Multiple sequence alignment - TraesCS2D01G385500

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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 TraesCS2D01G385500 chr2D 100.000 1770 0 0 1403 3172 490117824 490119593 0.000000e+00 3269.0
1 TraesCS2D01G385500 chr2D 100.000 1064 0 0 1 1064 490116422 490117485 0.000000e+00 1965.0
2 TraesCS2D01G385500 chr2D 85.823 790 72 18 1403 2158 148856306 148855523 0.000000e+00 802.0
3 TraesCS2D01G385500 chr2D 88.378 370 41 2 55 423 207239981 207240349 8.070000e-121 444.0
4 TraesCS2D01G385500 chr2D 81.030 369 34 22 711 1064 148856697 148856350 8.730000e-66 261.0
5 TraesCS2D01G385500 chr2D 86.207 232 17 6 2424 2649 148855478 148855256 1.470000e-58 237.0
6 TraesCS2D01G385500 chrUn 94.344 937 33 5 1403 2335 13023594 13024514 0.000000e+00 1419.0
7 TraesCS2D01G385500 chrUn 93.396 848 36 9 2337 3172 13024588 13025427 0.000000e+00 1238.0
8 TraesCS2D01G385500 chrUn 93.500 400 18 3 671 1064 13023157 13023554 3.520000e-164 588.0
9 TraesCS2D01G385500 chr2B 91.967 971 36 18 1405 2340 573974918 573975881 0.000000e+00 1323.0
10 TraesCS2D01G385500 chr2B 87.183 749 66 16 1434 2158 208211713 208210971 0.000000e+00 824.0
11 TraesCS2D01G385500 chr2B 89.514 658 30 16 1718 2340 573985068 573985721 0.000000e+00 797.0
12 TraesCS2D01G385500 chr2B 93.766 401 14 9 670 1064 573938826 573939221 2.720000e-165 592.0
13 TraesCS2D01G385500 chr2B 93.766 401 14 9 670 1064 573974481 573974876 2.720000e-165 592.0
14 TraesCS2D01G385500 chr2B 92.308 325 20 2 2335 2654 573985788 573986112 1.040000e-124 457.0
15 TraesCS2D01G385500 chr2B 91.743 327 19 5 2335 2654 573975948 573976273 6.240000e-122 448.0
16 TraesCS2D01G385500 chr2B 81.010 574 53 30 2424 2972 208210926 208210384 3.810000e-109 405.0
17 TraesCS2D01G385500 chr2B 95.142 247 11 1 2926 3172 573976596 573976841 3.840000e-104 388.0
18 TraesCS2D01G385500 chr2B 95.142 247 11 1 2926 3172 573986436 573986681 3.840000e-104 388.0
19 TraesCS2D01G385500 chr2B 91.093 247 15 5 2653 2895 573976354 573976597 8.480000e-86 327.0
20 TraesCS2D01G385500 chr2B 91.093 247 15 5 2653 2895 573986194 573986437 8.480000e-86 327.0
21 TraesCS2D01G385500 chr2B 82.143 364 32 18 711 1064 208212124 208211784 6.700000e-72 281.0
22 TraesCS2D01G385500 chr2A 86.551 751 67 18 1434 2158 153452438 153453180 0.000000e+00 797.0
23 TraesCS2D01G385500 chr2A 81.161 775 78 38 2424 3167 153453225 153453962 7.680000e-156 560.0
24 TraesCS2D01G385500 chr2A 84.259 432 50 12 2 426 14603622 14603202 3.810000e-109 405.0
25 TraesCS2D01G385500 chr1D 83.139 599 63 16 1 566 248987662 248987069 2.180000e-141 512.0
