Multiple sequence alignment - TraesCS3D01G432500

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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 TraesCS3D01G432500 chr3D 100.000 4992 0 0 1 4992 546243979 546248970 0.000000e+00 9219.0
1 TraesCS3D01G432500 chr3A 94.544 2859 114 22 897 3733 682972097 682974935 0.000000e+00 4377.0
2 TraesCS3D01G432500 chr3A 89.262 922 83 8 1 919 682971163 682972071 0.000000e+00 1140.0
3 TraesCS3D01G432500 chr3A 88.760 605 30 23 4419 4992 682976046 682976643 0.000000e+00 706.0
4 TraesCS3D01G432500 chr3A 83.453 278 34 6 3734 4001 682974893 682975168 1.070000e-61 248.0
5 TraesCS3D01G432500 chr3B 94.777 1570 69 11 897 2463 723027951 723029510 0.000000e+00 2433.0
6 TraesCS3D01G432500 chr3B 93.924 1547 72 9 2452 3982 723029600 723031140 0.000000e+00 2316.0
7 TraesCS3D01G432500 chr3B 88.201 1017 69 22 4017 4992 723031135 723032141 0.000000e+00 1166.0
8 TraesCS3D01G432500 chr3B 85.730 911 95 24 5 910 723027038 723027918 0.000000e+00 929.0
9 TraesCS3D01G432500 chr5D 100.000 28 0 0 1203 1230 394988550 394988523 9.000000e-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 TraesCS3D01G432500 chr3D 546243979 546248970 4991 False 9219.00 9219 100.00000 1 4992 1 chr3D.!!$F1 4991
1 TraesCS3D01G432500 chr3A 682971163 682976643 5480 False 1617.75 4377 89.00475 1 4992 4 chr3A.!!$F1 4991
2 TraesCS3D01G432500 chr3B 723027038 723032141 5103 False 1711.00 2433 90.65800 5 4992 4 chr3B.!!$F1 4987

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
663 665 1.076533 CAACGAGTTCCCGTCCGATG 61.077 60.000 0.00 0.0 42.54 3.84 F
1074 1131 1.081277 ACCAACCCTCCTCCTCCTC 59.919 63.158 0.00 0.0 0.00 3.71 F
1923 1993 1.211457 CTTGGCTGGCATCTAGGACTT 59.789 52.381 4.22 0.0 0.00 3.01 F
1964 2034 1.931906 TGCGCTGATTCACTGATCTC 58.068 50.000 9.73 0.0 0.00 2.75 F
3613 3806 0.465460 TGCCTGACAACTCCCACAAC 60.465 55.000 0.00 0.0 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1712 1.153881 GGAACCCGCTACGTCTCAC 60.154 63.158 0.00 0.0 0.00 3.51 R
1973 2043 2.308570 ACAGTTGGTCCATAGATGCCAA 59.691 45.455 0.00 0.0 38.51 4.52 R
3418 3606 0.460284 GGGTGTACTCTGCACGATGG 60.460 60.000 0.00 0.0 37.70 3.51 R
3751 3987 0.545171 ACAGACTCCAGCATCCCATG 59.455 55.000 0.00 0.0 0.00 3.66 R
4781 5561 1.330521 CTGGCCATCAAACGATTACCG 59.669 52.381 5.51 0.0 45.44 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 1.406539 CAGCAAGCAACAACAGGAAGT 59.593 47.619 0.00 0.00 0.00 3.01
87 88 8.630037 CAACAACAGGAAGTTAAGGTCTAAAAT 58.370 33.333 0.00 0.00 38.74 1.82
209 210 6.920758 GCACCATGAACATACAAAACTAACAA 59.079 34.615 0.00 0.00 0.00 2.83
210 211 7.436673 GCACCATGAACATACAAAACTAACAAA 59.563 33.333 0.00 0.00 0.00 2.83
354 356 7.442364 ACCATGAATCAGATATGTCTTTAACGG 59.558 37.037 0.00 0.00 30.42 4.44
375 377 7.712204 ACGGACATTTTGATAAATTAAGGGT 57.288 32.000 0.00 0.00 31.63 4.34
376 378 7.768240 ACGGACATTTTGATAAATTAAGGGTC 58.232 34.615 0.00 0.00 31.63 4.46
377 379 7.614192 ACGGACATTTTGATAAATTAAGGGTCT 59.386 33.333 0.00 0.00 31.63 3.85
