Multiple sequence alignment - TraesCS2A01G070000

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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 TraesCS2A01G070000 chr2A 100.000 3651 0 0 1 3651 30856277 30859927 0.000000e+00 6743.0
1 TraesCS2A01G070000 chr2A 85.000 920 114 13 1759 2664 30765490 30766399 0.000000e+00 913.0
2 TraesCS2A01G070000 chr2A 92.371 485 31 5 103 581 419483655 419484139 0.000000e+00 686.0
3 TraesCS2A01G070000 chr2A 87.500 400 34 9 852 1242 30764254 30764646 7.190000e-122 448.0
4 TraesCS2A01G070000 chr2A 86.611 239 24 7 1335 1568 30764711 30764946 1.300000e-64 257.0
5 TraesCS2A01G070000 chr2A 95.000 40 2 0 3257 3296 61842337 61842376 3.040000e-06 63.9
6 TraesCS2A01G070000 chr2D 92.661 2548 142 25 576 3096 28894582 28897111 0.000000e+00 3627.0
7 TraesCS2A01G070000 chr2D 84.911 676 86 10 2003 2665 28828616 28829288 0.000000e+00 669.0
8 TraesCS2A01G070000 chr2D 82.482 411 46 18 852 1242 28827464 28827868 1.620000e-88 337.0
9 TraesCS2A01G070000 chr2D 88.780 205 22 1 1364 1568 28827964 28828167 2.180000e-62 250.0
10 TraesCS2A01G070000 chr2D 99.099 111 1 0 1 111 101660433 101660323 2.220000e-47 200.0
11 TraesCS2A01G070000 chr2B 93.036 1479 83 11 1677 3145 46672537 46674005 0.000000e+00 2143.0
12 TraesCS2A01G070000 chr2B 84.591 941 131 11 1725 2659 46505121 46506053 0.000000e+00 922.0
13 TraesCS2A01G070000 chr2B 96.019 427 12 2 1266 1690 46671927 46672350 0.000000e+00 689.0
14 TraesCS2A01G070000 chr2B 91.102 472 33 5 808 1276 46669140 46669605 6.650000e-177 630.0
15 TraesCS2A01G070000 chr2B 86.717 399 41 9 852 1242 46504212 46504606 2.010000e-117 433.0
16 TraesCS2A01G070000 chr2B 92.647 136 10 0 677 812 46668978 46669113 2.880000e-46 196.0
17 TraesCS2A01G070000 chrUn 92.000 1450 89 16 1879 3316 359864169 359865603 0.000000e+00 2010.0
18 TraesCS2A01G070000 chrUn 94.293 841 38 3 1677 2515 423412862 423412030 0.000000e+00 1279.0
19 TraesCS2A01G070000 chrUn 92.768 885 49 7 808 1685 17182896 17183772 0.000000e+00 1266.0
20 TraesCS2A01G070000 chrUn 93.531 371 19 2 1677 2045 17183987 17184354 6.890000e-152 547.0
21 TraesCS2A01G070000 chrUn 94.706 340 15 2 3315 3651 359865697 359866036 3.230000e-145 525.0
22 TraesCS2A01G070000 chrUn 91.915 235 18 1 576 809 17182632 17182866 9.780000e-86 327.0
23 TraesCS2A01G070000 chrUn 95.028 181 4 2 1507 1685 423413254 423413077 2.780000e-71 279.0
24 TraesCS2A01G070000 chr6A 93.375 483 25 5 103 578 26630456 26629974 0.000000e+00 708.0
25 TraesCS2A01G070000 chr6A 81.633 98 14 4 3199 3296 101985614 101985521 1.090000e-10 78.7
26 TraesCS2A01G070000 chr5A 92.668 491 31 4 103 588 467416266 467415776 0.000000e+00 702.0
27 TraesCS2A01G070000 chr5A 82.324 611 86 13 2060 2652 512601072 512601678 9.040000e-141 510.0
