Multiple sequence alignment - TraesCS1A01G230200

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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 TraesCS1A01G230200 chr1A 100.000 2669 0 0 1 2669 402937827 402940495 0.000000e+00 4929.0
1 TraesCS1A01G230200 chr1B 89.164 1855 117 38 584 2398 433112059 433110249 0.000000e+00 2235.0
2 TraesCS1A01G230200 chr1B 91.791 268 11 2 2398 2665 433110218 433109962 1.950000e-96 363.0
3 TraesCS1A01G230200 chr1D 88.929 1120 58 23 891 1998 320195517 320194452 0.000000e+00 1321.0
4 TraesCS1A01G230200 chr1D 88.520 331 13 10 583 898 320195868 320195548 6.970000e-101 377.0
5 TraesCS1A01G230200 chr5B 93.391 575 38 0 1 575 537609630 537609056 0.000000e+00 852.0
6 TraesCS1A01G230200 chr5B 94.286 35 1 1 2394 2428 549974311 549974278 5.000000e-03 52.8
7 TraesCS1A01G230200 chr2D 92.443 569 43 0 5 573 111223575 111224143 0.000000e+00 813.0
8 TraesCS1A01G230200 chr2D 100.000 28 0 0 2398 2425 302248035 302248008 5.000000e-03 52.8
9 TraesCS1A01G230200 chr3B 89.792 578 58 1 1 577 445156351 445156928 0.000000e+00 739.0
10 TraesCS1A01G230200 chr3B 87.215 571 73 0 5 575 816249121 816248551 0.000000e+00 651.0
11 TraesCS1A01G230200 chr3D 89.667 571 59 0 5 575 609356400 609356970 0.000000e+00 728.0
12 TraesCS1A01G230200 chr4A 88.328 574 63 3 2 575 706872458 706873027 0.000000e+00 686.0
13 TraesCS1A01G230200 chr3A 88.225 569 66 1 5 573 60196767 60196200 0.000000e+00 678.0
14 TraesCS1A01G230200 chr3A 87.698 569 70 0 5 573 747300572 747300004 0.000000e+00 664.0
15 TraesCS1A01G230200 chr5D 87.741 571 70 0 5 575 435799484 435798914 0.000000e+00 667.0
16 TraesCS1A01G230200 chr5D 100.000 28 0 0 2398 2425 324588075 324588102 5.000000e-03 52.8
17 TraesCS1A01G230200 chr6B 94.444 36 1 1 2388 2422 58320189 58320154 1.000000e-03 54.7
18 TraesCS1A01G230200 chr5A 96.774 31 1 0 2398 2428 588845516 588845486 5.000000e-03 52.8
19 TraesCS1A01G230200 chr4D 96.774 31 1 0 2398 2428 494787218 494787188 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 TraesCS1A01G230200 chr1A 402937827 402940495 2668 False 4929 4929 100.0000 1 2669 1 chr1A.!!$F1 2668
1 TraesCS1A01G230200 chr1B 433109962 433112059 2097 True 1299 2235 90.4775 584 2665 2 chr1B.!!$R1 2081
2 TraesCS1A01G230200 chr1D 320194452 320195868 1416 True 849 1321 88.7245 583 1998 2 chr1D.!!$R1 1415
3 TraesCS1A01G230200 chr5B 537609056 537609630 574 True 852 852 93.3910 1 575 1 chr5B.!!$R1 574
4 TraesCS1A01G230200 chr2D 111223575 111224143 568 False 813 813 92.4430 5 573 1 chr2D.!!$F1 568
5 TraesCS1A01G230200 chr3B 445156351 445156928 577 False 739 739 89.7920 1 577 1 chr3B.!!$F1 576
6 TraesCS1A01G230200 chr3B 816248551 816249121 570 True 651 651 87.2150 5 575 1 chr3B.!!$R1 570
7 TraesCS1A01G230200 chr3D 609356400 609356970 570 False 728 728 89.6670 5 575 1 chr3D.!!$F1 570
