Multiple sequence alignment - TraesCS4A01G141600

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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 TraesCS4A01G141600 chr4A 100.000 2718 0 0 1 2718 222149271 222151988 0.000000e+00 5020
1 TraesCS4A01G141600 chr4A 92.123 1625 119 7 908 2526 173649742 173648121 0.000000e+00 2283
2 TraesCS4A01G141600 chr4A 83.333 570 64 9 30 599 173650646 173650108 5.230000e-137 497
3 TraesCS4A01G141600 chr4A 93.820 178 11 0 2541 2718 173648135 173647958 4.460000e-68 268
4 TraesCS4A01G141600 chr6D 91.693 1878 123 10 657 2526 5202727 5204579 0.000000e+00 2573
5 TraesCS4A01G141600 chr6D 86.093 604 55 11 1 601 5201814 5202391 8.260000e-175 623
6 TraesCS4A01G141600 chr2A 92.545 1717 116 10 817 2526 775685730 775684019 0.000000e+00 2451
7 TraesCS4A01G141600 chr2A 92.483 1716 120 7 817 2526 775736914 775738626 0.000000e+00 2446
8 TraesCS4A01G141600 chr2A 91.422 1772 138 10 766 2526 17555494 17557262 0.000000e+00 2418
9 TraesCS4A01G141600 chr2A 88.235 374 36 4 102 467 775686770 775686397 8.930000e-120 440
10 TraesCS4A01G141600 chr2A 87.332 371 39 4 102 464 775735878 775736248 4.190000e-113 418
11 TraesCS4A01G141600 chr2A 93.820 178 11 0 2541 2718 775684033 775683856 4.460000e-68 268
12 TraesCS4A01G141600 chr2A 93.820 178 11 0 2541 2718 775738612 775738789 4.460000e-68 268
13 TraesCS4A01G141600 chr5B 92.366 1716 121 8 817 2526 508017384 508019095 0.000000e+00 2435
14 TraesCS4A01G141600 chr5B 88.684 433 44 3 37 465 508015991 508016422 8.620000e-145 523
15 TraesCS4A01G141600 chr5B 88.759 427 43 3 43 465 21727433 21727008 4.010000e-143 518
16 TraesCS4A01G141600 chr5B 88.222 433 47 2 37 465 648746156 648745724 5.190000e-142 514
17 TraesCS4A01G141600 chr5B 93.258 178 12 0 2541 2718 21724589 21724412 2.080000e-66 263
18 TraesCS4A01G141600 chr5B 93.258 178 12 0 2541 2718 508019081 508019258 2.080000e-66 263
19 TraesCS4A01G141600 chr5B 93.258 178 12 0 2541 2718 596391718 596391541 2.080000e-66 263
20 TraesCS4A01G141600 chr7A 91.967 1718 125 10 817 2526 709847722 709849434 0.000000e+00 2396
21 TraesCS4A01G141600 chr5A 92.431 1625 114 7 908 2526 437172951 437174572 0.000000e+00 2311
22 TraesCS4A01G141600 chr5A 88.453 433 45 3 37 465 633000309 633000740 4.010000e-143 518
23 TraesCS4A01G141600 chr5A 82.867 572 67 8 30 601 437172047 437172587 4.070000e-133 484
24 TraesCS4A01G141600 chr5A 93.258 178 12 0 2541 2718 633003385 633003562 2.080000e-66 263
25 TraesCS4A01G141600 chr1A 92.308 1625 116 7 908 2526 539290017 539291638 0.000000e+00 2300
26 TraesCS4A01G141600 chr1A 83.072 573 64 10 30 601 539289113 539289653 8.750000e-135 490
27 TraesCS4A01G141600 chr1A 93.820 178 11 0 2541 2718 539291624 539291801 4.460000e-68 268
28 TraesCS4A01G141600 chr1D 90.211 1706 158 7 828 2526 18695600 18693897 0.000000e+00 2217
29 TraesCS4A01G141600 chr2D 86.567 603 58 7 1 601 565933458 565932877 0.000000e+00 643
