Multiple sequence alignment - TraesCS4B01G216400

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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 TraesCS4B01G216400 chr4B 100.000 2576 0 0 1 2576 456361609 456364184 0.000000e+00 4758.0
1 TraesCS4B01G216400 chr4B 93.500 1723 75 18 1 1713 456381626 456379931 0.000000e+00 2527.0
2 TraesCS4B01G216400 chr4B 85.480 1770 90 56 70 1713 599589529 599587801 0.000000e+00 1690.0
3 TraesCS4B01G216400 chr4B 86.189 1506 100 35 255 1713 668363776 668365220 0.000000e+00 1530.0
4 TraesCS4B01G216400 chr4B 87.008 1193 75 25 574 1713 599464344 599463179 0.000000e+00 1271.0
5 TraesCS4B01G216400 chr4B 85.430 1208 101 33 548 1713 669472215 669473389 0.000000e+00 1186.0
6 TraesCS4B01G216400 chr4B 84.783 1196 100 40 548 1713 668446233 668447376 0.000000e+00 1125.0
7 TraesCS4B01G216400 chr4B 84.878 1111 73 33 670 1711 673297428 673296344 0.000000e+00 1033.0
8 TraesCS4B01G216400 chr4B 88.367 851 70 12 891 1713 668216606 668217455 0.000000e+00 996.0
9 TraesCS4B01G216400 chr4B 85.813 578 55 19 1714 2276 614260698 614261263 2.860000e-164 588.0
10 TraesCS4B01G216400 chr4B 85.147 579 15 20 70 578 599465971 599465394 6.310000e-146 527.0
11 TraesCS4B01G216400 chr4B 92.012 338 13 3 560 892 668216197 668216525 1.810000e-126 462.0
12 TraesCS4B01G216400 chr4B 93.133 233 12 2 2348 2576 614261294 614261526 3.180000e-89 339.0
13 TraesCS4B01G216400 chr4B 89.270 233 11 6 70 301 668649703 668649922 1.950000e-71 279.0
14 TraesCS4B01G216400 chr4B 89.270 233 11 6 70 301 668973022 668973241 1.950000e-71 279.0
15 TraesCS4B01G216400 chr4B 89.270 233 11 6 70 301 669342393 669342174 1.950000e-71 279.0
16 TraesCS4B01G216400 chr4B 89.270 233 11 6 70 301 669471750 669471969 1.950000e-71 279.0
17 TraesCS4B01G216400 chr4B 89.270 233 11 6 70 301 669558383 669558602 1.950000e-71 279.0
18 TraesCS4B01G216400 chr4B 97.872 47 1 0 2348 2394 614261590 614261636 5.910000e-12 82.4
19 TraesCS4B01G216400 chr4B 92.982 57 0 1 11 67 668216149 668216201 2.120000e-11 80.5
20 TraesCS4B01G216400 chr4B 92.982 57 0 1 11 67 668402915 668402967 2.120000e-11 80.5
21 TraesCS4B01G216400 chr4B 100.000 39 0 0 617 655 673297464 673297426 3.560000e-09 73.1
22 TraesCS4B01G216400 chrUn 85.380 1751 96 45 11 1645 79803280 79804986 0.000000e+00 1668.0
23 TraesCS4B01G216400 chrUn 84.331 1487 95 44 326 1713 134396295 134394848 0.000000e+00 1328.0
24 TraesCS4B01G216400 chrUn 83.198 1476 105 41 326 1713 30531054 30529634 0.000000e+00 1219.0
25 TraesCS4B01G216400 chrUn 85.807 1078 81 29 664 1713 28897549 28898582 0.000000e+00 1077.0
