Multiple sequence alignment - TraesCS3B01G005500

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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 TraesCS3B01G005500 chr3B 100.000 2468 0 0 1 2468 3099482 3101949 0.000000e+00 4558
1 TraesCS3B01G005500 chr3B 96.032 378 14 1 1018 1395 3064559 3064183 4.510000e-172 614
2 TraesCS3B01G005500 chr3B 86.974 499 44 11 1606 2099 3064189 3063707 2.160000e-150 542
3 TraesCS3B01G005500 chr3B 95.853 217 9 0 743 959 3064838 3064622 3.900000e-93 351
4 TraesCS3B01G005500 chr3B 76.891 238 40 11 717 951 3068788 3068563 1.200000e-23 121
5 TraesCS3B01G005500 chr3D 86.233 1707 126 50 58 1707 2752505 2754159 0.000000e+00 1749
6 TraesCS3B01G005500 chr3D 87.379 412 43 7 1734 2139 2754502 2754910 4.810000e-127 464
7 TraesCS3B01G005500 chr3D 78.003 791 90 38 1019 1772 2747153 2747896 1.060000e-113 420
8 TraesCS3B01G005500 chr3D 77.778 720 75 34 1045 1735 2718333 2718996 5.020000e-97 364
9 TraesCS3B01G005500 chr3D 90.435 115 8 2 1204 1318 2533153 2533042 5.500000e-32 148
10 TraesCS3B01G005500 chr3D 77.903 267 38 12 1204 1467 2462085 2461837 1.980000e-31 147
11 TraesCS3B01G005500 chr3D 88.889 117 10 1 1204 1320 2469408 2469295 9.200000e-30 141
12 TraesCS3B01G005500 chr3D 84.746 118 13 4 717 833 2734238 2734351 2.010000e-21 113
13 TraesCS3B01G005500 chrUn 92.442 1032 55 9 1 1022 32039725 32038707 0.000000e+00 1452
14 TraesCS3B01G005500 chrUn 91.284 1090 47 10 1020 2077 32038676 32037603 0.000000e+00 1443
15 TraesCS3B01G005500 chrUn 95.050 202 7 2 2074 2274 32037334 32037135 5.120000e-82 315
16 TraesCS3B01G005500 chrUn 86.207 203 26 2 744 946 63657873 63657673 4.130000e-53 219
17 TraesCS3B01G005500 chrUn 86.207 203 26 2 744 946 317285163 317285363 4.130000e-53 219
18 TraesCS3B01G005500 chrUn 86.207 203 26 2 744 946 372045088 372045288 4.130000e-53 219
19 TraesCS3B01G005500 chrUn 77.273 264 42 13 714 969 330705181 330705434 3.310000e-29 139
20 TraesCS3B01G005500 chr3A 86.777 121 12 3 1204 1324 1519516 1519632 5.540000e-27 132


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 TraesCS3B01G005500 chr3B 3099482 3101949 2467 False 4558.0 4558 100.000000 1 2468 1 chr3B.!!$F1 2467
1 TraesCS3B01G005500 chr3B 3063707 3068788 5081 True 407.0 614 88.937500 717 2099 4 chr3B.!!$R1 1382
2 TraesCS3B01G005500 chr3D 2752505 2754910 2405 False 1106.5 1749 86.806000 58 2139 2 chr3D.!!$F4 2081
3 TraesCS3B01G005500 chr3D 2747153 2747896 743 False 420.0 420 78.003000 1019 1772 1 chr3D.!!$F3 753
