Multiple sequence alignment - TraesCS1A01G318900

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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 TraesCS1A01G318900 chr1A 100.000 3145 0 0 1 3145 510184168 510187312 0.000000e+00 5808
1 TraesCS1A01G318900 chr1A 97.358 2271 38 14 28 2292 509494592 509492338 0.000000e+00 3842
2 TraesCS1A01G318900 chr1A 88.984 1280 96 29 1018 2276 509719875 509718620 0.000000e+00 1541
3 TraesCS1A01G318900 chr1A 88.828 1280 98 28 1018 2276 509793255 509792000 0.000000e+00 1530
4 TraesCS1A01G318900 chr1A 88.578 1287 108 26 1018 2284 509914760 509913493 0.000000e+00 1526
5 TraesCS1A01G318900 chr1D 96.205 3057 89 14 28 3076 413060719 413063756 0.000000e+00 4977
6 TraesCS1A01G318900 chr1D 89.043 1296 85 26 1018 2284 412897788 412899055 0.000000e+00 1554
7 TraesCS1A01G318900 chr1D 88.341 1338 94 33 990 2292 412642220 412643530 0.000000e+00 1550
8 TraesCS1A01G318900 chr1D 88.341 1338 94 33 990 2292 412746198 412747508 0.000000e+00 1550
9 TraesCS1A01G318900 chr1D 88.341 1338 94 33 990 2292 412763361 412764671 0.000000e+00 1550
10 TraesCS1A01G318900 chr1D 88.829 1298 84 29 1018 2284 412684094 412685361 0.000000e+00 1537
11 TraesCS1A01G318900 chr1D 89.011 1274 86 29 1042 2284 412814479 412815729 0.000000e+00 1528
12 TraesCS1A01G318900 chr1D 86.076 1185 120 28 990 2132 412507211 412508392 0.000000e+00 1232
13 TraesCS1A01G318900 chr1D 91.327 761 47 12 1522 2276 412855325 412856072 0.000000e+00 1022
14 TraesCS1A01G318900 chr1D 89.637 386 33 4 591 972 412897320 412897702 4.720000e-133 484
15 TraesCS1A01G318900 chr1D 88.101 395 34 8 591 972 412683614 412684008 1.030000e-124 457
16 TraesCS1A01G318900 chr1D 90.536 317 25 2 658 972 412814077 412814390 6.280000e-112 414
17 TraesCS1A01G318900 chr4B 87.839 1587 126 43 732 2276 633465802 633467363 0.000000e+00 1799
18 TraesCS1A01G318900 chr4B 87.398 1587 136 44 732 2276 633398670 633400234 0.000000e+00 1764
19 TraesCS1A01G318900 chr1B 87.759 1593 120 38 732 2284 556297072 556298629 0.000000e+00 1792
20 TraesCS1A01G318900 chr1B 87.800 1582 123 45 738 2276 556064578 556063024 0.000000e+00 1788
21 TraesCS1A01G318900 chr1B 91.675 1009 52 19 618 1613 556965929 556966918 0.000000e+00 1369
22 TraesCS1A01G318900 chr1B 86.758 1163 115 24 999 2132 556108107 556109259 0.000000e+00 1258
23 TraesCS1A01G318900 chr1B 90.713 926 36 14 2175 3076 556971236 556972135 0.000000e+00 1188
24 TraesCS1A01G318900 chr1B 87.500 744 57 19 997 1718 556969405 556970134 0.000000e+00 826
