Multiple sequence alignment - TraesCS3B01G032500

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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 TraesCS3B01G032500 chr3B 100.000 3136 0 0 1 3136 15075330 15078465 0.000000e+00 5792.0
1 TraesCS3B01G032500 chr3B 87.202 2516 232 47 674 3136 15173003 15170525 0.000000e+00 2780.0
2 TraesCS3B01G032500 chr3B 84.848 1518 160 32 671 2130 26190643 26192148 0.000000e+00 1465.0
3 TraesCS3B01G032500 chr3B 84.783 1518 161 32 671 2130 25906490 25907995 0.000000e+00 1459.0
4 TraesCS3B01G032500 chr3B 84.717 1518 162 32 671 2130 26042948 26044453 0.000000e+00 1454.0
5 TraesCS3B01G032500 chr3B 84.585 1518 164 32 671 2130 26385142 26386647 0.000000e+00 1443.0
6 TraesCS3B01G032500 chr3B 84.443 1517 168 34 671 2130 26341539 26343044 0.000000e+00 1432.0
7 TraesCS3B01G032500 chr3B 84.256 1518 169 32 671 2130 25869996 25871501 0.000000e+00 1415.0
8 TraesCS3B01G032500 chr3B 84.256 1518 169 32 671 2130 26003044 26004549 0.000000e+00 1415.0
9 TraesCS3B01G032500 chr3B 82.691 1271 179 24 1113 2368 15141712 15140468 0.000000e+00 1090.0
10 TraesCS3B01G032500 chr3B 82.242 1267 190 21 1115 2370 25921155 25922397 0.000000e+00 1061.0
11 TraesCS3B01G032500 chr3B 82.163 1267 191 21 1115 2370 26246266 26247508 0.000000e+00 1055.0
12 TraesCS3B01G032500 chr3B 80.980 1367 218 26 1115 2469 26430103 26431439 0.000000e+00 1046.0
13 TraesCS3B01G032500 chr3B 81.926 1267 194 21 1115 2370 26057278 26058520 0.000000e+00 1038.0
14 TraesCS3B01G032500 chr3B 83.723 1155 122 31 675 1774 26300807 26301950 0.000000e+00 1031.0
15 TraesCS3B01G032500 chr3B 80.435 414 62 8 2735 3136 26050129 26050535 6.580000e-77 298.0
16 TraesCS3B01G032500 chr3B 80.435 414 62 8 2735 3136 26392354 26392760 6.580000e-77 298.0
17 TraesCS3B01G032500 chr3B 79.952 414 63 9 2735 3136 26239132 26239537 1.420000e-73 287.0
18 TraesCS3B01G032500 chr3B 80.296 406 46 12 675 1052 15179017 15178618 3.080000e-70 276.0
19 TraesCS3B01G032500 chr3B 84.082 245 26 8 18 249 26189382 26189626 1.130000e-54 224.0
20 TraesCS3B01G032500 chr3B 84.082 245 26 8 18 249 26299440 26299684 1.130000e-54 224.0
21 TraesCS3B01G032500 chr3B 83.673 245 27 8 18 249 26001814 26002058 5.270000e-53 219.0
22 TraesCS3B01G032500 chr3B 82.857 245 29 8 18 249 25868678 25868922 1.140000e-49 207.0
23 TraesCS3B01G032500 chr3B 82.857 245 29 8 18 249 26071833 26072077 1.140000e-49 207.0
24 TraesCS3B01G032500 chr3B 82.449 245 30 8 18 249 26340115 26340359 5.300000e-48 202.0
