Multiple sequence alignment - TraesCS7D01G124500

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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 TraesCS7D01G124500 chr7D 100.000 3563 0 0 1 3563 78114486 78118048 0.000000e+00 6580.0
1 TraesCS7D01G124500 chr7D 88.034 1546 179 2 1006 2551 477641653 477643192 0.000000e+00 1825.0
2 TraesCS7D01G124500 chr7A 95.176 2695 90 15 1 2665 81547215 81549899 0.000000e+00 4220.0
3 TraesCS7D01G124500 chr7A 87.451 1530 167 10 1022 2550 518658792 518657287 0.000000e+00 1738.0
4 TraesCS7D01G124500 chr7A 90.214 562 28 12 2683 3241 81549883 81550420 0.000000e+00 708.0
5 TraesCS7D01G124500 chr7A 88.034 234 20 3 3330 3563 81552318 81552543 1.630000e-68 270.0
6 TraesCS7D01G124500 chr7A 84.000 150 24 0 7 156 537879509 537879658 1.030000e-30 145.0
7 TraesCS7D01G124500 chr7A 91.000 100 9 0 3243 3342 81550526 81550625 6.200000e-28 135.0
8 TraesCS7D01G124500 chr7B 86.985 1552 188 10 1007 2551 501965667 501967211 0.000000e+00 1735.0
9 TraesCS7D01G124500 chr7B 95.548 876 34 2 1792 2665 25340416 25341288 0.000000e+00 1397.0
10 TraesCS7D01G124500 chr7B 96.871 799 25 0 1005 1803 25339166 25339964 0.000000e+00 1338.0
11 TraesCS7D01G124500 chr7B 77.394 1504 295 42 1071 2554 502316792 502318270 0.000000e+00 852.0
12 TraesCS7D01G124500 chr7B 94.615 130 6 1 866 995 25338982 25339110 2.170000e-47 200.0
13 TraesCS7D01G124500 chr7B 92.143 140 11 0 669 808 25338834 25338973 7.800000e-47 198.0
14 TraesCS7D01G124500 chr7B 86.842 76 10 0 3428 3503 666014498 666014573 6.340000e-13 86.1
15 TraesCS7D01G124500 chr3A 85.756 1383 182 12 1175 2551 33137240 33138613 0.000000e+00 1448.0
16 TraesCS7D01G124500 chr2D 81.254 1499 245 24 1085 2550 73417409 73415914 0.000000e+00 1179.0
17 TraesCS7D01G124500 chr2D 93.548 62 4 0 3442 3503 607417926 607417865 3.790000e-15 93.5
18 TraesCS7D01G124500 chr2A 81.254 1499 242 28 1085 2550 72814090 72812598 0.000000e+00 1175.0
19 TraesCS7D01G124500 chr2B 80.978 1493 254 21 1085 2550 111081870 111080381 0.000000e+00 1157.0
20 TraesCS7D01G124500 chr3B 79.058 191 35 3 236 423 776354361 776354549 3.730000e-25 126.0
21 TraesCS7D01G124500 chr4A 89.362 94 10 0 72 165 499130412 499130505 6.250000e-23 119.0
22 TraesCS7D01G124500 chr5A 81.295 139 24 2 33 169 245435060 245434922 1.050000e-20 111.0
23 TraesCS7D01G124500 chr5D 79.104 134 24 2 33 165 205566346 205566216 4.900000e-14 89.8


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 TraesCS7D01G124500 chr7D 78114486 78118048 3562 False 6580.00 6580 100.00000 1 3563 1 chr7D.!!$F1 3562
1 TraesCS7D01G124500 chr7D 477641653 477643192 1539 False 1825.00 1825 88.03400 1006 2551 1 chr7D.!!$F2 1545
2 TraesCS7D01G124500 chr7A 518657287 518658792 1505 True 1738.00 1738 87.45100 1022 2550 1 chr7A.!!$R1 1528
3 TraesCS7D01G124500 chr7A 81547215 81552543 5328 False 1333.25 4220 91.10600 1 3563 4 chr7A.!!$F2 3562
4 TraesCS7D01G124500 chr7B 501965667 501967211 1544 False 1735.00 1735 86.98500 1007 2551 1 chr7B.!!$F1 1544