25 TraesCS1A01G318900 chr1B 92.920 565 37 3 28 591 596471565 596471003 0.000000e+00 819
26 TraesCS1A01G318900 chr1B 88.124 581 48 12 581 1151 556833740 556834309 0.000000e+00 671
27 TraesCS1A01G318900 chr1B 88.124 581 48 12 581 1151 556862161 556862730 0.000000e+00 671
28 TraesCS1A01G318900 chr1B 91.282 390 32 1 585 974 556968966 556969353 5.970000e-147 531
29 TraesCS1A01G318900 chr5B 91.213 569 47 3 28 594 377119125 377119692 0.000000e+00 771
30 TraesCS1A01G318900 chr2B 90.517 580 45 7 28 599 229186500 229185923 0.000000e+00 758
31 TraesCS1A01G318900 chr2A 89.492 571 49 10 28 594 84363333 84362770 0.000000e+00 712
32 TraesCS1A01G318900 chr7D 89.910 555 51 3 28 581 520394573 520395123 0.000000e+00 710
33 TraesCS1A01G318900 chr6D 80.810 568 101 7 29 591 458604757 458605321 3.720000e-119 438
34 TraesCS1A01G318900 chrUn 80.142 564 104 7 34 592 111150108 111150668 6.280000e-112 414


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 TraesCS1A01G318900 chr1A 510184168 510187312 3144 False 5808.0 5808 100.0000 1 3145 1 chr1A.!!$F1 3144
1 TraesCS1A01G318900 chr1A 509492338 509494592 2254 True 3842.0 3842 97.3580 28 2292 1 chr1A.!!$R1 2264
2 TraesCS1A01G318900 chr1A 509718620 509719875 1255 True 1541.0 1541 88.9840 1018 2276 1 chr1A.!!$R2 1258
3 TraesCS1A01G318900 chr1A 509792000 509793255 1255 True 1530.0 1530 88.8280 1018 2276 1 chr1A.!!$R3 1258
4 TraesCS1A01G318900 chr1A 509913493 509914760 1267 True 1526.0 1526 88.5780 1018 2284 1 chr1A.!!$R4 1266
5 TraesCS1A01G318900 chr1D 413060719 413063756 3037 False 4977.0 4977 96.2050 28 3076 1 chr1D.!!$F6 3048
6 TraesCS1A01G318900 chr1D 412642220 412643530 1310 False 1550.0 1550 88.3410 990 2292 1 chr1D.!!$F2 1302
7 TraesCS1A01G318900 chr1D 412746198 412747508 1310 False 1550.0 1550 88.3410 990 2292 1 chr1D.!!$F3 1302
8 TraesCS1A01G318900 chr1D 412763361 412764671 1310 False 1550.0 1550 88.3410 990 2292 1 chr1D.!!$F4 1302
9 TraesCS1A01G318900 chr1D 412507211 412508392 1181 False 1232.0 1232 86.0760 990 2132 1 chr1D.!!$F1 1142
10 TraesCS1A01G318900 chr1D 412855325 412856072 747 False 1022.0 1022 91.3270 1522 2276 1 chr1D.!!$F5 754
11 TraesCS1A01G318900 chr1D 412897320 412899055 1735 False 1019.0 1554 89.3400 591 2284 2 chr1D.!!$F9 1693
12 TraesCS1A01G318900 chr1D 412683614 412685361 1747 False 997.0 1537 88.4650 591 2284 2 chr1D.!!$F7 1693
13 TraesCS1A01G318900 chr1D 412814077 412815729 1652 False 971.0 1528 89.7735 658 2284 2 chr1D.!!$F8 1626
