Multiple sequence alignment - TraesCS6B01G272900

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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 TraesCS6B01G272900 chr6B 100.000 3824 0 0 1 3824 492490149 492493972 0.000000e+00 7062.0
1 TraesCS6B01G272900 chr6D 92.857 3850 185 40 1 3824 328611211 328614996 0.000000e+00 5504.0
2 TraesCS6B01G272900 chr6D 93.939 99 5 1 3358 3455 389141614 389141712 8.560000e-32 148.0
3 TraesCS6B01G272900 chr6D 90.265 113 9 2 3345 3455 439506366 439506478 3.080000e-31 147.0
4 TraesCS6B01G272900 chr6A 94.751 2591 113 13 782 3361 467485876 467488454 0.000000e+00 4010.0
5 TraesCS6B01G272900 chr6A 92.323 508 37 2 1 508 467469571 467470076 0.000000e+00 721.0
6 TraesCS6B01G272900 chr6A 86.937 222 11 7 543 746 467485668 467485889 2.300000e-57 233.0
7 TraesCS6B01G272900 chr6A 86.574 216 22 4 3453 3664 467488452 467488664 8.260000e-57 231.0
8 TraesCS6B01G272900 chr6A 92.727 110 7 1 3347 3455 532902252 532902361 1.420000e-34 158.0
9 TraesCS6B01G272900 chr7D 91.964 112 7 2 3359 3468 180531372 180531483 5.110000e-34 156.0
10 TraesCS6B01G272900 chr7D 96.875 32 0 1 3552 3583 409170326 409170296 7.000000e-03 52.8
11 TraesCS6B01G272900 chr3A 96.774 93 3 0 3368 3460 739275106 739275014 5.110000e-34 156.0
12 TraesCS6B01G272900 chr3A 100.000 30 0 0 752 781 641863337 641863308 5.340000e-04 56.5
13 TraesCS6B01G272900 chr3D 94.000 100 5 1 3360 3458 79532649 79532550 2.380000e-32 150.0
14 TraesCS6B01G272900 chr3B 92.381 105 6 2 3353 3456 417055018 417054915 8.560000e-32 148.0
15 TraesCS6B01G272900 chr3B 89.362 47 3 2 3534 3580 556644745 556644701 1.480000e-04 58.4
16 TraesCS6B01G272900 chr2D 90.991 111 8 2 3355 3464 9906334 9906443 8.560000e-32 148.0
17 TraesCS6B01G272900 chr4B 89.381 113 10 2 3344 3455 28229372 28229261 1.430000e-29 141.0
18 TraesCS6B01G272900 chr7A 93.182 44 1 2 3534 3577 602498134 602498093 3.190000e-06 63.9
19 TraesCS6B01G272900 chr1A 91.304 46 2 1 3534 3579 495674849 495674806 1.150000e-05 62.1
20 TraesCS6B01G272900 chr1A 100.000 28 0 0 3552 3579 570270235 570270262 7.000000e-03 52.8
21 TraesCS6B01G272900 chr5B 100.000 29 0 0 3552 3580 281174129 281174157 2.000000e-03 54.7
22 TraesCS6B01G272900 chr4D 100.000 29 0 0 3552 3580 77263571 77263543 2.000000e-03 54.7


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 TraesCS6B01G272900 chr6B 492490149 492493972 3823 False 7062.000000 7062 100.000000 1 3824 1 chr6B.!!$F1 3823
1 TraesCS6B01G272900 chr6D 328611211 328614996 3785 False 5504.000000 5504 92.857000 1 3824 1 chr6D.!!$F1 3823
2 TraesCS6B01G272900 chr6A 467485668 467488664 2996 False 1491.333333 4010 89.420667 543 3664 3 chr6A.!!$F3 3121
3 TraesCS6B01G272900 chr6A 467469571 467470076 505 False 721.000000 721 92.323000 1 508 1 chr6A.!!$F1 507

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
