Multiple sequence alignment - TraesCS2A01G581700

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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 TraesCS2A01G581700 chr2A 100.000 3364 0 0 1 3364 774083668 774080305 0.000000e+00 6213
1 TraesCS2A01G581700 chr2A 93.854 960 57 2 2406 3364 200116800 200117758 0.000000e+00 1445
2 TraesCS2A01G581700 chr2A 93.458 963 60 3 2402 3364 337575281 337576240 0.000000e+00 1426
3 TraesCS2A01G581700 chr4D 95.359 2090 96 1 318 2406 493214055 493216144 0.000000e+00 3321
4 TraesCS2A01G581700 chr4D 95.652 322 12 2 1 320 493213560 493213881 1.790000e-142 516
5 TraesCS2A01G581700 chr4D 94.198 293 15 2 1 291 251092931 251092639 2.380000e-121 446
6 TraesCS2A01G581700 chr4D 91.623 191 14 2 103 291 148418721 148418911 2.570000e-66 263
7 TraesCS2A01G581700 chr4D 78.598 271 28 24 460 726 329668421 329668177 5.810000e-33 152
8 TraesCS2A01G581700 chr3D 93.809 2116 103 4 318 2406 77841421 77843535 0.000000e+00 3157
9 TraesCS2A01G581700 chr3D 94.637 317 17 0 4 320 77840911 77841227 3.020000e-135 492
10 TraesCS2A01G581700 chr4A 93.589 2090 130 2 318 2406 234615792 234617878 0.000000e+00 3114
11 TraesCS2A01G581700 chr4A 93.854 960 54 4 2410 3364 585923768 585922809 0.000000e+00 1441
12 TraesCS2A01G581700 chr4A 93.375 966 61 2 2400 3364 541505717 541506680 0.000000e+00 1426
13 TraesCS2A01G581700 chr5B 93.500 1600 87 5 699 2292 7210505 7208917 0.000000e+00 2362
14 TraesCS2A01G581700 chr5B 92.812 1600 79 12 699 2292 484771535 484769966 0.000000e+00 2285
15 TraesCS2A01G581700 chr5B 93.431 274 16 2 20 291 711785039 711784766 4.040000e-109 405
16 TraesCS2A01G581700 chr5B 92.237 219 10 2 720 931 61757862 61758080 1.520000e-78 303
17 TraesCS2A01G581700 chr6B 93.062 1600 77 8 699 2292 86993513 86991942 0.000000e+00 2309
18 TraesCS2A01G581700 chr6B 94.074 270 10 4 28 291 49616645 49616376 4.040000e-109 405
19 TraesCS2A01G581700 chr6B 90.625 288 26 1 5 291 464409367 464409654 6.810000e-102 381
20 TraesCS2A01G581700 chr6B 92.593 216 9 2 723 931 464575038 464574823 1.520000e-78 303
21 TraesCS2A01G581700 chr6B 92.237 219 10 2 720 931 577618559 577618777 1.520000e-78 303
22 TraesCS2A01G581700 chr2B 92.938 1600 79 13 699 2292 24003634 24005205 0.000000e+00 2298
23 TraesCS2A01G581700 chr2B 92.938 1600 79 6 699 2292 24041716 24040145 0.000000e+00 2298
24 TraesCS2A01G581700 chr2B 93.328 1244 74 4 723 1957 765129971 765128728 0.000000e+00 1829
25 TraesCS2A01G581700 chr2B 94.881 293 13 2 1 291 733356211 733355919 1.100000e-124 457
26 TraesCS2A01G581700 chr2B 91.045 201 17 1 2205 2405 751594247 751594048 1.540000e-68 270
27 TraesCS2A01G581700 chr7B 92.655 1593 84 6 699 2285 114039805 114041370 0.000000e+00 2263
