Multiple sequence alignment - TraesCS1B01G281100

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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 TraesCS1B01G281100 chr1B 100.000 4823 0 0 508 5330 489253425 489248603 0.000000e+00 8907.0
1 TraesCS1B01G281100 chr1B 100.000 128 0 0 1 128 489253932 489253805 2.480000e-58 237.0
2 TraesCS1B01G281100 chr1B 82.677 127 18 4 4761 4885 211626907 211627031 5.640000e-20 110.0
3 TraesCS1B01G281100 chr1B 79.130 115 17 6 5174 5284 42347056 42347167 7.400000e-09 73.1
4 TraesCS1B01G281100 chr1D 94.418 4174 163 31 689 4816 365731476 365727327 0.000000e+00 6353.0
5 TraesCS1B01G281100 chr1D 89.024 492 34 6 4814 5285 365727166 365726675 4.600000e-165 592.0
6 TraesCS1B01G281100 chr1D 90.164 122 12 0 7 128 365731811 365731690 5.530000e-35 159.0
7 TraesCS1B01G281100 chr1A 92.569 2826 129 39 689 3453 464840727 464837922 0.000000e+00 3980.0
8 TraesCS1B01G281100 chr1A 93.730 1882 80 15 3438 5285 464837904 464836027 0.000000e+00 2787.0
9 TraesCS1B01G281100 chr1A 87.640 178 10 7 508 685 464840942 464840777 4.210000e-46 196.0
10 TraesCS1B01G281100 chr1A 94.203 69 2 2 3274 3341 257991317 257991384 2.630000e-18 104.0
11 TraesCS1B01G281100 chr1A 90.698 43 2 2 4969 5009 3223113 3223155 7.460000e-04 56.5
12 TraesCS1B01G281100 chr3B 91.262 103 9 0 2006 2108 650798574 650798676 2.000000e-29 141.0
13 TraesCS1B01G281100 chr3B 92.647 68 3 1 3274 3341 215014326 215014261 4.390000e-16 97.1
14 TraesCS1B01G281100 chr3D 91.089 101 9 0 2008 2108 487808646 487808746 2.590000e-28 137.0
15 TraesCS1B01G281100 chr3D 85.124 121 15 3 4759 4877 389633005 389633124 2.610000e-23 121.0
16 TraesCS1B01G281100 chr3D 94.118 68 2 2 3274 3340 10422105 10422039 9.440000e-18 102.0
17 TraesCS1B01G281100 chr3A 90.099 101 10 0 2008 2108 631577020 631577120 1.200000e-26 132.0
18 TraesCS1B01G281100 chr3A 97.368 38 1 0 4976 5013 432856058 432856021 1.240000e-06 65.8
19 TraesCS1B01G281100 chr7B 86.087 115 12 4 4764 4877 477814969 477814858 2.610000e-23 121.0
20 TraesCS1B01G281100 chr7B 89.610 77 7 1 3260 3336 222299646 222299571 4.390000e-16 97.1
21 TraesCS1B01G281100 chr7D 87.500 104 12 1 4764 4866 1744339 1744442 9.380000e-23 119.0
22 TraesCS1B01G281100 chr4A 85.586 111 14 2 4757 4866 742971504 742971395 1.210000e-21 115.0
23 TraesCS1B01G281100 chr4A 83.193 119 16 4 4772 4887 427456527 427456410 7.300000e-19 106.0
24 TraesCS1B01G281100 chr7A 84.211 114 14 4 4770 4880 674819454 674819342 2.030000e-19 108.0
25 TraesCS1B01G281100 chr7A 92.754 69 3 2 3274 3341 448488442 448488375 1.220000e-16 99.0
26 TraesCS1B01G281100 chr4D 93.846 65 2 1 3274 3338 489984017 489984079 4.390000e-16 97.1
