Multiple sequence alignment - TraesCS1A01G138800

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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 TraesCS1A01G138800 chr1A 100.000 6063 0 0 1 6063 233919989 233926051 0.000000e+00 11197.0
1 TraesCS1A01G138800 chr1A 90.850 306 24 1 402 707 540722868 540723169 2.030000e-109 407.0
2 TraesCS1A01G138800 chr1A 90.554 307 27 1 401 707 376346528 376346224 7.320000e-109 405.0
3 TraesCS1A01G138800 chr1A 89.535 258 12 3 3106 3349 37396569 37396313 4.560000e-81 313.0
4 TraesCS1A01G138800 chr1D 95.672 3281 76 22 2647 5896 159142000 159145245 0.000000e+00 5212.0
5 TraesCS1A01G138800 chr1D 93.914 2662 98 18 1 2619 159139004 159141644 0.000000e+00 3960.0
6 TraesCS1A01G138800 chr1D 90.159 315 28 2 397 711 276505103 276504792 2.030000e-109 407.0
7 TraesCS1A01G138800 chr1D 97.093 172 3 1 5894 6063 159145300 159145471 7.690000e-74 289.0
8 TraesCS1A01G138800 chr1D 81.102 127 23 1 5682 5808 70582307 70582432 3.870000e-17 100.0
9 TraesCS1A01G138800 chr1B 93.865 3325 112 39 2608 5891 217562057 217565330 0.000000e+00 4926.0
10 TraesCS1A01G138800 chr1B 93.800 1742 46 18 906 2619 217560088 217561795 0.000000e+00 2562.0
11 TraesCS1A01G138800 chr1B 90.598 234 8 2 3106 3325 122829839 122829606 1.280000e-76 298.0
12 TraesCS1A01G138800 chr1B 90.171 234 9 2 3106 3325 79979330 79979097 5.940000e-75 292.0
13 TraesCS1A01G138800 chr1B 100.000 28 0 0 2751 2778 217562050 217562023 1.100000e-02 52.8
14 TraesCS1A01G138800 chr2B 89.055 402 38 5 1 399 463454409 463454011 1.520000e-135 494.0
15 TraesCS1A01G138800 chr2B 84.383 397 33 11 6 401 333037528 333037896 4.470000e-96 363.0
16 TraesCS1A01G138800 chr2B 83.333 84 13 1 5680 5763 114518791 114518873 6.520000e-10 76.8
17 TraesCS1A01G138800 chr7B 87.192 406 45 4 1 401 80702113 80702516 7.160000e-124 455.0
18 TraesCS1A01G138800 chr7B 88.525 61 6 1 2674 2734 657604652 657604711 8.430000e-09 73.1
19 TraesCS1A01G138800 chr7B 93.617 47 2 1 2688 2734 657594935 657594980 1.090000e-07 69.4
20 TraesCS1A01G138800 chr7B 86.885 61 7 1 2674 2734 657372186 657372245 3.920000e-07 67.6
21 TraesCS1A01G138800 chr6A 90.625 320 26 1 398 717 588602432 588602117 7.270000e-114 422.0
22 TraesCS1A01G138800 chr3D 90.645 310 27 1 398 707 22573664 22573971 1.570000e-110 411.0
23 TraesCS1A01G138800 chr5D 90.645 310 25 1 398 707 351152808 351153113 5.660000e-110 409.0
24 TraesCS1A01G138800 chr5D 89.873 316 26 3 389 703 309686817 309687127 9.470000e-108 401.0
25 TraesCS1A01G138800 chr5A 89.873 316 29 1 398 713 549204646 549204334 2.630000e-108 403.0
26 TraesCS1A01G138800 chr4B 91.860 258 7 2 3106 3349 333372417 333372160 1.250000e-91 348.0
27 TraesCS1A01G138800 chrUn 91.085 258 9 2 3106 3349 114953319 114953062 2.710000e-88 337.0
