Multiple sequence alignment - TraesCS3A01G172000

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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 TraesCS3A01G172000 chr3A 100.000 5779 0 0 1 5779 186744929 186750707 0.000000e+00 10672.0
1 TraesCS3A01G172000 chr3A 94.934 829 26 3 3124 3937 740075080 740074253 0.000000e+00 1284.0
2 TraesCS3A01G172000 chr3A 90.940 596 13 11 1 569 647684024 647684605 0.000000e+00 763.0
3 TraesCS3A01G172000 chr3D 98.510 4968 28 10 594 5523 160556169 160561128 0.000000e+00 8722.0
4 TraesCS3A01G172000 chr3D 97.744 266 5 1 5515 5779 160561188 160561453 1.900000e-124 457.0
5 TraesCS3A01G172000 chr3B 95.843 5004 103 38 594 5528 237105899 237110866 0.000000e+00 7991.0
6 TraesCS3A01G172000 chr3B 88.686 274 13 2 5524 5779 237110923 237111196 9.340000e-83 318.0
7 TraesCS3A01G172000 chr7D 94.233 815 30 4 3124 3923 478676378 478675566 0.000000e+00 1229.0
8 TraesCS3A01G172000 chr4A 92.754 621 14 6 1 594 559507386 559508002 0.000000e+00 869.0
9 TraesCS3A01G172000 chr4A 84.496 129 13 3 2975 3103 65140897 65141018 2.830000e-23 121.0
10 TraesCS3A01G172000 chr4A 84.848 66 6 4 4055 4120 512025827 512025888 4.830000e-06 63.9
11 TraesCS3A01G172000 chr2D 94.000 400 22 2 3124 3523 302988646 302988249 6.410000e-169 604.0
12 TraesCS3A01G172000 chr6D 87.619 525 33 14 99 595 387604098 387604618 1.080000e-161 580.0
13 TraesCS3A01G172000 chr6D 95.833 48 1 1 4058 4105 368365364 368365318 6.210000e-10 76.8
14 TraesCS3A01G172000 chr6D 92.157 51 3 1 4051 4100 27848408 27848358 2.890000e-08 71.3
15 TraesCS3A01G172000 chrUn 91.866 418 10 5 3535 3937 11557360 11556952 3.910000e-156 562.0
16 TraesCS3A01G172000 chrUn 97.692 260 6 0 3124 3383 11557619 11557360 1.140000e-121 448.0
17 TraesCS3A01G172000 chr7B 92.246 374 13 3 3579 3937 173307737 173307365 3.090000e-142 516.0
18 TraesCS3A01G172000 chr7B 87.248 298 30 5 313 607 619432112 619431820 3.340000e-87 333.0
19 TraesCS3A01G172000 chr7B 86.806 288 32 4 309 595 444462900 444462618 3.360000e-82 316.0
20 TraesCS3A01G172000 chr4B 93.617 282 14 2 3245 3523 220391017 220390737 8.960000e-113 418.0
21 TraesCS3A01G172000 chr4B 93.382 136 8 1 3124 3258 220392572 220392437 3.530000e-47 200.0
22 TraesCS3A01G172000 chr6A 88.927 289 26 4 309 596 457040676 457040959 9.210000e-93 351.0
23 TraesCS3A01G172000 chr6A 83.117 154 20 4 131 282 333828025 333828174 1.010000e-27 135.0
