Multiple sequence alignment - TraesCS5B01G343700

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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 TraesCS5B01G343700 chr5B 100.000 2324 0 0 1 2324 527065731 527063408 0.000000e+00 4292
1 TraesCS5B01G343700 chr5B 84.327 453 45 10 877 1306 528537423 528537872 9.930000e-114 420
2 TraesCS5B01G343700 chr5B 80.000 435 58 12 1044 1451 526587394 526586962 6.280000e-76 294
3 TraesCS5B01G343700 chr5B 90.732 205 16 3 1452 1653 527058226 527058022 1.060000e-68 270
4 TraesCS5B01G343700 chr5A 96.705 880 23 4 1448 2324 548239117 548238241 0.000000e+00 1459
5 TraesCS5B01G343700 chr5A 86.592 977 66 24 510 1453 548240783 548239839 0.000000e+00 1018
6 TraesCS5B01G343700 chr5A 82.603 730 75 21 768 1450 548231004 548230280 4.270000e-167 597
7 TraesCS5B01G343700 chr5A 81.651 654 74 12 801 1414 549153623 549154270 3.450000e-138 501
8 TraesCS5B01G343700 chr5A 82.083 240 43 0 1067 1306 547645319 547645080 3.030000e-49 206
9 TraesCS5B01G343700 chr5D 92.491 879 56 7 1449 2324 434323907 434324778 0.000000e+00 1249
10 TraesCS5B01G343700 chr5D 89.718 992 43 7 521 1453 434322638 434323629 0.000000e+00 1212
11 TraesCS5B01G343700 chr5D 89.035 839 49 3 510 1305 434403395 434402557 0.000000e+00 1000
12 TraesCS5B01G343700 chr5D 79.130 1011 130 37 509 1450 434394201 434393203 7.050000e-175 623
13 TraesCS5B01G343700 chr5D 79.276 912 113 28 609 1451 435237217 435238121 3.350000e-158 568
14 TraesCS5B01G343700 chr5D 88.186 474 38 10 1 459 434403959 434403489 1.210000e-152 549
15 TraesCS5B01G343700 chr5D 85.658 509 52 9 1827 2323 434401681 434401182 1.230000e-142 516
16 TraesCS5B01G343700 chr5D 78.780 410 50 15 594 969 434329612 434330018 8.300000e-60 241
17 TraesCS5B01G343700 chr5D 91.391 151 10 3 1453 1600 435238361 435238511 1.090000e-48 204
18 TraesCS5B01G343700 chr7B 83.942 137 14 5 801 932 547947453 547947320 8.720000e-25 124


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 TraesCS5B01G343700 chr5B 527063408 527065731 2323 True 4292.000000 4292 100.000000 1 2324 1 chr5B.!!$R3 2323
1 TraesCS5B01G343700 chr5A 548238241 548240783 2542 True 1238.500000 1459 91.648500 510 2324 2 chr5A.!!$R3 1814
2 TraesCS5B01G343700 chr5A 548230280 548231004 724 True 597.000000 597 82.603000 768 1450 1 chr5A.!!$R2 682
