Multiple sequence alignment - TraesCS3B01G521000

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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 TraesCS3B01G521000 chr3B 100.000 3799 0 0 923 4721 764377613 764373815 0.000000e+00 7016.0
1 TraesCS3B01G521000 chr3B 91.803 976 72 5 2506 3474 764055132 764056106 0.000000e+00 1352.0
2 TraesCS3B01G521000 chr3B 100.000 560 0 0 1 560 764378535 764377976 0.000000e+00 1035.0
3 TraesCS3B01G521000 chr3B 90.894 604 54 1 1805 2407 764054192 764054795 0.000000e+00 809.0
4 TraesCS3B01G521000 chr3B 92.520 508 33 3 2109 2613 764050192 764050697 0.000000e+00 723.0
5 TraesCS3B01G521000 chr3B 80.261 998 147 29 1532 2502 44782641 44783615 0.000000e+00 706.0
6 TraesCS3B01G521000 chr3B 88.596 570 48 10 3364 3921 764050695 764051259 0.000000e+00 676.0
7 TraesCS3B01G521000 chr3B 84.076 471 52 11 2246 2712 44767362 44766911 2.610000e-117 433.0
8 TraesCS3B01G521000 chr3B 85.921 277 35 4 2829 3104 44783616 44783889 4.620000e-75 292.0
9 TraesCS3B01G521000 chr3A 94.684 3819 152 19 926 4721 709373593 709377383 0.000000e+00 5880.0
10 TraesCS3B01G521000 chr3A 85.388 657 78 9 2059 2712 36657675 36658316 0.000000e+00 665.0
11 TraesCS3B01G521000 chr3A 79.487 780 100 32 1837 2588 14768585 14769332 2.540000e-137 499.0
12 TraesCS3B01G521000 chr3A 77.273 484 68 25 1531 2012 36657234 36657677 3.650000e-61 246.0
13 TraesCS3B01G521000 chr3A 100.000 39 0 0 1067 1105 36657040 36657078 6.550000e-09 73.1
14 TraesCS3B01G521000 chr3D 95.204 3315 112 16 923 4215 574424688 574427977 0.000000e+00 5197.0
15 TraesCS3B01G521000 chr3D 79.583 1200 171 31 1531 2712 26574489 26573346 0.000000e+00 791.0
16 TraesCS3B01G521000 chr3D 82.448 621 97 10 1887 2502 26582070 26582683 2.500000e-147 532.0
17 TraesCS3B01G521000 chr3D 84.838 277 35 5 2829 3104 26582684 26582954 6.020000e-69 272.0
18 TraesCS3B01G521000 chr3D 91.146 192 11 2 4216 4406 574428069 574428255 6.060000e-64 255.0
19 TraesCS3B01G521000 chr3D 93.600 125 8 0 4434 4558 574428251 574428375 2.240000e-43 187.0
20 TraesCS3B01G521000 chr3D 85.135 74 8 3 1067 1140 26581595 26581665 6.550000e-09 73.1
21 TraesCS3B01G521000 chr3D 86.364 66 6 3 1067 1131 26574668 26574605 8.480000e-08 69.4
22 TraesCS3B01G521000 chr1B 93.839 422 25 1 1 422 12330811 12330391 6.660000e-178 634.0
23 TraesCS3B01G521000 chr1B 98.571 70 1 0 420 489 12328783 12328714 1.780000e-24 124.0
24 TraesCS3B01G521000 chr6D 85.246 61 9 0 433 493 9476036 9475976 3.940000e-06 63.9
25 TraesCS3B01G521000 chrUn 94.286 35 2 0 469 503 65893992 65894026 2.000000e-03 54.7


