Multiple sequence alignment - TraesCS1A01G192600

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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 TraesCS1A01G192600 chr1A 100.000 2636 0 0 1 2636 347921445 347924080 0.000000e+00 4868.0
1 TraesCS1A01G192600 chr1A 92.784 97 7 0 360 456 402551205 402551109 9.840000e-30 141.0
2 TraesCS1A01G192600 chr1A 90.099 101 10 0 356 456 587607413 587607313 5.920000e-27 132.0
3 TraesCS1A01G192600 chr1A 90.099 101 10 0 356 456 587610295 587610195 5.920000e-27 132.0
4 TraesCS1A01G192600 chr1B 95.036 1390 58 4 673 2059 374864751 374866132 0.000000e+00 2174.0
5 TraesCS1A01G192600 chr1B 94.433 485 18 7 2152 2636 374867784 374868259 0.000000e+00 737.0
6 TraesCS1A01G192600 chr1B 92.500 80 4 2 557 636 374864582 374864659 2.140000e-21 113.0
7 TraesCS1A01G192600 chr1D 95.508 1358 46 6 522 1871 275620937 275622287 0.000000e+00 2156.0
8 TraesCS1A01G192600 chr1D 94.608 779 34 7 1858 2636 275623579 275624349 0.000000e+00 1199.0
9 TraesCS1A01G192600 chr1D 88.806 402 27 11 1 400 275620496 275620881 6.600000e-131 477.0
10 TraesCS1A01G192600 chr1D 98.113 53 1 0 462 514 275620849 275620901 2.790000e-15 93.5
11 TraesCS1A01G192600 chr6A 92.784 97 7 0 360 456 438267724 438267628 9.840000e-30 141.0
12 TraesCS1A01G192600 chr6A 92.784 97 7 0 360 456 617742233 617742137 9.840000e-30 141.0
13 TraesCS1A01G192600 chr6A 89.744 78 4 3 2037 2111 89893788 89893712 2.160000e-16 97.1
14 TraesCS1A01G192600 chr6A 96.552 58 0 2 2048 2104 104056398 104056454 7.770000e-16 95.3
15 TraesCS1A01G192600 chr6A 93.846 65 1 3 2048 2111 146554497 146554559 7.770000e-16 95.3
16 TraesCS1A01G192600 chr4D 92.784 97 7 0 360 456 8411320 8411416 9.840000e-30 141.0
17 TraesCS1A01G192600 chr4A 92.000 100 8 0 357 456 594031437 594031536 9.840000e-30 141.0
18 TraesCS1A01G192600 chr2A 89.381 113 8 4 347 456 507768825 507768936 3.540000e-29 139.0
19 TraesCS1A01G192600 chr5D 89.623 106 11 0 351 456 233153532 233153637 4.580000e-28 135.0
20 TraesCS1A01G192600 chr5D 93.548 62 2 2 2047 2107 28023677 28023617 1.000000e-14 91.6
21 TraesCS1A01G192600 chr7A 93.846 65 1 3 2048 2111 335980747 335980809 7.770000e-16 95.3
22 TraesCS1A01G192600 chr6D 93.750 64 3 1 2048 2111 73497392 73497330 7.770000e-16 95.3
23 TraesCS1A01G192600 chr5A 91.304 69 4 2 2029 2096 382336290 382336357 2.790000e-15 93.5
