Multiple sequence alignment - TraesCS4A01G223200

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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 TraesCS4A01G223200 chr4A 100.000 3558 0 0 1 3558 530939446 530935889 0.000000e+00 6571
1 TraesCS4A01G223200 chr4A 83.975 649 49 21 2959 3558 531117662 531118304 3.980000e-159 571
2 TraesCS4A01G223200 chr4D 89.645 2955 204 42 4 2889 65077092 65074171 0.000000e+00 3668
3 TraesCS4A01G223200 chr4D 93.770 305 17 1 2878 3180 65072014 65071710 1.160000e-124 457
4 TraesCS4A01G223200 chr4D 90.341 352 21 5 3215 3558 65070428 65070082 1.950000e-122 449
5 TraesCS4A01G223200 chr4B 89.189 2775 203 47 88 2833 95375410 95372704 0.000000e+00 3373
6 TraesCS4A01G223200 chr4B 84.776 624 46 15 2959 3558 95371213 95370615 6.620000e-162 580
7 TraesCS4A01G223200 chr2D 78.567 1535 267 40 1026 2536 11045298 11046794 0.000000e+00 955
8 TraesCS4A01G223200 chr2D 82.230 287 34 13 88 363 526159346 526159066 7.680000e-57 231
9 TraesCS4A01G223200 chr2B 77.995 1536 275 41 1026 2537 17366299 17364803 0.000000e+00 905
10 TraesCS4A01G223200 chr7B 77.540 1545 270 45 1027 2537 78244573 78243072 0.000000e+00 859
11 TraesCS4A01G223200 chrUn 78.079 1437 249 42 1026 2440 12633298 12631906 0.000000e+00 848
12 TraesCS4A01G223200 chrUn 81.851 562 72 15 961 1512 400800180 400800721 2.520000e-121 446
13 TraesCS4A01G223200 chrUn 81.818 561 73 14 961 1512 362827157 362826617 9.060000e-121 444
14 TraesCS4A01G223200 chrUn 81.640 561 74 14 961 1512 38566819 38567359 4.220000e-119 438
15 TraesCS4A01G223200 chrUn 84.793 217 29 3 961 1176 440756938 440756725 7.740000e-52 215
16 TraesCS4A01G223200 chr2A 80.921 912 150 17 1637 2537 11910502 11909604 0.000000e+00 699
17 TraesCS4A01G223200 chr1D 79.064 769 151 5 1775 2535 382743039 382742273 1.460000e-143 520
18 TraesCS4A01G223200 chr1D 81.752 274 25 18 108 363 29883062 29882796 4.660000e-49 206
19 TraesCS4A01G223200 chr3A 83.156 564 64 19 961 1512 32415123 32415667 1.480000e-133 486
20 TraesCS4A01G223200 chr3A 78.046 747 135 23 1804 2534 32415762 32416495 9.060000e-121 444
21 TraesCS4A01G223200 chr3A 83.043 230 26 11 88 310 686187205 686187428 2.800000e-46 196
22 TraesCS4A01G223200 chr3A 82.553 235 25 13 88 313 494036456 494036683 3.620000e-45 193
23 TraesCS4A01G223200 chr3A 79.787 282 35 16 88 353 738100936 738100661 6.070000e-43 185
24 TraesCS4A01G223200 chr3A 79.110 292 38 17 88 363 244000067 243999783 2.820000e-41 180
25 TraesCS4A01G223200 chr3B 81.851 562 72 15 961 1512 41143278 41142737 2.520000e-121 446
26 TraesCS4A01G223200 chr3B 81.851 562 72 15 961 1512 42194711 42195252 2.520000e-121 446
27 TraesCS4A01G223200 chr3B 81.317 562 81 13 961 1512 41037407 41036860 5.460000e-118 435