26 TraesCS2D01G385500 chr6D 84.597 422 58 6 1 417 444890756 444890337 2.280000e-111 412.0
27 TraesCS2D01G385500 chr3A 83.933 417 64 1 1 417 218724606 218725019 2.290000e-106 396.0
28 TraesCS2D01G385500 chr3A 86.667 150 19 1 425 573 218725053 218725202 7.040000e-37 165.0
29 TraesCS2D01G385500 chr3A 100.000 30 0 0 2378 2407 653306643 653306672 4.420000e-04 56.5
30 TraesCS2D01G385500 chr3A 100.000 28 0 0 645 672 633048594 633048621 6.000000e-03 52.8
31 TraesCS2D01G385500 chr1A 82.727 440 53 9 1 417 298612891 298613330 1.390000e-98 370.0
32 TraesCS2D01G385500 chr7D 82.619 420 64 6 1 417 197956689 197957102 2.330000e-96 363.0
33 TraesCS2D01G385500 chr7B 80.754 504 62 14 45 519 284968723 284968226 8.360000e-96 361.0
34 TraesCS2D01G385500 chr7B 93.220 59 4 0 359 417 162152413 162152471 1.570000e-13 87.9
35 TraesCS2D01G385500 chr4A 85.600 250 34 2 425 673 84952130 84951882 8.730000e-66 261.0
36 TraesCS2D01G385500 chr4A 81.712 257 38 8 1600 1851 34027499 34027247 4.150000e-49 206.0
37 TraesCS2D01G385500 chr4D 74.870 386 83 9 3 383 223634153 223633777 2.530000e-36 163.0
38 TraesCS2D01G385500 chr4D 75.224 335 64 14 3 326 374596696 374596370 1.190000e-29 141.0
39 TraesCS2D01G385500 chr5B 89.855 69 7 0 351 419 13911908 13911976 4.360000e-14 89.8
40 TraesCS2D01G385500 chr5D 92.308 39 2 1 644 681 421868814 421868852 2.000000e-03 54.7
41 TraesCS2D01G385500 chr5A 100.000 29 0 0 644 672 503662500 503662528 2.000000e-03 54.7
42 TraesCS2D01G385500 chr3D 100.000 29 0 0 645 673 241678962 241678990 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 TraesCS2D01G385500 chr2D 490116422 490119593 3171 False 2617.000000 3269 100.000000 1 3172 2 chr2D.!!$F2 3171
1 TraesCS2D01G385500 chr2D 148855256 148856697 1441 True 433.333333 802 84.353333 711 2649 3 chr2D.!!$R1 1938
2 TraesCS2D01G385500 chrUn 13023157 13025427 2270 False 1081.666667 1419 93.746667 671 3172 3 chrUn.!!$F1 2501
3 TraesCS2D01G385500 chr2B 573974481 573976841 2360 False 615.600000 1323 92.742200 670 3172 5 chr2B.!!$F2 2502
4 TraesCS2D01G385500 chr2B 208210384 208212124 1740 True 503.333333 824 83.445333 711 2972 3 chr2B.!!$R1 2261
5 TraesCS2D01G385500 chr2B 573985068 573986681 1613 False 492.250000 797 92.014250 1718 3172 4 chr2B.!!$F3 1454
6 TraesCS2D01G385500 chr2A 153452438 153453962 1524 False 678.500000 797 83.856000 1434 3167 2 chr2A.!!$F1 1733
7 TraesCS2D01G385500 chr1D 248987069 248987662 593 True 512.000000 512 83.139000 1 566 1 chr1D.!!$R1 565
8 TraesCS2D01G385500 chr3A 218724606 218725202 596 False 280.500000 396 85.300000 1 573 2 chr3A.!!$F3 572

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