25 TraesCS3B01G032500 chr3B 82.418 182 20 3 2966 3136 25914246 25914426 7.010000e-32 148.0
26 TraesCS3B01G032500 chr3A 89.129 1527 143 11 1297 2813 17485350 17483837 0.000000e+00 1879.0
27 TraesCS3B01G032500 chr3A 83.856 1499 146 41 671 2115 17432884 17434340 0.000000e+00 1339.0
28 TraesCS3B01G032500 chr3A 83.864 1351 171 25 1113 2447 17452971 17451652 0.000000e+00 1243.0
29 TraesCS3B01G032500 chr3A 82.383 982 78 42 389 1302 17486715 17485761 0.000000e+00 767.0
30 TraesCS3B01G032500 chr3A 85.811 296 29 5 2853 3136 17483828 17483534 5.080000e-78 302.0
31 TraesCS3B01G032500 chr3D 84.380 1274 158 23 1113 2370 10804083 10805331 0.000000e+00 1212.0
32 TraesCS3B01G032500 chr3D 82.884 1075 105 35 674 1688 10898724 10897669 0.000000e+00 893.0
33 TraesCS3B01G032500 chr3D 88.227 688 60 11 1 672 10797712 10798394 0.000000e+00 802.0
34 TraesCS3B01G032500 chr3D 87.162 296 25 4 2853 3136 10799194 10799488 1.080000e-84 324.0
35 TraesCS3B01G032500 chr3D 88.940 217 12 7 736 950 10798747 10798541 1.120000e-64 257.0
36 TraesCS3B01G032500 chr1D 88.785 107 11 1 3030 3136 447661397 447661502 2.540000e-26 130.0
37 TraesCS3B01G032500 chr4B 92.593 54 3 1 472 524 404186375 404186322 3.350000e-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 TraesCS3B01G032500 chr3B 15075330 15078465 3135 False 5792.000000 5792 100.000000 1 3136 1 chr3B.!!$F1 3135
1 TraesCS3B01G032500 chr3B 15170525 15173003 2478 True 2780.000000 2780 87.202000 674 3136 1 chr3B.!!$R2 2462
2 TraesCS3B01G032500 chr3B 25906490 25907995 1505 False 1459.000000 1459 84.783000 671 2130 1 chr3B.!!$F2 1459
3 TraesCS3B01G032500 chr3B 26042948 26044453 1505 False 1454.000000 1454 84.717000 671 2130 1 chr3B.!!$F5 1459
4 TraesCS3B01G032500 chr3B 26385142 26386647 1505 False 1443.000000 1443 84.585000 671 2130 1 chr3B.!!$F11 1459
5 TraesCS3B01G032500 chr3B 15140468 15141712 1244 True 1090.000000 1090 82.691000 1113 2368 1 chr3B.!!$R1 1255
6 TraesCS3B01G032500 chr3B 25921155 25922397 1242 False 1061.000000 1061 82.242000 1115 2370 1 chr3B.!!$F4 1255
7 TraesCS3B01G032500 chr3B 26246266 26247508 1242 False 1055.000000 1055 82.163000 1115 2370 1 chr3B.!!$F10 1255
8 TraesCS3B01G032500 chr3B 26430103 26431439 1336 False 1046.000000 1046 80.980000 1115 2469 1 chr3B.!!$F13 1354
9 TraesCS3B01G032500 chr3B 26057278 26058520 1242 False 1038.000000 1038 81.926000 1115 2370 1 chr3B.!!$F7 1255
