Multiple sequence alignment - TraesCS4B01G241600

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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 TraesCS4B01G241600 chr4B 100.000 4334 0 0 1 4334 500263659 500259326 0.000000e+00 8004.0
1 TraesCS4B01G241600 chr4B 88.235 68 5 3 2840 2904 586071342 586071409 1.290000e-10 78.7
2 TraesCS4B01G241600 chr4D 92.478 3430 177 35 930 4334 403405027 403401654 0.000000e+00 4830.0
3 TraesCS4B01G241600 chr4D 89.201 713 52 11 297 1006 403405718 403405028 0.000000e+00 867.0
4 TraesCS4B01G241600 chr4D 89.124 331 19 6 1 320 403406065 403405741 3.140000e-106 396.0
5 TraesCS4B01G241600 chr4A 95.086 1506 58 8 2201 3696 60932979 60931480 0.000000e+00 2357.0
6 TraesCS4B01G241600 chr4A 89.274 1874 131 38 301 2144 60934814 60932981 0.000000e+00 2283.0
7 TraesCS4B01G241600 chr4A 88.626 422 36 9 1728 2140 728413665 728414083 1.800000e-138 503.0
8 TraesCS4B01G241600 chr4A 93.667 300 15 3 4039 4334 60931482 60931183 3.080000e-121 446.0
9 TraesCS4B01G241600 chr4A 93.443 122 8 0 1 122 60935241 60935120 9.570000e-42 182.0
10 TraesCS4B01G241600 chr4A 82.653 98 13 3 3706 3800 119801447 119801351 2.780000e-12 84.2
11 TraesCS4B01G241600 chr4A 97.143 35 1 0 3765 3799 457515410 457515444 4.680000e-05 60.2
12 TraesCS4B01G241600 chr6A 94.126 681 39 1 1824 2504 443328547 443327868 0.000000e+00 1035.0
13 TraesCS4B01G241600 chr6A 81.443 97 14 3 3706 3799 149118430 149118335 4.650000e-10 76.8
14 TraesCS4B01G241600 chr6B 89.019 428 35 6 1722 2140 104569933 104570357 1.790000e-143 520.0
15 TraesCS4B01G241600 chr3D 82.474 97 13 3 3706 3799 247039134 247039039 9.990000e-12 82.4
16 TraesCS4B01G241600 chr3D 87.143 70 4 5 2840 2904 534666742 534666673 1.670000e-09 75.0
17 TraesCS4B01G241600 chr7D 88.406 69 5 3 2839 2904 422150544 422150612 3.590000e-11 80.5
18 TraesCS4B01G241600 chr3A 79.808 104 13 6 3701 3799 466512162 466512062 7.780000e-08 69.4
19 TraesCS4B01G241600 chr3A 97.143 35 1 0 3765 3799 482634025 482633991 4.680000e-05 60.2
20 TraesCS4B01G241600 chr5A 97.143 35 1 0 3765 3799 340524607 340524641 4.680000e-05 60.2
21 TraesCS4B01G241600 chr3B 94.737 38 2 0 3765 3802 631809105 631809068 4.680000e-05 60.2


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 TraesCS4B01G241600 chr4B 500259326 500263659 4333 True 8004 8004 100.000000 1 4334 1 chr4B.!!$R1 4333
1 TraesCS4B01G241600 chr4D 403401654 403406065 4411 True 2031 4830 90.267667 1 4334 3 chr4D.!!$R1 4333
2 TraesCS4B01G241600 chr4A 60931183 60935241 4058 True 1317 2357 92.867500 1 4334 4 chr4A.!!$R2 4333
3 TraesCS4B01G241600 chr6A 443327868 443328547 679 True 1035 1035 94.126000 1824 2504 1 chr6A.!!$R2 680

