Multiple sequence alignment - TraesCS2A01G176300

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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 TraesCS2A01G176300 chr2A 100.000 2892 0 0 760 3651 135884570 135887461 0.000000e+00 5341.0
1 TraesCS2A01G176300 chr2A 100.000 445 0 0 1 445 135883811 135884255 0.000000e+00 822.0
2 TraesCS2A01G176300 chr2B 93.968 2039 68 18 760 2757 182569076 182571100 0.000000e+00 3033.0
3 TraesCS2A01G176300 chr2B 91.388 569 41 5 3083 3651 182571449 182572009 0.000000e+00 773.0
4 TraesCS2A01G176300 chr2B 91.333 450 21 9 2 437 182568563 182569008 1.880000e-167 599.0
5 TraesCS2A01G176300 chr2B 96.465 198 7 0 2749 2946 182571126 182571323 9.780000e-86 327.0
6 TraesCS2A01G176300 chr2B 92.754 69 3 1 3015 3083 182571358 182571424 8.340000e-17 99.0
7 TraesCS2A01G176300 chr2D 92.337 1292 52 19 760 2013 128963744 128965026 0.000000e+00 1794.0
8 TraesCS2A01G176300 chr2D 94.172 755 23 7 2003 2757 128965063 128965796 0.000000e+00 1131.0
9 TraesCS2A01G176300 chr2D 95.055 546 22 2 2749 3292 128965822 128966364 0.000000e+00 854.0
10 TraesCS2A01G176300 chr2D 93.668 458 13 7 2 445 128963225 128963680 0.000000e+00 671.0
11 TraesCS2A01G176300 chr2D 90.217 368 29 3 3284 3651 128971511 128971871 1.190000e-129 473.0
12 TraesCS2A01G176300 chr2D 94.872 78 3 1 1145 1222 7892629 7892705 1.780000e-23 121.0
13 TraesCS2A01G176300 chr4D 91.304 230 19 1 1085 1313 17743900 17743671 2.740000e-81 313.0
14 TraesCS2A01G176300 chr7B 84.677 124 19 0 1116 1239 2899374 2899251 1.380000e-24 124.0
15 TraesCS2A01G176300 chr3D 86.139 101 12 2 3540 3639 450277983 450277884 1.390000e-19 108.0
16 TraesCS2A01G176300 chr7D 97.727 44 1 0 1166 1209 204881872 204881829 3.910000e-10 76.8
17 TraesCS2A01G176300 chr5B 90.698 43 3 1 3536 3577 586871952 586871994 5.090000e-04 56.5


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 TraesCS2A01G176300 chr2A 135883811 135887461 3650 False 3081.5 5341 100.0000 1 3651 2 chr2A.!!$F1 3650
1 TraesCS2A01G176300 chr2B 182568563 182572009 3446 False 966.2 3033 93.1816 2 3651 5 chr2B.!!$F1 3649
2 TraesCS2A01G176300 chr2D 128963225 128966364 3139 False 1112.5 1794 93.8080 2 3292 4 chr2D.!!$F3 3290

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
868 894 1.153147 GGAGACCGAGAATTGCCCC 60.153 63.158 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2656 2787 0.105349 TCCCCCTAGGTACATTCCGG 60.105 60.0 8.29 0.0 36.75 5.14 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
