Multiple sequence alignment - TraesCS1A01G055000

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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 TraesCS1A01G055000 chr1A 100.000 3577 0 0 3550 7126 36273874 36277450 0.000000e+00 6606.0
1 TraesCS1A01G055000 chr1A 100.000 3215 0 0 1 3215 36270325 36273539 0.000000e+00 5938.0
2 TraesCS1A01G055000 chr1A 86.842 266 26 8 6298 6559 68157042 68157302 9.040000e-74 289.0
3 TraesCS1A01G055000 chr1B 94.944 3422 143 20 3715 7126 56885723 56889124 0.000000e+00 5334.0
4 TraesCS1A01G055000 chr1B 92.719 2802 135 33 40 2792 56882325 56885106 0.000000e+00 3980.0
5 TraesCS1A01G055000 chr1B 85.127 316 33 11 2788 3093 56885415 56885104 1.930000e-80 311.0
6 TraesCS1A01G055000 chr1B 82.759 87 8 6 8 92 303016794 303016713 3.570000e-08 71.3
7 TraesCS1A01G055000 chr1D 93.686 2946 120 30 312 3215 36835195 36838116 0.000000e+00 4349.0
8 TraesCS1A01G055000 chr1D 97.898 1427 22 6 5122 6544 36839718 36841140 0.000000e+00 2462.0
9 TraesCS1A01G055000 chr1D 96.565 1077 27 3 4045 5120 36838566 36839633 0.000000e+00 1775.0
10 TraesCS1A01G055000 chr1D 96.763 587 19 0 6540 7126 36841374 36841960 0.000000e+00 979.0
11 TraesCS1A01G055000 chr1D 96.296 405 7 4 3551 3952 36838164 36838563 0.000000e+00 658.0
12 TraesCS1A01G055000 chr1D 96.350 274 9 1 8 281 36834855 36835127 3.920000e-122 449.0
13 TraesCS1A01G055000 chr1D 88.372 215 21 4 6310 6523 303702761 303702550 9.170000e-64 255.0
14 TraesCS1A01G055000 chr1D 87.336 229 20 7 6298 6524 334816414 334816635 3.300000e-63 254.0
15 TraesCS1A01G055000 chr1D 92.453 53 3 1 3651 3702 18689362 18689414 2.760000e-09 75.0
16 TraesCS1A01G055000 chr4B 87.170 265 29 4 6291 6553 258762327 258762588 5.410000e-76 296.0
17 TraesCS1A01G055000 chr4B 81.319 91 10 5 8 96 340784345 340784260 4.610000e-07 67.6
18 TraesCS1A01G055000 chr7A 85.223 291 36 7 6298 6585 350641440 350641726 6.990000e-75 292.0
19 TraesCS1A01G055000 chr7A 86.842 266 26 9 6298 6559 442273597 442273857 9.040000e-74 289.0
20 TraesCS1A01G055000 chr7A 95.745 47 2 0 3656 3702 513221042 513221088 7.670000e-10 76.8
21 TraesCS1A01G055000 chr3D 87.072 263 26 7 6292 6551 386221081 386221338 2.510000e-74 291.0
22 TraesCS1A01G055000 chr2B 86.029 272 28 8 6285 6551 352860502 352860236 4.210000e-72 283.0
23 TraesCS1A01G055000 chr3A 85.305 279 31 9 6286 6559 175624699 175624426 5.440000e-71 279.0
