Multiple sequence alignment - TraesCS3D01G081200

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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 TraesCS3D01G081200 chr3D 100.000 3783 0 0 1 3783 40772894 40776676 0.000000e+00 6986
1 TraesCS3D01G081200 chr3D 98.284 874 15 0 2910 3783 448464897 448464024 0.000000e+00 1531
2 TraesCS3D01G081200 chr3D 93.220 177 9 3 1333 1509 40774151 40774324 1.350000e-64 257
3 TraesCS3D01G081200 chr3D 98.889 90 0 1 1 90 339967755 339967843 3.910000e-35 159
4 TraesCS3D01G081200 chr3D 93.878 98 5 1 1 98 395497525 395497429 3.050000e-31 147
5 TraesCS3D01G081200 chrUn 94.584 2585 98 25 79 2628 19785994 19783417 0.000000e+00 3960
6 TraesCS3D01G081200 chrUn 97.356 1437 20 2 1493 2911 19742818 19741382 0.000000e+00 2427
7 TraesCS3D01G081200 chrUn 96.440 1264 28 6 183 1431 19744437 19743176 0.000000e+00 2069
8 TraesCS3D01G081200 chrUn 93.277 595 14 4 2342 2911 19783667 19783074 0.000000e+00 854
9 TraesCS3D01G081200 chrUn 91.489 235 15 5 1333 1566 19784805 19784575 6.100000e-83 318
10 TraesCS3D01G081200 chrUn 93.782 193 9 3 1333 1525 19743349 19743160 1.720000e-73 287
11 TraesCS3D01G081200 chrUn 89.302 215 22 1 79 293 92963957 92963744 6.230000e-68 268
12 TraesCS3D01G081200 chr6A 92.922 1653 80 18 1271 2911 57424053 57425680 0.000000e+00 2370
13 TraesCS3D01G081200 chr6A 94.900 902 34 7 666 1563 57423374 57424267 0.000000e+00 1400
14 TraesCS3D01G081200 chr6A 94.350 177 7 3 1333 1509 57423962 57424135 6.230000e-68 268
15 TraesCS3D01G081200 chr6A 93.333 90 6 0 1271 1360 57424131 57424220 2.370000e-27 134
16 TraesCS3D01G081200 chr6B 89.020 1612 139 21 1320 2911 93017442 93019035 0.000000e+00 1962
17 TraesCS3D01G081200 chr6B 86.328 1280 96 23 676 1903 93101497 93102749 0.000000e+00 1321
18 TraesCS3D01G081200 chr6B 90.379 1029 65 11 1907 2911 93103526 93104544 0.000000e+00 1321
19 TraesCS3D01G081200 chr6B 85.846 325 17 11 676 984 93017132 93017443 6.100000e-83 318
20 TraesCS3D01G081200 chr6B 89.558 249 25 1 1307 1555 93102075 93102322 7.890000e-82 315
21 TraesCS3D01G081200 chr6B 92.500 80 6 0 1271 1350 93017471 93017550 8.590000e-22 115
22 TraesCS3D01G081200 chr6B 92.500 80 6 0 1271 1350 93102195 93102274 8.590000e-22 115
23 TraesCS3D01G081200 chr2D 98.398 874 13 1 2910 3783 627933279 627934151 0.000000e+00 1535
24 TraesCS3D01G081200 chr2D 85.949 548 39 12 79 598 615473927 615473390 5.520000e-153 551
25 TraesCS3D01G081200 chr2D 85.792 549 42 12 79 598 36236331 36236872 1.990000e-152 549
26 TraesCS3D01G081200 chr2D 85.793 542 42 15 79 593 558910265 558909732 3.320000e-150 542