30 TraesCS4A01G141600 chr4B 93.258 178 12 0 2541 2718 2450242 2450419 2.080000e-66 263


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 TraesCS4A01G141600 chr4A 222149271 222151988 2717 False 5020.000000 5020 100.000000 1 2718 1 chr4A.!!$F1 2717
1 TraesCS4A01G141600 chr4A 173647958 173650646 2688 True 1016.000000 2283 89.758667 30 2718 3 chr4A.!!$R1 2688
2 TraesCS4A01G141600 chr6D 5201814 5204579 2765 False 1598.000000 2573 88.893000 1 2526 2 chr6D.!!$F1 2525
3 TraesCS4A01G141600 chr2A 17555494 17557262 1768 False 2418.000000 2418 91.422000 766 2526 1 chr2A.!!$F1 1760
4 TraesCS4A01G141600 chr2A 775683856 775686770 2914 True 1053.000000 2451 91.533333 102 2718 3 chr2A.!!$R1 2616
5 TraesCS4A01G141600 chr2A 775735878 775738789 2911 False 1044.000000 2446 91.211667 102 2718 3 chr2A.!!$F2 2616
6 TraesCS4A01G141600 chr5B 508015991 508019258 3267 False 1073.666667 2435 91.436000 37 2718 3 chr5B.!!$F1 2681
7 TraesCS4A01G141600 chr5B 21724412 21727433 3021 True 390.500000 518 91.008500 43 2718 2 chr5B.!!$R3 2675
8 TraesCS4A01G141600 chr7A 709847722 709849434 1712 False 2396.000000 2396 91.967000 817 2526 1 chr7A.!!$F1 1709
9 TraesCS4A01G141600 chr5A 437172047 437174572 2525 False 1397.500000 2311 87.649000 30 2526 2 chr5A.!!$F1 2496
10 TraesCS4A01G141600 chr5A 633000309 633003562 3253 False 390.500000 518 90.855500 37 2718 2 chr5A.!!$F2 2681
11 TraesCS4A01G141600 chr1A 539289113 539291801 2688 False 1019.333333 2300 89.733333 30 2718 3 chr1A.!!$F1 2688
12 TraesCS4A01G141600 chr1D 18693897 18695600 1703 True 2217.000000 2217 90.211000 828 2526 1 chr1D.!!$R1 1698
13 TraesCS4A01G141600 chr2D 565932877 565933458 581 True 643.000000 643 86.567000 1 601 1 chr2D.!!$R1 600

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
528 543 0.320334 TCGCTGCCGTCTTGAATCAA 60.320 50.0 0.00 0.0 35.54 2.57 F
579 594 0.522705 CGTTGACGGACGACATCGAT 60.523 55.0 17.71 0.0 45.47 3.59 F
1398 2236 0.937441 TAGGAGGGCTCAGATGGTCT 59.063 55.0 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 2328 0.263172 TCCCCTTGTGGCCAAAAAGA 59.737 50.0 24.54 13.13 0.00 2.52 R
1571 2409 0.322546 GCACCCTTCCCTCGTTTCAT 60.323 55.0 0.00 0.00 0.00 2.57 R
2544 3389 0.337773 AGGCAGTCCATCTCTCCTCA 59.662 55.0 0.00 0.00 33.74 3.86 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
33 34 7.485913 GGTCATACGAATAAACGTGACTAAGAA 59.514 37.037 0.00 0.00 46.02 2.52
34 35 8.521860 GTCATACGAATAAACGTGACTAAGAAG 58.478 37.037 0.00 0.00 46.02 2.85
35 36 7.699391 TCATACGAATAAACGTGACTAAGAAGG 59.301 37.037 0.00 0.00 46.02 3.46
68 69 1.135139 CACGACCACTTGATCGATCCT 59.865 52.381 22.31 2.31 40.86 3.24
71 72 1.137872 GACCACTTGATCGATCCTGCT 59.862 52.381 22.31 3.04 0.00 4.24
79 80 4.845580 CGATCCTGCTTGCCGCCT 62.846 66.667 0.00 0.00 38.05 5.52
88 93 1.949847 GCTTGCCGCCTGACTAGAGA 61.950 60.000 0.00 0.00 0.00 3.10
178 185 1.079490 TGGGATGAGGAGTGGAAGACT 59.921 52.381 0.00 0.00 37.76 3.24
259 266 1.852965 CTAACCACCCCAATCTCCCAT 59.147 52.381 0.00 0.00 0.00 4.00