28 TraesCS4A01G223200 chr3D 81.272 283 29 17 88 353 372625150 372625425 1.290000e-49 207
29 TraesCS4A01G223200 chr1B 79.861 288 28 22 87 354 368711932 368712209 2.180000e-42 183


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 TraesCS4A01G223200 chr4A 530935889 530939446 3557 True 6571.000000 6571 100.0000 1 3558 1 chr4A.!!$R1 3557
1 TraesCS4A01G223200 chr4A 531117662 531118304 642 False 571.000000 571 83.9750 2959 3558 1 chr4A.!!$F1 599
2 TraesCS4A01G223200 chr4D 65070082 65077092 7010 True 1524.666667 3668 91.2520 4 3558 3 chr4D.!!$R1 3554
3 TraesCS4A01G223200 chr4B 95370615 95375410 4795 True 1976.500000 3373 86.9825 88 3558 2 chr4B.!!$R1 3470
4 TraesCS4A01G223200 chr2D 11045298 11046794 1496 False 955.000000 955 78.5670 1026 2536 1 chr2D.!!$F1 1510
5 TraesCS4A01G223200 chr2B 17364803 17366299 1496 True 905.000000 905 77.9950 1026 2537 1 chr2B.!!$R1 1511
6 TraesCS4A01G223200 chr7B 78243072 78244573 1501 True 859.000000 859 77.5400 1027 2537 1 chr7B.!!$R1 1510
7 TraesCS4A01G223200 chrUn 12631906 12633298 1392 True 848.000000 848 78.0790 1026 2440 1 chrUn.!!$R1 1414
8 TraesCS4A01G223200 chrUn 400800180 400800721 541 False 446.000000 446 81.8510 961 1512 1 chrUn.!!$F2 551
9 TraesCS4A01G223200 chrUn 362826617 362827157 540 True 444.000000 444 81.8180 961 1512 1 chrUn.!!$R2 551
10 TraesCS4A01G223200 chrUn 38566819 38567359 540 False 438.000000 438 81.6400 961 1512 1 chrUn.!!$F1 551
11 TraesCS4A01G223200 chr2A 11909604 11910502 898 True 699.000000 699 80.9210 1637 2537 1 chr2A.!!$R1 900
12 TraesCS4A01G223200 chr1D 382742273 382743039 766 True 520.000000 520 79.0640 1775 2535 1 chr1D.!!$R2 760
13 TraesCS4A01G223200 chr3A 32415123 32416495 1372 False 465.000000 486 80.6010 961 2534 2 chr3A.!!$F3 1573
14 TraesCS4A01G223200 chr3B 41142737 41143278 541 True 446.000000 446 81.8510 961 1512 1 chr3B.!!$R2 551
15 TraesCS4A01G223200 chr3B 42194711 42195252 541 False 446.000000 446 81.8510 961 1512 1 chr3B.!!$F1 551
16 TraesCS4A01G223200 chr3B 41036860 41037407 547 True 435.000000 435 81.3170 961 1512 1 chr3B.!!$R1 551

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
71 72 0.107993 CCATTGCTCTTGCCTCTCGA 60.108 55.0 0.0 0.0 38.71 4.04 F
691 717 0.321021 GCGCTCCATCCAGATCTCAT 59.679 55.0 0.0 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1236 1324 0.944386 CCGGCATTAATCCCTGTTCG 59.056 55.0 0.0 0.0 0.0 3.95 R
2638 2767 2.028112 TGGAGATTGGAGACCTGAAACG 60.028 50.0 0.0 0.0 0.0 3.60 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
29 30 9.129532 GTTTCAGCTCTAGTATACCCTAACTTA 57.870 37.037 0.00 0.00 0.00 2.24
52 53 5.385509 TTTAGGACTAATGGCTTTGTTGC 57.614 39.130 0.00 0.00 0.00 4.17
71 72 0.107993 CCATTGCTCTTGCCTCTCGA 60.108 55.000 0.00 0.00 38.71 4.04
