Multiple sequence alignment - TraesCS2A01G175200

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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 TraesCS2A01G175200 chr2A 100.000 4266 0 0 1 4266 133683370 133687635 0.000000e+00 7878.0
1 TraesCS2A01G175200 chr2A 79.897 388 49 16 2615 2990 525822929 525822559 1.520000e-64 257.0
2 TraesCS2A01G175200 chr2B 91.354 3389 163 52 569 3905 180604520 180607830 0.000000e+00 4516.0
3 TraesCS2A01G175200 chr2B 91.154 520 33 10 1 513 180603999 180604512 0.000000e+00 693.0
4 TraesCS2A01G175200 chr2B 87.056 394 6 5 3902 4266 180607870 180608247 1.850000e-108 403.0
5 TraesCS2A01G175200 chr2B 81.201 383 57 12 10 386 28347568 28347941 1.160000e-75 294.0
6 TraesCS2A01G175200 chr2B 100.000 28 0 0 501 528 615506835 615506862 8.000000e-03 52.8
7 TraesCS2A01G175200 chr2D 95.002 2601 92 22 1334 3905 126982750 126985341 0.000000e+00 4048.0
8 TraesCS2A01G175200 chr2D 86.976 668 66 11 651 1304 126982092 126982752 0.000000e+00 732.0
9 TraesCS2A01G175200 chr2D 88.769 463 37 10 1 461 126979412 126979861 1.730000e-153 553.0
10 TraesCS2A01G175200 chr2D 84.987 373 44 6 2620 2990 103370613 103370251 6.740000e-98 368.0
11 TraesCS2A01G175200 chr2D 84.987 373 44 6 2620 2990 104398127 104398489 6.740000e-98 368.0
12 TraesCS2A01G175200 chr2D 85.533 394 10 7 3902 4266 126985381 126985756 6.740000e-98 368.0
13 TraesCS2A01G175200 chr2D 83.500 200 11 4 455 654 126981549 126981726 2.640000e-37 167.0
14 TraesCS2A01G175200 chr4D 88.720 789 57 7 1651 2437 236934393 236935151 0.000000e+00 935.0
15 TraesCS2A01G175200 chr4D 93.886 458 28 0 2436 2893 236936017 236936474 0.000000e+00 691.0
16 TraesCS2A01G175200 chr4D 94.581 203 11 0 2892 3094 236936594 236936796 8.900000e-82 315.0
17 TraesCS2A01G175200 chr4D 91.441 222 13 5 3159 3378 236939871 236940088 2.490000e-77 300.0
18 TraesCS2A01G175200 chr4B 87.516 801 64 8 1638 2437 338424341 338425106 0.000000e+00 893.0
19 TraesCS2A01G175200 chr4B 93.886 458 28 0 2436 2893 338425980 338426437 0.000000e+00 691.0
20 TraesCS2A01G175200 chr4B 94.581 203 11 0 2892 3094 338426551 338426753 8.900000e-82 315.0
21 TraesCS2A01G175200 chr4B 90.541 222 15 5 3159 3378 338427912 338428129 5.400000e-74 289.0
22 TraesCS2A01G175200 chr4B 83.838 99 12 3 431 528 637381988 637382083 1.630000e-14 91.6
23 TraesCS2A01G175200 chr4A 87.173 803 70 9 1638 2437 282080812 282081584 0.000000e+00 881.0
24 TraesCS2A01G175200 chr4A 94.105 458 27 0 2436 2893 282082449 282082906 0.000000e+00 697.0
25 TraesCS2A01G175200 chr4A 93.596 203 13 0 2892 3094 282083027 282083229 1.930000e-78 303.0
26 TraesCS2A01G175200 chr4A 90.950 221 14 5 3159 3377 282085646 282085862 4.170000e-75 292.0