577 606 0.033504 TCGCGGCTGGGAATCTATTC 59.966 55.0 10.31 0.0 33.6 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2582 0.248498 GATTTAGCGGCGGCCTTTTC 60.248 55.0 18.34 3.47 41.24 2.29 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
108 109 4.864334 CCTCCCCGCAGCCACATC 62.864 72.222 0.00 0.00 0.00 3.06
155 156 4.072088 GGCGACCGTGTTGAAGCG 62.072 66.667 0.00 0.00 0.00 4.68
173 174 2.660064 GGGAGCACGAGGACATGGT 61.660 63.158 0.00 0.00 0.00 3.55
174 175 1.296715 GGAGCACGAGGACATGGTT 59.703 57.895 0.00 0.00 0.00 3.67
175 176 0.321653 GGAGCACGAGGACATGGTTT 60.322 55.000 0.00 0.00 0.00 3.27
181 182 0.037697 CGAGGACATGGTTTCCGACA 60.038 55.000 0.00 0.00 38.29 4.35
238 239 4.218578 CGCAGGAGATGGAGCGCT 62.219 66.667 11.27 11.27 43.80 5.92
261 262 1.875963 CCGTGCGCTGGAAGAAATT 59.124 52.632 9.73 0.00 34.07 1.82
306 307 4.865761 GGCGGCGTCATCGTGCTA 62.866 66.667 6.63 0.00 39.27 3.49
314 315 1.533129 CGTCATCGTGCTATCCGACAA 60.533 52.381 0.00 0.00 37.12 3.18
316 317 1.474879 TCATCGTGCTATCCGACAACA 59.525 47.619 0.00 0.00 37.12 3.33
329 330 1.779569 GACAACAACGACGAGGTCAT 58.220 50.000 0.00 0.00 32.09 3.06
333 334 0.249699 ACAACGACGAGGTCATTGCA 60.250 50.000 0.00 0.00 38.99 4.08
334 335 1.078709 CAACGACGAGGTCATTGCAT 58.921 50.000 0.00 0.00 29.50 3.96
389 390 3.081554 CTGCAACTAGGCCACCCT 58.918 61.111 5.01 0.00 45.61 4.34
510 537 9.931210 CCTATATTTCGTCCAAATTAACTGAAC 57.069 33.333 0.00 0.00 36.09 3.18
520 547 7.961283 GTCCAAATTAACTGAACTTTATCGACC 59.039 37.037 0.00 0.00 0.00 4.79
521 548 6.959311 CCAAATTAACTGAACTTTATCGACCG 59.041 38.462 0.00 0.00 0.00 4.79
524 551 2.334838 ACTGAACTTTATCGACCGTGC 58.665 47.619 0.00 0.00 0.00 5.34
573 602 4.162690 GGTCGCGGCTGGGAATCT 62.163 66.667 14.69 0.00 38.96 2.40
574 603 2.792947 GGTCGCGGCTGGGAATCTA 61.793 63.158 14.69 0.00 38.96 1.98
575 604 1.367840 GTCGCGGCTGGGAATCTAT 59.632 57.895 14.69 0.00 38.96 1.98
576 605 0.249911 GTCGCGGCTGGGAATCTATT 60.250 55.000 14.69 0.00 38.96 1.73
577 606 0.033504 TCGCGGCTGGGAATCTATTC 59.966 55.000 10.31 0.00 33.60 1.75
599 628 4.632538 CCCCCAAGACGAAATTATTGTC 57.367 45.455 0.00 0.00 0.00 3.18
600 629 3.064820 CCCCCAAGACGAAATTATTGTCG 59.935 47.826 0.00 7.56 42.91 4.35
601 630 3.064820 CCCCAAGACGAAATTATTGTCGG 59.935 47.826 11.73 0.00 41.56 4.79
602 631 3.486875 CCCAAGACGAAATTATTGTCGGC 60.487 47.826 11.73 9.54 45.90 5.54
607 636 4.279659 GACGAAATTATTGTCGGCAATCC 58.720 43.478 20.26 3.97 44.87 3.01
608 637 3.945285 ACGAAATTATTGTCGGCAATCCT 59.055 39.130 20.26 4.75 43.61 3.24
609 638 4.035208 ACGAAATTATTGTCGGCAATCCTC 59.965 41.667 20.26 10.34 43.61 3.71
