Multiple sequence alignment - TraesCS2B01G456300

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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 TraesCS2B01G456300 chr2B 100.000 4336 0 0 1 4336 651072547 651068212 0.000000e+00 8008.0
1 TraesCS2B01G456300 chr2B 91.289 287 23 2 41 325 373728410 373728124 1.460000e-104 390.0
2 TraesCS2B01G456300 chr2B 85.644 202 19 8 305 499 373728098 373727900 2.040000e-48 204.0
3 TraesCS2B01G456300 chr2B 100.000 39 0 0 1 39 373741442 373741404 6.010000e-09 73.1
4 TraesCS2B01G456300 chr2D 96.641 2233 57 7 2106 4336 544849710 544847494 0.000000e+00 3692.0
5 TraesCS2B01G456300 chr2D 93.103 1450 54 14 496 1926 544851470 544850048 0.000000e+00 2082.0
6 TraesCS2B01G456300 chr2D 93.989 183 10 1 1922 2103 544849969 544849787 4.270000e-70 276.0
7 TraesCS2B01G456300 chr2A 91.524 1640 80 14 496 2103 688635211 688636823 0.000000e+00 2204.0
8 TraesCS2B01G456300 chr2A 97.306 891 24 0 2919 3809 688637759 688638649 0.000000e+00 1513.0
9 TraesCS2B01G456300 chr2A 96.206 817 29 2 2106 2921 688636900 688637715 0.000000e+00 1336.0
10 TraesCS2B01G456300 chr2A 92.929 297 14 2 4041 4336 688641135 688641425 4.010000e-115 425.0
11 TraesCS2B01G456300 chr2A 92.032 251 13 2 3802 4045 688640584 688640834 3.210000e-91 346.0
12 TraesCS2B01G456300 chr6B 92.857 392 25 3 1 391 562464489 562464100 2.260000e-157 566.0
13 TraesCS2B01G456300 chr6A 91.930 285 23 0 41 325 142946725 142947009 2.430000e-107 399.0
14 TraesCS2B01G456300 chr6A 87.778 180 15 5 325 497 41928889 41928710 2.040000e-48 204.0
15 TraesCS2B01G456300 chr6A 100.000 29 0 0 511 539 607677226 607677254 2.000000e-03 54.7
16 TraesCS2B01G456300 chr1B 87.719 285 26 5 41 325 124699434 124699709 1.500000e-84 324.0
17 TraesCS2B01G456300 chr1B 81.614 223 35 5 89 306 664344909 664345130 3.450000e-41 180.0
18 TraesCS2B01G456300 chr3A 86.010 193 20 3 323 508 265181640 265181448 2.640000e-47 200.0
19 TraesCS2B01G456300 chrUn 78.646 192 32 6 311 494 445254118 445253928 7.620000e-23 119.0
20 TraesCS2B01G456300 chr6D 100.000 39 0 0 1 39 366687540 366687502 6.010000e-09 73.1
21 TraesCS2B01G456300 chr5D 85.484 62 9 0 436 497 442661230 442661291 1.010000e-06 65.8
22 TraesCS2B01G456300 chr1D 100.000 31 0 0 747 777 471859995 471860025 1.680000e-04 58.4


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 TraesCS2B01G456300 chr2B 651068212 651072547 4335 True 8008.000000 8008 100.000000 1 4336 1 chr2B.!!$R2 4335
