Multiple sequence alignment - TraesCS4B01G196700

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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 TraesCS4B01G196700 chr4B 100.000 4499 0 0 1 4499 423771040 423775538 0.000000e+00 8309.0
1 TraesCS4B01G196700 chr4B 97.531 324 8 0 4176 4499 424062264 424061941 5.080000e-154 555.0
2 TraesCS4B01G196700 chr4B 74.414 469 106 10 1 463 530017932 530017472 5.940000e-44 189.0
3 TraesCS4B01G196700 chr4B 83.766 154 10 8 2272 2411 366930300 366930148 1.020000e-26 132.0
4 TraesCS4B01G196700 chr4D 92.450 2980 125 40 512 3450 341691500 341694420 0.000000e+00 4165.0
5 TraesCS4B01G196700 chr4D 96.296 918 21 6 3590 4499 341694527 341695439 0.000000e+00 1495.0
6 TraesCS4B01G196700 chr4D 97.531 324 8 0 4176 4499 341924918 341924595 5.080000e-154 555.0
7 TraesCS4B01G196700 chr4D 84.564 149 9 7 2276 2411 296729541 296729394 7.850000e-28 135.0
8 TraesCS4B01G196700 chr4D 95.946 74 2 1 3522 3595 341694419 341694491 7.910000e-23 119.0
9 TraesCS4B01G196700 chr4D 81.818 154 13 9 2272 2412 481578910 481578759 1.020000e-21 115.0
10 TraesCS4B01G196700 chr4A 89.976 2973 144 60 512 3419 125041641 125038758 0.000000e+00 3698.0
11 TraesCS4B01G196700 chr4A 89.836 915 44 23 3620 4499 125030476 125029576 0.000000e+00 1129.0
12 TraesCS4B01G196700 chr4A 89.744 507 50 2 1 505 125042217 125041711 0.000000e+00 647.0
13 TraesCS4B01G196700 chr4A 96.605 324 11 0 4176 4499 124403980 124404303 5.120000e-149 538.0
14 TraesCS4B01G196700 chr4A 95.556 45 2 0 3471 3515 125030938 125030894 6.240000e-09 73.1
15 TraesCS4B01G196700 chr7D 84.024 507 78 3 1 505 254126185 254125680 6.770000e-133 484.0
16 TraesCS4B01G196700 chr5D 92.492 333 24 1 4167 4499 483226874 483227205 4.070000e-130 475.0
17 TraesCS4B01G196700 chr5D 92.705 329 24 0 4171 4499 483370493 483370821 4.070000e-130 475.0
18 TraesCS4B01G196700 chr5B 92.447 331 24 1 4169 4499 593658387 593658716 5.270000e-129 472.0
19 TraesCS4B01G196700 chr5A 92.169 332 25 1 4168 4499 603793416 603793746 6.810000e-128 468.0
20 TraesCS4B01G196700 chr6B 83.071 508 80 6 1 505 469273746 469274250 1.480000e-124 457.0
21 TraesCS4B01G196700 chr6B 79.398 432 80 6 66 496 129557127 129557550 3.400000e-76 296.0
22 TraesCS4B01G196700 chr7B 83.979 387 57 4 117 501 580728051 580728434 2.560000e-97 366.0
23 TraesCS4B01G196700 chr7B 84.713 157 8 10 2268 2411 477814816 477814969 4.690000e-30 143.0
24 TraesCS4B01G196700 chr6D 78.935 432 84 3 66 496 57518054 57518479 2.050000e-73 287.0
25 TraesCS4B01G196700 chr1B 86.452 155 8 6 2269 2411 632021080 632020927 1.680000e-34 158.0
26 TraesCS4B01G196700 chr3B 83.217 143 14 9 2264 2397 476956016 476956157 6.110000e-24 122.0
27 TraesCS4B01G196700 chr1A 81.333 150 17 9 2271 2411 340012303 340012450 1.320000e-20 111.0