8 TraesCS1A01G230200 chr4A 706872458 706873027 569 False 686 686 88.3280 2 575 1 chr4A.!!$F1 573
9 TraesCS1A01G230200 chr3A 60196200 60196767 567 True 678 678 88.2250 5 573 1 chr3A.!!$R1 568
10 TraesCS1A01G230200 chr3A 747300004 747300572 568 True 664 664 87.6980 5 573 1 chr3A.!!$R2 568
11 TraesCS1A01G230200 chr5D 435798914 435799484 570 True 667 667 87.7410 5 575 1 chr5D.!!$R1 570


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
140 141 0.322322 CCAAACCATGCACATGCCTT 59.678 50.0 5.06 0.0 41.18 4.35 F
774 784 0.332972 ACCAAATCTCTTCCCCCAGC 59.667 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1179 1248 1.922220 GTCGTCGTCATCGTCGTCG 60.922 63.158 0.0 0.0 45.27 5.12 R
2435 2565 0.036164 TACAGATGTTGCCGCCAAGT 59.964 50.000 0.0 0.0 0.00 3.16 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
46 47 2.109126 GTGGTGATCTTGGCTCGGC 61.109 63.158 0.00 0.00 0.00 5.54
140 141 0.322322 CCAAACCATGCACATGCCTT 59.678 50.000 5.06 0.00 41.18 4.35
163 164 1.236616 CCAGAAGTGTTGCGCATGGA 61.237 55.000 17.05 0.00 0.00 3.41
281 282 0.978151 TCCGGAAGAATCCCACGAAA 59.022 50.000 0.00 0.00 43.37 3.46
288 289 4.519350 GGAAGAATCCCACGAAAAACTCTT 59.481 41.667 0.00 0.00 40.10 2.85
292 293 3.269538 TCCCACGAAAAACTCTTCACA 57.730 42.857 0.00 0.00 0.00 3.58
323 324 7.050377 ACTCTCATTTTCGGTATGACATTCAT 58.950 34.615 0.00 0.00 40.72 2.57
324 325 7.225538 ACTCTCATTTTCGGTATGACATTCATC 59.774 37.037 0.00 0.00 38.26 2.92
337 338 4.079844 TGACATTCATCTTCCATAAGGCCA 60.080 41.667 5.01 0.00 33.22 5.36
343 344 1.140852 TCTTCCATAAGGCCATCCACG 59.859 52.381 5.01 0.00 33.22 4.94
358 359 5.545588 CCATCCACGACTATTGATCATCTT 58.454 41.667 0.00 0.00 0.00 2.40
359 360 5.994054 CCATCCACGACTATTGATCATCTTT 59.006 40.000 0.00 0.00 0.00 2.52
427 429 4.401202 TCTGAATCATTAGAGCACGGTACA 59.599 41.667 0.00 0.00 0.00 2.90
449 451 3.069158 ACCGTCTTTACAGTGTAGTTGCT 59.931 43.478 2.68 0.00 0.00 3.91
469 471 3.367292 GCTTGATTTCTCGAATGCCCAAA 60.367 43.478 0.00 0.00 0.00 3.28
485 487 3.321968 GCCCAAACAAAAGAATCCTCACT 59.678 43.478 0.00 0.00 0.00 3.41
490 492 4.731313 ACAAAAGAATCCTCACTTCCCT 57.269 40.909 0.00 0.00 0.00 4.20
494 496 6.044404 ACAAAAGAATCCTCACTTCCCTCTTA 59.956 38.462 0.00 0.00 0.00 2.10
525 527 1.083489 TGTTTAGAATGGCTTCGGCG 58.917 50.000 0.00 0.00 42.91 6.46
531 533 2.852495 GAATGGCTTCGGCGTCTGGA 62.852 60.000 6.85 0.00 42.91 3.86
577 579 4.329545 GCCGCCAAGACCAGTCCA 62.330 66.667 0.00 0.00 0.00 4.02
578 580 2.046892 CCGCCAAGACCAGTCCAG 60.047 66.667 0.00 0.00 0.00 3.86
579 581 2.046892 CGCCAAGACCAGTCCAGG 60.047 66.667 0.00 0.00 0.00 4.45
580 582 2.360475 GCCAAGACCAGTCCAGGC 60.360 66.667 13.32 13.32 40.92 4.85
581 583 2.046892 CCAAGACCAGTCCAGGCG 60.047 66.667 0.00 0.00 0.00 5.52
582 584 2.743928 CAAGACCAGTCCAGGCGC 60.744 66.667 0.00 0.00 0.00 6.53
