Multiple sequence alignment - TraesCS6A01G365000

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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 TraesCS6A01G365000 chr6A 100.000 2472 0 0 1 2472 593352733 593355204 0.000000e+00 4566.0
1 TraesCS6A01G365000 chr6A 88.489 139 16 0 559 697 576825087 576824949 4.230000e-38 169.0
2 TraesCS6A01G365000 chr6A 86.207 145 15 3 405 545 597698758 597698901 4.260000e-33 152.0
3 TraesCS6A01G365000 chr6B 88.172 1767 105 51 253 1944 674934666 674936403 0.000000e+00 2010.0
4 TraesCS6A01G365000 chr6B 88.555 533 46 10 1946 2472 674936491 674937014 1.250000e-177 632.0
5 TraesCS6A01G365000 chr6B 84.412 340 28 8 2006 2329 189634072 189634402 6.640000e-81 311.0
6 TraesCS6A01G365000 chr6B 85.507 69 7 2 144 211 19364536 19364602 4.410000e-08 69.4
7 TraesCS6A01G365000 chr6D 86.829 1640 94 54 230 1797 446488429 446490018 0.000000e+00 1720.0
8 TraesCS6A01G365000 chr6D 89.340 591 42 20 1893 2472 446490610 446491190 0.000000e+00 723.0
9 TraesCS6A01G365000 chr6D 84.792 480 43 14 2007 2467 429959874 429960342 2.900000e-124 455.0
10 TraesCS6A01G365000 chr6D 84.375 480 45 14 2007 2467 26596687 26597155 6.270000e-121 444.0
11 TraesCS6A01G365000 chr6D 91.739 230 15 3 1 230 446488146 446488371 1.430000e-82 316.0
12 TraesCS6A01G365000 chr6D 94.737 76 4 0 1790 1865 446490538 446490613 4.320000e-23 119.0
13 TraesCS6A01G365000 chr6D 86.301 73 9 1 143 215 50767846 50767917 7.330000e-11 78.7
14 TraesCS6A01G365000 chr4B 84.900 649 61 18 727 1347 658585591 658584952 2.700000e-174 621.0
15 TraesCS6A01G365000 chr4B 88.942 208 19 4 1802 2006 607287210 607287004 1.130000e-63 254.0
16 TraesCS6A01G365000 chr2D 85.000 480 42 14 2007 2467 422074512 422074980 6.230000e-126 460.0
17 TraesCS6A01G365000 chr2D 83.763 388 28 15 982 1350 582494941 582494570 3.940000e-88 335.0
18 TraesCS6A01G365000 chr2D 91.707 205 11 4 1076 1274 488229214 488229418 1.870000e-71 279.0
19 TraesCS6A01G365000 chr3A 85.084 476 42 14 2010 2467 734656587 734656123 2.240000e-125 459.0
20 TraesCS6A01G365000 chr3A 81.169 154 19 6 73 225 13565424 13565280 5.590000e-22 115.0
21 TraesCS6A01G365000 chr7B 84.407 481 44 16 2006 2467 442046420 442046888 6.270000e-121 444.0
22 TraesCS6A01G365000 chr7B 89.928 139 11 3 559 696 537460484 537460348 2.530000e-40 176.0
23 TraesCS6A01G365000 chr7B 88.406 138 16 0 559 696 615378068 615378205 1.520000e-37 167.0
24 TraesCS6A01G365000 chr7B 87.413 143 18 0 559 701 668921553 668921411 5.470000e-37 165.0
25 TraesCS6A01G365000 chr7B 86.111 144 15 3 407 547 383859148 383859289 1.530000e-32 150.0
26 TraesCS6A01G365000 chr5D 84.486 477 44 12 2010 2467 76781012 76780547 6.270000e-121 444.0
27 TraesCS6A01G365000 chr5D 86.548 394 25 17 1001 1372 371440921 371440534 2.290000e-110 409.0
