Multiple sequence alignment - TraesCS2B01G345600

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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 TraesCS2B01G345600 chr2B 100.000 3692 0 0 1 3692 492291647 492287956 0.000000e+00 6818.0
1 TraesCS2B01G345600 chr2B 77.188 377 74 10 93 465 150740347 150739979 3.740000e-50 209.0
2 TraesCS2B01G345600 chr2D 95.679 2939 83 23 521 3445 419805562 419802654 0.000000e+00 4684.0
3 TraesCS2B01G345600 chr2D 89.524 105 11 0 3551 3655 419802343 419802239 2.310000e-27 134.0
4 TraesCS2B01G345600 chr2A 95.194 2497 81 24 1017 3502 570149939 570152407 0.000000e+00 3910.0
5 TraesCS2B01G345600 chr2A 84.654 795 100 13 1 788 570147922 570148701 0.000000e+00 773.0
6 TraesCS2B01G345600 chr2A 93.117 247 8 5 779 1022 570149483 570149723 1.630000e-93 353.0
7 TraesCS2B01G345600 chr1D 79.191 346 66 6 87 428 35814304 35814647 6.160000e-58 235.0
8 TraesCS2B01G345600 chr1D 94.118 51 3 0 3502 3552 270999054 270999004 1.100000e-10 78.7
9 TraesCS2B01G345600 chr1D 92.593 54 1 1 3502 3552 182982932 182982985 1.420000e-09 75.0
10 TraesCS2B01G345600 chr7D 92.727 55 0 3 3502 3552 462634103 462634049 3.950000e-10 76.8
11 TraesCS2B01G345600 chr7B 92.727 55 0 1 3502 3552 540167765 540167819 3.950000e-10 76.8
12 TraesCS2B01G345600 chrUn 91.379 58 0 1 3502 3554 119198799 119198856 1.420000e-09 75.0
13 TraesCS2B01G345600 chr5B 90.164 61 1 1 3502 3557 282296690 282296750 1.420000e-09 75.0
14 TraesCS2B01G345600 chr3D 91.379 58 0 1 3502 3554 409922049 409922106 1.420000e-09 75.0
15 TraesCS2B01G345600 chr5D 90.000 60 1 1 3500 3554 331404942 331404883 5.110000e-09 73.1
16 TraesCS2B01G345600 chr5D 88.889 63 1 2 3502 3558 545990030 545989968 5.110000e-09 73.1


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 TraesCS2B01G345600 chr2B 492287956 492291647 3691 True 6818.000000 6818 100.000000 1 3692 1 chr2B.!!$R2 3691
1 TraesCS2B01G345600 chr2D 419802239 419805562 3323 True 2409.000000 4684 92.601500 521 3655 2 chr2D.!!$R1 3134
2 TraesCS2B01G345600 chr2A 570147922 570152407 4485 False 1678.666667 3910 90.988333 1 3502 3 chr2A.!!$F1 3501

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
103 104 0.031314 ATCCGTAGCTCGCATGTCTG 59.969 55.0 0.00 0.0 38.35 3.51 F
1294 2330 0.103208 GGCGTTCTGATCCGATCTGT 59.897 55.0 9.78 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2939 0.318441 TTGAGCAGCGCTTACTCTGT 59.682 50.0 28.27 3.15 39.88 3.41 R
2746 3783 2.943690 CTCTCCAATCTCCAGCAACATG 59.056 50.0 0.00 0.00 0.00 3.21 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
24 25 2.825836 CTGGCCGGGAGACAATGC 60.826 66.667 2.57 0.00 0.00 3.56
