Multiple sequence alignment - TraesCS2D01G023800

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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 TraesCS2D01G023800 chr2D 100.000 4355 0 0 1 4355 10713123 10717477 0.000000e+00 8043
1 TraesCS2D01G023800 chr2D 78.159 554 115 5 1 551 6729392 6728842 8.960000e-92 348
2 TraesCS2D01G023800 chr2B 90.095 2726 215 28 982 3669 14172988 14175696 0.000000e+00 3487
3 TraesCS2D01G023800 chr2B 96.915 551 17 0 1 551 598570034 598570584 0.000000e+00 924
4 TraesCS2D01G023800 chr2B 88.657 767 59 11 677 1415 14808395 14809161 0.000000e+00 909
5 TraesCS2D01G023800 chr2B 75.088 855 171 35 2465 3295 14477572 14476736 1.150000e-95 361
6 TraesCS2D01G023800 chr2B 74.942 862 157 41 2465 3295 14434061 14433228 1.500000e-89 340
7 TraesCS2D01G023800 chr2B 74.826 862 158 42 2465 3295 14459654 14458821 6.980000e-88 335
8 TraesCS2D01G023800 chr2B 73.754 903 190 36 2465 3336 14349961 14349075 1.180000e-80 311
9 TraesCS2D01G023800 chr2B 73.462 878 187 41 2474 3328 14405595 14404741 5.510000e-74 289
10 TraesCS2D01G023800 chr2B 73.303 884 178 47 2474 3328 14212632 14211778 5.550000e-69 272
11 TraesCS2D01G023800 chr2B 79.817 327 64 2 1741 2066 15462807 15463132 2.020000e-58 237
12 TraesCS2D01G023800 chr2B 73.786 721 131 43 2703 3385 14421314 14420614 9.420000e-57 231
13 TraesCS2D01G023800 chr2B 78.689 305 62 1 1752 2056 14618859 14618558 2.660000e-47 200
14 TraesCS2D01G023800 chr2B 80.000 260 42 10 3058 3312 14423139 14422885 2.680000e-42 183
15 TraesCS2D01G023800 chr2B 79.008 262 51 2 1743 2002 14213457 14213198 4.480000e-40 176
16 TraesCS2D01G023800 chr2B 79.245 265 45 7 1743 2002 14406442 14406183 4.480000e-40 176
17 TraesCS2D01G023800 chr2B 94.118 102 6 0 712 813 14172535 14172636 5.830000e-34 156
18 TraesCS2D01G023800 chr2B 90.816 98 5 2 555 648 14168923 14169020 1.270000e-25 128
19 TraesCS2D01G023800 chr2B 90.909 99 4 4 555 648 14808187 14808285 1.270000e-25 128
20 TraesCS2D01G023800 chr2B 78.035 173 38 0 1894 2066 13911275 13911447 4.600000e-20 110
21 TraesCS2D01G023800 chr2A 92.407 2239 131 16 1645 3853 10981542 10983771 0.000000e+00 3157
22 TraesCS2D01G023800 chr2A 91.975 947 67 6 677 1614 10980596 10981542 0.000000e+00 1319
23 TraesCS2D01G023800 chr2A 93.256 519 24 3 3837 4355 10984305 10984812 0.000000e+00 754
24 TraesCS2D01G023800 chr2A 74.943 874 168 40 2467 3312 10844412 10843562 1.930000e-93 353
25 TraesCS2D01G023800 chr2A 79.439 321 64 2 1747 2066 10736023 10735704 4.380000e-55 226
26 TraesCS2D01G023800 chr2A 78.405 301 65 0 1747 2047 10845123 10844823 3.440000e-46 196
27 TraesCS2D01G023800 chr2A 78.764 259 52 2 1298 1553 10751168 10750910 2.080000e-38 171
28 TraesCS2D01G023800 chr7D 98.911 551 6 0 1 551 56994110 56993560 0.000000e+00 985
29 TraesCS2D01G023800 chr7D 96.033 479 18 1 1 479 45586357 45586834 0.000000e+00 778
30 TraesCS2D01G023800 chr4B 96.007 551 22 0 1 551 479409849 479409299 0.000000e+00 896
