Multiple sequence alignment - TraesCS3D01G337500

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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 TraesCS3D01G337500 chr3D 100.000 2984 0 0 1 2984 449539751 449542734 0.000000e+00 5511.0
1 TraesCS3D01G337500 chr3D 86.264 728 73 16 1282 1996 449737749 449738462 0.000000e+00 765.0
2 TraesCS3D01G337500 chr3D 85.249 583 50 21 717 1268 449737129 449737706 4.320000e-158 568.0
3 TraesCS3D01G337500 chr3D 75.585 299 48 16 54 330 486125388 486125093 1.120000e-24 124.0
4 TraesCS3D01G337500 chr3D 76.132 243 51 7 2717 2955 126939119 126938880 1.450000e-23 121.0
5 TraesCS3D01G337500 chr3D 87.755 98 12 0 401 498 129015140 129015043 6.760000e-22 115.0
6 TraesCS3D01G337500 chr3D 82.707 133 19 4 224 353 512989362 512989231 6.760000e-22 115.0
7 TraesCS3D01G337500 chr3D 86.735 98 13 0 401 498 129015296 129015199 3.140000e-20 110.0
8 TraesCS3D01G337500 chr3A 90.172 2503 141 40 520 2984 593176276 593178711 0.000000e+00 3162.0
9 TraesCS3D01G337500 chr3A 92.432 555 39 3 1 553 593175701 593176254 0.000000e+00 789.0
10 TraesCS3D01G337500 chr3A 86.370 741 62 18 1282 1996 593340244 593340971 0.000000e+00 773.0
11 TraesCS3D01G337500 chr3A 87.608 581 44 19 708 1265 593339621 593340196 0.000000e+00 649.0
12 TraesCS3D01G337500 chr3A 90.000 50 3 2 717 764 593107339 593107388 2.480000e-06 63.9
13 TraesCS3D01G337500 chr3B 91.678 1538 80 24 787 2313 590623404 590624904 0.000000e+00 2087.0
14 TraesCS3D01G337500 chr3B 86.058 789 72 21 1282 2049 591365380 591366151 0.000000e+00 813.0
15 TraesCS3D01G337500 chr3B 87.456 574 46 17 717 1268 591364761 591365330 3.240000e-179 638.0
16 TraesCS3D01G337500 chr3B 83.826 507 58 8 3 505 590622368 590622854 7.540000e-126 460.0
17 TraesCS3D01G337500 chr3B 89.744 234 22 2 563 794 590622999 590623232 6.250000e-77 298.0
18 TraesCS3D01G337500 chr3B 76.562 384 66 7 1 360 423871428 423871811 3.930000e-44 189.0
19 TraesCS3D01G337500 chr5A 87.395 238 30 0 2718 2955 691841480 691841243 1.050000e-69 274.0
20 TraesCS3D01G337500 chr5D 79.538 303 40 15 221 508 332788545 332788250 2.350000e-46 196.0
21 TraesCS3D01G337500 chr4D 93.258 89 6 0 418 506 221244730 221244818 6.710000e-27 132.0
22 TraesCS3D01G337500 chr4D 89.011 91 10 0 416 506 67806296 67806206 2.430000e-21 113.0
23 TraesCS3D01G337500 chr4B 89.423 104 11 0 401 504 100330217 100330114 6.710000e-27 132.0
24 TraesCS3D01G337500 chr2B 85.039 127 16 1 230 353 499618119 499617993 3.120000e-25 126.0
