Multiple sequence alignment - TraesCS2B01G076700

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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 TraesCS2B01G076700 chr2B 100.000 3913 0 0 1 3913 41866833 41862921 0.000000e+00 7227.0
1 TraesCS2B01G076700 chr2B 96.367 1211 40 3 1924 3134 41848013 41846807 0.000000e+00 1989.0
2 TraesCS2B01G076700 chr2B 94.574 129 5 1 2925 3053 478189759 478189633 8.580000e-47 198.0
3 TraesCS2B01G076700 chr2B 94.444 126 7 0 2925 3050 291855047 291855172 1.110000e-45 195.0
4 TraesCS2B01G076700 chr2B 93.496 123 8 0 2924 3046 708240557 708240679 2.400000e-42 183.0
5 TraesCS2B01G076700 chr2A 92.564 2165 100 36 780 2923 28809864 28807740 0.000000e+00 3049.0
6 TraesCS2B01G076700 chr2A 88.530 558 56 4 1 553 682976628 682977182 0.000000e+00 669.0
7 TraesCS2B01G076700 chr2A 87.719 570 61 5 4 566 761449889 761449322 0.000000e+00 656.0
8 TraesCS2B01G076700 chr2D 89.909 1645 111 19 1 1602 26561200 26559568 0.000000e+00 2067.0
9 TraesCS2B01G076700 chr2D 92.903 1240 57 20 1690 2923 26559440 26558226 0.000000e+00 1773.0
10 TraesCS2B01G076700 chr2D 94.444 126 7 0 2924 3049 305514991 305514866 1.110000e-45 195.0
11 TraesCS2B01G076700 chr2D 90.361 83 5 3 3045 3127 26558172 26558093 5.350000e-19 106.0
12 TraesCS2B01G076700 chrUn 87.345 806 54 17 3142 3913 292610895 292611686 0.000000e+00 880.0
13 TraesCS2B01G076700 chrUn 87.719 570 61 5 4 566 314599269 314598702 0.000000e+00 656.0
14 TraesCS2B01G076700 chr5B 84.364 857 109 19 1001 1854 44225723 44224889 0.000000e+00 817.0
15 TraesCS2B01G076700 chr5B 85.104 819 97 15 1039 1854 43925307 43926103 0.000000e+00 813.0
16 TraesCS2B01G076700 chr5B 83.205 780 103 19 1934 2709 44224764 44224009 0.000000e+00 689.0
17 TraesCS2B01G076700 chr5B 83.355 769 97 20 1934 2695 43926229 43926973 0.000000e+00 682.0
18 TraesCS2B01G076700 chr5D 84.444 855 95 20 1001 1854 44494159 44494976 0.000000e+00 808.0
19 TraesCS2B01G076700 chr5D 81.683 1010 136 31 1690 2694 3766293 3767258 0.000000e+00 795.0
20 TraesCS2B01G076700 chr5D 84.073 766 95 18 1934 2695 44495105 44495847 0.000000e+00 713.0
21 TraesCS2B01G076700 chr5D 85.614 570 79 2 1030 1596 3765227 3765796 2.600000e-166 595.0
22 TraesCS2B01G076700 chr5D 94.531 128 6 1 2925 3051 478215947 478215820 3.080000e-46 196.0
23 TraesCS2B01G076700 chr5A 84.112 856 102 22 1001 1854 34908997 34909820 0.000000e+00 797.0
24 TraesCS2B01G076700 chr5A 82.927 779 107 17 1934 2709 34909955 34910710 0.000000e+00 678.0
25 TraesCS2B01G076700 chr5A 92.958 71 4 1 3827 3897 673852419 673852350 6.920000e-18 102.0
26 TraesCS2B01G076700 chr7D 87.958 573 59 6 1 566 488607025 488607594 0.000000e+00 667.0
27 TraesCS2B01G076700 chr7D 81.195 569 85 12 1039 1587 60499827 60499261 4.640000e-119 438.0
28 TraesCS2B01G076700 chr6B 88.468 555 57 3 4 553 638938348 638937796 0.000000e+00 664.0
