Multiple sequence alignment - TraesCS1D01G246500

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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 TraesCS1D01G246500 chr1D 100.000 7361 0 0 1 7361 339106287 339113647 0.000000e+00 13594
1 TraesCS1D01G246500 chr1D 75.281 267 58 7 5202 5464 16404237 16403975 3.610000e-23 121
2 TraesCS1D01G246500 chr1B 93.356 4485 164 60 6 4445 453873700 453878095 0.000000e+00 6508
3 TraesCS1D01G246500 chr1B 94.895 1430 58 8 5538 6962 453879437 453880856 0.000000e+00 2222
4 TraesCS1D01G246500 chr1B 93.510 1094 33 6 4446 5538 453878135 453879191 0.000000e+00 1592
5 TraesCS1D01G246500 chr1B 98.540 548 7 1 6814 7361 453881115 453881661 0.000000e+00 966
6 TraesCS1D01G246500 chr1B 92.105 76 5 1 6756 6830 453880863 453880938 1.010000e-18 106
7 TraesCS1D01G246500 chr1A 96.067 3585 110 17 878 4445 438693457 438697027 0.000000e+00 5810
8 TraesCS1D01G246500 chr1A 95.109 2924 72 11 4446 7361 438697067 438699927 0.000000e+00 4542
9 TraesCS1D01G246500 chr1A 89.375 800 41 26 12 791 438692623 438693398 0.000000e+00 966
10 TraesCS1D01G246500 chr1A 75.479 261 56 6 5196 5452 16917986 16918242 3.610000e-23 121
11 TraesCS1D01G246500 chr2D 86.000 350 49 0 3565 3914 318331103 318330754 6.970000e-100 375
12 TraesCS1D01G246500 chr2D 77.236 615 113 22 5761 6358 318329704 318329100 1.180000e-87 335
13 TraesCS1D01G246500 chr2D 88.649 185 21 0 2498 2682 318332332 318332148 7.430000e-55 226
14 TraesCS1D01G246500 chr2D 83.750 160 25 1 2815 2973 318331896 318331737 4.600000e-32 150
15 TraesCS1D01G246500 chr2B 89.189 185 20 0 2498 2682 386309636 386309452 1.600000e-56 231
16 TraesCS1D01G246500 chr2B 83.750 160 25 1 2815 2973 386309215 386309056 4.600000e-32 150
17 TraesCS1D01G246500 chr2A 90.798 163 15 0 2498 2660 413329300 413329462 1.240000e-52 219
18 TraesCS1D01G246500 chr2A 84.795 171 22 4 2805 2973 413329689 413329857 1.270000e-37 169
19 TraesCS1D01G246500 chr6D 97.619 84 2 0 4619 4702 168293761 168293844 2.140000e-30 145
20 TraesCS1D01G246500 chr6D 95.349 86 4 0 4619 4704 309072510 309072595 3.580000e-28 137
21 TraesCS1D01G246500 chr3D 97.531 81 2 0 4619 4699 384726631 384726711 9.960000e-29 139
22 TraesCS1D01G246500 chr7A 95.349 86 4 0 4619 4704 477234926 477234841 3.580000e-28 137
23 TraesCS1D01G246500 chr5D 95.349 86 4 0 4619 4704 111788722 111788637 3.580000e-28 137
24 TraesCS1D01G246500 chr4B 92.632 95 6 1 4619 4712 491017647 491017741 1.290000e-27 135
25 TraesCS1D01G246500 chr6A 88.991 109 8 3 4599 4707 594831600 594831704 1.670000e-26 132


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 TraesCS1D01G246500 chr1D 339106287 339113647 7360 False 13594.000000 13594 100.00000 1 7361 1 chr1D.!!$F1 7360
1 TraesCS1D01G246500 chr1B 453873700 453881661 7961 False 2278.800000 6508 94.48120 6 7361 5 chr1B.!!$F1 7355