14 TraesCS1A01G318900 chr4B 633465802 633467363 1561 False 1799.0 1799 87.8390 732 2276 1 chr4B.!!$F2 1544
15 TraesCS1A01G318900 chr4B 633398670 633400234 1564 False 1764.0 1764 87.3980 732 2276 1 chr4B.!!$F1 1544
16 TraesCS1A01G318900 chr1B 556297072 556298629 1557 False 1792.0 1792 87.7590 732 2284 1 chr1B.!!$F2 1552
17 TraesCS1A01G318900 chr1B 556063024 556064578 1554 True 1788.0 1788 87.8000 738 2276 1 chr1B.!!$R1 1538
18 TraesCS1A01G318900 chr1B 556108107 556109259 1152 False 1258.0 1258 86.7580 999 2132 1 chr1B.!!$F1 1133
19 TraesCS1A01G318900 chr1B 556965929 556972135 6206 False 978.5 1369 90.2925 585 3076 4 chr1B.!!$F5 2491
20 TraesCS1A01G318900 chr1B 596471003 596471565 562 True 819.0 819 92.9200 28 591 1 chr1B.!!$R2 563
21 TraesCS1A01G318900 chr1B 556833740 556834309 569 False 671.0 671 88.1240 581 1151 1 chr1B.!!$F3 570
22 TraesCS1A01G318900 chr1B 556862161 556862730 569 False 671.0 671 88.1240 581 1151 1 chr1B.!!$F4 570
23 TraesCS1A01G318900 chr5B 377119125 377119692 567 False 771.0 771 91.2130 28 594 1 chr5B.!!$F1 566
24 TraesCS1A01G318900 chr2B 229185923 229186500 577 True 758.0 758 90.5170 28 599 1 chr2B.!!$R1 571
25 TraesCS1A01G318900 chr2A 84362770 84363333 563 True 712.0 712 89.4920 28 594 1 chr2A.!!$R1 566
26 TraesCS1A01G318900 chr7D 520394573 520395123 550 False 710.0 710 89.9100 28 581 1 chr7D.!!$F1 553
27 TraesCS1A01G318900 chr6D 458604757 458605321 564 False 438.0 438 80.8100 29 591 1 chr6D.!!$F1 562
28 TraesCS1A01G318900 chrUn 111150108 111150668 560 False 414.0 414 80.1420 34 592 1 chrUn.!!$F1 558

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
19 20 0.890542 TGCAGGTGGAGATGTGCAAC 60.891 55.0 0.0 0.0 42.79 4.17 F
243 248 0.903236 GAGGAAGCGGAACTTAGGGT 59.097 55.0 0.0 0.0 39.29 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2120 2748 0.040425 GGTTAACCACGCTGCACTTG 60.040 55.0 20.12 0.0 35.64 3.16 R
2351 6524 6.183810 TGATTGATTGCATCTACTCAGGAT 57.816 37.5 0.00 0.0 0.00 3.24 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
17 18 3.159615 TGCAGGTGGAGATGTGCA 58.840 55.556 0.00 0.00 43.50 4.57
18 19 1.455412 TGCAGGTGGAGATGTGCAA 59.545 52.632 0.00 0.00 42.79 4.08
19 20 0.890542 TGCAGGTGGAGATGTGCAAC 60.891 55.000 0.00 0.00 42.79 4.17
97 102 2.749800 GCCACCCAACTCTGAGTTCTTT 60.750 50.000 19.65 4.50 36.03 2.52
100 105 5.130350 CCACCCAACTCTGAGTTCTTTAAA 58.870 41.667 19.65 0.00 36.03 1.52
128 133 3.698539 TGTTGATGCAAGTTTTGTGGAGA 59.301 39.130 0.00 0.00 0.00 3.71
243 248 0.903236 GAGGAAGCGGAACTTAGGGT 59.097 55.000 0.00 0.00 39.29 4.34
