Multiple sequence alignment - TraesCS2A01G589200

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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 TraesCS2A01G589200 chr2A 100.000 3222 0 0 1 3222 778018850 778022071 0.000000e+00 5951
1 TraesCS2A01G589200 chr2D 92.622 2304 117 28 1 2288 635094774 635092508 0.000000e+00 3264
2 TraesCS2A01G589200 chr2D 88.434 415 31 3 2273 2670 635092490 635092076 4.830000e-133 484
3 TraesCS2A01G589200 chr2D 77.119 236 35 11 2443 2668 635091728 635091502 5.650000e-23 119
4 TraesCS2A01G589200 chr2B 92.048 2314 121 26 1 2277 779103525 779101238 0.000000e+00 3195
5 TraesCS2A01G589200 chr2B 88.108 370 28 6 2273 2627 779101210 779100842 2.970000e-115 425
6 TraesCS2A01G589200 chr2B 81.292 449 53 22 2785 3218 779100287 779099855 5.150000e-88 335
7 TraesCS2A01G589200 chr2B 93.860 114 6 1 2666 2779 779100626 779100514 1.540000e-38 171


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 TraesCS2A01G589200 chr2A 778018850 778022071 3221 False 5951.0 5951 100.000000 1 3222 1 chr2A.!!$F1 3221
1 TraesCS2A01G589200 chr2D 635091502 635094774 3272 True 1289.0 3264 86.058333 1 2670 3 chr2D.!!$R1 2669
2 TraesCS2A01G589200 chr2B 779099855 779103525 3670 True 1031.5 3195 88.827000 1 3218 4 chr2B.!!$R1 3217

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
222 224 0.108992 GATCACGTGGTCGGCTACAA 60.109 55.0 14.02 0.0 41.85 2.41 F
292 294 0.184933 AGGCAAAGCAAGTGTGGGTA 59.815 50.0 0.00 0.0 0.00 3.69 F
1624 1669 0.179056 ACAACCGCTGCAACTACTGT 60.179 50.0 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1591 1636 0.250553 GGTTGTCCCCGATGTTGTCA 60.251 55.000 0.0 0.0 0.00 3.58 R
1819 1864 1.076923 GGCGAGGTGGGACTCTAGA 60.077 63.158 0.0 0.0 35.33 2.43 R
3051 3708 0.178950 TCTGCTCACTGACCAGGAGT 60.179 55.000 0.0 0.0 32.16 3.85 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
42 43 3.191581 TCAAGTGATCAACGAGGAGTCTC 59.808 47.826 0.00 0.00 36.69 3.36
48 49 3.646736 TCAACGAGGAGTCTCTGGATA 57.353 47.619 0.00 0.00 37.86 2.59
49 50 3.964411 TCAACGAGGAGTCTCTGGATAA 58.036 45.455 0.00 0.00 37.86 1.75
50 51 3.948473 TCAACGAGGAGTCTCTGGATAAG 59.052 47.826 0.00 0.00 37.86 1.73
51 52 3.935818 ACGAGGAGTCTCTGGATAAGA 57.064 47.619 0.00 0.00 37.86 2.10
52 53 4.237976 ACGAGGAGTCTCTGGATAAGAA 57.762 45.455 0.00 0.00 37.86 2.52
53 54 4.601084 ACGAGGAGTCTCTGGATAAGAAA 58.399 43.478 0.00 0.00 37.86 2.52
54 55 5.017490 ACGAGGAGTCTCTGGATAAGAAAA 58.983 41.667 0.00 0.00 37.86 2.29
55 56 5.480772 ACGAGGAGTCTCTGGATAAGAAAAA 59.519 40.000 0.00 0.00 37.86 1.94
81 82 9.651913 AAAAATCACCGCACATTTTTCTATTAT 57.348 25.926 0.00 0.00 37.55 1.28
161 163 7.066766 AGCTGCAACAATTTTATTTTGGTTCAA 59.933 29.630 1.02 0.00 0.00 2.69
180 182 3.131400 TCAATCGATGTCGTGGTAATGGA 59.869 43.478 0.00 0.00 40.80 3.41
187 189 1.520787 CGTGGTAATGGAGACCGGC 60.521 63.158 0.00 0.00 40.09 6.13
203 205 2.561373 GCCGAGCCGAAAACAAGG 59.439 61.111 0.00 0.00 0.00 3.61
209 211 1.128692 GAGCCGAAAACAAGGATCACG 59.871 52.381 0.00 0.00 42.11 4.35
