Multiple sequence alignment - TraesCS4B01G058600

Loading Multiple Alignment...

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 TraesCS4B01G058600 chr4B 100.000 3797 0 0 1 3797 49739711 49743507 0.000000e+00 7012
1 TraesCS4B01G058600 chr4B 87.273 165 15 3 563 727 483582139 483581981 2.330000e-42 183
2 TraesCS4B01G058600 chr4D 93.351 2978 149 25 824 3797 34665670 34668602 0.000000e+00 4357
3 TraesCS4B01G058600 chr4D 94.526 548 20 5 3 550 34664525 34665062 0.000000e+00 837
4 TraesCS4B01G058600 chr4A 92.224 3022 146 27 697 3696 567686062 567683108 0.000000e+00 4196
5 TraesCS4B01G058600 chr4A 94.523 493 19 5 62 553 567687011 567686526 0.000000e+00 754
6 TraesCS4B01G058600 chr5B 89.375 160 9 6 562 719 299602222 299602375 1.080000e-45 195
7 TraesCS4B01G058600 chr7B 88.199 161 13 4 562 722 78552429 78552583 1.800000e-43 187
8 TraesCS4B01G058600 chr2A 88.199 161 13 4 562 721 141506317 141506472 1.800000e-43 187
9 TraesCS4B01G058600 chr1B 87.500 168 14 5 555 722 632020920 632021080 1.800000e-43 187
10 TraesCS4B01G058600 chr3B 85.955 178 19 5 549 723 404830303 404830477 6.480000e-43 185
11 TraesCS4B01G058600 chr3D 87.730 163 13 6 564 723 315480578 315480420 2.330000e-42 183
12 TraesCS4B01G058600 chr1D 88.199 161 10 7 561 719 7349702 7349855 2.330000e-42 183
13 TraesCS4B01G058600 chr2D 87.349 166 12 7 557 719 617101220 617101061 8.380000e-42 182


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 TraesCS4B01G058600 chr4B 49739711 49743507 3796 False 7012 7012 100.0000 1 3797 1 chr4B.!!$F1 3796
1 TraesCS4B01G058600 chr4D 34664525 34668602 4077 False 2597 4357 93.9385 3 3797 2 chr4D.!!$F1 3794
2 TraesCS4B01G058600 chr4A 567683108 567687011 3903 True 2475 4196 93.3735 62 3696 2 chr4A.!!$R1 3634

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
198 199 0.663153 GTGAAGACTTGCGCCAGTTT 59.337 50.0 16.07 7.26 0.00 2.66 F
1899 2434 0.815734 CGGATTCTGTCACCTACGGT 59.184 55.0 0.00 0.00 35.78 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2449 1.123246 ACCTGCCTGCCTTGCAAAAT 61.123 50.000 0.00 0.0 38.41 1.82 R
2815 3350 2.094675 GTGCACTAGTTCATTGCCCAT 58.905 47.619 10.32 0.0 35.26 4.00 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
34 35 6.809196 TGTTTCTTGGTACACAATTGTTTGTC 59.191 34.615 8.77 1.11 44.24 3.18
46 47 6.412653 CACAATTGTTTGTCGTTGTAGTTACC 59.587 38.462 8.77 0.00 44.24 2.85
59 60 8.093307 TCGTTGTAGTTACCAATACCATTAACA 58.907 33.333 0.00 0.00 0.00 2.41
112 113 5.053978 AGTTCAAGGAGGTTGTCAAATCT 57.946 39.130 0.00 0.00 37.43 2.40
115 116 7.234355 AGTTCAAGGAGGTTGTCAAATCTTAT 58.766 34.615 0.00 0.00 37.43 1.73
121 122 3.941483 AGGTTGTCAAATCTTATGAGGCG 59.059 43.478 0.00 0.00 0.00 5.52
