Multiple sequence alignment - TraesCS6B01G226800

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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 TraesCS6B01G226800 chr6B 100.000 5995 0 0 1 5995 348851225 348857219 0.000000e+00 11071.0
1 TraesCS6B01G226800 chr6B 90.323 682 61 4 1425 2101 349467492 349468173 0.000000e+00 889.0
2 TraesCS6B01G226800 chr6B 92.358 615 44 3 3398 4010 349468658 349469271 0.000000e+00 872.0
3 TraesCS6B01G226800 chr6B 89.985 689 49 14 4074 4746 349470590 349471274 0.000000e+00 872.0
4 TraesCS6B01G226800 chr6B 90.184 489 43 3 924 1411 349467020 349467504 3.050000e-177 632.0
5 TraesCS6B01G226800 chr6B 89.785 186 13 2 2988 3167 349468324 349468509 3.610000e-57 233.0
6 TraesCS6B01G226800 chr6B 84.211 190 24 3 5607 5791 551985575 551985387 4.770000e-41 180.0
7 TraesCS6B01G226800 chr6B 87.162 148 16 2 3209 3353 349468513 349468660 1.340000e-36 165.0
8 TraesCS6B01G226800 chr6A 92.869 3015 165 32 1 2979 324285935 324288935 0.000000e+00 4331.0
9 TraesCS6B01G226800 chr6A 95.959 2549 88 8 2981 5524 324291240 324293778 0.000000e+00 4122.0
10 TraesCS6B01G226800 chr6A 88.718 1365 108 20 3398 4746 326392750 326394084 0.000000e+00 1626.0
11 TraesCS6B01G226800 chr6A 88.340 1175 103 16 924 2089 326391064 326392213 0.000000e+00 1380.0
12 TraesCS6B01G226800 chr6A 90.343 466 31 9 5540 5995 324293840 324294301 3.090000e-167 599.0
13 TraesCS6B01G226800 chr6A 89.744 351 29 4 2988 3332 326392382 326392731 5.510000e-120 442.0
14 TraesCS6B01G226800 chr6A 82.203 118 16 4 5743 5857 548396742 548396857 4.950000e-16 97.1
15 TraesCS6B01G226800 chr6D 96.503 2545 75 4 2988 5524 262181803 262179265 0.000000e+00 4194.0
16 TraesCS6B01G226800 chr6D 93.567 2394 105 18 606 2979 262186464 262184100 0.000000e+00 3522.0
17 TraesCS6B01G226800 chr6D 88.970 1369 93 26 3398 4746 248507439 248506109 0.000000e+00 1639.0
18 TraesCS6B01G226800 chr6D 90.045 673 58 5 1425 2089 248508648 248507977 0.000000e+00 863.0
19 TraesCS6B01G226800 chr6D 93.458 535 25 9 1 535 262187198 262186674 0.000000e+00 785.0
20 TraesCS6B01G226800 chr6D 92.457 464 25 4 5540 5995 262179204 262178743 0.000000e+00 654.0
21 TraesCS6B01G226800 chr6D 89.366 489 47 3 924 1411 248509120 248508636 1.430000e-170 610.0
22 TraesCS6B01G226800 chr6D 89.785 372 32 3 2988 3353 248507808 248507437 7.030000e-129 472.0
23 TraesCS6B01G226800 chr6D 80.256 390 66 7 5591 5972 287676183 287675797 3.540000e-72 283.0
24 TraesCS6B01G226800 chr6D 81.651 218 33 2 5592 5802 390831502 390831719 2.220000e-39 174.0
25 TraesCS6B01G226800 chr6D 79.630 108 20 2 2685 2790 308887200 308887307 6.440000e-10 76.8
26 TraesCS6B01G226800 chrUn 92.268 388 23 6 4081 4463 480163773 480164158 1.470000e-150 544.0
27 TraesCS6B01G226800 chr7D 82.933 416 53 6 5590 5995 239045714 239046121 5.710000e-95 359.0