212 214 1.196808 CCGAAAACAAGGATCACGTGG 59.803 52.381 17.00 0.08 32.45 4.94
213 215 1.871039 CGAAAACAAGGATCACGTGGT 59.129 47.619 17.00 8.94 32.45 4.16
214 216 2.096417 CGAAAACAAGGATCACGTGGTC 60.096 50.000 20.80 20.80 32.45 4.02
222 224 0.108992 GATCACGTGGTCGGCTACAA 60.109 55.000 14.02 0.00 41.85 2.41
223 225 0.389426 ATCACGTGGTCGGCTACAAC 60.389 55.000 17.00 0.00 41.85 3.32
292 294 0.184933 AGGCAAAGCAAGTGTGGGTA 59.815 50.000 0.00 0.00 0.00 3.69
300 302 1.358152 CAAGTGTGGGTAGGGAAGGA 58.642 55.000 0.00 0.00 0.00 3.36
303 305 0.903236 GTGTGGGTAGGGAAGGAGTC 59.097 60.000 0.00 0.00 0.00 3.36
304 306 0.490017 TGTGGGTAGGGAAGGAGTCA 59.510 55.000 0.00 0.00 0.00 3.41
306 308 0.790993 TGGGTAGGGAAGGAGTCACT 59.209 55.000 0.00 0.00 44.53 3.41
309 311 2.627217 GGGTAGGGAAGGAGTCACTGAT 60.627 54.545 0.00 0.00 41.45 2.90
340 343 1.219131 GGGGGTGGTTAAGGGATGGT 61.219 60.000 0.00 0.00 0.00 3.55
350 353 0.995024 AAGGGATGGTCAGGAAGGTG 59.005 55.000 0.00 0.00 0.00 4.00
354 357 1.001641 ATGGTCAGGAAGGTGCAGC 60.002 57.895 8.11 8.11 0.00 5.25
364 367 3.422303 GGTGCAGCGCGTCATTGA 61.422 61.111 8.43 0.00 0.00 2.57
396 399 0.255890 CTGACGGGGGATGATGGTTT 59.744 55.000 0.00 0.00 0.00 3.27
438 441 1.653114 CAACAACGTGGTGCACTTTTG 59.347 47.619 17.98 15.81 33.86 2.44
470 473 2.713877 CGGGGGAGAAAAATTTACCGA 58.286 47.619 0.00 0.00 42.42 4.69
472 475 3.066203 CGGGGGAGAAAAATTTACCGATG 59.934 47.826 0.00 0.00 42.42 3.84
475 478 4.440112 GGGGAGAAAAATTTACCGATGCAG 60.440 45.833 0.00 0.00 0.00 4.41
476 479 4.398044 GGGAGAAAAATTTACCGATGCAGA 59.602 41.667 0.00 0.00 0.00 4.26
491 494 2.066262 TGCAGATTTTCTTCCGTCGAC 58.934 47.619 5.18 5.18 0.00 4.20
492 495 1.393883 GCAGATTTTCTTCCGTCGACC 59.606 52.381 10.58 0.00 0.00 4.79
503 506 2.019249 TCCGTCGACCGAAAGATATGT 58.981 47.619 10.58 0.00 39.56 2.29
504 507 2.117137 CCGTCGACCGAAAGATATGTG 58.883 52.381 10.58 0.00 39.56 3.21
511 514 2.103263 ACCGAAAGATATGTGCTCCCTC 59.897 50.000 0.00 0.00 0.00 4.30
533 536 9.626045 CCCTCTTGTTTATTTATTTCAGAACAC 57.374 33.333 0.00 0.00 0.00 3.32
637 648 8.583765 GCGAATAGTGTTCCAATTTTTATCAAC 58.416 33.333 0.00 0.00 0.00 3.18
701 714 3.975168 TTTCTGGTAGTAACTGGGCTC 57.025 47.619 0.00 0.00 0.00 4.70
900 917 3.707640 CTCCGACGCTCCTCCTCCT 62.708 68.421 0.00 0.00 0.00 3.69
926 943 1.450312 CTGGTAAGCCCCTTCTGCG 60.450 63.158 0.00 0.00 0.00 5.18
1005 1027 2.755876 TCGGCGCCTGAGATGAGT 60.756 61.111 26.68 0.00 0.00 3.41
1008 1030 2.202987 GCGCCTGAGATGAGTGGG 60.203 66.667 0.00 0.00 0.00 4.61
1175 1197 4.117661 GTCGAGGTCGCGGCTTCT 62.118 66.667 20.85 5.07 39.60 2.85
1212 1234 0.756294 CGCCACCATACATAGGGTCA 59.244 55.000 0.00 0.00 38.49 4.02
1311 1339 1.038130 CAGAGGAGACGGACGGGAAT 61.038 60.000 0.00 0.00 0.00 3.01
1441 1469 4.783621 GCCACCGCATGCTCTCCA 62.784 66.667 17.13 0.00 34.03 3.86
1472 1506 1.851304 GAGGTGATGCCCATTTCCAA 58.149 50.000 5.81 0.00 38.26 3.53
1475 1511 1.560505 GTGATGCCCATTTCCAACCT 58.439 50.000 0.00 0.00 0.00 3.50
1479 1515 0.780637 TGCCCATTTCCAACCTACCA 59.219 50.000 0.00 0.00 0.00 3.25
