Multiple sequence alignment - TraesCS1B01G061600

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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 TraesCS1B01G061600 chr1B 100.000 3461 0 0 1 3461 46691271 46694731 0.000000e+00 6392.0
1 TraesCS1B01G061600 chr1B 90.696 1752 146 9 713 2452 4954423 4952677 0.000000e+00 2316.0
2 TraesCS1B01G061600 chr1B 90.732 1748 140 13 710 2452 4518956 4517226 0.000000e+00 2311.0
3 TraesCS1B01G061600 chr1B 90.233 1761 140 15 710 2449 70232822 70234571 0.000000e+00 2270.0
4 TraesCS1B01G061600 chr1B 90.034 1746 151 11 709 2449 4110220 4111947 0.000000e+00 2239.0
5 TraesCS1B01G061600 chr1B 93.145 1240 69 6 1777 3014 4933876 4932651 0.000000e+00 1805.0
6 TraesCS1B01G061600 chr1B 83.358 679 52 20 2450 3104 46828523 46827882 3.880000e-159 571.0
7 TraesCS1B01G061600 chr1B 81.641 719 67 31 31 713 4543363 4542674 1.410000e-148 536.0
8 TraesCS1B01G061600 chr1B 85.086 409 28 9 38 439 46830562 46830180 1.510000e-103 387.0
9 TraesCS1B01G061600 chr1B 83.002 453 48 19 2455 2897 4517191 4516758 1.950000e-102 383.0
10 TraesCS1B01G061600 chr1B 81.616 359 46 12 3020 3370 4516587 4516241 2.630000e-71 279.0
11 TraesCS1B01G061600 chr1B 86.508 252 22 4 45 296 4955100 4954861 2.050000e-67 267.0
12 TraesCS1B01G061600 chr1B 90.217 184 14 2 59 238 4109416 4109599 1.610000e-58 237.0
13 TraesCS1B01G061600 chr1B 77.612 402 57 19 1 382 4143938 4144326 2.710000e-51 213.0
14 TraesCS1B01G061600 chr1B 90.244 164 12 3 49 212 4597760 4597601 9.730000e-51 211.0
15 TraesCS1B01G061600 chr1B 89.937 159 6 4 300 456 585356800 585356950 2.730000e-46 196.0
16 TraesCS1B01G061600 chr1B 83.523 176 13 7 430 598 4143871 4144037 2.150000e-32 150.0
17 TraesCS1B01G061600 chr1B 81.967 183 11 9 3189 3370 3938713 3938874 6.030000e-28 135.0
18 TraesCS1B01G061600 chr1B 93.902 82 4 1 3308 3388 4797554 4797473 4.690000e-24 122.0
19 TraesCS1B01G061600 chr1B 92.683 82 5 1 3308 3388 4112705 4112786 2.180000e-22 117.0
20 TraesCS1B01G061600 chr1B 92.593 81 5 1 3308 3388 4594977 4594898 7.850000e-22 115.0
21 TraesCS1B01G061600 chr1B 85.088 114 12 5 431 543 4542474 4542365 1.020000e-20 111.0
22 TraesCS1B01G061600 chr1B 93.182 44 2 1 610 653 46830461 46830419 2.880000e-06 63.9
23 TraesCS1B01G061600 chr5B 90.450 1801 144 16 709 2504 617170752 617172529 0.000000e+00 2348.0
24 TraesCS1B01G061600 chr5B 90.422 1754 139 13 710 2452 60825950 60824215 0.000000e+00 2281.0
25 TraesCS1B01G061600 chr5B 85.308 211 23 6 233 439 60826023 60825817 9.730000e-51 211.0
26 TraesCS1B01G061600 chr5B 89.888 89 3 2 92 180 60826243 60826161 3.650000e-20 110.0
27 TraesCS1B01G061600 chr5D 90.520 1751 137 15 710 2449 57819574 57821306 0.000000e+00 2287.0
28 TraesCS1B01G061600 chr6B 90.313 1755 136 16 710 2453 120595399 120593668 0.000000e+00 2268.0