630 634 0.530744 TAGTTCCAGTCTCGCGCATT 59.469 50.0 8.75 0.00 0.00 3.56 F
663 685 0.596600 TCGTCAGAGGCGTTCAACAC 60.597 55.0 0.00 0.00 0.00 3.32 F
1761 1788 1.082690 GCTCTGTTACTGAGGCTTGC 58.917 55.0 18.41 3.57 31.52 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1788 0.387202 CCAGCCCAGTCTCACTATCG 59.613 60.0 0.0 0.0 0.00 2.92 R
1888 1918 0.886563 ACAGCTTCAGAATGGCAAGC 59.113 50.0 0.0 0.0 42.48 4.01 R
2911 2941 0.321122 AGCAGCAACCCTTTCTCTCG 60.321 55.0 0.0 0.0 0.00 4.04 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
56 57 6.319141 AGTTGAACTTGAGCTAAATTGGTC 57.681 37.500 0.00 0.00 35.28 4.02
97 98 1.028905 CGGGAAGCCAGACAAAAACA 58.971 50.000 0.00 0.00 0.00 2.83
101 102 2.866156 GGAAGCCAGACAAAAACAAAGC 59.134 45.455 0.00 0.00 0.00 3.51
142 143 2.597455 CAAGGAAGAAAAAGGAGCCCA 58.403 47.619 0.00 0.00 0.00 5.36
159 160 2.076863 CCCATCAGGTTTTCGTCTCAC 58.923 52.381 0.00 0.00 0.00 3.51
174 175 2.095213 GTCTCACGCAACACAGAAACAA 59.905 45.455 0.00 0.00 0.00 2.83
232 233 1.203994 GACACGTTAGCCTGGAAGCTA 59.796 52.381 0.00 0.00 42.70 3.32
278 279 3.760580 ACAGACTAAGGCATATCCTGC 57.239 47.619 0.00 0.00 46.94 4.85
447 451 3.181454 GGATGGTCGAGATACCCAACAAT 60.181 47.826 0.00 0.00 38.90 2.71
472 476 9.703892 ATTTTCATCTTAGTCTTGATAGATCCG 57.296 33.333 0.00 0.00 31.86 4.18
478 482 6.708502 TCTTAGTCTTGATAGATCCGTCTCAG 59.291 42.308 0.00 0.00 35.87 3.35
511 515 2.302260 CCTCTCTCATACAAGGCGAGA 58.698 52.381 0.00 0.00 34.69 4.04
512 516 2.890311 CCTCTCTCATACAAGGCGAGAT 59.110 50.000 0.00 0.00 35.35 2.75
533 537 8.173775 CGAGATATACATCAATCAAATCCAAGC 58.826 37.037 0.00 0.00 33.21 4.01
582 586 3.118075 AGGGTCCAAACAACAAAAATGGG 60.118 43.478 0.00 0.00 0.00 4.00
604 608 5.003804 GGTAAACAGTTCATGTGTGATCCT 58.996 41.667 0.00 0.00 43.00 3.24
630 634 0.530744 TAGTTCCAGTCTCGCGCATT 59.469 50.000 8.75 0.00 0.00 3.56
663 685 0.596600 TCGTCAGAGGCGTTCAACAC 60.597 55.000 0.00 0.00 0.00 3.32
801 823 5.163913 CGGCAAGAATCGAATAGATGAATCC 60.164 44.000 0.00 0.00 40.02 3.01
907 933 7.503230 AGAAAATAACCTCCCGTTTCTTTGTAA 59.497 33.333 0.00 0.00 35.53 2.41
941 967 3.642741 ATTCCGTGCCCCCTCCTCT 62.643 63.158 0.00 0.00 0.00 3.69
943 969 4.787280 CCGTGCCCCCTCCTCTCT 62.787 72.222 0.00 0.00 0.00 3.10
1206 1233 1.543429 GGTATGCAGAAGAATCCGGGG 60.543 57.143 0.00 0.00 0.00 5.73
1242 1269 2.334653 GATCTCGAGGAGGCGCTG 59.665 66.667 13.56 0.00 0.00 5.18
1656 1683 1.980844 GGGTAAGTTGCCCGACTCT 59.019 57.895 13.80 0.00 36.30 3.24
1683 1710 2.552031 GAGAAGGTTCTTGATACGCCC 58.448 52.381 0.00 0.00 37.73 6.13
1703 1730 1.371558 GAGAGGAAACTGTGGCCGT 59.628 57.895 0.00 0.00 44.43 5.68
1716 1743 1.133025 GTGGCCGTTCATGGAGAATTG 59.867 52.381 0.00 0.00 38.76 2.32
1756 1783 2.344950 CAGCAAGCTCTGTTACTGAGG 58.655 52.381 18.41 5.73 31.52 3.86
1761 1788 1.082690 GCTCTGTTACTGAGGCTTGC 58.917 55.000 18.41 3.57 31.52 4.01