3 TraesCS5B01G343700 chr5A 549153623 549154270 647 False 501.000000 501 81.651000 801 1414 1 chr5A.!!$F1 613
4 TraesCS5B01G343700 chr5D 434322638 434324778 2140 False 1230.500000 1249 91.104500 521 2324 2 chr5D.!!$F2 1803
5 TraesCS5B01G343700 chr5D 434401182 434403959 2777 True 688.333333 1000 87.626333 1 2323 3 chr5D.!!$R2 2322
6 TraesCS5B01G343700 chr5D 434393203 434394201 998 True 623.000000 623 79.130000 509 1450 1 chr5D.!!$R1 941
7 TraesCS5B01G343700 chr5D 435237217 435238511 1294 False 386.000000 568 85.333500 609 1600 2 chr5D.!!$F3 991

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
88 97 0.031721 CGACTATTCCACTACGCCCC 59.968 60.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1353 1550 0.100682 ACACTAGGCATCGTACAGCG 59.899 55.0 0.0 0.0 43.01 5.18 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 3.327757 TGCCTCTTCAGAAACTACATGGT 59.672 43.478 0.00 0.00 0.00 3.55
44 45 4.558226 TCAGAAACTACATGGTGCATCT 57.442 40.909 0.00 0.00 0.00 2.90
51 52 4.910195 ACTACATGGTGCATCTTCAGAAA 58.090 39.130 0.00 0.00 0.00 2.52
83 92 3.315749 AGCAGCTACGACTATTCCACTAC 59.684 47.826 0.00 0.00 0.00 2.73
86 95 2.604132 GCTACGACTATTCCACTACGCC 60.604 54.545 0.00 0.00 0.00 5.68
87 96 0.743097 ACGACTATTCCACTACGCCC 59.257 55.000 0.00 0.00 0.00 6.13
88 97 0.031721 CGACTATTCCACTACGCCCC 59.968 60.000 0.00 0.00 0.00 5.80
89 98 1.117150 GACTATTCCACTACGCCCCA 58.883 55.000 0.00 0.00 0.00 4.96
90 99 1.692519 GACTATTCCACTACGCCCCAT 59.307 52.381 0.00 0.00 0.00 4.00
91 100 1.692519 ACTATTCCACTACGCCCCATC 59.307 52.381 0.00 0.00 0.00 3.51
92 101 1.002087 CTATTCCACTACGCCCCATCC 59.998 57.143 0.00 0.00 0.00 3.51
106 115 1.907739 CATCCCCATGGACGACTGT 59.092 57.895 15.22 0.00 45.58 3.55
133 142 1.892474 GGAGCAATTTTGGTAGTGGCA 59.108 47.619 0.00 0.00 39.30 4.92
148 164 1.298014 GGCAACTCCTCCTGACCAG 59.702 63.158 0.00 0.00 0.00 4.00
165 181 1.306568 AGGGAACTGAGGAGAGCCC 60.307 63.158 0.00 0.00 41.13 5.19
194 214 1.668101 CCTCCGTCCCTTCCGAGAAG 61.668 65.000 6.66 6.66 0.00 2.85
223 243 0.537188 ACATGACGTCCTCCATCACC 59.463 55.000 14.12 0.00 0.00 4.02
224 244 0.528466 CATGACGTCCTCCATCACCG 60.528 60.000 14.12 0.00 0.00 4.94
248 268 4.247380 CATCCCCAGGAGCTCGCC 62.247 72.222 7.83 0.00 34.05 5.54
365 385 3.728221 CGTGAAGCGAGACAAGATGATAG 59.272 47.826 0.00 0.00 44.77 2.08
374 394 5.981915 CGAGACAAGATGATAGCAAATCAGA 59.018 40.000 7.68 0.00 0.00 3.27