28 TraesCS2A01G070000 chr5A 80.824 631 97 15 2060 2671 512459700 512460325 1.190000e-129 473.0
29 TraesCS2A01G070000 chr5A 88.649 185 21 0 1734 1918 512600801 512600985 3.670000e-55 226.0
30 TraesCS2A01G070000 chr3A 92.946 482 30 3 103 580 749288536 749288055 0.000000e+00 699.0
31 TraesCS2A01G070000 chr3A 92.464 491 28 6 103 585 660661595 660662084 0.000000e+00 693.0
32 TraesCS2A01G070000 chr3A 92.931 481 25 5 103 574 507125354 507125834 0.000000e+00 691.0
33 TraesCS2A01G070000 chr3A 92.387 486 30 5 103 581 648534055 648533570 0.000000e+00 686.0
34 TraesCS2A01G070000 chr3A 77.534 592 91 24 1 577 86473143 86473707 5.880000e-83 318.0
35 TraesCS2A01G070000 chr3A 99.099 111 1 0 1 111 22330048 22330158 2.220000e-47 200.0
36 TraesCS2A01G070000 chr7D 92.593 486 27 5 103 580 114467756 114467272 0.000000e+00 689.0
37 TraesCS2A01G070000 chr7D 79.899 592 84 27 1 577 628764843 628764272 5.680000e-108 401.0
38 TraesCS2A01G070000 chr6D 92.547 483 27 5 103 577 379092973 379093454 0.000000e+00 684.0
39 TraesCS2A01G070000 chr6D 98.214 112 1 1 1 111 86664117 86664006 1.030000e-45 195.0
40 TraesCS2A01G070000 chr6D 98.214 112 1 1 1 111 379092839 379092950 1.030000e-45 195.0
41 TraesCS2A01G070000 chr5B 80.902 665 100 16 2072 2716 488015898 488016555 1.960000e-137 499.0
42 TraesCS2A01G070000 chr5B 89.407 236 25 0 1003 1238 488014614 488014849 7.660000e-77 298.0
43 TraesCS2A01G070000 chr5B 99.099 111 1 0 1 111 541057839 541057949 2.220000e-47 200.0
44 TraesCS2A01G070000 chr5B 88.889 54 3 2 3498 3548 519021622 519021569 3.040000e-06 63.9
45 TraesCS2A01G070000 chr5B 96.875 32 1 0 3437 3468 127850713 127850682 2.000000e-03 54.7
46 TraesCS2A01G070000 chr5D 87.938 257 30 1 1734 1989 407107398 407107142 5.920000e-78 302.0
47 TraesCS2A01G070000 chr5D 88.400 250 26 1 992 1238 407108647 407108398 7.660000e-77 298.0
48 TraesCS2A01G070000 chr5D 84.746 177 27 0 1738 1914 117734590 117734766 1.040000e-40 178.0
49 TraesCS2A01G070000 chr5D 86.667 60 4 2 3498 3553 429745669 429745610 3.040000e-06 63.9
50 TraesCS2A01G070000 chr5D 96.875 32 1 0 3437 3468 197842412 197842443 2.000000e-03 54.7
51 TraesCS2A01G070000 chr3B 92.414 145 5 2 1 139 715143070 715142926 6.180000e-48 202.0
52 TraesCS2A01G070000 chr3D 99.099 111 1 0 1 111 214959280 214959170 2.220000e-47 200.0
53 TraesCS2A01G070000 chr3D 97.222 36 1 0 3255 3290 522308266 522308231 1.090000e-05 62.1
54 TraesCS2A01G070000 chr6B 90.909 55 3 2 3243 3296 161437855 161437802 5.060000e-09 73.1
55 TraesCS2A01G070000 chr6B 96.875 32 1 0 3437 3468 264843614 264843645 2.000000e-03 54.7
56 TraesCS2A01G070000 chr1D 94.737 38 2 0 3255 3292 414707861 414707824 3.940000e-05 60.2