391 393 8.934023 AATTAAGGGTCTCTTGTTTTGTGATA 57.066 30.769 0.00 0.00 36.93 2.15
408 410 9.595823 TTTTGTGATAACTATGGAACTAGCTAC 57.404 33.333 0.00 0.00 0.00 3.58
411 413 7.014326 TGTGATAACTATGGAACTAGCTACAGG 59.986 40.741 0.00 0.00 0.00 4.00
505 507 2.734606 TGTTGCGAGTCGTTGGATTAAG 59.265 45.455 15.08 0.00 0.00 1.85
561 563 1.212250 GCCCCCTTCCCCTCAAACTA 61.212 60.000 0.00 0.00 0.00 2.24
583 585 2.667470 TCATCTTCTTCCTCCTACCCG 58.333 52.381 0.00 0.00 0.00 5.28
594 596 3.839490 TCCTCCTACCCGACAAAAATACA 59.161 43.478 0.00 0.00 0.00 2.29
627 629 2.456840 CTCCTCCCTCCCAACCCT 59.543 66.667 0.00 0.00 0.00 4.34
663 665 1.076533 CAACGAGTTCCCGTCCGATG 61.077 60.000 0.00 0.00 42.54 3.84
722 724 2.517450 GCTTCGTCCGATCCAAGCG 61.517 63.158 0.00 0.00 32.47 4.68
846 848 2.482721 TCTCCTTTGCGAAAAATCGACC 59.517 45.455 1.91 0.00 34.64 4.79
847 849 2.222886 TCCTTTGCGAAAAATCGACCA 58.777 42.857 1.91 0.00 34.64 4.02
848 850 2.817258 TCCTTTGCGAAAAATCGACCAT 59.183 40.909 1.91 0.00 34.64 3.55
876 881 2.287547 TGCGATTTTCAAGCAACTGGAC 60.288 45.455 0.00 0.00 38.01 4.02
879 884 3.665323 CGATTTTCAAGCAACTGGACGAG 60.665 47.826 0.00 0.00 0.00 4.18
933 984 3.243737 GGTTCTTGGAACCGAAGCATTTT 60.244 43.478 12.74 0.00 36.03 1.82
978 1029 7.020914 GGCAAAACCTCACTAGAATATTGAG 57.979 40.000 0.00 0.00 44.99 3.02
990 1041 7.335422 CACTAGAATATTGAGCAACTTGGACTT 59.665 37.037 0.00 0.00 0.00 3.01
1071 1128 2.671682 GCACCAACCCTCCTCCTC 59.328 66.667 0.00 0.00 0.00 3.71
1072 1129 2.972819 GCACCAACCCTCCTCCTCC 61.973 68.421 0.00 0.00 0.00 4.30
1073 1130 1.229658 CACCAACCCTCCTCCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
1074 1131 1.081277 ACCAACCCTCCTCCTCCTC 59.919 63.158 0.00 0.00 0.00 3.71
1075 1132 1.690985 CCAACCCTCCTCCTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
1076 1133 1.394151 CAACCCTCCTCCTCCTCCT 59.606 63.158 0.00 0.00 0.00 3.69
1099 1156 3.239627 TTCTCCCCACCTCGCCTCT 62.240 63.158 0.00 0.00 0.00 3.69
1101 1158 2.683933 TCCCCACCTCGCCTCTTC 60.684 66.667 0.00 0.00 0.00 2.87
1297 1354 2.747855 GGTGCCTCTTCTTGCCGG 60.748 66.667 0.00 0.00 0.00 6.13
1596 1660 4.680237 TTCCACTGCAGGCGACGG 62.680 66.667 19.93 10.11 0.00 4.79
1610 1674 1.703438 CGACGGACGTCCTAGGTGAG 61.703 65.000 30.92 16.47 41.76 3.51
1613 1677 1.716826 CGGACGTCCTAGGTGAGAGC 61.717 65.000 30.92 1.49 0.00 4.09
1647 1712 5.579511 GGAATCAAAATGATGAAACTGGCAG 59.420 40.000 14.16 14.16 37.15 4.85
1766 1836 2.178890 CAGAGGCTTGATCTGCGCC 61.179 63.158 4.18 11.09 44.09 6.53
1852 1922 3.680490 TGCCCGTCTATGAATTTCACAA 58.320 40.909 0.15 0.00 0.00 3.33
1882 1952 5.122711 CCTGCCAATGATTTTGATTTTGGTC 59.877 40.000 0.00 0.00 39.21 4.02
1923 1993 1.211457 CTTGGCTGGCATCTAGGACTT 59.789 52.381 4.22 0.00 0.00 3.01
1933 2003 3.683847 GCATCTAGGACTTGTGCCTTCAT 60.684 47.826 0.00 0.00 36.96 2.57
1964 2034 1.931906 TGCGCTGATTCACTGATCTC 58.068 50.000 9.73 0.00 0.00 2.75
1970 2040 3.067461 GCTGATTCACTGATCTCTACGGT 59.933 47.826 0.00 0.00 0.00 4.83
1973 2043 4.462834 TGATTCACTGATCTCTACGGTTGT 59.537 41.667 0.00 0.00 0.00 3.32