28 TraesCS2A01G581700 chr7B 91.197 284 24 1 3 286 616912846 616913128 5.270000e-103 385
29 TraesCS2A01G581700 chr4B 92.500 1600 86 7 699 2292 164309644 164311215 0.000000e+00 2259
30 TraesCS2A01G581700 chr4B 91.003 289 26 0 3 291 548862618 548862330 1.130000e-104 390
31 TraesCS2A01G581700 chr4B 91.204 216 12 2 723 931 97763101 97762886 1.530000e-73 287
32 TraesCS2A01G581700 chr4B 93.284 134 9 0 1 134 164309426 164309559 7.360000e-47 198
33 TraesCS2A01G581700 chr4B 96.667 60 2 0 198 257 164309586 164309645 2.140000e-17 100
34 TraesCS2A01G581700 chr5D 91.881 1244 78 10 723 1957 484041466 484040237 0.000000e+00 1716
35 TraesCS2A01G581700 chr5D 89.000 100 2 1 1072 1171 528730527 528730437 7.630000e-22 115
36 TraesCS2A01G581700 chr6A 94.161 959 53 3 2407 3364 508442748 508443704 0.000000e+00 1458
37 TraesCS2A01G581700 chr6A 93.952 959 50 7 2410 3363 31251867 31250912 0.000000e+00 1443
38 TraesCS2A01G581700 chr6A 92.759 290 20 1 3 291 4928752 4928463 5.190000e-113 418
39 TraesCS2A01G581700 chr5A 93.861 961 53 6 2405 3364 583144216 583143261 0.000000e+00 1443
40 TraesCS2A01G581700 chr1A 93.854 960 56 3 2406 3364 350857607 350856650 0.000000e+00 1443
41 TraesCS2A01G581700 chr1A 93.828 956 56 3 2410 3364 57357443 57356490 0.000000e+00 1435
42 TraesCS2A01G581700 chr1A 94.531 256 12 2 38 291 503676665 503676410 8.750000e-106 394
43 TraesCS2A01G581700 chr3B 93.127 291 20 0 1 291 210822627 210822917 8.630000e-116 427
44 TraesCS2A01G581700 chr3B 93.796 274 15 2 20 291 727082412 727082685 8.690000e-111 411
45 TraesCS2A01G581700 chr3B 91.349 289 25 0 3 291 280585194 280585482 2.430000e-106 396
46 TraesCS2A01G581700 chr3A 92.784 291 19 2 3 291 612613173 612612883 1.440000e-113 420
47 TraesCS2A01G581700 chr2D 94.361 266 13 2 28 291 65812165 65812430 1.120000e-109 407
48 TraesCS2A01G581700 chr2D 83.553 152 16 4 723 866 518814248 518814098 2.110000e-27 134
49 TraesCS2A01G581700 chr7D 94.922 256 11 2 38 291 158645175 158644920 1.880000e-107 399
50 TraesCS2A01G581700 chr7D 94.969 159 6 2 135 291 139218360 139218202 7.210000e-62 248
51 TraesCS2A01G581700 chr7D 94.815 135 7 0 1 135 139228410 139228276 9.460000e-51 211
52 TraesCS2A01G581700 chr6D 92.063 189 15 0 103 291 234474333 234474521 1.990000e-67 267


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 TraesCS2A01G581700 chr2A 774080305 774083668 3363 True 6213.000000 6213 100.000000 1 3364 1 chr2A.!!$R1 3363
1 TraesCS2A01G581700 chr2A 200116800 200117758 958 False 1445.000000 1445 93.854000 2406 3364 1 chr2A.!!$F1 958
2 TraesCS2A01G581700 chr2A 337575281 337576240 959 False 1426.000000 1426 93.458000 2402 3364 1 chr2A.!!$F2 962
