Multiple sequence alignment - TraesCS1B01G318600

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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 TraesCS1B01G318600 chr1B 100.000 4575 0 0 1 4575 543085208 543080634 0.000000e+00 8449
1 TraesCS1B01G318600 chr1B 92.556 712 50 3 3865 4575 543397502 543396793 0.000000e+00 1018
2 TraesCS1B01G318600 chr1B 81.988 483 73 6 2827 3296 543082268 543081787 9.220000e-107 398
3 TraesCS1B01G318600 chr1B 81.988 483 73 6 2941 3422 543082382 543081913 9.220000e-107 398
4 TraesCS1B01G318600 chr1D 93.353 3355 178 17 551 3868 403723175 403719829 0.000000e+00 4918
5 TraesCS1B01G318600 chr1D 93.829 713 40 4 3865 4575 427042399 427041689 0.000000e+00 1070
6 TraesCS1B01G318600 chr1D 90.733 464 13 11 2 445 403723680 403723227 3.940000e-165 592
7 TraesCS1B01G318600 chr1D 83.505 485 62 8 2941 3422 403720900 403720431 1.950000e-118 436
8 TraesCS1B01G318600 chr1D 83.230 483 67 6 2827 3296 403720786 403720305 9.090000e-117 431
9 TraesCS1B01G318600 chr1A 91.454 2820 211 14 764 3558 499441665 499438851 0.000000e+00 3845
10 TraesCS1B01G318600 chr1A 80.861 674 54 32 2 642 499442304 499441673 1.160000e-125 460
11 TraesCS1B01G318600 chr1A 92.405 316 17 7 3553 3866 499438824 499438514 1.170000e-120 444
12 TraesCS1B01G318600 chr1A 82.062 485 69 9 2941 3422 499439579 499439110 9.220000e-107 398
13 TraesCS1B01G318600 chr1A 81.781 483 74 6 2827 3296 499439465 499438984 4.290000e-105 392
14 TraesCS1B01G318600 chr3B 92.978 712 48 2 3865 4575 276830555 276831265 0.000000e+00 1037
15 TraesCS1B01G318600 chr3B 92.426 713 51 3 3865 4575 582024817 582025528 0.000000e+00 1014
16 TraesCS1B01G318600 chr6A 92.697 712 50 2 3865 4575 203769195 203769905 0.000000e+00 1026
17 TraesCS1B01G318600 chr6B 92.556 712 51 2 3865 4575 648203442 648202732 0.000000e+00 1020
18 TraesCS1B01G318600 chr6B 92.286 713 52 3 3865 4575 32120182 32120893 0.000000e+00 1009
19 TraesCS1B01G318600 chr6B 92.146 713 52 4 3865 4575 636968428 636969138 0.000000e+00 1003
20 TraesCS1B01G318600 chr5B 92.416 712 52 2 3865 4575 645939994 645940704 0.000000e+00 1014


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 TraesCS1B01G318600 chr1B 543080634 543085208 4574 True 3081.666667 8449 87.99200 1 4575 3 chr1B.!!$R2 4574
1 TraesCS1B01G318600 chr1B 543396793 543397502 709 True 1018.000000 1018 92.55600 3865 4575 1 chr1B.!!$R1 710
2 TraesCS1B01G318600 chr1D 403719829 403723680 3851 True 1594.250000 4918 87.70525 2 3868 4 chr1D.!!$R2 3866
3 TraesCS1B01G318600 chr1D 427041689 427042399 710 True 1070.000000 1070 93.82900 3865 4575 1 chr1D.!!$R1 710
4 TraesCS1B01G318600 chr1A 499438514 499442304 3790 True 1107.800000 3845 85.71260 2 3866 5 chr1A.!!$R1 3864
5 TraesCS1B01G318600 chr3B 276830555 276831265 710 False 1037.000000 1037 92.97800 3865 4575 1 chr3B.!!$F1 710
