Multiple sequence alignment - TraesCS1D01G114100

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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 TraesCS1D01G114100 chr1D 100.000 3661 0 0 1 3661 110333621 110337281 0.000000e+00 6761.0
1 TraesCS1D01G114100 chr1A 89.600 2952 170 56 1 2873 114543707 114546600 0.000000e+00 3624.0
2 TraesCS1D01G114100 chr1A 90.854 164 4 4 3230 3385 114547311 114547471 3.700000e-50 209.0
3 TraesCS1D01G114100 chr1A 87.662 154 8 7 3030 3177 114547154 114547302 6.290000e-38 169.0
4 TraesCS1D01G114100 chr1A 95.098 102 4 1 3561 3661 114547960 114548061 3.780000e-35 159.0
5 TraesCS1D01G114100 chr1B 93.012 2347 84 22 588 2873 167712242 167714569 0.000000e+00 3352.0
6 TraesCS1D01G114100 chr1B 88.960 471 23 12 3217 3661 167714922 167715389 4.130000e-154 555.0
7 TraesCS1D01G114100 chr4B 86.240 516 69 2 1797 2311 119275144 119275658 3.190000e-155 558.0
8 TraesCS1D01G114100 chr4B 75.960 495 99 18 1800 2284 375790852 375791336 1.700000e-58 237.0
9 TraesCS1D01G114100 chr4A 86.240 516 69 2 1797 2311 497011898 497012412 3.190000e-155 558.0
10 TraesCS1D01G114100 chr4D 85.659 516 72 2 1797 2311 84278112 84278626 3.220000e-150 542.0
11 TraesCS1D01G114100 chr4D 75.506 494 103 16 1800 2284 301534900 301535384 3.680000e-55 226.0
12 TraesCS1D01G114100 chr5D 76.626 569 89 17 25 573 37122991 37122447 1.300000e-69 274.0
13 TraesCS1D01G114100 chrUn 76.020 588 85 27 1 573 101391046 101390500 1.690000e-63 254.0
14 TraesCS1D01G114100 chr2B 79.937 319 48 12 25 337 397607857 397607549 1.710000e-53 220.0
15 TraesCS1D01G114100 chr2A 76.333 469 73 24 1 458 434987089 434986648 2.210000e-52 217.0
16 TraesCS1D01G114100 chr7D 77.251 211 25 14 52 258 115244406 115244215 6.470000e-18 102.0
17 TraesCS1D01G114100 chr5B 82.353 102 18 0 52 153 27789106 27789005 5.040000e-14 89.8


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 TraesCS1D01G114100 chr1D 110333621 110337281 3660 False 6761.00 6761 100.0000 1 3661 1 chr1D.!!$F1 3660
1 TraesCS1D01G114100 chr1A 114543707 114548061 4354 False 1040.25 3624 90.8035 1 3661 4 chr1A.!!$F1 3660
2 TraesCS1D01G114100 chr1B 167712242 167715389 3147 False 1953.50 3352 90.9860 588 3661 2 chr1B.!!$F1 3073
3 TraesCS1D01G114100 chr4B 119275144 119275658 514 False 558.00 558 86.2400 1797 2311 1 chr4B.!!$F1 514
4 TraesCS1D01G114100 chr4A 497011898 497012412 514 False 558.00 558 86.2400 1797 2311 1 chr4A.!!$F1 514
5 TraesCS1D01G114100 chr4D 84278112 84278626 514 False 542.00 542 85.6590 1797 2311 1 chr4D.!!$F1 514
6 TraesCS1D01G114100 chr5D 37122447 37122991 544 True 274.00 274 76.6260 25 573 1 chr5D.!!$R1 548
7 TraesCS1D01G114100 chrUn 101390500 101391046 546 True 254.00 254 76.0200 1 573 1 chrUn.!!$R1 572

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
378 423 0.406361 AGGAGAGTGACGGAGGAAGT 59.594 55.0 0.00 0.00 0.00 3.01 F
1085 1186 0.249911 GGCTGGTAGCTATGGTTCGG 60.250 60.0 0.00 0.00 41.99 4.30 F
