Multiple sequence alignment - TraesCS1D01G060600

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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 TraesCS1D01G060600 chr1D 100.000 3728 0 0 1 3728 40798938 40795211 0.000000e+00 6885
1 TraesCS1D01G060600 chr1D 92.216 167 8 5 390 552 409539782 409539947 8.050000e-57 231
2 TraesCS1D01G060600 chr1A 93.082 2790 121 26 994 3728 39894826 39892054 0.000000e+00 4017
3 TraesCS1D01G060600 chr1A 84.080 402 35 11 6 396 39895784 39895401 9.840000e-96 361
4 TraesCS1D01G060600 chr1A 84.342 281 25 5 647 925 39895119 39894856 1.330000e-64 257
5 TraesCS1D01G060600 chr1A 96.000 150 5 1 390 538 393948471 393948620 3.720000e-60 243
6 TraesCS1D01G060600 chr1B 94.602 1908 87 9 906 2805 60255728 60257627 0.000000e+00 2939
7 TraesCS1D01G060600 chr1B 85.531 1092 93 31 2660 3726 60131355 60130304 0.000000e+00 1081
8 TraesCS1D01G060600 chr1B 88.345 695 64 12 3045 3725 60273046 60273737 0.000000e+00 819
9 TraesCS1D01G060600 chr1B 85.542 664 76 14 3075 3728 60165924 60165271 0.000000e+00 676
10 TraesCS1D01G060600 chr1B 88.235 561 52 10 3177 3725 60129124 60128566 0.000000e+00 658
11 TraesCS1D01G060600 chr1B 91.358 405 17 9 2396 2800 60194076 60193690 4.240000e-149 538
12 TraesCS1D01G060600 chr1B 85.856 403 29 11 1 393 60252726 60253110 1.610000e-108 403
13 TraesCS1D01G060600 chr1B 87.252 353 33 10 3380 3725 60193342 60192995 3.490000e-105 392
14 TraesCS1D01G060600 chr1B 88.037 326 29 5 2531 2855 60272560 60272876 9.770000e-101 377
15 TraesCS1D01G060600 chr1B 84.083 289 20 11 750 1027 60255457 60255730 4.780000e-64 255
16 TraesCS1D01G060600 chr3D 83.207 661 89 17 1168 1827 605568923 605568284 1.490000e-163 586
17 TraesCS1D01G060600 chr3D 86.486 259 27 1 996 1246 605490942 605490684 1.020000e-70 278
18 TraesCS1D01G060600 chr3D 80.392 306 30 11 1040 1333 605510729 605510442 4.880000e-49 206
19 TraesCS1D01G060600 chr3A 85.345 464 64 4 1282 1744 738726496 738726956 9.370000e-131 477
20 TraesCS1D01G060600 chr3A 96.000 150 5 1 390 538 585605785 585605636 3.720000e-60 243
21 TraesCS1D01G060600 chr3A 80.072 276 29 13 979 1229 738726240 738726514 8.230000e-42 182
22 TraesCS1D01G060600 chr6A 96.622 148 4 1 390 536 521988389 521988242 1.030000e-60 244
23 TraesCS1D01G060600 chr7B 96.000 150 5 1 390 538 141869049 141868900 3.720000e-60 243
24 TraesCS1D01G060600 chr7A 96.000 150 5 1 390 538 347249368 347249517 3.720000e-60 243
25 TraesCS1D01G060600 chr6D 96.000 150 5 1 390 538 97856437 97856586 3.720000e-60 243
26 TraesCS1D01G060600 chr5A 94.839 155 6 2 390 542 640948110 640948264 1.340000e-59 241
27 TraesCS1D01G060600 chr5A 92.262 168 10 3 390 555 589229051 589229217 6.220000e-58 235