25 TraesCS3D01G337500 chr2B 77.953 127 25 1 232 355 591134416 591134290 3.190000e-10 76.8
26 TraesCS3D01G337500 chr6B 84.496 129 17 1 230 355 509649460 509649332 1.120000e-24 124.0
27 TraesCS3D01G337500 chr6B 77.857 140 28 1 221 357 294007477 294007616 1.910000e-12 84.2
28 TraesCS3D01G337500 chr1A 86.239 109 11 4 401 506 419491341 419491234 6.760000e-22 115.0
29 TraesCS3D01G337500 chr2D 81.159 138 22 2 221 355 572059901 572059765 1.130000e-19 108.0
30 TraesCS3D01G337500 chr1D 78.431 153 24 5 28 176 402755093 402754946 1.140000e-14 91.6
31 TraesCS3D01G337500 chr4A 92.857 56 4 0 2900 2955 484370823 484370878 6.860000e-12 82.4


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 TraesCS3D01G337500 chr3D 449539751 449542734 2983 False 5511.000000 5511 100.0000 1 2984 1 chr3D.!!$F1 2983
1 TraesCS3D01G337500 chr3D 449737129 449738462 1333 False 666.500000 765 85.7565 717 1996 2 chr3D.!!$F2 1279
2 TraesCS3D01G337500 chr3A 593175701 593178711 3010 False 1975.500000 3162 91.3020 1 2984 2 chr3A.!!$F2 2983
3 TraesCS3D01G337500 chr3A 593339621 593340971 1350 False 711.000000 773 86.9890 708 1996 2 chr3A.!!$F3 1288
4 TraesCS3D01G337500 chr3B 590622368 590624904 2536 False 948.333333 2087 88.4160 3 2313 3 chr3B.!!$F2 2310
5 TraesCS3D01G337500 chr3B 591364761 591366151 1390 False 725.500000 813 86.7570 717 2049 2 chr3B.!!$F3 1332

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
699 793 0.116143 TGGGAGGAAATTTGGGGGTG 59.884 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2500 0.106708 TATCATGCTCCCGACAAGCC 59.893 55.0 0.0 0.0 39.05 4.35 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
82 87 3.443925 CAGCTCGCCGAGGAGTGA 61.444 66.667 16.95 0.00 36.41 3.41
125 130 4.980805 GGGAGCACGGCGACACAA 62.981 66.667 16.62 0.00 0.00 3.33
403 409 2.674380 GGGTGCCCTGCAGTTGAG 60.674 66.667 13.81 0.00 40.08 3.02
486 492 2.154854 TGCGCTGAAGCATATACCTC 57.845 50.000 9.73 0.00 42.92 3.85
514 535 0.617535 ATGACAGTCCGGACATGGGA 60.618 55.000 35.00 19.33 0.00 4.37
518 539 1.165270 CAGTCCGGACATGGGAAAAC 58.835 55.000 35.00 5.89 34.80 2.43
572 665 5.970317 AGTTTTACCTTAATCCGGTTTGG 57.030 39.130 8.06 4.23 35.98 3.28
660 754 1.536072 GCATCTATGTTCGCGGACTGA 60.536 52.381 20.15 14.22 0.00 3.41
677 771 1.006805 GATCCCGTCGGCTGATGAG 60.007 63.158 16.68 2.68 32.56 2.90
681 775 0.319040 CCCGTCGGCTGATGAGTATG 60.319 60.000 16.68 0.00 32.56 2.39
