Multiple sequence alignment - TraesCS4D01G084100

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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 TraesCS4D01G084100 chr4D 100.000 3211 0 0 1 3211 57880680 57877470 0.000000e+00 5930.0
1 TraesCS4D01G084100 chr4D 84.844 640 61 15 7 626 57898215 57897592 2.120000e-171 612.0
2 TraesCS4D01G084100 chr4D 85.846 325 32 11 2690 3004 320043061 320043381 1.850000e-87 333.0
3 TraesCS4D01G084100 chr4D 86.486 185 9 7 755 929 57896408 57896230 4.230000e-44 189.0
4 TraesCS4D01G084100 chr4A 91.892 1036 59 14 733 1750 538712730 538713758 0.000000e+00 1424.0
5 TraesCS4D01G084100 chr4A 93.588 733 40 6 2482 3211 538714338 538715066 0.000000e+00 1086.0
6 TraesCS4D01G084100 chr4A 92.192 730 40 2 7 722 538708772 538709498 0.000000e+00 1016.0
7 TraesCS4D01G084100 chr4A 87.389 674 35 15 1756 2427 538713719 538714344 0.000000e+00 728.0
8 TraesCS4D01G084100 chr4A 84.478 335 34 10 2690 3008 153246135 153245803 6.690000e-82 315.0
9 TraesCS4D01G084100 chr4B 86.173 810 91 6 954 1745 86768593 86767787 0.000000e+00 856.0
10 TraesCS4D01G084100 chr4B 85.393 445 37 12 1756 2199 86767821 86767404 1.370000e-118 436.0
11 TraesCS4D01G084100 chr4B 85.015 327 31 15 2690 3007 400685547 400685230 1.860000e-82 316.0
12 TraesCS4D01G084100 chr4B 76.939 477 53 30 2207 2658 86767104 86766660 5.390000e-53 219.0
13 TraesCS4D01G084100 chr6B 82.317 328 43 11 2690 3011 48958260 48958578 1.470000e-68 270.0
14 TraesCS4D01G084100 chr6B 81.402 328 43 11 2690 3011 49001383 49001698 5.320000e-63 252.0
15 TraesCS4D01G084100 chr5A 80.061 326 49 11 2690 3003 479849489 479849168 8.960000e-56 228.0
16 TraesCS4D01G084100 chr7D 79.525 337 47 12 2682 3008 515464201 515464525 1.500000e-53 220.0
17 TraesCS4D01G084100 chr2D 80.323 310 45 11 2690 2992 12289111 12289411 1.500000e-53 220.0
18 TraesCS4D01G084100 chr2D 84.577 201 21 9 3007 3199 2338715 2338913 1.180000e-44 191.0
19 TraesCS4D01G084100 chr5D 79.459 185 28 6 2481 2656 51507399 51507582 4.350000e-24 122.0
20 TraesCS4D01G084100 chr3B 83.951 81 10 3 3118 3195 52895588 52895508 1.240000e-09 75.0
21 TraesCS4D01G084100 chr6A 82.090 67 7 4 410 473 72446895 72446959 6.000000e-03 52.8


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 TraesCS4D01G084100 chr4D 57877470 57880680 3210 True 5930.000000 5930 100.00000 1 3211 1 chr4D.!!$R1 3210
1 TraesCS4D01G084100 chr4D 57896230 57898215 1985 True 400.500000 612 85.66500 7 929 2 chr4D.!!$R2 922
2 TraesCS4D01G084100 chr4A 538708772 538715066 6294 False 1063.500000 1424 91.26525 7 3211 4 chr4A.!!$F1 3204
3 TraesCS4D01G084100 chr4B 86766660 86768593 1933 True 503.666667 856 82.83500 954 2658 3 chr4B.!!$R2 1704