24 TraesCS1A01G192600 chr5A 86.905 84 5 6 2035 2114 398285979 398285898 3.610000e-14 89.8
25 TraesCS1A01G192600 chr5A 83.871 62 8 2 462 521 597688725 597688786 1.020000e-04 58.4
26 TraesCS1A01G192600 chrUn 89.231 65 7 0 2480 2544 134301423 134301487 6.050000e-12 82.4
27 TraesCS1A01G192600 chrUn 80.734 109 16 4 2432 2539 108249686 108249582 2.170000e-11 80.5
28 TraesCS1A01G192600 chrUn 89.831 59 6 0 2486 2544 134301242 134301300 2.810000e-10 76.8


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 TraesCS1A01G192600 chr1A 347921445 347924080 2635 False 4868.000 4868 100.000000 1 2636 1 chr1A.!!$F1 2635
1 TraesCS1A01G192600 chr1B 374864582 374868259 3677 False 1008.000 2174 93.989667 557 2636 3 chr1B.!!$F1 2079
2 TraesCS1A01G192600 chr1D 275620496 275624349 3853 False 981.375 2156 94.258750 1 2636 4 chr1D.!!$F1 2635

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
120 121 0.107017 ATAGCTTGCCTGCACCGATT 60.107 50.0 0.0 0.0 34.99 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1849 0.168788 CACACGTCCCATGCATGAAC 59.831 55.0 28.31 21.9 0.0 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
38 39 1.267121 TCTTTTCTAGACTGGGCGCT 58.733 50.000 7.64 0.00 0.00 5.92
60 61 1.405121 GGTCGCCGATCCAGTTTTACT 60.405 52.381 0.00 0.00 0.00 2.24
74 75 5.491982 CAGTTTTACTAGGACTGCCAAGAT 58.508 41.667 0.00 0.00 34.97 2.40
75 76 6.351881 CCAGTTTTACTAGGACTGCCAAGATA 60.352 42.308 10.51 0.00 39.48 1.98
85 86 3.384168 ACTGCCAAGATATAGGTGGACA 58.616 45.455 3.52 1.37 0.00 4.02
97 98 0.890683 GGTGGACAATGCAAGGAAGG 59.109 55.000 0.00 0.00 0.00 3.46
99 100 1.815003 GTGGACAATGCAAGGAAGGAG 59.185 52.381 0.00 0.00 0.00 3.69
108 109 1.674962 GCAAGGAAGGAGCATAGCTTG 59.325 52.381 0.00 0.00 39.88 4.01
116 117 2.803479 GCATAGCTTGCCTGCACC 59.197 61.111 11.29 0.00 46.15 5.01
117 118 3.104766 CATAGCTTGCCTGCACCG 58.895 61.111 0.00 0.00 34.99 4.94
118 119 1.450134 CATAGCTTGCCTGCACCGA 60.450 57.895 0.00 0.00 34.99 4.69
119 120 0.816825 CATAGCTTGCCTGCACCGAT 60.817 55.000 0.00 0.00 34.99 4.18
120 121 0.107017 ATAGCTTGCCTGCACCGATT 60.107 50.000 0.00 0.00 34.99 3.34
121 122 0.322456 TAGCTTGCCTGCACCGATTT 60.322 50.000 0.00 0.00 34.99 2.17
122 123 1.181098 AGCTTGCCTGCACCGATTTT 61.181 50.000 0.00 0.00 34.99 1.82
123 124 0.525761 GCTTGCCTGCACCGATTTTA 59.474 50.000 0.00 0.00 0.00 1.52
