Multiple sequence alignment - TraesCS1D01G060700

Loading Multiple Alignment...

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 TraesCS1D01G060700 chr1D 100.000 5854 0 0 1 5854 40880800 40874947 0.000000e+00 10811.0
1 TraesCS1D01G060700 chr1A 96.432 2242 61 9 2023 4257 40150816 40148587 0.000000e+00 3679.0
2 TraesCS1D01G060700 chr1A 96.677 1956 57 6 33 1985 40152765 40150815 0.000000e+00 3245.0
3 TraesCS1D01G060700 chr1A 94.815 1620 44 9 4272 5854 40148540 40146924 0.000000e+00 2490.0
4 TraesCS1D01G060700 chr5B 92.419 277 18 3 5463 5737 697520546 697520271 5.500000e-105 392.0
5 TraesCS1D01G060700 chr4D 90.311 289 22 6 5463 5746 131105423 131105136 1.990000e-99 374.0
6 TraesCS1D01G060700 chr4D 97.059 34 1 0 624 657 474686518 474686485 2.280000e-04 58.4
7 TraesCS1D01G060700 chr4D 100.000 29 0 0 629 657 100563881 100563909 3.000000e-03 54.7
8 TraesCS1D01G060700 chr6B 90.459 283 23 4 5457 5737 487207111 487207391 2.580000e-98 370.0
9 TraesCS1D01G060700 chr6B 90.942 276 22 3 5463 5737 39335608 39335335 9.270000e-98 368.0
10 TraesCS1D01G060700 chr6D 89.116 294 25 7 5457 5746 18859789 18859499 5.580000e-95 359.0
11 TraesCS1D01G060700 chr5A 90.217 276 23 4 5463 5737 169798885 169799157 2.010000e-94 357.0
12 TraesCS1D01G060700 chr1B 89.199 287 25 6 5463 5746 433178070 433177787 2.600000e-93 353.0
13 TraesCS1D01G060700 chr5D 88.927 289 27 5 5453 5737 423244150 423244437 9.330000e-93 351.0
14 TraesCS1D01G060700 chr3D 86.555 119 14 2 5735 5852 419929431 419929314 4.760000e-26 130.0
15 TraesCS1D01G060700 chr6A 79.474 190 20 12 414 596 409377361 409377538 3.710000e-22 117.0
16 TraesCS1D01G060700 chr6A 100.000 32 0 0 1 32 614293427 614293458 6.340000e-05 60.2
17 TraesCS1D01G060700 chr7D 85.981 107 15 0 5735 5841 59167244 59167350 1.330000e-21 115.0
18 TraesCS1D01G060700 chr2D 92.593 54 2 2 605 657 640180170 640180222 6.290000e-10 76.8
19 TraesCS1D01G060700 chr2B 78.571 112 17 7 575 683 801249331 801249224 3.790000e-07 67.6
20 TraesCS1D01G060700 chr4A 97.222 36 1 0 5735 5770 677120415 677120450 1.760000e-05 62.1
21 TraesCS1D01G060700 chr4A 100.000 30 0 0 628 657 45839424 45839453 8.200000e-04 56.5
22 TraesCS1D01G060700 chr4A 100.000 30 0 0 628 657 473290017 473289988 8.200000e-04 56.5
23 TraesCS1D01G060700 chr4B 100.000 30 0 0 628 657 516959378 516959349 8.200000e-04 56.5
24 TraesCS1D01G060700 chr4B 100.000 29 0 0 629 657 142915539 142915567 3.000000e-03 54.7


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 TraesCS1D01G060700 chr1D 40874947 40880800 5853 True 10811 10811 100.000000 1 5854 1 chr1D.!!$R1 5853
1 TraesCS1D01G060700 chr1A 40146924 40152765 5841 True 3138 3679 95.974667 33 5854 3 chr1A.!!$R1 5821

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
387 388 0.888736 CTTCCCACACATGTTGCGGA 60.889 55.000 0.00 0.00 27.16 5.54 F
1784 1787 1.205417 CATGGGTGGACAATTTGCTCC 59.795 52.381 9.68 9.68 0.00 4.70 F
2270 2274 0.481128 CTCCCTCTACCTCTCCCTCC 59.519 65.000 0.00 0.00 0.00 4.30 F