1497 1533 1.002900 CCAACAGCACGTTTCGTCATT 60.003 47.619 0.00 0.00 38.32 2.57
1624 1669 0.179056 ACAACCGCTGCAACTACTGT 60.179 50.000 0.00 0.00 0.00 3.55
1822 1867 2.599578 GGCCCGGCCTACGATCTA 60.600 66.667 22.31 0.00 46.69 1.98
1873 1918 2.103263 GGAGGTGATCAACTTCCGCTAT 59.897 50.000 15.99 0.00 44.37 2.97
2128 2173 2.041819 GGGATCGGTGAGGGGAGT 60.042 66.667 0.00 0.00 0.00 3.85
2197 2242 2.672996 GCCGTGGAGGTGTGCATT 60.673 61.111 0.00 0.00 43.70 3.56
2210 2255 3.354678 GCATTCGCAAGGTGGTGT 58.645 55.556 0.00 0.00 38.36 4.16
2289 2366 1.669779 CATTGCCTGCTAGAGTTCTGC 59.330 52.381 0.00 0.00 0.00 4.26
2304 2381 3.639094 AGTTCTGCTCATAGCCGAGTAAT 59.361 43.478 0.00 0.00 41.51 1.89
2310 2387 4.099419 TGCTCATAGCCGAGTAATCTTGAA 59.901 41.667 0.00 0.00 41.51 2.69
2311 2388 5.221521 TGCTCATAGCCGAGTAATCTTGAAT 60.222 40.000 0.00 0.00 41.51 2.57
2321 2398 5.290493 AGTAATCTTGAATGGCATCCGTA 57.710 39.130 0.00 0.00 0.00 4.02
2348 2425 3.930229 TGAATTCGTTAGTCGTTGATGGG 59.070 43.478 0.04 0.00 40.80 4.00
2384 2461 2.203209 GGAAGCATAGGCACCCCG 60.203 66.667 0.67 0.00 44.61 5.73
2385 2462 2.902343 GAAGCATAGGCACCCCGC 60.902 66.667 0.67 0.00 44.61 6.13
2417 2495 6.283694 TGATGTAGCAAACTGTCTGGATATC 58.716 40.000 0.00 0.00 0.00 1.63
2424 2502 5.220491 GCAAACTGTCTGGATATCGTCTTTC 60.220 44.000 0.00 0.00 0.00 2.62
2441 2519 3.657727 TCTTTCCTGAGGAGGGTGAATTT 59.342 43.478 0.00 0.00 40.25 1.82
2573 2653 1.450312 GATGTTGCTGTCTCCCGGG 60.450 63.158 16.85 16.85 0.00 5.73
2584 2664 3.934391 CTCCCGGGCGTGAGTTCAC 62.934 68.421 18.49 2.16 43.15 3.18
2586 2666 2.030562 CCGGGCGTGAGTTCACTT 59.969 61.111 10.27 0.00 44.34 3.16
2587 2667 2.027625 CCGGGCGTGAGTTCACTTC 61.028 63.158 10.27 2.59 44.34 3.01
2624 2720 3.009473 TGCCTGCTGGAGTTTATTCTTCT 59.991 43.478 14.77 0.00 34.57 2.85
2627 2723 4.813697 CCTGCTGGAGTTTATTCTTCTAGC 59.186 45.833 2.92 2.63 34.57 3.42
2657 2753 4.873827 TGAATGCCGAGGTAAACTGAATAC 59.126 41.667 0.00 0.00 0.00 1.89
2688 3047 0.107456 AGATGGAAGCATGGGTAGCG 59.893 55.000 0.00 0.00 37.01 4.26
2776 3179 5.538067 TTGTTGGTAAGCTTTTGTTTTGC 57.462 34.783 3.20 0.00 0.00 3.68
2779 3182 4.727507 TGGTAAGCTTTTGTTTTGCTGA 57.272 36.364 3.20 0.00 37.11 4.26
2781 3184 5.049167 TGGTAAGCTTTTGTTTTGCTGATG 58.951 37.500 3.20 0.00 37.11 3.07
2782 3185 4.084380 GGTAAGCTTTTGTTTTGCTGATGC 60.084 41.667 3.20 0.00 37.11 3.91
2791 3428 2.738139 TGCTGATGCACACCGTCG 60.738 61.111 0.00 0.00 45.31 5.12
2793 3430 2.317609 GCTGATGCACACCGTCGTT 61.318 57.895 0.00 0.00 39.41 3.85
2800 3437 2.000587 CACACCGTCGTTGTCGTTT 58.999 52.632 0.00 0.00 38.33 3.60
2806 3443 2.285950 ACCGTCGTTGTCGTTTTGATTG 60.286 45.455 0.00 0.00 38.33 2.67
2807 3444 1.701431 CGTCGTTGTCGTTTTGATTGC 59.299 47.619 0.00 0.00 38.33 3.56
2815 3452 6.247176 GTTGTCGTTTTGATTGCATTGTTTT 58.753 32.000 0.00 0.00 0.00 2.43
2817 3454 5.006165 TGTCGTTTTGATTGCATTGTTTTCC 59.994 36.000 0.00 0.00 0.00 3.13
2818 3455 5.006165 GTCGTTTTGATTGCATTGTTTTCCA 59.994 36.000 0.00 0.00 0.00 3.53