57 TraesCS2A01G070000 chr4A 89.362 47 3 2 3251 3295 709580732 709580686 1.420000e-04 58.4
58 TraesCS2A01G070000 chr4A 86.538 52 7 0 3245 3296 733634478 733634529 1.420000e-04 58.4
59 TraesCS2A01G070000 chr4A 96.875 32 1 0 3437 3468 48686382 48686413 2.000000e-03 54.7
60 TraesCS2A01G070000 chr4D 96.875 32 1 0 3437 3468 123523356 123523387 2.000000e-03 54.7
61 TraesCS2A01G070000 chr4D 96.875 32 1 0 3437 3468 483693837 483693806 2.000000e-03 54.7
62 TraesCS2A01G070000 chr4B 96.875 32 1 0 3437 3468 209044359 209044328 2.000000e-03 54.7
63 TraesCS2A01G070000 chr1B 100.000 29 0 0 3255 3283 56316406 56316434 2.000000e-03 54.7


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 TraesCS2A01G070000 chr2A 30856277 30859927 3650 False 6743.000000 6743 100.000000 1 3651 1 chr2A.!!$F1 3650
1 TraesCS2A01G070000 chr2A 30764254 30766399 2145 False 539.333333 913 86.370333 852 2664 3 chr2A.!!$F4 1812
2 TraesCS2A01G070000 chr2D 28894582 28897111 2529 False 3627.000000 3627 92.661000 576 3096 1 chr2D.!!$F1 2520
3 TraesCS2A01G070000 chr2D 28827464 28829288 1824 False 418.666667 669 85.391000 852 2665 3 chr2D.!!$F2 1813
4 TraesCS2A01G070000 chr2B 46668978 46674005 5027 False 914.500000 2143 93.201000 677 3145 4 chr2B.!!$F2 2468
5 TraesCS2A01G070000 chr2B 46504212 46506053 1841 False 677.500000 922 85.654000 852 2659 2 chr2B.!!$F1 1807
6 TraesCS2A01G070000 chrUn 359864169 359866036 1867 False 1267.500000 2010 93.353000 1879 3651 2 chrUn.!!$F2 1772
7 TraesCS2A01G070000 chrUn 423412030 423413254 1224 True 779.000000 1279 94.660500 1507 2515 2 chrUn.!!$R1 1008
8 TraesCS2A01G070000 chrUn 17182632 17184354 1722 False 713.333333 1266 92.738000 576 2045 3 chrUn.!!$F1 1469
9 TraesCS2A01G070000 chr5A 512459700 512460325 625 False 473.000000 473 80.824000 2060 2671 1 chr5A.!!$F1 611
10 TraesCS2A01G070000 chr5A 512600801 512601678 877 False 368.000000 510 85.486500 1734 2652 2 chr5A.!!$F2 918
11 TraesCS2A01G070000 chr3A 86473143 86473707 564 False 318.000000 318 77.534000 1 577 1 chr3A.!!$F2 576
12 TraesCS2A01G070000 chr7D 628764272 628764843 571 True 401.000000 401 79.899000 1 577 1 chr7D.!!$R2 576
13 TraesCS2A01G070000 chr6D 379092839 379093454 615 False 439.500000 684 95.380500 1 577 2 chr6D.!!$F1 576
14 TraesCS2A01G070000 chr5B 488014614 488016555 1941 False 398.500000 499 85.154500 1003 2716 2 chr5B.!!$F2 1713
15 TraesCS2A01G070000 chr5D 407107142 407108647 1505 True 300.000000 302 88.169000 992 1989 2 chr5D.!!$R2 997

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
430 484 0.108585 AAACAGATGTGTGGGCGACT 59.891 50.0 0.0 0.0 36.84 4.18 F
541 598 0.396435 ATGGAGGCGTGTGAAGTTGA 59.604 50.0 0.0 0.0 0.00 3.18 F
555 612 0.466543 AGTTGACTAACGCCCACACA 59.533 50.0 0.0 0.0 41.71 3.72 F