1 TraesCS2B01G456300 chr2B 373727900 373728410 510 True 297.000000 390 88.466500 41 499 2 chr2B.!!$R3 458
2 TraesCS2B01G456300 chr2D 544847494 544851470 3976 True 2016.666667 3692 94.577667 496 4336 3 chr2D.!!$R1 3840
3 TraesCS2B01G456300 chr2A 688635211 688641425 6214 False 1164.800000 2204 93.999400 496 4336 5 chr2A.!!$F1 3840


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
71 72 0.588252 GAGACAATGCGTGCAGTTGT 59.412 50.0 16.80 16.80 38.66 3.32 F
1304 1379 0.333993 ATATGGGGCCATGAGGATGC 59.666 55.0 4.39 0.00 37.82 3.91 F
2318 2569 0.106868 CTGAGGAAGGCCATGCATCA 60.107 55.0 5.01 6.09 36.29 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1800 1.005037 CGGTTGGCTAGAGCACACA 60.005 57.895 3.54 0.0 44.36 3.72 R
3050 3349 0.820871 AAACGCCACAACACCAATGT 59.179 45.000 0.00 0.0 42.46 2.71 R
4238 6799 0.108585 GTCAGCACCCAGTTTCCAGA 59.891 55.000 0.00 0.0 0.00 3.86 R


All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.568623 ACCATGAAAAAGACGCTCCT 57.431 45.000 0.00 0.00 0.00 3.69
22 23 2.154462 ACCATGAAAAAGACGCTCCTG 58.846 47.619 0.00 0.00 0.00 3.86
23 24 2.224523 ACCATGAAAAAGACGCTCCTGA 60.225 45.455 0.00 0.00 0.00 3.86
24 25 3.012518 CCATGAAAAAGACGCTCCTGAT 58.987 45.455 0.00 0.00 0.00 2.90
25 26 3.441572 CCATGAAAAAGACGCTCCTGATT 59.558 43.478 0.00 0.00 0.00 2.57
26 27 4.437930 CCATGAAAAAGACGCTCCTGATTC 60.438 45.833 0.00 0.00 0.00 2.52
27 28 4.008074 TGAAAAAGACGCTCCTGATTCT 57.992 40.909 0.00 0.00 0.00 2.40
28 29 3.748048 TGAAAAAGACGCTCCTGATTCTG 59.252 43.478 0.00 0.00 0.00 3.02
29 30 3.409026 AAAAGACGCTCCTGATTCTGT 57.591 42.857 0.00 0.00 0.00 3.41
30 31 4.537135 AAAAGACGCTCCTGATTCTGTA 57.463 40.909 0.00 0.00 0.00 2.74
31 32 3.791973 AAGACGCTCCTGATTCTGTAG 57.208 47.619 0.00 0.00 0.00 2.74
32 33 2.729194 AGACGCTCCTGATTCTGTAGT 58.271 47.619 0.00 0.00 0.00 2.73
33 34 3.887352 AGACGCTCCTGATTCTGTAGTA 58.113 45.455 0.00 0.00 0.00 1.82
34 35 4.465886 AGACGCTCCTGATTCTGTAGTAT 58.534 43.478 0.00 0.00 0.00 2.12
35 36 4.277174 AGACGCTCCTGATTCTGTAGTATG 59.723 45.833 0.00 0.00 0.00 2.39
36 37 3.954904 ACGCTCCTGATTCTGTAGTATGT 59.045 43.478 0.00 0.00 0.00 2.29
37 38 4.202060 ACGCTCCTGATTCTGTAGTATGTG 60.202 45.833 0.00 0.00 0.00 3.21
38 39 4.202060 CGCTCCTGATTCTGTAGTATGTGT 60.202 45.833 0.00 0.00 0.00 3.72
39 40 5.285651 GCTCCTGATTCTGTAGTATGTGTC 58.714 45.833 0.00 0.00 0.00 3.67
44 45 6.461648 CCTGATTCTGTAGTATGTGTCGGAAT 60.462 42.308 0.00 0.00 38.21 3.01
