Multiple sequence alignment - TraesCS7D01G140900

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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 TraesCS7D01G140900 chr7D 100.000 3542 0 0 1 3542 89895515 89891974 0.000000e+00 6541.0
1 TraesCS7D01G140900 chr7D 89.426 1551 105 27 1102 2615 89868241 89866713 0.000000e+00 1901.0
2 TraesCS7D01G140900 chr7D 86.139 101 10 2 973 1069 89868431 89868331 4.840000e-19 106.0
3 TraesCS7D01G140900 chr7A 91.524 2277 86 37 435 2648 91494246 91492014 0.000000e+00 3037.0
4 TraesCS7D01G140900 chr7A 88.228 1614 125 32 1102 2686 91418826 91420403 0.000000e+00 1868.0
5 TraesCS7D01G140900 chr7A 86.250 240 17 2 36 259 91494603 91494364 2.730000e-61 246.0
6 TraesCS7D01G140900 chr7B 88.420 1779 88 41 3 1759 41033269 41031587 0.000000e+00 2036.0
7 TraesCS7D01G140900 chr7B 95.873 727 30 0 1808 2534 41031503 41030777 0.000000e+00 1177.0
8 TraesCS7D01G140900 chr7B 90.537 708 32 9 2694 3398 41030483 41029808 0.000000e+00 904.0
9 TraesCS7D01G140900 chr7B 91.758 182 13 2 2522 2701 41030757 41030576 5.870000e-63 252.0
10 TraesCS7D01G140900 chr7B 94.521 73 2 1 3470 3542 41029510 41029440 1.040000e-20 111.0
11 TraesCS7D01G140900 chr2D 99.315 146 1 0 2446 2591 380071095 380070950 7.540000e-67 265.0
12 TraesCS7D01G140900 chrUn 80.952 210 37 3 3048 3256 93791289 93791082 2.830000e-36 163.0
13 TraesCS7D01G140900 chrUn 87.273 55 7 0 1700 1754 110658425 110658479 2.950000e-06 63.9
14 TraesCS7D01G140900 chr5D 78.077 260 55 2 3034 3293 320450687 320450944 2.830000e-36 163.0
15 TraesCS7D01G140900 chr5D 76.923 260 58 2 3034 3293 439207519 439207776 2.850000e-31 147.0
16 TraesCS7D01G140900 chr5D 95.122 41 2 0 1720 1760 43385387 43385427 8.210000e-07 65.8
17 TraesCS7D01G140900 chr3D 80.583 206 39 1 3034 3239 584165164 584164960 1.320000e-34 158.0
18 TraesCS7D01G140900 chr5A 97.561 41 1 0 1720 1760 33152922 33152962 1.760000e-08 71.3
19 TraesCS7D01G140900 chr5A 87.273 55 7 0 1700 1754 700663770 700663824 2.950000e-06 63.9
20 TraesCS7D01G140900 chr4B 87.273 55 7 0 1700 1754 660662051 660662105 2.950000e-06 63.9


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 TraesCS7D01G140900 chr7D 89891974 89895515 3541 True 6541.0 6541 100.0000 1 3542 1 chr7D.!!$R1 3541
1 TraesCS7D01G140900 chr7D 89866713 89868431 1718 True 1003.5 1901 87.7825 973 2615 2 chr7D.!!$R2 1642
2 TraesCS7D01G140900 chr7A 91418826 91420403 1577 False 1868.0 1868 88.2280 1102 2686 1 chr7A.!!$F1 1584
3 TraesCS7D01G140900 chr7A 91492014 91494603 2589 True 1641.5 3037 88.8870 36 2648 2 chr7A.!!$R1 2612
4 TraesCS7D01G140900 chr7B 41029440 41033269 3829 True 896.0 2036 92.2218 3 3542 5 chr7B.!!$R1 3539

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
769 818 0.105453 CTCCCTCCCTTGGCTAGCTA 60.105 60.0 15.72 5.44 0.0 3.32 F
1277 1415 0.672711 GCCTTCCACCGGTAAGACAC 60.673 60.0 17.11 4.36 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 1918 0.106708 TGAGGAACAGAGCAAGCGTT 59.893 50.0 0.0 0.0 0.0 4.84 R
