Multiple sequence alignment - TraesCS5D01G500400

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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 TraesCS5D01G500400 chr5D 100.000 3928 0 0 1 3928 528977403 528981330 0.000000e+00 7254
1 TraesCS5D01G500400 chr5B 92.270 3480 135 44 1 3389 666206314 666209750 0.000000e+00 4813
2 TraesCS5D01G500400 chr5B 91.558 462 29 5 3473 3928 666209746 666210203 2.580000e-176 628
3 TraesCS5D01G500400 chr5A 90.184 2007 115 25 1342 3314 657206150 657208108 0.000000e+00 2540
4 TraesCS5D01G500400 chr5A 89.620 1185 65 28 1 1152 657204861 657206020 0.000000e+00 1454
5 TraesCS5D01G500400 chr5A 91.640 311 18 5 3473 3777 657208133 657208441 1.300000e-114 424
6 TraesCS5D01G500400 chr6D 93.750 96 1 1 3386 3481 62245402 62245312 5.290000e-29 139
7 TraesCS5D01G500400 chr7A 94.444 90 0 1 3387 3476 485195289 485195205 2.460000e-27 134
8 TraesCS5D01G500400 chr6B 92.708 96 1 2 3386 3481 14523407 14523318 2.460000e-27 134
9 TraesCS5D01G500400 chr7B 89.189 111 2 5 3378 3486 829837 829735 3.190000e-26 130
10 TraesCS5D01G500400 chr7D 91.667 96 2 2 3382 3476 22964251 22964341 1.150000e-25 128
11 TraesCS5D01G500400 chr7D 90.196 102 2 4 3386 3487 379769589 379769496 4.120000e-25 126
12 TraesCS5D01G500400 chr7D 86.179 123 8 5 3370 3490 494673698 494673583 1.480000e-24 124
13 TraesCS5D01G500400 chr3D 91.579 95 3 1 3382 3476 441134576 441134487 4.120000e-25 126
14 TraesCS5D01G500400 chr2D 90.816 98 4 1 3380 3477 636385940 636386032 4.120000e-25 126


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 TraesCS5D01G500400 chr5D 528977403 528981330 3927 False 7254.000000 7254 100.000000 1 3928 1 chr5D.!!$F1 3927
1 TraesCS5D01G500400 chr5B 666206314 666210203 3889 False 2720.500000 4813 91.914000 1 3928 2 chr5B.!!$F1 3927
2 TraesCS5D01G500400 chr5A 657204861 657208441 3580 False 1472.666667 2540 90.481333 1 3777 3 chr5A.!!$F1 3776

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
624 664 0.959372 GAAGAGAGTCCGACCCGTGA 60.959 60.000 0.00 0.0 0.00 4.35 F
625 665 0.961358 AAGAGAGTCCGACCCGTGAG 60.961 60.000 0.00 0.0 0.00 3.51 F
1265 1383 1.064946 CCAGACGATCGAGCTGGTC 59.935 63.158 33.48 18.7 43.25 4.02 F
2561 2707 1.141053 CCTCCTTATGTGCCTACACCC 59.859 57.143 0.00 0.0 46.86 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1555 1678 0.106519 GGACTGGGTACGGTAGGCTA 60.107 60.0 0.00 0.0 36.00 3.93 R
1558 1681 0.324091 ACTGGACTGGGTACGGTAGG 60.324 60.0 0.00 0.0 33.68 3.18 R
2763 2909 0.315251 TCGTCAGTGCACCTCTTCAG 59.685 55.0 14.63 0.0 0.00 3.02 R
3461 3618 0.109342 TATCGTACTCCCTCCGTCCC 59.891 60.0 0.00 0.0 0.00 4.46 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
28 29 1.446966 GAGGCACTTGTCGAGGAGC 60.447 63.158 0.00 0.00 41.55 4.70
346 347 4.308458 TCCTTGGGCGTGGTCGTG 62.308 66.667 0.00 0.00 39.49 4.35
