Multiple sequence alignment - TraesCS2D01G457600

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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 TraesCS2D01G457600 chr2D 100.000 3323 0 0 1 3323 565089590 565092912 0.000000e+00 6137.0
1 TraesCS2D01G457600 chr2D 94.923 2206 61 10 168 2342 565076395 565078580 0.000000e+00 3406.0
2 TraesCS2D01G457600 chr2D 95.287 2143 60 6 222 2342 565051788 565053911 0.000000e+00 3360.0
3 TraesCS2D01G457600 chr2D 86.538 208 25 3 2962 3166 565079124 565079331 3.340000e-55 226.0
4 TraesCS2D01G457600 chr2D 85.648 216 23 6 2962 3171 565054061 565054274 1.550000e-53 220.0
5 TraesCS2D01G457600 chr2D 93.333 75 3 2 2361 2433 565078565 565078639 3.500000e-20 110.0
6 TraesCS2D01G457600 chr2A 94.189 2237 77 15 137 2337 705530780 705532999 0.000000e+00 3362.0
7 TraesCS2D01G457600 chr2A 87.959 872 52 22 2372 3220 705532994 705533835 0.000000e+00 979.0
8 TraesCS2D01G457600 chr2A 95.283 106 5 0 3218 3323 705534443 705534548 5.700000e-38 169.0
9 TraesCS2D01G457600 chr2A 95.745 47 1 1 66 111 342439534 342439488 1.280000e-09 75.0
10 TraesCS2D01G457600 chr2B 93.900 2246 73 17 137 2337 676746503 676748729 0.000000e+00 3330.0
11 TraesCS2D01G457600 chr2B 92.775 692 26 9 2535 3220 676750992 676751665 0.000000e+00 979.0
12 TraesCS2D01G457600 chr2B 84.512 297 35 9 2688 2979 24900678 24900388 1.950000e-72 283.0
13 TraesCS2D01G457600 chr2B 89.944 179 12 4 2361 2538 676748720 676748893 3.340000e-55 226.0
14 TraesCS2D01G457600 chr2B 96.226 106 4 0 3218 3323 676752248 676752353 1.230000e-39 174.0
15 TraesCS2D01G457600 chr2B 79.487 117 17 5 2857 2968 448713105 448712991 3.550000e-10 76.8
16 TraesCS2D01G457600 chr7A 82.012 1968 227 78 320 2255 30651189 30653061 0.000000e+00 1555.0
17 TraesCS2D01G457600 chr4A 81.032 1977 238 72 323 2253 698935408 698933523 0.000000e+00 1447.0
18 TraesCS2D01G457600 chr4A 80.774 1602 195 63 701 2255 698804979 698803444 0.000000e+00 1147.0
19 TraesCS2D01G457600 chr4A 85.201 946 89 25 1352 2255 698170116 698169180 0.000000e+00 924.0
20 TraesCS2D01G457600 chr4A 83.441 930 94 33 1355 2255 698920224 698919326 0.000000e+00 809.0
21 TraesCS2D01G457600 chr4A 83.248 782 82 26 1539 2281 698926088 698925317 0.000000e+00 673.0
22 TraesCS2D01G457600 chr4A 80.346 809 117 24 323 1128 698826684 698825915 2.880000e-160 575.0
23 TraesCS2D01G457600 chr4A 79.408 777 124 21 468 1243 698921044 698920303 1.770000e-142 516.0
24 TraesCS2D01G457600 chr4A 84.127 189 27 3 2089 2275 699014171 699014358 2.630000e-41 180.0