28 TraesCS6B01G226800 chr7A 78.610 374 61 14 5590 5949 231240353 231240721 4.670000e-56 230.0
29 TraesCS6B01G226800 chr4A 76.550 371 59 21 5607 5959 306112851 306112491 1.720000e-40 178.0
30 TraesCS6B01G226800 chr2D 77.972 286 41 14 5586 5857 93257421 93257698 6.220000e-35 159.0
31 TraesCS6B01G226800 chr1B 86.364 66 9 0 119 184 487923363 487923298 8.330000e-09 73.1
32 TraesCS6B01G226800 chr3B 89.130 46 3 2 5484 5529 53810750 53810793 8.390000e-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 TraesCS6B01G226800 chr6B 348851225 348857219 5994 False 11071.000000 11071 100.000000 1 5995 1 chr6B.!!$F1 5994
1 TraesCS6B01G226800 chr6B 349467020 349471274 4254 False 610.500000 889 89.966167 924 4746 6 chr6B.!!$F2 3822
2 TraesCS6B01G226800 chr6A 324285935 324294301 8366 False 3017.333333 4331 93.057000 1 5995 3 chr6A.!!$F2 5994
3 TraesCS6B01G226800 chr6A 326391064 326394084 3020 False 1149.333333 1626 88.934000 924 4746 3 chr6A.!!$F3 3822
4 TraesCS6B01G226800 chr6D 262178743 262187198 8455 True 2288.750000 4194 93.996250 1 5995 4 chr6D.!!$R3 5994
5 TraesCS6B01G226800 chr6D 248506109 248509120 3011 True 896.000000 1639 89.541500 924 4746 4 chr6D.!!$R2 3822

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
557 560 0.106217 GTGGGAGAGAGAGAGGGAGG 60.106 65.0 0.00 0.0 0.00 4.30 F
560 563 0.478507 GGAGAGAGAGAGGGAGGGAG 59.521 65.0 0.00 0.0 0.00 4.30 F
2376 2569 0.319083 ATAGAAACACGACACCCGCA 59.681 50.0 0.00 0.0 43.32 5.69 F
2839 3052 0.396435 ACACGGAGCCAGATCAAACA 59.604 50.0 0.00 0.0 0.00 2.83 F
2960 3173 0.534412 CAACACAAGGCAACCCAACA 59.466 50.0 0.00 0.0 37.17 3.33 F
3473 6025 0.813184 CCATGGCCAACTCACATGTC 59.187 55.0 10.96 0.0 40.16 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2569 1.660575 CGCTTTGGTGTCGACGACT 60.661 57.895 26.86 0.00 33.15 4.18 R
2426 2638 3.120385 CTTGTGCTCATCGCGGCA 61.120 61.111 6.13 4.65 43.27 5.69 R
3380 5931 0.320508 AACGAGGAACCGCTCTTTCC 60.321 55.000 0.00 0.67 42.68 3.13 R
4712 8573 2.605823 GGTATCTTCGATGACAGGAGCG 60.606 54.545 2.72 0.00 0.00 5.03 R
4808 8669 2.618053 ACCGATCTGGAAATGAACGTC 58.382 47.619 10.05 0.00 42.00 4.34 R
5356 9217 3.378112 GCAGTAGAGTAATTTGCCATGCA 59.622 43.478 0.00 0.00 36.47 3.96 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
88 89 7.692908 AAGTTCAACACATATTCAAAAACCG 57.307 32.000 0.00 0.00 0.00 4.44
101 102 3.675698 TCAAAAACCGTGCAGAAAAACAC 59.324 39.130 0.00 0.00 0.00 3.32
109 110 3.727673 CGTGCAGAAAAACACATATCCCG 60.728 47.826 0.00 0.00 36.57 5.14
514 517 0.537653 GAGAGGAAGTACAGGGCCAC 59.462 60.000 6.18 0.00 0.00 5.01
528 531 0.690744 GGCCACCCAAGCCCATAAAT 60.691 55.000 0.00 0.00 45.16 1.40
549 552 0.337773 AGGAGCATGTGGGAGAGAGA 59.662 55.000 0.00 0.00 0.00 3.10
