Multiple sequence alignment - TraesCS4D01G092900

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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 TraesCS4D01G092900 chr4D 100.000 2301 0 0 788 3088 68052976 68055276 0.000000e+00 4250
1 TraesCS4D01G092900 chr4D 100.000 531 0 0 1 531 68052189 68052719 0.000000e+00 981
2 TraesCS4D01G092900 chr4A 94.818 1814 52 19 788 2579 517884164 517885957 0.000000e+00 2791
3 TraesCS4D01G092900 chr4A 88.268 537 40 12 1 526 517883405 517883929 3.380000e-174 621
4 TraesCS4D01G092900 chr4A 93.590 312 11 3 2544 2853 517886288 517885984 1.010000e-124 457
5 TraesCS4D01G092900 chr4B 93.171 1933 61 27 788 2686 100576221 100578116 0.000000e+00 2772
6 TraesCS4D01G092900 chr4B 87.855 387 22 8 2716 3088 100578319 100578694 6.120000e-117 431
7 TraesCS4D01G092900 chr4B 81.978 455 50 21 103 531 100575539 100575987 1.050000e-94 357
8 TraesCS4D01G092900 chr5D 81.108 397 46 20 985 1360 200501037 200501425 1.080000e-74 291
9 TraesCS4D01G092900 chr5D 93.525 139 8 1 1473 1610 200501533 200501671 4.040000e-49 206
10 TraesCS4D01G092900 chr5D 91.045 134 12 0 1001 1134 425077485 425077352 6.800000e-42 182
11 TraesCS4D01G092900 chr5D 85.926 135 17 2 1226 1359 425077353 425077220 3.210000e-30 143
12 TraesCS4D01G092900 chr5B 80.357 392 54 15 986 1360 211146011 211146396 3.030000e-70 276
13 TraesCS4D01G092900 chr5B 93.525 139 8 1 1473 1610 211146504 211146642 4.040000e-49 206
14 TraesCS4D01G092900 chr5B 85.926 135 17 2 1226 1359 514279495 514279362 3.210000e-30 143
15 TraesCS4D01G092900 chr5A 93.525 139 8 1 1473 1610 214166884 214167022 4.040000e-49 206
16 TraesCS4D01G092900 chr5A 90.278 144 13 1 994 1136 214166396 214166539 1.460000e-43 187
17 TraesCS4D01G092900 chr5A 91.045 134 12 0 1001 1134 539093485 539093352 6.800000e-42 182
18 TraesCS4D01G092900 chr5A 88.571 140 16 0 1221 1360 214166633 214166772 1.470000e-38 171
19 TraesCS4D01G092900 chr5A 85.185 135 18 2 1226 1359 539093353 539093220 1.490000e-28 137
20 TraesCS4D01G092900 chr3A 90.972 144 12 1 988 1131 633922089 633922231 3.140000e-45 193
21 TraesCS4D01G092900 chr1B 89.103 156 15 2 1479 1632 487951128 487950973 3.140000e-45 193
22 TraesCS4D01G092900 chr3B 89.855 138 14 0 994 1131 653152044 653152181 8.800000e-41 178
23 TraesCS4D01G092900 chr1A 88.591 149 14 3 1480 1625 463461337 463461189 8.800000e-41 178
24 TraesCS4D01G092900 chr1D 91.339 127 11 0 1480 1606 364624919 364624793 1.140000e-39 174
25 TraesCS4D01G092900 chr3D 89.431 123 13 0 1479 1601 492131788 492131910 4.120000e-34 156
26 TraesCS4D01G092900 chr3D 82.759 145 24 1 1217 1360 352367952 352367808 8.990000e-26 128