10 TraesCS3B01G032500 chr3B 26189382 26192148 2766 False 844.500000 1465 84.465000 18 2130 2 chr3B.!!$F16 2112
11 TraesCS3B01G032500 chr3B 26001814 26004549 2735 False 817.000000 1415 83.964500 18 2130 2 chr3B.!!$F15 2112
12 TraesCS3B01G032500 chr3B 26340115 26343044 2929 False 817.000000 1432 83.446000 18 2130 2 chr3B.!!$F18 2112
13 TraesCS3B01G032500 chr3B 25868678 25871501 2823 False 811.000000 1415 83.556500 18 2130 2 chr3B.!!$F14 2112
14 TraesCS3B01G032500 chr3B 26299440 26301950 2510 False 627.500000 1031 83.902500 18 1774 2 chr3B.!!$F17 1756
15 TraesCS3B01G032500 chr3A 17432884 17434340 1456 False 1339.000000 1339 83.856000 671 2115 1 chr3A.!!$F1 1444
16 TraesCS3B01G032500 chr3A 17451652 17452971 1319 True 1243.000000 1243 83.864000 1113 2447 1 chr3A.!!$R1 1334
17 TraesCS3B01G032500 chr3A 17483534 17486715 3181 True 982.666667 1879 85.774333 389 3136 3 chr3A.!!$R2 2747
18 TraesCS3B01G032500 chr3D 10804083 10805331 1248 False 1212.000000 1212 84.380000 1113 2370 1 chr3D.!!$F1 1257
19 TraesCS3B01G032500 chr3D 10897669 10898724 1055 True 893.000000 893 82.884000 674 1688 1 chr3D.!!$R2 1014
20 TraesCS3B01G032500 chr3D 10797712 10799488 1776 False 563.000000 802 87.694500 1 3136 2 chr3D.!!$F2 3135

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
469 1328 0.609957 TTCACATGCTCCAAGGCCAG 60.610 55.000 5.01 0.0 0.00 4.85 F
1180 2220 0.536006 GGCTTTGTGCTCTCTGTGGT 60.536 55.000 0.00 0.0 42.39 4.16 F
1929 3674 1.487976 TCCATGGATGTCAAGAGCTCC 59.512 52.381 11.44 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 3493 0.179103 GCATTTGTATGGCAGTGGGC 60.179 55.0 0.00 0.00 43.74 5.36 R
2019 3764 1.084289 GTCCATCGGTGTTGGTTAGC 58.916 55.0 0.00 0.00 35.64 3.09 R
2800 4560 1.107114 ATTCGTGGAGCTCTCGACAT 58.893 50.0 25.08 19.56 38.06 3.06 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
74 75 6.311445 CAGAAGCACTATGTTTCTCGTACAAT 59.689 38.462 5.10 0.00 42.98 2.71
106 107 3.642848 TGCTTTTCCCTTTCAAGAAGCAT 59.357 39.130 8.56 0.00 42.97 3.79
191 205 1.250476 GCAAATACGTGCTTCTTGCG 58.750 50.000 0.00 0.00 46.63 4.85
210 224 1.134521 CGGAGGCACAGGTTATGCTTA 60.135 52.381 0.00 0.00 42.93 3.09
227 241 4.944048 TGCTTATCGCAGTAGCAAATCTA 58.056 39.130 0.00 0.00 45.47 1.98
252 266 4.024387 GCTTCCACGAGAAACACAATTGTA 60.024 41.667 11.53 0.00 33.55 2.41
297 712 5.488645 TTTAAGAAGGACGGTTGTGTTTC 57.511 39.130 0.00 0.00 0.00 2.78
334 750 7.610580 AAAATAATTTTCTCCAACACCCAGA 57.389 32.000 0.00 0.00 0.00 3.86