74 75 1.188219 TTGCTCTTGCCTCTCGACCT 61.188 55.000 0.00 0.00 38.71 3.85
75 76 1.140804 GCTCTTGCCTCTCGACCTC 59.859 63.158 0.00 0.00 0.00 3.85
76 77 1.813192 CTCTTGCCTCTCGACCTCC 59.187 63.158 0.00 0.00 0.00 4.30
115 116 4.708421 CAGGATGGAACATCCTTGAAATGT 59.292 41.667 24.24 2.87 45.78 2.71
120 121 5.573219 TGGAACATCCTTGAAATGTGATCT 58.427 37.500 0.00 0.00 37.42 2.75
121 122 6.720309 TGGAACATCCTTGAAATGTGATCTA 58.280 36.000 0.00 0.00 37.42 1.98
155 156 5.901413 AGTCATGGTATGAGTGGATGAAT 57.099 39.130 0.00 0.00 41.23 2.57
185 186 6.547880 TCATGTGTTAAAAAGCCTCAGGTTTA 59.452 34.615 0.00 0.00 42.73 2.01
201 202 5.127845 TCAGGTTTATTCTTTTGCACAACCA 59.872 36.000 0.00 0.00 35.61 3.67
206 207 7.816995 GGTTTATTCTTTTGCACAACCATCATA 59.183 33.333 0.00 0.00 33.71 2.15
210 211 6.587206 TCTTTTGCACAACCATCATATCAA 57.413 33.333 0.00 0.00 0.00 2.57
218 219 6.972328 GCACAACCATCATATCAACGTATTTT 59.028 34.615 0.00 0.00 0.00 1.82
338 339 0.897863 TTTCAAACCGGCCCCATGAG 60.898 55.000 0.00 0.00 0.00 2.90
357 358 2.044946 CTCGGCCTCCAAAAGGGG 60.045 66.667 0.00 0.00 46.32 4.79
416 418 4.794248 GCAAAGTTTTTGCCTCGATTTT 57.206 36.364 13.97 0.00 39.38 1.82
417 419 5.898630 GCAAAGTTTTTGCCTCGATTTTA 57.101 34.783 13.97 0.00 39.38 1.52
418 420 6.280537 GCAAAGTTTTTGCCTCGATTTTAA 57.719 33.333 13.97 0.00 39.38 1.52
454 467 2.793278 TTGCGGGAAAAAGAAGAAGC 57.207 45.000 0.00 0.00 0.00 3.86
455 468 0.958822 TGCGGGAAAAAGAAGAAGCC 59.041 50.000 0.00 0.00 0.00 4.35
456 469 1.248486 GCGGGAAAAAGAAGAAGCCT 58.752 50.000 0.00 0.00 0.00 4.58
457 470 1.613925 GCGGGAAAAAGAAGAAGCCTT 59.386 47.619 0.00 0.00 34.81 4.35
458 471 2.608016 GCGGGAAAAAGAAGAAGCCTTG 60.608 50.000 0.00 0.00 31.62 3.61
575 595 6.463890 GCGATGCTGACATGATTTTATATTCG 59.536 38.462 0.00 0.00 36.35 3.34
583 606 8.208224 TGACATGATTTTATATTCGTAGTGGGT 58.792 33.333 0.00 0.00 0.00 4.51
587 610 6.259167 TGATTTTATATTCGTAGTGGGTGCAC 59.741 38.462 8.80 8.80 0.00 4.57
616 642 3.507162 TTTCCCAGAAAGACATCAGCA 57.493 42.857 0.00 0.00 0.00 4.41
657 683 2.213499 CCGCTTTGAGTCAAGTCAACT 58.787 47.619 5.56 0.00 36.15 3.16
691 717 0.321021 GCGCTCCATCCAGATCTCAT 59.679 55.000 0.00 0.00 0.00 2.90
695 721 2.552591 GCTCCATCCAGATCTCATTGGG 60.553 54.545 12.27 2.76 35.13 4.12
703 729 2.679837 CAGATCTCATTGGGTTGGTTCG 59.320 50.000 0.00 0.00 0.00 3.95
826 855 1.679032 CCCCCAAGTGTTCGATCTTCC 60.679 57.143 0.00 0.00 0.00 3.46
855 884 2.485814 AGTGCTTTTGAATCGAGAAGCC 59.514 45.455 13.83 8.19 42.81 4.35
891 947 5.065731 GCTTAGTTTCCAAGAGATCCATGTG 59.934 44.000 0.00 0.00 0.00 3.21
892 948 3.350833 AGTTTCCAAGAGATCCATGTGC 58.649 45.455 0.00 0.00 0.00 4.57
901 957 0.601311 GATCCATGTGCGCCTAGTCC 60.601 60.000 4.18 0.00 0.00 3.85
940 996 5.485353 TGTCCTTCTATATGGGGCATAAGAG 59.515 44.000 0.00 0.00 29.74 2.85