24 TraesCS1A01G055000 chr3A 100.000 37 0 0 5121 5157 140039330 140039294 1.280000e-07 69.4
25 TraesCS1A01G055000 chr5A 85.597 243 27 6 6285 6524 371479518 371479281 1.540000e-61 248.0
26 TraesCS1A01G055000 chr5A 84.706 85 8 5 8 92 384463928 384464007 5.930000e-11 80.5
27 TraesCS1A01G055000 chr3B 86.222 225 23 6 6298 6519 50047551 50047770 3.320000e-58 237.0
28 TraesCS1A01G055000 chr3B 84.416 77 8 3 8 84 254431914 254431986 9.920000e-09 73.1
29 TraesCS1A01G055000 chr2A 75.342 219 49 4 6310 6527 221300929 221300715 4.550000e-17 100.0
30 TraesCS1A01G055000 chr6D 93.220 59 4 0 3644 3702 9346295 9346237 3.540000e-13 87.9
31 TraesCS1A01G055000 chr6D 88.710 62 4 3 3648 3708 132661080 132661139 9.920000e-09 73.1
32 TraesCS1A01G055000 chr6D 88.710 62 4 3 3648 3708 132663200 132663141 9.920000e-09 73.1
33 TraesCS1A01G055000 chr5D 97.826 46 1 0 3657 3702 312136073 312136118 5.930000e-11 80.5
34 TraesCS1A01G055000 chr2D 95.745 47 2 0 3656 3702 459300556 459300602 7.670000e-10 76.8
35 TraesCS1A01G055000 chr4A 84.146 82 8 4 9 90 196772400 196772476 2.760000e-09 75.0
36 TraesCS1A01G055000 chr5B 82.418 91 9 5 8 95 235760072 235760158 9.920000e-09 73.1
37 TraesCS1A01G055000 chr5B 92.308 52 3 1 3650 3701 576291931 576291981 9.920000e-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 TraesCS1A01G055000 chr1A 36270325 36277450 7125 False 6272.000000 6606 100.000000 1 7126 2 chr1A.!!$F2 7125
1 TraesCS1A01G055000 chr1B 56882325 56889124 6799 False 4657.000000 5334 93.831500 40 7126 2 chr1B.!!$F1 7086
2 TraesCS1A01G055000 chr1D 36834855 36841960 7105 False 1778.666667 4349 96.259667 8 7126 6 chr1D.!!$F3 7118

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
620 673 0.317603 CGAATTACCTCGGATCGCGT 60.318 55.000 5.77 0.0 35.14 6.01 F
2064 2138 1.138859 AGTGCACTGTGTAAGCTCACA 59.861 47.619 20.97 7.9 44.54 3.58 F
2417 2491 1.219124 TGCCGGAGCAGTGATCTTC 59.781 57.895 5.05 0.0 46.52 2.87 F
3954 4125 0.473694 TCAGCCTCCTCCACTTTCCA 60.474 55.000 0.00 0.0 0.00 3.53 F
4518 4693 0.721718 CCCGCGTGATGTTTCTCTTC 59.278 55.000 4.92 0.0 0.00 2.87 F
5617 5877 1.417145 TGCCTTCTTGCTGCCATTTTT 59.583 42.857 0.00 0.0 0.00 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2417 2491 0.729116 GGATGATCAACACTGCACGG 59.271 55.000 0.00 0.00 0.00 4.94 R
2896 3023 1.073897 GGCTGGGGGTGCAGATATC 59.926 63.158 0.00 0.00 0.00 1.63 R
