Multiple sequence alignment - TraesCS6D01G373900

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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 TraesCS6D01G373900 chr6D 100.000 3395 0 0 1 3395 458532104 458528710 0.000000e+00 6270
1 TraesCS6D01G373900 chr6D 92.308 1443 87 12 1954 3393 458507536 458506115 0.000000e+00 2028
2 TraesCS6D01G373900 chr6D 90.777 1030 70 15 951 1966 458508974 458507956 0.000000e+00 1352
3 TraesCS6D01G373900 chr6B 91.418 2878 161 47 565 3393 697405998 697403158 0.000000e+00 3868
4 TraesCS6D01G373900 chr6B 89.762 2227 151 36 1182 3393 696995437 696993273 0.000000e+00 2778
5 TraesCS6D01G373900 chr6B 86.335 1449 114 35 1954 3393 697227068 697225695 0.000000e+00 1502
6 TraesCS6D01G373900 chr6B 86.138 1450 116 35 1954 3393 697261023 697259649 0.000000e+00 1485
7 TraesCS6D01G373900 chr6B 86.059 1449 118 35 1954 3393 697118099 697116726 0.000000e+00 1480
8 TraesCS6D01G373900 chr6B 90.019 1032 74 17 951 1966 697119396 697118378 0.000000e+00 1308
9 TraesCS6D01G373900 chr6B 90.127 1023 73 16 951 1957 697262319 697261309 0.000000e+00 1304
10 TraesCS6D01G373900 chr6B 89.922 1032 77 17 951 1966 697373414 697372394 0.000000e+00 1304
11 TraesCS6D01G373900 chr6B 89.729 1032 77 17 951 1966 697228364 697227346 0.000000e+00 1291
12 TraesCS6D01G373900 chr6B 85.842 1003 69 30 1954 2952 697372117 697371184 0.000000e+00 998
13 TraesCS6D01G373900 chr6B 88.941 425 39 3 2973 3393 697357326 697356906 5.020000e-143 518
14 TraesCS6D01G373900 chr6B 83.087 473 76 4 100 570 114967290 114966820 8.710000e-116 427
15 TraesCS6D01G373900 chr6B 91.250 80 5 1 951 1028 697014995 697014916 1.290000e-19 108
16 TraesCS6D01G373900 chr6B 91.250 80 5 1 951 1028 697229450 697229371 1.290000e-19 108
17 TraesCS6D01G373900 chr6B 91.250 80 5 1 951 1028 697231668 697231589 1.290000e-19 108
18 TraesCS6D01G373900 chr6A 90.741 2430 119 44 565 2948 605102033 605104402 0.000000e+00 3144
19 TraesCS6D01G373900 chr6A 90.356 477 35 6 2920 3393 605117789 605118257 1.730000e-172 616
20 TraesCS6D01G373900 chr7D 83.890 838 116 13 1106 1938 20727930 20727107 0.000000e+00 782
21 TraesCS6D01G373900 chr7D 82.143 532 83 10 43 570 549540819 549540296 2.400000e-121 446
22 TraesCS6D01G373900 chr7A 82.238 563 70 19 2051 2609 21205035 21204499 3.090000e-125 459
23 TraesCS6D01G373900 chr7A 81.544 531 80 10 44 570 515172578 515173094 4.050000e-114 422
24 TraesCS6D01G373900 chr1B 81.547 569 90 14 1 566 111921913 111922469 3.990000e-124 455
25 TraesCS6D01G373900 chr1B 82.453 530 76 11 44 570 192142024 192141509 6.680000e-122 448