550 553 0.752054 GGAGCATGTGGGAGAGAGAG 59.248 60.000 0.00 0.00 0.00 3.20
551 554 1.687682 GGAGCATGTGGGAGAGAGAGA 60.688 57.143 0.00 0.00 0.00 3.10
552 555 1.682854 GAGCATGTGGGAGAGAGAGAG 59.317 57.143 0.00 0.00 0.00 3.20
553 556 0.752054 GCATGTGGGAGAGAGAGAGG 59.248 60.000 0.00 0.00 0.00 3.69
554 557 1.412079 CATGTGGGAGAGAGAGAGGG 58.588 60.000 0.00 0.00 0.00 4.30
555 558 1.063341 CATGTGGGAGAGAGAGAGGGA 60.063 57.143 0.00 0.00 0.00 4.20
556 559 0.628522 TGTGGGAGAGAGAGAGGGAG 59.371 60.000 0.00 0.00 0.00 4.30
557 560 0.106217 GTGGGAGAGAGAGAGGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
558 561 1.292941 TGGGAGAGAGAGAGGGAGGG 61.293 65.000 0.00 0.00 0.00 4.30
559 562 0.996762 GGGAGAGAGAGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
560 563 0.478507 GGAGAGAGAGAGGGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
561 564 0.478507 GAGAGAGAGAGGGAGGGAGG 59.521 65.000 0.00 0.00 0.00 4.30
562 565 0.998945 AGAGAGAGAGGGAGGGAGGG 60.999 65.000 0.00 0.00 0.00 4.30
563 566 0.996762 GAGAGAGAGGGAGGGAGGGA 60.997 65.000 0.00 0.00 0.00 4.20
564 567 0.998945 AGAGAGAGGGAGGGAGGGAG 60.999 65.000 0.00 0.00 0.00 4.30
565 568 2.018086 AGAGAGGGAGGGAGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
566 569 3.039526 AGAGGGAGGGAGGGAGGG 61.040 72.222 0.00 0.00 0.00 4.30
595 598 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
681 853 9.959721 TGTTCTAAGATAGGTTATCTGCTTTTT 57.040 29.630 0.00 0.00 44.44 1.94
759 931 6.522054 TCCTTTTTCTTACTATCCTATGGCG 58.478 40.000 0.00 0.00 0.00 5.69
764 936 4.149598 TCTTACTATCCTATGGCGCTCAA 58.850 43.478 7.64 0.00 0.00 3.02
791 963 2.398554 CCACACATTCGCTTCCCCG 61.399 63.158 0.00 0.00 0.00 5.73
828 1000 2.517959 CTTTGGAGCTGGGAACAATGA 58.482 47.619 0.00 0.00 42.06 2.57
844 1016 4.769688 ACAATGAATGCGGAGTGAATAGA 58.230 39.130 0.00 0.00 0.00 1.98
849 1021 4.101585 TGAATGCGGAGTGAATAGATTCCT 59.898 41.667 0.00 0.00 35.97 3.36
850 1022 3.735237 TGCGGAGTGAATAGATTCCTC 57.265 47.619 10.13 10.13 35.97 3.71
886 1058 3.113260 AGACAGGAAGAACAAAGACCG 57.887 47.619 0.00 0.00 0.00 4.79
905 1077 6.678878 AGACCGAAGCCTTTAAAAAGATTTC 58.321 36.000 4.01 6.47 38.28 2.17
980 1152 6.017934 GCATGAATTAATTTAGCACGAGAGGA 60.018 38.462 1.43 0.00 0.00 3.71
1011 1183 7.663081 TGAATTCAGAAGACAATGTCTAGCTTT 59.337 33.333 17.04 8.43 42.59 3.51
1117 1289 1.980765 TCTTGAGGCCACTCTTGATGT 59.019 47.619 5.01 0.00 44.29 3.06
1148 1320 0.570272 CCGCGTTGTTTTCTTTGCAC 59.430 50.000 4.92 0.00 0.00 4.57
1308 1480 3.243907 CCGAGGAGGATATCACCAACTTC 60.244 52.174 16.75 7.57 45.00 3.01
1320 1492 1.412710 ACCAACTTCTTGAGCGAGTCA 59.587 47.619 0.00 0.00 0.00 3.41
1406 1578 5.070981 TGGCATACCTTTTGTTGATTCCAAA 59.929 36.000 0.00 0.00 36.63 3.28
1747 1925 2.887152 GGTGTTCTGCTTTGGTGAGATT 59.113 45.455 0.00 0.00 0.00 2.40