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
62 63 0.681733 ATAGCATCGTGGGTGGCTAG 59.318 55.0 0.0 0.0 41.63 3.42 F
1789 6169 0.108804 CCGTGTTGCTAGTCCGTGAT 60.109 55.0 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 6223 0.179056 ACTCATAATTGGCGACCCCG 60.179 55.000 0.00 0.0 35.87 5.73 R
2713 7411 1.154150 GAAGCGCACATCAAGCACC 60.154 57.895 11.47 0.0 0.00 5.01 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
47 48 3.060895 CGAACACAAAACCTCTCGATAGC 59.939 47.826 0.00 0.00 0.00 2.97
62 63 0.681733 ATAGCATCGTGGGTGGCTAG 59.318 55.000 0.00 0.00 41.63 3.42
134 136 2.551270 ACTAAGGAAGTGGCAGATCCA 58.449 47.619 17.95 1.03 44.18 3.41
504 524 6.992715 TGTTTCGAAGAAAAGAGAAGGAGAAT 59.007 34.615 0.00 0.00 45.90 2.40
512 532 9.500785 AAGAAAAGAGAAGGAGAATACAGAAAG 57.499 33.333 0.00 0.00 0.00 2.62
519 554 9.495572 GAGAAGGAGAATACAGAAAGAGAAAAA 57.504 33.333 0.00 0.00 0.00 1.94
579 614 6.213677 GGAAAATCCAGTACAGAAACAAACC 58.786 40.000 0.00 0.00 36.28 3.27
581 616 2.841215 TCCAGTACAGAAACAAACCGG 58.159 47.619 0.00 0.00 0.00 5.28
589 624 4.356289 ACAGAAACAAACCGGAAAAATCG 58.644 39.130 9.46 0.00 0.00 3.34
619 654 3.320673 ACGGACAGAATCTTCCAGAAC 57.679 47.619 10.51 0.00 0.00 3.01
733 1852 1.873591 GCGATACTCCGGCAATTTGAT 59.126 47.619 0.00 0.00 0.00 2.57
767 5109 7.306632 GCGTCATATAGCGAATTCCATAATACC 60.307 40.741 0.00 0.00 0.00 2.73
784 5126 2.607442 CTTTTGGGGGCAAGGGGG 60.607 66.667 0.00 0.00 0.00 5.40
836 5189 1.308998 GACAAATAGGCCCATCCACG 58.691 55.000 0.00 0.00 37.29 4.94
969 5325 4.927782 AGGAAAGCCACGCACGCA 62.928 61.111 0.00 0.00 36.29 5.24
1018 5390 0.250338 GCTATAAAGAGGCACGGGGG 60.250 60.000 0.00 0.00 0.00 5.40
1020 5392 0.983905 TATAAAGAGGCACGGGGGCA 60.984 55.000 6.57 0.00 46.44 5.36
1078 5450 1.464734 TACTCTGAGACCGCTCCAAG 58.535 55.000 12.44 0.00 40.55 3.61
1110 5484 2.092103 TCTACTCTGAGAAGAGGGGCTC 60.092 54.545 12.44 0.00 40.08 4.70
1178 5552 2.449525 GCGGTCAAGAATACGCGCA 61.450 57.895 5.73 0.00 42.66 6.09
1323 5697 1.403647 CGTCGACAAGCAAGACCCATA 60.404 52.381 17.16 0.00 0.00 2.74
1503 5883 0.396435 TCCGTGAACCAGCAGTCAAT 59.604 50.000 0.00 0.00 0.00 2.57
1529 5909 0.310854 GCCACTTGGAAACTTGTCCG 59.689 55.000 0.00 0.00 40.96 4.79
1549 5929 1.601419 CTTCCAAGGTCGAGCCCGTA 61.601 60.000 11.73 0.00 38.26 4.02
1590 5970 0.586802 GGGAACTGCACTTTCACGAC 59.413 55.000 5.82 0.00 0.00 4.34
1714 6094 3.925090 GGGTACCGGCCCGATGAG 61.925 72.222 3.71 0.00 40.86 2.90
1715 6095 3.925090 GGTACCGGCCCGATGAGG 61.925 72.222 3.71 0.00 40.63 3.86
1716 6096 2.836360 GTACCGGCCCGATGAGGA 60.836 66.667 3.71 0.00 45.00 3.71
1717 6097 2.042741 TACCGGCCCGATGAGGAA 60.043 61.111 3.71 0.00 45.00 3.36
1718 6098 2.428925 TACCGGCCCGATGAGGAAC 61.429 63.158 3.71 0.00 45.00 3.62
