Multiple sequence alignment - TraesCS4B01G312700

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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 TraesCS4B01G312700 chr4B 100.000 2585 0 0 1 2585 602629330 602631914 0.000000e+00 4774.0
1 TraesCS4B01G312700 chr4B 91.866 2545 175 14 50 2585 636160861 636158340 0.000000e+00 3524.0
2 TraesCS4B01G312700 chr7B 90.057 2112 191 13 482 2585 57863426 57861326 0.000000e+00 2719.0
3 TraesCS4B01G312700 chr7B 87.864 412 50 0 50 461 57863826 57863415 3.870000e-133 484.0
4 TraesCS4B01G312700 chr7B 96.000 50 1 1 3 52 511727456 511727504 2.130000e-11 80.5
5 TraesCS4B01G312700 chr7B 90.566 53 2 1 3 52 511888340 511888392 1.660000e-07 67.6
6 TraesCS4B01G312700 chr7B 85.965 57 6 2 3 59 141457685 141457631 2.780000e-05 60.2
7 TraesCS4B01G312700 chr3B 89.541 2113 207 12 480 2585 795564297 795562192 0.000000e+00 2665.0
8 TraesCS4B01G312700 chr3B 86.774 2117 262 14 482 2585 783743590 783741479 0.000000e+00 2342.0
9 TraesCS4B01G312700 chr3B 87.648 421 48 4 50 469 795564697 795564280 1.080000e-133 486.0
10 TraesCS4B01G312700 chr5B 92.430 1757 120 9 836 2585 50249529 50247779 0.000000e+00 2495.0
11 TraesCS4B01G312700 chr5B 85.092 2113 291 20 482 2584 477916514 477918612 0.000000e+00 2135.0
12 TraesCS4B01G312700 chr5B 80.984 2540 416 49 64 2585 456372590 456370100 0.000000e+00 1953.0
13 TraesCS4B01G312700 chr5B 85.958 1467 164 30 50 1509 619942684 619941253 0.000000e+00 1530.0
14 TraesCS4B01G312700 chr5B 90.296 371 35 1 53 423 50274692 50274323 3.870000e-133 484.0
15 TraesCS4B01G312700 chr1B 87.530 2109 238 18 490 2585 500686850 500684754 0.000000e+00 2414.0
16 TraesCS4B01G312700 chr2B 87.199 2117 246 19 482 2585 793909566 793911670 0.000000e+00 2385.0
17 TraesCS4B01G312700 chr2B 88.024 1645 184 10 482 2117 751601123 751599483 0.000000e+00 1934.0
18 TraesCS4B01G312700 chr2B 85.854 410 58 0 50 459 784600428 784600019 1.100000e-118 436.0
19 TraesCS4B01G312700 chr2B 84.461 399 58 4 64 460 793909180 793909576 8.670000e-105 390.0
20 TraesCS4B01G312700 chr2B 83.373 415 64 5 52 464 751601521 751601110 1.880000e-101 379.0
21 TraesCS4B01G312700 chr2B 92.157 51 2 2 1 49 762972168 762972218 1.280000e-08 71.3
22 TraesCS4B01G312700 chr6B 95.745 47 2 0 3 49 194242701 194242747 2.760000e-10 76.8


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 TraesCS4B01G312700 chr4B 602629330 602631914 2584 False 4774.0 4774 100.0000 1 2585 1 chr4B.!!$F1 2584
