Multiple sequence alignment - TraesCS6D01G156900

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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 TraesCS6D01G156900 chr6D 100.000 3921 0 0 464 4384 133215498 133211578 0.000000e+00 7241.0
1 TraesCS6D01G156900 chr6D 100.000 187 0 0 1 187 133215961 133215775 3.250000e-91 346.0
2 TraesCS6D01G156900 chr6A 94.056 2086 88 23 1564 3625 172119391 172117318 0.000000e+00 3133.0
3 TraesCS6D01G156900 chr6A 91.300 1092 57 16 478 1551 172120569 172119498 0.000000e+00 1456.0
4 TraesCS6D01G156900 chr6A 89.722 720 43 11 3680 4384 172117229 172116526 0.000000e+00 891.0
5 TraesCS6D01G156900 chr6A 97.326 187 5 0 1 187 172120818 172120632 7.080000e-83 318.0
6 TraesCS6D01G156900 chr6B 94.768 2007 74 19 1564 3554 231356100 231354109 0.000000e+00 3096.0
7 TraesCS6D01G156900 chr6B 90.573 785 48 10 772 1551 231356970 231356207 0.000000e+00 1016.0
8 TraesCS6D01G156900 chr6B 85.640 383 44 5 3688 4066 231353996 231353621 4.110000e-105 392.0
9 TraesCS6D01G156900 chr6B 96.889 225 4 1 4161 4382 231353541 231353317 1.490000e-99 374.0
10 TraesCS6D01G156900 chr6B 99.465 187 1 0 1 187 231672227 231672041 1.510000e-89 340.0
11 TraesCS6D01G156900 chr6B 92.105 228 13 3 490 716 231671983 231671760 2.540000e-82 316.0
12 TraesCS6D01G156900 chr6B 84.868 304 36 10 3768 4067 166114690 166114987 9.220000e-77 298.0
13 TraesCS6D01G156900 chr6B 94.828 58 2 1 708 765 231357061 231357005 6.040000e-14 89.8
14 TraesCS6D01G156900 chr5D 85.437 309 31 14 3767 4068 495614817 495615118 4.260000e-80 309.0
15 TraesCS6D01G156900 chr4B 85.016 307 34 11 3767 4068 579103350 579103649 7.130000e-78 302.0
16 TraesCS6D01G156900 chr4A 85.016 307 35 11 3767 4068 21844254 21844554 7.130000e-78 302.0
17 TraesCS6D01G156900 chr3B 85.113 309 30 14 3768 4068 708954584 708954884 7.130000e-78 302.0
18 TraesCS6D01G156900 chr3B 85.113 309 30 14 3768 4068 709075246 709075546 7.130000e-78 302.0
19 TraesCS6D01G156900 chr3A 84.641 306 35 11 3769 4068 645405794 645406093 1.190000e-75 294.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G156900 chr6D 133211578 133215961 4383 True 3793.50 7241 100.0000 1 4384 2 chr6D.!!$R1 4383
1 TraesCS6D01G156900 chr6A 172116526 172120818 4292 True 1449.50 3133 93.1010 1 4384 4 chr6A.!!$R1 4383
2 TraesCS6D01G156900 chr6B 231353317 231357061 3744 True 993.56 3096 92.5396 708 4382 5 chr6B.!!$R1 3674

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
900 935 0.107831 CAACCCGTCCCAGTCTTTGA 59.892 55.000 0.0 0.0 0.00 2.69 F
938 973 0.908198 GAGGTTGTCTCCATCCAGCT 59.092 55.000 0.0 0.0 36.52 4.24 F