693 787 5.009410 GCTGATGAGTATGGGAGGAAATTTG 59.991 44.000 0.00 0.00 0.00 2.32
698 792 1.101195 ATGGGAGGAAATTTGGGGGT 58.899 50.000 0.00 0.00 0.00 4.95
699 793 0.116143 TGGGAGGAAATTTGGGGGTG 59.884 55.000 0.00 0.00 0.00 4.61
700 794 0.411848 GGGAGGAAATTTGGGGGTGA 59.588 55.000 0.00 0.00 0.00 4.02
701 795 1.619704 GGGAGGAAATTTGGGGGTGAG 60.620 57.143 0.00 0.00 0.00 3.51
702 796 1.077169 GGAGGAAATTTGGGGGTGAGT 59.923 52.381 0.00 0.00 0.00 3.41
703 797 2.171003 GAGGAAATTTGGGGGTGAGTG 58.829 52.381 0.00 0.00 0.00 3.51
704 798 0.608130 GGAAATTTGGGGGTGAGTGC 59.392 55.000 0.00 0.00 0.00 4.40
706 800 2.556559 GGAAATTTGGGGGTGAGTGCTA 60.557 50.000 0.00 0.00 0.00 3.49
896 1196 3.186047 CACGACCCGCCGATTCAC 61.186 66.667 0.00 0.00 0.00 3.18
1239 1548 0.841961 CATCCTGCCATCTTCCCTCA 59.158 55.000 0.00 0.00 0.00 3.86
1334 1686 0.604073 TTGACAGGTTGCCGTCGATA 59.396 50.000 0.00 0.00 32.65 2.92
1510 1872 0.455633 CGGCAAGCTTGTTGATCAGC 60.456 55.000 26.55 10.26 0.00 4.26
1735 2104 1.959226 GGCTCAAACGCTCGTGGAA 60.959 57.895 0.00 0.00 0.00 3.53
2094 2485 0.902531 ACCGTGTACCTAAGCATGCT 59.097 50.000 16.30 16.30 0.00 3.79
2109 2500 1.762522 ATGCTATGTCGCCAGAGGGG 61.763 60.000 0.00 0.00 40.85 4.79
2130 2521 1.473257 GCTTGTCGGGAGCATGATACA 60.473 52.381 0.00 0.00 39.89 2.29
2138 2529 4.021981 TCGGGAGCATGATACATAAGACAG 60.022 45.833 0.00 0.00 0.00 3.51
2143 2534 4.584743 AGCATGATACATAAGACAGGTCGA 59.415 41.667 0.00 0.00 34.09 4.20
2163 2554 3.462021 GATGAGGTCTTTTGAGGATCCG 58.538 50.000 5.98 0.00 0.00 4.18
2167 2558 4.019321 TGAGGTCTTTTGAGGATCCGAAAT 60.019 41.667 5.98 0.00 0.00 2.17
2179 2570 1.720805 TCCGAAATGTCACATGTCCG 58.279 50.000 2.07 1.51 0.00 4.79
2183 2574 2.009774 GAAATGTCACATGTCCGGGAG 58.990 52.381 0.00 0.00 0.00 4.30
2204 2595 2.219325 GACTCTGTCAGGGCACGAGG 62.219 65.000 0.00 0.00 32.09 4.63
2264 2655 4.323028 GGGCCTTGAGATTCGATATCATCA 60.323 45.833 0.84 0.00 29.60 3.07
2269 2660 7.571026 CCTTGAGATTCGATATCATCAAACAC 58.429 38.462 3.12 0.00 29.60 3.32
2272 2663 6.978080 TGAGATTCGATATCATCAAACACGAA 59.022 34.615 3.12 0.00 41.15 3.85
2273 2664 7.168135 TGAGATTCGATATCATCAAACACGAAG 59.832 37.037 3.12 0.00 40.48 3.79
2274 2665 7.203218 AGATTCGATATCATCAAACACGAAGA 58.797 34.615 3.12 0.00 40.48 2.87
2275 2666 7.706607 AGATTCGATATCATCAAACACGAAGAA 59.293 33.333 3.12 0.00 40.48 2.52
2276 2667 6.569228 TCGATATCATCAAACACGAAGAAC 57.431 37.500 3.12 0.00 0.00 3.01
2277 2668 6.096695 TCGATATCATCAAACACGAAGAACA 58.903 36.000 3.12 0.00 0.00 3.18