2014 2133 0.457035 CTGCCCGTATTGCTTGCAAT 59.543 50.0 21.98 21.98 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 1373 0.530744 CGAACAGAGGATGAACCCGA 59.469 55.0 0.0 0.0 40.05 5.14 R
2399 2519 0.111253 AACTTGGTGAAGCCCCTGAG 59.889 55.0 0.0 0.0 36.04 3.35 R
3506 4050 0.100682 TATGTCCTCGTCGCTCTTGC 59.899 55.0 0.0 0.0 0.00 4.01 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
25 26 4.873827 GCAAACCATAGTTCACTTATCCGA 59.126 41.667 0.00 0.00 34.19 4.55
46 47 3.584733 ATCCCTAGAATTCCAGCAACC 57.415 47.619 0.65 0.00 0.00 3.77
47 48 1.209504 TCCCTAGAATTCCAGCAACCG 59.790 52.381 0.65 0.00 0.00 4.44
131 132 2.534019 CGACAGCTGTTGCCGTTGT 61.534 57.895 22.65 0.00 40.80 3.32
133 134 2.249309 CAGCTGTTGCCGTTGTCG 59.751 61.111 5.25 0.00 40.80 4.35
153 154 1.269309 GCTGGCGACGATGAGATACTT 60.269 52.381 0.00 0.00 0.00 2.24
190 208 6.604396 TGATATTGCCACAACAATCTTCATCT 59.396 34.615 0.00 0.00 40.64 2.90
334 379 0.478507 GAGAGGAGAGGGAGAGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
375 420 1.303615 GGAGGAGAGTGACGGAGGA 59.696 63.158 0.00 0.00 0.00 3.71
378 423 0.406361 AGGAGAGTGACGGAGGAAGT 59.594 55.000 0.00 0.00 0.00 3.01
410 455 4.162690 GGCCCAGTCGCTTCGGAT 62.163 66.667 0.00 0.00 0.00 4.18
472 527 1.231958 GGATCGGCCACGTCAAAACA 61.232 55.000 2.24 0.00 41.85 2.83
544 601 3.838550 GTGCGAAATGTCACAATCGTAAC 59.161 43.478 15.36 11.28 37.60 2.50
573 631 3.452755 TTCCGCTAATCATGACACGAT 57.547 42.857 0.00 0.00 0.00 3.73
601 659 2.492088 GCTTCTCGGCCTAAACCATTTT 59.508 45.455 0.00 0.00 0.00 1.82
604 662 4.028993 TCTCGGCCTAAACCATTTTCTT 57.971 40.909 0.00 0.00 0.00 2.52
612 670 1.620822 AACCATTTTCTTCTGCGGCT 58.379 45.000 0.00 0.00 0.00 5.52
649 707 1.456544 GCATGACGCAAACCAAATGTG 59.543 47.619 0.00 0.00 41.79 3.21
719 805 3.926058 AATCCAACGGCTAATACTGGT 57.074 42.857 0.00 0.00 0.00 4.00
744 830 1.568504 AGTGTGGCCCGAATCTTCTA 58.431 50.000 0.00 0.00 0.00 2.10
936 1026 1.751437 GATCCACACCAAACCCTAGC 58.249 55.000 0.00 0.00 0.00 3.42
1017 1107 1.340991 GCCATGGGGAGAAGTAAGCAA 60.341 52.381 15.13 0.00 35.59 3.91
1031 1121 4.303257 GCAAGCGCTTTACCCTCT 57.697 55.556 22.51 0.00 34.30 3.69
1069 1170 1.479709 AGTCTAGCGTTCATCTGGCT 58.520 50.000 0.00 0.00 40.68 4.75
1070 1171 1.135915 AGTCTAGCGTTCATCTGGCTG 59.864 52.381 0.00 0.00 37.62 4.85
1085 1186 0.249911 GGCTGGTAGCTATGGTTCGG 60.250 60.000 0.00 0.00 41.99 4.30
1172 1273 1.277842 TGTGATATGTGTTGCTCCCGT 59.722 47.619 0.00 0.00 0.00 5.28
1204 1305 4.338879 AGTTTCTGTCTGGATGATTTGGG 58.661 43.478 0.00 0.00 0.00 4.12
1206 1307 3.920231 TCTGTCTGGATGATTTGGGAG 57.080 47.619 0.00 0.00 0.00 4.30
1207 1308 3.453868 TCTGTCTGGATGATTTGGGAGA 58.546 45.455 0.00 0.00 0.00 3.71
1209 1310 3.944015 CTGTCTGGATGATTTGGGAGAAC 59.056 47.826 0.00 0.00 0.00 3.01
1231 1332 2.128771 ATTCATGCCCGTAGCTGTTT 57.871 45.000 0.00 0.00 44.23 2.83
1240 1341 1.535462 CCGTAGCTGTTTTCTTGTGGG 59.465 52.381 0.00 0.00 0.00 4.61
1272 1373 8.451908 AAAGAACATTTGAGTAGTACAAGCTT 57.548 30.769 2.52 0.00 0.00 3.74