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 TraesCS4B01G196700 chr4B 423771040 423775538 4498 False 8309.000000 8309 100.000000 1 4499 1 chr4B.!!$F1 4498
1 TraesCS4B01G196700 chr4D 341691500 341695439 3939 False 1926.333333 4165 94.897333 512 4499 3 chr4D.!!$F1 3987
2 TraesCS4B01G196700 chr4A 125038758 125042217 3459 True 2172.500000 3698 89.860000 1 3419 2 chr4A.!!$R2 3418
3 TraesCS4B01G196700 chr4A 125029576 125030938 1362 True 601.050000 1129 92.696000 3471 4499 2 chr4A.!!$R1 1028
4 TraesCS4B01G196700 chr7D 254125680 254126185 505 True 484.000000 484 84.024000 1 505 1 chr7D.!!$R1 504
5 TraesCS4B01G196700 chr6B 469273746 469274250 504 False 457.000000 457 83.071000 1 505 1 chr6B.!!$F2 504

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
846 924 0.030638 GCAAAGCAAGAAGGCGACAA 59.969 50.0 0.0 0.0 39.27 3.18 F
1593 1681 0.099436 CTGCCGTTGCTTAATCCAGC 59.901 55.0 0.0 0.0 40.55 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2737 2852 0.250684 TCTTTTGAGCGGTGATGCCA 60.251 50.000 0.0 0.0 36.97 4.92 R
3549 3694 1.004277 GGCCTACTGGTGAAATGTGGA 59.996 52.381 0.0 0.0 35.27 4.02 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
103 104 5.469084 CGGAATTACTTGGAATAGGTAAGGC 59.531 44.000 0.00 0.00 34.77 4.35
104 105 6.602278 GGAATTACTTGGAATAGGTAAGGCT 58.398 40.000 0.00 0.00 34.77 4.58
175 176 5.162075 AGACGAACTAAATGGAAGACGAAG 58.838 41.667 0.00 0.00 0.00 3.79
192 193 0.459237 AAGATGCTTGCCGAGACGAG 60.459 55.000 0.00 0.00 0.00 4.18
251 254 9.850628 CAAGAGAAAGAAAATCTTGCATCATTA 57.149 29.630 1.15 0.00 42.32 1.90
254 257 9.798994 GAGAAAGAAAATCTTGCATCATTATGT 57.201 29.630 1.15 0.00 36.71 2.29
385 388 1.591703 GCCAGGACTGTCACATCGA 59.408 57.895 10.38 0.00 0.00 3.59
414 417 0.534427 ATCCGAGTGCATGCATCCTG 60.534 55.000 25.64 14.49 0.00 3.86
418 421 1.747709 GAGTGCATGCATCCTGAACT 58.252 50.000 25.64 14.20 35.10 3.01
463 466 8.964420 ATTTCATAGTTACAAAATTGTCACGG 57.036 30.769 1.37 0.00 42.35 4.94
489 492 6.524101 AAAGGAACAGACAGAGACTAGATC 57.476 41.667 0.00 0.00 0.00 2.75
505 508 7.958088 AGACTAGATCTTTGATAAGGTTAGGC 58.042 38.462 0.00 0.00 31.62 3.93
506 509 7.787424 AGACTAGATCTTTGATAAGGTTAGGCT 59.213 37.037 0.00 0.00 31.62 4.58
511 514 8.718656 AGATCTTTGATAAGGTTAGGCTAATGT 58.281 33.333 10.65 1.70 32.02 2.71
512 515 9.343539 GATCTTTGATAAGGTTAGGCTAATGTT 57.656 33.333 10.65 9.38 32.02 2.71
514 517 9.528489 TCTTTGATAAGGTTAGGCTAATGTTTT 57.472 29.630 10.65 5.67 32.02 2.43
542 608 3.123620 GCTGCTCAGGAAGTGCCG 61.124 66.667 0.00 0.00 43.43 5.69
543 609 2.659016 CTGCTCAGGAAGTGCCGA 59.341 61.111 0.00 0.00 43.43 5.54
568 634 1.586154 GGTGAAGGATGTTGGTGCCG 61.586 60.000 0.00 0.00 0.00 5.69
571 637 0.321653 GAAGGATGTTGGTGCCGAGT 60.322 55.000 0.00 0.00 0.00 4.18
573 639 0.110486 AGGATGTTGGTGCCGAGTTT 59.890 50.000 0.00 0.00 0.00 2.66
589 655 4.323562 CCGAGTTTAGGGGATTCTTCAGTT 60.324 45.833 0.00 0.00 0.00 3.16
