Multiple sequence alignment - TraesCS2A01G107300

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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 TraesCS2A01G107300 chr2A 100.000 3553 0 0 1 3553 59716487 59720039 0.000000e+00 6562.0
1 TraesCS2A01G107300 chr2A 90.123 972 84 9 1655 2620 60760306 60759341 0.000000e+00 1253.0
2 TraesCS2A01G107300 chr2A 90.021 972 85 10 1655 2620 60283558 60282593 0.000000e+00 1247.0
3 TraesCS2A01G107300 chr2A 91.081 370 23 6 883 1243 60284132 60283764 3.190000e-135 492.0
4 TraesCS2A01G107300 chr2A 81.982 555 77 14 686 1221 60761488 60760938 1.950000e-122 449.0
5 TraesCS2A01G107300 chr2A 78.626 393 74 7 2161 2551 60068518 60068134 5.890000e-63 252.0
6 TraesCS2A01G107300 chr2A 77.672 421 69 20 2142 2551 59879969 59879563 2.130000e-57 233.0
7 TraesCS2A01G107300 chr2A 96.226 106 2 2 781 886 59706533 59706636 4.720000e-39 172.0
8 TraesCS2A01G107300 chr2A 89.062 64 3 1 2640 2699 60282592 60282529 3.800000e-10 76.8
9 TraesCS2A01G107300 chr2A 89.062 64 3 1 2640 2699 60759340 60759277 3.800000e-10 76.8
10 TraesCS2A01G107300 chr2D 92.757 2140 118 21 683 2810 59723603 59725717 0.000000e+00 3059.0
11 TraesCS2A01G107300 chr2D 90.731 971 80 8 1655 2620 60167048 60166083 0.000000e+00 1286.0
12 TraesCS2A01G107300 chr2D 92.868 659 31 8 2245 2894 59836615 59837266 0.000000e+00 942.0
13 TraesCS2A01G107300 chr2D 92.629 502 37 0 948 1449 59835318 59835819 0.000000e+00 723.0
14 TraesCS2A01G107300 chr2D 82.444 581 75 18 686 1243 60167916 60167340 1.920000e-132 483.0
15 TraesCS2A01G107300 chr2D 96.654 269 7 2 683 950 59830540 59830807 2.520000e-121 446.0
16 TraesCS2A01G107300 chr2D 90.244 287 24 3 1655 1939 59836260 59836544 4.330000e-99 372.0
17 TraesCS2A01G107300 chr2D 78.592 355 49 16 2565 2908 60164201 60163863 3.590000e-50 209.0
18 TraesCS2A01G107300 chr2D 89.381 113 7 3 1560 1669 59836135 59836245 1.720000e-28 137.0
19 TraesCS2A01G107300 chr2D 100.000 42 0 0 1323 1364 59724372 59724413 1.060000e-10 78.7
20 TraesCS2A01G107300 chr2B 92.643 1237 70 16 1667 2888 93408784 93410014 0.000000e+00 1760.0
21 TraesCS2A01G107300 chr2B 93.094 1115 68 7 1779 2888 93109161 93110271 0.000000e+00 1624.0
22 TraesCS2A01G107300 chr2B 90.363 965 84 5 1661 2620 94089962 94089002 0.000000e+00 1258.0
23 TraesCS2A01G107300 chr2B 88.900 1018 93 13 1614 2620 94251153 94250145 0.000000e+00 1236.0
24 TraesCS2A01G107300 chr2B 89.282 905 89 5 1658 2558 94099378 94098478 0.000000e+00 1127.0