56 60 9.823647 AGATACAATCATACAAACAGTAGGAAG 57.176 33.333 0.00 0.00 45.50 3.46
67 71 6.262496 ACAAACAGTAGGAAGTAGAAAAAGGC 59.738 38.462 0.00 0.00 0.00 4.35
69 73 5.552178 ACAGTAGGAAGTAGAAAAAGGCAG 58.448 41.667 0.00 0.00 0.00 4.85
70 74 5.307196 ACAGTAGGAAGTAGAAAAAGGCAGA 59.693 40.000 0.00 0.00 0.00 4.26
76 80 6.043358 AGGAAGTAGAAAAAGGCAGAAGTAGT 59.957 38.462 0.00 0.00 0.00 2.73
78 82 8.041919 GGAAGTAGAAAAAGGCAGAAGTAGTAT 58.958 37.037 0.00 0.00 0.00 2.12
80 84 9.438228 AAGTAGAAAAAGGCAGAAGTAGTATTC 57.562 33.333 0.00 0.00 0.00 1.75
81 85 8.041919 AGTAGAAAAAGGCAGAAGTAGTATTCC 58.958 37.037 0.00 0.00 0.00 3.01
86 96 2.694109 GGCAGAAGTAGTATTCCGGAGT 59.306 50.000 3.34 3.88 0.00 3.85
187 199 2.026262 GTCACACATCCCCAAGTACCAT 60.026 50.000 0.00 0.00 0.00 3.55
203 215 2.125269 ATCACTACCAACCGCGGC 60.125 61.111 28.58 0.00 0.00 6.53
788 814 2.200067 CGATTCTACTGGCTCTGCTTG 58.800 52.381 0.00 0.00 0.00 4.01
809 835 3.165498 GGCGCTCGTCGATTGTTT 58.835 55.556 7.64 0.00 41.67 2.83
868 894 1.153147 GGAGACCGAGAATTGCCCC 60.153 63.158 0.00 0.00 0.00 5.80
931 957 2.436824 GGCCGTCCTTGGAGCTTC 60.437 66.667 0.00 0.00 0.00 3.86
952 978 2.190578 GGAGGAGGGATTGGCGTG 59.809 66.667 0.00 0.00 0.00 5.34
1107 1137 2.183046 GTGGTCGAGCTCAGCCTC 59.817 66.667 16.64 11.60 0.00 4.70
1494 1524 2.123982 CCCTCCTCAAGCATGCCC 60.124 66.667 15.66 0.00 0.00 5.36
1528 1575 4.168760 GCACATGCTTTCACCAACTATTC 58.831 43.478 0.00 0.00 38.21 1.75
1576 1623 1.656652 TCTATTGCGCTTCCTTGCTC 58.343 50.000 9.73 0.00 0.00 4.26
1588 1635 5.447573 GCTTCCTTGCTCGAATTATTCATC 58.552 41.667 5.76 0.00 0.00 2.92
1648 1704 2.049767 TCATGCCGAGCTCACCGTA 61.050 57.895 15.40 0.00 0.00 4.02
1656 1712 2.251893 CGAGCTCACCGTAGTTCTTTC 58.748 52.381 15.40 0.00 0.00 2.62
1727 1783 2.291475 TGCCATGGATCTTGCTTTGGTA 60.291 45.455 18.40 0.00 0.00 3.25
1739 1795 6.919721 TCTTGCTTTGGTATTGTGATTTACC 58.080 36.000 0.00 0.00 38.68 2.85
1835 1907 4.216902 TCTTTTCTGCACAACCTGATGATG 59.783 41.667 0.00 0.00 0.00 3.07
1840 1912 1.133790 GCACAACCTGATGATGCTTCC 59.866 52.381 0.00 0.00 33.44 3.46
1940 2012 0.539051 CTGTTGCTCCTAGGGTCTGG 59.461 60.000 9.46 0.00 0.00 3.86
1973 2045 0.804989 ACGGCATGTTTCTAAGCAGC 59.195 50.000 0.00 0.00 0.00 5.25
2000 2072 8.859236 TCTAAGCTTTTAGTCACTACTAGTCA 57.141 34.615 3.20 0.00 39.36 3.41
2001 2073 8.948145 TCTAAGCTTTTAGTCACTACTAGTCAG 58.052 37.037 3.20 0.00 39.36 3.51
2019 2137 3.369147 GTCAGTAGTTACGTAGCGTCAGA 59.631 47.826 3.64 1.71 41.54 3.27
2022 2140 3.616379 AGTAGTTACGTAGCGTCAGAGTC 59.384 47.826 3.64 0.00 41.54 3.36
