Multiple sequence alignment - TraesCS7B01G412000

Loading Multiple Alignment...

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 TraesCS7B01G412000 chr7B 100.000 2602 0 0 1 2602 680122873 680125474 0.000000e+00 4806.0
1 TraesCS7B01G412000 chr7B 87.368 190 23 1 2282 2471 715570897 715571085 1.570000e-52 217.0
2 TraesCS7B01G412000 chr3B 91.042 2322 131 29 1 2286 131572667 131574947 0.000000e+00 3064.0
3 TraesCS7B01G412000 chr3B 94.667 150 8 0 2453 2602 131574958 131575107 1.560000e-57 233.0
4 TraesCS7B01G412000 chr3B 89.130 184 19 1 2278 2460 821121907 821122090 7.240000e-56 228.0
5 TraesCS7B01G412000 chr3B 83.500 200 30 3 458 655 578623729 578623531 1.590000e-42 183.0
6 TraesCS7B01G412000 chr2A 90.527 2333 143 16 1 2284 303743818 303741515 0.000000e+00 3013.0
7 TraesCS7B01G412000 chr2A 95.302 149 7 0 2454 2602 303741521 303741373 1.200000e-58 237.0
8 TraesCS7B01G412000 chr2A 94.444 90 4 1 2514 2602 303741362 303741273 1.260000e-28 137.0
9 TraesCS7B01G412000 chr6B 80.422 1328 218 28 709 2010 567601043 567602354 0.000000e+00 974.0
10 TraesCS7B01G412000 chr6B 94.872 39 2 0 657 695 567599750 567599788 7.780000e-06 62.1
11 TraesCS7B01G412000 chr5B 83.272 1082 157 17 942 2010 490356496 490357566 0.000000e+00 974.0
12 TraesCS7B01G412000 chr5B 92.169 166 12 1 2289 2454 331656649 331656485 1.560000e-57 233.0
13 TraesCS7B01G412000 chr1A 81.164 1237 187 33 809 2013 29194248 29193026 0.000000e+00 952.0
14 TraesCS7B01G412000 chr1A 81.448 663 116 4 1310 1965 155082045 155082707 1.060000e-148 536.0
15 TraesCS7B01G412000 chr1A 81.569 510 79 11 708 1211 155081401 155081901 8.670000e-110 407.0
16 TraesCS7B01G412000 chr4A 92.835 656 42 5 3 655 136860483 136861136 0.000000e+00 946.0
17 TraesCS7B01G412000 chr4A 86.541 847 88 13 977 1818 136873592 136874417 0.000000e+00 909.0
18 TraesCS7B01G412000 chr4A 85.321 436 44 8 1865 2289 136874422 136874848 1.430000e-117 433.0
19 TraesCS7B01G412000 chr4A 86.667 150 9 4 2451 2600 136874836 136874974 3.470000e-34 156.0
20 TraesCS7B01G412000 chr5D 80.796 854 132 23 709 1550 559668885 559668052 7.850000e-180 640.0
21 TraesCS7B01G412000 chr4D 84.475 657 89 9 1312 1959 278249994 278249342 1.020000e-178 636.0
22 TraesCS7B01G412000 chr4B 83.902 615 90 7 1226 1834 622813890 622814501 1.740000e-161 579.0
23 TraesCS7B01G412000 chr4B 83.000 200 31 3 458 655 476947616 476947418 7.400000e-41 178.0
24 TraesCS7B01G412000 chr6D 81.449 690 99 17 777 1443 129172486 129171803 2.950000e-149 538.0
25 TraesCS7B01G412000 chr5A 81.448 663 116 4 1310 1965 331865522 331866184 1.060000e-148 536.0
26 TraesCS7B01G412000 chr5A 82.192 511 74 14 708 1211 331864880 331865380 8.610000e-115 424.0
27 TraesCS7B01G412000 chr3D 84.298 484 65 8 1490 1964 419842756 419842275 1.820000e-126 462.0
28 TraesCS7B01G412000 chr3D 82.296 514 79 10 703 1209 419870682 419870174 3.980000e-118 435.0