3084 3449 0.036022 GGGAGATCTATGGTGGCAGC 59.964 60.0 10.3 10.3 0.0 5.25 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
212 229 0.785378 CACATTTGTGGCATGCAACG 59.215 50.000 20.19 8.41 42.10 4.10
227 244 4.002906 TGCAACGTATTCTTTGGAGTCT 57.997 40.909 0.00 0.00 0.00 3.24
286 303 5.477607 TGCTACACTTATAACCGCCATAT 57.522 39.130 0.00 0.00 0.00 1.78
287 304 6.593268 TGCTACACTTATAACCGCCATATA 57.407 37.500 0.00 0.00 0.00 0.86
289 306 8.296211 TGCTACACTTATAACCGCCATATATA 57.704 34.615 0.00 0.00 0.00 0.86
290 307 8.920174 TGCTACACTTATAACCGCCATATATAT 58.080 33.333 0.00 0.00 0.00 0.86
326 343 8.401709 GGTTTGCCAGAATTTGTTGAAAAATTA 58.598 29.630 0.00 0.00 36.07 1.40
327 344 9.780413 GTTTGCCAGAATTTGTTGAAAAATTAA 57.220 25.926 0.00 0.00 39.31 1.40
329 346 8.729805 TGCCAGAATTTGTTGAAAAATTAAGT 57.270 26.923 0.00 0.00 39.31 2.24
331 348 8.825745 GCCAGAATTTGTTGAAAAATTAAGTCA 58.174 29.630 0.00 0.00 39.31 3.41
364 381 3.088532 TGAACCAAACATACATGCCCTC 58.911 45.455 0.00 0.00 0.00 4.30
365 382 3.245229 TGAACCAAACATACATGCCCTCT 60.245 43.478 0.00 0.00 0.00 3.69
366 383 4.018870 TGAACCAAACATACATGCCCTCTA 60.019 41.667 0.00 0.00 0.00 2.43
367 384 4.584638 ACCAAACATACATGCCCTCTAA 57.415 40.909 0.00 0.00 0.00 2.10
368 385 5.129368 ACCAAACATACATGCCCTCTAAT 57.871 39.130 0.00 0.00 0.00 1.73
369 386 5.133221 ACCAAACATACATGCCCTCTAATC 58.867 41.667 0.00 0.00 0.00 1.75
370 387 4.214119 CCAAACATACATGCCCTCTAATCG 59.786 45.833 0.00 0.00 0.00 3.34
372 389 3.239449 ACATACATGCCCTCTAATCGGA 58.761 45.455 0.00 0.00 0.00 4.55
387 404 4.144703 GGAGAGACCCCGCGTTCC 62.145 72.222 4.92 0.00 0.00 3.62
408 438 1.317611 CAACGTGATCGATCGTGTGAC 59.682 52.381 20.03 11.23 40.19 3.67
426 456 2.083774 GACACCAGCGAAATGAATCCA 58.916 47.619 0.00 0.00 0.00 3.41
547 583 0.679002 GAGCATTGAAGGCAGGCAGA 60.679 55.000 4.17 0.00 0.00 4.26
550 586 1.379576 ATTGAAGGCAGGCAGAGGC 60.380 57.895 0.00 0.00 40.13 4.70
551 587 2.146146 ATTGAAGGCAGGCAGAGGCA 62.146 55.000 0.00 0.00 43.71 4.75
552 588 2.438075 GAAGGCAGGCAGAGGCAG 60.438 66.667 0.00 0.00 43.71 4.85
553 589 3.991725 GAAGGCAGGCAGAGGCAGG 62.992 68.421 0.00 0.00 43.71 4.85
613 654 8.150296 AGCAAAATATTTCCTATTAATGGTGCC 58.850 33.333 0.10 0.00 31.54 5.01
762 811 4.101448 CACCGCTCCCTCCCTTGG 62.101 72.222 0.00 0.00 0.00 3.61
765 814 2.764128 CGCTCCCTCCCTTGGCTA 60.764 66.667 0.00 0.00 0.00 3.93
766 815 2.801631 CGCTCCCTCCCTTGGCTAG 61.802 68.421 0.00 0.00 0.00 3.42
767 816 3.113514 GCTCCCTCCCTTGGCTAGC 62.114 68.421 6.04 6.04 0.00 3.42
768 817 1.383803 CTCCCTCCCTTGGCTAGCT 60.384 63.158 15.72 0.00 0.00 3.32
769 818 0.105453 CTCCCTCCCTTGGCTAGCTA 60.105 60.000 15.72 5.44 0.00 3.32
770 819 0.105453 TCCCTCCCTTGGCTAGCTAG 60.105 60.000 16.84 16.84 0.00 3.42
882 934 4.200283 CCTCGCTGCCTCCTCGTC 62.200 72.222 0.00 0.00 0.00 4.20
883 935 4.544689 CTCGCTGCCTCCTCGTCG 62.545 72.222 0.00 0.00 0.00 5.12
931 984 2.743718 GGCCGACGATCCATCCAT 59.256 61.111 0.00 0.00 0.00 3.41
