Multiple sequence alignment - TraesCS2B01G166400

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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 TraesCS2B01G166400 chr2B 100.000 4397 0 0 1 4397 139339708 139344104 0.000000e+00 8120.0
1 TraesCS2B01G166400 chr2A 91.976 2779 147 25 1648 4397 86962575 86965306 0.000000e+00 3827.0
2 TraesCS2B01G166400 chr2A 95.702 1745 48 6 842 2584 86898711 86900430 0.000000e+00 2782.0
3 TraesCS2B01G166400 chr2A 96.169 1540 49 4 2569 4101 86900382 86901918 0.000000e+00 2508.0
4 TraesCS2B01G166400 chr2A 94.118 170 4 4 4096 4263 86904537 86904702 2.030000e-63 254.0
5 TraesCS2B01G166400 chr2A 92.208 154 10 2 4245 4397 86904951 86905103 2.660000e-52 217.0
6 TraesCS2B01G166400 chr2A 89.286 56 3 3 1 56 498830606 498830658 2.840000e-07 67.6
7 TraesCS2B01G166400 chr2D 91.196 2601 149 44 36 2578 86490647 86493225 0.000000e+00 3461.0
8 TraesCS2B01G166400 chr2D 92.390 1866 94 14 2570 4397 86493184 86495039 0.000000e+00 2615.0
9 TraesCS2B01G166400 chr2D 87.097 62 3 5 1 59 337263007 337263066 1.020000e-06 65.8
10 TraesCS2B01G166400 chr5D 77.340 609 93 28 3645 4226 432029189 432029779 7.100000e-83 318.0
11 TraesCS2B01G166400 chr5A 79.928 279 44 9 3613 3886 547073318 547073589 1.250000e-45 195.0
12 TraesCS2B01G166400 chr5A 89.474 57 2 3 1 56 650019408 650019461 7.890000e-08 69.4
13 TraesCS2B01G166400 chr7D 84.211 95 11 4 38 129 30184767 30184860 6.060000e-14 89.8
14 TraesCS2B01G166400 chr7D 92.453 53 2 2 1 52 253604678 253604627 1.700000e-09 75.0
15 TraesCS2B01G166400 chr7D 92.157 51 2 2 1 51 48002360 48002312 2.190000e-08 71.3
16 TraesCS2B01G166400 chr6B 88.000 75 7 2 73 147 213235249 213235321 2.180000e-13 87.9
17 TraesCS2B01G166400 chr4D 90.909 55 1 3 1 55 22918699 22918749 2.190000e-08 71.3
18 TraesCS2B01G166400 chr4A 90.741 54 3 1 1 52 461577348 461577295 2.190000e-08 71.3
19 TraesCS2B01G166400 chr4A 90.741 54 2 3 1 54 609454700 609454750 7.890000e-08 69.4
20 TraesCS2B01G166400 chr1A 90.566 53 4 1 1 53 252674369 252674318 7.890000e-08 69.4
21 TraesCS2B01G166400 chr4B 96.970 33 1 0 188 220 62974375 62974343 6.140000e-04 56.5


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 TraesCS2B01G166400 chr2B 139339708 139344104 4396 False 8120.00 8120 100.00000 1 4397 1 chr2B.!!$F1 4396
1 TraesCS2B01G166400 chr2A 86962575 86965306 2731 False 3827.00 3827 91.97600 1648 4397 1 chr2A.!!$F1 2749
2 TraesCS2B01G166400 chr2A 86898711 86905103 6392 False 1440.25 2782 94.54925 842 4397 4 chr2A.!!$F3 3555
3 TraesCS2B01G166400 chr2D 86490647 86495039 4392 False 3038.00 3461 91.79300 36 4397 2 chr2D.!!$F2 4361
4 TraesCS2B01G166400 chr5D 432029189 432029779 590 False 318.00 318 77.34000 3645 4226 1 chr5D.!!$F1 581

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
372 403 0.306840 CGTCTAGGATTCGTAGCGCA 59.693 55.0 11.47 0.0 0.00 6.09 F
899 959 0.685097 TGGGGTAGAGTTGCTGTGAC 59.315 55.0 0.00 0.0 0.00 3.67 F
1442 1503 0.031716 TCCTCCCTCCACCTCATCAG 60.032 60.0 0.00 0.0 0.00 2.90 F
1470 1531 0.248296 GTCTCATCGTCCTCGCAGAC 60.248 60.0 0.00 0.0 36.96 3.51 F
1742 1803 0.321653 GCGGGCCTCTTCTTTCTTGA 60.322 55.0 0.84 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 1484 0.031716 CTGATGAGGTGGAGGGAGGA 60.032 60.000 0.0 0.0 0.00 3.71 R
2034 2095 1.575244 CCATGACAGCCTCATACACG 58.425 55.000 0.0 0.0 37.53 4.49 R