29 TraesCS7B01G412000 chr3A 83.943 492 58 12 740 1211 359579888 359580378 3.950000e-123 451.0
30 TraesCS7B01G412000 chr3A 100.000 167 0 0 2289 2455 655726606 655726772 2.510000e-80 309.0
31 TraesCS7B01G412000 chr3A 90.643 171 16 0 2289 2459 37458054 37457884 7.240000e-56 228.0
32 TraesCS7B01G412000 chr3A 90.000 170 17 0 2289 2458 31944339 31944170 1.210000e-53 220.0
33 TraesCS7B01G412000 chr2D 82.490 514 79 9 703 1209 500491585 500491076 8.550000e-120 440.0
34 TraesCS7B01G412000 chr7D 100.000 166 0 0 2289 2454 87366526 87366361 9.050000e-80 307.0
35 TraesCS7B01G412000 chr1B 98.844 173 1 1 2286 2458 332091164 332091335 9.050000e-80 307.0
36 TraesCS7B01G412000 chr1B 84.694 98 15 0 2067 2164 10554428 10554525 5.930000e-17 99.0
37 TraesCS7B01G412000 chr1D 88.043 184 20 2 2275 2458 413947314 413947495 1.570000e-52 217.0


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 TraesCS7B01G412000 chr7B 680122873 680125474 2601 False 4806.000000 4806 100.000000 1 2602 1 chr7B.!!$F1 2601
1 TraesCS7B01G412000 chr3B 131572667 131575107 2440 False 1648.500000 3064 92.854500 1 2602 2 chr3B.!!$F2 2601
2 TraesCS7B01G412000 chr2A 303741273 303743818 2545 True 1129.000000 3013 93.424333 1 2602 3 chr2A.!!$R1 2601
3 TraesCS7B01G412000 chr6B 567599750 567602354 2604 False 518.050000 974 87.647000 657 2010 2 chr6B.!!$F1 1353
4 TraesCS7B01G412000 chr5B 490356496 490357566 1070 False 974.000000 974 83.272000 942 2010 1 chr5B.!!$F1 1068
5 TraesCS7B01G412000 chr1A 29193026 29194248 1222 True 952.000000 952 81.164000 809 2013 1 chr1A.!!$R1 1204
6 TraesCS7B01G412000 chr1A 155081401 155082707 1306 False 471.500000 536 81.508500 708 1965 2 chr1A.!!$F1 1257
7 TraesCS7B01G412000 chr4A 136860483 136861136 653 False 946.000000 946 92.835000 3 655 1 chr4A.!!$F1 652
8 TraesCS7B01G412000 chr4A 136873592 136874974 1382 False 499.333333 909 86.176333 977 2600 3 chr4A.!!$F2 1623
9 TraesCS7B01G412000 chr5D 559668052 559668885 833 True 640.000000 640 80.796000 709 1550 1 chr5D.!!$R1 841
10 TraesCS7B01G412000 chr4D 278249342 278249994 652 True 636.000000 636 84.475000 1312 1959 1 chr4D.!!$R1 647
11 TraesCS7B01G412000 chr4B 622813890 622814501 611 False 579.000000 579 83.902000 1226 1834 1 chr4B.!!$F1 608
12 TraesCS7B01G412000 chr6D 129171803 129172486 683 True 538.000000 538 81.449000 777 1443 1 chr6D.!!$R1 666
13 TraesCS7B01G412000 chr5A 331864880 331866184 1304 False 480.000000 536 81.820000 708 1965 2 chr5A.!!$F1 1257
14 TraesCS7B01G412000 chr3D 419870174 419870682 508 True 435.000000 435 82.296000 703 1209 1 chr3D.!!$R2 506
15 TraesCS7B01G412000 chr2D 500491076 500491585 509 True 440.000000 440 82.490000 703 1209 1 chr2D.!!$R1 506

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
494 499 0.322008 GGTCAGAGTTGGGAAGGCAG 60.322 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 2955 0.179043 TTGTTACCAACGCCAGAGCA 60.179 50.0 0.0 0.0 39.83 4.26 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