25 TraesCS2D01G457600 chr4A 94.231 52 2 1 59 109 571068520 571068571 9.880000e-11 78.7
26 TraesCS2D01G457600 chr4A 95.745 47 2 0 65 111 653156708 653156662 3.550000e-10 76.8
27 TraesCS2D01G457600 chr7D 85.638 933 97 25 1352 2255 30265322 30266246 0.000000e+00 946.0
28 TraesCS2D01G457600 chr7D 79.374 1023 142 40 234 1245 30264284 30265248 0.000000e+00 656.0
29 TraesCS2D01G457600 chr7D 86.379 301 30 8 2685 2976 197344424 197344126 5.350000e-83 318.0
30 TraesCS2D01G457600 chr5A 89.172 314 30 2 2664 2973 667125481 667125794 4.020000e-104 388.0
31 TraesCS2D01G457600 chr6D 74.561 912 193 31 1354 2256 134741436 134740555 2.440000e-96 363.0
32 TraesCS2D01G457600 chr6D 74.334 939 199 32 1354 2281 134587304 134586397 8.760000e-96 361.0
33 TraesCS2D01G457600 chr6D 74.228 939 200 32 1354 2281 135040754 135039847 4.080000e-94 355.0
34 TraesCS2D01G457600 chr6D 86.218 312 37 5 2666 2972 419285811 419285501 1.910000e-87 333.0
35 TraesCS2D01G457600 chr5B 88.530 279 26 2 2698 2970 289594806 289594528 1.910000e-87 333.0
36 TraesCS2D01G457600 chr6B 76.212 660 129 22 1354 2005 233087917 233087278 1.150000e-84 324.0
37 TraesCS2D01G457600 chr6A 76.176 659 131 19 1354 2005 175996579 175995940 1.150000e-84 324.0
38 TraesCS2D01G457600 chr6A 95.745 47 2 0 63 109 539722630 539722676 3.550000e-10 76.8
39 TraesCS2D01G457600 chr3D 90.909 242 21 1 2664 2904 608605850 608605609 1.150000e-84 324.0
40 TraesCS2D01G457600 chr3D 93.878 49 3 0 62 110 582876346 582876298 1.280000e-09 75.0
41 TraesCS2D01G457600 chr1A 85.763 295 37 3 2690 2979 21408748 21409042 1.160000e-79 307.0
42 TraesCS2D01G457600 chr7B 95.833 48 2 0 65 112 491974109 491974062 9.880000e-11 78.7
43 TraesCS2D01G457600 chr1B 95.745 47 2 0 64 110 468250967 468250921 3.550000e-10 76.8
44 TraesCS2D01G457600 chr1B 95.745 47 2 0 64 110 468251356 468251310 3.550000e-10 76.8
45 TraesCS2D01G457600 chr5D 93.878 49 2 1 62 109 350947086 350947038 4.600000e-09 73.1


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 TraesCS2D01G457600 chr2D 565089590 565092912 3322 False 6137.000000 6137 100.00000 1 3323 1 chr2D.!!$F1 3322
1 TraesCS2D01G457600 chr2D 565051788 565054274 2486 False 1790.000000 3360 90.46750 222 3171 2 chr2D.!!$F2 2949
2 TraesCS2D01G457600 chr2D 565076395 565079331 2936 False 1247.333333 3406 91.59800 168 3166 3 chr2D.!!$F3 2998
3 TraesCS2D01G457600 chr2A 705530780 705534548 3768 False 1503.333333 3362 92.47700 137 3323 3 chr2A.!!$F1 3186
4 TraesCS2D01G457600 chr2B 676746503 676752353 5850 False 1177.250000 3330 93.21125 137 3323 4 chr2B.!!$F1 3186