628 630 0.679960 TCTGAATCGTGGAGCGGAGA 60.680 55.000 0.00 0.00 41.72 3.71
629 631 0.526524 CTGAATCGTGGAGCGGAGAC 60.527 60.000 0.00 0.00 41.72 3.36
667 677 2.167487 CCTCTCTGCCCAGAAGAAGTAC 59.833 54.545 0.00 0.00 36.94 2.73
753 763 3.488489 CTTCCGTTCATTTAACCGCAAG 58.512 45.455 0.00 0.00 34.33 4.01
772 782 2.358258 AGAACCAAATCTCTTCCCCCA 58.642 47.619 0.00 0.00 0.00 4.96
774 784 0.332972 ACCAAATCTCTTCCCCCAGC 59.667 55.000 0.00 0.00 0.00 4.85
795 812 3.377172 GCAAAGTAATCCACCACGCTTAT 59.623 43.478 0.00 0.00 0.00 1.73
796 813 4.495844 GCAAAGTAATCCACCACGCTTATC 60.496 45.833 0.00 0.00 0.00 1.75
797 814 4.755266 AAGTAATCCACCACGCTTATCT 57.245 40.909 0.00 0.00 0.00 1.98
798 815 4.323553 AGTAATCCACCACGCTTATCTC 57.676 45.455 0.00 0.00 0.00 2.75
799 816 3.961408 AGTAATCCACCACGCTTATCTCT 59.039 43.478 0.00 0.00 0.00 3.10
830 847 2.305927 GACATCAAGGAAGGAAGGACCA 59.694 50.000 0.00 0.00 42.04 4.02
832 849 0.693049 TCAAGGAAGGAAGGACCAGC 59.307 55.000 0.00 0.00 42.04 4.85
833 850 0.695347 CAAGGAAGGAAGGACCAGCT 59.305 55.000 0.00 0.00 42.04 4.24
834 851 1.074566 CAAGGAAGGAAGGACCAGCTT 59.925 52.381 0.00 0.00 42.04 3.74
835 852 0.695347 AGGAAGGAAGGACCAGCTTG 59.305 55.000 0.00 0.00 42.04 4.01
932 995 1.240256 AGCGCTTATCTACCCGAGAG 58.760 55.000 2.64 0.00 37.70 3.20
941 1004 1.379977 TACCCGAGAGCCACTCCTG 60.380 63.158 3.46 0.00 42.18 3.86
964 1027 2.838693 GGAGGAGGGGCCGTAGTC 60.839 72.222 0.00 0.00 43.43 2.59
974 1037 0.452585 GGCCGTAGTCACAGAGAGAC 59.547 60.000 0.00 0.00 36.26 3.36
978 1041 1.823797 GTAGTCACAGAGAGACCGGT 58.176 55.000 6.92 6.92 36.68 5.28
982 1045 2.203640 ACAGAGAGACCGGTGCCA 60.204 61.111 14.63 0.00 0.00 4.92
1243 1312 3.060020 GCCATCGACTCGTTCCCGA 62.060 63.158 0.00 0.00 41.73 5.14
1609 1690 2.389715 AGGACTGGCTCATGTACTACC 58.610 52.381 0.00 0.00 0.00 3.18
1692 1773 3.342627 CGTTGCGAGCGTGGGAAA 61.343 61.111 0.00 0.00 0.00 3.13
1693 1774 2.251371 GTTGCGAGCGTGGGAAAC 59.749 61.111 0.00 0.00 0.00 2.78
1799 1887 1.818850 CAGTATAACTGTACGCGCGT 58.181 50.000 39.05 39.05 41.19 6.01
1818 1910 4.607336 CGCGTACACGTATACGGTATACAA 60.607 45.833 25.90 13.94 46.39 2.41
1869 1961 1.348036 GTACTGGAAAGTGAGCAGGGT 59.652 52.381 0.00 0.00 0.00 4.34
1871 1963 0.397941 CTGGAAAGTGAGCAGGGTGA 59.602 55.000 0.00 0.00 0.00 4.02
1887 1979 2.952310 GGGTGACTTTTCATGATAGGGC 59.048 50.000 0.00 0.00 33.11 5.19
1943 2042 5.786311 TCATGGAAAAGATTTTGAAGCTGG 58.214 37.500 0.00 0.00 0.00 4.85
1964 2063 4.103153 TGGAGTTTTGTCCAATGTCTCTCT 59.897 41.667 0.00 0.00 44.01 3.10
1965 2064 4.693095 GGAGTTTTGTCCAATGTCTCTCTC 59.307 45.833 0.00 0.00 36.51 3.20
1966 2065 5.296151 AGTTTTGTCCAATGTCTCTCTCA 57.704 39.130 0.00 0.00 0.00 3.27
1967 2066 5.059833 AGTTTTGTCCAATGTCTCTCTCAC 58.940 41.667 0.00 0.00 0.00 3.51