27 TraesCS1B01G281100 chr6B 88.462 78 5 3 3274 3351 35707515 35707442 2.040000e-14 91.6
28 TraesCS1B01G281100 chr4B 94.286 35 2 0 4976 5010 11720745 11720779 3.000000e-03 54.7
29 TraesCS1B01G281100 chr5B 100.000 28 0 0 5173 5200 624199384 624199411 1.000000e-02 52.8
30 TraesCS1B01G281100 chr5B 100.000 28 0 0 5173 5200 627799781 627799808 1.000000e-02 52.8


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 TraesCS1B01G281100 chr1B 489248603 489253932 5329 True 4572 8907 100.000 1 5330 2 chr1B.!!$R1 5329
1 TraesCS1B01G281100 chr1D 365726675 365731811 5136 True 2368 6353 91.202 7 5285 3 chr1D.!!$R1 5278
2 TraesCS1B01G281100 chr1A 464836027 464840942 4915 True 2321 3980 91.313 508 5285 3 chr1A.!!$R1 4777

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
565 566 0.466189 CATGCTAGGGTTCGGGCATT 60.466 55.0 0.00 0.0 42.49 3.56 F
566 567 0.466189 ATGCTAGGGTTCGGGCATTG 60.466 55.0 0.00 0.0 41.80 2.82 F
1610 1705 0.667993 CACCGACACACCTTGCAATT 59.332 50.0 0.00 0.0 0.00 2.32 F
2543 2646 0.675083 TTGTTTGGCTGAGCACCATG 59.325 50.0 6.82 0.0 36.96 3.66 F
2790 2893 0.901827 GATGCCGGTTTTGGGGAAAT 59.098 50.0 1.90 0.0 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 2414 0.692476 TCCCATCATATTCCTGGCGG 59.308 55.000 0.00 0.00 0.00 6.13 R
2518 2621 1.824230 TGCTCAGCCAAACAACACTTT 59.176 42.857 0.00 0.00 0.00 2.66 R
2578 2681 1.341209 GGAACTTCCAACCTTTGCCAG 59.659 52.381 2.62 0.00 36.28 4.85 R
4257 4413 1.068741 ACCTTCTTGTCACACTCGTCC 59.931 52.381 0.00 0.00 0.00 4.79 R
4411 4570 1.297664 CAGATTACCTCTGCAGCAGC 58.702 55.000 18.43 1.49 44.73 5.25 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
34 35 2.257034 CTACAACCTAGTTCGAACCGC 58.743 52.381 24.22 0.00 0.00 5.68
92 93 2.507992 CGCTCCGTCTTGCCTGAG 60.508 66.667 0.00 0.00 0.00 3.35
117 118 2.341543 CTCCGGCATGCTATCGCT 59.658 61.111 18.92 0.00 36.97 4.93
118 119 2.025969 CTCCGGCATGCTATCGCTG 61.026 63.158 18.92 4.53 36.97 5.18
550 551 3.490759 CGCCACGTCCTCACATGC 61.491 66.667 0.00 0.00 0.00 4.06
565 566 0.466189 CATGCTAGGGTTCGGGCATT 60.466 55.000 0.00 0.00 42.49 3.56
566 567 0.466189 ATGCTAGGGTTCGGGCATTG 60.466 55.000 0.00 0.00 41.80 2.82
567 568 2.481471 GCTAGGGTTCGGGCATTGC 61.481 63.158 0.00 0.00 0.00 3.56
568 569 1.077787 CTAGGGTTCGGGCATTGCA 60.078 57.895 11.39 0.00 0.00 4.08
569 570 1.376609 CTAGGGTTCGGGCATTGCAC 61.377 60.000 11.39 5.77 0.00 4.57
570 571 2.130821 TAGGGTTCGGGCATTGCACA 62.131 55.000 12.14 0.00 0.00 4.57
571 572 2.350458 GGGTTCGGGCATTGCACAT 61.350 57.895 12.14 0.00 0.00 3.21
598 599 4.080356 TGGAGGAATCGACTGATCCAAAAT 60.080 41.667 8.39 0.00 32.24 1.82
601 602 6.127619 GGAGGAATCGACTGATCCAAAATTTT 60.128 38.462 0.00 0.00 32.24 1.82