25 TraesCS2A01G107300 chr2B 92.720 783 52 3 683 1463 93407779 93408558 0.000000e+00 1125.0
26 TraesCS2A01G107300 chr2B 93.230 709 36 7 683 1391 93108155 93108851 0.000000e+00 1033.0
27 TraesCS2A01G107300 chr2B 88.539 349 28 6 882 1219 94251864 94251517 2.550000e-111 412.0
28 TraesCS2A01G107300 chr2B 82.117 274 32 9 924 1186 94101827 94101560 5.970000e-53 219.0
29 TraesCS2A01G107300 chr2B 89.062 64 3 1 2640 2699 94089001 94088938 3.800000e-10 76.8
30 TraesCS2A01G107300 chr2B 89.062 64 3 1 2640 2699 94250144 94250081 3.800000e-10 76.8
31 TraesCS2A01G107300 chr3D 92.151 688 33 9 3 686 268156089 268155419 0.000000e+00 952.0
32 TraesCS2A01G107300 chr3D 85.843 664 85 7 2898 3553 508401325 508400663 0.000000e+00 697.0
33 TraesCS2A01G107300 chr3D 90.254 236 22 1 274 508 446093589 446093354 1.240000e-79 307.0
34 TraesCS2A01G107300 chr3D 83.860 285 36 7 2 284 446094202 446093926 2.720000e-66 263.0
35 TraesCS2A01G107300 chr7A 90.592 659 58 3 2898 3553 118333676 118334333 0.000000e+00 870.0
36 TraesCS2A01G107300 chr7A 87.764 662 73 7 2898 3553 595049340 595048681 0.000000e+00 767.0
37 TraesCS2A01G107300 chr7A 85.129 659 94 3 2898 3552 397780101 397780759 0.000000e+00 671.0
38 TraesCS2A01G107300 chr7A 83.942 685 79 17 2898 3553 207293112 207292430 8.370000e-176 627.0
39 TraesCS2A01G107300 chr7A 83.535 662 73 18 2898 3553 80567520 80566889 1.420000e-163 586.0
40 TraesCS2A01G107300 chr3A 88.182 660 73 4 2898 3553 158166342 158165684 0.000000e+00 782.0
41 TraesCS2A01G107300 chr3A 87.451 510 55 6 2 508 655989854 655990357 2.380000e-161 579.0
42 TraesCS2A01G107300 chr1D 89.280 625 54 2 2929 3553 405280411 405279800 0.000000e+00 771.0
43 TraesCS2A01G107300 chrUn 86.098 633 79 6 2929 3553 98221190 98220559 0.000000e+00 673.0
44 TraesCS2A01G107300 chrUn 88.696 115 13 0 2 116 455086617 455086503 1.330000e-29 141.0
45 TraesCS2A01G107300 chr1A 88.743 533 58 2 3022 3553 513929364 513929895 0.000000e+00 651.0
46 TraesCS2A01G107300 chr7D 83.560 663 100 6 2898 3553 7700162 7700822 2.340000e-171 612.0
47 TraesCS2A01G107300 chr7D 87.887 388 33 8 285 660 34962033 34962418 9.050000e-121 444.0
48 TraesCS2A01G107300 chr4D 82.867 572 84 8 2 566 145943890 145944454 5.300000e-138 501.0
49 TraesCS2A01G107300 chr4A 82.723 573 84 9 2 566 156794998 156794433 2.460000e-136 496.0
50 TraesCS2A01G107300 chr4A 81.913 575 84 10 2 566 326063676 326063112 5.370000e-128 468.0