24 TraesCS3A01G172000 chr6A 95.833 48 1 1 4058 4105 509279137 509279091 6.210000e-10 76.8
25 TraesCS3A01G172000 chr1B 87.108 287 31 5 309 594 12493700 12493419 2.600000e-83 320.0
26 TraesCS3A01G172000 chr1B 86.411 287 33 4 309 594 12563659 12563378 5.620000e-80 309.0
27 TraesCS3A01G172000 chr5B 86.242 298 35 5 309 605 57123103 57123395 9.340000e-83 318.0
28 TraesCS3A01G172000 chr5B 97.727 44 0 1 4057 4100 17982704 17982662 2.230000e-09 75.0
29 TraesCS3A01G172000 chr5B 95.652 46 0 2 4055 4100 113455078 113455121 8.030000e-09 73.1
30 TraesCS3A01G172000 chr1D 86.567 134 15 2 2970 3102 377160720 377160589 1.680000e-30 145.0
31 TraesCS3A01G172000 chr6B 95.833 48 1 1 4058 4105 553057123 553057169 6.210000e-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 TraesCS3A01G172000 chr3A 186744929 186750707 5778 False 10672.0 10672 100.0000 1 5779 1 chr3A.!!$F1 5778
1 TraesCS3A01G172000 chr3A 740074253 740075080 827 True 1284.0 1284 94.9340 3124 3937 1 chr3A.!!$R1 813
2 TraesCS3A01G172000 chr3A 647684024 647684605 581 False 763.0 763 90.9400 1 569 1 chr3A.!!$F2 568
3 TraesCS3A01G172000 chr3D 160556169 160561453 5284 False 4589.5 8722 98.1270 594 5779 2 chr3D.!!$F1 5185
4 TraesCS3A01G172000 chr3B 237105899 237111196 5297 False 4154.5 7991 92.2645 594 5779 2 chr3B.!!$F1 5185
5 TraesCS3A01G172000 chr7D 478675566 478676378 812 True 1229.0 1229 94.2330 3124 3923 1 chr7D.!!$R1 799
6 TraesCS3A01G172000 chr4A 559507386 559508002 616 False 869.0 869 92.7540 1 594 1 chr4A.!!$F3 593
7 TraesCS3A01G172000 chr6D 387604098 387604618 520 False 580.0 580 87.6190 99 595 1 chr6D.!!$F1 496
8 TraesCS3A01G172000 chrUn 11556952 11557619 667 True 505.0 562 94.7790 3124 3937 2 chrUn.!!$R1 813
9 TraesCS3A01G172000 chr4B 220390737 220392572 1835 True 309.0 418 93.4995 3124 3523 2 chr4B.!!$R1 399

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
588 618 0.440758 GCGTTGCACGTACATGCTTA 59.559 50.000 15.74 0.21 46.28 3.09 F
590 620 1.724623 CGTTGCACGTACATGCTTACT 59.275 47.619 15.74 0.00 46.28 2.24 F
2855 2911 1.059098 TTGATGCTGGTGTCTGTCCT 58.941 50.000 0.00 0.00 0.00 3.85 F
3007 3063 3.906720 TCACCTTCAGTGCTTATACCC 57.093 47.619 0.00 0.00 46.81 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2410 7.657761 CCAGGACAATATAAAACTAGTAGCCAG 59.342 40.741 0.0 0.0 0.00 4.85 R
3007 3063 1.493772 TTCCAACAGTTCGTAGTGCG 58.506 50.000 0.0 0.0 43.01 5.34 R