1852 2040 8.718734 CAGTTATTTCCTTACCTTGTACTGAAC 58.281 37.037 0.00 0.00 33.04 3.18
1874 2062 2.991190 CAGCAAGTTGATCAATGTTGCC 59.009 45.455 33.38 23.44 40.79 4.52
1922 2110 8.489489 AGAGCAATCAATACAAAGAAGGATCTA 58.511 33.333 0.00 0.00 33.77 1.98
1967 2155 3.134458 CCACACTCTTTGTCTCAACTCC 58.866 50.000 0.00 0.00 35.67 3.85
2191 2384 0.905337 ACAAAGTAGCGAGGGAGCCT 60.905 55.000 0.00 0.00 38.01 4.58
2220 2413 4.080356 CACAACATATCCCGGGATATCCAT 60.080 45.833 41.42 29.81 43.59 3.41
2238 2431 5.570205 TCCATACAACCTAAAAGGACACA 57.430 39.130 0.00 0.00 37.67 3.72
2249 2442 7.742767 ACCTAAAAGGACACAACTACATTACT 58.257 34.615 0.00 0.00 37.67 2.24
2273 2466 7.094463 ACTGAAAGATAATATAAGCATGCCTGC 60.094 37.037 15.66 5.76 43.24 4.85
2363 2556 4.062293 CACAACAACGTCCTCCATAGAAA 58.938 43.478 0.00 0.00 0.00 2.52
2376 2569 0.319083 ATAGAAACACGACACCCGCA 59.681 50.000 0.00 0.00 43.32 5.69
2386 2579 4.337060 CACCCGCAGTCGTCGACA 62.337 66.667 26.17 0.00 34.60 4.35
2396 2589 0.661187 GTCGTCGACACCAAAGCGTA 60.661 55.000 20.28 0.00 32.09 4.42
2426 2638 2.175202 CTCAGTAGCTCACCCAGAACT 58.825 52.381 0.00 0.00 0.00 3.01
2427 2639 1.895798 TCAGTAGCTCACCCAGAACTG 59.104 52.381 0.00 0.00 38.29 3.16
2484 2696 0.958382 GACGCCACTGCCCACAATAA 60.958 55.000 0.00 0.00 0.00 1.40
2490 2702 2.890311 CCACTGCCCACAATAAAGAACA 59.110 45.455 0.00 0.00 0.00 3.18
2605 2817 2.676265 GCGGACCACCATAAGGGGT 61.676 63.158 0.00 0.00 43.56 4.95
2608 2820 1.525442 GACCACCATAAGGGGTCGG 59.475 63.158 8.34 0.00 41.94 4.79
2637 2849 3.110705 ACATCCATGCTCCTAGACACTT 58.889 45.455 0.00 0.00 0.00 3.16
2638 2850 3.118482 ACATCCATGCTCCTAGACACTTG 60.118 47.826 0.00 0.00 0.00 3.16
2750 2962 1.077805 TGCCTCCACGGTAGGAAGA 59.922 57.895 1.04 0.00 37.20 2.87
2752 2964 0.971447 GCCTCCACGGTAGGAAGAGT 60.971 60.000 1.04 0.00 37.20 3.24
2839 3052 0.396435 ACACGGAGCCAGATCAAACA 59.604 50.000 0.00 0.00 0.00 2.83
2869 3082 3.771160 GGCCACCGGTGTCGATCT 61.771 66.667 31.80 0.00 39.00 2.75
2883 3096 2.638329 GATCTGTTCGACGACACGG 58.362 57.895 0.00 4.94 0.00 4.94
2925 3138 2.278989 ACCGACGTCACCAACACG 60.279 61.111 17.16 0.00 43.13 4.49
2945 3158 1.942657 GCAACAGAGAAGAGCACAACA 59.057 47.619 0.00 0.00 0.00 3.33
2960 3173 0.534412 CAACACAAGGCAACCCAACA 59.466 50.000 0.00 0.00 37.17 3.33
2965 3178 1.285578 CAAGGCAACCCAACAAAACG 58.714 50.000 0.00 0.00 37.17 3.60
2979 3192 3.199677 ACAAAACGAAATCACTCCGTCA 58.800 40.909 0.00 0.00 35.28 4.35
2981 3194 4.274950 ACAAAACGAAATCACTCCGTCATT 59.725 37.500 0.00 0.00 35.28 2.57
2982 3195 5.212194 CAAAACGAAATCACTCCGTCATTT 58.788 37.500 0.00 0.00 35.28 2.32
3088 5632 4.087507 GCTTTGCAACGGATAAAAACGTAC 59.912 41.667 0.00 0.00 43.31 3.67
3122 5666 1.671054 CGTTGTCATCGGCCTGGTT 60.671 57.895 0.00 0.00 0.00 3.67
3252 5799 5.757808 ACAAGCTTTGTTTTGTTTGTGTCTT 59.242 32.000 0.00 0.00 42.22 3.01