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 TraesCS3B01G521000 chr3B 764373815 764378535 4720 True 4025.500000 7016 100.000000 1 4721 2 chr3B.!!$R2 4720
1 TraesCS3B01G521000 chr3B 764050192 764056106 5914 False 890.000000 1352 90.953250 1805 3921 4 chr3B.!!$F2 2116
2 TraesCS3B01G521000 chr3B 44782641 44783889 1248 False 499.000000 706 83.091000 1532 3104 2 chr3B.!!$F1 1572
3 TraesCS3B01G521000 chr3A 709373593 709377383 3790 False 5880.000000 5880 94.684000 926 4721 1 chr3A.!!$F2 3795
4 TraesCS3B01G521000 chr3A 14768585 14769332 747 False 499.000000 499 79.487000 1837 2588 1 chr3A.!!$F1 751
5 TraesCS3B01G521000 chr3A 36657040 36658316 1276 False 328.033333 665 87.553667 1067 2712 3 chr3A.!!$F3 1645
6 TraesCS3B01G521000 chr3D 574424688 574428375 3687 False 1879.666667 5197 93.316667 923 4558 3 chr3D.!!$F2 3635
7 TraesCS3B01G521000 chr3D 26573346 26574668 1322 True 430.200000 791 82.973500 1067 2712 2 chr3D.!!$R1 1645
8 TraesCS3B01G521000 chr3D 26581595 26582954 1359 False 292.366667 532 84.140333 1067 3104 3 chr3D.!!$F1 2037
9 TraesCS3B01G521000 chr1B 12328714 12330811 2097 True 379.000000 634 96.205000 1 489 2 chr1B.!!$R1 488

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
535 2146 0.037326 GACATCCGTGCCAGTCTCAA 60.037 55.0 0.00 0.0 0.00 3.02 F
544 2155 0.037326 GCCAGTCTCAATGTCGTGGA 60.037 55.0 0.00 0.0 0.00 4.02 F
547 2158 0.247736 AGTCTCAATGTCGTGGAGCC 59.752 55.0 0.00 0.0 0.00 4.70 F
548 2159 0.741221 GTCTCAATGTCGTGGAGCCC 60.741 60.0 0.00 0.0 0.00 5.19 F
1701 3349 1.079503 CTTACTGCGAGGCCAGAAAC 58.920 55.0 5.01 0.0 36.67 2.78 F
3125 5642 0.179137 GGCTGCTTTCCAAATACCGC 60.179 55.0 0.00 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1875 4082 1.026182 ACCCATACACGAGCGTACGA 61.026 55.000 21.65 0.00 37.03 3.43 R
2349 4574 4.411013 TCTCAGTCATCTCACTCAGGAAA 58.589 43.478 0.00 0.00 0.00 3.13 R
2526 5038 4.588106 TCATCCATCTTTTTGTCCTTGCAA 59.412 37.500 0.00 0.00 0.00 4.08 R
2535 5047 5.330295 CGAGAAGCTTCATCCATCTTTTTG 58.670 41.667 27.57 3.76 0.00 2.44 R
3682 6206 1.550524 AGTATCTCGCTTGCTGGTCAA 59.449 47.619 0.00 0.00 0.00 3.18 R
4115 6644 1.402613 CCGGTTACAATTAAAGGCGGG 59.597 52.381 0.00 0.00 0.00 6.13 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
84 85 1.532868 CTCTCACAAAGGTTTCCGCTG 59.467 52.381 0.00 0.00 0.00 5.18
111 112 1.900486 CCTCCAAACCGGTAGAGTTCT 59.100 52.381 21.33 0.00 35.57 3.01
121 122 2.476519 CGGTAGAGTTCTTGTCTCTCGC 60.477 54.545 0.00 0.00 41.66 5.03
136 137 0.706729 CTCGCCACGTTACTTTCGAC 59.293 55.000 0.00 0.00 0.00 4.20
