Multiple sequence alignment - TraesCS2A01G408900

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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 TraesCS2A01G408900 chr2A 100.000 4406 0 0 1 4406 666294001 666289596 0.000000e+00 8137.0
1 TraesCS2A01G408900 chr2A 71.983 464 102 19 1487 1933 666021261 666021713 1.300000e-20 111.0
2 TraesCS2A01G408900 chr2B 94.203 3778 159 23 12 3779 614399901 614396174 0.000000e+00 5709.0
3 TraesCS2A01G408900 chr2B 91.974 1981 100 22 3 1973 614504868 614502937 0.000000e+00 2723.0
4 TraesCS2A01G408900 chr2B 96.629 1246 41 1 2534 3779 614502852 614501608 0.000000e+00 2067.0
5 TraesCS2A01G408900 chr2B 83.791 364 37 8 3772 4133 614395969 614395626 4.250000e-85 326.0
6 TraesCS2A01G408900 chr2B 83.702 362 37 8 3772 4131 614501403 614501062 5.500000e-84 322.0
7 TraesCS2A01G408900 chr2B 71.888 466 99 21 1487 1933 614241855 614242307 6.030000e-19 106.0
8 TraesCS2A01G408900 chr2D 96.292 3182 107 10 476 3653 521410264 521413438 0.000000e+00 5212.0
9 TraesCS2A01G408900 chr2D 85.246 793 74 13 3653 4406 521417723 521418511 0.000000e+00 776.0
10 TraesCS2A01G408900 chr2D 86.473 414 40 8 2 406 521409855 521410261 1.450000e-119 440.0
11 TraesCS2A01G408900 chr2D 72.258 465 99 19 1487 1933 521568153 521567701 2.780000e-22 117.0
12 TraesCS2A01G408900 chr6A 77.940 961 187 17 1132 2081 457020061 457019115 1.060000e-160 577.0
13 TraesCS2A01G408900 chr6B 77.570 963 188 18 1133 2081 504158258 504159206 1.380000e-154 556.0
14 TraesCS2A01G408900 chr6D 77.523 961 191 17 1132 2081 319053016 319052070 4.980000e-154 555.0
15 TraesCS2A01G408900 chrUn 83.702 362 37 8 3772 4131 480197366 480197025 5.500000e-84 322.0
16 TraesCS2A01G408900 chr7D 80.702 114 20 2 2676 2788 489114593 489114705 2.180000e-13 87.9
17 TraesCS2A01G408900 chr7B 80.702 114 20 2 2676 2788 517394238 517394350 2.180000e-13 87.9
18 TraesCS2A01G408900 chr7A 80.702 114 20 2 2676 2788 556299719 556299831 2.180000e-13 87.9


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 TraesCS2A01G408900 chr2A 666289596 666294001 4405 True 8137.0 8137 100.000000 1 4406 1 chr2A.!!$R1 4405
1 TraesCS2A01G408900 chr2B 614395626 614399901 4275 True 3017.5 5709 88.997000 12 4133 2 chr2B.!!$R1 4121
2 TraesCS2A01G408900 chr2B 614501062 614504868 3806 True 1704.0 2723 90.768333 3 4131 3 chr2B.!!$R2 4128
3 TraesCS2A01G408900 chr2D 521409855 521413438 3583 False 2826.0 5212 91.382500 2 3653 2 chr2D.!!$F2 3651
4 TraesCS2A01G408900 chr2D 521417723 521418511 788 False 776.0 776 85.246000 3653 4406 1 chr2D.!!$F1 753
5 TraesCS2A01G408900 chr6A 457019115 457020061 946 True 577.0 577 77.940000 1132 2081 1 chr6A.!!$R1 949
6 TraesCS2A01G408900 chr6B 504158258 504159206 948 False 556.0 556 77.570000 1133 2081 1 chr6B.!!$F1 948
7 TraesCS2A01G408900 chr6D 319052070 319053016 946 True 555.0 555 77.523000 1132 2081 1 chr6D.!!$R1 949

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
490 499 0.037139 TACGTTGAATGTGACCGGGG 60.037 55.000 6.32 0.00 0.00 5.73 F
1843 1857 0.737715 CTACCAGGTGTGCTTCGAGC 60.738 60.000 0.76 0.58 42.82 5.03 F