31 TraesCS2D01G023800 chr5B 95.644 551 24 0 1 551 57942978 57942428 0.000000e+00 885
32 TraesCS2D01G023800 chrUn 98.280 407 7 0 145 551 95302071 95302477 0.000000e+00 713
33 TraesCS2D01G023800 chr6B 86.196 623 68 10 3468 4086 523018981 523018373 0.000000e+00 658
34 TraesCS2D01G023800 chr3B 95.473 243 11 0 1 243 60739376 60739134 5.280000e-104 388


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 TraesCS2D01G023800 chr2D 10713123 10717477 4354 False 8043.000000 8043 100.000000 1 4355 1 chr2D.!!$F1 4354
1 TraesCS2D01G023800 chr2D 6728842 6729392 550 True 348.000000 348 78.159000 1 551 1 chr2D.!!$R1 550
2 TraesCS2D01G023800 chr2B 14168923 14175696 6773 False 1257.000000 3487 91.676333 555 3669 3 chr2B.!!$F4 3114
3 TraesCS2D01G023800 chr2B 598570034 598570584 550 False 924.000000 924 96.915000 1 551 1 chr2B.!!$F3 550
4 TraesCS2D01G023800 chr2B 14808187 14809161 974 False 518.500000 909 89.783000 555 1415 2 chr2B.!!$F5 860
5 TraesCS2D01G023800 chr2B 14476736 14477572 836 True 361.000000 361 75.088000 2465 3295 1 chr2B.!!$R4 830
6 TraesCS2D01G023800 chr2B 14433228 14434061 833 True 340.000000 340 74.942000 2465 3295 1 chr2B.!!$R2 830
7 TraesCS2D01G023800 chr2B 14458821 14459654 833 True 335.000000 335 74.826000 2465 3295 1 chr2B.!!$R3 830
8 TraesCS2D01G023800 chr2B 14349075 14349961 886 True 311.000000 311 73.754000 2465 3336 1 chr2B.!!$R1 871
9 TraesCS2D01G023800 chr2B 14404741 14406442 1701 True 232.500000 289 76.353500 1743 3328 2 chr2B.!!$R7 1585
10 TraesCS2D01G023800 chr2B 14211778 14213457 1679 True 224.000000 272 76.155500 1743 3328 2 chr2B.!!$R6 1585
11 TraesCS2D01G023800 chr2B 14420614 14423139 2525 True 207.000000 231 76.893000 2703 3385 2 chr2B.!!$R8 682
12 TraesCS2D01G023800 chr2A 10980596 10984812 4216 False 1743.333333 3157 92.546000 677 4355 3 chr2A.!!$F1 3678
13 TraesCS2D01G023800 chr2A 10843562 10845123 1561 True 274.500000 353 76.674000 1747 3312 2 chr2A.!!$R3 1565
14 TraesCS2D01G023800 chr7D 56993560 56994110 550 True 985.000000 985 98.911000 1 551 1 chr7D.!!$R1 550
15 TraesCS2D01G023800 chr4B 479409299 479409849 550 True 896.000000 896 96.007000 1 551 1 chr4B.!!$R1 550
16 TraesCS2D01G023800 chr5B 57942428 57942978 550 True 885.000000 885 95.644000 1 551 1 chr5B.!!$R1 550
17 TraesCS2D01G023800 chr6B 523018373 523018981 608 True 658.000000 658 86.196000 3468 4086 1 chr6B.!!$R1 618

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
165 166 0.398098 GGACTCAACGGATCCCCCTA 60.398 60.0 6.06 0.0 0.00 3.53 F
1382 5054 0.037877 AGCCTGCAATGCTCAGACTT 59.962 50.0 6.82 0.0 29.23 3.01 F
1524 5196 0.250901 TTCTGCAGCCTTGAGGTTCC 60.251 55.0 9.47 0.0 37.57 3.62 F
1744 5416 1.023513 GTGCACTCCAGAGGCATGAC 61.024 60.0 10.32 0.0 37.12 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 5183 0.323957 GTAACCGGAACCTCAAGGCT 59.676 55.000 9.46 0.0 39.32 4.58 R
2248 5986 1.600957 CGCAATGGAAGCACTCTATGG 59.399 52.381 0.00 0.0 0.00 2.74 R
2604 6416 1.664151 CTTACCGCATCCCGAAGAAAC 59.336 52.381 0.00 0.0 40.02 2.78 R
