Multiple sequence alignment - TraesCS2A01G339900

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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 TraesCS2A01G339900 chr2A 100.000 5821 0 0 1 5821 574966862 574961042 0.000000e+00 10750.0
1 TraesCS2A01G339900 chr2A 93.182 88 6 0 4550 4637 574962226 574962313 4.730000e-26 130.0
2 TraesCS2A01G339900 chr2B 93.988 3576 147 19 1 3565 482723257 482719739 0.000000e+00 5350.0
3 TraesCS2A01G339900 chr2B 95.287 2228 81 9 3597 5821 482719743 482717537 0.000000e+00 3511.0
4 TraesCS2A01G339900 chr2B 91.228 57 3 2 4550 4606 633577483 633577537 6.250000e-10 76.8
5 TraesCS2A01G339900 chr2D 95.824 2754 80 10 3074 5821 406943283 406940559 0.000000e+00 4416.0
6 TraesCS2A01G339900 chr2D 94.574 2838 102 18 1 2828 406946305 406943510 0.000000e+00 4340.0
7 TraesCS2A01G339900 chr2D 96.552 174 4 2 2904 3076 406943510 406943338 2.650000e-73 287.0
8 TraesCS2A01G339900 chr5A 84.615 169 22 4 5497 5662 691989949 691990116 1.300000e-36 165.0
9 TraesCS2A01G339900 chr5D 84.416 154 18 4 5298 5447 430721926 430722077 4.700000e-31 147.0
10 TraesCS2A01G339900 chr7A 79.808 208 32 7 5456 5662 327910345 327910147 6.080000e-30 143.0
11 TraesCS2A01G339900 chr7A 83.893 149 22 2 5298 5445 134510254 134510107 2.190000e-29 141.0
12 TraesCS2A01G339900 chr7A 100.000 29 0 0 2573 2601 128832316 128832344 3.000000e-03 54.7
13 TraesCS2A01G339900 chr5B 79.808 208 33 6 5456 5662 13078126 13077927 6.080000e-30 143.0
14 TraesCS2A01G339900 chr1A 79.412 204 34 5 5456 5659 496421270 496421075 2.830000e-28 137.0
15 TraesCS2A01G339900 chr1A 77.889 199 34 7 5456 5653 529255049 529255238 1.330000e-21 115.0
16 TraesCS2A01G339900 chr4B 78.537 205 33 8 5456 5659 33625954 33626148 2.200000e-24 124.0
17 TraesCS2A01G339900 chr4A 89.691 97 7 2 4541 4637 638216693 638216786 2.850000e-23 121.0
18 TraesCS2A01G339900 chr4A 88.636 88 8 1 4550 4637 638216786 638216701 7.980000e-19 106.0
19 TraesCS2A01G339900 chrUn 79.235 183 23 10 5456 5635 81660714 81660884 4.770000e-21 113.0
20 TraesCS2A01G339900 chr1D 96.825 63 1 1 2491 2552 198282976 198283038 2.870000e-18 104.0
21 TraesCS2A01G339900 chr6D 98.246 57 1 0 2495 2551 409547374 409547318 3.710000e-17 100.0
22 TraesCS2A01G339900 chr6B 98.246 57 1 0 2495 2551 615187028 615186972 3.710000e-17 100.0
23 TraesCS2A01G339900 chr7B 89.610 77 5 3 2477 2552 561753571 561753497 1.730000e-15 95.3
24 TraesCS2A01G339900 chr3D 96.491 57 2 0 2496 2552 324311164 324311108 1.730000e-15 95.3
25 TraesCS2A01G339900 chr3D 96.552 58 1 1 2496 2552 591382664 591382607 1.730000e-15 95.3
26 TraesCS2A01G339900 chr3D 94.915 59 3 0 2495 2553 136724314 136724256 6.210000e-15 93.5