1295 1412 2.347731 GGTTCATCCTCTGTTCGGTTC 58.652 52.381 0.00 0.00 0.00 3.62
1296 1413 2.289444 GGTTCATCCTCTGTTCGGTTCA 60.289 50.000 0.00 0.00 0.00 3.18
1298 1415 4.382685 GGTTCATCCTCTGTTCGGTTCATA 60.383 45.833 0.00 0.00 0.00 2.15
1309 1426 3.847671 TCGGTTCATATAATGGTGCCA 57.152 42.857 0.00 0.00 0.00 4.92
1374 1492 6.071334 TGCTCTTCATGTAGTAGTTTGCTAGT 60.071 38.462 0.00 0.00 35.25 2.57
1433 1551 6.346477 TCTAATCACTCTTAACACTGCTGT 57.654 37.500 0.00 0.00 0.00 4.40
1465 1583 5.680619 TGGTTGTATGGTCAATGATACTCC 58.319 41.667 0.00 0.00 0.00 3.85
1523 1641 5.121105 GGTATGCGTTCCCTGTTAATAAGT 58.879 41.667 0.00 0.00 0.00 2.24
1524 1642 5.235831 GGTATGCGTTCCCTGTTAATAAGTC 59.764 44.000 0.00 0.00 0.00 3.01
1528 1646 4.201656 GCGTTCCCTGTTAATAAGTCGTTC 60.202 45.833 0.00 0.00 0.00 3.95
1532 1650 5.240121 TCCCTGTTAATAAGTCGTTCAACC 58.760 41.667 0.00 0.00 0.00 3.77
1564 1682 6.182627 TGCTCATTCTGAATCATGGTAGTTT 58.817 36.000 0.00 0.00 0.00 2.66
1617 1735 8.779354 AACCTATGTTAAATTGAGTCTGACTC 57.221 34.615 26.86 26.86 38.12 3.36
1720 1838 5.581605 TGAACTGAGTTGCACATTCTTTTC 58.418 37.500 0.90 0.00 0.00 2.29
1727 1845 7.487484 TGAGTTGCACATTCTTTTCAATGTTA 58.513 30.769 0.00 0.00 43.17 2.41
1782 1901 5.500771 GCTGCTTTTAGTTGTTTTGTTCTGC 60.501 40.000 0.00 0.00 0.00 4.26
1783 1902 4.560819 TGCTTTTAGTTGTTTTGTTCTGCG 59.439 37.500 0.00 0.00 0.00 5.18
1927 2046 2.814280 TGAAGAAGAAGGGTGTCGAC 57.186 50.000 9.11 9.11 0.00 4.20
2014 2133 0.457035 CTGCCCGTATTGCTTGCAAT 59.543 50.000 21.98 21.98 0.00 3.56
2358 2477 7.664318 TGCTGAGATGATATGATATGCTTGTTT 59.336 33.333 0.00 0.00 0.00 2.83
2371 2490 5.827568 ATGCTTGTTTAAATTTCTGTGCG 57.172 34.783 0.00 0.00 0.00 5.34
2372 2491 3.489047 TGCTTGTTTAAATTTCTGTGCGC 59.511 39.130 0.00 0.00 0.00 6.09
2399 2519 8.772705 CCATATCTCTAATTTGTGCTTCTTCTC 58.227 37.037 0.00 0.00 0.00 2.87
2428 2548 0.736053 TCACCAAGTTCAACCGCAAC 59.264 50.000 0.00 0.00 0.00 4.17
2519 2639 2.237393 TGCTGGGCAATTGTTTTGTC 57.763 45.000 7.40 0.00 34.76 3.18
2524 2644 2.363680 TGGGCAATTGTTTTGTCGATGT 59.636 40.909 7.40 0.00 0.00 3.06
2576 2696 4.458989 TGTCCCTGCATCAACTAATTGTTC 59.541 41.667 0.00 0.00 36.63 3.18
2577 2697 4.458989 GTCCCTGCATCAACTAATTGTTCA 59.541 41.667 0.00 0.00 36.63 3.18
2578 2698 5.126061 GTCCCTGCATCAACTAATTGTTCAT 59.874 40.000 0.00 0.00 36.63 2.57
2579 2699 5.125900 TCCCTGCATCAACTAATTGTTCATG 59.874 40.000 0.00 0.00 39.66 3.07
2580 2700 5.105635 CCCTGCATCAACTAATTGTTCATGT 60.106 40.000 0.00 0.00 39.02 3.21
2581 2701 6.392354 CCTGCATCAACTAATTGTTCATGTT 58.608 36.000 0.00 0.00 39.02 2.71
2690 2812 6.238786 GCAGAAGAAGTCTATCCGTTCTATCA 60.239 42.308 0.00 0.00 33.56 2.15
2691 2813 7.359595 CAGAAGAAGTCTATCCGTTCTATCAG 58.640 42.308 0.00 0.00 33.56 2.90
2819 2941 8.902540 TTGTGATGATGGTACTAATATGAACC 57.097 34.615 0.00 0.00 0.00 3.62
2837 2959 0.179129 CCGCCTGTTGAATCATTGCC 60.179 55.000 0.00 0.00 0.00 4.52