1 TraesCS4B01G312700 chr4B 636158340 636160861 2521 True 3524.0 3524 91.8660 50 2585 1 chr4B.!!$R1 2535
2 TraesCS4B01G312700 chr7B 57861326 57863826 2500 True 1601.5 2719 88.9605 50 2585 2 chr7B.!!$R2 2535
3 TraesCS4B01G312700 chr3B 783741479 783743590 2111 True 2342.0 2342 86.7740 482 2585 1 chr3B.!!$R1 2103
4 TraesCS4B01G312700 chr3B 795562192 795564697 2505 True 1575.5 2665 88.5945 50 2585 2 chr3B.!!$R2 2535
5 TraesCS4B01G312700 chr5B 50247779 50249529 1750 True 2495.0 2495 92.4300 836 2585 1 chr5B.!!$R1 1749
6 TraesCS4B01G312700 chr5B 477916514 477918612 2098 False 2135.0 2135 85.0920 482 2584 1 chr5B.!!$F1 2102
7 TraesCS4B01G312700 chr5B 456370100 456372590 2490 True 1953.0 1953 80.9840 64 2585 1 chr5B.!!$R3 2521
8 TraesCS4B01G312700 chr5B 619941253 619942684 1431 True 1530.0 1530 85.9580 50 1509 1 chr5B.!!$R4 1459
9 TraesCS4B01G312700 chr1B 500684754 500686850 2096 True 2414.0 2414 87.5300 490 2585 1 chr1B.!!$R1 2095
10 TraesCS4B01G312700 chr2B 793909180 793911670 2490 False 1387.5 2385 85.8300 64 2585 2 chr2B.!!$F2 2521
11 TraesCS4B01G312700 chr2B 751599483 751601521 2038 True 1156.5 1934 85.6985 52 2117 2 chr2B.!!$R2 2065

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
888 897 0.035458 ACAAAAGGTGGAGAGCTCGG 59.965 55.0 8.37 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2216 2.436417 TGTTTATCAGTTCCTGCTGCC 58.564 47.619 0.0 0.0 36.49 4.85 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
22 23 1.552578 AAAAACGCCTATTCACCCCC 58.447 50.000 0.00 0.00 0.00 5.40
23 24 0.406361 AAAACGCCTATTCACCCCCA 59.594 50.000 0.00 0.00 0.00 4.96
24 25 0.323087 AAACGCCTATTCACCCCCAC 60.323 55.000 0.00 0.00 0.00 4.61
25 26 1.205460 AACGCCTATTCACCCCCACT 61.205 55.000 0.00 0.00 0.00 4.00
26 27 1.146263 CGCCTATTCACCCCCACTC 59.854 63.158 0.00 0.00 0.00 3.51
27 28 1.338136 CGCCTATTCACCCCCACTCT 61.338 60.000 0.00 0.00 0.00 3.24
28 29 1.802553 GCCTATTCACCCCCACTCTA 58.197 55.000 0.00 0.00 0.00 2.43
29 30 1.694696 GCCTATTCACCCCCACTCTAG 59.305 57.143 0.00 0.00 0.00 2.43
30 31 2.960104 GCCTATTCACCCCCACTCTAGT 60.960 54.545 0.00 0.00 0.00 2.57
31 32 2.966516 CCTATTCACCCCCACTCTAGTC 59.033 54.545 0.00 0.00 0.00 2.59
32 33 1.486211 ATTCACCCCCACTCTAGTCG 58.514 55.000 0.00 0.00 0.00 4.18
33 34 0.406750 TTCACCCCCACTCTAGTCGA 59.593 55.000 0.00 0.00 0.00 4.20
34 35 0.323178 TCACCCCCACTCTAGTCGAC 60.323 60.000 7.70 7.70 0.00 4.20