2901 2974 1.644786 CGGTTTCTGGCGATTCCACC 61.645 60.000 0.0 0.0 40.72 4.61 R
3034 3107 5.450818 AGCCATCCCTTGTACTTGATTAA 57.549 39.130 0.0 0.0 0.00 1.40 R
3681 3776 3.636764 GGTTTCCTTTCTTTTCTGCTGGA 59.363 43.478 0.0 0.0 0.00 3.86 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
36 37 6.814506 CCTCTAGGGCATATTTTCTTCATG 57.185 41.667 0.00 0.00 0.00 3.07
37 38 5.182760 CCTCTAGGGCATATTTTCTTCATGC 59.817 44.000 0.00 0.00 43.43 4.06
38 39 5.945310 TCTAGGGCATATTTTCTTCATGCT 58.055 37.500 5.83 0.00 43.62 3.79
69 70 3.572584 GCACAAAGCAATTTCTCTCTGG 58.427 45.455 0.00 0.00 44.79 3.86
94 97 7.116519 GGCGTTTTTATGGCAATTTTAGTTACA 59.883 33.333 0.00 0.00 0.00 2.41
95 98 8.652463 GCGTTTTTATGGCAATTTTAGTTACAT 58.348 29.630 0.00 0.00 0.00 2.29
103 106 6.096705 TGGCAATTTTAGTTACATGAGGATGG 59.903 38.462 0.00 0.00 33.39 3.51
117 120 6.746900 ACATGAGGATGGCAACTTTAGTTGTA 60.747 38.462 20.31 12.30 43.33 2.41
129 132 8.273643 CAACTTTAGTTGTAAAGCATGTCAAG 57.726 34.615 13.22 0.00 46.40 3.02
134 137 6.449635 AGTTGTAAAGCATGTCAAGTTTCA 57.550 33.333 0.00 0.00 0.00 2.69
139 142 7.319646 TGTAAAGCATGTCAAGTTTCAGTTTT 58.680 30.769 0.00 0.00 0.00 2.43
140 143 6.892310 AAAGCATGTCAAGTTTCAGTTTTC 57.108 33.333 0.00 0.00 0.00 2.29
142 145 6.212888 AGCATGTCAAGTTTCAGTTTTCTT 57.787 33.333 0.00 0.00 0.00 2.52
144 147 5.807011 GCATGTCAAGTTTCAGTTTTCTTGT 59.193 36.000 0.00 0.00 38.53 3.16
145 148 6.311200 GCATGTCAAGTTTCAGTTTTCTTGTT 59.689 34.615 0.00 0.00 38.53 2.83
146 149 7.148590 GCATGTCAAGTTTCAGTTTTCTTGTTT 60.149 33.333 0.00 0.00 38.53 2.83
147 150 8.711457 CATGTCAAGTTTCAGTTTTCTTGTTTT 58.289 29.630 0.00 0.00 38.53 2.43
148 151 8.293114 TGTCAAGTTTCAGTTTTCTTGTTTTC 57.707 30.769 0.00 0.00 38.53 2.29
196 227 1.333619 GGCGATGTTATTTCGTGCCAT 59.666 47.619 0.00 0.00 40.66 4.40
198 229 3.541711 GCGATGTTATTTCGTGCCATAC 58.458 45.455 0.00 0.00 38.81 2.39
222 253 5.163513 GTGTGGCACTTATCATTTTGGAAG 58.836 41.667 19.83 0.00 0.00 3.46
248 279 1.361204 TCACCCTTCTCCTGATGCAA 58.639 50.000 0.00 0.00 0.00 4.08
301 332 6.127810 TCAATATATAGGCGATCGTGGTAC 57.872 41.667 17.81 0.00 0.00 3.34
303 334 1.882912 TATAGGCGATCGTGGTACGT 58.117 50.000 17.81 3.61 43.14 3.57
306 337 1.009222 GGCGATCGTGGTACGTAGG 60.009 63.158 17.81 0.00 43.14 3.18
341 372 1.557443 CGCCTGAGTCGACAACAACC 61.557 60.000 19.50 9.55 0.00 3.77
357 388 4.129737 CCCACGATCCACGCGTCT 62.130 66.667 9.86 0.00 46.94 4.18
358 389 2.767445 CCCACGATCCACGCGTCTA 61.767 63.158 9.86 0.00 46.94 2.59
370 401 0.721811 CGCGTCTAGGATTCGTAGCG 60.722 60.000 17.75 17.75 40.37 4.26
372 403 0.306840 CGTCTAGGATTCGTAGCGCA 59.693 55.000 11.47 0.00 0.00 6.09
404 435 8.697846 AATGACTCGTAATTAATTCAACTCGA 57.302 30.769 3.39 7.76 0.00 4.04
431 462 4.754818 GAAACACGACGCGCGCTC 62.755 66.667 32.58 23.99 46.04 5.03
457 488 3.827898 CAGGCGACGGAGGAGGAC 61.828 72.222 0.00 0.00 0.00 3.85
485 516 2.626840 GAACCACTCTTCTCATGCTCC 58.373 52.381 0.00 0.00 0.00 4.70
486 517 1.649321 ACCACTCTTCTCATGCTCCA 58.351 50.000 0.00 0.00 0.00 3.86
487 518 1.980765 ACCACTCTTCTCATGCTCCAA 59.019 47.619 0.00 0.00 0.00 3.53
488 519 2.289945 ACCACTCTTCTCATGCTCCAAC 60.290 50.000 0.00 0.00 0.00 3.77
489 520 2.289882 CCACTCTTCTCATGCTCCAACA 60.290 50.000 0.00 0.00 0.00 3.33
493 524 3.141398 TCTTCTCATGCTCCAACAACAC 58.859 45.455 0.00 0.00 0.00 3.32