4 TraesCS3B01G005500 chr3D 2718333 2718996 663 False 364.0 364 77.778000 1045 1735 1 chr3D.!!$F1 690
5 TraesCS3B01G005500 chrUn 32037135 32039725 2590 True 1070.0 1452 92.925333 1 2274 3 chrUn.!!$R2 2273

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
256 261 0.040246 GTAGCCACGATCGAGGTAGC 60.040 60.0 28.52 18.73 0.0 3.58 F
257 262 0.179026 TAGCCACGATCGAGGTAGCT 60.179 55.0 28.52 23.45 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 5260 0.530288 GAAGAGGCACGAGAAGAGCT 59.470 55.000 0.0 0.0 36.65 4.09 R
1744 6179 1.213678 TGGAGGCAGATCTTTCATGGG 59.786 52.381 0.0 0.0 0.00 4.00 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
45 46 7.489113 CCAGATTCGCAAATAAGCATTAAAAGT 59.511 33.333 0.00 0.00 32.17 2.66
152 153 0.109919 CATGGTCGTCGACGTGAAGA 60.110 55.000 34.40 14.92 40.80 2.87
210 211 5.952387 TCTCCAGATCTTTTTCCCTTTGAA 58.048 37.500 0.00 0.00 0.00 2.69
256 261 0.040246 GTAGCCACGATCGAGGTAGC 60.040 60.000 28.52 18.73 0.00 3.58
257 262 0.179026 TAGCCACGATCGAGGTAGCT 60.179 55.000 28.52 23.45 0.00 3.32
258 263 1.008309 GCCACGATCGAGGTAGCTC 60.008 63.158 28.52 12.04 0.00 4.09
259 264 1.655329 CCACGATCGAGGTAGCTCC 59.345 63.158 24.34 1.70 0.00 4.70
260 265 1.655329 CACGATCGAGGTAGCTCCC 59.345 63.158 24.34 5.16 36.75 4.30
261 266 1.892862 ACGATCGAGGTAGCTCCCG 60.893 63.158 24.34 17.40 36.75 5.14
262 267 2.618219 CGATCGAGGTAGCTCCCGG 61.618 68.421 10.26 0.00 36.75 5.73
263 268 2.203509 ATCGAGGTAGCTCCCGGG 60.204 66.667 16.85 16.85 36.75 5.73
264 269 2.693896 GATCGAGGTAGCTCCCGGGA 62.694 65.000 25.06 25.06 36.75 5.14
265 270 2.082836 ATCGAGGTAGCTCCCGGGAT 62.083 60.000 27.07 13.62 36.75 3.85
266 271 1.833049 CGAGGTAGCTCCCGGGATT 60.833 63.158 27.07 18.21 36.75 3.01
267 272 1.807495 CGAGGTAGCTCCCGGGATTC 61.807 65.000 27.07 19.07 36.75 2.52
340 357 1.017387 CGATTTAGCAAGTGGGAGCC 58.983 55.000 0.00 0.00 0.00 4.70
346 363 2.360852 CAAGTGGGAGCCTGCCTG 60.361 66.667 3.18 0.00 0.00 4.85
348 365 2.900106 AAGTGGGAGCCTGCCTGTC 61.900 63.158 3.18 0.00 0.00 3.51
349 366 3.640407 GTGGGAGCCTGCCTGTCA 61.640 66.667 3.18 0.00 0.00 3.58
350 367 2.611800 TGGGAGCCTGCCTGTCAT 60.612 61.111 3.18 0.00 0.00 3.06
351 368 2.124403 GGGAGCCTGCCTGTCATG 60.124 66.667 0.00 0.00 0.00 3.07
352 369 2.827642 GGAGCCTGCCTGTCATGC 60.828 66.667 0.00 0.00 36.70 4.06
353 370 2.827642 GAGCCTGCCTGTCATGCC 60.828 66.667 0.00 0.00 37.07 4.40
354 371 4.437587 AGCCTGCCTGTCATGCCC 62.438 66.667 0.00 0.00 37.07 5.36
355 372 4.746309 GCCTGCCTGTCATGCCCA 62.746 66.667 0.00 0.00 31.22 5.36