3586 7472 0.250234 GGGATCGCTGCATATAGCCA 59.750 55.000 1.84 0.0 44.83 4.75 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
165 166 0.398098 GGACTCAACGGATCCCCCTA 60.398 60.000 6.06 0.00 0.00 3.53
301 302 3.448686 CAGTTGTATAAGAGCACCCTCG 58.551 50.000 0.00 0.00 43.05 4.63
552 553 3.328382 AACGTTGCAGAGGCTTATGTA 57.672 42.857 0.00 0.00 41.91 2.29
553 554 2.893637 ACGTTGCAGAGGCTTATGTAG 58.106 47.619 0.00 0.00 41.91 2.74
578 579 6.592798 TCAAACACGGTTTTTCTACTACAG 57.407 37.500 0.03 0.00 0.00 2.74
628 635 7.649057 AGACCAAACAGTAAAAATAGCTTCAC 58.351 34.615 0.00 0.00 0.00 3.18
648 655 7.066766 GCTTCACAATCCTAAAATCTGATCAGT 59.933 37.037 21.92 7.26 0.00 3.41
650 657 7.397221 TCACAATCCTAAAATCTGATCAGTGT 58.603 34.615 21.92 11.79 31.67 3.55
652 659 7.335171 CACAATCCTAAAATCTGATCAGTGTCA 59.665 37.037 21.92 3.34 0.00 3.58
655 662 6.351711 TCCTAAAATCTGATCAGTGTCATGG 58.648 40.000 21.92 17.12 0.00 3.66
658 665 2.391616 TCTGATCAGTGTCATGGCAC 57.608 50.000 22.91 22.91 39.51 5.01
674 681 1.340114 GGCACAGGTTTAAGGGGAGAG 60.340 57.143 0.00 0.00 0.00 3.20
675 682 1.628846 GCACAGGTTTAAGGGGAGAGA 59.371 52.381 0.00 0.00 0.00 3.10
801 4260 4.526970 ACACGAAATAGGATTTCATGCCT 58.473 39.130 7.66 0.00 38.31 4.75
915 4454 7.333528 TCTGCTTACTTTGAAACAACAATCT 57.666 32.000 0.00 0.00 0.00 2.40
937 4476 2.629336 ATTGGCTTGGTAGCTAGAGC 57.371 50.000 7.59 12.87 46.90 4.09
965 4504 2.432510 GCTCCCTAGTGCTGTCAAGTAT 59.567 50.000 0.00 0.00 0.00 2.12
967 4506 4.099573 GCTCCCTAGTGCTGTCAAGTATTA 59.900 45.833 0.00 0.00 0.00 0.98
968 4507 5.737635 GCTCCCTAGTGCTGTCAAGTATTAG 60.738 48.000 0.00 0.00 31.01 1.73
971 4510 5.395768 CCCTAGTGCTGTCAAGTATTAGCTT 60.396 44.000 0.00 0.00 37.10 3.74
972 4511 5.521735 CCTAGTGCTGTCAAGTATTAGCTTG 59.478 44.000 0.00 0.00 45.18 4.01
974 4513 4.020218 AGTGCTGTCAAGTATTAGCTTGGA 60.020 41.667 0.00 0.00 44.26 3.53
975 4514 4.331168 GTGCTGTCAAGTATTAGCTTGGAG 59.669 45.833 0.00 4.43 44.26 3.86
976 4515 4.020218 TGCTGTCAAGTATTAGCTTGGAGT 60.020 41.667 0.00 0.00 44.26 3.85
977 4516 5.186992 TGCTGTCAAGTATTAGCTTGGAGTA 59.813 40.000 0.00 0.97 44.26 2.59
978 4517 5.520649 GCTGTCAAGTATTAGCTTGGAGTAC 59.479 44.000 0.00 0.00 44.26 2.73
979 4518 5.647589 TGTCAAGTATTAGCTTGGAGTACG 58.352 41.667 0.00 0.00 44.26 3.67
980 4519 5.184479 TGTCAAGTATTAGCTTGGAGTACGT 59.816 40.000 0.00 0.00 44.26 3.57
1003 4674 0.541392 AGATTGCTGCCGTACCATGA 59.459 50.000 0.00 0.00 0.00 3.07
1018 4689 3.925630 ATGACCTGGCAGCCAACGG 62.926 63.158 17.03 16.84 30.80 4.44
1128 4799 3.697747 CGGTCGGCCAACTACCCA 61.698 66.667 6.96 0.00 34.09 4.51
1271 4943 0.375454 TTAATACGTGTGCGCATGCC 59.625 50.000 15.91 0.09 42.83 4.40
1284 4956 1.897423 CATGCCTGGACGGTACAGA 59.103 57.895 21.95 2.87 38.20 3.41
1296 4968 1.226888 GTACAGATCGGCGGTCCAC 60.227 63.158 17.90 8.94 0.00 4.02
1382 5054 0.037877 AGCCTGCAATGCTCAGACTT 59.962 50.000 6.82 0.00 29.23 3.01
1385 5057 2.686915 GCCTGCAATGCTCAGACTTATT 59.313 45.455 6.82 0.00 33.54 1.40