378 398 7.774157 AGACAAGATGATAGCAAATCAGATTGT 59.226 33.333 21.66 21.66 40.34 2.71
419 439 1.514553 GGATGCTTGCAAGGCTTCC 59.485 57.895 27.10 26.04 43.33 3.46
426 446 2.495739 CTTGCAAGGCTTCCTGGGAAG 61.496 57.143 19.14 21.31 44.41 3.46
439 459 2.029649 CCTGGGAAGCACATGAACAAAG 60.030 50.000 0.00 0.00 0.00 2.77
459 479 0.178903 ACTCCCTCTGTAACAGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
460 480 1.207791 CTCCCTCTGTAACAGCCCAT 58.792 55.000 0.00 0.00 0.00 4.00
461 481 1.561542 CTCCCTCTGTAACAGCCCATT 59.438 52.381 0.00 0.00 0.00 3.16
462 482 1.559682 TCCCTCTGTAACAGCCCATTC 59.440 52.381 0.00 0.00 0.00 2.67
464 484 2.092212 CCCTCTGTAACAGCCCATTCAT 60.092 50.000 0.00 0.00 0.00 2.57
466 486 3.614092 CTCTGTAACAGCCCATTCATGT 58.386 45.455 0.00 0.00 0.00 3.21
467 487 3.609853 TCTGTAACAGCCCATTCATGTC 58.390 45.455 0.00 0.00 0.00 3.06
471 491 3.377253 AACAGCCCATTCATGTCAGAT 57.623 42.857 0.00 0.00 0.00 2.90
472 492 2.651455 ACAGCCCATTCATGTCAGATG 58.349 47.619 0.00 0.00 0.00 2.90
473 493 2.025605 ACAGCCCATTCATGTCAGATGT 60.026 45.455 0.00 0.00 0.00 3.06
474 494 3.021695 CAGCCCATTCATGTCAGATGTT 58.978 45.455 0.00 0.00 0.00 2.71
475 495 3.446161 CAGCCCATTCATGTCAGATGTTT 59.554 43.478 0.00 0.00 0.00 2.83
476 496 4.641541 CAGCCCATTCATGTCAGATGTTTA 59.358 41.667 0.00 0.00 0.00 2.01
477 497 4.641989 AGCCCATTCATGTCAGATGTTTAC 59.358 41.667 0.00 0.00 0.00 2.01
478 498 4.398988 GCCCATTCATGTCAGATGTTTACA 59.601 41.667 0.00 0.00 0.00 2.41
479 499 5.449588 GCCCATTCATGTCAGATGTTTACAG 60.450 44.000 0.00 0.00 0.00 2.74
480 500 5.449588 CCCATTCATGTCAGATGTTTACAGC 60.450 44.000 0.00 0.00 0.00 4.40
481 501 5.449588 CCATTCATGTCAGATGTTTACAGCC 60.450 44.000 0.00 0.00 31.57 4.85
482 502 3.609853 TCATGTCAGATGTTTACAGCCC 58.390 45.455 0.00 0.00 31.57 5.19
483 503 3.008923 TCATGTCAGATGTTTACAGCCCA 59.991 43.478 0.00 0.00 31.57 5.36
484 504 3.719268 TGTCAGATGTTTACAGCCCAT 57.281 42.857 0.00 0.00 31.57 4.00
486 506 4.009675 TGTCAGATGTTTACAGCCCATTC 58.990 43.478 0.00 0.00 31.57 2.67
488 508 4.702131 GTCAGATGTTTACAGCCCATTCTT 59.298 41.667 0.00 0.00 31.57 2.52
489 509 4.701651 TCAGATGTTTACAGCCCATTCTTG 59.298 41.667 0.00 0.00 31.57 3.02
491 511 1.892474 TGTTTACAGCCCATTCTTGCC 59.108 47.619 0.00 0.00 0.00 4.52
493 513 2.562738 GTTTACAGCCCATTCTTGCCTT 59.437 45.455 0.00 0.00 0.00 4.35