35 36 1.378250 ACCCCCACTCTAGTCGACG 60.378 63.158 10.46 0.00 0.00 5.12
36 37 1.378250 CCCCCACTCTAGTCGACGT 60.378 63.158 10.46 0.00 0.00 4.34
37 38 0.107508 CCCCCACTCTAGTCGACGTA 60.108 60.000 10.46 2.39 0.00 3.57
38 39 1.679944 CCCCCACTCTAGTCGACGTAA 60.680 57.143 10.46 0.00 0.00 3.18
39 40 2.295885 CCCCACTCTAGTCGACGTAAT 58.704 52.381 10.46 0.00 0.00 1.89
40 41 2.033049 CCCCACTCTAGTCGACGTAATG 59.967 54.545 10.46 6.42 0.00 1.90
41 42 2.541178 CCCACTCTAGTCGACGTAATGC 60.541 54.545 10.46 0.00 0.00 3.56
42 43 2.096980 CCACTCTAGTCGACGTAATGCA 59.903 50.000 10.46 0.00 0.00 3.96
43 44 3.099362 CACTCTAGTCGACGTAATGCAC 58.901 50.000 10.46 0.00 0.00 4.57
44 45 3.008330 ACTCTAGTCGACGTAATGCACT 58.992 45.455 10.46 0.00 0.00 4.40
45 46 3.439476 ACTCTAGTCGACGTAATGCACTT 59.561 43.478 10.46 0.00 0.00 3.16
46 47 4.082895 ACTCTAGTCGACGTAATGCACTTT 60.083 41.667 10.46 0.00 0.00 2.66
47 48 4.409570 TCTAGTCGACGTAATGCACTTTC 58.590 43.478 10.46 0.00 0.00 2.62
48 49 3.021269 AGTCGACGTAATGCACTTTCA 57.979 42.857 10.46 0.00 0.00 2.69
60 61 9.363763 CGTAATGCACTTTCAGATCTGATATAT 57.636 33.333 25.64 9.77 39.64 0.86
259 260 5.527026 TTTGGCAATTATTCCCCCATTTT 57.473 34.783 0.00 0.00 0.00 1.82
280 282 4.591321 TGGGTGAAAAAGGAGCTGATAT 57.409 40.909 0.00 0.00 0.00 1.63
289 291 8.443176 TGAAAAAGGAGCTGATATAGATGGATT 58.557 33.333 0.00 0.00 0.00 3.01
296 298 9.732130 GGAGCTGATATAGATGGATTAACTTTT 57.268 33.333 0.00 0.00 0.00 2.27
334 336 0.391228 ACGGGTTTTGGAAATGCACC 59.609 50.000 0.00 0.00 0.00 5.01
348 350 1.114722 TGCACCTTCCCAAGCCTTTG 61.115 55.000 0.00 0.00 0.00 2.77
352 354 1.147817 ACCTTCCCAAGCCTTTGTGAT 59.852 47.619 0.00 0.00 32.21 3.06
364 366 8.686334 CCAAGCCTTTGTGATTATAAATAGTGT 58.314 33.333 0.00 0.00 32.21 3.55
367 369 7.339212 AGCCTTTGTGATTATAAATAGTGTGCA 59.661 33.333 0.00 0.00 0.00 4.57
420 422 3.935605 CCTTGAGGATTTAGGGTTTCCCG 60.936 52.174 0.00 0.00 43.24 5.14
469 471 5.127845 GTGAAGAGAGAGAGAGAGAGAGAGA 59.872 48.000 0.00 0.00 0.00 3.10
470 472 5.362143 TGAAGAGAGAGAGAGAGAGAGAGAG 59.638 48.000 0.00 0.00 0.00 3.20
471 473 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
472 474 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
473 475 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
474 476 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
475 477 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
476 478 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
477 479 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