2873 2995 4.869215 TGTCAATGTATTTTGCTGTGGTG 58.131 39.130 0.00 0.00 0.00 4.17
2921 3063 9.010029 ACATCAGGAAAATGTTATACGTTCTTT 57.990 29.630 0.00 0.00 33.62 2.52
2922 3064 9.277565 CATCAGGAAAATGTTATACGTTCTTTG 57.722 33.333 0.00 0.00 0.00 2.77
2923 3065 8.610248 TCAGGAAAATGTTATACGTTCTTTGA 57.390 30.769 0.00 0.00 0.00 2.69
2925 3067 9.672086 CAGGAAAATGTTATACGTTCTTTGAAA 57.328 29.630 0.00 0.00 0.00 2.69
2926 3068 9.673454 AGGAAAATGTTATACGTTCTTTGAAAC 57.327 29.630 0.00 0.00 0.00 2.78
2950 3127 3.196254 AGCAAAATTCTGGCCCAGTAATG 59.804 43.478 11.27 5.64 32.61 1.90
2960 3146 3.964031 TGGCCCAGTAATGTTTTTGAAGT 59.036 39.130 0.00 0.00 0.00 3.01
2961 3147 5.141182 TGGCCCAGTAATGTTTTTGAAGTA 58.859 37.500 0.00 0.00 0.00 2.24
2962 3148 5.010213 TGGCCCAGTAATGTTTTTGAAGTAC 59.990 40.000 0.00 0.00 0.00 2.73
2986 3172 6.325545 ACCAGTATACAATTTCCGGATGTCTA 59.674 38.462 12.37 5.22 0.00 2.59
2987 3173 7.147620 ACCAGTATACAATTTCCGGATGTCTAA 60.148 37.037 12.37 0.00 0.00 2.10
2988 3174 7.878127 CCAGTATACAATTTCCGGATGTCTAAT 59.122 37.037 12.37 2.41 0.00 1.73
2989 3175 9.273016 CAGTATACAATTTCCGGATGTCTAATT 57.727 33.333 12.37 8.67 0.00 1.40
3004 3190 7.169308 GGATGTCTAATTGGTTAGTGTATCGTG 59.831 40.741 0.00 0.00 38.72 4.35
3031 3217 2.986479 GTCAATTTTGCTGGCGTTTAGG 59.014 45.455 0.00 0.00 0.00 2.69
3038 3563 2.108168 TGCTGGCGTTTAGGAGAGTAT 58.892 47.619 0.00 0.00 0.00 2.12
3041 3566 4.049869 GCTGGCGTTTAGGAGAGTATTAC 58.950 47.826 0.00 0.00 0.00 1.89
3090 3615 1.098712 TGGTTGGTGTTTCGTCTGCC 61.099 55.000 0.00 0.00 0.00 4.85
3113 3638 2.744202 GTGTCTTTGATGCATCCGAACT 59.256 45.455 23.67 0.00 0.00 3.01
3177 3707 2.329267 CTTTGCCTTCCTTTTTCCCCT 58.671 47.619 0.00 0.00 0.00 4.79
3178 3708 1.715785 TTGCCTTCCTTTTTCCCCTG 58.284 50.000 0.00 0.00 0.00 4.45
3180 3710 1.783979 TGCCTTCCTTTTTCCCCTGTA 59.216 47.619 0.00 0.00 0.00 2.74
3181 3711 2.225017 TGCCTTCCTTTTTCCCCTGTAG 60.225 50.000 0.00 0.00 0.00 2.74
3182 3712 2.225041 GCCTTCCTTTTTCCCCTGTAGT 60.225 50.000 0.00 0.00 0.00 2.73
3184 3714 3.826729 CCTTCCTTTTTCCCCTGTAGTTG 59.173 47.826 0.00 0.00 0.00 3.16
3185 3715 4.447180 CCTTCCTTTTTCCCCTGTAGTTGA 60.447 45.833 0.00 0.00 0.00 3.18
3186 3716 5.325239 CTTCCTTTTTCCCCTGTAGTTGAT 58.675 41.667 0.00 0.00 0.00 2.57
3187 3717 5.333566 TCCTTTTTCCCCTGTAGTTGATT 57.666 39.130 0.00 0.00 0.00 2.57
3188 3718 5.321927 TCCTTTTTCCCCTGTAGTTGATTC 58.678 41.667 0.00 0.00 0.00 2.52
3189 3719 5.074515 TCCTTTTTCCCCTGTAGTTGATTCT 59.925 40.000 0.00 0.00 0.00 2.40
3190 3720 5.775195 CCTTTTTCCCCTGTAGTTGATTCTT 59.225 40.000 0.00 0.00 0.00 2.52
3191 3721 6.267699 CCTTTTTCCCCTGTAGTTGATTCTTT 59.732 38.462 0.00 0.00 0.00 2.52
3192 3722 7.202001 CCTTTTTCCCCTGTAGTTGATTCTTTT 60.202 37.037 0.00 0.00 0.00 2.27
3193 3723 7.669089 TTTTCCCCTGTAGTTGATTCTTTTT 57.331 32.000 0.00 0.00 0.00 1.94
3211 3741 4.327982 TTTTTCATCCGTGCCAAATTGA 57.672 36.364 0.00 0.00 0.00 2.57
3212 3742 4.327982 TTTTCATCCGTGCCAAATTGAA 57.672 36.364 0.00 0.00 0.00 2.69