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 TraesCS2A01G339900 chr2A 574961042 574966862 5820 True 10750.000000 10750 100.0000 1 5821 1 chr2A.!!$R1 5820
1 TraesCS2A01G339900 chr2B 482717537 482723257 5720 True 4430.500000 5350 94.6375 1 5821 2 chr2B.!!$R1 5820
2 TraesCS2A01G339900 chr2D 406940559 406946305 5746 True 3014.333333 4416 95.6500 1 5821 3 chr2D.!!$R1 5820

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
817 820 0.038343 TCGCCATCTTTTTGCTTGCC 60.038 50.0 0.00 0.00 0.00 4.52 F
1631 1644 0.889994 GTTGACAGGGCATGCATCAA 59.110 50.0 21.36 18.71 0.00 2.57 F
2105 2121 0.944386 CTAATGTTGGGGATTCGCGG 59.056 55.0 6.13 0.00 0.00 6.46 F
2687 2709 0.106149 GTGGATACTAAGCCCCGTGG 59.894 60.0 0.00 0.00 37.61 4.94 F
3047 3070 0.109723 ACAAGGCCCTAGCACGAAAA 59.890 50.0 0.00 0.00 42.56 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 2598 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.0 0.00 4.17 R
2664 2686 1.485066 CGGGGCTTAGTATCCACTTGT 59.515 52.381 0.00 0.0 36.14 3.16 R
3963 4046 1.135527 TCTACATTTCCGTGGCTACCG 59.864 52.381 0.00 0.0 0.00 4.02 R
4181 4267 3.056458 CCAGTGTACGTCCTGGCA 58.944 61.111 13.83 0.0 41.65 4.92 R
5010 5097 1.138859 CTCGCATGTACCCTGGAATCA 59.861 52.381 0.00 0.0 0.00 2.57 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
32 33 3.631250 ACAAAACATGGTCCACAGAACT 58.369 40.909 0.00 0.00 0.00 3.01
111 112 3.431725 CCCGAGAAGCCAAACGCC 61.432 66.667 0.00 0.00 38.78 5.68
232 233 0.867746 GAACAGCAGCACATGACGAA 59.132 50.000 0.00 0.00 0.00 3.85
233 234 1.466167 GAACAGCAGCACATGACGAAT 59.534 47.619 0.00 0.00 0.00 3.34
387 389 2.750888 GGAAGCATCGCCACCGTTC 61.751 63.158 0.00 0.00 35.54 3.95
400 402 1.153168 CCGTTCATTCCGCCTGGAT 60.153 57.895 0.00 0.00 45.91 3.41
415 417 2.628178 CCTGGATAGTGTGGCTCGATTA 59.372 50.000 0.00 0.00 0.00 1.75
615 617 2.203126 CCTCCATCGCTCAAGGCC 60.203 66.667 0.00 0.00 37.74 5.19
680 682 1.736586 GCTGGATCGATCGGTGAGT 59.263 57.895 18.81 0.00 0.00 3.41
710 712 1.296056 CGCCGGAGAAAACCACGATT 61.296 55.000 5.05 0.00 33.07 3.34
759 761 3.427638 GCCGTTCTTTAATTCTGCTTCCC 60.428 47.826 0.00 0.00 0.00 3.97
817 820 0.038343 TCGCCATCTTTTTGCTTGCC 60.038 50.000 0.00 0.00 0.00 4.52
1194 1203 6.056090 ACTCCTACGATGATATCTAGAGCA 57.944 41.667 3.98 0.00 0.00 4.26
1236 1247 7.572759 CAAAGCTGTACTTTCTTCACGAATTA 58.427 34.615 0.00 0.00 45.78 1.40
1249 1260 4.323417 TCACGAATTACACTGCCTTTGAT 58.677 39.130 0.00 0.00 0.00 2.57
1293 1304 5.504010 CGGTGACATATGCTTTGTGGTAATC 60.504 44.000 1.58 0.00 0.00 1.75
1330 1341 9.450807 CTAAAGTTGACTTATTGGACACAAAAG 57.549 33.333 0.00 0.00 36.19 2.27
1439 1452 5.184864 TGCTCTGTGTTTCCTTTCAAAAAGA 59.815 36.000 1.06 0.00 0.00 2.52
1464 1477 6.742559 AAAAGAAGAACTACACCTCACCTA 57.257 37.500 0.00 0.00 0.00 3.08
1474 1487 6.123651 ACTACACCTCACCTACTCTAAGATG 58.876 44.000 0.00 0.00 0.00 2.90
