Multiple sequence alignment - TraesCS2A01G452900

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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 TraesCS2A01G452900 chr2A 100.000 2339 0 0 1 2339 702303210 702300872 0.000000e+00 4320
1 TraesCS2A01G452900 chr2A 90.521 633 46 11 1719 2339 670281208 670280578 0.000000e+00 824
2 TraesCS2A01G452900 chr2A 90.789 152 12 2 105 254 759649015 759649166 3.940000e-48 202
3 TraesCS2A01G452900 chr5D 84.531 1642 176 54 105 1718 434472337 434470746 0.000000e+00 1554
4 TraesCS2A01G452900 chr5D 90.491 631 45 12 1719 2339 512189877 512190502 0.000000e+00 819
5 TraesCS2A01G452900 chr5D 94.231 104 6 0 2 105 159652932 159652829 2.410000e-35 159
6 TraesCS2A01G452900 chr5A 83.973 1641 191 48 105 1718 520469850 520468255 0.000000e+00 1507
7 TraesCS2A01G452900 chr5A 92.767 636 29 10 1718 2339 494293066 494293698 0.000000e+00 904
8 TraesCS2A01G452900 chr5A 91.311 633 38 12 1719 2339 428620270 428619643 0.000000e+00 848
9 TraesCS2A01G452900 chr5A 90.694 634 44 12 1718 2339 428639488 428638858 0.000000e+00 830
10 TraesCS2A01G452900 chr5A 89.163 203 19 3 105 305 708852212 708852413 1.390000e-62 250
11 TraesCS2A01G452900 chr5A 87.363 182 23 0 105 286 677937094 677936913 2.360000e-50 209
12 TraesCS2A01G452900 chr5A 91.071 112 9 1 2 113 677937228 677937118 1.450000e-32 150
13 TraesCS2A01G452900 chr5A 90.179 112 10 1 2 113 524940221 524940331 6.740000e-31 145
14 TraesCS2A01G452900 chr1A 89.342 1079 99 9 648 1718 60029105 60030175 0.000000e+00 1341
15 TraesCS2A01G452900 chr1A 91.009 634 40 15 1719 2339 434696489 434697118 0.000000e+00 839
16 TraesCS2A01G452900 chr4D 89.259 1080 90 21 648 1718 443736522 443737584 0.000000e+00 1328
17 TraesCS2A01G452900 chr1B 92.637 910 64 2 812 1718 309928411 309929320 0.000000e+00 1306
18 TraesCS2A01G452900 chr1B 85.802 162 15 7 105 261 309927682 309927840 5.170000e-37 165
19 TraesCS2A01G452900 chr6D 88.284 1084 108 8 644 1718 148227514 148226441 0.000000e+00 1280
20 TraesCS2A01G452900 chr6B 89.234 1031 87 16 698 1718 553384325 553385341 0.000000e+00 1267
21 TraesCS2A01G452900 chr6B 85.410 329 39 8 105 429 264645912 264646235 1.340000e-87 333
22 TraesCS2A01G452900 chr6B 91.071 112 9 1 2 113 553383565 553383675 1.450000e-32 150
23 TraesCS2A01G452900 chr7A 89.084 1026 100 6 701 1718 498604662 498603641 0.000000e+00 1264
24 TraesCS2A01G452900 chr7A 92.114 634 36 12 1718 2339 288741347 288741978 0.000000e+00 881
25 TraesCS2A01G452900 chr2D 87.419 1081 98 27 649 1718 71956716 71955663 0.000000e+00 1208
26 TraesCS2A01G452900 chr6A 91.469 633 41 8 1719 2339 186913902 186914533 0.000000e+00 857
27 TraesCS2A01G452900 chr6A 91.456 632 37 12 1719 2339 537467000 537467625 0.000000e+00 852
28 TraesCS2A01G452900 chr3B 76.316 380 56 25 2 357 822804042 822804411 3.090000e-39 172
29 TraesCS2A01G452900 chr3B 90.179 112 10 1 2 113 215114225 215114115 6.740000e-31 145
30 TraesCS2A01G452900 chr1D 86.164 159 19 3 105 261 107594570 107594727 4.000000e-38 169
31 TraesCS2A01G452900 chr1D 90.265 113 10 1 1 113 107594435 107594546 1.870000e-31 147