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
539 708 0.249489 GGGATGATCGCGCAACTACT 60.249 55.0 8.75 0.0 0.0 2.57 F
1244 1500 0.609681 ACGTCTCCTCACCTGACCTC 60.610 60.0 0.00 0.0 0.0 3.85 F
1645 1911 0.033699 GCAGCTTGAGGAAGGGGAAT 60.034 55.0 0.00 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1884 0.106769 TCCTCAAGCTGCCACAACAA 60.107 50.000 0.0 0.0 0.0 2.83 R
2946 3234 0.472925 TTAGGTGGAGTGGAGTGGCA 60.473 55.000 0.0 0.0 0.0 4.92 R
3555 3863 2.297701 TGTTGTTCTGGGTGCTTCTTC 58.702 47.619 0.0 0.0 0.0 2.87 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
64 65 2.239907 ACTAAAGGGAACTCAGGGCATC 59.760 50.000 0.00 0.00 42.68 3.91
75 76 0.747283 CAGGGCATCTCAGTTCCTGC 60.747 60.000 0.00 0.00 38.55 4.85
88 89 5.604112 TCAGTTCCTGCTGATGGTACATCA 61.604 45.833 11.06 11.06 40.23 3.07
136 137 9.144747 AGTTAGCATCTTAATATCTTATGCACG 57.855 33.333 8.17 0.00 44.18 5.34
137 138 6.414408 AGCATCTTAATATCTTATGCACGC 57.586 37.500 8.17 0.00 44.18 5.34
153 154 9.265938 CTTATGCACGCATACATAACATAATTC 57.734 33.333 11.18 0.00 38.48 2.17
154 155 5.674989 TGCACGCATACATAACATAATTCG 58.325 37.500 0.00 0.00 0.00 3.34
227 240 4.263639 ACTTGAGAAGCCATCATTCTTCCA 60.264 41.667 0.00 0.00 39.48 3.53
419 588 1.067425 CCACGGTGGACTTATCAACGA 60.067 52.381 22.77 0.00 46.99 3.85
423 592 2.094390 CGGTGGACTTATCAACGAGGAA 60.094 50.000 0.00 0.00 46.99 3.36
425 594 4.120589 GGTGGACTTATCAACGAGGAATC 58.879 47.826 0.00 0.00 28.01 2.52
441 610 2.578586 AATCCATCCTGCTGCCCCAC 62.579 60.000 0.00 0.00 0.00 4.61
487 656 3.806521 GCAGCACTCATCTTCGTGATATT 59.193 43.478 0.00 0.00 33.36 1.28
507 676 0.533951 CAGAAGGGGCAAATTCAGGC 59.466 55.000 0.00 0.00 0.00 4.85
531 700 1.301244 CTGAAGGGGGATGATCGCG 60.301 63.158 0.00 0.00 0.00 5.87
538 707 1.222115 GGGGATGATCGCGCAACTAC 61.222 60.000 8.75 0.00 0.00 2.73
539 708 0.249489 GGGATGATCGCGCAACTACT 60.249 55.000 8.75 0.00 0.00 2.57
540 709 1.571919 GGATGATCGCGCAACTACTT 58.428 50.000 8.75 0.00 0.00 2.24
541 710 1.933853 GGATGATCGCGCAACTACTTT 59.066 47.619 8.75 0.00 0.00 2.66
562 731 6.830838 ACTTTTGAAGATGGAGAGTGAAGTTT 59.169 34.615 0.00 0.00 0.00 2.66
578 747 1.602377 AGTTTGGTAGCGCTGTTTGTC 59.398 47.619 22.90 6.75 0.00 3.18
594 763 6.474819 TGTTTGTCGGATGTTAATAGTGTG 57.525 37.500 0.00 0.00 0.00 3.82
626 795 2.852449 TCCGGTTGCACAAATCTGTTA 58.148 42.857 0.00 0.00 31.64 2.41
743 912 7.228507 AGTGAACATAGAACAGCACATTTTGTA 59.771 33.333 0.00 0.00 0.00 2.41
749 918 9.366216 CATAGAACAGCACATTTTGTACTAGTA 57.634 33.333 0.00 0.00 0.00 1.82
750 919 7.653767 AGAACAGCACATTTTGTACTAGTAC 57.346 36.000 23.58 23.58 36.63 2.73
752 921 7.931948 AGAACAGCACATTTTGTACTAGTACTT 59.068 33.333 28.56 13.28 37.00 2.24
753 922 7.653767 ACAGCACATTTTGTACTAGTACTTC 57.346 36.000 28.56 8.12 37.00 3.01