2031 2149 4.672862 CGTAGCGTCAGAGTCTGATTATTG 59.327 45.833 25.17 13.70 42.73 1.90
2042 2160 7.384660 CAGAGTCTGATTATTGAGGCTAATCAC 59.615 40.741 15.46 0.02 39.48 3.06
2056 2174 2.522836 AATCACTATCCGAGCAGCTG 57.477 50.000 10.11 10.11 0.00 4.24
2127 2252 6.585322 ACTGACGATTAGTAAACGGAAAAGAG 59.415 38.462 15.76 5.70 0.00 2.85
2182 2307 8.461222 TGTTGGAATATGAAAATGTGACATCTC 58.539 33.333 0.00 0.00 0.00 2.75
2183 2308 7.572523 TGGAATATGAAAATGTGACATCTCC 57.427 36.000 0.00 0.00 32.02 3.71
2184 2309 7.348815 TGGAATATGAAAATGTGACATCTCCT 58.651 34.615 0.00 0.00 32.33 3.69
2185 2310 7.500227 TGGAATATGAAAATGTGACATCTCCTC 59.500 37.037 0.00 0.00 32.33 3.71
2226 2351 4.457496 CGGTGATGGCGCTGAGGT 62.457 66.667 7.64 0.00 32.55 3.85
2257 2382 4.081752 ACATCGAGCATGGAGATATCTTCC 60.082 45.833 8.62 10.63 36.72 3.46
2494 2625 0.457851 AGAAGATCGACGGCTTCCTG 59.542 55.000 20.28 0.00 41.01 3.86
2536 2667 1.204941 GAGGTGAGGATAGTGTGCGTT 59.795 52.381 0.00 0.00 0.00 4.84
2656 2787 0.373716 CGGTCTTCTTGTAATGCCGC 59.626 55.000 0.00 0.00 0.00 6.53
2657 2788 0.733150 GGTCTTCTTGTAATGCCGCC 59.267 55.000 0.00 0.00 0.00 6.13
2658 2789 0.373716 GTCTTCTTGTAATGCCGCCG 59.626 55.000 0.00 0.00 0.00 6.46
2680 2811 3.232662 GAATGTACCTAGGGGGAGAGAC 58.767 54.545 14.81 0.02 38.76 3.36
2917 3084 3.634568 TTTTGCCATGTTCAGTTACCG 57.365 42.857 0.00 0.00 0.00 4.02
2946 3113 1.058695 GAACGCGTATCAACTCCAACG 59.941 52.381 14.46 0.00 38.34 4.10
2952 3119 2.627945 GTATCAACTCCAACGCCATCA 58.372 47.619 0.00 0.00 0.00 3.07
2954 3121 0.321564 TCAACTCCAACGCCATCAGG 60.322 55.000 0.00 0.00 38.23 3.86
2991 3158 1.265365 GCTATTGCGCTTTGGAGATCC 59.735 52.381 9.73 0.00 0.00 3.36
3005 3172 0.912487 AGATCCCGGCCAAGTTGGTA 60.912 55.000 22.85 4.84 40.46 3.25
3030 3197 5.280654 ACTGGTTGGTAACGAAGAGTTTA 57.719 39.130 0.00 0.00 43.86 2.01
3031 3198 5.673514 ACTGGTTGGTAACGAAGAGTTTAA 58.326 37.500 0.00 0.00 43.86 1.52
3156 3346 2.370189 CACCCACAGTTCCTCTCTTTCT 59.630 50.000 0.00 0.00 0.00 2.52
3177 3367 6.227298 TCTCCTCTTCATTTAGACCATGAC 57.773 41.667 0.00 0.00 30.09 3.06
3188 3381 4.883240 CCATGACGATGGCCATGA 57.117 55.556 26.56 4.20 43.00 3.07
3189 3382 2.625375 CCATGACGATGGCCATGAG 58.375 57.895 26.56 19.26 43.00 2.90
3190 3383 0.107268 CCATGACGATGGCCATGAGA 59.893 55.000 26.56 4.19 43.00 3.27
3344 3537 2.093658 TCTACTGCGTTTTGGGGATCTC 60.094 50.000 0.00 0.00 0.00 2.75
3375 3568 9.654919 AAATTGGTATAGCTGGTAAATGGTAAT 57.345 29.630 0.00 0.00 0.00 1.89
3385 3578 7.121315 AGCTGGTAAATGGTAATGAAGAGTTTC 59.879 37.037 0.00 0.00 0.00 2.78