356 373 2.277737 CCTGCCTGTCATGCCCAT 59.722 61.111 0.00 0.00 0.00 4.00
357 374 2.125326 CCTGCCTGTCATGCCCATG 61.125 63.158 1.86 1.86 40.09 3.66
358 375 2.043752 TGCCTGTCATGCCCATGG 60.044 61.111 4.14 4.14 39.24 3.66
383 421 1.128692 GTCCACATACTTCGTGCTTGC 59.871 52.381 0.00 0.00 32.85 4.01
407 445 3.186909 TGATGCTATGGTTCGTTCTTCG 58.813 45.455 0.00 0.00 41.41 3.79
456 494 1.730501 ATGTGTGCATGGAGTCGAAG 58.269 50.000 0.00 0.00 33.37 3.79
481 519 8.034804 AGTAATCAGCAAAGAGTTTTGTTTTGT 58.965 29.630 2.44 0.00 44.41 2.83
499 538 6.538021 TGTTTTGTTGAAAAATGGACAGATGG 59.462 34.615 0.00 0.00 32.81 3.51
532 571 4.832823 AGTAGCACAAGCCCTTAAAAATGT 59.167 37.500 0.00 0.00 43.56 2.71
533 572 4.687901 AGCACAAGCCCTTAAAAATGTT 57.312 36.364 0.00 0.00 43.56 2.71
534 573 5.034852 AGCACAAGCCCTTAAAAATGTTT 57.965 34.783 0.00 0.00 43.56 2.83
536 575 5.527214 AGCACAAGCCCTTAAAAATGTTTTC 59.473 36.000 0.00 0.00 43.56 2.29
631 670 6.840780 ATCTAAAACTTCAACTCCAATGGG 57.159 37.500 0.00 0.00 0.00 4.00
664 703 0.598065 CCTTGCTTGCTACACCCAAC 59.402 55.000 0.00 0.00 0.00 3.77
703 742 7.846644 TTTTGCTTGCCAAGATATATTTTGG 57.153 32.000 24.31 24.31 45.28 3.28
714 753 9.313118 CCAAGATATATTTTGGCAAAAACTACC 57.687 33.333 27.25 16.55 38.07 3.18
724 763 4.288626 TGGCAAAAACTACCTCCACTAGAT 59.711 41.667 0.00 0.00 0.00 1.98
727 766 6.208797 GGCAAAAACTACCTCCACTAGATTTT 59.791 38.462 0.00 0.00 30.47 1.82
740 4733 4.827284 CACTAGATTTTGTTTGTGGGTCCT 59.173 41.667 0.00 0.00 0.00 3.85
835 4834 1.765314 GTAGACATGCTGGACCTCCAT 59.235 52.381 0.00 0.00 46.46 3.41
959 4958 4.614555 TTCATGGCAGCTATAACAAACG 57.385 40.909 0.00 0.00 0.00 3.60
1016 5023 0.417437 TCCATGGAGGAAGGTGGAGA 59.583 55.000 11.44 0.00 45.65 3.71
1170 5225 0.973632 TTCCTTCTTCTACAGGCGCA 59.026 50.000 10.83 0.00 0.00 6.09
1202 5260 2.556216 ATGGCCATGGTGGTGGGAA 61.556 57.895 20.04 0.00 40.46 3.97
1225 5283 0.037882 CTTCTCGTGCCTCTTCTGCA 60.038 55.000 0.00 0.00 36.12 4.41
1326 5384 1.987855 CCACCTCTACCTTCCCGCA 60.988 63.158 0.00 0.00 0.00 5.69
1431 5510 2.807045 GACGACCACGAGCAGCAG 60.807 66.667 0.00 0.00 42.66 4.24
1622 5730 0.179215 GTGCACTACTCGCATGTTGC 60.179 55.000 10.32 0.00 42.32 4.17
1638 5746 4.414337 TGTTGCCCATTTTACTTTGCTT 57.586 36.364 0.00 0.00 0.00 3.91
1652 5760 3.260632 ACTTTGCTTAATTTTGCCCCGAT 59.739 39.130 0.00 0.00 0.00 4.18
1682 5793 6.500684 TGCAAAAAGGAGTAGCTCATTAAG 57.499 37.500 0.00 0.00 33.23 1.85
1751 6186 2.398588 CTACCTCTGTAGCCCCATGAA 58.601 52.381 0.00 0.00 38.20 2.57