2 TraesCS1D01G246500 chr1A 438692623 438699927 7304 False 3772.666667 5810 93.51700 12 7361 3 chr1A.!!$F2 7349
3 TraesCS1D01G246500 chr2D 318329100 318332332 3232 True 271.500000 375 83.90875 2498 6358 4 chr2D.!!$R1 3860

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
703 751 0.036765 TATCCTGCTGGTTTTCGCGT 60.037 50.000 5.77 0.0 34.23 6.01 F
1024 1097 0.035598 TTCCCTCAACGAAATCGCCA 59.964 50.000 2.15 0.0 44.43 5.69 F
1233 1306 1.097232 TTCTGAATTGGATGCCAGCG 58.903 50.000 0.00 0.0 33.81 5.18 F
2653 2736 1.604438 CGTCGACCTGACCAATTCACA 60.604 52.381 10.58 0.0 45.23 3.58 F
3705 3985 1.375523 CCGACAGTGTGGCTAACCC 60.376 63.158 0.00 0.0 33.59 4.11 F
4938 5268 2.105128 GACAGGAGGACCGCATCG 59.895 66.667 0.00 0.0 41.83 3.84 F
5365 5700 1.274703 TGGATCCTGGGAGCTTGGAC 61.275 60.000 14.23 0.0 32.16 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1688 1762 0.549469 ATGATCCATGCCTGTGCTGA 59.451 50.000 0.00 0.00 38.71 4.26 R
2143 2225 3.560636 TCCTAGAGGGTTATGCAAAGC 57.439 47.619 0.00 0.00 36.25 3.51 R
2928 3139 4.635765 CAGTGGAGATAAGATCGGCAAAAA 59.364 41.667 0.00 0.00 0.00 1.94 R
4032 4314 0.532862 ACCGAGTCACAAGCCAGTTG 60.533 55.000 0.00 0.00 42.48 3.16 R
5365 5700 0.385390 GTGGTTCAGTGGTGCCAAAG 59.615 55.000 0.00 0.00 32.26 2.77 R
5801 6394 1.226974 GAATAGTGCGCCGCTCTCA 60.227 57.895 17.69 5.01 34.22 3.27 R
6631 7252 4.009675 TCCTGTAGCTTGCATTTGTAAGG 58.990 43.478 9.88 0.00 38.05 2.69 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
23 24 4.527816 AGTCCAAATGGTAAGTACACCGTA 59.472 41.667 0.00 0.00 41.88 4.02
237 249 4.320456 CCATCCCCTCGCCATCGG 62.320 72.222 0.00 0.00 36.13 4.18
277 302 5.693769 AAATCCAAATCTCCTCTCCGTTA 57.306 39.130 0.00 0.00 0.00 3.18
278 303 5.693769 AATCCAAATCTCCTCTCCGTTAA 57.306 39.130 0.00 0.00 0.00 2.01
279 304 4.467198 TCCAAATCTCCTCTCCGTTAAC 57.533 45.455 0.00 0.00 0.00 2.01
280 305 3.119245 TCCAAATCTCCTCTCCGTTAACG 60.119 47.826 20.99 20.99 39.44 3.18
281 306 3.368116 CCAAATCTCCTCTCCGTTAACGT 60.368 47.826 25.15 1.73 37.74 3.99
282 307 4.243270 CAAATCTCCTCTCCGTTAACGTT 58.757 43.478 25.15 5.88 37.74 3.99
288 313 2.493278 CCTCTCCGTTAACGTTTCCCTA 59.507 50.000 25.15 4.18 37.74 3.53
301 326 2.363795 CCCTACCGTCTCTGCCCA 60.364 66.667 0.00 0.00 0.00 5.36
315 340 4.293671 CCCACGGGCCTTTTCCCA 62.294 66.667 0.84 0.00 46.92 4.37
381 406 4.162690 CGTGAGGGGTGCCTAGCC 62.163 72.222 0.00 0.00 43.86 3.93
382 407 2.689034 GTGAGGGGTGCCTAGCCT 60.689 66.667 0.00 0.00 44.05 4.58
383 408 1.382695 GTGAGGGGTGCCTAGCCTA 60.383 63.158 0.00 0.00 44.05 3.93
384 409 1.075226 TGAGGGGTGCCTAGCCTAG 60.075 63.158 0.00 0.00 44.05 3.02
385 410 2.446802 AGGGGTGCCTAGCCTAGC 60.447 66.667 0.00 0.00 44.05 3.42
486 517 1.021390 CGTCAAGGCATTTCTCGGCT 61.021 55.000 0.00 0.00 41.78 5.52