6 TraesCS1B01G318600 chr3B 582024817 582025528 711 False 1014.000000 1014 92.42600 3865 4575 1 chr3B.!!$F2 710
7 TraesCS1B01G318600 chr6A 203769195 203769905 710 False 1026.000000 1026 92.69700 3865 4575 1 chr6A.!!$F1 710
8 TraesCS1B01G318600 chr6B 648202732 648203442 710 True 1020.000000 1020 92.55600 3865 4575 1 chr6B.!!$R1 710
9 TraesCS1B01G318600 chr6B 32120182 32120893 711 False 1009.000000 1009 92.28600 3865 4575 1 chr6B.!!$F1 710
10 TraesCS1B01G318600 chr6B 636968428 636969138 710 False 1003.000000 1003 92.14600 3865 4575 1 chr6B.!!$F2 710
11 TraesCS1B01G318600 chr5B 645939994 645940704 710 False 1014.000000 1014 92.41600 3865 4575 1 chr5B.!!$F1 710

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
478 520 0.033642 GATCGCCCTACCTTACTGGC 59.966 60.0 0.00 0.0 40.22 4.85 F
1965 2035 0.373716 GCGACCATGATGTTTCGTCC 59.626 55.0 13.15 0.0 33.95 4.79 F
2301 2371 0.037232 CCAAGGACGGAGAGGTGAAC 60.037 60.0 0.00 0.0 0.00 3.18 F
3481 3554 0.401738 TCTTGGAAGTGCTGGAAGGG 59.598 55.0 0.00 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2219 1.037030 GGGCTCGGGAATTCATTGCA 61.037 55.0 7.93 0.0 0.00 4.08 R
3490 3563 0.386731 CCGCAAAATCAACCGTGTCC 60.387 55.0 0.00 0.0 0.00 4.02 R
3536 3609 0.415429 AGAGACTCCATCCCACTGGT 59.585 55.0 0.00 0.0 37.57 4.00 R
4397 4506 2.175069 AGTATCCTCCCAGAAGCGAGTA 59.825 50.0 0.00 0.0 0.00 2.59 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
56 57 1.957186 CGAACAACGCGGGAAAGGA 60.957 57.895 12.47 0.00 34.51 3.36
60 61 1.104630 ACAACGCGGGAAAGGAAAAA 58.895 45.000 12.47 0.00 0.00 1.94
65 66 0.888619 GCGGGAAAGGAAAAAGGGAG 59.111 55.000 0.00 0.00 0.00 4.30
219 230 3.244353 ACCAACAGAAGAGATGGTGTGAG 60.244 47.826 0.00 0.00 44.25 3.51
298 319 3.343788 CTCGCCAGTCGGTCAGTCC 62.344 68.421 0.00 0.00 39.05 3.85
356 394 2.619074 CCATTTCCTTTCCTTCGCTCCT 60.619 50.000 0.00 0.00 0.00 3.69
449 491 3.040763 GCAGCCGGCGATCTCATC 61.041 66.667 23.20 1.08 0.00 2.92
450 492 2.733301 CAGCCGGCGATCTCATCT 59.267 61.111 23.20 0.00 0.00 2.90
452 494 1.829970 AGCCGGCGATCTCATCTGA 60.830 57.895 23.20 0.00 0.00 3.27
453 495 1.068083 GCCGGCGATCTCATCTGAA 59.932 57.895 12.58 0.00 0.00 3.02
454 496 0.943359 GCCGGCGATCTCATCTGAAG 60.943 60.000 12.58 0.00 0.00 3.02
455 497 0.943359 CCGGCGATCTCATCTGAAGC 60.943 60.000 9.30 0.00 0.00 3.86
456 498 1.274126 CGGCGATCTCATCTGAAGCG 61.274 60.000 0.00 0.00 0.00 4.68
457 499 0.943359 GGCGATCTCATCTGAAGCGG 60.943 60.000 0.00 0.00 0.00 5.52
460 502 1.606189 CGATCTCATCTGAAGCGGAGA 59.394 52.381 0.00 0.00 40.37 3.71
461 503 2.228582 CGATCTCATCTGAAGCGGAGAT 59.771 50.000 11.15 11.15 46.69 2.75
462 504 3.940209 ATCTCATCTGAAGCGGAGATC 57.060 47.619 0.00 0.00 41.91 2.75
463 505 1.606189 TCTCATCTGAAGCGGAGATCG 59.394 52.381 0.00 0.00 42.76 3.69
472 514 3.857764 CGGAGATCGCCCTACCTT 58.142 61.111 10.18 0.00 0.00 3.50
473 515 3.031916 CGGAGATCGCCCTACCTTA 57.968 57.895 10.18 0.00 0.00 2.69
