Multiple sequence alignment - TraesCS4A01G197800

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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 TraesCS4A01G197800 chr4A 100.000 2837 0 0 1 2837 482134512 482131676 0.000000e+00 5240.0
1 TraesCS4A01G197800 chr4A 80.556 108 15 6 2137 2240 537287651 537287756 8.430000e-11 78.7
2 TraesCS4A01G197800 chr4D 91.610 2193 108 26 1 2158 96522595 96524746 0.000000e+00 2961.0
3 TraesCS4A01G197800 chr4D 87.671 511 37 6 2348 2834 96525782 96526290 3.170000e-159 571.0
4 TraesCS4A01G197800 chr4B 91.478 2030 104 25 1 2005 136531467 136533452 0.000000e+00 2726.0
5 TraesCS4A01G197800 chr4B 89.273 289 12 1 2350 2619 136534033 136534321 7.520000e-91 344.0
6 TraesCS4A01G197800 chr4B 87.086 302 19 10 2012 2309 136533746 136534031 9.800000e-85 324.0
7 TraesCS4A01G197800 chr1B 89.474 76 8 0 1308 1383 592650907 592650982 2.330000e-16 97.1
8 TraesCS4A01G197800 chr1B 81.731 104 12 4 2137 2237 643058665 643058764 2.340000e-11 80.5
9 TraesCS4A01G197800 chr1B 100.000 34 0 0 1308 1341 654526217 654526184 2.360000e-06 63.9
10 TraesCS4A01G197800 chr6B 81.897 116 13 5 2140 2250 82538667 82538555 1.080000e-14 91.6
11 TraesCS4A01G197800 chr2B 83.168 101 11 4 2139 2236 557342547 557342450 1.400000e-13 87.9
12 TraesCS4A01G197800 chr2B 100.000 33 0 0 1308 1340 111369903 111369871 8.490000e-06 62.1
13 TraesCS4A01G197800 chr3D 80.342 117 20 3 2136 2251 578283375 578283261 5.040000e-13 86.1
14 TraesCS4A01G197800 chr3D 79.661 118 19 5 2136 2250 574338442 574338327 2.340000e-11 80.5
15 TraesCS4A01G197800 chr3D 78.512 121 19 4 2137 2253 495315099 495315216 3.920000e-09 73.1
16 TraesCS4A01G197800 chr3B 80.672 119 16 4 2136 2250 97725488 97725603 5.040000e-13 86.1
17 TraesCS4A01G197800 chr3B 95.238 42 2 0 2308 2349 651887496 651887455 1.820000e-07 67.6
18 TraesCS4A01G197800 chr3B 93.023 43 3 0 2307 2349 738120332 738120290 2.360000e-06 63.9
19 TraesCS4A01G197800 chr5D 95.122 41 2 0 2309 2349 255700781 255700741 6.560000e-07 65.8
20 TraesCS4A01G197800 chr5D 93.023 43 3 0 2307 2349 229934216 229934174 2.360000e-06 63.9
21 TraesCS4A01G197800 chr5B 95.122 41 2 0 2309 2349 411429009 411429049 6.560000e-07 65.8
22 TraesCS4A01G197800 chr1A 95.122 41 2 0 2309 2349 394029061 394029101 6.560000e-07 65.8
23 TraesCS4A01G197800 chr1A 93.023 43 3 0 2307 2349 426880167 426880125 2.360000e-06 63.9