127 128 7.482654 TGTCAAATCTTATGAGGCGATAAAG 57.517 36.000 0.00 0.00 0.00 1.85
175 176 2.346803 TGCGTTTGTCTATTGGAGCTC 58.653 47.619 4.71 4.71 0.00 4.09
198 199 0.663153 GTGAAGACTTGCGCCAGTTT 59.337 50.000 16.07 7.26 0.00 2.66
214 215 0.820482 GTTTGTTACAGCCCCGGTGT 60.820 55.000 0.00 0.06 46.27 4.16
222 223 2.748647 GCCCCGGTGTACGCAATT 60.749 61.111 8.97 0.00 42.52 2.32
570 597 8.623030 GTGTTTGTTGTAAAATTGTACTCCCTA 58.377 33.333 7.31 0.00 0.00 3.53
571 598 8.623030 TGTTTGTTGTAAAATTGTACTCCCTAC 58.377 33.333 7.31 1.89 0.00 3.18
584 613 9.706691 ATTGTACTCCCTACGTTCATAAATATG 57.293 33.333 0.00 0.00 35.04 1.78
648 677 7.821652 TGAAATGAGTGAACAAACACACTAAA 58.178 30.769 0.00 0.00 45.54 1.85
649 678 8.465999 TGAAATGAGTGAACAAACACACTAAAT 58.534 29.630 0.00 0.00 45.54 1.40
650 679 9.944663 GAAATGAGTGAACAAACACACTAAATA 57.055 29.630 0.00 0.00 45.54 1.40
652 681 9.897744 AATGAGTGAACAAACACACTAAATATG 57.102 29.630 0.00 0.00 45.54 1.78
653 682 7.359595 TGAGTGAACAAACACACTAAATATGC 58.640 34.615 0.00 0.00 45.54 3.14
675 705 7.024345 TGCCCATATACATCTGATTCAGAAT 57.976 36.000 19.73 13.37 44.04 2.40
709 1219 8.018677 AGAACATCTTGTAGTATTTGTGAACG 57.981 34.615 0.00 0.00 0.00 3.95
728 1238 5.768662 TGAACGGAAGGAGTATATACTGAGG 59.231 44.000 20.13 5.92 36.50 3.86
729 1239 5.321934 ACGGAAGGAGTATATACTGAGGT 57.678 43.478 20.13 6.48 36.50 3.85
730 1240 5.703310 ACGGAAGGAGTATATACTGAGGTT 58.297 41.667 20.13 7.56 36.50 3.50
731 1241 6.134754 ACGGAAGGAGTATATACTGAGGTTT 58.865 40.000 20.13 6.83 36.50 3.27
732 1242 6.610425 ACGGAAGGAGTATATACTGAGGTTTT 59.390 38.462 20.13 5.26 36.50 2.43
733 1243 6.924060 CGGAAGGAGTATATACTGAGGTTTTG 59.076 42.308 20.13 0.09 36.50 2.44
734 1244 7.417570 CGGAAGGAGTATATACTGAGGTTTTGT 60.418 40.741 20.13 0.00 36.50 2.83
735 1245 8.921205 GGAAGGAGTATATACTGAGGTTTTGTA 58.079 37.037 20.13 0.00 36.50 2.41
736 1246 9.968870 GAAGGAGTATATACTGAGGTTTTGTAG 57.031 37.037 20.13 0.00 36.50 2.74
741 1251 8.925338 AGTATATACTGAGGTTTTGTAGAAGGG 58.075 37.037 14.71 0.00 34.72 3.95
744 1254 3.328050 ACTGAGGTTTTGTAGAAGGGGAG 59.672 47.826 0.00 0.00 0.00 4.30
754 1264 8.674607 GTTTTGTAGAAGGGGAGTTTGTATATG 58.325 37.037 0.00 0.00 0.00 1.78
786 1299 2.001872 CTATGCAGCAACGACACATCA 58.998 47.619 0.00 0.00 0.00 3.07
797 1310 5.120830 GCAACGACACATCATTTAGAGAACT 59.879 40.000 0.00 0.00 0.00 3.01
813 1326 9.897744 TTTAGAGAACTTGTAATGCAGAAAATG 57.102 29.630 0.00 0.00 0.00 2.32
824 1337 2.253392 CAGAAAATGCTGCGAGGTTC 57.747 50.000 0.00 0.00 0.00 3.62
825 1338 1.536766 CAGAAAATGCTGCGAGGTTCA 59.463 47.619 0.00 0.00 0.00 3.18
826 1339 1.808945 AGAAAATGCTGCGAGGTTCAG 59.191 47.619 0.00 0.00 34.79 3.02
831 1344 4.928398 CTGCGAGGTTCAGCTGAT 57.072 55.556 19.04 1.77 34.83 2.90