5 TraesCS7D01G124500 chr7B 502316792 502318270 1478 False 852.00 852 77.39400 1071 2554 1 chr7B.!!$F2 1483
6 TraesCS7D01G124500 chr7B 25338834 25341288 2454 False 783.25 1397 94.79425 669 2665 4 chr7B.!!$F4 1996
7 TraesCS7D01G124500 chr3A 33137240 33138613 1373 False 1448.00 1448 85.75600 1175 2551 1 chr3A.!!$F1 1376
8 TraesCS7D01G124500 chr2D 73415914 73417409 1495 True 1179.00 1179 81.25400 1085 2550 1 chr2D.!!$R1 1465
9 TraesCS7D01G124500 chr2A 72812598 72814090 1492 True 1175.00 1175 81.25400 1085 2550 1 chr2A.!!$R1 1465
10 TraesCS7D01G124500 chr2B 111080381 111081870 1489 True 1157.00 1157 80.97800 1085 2550 1 chr2B.!!$R1 1465

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
373 393 0.517316 GTTGTGCCATCTTCGTGGTC 59.483 55.0 0.0 0.0 41.47 4.02 F
1784 1900 0.037975 TTCACCGTCCTAAAGTCCGC 60.038 55.0 0.0 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2753 0.107456 GTCCATGATCATCAGCCCGT 59.893 55.0 4.86 0.0 0.0 5.28 R
3035 3633 0.036448 TGGGTAAAATCGTGCCGGAA 59.964 50.0 5.05 0.0 0.0 4.30 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
31 32 1.915489 ACCAATCCATCACCACTAGCA 59.085 47.619 0.00 0.00 0.00 3.49
32 33 2.308570 ACCAATCCATCACCACTAGCAA 59.691 45.455 0.00 0.00 0.00 3.91
53 54 5.562917 CAACCACAACATCATATTCTCACG 58.437 41.667 0.00 0.00 0.00 4.35
59 60 6.037500 CACAACATCATATTCTCACGGATTGT 59.962 38.462 0.00 0.00 0.00 2.71
63 64 4.371786 TCATATTCTCACGGATTGTCAGC 58.628 43.478 0.00 0.00 0.00 4.26
108 109 7.550712 TCACATATCTACTCATATCACATGCC 58.449 38.462 0.00 0.00 0.00 4.40
126 127 4.737855 TGCCCACAGATCTAGTTAGAAC 57.262 45.455 0.00 0.00 35.69 3.01
128 129 3.380637 GCCCACAGATCTAGTTAGAACGA 59.619 47.826 0.00 0.00 35.69 3.85
129 130 4.498345 GCCCACAGATCTAGTTAGAACGAG 60.498 50.000 0.00 0.00 35.69 4.18
170 190 3.682858 CGAACTTACAACCATCGTGGAAT 59.317 43.478 10.46 0.00 40.96 3.01
201 221 0.528684 GACGCGCCTCTTATCTGCTT 60.529 55.000 5.73 0.00 0.00 3.91
232 252 3.499737 CGCATGGAACGGTGAGCC 61.500 66.667 0.00 0.00 0.00 4.70
296 316 6.378848 GGTGAGGGTGACTATATTAGGAGATC 59.621 46.154 0.00 0.00 0.00 2.75
312 332 1.202734 AGATCGATTCGACGGGAGGTA 60.203 52.381 11.56 0.00 39.18 3.08
330 350 0.693622 TAACCCCAATTCGTCCTGCA 59.306 50.000 0.00 0.00 0.00 4.41
350 370 6.012658 TGCAAAATTTTTAGAGACTCGCAT 57.987 33.333 0.00 0.00 0.00 4.73
373 393 0.517316 GTTGTGCCATCTTCGTGGTC 59.483 55.000 0.00 0.00 41.47 4.02
385 405 2.887568 GTGGTCGCATGAGCTCGG 60.888 66.667 9.64 4.96 43.09 4.63
412 432 4.883354 CCCTTCCCCTGCATCGCC 62.883 72.222 0.00 0.00 0.00 5.54
453 473 2.442084 ACGATTCGGACGTTCTTGC 58.558 52.632 11.29 0.00 41.18 4.01
535 564 1.070038 GCCATTTTTGCATCACGTGG 58.930 50.000 17.00 0.92 0.00 4.94
586 615 5.403897 AACACGTCACTAATGTTTCACTG 57.596 39.130 0.00 0.00 32.70 3.66
671 702 3.238108 AGAATGGACGACAAGCTAGTG 57.762 47.619 0.00 0.00 0.00 2.74
816 847 2.802816 GTCGATTATCACCACATCAGCC 59.197 50.000 0.00 0.00 0.00 4.85