26 27 2.825836 GGCCGGGAGACAATGCTG 60.826 66.667 2.18 0.00 0.00 4.41
34 35 2.550855 GGGAGACAATGCTGTGAGTGAA 60.551 50.000 0.00 0.00 35.30 3.18
36 37 3.373439 GGAGACAATGCTGTGAGTGAATC 59.627 47.826 0.00 0.00 35.30 2.52
67 68 0.819582 CACCATCATTGCCCACCTTC 59.180 55.000 0.00 0.00 0.00 3.46
69 70 1.434696 CATCATTGCCCACCTTCGC 59.565 57.895 0.00 0.00 0.00 4.70
97 98 1.842698 CGCTAGATCCGTAGCTCGCA 61.843 60.000 11.09 0.00 42.91 5.10
98 99 0.523966 GCTAGATCCGTAGCTCGCAT 59.476 55.000 6.71 0.00 41.99 4.73
103 104 0.031314 ATCCGTAGCTCGCATGTCTG 59.969 55.000 0.00 0.00 38.35 3.51
112 113 3.058160 GCATGTCTGGTGGCGCTT 61.058 61.111 7.64 0.00 0.00 4.68
114 115 1.672030 CATGTCTGGTGGCGCTTGA 60.672 57.895 7.64 0.00 0.00 3.02
125 126 2.817423 GCGCTTGATGCCTCCTTCG 61.817 63.158 0.00 0.00 38.78 3.79
176 177 1.075482 AGTTCCGACCTACGACCCA 59.925 57.895 0.00 0.00 45.77 4.51
197 198 5.241662 CCAACTTCCTCTTCTTCGAATCTT 58.758 41.667 0.00 0.00 0.00 2.40
202 203 3.118956 TCCTCTTCTTCGAATCTTGCTCC 60.119 47.826 0.00 0.00 0.00 4.70
221 222 0.798776 CGACGGCTTCAGATTGCTTT 59.201 50.000 0.00 0.00 0.00 3.51
229 230 2.839486 TCAGATTGCTTTGACTCGGT 57.161 45.000 0.00 0.00 0.00 4.69
234 235 0.250295 TTGCTTTGACTCGGTCAGGG 60.250 55.000 6.79 5.75 43.69 4.45
235 236 2.035442 GCTTTGACTCGGTCAGGGC 61.035 63.158 6.79 10.41 43.69 5.19
246 247 1.657751 GGTCAGGGCGAAATCCTTGC 61.658 60.000 0.00 0.00 33.66 4.01
249 250 0.677731 CAGGGCGAAATCCTTGCTCA 60.678 55.000 0.00 0.00 31.06 4.26
255 256 2.414691 GCGAAATCCTTGCTCAACCTTC 60.415 50.000 0.00 0.00 0.00 3.46
265 267 0.674581 CTCAACCTTCGATGCTGGCA 60.675 55.000 0.00 0.00 0.00 4.92
281 283 2.815211 CAGCGATGACACCCACGG 60.815 66.667 0.00 0.00 0.00 4.94
307 309 1.449246 CCTCTTCTTGGAGGCGCTG 60.449 63.158 7.64 0.00 45.07 5.18
308 310 1.593787 CTCTTCTTGGAGGCGCTGA 59.406 57.895 7.64 0.00 0.00 4.26
323 325 2.871637 GCGCTGACATGGCCATTATCTA 60.872 50.000 17.92 7.04 0.00 1.98
340 342 1.017387 CTATGCCCCTTTTCGAGCAC 58.983 55.000 0.00 0.00 38.21 4.40
341 343 0.742990 TATGCCCCTTTTCGAGCACG 60.743 55.000 0.00 0.00 38.21 5.34
363 365 1.624391 GGGAAGCCCTAGGTCCAGTTA 60.624 57.143 16.63 0.00 41.34 2.24
367 369 2.040178 AGCCCTAGGTCCAGTTATTCG 58.960 52.381 8.29 0.00 0.00 3.34
373 375 2.662866 AGGTCCAGTTATTCGGATCGA 58.337 47.619 0.00 0.00 37.50 3.59
405 407 2.414293 CGTCTCGACATCGTTCTCCTTT 60.414 50.000 0.54 0.00 40.80 3.11
426 428 1.852280 GTGAAGGCGTTGTCTTTTTGC 59.148 47.619 0.00 0.00 0.00 3.68
432 434 0.845768 CGTTGTCTTTTTGCTTGCGG 59.154 50.000 0.00 0.00 0.00 5.69
473 475 2.962421 GGAGATGTTGGTTTGGTTTGGA 59.038 45.455 0.00 0.00 0.00 3.53
474 476 3.243737 GGAGATGTTGGTTTGGTTTGGAC 60.244 47.826 0.00 0.00 0.00 4.02