646 712 4.952262 TTGTGCAAAAGCTAGCTATCTG 57.048 40.909 19.70 15.93 0.00 2.90
650 716 3.562973 TGCAAAAGCTAGCTATCTGATGC 59.437 43.478 19.70 20.08 0.00 3.91
804 872 4.697352 AGCCGATGAATAATATGAACTGCC 59.303 41.667 0.00 0.00 0.00 4.85
805 873 4.697352 GCCGATGAATAATATGAACTGCCT 59.303 41.667 0.00 0.00 0.00 4.75
845 923 1.654220 GCAAAGCAAGAAGGCGACA 59.346 52.632 0.00 0.00 39.27 4.35
846 924 0.030638 GCAAAGCAAGAAGGCGACAA 59.969 50.000 0.00 0.00 39.27 3.18
847 925 1.758783 CAAAGCAAGAAGGCGACAAC 58.241 50.000 0.00 0.00 39.27 3.32
848 926 1.065401 CAAAGCAAGAAGGCGACAACA 59.935 47.619 0.00 0.00 39.27 3.33
849 927 1.388547 AAGCAAGAAGGCGACAACAA 58.611 45.000 0.00 0.00 39.27 2.83
850 928 0.947244 AGCAAGAAGGCGACAACAAG 59.053 50.000 0.00 0.00 39.27 3.16
851 929 0.661483 GCAAGAAGGCGACAACAAGC 60.661 55.000 0.00 0.00 0.00 4.01
852 930 0.947244 CAAGAAGGCGACAACAAGCT 59.053 50.000 0.00 0.00 0.00 3.74
853 931 1.069636 CAAGAAGGCGACAACAAGCTC 60.070 52.381 0.00 0.00 0.00 4.09
854 932 0.106708 AGAAGGCGACAACAAGCTCA 59.893 50.000 0.00 0.00 0.00 4.26
855 933 0.944386 GAAGGCGACAACAAGCTCAA 59.056 50.000 0.00 0.00 0.00 3.02
856 934 1.333619 GAAGGCGACAACAAGCTCAAA 59.666 47.619 0.00 0.00 0.00 2.69
857 935 1.388547 AGGCGACAACAAGCTCAAAA 58.611 45.000 0.00 0.00 0.00 2.44
858 936 1.748493 AGGCGACAACAAGCTCAAAAA 59.252 42.857 0.00 0.00 0.00 1.94
1040 1118 3.292936 ACCCCGGCTAGCGTATCG 61.293 66.667 9.00 6.38 0.00 2.92
1126 1210 3.774336 TCCCGCCTCCCTACCCAT 61.774 66.667 0.00 0.00 0.00 4.00
1156 1240 3.530104 GCCGTGACGTTACTCGCG 61.530 66.667 8.95 0.00 44.19 5.87
1250 1334 1.896465 CTTTCCCCTTCTCGTGTCTCT 59.104 52.381 0.00 0.00 0.00 3.10
1277 1361 0.857675 TCCACCTCCCCATCGAGATA 59.142 55.000 0.00 0.00 30.97 1.98
1326 1410 1.815408 GCAGACCCAAGAACAGCTGAA 60.815 52.381 23.35 0.00 0.00 3.02
1395 1481 4.152402 GGTGTGCTTAGTTACTGACATGTG 59.848 45.833 1.15 0.00 0.00 3.21
1497 1583 0.326927 TCCCAATCACGGAAGGTTCC 59.673 55.000 0.00 0.00 44.05 3.62
1526 1612 3.576356 CGGCGCGCCATCTCAATT 61.576 61.111 45.26 0.00 35.37 2.32
1527 1613 2.800736 GGCGCGCCATCTCAATTT 59.199 55.556 43.55 0.00 35.81 1.82
1528 1614 1.139520 GGCGCGCCATCTCAATTTT 59.860 52.632 43.55 0.00 35.81 1.82
1588 1676 0.240945 GTGCACTGCCGTTGCTTAAT 59.759 50.000 10.32 0.00 38.71 1.40
1593 1681 0.099436 CTGCCGTTGCTTAATCCAGC 59.901 55.000 0.00 0.00 40.55 4.85
1616 1704 5.240403 GCTTGGATTTTCTCTCTCTTGTGTT 59.760 40.000 0.00 0.00 0.00 3.32
1699 1787 2.361438 GGTAAGCTCTACATGCCGTAGT 59.639 50.000 9.51 0.00 46.66 2.73
1719 1807 6.808704 CGTAGTGGTGACATGGATATATCAAG 59.191 42.308 14.60 6.00 46.14 3.02
1728 1816 8.156165 TGACATGGATATATCAAGTACAATGCA 58.844 33.333 14.60 0.00 0.00 3.96
1730 1818 9.524496 ACATGGATATATCAAGTACAATGCAAT 57.476 29.630 14.60 0.00 0.00 3.56
1740 1828 9.979578 ATCAAGTACAATGCAATTTTTGACTAA 57.020 25.926 4.82 0.00 31.22 2.24