511 542 3.617284 ACACGTGGAAGAGAACCTTTTT 58.383 40.909 21.57 0.00 34.68 1.94
513 544 4.573607 ACACGTGGAAGAGAACCTTTTTAC 59.426 41.667 21.57 0.00 34.68 2.01
514 545 3.805971 ACGTGGAAGAGAACCTTTTTACG 59.194 43.478 0.00 0.00 39.42 3.18
515 546 4.053295 CGTGGAAGAGAACCTTTTTACGA 58.947 43.478 0.00 0.00 37.64 3.43
531 562 4.742438 TTACGAAGGTGCAAATCTTCAC 57.258 40.909 19.17 0.00 39.30 3.18
537 568 1.068541 GGTGCAAATCTTCACCCGTTC 60.069 52.381 0.00 0.00 45.26 3.95
540 571 1.128692 GCAAATCTTCACCCGTTCTCG 59.871 52.381 0.00 0.00 0.00 4.04
546 577 1.472878 CTTCACCCGTTCTCGAGATGA 59.527 52.381 17.44 13.62 39.71 2.92
557 588 6.633634 CCGTTCTCGAGATGATACTAAACTTC 59.366 42.308 17.44 0.00 39.71 3.01
558 589 7.411274 CGTTCTCGAGATGATACTAAACTTCT 58.589 38.462 17.44 0.00 39.71 2.85
573 604 8.954950 ACTAAACTTCTCATCACCTATTCATG 57.045 34.615 0.00 0.00 0.00 3.07
574 605 8.543774 ACTAAACTTCTCATCACCTATTCATGT 58.456 33.333 0.00 0.00 0.00 3.21
587 618 5.070981 ACCTATTCATGTCACCCACATAGAG 59.929 44.000 0.00 0.00 44.60 2.43
627 658 5.530712 TGAAATTGTTTTACGGGCCTAAAC 58.469 37.500 0.84 14.90 33.50 2.01
641 672 5.016831 GGGCCTAAACCCCATCTATATTTG 58.983 45.833 0.84 0.00 45.00 2.32
645 676 6.072673 GCCTAAACCCCATCTATATTTGAACG 60.073 42.308 0.00 0.00 0.00 3.95
669 700 1.586564 GAGGCGACGTCGATCTTGG 60.587 63.158 39.74 11.11 43.02 3.61
673 704 1.516386 CGACGTCGATCTTGGTGGG 60.516 63.158 33.35 0.00 43.02 4.61
676 707 2.100631 CGTCGATCTTGGTGGGTGC 61.101 63.158 0.00 0.00 0.00 5.01
682 713 1.072331 GATCTTGGTGGGTGCGGATAT 59.928 52.381 0.00 0.00 0.00 1.63
686 717 1.071471 GGTGGGTGCGGATATGGAG 59.929 63.158 0.00 0.00 0.00 3.86
687 718 1.598130 GTGGGTGCGGATATGGAGC 60.598 63.158 0.00 0.00 0.00 4.70
720 751 2.124278 GGCACCCCGAAATCTCCC 60.124 66.667 0.00 0.00 0.00 4.30
721 752 2.680370 GGCACCCCGAAATCTCCCT 61.680 63.158 0.00 0.00 0.00 4.20
725 756 1.212935 CACCCCGAAATCTCCCTCAAT 59.787 52.381 0.00 0.00 0.00 2.57
733 764 5.863935 CCGAAATCTCCCTCAATTTTGTTTC 59.136 40.000 0.00 0.00 0.00 2.78
735 766 7.147976 CGAAATCTCCCTCAATTTTGTTTCTT 58.852 34.615 0.00 0.00 0.00 2.52
758 789 2.665649 TGACATACGAAGTGCGGATT 57.334 45.000 0.00 0.00 41.99 3.01
759 790 2.267426 TGACATACGAAGTGCGGATTG 58.733 47.619 0.00 0.00 41.99 2.67
780 811 5.423704 TGGTCCATGAAAATTTGATGCAT 57.576 34.783 0.00 0.00 0.00 3.96
785 816 4.201871 CCATGAAAATTTGATGCATGGTGC 60.202 41.667 22.11 0.00 46.75 5.01
788 819 2.684001 AATTTGATGCATGGTGCTGG 57.316 45.000 2.46 0.00 45.31 4.85
797 828 2.300433 GCATGGTGCTGGATGACATAA 58.700 47.619 0.00 0.00 40.96 1.90
798 829 2.033801 GCATGGTGCTGGATGACATAAC 59.966 50.000 0.00 0.00 40.96 1.89
799 830 2.418368 TGGTGCTGGATGACATAACC 57.582 50.000 0.00 0.00 35.85 2.85
800 831 1.632920 TGGTGCTGGATGACATAACCA 59.367 47.619 0.00 0.00 40.31 3.67
808 839 5.928976 CTGGATGACATAACCAGGTTATCA 58.071 41.667 20.53 17.64 44.96 2.15
822 879 5.331902 CAGGTTATCAAATGTTTAGCACCG 58.668 41.667 0.00 0.00 0.00 4.94
825 882 6.655848 AGGTTATCAAATGTTTAGCACCGTTA 59.344 34.615 0.00 0.00 0.00 3.18
864 922 6.612306 GTTGGAGATGACCTAAAATGACAAC 58.388 40.000 0.00 0.00 0.00 3.32
896 956 3.306472 TTTTTGGGGTAGAGTTGCTGT 57.694 42.857 0.00 0.00 0.00 4.40
897 957 2.270352 TTTGGGGTAGAGTTGCTGTG 57.730 50.000 0.00 0.00 0.00 3.66
898 958 1.429930 TTGGGGTAGAGTTGCTGTGA 58.570 50.000 0.00 0.00 0.00 3.58