4415 4590 1.562475 GAGTAATGGGGTGGCCTGTAA 59.438 52.381 3.32 0.00 0.00 2.41 R
5620 5880 0.746063 CAATACATGCGCATGGGGTT 59.254 50.000 43.46 32.48 42.91 4.11 R
5835 6098 2.293122 GCCAACAGCAATAAGTGACACA 59.707 45.455 8.59 0.00 42.97 3.72 R
6725 7226 1.135199 CAAGCATGCACAAAGCCCTAG 60.135 52.381 21.98 0.00 44.83 3.02 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
38 39 6.350612 CCCCTGAAACACAAAACTAAAACTCA 60.351 38.462 0.00 0.00 0.00 3.41
188 189 3.306502 CCACCACCTACGTTGTACTCATT 60.307 47.826 0.00 0.00 0.00 2.57
245 246 1.064758 ACACTTCAGCTCACCCACAAA 60.065 47.619 0.00 0.00 0.00 2.83
252 253 1.143684 AGCTCACCCACAAATCACAGT 59.856 47.619 0.00 0.00 0.00 3.55
276 277 0.806102 GCAGAAATCAGTAGCGCGGA 60.806 55.000 8.83 0.00 0.00 5.54
283 284 0.806102 TCAGTAGCGCGGATGCTTTC 60.806 55.000 8.83 0.00 44.46 2.62
284 285 1.083806 CAGTAGCGCGGATGCTTTCA 61.084 55.000 8.83 0.00 44.46 2.69
285 286 1.084370 AGTAGCGCGGATGCTTTCAC 61.084 55.000 8.83 0.00 44.46 3.18
288 289 1.512734 GCGCGGATGCTTTCACAAG 60.513 57.895 8.83 0.00 39.65 3.16
291 292 1.725931 CGCGGATGCTTTCACAAGAAC 60.726 52.381 0.00 0.00 39.65 3.01
293 294 2.666619 GCGGATGCTTTCACAAGAACAG 60.667 50.000 0.00 0.00 38.39 3.16
295 296 3.364366 CGGATGCTTTCACAAGAACAGAC 60.364 47.826 0.00 0.00 32.39 3.51
296 297 3.565482 GGATGCTTTCACAAGAACAGACA 59.435 43.478 0.00 0.00 32.39 3.41
298 299 5.278660 GGATGCTTTCACAAGAACAGACAAT 60.279 40.000 0.00 0.00 32.39 2.71
300 301 6.060028 TGCTTTCACAAGAACAGACAATAC 57.940 37.500 0.00 0.00 32.39 1.89
301 302 5.140177 GCTTTCACAAGAACAGACAATACG 58.860 41.667 0.00 0.00 32.39 3.06
303 304 5.900339 TTCACAAGAACAGACAATACGAC 57.100 39.130 0.00 0.00 0.00 4.34
304 305 3.978855 TCACAAGAACAGACAATACGACG 59.021 43.478 0.00 0.00 0.00 5.12
306 307 3.979495 ACAAGAACAGACAATACGACGTC 59.021 43.478 2.43 5.18 0.00 4.34
307 308 3.213249 AGAACAGACAATACGACGTCC 57.787 47.619 10.58 0.00 32.33 4.79
308 309 2.818432 AGAACAGACAATACGACGTCCT 59.182 45.455 10.58 0.34 32.33 3.85
310 311 4.094590 AGAACAGACAATACGACGTCCTAG 59.905 45.833 10.58 0.00 32.33 3.02
445 495 3.519930 GGCGAGGTCGAGGTCTCC 61.520 72.222 2.94 0.00 43.02 3.71
533 586 3.730061 GCATCAGGAAATTCACGAAGCAG 60.730 47.826 6.33 0.00 0.00 4.24
534 587 1.806542 TCAGGAAATTCACGAAGCAGC 59.193 47.619 0.00 0.00 0.00 5.25
535 588 1.536766 CAGGAAATTCACGAAGCAGCA 59.463 47.619 0.00 0.00 0.00 4.41