32 TraesCS2A01G452900 chr1D 90.816 98 9 0 105 202 203230699 203230796 5.240000e-27 132
33 TraesCS2A01G452900 chr3A 90.179 112 10 1 2 113 534371536 534371646 6.740000e-31 145
34 TraesCS2A01G452900 chr3A 90.179 112 10 1 2 113 534377495 534377605 6.740000e-31 145
35 TraesCS2A01G452900 chr4B 80.690 145 27 1 105 248 120462850 120462994 6.830000e-21 111


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 TraesCS2A01G452900 chr2A 702300872 702303210 2338 True 4320.0 4320 100.0000 1 2339 1 chr2A.!!$R2 2338
1 TraesCS2A01G452900 chr2A 670280578 670281208 630 True 824.0 824 90.5210 1719 2339 1 chr2A.!!$R1 620
2 TraesCS2A01G452900 chr5D 434470746 434472337 1591 True 1554.0 1554 84.5310 105 1718 1 chr5D.!!$R2 1613
3 TraesCS2A01G452900 chr5D 512189877 512190502 625 False 819.0 819 90.4910 1719 2339 1 chr5D.!!$F1 620
4 TraesCS2A01G452900 chr5A 520468255 520469850 1595 True 1507.0 1507 83.9730 105 1718 1 chr5A.!!$R3 1613
5 TraesCS2A01G452900 chr5A 494293066 494293698 632 False 904.0 904 92.7670 1718 2339 1 chr5A.!!$F1 621
6 TraesCS2A01G452900 chr5A 428619643 428620270 627 True 848.0 848 91.3110 1719 2339 1 chr5A.!!$R1 620
7 TraesCS2A01G452900 chr5A 428638858 428639488 630 True 830.0 830 90.6940 1718 2339 1 chr5A.!!$R2 621
8 TraesCS2A01G452900 chr1A 60029105 60030175 1070 False 1341.0 1341 89.3420 648 1718 1 chr1A.!!$F1 1070
9 TraesCS2A01G452900 chr1A 434696489 434697118 629 False 839.0 839 91.0090 1719 2339 1 chr1A.!!$F2 620
10 TraesCS2A01G452900 chr4D 443736522 443737584 1062 False 1328.0 1328 89.2590 648 1718 1 chr4D.!!$F1 1070
11 TraesCS2A01G452900 chr1B 309927682 309929320 1638 False 735.5 1306 89.2195 105 1718 2 chr1B.!!$F1 1613
12 TraesCS2A01G452900 chr6D 148226441 148227514 1073 True 1280.0 1280 88.2840 644 1718 1 chr6D.!!$R1 1074
13 TraesCS2A01G452900 chr6B 553383565 553385341 1776 False 708.5 1267 90.1525 2 1718 2 chr6B.!!$F2 1716
14 TraesCS2A01G452900 chr7A 498603641 498604662 1021 True 1264.0 1264 89.0840 701 1718 1 chr7A.!!$R1 1017
15 TraesCS2A01G452900 chr7A 288741347 288741978 631 False 881.0 881 92.1140 1718 2339 1 chr7A.!!$F1 621
16 TraesCS2A01G452900 chr2D 71955663 71956716 1053 True 1208.0 1208 87.4190 649 1718 1 chr2D.!!$R1 1069
17 TraesCS2A01G452900 chr6A 186913902 186914533 631 False 857.0 857 91.4690 1719 2339 1 chr6A.!!$F1 620
18 TraesCS2A01G452900 chr6A 537467000 537467625 625 False 852.0 852 91.4560 1719 2339 1 chr6A.!!$F2 620

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
688 852 0.033109 AGGAAAATACAGGGCCAGGC 60.033 55.0 6.18 1.26 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 2041 0.313043 CGTGTACGACTCCACCAACT 59.687 55.0 0.0 0.0 43.02 3.16 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
30 31 0.958822 GTTGTGGAGGCAACGGATTT 59.041 50.000 0.00 0.00 46.39 2.17
43 44 1.825285 CGGATTTGGCTCGCGATCAG 61.825 60.000 10.36 0.00 0.00 2.90
47 48 2.166130 TTTGGCTCGCGATCAGACCA 62.166 55.000 10.36 10.05 0.00 4.02
69 70 3.077907 CCAGACGTGGGGGACAAT 58.922 61.111 0.00 0.00 40.67 2.71