1631 1764 1.495951 GTTGGCGCCGTTTACTCTG 59.504 57.895 23.9 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2109 4.405680 CCGACCCATGGATAGCATAGATTA 59.594 45.833 15.22 0.0 0.0 1.75 R
2023 2166 5.990120 AGCTCAGCAGGTGAAATATTTTT 57.010 34.783 0.00 0.0 33.6 1.94 R
3491 3649 0.453793 TTTCCAACACAGTGCCAACG 59.546 50.000 0.00 0.0 0.0 4.10 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
100 101 1.523501 CGTTTTTGATGATGCGGTCG 58.476 50.000 0.00 0.00 0.00 4.79
105 106 3.696426 GATGATGCGGTCGAGCGC 61.696 66.667 44.61 44.61 40.67 5.92
497 498 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
500 501 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
503 504 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
504 505 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
505 506 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
506 507 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
507 508 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
508 509 3.312890 AGAGAGAGAGAGAGAGAGAGGG 58.687 54.545 0.00 0.00 0.00 4.30
509 510 3.051803 AGAGAGAGAGAGAGAGAGAGGGA 60.052 52.174 0.00 0.00 0.00 4.20
510 511 3.041946 AGAGAGAGAGAGAGAGAGGGAC 58.958 54.545 0.00 0.00 0.00 4.46
511 512 2.771943 GAGAGAGAGAGAGAGAGGGACA 59.228 54.545 0.00 0.00 0.00 4.02
512 513 2.774234 AGAGAGAGAGAGAGAGGGACAG 59.226 54.545 0.00 0.00 0.00 3.51
513 514 1.846439 AGAGAGAGAGAGAGGGACAGG 59.154 57.143 0.00 0.00 0.00 4.00
514 515 0.926293 AGAGAGAGAGAGGGACAGGG 59.074 60.000 0.00 0.00 0.00 4.45
555 556 1.987807 ATGGGAATGCGAGGGAGGTG 61.988 60.000 0.00 0.00 0.00 4.00
556 557 2.190578 GGAATGCGAGGGAGGTGG 59.809 66.667 0.00 0.00 0.00 4.61
557 558 2.670148 GGAATGCGAGGGAGGTGGT 61.670 63.158 0.00 0.00 0.00 4.16
658 659 1.578206 GCCACTGCGGAACTTTCCTC 61.578 60.000 0.00 0.00 45.33 3.71
659 660 1.291877 CCACTGCGGAACTTTCCTCG 61.292 60.000 0.00 0.00 45.33 4.63
688 689 4.260456 GCATTACCGAACTAATGCGCTTTA 60.260 41.667 9.73 12.49 45.52 1.85
727 728 1.471119 TTCTGGTATTCTCGTCGCCT 58.529 50.000 0.00 0.00 0.00 5.52
765 766 2.924101 AACCCCGTCGTGCCCTAA 60.924 61.111 0.00 0.00 0.00 2.69
767 768 3.697747 CCCCGTCGTGCCCTAACA 61.698 66.667 0.00 0.00 0.00 2.41
770 778 3.179265 CGTCGTGCCCTAACAGCG 61.179 66.667 0.00 0.00 0.00 5.18
879 914 1.446792 CATCGCGTTCCTGCTGTCT 60.447 57.895 5.77 0.00 0.00 3.41
883 918 1.301716 GCGTTCCTGCTGTCTCCAA 60.302 57.895 0.00 0.00 0.00 3.53
900 935 0.107831 CAACCCGTCCCAGTCTTTGA 59.892 55.000 0.00 0.00 0.00 2.69
938 973 0.908198 GAGGTTGTCTCCATCCAGCT 59.092 55.000 0.00 0.00 36.52 4.24