2278 2282 0.553862 ACCTCTCCCTCCCTCTCTCA 60.554 60.000 0.00 0.00 0.00 3.27 F
3677 3687 0.661020 GTCTCTGTCTCTAGGCTCGC 59.339 60.000 0.00 0.00 0.00 5.03 F
4035 4046 0.821517 ATGCTTGTGATGGCATGGTG 59.178 50.000 3.81 0.00 45.81 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 2243 0.467290 AGAGGGAGAGAGATCACGGC 60.467 60.000 0.0 0.00 0.00 5.68 R
2874 2879 3.240884 CATAGTCGATCAAGAGGATGCG 58.759 50.000 0.0 0.00 36.00 4.73 R
4017 4028 1.252215 CCACCATGCCATCACAAGCA 61.252 55.000 0.0 0.00 44.45 3.91 R
4044 4055 1.318934 ATGGTAGGCCCCTTTCCAAT 58.681 50.000 0.0 3.06 34.50 3.16 R
4540 4592 1.176527 CACGAGTTTTGGATGCCCAT 58.823 50.000 0.0 0.00 43.12 4.00 R
5196 5248 2.006888 CCATTCGAACGCCTAATGTGT 58.993 47.619 0.0 0.00 40.09 3.72 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
24 25 7.404671 CACAACTAGGGGCATAAAACTAATT 57.595 36.000 0.00 0.00 0.00 1.40
25 26 8.514330 CACAACTAGGGGCATAAAACTAATTA 57.486 34.615 0.00 0.00 0.00 1.40
26 27 9.131791 CACAACTAGGGGCATAAAACTAATTAT 57.868 33.333 0.00 0.00 0.00 1.28
27 28 9.709387 ACAACTAGGGGCATAAAACTAATTATT 57.291 29.630 0.00 0.00 0.00 1.40
29 30 8.935614 ACTAGGGGCATAAAACTAATTATTCC 57.064 34.615 0.00 0.00 30.55 3.01
30 31 8.733808 ACTAGGGGCATAAAACTAATTATTCCT 58.266 33.333 0.00 0.00 31.62 3.36
67 68 8.703336 GTTCTTTATCACAGGAAAAATTTCTGC 58.297 33.333 5.91 0.00 37.35 4.26
73 74 6.218019 TCACAGGAAAAATTTCTGCTGATTG 58.782 36.000 18.61 8.34 37.35 2.67
91 92 2.284754 TGGCATGTCCAGCTTTACAA 57.715 45.000 4.93 0.00 40.72 2.41
206 207 7.096023 GGCTATGTGTCTCAACGATTTGTATAG 60.096 40.741 0.00 0.00 34.02 1.31
373 374 8.732746 TTCTTTAATTGTACTAGATGCTTCCC 57.267 34.615 0.00 0.00 0.00 3.97
374 375 7.857456 TCTTTAATTGTACTAGATGCTTCCCA 58.143 34.615 0.00 0.00 0.00 4.37
386 387 1.580942 CTTCCCACACATGTTGCGG 59.419 57.895 0.00 0.00 0.00 5.69
387 388 0.888736 CTTCCCACACATGTTGCGGA 60.889 55.000 0.00 0.00 27.16 5.54
391 393 1.669502 CCCACACATGTTGCGGAATTG 60.670 52.381 0.00 0.00 27.16 2.32
401 403 2.697431 TGCGGAATTGTTTGCACTAC 57.303 45.000 0.00 0.00 31.31 2.73
581 584 5.825593 TGTTGAGGTGAGTTCTTTCCTAT 57.174 39.130 0.00 0.00 0.00 2.57
587 590 3.557595 GGTGAGTTCTTTCCTATGCATCG 59.442 47.826 0.19 0.00 0.00 3.84
658 661 3.198409 TGTGTGCATGTTGAGAGAACT 57.802 42.857 0.00 0.00 0.00 3.01
679 682 4.656112 ACTACATTTGTGAGGGCTAGCTAT 59.344 41.667 15.72 2.98 0.00 2.97
811 814 9.944376 TCTAGGATATAAATGCACCTCATTAAC 57.056 33.333 0.00 0.00 44.23 2.01
907 910 8.525316 CCATTATGATCATGCTTTAAATGCCTA 58.475 33.333 18.72 0.00 0.00 3.93
925 928 4.716784 TGCCTATCACTAATTGTCCTCACT 59.283 41.667 0.00 0.00 0.00 3.41
938 941 6.996180 TTGTCCTCACTAAATCCTATAGGG 57.004 41.667 18.97 4.73 35.41 3.53
962 965 9.003658 GGGACCATGACATTTCATACTATTAAG 57.996 37.037 0.00 0.00 40.79 1.85
965 968 7.448469 ACCATGACATTTCATACTATTAAGGGC 59.552 37.037 0.00 0.00 40.79 5.19
1001 1004 2.416547 GCACATCGCTACATCAACACTT 59.583 45.455 0.00 0.00 37.77 3.16
1027 1030 3.418684 TCTCCTTTGGCTTTGAGGTAC 57.581 47.619 0.00 0.00 32.33 3.34