2119 2747 3.136750 CCAGGGCGAGATCAGGAG 58.863 66.667 0.00 0.00 0.00 3.69
2120 2748 2.420890 CAGGGCGAGATCAGGAGC 59.579 66.667 0.00 0.00 0.00 4.70
2237 6410 3.390819 TGTTATACCTCCTTTCTCCCCC 58.609 50.000 0.00 0.00 0.00 5.40
2334 6507 9.836864 TCATATATAAACACTGTCATTTCAGCT 57.163 29.630 0.00 0.00 38.84 4.24
2404 6577 1.330234 TGCAAACCTGACATGCATGT 58.670 45.000 31.82 31.82 44.52 3.21
2407 6580 3.510753 TGCAAACCTGACATGCATGTAAT 59.489 39.130 31.45 14.58 44.52 1.89
2426 6602 8.970691 ATGTAATGAATCAGTAACAAAGTTGC 57.029 30.769 0.00 0.00 0.00 4.17
2452 6628 1.135603 ACATCAACACATCACATGCGC 60.136 47.619 0.00 0.00 0.00 6.09
2601 6777 0.602638 TCCGTTGTGTTAGCAGCCAG 60.603 55.000 0.00 0.00 0.00 4.85
2633 6809 4.394300 CCTCTCTGGCACTAAACATTTCTG 59.606 45.833 0.00 0.00 0.00 3.02
2641 6817 1.401905 CTAAACATTTCTGAGCCGGCC 59.598 52.381 26.15 15.80 0.00 6.13
2642 6818 1.586154 AAACATTTCTGAGCCGGCCG 61.586 55.000 26.15 21.04 0.00 6.13
2643 6819 3.204827 CATTTCTGAGCCGGCCGG 61.205 66.667 40.26 40.26 38.57 6.13
2664 6840 1.527034 GTGCAACTGATCTGCTGGAA 58.473 50.000 6.93 0.00 40.59 3.53
2668 6844 3.244526 TGCAACTGATCTGCTGGAAGTTA 60.245 43.478 6.93 0.00 40.59 2.24
2685 6861 5.533528 GGAAGTTAGTACAAAAGGGAAGCAA 59.466 40.000 0.00 0.00 0.00 3.91
2694 6870 6.618287 ACAAAAGGGAAGCAATTTTTAAGC 57.382 33.333 0.00 0.00 0.00 3.09
2982 7176 1.619654 CCAATGTTGGCTTCAGACCA 58.380 50.000 0.00 0.00 42.21 4.02
3030 7225 7.120285 TCTGGATGATTTCTGTTTCATGTCTTC 59.880 37.037 0.00 0.00 32.84 2.87
3076 7273 8.415950 AAATGGTTGTGGTATCTTGATAACAA 57.584 30.769 9.63 6.82 34.65 2.83
3077 7274 6.811253 TGGTTGTGGTATCTTGATAACAAC 57.189 37.500 19.68 19.68 44.08 3.32
3079 7276 6.190954 GTTGTGGTATCTTGATAACAACCC 57.809 41.667 18.34 7.16 40.78 4.11
3080 7277 5.772393 TGTGGTATCTTGATAACAACCCT 57.228 39.130 9.63 0.00 32.27 4.34
3081 7278 5.496556 TGTGGTATCTTGATAACAACCCTG 58.503 41.667 9.63 0.00 32.27 4.45
3082 7279 5.013704 TGTGGTATCTTGATAACAACCCTGT 59.986 40.000 9.63 0.00 37.39 4.00
3084 7281 6.093633 GTGGTATCTTGATAACAACCCTGTTC 59.906 42.308 9.63 0.00 42.25 3.18
3085 7282 6.177610 GGTATCTTGATAACAACCCTGTTCA 58.822 40.000 1.18 0.00 42.25 3.18
3086 7283 6.657541 GGTATCTTGATAACAACCCTGTTCAA 59.342 38.462 1.18 0.00 42.25 2.69
3087 7284 6.824305 ATCTTGATAACAACCCTGTTCAAG 57.176 37.500 11.10 11.10 44.61 3.02
3088 7285 5.935945 TCTTGATAACAACCCTGTTCAAGA 58.064 37.500 14.17 14.17 46.99 3.02
3089 7286 6.361433 TCTTGATAACAACCCTGTTCAAGAA 58.639 36.000 15.17 4.88 46.60 2.52
3090 7287 7.004086 TCTTGATAACAACCCTGTTCAAGAAT 58.996 34.615 15.17 0.00 46.60 2.40
