Multiple sequence alignment - TraesCS7B01G266600

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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 TraesCS7B01G266600 chr7B 100.000 2732 0 0 1 2732 489553248 489550517 0.000000e+00 5046.0
1 TraesCS7B01G266600 chr7B 83.014 783 87 26 950 1715 489781329 489780576 0.000000e+00 667.0
2 TraesCS7B01G266600 chr7B 86.047 86 10 2 504 587 10240058 10239973 1.040000e-14 91.6
3 TraesCS7B01G266600 chr7D 95.243 1955 61 15 805 2732 464137958 464136009 0.000000e+00 3066.0
4 TraesCS7B01G266600 chr7D 84.514 762 89 16 950 1695 464361422 464360674 0.000000e+00 726.0
5 TraesCS7B01G266600 chr7D 79.682 817 91 35 932 1707 464947901 464947119 1.120000e-143 520.0
6 TraesCS7B01G266600 chr7A 90.603 1394 68 22 619 1975 535590408 535591775 0.000000e+00 1790.0
7 TraesCS7B01G266600 chr7A 80.888 811 86 31 929 1695 534766214 534766999 2.360000e-160 575.0
8 TraesCS7B01G266600 chr7A 80.808 792 74 32 1972 2732 535591801 535592545 1.430000e-152 549.0
9 TraesCS7B01G266600 chr7A 87.637 364 33 7 131 482 535590025 535590388 1.960000e-111 412.0
10 TraesCS7B01G266600 chr7A 94.949 99 5 0 3 101 535589927 535590025 3.640000e-34 156.0
11 TraesCS7B01G266600 chr7A 93.103 58 4 0 425 482 535589511 535589568 4.850000e-13 86.1
12 TraesCS7B01G266600 chr6B 77.986 427 74 15 4 416 560799088 560799508 1.620000e-62 250.0
13 TraesCS7B01G266600 chr5A 77.904 439 72 19 4 431 593435831 593435407 1.620000e-62 250.0
14 TraesCS7B01G266600 chr5A 96.875 32 1 0 585 616 6296879 6296848 1.000000e-03 54.7
15 TraesCS7B01G266600 chr2B 77.098 441 83 14 3 431 741864857 741865291 3.520000e-59 239.0
16 TraesCS7B01G266600 chr3B 76.888 437 90 9 4 431 823937701 823937267 1.260000e-58 237.0
17 TraesCS7B01G266600 chr3B 76.484 438 80 16 4 431 536265941 536266365 1.650000e-52 217.0
18 TraesCS7B01G266600 chr3D 77.641 407 77 7 34 431 503776130 503776531 4.550000e-58 235.0
19 TraesCS7B01G266600 chr5D 80.743 296 49 5 143 431 409296417 409296711 9.840000e-55 224.0
20 TraesCS7B01G266600 chr5D 85.437 103 14 1 486 587 420700319 420700217 3.720000e-19 106.0
21 TraesCS7B01G266600 chr6D 80.537 298 48 7 143 431 465053556 465053260 1.270000e-53 220.0
22 TraesCS7B01G266600 chr4B 90.426 94 7 2 478 570 506929540 506929448 3.690000e-24 122.0
23 TraesCS7B01G266600 chr4B 85.965 114 15 1 476 588 541906374 541906261 1.330000e-23 121.0
24 TraesCS7B01G266600 chr3A 86.667 105 13 1 480 583 46728139 46728243 6.180000e-22 115.0
25 TraesCS7B01G266600 chr1D 85.714 105 13 2 480 583 230977628 230977731 2.880000e-20 110.0
26 TraesCS7B01G266600 chr1A 89.796 49 5 0 425 473 375116806 375116758 2.270000e-06 63.9


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 TraesCS7B01G266600 chr7B 489550517 489553248 2731 True 5046.00 5046 100.000 1 2732 1 chr7B.!!$R2 2731
1 TraesCS7B01G266600 chr7B 489780576 489781329 753 True 667.00 667 83.014 950 1715 1 chr7B.!!$R3 765
2 TraesCS7B01G266600 chr7D 464136009 464137958 1949 True 3066.00 3066 95.243 805 2732 1 chr7D.!!$R1 1927
3 TraesCS7B01G266600 chr7D 464360674 464361422 748 True 726.00 726 84.514 950 1695 1 chr7D.!!$R2 745