29 TraesCS2B01G076700 chr3B 87.852 568 63 2 4 566 756623591 756623025 0.000000e+00 662.0
30 TraesCS2B01G076700 chr3B 93.798 129 8 0 2924 3052 540175051 540174923 1.110000e-45 195.0
31 TraesCS2B01G076700 chr3A 88.288 555 59 2 4 553 447635227 447634674 0.000000e+00 660.0
32 TraesCS2B01G076700 chr3A 87.544 570 63 4 1 564 713638362 713638929 0.000000e+00 652.0
33 TraesCS2B01G076700 chr3D 87.522 569 65 2 4 566 50544507 50543939 0.000000e+00 652.0
34 TraesCS2B01G076700 chr3D 96.721 122 4 0 2925 3046 507038702 507038581 1.840000e-48 204.0
35 TraesCS2B01G076700 chr4A 77.821 514 72 20 3388 3880 658378395 658378887 2.980000e-71 279.0
36 TraesCS2B01G076700 chr4B 95.161 124 6 0 2924 3047 483266418 483266541 3.080000e-46 196.0
37 TraesCS2B01G076700 chr7A 100.000 29 0 0 3160 3188 63785390 63785418 2.000000e-03 54.7
38 TraesCS2B01G076700 chr1B 96.875 32 1 0 3142 3173 621465030 621464999 2.000000e-03 54.7


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 TraesCS2B01G076700 chr2B 41862921 41866833 3912 True 7227.000000 7227 100.000000 1 3913 1 chr2B.!!$R2 3912
1 TraesCS2B01G076700 chr2B 41846807 41848013 1206 True 1989.000000 1989 96.367000 1924 3134 1 chr2B.!!$R1 1210
2 TraesCS2B01G076700 chr2A 28807740 28809864 2124 True 3049.000000 3049 92.564000 780 2923 1 chr2A.!!$R1 2143
3 TraesCS2B01G076700 chr2A 682976628 682977182 554 False 669.000000 669 88.530000 1 553 1 chr2A.!!$F1 552
4 TraesCS2B01G076700 chr2A 761449322 761449889 567 True 656.000000 656 87.719000 4 566 1 chr2A.!!$R2 562
5 TraesCS2B01G076700 chr2D 26558093 26561200 3107 True 1315.333333 2067 91.057667 1 3127 3 chr2D.!!$R2 3126
6 TraesCS2B01G076700 chrUn 292610895 292611686 791 False 880.000000 880 87.345000 3142 3913 1 chrUn.!!$F1 771
7 TraesCS2B01G076700 chrUn 314598702 314599269 567 True 656.000000 656 87.719000 4 566 1 chrUn.!!$R1 562
8 TraesCS2B01G076700 chr5B 44224009 44225723 1714 True 753.000000 817 83.784500 1001 2709 2 chr5B.!!$R1 1708
9 TraesCS2B01G076700 chr5B 43925307 43926973 1666 False 747.500000 813 84.229500 1039 2695 2 chr5B.!!$F1 1656
10 TraesCS2B01G076700 chr5D 44494159 44495847 1688 False 760.500000 808 84.258500 1001 2695 2 chr5D.!!$F2 1694
11 TraesCS2B01G076700 chr5D 3765227 3767258 2031 False 695.000000 795 83.648500 1030 2694 2 chr5D.!!$F1 1664
12 TraesCS2B01G076700 chr5A 34908997 34910710 1713 False 737.500000 797 83.519500 1001 2709 2 chr5A.!!$F1 1708
13 TraesCS2B01G076700 chr7D 488607025 488607594 569 False 667.000000 667 87.958000 1 566 1 chr7D.!!$F1 565
14 TraesCS2B01G076700 chr7D 60499261 60499827 566 True 438.000000 438 81.195000 1039 1587 1 chr7D.!!$R1 548
15 TraesCS2B01G076700 chr6B 638937796 638938348 552 True 664.000000 664 88.468000 4 553 1 chr6B.!!$R1 549