3091 7288 7.505585 TCTTGATAACAACCCTGTTCAAGAATT 59.494 33.333 15.17 0.00 46.60 2.17
3092 7289 7.214467 TGATAACAACCCTGTTCAAGAATTC 57.786 36.000 0.00 0.00 42.25 2.17
3093 7290 6.775142 TGATAACAACCCTGTTCAAGAATTCA 59.225 34.615 8.44 0.00 42.25 2.57
3094 7291 7.451255 TGATAACAACCCTGTTCAAGAATTCAT 59.549 33.333 8.44 0.00 42.25 2.57
3095 7292 6.484364 AACAACCCTGTTCAAGAATTCATT 57.516 33.333 8.44 0.00 42.25 2.57
3096 7293 6.089249 ACAACCCTGTTCAAGAATTCATTC 57.911 37.500 8.44 0.00 32.39 2.67
3097 7294 5.156355 CAACCCTGTTCAAGAATTCATTCG 58.844 41.667 8.44 0.00 41.56 3.34
3098 7295 4.651778 ACCCTGTTCAAGAATTCATTCGA 58.348 39.130 8.44 0.00 41.56 3.71
3099 7296 5.256474 ACCCTGTTCAAGAATTCATTCGAT 58.744 37.500 8.44 0.00 41.56 3.59
3100 7297 5.711976 ACCCTGTTCAAGAATTCATTCGATT 59.288 36.000 8.44 0.00 41.56 3.34
3101 7298 6.209391 ACCCTGTTCAAGAATTCATTCGATTT 59.791 34.615 8.44 0.00 41.56 2.17
3102 7299 7.393234 ACCCTGTTCAAGAATTCATTCGATTTA 59.607 33.333 8.44 0.00 41.56 1.40
3103 7300 7.698130 CCCTGTTCAAGAATTCATTCGATTTAC 59.302 37.037 8.44 0.00 41.56 2.01
3104 7301 7.698130 CCTGTTCAAGAATTCATTCGATTTACC 59.302 37.037 8.44 0.00 41.56 2.85
3105 7302 8.105097 TGTTCAAGAATTCATTCGATTTACCA 57.895 30.769 8.44 0.00 41.56 3.25
3106 7303 8.236586 TGTTCAAGAATTCATTCGATTTACCAG 58.763 33.333 8.44 0.00 41.56 4.00
3107 7304 7.921786 TCAAGAATTCATTCGATTTACCAGT 57.078 32.000 8.44 0.00 41.56 4.00
3108 7305 8.335532 TCAAGAATTCATTCGATTTACCAGTT 57.664 30.769 8.44 0.00 41.56 3.16
3109 7306 9.443323 TCAAGAATTCATTCGATTTACCAGTTA 57.557 29.630 8.44 0.00 41.56 2.24
3116 7313 9.834628 TTCATTCGATTTACCAGTTAATTTGTC 57.165 29.630 0.00 0.00 0.00 3.18
3117 7314 8.172484 TCATTCGATTTACCAGTTAATTTGTCG 58.828 33.333 0.00 0.00 0.00 4.35
3118 7315 7.655236 TTCGATTTACCAGTTAATTTGTCGA 57.345 32.000 0.00 0.00 0.00 4.20
3119 7316 7.837202 TCGATTTACCAGTTAATTTGTCGAT 57.163 32.000 0.00 0.00 0.00 3.59
3120 7317 8.259049 TCGATTTACCAGTTAATTTGTCGATT 57.741 30.769 0.00 0.00 0.00 3.34
3121 7318 9.368674 TCGATTTACCAGTTAATTTGTCGATTA 57.631 29.630 0.00 0.00 0.00 1.75
3122 7319 9.976255 CGATTTACCAGTTAATTTGTCGATTAA 57.024 29.630 0.00 0.00 0.00 1.40
3126 7323 9.675464 TTACCAGTTAATTTGTCGATTAATCCT 57.325 29.630 9.87 0.00 34.87 3.24
3128 7325 9.106070 ACCAGTTAATTTGTCGATTAATCCTAC 57.894 33.333 9.87 8.87 34.87 3.18
3129 7326 9.326413 CCAGTTAATTTGTCGATTAATCCTACT 57.674 33.333 9.87 0.00 34.87 2.57
3131 7328 9.245962 AGTTAATTTGTCGATTAATCCTACTCG 57.754 33.333 9.87 0.00 34.87 4.18