28 TraesCS1A01G138800 chr4A 91.085 258 8 8 3106 3349 610428503 610428759 9.740000e-88 335.0
29 TraesCS1A01G138800 chr4A 89.147 258 14 4 3106 3349 555158802 555158545 5.900000e-80 309.0
30 TraesCS1A01G138800 chr3B 90.310 258 11 6 3106 3349 365739429 365739686 5.860000e-85 326.0
31 TraesCS1A01G138800 chr2A 89.706 204 20 1 5 207 714440516 714440719 6.030000e-65 259.0
32 TraesCS1A01G138800 chr2A 87.440 207 23 3 196 401 714516526 714516730 1.020000e-57 235.0
33 TraesCS1A01G138800 chr2A 88.060 67 8 0 5675 5741 74585752 74585818 5.040000e-11 80.5
34 TraesCS1A01G138800 chr2A 85.333 75 8 3 5690 5763 74785830 74785902 2.340000e-09 75.0
35 TraesCS1A01G138800 chr3A 92.697 178 12 1 225 401 703418398 703418221 7.800000e-64 255.0
36 TraesCS1A01G138800 chr2D 81.600 125 21 2 5640 5763 74999574 74999697 1.080000e-17 102.0


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 TraesCS1A01G138800 chr1A 233919989 233926051 6062 False 11197.000000 11197 100.000000 1 6063 1 chr1A.!!$F1 6062
1 TraesCS1A01G138800 chr1D 159139004 159145471 6467 False 3153.666667 5212 95.559667 1 6063 3 chr1D.!!$F2 6062
2 TraesCS1A01G138800 chr1B 217560088 217565330 5242 False 3744.000000 4926 93.832500 906 5891 2 chr1B.!!$F1 4985

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
62 63 0.036732 TCCTGACAGATTGGTGCACC 59.963 55.000 29.67 29.67 0.00 5.01 F
345 347 0.098376 GCAGAGTAGTGCTTGCATGC 59.902 55.000 17.19 17.19 40.54 4.06 F
1282 1297 0.592247 GCGAATGTATGGCGCCTTTG 60.592 55.000 29.70 17.53 44.55 2.77 F
1456 1473 0.937304 CTTCTCGTGGTGTTGTGGTG 59.063 55.000 0.00 0.00 0.00 4.17 F
1889 1907 1.906574 TCCTAAGTTGTGGCCCACTAG 59.093 52.381 16.23 8.09 35.11 2.57 F
2191 2209 2.422597 TCCAACCTGTTCTGTATTGCG 58.577 47.619 0.00 0.00 0.00 4.85 F
3753 4142 1.016627 GGTAATCGCAATGCAGCTGA 58.983 50.000 20.43 2.70 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 1982 0.871722 GAAGCACGGCATTGTGTGTA 59.128 50.000 11.18 0.00 41.94 2.90 R
2203 2221 2.627945 TCAGGCCAATGAATACGACAC 58.372 47.619 5.01 0.00 0.00 3.67 R
2476 2495 0.035056 ACAGCCACCAGTCCATTAGC 60.035 55.000 0.00 0.00 0.00 3.09 R
2477 2496 2.359900 GAACAGCCACCAGTCCATTAG 58.640 52.381 0.00 0.00 0.00 1.73 R
3523 3912 2.158842 GGATAGAGGCATGCTCTGTTGT 60.159 50.000 18.92 4.46 32.79 3.32 R
3884 4273 2.288395 CCTGGAAAACACATGTGCCTTC 60.288 50.000 25.68 24.13 0.00 3.46 R
5205 5604 0.026803 GAAGCAAGGTTGATAGCGCG 59.973 55.000 0.00 0.00 0.00 6.86 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
26 27 4.409218 GAGTCGCCCACGTACGCA 62.409 66.667 16.72 0.00 41.18 5.24
43 44 2.770904 ACCCACCCAACTGGACGT 60.771 61.111 0.00 0.00 37.39 4.34
62 63 0.036732 TCCTGACAGATTGGTGCACC 59.963 55.000 29.67 29.67 0.00 5.01
79 80 0.957395 ACCAGCAGGACAAGCAATCG 60.957 55.000 0.35 0.00 38.69 3.34