610 639 4.273480 CGAAATTATTGTCGGCAATCCTCT 59.727 41.667 20.26 2.65 43.61 3.69
611 640 5.465390 CGAAATTATTGTCGGCAATCCTCTA 59.535 40.000 20.26 0.00 43.61 2.43
612 641 6.018262 CGAAATTATTGTCGGCAATCCTCTAA 60.018 38.462 20.26 7.97 43.61 2.10
613 642 6.867662 AATTATTGTCGGCAATCCTCTAAG 57.132 37.500 20.26 0.00 43.61 2.18
614 643 5.607939 TTATTGTCGGCAATCCTCTAAGA 57.392 39.130 20.26 0.00 43.61 2.10
615 644 3.526931 TTGTCGGCAATCCTCTAAGAG 57.473 47.619 0.00 0.00 0.00 2.85
616 645 3.181461 ATTGTCGGCAATCCTCTAAGAGG 60.181 47.826 10.00 0.00 41.08 3.69
617 646 6.783963 ATTGTCGGCAATCCTCTAAGAGGC 62.784 50.000 10.00 0.00 41.08 4.70
624 653 3.669354 CCTCTAAGAGGCGCGATTT 57.331 52.632 12.10 0.00 43.29 2.17
625 654 1.941325 CCTCTAAGAGGCGCGATTTT 58.059 50.000 12.10 0.92 43.29 1.82
626 655 2.280628 CCTCTAAGAGGCGCGATTTTT 58.719 47.619 12.10 0.19 43.29 1.94
627 656 2.285488 CCTCTAAGAGGCGCGATTTTTC 59.715 50.000 12.10 0.00 43.29 2.29
628 657 1.924524 TCTAAGAGGCGCGATTTTTCG 59.075 47.619 12.10 0.00 0.00 3.46
645 674 4.889427 GCCTAAAAGCGCCTTTGG 57.111 55.556 14.18 10.91 33.64 3.28
646 675 1.215382 GCCTAAAAGCGCCTTTGGG 59.785 57.895 24.97 24.97 33.64 4.12
647 676 1.890174 CCTAAAAGCGCCTTTGGGG 59.110 57.895 22.44 15.67 33.64 4.96
648 677 1.604147 CCTAAAAGCGCCTTTGGGGG 61.604 60.000 22.44 13.58 46.78 5.40
666 695 3.096791 GCGAACAGCTGGAGATGC 58.903 61.111 19.93 10.58 44.04 3.91
667 696 1.449246 GCGAACAGCTGGAGATGCT 60.449 57.895 19.93 0.00 44.04 3.79
668 697 1.427592 GCGAACAGCTGGAGATGCTC 61.428 60.000 19.93 1.91 44.04 4.26
682 711 4.585162 GGAGATGCTCTAAGTACTTGGCTA 59.415 45.833 18.56 5.39 0.00 3.93
687 716 5.201243 TGCTCTAAGTACTTGGCTAGATCA 58.799 41.667 18.56 11.20 0.00 2.92
688 717 5.835819 TGCTCTAAGTACTTGGCTAGATCAT 59.164 40.000 18.56 0.00 0.00 2.45
690 719 7.671819 TGCTCTAAGTACTTGGCTAGATCATAT 59.328 37.037 18.56 0.00 0.00 1.78
710 740 3.323758 TTTGCCCCGATCACCCTCG 62.324 63.158 0.00 0.00 38.37 4.63
714 744 2.280389 CCCGATCACCCTCGCATG 60.280 66.667 0.00 0.00 37.33 4.06
837 867 0.396556 GGTCTCTCTCCCTCCAGACC 60.397 65.000 1.31 1.31 46.26 3.85
847 877 1.738099 CTCCAGACCCGCACTTTCG 60.738 63.158 0.00 0.00 0.00 3.46
853 893 4.394712 CCCGCACTTTCGCCTCCT 62.395 66.667 0.00 0.00 0.00 3.69
854 894 2.815647 CCGCACTTTCGCCTCCTC 60.816 66.667 0.00 0.00 0.00 3.71
993 1043 2.492090 CCTCCTCAGCTCCGAACG 59.508 66.667 0.00 0.00 0.00 3.95
994 1044 2.202676 CTCCTCAGCTCCGAACGC 60.203 66.667 0.00 0.00 0.00 4.84
1865 1925 0.531753 TAAGCTTGCTCGCACACACA 60.532 50.000 9.86 0.00 0.00 3.72
1871 1931 2.620459 CTCGCACACACACACACG 59.380 61.111 0.00 0.00 0.00 4.49
1918 2003 1.003116 CTTGCACAAGCTGACTGACAC 60.003 52.381 0.00 0.00 42.74 3.67