3132 7329 9.028185 GTTAATTTGTCGATTAATCCTACTCGT 57.972 33.333 9.87 0.00 34.87 4.18
3134 7331 8.798748 AATTTGTCGATTAATCCTACTCGTAG 57.201 34.615 9.87 0.00 33.30 3.51
3135 7332 5.354054 TGTCGATTAATCCTACTCGTAGC 57.646 43.478 9.87 0.00 33.30 3.58
3136 7333 4.084171 TGTCGATTAATCCTACTCGTAGCG 60.084 45.833 9.87 0.00 33.30 4.26
3137 7334 4.060900 TCGATTAATCCTACTCGTAGCGT 58.939 43.478 9.87 0.00 33.30 5.07
3138 7335 4.151335 TCGATTAATCCTACTCGTAGCGTC 59.849 45.833 9.87 0.00 33.30 5.19
3139 7336 4.084171 CGATTAATCCTACTCGTAGCGTCA 60.084 45.833 9.87 0.00 31.95 4.35
3140 7337 4.542662 TTAATCCTACTCGTAGCGTCAC 57.457 45.455 0.00 0.00 31.95 3.67
3141 7338 2.328819 ATCCTACTCGTAGCGTCACT 57.671 50.000 0.00 0.00 31.95 3.41
3142 7339 1.366679 TCCTACTCGTAGCGTCACTG 58.633 55.000 0.00 0.00 31.95 3.66
3143 7340 1.066645 TCCTACTCGTAGCGTCACTGA 60.067 52.381 0.00 0.00 31.95 3.41
3144 7341 1.736126 CCTACTCGTAGCGTCACTGAA 59.264 52.381 0.00 0.00 31.95 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.270550 CCTTTGTTGCACATCTCCACC 59.729 52.381 0.00 0.00 0.00 4.61
5 6 1.956477 ACCTTTGTTGCACATCTCCAC 59.044 47.619 0.00 0.00 0.00 4.02
7 8 2.749621 CCTACCTTTGTTGCACATCTCC 59.250 50.000 0.00 0.00 0.00 3.71
8 9 2.749621 CCCTACCTTTGTTGCACATCTC 59.250 50.000 0.00 0.00 0.00 2.75
9 10 2.375174 TCCCTACCTTTGTTGCACATCT 59.625 45.455 0.00 0.00 0.00 2.90
10 11 2.790433 TCCCTACCTTTGTTGCACATC 58.210 47.619 0.00 0.00 0.00 3.06
11 12 2.969821 TCCCTACCTTTGTTGCACAT 57.030 45.000 0.00 0.00 0.00 3.21
12 13 2.092103 ACTTCCCTACCTTTGTTGCACA 60.092 45.455 0.00 0.00 0.00 4.57
13 14 2.583143 ACTTCCCTACCTTTGTTGCAC 58.417 47.619 0.00 0.00 0.00 4.57
14 15 3.219281 GAACTTCCCTACCTTTGTTGCA 58.781 45.455 0.00 0.00 0.00 4.08
15 16 3.219281 TGAACTTCCCTACCTTTGTTGC 58.781 45.455 0.00 0.00 0.00 4.17
16 17 3.253432 GCTGAACTTCCCTACCTTTGTTG 59.747 47.826 0.00 0.00 0.00 3.33
17 18 3.487372 GCTGAACTTCCCTACCTTTGTT 58.513 45.455 0.00 0.00 0.00 2.83
18 19 2.224793 GGCTGAACTTCCCTACCTTTGT 60.225 50.000 0.00 0.00 0.00 2.83
19 20 2.224769 TGGCTGAACTTCCCTACCTTTG 60.225 50.000 0.00 0.00 0.00 2.77
20 21 2.062636 TGGCTGAACTTCCCTACCTTT 58.937 47.619 0.00 0.00 0.00 3.11
21 22 1.742308 TGGCTGAACTTCCCTACCTT 58.258 50.000 0.00 0.00 0.00 3.50
22 23 1.351350 GTTGGCTGAACTTCCCTACCT 59.649 52.381 0.00 0.00 0.00 3.08
23 24 1.613520 GGTTGGCTGAACTTCCCTACC 60.614 57.143 3.24 3.24 37.37 3.18
24 25 1.073284 TGGTTGGCTGAACTTCCCTAC 59.927 52.381 0.00 0.00 34.66 3.18
25 26 1.073284 GTGGTTGGCTGAACTTCCCTA 59.927 52.381 0.00 0.00 34.66 3.53
26 27 0.178990 GTGGTTGGCTGAACTTCCCT 60.179 55.000 0.00 0.00 34.66 4.20