685 686 7.154656 CGGGATAACATTAGATCATGTTCTCA 58.845 38.462 18.18 0.00 42.63 3.27
687 688 9.512588 GGGATAACATTAGATCATGTTCTCAAT 57.487 33.333 18.18 8.23 42.63 2.57
704 751 9.748708 TGTTCTCAATAAAAGGATTGTTGAAAG 57.251 29.630 2.76 0.00 37.92 2.62
887 952 4.404098 CACCGCCACCTGTACCCC 62.404 72.222 0.00 0.00 0.00 4.95
1145 1210 2.644676 GCTCCTTCCGCTCCTTAAATT 58.355 47.619 0.00 0.00 0.00 1.82
1146 1211 3.017442 GCTCCTTCCGCTCCTTAAATTT 58.983 45.455 0.00 0.00 0.00 1.82
1148 1213 4.273724 GCTCCTTCCGCTCCTTAAATTTAG 59.726 45.833 0.00 0.00 0.00 1.85
1192 1258 2.281002 CCGTTCCGGGGTTCGTTT 60.281 61.111 0.00 0.00 44.15 3.60
1295 1362 2.035626 CTCCGGCACCCCAACATT 59.964 61.111 0.00 0.00 0.00 2.71
1316 1383 1.557099 TCCAGTTCATAGAGGTGCGT 58.443 50.000 0.00 0.00 0.00 5.24
1323 1390 1.671328 TCATAGAGGTGCGTCTTCTCG 59.329 52.381 0.00 0.00 34.35 4.04
1391 1458 5.300792 TGTGTTTGTCCTCTTGGGTTTAATC 59.699 40.000 0.00 0.00 36.25 1.75
1404 1471 3.467803 GGTTTAATCGGCTGCTCTGTAT 58.532 45.455 0.00 0.00 0.00 2.29
1443 1510 2.066262 GGTGACGTGTAGTGAATGTGG 58.934 52.381 0.00 0.00 0.00 4.17
1449 1516 5.992829 TGACGTGTAGTGAATGTGGTTTTAT 59.007 36.000 0.00 0.00 0.00 1.40
1451 1518 7.116662 TGACGTGTAGTGAATGTGGTTTTATAC 59.883 37.037 0.00 0.00 0.00 1.47
1502 1577 9.136323 GGATATGTAACTGATTGGGAAATTTCT 57.864 33.333 17.42 0.00 0.00 2.52
1507 1582 6.983906 AACTGATTGGGAAATTTCTGAGTT 57.016 33.333 17.42 10.39 0.00 3.01
1509 1584 6.986250 ACTGATTGGGAAATTTCTGAGTTTC 58.014 36.000 17.42 8.29 34.42 2.78
1512 1587 7.790027 TGATTGGGAAATTTCTGAGTTTCAAA 58.210 30.769 17.42 0.00 36.34 2.69
1513 1588 7.710475 TGATTGGGAAATTTCTGAGTTTCAAAC 59.290 33.333 17.42 0.00 36.34 2.93
1610 1705 0.667993 CACCGACACACCTTGCAATT 59.332 50.000 0.00 0.00 0.00 2.32
1685 1780 1.098050 GGTTTAGCGAGGACGAGGTA 58.902 55.000 0.00 0.00 42.66 3.08
1719 1814 3.526534 CCTCGTCTTGATCTTCTTTCCC 58.473 50.000 0.00 0.00 0.00 3.97
1720 1815 3.526534 CTCGTCTTGATCTTCTTTCCCC 58.473 50.000 0.00 0.00 0.00 4.81
1764 1862 7.432252 CCAGAGTCAATTTACTGTTTTGTGTTC 59.568 37.037 0.00 0.00 0.00 3.18
1765 1863 7.967854 CAGAGTCAATTTACTGTTTTGTGTTCA 59.032 33.333 0.00 0.00 0.00 3.18
1795 1895 7.482169 TCTTTTCTCTCCTTATTACTGCAGA 57.518 36.000 23.35 0.00 0.00 4.26
2207 2307 7.218204 GCGTAAGAATAACTATTTGCTGTTTGG 59.782 37.037 0.00 0.00 43.02 3.28
2314 2414 1.503818 TTGCACCGGAAGTTCTTCGC 61.504 55.000 9.46 1.95 0.00 4.70
2408 2508 4.067896 CTGACCTTTGTAAGCACATCTGT 58.932 43.478 0.00 0.00 33.76 3.41
2518 2621 1.103987 TGCCACGCAAAGCAAACCTA 61.104 50.000 0.00 0.00 34.76 3.08
2543 2646 0.675083 TTGTTTGGCTGAGCACCATG 59.325 50.000 6.82 0.00 36.96 3.66