494 514 1.838112 TACAGCCCATTCTTGCCTTG 58.162 50.000 0.00 0.00 0.00 3.61
495 515 0.178953 ACAGCCCATTCTTGCCTTGT 60.179 50.000 0.00 0.00 0.00 3.16
497 517 1.079612 GCCCATTCTTGCCTTGTGC 60.080 57.895 0.00 0.00 41.77 4.57
498 518 1.538687 GCCCATTCTTGCCTTGTGCT 61.539 55.000 0.00 0.00 42.00 4.40
499 519 0.529378 CCCATTCTTGCCTTGTGCTC 59.471 55.000 0.00 0.00 42.00 4.26
500 520 0.169672 CCATTCTTGCCTTGTGCTCG 59.830 55.000 0.00 0.00 42.00 5.03
501 521 0.169672 CATTCTTGCCTTGTGCTCGG 59.830 55.000 0.00 0.00 42.00 4.63
502 522 0.036732 ATTCTTGCCTTGTGCTCGGA 59.963 50.000 0.00 0.00 42.00 4.55
505 525 0.392193 CTTGCCTTGTGCTCGGAGAT 60.392 55.000 9.69 0.00 42.00 2.75
506 526 0.036732 TTGCCTTGTGCTCGGAGATT 59.963 50.000 9.69 0.00 42.00 2.40
513 576 2.972625 TGTGCTCGGAGATTAAACAGG 58.027 47.619 9.69 0.00 33.89 4.00
517 580 2.937149 GCTCGGAGATTAAACAGGGAAC 59.063 50.000 9.69 0.00 33.89 3.62
532 595 3.054875 CAGGGAACAGATTGATCAGGTGA 60.055 47.826 0.00 0.00 0.00 4.02
658 728 2.999331 ACCCATTGTTGTATTCCTCGG 58.001 47.619 0.00 0.00 0.00 4.63
714 798 2.152297 TTGGCTACGCGGTTCGGTAA 62.152 55.000 12.47 0.00 43.86 2.85
720 804 2.263540 GCGGTTCGGTAAGGCAGA 59.736 61.111 0.00 0.00 0.00 4.26
723 807 1.291272 GGTTCGGTAAGGCAGACGT 59.709 57.895 0.00 0.00 0.00 4.34
746 830 5.415701 GTGAATGATAAGAAAGCAGACCCAA 59.584 40.000 0.00 0.00 0.00 4.12
840 963 0.895559 CCTTGTCCCCTGCCAACTTC 60.896 60.000 0.00 0.00 0.00 3.01
849 972 2.089980 CCTGCCAACTTCTCTCAATGG 58.910 52.381 0.00 0.00 0.00 3.16
920 1063 3.114616 CGGCTCAGCTCAACACCG 61.115 66.667 0.00 0.00 0.00 4.94
938 1081 0.994995 CGTCACTTCTTCATCCGCTG 59.005 55.000 0.00 0.00 0.00 5.18
955 1098 1.735386 CTGATCCACCAACTGAGCAG 58.265 55.000 0.00 0.00 38.49 4.24
1143 1312 1.289160 AGGGCCACTGTGTCATGTAT 58.711 50.000 6.18 0.00 0.00 2.29
1145 1314 3.048600 AGGGCCACTGTGTCATGTATAT 58.951 45.455 6.18 0.00 0.00 0.86
1148 1317 3.433598 GGCCACTGTGTCATGTATATGGT 60.434 47.826 7.08 0.00 34.97 3.55
1157 1326 4.021456 TGTCATGTATATGGTCGATGGGAC 60.021 45.833 0.00 0.00 45.31 4.46
1194 1363 1.248785 TGGAGTACCTCAGCACGACC 61.249 60.000 0.00 0.00 37.04 4.79
1344 1541 0.176680 CTCTATGGTGGCGTCTTGCT 59.823 55.000 0.00 0.00 45.43 3.91
1353 1550 1.201647 TGGCGTCTTGCTACTACACTC 59.798 52.381 0.00 0.00 45.43 3.51
1398 1595 2.162408 GCCAGCAACCAGATTTACTGTC 59.838 50.000 0.00 0.00 44.40 3.51