1993 2092 8.792830 TCACTTTTTCTCTTCTCTTTTCTTGA 57.207 30.769 0.00 0.00 0.00 3.02
2085 2184 9.990360 TGTTATGTCAGTATTTTGTTGAGAGTA 57.010 29.630 0.00 0.00 0.00 2.59
2089 2188 5.932303 GTCAGTATTTTGTTGAGAGTAGCCA 59.068 40.000 0.00 0.00 0.00 4.75
2106 2205 4.510038 AGCCAAAGATGAAACATCACAC 57.490 40.909 13.06 0.28 0.00 3.82
2113 2212 8.298854 CCAAAGATGAAACATCACACTCATAAA 58.701 33.333 13.06 0.00 0.00 1.40
2115 2214 9.850628 AAAGATGAAACATCACACTCATAAATG 57.149 29.630 13.06 0.00 0.00 2.32
2138 2237 7.727578 TGTATGAAGTACTAATCTTGGGTCA 57.272 36.000 0.00 0.00 34.27 4.02
2158 2257 6.410540 GGTCATGGATATAATTCTCCTCCAC 58.589 44.000 0.00 0.00 38.74 4.02
2162 2261 5.158141 TGGATATAATTCTCCTCCACTGCT 58.842 41.667 3.97 0.00 31.19 4.24
2171 2270 0.177604 CCTCCACTGCTCTGCCTTAG 59.822 60.000 0.00 0.00 0.00 2.18
2178 2277 0.174389 TGCTCTGCCTTAGCTCGAAG 59.826 55.000 0.00 0.00 40.73 3.79
2247 2346 5.011943 CAGAAGTTTTGGGGGATTTGAATCA 59.988 40.000 6.11 0.00 37.15 2.57
2252 2351 6.730507 AGTTTTGGGGGATTTGAATCATAAGT 59.269 34.615 6.11 0.00 37.15 2.24
2280 2379 8.950007 TTTATTTTATCTTTTCTGGTGGAGGT 57.050 30.769 0.00 0.00 0.00 3.85
2281 2380 8.575649 TTATTTTATCTTTTCTGGTGGAGGTC 57.424 34.615 0.00 0.00 0.00 3.85
2282 2381 5.576563 TTTATCTTTTCTGGTGGAGGTCA 57.423 39.130 0.00 0.00 0.00 4.02
2285 2384 4.453480 TCTTTTCTGGTGGAGGTCATTT 57.547 40.909 0.00 0.00 0.00 2.32
2286 2385 4.144297 TCTTTTCTGGTGGAGGTCATTTG 58.856 43.478 0.00 0.00 0.00 2.32
2287 2386 2.584835 TTCTGGTGGAGGTCATTTGG 57.415 50.000 0.00 0.00 0.00 3.28
2288 2387 1.444933 TCTGGTGGAGGTCATTTGGT 58.555 50.000 0.00 0.00 0.00 3.67
2289 2388 1.780309 TCTGGTGGAGGTCATTTGGTT 59.220 47.619 0.00 0.00 0.00 3.67
2290 2389 2.162681 CTGGTGGAGGTCATTTGGTTC 58.837 52.381 0.00 0.00 0.00 3.62
2291 2390 1.496857 TGGTGGAGGTCATTTGGTTCA 59.503 47.619 0.00 0.00 0.00 3.18
2292 2391 1.886542 GGTGGAGGTCATTTGGTTCAC 59.113 52.381 0.00 0.00 0.00 3.18
2293 2392 2.582052 GTGGAGGTCATTTGGTTCACA 58.418 47.619 0.00 0.00 0.00 3.58
2341 2440 7.952930 TGTCCTAAGGATTCTATATGAGCTCTT 59.047 37.037 16.19 11.54 32.73 2.85
2346 2445 8.600449 AAGGATTCTATATGAGCTCTTTTTCG 57.400 34.615 16.19 0.00 0.00 3.46
2351 2450 2.409948 ATGAGCTCTTTTTCGGAGGG 57.590 50.000 16.19 0.00 0.00 4.30
2383 2482 3.826157 CCAACCCAAATCTCTTGCTACAA 59.174 43.478 0.00 0.00 0.00 2.41
2388 2487 5.416952 ACCCAAATCTCTTGCTACAATTCTG 59.583 40.000 0.00 0.00 0.00 3.02
2430 2560 5.263872 ACGGAGGGAGTATTAGAGATCAT 57.736 43.478 0.00 0.00 0.00 2.45
2431 2561 5.646215 ACGGAGGGAGTATTAGAGATCATT 58.354 41.667 0.00 0.00 0.00 2.57
2432 2562 5.478679 ACGGAGGGAGTATTAGAGATCATTG 59.521 44.000 0.00 0.00 0.00 2.82
2433 2563 5.105554 CGGAGGGAGTATTAGAGATCATTGG 60.106 48.000 0.00 0.00 0.00 3.16
2434 2564 5.337975 GGAGGGAGTATTAGAGATCATTGGC 60.338 48.000 0.00 0.00 0.00 4.52