2356 2370 1.141881 GGCATGATCGTCGTCACCT 59.858 57.895 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2457 0.892358 TTCTCGGACTGCACGTAGGT 60.892 55.0 0.00 0.0 0.00 3.08 R
2806 2820 0.249573 TCGGCGAACGGTTTCTTCTT 60.250 50.0 7.35 0.0 44.45 2.52 R
4002 4232 0.251832 ACCTCACCTCGTCCTCATGT 60.252 55.0 0.00 0.0 0.00 3.21 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
55 57 2.788191 CTTTGCGCTCGGAAGACCCT 62.788 60.000 9.73 0.00 35.39 4.34
74 76 1.002468 CTTGTTGTCTTGTCGGGCTTG 60.002 52.381 0.00 0.00 0.00 4.01
75 77 0.817634 TGTTGTCTTGTCGGGCTTGG 60.818 55.000 0.00 0.00 0.00 3.61
79 81 2.282462 CTTGTCGGGCTTGGGCTT 60.282 61.111 0.00 0.00 38.73 4.35
80 82 2.282180 TTGTCGGGCTTGGGCTTC 60.282 61.111 0.00 0.00 38.73 3.86
81 83 3.126703 TTGTCGGGCTTGGGCTTCA 62.127 57.895 0.00 0.00 38.73 3.02
83 85 4.722700 TCGGGCTTGGGCTTCAGC 62.723 66.667 0.00 0.00 38.73 4.26
127 129 2.746277 AAGATCAACACCGGCGGC 60.746 61.111 28.71 7.72 0.00 6.53
128 130 3.254024 AAGATCAACACCGGCGGCT 62.254 57.895 28.71 10.32 0.00 5.52
140 142 0.168128 CGGCGGCTCCTTAAACTTTG 59.832 55.000 7.61 0.00 0.00 2.77
148 150 3.507622 GCTCCTTAAACTTTGCTGATGGT 59.492 43.478 0.00 0.00 0.00 3.55
159 161 4.386951 TGATGGTCGGGTGGTGCG 62.387 66.667 0.00 0.00 0.00 5.34
182 184 1.578206 GGGGTTGCACGCTCTTCTTC 61.578 60.000 0.00 0.00 0.00 2.87
214 216 2.144730 GTGCATGGTGTAAACCGTACA 58.855 47.619 0.00 0.00 0.00 2.90
224 226 6.539464 TGGTGTAAACCGTACATGGATATTTC 59.461 38.462 0.00 0.00 0.00 2.17
228 230 3.740115 ACCGTACATGGATATTTCTGGC 58.260 45.455 0.00 0.00 0.00 4.85
232 234 3.909427 ACATGGATATTTCTGGCCCAT 57.091 42.857 0.00 0.00 38.07 4.00
233 235 4.203342 ACATGGATATTTCTGGCCCATT 57.797 40.909 0.00 0.00 35.60 3.16
254 256 5.682943 TTGATACCTGAAACCTTTTCACG 57.317 39.130 0.00 0.00 0.00 4.35
264 266 1.234615 CCTTTTCACGGTGCGATGGT 61.235 55.000 2.51 0.00 0.00 3.55
310 312 4.670896 TTCTCGCATGTGATAATGGAGA 57.329 40.909 9.87 0.00 34.67 3.71
336 338 1.255667 GCCCGGAGTTGGAGACACTA 61.256 60.000 0.73 0.00 42.67 2.74
338 340 2.662866 CCCGGAGTTGGAGACACTATA 58.337 52.381 0.73 0.00 42.67 1.31
339 341 3.028850 CCCGGAGTTGGAGACACTATAA 58.971 50.000 0.73 0.00 42.67 0.98
340 342 3.181478 CCCGGAGTTGGAGACACTATAAC 60.181 52.174 0.73 0.00 42.67 1.89
343 345 4.158025 CGGAGTTGGAGACACTATAACACT 59.842 45.833 0.00 0.00 42.67 3.55
344 346 5.336531 CGGAGTTGGAGACACTATAACACTT 60.337 44.000 0.00 0.00 42.67 3.16
345 347 5.869888 GGAGTTGGAGACACTATAACACTTG 59.130 44.000 0.00 0.00 42.67 3.16
347 349 4.202245 TGGAGACACTATAACACTTGCC 57.798 45.455 0.00 0.00 33.40 4.52
366 375 3.953612 TGCCTCTTGTTCAATTGTGACTT 59.046 39.130 5.13 0.00 31.90 3.01
408 417 4.565022 AGAGCTTGCTAGTGTTTTCTCTC 58.435 43.478 0.00 0.00 0.00 3.20
409 418 3.669536 AGCTTGCTAGTGTTTTCTCTCC 58.330 45.455 0.00 0.00 0.00 3.71
414 423 6.377327 TTGCTAGTGTTTTCTCTCCTTTTG 57.623 37.500 0.00 0.00 0.00 2.44
415 424 5.680619 TGCTAGTGTTTTCTCTCCTTTTGA 58.319 37.500 0.00 0.00 0.00 2.69
416 425 5.527582 TGCTAGTGTTTTCTCTCCTTTTGAC 59.472 40.000 0.00 0.00 0.00 3.18
417 426 5.527582 GCTAGTGTTTTCTCTCCTTTTGACA 59.472 40.000 0.00 0.00 0.00 3.58