1058 1093 2.446435 ACTGTGCCTCTTTTGTGTGTT 58.554 42.857 0.00 0.00 0.00 3.32
1066 1101 4.740205 GCCTCTTTTGTGTGTTTTTCTAGC 59.260 41.667 0.00 0.00 0.00 3.42
1067 1102 4.970003 CCTCTTTTGTGTGTTTTTCTAGCG 59.030 41.667 0.00 0.00 0.00 4.26
1102 1137 1.534595 GCAGTAGCTATCCATTGCTGC 59.465 52.381 12.70 12.70 39.16 5.25
1109 1144 2.303022 GCTATCCATTGCTGCTAGGGTA 59.697 50.000 13.94 6.55 0.00 3.69
1159 1195 3.940657 GCATATGCTGTCTGACTGTTC 57.059 47.619 20.64 1.87 38.21 3.18
1217 1253 3.229293 TGACTGATTTGAACAATGGCCA 58.771 40.909 8.56 8.56 0.00 5.36
1236 1272 5.127519 TGGCCAGGAAAAATCATATGTCAAG 59.872 40.000 0.00 0.00 0.00 3.02
1301 1337 2.877360 TTCGTCGTAGGATGGCGCAC 62.877 60.000 10.83 0.00 0.00 5.34
1471 1507 3.662759 TTCCCTTTGTTGGAGTTGTCT 57.337 42.857 0.00 0.00 32.37 3.41
1498 1537 7.095607 GCACAACTATCTCCACCTAATTTATCG 60.096 40.741 0.00 0.00 0.00 2.92
1524 1563 4.469469 TTTTCTCATGAAAAGGGGTCCT 57.531 40.909 0.00 0.00 44.39 3.85
1609 1742 2.593026 TGTCCAACTCCCCATGAAAAC 58.407 47.619 0.00 0.00 0.00 2.43
1619 1752 1.605202 CCCATGAAAACTTGGTTGGCG 60.605 52.381 0.00 0.00 0.00 5.69
1631 1764 1.495951 GTTGGCGCCGTTTACTCTG 59.504 57.895 23.90 0.00 0.00 3.35
1660 1793 9.683069 AGAATGAATCAACATGACACTTTTAAC 57.317 29.630 0.00 0.00 0.00 2.01
1700 1837 6.692849 TGATATTTAGATCCTGCTGACCAT 57.307 37.500 0.00 0.00 0.00 3.55
1800 1937 4.454161 TGGAGGAATCACGTAATTTGTGTG 59.546 41.667 9.51 4.73 38.48 3.82
1945 2085 9.815306 AGAGTCTCTATGGCTGTAAGATTTATA 57.185 33.333 0.00 0.00 34.07 0.98
2022 2165 7.758076 CACCTCGTGTTGAACTAGAATTACATA 59.242 37.037 0.00 0.00 0.00 2.29
2023 2166 8.308931 ACCTCGTGTTGAACTAGAATTACATAA 58.691 33.333 0.00 0.00 0.00 1.90
2048 2191 1.818642 ATTTCACCTGCTGAGCTGAC 58.181 50.000 13.17 0.00 0.00 3.51
2311 2455 3.993081 CTCCACTTTGAGAGCACTACTTG 59.007 47.826 0.00 0.00 34.11 3.16
2634 2783 9.709495 ATCATAAGCAATTGTTTCTTTTTAGCA 57.291 25.926 11.08 0.00 0.00 3.49
2635 2784 9.539825 TCATAAGCAATTGTTTCTTTTTAGCAA 57.460 25.926 11.08 0.00 0.00 3.91
2806 2955 2.315925 TACACTAATCTGCAGCTGGC 57.684 50.000 17.12 8.54 45.13 4.85
3014 3165 2.743718 CGAGGTGCCCAGTTCACT 59.256 61.111 0.00 0.00 34.97 3.41
3032 3183 1.759445 ACTGTGACTGTGACTTCTGCT 59.241 47.619 0.00 0.00 0.00 4.24
3188 3339 0.590195 ATCTAGCGCCGTAAGTACCG 59.410 55.000 2.29 0.00 0.00 4.02
3192 3343 1.870901 GCGCCGTAAGTACCGTCAG 60.871 63.158 0.00 0.00 0.00 3.51
3228 3381 5.661056 ACTTCAGTTCGATAATCTCCACA 57.339 39.130 0.00 0.00 0.00 4.17
3235 3388 6.019237 CAGTTCGATAATCTCCACATGTCTTG 60.019 42.308 0.00 0.00 0.00 3.02
3242 3395 5.954296 ATCTCCACATGTCTTGTTTTGAG 57.046 39.130 0.00 0.00 36.00 3.02