1719 6099 4.891727 CCGGCCCGATGAGGAACG 62.892 72.222 3.71 0.00 45.00 3.95
1721 6101 4.467084 GGCCCGATGAGGAACGCA 62.467 66.667 0.00 0.00 45.75 5.24
1729 6109 3.157727 TGAGGAACGCATGTCCATG 57.842 52.632 2.86 2.86 41.60 3.66
1730 6110 0.324614 TGAGGAACGCATGTCCATGT 59.675 50.000 8.91 0.00 40.80 3.21
1731 6111 1.271325 TGAGGAACGCATGTCCATGTT 60.271 47.619 8.91 0.00 40.80 2.71
1732 6112 1.131126 GAGGAACGCATGTCCATGTTG 59.869 52.381 8.91 4.97 40.80 3.33
1733 6113 0.456653 GGAACGCATGTCCATGTTGC 60.457 55.000 8.91 0.00 40.80 4.17
1734 6114 0.523072 GAACGCATGTCCATGTTGCT 59.477 50.000 8.91 0.00 40.80 3.91
1735 6115 1.737236 GAACGCATGTCCATGTTGCTA 59.263 47.619 8.91 0.00 40.80 3.49
1736 6116 1.372582 ACGCATGTCCATGTTGCTAG 58.627 50.000 8.91 0.00 40.80 3.42
1737 6117 1.339055 ACGCATGTCCATGTTGCTAGT 60.339 47.619 8.91 0.00 40.80 2.57
1738 6118 1.328680 CGCATGTCCATGTTGCTAGTC 59.671 52.381 8.91 0.00 40.80 2.59
1739 6119 1.672881 GCATGTCCATGTTGCTAGTCC 59.327 52.381 8.91 0.00 40.80 3.85
1740 6120 2.940971 GCATGTCCATGTTGCTAGTCCA 60.941 50.000 8.91 0.00 40.80 4.02
1741 6121 3.548770 CATGTCCATGTTGCTAGTCCAT 58.451 45.455 0.00 0.00 34.23 3.41
1742 6122 2.989909 TGTCCATGTTGCTAGTCCATG 58.010 47.619 9.91 9.91 36.56 3.66
1743 6123 2.571202 TGTCCATGTTGCTAGTCCATGA 59.429 45.455 15.56 4.42 38.56 3.07
1744 6124 3.008923 TGTCCATGTTGCTAGTCCATGAA 59.991 43.478 15.56 0.00 38.56 2.57
1745 6125 3.624861 GTCCATGTTGCTAGTCCATGAAG 59.375 47.826 15.56 4.99 38.56 3.02
1746 6126 3.519107 TCCATGTTGCTAGTCCATGAAGA 59.481 43.478 15.56 6.62 38.56 2.87
1747 6127 4.164796 TCCATGTTGCTAGTCCATGAAGAT 59.835 41.667 15.56 0.00 38.56 2.40
1748 6128 4.275196 CCATGTTGCTAGTCCATGAAGATG 59.725 45.833 15.56 0.00 38.56 2.90
1749 6129 4.824479 TGTTGCTAGTCCATGAAGATGA 57.176 40.909 0.00 0.00 0.00 2.92
1750 6130 5.164620 TGTTGCTAGTCCATGAAGATGAA 57.835 39.130 0.00 0.00 0.00 2.57
1751 6131 5.181009 TGTTGCTAGTCCATGAAGATGAAG 58.819 41.667 0.00 0.00 0.00 3.02
1752 6132 5.046376 TGTTGCTAGTCCATGAAGATGAAGA 60.046 40.000 0.00 0.00 0.00 2.87
1753 6133 5.016051 TGCTAGTCCATGAAGATGAAGAC 57.984 43.478 0.00 0.00 0.00 3.01
1754 6134 4.141846 TGCTAGTCCATGAAGATGAAGACC 60.142 45.833 0.00 0.00 0.00 3.85
1755 6135 4.141846 GCTAGTCCATGAAGATGAAGACCA 60.142 45.833 0.00 0.00 0.00 4.02
1789 6169 0.108804 CCGTGTTGCTAGTCCGTGAT 60.109 55.000 0.00 0.00 0.00 3.06
1804 6184 0.999406 GTGATGATGACGACCAACCG 59.001 55.000 0.00 0.00 0.00 4.44
1806 6186 0.739462 GATGATGACGACCAACCGCA 60.739 55.000 0.00 0.00 0.00 5.69
1807 6187 0.321210 ATGATGACGACCAACCGCAA 60.321 50.000 0.00 0.00 0.00 4.85
1808 6188 1.225376 TGATGACGACCAACCGCAAC 61.225 55.000 0.00 0.00 0.00 4.17
1809 6189 2.222953 GATGACGACCAACCGCAACG 62.223 60.000 0.00 0.00 0.00 4.10
