Multiple sequence alignment - TraesCS5B01G282900

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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 TraesCS5B01G282900 chr5B 100.000 6080 0 0 1 6080 467516437 467510358 0.000000e+00 11228.0
1 TraesCS5B01G282900 chr5B 91.739 230 19 0 3732 3961 465871200 465870971 2.730000e-83 320.0
2 TraesCS5B01G282900 chr5B 81.974 233 40 2 9 239 24638045 24638277 4.810000e-46 196.0
3 TraesCS5B01G282900 chr5B 75.204 367 76 13 13 371 532429809 532430168 6.310000e-35 159.0
4 TraesCS5B01G282900 chr5A 96.150 5350 172 20 670 6006 492035423 492030095 0.000000e+00 8708.0
5 TraesCS5B01G282900 chr5A 86.066 366 37 7 14 371 492036222 492035863 1.240000e-101 381.0
6 TraesCS5B01G282900 chr5A 78.912 441 57 14 4664 5072 489870695 489871131 3.610000e-67 267.0
7 TraesCS5B01G282900 chr5A 89.937 159 10 1 450 602 492035711 492035553 3.720000e-47 200.0
8 TraesCS5B01G282900 chr5A 74.176 364 85 8 13 371 242848571 242848930 6.350000e-30 143.0
9 TraesCS5B01G282900 chr5A 96.875 64 2 0 6017 6080 492029933 492029870 2.320000e-19 108.0
10 TraesCS5B01G282900 chr5D 93.942 5695 250 41 370 6017 389114456 389108810 0.000000e+00 8517.0
11 TraesCS5B01G282900 chr5D 87.143 630 77 3 2147 2775 387114015 387114641 0.000000e+00 712.0
12 TraesCS5B01G282900 chr5D 82.782 726 86 21 3405 4112 387114902 387115606 4.030000e-171 612.0
13 TraesCS5B01G282900 chr5D 91.153 373 31 2 1 371 389114882 389114510 7.030000e-139 505.0
14 TraesCS5B01G282900 chr5D 85.950 121 13 4 4120 4239 387115688 387115805 6.400000e-25 126.0
15 TraesCS5B01G282900 chr5D 89.011 91 7 2 375 463 509546427 509546338 6.440000e-20 110.0
16 TraesCS5B01G282900 chr5D 98.305 59 1 0 6022 6080 389108661 389108603 3.000000e-18 104.0
17 TraesCS5B01G282900 chr7D 79.189 370 68 6 9 371 185303585 185303218 1.310000e-61 248.0
18 TraesCS5B01G282900 chr7D 89.011 91 7 2 367 454 161971368 161971458 6.440000e-20 110.0
19 TraesCS5B01G282900 chr3A 85.776 232 29 4 9 238 220604478 220604707 6.090000e-60 243.0
20 TraesCS5B01G282900 chr1D 78.108 370 72 7 9 371 190109210 190109577 6.130000e-55 226.0
21 TraesCS5B01G282900 chr1D 94.737 38 1 1 576 612 403702607 403702570 2.370000e-04 58.4
22 TraesCS5B01G282900 chr7A 80.870 230 42 2 18 245 628898363 628898134 4.840000e-41 180.0