4 TraesCS7B01G266600 chr7D 464947119 464947901 782 True 520.00 520 79.682 932 1707 1 chr7D.!!$R3 775
5 TraesCS7B01G266600 chr7A 535589511 535592545 3034 False 598.62 1790 89.420 3 2732 5 chr7A.!!$F2 2729
6 TraesCS7B01G266600 chr7A 534766214 534766999 785 False 575.00 575 80.888 929 1695 1 chr7A.!!$F1 766

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
260 684 0.237235 CACGCAACTAACACGCCAAT 59.763 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 2280 0.319383 CTCATTCTCCCCGCATCTCG 60.319 60.0 0.0 0.0 38.08 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
55 470 2.948720 GCCAACCGTCCTGCTCTCT 61.949 63.158 0.00 0.00 0.00 3.10
60 475 3.073735 CGTCCTGCTCTCTGCCCT 61.074 66.667 0.00 0.00 42.00 5.19
73 488 0.984961 CTGCCCTGATCCCCTCTTCA 60.985 60.000 0.00 0.00 0.00 3.02
75 490 1.826024 CCCTGATCCCCTCTTCACG 59.174 63.158 0.00 0.00 0.00 4.35
123 538 2.746277 GGGGGACACGATGTGCAC 60.746 66.667 10.75 10.75 41.74 4.57
124 539 2.746277 GGGGACACGATGTGCACC 60.746 66.667 15.69 0.00 40.73 5.01
125 540 2.031919 GGGACACGATGTGCACCA 59.968 61.111 15.69 2.61 40.73 4.17
126 541 2.325082 GGGACACGATGTGCACCAC 61.325 63.158 15.69 7.34 40.73 4.16
127 542 2.325082 GGACACGATGTGCACCACC 61.325 63.158 15.69 2.14 38.66 4.61
128 543 2.281484 ACACGATGTGCACCACCC 60.281 61.111 15.69 0.00 36.98 4.61
129 544 3.422303 CACGATGTGCACCACCCG 61.422 66.667 15.69 14.15 36.23 5.28
130 545 3.621805 ACGATGTGCACCACCCGA 61.622 61.111 15.69 0.00 34.99 5.14
134 549 3.589654 ATGTGCACCACCCGAGACG 62.590 63.158 15.69 0.00 32.73 4.18
157 572 1.065854 CCTCGGCCAAGAAGACAGATT 60.066 52.381 2.24 0.00 0.00 2.40
179 594 1.067295 TTGTCTCCTCCACCATTGCT 58.933 50.000 0.00 0.00 0.00 3.91
181 596 1.555075 TGTCTCCTCCACCATTGCTAC 59.445 52.381 0.00 0.00 0.00 3.58
182 597 1.555075 GTCTCCTCCACCATTGCTACA 59.445 52.381 0.00 0.00 0.00 2.74
193 608 6.317642 TCCACCATTGCTACATTGTAACATAC 59.682 38.462 1.00 0.00 0.00 2.39
213 633 6.714810 ACATACAATTACATCCCGTGCATTAT 59.285 34.615 0.00 0.00 0.00 1.28
216 636 5.592282 ACAATTACATCCCGTGCATTATCAA 59.408 36.000 0.00 0.00 0.00 2.57
217 637 6.096141 ACAATTACATCCCGTGCATTATCAAA 59.904 34.615 0.00 0.00 0.00 2.69
243 667 1.164411 TGATGTCCATCGTTTGGCAC 58.836 50.000 3.04 3.63 46.01 5.01
257 681 2.127383 GCACGCAACTAACACGCC 60.127 61.111 0.00 0.00 0.00 5.68
258 682 2.887889 GCACGCAACTAACACGCCA 61.888 57.895 0.00 0.00 0.00 5.69
259 683 1.644372 CACGCAACTAACACGCCAA 59.356 52.632 0.00 0.00 0.00 4.52
260 684 0.237235 CACGCAACTAACACGCCAAT 59.763 50.000 0.00 0.00 0.00 3.16
273 697 3.491356 CACGCCAATGTGTCTGTTATTG 58.509 45.455 0.00 0.00 35.12 1.90
277 701 4.083324 CGCCAATGTGTCTGTTATTGACTT 60.083 41.667 0.00 0.00 34.55 3.01
280 704 6.144402 GCCAATGTGTCTGTTATTGACTTTTG 59.856 38.462 0.00 0.00 34.55 2.44
287 711 7.166473 GTGTCTGTTATTGACTTTTGAAGCAAG 59.834 37.037 0.00 0.00 35.63 4.01
358 784 6.525121 TGATAAGAAAATATGAACCGCTCG 57.475 37.500 0.00 0.00 0.00 5.03
363 789 2.533266 AATATGAACCGCTCGCTCAT 57.467 45.000 9.11 9.11 34.29 2.90
375 801 2.923605 GCTCGCTCATGCAATTTGTTGT 60.924 45.455 0.00 0.00 39.64 3.32