80 81 0.674581 CCAGCAGGACAAGCAATCGA 60.675 55.000 0.00 0.00 36.89 3.59
91 92 3.814842 ACAAGCAATCGACATTCAGACAA 59.185 39.130 0.00 0.00 0.00 3.18
98 99 4.271696 TCGACATTCAGACAAGGACAAT 57.728 40.909 0.00 0.00 0.00 2.71
134 135 3.841255 TGTTGGGTATGTGGACACTATGA 59.159 43.478 3.91 0.00 0.00 2.15
138 139 4.534500 TGGGTATGTGGACACTATGAAAGT 59.466 41.667 3.91 0.00 39.81 2.66
140 141 6.385759 TGGGTATGTGGACACTATGAAAGTAT 59.614 38.462 3.91 0.00 35.76 2.12
143 144 5.907866 TGTGGACACTATGAAAGTATCGA 57.092 39.130 3.91 0.00 35.76 3.59
190 192 1.344763 CCCTCCTTACATCGGGTCATC 59.655 57.143 0.00 0.00 31.89 2.92
192 194 1.000163 CTCCTTACATCGGGTCATCGG 60.000 57.143 0.00 0.00 0.00 4.18
273 275 4.061596 GACCATTTCATAGTGGAGCTAGC 58.938 47.826 6.62 6.62 38.86 3.42
274 276 3.713764 ACCATTTCATAGTGGAGCTAGCT 59.286 43.478 19.45 19.45 38.86 3.32
275 277 4.901849 ACCATTTCATAGTGGAGCTAGCTA 59.098 41.667 19.38 0.97 38.86 3.32
276 278 5.011533 ACCATTTCATAGTGGAGCTAGCTAG 59.988 44.000 19.38 16.84 38.86 3.42
277 279 5.477510 CATTTCATAGTGGAGCTAGCTAGG 58.522 45.833 19.38 3.14 32.45 3.02
278 280 3.885976 TCATAGTGGAGCTAGCTAGGT 57.114 47.619 24.94 24.94 36.62 3.08
279 281 3.491342 TCATAGTGGAGCTAGCTAGGTG 58.509 50.000 29.22 13.22 33.58 4.00
280 282 2.366640 TAGTGGAGCTAGCTAGGTGG 57.633 55.000 29.22 2.14 33.58 4.61
281 283 0.631753 AGTGGAGCTAGCTAGGTGGA 59.368 55.000 29.22 12.71 33.58 4.02
282 284 1.219213 AGTGGAGCTAGCTAGGTGGAT 59.781 52.381 29.22 10.02 33.58 3.41
283 285 2.043227 GTGGAGCTAGCTAGGTGGATT 58.957 52.381 29.22 0.00 33.58 3.01
284 286 3.117093 AGTGGAGCTAGCTAGGTGGATTA 60.117 47.826 29.22 8.37 33.58 1.75
285 287 3.257127 GTGGAGCTAGCTAGGTGGATTAG 59.743 52.174 29.22 0.00 33.58 1.73
288 290 2.630580 AGCTAGCTAGGTGGATTAGCAC 59.369 50.000 24.15 1.76 44.65 4.40
321 323 1.373435 CCAACTAGGCCGGTTGTGA 59.627 57.895 29.15 1.53 41.47 3.58
343 345 0.393537 GGGCAGAGTAGTGCTTGCAT 60.394 55.000 13.95 0.00 43.45 3.96
345 347 0.098376 GCAGAGTAGTGCTTGCATGC 59.902 55.000 17.19 17.19 40.54 4.06
357 359 4.922692 GTGCTTGCATGCAATTACTTGTAA 59.077 37.500 31.96 7.39 45.12 2.41
363 365 7.389803 TGCATGCAATTACTTGTAACACTAT 57.610 32.000 20.30 0.00 34.69 2.12
366 368 8.586273 GCATGCAATTACTTGTAACACTATTTG 58.414 33.333 14.21 0.00 34.69 2.32
403 405 6.200878 TCACCCATTTCTCTTCTTTAAGGT 57.799 37.500 0.00 0.00 33.22 3.50
404 406 6.238648 TCACCCATTTCTCTTCTTTAAGGTC 58.761 40.000 0.00 0.00 33.22 3.85
406 408 6.717084 CACCCATTTCTCTTCTTTAAGGTCTT 59.283 38.462 0.00 0.00 33.22 3.01
421 423 5.843019 AAGGTCTTCTTTGGTTCATAGGA 57.157 39.130 0.00 0.00 29.99 2.94
425 427 6.100424 AGGTCTTCTTTGGTTCATAGGATAGG 59.900 42.308 0.00 0.00 0.00 2.57
439 441 7.893658 TCATAGGATAGGAAAATCGTAGGAAC 58.106 38.462 0.00 0.00 35.39 3.62
447 449 6.296803 AGGAAAATCGTAGGAACAGAAAAGT 58.703 36.000 0.00 0.00 0.00 2.66