3356 5907 6.618287 TCCTTGTGTCTCAATTAGTTTGTG 57.382 37.500 0.00 0.00 36.65 3.33
3453 6005 5.723672 AAGATACGATGGGATATGTCGTT 57.276 39.130 4.94 0.00 45.27 3.85
3458 6010 2.995939 CGATGGGATATGTCGTTCCATG 59.004 50.000 3.93 0.00 38.23 3.66
3473 6025 0.813184 CCATGGCCAACTCACATGTC 59.187 55.000 10.96 0.00 40.16 3.06
3590 6145 5.543790 AGTTCTTGGTTTGCTATCCCAAATT 59.456 36.000 0.00 0.00 37.77 1.82
3602 6157 6.040391 TGCTATCCCAAATTATAAAGGTGTGC 59.960 38.462 0.00 0.00 0.00 4.57
3701 6257 8.366401 TGAATGCTATCTTTCCAAATTGTTTCA 58.634 29.630 0.00 0.00 0.00 2.69
3951 6507 5.184892 ACTTCCATATCAAGAAAGCAGGT 57.815 39.130 0.00 0.00 0.00 4.00
4140 7983 4.447724 TGCGAGAATAAACACTGTGACTTC 59.552 41.667 15.86 10.64 0.00 3.01
4207 8050 5.064707 TGACGGCTATTTCAGAAATGCTAAC 59.935 40.000 17.38 12.74 32.38 2.34
4215 8058 7.951530 ATTTCAGAAATGCTAACACAAAAGG 57.048 32.000 7.64 0.00 0.00 3.11
4627 8482 6.151985 ACAACTTTGTAACTGTGGAAATGTCA 59.848 34.615 0.00 0.00 40.16 3.58
4630 8485 8.458573 ACTTTGTAACTGTGGAAATGTCATTA 57.541 30.769 0.00 0.00 0.00 1.90
4712 8573 8.184192 AGAAATGGTTTATCATCGAACAATGTC 58.816 33.333 0.00 0.00 0.00 3.06
4801 8662 8.940768 TTAGCCTTGAAATATATTTTTGGCAC 57.059 30.769 29.96 14.52 39.64 5.01
4808 8669 9.868277 TTGAAATATATTTTTGGCACCTTACAG 57.132 29.630 11.92 0.00 0.00 2.74
5024 8885 4.508124 AGCTGACGTTTTCTAGAAGTGTTG 59.492 41.667 5.12 4.90 0.00 3.33
5141 9002 4.942852 TCGAAGGAACAATGCAAACATTT 58.057 34.783 0.00 0.00 44.21 2.32
5343 9204 6.484643 GGCAATTCTCTCTACTGCATTATGAA 59.515 38.462 0.00 0.00 34.66 2.57
5350 9211 8.489489 TCTCTCTACTGCATTATGAAAAATCCT 58.511 33.333 0.00 0.00 0.00 3.24
5380 9241 4.142403 GCATGGCAAATTACTCTACTGCAA 60.142 41.667 0.00 0.00 34.66 4.08
5418 9279 5.824904 ACAAATCTTTTCGCTAGCATGAT 57.175 34.783 16.45 5.87 0.00 2.45
5457 9318 9.288576 TCACATGGCAAATCTTTCTATAATAGG 57.711 33.333 0.00 0.00 0.00 2.57
5577 9484 1.811965 CATGCAAGGAACGTCCATTCA 59.188 47.619 0.00 0.00 39.61 2.57
5655 9563 0.255033 TGGAAGTCTCGGATCGGAGA 59.745 55.000 24.61 24.61 40.64 3.71
5674 9586 3.673484 CGCACAAAGGCCCAGGTG 61.673 66.667 12.55 12.55 0.00 4.00
5761 9673 4.122046 TCATGCGAGAGATTACAATGGTG 58.878 43.478 0.00 0.00 0.00 4.17
5864 9776 2.740447 GTCAAGGGTTTACACGATGGTC 59.260 50.000 0.00 0.00 0.00 4.02
5880 9797 1.270094 TGGTCGATCTTCAGCGTTGTT 60.270 47.619 0.00 0.00 0.00 2.83
5912 9829 0.747852 GAGGGCTAGAAGGTCTTCGG 59.252 60.000 0.00 4.35 43.97 4.30
5921 9838 4.516195 GGTCTTCGGCGCTCCCTC 62.516 72.222 7.64 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 4.742167 TGCACGGTTTTTGAATATGTGTTG 59.258 37.500 0.00 0.00 0.00 3.33
88 89 3.438781 TCGGGATATGTGTTTTTCTGCAC 59.561 43.478 0.00 0.00 36.26 4.57
101 102 6.098679 TGCTTTGAACATTTTTCGGGATATG 58.901 36.000 0.00 0.00 0.00 1.78
