Multiple sequence alignment - TraesCS4A01G051600

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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 TraesCS4A01G051600 chr4A 100.000 3821 0 0 1 3821 42272012 42275832 0.000000e+00 7057.0
1 TraesCS4A01G051600 chr4A 97.059 34 1 0 1459 1492 42273439 42273472 1.480000e-04 58.4
2 TraesCS4A01G051600 chr4A 97.059 34 1 0 1428 1461 42273470 42273503 1.480000e-04 58.4
3 TraesCS4A01G051600 chr4D 95.288 2016 67 18 1462 3461 421532523 421530520 0.000000e+00 3171.0
4 TraesCS4A01G051600 chr4D 94.343 990 46 7 474 1461 421533474 421532493 0.000000e+00 1509.0
5 TraesCS4A01G051600 chr4D 94.366 355 16 2 3470 3821 421530454 421530101 3.360000e-150 542.0
6 TraesCS4A01G051600 chr4D 89.059 393 23 11 35 427 421534244 421533872 1.610000e-128 470.0
7 TraesCS4A01G051600 chr4B 94.453 1965 82 13 1507 3469 518643490 518641551 0.000000e+00 3000.0
8 TraesCS4A01G051600 chr4B 92.255 581 34 5 482 1062 518644416 518643847 0.000000e+00 813.0
9 TraesCS4A01G051600 chr4B 89.937 636 52 7 506 1141 478184936 478184313 0.000000e+00 809.0
10 TraesCS4A01G051600 chr4B 93.103 348 20 2 3475 3819 518641496 518641150 1.220000e-139 507.0
11 TraesCS4A01G051600 chr4B 90.110 364 14 2 1095 1437 518643852 518643490 1.620000e-123 453.0
12 TraesCS4A01G051600 chr4B 95.238 231 8 3 223 451 518644921 518644692 2.810000e-96 363.0
13 TraesCS4A01G051600 chr4B 88.485 165 18 1 65 229 518646526 518646363 8.370000e-47 198.0
14 TraesCS4A01G051600 chr4B 95.745 94 4 0 1368 1461 478184316 478184223 6.610000e-33 152.0
15 TraesCS4A01G051600 chr4B 96.552 87 3 0 1459 1545 478184256 478184170 1.110000e-30 145.0
16 TraesCS4A01G051600 chr2B 89.143 700 63 10 443 1141 31122650 31123337 0.000000e+00 859.0
17 TraesCS4A01G051600 chr2B 96.809 94 3 0 1368 1461 31123334 31123427 1.420000e-34 158.0
18 TraesCS4A01G051600 chr2B 96.552 87 3 0 1459 1545 31123394 31123480 1.110000e-30 145.0
19 TraesCS4A01G051600 chr2A 88.856 673 57 11 443 1114 72566645 72565990 0.000000e+00 811.0
20 TraesCS4A01G051600 chr2A 91.837 98 4 1 1368 1461 72521229 72521132 2.390000e-27 134.0
21 TraesCS4A01G051600 chr2A 91.954 87 5 2 332 416 72604226 72604140 1.860000e-23 121.0
22 TraesCS4A01G051600 chr2A 91.111 90 4 1 1459 1544 72521169 72521080 6.710000e-23 119.0
23 TraesCS4A01G051600 chr6A 85.116 215 30 2 2047 2259 612120992 612121206 6.430000e-53 219.0
24 TraesCS4A01G051600 chr1A 100.000 32 0 0 1 32 11178665 11178634 4.120000e-05 60.2
25 TraesCS4A01G051600 chrUn 100.000 31 0 0 1 31 404962654 404962624 1.480000e-04 58.4
26 TraesCS4A01G051600 chr3A 100.000 31 0 0 1 31 745420723 745420693 1.480000e-04 58.4


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 TraesCS4A01G051600 chr4A 42272012 42275832 3820 False 2391.266667 7057 98.039333 1 3821 3 chr4A.!!$F1 3820
1 TraesCS4A01G051600 chr4D 421530101 421534244 4143 True 1423.000000 3171 93.264000 35 3821 4 chr4D.!!$R1 3786
2 TraesCS4A01G051600 chr4B 518641150 518646526 5376 True 889.000000 3000 92.274000 65 3819 6 chr4B.!!$R2 3754