3390 3583 7.781324 AAATGGTAATGAAGAGTTTCCATGT 57.219 32.000 0.00 0.00 36.99 3.21
3446 3639 7.414429 GCACAATAGTAGCAATCTGTCATTTGA 60.414 37.037 0.00 0.00 0.00 2.69
3448 3641 9.182214 ACAATAGTAGCAATCTGTCATTTGATT 57.818 29.630 0.00 0.00 33.69 2.57
3464 3657 6.713903 TCATTTGATTTGTGCTCTCTCTTCTT 59.286 34.615 0.00 0.00 0.00 2.52
3465 3658 6.551385 TTTGATTTGTGCTCTCTCTTCTTC 57.449 37.500 0.00 0.00 0.00 2.87
3466 3659 4.573900 TGATTTGTGCTCTCTCTTCTTCC 58.426 43.478 0.00 0.00 0.00 3.46
3467 3660 4.285517 TGATTTGTGCTCTCTCTTCTTCCT 59.714 41.667 0.00 0.00 0.00 3.36
3478 3671 4.877773 TCTCTTCTTCCTTATGCTCCTCT 58.122 43.478 0.00 0.00 0.00 3.69
3479 3672 4.648762 TCTCTTCTTCCTTATGCTCCTCTG 59.351 45.833 0.00 0.00 0.00 3.35
3485 3678 1.137872 CCTTATGCTCCTCTGTCGCTT 59.862 52.381 0.00 0.00 0.00 4.68
3490 3683 0.459411 GCTCCTCTGTCGCTTCCTTC 60.459 60.000 0.00 0.00 0.00 3.46
3493 3686 1.544825 CCTCTGTCGCTTCCTTCCCA 61.545 60.000 0.00 0.00 0.00 4.37
3510 3703 0.246635 CCATTCTTGTCCTCGACCGT 59.753 55.000 0.00 0.00 0.00 4.83
3519 3712 2.439701 CTCGACCGTAGAGGGGCA 60.440 66.667 0.88 0.00 46.96 5.36
3530 3723 1.068352 AGAGGGGCAGAGTGGGTTTT 61.068 55.000 0.00 0.00 0.00 2.43
3532 3725 1.068352 AGGGGCAGAGTGGGTTTTCT 61.068 55.000 0.00 0.00 0.00 2.52
3533 3726 0.609406 GGGGCAGAGTGGGTTTTCTC 60.609 60.000 0.00 0.00 0.00 2.87
3534 3727 0.609406 GGGCAGAGTGGGTTTTCTCC 60.609 60.000 0.00 0.00 0.00 3.71
3535 3728 0.402121 GGCAGAGTGGGTTTTCTCCT 59.598 55.000 0.00 0.00 0.00 3.69
3536 3729 1.202940 GGCAGAGTGGGTTTTCTCCTT 60.203 52.381 0.00 0.00 0.00 3.36
3537 3730 1.882623 GCAGAGTGGGTTTTCTCCTTG 59.117 52.381 0.00 0.00 0.00 3.61
3538 3731 2.508526 CAGAGTGGGTTTTCTCCTTGG 58.491 52.381 0.00 0.00 0.00 3.61
3556 3749 0.808755 GGGGGACTAATGTGTTTGCG 59.191 55.000 0.00 0.00 0.00 4.85
3559 3752 2.423577 GGGACTAATGTGTTTGCGAGT 58.576 47.619 0.00 0.00 0.00 4.18
3563 3756 5.233689 GGGACTAATGTGTTTGCGAGTATAC 59.766 44.000 0.00 0.00 0.00 1.47
3577 3770 6.684686 TGCGAGTATACACAAGAAGTAAGTT 58.315 36.000 5.50 0.00 0.00 2.66
3578 3771 7.149973 TGCGAGTATACACAAGAAGTAAGTTT 58.850 34.615 5.50 0.00 0.00 2.66
3580 3773 7.541437 GCGAGTATACACAAGAAGTAAGTTTCT 59.459 37.037 5.50 0.00 39.03 2.52
3581 3774 9.063739 CGAGTATACACAAGAAGTAAGTTTCTC 57.936 37.037 5.50 0.00 36.42 2.87
3598 3791 8.480133 AAGTTTCTCAGGAGTTAAGAGAAGTA 57.520 34.615 0.00 0.00 45.79 2.24
3608 3801 5.971763 AGTTAAGAGAAGTATGCTGGAGTG 58.028 41.667 0.00 0.00 0.00 3.51