832 1345 2.381109 CTGCGAGGTTCAGCTGATG 58.619 57.895 19.04 6.65 34.83 3.07
833 1346 1.703438 CTGCGAGGTTCAGCTGATGC 61.703 60.000 19.04 16.24 40.05 3.91
850 1363 4.910195 TGATGCACTATTGGTTCAGTCTT 58.090 39.130 0.00 0.00 0.00 3.01
913 1440 1.092921 TTGTGGTGTCCGTCACAAGC 61.093 55.000 4.98 0.00 45.40 4.01
946 1481 4.489810 ACATGCAGTTGTTCGTTTTCAAA 58.510 34.783 0.00 0.00 0.00 2.69
981 1516 3.787001 AGCAGAACCCCCGCTAGC 61.787 66.667 4.06 4.06 33.25 3.42
1290 1825 4.465446 CTCCCCTCCTCCCTCGCA 62.465 72.222 0.00 0.00 0.00 5.10
1371 1906 2.041405 CCCTCCCACCTCCTCTCC 60.041 72.222 0.00 0.00 0.00 3.71
1485 2020 0.858139 ACCCCTCCCTCTTCCTCTCT 60.858 60.000 0.00 0.00 0.00 3.10
1507 2042 1.027255 CCTCGAGTCGCTCTCCAAGA 61.027 60.000 12.31 0.00 39.84 3.02
1899 2434 0.815734 CGGATTCTGTCACCTACGGT 59.184 55.000 0.00 0.00 35.78 4.83
1908 2443 1.742268 GTCACCTACGGTACTCTGGTC 59.258 57.143 0.00 0.00 32.11 4.02
1914 2449 0.826256 ACGGTACTCTGGTCACTGCA 60.826 55.000 0.00 0.00 0.00 4.41
1938 2473 0.394899 GCAAGGCAGGCAGGTTATCT 60.395 55.000 0.00 0.00 0.00 1.98
1944 2479 1.207791 CAGGCAGGTTATCTCAGGGT 58.792 55.000 0.00 0.00 0.00 4.34
1947 2482 2.772515 AGGCAGGTTATCTCAGGGTTAC 59.227 50.000 0.00 0.00 0.00 2.50
2056 2591 1.835927 GCTGGAGGAGTGCTTGGAGT 61.836 60.000 0.00 0.00 0.00 3.85
2122 2657 2.627945 TCTACAATGTGGTGATTCGGC 58.372 47.619 0.00 0.00 0.00 5.54
2156 2691 1.149148 GGAGAGACGAAACAAGCCAC 58.851 55.000 0.00 0.00 0.00 5.01
2158 2693 0.387929 AGAGACGAAACAAGCCACGA 59.612 50.000 0.00 0.00 0.00 4.35
2238 2773 1.152756 GGTGACTGGGCTTGTTGGT 60.153 57.895 0.00 0.00 0.00 3.67
2244 2779 2.991540 GGGCTTGTTGGTCAGGGC 60.992 66.667 0.00 0.00 45.42 5.19
2320 2855 1.366366 GCACCACAGTACGGAGTGT 59.634 57.895 1.00 1.00 45.73 3.55
2331 2866 1.129058 ACGGAGTGTTGAAGGACCTT 58.871 50.000 6.40 6.40 42.51 3.50
2341 2876 0.729690 GAAGGACCTTCTCAATGCGC 59.270 55.000 24.55 0.00 37.49 6.09
2349 2884 2.200067 CTTCTCAATGCGCTAGTCAGG 58.800 52.381 9.73 0.00 0.00 3.86
2466 3001 4.397382 CACTGTATGCGAAGAAACATGTG 58.603 43.478 0.00 0.00 0.00 3.21
2481 3016 1.919600 ATGTGAAGGAGGCCTGCTCC 61.920 60.000 28.68 16.95 41.15 4.70
2556 3091 4.142513 GCAAAGCTAATGAAGGGACTGAAG 60.143 45.833 3.72 0.00 40.86 3.02
2605 3140 2.777832 AATCACTGAGAAGGTGAGGC 57.222 50.000 0.00 0.00 45.14 4.70
2733 3268 2.747686 GGGAGGCAGACCGTTCAA 59.252 61.111 0.00 0.00 42.76 2.69
2735 3270 1.671742 GGAGGCAGACCGTTCAAGA 59.328 57.895 0.00 0.00 42.76 3.02
2740 3275 0.723981 GCAGACCGTTCAAGATCAGC 59.276 55.000 0.00 0.00 0.00 4.26
2797 3332 4.905429 TGATGAAGAATTCCCGAGTTGAA 58.095 39.130 0.65 0.00 46.93 2.69
2828 3363 5.461327 AGGATCATAAATGGGCAATGAACT 58.539 37.500 0.00 0.00 33.60 3.01
