Multiple sequence alignment - TraesCS6D01G280900

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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 TraesCS6D01G280900 chr6D 100.000 2655 0 0 1 2655 388335105 388332451 0.000000e+00 4903.0
1 TraesCS6D01G280900 chr6D 89.123 570 30 6 1 568 290813007 290813546 0.000000e+00 680.0
2 TraesCS6D01G280900 chr6A 91.580 1247 52 29 703 1936 534961250 534960044 0.000000e+00 1672.0
3 TraesCS6D01G280900 chr6A 79.296 710 78 35 1980 2653 534960041 534959365 1.460000e-117 433.0
4 TraesCS6D01G280900 chr6A 87.285 291 34 3 4 292 70915005 70914716 1.970000e-86 329.0
5 TraesCS6D01G280900 chr6B 88.921 1381 89 26 949 2288 580376378 580375021 0.000000e+00 1644.0
6 TraesCS6D01G280900 chr6B 87.781 401 41 5 1 394 203285819 203286218 1.860000e-126 462.0
7 TraesCS6D01G280900 chr6B 85.227 352 29 15 573 914 580377026 580376688 9.100000e-90 340.0
8 TraesCS6D01G280900 chr1A 87.153 1082 77 34 986 2034 566611147 566610095 0.000000e+00 1171.0
9 TraesCS6D01G280900 chr7D 90.223 583 36 9 1 568 388966199 388965623 0.000000e+00 741.0
10 TraesCS6D01G280900 chr7D 88.963 598 38 7 1 571 28334050 28334646 0.000000e+00 713.0
11 TraesCS6D01G280900 chr7D 87.822 583 36 15 1 570 210058789 210058229 0.000000e+00 651.0
12 TraesCS6D01G280900 chr7D 82.793 401 43 19 1 392 593671179 593670796 4.230000e-88 335.0
13 TraesCS6D01G280900 chr7A 89.626 588 42 6 1 572 316540918 316541502 0.000000e+00 730.0
14 TraesCS6D01G280900 chr3A 86.897 580 48 7 1 568 50934039 50933476 2.240000e-175 625.0
15 TraesCS6D01G280900 chr3A 82.824 425 32 25 1 392 623603800 623604216 2.530000e-90 342.0
16 TraesCS6D01G280900 chr4D 88.499 513 40 7 69 566 479407859 479407351 1.050000e-168 603.0
17 TraesCS6D01G280900 chr2D 85.340 573 62 13 1 568 306337229 306337784 8.240000e-160 573.0
18 TraesCS6D01G280900 chr2D 93.548 279 10 1 1 279 65640586 65640316 2.460000e-110 409.0
19 TraesCS6D01G280900 chr2D 80.457 394 72 5 1227 1619 410954175 410954564 2.000000e-76 296.0
20 TraesCS6D01G280900 chr5D 87.873 503 37 6 1 489 51029572 51029080 1.070000e-158 569.0
21 TraesCS6D01G280900 chr5D 90.545 275 23 2 292 566 455610663 455610392 6.990000e-96 361.0
22 TraesCS6D01G280900 chr2A 85.064 549 47 11 31 568 599777803 599777279 6.510000e-146 527.0
23 TraesCS6D01G280900 chr2A 80.250 400 74 5 1227 1625 578903545 578903150 2.000000e-76 296.0
24 TraesCS6D01G280900 chr2A 89.394 132 14 0 437 568 735566864 735566733 1.630000e-37 167.0
25 TraesCS6D01G280900 chr4B 86.711 301 34 4 6 306 642448501 642448207 1.970000e-86 329.0
26 TraesCS6D01G280900 chrUn 87.329 292 27 9 1 287 21561586 21561300 2.550000e-85 326.0
27 TraesCS6D01G280900 chr2B 86.139 303 34 6 5 306 777070266 777070561 1.190000e-83 320.0
28 TraesCS6D01G280900 chr2B 81.132 371 61 8 1231 1598 485161645 485162009 3.340000e-74 289.0