899 959 0.685097 TGGGGTAGAGTTGCTGTGAC 59.315 55.000 0.00 0.00 0.00 3.67
1023 1084 2.597510 GCCCCTCACCGTGCTTTT 60.598 61.111 0.00 0.00 0.00 2.27
1423 1484 2.042435 CCCTTCTCCTCCGGCTCT 60.042 66.667 0.00 0.00 0.00 4.09
1442 1503 0.031716 TCCTCCCTCCACCTCATCAG 60.032 60.000 0.00 0.00 0.00 2.90
1443 1504 0.326048 CCTCCCTCCACCTCATCAGT 60.326 60.000 0.00 0.00 0.00 3.41
1470 1531 0.248296 GTCTCATCGTCCTCGCAGAC 60.248 60.000 0.00 0.00 36.96 3.51
1563 1624 4.072088 GTTTCGCTGGCGGTCGTG 62.072 66.667 14.94 0.00 40.25 4.35
1593 1654 1.080501 CTCCGTGCTTCTTCTCGCA 60.081 57.895 0.00 0.00 0.00 5.10
1624 1685 4.824515 CCGGCCTCCTCTCCTCGT 62.825 72.222 0.00 0.00 0.00 4.18
1742 1803 0.321653 GCGGGCCTCTTCTTTCTTGA 60.322 55.000 0.84 0.00 0.00 3.02
1761 1822 3.044305 GGCACTGACACCAGCGAC 61.044 66.667 0.00 0.00 44.16 5.19
1863 1924 1.203523 GACAGCAGTAGCAGTAGCAGT 59.796 52.381 0.00 0.00 40.89 4.40
2034 2095 1.816863 TTGGGAGCACTGACGAGTCC 61.817 60.000 0.34 0.00 0.00 3.85
2292 2353 1.382914 ACTATGGAAGGGGCAGGTTT 58.617 50.000 0.00 0.00 0.00 3.27
2517 2578 1.991813 TCCCACTCCCATTCACATTCA 59.008 47.619 0.00 0.00 0.00 2.57
2518 2579 2.094675 CCCACTCCCATTCACATTCAC 58.905 52.381 0.00 0.00 0.00 3.18
2519 2580 2.555006 CCCACTCCCATTCACATTCACA 60.555 50.000 0.00 0.00 0.00 3.58
2520 2581 3.359033 CCACTCCCATTCACATTCACAT 58.641 45.455 0.00 0.00 0.00 3.21
2521 2582 3.765511 CCACTCCCATTCACATTCACATT 59.234 43.478 0.00 0.00 0.00 2.71
2522 2583 4.142315 CCACTCCCATTCACATTCACATTC 60.142 45.833 0.00 0.00 0.00 2.67
2523 2584 4.703575 CACTCCCATTCACATTCACATTCT 59.296 41.667 0.00 0.00 0.00 2.40
2531 2592 7.148137 CCATTCACATTCACATTCTCATTCTCA 60.148 37.037 0.00 0.00 0.00 3.27
2539 2600 9.623000 ATTCACATTCTCATTCTCATTCACATA 57.377 29.630 0.00 0.00 0.00 2.29
2546 2607 9.623000 TTCTCATTCTCATTCACATAATCATGT 57.377 29.630 0.00 0.00 46.58 3.21
2560 2621 8.074370 CACATAATCATGTTCATGAAGATCACC 58.926 37.037 14.80 0.00 42.98 4.02
2561 2622 7.776500 ACATAATCATGTTCATGAAGATCACCA 59.224 33.333 14.80 5.92 42.98 4.17
2562 2623 8.793592 CATAATCATGTTCATGAAGATCACCAT 58.206 33.333 14.80 7.96 33.83 3.55
2563 2624 6.879276 ATCATGTTCATGAAGATCACCATC 57.121 37.500 14.80 0.00 33.83 3.51
2564 2625 5.747342 TCATGTTCATGAAGATCACCATCA 58.253 37.500 14.80 3.80 0.00 3.07
2565 2626 5.587443 TCATGTTCATGAAGATCACCATCAC 59.413 40.000 14.80 0.00 0.00 3.06
2579 2652 4.141344 TCACCATCACCATCATGATCATGT 60.141 41.667 30.01 17.46 37.20 3.21
2901 2974 6.979817 CAGAATCTCAGTCTTGTAATGGAGAG 59.020 42.308 0.00 0.00 35.15 3.20
3012 3085 1.238439 CTGACACAATGGGAAGCGTT 58.762 50.000 0.00 0.00 0.00 4.84
3030 3103 2.872245 CGTTGGTGTTGTGATCTCAACT 59.128 45.455 30.30 0.00 45.26 3.16
3034 3107 5.745312 TGGTGTTGTGATCTCAACTCTAT 57.255 39.130 30.30 0.00 45.26 1.98
3681 3776 9.598517 TTAATGAAGAAAACAAAGAGCACAATT 57.401 25.926 0.00 0.00 0.00 2.32
3713 3808 9.593565 AGAAAAGAAAGGAAACCAGAGAATAAT 57.406 29.630 0.00 0.00 0.00 1.28
3758 3855 4.749245 ATAACCAGTTCAAACTTGAGCG 57.251 40.909 1.38 0.00 42.34 5.03
3782 3880 5.173664 AGCAAATTAATGGAGAAAGCAAGC 58.826 37.500 0.00 0.00 0.00 4.01
3848 3950 2.270923 CACTGAGTAATGCAAGCGCTA 58.729 47.619 12.05 0.00 39.64 4.26
3867 3969 2.879907 CATTGTTGGGGCAGAGCG 59.120 61.111 0.00 0.00 0.00 5.03
3888 3990 2.761208 GACTGGAGCCTTAGTTCAGCTA 59.239 50.000 0.00 0.00 36.87 3.32
4244 6999 8.340618 AGCAACAAGTGAGTAATTAATGTCAT 57.659 30.769 0.00 0.00 0.00 3.06