2601 2704 3.181423 TGGCAAAGGTTGGAAGTTCCTAT 60.181 43.478 22.41 3.45 37.46 2.57
2790 2893 0.901827 GATGCCGGTTTTGGGGAAAT 59.098 50.000 1.90 0.00 0.00 2.17
3039 3143 7.615582 TGATTGAACAACCTCTTAATAGCTG 57.384 36.000 0.00 0.00 0.00 4.24
3157 3271 4.666412 TTTTATCCAACACCCTCCATCA 57.334 40.909 0.00 0.00 0.00 3.07
3214 3328 3.015327 AGAGGCTCAAGATGTGAATTGC 58.985 45.455 18.26 0.00 35.22 3.56
3240 3355 2.159366 AGCGGAGTTCATACTTCACTCG 60.159 50.000 0.00 0.00 38.28 4.18
3243 3358 3.673594 CGGAGTTCATACTTCACTCGCTT 60.674 47.826 0.00 0.00 38.28 4.68
3263 3378 4.624452 GCTTTGTTCCTGAAGAAATGATGC 59.376 41.667 3.09 0.66 35.85 3.91
3329 3448 5.769367 AGGCAAATCTTTTACCTTCGTTTC 58.231 37.500 0.00 0.00 0.00 2.78
3373 3495 8.948631 TTTCATCATTGTTCTGTAGATCCTAC 57.051 34.615 0.00 0.00 0.00 3.18
3564 3719 9.045223 TGAAGGTCATTCAATCGATAAACATAG 57.955 33.333 0.00 0.00 45.00 2.23
3607 3762 7.042797 ACTGAATGCTGACAAGTGTATTTTT 57.957 32.000 0.00 0.00 0.00 1.94
3706 3861 2.290323 CCCGGATGACCCCAAGAATATC 60.290 54.545 0.73 0.00 0.00 1.63
3780 3935 8.619546 CACCCAAAATTTACAAATCACAAATGT 58.380 29.630 0.00 0.00 0.00 2.71
3826 3981 4.784329 CGAATAGCAGCAGTCGACTATAA 58.216 43.478 19.57 1.22 35.54 0.98
3839 3994 5.041940 GTCGACTATAACATCCCAGACAAC 58.958 45.833 8.70 0.00 0.00 3.32
3857 4012 6.201234 CAGACAACATTCTCATATCTGCTGAG 59.799 42.308 0.00 0.00 41.23 3.35
3947 4102 2.100749 TGCAAGATCGACGTGTCCATAT 59.899 45.455 0.00 0.00 0.00 1.78
3956 4111 1.626321 ACGTGTCCATATGTGAACCCA 59.374 47.619 1.24 0.00 0.00 4.51
4092 4248 1.638529 ACTACAAGAGGAGCAGCAGT 58.361 50.000 0.00 0.00 0.00 4.40
4118 4274 4.733523 GCCTTCTTTCTCGAAGCAAACAAA 60.734 41.667 0.00 0.00 39.21 2.83
4173 4329 1.446907 AGAAGCCAAGATCAAGCACG 58.553 50.000 0.00 0.00 0.00 5.34
4217 4373 4.681942 CGAGTTATCGGATGATGAGGAAAC 59.318 45.833 0.00 0.00 45.39 2.78
4232 4388 1.737793 GGAAACGAATGCGAAGGTCAT 59.262 47.619 0.00 0.00 41.64 3.06
4233 4389 2.223044 GGAAACGAATGCGAAGGTCATC 60.223 50.000 0.00 0.00 41.64 2.92
4257 4413 3.919216 ACCAGAACAGAATGACGAAGAG 58.081 45.455 0.00 0.00 39.69 2.85
4260 4416 3.923461 CAGAACAGAATGACGAAGAGGAC 59.077 47.826 0.00 0.00 39.69 3.85
4346 4502 3.138304 TCTAAACGCTGCTTGTGATGTT 58.862 40.909 0.00 0.00 0.00 2.71
4353 4509 2.497138 CTGCTTGTGATGTTGGACTGA 58.503 47.619 0.00 0.00 0.00 3.41
4358 4514 1.625315 TGTGATGTTGGACTGAGAGGG 59.375 52.381 0.00 0.00 0.00 4.30
4411 4570 4.379082 GGTTTTGGTAGGACGTATGCTTTG 60.379 45.833 0.00 0.00 0.00 2.77
4600 4763 4.065088 TGCTTACTACAGGTTTGCTGAAG 58.935 43.478 0.00 0.00 0.00 3.02
4603 4766 2.772287 ACTACAGGTTTGCTGAAGCTC 58.228 47.619 3.61 0.00 43.93 4.09
4702 4865 5.239306 TCAGATTTTGTTGCTAGGACTTGTG 59.761 40.000 0.00 0.00 0.00 3.33