1080 1083 9.166126 GTTGTTTGTTGTATTACTTCTTGCTAC 57.834 33.333 0.00 0.00 0.00 3.58
1361 1364 1.722011 TAAGTGAACTTAGCGCCTGC 58.278 50.000 2.29 0.00 38.20 4.85
1560 1563 3.206034 TCAAGTGCAGCAATGATTTCG 57.794 42.857 0.00 0.00 0.00 3.46
1614 1617 2.368439 CTCAGCGGGATTCAATTTGGA 58.632 47.619 0.00 0.00 0.00 3.53
1784 1787 1.205417 CATGGGTGGACAATTTGCTCC 59.795 52.381 9.68 9.68 0.00 4.70
1892 1895 9.555411 AATATACATACACCCCATGTACATAGA 57.445 33.333 8.32 0.00 46.65 1.98
1893 1896 7.865530 ATACATACACCCCATGTACATAGAA 57.134 36.000 8.32 0.00 46.65 2.10
1917 1920 9.604626 GAAAATTCATCAAGCATATGTAGCTAC 57.395 33.333 17.30 17.30 42.53 3.58
1997 2001 9.646427 GATTATCTATTTATCAGGACACTCACC 57.354 37.037 0.00 0.00 0.00 4.02
1998 2002 5.871396 TCTATTTATCAGGACACTCACCC 57.129 43.478 0.00 0.00 0.00 4.61
1999 2003 5.529289 TCTATTTATCAGGACACTCACCCT 58.471 41.667 0.00 0.00 0.00 4.34
2000 2004 6.679542 TCTATTTATCAGGACACTCACCCTA 58.320 40.000 0.00 0.00 0.00 3.53
2001 2005 7.306013 TCTATTTATCAGGACACTCACCCTAT 58.694 38.462 0.00 0.00 0.00 2.57
2002 2006 5.614324 TTTATCAGGACACTCACCCTATG 57.386 43.478 0.00 0.00 0.00 2.23
2003 2007 2.919772 TCAGGACACTCACCCTATGA 57.080 50.000 0.00 0.00 35.45 2.15
2004 2008 3.184382 TCAGGACACTCACCCTATGAA 57.816 47.619 0.00 0.00 36.69 2.57
2005 2009 3.099905 TCAGGACACTCACCCTATGAAG 58.900 50.000 0.00 0.00 36.69 3.02
2006 2010 2.169352 CAGGACACTCACCCTATGAAGG 59.831 54.545 0.00 0.00 43.25 3.46
2016 2020 2.787473 CCTATGAAGGGTTGTGCTGA 57.213 50.000 0.00 0.00 39.48 4.26
2017 2021 3.287867 CCTATGAAGGGTTGTGCTGAT 57.712 47.619 0.00 0.00 39.48 2.90
2018 2022 4.422073 CCTATGAAGGGTTGTGCTGATA 57.578 45.455 0.00 0.00 39.48 2.15
2019 2023 4.780815 CCTATGAAGGGTTGTGCTGATAA 58.219 43.478 0.00 0.00 39.48 1.75
2020 2024 5.380043 CCTATGAAGGGTTGTGCTGATAAT 58.620 41.667 0.00 0.00 39.48 1.28
2021 2025 5.240183 CCTATGAAGGGTTGTGCTGATAATG 59.760 44.000 0.00 0.00 39.48 1.90
2123 2127 6.709018 TTTGGGAACTTCTAAACAAAGGAG 57.291 37.500 0.00 0.00 0.00 3.69
2147 2151 6.149474 AGGTCTTTCATGGTAAATGAAGTTCG 59.851 38.462 0.00 0.00 38.98 3.95
2171 2175 6.537301 CGTACAATGTAGTTATGTGGTTCCAT 59.463 38.462 0.00 0.00 0.00 3.41
2190 2194 3.454447 CCATACTTCCCACCACATAGACA 59.546 47.826 0.00 0.00 0.00 3.41
2237 2241 5.725316 GCGCTAATTAGCTCTTCTTTGACAC 60.725 44.000 29.66 2.14 46.85 3.67
2239 2243 5.220491 GCTAATTAGCTCTTCTTTGACACCG 60.220 44.000 26.79 0.00 45.62 4.94
2240 2244 2.080286 TAGCTCTTCTTTGACACCGC 57.920 50.000 0.00 0.00 0.00 5.68
2242 2246 1.901650 GCTCTTCTTTGACACCGCCG 61.902 60.000 0.00 0.00 0.00 6.46
2262 2266 2.105821 CGTGATCTCTCTCCCTCTACCT 59.894 54.545 0.00 0.00 0.00 3.08
2263 2267 3.751518 GTGATCTCTCTCCCTCTACCTC 58.248 54.545 0.00 0.00 0.00 3.85
2265 2269 3.650942 TGATCTCTCTCCCTCTACCTCTC 59.349 52.174 0.00 0.00 0.00 3.20
2266 2270 2.414612 TCTCTCTCCCTCTACCTCTCC 58.585 57.143 0.00 0.00 0.00 3.71
2267 2271 1.423921 CTCTCTCCCTCTACCTCTCCC 59.576 61.905 0.00 0.00 0.00 4.30