201 202 4.268720 CCCCCTCTCTTCTCCTCG 57.731 66.667 0.00 0.00 0.00 4.63
205 206 1.388547 CCCTCTCTTCTCCTCGTCAG 58.611 60.000 0.00 0.00 0.00 3.51
206 207 0.738389 CCTCTCTTCTCCTCGTCAGC 59.262 60.000 0.00 0.00 0.00 4.26
216 217 1.803519 CTCGTCAGCTCGCTTCCAC 60.804 63.158 0.00 0.00 0.00 4.02
217 218 2.811317 CGTCAGCTCGCTTCCACC 60.811 66.667 0.00 0.00 0.00 4.61
271 272 0.179056 CTGTTCACGTCCCACCACTT 60.179 55.000 0.00 0.00 0.00 3.16
289 290 0.605050 TTGCGCACCAATCTGCTACA 60.605 50.000 11.12 0.00 34.77 2.74
295 296 1.556911 CACCAATCTGCTACACCTCCT 59.443 52.381 0.00 0.00 0.00 3.69
300 301 0.614979 TCTGCTACACCTCCTCCCAC 60.615 60.000 0.00 0.00 0.00 4.61
343 344 4.636249 CTGCAGAATATTCTACTCCCACC 58.364 47.826 17.53 0.99 35.34 4.61
364 365 1.001641 GTCACCCCATGCTGCTTCT 60.002 57.895 0.00 0.00 0.00 2.85
369 370 1.751927 CCCATGCTGCTTCTCCCAC 60.752 63.158 0.00 0.00 0.00 4.61
378 379 2.036098 TTCTCCCACTACGCCGGA 59.964 61.111 5.05 0.00 0.00 5.14
379 380 1.601419 CTTCTCCCACTACGCCGGAA 61.601 60.000 5.05 0.00 0.00 4.30
401 402 2.074948 CCCACCATCCCTCCTCCTG 61.075 68.421 0.00 0.00 0.00 3.86
418 419 0.250081 CTGCCTATTCCTTCGAGCCC 60.250 60.000 0.00 0.00 0.00 5.19
422 2033 1.211949 CCTATTCCTTCGAGCCCCAAA 59.788 52.381 0.00 0.00 0.00 3.28
489 2100 4.143543 TCAATTTGCTGACATCTTCACCA 58.856 39.130 0.00 0.00 0.00 4.17
490 2101 4.583907 TCAATTTGCTGACATCTTCACCAA 59.416 37.500 0.00 0.00 29.40 3.67
491 2102 4.778534 ATTTGCTGACATCTTCACCAAG 57.221 40.909 0.00 0.00 32.49 3.61
493 2104 1.271543 TGCTGACATCTTCACCAAGGG 60.272 52.381 0.00 0.00 0.00 3.95
495 2106 0.038166 TGACATCTTCACCAAGGGGC 59.962 55.000 0.00 0.00 37.90 5.80
496 2107 0.681243 GACATCTTCACCAAGGGGCC 60.681 60.000 0.00 0.00 37.90 5.80
497 2108 1.750399 CATCTTCACCAAGGGGCCG 60.750 63.158 0.00 0.00 37.90 6.13
498 2109 3.645268 ATCTTCACCAAGGGGCCGC 62.645 63.158 12.88 12.88 37.90 6.53
515 2126 2.974698 CCGCCCGCATCCTTCATC 60.975 66.667 0.00 0.00 0.00 2.92
516 2127 3.341043 CGCCCGCATCCTTCATCG 61.341 66.667 0.00 0.00 0.00 3.84
517 2128 2.108976 GCCCGCATCCTTCATCGA 59.891 61.111 0.00 0.00 0.00 3.59
518 2129 2.247437 GCCCGCATCCTTCATCGAC 61.247 63.158 0.00 0.00 0.00 4.20
519 2130 1.143838 CCCGCATCCTTCATCGACA 59.856 57.895 0.00 0.00 0.00 4.35
520 2131 0.250038 CCCGCATCCTTCATCGACAT 60.250 55.000 0.00 0.00 0.00 3.06
521 2132 1.143305 CCGCATCCTTCATCGACATC 58.857 55.000 0.00 0.00 0.00 3.06
522 2133 1.143305 CGCATCCTTCATCGACATCC 58.857 55.000 0.00 0.00 0.00 3.51
523 2134 1.143305 GCATCCTTCATCGACATCCG 58.857 55.000 0.00 0.00 40.25 4.18