26 TraesCS6D01G373900 chr1A 83.166 499 74 5 74 570 554782858 554783348 6.680000e-122 448
27 TraesCS6D01G373900 chr2A 80.367 545 88 14 1 541 748957688 748958217 2.460000e-106 396
28 TraesCS6D01G373900 chr3B 80.337 534 88 12 34 563 749489219 749488699 4.110000e-104 388
29 TraesCS6D01G373900 chr5A 79.189 567 105 11 7 569 583689250 583689807 6.870000e-102 381


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 TraesCS6D01G373900 chr6D 458528710 458532104 3394 True 6270.00 6270 100.0000 1 3395 1 chr6D.!!$R1 3394
1 TraesCS6D01G373900 chr6D 458506115 458508974 2859 True 1690.00 2028 91.5425 951 3393 2 chr6D.!!$R2 2442
2 TraesCS6D01G373900 chr6B 697403158 697405998 2840 True 3868.00 3868 91.4180 565 3393 1 chr6B.!!$R5 2828
3 TraesCS6D01G373900 chr6B 696993273 696995437 2164 True 2778.00 2778 89.7620 1182 3393 1 chr6B.!!$R2 2211
4 TraesCS6D01G373900 chr6B 697259649 697262319 2670 True 1394.50 1485 88.1325 951 3393 2 chr6B.!!$R8 2442
5 TraesCS6D01G373900 chr6B 697116726 697119396 2670 True 1394.00 1480 88.0390 951 3393 2 chr6B.!!$R6 2442
6 TraesCS6D01G373900 chr6B 697371184 697373414 2230 True 1151.00 1304 87.8820 951 2952 2 chr6B.!!$R9 2001
7 TraesCS6D01G373900 chr6B 697225695 697231668 5973 True 752.25 1502 89.6410 951 3393 4 chr6B.!!$R7 2442
8 TraesCS6D01G373900 chr6A 605102033 605104402 2369 False 3144.00 3144 90.7410 565 2948 1 chr6A.!!$F1 2383
9 TraesCS6D01G373900 chr7D 20727107 20727930 823 True 782.00 782 83.8900 1106 1938 1 chr7D.!!$R1 832
10 TraesCS6D01G373900 chr7D 549540296 549540819 523 True 446.00 446 82.1430 43 570 1 chr7D.!!$R2 527
11 TraesCS6D01G373900 chr7A 21204499 21205035 536 True 459.00 459 82.2380 2051 2609 1 chr7A.!!$R1 558
12 TraesCS6D01G373900 chr7A 515172578 515173094 516 False 422.00 422 81.5440 44 570 1 chr7A.!!$F1 526
13 TraesCS6D01G373900 chr1B 111921913 111922469 556 False 455.00 455 81.5470 1 566 1 chr1B.!!$F1 565
14 TraesCS6D01G373900 chr1B 192141509 192142024 515 True 448.00 448 82.4530 44 570 1 chr1B.!!$R1 526
15 TraesCS6D01G373900 chr2A 748957688 748958217 529 False 396.00 396 80.3670 1 541 1 chr2A.!!$F1 540
16 TraesCS6D01G373900 chr3B 749488699 749489219 520 True 388.00 388 80.3370 34 563 1 chr3B.!!$R1 529
17 TraesCS6D01G373900 chr5A 583689250 583689807 557 False 381.00 381 79.1890 7 569 1 chr5A.!!$F1 562

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
622 634 0.036388 TTGGCGGCAACCAAACAAAA 60.036 45.0 21.79 0.0 46.65 2.44 F