774 944 3.053619 TCCTAGACTGGTGCTCATGACTA 60.054 47.826 0.00 0.00 0.00 2.59
811 990 7.068593 CAGTATGTGATGGAAAATACCCACAAT 59.931 37.037 0.00 0.00 36.36 2.71
829 1008 6.018016 CCCACAATTTTTAAAGAAGCTGTTGG 60.018 38.462 0.00 0.00 0.00 3.77
846 1025 3.761218 TGTTGGCTCAAAGAGTGAAACAA 59.239 39.130 8.04 0.00 41.43 2.83
879 1058 9.598517 TGCAAAAGGGATTGAAATATGTTTATC 57.401 29.630 0.00 0.00 31.84 1.75
880 1059 9.598517 GCAAAAGGGATTGAAATATGTTTATCA 57.401 29.630 0.00 0.00 31.84 2.15
912 1091 2.146073 GAAGCTGGTGGCAAATGCGT 62.146 55.000 0.00 0.00 44.79 5.24
1028 1281 3.374402 ACGGGGCAGAGACAGACG 61.374 66.667 0.00 0.00 0.00 4.18
1031 1284 4.803426 GGGCAGAGACAGACGCCG 62.803 72.222 0.00 0.00 45.85 6.46
1244 1500 0.609681 ACGTCTCCTCACCTGACCTC 60.610 60.000 0.00 0.00 0.00 3.85
1314 1573 0.904865 TGCAGGACAAGGAGATCCGT 60.905 55.000 0.00 0.00 40.20 4.69
1367 1633 4.418401 GTACGTGGCCGCCGTGTA 62.418 66.667 25.38 13.30 39.22 2.90
1377 1643 2.509336 GCCGTGTATGCTGCTCGT 60.509 61.111 0.00 0.00 0.00 4.18
1416 1682 4.196193 TCTGATGTTGTTTCTGACGGTTT 58.804 39.130 0.00 0.00 0.00 3.27
1464 1730 3.195698 GGATTCGCGTGCAGGTCC 61.196 66.667 5.77 3.19 0.00 4.46
1553 1819 2.105128 CGATCCGGTGAGTGGAGC 59.895 66.667 0.00 0.00 39.30 4.70
1599 1865 9.597170 TTTGTGATGTTTGATTTGATTTCTGAA 57.403 25.926 0.00 0.00 0.00 3.02
1606 1872 8.431222 TGTTTGATTTGATTTCTGAAGGGATTT 58.569 29.630 0.00 0.00 0.00 2.17
1607 1873 9.276590 GTTTGATTTGATTTCTGAAGGGATTTT 57.723 29.630 0.00 0.00 0.00 1.82
1608 1874 9.850198 TTTGATTTGATTTCTGAAGGGATTTTT 57.150 25.926 0.00 0.00 0.00 1.94
1644 1910 1.380302 GCAGCTTGAGGAAGGGGAA 59.620 57.895 0.00 0.00 0.00 3.97
1645 1911 0.033699 GCAGCTTGAGGAAGGGGAAT 60.034 55.000 0.00 0.00 0.00 3.01
1647 1913 2.097825 CAGCTTGAGGAAGGGGAATTG 58.902 52.381 0.00 0.00 0.00 2.32
1697 1963 2.549754 ACTGCATGCACAAGTAAGACAC 59.450 45.455 18.46 0.00 0.00 3.67
1700 1966 2.489329 GCATGCACAAGTAAGACACCAT 59.511 45.455 14.21 0.00 0.00 3.55
1704 1970 4.397420 TGCACAAGTAAGACACCATGAAT 58.603 39.130 0.00 0.00 0.00 2.57
1768 2036 7.230913 ACTGATTGTACGTATCTACCTAGCATT 59.769 37.037 0.00 0.00 0.00 3.56
1774 2042 8.131100 TGTACGTATCTACCTAGCATTGTAAAC 58.869 37.037 0.00 0.00 0.00 2.01
1776 2044 6.038603 ACGTATCTACCTAGCATTGTAAACGA 59.961 38.462 0.00 0.00 0.00 3.85
1797 2065 4.614306 CGATTGCATTGTTTTGCTCTCTGA 60.614 41.667 0.00 0.00 43.18 3.27
1935 2204 6.572119 GCAATTCTCACCACATACCAATTTCA 60.572 38.462 0.00 0.00 0.00 2.69
1937 2206 6.513806 TTCTCACCACATACCAATTTCATG 57.486 37.500 0.00 0.00 0.00 3.07
1997 2266 6.700520 GCAGTCTTAGGTATATGTTTAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2028 2297 5.359194 AGACTTGATGTACTTATGGTGGG 57.641 43.478 0.00 0.00 0.00 4.61