1631 1644 0.889994 GTTGACAGGGCATGCATCAA 59.110 50.000 21.36 18.71 0.00 2.57
1858 1871 5.728351 TTCCTAATATTTTGAACGAGGCG 57.272 39.130 0.00 0.00 0.00 5.52
1865 1879 3.328237 TTTTGAACGAGGCGAGTTTTC 57.672 42.857 0.00 0.00 31.14 2.29
1883 1897 6.590357 AGTTTTCGACATCTGTTTCAATACG 58.410 36.000 0.00 0.00 0.00 3.06
1908 1924 4.993028 TGGCCCATTCACTAGTACTTTTT 58.007 39.130 0.00 0.00 0.00 1.94
2066 2082 4.760204 GCCGTAACTGCCATCCTTATAAAT 59.240 41.667 0.00 0.00 0.00 1.40
2105 2121 0.944386 CTAATGTTGGGGATTCGCGG 59.056 55.000 6.13 0.00 0.00 6.46
2233 2249 5.201243 GCCAGGTGGGTCTTCTATTTTAAT 58.799 41.667 0.00 0.00 39.65 1.40
2276 2298 0.963962 CAGGCTTGCATCCAGTTGTT 59.036 50.000 8.07 0.00 0.00 2.83
2506 2528 2.548067 CCATGTAATGTACTCCCTCCGC 60.548 54.545 0.00 0.00 44.81 5.54
2516 2538 1.385347 TCCCTCCGCCCCACAATAT 60.385 57.895 0.00 0.00 0.00 1.28
2523 2545 2.976185 TCCGCCCCACAATATAAGATCA 59.024 45.455 0.00 0.00 0.00 2.92
2559 2581 9.282247 CTAACATAGCTTGAAAAACATAGCTTG 57.718 33.333 0.00 0.00 40.50 4.01
2560 2582 7.452880 ACATAGCTTGAAAAACATAGCTTGA 57.547 32.000 0.00 0.00 40.50 3.02
2561 2583 7.885297 ACATAGCTTGAAAAACATAGCTTGAA 58.115 30.769 0.00 0.00 40.50 2.69
2562 2584 8.359642 ACATAGCTTGAAAAACATAGCTTGAAA 58.640 29.630 0.00 0.00 40.50 2.69
2563 2585 9.195411 CATAGCTTGAAAAACATAGCTTGAAAA 57.805 29.630 0.00 0.00 40.50 2.29
2564 2586 9.762933 ATAGCTTGAAAAACATAGCTTGAAAAA 57.237 25.926 0.00 0.00 40.50 1.94
2565 2587 8.667076 AGCTTGAAAAACATAGCTTGAAAAAT 57.333 26.923 0.00 0.00 38.66 1.82
2686 2708 1.120530 AGTGGATACTAAGCCCCGTG 58.879 55.000 0.00 0.00 34.74 4.94
2687 2709 0.106149 GTGGATACTAAGCCCCGTGG 59.894 60.000 0.00 0.00 37.61 4.94
2688 2710 0.325860 TGGATACTAAGCCCCGTGGT 60.326 55.000 0.00 0.00 37.61 4.16
2689 2711 0.391966 GGATACTAAGCCCCGTGGTC 59.608 60.000 0.00 0.00 0.00 4.02
2690 2712 1.117150 GATACTAAGCCCCGTGGTCA 58.883 55.000 0.00 0.00 0.00 4.02
2691 2713 1.483415 GATACTAAGCCCCGTGGTCAA 59.517 52.381 0.00 0.00 0.00 3.18
2692 2714 1.575419 TACTAAGCCCCGTGGTCAAT 58.425 50.000 0.00 0.00 0.00 2.57
2693 2715 1.575419 ACTAAGCCCCGTGGTCAATA 58.425 50.000 0.00 0.00 0.00 1.90
2800 2822 7.862512 TTTCCGTCTACTTTAAGGTTTTCAA 57.137 32.000 0.00 0.00 0.00 2.69
2865 2887 8.780249 GCTAACCTTAAAGTGTCTGAACAAATA 58.220 33.333 0.00 0.00 37.08 1.40
2922 2944 5.324409 AGCTTTGTAAATCCATCCTTGTCA 58.676 37.500 0.00 0.00 0.00 3.58
2933 2955 9.577222 AAATCCATCCTTGTCAATTCAATTTTT 57.423 25.926 0.00 0.00 0.00 1.94
3047 3070 0.109723 ACAAGGCCCTAGCACGAAAA 59.890 50.000 0.00 0.00 42.56 2.29
3335 3415 6.551385 TTGCGATTAGTAGCTAGTAGGTAC 57.449 41.667 25.45 25.45 46.47 3.34
3348 3428 8.336801 AGCTAGTAGGTACAAAAATTGAAAGG 57.663 34.615 0.00 0.00 0.00 3.11
3349 3429 7.393515 AGCTAGTAGGTACAAAAATTGAAAGGG 59.606 37.037 0.00 0.00 0.00 3.95