62 63 3.721625 TCGGAAGAGAGACAATGCG 57.278 52.632 0.00 0.00 34.84 4.73
70 71 0.870393 AGAGACAATGCGTGCAGTTG 59.130 50.000 0.00 7.84 0.00 3.16
71 72 0.588252 GAGACAATGCGTGCAGTTGT 59.412 50.000 16.80 16.80 38.66 3.32
114 115 6.369065 GGTGTATTCTTTTTCTGAGATCGTGT 59.631 38.462 0.00 0.00 0.00 4.49
120 121 6.277605 TCTTTTTCTGAGATCGTGTGTGTTA 58.722 36.000 0.00 0.00 0.00 2.41
143 144 4.585879 TGTAGGCCAAGTCCTTATGTTTC 58.414 43.478 5.01 0.00 37.66 2.78
215 216 8.746922 TTTCAAAATCAAACATGCTAGTCATC 57.253 30.769 0.00 0.00 31.79 2.92
264 265 9.862585 AATAATGTTCTCGAAAATTGCAAAAAC 57.137 25.926 1.71 0.00 31.20 2.43
265 266 5.710613 TGTTCTCGAAAATTGCAAAAACC 57.289 34.783 1.71 0.00 0.00 3.27
272 273 6.846350 TCGAAAATTGCAAAAACCACATTTT 58.154 28.000 1.71 2.84 42.55 1.82
336 384 7.489435 TGAAAGACTATTCTGATGAACGATGTC 59.511 37.037 0.00 0.00 34.71 3.06
366 414 6.016777 AGGTTTCTTCACATTCACACTTCATC 60.017 38.462 0.00 0.00 0.00 2.92
376 424 4.286297 TCACACTTCATCGAGGGAAAAT 57.714 40.909 0.00 0.00 0.00 1.82
400 455 9.614792 AATGATACTCAGGTTACCTTATTGTTC 57.385 33.333 0.00 0.00 0.00 3.18
403 458 5.861727 ACTCAGGTTACCTTATTGTTCGTT 58.138 37.500 0.00 0.00 0.00 3.85
427 482 8.647226 GTTAAAATTGGATATGTGAAGTGTTGC 58.353 33.333 0.00 0.00 0.00 4.17
433 488 4.814234 GGATATGTGAAGTGTTGCGGAATA 59.186 41.667 0.00 0.00 0.00 1.75
444 499 2.689553 TGCGGAATAGCACATTGAGA 57.310 45.000 0.00 0.00 42.92 3.27
460 515 9.860898 GCACATTGAGAAGGTTCTATTAATTTT 57.139 29.630 0.00 0.00 37.73 1.82
466 521 9.052759 TGAGAAGGTTCTATTAATTTTATCGCC 57.947 33.333 0.00 0.00 37.73 5.54
468 523 7.996644 AGAAGGTTCTATTAATTTTATCGCCCA 59.003 33.333 0.00 0.00 35.34 5.36
469 524 7.745620 AGGTTCTATTAATTTTATCGCCCAG 57.254 36.000 0.00 0.00 0.00 4.45
572 627 6.539826 TGAGCATATTCATCAAACTCACGAAT 59.460 34.615 0.00 0.00 0.00 3.34
703 758 4.262249 CGAAAGGAAATAAAAACAGGGGCA 60.262 41.667 0.00 0.00 0.00 5.36
933 993 1.377725 CCAACGCCAGGCATCTCTT 60.378 57.895 13.30 0.00 0.00 2.85
934 994 1.372087 CCAACGCCAGGCATCTCTTC 61.372 60.000 13.30 0.00 0.00 2.87
935 995 1.078143 AACGCCAGGCATCTCTTCC 60.078 57.895 13.30 0.00 0.00 3.46
936 996 2.203126 CGCCAGGCATCTCTTCCC 60.203 66.667 13.30 0.00 0.00 3.97
937 997 2.203126 GCCAGGCATCTCTTCCCG 60.203 66.667 6.55 0.00 0.00 5.14
938 998 2.203126 CCAGGCATCTCTTCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
1158 1218 0.976641 TCTTTGCCATCCAGAGACGT 59.023 50.000 0.00 0.00 30.39 4.34