3 TraesCS2A01G581700 chr4D 493213560 493216144 2584 False 1918.500000 3321 95.505500 1 2406 2 chr4D.!!$F2 2405
4 TraesCS2A01G581700 chr3D 77840911 77843535 2624 False 1824.500000 3157 94.223000 4 2406 2 chr3D.!!$F1 2402
5 TraesCS2A01G581700 chr4A 234615792 234617878 2086 False 3114.000000 3114 93.589000 318 2406 1 chr4A.!!$F1 2088
6 TraesCS2A01G581700 chr4A 585922809 585923768 959 True 1441.000000 1441 93.854000 2410 3364 1 chr4A.!!$R1 954
7 TraesCS2A01G581700 chr4A 541505717 541506680 963 False 1426.000000 1426 93.375000 2400 3364 1 chr4A.!!$F2 964
8 TraesCS2A01G581700 chr5B 7208917 7210505 1588 True 2362.000000 2362 93.500000 699 2292 1 chr5B.!!$R1 1593
9 TraesCS2A01G581700 chr5B 484769966 484771535 1569 True 2285.000000 2285 92.812000 699 2292 1 chr5B.!!$R2 1593
10 TraesCS2A01G581700 chr6B 86991942 86993513 1571 True 2309.000000 2309 93.062000 699 2292 1 chr6B.!!$R2 1593
11 TraesCS2A01G581700 chr2B 24003634 24005205 1571 False 2298.000000 2298 92.938000 699 2292 1 chr2B.!!$F1 1593
12 TraesCS2A01G581700 chr2B 24040145 24041716 1571 True 2298.000000 2298 92.938000 699 2292 1 chr2B.!!$R1 1593
13 TraesCS2A01G581700 chr2B 765128728 765129971 1243 True 1829.000000 1829 93.328000 723 1957 1 chr2B.!!$R4 1234
14 TraesCS2A01G581700 chr7B 114039805 114041370 1565 False 2263.000000 2263 92.655000 699 2285 1 chr7B.!!$F1 1586
15 TraesCS2A01G581700 chr4B 164309426 164311215 1789 False 852.333333 2259 94.150333 1 2292 3 chr4B.!!$F1 2291
16 TraesCS2A01G581700 chr5D 484040237 484041466 1229 True 1716.000000 1716 91.881000 723 1957 1 chr5D.!!$R1 1234
17 TraesCS2A01G581700 chr6A 508442748 508443704 956 False 1458.000000 1458 94.161000 2407 3364 1 chr6A.!!$F1 957
18 TraesCS2A01G581700 chr6A 31250912 31251867 955 True 1443.000000 1443 93.952000 2410 3363 1 chr6A.!!$R2 953
19 TraesCS2A01G581700 chr5A 583143261 583144216 955 True 1443.000000 1443 93.861000 2405 3364 1 chr5A.!!$R1 959
20 TraesCS2A01G581700 chr1A 350856650 350857607 957 True 1443.000000 1443 93.854000 2406 3364 1 chr1A.!!$R2 958
21 TraesCS2A01G581700 chr1A 57356490 57357443 953 True 1435.000000 1435 93.828000 2410 3364 1 chr1A.!!$R1 954

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
442 641 0.235665 AAAGCATCGCAGACAACACG 59.764 50.0 0.0 0.0 42.51 4.49 F
1566 1820 0.460987 GTCCGCTAGTGCTGCTGAAT 60.461 55.0 0.0 0.0 36.97 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2439 0.743688 CACGAGCATCTACTCTGCCT 59.256 55.0 0.0 0.0 40.56 4.75 R
2912 3172 0.592637 CCACAATGCTCGCTGTTCAA 59.407 50.0 0.0 0.0 0.00 2.69 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
48 49 6.071896 ACAGATTTTACTTAAAAGCTCCCTGC 60.072 38.462 8.86 0.00 45.52 4.85
75 76 5.641209 CCTTTTGTTTCATTGGTCAAACACA 59.359 36.000 2.60 0.00 41.18 3.72