46 47 9.679661 TGCTATTCATCCAAACTGAAATTAGTA 57.320 29.630 0.00 0.00 36.30 1.82
216 218 2.064434 TTTTGCACACTGGATGGACA 57.936 45.000 0.00 0.00 0.00 4.02
309 314 7.918562 GCCACATAAACATGTTCGGTAATTATT 59.081 33.333 12.39 0.00 31.37 1.40
316 321 8.934023 AACATGTTCGGTAATTATTATCCCAT 57.066 30.769 4.92 0.00 0.00 4.00
393 398 1.064314 CCCCCGTTTCATGTATTGGGA 60.064 52.381 14.64 0.00 39.03 4.37
452 457 5.926542 CCTCGTTGAACTTGATTTCTGACTA 59.073 40.000 0.00 0.00 0.00 2.59
494 499 0.322008 GGTCAGAGTTGGGAAGGCAG 60.322 60.000 0.00 0.00 0.00 4.85
527 532 1.604378 CCGAGCCCTTCAAGGATGT 59.396 57.895 4.43 0.00 37.67 3.06
535 540 1.407989 CCTTCAAGGATGTCTGCCCTC 60.408 57.143 0.00 0.00 37.67 4.30
655 661 8.778059 AGTTTTACAATATGTATTCCTGGGAGA 58.222 33.333 0.00 0.00 32.20 3.71
698 704 5.664294 AAAAATGCATGCAGGAGATTGTA 57.336 34.783 26.69 0.00 0.00 2.41
700 706 3.572632 ATGCATGCAGGAGATTGTACT 57.427 42.857 26.69 0.84 0.00 2.73
866 2113 7.419204 ACTAGTAAGTTCGAATATGTCTCTGC 58.581 38.462 0.00 0.00 29.00 4.26
1018 2287 7.497249 CCAGGACAATGTTTGAAAATTTTGGTA 59.503 33.333 8.47 0.00 0.00 3.25
1066 2335 4.755411 TGATCTAGTAAAAGTCAAGCCGG 58.245 43.478 0.00 0.00 0.00 6.13
1279 2597 4.608269 TGGGCATGGATGAAAATCACTAA 58.392 39.130 0.00 0.00 0.00 2.24
1371 2692 1.725665 CATGTGCTCAAGCGATGGG 59.274 57.895 0.00 0.00 45.83 4.00
1395 2720 7.069331 GGGCTACAGATGCAAGAGATATACTAT 59.931 40.741 0.00 0.00 0.00 2.12
1472 2798 1.595794 CGACGCAACACTTTGTACCTT 59.404 47.619 0.00 0.00 34.90 3.50
1477 2803 4.056050 CGCAACACTTTGTACCTTCTAGT 58.944 43.478 0.00 0.00 34.90 2.57
1522 2848 1.271379 CAGCAATGTGGAAGCATGTGT 59.729 47.619 0.00 0.00 0.00 3.72
1528 2854 3.207265 TGTGGAAGCATGTGTACTTGT 57.793 42.857 0.00 0.00 0.00 3.16
1671 2999 0.250338 ACTTTGGCCGAACTGAGTCC 60.250 55.000 0.00 0.00 0.00 3.85
1768 3108 0.739462 CCGCGACAAAGCTCCATACA 60.739 55.000 8.23 0.00 34.40 2.29
1784 3128 6.078456 TCCATACAAGGAACCATCAAAGAT 57.922 37.500 0.00 0.00 33.93 2.40
1903 3248 4.211125 TGCTCAAAATGTGGGTTAACAGA 58.789 39.130 8.10 0.00 32.52 3.41
1929 3279 1.514678 GAACACATGCAGCAACCCGA 61.515 55.000 0.00 0.00 0.00 5.14
1972 3325 6.767524 AATTTCAGTGTTGTTTACTGGTGA 57.232 33.333 5.42 0.00 44.33 4.02
2000 3354 5.634896 CATTTGGCTATGTCTCACTTTGTC 58.365 41.667 0.00 0.00 0.00 3.18
2029 3386 4.981806 ACAGTCTCTAGAATGAGCTGAC 57.018 45.455 13.85 7.75 42.16 3.51
2030 3387 3.699038 ACAGTCTCTAGAATGAGCTGACC 59.301 47.826 13.85 0.00 42.16 4.02
2043 3400 2.605366 GAGCTGACCAATAAGAAGACGC 59.395 50.000 0.00 0.00 0.00 5.19
2044 3401 1.666189 GCTGACCAATAAGAAGACGCC 59.334 52.381 0.00 0.00 0.00 5.68
2045 3402 2.935238 GCTGACCAATAAGAAGACGCCA 60.935 50.000 0.00 0.00 0.00 5.69
2046 3403 3.535561 CTGACCAATAAGAAGACGCCAT 58.464 45.455 0.00 0.00 0.00 4.40
2047 3404 3.270027 TGACCAATAAGAAGACGCCATG 58.730 45.455 0.00 0.00 0.00 3.66