2065 2341 4.217550 GCTTGTGTTAAAAGCCTGACCATA 59.782 41.667 0.00 0.00 43.45 2.74
2086 2362 7.613801 ACCATAAAGCCTGTCATAACATGTTAA 59.386 33.333 21.57 4.15 34.13 2.01
2124 2400 3.514309 AGTAAGGGAGATTACGTTGCACT 59.486 43.478 0.00 0.00 40.00 4.40
2133 2409 4.807834 AGATTACGTTGCACTCATCTCATG 59.192 41.667 0.00 0.00 0.00 3.07
2302 2585 0.112218 CACCCACATTCCCAACCTCA 59.888 55.000 0.00 0.00 0.00 3.86
2303 2586 0.405585 ACCCACATTCCCAACCTCAG 59.594 55.000 0.00 0.00 0.00 3.35
2359 2642 4.402793 TGTATTCTACCCAGCTGTCTCTTC 59.597 45.833 13.81 0.00 0.00 2.87
2475 2758 2.181975 CTGCTGGATCCATTGGGTTTT 58.818 47.619 16.63 0.00 34.93 2.43
2495 2778 9.233232 GGGTTTTTAATTCTTGTTGCTATATCG 57.767 33.333 0.00 0.00 0.00 2.92
2510 2793 4.376109 GCTATATCGCGCAGTTTTACTTCC 60.376 45.833 8.75 0.00 0.00 3.46
2691 2974 9.516314 GGTGTTTTGGATAATTTACATTAGAGC 57.484 33.333 0.00 0.00 0.00 4.09
2944 3232 4.405358 ACATTCAAACTTTCACACCCACAT 59.595 37.500 0.00 0.00 0.00 3.21
2946 3234 5.413309 TTCAAACTTTCACACCCACATTT 57.587 34.783 0.00 0.00 0.00 2.32
3140 3428 3.760684 GCCAATGGAGTGAACAGAGAAAT 59.239 43.478 2.05 0.00 0.00 2.17
3365 3659 4.021104 CCTGTGTTTCCACTGTCATCTCTA 60.021 45.833 0.00 0.00 42.34 2.43
3369 3663 5.809562 GTGTTTCCACTGTCATCTCTATCTG 59.190 44.000 0.00 0.00 38.61 2.90
3370 3664 5.716703 TGTTTCCACTGTCATCTCTATCTGA 59.283 40.000 0.00 0.00 0.00 3.27
3371 3665 6.382282 TGTTTCCACTGTCATCTCTATCTGAT 59.618 38.462 0.00 0.00 0.00 2.90
3372 3666 7.561356 TGTTTCCACTGTCATCTCTATCTGATA 59.439 37.037 0.00 0.00 0.00 2.15
3373 3667 8.584157 GTTTCCACTGTCATCTCTATCTGATAT 58.416 37.037 0.00 0.00 0.00 1.63
3374 3668 7.936496 TCCACTGTCATCTCTATCTGATATC 57.064 40.000 0.00 0.00 0.00 1.63
3375 3669 6.889177 TCCACTGTCATCTCTATCTGATATCC 59.111 42.308 0.00 0.00 0.00 2.59
3376 3670 6.096705 CCACTGTCATCTCTATCTGATATCCC 59.903 46.154 0.00 0.00 0.00 3.85
3377 3671 6.662663 CACTGTCATCTCTATCTGATATCCCA 59.337 42.308 0.00 0.00 0.00 4.37
3378 3672 7.178097 CACTGTCATCTCTATCTGATATCCCAA 59.822 40.741 0.00 0.00 0.00 4.12
3379 3673 7.900246 ACTGTCATCTCTATCTGATATCCCAAT 59.100 37.037 0.00 0.00 0.00 3.16
3380 3674 9.418839 CTGTCATCTCTATCTGATATCCCAATA 57.581 37.037 0.00 0.00 0.00 1.90
3430 3735 5.689819 ACGAAACAAGTCAGATATGCAAAC 58.310 37.500 0.00 0.00 0.00 2.93
3555 3863 3.450817 ACAAAGGAAAGGGTTCAACAAGG 59.549 43.478 0.00 0.00 35.25 3.61
3577 3885 2.301346 AGAAGCACCCAGAACAACAAG 58.699 47.619 0.00 0.00 0.00 3.16
3586 3894 3.152341 CCAGAACAACAAGCTCCTGAAT 58.848 45.455 0.00 0.00 0.00 2.57
3589 3897 5.452356 CCAGAACAACAAGCTCCTGAATTTT 60.452 40.000 0.00 0.00 0.00 1.82
3620 3928 5.047802 ACATTCAGGTTTTACTGCCAATGAG 60.048 40.000 11.94 0.00 36.73 2.90