29 TraesCS6D01G280900 chr2B 81.203 133 13 5 437 568 631728955 631728834 2.180000e-16 97.1


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 TraesCS6D01G280900 chr6D 388332451 388335105 2654 True 4903.0 4903 100.000 1 2655 1 chr6D.!!$R1 2654
1 TraesCS6D01G280900 chr6D 290813007 290813546 539 False 680.0 680 89.123 1 568 1 chr6D.!!$F1 567
2 TraesCS6D01G280900 chr6A 534959365 534961250 1885 True 1052.5 1672 85.438 703 2653 2 chr6A.!!$R2 1950
3 TraesCS6D01G280900 chr6B 580375021 580377026 2005 True 992.0 1644 87.074 573 2288 2 chr6B.!!$R1 1715
4 TraesCS6D01G280900 chr1A 566610095 566611147 1052 True 1171.0 1171 87.153 986 2034 1 chr1A.!!$R1 1048
5 TraesCS6D01G280900 chr7D 388965623 388966199 576 True 741.0 741 90.223 1 568 1 chr7D.!!$R2 567
6 TraesCS6D01G280900 chr7D 28334050 28334646 596 False 713.0 713 88.963 1 571 1 chr7D.!!$F1 570
7 TraesCS6D01G280900 chr7D 210058229 210058789 560 True 651.0 651 87.822 1 570 1 chr7D.!!$R1 569
8 TraesCS6D01G280900 chr7A 316540918 316541502 584 False 730.0 730 89.626 1 572 1 chr7A.!!$F1 571
9 TraesCS6D01G280900 chr3A 50933476 50934039 563 True 625.0 625 86.897 1 568 1 chr3A.!!$R1 567
10 TraesCS6D01G280900 chr4D 479407351 479407859 508 True 603.0 603 88.499 69 566 1 chr4D.!!$R1 497
11 TraesCS6D01G280900 chr2D 306337229 306337784 555 False 573.0 573 85.340 1 568 1 chr2D.!!$F1 567
12 TraesCS6D01G280900 chr2A 599777279 599777803 524 True 527.0 527 85.064 31 568 1 chr2A.!!$R2 537

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
642 707 0.673985 TGCGATCGGATCCTAGGTTG 59.326 55.0 18.3 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2038 2467 0.098376 GACACCACGAGTAGGCTACG 59.902 60.0 18.41 10.71 0.0 3.51 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
110 111 1.497991 CGAGACTGAGGCGTTTTTCA 58.502 50.000 0.00 0.00 0.00 2.69
141 142 4.129737 CGAAGGAGAAGGCGCCGA 62.130 66.667 23.20 0.00 39.22 5.54
441 500 1.299089 GCGCGGACATAAAATGGGC 60.299 57.895 8.83 0.00 33.60 5.36
586 645 4.670221 GCTCTAACTGCTTCAAATTCCACG 60.670 45.833 0.00 0.00 0.00 4.94
590 649 3.149196 ACTGCTTCAAATTCCACGATGT 58.851 40.909 0.00 0.00 0.00 3.06
594 653 6.258727 ACTGCTTCAAATTCCACGATGTATAG 59.741 38.462 0.00 0.00 0.00 1.31
596 655 6.992123 TGCTTCAAATTCCACGATGTATAGAT 59.008 34.615 0.00 0.00 0.00 1.98
614 673 9.815306 TGTATAGATCATCTTAAGCTTAGACCT 57.185 33.333 6.24 0.00 0.00 3.85
617 676 7.912778 AGATCATCTTAAGCTTAGACCTTCT 57.087 36.000 6.24 4.12 0.00 2.85
618 677 7.725251 AGATCATCTTAAGCTTAGACCTTCTG 58.275 38.462 6.24 2.70 0.00 3.02
619 678 6.859112 TCATCTTAAGCTTAGACCTTCTGT 57.141 37.500 6.24 0.00 0.00 3.41
635 700 1.143305 CTGTCATTGCGATCGGATCC 58.857 55.000 18.30 0.00 0.00 3.36
638 703 2.029918 TGTCATTGCGATCGGATCCTAG 60.030 50.000 18.30 2.81 0.00 3.02
640 705 1.273606 CATTGCGATCGGATCCTAGGT 59.726 52.381 18.30 0.00 0.00 3.08