2048 3405 3.055458 TGACCAATAAGAAGACGCCATGA 60.055 43.478 0.00 0.00 0.00 3.07
2049 3406 3.535561 ACCAATAAGAAGACGCCATGAG 58.464 45.455 0.00 0.00 0.00 2.90
2050 3407 3.055094 ACCAATAAGAAGACGCCATGAGT 60.055 43.478 0.00 0.00 0.00 3.41
2089 3446 1.474879 GGAGAGGTTCAGAAGAGTCGG 59.525 57.143 0.00 0.00 0.00 4.79
2152 3509 8.826710 TGTTTTTCTGCGGTATAAATAGATGAG 58.173 33.333 0.00 0.00 0.00 2.90
2164 3521 9.106070 GTATAAATAGATGAGTTCCAAACGGTT 57.894 33.333 0.00 0.00 36.23 4.44
2185 3542 3.430453 TGGATTCCCAAAATGGTCTGAC 58.570 45.455 0.00 0.00 40.09 3.51
2193 3550 3.566322 CCAAAATGGTCTGACCGTAAACA 59.434 43.478 21.29 3.32 42.58 2.83
2216 3573 0.395312 ACGTTCGGATTCCAGTTGGT 59.605 50.000 3.09 0.00 36.34 3.67
2220 3577 0.037590 TCGGATTCCAGTTGGTTGGG 59.962 55.000 3.09 0.00 38.81 4.12
2223 3580 2.723273 GGATTCCAGTTGGTTGGGTAG 58.277 52.381 0.00 0.00 38.81 3.18
2286 3652 3.140623 CCATGTTCATCAGTGTGTGTGA 58.859 45.455 0.00 0.00 0.00 3.58
2288 3654 2.212652 TGTTCATCAGTGTGTGTGAGC 58.787 47.619 0.00 0.00 0.00 4.26
2289 3655 2.212652 GTTCATCAGTGTGTGTGAGCA 58.787 47.619 0.00 0.00 0.00 4.26
2290 3656 2.159327 TCATCAGTGTGTGTGAGCAG 57.841 50.000 0.00 0.00 0.00 4.24
2291 3657 1.413812 TCATCAGTGTGTGTGAGCAGT 59.586 47.619 0.00 0.00 0.00 4.40
2292 3658 1.529865 CATCAGTGTGTGTGAGCAGTG 59.470 52.381 0.00 0.00 37.38 3.66
2294 3660 1.524621 AGTGTGTGTGAGCAGTGGC 60.525 57.895 0.00 0.00 41.61 5.01
2311 3677 3.547513 CGTAGCTAGGGGGTGGCC 61.548 72.222 5.50 0.00 31.44 5.36
2312 3678 2.366435 GTAGCTAGGGGGTGGCCA 60.366 66.667 0.00 0.00 31.44 5.36
2313 3679 2.040884 TAGCTAGGGGGTGGCCAG 60.041 66.667 5.11 0.00 31.44 4.85
2314 3680 3.714078 TAGCTAGGGGGTGGCCAGG 62.714 68.421 5.11 0.00 31.44 4.45
2316 3682 4.760220 CTAGGGGGTGGCCAGGGT 62.760 72.222 5.11 0.00 0.00 4.34
2335 3701 4.016706 GTCCGTGGACCACCCTGG 62.017 72.222 19.11 14.18 45.02 4.45
2336 3702 4.242586 TCCGTGGACCACCCTGGA 62.243 66.667 19.11 16.25 40.96 3.86
2337 3703 3.246112 CCGTGGACCACCCTGGAA 61.246 66.667 19.11 0.00 40.96 3.53
2338 3704 2.602676 CCGTGGACCACCCTGGAAT 61.603 63.158 19.11 0.00 40.96 3.01
2339 3705 1.378762 CGTGGACCACCCTGGAATT 59.621 57.895 19.11 0.00 40.96 2.17
2340 3706 0.251165 CGTGGACCACCCTGGAATTT 60.251 55.000 19.11 0.00 40.96 1.82
2341 3707 1.545841 GTGGACCACCCTGGAATTTC 58.454 55.000 14.16 0.00 40.96 2.17
2342 3708 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
2343 3709 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
2344 3710 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
2345 3711 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
2346 3712 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
2347 3713 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
2348 3714 2.023501 CCACCCTGGAATTTCCCCATAA 60.024 50.000 12.90 0.00 40.96 1.90
2349 3715 3.031013 CACCCTGGAATTTCCCCATAAC 58.969 50.000 12.90 0.00 35.03 1.89