27 TraesCS3D01G081200 chr2D 84.000 525 59 18 79 598 373764804 373765308 7.350000e-132 481
28 TraesCS3D01G081200 chr2D 94.949 99 4 1 1 99 68834855 68834952 1.820000e-33 154
29 TraesCS3D01G081200 chr2D 94.949 99 4 1 1 99 68892820 68892723 1.820000e-33 154
30 TraesCS3D01G081200 chr2D 93.137 102 4 3 1 101 441839795 441839696 3.050000e-31 147
31 TraesCS3D01G081200 chr1D 97.826 874 19 0 2910 3783 110003677 110002804 0.000000e+00 1509
32 TraesCS3D01G081200 chr1D 95.876 97 2 2 1 97 85486139 85486233 5.060000e-34 156
33 TraesCS3D01G081200 chr7D 97.254 874 24 0 2910 3783 183311079 183311952 0.000000e+00 1482
34 TraesCS3D01G081200 chr7D 84.954 545 43 17 79 598 631440058 631440588 2.010000e-142 516
35 TraesCS3D01G081200 chr5D 96.918 876 24 3 2910 3783 280763969 280764843 0.000000e+00 1465
36 TraesCS3D01G081200 chr5D 95.995 874 30 2 2910 3783 502865076 502864208 0.000000e+00 1415
37 TraesCS3D01G081200 chr5D 95.886 875 33 2 2910 3783 537374568 537373696 0.000000e+00 1413
38 TraesCS3D01G081200 chr5D 84.190 525 56 20 79 598 546675812 546676314 5.680000e-133 484
39 TraesCS3D01G081200 chr5D 83.704 540 36 20 79 593 396445216 396444704 2.660000e-126 462
40 TraesCS3D01G081200 chr4D 96.689 876 26 3 2910 3783 37501200 37502074 0.000000e+00 1454
41 TraesCS3D01G081200 chr4D 85.455 550 43 14 79 598 464169348 464169890 4.300000e-149 538
42 TraesCS3D01G081200 chr4D 83.206 524 62 18 79 598 296724810 296725311 1.240000e-124 457
43 TraesCS3D01G081200 chr4D 97.802 91 0 1 1 89 404904254 404904164 5.060000e-34 156
44 TraesCS3D01G081200 chr4D 95.745 94 0 4 1 94 381854823 381854912 8.470000e-32 148
45 TraesCS3D01G081200 chr6D 95.771 875 33 3 2910 3783 439677131 439676260 0.000000e+00 1408
46 TraesCS3D01G081200 chr6D 98.795 83 0 1 1 83 322994348 322994429 3.050000e-31 147
47 TraesCS3D01G081200 chr1A 91.776 535 25 5 79 598 482331266 482330736 0.000000e+00 726
48 TraesCS3D01G081200 chr5B 85.595 479 28 19 153 598 572740659 572740189 7.400000e-127 464
49 TraesCS3D01G081200 chr4B 85.132 491 32 19 153 608 650784589 650784105 7.400000e-127 464
50 TraesCS3D01G081200 chr4B 83.880 366 30 11 79 420 480830025 480829665 4.710000e-84 322


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 TraesCS3D01G081200 chr3D 40772894 40776676 3782 False 3621.500000 6986 96.610000 1 3783 2 chr3D.!!$F2 3782
1 TraesCS3D01G081200 chr3D 448464024 448464897 873 True 1531.000000 1531 98.284000 2910 3783 1 chr3D.!!$R2 873
2 TraesCS3D01G081200 chrUn 19783074 19785994 2920 True 1710.666667 3960 93.116667 79 2911 3 chrUn.!!$R3 2832
