Multiple sequence alignment - TraesCS7A01G282500

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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 TraesCS7A01G282500 chr7A 100.000 5651 0 0 1 5651 309672187 309666537 0.000000e+00 10436
1 TraesCS7A01G282500 chr7A 83.519 898 94 21 4737 5601 37127435 37126559 0.000000e+00 789
2 TraesCS7A01G282500 chr4A 94.332 4552 186 26 341 4862 76720514 76716005 0.000000e+00 6911
3 TraesCS7A01G282500 chr4A 95.702 791 27 3 4861 5651 76715923 76715140 0.000000e+00 1266
4 TraesCS7A01G282500 chr4A 85.357 280 13 5 1 279 76721110 76720858 1.210000e-66 265
5 TraesCS7A01G282500 chr7B 95.866 3774 126 10 1899 5651 123774254 123778018 0.000000e+00 6078
6 TraesCS7A01G282500 chr7B 95.217 3763 138 12 1916 5651 716355510 716359257 0.000000e+00 5914
7 TraesCS7A01G282500 chr7B 89.383 3664 282 56 1042 4660 615264091 615267692 0.000000e+00 4512
8 TraesCS7A01G282500 chr7B 95.424 1486 47 10 422 1903 123767428 123768896 0.000000e+00 2348
9 TraesCS7A01G282500 chr7B 89.384 292 9 6 1 291 123766778 123767048 1.170000e-91 348
10 TraesCS7A01G282500 chrUn 93.762 2613 130 17 9 2615 301885919 301888504 0.000000e+00 3892
11 TraesCS7A01G282500 chrUn 95.126 1826 81 5 2612 4435 357104969 357103150 0.000000e+00 2872
12 TraesCS7A01G282500 chrUn 95.215 1233 41 10 4431 5651 389019832 389018606 0.000000e+00 1934
13 TraesCS7A01G282500 chr2B 93.762 2613 130 17 9 2615 568857687 568855102 0.000000e+00 3892
14 TraesCS7A01G282500 chr2B 83.080 1318 193 17 3322 4626 182871133 182869833 0.000000e+00 1171
15 TraesCS7A01G282500 chr5A 94.570 2523 95 19 327 2845 565666211 565663727 0.000000e+00 3862
16 TraesCS7A01G282500 chr5A 95.322 791 30 3 4861 5651 565662939 565662156 0.000000e+00 1249
17 TraesCS7A01G282500 chr5A 93.360 497 16 3 4383 4862 565663728 565663232 0.000000e+00 719
18 TraesCS7A01G282500 chr5A 86.842 266 9 9 1 265 565666864 565666624 2.010000e-69 274
19 TraesCS7A01G282500 chr4B 90.072 2095 161 27 2572 4660 63651729 63653782 0.000000e+00 2673
20 TraesCS7A01G282500 chr4B 90.669 1897 147 19 2572 4462 63684746 63686618 0.000000e+00 2495
21 TraesCS7A01G282500 chr3D 85.407 2371 319 18 1879 4240 49437741 49440093 0.000000e+00 2436
22 TraesCS7A01G282500 chr3D 83.712 792 87 17 4887 5651 562329010 562328234 0.000000e+00 710
23 TraesCS7A01G282500 chr4D 83.302 2635 399 28 1917 4536 448171070 448173678 0.000000e+00 2390
24 TraesCS7A01G282500 chr4D 94.959 1468 49 5 4203 5651 461379771 461381232 0.000000e+00 2278