3660 5157 2.213499 GTGAGAATATGCAGAACCCGG 58.787 52.381 0.0 0.0 0.00 5.73 R
5231 6744 2.656947 TTCCTGAAGAACCCCACAAG 57.343 50.000 0.0 0.0 0.00 3.16 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
63 64 0.813210 GCTCCCGCAGAAATCTCCTG 60.813 60.000 0.00 0.00 35.78 3.86
90 91 3.256704 TGTCTTAAACATGGAGAGGGGT 58.743 45.455 0.00 0.00 31.20 4.95
136 140 6.317893 GGTCTACAAAAACTTGGTCTTCTTGA 59.682 38.462 0.00 0.00 0.00 3.02
211 215 1.320344 ATCTGCTGGAACCGAGCGTA 61.320 55.000 0.00 0.00 39.47 4.42
486 516 9.902196 TTATCCGGATTACTTTTTGTTTCTTTC 57.098 29.630 24.71 0.00 0.00 2.62
487 517 7.336161 TCCGGATTACTTTTTGTTTCTTTCA 57.664 32.000 0.00 0.00 0.00 2.69
488 518 7.947282 TCCGGATTACTTTTTGTTTCTTTCAT 58.053 30.769 0.00 0.00 0.00 2.57
489 519 7.865385 TCCGGATTACTTTTTGTTTCTTTCATG 59.135 33.333 0.00 0.00 0.00 3.07
490 520 7.359181 CCGGATTACTTTTTGTTTCTTTCATGC 60.359 37.037 0.00 0.00 0.00 4.06
491 521 7.382218 CGGATTACTTTTTGTTTCTTTCATGCT 59.618 33.333 0.00 0.00 0.00 3.79
492 522 9.045223 GGATTACTTTTTGTTTCTTTCATGCTT 57.955 29.630 0.00 0.00 0.00 3.91
494 524 8.994429 TTACTTTTTGTTTCTTTCATGCTTCA 57.006 26.923 0.00 0.00 0.00 3.02
495 525 7.903995 ACTTTTTGTTTCTTTCATGCTTCAA 57.096 28.000 0.00 0.00 0.00 2.69
496 526 8.496707 ACTTTTTGTTTCTTTCATGCTTCAAT 57.503 26.923 0.00 0.00 0.00 2.57
497 527 8.606602 ACTTTTTGTTTCTTTCATGCTTCAATC 58.393 29.630 0.00 0.00 0.00 2.67
498 528 8.721019 TTTTTGTTTCTTTCATGCTTCAATCT 57.279 26.923 0.00 0.00 0.00 2.40
499 529 8.721019 TTTTGTTTCTTTCATGCTTCAATCTT 57.279 26.923 0.00 0.00 0.00 2.40
500 530 7.703298 TTGTTTCTTTCATGCTTCAATCTTG 57.297 32.000 0.00 0.00 0.00 3.02
501 531 7.041635 TGTTTCTTTCATGCTTCAATCTTGA 57.958 32.000 0.00 0.00 34.92 3.02
502 532 7.490840 TGTTTCTTTCATGCTTCAATCTTGAA 58.509 30.769 5.33 5.33 44.31 2.69
503 533 7.980662 TGTTTCTTTCATGCTTCAATCTTGAAA 59.019 29.630 6.79 3.18 45.61 2.69
504 534 8.985805 GTTTCTTTCATGCTTCAATCTTGAAAT 58.014 29.630 6.79 0.00 45.61 2.17
506 536 9.850628 TTCTTTCATGCTTCAATCTTGAAATAG 57.149 29.630 6.79 0.00 45.61 1.73
507 537 9.234827 TCTTTCATGCTTCAATCTTGAAATAGA 57.765 29.630 6.79 0.42 45.61 1.98
522 552 9.519191 TCTTGAAATAGATTGTTCAATGAAGGA 57.481 29.630 0.00 0.00 41.57 3.36
541 571 7.330900 GAAGGATTCACATTGTGATCAATCT 57.669 36.000 19.63 10.46 46.62 2.40
542 572 7.713734 AAGGATTCACATTGTGATCAATCTT 57.286 32.000 19.63 13.05 42.40 2.40
543 573 7.096884 AGGATTCACATTGTGATCAATCTTG 57.903 36.000 19.63 0.00 42.40 3.02