2848 3383 5.483685 ACTAGTGCACCTTCACTTGATTA 57.516 39.130 14.63 0.00 44.26 1.75
2849 3384 5.238583 ACTAGTGCACCTTCACTTGATTAC 58.761 41.667 14.63 0.00 44.26 1.89
2871 3406 1.993956 TGTTTGTGGGAGTGATTGGG 58.006 50.000 0.00 0.00 0.00 4.12
2895 3430 6.811665 GGTTATGAAGCAACCAATAAGGAAAC 59.188 38.462 0.00 0.00 44.12 2.78
2900 3435 6.041409 TGAAGCAACCAATAAGGAAACATTGA 59.959 34.615 0.00 0.00 41.22 2.57
2943 3478 5.480073 AGGTTTGCAGTATTTCTATTGGCAA 59.520 36.000 0.68 0.68 0.00 4.52
2995 3530 4.624913 TCTGGTCCTATCTGAAGTCCATT 58.375 43.478 0.00 0.00 0.00 3.16
3003 3538 2.507484 TCTGAAGTCCATTTGCCAGTG 58.493 47.619 0.00 0.00 0.00 3.66
3018 3553 3.625764 TGCCAGTGTGTACTTCAGTTTTC 59.374 43.478 0.00 0.00 34.07 2.29
3023 3558 6.526674 CCAGTGTGTACTTCAGTTTTCAAAAC 59.473 38.462 4.72 4.72 34.07 2.43
3039 3574 5.263872 TCAAAACCTTTCAGGGGCTAATA 57.736 39.130 0.00 0.00 40.58 0.98
3048 3583 5.941146 TTCAGGGGCTAATAATATTGGGT 57.059 39.130 0.00 0.00 0.00 4.51
3125 3660 2.171840 GAAGTGAGTCCAGCCTGTCTA 58.828 52.381 0.00 0.00 0.00 2.59
3130 3665 1.552792 GAGTCCAGCCTGTCTAAGCTT 59.447 52.381 3.48 3.48 37.18 3.74
3168 3703 3.385755 AGCTTGTTGCAACTGGAAGATTT 59.614 39.130 28.61 11.31 45.94 2.17
3203 3738 1.865970 GAGCTGAGATTGAAGATGCCG 59.134 52.381 0.00 0.00 0.00 5.69
3337 3874 6.728089 TCACTCTTCATGCTTATCTCTGAT 57.272 37.500 0.00 0.00 0.00 2.90
3362 3899 7.800155 ATACTAAGAGGAGTTACTTACCGAC 57.200 40.000 0.00 0.00 0.00 4.79
3392 3929 7.850193 TGTACGAATATACCTAAACCCACTTT 58.150 34.615 0.00 0.00 0.00 2.66
3410 3947 6.940298 CCCACTTTAAAGTCTGATCTTGGTAA 59.060 38.462 18.00 0.00 37.08 2.85
3414 3951 9.793259 ACTTTAAAGTCTGATCTTGGTAATTGA 57.207 29.630 15.22 0.00 32.86 2.57
3424 3961 8.681486 TGATCTTGGTAATTGATACAGAATGG 57.319 34.615 0.00 0.00 43.62 3.16
3459 3996 6.173339 TGTGATTGAAGAGTTGATACCTTCC 58.827 40.000 0.00 0.00 33.89 3.46
3461 3998 6.314896 GTGATTGAAGAGTTGATACCTTCCTG 59.685 42.308 0.00 0.00 33.89 3.86
3502 4039 9.428097 TCTGATCATGTATTAGTTGTGATATGC 57.572 33.333 0.00 0.00 30.24 3.14
3504 4041 9.783081 TGATCATGTATTAGTTGTGATATGCTT 57.217 29.630 0.00 0.00 30.24 3.91
3585 4123 8.836413 GCAGTTGCTTATGTGGAAGTAAATATA 58.164 33.333 0.00 0.00 33.58 0.86
3621 4159 2.289002 GTCTATTACATGCTGGTGCTGC 59.711 50.000 0.00 0.00 40.48 5.25
3630 4168 3.003394 TGCTGGTGCTGCTATTAACAT 57.997 42.857 0.00 0.00 40.48 2.71
3653 4192 2.887151 ATCAAGTTGAACCCCCTCAG 57.113 50.000 10.14 0.00 0.00 3.35
3657 4196 1.821088 AGTTGAACCCCCTCAGTTCT 58.179 50.000 5.36 0.00 43.28 3.01
3667 4206 6.002653 ACCCCCTCAGTTCTATAACATTTC 57.997 41.667 0.00 0.00 38.12 2.17
3673 4212 9.793252 CCCTCAGTTCTATAACATTTCAATTTG 57.207 33.333 0.00 0.00 38.12 2.32