23 TraesCS5B01G282900 chr4A 85.841 113 12 3 370 480 681652682 681652792 3.850000e-22 117.0
24 TraesCS5B01G282900 chr3D 90.110 91 6 2 367 454 150829192 150829282 1.380000e-21 115.0
25 TraesCS5B01G282900 chr3D 88.636 88 8 1 370 455 64417730 64417817 8.330000e-19 106.0
26 TraesCS5B01G282900 chr4B 90.588 85 6 1 370 452 444329057 444328973 1.790000e-20 111.0
27 TraesCS5B01G282900 chr1B 89.655 87 7 1 370 454 575147953 575147867 6.440000e-20 110.0
28 TraesCS5B01G282900 chr2D 88.764 89 8 1 370 456 88309520 88309608 2.320000e-19 108.0
29 TraesCS5B01G282900 chr4D 82.645 121 13 7 367 482 101061142 101061025 3.880000e-17 100.0


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 TraesCS5B01G282900 chr5B 467510358 467516437 6079 True 11228.000000 11228 100.000000 1 6080 1 chr5B.!!$R2 6079
1 TraesCS5B01G282900 chr5A 492029870 492036222 6352 True 2349.250000 8708 92.257000 14 6080 4 chr5A.!!$R1 6066
2 TraesCS5B01G282900 chr5D 389108603 389114882 6279 True 3042.000000 8517 94.466667 1 6080 3 chr5D.!!$R2 6079
3 TraesCS5B01G282900 chr5D 387114015 387115805 1790 False 483.333333 712 85.291667 2147 4239 3 chr5D.!!$F1 2092

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
95 97 0.249868 TGTGAAACAGCCGAGGTGAG 60.250 55.000 9.57 0.00 45.67 3.51 F
199 202 1.839296 TGATGGGGACGTGGTGACA 60.839 57.895 0.00 0.00 38.70 3.58 F
1300 1470 0.729478 CTACAGCCGTGACAGTCGTG 60.729 60.000 0.00 0.00 0.00 4.35 F
2617 2787 0.534412 AGCAGGACAGATCTGGAACG 59.466 55.000 26.08 12.87 33.16 3.95 F
3343 3570 1.071699 ACATGTGCTGTAACGAAGGGT 59.928 47.619 0.00 0.00 35.91 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1202 0.179001 CTGGAGTTCGGTGGGGTTTT 60.179 55.000 0.0 0.0 0.00 2.43 R
1317 1487 1.179174 TGGCAGATACGATCTCCCGG 61.179 60.000 0.0 0.0 40.27 5.73 R
3237 3464 0.962489 AGCTCGGGACCTTATCATCG 59.038 55.000 0.0 0.0 0.00 3.84 R
3939 4176 1.201647 TCGAGTGTCTCCTTAAAGCGG 59.798 52.381 0.0 0.0 0.00 5.52 R
5135 5463 0.247460 TCACCTCTTGCTCGACATGG 59.753 55.000 0.0 0.0 0.00 3.66 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
39 40 1.270518 GGCATAGATCCAGTGCACGAT 60.271 52.381 12.01 9.15 40.53 3.73
95 97 0.249868 TGTGAAACAGCCGAGGTGAG 60.250 55.000 9.57 0.00 45.67 3.51
152 154 2.233676 TGAAGAAGAAGCGATGCCACTA 59.766 45.455 0.00 0.00 0.00 2.74