3326 3479 2.420058 ATTCAACTGGAATCGTCCCC 57.580 50.000 0.00 0.00 42.62 4.81
3370 3523 1.815408 GCTCATGTCAAGTGGTGGTGT 60.815 52.381 0.00 0.00 0.00 4.16
3409 3562 8.862325 TGTTTGTCATATGTAATCCTTCAAGT 57.138 30.769 1.90 0.00 0.00 3.16
3410 3563 9.952030 TGTTTGTCATATGTAATCCTTCAAGTA 57.048 29.630 1.90 0.00 0.00 2.24
3427 3585 6.814506 TCAAGTAGTGGTCTGTACTTCTAC 57.185 41.667 0.00 0.00 37.37 2.59
3437 3595 6.151312 TGGTCTGTACTTCTACTCAGTTGATC 59.849 42.308 0.00 0.00 0.00 2.92
3518 3677 5.105146 TGGCACTGTGTTGGAAAAAGTATTT 60.105 36.000 9.86 0.00 42.41 1.40
3556 3715 8.685838 TTTTGTAACTTGTATAAGAGTTGGCT 57.314 30.769 6.19 0.00 36.79 4.75
3558 3717 6.999950 TGTAACTTGTATAAGAGTTGGCTGA 58.000 36.000 6.19 0.00 36.79 4.26
3559 3718 7.620880 TGTAACTTGTATAAGAGTTGGCTGAT 58.379 34.615 6.19 0.00 36.79 2.90
3560 3719 6.992063 AACTTGTATAAGAGTTGGCTGATG 57.008 37.500 6.19 0.00 37.36 3.07
3561 3720 6.299805 ACTTGTATAAGAGTTGGCTGATGA 57.700 37.500 6.19 0.00 37.36 2.92
3562 3721 6.893583 ACTTGTATAAGAGTTGGCTGATGAT 58.106 36.000 6.19 0.00 37.36 2.45
3564 3723 8.486210 ACTTGTATAAGAGTTGGCTGATGATAA 58.514 33.333 6.19 0.00 37.36 1.75
3565 3724 9.499479 CTTGTATAAGAGTTGGCTGATGATAAT 57.501 33.333 0.00 0.00 35.92 1.28
3566 3725 8.837788 TGTATAAGAGTTGGCTGATGATAATG 57.162 34.615 0.00 0.00 0.00 1.90
3592 3752 6.434018 GCATCTCTGCTTAGTTGAAATTCT 57.566 37.500 0.00 0.00 45.32 2.40
3593 3753 6.485393 GCATCTCTGCTTAGTTGAAATTCTC 58.515 40.000 0.00 0.00 45.32 2.87
3594 3754 6.315891 GCATCTCTGCTTAGTTGAAATTCTCT 59.684 38.462 0.00 0.00 45.32 3.10
3595 3755 7.465781 GCATCTCTGCTTAGTTGAAATTCTCTC 60.466 40.741 0.00 0.00 45.32 3.20
3596 3756 6.096036 TCTCTGCTTAGTTGAAATTCTCTCG 58.904 40.000 0.00 0.00 0.00 4.04
3597 3757 6.025749 TCTGCTTAGTTGAAATTCTCTCGA 57.974 37.500 0.00 0.00 0.00 4.04
3630 3794 4.282496 ACATCTCCCCGGCTTATCTATAG 58.718 47.826 0.00 0.00 0.00 1.31
3631 3795 4.264442 ACATCTCCCCGGCTTATCTATAGT 60.264 45.833 0.00 0.00 0.00 2.12
3634 3798 6.088541 TCTCCCCGGCTTATCTATAGTATT 57.911 41.667 0.00 0.00 0.00 1.89
3636 3800 7.645942 TCTCCCCGGCTTATCTATAGTATTAA 58.354 38.462 0.00 0.00 0.00 1.40
3639 3803 8.921205 TCCCCGGCTTATCTATAGTATTAATTC 58.079 37.037 0.00 0.00 0.00 2.17
3640 3804 8.701895 CCCCGGCTTATCTATAGTATTAATTCA 58.298 37.037 0.00 0.00 0.00 2.57
3641 3805 9.530633 CCCGGCTTATCTATAGTATTAATTCAC 57.469 37.037 0.00 0.00 0.00 3.18
3658 3858 9.877178 ATTAATTCACTTTGTTGTTTGTTACCA 57.123 25.926 0.00 0.00 0.00 3.25
3659 3859 7.826260 AATTCACTTTGTTGTTTGTTACCAG 57.174 32.000 0.00 0.00 0.00 4.00