265 272 2.597340 CCAATCTCCCATGCCGGT 59.403 61.111 1.90 0.00 0.00 5.28
290 297 4.608774 ACCCCGTCGTCTCCCACA 62.609 66.667 0.00 0.00 0.00 4.17
294 301 1.676678 CCCGTCGTCTCCCACATCAT 61.677 60.000 0.00 0.00 0.00 2.45
309 316 2.660258 ATCATGGTCGGCGGTTAGGC 62.660 60.000 7.21 0.00 42.76 3.93
356 371 2.733593 GTCTTCCGCAACGACGCT 60.734 61.111 0.00 0.00 0.00 5.07
393 408 3.072468 GTCCGGACGTCCCATGGA 61.072 66.667 28.52 24.76 34.14 3.41
478 493 2.838202 GGTACTCCCTCTTGTGGATTCA 59.162 50.000 0.00 0.00 0.00 2.57
480 495 3.922171 ACTCCCTCTTGTGGATTCATC 57.078 47.619 0.00 0.00 0.00 2.92
481 496 2.169352 ACTCCCTCTTGTGGATTCATCG 59.831 50.000 0.00 0.00 0.00 3.84
482 497 2.169352 CTCCCTCTTGTGGATTCATCGT 59.831 50.000 0.00 0.00 0.00 3.73
483 498 2.168521 TCCCTCTTGTGGATTCATCGTC 59.831 50.000 0.00 0.00 0.00 4.20
484 499 2.169352 CCCTCTTGTGGATTCATCGTCT 59.831 50.000 0.00 0.00 0.00 4.18
485 500 3.369892 CCCTCTTGTGGATTCATCGTCTT 60.370 47.826 0.00 0.00 0.00 3.01
486 501 4.256920 CCTCTTGTGGATTCATCGTCTTT 58.743 43.478 0.00 0.00 0.00 2.52
487 502 4.331168 CCTCTTGTGGATTCATCGTCTTTC 59.669 45.833 0.00 0.00 0.00 2.62
488 503 4.893608 TCTTGTGGATTCATCGTCTTTCA 58.106 39.130 0.00 0.00 0.00 2.69
489 504 4.690748 TCTTGTGGATTCATCGTCTTTCAC 59.309 41.667 0.00 0.00 0.00 3.18
497 512 2.465920 CGTCTTTCACGTCGCTGC 59.534 61.111 0.00 0.00 44.07 5.25
528 543 0.320334 TCGCTGCCGTCTTGAATCAA 60.320 50.000 0.00 0.00 35.54 2.57
579 594 0.522705 CGTTGACGGACGACATCGAT 60.523 55.000 17.71 0.00 45.47 3.59
584 599 1.266175 GACGGACGACATCGATACCAT 59.734 52.381 8.54 0.00 43.02 3.55
601 616 2.086869 CCATCGCTGAAGGTTTGTCAT 58.913 47.619 0.00 0.00 0.00 3.06
603 618 2.839486 TCGCTGAAGGTTTGTCATCT 57.161 45.000 0.00 0.00 0.00 2.90
604 619 3.953712 TCGCTGAAGGTTTGTCATCTA 57.046 42.857 0.00 0.00 0.00 1.98
605 620 4.471904 TCGCTGAAGGTTTGTCATCTAT 57.528 40.909 0.00 0.00 0.00 1.98
606 621 4.433615 TCGCTGAAGGTTTGTCATCTATC 58.566 43.478 0.00 0.00 0.00 2.08
613 1088 6.157820 TGAAGGTTTGTCATCTATCCCACATA 59.842 38.462 0.00 0.00 0.00 2.29
616 1091 5.239525 GGTTTGTCATCTATCCCACATAAGC 59.760 44.000 0.00 0.00 0.00 3.09
618 1093 6.994421 TTGTCATCTATCCCACATAAGCTA 57.006 37.500 0.00 0.00 0.00 3.32
621 1096 8.664669 TGTCATCTATCCCACATAAGCTATAA 57.335 34.615 0.00 0.00 0.00 0.98
639 1407 8.846423 AGCTATAAATATCCTATACCACTGCT 57.154 34.615 0.00 0.00 0.00 4.24
640 1408 9.937876 AGCTATAAATATCCTATACCACTGCTA 57.062 33.333 0.00 0.00 0.00 3.49
641 1409 9.968870 GCTATAAATATCCTATACCACTGCTAC 57.031 37.037 0.00 0.00 0.00 3.58
645 1413 8.728596 AAATATCCTATACCACTGCTACTTCT 57.271 34.615 0.00 0.00 0.00 2.85
646 1414 8.728596 AATATCCTATACCACTGCTACTTCTT 57.271 34.615 0.00 0.00 0.00 2.52
647 1415 8.728596 ATATCCTATACCACTGCTACTTCTTT 57.271 34.615 0.00 0.00 0.00 2.52
648 1416 9.824216 ATATCCTATACCACTGCTACTTCTTTA 57.176 33.333 0.00 0.00 0.00 1.85
650 1418 6.550108 TCCTATACCACTGCTACTTCTTTAGG 59.450 42.308 0.00 0.00 0.00 2.69