932 985 1.071471 GGCCGACGATCCATCCATT 59.929 57.895 0.00 0.00 0.00 3.16
940 993 2.036475 ACGATCCATCCATTCTTCTCCG 59.964 50.000 0.00 0.00 0.00 4.63
963 1025 2.595463 GCAGGTGTGCCAGCTTGA 60.595 61.111 4.42 0.00 44.72 3.02
1224 1362 2.202401 GGCGACGACGTGGAGTAC 60.202 66.667 14.57 0.00 41.98 2.73
1277 1415 0.672711 GCCTTCCACCGGTAAGACAC 60.673 60.000 17.11 4.36 0.00 3.67
1283 1421 2.682856 TCCACCGGTAAGACACGTATAC 59.317 50.000 6.87 0.00 0.00 1.47
1365 1511 6.792250 GCCGATCTTGATTAATTATTCACACG 59.208 38.462 9.10 11.13 0.00 4.49
1366 1512 6.792250 CCGATCTTGATTAATTATTCACACGC 59.208 38.462 9.10 1.43 0.00 5.34
1367 1513 6.512982 CGATCTTGATTAATTATTCACACGCG 59.487 38.462 3.53 3.53 0.00 6.01
1368 1514 5.498159 TCTTGATTAATTATTCACACGCGC 58.502 37.500 5.73 0.00 0.00 6.86
1759 1913 1.534476 TCCTGCCACGACTGGGTAA 60.534 57.895 0.00 0.00 38.13 2.85
1760 1914 1.122632 TCCTGCCACGACTGGGTAAA 61.123 55.000 0.00 0.00 38.13 2.01
1764 1918 1.667151 CCACGACTGGGTAAACCGA 59.333 57.895 0.00 0.00 44.64 4.69
1769 1929 0.320160 GACTGGGTAAACCGAACGCT 60.320 55.000 0.00 0.00 44.64 5.07
1773 1933 1.232621 GGGTAAACCGAACGCTTGCT 61.233 55.000 0.00 0.00 36.71 3.91
1775 1935 1.145803 GTAAACCGAACGCTTGCTCT 58.854 50.000 0.00 0.00 0.00 4.09
1776 1936 1.136336 GTAAACCGAACGCTTGCTCTG 60.136 52.381 0.00 0.00 0.00 3.35
1777 1937 0.814010 AAACCGAACGCTTGCTCTGT 60.814 50.000 0.00 0.00 0.00 3.41
1778 1938 0.814010 AACCGAACGCTTGCTCTGTT 60.814 50.000 0.00 0.00 0.00 3.16
1779 1939 1.222115 ACCGAACGCTTGCTCTGTTC 61.222 55.000 0.00 0.00 38.83 3.18
1780 1940 1.493311 CGAACGCTTGCTCTGTTCC 59.507 57.895 6.38 0.00 38.97 3.62
1781 1941 0.946221 CGAACGCTTGCTCTGTTCCT 60.946 55.000 6.38 0.00 38.97 3.36
1782 1942 0.793250 GAACGCTTGCTCTGTTCCTC 59.207 55.000 0.00 0.00 36.79 3.71
1783 1943 0.106708 AACGCTTGCTCTGTTCCTCA 59.893 50.000 0.00 0.00 0.00 3.86
1784 1944 0.320247 ACGCTTGCTCTGTTCCTCAG 60.320 55.000 0.00 0.00 44.85 3.35
1786 1946 0.036022 GCTTGCTCTGTTCCTCAGGT 59.964 55.000 0.00 0.00 43.76 4.00
1787 1947 1.805869 CTTGCTCTGTTCCTCAGGTG 58.194 55.000 0.00 0.00 43.76 4.00
1791 1951 1.342074 CTCTGTTCCTCAGGTGTCCA 58.658 55.000 0.00 0.00 43.76 4.02
2049 2247 3.274586 CATGGCCACATCCGCGAG 61.275 66.667 8.16 0.00 34.35 5.03
2110 2308 1.298157 CCCCGTGTACGAGTACGACA 61.298 60.000 5.91 0.00 42.54 4.35
2175 2388 2.835705 CGACCGGCAGAGCGACTAT 61.836 63.158 0.00 0.00 0.00 2.12
2364 2577 3.461773 CCGGTCGCTGACATCCCT 61.462 66.667 10.14 0.00 33.68 4.20
2534 2779 0.605589 AGGCTCAACTTCAGACTCGG 59.394 55.000 0.00 0.00 0.00 4.63
2727 3090 8.794335 AGTGAAGGTTAAAAACTATCATCCTC 57.206 34.615 0.00 0.00 31.97 3.71
2782 3145 5.327737 TCACCCCCAATACAACTAAAACT 57.672 39.130 0.00 0.00 0.00 2.66
2785 3148 6.005198 CACCCCCAATACAACTAAAACTGTA 58.995 40.000 0.00 0.00 32.79 2.74
2789 3152 8.422566 CCCCCAATACAACTAAAACTGTAAAAA 58.577 33.333 0.00 0.00 32.05 1.94
2842 3206 3.244976 CAGTTGCCAATTAGCTTTTCCG 58.755 45.455 0.00 0.00 0.00 4.30