3655 3963 3.684788 GGTCAGCAAATACATCACTTCGT 59.315 43.478 0.00 0.00 0.00 3.85
3697 4005 1.039068 CTTTCCCACACATTGCCACA 58.961 50.000 0.00 0.00 0.00 4.17
3735 4043 3.057526 GTGTTTGATTCTAAGCCACACCC 60.058 47.826 0.00 0.00 0.00 4.61
3738 4046 4.487714 TTGATTCTAAGCCACACCCTAG 57.512 45.455 0.00 0.00 0.00 3.02
3814 4122 0.173708 GATTTCTCGACCGACAGCCT 59.826 55.000 0.00 0.00 0.00 4.58
3823 4131 0.250901 ACCGACAGCCTCTTGCATTT 60.251 50.000 0.00 0.00 44.83 2.32
3825 4133 1.401931 CCGACAGCCTCTTGCATTTTG 60.402 52.381 0.00 0.00 44.83 2.44
3839 4147 7.483307 TCTTGCATTTTGAGATAATAAGTGCC 58.517 34.615 0.00 0.00 0.00 5.01
3840 4148 6.772360 TGCATTTTGAGATAATAAGTGCCA 57.228 33.333 0.00 0.00 0.00 4.92
3859 4167 1.135141 CAAGTCAAGAGGAGAGGCTCG 60.135 57.143 9.22 0.00 0.00 5.03
3879 4187 5.539582 TCGTGATAATTGTTGCCACTAAC 57.460 39.130 0.00 0.00 0.00 2.34
3915 4223 5.979993 AGGCATATTTGACAATCATGCAAA 58.020 33.333 24.55 0.00 42.94 3.68
3935 4244 6.016024 TGCAAAATGCTTTCAGAATCAGTACT 60.016 34.615 3.78 0.00 45.31 2.73
3996 4305 4.454678 AGCTTCAATATTCTGCCGATTCA 58.545 39.130 0.00 0.00 0.00 2.57
4037 4346 2.031683 CGACTGTGACAAGTGGGAAAAC 59.968 50.000 0.00 0.00 0.00 2.43
4045 4354 0.966179 AAGTGGGAAAACCCATTCGC 59.034 50.000 11.25 0.00 42.29 4.70
4064 4374 2.519013 GCCTGGTCACTCTTTGGAAAT 58.481 47.619 0.00 0.00 0.00 2.17
4068 4378 4.326826 CTGGTCACTCTTTGGAAATAGCA 58.673 43.478 0.00 0.00 0.00 3.49
4072 4382 5.529060 GGTCACTCTTTGGAAATAGCATAGG 59.471 44.000 0.00 0.00 0.00 2.57
4157 4470 3.904136 ATTTTGCTCTCGGTTGACTTG 57.096 42.857 0.00 0.00 0.00 3.16
4193 4506 3.305720 CCAGTTGGGTAGCCTCTACATA 58.694 50.000 13.11 0.00 0.00 2.29
4223 4536 6.648879 TCTTGGAAGGTGTTTAATTCCTTG 57.351 37.500 9.89 2.79 42.50 3.61
4264 4577 2.545952 CGATTCCGCTATAGTTGCTGGT 60.546 50.000 0.84 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.724582 AACAAGTGAACGTGCCTGGC 61.725 55.000 12.87 12.87 0.00 4.85
75 76 5.987953 CAGGAACAGTATGATGTACCATCAG 59.012 44.000 12.02 2.31 39.69 2.90
123 124 8.722480 ATGTTATGTATGCGTGCATAAGATAT 57.278 30.769 26.98 18.97 41.62 1.63
124 125 9.646427 TTATGTTATGTATGCGTGCATAAGATA 57.354 29.630 27.71 27.71 41.62 1.98
125 126 8.546597 TTATGTTATGTATGCGTGCATAAGAT 57.453 30.769 29.18 29.18 43.84 2.40
126 127 7.954788 TTATGTTATGTATGCGTGCATAAGA 57.045 32.000 24.39 23.48 41.52 2.10
127 128 9.265938 GAATTATGTTATGTATGCGTGCATAAG 57.734 33.333 24.39 0.00 41.52 1.73
128 129 7.954786 CGAATTATGTTATGTATGCGTGCATAA 59.045 33.333 21.24 21.24 40.15 1.90
129 130 7.452231 CGAATTATGTTATGTATGCGTGCATA 58.548 34.615 12.14 12.14 37.82 3.14
132 133 4.549599 GCGAATTATGTTATGTATGCGTGC 59.450 41.667 0.00 0.00 0.00 5.34
133 134 5.674989 TGCGAATTATGTTATGTATGCGTG 58.325 37.500 0.00 0.00 0.00 5.34