623 635 0.179000 TGGCGGCAACCAAACAAAAT 59.821 45.0 10.22 0.0 36.55 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 4891 0.969894 AGTCCTTCCTGAACCAGTCG 59.030 55.000 0.0 0.0 0.0 4.18 R
2609 6482 3.138884 TGGAAAATCACTGTAGCTGCA 57.861 42.857 3.9 3.9 0.0 4.41 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
61 63 2.220586 TCATGGAGGCGTGGTGGAA 61.221 57.895 0.00 0.00 0.00 3.53
66 68 3.222354 GAGGCGTGGTGGAACTCGT 62.222 63.158 0.00 0.00 36.78 4.18
67 69 2.280592 GGCGTGGTGGAACTCGTT 60.281 61.111 0.00 0.00 36.78 3.85
68 70 2.315386 GGCGTGGTGGAACTCGTTC 61.315 63.158 1.22 1.22 36.78 3.95
69 71 2.654912 GCGTGGTGGAACTCGTTCG 61.655 63.158 3.93 0.00 40.37 3.95
97 105 2.140792 GGCGGGAGGGCTTCAGATA 61.141 63.158 0.00 0.00 38.40 1.98
121 129 4.879545 TGTTTTTAGGTGTCCTTCTGTGTC 59.120 41.667 0.00 0.00 34.61 3.67
213 222 2.124403 TCTAGCCCCCGTCTCGAC 60.124 66.667 0.00 0.00 0.00 4.20
232 241 4.783621 GTGCATCCAGCCTCGCCA 62.784 66.667 0.00 0.00 44.83 5.69
261 270 3.197614 GAGATGTGTCTCCGGCGA 58.802 61.111 9.30 0.00 44.20 5.54
288 297 1.303091 GGGATTCGGTCGGTGTTTGG 61.303 60.000 0.00 0.00 0.00 3.28
290 299 0.515564 GATTCGGTCGGTGTTTGGTG 59.484 55.000 0.00 0.00 0.00 4.17
292 301 0.810823 TTCGGTCGGTGTTTGGTGTC 60.811 55.000 0.00 0.00 0.00 3.67
335 345 5.223382 CGGTCTCATTTATCTGCGTCTATT 58.777 41.667 0.00 0.00 0.00 1.73
337 347 6.201044 CGGTCTCATTTATCTGCGTCTATTTT 59.799 38.462 0.00 0.00 0.00 1.82
345 355 5.824904 ATCTGCGTCTATTTTTCTGCAAT 57.175 34.783 0.00 0.00 31.16 3.56
351 361 5.060940 GCGTCTATTTTTCTGCAATTTGGAC 59.939 40.000 0.00 0.00 0.00 4.02
361 371 1.134946 GCAATTTGGACCCTTCCGATG 59.865 52.381 0.00 0.00 46.37 3.84
377 387 5.661056 TCCGATGTACACTTCTCTTCATT 57.339 39.130 0.00 0.00 0.00 2.57
388 398 1.586154 CTCTTCATTGGCGGCGGTTT 61.586 55.000 9.78 0.00 0.00 3.27
408 418 0.107456 CTGTTCTGGTGCACTGGTCT 59.893 55.000 17.98 0.00 0.00 3.85
450 460 4.094590 CGACTTTCCGACTGTCTACTACAT 59.905 45.833 6.21 0.00 37.50 2.29
622 634 0.036388 TTGGCGGCAACCAAACAAAA 60.036 45.000 21.79 0.00 46.65 2.44
623 635 0.179000 TGGCGGCAACCAAACAAAAT 59.821 45.000 10.22 0.00 36.55 1.82
624 636 0.585838 GGCGGCAACCAAACAAAATG 59.414 50.000 3.07 0.00 0.00 2.32
625 637 1.576356 GCGGCAACCAAACAAAATGA 58.424 45.000 0.00 0.00 0.00 2.57
626 638 1.936547 GCGGCAACCAAACAAAATGAA 59.063 42.857 0.00 0.00 0.00 2.57
627 639 2.352960 GCGGCAACCAAACAAAATGAAA 59.647 40.909 0.00 0.00 0.00 2.69
628 640 3.181506 GCGGCAACCAAACAAAATGAAAA 60.182 39.130 0.00 0.00 0.00 2.29
629 641 4.672801 GCGGCAACCAAACAAAATGAAAAA 60.673 37.500 0.00 0.00 0.00 1.94
630 642 5.576895 CGGCAACCAAACAAAATGAAAAAT 58.423 33.333 0.00 0.00 0.00 1.82