254 288 0.962356 ATTGCTGGCGAGAACCAAGG 60.962 55.000 0.00 0.00 39.86 3.61
263 297 2.931320 GCGAGAACCAAGGTTAGAGGTG 60.931 54.545 4.14 0.00 38.60 4.00
265 299 3.614390 CGAGAACCAAGGTTAGAGGTGAC 60.614 52.174 4.14 0.00 38.60 3.67
297 332 3.818787 GTCGGAACTAGCGGCGGA 61.819 66.667 9.78 0.00 0.00 5.54
299 334 1.526686 TCGGAACTAGCGGCGGATA 60.527 57.895 9.78 0.00 0.00 2.59
305 340 3.391049 GAACTAGCGGCGGATATTTTCT 58.609 45.455 9.78 0.00 0.00 2.52
308 343 2.550830 AGCGGCGGATATTTTCTGAT 57.449 45.000 9.78 0.00 31.81 2.90
310 345 4.002906 AGCGGCGGATATTTTCTGATAA 57.997 40.909 9.78 0.00 31.81 1.75
312 347 4.213482 AGCGGCGGATATTTTCTGATAAAC 59.787 41.667 9.78 0.00 31.81 2.01
313 348 4.698276 CGGCGGATATTTTCTGATAAACG 58.302 43.478 0.00 0.00 31.81 3.60
322 359 5.351233 TTTTCTGATAAACGTGCAATCGT 57.649 34.783 0.00 0.00 46.19 3.73
340 385 2.545106 TCGTGAAAAGGAAAGTTACGGC 59.455 45.455 0.00 0.00 0.00 5.68
358 412 1.502190 CTGCTGCGTACGAGAGACA 59.498 57.895 21.65 13.69 0.00 3.41
393 504 1.588674 CGTACAGCAACAGGTTTCCA 58.411 50.000 0.00 0.00 0.00 3.53
401 512 2.436417 CAACAGGTTTCCACGGATGAT 58.564 47.619 0.00 0.00 0.00 2.45
404 515 2.224769 ACAGGTTTCCACGGATGATGTT 60.225 45.455 0.00 0.00 0.00 2.71
407 518 4.007659 AGGTTTCCACGGATGATGTTTAC 58.992 43.478 0.00 0.00 0.00 2.01
413 524 0.300491 CGGATGATGTTTACCGTGCG 59.700 55.000 0.00 0.00 40.42 5.34
414 525 1.365699 GGATGATGTTTACCGTGCGT 58.634 50.000 0.00 0.00 0.00 5.24
419 530 0.663688 ATGTTTACCGTGCGTGCAAA 59.336 45.000 0.00 0.00 0.00 3.68
430 541 3.242712 CGTGCGTGCAAAGAAAGAAAAAT 59.757 39.130 0.00 0.00 0.00 1.82
431 542 4.603825 CGTGCGTGCAAAGAAAGAAAAATC 60.604 41.667 0.00 0.00 0.00 2.17
432 543 4.267452 GTGCGTGCAAAGAAAGAAAAATCA 59.733 37.500 0.00 0.00 0.00 2.57
433 544 4.503734 TGCGTGCAAAGAAAGAAAAATCAG 59.496 37.500 0.00 0.00 0.00 2.90
434 545 4.739716 GCGTGCAAAGAAAGAAAAATCAGA 59.260 37.500 0.00 0.00 0.00 3.27
435 546 5.231991 GCGTGCAAAGAAAGAAAAATCAGAA 59.768 36.000 0.00 0.00 0.00 3.02
436 547 6.560983 GCGTGCAAAGAAAGAAAAATCAGAAG 60.561 38.462 0.00 0.00 0.00 2.85
437 548 6.473455 CGTGCAAAGAAAGAAAAATCAGAAGT 59.527 34.615 0.00 0.00 0.00 3.01
438 549 7.514125 CGTGCAAAGAAAGAAAAATCAGAAGTG 60.514 37.037 0.00 0.00 0.00 3.16
440 551 8.199449 TGCAAAGAAAGAAAAATCAGAAGTGAT 58.801 29.630 0.00 0.00 46.01 3.06
441 552 8.697960 GCAAAGAAAGAAAAATCAGAAGTGATC 58.302 33.333 0.00 0.00 43.04 2.92
442 553 9.962783 CAAAGAAAGAAAAATCAGAAGTGATCT 57.037 29.630 0.00 0.00 43.04 2.75
471 582 1.997311 TGCAGGAGTCCAGGGGATG 60.997 63.158 12.86 0.20 32.73 3.51
472 583 1.997874 GCAGGAGTCCAGGGGATGT 60.998 63.158 12.86 0.00 32.73 3.06
474 585 2.042301 GCAGGAGTCCAGGGGATGTAT 61.042 57.143 12.86 0.00 32.73 2.29
500 625 2.161211 GCATGAGCAGTTTCAGAGGAAC 59.839 50.000 0.00 0.00 41.58 3.62
505 630 1.261619 GCAGTTTCAGAGGAACGTGTG 59.738 52.381 0.00 0.00 31.35 3.82
513 638 1.005512 AGGAACGTGTGCATGCGTA 60.006 52.632 14.09 0.72 40.70 4.42
524 655 1.339535 TGCATGCGTATTTGGTCCAGA 60.340 47.619 14.09 0.00 0.00 3.86
538 669 0.322975 TCCAGAGGACAAGAGCTTGC 59.677 55.000 9.99 3.65 44.03 4.01
544 675 2.675348 GAGGACAAGAGCTTGCATACAC 59.325 50.000 9.99 0.00 44.03 2.90