27 TraesCS4D01G092900 chr7B 90.909 99 8 1 1707 1805 144973720 144973623 6.950000e-27 132


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 TraesCS4D01G092900 chr4D 68052189 68055276 3087 False 2615.500000 4250 100.0000 1 3088 2 chr4D.!!$F1 3087
1 TraesCS4D01G092900 chr4A 517883405 517885957 2552 False 1706.000000 2791 91.5430 1 2579 2 chr4A.!!$F1 2578
2 TraesCS4D01G092900 chr4B 100575539 100578694 3155 False 1186.666667 2772 87.6680 103 3088 3 chr4B.!!$F1 2985
3 TraesCS4D01G092900 chr5D 200501037 200501671 634 False 248.500000 291 87.3165 985 1610 2 chr5D.!!$F1 625
4 TraesCS4D01G092900 chr5B 211146011 211146642 631 False 241.000000 276 86.9410 986 1610 2 chr5B.!!$F1 624

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
405 435 0.105709 AACCTCACCCCAAAACCCAG 60.106 55.0 0.0 0.0 0.00 4.45 F
431 461 2.133281 TGCATTCATTAGGCTGCACT 57.867 45.0 0.5 0.0 39.54 4.40 F
1850 1931 0.907486 TCAACCTCTCCATCAGCCTG 59.093 55.0 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1610 0.310543 GCTTGATGTGCGTGTTCCAA 59.689 50.000 0.0 0.0 0.0 3.53 R
1877 1958 3.056328 GCCTCCTGTTTCACCGCC 61.056 66.667 0.0 0.0 0.0 6.13 R
3001 3299 0.034670 ATCCAGACTGCTCAAAGGCC 60.035 55.000 0.0 0.0 0.0 5.19 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
58 59 8.602472 AATTAAAGTGTATGCCCAAAGGAATA 57.398 30.769 0.00 0.00 31.63 1.75
85 86 4.891566 GGCCTAGATCGCCATACG 57.108 61.111 5.33 0.00 46.27 3.06
99 100 3.695022 ATACGCCACCACGCTCGTC 62.695 63.158 0.00 0.00 36.50 4.20
174 184 1.179152 CACAGGGCAATTGCTCATCA 58.821 50.000 31.10 0.00 46.01 3.07
181 191 2.610232 GGCAATTGCTCATCAAAACGGT 60.610 45.455 28.42 0.00 41.70 4.83
210 220 8.383264 CGCAGGTAAGAAATAAGATAGTATCG 57.617 38.462 4.48 0.00 0.00 2.92
219 229 8.211629 AGAAATAAGATAGTATCGCCCTTTTGT 58.788 33.333 4.48 0.00 0.00 2.83
228 238 3.053896 CCCTTTTGTCCCGGTCGC 61.054 66.667 0.00 0.00 0.00 5.19
229 239 3.053896 CCTTTTGTCCCGGTCGCC 61.054 66.667 0.00 0.00 0.00 5.54
299 312 0.322322 TTCGACCAACCGCCAAGTAT 59.678 50.000 0.00 0.00 0.00 2.12
300 313 0.322322 TCGACCAACCGCCAAGTATT 59.678 50.000 0.00 0.00 0.00 1.89
359 388 7.440523 AGAACTAGTCATTTGATGTTGAACC 57.559 36.000 0.00 0.00 0.00 3.62
362 391 6.299141 ACTAGTCATTTGATGTTGAACCACT 58.701 36.000 0.00 0.00 0.00 4.00
364 393 4.520492 AGTCATTTGATGTTGAACCACTCC 59.480 41.667 0.00 0.00 0.00 3.85
382 411 1.576272 TCCCCCTCCAAAAACCAAGAA 59.424 47.619 0.00 0.00 0.00 2.52
384 413 2.677914 CCCCTCCAAAAACCAAGAACT 58.322 47.619 0.00 0.00 0.00 3.01
385 414 2.365293 CCCCTCCAAAAACCAAGAACTG 59.635 50.000 0.00 0.00 0.00 3.16
386 415 3.295973 CCCTCCAAAAACCAAGAACTGA 58.704 45.455 0.00 0.00 0.00 3.41
387 416 3.704061 CCCTCCAAAAACCAAGAACTGAA 59.296 43.478 0.00 0.00 0.00 3.02