770 794 4.082523 GTGCTAGCCACTCCGCCA 62.083 66.667 13.29 0.00 41.35 5.69
814 846 9.448438 TGCTAGCTGTTAGATTTTTCAAAGATA 57.552 29.630 17.23 0.00 0.00 1.98
815 847 9.709600 GCTAGCTGTTAGATTTTTCAAAGATAC 57.290 33.333 7.70 0.00 0.00 2.24
849 882 0.468400 AGCTAAACCACCGGCCAAAA 60.468 50.000 0.00 0.00 0.00 2.44
1011 4369 2.807967 TCCACGAGAAATGACAGCAAAG 59.192 45.455 0.00 0.00 0.00 2.77
1012 4370 2.095567 CCACGAGAAATGACAGCAAAGG 60.096 50.000 0.00 0.00 0.00 3.11
1048 4415 2.050144 GCAGTCCTCCATCCCTTATCA 58.950 52.381 0.00 0.00 0.00 2.15
1049 4416 2.641815 GCAGTCCTCCATCCCTTATCAT 59.358 50.000 0.00 0.00 0.00 2.45
1052 4419 4.349048 CAGTCCTCCATCCCTTATCATTCA 59.651 45.833 0.00 0.00 0.00 2.57
1054 4421 5.433051 AGTCCTCCATCCCTTATCATTCAAA 59.567 40.000 0.00 0.00 0.00 2.69
1060 4427 5.009410 CCATCCCTTATCATTCAAAGCAGAC 59.991 44.000 0.00 0.00 0.00 3.51
1065 4432 5.123820 CCTTATCATTCAAAGCAGACCGAAA 59.876 40.000 0.00 0.00 0.00 3.46
1067 4434 7.012327 CCTTATCATTCAAAGCAGACCGAAATA 59.988 37.037 0.00 0.00 0.00 1.40
1081 4448 4.309099 ACCGAAATACACAACACGTACAT 58.691 39.130 0.00 0.00 0.00 2.29
1084 4451 5.062934 CCGAAATACACAACACGTACATCAT 59.937 40.000 0.00 0.00 0.00 2.45
1086 4459 6.676995 CGAAATACACAACACGTACATCATTC 59.323 38.462 0.00 0.00 0.00 2.67
1091 4464 3.679980 ACAACACGTACATCATTCAGAGC 59.320 43.478 0.00 0.00 0.00 4.09
1095 4468 4.399618 ACACGTACATCATTCAGAGCTAGT 59.600 41.667 0.00 0.00 0.00 2.57
1096 4469 4.973051 CACGTACATCATTCAGAGCTAGTC 59.027 45.833 0.00 0.00 0.00 2.59
1097 4470 4.215201 CGTACATCATTCAGAGCTAGTCG 58.785 47.826 0.00 0.00 0.00 4.18
1125 4500 2.347490 GCAGGTCAGGCCGAGAAA 59.653 61.111 0.00 0.00 43.70 2.52
1834 5213 2.480802 GACAAAGTTCTTCTTCCCGCTC 59.519 50.000 0.00 0.00 35.02 5.03
1835 5214 2.158813 ACAAAGTTCTTCTTCCCGCTCA 60.159 45.455 0.00 0.00 35.02 4.26
1836 5215 2.878406 CAAAGTTCTTCTTCCCGCTCAA 59.122 45.455 0.00 0.00 35.02 3.02
1960 5794 9.381033 CCATAATTTTTATGCCAAGTGAAATGA 57.619 29.630 2.40 0.00 0.00 2.57
2414 6259 3.306472 AGGTTGTGCTCCCAAAGTAAA 57.694 42.857 0.00 0.00 0.00 2.01
2552 6400 7.518370 GCGGTTATGTCTTGTTACCTTATGATG 60.518 40.741 0.00 0.00 0.00 3.07
2553 6401 7.709182 CGGTTATGTCTTGTTACCTTATGATGA 59.291 37.037 0.00 0.00 0.00 2.92
2558 6406 8.319057 TGTCTTGTTACCTTATGATGATACCT 57.681 34.615 0.00 0.00 0.00 3.08
2559 6407 9.429109 TGTCTTGTTACCTTATGATGATACCTA 57.571 33.333 0.00 0.00 0.00 3.08
2560 6408 9.694137 GTCTTGTTACCTTATGATGATACCTAC 57.306 37.037 0.00 0.00 0.00 3.18
2606 6479 8.737168 ATAGTATGCATTTAGAGTGCTTTTCA 57.263 30.769 3.54 0.00 42.92 2.69