460 462 7.609532 AGGAACAGAAAAGTCATAGGAAATGAG 59.390 37.037 0.00 0.00 0.00 2.90
526 528 5.768662 AGATGCCCTTTGATTCACATCATAG 59.231 40.000 13.54 1.71 39.28 2.23
597 599 8.906867 TGGAATGTGAATGATAGAAAGAATTCC 58.093 33.333 0.65 0.00 39.71 3.01
598 600 9.129532 GGAATGTGAATGATAGAAAGAATTCCT 57.870 33.333 0.65 0.00 37.45 3.36
635 637 8.343787 AGGATTCCATTTCTATAAACCAAAGGA 58.656 33.333 5.29 0.00 0.00 3.36
640 642 9.053472 TCCATTTCTATAAACCAAAGGACTCTA 57.947 33.333 0.00 0.00 0.00 2.43
730 733 8.648698 AGATCTAAGTAGATGATATGCACACT 57.351 34.615 5.56 0.00 42.79 3.55
734 737 4.864633 AGTAGATGATATGCACACTCGTG 58.135 43.478 0.00 0.00 46.56 4.35
848 852 1.927527 ACATTCTGCCTCAGCCCCT 60.928 57.895 0.00 0.00 38.69 4.79
865 869 2.225267 CCCCTTTTAAAGAGGCCCTTCA 60.225 50.000 6.24 0.00 33.02 3.02
888 892 2.061182 CTACTGTAGGGCTCGTCCGC 62.061 65.000 6.95 0.00 34.94 5.54
1282 1297 0.592247 GCGAATGTATGGCGCCTTTG 60.592 55.000 29.70 17.53 44.55 2.77
1456 1473 0.937304 CTTCTCGTGGTGTTGTGGTG 59.063 55.000 0.00 0.00 0.00 4.17
1599 1616 8.759481 TGTCCAAAGATTATGGCATTATGTTA 57.241 30.769 4.78 0.00 37.88 2.41
1882 1900 6.246420 CATATTATGCTCCTAAGTTGTGGC 57.754 41.667 0.00 0.00 0.00 5.01
1889 1907 1.906574 TCCTAAGTTGTGGCCCACTAG 59.093 52.381 16.23 8.09 35.11 2.57
1964 1982 7.279981 GGCTTTGTTAATTTGGTTTCACTTTCT 59.720 33.333 0.00 0.00 0.00 2.52
2191 2209 2.422597 TCCAACCTGTTCTGTATTGCG 58.577 47.619 0.00 0.00 0.00 4.85
2476 2495 3.796504 GCCAACAGTCTTGTCCATTGTTG 60.797 47.826 8.29 8.29 44.92 3.33
2477 2496 3.374745 CAACAGTCTTGTCCATTGTTGC 58.625 45.455 3.15 0.00 41.19 4.17
2667 3040 8.895932 GTCATGTGACATTAAAATTCTACCAC 57.104 34.615 8.22 0.00 44.18 4.16
2756 3130 8.854614 ATTAGTTAGTTGAGCTCTGATTTTGT 57.145 30.769 16.19 0.00 0.00 2.83
2810 3184 6.479972 AGTGATTGAAAGACACGGGATATA 57.520 37.500 0.00 0.00 39.19 0.86
2824 3198 9.194271 GACACGGGATATATCTTTAGTTTCTTC 57.806 37.037 12.42 0.00 0.00 2.87
2921 3295 3.942115 GGGCTCTTTTGACACCTTAGATC 59.058 47.826 0.00 0.00 0.00 2.75
3058 3432 6.660521 TGTTCTTCTTGCAAGACCATGAATAT 59.339 34.615 28.46 0.00 34.13 1.28
3522 3911 8.657712 AGACCTTGTACCTTCTAAAACATTAGT 58.342 33.333 0.00 0.00 0.00 2.24
3523 3912 9.933723 GACCTTGTACCTTCTAAAACATTAGTA 57.066 33.333 0.00 0.00 0.00 1.82
3605 3994 5.985530 GCTTTCTGAGTTGGCTTATTTGTTT 59.014 36.000 0.00 0.00 0.00 2.83
3642 4031 1.208052 TCTAACTGCATGGACAGCTCC 59.792 52.381 0.00 0.00 41.60 4.70
3753 4142 1.016627 GGTAATCGCAATGCAGCTGA 58.983 50.000 20.43 2.70 0.00 4.26
4131 4520 9.990868 AAGGTTTATGTGTATATTTTCCCTCTT 57.009 29.630 0.00 0.00 0.00 2.85
4132 4521 9.990868 AGGTTTATGTGTATATTTTCCCTCTTT 57.009 29.630 0.00 0.00 0.00 2.52
4141 4530 8.739039 TGTATATTTTCCCTCTTTGTGTGAATG 58.261 33.333 0.00 0.00 0.00 2.67