51 TraesCS2A01G107300 chr4A 77.297 185 40 2 1038 1221 191375780 191375963 1.350000e-19 108.0
52 TraesCS2A01G107300 chr7B 82.278 79 12 2 2461 2538 22436935 22437012 2.290000e-07 67.6


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 TraesCS2A01G107300 chr2A 59716487 59720039 3552 False 6562.000000 6562 100.000000 1 3553 1 chr2A.!!$F2 3552
1 TraesCS2A01G107300 chr2A 60282529 60284132 1603 True 605.266667 1247 90.054667 883 2699 3 chr2A.!!$R3 1816
2 TraesCS2A01G107300 chr2A 60759277 60761488 2211 True 592.933333 1253 87.055667 686 2699 3 chr2A.!!$R4 2013
3 TraesCS2A01G107300 chr2D 59723603 59725717 2114 False 1568.850000 3059 96.378500 683 2810 2 chr2D.!!$F2 2127
4 TraesCS2A01G107300 chr2D 60163863 60167916 4053 True 659.333333 1286 83.922333 686 2908 3 chr2D.!!$R1 2222
5 TraesCS2A01G107300 chr2D 59835318 59837266 1948 False 543.500000 942 91.280500 948 2894 4 chr2D.!!$F3 1946
6 TraesCS2A01G107300 chr2B 93407779 93410014 2235 False 1442.500000 1760 92.681500 683 2888 2 chr2B.!!$F2 2205
7 TraesCS2A01G107300 chr2B 93108155 93110271 2116 False 1328.500000 1624 93.162000 683 2888 2 chr2B.!!$F1 2205
8 TraesCS2A01G107300 chr2B 94098478 94101827 3349 True 673.000000 1127 85.699500 924 2558 2 chr2B.!!$R2 1634
9 TraesCS2A01G107300 chr2B 94088938 94089962 1024 True 667.400000 1258 89.712500 1661 2699 2 chr2B.!!$R1 1038
10 TraesCS2A01G107300 chr2B 94250081 94251864 1783 True 574.933333 1236 88.833667 882 2699 3 chr2B.!!$R3 1817
11 TraesCS2A01G107300 chr3D 268155419 268156089 670 True 952.000000 952 92.151000 3 686 1 chr3D.!!$R1 683
12 TraesCS2A01G107300 chr3D 508400663 508401325 662 True 697.000000 697 85.843000 2898 3553 1 chr3D.!!$R2 655
13 TraesCS2A01G107300 chr3D 446093354 446094202 848 True 285.000000 307 87.057000 2 508 2 chr3D.!!$R3 506
14 TraesCS2A01G107300 chr7A 118333676 118334333 657 False 870.000000 870 90.592000 2898 3553 1 chr7A.!!$F1 655
15 TraesCS2A01G107300 chr7A 595048681 595049340 659 True 767.000000 767 87.764000 2898 3553 1 chr7A.!!$R3 655
16 TraesCS2A01G107300 chr7A 397780101 397780759 658 False 671.000000 671 85.129000 2898 3552 1 chr7A.!!$F2 654
17 TraesCS2A01G107300 chr7A 207292430 207293112 682 True 627.000000 627 83.942000 2898 3553 1 chr7A.!!$R2 655
18 TraesCS2A01G107300 chr7A 80566889 80567520 631 True 586.000000 586 83.535000 2898 3553 1 chr7A.!!$R1 655
19 TraesCS2A01G107300 chr3A 158165684 158166342 658 True 782.000000 782 88.182000 2898 3553 1 chr3A.!!$R1 655