5 TraesCS2D01G457600 chr7A 30651189 30653061 1872 False 1555.000000 1555 82.01200 320 2255 1 chr7A.!!$F1 1935
6 TraesCS2D01G457600 chr4A 698933523 698935408 1885 True 1447.000000 1447 81.03200 323 2253 1 chr4A.!!$R6 1930
7 TraesCS2D01G457600 chr4A 698803444 698804979 1535 True 1147.000000 1147 80.77400 701 2255 1 chr4A.!!$R3 1554
8 TraesCS2D01G457600 chr4A 698169180 698170116 936 True 924.000000 924 85.20100 1352 2255 1 chr4A.!!$R2 903
9 TraesCS2D01G457600 chr4A 698925317 698926088 771 True 673.000000 673 83.24800 1539 2281 1 chr4A.!!$R5 742
10 TraesCS2D01G457600 chr4A 698919326 698921044 1718 True 662.500000 809 81.42450 468 2255 2 chr4A.!!$R7 1787
11 TraesCS2D01G457600 chr4A 698825915 698826684 769 True 575.000000 575 80.34600 323 1128 1 chr4A.!!$R4 805
12 TraesCS2D01G457600 chr7D 30264284 30266246 1962 False 801.000000 946 82.50600 234 2255 2 chr7D.!!$F1 2021
13 TraesCS2D01G457600 chr6D 134740555 134741436 881 True 363.000000 363 74.56100 1354 2256 1 chr6D.!!$R2 902
14 TraesCS2D01G457600 chr6D 134586397 134587304 907 True 361.000000 361 74.33400 1354 2281 1 chr6D.!!$R1 927
15 TraesCS2D01G457600 chr6D 135039847 135040754 907 True 355.000000 355 74.22800 1354 2281 1 chr6D.!!$R3 927
16 TraesCS2D01G457600 chr6B 233087278 233087917 639 True 324.000000 324 76.21200 1354 2005 1 chr6B.!!$R1 651
17 TraesCS2D01G457600 chr6A 175995940 175996579 639 True 324.000000 324 76.17600 1354 2005 1 chr6A.!!$R1 651

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
24 25 0.465287 TTCTAATTCGTACCCCGGCC 59.535 55.0 0.00 0.0 37.11 6.13 F
36 37 0.752376 CCCCGGCCGCCTAAAAATTA 60.752 55.0 22.85 0.0 0.00 1.40 F
37 38 1.104630 CCCGGCCGCCTAAAAATTAA 58.895 50.0 22.85 0.0 0.00 1.40 F
1325 1391 1.128188 AAGGGAGCTTTGACGAGGGT 61.128 55.0 0.00 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1192 1258 0.610174 AAGAAGAGAGCATGCACGGA 59.390 50.000 21.98 0.00 0.00 4.69 R
1601 1694 1.441515 TTCTCGGCGAACTCGAACG 60.442 57.895 12.13 6.79 43.02 3.95 R
1942 2050 2.649034 GAACACGTCGAGCTGGGA 59.351 61.111 0.00 0.00 0.00 4.37 R
2366 2553 0.179121 TTGGATGCGGCAGTACGTAG 60.179 55.000 9.25 0.00 35.98 3.51 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
23 24 2.314323 TTTCTAATTCGTACCCCGGC 57.686 50.000 0.00 0.00 37.11 6.13
24 25 0.465287 TTCTAATTCGTACCCCGGCC 59.535 55.000 0.00 0.00 37.11 6.13
25 26 1.300388 CTAATTCGTACCCCGGCCG 60.300 63.158 21.04 21.04 37.11 6.13
26 27 3.444014 TAATTCGTACCCCGGCCGC 62.444 63.158 22.85 4.27 37.11 6.53