817 848 2.146342 CGATTATCACCACATCAGCCC 58.854 52.381 0.00 0.00 0.00 5.19
944 975 4.097361 GGAAGGTGGAGCCGGACC 62.097 72.222 5.05 8.64 43.70 4.46
1147 1229 0.038251 CAAGCAGCTCCTGTACACGA 60.038 55.000 0.00 0.00 33.43 4.35
1338 1420 3.066814 GGGCACGACTACGAGGGT 61.067 66.667 0.00 0.00 42.66 4.34
1350 1432 4.950479 GAGGGTCTCTCGTACCGA 57.050 61.111 0.00 0.00 37.93 4.69
1652 1752 2.031163 GCTCGTGGACAAGCAGGT 59.969 61.111 0.00 0.00 38.42 4.00
1784 1900 0.037975 TTCACCGTCCTAAAGTCCGC 60.038 55.000 0.00 0.00 0.00 5.54
1872 2451 4.760047 ATCACGGTGCGCCTCCAC 62.760 66.667 15.69 3.45 35.00 4.02
2075 2663 2.285368 CACCTCCAGCACCCCCTA 60.285 66.667 0.00 0.00 0.00 3.53
2469 3066 4.705996 GGCGAGAAGTACTACGGC 57.294 61.111 20.55 20.55 42.98 5.68
2516 3113 0.977395 AAGGCCATAGCGGATCCTAC 59.023 55.000 10.75 1.43 41.24 3.18
2563 3160 0.107508 CCCACCATTCAGCGAGTGAT 60.108 55.000 0.00 0.00 34.17 3.06
2572 3169 1.474478 TCAGCGAGTGATGAGGAAGAC 59.526 52.381 0.00 0.00 35.14 3.01
2575 3172 0.453793 CGAGTGATGAGGAAGACGCT 59.546 55.000 0.00 0.00 0.00 5.07
2630 3227 0.250295 TCGCTTGACCTTGGAGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
2654 3251 4.916983 TGGCAGGTGAATATTACATTGC 57.083 40.909 13.02 13.02 33.37 3.56
2656 3253 3.315191 GGCAGGTGAATATTACATTGCGT 59.685 43.478 13.98 0.00 34.22 5.24
2657 3254 4.202010 GGCAGGTGAATATTACATTGCGTT 60.202 41.667 13.98 0.00 34.22 4.84
2658 3255 4.734854 GCAGGTGAATATTACATTGCGTTG 59.265 41.667 0.00 0.00 0.00 4.10
2659 3256 5.273170 CAGGTGAATATTACATTGCGTTGG 58.727 41.667 0.00 0.00 0.00 3.77
2663 3260 6.090129 GTGAATATTACATTGCGTTGGTGTT 58.910 36.000 0.00 0.00 0.00 3.32
2664 3261 6.250527 GTGAATATTACATTGCGTTGGTGTTC 59.749 38.462 0.00 0.00 0.00 3.18
2666 3263 4.846779 ATTACATTGCGTTGGTGTTCTT 57.153 36.364 0.00 0.00 0.00 2.52
2667 3264 4.640789 TTACATTGCGTTGGTGTTCTTT 57.359 36.364 0.00 0.00 0.00 2.52
2668 3265 3.518634 ACATTGCGTTGGTGTTCTTTT 57.481 38.095 0.00 0.00 0.00 2.27
2669 3266 3.855858 ACATTGCGTTGGTGTTCTTTTT 58.144 36.364 0.00 0.00 0.00 1.94
2748 3345 6.583050 TCGAACGTTGACAAAAGTTTGAATTT 59.417 30.769 5.00 0.00 41.97 1.82
2777 3374 0.109532 TGGGCTCCAATTCACGTTGA 59.890 50.000 0.00 0.00 0.00 3.18
2781 3378 3.306019 GGGCTCCAATTCACGTTGAAAAT 60.306 43.478 4.87 0.00 40.12 1.82
2799 3396 5.841237 TGAAAATTTTCCCTGGTATGTTGGA 59.159 36.000 24.51 1.77 36.36 3.53
2934 3532 7.263100 TGTTATATTCATGATGTGTTGGAGC 57.737 36.000 0.00 0.00 0.00 4.70
2941 3539 8.701908 ATTCATGATGTGTTGGAGCTATTTAT 57.298 30.769 0.00 0.00 0.00 1.40
2978 3576 3.974222 GCATAAGCTTTGCCCCATC 57.026 52.632 17.56 0.00 37.91 3.51
2999 3597 7.946776 CCCATCCATTAATTAAGAGAGGACAAT 59.053 37.037 11.45 0.00 0.00 2.71
3019 3617 5.068987 ACAATAGAGTTTGGCACACACATTT 59.931 36.000 6.55 0.00 42.21 2.32
3027 3625 7.145323 AGTTTGGCACACACATTTCTTATTAC 58.855 34.615 6.55 0.00 42.21 1.89
3031 3629 6.937465 TGGCACACACATTTCTTATTACACTA 59.063 34.615 0.00 0.00 0.00 2.74
3032 3630 7.094975 TGGCACACACATTTCTTATTACACTAC 60.095 37.037 0.00 0.00 0.00 2.73
