Multiple sequence alignment - TraesCS1B01G397000

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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 TraesCS1B01G397000 chr1B 100.000 5794 0 0 1 5794 628622131 628616338 0.000000e+00 10700.0
1 TraesCS1B01G397000 chr1B 96.272 751 25 1 1 751 272386326 272387073 0.000000e+00 1229.0
2 TraesCS1B01G397000 chr1B 76.990 1030 143 61 5 969 3885984 3884984 2.410000e-138 503.0
3 TraesCS1B01G397000 chr1B 88.710 186 8 5 787 970 272387069 272387243 1.260000e-51 215.0
4 TraesCS1B01G397000 chr1B 80.812 271 42 7 2175 2443 484287041 484287303 2.740000e-48 204.0
5 TraesCS1B01G397000 chr1A 95.775 2556 89 8 3245 5794 550636395 550633853 0.000000e+00 4104.0
6 TraesCS1B01G397000 chr1A 97.710 262 6 0 968 1229 550637045 550636784 8.850000e-123 451.0
7 TraesCS1B01G397000 chr1A 78.269 520 77 14 1967 2459 518772207 518771697 9.440000e-78 302.0
8 TraesCS1B01G397000 chr1A 96.429 56 2 0 3191 3246 550636792 550636737 6.180000e-15 93.5
9 TraesCS1B01G397000 chr1D 95.195 2560 95 10 3248 5794 458145512 458142968 0.000000e+00 4021.0
10 TraesCS1B01G397000 chr1D 95.802 262 11 0 968 1229 458146164 458145903 1.930000e-114 424.0
11 TraesCS1B01G397000 chr1D 83.406 229 33 5 3966 4192 386257562 386257787 2.120000e-49 207.0
12 TraesCS1B01G397000 chr2B 95.921 1986 45 18 1231 3194 788535172 788537143 0.000000e+00 3186.0
13 TraesCS1B01G397000 chr2B 98.018 1564 25 5 1631 3190 765370682 765372243 0.000000e+00 2712.0
14 TraesCS1B01G397000 chr2B 88.212 1001 76 15 5 968 13676412 13675417 0.000000e+00 1157.0
15 TraesCS1B01G397000 chr2B 98.254 401 7 0 1231 1631 765368560 765368960 0.000000e+00 702.0
16 TraesCS1B01G397000 chr2B 90.323 62 6 0 912 973 785593353 785593292 1.340000e-11 82.4
17 TraesCS1B01G397000 chr7B 95.904 1953 51 9 1261 3189 725404549 725402602 0.000000e+00 3136.0
18 TraesCS1B01G397000 chr7B 84.655 769 61 27 1231 1971 605648977 605648238 0.000000e+00 713.0
19 TraesCS1B01G397000 chr7B 88.748 551 45 9 2457 2995 605647987 605647442 0.000000e+00 658.0
20 TraesCS1B01G397000 chr7B 89.077 531 47 5 448 969 656241392 656240864 0.000000e+00 649.0
21 TraesCS1B01G397000 chr3B 96.335 1255 42 4 1942 3192 739937791 739936537 0.000000e+00 2060.0
22 TraesCS1B01G397000 chr3B 94.993 739 16 12 1231 1952 739942910 739942176 0.000000e+00 1140.0
23 TraesCS1B01G397000 chr3B 84.541 207 29 2 1237 1440 824129521 824129315 9.840000e-48 202.0
24 TraesCS1B01G397000 chr3A 98.049 974 14 3 1 972 671734569 671733599 0.000000e+00 1688.0
25 TraesCS1B01G397000 chr3A 73.638 2166 507 55 3566 5703 24012214 24014343 0.000000e+00 778.0
26 TraesCS1B01G397000 chr2A 97.336 976 16 4 1 969 154813021 154812049 0.000000e+00 1650.0