1765 1792 2.758423 TCTGTTACTGAGGCTTGCGATA 59.242 45.455 0.00 0.00 0.00 2.92
1767 1794 2.496070 TGTTACTGAGGCTTGCGATAGT 59.504 45.455 0.00 0.00 39.35 2.12
1790 1817 3.016971 TGGGCTGGGAGGTGATGG 61.017 66.667 0.00 0.00 0.00 3.51
1794 1824 1.453669 GCTGGGAGGTGATGGGATC 59.546 63.158 0.00 0.00 0.00 3.36
1796 1826 2.388890 CTGGGAGGTGATGGGATCGC 62.389 65.000 2.14 2.14 39.02 4.58
1822 1852 4.888896 ACCGAGCTCTGGTAATGGAACAA 61.889 47.826 23.11 0.00 39.47 2.83
1888 1918 3.758023 TGATATTGAACCTGCAGTTGGTG 59.242 43.478 13.81 0.00 39.40 4.17
1908 1938 1.402456 GCTTGCCATTCTGAAGCTGTG 60.402 52.381 0.00 0.00 39.24 3.66
1912 1942 0.809385 CCATTCTGAAGCTGTGCCAG 59.191 55.000 0.00 0.00 34.12 4.85
1971 2001 1.136690 GTTCAGTCGATGTCGTTGCA 58.863 50.000 2.04 0.00 40.80 4.08
2003 2033 8.103305 TGTAGCTGAGAAGGAGAATAATTTTGT 58.897 33.333 0.00 0.00 0.00 2.83
2064 2094 8.743714 ACAAATATTCAGAAGGAAAATGGAGAC 58.256 33.333 0.00 0.00 39.39 3.36
2092 2122 4.038642 GTCCCCTGCTGAAAAACACATTTA 59.961 41.667 0.00 0.00 0.00 1.40
2235 2265 4.922206 TCATTTCCTTCACTGCCAATAGT 58.078 39.130 0.00 0.00 0.00 2.12
2244 2274 3.751175 TCACTGCCAATAGTGTTGTTAGC 59.249 43.478 5.89 0.00 46.32 3.09
2301 2331 1.200948 GGGCAGAGTTTCATGCTTCAC 59.799 52.381 0.00 0.00 42.19 3.18
2370 2400 4.162888 TGTGCACCTGAGTCAATCTATGAT 59.837 41.667 15.69 0.00 40.97 2.45
2449 2479 6.765989 ACAATCTAGTCAGTTTGTGTTGCTTA 59.234 34.615 1.38 0.00 41.18 3.09
2508 2538 6.166982 GGATATCAGACTTAATGTGCCTACC 58.833 44.000 4.83 0.00 0.00 3.18
2553 2583 3.555547 TCGATGAATGCATGTTTACCTCG 59.444 43.478 0.00 3.03 34.11 4.63
2625 2655 1.003003 GCTGAGGAGGCTGAAGAGTTT 59.997 52.381 0.00 0.00 0.00 2.66
2712 2742 1.241165 TGCACTCATTGAACAGCAGG 58.759 50.000 3.94 0.00 0.00 4.85
2734 2764 3.644884 ACTATCCAGATTTCCGCTACG 57.355 47.619 0.00 0.00 0.00 3.51
2792 2822 6.458070 GCTGAAGTTGAGAATATGGAAGAAGC 60.458 42.308 0.00 0.00 0.00 3.86
2793 2823 6.475504 TGAAGTTGAGAATATGGAAGAAGCA 58.524 36.000 0.00 0.00 0.00 3.91
2834 2864 8.438676 AATATAAGCGAGTAACTTCTTGCAAT 57.561 30.769 0.00 0.00 44.65 3.56
2835 2865 6.743575 ATAAGCGAGTAACTTCTTGCAATT 57.256 33.333 0.00 0.00 44.65 2.32
2911 2941 7.370383 TGAAACATTGCTTGGAATAAAGACTC 58.630 34.615 0.00 0.00 0.00 3.36
2912 2942 5.551760 ACATTGCTTGGAATAAAGACTCG 57.448 39.130 0.00 0.00 0.00 4.18
2970 3000 1.469767 GCATCAAAATGGTCGGAAGCC 60.470 52.381 0.00 0.00 33.19 4.35
3003 3034 5.412594 TGCTTCAGTGTTATCTTAAGGCAAG 59.587 40.000 1.85 0.00 35.38 4.01
3022 3053 4.499865 GCAAGATCTGTTACAGCGGAGATA 60.500 45.833 7.61 0.00 0.00 1.98
3023 3054 4.839668 AGATCTGTTACAGCGGAGATAC 57.160 45.455 7.61 0.00 0.00 2.24
3093 3124 4.688021 ACACTCTGAGACAGTTTTGAGAC 58.312 43.478 12.44 0.00 32.61 3.36
3132 3164 5.973565 GGAAAATACTTCATTGAATCCAGCG 59.026 40.000 8.82 0.00 30.49 5.18
3139 3171 2.009051 CATTGAATCCAGCGTGCAGTA 58.991 47.619 0.00 0.00 0.00 2.74