350 977 5.186992 ACACCCAGATAATTAGGCAAAAACC 59.813 40.000 0.00 0.00 0.00 3.27
351 978 5.422012 CACCCAGATAATTAGGCAAAAACCT 59.578 40.000 0.00 0.00 44.31 3.50
387 1016 4.835678 ACCCATCTAAAATCCGTAAACGT 58.164 39.130 1.41 0.00 37.74 3.99
455 1314 1.227527 CTGGACGCACCACTTCACA 60.228 57.895 0.00 0.00 44.64 3.58
469 1328 0.609957 TTCACATGCTCCAAGGCCAG 60.610 55.000 5.01 0.00 0.00 4.85
480 1341 3.765511 CTCCAAGGCCAGAAAAATGATCA 59.234 43.478 5.01 0.00 0.00 2.92
489 1350 5.163561 GCCAGAAAAATGATCATTACGGGAA 60.164 40.000 26.50 0.00 0.00 3.97
490 1351 6.461509 GCCAGAAAAATGATCATTACGGGAAT 60.462 38.462 26.50 10.53 0.00 3.01
614 1491 5.945155 GTGAAACCGATAAATTGCTAACCA 58.055 37.500 0.00 0.00 0.00 3.67
628 1507 0.751452 TAACCAAAAACGTTGCCCCC 59.249 50.000 0.00 0.00 0.00 5.40
657 1544 1.017387 GGGCAACTTGAGGATTAGCG 58.983 55.000 0.00 0.00 0.00 4.26
658 1545 1.406887 GGGCAACTTGAGGATTAGCGA 60.407 52.381 0.00 0.00 0.00 4.93
672 1612 3.648339 TTAGCGAGTTTAACGTCCACT 57.352 42.857 0.00 0.00 0.00 4.00
699 1670 5.391843 CGAACATTACTTCATGACCATGCAA 60.392 40.000 0.00 1.26 38.65 4.08
703 1674 7.388437 ACATTACTTCATGACCATGCAAAAAT 58.612 30.769 0.00 1.38 38.65 1.82
783 1754 5.400066 TCTTCACGACCTAATCATCACAA 57.600 39.130 0.00 0.00 0.00 3.33
784 1755 5.977635 TCTTCACGACCTAATCATCACAAT 58.022 37.500 0.00 0.00 0.00 2.71
785 1756 6.406370 TCTTCACGACCTAATCATCACAATT 58.594 36.000 0.00 0.00 0.00 2.32
787 1758 5.729510 TCACGACCTAATCATCACAATTCA 58.270 37.500 0.00 0.00 0.00 2.57
788 1759 5.580691 TCACGACCTAATCATCACAATTCAC 59.419 40.000 0.00 0.00 0.00 3.18
789 1760 5.351189 CACGACCTAATCATCACAATTCACA 59.649 40.000 0.00 0.00 0.00 3.58
793 1771 4.949238 CCTAATCATCACAATTCACACCCA 59.051 41.667 0.00 0.00 0.00 4.51
876 1858 1.440850 GTGTCTGCGCGTACGTACA 60.441 57.895 24.50 13.98 42.83 2.90
877 1859 0.795735 GTGTCTGCGCGTACGTACAT 60.796 55.000 24.50 0.00 42.83 2.29
953 1939 3.137484 CACCTTTGCACGCTAGCTA 57.863 52.632 13.93 0.00 34.99 3.32
1065 2094 2.731217 GTCAGCAACAAATCACACACC 58.269 47.619 0.00 0.00 0.00 4.16
1096 2125 2.551270 TCCACAGATACTTGAAGGGCT 58.449 47.619 0.00 0.00 0.00 5.19
1124 2164 1.877576 TAGCGGCAGATATGGCTCCG 61.878 60.000 12.41 6.43 42.68 4.63
1180 2220 0.536006 GGCTTTGTGCTCTCTGTGGT 60.536 55.000 0.00 0.00 42.39 4.16
1257 2298 4.728102 CGTTCTACGGCGGCACCA 62.728 66.667 13.24 0.00 38.08 4.17
1272 2313 4.778415 CCAGACGCCTCCGACACG 62.778 72.222 0.00 0.00 38.29 4.49
1311 2768 2.724977 TTCAACTCACGCCTCTACAG 57.275 50.000 0.00 0.00 0.00 2.74