27 TraesCS1B01G397000 chr2A 97.228 974 22 3 1 972 67975157 67976127 0.000000e+00 1644.0
28 TraesCS1B01G397000 chr2A 87.790 991 80 14 5 959 81482369 81483354 0.000000e+00 1122.0
29 TraesCS1B01G397000 chr2A 76.690 1124 232 29 3570 4678 727175356 727174248 1.070000e-166 597.0
30 TraesCS1B01G397000 chr2A 91.176 272 22 2 702 971 81483700 81483971 9.170000e-98 368.0
31 TraesCS1B01G397000 chr6B 95.160 971 26 5 1 969 448366245 448365294 0.000000e+00 1513.0
32 TraesCS1B01G397000 chr6B 71.075 1535 378 56 3570 5067 47092699 47091194 1.210000e-81 315.0
33 TraesCS1B01G397000 chr6B 81.481 216 38 2 2224 2438 703665180 703664966 5.970000e-40 176.0
34 TraesCS1B01G397000 chr6B 78.431 204 21 8 1240 1440 716290777 716290594 1.710000e-20 111.0
35 TraesCS1B01G397000 chr4D 75.138 2176 493 41 3573 5723 1823272 1825424 0.000000e+00 977.0
36 TraesCS1B01G397000 chr4D 85.657 495 65 4 1967 2457 446104212 446103720 3.100000e-142 516.0
37 TraesCS1B01G397000 chr4D 81.034 232 34 7 5558 5781 2889493 2889722 5.970000e-40 176.0
38 TraesCS1B01G397000 chr4D 79.832 238 35 7 5567 5794 2117065 2116831 1.670000e-35 161.0
39 TraesCS1B01G397000 chrUn 75.129 2127 459 57 3577 5664 47631565 47633660 0.000000e+00 933.0
40 TraesCS1B01G397000 chrUn 74.728 2117 482 46 3577 5664 47452166 47454258 0.000000e+00 896.0
41 TraesCS1B01G397000 chrUn 74.134 2223 491 72 3599 5777 47949888 47952070 0.000000e+00 843.0
42 TraesCS1B01G397000 chrUn 90.487 431 28 7 2770 3191 297566645 297567071 1.820000e-154 556.0
43 TraesCS1B01G397000 chrUn 90.487 431 28 7 2770 3191 297571582 297572008 1.820000e-154 556.0
44 TraesCS1B01G397000 chrUn 72.277 1111 256 42 3570 4654 96217856 96216772 1.220000e-76 298.0
45 TraesCS1B01G397000 chrUn 88.108 185 22 0 968 1152 48045740 48045924 2.720000e-53 220.0
46 TraesCS1B01G397000 chrUn 88.108 185 22 0 968 1152 48076011 48076195 2.720000e-53 220.0
47 TraesCS1B01G397000 chr4B 74.188 2185 496 52 3577 5723 3733780 3735934 0.000000e+00 848.0
48 TraesCS1B01G397000 chr4B 84.686 764 75 24 1231 1971 382786584 382787328 0.000000e+00 725.0
49 TraesCS1B01G397000 chr4B 87.703 553 49 11 2458 2995 382787583 382788131 1.370000e-175 627.0
50 TraesCS1B01G397000 chr4B 87.179 195 23 1 968 1160 3483367 3483173 2.720000e-53 220.0
51 TraesCS1B01G397000 chr4B 87.179 195 23 1 968 1160 3513340 3513146 2.720000e-53 220.0
52 TraesCS1B01G397000 chr4B 86.667 195 24 1 968 1160 3430817 3430623 1.260000e-51 215.0
53 TraesCS1B01G397000 chr4B 80.513 195 16 4 968 1160 3453252 3453078 4.710000e-26 130.0
54 TraesCS1B01G397000 chr4B 92.754 69 3 1 1094 1160 3426309 3426241 1.330000e-16 99.0
55 TraesCS1B01G397000 chr5D 75.085 1774 368 53 3553 5288 43962342 43964079 0.000000e+00 760.0