954 1010 3.302092 GCATAAGAGTTTCTGACGATGCG 60.302 47.826 0.00 0.00 30.87 4.73
955 1011 2.440539 AAGAGTTTCTGACGATGCGT 57.559 45.000 0.00 0.00 45.10 5.24
1008 1069 1.133025 CAACCATCAGAAATGGCGACC 59.867 52.381 3.98 0.00 42.82 4.79
1101 1163 0.959553 TCACCGACCAGTTCTCAGAC 59.040 55.000 0.00 0.00 0.00 3.51
1197 1265 3.070018 ACCTTCGCATGAGTTTCTGAAG 58.930 45.455 0.00 0.00 34.17 3.02
1236 1324 6.560253 TGCTGAAAAAGTATCTTTGAGGTC 57.440 37.500 0.00 0.00 0.00 3.85
1246 1334 2.257207 TCTTTGAGGTCGAACAGGGAT 58.743 47.619 1.87 0.00 0.00 3.85
1287 1375 2.806608 TTACCGTGAAGAAACTCGCT 57.193 45.000 0.00 0.00 0.00 4.93
1311 1399 0.168788 ATTCACCAATTGCGCGTGAG 59.831 50.000 8.43 0.00 37.78 3.51
1371 1465 7.094377 GCTCTCCACCATGAAAATGTAGTAAAA 60.094 37.037 0.00 0.00 0.00 1.52
1377 1471 8.924691 CACCATGAAAATGTAGTAAAATTGGTG 58.075 33.333 0.00 0.00 42.05 4.17
1431 1525 6.712095 TGGTGCTGAACAATGGAAGATATATC 59.288 38.462 4.42 4.42 0.00 1.63
1471 1565 3.054878 AGTTTACTTTGCCACGAGTACG 58.945 45.455 0.00 0.00 45.75 3.67
1508 1602 6.777580 AGCCTTCAGAAGAATCTTTTTGGTAA 59.222 34.615 12.14 0.00 32.03 2.85
1551 1645 4.997395 AGACTGCATTCGTGTTAATGTTCT 59.003 37.500 0.00 0.00 38.78 3.01
1552 1646 5.034554 ACTGCATTCGTGTTAATGTTCTG 57.965 39.130 0.00 0.00 38.78 3.02
1560 1654 9.773328 CATTCGTGTTAATGTTCTGATATGTTT 57.227 29.630 0.00 0.00 33.11 2.83
1584 1681 8.523915 TTATAGTACTACGGATTGGAGTTTGA 57.476 34.615 4.31 0.00 0.00 2.69
1590 1687 3.074412 ACGGATTGGAGTTTGACATCAC 58.926 45.455 0.00 0.00 0.00 3.06
1621 1726 9.912634 TTCCTTTAACTTTTCAATGCTCAATAG 57.087 29.630 0.00 0.00 0.00 1.73
1685 1791 8.952278 ACTTGTTATTGTACTGAAAACTTGTCA 58.048 29.630 0.00 0.00 0.00 3.58
1706 1816 6.145858 TGTCATTGTGAACATATTTTTGCTGC 59.854 34.615 0.00 0.00 0.00 5.25
1792 1902 6.920569 TCCTGTGTTTTACTTCTTCAGAAC 57.079 37.500 0.00 0.00 0.00 3.01
1848 1958 7.327214 TCAACATAATTAAGGGGATTTGCAAC 58.673 34.615 0.00 0.00 0.00 4.17
2019 2129 7.174946 CAGAATGTTGTTGGGTCATAGTAAGTT 59.825 37.037 0.00 0.00 0.00 2.66
2039 2149 4.154195 AGTTGACCACAAACTGCGATAATC 59.846 41.667 0.00 0.00 37.77 1.75
2093 2203 9.646427 GCATTCTAATCTCTCCGATAATACTTT 57.354 33.333 0.00 0.00 0.00 2.66
2239 2355 2.683211 ATTGTCCAGGCAAAGAACCT 57.317 45.000 1.06 0.00 38.35 3.50
2424 2551 6.586344 CATCTGAGTACCCATTGTTAGATGT 58.414 40.000 0.00 0.00 36.92 3.06
2589 2716 4.082026 GCCAGGTATGCAATTTTCACTCTT 60.082 41.667 0.00 0.00 0.00 2.85
2591 2718 6.350110 GCCAGGTATGCAATTTTCACTCTTTA 60.350 38.462 0.00 0.00 0.00 1.85
2592 2719 7.631377 GCCAGGTATGCAATTTTCACTCTTTAT 60.631 37.037 0.00 0.00 0.00 1.40
2638 2767 7.032580 CAGCTGCTGATAACCTACTATATGAC 58.967 42.308 24.88 0.00 32.44 3.06
2712 2841 3.635373 GACATGTGCAAGATGGAATGGAT 59.365 43.478 1.15 0.00 42.83 3.41