2278 2669 6.588373 TCGATATCATCAAACACGAAGAACAA 59.412 34.615 3.12 0.00 0.00 2.83
2279 2670 6.678663 CGATATCATCAAACACGAAGAACAAC 59.321 38.462 3.12 0.00 0.00 3.32
2280 2671 4.190304 TCATCAAACACGAAGAACAACG 57.810 40.909 0.00 0.00 0.00 4.10
2281 2672 3.866327 TCATCAAACACGAAGAACAACGA 59.134 39.130 0.00 0.00 0.00 3.85
2295 2686 2.740452 ACAACGAAGAACGAGGAAGTC 58.260 47.619 0.00 0.00 45.77 3.01
2328 2719 8.842942 AAACGAAGAATGAGAAAGAAGAAAAC 57.157 30.769 0.00 0.00 0.00 2.43
2397 2788 4.759516 ATGTGGTGTTTAATTGGTCGTC 57.240 40.909 0.00 0.00 0.00 4.20
2398 2789 3.542648 TGTGGTGTTTAATTGGTCGTCA 58.457 40.909 0.00 0.00 0.00 4.35
2407 2798 6.535150 TGTTTAATTGGTCGTCATCTCTCATC 59.465 38.462 0.00 0.00 0.00 2.92
2411 2802 5.444663 TTGGTCGTCATCTCTCATCTATG 57.555 43.478 0.00 0.00 0.00 2.23
2416 2807 6.372937 GGTCGTCATCTCTCATCTATGTATGA 59.627 42.308 0.00 0.00 34.72 2.15
2436 2827 9.078990 TGTATGAGATAGATGGACTTTTCGTAT 57.921 33.333 0.00 0.00 0.00 3.06
2466 2858 8.600449 AAAAGACTCAAAAACATGTTCAACAA 57.400 26.923 12.39 0.00 0.00 2.83
2499 2891 5.986501 AGACTAACTCGGACAGAAAATCT 57.013 39.130 0.00 0.00 0.00 2.40
2500 2892 7.282675 CCTAGACTAACTCGGACAGAAAATCTA 59.717 40.741 0.00 0.00 33.87 1.98
2503 2895 6.388278 ACTAACTCGGACAGAAAATCTACAC 58.612 40.000 0.00 0.00 0.00 2.90
2505 2897 5.407407 ACTCGGACAGAAAATCTACACAT 57.593 39.130 0.00 0.00 0.00 3.21
2510 2902 8.420374 TCGGACAGAAAATCTACACATAAATC 57.580 34.615 0.00 0.00 0.00 2.17
2511 2903 7.222031 TCGGACAGAAAATCTACACATAAATCG 59.778 37.037 0.00 0.00 0.00 3.34
2512 2904 7.516785 CGGACAGAAAATCTACACATAAATCGG 60.517 40.741 0.00 0.00 0.00 4.18
2513 2905 7.494625 GGACAGAAAATCTACACATAAATCGGA 59.505 37.037 0.00 0.00 0.00 4.55
2514 2906 8.197988 ACAGAAAATCTACACATAAATCGGAC 57.802 34.615 0.00 0.00 0.00 4.79
2515 2907 7.822334 ACAGAAAATCTACACATAAATCGGACA 59.178 33.333 0.00 0.00 0.00 4.02
2516 2908 8.830580 CAGAAAATCTACACATAAATCGGACAT 58.169 33.333 0.00 0.00 0.00 3.06
2532 2924 2.494059 GACATATCGGACATGTTGGGG 58.506 52.381 3.05 0.00 36.76 4.96
2584 2988 4.181578 AGTCGGACATTTAAGTCGGAATG 58.818 43.478 11.27 0.00 45.46 2.67
2599 3003 4.753107 GTCGGAATGTCCAACTTGACTTTA 59.247 41.667 0.00 0.00 35.91 1.85
2602 3006 5.181245 CGGAATGTCCAACTTGACTTTACAT 59.819 40.000 0.00 0.00 35.91 2.29
2615 3022 6.174720 TGACTTTACATTTGTCTCTGACCT 57.825 37.500 0.00 0.00 0.00 3.85
2653 3060 4.485163 GTTGTATGCCACTTTGGATTGAC 58.515 43.478 0.00 0.00 40.96 3.18
2665 3072 9.703892 CCACTTTGGATTGACATAATACAAAAA 57.296 29.630 10.28 0.00 40.96 1.94