56 TraesCS1B01G397000 chr5D 85.600 250 29 3 1967 2211 557937817 557938064 7.450000e-64 255.0
57 TraesCS1B01G397000 chr3D 73.441 2165 511 56 3566 5703 13179916 13177789 0.000000e+00 754.0
58 TraesCS1B01G397000 chr3D 85.246 183 23 4 1967 2147 539576000 539576180 9.910000e-43 185.0
59 TraesCS1B01G397000 chr4A 87.862 552 49 10 2458 2995 722494731 722495278 2.950000e-177 632.0
60 TraesCS1B01G397000 chr4A 90.153 457 35 4 2743 3190 645463055 645463510 2.330000e-163 586.0
61 TraesCS1B01G397000 chr4A 89.934 457 36 3 2743 3190 645523101 645523556 1.080000e-161 580.0
62 TraesCS1B01G397000 chr4A 90.487 431 28 7 2770 3191 645461894 645461468 1.820000e-154 556.0
63 TraesCS1B01G397000 chr4A 90.487 431 28 7 2770 3191 645521940 645521514 1.820000e-154 556.0
64 TraesCS1B01G397000 chr4A 78.068 497 80 10 1967 2442 712114302 712114790 2.640000e-73 287.0
65 TraesCS1B01G397000 chr4A 85.890 163 20 2 5563 5722 603047697 603047859 2.780000e-38 171.0
66 TraesCS1B01G397000 chr2D 76.854 1119 239 20 3570 4678 592621055 592619947 1.070000e-171 614.0
67 TraesCS1B01G397000 chr2D 78.733 442 59 15 2022 2457 76880923 76881335 4.450000e-66 263.0
68 TraesCS1B01G397000 chr6D 87.174 499 57 5 1964 2457 379559273 379559769 1.410000e-155 560.0
69 TraesCS1B01G397000 chr6D 87.121 396 23 8 5 373 42940288 42939894 1.930000e-114 424.0
70 TraesCS1B01G397000 chr7A 85.185 486 65 6 1966 2448 28155389 28154908 5.220000e-135 492.0
71 TraesCS1B01G397000 chr7A 80.836 287 45 6 2156 2440 642525126 642525404 3.520000e-52 217.0
72 TraesCS1B01G397000 chr6A 71.217 1758 432 59 3570 5289 27106480 27104759 5.480000e-100 375.0
73 TraesCS1B01G397000 chr5B 80.901 466 70 12 3543 4002 41907240 41907692 3.320000e-92 350.0
74 TraesCS1B01G397000 chr7D 78.252 515 94 10 3966 4478 45171971 45171473 1.210000e-81 315.0
75 TraesCS1B01G397000 chr7D 83.843 229 33 4 3966 4192 590795792 590795566 1.260000e-51 215.0


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 TraesCS1B01G397000 chr1B 628616338 628622131 5793 True 10700.0 10700 100.0000 1 5794 1 chr1B.!!$R2 5793
1 TraesCS1B01G397000 chr1B 272386326 272387243 917 False 722.0 1229 92.4910 1 970 2 chr1B.!!$F2 969
2 TraesCS1B01G397000 chr1B 3884984 3885984 1000 True 503.0 503 76.9900 5 969 1 chr1B.!!$R1 964
3 TraesCS1B01G397000 chr1A 550633853 550637045 3192 True 1549.5 4104 96.6380 968 5794 3 chr1A.!!$R2 4826
4 TraesCS1B01G397000 chr1A 518771697 518772207 510 True 302.0 302 78.2690 1967 2459 1 chr1A.!!$R1 492
5 TraesCS1B01G397000 chr1D 458142968 458146164 3196 True 2222.5 4021 95.4985 968 5794 2 chr1D.!!$R1 4826
6 TraesCS1B01G397000 chr2B 788535172 788537143 1971 False 3186.0 3186 95.9210 1231 3194 1 chr2B.!!$F1 1963