477 479 1.205893 TGTTGGTTTGGTTTGGACTGC 59.794 47.619 0.00 0.00 0.00 4.40
478 480 1.480545 GTTGGTTTGGTTTGGACTGCT 59.519 47.619 0.00 0.00 0.00 4.24
479 481 1.859302 TGGTTTGGTTTGGACTGCTT 58.141 45.000 0.00 0.00 0.00 3.91
480 482 1.754226 TGGTTTGGTTTGGACTGCTTC 59.246 47.619 0.00 0.00 0.00 3.86
481 483 1.068588 GGTTTGGTTTGGACTGCTTCC 59.931 52.381 0.00 0.00 46.13 3.46
483 485 0.260230 TTGGTTTGGACTGCTTCCCA 59.740 50.000 2.82 0.00 45.17 4.37
485 487 1.527433 GGTTTGGACTGCTTCCCAGC 61.527 60.000 2.82 0.00 45.17 4.85
501 503 1.200716 CCAGCACGACGAGTTTAGGTA 59.799 52.381 0.00 0.00 0.00 3.08
505 507 2.850647 GCACGACGAGTTTAGGTATGTC 59.149 50.000 0.00 0.00 0.00 3.06
578 587 0.174845 CCCAGCTTTGCATGGTCATG 59.825 55.000 6.59 6.59 41.60 3.07
584 593 4.151689 CAGCTTTGCATGGTCATGAAAAAG 59.848 41.667 21.87 21.87 43.63 2.27
589 598 5.787953 TGCATGGTCATGAAAAAGAAAGA 57.212 34.783 14.43 0.00 41.20 2.52
757 771 1.090052 GGCAGTCTGGTCATTACGCC 61.090 60.000 1.14 0.00 0.00 5.68
789 1594 2.609610 CCCGTTTCCCTCCCTCCA 60.610 66.667 0.00 0.00 0.00 3.86
802 1607 2.821366 CTCCATCGCCACCTGTGC 60.821 66.667 0.00 0.00 0.00 4.57
905 1713 1.227556 CCAATAACCTCCGCCCTCG 60.228 63.158 0.00 0.00 0.00 4.63
906 1714 1.520666 CAATAACCTCCGCCCTCGT 59.479 57.895 0.00 0.00 0.00 4.18
962 1770 1.206811 TCCTGCACATCCACCCATCA 61.207 55.000 0.00 0.00 0.00 3.07
1197 2233 3.339141 GCCAAGAAGAAGAGGGTAAGTG 58.661 50.000 0.00 0.00 0.00 3.16
1223 2259 1.227999 CCGTGTGTGTGGTGTGATCC 61.228 60.000 0.00 0.00 0.00 3.36
1294 2330 0.103208 GGCGTTCTGATCCGATCTGT 59.897 55.000 9.78 0.00 0.00 3.41
1295 2331 1.471676 GGCGTTCTGATCCGATCTGTT 60.472 52.381 9.78 0.00 0.00 3.16
1749 2786 3.625897 TCGCCACACCCTCCACTG 61.626 66.667 0.00 0.00 0.00 3.66
1785 2822 2.283173 GCAAGGTCAAGGGGTGGG 60.283 66.667 0.00 0.00 0.00 4.61
1787 2824 3.590574 AAGGTCAAGGGGTGGGGC 61.591 66.667 0.00 0.00 0.00 5.80
1797 2834 3.403558 GGTGGGGCTCTGGAGGAC 61.404 72.222 0.00 0.00 0.00 3.85
1815 2852 1.817099 CGACAAGGAGGATGCTGGC 60.817 63.158 0.00 0.00 36.28 4.85
1920 2957 0.389037 CACAGAGTAAGCGCTGCTCA 60.389 55.000 30.92 10.27 44.72 4.26
2376 3413 2.303022 GGATCTTGACCCAACAGACTCA 59.697 50.000 0.00 0.00 0.00 3.41
2472 3509 2.360852 CCAGGGTGCAGGAAGCTG 60.361 66.667 0.00 0.00 45.94 4.24
2498 3535 1.601171 CAGGGTCTGCAGGAGAAGG 59.399 63.158 15.13 0.00 30.26 3.46
2499 3536 0.906756 CAGGGTCTGCAGGAGAAGGA 60.907 60.000 15.13 0.00 30.26 3.36
2746 3783 4.895854 GCATTGGGTGTGATGCAC 57.104 55.556 0.00 0.00 46.03 4.57
2941 3988 3.584848 ACTAAGGCAAGTGGACATTCTCT 59.415 43.478 0.00 0.00 0.00 3.10
2994 4041 9.799106 ATAGCCTACTTTACATAAATGCTGATT 57.201 29.630 0.00 0.00 0.00 2.57