25 TraesCS7A01G282500 chr4D 94.335 1112 48 6 387 1497 461376785 461377882 0.000000e+00 1690
26 TraesCS7A01G282500 chr4D 93.143 175 8 3 105 278 461376214 461376385 2.610000e-63 254
27 TraesCS7A01G282500 chr4D 78.233 317 56 9 1241 1551 209913918 209914227 2.080000e-44 191
28 TraesCS7A01G282500 chr4D 97.674 43 1 0 1 43 461375857 461375899 2.180000e-09 75
29 TraesCS7A01G282500 chr3B 88.648 1709 118 33 1042 2713 828397168 828398837 0.000000e+00 2012
30 TraesCS7A01G282500 chr3B 82.943 598 72 14 101 679 828395868 828396454 3.900000e-141 512
31 TraesCS7A01G282500 chr1A 86.467 1766 231 7 1896 3657 543179848 543181609 0.000000e+00 1930
32 TraesCS7A01G282500 chr1B 89.689 805 66 12 3860 4660 550957143 550957934 0.000000e+00 1011
33 TraesCS7A01G282500 chr1B 87.559 852 77 11 4819 5651 518797714 518798555 0.000000e+00 959
34 TraesCS7A01G282500 chr1B 84.157 688 78 15 1 679 518795798 518796463 6.170000e-179 638
35 TraesCS7A01G282500 chr1B 89.412 425 40 2 4240 4660 518797259 518797682 1.080000e-146 531
36 TraesCS7A01G282500 chr6A 86.107 763 60 23 4895 5651 416296201 416295479 0.000000e+00 780
37 TraesCS7A01G282500 chr6A 85.901 766 62 23 4892 5651 38432416 38433141 0.000000e+00 774
38 TraesCS7A01G282500 chr6A 88.104 538 31 13 940 1451 416297322 416296792 4.840000e-170 608
39 TraesCS7A01G282500 chr6A 87.755 539 33 13 940 1451 38431296 38431828 2.910000e-167 599
40 TraesCS7A01G282500 chr6A 85.430 604 51 11 4360 4931 38431825 38432423 1.360000e-165 593
41 TraesCS7A01G282500 chr6A 85.430 604 51 11 4360 4931 416296795 416296197 1.360000e-165 593
42 TraesCS7A01G282500 chr6A 85.167 600 57 21 92 679 38430332 38430911 2.270000e-163 586
43 TraesCS7A01G282500 chr6A 90.547 201 16 3 737 937 38430919 38431116 4.340000e-66 263
44 TraesCS7A01G282500 chr6A 90.050 201 17 3 737 937 416297701 416297504 2.020000e-64 257
45 TraesCS7A01G282500 chr2A 86.013 765 63 20 4892 5651 731250743 731251468 0.000000e+00 780
46 TraesCS7A01G282500 chr2A 85.667 600 55 19 92 679 731248656 731249236 2.250000e-168 603
47 TraesCS7A01G282500 chr2A 87.755 539 33 10 940 1451 731249623 731250155 2.910000e-167 599
48 TraesCS7A01G282500 chr2A 85.430 604 51 11 4360 4931 731250152 731250750 1.360000e-165 593
49 TraesCS7A01G282500 chr2A 90.050 201 17 3 737 937 731249244 731249441 2.020000e-64 257


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 TraesCS7A01G282500 chr7A 309666537 309672187 5650 True 10436.000000 10436 100.000000 1 5651 1 chr7A.!!$R2 5650
1 TraesCS7A01G282500 chr7A 37126559 37127435 876 True 789.000000 789 83.519000 4737 5601 1 chr7A.!!$R1 864