1984 2054 3.792401 TCTACGGTTGTTGGCATCTATG 58.208 45.455 0.00 0.00 0.00 2.23
1997 2067 2.945668 GCATCTATGGACCAACTGTTCC 59.054 50.000 0.00 0.00 0.00 3.62
2212 2282 5.356470 ACTTCTGATCTTTGCTATTTCCAGC 59.644 40.000 0.00 0.00 42.15 4.85
2313 2383 3.755378 GACAATGCATATCCCTAAGGCAG 59.245 47.826 0.00 0.00 37.96 4.85
2609 2790 7.633193 AAAATATAACACCAATGGCGAACTA 57.367 32.000 0.00 0.00 0.00 2.24
2693 2881 4.401022 TGACCTGTTCTTGATCTTGCATT 58.599 39.130 0.00 0.00 0.00 3.56
2733 2921 5.193663 TGTGTTCAACCACATTTACATGG 57.806 39.130 0.00 0.00 40.30 3.66
2812 3000 6.389830 TCACAAACAAATGTAGAGCATGTT 57.610 33.333 0.00 0.00 37.96 2.71
3174 3362 1.986575 GACGAAATGGCAGCAGCTCC 61.987 60.000 0.00 0.00 41.70 4.70
3394 3582 2.679837 CAGAGGACATGTTATGGTGTGC 59.320 50.000 0.00 0.00 37.00 4.57
3418 3606 3.243501 TGAACATTTTCTCACTGCTTGCC 60.244 43.478 0.00 0.00 32.36 4.52
3544 3732 3.169512 CCAATTTGTGGGAAGGTACCT 57.830 47.619 9.21 9.21 44.64 3.08
3564 3752 3.490078 CCTTATCTCGTGCTCCAGACTTC 60.490 52.174 0.00 0.00 0.00 3.01
3575 3768 6.529220 GTGCTCCAGACTTCATATTCCTAAT 58.471 40.000 0.00 0.00 0.00 1.73
3613 3806 0.465460 TGCCTGACAACTCCCACAAC 60.465 55.000 0.00 0.00 0.00 3.32
3622 3815 1.302832 CTCCCACAACCTGCTGGAC 60.303 63.158 17.64 0.00 37.04 4.02
3671 3864 2.363683 CCTGAGAGAAACTTCCATGCC 58.636 52.381 0.00 0.00 0.00 4.40
3704 3940 3.491792 GGAAGAGCGGGAAGAAGTATCTG 60.492 52.174 0.00 0.00 35.59 2.90
3733 3969 3.431486 GGGATGCTGGAGAGTCTGTAAAG 60.431 52.174 0.00 0.00 0.00 1.85
3734 3970 3.431486 GGATGCTGGAGAGTCTGTAAAGG 60.431 52.174 0.00 0.00 0.00 3.11
3735 3971 1.902508 TGCTGGAGAGTCTGTAAAGGG 59.097 52.381 0.00 0.00 0.00 3.95
3736 3972 2.180276 GCTGGAGAGTCTGTAAAGGGA 58.820 52.381 0.00 0.00 0.00 4.20
3737 3973 2.567615 GCTGGAGAGTCTGTAAAGGGAA 59.432 50.000 0.00 0.00 0.00 3.97
3738 3974 3.008049 GCTGGAGAGTCTGTAAAGGGAAA 59.992 47.826 0.00 0.00 0.00 3.13
3739 3975 4.505039 GCTGGAGAGTCTGTAAAGGGAAAA 60.505 45.833 0.00 0.00 0.00 2.29
3740 3976 5.621193 CTGGAGAGTCTGTAAAGGGAAAAA 58.379 41.667 0.00 0.00 0.00 1.94
3741 3977 5.621193 TGGAGAGTCTGTAAAGGGAAAAAG 58.379 41.667 0.00 0.00 0.00 2.27
3742 3978 5.132144 TGGAGAGTCTGTAAAGGGAAAAAGT 59.868 40.000 0.00 0.00 0.00 2.66
3743 3979 6.328148 TGGAGAGTCTGTAAAGGGAAAAAGTA 59.672 38.462 0.00 0.00 0.00 2.24
3744 3980 7.017254 TGGAGAGTCTGTAAAGGGAAAAAGTAT 59.983 37.037 0.00 0.00 0.00 2.12
3745 3981 7.549842 GGAGAGTCTGTAAAGGGAAAAAGTATC 59.450 40.741 0.00 0.00 0.00 2.24
3746 3982 8.208575 AGAGTCTGTAAAGGGAAAAAGTATCT 57.791 34.615 0.00 0.00 0.00 1.98
3747 3983 9.322769 AGAGTCTGTAAAGGGAAAAAGTATCTA 57.677 33.333 0.00 0.00 0.00 1.98
3748 3984 9.368674 GAGTCTGTAAAGGGAAAAAGTATCTAC 57.631 37.037 0.00 0.00 0.00 2.59
3749 3985 8.877195 AGTCTGTAAAGGGAAAAAGTATCTACA 58.123 33.333 0.00 0.00 0.00 2.74
3750 3986 9.152595 GTCTGTAAAGGGAAAAAGTATCTACAG 57.847 37.037 0.00 0.00 36.60 2.74
3751 3987 7.822822 TCTGTAAAGGGAAAAAGTATCTACAGC 59.177 37.037 0.00 0.00 35.70 4.40
3752 3988 7.455058 TGTAAAGGGAAAAAGTATCTACAGCA 58.545 34.615 0.00 0.00 0.00 4.41
3753 3989 8.107095 TGTAAAGGGAAAAAGTATCTACAGCAT 58.893 33.333 0.00 0.00 0.00 3.79