27 TraesCS2A01G175200 chr5B 83.260 681 84 21 55 718 528935537 528936204 2.200000e-167 599.0
28 TraesCS2A01G175200 chr3D 86.207 551 59 10 11 554 72256833 72257373 7.950000e-162 580.0
29 TraesCS2A01G175200 chr3A 81.907 713 89 26 2 692 85676669 85677363 2.230000e-157 566.0
30 TraesCS2A01G175200 chr1D 88.015 267 30 1 590 854 338533644 338533910 8.900000e-82 315.0
31 TraesCS2A01G175200 chr1B 86.058 208 27 1 650 855 453200035 453200242 5.550000e-54 222.0
32 TraesCS2A01G175200 chr1B 89.720 107 10 1 431 537 453198447 453198552 7.440000e-28 135.0
33 TraesCS2A01G175200 chr6D 94.872 39 1 1 234 272 308936647 308936684 4.610000e-05 60.2


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 TraesCS2A01G175200 chr2A 133683370 133687635 4265 False 7878.000000 7878 100.000000 1 4266 1 chr2A.!!$F1 4265
1 TraesCS2A01G175200 chr2B 180603999 180608247 4248 False 1870.666667 4516 89.854667 1 4266 3 chr2B.!!$F3 4265
2 TraesCS2A01G175200 chr2D 126979412 126985756 6344 False 1173.600000 4048 87.956000 1 4266 5 chr2D.!!$F2 4265
3 TraesCS2A01G175200 chr4D 236934393 236940088 5695 False 560.250000 935 92.157000 1651 3378 4 chr4D.!!$F1 1727
4 TraesCS2A01G175200 chr4B 338424341 338428129 3788 False 547.000000 893 91.631000 1638 3378 4 chr4B.!!$F2 1740
5 TraesCS2A01G175200 chr4A 282080812 282085862 5050 False 543.250000 881 91.456000 1638 3377 4 chr4A.!!$F1 1739
6 TraesCS2A01G175200 chr5B 528935537 528936204 667 False 599.000000 599 83.260000 55 718 1 chr5B.!!$F1 663
7 TraesCS2A01G175200 chr3D 72256833 72257373 540 False 580.000000 580 86.207000 11 554 1 chr3D.!!$F1 543
8 TraesCS2A01G175200 chr3A 85676669 85677363 694 False 566.000000 566 81.907000 2 692 1 chr3A.!!$F1 690

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
778 2897 0.102663 GGGAAGCCTCGCTAGTACAC 59.897 60.000 0.00 0.0 38.25 2.90 F
1449 3590 0.034477 CGGATTGTGGCCTAGGGTTT 60.034 55.000 11.72 0.0 0.00 3.27 F
2133 4311 1.006102 CGCAGGAGGACGAACAAGT 60.006 57.895 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 4346 0.530870 GGGTACTTGATCTGCTCCGC 60.531 60.0 0.0 0.0 0.00 5.54 R
2786 5996 0.389426 GCAGCTAAAGAACCGTCCGA 60.389 55.0 0.0 0.0 0.00 4.55 R
3530 11527 2.286184 GCTGCATGTTACCCGAATAACG 60.286 50.0 0.0 0.0 37.79 3.18 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
81 83 6.238103 CCAGAAAATGTAGTACTAATGGCACG 60.238 42.308 3.61 0.00 0.00 5.34
186 189 7.596995 GCTATTTTTGGTGTAAATAGTGTGCAA 59.403 33.333 13.70 0.00 43.02 4.08
194 197 7.766278 TGGTGTAAATAGTGTGCAATTTTTGTT 59.234 29.630 0.00 0.00 0.00 2.83
274 280 7.630728 GCCACTAATTCATTCTTAGAAAACCCC 60.631 40.741 0.00 0.00 31.89 4.95
280 288 9.559732 AATTCATTCTTAGAAAACCCCTTTTTG 57.440 29.630 0.00 0.00 37.54 2.44