2350 3716 2.933139 ACCCTGGAATTTCCCCATAACT 59.067 45.455 12.90 0.00 35.03 2.24
2351 3717 3.339742 ACCCTGGAATTTCCCCATAACTT 59.660 43.478 12.90 0.00 35.03 2.66
2352 3718 3.706086 CCCTGGAATTTCCCCATAACTTG 59.294 47.826 12.90 0.00 35.03 3.16
2353 3719 4.352893 CCTGGAATTTCCCCATAACTTGT 58.647 43.478 12.90 0.00 35.03 3.16
2354 3720 5.515106 CCTGGAATTTCCCCATAACTTGTA 58.485 41.667 12.90 0.00 35.03 2.41
2355 3721 6.136155 CCTGGAATTTCCCCATAACTTGTAT 58.864 40.000 12.90 0.00 35.03 2.29
2356 3722 7.294584 CCTGGAATTTCCCCATAACTTGTATA 58.705 38.462 12.90 0.00 35.03 1.47
2357 3723 7.950124 CCTGGAATTTCCCCATAACTTGTATAT 59.050 37.037 12.90 0.00 35.03 0.86
2365 3731 9.664777 TTCCCCATAACTTGTATATAGTGTAGT 57.335 33.333 0.00 0.00 0.00 2.73
2426 3792 9.883142 TTAAATATTTTCATCAATTGACCACCC 57.117 29.630 11.07 0.00 32.84 4.61
2427 3793 7.738437 AATATTTTCATCAATTGACCACCCT 57.262 32.000 11.07 0.00 32.84 4.34
2428 3794 4.870123 TTTTCATCAATTGACCACCCTG 57.130 40.909 11.07 4.15 32.84 4.45
2429 3795 2.512692 TCATCAATTGACCACCCTGG 57.487 50.000 11.07 0.00 45.02 4.45
2430 3796 1.991813 TCATCAATTGACCACCCTGGA 59.008 47.619 11.07 0.00 40.96 3.86
2431 3797 2.025981 TCATCAATTGACCACCCTGGAG 60.026 50.000 11.07 0.00 40.96 3.86
2432 3798 1.444933 TCAATTGACCACCCTGGAGT 58.555 50.000 3.38 0.00 40.96 3.85
2433 3799 2.626785 TCAATTGACCACCCTGGAGTA 58.373 47.619 3.38 0.00 40.96 2.59
2434 3800 3.189606 TCAATTGACCACCCTGGAGTAT 58.810 45.455 3.38 0.00 40.96 2.12
2435 3801 3.591527 TCAATTGACCACCCTGGAGTATT 59.408 43.478 3.38 0.00 40.96 1.89
2436 3802 3.652057 ATTGACCACCCTGGAGTATTG 57.348 47.619 0.00 0.00 40.96 1.90
2437 3803 1.285280 TGACCACCCTGGAGTATTGG 58.715 55.000 0.00 0.00 40.96 3.16
2438 3804 1.286248 GACCACCCTGGAGTATTGGT 58.714 55.000 0.00 0.00 40.96 3.67
2439 3805 1.286248 ACCACCCTGGAGTATTGGTC 58.714 55.000 0.00 0.00 40.96 4.02
2440 3806 1.203440 ACCACCCTGGAGTATTGGTCT 60.203 52.381 0.00 0.00 40.96 3.85
2441 3807 1.210478 CCACCCTGGAGTATTGGTCTG 59.790 57.143 0.00 0.00 40.96 3.51
2442 3808 1.210478 CACCCTGGAGTATTGGTCTGG 59.790 57.143 0.00 0.00 0.00 3.86
2443 3809 0.181350 CCCTGGAGTATTGGTCTGGC 59.819 60.000 0.00 0.00 0.00 4.85
2444 3810 1.207791 CCTGGAGTATTGGTCTGGCT 58.792 55.000 0.00 0.00 0.00 4.75
2445 3811 2.398588 CCTGGAGTATTGGTCTGGCTA 58.601 52.381 0.00 0.00 0.00 3.93
2446 3812 2.103263 CCTGGAGTATTGGTCTGGCTAC 59.897 54.545 0.00 0.00 0.00 3.58
2447 3813 1.754803 TGGAGTATTGGTCTGGCTACG 59.245 52.381 0.00 0.00 0.00 3.51
2448 3814 1.538419 GGAGTATTGGTCTGGCTACGC 60.538 57.143 0.00 0.00 0.00 4.42
2512 3878 0.747255 ATGGATTCGCACGTCTAGCT 59.253 50.000 0.00 0.00 0.00 3.32
2544 3910 1.153549 GCTCTGGACGACATGGGAC 60.154 63.158 0.00 0.00 0.00 4.46
2551 3917 0.172803 GACGACATGGGACGCTACTT 59.827 55.000 0.00 0.00 35.61 2.24
2580 3946 0.913205 ACATAATACGGTGTGGGGCA 59.087 50.000 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.729281 AATTTCAGTTTGGATGAATAGCATTTT 57.271 25.926 0.00 0.00 37.34 1.82