554 593 2.821969 CACCACTGGGGAGAGATTTTTG 59.178 50.000 1.10 0.00 41.15 2.44
577 616 1.592669 CGCTGCCGAAGTGGATAGG 60.593 63.158 0.00 0.00 42.00 2.57
581 620 1.300233 GCCGAAGTGGATAGGCTCG 60.300 63.158 0.00 0.00 45.67 5.03
623 663 1.507174 GAAGAGAGTCCGACCCGTG 59.493 63.158 0.00 0.00 0.00 4.94
624 664 0.959372 GAAGAGAGTCCGACCCGTGA 60.959 60.000 0.00 0.00 0.00 4.35
625 665 0.961358 AAGAGAGTCCGACCCGTGAG 60.961 60.000 0.00 0.00 0.00 3.51
770 861 2.838225 GCCCTCCCGCACTAGCTA 60.838 66.667 0.00 0.00 39.10 3.32
771 862 3.130227 CCCTCCCGCACTAGCTAC 58.870 66.667 0.00 0.00 39.10 3.58
772 863 2.499827 CCCTCCCGCACTAGCTACC 61.500 68.421 0.00 0.00 39.10 3.18
773 864 2.499827 CCTCCCGCACTAGCTACCC 61.500 68.421 0.00 0.00 39.10 3.69
774 865 2.443390 TCCCGCACTAGCTACCCC 60.443 66.667 0.00 0.00 39.10 4.95
775 866 2.444140 CCCGCACTAGCTACCCCT 60.444 66.667 0.00 0.00 39.10 4.79
776 867 2.499827 CCCGCACTAGCTACCCCTC 61.500 68.421 0.00 0.00 39.10 4.30
777 868 2.499827 CCGCACTAGCTACCCCTCC 61.500 68.421 0.00 0.00 39.10 4.30
859 950 3.546714 CTCCGGGCAGGTTCGGTTT 62.547 63.158 0.00 0.00 45.79 3.27
988 1080 3.384014 CTCGTCTGTCGCGGGTCTC 62.384 68.421 6.13 0.00 39.67 3.36
1080 1172 3.753434 AGCTGCGACCTCAGGACG 61.753 66.667 11.58 11.58 43.00 4.79
1112 1204 2.348998 CAAGGTCAGCCCGCTCTT 59.651 61.111 0.00 0.00 38.74 2.85
1114 1206 1.915769 AAGGTCAGCCCGCTCTTCT 60.916 57.895 0.00 0.00 38.74 2.85
1115 1207 1.893919 AAGGTCAGCCCGCTCTTCTC 61.894 60.000 0.00 0.00 38.74 2.87
1116 1208 2.650116 GGTCAGCCCGCTCTTCTCA 61.650 63.158 0.00 0.00 0.00 3.27
1117 1209 1.153667 GTCAGCCCGCTCTTCTCAG 60.154 63.158 0.00 0.00 0.00 3.35
1118 1210 2.511145 CAGCCCGCTCTTCTCAGC 60.511 66.667 0.00 0.00 35.90 4.26
1137 1229 4.101448 CTCACCCTCCCGCCTTGG 62.101 72.222 0.00 0.00 37.55 3.61
1152 1244 4.142249 CCGCCTTGGTTTATTTTCCTTAGG 60.142 45.833 0.00 0.00 33.03 2.69
1154 1246 5.359860 CGCCTTGGTTTATTTTCCTTAGGAT 59.640 40.000 0.12 0.00 32.23 3.24
1155 1247 6.459710 CGCCTTGGTTTATTTTCCTTAGGATC 60.460 42.308 0.12 0.00 32.23 3.36
1166 1264 2.378886 TCCTTAGGATCATCGGCCTCTA 59.621 50.000 0.00 0.00 35.73 2.43
1265 1383 1.064946 CCAGACGATCGAGCTGGTC 59.935 63.158 33.48 18.70 43.25 4.02
1297 1415 3.748568 GCGGTTTCAGAATCTCTCAAGTT 59.251 43.478 0.00 0.00 0.00 2.66
1314 1433 6.365247 TCTCAAGTTTTAAGTCTATCGTGTGC 59.635 38.462 0.00 0.00 0.00 4.57
1376 1497 5.239525 GGAAATTGGATGATGCTGTACTACC 59.760 44.000 0.00 0.00 0.00 3.18
1379 1500 2.100749 TGGATGATGCTGTACTACCGTG 59.899 50.000 0.00 0.00 0.00 4.94
1380 1501 2.361119 GGATGATGCTGTACTACCGTGA 59.639 50.000 0.00 0.00 0.00 4.35
1391 1512 5.345702 TGTACTACCGTGATGTTCTATTGC 58.654 41.667 0.00 0.00 0.00 3.56
1395 1516 2.159156 ACCGTGATGTTCTATTGCGCTA 60.159 45.455 9.73 0.00 0.00 4.26
1468 1591 8.752005 TTTTTGCTCTTATGCCTACAAGATAT 57.248 30.769 0.00 0.00 30.70 1.63