2853 3217 8.842280 CCAATTAGCTTTTCCGTATAAATACCA 58.158 33.333 0.00 0.00 0.00 3.25
2867 3231 9.607285 CGTATAAATACCAAATACCAGATTTGC 57.393 33.333 4.79 0.00 37.60 3.68
3010 3374 6.321848 TCTTGTGTTCTTCGTAGTATCACA 57.678 37.500 10.40 10.40 33.53 3.58
3019 3383 0.838229 GTAGTATCACAAGCGTCGCG 59.162 55.000 12.30 0.00 0.00 5.87
3037 3401 1.227556 GCCATACTGTAGTGCCCCG 60.228 63.158 0.00 0.00 0.00 5.73
3038 3402 1.968050 GCCATACTGTAGTGCCCCGT 61.968 60.000 0.00 0.00 0.00 5.28
3074 3439 0.755686 CTACTTAGGAGGCAGCCTGG 59.244 60.000 22.26 6.06 39.08 4.45
3075 3440 0.338467 TACTTAGGAGGCAGCCTGGA 59.662 55.000 22.26 0.00 39.08 3.86
3076 3441 1.268283 ACTTAGGAGGCAGCCTGGAC 61.268 60.000 22.26 9.13 39.08 4.02
3077 3442 1.977293 CTTAGGAGGCAGCCTGGACC 61.977 65.000 22.26 14.73 39.08 4.46
3080 3445 2.365635 GAGGCAGCCTGGACCCTA 60.366 66.667 22.26 0.00 31.76 3.53
3081 3446 2.366167 AGGCAGCCTGGACCCTAG 60.366 66.667 15.24 0.00 29.57 3.02
3082 3447 2.689034 GGCAGCCTGGACCCTAGT 60.689 66.667 3.29 0.00 0.00 2.57
3083 3448 2.301738 GGCAGCCTGGACCCTAGTT 61.302 63.158 3.29 0.00 0.00 2.24
3084 3449 1.078143 GCAGCCTGGACCCTAGTTG 60.078 63.158 0.00 0.00 0.00 3.16
3085 3450 1.078143 CAGCCTGGACCCTAGTTGC 60.078 63.158 0.00 0.00 0.00 4.17
3086 3451 1.229658 AGCCTGGACCCTAGTTGCT 60.230 57.895 0.00 0.00 0.00 3.91
3087 3452 1.078143 GCCTGGACCCTAGTTGCTG 60.078 63.158 0.00 0.00 0.00 4.41
3088 3453 1.078143 CCTGGACCCTAGTTGCTGC 60.078 63.158 0.00 0.00 0.00 5.25
3089 3454 1.078143 CTGGACCCTAGTTGCTGCC 60.078 63.158 0.00 0.00 0.00 4.85
3090 3455 1.841302 CTGGACCCTAGTTGCTGCCA 61.841 60.000 0.00 0.00 0.00 4.92
3094 3459 1.304282 CCCTAGTTGCTGCCACCAT 59.696 57.895 0.00 0.00 0.00 3.55
3121 3486 2.514582 TCCCTTTCCTCCTCTCTATCGT 59.485 50.000 0.00 0.00 0.00 3.73
3233 3598 3.664025 TTCTCATGGACAGCGGCGG 62.664 63.158 9.78 0.00 0.00 6.13
3307 3672 4.332591 TGGGGTTGGGGCGTAACG 62.333 66.667 0.00 0.00 0.00 3.18
3334 3699 3.628646 ATGGTTGGCGGTGGCTCTC 62.629 63.158 0.00 0.00 39.81 3.20
3341 3707 4.864334 CGGTGGCTCTCCATGGCC 62.864 72.222 6.96 5.18 45.62 5.36
3351 3717 2.600173 CCATGGCCGTGTGGGTTT 60.600 61.111 23.39 0.00 38.44 3.27
3393 3759 1.767127 GAGATCAGCGACTCGAGCGA 61.767 60.000 26.02 11.28 40.04 4.93
3423 3789 3.195698 GACGCCACAATCGCCCTC 61.196 66.667 0.00 0.00 0.00 4.30
3424 3790 3.665675 GACGCCACAATCGCCCTCT 62.666 63.158 0.00 0.00 0.00 3.69
3425 3791 2.892425 CGCCACAATCGCCCTCTC 60.892 66.667 0.00 0.00 0.00 3.20
3426 3792 2.514824 GCCACAATCGCCCTCTCC 60.515 66.667 0.00 0.00 0.00 3.71
3427 3793 3.036429 GCCACAATCGCCCTCTCCT 62.036 63.158 0.00 0.00 0.00 3.69
3428 3794 1.144936 CCACAATCGCCCTCTCCTC 59.855 63.158 0.00 0.00 0.00 3.71
3429 3795 1.144936 CACAATCGCCCTCTCCTCC 59.855 63.158 0.00 0.00 0.00 4.30
3430 3796 1.306141 ACAATCGCCCTCTCCTCCA 60.306 57.895 0.00 0.00 0.00 3.86
3431 3797 0.692419 ACAATCGCCCTCTCCTCCAT 60.692 55.000 0.00 0.00 0.00 3.41
3432 3798 0.250209 CAATCGCCCTCTCCTCCATG 60.250 60.000 0.00 0.00 0.00 3.66
3433 3799 2.049627 AATCGCCCTCTCCTCCATGC 62.050 60.000 0.00 0.00 0.00 4.06