16 TraesCS2B01G076700 chr3B 756623025 756623591 566 True 662.000000 662 87.852000 4 566 1 chr3B.!!$R2 562
17 TraesCS2B01G076700 chr3A 447634674 447635227 553 True 660.000000 660 88.288000 4 553 1 chr3A.!!$R1 549
18 TraesCS2B01G076700 chr3A 713638362 713638929 567 False 652.000000 652 87.544000 1 564 1 chr3A.!!$F1 563
19 TraesCS2B01G076700 chr3D 50543939 50544507 568 True 652.000000 652 87.522000 4 566 1 chr3D.!!$R1 562

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
704 730 0.238289 CCAGTACGTGCTGCCAAAAG 59.762 55.0 26.10 9.27 35.28 2.27 F
896 938 0.399091 TTGGGATCCTGGCTCGATCT 60.399 55.0 12.58 0.00 37.02 2.75 F
984 1031 0.622665 ATCCAGTGCCAGCTTAGCTT 59.377 50.0 3.00 0.00 36.40 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2619 3209 2.677524 AGCATGTTGCCGGCACAT 60.678 55.556 32.95 29.74 46.52 3.21 R
2784 3380 9.563748 TCTGAATAAAATGATCACATATGCTGA 57.436 29.630 1.58 6.54 35.50 4.26 R
2996 3592 8.986991 AGTCTTTGTAGAGATTTCACTATGGAT 58.013 33.333 0.00 0.00 0.00 3.41 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
35 36 4.669206 ATGTTCAGTGCACATGGAAAAA 57.331 36.364 21.04 11.27 33.42 1.94
144 147 5.888724 TCAATTTGACTTAGGGTGACACAAA 59.111 36.000 8.08 0.00 0.00 2.83
271 275 8.262715 TCATTTTCACGCAGATAAGTTATTGA 57.737 30.769 0.00 0.00 0.00 2.57
291 295 1.889545 TGTGTGATGGCGTTGAATGA 58.110 45.000 0.00 0.00 0.00 2.57
313 318 1.604378 CTCCGGAAGTTGGGAGCAT 59.396 57.895 5.23 0.00 43.03 3.79
357 364 6.704493 ACTTAATTTTGCTCGAGTGTTGACTA 59.296 34.615 15.13 0.00 30.16 2.59
494 506 6.995511 TTTAAGGTGGTGAAGAATATTCGG 57.004 37.500 9.78 0.00 0.00 4.30
501 513 4.080807 TGGTGAAGAATATTCGGCAAGGTA 60.081 41.667 9.78 0.00 0.00 3.08
502 514 4.879545 GGTGAAGAATATTCGGCAAGGTAA 59.120 41.667 9.78 0.00 0.00 2.85
513 525 3.816523 TCGGCAAGGTAAAGTTTGTTAGG 59.183 43.478 0.00 0.00 0.00 2.69
514 526 3.566742 CGGCAAGGTAAAGTTTGTTAGGT 59.433 43.478 0.00 0.00 0.00 3.08
553 565 6.599356 TTATACAAGCTAGGTCACAGTTGA 57.401 37.500 0.00 0.00 0.00 3.18
558 570 6.296026 ACAAGCTAGGTCACAGTTGAATTTA 58.704 36.000 0.00 0.00 31.90 1.40
572 584 6.017440 CAGTTGAATTTAGTTTTGGTCCTCGA 60.017 38.462 0.00 0.00 0.00 4.04
597 609 0.523072 CAGCGGTGGTCTTGGATTTG 59.477 55.000 6.74 0.00 0.00 2.32
608 620 6.206634 GTGGTCTTGGATTTGTTCTAACATGA 59.793 38.462 0.00 0.00 38.95 3.07
612 624 7.965107 GTCTTGGATTTGTTCTAACATGATGAC 59.035 37.037 0.00 0.00 38.95 3.06
613 625 6.757897 TGGATTTGTTCTAACATGATGACC 57.242 37.500 0.00 0.00 38.95 4.02
704 730 0.238289 CCAGTACGTGCTGCCAAAAG 59.762 55.000 26.10 9.27 35.28 2.27
740 766 1.068434 CCAAAACCACACACATCACCC 59.932 52.381 0.00 0.00 0.00 4.61
747 773 1.045407 ACACACATCACCCGTGTAGT 58.955 50.000 0.00 0.00 45.63 2.73
773 799 0.508213 GCCAAAATCACAACGCAAGC 59.492 50.000 0.00 0.00 45.62 4.01
802 830 3.458189 ACCCAAAGAGATTTATCGAGCG 58.542 45.455 0.00 0.00 0.00 5.03