1843 6223 4.672409 CCCAGTTCAACTTTGAGTTTGAC 58.328 43.478 0.00 0.00 36.03 3.18
1866 6246 3.008049 GGGGTCGCCAATTATGAGTCTAT 59.992 47.826 0.00 0.00 0.00 1.98
1925 6305 1.626654 CGAATATAAGCTGCCGCCGG 61.627 60.000 0.00 0.00 36.60 6.13
1987 6367 3.317430 GTCGTCTCACCGTTATAGGGATT 59.683 47.826 0.00 0.00 35.02 3.01
1996 6376 2.035449 CGTTATAGGGATTGAGACGCCA 59.965 50.000 0.00 0.00 0.00 5.69
2057 6437 3.881089 CCCGTGACAGTTTTAACTCCTTT 59.119 43.478 0.00 0.00 37.08 3.11
2065 6445 7.825270 TGACAGTTTTAACTCCTTTGTTGAGTA 59.175 33.333 0.00 0.00 42.10 2.59
2080 6460 4.083164 TGTTGAGTAACATGCATGCTTGAG 60.083 41.667 33.07 16.71 41.66 3.02
2084 6464 5.009911 TGAGTAACATGCATGCTTGAGTTTT 59.990 36.000 33.07 21.17 0.00 2.43
2085 6465 5.846203 AGTAACATGCATGCTTGAGTTTTT 58.154 33.333 33.07 20.87 0.00 1.94
2117 6497 0.320421 TTGCGGGTGAGCTTGAGTAC 60.320 55.000 0.00 0.00 38.13 2.73
2132 6512 6.594159 AGCTTGAGTACTTGTTTAATGCGTAT 59.406 34.615 0.00 0.00 0.00 3.06
2135 6515 8.760103 TTGAGTACTTGTTTAATGCGTATGTA 57.240 30.769 0.00 0.00 0.00 2.29
2136 6516 8.936070 TGAGTACTTGTTTAATGCGTATGTAT 57.064 30.769 0.00 0.00 0.00 2.29
2169 6549 2.780065 TGCTTGTGATGCTTGTGTTC 57.220 45.000 0.00 0.00 0.00 3.18
2295 6972 0.032952 TGTGCACCGGTGTCTTCTAC 59.967 55.000 33.92 21.81 0.00 2.59
2297 6974 2.092882 GCACCGGTGTCTTCTACGC 61.093 63.158 33.92 14.12 37.91 4.42
2302 6989 3.908737 GGTGTCTTCTACGCACCTT 57.091 52.632 5.77 0.00 46.57 3.50
2307 6994 1.544691 GTCTTCTACGCACCTTCCTCA 59.455 52.381 0.00 0.00 0.00 3.86
2314 7001 1.072331 ACGCACCTTCCTCAATGAGTT 59.928 47.619 9.63 0.00 0.00 3.01
2345 7032 1.757118 TGATAGGGAGCGAAAGTCAGG 59.243 52.381 0.00 0.00 0.00 3.86
2363 7050 1.886542 AGGTTTTTAAGAAGCCCAGCG 59.113 47.619 4.46 0.00 0.00 5.18
2388 7075 5.763204 TCCTTTTAGAAGTTGCGTCTGAAAT 59.237 36.000 3.52 0.00 32.22 2.17
2391 7078 6.371809 TTTAGAAGTTGCGTCTGAAATGTT 57.628 33.333 0.00 0.00 0.00 2.71
2430 7117 8.226448 GGATATTAATCACAAATCTCGAAGCAG 58.774 37.037 0.00 0.00 33.41 4.24
2432 7119 3.616956 ATCACAAATCTCGAAGCAGGA 57.383 42.857 0.00 0.00 0.00 3.86
2437 7124 4.033358 CACAAATCTCGAAGCAGGATACAC 59.967 45.833 0.00 0.00 41.41 2.90
2440 7127 1.135139 TCTCGAAGCAGGATACACAGC 59.865 52.381 0.00 0.00 41.41 4.40
2443 7130 1.473965 CGAAGCAGGATACACAGCCAT 60.474 52.381 0.00 0.00 41.41 4.40
2455 7142 0.106769 ACAGCCATGTCACCACACAA 60.107 50.000 0.00 0.00 32.99 3.33
2465 7152 0.315869 CACCACACAAAGTCGTTCGC 60.316 55.000 0.00 0.00 0.00 4.70
2466 7153 0.461339 ACCACACAAAGTCGTTCGCT 60.461 50.000 0.00 0.00 0.00 4.93
2470 7157 2.032894 CACACAAAGTCGTTCGCTGATT 60.033 45.455 0.00 0.00 0.00 2.57
2480 7167 2.128035 GTTCGCTGATTAGTCCATCCG 58.872 52.381 0.00 0.00 0.00 4.18
2485 7172 0.387929 TGATTAGTCCATCCGTCGCC 59.612 55.000 0.00 0.00 0.00 5.54