7 TraesCS1B01G397000 chr2B 765368560 765372243 3683 False 1707.0 2712 98.1360 1231 3190 2 chr2B.!!$F2 1959
8 TraesCS1B01G397000 chr2B 13675417 13676412 995 True 1157.0 1157 88.2120 5 968 1 chr2B.!!$R1 963
9 TraesCS1B01G397000 chr7B 725402602 725404549 1947 True 3136.0 3136 95.9040 1261 3189 1 chr7B.!!$R2 1928
10 TraesCS1B01G397000 chr7B 605647442 605648977 1535 True 685.5 713 86.7015 1231 2995 2 chr7B.!!$R3 1764
11 TraesCS1B01G397000 chr7B 656240864 656241392 528 True 649.0 649 89.0770 448 969 1 chr7B.!!$R1 521
12 TraesCS1B01G397000 chr3B 739936537 739937791 1254 True 2060.0 2060 96.3350 1942 3192 1 chr3B.!!$R1 1250
13 TraesCS1B01G397000 chr3B 739942176 739942910 734 True 1140.0 1140 94.9930 1231 1952 1 chr3B.!!$R2 721
14 TraesCS1B01G397000 chr3A 671733599 671734569 970 True 1688.0 1688 98.0490 1 972 1 chr3A.!!$R1 971
15 TraesCS1B01G397000 chr3A 24012214 24014343 2129 False 778.0 778 73.6380 3566 5703 1 chr3A.!!$F1 2137
16 TraesCS1B01G397000 chr2A 154812049 154813021 972 True 1650.0 1650 97.3360 1 969 1 chr2A.!!$R1 968
17 TraesCS1B01G397000 chr2A 67975157 67976127 970 False 1644.0 1644 97.2280 1 972 1 chr2A.!!$F1 971
18 TraesCS1B01G397000 chr2A 81482369 81483971 1602 False 745.0 1122 89.4830 5 971 2 chr2A.!!$F2 966
19 TraesCS1B01G397000 chr2A 727174248 727175356 1108 True 597.0 597 76.6900 3570 4678 1 chr2A.!!$R2 1108
20 TraesCS1B01G397000 chr6B 448365294 448366245 951 True 1513.0 1513 95.1600 1 969 1 chr6B.!!$R2 968
21 TraesCS1B01G397000 chr6B 47091194 47092699 1505 True 315.0 315 71.0750 3570 5067 1 chr6B.!!$R1 1497
22 TraesCS1B01G397000 chr4D 1823272 1825424 2152 False 977.0 977 75.1380 3573 5723 1 chr4D.!!$F1 2150
23 TraesCS1B01G397000 chrUn 47631565 47633660 2095 False 933.0 933 75.1290 3577 5664 1 chrUn.!!$F2 2087
24 TraesCS1B01G397000 chrUn 47452166 47454258 2092 False 896.0 896 74.7280 3577 5664 1 chrUn.!!$F1 2087
25 TraesCS1B01G397000 chrUn 47949888 47952070 2182 False 843.0 843 74.1340 3599 5777 1 chrUn.!!$F3 2178
26 TraesCS1B01G397000 chrUn 96216772 96217856 1084 True 298.0 298 72.2770 3570 4654 1 chrUn.!!$R1 1084
27 TraesCS1B01G397000 chr4B 3733780 3735934 2154 False 848.0 848 74.1880 3577 5723 1 chr4B.!!$F1 2146
28 TraesCS1B01G397000 chr4B 382786584 382788131 1547 False 676.0 725 86.1945 1231 2995 2 chr4B.!!$F2 1764
29 TraesCS1B01G397000 chr5D 43962342 43964079 1737 False 760.0 760 75.0850 3553 5288 1 chr5D.!!$F1 1735
30 TraesCS1B01G397000 chr3D 13177789 13179916 2127 True 754.0 754 73.4410 3566 5703 1 chr3D.!!$R1 2137
31 TraesCS1B01G397000 chr4A 722494731 722495278 547 False 632.0 632 87.8620 2458 2995 1 chr4A.!!$F5 537