2176 2298 4.553429 CGAGTGGTTTTTCGCATGAATTAC 59.447 41.667 0.00 0.00 33.20 1.89
2263 2411 4.101898 TCTCCCACAAAATAGGCGCTATAA 59.898 41.667 7.64 0.00 0.00 0.98
2272 2420 1.107538 AGGCGCTATAACTGCTCGGA 61.108 55.000 7.64 0.00 0.00 4.55
2297 2445 2.684843 GCCGCTATGCTATGGCTGC 61.685 63.158 1.68 3.55 44.16 5.25
2298 2446 1.301953 CCGCTATGCTATGGCTGCA 60.302 57.895 1.68 3.31 44.95 4.41
2328 2476 3.444029 CCAAATCCTCCACAAATCCCTT 58.556 45.455 0.00 0.00 0.00 3.95
2347 2567 1.750399 CAAAGGCCTGCTATGCGGT 60.750 57.895 5.69 0.00 32.22 5.68
2362 2582 1.372251 CGGTCGCTATAGCTGCTGG 60.372 63.158 21.98 6.69 39.32 4.85
2363 2583 1.796190 CGGTCGCTATAGCTGCTGGA 61.796 60.000 21.98 8.98 39.32 3.86
2365 2585 1.202533 GGTCGCTATAGCTGCTGGAAA 60.203 52.381 21.98 0.00 39.32 3.13
2391 2613 2.010043 GCCGCTAAATCGTTTCTCCCA 61.010 52.381 0.00 0.00 0.00 4.37
2481 2709 5.979517 TCAACTACATGCTGATCGATTACTG 59.020 40.000 0.00 0.00 0.00 2.74
2710 3039 3.813166 GCACTGTGTATGTACAAGTTGGT 59.187 43.478 9.86 0.00 38.04 3.67
2731 3086 6.632909 TGGTAATCATCTTTGCAAATGAAGG 58.367 36.000 17.03 11.26 35.64 3.46
2773 3131 1.614903 TGGTGGTGACTGGTTAGTACG 59.385 52.381 0.00 0.00 37.25 3.67
2895 3285 4.397103 CACGGCCAATGATGATTATATGCT 59.603 41.667 2.24 0.00 0.00 3.79
2896 3286 4.637534 ACGGCCAATGATGATTATATGCTC 59.362 41.667 2.24 0.00 0.00 4.26
2897 3287 4.880120 CGGCCAATGATGATTATATGCTCT 59.120 41.667 2.24 0.00 0.00 4.09
2898 3288 6.051074 CGGCCAATGATGATTATATGCTCTA 58.949 40.000 2.24 0.00 0.00 2.43
2899 3289 6.539826 CGGCCAATGATGATTATATGCTCTAA 59.460 38.462 2.24 0.00 0.00 2.10
2900 3290 7.228108 CGGCCAATGATGATTATATGCTCTAAT 59.772 37.037 2.24 0.00 0.00 1.73
2901 3291 9.565090 GGCCAATGATGATTATATGCTCTAATA 57.435 33.333 0.00 0.00 0.00 0.98
3066 3460 4.202182 ACTCTTTGGTACAGTTAAGTGCGA 60.202 41.667 10.30 0.00 42.39 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 0.036765 TTTATGACGAGGTTGCCGCT 60.037 50.000 0.00 0.00 0.00 5.52
77 78 2.363361 GAGGGGAAGGGACGAGGA 59.637 66.667 0.00 0.00 0.00 3.71
80 81 4.410033 GGGGAGGGGAAGGGACGA 62.410 72.222 0.00 0.00 0.00 4.20
145 146 2.946762 GTGCTCCCGCTTCAACAC 59.053 61.111 0.00 0.00 36.97 3.32
148 149 2.048222 CTCGTGCTCCCGCTTCAA 60.048 61.111 0.00 0.00 36.97 2.69
155 156 2.185310 AACCATGTCCTCGTGCTCCC 62.185 60.000 0.00 0.00 0.00 4.30
173 174 1.138883 CCGCTCTCGATGTCGGAAA 59.861 57.895 12.26 0.00 44.23 3.13
174 175 2.798689 CCGCTCTCGATGTCGGAA 59.201 61.111 12.26 0.00 44.23 4.30
175 176 3.889044 GCCGCTCTCGATGTCGGA 61.889 66.667 19.21 0.00 44.23 4.55
209 210 4.063967 CCTGCGCCACGTAGTCCA 62.064 66.667 4.18 0.00 41.61 4.02