2607 6480 7.636150 AGTATGCATTTAGAGTGCTTTTCAT 57.364 32.000 3.54 0.00 42.92 2.57
2608 6481 8.737168 AGTATGCATTTAGAGTGCTTTTCATA 57.263 30.769 3.54 0.00 42.92 2.15
2609 6482 9.347240 AGTATGCATTTAGAGTGCTTTTCATAT 57.653 29.630 3.54 0.00 42.92 1.78
2610 6483 9.390795 GTATGCATTTAGAGTGCTTTTCATATG 57.609 33.333 3.54 0.00 42.92 1.78
2611 6484 6.267817 TGCATTTAGAGTGCTTTTCATATGC 58.732 36.000 0.00 0.00 42.92 3.14
2612 6485 6.127675 TGCATTTAGAGTGCTTTTCATATGCA 60.128 34.615 0.00 0.00 42.92 3.96
2613 6486 6.417044 GCATTTAGAGTGCTTTTCATATGCAG 59.583 38.462 0.00 0.00 37.56 4.41
2614 6487 5.490139 TTAGAGTGCTTTTCATATGCAGC 57.510 39.130 12.17 12.17 37.56 5.25
2615 6488 3.618351 AGAGTGCTTTTCATATGCAGCT 58.382 40.909 17.26 5.39 37.56 4.24
2616 6489 4.774124 AGAGTGCTTTTCATATGCAGCTA 58.226 39.130 17.26 6.32 37.56 3.32
2617 6490 4.574013 AGAGTGCTTTTCATATGCAGCTAC 59.426 41.667 17.26 14.11 37.56 3.58
2618 6491 4.264253 AGTGCTTTTCATATGCAGCTACA 58.736 39.130 17.26 0.00 37.56 2.74
2619 6492 4.334759 AGTGCTTTTCATATGCAGCTACAG 59.665 41.667 17.26 2.01 37.56 2.74
2620 6493 4.095483 GTGCTTTTCATATGCAGCTACAGT 59.905 41.667 17.26 0.00 37.56 3.55
2621 6494 4.095334 TGCTTTTCATATGCAGCTACAGTG 59.905 41.667 17.26 0.00 33.44 3.66
2622 6495 4.333649 GCTTTTCATATGCAGCTACAGTGA 59.666 41.667 11.92 0.00 0.00 3.41
2623 6496 5.008415 GCTTTTCATATGCAGCTACAGTGAT 59.992 40.000 11.92 0.00 0.00 3.06
2627 6500 6.609237 TCATATGCAGCTACAGTGATTTTC 57.391 37.500 0.00 0.00 0.00 2.29
2633 6506 5.297527 TGCAGCTACAGTGATTTTCCATATG 59.702 40.000 0.00 0.00 0.00 1.78
2773 6653 3.802862 TAGAGGCCTCTAGTGGTCG 57.197 57.895 34.33 0.00 40.93 4.79
2785 6665 0.751643 AGTGGTCGCTTTGTGGCTTT 60.752 50.000 0.00 0.00 0.00 3.51
2854 6734 7.451731 TTTCTATATCCATCAGGTTCACCTT 57.548 36.000 0.00 0.00 46.09 3.50
2857 6737 3.567478 ATCCATCAGGTTCACCTTAGC 57.433 47.619 0.00 0.00 46.09 3.09
2859 6739 2.237143 TCCATCAGGTTCACCTTAGCAG 59.763 50.000 0.00 0.00 46.09 4.24
2865 6745 4.021368 TCAGGTTCACCTTAGCAGACTTAC 60.021 45.833 0.00 0.00 46.09 2.34
2969 6849 5.069251 TGTGCATATGCCAAATGATCATGAA 59.931 36.000 24.54 0.00 41.18 2.57
2997 6877 7.444183 GGTTCGTGGATGGAGATTTCAATTATA 59.556 37.037 0.00 0.00 0.00 0.98
3029 6910 6.183361 ACCCTGAGAACAAAAATAGAGAAGGT 60.183 38.462 0.00 0.00 0.00 3.50
3280 7174 7.202047 GGATTGGTACATCTATTCTTGAGTCCT 60.202 40.741 0.00 0.00 39.30 3.85
3281 7175 6.716934 TGGTACATCTATTCTTGAGTCCTC 57.283 41.667 0.00 0.00 0.00 3.71
3282 7176 5.299531 TGGTACATCTATTCTTGAGTCCTCG 59.700 44.000 0.00 0.00 0.00 4.63
3283 7177 5.531659 GGTACATCTATTCTTGAGTCCTCGA 59.468 44.000 0.00 0.00 0.00 4.04