641 706 1.410004 TTGCGATCGGATCCTAGGTT 58.590 50.000 18.30 0.00 0.00 3.50
642 707 0.673985 TGCGATCGGATCCTAGGTTG 59.326 55.000 18.30 0.00 0.00 3.77
643 708 0.674534 GCGATCGGATCCTAGGTTGT 59.325 55.000 18.30 0.00 0.00 3.32
646 711 3.381949 CGATCGGATCCTAGGTTGTTTC 58.618 50.000 10.75 0.00 0.00 2.78
647 712 3.181479 CGATCGGATCCTAGGTTGTTTCA 60.181 47.826 10.75 0.00 0.00 2.69
648 713 4.501571 CGATCGGATCCTAGGTTGTTTCAT 60.502 45.833 10.75 0.00 0.00 2.57
649 714 4.837093 TCGGATCCTAGGTTGTTTCATT 57.163 40.909 10.75 0.00 0.00 2.57
650 715 4.513442 TCGGATCCTAGGTTGTTTCATTG 58.487 43.478 10.75 0.00 0.00 2.82
652 717 4.273318 GGATCCTAGGTTGTTTCATTGCT 58.727 43.478 9.08 0.00 0.00 3.91
653 718 4.706962 GGATCCTAGGTTGTTTCATTGCTT 59.293 41.667 9.08 0.00 0.00 3.91
654 719 5.393461 GGATCCTAGGTTGTTTCATTGCTTG 60.393 44.000 9.08 0.00 0.00 4.01
655 720 4.724399 TCCTAGGTTGTTTCATTGCTTGA 58.276 39.130 9.08 0.00 0.00 3.02
656 721 4.518970 TCCTAGGTTGTTTCATTGCTTGAC 59.481 41.667 9.08 0.00 32.84 3.18
657 722 3.354089 AGGTTGTTTCATTGCTTGACG 57.646 42.857 0.00 0.00 32.84 4.35
658 723 2.948979 AGGTTGTTTCATTGCTTGACGA 59.051 40.909 0.00 0.00 32.84 4.20
659 724 3.569701 AGGTTGTTTCATTGCTTGACGAT 59.430 39.130 0.00 0.00 32.84 3.73
660 725 3.914364 GGTTGTTTCATTGCTTGACGATC 59.086 43.478 0.00 0.00 32.84 3.69
673 738 4.841306 GCTTGACGATCTTTTCTTTCGAAC 59.159 41.667 0.00 0.00 36.73 3.95
692 758 4.967437 GAACTCAGTGTTCGTATCGTACT 58.033 43.478 0.00 0.00 44.49 2.73
694 760 5.462034 ACTCAGTGTTCGTATCGTACTAC 57.538 43.478 0.00 0.00 0.00 2.73
695 761 5.174395 ACTCAGTGTTCGTATCGTACTACT 58.826 41.667 0.00 0.00 0.00 2.57
697 763 6.475076 ACTCAGTGTTCGTATCGTACTACTAG 59.525 42.308 0.00 0.00 0.00 2.57
698 764 6.333416 TCAGTGTTCGTATCGTACTACTAGT 58.667 40.000 0.00 0.00 0.00 2.57
699 765 7.480810 TCAGTGTTCGTATCGTACTACTAGTA 58.519 38.462 1.89 1.89 0.00 1.82
700 766 8.138074 TCAGTGTTCGTATCGTACTACTAGTAT 58.862 37.037 2.33 0.00 32.65 2.12
701 767 8.759641 CAGTGTTCGTATCGTACTACTAGTATT 58.240 37.037 2.33 0.00 32.65 1.89
731 797 4.579869 AGATATTTGGAACGAGCAACTGT 58.420 39.130 0.00 0.00 0.00 3.55
962 1307 1.164662 CCCAGCAATCTCCGCATCTG 61.165 60.000 0.00 0.00 0.00 2.90
983 1328 2.507102 ACACCAAGCTCGATCGCG 60.507 61.111 11.09 5.24 39.35 5.87
1123 1473 1.150536 CCTCCCTCTCCTCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1124 1474 1.528309 CTCCCTCTCCTCTCCTCGC 60.528 68.421 0.00 0.00 0.00 5.03
1204 1554 4.335647 CAGCTGACCAAGGGCGGT 62.336 66.667 8.42 0.00 43.91 5.68
1664 2020 2.877168 GCCGAGGAGTAAGATCGAGTAA 59.123 50.000 0.00 0.00 38.72 2.24
1667 2023 3.810941 CGAGGAGTAAGATCGAGTAAGCT 59.189 47.826 0.00 0.00 38.72 3.74
1668 2024 4.319190 CGAGGAGTAAGATCGAGTAAGCTG 60.319 50.000 0.00 0.00 38.72 4.24
1669 2025 4.528920 AGGAGTAAGATCGAGTAAGCTGT 58.471 43.478 0.00 0.00 0.00 4.40