478 480 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
479 481 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
480 482 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
571 579 7.663493 GGGAGAGATAATTTCCAATACAGAAGG 59.337 40.741 0.00 0.00 32.50 3.46
580 588 5.422214 TCCAATACAGAAGGAAGGAAGAC 57.578 43.478 0.00 0.00 0.00 3.01
649 657 2.990284 TGGAAGATTTGGGTACAGGGAA 59.010 45.455 0.00 0.00 0.00 3.97
654 662 4.375313 AGATTTGGGTACAGGGAAGAGAT 58.625 43.478 0.00 0.00 0.00 2.75
677 685 6.916360 TTTGGGAAATCTAATCAGCAAGTT 57.084 33.333 0.00 0.00 0.00 2.66
721 730 1.115467 GATCTGAAGCTCCCCTCGAA 58.885 55.000 0.00 0.00 0.00 3.71
753 762 3.053320 GGAAACTGGGAAGAGGATGGAAT 60.053 47.826 0.00 0.00 0.00 3.01
758 767 4.596643 ACTGGGAAGAGGATGGAATATGAG 59.403 45.833 0.00 0.00 0.00 2.90
766 775 5.605908 AGAGGATGGAATATGAGCAGAAAGA 59.394 40.000 0.00 0.00 0.00 2.52
819 828 4.338118 TGTTGCCTGTTTCTTCTTTCGATT 59.662 37.500 0.00 0.00 0.00 3.34
827 836 6.902341 TGTTTCTTCTTTCGATTTGATCCAG 58.098 36.000 0.00 0.00 0.00 3.86
828 837 6.486657 TGTTTCTTCTTTCGATTTGATCCAGT 59.513 34.615 0.00 0.00 0.00 4.00
888 897 0.035458 ACAAAAGGTGGAGAGCTCGG 59.965 55.000 8.37 0.00 0.00 4.63
903 912 3.006728 CGGCTGGGGGTGGAACTA 61.007 66.667 0.00 0.00 36.74 2.24
953 965 7.782897 TCAGATTGAGGAGACTAAGAAAGAA 57.217 36.000 0.00 0.00 44.43 2.52
1012 1024 3.129287 GCTAACATGGATGTGGGAAACAG 59.871 47.826 0.00 0.00 43.64 3.16
1019 1031 0.482446 ATGTGGGAAACAGGCAAGGA 59.518 50.000 0.00 0.00 43.64 3.36
1020 1032 0.482446 TGTGGGAAACAGGCAAGGAT 59.518 50.000 0.00 0.00 33.78 3.24
1021 1033 0.890683 GTGGGAAACAGGCAAGGATG 59.109 55.000 0.00 0.00 0.00 3.51
1024 1036 1.342374 GGGAAACAGGCAAGGATGGAT 60.342 52.381 0.00 0.00 0.00 3.41
1046 1060 2.489073 GGGATGGTTCCAGAACAACAGT 60.489 50.000 12.32 0.00 44.60 3.55
1049 1063 4.499696 GGATGGTTCCAGAACAACAGTTTG 60.500 45.833 12.32 0.00 42.85 2.93
1051 1065 2.481276 GGTTCCAGAACAACAGTTTGGC 60.481 50.000 12.32 0.00 42.85 4.52
1080 1099 5.002516 AGAGAGAGCTTGGATCAAAACAAG 58.997 41.667 5.38 5.38 45.19 3.16
1269 1288 0.909610 CCAGAGGGTTGGGAGTGCTA 60.910 60.000 0.00 0.00 34.46 3.49
1360 1380 6.683537 TCTTCTGGGGAGATTAATGAGACTA 58.316 40.000 0.00 0.00 0.00 2.59
1555 1576 4.511527 CTGGACATATGACACTCAAGCTT 58.488 43.478 10.38 0.00 0.00 3.74
1563 1584 2.159254 TGACACTCAAGCTTTTGGCAAC 60.159 45.455 0.00 0.00 44.79 4.17
1569 1590 4.342092 ACTCAAGCTTTTGGCAACTTACAT 59.658 37.500 0.00 0.00 44.79 2.29