31 32 3.784719 GTACCCCGGCCGCCTAAA 61.785 66.667 22.85 0.00 0.00 1.85
32 33 3.007920 TACCCCGGCCGCCTAAAA 61.008 61.111 22.85 0.00 0.00 1.52
33 34 2.600729 TACCCCGGCCGCCTAAAAA 61.601 57.895 22.85 0.00 0.00 1.94
34 35 1.924145 TACCCCGGCCGCCTAAAAAT 61.924 55.000 22.85 0.60 0.00 1.82
35 36 2.055633 CCCCGGCCGCCTAAAAATT 61.056 57.895 22.85 0.00 0.00 1.82
36 37 0.752376 CCCCGGCCGCCTAAAAATTA 60.752 55.000 22.85 0.00 0.00 1.40
37 38 1.104630 CCCGGCCGCCTAAAAATTAA 58.895 50.000 22.85 0.00 0.00 1.40
38 39 1.202325 CCCGGCCGCCTAAAAATTAAC 60.202 52.381 22.85 0.00 0.00 2.01
39 40 1.532298 CCGGCCGCCTAAAAATTAACG 60.532 52.381 22.85 0.00 0.00 3.18
40 41 1.532298 CGGCCGCCTAAAAATTAACGG 60.532 52.381 14.67 0.00 43.37 4.44
41 42 1.744522 GGCCGCCTAAAAATTAACGGA 59.255 47.619 0.71 0.00 43.19 4.69
42 43 2.478370 GGCCGCCTAAAAATTAACGGAC 60.478 50.000 0.71 7.91 43.19 4.79
43 44 2.162008 GCCGCCTAAAAATTAACGGACA 59.838 45.455 12.72 0.00 43.19 4.02
44 45 3.366171 GCCGCCTAAAAATTAACGGACAA 60.366 43.478 12.72 0.00 43.19 3.18
45 46 4.675933 GCCGCCTAAAAATTAACGGACAAT 60.676 41.667 12.72 0.00 43.19 2.71
46 47 5.448904 GCCGCCTAAAAATTAACGGACAATA 60.449 40.000 12.72 0.00 43.19 1.90
47 48 5.967088 CCGCCTAAAAATTAACGGACAATAC 59.033 40.000 0.00 0.00 43.19 1.89
48 49 6.403418 CCGCCTAAAAATTAACGGACAATACA 60.403 38.462 0.00 0.00 43.19 2.29
49 50 7.022384 CGCCTAAAAATTAACGGACAATACAA 58.978 34.615 0.00 0.00 0.00 2.41
50 51 7.537991 CGCCTAAAAATTAACGGACAATACAAA 59.462 33.333 0.00 0.00 0.00 2.83
51 52 9.194271 GCCTAAAAATTAACGGACAATACAAAA 57.806 29.630 0.00 0.00 0.00 2.44
55 56 9.471084 AAAAATTAACGGACAATACAAAAGGAG 57.529 29.630 0.00 0.00 0.00 3.69
56 57 7.754851 AATTAACGGACAATACAAAAGGAGT 57.245 32.000 0.00 0.00 0.00 3.85
57 58 6.790285 TTAACGGACAATACAAAAGGAGTC 57.210 37.500 0.00 0.00 0.00 3.36
58 59 3.323243 ACGGACAATACAAAAGGAGTCG 58.677 45.455 0.00 0.00 0.00 4.18
59 60 3.006110 ACGGACAATACAAAAGGAGTCGA 59.994 43.478 0.00 0.00 0.00 4.20
60 61 4.181578 CGGACAATACAAAAGGAGTCGAT 58.818 43.478 0.00 0.00 0.00 3.59
61 62 4.032900 CGGACAATACAAAAGGAGTCGATG 59.967 45.833 0.00 0.00 0.00 3.84
62 63 5.175859 GGACAATACAAAAGGAGTCGATGA 58.824 41.667 0.00 0.00 0.00 2.92
63 64 5.063564 GGACAATACAAAAGGAGTCGATGAC 59.936 44.000 0.00 0.00 0.00 3.06
64 65 4.625742 ACAATACAAAAGGAGTCGATGACG 59.374 41.667 0.00 0.00 37.67 4.35
65 66 4.713824 ATACAAAAGGAGTCGATGACGA 57.286 40.909 0.00 0.00 46.56 4.20
124 125 7.827819 GGTAAAGATTTGCCTTCAAAATACC 57.172 36.000 5.30 3.31 44.44 2.73