3 TraesCS4A01G051600 chr4B 478184170 478184936 766 True 368.666667 809 94.078000 506 1545 3 chr4B.!!$R1 1039
4 TraesCS4A01G051600 chr2B 31122650 31123480 830 False 387.333333 859 94.168000 443 1545 3 chr2B.!!$F1 1102
5 TraesCS4A01G051600 chr2A 72565990 72566645 655 True 811.000000 811 88.856000 443 1114 1 chr2A.!!$R1 671

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
25 26 0.038709 GGCAACGCACAGGCATTTTA 60.039 50.0 0.0 0.0 41.24 1.52 F
150 151 0.249398 GCACACGTTCCTATCCACCT 59.751 55.0 0.0 0.0 0.00 4.00 F
1461 3286 0.828022 TGCATTACCCTGACCCTACG 59.172 55.0 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 3302 0.043637 CCAGGGTAGGGTCAGGGTAA 59.956 60.0 0.00 0.0 0.00 2.85 R
1486 3311 0.107165 GCTAAACTGCCAGGGTAGGG 60.107 60.0 8.32 0.0 32.04 3.53 R
3441 5284 0.676466 CTGCCAATCGGTTGCTGGTA 60.676 55.0 1.86 0.0 33.90 3.25 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 2.911509 TGGCAACGCACAGGCATT 60.912 55.556 0.00 0.00 41.24 3.56
23 24 2.339712 GGCAACGCACAGGCATTT 59.660 55.556 0.00 0.00 41.24 2.32
24 25 1.300853 GGCAACGCACAGGCATTTT 60.301 52.632 0.00 0.00 41.24 1.82
25 26 0.038709 GGCAACGCACAGGCATTTTA 60.039 50.000 0.00 0.00 41.24 1.52
26 27 1.059942 GCAACGCACAGGCATTTTAC 58.940 50.000 0.00 0.00 41.24 2.01
27 28 1.335872 GCAACGCACAGGCATTTTACT 60.336 47.619 0.00 0.00 41.24 2.24
28 29 2.095466 GCAACGCACAGGCATTTTACTA 60.095 45.455 0.00 0.00 41.24 1.82
29 30 3.747193 CAACGCACAGGCATTTTACTAG 58.253 45.455 0.00 0.00 41.24 2.57
30 31 3.053831 ACGCACAGGCATTTTACTAGT 57.946 42.857 0.00 0.00 41.24 2.57
31 32 3.408634 ACGCACAGGCATTTTACTAGTT 58.591 40.909 0.00 0.00 41.24 2.24
32 33 3.818773 ACGCACAGGCATTTTACTAGTTT 59.181 39.130 0.00 0.00 41.24 2.66
33 34 4.083484 ACGCACAGGCATTTTACTAGTTTC 60.083 41.667 0.00 0.00 41.24 2.78
63 64 3.905900 GAGTAAAATGCTCGGCTGC 57.094 52.632 0.00 0.00 0.00 5.25
70 71 1.859427 AATGCTCGGCTGCAGTGTTG 61.859 55.000 16.64 5.14 46.71 3.33
100 101 9.603921 CATTTGGACTGGATAGCAAATTTTAAT 57.396 29.630 0.00 0.00 29.64 1.40
114 115 4.957759 ATTTTAATAGTTGCGAGGCGTT 57.042 36.364 0.00 0.00 0.00 4.84
119 120 4.579454 AATAGTTGCGAGGCGTTATCTA 57.421 40.909 0.00 0.00 0.00 1.98
125 126 3.527533 TGCGAGGCGTTATCTACAAAAT 58.472 40.909 0.00 0.00 0.00 1.82
127 128 4.393680 TGCGAGGCGTTATCTACAAAATTT 59.606 37.500 0.00 0.00 0.00 1.82
136 137 6.032042 CGTTATCTACAAAATTTTCCGCACAC 59.968 38.462 0.00 0.00 0.00 3.82
142 143 1.314730 AATTTTCCGCACACGTTCCT 58.685 45.000 0.00 0.00 37.70 3.36
150 151 0.249398 GCACACGTTCCTATCCACCT 59.751 55.000 0.00 0.00 0.00 4.00
161 162 1.686587 CTATCCACCTGATGCACCGTA 59.313 52.381 0.00 0.00 34.76 4.02
176 177 1.955080 ACCGTAGATTCTCCATCGGAC 59.045 52.381 18.98 0.22 40.90 4.79
304 1756 4.093472 TCTCCATTCCCGAACAGAAAAA 57.907 40.909 0.00 0.00 0.00 1.94
457 1909 1.613836 AGTACGGTTCGTCCTCTGTT 58.386 50.000 0.00 0.00 41.54 3.16
479 2282 3.207669 CCCTACCCGGTCGTCTCG 61.208 72.222 0.00 0.00 0.00 4.04
544 2347 2.353607 GCGGTGGCGATCTACGAG 60.354 66.667 0.00 0.00 45.77 4.18