124 125 1.134946 GCTTGCCTGCACCGATTTTAT 59.865 47.619 0.00 0.00 0.00 1.40
154 155 2.540361 GGCAACAATGTCTCGATGCATC 60.540 50.000 17.10 17.10 35.57 3.91
247 248 8.311109 TCATTGCTGTGATTTAGTAGTACAAGA 58.689 33.333 2.52 0.00 0.00 3.02
314 315 1.666011 CTCACTACGTGTGCCAGGT 59.334 57.895 0.00 5.95 45.81 4.00
334 335 6.295236 CCAGGTGGTGATAAAAATGTGACATT 60.295 38.462 4.72 4.72 0.00 2.71
339 340 8.702438 GTGGTGATAAAAATGTGACATTTTCTG 58.298 33.333 29.73 0.00 31.53 3.02
355 356 8.489990 ACATTTTCTGTCAGTGATAGATCAAG 57.510 34.615 18.98 12.46 33.58 3.02
356 357 8.316946 ACATTTTCTGTCAGTGATAGATCAAGA 58.683 33.333 18.98 2.59 33.58 3.02
358 359 9.902684 ATTTTCTGTCAGTGATAGATCAAGATT 57.097 29.630 18.98 0.76 38.75 2.40
359 360 9.730705 TTTTCTGTCAGTGATAGATCAAGATTT 57.269 29.630 18.98 0.00 38.75 2.17
364 365 9.809096 TGTCAGTGATAGATCAAGATTTACTTC 57.191 33.333 0.00 0.00 38.75 3.01
365 366 9.255304 GTCAGTGATAGATCAAGATTTACTTCC 57.745 37.037 0.00 0.00 38.75 3.46
366 367 9.206690 TCAGTGATAGATCAAGATTTACTTCCT 57.793 33.333 0.00 0.00 38.75 3.36
367 368 9.829507 CAGTGATAGATCAAGATTTACTTCCTT 57.170 33.333 0.00 0.00 38.75 3.36
369 370 8.973378 GTGATAGATCAAGATTTACTTCCTTCG 58.027 37.037 0.00 0.00 38.75 3.79
370 371 8.696374 TGATAGATCAAGATTTACTTCCTTCGT 58.304 33.333 0.00 0.00 36.61 3.85
371 372 9.535878 GATAGATCAAGATTTACTTCCTTCGTT 57.464 33.333 0.00 0.00 36.61 3.85
372 373 9.892130 ATAGATCAAGATTTACTTCCTTCGTTT 57.108 29.630 0.00 0.00 36.61 3.60
373 374 8.257830 AGATCAAGATTTACTTCCTTCGTTTC 57.742 34.615 0.00 0.00 36.61 2.78
374 375 7.878127 AGATCAAGATTTACTTCCTTCGTTTCA 59.122 33.333 0.00 0.00 36.61 2.69
375 376 7.795482 TCAAGATTTACTTCCTTCGTTTCAA 57.205 32.000 0.00 0.00 36.61 2.69
376 377 8.215926 TCAAGATTTACTTCCTTCGTTTCAAA 57.784 30.769 0.00 0.00 36.61 2.69
377 378 8.846211 TCAAGATTTACTTCCTTCGTTTCAAAT 58.154 29.630 0.00 0.00 36.61 2.32
378 379 9.463443 CAAGATTTACTTCCTTCGTTTCAAATT 57.537 29.630 0.00 0.00 36.61 1.82
386 387 7.962918 ACTTCCTTCGTTTCAAATTATTCATCG 59.037 33.333 0.00 0.00 0.00 3.84
387 388 7.372451 TCCTTCGTTTCAAATTATTCATCGT 57.628 32.000 0.00 0.00 0.00 3.73
388 389 8.481974 TCCTTCGTTTCAAATTATTCATCGTA 57.518 30.769 0.00 0.00 0.00 3.43
389 390 8.937884 TCCTTCGTTTCAAATTATTCATCGTAA 58.062 29.630 0.00 0.00 0.00 3.18
390 391 9.549509 CCTTCGTTTCAAATTATTCATCGTAAA 57.450 29.630 0.00 0.00 0.00 2.01