2435 2565 5.158141 AGGGAGTATTAGAGATCATTGGCA 58.842 41.667 0.00 0.00 0.00 4.92
2436 2566 5.012561 AGGGAGTATTAGAGATCATTGGCAC 59.987 44.000 0.00 0.00 0.00 5.01
2458 2588 0.727398 GGCGGCAACATCTGTAGTTC 59.273 55.000 3.07 0.00 0.00 3.01
2459 2589 1.676014 GGCGGCAACATCTGTAGTTCT 60.676 52.381 3.07 0.00 0.00 3.01
2460 2590 1.661112 GCGGCAACATCTGTAGTTCTC 59.339 52.381 0.00 0.00 0.00 2.87
2461 2591 2.675317 GCGGCAACATCTGTAGTTCTCT 60.675 50.000 0.00 0.00 0.00 3.10
2497 2627 9.717892 GATAGGATTTCAATTCTACGTTTTTCC 57.282 33.333 0.00 0.00 29.50 3.13
2546 2676 3.706086 AGAGGCCTTGAATTGTTTTGTGT 59.294 39.130 6.77 0.00 0.00 3.72
2569 2699 4.398044 TGGAACTCAAACAGAACCAACTTC 59.602 41.667 0.00 0.00 31.49 3.01
2588 2718 8.385849 CCAACTTCTGGTTTCTGAAAGAGATGA 61.386 40.741 20.53 8.48 42.17 2.92
2612 2742 1.272147 GGAGTTGCCTTCCACATTCCT 60.272 52.381 0.00 0.00 34.74 3.36
2617 2747 2.676748 TGCCTTCCACATTCCTTTTGT 58.323 42.857 0.00 0.00 0.00 2.83
2622 2752 4.262164 CCTTCCACATTCCTTTTGTCCAAG 60.262 45.833 0.00 0.00 0.00 3.61
2623 2753 2.627699 TCCACATTCCTTTTGTCCAAGC 59.372 45.455 0.00 0.00 0.00 4.01
2630 2760 5.675684 TTCCTTTTGTCCAAGCTTTTCTT 57.324 34.783 0.00 0.00 34.78 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 1.475751 CCCCCGTTTCTCTGATGATGG 60.476 57.143 0.00 0.00 0.00 3.51
140 141 1.891919 GCGCAACACTTCTGGGACA 60.892 57.895 0.30 0.00 0.00 4.02
163 164 4.142227 GGAGCATGCTCTCATTCATTGTTT 60.142 41.667 38.84 6.15 42.38 2.83
219 220 5.755861 TCGTCATATTGCACCAATTAATCGA 59.244 36.000 0.00 0.00 35.54 3.59
288 289 4.991056 CCGAAAATGAGAGTCTTCTTGTGA 59.009 41.667 0.00 0.00 32.53 3.58
292 293 6.814146 GTCATACCGAAAATGAGAGTCTTCTT 59.186 38.462 0.00 0.00 34.12 2.52
297 298 6.535150 TGAATGTCATACCGAAAATGAGAGTC 59.465 38.462 10.20 10.20 40.26 3.36
305 306 6.176896 TGGAAGATGAATGTCATACCGAAAA 58.823 36.000 0.00 0.00 37.20 2.29
323 324 1.140852 CGTGGATGGCCTTATGGAAGA 59.859 52.381 3.32 0.00 34.25 2.87
324 325 1.140852 TCGTGGATGGCCTTATGGAAG 59.859 52.381 3.32 0.00 34.57 3.46
337 338 7.275183 TCAAAAGATGATCAATAGTCGTGGAT 58.725 34.615 0.00 0.00 31.50 3.41
343 344 7.254590 CGGAACCTCAAAAGATGATCAATAGTC 60.255 40.741 0.00 0.00 37.44 2.59
358 359 1.294138 CGGCTACCGGAACCTCAAA 59.706 57.895 9.46 0.00 44.15 2.69
359 360 2.975536 CGGCTACCGGAACCTCAA 59.024 61.111 9.46 0.00 44.15 3.02
409 411 3.454371 GGTGTACCGTGCTCTAATGAT 57.546 47.619 0.00 0.00 0.00 2.45
427 429 3.069158 AGCAACTACACTGTAAAGACGGT 59.931 43.478 0.00 0.00 46.63 4.83
435 437 5.633601 CGAGAAATCAAGCAACTACACTGTA 59.366 40.000 0.00 0.00 0.00 2.74
449 451 3.571828 TGTTTGGGCATTCGAGAAATCAA 59.428 39.130 0.00 0.00 0.00 2.57
469 471 4.352298 AGAGGGAAGTGAGGATTCTTTTGT 59.648 41.667 0.00 0.00 0.00 2.83
485 487 8.401955 AAACATTCCTATTAGGTAAGAGGGAA 57.598 34.615 9.57 6.86 43.19 3.97
494 496 7.816411 AGCCATTCTAAACATTCCTATTAGGT 58.184 34.615 9.57 0.00 36.53 3.08