29 TraesCS1B01G061600 chr6B 81.711 678 70 21 2450 3102 120131110 120130462 1.840000e-142 516.0
30 TraesCS1B01G061600 chr6B 81.726 394 42 16 2625 3017 655217320 655216956 5.610000e-78 302.0
31 TraesCS1B01G061600 chr6B 84.252 254 16 16 3124 3365 120130360 120130119 3.480000e-55 226.0
32 TraesCS1B01G061600 chr6D 89.766 1749 143 19 710 2453 51348850 51350567 0.000000e+00 2206.0
33 TraesCS1B01G061600 chr6D 83.041 684 57 26 2450 3102 53143040 53142385 1.800000e-157 566.0
34 TraesCS1B01G061600 chr6D 83.663 202 14 8 238 439 51074013 51074195 4.590000e-39 172.0
35 TraesCS1B01G061600 chr6D 83.500 200 14 8 240 439 50949098 50949278 5.940000e-38 169.0
36 TraesCS1B01G061600 chr6D 95.455 44 2 0 96 139 51342725 51342768 1.720000e-08 71.3
37 TraesCS1B01G061600 chr6A 86.567 1474 132 36 1672 3104 64065208 64063760 0.000000e+00 1565.0
38 TraesCS1B01G061600 chr6A 80.307 782 78 37 2450 3193 613495427 613496170 3.960000e-144 521.0
39 TraesCS1B01G061600 chr6A 84.921 252 17 12 3124 3365 64063662 64063422 5.770000e-58 235.0
40 TraesCS1B01G061600 chr4A 87.755 588 37 11 284 853 666694465 666693895 0.000000e+00 654.0
41 TraesCS1B01G061600 chr3B 87.585 588 38 11 284 853 409335663 409335093 0.000000e+00 649.0
42 TraesCS1B01G061600 chr1D 79.843 764 74 37 2482 3193 387236 387971 5.190000e-133 484.0
43 TraesCS1B01G061600 chr1D 97.260 146 4 0 2925 3070 665751 665896 7.420000e-62 248.0
44 TraesCS1B01G061600 chr3D 82.971 552 56 25 2451 2978 560023081 560022544 6.770000e-127 464.0
45 TraesCS1B01G061600 chr3D 83.200 500 29 28 1 467 560025718 560025241 1.160000e-109 407.0
46 TraesCS1B01G061600 chr3D 87.356 87 5 1 3308 3388 560022360 560022274 1.020000e-15 95.3
47 TraesCS1B01G061600 chr1A 81.379 580 50 18 2455 3013 2945047 2945589 1.490000e-113 420.0
48 TraesCS1B01G061600 chr1A 89.615 260 22 4 2826 3085 3520959 3520705 3.330000e-85 326.0
49 TraesCS1B01G061600 chr1A 83.799 358 28 12 359 711 2949333 2949665 2.590000e-81 313.0
50 TraesCS1B01G061600 chr1A 91.204 216 12 4 315 525 3542288 3542075 1.570000e-73 287.0
51 TraesCS1B01G061600 chr1A 86.022 186 9 6 543 711 3533376 3533191 2.120000e-42 183.0
52 TraesCS1B01G061600 chr1A 85.207 169 14 6 428 596 32545238 32545395 2.760000e-36 163.0
53 TraesCS1B01G061600 chr1A 82.738 168 13 7 218 372 586300457 586300293 6.030000e-28 135.0
54 TraesCS1B01G061600 chr1A 92.308 91 7 0 508 598 3012797 3012887 2.800000e-26 130.0
55 TraesCS1B01G061600 chr1A 96.923 65 2 0 3397 3461 3520470 3520406 3.650000e-20 110.0
56 TraesCS1B01G061600 chrUn 83.799 358 28 12 359 711 325465674 325466006 2.590000e-81 313.0
57 TraesCS1B01G061600 chrUn 89.062 128 10 3 2451 2577 318171241 318171365 4.620000e-34 156.0