3754 3990 7.396540 AAAGGGAAAAAGTATCTACAGCATG 57.603 36.000 0.00 0.00 46.00 4.06
3755 3991 5.440610 AGGGAAAAAGTATCTACAGCATGG 58.559 41.667 0.00 0.00 43.62 3.66
3756 3992 4.580580 GGGAAAAAGTATCTACAGCATGGG 59.419 45.833 0.00 0.00 43.62 4.00
3757 3993 5.437060 GGAAAAAGTATCTACAGCATGGGA 58.563 41.667 0.00 0.00 43.62 4.37
3758 3994 6.064717 GGAAAAAGTATCTACAGCATGGGAT 58.935 40.000 0.00 0.00 43.62 3.85
3759 3995 6.016777 GGAAAAAGTATCTACAGCATGGGATG 60.017 42.308 0.00 0.00 43.62 3.51
3769 4005 3.398694 CATGGGATGCTGGAGTCTG 57.601 57.895 0.00 0.00 0.00 3.51
3770 4006 0.545171 CATGGGATGCTGGAGTCTGT 59.455 55.000 0.00 0.00 0.00 3.41
3771 4007 1.764723 CATGGGATGCTGGAGTCTGTA 59.235 52.381 0.00 0.00 0.00 2.74
3772 4008 1.951209 TGGGATGCTGGAGTCTGTAA 58.049 50.000 0.00 0.00 0.00 2.41
3773 4009 2.265367 TGGGATGCTGGAGTCTGTAAA 58.735 47.619 0.00 0.00 0.00 2.01
3897 4136 6.527722 GTGTGTATATTGTTGAATGGCAGTTG 59.472 38.462 0.00 0.00 0.00 3.16
3950 4190 0.034337 TGGGAATATAAGTCGGGCGC 59.966 55.000 0.00 0.00 0.00 6.53
3965 4205 1.807226 GCGCGGGCCTAAGAATTTT 59.193 52.632 14.45 0.00 0.00 1.82
3975 4215 6.183360 CGGGCCTAAGAATTTTGATTGGTTAT 60.183 38.462 0.84 0.00 0.00 1.89
3983 4226 9.612066 AAGAATTTTGATTGGTTATTGTGTGTT 57.388 25.926 0.00 0.00 0.00 3.32
4030 4303 6.811954 TGTCTTCGACTGTATGGCATATTAA 58.188 36.000 10.92 0.00 33.15 1.40
4070 4343 5.880054 AATGGACGACCTAAAATCAAGTG 57.120 39.130 5.33 0.00 37.04 3.16
4092 4365 4.061596 GCCTGACTTATATTCCTGTCTGC 58.938 47.826 0.00 0.00 0.00 4.26
4137 4410 4.200092 GTTCATGAGTTAATGGGTCCTCC 58.800 47.826 0.00 0.00 0.00 4.30
4138 4411 2.434336 TCATGAGTTAATGGGTCCTCCG 59.566 50.000 0.00 0.00 38.76 4.63
4153 4427 4.462280 CCGGGGGCGTGAAGTACC 62.462 72.222 0.00 0.00 0.00 3.34
4164 4438 3.508762 CGTGAAGTACCGCAAATAGAGT 58.491 45.455 0.00 0.00 0.00 3.24
4165 4439 4.665212 CGTGAAGTACCGCAAATAGAGTA 58.335 43.478 0.00 0.00 0.00 2.59
4166 4440 4.498323 CGTGAAGTACCGCAAATAGAGTAC 59.502 45.833 0.00 0.00 36.23 2.73
4194 4625 2.161410 TGGCTCATTATTGTTGCGACAC 59.839 45.455 6.19 0.00 34.98 3.67
4196 4627 3.485877 GGCTCATTATTGTTGCGACACTC 60.486 47.826 6.19 0.00 34.98 3.51
4218 4669 4.279671 TCGCCATTGTCCAAATAAAGTGTT 59.720 37.500 0.00 0.00 0.00 3.32
4230 4681 6.715264 CCAAATAAAGTGTTCCTAAGGTGTCT 59.285 38.462 0.00 0.00 0.00 3.41
4248 4699 8.475331 AGGTGTCTTGTGTTTAAGAATATACG 57.525 34.615 0.00 0.00 38.33 3.06
4290 4793 4.380531 CAAACTGCAGTTAGAGGACTTCA 58.619 43.478 31.31 0.00 37.25 3.02
4324 4828 0.902531 ATAGCAGTAGTTGTGGGCGT 59.097 50.000 0.00 0.00 0.00 5.68
4342 4972 2.064014 CGTAACCCGTCCTTGAAGTTC 58.936 52.381 0.00 0.00 0.00 3.01
4356 4986 4.314740 TGAAGTTCCAAAATTTCACCCG 57.685 40.909 0.00 0.00 36.52 5.28
4399 5030 4.694339 AGTGAGCGGTATAAAGGACAATC 58.306 43.478 0.00 0.00 0.00 2.67
4409 5040 6.037610 GGTATAAAGGACAATCTTGAGCACAG 59.962 42.308 0.00 0.00 0.00 3.66
4489 5216 8.918202 ATTGTTTAGTTAGATCAAAGTGTCCA 57.082 30.769 0.00 0.00 0.00 4.02
4502 5242 7.053316 TCAAAGTGTCCATCAATGAAAACAT 57.947 32.000 0.00 0.00 0.00 2.71