32 TraesCS1B01G397000 chr2D 592619947 592621055 1108 True 614.0 614 76.8540 3570 4678 1 chr2D.!!$R1 1108
33 TraesCS1B01G397000 chr6A 27104759 27106480 1721 True 375.0 375 71.2170 3570 5289 1 chr6A.!!$R1 1719

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
265 330 1.521906 CGACCGACCACCACAAACA 60.522 57.895 0.00 0.0 0.00 2.83 F
399 464 2.345991 CGGTCGCCTCCCTTGAAA 59.654 61.111 0.00 0.0 0.00 2.69 F
1418 2134 1.138047 GCTGATGCTTGCGAACATGC 61.138 55.000 0.00 0.0 44.91 4.06 F
1431 2147 0.316204 AACATGCTGTGCTTTCTGGC 59.684 50.000 0.00 0.0 0.00 4.85 F
2982 5542 0.034574 TGCACTGTGTGGACAAGGTT 60.035 50.000 9.86 0.0 33.64 3.50 F
3036 5596 1.378531 GGCAGCGTCATTAACATGGA 58.621 50.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 1943 0.606673 GCCTCCAAAACGCCTCTCTT 60.607 55.000 0.00 0.0 0.00 2.85 R
1431 2147 1.211709 GAACGTTCCCCAAATGCGG 59.788 57.895 17.68 0.0 0.00 5.69 R
2982 5542 0.038618 CACGTTCCATCGTCTCACCA 60.039 55.000 0.00 0.0 42.27 4.17 R
3065 5625 2.627699 CTGGCACCTTTTTACACCACAT 59.372 45.455 0.00 0.0 0.00 3.21 R
4398 7326 5.048713 GGAATTTCAACTCGTGGATGTTCTT 60.049 40.000 0.00 0.0 0.00 2.52 R
4794 7730 5.067674 CACCTCAATTTTCTGTTGTTCCTCA 59.932 40.000 0.00 0.0 0.00 3.86 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
78 79 4.530857 CGGGATGTGCCGAGGACC 62.531 72.222 7.19 0.00 37.63 4.46
265 330 1.521906 CGACCGACCACCACAAACA 60.522 57.895 0.00 0.00 0.00 2.83
398 463 3.702048 CCGGTCGCCTCCCTTGAA 61.702 66.667 0.00 0.00 0.00 2.69
399 464 2.345991 CGGTCGCCTCCCTTGAAA 59.654 61.111 0.00 0.00 0.00 2.69
1164 1878 6.320164 AGAAGCAGGTCAGTACTTACTCATAG 59.680 42.308 7.13 0.00 33.46 2.23
1167 1881 5.357314 GCAGGTCAGTACTTACTCATAGTCA 59.643 44.000 7.13 0.00 33.46 3.41
1418 2134 1.138047 GCTGATGCTTGCGAACATGC 61.138 55.000 0.00 0.00 44.91 4.06
1431 2147 0.316204 AACATGCTGTGCTTTCTGGC 59.684 50.000 0.00 0.00 0.00 4.85
1441 2157 1.216178 CTTTCTGGCCGCATTTGGG 59.784 57.895 0.00 0.00 0.00 4.12
1614 2367 7.647907 TTTTAGTTCGATCTGTTTCTACCAC 57.352 36.000 6.25 0.00 0.00 4.16
2067 4580 5.931146 GCTTCTGCATAGCTAGAATGTACAT 59.069 40.000 1.41 1.41 39.41 2.29
2528 5069 8.623030 ACATTTTGTTGTAACGGTTGTTAGTAT 58.377 29.630 3.07 0.00 41.09 2.12
2572 5115 4.798387 GGTTGTTGAAACACATGAACAGTC 59.202 41.667 0.00 0.00 38.92 3.51
2603 5146 8.792633 ACGGAGAAGAACATTATTGAAAAATGA 58.207 29.630 3.01 0.00 37.68 2.57
2982 5542 0.034574 TGCACTGTGTGGACAAGGTT 60.035 50.000 9.86 0.00 33.64 3.50
3036 5596 1.378531 GGCAGCGTCATTAACATGGA 58.621 50.000 0.00 0.00 0.00 3.41
3065 5625 8.909708 GCACTGTGCATAATTTAAGAATACAA 57.090 30.769 26.70 0.00 44.26 2.41
3180 5741 2.281484 GTGCTCGGCCTCCAAACA 60.281 61.111 0.00 0.00 0.00 2.83