887 929 2.335092 ATCAGCCGCTTGGGATCCTG 62.335 60.000 12.58 3.69 38.47 3.86
896 938 0.399091 TTGGGATCCTGGCTCGATCT 60.399 55.000 12.58 0.00 37.02 2.75
906 948 7.232534 GGATCCTGGCTCGATCTTCTATATATT 59.767 40.741 3.84 0.00 37.02 1.28
912 954 6.015772 GGCTCGATCTTCTATATATTCCTCCC 60.016 46.154 0.00 0.00 0.00 4.30
939 986 3.619733 CGTCTCCTCCAATCATCACCAAA 60.620 47.826 0.00 0.00 0.00 3.28
973 1020 3.324993 GCTTCAGCTATCTATCCAGTGC 58.675 50.000 0.00 0.00 38.21 4.40
979 1026 2.038295 GCTATCTATCCAGTGCCAGCTT 59.962 50.000 0.00 0.00 0.00 3.74
984 1031 0.622665 ATCCAGTGCCAGCTTAGCTT 59.377 50.000 3.00 0.00 36.40 3.74
985 1032 1.275666 TCCAGTGCCAGCTTAGCTTA 58.724 50.000 3.00 0.00 36.40 3.09
987 1034 1.012841 CAGTGCCAGCTTAGCTTAGC 58.987 55.000 16.83 16.83 36.40 3.09
995 1042 2.147436 GCTTAGCTTAGCTGCTCGAT 57.853 50.000 17.97 0.00 42.97 3.59
996 1043 1.791785 GCTTAGCTTAGCTGCTCGATG 59.208 52.381 17.97 0.00 42.97 3.84
997 1044 2.402305 CTTAGCTTAGCTGCTCGATGG 58.598 52.381 17.97 0.00 42.97 3.51
1227 1295 1.900016 CTGGCACTTCAAGCTGGCA 60.900 57.895 13.15 13.15 40.40 4.92
1232 1300 2.979676 CTTCAAGCTGGCACGCCA 60.980 61.111 10.95 10.95 45.02 5.69
1252 1320 4.812476 CGGACGCCTTCATCGCCA 62.812 66.667 0.00 0.00 0.00 5.69
1254 1322 3.554692 GACGCCTTCATCGCCACG 61.555 66.667 0.00 0.00 0.00 4.94
1257 1325 2.387445 CGCCTTCATCGCCACGAAA 61.387 57.895 0.00 0.00 39.99 3.46
1470 1541 3.854669 CGGGGCTTCATCCTCGCT 61.855 66.667 0.00 0.00 43.85 4.93
1588 1659 2.202932 CCGCCACCGAGATCAAGG 60.203 66.667 5.09 5.09 36.29 3.61
1655 2029 5.346281 GCATGCGTAGTATTTCTCTATGTCC 59.654 44.000 0.00 0.00 0.00 4.02
1800 2288 3.376918 GCTTGGTTGCTGGCCTCC 61.377 66.667 3.32 0.00 0.00 4.30
1859 2347 5.420739 TCATGGTGCTCGCAAGGTATATATA 59.579 40.000 0.00 0.00 38.47 0.86
1866 2354 7.585573 GTGCTCGCAAGGTATATATATACGTAC 59.414 40.741 22.19 17.39 39.48 3.67
1868 2356 7.496529 TCGCAAGGTATATATATACGTACCC 57.503 40.000 22.19 11.62 39.48 3.69
1869 2357 7.053498 TCGCAAGGTATATATATACGTACCCA 58.947 38.462 22.19 9.45 39.48 4.51
1872 2360 9.472361 GCAAGGTATATATATACGTACCCATTG 57.528 37.037 22.19 17.40 39.48 2.82
2323 2888 1.730547 GCCAATATCGCGCCAATGC 60.731 57.895 0.00 0.00 0.00 3.56
2451 3016 1.211457 CAGGATCCCCTCACCTTCAAG 59.789 57.143 8.55 0.00 42.02 3.02
2619 3209 2.495409 CGGTGGCGGCTACAGGATA 61.495 63.158 18.37 0.00 0.00 2.59
3057 3653 3.124636 CGAAGGGAGTAAATTTGTGACGG 59.875 47.826 0.00 0.00 0.00 4.79
3172 3768 4.390909 GGGAGTTTTCGCTAGAAATTTCGA 59.609 41.667 12.42 6.68 44.82 3.71
3194 3790 0.294887 GCATAACGCGTCGAGAACAG 59.705 55.000 14.44 0.00 0.00 3.16
3207 3803 1.461127 GAGAACAGACGCATCCACAAC 59.539 52.381 0.00 0.00 0.00 3.32
3209 3805 1.227999 AACAGACGCATCCACAACCG 61.228 55.000 0.00 0.00 0.00 4.44
3269 3865 5.335583 CCAAACATGTCAACACGGTCATATT 60.336 40.000 0.00 0.00 0.00 1.28