651 1419 3.983044 ACCACTGCTACTTCTTTAGGG 57.017 47.619 0.00 0.00 0.00 3.53
652 1420 2.572104 ACCACTGCTACTTCTTTAGGGG 59.428 50.000 0.00 0.00 37.94 4.79
692 1522 5.313520 TCATTAGCATTGACATTGTGTGG 57.686 39.130 0.00 0.00 0.00 4.17
694 1524 4.764679 TTAGCATTGACATTGTGTGGTC 57.235 40.909 0.00 0.00 34.63 4.02
709 1539 8.820933 CATTGTGTGGTCTACAATATTGACTAG 58.179 37.037 22.16 13.42 44.50 2.57
735 1565 8.971321 GCAACATAATATTGTCATGGAAATCAC 58.029 33.333 0.00 0.00 0.00 3.06
788 1618 7.445707 TGCAACTATACACAAAGTACAATCCAA 59.554 33.333 0.00 0.00 35.05 3.53
803 1633 6.391227 ACAATCCAACAGAAGAAATTTCGT 57.609 33.333 12.42 9.49 0.00 3.85
819 1649 7.491696 AGAAATTTCGTTCTAGCACCTATGTAC 59.508 37.037 12.42 0.00 36.06 2.90
826 1656 6.210078 GTTCTAGCACCTATGTACATGAGTC 58.790 44.000 18.81 9.18 0.00 3.36
844 1674 8.877779 ACATGAGTCAGATTTAGAAAGAAATCG 58.122 33.333 0.00 0.85 46.19 3.34
921 1751 8.796475 AGTGCATGAACTTAGAATTTAACATGT 58.204 29.630 0.00 0.00 37.02 3.21
974 1804 7.909641 GTGTTGGTAGTAACGTGTGTTTAAATT 59.090 33.333 0.00 0.00 39.54 1.82
983 1813 5.495502 ACGTGTGTTTAAATTGACGAAGAC 58.504 37.500 17.47 0.00 0.00 3.01
995 1825 4.594123 TGACGAAGACACCTCATTTACA 57.406 40.909 0.00 0.00 0.00 2.41
996 1826 4.951254 TGACGAAGACACCTCATTTACAA 58.049 39.130 0.00 0.00 0.00 2.41
1004 1834 6.169094 AGACACCTCATTTACAACTGATGAG 58.831 40.000 5.77 5.77 43.95 2.90
1058 1892 9.562583 GATAACGATCCTAGTAATGAAGATGAC 57.437 37.037 0.00 0.00 0.00 3.06
1066 1900 6.811665 CCTAGTAATGAAGATGACGACAACAA 59.188 38.462 0.00 0.00 0.00 2.83
1131 1966 9.158233 CAGAGGATTTTGCAAATAATGAACATT 57.842 29.630 13.65 5.40 34.93 2.71
1149 1986 4.573900 ACATTGGTGCAAACAGTGAAAAA 58.426 34.783 18.05 0.00 31.05 1.94
1150 1987 4.630940 ACATTGGTGCAAACAGTGAAAAAG 59.369 37.500 18.05 0.00 31.05 2.27
1248 2086 7.972832 AATTTACAAGAAGATGTGGACGTTA 57.027 32.000 0.00 0.00 34.75 3.18
1398 2236 0.937441 TAGGAGGGCTCAGATGGTCT 59.063 55.000 0.00 0.00 0.00 3.85
1408 2246 1.065199 TCAGATGGTCTTGATGGTGGC 60.065 52.381 0.00 0.00 0.00 5.01
1453 2291 2.642311 TGAGGAGGCTCAATACCAACAA 59.358 45.455 17.69 0.00 0.00 2.83
1490 2328 3.053395 ACATTGGAAGGTCATGGCTATGT 60.053 43.478 10.12 0.00 35.73 2.29
1499 2337 3.429410 GGTCATGGCTATGTCTTTTTGGC 60.429 47.826 10.12 0.00 35.73 4.52
1534 2372 7.806409 TGCATACATATTCTACAACAAGCAT 57.194 32.000 0.00 0.00 0.00 3.79
1571 2409 3.378861 TCAGCATCAGGAGAGAGAAGA 57.621 47.619 0.00 0.00 0.00 2.87
1593 2431 0.185175 AAACGAGGGAAGGGTGCTTT 59.815 50.000 0.00 0.00 0.00 3.51
1652 2490 1.352352 CAGGGAGAAGGCAGAGGAAAA 59.648 52.381 0.00 0.00 0.00 2.29
1761 2599 0.872881 CGTGGAGTTTGGTTCGTCGT 60.873 55.000 0.00 0.00 0.00 4.34
1769 2607 2.226602 TTGGTTCGTCGTGTCATTCA 57.773 45.000 0.00 0.00 0.00 2.57
1804 2642 1.153369 CGTGATGGCTCGACCCAAT 60.153 57.895 2.98 0.00 38.61 3.16
1878 2716 1.421646 GATACTGGCTATGCAAGGGGT 59.578 52.381 0.00 0.00 33.11 4.95
1923 2761 4.396166 GGTGGACAACTTCATCAATAGGTG 59.604 45.833 0.00 0.00 35.22 4.00