125 126 7.611770 GGTAAAGATTTGCCTTCAAAATACCT 58.388 34.615 5.30 0.00 44.44 3.08
126 127 8.745590 GGTAAAGATTTGCCTTCAAAATACCTA 58.254 33.333 5.30 0.00 44.44 3.08
135 136 9.713713 TTGCCTTCAAAATACCTAAATTTTACC 57.286 29.630 0.00 0.00 37.03 2.85
180 181 3.181461 ACTCCTGAGTCTTCACTTGGTTG 60.181 47.826 0.00 0.00 36.92 3.77
224 237 3.751246 GCATCCTGCAAGCGCCAA 61.751 61.111 2.29 0.00 44.26 4.52
225 238 3.072486 GCATCCTGCAAGCGCCAAT 62.072 57.895 2.29 0.00 44.26 3.16
499 543 3.916438 TACCTGGCCTTCCGCTCCA 62.916 63.158 3.32 0.00 37.74 3.86
893 937 1.134580 CGTGACCTACCTCCTCGACTA 60.135 57.143 0.00 0.00 0.00 2.59
1128 1182 1.734465 GCGAGTTCCACTGAATCAAGG 59.266 52.381 0.00 0.00 31.98 3.61
1192 1258 3.626930 TGCAGTGTTCTTACTTTGGGTT 58.373 40.909 0.00 0.00 0.00 4.11
1199 1265 1.141254 TCTTACTTTGGGTTCCGTGCA 59.859 47.619 0.00 0.00 0.00 4.57
1325 1391 1.128188 AAGGGAGCTTTGACGAGGGT 61.128 55.000 0.00 0.00 0.00 4.34
1432 1510 1.545706 GGGTTTCTCGGAGGAGCAGT 61.546 60.000 4.96 0.00 40.26 4.40
1601 1694 1.887707 GCGGCTACACCTACATGGC 60.888 63.158 0.00 0.00 40.22 4.40
2312 2491 4.452733 GGGCACCGGAACTCCTCG 62.453 72.222 9.46 0.00 40.86 4.63
2336 2523 5.690857 GCGAACAATAGGTCCAGATTACTAC 59.309 44.000 0.00 0.00 0.00 2.73
2337 2524 5.913514 CGAACAATAGGTCCAGATTACTACG 59.086 44.000 0.00 0.00 0.00 3.51
2338 2525 6.459298 CGAACAATAGGTCCAGATTACTACGT 60.459 42.308 0.00 0.00 0.00 3.57
2339 2526 7.254898 CGAACAATAGGTCCAGATTACTACGTA 60.255 40.741 0.00 0.00 0.00 3.57
2340 2527 7.269477 ACAATAGGTCCAGATTACTACGTAC 57.731 40.000 0.00 0.00 0.00 3.67
2341 2528 7.059156 ACAATAGGTCCAGATTACTACGTACT 58.941 38.462 0.00 0.00 0.00 2.73
2342 2529 7.013083 ACAATAGGTCCAGATTACTACGTACTG 59.987 40.741 0.00 0.00 0.00 2.74
2343 2530 4.853007 AGGTCCAGATTACTACGTACTGT 58.147 43.478 8.73 1.82 0.00 3.55
2344 2531 4.880696 AGGTCCAGATTACTACGTACTGTC 59.119 45.833 8.73 3.17 0.00 3.51
2345 2532 4.036144 GGTCCAGATTACTACGTACTGTCC 59.964 50.000 8.73 7.30 0.00 4.02
2346 2533 4.036144 GTCCAGATTACTACGTACTGTCCC 59.964 50.000 8.73 0.00 0.00 4.46
2347 2534 4.080129 TCCAGATTACTACGTACTGTCCCT 60.080 45.833 8.73 0.00 0.00 4.20
2348 2535 5.130975 TCCAGATTACTACGTACTGTCCCTA 59.869 44.000 8.73 0.00 0.00 3.53
2349 2536 5.824624 CCAGATTACTACGTACTGTCCCTAA 59.175 44.000 8.73 0.00 0.00 2.69
2350 2537 6.319658 CCAGATTACTACGTACTGTCCCTAAA 59.680 42.308 8.73 0.00 0.00 1.85
2351 2538 7.148018 CCAGATTACTACGTACTGTCCCTAAAA 60.148 40.741 8.73 0.00 0.00 1.52
2352 2539 8.246180 CAGATTACTACGTACTGTCCCTAAAAA 58.754 37.037 0.00 0.00 0.00 1.94