100 105 7.714377 TCCACAAAACTTGCATCAACATTAATT 59.286 29.630 0.00 0.00 0.00 1.40
109 114 2.622942 GGTCTCCACAAAACTTGCATCA 59.377 45.455 0.00 0.00 0.00 3.07
128 133 2.552315 CCACACTCGCAACTTTAATGGT 59.448 45.455 0.00 0.00 0.00 3.55
380 385 5.361285 CACCAGTAGCTTCTAGGTATTGACT 59.639 44.000 11.97 0.00 37.90 3.41
607 616 2.798976 ACTGGTAGTTCGCAAACGTA 57.201 45.000 0.00 0.00 40.48 3.57
2119 2747 0.660300 GTTAACCACGCTGCACTTGC 60.660 55.000 0.00 0.00 42.50 4.01
2120 2748 0.040425 GGTTAACCACGCTGCACTTG 60.040 55.000 20.12 0.00 35.64 3.16
2351 6524 6.183810 TGATTGATTGCATCTACTCAGGAT 57.816 37.500 0.00 0.00 0.00 3.24
2404 6577 8.440059 CGTAGCAACTTTGTTACTGATTCATTA 58.560 33.333 12.40 0.00 41.07 1.90
2407 6580 6.223138 CGTAGCAACTTTGTTACTGATTCA 57.777 37.500 12.40 0.00 41.07 2.57
2426 6602 2.736192 TGTGATGTGTTGATGTGCGTAG 59.264 45.455 0.00 0.00 0.00 3.51
2507 6683 5.008019 CCAATAATGAGTCCATTCTTGACCG 59.992 44.000 14.01 0.32 43.65 4.79
2621 6797 1.401905 GGCCGGCTCAGAAATGTTTAG 59.598 52.381 28.56 0.00 0.00 1.85
2641 6817 2.780643 CAGATCAGTTGCACGCCG 59.219 61.111 0.00 0.00 0.00 6.46
2642 6818 2.037136 AGCAGATCAGTTGCACGCC 61.037 57.895 8.02 0.00 43.92 5.68
2643 6819 1.134075 CAGCAGATCAGTTGCACGC 59.866 57.895 8.02 0.00 43.92 5.34
2644 6820 0.671472 TCCAGCAGATCAGTTGCACG 60.671 55.000 8.02 0.00 43.92 5.34
2645 6821 1.467734 CTTCCAGCAGATCAGTTGCAC 59.532 52.381 8.02 0.00 43.92 4.57
2664 6840 7.597288 AAATTGCTTCCCTTTTGTACTAACT 57.403 32.000 0.00 0.00 0.00 2.24
2668 6844 7.441157 GCTTAAAAATTGCTTCCCTTTTGTACT 59.559 33.333 0.00 0.00 0.00 2.73
2685 6861 2.888212 TGTGGGAGGCTGCTTAAAAAT 58.112 42.857 5.84 0.00 0.00 1.82
2694 6870 2.125326 CATGGCATGTGGGAGGCTG 61.125 63.158 19.32 0.00 0.00 4.85
2795 6971 2.191128 ACTGGCATCTCAAGTGTTCC 57.809 50.000 0.00 0.00 0.00 3.62
2831 7007 8.573035 AGGACACGTTTCATTTTTGTATACAAT 58.427 29.630 18.69 1.73 35.55 2.71
3050 7247 8.415950 TGTTATCAAGATACCACAACCATTTT 57.584 30.769 0.00 0.00 0.00 1.82
3076 7273 4.651778 TCGAATGAATTCTTGAACAGGGT 58.348 39.130 7.05 0.00 34.69 4.34
3077 7274 5.824904 ATCGAATGAATTCTTGAACAGGG 57.175 39.130 7.05 0.00 34.69 4.45
3078 7275 7.698130 GGTAAATCGAATGAATTCTTGAACAGG 59.302 37.037 7.05 0.00 34.69 4.00
3079 7276 8.236586 TGGTAAATCGAATGAATTCTTGAACAG 58.763 33.333 7.05 0.00 34.69 3.16
3080 7277 8.105097 TGGTAAATCGAATGAATTCTTGAACA 57.895 30.769 7.05 0.00 34.69 3.18
3081 7278 8.237267 ACTGGTAAATCGAATGAATTCTTGAAC 58.763 33.333 7.05 0.00 34.69 3.18