3434 3800 3.473647 CGCCCTCTCCTCCATGCA 61.474 66.667 0.00 0.00 0.00 3.96
3435 3801 2.191641 GCCCTCTCCTCCATGCAC 59.808 66.667 0.00 0.00 0.00 4.57
3436 3802 2.914289 CCCTCTCCTCCATGCACC 59.086 66.667 0.00 0.00 0.00 5.01
3437 3803 2.750657 CCCTCTCCTCCATGCACCC 61.751 68.421 0.00 0.00 0.00 4.61
3438 3804 2.750657 CCTCTCCTCCATGCACCCC 61.751 68.421 0.00 0.00 0.00 4.95
3439 3805 1.692042 CTCTCCTCCATGCACCCCT 60.692 63.158 0.00 0.00 0.00 4.79
3440 3806 1.690633 TCTCCTCCATGCACCCCTC 60.691 63.158 0.00 0.00 0.00 4.30
3441 3807 2.692368 TCCTCCATGCACCCCTCC 60.692 66.667 0.00 0.00 0.00 4.30
3442 3808 3.813724 CCTCCATGCACCCCTCCC 61.814 72.222 0.00 0.00 0.00 4.30
3443 3809 4.181010 CTCCATGCACCCCTCCCG 62.181 72.222 0.00 0.00 0.00 5.14
3458 3824 4.596585 CCGCCCAACCCCACAACT 62.597 66.667 0.00 0.00 0.00 3.16
3459 3825 3.294493 CGCCCAACCCCACAACTG 61.294 66.667 0.00 0.00 0.00 3.16
3460 3826 2.917227 GCCCAACCCCACAACTGG 60.917 66.667 0.00 0.00 37.29 4.00
3461 3827 2.606449 CCCAACCCCACAACTGGT 59.394 61.111 0.00 0.00 35.46 4.00
3462 3828 1.075600 CCCAACCCCACAACTGGTT 60.076 57.895 0.00 0.00 45.60 3.67
3532 4124 5.457148 CGTGAGTTGGATTCTTCTTATCTCG 59.543 44.000 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.396811 GTGTCCCTCCGATTATGGGG 59.603 60.000 0.00 0.00 41.22 4.96
1 2 0.396811 GGTGTCCCTCCGATTATGGG 59.603 60.000 0.00 0.00 42.20 4.00
14 15 3.255888 GGGATTTTGAGAACTTGGTGTCC 59.744 47.826 0.00 0.00 0.00 4.02
55 57 5.581479 GGATCGTTTTTCTCTAGAAGGTTCC 59.419 44.000 0.00 0.00 35.21 3.62
206 223 4.002906 AGACTCCAAAGAATACGTTGCA 57.997 40.909 0.00 0.00 34.97 4.08
227 244 4.081642 GTGCTAATGAGAAGTGTGGGAGTA 60.082 45.833 0.00 0.00 0.00 2.59
326 343 9.313118 GTTTGGTTCATAATCAAAGTTTGACTT 57.687 29.630 20.26 16.34 43.48 3.01
327 344 8.474025 TGTTTGGTTCATAATCAAAGTTTGACT 58.526 29.630 20.26 12.60 43.48 3.41
336 353 7.264221 GGCATGTATGTTTGGTTCATAATCAA 58.736 34.615 0.00 0.00 31.00 2.57
370 387 4.144703 GGAACGCGGGGTCTCTCC 62.145 72.222 17.75 4.48 0.00 3.71
385 402 0.179148 CACGATCGATCACGTTGGGA 60.179 55.000 24.34 0.00 40.76 4.37
387 404 0.640262 CACACGATCGATCACGTTGG 59.360 55.000 24.34 9.86 40.76 3.77
394 411 1.550065 CTGGTGTCACACGATCGATC 58.450 55.000 24.34 15.68 34.83 3.69
408 438 3.788333 AATGGATTCATTTCGCTGGTG 57.212 42.857 0.00 0.00 40.42 4.17
426 456 6.604171 TGAGCTGGATATATGTGGTCAAAAT 58.396 36.000 0.00 0.00 33.18 1.82
520 556 1.081892 CCTTCAATGCTCACTCGGTG 58.918 55.000 0.00 0.00 34.45 4.94
522 558 0.674581 TGCCTTCAATGCTCACTCGG 60.675 55.000 0.00 0.00 0.00 4.63
550 586 3.209812 TCTCGATCGACGCCCCTG 61.210 66.667 15.15 2.55 42.26 4.45
551 587 3.210528 GTCTCGATCGACGCCCCT 61.211 66.667 15.15 0.00 42.26 4.79
552 588 2.938539 CTTGTCTCGATCGACGCCCC 62.939 65.000 15.15 0.94 42.26 5.80
553 589 1.586564 CTTGTCTCGATCGACGCCC 60.587 63.158 15.15 2.77 42.26 6.13
713 762 1.897133 TGGTTCTACGCAAGCCTTCTA 59.103 47.619 0.00 0.00 45.62 2.10
714 763 0.685097 TGGTTCTACGCAAGCCTTCT 59.315 50.000 0.00 0.00 45.62 2.85