2713 2842 4.795469 ACATGTGCAAGATGGAATGGATA 58.205 39.130 0.00 0.00 42.83 2.59
2717 2846 3.817647 GTGCAAGATGGAATGGATACTCC 59.182 47.826 0.00 0.00 36.96 3.85
2730 2860 8.207545 GGAATGGATACTCCCTATTATTGCTAG 58.792 40.741 0.00 0.00 35.03 3.42
2833 2970 5.238868 TGCTACGTACTCCACATATCTCTTC 59.761 44.000 0.00 0.00 0.00 2.87
2874 3011 9.739276 TTTTATTCTCCAGATACAATGTTGTCT 57.261 29.630 0.99 0.00 42.35 3.41
2875 3012 8.722480 TTATTCTCCAGATACAATGTTGTCTG 57.278 34.615 16.55 16.55 42.35 3.51
2876 3013 5.745312 TCTCCAGATACAATGTTGTCTGT 57.255 39.130 19.74 0.00 42.35 3.41
2945 5255 5.799435 GGGAAAAATGCAAAAACTTTGTGTG 59.201 36.000 0.00 0.00 0.00 3.82
2949 5259 2.600731 TGCAAAAACTTTGTGTGTCGG 58.399 42.857 1.45 0.00 0.00 4.79
2962 6687 1.453015 TGTCGGTGCTTTGTGGCTT 60.453 52.632 0.00 0.00 0.00 4.35
2998 6723 6.364435 GTCCAAGTTAGTCTAGTTTACAACCG 59.636 42.308 0.00 0.00 0.00 4.44
3086 6815 4.147321 GGGATGATACCAACCGTAGTCTA 58.853 47.826 0.00 0.00 36.21 2.59
3124 6869 8.954350 AGATGATCGATTCAACAATCTTCTTTT 58.046 29.630 0.00 0.00 38.03 2.27
3126 6871 7.236474 TGATCGATTCAACAATCTTCTTTTCG 58.764 34.615 0.00 0.00 36.93 3.46
3181 6926 9.880157 ATTTGCTCAATTGACTTTTAGCATTAT 57.120 25.926 15.84 10.94 39.50 1.28
3190 6935 9.914834 ATTGACTTTTAGCATTATTACTACCCA 57.085 29.630 0.00 0.00 0.00 4.51
3192 6937 7.771826 TGACTTTTAGCATTATTACTACCCACC 59.228 37.037 0.00 0.00 0.00 4.61
3193 6938 7.635648 ACTTTTAGCATTATTACTACCCACCA 58.364 34.615 0.00 0.00 0.00 4.17
3194 6939 7.555195 ACTTTTAGCATTATTACTACCCACCAC 59.445 37.037 0.00 0.00 0.00 4.16
3196 6941 5.646692 AGCATTATTACTACCCACCACAT 57.353 39.130 0.00 0.00 0.00 3.21
3198 6943 4.023193 GCATTATTACTACCCACCACATGC 60.023 45.833 0.00 0.00 0.00 4.06
3199 6944 2.325583 ATTACTACCCACCACATGCG 57.674 50.000 0.00 0.00 0.00 4.73
3200 6945 0.978151 TTACTACCCACCACATGCGT 59.022 50.000 0.00 0.00 0.00 5.24
3202 6947 1.809619 CTACCCACCACATGCGTCG 60.810 63.158 0.00 0.00 0.00 5.12
3205 6950 4.088762 CCACCACATGCGTCGCAC 62.089 66.667 24.34 0.00 43.04 5.34
3210 6965 0.317770 CCACATGCGTCGCACTTTTT 60.318 50.000 24.34 2.64 43.04 1.94
3260 8265 6.878923 CGGACTTCATATGCCATAATTTCCTA 59.121 38.462 0.00 0.00 0.00 2.94
3274 8279 9.512588 CCATAATTTCCTAGTTTGCTCTCATAT 57.487 33.333 0.00 0.00 0.00 1.78
3307 8312 7.544566 TCAGATGTTTAAGATGTCGTCTAAACC 59.455 37.037 16.32 8.43 35.67 3.27
3313 8318 4.612932 AGATGTCGTCTAAACCTCGTAC 57.387 45.455 0.00 0.00 34.69 3.67
3314 8319 4.005650 AGATGTCGTCTAAACCTCGTACA 58.994 43.478 0.00 0.00 34.69 2.90
3324 8329 7.637907 CGTCTAAACCTCGTACAGTAATAACTC 59.362 40.741 0.00 0.00 31.97 3.01
3347 8352 6.331845 TCAATATTTAGGCTGTGTTTGCATG 58.668 36.000 0.00 0.00 0.00 4.06
3349 8354 0.240678 TTAGGCTGTGTTTGCATGCG 59.759 50.000 14.09 0.00 0.00 4.73