3213 3743 4.533919 TTTCATCCGTGCCAAATTGAAT 57.466 36.364 0.00 0.00 0.00 2.57
3214 3744 5.651387 TTTCATCCGTGCCAAATTGAATA 57.349 34.783 0.00 0.00 0.00 1.75
3215 3745 4.898829 TCATCCGTGCCAAATTGAATAG 57.101 40.909 0.00 0.00 0.00 1.73
3220 3750 2.543641 GTGCCAAATTGAATAGCCTGC 58.456 47.619 0.00 0.00 0.00 4.85
3252 3782 5.758784 GGTTCGAAATCCCTAGAATTACCAG 59.241 44.000 0.00 0.00 0.00 4.00
3253 3783 4.957296 TCGAAATCCCTAGAATTACCAGC 58.043 43.478 0.00 0.00 0.00 4.85
3254 3784 3.741344 CGAAATCCCTAGAATTACCAGCG 59.259 47.826 0.00 0.00 0.00 5.18
3277 3807 4.325030 GGTAGGGTGATCTGAATTTGGGAA 60.325 45.833 0.00 0.00 0.00 3.97
3287 3817 5.841810 TCTGAATTTGGGAACACAATTGAC 58.158 37.500 13.59 0.62 42.67 3.18
3288 3818 4.954875 TGAATTTGGGAACACAATTGACC 58.045 39.130 13.59 9.42 42.67 4.02
3295 3833 3.059166 GGAACACAATTGACCAACATGC 58.941 45.455 13.59 0.00 0.00 4.06
3404 3942 1.000896 CCATCGAAAGCAAGGGGGT 60.001 57.895 0.00 0.00 0.00 4.95
3430 3968 0.094730 GGCGAGACGAACAAAATCCG 59.905 55.000 0.00 0.00 0.00 4.18
3442 3980 0.605319 AAAATCCGAACGCAGGAGCA 60.605 50.000 0.81 0.00 41.66 4.26
3452 3990 2.513204 CAGGAGCATCGCCCACAG 60.513 66.667 0.00 0.00 34.37 3.66
3458 3996 2.047274 CATCGCCCACAGGAACGT 60.047 61.111 0.00 0.00 33.47 3.99
3459 3997 1.671054 CATCGCCCACAGGAACGTT 60.671 57.895 0.00 0.00 33.47 3.99
3460 3998 1.375523 ATCGCCCACAGGAACGTTC 60.376 57.895 20.14 20.14 33.47 3.95
3506 4050 1.864082 GTTGCCCACAAAATCCAAACG 59.136 47.619 0.00 0.00 37.58 3.60
3542 4086 3.001086 ACATAAACCCCCTTCCTTCCTT 58.999 45.455 0.00 0.00 0.00 3.36
3545 4089 0.103337 AACCCCCTTCCTTCCTTCCT 60.103 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.685550 CGGTTGCTGGAATTCTAGGGATT 60.686 47.826 19.20 0.00 0.00 3.01
47 48 3.347216 TCCTTTCTCCACTAGCAAATGC 58.653 45.455 0.00 0.00 42.49 3.56
131 132 1.164041 TATCTCATCGTCGCCAGCGA 61.164 55.000 11.27 11.27 46.87 4.93
133 134 0.312416 AGTATCTCATCGTCGCCAGC 59.688 55.000 0.00 0.00 0.00 4.85
153 154 9.531942 GTTGTGGCAATATCATATTCATTTCAA 57.468 29.630 0.00 0.00 0.00 2.69
167 185 6.040166 GGAGATGAAGATTGTTGTGGCAATAT 59.960 38.462 0.00 0.00 38.98 1.28
169 187 4.159135 GGAGATGAAGATTGTTGTGGCAAT 59.841 41.667 0.00 0.00 41.28 3.56
219 238 2.047560 GAAGCGTAGTTGGCCGGT 60.048 61.111 1.90 0.00 36.18 5.28
312 333 2.244769 CTCCTCTCCCTCTCCTCTCTTT 59.755 54.545 0.00 0.00 0.00 2.52
313 334 1.852965 CTCCTCTCCCTCTCCTCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
334 379 1.468395 CGCTTTCTCTCCCTCGAGTTC 60.468 57.143 12.31 0.00 37.40 3.01
339 384 1.435515 CCTCGCTTTCTCTCCCTCG 59.564 63.158 0.00 0.00 0.00 4.63
375 420 4.660938 GGCCCAACCCGAGCACTT 62.661 66.667 0.00 0.00 0.00 3.16
458 513 0.387239 GAGCATGTTTTGACGTGGCC 60.387 55.000 0.00 0.00 0.00 5.36
503 559 2.546368 CACCGAACCGAAAATCTGACAA 59.454 45.455 0.00 0.00 0.00 3.18
544 601 4.982295 TCATGATTAGCGGAAACTATCACG 59.018 41.667 0.00 0.00 0.00 4.35
573 631 1.476845 TAGGCCGAGAAGCACCACAA 61.477 55.000 0.00 0.00 0.00 3.33