28 TraesCS6A01G365000 chr5D 83.459 133 16 5 281 407 371441333 371441201 4.320000e-23 119.0
29 TraesCS6A01G365000 chr5D 84.524 84 11 2 143 226 6051714 6051795 5.670000e-12 82.4
30 TraesCS6A01G365000 chr5D 84.706 85 9 4 144 227 54776131 54776050 5.670000e-12 82.4
31 TraesCS6A01G365000 chr5A 84.375 480 45 14 2007 2467 474049412 474049880 6.270000e-121 444.0
32 TraesCS6A01G365000 chr5A 86.250 400 36 11 982 1372 456485669 456485280 1.370000e-112 416.0
33 TraesCS6A01G365000 chr5A 85.891 404 28 16 982 1372 474537627 474537240 1.060000e-108 403.0
34 TraesCS6A01G365000 chr5A 94.000 50 3 0 765 814 474537834 474537785 2.640000e-10 76.8
35 TraesCS6A01G365000 chr3D 84.486 477 44 16 2010 2467 505057331 505056866 6.270000e-121 444.0
36 TraesCS6A01G365000 chr3D 84.167 480 46 14 2007 2467 10131655 10132123 2.920000e-119 438.0
37 TraesCS6A01G365000 chr3D 86.806 144 16 3 404 545 522508568 522508710 9.150000e-35 158.0
38 TraesCS6A01G365000 chr3B 85.912 433 38 17 2054 2467 97996144 97996572 8.110000e-120 440.0
39 TraesCS6A01G365000 chr3B 82.773 476 52 11 2011 2467 16190735 16191199 4.950000e-107 398.0
40 TraesCS6A01G365000 chr4A 81.250 608 53 30 934 1492 686385707 686385112 3.780000e-118 435.0
41 TraesCS6A01G365000 chr4A 82.186 494 36 21 1539 2006 686384791 686384324 6.450000e-101 377.0
42 TraesCS6A01G365000 chr4A 90.678 118 9 1 1 116 641612251 641612368 3.290000e-34 156.0
43 TraesCS6A01G365000 chr4A 87.395 119 10 5 746 860 641610316 641610433 5.550000e-27 132.0
44 TraesCS6A01G365000 chr4A 92.308 52 1 2 1491 1539 686384880 686384829 1.230000e-08 71.3
45 TraesCS6A01G365000 chr5B 86.520 408 32 14 982 1370 441446435 441446032 6.320000e-116 427.0
46 TraesCS6A01G365000 chr5B 86.006 343 23 14 1036 1356 448803966 448803627 6.550000e-91 344.0
47 TraesCS6A01G365000 chr5B 86.207 145 16 2 404 545 136277928 136278071 1.180000e-33 154.0
48 TraesCS6A01G365000 chr5B 86.207 87 9 1 728 814 441446676 441446593 9.410000e-15 91.6
49 TraesCS6A01G365000 chr1B 84.703 438 45 9 2049 2467 321122630 321123064 3.800000e-113 418.0
50 TraesCS6A01G365000 chr1B 85.385 130 3 3 2049 2162 670771802 670771931 1.200000e-23 121.0
51 TraesCS6A01G365000 chr7D 83.402 482 46 15 2007 2467 64462028 64462496 1.370000e-112 416.0
52 TraesCS6A01G365000 chr2B 83.636 385 34 19 982 1347 701491030 701490656 3.940000e-88 335.0
53 TraesCS6A01G365000 chr2B 83.041 342 25 17 1064 1372 572586514 572586855 1.870000e-71 279.0
54 TraesCS6A01G365000 chr4D 87.625 299 22 11 1720 2006 479961708 479961413 1.420000e-87 333.0
55 TraesCS6A01G365000 chr4D 88.489 139 16 0 559 697 77371334 77371196 4.230000e-38 169.0
56 TraesCS6A01G365000 chrUn 90.435 230 21 1 1 230 79346614 79346842 4.000000e-78 302.0
57 TraesCS6A01G365000 chr7A 88.652 141 16 0 559 699 149170743 149170603 3.270000e-39 172.0