3082 7279 8.335532 ACTGGTAAATCGAATGAATTCTTGAA 57.664 30.769 7.05 0.00 34.69 2.69
3083 7280 7.921786 ACTGGTAAATCGAATGAATTCTTGA 57.078 32.000 7.05 0.00 34.69 3.02
3090 7287 9.834628 GACAAATTAACTGGTAAATCGAATGAA 57.165 29.630 0.00 0.00 0.00 2.57
3091 7288 8.172484 CGACAAATTAACTGGTAAATCGAATGA 58.828 33.333 0.00 0.00 0.00 2.57
3092 7289 8.172484 TCGACAAATTAACTGGTAAATCGAATG 58.828 33.333 10.21 0.00 0.00 2.67
3093 7290 8.259049 TCGACAAATTAACTGGTAAATCGAAT 57.741 30.769 10.21 0.00 0.00 3.34
3094 7291 7.655236 TCGACAAATTAACTGGTAAATCGAA 57.345 32.000 10.21 0.00 0.00 3.71
3095 7292 7.837202 ATCGACAAATTAACTGGTAAATCGA 57.163 32.000 13.24 13.24 0.00 3.59
3096 7293 9.976255 TTAATCGACAAATTAACTGGTAAATCG 57.024 29.630 0.00 0.00 0.00 3.34
3100 7297 9.675464 AGGATTAATCGACAAATTAACTGGTAA 57.325 29.630 9.32 0.00 34.75 2.85
3102 7299 9.106070 GTAGGATTAATCGACAAATTAACTGGT 57.894 33.333 9.32 0.00 34.75 4.00
3103 7300 9.326413 AGTAGGATTAATCGACAAATTAACTGG 57.674 33.333 16.96 0.00 34.75 4.00
3105 7302 9.245962 CGAGTAGGATTAATCGACAAATTAACT 57.754 33.333 16.96 5.68 46.95 2.24
3106 7303 9.028185 ACGAGTAGGATTAATCGACAAATTAAC 57.972 33.333 16.96 3.97 46.95 2.01
3108 7305 9.888878 CTACGAGTAGGATTAATCGACAAATTA 57.111 33.333 16.96 2.82 46.95 1.40
3109 7306 7.381678 GCTACGAGTAGGATTAATCGACAAATT 59.618 37.037 16.96 1.83 46.95 1.82
3110 7307 6.862090 GCTACGAGTAGGATTAATCGACAAAT 59.138 38.462 16.96 0.00 46.95 2.32
3111 7308 6.204359 GCTACGAGTAGGATTAATCGACAAA 58.796 40.000 16.96 0.00 46.95 2.83
3112 7309 5.559608 CGCTACGAGTAGGATTAATCGACAA 60.560 44.000 16.96 0.00 46.95 3.18
3113 7310 4.084171 CGCTACGAGTAGGATTAATCGACA 60.084 45.833 16.96 1.37 46.95 4.35
3114 7311 4.084118 ACGCTACGAGTAGGATTAATCGAC 60.084 45.833 9.32 9.65 46.95 4.20
3115 7312 4.060900 ACGCTACGAGTAGGATTAATCGA 58.939 43.478 9.32 0.00 46.95 3.59
3117 7314 5.049543 AGTGACGCTACGAGTAGGATTAATC 60.050 44.000 6.93 6.93 33.87 1.75
3118 7315 4.820716 AGTGACGCTACGAGTAGGATTAAT 59.179 41.667 11.69 0.00 33.87 1.40
3119 7316 4.034858 CAGTGACGCTACGAGTAGGATTAA 59.965 45.833 11.69 0.00 33.87 1.40
3120 7317 3.558829 CAGTGACGCTACGAGTAGGATTA 59.441 47.826 11.69 0.00 33.87 1.75
3121 7318 2.355132 CAGTGACGCTACGAGTAGGATT 59.645 50.000 11.69 0.00 33.87 3.01
3122 7319 1.941294 CAGTGACGCTACGAGTAGGAT 59.059 52.381 11.69 0.00 33.87 3.24
3123 7320 1.066645 TCAGTGACGCTACGAGTAGGA 60.067 52.381 11.69 0.00 33.87 2.94
3124 7321 1.366679 TCAGTGACGCTACGAGTAGG 58.633 55.000 11.69 5.16 33.87 3.18


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

AutoCloner maintained by Alex Coulton.