4245 7000 8.239314 AGCAACAAGTGAGTAATTAATGTCATG 58.761 33.333 0.00 0.00 0.00 3.07
4246 7001 8.023128 GCAACAAGTGAGTAATTAATGTCATGT 58.977 33.333 0.00 0.00 0.00 3.21
4281 7304 3.627123 GCATGTGCATGTATGTAGGACAA 59.373 43.478 12.96 0.00 40.80 3.18
4285 7308 5.660460 TGTGCATGTATGTAGGACAACTAG 58.340 41.667 0.00 0.00 30.77 2.57
4310 7338 9.349713 AGAGGAGTGTAGAAAGATGTAATAGAG 57.650 37.037 0.00 0.00 0.00 2.43
4344 7373 9.265901 ACTTAATTCCTCTGTTGATGAATATCG 57.734 33.333 0.00 0.00 36.83 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.182760 GCATGAAGAAAATATGCCCTAGAGG 59.817 44.000 0.00 0.00 40.89 3.69
14 15 6.002704 AGCATGAAGAAAATATGCCCTAGAG 58.997 40.000 0.00 0.00 46.26 2.43
15 16 5.945310 AGCATGAAGAAAATATGCCCTAGA 58.055 37.500 0.00 0.00 46.26 2.43
16 17 6.712095 TGTAGCATGAAGAAAATATGCCCTAG 59.288 38.462 0.00 0.00 46.26 3.02
17 18 6.486657 GTGTAGCATGAAGAAAATATGCCCTA 59.513 38.462 0.00 0.00 46.26 3.53
18 19 5.300286 GTGTAGCATGAAGAAAATATGCCCT 59.700 40.000 0.00 0.00 46.26 5.19
19 20 5.523369 GTGTAGCATGAAGAAAATATGCCC 58.477 41.667 0.00 0.00 46.26 5.36
20 21 5.207768 CGTGTAGCATGAAGAAAATATGCC 58.792 41.667 0.00 0.00 46.26 4.40
21 22 5.678483 CACGTGTAGCATGAAGAAAATATGC 59.322 40.000 7.58 0.00 45.64 3.14
22 23 6.684131 CACACGTGTAGCATGAAGAAAATATG 59.316 38.462 22.90 0.00 0.00 1.78
23 24 6.183360 CCACACGTGTAGCATGAAGAAAATAT 60.183 38.462 22.90 0.00 0.00 1.28
24 25 5.121611 CCACACGTGTAGCATGAAGAAAATA 59.878 40.000 22.90 0.00 0.00 1.40
25 26 4.083324 CCACACGTGTAGCATGAAGAAAAT 60.083 41.667 22.90 0.00 0.00 1.82
26 27 3.249799 CCACACGTGTAGCATGAAGAAAA 59.750 43.478 22.90 0.00 0.00 2.29
27 28 2.805671 CCACACGTGTAGCATGAAGAAA 59.194 45.455 22.90 0.00 0.00 2.52
28 29 2.412870 CCACACGTGTAGCATGAAGAA 58.587 47.619 22.90 0.00 0.00 2.52
29 30 1.939381 GCCACACGTGTAGCATGAAGA 60.939 52.381 30.03 0.00 32.91 2.87
30 31 0.443869 GCCACACGTGTAGCATGAAG 59.556 55.000 30.03 12.20 32.91 3.02
31 32 0.250081 TGCCACACGTGTAGCATGAA 60.250 50.000 32.98 14.47 37.73 2.57
32 33 0.948623 GTGCCACACGTGTAGCATGA 60.949 55.000 37.17 17.78 43.83 3.07
33 34 1.227342 TGTGCCACACGTGTAGCATG 61.227 55.000 37.17 18.83 43.83 4.06
34 35 0.533978 TTGTGCCACACGTGTAGCAT 60.534 50.000 37.17 7.46 43.83 3.79
35 36 0.744771 TTTGTGCCACACGTGTAGCA 60.745 50.000 32.98 32.98 40.17 3.49
36 37 0.041312 CTTTGTGCCACACGTGTAGC 60.041 55.000 28.70 28.70 37.14 3.58
37 38 0.041312 GCTTTGTGCCACACGTGTAG 60.041 55.000 22.90 16.17 37.14 2.74
38 39 0.744771 TGCTTTGTGCCACACGTGTA 60.745 50.000 22.90 2.55 42.00 2.90
52 53 2.508526 ACGCCAGAGAGAAATTGCTTT 58.491 42.857 0.00 0.00 0.00 3.51
53 54 2.191128 ACGCCAGAGAGAAATTGCTT 57.809 45.000 0.00 0.00 0.00 3.91
61 62 2.290008 TGCCATAAAAACGCCAGAGAGA 60.290 45.455 0.00 0.00 0.00 3.10
62 63 2.083774 TGCCATAAAAACGCCAGAGAG 58.916 47.619 0.00 0.00 0.00 3.20
65 66 3.951775 AATTGCCATAAAAACGCCAGA 57.048 38.095 0.00 0.00 0.00 3.86
69 70 8.008902 TGTAACTAAAATTGCCATAAAAACGC 57.991 30.769 0.00 0.00 0.00 4.84
117 120 6.633856 AGAAAACTGAAACTTGACATGCTTT 58.366 32.000 0.00 0.00 0.00 3.51
129 132 9.567848 TGTCATAGAAAACAAGAAAACTGAAAC 57.432 29.630 0.00 0.00 0.00 2.78
162 191 5.705609 AACATCGCCTTGACTTTTACAAT 57.294 34.783 0.00 0.00 0.00 2.71
171 200 3.670203 CACGAAATAACATCGCCTTGAC 58.330 45.455 0.00 0.00 43.88 3.18