1836 6273 0.811281 GCCTGTTGGATGTTAGTGCC 59.189 55.000 0.00 0.00 34.57 5.01
1950 6390 1.633774 TCTGTTGGTCCAGGAGAGAC 58.366 55.000 0.00 0.00 33.14 3.36
2025 6484 0.974383 CCCCCGGTATATCTGGTGTC 59.026 60.000 0.00 0.00 40.86 3.67
2132 6866 2.202919 TCCGACTCATGCATGCGG 60.203 61.111 28.17 28.17 43.11 5.69
2145 6879 1.527034 CATGCGGTGATCCCATTAGG 58.473 55.000 0.00 0.00 0.00 2.69
2202 6936 2.810488 TACCCCCGAAGAGACACCCC 62.810 65.000 0.00 0.00 0.00 4.95
2203 6937 3.400054 CCCCGAAGAGACACCCCC 61.400 72.222 0.00 0.00 0.00 5.40
2217 6951 2.511452 CCCCCGTGCTGATCCTAGG 61.511 68.421 0.82 0.82 0.00 3.02
2246 6980 2.408835 CGCCAACGCCAATCATCC 59.591 61.111 0.00 0.00 0.00 3.51
2251 6985 1.001020 AACGCCAATCATCCAGCCA 60.001 52.632 0.00 0.00 0.00 4.75
2259 6993 0.839277 ATCATCCAGCCATCGGTTCA 59.161 50.000 0.00 0.00 0.00 3.18
2274 7008 8.999431 GCCATCGGTTCATTATCTATTTTAAGA 58.001 33.333 0.00 0.00 0.00 2.10
2296 7030 8.715190 AAGATAAATCTACTCCCTAGACCTTC 57.285 38.462 0.00 0.00 35.76 3.46
2297 7031 7.827787 AGATAAATCTACTCCCTAGACCTTCA 58.172 38.462 0.00 0.00 34.08 3.02
2298 7032 8.461033 AGATAAATCTACTCCCTAGACCTTCAT 58.539 37.037 0.00 0.00 34.08 2.57
2299 7033 9.756571 GATAAATCTACTCCCTAGACCTTCATA 57.243 37.037 0.00 0.00 34.08 2.15
2300 7034 7.842887 AAATCTACTCCCTAGACCTTCATAC 57.157 40.000 0.00 0.00 34.08 2.39
2301 7035 5.988865 TCTACTCCCTAGACCTTCATACA 57.011 43.478 0.00 0.00 0.00 2.29
2302 7036 6.532119 TCTACTCCCTAGACCTTCATACAT 57.468 41.667 0.00 0.00 0.00 2.29
2303 7037 7.643612 TCTACTCCCTAGACCTTCATACATA 57.356 40.000 0.00 0.00 0.00 2.29
2304 7038 8.053776 TCTACTCCCTAGACCTTCATACATAA 57.946 38.462 0.00 0.00 0.00 1.90
2305 7039 8.508601 TCTACTCCCTAGACCTTCATACATAAA 58.491 37.037 0.00 0.00 0.00 1.40
2306 7040 7.989947 ACTCCCTAGACCTTCATACATAAAA 57.010 36.000 0.00 0.00 0.00 1.52
2307 7041 8.568617 ACTCCCTAGACCTTCATACATAAAAT 57.431 34.615 0.00 0.00 0.00 1.82
2308 7042 8.652290 ACTCCCTAGACCTTCATACATAAAATC 58.348 37.037 0.00 0.00 0.00 2.17
2309 7043 7.667557 TCCCTAGACCTTCATACATAAAATCG 58.332 38.462 0.00 0.00 0.00 3.34
2310 7044 7.289317 TCCCTAGACCTTCATACATAAAATCGT 59.711 37.037 0.00 0.00 0.00 3.73
2311 7045 7.931948 CCCTAGACCTTCATACATAAAATCGTT 59.068 37.037 0.00 0.00 0.00 3.85
2312 7046 9.326413 CCTAGACCTTCATACATAAAATCGTTT 57.674 33.333 0.00 0.00 0.00 3.60
2316 7050 9.712359 GACCTTCATACATAAAATCGTTTTACC 57.288 33.333 5.47 0.00 37.88 2.85
2317 7051 9.233649 ACCTTCATACATAAAATCGTTTTACCA 57.766 29.630 5.47 0.00 37.88 3.25