3027 4074 5.527951 TCACTGACAAAATGCAATGTTACC 58.472 37.500 0.00 0.00 0.00 2.85
3048 4095 4.657039 ACCCAACTCAAGTAAACTCCTACA 59.343 41.667 0.00 0.00 0.00 2.74
3258 4309 6.882610 TTCATAATGTGTTTTGACTCAGCT 57.117 33.333 0.00 0.00 0.00 4.24
3315 4366 8.622948 ATTTAGTAAAGAAACTCCTTGGACTG 57.377 34.615 1.21 0.00 30.49 3.51
3360 4411 3.995048 ACTTTCTACAAGCTAGCGTTTCC 59.005 43.478 9.55 0.00 0.00 3.13
3367 4418 2.866762 CAAGCTAGCGTTTCCTGGTATC 59.133 50.000 9.55 0.00 0.00 2.24
3423 4474 9.692749 AGTTTCTTGCGATCGATCTTATTATAA 57.307 29.630 21.57 6.67 0.00 0.98
3429 4480 7.782049 TGCGATCGATCTTATTATAATCCCTT 58.218 34.615 21.57 0.00 0.00 3.95
3506 4557 8.954950 AGTTTGATCAAGTCTATAGAATGTGG 57.045 34.615 8.41 0.00 0.00 4.17
3507 4558 8.543774 AGTTTGATCAAGTCTATAGAATGTGGT 58.456 33.333 8.41 1.27 0.00 4.16
3510 4561 8.768501 TGATCAAGTCTATAGAATGTGGTAGT 57.231 34.615 3.40 0.00 0.00 2.73
3511 4562 8.851145 TGATCAAGTCTATAGAATGTGGTAGTC 58.149 37.037 3.40 0.00 0.00 2.59
3512 4563 7.584122 TCAAGTCTATAGAATGTGGTAGTCC 57.416 40.000 3.40 0.00 0.00 3.85
3513 4564 7.123383 TCAAGTCTATAGAATGTGGTAGTCCA 58.877 38.462 3.40 0.00 42.05 4.02
3514 4565 7.785028 TCAAGTCTATAGAATGTGGTAGTCCAT 59.215 37.037 3.40 0.00 46.20 3.41
3517 4568 8.424918 AGTCTATAGAATGTGGTAGTCCATTTG 58.575 37.037 3.40 0.00 46.20 2.32
3519 4570 8.988060 TCTATAGAATGTGGTAGTCCATTTGAA 58.012 33.333 0.00 0.00 46.20 2.69
3522 4573 7.396540 AGAATGTGGTAGTCCATTTGAAATC 57.603 36.000 0.00 0.00 46.20 2.17
3523 4574 7.177878 AGAATGTGGTAGTCCATTTGAAATCT 58.822 34.615 0.00 0.00 46.20 2.40
3525 4576 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
3527 4578 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
3529 4580 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
3562 4844 7.070571 AGGAACAGAGGGAGTAGAAATAATGAG 59.929 40.741 0.00 0.00 0.00 2.90
3563 4845 7.147637 GGAACAGAGGGAGTAGAAATAATGAGT 60.148 40.741 0.00 0.00 0.00 3.41
3571 4853 9.682465 GGGAGTAGAAATAATGAGTAACCTTTT 57.318 33.333 0.00 0.00 0.00 2.27
3592 4874 6.839124 TTTGACATTTGATAACTGATGGCT 57.161 33.333 0.00 0.00 0.00 4.75
3596 4878 6.883756 TGACATTTGATAACTGATGGCTGTAA 59.116 34.615 0.00 0.00 0.00 2.41
3601 4883 6.925610 TGATAACTGATGGCTGTAACATTC 57.074 37.500 0.00 0.00 0.00 2.67
3607 4889 2.831685 TGGCTGTAACATTCGACAGT 57.168 45.000 4.15 0.00 44.10 3.55
3611 4893 3.575630 GCTGTAACATTCGACAGTCTCA 58.424 45.455 0.00 0.00 44.10 3.27
3614 4896 5.120830 GCTGTAACATTCGACAGTCTCAAAT 59.879 40.000 0.00 0.00 44.10 2.32
3620 4902 5.765182 ACATTCGACAGTCTCAAATTCCTTT 59.235 36.000 0.00 0.00 0.00 3.11
3621 4903 6.263168 ACATTCGACAGTCTCAAATTCCTTTT 59.737 34.615 0.00 0.00 0.00 2.27