4718 4881 0.034186 TGTGTGGATGGGGCAGAATC 60.034 55.000 0.00 0.00 0.00 2.52
4783 4946 4.003648 GGTACTCCCTCTGTTCACAAATG 58.996 47.826 0.00 0.00 0.00 2.32
4790 4953 7.038302 ACTCCCTCTGTTCACAAATGTAAGATA 60.038 37.037 0.00 0.00 0.00 1.98
4834 5160 8.539544 TGAACTACATATGAACTGAAATGAGGA 58.460 33.333 10.38 0.00 0.00 3.71
4836 5162 8.954950 ACTACATATGAACTGAAATGAGGAAG 57.045 34.615 10.38 0.00 0.00 3.46
4844 5171 3.003689 ACTGAAATGAGGAAGCAAACACG 59.996 43.478 0.00 0.00 0.00 4.49
4860 5187 5.894807 GCAAACACGCTAAAATACGTCTATC 59.105 40.000 0.00 0.00 41.32 2.08
4992 5322 2.841215 TGGACTAAAACCACGACAAGG 58.159 47.619 0.00 0.00 32.03 3.61
5019 5349 0.249398 AACGGAGGGAGTACATGCAC 59.751 55.000 0.00 0.00 0.00 4.57
5091 5432 1.461897 GTGTAATTTGGTGGACCGACG 59.538 52.381 0.00 0.00 39.43 5.12
5209 5554 0.032130 CCATGGGTACTCGATCCACG 59.968 60.000 2.85 0.00 44.09 4.94
5212 5557 2.127271 TGGGTACTCGATCCACGTAA 57.873 50.000 0.00 0.00 43.13 3.18
5273 5627 5.542635 TCAAACCCTACTTGACTAGTCATGT 59.457 40.000 33.87 33.87 45.82 3.21
5285 5639 3.389329 ACTAGTCATGTTAGGGCATGGAG 59.611 47.826 6.26 4.78 44.54 3.86
5286 5640 2.200081 AGTCATGTTAGGGCATGGAGT 58.800 47.619 6.26 0.00 44.54 3.85
5287 5641 2.171448 AGTCATGTTAGGGCATGGAGTC 59.829 50.000 6.26 0.00 44.54 3.36
5288 5642 2.092968 GTCATGTTAGGGCATGGAGTCA 60.093 50.000 6.26 0.00 44.54 3.41
5289 5643 2.779430 TCATGTTAGGGCATGGAGTCAT 59.221 45.455 6.26 0.00 44.54 3.06
5297 5651 3.713902 CATGGAGTCATGGTAGGGC 57.286 57.895 0.00 0.00 45.19 5.19
5298 5652 0.839277 CATGGAGTCATGGTAGGGCA 59.161 55.000 0.00 0.00 45.19 5.36
5299 5653 1.422781 CATGGAGTCATGGTAGGGCAT 59.577 52.381 0.00 0.00 45.19 4.40
5300 5654 2.487746 TGGAGTCATGGTAGGGCATA 57.512 50.000 0.00 0.00 0.00 3.14
5301 5655 2.990195 TGGAGTCATGGTAGGGCATAT 58.010 47.619 0.00 0.00 0.00 1.78
5302 5656 4.140575 TGGAGTCATGGTAGGGCATATA 57.859 45.455 0.00 0.00 0.00 0.86
5303 5657 4.498493 TGGAGTCATGGTAGGGCATATAA 58.502 43.478 0.00 0.00 0.00 0.98
5304 5658 4.286032 TGGAGTCATGGTAGGGCATATAAC 59.714 45.833 0.00 0.00 0.00 1.89
5305 5659 4.532521 GGAGTCATGGTAGGGCATATAACT 59.467 45.833 0.00 0.00 0.00 2.24
5306 5660 5.720041 GGAGTCATGGTAGGGCATATAACTA 59.280 44.000 0.00 0.00 0.00 2.24
5307 5661 6.212791 GGAGTCATGGTAGGGCATATAACTAA 59.787 42.308 0.00 0.00 0.00 2.24
5308 5662 7.246171 AGTCATGGTAGGGCATATAACTAAG 57.754 40.000 0.00 0.00 0.00 2.18
5309 5663 6.787957 AGTCATGGTAGGGCATATAACTAAGT 59.212 38.462 0.00 0.00 0.00 2.24
5310 5664 7.292591 AGTCATGGTAGGGCATATAACTAAGTT 59.707 37.037 0.00 0.00 0.00 2.66
5311 5665 8.591072 GTCATGGTAGGGCATATAACTAAGTTA 58.409 37.037 0.00 0.00 32.36 2.24
5312 5666 9.333961 TCATGGTAGGGCATATAACTAAGTTAT 57.666 33.333 0.00 0.00 41.02 1.89