524 2135 1.539065 GCATCCTTCATCGACATCCGT 60.539 52.381 0.00 0.00 39.75 4.69
525 2136 2.130395 CATCCTTCATCGACATCCGTG 58.870 52.381 0.00 0.00 39.75 4.94
526 2137 0.179111 TCCTTCATCGACATCCGTGC 60.179 55.000 0.00 0.00 39.75 5.34
527 2138 1.154205 CCTTCATCGACATCCGTGCC 61.154 60.000 0.00 0.00 39.75 5.01
528 2139 0.460109 CTTCATCGACATCCGTGCCA 60.460 55.000 0.00 0.00 39.75 4.92
529 2140 0.460109 TTCATCGACATCCGTGCCAG 60.460 55.000 0.00 0.00 39.75 4.85
530 2141 1.153568 CATCGACATCCGTGCCAGT 60.154 57.895 0.00 0.00 39.75 4.00
531 2142 1.141881 ATCGACATCCGTGCCAGTC 59.858 57.895 0.00 0.00 39.75 3.51
533 2144 1.517257 CGACATCCGTGCCAGTCTC 60.517 63.158 0.00 0.00 0.00 3.36
535 2146 0.037326 GACATCCGTGCCAGTCTCAA 60.037 55.000 0.00 0.00 0.00 3.02
537 2148 1.012086 CATCCGTGCCAGTCTCAATG 58.988 55.000 0.00 0.00 0.00 2.82
538 2149 0.615331 ATCCGTGCCAGTCTCAATGT 59.385 50.000 0.00 0.00 0.00 2.71
540 2151 1.354337 CCGTGCCAGTCTCAATGTCG 61.354 60.000 0.00 0.00 0.00 4.35
541 2152 0.667487 CGTGCCAGTCTCAATGTCGT 60.667 55.000 0.00 0.00 0.00 4.34
542 2153 0.792640 GTGCCAGTCTCAATGTCGTG 59.207 55.000 0.00 0.00 0.00 4.35
543 2154 0.320683 TGCCAGTCTCAATGTCGTGG 60.321 55.000 0.00 0.00 0.00 4.94
544 2155 0.037326 GCCAGTCTCAATGTCGTGGA 60.037 55.000 0.00 0.00 0.00 4.02
545 2156 2.001812 CCAGTCTCAATGTCGTGGAG 57.998 55.000 0.00 0.00 0.00 3.86
546 2157 1.354040 CAGTCTCAATGTCGTGGAGC 58.646 55.000 0.00 0.00 0.00 4.70
547 2158 0.247736 AGTCTCAATGTCGTGGAGCC 59.752 55.000 0.00 0.00 0.00 4.70
548 2159 0.741221 GTCTCAATGTCGTGGAGCCC 60.741 60.000 0.00 0.00 0.00 5.19
549 2160 1.811266 CTCAATGTCGTGGAGCCCG 60.811 63.158 0.00 0.00 0.00 6.13
555 2166 3.680786 TCGTGGAGCCCGACACTG 61.681 66.667 0.00 0.00 35.51 3.66
1195 2818 1.226262 GTCTCCTCGCTCCTCCTCT 59.774 63.158 0.00 0.00 0.00 3.69
1206 2829 3.080121 CTCCTCTTGCCGGCCTCT 61.080 66.667 26.77 0.00 0.00 3.69
1209 2832 2.664081 CCTCTTGCCGGCCTCTCTT 61.664 63.158 26.77 0.00 0.00 2.85
1210 2833 1.298014 CTCTTGCCGGCCTCTCTTT 59.702 57.895 26.77 0.00 0.00 2.52
1248 2871 2.498726 CGCTTCCTCCTCCTGCTC 59.501 66.667 0.00 0.00 0.00 4.26
1578 3226 3.421844 GGCTTCCCACATACTGTTTTCT 58.578 45.455 0.00 0.00 0.00 2.52
1635 3283 3.426695 CCCTGTTCGATGAAATGCTTCAC 60.427 47.826 0.00 0.00 44.28 3.18
1701 3349 1.079503 CTTACTGCGAGGCCAGAAAC 58.920 55.000 5.01 0.00 36.67 2.78
1863 4070 1.742268 GCCAGAGGAATCAAAGCTGAC 59.258 52.381 0.00 0.00 33.30 3.51
1958 4174 3.419580 CATGGCCAGGCTGGGGTA 61.420 66.667 33.43 4.19 38.19 3.69
2315 4538 7.394923 TCCGTACAATTCCTTGATTAATGGTTT 59.605 33.333 0.00 0.00 36.20 3.27