1929 2767 3.686016 ACTTCATCAATAGGTGCGGTTT 58.314 40.909 0.00 0.00 0.00 3.27
1936 2774 2.288961 ATAGGTGCGGTTTGTACGAG 57.711 50.000 0.00 0.00 33.41 4.18
1961 2799 0.748450 CGGACTTATTAGGCGGGACA 59.252 55.000 0.00 0.00 0.00 4.02
1979 2817 2.554032 GACATGTACAACCTTTGCTGCT 59.446 45.455 0.00 0.00 0.00 4.24
1990 2828 3.091545 CCTTTGCTGCTGGGAGAAAATA 58.908 45.455 0.00 0.00 0.00 1.40
2041 2879 1.133976 GCAGTGGGCATTATGAGGAGT 60.134 52.381 0.00 0.00 43.97 3.85
2048 2886 4.068599 GGGCATTATGAGGAGTAGAAAGC 58.931 47.826 0.00 0.00 0.00 3.51
2091 2932 6.090483 TGAGTATGTGCTAGATAAGGAAGC 57.910 41.667 0.00 0.00 36.77 3.86
2092 2933 5.598417 TGAGTATGTGCTAGATAAGGAAGCA 59.402 40.000 0.00 0.00 43.66 3.91
2123 2964 1.942657 GTATGTTCTGGTGCGATGCAT 59.057 47.619 0.00 0.00 41.91 3.96
2129 2970 0.528466 CTGGTGCGATGCATAGTCGT 60.528 55.000 8.67 0.00 41.91 4.34
2299 3141 3.043713 CGACGCATGTGTGGCTGT 61.044 61.111 18.34 0.00 0.00 4.40
2374 3216 2.772739 GGTGACGCTGCAATGATCT 58.227 52.632 0.00 0.00 0.00 2.75
2378 3220 1.066645 TGACGCTGCAATGATCTGAGT 60.067 47.619 0.00 0.00 0.00 3.41
2383 3225 3.064958 CGCTGCAATGATCTGAGTGATTT 59.935 43.478 0.00 0.00 35.14 2.17
2403 3245 4.437682 TTGGAGTGTCCTTTCAGATGTT 57.562 40.909 0.00 0.00 37.46 2.71
2502 3347 1.202580 GCTCCTGTACTATGCCACCTG 60.203 57.143 0.00 0.00 0.00 4.00
2526 3371 6.042552 TGTCAAGAGAACTTTGAGGAGAGATT 59.957 38.462 0.00 0.00 33.70 2.40
2527 3372 6.934083 GTCAAGAGAACTTTGAGGAGAGATTT 59.066 38.462 0.00 0.00 33.70 2.17
2528 3373 7.443879 GTCAAGAGAACTTTGAGGAGAGATTTT 59.556 37.037 0.00 0.00 33.70 1.82
2529 3374 7.995488 TCAAGAGAACTTTGAGGAGAGATTTTT 59.005 33.333 0.00 0.00 33.70 1.94
2552 3397 7.969536 TTTTGACTATTGACTTTGAGGAGAG 57.030 36.000 0.00 0.00 0.00 3.20
2553 3398 6.918067 TTGACTATTGACTTTGAGGAGAGA 57.082 37.500 0.00 0.00 0.00 3.10
2554 3399 7.487822 TTGACTATTGACTTTGAGGAGAGAT 57.512 36.000 0.00 0.00 0.00 2.75
2591 3436 9.184523 TGTCAATAAATGGAAGACGGATAAAAT 57.815 29.630 0.00 0.00 32.08 1.82
2606 3451 5.123820 CGGATAAAATTGAAGAGTGGCTGAA 59.876 40.000 0.00 0.00 0.00 3.02
2607 3452 6.325596 GGATAAAATTGAAGAGTGGCTGAAC 58.674 40.000 0.00 0.00 0.00 3.18
2657 3502 5.001874 GGCAGCATCATATCTTTCAGATGA 58.998 41.667 0.00 0.00 40.10 2.92
2658 3503 5.472478 GGCAGCATCATATCTTTCAGATGAA 59.528 40.000 0.00 0.00 40.10 2.57
2689 3534 2.035576 GGTATGCGTAGTAACCAGAGGG 59.964 54.545 0.00 0.00 41.29 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 1.227350 CGGCAAGCAGGATCGATCA 60.227 57.895 25.93 0.00 0.00 2.92
71 72 0.973632 TTTCTCTAGTCAGGCGGCAA 59.026 50.000 13.08 0.00 0.00 4.52
135 142 1.735973 CGACGATCCAGATCAGCCA 59.264 57.895 8.31 0.00 37.69 4.75
162 169 1.554160 CAGCAGTCTTCCACTCCTCAT 59.446 52.381 0.00 0.00 30.26 2.90
290 297 1.445942 CCTAACCGCCGACCATGAT 59.554 57.895 0.00 0.00 0.00 2.45
294 301 3.599285 CTTGCCTAACCGCCGACCA 62.599 63.158 0.00 0.00 0.00 4.02
336 351 1.371267 CGTCGTTGCGGAAGACAGA 60.371 57.895 15.46 1.42 34.80 3.41
338 353 3.033764 GCGTCGTTGCGGAAGACA 61.034 61.111 15.46 0.00 34.80 3.41