545 676 1.740025 GGACAAGAGCTTGCATACACC 59.260 52.381 9.99 2.02 44.03 4.16
546 677 1.394917 GACAAGAGCTTGCATACACCG 59.605 52.381 9.99 0.00 44.03 4.94
547 678 1.001974 ACAAGAGCTTGCATACACCGA 59.998 47.619 9.99 0.00 44.03 4.69
548 679 1.662629 CAAGAGCTTGCATACACCGAG 59.337 52.381 0.00 0.00 33.45 4.63
549 680 0.460987 AGAGCTTGCATACACCGAGC 60.461 55.000 0.00 0.00 39.51 5.03
572 715 9.099454 GAGCGGTTATGATTAATATAAGGAAGG 57.901 37.037 0.00 0.00 0.00 3.46
574 717 8.044908 GCGGTTATGATTAATATAAGGAAGGGA 58.955 37.037 0.00 0.00 0.00 4.20
581 724 9.905713 TGATTAATATAAGGAAGGGATATGCAC 57.094 33.333 0.00 0.00 0.00 4.57
582 725 8.964476 ATTAATATAAGGAAGGGATATGCACG 57.036 34.615 0.00 0.00 0.00 5.34
583 726 6.374417 AATATAAGGAAGGGATATGCACGT 57.626 37.500 0.00 0.00 0.00 4.49
585 728 3.307379 GGAAGGGATATGCACGTCC 57.693 57.895 10.10 10.10 41.38 4.79
586 729 0.468226 GGAAGGGATATGCACGTCCA 59.532 55.000 18.11 0.00 46.51 4.02
587 730 1.072331 GGAAGGGATATGCACGTCCAT 59.928 52.381 18.11 10.38 46.51 3.41
590 733 1.490490 AGGGATATGCACGTCCATGTT 59.510 47.619 18.11 0.00 36.19 2.71
594 737 3.242739 GGATATGCACGTCCATGTTTGTC 60.243 47.826 1.14 0.00 34.57 3.18
596 739 2.535012 TGCACGTCCATGTTTGTCTA 57.465 45.000 0.00 0.00 0.00 2.59
598 741 2.741517 TGCACGTCCATGTTTGTCTATG 59.258 45.455 0.00 0.00 0.00 2.23
599 742 3.000041 GCACGTCCATGTTTGTCTATGA 59.000 45.455 0.00 0.00 0.00 2.15
601 744 4.083537 GCACGTCCATGTTTGTCTATGAAA 60.084 41.667 0.00 0.00 0.00 2.69
602 745 5.391950 GCACGTCCATGTTTGTCTATGAAAT 60.392 40.000 0.00 0.00 0.00 2.17
603 746 6.023435 CACGTCCATGTTTGTCTATGAAATG 58.977 40.000 0.00 0.00 0.00 2.32
604 747 5.123820 ACGTCCATGTTTGTCTATGAAATGG 59.876 40.000 0.00 0.00 35.47 3.16
605 748 5.343249 GTCCATGTTTGTCTATGAAATGGC 58.657 41.667 0.00 0.00 34.40 4.40
606 749 5.015515 TCCATGTTTGTCTATGAAATGGCA 58.984 37.500 0.00 0.00 34.40 4.92
627 784 3.762407 TCAGACTTGGTTTGATTCCGA 57.238 42.857 0.00 0.00 0.00 4.55
628 785 4.079980 TCAGACTTGGTTTGATTCCGAA 57.920 40.909 0.00 0.00 0.00 4.30
634 791 4.887655 ACTTGGTTTGATTCCGAAGAAACT 59.112 37.500 14.02 0.00 35.09 2.66
641 798 7.548075 GGTTTGATTCCGAAGAAACTATGACTA 59.452 37.037 14.02 0.00 35.09 2.59
662 826 4.665833 ATTATGGACTCGATTTCCGTGA 57.334 40.909 15.23 9.41 39.75 4.35
688 852 0.033109 AGGAAAATACAGGGCCAGGC 60.033 55.000 6.18 1.26 0.00 4.85
690 854 0.679960 GAAAATACAGGGCCAGGCGT 60.680 55.000 6.18 0.00 0.00 5.68
691 855 0.679960 AAAATACAGGGCCAGGCGTC 60.680 55.000 6.18 0.00 0.00 5.19
764 930 3.695830 TGTCTGCGAGTTAAGGGAAAT 57.304 42.857 0.00 0.00 0.00 2.17
783 949 2.338984 GTGGAGCGGACGAGTTGT 59.661 61.111 0.00 0.00 0.00 3.32
795 962 1.652563 GAGTTGTTGTGGGCGGAAC 59.347 57.895 0.00 0.00 0.00 3.62
804 971 2.181125 TGTGGGCGGAACTAATCTACA 58.819 47.619 0.00 0.00 0.00 2.74
835 1003 4.802999 CAAGAGGCTTCAAGTGATTTTCC 58.197 43.478 0.00 0.00 0.00 3.13
864 1034 1.300620 CAGGAACGGTGCGAGTCAA 60.301 57.895 0.00 0.00 0.00 3.18
865 1035 1.006102 AGGAACGGTGCGAGTCAAG 60.006 57.895 0.00 0.00 0.00 3.02
866 1038 2.027625 GGAACGGTGCGAGTCAAGG 61.028 63.158 0.00 0.00 0.00 3.61
