Multiple sequence alignment - TraesCS5D01G173000

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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 TraesCS5D01G173000 chr5D 100.000 4649 0 0 1 4649 270240479 270245127 0.000000e+00 8586.0
1 TraesCS5D01G173000 chr5D 100.000 29 0 0 4561 4589 270245009 270245037 2.000000e-03 54.7
2 TraesCS5D01G173000 chr5D 100.000 29 0 0 4531 4559 270245039 270245067 2.000000e-03 54.7
3 TraesCS5D01G173000 chr5B 91.415 4042 207 57 550 4559 307262731 307266664 0.000000e+00 5413.0
4 TraesCS5D01G173000 chr5B 85.019 267 28 7 1 262 507692039 507692298 1.280000e-65 261.0
5 TraesCS5D01G173000 chr5B 80.357 336 42 17 4 324 680969931 680969605 2.800000e-57 233.0
6 TraesCS5D01G173000 chr5B 91.954 87 7 0 4561 4647 307266636 307266722 6.320000e-24 122.0
7 TraesCS5D01G173000 chr5A 91.032 3267 166 51 1 3221 359695143 359698328 0.000000e+00 4292.0
8 TraesCS5D01G173000 chr5A 94.685 1317 61 8 3249 4559 359698325 359699638 0.000000e+00 2036.0
9 TraesCS5D01G173000 chr5A 85.606 264 23 10 4 258 641377212 641376955 3.570000e-66 263.0
10 TraesCS5D01G173000 chr2D 81.197 468 37 34 1 453 608194700 608195131 3.470000e-86 329.0
11 TraesCS5D01G173000 chr3A 85.714 273 25 10 2 265 13833744 13833477 4.580000e-70 276.0
12 TraesCS5D01G173000 chr3D 82.059 340 38 16 4 330 12193557 12193228 7.670000e-68 268.0
13 TraesCS5D01G173000 chr7D 81.303 353 43 18 1 339 403802987 403803330 9.920000e-67 265.0
14 TraesCS5D01G173000 chr2B 85.130 269 24 12 1 263 495815794 495815536 1.280000e-65 261.0
15 TraesCS5D01G173000 chr2B 86.250 80 8 2 253 329 495815565 495815486 2.980000e-12 84.2
16 TraesCS5D01G173000 chr7B 83.158 95 15 1 4204 4297 720216902 720216996 8.290000e-13 86.1


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 TraesCS5D01G173000 chr5D 270240479 270245127 4648 False 2898.466667 8586 100.0000 1 4649 3 chr5D.!!$F1 4648
1 TraesCS5D01G173000 chr5B 307262731 307266722 3991 False 2767.500000 5413 91.6845 550 4647 2 chr5B.!!$F2 4097
2 TraesCS5D01G173000 chr5A 359695143 359699638 4495 False 3164.000000 4292 92.8585 1 4559 2 chr5A.!!$F1 4558

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
954 970 0.976641 ATCTGGGTGCGTTTCTCTCA 59.023 50.0 0.00 0.0 0.00 3.27 F
1053 1076 0.035343 GCTGTTCCTGTTACTCCCCC 60.035 60.0 0.00 0.0 0.00 5.40 F
1397 1432 1.067295 TGGGCTGTCAACTCAATCCT 58.933 50.0 0.00 0.0 0.00 3.24 F
3096 3150 0.321996 GGGAGCTCTCGTGGAGTTTT 59.678 55.0 14.64 0.0 43.62 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2435 2485 0.413037 ATTGGGCATTCAGGGTTCCA 59.587 50.000 0.00 0.0 0.00 3.53 R