474 516 0.597072 CGGAGATCGCCCTACCTTAC 59.403 60.000 10.18 0.00 0.00 2.34
475 517 1.818522 CGGAGATCGCCCTACCTTACT 60.819 57.143 10.18 0.00 0.00 2.24
476 518 1.614413 GGAGATCGCCCTACCTTACTG 59.386 57.143 3.71 0.00 0.00 2.74
477 519 1.614413 GAGATCGCCCTACCTTACTGG 59.386 57.143 0.00 0.00 42.93 4.00
478 520 0.033642 GATCGCCCTACCTTACTGGC 59.966 60.000 0.00 0.00 40.22 4.85
479 521 1.408453 ATCGCCCTACCTTACTGGCC 61.408 60.000 0.00 0.00 40.87 5.36
480 522 2.064581 CGCCCTACCTTACTGGCCT 61.065 63.158 3.32 0.00 40.87 5.19
492 534 4.584743 CCTTACTGGCCTTTTTCTTGTTCT 59.415 41.667 3.32 0.00 0.00 3.01
493 535 5.069119 CCTTACTGGCCTTTTTCTTGTTCTT 59.931 40.000 3.32 0.00 0.00 2.52
494 536 4.391405 ACTGGCCTTTTTCTTGTTCTTG 57.609 40.909 3.32 0.00 0.00 3.02
495 537 4.023291 ACTGGCCTTTTTCTTGTTCTTGA 58.977 39.130 3.32 0.00 0.00 3.02
511 557 3.525537 TCTTGATTGATCTGCCTTCGAC 58.474 45.455 0.00 0.00 0.00 4.20
519 566 2.604686 TGCCTTCGACCTCTGCCT 60.605 61.111 0.00 0.00 0.00 4.75
613 661 3.197790 CCCATCGCCGTCAGCTTG 61.198 66.667 0.00 0.00 40.39 4.01
634 682 3.072330 TGAAGGTACCAACTTCTGATGCA 59.928 43.478 15.94 0.00 43.59 3.96
647 695 3.642705 TCTGATGCAACCGATCGATTAG 58.357 45.455 18.66 7.88 0.00 1.73
654 702 6.510879 TGCAACCGATCGATTAGTCTATAT 57.489 37.500 18.66 0.00 0.00 0.86
685 733 8.309656 TGTGATTGTGACATTTTAATTATGCCA 58.690 29.630 0.00 0.00 0.00 4.92
718 766 6.270231 GGAGGGTCTTAGAGATTAATTAGCCA 59.730 42.308 0.00 0.00 0.00 4.75
749 797 1.595093 GGTTGGATTTGGCCTGGTCG 61.595 60.000 3.32 0.00 0.00 4.79
791 839 2.069273 GTTTCCAGAGTGATCGTGTGG 58.931 52.381 5.01 5.01 0.00 4.17
948 997 8.746530 AGAATTCATTCAATGAGCTAATGTTGT 58.253 29.630 8.44 0.00 40.94 3.32
950 999 7.692460 TTCATTCAATGAGCTAATGTTGTCT 57.308 32.000 0.00 0.00 40.94 3.41
983 1032 1.449246 CTAGGTCTGTGCTGGCAGC 60.449 63.158 31.91 31.91 42.82 5.25
987 1036 1.598962 GTCTGTGCTGGCAGCTGAA 60.599 57.895 36.50 21.85 42.97 3.02
1119 1168 2.060050 TCAGTCTAGCCCTACTGCTC 57.940 55.000 4.76 0.00 42.31 4.26
1164 1213 3.428999 CGGGTCTCTTCGCTTTCATTCTA 60.429 47.826 0.00 0.00 0.00 2.10
1168 1217 5.452636 GGTCTCTTCGCTTTCATTCTATCCT 60.453 44.000 0.00 0.00 0.00 3.24
1170 1219 4.611943 TCTTCGCTTTCATTCTATCCTCG 58.388 43.478 0.00 0.00 0.00 4.63
1188 1237 5.399991 TCCTCGTCCCCTGTAATTATATGT 58.600 41.667 0.00 0.00 0.00 2.29
1310 1359 5.759763 AGTTTGGATGTTTTTCCAGAAATGC 59.240 36.000 0.00 0.00 46.22 3.56
1326 1375 5.464057 CAGAAATGCTCATTTTGAAGCACAA 59.536 36.000 8.98 0.00 40.77 3.33
1421 1491 1.207791 GGCAAGGAGAGGGATGAGAA 58.792 55.000 0.00 0.00 0.00 2.87
1446 1516 4.559862 TCCTCTTTTGAAGGGATCAGTC 57.440 45.455 0.00 0.00 39.77 3.51
1641 1711 2.157738 AGCTTGTTTGAGGATGCTGAC 58.842 47.619 0.00 0.00 0.00 3.51
1693 1763 4.871871 TTTGGATTATGCCCTTCCAGTA 57.128 40.909 0.00 0.00 40.48 2.74
1694 1764 4.437682 TTGGATTATGCCCTTCCAGTAG 57.562 45.455 0.00 0.00 40.48 2.57
1717 1787 4.141869 GGAATGATGGGGAAAATGGTGAAG 60.142 45.833 0.00 0.00 0.00 3.02