1670 2026 5.682659 AGGAGTAAGATCGAGTAAGCTGTA 58.317 41.667 0.00 0.00 0.00 2.74
1671 2027 5.528320 AGGAGTAAGATCGAGTAAGCTGTAC 59.472 44.000 0.00 0.00 0.00 2.90
1672 2028 5.406767 AGTAAGATCGAGTAAGCTGTACG 57.593 43.478 0.00 0.00 0.00 3.67
1673 2029 2.759538 AGATCGAGTAAGCTGTACGC 57.240 50.000 0.00 2.08 39.57 4.42
1686 2082 3.818787 TACGCCGGCCTCTTCGTC 61.819 66.667 23.46 0.00 36.50 4.20
1688 2084 4.514577 CGCCGGCCTCTTCGTCAT 62.515 66.667 23.46 0.00 0.00 3.06
1689 2085 2.586357 GCCGGCCTCTTCGTCATC 60.586 66.667 18.11 0.00 0.00 2.92
1690 2086 2.278857 CCGGCCTCTTCGTCATCG 60.279 66.667 0.00 0.00 38.55 3.84
1691 2087 2.490217 CGGCCTCTTCGTCATCGT 59.510 61.111 0.00 0.00 38.33 3.73
1692 2088 1.874019 CGGCCTCTTCGTCATCGTG 60.874 63.158 0.00 0.00 38.33 4.35
1693 2089 1.215647 GGCCTCTTCGTCATCGTGT 59.784 57.895 0.00 0.00 38.33 4.49
1696 2092 1.340658 CCTCTTCGTCATCGTGTGTG 58.659 55.000 0.00 0.00 38.33 3.82
1698 2094 0.671796 TCTTCGTCATCGTGTGTGGT 59.328 50.000 0.00 0.00 38.33 4.16
1724 2130 3.638592 AATAAGCTGCGGGGCCGTT 62.639 57.895 0.00 0.00 42.09 4.44
1801 2218 2.591715 GTTCGTGCTGCTGGTGGT 60.592 61.111 0.00 0.00 0.00 4.16
1803 2220 4.624364 TCGTGCTGCTGGTGGTGG 62.624 66.667 0.00 0.00 0.00 4.61
1810 2227 0.676466 CTGCTGGTGGTGGCGAAATA 60.676 55.000 0.00 0.00 0.00 1.40
1946 2372 5.824904 ATGTTTTCATGCACTCCTACATC 57.175 39.130 0.00 0.00 39.30 3.06
1947 2373 4.650734 TGTTTTCATGCACTCCTACATCA 58.349 39.130 0.00 0.00 0.00 3.07
1948 2374 4.696877 TGTTTTCATGCACTCCTACATCAG 59.303 41.667 0.00 0.00 0.00 2.90
1949 2375 4.558226 TTTCATGCACTCCTACATCAGT 57.442 40.909 0.00 0.00 0.00 3.41
1950 2376 5.675684 TTTCATGCACTCCTACATCAGTA 57.324 39.130 0.00 0.00 0.00 2.74
2058 2487 0.455005 GTAGCCTACTCGTGGTGTCC 59.545 60.000 0.00 0.00 0.00 4.02
2059 2488 1.028330 TAGCCTACTCGTGGTGTCCG 61.028 60.000 0.00 0.00 0.00 4.79
2061 2490 2.181021 CTACTCGTGGTGTCCGGC 59.819 66.667 0.00 0.00 0.00 6.13
2062 2491 2.282674 TACTCGTGGTGTCCGGCT 60.283 61.111 0.00 0.00 0.00 5.52
2064 2493 4.436998 CTCGTGGTGTCCGGCTCC 62.437 72.222 0.00 3.09 0.00 4.70
2221 2682 5.320723 TCAGCGAGCAATTTATAAACAACG 58.679 37.500 0.00 4.33 0.00 4.10
2268 2731 2.029623 TCTGGGTATCTGCCGACTAAC 58.970 52.381 0.00 0.00 0.00 2.34
2275 2738 3.296709 CTGCCGACTAACGCCCACT 62.297 63.158 0.00 0.00 41.07 4.00
2331 2794 3.791245 AGGATTCTCTGCGAAGATGTTC 58.209 45.455 0.00 0.00 34.56 3.18
2332 2795 3.450457 AGGATTCTCTGCGAAGATGTTCT 59.550 43.478 0.00 0.00 34.56 3.01
2338 2810 9.284594 GATTCTCTGCGAAGATGTTCTATATAC 57.715 37.037 0.00 0.00 34.56 1.47
2361 2833 5.182001 ACGATGAAAAAGGGAGAAATGACTG 59.818 40.000 0.00 0.00 0.00 3.51
2376 2848 1.211212 TGACTGAGGGCATCTCCAATG 59.789 52.381 0.00 0.00 41.76 2.82
2409 2881 3.360340 GACTCACCGTCCGTCCGT 61.360 66.667 0.00 0.00 36.62 4.69
2417 2889 1.497223 CCGTCCGTCCGTAGAGCTAG 61.497 65.000 0.00 0.00 0.00 3.42