2819 3456 5.757320 TCGTTTTGATTGCATTGTTTTCCAT 59.243 32.000 0.00 0.00 0.00 3.41
2820 3457 6.925718 TCGTTTTGATTGCATTGTTTTCCATA 59.074 30.769 0.00 0.00 0.00 2.74
2821 3458 7.601886 TCGTTTTGATTGCATTGTTTTCCATAT 59.398 29.630 0.00 0.00 0.00 1.78
2828 3465 9.970395 GATTGCATTGTTTTCCATATATGAAGA 57.030 29.630 14.54 0.99 0.00 2.87
2829 3466 9.976511 ATTGCATTGTTTTCCATATATGAAGAG 57.023 29.630 14.54 0.00 0.00 2.85
2830 3467 7.944061 TGCATTGTTTTCCATATATGAAGAGG 58.056 34.615 14.54 0.00 0.00 3.69
2831 3468 7.560991 TGCATTGTTTTCCATATATGAAGAGGT 59.439 33.333 14.54 0.00 0.00 3.85
2832 3469 8.416329 GCATTGTTTTCCATATATGAAGAGGTT 58.584 33.333 14.54 0.00 0.00 3.50
2833 3470 9.956720 CATTGTTTTCCATATATGAAGAGGTTC 57.043 33.333 14.54 0.00 0.00 3.62
2834 3471 9.927081 ATTGTTTTCCATATATGAAGAGGTTCT 57.073 29.630 14.54 0.00 33.38 3.01
2835 3472 8.737168 TGTTTTCCATATATGAAGAGGTTCTG 57.263 34.615 14.54 0.00 33.38 3.02
2853 3490 5.221541 GGTTCTGTCTAGGATTACCATCTGG 60.222 48.000 0.00 0.00 38.94 3.86
2856 3493 6.202331 TCTGTCTAGGATTACCATCTGGAAA 58.798 40.000 2.55 0.00 38.94 3.13
2874 3511 7.535139 TCTGGAAAGTTGTCTGTTAGTTTTTG 58.465 34.615 0.00 0.00 0.00 2.44
2879 3517 6.995511 AGTTGTCTGTTAGTTTTTGTGCTA 57.004 33.333 0.00 0.00 0.00 3.49
2896 3534 1.789464 GCTACGATGAAGCTCGATTGG 59.211 52.381 0.00 0.00 41.12 3.16
2922 3560 8.523915 AATGCACATTCCTGACTTTTATATCA 57.476 30.769 0.00 0.00 0.00 2.15
2960 3598 4.330074 CAGGGAGCAGTACAATTTTCTACG 59.670 45.833 0.00 0.00 0.00 3.51
2965 3603 3.187637 GCAGTACAATTTTCTACGTGGCA 59.812 43.478 0.00 0.00 0.00 4.92
2976 3614 3.585862 TCTACGTGGCACTGAGAAAATC 58.414 45.455 16.72 0.00 0.00 2.17
3023 3680 2.101125 CATTATTTCGAACTTGCGGCG 58.899 47.619 0.51 0.51 0.00 6.46
3051 3708 6.830912 TGAAATCTCTCTTTGAGGTGAAGAA 58.169 36.000 0.00 0.00 42.86 2.52
3052 3709 6.708054 TGAAATCTCTCTTTGAGGTGAAGAAC 59.292 38.462 0.00 0.00 42.86 3.01
3053 3710 6.432403 AATCTCTCTTTGAGGTGAAGAACT 57.568 37.500 0.00 0.00 42.86 3.01
3054 3711 5.461032 TCTCTCTTTGAGGTGAAGAACTC 57.539 43.478 0.00 0.00 42.86 3.01
3055 3712 4.282195 TCTCTCTTTGAGGTGAAGAACTCC 59.718 45.833 0.00 0.00 42.86 3.85
3056 3713 4.227197 TCTCTTTGAGGTGAAGAACTCCT 58.773 43.478 0.00 0.00 44.02 3.69
3057 3714 4.039730 TCTCTTTGAGGTGAAGAACTCCTG 59.960 45.833 0.00 0.00 41.80 3.86
3058 3715 3.071602 TCTTTGAGGTGAAGAACTCCTGG 59.928 47.826 0.00 0.00 41.80 4.45
3059 3716 2.103153 TGAGGTGAAGAACTCCTGGT 57.897 50.000 0.00 0.00 41.80 4.00
3060 3717 1.971357 TGAGGTGAAGAACTCCTGGTC 59.029 52.381 0.00 0.00 41.80 4.02
3061 3718 1.971357 GAGGTGAAGAACTCCTGGTCA 59.029 52.381 0.00 0.00 41.80 4.02
3062 3719 1.974236 AGGTGAAGAACTCCTGGTCAG 59.026 52.381 0.00 0.00 40.46 3.51
3063 3720 1.694696 GGTGAAGAACTCCTGGTCAGT 59.305 52.381 0.00 0.00 0.00 3.41
3064 3721 2.548920 GGTGAAGAACTCCTGGTCAGTG 60.549 54.545 0.00 0.00 0.00 3.66
3065 3722 2.365617 GTGAAGAACTCCTGGTCAGTGA 59.634 50.000 0.00 0.00 0.00 3.41
3066 3723 2.630098 TGAAGAACTCCTGGTCAGTGAG 59.370 50.000 0.00 11.97 34.24 3.51
3067 3724 0.972883 AGAACTCCTGGTCAGTGAGC 59.027 55.000 15.47 15.47 32.52 4.26