1165 1225 0.803768 CATCCAGAGACGTTGCTCGG 60.804 60.000 0.00 0.00 44.69 4.63
1304 1379 0.333993 ATATGGGGCCATGAGGATGC 59.666 55.000 4.39 0.00 37.82 3.91
1348 1423 4.046286 TCCAACTGGATTGCTATTGGTT 57.954 40.909 9.61 0.00 40.61 3.67
1493 1571 7.063308 GCATTTAACTGACAAATAACCATGGTG 59.937 37.037 20.60 8.06 0.00 4.17
1496 1574 8.693120 TTAACTGACAAATAACCATGGTGTAA 57.307 30.769 20.60 7.79 0.00 2.41
1586 1664 5.033589 AGCTACCGAGTACTATACTGTGT 57.966 43.478 0.00 0.00 39.59 3.72
1610 1691 8.065007 TGTTAAATTTAGGGGATAAGGAGCAAT 58.935 33.333 0.00 0.00 0.00 3.56
1674 1757 4.515567 CCTTTTAGAAGAAACAAGGCGTCT 59.484 41.667 0.00 0.00 34.71 4.18
1717 1800 1.485066 CGGGTGGGTAAGCTTACAGAT 59.515 52.381 31.98 0.00 35.37 2.90
1806 1899 4.889409 TCAAGCTCCAAAATCAGAAAGTGT 59.111 37.500 0.00 0.00 0.00 3.55
2007 2184 0.975887 ACGTAACCCCGGCTCTAAAA 59.024 50.000 0.00 0.00 0.00 1.52
2035 2212 6.827586 TTAGTTCAACAACACCAAGAAAGT 57.172 33.333 0.00 0.00 34.60 2.66
2054 2231 6.318900 AGAAAGTCTTTAGTCCCAAACAAGTG 59.681 38.462 0.00 0.00 0.00 3.16
2086 2263 5.337975 GCTAGATCTGAAACCCATAGGATCC 60.338 48.000 2.48 2.48 36.73 3.36
2123 2374 5.448654 TGGCAATTTGACTGGATAATAGCT 58.551 37.500 3.47 0.00 0.00 3.32
2189 2440 9.674824 CATAAGATGGTCAAAAAGAATATGAGC 57.325 33.333 0.00 0.00 40.88 4.26
2229 2480 3.499202 CCATACTAGCCCAGCCAAATCAT 60.499 47.826 0.00 0.00 0.00 2.45
2270 2521 2.709475 CTATTTGCTCACCGGCGC 59.291 61.111 0.00 0.00 34.52 6.53
2316 2567 1.455217 GCTGAGGAAGGCCATGCAT 60.455 57.895 5.01 0.00 36.29 3.96
2318 2569 0.106868 CTGAGGAAGGCCATGCATCA 60.107 55.000 5.01 6.09 36.29 3.07
2447 2700 6.367983 AGAACATTACCATGCATAGATTGGT 58.632 36.000 13.24 13.24 45.48 3.67
2449 2702 4.279169 ACATTACCATGCATAGATTGGTGC 59.721 41.667 17.36 0.00 43.45 5.01
2474 2727 8.349983 GCCCGCTTCTTTATTTCATTTATCTTA 58.650 33.333 0.00 0.00 0.00 2.10
2871 3124 1.199327 CTCTGCATGTGCTCCAACTTG 59.801 52.381 6.55 0.00 42.66 3.16
2921 3220 7.886629 AAACATGGTGATAGTTCTGCATAAT 57.113 32.000 0.00 0.00 0.00 1.28
3050 3349 9.542462 GCAATCCAGTATCTACAGTTGTATTTA 57.458 33.333 0.00 0.00 0.00 1.40
3378 3677 4.537135 AGTTATTGAGTCCTCGCTTTCA 57.463 40.909 0.00 0.00 0.00 2.69
3723 4022 7.775120 AGTTTTGAGAATTGTGTTTGAGTCAT 58.225 30.769 0.00 0.00 0.00 3.06
3762 4061 2.418746 GGGCATCTCACGTCTTACACAT 60.419 50.000 0.00 0.00 0.00 3.21
3874 6123 5.820947 TGTTCAGGAGGTACAGTTTCTTTTC 59.179 40.000 0.00 0.00 0.00 2.29