2426 2898 1.192757 CCGTAGAGCTAGATGTCGTCG 59.807 57.143 0.00 0.00 0.00 5.12
2437 2909 2.820787 AGATGTCGTCGGATCCTATTCC 59.179 50.000 10.75 0.00 0.00 3.01
2442 2914 2.261671 CGGATCCTATTCCCCGCG 59.738 66.667 10.75 0.00 35.29 6.46
2444 2916 2.741092 GATCCTATTCCCCGCGCA 59.259 61.111 8.75 0.00 0.00 6.09
2445 2917 1.374758 GATCCTATTCCCCGCGCAG 60.375 63.158 8.75 0.00 0.00 5.18
2457 2929 4.301027 GCGCAGGTCGGGGGATAG 62.301 72.222 0.30 0.00 38.94 2.08
2467 2939 0.318445 CGGGGGATAGCGACTAAACG 60.318 60.000 0.00 0.00 0.00 3.60
2468 2940 1.035139 GGGGGATAGCGACTAAACGA 58.965 55.000 0.00 0.00 35.09 3.85
2471 2943 1.337387 GGGATAGCGACTAAACGAGCT 59.663 52.381 0.00 0.00 43.07 4.09
2473 2945 3.445857 GGATAGCGACTAAACGAGCTTT 58.554 45.455 0.00 0.00 40.73 3.51
2496 2968 2.437359 CTGCAGTACTGGGCTGGC 60.437 66.667 23.95 9.23 34.73 4.85
2513 2985 3.134458 CTGGCCCATTTCGTATCTTCTC 58.866 50.000 0.00 0.00 0.00 2.87
2515 2987 3.964688 TGGCCCATTTCGTATCTTCTCTA 59.035 43.478 0.00 0.00 0.00 2.43
2519 2991 6.147985 GGCCCATTTCGTATCTTCTCTATTTC 59.852 42.308 0.00 0.00 0.00 2.17
2521 2993 7.117092 GCCCATTTCGTATCTTCTCTATTTCTC 59.883 40.741 0.00 0.00 0.00 2.87
2523 2995 8.144478 CCATTTCGTATCTTCTCTATTTCTCCA 58.856 37.037 0.00 0.00 0.00 3.86
2524 2996 9.534565 CATTTCGTATCTTCTCTATTTCTCCAA 57.465 33.333 0.00 0.00 0.00 3.53
2526 2998 9.938280 TTTCGTATCTTCTCTATTTCTCCAAAA 57.062 29.630 0.00 0.00 0.00 2.44
2527 2999 8.928270 TCGTATCTTCTCTATTTCTCCAAAAC 57.072 34.615 0.00 0.00 0.00 2.43
2528 3000 7.980099 TCGTATCTTCTCTATTTCTCCAAAACC 59.020 37.037 0.00 0.00 0.00 3.27
2529 3001 7.224949 CGTATCTTCTCTATTTCTCCAAAACCC 59.775 40.741 0.00 0.00 0.00 4.11
2531 3003 7.091533 TCTTCTCTATTTCTCCAAAACCCTT 57.908 36.000 0.00 0.00 0.00 3.95
2532 3004 7.526918 TCTTCTCTATTTCTCCAAAACCCTTT 58.473 34.615 0.00 0.00 0.00 3.11
2578 3058 6.373186 TTTCGGTTTTCTCTTCTTCTTTCC 57.627 37.500 0.00 0.00 0.00 3.13
2582 3062 7.277396 TCGGTTTTCTCTTCTTCTTTCCTTTA 58.723 34.615 0.00 0.00 0.00 1.85
2583 3063 7.937394 TCGGTTTTCTCTTCTTCTTTCCTTTAT 59.063 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.072476 TCTCCTTCGAAATCTGGTTTGGT 59.928 43.478 0.00 0.00 0.00 3.67
160 161 2.478746 GCGCTTCGGATTTTCGCA 59.521 55.556 0.00 0.00 44.50 5.10
378 421 0.035881 CGGCCATAGATCATGCCAGT 59.964 55.000 2.24 0.00 33.09 4.00
414 457 0.169230 TATGTCCGCGCGCAATTTTT 59.831 45.000 32.61 13.05 0.00 1.94
454 513 1.377202 GATTTGAGTCGGCAGGGCA 60.377 57.895 0.00 0.00 0.00 5.36
576 635 8.768957 AGATGATCTATACATCGTGGAATTTG 57.231 34.615 0.00 0.00 45.77 2.32
594 653 7.496747 ACAGAAGGTCTAAGCTTAAGATGATC 58.503 38.462 6.67 1.76 35.86 2.92
596 655 6.859112 ACAGAAGGTCTAAGCTTAAGATGA 57.141 37.500 6.67 0.00 35.86 2.92
611 670 1.645034 CGATCGCAATGACAGAAGGT 58.355 50.000 0.26 0.00 0.00 3.50