58 TraesCS1B01G061600 chr2B 81.218 394 44 15 2625 3017 472576724 472577088 1.220000e-74 291.0
59 TraesCS1B01G061600 chr2A 83.929 168 11 7 218 372 27942850 27943014 2.780000e-31 147.0
60 TraesCS1B01G061600 chr7A 83.929 168 10 8 218 372 725598550 725598387 1.000000e-30 145.0
61 TraesCS1B01G061600 chr7A 83.333 168 12 7 218 372 74733357 74733521 1.300000e-29 141.0
62 TraesCS1B01G061600 chr5A 83.333 168 12 7 218 372 72758661 72758497 1.300000e-29 141.0
63 TraesCS1B01G061600 chr7D 89.412 85 4 1 96 180 548230852 548230931 6.110000e-18 102.0


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 TraesCS1B01G061600 chr1B 46691271 46694731 3460 False 6392.000000 6392 100.000000 1 3461 1 chr1B.!!$F2 3460
1 TraesCS1B01G061600 chr1B 70232822 70234571 1749 False 2270.000000 2270 90.233000 710 2449 1 chr1B.!!$F3 1739
2 TraesCS1B01G061600 chr1B 4932651 4933876 1225 True 1805.000000 1805 93.145000 1777 3014 1 chr1B.!!$R2 1237
3 TraesCS1B01G061600 chr1B 4952677 4955100 2423 True 1291.500000 2316 88.602000 45 2452 2 chr1B.!!$R6 2407
4 TraesCS1B01G061600 chr1B 4516241 4518956 2715 True 991.000000 2311 85.116667 710 3370 3 chr1B.!!$R3 2660
5 TraesCS1B01G061600 chr1B 4109416 4112786 3370 False 864.333333 2239 90.978000 59 3388 3 chr1B.!!$F5 3329
6 TraesCS1B01G061600 chr1B 46827882 46830562 2680 True 340.633333 571 87.208667 38 3104 3 chr1B.!!$R7 3066
7 TraesCS1B01G061600 chr1B 4542365 4543363 998 True 323.500000 536 83.364500 31 713 2 chr1B.!!$R4 682
8 TraesCS1B01G061600 chr5B 617170752 617172529 1777 False 2348.000000 2348 90.450000 709 2504 1 chr5B.!!$F1 1795
9 TraesCS1B01G061600 chr5B 60824215 60826243 2028 True 867.333333 2281 88.539333 92 2452 3 chr5B.!!$R1 2360
10 TraesCS1B01G061600 chr5D 57819574 57821306 1732 False 2287.000000 2287 90.520000 710 2449 1 chr5D.!!$F1 1739
11 TraesCS1B01G061600 chr6B 120593668 120595399 1731 True 2268.000000 2268 90.313000 710 2453 1 chr6B.!!$R1 1743
12 TraesCS1B01G061600 chr6B 120130119 120131110 991 True 371.000000 516 82.981500 2450 3365 2 chr6B.!!$R3 915
13 TraesCS1B01G061600 chr6D 51348850 51350567 1717 False 2206.000000 2206 89.766000 710 2453 1 chr6D.!!$F4 1743
14 TraesCS1B01G061600 chr6D 53142385 53143040 655 True 566.000000 566 83.041000 2450 3102 1 chr6D.!!$R1 652
15 TraesCS1B01G061600 chr6A 64063422 64065208 1786 True 900.000000 1565 85.744000 1672 3365 2 chr6A.!!$R1 1693
16 TraesCS1B01G061600 chr6A 613495427 613496170 743 False 521.000000 521 80.307000 2450 3193 1 chr6A.!!$F1 743
17 TraesCS1B01G061600 chr4A 666693895 666694465 570 True 654.000000 654 87.755000 284 853 1 chr4A.!!$R1 569
18 TraesCS1B01G061600 chr3B 409335093 409335663 570 True 649.000000 649 87.585000 284 853 1 chr3B.!!$R1 569
19 TraesCS1B01G061600 chr1D 387236 387971 735 False 484.000000 484 79.843000 2482 3193 1 chr1D.!!$F1 711