24 TraesCS4A01G197800 chrUn 100.000 34 0 0 1308 1341 473127812 473127845 2.360000e-06 63.9
25 TraesCS4A01G197800 chrUn 100.000 33 0 0 1309 1341 473127891 473127923 8.490000e-06 62.1
26 TraesCS4A01G197800 chrUn 100.000 33 0 0 1309 1341 475075511 475075543 8.490000e-06 62.1
27 TraesCS4A01G197800 chr5A 93.023 43 3 0 2307 2349 539091456 539091414 2.360000e-06 63.9
28 TraesCS4A01G197800 chr5A 97.297 37 1 0 2307 2343 546393825 546393861 2.360000e-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 TraesCS4A01G197800 chr4A 482131676 482134512 2836 True 5240.000000 5240 100.0000 1 2837 1 chr4A.!!$R1 2836
1 TraesCS4A01G197800 chr4D 96522595 96526290 3695 False 1766.000000 2961 89.6405 1 2834 2 chr4D.!!$F1 2833
2 TraesCS4A01G197800 chr4B 136531467 136534321 2854 False 1131.333333 2726 89.2790 1 2619 3 chr4B.!!$F1 2618

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
764 789 0.322816 TCCTCATCCCAAGTTGCAGC 60.323 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 3588 0.323629 CCAAGTGGCCCTTCTTCGTA 59.676 55.0 0.0 0.0 0.0 3.43 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
25 26 5.278758 GCCTTTGCTTCCTTTGTTGTACATA 60.279 40.000 0.00 0.00 33.53 2.29
85 86 5.163953 CGTCCTGAACATGTGTTATTCTCAC 60.164 44.000 0.00 0.00 38.56 3.51
166 167 5.871524 TCATCGCATCAGATAGCTTTATTCC 59.128 40.000 0.00 0.00 0.00 3.01
167 168 5.213891 TCGCATCAGATAGCTTTATTCCA 57.786 39.130 0.00 0.00 0.00 3.53
183 184 1.452108 CCACCTTCCGCCCTTCATC 60.452 63.158 0.00 0.00 0.00 2.92
195 196 2.296190 GCCCTTCATCCTTTTCGTTTGT 59.704 45.455 0.00 0.00 0.00 2.83
221 222 3.664107 TCTGTCCCGAGATTTTCACAAG 58.336 45.455 0.00 0.00 0.00 3.16
224 225 4.456535 TGTCCCGAGATTTTCACAAGAAA 58.543 39.130 0.00 0.00 41.78 2.52
282 283 1.154169 TCGTTCGTCGAATCCACCG 60.154 57.895 11.45 9.57 45.98 4.94
284 285 1.670971 CGTTCGTCGAATCCACCGTG 61.671 60.000 11.45 0.00 42.86 4.94
358 359 1.712081 CGAGAGGAATTGCAGTGCG 59.288 57.895 11.20 0.00 0.00 5.34
361 362 1.537202 GAGAGGAATTGCAGTGCGTTT 59.463 47.619 11.20 6.33 0.00 3.60
364 365 1.000274 AGGAATTGCAGTGCGTTTTCC 60.000 47.619 24.94 24.94 35.30 3.13
441 447 1.229428 CACTTGACACCAGTGCGATT 58.771 50.000 0.00 0.00 0.00 3.34
442 448 1.603802 CACTTGACACCAGTGCGATTT 59.396 47.619 0.00 0.00 0.00 2.17
460 466 4.319694 CGATTTTCAGTGACAAGTGCATCA 60.320 41.667 0.00 0.00 0.00 3.07
461 467 3.969117 TTTCAGTGACAAGTGCATCAC 57.031 42.857 9.67 9.67 44.64 3.06