1535 1658 1.527433 GCTCCCCAAAAGCACCTCAC 61.527 60.000 0.00 0.00 39.61 3.51
1553 1676 4.320494 CCTCACATAGTTTGCCTTGTTGTC 60.320 45.833 0.00 0.00 0.00 3.18
1555 1678 4.826733 TCACATAGTTTGCCTTGTTGTCAT 59.173 37.500 0.00 0.00 0.00 3.06
1556 1679 6.000840 TCACATAGTTTGCCTTGTTGTCATA 58.999 36.000 0.00 0.00 0.00 2.15
1557 1680 6.149308 TCACATAGTTTGCCTTGTTGTCATAG 59.851 38.462 0.00 0.00 0.00 2.23
1558 1681 3.923017 AGTTTGCCTTGTTGTCATAGC 57.077 42.857 0.00 0.00 0.00 2.97
1559 1682 2.558359 AGTTTGCCTTGTTGTCATAGCC 59.442 45.455 0.00 0.00 0.00 3.93
1562 1685 2.985896 TGCCTTGTTGTCATAGCCTAC 58.014 47.619 0.00 0.00 0.00 3.18
1564 1687 2.550978 CCTTGTTGTCATAGCCTACCG 58.449 52.381 0.00 0.00 0.00 4.02
1597 1721 4.349365 AGTTGGAACTGTTTCTTCCCAAA 58.651 39.130 10.97 0.00 37.98 3.28
1616 1740 8.964476 TCCCAAAATCACACTTATCTTATCTC 57.036 34.615 0.00 0.00 0.00 2.75
1633 1757 3.880168 TCTCTACCCTTACCCTAGCTC 57.120 52.381 0.00 0.00 0.00 4.09
1866 2004 4.041740 TGTCCCGAAGATATTCGAAGTG 57.958 45.455 23.23 6.76 46.52 3.16
1935 2076 2.610438 AAACATGAGCATCCCAAGGT 57.390 45.000 0.00 0.00 0.00 3.50
2012 2155 5.353394 AAGGCATCCGTCTACAAAAGATA 57.647 39.130 0.00 0.00 36.36 1.98
2246 2392 7.943079 AGTTTATGAACCATGTGATGATTCA 57.057 32.000 0.00 0.00 36.39 2.57
2321 2467 1.942657 CCGAGTTTATGCATGGAGGTG 59.057 52.381 10.16 0.00 0.00 4.00
2531 2677 1.745087 GCTGGTATGGTTGATGTGGTG 59.255 52.381 0.00 0.00 0.00 4.17
2555 2701 1.282157 GTGAACCCTCCTTATGTGCCT 59.718 52.381 0.00 0.00 0.00 4.75
2561 2707 1.141053 CCTCCTTATGTGCCTACACCC 59.859 57.143 0.00 0.00 46.86 4.61
2774 2920 0.871057 GTGTTCTGCTGAAGAGGTGC 59.129 55.000 6.24 0.00 35.91 5.01
2846 2992 0.801251 GCGCAAATGCTTCTCAGTCT 59.199 50.000 0.30 0.00 39.32 3.24
3009 3155 6.801539 AATTCATATGGCGGTAATGTGTAG 57.198 37.500 2.13 0.00 0.00 2.74
3035 3181 4.686554 GTGTCTGAATGAGGTGTTACTGTC 59.313 45.833 0.00 0.00 0.00 3.51
3050 3196 0.600557 CTGTCGAGTTCAGACCTGCT 59.399 55.000 0.00 0.00 37.80 4.24
3051 3197 1.813178 CTGTCGAGTTCAGACCTGCTA 59.187 52.381 0.00 0.00 37.80 3.49
3093 3240 3.003480 GACTGACATGGTGAACTTAGCC 58.997 50.000 0.00 0.00 0.00 3.93
3239 3396 2.945668 GCCTTCCTGAATGTGACATACC 59.054 50.000 0.00 0.00 0.00 2.73
3320 3477 4.201960 GCAAAATTAGCTACTTCCTCCAGC 60.202 45.833 0.00 0.00 35.49 4.85
3329 3486 4.323104 GCTACTTCCTCCAGCCCATATTAG 60.323 50.000 0.00 0.00 0.00 1.73
3349 3506 3.131396 AGTTGACGCTCCTTTAGTTGTG 58.869 45.455 0.00 0.00 0.00 3.33
3363 3520 1.352352 AGTTGTGGATTGGAGGGAGTG 59.648 52.381 0.00 0.00 0.00 3.51
3389 3546 9.463443 GCAAAAATTTGATGTCTGTTTAGTACT 57.537 29.630 9.96 0.00 40.55 2.73
3392 3549 7.923414 AATTTGATGTCTGTTTAGTACTCCC 57.077 36.000 0.00 0.00 0.00 4.30
3393 3550 6.681729 TTTGATGTCTGTTTAGTACTCCCT 57.318 37.500 0.00 0.00 0.00 4.20
3394 3551 5.916661 TGATGTCTGTTTAGTACTCCCTC 57.083 43.478 0.00 0.00 0.00 4.30