586 644 3.673323 GCAGAAGAAAATGGTTTAGGCCG 60.673 47.826 0.00 0.00 0.00 6.13
601 659 0.320771 GGAGTTTGAGCCGCAGAAGA 60.321 55.000 0.00 0.00 0.00 2.87
604 662 2.347490 GGGAGTTTGAGCCGCAGA 59.653 61.111 0.00 0.00 0.00 4.26
612 670 1.070786 GCGTGACCTGGGAGTTTGA 59.929 57.895 0.00 0.00 0.00 2.69
719 805 2.835764 AGATTCGGGCCACACTTTACTA 59.164 45.455 4.39 0.00 0.00 1.82
744 830 0.178990 GTCCAGGCCCAGAAAACACT 60.179 55.000 0.00 0.00 0.00 3.55
936 1026 2.202676 GAGACGGAAGAGCTGCGG 60.203 66.667 0.00 0.00 44.35 5.69
1017 1107 1.306226 AGGGAGAGGGTAAAGCGCT 60.306 57.895 2.64 2.64 43.54 5.92
1031 1121 6.578313 AGACTAGAGTAACATACAGAGGGA 57.422 41.667 0.00 0.00 0.00 4.20
1069 1170 0.978667 TGCCCGAACCATAGCTACCA 60.979 55.000 0.00 0.00 0.00 3.25
1070 1171 0.179468 TTGCCCGAACCATAGCTACC 59.821 55.000 0.00 0.00 0.00 3.18
1085 1186 0.991344 CGCCAATTCAAACGATTGCC 59.009 50.000 0.00 0.00 36.45 4.52
1172 1273 9.567776 TCATCCAGACAGAAACTAAATAAACAA 57.432 29.630 0.00 0.00 0.00 2.83
1204 1305 3.487544 GCTACGGGCATGAATTTGTTCTC 60.488 47.826 0.00 0.00 41.35 2.87
1206 1307 2.423538 AGCTACGGGCATGAATTTGTTC 59.576 45.455 0.00 0.00 44.79 3.18
1207 1308 2.164219 CAGCTACGGGCATGAATTTGTT 59.836 45.455 0.00 0.00 44.79 2.83
1209 1310 1.745087 ACAGCTACGGGCATGAATTTG 59.255 47.619 0.00 0.00 44.79 2.32
1231 1332 3.780804 TCTTTCGAATCCCCACAAGAA 57.219 42.857 0.00 0.00 0.00 2.52
1240 1341 7.365840 ACTACTCAAATGTTCTTTCGAATCC 57.634 36.000 0.00 0.00 0.00 3.01
1272 1373 0.530744 CGAACAGAGGATGAACCCGA 59.469 55.000 0.00 0.00 40.05 5.14
1295 1412 6.518493 AGCATTTTTCTGGCACCATTATATG 58.482 36.000 0.00 0.00 0.00 1.78
1296 1413 6.552350 AGAGCATTTTTCTGGCACCATTATAT 59.448 34.615 0.00 0.00 0.00 0.86
1298 1415 4.713321 AGAGCATTTTTCTGGCACCATTAT 59.287 37.500 0.00 0.00 0.00 1.28
1333 1450 7.377766 TGAAGAGCACAGGAAATATTAACAC 57.622 36.000 0.00 0.00 0.00 3.32
1374 1492 7.278135 AGCAAGAGCATACATCTCTTCATTTA 58.722 34.615 2.59 0.00 46.01 1.40
1433 1551 4.986783 TGACCATACAACCATACCAACAA 58.013 39.130 0.00 0.00 0.00 2.83
1465 1583 6.128090 ACAGCAACTACTCATTCACATTCATG 60.128 38.462 0.00 0.00 0.00 3.07
1523 1641 1.890041 CAGTTGGCGGGTTGAACGA 60.890 57.895 0.00 0.00 0.00 3.85
1524 1642 2.637025 CAGTTGGCGGGTTGAACG 59.363 61.111 0.00 0.00 0.00 3.95
1532 1650 0.674581 TCAGAATGAGCAGTTGGCGG 60.675 55.000 0.00 0.00 42.56 6.13
1564 1682 4.713553 TGACAGGCAAACAAGAGATTACA 58.286 39.130 0.00 0.00 0.00 2.41
1727 1845 8.885494 TGCAAAGAAAATAACTAAATGCAGTT 57.115 26.923 4.23 4.23 41.56 3.16
1737 1855 6.293027 GCAGCAAACATGCAAAGAAAATAACT 60.293 34.615 3.41 0.00 43.31 2.24
1782 1901 5.391310 CCTGACCAGAGAATTTTGTCATTCG 60.391 44.000 0.00 0.00 38.10 3.34
1783 1902 5.707298 TCCTGACCAGAGAATTTTGTCATTC 59.293 40.000 0.00 0.00 35.59 2.67
1927 2046 3.046390 GTGAACACAGTGAGAGAACTCG 58.954 50.000 7.81 0.00 45.25 4.18
2014 2133 3.940852 CTGCATGCTTGGTCATGTACTTA 59.059 43.478 20.33 0.00 44.20 2.24
2351 2470 3.121025 GGCGCACAGAAATTTAAACAAGC 60.121 43.478 10.83 0.00 0.00 4.01