2 TraesCS7A01G282500 chr4A 76715140 76721110 5970 True 2814.000000 6911 91.797000 1 5651 3 chr4A.!!$R1 5650
3 TraesCS7A01G282500 chr7B 123774254 123778018 3764 False 6078.000000 6078 95.866000 1899 5651 1 chr7B.!!$F1 3752
4 TraesCS7A01G282500 chr7B 716355510 716359257 3747 False 5914.000000 5914 95.217000 1916 5651 1 chr7B.!!$F3 3735
5 TraesCS7A01G282500 chr7B 615264091 615267692 3601 False 4512.000000 4512 89.383000 1042 4660 1 chr7B.!!$F2 3618
6 TraesCS7A01G282500 chr7B 123766778 123768896 2118 False 1348.000000 2348 92.404000 1 1903 2 chr7B.!!$F4 1902
7 TraesCS7A01G282500 chrUn 301885919 301888504 2585 False 3892.000000 3892 93.762000 9 2615 1 chrUn.!!$F1 2606
8 TraesCS7A01G282500 chrUn 357103150 357104969 1819 True 2872.000000 2872 95.126000 2612 4435 1 chrUn.!!$R1 1823
9 TraesCS7A01G282500 chrUn 389018606 389019832 1226 True 1934.000000 1934 95.215000 4431 5651 1 chrUn.!!$R2 1220
10 TraesCS7A01G282500 chr2B 568855102 568857687 2585 True 3892.000000 3892 93.762000 9 2615 1 chr2B.!!$R2 2606
11 TraesCS7A01G282500 chr2B 182869833 182871133 1300 True 1171.000000 1171 83.080000 3322 4626 1 chr2B.!!$R1 1304
12 TraesCS7A01G282500 chr5A 565662156 565666864 4708 True 1526.000000 3862 92.523500 1 5651 4 chr5A.!!$R1 5650
13 TraesCS7A01G282500 chr4B 63651729 63653782 2053 False 2673.000000 2673 90.072000 2572 4660 1 chr4B.!!$F1 2088
14 TraesCS7A01G282500 chr4B 63684746 63686618 1872 False 2495.000000 2495 90.669000 2572 4462 1 chr4B.!!$F2 1890
15 TraesCS7A01G282500 chr3D 49437741 49440093 2352 False 2436.000000 2436 85.407000 1879 4240 1 chr3D.!!$F1 2361
16 TraesCS7A01G282500 chr3D 562328234 562329010 776 True 710.000000 710 83.712000 4887 5651 1 chr3D.!!$R1 764
17 TraesCS7A01G282500 chr4D 448171070 448173678 2608 False 2390.000000 2390 83.302000 1917 4536 1 chr4D.!!$F2 2619
18 TraesCS7A01G282500 chr4D 461375857 461381232 5375 False 1074.250000 2278 95.027750 1 5651 4 chr4D.!!$F3 5650
19 TraesCS7A01G282500 chr3B 828395868 828398837 2969 False 1262.000000 2012 85.795500 101 2713 2 chr3B.!!$F1 2612
20 TraesCS7A01G282500 chr1A 543179848 543181609 1761 False 1930.000000 1930 86.467000 1896 3657 1 chr1A.!!$F1 1761
21 TraesCS7A01G282500 chr1B 550957143 550957934 791 False 1011.000000 1011 89.689000 3860 4660 1 chr1B.!!$F1 800
22 TraesCS7A01G282500 chr1B 518795798 518798555 2757 False 709.333333 959 87.042667 1 5651 3 chr1B.!!$F2 5650
23 TraesCS7A01G282500 chr6A 38430332 38433141 2809 False 563.000000 774 86.960000 92 5651 5 chr6A.!!$F1 5559