2268 2272 1.011545 TCTCTCCCTCTACCTCTCCCT 59.988 57.143 0.00 0.00 0.00 4.20
2269 2273 1.423921 CTCTCCCTCTACCTCTCCCTC 59.576 61.905 0.00 0.00 0.00 4.30
2270 2274 0.481128 CTCCCTCTACCTCTCCCTCC 59.519 65.000 0.00 0.00 0.00 4.30
2278 2282 0.553862 ACCTCTCCCTCCCTCTCTCA 60.554 60.000 0.00 0.00 0.00 3.27
2285 2289 1.133792 CCCTCCCTCTCTCACTCTCTC 60.134 61.905 0.00 0.00 0.00 3.20
2292 2296 3.181461 CCTCTCTCACTCTCTCTCTCTCC 60.181 56.522 0.00 0.00 0.00 3.71
2334 2338 8.590470 CATCATCGATACACATGTATAGCTTTC 58.410 37.037 0.00 0.00 40.99 2.62
2474 2478 9.474313 AACAATGTGCCTAAAGATTATAGGAAA 57.526 29.630 3.83 0.00 42.16 3.13
2502 2506 4.447138 TGGGGTGAATTATGGGATACAC 57.553 45.455 0.00 0.00 39.74 2.90
2607 2611 9.470399 TCCCTTGGTTAATTTCCTCTTATAAAC 57.530 33.333 0.00 0.00 0.00 2.01
2748 2753 6.112734 AGAACCGCTTGACATGATACATTTA 58.887 36.000 0.00 0.00 0.00 1.40
2784 2789 7.383029 ACATCATAGTTTGAAATGTTGTGCTTG 59.617 33.333 0.00 0.00 38.03 4.01
2874 2879 4.694037 ACCAAGCTTCTTAACGGTTATCAC 59.306 41.667 0.00 0.00 0.00 3.06
2921 2926 9.704098 GGATTTATCTTGAACACTTTTATCGTC 57.296 33.333 0.00 0.00 0.00 4.20
2944 2949 6.033513 GTCGATTGTAGTTTTATTTGCAAGGC 59.966 38.462 0.00 0.00 0.00 4.35
3105 3114 5.255397 TGTTGTCTAGATTTTCCCATGGT 57.745 39.130 11.73 0.00 0.00 3.55
3454 3464 4.462483 GGTTAGGAATTGCCACATTCTCAA 59.538 41.667 0.00 0.00 40.02 3.02
3642 3652 8.034804 TCATCATTACCATATACCATGAACGAG 58.965 37.037 0.00 0.00 0.00 4.18
3652 3662 3.804036 ACCATGAACGAGAACTTTGTGA 58.196 40.909 0.00 0.00 0.00 3.58
3677 3687 0.661020 GTCTCTGTCTCTAGGCTCGC 59.339 60.000 0.00 0.00 0.00 5.03
3761 3771 2.910688 CCTGTGTGGTACTGTGAACT 57.089 50.000 0.00 0.00 0.00 3.01
3772 3782 4.755123 GGTACTGTGAACTTTGTAGCACAT 59.245 41.667 0.00 0.00 40.12 3.21
4000 4010 2.415983 TGGTCTCTTGGGAGGAAAGA 57.584 50.000 0.00 0.00 39.86 2.52
4012 4023 6.798544 TGGGAGGAAAGAGGTATCTAGATA 57.201 41.667 8.44 8.44 33.45 1.98
4017 4028 7.344352 GGAGGAAAGAGGTATCTAGATATGCAT 59.656 40.741 15.43 3.79 33.45 3.96
4035 4046 0.821517 ATGCTTGTGATGGCATGGTG 59.178 50.000 3.81 0.00 45.81 4.17
4044 4055 3.938048 GGCATGGTGGCATTAGCA 58.062 55.556 0.00 0.00 43.14 3.49
4118 4129 7.925703 ATCGTATATAATATACGGTGCAAGC 57.074 36.000 5.35 0.00 45.13 4.01
4245 4256 8.995027 AGTTCCTAATGATTGCCATTGTTATA 57.005 30.769 0.00 0.00 44.67 0.98
4246 4257 9.592196 AGTTCCTAATGATTGCCATTGTTATAT 57.408 29.630 0.00 0.00 44.67 0.86
4247 4258 9.630098 GTTCCTAATGATTGCCATTGTTATATG 57.370 33.333 0.00 0.00 44.67 1.78
4248 4259 8.938801 TCCTAATGATTGCCATTGTTATATGT 57.061 30.769 0.00 0.00 44.67 2.29
4249 4260 9.013229 TCCTAATGATTGCCATTGTTATATGTC 57.987 33.333 0.00 0.00 44.67 3.06
4250 4261 9.017509 CCTAATGATTGCCATTGTTATATGTCT 57.982 33.333 0.00 0.00 44.67 3.41
4252 4263 6.882610 TGATTGCCATTGTTATATGTCTCC 57.117 37.500 0.00 0.00 0.00 3.71
4264 4275 2.638480 ATGTCTCCCTCTCTCTCTCG 57.362 55.000 0.00 0.00 0.00 4.04
4265 4276 1.574263 TGTCTCCCTCTCTCTCTCGA 58.426 55.000 0.00 0.00 0.00 4.04
4295 4346 9.712305 GTGCATAATTAGGAGACTATATTGTGT 57.288 33.333 0.32 0.00 43.94 3.72