3 TraesCS3D01G081200 chrUn 19741382 19744437 3055 True 1594.333333 2427 95.859333 183 2911 3 chrUn.!!$R2 2728
4 TraesCS3D01G081200 chr6A 57423374 57425680 2306 False 1043.000000 2370 93.876250 666 2911 4 chr6A.!!$F1 2245
5 TraesCS3D01G081200 chr6B 93017132 93019035 1903 False 798.333333 1962 89.122000 676 2911 3 chr6B.!!$F1 2235
6 TraesCS3D01G081200 chr6B 93101497 93104544 3047 False 768.000000 1321 89.691250 676 2911 4 chr6B.!!$F2 2235
7 TraesCS3D01G081200 chr2D 627933279 627934151 872 False 1535.000000 1535 98.398000 2910 3783 1 chr2D.!!$F4 873
8 TraesCS3D01G081200 chr2D 615473390 615473927 537 True 551.000000 551 85.949000 79 598 1 chr2D.!!$R4 519
9 TraesCS3D01G081200 chr2D 36236331 36236872 541 False 549.000000 549 85.792000 79 598 1 chr2D.!!$F1 519
10 TraesCS3D01G081200 chr2D 558909732 558910265 533 True 542.000000 542 85.793000 79 593 1 chr2D.!!$R3 514
11 TraesCS3D01G081200 chr2D 373764804 373765308 504 False 481.000000 481 84.000000 79 598 1 chr2D.!!$F3 519
12 TraesCS3D01G081200 chr1D 110002804 110003677 873 True 1509.000000 1509 97.826000 2910 3783 1 chr1D.!!$R1 873
13 TraesCS3D01G081200 chr7D 183311079 183311952 873 False 1482.000000 1482 97.254000 2910 3783 1 chr7D.!!$F1 873
14 TraesCS3D01G081200 chr7D 631440058 631440588 530 False 516.000000 516 84.954000 79 598 1 chr7D.!!$F2 519
15 TraesCS3D01G081200 chr5D 280763969 280764843 874 False 1465.000000 1465 96.918000 2910 3783 1 chr5D.!!$F1 873
16 TraesCS3D01G081200 chr5D 502864208 502865076 868 True 1415.000000 1415 95.995000 2910 3783 1 chr5D.!!$R2 873
17 TraesCS3D01G081200 chr5D 537373696 537374568 872 True 1413.000000 1413 95.886000 2910 3783 1 chr5D.!!$R3 873
18 TraesCS3D01G081200 chr5D 546675812 546676314 502 False 484.000000 484 84.190000 79 598 1 chr5D.!!$F2 519
19 TraesCS3D01G081200 chr5D 396444704 396445216 512 True 462.000000 462 83.704000 79 593 1 chr5D.!!$R1 514
20 TraesCS3D01G081200 chr4D 37501200 37502074 874 False 1454.000000 1454 96.689000 2910 3783 1 chr4D.!!$F1 873
21 TraesCS3D01G081200 chr4D 464169348 464169890 542 False 538.000000 538 85.455000 79 598 1 chr4D.!!$F4 519
22 TraesCS3D01G081200 chr4D 296724810 296725311 501 False 457.000000 457 83.206000 79 598 1 chr4D.!!$F2 519
23 TraesCS3D01G081200 chr6D 439676260 439677131 871 True 1408.000000 1408 95.771000 2910 3783 1 chr6D.!!$R1 873
24 TraesCS3D01G081200 chr1A 482330736 482331266 530 True 726.000000 726 91.776000 79 598 1 chr1A.!!$R1 519


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