24 TraesCS7A01G282500 chr6A 416295479 416297701 2222 True 559.500000 780 87.422750 737 5651 4 chr6A.!!$R1 4914
25 TraesCS7A01G282500 chr2A 731248656 731251468 2812 False 566.400000 780 86.983000 92 5651 5 chr2A.!!$F1 5559

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
385 1055 1.079405 CCGGCCGCTTCTTGTTCTA 60.079 57.895 22.85 0.00 0.00 2.10 F
2053 3607 1.075542 CGGATTTGCTGTGCGTCTTA 58.924 50.000 0.00 0.00 0.00 2.10 F
2699 4259 0.605319 CACCTTTGCGCCCTTCACTA 60.605 55.000 4.18 0.00 0.00 2.74 F
3108 4673 1.802880 GCTTCGTGCGACATGGATACT 60.803 52.381 0.00 0.00 37.61 2.12 F
3345 4911 2.559381 ATAGAGAGACAAGGCAGGGT 57.441 50.000 0.00 0.00 0.00 4.34 F
4242 7281 1.335597 CGTGCTTCGAAGACTACCACA 60.336 52.381 28.95 11.97 42.86 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2280 3840 1.985473 AATCAAGTGTTGCTGGCTCA 58.015 45.000 0.00 0.00 0.00 4.26 R
2897 4457 1.023502 TCCATAATGTGCCACATGCG 58.976 50.000 11.79 2.88 45.60 4.73 R
3938 5514 2.028020 TGTGTATTGCATGGTACGGTCA 60.028 45.455 0.00 0.00 0.00 4.02 R
4223 7262 2.433868 TGTGGTAGTCTTCGAAGCAC 57.566 50.000 20.56 20.05 40.96 4.40 R
4251 7291 3.786635 CCTAGTTGAGTGGTCATAGCAC 58.213 50.000 1.09 1.09 46.20 4.40 R
5572 9022 4.451096 GCACCTCAAGTCTTCGTGAAATAA 59.549 41.667 7.76 0.00 32.36 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
43 321 4.383770 CCCACGTCTGTACCAAATCCTTAT 60.384 45.833 0.00 0.00 0.00 1.73
78 374 3.492656 CGGGATCGAAGATTTCTTGGCTA 60.493 47.826 0.00 0.00 45.12 3.93
186 488 3.875762 GCTGATCCATCTCCTCCTCGATA 60.876 52.174 0.00 0.00 0.00 2.92
285 602 2.429767 CCAGATCAGCTCTCCGCCA 61.430 63.158 0.00 0.00 40.39 5.69
385 1055 1.079405 CCGGCCGCTTCTTGTTCTA 60.079 57.895 22.85 0.00 0.00 2.10
420 1095 4.562757 CCACGGTTCTTCATTCTTCAGGTA 60.563 45.833 0.00 0.00 0.00 3.08
650 1347 5.674525 AGCAGCAAGTTGATTAGTGCTATA 58.325 37.500 7.16 0.00 45.33 1.31
675 1375 5.699458 ACTTAGTTATGGTGTTGTGTAGTGC 59.301 40.000 0.00 0.00 0.00 4.40
676 1376 4.351874 AGTTATGGTGTTGTGTAGTGCT 57.648 40.909 0.00 0.00 0.00 4.40
677 1377 5.477607 AGTTATGGTGTTGTGTAGTGCTA 57.522 39.130 0.00 0.00 0.00 3.49
678 1378 5.235516 AGTTATGGTGTTGTGTAGTGCTAC 58.764 41.667 2.60 2.60 36.63 3.58
679 1379 5.011738 AGTTATGGTGTTGTGTAGTGCTACT 59.988 40.000 10.28 0.00 37.00 2.57
680 1380 3.106242 TGGTGTTGTGTAGTGCTACTG 57.894 47.619 10.28 0.00 37.00 2.74
681 1381 1.798813 GGTGTTGTGTAGTGCTACTGC 59.201 52.381 10.28 4.79 37.00 4.40
723 1423 1.885887 GTGTTGGCTTCAATGGCTACA 59.114 47.619 0.00 0.00 43.12 2.74