2993 3044 0.461870 GCACACGAGTATGATGCCCA 60.462 55.000 0.00 0.0 0.00 5.36 R
3102 3156 1.220493 GGGGCCTCCTTTTCCCATATT 59.780 52.381 0.84 0.0 41.85 1.28 R
4604 4667 1.142870 CTCAGTGGTTGAACTTGGGGA 59.857 52.381 0.00 0.0 34.81 4.81 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
284 285 6.687081 TTTCTACACGTTCAACATTTTCCT 57.313 33.333 0.00 0.00 0.00 3.36
297 298 8.579850 TCAACATTTTCCTAATGCTTGAGTAT 57.420 30.769 0.00 0.00 31.13 2.12
303 304 9.875691 ATTTTCCTAATGCTTGAGTATTTTTCC 57.124 29.630 0.00 0.00 32.67 3.13
304 305 8.415950 TTTCCTAATGCTTGAGTATTTTTCCA 57.584 30.769 0.00 0.00 32.67 3.53
305 306 8.415950 TTCCTAATGCTTGAGTATTTTTCCAA 57.584 30.769 0.00 0.00 32.67 3.53
306 307 8.415950 TCCTAATGCTTGAGTATTTTTCCAAA 57.584 30.769 0.00 0.00 32.67 3.28
307 308 9.034800 TCCTAATGCTTGAGTATTTTTCCAAAT 57.965 29.630 0.00 0.00 36.52 2.32
421 426 5.784750 AGCAAAAACAGAAAACAGAAAGC 57.215 34.783 0.00 0.00 0.00 3.51
422 427 5.237048 AGCAAAAACAGAAAACAGAAAGCA 58.763 33.333 0.00 0.00 0.00 3.91
423 428 5.700373 AGCAAAAACAGAAAACAGAAAGCAA 59.300 32.000 0.00 0.00 0.00 3.91
424 429 6.204495 AGCAAAAACAGAAAACAGAAAGCAAA 59.796 30.769 0.00 0.00 0.00 3.68
425 430 6.855403 GCAAAAACAGAAAACAGAAAGCAAAA 59.145 30.769 0.00 0.00 0.00 2.44
426 431 7.378194 GCAAAAACAGAAAACAGAAAGCAAAAA 59.622 29.630 0.00 0.00 0.00 1.94
427 432 8.894864 CAAAAACAGAAAACAGAAAGCAAAAAG 58.105 29.630 0.00 0.00 0.00 2.27
428 433 5.784750 ACAGAAAACAGAAAGCAAAAAGC 57.215 34.783 0.00 0.00 46.19 3.51
485 490 1.654954 GCGAGTCGGAAGCTGGACTA 61.655 60.000 15.52 0.00 43.23 2.59
848 864 2.540931 CAGCTTTCGTTGCATGCTTTTT 59.459 40.909 20.33 0.00 0.00 1.94
930 946 2.696506 TGAGCTGCTTCTGTTGATCTG 58.303 47.619 2.53 0.00 0.00 2.90
954 970 0.976641 ATCTGGGTGCGTTTCTCTCA 59.023 50.000 0.00 0.00 0.00 3.27
963 986 1.136113 GCGTTTCTCTCAGAAGCTTGC 60.136 52.381 2.10 0.00 35.37 4.01
968 991 1.004560 TCTCAGAAGCTTGCACCGG 60.005 57.895 2.10 0.00 0.00 5.28
983 1006 3.452786 CGGAGGAAGGCGCTGAGA 61.453 66.667 7.64 0.00 0.00 3.27
984 1007 2.498726 GGAGGAAGGCGCTGAGAG 59.501 66.667 7.64 0.00 0.00 3.20
985 1008 2.498726 GAGGAAGGCGCTGAGAGG 59.501 66.667 7.64 0.00 0.00 3.69
986 1009 3.080121 AGGAAGGCGCTGAGAGGG 61.080 66.667 7.64 0.00 0.00 4.30
1024 1047 1.683319 GGGAATTCTCCAAGGTCTGCC 60.683 57.143 5.23 0.00 44.51 4.85
1053 1076 0.035343 GCTGTTCCTGTTACTCCCCC 60.035 60.000 0.00 0.00 0.00 5.40
1097 1124 2.798834 TTCGAATTCGGCGTTCATTC 57.201 45.000 26.47 12.19 40.29 2.67