20 TraesCS1B01G061600 chr3D 560022274 560025718 3444 True 322.100000 464 84.509000 1 3388 3 chr3D.!!$R1 3387
21 TraesCS1B01G061600 chr1A 2945047 2949665 4618 False 366.500000 420 82.589000 359 3013 2 chr1A.!!$F3 2654
22 TraesCS1B01G061600 chr1A 3520406 3520959 553 True 218.000000 326 93.269000 2826 3461 2 chr1A.!!$R4 635

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
303 378 0.395586 TTATGATGTGGCCCACCTGC 60.396 55.0 12.25 0.88 36.63 4.85 F
1056 1601 0.038618 TCAACAGGATCACCACGACG 60.039 55.0 0.00 0.00 38.94 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2470 0.179150 ACATCACTCGAGAAGCGCTC 60.179 55.0 21.68 4.3 40.61 5.03 R
2490 3094 0.880441 TGTCCAATGGTGCACAATCG 59.120 50.0 20.43 1.2 0.00 3.34 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
22 23 5.943349 TGCAGCAAATAGTAAGGGTAGTA 57.057 39.130 0.00 0.00 0.00 1.82
23 24 6.494666 TGCAGCAAATAGTAAGGGTAGTAT 57.505 37.500 0.00 0.00 0.00 2.12
25 26 6.990349 TGCAGCAAATAGTAAGGGTAGTATTC 59.010 38.462 0.00 0.00 35.60 1.75
26 27 7.147549 TGCAGCAAATAGTAAGGGTAGTATTCT 60.148 37.037 0.00 0.00 35.60 2.40
27 28 7.385478 GCAGCAAATAGTAAGGGTAGTATTCTC 59.615 40.741 0.00 0.00 35.60 2.87
29 30 9.878737 AGCAAATAGTAAGGGTAGTATTCTCTA 57.121 33.333 0.00 0.00 35.60 2.43
52 53 8.928448 TCTAGTTGAACAGATATTAGATTGGCT 58.072 33.333 0.00 0.00 0.00 4.75
68 74 1.269778 TGGCTCTGTGAACTCAACTCG 60.270 52.381 0.00 0.00 0.00 4.18
82 88 4.363990 CTCGTCGGCTGTGGCTGT 62.364 66.667 0.00 0.00 44.62 4.40
83 89 3.865929 CTCGTCGGCTGTGGCTGTT 62.866 63.158 0.00 0.00 44.62 3.16
192 202 5.693104 GCTTTTCATGTTCAGATTCAGCAAA 59.307 36.000 0.00 0.00 0.00 3.68
197 207 7.080353 TCATGTTCAGATTCAGCAAATAGTG 57.920 36.000 0.00 0.00 0.00 2.74
213 223 6.389091 CAAATAGTGGTAATTCTGCTTGCAA 58.611 36.000 0.00 0.00 0.00 4.08
252 320 6.491714 TTCTAGCTCATTATTCAGGCTCTT 57.508 37.500 0.00 0.00 34.88 2.85
271 343 5.755861 GCTCTTCTACTTAATCATGGTGGTC 59.244 44.000 0.00 0.00 0.00 4.02
281 353 3.241067 TCATGGTGGTCGCTAGTTTAC 57.759 47.619 0.00 0.00 0.00 2.01
282 354 2.093869 TCATGGTGGTCGCTAGTTTACC 60.094 50.000 0.00 0.00 0.00 2.85
285 357 2.369532 TGGTGGTCGCTAGTTTACCTTT 59.630 45.455 10.40 0.00 34.23 3.11
303 378 0.395586 TTATGATGTGGCCCACCTGC 60.396 55.000 12.25 0.88 36.63 4.85
540 649 8.881743 ACTACTGTAGTATTCTCTAGTTGAACG 58.118 37.037 18.42 0.00 37.23 3.95
543 655 7.081526 TGTAGTATTCTCTAGTTGAACGGAC 57.918 40.000 3.77 3.76 0.00 4.79
601 741 6.284891 GGAAAATGATTGATTTCCCTGTGA 57.715 37.500 6.09 0.00 45.74 3.58
602 742 6.700352 GGAAAATGATTGATTTCCCTGTGAA 58.300 36.000 6.09 0.00 45.74 3.18
605 745 6.521151 AATGATTGATTTCCCTGTGAACTC 57.479 37.500 0.00 0.00 34.22 3.01
701 1003 3.567164 AGTTGTTGGTTCAGATTCTGCAG 59.433 43.478 7.63 7.63 0.00 4.41