438 439 6.398234 ACATCTAGATACATCCATATCCGC 57.602 41.667 4.54 0.00 32.76 5.54
439 440 5.009110 ACATCTAGATACATCCATATCCGCG 59.991 44.000 4.54 0.00 32.76 6.46
440 441 4.777463 TCTAGATACATCCATATCCGCGA 58.223 43.478 8.23 0.00 32.76 5.87
441 442 3.784701 AGATACATCCATATCCGCGAC 57.215 47.619 8.23 0.00 32.76 5.19
442 443 3.089284 AGATACATCCATATCCGCGACA 58.911 45.455 8.23 0.00 32.76 4.35
443 444 3.509967 AGATACATCCATATCCGCGACAA 59.490 43.478 8.23 0.00 32.76 3.18
444 445 2.154854 ACATCCATATCCGCGACAAG 57.845 50.000 8.23 0.00 0.00 3.16
445 446 1.412710 ACATCCATATCCGCGACAAGT 59.587 47.619 8.23 0.00 0.00 3.16
446 447 2.626266 ACATCCATATCCGCGACAAGTA 59.374 45.455 8.23 0.00 0.00 2.24
447 448 3.069016 ACATCCATATCCGCGACAAGTAA 59.931 43.478 8.23 0.00 0.00 2.24
448 449 4.245660 CATCCATATCCGCGACAAGTAAT 58.754 43.478 8.23 0.00 0.00 1.89
449 450 4.330944 TCCATATCCGCGACAAGTAATT 57.669 40.909 8.23 0.00 0.00 1.40
450 451 4.304110 TCCATATCCGCGACAAGTAATTC 58.696 43.478 8.23 0.00 0.00 2.17
451 452 3.121279 CCATATCCGCGACAAGTAATTCG 59.879 47.826 8.23 0.00 38.31 3.34
452 453 1.567504 ATCCGCGACAAGTAATTCGG 58.432 50.000 8.23 0.00 35.73 4.30
453 454 0.527113 TCCGCGACAAGTAATTCGGA 59.473 50.000 8.23 0.00 42.86 4.55
454 455 1.067706 TCCGCGACAAGTAATTCGGAA 60.068 47.619 8.23 0.00 42.25 4.30
455 456 1.060122 CCGCGACAAGTAATTCGGAAC 59.940 52.381 8.23 0.00 39.23 3.62
456 457 1.990563 CGCGACAAGTAATTCGGAACT 59.009 47.619 0.00 0.00 35.73 3.01
457 458 2.410730 CGCGACAAGTAATTCGGAACTT 59.589 45.455 0.00 0.00 36.38 2.66
458 459 3.481467 CGCGACAAGTAATTCGGAACTTC 60.481 47.826 0.00 0.00 33.72 3.01
459 460 3.678548 GCGACAAGTAATTCGGAACTTCT 59.321 43.478 0.00 0.00 33.72 2.85
460 461 4.860907 GCGACAAGTAATTCGGAACTTCTA 59.139 41.667 0.00 0.00 33.72 2.10
526 555 3.372206 AGATCCATTTTCGCGACTTTCTG 59.628 43.478 9.15 2.13 0.00 3.02
539 568 4.851558 GCGACTTTCTGCGACAAATAATTT 59.148 37.500 0.00 0.00 0.00 1.82
540 569 6.019152 GCGACTTTCTGCGACAAATAATTTA 58.981 36.000 0.00 0.00 0.00 1.40
545 574 4.265893 TCTGCGACAAATAATTTAGGGCA 58.734 39.130 0.00 0.00 0.00 5.36
956 1048 2.643551 CACACCTAAAAGCCCATCGAT 58.356 47.619 0.00 0.00 0.00 3.59
1140 1232 0.033991 TCCTCCTCTTCGTCCTCCTG 60.034 60.000 0.00 0.00 0.00 3.86
1539 1634 2.028337 GAGGAGATCGCCTTCGCC 59.972 66.667 19.87 2.71 38.73 5.54
1562 1657 2.660258 GAACACGGACACAGTGGCCT 62.660 60.000 23.90 3.92 45.79 5.19