3068 3725 0.681733 GAACTCCTGGTCAGTGAGCA 59.318 55.000 22.86 22.86 37.74 4.26
3090 3747 1.906574 AGTCTTTCAATCTACGGCCCA 59.093 47.619 0.00 0.00 0.00 5.36
3094 3751 4.879545 GTCTTTCAATCTACGGCCCATAAA 59.120 41.667 0.00 0.00 0.00 1.40
3108 3765 2.549754 CCCATAAAAGCATCTACAGCCG 59.450 50.000 0.00 0.00 0.00 5.52
3114 3771 0.176680 AGCATCTACAGCCGGACTTG 59.823 55.000 5.05 1.91 0.00 3.16
3157 3818 1.070786 ACATGTTCGGGCGTGTTCT 59.929 52.632 0.00 0.00 35.28 3.01
3162 3823 2.286872 TGTTCGGGCGTGTTCTTTTTA 58.713 42.857 0.00 0.00 0.00 1.52
3163 3824 2.031930 TGTTCGGGCGTGTTCTTTTTAC 59.968 45.455 0.00 0.00 0.00 2.01
3169 3830 2.798847 GGCGTGTTCTTTTTACGTCTCT 59.201 45.455 0.00 0.00 39.16 3.10
3197 3861 3.069586 TCCGTCCATTCACCATACTCATC 59.930 47.826 0.00 0.00 0.00 2.92
3204 3868 2.587522 TCACCATACTCATCTCCTCCG 58.412 52.381 0.00 0.00 0.00 4.63
3218 3882 0.179048 CCTCCGCCACTTGCATATGA 60.179 55.000 6.97 0.00 41.33 2.15
3219 3883 1.544093 CCTCCGCCACTTGCATATGAT 60.544 52.381 6.97 0.00 41.33 2.45
3220 3884 1.802960 CTCCGCCACTTGCATATGATC 59.197 52.381 6.97 0.00 41.33 2.92
3221 3885 0.514255 CCGCCACTTGCATATGATCG 59.486 55.000 6.97 0.00 41.33 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 5.584253 TTTTCTTATCCAGAGACTCCTCG 57.416 43.478 0.00 0.00 44.08 4.63
55 56 7.961325 AATAGAAAAATGTGCGGTGATTTTT 57.039 28.000 0.00 0.00 41.98 1.94
57 58 9.730420 GTATAATAGAAAAATGTGCGGTGATTT 57.270 29.630 0.00 0.00 0.00 2.17
58 59 9.120538 AGTATAATAGAAAAATGTGCGGTGATT 57.879 29.630 0.00 0.00 0.00 2.57
59 60 8.677148 AGTATAATAGAAAAATGTGCGGTGAT 57.323 30.769 0.00 0.00 0.00 3.06
60 61 9.772973 ATAGTATAATAGAAAAATGTGCGGTGA 57.227 29.630 0.00 0.00 0.00 4.02
80 81 9.762933 AACTTGTTTTGCATGTTTGAATAGTAT 57.237 25.926 0.00 0.00 40.99 2.12
81 82 9.593134 AAACTTGTTTTGCATGTTTGAATAGTA 57.407 25.926 9.40 0.00 46.73 1.82
161 163 2.956333 TCTCCATTACCACGACATCGAT 59.044 45.455 8.54 0.00 43.02 3.59
187 189 0.727398 GATCCTTGTTTTCGGCTCGG 59.273 55.000 0.00 0.00 0.00 4.63
203 205 0.108992 TTGTAGCCGACCACGTGATC 60.109 55.000 19.30 8.99 37.88 2.92
209 211 1.084289 GGAATGTTGTAGCCGACCAC 58.916 55.000 0.00 0.00 0.00 4.16
212 214 2.202566 GCTAGGAATGTTGTAGCCGAC 58.797 52.381 0.00 0.00 34.30 4.79
213 215 1.828595 TGCTAGGAATGTTGTAGCCGA 59.171 47.619 0.00 0.00 38.76 5.54
214 216 2.309528 TGCTAGGAATGTTGTAGCCG 57.690 50.000 0.00 0.00 38.76 5.52
222 224 1.224592 CGCCCCTTGCTAGGAATGT 59.775 57.895 16.43 0.00 45.05 2.71
223 225 0.533755 CTCGCCCCTTGCTAGGAATG 60.534 60.000 16.43 5.00 45.05 2.67
277 279 1.145571 TCCCTACCCACACTTGCTTT 58.854 50.000 0.00 0.00 0.00 3.51
292 294 2.753247 GGTATCAGTGACTCCTTCCCT 58.247 52.381 0.00 0.00 0.00 4.20
300 302 2.761208 CCTTCTTCCGGTATCAGTGACT 59.239 50.000 0.00 0.00 0.00 3.41
303 305 1.139058 CCCCTTCTTCCGGTATCAGTG 59.861 57.143 0.00 0.00 0.00 3.66
304 306 1.497161 CCCCTTCTTCCGGTATCAGT 58.503 55.000 0.00 0.00 0.00 3.41
306 308 2.925078 CCCCCTTCTTCCGGTATCA 58.075 57.895 0.00 0.00 0.00 2.15