421 483 0.188342 AAAAGCCACACACCCCTCAT 59.812 50.0 0.0 0.0 0.0 2.90 F
1049 1143 0.617820 ACCACCCAGAGCTACCGATT 60.618 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1640 0.100861 GGCGTAGAGTCAGTGTAGCC 59.899 60.0 0.0 0.0 36.32 3.93 R
2869 4266 0.608640 ACGGCTGACAGGGACTTAAG 59.391 55.0 0.0 0.0 34.60 1.85 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
22 23 3.073274 ACTCAAGGCAACCATTAGTCC 57.927 47.619 0.00 0.00 37.17 3.85
23 24 2.375174 ACTCAAGGCAACCATTAGTCCA 59.625 45.455 0.00 0.00 37.17 4.02
24 25 3.010584 ACTCAAGGCAACCATTAGTCCAT 59.989 43.478 0.00 0.00 37.17 3.41
25 26 4.227300 ACTCAAGGCAACCATTAGTCCATA 59.773 41.667 0.00 0.00 37.17 2.74
26 27 4.780815 TCAAGGCAACCATTAGTCCATAG 58.219 43.478 0.00 0.00 37.17 2.23
27 28 4.473196 TCAAGGCAACCATTAGTCCATAGA 59.527 41.667 0.00 0.00 37.17 1.98
28 29 4.696479 AGGCAACCATTAGTCCATAGAG 57.304 45.455 0.00 0.00 37.17 2.43
29 30 4.298626 AGGCAACCATTAGTCCATAGAGA 58.701 43.478 0.00 0.00 37.17 3.10
30 31 4.910304 AGGCAACCATTAGTCCATAGAGAT 59.090 41.667 0.00 0.00 37.17 2.75
31 32 5.370880 AGGCAACCATTAGTCCATAGAGATT 59.629 40.000 0.00 0.00 37.17 2.40
32 33 5.471456 GGCAACCATTAGTCCATAGAGATTG 59.529 44.000 0.00 0.00 0.00 2.67
33 34 6.058183 GCAACCATTAGTCCATAGAGATTGT 58.942 40.000 0.00 0.00 0.00 2.71
34 35 6.203723 GCAACCATTAGTCCATAGAGATTGTC 59.796 42.308 0.00 0.00 0.00 3.18
35 36 7.275183 CAACCATTAGTCCATAGAGATTGTCA 58.725 38.462 0.00 0.00 0.00 3.58
36 37 7.623999 ACCATTAGTCCATAGAGATTGTCAT 57.376 36.000 0.00 0.00 0.00 3.06
37 38 7.675062 ACCATTAGTCCATAGAGATTGTCATC 58.325 38.462 0.00 0.00 0.00 2.92
38 39 7.290948 ACCATTAGTCCATAGAGATTGTCATCA 59.709 37.037 0.00 0.00 0.00 3.07
39 40 8.152898 CCATTAGTCCATAGAGATTGTCATCAA 58.847 37.037 0.00 0.00 37.98 2.57
40 41 9.722184 CATTAGTCCATAGAGATTGTCATCAAT 57.278 33.333 0.00 0.00 45.57 2.57
44 45 8.153550 AGTCCATAGAGATTGTCATCAATTACC 58.846 37.037 0.00 0.00 43.33 2.85
45 46 7.933577 GTCCATAGAGATTGTCATCAATTACCA 59.066 37.037 0.00 0.00 43.33 3.25
46 47 8.493607 TCCATAGAGATTGTCATCAATTACCAA 58.506 33.333 0.00 0.00 43.33 3.67
47 48 9.123902 CCATAGAGATTGTCATCAATTACCAAA 57.876 33.333 0.00 0.00 43.33 3.28
50 51 7.830739 AGAGATTGTCATCAATTACCAAAACC 58.169 34.615 0.00 0.00 43.33 3.27
51 52 7.451255 AGAGATTGTCATCAATTACCAAAACCA 59.549 33.333 0.00 0.00 43.33 3.67
52 53 7.961351 AGATTGTCATCAATTACCAAAACCAA 58.039 30.769 0.00 0.00 43.33 3.67
53 54 8.428063 AGATTGTCATCAATTACCAAAACCAAA 58.572 29.630 0.00 0.00 43.33 3.28
54 55 7.778470 TTGTCATCAATTACCAAAACCAAAC 57.222 32.000 0.00 0.00 0.00 2.93
55 56 6.878317 TGTCATCAATTACCAAAACCAAACA 58.122 32.000 0.00 0.00 0.00 2.83