1563 1658 2.357517 CACGGACACAGTGGCCTC 60.358 66.667 23.90 0.00 45.79 4.70
1564 1659 2.842462 ACGGACACAGTGGCCTCA 60.842 61.111 23.90 0.00 45.79 3.86
1608 1703 2.358193 CTGGACACCGGACAACGTCA 62.358 60.000 9.46 0.00 42.24 4.35
1622 1717 2.100631 CGTCATCACCTCCGGCAAC 61.101 63.158 0.00 0.00 0.00 4.17
1625 1720 1.191489 TCATCACCTCCGGCAACTGA 61.191 55.000 0.00 0.00 0.00 3.41
1629 1724 2.358737 CCTCCGGCAACTGACCAC 60.359 66.667 0.00 0.00 0.00 4.16
1714 1809 9.898152 TCCAAATTTTGTTGAATCCTTTTTAGT 57.102 25.926 8.26 0.00 0.00 2.24
1749 1847 5.531198 TGGTAGGAATTGGTAGCTTAGGTA 58.469 41.667 0.00 0.00 0.00 3.08
1751 1849 4.667519 AGGAATTGGTAGCTTAGGTACG 57.332 45.455 14.29 0.00 37.39 3.67
1892 3295 1.112916 TGAACGTCTGCTGGACCTGA 61.113 55.000 1.91 0.00 41.64 3.86
1922 3325 5.992217 CACTAAGCAAGTCTGTTCTAAACCT 59.008 40.000 0.00 0.00 35.76 3.50
1925 3328 4.570930 AGCAAGTCTGTTCTAAACCTAGC 58.429 43.478 0.00 0.00 0.00 3.42
1973 3376 6.744175 AGATGCTAATGAGATTCCTTCAGA 57.256 37.500 0.00 0.00 0.00 3.27
2046 3449 5.880164 TGGGTTCCTGATATTATCAACGA 57.120 39.130 7.73 3.99 39.11 3.85
2047 3450 6.433847 TGGGTTCCTGATATTATCAACGAT 57.566 37.500 7.73 0.00 39.11 3.73
2172 5153 8.126700 GGGGAAAACATTGTTAATATACAGTCG 58.873 37.037 1.76 0.00 0.00 4.18
2178 5159 8.552469 ACATTGTTAATATACAGTCGTACGAC 57.448 34.615 35.26 35.26 44.86 4.34
2234 5215 7.820044 TGAAGTTGATTTTTGTACAAACCAC 57.180 32.000 20.43 13.87 0.00 4.16
2266 5247 6.145534 ACAATTCACACGTATACAGAGTTGTG 59.854 38.462 16.95 13.78 37.63 3.33
2425 5406 3.263503 TACAACACTCGCTCGCGCT 62.264 57.895 5.56 0.00 39.59 5.92
2579 5560 9.162764 GTATAGTCATTTTACACCACAGTTCAT 57.837 33.333 0.00 0.00 0.00 2.57
2580 5561 6.317789 AGTCATTTTACACCACAGTTCATG 57.682 37.500 0.00 0.00 0.00 3.07
2581 5562 6.061441 AGTCATTTTACACCACAGTTCATGA 58.939 36.000 0.00 0.00 0.00 3.07
2586 5567 7.523293 TTTTACACCACAGTTCATGATTGAT 57.477 32.000 13.04 0.00 0.00 2.57
2591 5572 6.209986 ACACCACAGTTCATGATTGATTGAAT 59.790 34.615 13.04 0.00 34.60 2.57
2592 5573 6.530181 CACCACAGTTCATGATTGATTGAATG 59.470 38.462 13.04 1.70 34.60 2.67
2593 5574 6.434965 ACCACAGTTCATGATTGATTGAATGA 59.565 34.615 13.04 0.00 34.60 2.57
2594 5575 7.039574 ACCACAGTTCATGATTGATTGAATGAA 60.040 33.333 13.04 0.00 36.85 2.57
2598 5579 7.751047 GTTCATGATTGATTGAATGAACCAG 57.249 36.000 13.74 0.00 46.83 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 1.267121 AGCGCCCAGTCTAGAAAAGA 58.733 50.000 2.29 0.00 0.00 2.52