3665 3865 7.595502 CACTTTGTTGTTTGTTACCAGTTTACA 59.404 33.333 0.00 0.00 0.00 2.41
3666 3866 8.142551 ACTTTGTTGTTTGTTACCAGTTTACAA 58.857 29.630 0.00 0.00 0.00 2.41
3667 3867 8.522178 TTTGTTGTTTGTTACCAGTTTACAAG 57.478 30.769 0.00 0.00 33.74 3.16
3668 3868 7.450124 TGTTGTTTGTTACCAGTTTACAAGA 57.550 32.000 0.00 0.00 33.74 3.02
3669 3869 7.883217 TGTTGTTTGTTACCAGTTTACAAGAA 58.117 30.769 0.00 0.00 33.74 2.52
3670 3870 8.358148 TGTTGTTTGTTACCAGTTTACAAGAAA 58.642 29.630 0.00 0.00 33.74 2.52
3742 3954 4.853924 TCATTGAAAGGAAAGAACAGGC 57.146 40.909 0.00 0.00 0.00 4.85
3745 3957 1.956477 TGAAAGGAAAGAACAGGCTGC 59.044 47.619 15.89 0.00 0.00 5.25
3746 3958 1.270826 GAAAGGAAAGAACAGGCTGCC 59.729 52.381 15.89 11.65 0.00 4.85
3775 3988 7.220875 GTCTGTTTTCCTGACTGACAAATTTTC 59.779 37.037 8.70 0.00 42.22 2.29
3990 4203 0.466124 AGGCCGAGAAAGGTATGAGC 59.534 55.000 0.00 0.00 0.00 4.26
3995 4208 3.712187 CCGAGAAAGGTATGAGCTCTTC 58.288 50.000 16.19 9.05 0.00 2.87
4021 4234 2.807108 GCCCTGCCTCTCCTTTTATACG 60.807 54.545 0.00 0.00 0.00 3.06
4028 4241 3.304794 CCTCTCCTTTTATACGCCTCTCG 60.305 52.174 0.00 0.00 45.38 4.04
4045 4258 4.459089 GCGGCTCCCTCCACTCAC 62.459 72.222 0.00 0.00 0.00 3.51
4077 4290 2.159627 GTGGGACTAAACTTGCATCACG 59.840 50.000 0.00 0.00 0.00 4.35
4079 4292 1.201921 GGACTAAACTTGCATCACGCG 60.202 52.381 3.53 3.53 46.97 6.01
4080 4293 0.165944 ACTAAACTTGCATCACGCGC 59.834 50.000 5.73 0.00 46.97 6.86
4081 4294 0.853224 CTAAACTTGCATCACGCGCG 60.853 55.000 30.96 30.96 46.97 6.86
4083 4296 2.498761 AAACTTGCATCACGCGCGAG 62.499 55.000 39.36 30.24 46.97 5.03
4110 4323 1.520342 GAGCGCTCTGTGTGGGATC 60.520 63.158 29.88 0.00 0.00 3.36
4111 4324 1.954362 GAGCGCTCTGTGTGGGATCT 61.954 60.000 29.88 0.00 31.55 2.75
4118 4331 0.532573 CTGTGTGGGATCTGCGTAGT 59.467 55.000 0.00 0.00 0.00 2.73
4125 4338 0.750850 GGATCTGCGTAGTTGGGCTA 59.249 55.000 0.00 0.00 0.00 3.93
4137 4351 6.626402 GCGTAGTTGGGCTATTTTAACCAAAT 60.626 38.462 0.00 0.00 43.88 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
497 498 1.309688 GCCCTGTCCCTCTCTCTCT 59.690 63.158 0.00 0.00 0.00 3.10
500 501 2.043852 TCGCCCTGTCCCTCTCTC 60.044 66.667 0.00 0.00 0.00 3.20
503 504 3.239627 TTCCTCGCCCTGTCCCTCT 62.240 63.158 0.00 0.00 0.00 3.69
504 505 2.683933 TTCCTCGCCCTGTCCCTC 60.684 66.667 0.00 0.00 0.00 4.30
505 506 2.685380 CTTCCTCGCCCTGTCCCT 60.685 66.667 0.00 0.00 0.00 4.20
506 507 2.683933 TCTTCCTCGCCCTGTCCC 60.684 66.667 0.00 0.00 0.00 4.46
507 508 2.726351 CCTCTTCCTCGCCCTGTCC 61.726 68.421 0.00 0.00 0.00 4.02
508 509 2.726351 CCCTCTTCCTCGCCCTGTC 61.726 68.421 0.00 0.00 0.00 3.51