325 328 1.913419 TCCTGACCATCCCTTAACCAC 59.087 52.381 0.00 0.00 0.00 4.16
326 329 2.352561 TCCTGACCATCCCTTAACCA 57.647 50.000 0.00 0.00 0.00 3.67
327 330 2.092375 CCTTCCTGACCATCCCTTAACC 60.092 54.545 0.00 0.00 0.00 2.85
358 361 0.666274 GCAGTGGTCGTCGTCAATGA 60.666 55.000 17.55 0.00 31.55 2.57
364 367 2.335369 GTCAGCAGTGGTCGTCGT 59.665 61.111 0.00 0.00 0.00 4.34
410 413 0.105224 ACCACGTTGTTGATCCGTCA 59.895 50.000 0.00 0.00 31.46 4.35
470 473 2.673368 GTCGACGGAAGAAAATCTGCAT 59.327 45.455 0.00 0.00 0.00 3.96
472 475 1.393883 GGTCGACGGAAGAAAATCTGC 59.606 52.381 9.92 0.00 0.00 4.26
475 478 1.986698 TCGGTCGACGGAAGAAAATC 58.013 50.000 21.91 0.00 44.45 2.17
476 479 2.443887 TTCGGTCGACGGAAGAAAAT 57.556 45.000 28.39 0.00 44.45 1.82
491 494 2.366916 AGAGGGAGCACATATCTTTCGG 59.633 50.000 0.00 0.00 0.00 4.30
492 495 3.742433 AGAGGGAGCACATATCTTTCG 57.258 47.619 0.00 0.00 0.00 3.46
503 506 7.888021 TCTGAAATAAATAAACAAGAGGGAGCA 59.112 33.333 0.00 0.00 0.00 4.26
504 507 8.281212 TCTGAAATAAATAAACAAGAGGGAGC 57.719 34.615 0.00 0.00 0.00 4.70
604 611 0.645868 GAACACTATTCGCAGCCGAC 59.354 55.000 0.00 0.00 44.30 4.79
653 665 8.826710 TGGAGTATTGCTACTTGATAAAAATCG 58.173 33.333 0.00 0.00 38.33 3.34
687 700 1.203994 TGCTTCGAGCCCAGTTACTAC 59.796 52.381 4.73 0.00 41.51 2.73
808 821 1.186200 GATTTGGGGGAAGGAGTTGC 58.814 55.000 0.00 0.00 0.00 4.17
937 954 1.753078 CACCACCCGAGATCGAGGA 60.753 63.158 14.15 0.00 43.02 3.71
1212 1234 1.458967 GTATGGGGCGTAGGAGGGT 60.459 63.158 0.00 0.00 0.00 4.34
1441 1469 3.437795 CACCTCGTAGACCGGCGT 61.438 66.667 6.01 0.00 37.11 5.68
1461 1495 1.548719 GTTGGTAGGTTGGAAATGGGC 59.451 52.381 0.00 0.00 0.00 5.36
1472 1506 1.589803 GAAACGTGCTGTTGGTAGGT 58.410 50.000 0.00 0.00 40.84 3.08
1475 1511 1.210870 GACGAAACGTGCTGTTGGTA 58.789 50.000 0.62 0.00 41.37 3.25
1479 1515 2.096819 ACAAATGACGAAACGTGCTGTT 59.903 40.909 0.62 0.00 41.37 3.16
1497 1533 1.005037 ACGGCGAGCTGATCAACAA 60.005 52.632 16.62 0.00 0.00 2.83
1591 1636 0.250553 GGTTGTCCCCGATGTTGTCA 60.251 55.000 0.00 0.00 0.00 3.58
1750 1795 1.079127 GTCATAGTGGCAGGTGCGT 60.079 57.895 0.00 0.00 43.26 5.24
1819 1864 1.076923 GGCGAGGTGGGACTCTAGA 60.077 63.158 0.00 0.00 35.33 2.43
1822 1867 2.997897 GTGGCGAGGTGGGACTCT 60.998 66.667 0.00 0.00 35.33 3.24
1873 1918 4.087892 GCCTGGAAGCTCTCGCCA 62.088 66.667 0.00 0.00 36.60 5.69
2128 2173 1.666011 GACCAGCAGGAAGACGTCA 59.334 57.895 19.50 0.00 38.69 4.35
2197 2242 1.116536 TACCAGACACCACCTTGCGA 61.117 55.000 0.00 0.00 0.00 5.10
2289 2366 5.636965 CCATTCAAGATTACTCGGCTATGAG 59.363 44.000 0.00 0.58 41.86 2.90
2304 2381 3.213506 CCAATACGGATGCCATTCAAGA 58.786 45.455 0.00 0.00 36.56 3.02
2310 2387 2.727123 TTCACCAATACGGATGCCAT 57.273 45.000 0.00 0.00 38.63 4.40
2311 2388 2.727123 ATTCACCAATACGGATGCCA 57.273 45.000 0.00 0.00 38.63 4.92
2321 2398 4.992319 TCAACGACTAACGAATTCACCAAT 59.008 37.500 6.22 0.00 45.77 3.16
2348 2425 5.407407 TTCCATCTCACTTACCAGAAGAC 57.593 43.478 0.00 0.00 0.00 3.01
2398 2476 4.645136 AGACGATATCCAGACAGTTTGCTA 59.355 41.667 0.00 0.00 0.00 3.49