1147 1273 0.605319 GGCGGTGATGGTGAAGAACA 60.605 55.0 0.0 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 5098 0.179004 TGCCCAACAAGTTGTCCGAT 60.179 50.000 9.40 0.00 38.85 4.18 R
2389 5681 1.561076 TCATGCAGCTCCAGGTTGTAT 59.439 47.619 0.00 0.00 32.53 2.29 R
2461 5753 3.487042 CGAAGTACTCCGTCACGATGAAT 60.487 47.826 0.00 0.00 0.00 2.57 R
2756 6048 1.062587 CCACTAAACACTAGCGCATGC 59.937 52.381 11.47 7.91 43.24 4.06 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
42 44 3.461378 TGCCACCTACTAACACTAGGA 57.539 47.619 0.00 0.00 35.23 2.94
111 116 4.336280 GGGTAAAAGAGAGAGTTGCCATT 58.664 43.478 0.00 0.00 0.00 3.16
117 155 9.744468 GTAAAAGAGAGAGTTGCCATTTAAAAA 57.256 29.630 0.00 0.00 0.00 1.94
232 274 1.480789 TGCCATCTGCTTGCAATCAT 58.519 45.000 3.01 0.00 42.00 2.45
363 411 2.206750 GTGCGTGACTGAAAACTGGTA 58.793 47.619 0.00 0.00 0.00 3.25
376 424 0.249398 ACTGGTATGTGGGCGAACTC 59.751 55.000 0.00 0.00 0.00 3.01
384 432 0.320160 GTGGGCGAACTCCTAAACGT 60.320 55.000 0.00 0.00 0.00 3.99
415 469 1.002315 GCCCCTCCGTGTAGTAAAACA 59.998 52.381 0.00 0.00 0.00 2.83
430 484 0.108585 AAACAGATGTGTGGGCGACT 59.891 50.000 0.00 0.00 36.84 4.18
454 508 2.125472 ACACACCACACACGCGAA 60.125 55.556 15.93 0.00 0.00 4.70
488 542 7.228507 ACGTGGCATATAAAATCAGCTAATTCA 59.771 33.333 0.00 0.00 0.00 2.57
503 557 4.201950 GCTAATTCATGCCAAGATTCGTGT 60.202 41.667 0.00 0.00 0.00 4.49
535 589 2.662596 GGTGATGGAGGCGTGTGA 59.337 61.111 0.00 0.00 0.00 3.58
541 598 0.396435 ATGGAGGCGTGTGAAGTTGA 59.604 50.000 0.00 0.00 0.00 3.18
555 612 0.466543 AGTTGACTAACGCCCACACA 59.533 50.000 0.00 0.00 41.71 3.72
580 637 5.875359 TGTGGGCTTTAACATTTTCGTTTTT 59.125 32.000 0.00 0.00 0.00 1.94
604 661 2.802787 AATGGAAGTCGCCTATCTCG 57.197 50.000 0.00 0.00 0.00 4.04
635 694 6.374417 AAAGACACAGTTATCAGGTATGGT 57.626 37.500 0.00 0.00 0.00 3.55
652 711 0.959553 GGTCACGTGTCTCCTCTCAA 59.040 55.000 16.51 0.00 0.00 3.02
765 827 6.599244 ACAAAGATCTTATTCGAAATCAGCCA 59.401 34.615 8.75 0.00 0.00 4.75
769 831 2.708216 TATTCGAAATCAGCCAGCCA 57.292 45.000 0.00 0.00 0.00 4.75
771 833 1.382522 TTCGAAATCAGCCAGCCATC 58.617 50.000 0.00 0.00 0.00 3.51
774 836 2.141517 CGAAATCAGCCAGCCATCTAG 58.858 52.381 0.00 0.00 0.00 2.43
847 940 2.997897 GACGAGGGGTGGTCTGCT 60.998 66.667 0.00 0.00 0.00 4.24
965 1078 3.375299 CCGAGAAAATCACCAGTTCATCC 59.625 47.826 0.00 0.00 0.00 3.51
966 1079 3.375299 CGAGAAAATCACCAGTTCATCCC 59.625 47.826 0.00 0.00 0.00 3.85
967 1080 3.696548 GAGAAAATCACCAGTTCATCCCC 59.303 47.826 0.00 0.00 0.00 4.81
973 1086 2.106683 CCAGTTCATCCCCGCGTTC 61.107 63.158 4.92 0.00 0.00 3.95
1147 1273 0.605319 GGCGGTGATGGTGAAGAACA 60.605 55.000 0.00 0.00 0.00 3.18
1241 1367 1.935400 TCCCAGGGGAGGTACCGTA 60.935 63.158 5.33 0.00 39.76 4.02