3033 3631 7.119262 GGCACACACATTTCTTATTACACTACT 59.881 37.037 0.00 0.00 0.00 2.57
3034 3632 8.169268 GCACACACATTTCTTATTACACTACTC 58.831 37.037 0.00 0.00 0.00 2.59
3035 3633 9.424319 CACACACATTTCTTATTACACTACTCT 57.576 33.333 0.00 0.00 0.00 3.24
3036 3634 9.998106 ACACACATTTCTTATTACACTACTCTT 57.002 29.630 0.00 0.00 0.00 2.85
3038 3636 9.654663 ACACATTTCTTATTACACTACTCTTCC 57.345 33.333 0.00 0.00 0.00 3.46
3039 3637 8.808529 CACATTTCTTATTACACTACTCTTCCG 58.191 37.037 0.00 0.00 0.00 4.30
3040 3638 7.980099 ACATTTCTTATTACACTACTCTTCCGG 59.020 37.037 0.00 0.00 0.00 5.14
3041 3639 5.511234 TCTTATTACACTACTCTTCCGGC 57.489 43.478 0.00 0.00 0.00 6.13
3042 3640 4.951715 TCTTATTACACTACTCTTCCGGCA 59.048 41.667 0.00 0.00 0.00 5.69
3043 3641 3.521947 ATTACACTACTCTTCCGGCAC 57.478 47.619 0.00 0.00 0.00 5.01
3075 3673 4.708386 TTTTCCGCCCGCCGTGAT 62.708 61.111 0.00 0.00 34.38 3.06
3081 3679 3.585990 GCCCGCCGTGATCCAATG 61.586 66.667 0.00 0.00 0.00 2.82
3100 3699 3.243359 TGTTTTGCCTCCCTCTTGATT 57.757 42.857 0.00 0.00 0.00 2.57
3107 3706 2.484594 GCCTCCCTCTTGATTGAGCTAC 60.485 54.545 0.00 0.00 33.02 3.58
3147 3747 9.498176 TGATATATTTGAGTCAATCATGAGGTG 57.502 33.333 6.36 2.00 37.89 4.00
3149 3749 9.857656 ATATATTTGAGTCAATCATGAGGTGTT 57.142 29.630 6.36 0.00 37.89 3.32
3151 3751 4.897509 TGAGTCAATCATGAGGTGTTCT 57.102 40.909 0.09 5.65 35.88 3.01
3152 3752 5.233083 TGAGTCAATCATGAGGTGTTCTT 57.767 39.130 0.09 0.00 35.88 2.52
3153 3753 5.624159 TGAGTCAATCATGAGGTGTTCTTT 58.376 37.500 0.09 0.00 35.88 2.52
3154 3754 5.471116 TGAGTCAATCATGAGGTGTTCTTTG 59.529 40.000 0.09 0.00 35.88 2.77
3155 3755 4.217118 AGTCAATCATGAGGTGTTCTTTGC 59.783 41.667 0.09 0.00 35.88 3.68
3156 3756 4.022935 GTCAATCATGAGGTGTTCTTTGCA 60.023 41.667 0.09 0.00 35.88 4.08
3168 3768 6.039616 GGTGTTCTTTGCACAAACATTTAGA 58.960 36.000 10.03 0.00 38.51 2.10
3219 3819 7.982224 TCATCTCTTCTTTGAATGCATTGTAG 58.018 34.615 18.59 10.78 0.00 2.74
3221 3821 5.124457 TCTCTTCTTTGAATGCATTGTAGCC 59.876 40.000 18.59 2.04 0.00 3.93
3231 3831 2.754552 TGCATTGTAGCCAGATTGGTTC 59.245 45.455 0.00 0.00 40.46 3.62
3263 3967 7.027161 GGGTGTTTGTTACAAATATAGCACAG 58.973 38.462 21.42 0.00 38.80 3.66
3266 3970 8.286800 GTGTTTGTTACAAATATAGCACAGACA 58.713 33.333 13.84 0.63 38.80 3.41
3272 3976 8.450964 GTTACAAATATAGCACAGACACAACAT 58.549 33.333 0.00 0.00 0.00 2.71
3273 3977 7.076842 ACAAATATAGCACAGACACAACATC 57.923 36.000 0.00 0.00 0.00 3.06
3277 3981 0.512952 GCACAGACACAACATCGTCC 59.487 55.000 0.00 0.00 32.33 4.79
3307 4011 5.243981 CACAAGAGATAATAGGCATCCCAG 58.756 45.833 0.00 0.00 0.00 4.45
3312 4016 2.936919 TAATAGGCATCCCAGCACAG 57.063 50.000 0.00 0.00 35.83 3.66
3351 5760 7.117667 CCCCAAAGAAAAAGAAAATACAATCCG 59.882 37.037 0.00 0.00 0.00 4.18
3352 5761 7.360017 CCCAAAGAAAAAGAAAATACAATCCGC 60.360 37.037 0.00 0.00 0.00 5.54
3353 5762 7.384932 CCAAAGAAAAAGAAAATACAATCCGCT 59.615 33.333 0.00 0.00 0.00 5.52