715 764 1.197036 GTTGGTTCTACGCAAGCCTTC 59.803 52.381 0.00 0.00 45.62 3.46
770 819 2.459442 CGGCACAGCTCAGCTAAGC 61.459 63.158 12.89 12.89 42.82 3.09
771 820 1.812922 CCGGCACAGCTCAGCTAAG 60.813 63.158 0.00 0.00 36.40 2.18
772 821 2.265739 CCGGCACAGCTCAGCTAA 59.734 61.111 0.00 0.00 36.40 3.09
882 934 1.444553 GAGACGGAGCTGGTCAACG 60.445 63.158 14.91 6.58 36.87 4.10
883 935 1.444553 CGAGACGGAGCTGGTCAAC 60.445 63.158 14.91 8.63 36.87 3.18
884 936 1.863662 GACGAGACGGAGCTGGTCAA 61.864 60.000 14.91 0.00 41.50 3.18
929 982 2.697425 CGCGCACGGAGAAGAATG 59.303 61.111 8.75 0.00 34.97 2.67
930 983 3.188786 GCGCGCACGGAGAAGAAT 61.189 61.111 29.10 0.00 40.57 2.40
931 984 4.656117 TGCGCGCACGGAGAAGAA 62.656 61.111 33.09 2.14 40.57 2.52
963 1025 1.449601 CGGCCTTGACGTGCCTTAT 60.450 57.895 12.27 0.00 45.71 1.73
1206 1344 3.434319 TACTCCACGTCGTCGCCC 61.434 66.667 0.99 0.00 41.18 6.13
1234 1372 2.345760 GGTTGCGGTAGACCCTCGA 61.346 63.158 0.00 0.00 0.00 4.04
1365 1511 3.913573 CACCATGAGTACGCGCGC 61.914 66.667 32.58 23.91 0.00 6.86
1366 1512 1.588932 ATCACCATGAGTACGCGCG 60.589 57.895 30.96 30.96 0.00 6.86
1367 1513 1.490693 CCATCACCATGAGTACGCGC 61.491 60.000 5.73 0.00 30.57 6.86
1368 1514 1.490693 GCCATCACCATGAGTACGCG 61.491 60.000 3.53 3.53 30.57 6.01
1759 1913 0.814010 AACAGAGCAAGCGTTCGGTT 60.814 50.000 3.83 3.83 36.29 4.44
1760 1914 1.222115 GAACAGAGCAAGCGTTCGGT 61.222 55.000 0.00 0.00 32.46 4.69
1764 1918 0.106708 TGAGGAACAGAGCAAGCGTT 59.893 50.000 0.00 0.00 0.00 4.84
1775 1935 0.764369 AGCTGGACACCTGAGGAACA 60.764 55.000 4.99 0.00 0.00 3.18
1776 1936 0.398318 AAGCTGGACACCTGAGGAAC 59.602 55.000 4.99 0.00 0.00 3.62
1777 1937 0.397941 CAAGCTGGACACCTGAGGAA 59.602 55.000 4.99 0.00 0.00 3.36
1778 1938 0.471780 TCAAGCTGGACACCTGAGGA 60.472 55.000 4.99 0.00 0.00 3.71
1779 1939 0.617413 ATCAAGCTGGACACCTGAGG 59.383 55.000 0.00 0.00 0.00 3.86
1780 1940 1.277273 TCATCAAGCTGGACACCTGAG 59.723 52.381 0.00 0.00 0.00 3.35
1781 1941 1.351076 TCATCAAGCTGGACACCTGA 58.649 50.000 0.00 0.00 0.00 3.86
1782 1942 2.414994 ATCATCAAGCTGGACACCTG 57.585 50.000 0.00 0.00 0.00 4.00
1783 1943 3.776969 TCTAATCATCAAGCTGGACACCT 59.223 43.478 0.00 0.00 0.00 4.00
1784 1944 4.125703 CTCTAATCATCAAGCTGGACACC 58.874 47.826 0.00 0.00 0.00 4.16
1786 1946 3.453717 AGCTCTAATCATCAAGCTGGACA 59.546 43.478 0.00 0.00 43.21 4.02
1787 1947 4.070630 AGCTCTAATCATCAAGCTGGAC 57.929 45.455 0.00 0.00 43.21 4.02
1791 1951 6.038382 CACAATGAAGCTCTAATCATCAAGCT 59.962 38.462 0.00 0.00 46.66 3.74
2175 2388 2.395360 GCGGTGCATGTAGGCGAAA 61.395 57.895 0.00 0.00 36.28 3.46
2349 2562 1.742768 CCTAGGGATGTCAGCGACC 59.257 63.158 0.00 0.00 0.00 4.79
2355 2568 1.008327 TCCTTCAGCCTAGGGATGTCA 59.992 52.381 11.72 0.00 40.37 3.58
2364 2577 1.267574 CCAGCACCTCCTTCAGCCTA 61.268 60.000 0.00 0.00 0.00 3.93
2534 2779 0.610687 AGTCTGAACTGGCTAGTGGC 59.389 55.000 2.40 0.00 37.19 5.01
2701 2964 9.232473 GAGGATGATAGTTTTTAACCTTCACTT 57.768 33.333 0.00 0.00 0.00 3.16