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 TraesCS1D01G060600 chr1D 40795211 40798938 3727 True 6885.0 6885 100.000000 1 3728 1 chr1D.!!$R1 3727
1 TraesCS1D01G060600 chr1A 39892054 39895784 3730 True 1545.0 4017 87.168000 6 3728 3 chr1A.!!$R1 3722
2 TraesCS1D01G060600 chr1B 60252726 60257627 4901 False 1199.0 2939 88.180333 1 2805 3 chr1B.!!$F1 2804
3 TraesCS1D01G060600 chr1B 60128566 60131355 2789 True 869.5 1081 86.883000 2660 3726 2 chr1B.!!$R2 1066
4 TraesCS1D01G060600 chr1B 60165271 60165924 653 True 676.0 676 85.542000 3075 3728 1 chr1B.!!$R1 653
5 TraesCS1D01G060600 chr1B 60272560 60273737 1177 False 598.0 819 88.191000 2531 3725 2 chr1B.!!$F2 1194
6 TraesCS1D01G060600 chr1B 60192995 60194076 1081 True 465.0 538 89.305000 2396 3725 2 chr1B.!!$R3 1329
7 TraesCS1D01G060600 chr3D 605568284 605568923 639 True 586.0 586 83.207000 1168 1827 1 chr3D.!!$R3 659
8 TraesCS1D01G060600 chr3A 738726240 738726956 716 False 329.5 477 82.708500 979 1744 2 chr3A.!!$F1 765

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
324 337 0.331954 TTGAGGGAGCGTCTAGGTCT 59.668 55.0 0.0 0.0 46.05 3.85 F
932 3221 0.624500 CCCCTCCCTCCCTGAATCAA 60.625 60.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1605 4057 1.404181 CCGATGAACGCCAAGAAGAGA 60.404 52.381 0.0 0.0 41.07 3.10 R
2915 5430 0.505655 GTACGAGCAACCGACACAAC 59.494 55.000 0.0 0.0 0.00 3.32 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
33 43 0.599204 GCAAGGTCCAACGAACGAGA 60.599 55.000 0.14 0.00 0.00 4.04
43 53 0.529119 ACGAACGAGACCAACACACC 60.529 55.000 0.14 0.00 0.00 4.16
51 61 4.701171 ACGAGACCAACACACCTTTAAAAA 59.299 37.500 0.00 0.00 0.00 1.94
56 67 7.433680 AGACCAACACACCTTTAAAAATCATC 58.566 34.615 0.00 0.00 0.00 2.92
96 107 9.683069 AGAGCAACACTTCAAAAACATATTTAG 57.317 29.630 0.00 0.00 0.00 1.85
174 187 3.444742 TCCGAGGCACTTAAATTAGACGA 59.555 43.478 0.00 0.00 41.55 4.20
176 189 4.267928 CCGAGGCACTTAAATTAGACGAAG 59.732 45.833 0.00 0.00 41.55 3.79
209 222 0.771127 AGCAACCTTGTCCTAAGCCA 59.229 50.000 0.00 0.00 0.00 4.75
275 288 2.287788 CCATATTCTCCCAAATGCACGC 60.288 50.000 0.00 0.00 0.00 5.34
281 294 2.703798 CCCAAATGCACGCTCCCAG 61.704 63.158 0.00 0.00 0.00 4.45
319 332 3.300388 AGATGATTTGAGGGAGCGTCTA 58.700 45.455 0.00 0.00 0.00 2.59
320 333 3.320541 AGATGATTTGAGGGAGCGTCTAG 59.679 47.826 0.00 0.00 0.00 2.43
324 337 0.331954 TTGAGGGAGCGTCTAGGTCT 59.668 55.000 0.00 0.00 46.05 3.85
325 338 1.210538 TGAGGGAGCGTCTAGGTCTA 58.789 55.000 0.00 0.00 46.05 2.59
326 339 1.134159 TGAGGGAGCGTCTAGGTCTAC 60.134 57.143 0.00 0.00 46.05 2.59
327 340 0.917533 AGGGAGCGTCTAGGTCTACA 59.082 55.000 0.00 0.00 46.05 2.74