3878 6127 6.542370 TCAGGAGGTACAGTTTCTTTTCTTTG 59.458 38.462 0.00 0.00 0.00 2.77
3972 6228 6.753279 AGATACATTGGAATCGCAAATTTGTG 59.247 34.615 22.90 22.90 39.93 3.33
4022 6278 9.724839 TTACAAACTGCACAAAGTAAGAAATAC 57.275 29.630 0.00 0.00 34.52 1.89
4093 6654 2.662866 CCAATCCATGAGCTCATTGGT 58.337 47.619 27.80 19.79 33.61 3.67
4202 6763 0.179108 GGTCACCAGCGATACAGACC 60.179 60.000 0.00 2.49 38.77 3.85
4222 6783 6.150474 CAGACCGTTTTTGTCCCTTATAATGT 59.850 38.462 0.00 0.00 33.09 2.71
4223 6784 7.334921 CAGACCGTTTTTGTCCCTTATAATGTA 59.665 37.037 0.00 0.00 33.09 2.29
4224 6785 7.884354 AGACCGTTTTTGTCCCTTATAATGTAA 59.116 33.333 0.00 0.00 33.09 2.41
4225 6786 8.406730 ACCGTTTTTGTCCCTTATAATGTAAA 57.593 30.769 0.00 0.00 0.00 2.01
4226 6787 9.027202 ACCGTTTTTGTCCCTTATAATGTAAAT 57.973 29.630 0.00 0.00 0.00 1.40
4252 6813 6.780457 AAATATGAATCTGGAAACTGGGTG 57.220 37.500 0.00 0.00 0.00 4.61
4257 6818 0.108585 TCTGGAAACTGGGTGCTGAC 59.891 55.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.751175 CAGGAGCGTCTTTTTCATGGTTA 59.249 43.478 0.00 0.00 0.00 2.85
1 2 2.554032 CAGGAGCGTCTTTTTCATGGTT 59.446 45.455 0.00 0.00 0.00 3.67
2 3 2.154462 CAGGAGCGTCTTTTTCATGGT 58.846 47.619 0.00 0.00 0.00 3.55
3 4 2.426522 TCAGGAGCGTCTTTTTCATGG 58.573 47.619 0.00 0.00 0.00 3.66
4 5 4.394300 AGAATCAGGAGCGTCTTTTTCATG 59.606 41.667 0.00 0.00 0.00 3.07
5 6 4.394300 CAGAATCAGGAGCGTCTTTTTCAT 59.606 41.667 0.00 0.00 0.00 2.57
6 7 3.748048 CAGAATCAGGAGCGTCTTTTTCA 59.252 43.478 0.00 0.00 0.00 2.69
7 8 3.748568 ACAGAATCAGGAGCGTCTTTTTC 59.251 43.478 0.00 0.00 0.00 2.29
8 9 3.744660 ACAGAATCAGGAGCGTCTTTTT 58.255 40.909 0.00 0.00 0.00 1.94
9 10 3.409026 ACAGAATCAGGAGCGTCTTTT 57.591 42.857 0.00 0.00 0.00 2.27
10 11 3.511934 ACTACAGAATCAGGAGCGTCTTT 59.488 43.478 0.00 0.00 0.00 2.52
11 12 3.093057 ACTACAGAATCAGGAGCGTCTT 58.907 45.455 0.00 0.00 0.00 3.01
12 13 2.729194 ACTACAGAATCAGGAGCGTCT 58.271 47.619 0.00 0.00 0.00 4.18
13 14 4.036971 ACATACTACAGAATCAGGAGCGTC 59.963 45.833 0.00 0.00 0.00 5.19
14 15 3.954904 ACATACTACAGAATCAGGAGCGT 59.045 43.478 0.00 0.00 0.00 5.07
15 16 4.202060 ACACATACTACAGAATCAGGAGCG 60.202 45.833 0.00 0.00 0.00 5.03
16 17 5.269505 ACACATACTACAGAATCAGGAGC 57.730 43.478 0.00 0.00 0.00 4.70
17 18 5.506483 CCGACACATACTACAGAATCAGGAG 60.506 48.000 0.00 0.00 0.00 3.69
18 19 4.338400 CCGACACATACTACAGAATCAGGA 59.662 45.833 0.00 0.00 0.00 3.86
19 20 4.338400 TCCGACACATACTACAGAATCAGG 59.662 45.833 0.00 0.00 0.00 3.86