38 39 0.899720 AAAACTGGATCGGCGACCTA 59.100 50.000 13.76 0.00 0.00 3.08
46 47 4.113354 GCAGTCCTAGTAAAACTGGATCG 58.887 47.826 11.56 0.00 40.57 3.69
60 61 4.140782 TCCACCTATATCTTGGCAGTCCTA 60.141 45.833 0.00 0.00 0.00 2.94
74 75 4.385199 CCTTCCTTGCATTGTCCACCTATA 60.385 45.833 0.00 0.00 0.00 1.31
75 76 3.624777 CTTCCTTGCATTGTCCACCTAT 58.375 45.455 0.00 0.00 0.00 2.57
85 86 2.091994 AGCTATGCTCCTTCCTTGCATT 60.092 45.455 5.02 0.00 43.85 3.56
108 109 1.880027 CCCTATAAAATCGGTGCAGGC 59.120 52.381 0.00 0.00 0.00 4.85
112 113 1.607148 GGTGCCCTATAAAATCGGTGC 59.393 52.381 0.00 0.00 0.00 5.01
113 114 1.871039 CGGTGCCCTATAAAATCGGTG 59.129 52.381 0.00 0.00 0.00 4.94
114 115 1.202722 CCGGTGCCCTATAAAATCGGT 60.203 52.381 0.00 0.00 0.00 4.69
115 116 1.519408 CCGGTGCCCTATAAAATCGG 58.481 55.000 0.00 0.00 0.00 4.18
116 117 0.872388 GCCGGTGCCCTATAAAATCG 59.128 55.000 1.90 0.00 0.00 3.34
117 118 1.975660 TGCCGGTGCCCTATAAAATC 58.024 50.000 1.90 0.00 36.33 2.17
118 119 2.028876 GTTGCCGGTGCCCTATAAAAT 58.971 47.619 1.90 0.00 36.33 1.82
119 120 1.271982 TGTTGCCGGTGCCCTATAAAA 60.272 47.619 1.90 0.00 36.33 1.52
120 121 0.328592 TGTTGCCGGTGCCCTATAAA 59.671 50.000 1.90 0.00 36.33 1.40
121 122 0.328592 TTGTTGCCGGTGCCCTATAA 59.671 50.000 1.90 0.00 36.33 0.98
122 123 0.548989 ATTGTTGCCGGTGCCCTATA 59.451 50.000 1.90 0.00 36.33 1.31
123 124 1.037030 CATTGTTGCCGGTGCCCTAT 61.037 55.000 1.90 0.00 36.33 2.57
124 125 1.677300 CATTGTTGCCGGTGCCCTA 60.677 57.895 1.90 0.00 36.33 3.53
154 155 6.884295 TGTGTTATTTTTAGGGATGAGACCAG 59.116 38.462 0.00 0.00 0.00 4.00
314 315 8.420222 ACAGAAAATGTCACATTTTTATCACCA 58.580 29.630 25.76 0.00 37.75 4.17
339 340 9.255304 GGAAGTAAATCTTGATCTATCACTGAC 57.745 37.037 0.00 0.00 36.36 3.51
349 350 8.029642 TGAAACGAAGGAAGTAAATCTTGATC 57.970 34.615 0.00 0.00 36.40 2.92
350 351 7.979444 TGAAACGAAGGAAGTAAATCTTGAT 57.021 32.000 0.00 0.00 36.40 2.57
351 352 7.795482 TTGAAACGAAGGAAGTAAATCTTGA 57.205 32.000 0.00 0.00 36.40 3.02
352 353 9.463443 AATTTGAAACGAAGGAAGTAAATCTTG 57.537 29.630 0.00 0.00 36.40 3.02
360 361 7.962918 CGATGAATAATTTGAAACGAAGGAAGT 59.037 33.333 0.00 0.00 0.00 3.01
364 365 9.549509 TTTACGATGAATAATTTGAAACGAAGG 57.450 29.630 0.00 0.00 0.00 3.46