3395 3552 5.580998 TGATGTCTGTTTAGTACTCCCTCT 58.419 41.667 0.00 0.00 0.00 3.69
3396 3553 5.419155 TGATGTCTGTTTAGTACTCCCTCTG 59.581 44.000 0.00 0.00 0.00 3.35
3397 3554 4.737578 TGTCTGTTTAGTACTCCCTCTGT 58.262 43.478 0.00 0.00 0.00 3.41
3398 3555 4.765856 TGTCTGTTTAGTACTCCCTCTGTC 59.234 45.833 0.00 0.00 0.00 3.51
3399 3556 4.158209 GTCTGTTTAGTACTCCCTCTGTCC 59.842 50.000 0.00 0.00 0.00 4.02
3400 3557 3.438183 TGTTTAGTACTCCCTCTGTCCC 58.562 50.000 0.00 0.00 0.00 4.46
3401 3558 3.181415 TGTTTAGTACTCCCTCTGTCCCA 60.181 47.826 0.00 0.00 0.00 4.37
3402 3559 4.031611 GTTTAGTACTCCCTCTGTCCCAT 58.968 47.826 0.00 0.00 0.00 4.00
3403 3560 5.206587 GTTTAGTACTCCCTCTGTCCCATA 58.793 45.833 0.00 0.00 0.00 2.74
3404 3561 5.476950 TTAGTACTCCCTCTGTCCCATAA 57.523 43.478 0.00 0.00 0.00 1.90
3405 3562 4.561254 AGTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
3406 3563 5.681494 AGTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
3407 3564 6.234404 AGTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
3408 3565 7.358255 AGTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
3409 3566 7.776745 AGTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
3410 3567 7.896496 AGTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
3411 3568 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
3412 3569 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
3413 3570 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
3414 3571 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
3415 3572 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
3416 3573 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
3417 3574 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
3418 3575 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
3419 3576 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
3444 3601 2.546789 ACTAGTGTAGTGCCAAAAACGC 59.453 45.455 0.00 0.00 37.69 4.84
3445 3602 1.675552 AGTGTAGTGCCAAAAACGCT 58.324 45.000 0.00 0.00 0.00 5.07
3446 3603 1.602377 AGTGTAGTGCCAAAAACGCTC 59.398 47.619 0.00 0.00 0.00 5.03
3447 3604 0.948678 TGTAGTGCCAAAAACGCTCC 59.051 50.000 0.00 0.00 0.00 4.70
3448 3605 1.235724 GTAGTGCCAAAAACGCTCCT 58.764 50.000 0.00 0.00 0.00 3.69
3449 3606 2.224329 TGTAGTGCCAAAAACGCTCCTA 60.224 45.455 0.00 0.00 0.00 2.94
3450 3607 2.200373 AGTGCCAAAAACGCTCCTAT 57.800 45.000 0.00 0.00 0.00 2.57
3451 3608 3.343941 AGTGCCAAAAACGCTCCTATA 57.656 42.857 0.00 0.00 0.00 1.31
3452 3609 3.886123 AGTGCCAAAAACGCTCCTATAT 58.114 40.909 0.00 0.00 0.00 0.86
3453 3610 4.270008 AGTGCCAAAAACGCTCCTATATT 58.730 39.130 0.00 0.00 0.00 1.28
3454 3611 5.433526 AGTGCCAAAAACGCTCCTATATTA 58.566 37.500 0.00 0.00 0.00 0.98
3455 3612 6.062095 AGTGCCAAAAACGCTCCTATATTAT 58.938 36.000 0.00 0.00 0.00 1.28