405 435 0.105709 AACCTCACCCCAAAACCCAG 60.106 55.000 0.00 0.00 0.00 4.45
431 461 2.133281 TGCATTCATTAGGCTGCACT 57.867 45.000 0.50 0.00 39.54 4.40
498 530 2.632996 CCTCCTCCCCCAAAAGAAAAAC 59.367 50.000 0.00 0.00 0.00 2.43
503 538 4.116961 CTCCCCCAAAAGAAAAACGAAAC 58.883 43.478 0.00 0.00 0.00 2.78
504 539 2.861335 CCCCCAAAAGAAAAACGAAACG 59.139 45.455 0.00 0.00 0.00 3.60
505 540 3.429135 CCCCCAAAAGAAAAACGAAACGA 60.429 43.478 0.00 0.00 0.00 3.85
506 541 4.174762 CCCCAAAAGAAAAACGAAACGAA 58.825 39.130 0.00 0.00 0.00 3.85
507 542 4.626172 CCCCAAAAGAAAAACGAAACGAAA 59.374 37.500 0.00 0.00 0.00 3.46
508 543 5.444877 CCCCAAAAGAAAAACGAAACGAAAC 60.445 40.000 0.00 0.00 0.00 2.78
509 544 5.234766 CCAAAAGAAAAACGAAACGAAACG 58.765 37.500 0.00 0.00 0.00 3.60
510 545 5.059465 CCAAAAGAAAAACGAAACGAAACGA 59.941 36.000 0.00 0.00 0.00 3.85
1182 1239 2.428902 GCGTGTACGTGTACGGCA 60.429 61.111 22.08 4.80 44.95 5.69
1367 1429 4.712763 CTCGGCAACAAGTAACAATTCTC 58.287 43.478 0.00 0.00 0.00 2.87
1381 1443 7.821846 AGTAACAATTCTCATCCTTCTTCTGAC 59.178 37.037 0.00 0.00 0.00 3.51
1383 1445 3.876274 TTCTCATCCTTCTTCTGACGG 57.124 47.619 0.00 0.00 33.37 4.79
1405 1467 6.153067 CGGTGATATATCAGTGGAGAAAGAC 58.847 44.000 15.83 0.00 37.51 3.01
1406 1468 6.153067 GGTGATATATCAGTGGAGAAAGACG 58.847 44.000 15.83 0.00 37.51 4.18
1850 1931 0.907486 TCAACCTCTCCATCAGCCTG 59.093 55.000 0.00 0.00 0.00 4.85
1960 2041 1.653667 CGTGCATGTGCTTGAACCA 59.346 52.632 6.55 0.00 42.66 3.67
2097 2181 2.395654 GACGCCAATAGTAGCACTAGC 58.604 52.381 0.00 0.00 33.66 3.42
2118 2202 4.630069 AGCAACAGTAACATTCGGACATAC 59.370 41.667 0.00 0.00 0.00 2.39
2325 2429 5.935206 CCTACCTTCTTTCCTTCTTGTCTTC 59.065 44.000 0.00 0.00 0.00 2.87
2344 2448 8.853077 TGTCTTCATTAATATTGCCATAGGAG 57.147 34.615 0.00 0.00 0.00 3.69
2376 2480 6.078202 TCTTCCACTAGATCTAATCAAGCG 57.922 41.667 3.57 0.00 0.00 4.68
2505 2616 2.957402 AGGTTCTTGGATGTCTGCAA 57.043 45.000 0.00 0.00 0.00 4.08
2597 2708 1.028905 CCGCCTTGTAGAGAGGAGAG 58.971 60.000 0.00 0.00 36.32 3.20
2602 2713 1.571457 CTTGTAGAGAGGAGAGGGGGA 59.429 57.143 0.00 0.00 0.00 4.81
2603 2714 1.227249 TGTAGAGAGGAGAGGGGGAG 58.773 60.000 0.00 0.00 0.00 4.30
2604 2715 1.228190 GTAGAGAGGAGAGGGGGAGT 58.772 60.000 0.00 0.00 0.00 3.85
2605 2716 1.133606 GTAGAGAGGAGAGGGGGAGTG 60.134 61.905 0.00 0.00 0.00 3.51
2606 2717 1.075600 GAGAGGAGAGGGGGAGTGG 60.076 68.421 0.00 0.00 0.00 4.00
2607 2718 2.041405 GAGGAGAGGGGGAGTGGG 60.041 72.222 0.00 0.00 0.00 4.61
2648 2759 4.941713 TGCCCATATTTTCTGGTTAGGTT 58.058 39.130 0.00 0.00 31.44 3.50
2686 2797 2.092375 GGGAGAGGTGTTAATGAAGGGG 60.092 54.545 0.00 0.00 0.00 4.79
2687 2798 2.844348 GGAGAGGTGTTAATGAAGGGGA 59.156 50.000 0.00 0.00 0.00 4.81