2358 2477 4.460263 AGATATGGGCGCACAGAAATTTA 58.540 39.130 21.09 4.33 0.00 1.40
2371 2490 5.767168 AGAAGCACAAATTAGAGATATGGGC 59.233 40.000 0.00 0.00 40.66 5.36
2372 2491 7.718753 AGAAGAAGCACAAATTAGAGATATGGG 59.281 37.037 0.00 0.00 0.00 4.00
2399 2519 0.111253 AACTTGGTGAAGCCCCTGAG 59.889 55.000 0.00 0.00 36.04 3.35
2428 2548 4.023107 TCACTCTTGAACTTGAGGTAGTCG 60.023 45.833 0.00 0.00 34.84 4.18
2519 2639 4.446371 AGGCAGGATAAAGAAGAACATCG 58.554 43.478 0.00 0.00 0.00 3.84
2524 2644 7.827729 GGTTTACTAAGGCAGGATAAAGAAGAA 59.172 37.037 0.00 0.00 0.00 2.52
2576 2696 2.475111 CAGCTGCAAAGCAAGAAACATG 59.525 45.455 0.00 0.00 38.41 3.21
2577 2697 2.750948 CAGCTGCAAAGCAAGAAACAT 58.249 42.857 0.00 0.00 38.41 2.71
2578 2698 1.803625 GCAGCTGCAAAGCAAGAAACA 60.804 47.619 33.36 0.00 38.41 2.83
2579 2699 0.857287 GCAGCTGCAAAGCAAGAAAC 59.143 50.000 33.36 0.00 38.41 2.78
2580 2700 0.748450 AGCAGCTGCAAAGCAAGAAA 59.252 45.000 38.24 0.00 45.16 2.52
2581 2701 0.313043 GAGCAGCTGCAAAGCAAGAA 59.687 50.000 38.24 0.00 45.16 2.52
2690 2812 8.747538 AAGTTCCACACAGTAAAATAAGTTCT 57.252 30.769 0.00 0.00 0.00 3.01
2818 2940 0.179129 GGCAATGATTCAACAGGCGG 60.179 55.000 0.00 0.00 0.00 6.13
2819 2941 0.523968 CGGCAATGATTCAACAGGCG 60.524 55.000 14.40 14.40 38.61 5.52
2837 2959 3.974401 ACATTGACAAACGAATTCAAGCG 59.026 39.130 6.22 0.00 32.91 4.68
2899 3041 9.672086 TTTCAAAGAACGTATAACATTTTCCTG 57.328 29.630 0.00 0.00 0.00 3.86
2921 3063 3.465871 GGCCAGAATTTTGCTTGTTTCA 58.534 40.909 0.00 0.00 0.00 2.69
2922 3064 2.807967 GGGCCAGAATTTTGCTTGTTTC 59.192 45.455 4.39 0.00 0.00 2.78
2923 3065 2.172293 TGGGCCAGAATTTTGCTTGTTT 59.828 40.909 0.00 0.00 0.00 2.83
2925 3067 1.345415 CTGGGCCAGAATTTTGCTTGT 59.655 47.619 29.96 0.00 32.44 3.16
2926 3068 1.345415 ACTGGGCCAGAATTTTGCTTG 59.655 47.619 38.99 10.09 35.18 4.01
2960 3146 6.325545 AGACATCCGGAAATTGTATACTGGTA 59.674 38.462 9.01 0.00 0.00 3.25
2961 3147 5.130477 AGACATCCGGAAATTGTATACTGGT 59.870 40.000 9.01 0.00 0.00 4.00
2962 3148 5.611374 AGACATCCGGAAATTGTATACTGG 58.389 41.667 9.01 0.00 0.00 4.00
2986 3172 4.391830 CAGCACACGATACACTAACCAATT 59.608 41.667 0.00 0.00 0.00 2.32
2987 3173 3.932710 CAGCACACGATACACTAACCAAT 59.067 43.478 0.00 0.00 0.00 3.16
2988 3174 3.322369 CAGCACACGATACACTAACCAA 58.678 45.455 0.00 0.00 0.00 3.67
2989 3175 2.353307 CCAGCACACGATACACTAACCA 60.353 50.000 0.00 0.00 0.00 3.67
3004 3190 1.787012 CCAGCAAAATTGACCAGCAC 58.213 50.000 0.00 0.00 0.00 4.40
3031 3217 5.231568 CGTCCGGAAATTGTGTAATACTCTC 59.768 44.000 5.23 0.00 0.00 3.20
3038 3563 1.158434 GGCGTCCGGAAATTGTGTAA 58.842 50.000 5.23 0.00 0.00 2.41
3041 3566 1.006832 CTAGGCGTCCGGAAATTGTG 58.993 55.000 5.23 0.00 0.00 3.33
3090 3615 0.374758 CGGATGCATCAAAGACACCG 59.625 55.000 27.25 15.93 0.00 4.94
3157 3687 2.037641 CAGGGGAAAAAGGAAGGCAAAG 59.962 50.000 0.00 0.00 0.00 2.77
3190 3720 4.327982 TCAATTTGGCACGGATGAAAAA 57.672 36.364 0.00 0.00 0.00 1.94