1136 1169 5.464069 ACTAAATTTGGGTCCCAAGAACTT 58.536 37.500 22.66 15.88 44.84 2.66
1176 1210 6.592994 CAGATAGAAATGTCGACCATGCATAT 59.407 38.462 14.12 4.68 32.82 1.78
1177 1211 7.761249 CAGATAGAAATGTCGACCATGCATATA 59.239 37.037 14.12 0.00 32.82 0.86
1183 1217 4.559153 TGTCGACCATGCATATAGATGTG 58.441 43.478 14.12 0.00 35.30 3.21
1226 1261 5.127031 CGGTTTTTGATTTCCCATCTACCAT 59.873 40.000 0.00 0.00 0.00 3.55
1231 1266 1.507140 TTTCCCATCTACCATCGGCT 58.493 50.000 0.00 0.00 0.00 5.52
1294 1329 5.059161 CGCCATTCTGGAAATCTATGAAGA 58.941 41.667 0.00 0.00 40.96 2.87
1346 1381 8.531146 AGTTATGTTAATTGGCTGTTAGCATTT 58.469 29.630 13.51 0.00 44.75 2.32
1357 1392 5.811613 GGCTGTTAGCATTTTTGCAATATGA 59.188 36.000 20.29 3.77 44.75 2.15
1389 1424 2.550606 TCGTGTAAATTGGGCTGTCAAC 59.449 45.455 0.00 0.00 0.00 3.18
1392 1427 3.568007 GTGTAAATTGGGCTGTCAACTCA 59.432 43.478 0.00 0.00 0.00 3.41
1393 1428 4.037446 GTGTAAATTGGGCTGTCAACTCAA 59.963 41.667 0.00 0.00 0.00 3.02
1395 1430 4.525912 AAATTGGGCTGTCAACTCAATC 57.474 40.909 1.82 0.00 0.00 2.67
1397 1432 1.067295 TGGGCTGTCAACTCAATCCT 58.933 50.000 0.00 0.00 0.00 3.24
1398 1433 1.271543 TGGGCTGTCAACTCAATCCTG 60.272 52.381 0.00 0.00 0.00 3.86
1399 1434 1.271597 GGGCTGTCAACTCAATCCTGT 60.272 52.381 0.00 0.00 0.00 4.00
1400 1435 2.027192 GGGCTGTCAACTCAATCCTGTA 60.027 50.000 0.00 0.00 0.00 2.74
1401 1436 3.265791 GGCTGTCAACTCAATCCTGTAG 58.734 50.000 0.00 0.00 0.00 2.74
1419 1454 8.362464 TCCTGTAGTATGAAGTGTAAACTGAT 57.638 34.615 0.00 0.00 0.00 2.90
1429 1464 8.365399 TGAAGTGTAAACTGATACTGAAACTG 57.635 34.615 0.00 0.00 0.00 3.16
1487 1530 8.248945 TGTAAAGCTTAACTACTCCACATAGAC 58.751 37.037 0.00 0.00 0.00 2.59
1576 1624 5.991328 TTTCAGAAGCAGAGTTACAGTTG 57.009 39.130 0.00 0.00 0.00 3.16
1609 1657 3.258372 GCTAAAGGGAAAAAGACCAAGGG 59.742 47.826 0.00 0.00 0.00 3.95
1754 1802 5.646606 TCACTGTGGTTAGCTTTGTTTTTC 58.353 37.500 8.11 0.00 0.00 2.29
1832 1881 6.560253 TTATTTGTCTGGAGAAAGTCTTGC 57.440 37.500 0.00 0.00 0.00 4.01
1972 2021 2.932614 CGCATCTAGGTTGACCTTTGAG 59.067 50.000 8.18 0.07 46.09 3.02
1984 2033 6.209361 GTTGACCTTTGAGAAGTCCATTTTC 58.791 40.000 0.00 0.00 0.00 2.29
2088 2137 4.022329 ACTGTAGCACTGGTTTTAATTGCC 60.022 41.667 0.00 0.00 33.48 4.52
2114 2163 5.618236 TGCCATTTTTCATCATTGGTCAAA 58.382 33.333 0.00 0.00 0.00 2.69
2119 2168 9.005777 CCATTTTTCATCATTGGTCAAAGATTT 57.994 29.630 0.00 0.00 0.00 2.17
2216 2265 1.340697 CCCGGCCTTAAGTTAAAGCCT 60.341 52.381 25.67 0.00 0.00 4.58
2372 2422 4.083484 ACGTGTTAACAAAGAGCCATTAGC 60.083 41.667 10.51 0.00 44.25 3.09