109 110 8.351495 TCAAGTACATGCTTTGAACATTTTTC 57.649 30.769 0.00 0.00 0.00 2.29
371 374 5.923114 GCATTGGGTTTTTCTCTTTCTTCTC 59.077 40.000 0.00 0.00 0.00 2.87
373 376 5.600696 TGCATTGGGTTTTTCTCTTTCTTC 58.399 37.500 0.00 0.00 0.00 2.87
379 382 5.070847 ACTGATTTGCATTGGGTTTTTCTCT 59.929 36.000 0.00 0.00 0.00 3.10
380 383 5.178067 CACTGATTTGCATTGGGTTTTTCTC 59.822 40.000 0.00 0.00 0.00 2.87
381 384 5.058490 CACTGATTTGCATTGGGTTTTTCT 58.942 37.500 0.00 0.00 0.00 2.52
382 385 5.055812 TCACTGATTTGCATTGGGTTTTTC 58.944 37.500 0.00 0.00 0.00 2.29
482 485 2.833631 TCCTCTCGACTTTTGTTCCC 57.166 50.000 0.00 0.00 0.00 3.97
514 517 2.590821 CTCCTCATTTATGGGCTTGGG 58.409 52.381 0.00 0.00 0.00 4.12
528 531 0.041684 TCTCTCCCACATGCTCCTCA 59.958 55.000 0.00 0.00 0.00 3.86
549 552 3.039526 CCCTCCCTCCCTCCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
550 553 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
551 554 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
552 555 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
553 556 2.015726 TCTCTCCCTCCCTCCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
554 557 0.996762 TCTCTCTCCCTCCCTCCCTC 60.997 65.000 0.00 0.00 0.00 4.30
555 558 0.998945 CTCTCTCTCCCTCCCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
556 559 0.996762 TCTCTCTCTCCCTCCCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
557 560 0.478507 CTCTCTCTCTCCCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
558 561 1.421646 CTCTCTCTCTCTCCCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
559 562 1.010793 TCTCTCTCTCTCTCCCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
560 563 1.421646 CTCTCTCTCTCTCTCCCTCCC 59.578 61.905 0.00 0.00 0.00 4.30
561 564 2.370189 CTCTCTCTCTCTCTCTCCCTCC 59.630 59.091 0.00 0.00 0.00 4.30
562 565 3.309296 TCTCTCTCTCTCTCTCTCCCTC 58.691 54.545 0.00 0.00 0.00 4.30
563 566 3.051803 TCTCTCTCTCTCTCTCTCTCCCT 60.052 52.174 0.00 0.00 0.00 4.20
564 567 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
565 568 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
566 569 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
595 598 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
759 931 1.680735 TGTGTGGTTGGATTGTTGAGC 59.319 47.619 0.00 0.00 0.00 4.26
764 936 1.269448 GCGAATGTGTGGTTGGATTGT 59.731 47.619 0.00 0.00 0.00 2.71
791 963 3.186613 CCAAAGCGAACTCCAAGAACTAC 59.813 47.826 0.00 0.00 0.00 2.73
828 1000 4.636249 GAGGAATCTATTCACTCCGCATT 58.364 43.478 5.15 0.00 38.53 3.56
849 1021 3.437213 TGTCTTCCTTCCTCCAATACGA 58.563 45.455 0.00 0.00 0.00 3.43
850 1022 3.430929 CCTGTCTTCCTTCCTCCAATACG 60.431 52.174 0.00 0.00 0.00 3.06
886 1058 9.278734 CGATACAGAAATCTTTTTAAAGGCTTC 57.721 33.333 0.00 5.96 36.67 3.86