3191 3721 4.327982 TTCAATTTGGCACGGATGAAAA 57.672 36.364 0.00 0.00 0.00 2.29
3192 3722 4.533919 ATTCAATTTGGCACGGATGAAA 57.466 36.364 7.86 0.00 0.00 2.69
3193 3723 4.439974 GCTATTCAATTTGGCACGGATGAA 60.440 41.667 6.64 6.64 0.00 2.57
3194 3724 3.066621 GCTATTCAATTTGGCACGGATGA 59.933 43.478 0.00 0.00 0.00 2.92
3195 3725 3.374745 GCTATTCAATTTGGCACGGATG 58.625 45.455 0.00 0.00 0.00 3.51
3196 3726 2.362077 GGCTATTCAATTTGGCACGGAT 59.638 45.455 0.00 0.00 0.00 4.18
3197 3727 1.748493 GGCTATTCAATTTGGCACGGA 59.252 47.619 0.00 0.00 0.00 4.69
3198 3728 1.750778 AGGCTATTCAATTTGGCACGG 59.249 47.619 0.00 0.00 0.00 4.94
3199 3729 2.801063 CAGGCTATTCAATTTGGCACG 58.199 47.619 0.00 0.00 0.00 5.34
3200 3730 2.094078 TGCAGGCTATTCAATTTGGCAC 60.094 45.455 0.00 0.00 0.00 5.01
3201 3731 2.166870 CTGCAGGCTATTCAATTTGGCA 59.833 45.455 5.57 0.00 0.00 4.92
3202 3732 2.167075 ACTGCAGGCTATTCAATTTGGC 59.833 45.455 19.93 0.00 0.00 4.52
3203 3733 4.082081 TCAACTGCAGGCTATTCAATTTGG 60.082 41.667 19.93 0.00 0.00 3.28
3204 3734 5.063180 TCAACTGCAGGCTATTCAATTTG 57.937 39.130 19.93 9.20 0.00 2.32
3205 3735 5.394883 CCATCAACTGCAGGCTATTCAATTT 60.395 40.000 19.93 0.00 0.00 1.82
3206 3736 4.098960 CCATCAACTGCAGGCTATTCAATT 59.901 41.667 19.93 0.00 0.00 2.32
3207 3737 3.635373 CCATCAACTGCAGGCTATTCAAT 59.365 43.478 19.93 0.00 0.00 2.57
3208 3738 3.018856 CCATCAACTGCAGGCTATTCAA 58.981 45.455 19.93 0.00 0.00 2.69
3209 3739 2.025981 ACCATCAACTGCAGGCTATTCA 60.026 45.455 19.93 0.00 0.00 2.57
3210 3740 2.648059 ACCATCAACTGCAGGCTATTC 58.352 47.619 19.93 0.00 0.00 1.75
3211 3741 2.814805 ACCATCAACTGCAGGCTATT 57.185 45.000 19.93 0.00 0.00 1.73
3212 3742 2.648059 GAACCATCAACTGCAGGCTAT 58.352 47.619 19.93 4.87 0.00 2.97
3213 3743 1.675714 CGAACCATCAACTGCAGGCTA 60.676 52.381 19.93 2.32 0.00 3.93
3214 3744 0.957395 CGAACCATCAACTGCAGGCT 60.957 55.000 19.93 0.99 0.00 4.58
3215 3745 0.955428 TCGAACCATCAACTGCAGGC 60.955 55.000 19.93 0.00 0.00 4.85
3220 3750 3.347216 AGGGATTTCGAACCATCAACTG 58.653 45.455 11.04 0.00 0.00 3.16
3252 3782 2.614057 CAAATTCAGATCACCCTACCGC 59.386 50.000 0.00 0.00 0.00 5.68
3253 3783 3.206150 CCAAATTCAGATCACCCTACCG 58.794 50.000 0.00 0.00 0.00 4.02
3254 3784 3.202151 TCCCAAATTCAGATCACCCTACC 59.798 47.826 0.00 0.00 0.00 3.18
3277 3807 4.158394 GGATAGCATGTTGGTCAATTGTGT 59.842 41.667 5.13 0.00 0.00 3.72
3287 3817 0.846015 TCCCTGGGATAGCATGTTGG 59.154 55.000 12.53 0.00 0.00 3.77
3288 3818 2.965671 ATCCCTGGGATAGCATGTTG 57.034 50.000 26.78 0.00 41.16 3.33
3404 3942 2.046023 TTCGTCTCGCCGGGTCTA 60.046 61.111 2.18 0.00 0.00 2.59
3413 3951 2.470140 CGTTCGGATTTTGTTCGTCTCG 60.470 50.000 0.00 0.00 0.00 4.04
3430 3968 3.567797 GGCGATGCTCCTGCGTTC 61.568 66.667 0.00 0.00 43.34 3.95
3442 3980 1.375523 GAACGTTCCTGTGGGCGAT 60.376 57.895 17.68 0.00 0.00 4.58
3506 4050 0.100682 TATGTCCTCGTCGCTCTTGC 59.899 55.000 0.00 0.00 0.00 4.01
3542 4086 0.849540 GGGGGAAAGGGGAAGAAGGA 60.850 60.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.