2685 3092 1.003866 AGCAAAGTTGTTCGCTTCGAC 60.004 47.619 0.00 0.00 34.89 4.20
2730 3147 8.740123 TGAGGACTTTTGTGTTGAGTAAATAA 57.260 30.769 0.00 0.00 0.00 1.40
2778 3195 7.620491 TGCAGGAAATAATTATGGATATGGCAT 59.380 33.333 4.88 4.88 0.00 4.40
2782 3199 9.807649 GGAAATAATTATGGATATGGCATTGAC 57.192 33.333 4.78 0.00 0.00 3.18
2795 3212 3.936453 TGGCATTGACAGTATTAACGACC 59.064 43.478 0.00 0.00 0.00 4.79
2800 3217 7.198390 GCATTGACAGTATTAACGACCTACTA 58.802 38.462 0.00 0.00 0.00 1.82
2819 3236 8.148351 ACCTACTAATTGCGATCTAAATAAGCA 58.852 33.333 0.00 0.00 35.90 3.91
2821 3238 6.877855 ACTAATTGCGATCTAAATAAGCACG 58.122 36.000 0.00 0.00 37.57 5.34
2857 3274 2.748605 AGAAGCATCTACGCACATAGC 58.251 47.619 0.00 0.00 35.09 2.97
2858 3275 2.363680 AGAAGCATCTACGCACATAGCT 59.636 45.455 0.00 0.00 35.92 3.32
2859 3276 3.570125 AGAAGCATCTACGCACATAGCTA 59.430 43.478 0.00 0.00 35.92 3.32
2861 3278 2.887783 AGCATCTACGCACATAGCTAGT 59.112 45.455 0.00 0.00 42.61 2.57
2863 3280 3.827625 CATCTACGCACATAGCTAGTCC 58.172 50.000 0.00 0.00 42.61 3.85
2865 3282 2.879026 TCTACGCACATAGCTAGTCCTG 59.121 50.000 0.00 0.00 42.61 3.86
2866 3283 1.475403 ACGCACATAGCTAGTCCTGT 58.525 50.000 0.00 0.00 42.61 4.00
2867 3284 1.825474 ACGCACATAGCTAGTCCTGTT 59.175 47.619 0.00 0.00 42.61 3.16
2868 3285 3.021695 ACGCACATAGCTAGTCCTGTTA 58.978 45.455 0.00 0.00 42.61 2.41
2869 3286 3.446161 ACGCACATAGCTAGTCCTGTTAA 59.554 43.478 0.00 0.00 42.61 2.01
2870 3287 4.045104 CGCACATAGCTAGTCCTGTTAAG 58.955 47.826 0.00 0.00 42.61 1.85
2871 3288 4.202020 CGCACATAGCTAGTCCTGTTAAGA 60.202 45.833 0.00 0.00 42.61 2.10
2872 3289 5.044558 GCACATAGCTAGTCCTGTTAAGAC 58.955 45.833 0.00 0.00 41.15 3.01
2873 3290 5.394224 GCACATAGCTAGTCCTGTTAAGACA 60.394 44.000 0.00 0.00 41.15 3.41
2874 3291 7.172480 GCACATAGCTAGTCCTGTTAAGACAG 61.172 46.154 0.00 0.00 45.51 3.51
2900 3317 4.503714 AACAGGAACGGGATAATCATGT 57.496 40.909 0.00 0.00 39.50 3.21
2909 3326 6.697641 ACGGGATAATCATGTTATACCCTT 57.302 37.500 17.05 11.93 32.79 3.95
2910 3327 6.708285 ACGGGATAATCATGTTATACCCTTC 58.292 40.000 17.05 2.04 32.79 3.46
2935 3352 2.358615 CAGTTGGCCGTAGCAGCA 60.359 61.111 0.00 0.00 42.56 4.41
2961 3378 4.475135 GGCGGCCTCCTTCTGGTC 62.475 72.222 12.87 0.00 34.23 4.02
2967 3384 1.984570 CCTCCTTCTGGTCAGCGGA 60.985 63.158 8.01 8.01 34.23 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 87 1.826024 CCGGCCTAGAGCAAGTCAT 59.174 57.895 0.00 0.00 46.50 3.06