58 TraesCS6A01G365000 chr7A 88.571 140 12 2 407 543 63409493 63409631 1.520000e-37 167.0
59 TraesCS6A01G365000 chr7A 86.620 142 13 5 407 545 243351836 243351974 4.260000e-33 152.0
60 TraesCS6A01G365000 chr7A 86.014 143 16 2 406 545 730579835 730579976 1.530000e-32 150.0
61 TraesCS6A01G365000 chr2A 86.667 150 18 2 555 702 516212444 516212295 5.470000e-37 165.0


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 TraesCS6A01G365000 chr6A 593352733 593355204 2471 False 4566.000000 4566 100.00000 1 2472 1 chr6A.!!$F1 2471
1 TraesCS6A01G365000 chr6B 674934666 674937014 2348 False 1321.000000 2010 88.36350 253 2472 2 chr6B.!!$F3 2219
2 TraesCS6A01G365000 chr6D 446488146 446491190 3044 False 719.500000 1720 90.66125 1 2472 4 chr6D.!!$F4 2471
3 TraesCS6A01G365000 chr4B 658584952 658585591 639 True 621.000000 621 84.90000 727 1347 1 chr4B.!!$R2 620
4 TraesCS6A01G365000 chr5D 371440534 371441333 799 True 264.000000 409 85.00350 281 1372 2 chr5D.!!$R3 1091
5 TraesCS6A01G365000 chr5A 474537240 474537834 594 True 239.900000 403 89.94550 765 1372 2 chr5A.!!$R2 607
6 TraesCS6A01G365000 chr4A 686384324 686385707 1383 True 294.433333 435 85.24800 934 2006 3 chr4A.!!$R1 1072
7 TraesCS6A01G365000 chr5B 441446032 441446676 644 True 259.300000 427 86.36350 728 1370 2 chr5B.!!$R2 642

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
811 905 0.461961 CCCGTTTGCACTTGGGAAAA 59.538 50.0 10.19 0.0 44.88 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 3105 0.469917 TGATGCCGAAATCTCCCTCC 59.53 55.0 0.0 0.0 0.0 4.3 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
48 49 2.036256 CCAGGGCTCCACCTTTGG 59.964 66.667 0.00 0.00 45.56 3.28
74 75 5.051816 CCACTTGATTTTGATGTTGCTTGT 58.948 37.500 0.00 0.00 0.00 3.16
108 109 7.229907 ACTTGATGTCGTTTAATTACCTTGGTT 59.770 33.333 0.00 0.00 0.00 3.67
186 187 8.193438 AGATATTAACAGGTAGTCGTTGGTTAC 58.807 37.037 0.00 0.00 0.00 2.50
188 189 3.930634 ACAGGTAGTCGTTGGTTACTC 57.069 47.619 0.00 0.00 0.00 2.59
190 191 3.505293 ACAGGTAGTCGTTGGTTACTCTC 59.495 47.826 0.00 0.00 0.00 3.20
191 192 3.087781 AGGTAGTCGTTGGTTACTCTCC 58.912 50.000 0.00 0.00 0.00 3.71
192 193 2.821969 GGTAGTCGTTGGTTACTCTCCA 59.178 50.000 0.00 0.00 0.00 3.86
193 194 3.119566 GGTAGTCGTTGGTTACTCTCCAG 60.120 52.174 0.00 0.00 36.28 3.86
259 318 1.967319 ACTGAACCAACAGCGTCATT 58.033 45.000 0.00 0.00 41.06 2.57
305 366 7.069578 GGATTAGATACACCACTCAACTAAGGA 59.930 40.741 0.00 0.00 0.00 3.36
335 410 4.211164 CCGCATCGATAAGCTTTATCAACA 59.789 41.667 3.20 0.00 0.00 3.33
377 452 6.486657 TGAACTGACGGAGAAAAAGAATGAAT 59.513 34.615 0.00 0.00 0.00 2.57
399 474 1.005450 GCCATCTGGACTTTTACCCCA 59.995 52.381 0.00 0.00 37.39 4.96
425 500 2.830321 TCTACTCCCTCCGTTTCCTTTC 59.170 50.000 0.00 0.00 0.00 2.62
431 506 2.565834 CCCTCCGTTTCCTTTCAGTCTA 59.434 50.000 0.00 0.00 0.00 2.59