199 202 1.839296 TGATGGGGACGTGGTGACA 60.839 57.895 0.00 0.00 38.70 3.58
258 261 4.266070 GAGCGGACGATGGCGCTA 62.266 66.667 7.64 0.00 42.48 4.26
309 312 2.291043 AAGGCGGAATGGAGGACGT 61.291 57.895 0.00 0.00 0.00 4.34
318 321 4.324991 GGAGGACGTTGGCCGGTT 62.325 66.667 1.90 0.00 42.24 4.44
319 322 2.281276 GAGGACGTTGGCCGGTTT 60.281 61.111 1.90 0.00 42.24 3.27
342 345 2.144730 GTGCATCATCATCAGAGGAGC 58.855 52.381 0.00 0.00 38.06 4.70
361 371 4.551148 GGGGGAGGCTAGAGGATC 57.449 66.667 0.00 0.00 0.00 3.36
392 457 7.895962 TCCATACCATATAGAAGTGTGCTCTAT 59.104 37.037 0.00 0.00 0.00 1.98
449 514 9.293404 AGAGACTAGGCAATACATTTATACGTA 57.707 33.333 0.00 0.00 0.00 3.57
556 654 2.731217 GATTCCGCATTGGTGTATTGC 58.269 47.619 0.00 0.00 39.52 3.56
626 724 7.898014 AAATGGAGGAAGTAAAGTTTCAAGT 57.102 32.000 0.00 0.00 0.00 3.16
627 725 7.511959 AATGGAGGAAGTAAAGTTTCAAGTC 57.488 36.000 0.00 0.00 0.00 3.01
628 726 6.248569 TGGAGGAAGTAAAGTTTCAAGTCT 57.751 37.500 0.00 0.00 0.00 3.24
629 727 6.659824 TGGAGGAAGTAAAGTTTCAAGTCTT 58.340 36.000 0.00 0.00 0.00 3.01
631 729 6.378710 AGGAAGTAAAGTTTCAAGTCTTGC 57.621 37.500 7.78 0.00 0.00 4.01
634 732 7.033185 GGAAGTAAAGTTTCAAGTCTTGCAAA 58.967 34.615 7.78 6.86 0.00 3.68
635 733 7.544217 GGAAGTAAAGTTTCAAGTCTTGCAAAA 59.456 33.333 7.78 1.82 0.00 2.44
636 734 8.466086 AAGTAAAGTTTCAAGTCTTGCAAAAG 57.534 30.769 7.78 0.00 0.00 2.27
638 736 8.303876 AGTAAAGTTTCAAGTCTTGCAAAAGAA 58.696 29.630 7.78 0.00 0.00 2.52
639 737 7.961325 AAAGTTTCAAGTCTTGCAAAAGAAA 57.039 28.000 7.78 4.22 0.00 2.52
640 738 7.961325 AAGTTTCAAGTCTTGCAAAAGAAAA 57.039 28.000 7.78 0.00 0.00 2.29
641 739 7.586714 AGTTTCAAGTCTTGCAAAAGAAAAG 57.413 32.000 7.78 0.00 0.00 2.27
642 740 6.591448 AGTTTCAAGTCTTGCAAAAGAAAAGG 59.409 34.615 7.78 0.00 0.00 3.11
643 741 5.009854 TCAAGTCTTGCAAAAGAAAAGGG 57.990 39.130 7.78 0.00 0.00 3.95
644 742 4.709397 TCAAGTCTTGCAAAAGAAAAGGGA 59.291 37.500 7.78 0.00 0.00 4.20
645 743 5.363580 TCAAGTCTTGCAAAAGAAAAGGGAT 59.636 36.000 7.78 0.00 0.00 3.85
646 744 5.876651 AGTCTTGCAAAAGAAAAGGGATT 57.123 34.783 0.00 0.00 0.00 3.01
678 838 8.313292 TGTATGGGTATGTTTAGTTTTCGTAGT 58.687 33.333 0.00 0.00 0.00 2.73
1032 1202 2.028748 GTCCTCCAGCGGTTAGTTGTTA 60.029 50.000 0.00 0.00 0.00 2.41
1077 1247 2.851102 CCATCTGGATCCGCCCCT 60.851 66.667 7.39 0.00 37.39 4.79