875 1048 0.868406 GCGAGTCAAGGTTCTTGGTG 59.132 55.000 7.67 0.00 0.00 4.17
1032 1211 3.573967 GGTTCACCAAGTTTGATGTGGAT 59.426 43.478 0.00 0.00 36.23 3.41
1145 1324 3.365265 GCCGGCCAAGGTTGACAG 61.365 66.667 18.11 0.00 0.00 3.51
1159 1338 3.356639 GACAGCGATGCGTGGGAGA 62.357 63.158 0.00 0.00 0.00 3.71
1210 1389 2.170397 TGGCTTTATCTTGCGGATCAGA 59.830 45.455 0.00 0.00 35.98 3.27
1271 1450 2.079170 TGGGACAAGTTGGCAAATCA 57.921 45.000 11.70 0.14 31.92 2.57
1285 1464 6.088016 TGGCAAATCATTATATGTCCAAGC 57.912 37.500 0.00 0.00 0.00 4.01
1289 1468 6.239120 GCAAATCATTATATGTCCAAGCCAGT 60.239 38.462 0.00 0.00 0.00 4.00
1327 1506 6.916360 ATTTGAAGCAAAAGTTCTATGGGA 57.084 33.333 0.00 0.00 36.90 4.37
1388 1567 5.188163 TGAATGCCTTCAATCAATTGGTCAT 59.812 36.000 5.42 0.00 38.43 3.06
1400 1579 0.829990 TTGGTCATGGATCTAGCGCA 59.170 50.000 11.47 0.00 0.00 6.09
1434 1613 1.120530 TTGAGGACGAGGATAAGGCC 58.879 55.000 0.00 0.00 35.21 5.19
1441 1620 3.893813 GGACGAGGATAAGGCCTTACTTA 59.106 47.826 27.46 7.87 38.73 2.24
1471 1650 0.249398 GTTGCCACCGTCCTATGAGT 59.751 55.000 0.00 0.00 0.00 3.41
1522 1701 7.396540 AAGACAACCATCAATAATGAGGAAC 57.603 36.000 0.00 0.00 39.70 3.62
1613 1797 2.696187 GTTTGGGGTTGGCAGTTAAAGA 59.304 45.455 0.00 0.00 0.00 2.52
1697 1883 2.705658 TGCAAGGACTGGGGACATATAG 59.294 50.000 0.00 0.00 41.51 1.31
1973 2164 2.697751 CGTCTCCTCCTTCTTGATCCAT 59.302 50.000 0.00 0.00 0.00 3.41
2089 2283 1.089978 TGGAGGAGGAGGTGTAGGAA 58.910 55.000 0.00 0.00 0.00 3.36
2158 2360 6.146760 CCCACTATATATAGAGGCAAGGGAT 58.853 44.000 23.73 0.00 39.07 3.85
2199 2406 3.449126 ATCTAGGGGAGGGGCGGT 61.449 66.667 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.976474 GCCAAATCCGTTGCCTCCA 60.976 57.895 0.00 0.00 35.74 3.86
30 31 3.068064 TGGTCTGATCGCGAGCCA 61.068 61.111 23.12 17.04 0.00 4.75
43 44 2.430921 CACGTCTGGTCGCTGGTC 60.431 66.667 0.00 0.00 0.00 4.02
65 66 3.004839 CACACTCCGATCTATCCGATTGT 59.995 47.826 0.00 0.66 31.76 2.71
67 68 3.487372 TCACACTCCGATCTATCCGATT 58.513 45.455 0.00 0.00 30.84 3.34
68 69 3.078097 CTCACACTCCGATCTATCCGAT 58.922 50.000 0.00 0.00 34.25 4.18
69 70 2.104281 TCTCACACTCCGATCTATCCGA 59.896 50.000 0.00 0.00 0.00 4.55
254 288 2.164624 AGCTCATGTCGTCACCTCTAAC 59.835 50.000 0.00 0.00 0.00 2.34
263 297 0.985549 GACGAACAGCTCATGTCGTC 59.014 55.000 15.60 15.60 45.72 4.20
265 299 1.983907 CGACGAACAGCTCATGTCG 59.016 57.895 11.39 11.39 43.00 4.35
287 322 3.026630 TCAGAAAATATCCGCCGCTAG 57.973 47.619 0.00 0.00 0.00 3.42
296 331 7.850982 ACGATTGCACGTTTATCAGAAAATATC 59.149 33.333 0.00 0.00 44.14 1.63
297 332 7.639850 CACGATTGCACGTTTATCAGAAAATAT 59.360 33.333 0.00 0.00 44.76 1.28
299 334 5.794945 CACGATTGCACGTTTATCAGAAAAT 59.205 36.000 0.00 0.00 44.76 1.82
305 340 4.733972 TTTCACGATTGCACGTTTATCA 57.266 36.364 0.00 0.00 44.76 2.15
308 343 3.560481 TCCTTTTCACGATTGCACGTTTA 59.440 39.130 0.00 0.00 44.76 2.01
310 345 1.944024 TCCTTTTCACGATTGCACGTT 59.056 42.857 0.00 0.00 44.76 3.99
312 347 2.679355 TTCCTTTTCACGATTGCACG 57.321 45.000 0.00 0.00 39.31 5.34