125 130 3.818210 TCGTCCACAATAGCAATGTTGTT 59.182 39.130 0.00 0.00 36.48 2.83
157 162 4.509737 GCACGGGAGGAGCGGTAC 62.510 72.222 0.00 0.00 0.00 3.34
195 200 0.309612 ACGGTTCCGCAAATGTTGAC 59.690 50.000 11.32 0.00 0.00 3.18
271 276 6.464222 TGTTCTACTTTTCTTCGATGATGGT 58.536 36.000 1.37 4.66 0.00 3.55
374 380 2.272471 GCACCCTTCCCCACTAGC 59.728 66.667 0.00 0.00 0.00 3.42
486 492 1.222936 GGACTGTCATGAGCCCCAG 59.777 63.158 10.38 8.99 0.00 4.45
514 535 1.953686 CCGGCGGATATCCATTGTTTT 59.046 47.619 24.41 0.00 35.14 2.43
518 539 2.390599 CGCCGGCGGATATCCATTG 61.391 63.158 40.50 8.19 35.14 2.82
540 617 8.348507 CGGATTAAGGTAAAACTAGTCTACGAT 58.651 37.037 0.00 0.00 0.00 3.73
541 618 7.201732 CCGGATTAAGGTAAAACTAGTCTACGA 60.202 40.741 0.00 0.00 0.00 3.43
572 665 4.663636 AACAAATCGGACGAACTTCATC 57.336 40.909 0.00 0.00 0.00 2.92
660 754 0.467474 TACTCATCAGCCGACGGGAT 60.467 55.000 17.22 7.95 34.06 3.85
677 771 2.023404 ACCCCCAAATTTCCTCCCATAC 60.023 50.000 0.00 0.00 0.00 2.39
681 775 0.411848 TCACCCCCAAATTTCCTCCC 59.588 55.000 0.00 0.00 0.00 4.30
693 787 0.755686 CATCTCTAGCACTCACCCCC 59.244 60.000 0.00 0.00 0.00 5.40
698 792 1.871418 AAGGGCATCTCTAGCACTCA 58.129 50.000 0.00 0.00 46.98 3.41
699 793 3.831911 AGATAAGGGCATCTCTAGCACTC 59.168 47.826 0.00 0.00 46.98 3.51
701 795 4.186856 GAGATAAGGGCATCTCTAGCAC 57.813 50.000 6.16 0.00 45.04 4.40
896 1196 0.038801 TCTGAGCTTGTGAGTGCGAG 60.039 55.000 0.00 0.00 0.00 5.03
1451 1803 4.501071 GGGCATTTCTTTCTACTGTACGA 58.499 43.478 0.00 0.00 0.00 3.43
1707 2076 1.006571 GTTTGAGCCGGAGTCGACA 60.007 57.895 19.50 0.00 39.00 4.35
1735 2104 4.430765 GTCGATGGCACCGACGGT 62.431 66.667 19.99 15.37 45.23 4.83
1747 2116 1.613630 AGCCCCTGTTCCAGTCGAT 60.614 57.895 0.00 0.00 0.00 3.59
2036 2425 6.294342 CCGAACACAAATATACTCCGGATCTA 60.294 42.308 3.57 0.00 36.86 1.98
2094 2485 3.161450 GCCCCCTCTGGCGACATA 61.161 66.667 0.00 0.00 42.54 2.29
2109 2500 0.106708 TATCATGCTCCCGACAAGCC 59.893 55.000 0.00 0.00 39.05 4.35
2113 2504 3.895041 TCTTATGTATCATGCTCCCGACA 59.105 43.478 0.00 0.00 0.00 4.35
2130 2521 3.904717 AGACCTCATCGACCTGTCTTAT 58.095 45.455 0.00 0.00 32.61 1.73
2138 2529 2.233922 TCCTCAAAAGACCTCATCGACC 59.766 50.000 0.00 0.00 0.00 4.79
2143 2534 3.107601 TCGGATCCTCAAAAGACCTCAT 58.892 45.455 10.75 0.00 0.00 2.90
2163 2554 2.009774 CTCCCGGACATGTGACATTTC 58.990 52.381 1.15 3.20 0.00 2.17
2167 2558 2.290287 CCCTCCCGGACATGTGACA 61.290 63.158 1.15 0.00 0.00 3.58