5313 5667 9.959721 CATGGTAGGGCATATAACTAAGTTATT 57.040 33.333 0.00 0.00 39.18 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.158579 GGTTGTAGGGTGGTTGAAGGAA 60.159 50.000 0.00 0.00 0.00 3.36
1 2 1.422402 GGTTGTAGGGTGGTTGAAGGA 59.578 52.381 0.00 0.00 0.00 3.36
2 3 1.423921 AGGTTGTAGGGTGGTTGAAGG 59.576 52.381 0.00 0.00 0.00 3.46
3 4 2.951229 AGGTTGTAGGGTGGTTGAAG 57.049 50.000 0.00 0.00 0.00 3.02
4 5 3.320129 ACTAGGTTGTAGGGTGGTTGAA 58.680 45.455 0.00 0.00 0.00 2.69
5 6 2.980548 ACTAGGTTGTAGGGTGGTTGA 58.019 47.619 0.00 0.00 0.00 3.18
537 538 0.614979 ACCCTAGCATGTGAGGACGT 60.615 55.000 14.66 0.00 34.46 4.34
550 551 1.077787 TGCAATGCCCGAACCCTAG 60.078 57.895 1.53 0.00 0.00 3.02
566 567 0.309922 CGATTCCTCCATGCATGTGC 59.690 55.000 24.58 0.00 42.50 4.57
567 568 1.600957 GTCGATTCCTCCATGCATGTG 59.399 52.381 24.58 15.94 0.00 3.21
568 569 1.487976 AGTCGATTCCTCCATGCATGT 59.512 47.619 24.58 5.40 0.00 3.21
569 570 1.871676 CAGTCGATTCCTCCATGCATG 59.128 52.381 20.19 20.19 0.00 4.06
570 571 1.764723 TCAGTCGATTCCTCCATGCAT 59.235 47.619 0.00 0.00 0.00 3.96
571 572 1.194218 TCAGTCGATTCCTCCATGCA 58.806 50.000 0.00 0.00 0.00 3.96
576 577 3.543680 TTTGGATCAGTCGATTCCTCC 57.456 47.619 0.00 0.00 29.66 4.30
598 599 4.966965 TCCTAAGTTGCGTGAAACAAAA 57.033 36.364 0.00 0.00 35.74 2.44
601 602 4.153475 GCTAATCCTAAGTTGCGTGAAACA 59.847 41.667 0.00 0.00 35.74 2.83
709 756 7.535997 ACCGTATTCCTTTCAAGATTTTTAGC 58.464 34.615 0.00 0.00 0.00 3.09
797 853 1.266175 CGCTCGCCGGGTATATATAGG 59.734 57.143 2.18 0.00 0.00 2.57
887 952 3.971780 CTCGACGAACCGACCGACG 62.972 68.421 0.00 0.00 43.83 5.12
888 953 2.202272 CTCGACGAACCGACCGAC 60.202 66.667 0.00 0.00 34.02 4.79
889 954 4.093952 GCTCGACGAACCGACCGA 62.094 66.667 0.00 0.00 35.44 4.69
1159 1224 3.316868 GGAACGGAGACCAACAAAAATCA 59.683 43.478 0.00 0.00 0.00 2.57
1192 1258 2.136196 GACCCAATTGGAACGCGCAA 62.136 55.000 26.60 2.37 37.39 4.85
1295 1362 3.296854 ACGCACCTCTATGAACTGGATA 58.703 45.455 0.00 0.00 0.00 2.59
1366 1433 3.312736 AACCCAAGAGGACAAACACAT 57.687 42.857 0.00 0.00 39.89 3.21
1391 1458 1.009829 GTTTCCATACAGAGCAGCCG 58.990 55.000 0.00 0.00 0.00 5.52
1422 1489 2.066262 CACATTCACTACACGTCACCC 58.934 52.381 0.00 0.00 0.00 4.61
1443 1510 6.952083 CGTCCAAACTCTAAAGCGTATAAAAC 59.048 38.462 0.00 0.00 0.00 2.43
1449 1516 2.353011 CCCGTCCAAACTCTAAAGCGTA 60.353 50.000 0.00 0.00 0.00 4.42
1451 1518 1.076332 CCCGTCCAAACTCTAAAGCG 58.924 55.000 0.00 0.00 0.00 4.68
1502 1577 5.643379 AGTGCAGAAAAGTTTGAAACTCA 57.357 34.783 11.44 0.96 41.91 3.41
1507 1582 5.407995 CCAAACAAGTGCAGAAAAGTTTGAA 59.592 36.000 21.71 0.00 45.04 2.69