1428 5100 0.319211 CGCCTACCACTTCAACGACA 60.319 55.000 0.00 0.00 0.00 4.35
1451 5123 0.465097 TCGTCGGTATCCTCACCTCC 60.465 60.000 0.00 0.00 36.35 4.30
1455 5127 0.598562 CGGTATCCTCACCTCCATCG 59.401 60.000 0.00 0.00 36.35 3.84
1508 5180 0.615331 ATGACGGTGATGTGGCTTCT 59.385 50.000 0.00 0.00 0.00 2.85
1511 5183 1.672030 CGGTGATGTGGCTTCTGCA 60.672 57.895 0.00 0.00 41.91 4.41
1524 5196 0.250901 TTCTGCAGCCTTGAGGTTCC 60.251 55.000 9.47 0.00 37.57 3.62
1543 5215 3.681593 TCCGGTTACTCAGGGAAAATTG 58.318 45.455 0.00 0.00 32.28 2.32
1557 5229 3.699538 GGAAAATTGTATCCCAGTGTCCC 59.300 47.826 0.00 0.00 0.00 4.46
1569 5241 1.918800 GTGTCCCCTGCAGGTACCT 60.919 63.158 30.63 9.21 0.00 3.08
1573 5245 1.689233 CCCCTGCAGGTACCTAGCA 60.689 63.158 30.63 26.85 36.72 3.49
1581 5253 4.320870 TGCAGGTACCTAGCAAGTTAAAC 58.679 43.478 26.68 5.29 34.97 2.01
1594 5266 7.319142 AGCAAGTTAAACATTGTTGCAAAAT 57.681 28.000 0.00 0.71 44.80 1.82
1595 5267 8.430801 AGCAAGTTAAACATTGTTGCAAAATA 57.569 26.923 0.00 0.00 44.80 1.40
1596 5268 9.054922 AGCAAGTTAAACATTGTTGCAAAATAT 57.945 25.926 0.00 0.00 44.80 1.28
1683 5355 1.481772 GTTGCATGCATGGTACCCATT 59.518 47.619 27.34 0.00 42.23 3.16
1684 5356 1.863325 TGCATGCATGGTACCCATTT 58.137 45.000 27.34 0.00 42.23 2.32
1685 5357 3.023939 TGCATGCATGGTACCCATTTA 57.976 42.857 27.34 0.00 42.23 1.40
1696 5368 8.540388 GCATGGTACCCATTTATAGAATCTCTA 58.460 37.037 10.07 0.00 42.23 2.43
1716 5388 7.090173 TCTCTAAAAATTCCCGCAAAGAATTG 58.910 34.615 6.41 0.00 41.84 2.32
1739 5411 2.740055 CACGTGCACTCCAGAGGC 60.740 66.667 16.19 0.88 0.00 4.70
1744 5416 1.023513 GTGCACTCCAGAGGCATGAC 61.024 60.000 10.32 0.00 37.12 3.06
1840 5512 3.389925 ACATTTTGTGCCAATGGTCTG 57.610 42.857 0.00 0.00 36.15 3.51
1897 5569 5.348997 GCAGAGTAGTGTGGTTCATACTTTC 59.651 44.000 2.87 2.93 37.10 2.62
2003 5675 1.201965 CGTTGCTTCTCCGATTTGCTC 60.202 52.381 0.00 0.00 0.00 4.26
2069 5741 6.722129 ACTTCAGAGACTTGTGAGGTAAGTAT 59.278 38.462 2.72 0.00 35.54 2.12
2187 5922 9.836076 CCATGTTATGATTGATCATACATGTTC 57.164 33.333 27.60 0.00 46.28 3.18
2209 5944 5.832221 TCAATATAGATGGAGGACGGAGAT 58.168 41.667 0.00 0.00 0.00 2.75
2248 5986 1.087501 GGGTTTGCAAGAGATCGTCC 58.912 55.000 0.00 0.00 0.00 4.79
2345 6083 6.809196 CCAAAGTTATTAATTTAGCCGCACAA 59.191 34.615 0.00 0.00 0.00 3.33
2604 6416 2.159531 ACATGGCGTCAATGTGATTTCG 60.160 45.455 0.00 0.00 0.00 3.46
2643 6455 6.366332 CGGTAAGGCACTAAGTCATATGATTC 59.634 42.308 9.02 0.00 38.49 2.52
2679 6491 3.123621 CAGCGAACTTCCTAATCACACAC 59.876 47.826 0.00 0.00 0.00 3.82
2688 6500 6.205464 ACTTCCTAATCACACACACAGAATTG 59.795 38.462 0.00 0.00 0.00 2.32
2689 6501 5.863965 TCCTAATCACACACACAGAATTGA 58.136 37.500 0.00 0.00 0.00 2.57
2967 6810 5.181245 ACACACTCCGTATGGAAAATTCTTG 59.819 40.000 4.92 0.00 45.87 3.02
3314 7185 8.257306 GGATGGTAAAATAAAGGAGCAAATCAA 58.743 33.333 0.00 0.00 0.00 2.57
3386 7258 3.189287 GCCCGCAATATTGATAGGAGTTG 59.811 47.826 19.73 7.03 0.00 3.16
3400 7275 2.851195 GGAGTTGCTCCTTTCAAGTCA 58.149 47.619 7.86 0.00 46.41 3.41