525 527 3.006247 GGAGACTTTCATTGCTCCAGAC 58.994 50.000 0.00 0.00 44.91 3.51
531 533 3.330701 TGGTTAGGGAGACTTTCATTGCT 59.669 43.478 0.00 0.00 0.00 3.91
577 579 4.711949 CAACTCTGCTGGGCGCCT 62.712 66.667 28.56 0.00 38.05 5.52
579 581 4.704833 TCCAACTCTGCTGGGCGC 62.705 66.667 0.00 0.00 34.46 6.53
580 582 2.743928 GTCCAACTCTGCTGGGCG 60.744 66.667 0.00 0.00 34.46 6.13
581 583 1.376553 GAGTCCAACTCTGCTGGGC 60.377 63.158 0.00 0.00 41.88 5.36
582 584 0.397941 TTGAGTCCAACTCTGCTGGG 59.602 55.000 8.44 0.00 45.27 4.45
594 596 5.242838 ACGATTCAGAGGATAGATTGAGTCC 59.757 44.000 0.00 0.00 0.00 3.85
600 602 4.021544 GCTCCACGATTCAGAGGATAGATT 60.022 45.833 0.00 0.00 30.74 2.40
628 630 3.364441 TGCGGCCTACACGTACGT 61.364 61.111 16.72 16.72 0.00 3.57
629 631 2.877582 GTGCGGCCTACACGTACG 60.878 66.667 15.01 15.01 37.22 3.67
630 632 2.507769 GGTGCGGCCTACACGTAC 60.508 66.667 16.80 5.94 44.40 3.67
651 657 0.895530 TCGGTACTTCTTCTGGGCAG 59.104 55.000 0.00 0.00 0.00 4.85
667 677 1.364171 CTTCGGCTGGGTAGATCGG 59.636 63.158 0.00 0.00 0.00 4.18
753 763 2.728007 CTGGGGGAAGAGATTTGGTTC 58.272 52.381 0.00 0.00 0.00 3.62
772 782 1.165270 GCGTGGTGGATTACTTTGCT 58.835 50.000 0.00 0.00 0.00 3.91
774 784 4.876107 AGATAAGCGTGGTGGATTACTTTG 59.124 41.667 0.00 0.00 0.00 2.77
795 812 4.081254 CCTTGATGTCATGTGGAGAAGAGA 60.081 45.833 0.00 0.00 0.00 3.10
796 813 4.081254 TCCTTGATGTCATGTGGAGAAGAG 60.081 45.833 0.00 0.00 0.00 2.85
797 814 3.840078 TCCTTGATGTCATGTGGAGAAGA 59.160 43.478 0.00 0.00 0.00 2.87
798 815 4.212143 TCCTTGATGTCATGTGGAGAAG 57.788 45.455 0.00 0.00 0.00 2.85
799 816 4.566278 CCTTCCTTGATGTCATGTGGAGAA 60.566 45.833 0.00 0.00 0.00 2.87
835 852 1.666580 GGTAGGTATGCGAGGAGGC 59.333 63.158 0.00 0.00 0.00 4.70
880 902 2.162809 GAGTGAAAGAGAGGGAGACGAC 59.837 54.545 0.00 0.00 0.00 4.34
955 1018 0.452585 GTCTCTCTGTGACTACGGCC 59.547 60.000 0.00 0.00 33.03 6.13
960 1023 1.822506 CACCGGTCTCTCTGTGACTA 58.177 55.000 2.59 0.00 35.04 2.59
964 1027 2.262915 GGCACCGGTCTCTCTGTG 59.737 66.667 2.59 0.00 0.00 3.66
1174 1243 2.943034 GTCATCGTCGTCGCCGTC 60.943 66.667 0.00 0.00 36.96 4.79
1175 1244 4.806481 CGTCATCGTCGTCGCCGT 62.806 66.667 0.00 0.00 36.96 5.68
1176 1245 4.509883 TCGTCATCGTCGTCGCCG 62.510 66.667 0.00 0.00 38.33 6.46
1177 1246 2.943034 GTCGTCATCGTCGTCGCC 60.943 66.667 0.00 0.00 38.33 5.54
1178 1247 3.295462 CGTCGTCATCGTCGTCGC 61.295 66.667 0.00 0.00 41.73 5.19
1179 1248 1.922220 GTCGTCGTCATCGTCGTCG 60.922 63.158 0.00 0.00 45.27 5.12
1180 1249 1.922220 CGTCGTCGTCATCGTCGTC 60.922 63.158 7.05 2.04 45.27 4.20
1181 1250 2.095282 CGTCGTCGTCATCGTCGT 59.905 61.111 7.05 0.00 45.27 4.34
1182 1251 1.922220 GTCGTCGTCGTCATCGTCG 60.922 63.158 1.33 1.62 46.06 5.12
1579 1660 2.125673 CCAGTCCTTGTACCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