640 2443 1.064060 GTCGGCTCGATTTGAATTGGG 59.936 52.381 0.67 0.00 38.42 4.12
643 2446 1.064060 GGCTCGATTTGAATTGGGACG 59.936 52.381 0.00 0.00 0.00 4.79
667 2470 2.251893 GTTTCGCCTGAGACTAGTTCG 58.748 52.381 0.00 0.00 0.00 3.95
679 2482 8.460428 CCTGAGACTAGTTCGTCTTAGTTTATT 58.540 37.037 0.00 0.00 43.91 1.40
714 2517 6.760291 AGTACCTCTTAGAAGTGTTTTCTGG 58.240 40.000 0.00 0.00 0.00 3.86
717 2520 5.130477 ACCTCTTAGAAGTGTTTTCTGGTGA 59.870 40.000 0.00 0.00 0.00 4.02
725 2528 3.136443 AGTGTTTTCTGGTGACATCCTCA 59.864 43.478 0.00 0.00 41.51 3.86
745 2548 2.576847 CGCAAAATTCCGCGCTCC 60.577 61.111 5.56 0.00 45.57 4.70
761 2564 1.534175 GCTCCTCCGTGTATCGAGTTG 60.534 57.143 0.00 0.00 42.86 3.16
977 2780 3.730761 GCAGGGCTTCGTGTGCTG 61.731 66.667 0.00 0.00 32.97 4.41
981 2784 2.617274 GGGCTTCGTGTGCTGTTCC 61.617 63.158 0.00 0.00 0.00 3.62
1155 2959 9.841880 GGTTTTCTTATCTGTTTTTACTCCATC 57.158 33.333 0.00 0.00 0.00 3.51
1265 3069 4.260375 GCTTATTCGTCATGCTTGTGGTAG 60.260 45.833 0.00 0.00 0.00 3.18
1274 3078 6.338146 GTCATGCTTGTGGTAGACAGTTATA 58.662 40.000 0.00 0.00 35.44 0.98
1284 3088 8.100791 TGTGGTAGACAGTTATATTGCTTTTCT 58.899 33.333 0.00 0.00 0.00 2.52
1461 3286 0.828022 TGCATTACCCTGACCCTACG 59.172 55.000 0.00 0.00 0.00 3.51
1462 3287 1.117150 GCATTACCCTGACCCTACGA 58.883 55.000 0.00 0.00 0.00 3.43
1463 3288 1.692519 GCATTACCCTGACCCTACGAT 59.307 52.381 0.00 0.00 0.00 3.73
1464 3289 2.895404 GCATTACCCTGACCCTACGATA 59.105 50.000 0.00 0.00 0.00 2.92
1465 3290 3.514309 GCATTACCCTGACCCTACGATAT 59.486 47.826 0.00 0.00 0.00 1.63
1466 3291 4.020485 GCATTACCCTGACCCTACGATATT 60.020 45.833 0.00 0.00 0.00 1.28
1467 3292 5.186409 GCATTACCCTGACCCTACGATATTA 59.814 44.000 0.00 0.00 0.00 0.98
1468 3293 6.627508 GCATTACCCTGACCCTACGATATTAG 60.628 46.154 0.00 0.00 0.00 1.73
1469 3294 4.736611 ACCCTGACCCTACGATATTAGA 57.263 45.455 0.00 0.00 0.00 2.10
1470 3295 5.272405 ACCCTGACCCTACGATATTAGAT 57.728 43.478 0.00 0.00 0.00 1.98
1471 3296 5.652324 ACCCTGACCCTACGATATTAGATT 58.348 41.667 0.00 0.00 0.00 2.40
1472 3297 5.480772 ACCCTGACCCTACGATATTAGATTG 59.519 44.000 0.00 0.00 0.00 2.67
1473 3298 5.480772 CCCTGACCCTACGATATTAGATTGT 59.519 44.000 0.00 0.00 0.00 2.71
1474 3299 6.390721 CCTGACCCTACGATATTAGATTGTG 58.609 44.000 0.00 0.00 0.00 3.33
1475 3300 5.779922 TGACCCTACGATATTAGATTGTGC 58.220 41.667 0.00 0.00 0.00 4.57
1476 3301 5.303333 TGACCCTACGATATTAGATTGTGCA 59.697 40.000 0.00 0.00 0.00 4.57
1477 3302 6.014584 TGACCCTACGATATTAGATTGTGCAT 60.015 38.462 0.00 0.00 0.00 3.96
1478 3303 6.769512 ACCCTACGATATTAGATTGTGCATT 58.230 36.000 0.00 0.00 0.00 3.56
1479 3304 7.903145 ACCCTACGATATTAGATTGTGCATTA 58.097 34.615 0.00 0.00 0.00 1.90
1480 3305 7.817962 ACCCTACGATATTAGATTGTGCATTAC 59.182 37.037 0.00 0.00 0.00 1.89
1481 3306 7.277981 CCCTACGATATTAGATTGTGCATTACC 59.722 40.741 0.00 0.00 0.00 2.85
1482 3307 7.277981 CCTACGATATTAGATTGTGCATTACCC 59.722 40.741 0.00 0.00 0.00 3.69
1483 3308 6.769512 ACGATATTAGATTGTGCATTACCCT 58.230 36.000 0.00 0.00 0.00 4.34