3262 3294 8.028540 TGTTATCATATTATGTGCATTCGTCC 57.971 34.615 3.67 0.00 0.00 4.79
3275 3307 2.032528 CGTCCTGGCAAGCTCCAA 59.967 61.111 0.00 0.00 35.36 3.53
3293 3325 6.541641 AGCTCCAAATTGATTCAGACTCATAC 59.458 38.462 0.00 0.00 0.00 2.39
3302 3334 3.827008 TCAGACTCATACCCATTGCTC 57.173 47.619 0.00 0.00 0.00 4.26
3311 3343 5.630121 TCATACCCATTGCTCGGATAATTT 58.370 37.500 0.00 0.00 0.00 1.82
3339 3373 6.844279 GTGTTTACTGTTACTCGACAAATGTG 59.156 38.462 0.00 0.00 0.00 3.21
3364 3398 6.728200 CAATTTGCTCACTTTGAAGTACTCA 58.272 36.000 0.00 0.00 37.08 3.41
3368 3402 3.670991 GCTCACTTTGAAGTACTCACTCG 59.329 47.826 0.00 0.00 37.08 4.18
3369 3403 4.793353 GCTCACTTTGAAGTACTCACTCGT 60.793 45.833 0.00 0.00 37.08 4.18
3370 3404 4.856664 TCACTTTGAAGTACTCACTCGTC 58.143 43.478 0.00 0.00 37.08 4.20
3371 3405 3.982058 CACTTTGAAGTACTCACTCGTCC 59.018 47.826 0.00 0.00 37.08 4.79
3373 3407 2.281539 TGAAGTACTCACTCGTCCCA 57.718 50.000 0.00 0.00 32.29 4.37
3374 3408 2.589720 TGAAGTACTCACTCGTCCCAA 58.410 47.619 0.00 0.00 32.29 4.12
3377 3411 4.039973 TGAAGTACTCACTCGTCCCAAAAT 59.960 41.667 0.00 0.00 32.29 1.82
3378 3412 5.244402 TGAAGTACTCACTCGTCCCAAAATA 59.756 40.000 0.00 0.00 32.29 1.40
3379 3413 5.733620 AGTACTCACTCGTCCCAAAATAA 57.266 39.130 0.00 0.00 0.00 1.40
3380 3414 5.721232 AGTACTCACTCGTCCCAAAATAAG 58.279 41.667 0.00 0.00 0.00 1.73
3381 3415 4.618920 ACTCACTCGTCCCAAAATAAGT 57.381 40.909 0.00 0.00 0.00 2.24
3382 3416 4.315803 ACTCACTCGTCCCAAAATAAGTG 58.684 43.478 0.00 0.00 36.36 3.16
3383 3417 4.039973 ACTCACTCGTCCCAAAATAAGTGA 59.960 41.667 0.00 0.00 40.42 3.41
3384 3418 4.312443 TCACTCGTCCCAAAATAAGTGAC 58.688 43.478 0.00 0.00 38.47 3.67
3385 3419 4.039973 TCACTCGTCCCAAAATAAGTGACT 59.960 41.667 0.00 0.00 38.47 3.41
3386 3420 4.389077 CACTCGTCCCAAAATAAGTGACTC 59.611 45.833 0.00 0.00 36.99 3.36
3387 3421 3.581755 TCGTCCCAAAATAAGTGACTCG 58.418 45.455 0.00 0.00 0.00 4.18
3388 3422 3.256383 TCGTCCCAAAATAAGTGACTCGA 59.744 43.478 0.00 0.00 0.00 4.04
3389 3423 3.367025 CGTCCCAAAATAAGTGACTCGAC 59.633 47.826 0.00 0.00 0.00 4.20
3394 3428 5.238650 CCCAAAATAAGTGACTCGACTTTGT 59.761 40.000 0.00 0.00 37.38 2.83
3395 3429 6.425721 CCCAAAATAAGTGACTCGACTTTGTA 59.574 38.462 0.00 0.00 37.38 2.41
3396 3430 7.288672 CCAAAATAAGTGACTCGACTTTGTAC 58.711 38.462 0.00 0.00 37.38 2.90
3397 3431 7.170998 CCAAAATAAGTGACTCGACTTTGTACT 59.829 37.037 0.00 0.00 37.38 2.73
3398 3432 9.188588 CAAAATAAGTGACTCGACTTTGTACTA 57.811 33.333 0.00 0.00 37.38 1.82
3400 3434 9.924650 AAATAAGTGACTCGACTTTGTACTAAT 57.075 29.630 0.00 0.00 37.38 1.73
3402 3436 9.924650 ATAAGTGACTCGACTTTGTACTAATTT 57.075 29.630 0.00 0.00 37.38 1.82
3403 3437 8.658499 AAGTGACTCGACTTTGTACTAATTTT 57.342 30.769 0.00 0.00 31.92 1.82
3404 3438 8.073355 AGTGACTCGACTTTGTACTAATTTTG 57.927 34.615 0.00 0.00 0.00 2.44
3405 3439 7.709613 AGTGACTCGACTTTGTACTAATTTTGT 59.290 33.333 0.00 0.00 0.00 2.83