1763 1851 0.729116 CTGCTAAACACGGATGCCTG 59.271 55.000 0.00 0.00 0.00 4.85
1806 1896 1.705745 GGAACTCTTTGGGAGGACCTT 59.294 52.381 0.00 0.00 45.83 3.50
2049 2139 4.641541 TGGAATCTATTGCATGTGGTTCAG 59.358 41.667 0.00 0.00 33.04 3.02
2334 2427 9.147732 TGTCTGAATTGGATGTATATAGACACT 57.852 33.333 1.52 0.00 37.63 3.55
2335 2428 9.416794 GTCTGAATTGGATGTATATAGACACTG 57.583 37.037 1.52 0.00 33.94 3.66
2336 2429 8.588472 TCTGAATTGGATGTATATAGACACTGG 58.412 37.037 1.52 0.00 30.52 4.00
2439 2545 3.388024 AGTTCTTAACAGCAGAGGTGACA 59.612 43.478 2.94 0.00 34.87 3.58
2495 2601 5.867174 AGGAAAACTTTGTGTACAACTTTGC 59.133 36.000 0.00 3.94 35.28 3.68
2508 2614 7.693951 GTGTACAACTTTGCTCACATATCATTC 59.306 37.037 0.00 0.00 36.13 2.67
2678 2793 6.271585 ACCATCAATTCATAATCCTGGACT 57.728 37.500 0.00 0.00 0.00 3.85
2916 3053 3.155167 GGCCTAGGGACGTGGAGG 61.155 72.222 11.72 0.00 0.00 4.30
3016 3153 2.217112 GCACATGCCGATAGACGAC 58.783 57.895 0.00 0.00 45.77 4.34
3063 3200 2.566913 TGCTGCTCGACCTGTTTAAAA 58.433 42.857 0.00 0.00 0.00 1.52
3128 3265 7.108841 TGTGGCTAACTTAGAATGGTACTAG 57.891 40.000 0.00 0.00 0.00 2.57
3134 3271 6.793505 AACTTAGAATGGTACTAGGTCAGG 57.206 41.667 0.00 0.00 30.89 3.86
3268 3405 8.887036 TTGATGTATACAAGATACACCATGTC 57.113 34.615 10.14 0.00 37.33 3.06
3275 3412 5.601662 ACAAGATACACCATGTCCTATTCG 58.398 41.667 0.00 0.00 0.00 3.34
3359 3497 4.327357 ACTCGAATTGCTAAACTCGACATG 59.673 41.667 0.00 0.00 35.52 3.21
3367 3505 5.534407 TGCTAAACTCGACATGACACTTTA 58.466 37.500 0.00 0.00 0.00 1.85
3386 3531 5.105023 ACTTTAGAACGGTCTTATTCCCTCC 60.105 44.000 9.04 0.00 35.12 4.30
3387 3532 2.829023 AGAACGGTCTTATTCCCTCCA 58.171 47.619 0.00 0.00 0.00 3.86
3475 3620 5.305644 CAGAGGGGTACTATACATCAGCTTT 59.694 44.000 0.00 0.00 0.00 3.51
3476 3621 5.905913 AGAGGGGTACTATACATCAGCTTTT 59.094 40.000 0.00 0.00 0.00 2.27
3509 3654 0.462047 CCAAGGTGAGGATGTACCGC 60.462 60.000 0.00 0.00 44.74 5.68
3510 3655 0.462047 CAAGGTGAGGATGTACCGCC 60.462 60.000 0.00 0.00 44.74 6.13
3511 3656 1.956629 AAGGTGAGGATGTACCGCCG 61.957 60.000 0.00 0.00 44.74 6.46
3512 3657 2.106332 GTGAGGATGTACCGCCGG 59.894 66.667 0.00 0.00 44.74 6.13
3513 3658 3.845259 TGAGGATGTACCGCCGGC 61.845 66.667 19.07 19.07 44.74 6.13
3514 3659 3.537874 GAGGATGTACCGCCGGCT 61.538 66.667 26.68 9.55 44.74 5.52
3515 3660 3.792053 GAGGATGTACCGCCGGCTG 62.792 68.421 26.68 21.87 44.74 4.85
3516 3661 4.910585 GGATGTACCGCCGGCTGG 62.911 72.222 28.27 28.27 38.77 4.85
3564 3709 1.238439 CGCTTCCACATTTCACCAGT 58.762 50.000 0.00 0.00 0.00 4.00
3568 3713 2.489938 TCCACATTTCACCAGTAGGC 57.510 50.000 0.00 0.00 39.06 3.93
3683 4197 6.406400 GGGTGTATGCTAATTATTTTGCACCA 60.406 38.462 20.27 10.50 44.33 4.17
3703 4217 5.804473 CACCATTTATTTGCGCATTAGTTCA 59.196 36.000 12.75 0.00 0.00 3.18
3717 4231 7.044706 GCGCATTAGTTCAGATTTGATTGTAAC 60.045 37.037 0.30 0.00 32.27 2.50