1334 2791 4.386951 TAGTGCGTGCATGCCCGT 62.387 61.111 27.43 14.30 0.00 5.28
1349 2806 3.745799 TGCCCGTTTGATCTTGTTCTTA 58.254 40.909 0.00 0.00 0.00 2.10
1358 2815 7.571983 CGTTTGATCTTGTTCTTATCTGCACTT 60.572 37.037 0.00 0.00 0.00 3.16
1433 2897 2.024273 TCTTCTCTGAAGGGTACGGGAT 60.024 50.000 7.37 0.00 0.00 3.85
1476 2940 2.680913 GCTGTTCAATGACGGCGCT 61.681 57.895 6.90 0.00 41.59 5.92
1698 3162 2.429933 ATAGAGGTGGCATCATCCCT 57.570 50.000 0.00 0.00 0.00 4.20
1736 3200 7.942990 AGGTATATATGCGCCTCTTATAAGTC 58.057 38.462 12.19 2.92 0.00 3.01
1760 3224 5.049954 CCAAAAATTAGTTCGAAGTCACCGA 60.050 40.000 9.20 0.00 0.00 4.69
1780 3489 4.094442 CCGAAGCCACATAACTTTAACTCC 59.906 45.833 0.00 0.00 0.00 3.85
1782 3491 6.103997 CGAAGCCACATAACTTTAACTCCTA 58.896 40.000 0.00 0.00 0.00 2.94
1783 3492 6.761714 CGAAGCCACATAACTTTAACTCCTAT 59.238 38.462 0.00 0.00 0.00 2.57
1784 3493 7.254455 CGAAGCCACATAACTTTAACTCCTATG 60.254 40.741 0.00 0.00 0.00 2.23
1785 3494 5.823045 AGCCACATAACTTTAACTCCTATGC 59.177 40.000 0.00 0.00 0.00 3.14
1929 3674 1.487976 TCCATGGATGTCAAGAGCTCC 59.512 52.381 11.44 0.00 0.00 4.70
2019 3764 3.008330 CAACAAGATGCTCTCCTTCAGG 58.992 50.000 0.00 0.00 0.00 3.86
2031 3776 1.073284 TCCTTCAGGCTAACCAACACC 59.927 52.381 0.00 0.00 39.06 4.16
2123 3869 5.164022 GCAAATTGCAATTCTACTGAGCAAC 60.164 40.000 24.28 3.35 46.43 4.17
2197 3944 2.691526 ACAGCATTGCGATGAAATGGAT 59.308 40.909 18.58 0.00 35.88 3.41
2198 3945 3.131577 ACAGCATTGCGATGAAATGGATT 59.868 39.130 18.58 0.00 35.88 3.01
2220 3969 8.413229 GGATTTTATGGTGCTTAATGTGTATGT 58.587 33.333 0.00 0.00 0.00 2.29
2518 4275 8.181904 AGCTGAGGAGAAAAACAAAATAATCA 57.818 30.769 0.00 0.00 0.00 2.57
2592 4349 6.507900 TGCAAAATTTTATCGTTCAAGTCCA 58.492 32.000 2.44 0.00 0.00 4.02
2599 4356 9.667107 AATTTTATCGTTCAAGTCCATTCTAGA 57.333 29.630 0.00 0.00 0.00 2.43
2600 4357 8.475331 TTTTATCGTTCAAGTCCATTCTAGAC 57.525 34.615 0.00 0.00 34.31 2.59
2651 4408 8.876275 TGTAGAAGACGTTGTAACAATAAGTT 57.124 30.769 0.00 0.00 44.27 2.66
2652 4409 9.316730 TGTAGAAGACGTTGTAACAATAAGTTT 57.683 29.630 0.00 0.00 41.64 2.66
2774 4534 5.763876 ATAATAACCTGATAGACCAGCCC 57.236 43.478 0.00 0.00 32.97 5.19
2800 4560 2.828877 ACGTTCAAAGATGTCCACGAA 58.171 42.857 0.00 0.00 33.13 3.85
2805 4565 2.993220 TCAAAGATGTCCACGAATGTCG 59.007 45.455 0.00 0.00 46.93 4.35
2813 4573 0.526524 CCACGAATGTCGAGAGCTCC 60.527 60.000 10.93 0.68 43.74 4.70
2814 4574 0.171231 CACGAATGTCGAGAGCTCCA 59.829 55.000 10.93 0.80 43.74 3.86