509 510 2.685380 CCCTCTTCCTCGCCCTGT 60.685 66.667 0.00 0.00 0.00 4.00
510 511 3.474570 CCCCTCTTCCTCGCCCTG 61.475 72.222 0.00 0.00 0.00 4.45
511 512 4.012721 ACCCCTCTTCCTCGCCCT 62.013 66.667 0.00 0.00 0.00 5.19
512 513 3.787001 CACCCCTCTTCCTCGCCC 61.787 72.222 0.00 0.00 0.00 6.13
513 514 3.787001 CCACCCCTCTTCCTCGCC 61.787 72.222 0.00 0.00 0.00 5.54
514 515 2.291043 TTCCACCCCTCTTCCTCGC 61.291 63.158 0.00 0.00 0.00 5.03
658 659 4.841861 TTCGGTAATGCCCCGCCG 62.842 66.667 0.00 0.00 45.09 6.46
659 660 2.314415 TAGTTCGGTAATGCCCCGCC 62.314 60.000 0.00 0.00 45.09 6.13
667 668 4.271776 GGTAAAGCGCATTAGTTCGGTAAT 59.728 41.667 11.47 0.00 35.22 1.89
679 680 1.200020 GAGCAAAGTGGTAAAGCGCAT 59.800 47.619 11.47 0.00 0.00 4.73
688 689 2.281761 CGCAGGGAGCAAAGTGGT 60.282 61.111 0.00 0.00 46.13 4.16
799 828 2.032071 GAGGTGTTGGTCGTGGGG 59.968 66.667 0.00 0.00 0.00 4.96
805 834 2.047179 GAGGCGGAGGTGTTGGTC 60.047 66.667 0.00 0.00 0.00 4.02
879 914 1.057851 AAAGACTGGGACGGGTTGGA 61.058 55.000 0.00 0.00 40.47 3.53
883 918 1.752833 GTCAAAGACTGGGACGGGT 59.247 57.895 0.00 0.00 40.47 5.28
900 935 3.372349 CCTCAGATGTCAATCCCAATGGT 60.372 47.826 0.00 0.00 32.77 3.55
938 973 4.684724 AGGTCAGTGGGATTTCACTACTA 58.315 43.478 0.00 0.00 45.24 1.82
1051 1086 5.940192 ATGAATCGCTAGAAAAACACACA 57.060 34.783 0.00 0.00 0.00 3.72
1058 1093 6.545508 CACACATGAATGAATCGCTAGAAAA 58.454 36.000 0.00 0.00 0.00 2.29
1066 1101 3.752412 ACTGCACACATGAATGAATCG 57.248 42.857 0.00 0.00 0.00 3.34
1067 1102 4.334759 AGCTACTGCACACATGAATGAATC 59.665 41.667 0.00 0.00 42.74 2.52
1102 1137 4.020543 AGAGTTCACTTGAGCTACCCTAG 58.979 47.826 0.00 0.00 35.71 3.02
1159 1195 5.878116 TCCTTGACAAGTTAATTCCGTATGG 59.122 40.000 14.03 0.00 0.00 2.74
1172 1208 3.441572 GCATTACAGCATCCTTGACAAGT 59.558 43.478 14.03 0.00 0.00 3.16
1217 1253 9.347240 CCTATGTCTTGACATATGATTTTTCCT 57.653 33.333 19.74 0.00 32.80 3.36
1236 1272 6.933521 ACATAAATCATCACTCTGCCTATGTC 59.066 38.462 0.00 0.00 0.00 3.06
1301 1337 4.614946 CAAGAGGCAACAAGAAAGAAAGG 58.385 43.478 0.00 0.00 41.41 3.11
1471 1507 5.435686 AATTAGGTGGAGATAGTTGTGCA 57.564 39.130 0.00 0.00 0.00 4.57
1551 1590 7.715249 TGAAAAACTCTAGCAGACAAGTACATT 59.285 33.333 0.00 0.00 0.00 2.71
1552 1591 7.217200 TGAAAAACTCTAGCAGACAAGTACAT 58.783 34.615 0.00 0.00 0.00 2.29
1553 1592 6.578944 TGAAAAACTCTAGCAGACAAGTACA 58.421 36.000 0.00 0.00 0.00 2.90
1554 1593 7.659652 ATGAAAAACTCTAGCAGACAAGTAC 57.340 36.000 0.00 0.00 0.00 2.73
1555 1594 7.931407 TCAATGAAAAACTCTAGCAGACAAGTA 59.069 33.333 0.00 0.00 0.00 2.24