544 574 6.888088 AGGATTCACATTGTGATCAATCTTGA 59.112 34.615 19.63 2.64 42.40 3.02
545 575 7.395206 AGGATTCACATTGTGATCAATCTTGAA 59.605 33.333 19.63 3.85 42.40 2.69
546 576 8.030692 GGATTCACATTGTGATCAATCTTGAAA 58.969 33.333 19.63 1.42 42.40 2.69
547 577 8.752766 ATTCACATTGTGATCAATCTTGAAAC 57.247 30.769 19.63 0.32 42.40 2.78
548 578 7.274603 TCACATTGTGATCAATCTTGAAACA 57.725 32.000 15.41 2.79 41.66 2.83
549 579 7.714703 TCACATTGTGATCAATCTTGAAACAA 58.285 30.769 15.41 18.77 44.54 2.83
550 580 8.196103 TCACATTGTGATCAATCTTGAAACAAA 58.804 29.630 15.41 8.16 44.09 2.83
551 581 8.984764 CACATTGTGATCAATCTTGAAACAAAT 58.015 29.630 19.67 12.78 44.09 2.32
567 597 8.610855 TGAAACAAATAGTATTAGTCGAGACG 57.389 34.615 0.00 0.00 36.20 4.18
568 598 8.239314 TGAAACAAATAGTATTAGTCGAGACGT 58.761 33.333 0.00 0.00 36.20 4.34
569 599 7.966157 AACAAATAGTATTAGTCGAGACGTG 57.034 36.000 0.00 0.00 36.20 4.49
570 600 5.970023 ACAAATAGTATTAGTCGAGACGTGC 59.030 40.000 0.00 0.00 36.20 5.34
571 601 2.733820 AGTATTAGTCGAGACGTGCG 57.266 50.000 0.00 0.00 36.20 5.34
572 602 2.005451 AGTATTAGTCGAGACGTGCGT 58.995 47.619 0.00 0.00 36.20 5.24
573 603 2.417933 AGTATTAGTCGAGACGTGCGTT 59.582 45.455 0.00 0.00 36.20 4.84
574 604 1.614385 ATTAGTCGAGACGTGCGTTG 58.386 50.000 0.00 0.00 36.20 4.10
575 605 1.000233 TTAGTCGAGACGTGCGTTGC 61.000 55.000 0.00 0.00 36.20 4.17
576 606 2.120355 TAGTCGAGACGTGCGTTGCA 62.120 55.000 0.00 0.00 34.20 4.08
585 615 2.553770 TGCGTTGCACGTACATGC 59.446 55.556 7.04 7.04 44.73 4.06
586 616 1.958715 TGCGTTGCACGTACATGCT 60.959 52.632 15.74 0.00 46.28 3.79
587 617 1.206578 GCGTTGCACGTACATGCTT 59.793 52.632 15.74 0.00 46.28 3.91
588 618 0.440758 GCGTTGCACGTACATGCTTA 59.559 50.000 15.74 0.21 46.28 3.09
589 619 1.785518 GCGTTGCACGTACATGCTTAC 60.786 52.381 15.74 11.77 46.28 2.34
590 620 1.724623 CGTTGCACGTACATGCTTACT 59.275 47.619 15.74 0.00 46.28 2.24
591 621 2.918600 CGTTGCACGTACATGCTTACTA 59.081 45.455 15.74 0.00 46.28 1.82
592 622 3.001070 CGTTGCACGTACATGCTTACTAG 60.001 47.826 15.74 0.00 46.28 2.57
941 975 1.903860 TCGCCTAGCTAGGGTTTTTGA 59.096 47.619 35.44 10.48 43.82 2.69
1626 1671 2.297597 CTCGTGACCTCTCTGTCCTTTT 59.702 50.000 0.00 0.00 34.25 2.27
2124 2173 2.282462 CCCCAACTCCAGGTGTGC 60.282 66.667 0.00 0.00 0.00 4.57
2361 2410 3.019564 AGCAGGTATTTGATCACTTGCC 58.980 45.455 12.62 8.35 45.83 4.52
2682 2738 6.988522 TGTGATTAGTAGTCAACAGCAGTTA 58.011 36.000 0.00 0.00 35.85 2.24