2435 2485 4.029520 TGCCAATTGTATGCCCTAATTGT 58.970 39.130 4.43 0.00 39.14 2.71
2449 2499 3.131046 CCTAATTGTGGAACCCTGAATGC 59.869 47.826 0.00 0.00 34.36 3.56
2548 2598 9.730420 AATAATATCAACTATTTTGTTGTCCGC 57.270 29.630 7.17 0.00 45.26 5.54
2583 2633 8.364142 TGGATTTACCTTTGACACCTATTTTTG 58.636 33.333 0.00 0.00 39.86 2.44
2649 2699 7.690952 TGTTTACAAGTTTGTACAAGACCTT 57.309 32.000 8.56 9.42 42.84 3.50
2679 2729 1.134699 GTCACTGCCGGAGATGATGAA 60.135 52.381 5.05 0.00 0.00 2.57
2727 2777 1.200020 CAGGGTTTTGCTGATTCGGTC 59.800 52.381 0.00 0.00 0.00 4.79
2963 3014 8.563732 TGTAAATTTGAATCGTCTCATGTTTCA 58.436 29.630 0.00 0.00 0.00 2.69
2992 3043 3.879295 CTCTGTTGACATGAAGGTGTTGT 59.121 43.478 0.00 0.00 31.16 3.32
2993 3044 4.269183 TCTGTTGACATGAAGGTGTTGTT 58.731 39.130 0.00 0.00 31.16 2.83
2994 3045 4.096231 TCTGTTGACATGAAGGTGTTGTTG 59.904 41.667 0.00 0.00 31.16 3.33
3007 3058 2.095853 GTGTTGTTGGGCATCATACTCG 59.904 50.000 0.00 0.00 0.00 4.18
3029 3080 1.987770 GTGCCATTTCAACATTCTGCG 59.012 47.619 0.00 0.00 0.00 5.18
3048 3099 5.586643 TCTGCGGCATGTTTATGTTGTATTA 59.413 36.000 1.75 0.00 36.65 0.98
3087 3141 3.459232 TGTCATTTATGGGAGCTCTCG 57.541 47.619 14.64 0.00 0.00 4.04
3096 3150 0.321996 GGGAGCTCTCGTGGAGTTTT 59.678 55.000 14.64 0.00 43.62 2.43
3097 3151 1.270893 GGGAGCTCTCGTGGAGTTTTT 60.271 52.381 14.64 0.00 43.62 1.94
3102 3156 4.448210 AGCTCTCGTGGAGTTTTTGTAAA 58.552 39.130 9.16 0.00 43.62 2.01
3151 3206 5.751243 AACACATGAGTTTTACAGGACAC 57.249 39.130 0.00 0.00 0.00 3.67
3152 3207 4.776349 ACACATGAGTTTTACAGGACACA 58.224 39.130 0.00 0.00 0.00 3.72
3156 3211 5.527582 ACATGAGTTTTACAGGACACAGTTC 59.472 40.000 0.00 0.00 0.00 3.01
3294 3349 9.923143 CATGGTTGATGCTGATTTCATATAATT 57.077 29.630 0.00 0.00 0.00 1.40
3318 3373 3.245658 TGACCTTAGCTCCTTAGACCACT 60.246 47.826 0.00 0.00 0.00 4.00
3322 3377 5.965091 ACCTTAGCTCCTTAGACCACTAAAT 59.035 40.000 0.00 0.00 38.01 1.40
3503 3562 1.546323 CCCTTCTCTGAGCAGGCAAAA 60.546 52.381 16.72 0.00 0.00 2.44
3516 3575 3.194116 GCAGGCAAAATTCTGAATCTCCA 59.806 43.478 2.92 0.00 33.11 3.86
3526 3585 3.378512 TCTGAATCTCCATACCTGCACT 58.621 45.455 0.00 0.00 0.00 4.40
3654 3713 6.549433 AGATCTCTTCTGAAATGAGAAGCT 57.451 37.500 11.81 9.88 45.93 3.74
3665 3724 2.831685 TGAGAAGCTGCCGTTTCTTA 57.168 45.000 8.54 2.19 40.25 2.10
3826 3887 6.237901 TGCTGTGTATCTTACATTTTCTGGT 58.762 36.000 0.00 0.00 41.34 4.00
3951 4012 7.312657 TCTTTGCAAGAATGATGTCTGTATC 57.687 36.000 0.00 0.00 33.83 2.24
4003 4064 1.687123 TGAAACGCTATCTCTAGGGGC 59.313 52.381 0.00 0.00 41.10 5.80