4335 4731 5.834742 AGGCATATATGAATTTGTGCTTCCA 59.165 36.000 17.10 0.00 33.38 3.53
4363 4760 3.413558 GTGCTCGCTTAATTTGTTACCG 58.586 45.455 0.00 0.00 0.00 4.02
4597 4994 2.799017 TGATTTCTGTGGCATTGCTCT 58.201 42.857 8.82 0.00 0.00 4.09
4633 5030 8.268850 AGTTCCAAGTTATTAGCATGTTAGTG 57.731 34.615 0.00 0.00 0.00 2.74
4692 5089 4.437239 TGAAATTTTGTTGCCACGACATT 58.563 34.783 0.00 0.00 0.00 2.71
4702 5099 4.354071 TGCCACGACATTGTTGATAATG 57.646 40.909 11.07 0.00 42.38 1.90
4861 5258 4.595781 TGACATACAACAGGTTACCCTTCT 59.404 41.667 0.00 0.00 39.89 2.85
4862 5259 5.781306 TGACATACAACAGGTTACCCTTCTA 59.219 40.000 0.00 0.00 39.89 2.10
4863 5260 6.070995 TGACATACAACAGGTTACCCTTCTAG 60.071 42.308 0.00 0.00 39.89 2.43
4864 5261 3.697619 ACAACAGGTTACCCTTCTAGC 57.302 47.619 0.00 0.00 39.89 3.42
4865 5262 3.248888 ACAACAGGTTACCCTTCTAGCT 58.751 45.455 0.00 0.00 39.89 3.32
4866 5263 3.651423 ACAACAGGTTACCCTTCTAGCTT 59.349 43.478 0.00 0.00 39.89 3.74
4867 5264 4.104261 ACAACAGGTTACCCTTCTAGCTTT 59.896 41.667 0.00 0.00 39.89 3.51
4868 5265 4.554960 ACAGGTTACCCTTCTAGCTTTC 57.445 45.455 0.00 0.00 39.89 2.62
4869 5266 3.908103 ACAGGTTACCCTTCTAGCTTTCA 59.092 43.478 0.00 0.00 39.89 2.69
5076 5475 8.277197 TCTTGAGGGATGATGATGAAACTTTAT 58.723 33.333 0.00 0.00 0.00 1.40
5080 5479 5.279156 GGGATGATGATGAAACTTTATGCCC 60.279 44.000 0.00 0.00 0.00 5.36
5085 5484 6.608405 TGATGATGAAACTTTATGCCCTCATT 59.392 34.615 0.00 0.00 34.22 2.57
5187 5586 7.938490 TGAGCATCAATAATTAGCCTGAATACA 59.062 33.333 0.00 0.00 45.97 2.29
5205 5604 1.139058 ACAGGACGGATATGCCTTGTC 59.861 52.381 0.00 0.00 0.00 3.18
5253 5652 4.025040 TCAAAGTTCAGCAGATGTCCAT 57.975 40.909 0.00 0.00 0.00 3.41
5265 5664 8.843262 TCAGCAGATGTCCATTTATAATTTGAG 58.157 33.333 0.00 0.00 0.00 3.02
5275 5674 6.480981 CCATTTATAATTTGAGGCAGCCTTTG 59.519 38.462 17.46 0.00 31.76 2.77
5482 5885 3.443099 AAAGCTTGGAGCACTTTTGTC 57.557 42.857 0.00 0.00 45.56 3.18
5516 5919 1.654220 CAGGCAACGTGGGACAAAG 59.346 57.895 0.00 0.00 44.16 2.77
5808 6223 9.638239 GACAATGGCTAAAATATTTCTGAAACA 57.362 29.630 4.73 0.00 0.00 2.83
5809 6224 9.643693 ACAATGGCTAAAATATTTCTGAAACAG 57.356 29.630 4.73 0.00 0.00 3.16
5852 6267 3.565482 GGCCAACGATCAATGATGTACAT 59.435 43.478 8.43 8.43 41.45 2.29
5892 6308 8.641499 TTGAACTTATTTGGAATTGTGAACAC 57.359 30.769 0.00 0.00 0.00 3.32
5927 6400 0.038892 AGCGGATTTGCAAACTGCTG 60.039 50.000 30.34 21.69 45.31 4.41
5943 6416 1.004628 TGCTGCCTATGACCAATGTGT 59.995 47.619 0.00 0.00 0.00 3.72
5964 6437 4.276183 TGTAGCATCTCCTCGTACTTCATC 59.724 45.833 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.770904 ACGTCCAGTTGGGTGGGT 60.771 61.111 0.00 0.00 38.26 4.51
43 44 0.036732 GGTGCACCAATCTGTCAGGA 59.963 55.000 31.23 0.00 35.64 3.86
62 63 0.445436 GTCGATTGCTTGTCCTGCTG 59.555 55.000 0.00 0.00 0.00 4.41