467 473 2.918571 ACAAGTGCATCACTGGTCG 58.081 52.632 1.34 0.00 44.40 4.79
470 481 2.436646 GTGCATCACTGGTCGGGG 60.437 66.667 0.00 0.00 0.00 5.73
479 490 2.045731 TGGTCGGGGGAAAATCGC 60.046 61.111 0.00 0.00 0.00 4.58
528 546 1.538276 GCGGAATGTGCGAATTTGAG 58.462 50.000 0.00 0.00 30.86 3.02
675 700 1.488393 AGCTCTACCTGCAGATTTCCC 59.512 52.381 17.39 0.00 0.00 3.97
677 702 2.092699 GCTCTACCTGCAGATTTCCCTT 60.093 50.000 17.39 0.00 0.00 3.95
678 703 3.802866 CTCTACCTGCAGATTTCCCTTC 58.197 50.000 17.39 0.00 0.00 3.46
680 705 1.376649 ACCTGCAGATTTCCCTTCCT 58.623 50.000 17.39 0.00 0.00 3.36
691 716 5.488919 AGATTTCCCTTCCTCTGACATGTTA 59.511 40.000 0.00 0.00 0.00 2.41
750 775 4.346730 AGATGCACATTTCCATTTCCTCA 58.653 39.130 0.00 0.00 0.00 3.86
764 789 0.322816 TCCTCATCCCAAGTTGCAGC 60.323 55.000 0.00 0.00 0.00 5.25
787 812 2.754002 GGAGTATATACCGGCTCCACTC 59.246 54.545 16.17 14.41 45.00 3.51
794 819 2.027625 CCGGCTCCACTCGTGAAAC 61.028 63.158 0.00 0.00 0.00 2.78
819 847 6.035975 CGAAAAGCCTGAAAAACAAGAAACAT 59.964 34.615 0.00 0.00 0.00 2.71
824 852 8.962884 AGCCTGAAAAACAAGAAACATATTTT 57.037 26.923 0.00 0.00 0.00 1.82
852 880 2.872245 CCGATTCGACAGCCACATAAAT 59.128 45.455 7.83 0.00 0.00 1.40
859 887 2.689471 GACAGCCACATAAATGCATCCA 59.311 45.455 0.00 0.00 0.00 3.41
886 914 1.905215 CTGGCCTCTCCTTTTCTCTCA 59.095 52.381 3.32 0.00 35.26 3.27
970 999 3.124636 CGCAGCCTTTTTATTACGTCTGT 59.875 43.478 0.00 0.00 0.00 3.41
979 1008 7.148787 CCTTTTTATTACGTCTGTCTGACTGAC 60.149 40.741 27.85 27.85 43.25 3.51
980 1009 6.570672 TTTATTACGTCTGTCTGACTGACT 57.429 37.500 31.49 23.87 45.54 3.41
981 1010 3.898517 TTACGTCTGTCTGACTGACTG 57.101 47.619 31.49 27.24 45.54 3.51
982 1011 1.968704 ACGTCTGTCTGACTGACTGA 58.031 50.000 31.49 15.12 46.59 3.41
987 1016 2.107378 TCTGTCTGACTGACTGAGGAGT 59.893 50.000 12.62 0.00 44.84 3.85
1112 1141 1.299316 CGGCTTGCAACAACCACAG 60.299 57.895 0.00 0.00 0.00 3.66
1127 1156 1.102809 CACAGCCACCACAAGAAGCA 61.103 55.000 0.00 0.00 0.00 3.91
1158 1187 4.754667 GACCCGGCGTCCTTCACC 62.755 72.222 6.01 0.00 35.23 4.02
1299 1328 0.107945 GTCAGGCCGAGAAGAGCAAT 60.108 55.000 0.00 0.00 0.00 3.56
1527 1556 4.150454 AGGGAGAGGGAGGAGGCG 62.150 72.222 0.00 0.00 0.00 5.52
1571 1600 3.721706 GGAGTCAGGGCTGGTGGG 61.722 72.222 0.00 0.00 0.00 4.61
1572 1601 2.930562 GAGTCAGGGCTGGTGGGT 60.931 66.667 0.00 0.00 0.00 4.51