1242 1368 1.759692 CCCAGGGGAGGTACCGTAC 60.760 68.421 6.18 0.00 40.11 3.67
1243 1369 2.123428 CCAGGGGAGGTACCGTACG 61.123 68.421 8.69 8.69 40.11 3.67
1667 4597 5.587844 ACTGAAACCTAGTTCATCATGCATC 59.412 40.000 0.00 0.00 36.92 3.91
1881 5142 1.740025 GCCAAGATGACAGGTTGCTAC 59.260 52.381 0.00 0.00 0.00 3.58
1963 5225 4.760047 CGTGCCTTCCCCAGACGG 62.760 72.222 0.00 0.00 34.50 4.79
2045 5312 7.862372 CCCCAAATATCAATGTCTTTCATAACG 59.138 37.037 0.00 0.00 35.48 3.18
2052 5319 7.987268 TCAATGTCTTTCATAACGTAGCTAG 57.013 36.000 0.00 0.00 35.48 3.42
2262 5553 6.094603 AGAGTAATTGGTGTCATGATGCTTTC 59.905 38.462 0.00 0.00 0.00 2.62
2417 5709 3.965539 GAGCTGCATGAGGGCGTGT 62.966 63.158 1.02 0.00 36.28 4.49
2461 5753 3.592814 CGCGTCCGCATAGAGGGA 61.593 66.667 12.58 0.00 42.06 4.20
2532 5824 1.056660 GTGGGTCACCTCAAGGAAGA 58.943 55.000 2.30 0.00 38.94 2.87
2702 5994 3.084039 ACAAGTACCGATCTACGTTCCA 58.916 45.455 0.00 0.00 40.78 3.53
2712 6004 4.973051 CGATCTACGTTCCAAGATCAGAAG 59.027 45.833 20.51 5.86 45.56 2.85
2716 6008 3.654414 ACGTTCCAAGATCAGAAGTCAC 58.346 45.455 0.00 0.00 0.00 3.67
2718 6010 3.677121 CGTTCCAAGATCAGAAGTCACAG 59.323 47.826 0.00 0.00 0.00 3.66
2727 6019 2.630098 TCAGAAGTCACAGAGGTTCCTG 59.370 50.000 0.00 0.00 39.93 3.86
2754 6046 0.770499 TTGCTGGATCCAGAACACCA 59.230 50.000 40.29 26.30 46.30 4.17
2755 6047 0.994247 TGCTGGATCCAGAACACCAT 59.006 50.000 40.29 0.00 46.30 3.55
2756 6048 1.340308 TGCTGGATCCAGAACACCATG 60.340 52.381 40.29 15.88 46.30 3.66
2757 6049 1.386533 CTGGATCCAGAACACCATGC 58.613 55.000 34.54 0.00 46.30 4.06
2758 6050 0.697658 TGGATCCAGAACACCATGCA 59.302 50.000 11.44 0.00 0.00 3.96
2783 6075 4.304110 CGCTAGTGTTTAGTGGAAGTTGA 58.696 43.478 0.00 0.00 0.00 3.18
2847 6140 6.468333 TGCTACATAATAAGTGGAACCGTA 57.532 37.500 0.00 0.00 37.80 4.02
2852 6145 3.975168 AATAAGTGGAACCGTAGCACT 57.025 42.857 0.00 0.00 37.80 4.40
2880 6173 0.609131 CCCGGGTGCACTTCAAGATT 60.609 55.000 17.98 0.00 0.00 2.40
2888 6181 5.402398 GGTGCACTTCAAGATTTATGTTCC 58.598 41.667 17.98 0.00 0.00 3.62
2894 6187 7.550906 GCACTTCAAGATTTATGTTCCTCTACT 59.449 37.037 0.00 0.00 0.00 2.57
2999 6299 6.511444 GCACACGGTTACTTAAATGTGTACAA 60.511 38.462 0.00 0.00 39.65 2.41
3053 6361 0.250640 CTGCAGCTTCCTCAGGTTGT 60.251 55.000 0.00 0.00 0.00 3.32
3100 6408 8.762645 ACAGTAAATTCTCTAGATGATTGGACA 58.237 33.333 0.00 0.00 0.00 4.02
3126 6438 8.828688 AAATAAAGTACTGTAGTCACTCCAAC 57.171 34.615 0.00 0.00 0.00 3.77
3133 6445 6.086785 ACTGTAGTCACTCCAACTTCTAAC 57.913 41.667 0.00 0.00 0.00 2.34
3152 6465 3.637911 ACGCCCCTCATATTTTGTGTA 57.362 42.857 0.00 0.00 0.00 2.90
3341 6751 2.572104 ACAAGGGAGCCTTACAACCTAG 59.428 50.000 0.00 0.00 42.67 3.02
3358 6769 6.602009 ACAACCTAGCTTGTACACTTCTTTTT 59.398 34.615 1.42 0.00 32.38 1.94