175 206 1.014352 GGCACGAAATAACATCGCCT 58.986 50.000 0.00 0.00 43.88 5.52
196 227 4.155099 CCAAAATGATAAGTGCCACACGTA 59.845 41.667 0.00 0.00 39.64 3.57
198 229 3.190327 TCCAAAATGATAAGTGCCACACG 59.810 43.478 0.00 0.00 39.64 4.49
203 234 6.705863 AGATCTTCCAAAATGATAAGTGCC 57.294 37.500 0.00 0.00 0.00 5.01
204 235 9.890352 GATTAGATCTTCCAAAATGATAAGTGC 57.110 33.333 0.00 0.00 0.00 4.40
222 253 5.792741 CATCAGGAGAAGGGTGATTAGATC 58.207 45.833 0.00 0.00 0.00 2.75
278 309 5.220719 CGTACCACGATCGCCTATATATTGA 60.221 44.000 16.60 0.00 46.05 2.57
322 353 1.557443 GGTTGTTGTCGACTCAGGCG 61.557 60.000 17.92 0.00 0.00 5.52
326 357 0.528901 CGTGGGTTGTTGTCGACTCA 60.529 55.000 17.92 12.95 36.21 3.41
357 388 0.949397 ACGATGCGCTACGAATCCTA 59.051 50.000 26.61 0.00 38.58 2.94
358 389 0.102481 AACGATGCGCTACGAATCCT 59.898 50.000 26.61 7.25 38.58 3.24
370 401 9.646336 AATTAATTACGAGTCATTAAACGATGC 57.354 29.630 0.00 0.00 30.51 3.91
397 428 3.489416 TGTTTCGTGATTGAGTCGAGTTG 59.511 43.478 0.00 0.00 35.13 3.16
399 430 3.050619 GTGTTTCGTGATTGAGTCGAGT 58.949 45.455 0.00 0.00 35.13 4.18
400 431 2.089121 CGTGTTTCGTGATTGAGTCGAG 59.911 50.000 0.00 0.00 35.13 4.04
404 435 1.784856 CGTCGTGTTTCGTGATTGAGT 59.215 47.619 0.00 0.00 40.80 3.41
464 495 2.626840 GAGCATGAGAAGAGTGGTTCC 58.373 52.381 0.00 0.00 0.00 3.62
485 516 2.031683 GGTTCTCTTCCACGTGTTGTTG 59.968 50.000 15.65 0.00 0.00 3.33
486 517 2.093128 AGGTTCTCTTCCACGTGTTGTT 60.093 45.455 15.65 0.00 0.00 2.83
487 518 1.485066 AGGTTCTCTTCCACGTGTTGT 59.515 47.619 15.65 0.00 0.00 3.32
488 519 2.240493 AGGTTCTCTTCCACGTGTTG 57.760 50.000 15.65 4.10 0.00 3.33
489 520 3.277142 AAAGGTTCTCTTCCACGTGTT 57.723 42.857 15.65 0.00 33.94 3.32
493 524 4.053295 TCGTAAAAAGGTTCTCTTCCACG 58.947 43.478 0.00 0.00 36.26 4.94
520 551 1.128692 CGAGAACGGGTGAAGATTTGC 59.871 52.381 0.00 0.00 35.72 3.68
521 552 2.668457 CTCGAGAACGGGTGAAGATTTG 59.332 50.000 6.58 0.00 40.21 2.32
531 562 5.008811 AGTTTAGTATCATCTCGAGAACGGG 59.991 44.000 20.91 9.63 41.91 5.28
537 568 8.563732 TGATGAGAAGTTTAGTATCATCTCGAG 58.436 37.037 5.93 5.93 44.19 4.04
540 571 8.637986 AGGTGATGAGAAGTTTAGTATCATCTC 58.362 37.037 12.99 9.88 44.19 2.75
557 588 4.141642 TGGGTGACATGAATAGGTGATGAG 60.142 45.833 0.00 0.00 0.00 2.90
558 589 3.779738 TGGGTGACATGAATAGGTGATGA 59.220 43.478 0.00 0.00 0.00 2.92
569 600 4.908601 AAACTCTATGTGGGTGACATGA 57.091 40.909 0.00 0.00 45.43 3.07
570 601 6.406370 TCTAAAACTCTATGTGGGTGACATG 58.594 40.000 0.00 0.00 45.43 3.21
572 603 5.778241 TCTCTAAAACTCTATGTGGGTGACA 59.222 40.000 0.00 0.00 39.53 3.58
573 604 6.282199 TCTCTAAAACTCTATGTGGGTGAC 57.718 41.667 0.00 0.00 0.00 3.67
574 605 7.496346 AATCTCTAAAACTCTATGTGGGTGA 57.504 36.000 0.00 0.00 0.00 4.02
602 633 3.492337 AGGCCCGTAAAACAATTTCAGA 58.508 40.909 0.00 0.00 0.00 3.27
603 634 3.934457 AGGCCCGTAAAACAATTTCAG 57.066 42.857 0.00 0.00 0.00 3.02
604 635 5.509332 GGTTTAGGCCCGTAAAACAATTTCA 60.509 40.000 17.38 0.00 35.33 2.69
605 636 4.925054 GGTTTAGGCCCGTAAAACAATTTC 59.075 41.667 17.38 2.39 35.33 2.17
609 640 2.237643 GGGTTTAGGCCCGTAAAACAA 58.762 47.619 13.02 0.00 39.17 2.83
627 658 4.714632 ACACCGTTCAAATATAGATGGGG 58.285 43.478 0.00 0.00 0.00 4.96
631 662 6.456501 GCCTCTACACCGTTCAAATATAGAT 58.543 40.000 0.00 0.00 0.00 1.98
641 672 1.513586 CGTCGCCTCTACACCGTTC 60.514 63.158 0.00 0.00 0.00 3.95