1484 3309 6.650807 ACGATATTAGATTGTGCATTACCCTG 59.349 38.462 0.00 0.00 0.00 4.45
1485 3310 6.873605 CGATATTAGATTGTGCATTACCCTGA 59.126 38.462 0.00 0.00 0.00 3.86
1486 3311 7.148573 CGATATTAGATTGTGCATTACCCTGAC 60.149 40.741 0.00 0.00 0.00 3.51
1487 3312 3.004752 AGATTGTGCATTACCCTGACC 57.995 47.619 0.00 0.00 0.00 4.02
1488 3313 2.024414 GATTGTGCATTACCCTGACCC 58.976 52.381 0.00 0.00 0.00 4.46
1489 3314 1.072266 TTGTGCATTACCCTGACCCT 58.928 50.000 0.00 0.00 0.00 4.34
1490 3315 1.959710 TGTGCATTACCCTGACCCTA 58.040 50.000 0.00 0.00 0.00 3.53
1491 3316 1.557832 TGTGCATTACCCTGACCCTAC 59.442 52.381 0.00 0.00 0.00 3.18
1602 3427 7.175104 TGCCTTGTAGGAAGAGTGAAATTATT 58.825 34.615 0.00 0.00 37.67 1.40
1608 3433 9.547753 TGTAGGAAGAGTGAAATTATTAGATGC 57.452 33.333 0.00 0.00 0.00 3.91
1637 3462 5.090845 AGTGTAAATTTTGCCTTGGGGTAT 58.909 37.500 0.00 0.00 34.45 2.73
1639 3464 5.872617 GTGTAAATTTTGCCTTGGGGTATTC 59.127 40.000 0.00 0.00 34.45 1.75
1645 3470 1.483415 TGCCTTGGGGTATTCGTACTC 59.517 52.381 0.00 0.00 34.45 2.59
1731 3556 1.065126 AGTCTCCAATTGGCTACTGGC 60.065 52.381 23.20 12.05 40.90 4.85
1732 3557 1.065126 GTCTCCAATTGGCTACTGGCT 60.065 52.381 20.33 0.00 41.46 4.75
1775 3600 2.093500 ACAGGCGAATGATCAGCTGTTA 60.093 45.455 14.67 1.52 0.00 2.41
1778 3603 3.070734 AGGCGAATGATCAGCTGTTAGAT 59.929 43.478 14.67 0.00 0.00 1.98
1813 3638 4.384940 GGCAGCAAAACCCTTTAAATTCA 58.615 39.130 0.00 0.00 0.00 2.57
1896 3721 5.121768 GCAAGTAATGTTAGGTACAGTGTGG 59.878 44.000 5.88 0.00 40.83 4.17
2078 3903 5.985530 GCTATGGGCAATGTAAATTTCCTTC 59.014 40.000 0.00 0.00 41.35 3.46
2090 3915 8.256611 TGTAAATTTCCTTCTCTCAATCTTCG 57.743 34.615 0.00 0.00 0.00 3.79
2406 4231 6.929049 TCTTAGAGGCATATGGTTTTATCGTG 59.071 38.462 4.56 0.00 0.00 4.35
2421 4246 2.839486 TCGTGCTCTTCAGGTTTGAT 57.161 45.000 0.00 0.00 32.27 2.57
2620 4445 0.895100 GCAGTGGATTCTGGCCAACA 60.895 55.000 7.01 0.00 37.12 3.33
2737 4562 5.220777 CCTTTTTGTTGCTGAGAGTTACGAA 60.221 40.000 0.00 0.00 0.00 3.85
2745 4570 3.677424 GCTGAGAGTTACGAAGCCTGATT 60.677 47.826 0.00 0.00 0.00 2.57
2774 4599 2.087646 GACCAGTCTGATTTCCCTTGC 58.912 52.381 0.00 0.00 0.00 4.01
2826 4651 1.533338 CGAGTGCCGGTGTAGTATCAC 60.533 57.143 1.90 0.00 37.57 3.06
2844 4669 3.840468 TCACTTCGCGCTATGTTTCTTA 58.160 40.909 5.56 0.00 0.00 2.10
2920 4745 1.188863 CATCCTGGCCTTTCCCTTTG 58.811 55.000 3.32 0.00 0.00 2.77
2963 4788 5.163023 ACTGTCCTTTGTAAATTACACCCCT 60.163 40.000 5.19 0.00 38.63 4.79
3037 4862 1.734163 AACTTCATAAGCGAACCCGG 58.266 50.000 0.00 0.00 36.06 5.73
3103 4930 4.076394 AGCTACATCCTATCCGTCTCTTC 58.924 47.826 0.00 0.00 0.00 2.87
3176 5003 3.206642 GTTTGCTTTATTTTTGTGCGCG 58.793 40.909 0.00 0.00 0.00 6.86
3265 5106 3.181454 TGGAACTTTGTGGTTCTCTCTCC 60.181 47.826 7.19 0.00 43.43 3.71
3275 5116 3.328050 TGGTTCTCTCTCCCTCTTTTTCC 59.672 47.826 0.00 0.00 0.00 3.13
3276 5117 3.307833 GGTTCTCTCTCCCTCTTTTTCCC 60.308 52.174 0.00 0.00 0.00 3.97
3299 5140 1.592543 CTTTTTGTGTTTGGCGCTTCC 59.407 47.619 7.64 0.00 0.00 3.46
3347 5188 4.202295 TGTGCTCTGATGAGAAGTCTTTGT 60.202 41.667 0.00 0.00 42.73 2.83