1169 1339 0.853530 AAGAAGGTGAAGGCCAAGGT 59.146 50.000 5.01 0.00 0.00 3.50
1299 1469 1.170919 ACTACAGCCGTGACAGTCGT 61.171 55.000 0.00 0.00 0.00 4.34
1300 1470 0.729478 CTACAGCCGTGACAGTCGTG 60.729 60.000 0.00 0.00 0.00 4.35
1329 1499 1.150081 GGTCCTCCGGGAGATCGTA 59.850 63.158 25.60 2.54 43.12 3.43
1416 1586 3.443925 GGCAAGGAGAAAGGCGGC 61.444 66.667 0.00 0.00 0.00 6.53
1533 1703 4.980805 GGCGGTGCCGTGTCAGAA 62.981 66.667 12.46 0.00 39.62 3.02
1767 1937 4.342092 AGCCATGGTAATGTGATTAAAGGC 59.658 41.667 14.67 0.00 33.42 4.35
1809 1979 4.520111 ACATGTTTCTTCAATGCAGTGCTA 59.480 37.500 17.60 3.01 0.00 3.49
1849 2019 2.472695 TAAGTTCCGCAGCAAGATGT 57.527 45.000 0.00 0.00 0.00 3.06
2094 2264 1.687146 AGCGGAGGATGCTTCCAGA 60.687 57.895 19.98 0.00 45.30 3.86
2268 2438 2.964464 TGTTTCATCACCACCAGCAAAT 59.036 40.909 0.00 0.00 0.00 2.32
2617 2787 0.534412 AGCAGGACAGATCTGGAACG 59.466 55.000 26.08 12.87 33.16 3.95
2869 3044 1.265095 CAGCAGAAAATCACGCACAGT 59.735 47.619 0.00 0.00 0.00 3.55
2970 3197 2.548057 TGCTAAGAAAGAAACTGGCACG 59.452 45.455 0.00 0.00 0.00 5.34
3009 3236 2.332063 TGGCTTGGAGTAGCAATAGC 57.668 50.000 0.00 0.00 43.02 2.97
3123 3350 4.463539 TGGCATTGTGAGCATTGTTCTATT 59.536 37.500 2.11 0.00 0.00 1.73
3213 3440 1.198713 AGGACAGTGCGGAGATGATT 58.801 50.000 0.00 0.00 0.00 2.57
3237 3464 4.504097 GCAAGTGGTGATGAAAAACAAGTC 59.496 41.667 0.00 0.00 0.00 3.01
3343 3570 1.071699 ACATGTGCTGTAACGAAGGGT 59.928 47.619 0.00 0.00 35.91 4.34
3490 3717 4.946157 CAGCAGTGGAATTTACATCTTCCT 59.054 41.667 3.27 0.00 41.29 3.36
3500 3727 7.121315 GGAATTTACATCTTCCTGTAAGCAACT 59.879 37.037 0.00 0.00 41.32 3.16
3921 4158 1.819288 GACTCTCATGGTCGGTTCAGA 59.181 52.381 0.00 0.00 0.00 3.27
3939 4176 3.569701 TCAGAAAACTGAAAGGGCATGTC 59.430 43.478 0.00 0.00 39.30 3.06
4319 4645 4.122046 TGATGACGATTCATTGGCTGTAG 58.878 43.478 0.00 0.00 42.95 2.74
4328 4654 3.450904 TCATTGGCTGTAGAACCCTAGT 58.549 45.455 0.00 0.00 0.00 2.57
4414 4740 5.360714 GCCATGTCCATATCCTGAAAGAAAA 59.639 40.000 0.00 0.00 34.07 2.29
4674 5001 7.122204 TGTGTAGCTCTCAAGTTTAGTATGCTA 59.878 37.037 0.00 0.00 0.00 3.49
4675 5002 7.646130 GTGTAGCTCTCAAGTTTAGTATGCTAG 59.354 40.741 0.00 0.00 32.28 3.42
4706 5034 4.367039 TCCTCAAGTTTAGAACCCAAGG 57.633 45.455 0.00 0.00 0.00 3.61
4744 5072 0.828022 TAGGGACCTATTGTGCACCG 59.172 55.000 15.69 0.00 36.96 4.94