3277 3873 5.291128 GTCAACACGGTCATATTACTTCCTG 59.709 44.000 0.00 0.00 0.00 3.86
3312 3928 8.264347 TCTACTACATGCCAAATTCACTTATCA 58.736 33.333 0.00 0.00 0.00 2.15
3314 3930 7.934457 ACTACATGCCAAATTCACTTATCATC 58.066 34.615 0.00 0.00 0.00 2.92
3327 3943 6.528321 TCACTTATCATCTATGGGAGCAAAG 58.472 40.000 0.00 0.00 0.00 2.77
3349 3965 9.796062 CAAAGCATCATGTAACACAAATTTAAC 57.204 29.630 0.00 0.00 0.00 2.01
3414 4030 2.475339 ATATGCCCATGGGAGCAAAA 57.525 45.000 36.00 17.62 43.36 2.44
3461 4078 9.926158 GGATATACCTCTTATGATCTATGCATG 57.074 37.037 10.16 0.00 35.41 4.06
3475 4092 0.671796 TGCATGGCATGAGCATAAGC 59.328 50.000 30.69 13.07 44.61 3.09
3492 4109 5.347907 GCATAAGCGACCATGTAGTATTACC 59.652 44.000 0.00 0.00 0.00 2.85
3494 4111 5.347620 AAGCGACCATGTAGTATTACCAA 57.652 39.130 0.00 0.00 0.00 3.67
3498 4115 5.503520 GCGACCATGTAGTATTACCAAAAGC 60.504 44.000 0.00 0.00 0.00 3.51
3505 4122 8.993121 CATGTAGTATTACCAAAAGCTCATAGG 58.007 37.037 0.00 0.00 0.00 2.57
3508 4125 6.605119 AGTATTACCAAAAGCTCATAGGCAT 58.395 36.000 0.00 0.00 34.17 4.40
3558 4175 6.365247 TCGCTACTGTTAGTTTTCATCTTGAC 59.635 38.462 0.00 0.00 0.00 3.18
3578 4195 4.223700 TGACATTATCTTGTGCAGGAGTCT 59.776 41.667 0.00 0.00 0.00 3.24
3580 4197 6.098838 TGACATTATCTTGTGCAGGAGTCTAT 59.901 38.462 0.00 0.00 0.00 1.98
3589 4206 8.363390 TCTTGTGCAGGAGTCTATATTTCATAG 58.637 37.037 0.00 0.00 0.00 2.23
3595 4212 6.538021 CAGGAGTCTATATTTCATAGGCATGC 59.462 42.308 9.90 9.90 31.73 4.06
3622 4251 6.542735 TGTAGATATAGGCCGCATTCTACTAG 59.457 42.308 25.62 0.00 37.50 2.57
3625 4254 1.041437 AGGCCGCATTCTACTAGGAC 58.959 55.000 0.00 0.00 0.00 3.85
3629 4258 1.341531 CCGCATTCTACTAGGACTGGG 59.658 57.143 0.00 0.00 0.00 4.45
3640 4269 2.426023 GACTGGGCAAGTCGGTGT 59.574 61.111 6.22 0.00 45.76 4.16
3670 4299 0.322816 AGAAGCACGTGCATTGGGAT 60.323 50.000 39.21 16.76 45.16 3.85
3732 4361 5.197451 ACATGAACCTGAAACCAGTGTAAA 58.803 37.500 0.00 0.00 0.00 2.01
3741 4370 6.751888 CCTGAAACCAGTGTAAAGTTTTCTTG 59.248 38.462 0.00 0.00 40.37 3.02
3767 4396 6.600822 TGAGACAAGGAATGAATCAGGATTTC 59.399 38.462 0.00 0.00 0.00 2.17
3773 4402 4.262335 GGAATGAATCAGGATTTCATGCCC 60.262 45.833 11.00 7.07 33.07 5.36
3799 4428 3.071747 TGGCTCAATTATACATACCGCCA 59.928 43.478 0.00 0.00 42.16 5.69
3805 4434 7.362056 GCTCAATTATACATACCGCCAAATGAT 60.362 37.037 0.00 0.00 0.00 2.45
3856 4485 2.754552 GACATGTGGCAATAGGAAAGCA 59.245 45.455 1.15 0.00 0.00 3.91
3862 4491 7.287466 ACATGTGGCAATAGGAAAGCATATTTA 59.713 33.333 0.00 0.00 29.22 1.40
3867 4496 7.289782 TGGCAATAGGAAAGCATATTTACCAAT 59.710 33.333 0.00 0.00 34.25 3.16
3868 4497 7.599998 GGCAATAGGAAAGCATATTTACCAATG 59.400 37.037 0.00 0.00 29.22 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.588951 TCCTTCTATACTTGTCATCCGCAT 59.411 41.667 0.00 0.00 0.00 4.73
97 98 2.698797 AGTTGTCTCACCCTTTCTTCGA 59.301 45.455 0.00 0.00 0.00 3.71