313 348 3.964909 ACTTTCCTTTTCACGATTGCAC 58.035 40.909 0.00 0.00 0.00 4.57
322 359 2.292292 GCAGCCGTAACTTTCCTTTTCA 59.708 45.455 0.00 0.00 0.00 2.69
340 385 0.522286 CTGTCTCTCGTACGCAGCAG 60.522 60.000 11.24 14.69 0.00 4.24
377 487 1.101049 CCGTGGAAACCTGTTGCTGT 61.101 55.000 0.00 0.00 0.00 4.40
383 494 1.351017 ACATCATCCGTGGAAACCTGT 59.649 47.619 0.00 0.00 0.00 4.00
401 512 0.028242 CTTTGCACGCACGGTAAACA 59.972 50.000 0.00 0.00 0.00 2.83
404 515 1.003331 CTTTCTTTGCACGCACGGTAA 60.003 47.619 0.00 0.00 0.00 2.85
407 518 0.028770 TTCTTTCTTTGCACGCACGG 59.971 50.000 0.00 0.00 0.00 4.94
410 521 4.428209 TGATTTTTCTTTCTTTGCACGCA 58.572 34.783 0.00 0.00 0.00 5.24
411 522 4.739716 TCTGATTTTTCTTTCTTTGCACGC 59.260 37.500 0.00 0.00 0.00 5.34
412 523 6.473455 ACTTCTGATTTTTCTTTCTTTGCACG 59.527 34.615 0.00 0.00 0.00 5.34
413 524 7.489113 TCACTTCTGATTTTTCTTTCTTTGCAC 59.511 33.333 0.00 0.00 0.00 4.57
414 525 7.546358 TCACTTCTGATTTTTCTTTCTTTGCA 58.454 30.769 0.00 0.00 0.00 4.08
432 543 5.174395 GCACTAACACATCAGATCACTTCT 58.826 41.667 0.00 0.00 33.90 2.85
433 544 4.931601 TGCACTAACACATCAGATCACTTC 59.068 41.667 0.00 0.00 0.00 3.01
434 545 4.898320 TGCACTAACACATCAGATCACTT 58.102 39.130 0.00 0.00 0.00 3.16
435 546 4.502016 CTGCACTAACACATCAGATCACT 58.498 43.478 0.00 0.00 0.00 3.41
436 547 3.620374 CCTGCACTAACACATCAGATCAC 59.380 47.826 0.00 0.00 0.00 3.06
437 548 3.515104 TCCTGCACTAACACATCAGATCA 59.485 43.478 0.00 0.00 0.00 2.92
438 549 4.118410 CTCCTGCACTAACACATCAGATC 58.882 47.826 0.00 0.00 0.00 2.75
440 551 2.899900 ACTCCTGCACTAACACATCAGA 59.100 45.455 0.00 0.00 0.00 3.27
441 552 3.257393 GACTCCTGCACTAACACATCAG 58.743 50.000 0.00 0.00 0.00 2.90
442 553 2.028112 GGACTCCTGCACTAACACATCA 60.028 50.000 0.00 0.00 0.00 3.07
443 554 2.028112 TGGACTCCTGCACTAACACATC 60.028 50.000 0.00 0.00 0.00 3.06
444 555 1.977854 TGGACTCCTGCACTAACACAT 59.022 47.619 0.00 0.00 0.00 3.21
445 556 1.344438 CTGGACTCCTGCACTAACACA 59.656 52.381 0.00 0.00 0.00 3.72
453 564 1.997311 CATCCCCTGGACTCCTGCA 60.997 63.158 0.00 0.00 32.98 4.41
491 602 0.950555 GCATGCACACGTTCCTCTGA 60.951 55.000 14.21 0.00 0.00 3.27
492 603 1.499056 GCATGCACACGTTCCTCTG 59.501 57.895 14.21 0.00 0.00 3.35
494 605 1.011968 TACGCATGCACACGTTCCTC 61.012 55.000 19.57 0.00 43.35 3.71
497 608 1.904412 CAAATACGCATGCACACGTTC 59.096 47.619 19.57 0.00 43.35 3.95
500 625 0.167908 ACCAAATACGCATGCACACG 59.832 50.000 19.57 8.54 0.00 4.49
505 630 1.331756 CTCTGGACCAAATACGCATGC 59.668 52.381 7.91 7.91 0.00 4.06
524 655 2.616510 GGTGTATGCAAGCTCTTGTCCT 60.617 50.000 10.86 0.28 42.31 3.85
532 663 1.811266 CGCTCGGTGTATGCAAGCT 60.811 57.895 0.00 0.00 0.00 3.74
533 664 2.703409 CGCTCGGTGTATGCAAGC 59.297 61.111 0.00 0.00 0.00 4.01
534 665 3.398920 CCGCTCGGTGTATGCAAG 58.601 61.111 0.00 0.00 0.00 4.01
544 675 7.262772 TCCTTATATTAATCATAACCGCTCGG 58.737 38.462 6.79 6.79 42.03 4.63
545 676 8.697846 TTCCTTATATTAATCATAACCGCTCG 57.302 34.615 0.00 0.00 0.00 5.03
546 677 9.099454 CCTTCCTTATATTAATCATAACCGCTC 57.901 37.037 0.00 0.00 0.00 5.03
547 678 8.047310 CCCTTCCTTATATTAATCATAACCGCT 58.953 37.037 0.00 0.00 0.00 5.52