26 TraesCS4B01G216400 chrUn 84.698 1111 74 37 664 1713 29365090 29364015 0.000000e+00 1022.0
27 TraesCS4B01G216400 chrUn 89.791 813 56 14 907 1698 99649764 99650570 0.000000e+00 1016.0
28 TraesCS4B01G216400 chrUn 84.268 1106 72 38 664 1713 29602640 29601581 0.000000e+00 985.0
29 TraesCS4B01G216400 chrUn 83.712 1099 87 43 664 1713 99741975 99740920 0.000000e+00 953.0
30 TraesCS4B01G216400 chrUn 83.712 1099 87 43 664 1713 100353319 100352264 0.000000e+00 953.0
31 TraesCS4B01G216400 chrUn 89.270 233 11 6 70 301 346448813 346449032 1.950000e-71 279.0
32 TraesCS4B01G216400 chrUn 89.270 233 11 6 70 301 348077119 348076900 1.950000e-71 279.0
33 TraesCS4B01G216400 chrUn 83.891 329 11 5 11 301 30531439 30531115 2.520000e-70 276.0
34 TraesCS4B01G216400 chrUn 96.364 110 4 0 330 439 99649532 99649641 5.660000e-42 182.0
35 TraesCS4B01G216400 chrUn 91.200 125 6 2 326 445 346449100 346449224 5.700000e-37 165.0
36 TraesCS4B01G216400 chrUn 91.200 125 6 2 326 445 348076832 348076708 5.700000e-37 165.0
37 TraesCS4B01G216400 chrUn 100.000 38 0 0 34 71 346448756 346448793 1.280000e-08 71.3
38 TraesCS4B01G216400 chr6D 83.095 1822 128 51 11 1713 1069358 1071118 0.000000e+00 1493.0
39 TraesCS4B01G216400 chr5A 83.265 1470 121 46 325 1713 709530294 709531719 0.000000e+00 1236.0
40 TraesCS4B01G216400 chr5A 85.784 1238 74 39 548 1713 707983761 707984968 0.000000e+00 1218.0
41 TraesCS4B01G216400 chr5A 93.043 230 15 1 2348 2576 663766673 663766902 4.110000e-88 335.0
42 TraesCS4B01G216400 chr5A 89.270 233 11 6 70 301 707848401 707848620 1.950000e-71 279.0
43 TraesCS4B01G216400 chr5A 84.543 317 9 8 11 301 707983213 707983515 7.020000e-71 278.0
44 TraesCS4B01G216400 chr5A 92.000 125 5 2 326 445 707848688 707848812 1.230000e-38 171.0
45 TraesCS4B01G216400 chr5A 92.000 125 5 2 326 445 707983583 707983707 1.230000e-38 171.0
46 TraesCS4B01G216400 chr5A 84.127 189 9 10 11 193 709530115 709530288 2.050000e-36 163.0
47 TraesCS4B01G216400 chr4D 87.091 519 35 16 2021 2534 483703713 483704204 2.240000e-155 558.0
48 TraesCS4B01G216400 chr4D 98.276 58 1 0 1846 1903 483703540 483703597 4.530000e-18 102.0
49 TraesCS4B01G216400 chr4D 97.872 47 1 0 2348 2394 483704282 483704328 5.910000e-12 82.4
50 TraesCS4B01G216400 chr3D 100.000 87 0 0 2434 2520 557703768 557703854 7.380000e-36 161.0
51 TraesCS4B01G216400 chr1B 96.875 96 3 0 2433 2528 677995367 677995462 7.380000e-36 161.0
52 TraesCS4B01G216400 chr1B 94.792 96 5 0 2433 2528 677990518 677990613 1.600000e-32 150.0
53 TraesCS4B01G216400 chr3B 95.000 100 5 0 2433 2532 739981946 739982045 9.540000e-35 158.0