3674 4213 9.294030 CCTCAGTTCTATAACATTTCAATTTGC 57.706 33.333 0.00 0.00 38.12 3.68
3675 4214 9.844790 CTCAGTTCTATAACATTTCAATTTGCA 57.155 29.630 0.00 0.00 38.12 4.08
3696 4235 6.554419 TGCATGTGCTGTATTGATCTTTAAC 58.446 36.000 6.55 0.00 42.66 2.01
3700 4239 6.237901 TGTGCTGTATTGATCTTTAACCAGT 58.762 36.000 0.00 0.00 0.00 4.00
3712 4251 6.952773 TCTTTAACCAGTTGCACACTAAAT 57.047 33.333 0.00 0.00 32.76 1.40
3742 4281 6.767423 TGAGCTTATCTACTTAAATGCATGCA 59.233 34.615 25.04 25.04 0.00 3.96
3783 4322 4.990257 CAGCTATGCTTATGTGCACTTTT 58.010 39.130 19.41 5.59 46.33 2.27
3788 4327 5.648178 ATGCTTATGTGCACTTTTCATCA 57.352 34.783 19.41 7.70 46.33 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.254178 TGTTAATGGTATTGGTAACTACAACG 57.746 34.615 0.00 0.00 37.61 4.10
112 113 3.641436 TCTCCAGCTTTATCGCCTCATAA 59.359 43.478 0.00 0.00 0.00 1.90
115 116 1.410517 CTCTCCAGCTTTATCGCCTCA 59.589 52.381 0.00 0.00 0.00 3.86
121 122 7.864882 GCATTATTTTTCCTCTCCAGCTTTATC 59.135 37.037 0.00 0.00 0.00 1.75
127 128 4.989279 TGCATTATTTTTCCTCTCCAGC 57.011 40.909 0.00 0.00 0.00 4.85
175 176 2.328099 GGCGCAAGTCTTCACTGGG 61.328 63.158 10.83 0.00 40.30 4.45
198 199 1.672898 GTACACCGGGGCTGTAACA 59.327 57.895 1.73 0.00 0.00 2.41
214 215 1.308047 CATGGCCTGCTAATTGCGTA 58.692 50.000 3.32 0.00 46.63 4.42
543 545 7.122948 AGGGAGTACAATTTTACAACAAACACA 59.877 33.333 4.66 0.00 0.00 3.72
570 597 9.173021 TCCAAAACATCTCATATTTATGAACGT 57.827 29.630 2.18 0.00 41.72 3.99
609 638 8.534333 TCACTCATTTCAGTTTGTATGTAGTC 57.466 34.615 0.00 0.00 0.00 2.59
612 641 8.669946 TGTTCACTCATTTCAGTTTGTATGTA 57.330 30.769 0.00 0.00 0.00 2.29
618 647 6.585702 TGTGTTTGTTCACTCATTTCAGTTTG 59.414 34.615 0.00 0.00 38.90 2.93
648 677 8.328055 TCTGAATCAGATGTATATGGGCATAT 57.672 34.615 9.18 0.00 35.39 1.78
649 678 7.738437 TCTGAATCAGATGTATATGGGCATA 57.262 36.000 9.18 0.00 35.39 3.14
650 679 6.631763 TCTGAATCAGATGTATATGGGCAT 57.368 37.500 9.18 0.00 35.39 4.40
651 680 6.438186 TTCTGAATCAGATGTATATGGGCA 57.562 37.500 14.31 0.00 40.39 5.36
652 681 9.453572 TTTATTCTGAATCAGATGTATATGGGC 57.546 33.333 14.31 0.00 40.39 5.36
695 725 5.733620 ACTCCTTCCGTTCACAAATACTA 57.266 39.130 0.00 0.00 0.00 1.82
709 1219 7.793036 ACAAAACCTCAGTATATACTCCTTCC 58.207 38.462 12.62 0.00 33.46 3.46
728 1238 8.674607 CATATACAAACTCCCCTTCTACAAAAC 58.325 37.037 0.00 0.00 0.00 2.43
729 1239 7.338449 GCATATACAAACTCCCCTTCTACAAAA 59.662 37.037 0.00 0.00 0.00 2.44
730 1240 6.826741 GCATATACAAACTCCCCTTCTACAAA 59.173 38.462 0.00 0.00 0.00 2.83
731 1241 6.069905 TGCATATACAAACTCCCCTTCTACAA 60.070 38.462 0.00 0.00 0.00 2.41
732 1242 5.427157 TGCATATACAAACTCCCCTTCTACA 59.573 40.000 0.00 0.00 0.00 2.74
733 1243 5.925509 TGCATATACAAACTCCCCTTCTAC 58.074 41.667 0.00 0.00 0.00 2.59