3438 7320 8.684386 TTCACCAAAGAAAGATGTTATGTGTA 57.316 30.769 0.00 0.00 0.00 2.90
3453 7335 8.124808 TGTTATGTGTAGTTGTATGTACTGGA 57.875 34.615 0.00 0.00 0.00 3.86
3457 7339 7.058023 TGTGTAGTTGTATGTACTGGACTTT 57.942 36.000 0.00 0.00 0.00 2.66
3528 7411 1.593196 CATGGGCCCATGTAAGTACG 58.407 55.000 44.55 24.87 46.20 3.67
3536 7419 3.119245 GCCCATGTAAGTACGTGAGAAGA 60.119 47.826 11.47 0.00 44.02 2.87
3583 7469 5.008514 GTCAATGTTTCAAAACCATTTGGGG 59.991 40.000 0.96 0.00 44.88 4.96
3584 7470 5.104360 TCAATGTTTCAAAACCATTTGGGGA 60.104 36.000 0.96 0.00 44.88 4.81
3585 7471 4.143986 TGTTTCAAAACCATTTGGGGAC 57.856 40.909 0.96 0.50 44.88 4.46
3586 7472 3.777522 TGTTTCAAAACCATTTGGGGACT 59.222 39.130 0.96 0.00 44.88 3.85
3587 7473 4.126437 GTTTCAAAACCATTTGGGGACTG 58.874 43.478 0.96 0.00 44.88 3.51
3605 7491 0.250234 TGGCTATATGCAGCGATCCC 59.750 55.000 0.00 0.00 45.15 3.85
3731 7619 1.055849 GGGTGCAAATCCTTGGGTTT 58.944 50.000 0.00 0.00 32.76 3.27
3743 7631 3.075884 CCTTGGGTTTTGCATTGAATGG 58.924 45.455 7.35 0.00 0.00 3.16
3766 7654 5.456186 GGTGCCCACAACCATCTACTATATT 60.456 44.000 0.40 0.00 0.00 1.28
3797 7685 0.690762 ACCTAAACACCTCGCATGGT 59.309 50.000 0.00 0.00 41.77 3.55
3967 8408 9.969001 AACCCATAGTTACTTATTTTAGCAAGA 57.031 29.630 0.00 0.00 36.74 3.02
3994 8435 3.366781 GGCAGAAAATCAAGAGCTCAACC 60.367 47.826 17.77 0.00 0.00 3.77
3997 8438 5.638783 CAGAAAATCAAGAGCTCAACCATC 58.361 41.667 17.77 5.27 0.00 3.51
4087 8528 3.383825 AGCTTAGTACTCCCAATGTACGG 59.616 47.826 0.00 0.00 43.41 4.02
4109 8550 4.384427 GGGTTTAAATGTCCATCCGGTCTA 60.384 45.833 0.00 0.00 0.00 2.59
4110 8551 4.814771 GGTTTAAATGTCCATCCGGTCTAG 59.185 45.833 0.00 0.00 0.00 2.43
4132 8573 1.979308 TCCGGTGTCCATAACTCCAAA 59.021 47.619 0.00 0.00 40.85 3.28
4142 8583 4.351407 TCCATAACTCCAAACCCAGTTGTA 59.649 41.667 0.00 0.00 34.60 2.41
4149 8590 4.537751 TCCAAACCCAGTTGTAATTGACA 58.462 39.130 0.00 0.00 35.78 3.58
4177 8618 2.479566 TTTTCCACTAGGCTCTGCTG 57.520 50.000 0.00 0.00 33.74 4.41
4270 8711 5.063944 GCGATGAACTGAGTGTCATAAACAT 59.936 40.000 9.24 0.00 40.80 2.71
4276 8717 8.093927 TGAACTGAGTGTCATAAACATATCACA 58.906 33.333 0.00 0.00 40.80 3.58
4298 8739 7.867909 TCACACATGTTACAAAAACTGAAAACA 59.132 29.630 0.00 0.00 38.17 2.83
4319 8760 7.878477 AACATGTGCTAGAAATTGAAACATG 57.122 32.000 0.00 10.45 45.53 3.21
4322 8763 8.385789 CATGTGCTAGAAATTGAAACATGTAC 57.614 34.615 0.00 0.00 38.90 2.90
4332 8773 1.326548 GAAACATGTACGTGGGATCGC 59.673 52.381 19.05 2.14 0.00 4.58
4344 8785 1.134367 TGGGATCGCTAACTCAACTCG 59.866 52.381 11.46 0.00 0.00 4.18
4348 8789 2.363788 TCGCTAACTCAACTCGCATT 57.636 45.000 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 2.043450 CCTCGAGAGGCCTGAGGT 60.043 66.667 23.71 1.62 43.48 3.85
204 205 6.642950 CACTTTTTCGGTTAAATGCAATGGTA 59.357 34.615 0.00 0.00 0.00 3.25
301 302 4.089361 ACAGGGTTGATTGGGATTTTCTC 58.911 43.478 0.00 0.00 0.00 2.87
552 553 6.594937 TGTAGTAGAAAAACCGTGTTTGAACT 59.405 34.615 0.00 0.00 0.00 3.01