774 1278 6.292150 AGGTGCTAGCTACTTCAATAAATCC 58.708 40.000 17.23 0.00 0.00 3.01
781 1285 4.584325 GCTACTTCAATAAATCCCCATGCA 59.416 41.667 0.00 0.00 0.00 3.96
793 1297 3.289836 TCCCCATGCATATGAACAACAG 58.710 45.455 6.97 0.00 36.36 3.16
865 1381 1.854743 CATAATGAGTGTCTGCCGTCG 59.145 52.381 0.00 0.00 0.00 5.12
888 1410 4.498345 GGTGTGATCTCCGTCTATCTTCAC 60.498 50.000 0.00 0.00 34.16 3.18
889 1411 4.096532 GTGTGATCTCCGTCTATCTTCACA 59.903 45.833 0.00 0.00 39.53 3.58
890 1412 4.889995 TGTGATCTCCGTCTATCTTCACAT 59.110 41.667 0.00 0.00 37.62 3.21
891 1413 5.218885 GTGATCTCCGTCTATCTTCACATG 58.781 45.833 0.00 0.00 33.84 3.21
901 1427 6.369005 GTCTATCTTCACATGCATGCATTAC 58.631 40.000 30.32 6.91 33.90 1.89
962 1504 8.950403 GTTGTTTTCTCAACCTTGATACATAC 57.050 34.615 0.00 0.00 40.97 2.39
999 1544 5.008613 GGTACAGCTGAATTTGTTCTGTTCA 59.991 40.000 23.35 0.00 38.71 3.18
1017 1562 1.200519 CAATGGAGGACCTACCGGAA 58.799 55.000 9.46 0.00 44.74 4.30
1056 1601 0.038618 TCAACAGGATCACCACGACG 60.039 55.000 0.00 0.00 38.94 5.12
1178 1723 3.244422 ACAAAAGCCCTGACATCGTTCTA 60.244 43.478 0.00 0.00 0.00 2.10
1179 1724 3.914426 AAAGCCCTGACATCGTTCTAT 57.086 42.857 0.00 0.00 0.00 1.98
1229 1774 4.571176 GGAAATCGATTACTCTGGTTGGAC 59.429 45.833 11.83 0.00 0.00 4.02
1258 1803 3.253188 ACATGGAAATCAGTTGGACAACG 59.747 43.478 9.31 5.38 45.50 4.10
1411 1956 2.814919 TCCGCACCAAAAATAACGTCAT 59.185 40.909 0.00 0.00 0.00 3.06
1516 2061 2.124411 GGCTGGAATACCTTGGTAGGA 58.876 52.381 5.71 0.00 45.05 2.94
1656 2205 9.640952 AGAGGAAGATATGATAGTCTTATAGCC 57.359 37.037 0.00 0.00 34.97 3.93
1657 2206 9.415008 GAGGAAGATATGATAGTCTTATAGCCA 57.585 37.037 0.00 0.00 34.97 4.75
1733 2288 5.311265 TGATTTCTGCTGTGAGAGTTTGAT 58.689 37.500 0.00 0.00 0.00 2.57
1738 2293 3.603532 TGCTGTGAGAGTTTGATGGATC 58.396 45.455 0.00 0.00 0.00 3.36
1911 2466 4.510038 AAGCATCACACTTTGGCTTAAG 57.490 40.909 0.00 0.00 42.51 1.85
1915 2470 2.229792 TCACACTTTGGCTTAAGCTGG 58.770 47.619 25.88 15.32 41.70 4.85
1949 2504 5.220359 CGAGTGATGTCAGCTATTGTGAAAG 60.220 44.000 0.00 0.00 0.00 2.62
2003 2558 3.129988 GCTCTAGCCCTAAACTGTCGTAA 59.870 47.826 0.00 0.00 34.31 3.18
2064 2619 2.173356 TGACTGGCCATCAGAAATAGGG 59.827 50.000 5.51 0.00 46.18 3.53
2083 2638 1.480545 GGTTCACACAGCAGGGTTTTT 59.519 47.619 0.00 0.00 0.00 1.94
2150 2705 2.549754 ACGCCAACTTCTTTGATGACAG 59.450 45.455 0.00 0.00 37.39 3.51
2243 2798 0.527565 GTTGGGATGCGCTTCATTGT 59.472 50.000 22.93 0.00 35.05 2.71
2490 3094 8.023128 TGCTGCTGAAGTCATTATTAAGTTTTC 58.977 33.333 0.00 0.00 0.00 2.29
2516 3125 1.880819 GCACCATTGGACAAGGCTGG 61.881 60.000 10.37 2.48 0.00 4.85
2539 3149 3.496130 GCATCATCCGACCAGATTTACTG 59.504 47.826 0.00 0.00 45.36 2.74
2680 3331 7.280205 CCGTAATTCTGGTTGCTTAGTTTCTAT 59.720 37.037 0.00 0.00 0.00 1.98