24 25 9.308000 TGGTTACTAATTTCAGTTTGGATGAAT 57.692 29.630 0.00 0.00 36.60 2.57
46 47 4.870123 TTTTGCAATGCTCATACTGGTT 57.130 36.364 6.82 0.00 0.00 3.67
84 86 6.013725 CCCTCCCATGTTGCTACTACAATATA 60.014 42.308 0.00 0.00 31.12 0.86
291 296 8.792633 CATGGGATAATAATTACCGAACATGTT 58.207 33.333 11.78 11.78 0.00 2.71
293 298 8.450964 GTCATGGGATAATAATTACCGAACATG 58.549 37.037 0.00 0.00 33.93 3.21
309 314 8.746052 AAAAATCAACGAATAGTCATGGGATA 57.254 30.769 0.00 0.00 0.00 2.59
310 315 7.645058 AAAAATCAACGAATAGTCATGGGAT 57.355 32.000 0.00 0.00 0.00 3.85
393 398 4.457466 AGTGGTGACGATGGTTTTTACTT 58.543 39.130 0.00 0.00 0.00 2.24
494 499 1.152652 TCGGCTCCCTCTCATCCTC 60.153 63.158 0.00 0.00 0.00 3.71
527 532 1.188219 ACAGAAGCTTCGAGGGCAGA 61.188 55.000 20.43 0.00 0.00 4.26
535 540 1.016130 ATGCACGGACAGAAGCTTCG 61.016 55.000 20.43 16.87 0.00 3.79
655 661 0.245539 CCGGTGTACATTCAGACGGT 59.754 55.000 0.00 0.00 35.65 4.83
698 704 0.897863 ACTCTCGCTTCTCTGCCAGT 60.898 55.000 0.00 0.00 0.00 4.00
700 706 1.588597 CACTCTCGCTTCTCTGCCA 59.411 57.895 0.00 0.00 0.00 4.92
866 2113 3.781079 ATGCAACATCACCCAAATACG 57.219 42.857 0.00 0.00 0.00 3.06
916 2165 5.062558 CCGCATCAAAATGAAATCAGTTTCC 59.937 40.000 5.92 0.00 41.46 3.13
1018 2287 2.151202 CCCACGTTCATACAGCACTTT 58.849 47.619 0.00 0.00 0.00 2.66
1066 2335 2.683362 GCCTAGCAATGTACTCCAAACC 59.317 50.000 0.00 0.00 0.00 3.27
1371 2692 7.855409 CGATAGTATATCTCTTGCATCTGTAGC 59.145 40.741 0.00 0.00 0.00 3.58
1375 2700 5.976534 GGCGATAGTATATCTCTTGCATCTG 59.023 44.000 0.00 0.00 33.09 2.90
1395 2720 0.818040 TAGCGCAGATACTCTGGCGA 60.818 55.000 11.47 9.36 44.43 5.54
1449 2775 1.856597 GTACAAAGTGTTGCGTCGACT 59.143 47.619 14.70 0.00 38.39 4.18
1472 2798 8.421784 CCTAACTTAATGGTATCAAGCACTAGA 58.578 37.037 0.00 0.00 35.57 2.43
1477 2803 4.814234 CGCCTAACTTAATGGTATCAAGCA 59.186 41.667 0.00 0.00 37.55 3.91
1522 2848 6.403049 TCTCGCATTTTCTCCATAACAAGTA 58.597 36.000 0.00 0.00 0.00 2.24
1528 2854 5.427378 TGACATCTCGCATTTTCTCCATAA 58.573 37.500 0.00 0.00 0.00 1.90
1569 2895 2.194056 CCATCCCTCAGCGGCAAT 59.806 61.111 1.45 0.00 0.00 3.56
1627 2955 0.179043 TTGTTACCAACGCCAGAGCA 60.179 50.000 0.00 0.00 39.83 4.26
1671 2999 0.453282 CTTGCGAAATGGTGTGCTCG 60.453 55.000 0.00 0.00 0.00 5.03
1744 3073 1.153823 GAGCTTTGTCGCGGCTAGA 60.154 57.895 13.81 0.00 36.37 2.43
1768 3108 6.627087 TCTACTCATCTTTGATGGTTCCTT 57.373 37.500 7.58 0.00 0.00 3.36
1784 3128 6.205270 TCCGCGTACATAACATAATCTACTCA 59.795 38.462 4.92 0.00 0.00 3.41
1804 3148 2.432628 GTGTCCCTGAACTCCGCG 60.433 66.667 0.00 0.00 0.00 6.46
1903 3248 1.521450 GCTGCATGTGTTCCTGTGCT 61.521 55.000 0.00 0.00 38.37 4.40
1972 3325 5.628130 AGTGAGACATAGCCAAATGCATAT 58.372 37.500 0.00 0.00 44.83 1.78
2000 3354 8.196771 AGCTCATTCTAGAGACTGTTTCTAATG 58.803 37.037 13.59 13.59 37.87 1.90
2021 3378 3.849911 CGTCTTCTTATTGGTCAGCTCA 58.150 45.455 0.00 0.00 0.00 4.26