1854 1924 1.429463 CTTTTTCCGTCCGTCAGAGG 58.571 55.000 0.00 0.00 0.00 3.69
1918 1988 3.257469 TCAGCAGCCAAATAGACTCTG 57.743 47.619 0.00 0.00 0.00 3.35
1940 2010 3.365364 GCTCTAGTTTCACCATGTGCAAC 60.365 47.826 2.21 2.21 39.28 4.17
1965 2035 0.373716 GCGACCATGATGTTTCGTCC 59.626 55.000 13.15 0.00 33.95 4.79
2122 2192 2.219458 CTATGGCTGATGTTGCTCCAG 58.781 52.381 0.00 0.00 0.00 3.86
2149 2219 6.941436 GCTTGATGAGATTGATCCTCCTTTAT 59.059 38.462 0.00 0.00 0.00 1.40
2208 2278 0.323725 ATTCTGGCTGCGGTTCCAAT 60.324 50.000 0.00 0.00 30.98 3.16
2215 2285 0.883833 CTGCGGTTCCAATTTCTGCT 59.116 50.000 0.00 0.00 34.91 4.24
2224 2294 4.038271 TCCAATTTCTGCTGTCAGGATT 57.962 40.909 1.14 0.00 40.69 3.01
2227 2297 4.142447 CCAATTTCTGCTGTCAGGATTCTG 60.142 45.833 1.14 0.00 40.69 3.02
2244 2314 5.123979 GGATTCTGAAATGGACAGTGGTAAC 59.876 44.000 0.00 0.00 36.81 2.50
2259 2329 3.349488 GGTAACAACAACAAGGCTGAC 57.651 47.619 0.00 0.00 0.00 3.51
2273 2343 2.234908 AGGCTGACACTAGTAAAGCTGG 59.765 50.000 18.02 0.00 37.56 4.85
2289 2359 1.135721 GCTGGAAATGATGCCAAGGAC 59.864 52.381 0.00 0.00 32.95 3.85
2295 2365 0.467384 ATGATGCCAAGGACGGAGAG 59.533 55.000 0.00 0.00 0.00 3.20
2296 2366 1.144936 GATGCCAAGGACGGAGAGG 59.855 63.158 0.00 0.00 0.00 3.69
2297 2367 1.613630 ATGCCAAGGACGGAGAGGT 60.614 57.895 0.00 0.00 0.00 3.85
2301 2371 0.037232 CCAAGGACGGAGAGGTGAAC 60.037 60.000 0.00 0.00 0.00 3.18
2565 2635 2.027745 TGACCTTGCTTCTGATCCTGAC 60.028 50.000 0.00 0.00 0.00 3.51
2592 2662 3.854669 ATTCCTGGCTCGGCTCCG 61.855 66.667 1.14 1.14 41.35 4.63
2636 2706 1.620822 CTGTTTGAACCCCCTTCTGG 58.379 55.000 0.00 0.00 0.00 3.86
2694 2764 9.823647 GATAACTTGGACTCTCAAGAAATCATA 57.176 33.333 10.99 0.00 44.98 2.15
2700 2770 5.295540 GGACTCTCAAGAAATCATAACAGGC 59.704 44.000 0.00 0.00 0.00 4.85
2716 2786 3.838271 GCTCCCGCCGAGACATGA 61.838 66.667 0.00 0.00 41.63 3.07
2727 2797 3.181482 GCCGAGACATGATCTTCAAGAGA 60.181 47.826 0.00 0.00 38.00 3.10
2763 2833 2.050836 TTGGCGGCCAAGAGAGACAA 62.051 55.000 29.66 5.15 38.75 3.18
2770 2840 2.029290 GGCCAAGAGAGACAACGTTCTA 60.029 50.000 0.00 0.00 0.00 2.10
2817 2887 5.415077 GGATGCAATGGATATTCAGGAAGAG 59.585 44.000 0.00 0.00 0.00 2.85
2819 2889 6.196918 TGCAATGGATATTCAGGAAGAGAT 57.803 37.500 0.00 0.00 0.00 2.75
2825 2898 4.018597 GGATATTCAGGAAGAGATGGGCAT 60.019 45.833 0.00 0.00 0.00 4.40
2832 2905 3.099141 GGAAGAGATGGGCATTTTCCAA 58.901 45.455 0.00 0.00 37.87 3.53
2880 2953 6.989759 TGTCAAAACTAAGTGCTGTATCTGAA 59.010 34.615 0.00 0.00 0.00 3.02
2922 2995 3.079578 TGCTGATCAAGAGGAAAGCAAG 58.920 45.455 0.00 0.00 42.77 4.01
2968 3041 1.475034 GGTGGTTCAGTGACAAGAGCA 60.475 52.381 0.00 0.00 0.00 4.26
2994 3067 2.748605 AGACTGAGCGTTGTTTCTGAG 58.251 47.619 0.00 0.00 0.00 3.35
3014 3087 1.609072 GTCTGACACCCTTTCTTTGGC 59.391 52.381 2.24 0.00 0.00 4.52
3043 3116 3.532896 GAGGAATGCAACGACCTCA 57.467 52.632 19.56 0.00 45.53 3.86