1575 1604 3.636231 TCAGGGCTGGTGGGTTCG 61.636 66.667 0.00 0.00 0.00 3.95
1811 1846 4.221703 AGAAGATGACCGAGAAGACAACAT 59.778 41.667 0.00 0.00 0.00 2.71
1827 1862 1.083847 CATGACATGCATCGACGCG 60.084 57.895 3.53 3.53 34.15 6.01
1904 1939 1.005340 CTGCAGAATCCGAAGCTGAC 58.995 55.000 8.42 0.00 0.00 3.51
1905 1940 0.737367 TGCAGAATCCGAAGCTGACG 60.737 55.000 6.59 6.59 0.00 4.35
1906 1941 0.458543 GCAGAATCCGAAGCTGACGA 60.459 55.000 13.82 0.00 0.00 4.20
1907 1942 1.554392 CAGAATCCGAAGCTGACGAG 58.446 55.000 13.82 5.70 0.00 4.18
1908 1943 1.135257 CAGAATCCGAAGCTGACGAGT 60.135 52.381 13.82 0.00 0.00 4.18
1909 1944 1.135257 AGAATCCGAAGCTGACGAGTG 60.135 52.381 13.82 0.00 0.00 3.51
1910 1945 0.888619 AATCCGAAGCTGACGAGTGA 59.111 50.000 13.82 4.78 0.00 3.41
1920 1955 2.416027 GCTGACGAGTGATGACAAGCTA 60.416 50.000 0.00 0.00 0.00 3.32
1965 2000 6.551227 ACTGCCTCTTGTTCCTTTTCTAAATT 59.449 34.615 0.00 0.00 0.00 1.82
2074 2401 8.621286 AGGAAGCAAAATATAAACTTCGTATGG 58.379 33.333 0.00 0.00 38.07 2.74
2081 2408 8.888579 AAATATAAACTTCGTATGGACTCTGG 57.111 34.615 0.00 0.00 0.00 3.86
2121 2448 9.917887 ACAGTACTATGGATTGTACTAGTAAGT 57.082 33.333 3.61 4.64 43.82 2.24
2158 2488 6.170506 AGGAGTACATACGAAGCAAAATGAA 58.829 36.000 0.00 0.00 0.00 2.57
2159 2489 6.653320 AGGAGTACATACGAAGCAAAATGAAA 59.347 34.615 0.00 0.00 0.00 2.69
2160 2490 7.336931 AGGAGTACATACGAAGCAAAATGAAAT 59.663 33.333 0.00 0.00 0.00 2.17
2161 2491 8.609176 GGAGTACATACGAAGCAAAATGAAATA 58.391 33.333 0.00 0.00 0.00 1.40
2311 3552 6.994221 AGCACATTGTTAACTAGTGAGTACT 58.006 36.000 21.48 0.00 40.99 2.73
2313 3554 7.599245 AGCACATTGTTAACTAGTGAGTACTTC 59.401 37.037 21.48 0.00 38.36 3.01
2314 3555 7.148623 GCACATTGTTAACTAGTGAGTACTTCC 60.149 40.741 21.48 0.00 38.36 3.46
2315 3556 8.088981 CACATTGTTAACTAGTGAGTACTTCCT 58.911 37.037 15.75 0.00 38.36 3.36
2316 3557 8.305317 ACATTGTTAACTAGTGAGTACTTCCTC 58.695 37.037 7.22 0.00 38.36 3.71
2317 3558 8.524487 CATTGTTAACTAGTGAGTACTTCCTCT 58.476 37.037 7.22 0.00 38.36 3.69
2318 3559 9.750783 ATTGTTAACTAGTGAGTACTTCCTCTA 57.249 33.333 7.22 0.00 38.36 2.43
2319 3560 9.750783 TTGTTAACTAGTGAGTACTTCCTCTAT 57.249 33.333 7.22 0.00 38.36 1.98
2383 3624 0.623194 TGGCGATGGAATCCTTTGGA 59.377 50.000 0.00 0.00 41.39 3.53
2546 3825 1.113788 CGGCATTGGAAATGATGGGT 58.886 50.000 4.18 0.00 0.00 4.51
2633 3912 0.323542 ACGTCTCCTTCCATCGACCT 60.324 55.000 0.00 0.00 0.00 3.85