387 813 4.627035 GCAATTTGTTGTAAAGCCATCTCC 59.373 41.667 0.00 0.00 0.00 3.71
403 829 6.016777 AGCCATCTCCGATGAAACATAATTTC 60.017 38.462 5.46 0.00 0.00 2.17
474 901 8.686334 TGAAAGAAGTTTCCAATGCTATTATCC 58.314 33.333 0.00 0.00 41.37 2.59
479 906 7.961326 AGTTTCCAATGCTATTATCCTTGTT 57.039 32.000 0.00 0.00 0.00 2.83
480 907 9.474313 AAGTTTCCAATGCTATTATCCTTGTTA 57.526 29.630 0.00 0.00 0.00 2.41
481 908 8.903820 AGTTTCCAATGCTATTATCCTTGTTAC 58.096 33.333 0.00 0.00 0.00 2.50
482 909 8.903820 GTTTCCAATGCTATTATCCTTGTTACT 58.096 33.333 0.00 0.00 0.00 2.24
483 910 8.677148 TTCCAATGCTATTATCCTTGTTACTC 57.323 34.615 0.00 0.00 0.00 2.59
484 911 7.224297 TCCAATGCTATTATCCTTGTTACTCC 58.776 38.462 0.00 0.00 0.00 3.85
485 912 6.431234 CCAATGCTATTATCCTTGTTACTCCC 59.569 42.308 0.00 0.00 0.00 4.30
486 913 7.227156 CAATGCTATTATCCTTGTTACTCCCT 58.773 38.462 0.00 0.00 0.00 4.20
487 914 6.420913 TGCTATTATCCTTGTTACTCCCTC 57.579 41.667 0.00 0.00 0.00 4.30
488 915 5.307196 TGCTATTATCCTTGTTACTCCCTCC 59.693 44.000 0.00 0.00 0.00 4.30
489 916 5.307196 GCTATTATCCTTGTTACTCCCTCCA 59.693 44.000 0.00 0.00 0.00 3.86
490 917 6.013293 GCTATTATCCTTGTTACTCCCTCCAT 60.013 42.308 0.00 0.00 0.00 3.41
491 918 6.848562 ATTATCCTTGTTACTCCCTCCATT 57.151 37.500 0.00 0.00 0.00 3.16
492 919 6.652205 TTATCCTTGTTACTCCCTCCATTT 57.348 37.500 0.00 0.00 0.00 2.32
493 920 7.758820 TTATCCTTGTTACTCCCTCCATTTA 57.241 36.000 0.00 0.00 0.00 1.40
494 921 6.848562 ATCCTTGTTACTCCCTCCATTTAT 57.151 37.500 0.00 0.00 0.00 1.40
495 922 6.652205 TCCTTGTTACTCCCTCCATTTATT 57.348 37.500 0.00 0.00 0.00 1.40
496 923 7.039722 TCCTTGTTACTCCCTCCATTTATTT 57.960 36.000 0.00 0.00 0.00 1.40
497 924 7.475299 TCCTTGTTACTCCCTCCATTTATTTT 58.525 34.615 0.00 0.00 0.00 1.82
498 925 7.396055 TCCTTGTTACTCCCTCCATTTATTTTG 59.604 37.037 0.00 0.00 0.00 2.44
499 926 7.178451 CCTTGTTACTCCCTCCATTTATTTTGT 59.822 37.037 0.00 0.00 0.00 2.83
500 927 9.238368 CTTGTTACTCCCTCCATTTATTTTGTA 57.762 33.333 0.00 0.00 0.00 2.41
501 928 9.762381 TTGTTACTCCCTCCATTTATTTTGTAT 57.238 29.630 0.00 0.00 0.00 2.29
502 929 9.184523 TGTTACTCCCTCCATTTATTTTGTATG 57.815 33.333 0.00 0.00 0.00 2.39
503 930 9.403583 GTTACTCCCTCCATTTATTTTGTATGA 57.596 33.333 0.00 0.00 0.00 2.15
504 931 7.881775 ACTCCCTCCATTTATTTTGTATGAC 57.118 36.000 0.00 0.00 0.00 3.06
505 932 7.643123 ACTCCCTCCATTTATTTTGTATGACT 58.357 34.615 0.00 0.00 0.00 3.41
506 933 8.116026 ACTCCCTCCATTTATTTTGTATGACTT 58.884 33.333 0.00 0.00 0.00 3.01
507 934 8.893563 TCCCTCCATTTATTTTGTATGACTTT 57.106 30.769 0.00 0.00 0.00 2.66
508 935 9.320295 TCCCTCCATTTATTTTGTATGACTTTT 57.680 29.630 0.00 0.00 0.00 2.27
509 936 9.942850 CCCTCCATTTATTTTGTATGACTTTTT 57.057 29.630 0.00 0.00 0.00 1.94
535 962 8.918202 AGACATTTAAGATAACACCTGAAACA 57.082 30.769 0.00 0.00 0.00 2.83
536 963 9.003658 AGACATTTAAGATAACACCTGAAACAG 57.996 33.333 0.00 0.00 0.00 3.16
537 964 8.918202 ACATTTAAGATAACACCTGAAACAGA 57.082 30.769 0.00 0.00 32.44 3.41
538 965 9.520515 ACATTTAAGATAACACCTGAAACAGAT 57.479 29.630 0.00 0.00 32.44 2.90
549 976 8.409358 ACACCTGAAACAGATTAATTTTAGCT 57.591 30.769 0.00 0.00 32.44 3.32