2458 2925 6.399639 TGGACTTGTATTGCTATCACGATA 57.600 37.500 0.00 0.00 0.00 2.92
2578 5156 0.807496 GAGCATCTCCAACAACAGCC 59.193 55.000 0.00 0.00 0.00 4.85
2579 5157 0.403271 AGCATCTCCAACAACAGCCT 59.597 50.000 0.00 0.00 0.00 4.58
2580 5158 1.202976 AGCATCTCCAACAACAGCCTT 60.203 47.619 0.00 0.00 0.00 4.35
2581 5159 1.068055 GCATCTCCAACAACAGCCTTG 60.068 52.381 0.00 0.00 0.00 3.61
2582 5160 2.507484 CATCTCCAACAACAGCCTTGA 58.493 47.619 0.00 0.00 0.00 3.02
2583 5161 2.727123 TCTCCAACAACAGCCTTGAA 57.273 45.000 0.00 0.00 0.00 2.69
2584 5162 3.011566 TCTCCAACAACAGCCTTGAAA 57.988 42.857 0.00 0.00 0.00 2.69
2620 5198 3.068024 GGACACTTGGTGCAAAAAGATCA 59.932 43.478 14.78 0.00 37.84 2.92
2726 5310 3.121113 GCGCTGAAATAATGTTTTTGCGT 59.879 39.130 17.68 0.00 40.52 5.24
2768 5352 1.939769 AAAAACACGGCGCACAACCT 61.940 50.000 10.83 0.00 0.00 3.50
2829 5414 1.738830 CAAATTTGCAGGCCCGCAG 60.739 57.895 14.50 0.00 44.14 5.18
2991 5578 7.361713 GCTCTAAACATATAAAGTTGTGGTGCA 60.362 37.037 0.00 0.00 0.00 4.57
3103 5693 1.415672 AAGTTTCACCCCGCCTCTCA 61.416 55.000 0.00 0.00 0.00 3.27
3296 6508 8.665643 TCTTAGACGGAAAAGTTGATTTGTAA 57.334 30.769 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.818291 TTTTTAGGCGGCCGGGGTAC 62.818 60.000 29.38 9.53 0.00 3.34
15 16 1.924145 ATTTTTAGGCGGCCGGGGTA 61.924 55.000 29.38 0.00 0.00 3.69
16 17 2.791613 AATTTTTAGGCGGCCGGGGT 62.792 55.000 29.38 0.00 0.00 4.95
17 18 0.752376 TAATTTTTAGGCGGCCGGGG 60.752 55.000 29.38 0.00 0.00 5.73
18 19 1.104630 TTAATTTTTAGGCGGCCGGG 58.895 50.000 29.38 0.00 0.00 5.73
19 20 1.532298 CGTTAATTTTTAGGCGGCCGG 60.532 52.381 29.38 8.95 0.00 6.13
20 21 1.532298 CCGTTAATTTTTAGGCGGCCG 60.532 52.381 24.05 24.05 32.73 6.13
21 22 1.744522 TCCGTTAATTTTTAGGCGGCC 59.255 47.619 12.11 12.11 39.11 6.13
22 23 2.162008 TGTCCGTTAATTTTTAGGCGGC 59.838 45.455 0.00 0.00 39.11 6.53
23 24 4.422546 TTGTCCGTTAATTTTTAGGCGG 57.577 40.909 0.00 0.00 40.43 6.13
24 25 6.544622 TGTATTGTCCGTTAATTTTTAGGCG 58.455 36.000 0.00 0.00 0.00 5.52
25 26 8.745464 TTTGTATTGTCCGTTAATTTTTAGGC 57.255 30.769 0.00 0.00 0.00 3.93
29 30 9.471084 CTCCTTTTGTATTGTCCGTTAATTTTT 57.529 29.630 0.00 0.00 0.00 1.94
30 31 8.635328 ACTCCTTTTGTATTGTCCGTTAATTTT 58.365 29.630 0.00 0.00 0.00 1.82
31 32 8.173542 ACTCCTTTTGTATTGTCCGTTAATTT 57.826 30.769 0.00 0.00 0.00 1.82
32 33 7.360607 CGACTCCTTTTGTATTGTCCGTTAATT 60.361 37.037 0.00 0.00 0.00 1.40
33 34 6.091713 CGACTCCTTTTGTATTGTCCGTTAAT 59.908 38.462 0.00 0.00 0.00 1.40
34 35 5.406175 CGACTCCTTTTGTATTGTCCGTTAA 59.594 40.000 0.00 0.00 0.00 2.01