4442 4494 4.873746 ATGTGGGATGGTAGAAGTATCG 57.126 45.455 0.00 0.00 0.00 2.92
4452 4504 7.501559 GGATGGTAGAAGTATCGCCTATACATA 59.498 40.741 6.63 0.00 42.63 2.29
4493 4545 8.691727 GTGTACTAACATGTCGATCAATACATC 58.308 37.037 0.00 0.00 38.08 3.06
4501 4553 6.085555 TGTCGATCAATACATCTAGGAACC 57.914 41.667 0.00 0.00 0.00 3.62
4518 4570 3.308402 GGAACCATCTTCAGGTGATTGGA 60.308 47.826 9.79 0.00 39.86 3.53
4663 4715 1.348064 TCACGACCAAGTCCTCCAAT 58.652 50.000 0.00 0.00 0.00 3.16
4747 4799 4.389992 CGATGCACAGGGTATTGATCATAC 59.610 45.833 0.00 1.68 37.61 2.39
5063 5115 1.950909 CGGAGGCAAACACAAAAGGTA 59.049 47.619 0.00 0.00 0.00 3.08
5064 5116 2.287368 CGGAGGCAAACACAAAAGGTAC 60.287 50.000 0.00 0.00 0.00 3.34
5078 5130 7.597743 ACACAAAAGGTACACGAGATAAGTAAG 59.402 37.037 0.00 0.00 0.00 2.34
5113 5165 1.974028 TTGTAGGCCCACCAAGGATA 58.026 50.000 0.00 0.00 41.22 2.59
5196 5248 5.222079 TGCAGTCACCAGTGAAAGTATTA 57.778 39.130 1.23 0.00 41.85 0.98
5255 5307 2.158325 AGGGGAAGGACAAATTCTTGCA 60.158 45.455 0.00 0.00 35.84 4.08
5259 5311 5.122519 GGGAAGGACAAATTCTTGCAAAAA 58.877 37.500 0.00 0.00 35.84 1.94
5289 5341 2.228582 CCTCAACAATCGAATGGTTGCA 59.771 45.455 17.37 9.23 41.17 4.08
5300 5352 3.614630 CGAATGGTTGCATGATGTGGTTT 60.615 43.478 0.00 0.00 0.00 3.27
5345 5398 6.127535 GCATTCTTGGATTTCTCTCATTTGGA 60.128 38.462 0.00 0.00 0.00 3.53
5370 5423 7.083875 TCTTCGTGTTTGAATCTTTTTGTCT 57.916 32.000 0.00 0.00 0.00 3.41
5436 5489 6.435428 ACTTGACTTTGGCAATTTTACTACG 58.565 36.000 0.00 0.00 0.00 3.51
5458 5511 6.507996 ACGTAGTCACAAGGGAAAGTATCCA 61.508 44.000 0.00 0.00 45.69 3.41
5545 5624 6.368791 TGTTCACACTGAATATGACTACAAGC 59.631 38.462 0.00 0.00 38.79 4.01
5557 5636 8.910351 ATATGACTACAAGCCCTAGAAATTTC 57.090 34.615 10.33 10.33 0.00 2.17
5570 5649 6.003950 CCTAGAAATTTCAGGTCCAAACTCA 58.996 40.000 19.99 0.00 0.00 3.41
5642 5722 5.343249 ACAAGAGACAAAAGCAACATTGAC 58.657 37.500 0.00 0.00 0.00 3.18
5651 5731 6.919662 ACAAAAGCAACATTGACACTATTCAG 59.080 34.615 0.00 0.00 0.00 3.02
5715 5795 7.733773 ATTTTGGACCTAAAATCTTTAGGGG 57.266 36.000 22.89 6.54 44.47 4.79
5720 5800 6.679303 TGGACCTAAAATCTTTAGGGGATGTA 59.321 38.462 22.89 6.50 44.47 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.404671 AATTAGTTTTATGCCCCTAGTTGTG 57.595 36.000 0.00 0.00 0.00 3.33
1 2 9.709387 AATAATTAGTTTTATGCCCCTAGTTGT 57.291 29.630 0.00 0.00 0.00 3.32
3 4 9.363401 GGAATAATTAGTTTTATGCCCCTAGTT 57.637 33.333 0.00 0.00 32.84 2.24
4 5 8.733808 AGGAATAATTAGTTTTATGCCCCTAGT 58.266 33.333 0.00 0.00 37.82 2.57
73 74 2.558359 ACTTTGTAAAGCTGGACATGCC 59.442 45.455 4.35 0.00 39.63 4.40
91 92 4.798882 TGGTTTTGGATCACCACTAACTT 58.201 39.130 0.00 0.00 46.80 2.66
373 374 2.420628 ACAATTCCGCAACATGTGTG 57.579 45.000 0.00 1.20 37.49 3.82
374 375 3.122297 CAAACAATTCCGCAACATGTGT 58.878 40.909 0.00 0.00 0.00 3.72
581 584 0.956902 ACATCAACTGCAGCGATGCA 60.957 50.000 31.74 28.41 40.15 3.96
587 590 3.360249 AAGACAAACATCAACTGCAGC 57.640 42.857 15.27 0.00 0.00 5.25