550 977 8.299570 ACACCTGAAACAGATTAATTTTAGCTG 58.700 33.333 0.00 0.00 32.44 4.24
551 978 8.299570 CACCTGAAACAGATTAATTTTAGCTGT 58.700 33.333 0.00 0.77 41.19 4.40
552 979 8.515414 ACCTGAAACAGATTAATTTTAGCTGTC 58.485 33.333 6.76 0.00 38.74 3.51
553 980 7.970614 CCTGAAACAGATTAATTTTAGCTGTCC 59.029 37.037 6.76 3.84 38.74 4.02
554 981 8.635765 TGAAACAGATTAATTTTAGCTGTCCT 57.364 30.769 6.76 0.00 38.74 3.85
555 982 9.733556 TGAAACAGATTAATTTTAGCTGTCCTA 57.266 29.630 6.76 0.00 38.74 2.94
559 986 8.665685 ACAGATTAATTTTAGCTGTCCTAAACG 58.334 33.333 0.00 0.00 43.73 3.60
560 987 8.879759 CAGATTAATTTTAGCTGTCCTAAACGA 58.120 33.333 0.00 0.00 43.73 3.85
561 988 8.880750 AGATTAATTTTAGCTGTCCTAAACGAC 58.119 33.333 0.00 0.00 43.73 4.34
562 989 8.788325 ATTAATTTTAGCTGTCCTAAACGACT 57.212 30.769 0.00 0.00 43.73 4.18
563 990 8.611654 TTAATTTTAGCTGTCCTAAACGACTT 57.388 30.769 0.00 0.00 43.73 3.01
564 991 9.709495 TTAATTTTAGCTGTCCTAAACGACTTA 57.291 29.630 0.00 0.00 43.73 2.24
565 992 7.592439 ATTTTAGCTGTCCTAAACGACTTAC 57.408 36.000 0.00 0.00 43.73 2.34
566 993 5.710513 TTAGCTGTCCTAAACGACTTACA 57.289 39.130 0.00 0.00 33.18 2.41
567 994 4.595762 AGCTGTCCTAAACGACTTACAA 57.404 40.909 0.00 0.00 33.70 2.41
568 995 4.952460 AGCTGTCCTAAACGACTTACAAA 58.048 39.130 0.00 0.00 33.70 2.83
569 996 5.362263 AGCTGTCCTAAACGACTTACAAAA 58.638 37.500 0.00 0.00 33.70 2.44
570 997 5.465724 AGCTGTCCTAAACGACTTACAAAAG 59.534 40.000 0.00 0.00 38.77 2.27
571 998 5.662211 TGTCCTAAACGACTTACAAAAGC 57.338 39.130 0.00 0.00 36.05 3.51
572 999 4.209703 TGTCCTAAACGACTTACAAAAGCG 59.790 41.667 0.00 0.00 37.86 4.68
573 1000 4.445385 GTCCTAAACGACTTACAAAAGCGA 59.555 41.667 0.00 0.00 36.44 4.93
574 1001 5.049167 TCCTAAACGACTTACAAAAGCGAA 58.951 37.500 0.00 0.00 36.44 4.70
575 1002 5.697633 TCCTAAACGACTTACAAAAGCGAAT 59.302 36.000 0.00 0.00 36.44 3.34
576 1003 6.867816 TCCTAAACGACTTACAAAAGCGAATA 59.132 34.615 0.00 0.00 36.44 1.75
577 1004 7.062605 TCCTAAACGACTTACAAAAGCGAATAG 59.937 37.037 0.00 0.00 36.44 1.73
578 1005 6.774354 AAACGACTTACAAAAGCGAATAGA 57.226 33.333 0.00 0.00 36.44 1.98
579 1006 6.390987 AACGACTTACAAAAGCGAATAGAG 57.609 37.500 0.00 0.00 36.44 2.43
580 1007 4.863131 ACGACTTACAAAAGCGAATAGAGG 59.137 41.667 0.00 0.00 36.44 3.69
581 1008 4.267928 CGACTTACAAAAGCGAATAGAGGG 59.732 45.833 0.00 0.00 36.05 4.30
582 1009 5.416271 ACTTACAAAAGCGAATAGAGGGA 57.584 39.130 0.00 0.00 36.05 4.20
583 1010 5.801380 ACTTACAAAAGCGAATAGAGGGAA 58.199 37.500 0.00 0.00 36.05 3.97
629 1056 7.944729 AGTTAAATGTATGGCAGACTTTGAT 57.055 32.000 14.03 2.48 0.00 2.57
632 1059 2.009051 TGTATGGCAGACTTTGATGCG 58.991 47.619 14.03 0.00 43.49 4.73
640 1067 3.062099 GCAGACTTTGATGCGAAATACGA 59.938 43.478 0.00 0.00 45.77 3.43
641 1068 4.780324 GCAGACTTTGATGCGAAATACGAG 60.780 45.833 0.00 0.00 45.77 4.18
656 1083 5.526506 AATACGAGGCGACTAATAAACCT 57.473 39.130 0.00 0.00 44.43 3.50
722 1149 5.091261 AGTTCGTCAAGGAGCAAATAGAT 57.909 39.130 0.00 0.00 0.00 1.98
735 1162 6.634436 GGAGCAAATAGATAATGAACAAAGCG 59.366 38.462 0.00 0.00 0.00 4.68
908 1354 2.608988 CCAGCACCCCCACTCTCT 60.609 66.667 0.00 0.00 0.00 3.10