56 57 7.504403 TGTCATCAATTACCAAAACCAAACAT 58.496 30.769 0.00 0.00 0.00 2.71
57 58 7.440556 TGTCATCAATTACCAAAACCAAACATG 59.559 33.333 0.00 0.00 0.00 3.21
58 59 6.933521 TCATCAATTACCAAAACCAAACATGG 59.066 34.615 0.00 0.00 38.91 3.66
59 60 5.615289 TCAATTACCAAAACCAAACATGGG 58.385 37.500 0.00 0.00 37.26 4.00
60 61 4.632327 ATTACCAAAACCAAACATGGGG 57.368 40.909 0.00 0.00 37.26 4.96
61 62 1.135960 ACCAAAACCAAACATGGGGG 58.864 50.000 0.00 0.00 37.26 5.40
62 63 0.250684 CCAAAACCAAACATGGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
63 64 0.471617 CAAAACCAAACATGGGGGCA 59.528 50.000 0.00 0.00 0.00 5.36
64 65 0.472044 AAAACCAAACATGGGGGCAC 59.528 50.000 0.00 0.00 0.00 5.01
76 77 3.365535 GGGCACCGCATGTTCTTT 58.634 55.556 0.00 0.00 40.86 2.52
77 78 1.212751 GGGCACCGCATGTTCTTTC 59.787 57.895 0.00 0.00 40.86 2.62
337 393 2.300437 AGCCCTATTAATCGCTCCTGTC 59.700 50.000 0.00 0.00 0.00 3.51
350 409 2.203139 CTGTCCCCACGCAACACA 60.203 61.111 0.00 0.00 0.00 3.72
421 483 0.188342 AAAAGCCACACACCCCTCAT 59.812 50.000 0.00 0.00 0.00 2.90
594 662 2.921754 CGAAGGTCAAAGTACATCGACC 59.078 50.000 15.95 15.95 46.85 4.79
603 671 5.643348 TCAAAGTACATCGACCGAGTTACTA 59.357 40.000 12.95 0.81 30.28 1.82
628 696 2.358939 AAGTACATTCGTGTCCGTCC 57.641 50.000 0.00 0.00 35.01 4.79
646 715 3.368116 CGTCCCCTTAAAACTCACTCGAT 60.368 47.826 0.00 0.00 0.00 3.59
1049 1143 0.617820 ACCACCCAGAGCTACCGATT 60.618 55.000 0.00 0.00 0.00 3.34
1458 1651 2.184579 GCGGGAGGCTACACTGAC 59.815 66.667 0.00 0.00 39.11 3.51
1459 1652 2.352032 GCGGGAGGCTACACTGACT 61.352 63.158 0.00 0.00 39.11 3.41
1460 1653 1.810532 CGGGAGGCTACACTGACTC 59.189 63.158 0.00 0.00 41.23 3.36
1461 1654 0.681564 CGGGAGGCTACACTGACTCT 60.682 60.000 0.00 0.00 41.65 3.24
1468 1667 0.377554 CTACACTGACTCTACGCCGG 59.622 60.000 0.00 0.00 0.00 6.13
2193 3497 4.722008 GCGTTCAAAAAGGCCGTT 57.278 50.000 0.00 0.00 39.74 4.44
2575 3969 1.476845 TACCAAGTCCGCTGCCAAGA 61.477 55.000 0.00 0.00 0.00 3.02
2869 4266 2.555757 GCAATCCCCATGATAAGTCAGC 59.444 50.000 0.00 0.00 37.87 4.26
2907 4304 6.479990 CAGCCGTGATAAATCTTCAGTTATGA 59.520 38.462 0.00 0.00 0.00 2.15
3016 4414 7.168905 CCTAACAAATAGAGGAGTGAAACCTT 58.831 38.462 0.00 0.00 37.93 3.50
3032 4430 1.766496 ACCTTCAACCGAGAAGAACCA 59.234 47.619 12.00 0.00 46.18 3.67
3352 4751 2.875672 GCACATGGTCCACTTGAGCTAA 60.876 50.000 7.43 0.00 42.12 3.09
3509 4908 0.314935 CACAATGGACGGCAAGCTTT 59.685 50.000 0.00 0.00 0.00 3.51
3699 5098 5.334879 GGTTAGTACACAAAGCACAATGGAG 60.335 44.000 0.00 0.00 0.00 3.86