352 362 6.917477 GTGCATTTTCTGAGTAAATTGTGTGA 59.083 34.615 0.00 0.00 0.00 3.58
483 2203 9.884465 CAATTCATTTCGTCTTAGAGAACTTTT 57.116 29.630 0.00 0.00 0.00 2.27
484 2204 9.884465 AATTCATTTCGTCTTAGAGAACTTTTG 57.116 29.630 0.00 0.00 0.00 2.44
555 2275 4.641989 ACAATCATACTGGCAATCTTCCAC 59.358 41.667 0.00 0.00 0.00 4.02
556 2276 2.905075 TCATACTGGCAATCTTCCACG 58.095 47.619 0.00 0.00 0.00 4.94
557 2277 1.331756 CATACTGGCAATCTTCCACGC 59.668 52.381 0.00 0.00 0.00 5.34
560 2280 2.435938 GGCAATCTTCCACGCCGA 60.436 61.111 0.00 0.00 34.26 5.54
562 2282 1.582610 GGCAATCTTCCACGCCGAAA 61.583 55.000 0.00 0.00 34.26 3.46
564 2284 1.335506 GCAATCTTCCACGCCGAAAAA 60.336 47.619 0.00 0.00 0.00 1.94
605 2344 4.546674 TCTAGCCATGTCTTATCCAGTCA 58.453 43.478 0.00 0.00 0.00 3.41
673 2785 3.281341 CACCGCTTGCTTATGAAACAA 57.719 42.857 0.00 0.00 0.00 2.83
706 2818 4.807304 ACAAAATTCAGCAACTCAGCTTTG 59.193 37.500 0.00 0.00 43.70 2.77
740 2854 4.218417 GTGAAAGGACAAGCATACATTGGT 59.782 41.667 0.00 0.00 37.77 3.67
764 2878 2.500504 GTCCACTACTACCCAAGGGAAG 59.499 54.545 13.15 6.14 38.96 3.46
765 2879 1.209747 CCACTACTACCCAAGGGAAGC 59.790 57.143 13.15 0.00 38.96 3.86
766 2880 1.209747 CACTACTACCCAAGGGAAGCC 59.790 57.143 13.15 0.00 38.96 4.35
767 2881 1.080666 ACTACTACCCAAGGGAAGCCT 59.919 52.381 13.15 0.00 38.96 4.58
768 2882 1.763545 CTACTACCCAAGGGAAGCCTC 59.236 57.143 13.15 0.00 38.96 4.70
778 2897 0.102663 GGGAAGCCTCGCTAGTACAC 59.897 60.000 0.00 0.00 38.25 2.90
780 2899 1.203994 GGAAGCCTCGCTAGTACACAA 59.796 52.381 0.00 0.00 38.25 3.33
785 2904 2.734492 GCCTCGCTAGTACACAAATCGT 60.734 50.000 0.00 0.00 0.00 3.73
806 2925 4.201910 CGTCTGAAACAAATTGTGGTCAGT 60.202 41.667 26.01 1.05 40.95 3.41
813 2932 2.169832 AATTGTGGTCAGTCGACTGG 57.830 50.000 37.82 22.94 43.91 4.00
853 2972 0.461961 AACTGTCATCTAGCCGCTCC 59.538 55.000 0.00 0.00 0.00 4.70
880 2999 0.695803 CATACCTCCTCCCCTGCCTT 60.696 60.000 0.00 0.00 0.00 4.35
923 3049 2.175931 AGGGTGGTATTGTTGTTGGTCA 59.824 45.455 0.00 0.00 0.00 4.02
940 3075 2.498167 GTCATGTTGAGCCTCTGTTGT 58.502 47.619 0.00 0.00 0.00 3.32
943 3078 2.936919 TGTTGAGCCTCTGTTGTCAT 57.063 45.000 0.00 0.00 0.00 3.06
978 3113 1.476471 CCATGCTCATTGTCCTCCTCC 60.476 57.143 0.00 0.00 0.00 4.30
979 3114 0.467384 ATGCTCATTGTCCTCCTCCG 59.533 55.000 0.00 0.00 0.00 4.63
1043 3178 2.109126 GCCCAACACCATCGCTCTC 61.109 63.158 0.00 0.00 0.00 3.20
1061 3196 2.765969 CACTGCATCCACCCCCTT 59.234 61.111 0.00 0.00 0.00 3.95
1084 3219 3.441922 CCTCTGATCCATATGTCGACGAT 59.558 47.826 11.62 6.83 0.00 3.73
1092 3227 2.595124 TATGTCGACGATGCCACATT 57.405 45.000 11.62 0.00 31.83 2.71
1139 3275 0.238289 CAACACCAATGACCACGAGC 59.762 55.000 0.00 0.00 0.00 5.03
1218 3354 2.692557 GCCATGACTAGAAGAGAGAGCA 59.307 50.000 0.00 0.00 0.00 4.26