612 671 0.933097 CCGATCGCAATGACAGAAGG 59.067 55.000 10.32 0.00 0.00 3.46
614 673 2.473816 GATCCGATCGCAATGACAGAA 58.526 47.619 10.32 0.00 0.00 3.02
616 675 1.143305 GGATCCGATCGCAATGACAG 58.857 55.000 10.32 0.00 0.00 3.51
617 676 0.752658 AGGATCCGATCGCAATGACA 59.247 50.000 10.32 0.00 0.00 3.58
618 677 2.600731 CTAGGATCCGATCGCAATGAC 58.399 52.381 10.32 1.36 0.00 3.06
619 678 1.546029 CCTAGGATCCGATCGCAATGA 59.454 52.381 10.32 1.38 0.00 2.57
621 680 1.633774 ACCTAGGATCCGATCGCAAT 58.366 50.000 17.98 5.18 0.00 3.56
625 690 3.181479 TGAAACAACCTAGGATCCGATCG 60.181 47.826 17.98 8.51 0.00 3.69
635 700 4.213270 TCGTCAAGCAATGAAACAACCTAG 59.787 41.667 0.00 0.00 40.50 3.02
638 703 3.347958 TCGTCAAGCAATGAAACAACC 57.652 42.857 0.00 0.00 40.50 3.77
640 705 5.437289 AAGATCGTCAAGCAATGAAACAA 57.563 34.783 0.00 0.00 40.50 2.83
641 706 5.437289 AAAGATCGTCAAGCAATGAAACA 57.563 34.783 0.00 0.00 40.50 2.83
642 707 6.145535 AGAAAAGATCGTCAAGCAATGAAAC 58.854 36.000 0.00 0.00 40.50 2.78
643 708 6.317789 AGAAAAGATCGTCAAGCAATGAAA 57.682 33.333 0.00 0.00 40.50 2.69
646 711 5.282310 CGAAAGAAAAGATCGTCAAGCAATG 59.718 40.000 0.00 0.00 0.00 2.82
647 712 5.179368 TCGAAAGAAAAGATCGTCAAGCAAT 59.821 36.000 0.00 0.00 37.79 3.56
648 713 4.509970 TCGAAAGAAAAGATCGTCAAGCAA 59.490 37.500 0.00 0.00 37.79 3.91
649 714 4.055360 TCGAAAGAAAAGATCGTCAAGCA 58.945 39.130 0.00 0.00 37.79 3.91
650 715 4.647291 TCGAAAGAAAAGATCGTCAAGC 57.353 40.909 0.00 0.00 37.79 4.01
673 738 5.715429 AGTAGTACGATACGAACACTGAG 57.285 43.478 0.00 0.00 0.00 3.35
699 765 9.209175 GCTCGTTCCAAATATCTTCATACTAAT 57.791 33.333 0.00 0.00 0.00 1.73
700 766 8.201464 TGCTCGTTCCAAATATCTTCATACTAA 58.799 33.333 0.00 0.00 0.00 2.24
701 767 7.722363 TGCTCGTTCCAAATATCTTCATACTA 58.278 34.615 0.00 0.00 0.00 1.82
706 772 5.122239 CAGTTGCTCGTTCCAAATATCTTCA 59.878 40.000 0.00 0.00 0.00 3.02
708 774 5.003804 ACAGTTGCTCGTTCCAAATATCTT 58.996 37.500 0.00 0.00 0.00 2.40
753 819 4.459089 GAGGACAGACAGGGCCGC 62.459 72.222 0.00 0.00 0.00 6.53
945 1015 1.598132 CTTCAGATGCGGAGATTGCTG 59.402 52.381 0.00 0.00 0.00 4.41
946 1016 1.483827 TCTTCAGATGCGGAGATTGCT 59.516 47.619 0.00 0.00 0.00 3.91
947 1017 1.596727 GTCTTCAGATGCGGAGATTGC 59.403 52.381 0.00 0.00 0.00 3.56
962 1307 1.272781 CGATCGAGCTTGGTGTCTTC 58.727 55.000 10.26 0.00 0.00 2.87
1074 1419 0.687757 CCTTGATCTGGGTCGGGAGA 60.688 60.000 0.00 0.00 0.00 3.71
1103 1448 0.185175 GAGGAGAGGAGAGGGAGGAC 59.815 65.000 0.00 0.00 0.00 3.85
1123 1473 2.547211 AGCAGAGCAATAATCATGTCGC 59.453 45.455 0.00 0.00 0.00 5.19
1124 1474 3.121092 CGAGCAGAGCAATAATCATGTCG 60.121 47.826 0.00 0.00 0.00 4.35
1255 1605 1.141881 CTTCCAGATCGACCCCGTG 59.858 63.158 0.00 0.00 37.05 4.94
1646 2002 4.577283 ACAGCTTACTCGATCTTACTCCTC 59.423 45.833 0.00 0.00 0.00 3.71
1647 2003 4.528920 ACAGCTTACTCGATCTTACTCCT 58.471 43.478 0.00 0.00 0.00 3.69