217 218 2.202987 CTCCATCTCCTGCGCCAC 60.203 66.667 4.18 0.00 0.00 5.01
249 250 0.179153 GCTCGGCAATTTCTTCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
306 307 0.388134 CCTCGTCGTTGTTGTCGGAT 60.388 55.000 0.00 0.00 0.00 4.18
316 317 1.359848 GATGCAATGACCTCGTCGTT 58.640 50.000 0.00 0.00 41.72 3.85
377 378 0.910088 GTCCTTCAGGGTGGCCTAGT 60.910 60.000 3.32 0.00 36.25 2.57
379 380 1.987855 CGTCCTTCAGGGTGGCCTA 60.988 63.158 3.32 0.00 36.25 3.93
417 418 1.284198 ACTACTCCTAGTTCCTCGCCA 59.716 52.381 0.00 0.00 27.62 5.69
419 420 4.453177 AAAACTACTCCTAGTTCCTCGC 57.547 45.455 0.00 0.00 41.58 5.03
421 422 6.507958 ACGTAAAACTACTCCTAGTTCCTC 57.492 41.667 0.00 0.00 41.58 3.71
423 424 7.953158 AAAACGTAAAACTACTCCTAGTTCC 57.047 36.000 0.00 0.00 41.58 3.62
480 507 8.403236 AGTTAATTTGGACGAAATATAGGCAAC 58.597 33.333 0.00 0.00 32.76 4.17
482 509 7.771361 TCAGTTAATTTGGACGAAATATAGGCA 59.229 33.333 0.00 0.00 32.76 4.75
510 537 0.719465 AAAGCGCACGGTCGATAAAG 59.281 50.000 11.47 0.00 0.00 1.85
578 607 3.064820 CGACAATAATTTCGTCTTGGGGG 59.935 47.826 0.00 0.00 0.00 5.40
579 608 3.064820 CCGACAATAATTTCGTCTTGGGG 59.935 47.826 0.00 0.00 33.23 4.96
580 609 3.486875 GCCGACAATAATTTCGTCTTGGG 60.487 47.826 0.00 0.00 33.23 4.12
581 610 3.126171 TGCCGACAATAATTTCGTCTTGG 59.874 43.478 0.00 0.00 33.23 3.61
582 611 4.335082 TGCCGACAATAATTTCGTCTTG 57.665 40.909 0.00 0.00 33.23 3.02
583 612 5.448632 GGATTGCCGACAATAATTTCGTCTT 60.449 40.000 0.00 0.00 46.59 3.01
584 613 4.035208 GGATTGCCGACAATAATTTCGTCT 59.965 41.667 0.00 0.00 46.59 4.18
585 614 4.035208 AGGATTGCCGACAATAATTTCGTC 59.965 41.667 0.00 0.00 46.59 4.20
586 615 3.945285 AGGATTGCCGACAATAATTTCGT 59.055 39.130 0.00 0.00 46.59 3.85
587 616 4.273480 AGAGGATTGCCGACAATAATTTCG 59.727 41.667 0.00 0.00 46.59 3.46
588 617 5.757850 AGAGGATTGCCGACAATAATTTC 57.242 39.130 0.00 0.00 46.59 2.17
589 618 7.054124 TCTTAGAGGATTGCCGACAATAATTT 58.946 34.615 0.00 0.00 46.59 1.82
590 619 6.591935 TCTTAGAGGATTGCCGACAATAATT 58.408 36.000 0.00 0.00 46.59 1.40
591 620 6.174720 TCTTAGAGGATTGCCGACAATAAT 57.825 37.500 0.00 0.00 46.59 1.28
592 621 5.601662 CTCTTAGAGGATTGCCGACAATAA 58.398 41.667 0.41 0.00 46.59 1.40
593 622 5.201713 CTCTTAGAGGATTGCCGACAATA 57.798 43.478 0.41 0.00 46.59 1.90
595 624 3.526931 CTCTTAGAGGATTGCCGACAA 57.473 47.619 0.41 0.00 40.87 3.18
607 636 2.034507 CGAAAAATCGCGCCTCTTAGAG 60.035 50.000 0.00 1.56 0.00 2.43
608 637 1.924524 CGAAAAATCGCGCCTCTTAGA 59.075 47.619 0.00 0.00 0.00 2.10
609 638 2.353257 CGAAAAATCGCGCCTCTTAG 57.647 50.000 0.00 0.00 0.00 2.18
628 657 1.215382 CCCAAAGGCGCTTTTAGGC 59.785 57.895 17.71 0.00 30.60 3.93