3769 5168 5.053811 TCTACGCTTTGTGAGTTGATCAAA 58.946 37.500 10.35 0.00 40.43 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.042311 TGGACTAATGGTTGCCTTGAGTTA 59.958 41.667 0.00 0.00 0.00 2.24
1 2 3.181434 TGGACTAATGGTTGCCTTGAGTT 60.181 43.478 0.00 0.00 0.00 3.01
2 3 2.375174 TGGACTAATGGTTGCCTTGAGT 59.625 45.455 0.00 0.00 0.00 3.41
3 4 3.071874 TGGACTAATGGTTGCCTTGAG 57.928 47.619 0.00 0.00 0.00 3.02
4 5 3.737559 ATGGACTAATGGTTGCCTTGA 57.262 42.857 0.00 0.00 0.00 3.02
5 6 4.780815 TCTATGGACTAATGGTTGCCTTG 58.219 43.478 0.00 0.00 0.00 3.61
6 7 4.721776 TCTCTATGGACTAATGGTTGCCTT 59.278 41.667 0.00 0.00 0.00 4.35
7 8 4.298626 TCTCTATGGACTAATGGTTGCCT 58.701 43.478 0.00 0.00 0.00 4.75
8 9 4.689612 TCTCTATGGACTAATGGTTGCC 57.310 45.455 0.00 0.00 0.00 4.52
9 10 6.058183 ACAATCTCTATGGACTAATGGTTGC 58.942 40.000 0.00 0.00 0.00 4.17
10 11 7.275183 TGACAATCTCTATGGACTAATGGTTG 58.725 38.462 0.00 0.00 0.00 3.77
11 12 7.437713 TGACAATCTCTATGGACTAATGGTT 57.562 36.000 0.00 0.00 0.00 3.67
12 13 7.290948 TGATGACAATCTCTATGGACTAATGGT 59.709 37.037 0.00 0.00 33.61 3.55
13 14 7.674120 TGATGACAATCTCTATGGACTAATGG 58.326 38.462 0.00 0.00 33.61 3.16
14 15 9.722184 ATTGATGACAATCTCTATGGACTAATG 57.278 33.333 0.00 0.00 42.20 1.90
18 19 8.153550 GGTAATTGATGACAATCTCTATGGACT 58.846 37.037 0.00 0.00 44.67 3.85
19 20 7.933577 TGGTAATTGATGACAATCTCTATGGAC 59.066 37.037 0.00 0.00 44.67 4.02
20 21 8.033178 TGGTAATTGATGACAATCTCTATGGA 57.967 34.615 0.00 0.00 44.67 3.41
21 22 8.681486 TTGGTAATTGATGACAATCTCTATGG 57.319 34.615 0.00 0.00 44.67 2.74
24 25 8.956426 GGTTTTGGTAATTGATGACAATCTCTA 58.044 33.333 0.00 0.00 44.67 2.43
25 26 7.451255 TGGTTTTGGTAATTGATGACAATCTCT 59.549 33.333 0.00 0.00 44.67 3.10
26 27 7.601856 TGGTTTTGGTAATTGATGACAATCTC 58.398 34.615 0.00 0.00 44.67 2.75
27 28 7.537596 TGGTTTTGGTAATTGATGACAATCT 57.462 32.000 0.00 0.00 44.67 2.40
28 29 8.495148 GTTTGGTTTTGGTAATTGATGACAATC 58.505 33.333 0.00 0.00 44.67 2.67
29 30 7.989741 TGTTTGGTTTTGGTAATTGATGACAAT 59.010 29.630 0.00 0.00 46.99 2.71
30 31 7.331026 TGTTTGGTTTTGGTAATTGATGACAA 58.669 30.769 0.00 0.00 40.42 3.18
31 32 6.878317 TGTTTGGTTTTGGTAATTGATGACA 58.122 32.000 0.00 0.00 0.00 3.58
32 33 7.095271 CCATGTTTGGTTTTGGTAATTGATGAC 60.095 37.037 0.00 0.00 38.30 3.06
33 34 6.933521 CCATGTTTGGTTTTGGTAATTGATGA 59.066 34.615 0.00 0.00 38.30 2.92
34 35 6.149142 CCCATGTTTGGTTTTGGTAATTGATG 59.851 38.462 0.00 0.00 41.91 3.07
35 36 6.237154 CCCATGTTTGGTTTTGGTAATTGAT 58.763 36.000 0.00 0.00 41.91 2.57
36 37 5.455326 CCCCATGTTTGGTTTTGGTAATTGA 60.455 40.000 0.00 0.00 41.91 2.57