3611 3804 7.561722 AGTTAAGAGAAGTATGCTGGAGTGATA 59.438 37.037 0.00 0.00 0.00 2.15
3621 3814 5.066913 TGCTGGAGTGATAGAGGAGATTA 57.933 43.478 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.271707 CCTCCGGTAAATGTTGGTGGT 60.272 52.381 0.00 0.00 31.92 4.16
55 59 8.041919 GGAATACTACTTCTGCCTTTTTCTACT 58.958 37.037 0.00 0.00 0.00 2.57
56 60 7.010275 CGGAATACTACTTCTGCCTTTTTCTAC 59.990 40.741 0.00 0.00 0.00 2.59
67 71 4.398358 TGTCACTCCGGAATACTACTTCTG 59.602 45.833 5.23 0.00 0.00 3.02
69 73 4.439837 GGTGTCACTCCGGAATACTACTTC 60.440 50.000 5.23 0.00 0.00 3.01
70 74 3.446516 GGTGTCACTCCGGAATACTACTT 59.553 47.826 5.23 0.00 0.00 2.24
76 80 1.252215 TGCGGTGTCACTCCGGAATA 61.252 55.000 19.51 0.00 44.90 1.75
78 82 3.228017 TGCGGTGTCACTCCGGAA 61.228 61.111 19.51 0.00 44.90 4.30
187 199 4.382320 GGCCGCGGTTGGTAGTGA 62.382 66.667 28.70 0.00 0.00 3.41
247 264 3.961414 TTGGACCCCGACAAGCCC 61.961 66.667 0.00 0.00 0.00 5.19
259 276 2.312436 GCGGGTACACGTGTTGGAC 61.312 63.158 28.55 18.71 38.54 4.02
899 925 0.447801 CGGCCAAATTCTCAGGAACG 59.552 55.000 2.24 0.00 33.96 3.95
931 957 3.171388 CCAATCCCTCCTCCCCCG 61.171 72.222 0.00 0.00 0.00 5.73
1081 1111 4.477975 CTCGACCACCTCGTCCGC 62.478 72.222 0.00 0.00 43.45 5.54
1477 1507 2.123982 GGGCATGCTTGAGGAGGG 60.124 66.667 18.92 0.00 0.00 4.30
1576 1623 3.058432 CAGGCAGCTGGATGAATAATTCG 60.058 47.826 17.12 0.00 0.00 3.34
1588 1635 0.035630 AGAGCTTAACAGGCAGCTGG 60.036 55.000 17.12 0.73 46.72 4.85
1648 1704 2.832129 TGCATCTCCTACCGAAAGAACT 59.168 45.455 0.00 0.00 0.00 3.01
1656 1712 1.302033 GCCCATGCATCTCCTACCG 60.302 63.158 0.00 0.00 37.47 4.02
1690 1746 2.639065 TGGCAAAGAACACTCGACTTT 58.361 42.857 0.00 0.00 34.77 2.66
1727 1783 3.830744 TCGATCCCGGTAAATCACAAT 57.169 42.857 0.00 0.00 36.24 2.71
1840 1912 1.083489 ACAAATCCCATGCGTACGTG 58.917 50.000 17.90 8.04 0.00 4.49
1973 2045 9.777575 GACTAGTAGTGACTAAAAGCTTAGAAG 57.222 37.037 7.76 0.00 37.72 2.85
1997 2069 3.369147 TCTGACGCTACGTAACTACTGAC 59.631 47.826 0.00 0.00 41.37 3.51
2000 2072 3.594134 ACTCTGACGCTACGTAACTACT 58.406 45.455 0.00 0.00 41.37 2.57
2001 2073 3.616379 AGACTCTGACGCTACGTAACTAC 59.384 47.826 0.00 0.00 41.37 2.73
2019 2137 7.372260 AGTGATTAGCCTCAATAATCAGACT 57.628 36.000 8.28 2.19 45.54 3.24
2022 2140 7.490725 CGGATAGTGATTAGCCTCAATAATCAG 59.509 40.741 8.28 0.00 45.54 2.90
2031 2149 2.558795 TGCTCGGATAGTGATTAGCCTC 59.441 50.000 0.00 0.00 35.60 4.70
2127 2252 8.579006 TCAATAAAGATTCATATCCCAATGTGC 58.421 33.333 0.00 0.00 0.00 4.57
2182 2307 0.107312 CACCAATGCAGAGGAGGAGG 60.107 60.000 13.66 0.00 0.00 4.30