434 509 3.986277 TCCGTTTCCTTTCAGTCTACAC 58.014 45.455 0.00 0.00 0.00 2.90
543 622 5.263599 TCAGATGCACCATGAAAGGTATTT 58.736 37.500 0.00 0.00 40.77 1.40
546 625 6.532657 CAGATGCACCATGAAAGGTATTTTTC 59.467 38.462 0.00 0.00 40.77 2.29
554 633 6.644592 CCATGAAAGGTATTTTTCTTTTGCGA 59.355 34.615 0.00 0.00 37.81 5.10
561 640 6.039382 AGGTATTTTTCTTTTGCGAGAACACT 59.961 34.615 0.00 0.00 35.50 3.55
652 731 2.485266 AACTTTGTGTAGTTTGGCGC 57.515 45.000 0.00 0.00 34.81 6.53
668 750 5.847670 TTGGCGCCAAACAAATTTTATAC 57.152 34.783 38.61 0.00 32.44 1.47
669 751 4.883083 TGGCGCCAAACAAATTTTATACA 58.117 34.783 30.74 0.00 0.00 2.29
670 752 5.482908 TGGCGCCAAACAAATTTTATACAT 58.517 33.333 30.74 0.00 0.00 2.29
672 754 5.578727 GGCGCCAAACAAATTTTATACATGA 59.421 36.000 24.80 0.00 0.00 3.07
711 793 6.105397 ACGGAGTATCTCTACTTCCTAGAG 57.895 45.833 0.00 0.00 44.66 2.43
718 800 5.356291 TCTCTACTTCCTAGAGTACGCTT 57.644 43.478 3.89 0.00 46.35 4.68
719 801 5.117584 TCTCTACTTCCTAGAGTACGCTTG 58.882 45.833 3.89 2.41 46.35 4.01
720 802 4.197750 TCTACTTCCTAGAGTACGCTTGG 58.802 47.826 18.46 18.46 32.92 3.61
721 803 1.477295 ACTTCCTAGAGTACGCTTGGC 59.523 52.381 19.45 0.00 31.91 4.52
722 804 1.476891 CTTCCTAGAGTACGCTTGGCA 59.523 52.381 19.45 10.17 31.91 4.92
723 805 0.815734 TCCTAGAGTACGCTTGGCAC 59.184 55.000 19.45 0.00 31.91 5.01
724 806 0.530744 CCTAGAGTACGCTTGGCACA 59.469 55.000 13.46 0.00 0.00 4.57
760 850 9.155785 TGTTAACCACAAAGGGGATTATTAAAA 57.844 29.630 2.48 0.00 43.89 1.52
811 905 0.461961 CCCGTTTGCACTTGGGAAAA 59.538 50.000 10.19 0.00 44.88 2.29
882 977 5.995282 TCAAGAATCCGTGTTTACTTGTGAT 59.005 36.000 0.00 0.00 36.91 3.06
883 978 6.147164 TCAAGAATCCGTGTTTACTTGTGATC 59.853 38.462 0.00 0.00 36.91 2.92
884 979 4.625742 AGAATCCGTGTTTACTTGTGATCG 59.374 41.667 0.00 0.00 0.00 3.69
889 1010 3.057739 CGTGTTTACTTGTGATCGTCTCG 59.942 47.826 0.00 0.00 0.00 4.04
923 1048 0.991920 TCTTTTCCCCTACAGCCCTG 59.008 55.000 0.00 0.00 0.00 4.45
968 1093 1.048724 TCCTCCTCAACATAGCCCGG 61.049 60.000 0.00 0.00 0.00 5.73
970 1095 1.689233 TCCTCAACATAGCCCGGCT 60.689 57.895 18.05 18.05 43.41 5.52
974 1099 1.224592 CAACATAGCCCGGCTTCCT 59.775 57.895 19.35 0.00 40.44 3.36
976 1101 1.984288 AACATAGCCCGGCTTCCTCC 61.984 60.000 19.35 0.00 40.44 4.30
977 1102 2.143419 CATAGCCCGGCTTCCTCCT 61.143 63.158 19.35 0.00 40.44 3.69
980 1105 2.815684 TAGCCCGGCTTCCTCCTCAA 62.816 60.000 19.35 0.00 40.44 3.02
984 1135 0.830648 CCGGCTTCCTCCTCAACATA 59.169 55.000 0.00 0.00 0.00 2.29
998 1149 2.295909 TCAACATAGCCACCAAAGCAAC 59.704 45.455 0.00 0.00 0.00 4.17
999 1150 1.993956 ACATAGCCACCAAAGCAACA 58.006 45.000 0.00 0.00 0.00 3.33
1000 1151 1.613437 ACATAGCCACCAAAGCAACAC 59.387 47.619 0.00 0.00 0.00 3.32
1001 1152 1.612950 CATAGCCACCAAAGCAACACA 59.387 47.619 0.00 0.00 0.00 3.72