3368 8381 4.052608 TGCGAAAATCGTCAGTTTCAGTA 58.947 39.130 1.45 0.00 42.81 2.74
3369 8382 4.508492 TGCGAAAATCGTCAGTTTCAGTAA 59.492 37.500 1.45 0.00 42.81 2.24
3437 8462 1.261238 GCAGCCAGAGTCACCCTACT 61.261 60.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.767670 AGGGTATACTAGAGCTGAAACTCA 58.232 41.667 2.25 0.00 39.26 3.41
1 2 7.503230 AGTTAGGGTATACTAGAGCTGAAACTC 59.497 40.741 2.25 0.00 36.91 3.01
2 3 7.355890 AGTTAGGGTATACTAGAGCTGAAACT 58.644 38.462 2.25 0.00 0.00 2.66
29 30 5.965922 GCAACAAAGCCATTAGTCCTAAAT 58.034 37.500 0.00 0.00 0.00 1.40
52 53 0.107993 TCGAGAGGCAAGAGCAATGG 60.108 55.000 0.00 0.00 44.61 3.16
53 54 1.005340 GTCGAGAGGCAAGAGCAATG 58.995 55.000 0.00 0.00 44.61 2.82
58 59 0.967887 TGGAGGTCGAGAGGCAAGAG 60.968 60.000 0.00 0.00 37.54 2.85
74 75 0.623194 TGAAATTCGGCCTCCATGGA 59.377 50.000 15.27 15.27 38.35 3.41
75 76 1.027357 CTGAAATTCGGCCTCCATGG 58.973 55.000 4.97 4.97 39.35 3.66
76 77 1.027357 CCTGAAATTCGGCCTCCATG 58.973 55.000 0.00 0.00 0.00 3.66
141 142 9.093458 ACACATGATACTATTCATCCACTCATA 57.907 33.333 0.00 0.00 34.09 2.15
142 143 7.971201 ACACATGATACTATTCATCCACTCAT 58.029 34.615 0.00 0.00 34.09 2.90
155 156 7.552687 CCTGAGGCTTTTTAACACATGATACTA 59.447 37.037 0.00 0.00 0.00 1.82
185 186 7.172868 TGATATGATGGTTGTGCAAAAGAAT 57.827 32.000 0.00 0.00 0.00 2.40
319 320 0.897863 CTCATGGGGCCGGTTTGAAA 60.898 55.000 1.90 0.00 0.00 2.69
320 321 1.304052 CTCATGGGGCCGGTTTGAA 60.304 57.895 1.90 0.00 0.00 2.69
321 322 2.354729 CTCATGGGGCCGGTTTGA 59.645 61.111 1.90 0.00 0.00 2.69
322 323 2.755469 CCTCATGGGGCCGGTTTG 60.755 66.667 0.00 0.00 0.00 2.93
384 386 6.228273 GCAAAAACTTTGCCTTTCCTATTC 57.772 37.500 12.10 0.00 39.38 1.75
432 445 3.868661 GCTTCTTCTTTTTCCCGCAAAAA 59.131 39.130 3.94 3.94 40.93 1.94
433 446 3.453424 GCTTCTTCTTTTTCCCGCAAAA 58.547 40.909 0.00 0.00 31.73 2.44
434 447 2.223947 GGCTTCTTCTTTTTCCCGCAAA 60.224 45.455 0.00 0.00 0.00 3.68
435 448 1.339929 GGCTTCTTCTTTTTCCCGCAA 59.660 47.619 0.00 0.00 0.00 4.85
436 449 0.958822 GGCTTCTTCTTTTTCCCGCA 59.041 50.000 0.00 0.00 0.00 5.69
437 450 1.248486 AGGCTTCTTCTTTTTCCCGC 58.752 50.000 0.00 0.00 0.00 6.13
438 451 2.608016 GCAAGGCTTCTTCTTTTTCCCG 60.608 50.000 0.00 0.00 0.00 5.14
439 452 2.289072 GGCAAGGCTTCTTCTTTTTCCC 60.289 50.000 0.00 0.00 0.00 3.97
440 453 2.630098 AGGCAAGGCTTCTTCTTTTTCC 59.370 45.455 0.00 0.00 0.00 3.13
441 454 4.053983 CAAGGCAAGGCTTCTTCTTTTTC 58.946 43.478 5.85 0.00 0.00 2.29
442 455 3.452264 ACAAGGCAAGGCTTCTTCTTTTT 59.548 39.130 5.85 0.00 0.00 1.94
443 456 3.033909 ACAAGGCAAGGCTTCTTCTTTT 58.966 40.909 5.85 0.00 0.00 2.27
444 457 2.363359 CACAAGGCAAGGCTTCTTCTTT 59.637 45.455 5.85 0.00 0.00 2.52
445 458 1.959282 CACAAGGCAAGGCTTCTTCTT 59.041 47.619 5.85 0.00 0.00 2.52