495 526 3.305744 GGCATTTCTCGGCTAACCAAAAA 60.306 43.478 0.00 0.00 34.57 1.94
496 527 3.673338 GCATTTCTCGGCTAACCAAAAAC 59.327 43.478 0.00 0.00 34.57 2.43
497 528 4.794655 GCATTTCTCGGCTAACCAAAAACA 60.795 41.667 0.00 0.00 34.57 2.83
498 529 5.469479 CATTTCTCGGCTAACCAAAAACAT 58.531 37.500 0.00 0.00 34.57 2.71
500 531 3.482436 TCTCGGCTAACCAAAAACATGT 58.518 40.909 0.00 0.00 34.57 3.21
501 532 3.886505 TCTCGGCTAACCAAAAACATGTT 59.113 39.130 4.92 4.92 34.57 2.71
502 533 4.023536 TCTCGGCTAACCAAAAACATGTTC 60.024 41.667 12.39 0.00 34.57 3.18
503 534 3.886505 TCGGCTAACCAAAAACATGTTCT 59.113 39.130 12.39 0.00 34.57 3.01
508 544 2.758130 ACCAAAAACATGTTCTGGGGT 58.242 42.857 29.50 22.63 32.64 4.95
557 593 5.586243 TGTCATTGAAAATCTCTTCGGATCC 59.414 40.000 0.00 0.00 0.00 3.36
577 613 2.936498 CCCATTCGTTCCTGTGTATGTC 59.064 50.000 0.00 0.00 0.00 3.06
603 639 5.652014 CACCTAACATGCATTTTCCTAGGAA 59.348 40.000 20.72 20.72 0.00 3.36
659 698 4.024048 ACGTGTTATTGCTATATTGGCTGC 60.024 41.667 0.00 0.00 0.00 5.25
699 747 6.024552 TCATTTTGTATCCTGCTGGTTTTC 57.975 37.500 9.73 0.57 34.23 2.29
703 751 0.036765 TATCCTGCTGGTTTTCGCGT 60.037 50.000 5.77 0.00 34.23 6.01
742 790 5.232463 TGAATTGCAGAAATCTTTCCAAGC 58.768 37.500 0.00 3.06 37.92 4.01
743 791 5.011329 TGAATTGCAGAAATCTTTCCAAGCT 59.989 36.000 11.22 0.00 37.92 3.74
744 792 3.928727 TGCAGAAATCTTTCCAAGCTG 57.071 42.857 0.00 0.00 37.92 4.24
750 798 2.206576 ATCTTTCCAAGCTGTGTCCC 57.793 50.000 0.00 0.00 0.00 4.46
872 920 5.407049 ACAGATGGCCATCCTACTAAGTAT 58.593 41.667 36.81 15.60 38.58 2.12
873 921 6.562228 ACAGATGGCCATCCTACTAAGTATA 58.438 40.000 36.81 0.00 38.58 1.47
1024 1097 0.035598 TTCCCTCAACGAAATCGCCA 59.964 50.000 2.15 0.00 44.43 5.69
1230 1303 1.818060 CGGTTTCTGAATTGGATGCCA 59.182 47.619 0.00 0.00 0.00 4.92
1233 1306 1.097232 TTCTGAATTGGATGCCAGCG 58.903 50.000 0.00 0.00 33.81 5.18
1393 1467 5.204409 TCATGTCTTGCAAGCTCAAAAAT 57.796 34.783 21.99 1.64 0.00 1.82
1408 1482 3.686241 TCAAAAATGATGACCTCGAGCTG 59.314 43.478 6.99 0.00 0.00 4.24
1441 1515 9.204570 GCTAGTACAAAACATGACTCTTTCTTA 57.795 33.333 0.00 0.00 0.00 2.10
1529 1603 1.868469 TTGTGCCAATTGCTTTGCTC 58.132 45.000 0.00 0.00 42.00 4.26
1560 1634 6.691255 TTGTCCTAGTACCTGTTAATTGGT 57.309 37.500 7.37 7.37 40.12 3.67
1561 1635 6.290294 TGTCCTAGTACCTGTTAATTGGTC 57.710 41.667 5.74 0.51 37.74 4.02
1571 1645 5.072600 ACCTGTTAATTGGTCTAGTGGAACA 59.927 40.000 0.00 0.00 40.31 3.18
1628 1702 8.452989 AAATTGACAAGCTTTCGATATCAAAC 57.547 30.769 0.00 0.00 0.00 2.93
2028 2107 5.877012 GCAGTCAATCTTTAGGATTCTGTCA 59.123 40.000 7.31 0.00 42.20 3.58
2246 2328 7.582667 AACAAACAGAAAAACCTAGCTGTAT 57.417 32.000 0.00 0.00 40.43 2.29
2402 2484 7.561021 TGTTTTGTATCTGCAACTGAAACTA 57.439 32.000 14.66 5.37 31.19 2.24
2653 2736 1.604438 CGTCGACCTGACCAATTCACA 60.604 52.381 10.58 0.00 45.23 3.58