4750 5078 1.153353 CCTATTGTGCACCGTTCGTT 58.847 50.000 15.69 0.00 0.00 3.85
4782 5110 4.686191 ATGGGCAGAGAGAGTCATTTAG 57.314 45.455 0.00 0.00 0.00 1.85
4822 5150 9.237846 GGATTGTATGCTTTAGAAATTAACTGC 57.762 33.333 0.00 0.00 0.00 4.40
4977 5305 2.665000 CAGAGCCGCTCCTCCAAA 59.335 61.111 16.99 0.00 32.17 3.28
5004 5332 1.635844 TTTACGCGAGCGATTCACAT 58.364 45.000 24.72 2.01 42.83 3.21
5049 5377 2.622436 GTTCTCAACTGCGAGGCTTAT 58.378 47.619 0.00 0.00 33.59 1.73
5073 5401 1.550976 CTTTTCTACGAGAGGGTGGCT 59.449 52.381 0.00 0.00 0.00 4.75
5135 5463 5.652891 TCAGTGAGTAGTTAGGGACAAGATC 59.347 44.000 0.00 0.00 0.00 2.75
5342 5675 3.696782 ACGGTTCGTTCAGATCTCG 57.303 52.632 0.00 0.00 36.35 4.04
5354 5687 3.625853 TCAGATCTCGACAAGGTCATCT 58.374 45.455 0.00 0.00 37.61 2.90
5387 5720 4.487948 TCGGTTGTATTGGTTTAGAGTCG 58.512 43.478 0.00 0.00 0.00 4.18
5432 5765 7.862372 GCCTGGTACATGTTTTTGATATATGTG 59.138 37.037 2.30 0.00 38.20 3.21
5558 5892 7.513856 TGTAGTATTACATTGTACCATGCCAT 58.486 34.615 6.84 2.52 34.91 4.40
5718 6056 5.407049 TGGATTTGGAGGTTTTTGGGATTA 58.593 37.500 0.00 0.00 0.00 1.75
5720 6058 6.070309 TGGATTTGGAGGTTTTTGGGATTATG 60.070 38.462 0.00 0.00 0.00 1.90
5727 6065 3.595173 GTTTTTGGGATTATGGGCACAC 58.405 45.455 0.00 0.00 0.00 3.82
5729 6067 1.034838 TTGGGATTATGGGCACACGC 61.035 55.000 0.00 0.00 37.44 5.34
5810 6148 8.986477 AGAGTTTTTGAAACATGGTATTATGC 57.014 30.769 0.00 0.00 0.00 3.14
5828 6166 2.025898 TGCAATGGCTGGTATCATGTG 58.974 47.619 0.00 0.00 41.91 3.21
5830 6168 2.033801 GCAATGGCTGGTATCATGTGAC 59.966 50.000 0.00 0.00 36.96 3.67
5936 6274 2.202676 GCGAGAAGCTGAGGACGG 60.203 66.667 0.00 0.00 44.04 4.79
5952 6290 4.481112 GGCGCCGGAATTGTGCTG 62.481 66.667 12.58 0.00 39.17 4.41
5974 6312 2.429971 CCTGTGCAGAGCAATCTAGAGA 59.570 50.000 5.08 0.00 41.47 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.179048 CTATGCCACGATCTTGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
11 12 2.968574 ACTGGATCTATGCCACGATCTT 59.031 45.455 0.00 0.00 36.97 2.40
63 65 2.449031 TTTCACATCGCTGCGACCCT 62.449 55.000 28.41 9.10 39.18 4.34
89 91 2.997897 GCGACCACCTCCTCACCT 60.998 66.667 0.00 0.00 0.00 4.00
92 94 4.671590 TCCGCGACCACCTCCTCA 62.672 66.667 8.23 0.00 0.00 3.86
95 97 4.736896 GTGTCCGCGACCACCTCC 62.737 72.222 8.23 0.00 0.00 4.30