1002 1153 1.769026 TAGCCACCAAAGCAACACAA 58.231 45.000 0.00 0.00 0.00 3.33
1003 1154 0.175531 AGCCACCAAAGCAACACAAC 59.824 50.000 0.00 0.00 0.00 3.32
1046 1207 4.313282 TCGTCTTCTTCTCTTCACGTAGA 58.687 43.478 0.00 0.00 0.00 2.59
1047 1208 4.152045 TCGTCTTCTTCTCTTCACGTAGAC 59.848 45.833 0.00 0.00 0.00 2.59
1048 1209 4.083961 CGTCTTCTTCTCTTCACGTAGACA 60.084 45.833 8.13 0.00 32.40 3.41
1277 1468 1.970917 GCTCCATGTTCGCCGACTTG 61.971 60.000 0.00 0.00 0.00 3.16
1298 1489 4.115199 GGAGGCGCCAAGGACCAT 62.115 66.667 31.54 4.27 36.34 3.55
1320 1511 1.282817 CTCAACGACCAACACAACGA 58.717 50.000 0.00 0.00 0.00 3.85
1344 1535 0.316278 CGTCCAGTCGCAGTAGATCG 60.316 60.000 0.00 0.00 0.00 3.69
1424 1637 6.702716 TTAGTTGGTTGGGTCTTTTTACTG 57.297 37.500 0.00 0.00 0.00 2.74
1555 2046 9.288576 CTCAATCAATAGCAATTTCCTGGTATA 57.711 33.333 0.00 0.00 38.69 1.47
1686 2188 0.179051 CCCAAGGCAAAGCAGCAAAA 60.179 50.000 0.00 0.00 35.83 2.44
1688 2190 2.223745 CCAAGGCAAAGCAGCAAAAAT 58.776 42.857 0.00 0.00 35.83 1.82
1693 2205 2.617774 GGCAAAGCAGCAAAAATTGGAA 59.382 40.909 0.00 0.00 35.83 3.53
1701 2213 7.748691 AGCAGCAAAAATTGGAATGTTTAAT 57.251 28.000 0.00 0.00 0.00 1.40
1734 2246 6.222038 ACTCAATGGTGTAATCACGTCTAT 57.778 37.500 0.00 0.00 44.68 1.98
1748 2260 1.515519 TCTATCGTGCGCCGTTGTC 60.516 57.895 16.00 0.00 37.94 3.18
1867 2914 8.352942 CCTATTGCTAATAATTTGACAACCTCC 58.647 37.037 0.00 0.00 0.00 4.30
1936 2986 7.703197 TCTCGTCATCATTGCGTTAATAAACTA 59.297 33.333 0.00 0.00 33.15 2.24
1969 3105 9.737427 AGATTAGTTTAGATACATGACTCAACG 57.263 33.333 0.00 0.00 0.00 4.10
1989 3125 1.587547 GAGGGAGATTTCGGCATCAC 58.412 55.000 0.00 0.00 0.00 3.06
2047 3187 8.311395 AGTTCAGATGGATTATGTGAAGACTA 57.689 34.615 0.00 0.00 46.13 2.59
2104 3244 4.941657 TCTTCTATGCACATGAGCTACAG 58.058 43.478 16.24 10.02 34.99 2.74
2145 3311 6.427974 GTCATGTGACAATCTTGCTGATATG 58.572 40.000 8.22 0.00 44.18 1.78
2146 3312 6.037940 GTCATGTGACAATCTTGCTGATATGT 59.962 38.462 8.22 0.00 44.18 2.29
2147 3313 6.600427 TCATGTGACAATCTTGCTGATATGTT 59.400 34.615 0.00 0.00 34.45 2.71
2148 3314 6.426980 TGTGACAATCTTGCTGATATGTTC 57.573 37.500 0.00 0.00 34.45 3.18
2149 3315 5.939296 TGTGACAATCTTGCTGATATGTTCA 59.061 36.000 0.00 0.00 34.45 3.18
2150 3316 6.128200 TGTGACAATCTTGCTGATATGTTCAC 60.128 38.462 0.00 0.00 34.45 3.18
2151 3317 6.093219 GTGACAATCTTGCTGATATGTTCACT 59.907 38.462 0.00 0.00 34.45 3.41
2152 3318 7.278646 GTGACAATCTTGCTGATATGTTCACTA 59.721 37.037 0.00 0.00 34.45 2.74
2153 3319 7.823799 TGACAATCTTGCTGATATGTTCACTAA 59.176 33.333 0.00 0.00 34.45 2.24
2154 3320 8.565896 ACAATCTTGCTGATATGTTCACTAAA 57.434 30.769 0.00 0.00 34.45 1.85
2155 3321 9.182214 ACAATCTTGCTGATATGTTCACTAAAT 57.818 29.630 0.00 0.00 34.45 1.40
2156 3322 9.661187 CAATCTTGCTGATATGTTCACTAAATC 57.339 33.333 0.00 0.00 34.45 2.17