2365 7099 6.877611 TTTTCTGTACAGGTCTTTTCCATC 57.122 37.500 22.48 0.00 0.00 3.51
2366 7100 5.825593 TTCTGTACAGGTCTTTTCCATCT 57.174 39.130 22.48 0.00 0.00 2.90
2367 7101 6.928348 TTCTGTACAGGTCTTTTCCATCTA 57.072 37.500 22.48 0.00 0.00 1.98
2368 7102 7.496346 TTCTGTACAGGTCTTTTCCATCTAT 57.504 36.000 22.48 0.00 0.00 1.98
2369 7103 7.496346 TCTGTACAGGTCTTTTCCATCTATT 57.504 36.000 22.48 0.00 0.00 1.73
2370 7104 7.918076 TCTGTACAGGTCTTTTCCATCTATTT 58.082 34.615 22.48 0.00 0.00 1.40
2371 7105 9.042450 TCTGTACAGGTCTTTTCCATCTATTTA 57.958 33.333 22.48 0.00 0.00 1.40
2372 7106 9.838339 CTGTACAGGTCTTTTCCATCTATTTAT 57.162 33.333 15.49 0.00 0.00 1.40
2376 7110 9.401058 ACAGGTCTTTTCCATCTATTTATTCTG 57.599 33.333 0.00 0.00 0.00 3.02
2377 7111 9.401058 CAGGTCTTTTCCATCTATTTATTCTGT 57.599 33.333 0.00 0.00 0.00 3.41
2378 7112 9.981460 AGGTCTTTTCCATCTATTTATTCTGTT 57.019 29.630 0.00 0.00 0.00 3.16
2454 7188 9.491675 TCTATGCATGTTCAAAATCAAAAATGT 57.508 25.926 10.16 0.00 0.00 2.71
2457 7191 9.804758 ATGCATGTTCAAAATCAAAAATGTTTT 57.195 22.222 0.00 0.00 0.00 2.43
2458 7192 9.635520 TGCATGTTCAAAATCAAAAATGTTTTT 57.364 22.222 0.00 0.00 40.75 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.906660 TCACTAACCACTTTTAATGCTTATTTG 57.093 29.630 0.00 0.00 0.00 2.32
45 46 4.290985 TCCCTTCAATCCATTCACTAACCA 59.709 41.667 0.00 0.00 0.00 3.67
92 93 5.357314 TCCTAGTGACTAGTGTTGTGATAGC 59.643 44.000 17.60 0.00 32.62 2.97
210 211 2.366533 CAGAAGTGCAGATCATTGCCT 58.633 47.619 4.64 0.00 43.43 4.75
256 261 2.310779 TATCAGAGGAATCCCGGGAG 57.689 55.000 30.42 13.56 37.58 4.30
257 262 4.264850 ACATATATCAGAGGAATCCCGGGA 60.265 45.833 29.18 29.18 37.58 5.14
258 263 4.033709 ACATATATCAGAGGAATCCCGGG 58.966 47.826 16.85 16.85 37.58 5.73
259 264 5.221067 CGTACATATATCAGAGGAATCCCGG 60.221 48.000 0.00 0.00 37.58 5.73
260 265 5.221067 CCGTACATATATCAGAGGAATCCCG 60.221 48.000 0.00 0.00 37.58 5.14
261 266 5.452077 GCCGTACATATATCAGAGGAATCCC 60.452 48.000 0.00 0.00 0.00 3.85
262 267 5.452077 GGCCGTACATATATCAGAGGAATCC 60.452 48.000 0.00 0.00 0.00 3.01
263 268 5.127194 TGGCCGTACATATATCAGAGGAATC 59.873 44.000 0.00 0.00 0.00 2.52
264 269 5.023452 TGGCCGTACATATATCAGAGGAAT 58.977 41.667 0.00 0.00 0.00 3.01
265 270 4.412843 TGGCCGTACATATATCAGAGGAA 58.587 43.478 0.00 0.00 0.00 3.36
266 271 4.017126 CTGGCCGTACATATATCAGAGGA 58.983 47.826 0.00 0.00 0.00 3.71
267 272 3.429547 GCTGGCCGTACATATATCAGAGG 60.430 52.174 0.00 0.00 0.00 3.69
340 357 2.125326 CCATGGGCATGACAGGCAG 61.125 63.158 14.83 0.52 41.20 4.85