658 661 5.630415 AATAGCTAGCCCTCACAAATGTA 57.370 39.130 12.13 0.00 0.00 2.29
785 788 9.944376 GTTAATGAGGTGCATTTATATCCTAGA 57.056 33.333 0.00 0.00 44.68 2.43
826 829 6.152932 ACACAATCTTGCTTGAAAGTCAAT 57.847 33.333 0.00 0.00 35.59 2.57
907 910 8.095452 AGGATTTAGTGAGGACAATTAGTGAT 57.905 34.615 0.00 0.00 0.00 3.06
938 941 9.003658 CCCTTAATAGTATGAAATGTCATGGTC 57.996 37.037 8.76 0.00 44.49 4.02
943 946 5.995282 CCGCCCTTAATAGTATGAAATGTCA 59.005 40.000 0.00 0.00 38.41 3.58
962 965 2.418083 CCTTTCATTGAGGCCGCCC 61.418 63.158 5.55 0.00 0.00 6.13
1001 1004 3.360867 TCAAAGCCAAAGGAGAAACACA 58.639 40.909 0.00 0.00 0.00 3.72
1027 1030 7.554118 ACAATATGTTGAAGAGAACTACCCATG 59.446 37.037 9.40 0.00 38.71 3.66
1069 1072 5.163447 TGTTGTGAGTGTAGTAGCAAGAAGT 60.163 40.000 0.00 0.00 0.00 3.01
1080 1083 4.818534 AAGCATTGTGTTGTGAGTGTAG 57.181 40.909 0.00 0.00 0.00 2.74
1161 1164 9.013229 TGAAAGCAAGTAAATCATTATGTGAGT 57.987 29.630 0.00 0.00 40.92 3.41
1560 1563 8.841300 GGTTTTCCATCTCCTCTATTTACAATC 58.159 37.037 0.00 0.00 40.31 2.67
1744 1747 6.071221 CCCATGTGGAATTTGAAAGAGAATCA 60.071 38.462 0.00 0.00 35.28 2.57
1892 1895 9.123902 TGTAGCTACATATGCTTGATGAATTTT 57.876 29.630 22.67 0.00 41.46 1.82
1893 1896 8.681486 TGTAGCTACATATGCTTGATGAATTT 57.319 30.769 22.67 0.00 41.46 1.82
1982 1986 4.536295 TCATAGGGTGAGTGTCCTGATA 57.464 45.455 0.00 0.00 34.75 2.15
1983 1987 3.404869 TCATAGGGTGAGTGTCCTGAT 57.595 47.619 0.00 0.00 34.75 2.90
1984 1988 2.919772 TCATAGGGTGAGTGTCCTGA 57.080 50.000 0.00 0.00 34.75 3.86
1985 1989 2.169352 CCTTCATAGGGTGAGTGTCCTG 59.831 54.545 0.00 0.00 38.29 3.86
1986 1990 2.472029 CCTTCATAGGGTGAGTGTCCT 58.528 52.381 0.00 0.00 38.29 3.85
1987 1991 2.990066 CCTTCATAGGGTGAGTGTCC 57.010 55.000 0.00 0.00 38.29 4.02
1997 2001 2.787473 TCAGCACAACCCTTCATAGG 57.213 50.000 0.00 0.00 41.60 2.57
1998 2002 6.057533 TCATTATCAGCACAACCCTTCATAG 58.942 40.000 0.00 0.00 0.00 2.23
1999 2003 6.000246 TCATTATCAGCACAACCCTTCATA 58.000 37.500 0.00 0.00 0.00 2.15
2000 2004 4.858850 TCATTATCAGCACAACCCTTCAT 58.141 39.130 0.00 0.00 0.00 2.57
2001 2005 4.299586 TCATTATCAGCACAACCCTTCA 57.700 40.909 0.00 0.00 0.00 3.02
2002 2006 5.841957 AATCATTATCAGCACAACCCTTC 57.158 39.130 0.00 0.00 0.00 3.46
2003 2007 7.902920 ATTAATCATTATCAGCACAACCCTT 57.097 32.000 0.00 0.00 0.00 3.95
2004 2008 7.902920 AATTAATCATTATCAGCACAACCCT 57.097 32.000 0.00 0.00 0.00 4.34
2005 2009 9.463443 GTAAATTAATCATTATCAGCACAACCC 57.537 33.333 0.00 0.00 0.00 4.11
2123 2127 6.072673 ACGAACTTCATTTACCATGAAAGACC 60.073 38.462 0.00 0.00 37.55 3.85
2147 2151 7.859325 ATGGAACCACATAACTACATTGTAC 57.141 36.000 0.00 0.00 0.00 2.90
2171 2175 5.962031 ACTATTGTCTATGTGGTGGGAAGTA 59.038 40.000 0.00 0.00 0.00 2.24
2216 2220 5.220491 GCGGTGTCAAAGAAGAGCTAATTAG 60.220 44.000 8.20 8.20 0.00 1.73
2237 2241 2.725008 GGAGAGAGATCACGGCGG 59.275 66.667 13.24 0.00 0.00 6.13
2239 2243 0.467290 AGAGGGAGAGAGATCACGGC 60.467 60.000 0.00 0.00 0.00 5.68