2686 3337 8.362464 TCTGGTTGCTTAGTTTCTATTCTCTA 57.638 34.615 0.00 0.00 0.00 2.43
2734 3385 0.107165 CCCCAAGATTCCCCGTCTTC 60.107 60.000 0.00 0.00 33.82 2.87
2809 3472 3.737559 AGCAAATGTCATGGACCCTTA 57.262 42.857 0.00 0.00 0.00 2.69
3111 3971 2.666508 GGCATATAACATAGCCGTCACG 59.333 50.000 0.00 0.00 37.41 4.35
3118 3978 1.067142 ACATAGCCGTCACGTCATGTT 60.067 47.619 0.00 0.00 0.00 2.71
3144 4004 3.071671 TGGACATCCAGCACTCAGA 57.928 52.632 0.00 0.00 42.01 3.27
3227 4390 6.759497 AAATAGCAGGAATTAAGACACCAC 57.241 37.500 0.00 0.00 0.00 4.16
3243 4406 3.452627 ACACCACTTGAGGGATGAGATAC 59.547 47.826 0.00 0.00 0.00 2.24
3285 4453 5.643379 TGGTACAAAGATCCTGAAATTGC 57.357 39.130 0.00 0.00 31.92 3.56
3291 4459 6.527423 ACAAAGATCCTGAAATTGCAAATGT 58.473 32.000 1.71 0.00 0.00 2.71
3293 4461 8.149647 ACAAAGATCCTGAAATTGCAAATGTAA 58.850 29.630 1.71 0.00 0.00 2.41
3294 4462 8.437742 CAAAGATCCTGAAATTGCAAATGTAAC 58.562 33.333 1.71 0.00 0.00 2.50
3295 4463 7.230849 AGATCCTGAAATTGCAAATGTAACA 57.769 32.000 1.71 0.00 0.00 2.41
3296 4464 7.092716 AGATCCTGAAATTGCAAATGTAACAC 58.907 34.615 1.71 0.00 0.00 3.32
3379 8200 4.437239 CATCAGTTCAGCTCGTAGGAATT 58.563 43.478 0.00 0.00 0.00 2.17
3382 8203 1.324736 GTTCAGCTCGTAGGAATTGCG 59.675 52.381 0.00 0.00 36.12 4.85
3426 8268 6.825944 TTGCTGGCTATGTAATTTGTGTTA 57.174 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.964772 TGTTCAACTAGAGAATACTACCCTTAC 58.035 37.037 0.00 0.00 0.00 2.34
14 15 7.411808 TCTGTTCAACTAGAGAATACTACCCT 58.588 38.462 0.00 0.00 0.00 4.34
15 16 7.642082 TCTGTTCAACTAGAGAATACTACCC 57.358 40.000 0.00 0.00 0.00 3.69
25 26 9.202273 GCCAATCTAATATCTGTTCAACTAGAG 57.798 37.037 0.00 0.00 0.00 2.43
26 27 8.928448 AGCCAATCTAATATCTGTTCAACTAGA 58.072 33.333 0.00 0.00 0.00 2.43
27 28 9.202273 GAGCCAATCTAATATCTGTTCAACTAG 57.798 37.037 0.00 0.00 0.00 2.57
29 30 7.714377 CAGAGCCAATCTAATATCTGTTCAACT 59.286 37.037 0.00 0.00 36.10 3.16
52 53 1.001706 CCGACGAGTTGAGTTCACAGA 60.002 52.381 0.00 0.00 0.00 3.41
68 74 1.135689 CATTTAACAGCCACAGCCGAC 60.136 52.381 0.00 0.00 41.25 4.79
192 202 6.588719 TTTTGCAAGCAGAATTACCACTAT 57.411 33.333 0.00 0.00 0.00 2.12
197 207 6.544038 AACAATTTTGCAAGCAGAATTACC 57.456 33.333 19.10 0.00 38.25 2.85
213 223 5.772521 AGCTAGAATTGACGCAAACAATTT 58.227 33.333 11.89 6.96 44.46 1.82
252 320 3.704566 AGCGACCACCATGATTAAGTAGA 59.295 43.478 0.00 0.00 0.00 2.59
271 343 5.277345 GCCACATCATAAAGGTAAACTAGCG 60.277 44.000 0.00 0.00 0.00 4.26
281 353 1.063717 AGGTGGGCCACATCATAAAGG 60.064 52.381 35.69 0.00 35.86 3.11
282 354 2.026641 CAGGTGGGCCACATCATAAAG 58.973 52.381 35.69 14.04 35.86 1.85
285 357 1.227102 GCAGGTGGGCCACATCATA 59.773 57.895 35.69 0.00 35.86 2.15
330 408 7.392113 GCTAGCACCTTATCTGTCTCTAGATTA 59.608 40.741 10.63 0.00 38.35 1.75