2751 2837 6.051646 TCTTAGACTTGTTGCGTTTAAACC 57.948 37.500 12.66 6.35 0.00 3.27
2928 3139 6.681729 TTACCTCAGTCATCAGGTTTTACT 57.318 37.500 0.00 0.00 40.35 2.24
2966 3178 3.616219 TCCACTGTGGTATTGTTATGGC 58.384 45.455 25.15 0.00 39.03 4.40
3445 3675 1.532078 GGGTCTTTGGGGGCGAAAA 60.532 57.895 0.00 0.00 0.00 2.29
3705 3985 1.375523 CCGACAGTGTGGCTAACCC 60.376 63.158 0.00 0.00 33.59 4.11
3979 4260 3.296628 AGCATTTACAGCGTGTTTTTCG 58.703 40.909 0.00 0.00 37.01 3.46
4032 4314 7.389607 TCCTACTACTTCAACAATTTAGGCAAC 59.610 37.037 0.00 0.00 0.00 4.17
4082 4364 3.003897 GTCCTAAGAGCTACATGGAGACG 59.996 52.174 9.87 0.00 0.00 4.18
4091 4373 4.631813 AGCTACATGGAGACGTTTTGATTC 59.368 41.667 9.87 0.00 0.00 2.52
4166 4449 2.266279 TGTTAGGCTTACAAGAGGGCT 58.734 47.619 3.48 0.00 39.21 5.19
4169 4452 2.255770 AGGCTTACAAGAGGGCTACT 57.744 50.000 0.00 0.00 34.14 2.57
4170 4453 2.552367 AGGCTTACAAGAGGGCTACTT 58.448 47.619 0.00 0.00 34.14 2.24
4171 4454 2.913617 AGGCTTACAAGAGGGCTACTTT 59.086 45.455 0.00 0.00 34.14 2.66
4172 4455 3.330998 AGGCTTACAAGAGGGCTACTTTT 59.669 43.478 0.00 0.00 34.14 2.27
4173 4456 3.690139 GGCTTACAAGAGGGCTACTTTTC 59.310 47.826 0.00 0.00 0.00 2.29
4174 4457 4.324267 GCTTACAAGAGGGCTACTTTTCA 58.676 43.478 0.00 0.00 0.00 2.69
4288 4578 3.997021 AGTTCATTTGTAGCCGTTCTCAG 59.003 43.478 0.00 0.00 0.00 3.35
4531 4861 6.816140 ACCGATTAATAAAAATGTTGCCCAAG 59.184 34.615 0.00 0.00 0.00 3.61
4851 5181 5.882000 GCCAGGGATTGCATTAAAAATCTTT 59.118 36.000 0.00 0.00 34.01 2.52
4917 5247 6.214208 TGGAAGGTCATATATCAATCTCTGGG 59.786 42.308 0.00 0.00 0.00 4.45
4938 5268 2.105128 GACAGGAGGACCGCATCG 59.895 66.667 0.00 0.00 41.83 3.84
5126 5461 2.830923 CAATGGGGCCAATGTTTACTGA 59.169 45.455 4.39 0.00 0.00 3.41
5144 5479 3.826729 ACTGACACCTAATTCTTTTGCCC 59.173 43.478 0.00 0.00 0.00 5.36
5365 5700 1.274703 TGGATCCTGGGAGCTTGGAC 61.275 60.000 14.23 0.00 32.16 4.02
5491 5826 4.558226 TGCCTATCTTGTGTTCAGACAT 57.442 40.909 0.00 0.00 38.23 3.06
5569 6160 9.814899 TTTATTTCTTTTTGTGAGATCTTGCAA 57.185 25.926 0.00 0.00 0.00 4.08
5592 6183 5.361135 CAGTATGTTTGCTGTCATCACAA 57.639 39.130 0.00 0.00 31.56 3.33
5670 6261 7.626452 GCCATTCTTAGTAAACAACTGGATGTC 60.626 40.741 0.00 0.00 39.39 3.06
5723 6316 5.277731 GCTAGGCAGCTTTCATACTTCATTC 60.278 44.000 0.00 0.00 44.93 2.67
5786 6379 5.565592 TTCGCTGCAAGATCATTAATGTT 57.434 34.783 14.97 7.03 34.07 2.71
6051 6665 7.503549 TCTTCATTAAGATCTTCAGCATAGCA 58.496 34.615 12.24 0.00 36.80 3.49
6229 6843 6.239217 AGGATGACATGTATGAGCTTGTTA 57.761 37.500 0.00 0.00 0.00 2.41
6343 6960 4.081972 GCACTGATGAAGGAGAGTTCAGTA 60.082 45.833 3.79 0.00 43.76 2.74
6507 7125 4.724602 GCCGCCATGAAATTGAAAATTTCG 60.725 41.667 16.52 8.09 40.02 3.46
6508 7126 4.201705 CCGCCATGAAATTGAAAATTTCGG 60.202 41.667 16.52 14.03 40.02 4.30