20 21 5.500645 TCCGACACATACTACAGAATCAG 57.499 43.478 0.00 0.00 0.00 2.90
21 22 5.907866 TTCCGACACATACTACAGAATCA 57.092 39.130 0.00 0.00 0.00 2.57
22 23 5.625721 CGATTCCGACACATACTACAGAATC 59.374 44.000 0.00 0.00 38.22 2.52
23 24 5.507482 CCGATTCCGACACATACTACAGAAT 60.507 44.000 0.00 0.00 38.22 2.40
24 25 4.201980 CCGATTCCGACACATACTACAGAA 60.202 45.833 0.00 0.00 38.22 3.02
25 26 3.314357 CCGATTCCGACACATACTACAGA 59.686 47.826 0.00 0.00 38.22 3.41
26 27 3.314357 TCCGATTCCGACACATACTACAG 59.686 47.826 0.00 0.00 38.22 2.74
27 28 3.281158 TCCGATTCCGACACATACTACA 58.719 45.455 0.00 0.00 38.22 2.74
28 29 3.976793 TCCGATTCCGACACATACTAC 57.023 47.619 0.00 0.00 38.22 2.73
29 30 4.201657 TCTTCCGATTCCGACACATACTA 58.798 43.478 0.00 0.00 38.22 1.82
30 31 3.021695 TCTTCCGATTCCGACACATACT 58.978 45.455 0.00 0.00 38.22 2.12
31 32 3.066342 TCTCTTCCGATTCCGACACATAC 59.934 47.826 0.00 0.00 38.22 2.39
32 33 3.284617 TCTCTTCCGATTCCGACACATA 58.715 45.455 0.00 0.00 38.22 2.29
33 34 2.099921 CTCTCTTCCGATTCCGACACAT 59.900 50.000 0.00 0.00 38.22 3.21
34 35 1.472878 CTCTCTTCCGATTCCGACACA 59.527 52.381 0.00 0.00 38.22 3.72
35 36 1.743958 TCTCTCTTCCGATTCCGACAC 59.256 52.381 0.00 0.00 38.22 3.67
36 37 1.743958 GTCTCTCTTCCGATTCCGACA 59.256 52.381 0.00 0.00 38.22 4.35
37 38 1.743958 TGTCTCTCTTCCGATTCCGAC 59.256 52.381 0.00 0.00 38.22 4.79
38 39 2.124277 TGTCTCTCTTCCGATTCCGA 57.876 50.000 0.00 0.00 38.22 4.55
39 40 2.941453 TTGTCTCTCTTCCGATTCCG 57.059 50.000 0.00 0.00 0.00 4.30
44 45 0.888619 ACGCATTGTCTCTCTTCCGA 59.111 50.000 0.00 0.00 0.00 4.55
56 57 0.661187 GACCACAACTGCACGCATTG 60.661 55.000 10.59 10.59 0.00 2.82
58 59 1.227943 AGACCACAACTGCACGCAT 60.228 52.632 0.00 0.00 0.00 4.73
62 63 0.463654 TGGTGAGACCACAACTGCAC 60.464 55.000 0.00 0.00 44.79 4.57
70 71 2.104963 ACCTTCTTTCTGGTGAGACCAC 59.895 50.000 0.00 0.00 44.79 4.16
105 106 3.797256 GCCTACATAACACACACGATCTC 59.203 47.826 0.00 0.00 0.00 2.75
109 110 1.619332 TGGCCTACATAACACACACGA 59.381 47.619 3.32 0.00 0.00 4.35
114 115 2.910319 AGGACTTGGCCTACATAACACA 59.090 45.455 3.32 0.00 36.22 3.72
120 121 4.862641 AACATAAGGACTTGGCCTACAT 57.137 40.909 3.32 0.00 37.26 2.29
143 144 0.394352 ACTCTATTTGGGCTTGCCCG 60.394 55.000 23.81 10.66 0.00 6.13
247 248 5.655893 ATGTGGTTTTTGCAATTTTCGAG 57.344 34.783 0.00 0.00 0.00 4.04
276 277 8.918961 TTGTTGTTCAGAATAACACGAATTTT 57.081 26.923 21.46 0.00 41.30 1.82