412 413 8.580720 GCGGATATGGATGTATCTAGATGTATT 58.419 37.037 15.79 0.00 32.78 1.89
413 414 7.094592 CGCGGATATGGATGTATCTAGATGTAT 60.095 40.741 15.79 9.11 32.78 2.29
414 415 6.204882 CGCGGATATGGATGTATCTAGATGTA 59.795 42.308 15.79 4.44 32.78 2.29
415 416 5.009110 CGCGGATATGGATGTATCTAGATGT 59.991 44.000 15.79 1.25 32.78 3.06
416 417 5.239525 TCGCGGATATGGATGTATCTAGATG 59.760 44.000 15.79 0.00 32.78 2.90
417 418 5.239744 GTCGCGGATATGGATGTATCTAGAT 59.760 44.000 10.73 10.73 32.78 1.98
418 419 4.575236 GTCGCGGATATGGATGTATCTAGA 59.425 45.833 6.13 0.00 32.78 2.43
419 420 4.335594 TGTCGCGGATATGGATGTATCTAG 59.664 45.833 6.13 0.00 32.78 2.43
420 421 4.266714 TGTCGCGGATATGGATGTATCTA 58.733 43.478 6.13 0.00 32.78 1.98
421 422 3.089284 TGTCGCGGATATGGATGTATCT 58.911 45.455 6.13 0.00 32.78 1.98
422 423 3.503827 TGTCGCGGATATGGATGTATC 57.496 47.619 6.13 0.00 0.00 2.24
423 424 3.258372 ACTTGTCGCGGATATGGATGTAT 59.742 43.478 6.13 0.00 0.00 2.29
424 425 2.626266 ACTTGTCGCGGATATGGATGTA 59.374 45.455 6.13 0.00 0.00 2.29
425 426 1.412710 ACTTGTCGCGGATATGGATGT 59.587 47.619 6.13 0.00 0.00 3.06
426 427 2.154854 ACTTGTCGCGGATATGGATG 57.845 50.000 6.13 0.00 0.00 3.51
427 428 4.537135 ATTACTTGTCGCGGATATGGAT 57.463 40.909 6.13 0.00 0.00 3.41
428 429 4.304110 GAATTACTTGTCGCGGATATGGA 58.696 43.478 6.13 0.00 0.00 3.41
429 430 3.121279 CGAATTACTTGTCGCGGATATGG 59.879 47.826 6.13 0.00 0.00 2.74
430 431 3.121279 CCGAATTACTTGTCGCGGATATG 59.879 47.826 6.13 0.00 41.11 1.78
431 432 3.005050 TCCGAATTACTTGTCGCGGATAT 59.995 43.478 6.13 0.00 42.29 1.63
432 433 2.358582 TCCGAATTACTTGTCGCGGATA 59.641 45.455 6.13 0.00 42.29 2.59
433 434 1.135527 TCCGAATTACTTGTCGCGGAT 59.864 47.619 6.13 0.00 42.29 4.18
434 435 0.527113 TCCGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 44.60 5.54
435 436 1.060122 GTTCCGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 40.06 6.46
436 437 1.990563 AGTTCCGAATTACTTGTCGCG 59.009 47.619 0.00 0.00 35.93 5.87
437 438 3.678548 AGAAGTTCCGAATTACTTGTCGC 59.321 43.478 0.00 0.00 34.88 5.19
438 439 5.287992 GGTAGAAGTTCCGAATTACTTGTCG 59.712 44.000 0.00 0.00 34.88 4.35
439 440 6.644191 GGTAGAAGTTCCGAATTACTTGTC 57.356 41.667 0.00 0.00 34.88 3.18
508 509 1.606606 GCAGAAAGTCGCGAAAATGG 58.393 50.000 12.06 0.00 0.00 3.16
526 555 4.261197 CCTCTGCCCTAAATTATTTGTCGC 60.261 45.833 0.00 0.00 0.00 5.19