3655 4937 4.006319 GCTACTTATTCCCATCAGGCATC 58.994 47.826 0.00 0.00 34.51 3.91
3656 4938 4.505566 GCTACTTATTCCCATCAGGCATCA 60.506 45.833 0.00 0.00 34.51 3.07
3657 4939 4.096190 ACTTATTCCCATCAGGCATCAG 57.904 45.455 0.00 0.00 34.51 2.90
3658 4940 3.181436 ACTTATTCCCATCAGGCATCAGG 60.181 47.826 0.00 0.00 34.51 3.86
3659 4941 0.178970 ATTCCCATCAGGCATCAGGC 60.179 55.000 0.00 0.00 43.74 4.85
3672 4954 4.000331 GCATCAGGCATATAGTGTGAGT 58.000 45.455 0.00 0.00 43.97 3.41
3673 4955 3.744942 GCATCAGGCATATAGTGTGAGTG 59.255 47.826 0.00 0.00 43.97 3.51
3674 4956 3.459232 TCAGGCATATAGTGTGAGTGC 57.541 47.619 0.00 0.00 35.17 4.40
3675 4957 3.033909 TCAGGCATATAGTGTGAGTGCT 58.966 45.455 0.00 0.00 36.15 4.40
3676 4958 3.452264 TCAGGCATATAGTGTGAGTGCTT 59.548 43.478 0.00 0.00 36.15 3.91
3677 4959 4.080919 TCAGGCATATAGTGTGAGTGCTTT 60.081 41.667 0.00 0.00 36.15 3.51
3678 4960 5.128663 TCAGGCATATAGTGTGAGTGCTTTA 59.871 40.000 0.00 0.00 36.15 1.85
3679 4961 5.817296 CAGGCATATAGTGTGAGTGCTTTAA 59.183 40.000 0.00 0.00 36.15 1.52
3680 4962 5.817816 AGGCATATAGTGTGAGTGCTTTAAC 59.182 40.000 0.00 0.00 36.15 2.01
3681 4963 5.007724 GGCATATAGTGTGAGTGCTTTAACC 59.992 44.000 0.00 0.00 36.15 2.85
3682 4964 5.007724 GCATATAGTGTGAGTGCTTTAACCC 59.992 44.000 0.00 0.00 33.25 4.11
3683 4965 2.271944 AGTGTGAGTGCTTTAACCCC 57.728 50.000 0.00 0.00 0.00 4.95
3684 4966 1.774856 AGTGTGAGTGCTTTAACCCCT 59.225 47.619 0.00 0.00 0.00 4.79
3685 4967 1.880027 GTGTGAGTGCTTTAACCCCTG 59.120 52.381 0.00 0.00 0.00 4.45
3686 4968 1.771854 TGTGAGTGCTTTAACCCCTGA 59.228 47.619 0.00 0.00 0.00 3.86
3687 4969 2.224523 TGTGAGTGCTTTAACCCCTGAG 60.225 50.000 0.00 0.00 0.00 3.35
3688 4970 2.038557 GTGAGTGCTTTAACCCCTGAGA 59.961 50.000 0.00 0.00 0.00 3.27
3689 4971 2.038557 TGAGTGCTTTAACCCCTGAGAC 59.961 50.000 0.00 0.00 0.00 3.36
3690 4972 1.351350 AGTGCTTTAACCCCTGAGACC 59.649 52.381 0.00 0.00 0.00 3.85
3691 4973 1.351350 GTGCTTTAACCCCTGAGACCT 59.649 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.742281 CTCACAGCATTGTCTCCCGG 60.742 60.000 0.00 0.00 34.62 5.73
13 14 1.002430 TCACTCACAGCATTGTCTCCC 59.998 52.381 0.00 0.00 34.62 4.30
69 70 2.336809 GATCTAGCGGACAGGGCG 59.663 66.667 0.00 0.00 35.00 6.13
73 74 0.238817 GCTACGGATCTAGCGGACAG 59.761 60.000 0.00 0.00 30.19 3.51
97 98 1.028330 CATCAAGCGCCACCAGACAT 61.028 55.000 2.29 0.00 0.00 3.06
98 99 1.672030 CATCAAGCGCCACCAGACA 60.672 57.895 2.29 0.00 0.00 3.41
121 122 2.509336 CTACGCCCACTGCCGAAG 60.509 66.667 0.00 0.00 36.24 3.79
125 126 4.840005 GGAGCTACGCCCACTGCC 62.840 72.222 0.00 0.00 36.24 4.85
135 136 4.222847 CGCGGGAAGGGGAGCTAC 62.223 72.222 0.00 0.00 0.00 3.58