20 TraesCS2A01G107300 chr3A 655989854 655990357 503 False 579.000000 579 87.451000 2 508 1 chr3A.!!$F1 506
21 TraesCS2A01G107300 chr1D 405279800 405280411 611 True 771.000000 771 89.280000 2929 3553 1 chr1D.!!$R1 624
22 TraesCS2A01G107300 chrUn 98220559 98221190 631 True 673.000000 673 86.098000 2929 3553 1 chrUn.!!$R1 624
23 TraesCS2A01G107300 chr1A 513929364 513929895 531 False 651.000000 651 88.743000 3022 3553 1 chr1A.!!$F1 531
24 TraesCS2A01G107300 chr7D 7700162 7700822 660 False 612.000000 612 83.560000 2898 3553 1 chr7D.!!$F1 655
25 TraesCS2A01G107300 chr4D 145943890 145944454 564 False 501.000000 501 82.867000 2 566 1 chr4D.!!$F1 564
26 TraesCS2A01G107300 chr4A 156794433 156794998 565 True 496.000000 496 82.723000 2 566 1 chr4A.!!$R1 564
27 TraesCS2A01G107300 chr4A 326063112 326063676 564 True 468.000000 468 81.913000 2 566 1 chr4A.!!$R2 564

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
254 266 0.239347 AGCAGCTTTGATTCGCACAC 59.761 50.000 0.0 0.0 0.0 3.82 F
603 974 2.668144 TGAAAGAACCCAAACCCGAT 57.332 45.000 0.0 0.0 0.0 4.18 F
1743 4867 1.801913 CGTACTGCTGAGCGACACC 60.802 63.158 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1494 3546 0.03759 AGCGGGGCAACAAGAACATA 59.962 50.0 0.00 0.00 39.74 2.29 R
1794 4964 0.03779 TGTCGATGACGTTCATGCCA 60.038 50.0 5.41 0.00 37.20 4.92 R
2988 8148 0.37441 GTTTCCCGCGCGCTAATTTA 59.626 50.0 30.48 7.06 0.00 1.40 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
123 135 6.176183 GCAATGCCTGAGTAATACTGGATAT 58.824 40.000 0.00 0.00 0.00 1.63
124 136 6.314896 GCAATGCCTGAGTAATACTGGATATC 59.685 42.308 0.00 0.00 0.00 1.63
125 137 5.644977 TGCCTGAGTAATACTGGATATCG 57.355 43.478 0.00 0.00 0.00 2.92
126 138 5.321927 TGCCTGAGTAATACTGGATATCGA 58.678 41.667 0.00 0.00 0.00 3.59
127 139 5.773176 TGCCTGAGTAATACTGGATATCGAA 59.227 40.000 0.00 0.00 0.00 3.71
128 140 6.266786 TGCCTGAGTAATACTGGATATCGAAA 59.733 38.462 0.00 0.00 0.00 3.46
142 154 6.127168 TGGATATCGAAATAGTGTCACCAAGT 60.127 38.462 0.00 0.00 0.00 3.16
245 257 4.720649 ACTACTTATCGAGCAGCTTTGA 57.279 40.909 0.00 0.00 0.00 2.69
254 266 0.239347 AGCAGCTTTGATTCGCACAC 59.761 50.000 0.00 0.00 0.00 3.82
255 267 0.239347 GCAGCTTTGATTCGCACACT 59.761 50.000 0.00 0.00 0.00 3.55
298 657 9.243637 GTTTATAGTCAATGCAAGAACAAACAA 57.756 29.630 0.00 0.00 0.00 2.83
338 697 6.863126 GCTAAATCAAGCACTGCTAAAGAAAA 59.137 34.615 3.33 0.00 42.30 2.29
510 881 8.669243 CAAAAAGGAGTAGAACATAATCCTGAC 58.331 37.037 4.79 0.00 40.68 3.51