54 TraesCS4B01G216400 chr3A 94.000 100 6 0 2433 2532 693460335 693460434 4.440000e-33 152.0
55 TraesCS4B01G216400 chr7B 90.435 115 7 2 2432 2542 593921339 593921225 5.740000e-32 148.0
56 TraesCS4B01G216400 chr7B 97.872 47 1 0 2348 2394 593921454 593921408 5.910000e-12 82.4
57 TraesCS4B01G216400 chr7D 97.872 47 1 0 2348 2394 549544754 549544708 5.910000e-12 82.4
58 TraesCS4B01G216400 chr7A 97.872 47 1 0 2348 2394 635031912 635031866 5.910000e-12 82.4
59 TraesCS4B01G216400 chr1D 97.872 47 1 0 2348 2394 481828474 481828520 5.910000e-12 82.4


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 TraesCS4B01G216400 chr4B 456361609 456364184 2575 False 4758.000000 4758 100.000000 1 2576 1 chr4B.!!$F1 2575
1 TraesCS4B01G216400 chr4B 456379931 456381626 1695 True 2527.000000 2527 93.500000 1 1713 1 chr4B.!!$R1 1712
2 TraesCS4B01G216400 chr4B 599587801 599589529 1728 True 1690.000000 1690 85.480000 70 1713 1 chr4B.!!$R2 1643
3 TraesCS4B01G216400 chr4B 668363776 668365220 1444 False 1530.000000 1530 86.189000 255 1713 1 chr4B.!!$F2 1458
4 TraesCS4B01G216400 chr4B 668446233 668447376 1143 False 1125.000000 1125 84.783000 548 1713 1 chr4B.!!$F4 1165
5 TraesCS4B01G216400 chr4B 599463179 599465971 2792 True 899.000000 1271 86.077500 70 1713 2 chr4B.!!$R4 1643
6 TraesCS4B01G216400 chr4B 669471750 669473389 1639 False 732.500000 1186 87.350000 70 1713 2 chr4B.!!$F10 1643
7 TraesCS4B01G216400 chr4B 673296344 673297464 1120 True 553.050000 1033 92.439000 617 1711 2 chr4B.!!$R5 1094
8 TraesCS4B01G216400 chr4B 668216149 668217455 1306 False 512.833333 996 91.120333 11 1713 3 chr4B.!!$F9 1702
9 TraesCS4B01G216400 chr4B 614260698 614261636 938 False 336.466667 588 92.272667 1714 2576 3 chr4B.!!$F8 862
10 TraesCS4B01G216400 chrUn 79803280 79804986 1706 False 1668.000000 1668 85.380000 11 1645 1 chrUn.!!$F2 1634
11 TraesCS4B01G216400 chrUn 134394848 134396295 1447 True 1328.000000 1328 84.331000 326 1713 1 chrUn.!!$R5 1387
12 TraesCS4B01G216400 chrUn 28897549 28898582 1033 False 1077.000000 1077 85.807000 664 1713 1 chrUn.!!$F1 1049
13 TraesCS4B01G216400 chrUn 29364015 29365090 1075 True 1022.000000 1022 84.698000 664 1713 1 chrUn.!!$R1 1049
14 TraesCS4B01G216400 chrUn 29601581 29602640 1059 True 985.000000 985 84.268000 664 1713 1 chrUn.!!$R2 1049
15 TraesCS4B01G216400 chrUn 99740920 99741975 1055 True 953.000000 953 83.712000 664 1713 1 chrUn.!!$R3 1049
16 TraesCS4B01G216400 chrUn 100352264 100353319 1055 True 953.000000 953 83.712000 664 1713 1 chrUn.!!$R4 1049