158 159 0.540365 TTGGGTCGTAGGTCGGAACT 60.540 55.000 0.00 0.00 40.32 3.01
165 166 1.203149 AGAGGAAGTTGGGTCGTAGGT 60.203 52.381 0.00 0.00 0.00 3.08
176 177 4.693095 GCAAGATTCGAAGAAGAGGAAGTT 59.307 41.667 3.35 0.00 45.90 2.66
197 198 1.888436 AATCTGAAGCCGTCGGAGCA 61.888 55.000 17.49 8.19 45.06 4.26
202 203 0.798776 AAAGCAATCTGAAGCCGTCG 59.201 50.000 2.37 0.00 0.00 5.12
221 222 1.541310 ATTTCGCCCTGACCGAGTCA 61.541 55.000 6.57 6.57 40.50 3.41
229 230 0.392998 GAGCAAGGATTTCGCCCTGA 60.393 55.000 0.00 0.00 33.55 3.86
234 235 1.168714 AGGTTGAGCAAGGATTTCGC 58.831 50.000 0.00 0.00 0.00 4.70
235 236 2.159653 CGAAGGTTGAGCAAGGATTTCG 60.160 50.000 0.00 0.00 0.00 3.46
246 247 0.674581 TGCCAGCATCGAAGGTTGAG 60.675 55.000 5.98 0.00 0.00 3.02
249 250 2.042831 GCTGCCAGCATCGAAGGTT 61.043 57.895 12.82 0.00 41.89 3.50
255 256 2.586914 TCATCGCTGCCAGCATCG 60.587 61.111 18.21 9.45 42.58 3.84
265 267 4.082523 CCCGTGGGTGTCATCGCT 62.083 66.667 0.00 0.00 0.00 4.93
281 283 0.966920 TCCAAGAAGAGGACGACACC 59.033 55.000 0.00 0.00 0.00 4.16
302 304 0.239347 GATAATGGCCATGTCAGCGC 59.761 55.000 21.63 0.00 0.00 5.92
323 325 2.040544 CGTGCTCGAAAAGGGGCAT 61.041 57.895 1.00 0.00 39.71 4.40
348 350 1.070289 CCGAATAACTGGACCTAGGGC 59.930 57.143 14.81 10.79 0.00 5.19
378 380 0.452287 ACGATGTCGAGACGTTGTCG 60.452 55.000 9.67 13.45 40.03 4.35
405 407 2.733858 GCAAAAAGACAACGCCTTCACA 60.734 45.455 0.00 0.00 0.00 3.58
413 415 0.845768 CCGCAAGCAAAAAGACAACG 59.154 50.000 0.00 0.00 0.00 4.10
432 434 3.188786 GTCCACTGTCGCGGATGC 61.189 66.667 6.13 0.00 32.83 3.91
438 440 0.247736 ATCTCCAAGTCCACTGTCGC 59.752 55.000 0.00 0.00 0.00 5.19
441 443 2.224621 CCAACATCTCCAAGTCCACTGT 60.225 50.000 0.00 0.00 0.00 3.55
449 451 4.370917 CAAACCAAACCAACATCTCCAAG 58.629 43.478 0.00 0.00 0.00 3.61
473 475 2.031163 GTCGTGCTGGGAAGCAGT 59.969 61.111 0.00 0.00 46.32 4.40
474 476 3.114616 CGTCGTGCTGGGAAGCAG 61.115 66.667 0.00 0.00 46.32 4.24
477 479 0.600255 AAACTCGTCGTGCTGGGAAG 60.600 55.000 0.00 0.00 0.00 3.46
478 480 0.675083 TAAACTCGTCGTGCTGGGAA 59.325 50.000 0.00 0.00 0.00 3.97
479 481 0.242825 CTAAACTCGTCGTGCTGGGA 59.757 55.000 0.00 0.00 0.00 4.37
480 482 0.736325 CCTAAACTCGTCGTGCTGGG 60.736 60.000 0.00 0.00 0.00 4.45
481 483 0.038526 ACCTAAACTCGTCGTGCTGG 60.039 55.000 0.00 0.00 0.00 4.85
483 485 2.490903 ACATACCTAAACTCGTCGTGCT 59.509 45.455 0.00 0.00 0.00 4.40
485 487 3.096461 CGACATACCTAAACTCGTCGTG 58.904 50.000 0.00 0.00 40.85 4.35
490 492 5.287035 GTGGTAAACGACATACCTAAACTCG 59.713 44.000 14.07 0.00 42.73 4.18
501 503 3.764237 ACAAGAGGTGGTAAACGACAT 57.236 42.857 0.00 0.00 0.00 3.06