6722 7343 0.391528 GGGCAAATGGGTGCATCAAC 60.392 55.000 0.00 0.00 46.81 3.18
6741 7362 7.761704 GCATCAACTCAGAACTTCTACTGATAA 59.238 37.037 0.00 0.00 41.35 1.75
6751 7372 7.554476 AGAACTTCTACTGATAATTTCAAGCCC 59.446 37.037 0.00 0.00 32.78 5.19
6831 7855 3.801114 AACAGCAACTGGAAAAAGGAC 57.199 42.857 0.00 0.00 35.51 3.85
6911 7935 4.881850 ACAGAACTGGAATTTCTTTCGTGT 59.118 37.500 6.76 2.52 34.98 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.667360 ACGGTGTACTTACCATTTGGAC 58.333 45.455 3.01 0.00 40.89 4.02
2 3 4.282957 TGTACGGTGTACTTACCATTTGGA 59.717 41.667 3.01 0.00 40.89 3.53
3 4 4.567971 TGTACGGTGTACTTACCATTTGG 58.432 43.478 8.41 0.00 40.89 3.28
4 5 5.870433 TCATGTACGGTGTACTTACCATTTG 59.130 40.000 8.41 0.00 40.89 2.32
6 7 5.664294 TCATGTACGGTGTACTTACCATT 57.336 39.130 8.41 0.00 40.89 3.16
8 9 5.465532 TTTCATGTACGGTGTACTTACCA 57.534 39.130 8.41 0.00 40.89 3.25
10 11 7.095102 ACCAAATTTCATGTACGGTGTACTTAC 60.095 37.037 8.41 0.00 0.00 2.34
11 12 6.935771 ACCAAATTTCATGTACGGTGTACTTA 59.064 34.615 8.41 0.00 0.00 2.24
12 13 5.766174 ACCAAATTTCATGTACGGTGTACTT 59.234 36.000 8.41 0.00 0.00 2.24
13 14 5.310451 ACCAAATTTCATGTACGGTGTACT 58.690 37.500 8.41 0.00 0.00 2.73
14 15 5.391203 GGACCAAATTTCATGTACGGTGTAC 60.391 44.000 0.00 0.22 0.00 2.90
15 16 4.696402 GGACCAAATTTCATGTACGGTGTA 59.304 41.667 0.00 0.00 0.00 2.90
16 17 3.504520 GGACCAAATTTCATGTACGGTGT 59.495 43.478 0.00 0.00 0.00 4.16
17 18 3.504134 TGGACCAAATTTCATGTACGGTG 59.496 43.478 0.00 0.00 0.00 4.94
20 21 4.695455 ACTCTGGACCAAATTTCATGTACG 59.305 41.667 0.00 0.00 0.00 3.67
23 24 6.068010 TGTAACTCTGGACCAAATTTCATGT 58.932 36.000 0.00 0.00 0.00 3.21
75 81 2.481185 GTCCTCGTCGGTTAAATTGCAA 59.519 45.455 0.00 0.00 0.00 4.08
148 155 4.641645 CCTTGTGTCCGGCTGGCA 62.642 66.667 6.73 5.56 34.14 4.92
150 157 3.612247 CTCCCTTGTGTCCGGCTGG 62.612 68.421 4.71 4.71 0.00 4.85
237 249 1.828979 TTTGTCGGGTTTGGCTATCC 58.171 50.000 0.00 0.00 0.00 2.59
277 302 1.271656 CAGAGACGGTAGGGAAACGTT 59.728 52.381 0.00 0.00 41.40 3.99
278 303 0.886563 CAGAGACGGTAGGGAAACGT 59.113 55.000 0.00 0.00 44.35 3.99
279 304 0.458025 GCAGAGACGGTAGGGAAACG 60.458 60.000 0.00 0.00 0.00 3.60
280 305 0.108281 GGCAGAGACGGTAGGGAAAC 60.108 60.000 0.00 0.00 0.00 2.78
281 306 1.262640 GGGCAGAGACGGTAGGGAAA 61.263 60.000 0.00 0.00 0.00 3.13
282 307 1.684734 GGGCAGAGACGGTAGGGAA 60.685 63.158 0.00 0.00 0.00 3.97
381 406 1.903183 GGGCATTACCTCCTAGGCTAG 59.097 57.143 14.77 14.77 39.63 3.42
382 407 1.508185 AGGGCATTACCTCCTAGGCTA 59.492 52.381 2.96 0.00 39.63 3.93
383 408 0.269173 AGGGCATTACCTCCTAGGCT 59.731 55.000 2.96 0.00 39.63 4.58
384 409 2.855669 AGGGCATTACCTCCTAGGC 58.144 57.895 2.96 0.00 39.63 3.93
455 480 2.170397 TGCCTTGACGATATCACCATGT 59.830 45.455 3.12 0.00 36.92 3.21