3350 3430 6.340962 AGTAGGTACAAAAATTGAAAGGGC 57.659 37.500 0.00 0.00 0.00 5.19
3351 3431 5.836358 AGTAGGTACAAAAATTGAAAGGGCA 59.164 36.000 0.00 0.00 0.00 5.36
3352 3432 5.213891 AGGTACAAAAATTGAAAGGGCAG 57.786 39.130 0.00 0.00 0.00 4.85
3353 3433 4.040339 AGGTACAAAAATTGAAAGGGCAGG 59.960 41.667 0.00 0.00 0.00 4.85
3354 3434 4.039852 GGTACAAAAATTGAAAGGGCAGGA 59.960 41.667 0.00 0.00 0.00 3.86
3355 3435 4.341366 ACAAAAATTGAAAGGGCAGGAG 57.659 40.909 0.00 0.00 0.00 3.69
3356 3436 3.711190 ACAAAAATTGAAAGGGCAGGAGT 59.289 39.130 0.00 0.00 0.00 3.85
3357 3437 4.898861 ACAAAAATTGAAAGGGCAGGAGTA 59.101 37.500 0.00 0.00 0.00 2.59
3423 3503 5.700722 ATGGTATCATGCATTGTGATGTC 57.299 39.130 10.84 4.94 36.96 3.06
3458 3538 1.529309 GGGATGGCTTGGAGAGGAC 59.471 63.158 0.00 0.00 0.00 3.85
3459 3539 0.985490 GGGATGGCTTGGAGAGGACT 60.985 60.000 0.00 0.00 0.00 3.85
3484 3564 5.036916 AGGTATTGAAAGGGGAGACATACA 58.963 41.667 0.00 0.00 0.00 2.29
3492 3572 1.978580 GGGGAGACATACATAGTGGGG 59.021 57.143 0.00 0.00 0.00 4.96
3573 3653 5.591099 TGGAGATTTCTTTGTTGCTTGAAC 58.409 37.500 0.00 0.00 34.84 3.18
3574 3654 4.984785 GGAGATTTCTTTGTTGCTTGAACC 59.015 41.667 0.00 0.00 33.07 3.62
3646 3726 5.337169 GCTCCTAACATGACTCAGAACTTCT 60.337 44.000 0.00 0.00 0.00 2.85
3892 3975 4.566659 GCATAAATGCGTGTTGAAAAGG 57.433 40.909 0.00 0.00 44.67 3.11
3896 3979 3.791973 AATGCGTGTTGAAAAGGAACA 57.208 38.095 0.00 0.00 0.00 3.18
3963 4046 5.915196 GCTGAAAGGTTGTGAATGAGTAAAC 59.085 40.000 0.00 0.00 0.00 2.01
3999 4082 6.653273 AATGTAGAACATGATCGTGTGAAG 57.347 37.500 21.05 0.00 37.97 3.02
4149 4235 1.378250 GAGCCAGCCTCAGCAATGT 60.378 57.895 0.00 0.00 43.56 2.71
4181 4267 9.878599 CAGAGTAGAATACAAACGACAAAAATT 57.121 29.630 0.00 0.00 46.26 1.82
4517 4604 4.158949 AGTTTGGAAGGTGTGGTTTGTTAC 59.841 41.667 0.00 0.00 0.00 2.50
4559 4646 5.214293 GGATAAAACCTAGTACTCCCTCCA 58.786 45.833 0.00 0.00 0.00 3.86
4571 4658 4.614967 ACTCCCTCCAATCCAAATCAAT 57.385 40.909 0.00 0.00 0.00 2.57
4597 4684 5.395486 GTCGCAGCTTTAGTACAAAGTTTTG 59.605 40.000 14.90 3.17 43.62 2.44
4617 4704 4.661993 TGTACTAAAGCTGCGACAATTG 57.338 40.909 3.24 3.24 0.00 2.32
4882 4969 6.352516 AGGAGAGCACAAGGAATTATAACAG 58.647 40.000 0.00 0.00 0.00 3.16
4898 4985 1.915141 ACAGCAAAACATAGCCTGCT 58.085 45.000 0.00 0.00 45.83 4.24
4953 5040 2.681848 CTCTGGAATGCTGGCTGTAAAG 59.318 50.000 0.00 0.00 0.00 1.85
4966 5053 4.010349 GGCTGTAAAGGATGTGTTAGCTT 58.990 43.478 0.00 0.00 0.00 3.74
5138 5225 4.821805 GGTTGTCTTCATCTTCCAACTTGA 59.178 41.667 0.00 0.00 36.52 3.02
5234 5321 8.602328 CATTGCTTTTCTACAAAATCACAAACA 58.398 29.630 0.00 0.00 29.40 2.83
5294 5381 8.823220 AACTCCCAGTTTTTATAAGCATGTAT 57.177 30.769 0.00 0.00 34.11 2.29
5295 5382 8.225603 ACTCCCAGTTTTTATAAGCATGTATG 57.774 34.615 0.00 0.00 0.00 2.39