3393 7288 9.219603 TGAACATGATAGTTCCAAAAGAGTAAG 57.780 33.333 0.00 0.00 45.62 2.34
3394 7289 9.220767 GAACATGATAGTTCCAAAAGAGTAAGT 57.779 33.333 0.00 0.00 41.52 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.966920 CACAACAGACGGGGTAGACT 59.033 55.000 0.00 0.00 0.00 3.24
61 63 4.355925 GGCAAGAACCGAACGAGT 57.644 55.556 0.00 0.00 0.00 4.18
91 93 7.824289 CAGAAGGACACCTAAAAACATATCTGA 59.176 37.037 0.00 0.00 31.13 3.27
95 103 7.231467 ACACAGAAGGACACCTAAAAACATAT 58.769 34.615 0.00 0.00 31.13 1.78
97 105 5.445964 ACACAGAAGGACACCTAAAAACAT 58.554 37.500 0.00 0.00 31.13 2.71
121 129 2.293399 GCAGGACACAAACCCTAAACAG 59.707 50.000 0.00 0.00 0.00 3.16
174 183 3.181443 ACGGGGAGAACATTATTCCATCC 60.181 47.826 0.00 0.00 32.50 3.51
230 239 2.362369 ATCTCCACACGCCCTCTGG 61.362 63.158 0.00 0.00 0.00 3.86
232 241 1.610673 ACATCTCCACACGCCCTCT 60.611 57.895 0.00 0.00 0.00 3.69
261 270 0.102481 CGACCGAATCCCACGAGATT 59.898 55.000 0.00 0.00 39.19 2.40
335 345 3.070878 GGAAGGGTCCAAATTGCAGAAAA 59.929 43.478 0.00 0.00 44.26 2.29
337 347 2.247358 GGAAGGGTCCAAATTGCAGAA 58.753 47.619 0.00 0.00 44.26 3.02
345 355 1.979308 TGTACATCGGAAGGGTCCAAA 59.021 47.619 0.00 0.00 45.26 3.28
351 361 2.761208 AGAGAAGTGTACATCGGAAGGG 59.239 50.000 0.00 0.00 0.00 3.95
361 371 2.673368 CCGCCAATGAAGAGAAGTGTAC 59.327 50.000 0.00 0.00 0.00 2.90
377 387 2.975799 GAACAGAAACCGCCGCCA 60.976 61.111 0.00 0.00 0.00 5.69
388 398 0.106708 GACCAGTGCACCAGAACAGA 59.893 55.000 14.63 0.00 0.00 3.41
408 418 0.179468 GTCGTGCTAAGGCCCCATAA 59.821 55.000 0.00 0.00 37.74 1.90
450 460 2.282180 GAGCCGGGCAAACCTTGA 60.282 61.111 23.09 0.00 36.97 3.02
570 582 3.118112 CCTGGTGAGGATATGCTCAACTT 60.118 47.826 33.67 0.00 42.93 2.66
571 583 2.437281 CCTGGTGAGGATATGCTCAACT 59.563 50.000 33.67 0.00 42.93 3.16
572 584 2.843701 CCTGGTGAGGATATGCTCAAC 58.156 52.381 29.62 29.62 42.93 3.18
573 585 1.141657 GCCTGGTGAGGATATGCTCAA 59.858 52.381 26.30 12.67 42.93 3.02
628 640 8.694540 CGGATCTGGAGAGATTATCTTCATATT 58.305 37.037 0.00 0.00 42.96 1.28
629 641 7.838696 ACGGATCTGGAGAGATTATCTTCATAT 59.161 37.037 6.47 0.00 42.96 1.78
630 642 7.178573 ACGGATCTGGAGAGATTATCTTCATA 58.821 38.462 6.47 0.00 42.96 2.15
636 648 5.258051 AGGTACGGATCTGGAGAGATTATC 58.742 45.833 6.47 0.00 39.19 1.75
676 697 1.738099 CTCGTGGTACAGGTGCTGC 60.738 63.158 0.00 0.00 45.38 5.25
814 846 1.339097 AGCTAGGGTTTCGAGTGTGT 58.661 50.000 0.00 0.00 0.00 3.72
815 847 3.587797 TTAGCTAGGGTTTCGAGTGTG 57.412 47.619 0.00 0.00 0.00 3.82
902 935 4.275810 AGAGAAATGAATGACCATGGTGG 58.724 43.478 25.52 0.00 45.02 4.61