215 218 2.920912 TTCCCCTCGTCCGTGCTT 60.921 61.111 0.00 0.00 0.00 3.91
247 250 2.186903 CAACCCTAGCGCCATCGT 59.813 61.111 2.29 0.00 38.14 3.73
298 301 2.046314 CGGCCAACGTCCTCCATT 60.046 61.111 2.24 0.00 37.93 3.16
309 312 2.093537 GATGCACCAAAACCGGCCAA 62.094 55.000 0.00 0.00 0.00 4.52
318 321 3.054213 TCCTCTGATGATGATGCACCAAA 60.054 43.478 0.00 0.00 0.00 3.28
319 322 2.506644 TCCTCTGATGATGATGCACCAA 59.493 45.455 0.00 0.00 0.00 3.67
348 351 0.955905 GACACCGATCCTCTAGCCTC 59.044 60.000 0.00 0.00 0.00 4.70
361 371 5.010719 ACACTTCTATATGGTATGGACACCG 59.989 44.000 0.00 0.00 41.88 4.94
491 581 8.628630 TTGTATCCAACATGAACATTCAAGTA 57.371 30.769 0.00 0.00 38.06 2.24
602 700 7.780271 AGACTTGAAACTTTACTTCCTCCATTT 59.220 33.333 0.00 0.00 0.00 2.32
603 701 7.290813 AGACTTGAAACTTTACTTCCTCCATT 58.709 34.615 0.00 0.00 0.00 3.16
604 702 6.842676 AGACTTGAAACTTTACTTCCTCCAT 58.157 36.000 0.00 0.00 0.00 3.41
606 704 6.513556 GCAAGACTTGAAACTTTACTTCCTCC 60.514 42.308 19.51 0.00 0.00 4.30
607 705 6.038271 TGCAAGACTTGAAACTTTACTTCCTC 59.962 38.462 19.51 0.00 0.00 3.71
609 707 6.131544 TGCAAGACTTGAAACTTTACTTCC 57.868 37.500 19.51 0.00 0.00 3.46
613 711 8.460831 TTCTTTTGCAAGACTTGAAACTTTAC 57.539 30.769 19.51 0.00 38.86 2.01
614 712 9.482627 TTTTCTTTTGCAAGACTTGAAACTTTA 57.517 25.926 19.51 0.00 38.86 1.85
615 713 7.961325 TTTCTTTTGCAAGACTTGAAACTTT 57.039 28.000 19.51 0.00 38.86 2.66
618 716 6.183360 CCCTTTTCTTTTGCAAGACTTGAAAC 60.183 38.462 19.51 1.95 38.86 2.78
620 718 5.186797 TCCCTTTTCTTTTGCAAGACTTGAA 59.813 36.000 19.51 5.41 38.86 2.69
621 719 4.709397 TCCCTTTTCTTTTGCAAGACTTGA 59.291 37.500 19.51 1.50 38.86 3.02
622 720 5.009854 TCCCTTTTCTTTTGCAAGACTTG 57.990 39.130 11.02 11.02 38.86 3.16
623 721 5.876651 ATCCCTTTTCTTTTGCAAGACTT 57.123 34.783 0.00 0.00 38.86 3.01
624 722 5.876651 AATCCCTTTTCTTTTGCAAGACT 57.123 34.783 0.00 0.00 38.86 3.24
625 723 9.705290 TTTATAATCCCTTTTCTTTTGCAAGAC 57.295 29.630 0.00 0.00 38.86 3.01
634 732 9.951866 ACCCATACATTTATAATCCCTTTTCTT 57.048 29.630 0.00 0.00 0.00 2.52
678 838 7.151976 TGAACAATCTGTCATAGTCTTTTCGA 58.848 34.615 0.00 0.00 0.00 3.71
690 850 2.835156 TCGGGGTATGAACAATCTGTCA 59.165 45.455 0.00 0.00 0.00 3.58
834 997 2.101575 CTAAGCTACGACGGCGCA 59.898 61.111 12.58 0.00 42.48 6.09