1667 2023 4.124351 CGAAGAGGCCGGCGTACA 62.124 66.667 23.69 0.00 0.00 2.90
1668 2024 4.125695 ACGAAGAGGCCGGCGTAC 62.126 66.667 23.69 15.33 34.93 3.67
1669 2025 3.818787 GACGAAGAGGCCGGCGTA 61.819 66.667 23.69 0.00 37.07 4.42
1671 2027 4.514577 ATGACGAAGAGGCCGGCG 62.515 66.667 22.54 7.92 38.00 6.46
1672 2028 2.586357 GATGACGAAGAGGCCGGC 60.586 66.667 21.18 21.18 35.21 6.13
1673 2029 2.278857 CGATGACGAAGAGGCCGG 60.279 66.667 0.00 0.00 42.66 6.13
1686 2082 0.796312 GCTACCAACCACACACGATG 59.204 55.000 0.00 0.00 0.00 3.84
1687 2083 0.394938 TGCTACCAACCACACACGAT 59.605 50.000 0.00 0.00 0.00 3.73
1688 2084 0.178301 TTGCTACCAACCACACACGA 59.822 50.000 0.00 0.00 0.00 4.35
1689 2085 1.234821 ATTGCTACCAACCACACACG 58.765 50.000 0.00 0.00 32.95 4.49
1690 2086 3.365969 GCTTATTGCTACCAACCACACAC 60.366 47.826 0.00 0.00 38.95 3.82
1691 2087 2.817258 GCTTATTGCTACCAACCACACA 59.183 45.455 0.00 0.00 38.95 3.72
1692 2088 3.487563 GCTTATTGCTACCAACCACAC 57.512 47.619 0.00 0.00 38.95 3.82
1761 2174 3.995048 TCATCTAGTAGTACATCTCCGCG 59.005 47.826 0.00 0.00 0.00 6.46
1762 2175 4.998672 ACTCATCTAGTAGTACATCTCCGC 59.001 45.833 2.52 0.00 36.36 5.54
1763 2176 6.128769 CGAACTCATCTAGTAGTACATCTCCG 60.129 46.154 2.52 0.00 37.50 4.63
1764 2177 6.707161 ACGAACTCATCTAGTAGTACATCTCC 59.293 42.308 2.52 0.00 37.50 3.71
1765 2178 7.569297 CACGAACTCATCTAGTAGTACATCTC 58.431 42.308 2.52 0.00 37.50 2.75
1766 2179 6.017770 GCACGAACTCATCTAGTAGTACATCT 60.018 42.308 2.52 0.00 37.50 2.90
1801 2218 0.834612 AGGTCCCGATTATTTCGCCA 59.165 50.000 0.00 0.00 46.71 5.69
1803 2220 2.234300 TCAGGTCCCGATTATTTCGC 57.766 50.000 0.00 0.00 46.71 4.70
1805 2222 6.766467 AGTACAAATCAGGTCCCGATTATTTC 59.234 38.462 0.55 0.00 32.79 2.17
1806 2223 6.542370 CAGTACAAATCAGGTCCCGATTATTT 59.458 38.462 0.55 0.00 32.79 1.40
1810 2227 3.263425 ACAGTACAAATCAGGTCCCGATT 59.737 43.478 0.00 0.00 34.56 3.34
1937 2363 7.068103 AGAGAAGACATGTTACTGATGTAGGAG 59.932 40.741 0.00 0.00 34.10 3.69
1939 2365 7.068103 AGAGAGAAGACATGTTACTGATGTAGG 59.932 40.741 0.00 0.00 34.10 3.18
1940 2366 7.914871 CAGAGAGAAGACATGTTACTGATGTAG 59.085 40.741 0.00 0.00 34.10 2.74
1941 2367 7.629437 GCAGAGAGAAGACATGTTACTGATGTA 60.629 40.741 0.00 0.00 34.10 2.29
1942 2368 6.629128 CAGAGAGAAGACATGTTACTGATGT 58.371 40.000 0.00 0.00 36.73 3.06
1943 2369 5.519566 GCAGAGAGAAGACATGTTACTGATG 59.480 44.000 0.00 0.00 0.00 3.07
1944 2370 5.421693 AGCAGAGAGAAGACATGTTACTGAT 59.578 40.000 0.00 0.00 0.00 2.90
1945 2371 4.769488 AGCAGAGAGAAGACATGTTACTGA 59.231 41.667 0.00 0.00 0.00 3.41
1946 2372 4.863689 CAGCAGAGAGAAGACATGTTACTG 59.136 45.833 0.00 4.02 0.00 2.74
1947 2373 4.081752 CCAGCAGAGAGAAGACATGTTACT 60.082 45.833 0.00 0.00 0.00 2.24
1948 2374 4.180057 CCAGCAGAGAGAAGACATGTTAC 58.820 47.826 0.00 0.00 0.00 2.50