37 38 4.759183 CCCCATGTTTGGTTTTGGTAATTG 59.241 41.667 0.00 0.00 41.91 2.32
38 39 4.202514 CCCCCATGTTTGGTTTTGGTAATT 60.203 41.667 0.00 0.00 41.91 1.40
39 40 3.329225 CCCCCATGTTTGGTTTTGGTAAT 59.671 43.478 0.00 0.00 41.91 1.89
40 41 2.706190 CCCCCATGTTTGGTTTTGGTAA 59.294 45.455 0.00 0.00 41.91 2.85
41 42 2.330216 CCCCCATGTTTGGTTTTGGTA 58.670 47.619 0.00 0.00 41.91 3.25
42 43 1.135960 CCCCCATGTTTGGTTTTGGT 58.864 50.000 0.00 0.00 41.91 3.67
43 44 0.250684 GCCCCCATGTTTGGTTTTGG 60.251 55.000 0.00 0.00 41.91 3.28
44 45 0.471617 TGCCCCCATGTTTGGTTTTG 59.528 50.000 0.00 0.00 41.91 2.44
45 46 0.472044 GTGCCCCCATGTTTGGTTTT 59.528 50.000 0.00 0.00 41.91 2.43
46 47 1.414866 GGTGCCCCCATGTTTGGTTT 61.415 55.000 0.00 0.00 41.91 3.27
47 48 1.841103 GGTGCCCCCATGTTTGGTT 60.841 57.895 0.00 0.00 41.91 3.67
48 49 2.203773 GGTGCCCCCATGTTTGGT 60.204 61.111 0.00 0.00 41.91 3.67
49 50 3.381136 CGGTGCCCCCATGTTTGG 61.381 66.667 0.00 0.00 43.23 3.28
50 51 4.067913 GCGGTGCCCCCATGTTTG 62.068 66.667 0.00 0.00 0.00 2.93
51 52 3.903281 ATGCGGTGCCCCCATGTTT 62.903 57.895 0.00 0.00 0.00 2.83
52 53 4.380945 ATGCGGTGCCCCCATGTT 62.381 61.111 0.00 0.00 0.00 2.71
55 56 4.380945 AACATGCGGTGCCCCCAT 62.381 61.111 0.00 0.00 0.00 4.00
57 58 4.740822 AGAACATGCGGTGCCCCC 62.741 66.667 0.00 0.00 0.00 5.40
58 59 2.212900 GAAAGAACATGCGGTGCCCC 62.213 60.000 0.00 0.00 0.00 5.80
59 60 1.212751 GAAAGAACATGCGGTGCCC 59.787 57.895 0.00 0.00 0.00 5.36
60 61 0.387239 GTGAAAGAACATGCGGTGCC 60.387 55.000 0.00 0.00 0.00 5.01
61 62 0.310543 TGTGAAAGAACATGCGGTGC 59.689 50.000 0.00 0.00 0.00 5.01
62 63 2.995466 ATGTGAAAGAACATGCGGTG 57.005 45.000 0.00 0.00 39.32 4.94
63 64 3.407698 TGTATGTGAAAGAACATGCGGT 58.592 40.909 0.00 0.00 43.64 5.68
64 65 4.621068 ATGTATGTGAAAGAACATGCGG 57.379 40.909 0.00 0.00 43.64 5.69
65 66 6.105657 TGTATGTATGTGAAAGAACATGCG 57.894 37.500 0.00 0.00 43.64 4.73
66 67 7.530010 AGTTGTATGTATGTGAAAGAACATGC 58.470 34.615 0.00 0.00 40.93 4.06
77 78 6.090763 CGGCCACATATAGTTGTATGTATGTG 59.909 42.308 2.24 14.29 46.53 3.21
296 321 1.902508 TGTTGGCTTTGGTTTGTTCCA 59.097 42.857 0.00 0.00 35.49 3.53
312 367 2.808543 GGAGCGATTAATAGGGCTGTTG 59.191 50.000 11.56 0.00 35.54 3.33
337 393 3.215568 TGCTTGTGTTGCGTGGGG 61.216 61.111 0.00 0.00 0.00 4.96
350 409 4.829492 AGGCTGAATTTTCTGTTAGTGCTT 59.171 37.500 0.00 0.00 0.00 3.91
544 611 5.405935 TTCTGTTTGAGATTCAGGATCGA 57.594 39.130 0.00 0.00 39.85 3.59
611 679 0.459063 GGGGACGGACACGAATGTAC 60.459 60.000 0.00 0.00 44.60 2.90
612 680 0.612732 AGGGGACGGACACGAATGTA 60.613 55.000 0.00 0.00 44.60 2.29