144 147 6.937436 ACTTAAAAGAATTTCACCGTCACT 57.063 33.333 0.00 0.00 37.28 3.41
271 275 2.435422 TCATTCAACGCCATCACACAT 58.565 42.857 0.00 0.00 0.00 3.21
291 295 1.818131 GCTCCCAACTTCCGGAGTTTT 60.818 52.381 14.28 3.05 46.34 2.43
357 364 3.436243 AGTCCCTTCTCGTCTTCTTCAT 58.564 45.455 0.00 0.00 0.00 2.57
394 406 2.019984 GCTGCTACTCCCAAATTCCAG 58.980 52.381 0.00 0.00 0.00 3.86
399 411 0.392998 CACCGCTGCTACTCCCAAAT 60.393 55.000 0.00 0.00 0.00 2.32
401 413 2.662596 CACCGCTGCTACTCCCAA 59.337 61.111 0.00 0.00 0.00 4.12
494 506 6.254804 CACAAACCTAACAAACTTTACCTTGC 59.745 38.462 0.00 0.00 0.00 4.01
501 513 5.883503 TCGACACAAACCTAACAAACTTT 57.116 34.783 0.00 0.00 0.00 2.66
502 514 5.883503 TTCGACACAAACCTAACAAACTT 57.116 34.783 0.00 0.00 0.00 2.66
539 551 8.076178 CCAAAACTAAATTCAACTGTGACCTAG 58.924 37.037 0.00 0.00 31.90 3.02
545 557 6.805713 AGGACCAAAACTAAATTCAACTGTG 58.194 36.000 0.00 0.00 0.00 3.66
553 565 8.265055 TGATCTATCGAGGACCAAAACTAAATT 58.735 33.333 0.00 0.00 0.00 1.82
558 570 4.442192 GCTGATCTATCGAGGACCAAAACT 60.442 45.833 0.00 0.00 0.00 2.66
572 584 1.414181 CCAAGACCACCGCTGATCTAT 59.586 52.381 0.00 0.00 0.00 1.98
580 592 0.958822 AACAAATCCAAGACCACCGC 59.041 50.000 0.00 0.00 0.00 5.68
583 595 6.206634 TCATGTTAGAACAAATCCAAGACCAC 59.793 38.462 0.00 0.00 43.03 4.16
597 609 3.063997 CCAAGCGGTCATCATGTTAGAAC 59.936 47.826 0.00 0.00 0.00 3.01
608 620 1.279271 AGCTAAGTTCCAAGCGGTCAT 59.721 47.619 0.00 0.00 43.63 3.06
612 624 1.796796 GCAGCTAAGTTCCAAGCGG 59.203 57.895 0.00 0.00 43.63 5.52
613 625 1.014044 TCGCAGCTAAGTTCCAAGCG 61.014 55.000 3.18 3.18 43.63 4.68
654 672 0.744414 ATCAGCGTGATTGTTCCGGG 60.744 55.000 0.00 0.00 32.13 5.73
655 673 1.086696 AATCAGCGTGATTGTTCCGG 58.913 50.000 10.97 0.00 44.68 5.14
704 730 3.658757 TTTGGCTTGATTTGGTAGTGC 57.341 42.857 0.00 0.00 0.00 4.40
740 766 4.154015 TGATTTTGGCTTGATGACTACACG 59.846 41.667 0.00 0.00 0.00 4.49
747 773 3.856638 GCGTTGTGATTTTGGCTTGATGA 60.857 43.478 0.00 0.00 0.00 2.92
773 799 6.586082 CGATAAATCTCTTTGGGTTTTGGTTG 59.414 38.462 0.00 0.00 0.00 3.77
802 830 4.202959 CGAGAAATTACATCGCAATTGCAC 59.797 41.667 28.77 2.01 42.21 4.57
878 920 0.399091 AAGATCGAGCCAGGATCCCA 60.399 55.000 8.55 0.00 40.93 4.37
887 929 6.015772 GGGAGGAATATATAGAAGATCGAGCC 60.016 46.154 0.00 0.00 0.00 4.70
896 938 7.644062 AGACGATGAGGGAGGAATATATAGAA 58.356 38.462 0.00 0.00 0.00 2.10
906 948 0.183971 GAGGAGACGATGAGGGAGGA 59.816 60.000 0.00 0.00 0.00 3.71
912 954 3.320256 TGATGATTGGAGGAGACGATGAG 59.680 47.826 0.00 0.00 0.00 2.90
939 986 1.268999 GCTGAAGCTCGATCGATCTGT 60.269 52.381 21.12 11.72 38.21 3.41
979 1026 0.032678 GCCATCGAGCAGCTAAGCTA 59.967 55.000 0.00 0.00 46.75 3.32
993 1040 3.730761 GCCATCGCCATCGCCATC 61.731 66.667 0.00 0.00 35.26 3.51
1232 1300 4.143333 CGATGAAGGCGTCCGGGT 62.143 66.667 0.00 0.00 0.00 5.28