4586 5366 6.449698 ACAACAGTAAGGAGAAATGCATTTG 58.550 36.000 28.67 14.05 0.00 2.32
4635 5415 6.921857 ACTTGCTCAAAAACAATTGATCAGAG 59.078 34.615 13.59 12.62 36.94 3.35
4703 5483 2.205074 CAGGCACGCCTAGAATACAAG 58.795 52.381 10.95 0.00 46.28 3.16
4704 5484 2.108168 AGGCACGCCTAGAATACAAGA 58.892 47.619 9.35 0.00 46.14 3.02
4705 5485 2.500098 AGGCACGCCTAGAATACAAGAA 59.500 45.455 9.35 0.00 46.14 2.52
4706 5486 2.866762 GGCACGCCTAGAATACAAGAAG 59.133 50.000 0.00 0.00 0.00 2.85
4707 5487 2.285488 GCACGCCTAGAATACAAGAAGC 59.715 50.000 0.00 0.00 0.00 3.86
4781 5561 4.852609 CAGCAAGCTGGCATTTTTATTC 57.147 40.909 17.28 0.00 40.17 1.75
4855 5635 4.715523 GCCTACAGGTTGGCGGCA 62.716 66.667 7.97 7.97 41.22 5.69
4927 5707 1.201429 TCCCCTTGAAGGAGCTCACC 61.201 60.000 13.97 0.00 37.67 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 5.702670 CACACTCTGAGCTAATTCCTGAAAA 59.297 40.000 4.19 0.00 0.00 2.29
209 210 7.985184 TGTCGGAGTACATTATAAGATTTGCTT 59.015 33.333 0.00 0.00 40.68 3.91
210 211 7.497595 TGTCGGAGTACATTATAAGATTTGCT 58.502 34.615 0.00 0.00 0.00 3.91
375 377 8.999431 GTTCCATAGTTATCACAAAACAAGAGA 58.001 33.333 0.00 0.00 0.00 3.10
376 378 9.003658 AGTTCCATAGTTATCACAAAACAAGAG 57.996 33.333 0.00 0.00 0.00 2.85
377 379 8.918202 AGTTCCATAGTTATCACAAAACAAGA 57.082 30.769 0.00 0.00 0.00 3.02
391 393 6.869206 TTTCCTGTAGCTAGTTCCATAGTT 57.131 37.500 0.00 0.00 0.00 2.24
463 465 4.039488 ACAAATTGGCTGATGCAAAAGAGA 59.961 37.500 0.00 0.00 41.91 3.10
464 466 4.312443 ACAAATTGGCTGATGCAAAAGAG 58.688 39.130 0.00 0.00 41.91 2.85
465 467 4.339872 ACAAATTGGCTGATGCAAAAGA 57.660 36.364 0.00 0.00 41.91 2.52
478 480 2.043411 CAACGACTCGCAACAAATTGG 58.957 47.619 0.00 0.00 36.23 3.16
505 507 1.079503 GACAATCTGGCCACTCGTTC 58.920 55.000 0.00 0.00 0.00 3.95
561 563 3.643792 CGGGTAGGAGGAAGAAGATGAAT 59.356 47.826 0.00 0.00 0.00 2.57
583 585 6.149633 AGAAATCGTGGCTTGTATTTTTGTC 58.850 36.000 0.00 0.00 0.00 3.18
594 596 1.630878 AGGAGGAAGAAATCGTGGCTT 59.369 47.619 0.00 0.00 0.00 4.35
627 629 0.040646 TTGGAGGCGAGGTAGGAGAA 59.959 55.000 0.00 0.00 0.00 2.87
663 665 3.757248 ATTGCGTCCCCGATGAGGC 62.757 63.158 10.59 10.59 44.29 4.70
685 687 1.014564 CCCGAGTTGGAGACGAAAGC 61.015 60.000 0.00 0.00 42.00 3.51
689 691 1.874345 GAAGCCCGAGTTGGAGACGA 61.874 60.000 0.00 0.00 42.00 4.20
722 724 3.017442 GGGGCTTTTAACTCTGACCATC 58.983 50.000 0.00 0.00 0.00 3.51
818 820 2.774439 TTCGCAAAGGAGAAGCAAAC 57.226 45.000 0.00 0.00 0.00 2.93
819 821 3.791973 TTTTCGCAAAGGAGAAGCAAA 57.208 38.095 0.00 0.00 34.26 3.68
876 881 0.878416 TTCGGTTTTGCCATTCCTCG 59.122 50.000 0.00 0.00 36.97 4.63
879 884 2.223947 ACTTGTTCGGTTTTGCCATTCC 60.224 45.455 0.00 0.00 36.97 3.01
933 984 7.113658 TGCCTACTTTTGTTTCCATTTTGTA 57.886 32.000 0.00 0.00 0.00 2.41
976 1027 1.202818 AGTCCCAAGTCCAAGTTGCTC 60.203 52.381 0.00 0.00 0.00 4.26
978 1029 0.954452 CAGTCCCAAGTCCAAGTTGC 59.046 55.000 0.00 0.00 0.00 4.17
990 1041 2.276116 GCGAGGTCAGTCAGTCCCA 61.276 63.158 0.00 0.00 0.00 4.37
1071 1128 0.621082 GTGGGGAGAAGGAAAGGAGG 59.379 60.000 0.00 0.00 0.00 4.30