352 369 0.108396 TATGTGGACGATGCCATGGG 59.892 55.000 15.13 0.00 40.68 4.00
353 370 1.202687 AGTATGTGGACGATGCCATGG 60.203 52.381 7.63 7.63 40.68 3.66
354 371 2.245159 AGTATGTGGACGATGCCATG 57.755 50.000 0.00 0.00 40.68 3.66
355 372 2.803133 CGAAGTATGTGGACGATGCCAT 60.803 50.000 0.00 0.00 40.68 4.40
356 373 1.470805 CGAAGTATGTGGACGATGCCA 60.471 52.381 0.00 0.00 35.02 4.92
357 374 1.209128 CGAAGTATGTGGACGATGCC 58.791 55.000 0.00 0.00 0.00 4.40
358 375 1.588404 CACGAAGTATGTGGACGATGC 59.412 52.381 0.00 0.00 41.61 3.91
359 376 1.588404 GCACGAAGTATGTGGACGATG 59.412 52.381 0.00 0.00 41.61 3.84
360 377 1.476891 AGCACGAAGTATGTGGACGAT 59.523 47.619 0.00 0.00 41.61 3.73
361 378 0.885879 AGCACGAAGTATGTGGACGA 59.114 50.000 0.00 0.00 41.61 4.20
362 379 1.390123 CAAGCACGAAGTATGTGGACG 59.610 52.381 0.00 0.00 41.61 4.79
363 380 1.128692 GCAAGCACGAAGTATGTGGAC 59.871 52.381 0.00 0.00 41.61 4.02
364 381 1.001974 AGCAAGCACGAAGTATGTGGA 59.998 47.619 0.00 0.00 41.61 4.02
365 382 1.442769 AGCAAGCACGAAGTATGTGG 58.557 50.000 0.00 0.00 41.61 4.17
366 383 3.058983 TCAAAGCAAGCACGAAGTATGTG 60.059 43.478 0.00 0.00 41.61 3.21
367 384 3.138304 TCAAAGCAAGCACGAAGTATGT 58.862 40.909 0.00 0.00 41.61 2.29
383 421 5.551760 AAGAACGAACCATAGCATCAAAG 57.448 39.130 0.00 0.00 0.00 2.77
407 445 5.388408 AGCTTGTACTTGTAGTGTAGACC 57.612 43.478 0.00 0.00 0.00 3.85
456 494 8.185003 ACAAAACAAAACTCTTTGCTGATTAC 57.815 30.769 0.00 0.00 44.96 1.89
481 519 6.154877 ACATATGCCATCTGTCCATTTTTCAA 59.845 34.615 1.58 0.00 0.00 2.69
499 538 4.261197 GGGCTTGTGCTACTTAACATATGC 60.261 45.833 1.58 0.00 39.59 3.14
678 717 8.266392 CCAAAATATATCTTGGCAAGCAAAAA 57.734 30.769 22.31 5.15 35.97 1.94
679 718 7.846644 CCAAAATATATCTTGGCAAGCAAAA 57.153 32.000 22.31 5.56 35.97 2.44
688 727 9.313118 GGTAGTTTTTGCCAAAATATATCTTGG 57.687 33.333 12.77 12.77 44.23 3.61
691 730 8.914011 GGAGGTAGTTTTTGCCAAAATATATCT 58.086 33.333 3.01 5.56 34.35 1.98
692 731 8.691797 TGGAGGTAGTTTTTGCCAAAATATATC 58.308 33.333 3.01 0.91 34.35 1.63
693 732 8.474831 GTGGAGGTAGTTTTTGCCAAAATATAT 58.525 33.333 3.01 0.00 34.35 0.86
694 733 7.672239 AGTGGAGGTAGTTTTTGCCAAAATATA 59.328 33.333 3.01 0.00 34.35 0.86
695 734 6.496911 AGTGGAGGTAGTTTTTGCCAAAATAT 59.503 34.615 3.01 0.00 34.35 1.28
696 735 5.836358 AGTGGAGGTAGTTTTTGCCAAAATA 59.164 36.000 3.01 0.00 34.35 1.40
697 736 4.653801 AGTGGAGGTAGTTTTTGCCAAAAT 59.346 37.500 3.01 0.00 34.35 1.82
698 737 4.027437 AGTGGAGGTAGTTTTTGCCAAAA 58.973 39.130 0.00 0.00 33.26 2.44