3363 5204 1.412079 TTGTTTGCTGGAATGTGGCT 58.588 45.000 0.00 0.00 0.00 4.75
3383 5224 2.793790 CTCTGTGCTCGTATGATTCAGC 59.206 50.000 0.00 0.00 0.00 4.26
3407 5248 1.068333 CAGTAGCGCCATTGTTTGCTT 60.068 47.619 2.29 0.00 38.82 3.91
3441 5284 7.005902 TGCCATTGGTAGATCACATCATAATT 58.994 34.615 4.26 0.00 0.00 1.40
3461 5304 2.703798 CCAGCAACCGATTGGCAGG 61.704 63.158 0.00 0.00 39.70 4.85
3462 5305 3.064324 AGCAACCGATTGGCAGGC 61.064 61.111 0.00 0.09 39.70 4.85
3463 5306 3.372730 GCAACCGATTGGCAGGCA 61.373 61.111 0.00 0.00 39.70 4.75
3464 5307 2.929903 GCAACCGATTGGCAGGCAA 61.930 57.895 12.53 12.53 39.70 4.52
3466 5309 1.978617 AACCGATTGGCAGGCAAGG 60.979 57.895 15.57 13.70 39.70 3.61
3467 5310 2.361610 CCGATTGGCAGGCAAGGT 60.362 61.111 15.57 0.00 0.00 3.50
3468 5311 1.077787 CCGATTGGCAGGCAAGGTA 60.078 57.895 15.57 0.00 0.00 3.08
3488 5388 3.712091 AAAGACGAGCGGTAATAGAGG 57.288 47.619 0.00 0.00 0.00 3.69
3533 5436 5.105997 ACTGAATTGAGCTTAACTGCAATCC 60.106 40.000 0.00 0.00 34.99 3.01
3548 5451 1.070175 CAATCCGTCGAAACACACCAC 60.070 52.381 0.00 0.00 0.00 4.16
3678 5581 0.185901 TTTCCCCAGCTTTGCTCTGT 59.814 50.000 0.00 0.00 36.40 3.41
3686 5589 2.033049 CAGCTTTGCTCTGTCATATGCC 59.967 50.000 0.00 0.00 36.40 4.40
3687 5590 2.019249 GCTTTGCTCTGTCATATGCCA 58.981 47.619 0.00 0.00 0.00 4.92
3688 5591 2.424601 GCTTTGCTCTGTCATATGCCAA 59.575 45.455 0.00 0.00 0.00 4.52
3695 5598 4.122046 CTCTGTCATATGCCAACGATTCA 58.878 43.478 0.00 0.00 0.00 2.57
3700 5603 3.118445 TCATATGCCAACGATTCACCAGA 60.118 43.478 0.00 0.00 0.00 3.86
3708 5611 2.888594 ACGATTCACCAGATACCAACG 58.111 47.619 0.00 0.00 0.00 4.10
3737 5640 5.734720 CAGCTTCTTCCTACCATTTCTGTA 58.265 41.667 0.00 0.00 0.00 2.74
3765 5668 7.328249 GTCAGATGAGCACATATAACTAGCTTC 59.672 40.741 0.00 0.00 36.82 3.86
3766 5669 6.307558 CAGATGAGCACATATAACTAGCTTCG 59.692 42.308 0.00 0.00 36.82 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.697992 AAATGCCTGTGCGTTGCCAC 62.698 55.000 0.00 0.00 45.88 5.01
6 7 0.038709 TAAAATGCCTGTGCGTTGCC 60.039 50.000 0.00 0.00 45.88 4.52
7 8 1.059942 GTAAAATGCCTGTGCGTTGC 58.940 50.000 0.00 0.00 45.88 4.17
8 9 2.704725 AGTAAAATGCCTGTGCGTTG 57.295 45.000 0.00 0.00 45.88 4.10
10 11 3.053831 ACTAGTAAAATGCCTGTGCGT 57.946 42.857 0.00 0.00 41.78 5.24
11 12 4.154195 AGAAACTAGTAAAATGCCTGTGCG 59.846 41.667 0.00 0.00 41.78 5.34
12 13 5.629079 AGAAACTAGTAAAATGCCTGTGC 57.371 39.130 0.00 0.00 38.26 4.57
47 48 0.804989 ACTGCAGCCGAGCATTTTAC 59.195 50.000 15.27 0.00 44.68 2.01
61 62 2.100584 GTCCAAATGAACCAACACTGCA 59.899 45.455 0.00 0.00 0.00 4.41
63 64 3.243501 CCAGTCCAAATGAACCAACACTG 60.244 47.826 0.00 0.00 0.00 3.66
70 71 3.620488 TGCTATCCAGTCCAAATGAACC 58.380 45.455 0.00 0.00 0.00 3.62
100 101 2.684374 TGTAGATAACGCCTCGCAACTA 59.316 45.455 0.00 0.00 0.00 2.24
114 115 5.179742 ACGTGTGCGGAAAATTTTGTAGATA 59.820 36.000 8.47 0.00 43.45 1.98
119 120 2.570442 ACGTGTGCGGAAAATTTTGT 57.430 40.000 8.47 0.00 43.45 2.83
125 126 2.070783 GATAGGAACGTGTGCGGAAAA 58.929 47.619 0.00 0.00 43.45 2.29