1458 1529 0.179065 TGATGGCAGCGAGGATGAAG 60.179 55.000 0.00 0.00 0.00 3.02
1470 1541 2.350895 CTGGGACGGTTGATGGCA 59.649 61.111 0.00 0.00 0.00 4.92
1588 1659 8.100508 ACTGAACTGGCTTAATTTCTTACTTC 57.899 34.615 0.00 0.00 0.00 3.01
1639 2013 6.239064 GGTCGACATGGACATAGAGAAATACT 60.239 42.308 18.91 0.00 38.70 2.12
1640 2014 5.921408 GGTCGACATGGACATAGAGAAATAC 59.079 44.000 18.91 0.00 38.70 1.89
1641 2015 5.833667 AGGTCGACATGGACATAGAGAAATA 59.166 40.000 18.91 0.00 38.70 1.40
1642 2016 4.651503 AGGTCGACATGGACATAGAGAAAT 59.348 41.667 18.91 0.00 38.70 2.17
1655 2029 5.326200 AGGAGTAAACTAAGGTCGACATG 57.674 43.478 18.91 1.48 0.00 3.21
1911 2474 9.953565 ACAAGCCATTAATTTCAGTACTAGTAA 57.046 29.630 3.61 0.00 0.00 2.24
1918 2481 7.361713 GCACTACACAAGCCATTAATTTCAGTA 60.362 37.037 0.00 0.00 0.00 2.74
1919 2482 6.570378 GCACTACACAAGCCATTAATTTCAGT 60.570 38.462 0.00 0.00 0.00 3.41
1920 2483 5.801947 GCACTACACAAGCCATTAATTTCAG 59.198 40.000 0.00 0.00 0.00 3.02
1921 2484 5.708948 GCACTACACAAGCCATTAATTTCA 58.291 37.500 0.00 0.00 0.00 2.69
2451 3016 2.678190 GCTTACATCCCATCTATCGGGC 60.678 54.545 0.00 0.00 44.11 6.13
2485 3050 4.336713 TGAATGATCGATGAGAGAACGAGT 59.663 41.667 0.54 0.00 39.31 4.18
2528 3118 8.877779 CCATATCGATTCATCCATTAGTTTCTC 58.122 37.037 1.71 0.00 0.00 2.87
2619 3209 2.677524 AGCATGTTGCCGGCACAT 60.678 55.556 32.95 29.74 46.52 3.21
2784 3380 9.563748 TCTGAATAAAATGATCACATATGCTGA 57.436 29.630 1.58 6.54 35.50 4.26
2996 3592 8.986991 AGTCTTTGTAGAGATTTCACTATGGAT 58.013 33.333 0.00 0.00 0.00 3.41
3031 3627 4.758165 TCACAAATTTACTCCCTTCGTTCC 59.242 41.667 0.00 0.00 0.00 3.62
3057 3653 3.004106 AGAAAACACAGACTTGATGCAGC 59.996 43.478 0.00 0.00 0.00 5.25
3134 3730 1.364626 CTCCCACGACTTGATGCAGC 61.365 60.000 0.00 0.00 0.00 5.25
3135 3731 0.036952 ACTCCCACGACTTGATGCAG 60.037 55.000 0.00 0.00 0.00 4.41
3136 3732 0.396435 AACTCCCACGACTTGATGCA 59.604 50.000 0.00 0.00 0.00 3.96
3137 3733 1.523758 AAACTCCCACGACTTGATGC 58.476 50.000 0.00 0.00 0.00 3.91
3138 3734 2.157668 CGAAAACTCCCACGACTTGATG 59.842 50.000 0.00 0.00 0.00 3.07
3139 3735 2.413837 CGAAAACTCCCACGACTTGAT 58.586 47.619 0.00 0.00 0.00 2.57
3140 3736 1.860676 CGAAAACTCCCACGACTTGA 58.139 50.000 0.00 0.00 0.00 3.02
3172 3768 0.109458 TTCTCGACGCGTTATGCTGT 60.109 50.000 15.53 0.00 43.27 4.40
3194 3790 3.047280 TGCGGTTGTGGATGCGTC 61.047 61.111 0.00 0.00 0.00 5.19
3238 3834 1.068816 GTTGACATGTTTGGTACCGCC 60.069 52.381 7.57 0.00 37.90 6.13
3239 3835 1.604755 TGTTGACATGTTTGGTACCGC 59.395 47.619 7.57 0.50 0.00 5.68
3240 3836 2.349060 CGTGTTGACATGTTTGGTACCG 60.349 50.000 7.57 0.00 0.00 4.02
3312 3928 3.870538 TGATGCTTTGCTCCCATAGAT 57.129 42.857 0.00 0.00 0.00 1.98
3314 3930 3.220110 ACATGATGCTTTGCTCCCATAG 58.780 45.455 0.00 0.00 0.00 2.23