328 341 1.023502 GGGAGCGTCTAGGTCTACAC 58.976 60.000 0.00 0.00 46.05 2.90
329 342 1.408544 GGGAGCGTCTAGGTCTACACT 60.409 57.143 0.00 0.00 46.05 3.55
334 347 3.197333 AGCGTCTAGGTCTACACTCACTA 59.803 47.826 0.00 0.00 0.00 2.74
337 350 4.512198 CGTCTAGGTCTACACTCACTATGG 59.488 50.000 0.00 0.00 0.00 2.74
355 368 8.435187 TCACTATGGATCAATAAATTCTCAGCT 58.565 33.333 0.00 0.00 0.00 4.24
407 564 9.552114 CTGCAAACAATATTTGTCTTTCTAGAG 57.448 33.333 0.00 0.00 44.59 2.43
431 588 8.475331 AGATTTCAACAAGTAACTACATACGG 57.525 34.615 0.00 0.00 0.00 4.02
436 593 4.741342 ACAAGTAACTACATACGGAGCAC 58.259 43.478 0.00 0.00 0.00 4.40
496 653 9.716531 ATACATCTGTATGTGATAGTCCATTTG 57.283 33.333 2.10 0.00 45.99 2.32
507 664 9.383519 TGTGATAGTCCATTTGAAATCTCTAAC 57.616 33.333 0.00 0.00 0.00 2.34
528 685 8.662141 TCTAACAAGACAAATATTTAGGAACGC 58.338 33.333 0.00 0.00 0.00 4.84
529 686 5.864986 ACAAGACAAATATTTAGGAACGCG 58.135 37.500 3.53 3.53 0.00 6.01
532 689 3.872771 GACAAATATTTAGGAACGCGGGA 59.127 43.478 12.47 0.00 0.00 5.14
533 690 3.875134 ACAAATATTTAGGAACGCGGGAG 59.125 43.478 12.47 0.00 0.00 4.30
534 691 3.832615 AATATTTAGGAACGCGGGAGT 57.167 42.857 12.47 0.00 0.00 3.85
535 692 4.942761 AATATTTAGGAACGCGGGAGTA 57.057 40.909 12.47 0.00 0.00 2.59
536 693 5.479124 AATATTTAGGAACGCGGGAGTAT 57.521 39.130 12.47 0.00 0.00 2.12
537 694 6.594788 AATATTTAGGAACGCGGGAGTATA 57.405 37.500 12.47 0.00 0.00 1.47
538 695 4.942761 ATTTAGGAACGCGGGAGTATAA 57.057 40.909 12.47 0.00 0.00 0.98
539 696 4.734398 TTTAGGAACGCGGGAGTATAAA 57.266 40.909 12.47 5.29 0.00 1.40
540 697 2.591571 AGGAACGCGGGAGTATAAAC 57.408 50.000 12.47 0.00 0.00 2.01
541 698 1.826720 AGGAACGCGGGAGTATAAACA 59.173 47.619 12.47 0.00 0.00 2.83
542 699 2.234414 AGGAACGCGGGAGTATAAACAA 59.766 45.455 12.47 0.00 0.00 2.83
543 700 2.349580 GGAACGCGGGAGTATAAACAAC 59.650 50.000 12.47 0.00 0.00 3.32
544 701 3.256558 GAACGCGGGAGTATAAACAACT 58.743 45.455 12.47 0.00 0.00 3.16
545 702 2.613691 ACGCGGGAGTATAAACAACTG 58.386 47.619 12.47 0.00 0.00 3.16
546 703 2.028748 ACGCGGGAGTATAAACAACTGT 60.029 45.455 12.47 0.00 0.00 3.55
547 704 2.601763 CGCGGGAGTATAAACAACTGTC 59.398 50.000 0.00 0.00 0.00 3.51
548 705 2.934553 GCGGGAGTATAAACAACTGTCC 59.065 50.000 0.00 0.00 0.00 4.02
549 706 3.618019 GCGGGAGTATAAACAACTGTCCA 60.618 47.826 0.00 0.00 0.00 4.02
550 707 4.766375 CGGGAGTATAAACAACTGTCCAT 58.234 43.478 0.00 0.00 0.00 3.41
551 708 5.183228 CGGGAGTATAAACAACTGTCCATT 58.817 41.667 0.00 0.00 0.00 3.16
552 709 5.646360 CGGGAGTATAAACAACTGTCCATTT 59.354 40.000 0.00 0.00 0.00 2.32
553 710 6.819649 CGGGAGTATAAACAACTGTCCATTTA 59.180 38.462 0.00 0.00 0.00 1.40
554 711 7.497909 CGGGAGTATAAACAACTGTCCATTTAT 59.502 37.037 8.19 8.19 33.12 1.40