553 606 2.412089 AGCAACGATTACAGCGAGAAAC 59.588 45.455 0.00 0.00 0.00 2.78
618 671 1.406447 GTCGAATTACCTCGGATCGC 58.594 55.000 0.00 0.00 39.35 4.58
620 673 0.317603 CGAATTACCTCGGATCGCGT 60.318 55.000 5.77 0.00 35.14 6.01
763 822 4.918037 GACACGTGTCGAGGAATTAGTAT 58.082 43.478 31.03 0.00 35.12 2.12
1119 1180 4.778415 CTCCTCACGGTGGTCGCG 62.778 72.222 8.50 0.00 43.89 5.87
1278 1339 4.451150 CTCCGGGCACTGCGCTTA 62.451 66.667 9.73 3.31 41.91 3.09
1335 1402 9.985318 CTTAATTAGAATTGCTTGAGAACTCAG 57.015 33.333 4.72 1.85 41.13 3.35
1336 1403 5.869753 TTAGAATTGCTTGAGAACTCAGC 57.130 39.130 14.46 14.46 41.13 4.26
1337 1404 3.748083 AGAATTGCTTGAGAACTCAGCA 58.252 40.909 17.73 17.73 41.13 4.41
1338 1405 3.501445 AGAATTGCTTGAGAACTCAGCAC 59.499 43.478 19.81 13.09 40.59 4.40
1339 1406 2.627515 TTGCTTGAGAACTCAGCACT 57.372 45.000 19.81 0.00 40.59 4.40
1340 1407 2.160822 TGCTTGAGAACTCAGCACTC 57.839 50.000 17.73 0.00 41.13 3.51
1344 1411 3.577667 CTTGAGAACTCAGCACTCAGAG 58.422 50.000 4.72 0.00 40.82 3.35
1366 1433 6.773200 AGAGCCTAAGGATATTTTTGTTAGCC 59.227 38.462 0.00 0.00 0.00 3.93
1369 1436 7.939588 AGCCTAAGGATATTTTTGTTAGCCTAG 59.060 37.037 0.00 0.00 34.43 3.02
1375 1442 9.785982 AGGATATTTTTGTTAGCCTAGAGATTC 57.214 33.333 0.00 0.00 33.78 2.52
1379 1446 7.672983 TTTTTGTTAGCCTAGAGATTCTGTG 57.327 36.000 0.00 0.00 0.00 3.66
1380 1447 6.605471 TTTGTTAGCCTAGAGATTCTGTGA 57.395 37.500 0.00 0.00 0.00 3.58
1382 1449 6.154203 TGTTAGCCTAGAGATTCTGTGATG 57.846 41.667 0.00 0.00 0.00 3.07
1383 1450 5.069648 TGTTAGCCTAGAGATTCTGTGATGG 59.930 44.000 0.00 0.00 0.00 3.51
1389 1458 6.279882 CCTAGAGATTCTGTGATGGTTTCTC 58.720 44.000 0.00 0.00 0.00 2.87
1399 1468 6.491062 TCTGTGATGGTTTCTCAACATGAATT 59.509 34.615 0.00 0.00 34.15 2.17
1454 1525 1.209019 AGCTATCCACTGAAGCACTGG 59.791 52.381 0.00 0.00 38.75 4.00
1477 1548 7.761409 TGGTCATATTTGTTGTGAGCTTAATC 58.239 34.615 0.00 0.00 42.50 1.75
1492 1563 5.753716 AGCTTAATCATGAGCTTCCTCTTT 58.246 37.500 0.09 0.00 45.44 2.52
1511 1582 4.701651 TCTTTTGGACATATGTTGCAGAGG 59.298 41.667 10.30 2.19 0.00 3.69
1518 1589 3.264193 ACATATGTTGCAGAGGTGGAGAA 59.736 43.478 1.41 0.00 0.00 2.87
1531 1602 2.678324 GTGGAGAAGAAGAGTTCCACG 58.322 52.381 6.74 0.00 46.98 4.94
1740 1811 2.459442 GCAGGTCATCGCTGCAGTC 61.459 63.158 16.64 6.83 42.98 3.51
1840 1911 8.768955 GCATCTCGACTAATCTTTAACATTGAT 58.231 33.333 0.00 0.00 0.00 2.57