1429 1627 2.743664 TGAAGAACATGCATTCAGGACG 59.256 45.455 0.00 0.00 0.00 4.79
1540 2567 8.139350 TGCAATGACATCAATCCAATAGAAATC 58.861 33.333 0.00 0.00 0.00 2.17
1637 2665 8.260114 AGATTTCAATTATTGGGGTAAAAGCAG 58.740 33.333 5.02 0.00 0.00 4.24
1693 2721 3.867857 TGCAGCTCCGAATGTTTATGTA 58.132 40.909 0.00 0.00 0.00 2.29
1768 2809 6.778834 AGTGTTCATGAAATCATTGGCATA 57.221 33.333 10.35 0.00 33.61 3.14
1782 2823 0.179018 GGCATACTTCCCGCTTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
1831 2872 7.408756 TTTCAATATCTTGCAAGGCTGTAAT 57.591 32.000 25.73 13.18 32.11 1.89
1979 3023 7.549134 CCCTCTTTTAAATGCCAGTAAAAATCC 59.451 37.037 0.00 0.00 30.85 3.01
2013 3057 7.077605 CACAGTATGACCATGTTAAGTGTTTG 58.922 38.462 0.00 0.00 39.69 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 5.921962 TCTAGCTAGTTTCTGAAGATGCA 57.078 39.130 20.10 0.00 0.00 3.96
44 45 4.499183 GCTGCTTCTAGCTAGTTTCTGAA 58.501 43.478 20.10 5.74 42.97 3.02
70 76 1.117150 TGGGGCGTAGTGGAATAGTC 58.883 55.000 0.00 0.00 0.00 2.59
71 77 1.692519 GATGGGGCGTAGTGGAATAGT 59.307 52.381 0.00 0.00 0.00 2.12
90 99 1.125093 ACAACAGTCGTCCATGGGGA 61.125 55.000 13.02 7.13 42.29 4.81
91 100 0.955428 CACAACAGTCGTCCATGGGG 60.955 60.000 13.02 4.51 0.00 4.96
92 101 0.034756 TCACAACAGTCGTCCATGGG 59.965 55.000 13.02 0.00 0.00 4.00
100 109 1.511850 TTGCTCCATCACAACAGTCG 58.488 50.000 0.00 0.00 0.00 4.18
106 115 4.832266 ACTACCAAAATTGCTCCATCACAA 59.168 37.500 0.00 0.00 0.00 3.33
148 164 1.306568 AGGGCTCTCCTCAGTTCCC 60.307 63.158 0.00 0.00 44.06 3.97
165 181 3.213402 GACGGAGGAGGCGGAGAG 61.213 72.222 0.00 0.00 0.00 3.20
170 186 3.839432 GAAGGGACGGAGGAGGCG 61.839 72.222 0.00 0.00 0.00 5.52
186 206 0.966920 GTGTGTCTTCCCTTCTCGGA 59.033 55.000 0.00 0.00 33.16 4.55
194 214 1.429463 GACGTCATGTGTGTCTTCCC 58.571 55.000 11.55 0.00 0.00 3.97
351 371 7.966246 ATCTGATTTGCTATCATCTTGTCTC 57.034 36.000 3.13 0.00 0.00 3.36
354 374 7.876936 ACAATCTGATTTGCTATCATCTTGT 57.123 32.000 0.00 15.64 32.54 3.16
365 385 6.101332 TCAGGCATTAAACAATCTGATTTGC 58.899 36.000 11.97 11.97 0.00 3.68
378 398 8.871629 TCCTGTTTAACTAATCAGGCATTAAA 57.128 30.769 16.80 2.30 45.91 1.52
398 418 0.541296 AAGCCTTGCAAGCATCCTGT 60.541 50.000 21.43 0.00 0.00 4.00
399 419 0.172803 GAAGCCTTGCAAGCATCCTG 59.827 55.000 21.43 7.34 0.00 3.86
407 427 0.540365 CTTCCCAGGAAGCCTTGCAA 60.540 55.000 13.33 0.00 43.95 4.08