279 280 8.918961 TTTTTGTTGTTCAGAATAACACGAAT 57.081 26.923 21.46 0.00 41.30 3.34
314 317 6.456795 TGACATCGTTCATCAGAATAGTCT 57.543 37.500 0.00 0.00 35.92 3.24
336 384 3.503748 GTGAATGTGAAGAAACCTCCCTG 59.496 47.826 0.00 0.00 0.00 4.45
376 424 7.093640 ACGAACAATAAGGTAACCTGAGTATCA 60.094 37.037 0.00 0.00 46.23 2.15
400 455 8.849490 CAACACTTCACATATCCAATTTTAACG 58.151 33.333 0.00 0.00 0.00 3.18
403 458 7.026562 CGCAACACTTCACATATCCAATTTTA 58.973 34.615 0.00 0.00 0.00 1.52
427 482 3.535561 ACCTTCTCAATGTGCTATTCCG 58.464 45.455 0.00 0.00 0.00 4.30
433 488 8.814038 AATTAATAGAACCTTCTCAATGTGCT 57.186 30.769 0.00 0.00 38.70 4.40
444 499 7.778382 ACTGGGCGATAAAATTAATAGAACCTT 59.222 33.333 0.00 0.00 0.00 3.50
485 540 9.132521 CATGCTTTTGAAAATAACTAGGACAAG 57.867 33.333 0.00 0.00 0.00 3.16
621 676 6.578023 TGTTCGGGATTTCAAACAAAAATCT 58.422 32.000 8.10 0.00 41.04 2.40
727 782 0.107268 AAGGTACGCACGGGACTTTT 59.893 50.000 0.00 0.00 0.00 2.27
924 984 2.110006 GGAGCGGGAAGAGATGCC 59.890 66.667 0.00 0.00 35.86 4.40
1158 1218 2.735151 TCTAGACAATCTCCCGAGCAA 58.265 47.619 0.00 0.00 0.00 3.91
1165 1225 8.158789 ACCAGTAGTAGTATCTAGACAATCTCC 58.841 40.741 0.00 0.00 0.00 3.71
1304 1379 3.924073 TCAGACGAAACGACACATATTGG 59.076 43.478 0.00 0.00 0.00 3.16
1417 1492 6.539173 ACACCGATTATTATGCAAATAGGGA 58.461 36.000 11.28 0.00 33.56 4.20
1493 1571 4.839668 ATAGATCGGACAGCAGAGTTAC 57.160 45.455 0.00 0.00 0.00 2.50
1496 1574 3.192422 GCATATAGATCGGACAGCAGAGT 59.808 47.826 0.00 0.00 0.00 3.24
1717 1800 1.005037 CGGTTGGCTAGAGCACACA 60.005 57.895 3.54 0.00 44.36 3.72
1849 1942 8.591072 AGGAAATTAATTCATCAGGCATATTGG 58.409 33.333 0.10 0.00 39.98 3.16
1990 2167 3.555527 AGATTTTAGAGCCGGGGTTAC 57.444 47.619 2.18 0.00 0.00 2.50
2007 2184 7.639113 TCTTGGTGTTGTTGAACTAAAAGAT 57.361 32.000 0.00 0.00 32.79 2.40
2026 2203 5.592688 TGTTTGGGACTAAAGACTTTCTTGG 59.407 40.000 3.07 0.00 36.71 3.61
2103 2280 8.843262 TGATTGAGCTATTATCCAGTCAAATTG 58.157 33.333 0.00 0.00 0.00 2.32
2104 2281 8.985315 TGATTGAGCTATTATCCAGTCAAATT 57.015 30.769 0.00 0.00 0.00 1.82
2123 2374 9.613428 ACCTACGATTATGAATTTTCTGATTGA 57.387 29.630 0.00 0.00 0.00 2.57
2156 2407 8.231692 TCTTTTTGACCATCTTATGTGTCAAA 57.768 30.769 20.50 20.50 46.39 2.69
2189 2440 1.080569 GGCAACATCCAAACAGCCG 60.081 57.895 0.00 0.00 31.88 5.52
2279 2530 3.632145 CAGCTCACTTTTACACCAAACCT 59.368 43.478 0.00 0.00 0.00 3.50
2290 2541 1.546548 GGCCTTCCTCAGCTCACTTTT 60.547 52.381 0.00 0.00 0.00 2.27