17 TraesCS4B01G216400 chrUn 30529634 30531439 1805 True 747.500000 1219 83.544500 11 1713 2 chrUn.!!$R6 1702
18 TraesCS4B01G216400 chrUn 99649532 99650570 1038 False 599.000000 1016 93.077500 330 1698 2 chrUn.!!$F3 1368
19 TraesCS4B01G216400 chr6D 1069358 1071118 1760 False 1493.000000 1493 83.095000 11 1713 1 chr6D.!!$F1 1702
20 TraesCS4B01G216400 chr5A 709530115 709531719 1604 False 699.500000 1236 83.696000 11 1713 2 chr5A.!!$F4 1702
21 TraesCS4B01G216400 chr5A 707983213 707984968 1755 False 555.666667 1218 87.442333 11 1713 3 chr5A.!!$F3 1702
22 TraesCS4B01G216400 chr4D 483703540 483704328 788 False 247.466667 558 94.413000 1846 2534 3 chr4D.!!$F1 688

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
931 2336 2.763448 GCTGTATGGTCTCTTCCTGACT 59.237 50.0 0.0 0.0 35.04 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 3814 0.8501 TGAGGCTCCTTTGGTTTCCA 59.15 50.0 12.86 0.0 0.0 3.53 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
694 1933 4.806330 AGATGCAATTTTCTTGCTCACAG 58.194 39.130 10.87 0.00 45.13 3.66
725 1970 8.833734 ACAATGAATGATGGGATCTCTATGTAT 58.166 33.333 0.00 0.00 0.00 2.29
931 2336 2.763448 GCTGTATGGTCTCTTCCTGACT 59.237 50.000 0.00 0.00 35.04 3.41
1003 2464 1.067635 CAGTCCGCCAAAAGGAAATGG 60.068 52.381 0.00 0.00 39.84 3.16
1052 2516 3.970410 CCAAGACCTGCAGGCCCA 61.970 66.667 33.06 0.00 39.32 5.36
1080 2562 0.929244 AGCTGGGCCACTCCAATAAT 59.071 50.000 0.00 0.00 36.21 1.28
1164 2646 2.969238 CGCCCGCTGATCATGGAC 60.969 66.667 14.17 3.48 0.00 4.02
1177 2659 0.729116 CATGGACGTGATGTTCTGGC 59.271 55.000 0.00 0.00 0.00 4.85
1244 2726 1.268234 GGAAATCCAAATGCTCGAGCG 60.268 52.381 30.75 17.07 38.96 5.03
1483 2980 1.985473 TTGCAACATGCTTCAGGAGT 58.015 45.000 0.00 0.00 45.31 3.85
1484 2981 1.527034 TGCAACATGCTTCAGGAGTC 58.473 50.000 3.78 0.00 45.31 3.36
1541 3038 1.520494 GAGACCCCGGTTTGTTTCTC 58.480 55.000 0.00 0.00 0.00 2.87
1557 3072 4.081254 TGTTTCTCTGATCCTGATGAGTGG 60.081 45.833 0.00 0.00 0.00 4.00
1558 3073 3.677156 TCTCTGATCCTGATGAGTGGA 57.323 47.619 0.00 0.00 36.72 4.02
1559 3074 3.986435 TCTCTGATCCTGATGAGTGGAA 58.014 45.455 0.00 0.00 35.81 3.53
1560 3075 3.959449 TCTCTGATCCTGATGAGTGGAAG 59.041 47.826 0.00 0.00 35.81 3.46
1561 3076 3.959449 CTCTGATCCTGATGAGTGGAAGA 59.041 47.826 0.00 0.00 35.81 2.87
1562 3077 3.959449 TCTGATCCTGATGAGTGGAAGAG 59.041 47.826 0.00 0.00 35.81 2.85
1715 3309 7.685481 TCTTGGGTAGTGTTTTCTCATTCATA 58.315 34.615 0.00 0.00 0.00 2.15
1738 3332 9.959749 CATATGAATCATCATCACATCACAAAA 57.040 29.630 0.00 0.00 42.75 2.44
1791 3385 6.861065 ATGTAACGACATGAACCAATATCC 57.139 37.500 0.00 0.00 44.90 2.59