2157 3323 8.969260 ATCTTGCTGATATGTTCACTAAATCA 57.031 30.769 0.00 0.00 32.79 2.57
2158 3324 8.969260 TCTTGCTGATATGTTCACTAAATCAT 57.031 30.769 0.00 0.00 0.00 2.45
2159 3325 9.399797 TCTTGCTGATATGTTCACTAAATCATT 57.600 29.630 0.00 0.00 0.00 2.57
2256 3422 2.732001 AAACTTCACAAACTCGTCGC 57.268 45.000 0.00 0.00 0.00 5.19
2413 3583 5.231357 CGTATACTATGCGCTTTGTCTTCAA 59.769 40.000 13.18 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.754621 CTCGGCTGCTCCTGGACTA 60.755 63.158 0.00 0.00 0.00 2.59
48 49 5.772521 AGCAACATCAAAATCAAGTGGTAC 58.227 37.500 0.00 0.00 0.00 3.34
74 75 8.542497 AATTAAACGACATCAAGTAGTAGCAA 57.458 30.769 0.00 0.00 34.81 3.91
163 164 7.394359 AGAGTAACCAACGACTACCTGTTAATA 59.606 37.037 0.00 0.00 0.00 0.98
171 172 2.821969 TGGAGAGTAACCAACGACTACC 59.178 50.000 0.00 0.00 34.25 3.18
175 176 3.056749 ACATCTGGAGAGTAACCAACGAC 60.057 47.826 0.00 0.00 36.95 4.34
178 179 4.537135 TCACATCTGGAGAGTAACCAAC 57.463 45.455 0.00 0.00 36.95 3.77
248 307 0.534203 ACCGAACCAATGACGCTGTT 60.534 50.000 0.00 0.00 0.00 3.16
254 313 7.327518 CCATAGTTTAAAAACCGAACCAATGAC 59.672 37.037 2.02 0.00 39.71 3.06
259 318 7.527568 AATCCATAGTTTAAAAACCGAACCA 57.472 32.000 2.02 0.00 39.71 3.67
305 366 3.733337 AGCTTATCGATGCGGAAATCTT 58.267 40.909 8.54 0.00 0.00 2.40
335 410 7.261325 GTCAGTTCAGTGATGTATGTAGTGAT 58.739 38.462 0.00 0.00 31.55 3.06
377 452 1.005450 GGGTAAAAGTCCAGATGGCCA 59.995 52.381 8.56 8.56 34.44 5.36
399 474 3.055312 GGAAACGGAGGGAGTAGATTTGT 60.055 47.826 0.00 0.00 0.00 2.83
512 591 9.234827 CCTTTCATGGTGCATCTGATAATATTA 57.765 33.333 0.00 0.00 0.00 0.98
537 616 6.206498 AGTGTTCTCGCAAAAGAAAAATACC 58.794 36.000 0.00 0.00 37.04 2.73
543 622 6.612247 TTCATAGTGTTCTCGCAAAAGAAA 57.388 33.333 0.00 0.00 37.04 2.52
546 625 6.373779 ACATTTCATAGTGTTCTCGCAAAAG 58.626 36.000 0.00 0.00 0.00 2.27
668 750 5.049954 TCCGTCCGTTTCTTTTTACTTCATG 60.050 40.000 0.00 0.00 0.00 3.07
669 751 5.058490 TCCGTCCGTTTCTTTTTACTTCAT 58.942 37.500 0.00 0.00 0.00 2.57
670 752 4.440880 TCCGTCCGTTTCTTTTTACTTCA 58.559 39.130 0.00 0.00 0.00 3.02
672 754 4.445453 ACTCCGTCCGTTTCTTTTTACTT 58.555 39.130 0.00 0.00 0.00 2.24
685 767 2.807392 GGAAGTAGAGATACTCCGTCCG 59.193 54.545 0.00 0.00 0.00 4.79
711 793 1.154035 GCCATTGTGCCAAGCGTAC 60.154 57.895 0.00 0.00 0.00 3.67
718 800 0.757512 AACAATGTGCCATTGTGCCA 59.242 45.000 24.82 0.00 40.94 4.92
719 801 2.736192 GTTAACAATGTGCCATTGTGCC 59.264 45.455 24.82 15.79 40.94 5.01
720 802 2.736192 GGTTAACAATGTGCCATTGTGC 59.264 45.455 24.82 19.09 40.94 4.57
721 803 3.740321 GTGGTTAACAATGTGCCATTGTG 59.260 43.478 24.82 8.92 40.94 3.33
722 804 3.386078 TGTGGTTAACAATGTGCCATTGT 59.614 39.130 20.95 20.95 43.35 2.71
723 805 3.987547 TGTGGTTAACAATGTGCCATTG 58.012 40.909 19.95 19.95 35.24 2.82
724 806 4.679373 TTGTGGTTAACAATGTGCCATT 57.321 36.364 8.10 0.00 43.96 3.16