134 135 5.915812 TGCGAATTATGTTATGTATGCGT 57.084 34.783 0.00 0.00 0.00 5.24
135 136 6.516355 GTCTTGCGAATTATGTTATGTATGCG 59.484 38.462 0.00 0.00 0.00 4.73
136 137 7.576236 AGTCTTGCGAATTATGTTATGTATGC 58.424 34.615 0.00 0.00 0.00 3.14
137 138 9.935682 AAAGTCTTGCGAATTATGTTATGTATG 57.064 29.630 0.00 0.00 0.00 2.39
198 205 3.679389 TGATGGCTTCTCAAGTTTCCTC 58.321 45.455 1.86 0.00 0.00 3.71
227 240 4.218417 CCAAAACGATGATTTCTTCCCTGT 59.782 41.667 0.00 0.00 0.00 4.00
423 592 2.697263 TGGGGCAGCAGGATGGAT 60.697 61.111 0.00 0.00 35.86 3.41
425 594 3.736224 AGTGGGGCAGCAGGATGG 61.736 66.667 0.00 0.00 35.86 3.51
430 599 0.036732 TTCTAACAGTGGGGCAGCAG 59.963 55.000 0.00 0.00 0.00 4.24
441 610 5.177142 CGATCATGAAGCATCCTTCTAACAG 59.823 44.000 0.00 0.00 46.13 3.16
487 656 1.892329 GCCTGAATTTGCCCCTTCTGA 60.892 52.381 0.00 0.00 0.00 3.27
507 676 0.332632 TCATCCCCCTTCAGGCAAAG 59.667 55.000 0.00 0.00 0.00 2.77
531 700 5.703130 ACTCTCCATCTTCAAAAGTAGTTGC 59.297 40.000 0.00 0.00 0.00 4.17
538 707 6.874288 AACTTCACTCTCCATCTTCAAAAG 57.126 37.500 0.00 0.00 0.00 2.27
539 708 6.039717 CCAAACTTCACTCTCCATCTTCAAAA 59.960 38.462 0.00 0.00 0.00 2.44
540 709 5.532406 CCAAACTTCACTCTCCATCTTCAAA 59.468 40.000 0.00 0.00 0.00 2.69
541 710 5.065914 CCAAACTTCACTCTCCATCTTCAA 58.934 41.667 0.00 0.00 0.00 2.69
562 731 1.666553 CCGACAAACAGCGCTACCA 60.667 57.895 10.99 0.00 0.00 3.25
578 747 5.346011 CGATCCATCACACTATTAACATCCG 59.654 44.000 0.00 0.00 0.00 4.18
626 795 0.103208 GATCGCCAATCTGTCCGAGT 59.897 55.000 0.00 0.00 32.86 4.18
743 912 4.018233 AGCACCAGTCTAGGAAGTACTAGT 60.018 45.833 0.00 0.00 40.97 2.57
749 918 2.310779 TGAGCACCAGTCTAGGAAGT 57.689 50.000 0.00 0.00 0.00 3.01
750 919 2.762887 TCATGAGCACCAGTCTAGGAAG 59.237 50.000 0.00 0.00 0.00 3.46
752 921 2.103373 GTCATGAGCACCAGTCTAGGA 58.897 52.381 0.00 0.00 0.00 2.94
753 922 2.106566 AGTCATGAGCACCAGTCTAGG 58.893 52.381 0.00 0.00 0.00 3.02
774 944 5.483937 TCCATCACATACTGTAACCTGTTCT 59.516 40.000 0.00 0.00 0.00 3.01
803 973 6.233905 ACAGCTTCTTTAAAAATTGTGGGT 57.766 33.333 0.00 0.00 0.00 4.51
806 985 6.421405 GCCAACAGCTTCTTTAAAAATTGTG 58.579 36.000 0.00 0.00 38.99 3.33
829 1008 6.119144 TGTAACTTGTTTCACTCTTTGAGC 57.881 37.500 0.00 0.00 34.94 4.26
835 1014 6.449635 TTTGCATGTAACTTGTTTCACTCT 57.550 33.333 0.00 0.00 0.00 3.24
838 1017 5.234116 CCCTTTTGCATGTAACTTGTTTCAC 59.766 40.000 0.00 0.00 0.00 3.18
846 1025 6.418057 TTTCAATCCCTTTTGCATGTAACT 57.582 33.333 0.00 0.00 0.00 2.24
879 1058 5.006941 CCACCAGCTTCTTCAAACAATTTTG 59.993 40.000 0.00 0.00 43.17 2.44
880 1059 5.118286 CCACCAGCTTCTTCAAACAATTTT 58.882 37.500 0.00 0.00 0.00 1.82
881 1060 4.696455 CCACCAGCTTCTTCAAACAATTT 58.304 39.130 0.00 0.00 0.00 1.82