1571 1592 6.040391 ACTCAAGCTTTTGGCAACTTACATAA 59.960 34.615 0.00 0.00 44.79 1.90
1596 1617 4.100344 GTGTGGGTGTAGTTTGGGAAAATT 59.900 41.667 0.00 0.00 0.00 1.82
1605 1626 3.321968 AGTTTGGGAAAATTCCTGAGTGC 59.678 43.478 11.75 0.00 46.72 4.40
1637 1659 0.850100 TTTGGGATGTGTGAGGTGGT 59.150 50.000 0.00 0.00 0.00 4.16
1644 1666 0.254462 TGTGTGAGGTGGTTGCTTCA 59.746 50.000 0.00 0.00 0.00 3.02
1651 1673 0.392336 GGTGGTTGCTTCAATTGGCA 59.608 50.000 5.42 5.41 36.62 4.92
1707 1729 6.012858 TGAAAGAGAAAATCAGGGCTAAGGTA 60.013 38.462 0.00 0.00 0.00 3.08
1792 1821 4.259356 CAGAATCAGCATTGAGTTGGAGA 58.741 43.478 0.00 0.00 36.61 3.71
1801 1830 7.882791 TCAGCATTGAGTTGGAGAAAGTAATTA 59.117 33.333 0.00 0.00 0.00 1.40
1859 1888 3.662759 TTTGGAACCTGAACTTGAGGT 57.337 42.857 0.00 0.00 46.36 3.85
1925 1955 4.405358 AGGAGCTGATGGAACTAAAGAGAG 59.595 45.833 0.00 0.00 0.00 3.20
2100 2132 5.507637 AGGTTGAAGAAATCAGATGCAGAT 58.492 37.500 0.00 0.00 39.77 2.90
2117 2149 4.098349 TGCAGATATGATGCTTGGAAAACC 59.902 41.667 10.09 0.00 44.17 3.27
2183 2216 2.029623 CTGCTGGAAATGATTCAGGGG 58.970 52.381 0.00 0.00 37.29 4.79
2184 2217 1.342275 TGCTGGAAATGATTCAGGGGG 60.342 52.381 0.00 0.00 37.29 5.40
2314 2348 4.408921 CCCAGGATAACACACCAGAAGATA 59.591 45.833 0.00 0.00 0.00 1.98
2321 2355 7.657761 GGATAACACACCAGAAGATACTTATGG 59.342 40.741 19.26 19.26 37.07 2.74
2339 2373 6.215636 ACTTATGGAGAACCTGTGGACTATTT 59.784 38.462 0.00 0.00 37.04 1.40
2511 2545 2.564504 GGAAAGGGCAGCTGAAAAGAAT 59.435 45.455 20.43 0.00 0.00 2.40
2546 2581 6.779539 AGAACCCTGTTCTTTCTGATGAAAAT 59.220 34.615 3.71 0.00 41.09 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.203075 TGGGGGTGAATAGGCGTTTTT 60.203 47.619 0.00 0.00 0.00 1.94
4 5 0.406361 TGGGGGTGAATAGGCGTTTT 59.594 50.000 0.00 0.00 0.00 2.43
5 6 0.323087 GTGGGGGTGAATAGGCGTTT 60.323 55.000 0.00 0.00 0.00 3.60
6 7 1.205460 AGTGGGGGTGAATAGGCGTT 61.205 55.000 0.00 0.00 0.00 4.84
7 8 1.615424 AGTGGGGGTGAATAGGCGT 60.615 57.895 0.00 0.00 0.00 5.68
8 9 1.146263 GAGTGGGGGTGAATAGGCG 59.854 63.158 0.00 0.00 0.00 5.52
9 10 1.694696 CTAGAGTGGGGGTGAATAGGC 59.305 57.143 0.00 0.00 0.00 3.93
10 11 2.966516 GACTAGAGTGGGGGTGAATAGG 59.033 54.545 0.00 0.00 0.00 2.57
11 12 2.623889 CGACTAGAGTGGGGGTGAATAG 59.376 54.545 0.00 0.00 0.00 1.73
12 13 2.242965 TCGACTAGAGTGGGGGTGAATA 59.757 50.000 0.00 0.00 0.00 1.75
13 14 1.006758 TCGACTAGAGTGGGGGTGAAT 59.993 52.381 0.00 0.00 0.00 2.57