3741 4265 4.970662 ACTGCATTTTACTACATGGCTG 57.029 40.909 0.00 0.00 0.00 4.85
3788 4313 6.769822 TCAAAGCCTATGATTTTTGCCAAAAA 59.230 30.769 16.94 16.94 43.76 1.94
3802 4327 9.798994 TTTTTGCCAAAAATTTCGTAGTTAGTA 57.201 25.926 11.16 0.00 35.57 1.82
3803 4328 8.785468 TTTGCCAAAAATTTCGTAGTTAGTAC 57.215 30.769 0.00 0.00 0.00 2.73
3804 4329 7.733402 TGCCAAAAATTTCGTAGTTAGTACT 57.267 32.000 0.00 0.00 38.44 2.73
3843 4368 6.096705 CCAACATTTTGGTCATGCCTCTATTA 59.903 38.462 2.21 0.00 46.63 0.98
3928 4453 6.128282 ACAACCTGCTATTATCACGACAAAAG 60.128 38.462 0.00 0.00 0.00 2.27
3930 4455 6.170506 ACCTGCTATTATCACGACAAAAGAA 58.829 36.000 0.00 0.00 0.00 2.52
4044 4586 1.487976 TCCATGTTTTGCCAAAAGCCA 59.512 42.857 2.15 0.00 42.71 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.229209 TGGACCTTTCCTCTCCGCT 60.229 57.895 0.00 0.00 43.31 5.52
78 79 6.687139 GCCTTACCTATTCCAAGTAATTCCGA 60.687 42.308 0.00 0.00 0.00 4.55
79 80 5.469084 GCCTTACCTATTCCAAGTAATTCCG 59.531 44.000 0.00 0.00 0.00 4.30
134 135 3.745975 CGTCTTCCACAGTTGCATCTTTA 59.254 43.478 0.00 0.00 0.00 1.85
175 176 0.249238 ATCTCGTCTCGGCAAGCATC 60.249 55.000 0.00 0.00 0.00 3.91
192 193 4.913376 GACAACCATACTTGTCATGCATC 58.087 43.478 0.00 0.00 46.38 3.91
247 250 2.009051 TCCGCTGCACTTCACATAATG 58.991 47.619 0.00 0.00 0.00 1.90
251 254 2.037136 GCTCCGCTGCACTTCACAT 61.037 57.895 0.00 0.00 0.00 3.21
254 257 4.704833 GGGCTCCGCTGCACTTCA 62.705 66.667 0.00 0.00 32.79 3.02
308 311 4.680537 ACCGGTCGCCCTCTCTGT 62.681 66.667 0.00 0.00 0.00 3.41
347 350 0.468400 GATCTCTACCCCGTCCAGCT 60.468 60.000 0.00 0.00 0.00 4.24
385 388 3.198409 TGCACTCGGATAATTCTGCAT 57.802 42.857 0.00 0.00 29.85 3.96
414 417 4.389374 TGATGGAGTTGGTTTCTCAGTTC 58.611 43.478 0.00 0.00 34.04 3.01
418 421 6.323482 TGAAATTTGATGGAGTTGGTTTCTCA 59.677 34.615 0.00 0.00 34.04 3.27
452 455 4.208746 TGTTCCTTTACCCGTGACAATTT 58.791 39.130 0.00 0.00 0.00 1.82
453 456 3.818773 CTGTTCCTTTACCCGTGACAATT 59.181 43.478 0.00 0.00 0.00 2.32
463 466 4.875561 AGTCTCTGTCTGTTCCTTTACC 57.124 45.455 0.00 0.00 0.00 2.85
516 519 0.106268 TCCTGAGCAGCCACCAAAAA 60.106 50.000 0.00 0.00 0.00 1.94
517 520 0.106268 TTCCTGAGCAGCCACCAAAA 60.106 50.000 0.00 0.00 0.00 2.44
542 608 1.815003 CAACATCCTTCACCTGCCTTC 59.185 52.381 0.00 0.00 0.00 3.46
543 609 1.548582 CCAACATCCTTCACCTGCCTT 60.549 52.381 0.00 0.00 0.00 4.35
568 634 6.715264 TCAAAACTGAAGAATCCCCTAAACTC 59.285 38.462 0.00 0.00 0.00 3.01
571 637 7.508977 ACAATCAAAACTGAAGAATCCCCTAAA 59.491 33.333 0.00 0.00 0.00 1.85
573 639 6.552008 ACAATCAAAACTGAAGAATCCCCTA 58.448 36.000 0.00 0.00 0.00 3.53
606 672 5.410067 CACAAACAAACACCAGTCAGAAAT 58.590 37.500 0.00 0.00 0.00 2.17
610 676 2.094803 TGCACAAACAAACACCAGTCAG 60.095 45.455 0.00 0.00 0.00 3.51
646 712 5.539582 TTACAAGTCACGTTAATGGCATC 57.460 39.130 0.00 0.00 0.00 3.91