1792 3386 4.806775 TGTAACGACATGAACCAATATCCG 59.193 41.667 0.00 0.00 0.00 4.18
1794 3388 2.169769 ACGACATGAACCAATATCCGGT 59.830 45.455 0.00 0.00 38.85 5.28
1796 3390 2.878406 GACATGAACCAATATCCGGTGG 59.122 50.000 7.26 7.26 41.00 4.61
1797 3391 2.507886 ACATGAACCAATATCCGGTGGA 59.492 45.455 15.35 0.00 38.36 4.02
1820 3414 7.155328 GGACGAATTGATATCACCAGAATACT 58.845 38.462 4.48 0.00 0.00 2.12
1833 3427 9.836179 ATCACCAGAATACTCTAAGATAATCCT 57.164 33.333 0.00 0.00 0.00 3.24
1964 3615 4.938832 CGTACAATTCCTGTATCCAAACCA 59.061 41.667 0.00 0.00 42.50 3.67
1983 3634 3.681593 CAGAATGGATGCAAACCCAAA 57.318 42.857 9.44 0.00 35.85 3.28
1984 3635 4.210724 CAGAATGGATGCAAACCCAAAT 57.789 40.909 9.44 3.13 35.85 2.32
1985 3636 5.341872 CAGAATGGATGCAAACCCAAATA 57.658 39.130 9.44 0.00 35.85 1.40
1986 3637 5.732633 CAGAATGGATGCAAACCCAAATAA 58.267 37.500 9.44 0.00 35.85 1.40
1987 3638 6.171921 CAGAATGGATGCAAACCCAAATAAA 58.828 36.000 9.44 0.00 35.85 1.40
1988 3639 6.092533 CAGAATGGATGCAAACCCAAATAAAC 59.907 38.462 9.44 0.69 35.85 2.01
1989 3640 5.760484 ATGGATGCAAACCCAAATAAACT 57.240 34.783 9.44 0.00 35.85 2.66
1990 3641 6.865834 ATGGATGCAAACCCAAATAAACTA 57.134 33.333 9.44 0.00 35.85 2.24
1991 3642 6.672266 TGGATGCAAACCCAAATAAACTAA 57.328 33.333 10.15 0.00 0.00 2.24
1992 3643 7.251321 TGGATGCAAACCCAAATAAACTAAT 57.749 32.000 10.15 0.00 0.00 1.73
1999 3650 8.440059 GCAAACCCAAATAAACTAATTTAGCAC 58.560 33.333 3.28 0.00 33.78 4.40
2003 3654 7.039270 CCCAAATAAACTAATTTAGCACACCC 58.961 38.462 3.28 0.00 33.78 4.61
2070 3722 4.331968 TGATTTAGCACACCCACTTAAGG 58.668 43.478 7.53 0.00 0.00 2.69
2130 3782 3.140144 TGAGGTTCACCCCTGAGATTTTT 59.860 43.478 0.00 0.00 34.03 1.94
2131 3783 3.759086 GAGGTTCACCCCTGAGATTTTTC 59.241 47.826 0.00 0.00 34.03 2.29
2136 3788 2.609459 CACCCCTGAGATTTTTCGATCG 59.391 50.000 9.36 9.36 0.00 3.69
2162 3814 5.193099 AGAAAGCAACCCATACCAAGTAT 57.807 39.130 0.00 0.00 0.00 2.12
2182 3836 1.248486 GGAAACCAAAGGAGCCTCAC 58.752 55.000 0.00 0.00 0.00 3.51
2198 3852 2.440501 CTCACAACACGTTGCAGTTTC 58.559 47.619 9.79 0.00 44.03 2.78
2274 3928 4.428209 TCAAAGCATGAGATCGAGAACTC 58.572 43.478 0.00 3.78 33.04 3.01
2276 3930 3.988379 AGCATGAGATCGAGAACTCTC 57.012 47.619 10.87 11.26 38.69 3.20
2294 3948 4.098055 TCTCATCAACTGTAGCGAAGAC 57.902 45.455 0.00 0.00 0.00 3.01
2320 3974 9.778993 CACAAAATCAAGTGAATAGGATTACAG 57.221 33.333 0.00 0.00 37.97 2.74
2321 3975 9.520515 ACAAAATCAAGTGAATAGGATTACAGT 57.479 29.630 0.00 0.00 30.29 3.55
2326 3980 7.685481 TCAAGTGAATAGGATTACAGTTTGGA 58.315 34.615 0.00 0.00 0.00 3.53
2327 3981 7.824289 TCAAGTGAATAGGATTACAGTTTGGAG 59.176 37.037 0.00 0.00 0.00 3.86