3354 5763 8.427774 CAAAGAAAAAGAAAATACAATCCGCTC 58.572 33.333 0.00 0.00 0.00 5.03
3355 5764 6.621613 AGAAAAAGAAAATACAATCCGCTCC 58.378 36.000 0.00 0.00 0.00 4.70
3356 5765 4.983671 AAAGAAAATACAATCCGCTCCC 57.016 40.909 0.00 0.00 0.00 4.30
3357 5766 3.933861 AGAAAATACAATCCGCTCCCT 57.066 42.857 0.00 0.00 0.00 4.20
3358 5767 3.545703 AGAAAATACAATCCGCTCCCTG 58.454 45.455 0.00 0.00 0.00 4.45
3359 5768 2.348411 AAATACAATCCGCTCCCTGG 57.652 50.000 0.00 0.00 0.00 4.45
3360 5769 0.474184 AATACAATCCGCTCCCTGGG 59.526 55.000 6.33 6.33 0.00 4.45
3361 5770 0.694444 ATACAATCCGCTCCCTGGGT 60.694 55.000 13.56 0.00 0.00 4.51
3371 5780 4.489771 CCCTGGGTGCCTTAGCGG 62.490 72.222 3.97 0.00 44.31 5.52
3400 5809 0.179200 CAACACCAATCGCTAACCGC 60.179 55.000 0.00 0.00 36.73 5.68
3402 5811 1.743623 CACCAATCGCTAACCGCCA 60.744 57.895 0.00 0.00 36.73 5.69
3404 5813 0.393808 ACCAATCGCTAACCGCCATT 60.394 50.000 0.00 0.00 36.73 3.16
3410 5819 1.632046 CGCTAACCGCCATTGTCGTT 61.632 55.000 0.00 0.00 34.21 3.85
3413 5822 1.127951 CTAACCGCCATTGTCGTTGAC 59.872 52.381 0.00 0.00 0.00 3.18
3415 5824 1.206578 CCGCCATTGTCGTTGACAC 59.793 57.895 0.00 0.00 42.60 3.67
3435 5844 4.269844 ACACGAACAACAATGAAAAATGCC 59.730 37.500 0.00 0.00 0.00 4.40
3448 5857 1.815817 AAATGCCGGAAGCCACCAAC 61.816 55.000 5.05 0.00 42.71 3.77
3463 5872 1.376037 CAACTCCTGAACCGAGGGC 60.376 63.158 0.00 0.00 33.41 5.19
3464 5873 1.841556 AACTCCTGAACCGAGGGCA 60.842 57.895 0.00 0.00 33.41 5.36
3470 5879 2.351276 GAACCGAGGGCACACCAT 59.649 61.111 0.00 0.00 43.89 3.55
3505 5914 5.484958 GCTTTCTGAGTCGAATATGAAACG 58.515 41.667 8.14 6.80 0.00 3.60
3507 5916 3.444916 TCTGAGTCGAATATGAAACGCC 58.555 45.455 0.00 0.00 0.00 5.68
3523 5932 1.803289 GCCTTCATTTGACCGGAGC 59.197 57.895 9.46 0.00 0.00 4.70
3525 5934 1.369091 CCTTCATTTGACCGGAGCCG 61.369 60.000 9.46 1.06 39.44 5.52
3529 5938 1.146263 ATTTGACCGGAGCCGATCC 59.854 57.895 9.46 0.00 45.64 3.36
3530 5939 2.325393 ATTTGACCGGAGCCGATCCC 62.325 60.000 9.46 0.00 46.50 3.85
3548 5957 0.038455 CCGTGGGGGTTGTGGAAATA 59.962 55.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.635765 CCGTGAGAATATGATGTTGTGGTT 59.364 41.667 0.00 0.00 0.00 3.67
32 33 4.081142 TCCGTGAGAATATGATGTTGTGGT 60.081 41.667 0.00 0.00 0.00 4.16
53 54 1.133976 AGCATGGTAGGCTGACAATCC 60.134 52.381 0.00 0.00 40.80 3.01
59 60 0.830648 GTGGTAGCATGGTAGGCTGA 59.169 55.000 4.51 0.00 42.62 4.26
63 64 1.597742 GCATGTGGTAGCATGGTAGG 58.402 55.000 4.51 0.00 44.58 3.18
108 109 5.821516 ACTCGTTCTAACTAGATCTGTGG 57.178 43.478 5.18 0.00 31.40 4.17
126 127 1.487142 TCACTCCCTCCTCTCTACTCG 59.513 57.143 0.00 0.00 0.00 4.18
128 129 2.105821 CGATCACTCCCTCCTCTCTACT 59.894 54.545 0.00 0.00 0.00 2.57
129 130 2.105134 TCGATCACTCCCTCCTCTCTAC 59.895 54.545 0.00 0.00 0.00 2.59
170 190 2.758089 GCGCGTCTTCTCCGTCCTA 61.758 63.158 8.43 0.00 0.00 2.94
242 262 0.898326 AAACTCCCGCCACAATTCCC 60.898 55.000 0.00 0.00 0.00 3.97
296 316 0.248784 GGTTACCTCCCGTCGAATCG 60.249 60.000 0.00 0.00 0.00 3.34