650 716 9.261180 AGATCATATTACAAGTCACGTTAATGG 57.739 33.333 0.00 0.00 0.00 3.16
770 838 4.574599 ATTCATCGGCTTTATTTGCTCC 57.425 40.909 0.00 0.00 0.00 4.70
804 872 2.740055 GCCGTCAGCCACAGTGAG 60.740 66.667 0.62 0.00 34.35 3.51
858 936 1.599797 CCCCTGTCGTCGCCTTTTT 60.600 57.895 0.00 0.00 0.00 1.94
859 937 2.032071 CCCCTGTCGTCGCCTTTT 59.968 61.111 0.00 0.00 0.00 2.27
860 938 4.699522 GCCCCTGTCGTCGCCTTT 62.700 66.667 0.00 0.00 0.00 3.11
935 1013 1.424638 TAAGCATAGCCCTGACCTCC 58.575 55.000 0.00 0.00 0.00 4.30
1040 1118 1.604915 GGGAGACAAGGAGAAGGCC 59.395 63.158 0.00 0.00 0.00 5.19
1068 1146 3.458163 GATCGGAGGACGGCCACA 61.458 66.667 11.69 0.00 44.45 4.17
1144 1228 4.125695 AGGGCCGCGAGTAACGTC 62.126 66.667 8.23 0.00 44.60 4.34
1250 1334 2.454941 GGGAGGTGGAAGAGGGGA 59.545 66.667 0.00 0.00 0.00 4.81
1277 1361 9.434420 CGTGCCTTAGAGTACTACTACTATTAT 57.566 37.037 0.00 0.00 32.96 1.28
1326 1410 5.291128 CGTAGCCAAGTGATAAGTCGAAAAT 59.709 40.000 0.00 0.00 0.00 1.82
1395 1481 1.215382 GCAAATCTGGGAAACGGCC 59.785 57.895 0.00 0.00 0.00 6.13
1479 1565 2.868253 GGAACCTTCCGTGATTGGG 58.132 57.895 0.00 0.00 37.65 4.12
1497 1583 2.021380 GCGCCGCATCTAAACACG 59.979 61.111 3.15 0.00 0.00 4.49
1522 1608 6.237808 CGAACCAAAACAGGAGTTCAAAATTG 60.238 38.462 0.00 0.00 38.80 2.32
1523 1609 5.810074 CGAACCAAAACAGGAGTTCAAAATT 59.190 36.000 0.00 0.00 38.80 1.82
1524 1610 5.126384 TCGAACCAAAACAGGAGTTCAAAAT 59.874 36.000 0.00 0.00 38.80 1.82
1525 1611 4.459685 TCGAACCAAAACAGGAGTTCAAAA 59.540 37.500 0.00 0.00 38.80 2.44
1526 1612 4.011023 TCGAACCAAAACAGGAGTTCAAA 58.989 39.130 0.00 0.00 38.80 2.69
1527 1613 3.611970 TCGAACCAAAACAGGAGTTCAA 58.388 40.909 0.00 0.00 38.80 2.69
1528 1614 3.202906 CTCGAACCAAAACAGGAGTTCA 58.797 45.455 0.00 0.00 38.80 3.18
1593 1681 6.874288 AACACAAGAGAGAGAAAATCCAAG 57.126 37.500 0.00 0.00 0.00 3.61
1603 1691 8.744652 TCTCCTTTATCTAAACACAAGAGAGAG 58.255 37.037 0.00 0.00 0.00 3.20
1605 1693 9.364989 CTTCTCCTTTATCTAAACACAAGAGAG 57.635 37.037 0.00 0.00 0.00 3.20
1616 1704 6.497259 ACACTGTGTCCTTCTCCTTTATCTAA 59.503 38.462 7.80 0.00 0.00 2.10
1699 1787 7.610580 TGTACTTGATATATCCATGTCACCA 57.389 36.000 10.25 2.86 32.60 4.17
1730 1818 7.646130 CCGTGTTTAGCAGAAATTAGTCAAAAA 59.354 33.333 0.00 0.00 0.00 1.94
1738 1826 4.095782 GGCATCCGTGTTTAGCAGAAATTA 59.904 41.667 0.00 0.00 0.00 1.40
1739 1827 3.119495 GGCATCCGTGTTTAGCAGAAATT 60.119 43.478 0.00 0.00 0.00 1.82
1740 1828 2.423538 GGCATCCGTGTTTAGCAGAAAT 59.576 45.455 0.00 0.00 0.00 2.17
1743 1831 0.613260 AGGCATCCGTGTTTAGCAGA 59.387 50.000 0.00 0.00 0.00 4.26
1754 1842 2.545526 CTGTAAATGTAGCAGGCATCCG 59.454 50.000 0.00 0.00 0.00 4.18
1763 1851 3.274288 AGGCTCTTGCTGTAAATGTAGC 58.726 45.455 0.00 0.00 40.29 3.58
1806 1896 3.054948 CCGTACCTTCAATAACCTTCCCA 60.055 47.826 0.00 0.00 0.00 4.37
2049 2139 4.585955 TCTATCGCCATTCCAAGAGTAC 57.414 45.455 0.00 0.00 0.00 2.73