486 517 4.100189 CACCCCAGAACATGTTTTTGGTTA 59.900 41.667 27.59 0.00 0.00 2.85
495 526 2.034066 CGGCACCCCAGAACATGT 59.966 61.111 0.00 0.00 0.00 3.21
496 527 3.443045 GCGGCACCCCAGAACATG 61.443 66.667 0.00 0.00 0.00 3.21
497 528 3.210012 AAGCGGCACCCCAGAACAT 62.210 57.895 1.45 0.00 0.00 2.71
498 529 3.842925 GAAGCGGCACCCCAGAACA 62.843 63.158 1.45 0.00 0.00 3.18
500 531 1.558167 TATGAAGCGGCACCCCAGAA 61.558 55.000 1.45 0.00 0.00 3.02
501 532 1.971505 CTATGAAGCGGCACCCCAGA 61.972 60.000 1.45 0.00 0.00 3.86
502 533 1.524621 CTATGAAGCGGCACCCCAG 60.525 63.158 1.45 0.00 0.00 4.45
503 534 1.344953 ATCTATGAAGCGGCACCCCA 61.345 55.000 1.45 0.00 0.00 4.96
508 544 0.315251 CGAGGATCTATGAAGCGGCA 59.685 55.000 1.45 0.00 0.00 5.69
557 593 2.603110 CGACATACACAGGAACGAATGG 59.397 50.000 0.00 0.00 0.00 3.16
577 613 2.164219 AGGAAAATGCATGTTAGGTGCG 59.836 45.455 0.95 0.00 45.37 5.34
659 698 8.567285 ACAAAATGAAAACCTAGTCCTAGATG 57.433 34.615 2.86 0.00 35.21 2.90
699 747 4.055360 TCATACCAGAATTCCATAACGCG 58.945 43.478 3.53 3.53 0.00 6.01
703 751 7.779326 TCTGCAATTCATACCAGAATTCCATAA 59.221 33.333 0.65 0.00 44.16 1.90
742 790 3.927142 GTGAGTAATTCTTCGGGACACAG 59.073 47.826 0.00 0.00 0.00 3.66
743 791 3.322541 TGTGAGTAATTCTTCGGGACACA 59.677 43.478 0.00 0.00 34.24 3.72
744 792 3.921677 TGTGAGTAATTCTTCGGGACAC 58.078 45.455 0.00 0.00 0.00 3.67
750 798 9.270576 CATCAAATCTTTGTGAGTAATTCTTCG 57.729 33.333 2.82 0.00 39.18 3.79
807 855 6.367161 ACCATGGTCATGATCATCAACATTA 58.633 36.000 18.79 0.42 41.20 1.90
970 1043 4.101114 TCTCTAGAGAGACTCACTCCAGT 58.899 47.826 18.76 0.00 45.48 4.00
1024 1097 4.826733 TGATATGTTTATTCCCGCAGCAAT 59.173 37.500 0.00 0.00 0.00 3.56
1035 1108 7.844493 ACCCAATGCTGATGATATGTTTATT 57.156 32.000 0.00 0.00 0.00 1.40
1203 1276 4.780815 TCCAATTCAGAAACCGCAGATAT 58.219 39.130 0.00 0.00 0.00 1.63
1230 1303 3.508840 GGCATTTGTAGCGCCGCT 61.509 61.111 18.67 18.67 43.41 5.52
1233 1306 0.179163 GTTCTGGCATTTGTAGCGCC 60.179 55.000 2.29 0.00 46.43 6.53
1335 1408 6.889301 AAACACAGTGATGTGAGAATTGAT 57.111 33.333 14.85 0.00 42.02 2.57
1355 1428 6.892310 AGACATGAAAGTGAAAGCAAAAAC 57.108 33.333 0.00 0.00 0.00 2.43
1393 1467 0.676782 TCGACAGCTCGAGGTCATCA 60.677 55.000 15.54 4.20 44.14 3.07
1408 1482 4.921515 TCATGTTTTGTACTAGCAGTCGAC 59.078 41.667 7.70 7.70 0.00 4.20
1422 1496 9.604626 GTCATCTTAAGAAAGAGTCATGTTTTG 57.395 33.333 9.71 0.00 44.79 2.44
1529 1603 3.804325 CAGGTACTAGGACAATGAATGCG 59.196 47.826 7.57 0.00 36.02 4.73
1560 1634 5.497464 TCATGTTCCAATGTTCCACTAGA 57.503 39.130 0.00 0.00 0.00 2.43
1561 1635 6.573664 TTTCATGTTCCAATGTTCCACTAG 57.426 37.500 0.00 0.00 0.00 2.57
1571 1645 7.729124 ATTCAGATCCTTTTCATGTTCCAAT 57.271 32.000 0.00 0.00 0.00 3.16
1688 1762 0.549469 ATGATCCATGCCTGTGCTGA 59.451 50.000 0.00 0.00 38.71 4.26
1901 1977 6.173427 ACATGGCTAAGTTTCAAATGGTTT 57.827 33.333 0.00 0.00 0.00 3.27