2688 2799 3.459969 GGAGAGGTGTTAATGAAGGGGAT 59.540 47.826 0.00 0.00 0.00 3.85
2689 2800 4.658901 GGAGAGGTGTTAATGAAGGGGATA 59.341 45.833 0.00 0.00 0.00 2.59
2690 2801 5.132144 GGAGAGGTGTTAATGAAGGGGATAA 59.868 44.000 0.00 0.00 0.00 1.75
2691 2802 6.353602 GGAGAGGTGTTAATGAAGGGGATAAA 60.354 42.308 0.00 0.00 0.00 1.40
2692 2803 6.663734 AGAGGTGTTAATGAAGGGGATAAAG 58.336 40.000 0.00 0.00 0.00 1.85
2693 2804 6.217693 AGAGGTGTTAATGAAGGGGATAAAGT 59.782 38.462 0.00 0.00 0.00 2.66
2694 2805 6.187682 AGGTGTTAATGAAGGGGATAAAGTG 58.812 40.000 0.00 0.00 0.00 3.16
2695 2806 5.163550 GGTGTTAATGAAGGGGATAAAGTGC 60.164 44.000 0.00 0.00 0.00 4.40
2696 2807 4.953579 TGTTAATGAAGGGGATAAAGTGCC 59.046 41.667 0.00 0.00 37.65 5.01
2697 2808 3.756082 AATGAAGGGGATAAAGTGCCA 57.244 42.857 0.00 0.00 40.78 4.92
2698 2809 3.979501 ATGAAGGGGATAAAGTGCCAT 57.020 42.857 0.00 0.00 40.78 4.40
2699 2810 3.017048 TGAAGGGGATAAAGTGCCATG 57.983 47.619 0.00 0.00 40.78 3.66
2700 2811 2.310538 GAAGGGGATAAAGTGCCATGG 58.689 52.381 7.63 7.63 40.78 3.66
2701 2812 1.607225 AGGGGATAAAGTGCCATGGA 58.393 50.000 18.40 0.00 40.78 3.41
2702 2813 1.496429 AGGGGATAAAGTGCCATGGAG 59.504 52.381 18.40 0.00 40.78 3.86
2703 2814 1.479389 GGGGATAAAGTGCCATGGAGG 60.479 57.143 18.40 0.00 40.78 4.30
2704 2815 1.494721 GGGATAAAGTGCCATGGAGGA 59.505 52.381 18.40 0.00 41.22 3.71
2705 2816 2.487986 GGGATAAAGTGCCATGGAGGAG 60.488 54.545 18.40 0.00 41.22 3.69
2706 2817 2.487986 GGATAAAGTGCCATGGAGGAGG 60.488 54.545 18.40 0.00 41.22 4.30
2707 2818 1.965414 TAAAGTGCCATGGAGGAGGA 58.035 50.000 18.40 0.00 41.22 3.71
2708 2819 0.622665 AAAGTGCCATGGAGGAGGAG 59.377 55.000 18.40 0.00 41.22 3.69
2709 2820 1.277580 AAGTGCCATGGAGGAGGAGG 61.278 60.000 18.40 0.00 41.22 4.30
2710 2821 1.690633 GTGCCATGGAGGAGGAGGA 60.691 63.158 18.40 0.00 41.22 3.71
2711 2822 1.383664 TGCCATGGAGGAGGAGGAG 60.384 63.158 18.40 0.00 41.22 3.69
2712 2823 2.146061 GCCATGGAGGAGGAGGAGG 61.146 68.421 18.40 0.00 41.22 4.30
2713 2824 1.461075 CCATGGAGGAGGAGGAGGG 60.461 68.421 5.56 0.00 41.22 4.30
2714 2825 1.461075 CATGGAGGAGGAGGAGGGG 60.461 68.421 0.00 0.00 0.00 4.79
2775 3059 0.990374 AATGGTCAGAGAGCTTGGCT 59.010 50.000 0.00 0.00 43.88 4.75
2803 3087 2.036256 CTGGCCTTCTTGGGGGTG 59.964 66.667 3.32 0.00 36.00 4.61
2804 3088 3.589542 TGGCCTTCTTGGGGGTGG 61.590 66.667 3.32 0.00 36.00 4.61
2805 3089 3.264845 GGCCTTCTTGGGGGTGGA 61.265 66.667 0.00 0.00 36.00 4.02
2806 3090 2.626467 GGCCTTCTTGGGGGTGGAT 61.626 63.158 0.00 0.00 36.00 3.41
2807 3091 1.380380 GCCTTCTTGGGGGTGGATG 60.380 63.158 0.00 0.00 36.00 3.51
2864 3148 5.441718 AATCATGGATCAGTACCACAGTT 57.558 39.130 0.00 0.00 40.36 3.16