1556 1595 6.767902 TCAATGAAAAACTCTAGCAGACAAGT 59.232 34.615 0.00 0.00 0.00 3.16
1559 1598 7.445096 TGAATCAATGAAAAACTCTAGCAGACA 59.555 33.333 0.00 0.00 0.00 3.41
1560 1599 7.810658 TGAATCAATGAAAAACTCTAGCAGAC 58.189 34.615 0.00 0.00 0.00 3.51
1561 1600 7.984422 TGAATCAATGAAAAACTCTAGCAGA 57.016 32.000 0.00 0.00 0.00 4.26
1590 1723 2.876581 AGTTTTCATGGGGAGTTGGAC 58.123 47.619 0.00 0.00 0.00 4.02
1609 1742 1.081708 GTAAACGGCGCCAACCAAG 60.082 57.895 28.98 11.60 0.00 3.61
1619 1752 3.585862 TCATTCTGACAGAGTAAACGGC 58.414 45.455 5.10 0.00 0.00 5.68
1631 1764 6.492007 AGTGTCATGTTGATTCATTCTGAC 57.508 37.500 12.51 12.51 0.00 3.51
1700 1837 5.754782 AGTGGAGCAATGGTTAACATATCA 58.245 37.500 8.10 0.00 39.40 2.15
1819 1959 7.781324 AGTCAAATATGTGGGACTGAATTTT 57.219 32.000 0.00 0.00 39.04 1.82
1964 2106 5.353986 ACCCATGGATAGCATAGATTACCT 58.646 41.667 15.22 0.00 0.00 3.08
1966 2108 5.352284 CGACCCATGGATAGCATAGATTAC 58.648 45.833 15.22 0.00 0.00 1.89
1967 2109 4.405680 CCGACCCATGGATAGCATAGATTA 59.594 45.833 15.22 0.00 0.00 1.75
2023 2166 5.990120 AGCTCAGCAGGTGAAATATTTTT 57.010 34.783 0.00 0.00 33.60 1.94
2232 2376 6.381994 AGCATGATCTACCCATCATTTTTGTT 59.618 34.615 0.00 0.00 40.86 2.83
2643 2792 8.814038 AAGAGGTCAGCAGATATAACAATTTT 57.186 30.769 0.00 0.00 0.00 1.82
2644 2793 8.814038 AAAGAGGTCAGCAGATATAACAATTT 57.186 30.769 0.00 0.00 0.00 1.82
3014 3165 3.132111 TGTTAGCAGAAGTCACAGTCACA 59.868 43.478 0.00 0.00 0.00 3.58
3032 3183 3.153369 TGGAGCTTTGGCATCTTGTTA 57.847 42.857 0.00 0.00 41.70 2.41
3188 3339 6.500684 TGAAGTATCAAAATTCAGGCTGAC 57.499 37.500 18.55 2.65 30.99 3.51
3228 3381 6.706270 AGTGACGATTACTCAAAACAAGACAT 59.294 34.615 0.00 0.00 0.00 3.06
3263 3416 1.277495 GCCTGCAACAATGTTCGTGC 61.277 55.000 0.00 0.00 0.00 5.34
3407 3560 6.124316 TGAGTAGAAGTACAGACCACTACT 57.876 41.667 0.00 0.00 42.49 2.57
3409 3562 6.124316 ACTGAGTAGAAGTACAGACCACTA 57.876 41.667 0.00 0.00 34.88 2.74
3410 3563 4.988029 ACTGAGTAGAAGTACAGACCACT 58.012 43.478 0.00 0.00 34.88 4.00
3427 3585 5.813080 TTCATGCATTCTGATCAACTGAG 57.187 39.130 0.00 0.00 0.00 3.35
3491 3649 0.453793 TTTCCAACACAGTGCCAACG 59.546 50.000 0.00 0.00 0.00 4.10
3518 3677 5.652994 AGTTACAAAAACTCAGTGCCAAA 57.347 34.783 0.00 0.00 0.00 3.28
3554 3713 4.632251 CAGAGATGCCTCATTATCATCAGC 59.368 45.833 0.00 0.00 41.87 4.26
3556 3715 4.286291 AGCAGAGATGCCTCATTATCATCA 59.714 41.667 0.00 0.00 41.87 3.07
3558 3717 4.912317 AGCAGAGATGCCTCATTATCAT 57.088 40.909 0.00 0.00 41.87 2.45
3559 3718 4.701651 AAGCAGAGATGCCTCATTATCA 57.298 40.909 0.00 0.00 41.87 2.15
3560 3719 5.792741 ACTAAGCAGAGATGCCTCATTATC 58.207 41.667 0.00 0.00 41.87 1.75