930 1376 3.172106 TTCCCCACCACCGCTTCA 61.172 61.111 0.00 0.00 0.00 3.02
938 1384 4.410400 CACCGCTTCACCCCCTCC 62.410 72.222 0.00 0.00 0.00 4.30
1779 2280 3.137533 GGCCTAGATGCAAGAATGAGAC 58.862 50.000 0.00 0.00 0.00 3.36
1865 2366 0.754472 TCGTTCCCCTTCTGTTTCGT 59.246 50.000 0.00 0.00 0.00 3.85
1866 2367 1.139455 TCGTTCCCCTTCTGTTTCGTT 59.861 47.619 0.00 0.00 0.00 3.85
1907 2408 3.144506 CCCTGCTTGGATGCTAGTAATG 58.855 50.000 0.00 0.00 38.35 1.90
1952 2460 3.081061 TCTGTGCAATGTGGAACCATAC 58.919 45.455 0.00 0.00 34.36 2.39
1991 2528 6.481313 GCAACAGCTAGTTAATCTCATCATGA 59.519 38.462 0.00 0.00 38.74 3.07
2079 2621 2.029623 CCCATTTCTGCAGGATTCTGG 58.970 52.381 15.13 12.30 41.19 3.86
2082 2624 1.830279 TTTCTGCAGGATTCTGGCTG 58.170 50.000 15.13 0.00 41.19 4.85
2137 2686 1.462616 AGTTCGCAGCAATGGCAATA 58.537 45.000 0.00 0.00 44.61 1.90
2138 2687 1.818060 AGTTCGCAGCAATGGCAATAA 59.182 42.857 0.00 0.00 44.61 1.40
2139 2688 2.428171 AGTTCGCAGCAATGGCAATAAT 59.572 40.909 0.00 0.00 44.61 1.28
2144 2693 3.551250 CGCAGCAATGGCAATAATCATCA 60.551 43.478 0.00 0.00 44.61 3.07
2157 2706 1.308069 ATCATCACTGGCACCGCAAC 61.308 55.000 0.00 0.00 0.00 4.17
2183 2732 2.464459 CCGAATTCCTCCGTGCTGC 61.464 63.158 0.00 0.00 0.00 5.25
2184 2733 2.464459 CGAATTCCTCCGTGCTGCC 61.464 63.158 0.00 0.00 0.00 4.85
2376 2935 1.205655 GGTACGGTCAGGGTTAACTCC 59.794 57.143 0.61 3.43 0.00 3.85
2398 2963 9.303116 ACTCCCTAATCACACATAGAGTATTAG 57.697 37.037 0.00 0.00 31.84 1.73
2448 3013 2.029073 CGCCACACGTCTGGAGTT 59.971 61.111 14.69 0.00 36.87 3.01
2449 3014 1.594293 CGCCACACGTCTGGAGTTT 60.594 57.895 14.69 0.00 36.87 2.66
2450 3015 0.319211 CGCCACACGTCTGGAGTTTA 60.319 55.000 14.69 0.00 36.87 2.01
2719 3311 5.516339 GCGTTAATCTTGATTGTTGATTGGG 59.484 40.000 6.15 0.00 33.24 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.595357 GGTCCGTGGGGAAGTACAG 59.405 63.158 0.00 0.00 46.08 2.74
1 2 2.277591 CGGTCCGTGGGGAAGTACA 61.278 63.158 2.08 0.00 46.08 2.90
2 3 2.575461 CGGTCCGTGGGGAAGTAC 59.425 66.667 2.08 0.00 46.08 2.73
11 12 0.797249 CTTCTACTTCGCGGTCCGTG 60.797 60.000 18.95 18.95 38.82 4.94
12 13 1.239968 ACTTCTACTTCGCGGTCCGT 61.240 55.000 13.94 0.71 38.35 4.69
13 14 0.522915 GACTTCTACTTCGCGGTCCG 60.523 60.000 6.99 6.99 38.61 4.79
55 470 1.082766 TGAAGAGGGGATCAGGGCA 59.917 57.895 0.00 0.00 0.00 5.36
60 475 1.275291 GAACACGTGAAGAGGGGATCA 59.725 52.381 25.01 0.00 0.00 2.92
73 488 1.922135 GCGGATTGGCATGAACACGT 61.922 55.000 0.00 0.00 0.00 4.49
75 490 1.139520 GGCGGATTGGCATGAACAC 59.860 57.895 0.00 0.00 44.08 3.32
106 521 2.746277 GTGCACATCGTGTCCCCC 60.746 66.667 13.17 0.00 35.75 5.40
107 522 2.746277 GGTGCACATCGTGTCCCC 60.746 66.667 20.43 0.00 35.75 4.81
108 523 2.031919 TGGTGCACATCGTGTCCC 59.968 61.111 20.43 0.00 35.75 4.46
109 524 2.325082 GGTGGTGCACATCGTGTCC 61.325 63.158 20.43 5.86 35.86 4.02
110 525 2.325082 GGGTGGTGCACATCGTGTC 61.325 63.158 20.43 0.00 35.86 3.67
111 526 2.281484 GGGTGGTGCACATCGTGT 60.281 61.111 20.43 0.00 35.86 4.49
112 527 3.422303 CGGGTGGTGCACATCGTG 61.422 66.667 20.43 0.87 35.86 4.35