418 427 6.205658 GCTAGTGTTTTCTCTCCTTTTGACAT 59.794 38.462 0.00 0.00 0.00 3.06
420 429 7.032377 AGTGTTTTCTCTCCTTTTGACATTC 57.968 36.000 0.00 0.00 0.00 2.67
421 430 6.603201 AGTGTTTTCTCTCCTTTTGACATTCA 59.397 34.615 0.00 0.00 0.00 2.57
422 431 6.914757 GTGTTTTCTCTCCTTTTGACATTCAG 59.085 38.462 0.00 0.00 0.00 3.02
423 432 6.603201 TGTTTTCTCTCCTTTTGACATTCAGT 59.397 34.615 0.00 0.00 0.00 3.41
424 433 7.773224 TGTTTTCTCTCCTTTTGACATTCAGTA 59.227 33.333 0.00 0.00 0.00 2.74
425 434 8.787852 GTTTTCTCTCCTTTTGACATTCAGTAT 58.212 33.333 0.00 0.00 0.00 2.12
426 435 7.912056 TTCTCTCCTTTTGACATTCAGTATG 57.088 36.000 0.00 0.00 40.26 2.39
439 448 7.435068 ACATTCAGTATGTAAACAGGTCAAC 57.565 36.000 0.00 0.00 45.62 3.18
440 449 6.995686 ACATTCAGTATGTAAACAGGTCAACA 59.004 34.615 0.00 0.00 45.62 3.33
441 450 7.500892 ACATTCAGTATGTAAACAGGTCAACAA 59.499 33.333 0.00 0.00 45.62 2.83
442 451 7.490962 TTCAGTATGTAAACAGGTCAACAAG 57.509 36.000 0.00 0.00 37.40 3.16
443 452 5.468746 TCAGTATGTAAACAGGTCAACAAGC 59.531 40.000 0.00 0.00 37.40 4.01
444 453 4.760204 AGTATGTAAACAGGTCAACAAGCC 59.240 41.667 0.00 0.00 0.00 4.35
445 454 3.290948 TGTAAACAGGTCAACAAGCCT 57.709 42.857 0.00 0.00 35.04 4.58
447 456 4.020543 TGTAAACAGGTCAACAAGCCTTT 58.979 39.130 0.00 0.00 31.73 3.11
449 458 5.652891 TGTAAACAGGTCAACAAGCCTTTTA 59.347 36.000 0.00 0.00 31.73 1.52
460 469 5.200368 ACAAGCCTTTTACCACATCTTTG 57.800 39.130 0.00 0.00 0.00 2.77
474 483 4.965762 CACATCTTTGTGCATGCTTATACG 59.034 41.667 20.33 3.31 46.20 3.06
488 497 3.000925 GCTTATACGTTGAATGTGACCGG 59.999 47.826 0.00 0.00 0.00 5.28
490 499 0.037139 TACGTTGAATGTGACCGGGG 60.037 55.000 6.32 0.00 0.00 5.73
493 502 3.577334 TTGAATGTGACCGGGGGCC 62.577 63.158 6.32 0.00 0.00 5.80
506 516 1.755265 CGGGGGCCATCTTGATGAAAT 60.755 52.381 4.39 0.00 0.00 2.17
512 522 3.451902 GGCCATCTTGATGAAATTCCCAA 59.548 43.478 11.76 0.00 0.00 4.12
544 554 1.611673 CCGGCCTCTTGACTGATTGTT 60.612 52.381 0.00 0.00 0.00 2.83
560 570 8.579682 ACTGATTGTTCAAAGAATGCTTTTAC 57.420 30.769 0.00 0.00 42.27 2.01
573 583 5.573337 ATGCTTTTACCTGAATCAAGCTC 57.427 39.130 4.32 0.00 40.48 4.09
578 588 5.489792 TTTACCTGAATCAAGCTCTCTGT 57.510 39.130 0.00 0.00 0.00 3.41
584 594 5.702670 CCTGAATCAAGCTCTCTGTTTTACA 59.297 40.000 0.00 0.00 0.00 2.41
589 599 3.051081 AGCTCTCTGTTTTACAGGCAG 57.949 47.619 6.96 4.76 45.94 4.85
718 728 3.469739 GCATTTAGCAAAATCATGGGGG 58.530 45.455 0.00 0.00 44.79 5.40
722 732 6.358991 CATTTAGCAAAATCATGGGGGAAAT 58.641 36.000 0.00 0.00 32.87 2.17
763 774 4.639310 CAGCTTCATTTCAAGGCATCTAGT 59.361 41.667 0.00 0.00 0.00 2.57
764 775 4.880696 AGCTTCATTTCAAGGCATCTAGTC 59.119 41.667 0.00 0.00 0.00 2.59
805 816 5.988287 ACAAGAAAAGCCCTGAAATGAAAA 58.012 33.333 0.00 0.00 0.00 2.29
807 818 5.612725 AGAAAAGCCCTGAAATGAAAACA 57.387 34.783 0.00 0.00 0.00 2.83
816 827 5.997746 CCCTGAAATGAAAACACAGAGTCTA 59.002 40.000 0.00 0.00 0.00 2.59
936 947 5.423290 TCCATCTTTAGAGATCACAAGAGCA 59.577 40.000 0.00 0.00 40.67 4.26
1314 1325 2.314647 CCGCAACGTCGTCAATGGT 61.315 57.895 0.00 0.00 0.00 3.55