4070 4131 3.355378 CCAAATGTGTGCAAGAGGGATA 58.645 45.455 0.00 0.00 0.00 2.59
4093 4154 0.747283 AGCCTCCCGTACAGTAGTCG 60.747 60.000 0.00 0.00 0.00 4.18
4100 4161 0.723414 CGTACAGTAGTCGCCGAGAA 59.277 55.000 0.00 0.00 0.00 2.87
4122 4183 9.159470 GAGAAAAGTGACGAAAATTCTAAGTTG 57.841 33.333 0.00 0.00 0.00 3.16
4236 4298 3.515901 GTGAAGTTGAGATCTACCACCCT 59.484 47.826 0.00 0.00 0.00 4.34
4269 4331 3.512724 AGCTTTGGTTCCATCATCTTTGG 59.487 43.478 0.00 0.00 35.45 3.28
4353 4415 7.006865 AGTGATATCTTAATGCATGAGAGCT 57.993 36.000 15.67 7.71 34.99 4.09
4369 4431 7.223777 GCATGAGAGCTTCTAAAACTACTTAGG 59.776 40.741 0.00 0.00 31.02 2.69
4377 4439 7.549842 GCTTCTAAAACTACTTAGGGAGGAAAG 59.450 40.741 0.00 0.00 31.02 2.62
4442 4505 4.222145 TCGCTTCATCTAGTGGGTTTTACT 59.778 41.667 0.00 0.00 0.00 2.24
4490 4553 9.554724 GTTAATATTTGGTGTCTATGTGTGTTG 57.445 33.333 0.00 0.00 0.00 3.33
4503 4566 9.212641 GTCTATGTGTGTTGATATTGATGCTAT 57.787 33.333 0.00 0.00 0.00 2.97
4531 4594 6.545504 TTCTAGAAGAATGTGTGAAAGCAC 57.454 37.500 0.00 0.00 45.35 4.40
4535 4598 5.564550 AGAAGAATGTGTGAAAGCACCTAT 58.435 37.500 0.00 0.00 44.51 2.57
4566 4629 2.938956 GCTATGTGCTGGGACCTATT 57.061 50.000 0.00 0.00 38.95 1.73
4620 4683 1.068588 GCTTTCCCCAAGTTCAACCAC 59.931 52.381 0.00 0.00 34.56 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 250 6.466413 TGAACGTGTAGAAAAATTGTTGAACG 59.534 34.615 0.00 0.00 0.00 3.95
254 255 8.696410 AATGTTGAACGTGTAGAAAAATTGTT 57.304 26.923 0.00 0.00 0.00 2.83
260 261 7.090953 AGGAAAATGTTGAACGTGTAGAAAA 57.909 32.000 0.00 0.00 0.00 2.29
399 404 5.237048 TGCTTTCTGTTTTCTGTTTTTGCT 58.763 33.333 0.00 0.00 0.00 3.91
400 405 5.529014 TGCTTTCTGTTTTCTGTTTTTGC 57.471 34.783 0.00 0.00 0.00 3.68
401 406 8.779603 TTTTTGCTTTCTGTTTTCTGTTTTTG 57.220 26.923 0.00 0.00 0.00 2.44
402 407 7.591057 GCTTTTTGCTTTCTGTTTTCTGTTTTT 59.409 29.630 0.00 0.00 38.95 1.94
403 408 7.077605 GCTTTTTGCTTTCTGTTTTCTGTTTT 58.922 30.769 0.00 0.00 38.95 2.43
404 409 6.204495 TGCTTTTTGCTTTCTGTTTTCTGTTT 59.796 30.769 0.00 0.00 43.37 2.83
405 410 5.700373 TGCTTTTTGCTTTCTGTTTTCTGTT 59.300 32.000 0.00 0.00 43.37 3.16
406 411 5.237048 TGCTTTTTGCTTTCTGTTTTCTGT 58.763 33.333 0.00 0.00 43.37 3.41
407 412 5.783100 TGCTTTTTGCTTTCTGTTTTCTG 57.217 34.783 0.00 0.00 43.37 3.02
408 413 6.799926 TTTGCTTTTTGCTTTCTGTTTTCT 57.200 29.167 0.00 0.00 43.37 2.52
409 414 7.850268 TTTTTGCTTTTTGCTTTCTGTTTTC 57.150 28.000 0.00 0.00 43.37 2.29
436 441 3.684305 GCACAGCCTGTTTTTCTGTTTTT 59.316 39.130 0.00 0.00 38.85 1.94