553 554 6.774084 TGTAGTAGAAAAACCGTGTTTGAAC 58.226 36.000 0.00 0.00 0.00 3.18
578 579 2.749621 CCCTTATGTCTGGTCTTGTTGC 59.250 50.000 0.00 0.00 0.00 4.17
628 635 7.854557 TGACACTGATCAGATTTTAGGATTG 57.145 36.000 29.27 14.36 0.00 2.67
648 655 2.513753 CCTTAAACCTGTGCCATGACA 58.486 47.619 0.00 0.00 0.00 3.58
650 657 1.272425 CCCCTTAAACCTGTGCCATGA 60.272 52.381 0.00 0.00 0.00 3.07
652 659 1.005924 CTCCCCTTAAACCTGTGCCAT 59.994 52.381 0.00 0.00 0.00 4.40
655 662 1.628846 TCTCTCCCCTTAAACCTGTGC 59.371 52.381 0.00 0.00 0.00 4.57
658 665 2.552367 AGGTCTCTCCCCTTAAACCTG 58.448 52.381 0.00 0.00 35.84 4.00
659 666 2.913617 CAAGGTCTCTCCCCTTAAACCT 59.086 50.000 0.00 0.00 40.35 3.50
661 668 2.026169 CCCAAGGTCTCTCCCCTTAAAC 60.026 54.545 0.00 0.00 40.35 2.01
664 671 0.797579 ACCCAAGGTCTCTCCCCTTA 59.202 55.000 0.00 0.00 40.35 2.69
665 672 0.103876 AACCCAAGGTCTCTCCCCTT 60.104 55.000 0.00 0.00 43.11 3.95
666 673 0.103876 AAACCCAAGGTCTCTCCCCT 60.104 55.000 0.00 0.00 33.12 4.79
667 674 0.328592 GAAACCCAAGGTCTCTCCCC 59.671 60.000 0.00 0.00 33.12 4.81
668 675 1.279558 GAGAAACCCAAGGTCTCTCCC 59.720 57.143 5.91 0.00 42.27 4.30
670 677 1.893801 TCGAGAAACCCAAGGTCTCTC 59.106 52.381 6.99 6.99 44.01 3.20
674 681 1.619332 ACTCTCGAGAAACCCAAGGTC 59.381 52.381 17.36 0.00 33.12 3.85
675 682 1.619332 GACTCTCGAGAAACCCAAGGT 59.381 52.381 17.36 7.99 37.65 3.50
726 4185 3.562973 GCCATGACACTGATCGAAATGAT 59.437 43.478 0.00 0.00 41.06 2.45
828 4348 0.950836 TTCAATGGTTCAGCCGTGTG 59.049 50.000 0.00 0.00 41.21 3.82
937 4476 2.862223 GCACTAGGGAGCGGGCTAG 61.862 68.421 0.00 0.00 0.00 3.42
965 4504 4.859304 TCTTGAACGTACTCCAAGCTAA 57.141 40.909 12.27 0.00 37.71 3.09
967 4506 3.963428 ATCTTGAACGTACTCCAAGCT 57.037 42.857 12.27 0.00 37.71 3.74
968 4507 3.424962 GCAATCTTGAACGTACTCCAAGC 60.425 47.826 12.27 0.00 37.71 4.01
971 4510 3.325870 CAGCAATCTTGAACGTACTCCA 58.674 45.455 0.00 0.00 0.00 3.86
972 4511 2.094417 GCAGCAATCTTGAACGTACTCC 59.906 50.000 0.00 0.00 0.00 3.85
974 4513 2.076863 GGCAGCAATCTTGAACGTACT 58.923 47.619 0.00 0.00 0.00 2.73
975 4514 1.201921 CGGCAGCAATCTTGAACGTAC 60.202 52.381 0.00 0.00 0.00 3.67
976 4515 1.075542 CGGCAGCAATCTTGAACGTA 58.924 50.000 0.00 0.00 0.00 3.57
977 4516 0.884704 ACGGCAGCAATCTTGAACGT 60.885 50.000 0.00 0.00 0.00 3.99
978 4517 1.075542 TACGGCAGCAATCTTGAACG 58.924 50.000 0.00 0.00 0.00 3.95
979 4518 1.130561 GGTACGGCAGCAATCTTGAAC 59.869 52.381 0.00 0.00 0.00 3.18
980 4519 1.271108 TGGTACGGCAGCAATCTTGAA 60.271 47.619 0.00 0.00 0.00 2.69
1003 4674 4.643387 GACCGTTGGCTGCCAGGT 62.643 66.667 27.17 27.17 35.21 4.00
1082 4753 2.279120 CCGATGAGCAGCGAGTCC 60.279 66.667 9.94 0.00 43.75 3.85
1251 4923 1.002900 GGCATGCGCACACGTATTAAT 60.003 47.619 14.90 0.00 42.26 1.40
1271 4943 1.065928 GCCGATCTGTACCGTCCAG 59.934 63.158 0.00 0.00 0.00 3.86
1296 4968 2.412089 CCTTTAACTTGTCGAAGCTCCG 59.588 50.000 0.00 0.00 31.68 4.63
1304 4976 1.500396 GCCGGCCTTTAACTTGTCG 59.500 57.895 18.11 0.00 0.00 4.35
1382 5054 2.158559 AGCCGTTGCATTGTGTCAATA 58.841 42.857 0.00 0.00 41.13 1.90