699 738 3.637769 AGTGGAGGTAGTTTTTGCCAAA 58.362 40.909 0.00 0.00 33.26 3.28
700 739 3.306472 AGTGGAGGTAGTTTTTGCCAA 57.694 42.857 0.00 0.00 33.26 4.52
701 740 3.649023 TCTAGTGGAGGTAGTTTTTGCCA 59.351 43.478 0.00 0.00 33.26 4.92
702 741 4.281898 TCTAGTGGAGGTAGTTTTTGCC 57.718 45.455 0.00 0.00 0.00 4.52
703 742 6.819397 AAATCTAGTGGAGGTAGTTTTTGC 57.181 37.500 0.00 0.00 0.00 3.68
704 743 8.166422 ACAAAATCTAGTGGAGGTAGTTTTTG 57.834 34.615 17.13 17.13 44.13 2.44
705 744 8.762481 AACAAAATCTAGTGGAGGTAGTTTTT 57.238 30.769 0.00 0.00 32.98 1.94
706 745 8.630037 CAAACAAAATCTAGTGGAGGTAGTTTT 58.370 33.333 0.00 0.00 0.00 2.43
707 746 7.778382 ACAAACAAAATCTAGTGGAGGTAGTTT 59.222 33.333 0.00 0.00 0.00 2.66
708 747 7.228706 CACAAACAAAATCTAGTGGAGGTAGTT 59.771 37.037 0.00 0.00 0.00 2.24
709 748 6.710744 CACAAACAAAATCTAGTGGAGGTAGT 59.289 38.462 0.00 0.00 0.00 2.73
710 749 7.133891 CACAAACAAAATCTAGTGGAGGTAG 57.866 40.000 0.00 0.00 0.00 3.18
724 763 2.104170 GGTGAGGACCCACAAACAAAA 58.896 47.619 13.16 0.00 38.74 2.44
740 4733 3.389656 TCATGCGTTATTCATAGGGGTGA 59.610 43.478 0.00 0.00 0.00 4.02
835 4834 0.834612 ACGACAAAGGACCTTGGACA 59.165 50.000 16.05 0.00 0.00 4.02
959 4958 0.818040 AGTGGGTTTTGAGTGGCGAC 60.818 55.000 0.00 0.00 0.00 5.19
1170 5225 0.687427 GGCCATGGTAATTGCCACCT 60.687 55.000 18.22 0.00 42.86 4.00
1202 5260 0.530288 GAAGAGGCACGAGAAGAGCT 59.470 55.000 0.00 0.00 36.65 4.09
1225 5283 3.260884 TGCGACTTGAGGAAGGTCTTATT 59.739 43.478 0.00 0.00 32.95 1.40
1484 5563 2.800544 GTGCGTTGACTTGACACTACAT 59.199 45.455 0.00 0.00 0.00 2.29
1622 5730 7.304735 GGCAAAATTAAGCAAAGTAAAATGGG 58.695 34.615 4.67 0.00 0.00 4.00
1652 5760 3.492482 GCTACTCCTTTTTGCAAAGCCAA 60.492 43.478 12.41 3.32 38.53 4.52
1682 5793 1.570813 TCGATGTCGATCAACATGCC 58.429 50.000 3.45 0.00 44.22 4.40
1743 6178 1.478288 GGAGGCAGATCTTTCATGGGG 60.478 57.143 0.00 0.00 0.00 4.96
1744 6179 1.213678 TGGAGGCAGATCTTTCATGGG 59.786 52.381 0.00 0.00 0.00 4.00
1751 6186 2.172293 GAGGAACATGGAGGCAGATCTT 59.828 50.000 0.00 0.00 0.00 2.40
1950 6390 1.227263 CATTAGCAGGTCGGACCCG 60.227 63.158 23.21 14.83 39.75 5.28
2025 6484 4.525912 AAGCTTCCAAATAGCCAACAAG 57.474 40.909 0.00 0.00 39.47 3.16
2132 6866 2.364324 TCTACGCACCTAATGGGATCAC 59.636 50.000 0.00 0.00 43.98 3.06
2145 6879 2.438583 GTATCTCACACGTCTACGCAC 58.561 52.381 1.74 0.00 44.43 5.34
2202 6936 2.751991 ATCCCTAGGATCAGCACGG 58.248 57.895 11.48 0.00 38.09 4.94
2217 6951 2.036572 TTGGCGGGGGTTTGATCC 59.963 61.111 0.00 0.00 0.00 3.36