528 899 5.815222 TCCTGACATTTGAACCATGTATACG 59.185 40.000 0.00 0.00 34.89 3.06
542 913 8.867112 ACCATGTATACGTTACACATAAGAAG 57.133 34.615 11.16 0.78 31.81 2.85
566 937 5.590259 GTGCCAGACAACTGATAATACCAAT 59.410 40.000 0.00 0.00 46.03 3.16
600 971 5.029807 TCAATTTGAAAGAACCCAAACCC 57.970 39.130 0.00 0.00 35.42 4.11
603 974 2.668144 TGAAAGAACCCAAACCCGAT 57.332 45.000 0.00 0.00 0.00 4.18
627 998 9.982651 GATAGCTCACTTGGTAAATAACTGATA 57.017 33.333 0.00 0.00 0.00 2.15
719 1090 5.339008 ACGATAATTCTGAGCTTGTGGTA 57.661 39.130 0.00 0.00 0.00 3.25
818 1189 6.499350 ACCATACCAACCGTACTATATCCATT 59.501 38.462 0.00 0.00 0.00 3.16
833 1231 9.799106 ACTATATCCATTCTCCAACCAAAATAG 57.201 33.333 0.00 0.00 0.00 1.73
914 1312 8.725405 TGAAATTTGTCAGCTATATAAACGGA 57.275 30.769 0.00 0.00 0.00 4.69
1463 3515 9.967451 TCGATAATCCTAGATCTAAGAATGACT 57.033 33.333 5.16 0.00 0.00 3.41
1467 3519 7.775053 ATCCTAGATCTAAGAATGACTCACC 57.225 40.000 5.16 0.00 0.00 4.02
1469 3521 8.046867 TCCTAGATCTAAGAATGACTCACCTA 57.953 38.462 3.57 0.00 0.00 3.08
1470 3522 7.940137 TCCTAGATCTAAGAATGACTCACCTAC 59.060 40.741 3.57 0.00 0.00 3.18
1472 3524 6.678547 AGATCTAAGAATGACTCACCTACCT 58.321 40.000 0.00 0.00 0.00 3.08
1473 3525 7.817440 AGATCTAAGAATGACTCACCTACCTA 58.183 38.462 0.00 0.00 0.00 3.08
1474 3526 7.722285 AGATCTAAGAATGACTCACCTACCTAC 59.278 40.741 0.00 0.00 0.00 3.18
1475 3527 6.728411 TCTAAGAATGACTCACCTACCTACA 58.272 40.000 0.00 0.00 0.00 2.74
1476 3528 5.923733 AAGAATGACTCACCTACCTACAG 57.076 43.478 0.00 0.00 0.00 2.74
1477 3529 4.282496 AGAATGACTCACCTACCTACAGG 58.718 47.826 0.00 0.00 41.87 4.00
1494 3546 7.613551 CCTACAGGTTAACATACCTTCCTAT 57.386 40.000 8.10 0.00 46.39 2.57
1495 3547 8.716674 CCTACAGGTTAACATACCTTCCTATA 57.283 38.462 8.10 0.00 46.39 1.31
1496 3548 9.322769 CCTACAGGTTAACATACCTTCCTATAT 57.677 37.037 8.10 0.00 46.39 0.86
1498 3550 8.562949 ACAGGTTAACATACCTTCCTATATGT 57.437 34.615 8.10 0.00 46.39 2.29
1499 3551 8.999895 ACAGGTTAACATACCTTCCTATATGTT 58.000 33.333 8.10 12.71 46.39 2.71
1500 3552 9.490379 CAGGTTAACATACCTTCCTATATGTTC 57.510 37.037 11.74 1.56 46.39 3.18
1501 3553 9.448587 AGGTTAACATACCTTCCTATATGTTCT 57.551 33.333 11.74 3.05 46.39 3.01
1644 4643 9.226345 GTGACTTTTCAGTTCAAATCAACTAAG 57.774 33.333 0.00 0.00 34.70 2.18
1697 4815 7.095397 CGGAAGTAATTTCTTATGTGTGTGACA 60.095 37.037 0.00 0.00 36.05 3.58
1743 4867 1.801913 CGTACTGCTGAGCGACACC 60.802 63.158 0.00 0.00 0.00 4.16