1374 1385 8.712228 AGATGAAAAAGAAGGACTGGTTTTAT 57.288 30.769 0.00 0.00 0.00 1.40
1843 1857 0.737715 CTACCAGGTGTGCTTCGAGC 60.738 60.000 0.76 0.58 42.82 5.03
2244 2258 1.591594 CAGCGACACCGTGTTGAGT 60.592 57.895 21.17 5.84 33.58 3.41
2281 2295 2.540515 GGAAGATCGTCATTTGCGAGA 58.459 47.619 10.88 0.00 41.83 4.04
2356 2370 1.141881 GGCATGATCGTCGTCACCT 59.858 57.895 0.00 0.00 0.00 4.00
2443 2457 1.188219 AGTCGGGCAGAAGCTCAAGA 61.188 55.000 0.00 0.00 43.19 3.02
2790 2804 3.188786 GCGCTGATGACGACCACC 61.189 66.667 0.00 0.00 0.00 4.61
2806 2820 1.608542 CCACCGAAACCACCGATAACA 60.609 52.381 0.00 0.00 0.00 2.41
2821 2835 4.433805 CCGATAACAAGAAGAAACCGTTCG 60.434 45.833 0.00 0.00 38.90 3.95
2822 2836 2.750301 AACAAGAAGAAACCGTTCGC 57.250 45.000 0.00 0.00 38.90 4.70
2853 2867 2.019951 CACGCAGGCGACGTACTTT 61.020 57.895 21.62 0.00 42.96 2.66
3029 3043 3.689161 TGCACCAAGATAACAAAGATCGG 59.311 43.478 0.00 0.00 0.00 4.18
3067 3081 0.389025 CCCGTCGATCACCATCATCA 59.611 55.000 0.00 0.00 0.00 3.07
3078 3092 1.210234 ACCATCATCATCGACAAGGCA 59.790 47.619 0.00 0.00 0.00 4.75
3085 3099 0.320683 CATCGACAAGGCAGACACCA 60.321 55.000 0.00 0.00 0.00 4.17
3438 3452 8.802856 GTTTTGTTTTGTTTTGTTTTCTTTGCT 58.197 25.926 0.00 0.00 0.00 3.91
3610 3624 7.310052 GCCCTCAATTAGAAAGAAATTTCCTGT 60.310 37.037 14.61 3.93 0.00 4.00
3685 3701 0.668535 GCAAACACACTGGGTTCCTC 59.331 55.000 0.00 0.00 0.00 3.71
3694 3710 1.202651 ACTGGGTTCCTCTTCAACACG 60.203 52.381 0.00 0.00 28.85 4.49
3733 3749 1.247567 TCCTACAGCAAAAGCCTTGC 58.752 50.000 12.14 12.14 45.22 4.01
3752 3768 1.864711 GCTGCGAAAAGGTATATGCGA 59.135 47.619 0.00 0.00 0.00 5.10
3811 4039 1.005097 TCTTTGGCTCATGCATGTCCT 59.995 47.619 27.96 0.00 41.91 3.85
3820 4048 2.509131 TCATGCATGTCCTGTCCCATTA 59.491 45.455 25.43 0.00 0.00 1.90
3832 4060 1.737793 GTCCCATTACAACAAGAGCCG 59.262 52.381 0.00 0.00 0.00 5.52
3833 4061 0.451783 CCCATTACAACAAGAGCCGC 59.548 55.000 0.00 0.00 0.00 6.53
3837 4065 0.863144 TTACAACAAGAGCCGCGTTC 59.137 50.000 4.92 2.05 0.00 3.95
3847 4075 0.240945 AGCCGCGTTCCAATTTCAAG 59.759 50.000 4.92 0.00 0.00 3.02
3849 4077 1.335506 GCCGCGTTCCAATTTCAAGAA 60.336 47.619 4.92 0.00 0.00 2.52
3853 4081 2.288152 GCGTTCCAATTTCAAGAAGGCA 60.288 45.455 10.70 0.00 45.77 4.75
3862 4090 4.734398 TTTCAAGAAGGCACATGTTTGT 57.266 36.364 0.00 0.00 36.15 2.83
3865 4093 5.181690 TCAAGAAGGCACATGTTTGTAAC 57.818 39.130 0.00 0.00 33.76 2.50
3868 4096 4.207165 AGAAGGCACATGTTTGTAACTGT 58.793 39.130 0.00 0.00 33.76 3.55
3875 4103 6.531948 GGCACATGTTTGTAACTGTAACAAAA 59.468 34.615 0.00 0.00 45.56 2.44
3885 4113 5.731957 AACTGTAACAAAACCCTTGTTGT 57.268 34.783 12.02 0.81 42.05 3.32
3955 4184 2.649516 CATGTTGCAATTTCGACACGT 58.350 42.857 0.59 0.00 33.53 4.49
3958 4187 1.263217 GTTGCAATTTCGACACGTCCT 59.737 47.619 0.59 0.00 0.00 3.85
3964 4193 4.347813 CAATTTCGACACGTCCTTTGTTT 58.652 39.130 0.00 0.00 0.00 2.83
3985 4215 4.838152 ATCTGGACGCGCCGCAAT 62.838 61.111 10.75 0.00 40.66 3.56
4016 4246 1.293498 GTGCACATGAGGACGAGGT 59.707 57.895 13.17 0.00 0.00 3.85
4017 4247 1.016130 GTGCACATGAGGACGAGGTG 61.016 60.000 13.17 0.00 0.00 4.00