3327 3943 8.434661 CCTTGTTAAATTTGTGTTACATGATGC 58.565 33.333 0.00 0.00 0.00 3.91
3385 4001 6.226272 TCCCATGGGCATATATTAACCTTT 57.774 37.500 27.41 0.00 34.68 3.11
3386 4002 5.811030 GCTCCCATGGGCATATATTAACCTT 60.811 44.000 27.41 0.00 34.68 3.50
3387 4003 4.325344 GCTCCCATGGGCATATATTAACCT 60.325 45.833 27.41 0.00 34.68 3.50
3388 4004 3.954258 GCTCCCATGGGCATATATTAACC 59.046 47.826 27.41 0.00 34.68 2.85
3389 4005 4.599041 TGCTCCCATGGGCATATATTAAC 58.401 43.478 27.41 1.89 33.23 2.01
3390 4006 4.944260 TGCTCCCATGGGCATATATTAA 57.056 40.909 27.41 4.20 33.23 1.40
3391 4007 4.944260 TTGCTCCCATGGGCATATATTA 57.056 40.909 27.41 5.01 38.30 0.98
3392 4008 3.831642 TTGCTCCCATGGGCATATATT 57.168 42.857 27.41 0.00 38.30 1.28
3435 4051 9.926158 CATGCATAGATCATAAGAGGTATATCC 57.074 37.037 0.00 0.00 0.00 2.59
3458 4075 1.069432 GTCGCTTATGCTCATGCCATG 60.069 52.381 0.00 0.00 38.71 3.66
3459 4076 1.233019 GTCGCTTATGCTCATGCCAT 58.767 50.000 0.00 4.47 38.71 4.40
3460 4077 0.815213 GGTCGCTTATGCTCATGCCA 60.815 55.000 0.00 0.00 38.71 4.92
3461 4078 0.815213 TGGTCGCTTATGCTCATGCC 60.815 55.000 0.00 0.00 38.71 4.40
3472 4089 5.347620 TTGGTAATACTACATGGTCGCTT 57.652 39.130 0.00 0.00 0.00 4.68
3475 4092 5.815740 AGCTTTTGGTAATACTACATGGTCG 59.184 40.000 0.00 0.00 0.00 4.79
3485 4102 6.263168 ACATGCCTATGAGCTTTTGGTAATAC 59.737 38.462 0.00 0.00 37.73 1.89
3520 4137 9.216117 ACTAACAGTAGCGAAATAATTCTTTGT 57.784 29.630 0.00 0.00 33.17 2.83
3535 4152 7.421530 TGTCAAGATGAAAACTAACAGTAGC 57.578 36.000 0.00 0.00 0.00 3.58
3558 4175 9.499479 AAATATAGACTCCTGCACAAGATAATG 57.501 33.333 0.00 0.00 0.00 1.90
3589 4206 3.209410 GGCCTATATCTACATGCATGCC 58.791 50.000 26.53 13.69 0.00 4.40
3595 4212 5.016051 AGAATGCGGCCTATATCTACATG 57.984 43.478 0.00 0.00 0.00 3.21
3625 4254 0.034896 AACTACACCGACTTGCCCAG 59.965 55.000 0.00 0.00 0.00 4.45
3629 4258 1.194772 GCTGAAACTACACCGACTTGC 59.805 52.381 0.00 0.00 0.00 4.01
3636 4265 3.680458 GTGCTTCTAGCTGAAACTACACC 59.320 47.826 0.00 0.00 42.97 4.16
3640 4269 3.575630 CACGTGCTTCTAGCTGAAACTA 58.424 45.455 0.82 0.00 42.97 2.24
3670 4299 8.846943 TGTTCTTATTTGATCTAGTTCTTGCA 57.153 30.769 2.61 0.00 0.00 4.08
3741 4370 4.836825 TCCTGATTCATTCCTTGTCTCAC 58.163 43.478 0.00 0.00 0.00 3.51
3773 4402 6.086222 GCGGTATGTATAATTGAGCCAATTG 58.914 40.000 18.02 0.00 42.91 2.32
3799 4428 6.518493 AGTTGTGACAATGCTTGAATCATTT 58.482 32.000 0.00 0.00 32.30 2.32
3805 4434 7.542890 TCTTAAAAGTTGTGACAATGCTTGAA 58.457 30.769 0.00 0.00 0.00 2.69
3856 4485 8.058847 TGCTTCCTTCCTTACATTGGTAAATAT 58.941 33.333 0.00 0.00 38.92 1.28
3862 4491 3.806949 TGCTTCCTTCCTTACATTGGT 57.193 42.857 0.00 0.00 0.00 3.67
3867 4496 5.755409 TGTTCTATGCTTCCTTCCTTACA 57.245 39.130 0.00 0.00 0.00 2.41
3868 4497 7.475840 CATTTGTTCTATGCTTCCTTCCTTAC 58.524 38.462 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.