3456 3613 7.221450 AGTGCCAAAAACGCTCCTATATTATA 58.779 34.615 0.00 0.00 0.00 0.98
3457 3614 7.883311 AGTGCCAAAAACGCTCCTATATTATAT 59.117 33.333 0.00 0.00 0.00 0.86
3458 3615 8.512138 GTGCCAAAAACGCTCCTATATTATATT 58.488 33.333 0.00 0.00 0.00 1.28
3459 3616 9.727859 TGCCAAAAACGCTCCTATATTATATTA 57.272 29.630 0.00 0.00 0.00 0.98
3466 3623 7.883217 ACGCTCCTATATTATATTATGGGACG 58.117 38.462 22.38 22.38 38.34 4.79
3467 3624 7.039923 ACGCTCCTATATTATATTATGGGACGG 60.040 40.741 24.61 17.70 37.65 4.79
3468 3625 7.176165 CGCTCCTATATTATATTATGGGACGGA 59.824 40.741 19.73 9.76 35.12 4.69
3469 3626 8.524487 GCTCCTATATTATATTATGGGACGGAG 58.476 40.741 13.04 11.53 35.12 4.63
3470 3627 8.951614 TCCTATATTATATTATGGGACGGAGG 57.048 38.462 13.04 4.31 35.12 4.30
3471 3628 7.954056 TCCTATATTATATTATGGGACGGAGGG 59.046 40.741 13.04 0.00 35.12 4.30
3476 3633 2.077687 TTATGGGACGGAGGGAGTAC 57.922 55.000 0.00 0.00 0.00 2.73
3480 3637 0.109342 GGGACGGAGGGAGTACGATA 59.891 60.000 0.00 0.00 0.00 2.92
3532 3691 1.815003 CATCTGGGTTTGTTCTCTGGC 59.185 52.381 0.00 0.00 0.00 4.85
3538 3697 1.525077 TTTGTTCTCTGGCCGCGTT 60.525 52.632 4.92 0.00 0.00 4.84
3566 3725 8.870160 TTGTTTTGATAGATTTGTTTGAGGTG 57.130 30.769 0.00 0.00 0.00 4.00
3614 3773 2.447887 GGATGCACTGTCGCGTCTG 61.448 63.158 5.77 7.42 45.46 3.51
3708 3873 9.383519 GAGTGAGTACCAATTTTTGATCAGATA 57.616 33.333 0.00 0.00 0.00 1.98
3730 3898 9.429359 AGATAATATTTGCTAAACCTGATCGAG 57.571 33.333 0.00 0.00 0.00 4.04
3752 3920 2.031333 CACAGAAACTTCAGCAAGGAGC 60.031 50.000 0.00 0.00 46.19 4.70
3848 4017 3.413327 TCTTGCATAGCGGGTACAAAAA 58.587 40.909 0.00 0.00 0.00 1.94
3901 4070 2.022718 AGCAGACTTGGAACCTCTCT 57.977 50.000 0.00 0.00 0.00 3.10
3902 4071 2.334023 AGCAGACTTGGAACCTCTCTT 58.666 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
581 620 1.676967 CCCAACTCCCAAGCTGAGC 60.677 63.158 0.00 0.00 32.98 4.26
623 663 0.620700 TTAGCCTGTTCCCCTCCCTC 60.621 60.000 0.00 0.00 0.00 4.30
624 664 0.621862 CTTAGCCTGTTCCCCTCCCT 60.622 60.000 0.00 0.00 0.00 4.20
625 665 1.915983 CTTAGCCTGTTCCCCTCCC 59.084 63.158 0.00 0.00 0.00 4.30
626 666 1.224870 GCTTAGCCTGTTCCCCTCC 59.775 63.158 0.00 0.00 0.00 4.30
756 847 2.499827 GGGGTAGCTAGTGCGGGAG 61.500 68.421 0.00 0.00 45.42 4.30
757 848 2.443390 GGGGTAGCTAGTGCGGGA 60.443 66.667 0.00 0.00 45.42 5.14
759 850 2.499827 GGAGGGGTAGCTAGTGCGG 61.500 68.421 0.00 0.00 45.42 5.69
760 851 2.499827 GGGAGGGGTAGCTAGTGCG 61.500 68.421 0.00 0.00 45.42 5.34
761 852 2.141448 GGGGAGGGGTAGCTAGTGC 61.141 68.421 0.00 0.00 40.05 4.40
762 853 1.459730 GGGGGAGGGGTAGCTAGTG 60.460 68.421 0.00 0.00 0.00 2.74
763 854 3.034991 GGGGGAGGGGTAGCTAGT 58.965 66.667 0.00 0.00 0.00 2.57
764 855 2.203655 CGGGGGAGGGGTAGCTAG 60.204 72.222 0.00 0.00 0.00 3.42
765 856 4.551960 GCGGGGGAGGGGTAGCTA 62.552 72.222 0.00 0.00 0.00 3.32