629 658 1.604147 CCCCCAAAGGCGCTTTTAGG 61.604 60.000 20.00 20.00 30.60 2.69
630 659 1.890174 CCCCCAAAGGCGCTTTTAG 59.110 57.895 17.71 10.38 30.60 1.85
631 660 4.105388 CCCCCAAAGGCGCTTTTA 57.895 55.556 17.71 0.00 30.60 1.52
645 674 4.785453 CTCCAGCTGTTCGCCCCC 62.785 72.222 13.81 0.00 40.39 5.40
646 675 3.036429 ATCTCCAGCTGTTCGCCCC 62.036 63.158 13.81 0.00 40.39 5.80
647 676 1.817099 CATCTCCAGCTGTTCGCCC 60.817 63.158 13.81 0.00 40.39 6.13
648 677 2.467826 GCATCTCCAGCTGTTCGCC 61.468 63.158 13.81 0.00 40.39 5.54
649 678 1.427592 GAGCATCTCCAGCTGTTCGC 61.428 60.000 13.81 7.78 43.58 4.70
650 679 2.675519 GAGCATCTCCAGCTGTTCG 58.324 57.895 13.81 0.00 43.58 3.95
662 691 5.776173 TCTAGCCAAGTACTTAGAGCATC 57.224 43.478 20.34 0.00 0.00 3.91
663 692 5.835819 TGATCTAGCCAAGTACTTAGAGCAT 59.164 40.000 16.37 7.40 0.00 3.79
664 693 5.201243 TGATCTAGCCAAGTACTTAGAGCA 58.799 41.667 16.37 16.37 0.00 4.26
665 694 5.776173 TGATCTAGCCAAGTACTTAGAGC 57.224 43.478 8.04 10.74 0.00 4.09
666 695 9.019656 ACATATGATCTAGCCAAGTACTTAGAG 57.980 37.037 10.38 3.63 0.00 2.43
667 696 8.941995 ACATATGATCTAGCCAAGTACTTAGA 57.058 34.615 10.38 8.01 0.00 2.10
668 697 9.988815 AAACATATGATCTAGCCAAGTACTTAG 57.011 33.333 10.38 1.59 0.00 2.18
682 711 3.072915 TGATCGGGGCAAACATATGATCT 59.927 43.478 10.38 0.00 33.64 2.75
687 716 1.478654 GGGTGATCGGGGCAAACATAT 60.479 52.381 0.00 0.00 0.00 1.78
688 717 0.106918 GGGTGATCGGGGCAAACATA 60.107 55.000 0.00 0.00 0.00 2.29
690 719 2.034999 GGGTGATCGGGGCAAACA 59.965 61.111 0.00 0.00 0.00 2.83
837 867 2.788191 AAGAGGAGGCGAAAGTGCGG 62.788 60.000 0.00 0.00 35.06 5.69
847 877 0.808060 GCGCTAGTTGAAGAGGAGGC 60.808 60.000 0.00 0.00 0.00 4.70
993 1043 2.283101 TGGTTGTCCATGCCTGGC 60.283 61.111 12.87 12.87 42.80 4.85
994 1044 2.345760 GCTGGTTGTCCATGCCTGG 61.346 63.158 0.78 0.78 43.43 4.45
1042 1092 1.305219 CCATTGGCCGCGAAGAAAGA 61.305 55.000 8.23 0.00 0.00 2.52
1585 1643 0.846870 CTTCTTGGGGTCCCCTCCTT 60.847 60.000 28.11 0.00 45.70 3.36
1865 1925 0.818938 TGATATGTACGCCCGTGTGT 59.181 50.000 3.22 0.00 39.01 3.72
1871 1931 4.273148 AGAGGAATTGATATGTACGCCC 57.727 45.455 0.00 0.00 0.00 6.13
1923 2008 0.612229 TTCTCCTTCAGCCTCAGCAG 59.388 55.000 0.00 0.00 43.56 4.24
2065 2159 1.874345 GCAGGTTCCCGTCGAGAAGA 61.874 60.000 0.00 0.00 0.00 2.87
2121 2215 3.461773 CAGGTCATCGTCCGGCCT 61.462 66.667 0.00 0.00 0.00 5.19
2176 2298 3.978687 CGTAGCCACCATAAACTCTAGG 58.021 50.000 0.00 0.00 0.00 3.02
2272 2420 1.821061 ATAGCATAGCGGCGAGGCTT 61.821 55.000 25.71 11.97 41.39 4.35
2297 2445 4.573950 GGATTTGGCGGCGGCATG 62.574 66.667 36.43 0.00 42.47 4.06
2298 2446 4.820744 AGGATTTGGCGGCGGCAT 62.821 61.111 36.43 23.43 42.47 4.40