2401 2479 5.292101 GGAAAGACGATATCCAGACAGTTTG 59.708 44.000 0.00 0.00 33.30 2.93
2417 2495 0.247736 CACCCTCCTCAGGAAAGACG 59.752 60.000 0.00 0.00 43.65 4.18
2424 2502 1.635487 TCCAAATTCACCCTCCTCAGG 59.365 52.381 0.00 0.00 39.98 3.86
2441 2519 3.634504 ACCAGCAAATTCAGCATATCCA 58.365 40.909 5.74 0.00 0.00 3.41
2527 2607 6.851222 ATAAACATCTAGAGGCAAATCACG 57.149 37.500 3.87 0.00 0.00 4.35
2584 2664 4.394300 CAGGCACCATCTGAAAACTAGAAG 59.606 45.833 0.00 0.00 34.36 2.85
2586 2666 3.869912 GCAGGCACCATCTGAAAACTAGA 60.870 47.826 0.00 0.00 34.36 2.43
2587 2667 2.421424 GCAGGCACCATCTGAAAACTAG 59.579 50.000 0.00 0.00 34.36 2.57
2657 2753 3.072038 TGCTTCCATCTCACCAGATATGG 59.928 47.826 4.39 4.39 45.28 2.74
2694 3053 1.067635 ACAATTTCCCGCATCAGCAAC 60.068 47.619 0.00 0.00 42.27 4.17
2776 3179 1.221466 ACAACGACGGTGTGCATCAG 61.221 55.000 19.50 0.00 0.00 2.90
2779 3182 2.307309 CGACAACGACGGTGTGCAT 61.307 57.895 25.61 0.00 42.66 3.96
2781 3184 2.027628 AAACGACAACGACGGTGTGC 62.028 55.000 25.61 13.73 42.66 4.57
2782 3185 0.370958 AAAACGACAACGACGGTGTG 59.629 50.000 25.61 17.41 42.66 3.82
2783 3186 0.370958 CAAAACGACAACGACGGTGT 59.629 50.000 20.36 20.36 42.66 4.16
2791 3428 5.388225 AACAATGCAATCAAAACGACAAC 57.612 34.783 0.00 0.00 0.00 3.32
2793 3430 5.006165 GGAAAACAATGCAATCAAAACGACA 59.994 36.000 0.00 0.00 0.00 4.35
2806 3443 7.945134 ACCTCTTCATATATGGAAAACAATGC 58.055 34.615 12.78 0.00 0.00 3.56
2807 3444 9.956720 GAACCTCTTCATATATGGAAAACAATG 57.043 33.333 12.78 0.00 0.00 2.82
2815 3452 7.671819 CCTAGACAGAACCTCTTCATATATGGA 59.328 40.741 12.78 2.95 0.00 3.41
2817 3454 8.642935 TCCTAGACAGAACCTCTTCATATATG 57.357 38.462 6.36 6.36 0.00 1.78
2818 3455 9.836179 AATCCTAGACAGAACCTCTTCATATAT 57.164 33.333 0.00 0.00 0.00 0.86
2820 3457 9.084533 GTAATCCTAGACAGAACCTCTTCATAT 57.915 37.037 0.00 0.00 0.00 1.78
2821 3458 7.506261 GGTAATCCTAGACAGAACCTCTTCATA 59.494 40.741 0.00 0.00 0.00 2.15
2823 3460 5.657302 GGTAATCCTAGACAGAACCTCTTCA 59.343 44.000 0.00 0.00 0.00 3.02
2825 3462 5.590818 TGGTAATCCTAGACAGAACCTCTT 58.409 41.667 0.00 0.00 34.23 2.85
2826 3463 5.208294 TGGTAATCCTAGACAGAACCTCT 57.792 43.478 0.00 0.00 34.23 3.69
2828 3465 5.600484 CAGATGGTAATCCTAGACAGAACCT 59.400 44.000 0.00 0.00 32.77 3.50
2829 3466 5.221541 CCAGATGGTAATCCTAGACAGAACC 60.222 48.000 0.00 0.00 32.77 3.62
2830 3467 5.598830 TCCAGATGGTAATCCTAGACAGAAC 59.401 44.000 0.00 0.00 36.34 3.01
2831 3468 5.777449 TCCAGATGGTAATCCTAGACAGAA 58.223 41.667 0.00 0.00 36.34 3.02
2832 3469 5.403558 TCCAGATGGTAATCCTAGACAGA 57.596 43.478 0.00 0.00 36.34 3.41
2833 3470 6.098982 ACTTTCCAGATGGTAATCCTAGACAG 59.901 42.308 0.00 0.00 36.34 3.51
2834 3471 5.964477 ACTTTCCAGATGGTAATCCTAGACA 59.036 40.000 0.00 0.00 36.34 3.41
2835 3472 6.487299 ACTTTCCAGATGGTAATCCTAGAC 57.513 41.667 0.00 0.00 36.34 2.59
2853 3490 6.806739 AGCACAAAAACTAACAGACAACTTTC 59.193 34.615 0.00 0.00 0.00 2.62
2856 3493 5.897377 AGCACAAAAACTAACAGACAACT 57.103 34.783 0.00 0.00 0.00 3.16