555 712 9.841295 GGGAGTATAAACAACTGTCCATTTATA 57.159 33.333 6.86 6.86 31.43 0.98
615 781 7.642071 TTTTCATCATAGCTGAAAAACTTGC 57.358 32.000 8.00 0.00 45.00 4.01
619 785 5.710513 TCATAGCTGAAAAACTTGCATGT 57.289 34.783 0.00 0.00 0.00 3.21
672 838 5.422214 AATGTCAAGATAGACGGTCCTTT 57.578 39.130 4.14 0.00 41.41 3.11
699 980 9.249457 TGTTGCTGAGATTTTATCTAATACTCG 57.751 33.333 0.00 0.00 40.38 4.18
702 983 7.867909 TGCTGAGATTTTATCTAATACTCGGTG 59.132 37.037 0.00 0.00 40.38 4.94
726 1010 7.769044 GTGAACTTAGGATTAGCAAATCTGGTA 59.231 37.037 0.00 0.00 41.18 3.25
748 3032 7.039270 GGTAAGTAATTTAAAGGGCATGGTTG 58.961 38.462 0.00 0.00 0.00 3.77
839 3123 2.668850 TTTGGAATCTCCTCCCCTCT 57.331 50.000 0.00 0.00 37.46 3.69
848 3132 2.283966 CTCCCCTCTCCGTGTGGT 60.284 66.667 0.00 0.00 36.30 4.16
865 3149 2.153913 GTCGTGTGGACACATCTGC 58.846 57.895 8.54 0.00 46.75 4.26
866 3150 1.005037 TCGTGTGGACACATCTGCC 60.005 57.895 8.54 0.00 46.75 4.85
931 3220 1.004758 CCCCTCCCTCCCTGAATCA 59.995 63.158 0.00 0.00 0.00 2.57
932 3221 0.624500 CCCCTCCCTCCCTGAATCAA 60.625 60.000 0.00 0.00 0.00 2.57
933 3222 1.527457 CCCTCCCTCCCTGAATCAAT 58.473 55.000 0.00 0.00 0.00 2.57
934 3223 1.423161 CCCTCCCTCCCTGAATCAATC 59.577 57.143 0.00 0.00 0.00 2.67
935 3224 1.423161 CCTCCCTCCCTGAATCAATCC 59.577 57.143 0.00 0.00 0.00 3.01
938 3227 1.527457 CCTCCCTGAATCAATCCCCT 58.473 55.000 0.00 0.00 0.00 4.79
940 3229 2.158549 CCTCCCTGAATCAATCCCCTTC 60.159 54.545 0.00 0.00 0.00 3.46
941 3230 1.852965 TCCCTGAATCAATCCCCTTCC 59.147 52.381 0.00 0.00 0.00 3.46
942 3231 1.855599 CCCTGAATCAATCCCCTTCCT 59.144 52.381 0.00 0.00 0.00 3.36
943 3232 2.245806 CCCTGAATCAATCCCCTTCCTT 59.754 50.000 0.00 0.00 0.00 3.36
973 3264 0.892358 ACCAGACGAACGCACTCCTA 60.892 55.000 0.00 0.00 0.00 2.94
985 3276 2.507102 CTCCTACAGCCACACGCG 60.507 66.667 3.53 3.53 44.76 6.01
1668 4120 2.432628 CTCGTCGGGTTCAGCACC 60.433 66.667 0.00 0.00 46.46 5.01
2109 4561 1.664873 TCCTCTACGTCGACATCCTG 58.335 55.000 17.16 0.66 0.00 3.86
2233 4685 2.490217 CCATCGTCTTCGGCTCGT 59.510 61.111 0.00 0.00 37.69 4.18
2562 5014 0.529337 CCTACATGCTGCTCCACTCG 60.529 60.000 0.00 0.00 0.00 4.18
2656 5108 0.594284 GCGAGCCGATACACCAGTAC 60.594 60.000 0.00 0.00 31.96 2.73
2730 5185 4.954202 TCTCACGTGGAATTGTCCTAGTAT 59.046 41.667 17.00 0.00 45.22 2.12
2731 5186 6.039047 GTCTCACGTGGAATTGTCCTAGTATA 59.961 42.308 17.00 0.00 45.22 1.47
2732 5187 6.262496 TCTCACGTGGAATTGTCCTAGTATAG 59.738 42.308 17.00 0.00 45.22 1.31
2733 5188 5.889853 TCACGTGGAATTGTCCTAGTATAGT 59.110 40.000 17.00 0.00 45.22 2.12
2734 5189 7.056006 TCACGTGGAATTGTCCTAGTATAGTA 58.944 38.462 17.00 0.00 45.22 1.82