2880 3164 4.333926 CCACAGTTATCTAAAGCCAGCTTC 59.666 45.833 5.17 0.00 34.84 3.86
2881 3165 4.937620 CACAGTTATCTAAAGCCAGCTTCA 59.062 41.667 5.17 0.00 34.84 3.02
2882 3166 5.064452 CACAGTTATCTAAAGCCAGCTTCAG 59.936 44.000 5.17 0.07 34.84 3.02
2929 3213 5.869888 CAGTCAGGGTATCAGTAGTTTGTTC 59.130 44.000 0.00 0.00 0.00 3.18
2933 3217 4.081807 AGGGTATCAGTAGTTTGTTCGGTC 60.082 45.833 0.00 0.00 0.00 4.79
2946 3230 1.461127 GTTCGGTCTGTCATGTTGCTC 59.539 52.381 0.00 0.00 0.00 4.26
2947 3231 0.969149 TCGGTCTGTCATGTTGCTCT 59.031 50.000 0.00 0.00 0.00 4.09
2979 3277 4.588899 TGATCCACAGGTATTCCAGTTTG 58.411 43.478 0.00 0.00 30.94 2.93
2990 3288 1.180907 TCCAGTTTGCAGCAACACAA 58.819 45.000 7.54 0.00 0.00 3.33
2992 3290 1.134753 CCAGTTTGCAGCAACACAAGA 59.865 47.619 7.54 0.00 0.00 3.02
3001 3299 5.941733 TGCAGCAACACAAGACATAAATAG 58.058 37.500 0.00 0.00 0.00 1.73
3004 3302 4.399303 AGCAACACAAGACATAAATAGGCC 59.601 41.667 0.00 0.00 0.00 5.19
3012 3310 5.116084 AGACATAAATAGGCCTTTGAGCA 57.884 39.130 12.58 0.00 0.00 4.26
3013 3311 5.128919 AGACATAAATAGGCCTTTGAGCAG 58.871 41.667 12.58 0.00 0.00 4.24
3023 3321 2.617532 GCCTTTGAGCAGTCTGGATCTT 60.618 50.000 1.14 0.00 0.00 2.40
3024 3322 3.683802 CCTTTGAGCAGTCTGGATCTTT 58.316 45.455 1.14 0.00 0.00 2.52
3025 3323 3.439476 CCTTTGAGCAGTCTGGATCTTTG 59.561 47.826 1.14 0.00 0.00 2.77
3026 3324 2.775911 TGAGCAGTCTGGATCTTTGG 57.224 50.000 1.14 0.00 0.00 3.28
3027 3325 1.280133 TGAGCAGTCTGGATCTTTGGG 59.720 52.381 1.14 0.00 0.00 4.12
3055 3353 8.015658 GCTGTTTCAACCTAACATAAGTACTTG 58.984 37.037 18.56 5.67 35.18 3.16
3059 3357 7.549147 TCAACCTAACATAAGTACTTGTCCT 57.451 36.000 18.56 3.45 0.00 3.85
3061 3359 9.092338 TCAACCTAACATAAGTACTTGTCCTTA 57.908 33.333 18.56 8.23 0.00 2.69
3063 3361 9.886132 AACCTAACATAAGTACTTGTCCTTATG 57.114 33.333 18.56 18.27 42.31 1.90
3076 3374 3.131396 GTCCTTATGTGCCCACTTATCG 58.869 50.000 0.00 0.00 0.00 2.92
3084 3382 2.354821 GTGCCCACTTATCGAACAATCC 59.645 50.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.504238 TGGGCATACACTTTAATTTCGGAATAT 59.496 33.333 0.00 0.00 0.00 1.28
31 32 6.930731 TCCTTTGGGCATACACTTTAATTTC 58.069 36.000 0.00 0.00 0.00 2.17
42 43 3.500343 AGGCATATTCCTTTGGGCATAC 58.500 45.455 0.00 0.00 30.82 2.39
99 100 2.036475 CACGAGAGATGGAAGGTATGGG 59.964 54.545 0.00 0.00 0.00 4.00
181 191 2.166870 TCTTATTTCTTACCTGCGGCGA 59.833 45.455 12.98 0.00 0.00 5.54
186 196 7.275999 GGCGATACTATCTTATTTCTTACCTGC 59.724 40.741 0.00 0.00 0.00 4.85
210 220 3.053896 CGACCGGGACAAAAGGGC 61.054 66.667 6.32 0.00 0.00 5.19
233 243 6.316890 TGCAACTATATTAGTTTTCCGGTTCC 59.683 38.462 0.00 0.00 46.27 3.62
237 247 7.860872 GGAAATGCAACTATATTAGTTTTCCGG 59.139 37.037 0.00 0.00 46.27 5.14