2683 2739 6.866770 TGTGATTAGTAGTCAACAGCAGTTAC 59.133 38.462 0.00 0.00 35.85 2.50
2684 2740 7.091443 GTGATTAGTAGTCAACAGCAGTTACT 58.909 38.462 0.00 0.00 35.85 2.24
2685 2741 7.599245 GTGATTAGTAGTCAACAGCAGTTACTT 59.401 37.037 0.00 0.00 35.85 2.24
2855 2911 1.059098 TTGATGCTGGTGTCTGTCCT 58.941 50.000 0.00 0.00 0.00 3.85
2926 2982 9.554724 CTCTCTGCTATACGATTCTTTATCTTC 57.445 37.037 0.00 0.00 0.00 2.87
3007 3063 3.906720 TCACCTTCAGTGCTTATACCC 57.093 47.619 0.00 0.00 46.81 3.69
3049 3105 6.550938 AATATTGTCACAGGAGATGACTCA 57.449 37.500 6.68 0.00 45.58 3.41
3114 3171 7.489113 GGATTCACTACATTTTGCACCATTAAG 59.511 37.037 0.00 0.00 0.00 1.85
3472 4969 8.540507 TGTGATTACTAGCTTCCTTAGAGATT 57.459 34.615 0.00 0.00 0.00 2.40
3692 5205 5.065090 TGCATATTCTCACATGGTTTCTTCG 59.935 40.000 0.00 0.00 0.00 3.79
4306 5819 0.981277 CTACCTCCGGTGGTTCCCAT 60.981 60.000 31.68 9.79 41.22 4.00
4637 6150 3.881089 TGCAGAGCCATGATAACAATGAG 59.119 43.478 0.00 0.00 0.00 2.90
4940 6453 1.612199 GGTGGTAATTCCCTTGTCGCA 60.612 52.381 0.00 0.00 34.77 5.10
5050 6563 4.566837 ACTGGTCCTGGGTATCAATATCA 58.433 43.478 0.33 0.00 0.00 2.15
5174 6687 5.677319 TTTTGCTACTGTATAGCCTGAGT 57.323 39.130 3.60 0.00 39.69 3.41
5231 6744 5.230182 GGACAATTCTTGAATGGTTTGGTC 58.770 41.667 5.02 0.00 0.00 4.02
5280 6793 0.950836 TGCAGTTTGTCCGAACATGG 59.049 50.000 0.00 0.00 34.73 3.66
5305 6818 7.433425 GGCAATGTCAGCTTTCACTTAATTATC 59.567 37.037 0.00 0.00 0.00 1.75
5309 6822 8.621532 TGTCAGCTTTCACTTAATTATCAGTT 57.378 30.769 0.00 0.00 0.00 3.16
5311 6824 9.899226 GTCAGCTTTCACTTAATTATCAGTTTT 57.101 29.630 0.00 0.00 0.00 2.43
5312 6825 9.897744 TCAGCTTTCACTTAATTATCAGTTTTG 57.102 29.630 0.00 0.00 0.00 2.44
5313 6826 9.683069 CAGCTTTCACTTAATTATCAGTTTTGT 57.317 29.630 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 6.127897 CCCTCTCCATGTTTAAGACAAATGAC 60.128 42.308 0.00 0.00 42.62 3.06
90 91 2.419990 CGTGGGATTCAATGACAGCCTA 60.420 50.000 0.00 0.00 0.00 3.93
136 140 8.424133 AGAGCAACCAAAATTTAGATGAAGTTT 58.576 29.630 0.00 0.00 0.00 2.66
157 161 3.631250 AGAACAAAAACTCCCAAGAGCA 58.369 40.909 0.00 0.00 44.65 4.26
211 215 1.402968 CTGCGGCATGTTAGCAAGATT 59.597 47.619 1.75 0.00 40.63 2.40
460 490 9.902196 GAAAGAAACAAAAAGTAATCCGGATAA 57.098 29.630 19.48 0.00 0.00 1.75
461 491 9.069082 TGAAAGAAACAAAAAGTAATCCGGATA 57.931 29.630 19.48 3.30 0.00 2.59