96 97 4.838152 GCAGCGATGCCGAGGGAA 62.838 66.667 16.30 0.00 38.22 3.97
140 141 8.232513 GCATTCTAATGGTCACATACATGTATG 58.767 37.037 34.18 34.18 41.14 2.39
201 202 1.386748 CAACACGTACACTCTCATGCG 59.613 52.381 0.00 0.00 0.00 4.73
264 265 4.336889 TGCTAGTCTTGCTTACACTGTT 57.663 40.909 7.78 0.00 0.00 3.16
268 269 5.007724 GCTAGTCTTGCTTACACTGTTTGTT 59.992 40.000 0.00 0.00 39.91 2.83
269 270 5.235305 AGTCTTGCTTACACTGTTTGTTG 57.765 39.130 0.00 0.00 39.91 3.33
270 271 4.096382 AGTCTTGCTTACACTGTTTGTTGG 59.904 41.667 0.00 0.00 39.91 3.77
272 273 1.407258 TGCTTACACTGTTTGTTGGGC 59.593 47.619 0.00 0.00 39.91 5.36
273 274 1.407258 GCTTACACTGTTTGTTGGGCA 59.593 47.619 0.00 0.00 39.91 5.36
274 275 2.035832 GCTTACACTGTTTGTTGGGCAT 59.964 45.455 0.00 0.00 39.91 4.40
354 553 5.212532 TGCTGGTTGTTTGAAAGCATTAT 57.787 34.783 0.00 0.00 38.88 1.28
414 613 2.432300 GCCTAACTCTGCCCGGCTA 61.432 63.158 11.61 0.00 37.76 3.93
437 636 2.357323 TGTTTTGAAAGCATCGCAGACA 59.643 40.909 0.00 0.00 42.51 3.41
442 641 0.235665 AAAGCATCGCAGACAACACG 59.764 50.000 0.00 0.00 42.51 4.49
491 690 9.877178 CTTGGTGTTACAAGTCTTAGATTAGAT 57.123 33.333 0.00 0.00 42.18 1.98
510 709 7.933215 TTAGATAGTCAACACACACTAGCTA 57.067 36.000 0.00 0.00 39.51 3.32
533 732 4.344102 AGTTTACAGGACAGTAACAGAGCA 59.656 41.667 0.00 0.00 33.96 4.26
569 768 6.503524 CCGTTTCTTTTGATTTCTTCTTCCA 58.496 36.000 0.00 0.00 0.00 3.53
590 789 1.909302 CATCCTTGGTGGGTACTCTGT 59.091 52.381 0.00 0.00 36.20 3.41
594 793 1.899814 CTTGGTGGGTACTCTGTAGCA 59.100 52.381 8.78 0.00 0.00 3.49
624 823 1.376553 GTCTTCCTGTGCCTGCTCC 60.377 63.158 0.00 0.00 0.00 4.70
625 824 1.537397 TCTTCCTGTGCCTGCTCCT 60.537 57.895 0.00 0.00 0.00 3.69
714 938 4.503741 ACACATTGCAGTAAACCATCAC 57.496 40.909 0.00 0.00 0.00 3.06
830 1073 5.918011 TGTTATTCTGAACCGTTTGCATTTC 59.082 36.000 0.00 0.00 0.00 2.17
885 1137 4.457496 ATGTCCAGGTCCGCTGCG 62.457 66.667 16.34 16.34 0.00 5.18
1024 1276 1.001641 GTGCTGCTGGAGTTCCCAT 60.002 57.895 0.00 0.00 45.57 4.00
1025 1277 0.610232 GTGCTGCTGGAGTTCCCATT 60.610 55.000 0.00 0.00 45.57 3.16
1037 1289 2.124151 CCCATTGGAAGCTCCGGG 60.124 66.667 3.62 0.00 40.17 5.73
1203 1455 7.505585 CACCAGTGGGGATAACAATAACATAAT 59.494 37.037 15.21 0.00 41.15 1.28
1266 1518 3.634448 CGGTCTTCCAGAGATCATACTGT 59.366 47.826 0.00 0.00 35.04 3.55
1281 1533 0.535102 ACTGTTGGTGGCTCTTTCCG 60.535 55.000 0.00 0.00 0.00 4.30
1315 1567 7.562821 ACATGCATCATCAGTCCTATATAGCTA 59.437 37.037 4.04 0.00 0.00 3.32
1352 1605 4.216472 CCTTTTGTTCTAGAAAGTGGGAGC 59.784 45.833 6.78 0.00 32.34 4.70
1474 1728 6.625532 AAGTTTTAAATGCAAGGATGGGAT 57.374 33.333 0.00 0.00 0.00 3.85
1481 1735 1.133699 TGCAAGGATGGGATGTGGATC 60.134 52.381 0.00 0.00 0.00 3.36