2229 6963 2.327002 CTGGATGATTGGCGTTGGCG 62.327 60.000 0.00 0.00 41.24 5.69
2246 6980 6.808008 AAATAGATAATGAACCGATGGCTG 57.192 37.500 0.00 0.00 0.00 4.85
2274 7008 9.536510 GTATGAAGGTCTAGGGAGTAGATTTAT 57.463 37.037 0.00 0.00 40.05 1.40
2275 7009 8.508601 TGTATGAAGGTCTAGGGAGTAGATTTA 58.491 37.037 0.00 0.00 40.05 1.40
2276 7010 7.363031 TGTATGAAGGTCTAGGGAGTAGATTT 58.637 38.462 0.00 0.00 40.05 2.17
2277 7011 6.923670 TGTATGAAGGTCTAGGGAGTAGATT 58.076 40.000 0.00 0.00 40.05 2.40
2278 7012 6.532119 TGTATGAAGGTCTAGGGAGTAGAT 57.468 41.667 0.00 0.00 40.05 1.98
2279 7013 5.988865 TGTATGAAGGTCTAGGGAGTAGA 57.011 43.478 0.00 0.00 35.20 2.59
2280 7014 8.707796 TTTATGTATGAAGGTCTAGGGAGTAG 57.292 38.462 0.00 0.00 0.00 2.57
2281 7015 9.670442 ATTTTATGTATGAAGGTCTAGGGAGTA 57.330 33.333 0.00 0.00 0.00 2.59
2282 7016 7.989947 TTTTATGTATGAAGGTCTAGGGAGT 57.010 36.000 0.00 0.00 0.00 3.85
2283 7017 7.815068 CGATTTTATGTATGAAGGTCTAGGGAG 59.185 40.741 0.00 0.00 0.00 4.30
2284 7018 7.289317 ACGATTTTATGTATGAAGGTCTAGGGA 59.711 37.037 0.00 0.00 0.00 4.20
2285 7019 7.442656 ACGATTTTATGTATGAAGGTCTAGGG 58.557 38.462 0.00 0.00 0.00 3.53
2286 7020 8.888579 AACGATTTTATGTATGAAGGTCTAGG 57.111 34.615 0.00 0.00 0.00 3.02
2290 7024 9.712359 GGTAAAACGATTTTATGTATGAAGGTC 57.288 33.333 0.00 0.00 37.44 3.85
2291 7025 9.233649 TGGTAAAACGATTTTATGTATGAAGGT 57.766 29.630 0.00 0.00 37.44 3.50
2341 7075 7.060421 AGATGGAAAAGACCTGTACAGAAAAA 58.940 34.615 24.68 0.48 0.00 1.94
2342 7076 6.601332 AGATGGAAAAGACCTGTACAGAAAA 58.399 36.000 24.68 0.00 0.00 2.29
2343 7077 6.187727 AGATGGAAAAGACCTGTACAGAAA 57.812 37.500 24.68 0.00 0.00 2.52
2344 7078 5.825593 AGATGGAAAAGACCTGTACAGAA 57.174 39.130 24.68 0.00 0.00 3.02
2345 7079 7.496346 AATAGATGGAAAAGACCTGTACAGA 57.504 36.000 24.68 0.72 0.00 3.41
2346 7080 9.838339 ATAAATAGATGGAAAAGACCTGTACAG 57.162 33.333 16.34 16.34 0.00 2.74
2350 7084 9.401058 CAGAATAAATAGATGGAAAAGACCTGT 57.599 33.333 0.00 0.00 0.00 4.00
2351 7085 9.401058 ACAGAATAAATAGATGGAAAAGACCTG 57.599 33.333 0.00 0.00 0.00 4.00
2352 7086 9.981460 AACAGAATAAATAGATGGAAAAGACCT 57.019 29.630 0.00 0.00 0.00 3.85
2428 7162 9.491675 ACATTTTTGATTTTGAACATGCATAGA 57.508 25.926 0.00 0.00 0.00 1.98
2431 7165 9.804758 AAAACATTTTTGATTTTGAACATGCAT 57.195 22.222 0.00 0.00 0.00 3.96
2432 7166 9.635520 AAAAACATTTTTGATTTTGAACATGCA 57.364 22.222 1.58 0.00 38.81 3.96


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

AutoCloner maintained by Alex Coulton.