462 492 7.947282 TGAAAGAAACAAAAAGTAATCCGGAT 58.053 30.769 12.38 12.38 0.00 4.18
463 493 7.336161 TGAAAGAAACAAAAAGTAATCCGGA 57.664 32.000 6.61 6.61 0.00 5.14
464 494 7.359181 GCATGAAAGAAACAAAAAGTAATCCGG 60.359 37.037 0.00 0.00 0.00 5.14
465 495 7.382218 AGCATGAAAGAAACAAAAAGTAATCCG 59.618 33.333 0.00 0.00 0.00 4.18
466 496 8.593492 AGCATGAAAGAAACAAAAAGTAATCC 57.407 30.769 0.00 0.00 0.00 3.01
468 498 9.598517 TGAAGCATGAAAGAAACAAAAAGTAAT 57.401 25.926 0.00 0.00 0.00 1.89
469 499 8.994429 TGAAGCATGAAAGAAACAAAAAGTAA 57.006 26.923 0.00 0.00 0.00 2.24
470 500 8.994429 TTGAAGCATGAAAGAAACAAAAAGTA 57.006 26.923 0.00 0.00 0.00 2.24
471 501 7.903995 TTGAAGCATGAAAGAAACAAAAAGT 57.096 28.000 0.00 0.00 0.00 2.66
472 502 8.823818 AGATTGAAGCATGAAAGAAACAAAAAG 58.176 29.630 0.00 0.00 0.00 2.27
473 503 8.721019 AGATTGAAGCATGAAAGAAACAAAAA 57.279 26.923 0.00 0.00 0.00 1.94
474 504 8.605746 CAAGATTGAAGCATGAAAGAAACAAAA 58.394 29.630 0.00 0.00 0.00 2.44
475 505 7.980662 TCAAGATTGAAGCATGAAAGAAACAAA 59.019 29.630 0.00 0.00 33.55 2.83
476 506 7.490840 TCAAGATTGAAGCATGAAAGAAACAA 58.509 30.769 0.00 0.00 33.55 2.83
477 507 7.041635 TCAAGATTGAAGCATGAAAGAAACA 57.958 32.000 0.00 0.00 33.55 2.83
478 508 7.935338 TTCAAGATTGAAGCATGAAAGAAAC 57.065 32.000 0.00 0.00 41.88 2.78
480 510 9.850628 CTATTTCAAGATTGAAGCATGAAAGAA 57.149 29.630 16.90 8.64 46.68 2.52
481 511 9.234827 TCTATTTCAAGATTGAAGCATGAAAGA 57.765 29.630 16.90 12.50 46.68 2.52
496 526 9.519191 TCCTTCATTGAACAATCTATTTCAAGA 57.481 29.630 0.00 0.00 43.21 3.02
502 532 9.246670 TGTGAATCCTTCATTGAACAATCTATT 57.753 29.630 0.00 0.00 42.47 1.73
503 533 8.812513 TGTGAATCCTTCATTGAACAATCTAT 57.187 30.769 0.00 0.00 42.47 1.98
504 534 8.812513 ATGTGAATCCTTCATTGAACAATCTA 57.187 30.769 0.00 0.00 42.47 1.98
505 535 7.713734 ATGTGAATCCTTCATTGAACAATCT 57.286 32.000 0.00 0.00 42.47 2.40
506 536 7.816031 ACAATGTGAATCCTTCATTGAACAATC 59.184 33.333 20.53 0.00 46.20 2.67
507 537 7.601130 CACAATGTGAATCCTTCATTGAACAAT 59.399 33.333 20.53 0.00 46.20 2.71
508 538 6.924612 CACAATGTGAATCCTTCATTGAACAA 59.075 34.615 20.53 0.00 46.20 2.83
509 539 6.264970 TCACAATGTGAATCCTTCATTGAACA 59.735 34.615 14.37 0.00 46.20 3.18
510 540 6.680810 TCACAATGTGAATCCTTCATTGAAC 58.319 36.000 14.37 0.00 46.20 3.18
511 541 6.897706 TCACAATGTGAATCCTTCATTGAA 57.102 33.333 14.37 0.00 46.20 2.69
512 542 6.660094 TGATCACAATGTGAATCCTTCATTGA 59.340 34.615 20.64 0.00 45.96 2.57