777 868 4.301027 GATCTAGTGGCGGCGGGG 62.301 72.222 9.78 0.00 0.00 5.73
791 882 1.116536 GGAGAGGAAGGGGACGGATC 61.117 65.000 0.00 0.00 0.00 3.36
871 962 2.198406 GGAAACCTCCAAAACGCAAAC 58.802 47.619 0.00 0.00 41.96 2.93
965 1057 2.202492 CGCGACAGACGAGGAAGG 60.202 66.667 0.00 0.00 45.77 3.46
988 1080 1.497278 CCGACATGGAGCAACAACG 59.503 57.895 0.00 0.00 42.00 4.10
1112 1204 1.000993 GGGAGGGTGAGAGCTGAGA 59.999 63.158 0.00 0.00 0.00 3.27
1114 1206 2.363018 CGGGAGGGTGAGAGCTGA 60.363 66.667 0.00 0.00 0.00 4.26
1115 1207 4.154347 GCGGGAGGGTGAGAGCTG 62.154 72.222 0.00 0.00 0.00 4.24
1118 1210 2.685380 AAGGCGGGAGGGTGAGAG 60.685 66.667 0.00 0.00 0.00 3.20
1137 1229 6.294010 GGCCGATGATCCTAAGGAAAATAAAC 60.294 42.308 0.00 0.00 34.34 2.01
1152 1244 1.214062 CCGCTAGAGGCCGATGATC 59.786 63.158 0.00 0.00 37.74 2.92
1171 1280 0.969149 TAGTATCCATCGGCTGCCTG 59.031 55.000 17.92 9.08 0.00 4.85
1229 1347 2.185867 GTAATGCTCACGCGGGGA 59.814 61.111 9.32 5.39 39.65 4.81
1265 1383 3.624326 TCTGAAACCGCATTCAAGTTG 57.376 42.857 0.00 0.00 38.75 3.16
1297 1415 2.492881 TCCCGCACACGATAGACTTAAA 59.507 45.455 0.00 0.00 43.93 1.52
1314 1433 5.609423 AGAAGAATCTGAAGATGATTCCCG 58.391 41.667 11.39 0.00 46.43 5.14
1366 1487 3.505464 AGAACATCACGGTAGTACAGC 57.495 47.619 2.06 0.00 0.00 4.40
1376 1497 3.120889 CCATAGCGCAATAGAACATCACG 60.121 47.826 11.47 0.00 0.00 4.35
1379 1500 5.641209 AGATTCCATAGCGCAATAGAACATC 59.359 40.000 11.47 3.22 0.00 3.06
1380 1501 5.555017 AGATTCCATAGCGCAATAGAACAT 58.445 37.500 11.47 0.00 0.00 2.71
1391 1512 4.572389 ACAGCAAACTAAGATTCCATAGCG 59.428 41.667 0.00 0.00 0.00 4.26
1395 1516 6.313519 TCCTACAGCAAACTAAGATTCCAT 57.686 37.500 0.00 0.00 0.00 3.41
1535 1658 5.335127 GCTATGACAACAAGGCAAACTATG 58.665 41.667 0.00 0.00 39.98 2.23
1553 1676 1.612463 GACTGGGTACGGTAGGCTATG 59.388 57.143 0.00 0.00 36.00 2.23
1555 1678 0.106519 GGACTGGGTACGGTAGGCTA 60.107 60.000 0.00 0.00 36.00 3.93
1556 1679 1.380920 GGACTGGGTACGGTAGGCT 60.381 63.158 0.00 0.00 36.00 4.58
1557 1680 1.673808 CTGGACTGGGTACGGTAGGC 61.674 65.000 0.00 0.00 36.00 3.93
1558 1681 0.324091 ACTGGACTGGGTACGGTAGG 60.324 60.000 0.00 0.00 33.68 3.18
1559 1682 1.203994 CAACTGGACTGGGTACGGTAG 59.796 57.143 0.00 0.00 34.46 3.18
1562 1685 1.189524 TCCAACTGGACTGGGTACGG 61.190 60.000 0.00 0.00 39.78 4.02
1564 1687 1.697982 AGTTCCAACTGGACTGGGTAC 59.302 52.381 0.00 0.00 45.39 3.34
1597 1721 9.440761 AAGGGTAGAGATAAGATAAGTGTGATT 57.559 33.333 0.00 0.00 0.00 2.57
1616 1740 2.317973 GGTGAGCTAGGGTAAGGGTAG 58.682 57.143 0.00 0.00 0.00 3.18
1633 1757 1.511613 ATGGGGTCAGTATCAGGGTG 58.488 55.000 0.00 0.00 0.00 4.61
1866 2004 4.976116 GCTCATCCAAAGTTAACAACACAC 59.024 41.667 8.61 0.00 0.00 3.82
1935 2076 2.949177 TGCCTTAAACTGAAGAGCCA 57.051 45.000 0.00 0.00 0.00 4.75
1986 2129 3.795623 TTGTAGACGGATGCCTTACTC 57.204 47.619 0.00 0.00 0.00 2.59