505 507 5.235516 AGTGAATACAAGAGGTGGTAAACG 58.764 41.667 0.00 0.00 0.00 3.60
557 566 1.607467 GACCATGCAAAGCTGGGGT 60.607 57.895 8.86 0.00 36.82 4.95
559 568 0.174845 CATGACCATGCAAAGCTGGG 59.825 55.000 8.86 5.54 36.82 4.45
561 570 3.306917 TTTCATGACCATGCAAAGCTG 57.693 42.857 0.00 0.00 38.65 4.24
918 1726 1.338973 GATAGATAACACACGGGGCGA 59.661 52.381 0.00 0.00 0.00 5.54
1223 2259 3.022287 CCCCCAAATCGAATCGCG 58.978 61.111 0.00 0.00 42.69 5.87
1254 2290 3.508840 CAATCCGCAACCGAGCCC 61.509 66.667 0.00 0.00 36.29 5.19
1731 2768 3.626924 AGTGGAGGGTGTGGCGAC 61.627 66.667 0.00 0.00 0.00 5.19
1761 2798 1.377725 CCTTGACCTTGCATCGGCT 60.378 57.895 2.65 0.00 41.91 5.52
1785 2822 1.216710 CTTGTCGTCCTCCAGAGCC 59.783 63.158 0.00 0.00 0.00 4.70
1787 2824 0.814457 CTCCTTGTCGTCCTCCAGAG 59.186 60.000 0.00 0.00 0.00 3.35
1797 2834 1.817099 GCCAGCATCCTCCTTGTCG 60.817 63.158 0.00 0.00 0.00 4.35
1815 2852 0.527817 CTACTTCTTGCCCGGTAGCG 60.528 60.000 7.49 7.49 34.65 4.26
1893 2930 1.630244 GCTTACTCTGTGCACAGCCG 61.630 60.000 36.76 30.17 43.46 5.52
1902 2939 0.318441 TTGAGCAGCGCTTACTCTGT 59.682 50.000 28.27 3.15 39.88 3.41
1920 2957 2.604382 GGGCCACCACCATTGCTT 60.604 61.111 4.39 0.00 36.50 3.91
1950 2987 0.817654 TGGACCATAGACTGCTCACG 59.182 55.000 0.00 0.00 0.00 4.35
2274 3311 4.431131 ATCCCCCAGCAGTTGCCG 62.431 66.667 0.00 0.00 43.38 5.69
2376 3413 3.342477 GGGCAGGGGAGGAAGCTT 61.342 66.667 0.00 0.00 0.00 3.74
2746 3783 2.943690 CTCTCCAATCTCCAGCAACATG 59.056 50.000 0.00 0.00 0.00 3.21
2808 3845 5.417580 GGCAAGGAAATAACAGTCACCATAA 59.582 40.000 0.00 0.00 0.00 1.90
2901 3948 6.399743 CCTTAGTAGAAGAAAGTCCCAAGAC 58.600 44.000 0.00 0.00 43.89 3.01
2907 3954 5.639931 CACTTGCCTTAGTAGAAGAAAGTCC 59.360 44.000 0.00 0.00 0.00 3.85
2994 4041 6.040278 TGCATTTTGTCAGTGAAGACCAAATA 59.960 34.615 7.28 1.53 40.06 1.40
2995 4042 5.163426 TGCATTTTGTCAGTGAAGACCAAAT 60.163 36.000 7.28 0.00 41.66 2.32
3027 4074 7.745620 AAATGTAGGAGTTTACTTGAGTTGG 57.254 36.000 0.00 0.00 0.00 3.77
3086 4133 6.126796 TGACCAGAGCCTGAAATGATAATACA 60.127 38.462 4.00 0.00 32.44 2.29
3234 4285 7.458409 AGCTGAGTCAAAACACATTATGAAT 57.542 32.000 0.00 0.00 0.00 2.57
3258 4309 5.466058 CACATTTGCATCTTAAAGTTGCCAA 59.534 36.000 6.71 3.12 39.53 4.52
3423 4474 6.721208 TGCAAAGTAAGAAGAAATGAAGGGAT 59.279 34.615 0.00 0.00 0.00 3.85
3527 4578 9.280456 TCTACTCCCTCTGTTCCTAAATATTTT 57.720 33.333 5.91 0.00 0.00 1.82
3529 4580 8.855804 TTCTACTCCCTCTGTTCCTAAATATT 57.144 34.615 0.00 0.00 0.00 1.28
3531 4582 8.855804 ATTTCTACTCCCTCTGTTCCTAAATA 57.144 34.615 0.00 0.00 0.00 1.40
3534 4585 8.705594 CATTATTTCTACTCCCTCTGTTCCTAA 58.294 37.037 0.00 0.00 0.00 2.69