1072 1129 0.621082 GGTGGGGAGAAGGAAAGGAG 59.379 60.000 0.00 0.00 0.00 3.69
1073 1130 0.196118 AGGTGGGGAGAAGGAAAGGA 59.804 55.000 0.00 0.00 0.00 3.36
1074 1131 0.621082 GAGGTGGGGAGAAGGAAAGG 59.379 60.000 0.00 0.00 0.00 3.11
1075 1132 0.250513 CGAGGTGGGGAGAAGGAAAG 59.749 60.000 0.00 0.00 0.00 2.62
1076 1133 1.838073 GCGAGGTGGGGAGAAGGAAA 61.838 60.000 0.00 0.00 0.00 3.13
1099 1156 1.497309 ATCTGCGGAGTTTGGGGGAA 61.497 55.000 3.10 0.00 0.00 3.97
1101 1158 1.000896 AATCTGCGGAGTTTGGGGG 60.001 57.895 3.10 0.00 0.00 5.40
1178 1235 2.181021 GGGTCGATGCTTCGTCGT 59.819 61.111 19.92 0.00 45.65 4.34
1297 1354 3.716539 TACGAGGACATGGCAGCGC 62.717 63.158 11.64 0.00 0.00 5.92
1306 1363 2.044555 CGCTCCTGGTACGAGGACA 61.045 63.158 21.57 3.93 37.20 4.02
1515 1579 2.032860 GCTGCGGATAAGGAGGAGCA 62.033 60.000 0.00 0.00 46.37 4.26
1596 1660 1.394618 ATGCTCTCACCTAGGACGTC 58.605 55.000 17.98 7.13 0.00 4.34
1610 1674 6.819649 TCATTTTGATTCCATGGAAAATGCTC 59.180 34.615 29.21 23.13 42.00 4.26
1613 1677 8.725405 TCATCATTTTGATTCCATGGAAAATG 57.275 30.769 28.63 28.63 42.92 2.32
1647 1712 1.153881 GGAACCCGCTACGTCTCAC 60.154 63.158 0.00 0.00 0.00 3.51
1766 1836 6.112734 TGCACATTCATTTACAGGGTAGTAG 58.887 40.000 0.00 0.00 0.00 2.57
1852 1922 4.346730 TCAAAATCATTGGCAGGACAGAT 58.653 39.130 0.00 0.00 0.00 2.90
1882 1952 3.962718 AGGGATAAGATTTGCCACCAATG 59.037 43.478 0.00 0.00 0.00 2.82
1923 1993 5.631512 GCAATAAACGTAAAATGAAGGCACA 59.368 36.000 0.00 0.00 0.00 4.57
1933 2003 5.566016 GTGAATCAGCGCAATAAACGTAAAA 59.434 36.000 11.47 0.00 0.00 1.52
1964 2034 2.872245 CCATAGATGCCAACAACCGTAG 59.128 50.000 0.00 0.00 0.00 3.51
1970 2040 3.448093 TTGGTCCATAGATGCCAACAA 57.552 42.857 0.00 0.00 36.23 2.83
1973 2043 2.308570 ACAGTTGGTCCATAGATGCCAA 59.691 45.455 0.00 0.00 38.51 4.52
1997 2067 4.844349 TGAGGAAAGTAGGGAATGAAGG 57.156 45.455 0.00 0.00 0.00 3.46
2096 2166 4.260334 GCTGTTTGGTGCATGAAAGAAAAC 60.260 41.667 0.00 0.00 0.00 2.43
2133 2203 7.679638 GCAGACAAACTTAAGTGTCATCAAGTT 60.680 37.037 21.68 3.91 45.40 2.66
2212 2282 2.954318 AGCAAAATCCTCCCATGATTCG 59.046 45.455 0.00 0.00 31.39 3.34
2565 2746 5.651387 TTTTGTCCAACAAACATCAGTGA 57.349 34.783 4.82 0.00 46.53 3.41
2609 2790 7.624360 AAATGTTGTGTACCGATCATTGTAT 57.376 32.000 0.00 0.00 0.00 2.29
2733 2921 6.914215 CCAGACAATGTGCATACATCATAAAC 59.086 38.462 0.00 0.00 46.54 2.01
2740 2928 6.691437 TCTGCCCAGACAATGTGCATACAT 62.691 45.833 0.00 0.00 41.70 2.29
2801 2989 6.135290 TGAAATATGCCAAACATGCTCTAC 57.865 37.500 0.00 0.00 40.06 2.59
3379 3567 2.177394 TCACGCACACCATAACATGT 57.823 45.000 0.00 0.00 0.00 3.21
3394 3582 3.885484 AGCAGTGAGAAAATGTTCACG 57.115 42.857 0.00 0.00 46.34 4.35
3418 3606 0.460284 GGGTGTACTCTGCACGATGG 60.460 60.000 0.00 0.00 37.70 3.51
3543 3731 3.129462 TGAAGTCTGGAGCACGAGATAAG 59.871 47.826 0.00 0.00 33.79 1.73
3544 3732 3.089284 TGAAGTCTGGAGCACGAGATAA 58.911 45.455 0.00 0.00 33.79 1.75
3575 3768 6.602803 TCAGGCATGCAGAGAAAATACATTTA 59.397 34.615 21.36 0.00 0.00 1.40