539 568 3.116707 AGCTAAATACTCCCTCTGCCCTA 60.117 47.826 0.00 0.00 0.00 3.53
540 569 2.050918 GCTAAATACTCCCTCTGCCCT 58.949 52.381 0.00 0.00 0.00 5.19
1093 1185 2.825836 CAGCATGGGGAAGGACGC 60.826 66.667 0.00 0.00 0.00 5.19
1140 1232 1.122227 AGATGGAGAGGAAGCAGAGC 58.878 55.000 0.00 0.00 0.00 4.09
1512 1607 4.162690 ATCTCCTCGTTGGGCGGC 62.163 66.667 0.00 0.00 41.72 6.53
1534 1629 1.662446 GTCCGTGTTCTTCGGCGAA 60.662 57.895 22.33 22.33 46.49 4.70
1539 1634 0.852777 CACTGTGTCCGTGTTCTTCG 59.147 55.000 0.00 0.00 0.00 3.79
1622 1717 0.947180 CGTTGGTTACCGGTGGTCAG 60.947 60.000 19.93 0.00 37.09 3.51
1625 1720 2.426887 CCGTTGGTTACCGGTGGT 59.573 61.111 19.93 0.00 39.38 4.16
1715 1810 9.364653 CTACCAATTCCTACCAACTACTATAGT 57.635 37.037 10.87 10.87 41.73 2.12
1716 1811 8.305317 GCTACCAATTCCTACCAACTACTATAG 58.695 40.741 0.00 0.00 0.00 1.31
1717 1812 8.008922 AGCTACCAATTCCTACCAACTACTATA 58.991 37.037 0.00 0.00 0.00 1.31
1718 1813 6.844917 AGCTACCAATTCCTACCAACTACTAT 59.155 38.462 0.00 0.00 0.00 2.12
1719 1814 6.200114 AGCTACCAATTCCTACCAACTACTA 58.800 40.000 0.00 0.00 0.00 1.82
1749 1847 1.003839 ACGTCCCATGCATGAACGT 60.004 52.632 34.66 34.66 0.00 3.99
1751 1849 0.168788 CACACGTCCCATGCATGAAC 59.831 55.000 28.31 21.90 0.00 3.18
1879 3282 2.037251 GTGTTTACTCAGGTCCAGCAGA 59.963 50.000 0.00 0.00 0.00 4.26
1892 3295 6.583562 AGAACAGACTTGCTTAGTGTTTACT 58.416 36.000 0.00 0.00 37.17 2.24
1922 3325 4.085733 AGTGTAAAATTGCCCATGTGCTA 58.914 39.130 0.86 0.00 0.00 3.49
1925 3328 6.206395 TGATAGTGTAAAATTGCCCATGTG 57.794 37.500 0.00 0.00 0.00 3.21
2014 3417 2.131854 TCAGGAACCCAAGTTTCTCCA 58.868 47.619 0.00 0.00 40.05 3.86
2172 5153 6.972901 TGTGTGATCTGAGAATAATGTCGTAC 59.027 38.462 0.00 0.00 0.00 3.67
2234 5215 9.030301 TCTGTATACGTGTGAATTGTGATATTG 57.970 33.333 0.00 0.00 0.00 1.90
2266 5247 4.722194 ACGTGTGAATTGTGATTATGCAC 58.278 39.130 0.00 0.00 39.22 4.57
2331 5312 1.720852 GGCGTTGCTTTGCATGTTAAG 59.279 47.619 0.00 0.00 38.76 1.85
2425 5406 5.888724 ACTCTCTCGATCAACAAATCCTCTA 59.111 40.000 0.00 0.00 0.00 2.43
2562 5543 6.951062 TCAATCATGAACTGTGGTGTAAAA 57.049 33.333 0.00 0.00 30.99 1.52
2604 5585 6.478512 AAGATTGAAGGTACAAGCCAAAAA 57.521 33.333 0.00 0.00 36.94 1.94
2609 5590 7.391148 TTCATAAAGATTGAAGGTACAAGCC 57.609 36.000 0.00 0.00 36.94 4.35


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

AutoCloner maintained by Alex Coulton.