2735 5190 7.228108 TCACGTGGAATTGTCCTAGTATAGTAG 59.772 40.741 17.00 7.53 45.22 2.57
2752 5207 8.254508 AGTATAGTAGCACTTTCTCCTTTTCAG 58.745 37.037 0.00 0.00 0.00 3.02
2884 5393 5.043248 ACAAAACAAGCAAAGCAGTATGTC 58.957 37.500 0.00 0.00 39.31 3.06
2889 5398 4.637534 ACAAGCAAAGCAGTATGTCTATGG 59.362 41.667 0.00 0.00 39.31 2.74
2910 5424 6.282199 TGGTTCTCCTGTGTAGTATTCTTC 57.718 41.667 0.00 0.00 34.23 2.87
2915 5430 5.821470 TCTCCTGTGTAGTATTCTTCTACGG 59.179 44.000 0.00 0.00 40.15 4.02
2918 5433 6.034591 CCTGTGTAGTATTCTTCTACGGTTG 58.965 44.000 0.00 0.00 40.15 3.77
2942 5549 3.676646 GTCGGTTGCTCGTACTATGTTTT 59.323 43.478 0.00 0.00 0.00 2.43
3009 5654 4.215399 TGTCTTATTTGAAAGCCCTCGTTG 59.785 41.667 0.00 0.00 0.00 4.10
3072 5717 7.676683 ACATGTGTCCTACTGGTAATATCTT 57.323 36.000 0.00 0.00 34.23 2.40
3143 5791 2.504367 ACAAACACTCTCGGGGAAATG 58.496 47.619 0.00 0.00 0.00 2.32
3243 7608 3.199677 CAATAAACCATGCAGGCCATTG 58.800 45.455 5.01 0.00 43.14 2.82
3251 7618 1.077930 GCAGGCCATTGCTCAGAGA 60.078 57.895 5.01 0.00 40.89 3.10
3255 7622 2.877168 CAGGCCATTGCTCAGAGAATAC 59.123 50.000 5.01 0.00 37.74 1.89
3257 7624 2.421952 GGCCATTGCTCAGAGAATACCA 60.422 50.000 0.00 0.00 37.74 3.25
3264 7631 2.166664 GCTCAGAGAATACCAACCGACT 59.833 50.000 0.00 0.00 0.00 4.18
3271 7639 5.469084 AGAGAATACCAACCGACTGAAAAAC 59.531 40.000 0.00 0.00 0.00 2.43
3302 7670 0.391528 CCATCGATGTCACACAGGCA 60.392 55.000 23.27 0.00 35.48 4.75
3355 7724 3.817653 TATTCGTTGGATCGGCACCGG 62.818 57.143 9.58 0.00 40.25 5.28
3358 7727 4.337177 TTGGATCGGCACCGGCAA 62.337 61.111 9.58 0.00 43.71 4.52
3373 7742 2.095263 CCGGCAACATCTACAAACAAGG 60.095 50.000 0.00 0.00 0.00 3.61
3607 7988 1.460504 TTGTACACTCGGAGATCGCT 58.539 50.000 12.86 0.00 39.05 4.93
3618 7999 1.989706 GAGATCGCTTCTCCTAGGGT 58.010 55.000 9.46 0.00 44.46 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.529119 GGTGTGTTGGTCTCGTTCGT 60.529 55.000 0.00 0.00 0.00 3.85
33 43 6.183360 ACGATGATTTTTAAAGGTGTGTTGGT 60.183 34.615 0.00 0.00 0.00 3.67
51 61 5.476254 TGCTCTAGAAGATGATGACGATGAT 59.524 40.000 0.00 0.00 0.00 2.45
56 67 4.502282 GTGTTGCTCTAGAAGATGATGACG 59.498 45.833 0.00 0.00 0.00 4.35
71 82 9.463443 ACTAAATATGTTTTTGAAGTGTTGCTC 57.537 29.630 0.00 0.00 0.00 4.26
124 136 8.015185 AGCTGCCAAAGTATTATTCATCAATT 57.985 30.769 0.00 0.00 0.00 2.32
125 137 7.592885 AGCTGCCAAAGTATTATTCATCAAT 57.407 32.000 0.00 0.00 0.00 2.57
126 138 7.340232 AGAAGCTGCCAAAGTATTATTCATCAA 59.660 33.333 0.00 0.00 0.00 2.57
127 139 6.830324 AGAAGCTGCCAAAGTATTATTCATCA 59.170 34.615 0.00 0.00 0.00 3.07
174 187 6.120507 AGGTTGCTTTCTCTCTCAATACTT 57.879 37.500 0.00 0.00 0.00 2.24
176 189 5.703130 ACAAGGTTGCTTTCTCTCTCAATAC 59.297 40.000 0.00 0.00 0.00 1.89