2486 7173 0.387929 GATTAGTCCATCCGTCGCCA 59.612 55.000 0.00 0.00 0.00 5.69
2569 7267 3.614092 CTCTGCCCAAACTCACATACAT 58.386 45.455 0.00 0.00 0.00 2.29
2634 7332 3.056821 AGGAAGACGACAACGAATCATCA 60.057 43.478 0.00 0.00 42.66 3.07
2722 7420 6.608405 TCATGGAAGATAATTTGGTGCTTGAT 59.392 34.615 0.00 0.00 0.00 2.57
2728 7426 0.388907 ATTTGGTGCTTGATGTGCGC 60.389 50.000 0.00 0.00 39.88 6.09
2751 7449 7.442657 CGCTTCAAATTTCAGATCATTTGAAC 58.557 34.615 19.81 16.45 46.87 3.18
2753 7451 8.932791 GCTTCAAATTTCAGATCATTTGAACAT 58.067 29.630 19.81 6.41 46.87 2.71
2840 7540 8.189119 AGACCTTAAATTTGTCTTTATTGCCA 57.811 30.769 0.00 0.00 35.93 4.92
2861 7561 4.380531 CAAGAGCTACTCAGTTGTCCAAA 58.619 43.478 0.00 0.00 32.06 3.28
2885 7585 4.278170 TGATCTGAAATTTTGAACGCACCT 59.722 37.500 0.00 0.00 0.00 4.00
2892 7592 0.730265 TTTGAACGCACCTCACACAC 59.270 50.000 0.00 0.00 0.00 3.82
2989 7689 3.972971 GAGTGCAGCTGAGCCTGGG 62.973 68.421 20.43 0.00 33.44 4.45
3070 7771 9.962759 GCAAATTTCTCATACAACATGAAATTC 57.037 29.630 0.00 0.00 42.67 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.005554 ACTCACATGTGCACTATTCTGC 58.994 45.455 21.38 0.00 37.70 4.26
1 2 4.248058 TCACTCACATGTGCACTATTCTG 58.752 43.478 21.38 9.91 37.81 3.02
2 3 4.541973 TCACTCACATGTGCACTATTCT 57.458 40.909 21.38 0.00 37.81 2.40
3 4 4.026228 CGATCACTCACATGTGCACTATTC 60.026 45.833 21.38 11.59 37.81 1.75
4 5 3.867493 CGATCACTCACATGTGCACTATT 59.133 43.478 21.38 3.99 37.81 1.73
5 6 3.131046 TCGATCACTCACATGTGCACTAT 59.869 43.478 21.38 11.47 37.81 2.12
15 16 3.311322 GGTTTTGTGTTCGATCACTCACA 59.689 43.478 23.26 13.53 38.90 3.58
47 48 2.203070 GGCTAGCCACCCACGATG 60.203 66.667 29.33 0.00 35.81 3.84
504 524 8.215926 TCGTTTTCCATTTTTCTCTTTCTGTA 57.784 30.769 0.00 0.00 0.00 2.74
553 588 4.710324 TGTTTCTGTACTGGATTTTCCGT 58.290 39.130 0.00 0.00 40.17 4.69
599 634 2.352814 CGTTCTGGAAGATTCTGTCCGT 60.353 50.000 9.10 0.00 46.36 4.69
632 667 0.468226 ACGTTCTGGAAGTTGCTCCA 59.532 50.000 0.00 0.00 43.45 3.86
633 668 1.531578 GAACGTTCTGGAAGTTGCTCC 59.468 52.381 20.97 0.00 35.88 4.70
634 669 1.531578 GGAACGTTCTGGAAGTTGCTC 59.468 52.381 26.32 2.83 34.18 4.26
646 681 1.014564 CCTCCGCTTCAGGAACGTTC 61.015 60.000 20.14 20.14 40.25 3.95
723 1842 0.925466 GCACGATGCATCAAATTGCC 59.075 50.000 25.70 9.44 44.26 4.52
733 1852 1.418373 GCTATATGACGCACGATGCA 58.582 50.000 9.95 0.00 45.36 3.96
767 5109 2.607442 CCCCCTTGCCCCCAAAAG 60.607 66.667 0.00 0.00 0.00 2.27
784 5126 1.820010 CTTGGGCTTTGGTTGGAGGC 61.820 60.000 0.00 0.00 37.69 4.70
814 5167 1.172812 GGATGGGCCTATTTGTCGGC 61.173 60.000 1.86 0.00 45.55 5.54
815 5168 0.182537 TGGATGGGCCTATTTGTCGG 59.817 55.000 1.86 0.00 37.63 4.79