2349 4574 2.172505 TGATTTAGACATGGCGATGGGT 59.827 45.455 13.62 2.20 33.39 4.51
2526 5038 6.215845 GTTCACAGCACTTATCAATGGTTTT 58.784 36.000 0.00 0.00 0.00 2.43
2535 5047 6.146021 CACTTATCAATGGTTTTTGCAAGGAC 59.854 38.462 0.00 2.39 0.00 3.85
2757 5274 1.367471 CTTGACCAGTGGAGCGTCA 59.633 57.895 18.40 6.09 34.80 4.35
2799 5316 2.173782 TGACCTAGAAAACAACTGCCCA 59.826 45.455 0.00 0.00 0.00 5.36
2859 5376 2.050144 TGCAGAGAAGGAAGGTTGACT 58.950 47.619 0.00 0.00 0.00 3.41
2932 5449 8.213518 TGATCTTGTCAGCTTTACCATTATTC 57.786 34.615 0.00 0.00 31.80 1.75
2953 5470 3.769300 TCTGTATACAGCCTTGAAGCAGA 59.231 43.478 25.31 3.75 43.46 4.26
2984 5501 7.144661 ACAGAAAAATCATGCGTGTTATTGAA 58.855 30.769 5.68 0.00 0.00 2.69
3125 5642 0.179137 GGCTGCTTTCCAAATACCGC 60.179 55.000 0.00 0.00 0.00 5.68
3656 6180 1.134640 ACCGAACTGGCGCACATATAA 60.135 47.619 10.83 0.00 43.94 0.98
3682 6206 6.042666 AGCTCTTTTCTTAGGAACTTCTCTGT 59.957 38.462 0.00 0.00 41.75 3.41
3751 6275 3.004171 TCACCGTTTCCAATGTTATCCG 58.996 45.455 0.00 0.00 0.00 4.18
3777 6301 3.010420 CCGAGTAGTCTGACTCACATCA 58.990 50.000 14.62 0.00 45.23 3.07
3782 6306 1.620819 AGTCTGACTCACATCACACCC 59.379 52.381 4.06 0.00 0.00 4.61
3918 6447 6.070995 CCTGTACCTCCTGTCATGTTTTAGTA 60.071 42.308 0.00 0.00 0.00 1.82
3952 6481 4.005650 ACCTGACAATGCTGTATCAGTTG 58.994 43.478 0.00 0.00 35.30 3.16
3956 6485 6.317140 CCTGACAATGCTGTATCAGTTGTTAT 59.683 38.462 7.02 0.00 35.30 1.89
4030 6559 4.464244 TGTTGGTGTTGTTTCTTCCATGAA 59.536 37.500 0.00 0.00 0.00 2.57
4063 6592 9.890629 TCTTTTGCATAGTATAATGAGTTGTCT 57.109 29.630 0.00 0.00 0.00 3.41
4066 6595 5.991606 TGCATAGTATAATGAGTTGTCTGGC 59.008 40.000 0.00 0.00 0.00 4.85
4158 6687 7.446625 CCGGAATGAATGAAATAAGGAAGATCT 59.553 37.037 0.00 0.00 0.00 2.75
4210 6739 9.997482 TCAGTTCTTAACATGTAAACAGAAAAC 57.003 29.630 0.00 0.00 0.00 2.43
4247 6866 6.297582 TGCATTGTCAAATTTGGGAAGAAAT 58.702 32.000 17.90 6.69 0.00 2.17
4248 6867 6.427547 TGCATTGTCAAATTTGGGAAGAAATC 59.572 34.615 17.90 2.05 0.00 2.17
4330 6950 4.935808 ACTTTTTAACAGTGATAGGGCGAG 59.064 41.667 0.00 0.00 0.00 5.03
4411 7031 1.329906 GAATCTGAAGCATGCAGGACG 59.670 52.381 21.98 4.07 44.09 4.79
4425 7045 1.971167 GGACGCATGCCTTGTTCCA 60.971 57.895 13.15 0.00 32.58 3.53
4427 7047 1.228245 ACGCATGCCTTGTTCCACT 60.228 52.632 13.15 0.00 0.00 4.00
4501 7121 2.948315 CCAGCTCCTCAAAATCTAAGCC 59.052 50.000 0.00 0.00 0.00 4.35
4504 7124 1.943340 CTCCTCAAAATCTAAGCCCGC 59.057 52.381 0.00 0.00 0.00 6.13
4524 7144 2.521126 CCGACCATAACCAGGGTTTTT 58.479 47.619 9.30 0.00 39.47 1.94