1230 3366 0.965866 AGAGAGCATCGGGTTGTCGA 60.966 55.000 0.00 0.00 42.67 4.20
1265 3401 1.868997 CACGCGGTCAAGCTTCATT 59.131 52.632 12.47 0.00 34.40 2.57
1269 3405 1.019278 GCGGTCAAGCTTCATTCGGA 61.019 55.000 0.00 0.00 0.00 4.55
1273 3409 1.059369 CAAGCTTCATTCGGACGCG 59.941 57.895 3.53 3.53 44.90 6.01
1274 3410 1.080093 AAGCTTCATTCGGACGCGA 60.080 52.632 15.93 0.00 44.90 5.87
1287 3424 3.822192 CGCGAGTCGATGTGGGGA 61.822 66.667 18.61 0.00 41.67 4.81
1325 3464 2.560861 CCATGCCAACCAACGACG 59.439 61.111 0.00 0.00 0.00 5.12
1330 3469 2.631428 CCAACCAACGACGTGCAG 59.369 61.111 0.00 0.00 0.00 4.41
1387 3526 1.626654 CGCCTTGCTCGAATCACGTT 61.627 55.000 0.00 0.00 43.13 3.99
1393 3532 2.048597 TCGAATCACGTTGCCGCT 60.049 55.556 0.00 0.00 43.13 5.52
1430 3571 1.448717 GAGGAAAGAGAGTGGCGCC 60.449 63.158 22.73 22.73 0.00 6.53
1449 3590 0.034477 CGGATTGTGGCCTAGGGTTT 60.034 55.000 11.72 0.00 0.00 3.27
1450 3591 1.210967 CGGATTGTGGCCTAGGGTTTA 59.789 52.381 11.72 0.00 0.00 2.01
1470 3612 5.950544 TTATGTAGTGGCTGTGAGGTTAT 57.049 39.130 0.00 0.00 0.00 1.89
1480 3622 6.806739 GTGGCTGTGAGGTTATTTATGTTTTC 59.193 38.462 0.00 0.00 0.00 2.29
1527 3696 5.467035 TTGACCAGATCCCAAATTCAAAC 57.533 39.130 0.00 0.00 0.00 2.93
1566 3736 1.669211 GCGGTCGGTATTCTGATAGCC 60.669 57.143 0.00 0.00 33.65 3.93
1592 3762 2.002018 AAGGCCGGAAAACTGGACCA 62.002 55.000 5.05 0.00 31.71 4.02
1601 3771 3.568430 GGAAAACTGGACCAACTTCGAAT 59.432 43.478 0.00 0.00 0.00 3.34
1608 3783 4.315803 TGGACCAACTTCGAATTCTCTTC 58.684 43.478 0.00 0.00 0.00 2.87
1622 3797 7.065803 TCGAATTCTCTTCTTCGGCAATAAAAT 59.934 33.333 3.52 0.00 43.29 1.82
1685 3860 1.338200 CGCAGCTCAAAACCCTAGTCT 60.338 52.381 0.00 0.00 0.00 3.24
1687 3862 2.744741 GCAGCTCAAAACCCTAGTCTTC 59.255 50.000 0.00 0.00 0.00 2.87
1759 3937 3.105928 ATCACCCCTCCCATGGCC 61.106 66.667 6.09 0.00 0.00 5.36
2131 4309 2.357034 GCGCAGGAGGACGAACAA 60.357 61.111 0.30 0.00 0.00 2.83
2133 4311 1.006102 CGCAGGAGGACGAACAAGT 60.006 57.895 0.00 0.00 0.00 3.16
2136 4314 1.272769 GCAGGAGGACGAACAAGTAGT 59.727 52.381 0.00 0.00 0.00 2.73
2165 4346 4.695231 ACGACAACGACGAGGGCG 62.695 66.667 15.14 15.14 42.66 6.13
2468 5678 2.103263 GGGATCGTCAAAGTATGGAGCT 59.897 50.000 0.00 0.00 0.00 4.09
2484 5694 2.012673 GAGCTTGCCACAGATAACCAG 58.987 52.381 0.00 0.00 0.00 4.00
2786 5996 5.046304 AGTGTATATGGTGTCAGCTTTCACT 60.046 40.000 14.90 9.43 35.26 3.41
2788 5998 1.800805 ATGGTGTCAGCTTTCACTCG 58.199 50.000 14.90 0.00 35.26 4.18
2848 6058 3.096852 TGCTCGAGTTTGGGATCTAAGA 58.903 45.455 15.13 0.00 0.00 2.10
2969 6301 6.867662 ACAATTTCTGTCGAATATGGGATC 57.132 37.500 0.00 0.00 29.87 3.36
3101 6924 0.036010 AGCAGCGCTATGGTCAACTT 60.036 50.000 10.99 0.00 36.99 2.66