485 490 2.106566 CCCTATATCTCGCATCCAGCT 58.893 52.381 0.00 0.00 42.61 4.24
490 495 0.818296 ACGCCCCTATATCTCGCATC 59.182 55.000 0.00 0.00 0.00 3.91
848 864 2.044352 TCGTCAGATCCGGGCTGA 60.044 61.111 19.70 19.70 39.90 4.26
930 946 1.207329 AGAAACGCACCCAGATAGGTC 59.793 52.381 0.00 0.00 38.39 3.85
954 970 1.768684 TTCCTCCGGTGCAAGCTTCT 61.769 55.000 0.00 0.00 0.00 2.85
968 991 2.498726 CCTCTCAGCGCCTTCCTC 59.501 66.667 2.29 0.00 0.00 3.71
980 1003 2.520741 CCTCCTCTCCGCCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
981 1004 4.851214 GCCTCCTCTCCGCCCTCT 62.851 72.222 0.00 0.00 0.00 3.69
985 1008 4.247380 CATGGCCTCCTCTCCGCC 62.247 72.222 3.32 0.00 43.32 6.13
986 1009 4.247380 CCATGGCCTCCTCTCCGC 62.247 72.222 3.32 0.00 0.00 5.54
987 1010 3.554342 CCCATGGCCTCCTCTCCG 61.554 72.222 6.09 0.00 0.00 4.63
988 1011 3.174265 CCCCATGGCCTCCTCTCC 61.174 72.222 6.09 0.00 0.00 3.71
1053 1076 8.818141 ATGTAAATACATGTAGTCAGAATCGG 57.182 34.615 11.91 0.00 44.66 4.18
1097 1124 2.299993 TAGTTGCGCAAGATCAGAGG 57.700 50.000 25.78 0.00 43.02 3.69
1136 1169 8.843262 CATTTCTATCTGGCAAATCAACTGATA 58.157 33.333 0.00 0.00 33.73 2.15
1176 1210 4.081917 TGGTCGAGTTATGTTGCACATCTA 60.082 41.667 5.25 0.00 39.88 1.98
1177 1211 3.262420 GGTCGAGTTATGTTGCACATCT 58.738 45.455 5.25 0.00 39.88 2.90
1183 1217 2.412325 CCGTTTGGTCGAGTTATGTTGC 60.412 50.000 0.00 0.00 0.00 4.17
1226 1261 5.070685 TCAGTTATCATAGAGCTTAGCCGA 58.929 41.667 0.00 0.00 0.00 5.54
1294 1329 6.099413 AGGTGATGAGATGACATATGTGAAGT 59.901 38.462 14.43 0.00 0.00 3.01
1346 1381 5.065090 CGATCTTCCAGTGTCATATTGCAAA 59.935 40.000 1.71 0.00 0.00 3.68
1389 1424 9.088512 GTTTACACTTCATACTACAGGATTGAG 57.911 37.037 0.00 0.00 0.00 3.02
1392 1427 8.812972 TCAGTTTACACTTCATACTACAGGATT 58.187 33.333 0.00 0.00 0.00 3.01
1393 1428 8.362464 TCAGTTTACACTTCATACTACAGGAT 57.638 34.615 0.00 0.00 0.00 3.24
1395 1430 9.517609 GTATCAGTTTACACTTCATACTACAGG 57.482 37.037 2.51 0.00 0.00 4.00
1437 1472 5.476945 AGAAAGGAAGGCGTTAATCACAAAT 59.523 36.000 0.00 0.00 0.00 2.32
1448 1483 2.152016 GCTTTACAGAAAGGAAGGCGT 58.848 47.619 0.02 0.00 42.12 5.68
1450 1485 5.473846 AGTTAAGCTTTACAGAAAGGAAGGC 59.526 40.000 17.19 0.00 42.12 4.35
1487 1530 1.254026 TTCAGACAGACCACCGGTAG 58.746 55.000 6.87 0.96 35.25 3.18
1649 1697 6.387041 AATGCATGATATGTCAGGTTTCAG 57.613 37.500 0.00 0.00 38.37 3.02
1754 1802 9.037737 CAATTGAAAGCACCATTTTCATATAGG 57.962 33.333 0.00 0.00 42.31 2.57
1815 1864 4.067896 TCATTGCAAGACTTTCTCCAGAC 58.932 43.478 4.94 0.00 0.00 3.51
1972 2021 8.154649 TCAGAGTTTTAGTGAAAATGGACTTC 57.845 34.615 0.00 0.00 36.92 3.01