747 1447 1.674817 GCCATACCAAGCACGTGTACT 60.675 52.381 18.38 3.34 0.00 2.73
752 1452 5.393352 CCATACCAAGCACGTGTACTAACTA 60.393 44.000 18.38 0.00 0.00 2.24
763 1463 7.429340 GCACGTGTACTAACTATACATAAACGT 59.571 37.037 18.38 0.00 35.11 3.99
856 1556 2.047844 GCTGCTCTGGCTTCGTCA 60.048 61.111 0.00 0.00 39.59 4.35
938 1645 8.774546 TTTCTCTCTCTCCAAGATACATATGT 57.225 34.615 13.93 13.93 32.19 2.29
1165 2684 1.615392 GCCATGCCTTTGATATGACCC 59.385 52.381 0.00 0.00 0.00 4.46
1166 2685 2.948115 CCATGCCTTTGATATGACCCA 58.052 47.619 0.00 0.00 0.00 4.51
1167 2686 3.503365 CCATGCCTTTGATATGACCCAT 58.497 45.455 0.00 0.00 0.00 4.00
1168 2687 3.257375 CCATGCCTTTGATATGACCCATG 59.743 47.826 0.00 0.00 0.00 3.66
1252 2772 3.471306 AGGATCCAGTAATGGAGGGTAGA 59.529 47.826 18.08 0.00 41.88 2.59
1261 2781 1.112113 TGGAGGGTAGAAGTGCGATC 58.888 55.000 0.00 0.00 0.00 3.69
1393 2915 8.588290 TTATGTTAATCCCTTGTGTGCTATTT 57.412 30.769 0.00 0.00 0.00 1.40
1394 2916 6.909550 TGTTAATCCCTTGTGTGCTATTTT 57.090 33.333 0.00 0.00 0.00 1.82
1395 2917 6.686630 TGTTAATCCCTTGTGTGCTATTTTG 58.313 36.000 0.00 0.00 0.00 2.44
1396 2918 6.491745 TGTTAATCCCTTGTGTGCTATTTTGA 59.508 34.615 0.00 0.00 0.00 2.69
1436 2960 2.752354 CAGCCATGGAATCGGTTAACAA 59.248 45.455 18.40 0.00 0.00 2.83
1504 3028 8.551682 AATTAATTCCCCAATGCTTCTCATTA 57.448 30.769 0.00 0.00 43.21 1.90
1554 3081 6.805016 ATCATTCTCTCAAGAGGTACACAT 57.195 37.500 7.17 0.00 42.30 3.21
1779 3307 6.183360 ACACTTGTCACAACCTGTAATACTCT 60.183 38.462 0.00 0.00 0.00 3.24
1836 3390 6.647334 TTTTGGCAGTGACAAAATGAGATA 57.353 33.333 29.05 9.06 44.33 1.98
1911 3465 5.570320 AGGGTAATGTTACTGAACTTGCAT 58.430 37.500 3.22 0.00 36.45 3.96
1920 3474 7.935520 TGTTACTGAACTTGCATTCAATGTTA 58.064 30.769 4.41 0.00 38.12 2.41
1978 3532 3.085952 TGAAGCCAAAAGTAGGGATGG 57.914 47.619 0.00 0.00 36.00 3.51
1998 3552 4.598022 TGGTATTTGATGACATTGCCTCA 58.402 39.130 0.00 0.00 0.00 3.86
2004 3558 2.236893 TGATGACATTGCCTCAGTGCTA 59.763 45.455 0.00 0.00 0.00 3.49
2042 3596 1.335780 TGCACACAATGTCGGATTTGC 60.336 47.619 4.22 0.00 0.00 3.68
2053 3607 1.075542 CGGATTTGCTGTGCGTCTTA 58.924 50.000 0.00 0.00 0.00 2.10
2112 3666 2.309613 TGCTTCCTGTGTGCAAAAGAT 58.690 42.857 0.00 0.00 33.48 2.40
2221 3781 7.598278 AGCTTATATATGTCACTCGAGAAAGG 58.402 38.462 21.68 5.64 0.00 3.11
2280 3840 1.688197 CAATCACCCTTTTGTGCCACT 59.312 47.619 0.00 0.00 36.17 4.00
2370 3930 2.686915 GTCAGAAAGCTAGCATTGGCAT 59.313 45.455 18.83 0.00 44.61 4.40
2403 3963 8.871125 AGCATATAGGCTACTTAATGTTAGTGT 58.129 33.333 10.76 0.00 43.70 3.55