2634 3913 1.064906 ACGTCTCCTTCCATCGACCTA 60.065 52.381 0.00 0.00 0.00 3.08
2654 3935 2.017138 AAAAAGGCCCGTTTTGTGTG 57.983 45.000 12.73 0.00 29.93 3.82
2662 3943 1.960689 CCCGTTTTGTGTGGGATTCTT 59.039 47.619 0.00 0.00 46.41 2.52
2664 3945 3.181470 CCCGTTTTGTGTGGGATTCTTTT 60.181 43.478 0.00 0.00 46.41 2.27
2667 3948 4.678622 GTTTTGTGTGGGATTCTTTTCGT 58.321 39.130 0.00 0.00 0.00 3.85
2671 3952 3.067461 TGTGTGGGATTCTTTTCGTTTGG 59.933 43.478 0.00 0.00 0.00 3.28
2677 3958 4.295870 GGATTCTTTTCGTTTGGGTCAAC 58.704 43.478 0.00 0.00 0.00 3.18
2684 3965 2.082231 TCGTTTGGGTCAACAAAACGA 58.918 42.857 14.02 14.02 41.53 3.85
2691 3972 4.900684 TGGGTCAACAAAACGATCATCTA 58.099 39.130 0.00 0.00 0.00 1.98
2701 3982 5.659048 AAACGATCATCTATTTTCGGCTC 57.341 39.130 0.00 0.00 35.98 4.70
2702 3983 4.592485 ACGATCATCTATTTTCGGCTCT 57.408 40.909 0.00 0.00 35.98 4.09
2703 3984 4.302455 ACGATCATCTATTTTCGGCTCTG 58.698 43.478 0.00 0.00 35.98 3.35
2705 3986 4.747108 CGATCATCTATTTTCGGCTCTGTT 59.253 41.667 0.00 0.00 0.00 3.16
2720 4001 5.491982 GGCTCTGTTAGATATACCCATTGG 58.508 45.833 0.00 0.00 37.80 3.16
2737 4018 3.149648 GGCGGCTGCATCCCAAAT 61.150 61.111 21.31 0.00 45.35 2.32
2746 4027 4.141869 GGCTGCATCCCAAATTTTATGTCT 60.142 41.667 0.50 0.00 0.00 3.41
2779 4060 3.942539 AAAAAGAAAAATGCACCGCAC 57.057 38.095 0.00 0.00 43.04 5.34
2784 4065 4.454728 AGAAAAATGCACCGCACAATAT 57.545 36.364 0.00 0.00 43.04 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.040412 GGTCCAGGGAGTGAAGAAATGT 59.960 50.000 0.00 0.00 0.00 2.71
85 86 2.289945 CCTCACTTCAGAAAGGTCAGGG 60.290 54.545 0.00 0.00 36.78 4.45
166 167 1.452108 GGATGAAGGGCGGAAGGTG 60.452 63.158 0.00 0.00 0.00 4.00
167 168 1.208165 AAGGATGAAGGGCGGAAGGT 61.208 55.000 0.00 0.00 0.00 3.50
183 184 4.976116 GGACAGATTCAACAAACGAAAAGG 59.024 41.667 0.00 0.00 0.00 3.11
195 196 4.695455 GTGAAAATCTCGGGACAGATTCAA 59.305 41.667 5.71 0.00 41.45 2.69
282 283 5.028375 CGTGAAAACTGGAAAAGAGTTCAC 58.972 41.667 0.00 0.00 42.90 3.18
284 285 4.334481 TCCGTGAAAACTGGAAAAGAGTTC 59.666 41.667 0.00 0.00 32.33 3.01
354 355 2.094130 AGCTAGGTAGAGGAAAACGCAC 60.094 50.000 0.00 0.00 0.00 5.34
358 359 4.632251 GCAGAAAGCTAGGTAGAGGAAAAC 59.368 45.833 0.00 0.00 41.15 2.43
361 362 2.766828 GGCAGAAAGCTAGGTAGAGGAA 59.233 50.000 0.00 0.00 44.79 3.36
364 365 2.763448 ACAGGCAGAAAGCTAGGTAGAG 59.237 50.000 0.00 0.00 44.79 2.43