4018 4248 1.184970 TGCACATGAGGACGAGGTGA 61.185 55.000 0.00 0.00 0.00 4.02
4046 4279 1.069765 CACTCCTTGTCAGCGTGGT 59.930 57.895 0.00 0.00 0.00 4.16
4070 4303 0.747255 CTCACCGGATCCATCGACTT 59.253 55.000 9.46 0.00 0.00 3.01
4078 4311 1.207089 GATCCATCGACTTGGTCACCA 59.793 52.381 0.00 0.00 38.01 4.17
4093 4326 3.541632 GTCACCAAGGAAGAGTTTGACA 58.458 45.455 0.00 0.00 33.59 3.58
4100 4333 2.703007 AGGAAGAGTTTGACAGCAGAGT 59.297 45.455 0.00 0.00 0.00 3.24
4105 4338 3.118261 AGAGTTTGACAGCAGAGTTCCAA 60.118 43.478 0.00 0.00 0.00 3.53
4139 4372 2.488153 CGATGACGATGACCTATAGGCA 59.512 50.000 19.25 17.01 42.66 4.75
4149 4382 0.106708 CCTATAGGCAAAGGCGCTCA 59.893 55.000 7.64 0.00 42.47 4.26
4165 4398 0.034059 CTCAGTCAGGCTCGGTTGTT 59.966 55.000 0.00 0.00 0.00 2.83
4170 4403 1.053424 TCAGGCTCGGTTGTTAGGTT 58.947 50.000 0.00 0.00 0.00 3.50
4182 4415 0.942410 GTTAGGTTGAGACACGCGCA 60.942 55.000 5.73 0.00 0.00 6.09
4219 4452 3.197790 CAATGCAGGGCGACTCCG 61.198 66.667 0.00 0.00 39.16 4.63
4233 4466 1.445410 CTCCGACGGCGATGAACAA 60.445 57.895 15.16 0.00 40.82 2.83
4237 4470 0.456142 CGACGGCGATGAACAAGAGA 60.456 55.000 16.62 0.00 40.82 3.10
4246 4479 3.194542 CGATGAACAAGAGAAGAGGAGGT 59.805 47.826 0.00 0.00 0.00 3.85
4297 4534 0.394565 GAAGACCAGCCATCGCCTAT 59.605 55.000 0.00 0.00 34.57 2.57
4323 4560 2.819154 CGCGTGATGGACATGGCA 60.819 61.111 0.00 0.00 36.16 4.92
4360 4606 1.283793 CACCTTGTTGCGCTCCTTG 59.716 57.895 9.73 0.00 0.00 3.61
4400 4646 0.112995 TGCAAAGGTTGGAGATGGCT 59.887 50.000 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.359848 CGCTATATGCCGGTTCATCC 58.640 55.000 1.90 0.00 38.78 3.51
5 6 0.179056 AGTTGCGCTATATGCCGGTT 60.179 50.000 9.73 0.00 38.78 4.44
55 57 1.021202 CAAGCCCGACAAGACAACAA 58.979 50.000 0.00 0.00 0.00 2.83
94 96 3.327464 TGATCTTGATAATGCCCGGATCA 59.673 43.478 0.73 0.00 36.71 2.92
100 102 3.003689 CGGTGTTGATCTTGATAATGCCC 59.996 47.826 0.00 0.00 0.00 5.36
127 129 4.142816 CGACCATCAGCAAAGTTTAAGGAG 60.143 45.833 0.00 0.00 0.00 3.69
128 130 3.751175 CGACCATCAGCAAAGTTTAAGGA 59.249 43.478 0.00 0.00 0.00 3.36
140 142 2.436646 CACCACCCGACCATCAGC 60.437 66.667 0.00 0.00 0.00 4.26
165 167 1.493311 CGAAGAAGAGCGTGCAACC 59.507 57.895 0.00 0.00 0.00 3.77
174 176 0.731417 CAAGCATGGCCGAAGAAGAG 59.269 55.000 0.00 0.00 0.00 2.85
214 216 4.474303 TCAATGGGCCAGAAATATCCAT 57.526 40.909 13.78 0.00 39.63 3.41
224 226 2.689983 GTTTCAGGTATCAATGGGCCAG 59.310 50.000 13.78 0.00 0.00 4.85
228 230 5.480073 TGAAAAGGTTTCAGGTATCAATGGG 59.520 40.000 0.00 0.00 0.00 4.00
232 234 4.517453 CCGTGAAAAGGTTTCAGGTATCAA 59.483 41.667 17.39 0.00 33.79 2.57
233 235 4.069304 CCGTGAAAAGGTTTCAGGTATCA 58.931 43.478 17.39 0.00 33.79 2.15
254 256 0.110373 GAAACGAACACCATCGCACC 60.110 55.000 0.00 0.00 46.51 5.01
264 266 1.267136 CGAAGTGTTGCGAAACGAACA 60.267 47.619 0.88 0.00 0.00 3.18
310 312 1.002134 CCAACTCCGGGCAGTTCAT 60.002 57.895 0.00 0.00 34.17 2.57
336 338 6.040842 ACAATTGAACAAGAGGCAAGTGTTAT 59.959 34.615 13.59 0.00 45.03 1.89
338 340 4.160252 ACAATTGAACAAGAGGCAAGTGTT 59.840 37.500 13.59 0.12 45.03 3.32