3407 3441 8.971321 TGACTCGACTTTGTACTAATTTTGTAC 58.029 33.333 12.39 12.39 40.27 2.90
3408 3442 9.189723 GACTCGACTTTGTACTAATTTTGTACT 57.810 33.333 17.79 2.73 40.44 2.73
3429 3463 9.991906 TGTACTAAAGCTAATACAAAGTTGAGT 57.008 29.630 0.00 0.00 0.00 3.41
3432 3466 8.989980 ACTAAAGCTAATACAAAGTTGAGTCAC 58.010 33.333 0.00 0.00 0.00 3.67
3433 3467 9.209175 CTAAAGCTAATACAAAGTTGAGTCACT 57.791 33.333 0.00 0.00 0.00 3.41
3451 3485 3.835978 TCACTTATTTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
3452 3486 4.081642 TCACTTATTTTGAGACGGAGGGAG 60.082 45.833 0.00 0.00 0.00 4.30
3453 3487 3.838903 ACTTATTTTGAGACGGAGGGAGT 59.161 43.478 0.00 0.00 0.00 3.85
3497 3531 9.845740 AACTTATTATGTTGATAGCCATGTACA 57.154 29.630 0.00 0.00 0.00 2.90
3532 3569 2.198304 CTGTTGGTACTCCCCCTGCC 62.198 65.000 0.00 0.00 0.00 4.85
3549 3586 4.455606 CCTGCCTTAGTGATCTAAAAGGG 58.544 47.826 16.99 5.26 35.98 3.95
3550 3587 4.455606 CTGCCTTAGTGATCTAAAAGGGG 58.544 47.826 16.99 4.01 35.98 4.79
3604 3641 6.142817 ACATTTGCTCACTTTGTCGTATTTC 58.857 36.000 0.00 0.00 0.00 2.17
3608 3645 4.020928 TGCTCACTTTGTCGTATTTCCCTA 60.021 41.667 0.00 0.00 0.00 3.53
3638 3675 0.834687 ACTCCGCTACTGGTTCCCAA 60.835 55.000 0.00 0.00 30.80 4.12
3668 3705 0.856982 TGGTGTCCTGACCCCAATTT 59.143 50.000 0.00 0.00 35.91 1.82
3680 3717 2.034124 CCCCAATTTCTGGTATGCAGG 58.966 52.381 0.00 0.00 44.76 4.85
3693 3730 2.512692 ATGCAGGGCACATTCTGTTA 57.487 45.000 0.00 0.00 43.04 2.41
3763 3800 0.990374 GATGCTGGATGGGATAGCCT 59.010 55.000 0.00 0.00 35.30 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.131731 AGCTCAAGTTCAACTTCTTAATCAAAC 58.868 33.333 0.00 0.00 36.03 2.93
56 57 4.447054 CGAGCAGCTTTGTGGATAGATAAG 59.553 45.833 0.00 0.00 0.00 1.73
97 98 5.184892 AGGGACACAGATAAATCAGCTTT 57.815 39.130 0.00 0.00 0.00 3.51
101 102 5.282055 TGCTAGGGACACAGATAAATCAG 57.718 43.478 0.00 0.00 0.00 2.90
142 143 1.270094 TGCGTGAGACGAAAACCTGAT 60.270 47.619 0.00 0.00 46.05 2.90
159 160 3.672867 AGTTTGTTTGTTTCTGTGTTGCG 59.327 39.130 0.00 0.00 0.00 4.85
174 175 2.024414 GTCAGTGGCCAAGAGTTTGTT 58.976 47.619 7.24 0.00 32.21 2.83
232 233 3.386237 GAGACCAGCCTGGCGACT 61.386 66.667 11.63 8.05 42.67 4.18
281 282 4.161295 CTTCATGCGGGGCGAGGA 62.161 66.667 0.00 0.00 0.00 3.71
376 377 4.174762 CGAGACCTAGGTTTACAAAGCTC 58.825 47.826 17.53 13.68 44.77 4.09
404 405 7.420680 CCATCCCCTAGGCCTCATATTATAAAG 60.421 44.444 9.68 0.00 0.00 1.85
407 408 5.041835 ACCATCCCCTAGGCCTCATATTATA 60.042 44.000 9.68 0.00 0.00 0.98
408 409 4.265957 ACCATCCCCTAGGCCTCATATTAT 60.266 45.833 9.68 0.00 0.00 1.28
409 410 3.080619 ACCATCCCCTAGGCCTCATATTA 59.919 47.826 9.68 0.00 0.00 0.98
410 411 2.157786 ACCATCCCCTAGGCCTCATATT 60.158 50.000 9.68 0.00 0.00 1.28
414 418 1.074471 GACCATCCCCTAGGCCTCA 60.074 63.158 9.68 0.00 0.00 3.86
418 422 0.543174 ATCTCGACCATCCCCTAGGC 60.543 60.000 2.05 0.00 0.00 3.93