359 388 0.187361 TGGTTTTTGGAGGGGGAGTG 59.813 55.000 0.00 0.00 0.00 3.51
362 391 1.236708 TCTTGGTTTTTGGAGGGGGA 58.763 50.000 0.00 0.00 0.00 4.81
364 393 2.365293 CAGTTCTTGGTTTTTGGAGGGG 59.635 50.000 0.00 0.00 0.00 4.79
382 411 1.411074 GGTTTTGGGGTGAGGTTCAGT 60.411 52.381 0.00 0.00 0.00 3.41
384 413 0.105913 GGGTTTTGGGGTGAGGTTCA 60.106 55.000 0.00 0.00 0.00 3.18
385 414 0.105913 TGGGTTTTGGGGTGAGGTTC 60.106 55.000 0.00 0.00 0.00 3.62
386 415 0.105709 CTGGGTTTTGGGGTGAGGTT 60.106 55.000 0.00 0.00 0.00 3.50
387 416 1.541672 CTGGGTTTTGGGGTGAGGT 59.458 57.895 0.00 0.00 0.00 3.85
405 435 0.385390 CCTAATGAATGCAACGGGGC 59.615 55.000 0.00 0.00 0.00 5.80
431 461 0.321671 GAGCACACCAGCAGGAGTAA 59.678 55.000 0.35 0.00 36.51 2.24
1174 1231 0.951525 CATTCACCCGTTGCCGTACA 60.952 55.000 0.00 0.00 0.00 2.90
1175 1232 0.671163 TCATTCACCCGTTGCCGTAC 60.671 55.000 0.00 0.00 0.00 3.67
1176 1233 0.250793 ATCATTCACCCGTTGCCGTA 59.749 50.000 0.00 0.00 0.00 4.02
1177 1234 1.002624 ATCATTCACCCGTTGCCGT 60.003 52.632 0.00 0.00 0.00 5.68
1178 1235 1.305219 ACATCATTCACCCGTTGCCG 61.305 55.000 0.00 0.00 0.00 5.69
1179 1236 0.171007 CACATCATTCACCCGTTGCC 59.829 55.000 0.00 0.00 0.00 4.52
1182 1239 1.879380 CACACACATCATTCACCCGTT 59.121 47.619 0.00 0.00 0.00 4.44
1367 1429 3.533606 ATCACCGTCAGAAGAAGGATG 57.466 47.619 4.50 0.47 45.06 3.51
1381 1443 6.153067 GTCTTTCTCCACTGATATATCACCG 58.847 44.000 11.49 5.93 32.50 4.94
1383 1445 6.016192 TCCGTCTTTCTCCACTGATATATCAC 60.016 42.308 11.49 0.00 32.50 3.06
1538 1610 0.310543 GCTTGATGTGCGTGTTCCAA 59.689 50.000 0.00 0.00 0.00 3.53
1877 1958 3.056328 GCCTCCTGTTTCACCGCC 61.056 66.667 0.00 0.00 0.00 6.13
2097 2181 6.147164 AGTTGTATGTCCGAATGTTACTGTTG 59.853 38.462 0.00 0.00 0.00 3.33
2198 2290 7.107542 TGCAAATTACGTAATAGGAAAGGAGT 58.892 34.615 20.62 0.00 0.00 3.85
2200 2292 6.037830 GCTGCAAATTACGTAATAGGAAAGGA 59.962 38.462 20.62 8.02 0.00 3.36
2201 2293 6.038271 AGCTGCAAATTACGTAATAGGAAAGG 59.962 38.462 20.62 9.42 0.00 3.11
2202 2294 7.016361 AGCTGCAAATTACGTAATAGGAAAG 57.984 36.000 20.62 14.77 0.00 2.62
2204 2296 6.202188 GCTAGCTGCAAATTACGTAATAGGAA 59.798 38.462 20.62 9.88 42.31 3.36
2206 2298 5.916969 GCTAGCTGCAAATTACGTAATAGG 58.083 41.667 20.62 15.90 42.31 2.57
2258 2357 4.672587 TCATGAACTATGTCACCTAGGC 57.327 45.455 9.30 0.00 38.01 3.93
2259 2358 8.183104 TCTATTCATGAACTATGTCACCTAGG 57.817 38.462 11.07 7.41 38.01 3.02
2325 2429 8.585471 ATGAACCTCCTATGGCAATATTAATG 57.415 34.615 0.00 0.00 0.00 1.90
2344 2448 6.418057 AGATCTAGTGGAAGATGATGAACC 57.582 41.667 0.00 0.00 36.33 3.62
2505 2616 0.107017 GGCCATGTCATGTGCTACCT 60.107 55.000 19.35 0.00 0.00 3.08
2507 2618 1.605710 GATGGCCATGTCATGTGCTAC 59.394 52.381 26.56 0.00 0.00 3.58