972 1138 0.451783 AACCAATGCTCGAAATCGGC 59.548 50.000 2.63 6.21 40.29 5.54
1032 1202 0.179001 CTGGAGTTCGGTGGGGTTTT 60.179 55.000 0.00 0.00 0.00 2.43
1169 1339 3.052082 GCTGCTGCGCCTTCTTCA 61.052 61.111 4.18 0.00 0.00 3.02
1317 1487 1.179174 TGGCAGATACGATCTCCCGG 61.179 60.000 0.00 0.00 40.27 5.73
1329 1499 1.886313 CGCGAGATGCTTGGCAGAT 60.886 57.895 0.00 0.00 43.65 2.90
1350 1520 3.947132 CTCCCGGCAGTGCTCACAG 62.947 68.421 16.11 2.78 0.00 3.66
1416 1586 2.351544 GCCTTTCTTCTTCTGCTGCTTG 60.352 50.000 0.00 0.00 0.00 4.01
1809 1979 1.684049 AAGCGCTAGGAGGCTCTGT 60.684 57.895 12.05 4.80 38.88 3.41
2094 2264 3.400054 GTAGGAACCCCAGCCGCT 61.400 66.667 0.00 0.00 33.88 5.52
2097 2267 1.272480 ACAATTGTAGGAACCCCAGCC 60.272 52.381 9.97 0.00 33.88 4.85
2268 2438 4.135306 CTCGTATAGACTGCTTGGTCCTA 58.865 47.826 0.00 0.00 36.95 2.94
2631 2804 2.557924 TCCACTGTGAAATGAACCATGC 59.442 45.455 9.86 0.00 0.00 4.06
2869 3044 1.548719 CCCATCTCCGCCATATAACGA 59.451 52.381 0.00 0.00 0.00 3.85
2970 3197 4.694509 GCCATCACATCAATATCTCCAGTC 59.305 45.833 0.00 0.00 0.00 3.51
3009 3236 2.830104 TCATCCACTTCATCATCAGCG 58.170 47.619 0.00 0.00 0.00 5.18
3213 3440 4.081752 ACTTGTTTTTCATCACCACTTGCA 60.082 37.500 0.00 0.00 0.00 4.08
3237 3464 0.962489 AGCTCGGGACCTTATCATCG 59.038 55.000 0.00 0.00 0.00 3.84
3343 3570 3.450457 ACCAAAGAAGGATTTGCACACAA 59.550 39.130 0.00 0.00 38.57 3.33
3490 3717 3.550639 GCAAAGTCATGCAGTTGCTTACA 60.551 43.478 15.57 0.00 45.70 2.41
3500 3727 1.868987 ATGCTGCGCAAAGTCATGCA 61.869 50.000 18.64 18.64 46.76 3.96
3921 4158 1.613437 CGGACATGCCCTTTCAGTTTT 59.387 47.619 0.00 0.00 0.00 2.43
3939 4176 1.201647 TCGAGTGTCTCCTTAAAGCGG 59.798 52.381 0.00 0.00 0.00 5.52
4126 4451 8.523915 TCTAGTCATATCATTGTGGCAAAATT 57.476 30.769 0.00 0.00 0.00 1.82
4319 4645 2.429610 TGCGGAGAATGTACTAGGGTTC 59.570 50.000 0.00 0.00 0.00 3.62
4364 4690 8.202811 CAGACCTGAATCAGAGAATAAGATTGA 58.797 37.037 12.53 0.00 32.51 2.57
4385 4711 1.701847 AGGATATGGACATGGCAGACC 59.298 52.381 0.00 0.00 0.00 3.85
4674 5001 9.654663 GTTCTAAACTTGAGGATAACACATACT 57.345 33.333 0.00 0.00 0.00 2.12
4675 5002 8.880750 GGTTCTAAACTTGAGGATAACACATAC 58.119 37.037 0.00 0.00 0.00 2.39
4687 5015 4.072839 GTCCCTTGGGTTCTAAACTTGAG 58.927 47.826 5.51 0.00 0.00 3.02
4706 5034 3.248602 CCTAAACTTATGCGAGCATGTCC 59.751 47.826 19.64 0.00 37.82 4.02