3366 6777 6.513556 GCTTGTACACTTCTTTTTCCTTCTCC 60.514 42.308 0.00 0.00 0.00 3.71
3377 6788 2.795231 TCCTTCTCCCATGCTTCAAG 57.205 50.000 0.00 0.00 0.00 3.02
3380 6791 3.160269 CCTTCTCCCATGCTTCAAGTTT 58.840 45.455 0.00 0.00 0.00 2.66
3387 6798 2.036217 CCATGCTTCAAGTTTTGCCTCA 59.964 45.455 0.00 0.00 0.00 3.86
3441 6852 6.427974 GCAAACACTAGTTCAAAGTAAGGTC 58.572 40.000 0.00 0.00 36.84 3.85
3480 6893 1.080025 GTTCCGTGACGCTAGCCTT 60.080 57.895 9.66 0.00 0.00 4.35
3496 6909 0.758734 CCTTATGACGAGATGGCCCA 59.241 55.000 0.00 0.00 0.00 5.36
3575 6988 7.939784 ATTCTAAGTTGAATAGGGGTGAAAC 57.060 36.000 0.00 0.00 35.18 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 1.338674 TGTAGCGCTACATGGCAACTT 60.339 47.619 39.24 4.05 40.77 2.66
117 155 5.050091 CACGTAAGCAGATGTCAACTCTTTT 60.050 40.000 0.00 0.00 45.62 2.27
127 165 1.626654 GCGTGCACGTAAGCAGATGT 61.627 55.000 36.80 0.00 46.69 3.06
168 206 3.674753 GTCAGTTGCCATATGTTTTGCAC 59.325 43.478 1.24 0.33 32.63 4.57
268 312 0.607489 CACCCAAGCTGCTAGTTGCT 60.607 55.000 0.90 5.92 43.37 3.91
275 319 3.177884 TCCCACACCCAAGCTGCT 61.178 61.111 0.00 0.00 0.00 4.24
304 349 0.184692 TTTGCCATCTCACCCACACA 59.815 50.000 0.00 0.00 0.00 3.72
334 379 2.591715 GTCACGCACAAGGGCTGT 60.592 61.111 0.00 0.00 39.56 4.40
363 411 1.674817 CGTTTAGGAGTTCGCCCACAT 60.675 52.381 0.00 0.00 0.00 3.21
376 424 0.947180 CCGGTGTGTGGACGTTTAGG 60.947 60.000 0.00 0.00 0.00 2.69
407 461 2.151202 CGCCCACACATCTGTTTTACT 58.849 47.619 0.00 0.00 0.00 2.24
415 469 0.247736 GAGAAGTCGCCCACACATCT 59.752 55.000 0.00 0.00 0.00 2.90
430 484 1.470805 CGTGTGTGGTGTGTGAGAGAA 60.471 52.381 0.00 0.00 0.00 2.87
454 508 6.995686 TGATTTTATATGCCACGTAGGACAAT 59.004 34.615 8.04 0.00 41.22 2.71
488 542 4.207891 ACTTCTACACGAATCTTGGCAT 57.792 40.909 0.00 0.00 0.00 4.40
503 557 4.712829 TCCATCACCGTCCAATAACTTCTA 59.287 41.667 0.00 0.00 0.00 2.10
535 589 1.134340 TGTGTGGGCGTTAGTCAACTT 60.134 47.619 0.00 0.00 32.09 2.66
541 598 2.927004 CACATGTGTGGGCGTTAGT 58.073 52.632 18.03 0.00 42.10 2.24
555 612 4.864704 ACGAAAATGTTAAAGCCCACAT 57.135 36.364 0.00 0.00 35.00 3.21
569 626 9.769093 CGACTTCCATTATAGAAAAACGAAAAT 57.231 29.630 0.00 0.00 0.00 1.82
580 637 5.354513 CGAGATAGGCGACTTCCATTATAGA 59.645 44.000 0.00 0.00 43.67 1.98
586 643 0.962489 CCGAGATAGGCGACTTCCAT 59.038 55.000 0.00 0.00 43.67 3.41
604 661 1.021968 AACTGTGTCTTTCGGCAACC 58.978 50.000 0.00 0.00 0.00 3.77
611 668 6.407202 ACCATACCTGATAACTGTGTCTTTC 58.593 40.000 0.00 0.00 0.00 2.62
616 673 4.381612 CGTGACCATACCTGATAACTGTGT 60.382 45.833 0.00 0.00 0.00 3.72
617 674 4.112634 CGTGACCATACCTGATAACTGTG 58.887 47.826 0.00 0.00 0.00 3.66
635 694 0.598562 GCTTGAGAGGAGACACGTGA 59.401 55.000 25.01 0.00 0.00 4.35
652 711 1.356124 CAGCTATACCAGGGATGGCT 58.644 55.000 17.05 17.05 41.33 4.75