3427 11424 7.294473 GTTGCGCCAAAATATTTGTATTTGTT 58.706 30.769 4.18 0.00 33.31 2.83
3428 11425 8.436200 GTTGCGCCAAAATATTTGTATTTGTTA 58.564 29.630 4.18 0.00 33.31 2.41
3466 11463 7.986889 GGTTTAGGGTACGAATTGTAATCCTTA 59.013 37.037 8.47 0.00 38.85 2.69
3659 11656 2.460669 AGGGCATCAATTGAAACCCTC 58.539 47.619 31.82 16.96 45.24 4.30
3719 11716 0.871722 ACTTGAGCGTGCGCAATTTA 59.128 45.000 14.00 0.00 44.88 1.40
3763 11760 5.418840 ACATGGGGTTGAAATAGCTGTTAAG 59.581 40.000 0.00 0.00 0.00 1.85
3826 11823 3.380479 TCAACGGTACACTTCTTCCAG 57.620 47.619 0.00 0.00 0.00 3.86
4019 12064 2.041976 CCTCCGACGATGCCACTAT 58.958 57.895 0.00 0.00 0.00 2.12
4078 12151 4.757149 AGAGAAACACAAGCAGTCCATAAC 59.243 41.667 0.00 0.00 0.00 1.89
4079 12152 4.718961 AGAAACACAAGCAGTCCATAACT 58.281 39.130 0.00 0.00 39.44 2.24
4171 12245 3.250762 GCTAACACATGTTCTTCACAGCA 59.749 43.478 0.00 0.00 39.40 4.41
4172 12246 4.261155 GCTAACACATGTTCTTCACAGCAA 60.261 41.667 0.00 0.00 39.40 3.91
4173 12247 4.924305 AACACATGTTCTTCACAGCAAT 57.076 36.364 0.00 0.00 39.40 3.56
4174 12248 6.348458 GCTAACACATGTTCTTCACAGCAATA 60.348 38.462 0.00 0.00 39.40 1.90
4175 12249 6.579666 AACACATGTTCTTCACAGCAATAT 57.420 33.333 0.00 0.00 39.40 1.28
4176 12250 6.579666 ACACATGTTCTTCACAGCAATATT 57.420 33.333 0.00 0.00 39.40 1.28
4177 12251 6.384224 ACACATGTTCTTCACAGCAATATTG 58.616 36.000 11.27 11.27 39.40 1.90
4178 12252 8.472669 AACACATGTTCTTCACAGCAATATTGC 61.473 37.037 29.21 29.21 43.80 3.56
4199 12273 3.349006 ACAGCGAACTTGGCAGCG 61.349 61.111 0.00 0.00 34.34 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 6.657836 ACGTGCCATTAGTACTACATTTTC 57.342 37.500 0.91 0.00 0.00 2.29
162 164 9.988815 AATTGCACACTATTTACACCAAAAATA 57.011 25.926 0.00 0.00 0.00 1.40
164 166 8.723942 AAATTGCACACTATTTACACCAAAAA 57.276 26.923 0.00 0.00 30.84 1.94
168 170 7.268586 ACAAAAATTGCACACTATTTACACCA 58.731 30.769 0.00 0.00 32.09 4.17
435 461 9.807921 AATTGGTTCCATTAGTATTACCCATAG 57.192 33.333 0.00 0.00 0.00 2.23
466 2186 6.092944 TGCAAAACAAAAGTTCTCTAAGACGA 59.907 34.615 0.00 0.00 0.00 4.20
530 2250 5.357878 TGGAAGATTGCCAGTATGATTGTTC 59.642 40.000 0.00 0.00 39.69 3.18
538 2258 1.668419 GCGTGGAAGATTGCCAGTAT 58.332 50.000 0.00 0.00 35.77 2.12
543 2263 1.582610 TTTCGGCGTGGAAGATTGCC 61.583 55.000 6.85 0.00 44.09 4.52
564 2284 7.287696 TGGCTAGAAGAAAAGGAAGATTGTTTT 59.712 33.333 0.00 0.00 0.00 2.43
566 2286 6.306987 TGGCTAGAAGAAAAGGAAGATTGTT 58.693 36.000 0.00 0.00 0.00 2.83
567 2287 5.880901 TGGCTAGAAGAAAAGGAAGATTGT 58.119 37.500 0.00 0.00 0.00 2.71
568 2288 6.376581 ACATGGCTAGAAGAAAAGGAAGATTG 59.623 38.462 0.00 0.00 0.00 2.67
569 2289 6.488715 ACATGGCTAGAAGAAAAGGAAGATT 58.511 36.000 0.00 0.00 0.00 2.40