2815 4575 0.171455 ACGAATGTCGAGAGCTCCAC 59.829 55.000 10.93 5.59 43.74 4.02
2816 4576 0.863538 CGAATGTCGAGAGCTCCACG 60.864 60.000 20.10 20.10 43.74 4.94
2817 4577 0.452184 GAATGTCGAGAGCTCCACGA 59.548 55.000 23.27 23.27 0.00 4.35
2823 4583 1.135083 TCGAGAGCTCCACGAATTTCC 60.135 52.381 24.34 0.00 33.20 3.13
2830 4590 1.726791 CTCCACGAATTTCCACGACTG 59.273 52.381 0.00 0.00 0.00 3.51
2859 4619 3.463585 CATGCAAATGGGGCGCCT 61.464 61.111 28.56 2.77 0.00 5.52
2945 4706 7.101652 TGGTCAAAAGCTTATGTACAACAAA 57.898 32.000 0.00 0.00 0.00 2.83
2946 4707 6.975772 TGGTCAAAAGCTTATGTACAACAAAC 59.024 34.615 0.00 0.00 0.00 2.93
2954 4715 2.834574 TGTACAACAAACTTGTGCCG 57.165 45.000 0.00 0.00 41.31 5.69
2975 4736 1.055849 GGGTGGAACTTTGGGCAAAT 58.944 50.000 0.00 0.00 36.74 2.32
2990 4751 7.790782 TTGGGCAAATATTTCCTAGAAACTT 57.209 32.000 0.00 0.00 0.00 2.66
3021 4782 2.296792 TGAACAATGTGTGTGGACCAG 58.703 47.619 0.00 0.00 40.60 4.00
3028 4789 3.847671 TGTGTGTGGACCAGTTAATCA 57.152 42.857 0.00 0.00 0.00 2.57
3043 4815 6.259608 CCAGTTAATCATGACAGATTCCTGAC 59.740 42.308 0.00 0.00 43.02 3.51
3102 4874 3.154589 GGGCTGTACTTGTAGCACC 57.845 57.895 5.41 1.26 41.63 5.01
3112 4884 2.167900 ACTTGTAGCACCGGTCCTATTC 59.832 50.000 8.87 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.441495 CCCTGGAAAAAGAGAAAACCACAC 60.441 45.833 0.00 0.00 0.00 3.82
50 51 5.386958 TGTACGAGAAACATAGTGCTTCT 57.613 39.130 0.00 0.00 35.69 2.85
74 75 3.806949 AGGGAAAAGCACAACCTATGA 57.193 42.857 0.00 0.00 0.00 2.15
179 193 3.793144 GCCTCCGCAAGAAGCACG 61.793 66.667 0.00 0.00 46.13 5.34
191 205 2.710096 TAAGCATAACCTGTGCCTCC 57.290 50.000 0.00 0.00 43.50 4.30
227 241 2.254546 TGTGTTTCTCGTGGAAGCAT 57.745 45.000 11.53 0.00 44.54 3.79
277 692 3.125316 CGAAACACAACCGTCCTTCTTA 58.875 45.455 0.00 0.00 0.00 2.10
284 699 1.897641 TTTTGCGAAACACAACCGTC 58.102 45.000 0.00 0.00 0.00 4.79
311 726 7.797121 ATCTGGGTGTTGGAGAAAATTATTT 57.203 32.000 0.00 0.00 0.00 1.40
315 731 7.797121 AATTATCTGGGTGTTGGAGAAAATT 57.203 32.000 0.00 0.00 0.00 1.82
316 732 7.561356 CCTAATTATCTGGGTGTTGGAGAAAAT 59.439 37.037 0.00 0.00 0.00 1.82
327 743 5.422012 AGGTTTTTGCCTAATTATCTGGGTG 59.578 40.000 0.00 0.00 37.04 4.61
334 750 7.912719 TGGCTTTTAGGTTTTTGCCTAATTAT 58.087 30.769 5.54 0.00 46.77 1.28
380 1009 6.784176 TCTGGGTTTCTTTTTACACGTTTAC 58.216 36.000 0.00 0.00 0.00 2.01
381 1010 6.038492 CCTCTGGGTTTCTTTTTACACGTTTA 59.962 38.462 0.00 0.00 0.00 2.01
387 1016 4.167307 ACTCCCTCTGGGTTTCTTTTTACA 59.833 41.667 2.25 0.00 44.74 2.41