441 447 3.969117 GTGATGCACTTGTCACTGAAA 57.031 42.857 10.29 0.00 41.10 2.69
460 466 1.298667 CGATTTTCCCCCGACCAGT 59.701 57.895 0.00 0.00 0.00 4.00
461 467 2.112815 GCGATTTTCCCCCGACCAG 61.113 63.158 0.00 0.00 0.00 4.00
462 468 2.045731 GCGATTTTCCCCCGACCA 60.046 61.111 0.00 0.00 0.00 4.02
463 469 2.827190 GGCGATTTTCCCCCGACC 60.827 66.667 0.00 0.00 0.00 4.79
464 470 2.827190 GGGCGATTTTCCCCCGAC 60.827 66.667 0.00 0.00 37.81 4.79
470 481 2.159099 GGAGAAAATGGGGCGATTTTCC 60.159 50.000 20.88 15.20 46.72 3.13
479 490 0.413434 AACCCTGGGAGAAAATGGGG 59.587 55.000 22.23 0.00 42.00 4.96
610 629 3.119531 TCGCACAAATTTGATGGTGATCC 60.120 43.478 24.64 4.95 33.16 3.36
675 700 3.875727 CCTGCATAACATGTCAGAGGAAG 59.124 47.826 12.56 1.85 36.90 3.46
677 702 2.420547 GCCTGCATAACATGTCAGAGGA 60.421 50.000 12.56 0.00 36.90 3.71
678 703 1.945394 GCCTGCATAACATGTCAGAGG 59.055 52.381 12.56 8.78 36.90 3.69
680 705 1.281577 TGGCCTGCATAACATGTCAGA 59.718 47.619 12.56 0.00 36.90 3.27
691 716 1.677966 CTTCAGCACTGGCCTGCAT 60.678 57.895 18.35 2.00 42.56 3.96
750 775 0.323178 CTCCTGCTGCAACTTGGGAT 60.323 55.000 3.02 0.00 0.00 3.85
787 812 2.748461 TTCAGGCTTTTCGTTTCACG 57.252 45.000 0.00 0.00 44.19 4.35
794 819 5.347364 TGTTTCTTGTTTTTCAGGCTTTTCG 59.653 36.000 0.00 0.00 0.00 3.46
852 880 1.304381 GCCAGGAAAGGTGGATGCA 60.304 57.895 0.00 0.00 37.23 3.96
859 887 0.476611 AAGGAGAGGCCAGGAAAGGT 60.477 55.000 5.01 0.00 40.02 3.50
886 914 7.624478 TCTCCGAGGAAGAGAGGTATATATAGT 59.376 40.741 0.00 0.00 35.46 2.12
947 976 3.369756 CAGACGTAATAAAAAGGCTGCGA 59.630 43.478 0.00 0.00 0.00 5.10
948 977 3.124636 ACAGACGTAATAAAAAGGCTGCG 59.875 43.478 0.00 0.00 0.00 5.18
970 999 1.202989 AGCACTCCTCAGTCAGTCAGA 60.203 52.381 0.00 0.00 0.00 3.27
979 1008 0.873054 CAACAAGCAGCACTCCTCAG 59.127 55.000 0.00 0.00 0.00 3.35
980 1009 0.535780 CCAACAAGCAGCACTCCTCA 60.536 55.000 0.00 0.00 0.00 3.86
981 1010 0.250467 TCCAACAAGCAGCACTCCTC 60.250 55.000 0.00 0.00 0.00 3.71
982 1011 0.403271 ATCCAACAAGCAGCACTCCT 59.597 50.000 0.00 0.00 0.00 3.69
987 1016 2.628696 CGCCATCCAACAAGCAGCA 61.629 57.895 0.00 0.00 0.00 4.41
1112 1141 1.900498 AGCTGCTTCTTGTGGTGGC 60.900 57.895 0.00 0.00 0.00 5.01
1557 1586 2.034221 GAACCCACCAGCCCTGAC 59.966 66.667 0.00 0.00 0.00 3.51
1558 1587 3.636231 CGAACCCACCAGCCCTGA 61.636 66.667 0.00 0.00 0.00 3.86
1811 1846 2.126110 ACGCGTCGATGCATGTCA 60.126 55.556 27.92 0.00 34.15 3.58