2328 3982 6.653989 AGTGAATAGGATTACAGTTTGGAGG 58.346 40.000 0.00 0.00 0.00 4.30
2329 3983 5.297029 GTGAATAGGATTACAGTTTGGAGGC 59.703 44.000 0.00 0.00 0.00 4.70
2330 3984 5.191722 TGAATAGGATTACAGTTTGGAGGCT 59.808 40.000 0.00 0.00 0.00 4.58
2331 3985 3.636153 AGGATTACAGTTTGGAGGCTC 57.364 47.619 5.78 5.78 0.00 4.70
2332 3986 2.239907 AGGATTACAGTTTGGAGGCTCC 59.760 50.000 26.95 26.95 36.96 4.70
2333 3987 2.239907 GGATTACAGTTTGGAGGCTCCT 59.760 50.000 32.28 14.99 37.46 3.69
2334 3988 3.308473 GGATTACAGTTTGGAGGCTCCTT 60.308 47.826 32.28 13.86 37.46 3.36
2335 3989 3.876309 TTACAGTTTGGAGGCTCCTTT 57.124 42.857 32.28 13.52 37.46 3.11
2336 3990 1.986882 ACAGTTTGGAGGCTCCTTTG 58.013 50.000 32.28 24.35 37.46 2.77
2337 3991 1.215423 ACAGTTTGGAGGCTCCTTTGT 59.785 47.619 32.28 24.91 37.46 2.83
2338 3992 2.310538 CAGTTTGGAGGCTCCTTTGTT 58.689 47.619 32.28 12.84 37.46 2.83
2339 3993 2.695147 CAGTTTGGAGGCTCCTTTGTTT 59.305 45.455 32.28 11.81 37.46 2.83
2340 3994 3.132824 CAGTTTGGAGGCTCCTTTGTTTT 59.867 43.478 32.28 10.30 37.46 2.43
2341 3995 3.384789 AGTTTGGAGGCTCCTTTGTTTTC 59.615 43.478 32.28 14.32 37.46 2.29
2342 3996 1.995376 TGGAGGCTCCTTTGTTTTCC 58.005 50.000 32.28 5.10 37.46 3.13
2343 3997 1.216678 TGGAGGCTCCTTTGTTTTCCA 59.783 47.619 32.28 7.90 37.46 3.53
2344 3998 2.158325 TGGAGGCTCCTTTGTTTTCCAT 60.158 45.455 32.28 0.00 37.46 3.41
2345 3999 2.899900 GGAGGCTCCTTTGTTTTCCATT 59.100 45.455 26.44 0.00 32.53 3.16
2346 4000 4.086457 GGAGGCTCCTTTGTTTTCCATTA 58.914 43.478 26.44 0.00 32.53 1.90
2415 4069 8.811994 CCATTAAGAGAAAATTTAGTTTGGGGA 58.188 33.333 0.00 0.00 0.00 4.81
2529 4187 3.913163 GGAAAGGATCCTCATACCCATCT 59.087 47.826 16.52 0.00 45.56 2.90
2534 4192 6.882768 AGGATCCTCATACCCATCTAAATC 57.117 41.667 9.02 0.00 0.00 2.17
2536 4194 7.028131 AGGATCCTCATACCCATCTAAATCTT 58.972 38.462 9.02 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
725 1970 7.070571 ACAGAGGGAATACAATTTGGTTCAAAA 59.929 33.333 14.63 0.00 36.90 2.44
931 2336 6.016610 GGTACAGCACAAACAGAGGATTTAAA 60.017 38.462 0.00 0.00 0.00 1.52
1013 2477 1.559368 TTGGGCATGGGAGTTGATTG 58.441 50.000 0.00 0.00 0.00 2.67
1018 2482 0.413037 TGGATTTGGGCATGGGAGTT 59.587 50.000 0.00 0.00 0.00 3.01
1052 2516 3.474570 GGCCCAGCTCATCGGAGT 61.475 66.667 0.00 0.00 43.37 3.85
1164 2646 1.430632 GCATGGCCAGAACATCACG 59.569 57.895 13.05 0.00 0.00 4.35
1177 2659 0.178981 ATTTCCATCTCCGGGCATGG 60.179 55.000 21.02 21.02 41.04 3.66
1189 2671 2.356125 CCACGACCAAGAGGATTTCCAT 60.356 50.000 0.00 0.00 38.89 3.41
1244 2726 2.778299 TGAGCTTGGGTAACACATCAC 58.222 47.619 0.00 0.00 39.74 3.06