3536 4587 6.903534 TCATTATTTCTACTCCCTCTGTTCCT 59.096 38.462 0.00 0.00 0.00 3.36
3537 4588 7.125792 TCATTATTTCTACTCCCTCTGTTCC 57.874 40.000 0.00 0.00 0.00 3.62
3538 4589 7.787028 ACTCATTATTTCTACTCCCTCTGTTC 58.213 38.462 0.00 0.00 0.00 3.18
3539 4590 7.741554 ACTCATTATTTCTACTCCCTCTGTT 57.258 36.000 0.00 0.00 0.00 3.16
3541 4592 8.145122 GGTTACTCATTATTTCTACTCCCTCTG 58.855 40.741 0.00 0.00 0.00 3.35
3543 4594 8.252624 AGGTTACTCATTATTTCTACTCCCTC 57.747 38.462 0.00 0.00 0.00 4.30
3544 4595 8.625467 AAGGTTACTCATTATTTCTACTCCCT 57.375 34.615 0.00 0.00 0.00 4.20
3545 4596 9.682465 AAAAGGTTACTCATTATTTCTACTCCC 57.318 33.333 0.00 0.00 0.00 4.30
3571 4853 5.255687 ACAGCCATCAGTTATCAAATGTCA 58.744 37.500 0.00 0.00 0.00 3.58
3592 4874 6.147164 GGAATTTGAGACTGTCGAATGTTACA 59.853 38.462 1.52 0.00 38.20 2.41
3596 4878 4.899502 AGGAATTTGAGACTGTCGAATGT 58.100 39.130 1.52 0.00 38.20 2.71
3601 4883 7.133891 ACATAAAAGGAATTTGAGACTGTCG 57.866 36.000 1.52 0.00 32.27 4.35
3614 4896 8.958119 AAGTAGCAATATCGACATAAAAGGAA 57.042 30.769 0.00 0.00 0.00 3.36
3620 4902 8.590204 TGGGAATAAGTAGCAATATCGACATAA 58.410 33.333 0.00 0.00 0.00 1.90
3621 4903 8.129496 TGGGAATAAGTAGCAATATCGACATA 57.871 34.615 0.00 0.00 0.00 2.29
3655 4937 3.465742 AGCACTCACACTATATGCCTG 57.534 47.619 0.00 0.00 36.96 4.85
3656 4938 4.494091 AAAGCACTCACACTATATGCCT 57.506 40.909 0.00 0.00 36.96 4.75
3657 4939 5.007724 GGTTAAAGCACTCACACTATATGCC 59.992 44.000 0.00 0.00 36.96 4.40
3658 4940 5.007724 GGGTTAAAGCACTCACACTATATGC 59.992 44.000 0.00 0.00 36.52 3.14
3659 4941 5.527582 GGGGTTAAAGCACTCACACTATATG 59.472 44.000 0.00 0.00 0.00 1.78
3660 4942 5.428783 AGGGGTTAAAGCACTCACACTATAT 59.571 40.000 0.00 0.00 0.00 0.86
3661 4943 4.781087 AGGGGTTAAAGCACTCACACTATA 59.219 41.667 0.00 0.00 0.00 1.31
3662 4944 3.587506 AGGGGTTAAAGCACTCACACTAT 59.412 43.478 0.00 0.00 0.00 2.12
3663 4945 2.976882 AGGGGTTAAAGCACTCACACTA 59.023 45.455 0.00 0.00 0.00 2.74
3664 4946 1.774856 AGGGGTTAAAGCACTCACACT 59.225 47.619 0.00 0.00 0.00 3.55
3665 4947 1.880027 CAGGGGTTAAAGCACTCACAC 59.120 52.381 0.00 0.00 0.00 3.82
3666 4948 1.771854 TCAGGGGTTAAAGCACTCACA 59.228 47.619 0.00 0.00 0.00 3.58
3667 4949 2.038557 TCTCAGGGGTTAAAGCACTCAC 59.961 50.000 0.00 0.00 0.00 3.51
3668 4950 2.038557 GTCTCAGGGGTTAAAGCACTCA 59.961 50.000 0.00 0.00 0.00 3.41
3669 4951 2.615747 GGTCTCAGGGGTTAAAGCACTC 60.616 54.545 0.00 0.00 0.00 3.51
3670 4952 1.351350 GGTCTCAGGGGTTAAAGCACT 59.649 52.381 0.00 0.00 0.00 4.40
3671 4953 1.351350 AGGTCTCAGGGGTTAAAGCAC 59.649 52.381 0.00 0.00 0.00 4.40
3672 4954 1.742308 AGGTCTCAGGGGTTAAAGCA 58.258 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.