79 80 6.183360 CGTTCTATTGTCCTTGTCTGAATGTC 60.183 42.308 0.00 0.00 0.00 3.06
80 81 5.639506 CGTTCTATTGTCCTTGTCTGAATGT 59.360 40.000 0.00 0.00 0.00 2.71
91 92 4.162320 ACATGGTGATCGTTCTATTGTCCT 59.838 41.667 0.00 0.00 0.00 3.85
98 99 2.569853 ACCCAACATGGTGATCGTTCTA 59.430 45.455 13.74 0.00 37.20 2.10
134 135 5.545658 ACACGATTGCATTTCGATACTTT 57.454 34.783 21.96 0.65 39.81 2.66
138 139 3.242016 GTCGACACGATTGCATTTCGATA 59.758 43.478 21.96 4.20 38.42 2.92
140 141 1.388768 GTCGACACGATTGCATTTCGA 59.611 47.619 21.96 11.53 38.42 3.71
217 219 0.250381 TTAAACCCGCTCGCTTCCAA 60.250 50.000 0.00 0.00 0.00 3.53
250 252 4.443457 GCTAGCTCCACTATGAAATGGTCA 60.443 45.833 7.70 0.00 35.00 4.02
273 275 3.215151 TCTCTCGTGCTAATCCACCTAG 58.785 50.000 0.00 0.00 32.10 3.02
274 276 3.292492 TCTCTCGTGCTAATCCACCTA 57.708 47.619 0.00 0.00 32.10 3.08
275 277 2.145397 TCTCTCGTGCTAATCCACCT 57.855 50.000 0.00 0.00 32.10 4.00
276 278 2.362397 TCATCTCTCGTGCTAATCCACC 59.638 50.000 0.00 0.00 32.10 4.61
277 279 3.067461 ACTCATCTCTCGTGCTAATCCAC 59.933 47.826 0.00 0.00 0.00 4.02
278 280 3.291584 ACTCATCTCTCGTGCTAATCCA 58.708 45.455 0.00 0.00 0.00 3.41
279 281 4.083003 CCTACTCATCTCTCGTGCTAATCC 60.083 50.000 0.00 0.00 0.00 3.01
280 282 4.614993 GCCTACTCATCTCTCGTGCTAATC 60.615 50.000 0.00 0.00 0.00 1.75
281 283 3.254657 GCCTACTCATCTCTCGTGCTAAT 59.745 47.826 0.00 0.00 0.00 1.73
282 284 2.619177 GCCTACTCATCTCTCGTGCTAA 59.381 50.000 0.00 0.00 0.00 3.09
283 285 2.222886 GCCTACTCATCTCTCGTGCTA 58.777 52.381 0.00 0.00 0.00 3.49
284 286 1.028905 GCCTACTCATCTCTCGTGCT 58.971 55.000 0.00 0.00 0.00 4.40
285 287 0.031449 GGCCTACTCATCTCTCGTGC 59.969 60.000 0.00 0.00 0.00 5.34
288 290 2.028130 AGTTGGCCTACTCATCTCTCG 58.972 52.381 14.58 0.00 0.00 4.04
318 320 1.215647 CACTACTCTGCCCGGTCAC 59.784 63.158 0.00 0.00 0.00 3.67
321 323 1.913762 AAGCACTACTCTGCCCGGT 60.914 57.895 0.00 0.00 37.96 5.28
324 326 0.393537 ATGCAAGCACTACTCTGCCC 60.394 55.000 0.00 0.00 37.96 5.36
363 365 4.729227 GGTGAAAGAAACCCTTCACAAA 57.271 40.909 14.79 0.00 36.01 2.83
386 388 9.072375 CCAAAGAAGACCTTAAAGAAGAGAAAT 57.928 33.333 0.00 0.00 34.25 2.17
391 393 7.343357 TGAACCAAAGAAGACCTTAAAGAAGA 58.657 34.615 0.00 0.00 34.25 2.87
403 405 7.749377 TTCCTATCCTATGAACCAAAGAAGA 57.251 36.000 0.00 0.00 0.00 2.87
404 406 8.807948 TTTTCCTATCCTATGAACCAAAGAAG 57.192 34.615 0.00 0.00 0.00 2.85
406 408 7.715249 CGATTTTCCTATCCTATGAACCAAAGA 59.285 37.037 0.00 0.00 0.00 2.52
421 423 8.101419 ACTTTTCTGTTCCTACGATTTTCCTAT 58.899 33.333 0.00 0.00 0.00 2.57
425 427 7.186021 TGACTTTTCTGTTCCTACGATTTTC 57.814 36.000 0.00 0.00 0.00 2.29
439 441 8.610896 GTCATCTCATTTCCTATGACTTTTCTG 58.389 37.037 0.00 0.00 43.07 3.02
447 449 9.097946 AGATACATGTCATCTCATTTCCTATGA 57.902 33.333 0.00 0.00 0.00 2.15