1483 2980 2.741092 GACCAGCAACGGGACAGA 59.259 61.111 0.00 0.00 0.00 3.41
1484 2981 2.358737 GGACCAGCAACGGGACAG 60.359 66.667 0.00 0.00 0.00 3.51
1541 3038 3.705579 ACTCTTCCACTCATCAGGATCAG 59.294 47.826 0.00 0.00 33.10 2.90
1557 3072 8.845227 TGATAAGTCTACTCATCATCACTCTTC 58.155 37.037 0.00 0.00 0.00 2.87
1558 3073 8.759481 TGATAAGTCTACTCATCATCACTCTT 57.241 34.615 0.00 0.00 0.00 2.85
1559 3074 7.040478 GCTGATAAGTCTACTCATCATCACTCT 60.040 40.741 0.00 0.00 0.00 3.24
1560 3075 7.083858 GCTGATAAGTCTACTCATCATCACTC 58.916 42.308 0.00 0.00 0.00 3.51
1561 3076 6.015519 GGCTGATAAGTCTACTCATCATCACT 60.016 42.308 0.00 0.00 0.00 3.41
1562 3077 6.155827 GGCTGATAAGTCTACTCATCATCAC 58.844 44.000 0.00 0.00 0.00 3.06
1680 3268 8.732746 AAAACACTACCCAAGATACATATCAC 57.267 34.615 1.88 0.00 35.17 3.06
1715 3309 8.288689 TCTTTTGTGATGTGATGATGATTCAT 57.711 30.769 0.00 0.00 45.39 2.57
1721 3315 8.806177 TTCTTTTCTTTTGTGATGTGATGATG 57.194 30.769 0.00 0.00 0.00 3.07
1738 3332 9.257651 CTGAAGCATTTTCTTTCATTCTTTTCT 57.742 29.630 0.00 0.00 0.00 2.52
1774 3368 2.543848 CACCGGATATTGGTTCATGTCG 59.456 50.000 9.46 0.00 37.72 4.35
1791 3385 2.800544 GGTGATATCAATTCGTCCACCG 59.199 50.000 7.07 0.00 34.16 4.94
1792 3386 3.804036 TGGTGATATCAATTCGTCCACC 58.196 45.455 7.07 2.26 41.98 4.61
1794 3388 5.351948 TTCTGGTGATATCAATTCGTCCA 57.648 39.130 7.07 8.52 0.00 4.02
1796 3390 8.085296 AGAGTATTCTGGTGATATCAATTCGTC 58.915 37.037 7.07 0.00 30.72 4.20
1797 3391 7.957002 AGAGTATTCTGGTGATATCAATTCGT 58.043 34.615 7.07 0.00 30.72 3.85
1820 3414 8.862325 TTTTGCAACAGAAGGATTATCTTAGA 57.138 30.769 0.00 0.00 0.00 2.10
1964 3615 6.013466 AGTTTATTTGGGTTTGCATCCATTCT 60.013 34.615 10.02 0.57 32.48 2.40
1973 3624 8.440059 GTGCTAAATTAGTTTATTTGGGTTTGC 58.560 33.333 1.68 0.00 0.00 3.68
1974 3625 9.482627 TGTGCTAAATTAGTTTATTTGGGTTTG 57.517 29.630 1.68 0.00 0.00 2.93
1975 3626 9.483916 GTGTGCTAAATTAGTTTATTTGGGTTT 57.516 29.630 1.68 0.00 0.00 3.27
1976 3627 8.092068 GGTGTGCTAAATTAGTTTATTTGGGTT 58.908 33.333 1.68 0.00 0.00 4.11
1977 3628 7.310175 GGGTGTGCTAAATTAGTTTATTTGGGT 60.310 37.037 1.68 0.00 0.00 4.51
1978 3629 7.039270 GGGTGTGCTAAATTAGTTTATTTGGG 58.961 38.462 1.68 0.00 0.00 4.12
1979 3630 7.544217 GTGGGTGTGCTAAATTAGTTTATTTGG 59.456 37.037 1.68 0.00 0.00 3.28
1980 3631 8.303876 AGTGGGTGTGCTAAATTAGTTTATTTG 58.696 33.333 1.68 0.00 0.00 2.32
1981 3632 8.417273 AGTGGGTGTGCTAAATTAGTTTATTT 57.583 30.769 1.68 0.00 0.00 1.40
1982 3633 8.417273 AAGTGGGTGTGCTAAATTAGTTTATT 57.583 30.769 1.68 0.00 0.00 1.40
1983 3634 8.417273 AAAGTGGGTGTGCTAAATTAGTTTAT 57.583 30.769 1.68 0.00 0.00 1.40