3120 3193 0.537188 TTTCTGGATCTGACGCCCTC 59.463 55.000 0.00 0.00 0.00 4.30
3132 3205 2.665603 GCCCTCTCTTTGGTCGCT 59.334 61.111 0.00 0.00 0.00 4.93
3134 3207 1.975327 CCCTCTCTTTGGTCGCTGA 59.025 57.895 0.00 0.00 0.00 4.26
3220 3293 3.678056 AGAGCATGTCGAAAGTAACCA 57.322 42.857 0.00 0.00 0.00 3.67
3345 3418 2.429351 CGTGTCGAAGCAGAGCGTC 61.429 63.158 0.00 0.00 33.97 5.19
3463 3536 0.813821 GCCAAGGCAGGAAAGTGATC 59.186 55.000 6.14 0.00 41.49 2.92
3470 3543 2.751806 GGCAGGAAAGTGATCTTGGAAG 59.248 50.000 0.00 0.00 33.79 3.46
3480 3553 2.290514 TGATCTTGGAAGTGCTGGAAGG 60.291 50.000 0.00 0.00 0.00 3.46
3481 3554 0.401738 TCTTGGAAGTGCTGGAAGGG 59.598 55.000 0.00 0.00 0.00 3.95
3536 3609 2.556144 AACTCTGAATGCTGCTGTCA 57.444 45.000 0.00 3.47 0.00 3.58
3577 3680 8.412456 TCTCTGAATCTTCTGATCAAGTGATAC 58.588 37.037 0.00 0.00 35.14 2.24
3654 3757 2.030540 CACTGTTCCTGTTGCCATTCTG 60.031 50.000 0.00 0.00 0.00 3.02
3680 3784 2.859165 TAGGCCTTGTGAAGTTCCAG 57.141 50.000 12.58 0.00 0.00 3.86
3758 3864 9.217278 CATCCTATAGAATGTTGAATCTCCTTG 57.783 37.037 0.00 0.00 0.00 3.61
3771 3877 9.264719 GTTGAATCTCCTTGTCAAATTTTCAAT 57.735 29.630 6.17 0.00 34.33 2.57
3819 3925 1.177895 TTTCCCAGCTGCGATGCAAA 61.178 50.000 8.66 0.00 38.41 3.68
3872 3978 2.776526 TAGCCCCGCCCCATTCAT 60.777 61.111 0.00 0.00 0.00 2.57
3964 4070 4.574674 AGGGCAAACTCATGTCTTATGA 57.425 40.909 0.00 0.00 0.00 2.15
4096 4203 4.260170 GTTTCTTCTGGCAGAGTGATGAT 58.740 43.478 17.91 0.00 0.00 2.45
4130 4237 1.134098 ACCGACTAGCCAAATGGGATG 60.134 52.381 0.90 0.00 40.01 3.51
4141 4248 2.951642 CAAATGGGATGTTATCTGCCGT 59.048 45.455 0.00 0.00 0.00 5.68
4192 4300 8.383318 TCAAGAATCTTGAAGTTAAGAACAGG 57.617 34.615 22.00 0.00 39.87 4.00
4222 4330 7.241042 TCTCAGTAAGTGGCTGTATAAGTTT 57.759 36.000 0.00 0.00 35.60 2.66
4223 4331 7.676947 TCTCAGTAAGTGGCTGTATAAGTTTT 58.323 34.615 0.00 0.00 35.60 2.43
4260 4369 3.160047 CCTGGGCGCAGATCCTCT 61.160 66.667 30.57 0.00 0.00 3.69
4268 4377 1.740380 GCGCAGATCCTCTGTAGCAAA 60.740 52.381 0.30 0.00 45.94 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 394 5.896678 TGGTGATCCCAAAGAAAGAAAAAGA 59.103 36.000 0.84 0.00 41.50 2.52
455 497 0.597072 GTAAGGTAGGGCGATCTCCG 59.403 60.000 0.00 0.00 42.21 4.63
456 498 1.614413 CAGTAAGGTAGGGCGATCTCC 59.386 57.143 0.00 0.00 0.00 3.71
457 499 1.614413 CCAGTAAGGTAGGGCGATCTC 59.386 57.143 0.00 0.00 0.00 2.75
460 502 2.134092 GCCAGTAAGGTAGGGCGAT 58.866 57.895 0.00 0.00 40.61 4.58
461 503 3.625099 GCCAGTAAGGTAGGGCGA 58.375 61.111 0.00 0.00 40.61 5.54
464 506 3.010250 AGAAAAAGGCCAGTAAGGTAGGG 59.990 47.826 5.01 0.00 40.61 3.53
465 507 4.302559 AGAAAAAGGCCAGTAAGGTAGG 57.697 45.455 5.01 0.00 40.61 3.18
466 508 5.070685 ACAAGAAAAAGGCCAGTAAGGTAG 58.929 41.667 5.01 0.00 40.61 3.18
467 509 5.056553 ACAAGAAAAAGGCCAGTAAGGTA 57.943 39.130 5.01 0.00 40.61 3.08
468 510 3.910989 ACAAGAAAAAGGCCAGTAAGGT 58.089 40.909 5.01 0.00 40.61 3.50