905 1077 3.915437 AAACCAACCTTTGCGATACAG 57.085 42.857 0.00 0.00 0.00 2.74
980 1152 8.230472 AGACATTGTCTTCTGAATTCAGTTTT 57.770 30.769 29.80 10.46 40.28 2.43
1011 1183 3.904800 TCAGAGACAAGAACACCAACA 57.095 42.857 0.00 0.00 0.00 3.33
1117 1289 3.357166 ACAACGCGGCTTTTCAAAATA 57.643 38.095 12.47 0.00 0.00 1.40
1308 1480 1.751351 TCAGGGTATGACTCGCTCAAG 59.249 52.381 0.00 0.00 31.12 3.02
1320 1492 6.519043 CGATTGACTGGTTCATATCAGGGTAT 60.519 42.308 0.00 0.00 35.47 2.73
1523 1701 3.243359 TCTTTTGGCCTCCTGATTTGT 57.757 42.857 3.32 0.00 0.00 2.83
1668 1846 5.248934 TGGATCCAATGGCAAGAAATTCTTT 59.751 36.000 13.46 0.00 33.78 2.52
1852 2040 2.991190 GCAACATTGATCAACTTGCTGG 59.009 45.455 29.16 13.99 35.78 4.85
1922 2110 2.171448 CTCATTCCTCTCCCACGGATTT 59.829 50.000 0.00 0.00 0.00 2.17
1928 2116 1.909302 TGGTTCTCATTCCTCTCCCAC 59.091 52.381 0.00 0.00 0.00 4.61
1967 2155 3.814268 CAACCAATGGCCTCGGCG 61.814 66.667 3.32 0.00 43.06 6.46
2136 2329 8.357402 CCTGTACTTTGGTTTGCTAGTTTAAAT 58.643 33.333 0.00 0.00 0.00 1.40
2140 2333 5.442391 TCCTGTACTTTGGTTTGCTAGTTT 58.558 37.500 0.00 0.00 0.00 2.66
2191 2384 3.775866 TCCCGGGATATGTTGTGTAAGAA 59.224 43.478 22.63 0.00 0.00 2.52
2220 2413 6.887013 TGTAGTTGTGTCCTTTTAGGTTGTA 58.113 36.000 0.00 0.00 36.53 2.41
2273 2466 3.931907 TTCCCCTCCTGATGTTGTATG 57.068 47.619 0.00 0.00 0.00 2.39
2376 2569 1.660575 CGCTTTGGTGTCGACGACT 60.661 57.895 26.86 0.00 33.15 4.18
2386 2579 4.246458 GAGTGAAAGATCTACGCTTTGGT 58.754 43.478 14.25 0.00 35.83 3.67
2396 2589 4.159506 GGTGAGCTACTGAGTGAAAGATCT 59.840 45.833 0.00 0.00 0.00 2.75
2426 2638 3.120385 CTTGTGCTCATCGCGGCA 61.120 61.111 6.13 4.65 43.27 5.69
2427 2639 4.527157 GCTTGTGCTCATCGCGGC 62.527 66.667 6.13 1.26 43.27 6.53
2484 2696 3.552384 TGGCCCCGACGTGTTCTT 61.552 61.111 0.00 0.00 0.00 2.52
2637 2849 2.646930 GTCATGAGATGGATGGTTGCA 58.353 47.619 0.00 0.00 0.00 4.08
2638 2850 1.952296 GGTCATGAGATGGATGGTTGC 59.048 52.381 0.00 0.00 0.00 4.17
2750 2962 0.252284 CTGGGAGGTAGGTGTGGACT 60.252 60.000 0.00 0.00 0.00 3.85
2752 2964 0.252103 GACTGGGAGGTAGGTGTGGA 60.252 60.000 0.00 0.00 0.00 4.02
2829 3042 1.133025 GGAATGGCGGTGTTTGATCTG 59.867 52.381 0.00 0.00 0.00 2.90
2869 3082 2.104530 TTGCCGTGTCGTCGAACA 59.895 55.556 0.00 0.00 0.00 3.18
2925 3138 1.942657 TGTTGTGCTCTTCTCTGTTGC 59.057 47.619 0.00 0.00 0.00 4.17
2945 3158 1.404851 CGTTTTGTTGGGTTGCCTTGT 60.405 47.619 0.00 0.00 0.00 3.16
2979 3192 6.393171 GTTAAGAGCCTCAAAATGCAGAAAT 58.607 36.000 0.00 0.00 0.00 2.17
2981 3194 4.218417 GGTTAAGAGCCTCAAAATGCAGAA 59.782 41.667 0.00 0.00 0.00 3.02
2982 3195 3.758554 GGTTAAGAGCCTCAAAATGCAGA 59.241 43.478 0.00 0.00 0.00 4.26
3088 5632 2.812178 CGCCTTAACACGACCGGG 60.812 66.667 6.32 0.00 0.00 5.73
3376 5927 1.128188 AGGAACCGCTCTTTCCCACT 61.128 55.000 4.66 0.00 43.29 4.00