2183 2308 3.473147 CACCAATGCAGAGGAGGAG 57.527 57.895 13.66 0.00 0.00 3.69
2226 2351 1.648504 CATGCTCGATGTGCTCTTCA 58.351 50.000 0.00 0.00 0.00 3.02
2257 2382 6.582295 GGTTGCTGGCATTGTTATTATTATCG 59.418 38.462 0.00 0.00 0.00 2.92
2494 2625 3.055312 CCTCCCCTTTCCTGTACTTGTAC 60.055 52.174 4.14 4.14 0.00 2.90
2656 2787 0.105349 TCCCCCTAGGTACATTCCGG 60.105 60.000 8.29 0.00 36.75 5.14
2657 2788 1.133262 TCTCCCCCTAGGTACATTCCG 60.133 57.143 8.29 0.00 36.75 4.30
2658 2789 2.179424 TCTCTCCCCCTAGGTACATTCC 59.821 54.545 8.29 0.00 36.75 3.01
2680 2811 3.326836 AGGAAAGAGAGGAAAAGAGCG 57.673 47.619 0.00 0.00 0.00 5.03
2862 3027 9.715121 TCCTAAACCTTACACATTTACAGTTAG 57.285 33.333 0.00 0.00 0.00 2.34
2917 3084 2.793933 TGATACGCGTTCAGAGTAAGC 58.206 47.619 20.78 0.00 38.57 3.09
2946 3113 3.003689 CCGAATATGTGAAACCTGATGGC 59.996 47.826 0.00 0.00 36.63 4.40
2952 3119 4.222124 AGCTTCCGAATATGTGAAACCT 57.778 40.909 0.00 0.00 34.36 3.50
2954 3121 5.909610 GCAATAGCTTCCGAATATGTGAAAC 59.090 40.000 0.00 0.00 37.91 2.78
2991 3158 2.014128 CAGTTATACCAACTTGGCCGG 58.986 52.381 7.81 0.00 42.67 6.13
3005 3172 5.479124 ACTCTTCGTTACCAACCAGTTAT 57.521 39.130 0.00 0.00 0.00 1.89
3030 3197 6.427547 CCTTGCAAACCACAACATATTCATTT 59.572 34.615 0.00 0.00 0.00 2.32
3031 3198 5.933463 CCTTGCAAACCACAACATATTCATT 59.067 36.000 0.00 0.00 0.00 2.57
3140 3330 4.126520 AGAGGAGAAAGAGAGGAACTGT 57.873 45.455 0.00 0.00 41.55 3.55
3156 3346 4.709886 TCGTCATGGTCTAAATGAAGAGGA 59.290 41.667 0.00 0.00 37.54 3.71
3177 3367 0.250209 CCTCCTTCTCATGGCCATCG 60.250 60.000 17.61 11.99 0.00 3.84
3188 3381 1.661463 TCTCATTGGTGCCTCCTTCT 58.339 50.000 0.00 0.00 37.07 2.85
3189 3382 2.496899 TTCTCATTGGTGCCTCCTTC 57.503 50.000 0.00 0.00 37.07 3.46
3190 3383 3.094572 CAATTCTCATTGGTGCCTCCTT 58.905 45.455 0.00 0.00 36.82 3.36
3328 3521 0.672401 GTCGAGATCCCCAAAACGCA 60.672 55.000 0.00 0.00 0.00 5.24
3360 3553 6.759497 AACTCTTCATTACCATTTACCAGC 57.241 37.500 0.00 0.00 0.00 4.85
3369 3562 8.877864 AAATACATGGAAACTCTTCATTACCA 57.122 30.769 0.00 0.00 32.75 3.25
3375 3568 9.295825 ACAACATAAATACATGGAAACTCTTCA 57.704 29.630 0.00 0.00 32.75 3.02
3385 3578 5.868258 TGCAAAGCACAACATAAATACATGG 59.132 36.000 0.00 0.00 31.71 3.66
3390 3583 6.338214 TCCTTGCAAAGCACAACATAAATA 57.662 33.333 0.00 0.00 44.44 1.40
3425 3618 9.182214 ACAAATCAAATGACAGATTGCTACTAT 57.818 29.630 0.00 0.00 34.86 2.12
3427 3620 7.310664 CACAAATCAAATGACAGATTGCTACT 58.689 34.615 0.00 0.00 34.86 2.57