35 36 4.925054 CGACTCCTTTTGTATTGTCCGTTA 59.075 41.667 0.00 0.00 0.00 3.18
36 37 3.744426 CGACTCCTTTTGTATTGTCCGTT 59.256 43.478 0.00 0.00 0.00 4.44
37 38 3.006110 TCGACTCCTTTTGTATTGTCCGT 59.994 43.478 0.00 0.00 0.00 4.69
38 39 3.581755 TCGACTCCTTTTGTATTGTCCG 58.418 45.455 0.00 0.00 0.00 4.79
39 40 5.063564 GTCATCGACTCCTTTTGTATTGTCC 59.936 44.000 0.00 0.00 0.00 4.02
40 41 5.220228 CGTCATCGACTCCTTTTGTATTGTC 60.220 44.000 0.00 0.00 39.71 3.18
41 42 4.625742 CGTCATCGACTCCTTTTGTATTGT 59.374 41.667 0.00 0.00 39.71 2.71
42 43 4.862574 TCGTCATCGACTCCTTTTGTATTG 59.137 41.667 0.00 0.00 41.35 1.90
43 44 5.068234 TCGTCATCGACTCCTTTTGTATT 57.932 39.130 0.00 0.00 41.35 1.89
44 45 4.713824 TCGTCATCGACTCCTTTTGTAT 57.286 40.909 0.00 0.00 41.35 2.29
45 46 4.508461 TTCGTCATCGACTCCTTTTGTA 57.492 40.909 0.00 0.00 46.03 2.41
46 47 3.380479 TTCGTCATCGACTCCTTTTGT 57.620 42.857 0.00 0.00 46.03 2.83
47 48 4.725556 TTTTCGTCATCGACTCCTTTTG 57.274 40.909 0.00 0.00 46.03 2.44
98 99 8.745590 GGTATTTTGAAGGCAAATCTTTACCTA 58.254 33.333 0.00 0.00 43.07 3.08
99 100 7.454694 AGGTATTTTGAAGGCAAATCTTTACCT 59.545 33.333 0.44 0.44 43.07 3.08
100 101 7.611770 AGGTATTTTGAAGGCAAATCTTTACC 58.388 34.615 0.00 0.00 43.07 2.85
109 110 9.713713 GGTAAAATTTAGGTATTTTGAAGGCAA 57.286 29.630 0.00 0.00 38.01 4.52
110 111 9.095700 AGGTAAAATTTAGGTATTTTGAAGGCA 57.904 29.630 0.00 0.00 38.01 4.75
111 112 9.582431 GAGGTAAAATTTAGGTATTTTGAAGGC 57.418 33.333 0.00 0.00 38.01 4.35
112 113 9.783256 CGAGGTAAAATTTAGGTATTTTGAAGG 57.217 33.333 0.00 0.00 38.01 3.46
115 116 9.169592 CCTCGAGGTAAAATTTAGGTATTTTGA 57.830 33.333 24.04 0.00 38.01 2.69
134 135 2.746362 ACTAGTACAAACGACCTCGAGG 59.254 50.000 30.11 30.11 43.02 4.63
135 136 3.683822 AGACTAGTACAAACGACCTCGAG 59.316 47.826 5.13 5.13 43.02 4.04
180 181 1.209747 AGAGTGGAGCCGGGAATTAAC 59.790 52.381 2.18 0.00 0.00 2.01
217 230 3.821033 GGACTTGGAATAATATTGGCGCT 59.179 43.478 7.64 0.00 0.00 5.92
219 232 5.299279 ACTTGGACTTGGAATAATATTGGCG 59.701 40.000 0.00 0.00 0.00 5.69
221 234 8.352942 GCTTACTTGGACTTGGAATAATATTGG 58.647 37.037 0.00 0.00 0.00 3.16
222 235 8.902806 TGCTTACTTGGACTTGGAATAATATTG 58.097 33.333 0.00 0.00 0.00 1.90
223 236 9.474313 TTGCTTACTTGGACTTGGAATAATATT 57.526 29.630 0.00 0.00 0.00 1.28
224 237 9.474313 TTTGCTTACTTGGACTTGGAATAATAT 57.526 29.630 0.00 0.00 0.00 1.28
225 238 8.871629 TTTGCTTACTTGGACTTGGAATAATA 57.128 30.769 0.00 0.00 0.00 0.98
1128 1182 2.722201 CCGCCACCTAGGACCACTC 61.722 68.421 17.98 0.00 41.22 3.51
1192 1258 0.610174 AAGAAGAGAGCATGCACGGA 59.390 50.000 21.98 0.00 0.00 4.69