3561 3720 5.822132 ACTAAGCAGAGATGCCTCATTAT 57.178 39.130 0.00 0.00 41.87 1.28
3562 3721 5.129320 TCAACTAAGCAGAGATGCCTCATTA 59.871 40.000 0.00 0.00 41.87 1.90
3564 3723 3.453717 TCAACTAAGCAGAGATGCCTCAT 59.546 43.478 0.00 0.00 41.87 2.90
3565 3724 2.833943 TCAACTAAGCAGAGATGCCTCA 59.166 45.455 0.00 0.00 41.87 3.86
3566 3725 3.533606 TCAACTAAGCAGAGATGCCTC 57.466 47.619 0.00 0.00 39.72 4.70
3586 3746 6.683110 ATGTACCGCATACTTCGAGAGAATTT 60.683 38.462 0.00 0.00 42.15 1.82
3589 3749 3.630769 ATGTACCGCATACTTCGAGAGAA 59.369 43.478 0.00 0.00 41.35 2.87
3591 3751 3.251245 AGATGTACCGCATACTTCGAGAG 59.749 47.826 0.00 0.00 40.99 3.20
3592 3752 3.211865 AGATGTACCGCATACTTCGAGA 58.788 45.455 0.00 0.00 40.99 4.04
3593 3753 3.556513 GAGATGTACCGCATACTTCGAG 58.443 50.000 0.00 0.00 40.99 4.04
3594 3754 2.292569 GGAGATGTACCGCATACTTCGA 59.707 50.000 0.00 0.00 40.99 3.71
3595 3755 2.607282 GGGAGATGTACCGCATACTTCG 60.607 54.545 0.00 0.00 40.99 3.79
3596 3756 2.288886 GGGGAGATGTACCGCATACTTC 60.289 54.545 0.00 3.88 38.06 3.01
3597 3757 1.692519 GGGGAGATGTACCGCATACTT 59.307 52.381 0.00 0.00 38.06 2.24
3678 3878 9.357161 TCCACCTTTTGCTAATCTTAAACTAAA 57.643 29.630 0.00 0.00 0.00 1.85
3686 3886 4.460731 GCTTCTCCACCTTTTGCTAATCTT 59.539 41.667 0.00 0.00 0.00 2.40
3690 3890 2.158534 TGGCTTCTCCACCTTTTGCTAA 60.159 45.455 0.00 0.00 40.72 3.09
3719 3925 5.010415 AGCCTGTTCTTTCCTTTCAATGAAG 59.990 40.000 0.00 0.00 0.00 3.02
3742 3954 1.202806 TCAGGAAAACAGACAGGGCAG 60.203 52.381 0.00 0.00 0.00 4.85
3745 3957 2.104792 TCAGTCAGGAAAACAGACAGGG 59.895 50.000 0.00 0.00 38.01 4.45
3746 3958 3.134458 GTCAGTCAGGAAAACAGACAGG 58.866 50.000 0.00 0.00 38.01 4.00
3775 3988 1.881591 CACCCCAACCAAAGCAAATG 58.118 50.000 0.00 0.00 0.00 2.32
3833 4046 3.204467 TTGCTACTGGGGCCCACAC 62.204 63.158 24.76 11.83 0.00 3.82
3863 4076 2.332312 TTTGTGAGGGTGGTGGGTCG 62.332 60.000 0.00 0.00 0.00 4.79
4028 4241 4.459089 GTGAGTGGAGGGAGCCGC 62.459 72.222 0.00 0.00 38.73 6.53
4110 4323 4.201881 GGTTAAAATAGCCCAACTACGCAG 60.202 45.833 0.00 0.00 32.32 5.18
4111 4324 3.690628 GGTTAAAATAGCCCAACTACGCA 59.309 43.478 0.00 0.00 32.32 5.24
4118 4331 5.126384 CGGAGATTTGGTTAAAATAGCCCAA 59.874 40.000 0.00 0.00 38.64 4.12
4125 4338 4.159693 GGCCTTCGGAGATTTGGTTAAAAT 59.840 41.667 0.00 0.00 41.33 1.82
4137 4351 1.497309 ATGGTTTGGGCCTTCGGAGA 61.497 55.000 4.53 0.00 0.00 3.71
4193 4407 2.683968 CTGCTAAGCGTGTAGTTTGGA 58.316 47.619 0.00 0.00 0.00 3.53
4323 4543 2.551270 CTTGAACGGTGACTGCGC 59.449 61.111 0.00 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.