548 679 8.044908 TCCCTTCCTTATATTAATCATAACCGC 58.955 37.037 0.00 0.00 0.00 5.68
562 693 4.222145 GGACGTGCATATCCCTTCCTTATA 59.778 45.833 0.63 0.00 0.00 0.98
566 697 0.759346 GGACGTGCATATCCCTTCCT 59.241 55.000 0.63 0.00 0.00 3.36
572 715 2.682856 ACAAACATGGACGTGCATATCC 59.317 45.455 22.75 11.38 35.37 2.59
574 717 3.609853 AGACAAACATGGACGTGCATAT 58.390 40.909 22.75 8.98 0.00 1.78
575 718 3.052455 AGACAAACATGGACGTGCATA 57.948 42.857 22.75 0.00 0.00 3.14
576 719 1.896220 AGACAAACATGGACGTGCAT 58.104 45.000 17.64 17.64 0.00 3.96
577 720 2.535012 TAGACAAACATGGACGTGCA 57.465 45.000 13.59 13.59 0.00 4.57
578 721 3.000041 TCATAGACAAACATGGACGTGC 59.000 45.455 0.00 0.00 0.00 5.34
579 722 5.605564 TTTCATAGACAAACATGGACGTG 57.394 39.130 0.00 0.00 0.00 4.49
580 723 5.123820 CCATTTCATAGACAAACATGGACGT 59.876 40.000 0.00 0.00 0.00 4.34
581 724 5.572211 CCATTTCATAGACAAACATGGACG 58.428 41.667 0.00 0.00 0.00 4.79
582 725 5.105797 TGCCATTTCATAGACAAACATGGAC 60.106 40.000 0.00 0.00 0.00 4.02
583 726 5.015515 TGCCATTTCATAGACAAACATGGA 58.984 37.500 0.00 0.00 0.00 3.41
585 728 6.566141 TGATGCCATTTCATAGACAAACATG 58.434 36.000 0.00 0.00 0.00 3.21
586 729 6.604396 TCTGATGCCATTTCATAGACAAACAT 59.396 34.615 0.00 0.00 0.00 2.71
587 730 5.945191 TCTGATGCCATTTCATAGACAAACA 59.055 36.000 0.00 0.00 0.00 2.83
590 733 5.748402 AGTCTGATGCCATTTCATAGACAA 58.252 37.500 0.00 0.00 33.96 3.18
594 737 4.885907 ACCAAGTCTGATGCCATTTCATAG 59.114 41.667 0.00 0.00 0.00 2.23
596 739 3.705051 ACCAAGTCTGATGCCATTTCAT 58.295 40.909 0.00 0.00 0.00 2.57
598 741 4.022068 TCAAACCAAGTCTGATGCCATTTC 60.022 41.667 0.00 0.00 0.00 2.17
599 742 3.896888 TCAAACCAAGTCTGATGCCATTT 59.103 39.130 0.00 0.00 0.00 2.32
601 744 3.159213 TCAAACCAAGTCTGATGCCAT 57.841 42.857 0.00 0.00 0.00 4.40
602 745 2.655090 TCAAACCAAGTCTGATGCCA 57.345 45.000 0.00 0.00 0.00 4.92
603 746 3.119352 GGAATCAAACCAAGTCTGATGCC 60.119 47.826 0.00 0.00 37.97 4.40
604 747 3.426695 CGGAATCAAACCAAGTCTGATGC 60.427 47.826 0.00 0.00 30.28 3.91
605 748 4.002982 TCGGAATCAAACCAAGTCTGATG 58.997 43.478 0.00 0.00 30.28 3.07
606 749 4.286297 TCGGAATCAAACCAAGTCTGAT 57.714 40.909 0.00 0.00 0.00 2.90
627 784 9.132923 TCGAGTCCATAATAGTCATAGTTTCTT 57.867 33.333 0.00 0.00 0.00 2.52
628 785 8.693120 TCGAGTCCATAATAGTCATAGTTTCT 57.307 34.615 0.00 0.00 0.00 2.52
634 791 7.176165 ACGGAAATCGAGTCCATAATAGTCATA 59.824 37.037 16.04 0.00 42.43 2.15
641 798 4.665833 TCACGGAAATCGAGTCCATAAT 57.334 40.909 16.04 0.00 42.43 1.28
645 802 2.611971 CCTTTCACGGAAATCGAGTCCA 60.612 50.000 16.04 0.00 42.43 4.02
662 826 2.567169 GCCCTGTATTTTCCTTGCCTTT 59.433 45.455 0.00 0.00 0.00 3.11
688 852 3.506067 AGCCTTTTATTTCCTGTTGGACG 59.494 43.478 0.00 0.00 43.06 4.79
690 854 5.261216 CCTAGCCTTTTATTTCCTGTTGGA 58.739 41.667 0.00 0.00 41.36 3.53
691 855 4.402474 CCCTAGCCTTTTATTTCCTGTTGG 59.598 45.833 0.00 0.00 0.00 3.77
693 857 5.262009 GACCCTAGCCTTTTATTTCCTGTT 58.738 41.667 0.00 0.00 0.00 3.16
695 859 3.877508 CGACCCTAGCCTTTTATTTCCTG 59.122 47.826 0.00 0.00 0.00 3.86