2250 2340 7.868415 GGAGTATATCAGTAACATCCAAGTCAC 59.132 40.741 0.00 0.00 0.00 3.67
2297 2390 8.912988 ACATCCAATTCAGACAAAAGTTAGAAA 58.087 29.630 0.00 0.00 0.00 2.52
2334 2427 6.097554 ACATTGAAATGAGTGTAACAAACCCA 59.902 34.615 9.94 0.00 38.54 4.51
2335 2428 6.420604 CACATTGAAATGAGTGTAACAAACCC 59.579 38.462 9.94 0.00 38.54 4.11
2336 2429 6.420604 CCACATTGAAATGAGTGTAACAAACC 59.579 38.462 9.94 0.00 38.54 3.27
2532 2638 3.307674 TGAAAAAGCACGCATTCATGAC 58.692 40.909 0.00 0.00 0.00 3.06
2630 2745 2.028130 AGTGGAGACTCGCCATAGAAG 58.972 52.381 4.65 0.00 35.49 2.85
2631 2746 2.145397 AGTGGAGACTCGCCATAGAA 57.855 50.000 4.65 0.00 35.49 2.10
2632 2747 2.145397 AAGTGGAGACTCGCCATAGA 57.855 50.000 4.65 0.00 35.49 1.98
2633 2748 2.166459 TGAAAGTGGAGACTCGCCATAG 59.834 50.000 4.65 0.00 35.49 2.23
2634 2749 2.176045 TGAAAGTGGAGACTCGCCATA 58.824 47.619 4.65 0.00 35.49 2.74
2635 2750 0.976641 TGAAAGTGGAGACTCGCCAT 59.023 50.000 4.65 0.00 35.49 4.40
2636 2751 0.756294 TTGAAAGTGGAGACTCGCCA 59.244 50.000 0.00 0.00 0.00 5.69
2637 2752 1.149148 GTTGAAAGTGGAGACTCGCC 58.851 55.000 0.00 0.00 0.00 5.54
2678 2793 5.698741 ATCAACTTCAGGGACATGATACA 57.301 39.130 0.00 0.00 0.00 2.29
2737 2852 0.250684 TCTTTTGAGCGGTGATGCCA 60.251 50.000 0.00 0.00 36.97 4.92
2784 2899 5.283717 GTGTGTATACAAAGAAAATGCAGCG 59.716 40.000 7.25 0.00 38.82 5.18
2916 3053 3.206150 TCAACACAAAGGTCTTGAGAGC 58.794 45.455 2.07 2.07 42.47 4.09
3016 3153 1.135083 AGTTGCTTGACCGGAGTATCG 60.135 52.381 9.46 0.00 34.37 2.92
3063 3200 1.535462 CAAGCCAACTCGGTCGAAAAT 59.465 47.619 0.00 0.00 36.97 1.82
3128 3265 2.687935 TGTTTTCTTCTTGCACCTGACC 59.312 45.455 0.00 0.00 0.00 4.02
3134 3271 8.655970 AGTTACAAAAATGTTTTCTTCTTGCAC 58.344 29.630 0.00 0.00 0.00 4.57
3275 3412 6.342338 TCTAGTCTTTGTCTTTAGGTCACC 57.658 41.667 0.00 0.00 0.00 4.02
3359 3497 5.579904 GGGAATAAGACCGTTCTAAAGTGTC 59.420 44.000 0.00 0.00 0.00 3.67
3367 3505 2.829023 TGGAGGGAATAAGACCGTTCT 58.171 47.619 0.00 0.00 0.00 3.01
3446 3591 7.201974 GCTGATGTATAGTACCCCTCTGTAAAA 60.202 40.741 0.00 0.00 0.00 1.52
3447 3592 6.267014 GCTGATGTATAGTACCCCTCTGTAAA 59.733 42.308 0.00 0.00 0.00 2.01
3448 3593 5.773680 GCTGATGTATAGTACCCCTCTGTAA 59.226 44.000 0.00 0.00 0.00 2.41
3449 3594 5.074652 AGCTGATGTATAGTACCCCTCTGTA 59.925 44.000 0.00 0.00 0.00 2.74
3450 3595 4.140900 AGCTGATGTATAGTACCCCTCTGT 60.141 45.833 0.00 0.00 0.00 3.41
3451 3596 4.411927 AGCTGATGTATAGTACCCCTCTG 58.588 47.826 0.00 0.00 0.00 3.35
3452 3597 4.750833 AGCTGATGTATAGTACCCCTCT 57.249 45.455 0.00 0.00 0.00 3.69
3453 3598 5.810080 AAAGCTGATGTATAGTACCCCTC 57.190 43.478 0.00 0.00 0.00 4.30
3454 3599 5.665812 TGAAAAGCTGATGTATAGTACCCCT 59.334 40.000 0.00 0.00 0.00 4.79
3455 3600 5.925509 TGAAAAGCTGATGTATAGTACCCC 58.074 41.667 0.00 0.00 0.00 4.95