113 528 3.589654 CTCGGGTGGTGCACATCGT 62.590 63.158 20.43 0.00 35.86 3.73
114 529 2.815211 CTCGGGTGGTGCACATCG 60.815 66.667 20.43 15.40 35.86 3.84
115 530 1.741770 GTCTCGGGTGGTGCACATC 60.742 63.158 20.43 10.48 35.86 3.06
116 531 2.347490 GTCTCGGGTGGTGCACAT 59.653 61.111 20.43 0.00 35.86 3.21
117 532 4.293648 CGTCTCGGGTGGTGCACA 62.294 66.667 20.43 1.62 35.86 4.57
141 556 3.760684 ACAATGAATCTGTCTTCTTGGCC 59.239 43.478 0.00 0.00 0.00 5.36
151 566 3.054802 GGTGGAGGAGACAATGAATCTGT 60.055 47.826 0.00 0.00 0.00 3.41
157 572 2.618816 GCAATGGTGGAGGAGACAATGA 60.619 50.000 0.00 0.00 0.00 2.57
170 585 7.082700 TGTATGTTACAATGTAGCAATGGTG 57.917 36.000 13.61 0.00 35.38 4.17
193 608 5.687770 TGATAATGCACGGGATGTAATTG 57.312 39.130 0.00 0.00 0.00 2.32
238 662 2.887889 GCGTGTTAGTTGCGTGCCA 61.888 57.895 0.00 0.00 0.00 4.92
243 667 0.237235 ACATTGGCGTGTTAGTTGCG 59.763 50.000 0.00 0.00 0.00 4.85
257 681 8.854979 TTCAAAAGTCAATAACAGACACATTG 57.145 30.769 0.00 0.00 38.46 2.82
258 682 7.649306 GCTTCAAAAGTCAATAACAGACACATT 59.351 33.333 0.00 0.00 38.46 2.71
259 683 7.141363 GCTTCAAAAGTCAATAACAGACACAT 58.859 34.615 0.00 0.00 38.46 3.21
260 684 6.094742 TGCTTCAAAAGTCAATAACAGACACA 59.905 34.615 0.00 0.00 38.46 3.72
267 691 6.292328 GGTTGCTTGCTTCAAAAGTCAATAAC 60.292 38.462 0.00 0.00 0.00 1.89
273 697 3.163630 TGGTTGCTTGCTTCAAAAGTC 57.836 42.857 0.00 0.00 0.00 3.01
338 762 4.439057 AGCGAGCGGTTCATATTTTCTTA 58.561 39.130 0.00 0.00 0.00 2.10
351 777 1.308069 AAATTGCATGAGCGAGCGGT 61.308 50.000 0.00 0.00 46.23 5.68
358 784 4.143052 GGCTTTACAACAAATTGCATGAGC 60.143 41.667 0.00 5.16 39.66 4.26
363 789 5.212532 AGATGGCTTTACAACAAATTGCA 57.787 34.783 0.00 0.00 39.66 4.08
375 801 4.214986 TGTTTCATCGGAGATGGCTTTA 57.785 40.909 9.77 0.00 45.12 1.85
387 813 8.477984 AAAATGTGGGAAATTATGTTTCATCG 57.522 30.769 7.45 0.00 0.00 3.84
464 891 5.307196 GGAGGGAGTAACAAGGATAATAGCA 59.693 44.000 0.00 0.00 0.00 3.49
474 901 8.122472 ACAAAATAAATGGAGGGAGTAACAAG 57.878 34.615 0.00 0.00 0.00 3.16
479 906 8.778059 AGTCATACAAAATAAATGGAGGGAGTA 58.222 33.333 0.00 0.00 0.00 2.59
480 907 7.643123 AGTCATACAAAATAAATGGAGGGAGT 58.357 34.615 0.00 0.00 0.00 3.85
481 908 8.525290 AAGTCATACAAAATAAATGGAGGGAG 57.475 34.615 0.00 0.00 0.00 4.30
482 909 8.893563 AAAGTCATACAAAATAAATGGAGGGA 57.106 30.769 0.00 0.00 0.00 4.20
483 910 9.942850 AAAAAGTCATACAAAATAAATGGAGGG 57.057 29.630 0.00 0.00 0.00 4.30
510 937 8.918202 TGTTTCAGGTGTTATCTTAAATGTCT 57.082 30.769 0.00 0.00 0.00 3.41
511 938 8.999431 TCTGTTTCAGGTGTTATCTTAAATGTC 58.001 33.333 0.00 0.00 31.51 3.06
512 939 8.918202 TCTGTTTCAGGTGTTATCTTAAATGT 57.082 30.769 0.00 0.00 31.51 2.71
523 950 8.860088 AGCTAAAATTAATCTGTTTCAGGTGTT 58.140 29.630 0.00 0.00 31.51 3.32
524 951 8.299570 CAGCTAAAATTAATCTGTTTCAGGTGT 58.700 33.333 0.00 0.00 31.51 4.16
525 952 8.299570 ACAGCTAAAATTAATCTGTTTCAGGTG 58.700 33.333 1.86 1.79 34.69 4.00
526 953 8.409358 ACAGCTAAAATTAATCTGTTTCAGGT 57.591 30.769 1.86 0.00 34.69 4.00
527 954 7.970614 GGACAGCTAAAATTAATCTGTTTCAGG 59.029 37.037 7.85 0.00 38.03 3.86
528 955 8.734386 AGGACAGCTAAAATTAATCTGTTTCAG 58.266 33.333 7.85 0.00 38.03 3.02