2702 2965 8.606830 AGAGGATGATAGTTTTTAACCTTCACT 58.393 33.333 0.00 0.00 0.00 3.41
2789 3152 7.899973 AGGAGAGCATGACATTTTAAACATTT 58.100 30.769 0.00 0.00 0.00 2.32
2792 3155 7.394016 TCTAGGAGAGCATGACATTTTAAACA 58.606 34.615 0.00 0.00 0.00 2.83
2793 3156 7.849804 TCTAGGAGAGCATGACATTTTAAAC 57.150 36.000 0.00 0.00 0.00 2.01
2794 3157 8.862325 TTTCTAGGAGAGCATGACATTTTAAA 57.138 30.769 0.00 0.00 0.00 1.52
2853 3217 8.584157 TGTTTATCAACAGCAAATCTGGTATTT 58.416 29.630 0.00 0.00 41.81 1.40
2867 3231 5.984627 TGACACACGATTGTTTATCAACAG 58.015 37.500 0.00 0.00 43.92 3.16
2929 3293 0.810031 AATATCCAGTCGCACCGCAC 60.810 55.000 0.00 0.00 0.00 5.34
3019 3383 1.227556 CGGGGCACTACAGTATGGC 60.228 63.158 7.58 7.58 43.62 4.40
3026 3390 2.281208 GCAACACGGGGCACTACA 60.281 61.111 0.00 0.00 0.00 2.74
3037 3401 3.022287 CCCACACGACAGCAACAC 58.978 61.111 0.00 0.00 0.00 3.32
3038 3402 2.034048 TAGCCCACACGACAGCAACA 62.034 55.000 0.00 0.00 0.00 3.33
3074 3439 1.377333 GGTGGCAGCAACTAGGGTC 60.377 63.158 12.58 0.00 0.00 4.46
3075 3440 1.500783 ATGGTGGCAGCAACTAGGGT 61.501 55.000 24.45 1.70 0.00 4.34
3076 3441 0.546122 TATGGTGGCAGCAACTAGGG 59.454 55.000 24.45 0.00 0.00 3.53
3077 3442 1.486310 TCTATGGTGGCAGCAACTAGG 59.514 52.381 24.45 11.56 0.00 3.02
3078 3443 2.988010 TCTATGGTGGCAGCAACTAG 57.012 50.000 24.45 20.16 0.00 2.57
3079 3444 3.041211 AGATCTATGGTGGCAGCAACTA 58.959 45.455 24.45 11.46 0.00 2.24
3080 3445 1.842562 AGATCTATGGTGGCAGCAACT 59.157 47.619 24.45 10.85 0.00 3.16
3081 3446 2.216898 GAGATCTATGGTGGCAGCAAC 58.783 52.381 24.45 12.22 0.00 4.17
3082 3447 1.141657 GGAGATCTATGGTGGCAGCAA 59.858 52.381 24.45 7.83 0.00 3.91
3083 3448 0.761187 GGAGATCTATGGTGGCAGCA 59.239 55.000 22.88 22.88 0.00 4.41
3084 3449 0.036022 GGGAGATCTATGGTGGCAGC 59.964 60.000 10.30 10.30 0.00 5.25
3085 3450 1.727062 AGGGAGATCTATGGTGGCAG 58.273 55.000 0.00 0.00 0.00 4.85
3086 3451 2.196742 AAGGGAGATCTATGGTGGCA 57.803 50.000 0.00 0.00 0.00 4.92
3087 3452 2.224646 GGAAAGGGAGATCTATGGTGGC 60.225 54.545 0.00 0.00 0.00 5.01
3088 3453 3.321950 AGGAAAGGGAGATCTATGGTGG 58.678 50.000 0.00 0.00 0.00 4.61
3089 3454 3.326297 GGAGGAAAGGGAGATCTATGGTG 59.674 52.174 0.00 0.00 0.00 4.17
3090 3455 3.211000 AGGAGGAAAGGGAGATCTATGGT 59.789 47.826 0.00 0.00 0.00 3.55
3094 3459 4.058731 AGAGAGGAGGAAAGGGAGATCTA 58.941 47.826 0.00 0.00 0.00 1.98
3121 3486 1.666553 CTGCGGCGTCCTACAACAA 60.667 57.895 9.37 0.00 0.00 2.83
3168 3533 0.595310 GTACCGCGAGCAAGATCCTC 60.595 60.000 8.23 0.00 0.00 3.71
3205 3570 0.391661 TCCATGAGAAGCTTGTCGCC 60.392 55.000 17.82 0.00 40.39 5.54
3334 3699 2.600173 AAACCCACACGGCCATGG 60.600 61.111 7.63 7.63 35.59 3.66
3341 3707 2.330041 GTTCCGCAAACCCACACG 59.670 61.111 0.00 0.00 31.20 4.49
3351 3717 2.888464 TTTTGGGTGTCGGTTCCGCA 62.888 55.000 6.35 5.44 0.00 5.69
3406 3772 3.195698 GAGGGCGATTGTGGCGTC 61.196 66.667 0.00 0.00 41.13 5.19
3407 3773 3.665675 GAGAGGGCGATTGTGGCGT 62.666 63.158 0.00 0.00 34.76 5.68