1482 1736 1.144503 GCAAGGATGGGATGTGGATCT 59.855 52.381 0.00 0.00 0.00 2.75
1565 1819 1.079819 GTCCGCTAGTGCTGCTGAA 60.080 57.895 0.00 0.00 36.97 3.02
1566 1820 0.460987 GTCCGCTAGTGCTGCTGAAT 60.461 55.000 0.00 0.00 36.97 2.57
1569 1823 1.649664 CGCTAGTGCTGCTGAATCTT 58.350 50.000 0.00 0.00 36.97 2.40
1583 1837 3.861840 TGAATCTTCTTGGACGGACATC 58.138 45.455 0.00 0.00 0.00 3.06
1586 1840 3.095912 TCTTCTTGGACGGACATCCTA 57.904 47.619 0.00 0.00 39.75 2.94
1653 1907 2.939103 CCCTGCATCTTACAGTAGTTGC 59.061 50.000 0.00 0.00 39.93 4.17
1659 1913 4.571176 GCATCTTACAGTAGTTGCCCTAAC 59.429 45.833 0.00 0.00 35.70 2.34
1886 2140 5.100943 GTGACTTTCATCGGTACCTACTTC 58.899 45.833 10.90 0.00 0.00 3.01
1957 2211 6.093082 TGTTGTCAGCTTCATATGTTCTGATG 59.907 38.462 19.25 10.91 36.37 3.07
2185 2439 8.215926 AGTTAAGTACATGTTTGTTACAGCAA 57.784 30.769 2.30 0.00 40.83 3.91
2199 2454 1.297664 CAGCAAGGCAGAGTAGATGC 58.702 55.000 0.00 0.00 43.09 3.91
2201 2456 1.138661 AGCAAGGCAGAGTAGATGCTC 59.861 52.381 0.00 0.00 39.80 4.26
2285 2540 7.119699 CACTGCCATCTTACATTCTGTTCTTTA 59.880 37.037 0.00 0.00 0.00 1.85
2361 2616 2.579201 CTCTTCGCCCCATCGTGT 59.421 61.111 0.00 0.00 0.00 4.49
2408 2663 4.479993 GCGAGGGCTGGCAGACAT 62.480 66.667 24.18 17.06 34.31 3.06
2441 2697 1.885887 CACATCCGTGACATTTTGGGT 59.114 47.619 0.00 0.00 46.80 4.51
2513 2772 2.350498 GTGACAAAACCCGGTATCATCG 59.650 50.000 0.00 0.00 0.00 3.84
2573 2832 2.227865 TGACAGTAAATGGGCTTTTCGC 59.772 45.455 0.00 0.00 38.13 4.70
2593 2852 0.692419 CCTGGGTAGGCCAGAGACAT 60.692 60.000 5.01 0.00 37.25 3.06
2652 2911 2.202756 CGTGGTAGAAGCGAGGGC 60.203 66.667 0.00 0.00 40.37 5.19
2816 3076 1.442526 GCGATTGCACTGCAGGCTAT 61.443 55.000 19.93 19.06 40.61 2.97
2828 3088 2.213499 GCAGGCTATGCGTTACTGAAT 58.787 47.619 7.99 0.00 46.99 2.57
2830 3090 3.722147 CAGGCTATGCGTTACTGAATCT 58.278 45.455 0.00 0.00 0.00 2.40
2905 3165 1.339055 TGCTGCTAACTGAAGCCGATT 60.339 47.619 0.00 0.00 46.96 3.34
2912 3172 0.620556 ACTGAAGCCGATTGATGGGT 59.379 50.000 0.00 0.00 39.32 4.51
2920 3180 1.133025 CCGATTGATGGGTTGAACAGC 59.867 52.381 0.00 0.00 0.00 4.40
2931 3191 0.592637 TTGAACAGCGAGCATTGTGG 59.407 50.000 0.00 0.00 0.00 4.17
2932 3192 0.250252 TGAACAGCGAGCATTGTGGA 60.250 50.000 0.00 0.00 0.00 4.02
3123 3394 1.378762 CGTGGAGGGGTGGTTGAAT 59.621 57.895 0.00 0.00 0.00 2.57
3130 3401 1.203570 AGGGGTGGTTGAATAGGACCT 60.204 52.381 0.00 0.00 36.86 3.85
3170 3441 1.202964 TGAACAGTAGACGGTGGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
3171 3442 2.100989 GAACAGTAGACGGTGGAGGAT 58.899 52.381 0.00 0.00 0.00 3.24
3232 3504 1.296715 GATGAACAGGAGCCCGTGT 59.703 57.895 0.00 0.00 42.54 4.49