361 376 2.507547 GACGGTTACATGCGGCGA 60.508 61.111 12.98 0.00 0.00 5.54
390 405 1.228769 ACGAGTGTGGTAGGCTCCA 60.229 57.895 0.00 0.00 34.85 3.86
393 408 0.830444 TTGGACGAGTGTGGTAGGCT 60.830 55.000 0.00 0.00 0.00 4.58
466 481 4.690748 GTGAAAGACGATGAATCCACAAGA 59.309 41.667 0.00 0.00 0.00 3.02
481 496 2.853914 GGCAGCGACGTGAAAGAC 59.146 61.111 0.00 0.00 0.00 3.01
482 497 2.733218 CGGCAGCGACGTGAAAGA 60.733 61.111 0.00 0.00 0.00 2.52
489 504 4.717629 TGGAAGACGGCAGCGACG 62.718 66.667 0.00 2.24 41.40 5.12
490 505 3.112709 GTGGAAGACGGCAGCGAC 61.113 66.667 0.00 0.00 0.00 5.19
491 506 4.717629 CGTGGAAGACGGCAGCGA 62.718 66.667 0.00 0.00 44.85 4.93
513 528 2.555123 GGCTTGATTCAAGACGGCA 58.445 52.632 26.72 0.00 43.42 5.69
579 594 2.037902 TGACAAACCTTCAGCGATGGTA 59.962 45.455 0.00 0.00 38.82 3.25
584 599 2.839486 AGATGACAAACCTTCAGCGA 57.161 45.000 0.00 0.00 34.50 4.93
613 1088 9.273137 AGCAGTGGTATAGGATATTTATAGCTT 57.727 33.333 0.00 0.00 34.30 3.74
621 1096 8.728596 AAGAAGTAGCAGTGGTATAGGATATT 57.271 34.615 5.16 0.00 0.00 1.28
624 1392 7.233757 CCTAAAGAAGTAGCAGTGGTATAGGAT 59.766 40.741 15.02 1.84 0.00 3.24
625 1393 6.550108 CCTAAAGAAGTAGCAGTGGTATAGGA 59.450 42.308 15.02 0.00 0.00 2.94
627 1395 6.239345 CCCCTAAAGAAGTAGCAGTGGTATAG 60.239 46.154 5.16 2.33 0.00 1.31
630 1398 3.773119 CCCCTAAAGAAGTAGCAGTGGTA 59.227 47.826 0.00 0.00 0.00 3.25
632 1400 2.092914 CCCCCTAAAGAAGTAGCAGTGG 60.093 54.545 0.00 0.00 0.00 4.00
633 1401 3.268023 CCCCCTAAAGAAGTAGCAGTG 57.732 52.381 0.00 0.00 0.00 3.66
650 1418 1.826447 AGATCCCTCTGATTTCCCCC 58.174 55.000 0.00 0.00 32.41 5.40
651 1419 2.780010 TGAAGATCCCTCTGATTTCCCC 59.220 50.000 0.00 0.00 32.41 4.81
652 1420 4.720775 ATGAAGATCCCTCTGATTTCCC 57.279 45.455 0.00 0.00 32.41 3.97
654 1422 6.294473 TGCTAATGAAGATCCCTCTGATTTC 58.706 40.000 0.00 0.00 32.41 2.17
655 1423 6.257994 TGCTAATGAAGATCCCTCTGATTT 57.742 37.500 0.00 0.00 32.41 2.17
665 1495 7.431376 CACACAATGTCAATGCTAATGAAGATC 59.569 37.037 0.00 0.00 0.00 2.75
709 1539 8.971321 GTGATTTCCATGACAATATTATGTTGC 58.029 33.333 1.60 0.00 32.57 4.17
735 1565 1.599419 GCGTGTAAACTTTGGCACCAG 60.599 52.381 0.00 0.00 0.00 4.00
788 1618 5.179555 GGTGCTAGAACGAAATTTCTTCTGT 59.820 40.000 26.33 13.63 37.09 3.41
803 1633 5.891551 TGACTCATGTACATAGGTGCTAGAA 59.108 40.000 8.32 0.00 0.00 2.10
819 1649 8.877779 ACGATTTCTTTCTAAATCTGACTCATG 58.122 33.333 7.49 0.00 41.62 3.07
921 1751 7.871463 TGCACATCATTGAAAAACACATTATCA 59.129 29.630 0.00 0.00 0.00 2.15
974 1804 4.594123 TGTAAATGAGGTGTCTTCGTCA 57.406 40.909 0.00 0.00 36.81 4.35
983 1813 7.414873 CCATTCTCATCAGTTGTAAATGAGGTG 60.415 40.741 10.69 4.94 44.19 4.00
995 1825 7.613022 ACATCATTTGTACCATTCTCATCAGTT 59.387 33.333 0.00 0.00 36.57 3.16
996 1826 7.114754 ACATCATTTGTACCATTCTCATCAGT 58.885 34.615 0.00 0.00 36.57 3.41
1004 1834 5.220662 CCGACTGACATCATTTGTACCATTC 60.221 44.000 0.00 0.00 39.18 2.67