14 15 0.406750 TCGACTAGAGTGGGGGTGAA 59.593 55.000 0.00 0.00 0.00 3.18
15 16 0.323178 GTCGACTAGAGTGGGGGTGA 60.323 60.000 8.70 0.00 0.00 4.02
16 17 1.654954 CGTCGACTAGAGTGGGGGTG 61.655 65.000 14.70 0.00 0.00 4.61
17 18 1.378250 CGTCGACTAGAGTGGGGGT 60.378 63.158 14.70 0.00 0.00 4.95
18 19 0.107508 TACGTCGACTAGAGTGGGGG 60.108 60.000 14.70 0.00 0.00 5.40
19 20 1.742761 TTACGTCGACTAGAGTGGGG 58.257 55.000 14.70 0.00 0.00 4.96
20 21 2.541178 GCATTACGTCGACTAGAGTGGG 60.541 54.545 14.70 0.00 0.00 4.61
21 22 2.096980 TGCATTACGTCGACTAGAGTGG 59.903 50.000 14.70 0.00 0.00 4.00
22 23 3.099362 GTGCATTACGTCGACTAGAGTG 58.901 50.000 14.70 6.67 0.00 3.51
23 24 3.008330 AGTGCATTACGTCGACTAGAGT 58.992 45.455 14.70 6.52 0.00 3.24
24 25 3.677190 AGTGCATTACGTCGACTAGAG 57.323 47.619 14.70 0.00 0.00 2.43
25 26 4.083164 TGAAAGTGCATTACGTCGACTAGA 60.083 41.667 14.70 0.00 0.00 2.43
26 27 4.163552 TGAAAGTGCATTACGTCGACTAG 58.836 43.478 14.70 0.96 0.00 2.57
27 28 4.083164 TCTGAAAGTGCATTACGTCGACTA 60.083 41.667 14.70 2.35 33.76 2.59
28 29 2.987149 CTGAAAGTGCATTACGTCGACT 59.013 45.455 14.70 3.37 0.00 4.18
29 30 2.984471 TCTGAAAGTGCATTACGTCGAC 59.016 45.455 5.18 5.18 33.76 4.20
30 31 3.291809 TCTGAAAGTGCATTACGTCGA 57.708 42.857 0.00 0.00 33.76 4.20
31 32 3.859961 AGATCTGAAAGTGCATTACGTCG 59.140 43.478 0.00 0.00 33.76 5.12
32 33 4.864806 TCAGATCTGAAAGTGCATTACGTC 59.135 41.667 23.17 0.00 36.53 4.34
33 34 4.820897 TCAGATCTGAAAGTGCATTACGT 58.179 39.130 23.17 0.00 36.53 3.57
34 35 5.980698 ATCAGATCTGAAAGTGCATTACG 57.019 39.130 28.40 0.00 43.58 3.18
39 40 9.060347 GGAAAATATATCAGATCTGAAAGTGCA 57.940 33.333 28.40 11.48 43.58 4.57
40 41 9.060347 TGGAAAATATATCAGATCTGAAAGTGC 57.940 33.333 28.40 14.63 43.58 4.40
45 46 9.060347 GCAACTGGAAAATATATCAGATCTGAA 57.940 33.333 28.40 17.61 43.58 3.02
46 47 8.212995 TGCAACTGGAAAATATATCAGATCTGA 58.787 33.333 27.03 27.03 44.59 3.27
47 48 8.387190 TGCAACTGGAAAATATATCAGATCTG 57.613 34.615 17.07 17.07 0.00 2.90
48 49 8.985315 TTGCAACTGGAAAATATATCAGATCT 57.015 30.769 0.00 0.00 0.00 2.75
60 61 3.440173 GGATCGATCTTGCAACTGGAAAA 59.560 43.478 23.96 0.00 0.00 2.29
61 62 3.009723 GGATCGATCTTGCAACTGGAAA 58.990 45.455 23.96 0.00 0.00 3.13
259 260 2.978156 ATCAGCTCCTTTTTCACCCA 57.022 45.000 0.00 0.00 0.00 4.51
280 282 6.210385 TGCTTTGCCAAAAGTTAATCCATCTA 59.790 34.615 0.00 0.00 44.02 1.98
310 312 2.514803 CATTTCCAAAACCCGTCTCCT 58.485 47.619 0.00 0.00 0.00 3.69