2179 2570 1.687493 CCCTGACAGAGTCCCTCCC 60.687 68.421 3.32 0.00 0.00 4.30
2183 2574 2.665603 GTGCCCTGACAGAGTCCC 59.334 66.667 3.32 0.00 0.00 4.46
2187 2578 2.575993 CCTCGTGCCCTGACAGAG 59.424 66.667 3.32 0.00 0.00 3.35
2188 2579 3.695606 GCCTCGTGCCCTGACAGA 61.696 66.667 3.32 0.00 0.00 3.41
2195 2586 1.300697 CTATAACCGCCTCGTGCCC 60.301 63.158 0.00 0.00 36.24 5.36
2204 2595 0.320697 CCTGGGTAGCCTATAACCGC 59.679 60.000 13.11 0.00 36.57 5.68
2264 2655 4.644954 GTTCTTCGTTGTTCTTCGTGTTT 58.355 39.130 0.00 0.00 0.00 2.83
2269 2660 2.153247 CCTCGTTCTTCGTTGTTCTTCG 59.847 50.000 0.00 0.00 40.80 3.79
2272 2663 3.181478 ACTTCCTCGTTCTTCGTTGTTCT 60.181 43.478 0.00 0.00 40.80 3.01
2273 2664 3.121544 ACTTCCTCGTTCTTCGTTGTTC 58.878 45.455 0.00 0.00 40.80 3.18
2274 2665 3.121544 GACTTCCTCGTTCTTCGTTGTT 58.878 45.455 0.00 0.00 40.80 2.83
2275 2666 2.545322 GGACTTCCTCGTTCTTCGTTGT 60.545 50.000 0.00 0.00 40.80 3.32
2276 2667 2.059541 GGACTTCCTCGTTCTTCGTTG 58.940 52.381 0.00 0.00 40.80 4.10
2277 2668 1.962100 AGGACTTCCTCGTTCTTCGTT 59.038 47.619 0.00 0.00 44.77 3.85
2278 2669 1.618487 AGGACTTCCTCGTTCTTCGT 58.382 50.000 0.00 0.00 44.77 3.85
2407 2798 9.566530 CGAAAAGTCCATCTATCTCATACATAG 57.433 37.037 0.00 0.00 0.00 2.23
2456 2848 6.828785 AGTCTAGGTTTTGACTTGTTGAACAT 59.171 34.615 0.00 0.00 40.21 2.71
2466 2858 5.048154 GTCCGAGTTAGTCTAGGTTTTGACT 60.048 44.000 0.00 0.00 44.56 3.41
2499 2891 6.016108 TGTCCGATATGTCCGATTTATGTGTA 60.016 38.462 0.00 0.00 0.00 2.90
2500 2892 5.221362 TGTCCGATATGTCCGATTTATGTGT 60.221 40.000 0.00 0.00 0.00 3.72
2503 2895 5.869344 ACATGTCCGATATGTCCGATTTATG 59.131 40.000 5.01 0.00 33.72 1.90
2505 2897 5.462530 ACATGTCCGATATGTCCGATTTA 57.537 39.130 5.01 0.00 33.72 1.40
2510 2902 2.135139 CCAACATGTCCGATATGTCCG 58.865 52.381 10.82 6.08 37.77 4.79
2511 2903 2.494059 CCCAACATGTCCGATATGTCC 58.506 52.381 10.82 0.00 37.77 4.02
2512 2904 2.158813 ACCCCAACATGTCCGATATGTC 60.159 50.000 10.82 0.00 37.77 3.06
2513 2905 1.843851 ACCCCAACATGTCCGATATGT 59.156 47.619 0.00 5.01 40.30 2.29
2514 2906 2.158827 TCACCCCAACATGTCCGATATG 60.159 50.000 0.00 3.71 0.00 1.78
2515 2907 2.123589 TCACCCCAACATGTCCGATAT 58.876 47.619 0.00 0.00 0.00 1.63
2516 2908 1.574263 TCACCCCAACATGTCCGATA 58.426 50.000 0.00 0.00 0.00 2.92
2517 2909 0.695924 TTCACCCCAACATGTCCGAT 59.304 50.000 0.00 0.00 0.00 4.18
2518 2910 0.474614 TTTCACCCCAACATGTCCGA 59.525 50.000 0.00 0.00 0.00 4.55
2519 2911 1.544724 ATTTCACCCCAACATGTCCG 58.455 50.000 0.00 0.00 0.00 4.79