836 5189 6.646653 CCAGGTTTTCTTTATTCCTTTTGAGC 59.353 38.462 0.00 0.00 0.00 4.26
916 5269 1.746517 CGCCCCGGTATTTAGCTCT 59.253 57.895 0.00 0.00 0.00 4.09
917 5270 1.301479 CCGCCCCGGTATTTAGCTC 60.301 63.158 0.00 0.00 42.73 4.09
918 5271 2.826702 CCGCCCCGGTATTTAGCT 59.173 61.111 0.00 0.00 42.73 3.32
929 5282 1.153025 GGAAGTCCATAACCGCCCC 60.153 63.158 0.00 0.00 35.64 5.80
991 5347 5.504665 CCGTGCCTCTTTATAGCAGAAAATG 60.505 44.000 0.00 0.00 37.15 2.32
1078 5450 7.210873 TCTTCTCAGAGTAGACCAACTTTTTC 58.789 38.462 2.67 0.00 0.00 2.29
1503 5883 0.534203 GTTTCCAAGTGGCCACTCGA 60.534 55.000 37.75 30.34 41.58 4.04
1529 5909 2.436824 GGGCTCGACCTTGGAAGC 60.437 66.667 0.00 0.00 39.10 3.86
1549 5929 3.011517 ATGGCGGGCTCCAAGTCT 61.012 61.111 2.38 0.00 39.96 3.24
1574 5954 1.400494 GTTGGTCGTGAAAGTGCAGTT 59.600 47.619 0.00 0.00 0.00 3.16
1629 6009 1.529152 TTTGGAGTAGGCGCACTCGA 61.529 55.000 18.41 13.61 44.93 4.04
1670 6050 4.040584 GGGGTAGATCTTGAGGAACCATAC 59.959 50.000 11.34 0.00 0.00 2.39
1671 6051 4.232091 GGGGTAGATCTTGAGGAACCATA 58.768 47.826 11.34 0.00 0.00 2.74
1711 6091 0.324614 ACATGGACATGCGTTCCTCA 59.675 50.000 11.96 0.00 42.39 3.86
1712 6092 1.131126 CAACATGGACATGCGTTCCTC 59.869 52.381 11.96 0.00 42.39 3.71
1713 6093 1.167851 CAACATGGACATGCGTTCCT 58.832 50.000 11.96 0.00 42.39 3.36
1714 6094 0.456653 GCAACATGGACATGCGTTCC 60.457 55.000 11.96 0.00 42.39 3.62
1715 6095 0.523072 AGCAACATGGACATGCGTTC 59.477 50.000 11.96 0.35 44.60 3.95
1716 6096 1.739466 CTAGCAACATGGACATGCGTT 59.261 47.619 11.96 4.88 44.60 4.84
1717 6097 1.339055 ACTAGCAACATGGACATGCGT 60.339 47.619 11.96 0.00 44.60 5.24
1718 6098 1.328680 GACTAGCAACATGGACATGCG 59.671 52.381 11.96 5.26 44.60 4.73
1719 6099 1.672881 GGACTAGCAACATGGACATGC 59.327 52.381 11.96 2.22 42.39 4.06
1720 6100 2.989909 TGGACTAGCAACATGGACATG 58.010 47.619 10.57 10.57 44.15 3.21
1721 6101 3.200605 TCATGGACTAGCAACATGGACAT 59.799 43.478 16.94 0.00 41.64 3.06
1722 6102 2.571202 TCATGGACTAGCAACATGGACA 59.429 45.455 16.94 1.75 41.64 4.02
1723 6103 3.266510 TCATGGACTAGCAACATGGAC 57.733 47.619 16.94 0.00 41.64 4.02
1724 6104 3.519107 TCTTCATGGACTAGCAACATGGA 59.481 43.478 16.94 10.70 41.64 3.41
1725 6105 3.877559 TCTTCATGGACTAGCAACATGG 58.122 45.455 16.94 6.83 41.64 3.66
1726 6106 5.121105 TCATCTTCATGGACTAGCAACATG 58.879 41.667 13.00 13.00 42.44 3.21
1727 6107 5.363562 TCATCTTCATGGACTAGCAACAT 57.636 39.130 0.00 0.00 0.00 2.71
1728 6108 4.824479 TCATCTTCATGGACTAGCAACA 57.176 40.909 0.00 0.00 0.00 3.33
1729 6109 5.293079 GTCTTCATCTTCATGGACTAGCAAC 59.707 44.000 0.00 0.00 0.00 4.17
1730 6110 5.423015 GTCTTCATCTTCATGGACTAGCAA 58.577 41.667 0.00 0.00 0.00 3.91
1731 6111 4.141846 GGTCTTCATCTTCATGGACTAGCA 60.142 45.833 0.00 0.00 0.00 3.49