127 128 0.108520 GGATAGGAACGTGTGCGGAA 60.109 55.000 0.00 0.00 43.45 4.30
136 137 1.138859 TGCATCAGGTGGATAGGAACG 59.861 52.381 0.00 0.00 33.95 3.95
142 143 1.686587 CTACGGTGCATCAGGTGGATA 59.313 52.381 0.00 0.00 33.95 2.59
150 151 2.107366 TGGAGAATCTACGGTGCATCA 58.893 47.619 0.00 0.00 33.73 3.07
161 162 1.409427 GAACCGTCCGATGGAGAATCT 59.591 52.381 13.92 0.00 32.61 2.40
304 1756 1.476488 GCCTGTGTGTGTGTTCCTTTT 59.524 47.619 0.00 0.00 0.00 2.27
473 1926 1.869574 CATCACAGACGCCGAGACG 60.870 63.158 0.00 0.00 39.50 4.18
479 2282 3.188786 GGACGCATCACAGACGCC 61.189 66.667 0.00 0.00 0.00 5.68
680 2483 9.344772 CACTTCTAAGAGGTACTAGTATGTGAT 57.655 37.037 5.75 0.00 41.55 3.06
681 2484 8.327271 ACACTTCTAAGAGGTACTAGTATGTGA 58.673 37.037 5.75 0.00 41.55 3.58
691 2494 6.424207 CACCAGAAAACACTTCTAAGAGGTAC 59.576 42.308 0.00 0.00 0.00 3.34
692 2495 6.325545 TCACCAGAAAACACTTCTAAGAGGTA 59.674 38.462 0.00 0.00 0.00 3.08
693 2496 5.130477 TCACCAGAAAACACTTCTAAGAGGT 59.870 40.000 0.00 0.00 0.00 3.85
694 2497 5.467063 GTCACCAGAAAACACTTCTAAGAGG 59.533 44.000 0.00 0.00 0.00 3.69
695 2498 6.049149 TGTCACCAGAAAACACTTCTAAGAG 58.951 40.000 0.00 0.00 0.00 2.85
696 2499 5.984725 TGTCACCAGAAAACACTTCTAAGA 58.015 37.500 0.00 0.00 0.00 2.10
714 2517 0.955428 TTTGCGCCTGAGGATGTCAC 60.955 55.000 0.65 0.00 0.00 3.67
717 2520 1.474077 GAATTTTGCGCCTGAGGATGT 59.526 47.619 0.65 0.00 0.00 3.06
745 2548 0.527817 GCCCAACTCGATACACGGAG 60.528 60.000 0.00 0.00 42.82 4.63
776 2579 3.545724 TGCAGATCAGCAACAGGAG 57.454 52.632 10.74 0.00 42.46 3.69
801 2604 0.460284 GACGACATGGCATCTCGGTT 60.460 55.000 25.19 8.75 0.00 4.44
965 2768 0.880278 TGAGGAACAGCACACGAAGC 60.880 55.000 0.00 0.00 0.00 3.86
977 2780 1.668151 GACGGCACTGGTGAGGAAC 60.668 63.158 4.79 0.00 0.00 3.62
981 2784 0.888619 TCTTAGACGGCACTGGTGAG 59.111 55.000 4.79 0.56 0.00 3.51
1115 2919 8.437575 AGATAAGAAAACCTAGACCAGTTCAAA 58.562 33.333 0.00 0.00 0.00 2.69
1461 3286 7.119846 GGTCAGGGTAATGCACAATCTAATATC 59.880 40.741 0.00 0.00 0.00 1.63
1462 3287 6.942576 GGTCAGGGTAATGCACAATCTAATAT 59.057 38.462 0.00 0.00 0.00 1.28
1463 3288 6.296026 GGTCAGGGTAATGCACAATCTAATA 58.704 40.000 0.00 0.00 0.00 0.98
1464 3289 5.133221 GGTCAGGGTAATGCACAATCTAAT 58.867 41.667 0.00 0.00 0.00 1.73
1465 3290 4.523083 GGTCAGGGTAATGCACAATCTAA 58.477 43.478 0.00 0.00 0.00 2.10
1466 3291 3.118038 GGGTCAGGGTAATGCACAATCTA 60.118 47.826 0.00 0.00 0.00 1.98
1467 3292 2.357154 GGGTCAGGGTAATGCACAATCT 60.357 50.000 0.00 0.00 0.00 2.40
1468 3293 2.024414 GGGTCAGGGTAATGCACAATC 58.976 52.381 0.00 0.00 0.00 2.67
1469 3294 1.640670 AGGGTCAGGGTAATGCACAAT 59.359 47.619 0.00 0.00 0.00 2.71
1470 3295 1.072266 AGGGTCAGGGTAATGCACAA 58.928 50.000 0.00 0.00 0.00 3.33
1471 3296 1.557832 GTAGGGTCAGGGTAATGCACA 59.442 52.381 0.00 0.00 0.00 4.57
1472 3297 1.134189 GGTAGGGTCAGGGTAATGCAC 60.134 57.143 0.00 0.00 0.00 4.57
1473 3298 1.209621 GGTAGGGTCAGGGTAATGCA 58.790 55.000 0.00 0.00 0.00 3.96
1474 3299 0.472898 GGGTAGGGTCAGGGTAATGC 59.527 60.000 0.00 0.00 0.00 3.56