734 1244 6.157994 AGTTGCATATACAAACTCCCCTTCTA 59.842 38.462 0.00 0.00 0.00 2.10
735 1245 5.044846 AGTTGCATATACAAACTCCCCTTCT 60.045 40.000 0.00 0.00 0.00 2.85
736 1246 5.066505 CAGTTGCATATACAAACTCCCCTTC 59.933 44.000 0.00 0.00 0.00 3.46
741 1251 6.546395 CAACTCAGTTGCATATACAAACTCC 58.454 40.000 4.15 0.00 36.73 3.85
780 1293 8.453320 TGCATTACAAGTTCTCTAAATGATGTG 58.547 33.333 0.00 0.00 0.00 3.21
814 1327 1.703438 GCATCAGCTGAACCTCGCAG 61.703 60.000 22.50 4.66 37.91 5.18
815 1328 1.742880 GCATCAGCTGAACCTCGCA 60.743 57.895 22.50 0.00 37.91 5.10
816 1329 1.742880 TGCATCAGCTGAACCTCGC 60.743 57.895 22.50 17.64 42.74 5.03
817 1330 0.390866 AGTGCATCAGCTGAACCTCG 60.391 55.000 22.50 8.20 42.74 4.63
818 1331 2.680312 TAGTGCATCAGCTGAACCTC 57.320 50.000 22.50 14.57 42.74 3.85
819 1332 3.276857 CAATAGTGCATCAGCTGAACCT 58.723 45.455 22.50 15.44 42.74 3.50
820 1333 2.357009 CCAATAGTGCATCAGCTGAACC 59.643 50.000 22.50 14.82 42.74 3.62
821 1334 3.012518 ACCAATAGTGCATCAGCTGAAC 58.987 45.455 22.50 14.77 42.74 3.18
822 1335 3.354948 ACCAATAGTGCATCAGCTGAA 57.645 42.857 22.50 2.71 42.74 3.02
823 1336 3.273434 GAACCAATAGTGCATCAGCTGA 58.727 45.455 20.79 20.79 42.74 4.26
824 1337 3.011818 TGAACCAATAGTGCATCAGCTG 58.988 45.455 7.63 7.63 42.74 4.24
825 1338 3.276857 CTGAACCAATAGTGCATCAGCT 58.723 45.455 9.50 0.00 42.74 4.24
826 1339 3.012518 ACTGAACCAATAGTGCATCAGC 58.987 45.455 17.82 0.00 38.51 4.26
827 1340 4.511527 AGACTGAACCAATAGTGCATCAG 58.488 43.478 16.85 16.85 39.75 2.90
828 1341 4.558226 AGACTGAACCAATAGTGCATCA 57.442 40.909 0.00 0.00 31.77 3.07
829 1342 4.937620 TCAAGACTGAACCAATAGTGCATC 59.062 41.667 0.00 0.00 31.77 3.91
830 1343 4.910195 TCAAGACTGAACCAATAGTGCAT 58.090 39.130 0.00 0.00 31.77 3.96
831 1344 4.350368 TCAAGACTGAACCAATAGTGCA 57.650 40.909 0.00 0.00 31.13 4.57
832 1345 4.154918 CCTTCAAGACTGAACCAATAGTGC 59.845 45.833 0.00 0.00 36.62 4.40
833 1346 4.154918 GCCTTCAAGACTGAACCAATAGTG 59.845 45.833 0.00 0.00 36.62 2.74
850 1363 3.329542 GATCAGTGGGCCGCCTTCA 62.330 63.158 14.73 0.00 0.00 3.02
946 1481 1.610102 GCTGATCTGTTCTGTGTGCCT 60.610 52.381 1.27 0.00 0.00 4.75
1371 1906 4.292178 GGCGAGAGGATGGAGGCG 62.292 72.222 0.00 0.00 0.00 5.52
1485 2020 1.153329 GGAGAGCGACTCGAGGAGA 60.153 63.158 18.41 0.00 45.76 3.71
1588 2123 2.047274 GCACCAGCCGTAGAGCAA 60.047 61.111 0.00 0.00 34.23 3.91
1713 2248 3.744719 TCCTCGAACCTGCCGTCG 61.745 66.667 0.00 0.00 0.00 5.12
1899 2434 2.813754 GCAAAATGCAGTGACCAGAGTA 59.186 45.455 0.00 0.00 44.26 2.59
1914 2449 1.123246 ACCTGCCTGCCTTGCAAAAT 61.123 50.000 0.00 0.00 38.41 1.82
1926 2461 1.972588 AACCCTGAGATAACCTGCCT 58.027 50.000 0.00 0.00 0.00 4.75