1692 1773 3.305744 GCGGTAAAACAAACATGGATGGT 60.306 43.478 0.00 0.00 0.00 3.55
1693 1774 3.249917 GCGGTAAAACAAACATGGATGG 58.750 45.455 0.00 0.00 0.00 3.51
1694 1775 2.914214 CGCGGTAAAACAAACATGGATG 59.086 45.455 0.00 0.00 0.00 3.51
1695 1776 2.814919 TCGCGGTAAAACAAACATGGAT 59.185 40.909 6.13 0.00 0.00 3.41
1696 1777 2.219458 TCGCGGTAAAACAAACATGGA 58.781 42.857 6.13 0.00 0.00 3.41
1798 1886 5.734311 ACGTTGTATACCGTATACGTGTAC 58.266 41.667 22.87 20.19 43.05 2.90
1799 1887 5.977171 ACGTTGTATACCGTATACGTGTA 57.023 39.130 22.87 21.80 43.05 2.90
1810 1902 5.569059 GTGTGTGTACAGTACGTTGTATACC 59.431 44.000 18.72 12.94 41.92 2.73
1818 1910 2.864882 GCATGGTGTGTGTACAGTACGT 60.865 50.000 6.23 0.00 37.52 3.57
1869 1961 2.238646 ACGGCCCTATCATGAAAAGTCA 59.761 45.455 0.00 0.00 38.41 3.41
1871 1963 2.238646 TCACGGCCCTATCATGAAAAGT 59.761 45.455 0.00 0.00 0.00 2.66
1943 2042 5.178438 GTGAGAGAGACATTGGACAAAACTC 59.822 44.000 0.00 0.00 0.00 3.01
1964 2063 8.043710 AGAAAAGAGAAGAGAAAAAGTGAGTGA 58.956 33.333 0.00 0.00 0.00 3.41
1965 2064 8.207521 AGAAAAGAGAAGAGAAAAAGTGAGTG 57.792 34.615 0.00 0.00 0.00 3.51
1966 2065 8.672815 CAAGAAAAGAGAAGAGAAAAAGTGAGT 58.327 33.333 0.00 0.00 0.00 3.41
1967 2066 8.887717 TCAAGAAAAGAGAAGAGAAAAAGTGAG 58.112 33.333 0.00 0.00 0.00 3.51
2039 2138 3.119637 ACAAAATAATCAAAGCGGGTCCG 60.120 43.478 4.85 4.85 43.09 4.79
2041 2140 7.033185 ACATAACAAAATAATCAAAGCGGGTC 58.967 34.615 0.00 0.00 0.00 4.46
2045 2144 8.673626 ACTGACATAACAAAATAATCAAAGCG 57.326 30.769 0.00 0.00 0.00 4.68
2085 2184 4.147321 AGTGTGATGTTTCATCTTTGGCT 58.853 39.130 10.40 1.26 33.56 4.75
2089 2188 9.850628 CATTTATGAGTGTGATGTTTCATCTTT 57.149 29.630 10.40 0.00 33.56 2.52
2113 2212 8.319057 TGACCCAAGATTAGTACTTCATACAT 57.681 34.615 0.00 0.00 36.09 2.29
2115 2214 7.657761 CCATGACCCAAGATTAGTACTTCATAC 59.342 40.741 0.00 0.00 0.00 2.39
2118 2217 5.724370 TCCATGACCCAAGATTAGTACTTCA 59.276 40.000 0.00 0.00 0.00 3.02
2124 2223 9.965902 GAATTATATCCATGACCCAAGATTAGT 57.034 33.333 0.00 0.00 0.00 2.24
2138 2237 5.789575 AGCAGTGGAGGAGAATTATATCCAT 59.210 40.000 9.13 0.00 41.81 3.41
2158 2257 0.174389 TTCGAGCTAAGGCAGAGCAG 59.826 55.000 12.44 6.62 42.69 4.24
2162 2261 1.335182 CGATCTTCGAGCTAAGGCAGA 59.665 52.381 0.00 0.00 43.74 4.26
2194 2293 8.970691 AATTCGTTTGAATCAAAGATCGAATT 57.029 26.923 30.51 30.51 44.74 2.17
2196 2295 8.795786 AAAATTCGTTTGAATCAAAGATCGAA 57.204 26.923 24.35 24.35 44.02 3.71
2198 2297 9.112789 TGTAAAATTCGTTTGAATCAAAGATCG 57.887 29.630 8.88 9.47 44.02 3.69
2205 2304 9.796120 AAACTTCTGTAAAATTCGTTTGAATCA 57.204 25.926 0.00 0.00 44.02 2.57
2258 2357 6.552008 TGACCTCCACCAGAAAAGATAAAAT 58.448 36.000 0.00 0.00 0.00 1.82
2266 2365 3.230134 CCAAATGACCTCCACCAGAAAA 58.770 45.455 0.00 0.00 0.00 2.29