1794 4964 2.358247 AACGCCGGCTCAATTCGT 60.358 55.556 26.68 10.27 34.63 3.85
2480 5657 4.424711 TTCAGGGCGGCCATGGTC 62.425 66.667 30.78 10.70 35.84 4.02
2631 5822 9.371136 AGTTATTGTACTTGTACTGATCATGTG 57.629 33.333 11.53 0.00 0.00 3.21
2699 5894 4.406648 TGGAGTGTCATGTGATGTATCC 57.593 45.455 0.00 0.00 0.00 2.59
2731 7876 2.175811 GCCGTCGTGCAAATGGAC 59.824 61.111 11.84 5.76 0.00 4.02
2774 7923 6.147864 TCTTTGCTTATTAATCATGCCCAC 57.852 37.500 0.00 0.00 0.00 4.61
2785 7934 2.093890 TCATGCCCACTTGCACATAAG 58.906 47.619 0.00 0.00 45.48 1.73
2864 8017 3.740397 CACACCACCATGCGGCAG 61.740 66.667 9.25 0.00 34.57 4.85
2888 8042 6.713903 AGATCATATGGAATGATTTCAACGCT 59.286 34.615 2.13 0.00 38.73 5.07
2891 8045 7.864686 TCATATGGAATGATTTCAACGCTTAG 58.135 34.615 2.13 0.00 33.23 2.18
2894 8048 4.094887 TGGAATGATTTCAACGCTTAGAGC 59.905 41.667 0.00 0.00 33.93 4.09
2895 8049 4.094887 GGAATGATTTCAACGCTTAGAGCA 59.905 41.667 0.50 0.00 35.75 4.26
2896 8050 5.220931 GGAATGATTTCAACGCTTAGAGCAT 60.221 40.000 0.50 0.00 35.75 3.79
2943 8103 0.108898 GCATGCGTGGTAAATTGGCA 60.109 50.000 8.27 0.00 38.09 4.92
3086 8269 1.003972 GCGCGTCTATAAATTGCAGCA 60.004 47.619 8.43 0.00 0.00 4.41
3092 8296 3.565902 GTCTATAAATTGCAGCACCCTCC 59.434 47.826 0.00 0.00 0.00 4.30
3346 8560 1.697754 CCTGTGGCCCCCTTAGGAT 60.698 63.158 0.00 0.00 38.24 3.24
3535 8755 2.093128 AGACACCAACGAGGAACAGTTT 60.093 45.455 5.70 0.00 41.22 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 4.568359 CACTCAGATGATTTTGTCGGTAGG 59.432 45.833 0.00 0.00 0.00 3.18
123 135 4.330944 ACACTTGGTGACACTATTTCGA 57.669 40.909 5.39 0.00 42.67 3.71
124 136 5.466819 TCTACACTTGGTGACACTATTTCG 58.533 41.667 5.39 0.00 42.67 3.46
125 137 7.225931 TGTTTCTACACTTGGTGACACTATTTC 59.774 37.037 5.39 0.00 42.67 2.17
126 138 7.051623 TGTTTCTACACTTGGTGACACTATTT 58.948 34.615 5.39 0.00 42.67 1.40
127 139 6.588204 TGTTTCTACACTTGGTGACACTATT 58.412 36.000 5.39 0.00 42.67 1.73
128 140 6.041637 TCTGTTTCTACACTTGGTGACACTAT 59.958 38.462 5.39 0.00 42.67 2.12
142 154 6.646267 ACCAACTTAAGTGTCTGTTTCTACA 58.354 36.000 9.34 0.00 0.00 2.74
234 246 0.518636 TGTGCGAATCAAAGCTGCTC 59.481 50.000 1.00 0.00 0.00 4.26
254 266 9.756571 ACTATAAACCCTACTCACTATGGATAG 57.243 37.037 0.00 0.00 36.46 2.08
255 267 9.750783 GACTATAAACCCTACTCACTATGGATA 57.249 37.037 0.00 0.00 0.00 2.59
298 657 8.139989 GCTTGATTTAGCCATATGTTTCTCAAT 58.860 33.333 1.24 0.02 35.06 2.57
338 697 5.355670 ACATAGGAGGGGTCATACTATGT 57.644 43.478 10.55 10.55 45.46 2.29