2874 3511 2.126914 ATCGAGCTTCATCGTAGCAC 57.873 50.000 0.00 0.00 43.20 4.40
2879 3517 2.672961 TTCCAATCGAGCTTCATCGT 57.327 45.000 0.00 0.00 43.20 3.73
2896 3534 8.623903 TGATATAAAAGTCAGGAATGTGCATTC 58.376 33.333 14.59 14.59 44.82 2.67
2914 3552 5.660417 TGAGCTTTGGGGCAAATGATATAAA 59.340 36.000 0.00 0.00 32.70 1.40
2922 3560 0.906282 CCCTGAGCTTTGGGGCAAAT 60.906 55.000 15.05 0.00 39.76 2.32
2976 3614 9.069082 AGCTTGTACATACTAAGATACCTACTG 57.931 37.037 0.00 0.00 0.00 2.74
3051 3708 0.178950 TCTGCTCACTGACCAGGAGT 60.179 55.000 0.00 0.00 32.16 3.85
3052 3709 0.531657 CTCTGCTCACTGACCAGGAG 59.468 60.000 0.00 6.57 0.00 3.69
3053 3710 0.178950 ACTCTGCTCACTGACCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
3054 3711 0.246086 GACTCTGCTCACTGACCAGG 59.754 60.000 1.82 0.00 0.00 4.45
3055 3712 1.255882 AGACTCTGCTCACTGACCAG 58.744 55.000 0.00 0.00 0.00 4.00
3056 3713 1.709578 AAGACTCTGCTCACTGACCA 58.290 50.000 0.00 0.00 0.00 4.02
3057 3714 2.036475 TGAAAGACTCTGCTCACTGACC 59.964 50.000 0.00 0.00 0.00 4.02
3058 3715 3.377346 TGAAAGACTCTGCTCACTGAC 57.623 47.619 0.00 0.00 0.00 3.51
3059 3716 4.282957 AGATTGAAAGACTCTGCTCACTGA 59.717 41.667 0.00 0.00 0.00 3.41
3060 3717 4.567971 AGATTGAAAGACTCTGCTCACTG 58.432 43.478 0.00 0.00 0.00 3.66
3061 3718 4.888326 AGATTGAAAGACTCTGCTCACT 57.112 40.909 0.00 0.00 0.00 3.41
3062 3719 4.560819 CGTAGATTGAAAGACTCTGCTCAC 59.439 45.833 0.00 0.00 0.00 3.51
3063 3720 4.380973 CCGTAGATTGAAAGACTCTGCTCA 60.381 45.833 0.00 0.00 0.00 4.26
3064 3721 4.109050 CCGTAGATTGAAAGACTCTGCTC 58.891 47.826 0.00 0.00 0.00 4.26
3065 3722 3.677424 GCCGTAGATTGAAAGACTCTGCT 60.677 47.826 0.00 0.00 0.00 4.24
3066 3723 2.605366 GCCGTAGATTGAAAGACTCTGC 59.395 50.000 0.00 0.00 0.00 4.26
3067 3724 3.190874 GGCCGTAGATTGAAAGACTCTG 58.809 50.000 0.00 0.00 0.00 3.35
3068 3725 2.168728 GGGCCGTAGATTGAAAGACTCT 59.831 50.000 0.00 0.00 0.00 3.24
3069 3726 2.093658 TGGGCCGTAGATTGAAAGACTC 60.094 50.000 0.00 0.00 0.00 3.36
3070 3727 1.906574 TGGGCCGTAGATTGAAAGACT 59.093 47.619 0.00 0.00 0.00 3.24
3071 3728 2.396590 TGGGCCGTAGATTGAAAGAC 57.603 50.000 0.00 0.00 0.00 3.01
3072 3729 4.764050 TTATGGGCCGTAGATTGAAAGA 57.236 40.909 5.46 0.00 0.00 2.52
3090 3747 3.134804 AGTCCGGCTGTAGATGCTTTTAT 59.865 43.478 0.00 0.00 0.00 1.40
3094 3751 0.905357 AAGTCCGGCTGTAGATGCTT 59.095 50.000 0.00 0.00 0.00 3.91
3108 3765 1.402852 GGCGCTGAATTTTCCAAGTCC 60.403 52.381 7.64 0.00 0.00 3.85
3114 3771 3.908213 TGTTTAAGGCGCTGAATTTTCC 58.092 40.909 7.64 0.00 0.00 3.13
3146 3807 0.582960 ACGTAAAAAGAACACGCCCG 59.417 50.000 0.00 0.00 39.23 6.13
3157 3818 7.546358 TGGACGGATAAATAGAGACGTAAAAA 58.454 34.615 0.00 0.00 34.43 1.94
3162 3823 5.301045 TGAATGGACGGATAAATAGAGACGT 59.699 40.000 0.00 0.00 37.26 4.34
3163 3824 5.629849 GTGAATGGACGGATAAATAGAGACG 59.370 44.000 0.00 0.00 0.00 4.18
3169 3830 7.015779 TGAGTATGGTGAATGGACGGATAAATA 59.984 37.037 0.00 0.00 0.00 1.40
3177 3838 4.302455 GAGATGAGTATGGTGAATGGACG 58.698 47.826 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.