903 936 5.909621 AAGAGAAATGAATGACCATGGTG 57.090 39.130 25.52 0.00 0.00 4.17
904 937 5.124457 CGAAAGAGAAATGAATGACCATGGT 59.876 40.000 19.89 19.89 0.00 3.55
1028 4386 2.050144 TGATAAGGGATGGAGGACTGC 58.950 52.381 0.00 0.00 0.00 4.40
1029 4387 4.349048 TGAATGATAAGGGATGGAGGACTG 59.651 45.833 0.00 0.00 0.00 3.51
1038 4405 5.136105 GGTCTGCTTTGAATGATAAGGGAT 58.864 41.667 0.00 0.00 0.00 3.85
1048 4415 4.759693 TGTGTATTTCGGTCTGCTTTGAAT 59.240 37.500 0.00 0.00 0.00 2.57
1049 4416 4.130857 TGTGTATTTCGGTCTGCTTTGAA 58.869 39.130 0.00 0.00 0.00 2.69
1052 4419 3.880490 TGTTGTGTATTTCGGTCTGCTTT 59.120 39.130 0.00 0.00 0.00 3.51
1054 4421 2.806244 GTGTTGTGTATTTCGGTCTGCT 59.194 45.455 0.00 0.00 0.00 4.24
1060 4427 4.386350 TGATGTACGTGTTGTGTATTTCGG 59.614 41.667 0.00 0.00 0.00 4.30
1065 4432 6.394809 TCTGAATGATGTACGTGTTGTGTAT 58.605 36.000 0.00 0.00 0.00 2.29
1067 4434 4.627058 TCTGAATGATGTACGTGTTGTGT 58.373 39.130 0.00 0.00 0.00 3.72
1081 4448 2.550180 CCGATCGACTAGCTCTGAATGA 59.450 50.000 18.66 0.00 0.00 2.57
1084 4451 0.663688 GCCGATCGACTAGCTCTGAA 59.336 55.000 18.66 0.00 0.00 3.02
1086 4459 0.382158 TTGCCGATCGACTAGCTCTG 59.618 55.000 18.66 0.00 0.00 3.35
1091 4464 0.249447 TGCCATTGCCGATCGACTAG 60.249 55.000 18.66 0.00 36.33 2.57
1095 4468 2.203056 CCTGCCATTGCCGATCGA 60.203 61.111 18.66 0.00 36.33 3.59
1096 4469 2.514592 ACCTGCCATTGCCGATCG 60.515 61.111 8.51 8.51 36.33 3.69
1097 4470 1.442526 CTGACCTGCCATTGCCGATC 61.443 60.000 0.00 0.00 36.33 3.69
1125 4500 2.522436 TCGGTGGGGACGAACACT 60.522 61.111 0.00 0.00 37.42 3.55
1512 4891 0.969894 AGTCCTTCCTGAACCAGTCG 59.030 55.000 0.00 0.00 0.00 4.18
1834 5213 3.665190 ACTTAACCGCTCCTTCTTCTTG 58.335 45.455 0.00 0.00 0.00 3.02
1835 5214 5.046520 ACATACTTAACCGCTCCTTCTTCTT 60.047 40.000 0.00 0.00 0.00 2.52
1836 5215 4.466726 ACATACTTAACCGCTCCTTCTTCT 59.533 41.667 0.00 0.00 0.00 2.85
1947 5347 6.101332 TCATTGCTTTATCATTTCACTTGGC 58.899 36.000 0.00 0.00 0.00 4.52
2031 5868 9.747898 TTAATCAAGCCTAACTAGGATGAAAAA 57.252 29.630 6.98 6.27 46.63 1.94
2414 6259 6.830324 ACAATCCACAACATATGTAAGCATCT 59.170 34.615 9.21 0.00 41.46 2.90
2552 6400 7.173735 TTTCCAAAAGAAAGTTCCGTAGGTATC 59.826 37.037 0.00 0.00 44.16 2.24
2553 6401 6.999871 TTTCCAAAAGAAAGTTCCGTAGGTAT 59.000 34.615 0.00 0.00 44.16 2.73
2555 6403 5.195185 TTTCCAAAAGAAAGTTCCGTAGGT 58.805 37.500 0.00 0.00 44.16 3.08
2556 6404 5.761165 TTTCCAAAAGAAAGTTCCGTAGG 57.239 39.130 0.00 0.00 44.81 3.18
2591 6442 5.649395 AGCTGCATATGAAAAGCACTCTAAA 59.351 36.000 20.75 0.00 38.14 1.85