447 451 8.696374 ACGGATCTATCAAGACTAAGATGAAAA 58.304 33.333 0.00 0.00 33.57 2.29
472 476 2.158842 AGGCTACATTGGATGCTGAGAC 60.159 50.000 0.00 0.00 0.00 3.36
478 482 2.103771 TGAGAGAGGCTACATTGGATGC 59.896 50.000 0.00 0.00 0.00 3.91
511 515 7.727186 ACCTGCTTGGATTTGATTGATGTATAT 59.273 33.333 3.40 0.00 39.71 0.86
512 516 7.013559 CACCTGCTTGGATTTGATTGATGTATA 59.986 37.037 3.40 0.00 39.71 1.47
582 586 5.934625 AGAGGATCACACATGAACTGTTTAC 59.065 40.000 0.00 0.00 38.69 2.01
604 608 3.650139 GCGAGACTGGAACTACAAAAGA 58.350 45.455 0.00 0.00 0.00 2.52
630 634 2.775960 TCTGACGAGTCCTGATAGGGTA 59.224 50.000 0.34 0.00 35.59 3.69
654 676 5.290643 ACAAAACCAATGATTGTGTTGAACG 59.709 36.000 15.25 7.43 36.03 3.95
746 768 5.980715 CGCCTCCTCTCTAAAAAGAATCTAC 59.019 44.000 0.00 0.00 0.00 2.59
748 770 4.682050 GCGCCTCCTCTCTAAAAAGAATCT 60.682 45.833 0.00 0.00 0.00 2.40
749 771 3.558006 GCGCCTCCTCTCTAAAAAGAATC 59.442 47.826 0.00 0.00 0.00 2.52
750 772 3.198853 AGCGCCTCCTCTCTAAAAAGAAT 59.801 43.478 2.29 0.00 0.00 2.40
751 773 2.567615 AGCGCCTCCTCTCTAAAAAGAA 59.432 45.455 2.29 0.00 0.00 2.52
752 774 2.180276 AGCGCCTCCTCTCTAAAAAGA 58.820 47.619 2.29 0.00 0.00 2.52
753 775 2.675348 CAAGCGCCTCCTCTCTAAAAAG 59.325 50.000 2.29 0.00 0.00 2.27
801 823 3.879427 TCAATTTACAAAACAGCCGTCG 58.121 40.909 0.00 0.00 0.00 5.12
907 933 2.932614 CGGAATCGAATGAAACAGAGCT 59.067 45.455 0.00 0.00 39.00 4.09
941 967 2.038269 GGTGCGGATCGGCAAAAGA 61.038 57.895 27.17 3.87 45.93 2.52
943 969 3.059386 GGGTGCGGATCGGCAAAA 61.059 61.111 27.17 4.62 45.93 2.44
1286 1313 2.585247 GTGCCCACTCGTATCGGC 60.585 66.667 0.00 0.00 41.99 5.54
1338 1365 2.664851 CCGGAGACAACTTGCGCA 60.665 61.111 5.66 5.66 0.00 6.09
1641 1668 0.895530 CCTCAGAGTCGGGCAACTTA 59.104 55.000 0.00 0.00 0.00 2.24
1656 1683 3.260269 TCAAGAACCTTCTCCTCCTCA 57.740 47.619 0.00 0.00 36.28 3.86
1683 1710 1.376037 GGCCACAGTTTCCTCTCCG 60.376 63.158 0.00 0.00 0.00 4.63
1703 1730 2.690632 GCATCCCCCAATTCTCCATGAA 60.691 50.000 0.00 0.00 39.24 2.57
1716 1743 1.482182 GGAACAGATTTTGCATCCCCC 59.518 52.381 0.00 0.00 32.55 5.40
1756 1783 1.565305 CCAGTCTCACTATCGCAAGC 58.435 55.000 0.00 0.00 37.18 4.01
1761 1788 0.387202 CCAGCCCAGTCTCACTATCG 59.613 60.000 0.00 0.00 0.00 2.92
1765 1792 1.611851 CTCCCAGCCCAGTCTCACT 60.612 63.158 0.00 0.00 0.00 3.41
1767 1794 2.284921 CCTCCCAGCCCAGTCTCA 60.285 66.667 0.00 0.00 0.00 3.27
1796 1826 4.079970 TCCATTACCAGAGCTCGGTATAG 58.920 47.826 26.94 22.44 38.77 1.31
1822 1852 3.243975 CCCAGTTCAGCATTTTGAGCTTT 60.244 43.478 0.00 0.00 41.14 3.51
1888 1918 0.886563 ACAGCTTCAGAATGGCAAGC 59.113 50.000 0.00 0.00 42.48 4.01
1923 1953 4.115401 TGAATCAGAACAGATGGTCTCG 57.885 45.455 0.00 0.00 40.79 4.04
1971 2001 4.348486 TCTCCTTCTCAGCTACAACTGAT 58.652 43.478 0.00 0.00 45.34 2.90
2003 2033 2.305635 TCCTTTTCACTATCTGCAGGCA 59.694 45.455 15.13 0.50 0.00 4.75