250 263 3.462954 TGCATTTGGGAGAATATGGGAGA 59.537 43.478 0.00 0.00 0.00 3.71
251 264 3.571401 GTGCATTTGGGAGAATATGGGAG 59.429 47.826 0.00 0.00 0.00 4.30
252 265 3.565307 GTGCATTTGGGAGAATATGGGA 58.435 45.455 0.00 0.00 0.00 4.37
253 266 2.294233 CGTGCATTTGGGAGAATATGGG 59.706 50.000 0.00 0.00 0.00 4.00
254 267 2.287788 GCGTGCATTTGGGAGAATATGG 60.288 50.000 0.00 0.00 0.00 2.74
255 268 2.620115 AGCGTGCATTTGGGAGAATATG 59.380 45.455 0.00 0.00 0.00 1.78
256 269 2.880890 GAGCGTGCATTTGGGAGAATAT 59.119 45.455 0.00 0.00 0.00 1.28
257 270 2.288666 GAGCGTGCATTTGGGAGAATA 58.711 47.619 0.00 0.00 0.00 1.75
258 271 1.098050 GAGCGTGCATTTGGGAGAAT 58.902 50.000 0.00 0.00 0.00 2.40
275 288 6.881065 TCTTTCATGTATTCTTCAACTGGGAG 59.119 38.462 0.00 0.00 0.00 4.30
319 332 5.130705 TGATCCATAGTGAGTGTAGACCT 57.869 43.478 0.00 0.00 0.00 3.85
320 333 5.854010 TTGATCCATAGTGAGTGTAGACC 57.146 43.478 0.00 0.00 0.00 3.85
325 338 9.553064 GAGAATTTATTGATCCATAGTGAGTGT 57.447 33.333 0.00 0.00 0.00 3.55
326 339 9.551734 TGAGAATTTATTGATCCATAGTGAGTG 57.448 33.333 0.00 0.00 0.00 3.51
327 340 9.775854 CTGAGAATTTATTGATCCATAGTGAGT 57.224 33.333 0.00 0.00 0.00 3.41
328 341 8.719648 GCTGAGAATTTATTGATCCATAGTGAG 58.280 37.037 0.00 0.00 0.00 3.51
329 342 8.435187 AGCTGAGAATTTATTGATCCATAGTGA 58.565 33.333 0.00 0.00 0.00 3.41
407 564 8.470040 TCCGTATGTAGTTACTTGTTGAAATC 57.530 34.615 0.00 0.00 0.00 2.17
420 577 4.081642 ACTCATTGTGCTCCGTATGTAGTT 60.082 41.667 0.00 0.00 0.00 2.24
424 581 2.233676 TCACTCATTGTGCTCCGTATGT 59.766 45.455 0.00 0.00 45.81 2.29
431 588 5.174395 AGTGTAGATTCACTCATTGTGCTC 58.826 41.667 0.00 0.00 44.07 4.26
477 634 9.330063 GAGATTTCAAATGGACTATCACATACA 57.670 33.333 0.00 0.00 0.00 2.29
507 664 5.263185 CCGCGTTCCTAAATATTTGTCTTG 58.737 41.667 11.05 0.00 0.00 3.02
518 675 4.081752 TGTTTATACTCCCGCGTTCCTAAA 60.082 41.667 4.92 0.00 0.00 1.85
527 684 2.934553 GGACAGTTGTTTATACTCCCGC 59.065 50.000 0.00 0.00 0.00 6.13
528 685 4.196626 TGGACAGTTGTTTATACTCCCG 57.803 45.455 0.00 0.00 0.00 5.14
529 686 8.747538 ATAAATGGACAGTTGTTTATACTCCC 57.252 34.615 0.00 0.00 0.00 4.30
564 721 9.511144 CAAACGGTACAGTTTTTAAGATCTTTT 57.489 29.630 19.60 0.00 41.84 2.27
565 722 8.680001 ACAAACGGTACAGTTTTTAAGATCTTT 58.320 29.630 19.60 0.00 41.84 2.52
566 723 8.217131 ACAAACGGTACAGTTTTTAAGATCTT 57.783 30.769 19.60 13.56 41.84 2.40
567 724 7.797038 ACAAACGGTACAGTTTTTAAGATCT 57.203 32.000 19.60 0.00 41.84 2.75
568 725 8.845942 AAACAAACGGTACAGTTTTTAAGATC 57.154 30.769 19.60 0.00 41.84 2.75
569 726 9.292846 GAAAACAAACGGTACAGTTTTTAAGAT 57.707 29.630 19.60 6.32 42.33 2.40
570 727 8.295288 TGAAAACAAACGGTACAGTTTTTAAGA 58.705 29.630 19.60 2.55 42.33 2.10