2268 2367 1.780309 ACCAAATGACCTCCACCAGAA 59.220 47.619 0.00 0.00 0.00 3.02
2269 2368 1.444933 ACCAAATGACCTCCACCAGA 58.555 50.000 0.00 0.00 0.00 3.86
2270 2369 2.162681 GAACCAAATGACCTCCACCAG 58.837 52.381 0.00 0.00 0.00 4.00
2271 2370 1.496857 TGAACCAAATGACCTCCACCA 59.503 47.619 0.00 0.00 0.00 4.17
2272 2371 1.886542 GTGAACCAAATGACCTCCACC 59.113 52.381 0.00 0.00 0.00 4.61
2273 2372 2.554032 CTGTGAACCAAATGACCTCCAC 59.446 50.000 0.00 0.00 0.00 4.02
2274 2373 2.488891 CCTGTGAACCAAATGACCTCCA 60.489 50.000 0.00 0.00 0.00 3.86
2275 2374 2.162681 CCTGTGAACCAAATGACCTCC 58.837 52.381 0.00 0.00 0.00 4.30
2276 2375 3.140325 TCCTGTGAACCAAATGACCTC 57.860 47.619 0.00 0.00 0.00 3.85
2277 2376 3.814504 ATCCTGTGAACCAAATGACCT 57.185 42.857 0.00 0.00 0.00 3.85
2278 2377 4.280677 TCAAATCCTGTGAACCAAATGACC 59.719 41.667 0.00 0.00 0.00 4.02
2279 2378 5.452078 TCAAATCCTGTGAACCAAATGAC 57.548 39.130 0.00 0.00 0.00 3.06
2280 2379 6.669125 ATTCAAATCCTGTGAACCAAATGA 57.331 33.333 0.00 0.00 37.80 2.57
2281 2380 6.956299 GATTCAAATCCTGTGAACCAAATG 57.044 37.500 0.00 0.00 37.80 2.32
2327 2426 5.011125 CCCTCCGAAAAAGAGCTCATATAGA 59.989 44.000 17.77 2.79 0.00 1.98
2329 2428 4.899457 TCCCTCCGAAAAAGAGCTCATATA 59.101 41.667 17.77 0.00 0.00 0.86
2336 2435 2.186532 ACTTCCCTCCGAAAAAGAGC 57.813 50.000 0.00 0.00 0.00 4.09
2351 2450 3.641436 AGATTTGGGTTGGTGGAAACTTC 59.359 43.478 0.00 0.00 0.00 3.01
2388 2487 9.983804 CCTCCGTAAAGAAATATACAAGAAAAC 57.016 33.333 0.00 0.00 0.00 2.43
2406 2536 6.196918 TGATCTCTAATACTCCCTCCGTAA 57.803 41.667 0.00 0.00 0.00 3.18
2430 2560 3.910490 GTTGCCGCCAAGTGCCAA 61.910 61.111 0.00 0.00 36.24 4.52
2432 2562 3.631487 GATGTTGCCGCCAAGTGCC 62.631 63.158 0.00 0.00 36.24 5.01
2433 2563 2.126346 GATGTTGCCGCCAAGTGC 60.126 61.111 0.00 0.00 0.00 4.40
2434 2564 1.210931 CAGATGTTGCCGCCAAGTG 59.789 57.895 0.00 0.00 0.00 3.16
2435 2565 0.036164 TACAGATGTTGCCGCCAAGT 59.964 50.000 0.00 0.00 0.00 3.16
2436 2566 0.729116 CTACAGATGTTGCCGCCAAG 59.271 55.000 0.00 0.00 0.00 3.61
2486 2616 2.812011 CAGGGGAACAGGAAAAACGTAG 59.188 50.000 0.00 0.00 0.00 3.51
2497 2627 2.196595 TGTAGGATTCCAGGGGAACAG 58.803 52.381 5.29 0.00 45.07 3.16
2546 2676 3.963129 AGTTGGTTCTGTTTGAGTTCCA 58.037 40.909 0.00 0.00 0.00 3.53
2569 2699 5.125097 CCCAATCATCTCTTTCAGAAACCAG 59.875 44.000 0.00 0.00 33.62 4.00
2612 2742 5.675684 AGGAAAGAAAAGCTTGGACAAAA 57.324 34.783 0.00 0.00 36.80 2.44
2617 2747 4.709397 TCAACAAGGAAAGAAAAGCTTGGA 59.291 37.500 0.00 0.00 36.80 3.53
2622 2752 6.276091 ACAGAATCAACAAGGAAAGAAAAGC 58.724 36.000 0.00 0.00 0.00 3.51
2623 2753 8.840321 TCTACAGAATCAACAAGGAAAGAAAAG 58.160 33.333 0.00 0.00 0.00 2.27
2630 2760 4.997395 GTGCTCTACAGAATCAACAAGGAA 59.003 41.667 0.00 0.00 0.00 3.36



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

AutoCloner maintained by Alex Coulton.