1199 1265 2.806019 CGGCATAGCAAGAAGAGAGCAT 60.806 50.000 0.00 0.00 0.00 3.79
1325 1391 2.359850 GCCACATCAAGGACGCCA 60.360 61.111 0.00 0.00 0.00 5.69
1432 1510 2.559668 AGACCGACGAGTTTCCAATACA 59.440 45.455 0.00 0.00 0.00 2.29
1601 1694 1.441515 TTCTCGGCGAACTCGAACG 60.442 57.895 12.13 6.79 43.02 3.95
1650 1746 4.150454 CGGCCCTCCTCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
1942 2050 2.649034 GAACACGTCGAGCTGGGA 59.351 61.111 0.00 0.00 0.00 4.37
2292 2471 3.319198 GGAGTTCCGGTGCCCTCA 61.319 66.667 0.00 0.00 0.00 3.86
2312 2491 4.694339 AGTAATCTGGACCTATTGTTCGC 58.306 43.478 0.00 0.00 0.00 4.70
2364 2551 0.664761 GGATGCGGCAGTACGTAGTA 59.335 55.000 9.25 0.00 45.11 1.82
2366 2553 0.179121 TTGGATGCGGCAGTACGTAG 60.179 55.000 9.25 0.00 35.98 3.51
2367 2554 0.458889 GTTGGATGCGGCAGTACGTA 60.459 55.000 9.25 0.00 35.98 3.57
2368 2555 1.740296 GTTGGATGCGGCAGTACGT 60.740 57.895 9.25 0.00 35.98 3.57
2369 2556 1.739929 TGTTGGATGCGGCAGTACG 60.740 57.895 9.25 0.00 0.00 3.67
2370 2557 1.794222 GTGTTGGATGCGGCAGTAC 59.206 57.895 9.25 4.37 0.00 2.73
2371 2558 1.739929 CGTGTTGGATGCGGCAGTA 60.740 57.895 9.25 0.00 0.00 2.74
2372 2559 3.049674 CGTGTTGGATGCGGCAGT 61.050 61.111 9.25 0.00 0.00 4.40
2373 2560 3.803082 CCGTGTTGGATGCGGCAG 61.803 66.667 9.25 0.00 42.00 4.85
2458 2925 4.015872 TCAGTGCCGAGGTTTATTTCTT 57.984 40.909 0.00 0.00 0.00 2.52
2576 5154 2.159114 TGTTTCAAGGCTGTTTCAAGGC 60.159 45.455 0.00 0.00 42.87 4.35
2577 5155 3.491447 CCTGTTTCAAGGCTGTTTCAAGG 60.491 47.826 0.00 0.00 0.00 3.61
2578 5156 3.381272 TCCTGTTTCAAGGCTGTTTCAAG 59.619 43.478 0.00 0.00 37.24 3.02
2579 5157 3.130340 GTCCTGTTTCAAGGCTGTTTCAA 59.870 43.478 0.00 0.00 37.24 2.69
2580 5158 2.687935 GTCCTGTTTCAAGGCTGTTTCA 59.312 45.455 0.00 0.00 37.24 2.69
2581 5159 2.687935 TGTCCTGTTTCAAGGCTGTTTC 59.312 45.455 0.00 0.00 37.24 2.78
2582 5160 2.427095 GTGTCCTGTTTCAAGGCTGTTT 59.573 45.455 0.00 0.00 37.24 2.83
2583 5161 2.024414 GTGTCCTGTTTCAAGGCTGTT 58.976 47.619 0.00 0.00 37.24 3.16
2584 5162 1.212935 AGTGTCCTGTTTCAAGGCTGT 59.787 47.619 0.00 0.00 37.24 4.40
2726 5310 1.406341 GCGTATGGTAAACCTCCTGCA 60.406 52.381 0.02 0.00 36.82 4.41
2907 5492 3.981071 AAAGATGCCTATATAGCCGCA 57.019 42.857 13.83 13.83 35.35 5.69
3057 5647 3.209097 GTTGGCCACACACGCACT 61.209 61.111 3.88 0.00 0.00 4.40
3059 5649 3.208383 CAGTTGGCCACACACGCA 61.208 61.111 3.88 0.00 0.00 5.24
3296 6508 7.568349 TGAGCCATATGTAGAGAGAACAAAAT 58.432 34.615 1.24 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.