765 827 3.556999 AGATACACGACACTAGATGGCT 58.443 45.455 0.00 0.00 31.94 4.75
847 940 2.805295 CGGCCGGCAGATAAAACTATCA 60.805 50.000 30.85 0.00 0.00 2.15
913 1015 2.017113 GCCTTCGGGAGGGTATGTTTG 61.017 57.143 4.07 0.00 46.40 2.93
973 1086 4.628074 TCCTTTCTTTCTTGGACGTACAG 58.372 43.478 0.00 0.00 0.00 2.74
1015 1141 1.302033 CGCTCCTGTTGCTCACCTT 60.302 57.895 0.00 0.00 0.00 3.50
1147 1273 1.333177 GGATCGCAGGAGAGGTACAT 58.667 55.000 0.00 0.00 0.00 2.29
1241 1367 8.821147 TTAGATTACAGTGAAAACATACACGT 57.179 30.769 0.00 0.00 41.22 4.49
1242 1368 9.901724 GATTAGATTACAGTGAAAACATACACG 57.098 33.333 0.00 0.00 41.22 4.49
1327 4109 3.873952 CCAAAATTTCAAGGTTTTCGGCA 59.126 39.130 0.00 0.00 0.00 5.69
1571 4359 6.174760 TGTAGTAACAAACAACCAGACAAGT 58.825 36.000 0.00 0.00 30.91 3.16
1837 5098 0.179004 TGCCCAACAAGTTGTCCGAT 60.179 50.000 9.40 0.00 38.85 4.18
1869 5130 2.334838 CCAACTACGTAGCAACCTGTC 58.665 52.381 22.40 0.00 0.00 3.51
1963 5225 5.957842 TCAGTATGAACAAAACCATCCAC 57.042 39.130 0.00 0.00 45.97 4.02
2045 5312 5.986135 CCATGAGAAATGGTGTACTAGCTAC 59.014 44.000 0.00 0.00 34.56 3.58
2048 5315 4.130118 CCCATGAGAAATGGTGTACTAGC 58.870 47.826 0.00 0.00 37.48 3.42
2052 5319 7.823745 ATTTATCCCATGAGAAATGGTGTAC 57.176 36.000 0.00 0.00 40.08 2.90
2389 5681 1.561076 TCATGCAGCTCCAGGTTGTAT 59.439 47.619 0.00 0.00 32.53 2.29
2461 5753 3.487042 CGAAGTACTCCGTCACGATGAAT 60.487 47.826 0.00 0.00 0.00 2.57
2702 5994 4.020662 GGAACCTCTGTGACTTCTGATCTT 60.021 45.833 0.00 0.00 0.00 2.40
2712 6004 2.222027 CAAACCAGGAACCTCTGTGAC 58.778 52.381 0.00 0.00 33.14 3.67
2716 6008 2.362077 CAAACCAAACCAGGAACCTCTG 59.638 50.000 0.00 0.00 34.70 3.35
2718 6010 1.068588 GCAAACCAAACCAGGAACCTC 59.931 52.381 0.00 0.00 0.00 3.85
2727 6019 1.273327 CTGGATCCAGCAAACCAAACC 59.727 52.381 28.45 0.00 37.24 3.27
2754 6046 2.352651 CACTAAACACTAGCGCATGCAT 59.647 45.455 19.57 8.14 46.23 3.96
2755 6047 1.731709 CACTAAACACTAGCGCATGCA 59.268 47.619 19.57 0.00 46.23 3.96
2756 6048 1.062587 CCACTAAACACTAGCGCATGC 59.937 52.381 11.47 7.91 43.24 4.06
2757 6049 2.616960 TCCACTAAACACTAGCGCATG 58.383 47.619 11.47 7.56 0.00 4.06
2758 6050 3.262420 CTTCCACTAAACACTAGCGCAT 58.738 45.455 11.47 0.00 0.00 4.73
2783 6075 4.653801 ACCAAAGTAGCACCCAATTTTCTT 59.346 37.500 0.00 0.00 0.00 2.52
2847 6140 2.681778 CGGGGGTCAGAGAGTGCT 60.682 66.667 0.00 0.00 0.00 4.40
2867 6160 6.240894 AGAGGAACATAAATCTTGAAGTGCA 58.759 36.000 0.00 0.00 0.00 4.57
2880 6173 5.480422 TCTGCAGACAAGTAGAGGAACATAA 59.520 40.000 13.74 0.00 0.00 1.90
2888 6181 5.414454 AGAGTAGTTCTGCAGACAAGTAGAG 59.586 44.000 18.03 0.00 33.93 2.43
2894 6187 6.406692 AGTTTAGAGTAGTTCTGCAGACAA 57.593 37.500 18.03 0.00 36.61 3.18