1827 1862 6.954944 TCCATTCATAATTAACTAAGCGCAC 58.045 36.000 11.47 0.00 0.00 5.34
1904 1939 1.923204 GCTGTAGCTTGTCATCACTCG 59.077 52.381 0.00 0.00 38.21 4.18
1905 1940 2.964740 TGCTGTAGCTTGTCATCACTC 58.035 47.619 5.38 0.00 42.66 3.51
1906 1941 3.070018 GTTGCTGTAGCTTGTCATCACT 58.930 45.455 5.38 0.00 42.66 3.41
1907 1942 3.070018 AGTTGCTGTAGCTTGTCATCAC 58.930 45.455 5.38 0.00 42.66 3.06
1908 1943 3.407424 AGTTGCTGTAGCTTGTCATCA 57.593 42.857 5.38 0.00 42.66 3.07
1909 1944 4.499183 AGTAGTTGCTGTAGCTTGTCATC 58.501 43.478 5.38 0.00 42.66 2.92
1910 1945 4.543590 AGTAGTTGCTGTAGCTTGTCAT 57.456 40.909 5.38 0.00 42.66 3.06
1920 1955 6.239064 GGCAGTATATGAGTAGTAGTTGCTGT 60.239 42.308 0.00 0.00 0.00 4.40
2010 2050 8.718102 AGACATATTTTGCTTCGTATGTACTT 57.282 30.769 0.00 0.00 37.76 2.24
2049 2376 8.617809 TCCATACGAAGTTTATATTTTGCTTCC 58.382 33.333 0.00 0.00 37.78 3.46
2132 2462 6.755141 TCATTTTGCTTCGTATGTACTCCTAC 59.245 38.462 0.00 0.00 0.00 3.18
2133 2463 6.869695 TCATTTTGCTTCGTATGTACTCCTA 58.130 36.000 0.00 0.00 0.00 2.94
2328 3569 8.834465 TCTTCGTAGTATTCTAAACGCTCTTAT 58.166 33.333 0.00 0.00 0.00 1.73
2329 3570 8.201554 TCTTCGTAGTATTCTAAACGCTCTTA 57.798 34.615 0.00 0.00 0.00 2.10
2330 3571 7.081526 TCTTCGTAGTATTCTAAACGCTCTT 57.918 36.000 0.00 0.00 0.00 2.85
2331 3572 6.674694 TCTTCGTAGTATTCTAAACGCTCT 57.325 37.500 0.00 0.00 0.00 4.09
2332 3573 6.414402 CCTTCTTCGTAGTATTCTAAACGCTC 59.586 42.308 0.00 0.00 0.00 5.03
2333 3574 6.264088 CCTTCTTCGTAGTATTCTAAACGCT 58.736 40.000 0.00 0.00 0.00 5.07
2334 3575 5.458126 CCCTTCTTCGTAGTATTCTAAACGC 59.542 44.000 0.00 0.00 0.00 4.84
2335 3576 5.458126 GCCCTTCTTCGTAGTATTCTAAACG 59.542 44.000 0.00 0.00 0.00 3.60
2336 3577 5.752472 GGCCCTTCTTCGTAGTATTCTAAAC 59.248 44.000 0.00 0.00 0.00 2.01
2337 3578 5.422970 TGGCCCTTCTTCGTAGTATTCTAAA 59.577 40.000 0.00 0.00 0.00 1.85
2338 3579 4.957954 TGGCCCTTCTTCGTAGTATTCTAA 59.042 41.667 0.00 0.00 0.00 2.10
2339 3580 4.340381 GTGGCCCTTCTTCGTAGTATTCTA 59.660 45.833 0.00 0.00 0.00 2.10
2340 3581 3.132467 GTGGCCCTTCTTCGTAGTATTCT 59.868 47.826 0.00 0.00 0.00 2.40
2341 3582 3.132467 AGTGGCCCTTCTTCGTAGTATTC 59.868 47.826 0.00 0.00 0.00 1.75
2342 3583 3.105283 AGTGGCCCTTCTTCGTAGTATT 58.895 45.455 0.00 0.00 0.00 1.89
2343 3584 2.748388 AGTGGCCCTTCTTCGTAGTAT 58.252 47.619 0.00 0.00 0.00 2.12
2344 3585 2.226962 AGTGGCCCTTCTTCGTAGTA 57.773 50.000 0.00 0.00 0.00 1.82