469 511 4.584743 AGAACAAGAAAAAGGCCAGTAAGG 59.415 41.667 5.01 0.00 41.84 2.69
470 512 5.774498 AGAACAAGAAAAAGGCCAGTAAG 57.226 39.130 5.01 0.00 0.00 2.34
471 513 5.654650 TCAAGAACAAGAAAAAGGCCAGTAA 59.345 36.000 5.01 0.00 0.00 2.24
472 514 5.197451 TCAAGAACAAGAAAAAGGCCAGTA 58.803 37.500 5.01 0.00 0.00 2.74
473 515 4.023291 TCAAGAACAAGAAAAAGGCCAGT 58.977 39.130 5.01 0.00 0.00 4.00
474 516 4.654091 TCAAGAACAAGAAAAAGGCCAG 57.346 40.909 5.01 0.00 0.00 4.85
475 517 5.128499 TCAATCAAGAACAAGAAAAAGGCCA 59.872 36.000 5.01 0.00 0.00 5.36
476 518 5.600696 TCAATCAAGAACAAGAAAAAGGCC 58.399 37.500 0.00 0.00 0.00 5.19
477 519 7.115947 CAGATCAATCAAGAACAAGAAAAAGGC 59.884 37.037 0.00 0.00 0.00 4.35
478 520 7.115947 GCAGATCAATCAAGAACAAGAAAAAGG 59.884 37.037 0.00 0.00 0.00 3.11
479 521 7.115947 GGCAGATCAATCAAGAACAAGAAAAAG 59.884 37.037 0.00 0.00 0.00 2.27
480 522 6.925165 GGCAGATCAATCAAGAACAAGAAAAA 59.075 34.615 0.00 0.00 0.00 1.94
492 534 2.237143 AGGTCGAAGGCAGATCAATCAA 59.763 45.455 0.00 0.00 0.00 2.57
493 535 1.833630 AGGTCGAAGGCAGATCAATCA 59.166 47.619 0.00 0.00 0.00 2.57
494 536 2.102252 AGAGGTCGAAGGCAGATCAATC 59.898 50.000 0.00 0.00 0.00 2.67
495 537 2.114616 AGAGGTCGAAGGCAGATCAAT 58.885 47.619 0.00 0.00 0.00 2.57
511 557 2.125065 CAGCAGCAGAGGCAGAGG 60.125 66.667 0.00 0.00 44.61 3.69
613 661 3.674997 TGCATCAGAAGTTGGTACCTTC 58.325 45.455 14.36 8.83 38.87 3.46
634 682 5.879223 ACGGATATAGACTAATCGATCGGTT 59.121 40.000 18.99 18.99 30.16 4.44
647 695 6.040247 TGTCACAATCACAACGGATATAGAC 58.960 40.000 0.00 0.00 0.00 2.59
654 702 4.909696 AAAATGTCACAATCACAACGGA 57.090 36.364 0.00 0.00 0.00 4.69
685 733 3.529734 TCTCTAAGACCCTCCATCTCAGT 59.470 47.826 0.00 0.00 0.00 3.41
718 766 0.690762 ATCCAACCGTGTAAGCAGGT 59.309 50.000 0.00 0.00 40.50 4.00
749 797 4.673311 ACGATGAATTTTGTTACGCACAAC 59.327 37.500 0.33 0.00 45.54 3.32
791 839 5.184671 GGAAGGGATAATCAAGGATGCAATC 59.815 44.000 0.00 0.00 44.55 2.67
948 997 3.898123 ACCTAGCAGAGAAAACACAGAGA 59.102 43.478 0.00 0.00 0.00 3.10
950 999 3.898123 AGACCTAGCAGAGAAAACACAGA 59.102 43.478 0.00 0.00 0.00 3.41
983 1032 1.681166 CCATGGCCACTCCTCTTTCAG 60.681 57.143 8.16 0.00 35.26 3.02
987 1036 1.542375 ACCCATGGCCACTCCTCTT 60.542 57.895 8.16 0.00 35.26 2.85
1119 1168 4.440802 GGTGAAGATCTGTACAGCAGGTAG 60.441 50.000 18.45 0.00 45.08 3.18
1164 1213 6.023603 ACATATAATTACAGGGGACGAGGAT 58.976 40.000 0.00 0.00 0.00 3.24
1168 1217 4.262721 GGCACATATAATTACAGGGGACGA 60.263 45.833 0.00 0.00 0.00 4.20
1170 1219 4.760204 GTGGCACATATAATTACAGGGGAC 59.240 45.833 13.86 0.00 44.52 4.46
1206 1255 3.181479 TGCTCCCGTAACTTAGCAGTATG 60.181 47.826 0.00 0.00 39.92 2.39
1310 1359 3.318839 TCCCTGTTGTGCTTCAAAATGAG 59.681 43.478 0.00 0.00 37.81 2.90
1326 1375 1.915141 CAGGCACAGAAAATCCCTGT 58.085 50.000 0.00 0.00 44.92 4.00
1421 1491 5.222213 ACTGATCCCTTCAAAAGAGGAACAT 60.222 40.000 0.00 0.00 36.33 2.71