2999 6299 6.202954 GCGAAACTATTCAGGTTGCAGTATAT 59.797 38.462 0.00 0.00 35.15 0.86
3004 6312 2.744202 AGCGAAACTATTCAGGTTGCAG 59.256 45.455 0.00 0.00 35.15 4.41
3053 6361 2.758736 AACCAAAGTTTTGCAGCACA 57.241 40.000 0.00 0.00 36.86 4.57
3097 6405 8.923683 GGAGTGACTACAGTACTTTATTTTGTC 58.076 37.037 0.00 0.00 0.00 3.18
3099 6407 8.827177 TGGAGTGACTACAGTACTTTATTTTG 57.173 34.615 0.00 0.00 31.90 2.44
3100 6408 9.269453 GTTGGAGTGACTACAGTACTTTATTTT 57.731 33.333 0.00 0.00 31.90 1.82
3102 6410 8.191534 AGTTGGAGTGACTACAGTACTTTATT 57.808 34.615 0.00 0.00 31.90 1.40
3104 6412 7.504911 AGAAGTTGGAGTGACTACAGTACTTTA 59.495 37.037 14.31 0.00 30.61 1.85
3105 6413 6.324254 AGAAGTTGGAGTGACTACAGTACTTT 59.676 38.462 14.31 4.56 30.61 2.66
3116 6424 2.067013 GGCGTTAGAAGTTGGAGTGAC 58.933 52.381 0.00 0.00 0.00 3.67
3126 6438 4.881850 ACAAAATATGAGGGGCGTTAGAAG 59.118 41.667 0.00 0.00 0.00 2.85
3133 6445 4.974368 TTTACACAAAATATGAGGGGCG 57.026 40.909 0.00 0.00 0.00 6.13
3152 6465 9.533253 CCTATTCAAACTCACTGTCAAATTTTT 57.467 29.630 0.00 0.00 0.00 1.94
3284 6599 7.599630 AACATTGACCATGCATGAATTTAAC 57.400 32.000 28.31 10.58 36.14 2.01
3286 6601 7.384477 TCAAACATTGACCATGCATGAATTTA 58.616 30.769 28.31 9.33 36.14 1.40
3292 6607 5.006153 AGATCAAACATTGACCATGCATG 57.994 39.130 20.19 20.19 43.48 4.06
3293 6608 6.971726 ATAGATCAAACATTGACCATGCAT 57.028 33.333 0.00 0.00 43.48 3.96
3294 6609 6.778834 AATAGATCAAACATTGACCATGCA 57.221 33.333 0.00 0.00 43.48 3.96
3295 6610 9.831737 GTATAATAGATCAAACATTGACCATGC 57.168 33.333 0.00 0.00 43.48 4.06
3341 6751 6.378710 AGAAGGAAAAAGAAGTGTACAAGC 57.621 37.500 0.00 0.00 0.00 4.01
3358 6769 1.988107 ACTTGAAGCATGGGAGAAGGA 59.012 47.619 0.00 0.00 0.00 3.36
3366 6777 2.036217 TGAGGCAAAACTTGAAGCATGG 59.964 45.455 0.00 0.00 0.00 3.66
3377 6788 0.877743 GGAGTGAGCTGAGGCAAAAC 59.122 55.000 0.00 0.00 41.70 2.43
3380 6791 0.543883 AGAGGAGTGAGCTGAGGCAA 60.544 55.000 0.00 0.00 41.70 4.52
3387 6798 1.893919 GCGGGAAAGAGGAGTGAGCT 61.894 60.000 0.00 0.00 0.00 4.09
3421 6832 6.042781 TCCATGACCTTACTTTGAACTAGTGT 59.957 38.462 0.00 0.00 0.00 3.55
3426 6837 6.187727 TCTTCCATGACCTTACTTTGAACT 57.812 37.500 0.00 0.00 0.00 3.01
3427 6838 6.072452 CCTTCTTCCATGACCTTACTTTGAAC 60.072 42.308 0.00 0.00 0.00 3.18
3441 6852 1.026718 GCCACGACCCTTCTTCCATG 61.027 60.000 0.00 0.00 0.00 3.66
3480 6893 0.976641 GGATGGGCCATCTCGTCATA 59.023 55.000 37.80 0.40 40.39 2.15
3496 6909 6.653020 TGTTTCAACTACTCATGCTATGGAT 58.347 36.000 0.00 0.00 0.00 3.41
3546 6959 7.393234 TCACCCCTATTCAACTTAGAATTTGTG 59.607 37.037 0.00 0.00 38.97 3.33
3564 6977 3.203487 ACAAAACTCCAGTTTCACCCCTA 59.797 43.478 5.17 0.00 46.47 3.53
3575 6988 9.877178 ACTACTCTATTTATGACAAAACTCCAG 57.123 33.333 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.