339 341 3.701040 ACAATTGAACAAGAGGCAAGTGT 59.299 39.130 13.59 0.00 43.33 3.55
340 342 4.046462 CACAATTGAACAAGAGGCAAGTG 58.954 43.478 13.59 0.00 41.66 3.16
343 345 3.953612 AGTCACAATTGAACAAGAGGCAA 59.046 39.130 13.59 0.00 31.90 4.52
344 346 3.554934 AGTCACAATTGAACAAGAGGCA 58.445 40.909 13.59 0.00 31.90 4.75
345 347 4.276926 AGAAGTCACAATTGAACAAGAGGC 59.723 41.667 13.59 0.00 31.90 4.70
347 349 7.605691 AGGATAGAAGTCACAATTGAACAAGAG 59.394 37.037 13.59 0.00 31.90 2.85
366 375 7.531317 AGCTCTCCTATTTCTAACAGGATAGA 58.469 38.462 6.47 0.00 37.82 1.98
408 417 8.023128 CCTGTTTACATACTGAATGTCAAAAGG 58.977 37.037 6.80 6.80 46.15 3.11
409 418 8.567948 ACCTGTTTACATACTGAATGTCAAAAG 58.432 33.333 0.00 0.00 46.15 2.27
414 423 7.172532 TGTTGACCTGTTTACATACTGAATGTC 59.827 37.037 0.00 0.00 46.15 3.06
416 425 7.433708 TGTTGACCTGTTTACATACTGAATG 57.566 36.000 0.00 0.00 41.74 2.67
417 426 7.308589 GCTTGTTGACCTGTTTACATACTGAAT 60.309 37.037 0.00 0.00 0.00 2.57
418 427 6.017440 GCTTGTTGACCTGTTTACATACTGAA 60.017 38.462 0.00 0.00 0.00 3.02
420 429 5.334879 GGCTTGTTGACCTGTTTACATACTG 60.335 44.000 0.00 0.00 0.00 2.74
421 430 4.760204 GGCTTGTTGACCTGTTTACATACT 59.240 41.667 0.00 0.00 0.00 2.12
422 431 4.760204 AGGCTTGTTGACCTGTTTACATAC 59.240 41.667 0.00 0.00 34.07 2.39
423 432 4.980573 AGGCTTGTTGACCTGTTTACATA 58.019 39.130 0.00 0.00 34.07 2.29
424 433 3.832527 AGGCTTGTTGACCTGTTTACAT 58.167 40.909 0.00 0.00 34.07 2.29
425 434 3.290948 AGGCTTGTTGACCTGTTTACA 57.709 42.857 0.00 0.00 34.07 2.41
426 435 4.649088 AAAGGCTTGTTGACCTGTTTAC 57.351 40.909 0.00 0.00 36.07 2.01
427 436 5.068067 GGTAAAAGGCTTGTTGACCTGTTTA 59.932 40.000 0.00 0.00 35.12 2.01
428 437 4.142026 GGTAAAAGGCTTGTTGACCTGTTT 60.142 41.667 0.00 0.00 35.12 2.83
430 439 2.956333 GGTAAAAGGCTTGTTGACCTGT 59.044 45.455 0.00 0.00 36.07 4.00
431 440 2.955660 TGGTAAAAGGCTTGTTGACCTG 59.044 45.455 10.10 0.00 36.07 4.00
432 441 2.956333 GTGGTAAAAGGCTTGTTGACCT 59.044 45.455 10.10 0.00 38.14 3.85
433 442 2.691011 TGTGGTAAAAGGCTTGTTGACC 59.309 45.455 0.00 0.86 0.00 4.02
434 443 4.278419 AGATGTGGTAAAAGGCTTGTTGAC 59.722 41.667 0.00 0.00 0.00 3.18
435 444 4.469657 AGATGTGGTAAAAGGCTTGTTGA 58.530 39.130 0.00 0.00 0.00 3.18
436 445 4.853924 AGATGTGGTAAAAGGCTTGTTG 57.146 40.909 0.00 0.00 0.00 3.33
437 446 5.128663 ACAAAGATGTGGTAAAAGGCTTGTT 59.871 36.000 0.00 0.15 38.69 2.83
438 447 4.649218 ACAAAGATGTGGTAAAAGGCTTGT 59.351 37.500 0.00 0.00 38.69 3.16
439 448 5.200368 ACAAAGATGTGGTAAAAGGCTTG 57.800 39.130 0.00 0.00 38.69 4.01
460 469 4.730042 CACATTCAACGTATAAGCATGCAC 59.270 41.667 21.98 8.21 0.00 4.57
465 474 3.615056 CGGTCACATTCAACGTATAAGCA 59.385 43.478 0.00 0.00 0.00 3.91
467 476 3.554324 CCCGGTCACATTCAACGTATAAG 59.446 47.826 0.00 0.00 0.00 1.73
470 479 1.406341 CCCCGGTCACATTCAACGTAT 60.406 52.381 0.00 0.00 0.00 3.06
474 483 2.340328 GCCCCCGGTCACATTCAAC 61.340 63.158 0.00 0.00 0.00 3.18
488 497 2.366590 GGAATTTCATCAAGATGGCCCC 59.633 50.000 9.96 0.00 39.24 5.80
490 499 3.033184 TGGGAATTTCATCAAGATGGCC 58.967 45.455 9.96 0.00 39.24 5.36