1984 3635 7.826918 AAAGTGGGTGTGCTAAATTAGTTTA 57.173 32.000 1.68 0.00 0.00 2.01
1985 3636 6.724893 AAAGTGGGTGTGCTAAATTAGTTT 57.275 33.333 1.68 0.00 0.00 2.66
1986 3637 7.504574 ACTTAAAGTGGGTGTGCTAAATTAGTT 59.495 33.333 1.68 0.00 0.00 2.24
1987 3638 7.002276 ACTTAAAGTGGGTGTGCTAAATTAGT 58.998 34.615 1.68 0.00 0.00 2.24
1988 3639 7.448748 ACTTAAAGTGGGTGTGCTAAATTAG 57.551 36.000 0.00 0.00 0.00 1.73
1989 3640 8.921353 TTACTTAAAGTGGGTGTGCTAAATTA 57.079 30.769 0.00 0.00 0.00 1.40
1990 3641 7.826918 TTACTTAAAGTGGGTGTGCTAAATT 57.173 32.000 0.00 0.00 0.00 1.82
1991 3642 7.826918 TTTACTTAAAGTGGGTGTGCTAAAT 57.173 32.000 0.00 0.00 0.00 1.40
1992 3643 7.642082 TTTTACTTAAAGTGGGTGTGCTAAA 57.358 32.000 0.00 0.00 0.00 1.85
1999 3650 7.881232 TCAGGTCTATTTTACTTAAAGTGGGTG 59.119 37.037 0.00 0.00 0.00 4.61
2130 3782 2.607187 GGTTGCTTTCTTCTCGATCGA 58.393 47.619 18.32 18.32 0.00 3.59
2131 3783 1.661112 GGGTTGCTTTCTTCTCGATCG 59.339 52.381 9.36 9.36 0.00 3.69
2136 3788 3.686016 TGGTATGGGTTGCTTTCTTCTC 58.314 45.455 0.00 0.00 0.00 2.87
2162 3814 0.850100 TGAGGCTCCTTTGGTTTCCA 59.150 50.000 12.86 0.00 0.00 3.53
2168 3821 0.954452 GTGTTGTGAGGCTCCTTTGG 59.046 55.000 12.86 0.00 0.00 3.28
2182 3836 2.823196 TCAGAAACTGCAACGTGTTG 57.177 45.000 8.35 8.35 43.14 3.33
2233 3887 8.206189 TGCTTTGATCTACATAATGAGTCATCA 58.794 33.333 5.98 0.00 40.50 3.07
2239 3893 8.828688 TCTCATGCTTTGATCTACATAATGAG 57.171 34.615 13.83 13.83 32.72 2.90
2245 3899 6.015603 TCTCGATCTCATGCTTTGATCTACAT 60.016 38.462 12.44 0.00 35.68 2.29
2274 3928 3.610242 GTGTCTTCGCTACAGTTGATGAG 59.390 47.826 0.00 0.00 0.00 2.90
2276 3930 3.317150 TGTGTCTTCGCTACAGTTGATG 58.683 45.455 0.00 0.00 0.00 3.07
2294 3948 9.778993 CTGTAATCCTATTCACTTGATTTTGTG 57.221 33.333 0.00 0.00 35.68 3.33
2320 3974 3.492656 GGAAAACAAAGGAGCCTCCAAAC 60.493 47.826 14.46 0.00 39.61 2.93
2321 3975 2.698274 GGAAAACAAAGGAGCCTCCAAA 59.302 45.455 14.46 0.00 39.61 3.28
2323 3977 1.216678 TGGAAAACAAAGGAGCCTCCA 59.783 47.619 14.46 0.00 39.61 3.86
2324 3978 1.995376 TGGAAAACAAAGGAGCCTCC 58.005 50.000 1.26 1.26 36.58 4.30
2326 3980 5.147767 ACTTAATGGAAAACAAAGGAGCCT 58.852 37.500 0.00 0.00 0.00 4.58
2327 3981 5.468540 ACTTAATGGAAAACAAAGGAGCC 57.531 39.130 0.00 0.00 0.00 4.70
2346 4000 9.658799 CCCAAATGATCGACTATGATTATACTT 57.341 33.333 0.00 0.00 0.00 2.24
2359 4013 2.999331 TCCTTTCCCCAAATGATCGAC 58.001 47.619 0.00 0.00 0.00 4.20
2425 4083 6.359804 CCAGAAATCTGATCCATCCACTTTA 58.640 40.000 11.94 0.00 46.59 1.85


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

AutoCloner maintained by Alex Coulton.