1385 5057 1.840630 CGAGCCGTTGCATTGTGTCA 61.841 55.000 0.00 0.00 41.13 3.58
1428 5100 1.955080 GGTGAGGATACCGACGATCTT 59.045 52.381 0.00 0.00 37.17 2.40
1436 5108 0.598562 CGATGGAGGTGAGGATACCG 59.401 60.000 0.00 0.00 45.56 4.02
1508 5180 2.032528 CGGAACCTCAAGGCTGCA 59.967 61.111 0.50 0.00 39.32 4.41
1511 5183 0.323957 GTAACCGGAACCTCAAGGCT 59.676 55.000 9.46 0.00 39.32 4.58
1524 5196 5.296035 GGATACAATTTTCCCTGAGTAACCG 59.704 44.000 0.00 0.00 0.00 4.44
1543 5215 1.271840 TGCAGGGGACACTGGGATAC 61.272 60.000 3.45 0.00 38.90 2.24
1557 5229 0.905357 ACTTGCTAGGTACCTGCAGG 59.095 55.000 31.60 31.60 39.26 4.85
1569 5241 7.834068 TTTTGCAACAATGTTTAACTTGCTA 57.166 28.000 16.67 9.47 38.43 3.49
1660 5332 2.212869 GGTACCATGCATGCAACATG 57.787 50.000 26.68 18.38 43.67 3.21
1683 5355 9.621629 TTGCGGGAATTTTTAGAGATTCTATAA 57.378 29.630 0.00 0.00 33.75 0.98
1684 5356 9.621629 TTTGCGGGAATTTTTAGAGATTCTATA 57.378 29.630 0.00 0.00 33.75 1.31
1685 5357 8.519799 TTTGCGGGAATTTTTAGAGATTCTAT 57.480 30.769 0.00 0.00 33.75 1.98
1716 5388 3.044305 GGAGTGCACGTGTGAGGC 61.044 66.667 18.38 2.14 0.00 4.70
1726 5398 1.297689 GTCATGCCTCTGGAGTGCA 59.702 57.895 13.17 13.17 38.38 4.57
1739 5411 4.403752 TGAGAGTAGTCCCTTGATGTCATG 59.596 45.833 0.00 0.00 0.00 3.07
1744 5416 4.277476 AGAGTGAGAGTAGTCCCTTGATG 58.723 47.826 0.00 0.00 0.00 3.07
1840 5512 0.545646 AGGATGGCAGGAGCTCTTTC 59.454 55.000 14.64 0.00 41.70 2.62
1897 5569 0.461870 TCCGATGCAAGGGAATGTCG 60.462 55.000 11.11 3.65 0.00 4.35
2003 5675 1.742831 CACCCTCTCGAAGTCTCTCAG 59.257 57.143 0.00 0.00 0.00 3.35
2187 5922 6.336566 CAATCTCCGTCCTCCATCTATATTG 58.663 44.000 0.00 0.00 0.00 1.90
2191 5926 3.169099 CCAATCTCCGTCCTCCATCTAT 58.831 50.000 0.00 0.00 0.00 1.98
2209 5944 2.484770 CCGAACTTCTCACCAAGTCCAA 60.485 50.000 0.00 0.00 35.45 3.53
2248 5986 1.600957 CGCAATGGAAGCACTCTATGG 59.399 52.381 0.00 0.00 0.00 2.74
2345 6083 9.623000 CCATACACATCATATATGTCATCCAAT 57.377 33.333 12.42 0.00 0.00 3.16
2393 6131 2.426522 CTTCCAATCGCCTCAGTGAAA 58.573 47.619 0.00 0.00 35.78 2.69
2438 6233 8.629158 ACAGCACAAGTCAATTTGAAATTACTA 58.371 29.630 2.42 0.00 0.00 1.82
2513 6325 6.153067 ACAGAGTAAAGTGCTCGCATATATC 58.847 40.000 0.00 0.00 37.99 1.63
2590 6402 4.846137 CCGAAGAAACGAAATCACATTGAC 59.154 41.667 0.00 0.00 35.09 3.18
2604 6416 1.664151 CTTACCGCATCCCGAAGAAAC 59.336 52.381 0.00 0.00 40.02 2.78
2643 6455 5.095691 AGTTCGCTGTGTTTTTAGTGATG 57.904 39.130 0.00 0.00 33.86 3.07
2688 6500 5.872617 TGCCATGCCACTATAATATTACGTC 59.127 40.000 0.00 0.00 0.00 4.34
2689 6501 5.800296 TGCCATGCCACTATAATATTACGT 58.200 37.500 0.00 0.00 0.00 3.57
2967 6810 7.657336 TGGAACATGAAGGAACAAATAGAAAC 58.343 34.615 0.00 0.00 0.00 2.78
3318 7189 7.038659 CGGCATTAAAAGGATCCAAATACAAA 58.961 34.615 15.82 0.00 0.00 2.83
3368 7239 5.619625 GGAGCAACTCCTATCAATATTGC 57.380 43.478 10.76 0.00 46.41 3.56
3438 7320 7.736893 AGAAAGAAAGTCCAGTACATACAACT 58.263 34.615 0.00 0.00 0.00 3.16