5332 5419 5.191722 ACTGCTCCACTCCCTAAAATTCATA 59.808 40.000 0.00 0.00 0.00 2.15
5395 5482 6.719370 ACAATATGCCACTCCAAGAAAACTAA 59.281 34.615 0.00 0.00 0.00 2.24
5468 5555 3.197116 CGTTGGAGTTAAGTGGATACCCT 59.803 47.826 0.00 0.00 0.00 4.34
5470 5557 5.183969 GTTGGAGTTAAGTGGATACCCTTC 58.816 45.833 0.00 0.00 0.00 3.46
5496 5583 5.521906 TTTTTCCCACGACATTCATTCAA 57.478 34.783 0.00 0.00 0.00 2.69
5502 5589 5.584649 TCCCACGACATTCATTCAAATAGAC 59.415 40.000 0.00 0.00 0.00 2.59
5512 5599 8.954350 CATTCATTCAAATAGACTCTTTCCACT 58.046 33.333 0.00 0.00 0.00 4.00
5549 5636 2.291856 GCTGGAGCTACCTGGAAGT 58.708 57.895 0.00 0.00 39.86 3.01
5610 5711 0.963962 ATGCAACTGCTCCAAAGTGG 59.036 50.000 2.95 0.00 42.66 4.00
5611 5712 0.106769 TGCAACTGCTCCAAAGTGGA 60.107 50.000 2.95 0.00 45.34 4.02
5648 5749 3.563390 GCTGATTTTGATAGAGTGGAGCC 59.437 47.826 0.00 0.00 0.00 4.70
5655 5756 0.757188 ATAGAGTGGAGCCGTCCCAG 60.757 60.000 0.00 0.00 43.15 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.530497 GCACGGTGTTGACGCTTCA 61.530 57.895 10.24 0.00 34.00 3.02
111 112 0.784778 GCCGAGACGAGACAAAACAG 59.215 55.000 0.00 0.00 0.00 3.16
232 233 4.414956 TGGAGGAGTGGGGCCGAT 62.415 66.667 0.00 0.00 0.00 4.18
400 402 2.035449 CCGGATTAATCGAGCCACACTA 59.965 50.000 9.32 0.00 0.00 2.74
415 417 2.514592 CGGCTCATGCACCGGATT 60.515 61.111 9.46 0.00 45.74 3.01
566 568 3.408501 CTGCTCTCGCTCAGGGTCG 62.409 68.421 0.00 0.00 36.97 4.79
615 617 1.238439 GAGATGGAGGAGAGCTCGAG 58.762 60.000 8.45 8.45 0.00 4.04
715 717 5.750547 GGCCACAGAAAAGAAGAAGAAAAAG 59.249 40.000 0.00 0.00 0.00 2.27
717 719 4.202010 CGGCCACAGAAAAGAAGAAGAAAA 60.202 41.667 2.24 0.00 0.00 2.29
718 720 3.315191 CGGCCACAGAAAAGAAGAAGAAA 59.685 43.478 2.24 0.00 0.00 2.52
719 721 2.878406 CGGCCACAGAAAAGAAGAAGAA 59.122 45.455 2.24 0.00 0.00 2.52
720 722 2.158813 ACGGCCACAGAAAAGAAGAAGA 60.159 45.455 2.24 0.00 0.00 2.87
817 820 1.374758 GGAACTCTGCACCCTGACG 60.375 63.158 0.00 0.00 0.00 4.35
1102 1107 9.413734 CCTCACAGGAAAAATCCTATTCTATTT 57.586 33.333 0.00 0.00 37.67 1.40
1103 1108 7.503902 GCCTCACAGGAAAAATCCTATTCTATT 59.496 37.037 0.00 0.00 37.67 1.73
1148 1157 8.361592 AGTACTTAATTTCCCGAATTATCACG 57.638 34.615 0.00 0.00 39.34 4.35
1207 1218 4.273480 GTGAAGAAAGTACAGCTTTGCTCA 59.727 41.667 0.00 0.00 46.54 4.26
1330 1341 0.106318 AAAGATGAGGGCTGATGGGC 60.106 55.000 0.00 0.00 40.05 5.36
1356 1367 6.704050 GTCATAAGAAGATGAGGGCTAGTTTC 59.296 42.308 0.00 0.00 36.51 2.78
1858 1871 6.732392 CGTATTGAAACAGATGTCGAAAACTC 59.268 38.462 0.00 0.00 0.00 3.01
1865 1879 5.492854 CCATTCGTATTGAAACAGATGTCG 58.507 41.667 0.00 0.00 40.71 4.35
1903 1919 9.981114 ACCCAATTAAACTAAGATCACAAAAAG 57.019 29.630 0.00 0.00 0.00 2.27
1908 1924 8.877864 AATGACCCAATTAAACTAAGATCACA 57.122 30.769 0.00 0.00 0.00 3.58