1446 1516 4.916983 AACTCTCTCATCTCCTTGATCG 57.083 45.455 0.00 0.00 32.05 3.69
1693 1763 3.012730 TCACCATTTTCCCCATCATTCCT 59.987 43.478 0.00 0.00 0.00 3.36
1694 1764 3.373830 TCACCATTTTCCCCATCATTCC 58.626 45.455 0.00 0.00 0.00 3.01
1702 1772 1.273327 CACTGCTTCACCATTTTCCCC 59.727 52.381 0.00 0.00 0.00 4.81
1717 1787 2.818130 TGATTTTCCTTTGCCACTGC 57.182 45.000 0.00 0.00 38.26 4.40
1812 1882 1.510844 GCCCCATTTGCAAGTACCG 59.489 57.895 0.00 0.00 0.00 4.02
1854 1924 5.824904 TCTTTATGCCATCAAGCTTCTTC 57.175 39.130 0.00 0.00 0.00 2.87
1897 1967 3.603532 CAGAGTCTATTTGGCTGCTGAA 58.396 45.455 0.00 0.00 31.71 3.02
1918 1988 2.426522 TGCACATGGTGAAACTAGAGC 58.573 47.619 0.00 0.00 35.23 4.09
1940 2010 3.242091 CGAAACATCATGGTCGCTAACTG 60.242 47.826 0.57 0.00 0.00 3.16
1945 2015 1.359848 GACGAAACATCATGGTCGCT 58.640 50.000 11.74 1.74 33.95 4.93
1965 2035 2.159572 CGGCTTACCAGAATCAAAACCG 60.160 50.000 0.00 0.00 34.57 4.44
2096 2166 5.039920 AGCAACATCAGCCATAGTGATAA 57.960 39.130 0.00 0.00 32.69 1.75
2122 2192 3.814283 GGAGGATCAATCTCATCAAGCAC 59.186 47.826 0.00 0.00 36.25 4.40
2149 2219 1.037030 GGGCTCGGGAATTCATTGCA 61.037 55.000 7.93 0.00 0.00 4.08
2224 2294 4.698201 TGTTACCACTGTCCATTTCAGA 57.302 40.909 0.00 0.00 36.81 3.27
2227 2297 5.163602 TGTTGTTGTTACCACTGTCCATTTC 60.164 40.000 0.00 0.00 0.00 2.17
2244 2314 3.206150 ACTAGTGTCAGCCTTGTTGTTG 58.794 45.455 0.00 0.00 0.00 3.33
2254 2324 3.594603 TCCAGCTTTACTAGTGTCAGC 57.405 47.619 5.39 9.92 34.53 4.26
2259 2329 5.220931 GGCATCATTTCCAGCTTTACTAGTG 60.221 44.000 5.39 0.00 0.00 2.74
2273 2343 1.672881 CTCCGTCCTTGGCATCATTTC 59.327 52.381 0.00 0.00 0.00 2.17
2289 2359 1.550524 TCATCCTTGTTCACCTCTCCG 59.449 52.381 0.00 0.00 0.00 4.63
2295 2365 2.094675 CCACCATCATCCTTGTTCACC 58.905 52.381 0.00 0.00 0.00 4.02
2296 2366 2.094675 CCCACCATCATCCTTGTTCAC 58.905 52.381 0.00 0.00 0.00 3.18
2297 2367 1.991813 TCCCACCATCATCCTTGTTCA 59.008 47.619 0.00 0.00 0.00 3.18
2301 2371 1.767759 GGTTCCCACCATCATCCTTG 58.232 55.000 0.00 0.00 43.61 3.61
2565 2635 2.515523 CCAGGAATGGCTGCCTCG 60.516 66.667 21.03 1.70 30.41 4.63
2592 2662 0.657312 TTCGCCGATGCATGATTGAC 59.343 50.000 2.46 0.00 37.32 3.18
2636 2706 7.328982 CAGATACACTGCTATCATCTGATTGTC 59.671 40.741 4.27 0.00 43.37 3.18
2700 2770 1.006805 GATCATGTCTCGGCGGGAG 60.007 63.158 11.12 0.00 44.58 4.30
2716 2786 7.429374 TGAAGGTATCATGTCTCTTGAAGAT 57.571 36.000 0.00 0.00 32.27 2.40
2727 2797 3.440173 CGCCAAAGTTGAAGGTATCATGT 59.560 43.478 0.00 0.00 38.03 3.21
2763 2833 6.183360 CGAAACATGGCTTAAATCTAGAACGT 60.183 38.462 0.00 0.00 0.00 3.99
2770 2840 3.758554 AGCACGAAACATGGCTTAAATCT 59.241 39.130 0.00 0.00 31.34 2.40
2817 2887 1.278699 TGCCTTTGGAAAATGCCCATC 59.721 47.619 0.00 0.00 33.04 3.51
2819 2889 0.686224 CTGCCTTTGGAAAATGCCCA 59.314 50.000 0.00 0.00 0.00 5.36
2825 2898 3.130340 GTCACTGAACTGCCTTTGGAAAA 59.870 43.478 0.00 0.00 0.00 2.29