1509 1584 4.435917 GCCAAACAAGTGCAGAAAAGTTTG 60.436 41.667 16.78 16.78 43.08 2.93
1512 1587 2.233431 TGCCAAACAAGTGCAGAAAAGT 59.767 40.909 0.00 0.00 0.00 2.66
1513 1588 2.891112 TGCCAAACAAGTGCAGAAAAG 58.109 42.857 0.00 0.00 0.00 2.27
1610 1705 2.183300 GCCGCGTACTCCATCACA 59.817 61.111 4.92 0.00 0.00 3.58
1685 1780 8.047310 AGATCAAGACGAGGGTTATAAATTGTT 58.953 33.333 0.00 0.00 0.00 2.83
1719 1814 2.280628 GGATTTCGTACTTCTGCTGGG 58.719 52.381 0.00 0.00 0.00 4.45
1720 1815 2.932614 CTGGATTTCGTACTTCTGCTGG 59.067 50.000 0.00 0.00 0.00 4.85
1776 1876 4.610333 TGGTCTGCAGTAATAAGGAGAGA 58.390 43.478 14.67 0.00 32.72 3.10
1781 1881 8.153550 AGAAATATCTGGTCTGCAGTAATAAGG 58.846 37.037 14.67 0.00 33.59 2.69
1795 1895 3.201708 AGCTGCTGGAAGAAATATCTGGT 59.798 43.478 0.00 0.00 35.59 4.00
2219 2319 4.130857 TGTCACAAAATGGCGAAGAGTTA 58.869 39.130 0.00 0.00 34.72 2.24
2314 2414 0.692476 TCCCATCATATTCCTGGCGG 59.308 55.000 0.00 0.00 0.00 6.13
2378 2478 6.204688 TGTGCTTACAAAGGTCAGAAACATAG 59.795 38.462 0.00 0.00 0.00 2.23
2379 2479 6.058833 TGTGCTTACAAAGGTCAGAAACATA 58.941 36.000 0.00 0.00 0.00 2.29
2408 2508 2.038033 ACCTTAAGTGGCGTGCTCTTAA 59.962 45.455 15.67 15.67 34.14 1.85
2490 2593 3.019964 TTGCGTGGCAACTCATTCT 57.980 47.368 0.00 0.00 43.99 2.40
2518 2621 1.824230 TGCTCAGCCAAACAACACTTT 59.176 42.857 0.00 0.00 0.00 2.66
2578 2681 1.341209 GGAACTTCCAACCTTTGCCAG 59.659 52.381 2.62 0.00 36.28 4.85
2622 2725 5.182570 CACATCCTTTACCGTATCCTATCGA 59.817 44.000 0.00 0.00 0.00 3.59
3039 3143 7.412781 GCAGATATTGTATGATTACTCAGCAGC 60.413 40.741 0.00 0.00 34.12 5.25
3157 3271 2.571653 TCAGGCCATGCACTACTAAACT 59.428 45.455 5.01 0.00 0.00 2.66
3214 3328 4.441415 GTGAAGTATGAACTCCGCTTATCG 59.559 45.833 0.00 0.00 33.75 2.92
3230 3345 3.069016 TCAGGAACAAAGCGAGTGAAGTA 59.931 43.478 0.00 0.00 0.00 2.24
3240 3355 4.624452 GCATCATTTCTTCAGGAACAAAGC 59.376 41.667 0.00 0.00 33.13 3.51
3243 3358 4.828939 ACAGCATCATTTCTTCAGGAACAA 59.171 37.500 0.00 0.00 33.13 2.83
3263 3378 8.283291 GGAGAATAGAGTTTGTTTGTGTTACAG 58.717 37.037 0.00 0.00 0.00 2.74
3427 3549 4.219070 CCTCTTTCTCATTTGGCAATGTGA 59.781 41.667 0.00 8.14 40.78 3.58
3564 3719 6.824305 TCAGTTACACCCTGTACTACTAAC 57.176 41.667 0.00 0.00 31.69 2.34
3706 3861 5.469421 GGCTATCACCTGAATGATCTTCTTG 59.531 44.000 0.00 0.00 39.97 3.02
3780 3935 2.158841 GCAAACAAAGATAAGCGACCGA 59.841 45.455 0.00 0.00 0.00 4.69
3826 3981 4.581309 ATGAGAATGTTGTCTGGGATGT 57.419 40.909 0.00 0.00 0.00 3.06
3839 3994 4.994220 GCACTCAGCAGATATGAGAATG 57.006 45.455 9.78 0.44 45.80 2.67
3857 4012 2.697654 AGAGAAATGAGCTGTCTGCAC 58.302 47.619 0.00 0.00 45.94 4.57
3947 4102 2.948979 GTCACATCAAAGTGGGTTCACA 59.051 45.455 0.00 0.00 45.91 3.58