1927 1943 4.827284 TCCAAAACTCTTCCTGAAATGACC 59.173 41.667 0.00 0.00 0.00 4.02
2066 2082 1.271163 GCTACCCACAACTTACTGCCA 60.271 52.381 0.00 0.00 0.00 4.92
2105 2121 2.224646 ACCTCCTTTCAGAAGAACAGCC 60.225 50.000 0.00 0.00 34.71 4.85
2486 2508 2.548067 GGCGGAGGGAGTACATTACATG 60.548 54.545 0.00 0.00 0.00 3.21
2506 2528 9.754382 CTTGAAAAATGATCTTATATTGTGGGG 57.246 33.333 0.00 0.00 0.00 4.96
2535 2557 7.885297 TCAAGCTATGTTTTTCAAGCTATGTT 58.115 30.769 0.00 0.00 38.52 2.71
2554 2576 8.248945 CCACAATAGAAGATCATTTTTCAAGCT 58.751 33.333 0.00 0.00 0.00 3.74
2555 2577 7.490402 CCCACAATAGAAGATCATTTTTCAAGC 59.510 37.037 0.00 0.00 0.00 4.01
2556 2578 8.742777 TCCCACAATAGAAGATCATTTTTCAAG 58.257 33.333 0.00 0.00 0.00 3.02
2557 2579 8.522830 GTCCCACAATAGAAGATCATTTTTCAA 58.477 33.333 0.00 0.00 0.00 2.69
2558 2580 7.148255 CGTCCCACAATAGAAGATCATTTTTCA 60.148 37.037 0.00 0.00 0.00 2.69
2559 2581 7.189512 CGTCCCACAATAGAAGATCATTTTTC 58.810 38.462 0.00 0.00 0.00 2.29
2560 2582 6.095440 CCGTCCCACAATAGAAGATCATTTTT 59.905 38.462 0.00 0.00 0.00 1.94
2561 2583 5.590259 CCGTCCCACAATAGAAGATCATTTT 59.410 40.000 0.00 0.00 0.00 1.82
2562 2584 5.104527 TCCGTCCCACAATAGAAGATCATTT 60.105 40.000 0.00 0.00 0.00 2.32
2563 2585 4.408921 TCCGTCCCACAATAGAAGATCATT 59.591 41.667 0.00 0.00 0.00 2.57
2564 2586 3.967326 TCCGTCCCACAATAGAAGATCAT 59.033 43.478 0.00 0.00 0.00 2.45
2565 2587 3.371034 TCCGTCCCACAATAGAAGATCA 58.629 45.455 0.00 0.00 0.00 2.92
2576 2598 1.000019 CTACTCCCTCCGTCCCACA 60.000 63.158 0.00 0.00 0.00 4.17
2664 2686 1.485066 CGGGGCTTAGTATCCACTTGT 59.515 52.381 0.00 0.00 36.14 3.16
2686 2708 7.925993 TCGTTTTATGTGATCCAATATTGACC 58.074 34.615 17.23 5.98 0.00 4.02
2687 2709 9.385902 CATCGTTTTATGTGATCCAATATTGAC 57.614 33.333 17.23 7.47 0.00 3.18
2688 2710 9.119418 ACATCGTTTTATGTGATCCAATATTGA 57.881 29.630 17.23 3.72 38.65 2.57
2865 2887 9.880157 TTTTGAGTTGTAACACTAGTACTTCTT 57.120 29.630 0.00 0.00 0.00 2.52
3047 3070 4.397417 GTCAGAGCAGATATTTTGTTGGCT 59.603 41.667 0.00 0.00 0.00 4.75
3098 3178 2.158827 GGTGGTGGAAAAAGGCAACAAT 60.159 45.455 0.00 0.00 41.41 2.71
3335 3415 4.341366 ACTCCTGCCCTTTCAATTTTTG 57.659 40.909 0.00 0.00 0.00 2.44
3336 3416 6.686484 ATTACTCCTGCCCTTTCAATTTTT 57.314 33.333 0.00 0.00 0.00 1.94
3337 3417 6.686484 AATTACTCCTGCCCTTTCAATTTT 57.314 33.333 0.00 0.00 0.00 1.82
3338 3418 6.686484 AAATTACTCCTGCCCTTTCAATTT 57.314 33.333 0.00 0.00 0.00 1.82
3339 3419 6.269769 TCAAAATTACTCCTGCCCTTTCAATT 59.730 34.615 0.00 0.00 0.00 2.32
3340 3420 5.779771 TCAAAATTACTCCTGCCCTTTCAAT 59.220 36.000 0.00 0.00 0.00 2.57
3341 3421 5.144100 TCAAAATTACTCCTGCCCTTTCAA 58.856 37.500 0.00 0.00 0.00 2.69
3342 3422 4.735369 TCAAAATTACTCCTGCCCTTTCA 58.265 39.130 0.00 0.00 0.00 2.69