1972 2048 7.331026 TGACAACTATTCTCTGGAATAACCTG 58.669 38.462 0.00 0.00 41.93 4.00
2133 2215 5.011533 AGGGTTATGCAAAGCAAATTGTACA 59.988 36.000 0.00 0.00 43.62 2.90
2143 2225 3.560636 TCCTAGAGGGTTATGCAAAGC 57.439 47.619 0.00 0.00 36.25 3.51
2150 2232 5.911766 ACTAAATGGCTTCCTAGAGGGTTAT 59.088 40.000 0.00 0.00 36.25 1.89
2258 2340 7.064728 GCTTACTCCCAACTCTTAACATTGTAG 59.935 40.741 0.00 0.00 0.00 2.74
2451 2534 9.947669 ACGTAGACAGTACAAAACATAGATATC 57.052 33.333 0.00 0.00 0.00 1.63
2718 2804 8.784043 ACGCAACAAGTCTAAGAAGATAAAAAT 58.216 29.630 0.00 0.00 33.30 1.82
2796 2997 5.777732 ACCTAAATAGAGCAGGATAGGAGTG 59.222 44.000 3.80 0.00 35.12 3.51
2797 2998 5.971493 ACCTAAATAGAGCAGGATAGGAGT 58.029 41.667 3.80 0.00 35.12 3.85
2798 2999 7.179269 AGTACCTAAATAGAGCAGGATAGGAG 58.821 42.308 3.80 0.00 35.12 3.69
2799 3000 7.104974 AGTACCTAAATAGAGCAGGATAGGA 57.895 40.000 3.80 0.00 35.12 2.94
2801 3002 8.085296 CACAAGTACCTAAATAGAGCAGGATAG 58.915 40.741 0.00 0.00 33.44 2.08
2802 3003 7.783119 TCACAAGTACCTAAATAGAGCAGGATA 59.217 37.037 0.00 0.00 33.44 2.59
2805 3006 6.096987 TCTCACAAGTACCTAAATAGAGCAGG 59.903 42.308 0.00 0.00 35.45 4.85
2928 3139 4.635765 CAGTGGAGATAAGATCGGCAAAAA 59.364 41.667 0.00 0.00 0.00 1.94
3201 3425 4.644685 CCTTTCTTCTTCTCAACCAAACCA 59.355 41.667 0.00 0.00 0.00 3.67
3363 3591 7.148018 ACCACTTGCCAGATTAATAAATCACAG 60.148 37.037 0.00 0.00 43.44 3.66
3445 3675 8.919145 GCCTTATAGTATTCTATAGCATCCACT 58.081 37.037 0.00 0.00 39.39 4.00
3705 3985 3.316573 GAGGTTCCGGAGCCCACTG 62.317 68.421 31.54 0.00 31.34 3.66
3875 4155 3.222603 GGGTTTCAAGAAAGGAAGCAGA 58.777 45.455 0.00 0.00 0.00 4.26
3979 4260 3.946558 AGGATTCAGAAGATGCTTCTTGC 59.053 43.478 18.72 10.56 42.34 4.01
4032 4314 0.532862 ACCGAGTCACAAGCCAGTTG 60.533 55.000 0.00 0.00 42.48 3.16
4043 4325 1.891150 GGACCTGAACTAACCGAGTCA 59.109 52.381 0.00 0.00 37.44 3.41
4077 4359 8.328864 AGCTAATTTATCGAATCAAAACGTCTC 58.671 33.333 0.00 0.00 0.00 3.36
4079 4361 8.725046 CAAGCTAATTTATCGAATCAAAACGTC 58.275 33.333 0.00 0.00 0.00 4.34
4123 4406 7.734942 ACATGTCATGGTAGTTTGGAATTTTT 58.265 30.769 17.08 0.00 33.60 1.94
4124 4407 7.301868 ACATGTCATGGTAGTTTGGAATTTT 57.698 32.000 17.08 0.00 33.60 1.82
4128 4411 5.943416 CCTAACATGTCATGGTAGTTTGGAA 59.057 40.000 28.25 1.99 46.68 3.53
4130 4413 4.096382 GCCTAACATGTCATGGTAGTTTGG 59.904 45.833 28.25 18.78 46.68 3.28
4288 4578 7.541783 TGTTAAGATGCTGTTGTTAAATGATGC 59.458 33.333 0.00 0.00 0.00 3.91
4426 4716 8.239314 CAGCACTGTTTATAACATGTTCAGATT 58.761 33.333 23.58 10.57 41.26 2.40
4429 4719 6.149308 TCCAGCACTGTTTATAACATGTTCAG 59.851 38.462 15.85 17.17 41.26 3.02
4668 4998 5.661312 CCCTCCGTCCCATAATATAAGATCA 59.339 44.000 0.00 0.00 0.00 2.92
4739 5069 7.323049 TGAAACTAGATCCGTTGTTCAAAAA 57.677 32.000 0.00 0.00 0.00 1.94