2029 3386 3.535561 ACTCATGGCGTCTTCTTATTGG 58.464 45.455 0.00 0.00 0.00 3.16
2030 3387 3.557595 GGACTCATGGCGTCTTCTTATTG 59.442 47.826 13.34 0.00 0.00 1.90
2045 3402 4.039245 CCATAACCGTAGTCATGGACTCAT 59.961 45.833 1.55 0.00 42.40 2.90
2046 3403 3.383505 CCATAACCGTAGTCATGGACTCA 59.616 47.826 1.55 0.00 42.40 3.41
2047 3404 3.243771 CCCATAACCGTAGTCATGGACTC 60.244 52.174 1.55 0.00 42.40 3.36
2048 3405 2.698797 CCCATAACCGTAGTCATGGACT 59.301 50.000 4.13 4.13 45.54 3.85
2049 3406 2.224209 CCCCATAACCGTAGTCATGGAC 60.224 54.545 0.00 0.00 40.37 4.02
2050 3407 2.043992 CCCCATAACCGTAGTCATGGA 58.956 52.381 0.00 0.00 40.37 3.41
2130 3487 7.656137 GGAACTCATCTATTTATACCGCAGAAA 59.344 37.037 0.00 0.00 0.00 2.52
2164 3521 3.430453 GTCAGACCATTTTGGGAATCCA 58.570 45.455 0.09 0.00 43.37 3.41
2177 3534 1.121378 TGGTGTTTACGGTCAGACCA 58.879 50.000 20.13 5.44 38.47 4.02
2185 3542 0.232816 CCGAACGTTGGTGTTTACGG 59.767 55.000 5.00 5.90 41.81 4.02
2193 3550 0.395312 ACTGGAATCCGAACGTTGGT 59.605 50.000 5.00 0.00 0.00 3.67
2216 3573 1.305465 TGCTAGCCGGTCTACCCAA 60.305 57.895 13.29 0.00 0.00 4.12
2286 3652 2.427245 CCCTAGCTACGCCACTGCT 61.427 63.158 0.00 0.00 40.43 4.24
2288 3654 2.797278 CCCCCTAGCTACGCCACTG 61.797 68.421 0.00 0.00 0.00 3.66
2289 3655 2.444140 CCCCCTAGCTACGCCACT 60.444 66.667 0.00 0.00 0.00 4.00
2290 3656 2.762875 ACCCCCTAGCTACGCCAC 60.763 66.667 0.00 0.00 0.00 5.01
2291 3657 2.762459 CACCCCCTAGCTACGCCA 60.762 66.667 0.00 0.00 0.00 5.69
2292 3658 3.547513 CCACCCCCTAGCTACGCC 61.548 72.222 0.00 0.00 0.00 5.68
2294 3660 3.547513 GGCCACCCCCTAGCTACG 61.548 72.222 0.00 0.00 0.00 3.51
2299 3665 4.760220 ACCCTGGCCACCCCCTAG 62.760 72.222 0.00 0.00 0.00 3.02
2310 3676 4.016706 GTCCACGGACCACCCTGG 62.017 72.222 4.78 0.00 45.02 4.45
2318 3684 4.016706 CCAGGGTGGTCCACGGAC 62.017 72.222 15.93 7.75 43.87 4.79
2319 3685 3.777818 TTCCAGGGTGGTCCACGGA 62.778 63.158 15.93 13.70 39.03 4.69
2320 3686 2.137177 AATTCCAGGGTGGTCCACGG 62.137 60.000 15.93 11.57 39.03 4.94
2321 3687 0.251165 AAATTCCAGGGTGGTCCACG 60.251 55.000 15.93 2.12 39.03 4.94
2322 3688 1.545841 GAAATTCCAGGGTGGTCCAC 58.454 55.000 14.13 14.13 39.03 4.02
2323 3689 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
2324 3690 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
2325 3691 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
2326 3692 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
2327 3693 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
2328 3694 3.031013 GTTATGGGGAAATTCCAGGGTG 58.969 50.000 14.68 0.00 38.64 4.61
2329 3695 2.933139 AGTTATGGGGAAATTCCAGGGT 59.067 45.455 14.68 0.00 38.64 4.34
2330 3696 3.688049 AGTTATGGGGAAATTCCAGGG 57.312 47.619 14.68 0.00 38.64 4.45
2331 3697 4.352893 ACAAGTTATGGGGAAATTCCAGG 58.647 43.478 14.68 0.00 38.64 4.45
2332 3698 8.940397 ATATACAAGTTATGGGGAAATTCCAG 57.060 34.615 14.68 0.00 38.64 3.86