1949 2375 3.368843 GCCAGCAGAGAGAAGACATGTTA 60.369 47.826 0.00 0.00 0.00 2.41
1950 2376 2.614987 GCCAGCAGAGAGAAGACATGTT 60.615 50.000 0.00 0.00 0.00 2.71
2038 2467 0.098376 GACACCACGAGTAGGCTACG 59.902 60.000 18.41 10.71 0.00 3.51
2045 2474 2.282674 AGCCGGACACCACGAGTA 60.283 61.111 5.05 0.00 0.00 2.59
2047 2476 4.436998 GGAGCCGGACACCACGAG 62.437 72.222 5.05 0.00 0.00 4.18
2064 2493 2.126812 GAGCTACTATCCGCGCGG 60.127 66.667 42.13 42.13 0.00 6.46
2169 2626 9.860898 GCTGATTCCACTCTAATGTTTTAATTT 57.139 29.630 0.00 0.00 0.00 1.82
2187 2648 0.307146 GCTCGCTGAATGCTGATTCC 59.693 55.000 0.00 0.00 37.74 3.01
2268 2731 0.744281 AAAAACAGGTTGAGTGGGCG 59.256 50.000 0.00 0.00 0.00 6.13
2288 2751 7.237982 TCCTCTGGGAAAAATCTTATTTGACA 58.762 34.615 0.00 0.00 38.93 3.58
2289 2752 7.703058 TCCTCTGGGAAAAATCTTATTTGAC 57.297 36.000 0.00 0.00 38.93 3.18
2290 2753 8.899887 AATCCTCTGGGAAAAATCTTATTTGA 57.100 30.769 0.00 0.00 45.78 2.69
2291 2754 8.975295 AGAATCCTCTGGGAAAAATCTTATTTG 58.025 33.333 0.00 0.00 45.78 2.32
2292 2755 9.194972 GAGAATCCTCTGGGAAAAATCTTATTT 57.805 33.333 0.00 0.00 45.78 1.40
2293 2756 8.759481 GAGAATCCTCTGGGAAAAATCTTATT 57.241 34.615 0.00 0.00 45.78 1.40
2338 2810 5.412594 TCAGTCATTTCTCCCTTTTTCATCG 59.587 40.000 0.00 0.00 0.00 3.84
2348 2820 0.620556 TGCCCTCAGTCATTTCTCCC 59.379 55.000 0.00 0.00 0.00 4.30
2355 2827 1.588239 TTGGAGATGCCCTCAGTCAT 58.412 50.000 5.71 0.00 43.76 3.06
2356 2828 1.211212 CATTGGAGATGCCCTCAGTCA 59.789 52.381 5.71 0.00 43.76 3.41
2399 2871 0.529337 TCTAGCTCTACGGACGGACG 60.529 60.000 0.00 0.00 40.31 4.79
2408 2880 2.481854 TCCGACGACATCTAGCTCTAC 58.518 52.381 0.00 0.00 0.00 2.59
2409 2881 2.904697 TCCGACGACATCTAGCTCTA 57.095 50.000 0.00 0.00 0.00 2.43
2417 2889 2.094649 GGGAATAGGATCCGACGACATC 60.095 54.545 5.98 0.00 40.62 3.06
2426 2898 2.047179 GCGCGGGGAATAGGATCC 60.047 66.667 8.83 2.48 38.86 3.36
2442 2914 4.301027 CGCTATCCCCCGACCTGC 62.301 72.222 0.00 0.00 0.00 4.85
2444 2916 2.521224 GTCGCTATCCCCCGACCT 60.521 66.667 2.07 0.00 45.81 3.85
2450 2922 1.602416 GCTCGTTTAGTCGCTATCCCC 60.602 57.143 0.00 0.00 0.00 4.81
2453 2925 4.027540 GTGAAAGCTCGTTTAGTCGCTATC 60.028 45.833 0.00 0.00 31.48 2.08
2454 2926 3.858238 GTGAAAGCTCGTTTAGTCGCTAT 59.142 43.478 0.00 0.00 31.48 2.97
2455 2927 3.240069 GTGAAAGCTCGTTTAGTCGCTA 58.760 45.455 0.00 0.00 31.48 4.26
2457 2929 1.201672 CGTGAAAGCTCGTTTAGTCGC 60.202 52.381 0.00 0.00 0.00 5.19
2467 2939 0.670546 TACTGCAGGCGTGAAAGCTC 60.671 55.000 19.93 0.00 37.29 4.09
2468 2940 0.951040 GTACTGCAGGCGTGAAAGCT 60.951 55.000 19.93 0.00 37.29 3.74
2471 2943 0.602638 CCAGTACTGCAGGCGTGAAA 60.603 55.000 19.93 0.00 0.00 2.69
2473 2945 2.656646 CCAGTACTGCAGGCGTGA 59.343 61.111 19.93 0.00 0.00 4.35
2496 2968 7.600752 GGAGAAATAGAGAAGATACGAAATGGG 59.399 40.741 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.