4578 7198 9.585099 TTATCTGCCATTTTTATGCTTTAGTTG 57.415 29.630 0.00 0.00 0.00 3.16
4598 7218 7.624360 AGTTGAACTTTAACATCTGTGTGAA 57.376 32.000 0.00 0.00 38.92 3.18
4653 7277 3.769739 ACATGCTCTGTAACAGGAACA 57.230 42.857 0.00 0.00 35.91 3.18
4696 7320 5.781306 TCTGTACACCAAGACCAACCTAATA 59.219 40.000 0.00 0.00 0.00 0.98
4703 7327 6.484643 CACCAAGACCAACCTAATATCTGATG 59.515 42.308 0.00 0.00 0.00 3.07
4709 7333 5.428457 ACCAACCTAATATCTGATGGTGTGA 59.572 40.000 0.00 0.00 38.22 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.434359 CGGTTTGGAGGTCGAGGC 60.434 66.667 0.00 0.00 0.00 4.70
121 122 2.535166 TGTTTCGTCGAAAGTAACGTGG 59.465 45.455 20.27 0.00 39.78 4.94
188 189 1.670811 GAGCTGACGAGGAGAAGAGAG 59.329 57.143 0.00 0.00 0.00 3.20
201 202 2.435059 GGGTGGAAGCGAGCTGAC 60.435 66.667 0.00 0.00 33.03 3.51
205 206 4.785453 CTGGGGGTGGAAGCGAGC 62.785 72.222 0.00 0.00 33.03 5.03
206 207 4.785453 GCTGGGGGTGGAAGCGAG 62.785 72.222 0.00 0.00 33.03 5.03
325 326 2.296471 CGCGGTGGGAGTAGAATATTCT 59.704 50.000 21.28 21.28 41.24 2.40
364 365 3.384532 GGTTCCGGCGTAGTGGGA 61.385 66.667 6.01 0.00 0.00 4.37
369 370 3.697747 TGGGTGGTTCCGGCGTAG 61.698 66.667 6.01 0.00 37.00 3.51
378 379 2.238701 GGAGGGATGGTGGGTGGTT 61.239 63.158 0.00 0.00 0.00 3.67
379 380 2.614013 GGAGGGATGGTGGGTGGT 60.614 66.667 0.00 0.00 0.00 4.16
401 402 1.071642 GGGGCTCGAAGGAATAGGC 59.928 63.158 0.00 0.00 35.21 3.93
418 419 3.108376 ACTTCTCCTAGGGCTACTTTGG 58.892 50.000 9.46 0.00 0.00 3.28
422 2033 2.241685 TCGAACTTCTCCTAGGGCTACT 59.758 50.000 9.46 0.00 0.00 2.57
498 2109 2.974698 GATGAAGGATGCGGGCGG 60.975 66.667 0.00 0.00 0.00 6.13
501 2112 0.250038 ATGTCGATGAAGGATGCGGG 60.250 55.000 0.00 0.00 0.00 6.13
502 2113 1.143305 GATGTCGATGAAGGATGCGG 58.857 55.000 0.00 0.00 0.00 5.69
503 2114 1.143305 GGATGTCGATGAAGGATGCG 58.857 55.000 0.00 0.00 0.00 4.73
504 2115 1.143305 CGGATGTCGATGAAGGATGC 58.857 55.000 0.00 0.00 42.43 3.91
505 2116 2.130395 CACGGATGTCGATGAAGGATG 58.870 52.381 0.00 0.00 42.43 3.51
506 2117 1.539065 GCACGGATGTCGATGAAGGAT 60.539 52.381 0.00 0.00 42.43 3.24
507 2118 0.179111 GCACGGATGTCGATGAAGGA 60.179 55.000 0.00 0.00 42.43 3.36
509 2120 0.460109 TGGCACGGATGTCGATGAAG 60.460 55.000 0.00 0.00 42.43 3.02
511 2122 1.141665 CTGGCACGGATGTCGATGA 59.858 57.895 0.00 0.00 42.43 2.92
512 2123 1.148157 GACTGGCACGGATGTCGATG 61.148 60.000 0.00 0.00 42.43 3.84
513 2124 1.141881 GACTGGCACGGATGTCGAT 59.858 57.895 0.00 0.00 42.43 3.59
514 2125 1.934220 GAGACTGGCACGGATGTCGA 61.934 60.000 0.00 0.00 42.43 4.20