460 462 9.368674 CTCATAGGATTTGAGATACATGTCATC 57.631 37.037 0.00 4.47 42.63 2.92
501 503 3.949754 TGATGTGAATCAAAGGGCATCTC 59.050 43.478 10.68 0.00 35.22 2.75
552 554 9.479549 ACATTCCATAGGAAAATAAACATCAGT 57.520 29.630 2.16 0.00 45.41 3.41
707 709 7.175816 ACGAGTGTGCATATCATCTACTTAGAT 59.824 37.037 0.00 0.00 43.51 1.98
708 710 6.486993 ACGAGTGTGCATATCATCTACTTAGA 59.513 38.462 0.00 0.00 36.65 2.10
848 852 4.159557 AGCATTGAAGGGCCTCTTTAAAA 58.840 39.130 6.46 2.00 35.13 1.52
865 869 1.409427 GACGAGCCCTACAGTAGCATT 59.591 52.381 1.50 0.00 0.00 3.56
1279 1294 1.298264 CAGCAAACAGACGCGCAAA 60.298 52.632 5.73 0.00 0.00 3.68
1282 1297 2.127609 GTCAGCAAACAGACGCGC 60.128 61.111 5.73 0.00 0.00 6.86
1475 1492 3.553828 TGGTCCGAAATCTTGTATCCC 57.446 47.619 0.00 0.00 0.00 3.85
1599 1616 5.244626 AGTTGGAAGCAAGAAAGCACAATAT 59.755 36.000 0.00 0.00 36.85 1.28
1706 1723 8.519492 AGCACAAAACAAACATTATGTCATAC 57.481 30.769 0.00 0.00 0.00 2.39
1882 1900 9.445786 CGCATTATATTTTACAAAACTAGTGGG 57.554 33.333 0.00 0.00 0.00 4.61
1964 1982 0.871722 GAAGCACGGCATTGTGTGTA 59.128 50.000 11.18 0.00 41.94 2.90
2191 2209 5.113383 TGAATACGACACCATTCCATGTAC 58.887 41.667 0.00 0.00 31.43 2.90
2203 2221 2.627945 TCAGGCCAATGAATACGACAC 58.372 47.619 5.01 0.00 0.00 3.67
2213 2231 8.138365 CTGAAAATCATTAATTCAGGCCAATG 57.862 34.615 5.01 5.08 43.92 2.82
2446 2465 5.221224 TGGACAAGACTGTTGGCAATTAAAG 60.221 40.000 1.92 1.99 35.30 1.85
2476 2495 0.035056 ACAGCCACCAGTCCATTAGC 60.035 55.000 0.00 0.00 0.00 3.09
2477 2496 2.359900 GAACAGCCACCAGTCCATTAG 58.640 52.381 0.00 0.00 0.00 1.73
2600 2645 3.099905 TCATAGGCAAGATAGGCGCTAT 58.900 45.455 7.64 2.94 39.37 2.97
2921 3295 7.730364 AGTTTGTGTTGTAAGATCTAACTGG 57.270 36.000 0.00 0.00 0.00 4.00
3248 3622 8.846423 ACTAGAGTTATAAGCCATAGCCATAT 57.154 34.615 0.00 0.00 41.25 1.78
3249 3623 9.763837 TTACTAGAGTTATAAGCCATAGCCATA 57.236 33.333 0.00 0.00 41.25 2.74
3250 3624 8.666129 TTACTAGAGTTATAAGCCATAGCCAT 57.334 34.615 0.00 0.00 41.25 4.40
3251 3625 8.666129 ATTACTAGAGTTATAAGCCATAGCCA 57.334 34.615 0.00 0.00 41.25 4.75
3252 3626 8.750298 TGATTACTAGAGTTATAAGCCATAGCC 58.250 37.037 0.00 0.00 41.25 3.93
3386 3774 5.887754 ACCTGTGTGTAATTGATAGGGTTT 58.112 37.500 0.00 0.00 0.00 3.27
3521 3910 2.393271 AGAGGCATGCTCTGTTGTAC 57.607 50.000 18.92 0.00 0.00 2.90
3522 3911 3.070159 GGATAGAGGCATGCTCTGTTGTA 59.930 47.826 18.92 3.67 32.79 2.41
3523 3912 2.158842 GGATAGAGGCATGCTCTGTTGT 60.159 50.000 18.92 4.46 32.79 3.32
3605 3994 7.083858 GCAGTTAGAATCAACAATACTTGCAA 58.916 34.615 0.00 0.00 0.00 4.08
3642 4031 6.024552 ACTAAACCAACAATGCTTATGTGG 57.975 37.500 0.00 0.00 0.00 4.17
3726 4115 5.506317 GCTGCATTGCGATTACCTAAGATTT 60.506 40.000 3.84 0.00 0.00 2.17