2570 4130 5.400066 TGAATATGAAGTTGACGAGGTCA 57.600 39.130 0.00 0.00 41.09 4.02
2699 4259 0.605319 CACCTTTGCGCCCTTCACTA 60.605 55.000 4.18 0.00 0.00 2.74
2777 4337 7.220030 TGAGACAGAAGAATCCTATATTTGGC 58.780 38.462 0.00 0.00 0.00 4.52
2862 4422 7.384660 TGAATGTGTTAGGATGAAAAATGCAAC 59.615 33.333 0.00 0.00 0.00 4.17
2897 4457 2.029244 CCGAACACGACACATAGATTGC 59.971 50.000 0.00 0.00 0.00 3.56
3062 4627 5.087323 TCATAGAGTTTCAGTTGGAGGACT 58.913 41.667 0.00 0.00 0.00 3.85
3108 4673 1.802880 GCTTCGTGCGACATGGATACT 60.803 52.381 0.00 0.00 37.61 2.12
3137 4702 6.808321 ACTTTATGGACATTCACCTAGCTA 57.192 37.500 0.00 0.00 0.00 3.32
3232 4798 3.726291 TTGTTGAGTTTTGGCTAAGGC 57.274 42.857 0.00 0.00 37.82 4.35
3345 4911 2.559381 ATAGAGAGACAAGGCAGGGT 57.441 50.000 0.00 0.00 0.00 4.34
3432 4998 5.049198 GTGATGTTCAGCAGACAGAAAATCA 60.049 40.000 4.39 4.39 41.31 2.57
3456 5022 5.976458 TGAGGGGATTAAAATCATGTTTGC 58.024 37.500 5.15 0.00 37.15 3.68
3511 5077 4.699735 TGTTATGACACAACATCCATGACC 59.300 41.667 0.00 0.00 31.11 4.02
3577 5143 5.529800 GTGCCGTCACATTATTAGGGTATTT 59.470 40.000 0.00 0.00 42.66 1.40
3629 5195 4.574828 GCCTTTGTATTCTTAAGCGATGGA 59.425 41.667 0.00 0.00 0.00 3.41
3787 5362 8.992073 GGAATGTGCTTGAAGAAAATTTAACAT 58.008 29.630 0.00 0.00 0.00 2.71
3853 5428 5.774690 AGGGACAAGCTAGAAGATCTCATAG 59.225 44.000 0.00 2.73 0.00 2.23
3856 5431 6.071952 GGACAAGCTAGAAGATCTCATAGGAG 60.072 46.154 13.33 0.00 42.80 3.69
4223 7262 2.028930 AGTAGAGGTTTGTGCTCCTTCG 60.029 50.000 0.00 0.00 33.83 3.79
4242 7281 1.335597 CGTGCTTCGAAGACTACCACA 60.336 52.381 28.95 11.97 42.86 4.17
4251 7291 5.337554 TCGAAGACTACCACATATTTGTCG 58.662 41.667 0.00 0.00 32.34 4.35
4413 7458 0.729116 CGTCCATGACATGAGCCAAC 59.271 55.000 17.24 6.03 32.09 3.77
4716 7794 9.558396 TGCCATTTTATTTGATTTGAAAACTCT 57.442 25.926 0.00 0.00 0.00 3.24
4735 7813 4.774726 ACTCTCTTGTAGATGCTGGAAAGA 59.225 41.667 0.00 0.00 32.41 2.52
4837 7921 8.705594 CATATAGGTTATGTATCCTAGGTTGGG 58.294 40.741 9.08 0.00 39.30 4.12
4900 8284 8.178313 TCTTCTCGAGATATGCTATTTGGTAA 57.822 34.615 17.44 0.00 0.00 2.85
5020 8449 0.034896 ACCAGGAAGCACTAACACGG 59.965 55.000 0.00 0.00 0.00 4.94
5127 8556 6.477253 TGCCGGCCATATACTAAAAATGATA 58.523 36.000 26.77 0.00 0.00 2.15
5350 8799 5.142061 TGTATGTGTGGTCGTACTTGATT 57.858 39.130 0.00 0.00 32.80 2.57
5456 8906 9.180678 CTTCAAAAATTAGTGGTGTCACATAAC 57.819 33.333 5.12 0.11 45.91 1.89
5475 8925 9.559958 CACATAACTGTGTCTGGATTTTATTTC 57.440 33.333 0.00 0.00 46.33 2.17