3343 3423 5.654497 CATCAAAATTACTCCTGCCCTTTC 58.346 41.667 0.00 0.00 0.00 2.62
3344 3424 4.081476 GCATCAAAATTACTCCTGCCCTTT 60.081 41.667 0.00 0.00 0.00 3.11
3345 3425 3.448660 GCATCAAAATTACTCCTGCCCTT 59.551 43.478 0.00 0.00 0.00 3.95
3346 3426 3.026694 GCATCAAAATTACTCCTGCCCT 58.973 45.455 0.00 0.00 0.00 5.19
3347 3427 2.760092 TGCATCAAAATTACTCCTGCCC 59.240 45.455 0.00 0.00 0.00 5.36
3348 3428 4.340381 AGATGCATCAAAATTACTCCTGCC 59.660 41.667 27.81 0.00 0.00 4.85
3349 3429 5.066893 TCAGATGCATCAAAATTACTCCTGC 59.933 40.000 27.81 0.00 0.00 4.85
3350 3430 6.459298 GGTCAGATGCATCAAAATTACTCCTG 60.459 42.308 27.81 12.75 0.00 3.86
3351 3431 5.591877 GGTCAGATGCATCAAAATTACTCCT 59.408 40.000 27.81 0.00 0.00 3.69
3352 3432 5.221126 GGGTCAGATGCATCAAAATTACTCC 60.221 44.000 27.81 14.82 0.00 3.85
3353 3433 5.504665 CGGGTCAGATGCATCAAAATTACTC 60.505 44.000 27.81 14.19 0.00 2.59
3354 3434 4.336433 CGGGTCAGATGCATCAAAATTACT 59.664 41.667 27.81 2.07 0.00 2.24
3355 3435 4.096382 ACGGGTCAGATGCATCAAAATTAC 59.904 41.667 27.81 14.82 0.00 1.89
3356 3436 4.096231 CACGGGTCAGATGCATCAAAATTA 59.904 41.667 27.81 4.23 0.00 1.40
3357 3437 3.091545 ACGGGTCAGATGCATCAAAATT 58.908 40.909 27.81 4.42 0.00 1.82
3423 3503 2.549926 TCCCGATGTGAATCAATGTCG 58.450 47.619 6.30 6.30 0.00 4.35
3458 3538 5.693769 TGTCTCCCCTTTCAATACCTTAG 57.306 43.478 0.00 0.00 0.00 2.18
3459 3539 6.674861 TGTATGTCTCCCCTTTCAATACCTTA 59.325 38.462 0.00 0.00 0.00 2.69
3484 3564 4.988221 TCCCCTTTCAATTATCCCCACTAT 59.012 41.667 0.00 0.00 0.00 2.12
3492 3572 9.442047 CTATGTCTGTATCCCCTTTCAATTATC 57.558 37.037 0.00 0.00 0.00 1.75
3622 3702 4.464069 AGTTCTGAGTCATGTTAGGAGC 57.536 45.455 0.00 0.00 0.00 4.70
3674 3756 5.178623 TCAGGACTTGTTAACGTTTAGCATG 59.821 40.000 5.91 8.20 0.00 4.06
3880 3963 3.980646 TCCATGTTCCTTTTCAACACG 57.019 42.857 0.00 0.00 36.59 4.49
3892 3975 4.215399 TCGTCACCTTTTCATTCCATGTTC 59.785 41.667 0.00 0.00 0.00 3.18
3896 3979 3.129287 GCATCGTCACCTTTTCATTCCAT 59.871 43.478 0.00 0.00 0.00 3.41
3963 4046 1.135527 TCTACATTTCCGTGGCTACCG 59.864 52.381 0.00 0.00 0.00 4.02
3999 4082 5.464168 CGATGGCATTAAGATCCCATTTTC 58.536 41.667 0.00 0.00 38.15 2.29
4149 4235 4.253685 GTTTGTATTCTACTCTGCTGCCA 58.746 43.478 0.00 0.00 0.00 4.92
4181 4267 3.056458 CCAGTGTACGTCCTGGCA 58.944 61.111 13.83 0.00 41.65 4.92
4517 4604 4.897509 TCCCAGCAATCCACTATATCTG 57.102 45.455 0.00 0.00 0.00 2.90
4559 4646 3.194116 AGCTGCGACAATTGATTTGGATT 59.806 39.130 13.59 0.00 39.80 3.01
4571 4658 4.124238 ACTTTGTACTAAAGCTGCGACAA 58.876 39.130 14.06 0.00 0.00 3.18
4597 4684 4.921470 TCAATTGTCGCAGCTTTAGTAC 57.079 40.909 5.13 0.00 0.00 2.73
4598 4685 6.314018 CAAATCAATTGTCGCAGCTTTAGTA 58.686 36.000 5.13 0.00 34.16 1.82
4617 4704 3.389329 TGCTACTCCCTCTGATCCAAATC 59.611 47.826 0.00 0.00 0.00 2.17