3871 4260 8.486210 ACACATGTGCCTTCTATTCTAAGAATA 58.514 33.333 25.68 0.00 35.04 1.75
3884 4273 2.288395 CCTGGAAAACACATGTGCCTTC 60.288 50.000 25.68 24.13 0.00 3.46
4041 4430 9.717942 GATACAAGGCAGAGATACTTTCATTAT 57.282 33.333 0.00 0.00 0.00 1.28
4042 4431 8.704668 TGATACAAGGCAGAGATACTTTCATTA 58.295 33.333 0.00 0.00 0.00 1.90
4043 4432 7.568349 TGATACAAGGCAGAGATACTTTCATT 58.432 34.615 0.00 0.00 0.00 2.57
4044 4433 7.129457 TGATACAAGGCAGAGATACTTTCAT 57.871 36.000 0.00 0.00 0.00 2.57
4131 4520 7.867305 TTTTAGAACCAGTACATTCACACAA 57.133 32.000 0.00 0.00 0.00 3.33
4132 4521 7.717436 TCATTTTAGAACCAGTACATTCACACA 59.283 33.333 0.00 0.00 0.00 3.72
4166 4555 2.987547 CCAGCACAGCAACCTGGG 60.988 66.667 0.00 0.00 45.55 4.45
4335 4731 2.586258 ATTAAGCGAGCACGAGTCAT 57.414 45.000 8.01 0.00 42.66 3.06
4363 4760 6.759497 ATTGAAGCCAACATTACCTTAGTC 57.241 37.500 0.00 0.00 34.72 2.59
4633 5030 5.818136 TGTGCTATCCAAGAAATGCTTAC 57.182 39.130 0.00 0.00 34.31 2.34
4702 5099 5.863935 GCCAAGAGTACAAATTCCAAACATC 59.136 40.000 0.00 0.00 0.00 3.06
4863 5260 6.672147 TGAAAATCTGAAAGCTACTGAAAGC 58.328 36.000 0.00 0.00 43.11 3.51
4864 5261 9.125906 CATTGAAAATCTGAAAGCTACTGAAAG 57.874 33.333 0.00 0.00 42.29 2.62
4865 5262 7.596248 GCATTGAAAATCTGAAAGCTACTGAAA 59.404 33.333 0.00 0.00 0.00 2.69
4866 5263 7.086376 GCATTGAAAATCTGAAAGCTACTGAA 58.914 34.615 0.00 0.00 0.00 3.02
4867 5264 6.207221 TGCATTGAAAATCTGAAAGCTACTGA 59.793 34.615 0.00 0.00 0.00 3.41
4868 5265 6.384224 TGCATTGAAAATCTGAAAGCTACTG 58.616 36.000 0.00 0.00 0.00 2.74
4869 5266 6.579666 TGCATTGAAAATCTGAAAGCTACT 57.420 33.333 0.00 0.00 0.00 2.57
5187 5586 0.389391 CGACAAGGCATATCCGTCCT 59.611 55.000 0.00 0.00 40.77 3.85
5205 5604 0.026803 GAAGCAAGGTTGATAGCGCG 59.973 55.000 0.00 0.00 0.00 6.86
5253 5652 6.603940 ACAAAGGCTGCCTCAAATTATAAA 57.396 33.333 23.61 0.00 30.89 1.40
5482 5885 2.012673 GCCTGCTACTTTGTGGATCAG 58.987 52.381 0.00 0.00 0.00 2.90
5516 5919 1.909700 TTGATTGGCTGGTGAGGTTC 58.090 50.000 0.00 0.00 0.00 3.62
5779 6194 8.450578 TCAGAAATATTTTAGCCATTGTCGAT 57.549 30.769 1.43 0.00 0.00 3.59
5783 6198 9.643693 CTGTTTCAGAAATATTTTAGCCATTGT 57.356 29.630 1.43 0.00 32.44 2.71
5808 6223 0.971386 CATGGCAAGGCAGGTTTTCT 59.029 50.000 2.05 0.00 0.00 2.52
5809 6224 0.681175 ACATGGCAAGGCAGGTTTTC 59.319 50.000 8.14 0.00 0.00 2.29
5852 6267 3.631250 AGTTCAAGGCAGGTTCTGAAAA 58.369 40.909 0.00 0.00 32.44 2.29
5892 6308 2.287644 TCCGCTGATTGTCAATAATGCG 59.712 45.455 21.89 21.89 41.50 4.73
5927 6400 2.917933 TGCTACACATTGGTCATAGGC 58.082 47.619 0.00 0.00 0.00 3.93
5943 6416 4.276183 GTGATGAAGTACGAGGAGATGCTA 59.724 45.833 0.00 0.00 0.00 3.49
5964 6437 1.597854 TCGTGGCTTTGGCAGAGTG 60.598 57.895 6.91 0.00 39.19 3.51


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

AutoCloner maintained by Alex Coulton.