510 881 7.744059 TGTGTAACGTATACATGGTTCAAATG 58.256 34.615 11.81 0.00 42.39 2.32
528 899 4.994852 TGTCTGGCACTTCTTATGTGTAAC 59.005 41.667 0.00 0.00 37.70 2.50
542 913 4.513442 TGGTATTATCAGTTGTCTGGCAC 58.487 43.478 0.00 0.00 41.59 5.01
600 971 6.978659 TCAGTTATTTACCAAGTGAGCTATCG 59.021 38.462 0.00 0.00 31.88 2.92
627 998 9.488762 TGATATACATCCCTCGAGGTAAATAAT 57.511 33.333 29.25 16.79 38.65 1.28
639 1010 8.787852 GGAAAAATGACTTGATATACATCCCTC 58.212 37.037 0.00 0.00 0.00 4.30
668 1039 6.545666 TCACCAAATTGTGTCATACTTCTGTT 59.454 34.615 0.00 0.00 37.51 3.16
719 1090 1.896122 GCTAGGGTTGTGGTAGCGGT 61.896 60.000 0.00 0.00 30.50 5.68
818 1189 5.568023 CGGTACTGTCTATTTTGGTTGGAGA 60.568 44.000 0.00 0.00 0.00 3.71
833 1231 2.450609 ACATGACAACCGGTACTGTC 57.549 50.000 25.95 25.95 41.93 3.51
914 1312 6.233434 CCTGCATTACCATGACTACATACAT 58.767 40.000 0.00 0.00 35.09 2.29
1375 3390 2.829720 AGTGATCCACGCCACTAACTTA 59.170 45.455 0.00 0.00 41.38 2.24
1481 3533 7.499232 GCAACAAGAACATATAGGAAGGTATGT 59.501 37.037 0.00 0.00 41.85 2.29
1482 3534 7.041098 GGCAACAAGAACATATAGGAAGGTATG 60.041 40.741 0.00 0.00 35.08 2.39
1483 3535 6.998673 GGCAACAAGAACATATAGGAAGGTAT 59.001 38.462 0.00 0.00 0.00 2.73
1484 3536 6.354130 GGCAACAAGAACATATAGGAAGGTA 58.646 40.000 0.00 0.00 0.00 3.08
1485 3537 5.193679 GGCAACAAGAACATATAGGAAGGT 58.806 41.667 0.00 0.00 0.00 3.50
1486 3538 4.580580 GGGCAACAAGAACATATAGGAAGG 59.419 45.833 0.00 0.00 39.74 3.46
1488 3540 4.532834 GGGGCAACAAGAACATATAGGAA 58.467 43.478 0.00 0.00 39.74 3.36
1489 3541 3.433031 CGGGGCAACAAGAACATATAGGA 60.433 47.826 0.00 0.00 39.74 2.94
1490 3542 2.878406 CGGGGCAACAAGAACATATAGG 59.122 50.000 0.00 0.00 39.74 2.57
1491 3543 2.290641 GCGGGGCAACAAGAACATATAG 59.709 50.000 0.00 0.00 39.74 1.31
1493 3545 1.102978 GCGGGGCAACAAGAACATAT 58.897 50.000 0.00 0.00 39.74 1.78
1494 3546 0.037590 AGCGGGGCAACAAGAACATA 59.962 50.000 0.00 0.00 39.74 2.29
1495 3547 0.037590 TAGCGGGGCAACAAGAACAT 59.962 50.000 0.00 0.00 39.74 2.71
1496 3548 0.887387 GTAGCGGGGCAACAAGAACA 60.887 55.000 0.00 0.00 39.74 3.18
1497 3549 1.873863 GTAGCGGGGCAACAAGAAC 59.126 57.895 0.00 0.00 39.74 3.01
1498 3550 1.669760 CGTAGCGGGGCAACAAGAA 60.670 57.895 0.00 0.00 39.74 2.52
1499 3551 1.534336 TACGTAGCGGGGCAACAAGA 61.534 55.000 0.00 0.00 39.74 3.02
1500 3552 0.671163 TTACGTAGCGGGGCAACAAG 60.671 55.000 0.00 0.00 39.74 3.16
1501 3553 0.250209 TTTACGTAGCGGGGCAACAA 60.250 50.000 0.00 0.00 39.74 2.83