1475 3300 1.768870 CAGGGTAGGGTCAGGGTAATG 59.231 57.143 0.00 0.00 0.00 1.90
1476 3301 1.345112 CCAGGGTAGGGTCAGGGTAAT 60.345 57.143 0.00 0.00 0.00 1.89
1477 3302 0.043637 CCAGGGTAGGGTCAGGGTAA 59.956 60.000 0.00 0.00 0.00 2.85
1478 3303 1.707827 CCAGGGTAGGGTCAGGGTA 59.292 63.158 0.00 0.00 0.00 3.69
1479 3304 2.454941 CCAGGGTAGGGTCAGGGT 59.545 66.667 0.00 0.00 0.00 4.34
1480 3305 3.090532 GCCAGGGTAGGGTCAGGG 61.091 72.222 0.00 0.00 0.00 4.45
1481 3306 2.285368 TGCCAGGGTAGGGTCAGG 60.285 66.667 0.00 0.00 0.00 3.86
1482 3307 1.201429 AACTGCCAGGGTAGGGTCAG 61.201 60.000 8.32 0.00 36.37 3.51
1483 3308 0.770557 AAACTGCCAGGGTAGGGTCA 60.771 55.000 8.32 0.00 32.04 4.02
1484 3309 1.209747 CTAAACTGCCAGGGTAGGGTC 59.790 57.143 8.32 0.00 32.04 4.46
1485 3310 1.286248 CTAAACTGCCAGGGTAGGGT 58.714 55.000 8.32 0.00 32.04 4.34
1486 3311 0.107165 GCTAAACTGCCAGGGTAGGG 60.107 60.000 8.32 0.00 32.04 3.53
1487 3312 0.618458 TGCTAAACTGCCAGGGTAGG 59.382 55.000 8.32 0.00 32.04 3.18
1488 3313 1.679032 GGTGCTAAACTGCCAGGGTAG 60.679 57.143 1.56 1.56 0.00 3.18
1489 3314 0.326927 GGTGCTAAACTGCCAGGGTA 59.673 55.000 0.00 0.00 0.00 3.69
1490 3315 1.074951 GGTGCTAAACTGCCAGGGT 59.925 57.895 0.00 0.00 0.00 4.34
1491 3316 0.323725 ATGGTGCTAAACTGCCAGGG 60.324 55.000 0.00 0.00 34.18 4.45
1602 3427 7.414436 GCAAAATTTACACTAATCCGCATCTA 58.586 34.615 0.00 0.00 0.00 1.98
1608 3433 5.804979 CCAAGGCAAAATTTACACTAATCCG 59.195 40.000 0.00 0.00 0.00 4.18
1620 3445 3.169908 ACGAATACCCCAAGGCAAAATT 58.830 40.909 0.00 0.00 36.11 1.82
1637 3462 7.250569 ACGTTTCTAAATAATCCGAGTACGAA 58.749 34.615 0.00 0.00 42.66 3.85
1639 3464 7.441878 AACGTTTCTAAATAATCCGAGTACG 57.558 36.000 0.00 0.00 39.43 3.67
1731 3556 3.192001 ACTGAACAAGCACAATGGCATAG 59.808 43.478 0.00 0.00 35.83 2.23
1732 3557 3.156293 ACTGAACAAGCACAATGGCATA 58.844 40.909 0.00 0.00 35.83 3.14
1798 3623 8.150296 CCAGAAACATCTGAATTTAAAGGGTTT 58.850 33.333 7.39 0.00 39.99 3.27
1813 3638 6.884836 GGTGGACTAAAATACCAGAAACATCT 59.115 38.462 0.00 0.00 34.21 2.90
1831 3656 1.668419 GCATAAAGCATCGGTGGACT 58.332 50.000 0.00 0.00 44.79 3.85
1896 3721 7.769220 TGTAGTCTAAGCTCCAAAGTACATAC 58.231 38.462 0.00 0.00 0.00 2.39
1908 3733 7.093992 AGAAGAACACATTGTAGTCTAAGCTC 58.906 38.462 0.00 0.00 0.00 4.09
2078 3903 1.535015 GGTCGAGGCGAAGATTGAGAG 60.535 57.143 0.00 0.00 37.72 3.20
2090 3915 4.442706 TCATCTATTGAAAAGGTCGAGGC 58.557 43.478 0.00 0.00 0.00 4.70
2737 4562 4.018960 ACTGGTCAGAATACAAATCAGGCT 60.019 41.667 4.84 0.00 0.00 4.58
2745 4570 6.173339 GGAAATCAGACTGGTCAGAATACAA 58.827 40.000 1.81 0.00 0.00 2.41
2774 4599 1.308998 ACGGTCAAGGAACTGCAAAG 58.691 50.000 0.00 0.00 40.86 2.77
2826 4651 5.050769 ACATCATAAGAAACATAGCGCGAAG 60.051 40.000 12.10 0.00 0.00 3.79
2844 4669 5.972107 AAAAACTTCAGCTGCTACATCAT 57.028 34.783 9.47 0.00 0.00 2.45
2909 4734 3.230976 AGTAAACAGGCAAAGGGAAAGG 58.769 45.455 0.00 0.00 0.00 3.11
2920 4745 3.746492 CAGTCACCAGTAAGTAAACAGGC 59.254 47.826 0.00 0.00 29.43 4.85
2963 4788 6.310941 TCTTGGTCTTTGATAAAACCATCCA 58.689 36.000 0.00 0.00 41.23 3.41