2064 2094 1.604604 TTTTCAGCAGGGGACTTTCG 58.395 50.000 0.00 0.00 40.21 3.46
2076 2106 7.913297 TCAGTGTAAGTAAATGTGTTTTTCAGC 59.087 33.333 0.00 0.00 0.00 4.26
2235 2265 1.367346 TCCCATCCAGGCTAACAACA 58.633 50.000 0.00 0.00 35.39 3.33
2244 2274 4.025360 TGACAAAATCAATCCCATCCAGG 58.975 43.478 0.00 0.00 33.02 4.45
2301 2331 1.475751 CCAACCATCTTCCGGATCTGG 60.476 57.143 15.09 15.09 31.27 3.86
2480 2510 4.453819 GCACATTAAGTCTGATATCCCTGC 59.546 45.833 0.00 0.00 0.00 4.85
2508 2538 1.669115 CAGTCCAACCTCAGGTGCG 60.669 63.158 0.00 0.00 35.34 5.34
2553 2583 9.337396 TGTGTATCCATCCATTTTGAGTTATAC 57.663 33.333 0.00 0.00 0.00 1.47
2625 2655 7.921041 ATGAGGGAAGATGTACTTGATCTTA 57.079 36.000 6.85 0.00 39.72 2.10
2712 2742 3.982058 CGTAGCGGAAATCTGGATAGTTC 59.018 47.826 0.00 0.00 0.00 3.01
2734 2764 1.136695 CTCAGATCCAGCAGTCTCCAC 59.863 57.143 0.00 0.00 0.00 4.02
2792 2822 9.117145 CGCTTATATTATTACTTGGCATTTGTG 57.883 33.333 0.00 0.00 0.00 3.33
2793 2823 9.062524 TCGCTTATATTATTACTTGGCATTTGT 57.937 29.630 0.00 0.00 0.00 2.83
2834 2864 3.342377 TCCATCGGTCTTGCATGTTAA 57.658 42.857 0.00 0.00 0.00 2.01
2835 2865 3.558931 ATCCATCGGTCTTGCATGTTA 57.441 42.857 0.00 0.00 0.00 2.41
2911 2941 0.321122 AGCAGCAACCCTTTCTCTCG 60.321 55.000 0.00 0.00 0.00 4.04
2912 2942 1.902938 AAGCAGCAACCCTTTCTCTC 58.097 50.000 0.00 0.00 0.00 3.20
3003 3034 3.556513 CGTATCTCCGCTGTAACAGATC 58.443 50.000 0.00 0.00 32.44 2.75
3093 3124 2.065899 TTTCCAGGGGGCATAATTCG 57.934 50.000 0.00 0.00 0.00 3.34
3240 3272 6.818142 CCAGGACGAATGCACATAATATGATA 59.182 38.462 7.33 0.00 0.00 2.15
3245 3277 3.138304 GCCAGGACGAATGCACATAATA 58.862 45.455 0.00 0.00 0.00 0.98
3262 3294 3.056393 TGAATCAATTTGGAGCTTGCCAG 60.056 43.478 0.00 0.00 39.52 4.85
3275 3307 6.040166 GCAATGGGTATGAGTCTGAATCAATT 59.960 38.462 12.12 4.25 0.00 2.32
3293 3325 3.885297 ACAGAAATTATCCGAGCAATGGG 59.115 43.478 0.00 0.00 0.00 4.00
3302 3334 8.932791 AGTAACAGTAAACACAGAAATTATCCG 58.067 33.333 0.00 0.00 0.00 4.18
3311 3343 5.503662 TGTCGAGTAACAGTAAACACAGA 57.496 39.130 0.00 0.00 0.00 3.41
3339 3373 5.523369 AGTACTTCAAAGTGAGCAAATTGC 58.477 37.500 10.41 10.41 41.00 3.56
3364 3398 4.566987 GAGTCACTTATTTTGGGACGAGT 58.433 43.478 0.00 0.00 33.84 4.18
3368 3402 4.566987 AGTCGAGTCACTTATTTTGGGAC 58.433 43.478 0.00 0.00 0.00 4.46
3369 3403 4.884668 AGTCGAGTCACTTATTTTGGGA 57.115 40.909 0.00 0.00 0.00 4.37
3370 3404 5.238650 ACAAAGTCGAGTCACTTATTTTGGG 59.761 40.000 11.39 0.00 35.45 4.12
3371 3405 6.300354 ACAAAGTCGAGTCACTTATTTTGG 57.700 37.500 11.39 0.00 35.45 3.28
3373 3407 9.754382 TTAGTACAAAGTCGAGTCACTTATTTT 57.246 29.630 0.00 0.00 35.45 1.82
3374 3408 9.924650 ATTAGTACAAAGTCGAGTCACTTATTT 57.075 29.630 0.00 1.15 35.45 1.40
3377 3411 9.754382 AAAATTAGTACAAAGTCGAGTCACTTA 57.246 29.630 0.00 0.00 35.45 2.24