2532 2924 8.017946 GTGGATTCTCTGTTTCAACTATTTCAC 58.982 37.037 0.00 0.00 0.00 3.18
2584 2988 7.012421 AGAGACAAATGTAAAGTCAAGTTGGAC 59.988 37.037 2.34 0.42 38.08 4.02
2599 3003 3.213206 TGCAAGGTCAGAGACAAATGT 57.787 42.857 0.00 0.00 33.68 2.71
2602 3006 2.416747 CGATGCAAGGTCAGAGACAAA 58.583 47.619 0.00 0.00 33.68 2.83
2615 3022 2.028130 ACAACCTCAAAACCGATGCAA 58.972 42.857 0.00 0.00 0.00 4.08
2653 3060 7.735586 GCGAACAACTTTGCTTTTTGTATTATG 59.264 33.333 0.00 0.00 34.29 1.90
2753 3170 7.408756 TGCCATATCCATAATTATTTCCTGC 57.591 36.000 0.00 0.00 0.00 4.85
2756 3173 9.807649 GTCAATGCCATATCCATAATTATTTCC 57.192 33.333 0.00 0.00 0.00 3.13
2765 3182 9.448438 GTTAATACTGTCAATGCCATATCCATA 57.552 33.333 0.00 0.00 0.00 2.74
2766 3183 7.119699 CGTTAATACTGTCAATGCCATATCCAT 59.880 37.037 0.00 0.00 0.00 3.41
2769 3186 7.360101 GGTCGTTAATACTGTCAATGCCATATC 60.360 40.741 0.00 0.00 0.00 1.63
2770 3187 6.426937 GGTCGTTAATACTGTCAATGCCATAT 59.573 38.462 0.00 0.00 0.00 1.78
2778 3195 9.577110 CAATTAGTAGGTCGTTAATACTGTCAA 57.423 33.333 0.00 0.00 32.25 3.18
2782 3199 6.914215 TCGCAATTAGTAGGTCGTTAATACTG 59.086 38.462 0.00 0.00 32.25 2.74
2795 3212 8.156553 CGTGCTTATTTAGATCGCAATTAGTAG 58.843 37.037 7.38 0.00 31.77 2.57
2800 3217 5.734855 ACGTGCTTATTTAGATCGCAATT 57.265 34.783 0.00 0.00 31.77 2.32
2819 3236 5.698089 TGCTTCTACTATATGCGTAGTACGT 59.302 40.000 22.81 7.73 44.73 3.57
2821 3238 7.976826 AGATGCTTCTACTATATGCGTAGTAC 58.023 38.462 0.00 0.00 36.39 2.73
2848 3265 8.548987 TGTCTTAACAGGACTAGCTATGTGCG 62.549 46.154 0.00 0.67 39.34 5.34
2876 3293 5.714806 ACATGATTATCCCGTTCCTGTTTTT 59.285 36.000 0.00 0.00 0.00 1.94
2877 3294 5.261216 ACATGATTATCCCGTTCCTGTTTT 58.739 37.500 0.00 0.00 0.00 2.43
2878 3295 4.855340 ACATGATTATCCCGTTCCTGTTT 58.145 39.130 0.00 0.00 0.00 2.83
2879 3296 4.503714 ACATGATTATCCCGTTCCTGTT 57.496 40.909 0.00 0.00 0.00 3.16
2882 3299 6.296259 GGGTATAACATGATTATCCCGTTCCT 60.296 42.308 0.00 0.00 0.00 3.36
2886 3303 6.271391 TGAAGGGTATAACATGATTATCCCGT 59.729 38.462 0.00 10.37 38.72 5.28
2900 3317 2.916934 ACTGGCCAACTGAAGGGTATAA 59.083 45.455 7.01 0.00 0.00 0.98
2945 3362 3.672295 CTGACCAGAAGGAGGCCGC 62.672 68.421 0.00 0.00 38.69 6.53
2947 3364 2.270527 GCTGACCAGAAGGAGGCC 59.729 66.667 0.00 0.00 38.69 5.19
2961 3378 2.510238 CCGAGAAGGCTTCCGCTG 60.510 66.667 23.09 10.56 36.09 5.18


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

AutoCloner maintained by Alex Coulton.