437 522 7.961326 AGGAGAATGGCTTTACAACATTAAT 57.039 32.000 0.00 0.00 35.17 1.40
501 609 6.668541 ACTACAGTAGTATTTGCTGCAATG 57.331 37.500 16.77 11.70 42.63 2.82
528 637 4.177026 CCAATCTGTCCGTTCAACTAGAG 58.823 47.826 0.00 0.00 0.00 2.43
533 642 0.521735 GGCCAATCTGTCCGTTCAAC 59.478 55.000 0.00 0.00 0.00 3.18
540 649 0.038166 TTCACAGGGCCAATCTGTCC 59.962 55.000 6.18 0.00 42.87 4.02
543 655 1.271543 TGAGTTCACAGGGCCAATCTG 60.272 52.381 6.18 5.37 38.16 2.90
599 739 9.902684 ATTAGTTAGTACTAGTAGCTGAGTTCA 57.097 33.333 1.87 0.00 38.09 3.18
605 745 9.751542 ATGCAAATTAGTTAGTACTAGTAGCTG 57.248 33.333 1.87 0.00 38.09 4.24
636 797 9.788960 GCTAATTAATAACAAGAAAACCAGAGG 57.211 33.333 0.00 0.00 0.00 3.69
665 834 5.697067 ACCAACAACTTATTTGGAGGTACA 58.303 37.500 7.35 0.00 44.51 2.90
668 837 5.205056 TGAACCAACAACTTATTTGGAGGT 58.795 37.500 7.35 0.00 44.51 3.85
774 1278 3.695556 TGTCTGTTGTTCATATGCATGGG 59.304 43.478 10.16 0.77 32.61 4.00
781 1285 7.425606 GTCCAAAACTTGTCTGTTGTTCATAT 58.574 34.615 0.00 0.00 0.00 1.78
793 1297 4.312443 TCTGTATCCGTCCAAAACTTGTC 58.688 43.478 0.00 0.00 0.00 3.18
865 1381 3.632604 TGAAGATAGACGGAGATCACACC 59.367 47.826 0.00 0.00 0.00 4.16
877 1399 5.434352 AATGCATGCATGTGAAGATAGAC 57.566 39.130 32.79 7.53 36.68 2.59
888 1410 8.433421 TGATATATCAGAGTAATGCATGCATG 57.567 34.615 32.79 22.70 33.00 4.06
958 1499 5.928839 GCTGTACCAATCATCAGGTAGTATG 59.071 44.000 0.00 0.00 40.83 2.39
962 1504 4.100035 TCAGCTGTACCAATCATCAGGTAG 59.900 45.833 14.67 0.00 40.83 3.18
999 1544 1.497161 CTTCCGGTAGGTCCTCCATT 58.503 55.000 0.00 0.00 39.05 3.16
1056 1601 5.988287 AGGGAAAGAGAATTCAGATCACTC 58.012 41.667 8.44 0.00 0.00 3.51
1229 1774 4.801891 CAACTGATTTCCATGTTCAGGTG 58.198 43.478 12.78 12.78 45.63 4.00
1235 1780 4.261572 CGTTGTCCAACTGATTTCCATGTT 60.262 41.667 8.40 0.00 39.08 2.71
1258 1803 4.279420 AGATGAAAACACAGAAAGGCCTTC 59.721 41.667 20.79 12.47 0.00 3.46
1325 1870 1.137675 CAAGCCCAGAGTCATCGATGA 59.862 52.381 23.99 23.99 0.00 2.92
1411 1956 0.387565 GCAACCGAGAAAAGCCCAAA 59.612 50.000 0.00 0.00 0.00 3.28
1516 2061 3.012518 CAAGCTCTTCCAACGATCCATT 58.987 45.455 0.00 0.00 0.00 3.16
1608 2153 7.148000 CCTCTTTTCCTCTCAAACTCAAACTTT 60.148 37.037 0.00 0.00 0.00 2.66
1652 2201 3.619900 AGACCTCATCACCTATGGCTA 57.380 47.619 0.00 0.00 36.15 3.93
1653 2202 2.485966 AGACCTCATCACCTATGGCT 57.514 50.000 0.00 0.00 36.15 4.75
1654 2203 3.834813 TCATAGACCTCATCACCTATGGC 59.165 47.826 0.00 0.00 39.08 4.40
1655 2204 5.083122 AGTCATAGACCTCATCACCTATGG 58.917 45.833 0.00 0.00 39.08 2.74
1656 2205 5.184864 GGAGTCATAGACCTCATCACCTATG 59.815 48.000 0.00 0.00 39.63 2.23
1657 2206 5.075761 AGGAGTCATAGACCTCATCACCTAT 59.924 44.000 0.00 0.00 32.18 2.57
1733 2288 0.546122 ATGCGCCAACCTTAGATCCA 59.454 50.000 4.18 0.00 0.00 3.41