513 543 6.859017 TGATCACAATGTGAATCCTTCATTG 58.141 36.000 20.64 15.60 45.96 2.82
514 544 7.470935 TTGATCACAATGTGAATCCTTCATT 57.529 32.000 20.64 0.00 45.96 2.57
515 545 7.560262 AGATTGATCACAATGTGAATCCTTCAT 59.440 33.333 20.64 8.79 45.96 2.57
516 546 6.888088 AGATTGATCACAATGTGAATCCTTCA 59.112 34.615 20.64 15.34 45.96 3.02
517 547 7.330900 AGATTGATCACAATGTGAATCCTTC 57.669 36.000 20.64 12.92 45.96 3.46
518 548 7.395206 TCAAGATTGATCACAATGTGAATCCTT 59.605 33.333 20.64 14.77 45.96 3.36
519 549 6.888088 TCAAGATTGATCACAATGTGAATCCT 59.112 34.615 20.64 6.05 45.96 3.24
520 550 7.092137 TCAAGATTGATCACAATGTGAATCC 57.908 36.000 20.64 12.51 45.96 3.01
521 551 8.857216 GTTTCAAGATTGATCACAATGTGAATC 58.143 33.333 20.64 17.42 45.96 2.52
522 552 8.361889 TGTTTCAAGATTGATCACAATGTGAAT 58.638 29.630 20.64 9.43 45.96 2.57
523 553 7.714703 TGTTTCAAGATTGATCACAATGTGAA 58.285 30.769 20.64 4.32 45.96 3.18
524 554 7.274603 TGTTTCAAGATTGATCACAATGTGA 57.725 32.000 19.08 19.08 46.90 3.58
525 555 7.933728 TTGTTTCAAGATTGATCACAATGTG 57.066 32.000 7.12 7.12 45.30 3.21
541 571 9.069078 CGTCTCGACTAATACTATTTGTTTCAA 57.931 33.333 0.00 0.00 0.00 2.69
542 572 8.239314 ACGTCTCGACTAATACTATTTGTTTCA 58.761 33.333 0.00 0.00 0.00 2.69
543 573 8.521860 CACGTCTCGACTAATACTATTTGTTTC 58.478 37.037 0.00 0.00 0.00 2.78
544 574 7.008992 GCACGTCTCGACTAATACTATTTGTTT 59.991 37.037 0.00 0.00 0.00 2.83
545 575 6.471519 GCACGTCTCGACTAATACTATTTGTT 59.528 38.462 0.00 0.00 0.00 2.83
546 576 5.970023 GCACGTCTCGACTAATACTATTTGT 59.030 40.000 0.00 0.00 0.00 2.83
547 577 5.113678 CGCACGTCTCGACTAATACTATTTG 59.886 44.000 0.82 0.00 0.00 2.32
548 578 5.203370 CGCACGTCTCGACTAATACTATTT 58.797 41.667 0.82 0.00 0.00 1.40
549 579 4.272018 ACGCACGTCTCGACTAATACTATT 59.728 41.667 12.91 0.00 0.00 1.73
550 580 3.806521 ACGCACGTCTCGACTAATACTAT 59.193 43.478 12.91 0.00 0.00 2.12
551 581 3.190079 ACGCACGTCTCGACTAATACTA 58.810 45.455 12.91 0.00 0.00 1.82
552 582 2.005451 ACGCACGTCTCGACTAATACT 58.995 47.619 12.91 0.00 0.00 2.12
553 583 2.448726 ACGCACGTCTCGACTAATAC 57.551 50.000 12.91 0.00 0.00 1.89
554 584 2.777494 CAACGCACGTCTCGACTAATA 58.223 47.619 12.91 0.00 0.00 0.98
555 585 1.614385 CAACGCACGTCTCGACTAAT 58.386 50.000 12.91 0.00 0.00 1.73
556 586 1.000233 GCAACGCACGTCTCGACTAA 61.000 55.000 12.91 0.00 0.00 2.24
557 587 1.441515 GCAACGCACGTCTCGACTA 60.442 57.895 12.91 0.00 0.00 2.59