348 350 8.839310 AGGAGATGCACACTATTTATAATCAC 57.161 34.615 0.00 0.00 0.00 3.06
352 354 6.931281 GCAGAGGAGATGCACACTATTTATAA 59.069 38.462 0.00 0.00 43.31 0.98
364 366 1.904537 TCTCAAAGCAGAGGAGATGCA 59.095 47.619 0.00 0.00 46.31 3.96
367 369 3.956199 CTCTCTCTCAAAGCAGAGGAGAT 59.044 47.826 15.37 0.00 40.50 2.75
433 435 4.678256 TCTCTCTTCACTATCACCCAGTT 58.322 43.478 0.00 0.00 0.00 3.16
469 471 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
470 472 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.00 0.00 3.20
471 473 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.00 0.00 3.10
472 474 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.00 0.00 3.20
473 475 4.271807 TCCTCTCTCTCTCTCTCTCTCT 57.728 50.000 0.00 0.00 0.00 3.10
474 476 4.590647 TCATCCTCTCTCTCTCTCTCTCTC 59.409 50.000 0.00 0.00 0.00 3.20
475 477 4.560739 TCATCCTCTCTCTCTCTCTCTCT 58.439 47.826 0.00 0.00 0.00 3.10
476 478 4.963318 TCATCCTCTCTCTCTCTCTCTC 57.037 50.000 0.00 0.00 0.00 3.20
477 479 4.474651 TGTTCATCCTCTCTCTCTCTCTCT 59.525 45.833 0.00 0.00 0.00 3.10
478 480 4.780815 TGTTCATCCTCTCTCTCTCTCTC 58.219 47.826 0.00 0.00 0.00 3.20
479 481 4.385643 CCTGTTCATCCTCTCTCTCTCTCT 60.386 50.000 0.00 0.00 0.00 3.10
480 482 3.885297 CCTGTTCATCCTCTCTCTCTCTC 59.115 52.174 0.00 0.00 0.00 3.20
571 579 4.120589 ACTTGTCAAGTTCGTCTTCCTTC 58.879 43.478 12.62 0.00 39.04 3.46
580 588 7.574030 TAGATCTCTCTCAACTTGTCAAGTTCG 60.574 40.741 24.91 19.66 40.04 3.95
595 603 7.950512 TCTCATTGTTTGGATAGATCTCTCTC 58.049 38.462 0.00 0.00 32.66 3.20
654 662 6.493115 TCAACTTGCTGATTAGATTTCCCAAA 59.507 34.615 0.00 0.00 0.00 3.28
699 708 1.494960 GAGGGGAGCTTCAGATCTGT 58.505 55.000 21.92 2.70 0.00 3.41
753 762 5.595952 TGTGCTCTCTATCTTTCTGCTCATA 59.404 40.000 0.00 0.00 0.00 2.15
758 767 4.332268 CCTTTGTGCTCTCTATCTTTCTGC 59.668 45.833 0.00 0.00 0.00 4.26
766 775 6.773638 TCTTCTTTTCCTTTGTGCTCTCTAT 58.226 36.000 0.00 0.00 0.00 1.98
819 828 2.371841 ACCACTGTTGCTACTGGATCAA 59.628 45.455 12.38 0.00 0.00 2.57
827 836 0.958822 CCCCAAACCACTGTTGCTAC 59.041 55.000 0.00 0.00 34.13 3.58
828 837 0.825840 GCCCCAAACCACTGTTGCTA 60.826 55.000 0.00 0.00 34.13 3.49
888 897 1.037579 GCAATAGTTCCACCCCCAGC 61.038 60.000 0.00 0.00 0.00 4.85
903 912 2.363406 GCTGCTTCCAGGGGCAAT 60.363 61.111 8.89 0.00 39.54 3.56
953 965 4.410099 TGTGATCTTTTCCTCCAGCAAAT 58.590 39.130 0.00 0.00 0.00 2.32
1012 1024 0.541296 CCATCCCATCCATCCTTGCC 60.541 60.000 0.00 0.00 0.00 4.52