1058 1892 3.570576 CGAATCGTTATCGTTGTTGTCG 58.429 45.455 0.00 0.00 38.33 4.35
1131 1966 2.564947 ACCTTTTTCACTGTTTGCACCA 59.435 40.909 0.00 0.00 0.00 4.17
1149 1986 7.918076 TGGAATCAAATAGACTTCACTTACCT 58.082 34.615 0.00 0.00 0.00 3.08
1150 1987 7.824779 ACTGGAATCAAATAGACTTCACTTACC 59.175 37.037 0.00 0.00 0.00 2.85
1248 2086 8.529424 TCCTCATGATTATTTTGCTCATTCTT 57.471 30.769 0.00 0.00 0.00 2.52
1377 2215 2.119495 GACCATCTGAGCCCTCCTAAA 58.881 52.381 0.00 0.00 0.00 1.85
1378 2216 1.292242 AGACCATCTGAGCCCTCCTAA 59.708 52.381 0.00 0.00 0.00 2.69
1398 2236 2.423290 TTCGTCGTCGCCACCATCAA 62.423 55.000 0.00 0.00 36.96 2.57
1408 2246 0.863538 CCATCTCTGCTTCGTCGTCG 60.864 60.000 0.00 0.00 38.55 5.12
1453 2291 3.136443 TCCAATGTGTCTCCAACTTCTGT 59.864 43.478 0.00 0.00 0.00 3.41
1490 2328 0.263172 TCCCCTTGTGGCCAAAAAGA 59.737 50.000 24.54 13.13 0.00 2.52
1499 2337 2.369983 ATGTATGCATCCCCTTGTGG 57.630 50.000 0.19 0.00 0.00 4.17
1571 2409 0.322546 GCACCCTTCCCTCGTTTCAT 60.323 55.000 0.00 0.00 0.00 2.57
1593 2431 4.595781 ACCGCCTGAACCATATTATTCCTA 59.404 41.667 0.00 0.00 0.00 2.94
1652 2490 1.072331 GCGACCCTCCATGGTTATGAT 59.928 52.381 12.58 0.00 39.24 2.45
1678 2516 1.474677 CGAGTCTCGGGTCTAAGCCTA 60.475 57.143 14.68 0.00 36.00 3.93
1761 2599 4.641541 GGTTGTGATCATCCATGAATGACA 59.358 41.667 0.00 0.00 40.69 3.58
1769 2607 2.027285 TCACGTGGTTGTGATCATCCAT 60.027 45.455 17.00 3.75 43.62 3.41
1804 2642 3.442273 GTGACCACAGAAAACAAACCTCA 59.558 43.478 0.00 0.00 0.00 3.86
1878 2716 7.448161 CCACCATTATATGCTTACTGATTCCAA 59.552 37.037 0.00 0.00 0.00 3.53
1923 2761 1.785518 CGCATTTCTCGTACAAACCGC 60.786 52.381 0.00 0.00 0.00 5.68
1929 2767 2.736144 AAGTCCGCATTTCTCGTACA 57.264 45.000 0.00 0.00 0.00 2.90
1936 2774 2.223377 CCGCCTAATAAGTCCGCATTTC 59.777 50.000 0.00 0.00 0.00 2.17
1961 2799 1.888512 CCAGCAGCAAAGGTTGTACAT 59.111 47.619 0.00 0.00 0.00 2.29
1979 2817 4.771577 TGCAATGAGCTTTATTTTCTCCCA 59.228 37.500 0.00 0.00 45.94 4.37
1990 2828 2.318908 TCACCCTTTGCAATGAGCTTT 58.681 42.857 13.58 0.00 45.94 3.51
2041 2879 2.567615 GTCTGGGTCCTTCTGCTTTCTA 59.432 50.000 0.00 0.00 0.00 2.10
2048 2886 3.071602 TCAAAGAAGTCTGGGTCCTTCTG 59.928 47.826 2.93 0.00 45.01 3.02
2068 2906 5.598417 TGCTTCCTTATCTAGCACATACTCA 59.402 40.000 0.00 0.00 39.79 3.41
2091 2932 3.186409 CCAGAACATACACTTCAACCGTG 59.814 47.826 0.00 0.00 38.32 4.94
2092 2933 3.181458 ACCAGAACATACACTTCAACCGT 60.181 43.478 0.00 0.00 0.00 4.83
2123 2964 1.478837 CCTGATAGCCCTCCACGACTA 60.479 57.143 0.00 0.00 0.00 2.59
2129 2970 1.478837 CGTAGTCCTGATAGCCCTCCA 60.479 57.143 0.00 0.00 0.00 3.86
2199 3041 3.952628 GACGAAGGGGGCGAACAGG 62.953 68.421 0.00 0.00 0.00 4.00
2299 3141 6.152661 CAGTTTGCCCTCATAAAAGTATGGAA 59.847 38.462 0.00 0.00 38.15 3.53
2304 3146 5.626142 TGACAGTTTGCCCTCATAAAAGTA 58.374 37.500 0.00 0.00 0.00 2.24
2374 3216 4.141505 TGAAAGGACACTCCAAATCACTCA 60.142 41.667 0.00 0.00 39.61 3.41
2378 3220 4.705110 TCTGAAAGGACACTCCAAATCA 57.295 40.909 0.00 0.00 39.61 2.57