571 728 8.450385 TGAAAACAAACGGTACAGTTTTTAAG 57.550 30.769 19.60 11.93 42.33 1.85
572 729 8.983307 ATGAAAACAAACGGTACAGTTTTTAA 57.017 26.923 19.60 7.52 42.33 1.52
573 730 8.242053 TGATGAAAACAAACGGTACAGTTTTTA 58.758 29.630 19.60 11.99 42.33 1.52
574 731 7.091443 TGATGAAAACAAACGGTACAGTTTTT 58.909 30.769 19.60 12.19 42.33 1.94
575 732 6.622549 TGATGAAAACAAACGGTACAGTTTT 58.377 32.000 19.60 14.20 44.22 2.43
576 733 6.197364 TGATGAAAACAAACGGTACAGTTT 57.803 33.333 16.98 16.98 44.27 2.66
577 734 5.821516 TGATGAAAACAAACGGTACAGTT 57.178 34.783 5.49 5.49 35.59 3.16
578 735 6.348213 GCTATGATGAAAACAAACGGTACAGT 60.348 38.462 0.00 0.00 0.00 3.55
579 736 6.021596 GCTATGATGAAAACAAACGGTACAG 58.978 40.000 0.00 0.00 0.00 2.74
580 737 5.703592 AGCTATGATGAAAACAAACGGTACA 59.296 36.000 0.00 0.00 0.00 2.90
581 738 6.021596 CAGCTATGATGAAAACAAACGGTAC 58.978 40.000 0.00 0.00 0.00 3.34
582 739 5.935206 TCAGCTATGATGAAAACAAACGGTA 59.065 36.000 0.00 0.00 0.00 4.02
583 740 4.759693 TCAGCTATGATGAAAACAAACGGT 59.240 37.500 0.00 0.00 0.00 4.83
584 741 5.295431 TCAGCTATGATGAAAACAAACGG 57.705 39.130 0.00 0.00 0.00 4.44
585 742 7.621832 TTTTCAGCTATGATGAAAACAAACG 57.378 32.000 16.39 0.00 46.40 3.60
699 980 6.038714 CCAGATTTGCTAATCCTAAGTTCACC 59.961 42.308 15.88 0.00 40.91 4.02
702 983 8.732746 TTACCAGATTTGCTAATCCTAAGTTC 57.267 34.615 15.88 0.00 40.91 3.01
748 3032 4.392138 GTGTGAAGGATGTGGTAAACTAGC 59.608 45.833 0.00 0.00 0.00 3.42
839 3123 2.834043 TCCACACGACCACACGGA 60.834 61.111 0.00 0.00 37.61 4.69
866 3150 4.087892 CGCTGAGGTGTGAGGGGG 62.088 72.222 0.00 0.00 0.00 5.40
931 3220 5.958380 GTGGATCTTTTTAAGGAAGGGGATT 59.042 40.000 0.00 0.00 0.00 3.01
932 3221 5.519808 GTGGATCTTTTTAAGGAAGGGGAT 58.480 41.667 0.00 0.00 0.00 3.85
933 3222 4.264217 GGTGGATCTTTTTAAGGAAGGGGA 60.264 45.833 0.00 0.00 0.00 4.81
934 3223 4.023980 GGTGGATCTTTTTAAGGAAGGGG 58.976 47.826 0.00 0.00 0.00 4.79
935 3224 4.672899 TGGTGGATCTTTTTAAGGAAGGG 58.327 43.478 0.00 0.00 0.00 3.95
938 3227 5.001232 CGTCTGGTGGATCTTTTTAAGGAA 58.999 41.667 0.00 0.00 0.00 3.36
940 3229 4.575885 TCGTCTGGTGGATCTTTTTAAGG 58.424 43.478 0.00 0.00 0.00 2.69
941 3230 5.389516 CGTTCGTCTGGTGGATCTTTTTAAG 60.390 44.000 0.00 0.00 0.00 1.85
942 3231 4.449743 CGTTCGTCTGGTGGATCTTTTTAA 59.550 41.667 0.00 0.00 0.00 1.52
943 3232 3.991773 CGTTCGTCTGGTGGATCTTTTTA 59.008 43.478 0.00 0.00 0.00 1.52
1005 3436 4.996434 CGCGGGATGATGGGGCTC 62.996 72.222 0.00 0.00 0.00 4.70
1605 4057 1.404181 CCGATGAACGCCAAGAAGAGA 60.404 52.381 0.00 0.00 41.07 3.10
1968 4420 3.764466 CTGAAGCCCTCGTCGCCT 61.764 66.667 0.00 0.00 0.00 5.52
1978 4430 3.006247 CCTTCTTGAAGTAGCTGAAGCC 58.994 50.000 0.00 0.00 43.38 4.35