419 439 2.886523 TCTTTGTTCATGTGCTTCCCAG 59.113 45.455 0.00 0.00 0.00 4.45
426 446 2.485814 GAGGGAGTCTTTGTTCATGTGC 59.514 50.000 0.00 0.00 0.00 4.57
439 459 0.537653 GGGCTGTTACAGAGGGAGTC 59.462 60.000 17.40 0.00 32.44 3.36
459 479 4.641989 GGGCTGTAAACATCTGACATGAAT 59.358 41.667 0.00 0.00 0.00 2.57
460 480 4.009675 GGGCTGTAAACATCTGACATGAA 58.990 43.478 0.00 0.00 0.00 2.57
461 481 3.008923 TGGGCTGTAAACATCTGACATGA 59.991 43.478 0.00 0.00 0.00 3.07
462 482 3.346315 TGGGCTGTAAACATCTGACATG 58.654 45.455 0.00 0.00 0.00 3.21
464 484 3.719268 ATGGGCTGTAAACATCTGACA 57.281 42.857 0.00 0.00 0.00 3.58
466 486 4.574674 AGAATGGGCTGTAAACATCTGA 57.425 40.909 0.00 0.00 0.00 3.27
467 487 4.676196 GCAAGAATGGGCTGTAAACATCTG 60.676 45.833 0.00 0.00 0.00 2.90
471 491 1.892474 GGCAAGAATGGGCTGTAAACA 59.108 47.619 0.00 0.00 0.00 2.83
472 492 2.654749 GGCAAGAATGGGCTGTAAAC 57.345 50.000 0.00 0.00 0.00 2.01
479 499 1.079612 GCACAAGGCAAGAATGGGC 60.080 57.895 0.00 0.00 43.97 5.36
489 509 2.024176 TTAATCTCCGAGCACAAGGC 57.976 50.000 0.00 0.00 45.30 4.35
491 511 3.372206 CCTGTTTAATCTCCGAGCACAAG 59.628 47.826 0.00 0.00 0.00 3.16
493 513 2.354704 CCCTGTTTAATCTCCGAGCACA 60.355 50.000 0.00 0.00 0.00 4.57
494 514 2.093658 TCCCTGTTTAATCTCCGAGCAC 60.094 50.000 0.00 0.00 0.00 4.40
495 515 2.184533 TCCCTGTTTAATCTCCGAGCA 58.815 47.619 0.00 0.00 0.00 4.26
497 517 4.081642 TCTGTTCCCTGTTTAATCTCCGAG 60.082 45.833 0.00 0.00 0.00 4.63
498 518 3.835978 TCTGTTCCCTGTTTAATCTCCGA 59.164 43.478 0.00 0.00 0.00 4.55
499 519 4.202245 TCTGTTCCCTGTTTAATCTCCG 57.798 45.455 0.00 0.00 0.00 4.63
500 520 6.180472 TCAATCTGTTCCCTGTTTAATCTCC 58.820 40.000 0.00 0.00 0.00 3.71
501 521 7.554118 TGATCAATCTGTTCCCTGTTTAATCTC 59.446 37.037 0.00 0.00 0.00 2.75
502 522 7.405292 TGATCAATCTGTTCCCTGTTTAATCT 58.595 34.615 0.00 0.00 0.00 2.40
505 525 5.945784 CCTGATCAATCTGTTCCCTGTTTAA 59.054 40.000 0.00 0.00 0.00 1.52
506 526 5.014123 ACCTGATCAATCTGTTCCCTGTTTA 59.986 40.000 0.00 0.00 0.00 2.01
513 576 5.188434 TCATTCACCTGATCAATCTGTTCC 58.812 41.667 0.00 0.00 0.00 3.62
517 580 6.505044 TTGTTCATTCACCTGATCAATCTG 57.495 37.500 0.00 0.00 32.58 2.90
532 595 9.797556 CTGTCATCATAATGTTCATTGTTCATT 57.202 29.630 8.11 11.38 36.12 2.57
604 667 2.232239 CTGAACAATTTCGGTGAGCG 57.768 50.000 0.00 0.00 33.87 5.03