1938 2473 2.298163 GTCCAAGAACTCGTAACCCTGA 59.702 50.000 0.00 0.00 0.00 3.86
1944 2479 3.576982 ACATGGAGTCCAAGAACTCGTAA 59.423 43.478 20.95 0.00 45.45 3.18
1947 2482 2.611518 GACATGGAGTCCAAGAACTCG 58.388 52.381 20.95 4.40 45.45 4.18
1994 2529 3.315191 CACAAAGAACCCAAGGTACACTG 59.685 47.826 0.00 0.00 33.12 3.66
2056 2591 2.022625 ACTCCCTCATCCTCTCCATCAA 60.023 50.000 0.00 0.00 0.00 2.57
2099 2634 4.997395 GCCGAATCACCACATTGTAGATAT 59.003 41.667 0.00 0.00 0.00 1.63
2122 2657 1.403679 CTCTCCGAGCTTACAGGACAG 59.596 57.143 0.00 0.00 0.00 3.51
2156 2691 1.660607 CCATCTCGTTCCACAATGTCG 59.339 52.381 0.00 0.00 0.00 4.35
2158 2693 2.567169 TCTCCATCTCGTTCCACAATGT 59.433 45.455 0.00 0.00 0.00 2.71
2264 2799 3.377172 CCCGACCATGTCCTTGAAATAAC 59.623 47.826 0.00 0.00 0.00 1.89
2320 2855 2.426522 CGCATTGAGAAGGTCCTTCAA 58.573 47.619 29.36 19.01 42.37 2.69
2331 2866 0.461548 CCCTGACTAGCGCATTGAGA 59.538 55.000 11.47 0.00 0.00 3.27
2341 2876 5.659463 CTCAAGTTTCTCATCCCTGACTAG 58.341 45.833 0.00 0.00 0.00 2.57
2349 2884 2.816087 TGCAAGCTCAAGTTTCTCATCC 59.184 45.455 0.00 0.00 0.00 3.51
2372 2907 0.983467 AATGCAACCCCAAACATCCC 59.017 50.000 0.00 0.00 0.00 3.85
2481 3016 2.543012 CTCGAGCATGTCCAAGCAATAG 59.457 50.000 0.00 0.00 0.00 1.73
2556 3091 5.237344 AGCAATCTGTCTGTTGTACAGTTTC 59.763 40.000 6.71 1.18 46.03 2.78
2605 3140 1.039785 TGTCTCTCCTCCGCCATCAG 61.040 60.000 0.00 0.00 0.00 2.90
2733 3268 3.307506 AGCATGTTCTCTAGGCTGATCT 58.692 45.455 0.00 0.00 32.76 2.75
2740 3275 3.902881 AAGGTCAGCATGTTCTCTAGG 57.097 47.619 0.00 0.00 37.40 3.02
2797 3332 9.605951 ATTGCCCATTTATGATCCTAGTTTAAT 57.394 29.630 0.00 0.00 0.00 1.40
2815 3350 2.094675 GTGCACTAGTTCATTGCCCAT 58.905 47.619 10.32 0.00 35.26 4.00
2848 3383 3.321682 CCAATCACTCCCACAAACAATGT 59.678 43.478 0.00 0.00 45.34 2.71
2849 3384 3.306225 CCCAATCACTCCCACAAACAATG 60.306 47.826 0.00 0.00 0.00 2.82
2871 3406 7.375053 TGTTTCCTTATTGGTTGCTTCATAAC 58.625 34.615 0.00 0.00 37.07 1.89
2895 3430 4.804139 GCTCCATTTTCAGCAAGATCAATG 59.196 41.667 0.00 0.00 35.56 2.82
2900 3435 2.758979 CCTGCTCCATTTTCAGCAAGAT 59.241 45.455 0.00 0.00 44.98 2.40
2937 3472 6.038603 GCTCAAGTATCAATATCAGTTGCCAA 59.961 38.462 0.00 0.00 0.00 4.52
2939 3474 5.049129 GGCTCAAGTATCAATATCAGTTGCC 60.049 44.000 0.00 0.00 0.00 4.52
2940 3475 5.528690 TGGCTCAAGTATCAATATCAGTTGC 59.471 40.000 0.00 0.00 0.00 4.17
2969 3504 2.763448 ACTTCAGATAGGACCAGAGTGC 59.237 50.000 0.00 0.00 33.83 4.40
2975 3510 4.626287 GCAAATGGACTTCAGATAGGACCA 60.626 45.833 0.00 0.00 33.01 4.02
2977 3512 3.879892 GGCAAATGGACTTCAGATAGGAC 59.120 47.826 0.00 0.00 0.00 3.85
2995 3530 3.275617 AACTGAAGTACACACTGGCAA 57.724 42.857 0.00 0.00 34.36 4.52