529 956 8.635765 AGGACAGCTAAAATTAATCTGTTTCA 57.364 30.769 7.85 0.00 38.03 2.69
533 960 8.665685 CGTTTAGGACAGCTAAAATTAATCTGT 58.334 33.333 6.48 6.48 40.31 3.41
534 961 8.879759 TCGTTTAGGACAGCTAAAATTAATCTG 58.120 33.333 0.00 0.00 0.00 2.90
535 962 8.880750 GTCGTTTAGGACAGCTAAAATTAATCT 58.119 33.333 0.00 0.00 36.91 2.40
536 963 8.880750 AGTCGTTTAGGACAGCTAAAATTAATC 58.119 33.333 5.50 0.00 39.42 1.75
537 964 8.788325 AGTCGTTTAGGACAGCTAAAATTAAT 57.212 30.769 5.50 0.00 39.42 1.40
538 965 8.611654 AAGTCGTTTAGGACAGCTAAAATTAA 57.388 30.769 5.50 0.00 39.42 1.40
539 966 9.143631 GTAAGTCGTTTAGGACAGCTAAAATTA 57.856 33.333 5.50 0.00 39.42 1.40
540 967 7.658575 TGTAAGTCGTTTAGGACAGCTAAAATT 59.341 33.333 5.50 0.00 39.42 1.82
541 968 7.156673 TGTAAGTCGTTTAGGACAGCTAAAAT 58.843 34.615 5.50 0.00 39.42 1.82
542 969 6.514947 TGTAAGTCGTTTAGGACAGCTAAAA 58.485 36.000 5.50 0.00 39.42 1.52
543 970 6.088016 TGTAAGTCGTTTAGGACAGCTAAA 57.912 37.500 5.50 0.00 39.42 1.85
544 971 5.710513 TGTAAGTCGTTTAGGACAGCTAA 57.289 39.130 5.50 0.00 39.42 3.09
545 972 5.710513 TTGTAAGTCGTTTAGGACAGCTA 57.289 39.130 5.50 0.00 39.42 3.32
546 973 4.595762 TTGTAAGTCGTTTAGGACAGCT 57.404 40.909 5.50 0.00 39.42 4.24
547 974 5.662211 TTTTGTAAGTCGTTTAGGACAGC 57.338 39.130 5.50 0.00 39.42 4.40
548 975 5.611844 CGCTTTTGTAAGTCGTTTAGGACAG 60.612 44.000 5.50 0.00 39.42 3.51
549 976 4.209703 CGCTTTTGTAAGTCGTTTAGGACA 59.790 41.667 5.50 0.00 39.42 4.02
550 977 4.445385 TCGCTTTTGTAAGTCGTTTAGGAC 59.555 41.667 0.00 0.00 34.63 3.85
551 978 4.619973 TCGCTTTTGTAAGTCGTTTAGGA 58.380 39.130 0.00 0.00 34.63 2.94
552 979 4.977741 TCGCTTTTGTAAGTCGTTTAGG 57.022 40.909 0.00 0.00 34.63 2.69
553 980 7.946043 TCTATTCGCTTTTGTAAGTCGTTTAG 58.054 34.615 0.00 0.00 34.63 1.85
554 981 7.062605 CCTCTATTCGCTTTTGTAAGTCGTTTA 59.937 37.037 0.00 0.00 34.63 2.01
555 982 6.128634 CCTCTATTCGCTTTTGTAAGTCGTTT 60.129 38.462 0.00 0.00 34.63 3.60
556 983 5.347907 CCTCTATTCGCTTTTGTAAGTCGTT 59.652 40.000 0.00 0.00 34.63 3.85
557 984 4.863131 CCTCTATTCGCTTTTGTAAGTCGT 59.137 41.667 0.00 0.00 34.63 4.34
558 985 4.267928 CCCTCTATTCGCTTTTGTAAGTCG 59.732 45.833 0.00 0.00 33.74 4.18
559 986 5.416947 TCCCTCTATTCGCTTTTGTAAGTC 58.583 41.667 0.00 0.00 33.74 3.01
560 987 5.416271 TCCCTCTATTCGCTTTTGTAAGT 57.584 39.130 0.00 0.00 33.74 2.24
561 988 6.927294 ATTCCCTCTATTCGCTTTTGTAAG 57.073 37.500 0.00 0.00 34.36 2.34
562 989 7.332557 TGTATTCCCTCTATTCGCTTTTGTAA 58.667 34.615 0.00 0.00 0.00 2.41
563 990 6.880484 TGTATTCCCTCTATTCGCTTTTGTA 58.120 36.000 0.00 0.00 0.00 2.41
564 991 5.741011 TGTATTCCCTCTATTCGCTTTTGT 58.259 37.500 0.00 0.00 0.00 2.83
565 992 6.867662 ATGTATTCCCTCTATTCGCTTTTG 57.132 37.500 0.00 0.00 0.00 2.44
605 1032 7.629222 GCATCAAAGTCTGCCATACATTTAACT 60.629 37.037 0.00 0.00 32.15 2.24
606 1033 6.473455 GCATCAAAGTCTGCCATACATTTAAC 59.527 38.462 0.00 0.00 32.15 2.01
607 1034 6.563422 GCATCAAAGTCTGCCATACATTTAA 58.437 36.000 0.00 0.00 32.15 1.52
608 1035 5.220835 CGCATCAAAGTCTGCCATACATTTA 60.221 40.000 0.00 0.00 34.89 1.40