2246 2392 0.390209 GCGCATCAACAAGGGCAAAT 60.390 50.000 0.30 0.00 42.51 2.32
2321 2467 1.340991 ACATAACCACTGCCACATCCC 60.341 52.381 0.00 0.00 0.00 3.85
2555 2701 2.953466 CGATTTCTTCCTCGGGTGTA 57.047 50.000 0.00 0.00 0.00 2.90
2561 2707 2.890808 TCATCCCGATTTCTTCCTCG 57.109 50.000 0.00 0.00 34.73 4.63
2763 2909 0.315251 TCGTCAGTGCACCTCTTCAG 59.685 55.000 14.63 0.00 0.00 3.02
2774 2920 0.605589 AAAGGCTCTCCTCGTCAGTG 59.394 55.000 0.00 0.00 43.40 3.66
2846 2992 2.782222 GGCGCGTGGAGATCTACCA 61.782 63.158 8.43 6.16 34.84 3.25
3009 3155 5.406780 CAGTAACACCTCATTCAGACACTTC 59.593 44.000 0.00 0.00 0.00 3.01
3035 3181 2.028130 AGGATAGCAGGTCTGAACTCG 58.972 52.381 1.65 0.00 0.00 4.18
3050 3196 3.427573 TGGTTCGTGTTCTCAGAGGATA 58.572 45.455 0.00 0.00 0.00 2.59
3051 3197 2.232452 CTGGTTCGTGTTCTCAGAGGAT 59.768 50.000 0.00 0.00 0.00 3.24
3093 3240 1.955778 TGGTTTGATTGCTCACTGGTG 59.044 47.619 0.00 0.00 0.00 4.17
3239 3396 3.502211 AGACGAAGGCACAATTTAACAGG 59.498 43.478 0.00 0.00 0.00 4.00
3320 3477 3.753294 AGGAGCGTCAACTAATATGGG 57.247 47.619 0.00 0.00 0.00 4.00
3329 3486 2.223377 CCACAACTAAAGGAGCGTCAAC 59.777 50.000 0.00 0.00 0.00 3.18
3349 3506 1.923356 TTTTGCACTCCCTCCAATCC 58.077 50.000 0.00 0.00 0.00 3.01
3363 3520 9.463443 AGTACTAAACAGACATCAAATTTTTGC 57.537 29.630 0.00 0.00 38.05 3.68
3423 3580 2.546789 GCGTTTTTGGCACTACACTAGT 59.453 45.455 0.00 0.00 40.28 2.57
3424 3581 2.806244 AGCGTTTTTGGCACTACACTAG 59.194 45.455 0.00 0.00 0.00 2.57
3425 3582 2.803956 GAGCGTTTTTGGCACTACACTA 59.196 45.455 0.00 0.00 0.00 2.74
3426 3583 1.602377 GAGCGTTTTTGGCACTACACT 59.398 47.619 0.00 0.00 0.00 3.55
3427 3584 1.334689 GGAGCGTTTTTGGCACTACAC 60.335 52.381 0.00 0.00 0.00 2.90
3428 3585 0.948678 GGAGCGTTTTTGGCACTACA 59.051 50.000 0.00 0.00 0.00 2.74
3429 3586 1.235724 AGGAGCGTTTTTGGCACTAC 58.764 50.000 0.00 0.00 0.00 2.73
3430 3587 2.843401 TAGGAGCGTTTTTGGCACTA 57.157 45.000 0.00 0.00 0.00 2.74
3431 3588 2.200373 ATAGGAGCGTTTTTGGCACT 57.800 45.000 0.00 0.00 0.00 4.40
3432 3589 4.632538 AATATAGGAGCGTTTTTGGCAC 57.367 40.909 0.00 0.00 0.00 5.01
3433 3590 8.630054 AATATAATATAGGAGCGTTTTTGGCA 57.370 30.769 0.00 0.00 0.00 4.92
3440 3597 8.358148 CGTCCCATAATATAATATAGGAGCGTT 58.642 37.037 0.00 0.00 0.00 4.84
3441 3598 7.039923 CCGTCCCATAATATAATATAGGAGCGT 60.040 40.741 11.92 0.00 0.00 5.07
3442 3599 7.176165 TCCGTCCCATAATATAATATAGGAGCG 59.824 40.741 0.00 3.87 0.00 5.03
3443 3600 8.418597 TCCGTCCCATAATATAATATAGGAGC 57.581 38.462 0.00 0.00 0.00 4.70
3444 3601 9.026121 CCTCCGTCCCATAATATAATATAGGAG 57.974 40.741 0.00 0.00 38.84 3.69
3445 3602 7.954056 CCCTCCGTCCCATAATATAATATAGGA 59.046 40.741 0.00 0.00 0.00 2.94
3446 3603 7.954056 TCCCTCCGTCCCATAATATAATATAGG 59.046 40.741 0.00 0.00 0.00 2.57
3447 3604 8.951614 TCCCTCCGTCCCATAATATAATATAG 57.048 38.462 0.00 0.00 0.00 1.31