3192 5753 2.161609 CCTCCAAACAGCATTTCCGTAC 59.838 50.000 0.00 0.00 0.00 3.67
3193 5754 2.811431 CTCCAAACAGCATTTCCGTACA 59.189 45.455 0.00 0.00 0.00 2.90
3194 5755 3.417101 TCCAAACAGCATTTCCGTACAT 58.583 40.909 0.00 0.00 0.00 2.29
3195 5756 4.580868 TCCAAACAGCATTTCCGTACATA 58.419 39.130 0.00 0.00 0.00 2.29
3196 5757 5.189928 TCCAAACAGCATTTCCGTACATAT 58.810 37.500 0.00 0.00 0.00 1.78
3197 5758 5.295787 TCCAAACAGCATTTCCGTACATATC 59.704 40.000 0.00 0.00 0.00 1.63
3198 5759 5.065859 CCAAACAGCATTTCCGTACATATCA 59.934 40.000 0.00 0.00 0.00 2.15
3239 5800 6.978343 TTATATATGAACTTGCATACGGCC 57.022 37.500 0.00 0.00 43.89 6.13
3492 6399 1.597742 AGTGCACTGCTTGTGGTAAG 58.402 50.000 20.97 0.00 46.27 2.34
3496 6403 3.314080 GTGCACTGCTTGTGGTAAGTAAA 59.686 43.478 10.32 0.00 46.27 2.01
3497 6404 4.023193 GTGCACTGCTTGTGGTAAGTAAAT 60.023 41.667 10.32 0.00 46.27 1.40
3535 6442 4.827284 ACCTAGCCATTGCCAACATATTAC 59.173 41.667 0.00 0.00 38.69 1.89
4398 7326 5.539955 TGCACAGATATATCTAGACTGCCAA 59.460 40.000 14.92 3.32 34.85 4.52
4794 7730 1.555075 TGCTCAAAGCCCGAGTCTAAT 59.445 47.619 0.00 0.00 41.51 1.73
4849 7785 1.699634 TGATATGCCCTCTACCTTGCC 59.300 52.381 0.00 0.00 0.00 4.52
5010 7946 1.628340 TGTCGACTCCCATGTTTGGAT 59.372 47.619 17.92 0.00 46.92 3.41
5053 7989 0.878416 GGCAATCAAGCGTGTTGGTA 59.122 50.000 13.46 0.00 34.64 3.25
5124 8066 2.642154 TGGTTGGCTTTCCGAAACTA 57.358 45.000 0.00 0.00 34.14 2.24
5199 8141 1.369091 AAGTTCAAGCTATGCCCGCG 61.369 55.000 0.00 0.00 0.00 6.46
5289 8231 7.309805 GCAAGGGTTATGAAGAAGTTAACCATT 60.310 37.037 11.86 8.72 45.64 3.16
5340 8282 5.470047 AGAACTTCACTTCCGTAGTTCAT 57.530 39.130 14.14 0.36 45.52 2.57
5372 8314 2.440409 TGACTTACCCGACCTGACTAC 58.560 52.381 0.00 0.00 0.00 2.73
5373 8315 2.224843 TGACTTACCCGACCTGACTACA 60.225 50.000 0.00 0.00 0.00 2.74
5744 8689 6.111768 ACATATTGTTGATCGTTGCTCTTC 57.888 37.500 0.00 0.00 0.00 2.87
5745 8690 5.065218 ACATATTGTTGATCGTTGCTCTTCC 59.935 40.000 0.00 0.00 0.00 3.46
5746 8691 2.542020 TGTTGATCGTTGCTCTTCCA 57.458 45.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.288926 GATTGAGAGTGTGCAGCGCG 62.289 60.000 0.00 0.00 0.00 6.86
118 119 0.606401 CTCACGGATGGGTTGCTGTT 60.606 55.000 0.00 0.00 0.00 3.16
265 330 3.728373 GGTGGCGATGGAAGGGGT 61.728 66.667 0.00 0.00 0.00 4.95
397 462 1.452108 GTCCTAGCCGGCTGCATTT 60.452 57.895 38.98 14.66 44.83 2.32
398 463 2.190578 GTCCTAGCCGGCTGCATT 59.809 61.111 38.98 15.51 44.83 3.56
399 464 3.083349 TGTCCTAGCCGGCTGCAT 61.083 61.111 38.98 15.95 44.83 3.96
1164 1878 9.101655 ACACTAAAATACGGGTGTTATATTGAC 57.898 33.333 0.00 0.00 39.47 3.18
1167 1881 9.101655 GTGACACTAAAATACGGGTGTTATATT 57.898 33.333 0.00 0.00 42.01 1.28