2601 6474 7.395190 AAATCACTGTAGCTGCATATGAAAA 57.605 32.000 18.45 2.11 0.00 2.29
2602 6475 7.395190 AAAATCACTGTAGCTGCATATGAAA 57.605 32.000 18.45 2.68 0.00 2.69
2603 6476 6.038603 GGAAAATCACTGTAGCTGCATATGAA 59.961 38.462 18.45 0.00 0.00 2.57
2604 6477 5.528690 GGAAAATCACTGTAGCTGCATATGA 59.471 40.000 17.35 17.35 0.00 2.15
2605 6478 5.297527 TGGAAAATCACTGTAGCTGCATATG 59.702 40.000 4.51 7.39 0.00 1.78
2606 6479 5.439721 TGGAAAATCACTGTAGCTGCATAT 58.560 37.500 4.51 0.00 0.00 1.78
2607 6480 4.842574 TGGAAAATCACTGTAGCTGCATA 58.157 39.130 4.51 0.00 0.00 3.14
2608 6481 3.689347 TGGAAAATCACTGTAGCTGCAT 58.311 40.909 4.51 0.00 0.00 3.96
2609 6482 3.138884 TGGAAAATCACTGTAGCTGCA 57.861 42.857 3.90 3.90 0.00 4.41
2610 6483 5.297776 ACATATGGAAAATCACTGTAGCTGC 59.702 40.000 7.80 0.00 0.00 5.25
2611 6484 6.317140 ACACATATGGAAAATCACTGTAGCTG 59.683 38.462 7.80 0.00 0.00 4.24
2612 6485 6.418101 ACACATATGGAAAATCACTGTAGCT 58.582 36.000 7.80 0.00 0.00 3.32
2613 6486 6.683974 ACACATATGGAAAATCACTGTAGC 57.316 37.500 7.80 0.00 0.00 3.58
2614 6487 7.042725 CGGTACACATATGGAAAATCACTGTAG 60.043 40.741 7.80 0.00 0.00 2.74
2615 6488 6.759356 CGGTACACATATGGAAAATCACTGTA 59.241 38.462 7.80 0.64 0.00 2.74
2616 6489 5.584649 CGGTACACATATGGAAAATCACTGT 59.415 40.000 7.80 1.60 0.00 3.55
2617 6490 5.584649 ACGGTACACATATGGAAAATCACTG 59.415 40.000 7.80 3.05 0.00 3.66
2618 6491 5.584649 CACGGTACACATATGGAAAATCACT 59.415 40.000 7.80 0.00 0.00 3.41
2619 6492 5.353123 ACACGGTACACATATGGAAAATCAC 59.647 40.000 7.80 0.00 0.00 3.06
2620 6493 5.492895 ACACGGTACACATATGGAAAATCA 58.507 37.500 7.80 0.00 0.00 2.57
2621 6494 6.535865 TGTACACGGTACACATATGGAAAATC 59.464 38.462 7.80 0.00 0.00 2.17
2622 6495 6.408035 TGTACACGGTACACATATGGAAAAT 58.592 36.000 7.80 0.00 0.00 1.82
2623 6496 5.791666 TGTACACGGTACACATATGGAAAA 58.208 37.500 7.80 0.00 0.00 2.29
2627 6500 7.149307 TGATATTGTACACGGTACACATATGG 58.851 38.462 20.33 0.00 0.00 2.74
2633 6506 8.298854 TGGTATATGATATTGTACACGGTACAC 58.701 37.037 14.08 6.17 0.00 2.90
2773 6653 2.477754 GCTTCATTCAAAGCCACAAAGC 59.522 45.455 0.00 0.00 44.75 3.51
2829 6709 7.639062 AGGTGAACCTGATGGATATAGAAAT 57.361 36.000 0.00 0.00 46.55 2.17
2865 6745 4.188247 TGGTTAGAATCCAAGACTCACG 57.812 45.455 0.00 0.00 31.50 4.35
2969 6849 3.054434 TGAAATCTCCATCCACGAACCAT 60.054 43.478 0.00 0.00 0.00 3.55
3029 6910 4.807443 CAAACATGTCATGTGCATTACCA 58.193 39.130 19.08 0.00 44.07 3.25
3228 7117 4.026744 TGAAACAAGGGATGTGGTCAAAA 58.973 39.130 0.00 0.00 42.99 2.44


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

AutoCloner maintained by Alex Coulton.