2331 2583 4.895668 ATGTTTGGATGAGCACCAATTT 57.104 36.364 0.00 0.00 45.09 1.82
2447 2700 4.799564 AAATGAAATAAAGAAGCGGGCA 57.200 36.364 0.00 0.00 0.00 5.36
2921 3220 8.265055 AGAACATACTTTAGCAGCTATAACCAA 58.735 33.333 2.02 0.00 0.00 3.67
3050 3349 0.820871 AAACGCCACAACACCAATGT 59.179 45.000 0.00 0.00 42.46 2.71
3345 3644 8.232913 AGGACTCAATAACTTACTTTGCAAAA 57.767 30.769 13.84 0.00 0.00 2.44
3346 3645 7.307751 CGAGGACTCAATAACTTACTTTGCAAA 60.308 37.037 12.14 12.14 0.00 3.68
3378 3677 1.603802 CACGGTGTGAACAGAATGCTT 59.396 47.619 0.00 0.00 35.74 3.91
3616 3915 2.277084 GTGGTAAGGCGGACTTGTATG 58.723 52.381 6.30 0.00 40.37 2.39
3723 4022 2.394930 CCACAACATGGTATGGTCGA 57.605 50.000 0.00 0.00 44.46 4.20
3830 6079 8.267620 TGAACAAATCTGTCACGATATGATTT 57.732 30.769 0.00 0.00 40.28 2.17
3831 6080 7.011763 CCTGAACAAATCTGTCACGATATGATT 59.988 37.037 0.00 0.00 40.28 2.57
3832 6081 6.481313 CCTGAACAAATCTGTCACGATATGAT 59.519 38.462 0.00 0.00 40.28 2.45
3833 6082 5.812127 CCTGAACAAATCTGTCACGATATGA 59.188 40.000 0.00 0.00 33.45 2.15
3834 6083 5.812127 TCCTGAACAAATCTGTCACGATATG 59.188 40.000 0.00 0.00 33.45 1.78
3835 6084 5.977635 TCCTGAACAAATCTGTCACGATAT 58.022 37.500 0.00 0.00 33.45 1.63
3836 6085 5.400066 TCCTGAACAAATCTGTCACGATA 57.600 39.130 0.00 0.00 33.45 2.92
3837 6086 4.248859 CTCCTGAACAAATCTGTCACGAT 58.751 43.478 0.00 0.00 33.45 3.73
3851 6100 6.056236 AGAAAAGAAACTGTACCTCCTGAAC 58.944 40.000 0.00 0.00 0.00 3.18
3874 6123 9.553064 ACCTATAGAAGCACAATATCTTCAAAG 57.447 33.333 0.00 0.16 40.72 2.77
3878 6127 6.876257 CCCACCTATAGAAGCACAATATCTTC 59.124 42.308 0.00 0.00 39.08 2.87
3953 6202 5.389859 TCTCACAAATTTGCGATTCCAAT 57.610 34.783 18.12 0.00 0.00 3.16
3954 6203 4.844998 TCTCACAAATTTGCGATTCCAA 57.155 36.364 18.12 0.00 0.00 3.53
4022 6278 1.783284 TCAGCAGCTAGAACAACACG 58.217 50.000 0.00 0.00 0.00 4.49
4068 6629 0.179062 GAGCTCATGGATTGGCGACT 60.179 55.000 9.40 0.00 0.00 4.18
4093 6654 6.783708 AAATACTGGTTGGTTCAAGACAAA 57.216 33.333 0.00 0.00 0.00 2.83
4226 6787 9.573166 CACCCAGTTTCCAGATTCATATTTATA 57.427 33.333 0.00 0.00 0.00 0.98
4227 6788 7.014615 GCACCCAGTTTCCAGATTCATATTTAT 59.985 37.037 0.00 0.00 0.00 1.40
4238 6799 0.108585 GTCAGCACCCAGTTTCCAGA 59.891 55.000 0.00 0.00 0.00 3.86
4257 6818 9.438291 CGTTGCCTATAATAAAAATGAAGACAG 57.562 33.333 0.00 0.00 0.00 3.51



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

AutoCloner maintained by Alex Coulton.