1738 2293 4.096382 AGTTTCAATATGCGCCAACCTTAG 59.904 41.667 4.18 0.00 0.00 2.18
1911 2466 2.581953 CTCGAGAAGCGCTCCAGC 60.582 66.667 12.06 0.13 40.70 4.85
1915 2470 0.179150 ACATCACTCGAGAAGCGCTC 60.179 55.000 21.68 4.30 40.61 5.03
1922 2477 3.696548 ACAATAGCTGACATCACTCGAGA 59.303 43.478 21.68 0.00 0.00 4.04
1949 2504 4.868171 TGTTATCAGTAAATGACGTCCTGC 59.132 41.667 14.12 1.18 41.91 4.85
2003 2558 3.030291 CTGAGGTCTACCATCTGAAGCT 58.970 50.000 1.26 0.00 38.89 3.74
2064 2619 2.959507 AAAAACCCTGCTGTGTGAAC 57.040 45.000 0.00 0.00 0.00 3.18
2083 2638 1.883638 GCAGGACTGAATGAGCACCAA 60.884 52.381 3.00 0.00 0.00 3.67
2150 2705 2.368878 AGAGGGCCTTCATCCCCC 60.369 66.667 18.32 0.00 45.03 5.40
2243 2798 1.604308 CTCAAGCATGGGGTGTGCA 60.604 57.895 0.00 0.00 44.87 4.57
2490 3094 0.880441 TGTCCAATGGTGCACAATCG 59.120 50.000 20.43 1.20 0.00 3.34
2516 3125 1.972872 AAATCTGGTCGGATGATGCC 58.027 50.000 0.00 0.00 0.00 4.40
2539 3149 7.770801 AATAAGGCAACAAAAAGTTCAGAAC 57.229 32.000 5.00 5.00 38.74 3.01
2680 3331 3.490419 GGTTTCGAAGCGGCTATAGAGAA 60.490 47.826 1.35 2.34 0.00 2.87
2787 3450 3.737559 AGGGTCCATGACATTTGCTTA 57.262 42.857 0.00 0.00 33.68 3.09
2809 3472 7.968405 GTGCTCAAAATCACTTCCGTAATAAAT 59.032 33.333 0.00 0.00 0.00 1.40
3085 3842 4.315803 ACGGCTATGTTATATGCCTTGAC 58.684 43.478 0.00 0.00 42.90 3.18
3111 3971 3.988379 TGTCCAGAGCAAAAACATGAC 57.012 42.857 0.00 0.00 0.00 3.06
3227 4390 6.267242 TGAATCTCAGTATCTCATCCCTCAAG 59.733 42.308 0.00 0.00 0.00 3.02
3243 4406 4.022589 ACCAAGCAAACACATGAATCTCAG 60.023 41.667 0.00 0.00 0.00 3.35
3285 4453 3.617540 TTGAGCGGTGTGTTACATTTG 57.382 42.857 0.00 0.00 0.00 2.32
3291 4459 0.470766 ACCCTTTGAGCGGTGTGTTA 59.529 50.000 0.00 0.00 0.00 2.41
3293 4461 0.818040 GAACCCTTTGAGCGGTGTGT 60.818 55.000 0.00 0.00 30.96 3.72
3294 4462 0.535102 AGAACCCTTTGAGCGGTGTG 60.535 55.000 0.00 0.00 30.96 3.82
3295 4463 0.535102 CAGAACCCTTTGAGCGGTGT 60.535 55.000 0.00 0.00 30.96 4.16
3296 4464 0.250295 TCAGAACCCTTTGAGCGGTG 60.250 55.000 0.00 0.00 30.96 4.94
3379 8200 3.990141 GCGAAGTTTGCAAACGCA 58.010 50.000 30.90 0.00 46.75 5.24
3388 8209 2.195922 CAGCAAAGCAAAGCGAAGTTT 58.804 42.857 0.00 0.00 35.48 2.66
3389 8210 1.536709 CCAGCAAAGCAAAGCGAAGTT 60.537 47.619 0.00 0.00 35.48 2.66
3390 8211 0.031178 CCAGCAAAGCAAAGCGAAGT 59.969 50.000 0.00 0.00 35.48 3.01
3391 8212 1.280206 GCCAGCAAAGCAAAGCGAAG 61.280 55.000 0.00 0.00 35.48 3.79
3393 8214 0.888736 TAGCCAGCAAAGCAAAGCGA 60.889 50.000 0.00 0.00 35.48 4.93
3394 8215 0.171903 ATAGCCAGCAAAGCAAAGCG 59.828 50.000 0.00 0.00 35.48 4.68
3395 8216 1.067354 ACATAGCCAGCAAAGCAAAGC 60.067 47.619 0.00 0.00 0.00 3.51
3436 8278 4.030977 GCGCATGTTTCATTTTAGCTCAAG 59.969 41.667 0.30 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.