570 2290 6.069731 AGACATGGCTAGAAGAAAAGGAAGAT 60.070 38.462 0.00 0.00 0.00 2.40
571 2291 5.249393 AGACATGGCTAGAAGAAAAGGAAGA 59.751 40.000 0.00 0.00 0.00 2.87
572 2292 5.495640 AGACATGGCTAGAAGAAAAGGAAG 58.504 41.667 0.00 0.00 0.00 3.46
573 2293 5.505181 AGACATGGCTAGAAGAAAAGGAA 57.495 39.130 0.00 0.00 0.00 3.36
576 2296 7.050377 TGGATAAGACATGGCTAGAAGAAAAG 58.950 38.462 0.00 0.00 0.00 2.27
581 2301 5.069648 TGACTGGATAAGACATGGCTAGAAG 59.930 44.000 0.00 0.00 0.00 2.85
587 2325 2.843701 CCTGACTGGATAAGACATGGC 58.156 52.381 0.00 0.00 38.35 4.40
605 2344 4.713814 TGTAAGATGAGATGAGTTGAGCCT 59.286 41.667 0.00 0.00 0.00 4.58
684 2796 4.318546 GCAAAGCTGAGTTGCTGAATTTTG 60.319 41.667 13.22 0.00 46.31 2.44
686 2798 3.387397 GCAAAGCTGAGTTGCTGAATTT 58.613 40.909 13.22 0.00 46.31 1.82
695 2807 5.182001 CACCAACTAATAGCAAAGCTGAGTT 59.818 40.000 1.04 5.98 40.10 3.01
706 2818 5.392057 GCTTGTCCTTTCACCAACTAATAGC 60.392 44.000 0.00 0.00 0.00 2.97
740 2854 1.617804 CCTTGGGTAGTAGTGGACCGA 60.618 57.143 0.00 0.00 36.51 4.69
764 2878 1.852895 CGATTTGTGTACTAGCGAGGC 59.147 52.381 0.00 0.00 0.00 4.70
765 2879 3.106672 GACGATTTGTGTACTAGCGAGG 58.893 50.000 0.00 0.00 0.00 4.63
766 2880 3.786576 CAGACGATTTGTGTACTAGCGAG 59.213 47.826 0.00 0.00 0.00 5.03
767 2881 3.437741 TCAGACGATTTGTGTACTAGCGA 59.562 43.478 0.00 0.00 0.00 4.93
768 2882 3.754955 TCAGACGATTTGTGTACTAGCG 58.245 45.455 0.00 0.00 0.00 4.26
778 2897 5.748152 ACCACAATTTGTTTCAGACGATTTG 59.252 36.000 0.00 0.00 38.27 2.32
780 2899 5.067153 TGACCACAATTTGTTTCAGACGATT 59.933 36.000 0.00 0.00 0.00 3.34
785 2904 4.035091 CGACTGACCACAATTTGTTTCAGA 59.965 41.667 28.65 6.43 38.96 3.27
806 2925 5.471797 TGAAAACAATATTTGAGCCAGTCGA 59.528 36.000 0.00 0.00 0.00 4.20
813 2932 7.649306 ACAGTTGACTGAAAACAATATTTGAGC 59.351 33.333 17.42 0.00 46.59 4.26
815 2934 8.681806 TGACAGTTGACTGAAAACAATATTTGA 58.318 29.630 17.42 0.00 46.59 2.69
853 2972 2.092375 GGGGAGGAGGTATGTTTCTTGG 60.092 54.545 0.00 0.00 0.00 3.61
911 3037 2.100584 GGCTCAACATGACCAACAACAA 59.899 45.455 0.00 0.00 0.00 2.83
912 3038 1.680735 GGCTCAACATGACCAACAACA 59.319 47.619 0.00 0.00 0.00 3.33
915 3041 1.421268 AGAGGCTCAACATGACCAACA 59.579 47.619 18.26 0.00 0.00 3.33
917 3043 1.421268 ACAGAGGCTCAACATGACCAA 59.579 47.619 18.26 0.00 0.00 3.67
923 3049 2.936919 TGACAACAGAGGCTCAACAT 57.063 45.000 18.26 0.00 0.00 2.71
967 3102 1.415672 AACTTGGCGGAGGAGGACAA 61.416 55.000 0.00 0.00 0.00 3.18
1043 3178 2.843912 GAAGGGGGTGGATGCAGTGG 62.844 65.000 0.00 0.00 0.00 4.00
1061 3196 2.814336 CGTCGACATATGGATCAGAGGA 59.186 50.000 17.16 0.00 0.00 3.71
1084 3219 0.943673 CGCATCCGAATAATGTGGCA 59.056 50.000 0.00 0.00 36.29 4.92
1139 3275 3.535962 GGCCAGAGGGAGCTCGAG 61.536 72.222 8.45 8.45 35.59 4.04