739 821 7.256511 CCTTGTTTTAATAATCCCCTTTGTGGT 60.257 37.037 0.00 0.00 0.00 4.16
740 822 7.038658 TCCTTGTTTTAATAATCCCCTTTGTGG 60.039 37.037 0.00 0.00 0.00 4.17
741 823 7.902087 TCCTTGTTTTAATAATCCCCTTTGTG 58.098 34.615 0.00 0.00 0.00 3.33
744 826 8.499288 TGTTCCTTGTTTTAATAATCCCCTTT 57.501 30.769 0.00 0.00 0.00 3.11
760 850 2.514160 ACTCCTTTTCCCTGTTCCTTGT 59.486 45.455 0.00 0.00 0.00 3.16
832 926 5.296035 CACCAGTAAAAACGGAGTCTCTTTT 59.704 40.000 0.00 2.12 45.00 2.27
836 930 3.986277 TCACCAGTAAAAACGGAGTCTC 58.014 45.455 0.00 0.00 45.00 3.36
838 932 4.312443 TGATCACCAGTAAAAACGGAGTC 58.688 43.478 0.00 0.00 45.00 3.36
840 934 4.994852 TCTTGATCACCAGTAAAAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
853 948 4.935808 AGTAAACACGGATTCTTGATCACC 59.064 41.667 0.00 0.00 36.43 4.02
882 977 3.984508 AGAAACAAAGAGACGAGACGA 57.015 42.857 0.00 0.00 0.00 4.20
883 978 4.740695 AGAAAGAAACAAAGAGACGAGACG 59.259 41.667 0.00 0.00 0.00 4.18
884 979 6.591313 AAGAAAGAAACAAAGAGACGAGAC 57.409 37.500 0.00 0.00 0.00 3.36
889 1010 6.096987 AGGGGAAAAGAAAGAAACAAAGAGAC 59.903 38.462 0.00 0.00 0.00 3.36
923 1048 4.821589 CCGTCTCGGGCTTGGAGC 62.822 72.222 0.00 0.00 44.15 4.70
968 1093 1.210478 TGGCTATGTTGAGGAGGAAGC 59.790 52.381 0.00 0.00 0.00 3.86
970 1095 1.559682 GGTGGCTATGTTGAGGAGGAA 59.440 52.381 0.00 0.00 0.00 3.36
974 1099 2.879756 GCTTTGGTGGCTATGTTGAGGA 60.880 50.000 0.00 0.00 0.00 3.71
976 1101 2.161855 TGCTTTGGTGGCTATGTTGAG 58.838 47.619 0.00 0.00 0.00 3.02
977 1102 2.284754 TGCTTTGGTGGCTATGTTGA 57.715 45.000 0.00 0.00 0.00 3.18
980 1105 1.613437 GTGTTGCTTTGGTGGCTATGT 59.387 47.619 0.00 0.00 0.00 2.29
984 1135 0.175531 GTTGTGTTGCTTTGGTGGCT 59.824 50.000 0.00 0.00 0.00 4.75
998 1149 0.179150 CGGTTGTGGTTGTGGTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
999 1150 1.316706 CCGGTTGTGGTTGTGGTTGT 61.317 55.000 0.00 0.00 0.00 3.32
1000 1151 1.435515 CCGGTTGTGGTTGTGGTTG 59.564 57.895 0.00 0.00 0.00 3.77
1001 1152 2.419739 GCCGGTTGTGGTTGTGGTT 61.420 57.895 1.90 0.00 0.00 3.67
1002 1153 2.831284 GCCGGTTGTGGTTGTGGT 60.831 61.111 1.90 0.00 0.00 4.16
1003 1154 3.959975 CGCCGGTTGTGGTTGTGG 61.960 66.667 1.90 0.00 0.00 4.17
1046 1207 5.841957 AGCTGAGATTGAAAACTTGTTGT 57.158 34.783 0.00 0.00 0.00 3.32
1047 1208 7.514125 CGAAAAGCTGAGATTGAAAACTTGTTG 60.514 37.037 0.00 0.00 0.00 3.33
1048 1209 6.473455 CGAAAAGCTGAGATTGAAAACTTGTT 59.527 34.615 0.00 0.00 0.00 2.83
1129 1305 3.776659 TTGAAGCACGTCGACGCCA 62.777 57.895 35.92 22.10 44.43 5.69
1166 1351 1.815003 CCGCTCCATGAACGATGCA 60.815 57.895 0.00 0.00 0.00 3.96
1169 1354 2.203070 GCCCGCTCCATGAACGAT 60.203 61.111 0.00 0.00 0.00 3.73
1298 1489 0.393132 TTGTGTTGGTCGTTGAGCCA 60.393 50.000 0.00 0.00 0.00 4.75
1320 1511 4.039357 CTGCGACTGGACGGACGT 62.039 66.667 0.00 0.00 0.00 4.34