493 502 8.611654 AAAAAGTTGGGAATTTCATCAAGATG 57.388 30.769 3.67 3.67 40.09 2.90
506 516 3.006003 GCCGGTCATTAAAAAGTTGGGAA 59.994 43.478 1.90 0.00 0.00 3.97
512 522 3.434940 AGAGGCCGGTCATTAAAAAGT 57.565 42.857 9.71 0.00 0.00 2.66
544 554 7.523293 TGATTCAGGTAAAAGCATTCTTTGA 57.477 32.000 0.00 0.00 41.40 2.69
560 570 5.702670 TGTAAAACAGAGAGCTTGATTCAGG 59.297 40.000 0.00 0.00 0.00 3.86
578 588 6.094325 TCGTCTTTCTTTTTCTGCCTGTAAAA 59.906 34.615 0.00 0.00 0.00 1.52
584 594 3.503748 CCATCGTCTTTCTTTTTCTGCCT 59.496 43.478 0.00 0.00 0.00 4.75
589 599 4.489679 AGCACCATCGTCTTTCTTTTTC 57.510 40.909 0.00 0.00 0.00 2.29
763 774 6.256819 TCTTGTAGAGGAAATGAAGGAGAGA 58.743 40.000 0.00 0.00 0.00 3.10
764 775 6.537453 TCTTGTAGAGGAAATGAAGGAGAG 57.463 41.667 0.00 0.00 0.00 3.20
805 816 6.183361 ACCAGAAGTTCAATTAGACTCTGTGT 60.183 38.462 5.50 0.00 0.00 3.72
807 818 6.042093 TGACCAGAAGTTCAATTAGACTCTGT 59.958 38.462 5.50 0.00 0.00 3.41
816 827 4.090761 TGCTCTGACCAGAAGTTCAATT 57.909 40.909 5.50 0.00 36.94 2.32
936 947 3.926058 AGCGTTACATATGGGGAGTTT 57.074 42.857 7.80 0.00 0.00 2.66
1169 1180 1.603326 TGTACAGCTTCGTGTCGTACA 59.397 47.619 6.81 6.81 39.92 2.90
1314 1325 2.654877 GTGAGACGGGCGGAGAAA 59.345 61.111 0.00 0.00 0.00 2.52
2331 2345 1.144057 GACGATCATGCCGAACCCT 59.856 57.895 12.99 0.00 0.00 4.34
2356 2370 2.429930 CGGGCCAAACACCTCAGA 59.570 61.111 4.39 0.00 0.00 3.27
2367 2381 3.488569 GGGATGATCACCGGGCCA 61.489 66.667 6.32 0.00 0.00 5.36
2443 2457 0.892358 TTCTCGGACTGCACGTAGGT 60.892 55.000 0.00 0.00 0.00 3.08
2727 2741 4.090057 GGGTGCGCGTTCTTCAGC 62.090 66.667 8.43 6.11 0.00 4.26
2728 2742 3.777925 CGGGTGCGCGTTCTTCAG 61.778 66.667 8.43 0.00 0.00 3.02
2790 2804 3.991773 TCTTCTTGTTATCGGTGGTTTCG 59.008 43.478 0.00 0.00 0.00 3.46
2806 2820 0.249573 TCGGCGAACGGTTTCTTCTT 60.250 50.000 7.35 0.00 44.45 2.52
2937 2951 1.741770 GTTGAGCCCGCACAGGTAG 60.742 63.158 0.00 0.00 38.74 3.18
3029 3043 1.135053 GGTAGTTGAGGTCCTTCTCGC 60.135 57.143 0.00 0.00 36.61 5.03
3067 3081 0.320771 GTGGTGTCTGCCTTGTCGAT 60.321 55.000 0.00 0.00 0.00 3.59
3078 3092 2.279918 GCGTTCACGGTGGTGTCT 60.280 61.111 8.50 0.00 44.68 3.41
3268 3282 1.004440 ACTTGAGCTGCCCTTCGAC 60.004 57.895 0.00 0.00 0.00 4.20
3438 3452 3.562141 CCACACCTGTATTTCAACACGAA 59.438 43.478 0.00 0.00 0.00 3.85
3632 3646 7.559335 AATATAGGAACTCATGAGGCATACA 57.441 36.000 26.08 9.88 41.75 2.29
3665 3681 1.101049 AGGAACCCAGTGTGTTTGCG 61.101 55.000 0.00 0.00 0.00 4.85
3685 3701 2.949714 AAATCACGCTCGTGTTGAAG 57.050 45.000 19.95 0.00 45.55 3.02
3694 3710 6.670077 AGGATTTCTAAGAAAATCACGCTC 57.330 37.500 8.24 1.33 44.09 5.03
3733 3749 3.123804 AGTCGCATATACCTTTTCGCAG 58.876 45.455 0.00 0.00 0.00 5.18
3752 3768 1.166531 AAGGCTCTTTTTGCGCGAGT 61.167 50.000 12.10 0.00 0.00 4.18
3757 3773 0.854705 GCAACAAGGCTCTTTTTGCG 59.145 50.000 17.24 0.00 33.80 4.85
3820 4048 2.251642 GGAACGCGGCTCTTGTTGT 61.252 57.895 12.47 0.00 0.00 3.32
3832 4060 2.288152 TGCCTTCTTGAAATTGGAACGC 60.288 45.455 0.00 0.00 0.00 4.84
3833 4061 3.243367 TGTGCCTTCTTGAAATTGGAACG 60.243 43.478 0.00 0.00 0.00 3.95