4078 4234 1.302351 GCACACTGCTGCTCCTCTT 60.302 57.895 0.00 0.00 40.96 2.85
4092 4248 1.202639 TGCTTCGAGAAAGAAGGCACA 60.203 47.619 8.54 0.00 45.65 4.57
4118 4274 4.778579 CACAATCTCCATGATCTCTTGGT 58.221 43.478 10.82 0.00 40.77 3.67
4217 4373 1.517276 GTACGATGACCTTCGCATTCG 59.483 52.381 5.40 0.00 42.82 3.34
4232 4388 2.815503 TCGTCATTCTGTTCTGGTACGA 59.184 45.455 0.00 0.00 35.94 3.43
4233 4389 3.211803 TCGTCATTCTGTTCTGGTACG 57.788 47.619 0.00 0.00 0.00 3.67
4257 4413 1.068741 ACCTTCTTGTCACACTCGTCC 59.931 52.381 0.00 0.00 0.00 4.79
4260 4416 3.318017 CCTAACCTTCTTGTCACACTCG 58.682 50.000 0.00 0.00 0.00 4.18
4346 4502 4.603094 TTATCTACACCCTCTCAGTCCA 57.397 45.455 0.00 0.00 0.00 4.02
4353 4509 7.394144 AAATAGCCAATTATCTACACCCTCT 57.606 36.000 0.00 0.00 0.00 3.69
4411 4570 1.297664 CAGATTACCTCTGCAGCAGC 58.702 55.000 18.43 1.49 44.73 5.25
4551 4714 1.339055 CCTCCCAGATCGCACAAAAGA 60.339 52.381 0.00 0.00 0.00 2.52
4702 4865 3.106738 CAGATTCTGCCCCATCCAC 57.893 57.895 0.00 0.00 0.00 4.02
4718 4881 3.904136 AGAACTGAAAAATCGTGGCAG 57.096 42.857 0.00 0.00 0.00 4.85
4724 4887 5.280945 TCAGGCAAAAGAACTGAAAAATCG 58.719 37.500 0.00 0.00 38.22 3.34
4730 4893 3.384467 CCCTTTCAGGCAAAAGAACTGAA 59.616 43.478 12.37 0.00 46.20 3.02
4834 5160 4.212636 AGACGTATTTTAGCGTGTTTGCTT 59.787 37.500 0.00 0.00 44.46 3.91
4836 5162 4.061570 AGACGTATTTTAGCGTGTTTGC 57.938 40.909 0.00 0.00 41.70 3.68
4844 5171 7.709269 TTGGATGTGATAGACGTATTTTAGC 57.291 36.000 0.00 0.00 0.00 3.09
4974 5304 6.183360 CCATAATCCTTGTCGTGGTTTTAGTC 60.183 42.308 0.00 0.00 0.00 2.59
4992 5322 3.640029 TGTACTCCCTCCGTTCCATAATC 59.360 47.826 0.00 0.00 0.00 1.75
5069 5399 3.614630 CGTCGGTCCACCAAATTACACTA 60.615 47.826 0.00 0.00 35.14 2.74
5091 5432 7.610865 TCATGGATTTTGGTAATCACCTTTTC 58.389 34.615 0.00 0.00 45.98 2.29
5106 5447 8.696043 TTAATAGCATAGCACTCATGGATTTT 57.304 30.769 0.00 0.00 0.00 1.82
5167 5512 5.390613 GGTAAAATTGTCATCCTTCACACG 58.609 41.667 0.00 0.00 0.00 4.49
5209 5554 8.719648 ACATATACGTGCTCATACTCTACTTAC 58.280 37.037 0.00 0.00 0.00 2.34
5212 5557 7.135089 CACATATACGTGCTCATACTCTACT 57.865 40.000 0.00 0.00 0.00 2.57
5249 5603 5.542635 ACATGACTAGTCAAGTAGGGTTTGA 59.457 40.000 27.53 2.81 43.58 2.69
5273 5627 1.595311 ACCATGACTCCATGCCCTAA 58.405 50.000 0.00 0.00 46.73 2.69
5285 5639 7.005709 ACTTAGTTATATGCCCTACCATGAC 57.994 40.000 0.00 0.00 0.00 3.06
5286 5640 7.626999 AACTTAGTTATATGCCCTACCATGA 57.373 36.000 0.00 0.00 0.00 3.07
5287 5641 9.959721 AATAACTTAGTTATATGCCCTACCATG 57.040 33.333 16.78 0.00 37.69 3.66


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

AutoCloner maintained by Alex Coulton.