2656 5108 1.862123 CACTGCCACTGTTGCTACG 59.138 57.895 5.42 0.00 0.00 3.51
2730 5185 6.420913 ACTGAAAAGGAGAAAGTGCTACTA 57.579 37.500 0.00 0.00 0.00 1.82
2731 5186 5.297569 ACTGAAAAGGAGAAAGTGCTACT 57.702 39.130 0.00 0.00 0.00 2.57
2732 5187 6.261158 AGAAACTGAAAAGGAGAAAGTGCTAC 59.739 38.462 0.00 0.00 0.00 3.58
2733 5188 6.357367 AGAAACTGAAAAGGAGAAAGTGCTA 58.643 36.000 0.00 0.00 0.00 3.49
2734 5189 5.196695 AGAAACTGAAAAGGAGAAAGTGCT 58.803 37.500 0.00 0.00 0.00 4.40
2735 5190 5.506686 AGAAACTGAAAAGGAGAAAGTGC 57.493 39.130 0.00 0.00 0.00 4.40
2752 5207 6.656003 ACAAAACATAACTACAGCGAGAAAC 58.344 36.000 0.00 0.00 0.00 2.78
2808 5268 6.364165 GCGTCATTAATTTAGCACCGAGTATA 59.636 38.462 0.00 0.00 0.00 1.47
2809 5269 5.176958 GCGTCATTAATTTAGCACCGAGTAT 59.823 40.000 0.00 0.00 0.00 2.12
2810 5270 4.505191 GCGTCATTAATTTAGCACCGAGTA 59.495 41.667 0.00 0.00 0.00 2.59
2884 5393 7.589958 AGAATACTACACAGGAGAACCATAG 57.410 40.000 0.00 0.00 38.94 2.23
2889 5398 7.188157 CGTAGAAGAATACTACACAGGAGAAC 58.812 42.308 0.00 0.00 39.82 3.01
2910 5424 0.599204 AGCAACCGACACAACCGTAG 60.599 55.000 0.00 0.00 0.00 3.51
2915 5430 0.505655 GTACGAGCAACCGACACAAC 59.494 55.000 0.00 0.00 0.00 3.32
2918 5433 2.182825 CATAGTACGAGCAACCGACAC 58.817 52.381 0.00 0.00 0.00 3.67
2976 5621 7.867403 GGCTTTCAAATAAGACATTTTGAGTGA 59.133 33.333 0.00 0.00 41.42 3.41
2979 5624 7.381323 AGGGCTTTCAAATAAGACATTTTGAG 58.619 34.615 0.00 0.00 41.42 3.02
3009 5654 6.314784 GTTCATTAACATAGGTTGAGCACAC 58.685 40.000 2.37 0.00 37.88 3.82
3167 5815 1.186200 TGAAGATGGTCGACTCCCAG 58.814 55.000 16.46 0.00 34.92 4.45
3214 7579 1.858399 GCATGGTTTATTGGTACGCGC 60.858 52.381 5.73 0.00 0.00 6.86
3243 7608 2.166664 AGTCGGTTGGTATTCTCTGAGC 59.833 50.000 0.00 0.00 0.00 4.26
3251 7618 4.641094 TGTGTTTTTCAGTCGGTTGGTATT 59.359 37.500 0.00 0.00 0.00 1.89
3255 7622 2.478879 GGTGTGTTTTTCAGTCGGTTGG 60.479 50.000 0.00 0.00 0.00 3.77
3257 7624 1.746787 GGGTGTGTTTTTCAGTCGGTT 59.253 47.619 0.00 0.00 0.00 4.44
3264 7631 1.754226 GGCTCAAGGGTGTGTTTTTCA 59.246 47.619 0.00 0.00 0.00 2.69
3271 7639 0.107508 ATCGATGGCTCAAGGGTGTG 60.108 55.000 0.00 0.00 0.00 3.82
3302 7670 1.002087 GTCACCCCATCTCGACAGTTT 59.998 52.381 0.00 0.00 0.00 2.66
3355 7724 6.072175 TCCAATACCTTGTTTGTAGATGTTGC 60.072 38.462 0.00 0.00 0.00 4.17
3358 7727 7.016153 TCTCCAATACCTTGTTTGTAGATGT 57.984 36.000 0.00 0.00 0.00 3.06
3373 7742 6.183360 GCACTCAATGAAGTCTTCTCCAATAC 60.183 42.308 13.67 0.00 0.00 1.89
3607 7988 2.310945 TCCTCTCGAAACCCTAGGAGAA 59.689 50.000 11.48 0.00 35.31 2.87
3618 7999 4.994907 TCCATAATCGTTCCTCTCGAAA 57.005 40.909 0.00 0.00 40.61 3.46


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

AutoCloner maintained by Alex Coulton.