312 332 0.178975 TTGCAGGACGAATTGGGGTT 60.179 50.000 0.00 0.00 0.00 4.11
330 350 6.431234 ACCTCATGCGAGTCTCTAAAAATTTT 59.569 34.615 0.00 0.00 37.59 1.82
395 415 4.883354 GGCGATGCAGGGGAAGGG 62.883 72.222 0.00 0.00 0.00 3.95
412 432 2.124507 TTTCCTCCCAACCAGGCTCG 62.125 60.000 0.00 0.00 35.39 5.03
444 464 2.147387 ACCTCCCAGGCAAGAACGT 61.147 57.895 0.00 0.00 39.63 3.99
446 466 0.178990 AACACCTCCCAGGCAAGAAC 60.179 55.000 0.00 0.00 39.63 3.01
450 470 2.593026 CTTAAAACACCTCCCAGGCAA 58.407 47.619 0.00 0.00 39.63 4.52
453 473 2.971901 ACCTTAAAACACCTCCCAGG 57.028 50.000 0.00 0.00 42.49 4.45
535 564 1.754234 CATACAGCCCAACCAGCCC 60.754 63.158 0.00 0.00 0.00 5.19
557 586 3.314080 ACATTAGTGACGTGTTTGGTTGG 59.686 43.478 0.00 0.00 0.00 3.77
762 793 7.224753 CGCAAAGTGTAATGTAATCTAGTGGAT 59.775 37.037 0.00 0.00 35.97 3.41
816 847 0.252927 GGGAGGATCAGGATAGGGGG 60.253 65.000 0.00 0.00 36.25 5.40
817 848 0.493639 TGGGAGGATCAGGATAGGGG 59.506 60.000 0.00 0.00 36.25 4.79
944 975 2.783135 ACCTCGCTATATTTGCATGGG 58.217 47.619 0.00 0.00 0.00 4.00
1698 1801 3.390521 ACGATGCCGAAGCTCCCA 61.391 61.111 0.00 0.00 40.80 4.37
1762 1878 2.685100 GGACTTTAGGACGGTGAACAG 58.315 52.381 0.00 0.00 0.00 3.16
1809 2388 1.907739 GACCTGCTGCCATCTGGTA 59.092 57.895 0.00 0.00 36.16 3.25
1872 2451 1.576421 GAAGCGAGCCACCTGTTTG 59.424 57.895 0.00 0.00 0.00 2.93
2075 2663 4.335647 CGGAGGTGGCCTTGCTGT 62.336 66.667 3.32 0.00 31.76 4.40
2162 2753 0.107456 GTCCATGATCATCAGCCCGT 59.893 55.000 4.86 0.00 0.00 5.28
2301 2895 1.228583 TCTGAGCCACCTCGTCTGT 60.229 57.895 0.00 0.00 41.13 3.41
2469 3066 0.179134 CGAGCCTCTGGAAGTTACCG 60.179 60.000 0.00 0.00 33.76 4.02
2516 3113 1.467713 GCTCGTTCCTGAAGTAGTCGG 60.468 57.143 0.00 0.00 0.00 4.79
2563 3160 2.868196 CGACGAGCGTCTTCCTCA 59.132 61.111 19.23 0.00 42.54 3.86
2608 3205 2.554032 CAACTCCAAGGTCAAGCGATTT 59.446 45.455 0.00 0.00 0.00 2.17
2609 3206 2.154462 CAACTCCAAGGTCAAGCGATT 58.846 47.619 0.00 0.00 0.00 3.34
2610 3207 1.611673 CCAACTCCAAGGTCAAGCGAT 60.612 52.381 0.00 0.00 0.00 4.58
2619 3216 0.682209 CTGCCATCCCAACTCCAAGG 60.682 60.000 0.00 0.00 0.00 3.61
2630 3227 5.565439 GCAATGTAATATTCACCTGCCATCC 60.565 44.000 0.00 0.00 0.00 3.51
2671 3268 0.665835 ACGCAATGTCCTCGCAAAAA 59.334 45.000 0.00 0.00 0.00 1.94
2672 3269 0.665835 AACGCAATGTCCTCGCAAAA 59.334 45.000 0.00 0.00 0.00 2.44
2673 3270 0.040514 CAACGCAATGTCCTCGCAAA 60.041 50.000 0.00 0.00 0.00 3.68
2674 3271 1.573932 CAACGCAATGTCCTCGCAA 59.426 52.632 0.00 0.00 0.00 4.85
2675 3272 2.324330 CCAACGCAATGTCCTCGCA 61.324 57.895 0.00 0.00 0.00 5.10
2676 3273 2.325082 ACCAACGCAATGTCCTCGC 61.325 57.895 0.00 0.00 0.00 5.03
2677 3274 1.227999 ACACCAACGCAATGTCCTCG 61.228 55.000 0.00 0.00 0.00 4.63
2678 3275 0.951558 AACACCAACGCAATGTCCTC 59.048 50.000 0.00 0.00 0.00 3.71
2679 3276 0.951558 GAACACCAACGCAATGTCCT 59.048 50.000 0.00 0.00 0.00 3.85
2680 3277 0.665835 TGAACACCAACGCAATGTCC 59.334 50.000 0.00 0.00 0.00 4.02