3585 3778 1.072806 AGTTGTCAGGCATGCAGAGAA 59.927 47.619 21.36 17.60 0.00 2.87
3587 3780 1.085091 GAGTTGTCAGGCATGCAGAG 58.915 55.000 21.36 8.50 0.00 3.35
3622 3815 2.094854 GCAGAACTCCATTTCCTGCAAG 60.095 50.000 0.00 0.00 33.47 4.01
3671 3864 1.880340 GCTCTTCCTGATGCGACCG 60.880 63.158 0.00 0.00 0.00 4.79
3733 3969 4.580580 CCCATGCTGTAGATACTTTTTCCC 59.419 45.833 0.00 0.00 0.00 3.97
3734 3970 5.437060 TCCCATGCTGTAGATACTTTTTCC 58.563 41.667 0.00 0.00 0.00 3.13
3735 3971 6.963796 CATCCCATGCTGTAGATACTTTTTC 58.036 40.000 0.00 0.00 0.00 2.29
3736 3972 6.949352 CATCCCATGCTGTAGATACTTTTT 57.051 37.500 0.00 0.00 0.00 1.94
3751 3987 0.545171 ACAGACTCCAGCATCCCATG 59.455 55.000 0.00 0.00 0.00 3.66
3752 3988 2.180946 TACAGACTCCAGCATCCCAT 57.819 50.000 0.00 0.00 0.00 4.00
3753 3989 1.951209 TTACAGACTCCAGCATCCCA 58.049 50.000 0.00 0.00 0.00 4.37
3754 3990 3.567478 ATTTACAGACTCCAGCATCCC 57.433 47.619 0.00 0.00 0.00 3.85
3755 3991 6.651225 GGTATTATTTACAGACTCCAGCATCC 59.349 42.308 0.00 0.00 0.00 3.51
3756 3992 6.366332 CGGTATTATTTACAGACTCCAGCATC 59.634 42.308 0.00 0.00 0.00 3.91
3757 3993 6.183360 ACGGTATTATTTACAGACTCCAGCAT 60.183 38.462 0.00 0.00 0.00 3.79
3758 3994 5.128171 ACGGTATTATTTACAGACTCCAGCA 59.872 40.000 0.00 0.00 0.00 4.41
3759 3995 5.598769 ACGGTATTATTTACAGACTCCAGC 58.401 41.667 0.00 0.00 0.00 4.85
3760 3996 7.938715 ACTACGGTATTATTTACAGACTCCAG 58.061 38.462 0.00 0.00 0.00 3.86
3761 3997 7.886629 ACTACGGTATTATTTACAGACTCCA 57.113 36.000 0.00 0.00 0.00 3.86
3762 3998 8.628280 AGAACTACGGTATTATTTACAGACTCC 58.372 37.037 0.00 0.00 0.00 3.85
3771 4007 9.886132 AGACATCAAAGAACTACGGTATTATTT 57.114 29.630 0.00 0.00 0.00 1.40
3772 4008 9.314321 CAGACATCAAAGAACTACGGTATTATT 57.686 33.333 0.00 0.00 0.00 1.40
3773 4009 8.692710 TCAGACATCAAAGAACTACGGTATTAT 58.307 33.333 0.00 0.00 0.00 1.28
3792 4028 5.449314 CGAGAACGAGATAGGTTTCAGACAT 60.449 44.000 0.00 0.00 42.66 3.06
3897 4136 2.553172 AGTACTATCGAACTCCATCGCC 59.447 50.000 0.00 0.00 42.44 5.54
3950 4190 3.447229 ACCAATCAAAATTCTTAGGCCCG 59.553 43.478 0.00 0.00 0.00 6.13
3957 4197 9.612066 AACACACAATAACCAATCAAAATTCTT 57.388 25.926 0.00 0.00 0.00 2.52
3961 4201 9.995003 ATACAACACACAATAACCAATCAAAAT 57.005 25.926 0.00 0.00 0.00 1.82
3965 4205 6.385843 GCATACAACACACAATAACCAATCA 58.614 36.000 0.00 0.00 0.00 2.57
4009 4252 7.477144 TGTTTAATATGCCATACAGTCGAAG 57.523 36.000 0.00 0.00 0.00 3.79
4010 4253 7.497579 ACATGTTTAATATGCCATACAGTCGAA 59.502 33.333 1.60 0.00 0.00 3.71
4011 4254 6.989759 ACATGTTTAATATGCCATACAGTCGA 59.010 34.615 1.60 0.00 0.00 4.20
4012 4255 7.189693 ACATGTTTAATATGCCATACAGTCG 57.810 36.000 1.60 0.00 0.00 4.18
4013 4256 9.450807 GAAACATGTTTAATATGCCATACAGTC 57.549 33.333 23.33 1.75 32.11 3.51
4014 4257 8.128582 CGAAACATGTTTAATATGCCATACAGT 58.871 33.333 23.33 0.00 32.11 3.55
4016 4259 6.915300 GCGAAACATGTTTAATATGCCATACA 59.085 34.615 23.33 0.00 32.11 2.29
4017 4260 7.138736 AGCGAAACATGTTTAATATGCCATAC 58.861 34.615 23.33 6.05 32.11 2.39
4018 4261 7.270757 AGCGAAACATGTTTAATATGCCATA 57.729 32.000 23.33 0.00 32.11 2.74