1984 2033 6.634436 GTGCATTTGTCTTCAGAGTTTTAGTG 59.366 38.462 0.00 0.00 0.00 2.74
2034 2083 4.870426 AGACAGGAATTTACATGCTACACG 59.130 41.667 0.00 0.00 0.00 4.49
2046 2095 5.880901 ACAGTGATGGTAAGACAGGAATTT 58.119 37.500 0.00 0.00 0.00 1.82
2088 2137 5.701750 TGACCAATGATGAAAAATGGCAAAG 59.298 36.000 0.00 0.00 34.45 2.77
2249 2299 9.599866 AAATACTTTAAAGCCAATAAAGCATCC 57.400 29.630 15.24 0.00 41.78 3.51
2372 2422 6.402550 CGGTTCATGAAATACTTTCTGTCCAG 60.403 42.308 10.35 0.00 40.32 3.86
2375 2425 6.481954 ACGGTTCATGAAATACTTTCTGTC 57.518 37.500 10.35 0.00 40.32 3.51
2396 2446 5.351233 TTGGCAGTAAACTAACATGAACG 57.649 39.130 0.00 0.00 0.00 3.95
2435 2485 0.413037 ATTGGGCATTCAGGGTTCCA 59.587 50.000 0.00 0.00 0.00 3.53
2449 2499 3.756434 ACTAACATTTCACGGTCATTGGG 59.244 43.478 0.00 0.00 0.00 4.12
2546 2596 6.583050 TCAAAGGTAAATCCAAATTTAACGCG 59.417 34.615 3.53 3.53 45.72 6.01
2548 2598 8.696175 GTGTCAAAGGTAAATCCAAATTTAACG 58.304 33.333 0.00 0.00 45.72 3.18
2583 2633 3.854666 TGTTATCTCAGCTGCAGAGAAC 58.145 45.455 28.06 28.06 44.56 3.01
2623 2673 8.288689 AGGTCTTGTACAAACTTGTAAACAAT 57.711 30.769 10.03 0.00 44.46 2.71
2649 2699 0.934496 CGGCAGTGACGAAAAAGTGA 59.066 50.000 14.90 0.00 35.20 3.41
2679 2729 6.504398 CACATTTGCTATGATGAGCTCATTT 58.496 36.000 29.26 21.22 42.07 2.32
2727 2777 7.741027 TGTATATTACCTGAGTAGAAGACCG 57.259 40.000 0.00 0.00 0.00 4.79
2756 2806 7.792374 ATACCAGTTCATGCAGTAACATTAG 57.208 36.000 14.37 4.65 0.00 1.73
2963 3014 6.600822 CACCTTCATGTCAACAGAGGATTATT 59.399 38.462 13.67 0.00 32.26 1.40
2992 3043 2.011548 GCACACGAGTATGATGCCCAA 61.012 52.381 0.00 0.00 0.00 4.12
2993 3044 0.461870 GCACACGAGTATGATGCCCA 60.462 55.000 0.00 0.00 0.00 5.36
2994 3045 2.311294 GCACACGAGTATGATGCCC 58.689 57.895 0.00 0.00 0.00 5.36
3007 3058 2.733026 GCAGAATGTTGAAATGGCACAC 59.267 45.455 0.00 0.00 39.77 3.82
3062 3113 6.483307 CGAGAGCTCCCATAAATGACATAAAA 59.517 38.462 10.93 0.00 0.00 1.52
3066 3117 3.389329 ACGAGAGCTCCCATAAATGACAT 59.611 43.478 10.93 0.00 0.00 3.06
3067 3118 2.766263 ACGAGAGCTCCCATAAATGACA 59.234 45.455 10.93 0.00 0.00 3.58
3068 3119 3.126831 CACGAGAGCTCCCATAAATGAC 58.873 50.000 10.93 0.00 0.00 3.06
3069 3120 2.103094 CCACGAGAGCTCCCATAAATGA 59.897 50.000 10.93 0.00 0.00 2.57
3070 3121 2.103094 TCCACGAGAGCTCCCATAAATG 59.897 50.000 10.93 0.00 0.00 2.32
3071 3122 2.366916 CTCCACGAGAGCTCCCATAAAT 59.633 50.000 10.93 0.00 35.31 1.40
3072 3123 1.757118 CTCCACGAGAGCTCCCATAAA 59.243 52.381 10.93 0.00 35.31 1.40