446 459 1.613836 CACAAGGCAAGGCTTCTTCT 58.386 50.000 5.85 0.00 0.00 2.85
447 460 0.600057 CCACAAGGCAAGGCTTCTTC 59.400 55.000 5.85 0.00 0.00 2.87
449 462 4.507969 CCACAAGGCAAGGCTTCT 57.492 55.556 5.85 0.00 0.00 2.85
492 512 2.813908 GGCTTTCATCGACGGCGT 60.814 61.111 14.65 14.65 38.98 5.68
616 642 3.323403 GGTCTAGCCTATGATGCTCACTT 59.677 47.826 0.00 0.00 40.23 3.16
657 683 0.391130 AGCGCGTAGGCAAAGAATGA 60.391 50.000 8.43 0.00 39.92 2.57
665 691 4.221422 GGATGGAGCGCGTAGGCA 62.221 66.667 8.43 0.00 39.92 4.75
691 717 4.701171 GTGGATTTATACGAACCAACCCAA 59.299 41.667 0.00 0.00 32.32 4.12
695 721 3.310501 CGGGTGGATTTATACGAACCAAC 59.689 47.826 0.00 0.00 37.57 3.77
703 729 3.995048 GCTAGCTTCGGGTGGATTTATAC 59.005 47.826 7.70 0.00 0.00 1.47
826 855 3.119849 CGATTCAAAAGCACTAACCTGGG 60.120 47.826 0.00 0.00 0.00 4.45
891 947 0.531200 AAGTACACAGGACTAGGCGC 59.469 55.000 0.00 0.00 0.00 6.53
892 948 3.276857 TCTAAGTACACAGGACTAGGCG 58.723 50.000 0.00 0.00 0.00 5.52
901 957 6.767524 AGAAGGACAGATCTAAGTACACAG 57.232 41.667 0.00 0.00 0.00 3.66
940 996 1.059264 GCTACACGCATCGTCAGAAAC 59.941 52.381 0.00 0.00 38.32 2.78
1101 1163 1.850441 CCTGTACCGATTTTACGCTCG 59.150 52.381 0.00 0.00 34.73 5.03
1197 1265 3.916761 TCAGCAAACATTGGCATCTTTC 58.083 40.909 0.00 0.00 0.00 2.62
1236 1324 0.944386 CCGGCATTAATCCCTGTTCG 59.056 55.000 0.00 0.00 0.00 3.95
1287 1375 2.057316 CGCGCAATTGGTGAATTTTCA 58.943 42.857 8.75 0.00 34.20 2.69
1431 1525 2.033299 ACTTTCAACAATGTCAGCCACG 59.967 45.455 0.00 0.00 0.00 4.94
1508 1602 7.928706 GCAGTCTGAATCAGGTAGTATTGTATT 59.071 37.037 10.71 0.00 31.51 1.89
1512 1606 5.664457 TGCAGTCTGAATCAGGTAGTATTG 58.336 41.667 10.71 0.00 31.51 1.90
1513 1607 5.939764 TGCAGTCTGAATCAGGTAGTATT 57.060 39.130 10.71 0.00 31.51 1.89
1529 1623 5.082059 CAGAACATTAACACGAATGCAGTC 58.918 41.667 3.54 3.54 39.94 3.51
1531 1625 5.281693 TCAGAACATTAACACGAATGCAG 57.718 39.130 0.00 0.00 39.94 4.41
1560 1654 7.557358 TGTCAAACTCCAATCCGTAGTACTATA 59.443 37.037 5.75 0.00 0.00 1.31
1561 1655 6.379133 TGTCAAACTCCAATCCGTAGTACTAT 59.621 38.462 5.75 0.00 0.00 2.12
1562 1656 5.711506 TGTCAAACTCCAATCCGTAGTACTA 59.288 40.000 0.00 0.00 0.00 1.82
1563 1657 4.525487 TGTCAAACTCCAATCCGTAGTACT 59.475 41.667 0.00 0.00 0.00 2.73
1564 1658 4.813027 TGTCAAACTCCAATCCGTAGTAC 58.187 43.478 0.00 0.00 0.00 2.73
1565 1659 5.186215 TGATGTCAAACTCCAATCCGTAGTA 59.814 40.000 0.00 0.00 0.00 1.82
1570 1667 3.338249 AGTGATGTCAAACTCCAATCCG 58.662 45.455 0.00 0.00 0.00 4.18
1572 1669 8.778358 GGAATATAGTGATGTCAAACTCCAATC 58.222 37.037 0.00 0.00 0.00 2.67
1664 1769 9.729023 CACAATGACAAGTTTTCAGTACAATAA 57.271 29.630 0.00 0.00 0.00 1.40
1679 1784 8.218441 CAGCAAAAATATGTTCACAATGACAAG 58.782 33.333 0.00 0.00 0.00 3.16