882 1061 3.493176 GCCACCAGCTTCTTCAAACAATT 60.493 43.478 0.00 0.00 38.99 2.32
884 1063 1.408702 GCCACCAGCTTCTTCAAACAA 59.591 47.619 0.00 0.00 38.99 2.83
885 1064 1.032014 GCCACCAGCTTCTTCAAACA 58.968 50.000 0.00 0.00 38.99 2.83
886 1065 1.032014 TGCCACCAGCTTCTTCAAAC 58.968 50.000 0.00 0.00 44.23 2.93
887 1066 1.774110 TTGCCACCAGCTTCTTCAAA 58.226 45.000 0.00 0.00 44.23 2.69
888 1067 1.774110 TTTGCCACCAGCTTCTTCAA 58.226 45.000 0.00 0.00 44.23 2.69
889 1068 1.614903 CATTTGCCACCAGCTTCTTCA 59.385 47.619 0.00 0.00 44.23 3.02
1151 1407 0.750182 AGAGCGAGGAGTAGCAGGAC 60.750 60.000 0.00 0.00 35.48 3.85
1159 1415 0.550914 AGATGAGGAGAGCGAGGAGT 59.449 55.000 0.00 0.00 0.00 3.85
1222 1478 0.810016 GTCAGGTGAGGAGACGTACC 59.190 60.000 3.41 3.41 40.25 3.34
1235 1491 2.283966 CGTGGGGAGAGGTCAGGT 60.284 66.667 0.00 0.00 0.00 4.00
1244 1500 2.685380 AGGGAGAAGCGTGGGGAG 60.685 66.667 0.00 0.00 0.00 4.30
1314 1573 2.032528 CAGGCGGCCTTGTTCTCA 59.967 61.111 21.26 0.00 0.00 3.27
1377 1643 1.071987 GATGCATCCCCATCGAGCA 59.928 57.895 16.23 0.00 39.79 4.26
1503 1769 1.373748 GTTGTAGCACTCCGGCGAA 60.374 57.895 9.30 0.00 39.27 4.70
1618 1884 0.106769 TCCTCAAGCTGCCACAACAA 60.107 50.000 0.00 0.00 0.00 2.83
1768 2036 5.321983 GCAAAACAATGCAATCGTTTACA 57.678 34.783 10.70 0.00 45.70 2.41
1797 2065 2.053747 TTCCACCCTCTACACCCAAT 57.946 50.000 0.00 0.00 0.00 3.16
1837 2106 3.181495 CCATCTGACAGGAGACGTTACTC 60.181 52.174 1.81 0.00 36.31 2.59
1843 2112 1.407936 ATCCCATCTGACAGGAGACG 58.592 55.000 1.81 0.00 31.94 4.18
2028 2297 5.941948 AACACAAGCCATAACTAACTGTC 57.058 39.130 0.00 0.00 0.00 3.51
2065 2341 5.772672 TGGTTAACATGTTATGACAGGCTTT 59.227 36.000 18.69 0.00 41.08 3.51
2086 2362 6.980577 TCCCTTACTGAATTATCCATTTGGT 58.019 36.000 0.00 0.00 36.34 3.67
2124 2400 4.186856 TGCAGTAAACGACATGAGATGA 57.813 40.909 0.00 0.00 0.00 2.92
2133 2409 2.069273 AGACAGCATGCAGTAAACGAC 58.931 47.619 21.98 4.83 42.53 4.34
2302 2585 4.040952 ACCTTTGTTCTACTGCAGATCACT 59.959 41.667 23.35 0.00 33.60 3.41
2303 2586 4.319177 ACCTTTGTTCTACTGCAGATCAC 58.681 43.478 23.35 11.53 33.60 3.06
2359 2642 5.907945 CACAGTAATGTAGACCGTAGAATCG 59.092 44.000 0.00 0.00 0.00 3.34
2462 2745 7.174772 GCAACAAGAATTAAAAACCCAATGGAT 59.825 33.333 0.00 0.00 34.81 3.41
2475 2758 5.235401 TGCGCGATATAGCAACAAGAATTAA 59.765 36.000 12.10 0.00 40.78 1.40
2495 2778 0.521735 CTGGGGAAGTAAAACTGCGC 59.478 55.000 0.00 0.00 36.07 6.09
2657 2940 4.715534 TTATCCAAAACACCTCAGTCCA 57.284 40.909 0.00 0.00 0.00 4.02
2899 3187 4.041762 TCCACGGTGGATTGGGCC 62.042 66.667 25.53 0.00 42.67 5.80
2918 3206 5.298276 GTGGGTGTGAAAGTTTGAATGTAGA 59.702 40.000 0.00 0.00 0.00 2.59