1732 6112 4.141846 TGGTCTTCATCTTCATGGACTAGC 60.142 45.833 0.00 0.00 0.00 3.42
1733 6113 5.355596 GTGGTCTTCATCTTCATGGACTAG 58.644 45.833 0.00 0.00 0.00 2.57
1734 6114 4.142160 CGTGGTCTTCATCTTCATGGACTA 60.142 45.833 0.00 0.00 0.00 2.59
1735 6115 3.368843 CGTGGTCTTCATCTTCATGGACT 60.369 47.826 0.00 0.00 0.00 3.85
1736 6116 2.932614 CGTGGTCTTCATCTTCATGGAC 59.067 50.000 0.00 0.00 0.00 4.02
1737 6117 2.831526 TCGTGGTCTTCATCTTCATGGA 59.168 45.455 0.00 0.00 0.00 3.41
1738 6118 3.193263 CTCGTGGTCTTCATCTTCATGG 58.807 50.000 0.00 0.00 0.00 3.66
1739 6119 3.118992 TCCTCGTGGTCTTCATCTTCATG 60.119 47.826 2.99 0.00 34.23 3.07
1740 6120 3.099905 TCCTCGTGGTCTTCATCTTCAT 58.900 45.455 2.99 0.00 34.23 2.57
1741 6121 2.525368 TCCTCGTGGTCTTCATCTTCA 58.475 47.619 2.99 0.00 34.23 3.02
1742 6122 3.254892 GTTCCTCGTGGTCTTCATCTTC 58.745 50.000 2.99 0.00 34.23 2.87
1743 6123 2.352814 CGTTCCTCGTGGTCTTCATCTT 60.353 50.000 2.99 0.00 34.52 2.40
1744 6124 1.202582 CGTTCCTCGTGGTCTTCATCT 59.797 52.381 2.99 0.00 34.52 2.90
1745 6125 1.630148 CGTTCCTCGTGGTCTTCATC 58.370 55.000 2.99 0.00 34.52 2.92
1746 6126 0.389948 GCGTTCCTCGTGGTCTTCAT 60.390 55.000 2.99 0.00 42.13 2.57
1747 6127 1.006571 GCGTTCCTCGTGGTCTTCA 60.007 57.895 2.99 0.00 42.13 3.02
1748 6128 2.087009 CGCGTTCCTCGTGGTCTTC 61.087 63.158 0.00 0.00 44.94 2.87
1749 6129 2.049433 CGCGTTCCTCGTGGTCTT 60.049 61.111 0.00 0.00 44.94 3.01
1755 6135 4.695231 CGGACACGCGTTCCTCGT 62.695 66.667 26.62 16.36 42.13 4.18
1789 6169 1.069935 TTGCGGTTGGTCGTCATCA 59.930 52.632 0.00 0.00 0.00 3.07
1843 6223 0.179056 ACTCATAATTGGCGACCCCG 60.179 55.000 0.00 0.00 35.87 5.73
1866 6246 4.026393 CGTTGAACGTGTGTGTCATCTTAA 60.026 41.667 9.94 0.00 36.74 1.85
1925 6305 1.279840 GTTCGGCAGCAGTGTTGAC 59.720 57.895 11.60 7.00 0.00 3.18
1987 6367 1.669115 GAGCAAGCTTGGCGTCTCA 60.669 57.895 27.10 0.00 36.08 3.27
1996 6376 1.004511 AGCATGGAAGAGAGCAAGCTT 59.995 47.619 0.00 0.00 0.00 3.74
2039 6419 6.657541 ACTCAACAAAGGAGTTAAAACTGTCA 59.342 34.615 0.00 0.00 42.77 3.58
2095 6475 0.667993 CTCAAGCTCACCCGCAAAAA 59.332 50.000 0.00 0.00 0.00 1.94
2135 6515 9.533253 GCATCACAAGCATAAAAACCTAATTAT 57.467 29.630 0.00 0.00 0.00 1.28
2136 6516 8.748412 AGCATCACAAGCATAAAAACCTAATTA 58.252 29.630 0.00 0.00 0.00 1.40
2137 6517 7.614494 AGCATCACAAGCATAAAAACCTAATT 58.386 30.769 0.00 0.00 0.00 1.40
2151 6531 1.664016 CCGAACACAAGCATCACAAGC 60.664 52.381 0.00 0.00 0.00 4.01
2295 6972 1.813513 AACTCATTGAGGAAGGTGCG 58.186 50.000 17.66 0.00 33.35 5.34
2297 6974 7.693969 ATTTAGAAACTCATTGAGGAAGGTG 57.306 36.000 17.66 0.00 33.35 4.00
2314 7001 9.273016 CTTTCGCTCCCTATCATTTATTTAGAA 57.727 33.333 0.00 0.00 0.00 2.10
2345 7032 2.351447 GGACGCTGGGCTTCTTAAAAAC 60.351 50.000 0.00 0.00 0.00 2.43