515 2126 1.517257 GAGACTGGCACGGATGTCG 60.517 63.158 0.00 0.00 45.88 4.35
516 2127 0.037326 TTGAGACTGGCACGGATGTC 60.037 55.000 0.00 0.00 38.67 3.06
517 2128 0.615331 ATTGAGACTGGCACGGATGT 59.385 50.000 0.00 0.00 38.67 3.06
518 2129 1.012086 CATTGAGACTGGCACGGATG 58.988 55.000 0.00 0.00 38.67 3.51
519 2130 0.615331 ACATTGAGACTGGCACGGAT 59.385 50.000 0.00 0.00 38.67 4.18
520 2131 0.037326 GACATTGAGACTGGCACGGA 60.037 55.000 0.00 0.00 38.67 4.69
521 2132 1.354337 CGACATTGAGACTGGCACGG 61.354 60.000 0.00 0.00 42.99 4.94
522 2133 0.667487 ACGACATTGAGACTGGCACG 60.667 55.000 0.00 0.00 0.00 5.34
523 2134 0.792640 CACGACATTGAGACTGGCAC 59.207 55.000 0.00 0.00 0.00 5.01
524 2135 0.320683 CCACGACATTGAGACTGGCA 60.321 55.000 0.00 0.00 0.00 4.92
525 2136 0.037326 TCCACGACATTGAGACTGGC 60.037 55.000 0.00 0.00 0.00 4.85
526 2137 2.001812 CTCCACGACATTGAGACTGG 57.998 55.000 0.00 0.00 0.00 4.00
527 2138 1.354040 GCTCCACGACATTGAGACTG 58.646 55.000 0.00 0.00 0.00 3.51
528 2139 0.247736 GGCTCCACGACATTGAGACT 59.752 55.000 0.00 0.00 31.21 3.24
529 2140 0.741221 GGGCTCCACGACATTGAGAC 60.741 60.000 0.00 0.00 33.20 3.36
530 2141 1.596934 GGGCTCCACGACATTGAGA 59.403 57.895 0.00 0.00 0.00 3.27
531 2142 1.811266 CGGGCTCCACGACATTGAG 60.811 63.158 0.00 0.00 0.00 3.02
533 2144 2.264480 TCGGGCTCCACGACATTG 59.736 61.111 0.00 0.00 35.12 2.82
538 2149 3.680786 CAGTGTCGGGCTCCACGA 61.681 66.667 0.00 0.00 36.69 4.35
1034 2645 2.455532 TGGGGTTGGGGTTGGGAT 60.456 61.111 0.00 0.00 0.00 3.85
1035 2646 3.513566 GTGGGGTTGGGGTTGGGA 61.514 66.667 0.00 0.00 0.00 4.37
1173 2796 3.404141 GAGGAGCGAGGAGACGTGC 62.404 68.421 0.00 0.00 35.59 5.34
1195 2818 2.351276 GGAAAGAGAGGCCGGCAA 59.649 61.111 30.85 0.00 0.00 4.52
1248 2871 2.760385 GAGACGAGGTGGGGAGGG 60.760 72.222 0.00 0.00 0.00 4.30
1507 3148 2.214920 GGGACAGGTGAAGGACGGT 61.215 63.158 0.00 0.00 0.00 4.83
1578 3226 4.745125 GTGAACTGACGAATCTTGACAAGA 59.255 41.667 19.85 19.85 42.69 3.02
1635 3283 2.729479 ATCCAGGCGAGCACCAGAG 61.729 63.158 0.00 0.00 0.00 3.35
1863 4070 3.027710 GAGCGTACGATAAGTCACTTCG 58.972 50.000 21.65 0.00 38.76 3.79
1875 4082 1.026182 ACCCATACACGAGCGTACGA 61.026 55.000 21.65 0.00 37.03 3.43
2315 4538 5.559770 TGTCTAAATCATCCTGTTTGCAGA 58.440 37.500 0.00 0.00 45.28 4.26
2349 4574 4.411013 TCTCAGTCATCTCACTCAGGAAA 58.589 43.478 0.00 0.00 0.00 3.13
2526 5038 4.588106 TCATCCATCTTTTTGTCCTTGCAA 59.412 37.500 0.00 0.00 0.00 4.08
2535 5047 5.330295 CGAGAAGCTTCATCCATCTTTTTG 58.670 41.667 27.57 3.76 0.00 2.44