1019 1031 1.911454 TCTGGAACCATCCCATCCAT 58.089 50.000 0.00 0.00 45.95 3.41
1020 1032 1.284785 GTTCTGGAACCATCCCATCCA 59.715 52.381 2.35 0.00 45.95 3.41
1021 1033 1.284785 TGTTCTGGAACCATCCCATCC 59.715 52.381 10.44 0.00 45.95 3.51
1024 1036 1.496857 TGTTGTTCTGGAACCATCCCA 59.503 47.619 10.44 0.00 45.95 4.37
1046 1060 0.901124 GCTCTCTCTCTCTGGCCAAA 59.099 55.000 7.01 0.00 0.00 3.28
1049 1063 0.461135 CAAGCTCTCTCTCTCTGGCC 59.539 60.000 0.00 0.00 0.00 5.36
1051 1065 2.142356 TCCAAGCTCTCTCTCTCTGG 57.858 55.000 0.00 0.00 0.00 3.86
1080 1099 2.229784 CACTCTGAAATTTCCACCAGCC 59.770 50.000 15.48 0.00 0.00 4.85
1269 1288 5.010012 CACCTCTTTAGAATTTTGCACCAGT 59.990 40.000 0.00 0.00 0.00 4.00
1360 1380 7.654022 TGTAGTTGAAACCTTCCAAGAATTT 57.346 32.000 0.00 0.00 0.00 1.82
1518 1539 2.224843 TGTCCAGCTGTCCACATTGATT 60.225 45.455 13.81 0.00 0.00 2.57
1555 1576 5.221342 CCCACACTTTATGTAAGTTGCCAAA 60.221 40.000 0.00 0.00 44.73 3.28
1563 1584 7.308348 CCAAACTACACCCACACTTTATGTAAG 60.308 40.741 0.00 0.00 40.64 2.34
1569 1590 3.458857 TCCCAAACTACACCCACACTTTA 59.541 43.478 0.00 0.00 0.00 1.85
1571 1592 1.847737 TCCCAAACTACACCCACACTT 59.152 47.619 0.00 0.00 0.00 3.16
1623 1645 1.537202 GAAGCAACCACCTCACACATC 59.463 52.381 0.00 0.00 0.00 3.06
1637 1659 2.694628 AGAACAGTGCCAATTGAAGCAA 59.305 40.909 7.12 0.00 41.48 3.91
1644 1666 4.344679 TCAATTTCCAGAACAGTGCCAATT 59.655 37.500 0.00 0.00 0.00 2.32
1651 1673 6.375455 GTGGACATATCAATTTCCAGAACAGT 59.625 38.462 0.00 0.00 41.57 3.55
1801 1830 9.807921 TCTCTTTTCTTTATACCATCCTTGTTT 57.192 29.630 0.00 0.00 0.00 2.83
1839 1868 3.662759 ACCTCAAGTTCAGGTTCCAAA 57.337 42.857 0.00 0.00 41.95 3.28
1859 1888 6.395780 TTTTCTGACCTCCCATACCATTTA 57.604 37.500 0.00 0.00 0.00 1.40
1925 1955 2.569404 CCTATACTTCCCAGGGAGATGC 59.431 54.545 8.67 0.00 31.21 3.91
1933 1963 3.199946 TGTTTGAGCCCTATACTTCCCAG 59.800 47.826 0.00 0.00 0.00 4.45
2183 2216 2.436417 TGTTTATCAGTTCCTGCTGCC 58.564 47.619 0.00 0.00 36.49 4.85
2184 2217 3.503748 ACTTGTTTATCAGTTCCTGCTGC 59.496 43.478 0.00 0.00 36.49 5.25
2314 2348 3.521727 AGTCCACAGGTTCTCCATAAGT 58.478 45.455 0.00 0.00 35.89 2.24
2321 2355 5.346181 AGCTAAATAGTCCACAGGTTCTC 57.654 43.478 0.00 0.00 0.00 2.87
2339 2373 6.798427 ATTCCACAGAATCTTGACTAGCTA 57.202 37.500 0.00 0.00 38.36 3.32
2511 2545 8.832735 AGAAAGAACAGGGTTCTACCATAATTA 58.167 33.333 11.63 0.00 41.02 1.40


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

AutoCloner maintained by Alex Coulton.