558 588 2.729862 GCAACGCACGTCTCGACT 60.730 61.111 12.91 0.00 0.00 4.18
559 589 3.028019 TGCAACGCACGTCTCGAC 61.028 61.111 12.91 3.79 31.71 4.20
572 602 8.965480 ACTCTACTAGTAAGCATGTACGTGCAA 61.965 40.741 35.00 22.78 41.40 4.08
573 603 7.570400 ACTCTACTAGTAAGCATGTACGTGCA 61.570 42.308 35.00 17.77 41.40 4.57
574 604 5.165911 TCTACTAGTAAGCATGTACGTGC 57.834 43.478 28.92 28.92 45.38 5.34
575 605 6.360844 ACTCTACTAGTAAGCATGTACGTG 57.639 41.667 10.89 10.89 36.36 4.49
576 606 7.044181 TGTACTCTACTAGTAAGCATGTACGT 58.956 38.462 3.76 0.00 42.37 3.57
577 607 7.474398 TGTACTCTACTAGTAAGCATGTACG 57.526 40.000 3.76 0.00 42.37 3.67
1626 1671 8.734218 TGTGTGTCTTAACCATAACTAAAACA 57.266 30.769 0.00 0.00 0.00 2.83
2124 2173 9.907576 GATTACAAGAATAAGATTCAGTTGACG 57.092 33.333 7.70 0.00 0.00 4.35
2361 2410 7.657761 CCAGGACAATATAAAACTAGTAGCCAG 59.342 40.741 0.00 0.00 0.00 4.85
3007 3063 1.493772 TTCCAACAGTTCGTAGTGCG 58.506 50.000 0.00 0.00 43.01 5.34
3049 3105 7.823745 AAATGAATGAGTTACCTGAGTTTGT 57.176 32.000 0.00 0.00 0.00 2.83
3185 3245 6.716628 ACTTGTCAAATCTGATGTACAATGGT 59.283 34.615 0.00 6.30 33.05 3.55
3472 4969 9.453325 GGAAAAATGAACAAACGAAACTATACA 57.547 29.630 0.00 0.00 0.00 2.29
3660 5157 2.213499 GTGAGAATATGCAGAACCCGG 58.787 52.381 0.00 0.00 0.00 5.73
3692 5205 7.949690 AATACAAACAAAGGTAATCCCCTAC 57.050 36.000 0.00 0.00 33.33 3.18
4306 5819 8.298854 CAAATGAGAACATACTTGATTTGGTCA 58.701 33.333 0.00 0.00 35.50 4.02
4637 6150 5.528043 TCTTCACAGCCTTCTCATAGATC 57.472 43.478 0.00 0.00 0.00 2.75
5050 6563 4.803098 ATACTCCTCTTACAAACGCTGT 57.197 40.909 0.00 0.00 42.47 4.40
5231 6744 2.656947 TTCCTGAAGAACCCCACAAG 57.343 50.000 0.00 0.00 0.00 3.16
5280 6793 7.970061 TGATAATTAAGTGAAAGCTGACATTGC 59.030 33.333 0.00 0.00 0.00 3.56
5305 6818 9.991388 AAATCAAAATTGATCACAACAAAACTG 57.009 25.926 8.96 0.00 46.60 3.16
5309 6822 7.982224 TGCAAATCAAAATTGATCACAACAAA 58.018 26.923 8.96 0.00 46.60 2.83
5311 6824 7.226918 ACATGCAAATCAAAATTGATCACAACA 59.773 29.630 8.96 4.93 46.60 3.33
5312 6825 7.577979 ACATGCAAATCAAAATTGATCACAAC 58.422 30.769 8.96 0.05 46.60 3.32
5313 6826 7.731882 ACATGCAAATCAAAATTGATCACAA 57.268 28.000 8.96 0.00 46.60 3.33
5523 7073 1.202222 CGATGTTTGAATGCCTGAGCC 60.202 52.381 0.00 0.00 38.69 4.70
5606 7225 1.521457 GAATGCGCCGGAGATCACA 60.521 57.895 10.31 0.00 0.00 3.58
5659 7278 2.652095 CCCGTGTCGTACCCACCAT 61.652 63.158 5.10 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.