1540 3592 7.865385 GTCTAAAGAGGAGTAATGCTACATCTG 59.135 40.741 0.00 0.00 0.00 2.90
1644 4643 8.519526 TCAACACAAATTCAGTACATTATTCCC 58.480 33.333 0.00 0.00 0.00 3.97
1697 4815 1.170919 GCAGCCCTGATGCATCGATT 61.171 55.000 21.34 2.98 44.90 3.34
1788 4958 1.518325 TGACGTTCATGCCACGAATT 58.482 45.000 20.19 2.30 40.20 2.17
1794 4964 0.037790 TGTCGATGACGTTCATGCCA 60.038 50.000 5.41 0.00 37.20 4.92
1900 5070 1.658673 GCCGGATCGATCTTACGGT 59.341 57.895 29.75 0.00 45.85 4.83
1946 5119 5.682943 AAGTTGCTTAATTTACTGTCGCA 57.317 34.783 0.00 0.00 0.00 5.10
2699 5894 1.364171 CGGCCCCTTGAGATACTCG 59.636 63.158 0.00 0.00 32.35 4.18
2774 7923 5.750067 AGAAACAAAAGTGCTTATGTGCAAG 59.250 36.000 0.00 0.00 45.12 4.01
2785 7934 4.016113 AGTTCGTCAGAAACAAAAGTGC 57.984 40.909 0.00 0.00 38.23 4.40
2864 8017 6.906659 AGCGTTGAAATCATTCCATATGATC 58.093 36.000 3.65 0.00 37.75 2.92
2888 8042 3.538591 CTGTTGGAGATGCATGCTCTAA 58.461 45.455 20.33 11.84 31.58 2.10
2891 8045 0.381089 GCTGTTGGAGATGCATGCTC 59.619 55.000 20.33 13.56 0.00 4.26
2894 8048 1.725665 CGGCTGTTGGAGATGCATG 59.274 57.895 2.46 0.00 0.00 4.06
2895 8049 2.117156 GCGGCTGTTGGAGATGCAT 61.117 57.895 0.00 0.00 0.00 3.96
2896 8050 2.747460 GCGGCTGTTGGAGATGCA 60.747 61.111 0.00 0.00 0.00 3.96
2975 8135 2.817901 CTAATTTACCGCTACCGCTGT 58.182 47.619 0.00 0.00 37.38 4.40
2983 8143 2.867091 CGCGCGCTAATTTACCGCT 61.867 57.895 30.48 0.00 45.02 5.52
2988 8148 0.374410 GTTTCCCGCGCGCTAATTTA 59.626 50.000 30.48 7.06 0.00 1.40
2992 8152 3.993376 ATCGTTTCCCGCGCGCTAA 62.993 57.895 30.48 17.74 36.19 3.09
3020 8187 0.890996 CGAGTTGCTGCCTTTTCCCT 60.891 55.000 0.00 0.00 0.00 4.20
3063 8245 0.941542 GCAATTTATAGACGCGCCCA 59.058 50.000 5.73 0.00 0.00 5.36
3064 8246 0.941542 TGCAATTTATAGACGCGCCC 59.058 50.000 5.73 0.00 0.00 6.13
3071 8253 3.744214 CGGAGGGTGCTGCAATTTATAGA 60.744 47.826 2.77 0.00 0.00 1.98
3092 8296 2.128853 GAGAGATGGAGAGAGCGGCG 62.129 65.000 0.51 0.51 0.00 6.46
3332 8546 2.062636 GTTCATATCCTAAGGGGGCCA 58.937 52.381 4.39 0.00 35.33 5.36
3335 8549 3.557264 GCGAAGTTCATATCCTAAGGGGG 60.557 52.174 3.32 0.00 35.33 5.40
3339 8553 3.982058 GTCGGCGAAGTTCATATCCTAAG 59.018 47.826 12.92 0.00 0.00 2.18
3346 8560 0.457166 CCACGTCGGCGAAGTTCATA 60.457 55.000 25.22 0.00 42.00 2.15
3371 8585 3.385384 CTCTCGTGCCTGCTCCCA 61.385 66.667 0.00 0.00 0.00 4.37
3384 8598 1.014564 CGGGAAAGGCGTCAACTCTC 61.015 60.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.