3408 3774 2.892425 GAGAGGGCGATTGTGGCG 60.892 66.667 0.00 0.00 34.76 5.69
3409 3775 2.514824 GGAGAGGGCGATTGTGGC 60.515 66.667 0.00 0.00 0.00 5.01
3410 3776 1.144936 GAGGAGAGGGCGATTGTGG 59.855 63.158 0.00 0.00 0.00 4.17
3411 3777 1.144936 GGAGGAGAGGGCGATTGTG 59.855 63.158 0.00 0.00 0.00 3.33
3412 3778 0.692419 ATGGAGGAGAGGGCGATTGT 60.692 55.000 0.00 0.00 0.00 2.71
3413 3779 0.250209 CATGGAGGAGAGGGCGATTG 60.250 60.000 0.00 0.00 0.00 2.67
3414 3780 2.049627 GCATGGAGGAGAGGGCGATT 62.050 60.000 0.00 0.00 0.00 3.34
3415 3781 2.515071 GCATGGAGGAGAGGGCGAT 61.515 63.158 0.00 0.00 0.00 4.58
3416 3782 3.157252 GCATGGAGGAGAGGGCGA 61.157 66.667 0.00 0.00 0.00 5.54
3417 3783 3.473647 TGCATGGAGGAGAGGGCG 61.474 66.667 0.00 0.00 0.00 6.13
3418 3784 2.191641 GTGCATGGAGGAGAGGGC 59.808 66.667 0.00 0.00 0.00 5.19
3419 3785 2.750657 GGGTGCATGGAGGAGAGGG 61.751 68.421 0.00 0.00 0.00 4.30
3420 3786 2.750657 GGGGTGCATGGAGGAGAGG 61.751 68.421 0.00 0.00 0.00 3.69
3421 3787 1.692042 AGGGGTGCATGGAGGAGAG 60.692 63.158 0.00 0.00 0.00 3.20
3422 3788 1.690633 GAGGGGTGCATGGAGGAGA 60.691 63.158 0.00 0.00 0.00 3.71
3423 3789 2.750657 GGAGGGGTGCATGGAGGAG 61.751 68.421 0.00 0.00 0.00 3.69
3424 3790 2.692368 GGAGGGGTGCATGGAGGA 60.692 66.667 0.00 0.00 0.00 3.71
3425 3791 3.813724 GGGAGGGGTGCATGGAGG 61.814 72.222 0.00 0.00 0.00 4.30
3426 3792 4.181010 CGGGAGGGGTGCATGGAG 62.181 72.222 0.00 0.00 0.00 3.86
3441 3807 4.596585 AGTTGTGGGGTTGGGCGG 62.597 66.667 0.00 0.00 0.00 6.13
3442 3808 3.294493 CAGTTGTGGGGTTGGGCG 61.294 66.667 0.00 0.00 0.00 6.13
3443 3809 2.917227 CCAGTTGTGGGGTTGGGC 60.917 66.667 0.00 0.00 40.67 5.36
3454 3820 0.248743 CAGCAGCACACAACCAGTTG 60.249 55.000 8.95 8.95 45.58 3.16
3455 3821 1.386525 CCAGCAGCACACAACCAGTT 61.387 55.000 0.00 0.00 0.00 3.16
3456 3822 1.825191 CCAGCAGCACACAACCAGT 60.825 57.895 0.00 0.00 0.00 4.00
3457 3823 2.558286 CCCAGCAGCACACAACCAG 61.558 63.158 0.00 0.00 0.00 4.00
3458 3824 2.519063 CCCAGCAGCACACAACCA 60.519 61.111 0.00 0.00 0.00 3.67
3459 3825 3.982241 GCCCAGCAGCACACAACC 61.982 66.667 0.00 0.00 0.00 3.77
3460 3826 2.295472 TTTGCCCAGCAGCACACAAC 62.295 55.000 0.00 0.00 43.97 3.32
3461 3827 2.018727 CTTTGCCCAGCAGCACACAA 62.019 55.000 0.00 0.00 43.97 3.33
3462 3828 2.441717 TTTGCCCAGCAGCACACA 60.442 55.556 0.00 0.00 43.97 3.72
3463 3829 2.337532 CTTTGCCCAGCAGCACAC 59.662 61.111 0.00 0.00 43.97 3.82
3464 3830 3.608662 GCTTTGCCCAGCAGCACA 61.609 61.111 0.00 0.00 43.97 4.57
3465 3831 3.278592 GAGCTTTGCCCAGCAGCAC 62.279 63.158 6.97 0.00 43.97 4.40
3466 3832 2.987547 GAGCTTTGCCCAGCAGCA 60.988 61.111 6.97 0.00 42.84 4.41
3467 3833 2.675772 AGAGCTTTGCCCAGCAGC 60.676 61.111 6.97 0.00 42.84 5.25
3468 3834 2.396955 CGAGAGCTTTGCCCAGCAG 61.397 63.158 6.97 0.00 42.84 4.24
3511 4103 5.751028 CACCGAGATAAGAAGAATCCAACTC 59.249 44.000 0.00 0.00 0.00 3.01
3512 4104 5.395768 CCACCGAGATAAGAAGAATCCAACT 60.396 44.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.