2328 2476 1.451927 CCGCATAGCAGGCCTTTGA 60.452 57.895 0.00 0.00 0.00 2.69
2362 2582 0.248498 GATTTAGCGGCGGCCTTTTC 60.248 55.000 18.34 3.47 41.24 2.29
2363 2583 1.807226 GATTTAGCGGCGGCCTTTT 59.193 52.632 18.34 4.75 41.24 2.27
2365 2585 2.895372 CGATTTAGCGGCGGCCTT 60.895 61.111 18.34 7.79 41.24 4.35
2374 2596 2.613691 TCGTGGGAGAAACGATTTAGC 58.386 47.619 0.00 0.00 44.58 3.09
2391 2613 8.364894 AGGCTAAAAACCAAAGATTAAAATCGT 58.635 29.630 0.00 0.00 40.35 3.73
2662 2989 6.228258 TCACTAAGAAGACAATTTACGGCTT 58.772 36.000 0.00 0.00 0.00 4.35
2710 3039 7.707624 AGACCTTCATTTGCAAAGATGATTA 57.292 32.000 18.19 2.94 32.73 1.75
2731 3086 9.888878 CACCAACATCATCATCAATATTTAGAC 57.111 33.333 0.00 0.00 0.00 2.59
2814 3172 8.577048 TTTACCAAAACCAACGGATAATCATA 57.423 30.769 0.00 0.00 0.00 2.15
2823 3181 6.258947 ACATTCATTTTTACCAAAACCAACGG 59.741 34.615 0.00 0.00 34.63 4.44
2852 3211 6.158598 CCGTGAAAAATGTCATCCTTTTGAT 58.841 36.000 0.89 0.00 0.00 2.57
2904 3294 9.705290 AAGGGCTAATTAACATACAAAACTTTG 57.295 29.630 0.60 0.60 43.62 2.77
2905 3295 9.705290 CAAGGGCTAATTAACATACAAAACTTT 57.295 29.630 0.00 0.00 0.00 2.66
2906 3296 8.866093 ACAAGGGCTAATTAACATACAAAACTT 58.134 29.630 0.00 0.00 0.00 2.66
2907 3297 8.303876 CACAAGGGCTAATTAACATACAAAACT 58.696 33.333 0.00 0.00 0.00 2.66
2908 3298 8.085909 ACACAAGGGCTAATTAACATACAAAAC 58.914 33.333 0.00 0.00 0.00 2.43
2909 3299 8.184304 ACACAAGGGCTAATTAACATACAAAA 57.816 30.769 0.00 0.00 0.00 2.44
2910 3300 7.768807 ACACAAGGGCTAATTAACATACAAA 57.231 32.000 0.00 0.00 0.00 2.83
2911 3301 7.668052 AGAACACAAGGGCTAATTAACATACAA 59.332 33.333 0.00 0.00 0.00 2.41
2912 3302 7.172342 AGAACACAAGGGCTAATTAACATACA 58.828 34.615 0.00 0.00 0.00 2.29
2913 3303 7.625828 AGAACACAAGGGCTAATTAACATAC 57.374 36.000 0.00 0.00 0.00 2.39
2914 3304 9.914834 ATTAGAACACAAGGGCTAATTAACATA 57.085 29.630 0.00 0.00 31.45 2.29
2915 3305 8.823220 ATTAGAACACAAGGGCTAATTAACAT 57.177 30.769 0.00 0.00 31.45 2.71
2916 3306 9.914834 ATATTAGAACACAAGGGCTAATTAACA 57.085 29.630 0.00 0.00 35.71 2.41
2922 3312 9.969001 AAAGTTATATTAGAACACAAGGGCTAA 57.031 29.630 4.18 0.00 0.00 3.09
2923 3313 9.391006 CAAAGTTATATTAGAACACAAGGGCTA 57.609 33.333 4.18 0.00 0.00 3.93
2924 3314 7.888546 ACAAAGTTATATTAGAACACAAGGGCT 59.111 33.333 4.18 0.00 0.00 5.19
2925 3315 8.051901 ACAAAGTTATATTAGAACACAAGGGC 57.948 34.615 4.18 0.00 0.00 5.19
3066 3460 0.174389 CCATGTACGCTCTGCAGTCT 59.826 55.000 14.67 0.00 0.00 3.24
3112 3506 8.365399 TCATATATTTTGCGACCAGTTCTTAG 57.635 34.615 0.00 0.00 0.00 2.18


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

AutoCloner maintained by Alex Coulton.