2345 3586 1.002087 CAAGTGGCCCTTCTTCGTAGT 59.998 52.381 0.00 0.00 0.00 2.73
2346 3587 1.676014 CCAAGTGGCCCTTCTTCGTAG 60.676 57.143 0.00 0.00 0.00 3.51
2347 3588 0.323629 CCAAGTGGCCCTTCTTCGTA 59.676 55.000 0.00 0.00 0.00 3.43
2348 3589 1.073199 CCAAGTGGCCCTTCTTCGT 59.927 57.895 0.00 0.00 0.00 3.85
2349 3590 3.987404 CCAAGTGGCCCTTCTTCG 58.013 61.111 0.00 0.00 0.00 3.79
2396 3637 3.311322 TCGCGTTGGGTTGATTGATATTC 59.689 43.478 5.77 0.00 0.00 1.75
2533 3812 3.513515 GTGCCTTTTACCCATCATTTCCA 59.486 43.478 0.00 0.00 0.00 3.53
2546 3825 1.466950 CGGCGATCAAAGTGCCTTTTA 59.533 47.619 0.00 0.00 46.67 1.52
2642 3923 1.616159 AGAATCCCACACAAAACGGG 58.384 50.000 0.00 0.00 41.76 5.28
2650 3931 3.552068 CCCAAACGAAAAGAATCCCACAC 60.552 47.826 0.00 0.00 0.00 3.82
2652 3933 2.626266 ACCCAAACGAAAAGAATCCCAC 59.374 45.455 0.00 0.00 0.00 4.61
2653 3934 2.888414 GACCCAAACGAAAAGAATCCCA 59.112 45.455 0.00 0.00 0.00 4.37
2654 3935 2.888414 TGACCCAAACGAAAAGAATCCC 59.112 45.455 0.00 0.00 0.00 3.85
2662 3943 3.057736 TCGTTTTGTTGACCCAAACGAAA 60.058 39.130 19.97 2.64 39.84 3.46
2664 3945 2.082231 TCGTTTTGTTGACCCAAACGA 58.918 42.857 19.05 19.05 36.49 3.85
2667 3948 4.582656 AGATGATCGTTTTGTTGACCCAAA 59.417 37.500 0.00 0.00 32.70 3.28
2671 3952 7.216317 CGAAAATAGATGATCGTTTTGTTGACC 59.784 37.037 13.54 1.96 0.00 4.02
2677 3958 5.810525 AGCCGAAAATAGATGATCGTTTTG 58.189 37.500 13.54 7.54 33.65 2.44
2684 3965 7.055667 TCTAACAGAGCCGAAAATAGATGAT 57.944 36.000 0.00 0.00 0.00 2.45
2691 3972 6.042781 TGGGTATATCTAACAGAGCCGAAAAT 59.957 38.462 0.00 0.00 0.00 1.82
2701 3982 4.253685 CGCCCAATGGGTATATCTAACAG 58.746 47.826 21.02 0.00 46.51 3.16
2702 3983 3.008594 CCGCCCAATGGGTATATCTAACA 59.991 47.826 21.02 0.00 46.51 2.41
2703 3984 3.606687 CCGCCCAATGGGTATATCTAAC 58.393 50.000 21.02 0.00 46.51 2.34
2705 3986 1.557832 GCCGCCCAATGGGTATATCTA 59.442 52.381 21.02 0.00 46.51 1.98
2720 4001 2.242797 AAATTTGGGATGCAGCCGCC 62.243 55.000 16.15 2.07 37.32 6.13
2721 4002 0.391528 AAAATTTGGGATGCAGCCGC 60.392 50.000 16.15 8.76 39.24 6.53
2723 4004 4.122046 GACATAAAATTTGGGATGCAGCC 58.878 43.478 14.08 14.08 0.00 4.85
2726 4007 5.999205 ACAGACATAAAATTTGGGATGCA 57.001 34.783 0.00 0.00 0.00 3.96
2764 4045 5.529014 AAATATTGTGCGGTGCATTTTTC 57.471 34.783 0.00 0.00 41.91 2.29
2810 4094 9.277565 CAATGACTATCGTGGACTTTTTAATTG 57.722 33.333 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.