2681 3278 2.483583 TTGAACACCAACGCAATGTC 57.516 45.000 0.00 0.00 0.00 3.06
2682 3279 2.741612 CATTGAACACCAACGCAATGT 58.258 42.857 0.00 0.00 41.44 2.71
2684 3281 4.782019 ATACATTGAACACCAACGCAAT 57.218 36.364 0.00 0.00 37.63 3.56
2685 3282 4.757657 ACTATACATTGAACACCAACGCAA 59.242 37.500 0.00 0.00 37.63 4.85
2686 3283 4.320023 ACTATACATTGAACACCAACGCA 58.680 39.130 0.00 0.00 37.63 5.24
2687 3284 4.939509 ACTATACATTGAACACCAACGC 57.060 40.909 0.00 0.00 37.63 4.84
2688 3285 5.410132 TGGAACTATACATTGAACACCAACG 59.590 40.000 0.00 0.00 37.63 4.10
2748 3345 1.988293 TTGGAGCCCAATTCGAACAA 58.012 45.000 0.00 0.00 38.75 2.83
2777 3374 5.843969 ACTCCAACATACCAGGGAAAATTTT 59.156 36.000 2.28 2.28 0.00 1.82
2781 3378 3.396276 TGACTCCAACATACCAGGGAAAA 59.604 43.478 0.00 0.00 0.00 2.29
2816 3413 6.652481 GCAACACTGCCAATATGTATCTCTAT 59.348 38.462 0.00 0.00 43.26 1.98
2817 3414 5.991606 GCAACACTGCCAATATGTATCTCTA 59.008 40.000 0.00 0.00 43.26 2.43
2818 3415 4.818546 GCAACACTGCCAATATGTATCTCT 59.181 41.667 0.00 0.00 43.26 3.10
2819 3416 5.100751 GCAACACTGCCAATATGTATCTC 57.899 43.478 0.00 0.00 43.26 2.75
2999 3597 4.460263 AGAAATGTGTGTGCCAAACTCTA 58.540 39.130 0.00 0.00 0.00 2.43
3019 3617 4.951715 TGCCGGAAGAGTAGTGTAATAAGA 59.048 41.667 5.05 0.00 0.00 2.10
3027 3625 0.456221 ATCGTGCCGGAAGAGTAGTG 59.544 55.000 5.05 0.00 0.00 2.74
3031 3629 2.344025 GTAAAATCGTGCCGGAAGAGT 58.656 47.619 5.05 0.00 0.00 3.24
3032 3630 1.664151 GGTAAAATCGTGCCGGAAGAG 59.336 52.381 5.05 0.00 0.00 2.85
3033 3631 1.676615 GGGTAAAATCGTGCCGGAAGA 60.677 52.381 5.05 0.00 0.00 2.87
3034 3632 0.730840 GGGTAAAATCGTGCCGGAAG 59.269 55.000 5.05 0.00 0.00 3.46
3035 3633 0.036448 TGGGTAAAATCGTGCCGGAA 59.964 50.000 5.05 0.00 0.00 4.30
3036 3634 0.253610 ATGGGTAAAATCGTGCCGGA 59.746 50.000 5.05 0.00 0.00 5.14
3037 3635 1.099689 AATGGGTAAAATCGTGCCGG 58.900 50.000 0.00 0.00 0.00 6.13
3038 3636 2.931512 AAATGGGTAAAATCGTGCCG 57.068 45.000 0.00 0.00 0.00 5.69
3069 3667 1.545582 AGGCAAAACATTGGATCACGG 59.454 47.619 0.00 0.00 0.00 4.94
3075 3673 1.428912 AGAGGGAGGCAAAACATTGGA 59.571 47.619 0.00 0.00 0.00 3.53
3079 3677 2.978156 TCAAGAGGGAGGCAAAACAT 57.022 45.000 0.00 0.00 0.00 2.71
3081 3679 3.157087 TCAATCAAGAGGGAGGCAAAAC 58.843 45.455 0.00 0.00 0.00 2.43
3100 3699 3.067320 CACCTTCGATCATCTGTAGCTCA 59.933 47.826 0.00 0.00 0.00 4.26
3107 3706 8.992835 TCAAATATATCACCTTCGATCATCTG 57.007 34.615 0.00 0.00 0.00 2.90
3147 3747 6.751888 ACACTCTAAATGTTTGTGCAAAGAAC 59.248 34.615 0.00 0.00 32.49 3.01
3149 3749 6.127758 ACACACTCTAAATGTTTGTGCAAAGA 60.128 34.615 0.00 0.00 41.06 2.52
3151 3751 5.960113 ACACACTCTAAATGTTTGTGCAAA 58.040 33.333 0.00 0.00 41.06 3.68
3152 3752 5.574891 ACACACTCTAAATGTTTGTGCAA 57.425 34.783 0.00 0.00 41.06 4.08
3153 3753 5.124617 TGAACACACTCTAAATGTTTGTGCA 59.875 36.000 0.00 0.00 41.06 4.57
3154 3754 5.577835 TGAACACACTCTAAATGTTTGTGC 58.422 37.500 0.00 0.00 41.06 4.57