3528 7411 5.502153 TCGCTATCTACCTTTCTTCTCAC 57.498 43.478 0.00 0.00 0.00 3.51
3536 7419 7.606456 TGACTTTCATTTTCGCTATCTACCTTT 59.394 33.333 0.00 0.00 0.00 3.11
3583 7469 2.266554 GATCGCTGCATATAGCCAGTC 58.733 52.381 0.00 0.00 44.83 3.51
3584 7470 1.066573 GGATCGCTGCATATAGCCAGT 60.067 52.381 0.00 0.00 44.83 4.00
3585 7471 1.649664 GGATCGCTGCATATAGCCAG 58.350 55.000 0.00 0.00 44.83 4.85
3586 7472 0.250234 GGGATCGCTGCATATAGCCA 59.750 55.000 1.84 0.00 44.83 4.75
3587 7473 0.807667 CGGGATCGCTGCATATAGCC 60.808 60.000 8.28 0.00 44.83 3.93
3605 7491 0.453793 ACTTCATGAGAGTCTCGCCG 59.546 55.000 15.34 6.33 32.35 6.46
3687 7575 7.939039 CCTCTATTCAATAAAAGAGGCCATACA 59.061 37.037 5.01 0.00 46.32 2.29
3688 7576 8.329203 CCTCTATTCAATAAAAGAGGCCATAC 57.671 38.462 5.01 0.00 46.32 2.39
3743 7631 3.560636 ATAGTAGATGGTTGTGGGCAC 57.439 47.619 0.00 0.00 0.00 5.01
3774 7662 2.922740 TGCGAGGTGTTTAGGTCTTT 57.077 45.000 0.00 0.00 0.00 2.52
3779 7667 1.821216 AACCATGCGAGGTGTTTAGG 58.179 50.000 0.10 0.00 42.25 2.69
3797 7685 8.723942 TTCTTTTGCATTTTAGCCTTTTGTAA 57.276 26.923 0.00 0.00 0.00 2.41
3907 8348 7.065563 CACTTAGAGGCTATATTCATCCAATGC 59.934 40.741 0.00 0.00 0.00 3.56
3967 8408 3.265479 AGCTCTTGATTTTCTGCCTAGGT 59.735 43.478 11.31 0.00 0.00 3.08
3994 8435 6.020995 GTCCAAAACACACAACTTTTACGATG 60.021 38.462 0.00 0.00 0.00 3.84
3997 8438 5.154932 TGTCCAAAACACACAACTTTTACG 58.845 37.500 0.00 0.00 31.20 3.18
4087 8528 3.617284 AGACCGGATGGACATTTAAACC 58.383 45.455 9.46 0.00 39.21 3.27
4109 8550 2.040178 GGAGTTATGGACACCGGATCT 58.960 52.381 9.46 0.00 0.00 2.75
4110 8551 1.760613 TGGAGTTATGGACACCGGATC 59.239 52.381 9.46 4.97 41.43 3.36
4132 8573 4.261994 GCAATGTGTCAATTACAACTGGGT 60.262 41.667 0.00 0.00 40.63 4.51
4161 8602 2.362369 GCCAGCAGAGCCTAGTGGA 61.362 63.158 0.00 0.00 34.57 4.02
4164 8605 0.324738 TAGTGCCAGCAGAGCCTAGT 60.325 55.000 0.00 0.00 0.00 2.57
4170 8611 2.105006 ACATTGTAGTGCCAGCAGAG 57.895 50.000 0.00 0.00 0.00 3.35
4177 8618 2.230992 TGCCAATCAACATTGTAGTGCC 59.769 45.455 0.00 0.00 38.22 5.01
4208 8649 0.515564 GCCGCGCTTTTCTCAAACTA 59.484 50.000 5.56 0.00 0.00 2.24
4230 8671 2.303163 TCGCTAGTTTGTGTGTGTGT 57.697 45.000 0.00 0.00 0.00 3.72
4231 8672 2.799978 TCATCGCTAGTTTGTGTGTGTG 59.200 45.455 0.00 0.00 0.00 3.82
4232 8673 3.106242 TCATCGCTAGTTTGTGTGTGT 57.894 42.857 0.00 0.00 0.00 3.72
4233 8674 3.494626 AGTTCATCGCTAGTTTGTGTGTG 59.505 43.478 0.00 0.00 0.00 3.82
4234 8675 3.494626 CAGTTCATCGCTAGTTTGTGTGT 59.505 43.478 0.00 0.00 0.00 3.72
4235 8676 3.740832 TCAGTTCATCGCTAGTTTGTGTG 59.259 43.478 0.00 0.00 0.00 3.82
4298 8739 7.094805 ACGTACATGTTTCAATTTCTAGCACAT 60.095 33.333 2.30 0.00 0.00 3.21
4319 8760 1.402968 TGAGTTAGCGATCCCACGTAC 59.597 52.381 0.00 0.00 35.59 3.67
4320 8761 1.753930 TGAGTTAGCGATCCCACGTA 58.246 50.000 0.00 0.00 35.59 3.57
4321 8762 0.892755 TTGAGTTAGCGATCCCACGT 59.107 50.000 0.00 0.00 35.59 4.49
4322 8763 1.135083 AGTTGAGTTAGCGATCCCACG 60.135 52.381 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.