2832 2905 2.171448 ACTCTTGTCACTGAACTGCCTT 59.829 45.455 0.00 0.00 0.00 4.35
2880 2953 4.261801 CAACCGAAGAAAGGGTATCACAT 58.738 43.478 0.00 0.00 34.85 3.21
2922 2995 4.277423 TGGAAATCCTTTTTGACGAGGTTC 59.723 41.667 0.44 0.00 36.82 3.62
2968 3041 2.533266 ACAACGCTCAGTCTTGACAT 57.467 45.000 3.49 0.00 0.00 3.06
2994 3067 1.609072 GCCAAAGAAAGGGTGTCAGAC 59.391 52.381 0.00 0.00 0.00 3.51
3014 3087 1.502163 GCATTCCTCTTGATCGGCGG 61.502 60.000 7.21 0.00 0.00 6.13
3043 3116 4.774200 CCACCTCTGGAAATCCTTTTTGAT 59.226 41.667 0.44 0.00 40.55 2.57
3090 3163 2.037772 AGATCCAGAAACAACGCTCAGT 59.962 45.455 0.00 0.00 0.00 3.41
3120 3193 2.928757 CTCTTGATCAGCGACCAAAGAG 59.071 50.000 0.00 0.00 0.00 2.85
3132 3205 0.737367 CGCTGCGTTCCTCTTGATCA 60.737 55.000 14.93 0.00 0.00 2.92
3134 3207 0.737715 GTCGCTGCGTTCCTCTTGAT 60.738 55.000 22.48 0.00 0.00 2.57
3220 3293 2.689983 GGGCATCGGATTCAGAAACAAT 59.310 45.455 0.00 0.00 0.00 2.71
3335 3408 0.596577 TTCAGTAACGACGCTCTGCT 59.403 50.000 0.00 0.00 0.00 4.24
3345 3418 8.286996 ACGAAATGATATCAGATTCAGTAACG 57.713 34.615 23.35 15.72 0.00 3.18
3438 3511 3.574074 TTCCTGCCTTGGCAGCTCC 62.574 63.158 30.26 0.00 36.57 4.70
3463 3536 0.401738 TCCCTTCCAGCACTTCCAAG 59.598 55.000 0.00 0.00 0.00 3.61
3470 3543 1.893062 GGCATTTCCCTTCCAGCAC 59.107 57.895 0.00 0.00 0.00 4.40
3490 3563 0.386731 CCGCAAAATCAACCGTGTCC 60.387 55.000 0.00 0.00 0.00 4.02
3536 3609 0.415429 AGAGACTCCATCCCACTGGT 59.585 55.000 0.00 0.00 37.57 4.00
3577 3680 0.875059 GGGAAAACTCTGTGCTTCGG 59.125 55.000 0.00 0.00 0.00 4.30
3654 3757 3.412386 ACTTCACAAGGCCTATGTTCAC 58.588 45.455 5.16 0.00 0.00 3.18
3752 3858 6.985117 TCAGGATTGAAAATTTGACAAGGAG 58.015 36.000 13.66 6.78 0.00 3.69
3758 3864 7.381323 ACAGGAATCAGGATTGAAAATTTGAC 58.619 34.615 0.00 0.00 36.78 3.18
3771 3877 4.218417 GCTAAAAGCAAACAGGAATCAGGA 59.782 41.667 0.00 0.00 41.89 3.86
3872 3978 6.041423 TCTCTGTTTGTCAGCTTATGATGA 57.959 37.500 0.00 0.00 43.32 2.92
3964 4070 7.308589 CCGAATTAATAAGAATCAATCGGCCTT 60.309 37.037 0.00 0.00 0.00 4.35
4096 4203 6.379133 TGGCTAGTCGGTATTTTCTCTTAAGA 59.621 38.462 4.81 4.81 0.00 2.10
4130 4237 2.007608 GTCCTTTGGACGGCAGATAAC 58.992 52.381 0.67 0.00 43.14 1.89
4168 4276 8.072567 CACCTGTTCTTAACTTCAAGATTCTTG 58.927 37.037 18.49 18.49 34.59 3.02
4183 4291 2.972713 ACTGAGAAGGCACCTGTTCTTA 59.027 45.455 0.00 0.00 33.04 2.10
4192 4300 1.002544 AGCCACTTACTGAGAAGGCAC 59.997 52.381 0.00 0.00 45.84 5.01
4260 4369 8.206867 AGTCTTAGAATGCAGATATTTGCTACA 58.793 33.333 18.11 0.00 44.38 2.74
4268 4377 6.201806 GCGACAAAGTCTTAGAATGCAGATAT 59.798 38.462 0.00 0.00 0.00 1.63
4378 4487 3.687698 AGTATTGTTGCCATTACCGACAC 59.312 43.478 0.00 0.00 30.97 3.67
4397 4506 2.175069 AGTATCCTCCCAGAAGCGAGTA 59.825 50.000 0.00 0.00 0.00 2.59
4509 4618 4.439253 ACTGAATATTAAGGGGAGTGGC 57.561 45.455 4.78 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.