3277 3549 1.174783 GAACAGTAGCTCGTGGAGGA 58.825 55.000 0.00 0.00 0.00 3.71
3352 3624 4.176752 GCCACACCCCTCCCGATC 62.177 72.222 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.593134 TTTTAAGTAAAATCTGTTTGTGCACAT 57.407 25.926 22.39 4.56 30.83 3.21
48 49 6.148480 TGTTTGACCAATGAAACAAAAGGTTG 59.852 34.615 0.00 0.00 38.73 3.77
96 97 0.822164 GCATACGTGTGTAGGGGAGT 59.178 55.000 14.10 0.00 33.08 3.85
163 164 4.018490 TGTTGGAGCTTTATCATGCATGT 58.982 39.130 25.43 15.34 0.00 3.21
173 174 3.319972 AGAGTGTACGTGTTGGAGCTTTA 59.680 43.478 0.00 0.00 0.00 1.85
253 254 1.407258 TGCCCAACAAACAGTGTAAGC 59.593 47.619 0.00 0.00 40.60 3.09
264 265 8.646900 AGAAAATTAAAGTAGAATGCCCAACAA 58.353 29.630 0.00 0.00 0.00 2.83
268 269 7.775053 ACAGAAAATTAAAGTAGAATGCCCA 57.225 32.000 0.00 0.00 0.00 5.36
269 270 8.736244 TGTACAGAAAATTAAAGTAGAATGCCC 58.264 33.333 0.00 0.00 0.00 5.36
354 553 7.014230 ACAAAAATAACAGCCTAAAGAAGCAGA 59.986 33.333 0.00 0.00 0.00 4.26
414 613 3.983344 GTCTGCGATGCTTTCAAAACAAT 59.017 39.130 0.00 0.00 0.00 2.71
437 636 2.798283 CGTTCATAGGTGTGTTCGTGTT 59.202 45.455 0.00 0.00 0.00 3.32
442 641 5.007332 AGTTGTTTCGTTCATAGGTGTGTTC 59.993 40.000 0.00 0.00 0.00 3.18
491 690 6.401047 AAACTAGCTAGTGTGTGTTGACTA 57.599 37.500 26.70 0.00 36.50 2.59
510 709 4.344102 TGCTCTGTTACTGTCCTGTAAACT 59.656 41.667 0.00 0.00 34.67 2.66
569 768 1.909302 CAGAGTACCCACCAAGGATGT 59.091 52.381 0.00 0.00 41.22 3.06
624 823 3.429141 CAGCTGCCGGTGCTCAAG 61.429 66.667 18.71 6.98 38.92 3.02
714 938 8.028938 CAGTCCAGTAACCTCCAAATTAAATTG 58.971 37.037 0.00 0.00 0.00 2.32
830 1073 5.977635 TGAACACTGGTAATGAGATACAGG 58.022 41.667 0.00 0.00 0.00 4.00
1024 1276 1.907739 CTGATCCCGGAGCTTCCAA 59.092 57.895 0.73 0.00 35.91 3.53
1025 1277 2.735772 GCTGATCCCGGAGCTTCCA 61.736 63.158 0.73 0.00 35.91 3.53
1037 1289 2.690778 GGGTGCGTTGGTGCTGATC 61.691 63.158 0.00 0.00 35.36 2.92
1203 1455 7.436970 CGCAACCTACATAACACATTCATACTA 59.563 37.037 0.00 0.00 0.00 1.82
1266 1518 1.374947 CCTCGGAAAGAGCCACCAA 59.625 57.895 0.00 0.00 45.54 3.67
1281 1533 5.207110 ACTGATGATGCATGTACTACCTC 57.793 43.478 2.46 0.00 0.00 3.85
1315 1567 6.006449 AGAACAAAAGGAGTACATGAGCAAT 58.994 36.000 0.00 0.00 0.00 3.56
1330 1582 4.083802 CGCTCCCACTTTCTAGAACAAAAG 60.084 45.833 4.18 2.40 38.24 2.27
1352 1605 1.948721 GAAAATCAAGGGGCCCTGCG 61.949 60.000 29.60 21.06 32.13 5.18
1460 1713 0.928505 TCCACATCCCATCCTTGCAT 59.071 50.000 0.00 0.00 0.00 3.96
1474 1728 2.678580 TCCGTGCGGAGATCCACA 60.679 61.111 9.48 0.00 39.76 4.17
1554 1808 2.039480 TCCAAGAAGATTCAGCAGCACT 59.961 45.455 0.00 0.00 0.00 4.40
1565 1819 2.472029 AGGATGTCCGTCCAAGAAGAT 58.528 47.619 8.21 0.00 40.90 2.40
1566 1820 1.938585 AGGATGTCCGTCCAAGAAGA 58.061 50.000 8.21 0.00 40.90 2.87