2363 7050 4.056050 TCAGACGCAACTTCTAAAAGGAC 58.944 43.478 0.00 0.00 36.78 3.85
2388 7075 7.758820 TTAATATCCTAGGGTCCAGAAAACA 57.241 36.000 9.46 0.00 0.00 2.83
2391 7078 7.570982 TGTGATTAATATCCTAGGGTCCAGAAA 59.429 37.037 9.46 0.00 0.00 2.52
2430 7117 1.065491 TGGTGACATGGCTGTGTATCC 60.065 52.381 0.00 3.77 35.14 2.59
2432 7119 1.350684 TGTGGTGACATGGCTGTGTAT 59.649 47.619 0.00 0.00 46.14 2.29
2437 7124 1.001048 CTTTGTGTGGTGACATGGCTG 60.001 52.381 0.00 0.00 46.14 4.85
2440 7127 1.264020 CGACTTTGTGTGGTGACATGG 59.736 52.381 0.00 0.00 46.14 3.66
2443 7130 2.004017 GAACGACTTTGTGTGGTGACA 58.996 47.619 0.00 0.00 37.67 3.58
2455 7142 2.230508 TGGACTAATCAGCGAACGACTT 59.769 45.455 0.00 0.00 0.00 3.01
2465 7152 1.603172 GGCGACGGATGGACTAATCAG 60.603 57.143 0.00 0.00 0.00 2.90
2466 7153 0.387929 GGCGACGGATGGACTAATCA 59.612 55.000 0.00 0.00 0.00 2.57
2470 7157 1.252215 TGTTGGCGACGGATGGACTA 61.252 55.000 0.00 0.00 0.00 2.59
2480 7167 2.668550 GGAGGTGGTGTTGGCGAC 60.669 66.667 0.00 0.00 0.00 5.19
2485 7172 2.153401 TGAGGGGGAGGTGGTGTTG 61.153 63.158 0.00 0.00 0.00 3.33
2486 7173 2.154074 GTGAGGGGGAGGTGGTGTT 61.154 63.158 0.00 0.00 0.00 3.32
2569 7267 0.106015 TCTCGCCAGGGATCTGATCA 60.106 55.000 18.64 0.00 43.49 2.92
2658 7356 4.129737 CTGCCGTCCCGTCATCGT 62.130 66.667 0.00 0.00 35.01 3.73
2713 7411 1.154150 GAAGCGCACATCAAGCACC 60.154 57.895 11.47 0.00 0.00 5.01
2722 7420 3.252944 TGATCTGAAATTTGAAGCGCACA 59.747 39.130 11.47 6.70 0.00 4.57
2812 7511 9.346725 GCAATAAAGACAAATTTAAGGTCTCTG 57.653 33.333 9.40 6.95 40.80 3.35
2813 7512 8.523658 GGCAATAAAGACAAATTTAAGGTCTCT 58.476 33.333 9.40 0.47 40.80 3.10
2814 7513 8.303876 TGGCAATAAAGACAAATTTAAGGTCTC 58.696 33.333 9.40 0.00 40.80 3.36
2815 7514 8.189119 TGGCAATAAAGACAAATTTAAGGTCT 57.811 30.769 4.30 4.30 43.35 3.85
2816 7515 8.825667 TTGGCAATAAAGACAAATTTAAGGTC 57.174 30.769 0.00 0.00 32.51 3.85
2817 7516 8.646900 TCTTGGCAATAAAGACAAATTTAAGGT 58.353 29.630 0.00 0.00 35.78 3.50
2818 7517 9.143631 CTCTTGGCAATAAAGACAAATTTAAGG 57.856 33.333 0.00 0.00 35.78 2.69
2820 7519 8.367156 AGCTCTTGGCAATAAAGACAAATTTAA 58.633 29.630 0.00 0.00 44.79 1.52
2821 7520 7.895759 AGCTCTTGGCAATAAAGACAAATTTA 58.104 30.769 0.00 0.00 44.79 1.40
2840 7540 4.689612 TTTGGACAACTGAGTAGCTCTT 57.310 40.909 0.00 0.00 0.00 2.85
2861 7561 5.047802 AGGTGCGTTCAAAATTTCAGATCAT 60.048 36.000 0.00 0.00 0.00 2.45
2885 7585 5.105797 GCATGGAAGATAATTTGGTGTGTGA 60.106 40.000 0.00 0.00 0.00 3.58
2979 7679 4.463879 CTCGGTGCCCAGGCTCAG 62.464 72.222 10.58 7.38 42.51 3.35
3109 7810 4.877378 ATGAACAAAGAATGTGCCATGT 57.123 36.364 0.00 0.00 42.99 3.21


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

AutoCloner maintained by Alex Coulton.