421 1280 3.181499 CGTCCAGTCGCAGTAACTTATCT 60.181 47.826 0.00 0.00 0.00 1.98
455 1314 2.014010 TTTTTCTGGCCTTGGAGCAT 57.986 45.000 3.32 0.00 0.00 3.79
469 1328 6.447162 GGGATTCCCGTAATGATCATTTTTC 58.553 40.000 25.26 14.78 32.13 2.29
569 1435 7.648142 TCACCATATTTGTTGTTTCTCACTTC 58.352 34.615 0.00 0.00 0.00 3.01
614 1491 1.034356 GTGTAGGGGGCAACGTTTTT 58.966 50.000 0.00 0.00 37.60 1.94
628 1507 1.944024 TCAAGTTGCCCAAACGTGTAG 59.056 47.619 0.00 0.00 45.28 2.74
672 1612 4.888917 TGGTCATGAAGTAATGTTCGTCA 58.111 39.130 0.00 0.00 0.00 4.35
699 1670 5.060506 TCAATGCGTATCCGTCCATATTTT 58.939 37.500 0.00 0.00 36.15 1.82
703 1674 2.888414 TCTCAATGCGTATCCGTCCATA 59.112 45.455 0.00 0.00 36.15 2.74
811 1789 1.142748 GGTCCTGCATCTGTCCTCG 59.857 63.158 0.00 0.00 0.00 4.63
904 1889 4.041917 CCGTGCCATGCTTGCGTT 62.042 61.111 0.00 0.00 0.00 4.84
951 1937 2.877168 GAGGATTCTGCAAGGCATGTAG 59.123 50.000 1.15 1.15 42.56 2.74
953 1939 1.684248 GGAGGATTCTGCAAGGCATGT 60.684 52.381 0.00 0.00 38.13 3.21
997 2018 9.692749 TCTGATGATCGTTTGTTTATATAGTCC 57.307 33.333 0.00 0.00 0.00 3.85
1065 2094 0.806868 ATCTGTGGATGCGTTTGCTG 59.193 50.000 0.00 0.00 43.34 4.41
1096 2125 1.607801 ATCTGCCGCTAGCTGTGTCA 61.608 55.000 13.93 0.00 44.23 3.58
1124 2164 3.123620 CCTGCAGCAACTCGAGCC 61.124 66.667 13.61 0.84 0.00 4.70
1254 2295 3.681835 GTGTCGGAGGCGTCTGGT 61.682 66.667 14.95 0.00 28.88 4.00
1256 2297 3.052620 ATCGTGTCGGAGGCGTCTG 62.053 63.158 9.00 9.00 28.88 3.51
1257 2298 2.750637 ATCGTGTCGGAGGCGTCT 60.751 61.111 6.34 0.00 28.88 4.18
1272 2313 9.125026 AGTTGAATGATTAGTTGATTACCCATC 57.875 33.333 0.00 0.00 0.00 3.51
1311 2768 0.590732 GCATGCACGCACTAGATTGC 60.591 55.000 14.21 0.00 39.28 3.56
1334 2791 7.750229 AAGTGCAGATAAGAACAAGATCAAA 57.250 32.000 0.00 0.00 0.00 2.69
1349 2806 2.455674 TCGCAAGTGTAAGTGCAGAT 57.544 45.000 0.00 0.00 40.94 2.90
1395 2859 3.887335 GAGGTTGCCGTACCCGCAA 62.887 63.158 10.20 10.20 39.08 4.85
1433 2897 4.228567 TCAGAACCACCGTGCGCA 62.229 61.111 5.66 5.66 0.00 6.09
1627 3091 2.028484 GTCGAAGTGTGGCCGTGA 59.972 61.111 0.00 0.00 0.00 4.35
1698 3162 6.127730 CGCATATATACCTCTGGTACATGACA 60.128 42.308 0.00 0.00 41.31 3.58
1736 3200 5.049954 TCGGTGACTTCGAACTAATTTTTGG 60.050 40.000 0.00 0.00 33.42 3.28
1750 3214 2.380084 TATGTGGCTTCGGTGACTTC 57.620 50.000 0.00 0.00 0.00 3.01
1760 3224 6.318900 GCATAGGAGTTAAAGTTATGTGGCTT 59.681 38.462 0.00 0.00 0.00 4.35