2570 2681 1.002087 CTCTACAAGGCGGACAAACCT 59.998 52.381 0.00 0.00 38.14 3.50
2579 2690 1.028905 CCTCTCCTCTCTACAAGGCG 58.971 60.000 0.00 0.00 33.65 5.52
2580 2691 1.408969 CCCTCTCCTCTCTACAAGGC 58.591 60.000 0.00 0.00 33.65 4.35
2581 2692 1.412361 CCCCCTCTCCTCTCTACAAGG 60.412 61.905 0.00 0.00 35.05 3.61
2602 2713 2.937689 ATGCTGCCCACTCCCACT 60.938 61.111 0.00 0.00 0.00 4.00
2603 2714 2.753043 CATGCTGCCCACTCCCAC 60.753 66.667 0.00 0.00 0.00 4.61
2604 2715 3.259314 ACATGCTGCCCACTCCCA 61.259 61.111 0.00 0.00 0.00 4.37
2605 2716 2.753043 CACATGCTGCCCACTCCC 60.753 66.667 0.00 0.00 0.00 4.30
2606 2717 1.748122 CTCACATGCTGCCCACTCC 60.748 63.158 0.00 0.00 0.00 3.85
2607 2718 0.107312 ATCTCACATGCTGCCCACTC 60.107 55.000 0.00 0.00 0.00 3.51
2648 2759 3.795545 TCTCCCATACCTTCTACCTACCA 59.204 47.826 0.00 0.00 0.00 3.25
2686 2797 2.439507 TCCTCCTCCATGGCACTTTATC 59.560 50.000 6.96 0.00 35.26 1.75
2687 2798 2.441001 CTCCTCCTCCATGGCACTTTAT 59.559 50.000 6.96 0.00 35.26 1.40
2688 2799 1.839994 CTCCTCCTCCATGGCACTTTA 59.160 52.381 6.96 0.00 35.26 1.85
2689 2800 0.622665 CTCCTCCTCCATGGCACTTT 59.377 55.000 6.96 0.00 35.26 2.66
2690 2801 1.277580 CCTCCTCCTCCATGGCACTT 61.278 60.000 6.96 0.00 35.26 3.16
2691 2802 1.692042 CCTCCTCCTCCATGGCACT 60.692 63.158 6.96 0.00 35.26 4.40
2692 2803 1.690633 TCCTCCTCCTCCATGGCAC 60.691 63.158 6.96 0.00 35.26 5.01
2693 2804 1.383664 CTCCTCCTCCTCCATGGCA 60.384 63.158 6.96 0.00 35.26 4.92
2694 2805 2.146061 CCTCCTCCTCCTCCATGGC 61.146 68.421 6.96 0.00 35.26 4.40
2695 2806 1.461075 CCCTCCTCCTCCTCCATGG 60.461 68.421 4.97 4.97 37.10 3.66
2696 2807 1.461075 CCCCTCCTCCTCCTCCATG 60.461 68.421 0.00 0.00 0.00 3.66
2697 2808 1.630333 TCCCCTCCTCCTCCTCCAT 60.630 63.158 0.00 0.00 0.00 3.41
2698 2809 2.204624 TCCCCTCCTCCTCCTCCA 60.205 66.667 0.00 0.00 0.00 3.86
2699 2810 2.612251 CTCCCCTCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
2700 2811 2.612251 CCTCCCCTCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
2701 2812 3.039526 CCCTCCCCTCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
2702 2813 4.179599 CCCCTCCCCTCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
2703 2814 4.890306 GCCCCTCCCCTCCTCCTC 62.890 77.778 0.00 0.00 0.00 3.71
2705 2816 4.523282 ATGCCCCTCCCCTCCTCC 62.523 72.222 0.00 0.00 0.00 4.30
2706 2817 3.174265 CATGCCCCTCCCCTCCTC 61.174 72.222 0.00 0.00 0.00 3.71
2707 2818 4.851252 CCATGCCCCTCCCCTCCT 62.851 72.222 0.00 0.00 0.00 3.69
2708 2819 4.843331 TCCATGCCCCTCCCCTCC 62.843 72.222 0.00 0.00 0.00 4.30
2709 2820 3.493303 GTCCATGCCCCTCCCCTC 61.493 72.222 0.00 0.00 0.00 4.30
2710 2821 4.044390 AGTCCATGCCCCTCCCCT 62.044 66.667 0.00 0.00 0.00 4.79