714 798 4.471904 TTCTTATCATTCACGTCTGCCT 57.528 40.909 0.00 0.00 0.00 4.75
720 804 4.631813 GGTCTGCTTTCTTATCATTCACGT 59.368 41.667 0.00 0.00 0.00 4.49
723 807 5.178096 TGGGTCTGCTTTCTTATCATTCA 57.822 39.130 0.00 0.00 0.00 2.57
746 830 4.580580 GCCTATAGTTGCAATTGTTAGGCT 59.419 41.667 30.06 15.06 44.30 4.58
840 963 1.531423 ACTGTGCTTGCCATTGAGAG 58.469 50.000 0.00 0.00 0.00 3.20
849 972 1.279840 GACGGTGAACTGTGCTTGC 59.720 57.895 0.00 0.00 35.19 4.01
920 1063 2.370281 TCAGCGGATGAAGAAGTGAC 57.630 50.000 0.00 0.00 34.02 3.67
938 1081 1.446907 CACTGCTCAGTTGGTGGATC 58.553 55.000 0.00 0.00 40.20 3.36
955 1098 2.636830 AGTGAGCTATGGATGTTGCAC 58.363 47.619 0.00 0.00 0.00 4.57
1143 1312 1.669049 AACGCGTCCCATCGACCATA 61.669 55.000 14.44 0.00 38.36 2.74
1145 1314 2.718747 AAAACGCGTCCCATCGACCA 62.719 55.000 14.44 0.00 38.36 4.02
1148 1317 1.005984 TCAAAACGCGTCCCATCGA 60.006 52.632 14.44 0.44 0.00 3.59
1157 1326 2.248835 AACGGGACCTCAAAACGCG 61.249 57.895 3.53 3.53 43.48 6.01
1194 1363 4.421479 AGGAGCTCGCCGAACACG 62.421 66.667 7.83 0.00 0.00 4.49
1197 1366 2.202676 CTCAGGAGCTCGCCGAAC 60.203 66.667 7.83 0.00 0.00 3.95
1298 1467 0.319728 ATGCACTCTCGACAGCAAGT 59.680 50.000 0.00 0.00 40.76 3.16
1353 1550 0.100682 ACACTAGGCATCGTACAGCG 59.899 55.000 0.00 0.00 43.01 5.18
1369 1566 1.799258 CTGGTTGCTGGCTCCAACAC 61.799 60.000 17.87 10.57 43.24 3.32
1398 1595 3.999001 TGCATGTTCTTCAGAAGCTACAG 59.001 43.478 17.62 12.72 34.27 2.74
1429 1627 4.093115 CACAAGACAGAAGACATCATCAGC 59.907 45.833 0.00 0.00 0.00 4.26
1510 2535 9.134055 TCTATTGGATTGATGTCATTGCAATAA 57.866 29.630 21.31 1.79 43.27 1.40
1540 2567 8.877779 TCCATTTTGTTTTTGTTGTCATACTTG 58.122 29.630 0.00 0.00 0.00 3.16
1637 2665 3.146066 TGCTTGACAGTTAACCATCACC 58.854 45.455 8.53 4.89 0.00 4.02
1768 2809 1.351017 TCTCAAATGGAAGCGGGAAGT 59.649 47.619 0.00 0.00 0.00 3.01
1782 2823 7.466746 AGGCTTTACATAGCAATTTCTCAAA 57.533 32.000 0.00 0.00 43.02 2.69
1814 2855 5.198965 AGATTCATTACAGCCTTGCAAGAT 58.801 37.500 28.05 12.96 0.00 2.40
1815 2856 4.592942 AGATTCATTACAGCCTTGCAAGA 58.407 39.130 28.05 6.89 0.00 3.02
1831 2872 5.938125 GGTTAACAGGTTTCTGCTAGATTCA 59.062 40.000 8.10 0.00 44.59 2.57
2013 3057 3.964411 AGGCATTACCCCAAAAGTAGAC 58.036 45.455 0.00 0.00 40.58 2.59
2144 3188 6.630443 GCAAGTCGATCTGCTTTATGTAATTG 59.370 38.462 12.90 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.