3380 5931 0.320508 AACGAGGAACCGCTCTTTCC 60.321 55.000 0.00 0.67 42.68 3.13
3453 6005 0.405198 ACATGTGAGTTGGCCATGGA 59.595 50.000 18.40 0.00 40.16 3.41
3458 6010 1.538047 ACATGACATGTGAGTTGGCC 58.462 50.000 20.21 0.00 43.01 5.36
3473 6025 7.987268 TTGCTAGAATCTTTACTCGTACATG 57.013 36.000 0.00 0.00 0.00 3.21
3533 6088 7.643528 CTGAAAAAGGAAAAATACTTCAGCC 57.356 36.000 0.00 0.00 33.95 4.85
3590 6145 6.428771 GTGGTTGTAGAAAGCACACCTTTATA 59.571 38.462 13.79 0.00 43.64 0.98
3602 6157 4.641396 TCAGTGATGGTGGTTGTAGAAAG 58.359 43.478 0.00 0.00 0.00 2.62
3701 6257 6.667414 AGAGTTGTATCTGAGAGAAGTCCAAT 59.333 38.462 11.89 0.00 0.00 3.16
4095 7933 6.910433 CGCAAAACAAAGTCACAGTATTTACT 59.090 34.615 0.00 0.00 36.90 2.24
4112 7950 5.065346 TCACAGTGTTTATTCTCGCAAAACA 59.935 36.000 0.00 0.00 39.95 2.83
4113 7951 5.395486 GTCACAGTGTTTATTCTCGCAAAAC 59.605 40.000 0.00 0.00 34.45 2.43
4140 7983 4.456911 CAGGGCTACATAAACATGCCATAG 59.543 45.833 0.00 0.00 44.85 2.23
4207 8050 6.420604 ACGAAAGCATAATGAAACCTTTTGTG 59.579 34.615 0.00 0.00 38.21 3.33
4630 8485 9.492973 CATTAACCTGGAGAAAATGTTTGAAAT 57.507 29.630 0.00 0.00 0.00 2.17
4676 8537 7.517614 TGATAAACCATTTCTGCACAAGTTA 57.482 32.000 0.00 0.00 0.00 2.24
4712 8573 2.605823 GGTATCTTCGATGACAGGAGCG 60.606 54.545 2.72 0.00 0.00 5.03
4801 8662 4.566004 TCTGGAAATGAACGTCTGTAAGG 58.434 43.478 0.00 0.00 0.00 2.69
4808 8669 2.618053 ACCGATCTGGAAATGAACGTC 58.382 47.619 10.05 0.00 42.00 4.34
5024 8885 4.637977 CCAGAGAGCATTCCCTAGAAAAAC 59.362 45.833 0.00 0.00 35.09 2.43
5141 9002 3.837731 TCTCTGGATGGTGTATGTGAACA 59.162 43.478 0.00 0.00 0.00 3.18
5343 9204 4.289238 TGCCATGCATTTCAAGGATTTT 57.711 36.364 0.00 0.00 35.62 1.82
5350 9211 6.040209 AGAGTAATTTGCCATGCATTTCAA 57.960 33.333 0.00 0.90 38.76 2.69
5356 9217 3.378112 GCAGTAGAGTAATTTGCCATGCA 59.622 43.478 0.00 0.00 36.47 3.96
5418 9279 9.206870 GATTTGCCATGTGAAAGAGAAAAATTA 57.793 29.630 0.00 0.00 0.00 1.40
5577 9484 3.688694 TTGCACCGTTAGTATCCAAGT 57.311 42.857 0.00 0.00 0.00 3.16
5655 9563 2.361610 CCTGGGCCTTTGTGCGAT 60.362 61.111 4.53 0.00 0.00 4.58
5674 9586 1.411041 ATTACTCTACGGAGGCCCAC 58.589 55.000 0.00 0.00 43.46 4.61
5741 9653 4.142609 ACACCATTGTAATCTCTCGCAT 57.857 40.909 0.00 0.00 32.60 4.73
5748 9660 5.590259 GCAACCTCATACACCATTGTAATCT 59.410 40.000 0.00 0.00 41.64 2.40
5761 9673 3.858247 ACTTTCGGTAGCAACCTCATAC 58.142 45.455 0.00 0.00 44.35 2.39
5864 9776 0.179215 GGCAACAACGCTGAAGATCG 60.179 55.000 0.00 0.00 0.00 3.69
5880 9797 3.170362 CCCTCCAAGACAAGGGCA 58.830 61.111 0.00 0.00 45.63 5.36
5921 9838 4.009015 GGCAAAGGAGAAGCCCTG 57.991 61.111 0.00 0.00 42.58 4.45
5947 9864 0.613260 GTGTCTATCACAGGCCCACA 59.387 55.000 0.00 0.00 45.51 4.17


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

AutoCloner maintained by Alex Coulton.