2711 2822 3.813724 CAGTCCATGCCCCTCCCC 61.814 72.222 0.00 0.00 0.00 4.81
2712 2823 2.692368 TCAGTCCATGCCCCTCCC 60.692 66.667 0.00 0.00 0.00 4.30
2713 2824 2.750657 CCTCAGTCCATGCCCCTCC 61.751 68.421 0.00 0.00 0.00 4.30
2714 2825 1.690633 TCCTCAGTCCATGCCCCTC 60.691 63.158 0.00 0.00 0.00 4.30
2775 3059 0.819259 GAAGGCCAGACACAGCACAA 60.819 55.000 5.01 0.00 0.00 3.33
2803 3087 1.097547 CAACTCCGGCATCCACATCC 61.098 60.000 0.00 0.00 0.00 3.51
2804 3088 1.097547 CCAACTCCGGCATCCACATC 61.098 60.000 0.00 0.00 0.00 3.06
2805 3089 1.077501 CCAACTCCGGCATCCACAT 60.078 57.895 0.00 0.00 0.00 3.21
2806 3090 2.350895 CCAACTCCGGCATCCACA 59.649 61.111 0.00 0.00 0.00 4.17
2807 3091 2.040544 CACCAACTCCGGCATCCAC 61.041 63.158 0.00 0.00 0.00 4.02
2851 3135 5.482526 TGGCTTTAGATAACTGTGGTACTGA 59.517 40.000 0.00 0.00 0.00 3.41
2858 3142 4.937620 TGAAGCTGGCTTTAGATAACTGTG 59.062 41.667 9.28 0.00 36.26 3.66
2864 3148 4.844349 AACCTGAAGCTGGCTTTAGATA 57.156 40.909 22.77 3.84 40.67 1.98
2929 3213 2.263077 GTAGAGCAACATGACAGACCG 58.737 52.381 0.00 0.00 0.00 4.79
2946 3230 5.028549 ACCTGTGGATCAAATAGCTGTAG 57.971 43.478 0.00 0.00 0.00 2.74
2947 3231 6.747414 ATACCTGTGGATCAAATAGCTGTA 57.253 37.500 0.00 0.00 0.00 2.74
2959 3243 3.245229 TGCAAACTGGAATACCTGTGGAT 60.245 43.478 0.00 0.00 45.33 3.41
2964 3248 2.161855 TGCTGCAAACTGGAATACCTG 58.838 47.619 0.00 0.00 40.30 4.00
2979 3277 5.335127 CCTATTTATGTCTTGTGTTGCTGC 58.665 41.667 0.00 0.00 0.00 5.25
2990 3288 5.116084 TGCTCAAAGGCCTATTTATGTCT 57.884 39.130 5.16 0.00 0.00 3.41
2992 3290 4.860022 ACTGCTCAAAGGCCTATTTATGT 58.140 39.130 5.16 0.00 0.00 2.29
3001 3299 0.034670 ATCCAGACTGCTCAAAGGCC 60.035 55.000 0.00 0.00 0.00 5.19
3004 3302 3.439476 CCAAAGATCCAGACTGCTCAAAG 59.561 47.826 0.00 0.00 0.00 2.77
3012 3310 1.558756 CAGCTCCCAAAGATCCAGACT 59.441 52.381 0.00 0.00 0.00 3.24
3013 3311 1.280421 ACAGCTCCCAAAGATCCAGAC 59.720 52.381 0.00 0.00 0.00 3.51
3023 3321 3.219281 GTTAGGTTGAAACAGCTCCCAA 58.781 45.455 0.00 0.00 0.00 4.12
3024 3322 2.173782 TGTTAGGTTGAAACAGCTCCCA 59.826 45.455 0.00 0.00 33.13 4.37
3025 3323 2.858745 TGTTAGGTTGAAACAGCTCCC 58.141 47.619 0.00 0.00 33.13 4.30
3026 3324 5.705905 ACTTATGTTAGGTTGAAACAGCTCC 59.294 40.000 0.00 0.00 40.00 4.70
3027 3325 6.803154 ACTTATGTTAGGTTGAAACAGCTC 57.197 37.500 0.00 0.00 40.00 4.09
3055 3353 3.131396 CGATAAGTGGGCACATAAGGAC 58.869 50.000 0.00 0.00 0.00 3.85
3059 3357 4.209307 TGTTCGATAAGTGGGCACATAA 57.791 40.909 0.00 0.00 0.00 1.90
3061 3359 2.779755 TGTTCGATAAGTGGGCACAT 57.220 45.000 0.00 0.00 0.00 3.21
3063 3361 2.354821 GGATTGTTCGATAAGTGGGCAC 59.645 50.000 0.00 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.