2799 5316 4.082949 GCGGTTAGGCTAAATTTGTTCAGT 60.083 41.667 8.86 0.00 0.00 3.41
2859 5376 4.201657 CATTCCAGACATGGTATGCTTCA 58.798 43.478 0.00 0.00 44.38 3.02
2932 5449 4.128925 TCTGCTTCAAGGCTGTATACAG 57.871 45.455 25.68 25.68 46.40 2.74
2953 5470 6.855836 ACACGCATGATTTTTCTGTATCATT 58.144 32.000 0.00 0.00 38.97 2.57
2984 5501 5.624159 TGACACATTTTTCTGTCATCTCCT 58.376 37.500 0.00 0.00 36.51 3.69
3417 5937 5.105595 GCTAATGCAATCAGGAAAAAGACCT 60.106 40.000 0.00 0.00 39.41 3.85
3656 6180 6.934083 CAGAGAAGTTCCTAAGAAAAGAGCTT 59.066 38.462 0.00 0.00 34.31 3.74
3682 6206 1.550524 AGTATCTCGCTTGCTGGTCAA 59.449 47.619 0.00 0.00 0.00 3.18
3894 6423 5.794894 ACTAAAACATGACAGGAGGTACAG 58.205 41.667 0.00 0.00 0.00 2.74
3900 6429 9.449719 AACCTATTTACTAAAACATGACAGGAG 57.550 33.333 0.00 0.00 0.00 3.69
3929 6458 3.866651 ACTGATACAGCATTGTCAGGTC 58.133 45.455 13.53 0.00 38.76 3.85
3952 6481 7.603024 GGGCAGTATAATCCACTGAGTTATAAC 59.397 40.741 7.57 7.57 45.10 1.89
3956 6485 5.070446 CAGGGCAGTATAATCCACTGAGTTA 59.930 44.000 6.67 0.00 45.10 2.24
4054 6583 2.009681 TGGAGTAGCCAGACAACTCA 57.990 50.000 4.31 0.00 43.33 3.41
4115 6644 1.402613 CCGGTTACAATTAAAGGCGGG 59.597 52.381 0.00 0.00 0.00 6.13
4117 6646 4.095185 TCATTCCGGTTACAATTAAAGGCG 59.905 41.667 0.00 0.00 0.00 5.52
4158 6687 2.409378 GCAAACAGTACGCGTTAAGCTA 59.591 45.455 20.78 0.00 45.59 3.32
4217 6836 8.455903 TTCCCAAATTTGACAATGCAAAATTA 57.544 26.923 19.86 0.00 40.72 1.40
4247 6866 8.966868 GTATCCCAAATTTTATTCAGTCTTGGA 58.033 33.333 0.00 0.00 34.97 3.53
4248 6867 8.748412 TGTATCCCAAATTTTATTCAGTCTTGG 58.252 33.333 0.00 0.00 33.20 3.61
4284 6904 3.350219 AAATGCCCATGTTACTCGACT 57.650 42.857 0.00 0.00 0.00 4.18
4285 6905 3.936453 TGTAAATGCCCATGTTACTCGAC 59.064 43.478 5.18 0.00 0.00 4.20
4330 6950 2.128771 TATGCTCAAAACCTCAGGCC 57.871 50.000 0.00 0.00 0.00 5.19
4411 7031 2.531522 AAAAGTGGAACAAGGCATGC 57.468 45.000 9.90 9.90 44.16 4.06
4501 7121 2.203015 CCTGGTTATGGTCGGCGG 60.203 66.667 7.21 0.00 0.00 6.13
4504 7124 2.209690 AAAACCCTGGTTATGGTCGG 57.790 50.000 1.21 0.00 37.35 4.79
4578 7198 6.305693 AGCTTCACACAGATGTTAAAGTTC 57.694 37.500 0.00 0.00 36.72 3.01
4598 7218 5.817816 GTCCATTGCAGTTAACATACTAGCT 59.182 40.000 8.61 0.00 0.00 3.32
4653 7277 2.832129 AGACCACGATTACAGACACCAT 59.168 45.455 0.00 0.00 0.00 3.55
4683 7307 5.667626 ACACCATCAGATATTAGGTTGGTCT 59.332 40.000 0.00 0.00 33.88 3.85
4696 7320 5.364735 TGTACAGATGATCACACCATCAGAT 59.635 40.000 0.00 0.00 42.03 2.90


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

AutoCloner maintained by Alex Coulton.