2383 3225 3.648067 AGAACATCTGAAAGGACACTCCA 59.352 43.478 0.00 0.00 39.61 3.86
2403 3245 2.481276 CCACGAGCAAATACGATGGAGA 60.481 50.000 0.00 0.00 34.93 3.71
2502 3347 5.461032 TCTCTCCTCAAAGTTCTCTTGAC 57.539 43.478 0.00 0.00 33.79 3.18
2527 3372 8.210946 TCTCTCCTCAAAGTCAATAGTCAAAAA 58.789 33.333 0.00 0.00 0.00 1.94
2528 3373 7.735917 TCTCTCCTCAAAGTCAATAGTCAAAA 58.264 34.615 0.00 0.00 0.00 2.44
2529 3374 7.303182 TCTCTCCTCAAAGTCAATAGTCAAA 57.697 36.000 0.00 0.00 0.00 2.69
2530 3375 6.918067 TCTCTCCTCAAAGTCAATAGTCAA 57.082 37.500 0.00 0.00 0.00 3.18
2531 3376 6.127225 CCATCTCTCCTCAAAGTCAATAGTCA 60.127 42.308 0.00 0.00 0.00 3.41
2532 3377 6.097554 TCCATCTCTCCTCAAAGTCAATAGTC 59.902 42.308 0.00 0.00 0.00 2.59
2533 3378 5.960811 TCCATCTCTCCTCAAAGTCAATAGT 59.039 40.000 0.00 0.00 0.00 2.12
2534 3379 6.098124 AGTCCATCTCTCCTCAAAGTCAATAG 59.902 42.308 0.00 0.00 0.00 1.73
2535 3380 5.960811 AGTCCATCTCTCCTCAAAGTCAATA 59.039 40.000 0.00 0.00 0.00 1.90
2536 3381 4.782156 AGTCCATCTCTCCTCAAAGTCAAT 59.218 41.667 0.00 0.00 0.00 2.57
2537 3382 4.020751 CAGTCCATCTCTCCTCAAAGTCAA 60.021 45.833 0.00 0.00 0.00 3.18
2538 3383 3.513119 CAGTCCATCTCTCCTCAAAGTCA 59.487 47.826 0.00 0.00 0.00 3.41
2539 3384 3.678529 GCAGTCCATCTCTCCTCAAAGTC 60.679 52.174 0.00 0.00 0.00 3.01
2540 3385 2.235898 GCAGTCCATCTCTCCTCAAAGT 59.764 50.000 0.00 0.00 0.00 2.66
2541 3386 2.419851 GGCAGTCCATCTCTCCTCAAAG 60.420 54.545 0.00 0.00 0.00 2.77
2542 3387 1.556911 GGCAGTCCATCTCTCCTCAAA 59.443 52.381 0.00 0.00 0.00 2.69
2543 3388 1.198713 GGCAGTCCATCTCTCCTCAA 58.801 55.000 0.00 0.00 0.00 3.02
2544 3389 0.337773 AGGCAGTCCATCTCTCCTCA 59.662 55.000 0.00 0.00 33.74 3.86
2545 3390 1.494960 AAGGCAGTCCATCTCTCCTC 58.505 55.000 0.00 0.00 33.74 3.71
2546 3391 1.558756 CAAAGGCAGTCCATCTCTCCT 59.441 52.381 0.00 0.00 33.74 3.69
2547 3392 1.280421 ACAAAGGCAGTCCATCTCTCC 59.720 52.381 0.00 0.00 33.74 3.71
2548 3393 2.027745 TGACAAAGGCAGTCCATCTCTC 60.028 50.000 2.97 0.00 35.15 3.20
2549 3394 1.980765 TGACAAAGGCAGTCCATCTCT 59.019 47.619 2.97 0.00 35.15 3.10
2550 3395 2.479566 TGACAAAGGCAGTCCATCTC 57.520 50.000 2.97 0.00 35.15 2.75
2551 3396 2.957402 TTGACAAAGGCAGTCCATCT 57.043 45.000 2.97 0.00 35.15 2.90
2552 3397 5.643379 TTTATTGACAAAGGCAGTCCATC 57.357 39.130 0.00 0.00 35.15 3.51
2553 3398 5.105228 CCATTTATTGACAAAGGCAGTCCAT 60.105 40.000 0.00 0.90 35.15 3.41
2554 3399 4.220382 CCATTTATTGACAAAGGCAGTCCA 59.780 41.667 0.00 0.00 35.15 4.02
2591 3436 1.768275 TCCTGTTCAGCCACTCTTCAA 59.232 47.619 0.00 0.00 0.00 2.69
2606 3451 5.135362 AGTCTCCTCTTCCTATACATCCTGT 59.865 44.000 0.00 0.00 0.00 4.00
2607 3452 5.640147 AGTCTCCTCTTCCTATACATCCTG 58.360 45.833 0.00 0.00 0.00 3.86
2631 3476 5.791666 TCTGAAAGATATGATGCTGCCTAG 58.208 41.667 0.00 0.00 38.67 3.02
2633 3478 4.701651 TCTGAAAGATATGATGCTGCCT 57.298 40.909 0.00 0.00 38.67 4.75


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

AutoCloner maintained by Alex Coulton.