4744 5072 4.083003 TGCCCATAAATCACAGAAACGAAC 60.083 41.667 0.00 0.00 0.00 3.95
4750 5078 4.471025 TCTCTCTGCCCATAAATCACAGAA 59.529 41.667 0.00 0.00 36.96 3.02
4782 5110 7.555965 AGCATACAATCCAATTTTAAAGTCCC 58.444 34.615 0.00 0.00 0.00 4.46
4822 5150 8.455903 TCCTTTGATCTGCATATTAAGGAAAG 57.544 34.615 18.93 9.15 37.37 2.62
4834 5162 6.261603 GTGATGTCATTATCCTTTGATCTGCA 59.738 38.462 0.00 0.00 32.18 4.41
4842 5170 7.442364 CGATAAGTGGTGATGTCATTATCCTTT 59.558 37.037 7.80 0.00 0.00 3.11
4977 5305 0.719465 CGCTCGCGTAAAACCAAGAT 59.281 50.000 5.77 0.00 34.35 2.40
5049 5377 3.958798 CCACCCTCTCGTAGAAAAGGATA 59.041 47.826 0.00 0.00 34.09 2.59
5135 5463 0.247460 TCACCTCTTGCTCGACATGG 59.753 55.000 0.00 0.00 0.00 3.66
5136 5464 1.337167 TGTCACCTCTTGCTCGACATG 60.337 52.381 0.00 0.00 31.92 3.21
5175 5504 2.928757 CAACTGAGACAGTCATAGCAGC 59.071 50.000 2.66 0.00 44.62 5.25
5342 5675 2.413453 GACGCTCAAAGATGACCTTGTC 59.587 50.000 0.00 0.00 34.79 3.18
5354 5687 0.675083 TACAACCGAGGACGCTCAAA 59.325 50.000 0.00 0.00 38.29 2.69
5387 5720 2.159170 GGCTGTCTATGACTGACTGACC 60.159 54.545 8.42 0.00 36.73 4.02
5432 5765 1.135112 CAAAATTTAGGGGCGCACTCC 60.135 52.381 10.74 7.68 0.00 3.85
5558 5892 6.537453 TGAAACTTCCAGGTTTGATTTTCA 57.463 33.333 0.00 0.00 39.20 2.69
5619 5953 6.235664 TGGAGTTTTTAGGGATTGTAGACAC 58.764 40.000 0.00 0.00 0.00 3.67
5706 6044 3.595173 GTGTGCCCATAATCCCAAAAAC 58.405 45.455 0.00 0.00 0.00 2.43
5711 6049 1.453015 GCGTGTGCCCATAATCCCA 60.453 57.895 0.00 0.00 33.98 4.37
5727 6065 2.627791 TGTGAATGTCCACAAGGCG 58.372 52.632 0.00 0.00 43.32 5.52
5810 6148 3.281158 TGTCACATGATACCAGCCATTG 58.719 45.455 0.00 0.00 0.00 2.82
5828 6166 1.457346 CAGGCAACAGGGAAGATGTC 58.543 55.000 0.00 0.00 41.41 3.06
5830 6168 2.877975 CCAGGCAACAGGGAAGATG 58.122 57.895 0.00 0.00 40.18 2.90
5941 6279 1.080298 GCACAGGCAGCACAATTCC 60.080 57.895 0.00 0.00 40.72 3.01
5952 6290 1.134580 TCTAGATTGCTCTGCACAGGC 60.135 52.381 0.00 1.36 38.71 4.85
5953 6291 2.429971 TCTCTAGATTGCTCTGCACAGG 59.570 50.000 0.00 0.00 38.71 4.00
5974 6312 3.118454 CGCGCCGTTCCTGTTCAT 61.118 61.111 0.00 0.00 0.00 2.57
6006 6344 1.006832 GATGTTGATGGGTCGTTCGG 58.993 55.000 0.00 0.00 0.00 4.30
6008 6346 2.858344 CGTAGATGTTGATGGGTCGTTC 59.142 50.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.