4740 5070 6.928979 TGAAACTAGATCCGTTGTTCAAAA 57.071 33.333 0.00 0.00 0.00 2.44
4741 5071 8.786826 ATATGAAACTAGATCCGTTGTTCAAA 57.213 30.769 0.00 0.00 0.00 2.69
4742 5072 8.786826 AATATGAAACTAGATCCGTTGTTCAA 57.213 30.769 0.00 0.00 0.00 2.69
4743 5073 8.786826 AAATATGAAACTAGATCCGTTGTTCA 57.213 30.769 0.00 1.83 0.00 3.18
4744 5074 9.704098 GAAAATATGAAACTAGATCCGTTGTTC 57.296 33.333 0.00 0.00 0.00 3.18
4745 5075 9.226606 TGAAAATATGAAACTAGATCCGTTGTT 57.773 29.630 0.00 0.00 0.00 2.83
4746 5076 8.786826 TGAAAATATGAAACTAGATCCGTTGT 57.213 30.769 0.00 0.00 0.00 3.32
4851 5181 8.529424 TTAGAAACATCGGGAGAAGTATAAGA 57.471 34.615 0.00 0.00 40.30 2.10
4917 5247 2.047179 GCGGTCCTCCTGTCCAAC 60.047 66.667 0.00 0.00 0.00 3.77
5094 5425 6.670027 ACATTGGCCCCATTGTTATAAACTTA 59.330 34.615 0.00 0.00 37.27 2.24
5095 5426 5.487131 ACATTGGCCCCATTGTTATAAACTT 59.513 36.000 0.00 0.00 37.27 2.66
5096 5427 5.029474 ACATTGGCCCCATTGTTATAAACT 58.971 37.500 0.00 0.00 37.27 2.66
5097 5428 5.351948 ACATTGGCCCCATTGTTATAAAC 57.648 39.130 0.00 0.00 37.27 2.01
5098 5429 6.380079 AAACATTGGCCCCATTGTTATAAA 57.620 33.333 21.24 0.00 44.51 1.40
5099 5430 6.670027 AGTAAACATTGGCCCCATTGTTATAA 59.330 34.615 21.24 11.58 44.51 0.98
5126 5461 3.506067 CGAAGGGCAAAAGAATTAGGTGT 59.494 43.478 0.00 0.00 0.00 4.16
5144 5479 4.511454 TGTCATGACAAAAGGAGAACGAAG 59.489 41.667 26.02 0.00 38.56 3.79
5365 5700 0.385390 GTGGTTCAGTGGTGCCAAAG 59.615 55.000 0.00 0.00 32.26 2.77
5561 6152 4.279169 ACAGCAAACATACTGTTGCAAGAT 59.721 37.500 0.00 0.00 44.59 2.40
5635 6226 7.930217 TGTTTACTAAGAATGGCATGAATAGC 58.070 34.615 0.00 0.00 0.00 2.97
5723 6316 5.346181 AGTGGCCTAAGCTAGTAGAAAAG 57.654 43.478 3.32 0.00 39.73 2.27
5786 6379 5.237815 CCGCTCTCATATTGCTGGTTATAA 58.762 41.667 0.00 0.00 0.00 0.98
5801 6394 1.226974 GAATAGTGCGCCGCTCTCA 60.227 57.895 17.69 5.01 34.22 3.27
5840 6433 6.961554 GTGATACTATTAATGCGGCAATAAGC 59.038 38.462 15.01 0.00 44.65 3.09
6229 6843 4.141298 GGGATTCTTCTCTTCATCCATGGT 60.141 45.833 12.58 0.00 37.52 3.55
6325 6942 5.738783 GCATCCTACTGAACTCTCCTTCATC 60.739 48.000 0.00 0.00 29.71 2.92
6489 7107 8.853345 CAGTAGTCCGAAATTTTCAATTTCATG 58.147 33.333 17.79 10.55 37.76 3.07
6507 7125 7.519649 GCTCAAATCATAATCTTGCAGTAGTCC 60.520 40.741 0.00 0.00 0.00 3.85
6508 7126 7.351223 GCTCAAATCATAATCTTGCAGTAGTC 58.649 38.462 0.00 0.00 0.00 2.59
6631 7252 4.009675 TCCTGTAGCTTGCATTTGTAAGG 58.990 43.478 9.88 0.00 38.05 2.69
6741 7362 6.263617 TGTTTCGTAAGTTTAGGGCTTGAAAT 59.736 34.615 0.00 0.00 39.48 2.17
6795 7625 9.081997 CAGTTGCTGTTTATGTTGTTTTCTTTA 57.918 29.630 0.00 0.00 0.00 1.85
6799 7630 6.039616 TCCAGTTGCTGTTTATGTTGTTTTC 58.960 36.000 0.00 0.00 0.00 2.29
6803 7634 5.590530 TTTCCAGTTGCTGTTTATGTTGT 57.409 34.783 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.