2240 2244 2.500229 GTAGAGGGAGAGAGATCACGG 58.500 57.143 0.00 0.00 0.00 4.94
2242 2246 3.394606 AGAGGTAGAGGGAGAGAGATCAC 59.605 52.174 0.00 0.00 0.00 3.06
2262 2266 0.923358 GAGTGAGAGAGGGAGGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
2263 2267 0.926293 AGAGTGAGAGAGGGAGGGAG 59.074 60.000 0.00 0.00 0.00 4.30
2265 2269 0.926293 AGAGAGTGAGAGAGGGAGGG 59.074 60.000 0.00 0.00 0.00 4.30
2266 2270 1.846439 AGAGAGAGTGAGAGAGGGAGG 59.154 57.143 0.00 0.00 0.00 4.30
2267 2271 2.774234 AGAGAGAGAGTGAGAGAGGGAG 59.226 54.545 0.00 0.00 0.00 4.30
2268 2272 2.771943 GAGAGAGAGAGTGAGAGAGGGA 59.228 54.545 0.00 0.00 0.00 4.20
2269 2273 2.774234 AGAGAGAGAGAGTGAGAGAGGG 59.226 54.545 0.00 0.00 0.00 4.30
2270 2274 3.181461 GGAGAGAGAGAGAGTGAGAGAGG 60.181 56.522 0.00 0.00 0.00 3.69
2278 2282 3.041946 GAGAGAGGGAGAGAGAGAGAGT 58.958 54.545 0.00 0.00 0.00 3.24
2285 2289 8.884124 ATGAATAATTAGAGAGAGGGAGAGAG 57.116 38.462 0.00 0.00 0.00 3.20
2420 2424 5.959618 AACTTGCTACTTAACATGGAACC 57.040 39.130 0.00 0.00 0.00 3.62
2474 2478 9.100197 GTATCCCATAATTCACCCCATATTTTT 57.900 33.333 0.00 0.00 0.00 1.94
2481 2485 4.051478 AGTGTATCCCATAATTCACCCCA 58.949 43.478 0.00 0.00 29.87 4.96
2499 2503 6.429692 TCCATGATACGATGTTTGAAAAGTGT 59.570 34.615 0.00 0.00 0.00 3.55
2502 2506 8.611757 TGTATCCATGATACGATGTTTGAAAAG 58.388 33.333 9.09 0.00 45.41 2.27
2759 2764 7.148705 CCAAGCACAACATTTCAAACTATGATG 60.149 37.037 0.00 0.00 38.03 3.07
2784 2789 6.201806 CACAATGCTTAACATACTCTAGCTCC 59.798 42.308 0.00 0.00 38.34 4.70
2874 2879 3.240884 CATAGTCGATCAAGAGGATGCG 58.759 50.000 0.00 0.00 36.00 4.73
2916 2921 7.067532 TGCAAATAAAACTACAATCGACGAT 57.932 32.000 4.05 4.05 0.00 3.73
2918 2923 6.248420 CCTTGCAAATAAAACTACAATCGACG 59.752 38.462 0.00 0.00 0.00 5.12
2921 2926 6.092748 AGCCTTGCAAATAAAACTACAATCG 58.907 36.000 0.00 0.00 0.00 3.34
3105 3114 5.029807 TGAGTGTGTGAATCCTTGTACAA 57.970 39.130 8.28 8.28 0.00 2.41
3215 3224 6.377146 ACCACACATAATTCCTTCCATGTAAC 59.623 38.462 0.00 0.00 30.66 2.50
3217 3226 6.073447 ACCACACATAATTCCTTCCATGTA 57.927 37.500 0.00 0.00 30.66 2.29
3218 3227 4.934356 ACCACACATAATTCCTTCCATGT 58.066 39.130 0.00 0.00 31.91 3.21
3219 3228 5.418524 TCAACCACACATAATTCCTTCCATG 59.581 40.000 0.00 0.00 0.00 3.66
3220 3229 5.579047 TCAACCACACATAATTCCTTCCAT 58.421 37.500 0.00 0.00 0.00 3.41
3221 3230 4.991776 TCAACCACACATAATTCCTTCCA 58.008 39.130 0.00 0.00 0.00 3.53
3222 3231 5.975693 TTCAACCACACATAATTCCTTCC 57.024 39.130 0.00 0.00 0.00 3.46
3454 3464 8.956533 AAAAGTTAATGGTAAAAGTTGCATGT 57.043 26.923 0.00 0.00 0.00 3.21
3587 3597 9.778741 TCTAAATATATTAGCACCTCTGTTTGG 57.221 33.333 0.00 0.00 0.00 3.28
3642 3652 5.602628 ACAGAGACCTACTTCACAAAGTTC 58.397 41.667 0.00 0.00 43.28 3.01
3652 3662 3.526019 AGCCTAGAGACAGAGACCTACTT 59.474 47.826 0.00 0.00 0.00 2.24
4000 4010 6.212187 TCACAAGCATGCATATCTAGATACCT 59.788 38.462 21.98 0.00 0.00 3.08
4002 4012 7.011202 CCATCACAAGCATGCATATCTAGATAC 59.989 40.741 21.98 4.18 0.00 2.24