3448 3605 8.517047 ACTCCCTCCGTCCCATAATATAATATA 58.483 37.037 0.00 0.00 0.00 0.86
3449 3606 7.371043 ACTCCCTCCGTCCCATAATATAATAT 58.629 38.462 0.00 0.00 0.00 1.28
3450 3607 6.748969 ACTCCCTCCGTCCCATAATATAATA 58.251 40.000 0.00 0.00 0.00 0.98
3451 3608 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
3452 3609 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3453 3610 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3454 3611 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3455 3612 3.771216 GTACTCCCTCCGTCCCATAATA 58.229 50.000 0.00 0.00 0.00 0.98
3456 3613 2.606378 GTACTCCCTCCGTCCCATAAT 58.394 52.381 0.00 0.00 0.00 1.28
3457 3614 1.751733 CGTACTCCCTCCGTCCCATAA 60.752 57.143 0.00 0.00 0.00 1.90
3458 3615 0.179009 CGTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
3459 3616 1.455217 CGTACTCCCTCCGTCCCAT 60.455 63.158 0.00 0.00 0.00 4.00
3460 3617 1.929860 ATCGTACTCCCTCCGTCCCA 61.930 60.000 0.00 0.00 0.00 4.37
3461 3618 0.109342 TATCGTACTCCCTCCGTCCC 59.891 60.000 0.00 0.00 0.00 4.46
3462 3619 1.202746 ACTATCGTACTCCCTCCGTCC 60.203 57.143 0.00 0.00 0.00 4.79
3463 3620 2.252976 ACTATCGTACTCCCTCCGTC 57.747 55.000 0.00 0.00 0.00 4.79
3464 3621 3.672808 CATACTATCGTACTCCCTCCGT 58.327 50.000 0.00 0.00 0.00 4.69
3465 3622 2.419324 GCATACTATCGTACTCCCTCCG 59.581 54.545 0.00 0.00 0.00 4.63
3466 3623 3.688235 AGCATACTATCGTACTCCCTCC 58.312 50.000 0.00 0.00 0.00 4.30
3467 3624 4.616373 GCAAGCATACTATCGTACTCCCTC 60.616 50.000 0.00 0.00 0.00 4.30
3468 3625 3.256136 GCAAGCATACTATCGTACTCCCT 59.744 47.826 0.00 0.00 0.00 4.20
3469 3626 3.256136 AGCAAGCATACTATCGTACTCCC 59.744 47.826 0.00 0.00 0.00 4.30
3470 3627 4.477780 GAGCAAGCATACTATCGTACTCC 58.522 47.826 0.00 0.00 0.00 3.85
3471 3628 4.216687 AGGAGCAAGCATACTATCGTACTC 59.783 45.833 0.00 0.00 0.00 2.59
3476 3633 7.081349 GCTATATAGGAGCAAGCATACTATCG 58.919 42.308 11.72 0.00 39.84 2.92
3480 3637 5.026121 TGGCTATATAGGAGCAAGCATACT 58.974 41.667 11.72 0.00 41.98 2.12
3500 3659 0.822532 CCCAGATGCATCTTCCTGGC 60.823 60.000 26.70 0.00 43.56 4.85
3532 3691 3.879427 TCTATCAAAACAAACAACGCGG 58.121 40.909 12.47 0.00 0.00 6.46
3538 3697 9.311916 CCTCAAACAAATCTATCAAAACAAACA 57.688 29.630 0.00 0.00 0.00 2.83
3566 3725 6.212888 AGCTCATAAAATTCACCACCAATC 57.787 37.500 0.00 0.00 0.00 2.67
3614 3773 1.442769 TCTGTTCGAAGCTGCATTCC 58.557 50.000 0.00 0.00 0.00 3.01
3708 3873 5.822519 TGCTCGATCAGGTTTAGCAAATATT 59.177 36.000 0.00 0.00 40.05 1.28
3730 3898 1.949525 TCCTTGCTGAAGTTTCTGTGC 59.050 47.619 1.59 0.00 0.00 4.57
3752 3920 8.745837 GTCATTTTGTTGTAACTCAGTCATTTG 58.254 33.333 0.00 0.00 0.00 2.32
3819 3988 5.852282 ACCCGCTATGCAAGAAAATAAAT 57.148 34.783 0.00 0.00 0.00 1.40
3848 4017 7.395489 ACTTGATCTCCAGCATAATTTGTTCTT 59.605 33.333 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.