1152 3288 2.609299 TCCATCGACTTGGGGCCA 60.609 61.111 4.39 0.00 37.37 5.36
1157 3293 2.169789 CGCTGCTCCATCGACTTGG 61.170 63.158 0.00 0.00 38.18 3.61
1205 3341 2.690497 CAACCCGATGCTCTCTCTTCTA 59.310 50.000 0.00 0.00 0.00 2.10
1218 3354 1.616865 TGAAGTCTTCGACAACCCGAT 59.383 47.619 8.06 0.00 38.45 4.18
1245 3381 3.345808 GAAGCTTGACCGCGTGCA 61.346 61.111 2.10 0.00 34.40 4.57
1265 3401 3.122971 ACATCGACTCGCGTCCGA 61.123 61.111 18.31 18.31 42.01 4.55
1269 3405 4.129737 CCCCACATCGACTCGCGT 62.130 66.667 5.77 0.00 41.80 6.01
1273 3409 2.022240 GAGGCTCCCCACATCGACTC 62.022 65.000 2.15 0.00 0.00 3.36
1274 3410 2.039624 AGGCTCCCCACATCGACT 59.960 61.111 0.00 0.00 0.00 4.18
1304 3441 3.705289 GTTGGTTGGCATGGGGGC 61.705 66.667 0.00 0.00 43.73 5.80
1317 3456 2.249309 CAAGCTGCACGTCGTTGG 59.751 61.111 1.02 0.00 0.00 3.77
1330 3469 4.966787 TTCCGGGGGTGTGCAAGC 62.967 66.667 0.00 0.00 0.00 4.01
1373 3512 3.561429 GGCAACGTGATTCGAGCA 58.439 55.556 0.00 0.00 42.23 4.26
1393 3532 0.816018 CTTCTCTCTCTCGGCCGCTA 60.816 60.000 23.51 9.97 0.00 4.26
1400 3539 4.513442 TCTCTTTCCTCTTCTCTCTCTCG 58.487 47.826 0.00 0.00 0.00 4.04
1401 3540 5.355350 CACTCTCTTTCCTCTTCTCTCTCTC 59.645 48.000 0.00 0.00 0.00 3.20
1430 3571 0.034477 AAACCCTAGGCCACAATCCG 60.034 55.000 5.01 0.00 0.00 4.18
1449 3590 5.950544 AATAACCTCACAGCCACTACATA 57.049 39.130 0.00 0.00 0.00 2.29
1450 3591 4.844349 AATAACCTCACAGCCACTACAT 57.156 40.909 0.00 0.00 0.00 2.29
1470 3612 9.347934 CAGTACACACACAAAAGAAAACATAAA 57.652 29.630 0.00 0.00 0.00 1.40
1480 3622 2.286833 CGTCCCAGTACACACACAAAAG 59.713 50.000 0.00 0.00 0.00 2.27
1493 3635 3.637273 GGTCAAGCCCGTCCCAGT 61.637 66.667 0.00 0.00 0.00 4.00
1494 3636 3.612247 CTGGTCAAGCCCGTCCCAG 62.612 68.421 0.00 0.00 37.00 4.45
1495 3637 3.636231 CTGGTCAAGCCCGTCCCA 61.636 66.667 0.00 0.00 36.04 4.37
1584 3754 3.325135 AGAGAATTCGAAGTTGGTCCAGT 59.675 43.478 3.35 0.00 0.00 4.00
1585 3755 3.931578 AGAGAATTCGAAGTTGGTCCAG 58.068 45.455 3.35 0.00 0.00 3.86
1586 3756 4.040461 AGAAGAGAATTCGAAGTTGGTCCA 59.960 41.667 3.35 0.00 0.00 4.02
1601 3771 7.362056 CCAAGATTTTATTGCCGAAGAAGAGAA 60.362 37.037 0.00 0.00 0.00 2.87
1608 3783 5.095490 GTGACCAAGATTTTATTGCCGAAG 58.905 41.667 0.00 0.00 0.00 3.79
1622 3797 1.215382 CGGCGATCTGTGACCAAGA 59.785 57.895 0.00 0.00 0.00 3.02
1685 3860 2.113562 CCGGGGTTTGGGAACGAA 59.886 61.111 0.00 0.00 36.61 3.85
1687 3862 3.256824 TAGCCGGGGTTTGGGAACG 62.257 63.158 3.09 0.00 36.61 3.95
1849 4027 2.408022 CCGACCTCGTCATCGTCC 59.592 66.667 0.00 0.00 36.60 4.79
2131 4309 4.415150 TCGTCGCCCGGGACTACT 62.415 66.667 29.31 0.00 37.11 2.57
2148 4329 4.695231 CGCCCTCGTCGTTGTCGT 62.695 66.667 0.00 0.00 38.33 4.34
2165 4346 0.530870 GGGTACTTGATCTGCTCCGC 60.531 60.000 0.00 0.00 0.00 5.54