2339 3705 9.664777 ACTACACTATATACAAGTTATGGGGAA 57.335 33.333 0.00 0.00 0.00 3.97
2400 3766 9.883142 GGGTGGTCAATTGATGAAAATATTTAA 57.117 29.630 12.12 0.00 40.50 1.52
2401 3767 9.265862 AGGGTGGTCAATTGATGAAAATATTTA 57.734 29.630 12.12 0.00 40.50 1.40
2402 3768 8.042515 CAGGGTGGTCAATTGATGAAAATATTT 58.957 33.333 12.12 0.00 40.50 1.40
2403 3769 7.364939 CCAGGGTGGTCAATTGATGAAAATATT 60.365 37.037 12.12 0.00 40.50 1.28
2404 3770 6.098695 CCAGGGTGGTCAATTGATGAAAATAT 59.901 38.462 12.12 0.00 40.50 1.28
2405 3771 5.421693 CCAGGGTGGTCAATTGATGAAAATA 59.578 40.000 12.12 0.00 40.50 1.40
2406 3772 4.223477 CCAGGGTGGTCAATTGATGAAAAT 59.777 41.667 12.12 0.00 40.50 1.82
2407 3773 3.577848 CCAGGGTGGTCAATTGATGAAAA 59.422 43.478 12.12 0.00 40.50 2.29
2408 3774 3.164268 CCAGGGTGGTCAATTGATGAAA 58.836 45.455 12.12 0.00 40.50 2.69
2409 3775 2.378208 TCCAGGGTGGTCAATTGATGAA 59.622 45.455 12.12 0.00 40.50 2.57
2410 3776 1.991813 TCCAGGGTGGTCAATTGATGA 59.008 47.619 12.12 0.00 39.03 2.92
2411 3777 2.291153 ACTCCAGGGTGGTCAATTGATG 60.291 50.000 12.12 4.47 39.03 3.07
2412 3778 1.995542 ACTCCAGGGTGGTCAATTGAT 59.004 47.619 12.12 0.00 39.03 2.57
2413 3779 1.444933 ACTCCAGGGTGGTCAATTGA 58.555 50.000 3.38 3.38 39.03 2.57
2414 3780 3.652057 ATACTCCAGGGTGGTCAATTG 57.348 47.619 0.00 0.00 39.03 2.32
2415 3781 3.309121 CCAATACTCCAGGGTGGTCAATT 60.309 47.826 0.00 0.00 39.03 2.32
2416 3782 2.242196 CCAATACTCCAGGGTGGTCAAT 59.758 50.000 0.00 0.00 39.03 2.57
2417 3783 1.633432 CCAATACTCCAGGGTGGTCAA 59.367 52.381 0.00 0.00 39.03 3.18
2418 3784 1.285280 CCAATACTCCAGGGTGGTCA 58.715 55.000 0.00 0.00 39.03 4.02
2419 3785 1.286248 ACCAATACTCCAGGGTGGTC 58.714 55.000 0.00 0.00 38.16 4.02
2420 3786 1.203440 AGACCAATACTCCAGGGTGGT 60.203 52.381 0.00 0.00 45.23 4.16
2421 3787 1.210478 CAGACCAATACTCCAGGGTGG 59.790 57.143 0.00 0.00 39.43 4.61
2422 3788 1.210478 CCAGACCAATACTCCAGGGTG 59.790 57.143 0.00 0.00 32.77 4.61
2423 3789 1.584724 CCAGACCAATACTCCAGGGT 58.415 55.000 0.00 0.00 36.05 4.34
2424 3790 0.181350 GCCAGACCAATACTCCAGGG 59.819 60.000 0.00 0.00 0.00 4.45
2425 3791 1.207791 AGCCAGACCAATACTCCAGG 58.792 55.000 0.00 0.00 0.00 4.45
2426 3792 2.223829 CGTAGCCAGACCAATACTCCAG 60.224 54.545 0.00 0.00 0.00 3.86
2427 3793 1.754803 CGTAGCCAGACCAATACTCCA 59.245 52.381 0.00 0.00 0.00 3.86
2428 3794 2.510768 CGTAGCCAGACCAATACTCC 57.489 55.000 0.00 0.00 0.00 3.85
2450 3816 0.242286 CTAGCGAGCTCACACACAGT 59.758 55.000 15.40 0.00 0.00 3.55
2451 3817 1.075425 GCTAGCGAGCTCACACACAG 61.075 60.000 15.40 5.31 45.98 3.66
2452 3818 1.080501 GCTAGCGAGCTCACACACA 60.081 57.895 15.40 0.00 45.98 3.72
2453 3819 3.773974 GCTAGCGAGCTCACACAC 58.226 61.111 15.40 0.00 45.98 3.82
2512 3878 3.842923 GAGCTCGCTGGCAGGCTA 61.843 66.667 17.64 0.00 35.01 3.93
2551 3917 9.111613 CCCACACCGTATTATGTATTTTTCTAA 57.888 33.333 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.