1685 1791 4.626604 CGGCAGCAAAAATATGTTCACAAT 59.373 37.500 0.00 0.00 0.00 2.71
1792 1902 7.447374 TGTTCCAGTCCATTTTTGTATGTAG 57.553 36.000 0.00 0.00 0.00 2.74
1848 1958 2.715268 CTGTGTACAAAGTGCAAACCG 58.285 47.619 4.74 0.00 28.81 4.44
2019 2129 3.937814 AGATTATCGCAGTTTGTGGTCA 58.062 40.909 0.00 0.00 0.00 4.02
2039 2149 9.218359 GTTTACTTTAAGACGAAGGAACAAAAG 57.782 33.333 0.00 0.00 30.93 2.27
2455 2582 5.875224 TCAACACATTCCAGTCCTATTTCA 58.125 37.500 0.00 0.00 0.00 2.69
2589 2716 8.389779 TGAAATGCAGAACAAGTCAGTTATAA 57.610 30.769 0.00 0.00 0.00 0.98
2591 2718 6.882610 TGAAATGCAGAACAAGTCAGTTAT 57.117 33.333 0.00 0.00 0.00 1.89
2638 2767 2.028112 TGGAGATTGGAGACCTGAAACG 60.028 50.000 0.00 0.00 0.00 3.60
2743 2873 9.338291 CGTACATATCATAGCGTACTGTTTTAT 57.662 33.333 0.00 0.00 33.61 1.40
2749 2879 5.923665 TGACGTACATATCATAGCGTACTG 58.076 41.667 0.00 3.33 33.61 2.74
2751 2881 6.800408 ACAATGACGTACATATCATAGCGTAC 59.200 38.462 5.05 0.00 38.38 3.67
2833 2970 9.062524 TGGAGAATAAAAATATCCATTACCACG 57.937 33.333 0.00 0.00 35.16 4.94
2945 5255 0.948678 TTAAGCCACAAAGCACCGAC 59.051 50.000 0.00 0.00 34.23 4.79
2949 5259 2.979813 CGTTGATTAAGCCACAAAGCAC 59.020 45.455 0.00 0.00 34.23 4.40
2962 6687 3.583966 ACTAACTTGGACCCCGTTGATTA 59.416 43.478 5.92 0.00 0.00 1.75
2998 6723 9.027202 TGGTTTAATCCCCAAATAGTTTAAGTC 57.973 33.333 0.02 0.00 0.00 3.01
3086 6815 8.722480 TGAATCGATCATCTCTTGTTTATTGT 57.278 30.769 0.00 0.00 31.50 2.71
3124 6869 1.153449 CGGGCAAGTAGGCATTCGA 60.153 57.895 0.00 0.00 46.44 3.71
3126 6871 0.107654 ACTCGGGCAAGTAGGCATTC 60.108 55.000 0.00 0.00 46.44 2.67
3181 6926 3.844911 CGCATGTGGTGGGTAGTAA 57.155 52.632 0.00 0.00 36.12 2.24
3189 6934 2.116736 AAAGTGCGACGCATGTGGTG 62.117 55.000 27.23 3.40 41.91 4.17
3190 6935 1.444119 AAAAGTGCGACGCATGTGGT 61.444 50.000 27.23 7.96 41.91 4.16
3192 6937 3.162499 AAAAAGTGCGACGCATGTG 57.838 47.368 27.23 4.30 41.91 3.21
3213 8205 1.078778 TCGCCTAATCGCCTGCAAA 60.079 52.632 0.00 0.00 0.00 3.68
3260 8265 6.712095 TCTGAAACAACATATGAGAGCAAACT 59.288 34.615 10.38 0.00 0.00 2.66
3274 8279 7.011950 ACGACATCTTAAACATCTGAAACAACA 59.988 33.333 0.00 0.00 0.00 3.33
3324 8329 5.005971 GCATGCAAACACAGCCTAAATATTG 59.994 40.000 14.21 0.00 0.00 1.90
3347 8352 3.521524 ACTGAAACTGACGATTTTCGC 57.478 42.857 0.00 0.00 45.12 4.70
3368 8381 8.961634 GGATACTTCCTCTTGCTAAGAAAAATT 58.038 33.333 0.00 0.00 39.14 1.82
3369 8382 8.109634 TGGATACTTCCTCTTGCTAAGAAAAAT 58.890 33.333 0.00 0.00 43.07 1.82
3437 8462 3.636231 CGGACTGGGCCACTTGGA 61.636 66.667 0.00 0.00 37.39 3.53
3531 8563 0.899253 TTCGTGGTGGTCCATACGGA 60.899 55.000 23.26 16.49 46.20 4.69


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

AutoCloner maintained by Alex Coulton.