 6.86
909 995 2.780065 TATCCAATGATTGCTTGCGC 57.220 45.000 0.00 0.00 32.18 6.09
910 996 3.253921 TCCATATCCAATGATTGCTTGCG 59.746 43.478 0.00 0.00 32.18 4.85
1077 1169 4.052229 AAGAGCGACCGGGTGACG 62.052 66.667 3.30 3.77 43.80 4.35
1284 1376 2.413310 ACTTGTATTTCGGCCCGAAT 57.587 45.000 20.84 12.17 45.28 3.34
1286 1378 1.729284 GAACTTGTATTTCGGCCCGA 58.271 50.000 0.00 0.00 0.00 5.14
1343 1447 9.533253 ACATCTCGTTTCTGAATTTCAAATTTT 57.467 25.926 0.00 0.00 0.00 1.82
1344 1448 9.533253 AACATCTCGTTTCTGAATTTCAAATTT 57.467 25.926 0.00 0.00 32.35 1.82
1345 1449 9.185192 GAACATCTCGTTTCTGAATTTCAAATT 57.815 29.630 0.00 0.00 38.19 1.82
1346 1450 8.352201 TGAACATCTCGTTTCTGAATTTCAAAT 58.648 29.630 0.01 0.00 38.19 2.32
1347 1451 7.702386 TGAACATCTCGTTTCTGAATTTCAAA 58.298 30.769 0.01 0.00 38.19 2.69
1348 1452 7.258022 TGAACATCTCGTTTCTGAATTTCAA 57.742 32.000 0.01 0.00 38.19 2.69
1349 1453 6.566564 GCTGAACATCTCGTTTCTGAATTTCA 60.567 38.462 0.00 0.00 38.19 2.69
1350 1454 5.792468 GCTGAACATCTCGTTTCTGAATTTC 59.208 40.000 0.00 0.00 38.19 2.17
1363 1467 7.647907 ATGTTTCAAATTTGCTGAACATCTC 57.352 32.000 25.24 8.89 34.23 2.75
1365 1469 9.505995 AAAAATGTTTCAAATTTGCTGAACATC 57.494 25.926 27.91 11.06 36.19 3.06
1393 1509 1.401018 CCAATTCAAACTTCGCCGACC 60.401 52.381 0.00 0.00 0.00 4.79
1394 1510 1.401018 CCCAATTCAAACTTCGCCGAC 60.401 52.381 0.00 0.00 0.00 4.79
1413 1605 0.096976 CCACGCACGATCACATTTCC 59.903 55.000 0.00 0.00 0.00 3.13
1414 1606 0.096976 CCCACGCACGATCACATTTC 59.903 55.000 0.00 0.00 0.00 2.17
1486 1707 1.202313 GGATCGGATCGGATCGGATTC 60.202 57.143 29.95 26.64 45.65 2.52
1489 1710 2.038837 CGGATCGGATCGGATCGGA 61.039 63.158 30.76 24.59 42.89 4.55
1490 1711 2.485582 CGGATCGGATCGGATCGG 59.514 66.667 27.38 26.56 43.00 4.18
1508 1729 1.082366 CGCCGCGCCATTTATTACC 60.082 57.895 0.00 0.00 0.00 2.85
1611 2091 1.134694 CGCTTTACGCTTTCCAGCC 59.865 57.895 0.00 0.00 44.06 4.85
1709 2189 3.458163 CTCCCCGCTACGCTTCCA 61.458 66.667 0.00 0.00 0.00 3.53
2200 2716 2.183046 GTGTCAGAGCTCTCCCGC 59.817 66.667 14.96 10.06 0.00 6.13
2211 2727 2.490217 CCTACGCGGAGGTGTCAG 59.510 66.667 30.13 1.79 38.08 3.51


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

AutoCloner maintained by Alex Coulton.