2227 4408 1.200483 GTGAGTACATGGCGATGTCG 58.800 55.000 18.26 0.00 42.14 4.35
2468 5678 3.193267 GCAATTCTGGTTATCTGTGGCAA 59.807 43.478 0.00 0.00 0.00 4.52
2484 5694 1.338105 GGCCTTTCAGGGTTGCAATTC 60.338 52.381 0.59 0.00 35.37 2.17
2786 5996 0.389426 GCAGCTAAAGAACCGTCCGA 60.389 55.000 0.00 0.00 0.00 4.55
2788 5998 1.666189 GATGCAGCTAAAGAACCGTCC 59.334 52.381 0.00 0.00 0.00 4.79
2848 6058 5.281314 AGGGTACAGTACAATCTTCCTGAT 58.719 41.667 12.89 0.00 36.89 2.90
2969 6301 7.989741 AGAATATAACATTTGTCTGGTCCTCAG 59.010 37.037 0.00 0.00 44.68 3.35
3101 6924 7.309770 AGCTTTTAATTGGTTTGTAATCCCA 57.690 32.000 0.00 0.00 0.00 4.37
3373 11370 5.772393 TCTAGTATTTCAAAGGCCAAGGA 57.228 39.130 5.01 0.00 0.00 3.36
3427 11424 9.914834 TCGTACCCTAAACCTAAAGTTACTATA 57.085 33.333 0.00 0.00 37.88 1.31
3428 11425 8.823220 TCGTACCCTAAACCTAAAGTTACTAT 57.177 34.615 0.00 0.00 37.88 2.12
3530 11527 2.286184 GCTGCATGTTACCCGAATAACG 60.286 50.000 0.00 0.00 37.79 3.18
3659 11656 9.455847 GAGAAATCCTCATTAATTTTTCATCCG 57.544 33.333 0.00 0.00 41.58 4.18
3719 11716 6.405065 CCATGTTTCCAAATGTGATCGATTCT 60.405 38.462 0.00 0.00 0.00 2.40
3891 11893 3.549299 AAGAGCTGCAAATCAAAGACG 57.451 42.857 1.02 0.00 0.00 4.18
4019 12064 3.498397 GTCGGATGCTTTGTTGAGAGAAA 59.502 43.478 0.00 0.00 0.00 2.52
4104 12177 6.881602 TGCACATTGTGGTACATTTATAGTGA 59.118 34.615 18.05 0.00 44.52 3.41
4171 12245 4.379813 CCAAGTTCGCTGTGAAGCAATATT 60.380 41.667 3.49 0.00 37.23 1.28
4172 12246 3.127548 CCAAGTTCGCTGTGAAGCAATAT 59.872 43.478 3.49 0.00 37.23 1.28
4173 12247 2.483877 CCAAGTTCGCTGTGAAGCAATA 59.516 45.455 3.49 0.00 37.23 1.90
4174 12248 1.267806 CCAAGTTCGCTGTGAAGCAAT 59.732 47.619 3.49 0.00 37.23 3.56
4175 12249 0.662619 CCAAGTTCGCTGTGAAGCAA 59.337 50.000 3.49 0.00 37.23 3.91
4176 12250 1.785041 GCCAAGTTCGCTGTGAAGCA 61.785 55.000 3.49 0.00 37.23 3.91
4177 12251 1.081840 GCCAAGTTCGCTGTGAAGC 60.082 57.895 3.49 0.61 37.23 3.86
4178 12252 0.236711 CTGCCAAGTTCGCTGTGAAG 59.763 55.000 3.49 0.00 37.23 3.02
4179 12253 1.785041 GCTGCCAAGTTCGCTGTGAA 61.785 55.000 0.00 0.00 0.00 3.18
4180 12254 2.253758 GCTGCCAAGTTCGCTGTGA 61.254 57.895 1.70 0.00 0.00 3.58
4181 12255 2.253452 GCTGCCAAGTTCGCTGTG 59.747 61.111 1.70 0.00 0.00 3.66
4182 12256 3.349006 CGCTGCCAAGTTCGCTGT 61.349 61.111 1.70 0.00 0.00 4.40
4183 12257 4.748679 GCGCTGCCAAGTTCGCTG 62.749 66.667 0.00 0.00 43.70 5.18
4186 12260 1.143373 TATACGCGCTGCCAAGTTCG 61.143 55.000 5.73 0.00 0.00 3.95
4187 12261 1.003851 TTATACGCGCTGCCAAGTTC 58.996 50.000 5.73 0.00 0.00 3.01
4199 12273 3.678072 TCTGCAACTCTGTGTTTATACGC 59.322 43.478 0.00 0.00 36.63 4.42


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

AutoCloner maintained by Alex Coulton.