3456 3601 7.859325 TTTGAAAAGCTGATGTATAGTACCC 57.141 36.000 0.00 0.00 0.00 3.69
3457 3602 8.947115 AGTTTTGAAAAGCTGATGTATAGTACC 58.053 33.333 0.00 0.00 0.00 3.34
3460 3605 9.683069 CAAAGTTTTGAAAAGCTGATGTATAGT 57.317 29.630 0.00 0.00 40.55 2.12
3461 3606 9.132521 CCAAAGTTTTGAAAAGCTGATGTATAG 57.867 33.333 6.18 0.00 40.55 1.31
3462 3607 7.598493 GCCAAAGTTTTGAAAAGCTGATGTATA 59.402 33.333 6.18 0.00 40.55 1.47
3463 3608 6.424812 GCCAAAGTTTTGAAAAGCTGATGTAT 59.575 34.615 6.18 0.00 40.55 2.29
3464 3609 5.752955 GCCAAAGTTTTGAAAAGCTGATGTA 59.247 36.000 6.18 0.00 40.55 2.29
3465 3610 4.571984 GCCAAAGTTTTGAAAAGCTGATGT 59.428 37.500 6.18 0.00 40.55 3.06
3466 3611 4.571580 TGCCAAAGTTTTGAAAAGCTGATG 59.428 37.500 6.18 0.00 40.55 3.07
3467 3612 4.571984 GTGCCAAAGTTTTGAAAAGCTGAT 59.428 37.500 6.18 0.00 40.55 2.90
3468 3613 3.932089 GTGCCAAAGTTTTGAAAAGCTGA 59.068 39.130 6.18 0.00 40.55 4.26
3469 3614 3.063861 GGTGCCAAAGTTTTGAAAAGCTG 59.936 43.478 6.18 0.00 40.55 4.24
3475 3620 2.569404 ACCTTGGTGCCAAAGTTTTGAA 59.431 40.909 5.10 0.00 40.55 2.69
3476 3621 2.093764 CACCTTGGTGCCAAAGTTTTGA 60.094 45.455 6.88 0.00 40.55 2.69
3513 3658 3.058160 CAAGCCGGAACCAGCCAG 61.058 66.667 5.05 0.00 0.00 4.85
3514 3659 4.659172 CCAAGCCGGAACCAGCCA 62.659 66.667 5.05 0.00 36.56 4.75
3515 3660 4.660938 ACCAAGCCGGAACCAGCC 62.661 66.667 5.05 0.00 38.63 4.85
3516 3661 3.365265 CACCAAGCCGGAACCAGC 61.365 66.667 5.05 0.00 38.63 4.85
3517 3662 3.365265 GCACCAAGCCGGAACCAG 61.365 66.667 5.05 0.00 38.63 4.00
3549 3694 1.004277 GGCCTACTGGTGAAATGTGGA 59.996 52.381 0.00 0.00 35.27 4.02
3564 3709 2.528134 GGCTCCATGTACAGGCCTA 58.472 57.895 3.98 0.00 39.68 3.93
3568 3713 2.919043 GGGGGCTCCATGTACAGG 59.081 66.667 4.16 0.00 35.00 4.00
3683 4197 8.810427 CAAATCTGAACTAATGCGCAAATAAAT 58.190 29.630 17.11 0.00 0.00 1.40
3703 4217 5.940192 TGCAGTTCGTTACAATCAAATCT 57.060 34.783 0.00 0.00 0.00 2.40
3717 4231 4.094887 AGCCATGTAGTAAAATGCAGTTCG 59.905 41.667 0.00 0.00 0.00 3.95
3741 4265 6.449698 TGATCTGTTTTCAAGCCAAAAGATC 58.550 36.000 5.46 5.46 32.58 2.75
3788 4313 8.004087 TGCTTGGATAGTACTAACTACGAAAT 57.996 34.615 6.70 0.00 40.98 2.17
3800 4325 1.211949 TGGGGCTTGCTTGGATAGTAC 59.788 52.381 0.00 0.00 0.00 2.73
3802 4327 0.704076 TTGGGGCTTGCTTGGATAGT 59.296 50.000 0.00 0.00 0.00 2.12
3803 4328 1.106285 GTTGGGGCTTGCTTGGATAG 58.894 55.000 0.00 0.00 0.00 2.08
3804 4329 0.407528 TGTTGGGGCTTGCTTGGATA 59.592 50.000 0.00 0.00 0.00 2.59
3885 4410 5.182760 AGGTTGTTTTCATTCTCAGATCTGC 59.817 40.000 18.36 0.39 0.00 4.26
3928 4453 3.632145 TCTCTTTGAAGCCTTTGGTGTTC 59.368 43.478 0.00 0.00 0.00 3.18
3930 4455 3.297134 TCTCTTTGAAGCCTTTGGTGT 57.703 42.857 0.00 0.00 0.00 4.16
4044 4586 8.832521 TGTCATTTGAGTACTGTCGTTAATTTT 58.167 29.630 0.00 0.00 0.00 1.82
4294 4844 2.570302 GGAGACCTTTGCTACTTACCCA 59.430 50.000 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.