3837 4065 4.261578 ACATGTGCCTTCTTGAAATTGG 57.738 40.909 0.00 0.00 0.00 3.16
3847 4075 4.568152 ACAGTTACAAACATGTGCCTTC 57.432 40.909 0.00 0.00 0.00 3.46
3849 4077 4.884744 TGTTACAGTTACAAACATGTGCCT 59.115 37.500 0.00 0.00 0.00 4.75
3853 4081 7.036829 GGGTTTTGTTACAGTTACAAACATGT 58.963 34.615 15.73 0.00 43.11 3.21
3862 4090 6.837471 ACAACAAGGGTTTTGTTACAGTTA 57.163 33.333 5.10 0.00 40.30 2.24
3865 4093 8.535690 TTTTTACAACAAGGGTTTTGTTACAG 57.464 30.769 5.10 0.00 40.30 2.74
3906 4135 1.656818 GCAATGGGACGGGACACATG 61.657 60.000 0.00 0.00 33.91 3.21
3907 4136 1.378514 GCAATGGGACGGGACACAT 60.379 57.895 0.00 0.00 35.22 3.21
3955 4184 2.293122 CGTCCAGATTGCAAACAAAGGA 59.707 45.455 1.71 7.33 39.77 3.36
3958 4187 1.599171 CGCGTCCAGATTGCAAACAAA 60.599 47.619 1.71 0.00 39.77 2.83
3983 4213 0.396435 TGCACGTGAGTTCCTCCATT 59.604 50.000 22.23 0.00 46.40 3.16
3985 4215 1.069090 GTGCACGTGAGTTCCTCCA 59.931 57.895 22.23 1.36 46.40 3.86
4002 4232 0.251832 ACCTCACCTCGTCCTCATGT 60.252 55.000 0.00 0.00 0.00 3.21
4014 4244 4.643387 AGTGCCGCCAACCTCACC 62.643 66.667 0.00 0.00 0.00 4.02
4016 4246 4.329545 GGAGTGCCGCCAACCTCA 62.330 66.667 0.00 0.00 0.00 3.86
4017 4247 3.553095 AAGGAGTGCCGCCAACCTC 62.553 63.158 0.00 0.00 39.96 3.85
4018 4248 3.570212 AAGGAGTGCCGCCAACCT 61.570 61.111 0.00 0.00 39.96 3.50
4070 4303 2.507886 TCAAACTCTTCCTTGGTGACCA 59.492 45.455 0.00 0.00 0.00 4.02
4078 4311 3.135530 ACTCTGCTGTCAAACTCTTCCTT 59.864 43.478 0.00 0.00 0.00 3.36
4085 4318 2.945668 GTTGGAACTCTGCTGTCAAACT 59.054 45.455 0.00 0.00 0.00 2.66
4093 4326 2.787994 CCTTCATGTTGGAACTCTGCT 58.212 47.619 0.00 0.00 0.00 4.24
4100 4333 1.623311 TCGAGAGCCTTCATGTTGGAA 59.377 47.619 10.16 0.00 0.00 3.53
4105 4338 1.202348 CGTCATCGAGAGCCTTCATGT 60.202 52.381 0.00 0.00 39.71 3.21
4133 4366 0.462759 GACTGAGCGCCTTTGCCTAT 60.463 55.000 2.29 0.00 34.65 2.57
4134 4367 1.079127 GACTGAGCGCCTTTGCCTA 60.079 57.895 2.29 0.00 34.65 3.93
4139 4372 2.359230 GCCTGACTGAGCGCCTTT 60.359 61.111 2.29 0.00 0.00 3.11
4149 4382 0.608640 CCTAACAACCGAGCCTGACT 59.391 55.000 0.00 0.00 0.00 3.41
4159 4392 1.529865 GCGTGTCTCAACCTAACAACC 59.470 52.381 0.00 0.00 0.00 3.77
4160 4393 1.191647 CGCGTGTCTCAACCTAACAAC 59.808 52.381 0.00 0.00 0.00 3.32
4165 4398 1.080772 CTGCGCGTGTCTCAACCTA 60.081 57.895 8.43 0.00 0.00 3.08
4182 4415 2.270205 CCACCATGGAGCTTCGCT 59.730 61.111 21.47 0.00 40.96 4.93
4193 4426 3.454573 CCTGCATTGCGCCACCAT 61.455 61.111 4.18 0.00 41.33 3.55
4214 4447 2.149803 TTGTTCATCGCCGTCGGAGT 62.150 55.000 17.49 0.00 36.13 3.85
4219 4452 1.656095 CTTCTCTTGTTCATCGCCGTC 59.344 52.381 0.00 0.00 0.00 4.79
4233 4466 0.540830 ACGTGCACCTCCTCTTCTCT 60.541 55.000 12.15 0.00 0.00 3.10
4237 4470 2.743718 CCACGTGCACCTCCTCTT 59.256 61.111 10.91 0.00 0.00 2.85
4266 4503 4.771127 GTCTTCGACCACTGCCAA 57.229 55.556 0.00 0.00 0.00 4.52
4297 4534 2.104928 CATCACGCGCTAGCCTCA 59.895 61.111 5.73 0.00 41.18 3.86
4323 4560 2.022764 GCTTGTTGCAAAGGTTGGTT 57.977 45.000 0.00 0.00 42.31 3.67
4360 4606 1.001181 ACTTGACCCATGTTGCAATGC 59.999 47.619 0.59 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.