1784 3493 0.179103 GCATTTGTATGGCAGTGGGC 60.179 55.000 0.00 0.00 43.74 5.36
1785 3494 1.135527 CTGCATTTGTATGGCAGTGGG 59.864 52.381 4.78 0.00 34.26 4.61
1835 3546 8.991783 ATAATCATGACCATTGATTCTGAACT 57.008 30.769 0.00 0.00 34.55 3.01
1863 3574 6.882610 ACATTGCTCACAAGAACAAGATTA 57.117 33.333 0.00 0.00 39.69 1.75
1929 3674 0.652592 GCATCCAGTCGTCCGAATTG 59.347 55.000 0.00 0.00 0.00 2.32
1960 3705 2.481471 GCCAGTTAGCGCCCCAATC 61.481 63.158 2.29 0.00 0.00 2.67
2019 3764 1.084289 GTCCATCGGTGTTGGTTAGC 58.916 55.000 0.00 0.00 35.64 3.09
2123 3869 7.099266 TGGTAAATTAATTGGTCAGCAGATG 57.901 36.000 0.39 0.00 0.00 2.90
2178 3925 4.395959 AAATCCATTTCATCGCAATGCT 57.604 36.364 2.94 0.00 32.58 3.79
2198 3945 9.456147 AGTAACATACACATTAAGCACCATAAA 57.544 29.630 0.00 0.00 0.00 1.40
2374 4128 4.703575 TGGCGTACCACTATGTAGATATCC 59.296 45.833 0.00 0.00 42.67 2.59
2545 4302 8.565416 TGCATCAACAATTTGCATTATTCAAAA 58.435 25.926 0.00 0.00 41.18 2.44
2621 4378 7.599630 TTGTTACAACGTCTTCTACAAAACT 57.400 32.000 0.00 0.00 0.00 2.66
2653 4410 8.603181 GTTGAGCTAGAATTGCAAAAAGAAAAA 58.397 29.630 1.71 0.00 0.00 1.94
2654 4411 7.224557 GGTTGAGCTAGAATTGCAAAAAGAAAA 59.775 33.333 1.71 0.00 0.00 2.29
2665 4422 3.198635 TGAGGAGGGTTGAGCTAGAATTG 59.801 47.826 0.00 0.00 0.00 2.32
2717 4477 7.997223 CCACCTTATATATAGACCTATCGGTGA 59.003 40.741 0.00 0.00 45.73 4.02
2718 4478 7.778853 ACCACCTTATATATAGACCTATCGGTG 59.221 40.741 0.00 0.00 45.73 4.94
2736 4496 8.426489 CAGGTTATTATAGTAGCAACCACCTTA 58.574 37.037 4.75 0.00 40.92 2.69
2744 4504 9.596308 TGGTCTATCAGGTTATTATAGTAGCAA 57.404 33.333 0.00 0.00 0.00 3.91
2774 4534 3.559655 TGGACATCTTTGAACGTTGAGTG 59.440 43.478 5.00 5.06 0.00 3.51
2800 4560 1.107114 ATTCGTGGAGCTCTCGACAT 58.893 50.000 25.08 19.56 38.06 3.06
2805 4565 2.003301 GTGGAAATTCGTGGAGCTCTC 58.997 52.381 14.64 4.40 0.00 3.20
2823 4583 2.390599 CCATTGGCGTCCAGTCGTG 61.391 63.158 0.00 0.00 33.81 4.35
2837 4597 1.225148 GCCCCATTTGCATGCCATT 59.775 52.632 16.68 0.00 0.00 3.16
2946 4707 4.278513 TTCCACCCCCGGCACAAG 62.279 66.667 0.00 0.00 0.00 3.16
2954 4715 2.603473 GCCCAAAGTTCCACCCCC 60.603 66.667 0.00 0.00 0.00 5.40
2990 4751 6.971756 CACACACATTGTTCATTTCAACTACA 59.028 34.615 0.00 0.00 35.67 2.74
2997 4758 4.202101 TGGTCCACACACATTGTTCATTTC 60.202 41.667 0.00 0.00 35.67 2.17
3028 4789 6.124340 TGCATAATTGTCAGGAATCTGTCAT 58.876 36.000 0.00 0.00 41.59 3.06
3102 4874 6.986817 AGAAATTGTCACATAGAATAGGACCG 59.013 38.462 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.