3378 3412 8.548721 CAAAATTAGTACAAAGTCGAGTCACTT 58.451 33.333 0.00 3.11 38.30 3.16
3379 3413 7.709613 ACAAAATTAGTACAAAGTCGAGTCACT 59.290 33.333 0.00 0.00 0.00 3.41
3380 3414 7.848491 ACAAAATTAGTACAAAGTCGAGTCAC 58.152 34.615 0.00 0.00 0.00 3.67
3381 3415 8.971321 GTACAAAATTAGTACAAAGTCGAGTCA 58.029 33.333 13.38 0.00 41.08 3.41
3382 3416 9.189723 AGTACAAAATTAGTACAAAGTCGAGTC 57.810 33.333 18.07 0.00 43.24 3.36
3403 3437 9.991906 ACTCAACTTTGTATTAGCTTTAGTACA 57.008 29.630 0.00 0.00 0.00 2.90
3407 3441 9.209175 AGTGACTCAACTTTGTATTAGCTTTAG 57.791 33.333 0.00 0.00 0.00 1.85
3408 3442 9.555727 AAGTGACTCAACTTTGTATTAGCTTTA 57.444 29.630 0.00 0.00 37.05 1.85
3409 3443 8.451908 AAGTGACTCAACTTTGTATTAGCTTT 57.548 30.769 0.00 0.00 37.05 3.51
3410 3444 9.726438 ATAAGTGACTCAACTTTGTATTAGCTT 57.274 29.630 0.00 0.00 40.77 3.74
3417 3451 9.607988 TCTCAAAATAAGTGACTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
3418 3452 8.398665 GTCTCAAAATAAGTGACTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
3419 3453 7.584123 CGTCTCAAAATAAGTGACTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
3423 3457 5.694910 TCCGTCTCAAAATAAGTGACTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
3424 3458 5.849510 TCCGTCTCAAAATAAGTGACTCAA 58.150 37.500 0.00 0.00 0.00 3.02
3426 3460 4.865365 CCTCCGTCTCAAAATAAGTGACTC 59.135 45.833 0.00 0.00 0.00 3.36
3427 3461 4.322801 CCCTCCGTCTCAAAATAAGTGACT 60.323 45.833 0.00 0.00 0.00 3.41
3428 3462 3.933332 CCCTCCGTCTCAAAATAAGTGAC 59.067 47.826 0.00 0.00 0.00 3.67
3429 3463 3.835978 TCCCTCCGTCTCAAAATAAGTGA 59.164 43.478 0.00 0.00 0.00 3.41
3430 3464 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
3431 3465 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
3432 3466 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
3433 3467 6.555463 AATACTCCCTCCGTCTCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
3441 3475 6.787170 TGTATGTATAATACTCCCTCCGTCT 58.213 40.000 0.00 0.00 0.00 4.18
3479 3513 4.080356 ACAGGTGTACATGGCTATCAACAT 60.080 41.667 0.00 0.00 30.95 2.71
3484 3518 2.213499 GCACAGGTGTACATGGCTATC 58.787 52.381 0.00 0.00 30.95 2.08
3488 3522 1.303236 TGGCACAGGTGTACATGGC 60.303 57.895 12.46 12.46 38.08 4.40
3497 3531 0.694771 ACAGATCATGTGGCACAGGT 59.305 50.000 28.77 17.63 41.91 4.00
3549 3586 9.590828 ACTCCCTCTCTAAACTAATATAAGACC 57.409 37.037 0.00 0.00 0.00 3.85
3566 3603 5.163405 TGAGCAAATGTATGTACTCCCTCTC 60.163 44.000 0.00 0.00 0.00 3.20
3604 3641 3.890147 AGCGGAGTTGAACTACTATAGGG 59.110 47.826 5.94 0.00 0.00 3.53
3608 3645 4.338682 CCAGTAGCGGAGTTGAACTACTAT 59.661 45.833 5.94 0.00 42.56 2.12
3668 3705 0.625316 AATGTGCCCTGCATACCAGA 59.375 50.000 0.00 0.00 44.64 3.86
3693 3730 4.500545 CGTTATCAGCAGCAGGATAAGTCT 60.501 45.833 15.93 0.00 36.84 3.24
3763 3800 5.127845 CCCAAAGACAGAGAGTAGAGCAATA 59.872 44.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.