645 676 1.712977 ATCGACGTCGCCTCTACACC 61.713 60.000 32.19 0.00 39.60 4.16
669 700 1.598130 GCTCCATATCCGCACCCAC 60.598 63.158 0.00 0.00 0.00 4.61
673 704 0.320247 CTGGAGCTCCATATCCGCAC 60.320 60.000 35.11 4.03 46.46 5.34
676 707 0.894141 CCTCTGGAGCTCCATATCCG 59.106 60.000 35.11 22.72 46.46 4.18
710 741 6.681777 AGAAACAAAATTGAGGGAGATTTCG 58.318 36.000 0.00 0.00 0.00 3.46
711 742 7.928167 ACAAGAAACAAAATTGAGGGAGATTTC 59.072 33.333 0.00 0.00 0.00 2.17
712 743 7.795047 ACAAGAAACAAAATTGAGGGAGATTT 58.205 30.769 0.00 0.00 0.00 2.17
715 746 6.790232 AACAAGAAACAAAATTGAGGGAGA 57.210 33.333 0.00 0.00 0.00 3.71
721 752 8.802856 CGTATGTCAAACAAGAAACAAAATTGA 58.197 29.630 0.00 0.00 0.00 2.57
725 756 8.024285 ACTTCGTATGTCAAACAAGAAACAAAA 58.976 29.630 0.00 0.00 0.00 2.44
733 764 3.469629 CGCACTTCGTATGTCAAACAAG 58.530 45.455 0.00 0.00 0.00 3.16
735 766 1.795872 CCGCACTTCGTATGTCAAACA 59.204 47.619 0.00 0.00 36.19 2.83
758 789 4.886496 TGCATCAAATTTTCATGGACCA 57.114 36.364 0.00 0.00 0.00 4.02
759 790 5.728351 CATGCATCAAATTTTCATGGACC 57.272 39.130 0.00 0.00 33.01 4.46
780 811 1.632920 TGGTTATGTCATCCAGCACCA 59.367 47.619 0.00 0.00 36.96 4.17
785 816 5.928976 TGATAACCTGGTTATGTCATCCAG 58.071 41.667 31.21 11.91 45.67 3.86
788 819 8.225603 ACATTTGATAACCTGGTTATGTCATC 57.774 34.615 31.21 20.57 38.62 2.92
797 828 5.185056 GGTGCTAAACATTTGATAACCTGGT 59.815 40.000 0.00 0.00 0.00 4.00
798 829 5.650543 GGTGCTAAACATTTGATAACCTGG 58.349 41.667 0.00 0.00 0.00 4.45
799 830 5.106317 ACGGTGCTAAACATTTGATAACCTG 60.106 40.000 0.00 0.00 0.00 4.00
800 831 5.007682 ACGGTGCTAAACATTTGATAACCT 58.992 37.500 0.00 0.00 0.00 3.50
802 833 8.905103 AATAACGGTGCTAAACATTTGATAAC 57.095 30.769 0.00 0.00 0.00 1.89
803 834 9.915629 AAAATAACGGTGCTAAACATTTGATAA 57.084 25.926 0.00 0.00 0.00 1.75
806 837 9.915629 ATTAAAATAACGGTGCTAAACATTTGA 57.084 25.926 0.00 0.00 0.00 2.69
807 838 9.950858 CATTAAAATAACGGTGCTAAACATTTG 57.049 29.630 0.00 0.00 0.00 2.32
808 839 9.699703 ACATTAAAATAACGGTGCTAAACATTT 57.300 25.926 0.00 0.00 0.00 2.32
822 879 7.699566 TCTCCAACGCCATACATTAAAATAAC 58.300 34.615 0.00 0.00 0.00 1.89
825 882 6.545666 TCATCTCCAACGCCATACATTAAAAT 59.454 34.615 0.00 0.00 0.00 1.82
881 939 0.036294 GGTCACAGCAACTCTACCCC 60.036 60.000 0.00 0.00 0.00 4.95
884 944 2.035961 TCACAGGTCACAGCAACTCTAC 59.964 50.000 0.00 0.00 0.00 2.59
885 945 2.297315 CTCACAGGTCACAGCAACTCTA 59.703 50.000 0.00 0.00 0.00 2.43
886 946 1.069823 CTCACAGGTCACAGCAACTCT 59.930 52.381 0.00 0.00 0.00 3.24
887 947 1.506493 CTCACAGGTCACAGCAACTC 58.494 55.000 0.00 0.00 0.00 3.01
888 948 0.107456 CCTCACAGGTCACAGCAACT 59.893 55.000 0.00 0.00 0.00 3.16
889 949 1.510480 GCCTCACAGGTCACAGCAAC 61.510 60.000 0.00 0.00 37.80 4.17
891 951 2.427320 GCCTCACAGGTCACAGCA 59.573 61.111 0.00 0.00 37.80 4.41
892 952 2.359230 GGCCTCACAGGTCACAGC 60.359 66.667 0.00 0.00 40.51 4.40
893 953 3.150949 TGGCCTCACAGGTCACAG 58.849 61.111 3.32 0.00 43.71 3.66
897 957 0.615331 TTCAGATGGCCTCACAGGTC 59.385 55.000 3.32 0.00 41.40 3.85
898 958 1.004044 CTTTCAGATGGCCTCACAGGT 59.996 52.381 3.32 0.00 37.80 4.00
899 959 1.681166 CCTTTCAGATGGCCTCACAGG 60.681 57.143 3.32 0.00 38.80 4.00
1423 1484 0.031716 CTGATGAGGTGGAGGGAGGA 60.032 60.000 0.00 0.00 0.00 3.71
1442 1503 2.280823 GACGATGAGACCGGGGTCAC 62.281 65.000 19.38 13.73 46.76 3.67
1443 1504 2.036731 ACGATGAGACCGGGGTCA 59.963 61.111 19.38 8.65 46.76 4.02