4019 4262 6.147864 AGCGAAACATGTTTAATATGCCAT 57.852 33.333 23.33 6.01 32.11 4.40
4030 4303 4.214545 TCCATTTAACGAGCGAAACATGTT 59.785 37.500 4.92 4.92 0.00 2.71
4070 4343 4.061596 GCAGACAGGAATATAAGTCAGGC 58.938 47.826 0.00 0.00 33.56 4.85
4092 4365 8.831715 AACAAAAACTTATAAAGCATTCCCTG 57.168 30.769 0.00 0.00 0.00 4.45
4106 4379 8.919145 ACCCATTAACTCATGAACAAAAACTTA 58.081 29.630 0.00 0.00 0.00 2.24
4137 4410 4.807039 CGGTACTTCACGCCCCCG 62.807 72.222 0.00 0.00 41.14 5.73
4150 4424 4.796606 ACCTAGGTACTCTATTTGCGGTA 58.203 43.478 14.41 0.00 41.75 4.02
4153 4427 4.369182 CCAACCTAGGTACTCTATTTGCG 58.631 47.826 16.67 0.00 41.75 4.85
4161 4435 5.810080 ATAATGAGCCAACCTAGGTACTC 57.190 43.478 23.34 23.34 41.75 2.59
4162 4436 5.428783 ACAATAATGAGCCAACCTAGGTACT 59.571 40.000 16.67 13.24 46.37 2.73
4163 4437 5.681639 ACAATAATGAGCCAACCTAGGTAC 58.318 41.667 16.67 8.15 0.00 3.34
4164 4438 5.968676 ACAATAATGAGCCAACCTAGGTA 57.031 39.130 16.67 0.00 0.00 3.08
4165 4439 4.862641 ACAATAATGAGCCAACCTAGGT 57.137 40.909 9.21 9.21 0.00 3.08
4166 4440 4.202050 GCAACAATAATGAGCCAACCTAGG 60.202 45.833 7.41 7.41 0.00 3.02
4194 4625 4.082787 ACACTTTATTTGGACAATGGCGAG 60.083 41.667 0.00 0.00 0.00 5.03
4196 4627 4.173036 ACACTTTATTTGGACAATGGCG 57.827 40.909 0.00 0.00 0.00 5.69
4200 4631 7.728532 ACCTTAGGAACACTTTATTTGGACAAT 59.271 33.333 4.77 0.00 0.00 2.71
4201 4632 7.013846 CACCTTAGGAACACTTTATTTGGACAA 59.986 37.037 4.77 0.00 0.00 3.18
4218 4669 6.488769 TCTTAAACACAAGACACCTTAGGA 57.511 37.500 4.77 0.00 29.55 2.94
4290 4793 4.655963 ACTGCTATCAACATTGGTCTGTT 58.344 39.130 0.00 0.00 39.91 3.16
4324 4828 2.048601 TGGAACTTCAAGGACGGGTTA 58.951 47.619 0.00 0.00 0.00 2.85
4335 4965 3.954904 TCGGGTGAAATTTTGGAACTTCA 59.045 39.130 0.00 0.00 0.00 3.02
4399 5030 6.849085 AGGACCTATATATCTGTGCTCAAG 57.151 41.667 0.00 0.00 0.00 3.02
4489 5216 7.396907 TCAGACCCATGTTATGTTTTCATTGAT 59.603 33.333 0.00 0.00 41.25 2.57
4523 5263 7.413657 GGCAACTTTCGCTCAGTATATGTTTTA 60.414 37.037 0.00 0.00 0.00 1.52
4531 5271 2.472695 TGGCAACTTTCGCTCAGTAT 57.527 45.000 0.00 0.00 37.61 2.12
4540 5280 5.106475 TGTTATCCGTATGTTGGCAACTTTC 60.106 40.000 28.71 19.38 37.61 2.62
4586 5366 5.067674 TGAGCCATATTTGTGTATCTTTGGC 59.932 40.000 2.47 2.47 46.78 4.52
4635 5415 2.095768 TGCTTGCAACTGCTATTCGTTC 60.096 45.455 11.46 0.00 42.66 3.95
4660 5440 2.744202 CTGTCATTGTGTAACTGAGGCC 59.256 50.000 0.00 0.00 38.04 5.19
4703 5483 2.680339 GTTATCTGGGTGAGCTTGCTTC 59.320 50.000 0.00 0.00 0.00 3.86
4704 5484 2.307098 AGTTATCTGGGTGAGCTTGCTT 59.693 45.455 0.00 0.00 0.00 3.91
4705 5485 1.912043 AGTTATCTGGGTGAGCTTGCT 59.088 47.619 0.00 0.00 0.00 3.91
4706 5486 2.012673 CAGTTATCTGGGTGAGCTTGC 58.987 52.381 0.00 0.00 37.97 4.01
4781 5561 1.330521 CTGGCCATCAAACGATTACCG 59.669 52.381 5.51 0.00 45.44 4.02
4855 5635 2.032681 GGCAACGCCCTCAAGACT 59.967 61.111 0.00 0.00 44.06 3.24
4927 5707 4.463879 CAGCTGGAGCACGAGGGG 62.464 72.222 5.57 0.00 45.16 4.79


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

AutoCloner maintained by Alex Coulton.