5476 8926 9.295825 ACATAACTGTGTCTGGATTTTATTTCA 57.704 29.630 0.00 0.00 33.22 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 321 1.735376 GATCCCGTGCCTTCGCTCTA 61.735 60.000 0.00 0.00 35.36 2.43
113 415 2.107292 CAAGATCTGCGCTGCTGCT 61.107 57.895 9.73 3.24 36.97 4.24
116 418 1.814586 GCTCAAGATCTGCGCTGCT 60.815 57.895 9.73 0.00 32.75 4.24
119 421 0.743701 CTTGGCTCAAGATCTGCGCT 60.744 55.000 9.73 0.00 43.42 5.92
186 488 0.173708 CGAAGAAACGGCTAGGAGCT 59.826 55.000 0.00 0.00 41.99 4.09
214 530 2.905415 TCCAATCTGCCTCAAACCAT 57.095 45.000 0.00 0.00 0.00 3.55
313 631 4.449075 GCTAGTGCTGAATCGCGAGAGA 62.449 54.545 16.66 0.00 39.04 3.10
385 1055 1.833787 AACCGTGGTGGCCTATTCGT 61.834 55.000 3.32 0.00 43.94 3.85
650 1347 6.204108 GCACTACACAACACCATAACTAAGTT 59.796 38.462 0.00 0.00 0.00 2.66
664 1364 2.457366 AGGCAGTAGCACTACACAAC 57.543 50.000 10.30 0.00 44.61 3.32
681 1381 2.607499 AGATCTCCATGAGCCAGTAGG 58.393 52.381 0.00 0.00 38.23 3.18
723 1423 0.253044 ACGTGCTTGGTATGGCTGAT 59.747 50.000 0.00 0.00 0.00 2.90
752 1452 9.136952 GCTAGAAATCGGATAACGTTTATGTAT 57.863 33.333 5.91 0.00 44.69 2.29
763 1463 4.100963 TGCTTCCTGCTAGAAATCGGATAA 59.899 41.667 0.00 0.00 43.37 1.75
938 1645 6.839124 AATGGCATCTTTGTGTCTATTCAA 57.161 33.333 0.00 0.00 0.00 2.69
1168 2687 1.337703 TGTCAAACTTCTGCCACATGC 59.662 47.619 0.00 0.00 41.77 4.06
1252 2772 2.173782 TCCTAGAGGAGAGATCGCACTT 59.826 50.000 0.00 0.00 39.78 3.16
1436 2960 9.419297 CATCACTGAAATCTTGATTTTGAACAT 57.581 29.630 9.58 0.00 0.00 2.71
1504 3028 4.345859 TTTTCGGTGTACTGGAGTCATT 57.654 40.909 0.00 0.00 0.00 2.57
1713 3240 9.372369 GCTGTCTAATTTCTACCATACATATCC 57.628 37.037 0.00 0.00 0.00 2.59
1808 3336 7.984050 TCTCATTTTGTCACTGCCAAAAATTAA 59.016 29.630 2.30 0.00 42.95 1.40
1836 3390 9.832445 AAAGACTACATGTTATTCGGTTATGAT 57.168 29.630 2.30 0.00 0.00 2.45
1911 3465 9.575868 TTATACAAAGAACCCTGTAACATTGAA 57.424 29.630 0.00 0.00 32.05 2.69
1978 3532 5.575957 CACTGAGGCAATGTCATCAAATAC 58.424 41.667 0.00 0.00 0.00 1.89
1998 3552 7.227512 GCATATGTCCTGTAAAATTCTAGCACT 59.772 37.037 4.29 0.00 0.00 4.40
2004 3558 6.658816 TGTGTGCATATGTCCTGTAAAATTCT 59.341 34.615 4.29 0.00 0.00 2.40
2042 3596 2.983136 CTCTGTTGTCTAAGACGCACAG 59.017 50.000 1.61 1.61 42.67 3.66
2053 3607 2.581216 TCTACGACCCTCTGTTGTCT 57.419 50.000 0.00 0.00 40.89 3.41
2221 3781 8.897752 AGTGAAGCTATCTTGTATTTTCCATTC 58.102 33.333 0.00 0.00 31.48 2.67
2280 3840 1.985473 AATCAAGTGTTGCTGGCTCA 58.015 45.000 0.00 0.00 0.00 4.26
2389 3949 7.122948 TGAAAACCACCAACACTAACATTAAGT 59.877 33.333 0.00 0.00 0.00 2.24