4867 4954 9.023967 GCTATGTTTTGCTGTTATAATTCCTTG 57.976 33.333 0.00 0.00 0.00 3.61
4882 4969 2.030007 TGTCAAGCAGGCTATGTTTTGC 60.030 45.455 0.00 0.00 36.83 3.68
4898 4985 5.172687 TGCATTACCACTATCCTTGTCAA 57.827 39.130 0.00 0.00 0.00 3.18
4953 5040 6.743575 ACTTACAATCAAGCTAACACATCC 57.256 37.500 0.00 0.00 0.00 3.51
5010 5097 1.138859 CTCGCATGTACCCTGGAATCA 59.861 52.381 0.00 0.00 0.00 2.57
5164 5251 8.334263 ACATGAAAATCGCCCATTTTAAAATT 57.666 26.923 10.77 0.00 43.56 1.82
5186 5273 6.418057 TGAGTTGCCCTTGATTTTAAACAT 57.582 33.333 0.00 0.00 0.00 2.71
5234 5321 2.684001 TACCCGAAATCGCAATCACT 57.316 45.000 0.00 0.00 38.18 3.41
5242 5329 7.184800 TCACATTTTATCATACCCGAAATCG 57.815 36.000 0.00 0.00 39.44 3.34
5294 5381 2.520458 CAGTCCCAAACAGGCCCA 59.480 61.111 0.00 0.00 35.39 5.36
5295 5382 2.991540 GCAGTCCCAAACAGGCCC 60.992 66.667 0.00 0.00 35.39 5.80
5332 5419 8.515414 GTTTGGTTTGTAATTTCTAGAGCAGAT 58.485 33.333 0.00 0.00 31.77 2.90
5423 5510 1.065564 GCACTCCCTCAAGAGCTTCAT 60.066 52.381 0.00 0.00 37.39 2.57
5448 5535 5.045869 CAGAAGGGTATCCACTTAACTCCAA 60.046 44.000 0.00 0.00 34.83 3.53
5502 5589 9.837525 CAAGAATGAGAAATTTAGTGGAAAGAG 57.162 33.333 0.00 0.00 0.00 2.85
5512 5599 7.362401 GCTCCAGCTTCAAGAATGAGAAATTTA 60.362 37.037 0.00 0.00 36.78 1.40
5549 5636 8.461222 CCACAAAGAGCAGTTTATCATATTTGA 58.539 33.333 0.00 0.00 36.00 2.69
5610 5711 7.811236 TCAAAATCAGCTTCACTTCATCAAATC 59.189 33.333 0.00 0.00 0.00 2.17
5611 5712 7.663827 TCAAAATCAGCTTCACTTCATCAAAT 58.336 30.769 0.00 0.00 0.00 2.32
5612 5713 7.041635 TCAAAATCAGCTTCACTTCATCAAA 57.958 32.000 0.00 0.00 0.00 2.69
5613 5714 6.638096 TCAAAATCAGCTTCACTTCATCAA 57.362 33.333 0.00 0.00 0.00 2.57
5614 5715 6.829229 ATCAAAATCAGCTTCACTTCATCA 57.171 33.333 0.00 0.00 0.00 3.07
5615 5716 8.206325 TCTATCAAAATCAGCTTCACTTCATC 57.794 34.615 0.00 0.00 0.00 2.92
5616 5717 7.828223 ACTCTATCAAAATCAGCTTCACTTCAT 59.172 33.333 0.00 0.00 0.00 2.57
5617 5718 7.118825 CACTCTATCAAAATCAGCTTCACTTCA 59.881 37.037 0.00 0.00 0.00 3.02
5618 5719 7.413877 CCACTCTATCAAAATCAGCTTCACTTC 60.414 40.741 0.00 0.00 0.00 3.01
5619 5720 6.373774 CCACTCTATCAAAATCAGCTTCACTT 59.626 38.462 0.00 0.00 0.00 3.16
5620 5721 5.879223 CCACTCTATCAAAATCAGCTTCACT 59.121 40.000 0.00 0.00 0.00 3.41
5621 5722 5.877012 TCCACTCTATCAAAATCAGCTTCAC 59.123 40.000 0.00 0.00 0.00 3.18
5622 5723 6.053632 TCCACTCTATCAAAATCAGCTTCA 57.946 37.500 0.00 0.00 0.00 3.02
5623 5724 5.007528 GCTCCACTCTATCAAAATCAGCTTC 59.992 44.000 0.00 0.00 0.00 3.86
5648 5749 3.627123 TCAAATAATGCATGTCTGGGACG 59.373 43.478 0.00 0.00 34.95 4.79
5655 5756 9.531942 TCCACATTTTATCAAATAATGCATGTC 57.468 29.630 0.00 0.00 33.61 3.06


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

AutoCloner maintained by Alex Coulton.