3037 4862 7.327275 CCTCTACAGCTACATATTTGAATCGTC 59.673 40.741 0.00 0.00 0.00 4.20
3131 4958 2.603021 AGCTCAAGACTGGAGAGAACA 58.397 47.619 11.33 0.00 34.24 3.18
3140 4967 2.357009 AGCAAACACAAGCTCAAGACTG 59.643 45.455 0.00 0.00 36.00 3.51
3196 5023 6.839124 ATTTCAGTTCCAGCACATATTTGA 57.161 33.333 0.00 0.00 0.00 2.69
3265 5106 4.405680 ACACAAAAAGAGGGGAAAAAGAGG 59.594 41.667 0.00 0.00 0.00 3.69
3275 5116 1.851658 CGCCAAACACAAAAAGAGGG 58.148 50.000 0.00 0.00 0.00 4.30
3276 5117 1.202405 AGCGCCAAACACAAAAAGAGG 60.202 47.619 2.29 0.00 0.00 3.69
3318 5159 5.798132 ACTTCTCATCAGAGCACAAATACA 58.202 37.500 0.00 0.00 41.81 2.29
3319 5160 6.105333 AGACTTCTCATCAGAGCACAAATAC 58.895 40.000 0.00 0.00 41.81 1.89
3320 5161 6.291648 AGACTTCTCATCAGAGCACAAATA 57.708 37.500 0.00 0.00 41.81 1.40
3321 5162 5.163281 AGACTTCTCATCAGAGCACAAAT 57.837 39.130 0.00 0.00 41.81 2.32
3322 5163 4.613925 AGACTTCTCATCAGAGCACAAA 57.386 40.909 0.00 0.00 41.81 2.83
3323 5164 4.613925 AAGACTTCTCATCAGAGCACAA 57.386 40.909 0.00 0.00 41.81 3.33
3347 5188 1.250328 CAGAGCCACATTCCAGCAAA 58.750 50.000 0.00 0.00 0.00 3.68
3363 5204 2.166254 TGCTGAATCATACGAGCACAGA 59.834 45.455 0.00 0.00 36.54 3.41
3383 5224 3.173599 CAAACAATGGCGCTACTGAATG 58.826 45.455 9.81 3.43 0.00 2.67
3441 5284 0.676466 CTGCCAATCGGTTGCTGGTA 60.676 55.000 1.86 0.00 33.90 3.25
3461 5304 0.669625 ACCGCTCGTCTTTACCTTGC 60.670 55.000 0.00 0.00 0.00 4.01
3462 5305 2.642139 TACCGCTCGTCTTTACCTTG 57.358 50.000 0.00 0.00 0.00 3.61
3463 5306 3.881937 ATTACCGCTCGTCTTTACCTT 57.118 42.857 0.00 0.00 0.00 3.50
3464 5307 4.202441 TCTATTACCGCTCGTCTTTACCT 58.798 43.478 0.00 0.00 0.00 3.08
3466 5309 4.036144 ACCTCTATTACCGCTCGTCTTTAC 59.964 45.833 0.00 0.00 0.00 2.01
3467 5310 4.202441 ACCTCTATTACCGCTCGTCTTTA 58.798 43.478 0.00 0.00 0.00 1.85
3468 5311 3.022406 ACCTCTATTACCGCTCGTCTTT 58.978 45.455 0.00 0.00 0.00 2.52
3488 5388 9.809096 TTCAGTAGAAATTGTCTGATGATCTAC 57.191 33.333 0.00 0.00 37.12 2.59
3533 5436 1.919839 GCATTGTGGTGTGTTTCGACG 60.920 52.381 0.00 0.00 0.00 5.12
3662 5565 0.323178 ATGACAGAGCAAAGCTGGGG 60.323 55.000 0.00 0.00 39.88 4.96
3678 5581 3.118445 TCTGGTGAATCGTTGGCATATGA 60.118 43.478 6.97 0.00 0.00 2.15
3686 5589 3.062099 CGTTGGTATCTGGTGAATCGTTG 59.938 47.826 0.00 0.00 0.00 4.10
3687 5590 3.259064 CGTTGGTATCTGGTGAATCGTT 58.741 45.455 0.00 0.00 0.00 3.85
3688 5591 2.888594 CGTTGGTATCTGGTGAATCGT 58.111 47.619 0.00 0.00 0.00 3.73
3695 5598 1.079405 CGTGGCGTTGGTATCTGGT 60.079 57.895 0.00 0.00 0.00 4.00
3700 5603 3.124921 GCTGCGTGGCGTTGGTAT 61.125 61.111 0.00 0.00 0.00 2.73
3708 5611 1.079127 TAGGAAGAAGCTGCGTGGC 60.079 57.895 0.00 0.00 0.00 5.01
3737 5640 6.295011 GCTAGTTATATGTGCTCATCTGACCT 60.295 42.308 4.19 0.00 35.70 3.85
3765 5668 2.604614 GGTTTCTTAACAACAGCAGGCG 60.605 50.000 0.00 0.00 35.92 5.52
3766 5669 2.288213 GGGTTTCTTAACAACAGCAGGC 60.288 50.000 0.00 0.00 35.92 4.85


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

AutoCloner maintained by Alex Coulton.