3003 3538 7.810759 TGAAAGGTTTTGAAAACTGAAGTACAC 59.189 33.333 18.95 1.04 35.78 2.90
3039 3574 3.245586 TGGCACTGAAAGGACCCAATATT 60.246 43.478 0.00 0.00 39.30 1.28
3048 3583 4.481195 GCACTGGCACTGAAAGGA 57.519 55.556 0.00 0.00 39.30 3.36
3091 3626 3.449018 ACTCACTTCCAGCCATAGTAGTG 59.551 47.826 0.00 0.00 35.51 2.74
3125 3660 3.160679 AGTTCAGGCATAACCAAGCTT 57.839 42.857 0.00 0.00 43.14 3.74
3130 3665 3.009033 ACAAGCTAGTTCAGGCATAACCA 59.991 43.478 0.00 0.00 43.14 3.67
3224 3759 5.431420 TTGTTACTTGTGTAGTTGGCATG 57.569 39.130 0.00 0.00 38.33 4.06
3225 3760 6.096282 AGTTTTGTTACTTGTGTAGTTGGCAT 59.904 34.615 0.00 0.00 38.33 4.40
3226 3761 5.416326 AGTTTTGTTACTTGTGTAGTTGGCA 59.584 36.000 0.00 0.00 38.33 4.92
3227 3762 5.886992 AGTTTTGTTACTTGTGTAGTTGGC 58.113 37.500 0.00 0.00 38.33 4.52
3228 3763 7.079182 TGAGTTTTGTTACTTGTGTAGTTGG 57.921 36.000 0.00 0.00 38.33 3.77
3310 3847 7.879677 TCAGAGATAAGCATGAAGAGTGAAAAA 59.120 33.333 0.00 0.00 0.00 1.94
3311 3848 7.389232 TCAGAGATAAGCATGAAGAGTGAAAA 58.611 34.615 0.00 0.00 0.00 2.29
3337 3874 8.709308 AGTCGGTAAGTAACTCCTCTTAGTATA 58.291 37.037 0.00 0.00 0.00 1.47
3348 3885 7.464358 TCGTACAATAAGTCGGTAAGTAACTC 58.536 38.462 0.00 0.00 0.00 3.01
3356 3893 8.621532 AGGTATATTCGTACAATAAGTCGGTA 57.378 34.615 0.00 0.00 0.00 4.02
3357 3894 7.516198 AGGTATATTCGTACAATAAGTCGGT 57.484 36.000 0.00 0.00 0.00 4.69
3358 3895 9.897744 TTTAGGTATATTCGTACAATAAGTCGG 57.102 33.333 0.00 0.00 0.00 4.79
3362 3899 9.985730 TGGGTTTAGGTATATTCGTACAATAAG 57.014 33.333 0.00 0.00 0.00 1.73
3410 3947 8.896744 CAGTGAACATAACCATTCTGTATCAAT 58.103 33.333 0.00 0.00 0.00 2.57
3414 3951 7.394016 TCACAGTGAACATAACCATTCTGTAT 58.606 34.615 0.00 0.00 34.29 2.29
3424 3961 7.426929 ACTCTTCAATCACAGTGAACATAAC 57.573 36.000 7.50 0.00 31.78 1.89
3630 4168 5.068215 TGAGGGGGTTCAACTTGATTAAA 57.932 39.130 0.00 0.00 0.00 1.52
3644 4183 5.491078 TGAAATGTTATAGAACTGAGGGGGT 59.509 40.000 1.39 0.00 36.45 4.95
3657 4196 7.818446 ACAGCACATGCAAATTGAAATGTTATA 59.182 29.630 6.64 0.00 45.16 0.98
3667 4206 6.040247 AGATCAATACAGCACATGCAAATTG 58.960 36.000 6.64 11.78 45.16 2.32
3673 4212 5.973565 GGTTAAAGATCAATACAGCACATGC 59.026 40.000 0.00 0.00 42.49 4.06
3674 4213 7.087409 TGGTTAAAGATCAATACAGCACATG 57.913 36.000 0.00 0.00 0.00 3.21
3675 4214 6.886459 ACTGGTTAAAGATCAATACAGCACAT 59.114 34.615 0.00 0.00 0.00 3.21
3676 4215 6.237901 ACTGGTTAAAGATCAATACAGCACA 58.762 36.000 0.00 0.00 0.00 4.57
3696 4235 5.830912 TCAAAAGATTTAGTGTGCAACTGG 58.169 37.500 10.59 0.00 40.26 4.00
3700 4239 5.772825 AGCTCAAAAGATTTAGTGTGCAA 57.227 34.783 0.00 0.00 33.94 4.08
3712 4251 9.448438 TGCATTTAAGTAGATAAGCTCAAAAGA 57.552 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.