696 860 3.778629 TCGACCCTAGCCTTTTATTTCCT 59.221 43.478 0.00 0.00 0.00 3.36
756 922 1.000896 CCGCTCCACCATTTCCCTT 60.001 57.895 0.00 0.00 0.00 3.95
764 930 2.915659 AACTCGTCCGCTCCACCA 60.916 61.111 0.00 0.00 0.00 4.17
783 949 2.568062 TGTAGATTAGTTCCGCCCACAA 59.432 45.455 0.00 0.00 0.00 3.33
795 962 1.635844 TGCCGCAACGTGTAGATTAG 58.364 50.000 0.00 0.00 0.00 1.73
804 971 4.626081 AGCCTCTTGCCGCAACGT 62.626 61.111 0.38 0.00 42.71 3.99
835 1003 2.325082 CGTTCCTGTCCGCCCTTTG 61.325 63.158 0.00 0.00 0.00 2.77
864 1034 0.324943 CCGTGATCCACCAAGAACCT 59.675 55.000 0.00 0.00 0.00 3.50
865 1035 0.323629 TCCGTGATCCACCAAGAACC 59.676 55.000 0.00 0.00 0.00 3.62
866 1038 1.002087 AGTCCGTGATCCACCAAGAAC 59.998 52.381 0.00 0.00 0.00 3.01
875 1048 2.509336 CACCGCAGTCCGTGATCC 60.509 66.667 0.00 0.00 34.38 3.36
980 1159 2.411701 CGAGCCGCGATCTAACCA 59.588 61.111 8.23 0.00 44.57 3.67
1009 1188 2.692557 CCACATCAAACTTGGTGAACCA 59.307 45.455 9.65 0.00 41.81 3.67
1032 1211 4.337145 AGTTACCCGTGCCATCAAATTTA 58.663 39.130 0.00 0.00 0.00 1.40
1077 1256 2.992543 CTGCTGCGCTAGAATATCCTTC 59.007 50.000 9.73 0.00 0.00 3.46
1145 1324 0.792640 CATATTCTCCCACGCATCGC 59.207 55.000 0.00 0.00 0.00 4.58
1174 1353 2.741092 CCATATGGTAGCGGCCGT 59.259 61.111 28.70 16.08 0.00 5.68
1210 1389 5.473066 TCGTCCATGACATGATACATGAT 57.527 39.130 17.24 3.36 44.28 2.45
1271 1450 4.165950 TGGTCACTGGCTTGGACATATAAT 59.834 41.667 0.00 0.00 33.26 1.28
1285 1464 5.647658 TCAAATACAGCTTATTGGTCACTGG 59.352 40.000 0.00 0.00 32.60 4.00
1289 1468 5.709631 TGCTTCAAATACAGCTTATTGGTCA 59.290 36.000 0.00 0.00 36.92 4.02
1327 1506 2.780010 CCAACCCCTCCTACATCTTCAT 59.220 50.000 0.00 0.00 0.00 2.57
1374 1553 5.334646 CGCTAGATCCATGACCAATTGATTG 60.335 44.000 7.12 0.00 37.52 2.67
1388 1567 1.274447 CATCCAGATGCGCTAGATCCA 59.726 52.381 9.73 0.00 31.39 3.41
1400 1579 4.442612 CGTCCTCAATCTTCACATCCAGAT 60.443 45.833 0.00 0.00 0.00 2.90
1434 1613 6.577427 GTGGCAACGAAACAAGAATAAGTAAG 59.423 38.462 0.00 0.00 42.51 2.34
1435 1614 6.432107 GTGGCAACGAAACAAGAATAAGTAA 58.568 36.000 0.00 0.00 42.51 2.24
1441 1620 1.001815 CGGTGGCAACGAAACAAGAAT 60.002 47.619 22.63 0.00 42.51 2.40
1573 1752 4.893829 AACCTTGAGTACTCTCCCTTTC 57.106 45.455 23.01 0.00 39.75 2.62
1613 1797 5.488919 TCTTGTCCCTTCCTGAGTTGATAAT 59.511 40.000 0.00 0.00 0.00 1.28
1833 2023 5.529800 ACCAACTGTATTCTTGTAACGCTTT 59.470 36.000 0.00 0.00 0.00 3.51
1849 2039 1.068127 GTGTACGACTCCACCAACTGT 59.932 52.381 0.00 0.00 0.00 3.55
1851 2041 0.313043 CGTGTACGACTCCACCAACT 59.687 55.000 0.00 0.00 43.02 3.16
1937 2128 3.061260 GACGTCCTCGGGCTGTACC 62.061 68.421 3.51 0.00 41.85 3.34
1973 2164 2.158158 TCAACTTCTCCTCTCCCCTTGA 60.158 50.000 0.00 0.00 0.00 3.02
2070 2264 1.089978 TTCCTACACCTCCTCCTCCA 58.910 55.000 0.00 0.00 0.00 3.86
2148 2350 2.778717 GCCCCCTATCCCTTGCCT 60.779 66.667 0.00 0.00 0.00 4.75
2199 2406 3.264845 GTTTCCCCTCCCTGGCCA 61.265 66.667 4.71 4.71 0.00 5.36
2252 2460 0.927029 GCCTAGGGTTGAGGGGAAAT 59.073 55.000 11.72 0.00 34.35 2.17


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

AutoCloner maintained by Alex Coulton.