4012 4023 2.585876 TGCCATCACAAGCATGCAT 58.414 47.368 21.98 4.57 33.08 3.96
4017 4028 1.252215 CCACCATGCCATCACAAGCA 61.252 55.000 0.00 0.00 44.45 3.91
4032 4043 2.159057 CCTTTCCAATGCTAATGCCACC 60.159 50.000 0.00 0.00 38.71 4.61
4035 4046 1.413812 CCCCTTTCCAATGCTAATGCC 59.586 52.381 0.00 0.00 38.71 4.40
4044 4055 1.318934 ATGGTAGGCCCCTTTCCAAT 58.681 50.000 0.00 3.06 34.50 3.16
4118 4129 8.592105 TTTTCCAAACAAAGAATAGCATTCTG 57.408 30.769 10.78 5.04 0.00 3.02
4245 4256 2.123589 TCGAGAGAGAGAGGGAGACAT 58.876 52.381 0.00 0.00 34.84 3.06
4246 4257 1.574263 TCGAGAGAGAGAGGGAGACA 58.426 55.000 0.00 0.00 34.84 3.41
4379 4431 8.166422 TCCCAGAAAACTTAATCAAACTTCTC 57.834 34.615 0.00 0.00 0.00 2.87
4442 4494 9.765795 ACACTATCTTTGTTCTTATGTATAGGC 57.234 33.333 0.00 0.00 0.00 3.93
4452 4504 9.998106 ATGTTAGTACACACTATCTTTGTTCTT 57.002 29.630 0.00 0.00 37.12 2.52
4493 4545 5.121811 CAATCACCTGAAGATGGTTCCTAG 58.878 45.833 0.00 0.00 35.28 3.02
4518 4570 2.846206 TGTTAGCTCCCACATGGATCTT 59.154 45.455 0.00 0.00 44.07 2.40
4538 4590 1.545582 ACGAGTTTTGGATGCCCATTG 59.454 47.619 0.00 0.00 43.12 2.82
4540 4592 1.176527 CACGAGTTTTGGATGCCCAT 58.823 50.000 0.00 0.00 43.12 4.00
4663 4715 2.039216 TCGAAAACATAGCCACTTCCCA 59.961 45.455 0.00 0.00 0.00 4.37
4747 4799 2.028420 TGGAAGATCTGCAACGATGG 57.972 50.000 2.29 0.00 0.00 3.51
4781 4833 6.817765 TTTGAAGGAGTATAGCAACCTTTG 57.182 37.500 0.00 0.00 41.90 2.77
5063 5115 6.510879 TCACACATCTTACTTATCTCGTGT 57.489 37.500 0.00 0.00 36.84 4.49
5064 5116 8.346300 ACTATCACACATCTTACTTATCTCGTG 58.654 37.037 0.00 0.00 0.00 4.35
5113 5165 4.892934 ACCCAAACAACATGTGAATACAGT 59.107 37.500 0.00 0.00 40.79 3.55
5196 5248 2.006888 CCATTCGAACGCCTAATGTGT 58.993 47.619 0.00 0.00 40.09 3.72
5259 5311 2.026641 CGATTGTTGAGGGCATGGATT 58.973 47.619 0.00 0.00 0.00 3.01
5320 5373 6.040878 CCAAATGAGAGAAATCCAAGAATGC 58.959 40.000 0.00 0.00 0.00 3.56
5345 5398 7.707104 AGACAAAAAGATTCAAACACGAAGAT 58.293 30.769 0.00 0.00 0.00 2.40
5436 5489 5.046520 ACTGGATACTTTCCCTTGTGACTAC 60.047 44.000 0.00 0.00 44.77 2.73
5528 5607 6.656632 TCTAGGGCTTGTAGTCATATTCAG 57.343 41.667 0.00 0.00 0.00 3.02
5545 5624 5.325239 AGTTTGGACCTGAAATTTCTAGGG 58.675 41.667 26.59 22.25 35.89 3.53
5557 5636 3.192422 TGTGTGTTTTGAGTTTGGACCTG 59.808 43.478 0.00 0.00 0.00 4.00
5570 5649 8.281893 CACTTTTTGTTTCTCAATGTGTGTTTT 58.718 29.630 0.00 0.00 35.84 2.43
5620 5700 5.230726 GTGTCAATGTTGCTTTTGTCTCTTG 59.769 40.000 0.00 0.00 0.00 3.02
5642 5722 8.961294 AAAGAGAAATCCAGATCTGAATAGTG 57.039 34.615 24.62 6.18 0.00 2.74
5715 5795 5.578727 GTCTCACAAGGAATGTCACTACATC 59.421 44.000 0.00 0.00 45.79 3.06
5720 5800 4.696479 AAGTCTCACAAGGAATGTCACT 57.304 40.909 0.00 0.00 41.46 3.41
5730 5810 5.387444 CGACAAACGTGATAAGTCTCACAAG 60.387 44.000 0.00 0.00 44.69 3.16
5746 5834 7.000575 ATTGTCCATCTATTTACGACAAACG 57.999 36.000 5.17 0.00 44.16 3.60
5828 5916 4.281525 TGCAACGGAAGAAACAAACTAC 57.718 40.909 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.