3073 3124 1.403814 CTCCACGAGAGCTCCCATAA 58.596 55.000 10.93 0.00 35.31 1.90
3075 3126 3.947173 CTCCACGAGAGCTCCCAT 58.053 61.111 10.93 0.00 35.31 4.00
3087 3141 9.549078 TTTTCCCATATTTTACAAAAACTCCAC 57.451 29.630 0.00 0.00 0.00 4.02
3096 3150 5.423931 GGCCTCCTTTTCCCATATTTTACAA 59.576 40.000 0.00 0.00 0.00 2.41
3097 3151 4.959839 GGCCTCCTTTTCCCATATTTTACA 59.040 41.667 0.00 0.00 0.00 2.41
3102 3156 1.220493 GGGGCCTCCTTTTCCCATATT 59.780 52.381 0.84 0.00 41.85 1.28
3294 3349 4.894114 GTGGTCTAAGGAGCTAAGGTCATA 59.106 45.833 0.00 0.00 40.29 2.15
3473 3532 2.634940 CTCAGAGAAGGGAACAGAACCA 59.365 50.000 0.00 0.00 0.00 3.67
3476 3535 2.301296 CTGCTCAGAGAAGGGAACAGAA 59.699 50.000 0.00 0.00 30.67 3.02
3503 3562 4.411540 AGTGCAGGTATGGAGATTCAGAAT 59.588 41.667 0.00 0.00 0.00 2.40
3516 3575 4.307032 AATGACAGGAAAGTGCAGGTAT 57.693 40.909 0.00 0.00 0.00 2.73
3559 3618 7.706179 CAGAGAACAAACAGCCAAATAGAAAAA 59.294 33.333 0.00 0.00 0.00 1.94
3654 3713 1.807742 CGGGTGAAATAAGAAACGGCA 59.192 47.619 0.00 0.00 0.00 5.69
3951 4012 1.588824 TTTCTGGCTCATGCTTGGCG 61.589 55.000 0.00 0.00 39.59 5.69
4070 4131 3.635836 GACTACTGTACGGGAGGCTAAAT 59.364 47.826 18.47 0.00 0.00 1.40
4093 4154 3.537793 ATTTTCGTCACTTTTCTCGGC 57.462 42.857 0.00 0.00 0.00 5.54
4100 4161 6.206498 GCCAACTTAGAATTTTCGTCACTTT 58.794 36.000 0.00 0.00 0.00 2.66
4207 4269 5.409826 GGTAGATCTCAACTTCACAACCTTG 59.590 44.000 0.00 0.00 0.00 3.61
4208 4270 5.071788 TGGTAGATCTCAACTTCACAACCTT 59.928 40.000 0.00 0.00 0.00 3.50
4236 4298 3.632145 GGAACCAAAGCTTGAAAGAGACA 59.368 43.478 0.00 0.00 0.00 3.41
4269 4331 4.280929 AGCCAAGGATTAAAACAACCTCAC 59.719 41.667 0.00 0.00 31.89 3.51
4344 4406 7.708752 CCCTAAGTAGTTTTAGAAGCTCTCATG 59.291 40.741 0.00 0.00 33.42 3.07
4353 4415 7.736234 TCCTTTCCTCCCTAAGTAGTTTTAGAA 59.264 37.037 0.00 0.00 33.42 2.10
4369 4431 5.934781 ACATGTGATAGAATCCTTTCCTCC 58.065 41.667 0.00 0.00 31.84 4.30
4442 4505 4.076394 CGTGGAAAAGTCCCCAAATTAGA 58.924 43.478 0.00 0.00 44.23 2.10
4522 4585 5.246307 AGGACAAGTAATAGGTGCTTTCAC 58.754 41.667 0.00 0.00 42.40 3.18
4531 4594 6.159988 GCACATAGCTAGGACAAGTAATAGG 58.840 44.000 13.23 0.00 41.15 2.57
4559 4622 7.371936 CACATAGCTAGGACAAGTAATAGGTC 58.628 42.308 13.23 0.00 0.00 3.85
4560 4623 6.239345 GCACATAGCTAGGACAAGTAATAGGT 60.239 42.308 13.23 0.00 41.15 3.08
4561 4624 6.159988 GCACATAGCTAGGACAAGTAATAGG 58.840 44.000 13.23 0.00 41.15 2.57
4604 4667 1.142870 CTCAGTGGTTGAACTTGGGGA 59.857 52.381 0.00 0.00 34.81 4.81


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

AutoCloner maintained by Alex Coulton.