1229 1943 0.606673 GCCTCCAAAACGCCTCTCTT 60.607 55.000 0.00 0.00 0.00 2.85
1418 2134 1.870055 AATGCGGCCAGAAAGCACAG 61.870 55.000 2.24 0.00 44.12 3.66
1431 2147 1.211709 GAACGTTCCCCAAATGCGG 59.788 57.895 17.68 0.00 0.00 5.69
1612 2365 6.813152 CAGCACATTTTCCCCTATAAAAAGTG 59.187 38.462 10.59 10.59 43.30 3.16
1614 2367 6.935167 ACAGCACATTTTCCCCTATAAAAAG 58.065 36.000 0.00 0.00 30.20 2.27
1848 4325 9.797473 CTGTGTATTTTAGCAATATATGTGACG 57.203 33.333 0.00 0.00 0.00 4.35
2067 4580 3.283259 TGTGTGTGTTGGTGTTGGATA 57.717 42.857 0.00 0.00 0.00 2.59
2572 5115 7.364522 TCAATAATGTTCTTCTCCGTGAAAG 57.635 36.000 0.00 0.00 33.79 2.62
2652 5197 7.967890 AAATCACATTGTCCAAAGGAAAATC 57.032 32.000 0.00 0.00 37.53 2.17
2982 5542 0.038618 CACGTTCCATCGTCTCACCA 60.039 55.000 0.00 0.00 42.27 4.17
3065 5625 2.627699 CTGGCACCTTTTTACACCACAT 59.372 45.455 0.00 0.00 0.00 3.21
3180 5741 4.127171 GTGGTGATATGTACGGAAATGCT 58.873 43.478 0.00 0.00 0.00 3.79
3237 5798 6.391227 AGCAATAAAACTATATGTGGTGGC 57.609 37.500 0.00 0.00 0.00 5.01
3287 6194 7.761249 CCTTTTCATTTATCATCTTGGTGAACC 59.239 37.037 0.00 0.00 0.00 3.62
3449 6356 9.959721 ACTAGATCACCAAGAAAATAAGCTAAA 57.040 29.630 0.00 0.00 0.00 1.85
3535 6442 8.897872 AACATATAAAGTTAATGAGGGGTACG 57.102 34.615 0.00 0.00 0.00 3.67
3563 6470 2.654863 ACCTGCAAGCAGTTGTAAGTT 58.345 42.857 19.60 0.00 42.15 2.66
3564 6471 2.348411 ACCTGCAAGCAGTTGTAAGT 57.652 45.000 19.60 7.34 42.15 2.24
3565 6472 3.403038 AGTACCTGCAAGCAGTTGTAAG 58.597 45.455 19.60 6.74 42.15 2.34
3566 6473 3.181459 TGAGTACCTGCAAGCAGTTGTAA 60.181 43.478 19.60 0.57 42.15 2.41
3567 6474 2.367241 TGAGTACCTGCAAGCAGTTGTA 59.633 45.455 19.60 12.79 42.15 2.41
3568 6475 1.140852 TGAGTACCTGCAAGCAGTTGT 59.859 47.619 19.60 13.70 42.15 3.32
4398 7326 5.048713 GGAATTTCAACTCGTGGATGTTCTT 60.049 40.000 0.00 0.00 0.00 2.52
4794 7730 5.067674 CACCTCAATTTTCTGTTGTTCCTCA 59.932 40.000 0.00 0.00 0.00 3.86
5053 7989 2.524306 TCGGGGTTGCAAGAATTCATT 58.476 42.857 8.44 0.00 0.00 2.57
5124 8066 6.321181 ACATTCCACTTAAAATCAGTGTGTGT 59.679 34.615 0.00 0.00 40.19 3.72
5149 8091 1.214305 CCCCACTCCTCCCATTCCAA 61.214 60.000 0.00 0.00 0.00 3.53
5289 8231 1.663739 GAGACACTGTACGCCACCA 59.336 57.895 0.00 0.00 0.00 4.17
5298 8240 1.617322 TTAGCGACTGGAGACACTGT 58.383 50.000 0.00 0.00 35.60 3.55
5340 8282 3.889538 CGGGTAAGTCATACAGGATGAGA 59.110 47.826 0.00 0.00 45.46 3.27
5372 8314 6.171921 TGCAATTTGGGGAAATTAGACATTG 58.828 36.000 0.00 0.00 31.67 2.82
5373 8315 6.371595 TGCAATTTGGGGAAATTAGACATT 57.628 33.333 0.00 0.00 31.67 2.71
5604 8546 1.953686 TCGACATGCTGGATATGACGA 59.046 47.619 8.06 8.06 45.27 4.20


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

AutoCloner maintained by Alex Coulton.