613 681 1.477685 AAGGGGACGGACACGAATGT 61.478 55.000 0.00 0.00 44.60 2.71
614 682 0.533491 TAAGGGGACGGACACGAATG 59.467 55.000 0.00 0.00 44.60 2.67
615 683 1.269012 TTAAGGGGACGGACACGAAT 58.731 50.000 0.00 0.00 44.60 3.34
616 684 1.047002 TTTAAGGGGACGGACACGAA 58.953 50.000 0.00 0.00 44.60 3.85
620 688 2.048601 TGAGTTTTAAGGGGACGGACA 58.951 47.619 0.00 0.00 0.00 4.02
621 689 2.038164 AGTGAGTTTTAAGGGGACGGAC 59.962 50.000 0.00 0.00 0.00 4.79
623 691 2.696506 GAGTGAGTTTTAAGGGGACGG 58.303 52.381 0.00 0.00 0.00 4.79
624 692 2.029649 TCGAGTGAGTTTTAAGGGGACG 60.030 50.000 0.00 0.00 0.00 4.79
626 694 4.285003 TCAATCGAGTGAGTTTTAAGGGGA 59.715 41.667 12.21 0.00 0.00 4.81
628 696 5.786401 CTCAATCGAGTGAGTTTTAAGGG 57.214 43.478 29.64 6.64 40.22 3.95
646 715 1.061546 AGGGGACGGCTAAAACTCAA 58.938 50.000 0.00 0.00 0.00 3.02
1049 1143 1.018840 TGGAGGGAGGAAGAGGATCA 58.981 55.000 0.00 0.00 37.82 2.92
1432 1625 1.400530 TAGCCTCCCGCCTTCTTAGC 61.401 60.000 0.00 0.00 38.78 3.09
1434 1627 0.324923 TGTAGCCTCCCGCCTTCTTA 60.325 55.000 0.00 0.00 38.78 2.10
1438 1631 2.284699 AGTGTAGCCTCCCGCCTT 60.285 61.111 0.00 0.00 38.78 4.35
1439 1632 3.077556 CAGTGTAGCCTCCCGCCT 61.078 66.667 0.00 0.00 38.78 5.52
1440 1633 3.075005 TCAGTGTAGCCTCCCGCC 61.075 66.667 0.00 0.00 38.78 6.13
1443 1636 2.025898 GTAGAGTCAGTGTAGCCTCCC 58.974 57.143 0.00 0.00 0.00 4.30
1445 1638 1.064357 GCGTAGAGTCAGTGTAGCCTC 59.936 57.143 0.00 0.00 0.00 4.70
1446 1639 1.096416 GCGTAGAGTCAGTGTAGCCT 58.904 55.000 0.00 0.00 0.00 4.58
1447 1640 0.100861 GGCGTAGAGTCAGTGTAGCC 59.899 60.000 0.00 0.00 36.32 3.93
1450 1643 1.651240 GCCGGCGTAGAGTCAGTGTA 61.651 60.000 12.58 0.00 0.00 2.90
1451 1644 2.991076 GCCGGCGTAGAGTCAGTGT 61.991 63.158 12.58 0.00 0.00 3.55
1452 1645 2.202623 GCCGGCGTAGAGTCAGTG 60.203 66.667 12.58 0.00 0.00 3.66
1453 1646 3.450115 GGCCGGCGTAGAGTCAGT 61.450 66.667 22.54 0.00 0.00 3.41
1458 1651 4.253257 GAGTCGGCCGGCGTAGAG 62.253 72.222 26.29 9.24 0.00 2.43
2193 3497 4.467084 GAGGTGGCGGCGGATTCA 62.467 66.667 9.78 0.00 0.00 2.57
2869 4266 0.608640 ACGGCTGACAGGGACTTAAG 59.391 55.000 0.00 0.00 34.60 1.85
2907 4304 6.015940 CCTCTTTCCAACAAGCTTGAGTTTAT 60.016 38.462 32.50 6.30 0.00 1.40
3016 4414 0.756294 TGCTGGTTCTTCTCGGTTGA 59.244 50.000 0.00 0.00 0.00 3.18
3032 4430 3.627395 TTCGATGTTGGAGGTTATGCT 57.373 42.857 0.00 0.00 0.00 3.79
3352 4751 3.708631 AGGGAGTCAAGATCGTCATCATT 59.291 43.478 0.00 0.00 0.00 2.57
3509 4908 4.783764 TCACGAAGAGATCAAGTGCTTA 57.216 40.909 0.00 0.00 33.28 3.09



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

AutoCloner maintained by Alex Coulton.