3446 3639 4.906747 AGGAAGAAGAGAGAGCACAAAT 57.093 40.909 0.00 0.00 0.00 2.32
3448 3641 5.728471 CATAAGGAAGAAGAGAGAGCACAA 58.272 41.667 0.00 0.00 0.00 3.33
3464 3657 0.747255 GCGACAGAGGAGCATAAGGA 59.253 55.000 0.00 0.00 0.00 3.36
3465 3658 0.749649 AGCGACAGAGGAGCATAAGG 59.250 55.000 0.00 0.00 0.00 2.69
3466 3659 2.468831 GAAGCGACAGAGGAGCATAAG 58.531 52.381 0.00 0.00 0.00 1.73
3467 3660 1.137086 GGAAGCGACAGAGGAGCATAA 59.863 52.381 0.00 0.00 0.00 1.90
3478 3671 0.984230 AGAATGGGAAGGAAGCGACA 59.016 50.000 0.00 0.00 0.00 4.35
3479 3672 1.740025 CAAGAATGGGAAGGAAGCGAC 59.260 52.381 0.00 0.00 0.00 5.19
3485 3678 1.555075 CGAGGACAAGAATGGGAAGGA 59.445 52.381 0.00 0.00 0.00 3.36
3490 3683 0.460284 CGGTCGAGGACAAGAATGGG 60.460 60.000 0.00 0.00 33.68 4.00
3493 3686 2.683867 CTCTACGGTCGAGGACAAGAAT 59.316 50.000 1.91 0.00 33.68 2.40
3510 3703 0.178873 AAACCCACTCTGCCCCTCTA 60.179 55.000 0.00 0.00 0.00 2.43
3519 3712 1.425448 CCCAAGGAGAAAACCCACTCT 59.575 52.381 0.00 0.00 34.11 3.24
3532 3725 2.053747 ACACATTAGTCCCCCAAGGA 57.946 50.000 0.00 0.00 44.91 3.36
3533 3726 2.825532 CAAACACATTAGTCCCCCAAGG 59.174 50.000 0.00 0.00 0.00 3.61
3534 3727 2.231235 GCAAACACATTAGTCCCCCAAG 59.769 50.000 0.00 0.00 0.00 3.61
3535 3728 2.243810 GCAAACACATTAGTCCCCCAA 58.756 47.619 0.00 0.00 0.00 4.12
3536 3729 1.884497 CGCAAACACATTAGTCCCCCA 60.884 52.381 0.00 0.00 0.00 4.96
3537 3730 0.808755 CGCAAACACATTAGTCCCCC 59.191 55.000 0.00 0.00 0.00 5.40
3538 3731 1.737793 CTCGCAAACACATTAGTCCCC 59.262 52.381 0.00 0.00 0.00 4.81
3556 3749 9.909644 TGAGAAACTTACTTCTTGTGTATACTC 57.090 33.333 4.17 0.83 35.76 2.59
3559 3752 9.085645 TCCTGAGAAACTTACTTCTTGTGTATA 57.914 33.333 0.00 0.00 35.76 1.47
3563 3756 6.284459 ACTCCTGAGAAACTTACTTCTTGTG 58.716 40.000 0.22 0.00 35.76 3.33
3577 3770 6.665680 AGCATACTTCTCTTAACTCCTGAGAA 59.334 38.462 0.22 0.00 42.37 2.87
3578 3771 6.096141 CAGCATACTTCTCTTAACTCCTGAGA 59.904 42.308 0.22 0.00 35.36 3.27
3580 3773 5.127845 CCAGCATACTTCTCTTAACTCCTGA 59.872 44.000 0.00 0.00 0.00 3.86
3581 3774 5.127845 TCCAGCATACTTCTCTTAACTCCTG 59.872 44.000 0.00 0.00 0.00 3.86
3598 3791 3.609256 TCTCCTCTATCACTCCAGCAT 57.391 47.619 0.00 0.00 0.00 3.79
3608 3801 7.976734 CCCACACGAATAATAATCTCCTCTATC 59.023 40.741 0.00 0.00 0.00 2.08
3611 3804 5.839063 TCCCACACGAATAATAATCTCCTCT 59.161 40.000 0.00 0.00 0.00 3.69
3621 3814 3.181454 GGGTCATCTCCCACACGAATAAT 60.181 47.826 0.00 0.00 46.30 1.28


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

AutoCloner maintained by Alex Coulton.