2944 3232 1.150536 GGTGGAGTGGAGTGGCAAA 59.849 57.895 0.00 0.00 0.00 3.68
2946 3234 0.472925 TTAGGTGGAGTGGAGTGGCA 60.473 55.000 0.00 0.00 0.00 4.92
3109 3397 3.674997 TCACTCCATTGGCAGAAAGTAC 58.325 45.455 0.00 0.00 0.00 2.73
3140 3428 6.109156 TGTTTACAGCAGACTTGGAGAATA 57.891 37.500 0.00 0.00 0.00 1.75
3319 3613 8.792633 CAGGAATAACTTGACACAATTTTCCTA 58.207 33.333 0.00 0.00 38.63 2.94
3320 3614 7.287696 ACAGGAATAACTTGACACAATTTTCCT 59.712 33.333 0.00 0.00 40.70 3.36
3430 3735 7.798071 TGGTTTCCCTGTAGTACCTTATTATG 58.202 38.462 0.00 0.00 0.00 1.90
3445 3750 9.754382 CAATGAATCTTAAATATGGTTTCCCTG 57.246 33.333 0.00 0.00 0.00 4.45
3555 3863 2.297701 TGTTGTTCTGGGTGCTTCTTC 58.702 47.619 0.00 0.00 0.00 2.87
3577 3885 7.315142 TGAATGTTGACATAAAATTCAGGAGC 58.685 34.615 0.00 0.00 35.10 4.70
3586 3894 9.743057 CAGTAAAACCTGAATGTTGACATAAAA 57.257 29.630 0.00 0.00 35.10 1.52
3589 3897 6.072175 GGCAGTAAAACCTGAATGTTGACATA 60.072 38.462 0.00 0.00 32.74 2.29
3620 3928 2.858745 TGCTGACCCCTTTTTAGTCAC 58.141 47.619 0.00 0.00 35.67 3.67
3814 4122 7.122501 TGGCACTTATTATCTCAAAATGCAAGA 59.877 33.333 0.00 0.00 32.19 3.02
3823 4131 7.394016 TCTTGACTTGGCACTTATTATCTCAA 58.606 34.615 0.00 0.00 0.00 3.02
3825 4133 6.481644 CCTCTTGACTTGGCACTTATTATCTC 59.518 42.308 0.00 0.00 0.00 2.75
3839 4147 1.135141 CGAGCCTCTCCTCTTGACTTG 60.135 57.143 0.00 0.00 0.00 3.16
3840 4148 1.181786 CGAGCCTCTCCTCTTGACTT 58.818 55.000 0.00 0.00 0.00 3.01
3879 4187 0.465705 TATGCCTCCCAAGCTTCTCG 59.534 55.000 0.00 0.00 0.00 4.04
3915 4223 5.819901 GCCTAGTACTGATTCTGAAAGCATT 59.180 40.000 5.39 0.00 28.87 3.56
3935 4244 3.640498 CTCTGGATTGAGAGATGTGCCTA 59.360 47.826 0.00 0.00 41.95 3.93
3967 4276 5.105063 GGCAGAATATTGAAGCTTTTGACC 58.895 41.667 0.00 0.00 0.00 4.02
4037 4346 1.450312 GAGTGACCAGGCGAATGGG 60.450 63.158 10.66 0.00 45.25 4.00
4045 4354 3.691609 GCTATTTCCAAAGAGTGACCAGG 59.308 47.826 0.00 0.00 30.24 4.45
4068 4378 4.170449 TGATCCTACATGATGGCACCTAT 58.830 43.478 0.00 0.00 0.00 2.57
4072 4382 3.181462 TGACTGATCCTACATGATGGCAC 60.181 47.826 0.00 0.00 0.00 5.01
4077 4387 6.070596 TGTGAAGTTGACTGATCCTACATGAT 60.071 38.462 0.00 0.00 0.00 2.45
4157 4470 0.977395 ACTGGGTAACTCTGCACCTC 59.023 55.000 0.00 0.00 35.04 3.85
4193 4506 4.664688 AAACACCTTCCAAGATCCATCT 57.335 40.909 0.00 0.00 39.22 2.90
4223 4536 2.079925 GTTCAGCTTCACACCATCTCC 58.920 52.381 0.00 0.00 0.00 3.71
4252 4565 6.106003 CACTGACACAATACCAGCAACTATA 58.894 40.000 0.00 0.00 0.00 1.31
4255 4568 3.141398 CACTGACACAATACCAGCAACT 58.859 45.455 0.00 0.00 0.00 3.16
4264 4577 5.803552 TCATCCATTGACACTGACACAATA 58.196 37.500 0.00 0.00 33.73 1.90


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

AutoCloner maintained by Alex Coulton.