3155 3755 7.306167 GCAATGAACACACTCTAAATGTTTGTG 60.306 37.037 0.00 0.00 42.68 3.33
3156 3756 6.697019 GCAATGAACACACTCTAAATGTTTGT 59.303 34.615 0.00 0.00 36.70 2.83
3168 3768 4.065088 ACTGATAACGCAATGAACACACT 58.935 39.130 0.00 0.00 0.00 3.55
3207 3807 3.382546 ACCAATCTGGCTACAATGCATTC 59.617 43.478 9.53 0.00 42.67 2.67
3219 3819 1.452108 CCCTCCGAACCAATCTGGC 60.452 63.158 0.00 0.00 42.67 4.85
3221 3821 1.224592 CCCCCTCCGAACCAATCTG 59.775 63.158 0.00 0.00 0.00 2.90
3241 3841 8.286800 GTGTCTGTGCTATATTTGTAACAAACA 58.713 33.333 0.00 0.00 35.88 2.83
3243 3843 8.384607 TGTGTCTGTGCTATATTTGTAACAAA 57.615 30.769 0.00 0.00 0.00 2.83
3244 3844 7.971183 TGTGTCTGTGCTATATTTGTAACAA 57.029 32.000 0.00 0.00 0.00 2.83
3263 3967 1.798813 GGTTCTGGACGATGTTGTGTC 59.201 52.381 0.00 0.00 0.00 3.67
3266 3970 0.762418 TGGGTTCTGGACGATGTTGT 59.238 50.000 0.00 0.00 0.00 3.32
3272 3976 0.679505 CTCTTGTGGGTTCTGGACGA 59.320 55.000 0.00 0.00 0.00 4.20
3273 3977 0.679505 TCTCTTGTGGGTTCTGGACG 59.320 55.000 0.00 0.00 0.00 4.79
3277 3981 5.059833 GCCTATTATCTCTTGTGGGTTCTG 58.940 45.833 0.00 0.00 0.00 3.02
3312 4016 2.632512 TCTTTGGGGGTCTTTTTGCATC 59.367 45.455 0.00 0.00 0.00 3.91
3351 5760 2.592308 CTAAGGCACCCAGGGAGC 59.408 66.667 19.45 19.45 38.54 4.70
3352 5761 2.592308 GCTAAGGCACCCAGGGAG 59.408 66.667 14.54 5.21 38.54 4.30
3353 5762 3.399181 CGCTAAGGCACCCAGGGA 61.399 66.667 14.54 0.00 38.60 4.20
3354 5763 4.489771 CCGCTAAGGCACCCAGGG 62.490 72.222 2.85 2.85 38.60 4.45
3355 5764 2.478335 TTTCCGCTAAGGCACCCAGG 62.478 60.000 0.00 0.00 40.77 4.45
3356 5765 1.002624 TTTCCGCTAAGGCACCCAG 60.003 57.895 0.00 0.00 40.77 4.45
3357 5766 1.302993 GTTTCCGCTAAGGCACCCA 60.303 57.895 0.00 0.00 40.77 4.51
3358 5767 0.251073 TAGTTTCCGCTAAGGCACCC 59.749 55.000 0.00 0.00 40.77 4.61
3359 5768 2.103537 TTAGTTTCCGCTAAGGCACC 57.896 50.000 0.00 0.00 40.77 5.01
3360 5769 2.161012 GGTTTAGTTTCCGCTAAGGCAC 59.839 50.000 0.00 0.00 40.77 5.01
3361 5770 2.224572 TGGTTTAGTTTCCGCTAAGGCA 60.225 45.455 0.00 0.00 40.77 4.75
3371 5780 3.978855 GCGATTGGTGTTGGTTTAGTTTC 59.021 43.478 0.00 0.00 0.00 2.78
3410 5819 5.005203 GCATTTTTCATTGTTGTTCGTGTCA 59.995 36.000 0.00 0.00 0.00 3.58
3413 5822 4.605793 CGGCATTTTTCATTGTTGTTCGTG 60.606 41.667 0.00 0.00 0.00 4.35
3415 5824 3.121058 CCGGCATTTTTCATTGTTGTTCG 60.121 43.478 0.00 0.00 0.00 3.95
3435 5844 1.672356 CAGGAGTTGGTGGCTTCCG 60.672 63.158 0.00 0.00 0.00 4.30
3448 5857 2.266055 GTGCCCTCGGTTCAGGAG 59.734 66.667 0.00 0.00 35.20 3.69
3463 5872 1.431488 CCGATTCAGGCGATGGTGTG 61.431 60.000 0.00 0.00 0.00 3.82
3464 5873 1.153369 CCGATTCAGGCGATGGTGT 60.153 57.895 0.00 0.00 0.00 4.16
3505 5914 1.657751 GGCTCCGGTCAAATGAAGGC 61.658 60.000 0.00 0.00 0.00 4.35
3507 5916 0.391130 TCGGCTCCGGTCAAATGAAG 60.391 55.000 8.59 0.00 40.25 3.02
3529 5938 0.038455 TATTTCCACAACCCCCACGG 59.962 55.000 0.00 0.00 37.81 4.94
3530 5939 2.137810 ATATTTCCACAACCCCCACG 57.862 50.000 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.