609 1036 4.439153 CGCATCAAAGTCTGCCATACATTT 60.439 41.667 0.00 0.00 34.89 2.32
610 1037 3.065786 CGCATCAAAGTCTGCCATACATT 59.934 43.478 0.00 0.00 34.89 2.71
611 1038 2.615447 CGCATCAAAGTCTGCCATACAT 59.385 45.455 0.00 0.00 34.89 2.29
612 1039 2.009051 CGCATCAAAGTCTGCCATACA 58.991 47.619 0.00 0.00 34.89 2.29
613 1040 2.279741 TCGCATCAAAGTCTGCCATAC 58.720 47.619 0.00 0.00 34.89 2.39
614 1041 2.689553 TCGCATCAAAGTCTGCCATA 57.310 45.000 0.00 0.00 34.89 2.74
615 1042 1.825090 TTCGCATCAAAGTCTGCCAT 58.175 45.000 0.00 0.00 34.89 4.40
616 1043 1.603456 TTTCGCATCAAAGTCTGCCA 58.397 45.000 0.00 0.00 34.89 4.92
617 1044 2.927553 ATTTCGCATCAAAGTCTGCC 57.072 45.000 0.00 0.00 34.89 4.85
621 1048 3.544244 GCCTCGTATTTCGCATCAAAGTC 60.544 47.826 0.00 0.00 39.67 3.01
629 1056 0.734309 TAGTCGCCTCGTATTTCGCA 59.266 50.000 0.00 0.00 39.67 5.10
632 1059 5.981915 AGGTTTATTAGTCGCCTCGTATTTC 59.018 40.000 0.00 0.00 0.00 2.17
640 1067 2.835764 TGTCCAGGTTTATTAGTCGCCT 59.164 45.455 0.00 0.00 0.00 5.52
641 1068 3.255969 TGTCCAGGTTTATTAGTCGCC 57.744 47.619 0.00 0.00 0.00 5.54
684 1111 7.234187 TGACGAACTATGCACAAAATAGATC 57.766 36.000 0.00 0.00 32.85 2.75
722 1149 4.876125 TGCAATTTCCGCTTTGTTCATTA 58.124 34.783 0.00 0.00 0.00 1.90
735 1162 8.139989 AGTTCTATGATAAGCATTGCAATTTCC 58.860 33.333 9.83 1.20 38.44 3.13
908 1354 3.253838 CGGTGGTGGGGAAGGGAA 61.254 66.667 0.00 0.00 0.00 3.97
930 1376 3.369388 GAGAGGAGGGGAGGGGGT 61.369 72.222 0.00 0.00 0.00 4.95
932 1378 4.179599 GGGAGAGGAGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
934 1380 3.039526 AGGGGAGAGGAGGGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
936 1382 3.036959 GGAGGGGAGAGGAGGGGA 61.037 72.222 0.00 0.00 0.00 4.81
938 1384 4.179599 GGGGAGGGGAGAGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
1264 1731 2.202987 CAGATCCAGCACTCCGGC 60.203 66.667 0.00 0.00 0.00 6.13
1342 1815 3.043713 CATGTGCGTGTGCTCGGT 61.044 61.111 0.00 0.00 43.34 4.69
1650 2147 1.153745 GAAGGAGTCGATGCGCTGT 60.154 57.895 9.73 0.00 0.00 4.40
1779 2280 0.319383 CTCATTCTCCCCGCATCTCG 60.319 60.000 0.00 0.00 38.08 4.04
1952 2460 4.352088 GCTGTTGCAATCCACAGGATGG 62.352 54.545 16.05 0.00 42.27 3.51
1991 2528 7.201767 GCAGAAATGGCAAGAGATTTACATACT 60.202 37.037 0.00 0.00 0.00 2.12
2079 2621 3.733224 CGTGCTATTCACATACTCTCAGC 59.267 47.826 0.00 0.00 45.92 4.26
2082 2624 3.487574 GTGCGTGCTATTCACATACTCTC 59.512 47.826 0.00 0.00 45.92 3.20
2111 2657 2.679837 CCATTGCTGCGAACTAATGACT 59.320 45.455 10.22 0.00 33.50 3.41
2137 2686 0.608856 TTGCGGTGCCAGTGATGATT 60.609 50.000 0.00 0.00 0.00 2.57
2138 2687 1.002257 TTGCGGTGCCAGTGATGAT 60.002 52.632 0.00 0.00 0.00 2.45
2139 2688 1.965930 GTTGCGGTGCCAGTGATGA 60.966 57.895 0.00 0.00 0.00 2.92
2144 2693 2.112928 TGATGTTGCGGTGCCAGT 59.887 55.556 0.00 0.00 0.00 4.00
2157 2706 1.668419 GGAGGAATTCGGTGGTGATG 58.332 55.000 0.00 0.00 0.00 3.07
2183 2732 1.135083 CGGTGACTACTAAGCACCTGG 60.135 57.143 0.00 0.00 42.74 4.45
2184 2733 1.816835 TCGGTGACTACTAAGCACCTG 59.183 52.381 0.00 0.00 42.74 4.00
2398 2963 2.679837 TGACGACGGAGATGGTTAGTAC 59.320 50.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.