1569 1823 1.006758 AGGTAGGATGTCCGTCCAAGA 59.993 52.381 8.21 0.00 40.90 3.02
1583 1837 1.561542 AGCCAACATGGAAGAGGTAGG 59.438 52.381 0.00 0.00 40.96 3.18
1586 1840 1.985159 TGTAGCCAACATGGAAGAGGT 59.015 47.619 0.00 0.00 40.96 3.85
1610 1864 1.117994 CAGAGAGCTCACCATGGCTA 58.882 55.000 17.77 0.00 39.05 3.93
1653 1907 4.104102 TCCAGCCCAACTATAATGTTAGGG 59.896 45.833 0.00 0.00 39.27 3.53
1659 1913 6.322201 AGTTCATTTCCAGCCCAACTATAATG 59.678 38.462 0.00 0.00 0.00 1.90
1886 2140 8.628882 TGTATCTACTCATATTTTGTGTGTCG 57.371 34.615 0.00 0.00 34.13 4.35
1914 2168 9.823647 CTGACAACATAATATAACCAGAAGTCT 57.176 33.333 0.00 0.00 0.00 3.24
1947 2201 7.038516 TCCACAGATATCATAGCATCAGAACAT 60.039 37.037 5.32 0.00 0.00 2.71
1957 2211 5.873712 CCAATGTCTCCACAGATATCATAGC 59.126 44.000 5.32 0.00 35.41 2.97
2112 2366 8.898761 TGTTGTTCACATGTTACTACTTGATTT 58.101 29.630 17.25 0.00 34.47 2.17
2185 2439 0.743688 CACGAGCATCTACTCTGCCT 59.256 55.000 0.00 0.00 40.56 4.75
2285 2540 3.384789 TCTTCTGGCGAGCTGTATACAAT 59.615 43.478 7.06 0.00 0.00 2.71
2361 2616 0.906066 TACTTGCGGGTCTGGCATTA 59.094 50.000 0.00 0.00 40.62 1.90
2475 2734 9.820229 GTTTTGTCACAATTATCGTCATAGAAA 57.180 29.630 0.00 0.00 0.00 2.52
2513 2772 1.413077 GTAGGAGCCCACCACATCTAC 59.587 57.143 0.00 0.00 0.00 2.59
2580 2839 1.043816 GCAGCTATGTCTCTGGCCTA 58.956 55.000 3.32 0.00 0.00 3.93
2581 2840 0.979709 TGCAGCTATGTCTCTGGCCT 60.980 55.000 3.32 0.00 0.00 5.19
2586 2845 4.101274 AGAATGTCATGCAGCTATGTCTCT 59.899 41.667 0.00 0.00 0.00 3.10
2593 2852 3.018856 CCCAAAGAATGTCATGCAGCTA 58.981 45.455 0.00 0.00 0.00 3.32
2652 2911 5.139435 GGAACTCCCTGAAATTTTCCTTG 57.861 43.478 6.68 0.00 31.54 3.61
2760 3020 4.309950 AACGCCTCGCTCGGGTTT 62.310 61.111 0.00 0.00 33.04 3.27
2816 3076 1.201414 TCGCTCAGATTCAGTAACGCA 59.799 47.619 0.00 0.00 0.00 5.24
2847 3107 2.559668 TCGATCGGGTTCAGTTAACAGT 59.440 45.455 16.41 0.00 40.08 3.55
2905 3165 0.955428 GCTCGCTGTTCAACCCATCA 60.955 55.000 0.00 0.00 0.00 3.07
2912 3172 0.592637 CCACAATGCTCGCTGTTCAA 59.407 50.000 0.00 0.00 0.00 2.69
2920 3180 2.124570 CCCCCTCCACAATGCTCG 60.125 66.667 0.00 0.00 0.00 5.03
2931 3191 3.202151 TCACTATTCATCCAAACCCCCTC 59.798 47.826 0.00 0.00 0.00 4.30
2932 3192 3.197983 TCACTATTCATCCAAACCCCCT 58.802 45.455 0.00 0.00 0.00 4.79
3130 3401 3.625897 CAGCCCTCCACACCACGA 61.626 66.667 0.00 0.00 0.00 4.35
3170 3441 2.491693 CACCGGCTATTGTTCAACCAAT 59.508 45.455 0.00 0.00 38.54 3.16
3171 3442 1.883275 CACCGGCTATTGTTCAACCAA 59.117 47.619 0.00 0.00 0.00 3.67
3232 3504 1.076923 GTCGACCTCCTCCAGCCTA 60.077 63.158 3.51 0.00 0.00 3.93
3277 3549 4.393778 ACCGTCGACCCCCTCCAT 62.394 66.667 10.58 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.