1559 1620 2.915659 AGTGGGAAGGCGACACGA 60.916 61.111 0.00 0.00 39.95 4.35
1562 1623 3.691342 CGGAGTGGGAAGGCGACA 61.691 66.667 0.00 0.00 0.00 4.35
1563 1624 3.692406 ACGGAGTGGGAAGGCGAC 61.692 66.667 0.00 0.00 42.51 5.19
1593 1654 2.757077 CCGGAAGCAAAGGGGAGT 59.243 61.111 0.00 0.00 0.00 3.85
1624 1685 1.202188 CGCAGATACAGAGTGCTCGAA 60.202 52.381 0.00 0.00 34.92 3.71
1742 1803 2.359107 CGCTGGTGTCAGTGCCAT 60.359 61.111 0.00 0.00 43.42 4.40
1863 1924 5.465532 TTGCAAAATTCATGCTTGGTCTA 57.534 34.783 14.90 0.00 44.14 2.59
2034 2095 1.575244 CCATGACAGCCTCATACACG 58.425 55.000 0.00 0.00 37.53 4.49
2058 2119 1.968493 TCACTAAGGATATGCCGGACC 59.032 52.381 5.05 0.00 43.43 4.46
2292 2353 3.046283 ACATACCCAGATAGCACCTCA 57.954 47.619 0.00 0.00 0.00 3.86
2517 2578 9.623000 TGATTATGTGAATGAGAATGAGAATGT 57.377 29.630 0.00 0.00 0.00 2.71
2520 2581 9.623000 ACATGATTATGTGAATGAGAATGAGAA 57.377 29.630 1.71 0.00 45.54 2.87
2521 2582 9.623000 AACATGATTATGTGAATGAGAATGAGA 57.377 29.630 3.56 0.00 46.54 3.27
2522 2583 9.880064 GAACATGATTATGTGAATGAGAATGAG 57.120 33.333 3.56 0.00 46.54 2.90
2523 2584 9.398538 TGAACATGATTATGTGAATGAGAATGA 57.601 29.630 3.56 0.00 46.54 2.57
2539 2600 6.831868 TGATGGTGATCTTCATGAACATGATT 59.168 34.615 16.49 6.69 46.12 2.57
2546 2607 4.573021 TGGTGATGGTGATCTTCATGAA 57.427 40.909 8.12 8.12 33.08 2.57
2560 2621 6.575162 ATGAACATGATCATGATGGTGATG 57.425 37.500 36.37 13.42 41.20 3.07
2579 2652 4.573021 TGGTGATGGTGATCTTCATGAA 57.427 40.909 8.12 8.12 33.08 2.57
2671 2744 2.353357 TGGTGATTCTGATGATGGCC 57.647 50.000 0.00 0.00 0.00 5.36
2819 2892 3.797546 GTCCTTGCTCGCTGCTGC 61.798 66.667 5.34 5.34 43.37 5.25
2901 2974 1.644786 CGGTTTCTGGCGATTCCACC 61.645 60.000 0.00 0.00 40.72 4.61
3030 3103 7.072454 AGCCATCCCTTGTACTTGATTAATAGA 59.928 37.037 0.00 0.00 0.00 1.98
3034 3107 5.450818 AGCCATCCCTTGTACTTGATTAA 57.549 39.130 0.00 0.00 0.00 1.40
3681 3776 3.636764 GGTTTCCTTTCTTTTCTGCTGGA 59.363 43.478 0.00 0.00 0.00 3.86
3758 3855 5.290400 GCTTGCTTTCTCCATTAATTTGCTC 59.710 40.000 0.00 0.00 0.00 4.26
3782 3880 6.561614 TCACTTCTCGTTTATTGCTACCTAG 58.438 40.000 0.00 0.00 0.00 3.02
3848 3950 1.980772 GCTCTGCCCCAACAATGCT 60.981 57.895 0.00 0.00 0.00 3.79
3859 3961 4.828925 GGCTCCAGTCGCTCTGCC 62.829 72.222 0.00 0.00 42.38 4.85
3867 3969 1.552792 AGCTGAACTAAGGCTCCAGTC 59.447 52.381 2.54 0.00 0.00 3.51
3888 3990 8.021973 GTCGAAGATACACACGGATTATATCTT 58.978 37.037 4.84 4.84 42.50 2.40
4244 6999 5.689835 TGCACATGCCTCCTAATTAATACA 58.310 37.500 0.49 0.00 41.18 2.29
4245 7000 6.207417 ACATGCACATGCCTCCTAATTAATAC 59.793 38.462 10.50 0.00 42.39 1.89
4246 7001 6.306199 ACATGCACATGCCTCCTAATTAATA 58.694 36.000 10.50 0.00 42.39 0.98
4247 7002 5.142639 ACATGCACATGCCTCCTAATTAAT 58.857 37.500 10.50 0.00 42.39 1.40
4248 7003 4.535781 ACATGCACATGCCTCCTAATTAA 58.464 39.130 10.50 0.00 42.39 1.40
4285 7308 9.344772 TCTCTATTACATCTTTCTACACTCCTC 57.655 37.037 0.00 0.00 0.00 3.71
4310 7338 5.966742 ACAGAGGAATTAAGTGCCTTTTC 57.033 39.130 0.00 0.00 30.70 2.29
4315 7343 4.943705 TCATCAACAGAGGAATTAAGTGCC 59.056 41.667 0.00 0.00 0.00 5.01
4327 7356 6.653273 AACACACGATATTCATCAACAGAG 57.347 37.500 0.00 0.00 0.00 3.35
4330 7359 9.810545 TCTAATAACACACGATATTCATCAACA 57.189 29.630 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.