1344 1535 0.316032 GCCATCTAGACGACGACGAC 60.316 60.000 15.32 8.08 42.66 4.34
1424 1637 4.565564 ACGACGATACAAGTTTAATCCAGC 59.434 41.667 0.00 0.00 0.00 4.85
1555 2046 5.479027 AGGGAACACAAAGTAAACAACAACT 59.521 36.000 0.00 0.00 0.00 3.16
1686 2188 6.757237 TGTGCACTCATTAAACATTCCAATT 58.243 32.000 19.41 0.00 0.00 2.32
1688 2190 5.781210 TGTGCACTCATTAAACATTCCAA 57.219 34.783 19.41 0.00 0.00 3.53
1739 2251 1.504359 TTTTCTGGTAGACAACGGCG 58.496 50.000 4.80 4.80 0.00 6.46
1857 2904 2.043992 TCTTTCCTTCGGAGGTTGTCA 58.956 47.619 10.32 0.00 43.97 3.58
1884 2932 0.874175 GGTTCGTTTGTTTGCTGCCC 60.874 55.000 0.00 0.00 0.00 5.36
1895 2943 3.056821 TGACGAGATCATCTGGTTCGTTT 60.057 43.478 3.52 0.00 43.65 3.60
1969 3105 0.469917 TGATGCCGAAATCTCCCTCC 59.530 55.000 0.00 0.00 0.00 4.30
1989 3125 6.420604 AGACAAACAAAAGTTTATCAATGCGG 59.579 34.615 2.73 0.00 0.00 5.69
2020 3160 8.105829 AGTCTTCACATAATCCATCTGAACTTT 58.894 33.333 0.00 0.00 0.00 2.66
2047 3187 9.167311 CTAATATGCTTTGTGAGGTTACTCTTT 57.833 33.333 0.00 0.00 44.29 2.52
2104 3244 4.275936 ACATGACTTAGTTTGTCCAACTGC 59.724 41.667 0.00 0.00 45.98 4.40
2146 3312 9.330063 GGATGATGTCAGTAATGATTTAGTGAA 57.670 33.333 0.00 0.00 45.08 3.18
2147 3313 8.708378 AGGATGATGTCAGTAATGATTTAGTGA 58.292 33.333 0.00 0.31 42.70 3.41
2148 3314 8.899427 AGGATGATGTCAGTAATGATTTAGTG 57.101 34.615 0.00 0.00 39.25 2.74
2149 3315 9.553064 GAAGGATGATGTCAGTAATGATTTAGT 57.447 33.333 0.00 0.00 0.00 2.24
2150 3316 8.706936 CGAAGGATGATGTCAGTAATGATTTAG 58.293 37.037 0.00 0.00 0.00 1.85
2151 3317 8.421002 TCGAAGGATGATGTCAGTAATGATTTA 58.579 33.333 0.00 0.00 0.00 1.40
2152 3318 7.275183 TCGAAGGATGATGTCAGTAATGATTT 58.725 34.615 0.00 0.00 0.00 2.17
2153 3319 6.820335 TCGAAGGATGATGTCAGTAATGATT 58.180 36.000 0.00 0.00 0.00 2.57
2154 3320 6.266330 TCTCGAAGGATGATGTCAGTAATGAT 59.734 38.462 0.00 0.00 0.00 2.45
2155 3321 5.594317 TCTCGAAGGATGATGTCAGTAATGA 59.406 40.000 0.00 0.00 0.00 2.57
2156 3322 5.836347 TCTCGAAGGATGATGTCAGTAATG 58.164 41.667 0.00 0.00 0.00 1.90
2157 3323 6.083098 CTCTCGAAGGATGATGTCAGTAAT 57.917 41.667 0.00 0.00 0.00 1.89
2158 3324 5.506686 CTCTCGAAGGATGATGTCAGTAA 57.493 43.478 0.00 0.00 0.00 2.24
2181 3347 1.141645 TACCGATTTCACACACGCAC 58.858 50.000 0.00 0.00 0.00 5.34
2343 3511 3.181774 CGTCGAAAACTCGTGTGAGAAAT 59.818 43.478 0.00 0.00 45.57 2.17
2361 3530 2.661504 TTGCACAAATTGTCTCGTCG 57.338 45.000 0.00 0.00 0.00 5.12
2374 3543 7.042992 GCATAGTATACGTTCTTGTATTGCACA 60.043 37.037 0.00 0.00 35.99 4.57
2386 3555 4.738740 AGACAAAGCGCATAGTATACGTTC 59.261 41.667 11.47 0.00 0.00 3.95
2389 3558 4.738252 TGAAGACAAAGCGCATAGTATACG 59.262 41.667 11.47 0.00 0.00 3.06
2428 3598 3.974871 TGCCTTACAACTCCGAAAAAC 57.025 42.857 0.00 0.00 0.00 2.43
2434 3606 6.028368 CGTATATCTATGCCTTACAACTCCG 58.972 44.000 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.