2403 3963 2.158986 CCAACATGCTGAAAACCACCAA 60.159 45.455 0.00 0.00 0.00 3.67
2525 4085 3.837355 AGAAAAATGCAGGGTTCAGAGT 58.163 40.909 0.00 0.00 0.00 3.24
2570 4130 7.010183 CGTCCAGAATAAACGAATCAATGTACT 59.990 37.037 0.00 0.00 38.65 2.73
2699 4259 5.048504 CACTTTGCATGTGATGGTTTACTCT 60.049 40.000 13.16 0.00 37.60 3.24
2777 4337 5.240891 TGCTCTAAGAAATGACCTGAACAG 58.759 41.667 0.00 0.00 0.00 3.16
2862 4422 3.183775 CGTGTTCGGTAGAGTTTTTCTGG 59.816 47.826 0.00 0.00 36.61 3.86
2897 4457 1.023502 TCCATAATGTGCCACATGCG 58.976 50.000 11.79 2.88 45.60 4.73
3108 4673 7.195374 AGGTGAATGTCCATAAAGTAAGCTA 57.805 36.000 0.00 0.00 0.00 3.32
3137 4702 7.451877 TGAAATAGAAGTTGTCCTGAGTAGACT 59.548 37.037 0.00 0.00 35.21 3.24
3232 4798 4.923893 TGACATTTCAAAGCAGTGTCAAG 58.076 39.130 2.41 0.00 44.19 3.02
3258 4824 1.159285 CGGCAATCAGCTCACTTTGA 58.841 50.000 0.00 0.00 44.79 2.69
3300 4866 4.279169 CCCATGATGTCAACAACTCACTTT 59.721 41.667 0.00 0.00 0.00 2.66
3432 4998 6.408434 GGCAAACATGATTTTAATCCCCTCAT 60.408 38.462 0.00 0.00 34.50 2.90
3456 5022 5.998454 AATCTTCTTGTATTGATCGCTGG 57.002 39.130 0.00 0.00 0.00 4.85
3511 5077 3.207474 AGCTTGCAAGAACATTTAGCG 57.793 42.857 30.39 0.00 32.68 4.26
3577 5143 6.568869 CAATTCATTTATTTTCGCACCCCTA 58.431 36.000 0.00 0.00 0.00 3.53
3787 5362 5.781210 TTCACAGCAATGTCAACCAAATA 57.219 34.783 0.00 0.00 0.00 1.40
3853 5428 3.019564 CCATGGAGTGTTTGGATTCTCC 58.980 50.000 5.56 0.00 44.54 3.71
3856 5431 3.445096 CCTTCCATGGAGTGTTTGGATTC 59.555 47.826 15.53 0.00 39.22 2.52
3938 5514 2.028020 TGTGTATTGCATGGTACGGTCA 60.028 45.455 0.00 0.00 0.00 4.02
4223 7262 2.433868 TGTGGTAGTCTTCGAAGCAC 57.566 50.000 20.56 20.05 40.96 4.40
4251 7291 3.786635 CCTAGTTGAGTGGTCATAGCAC 58.213 50.000 1.09 1.09 46.20 4.40
4343 7388 4.150897 TCCTTGTTGTAGCCATACCATC 57.849 45.455 0.00 0.00 0.00 3.51
4716 7794 4.284490 ACTGTCTTTCCAGCATCTACAAGA 59.716 41.667 0.00 0.00 35.83 3.02
4900 8284 9.520515 AGTAAATAGGTGTCATTCAGAAACATT 57.479 29.630 0.00 0.00 36.08 2.71
5020 8449 5.940470 ACCGAAAATATCTATCATTCTGCCC 59.060 40.000 0.00 0.00 0.00 5.36
5350 8799 6.005823 CACATGAGATAATAAGCCATCCCAA 58.994 40.000 0.00 0.00 0.00 4.12
5456 8906 7.395190 TGGATGAAATAAAATCCAGACACAG 57.605 36.000 0.23 0.00 45.86 3.66
5488 8938 9.521503 CTCGTCTCATATAAGATCTGTGAAAAA 57.478 33.333 0.00 0.00 0.00 1.94
5572 9022 4.451096 GCACCTCAAGTCTTCGTGAAATAA 59.549 41.667 7.76 0.00 32.36 1.40


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

AutoCloner maintained by Alex Coulton.