1876 1948 2.291930 TGTTGGAGGTGTGGTTCCTTTT 60.292 45.455 0.00 0.00 35.20 2.27
1964 2036 6.187125 GCTTCACTAGATGCTTGAATGAAA 57.813 37.500 0.00 0.00 40.64 2.69
2064 2138 1.138859 AGTGCACTGTGTAAGCTCACA 59.861 47.619 20.97 7.90 44.54 3.58
2417 2491 1.219124 TGCCGGAGCAGTGATCTTC 59.781 57.895 5.05 0.00 46.52 2.87
2606 2680 5.605488 TCCTACAAGGTAAAACTGTTCTCCT 59.395 40.000 0.00 0.00 36.53 3.69
2705 2780 5.241403 TGGCAACTTCCTTTATGAGAAGA 57.759 39.130 6.75 0.00 41.69 2.87
2872 2999 3.626670 CAGCTGATCTAGGAAAGCAAAGG 59.373 47.826 8.42 0.00 38.14 3.11
2896 3023 9.620660 AGGTTTAAATGAACGCAAACTTATTAG 57.379 29.630 0.00 0.00 32.69 1.73
2904 3031 7.851508 TGAACGCAAACTTATTAGATATCTGC 58.148 34.615 15.79 6.61 0.00 4.26
2906 3033 7.178712 ACGCAAACTTATTAGATATCTGCAC 57.821 36.000 15.79 0.00 0.00 4.57
2968 3108 7.571798 GCATCAAACAAAGATTTTTGACCATCC 60.572 37.037 15.10 0.00 45.21 3.51
3016 3156 2.306219 AGCCCTCAGTTTTTAGTCCTCC 59.694 50.000 0.00 0.00 0.00 4.30
3133 3273 5.998363 AGTCTCATCCCTGTCTTTTAACAAC 59.002 40.000 0.00 0.00 0.00 3.32
3154 3294 8.068892 ACAACCTTGTTCAACCAATTTAGTTA 57.931 30.769 0.00 0.00 38.47 2.24
3687 3855 4.261801 CGATCCAAAATAAGTGTCCTGGT 58.738 43.478 0.00 0.00 0.00 4.00
3691 3859 6.155475 TCCAAAATAAGTGTCCTGGTTTTG 57.845 37.500 8.60 8.60 36.54 2.44
3891 4062 4.935808 CCTGTCACTGGTAAATAACTCCAC 59.064 45.833 0.00 0.00 0.00 4.02
3954 4125 0.473694 TCAGCCTCCTCCACTTTCCA 60.474 55.000 0.00 0.00 0.00 3.53
3990 4161 2.028130 ACGATGACCAGATCCTCACTC 58.972 52.381 0.00 0.00 0.00 3.51
3994 4165 1.819288 TGACCAGATCCTCACTCGAAC 59.181 52.381 0.00 0.00 0.00 3.95
4008 4179 7.659799 TCCTCACTCGAACTTTGAAATATTTCA 59.340 33.333 23.86 23.86 44.78 2.69
4168 4342 6.857964 GTCCGATTTAAGCATGACCAATTATG 59.142 38.462 0.00 0.00 0.00 1.90
4203 4377 7.880160 TTGCATAAGCTTGTTACCAGATATT 57.120 32.000 9.86 0.00 42.74 1.28
4354 4529 4.040829 TGTGTCTGAGTGAACCATCTCAAT 59.959 41.667 0.00 0.00 39.67 2.57
4453 4628 7.364232 CCATTACTCTTGACTCTGGTAGTGATT 60.364 40.741 0.00 0.00 39.07 2.57
4514 4689 1.821216 ATTTCCCGCGTGATGTTTCT 58.179 45.000 4.92 0.00 0.00 2.52
4518 4693 0.721718 CCCGCGTGATGTTTCTCTTC 59.278 55.000 4.92 0.00 0.00 2.87
4677 4852 3.674997 TCTGTCCCTATGAACAAACTGC 58.325 45.455 0.00 0.00 0.00 4.40
4715 4891 9.965824 TTTTTCTCTTTTCATAGACAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
4957 5133 3.253188 GCTTCTGTTAATTCAGCCACACA 59.747 43.478 0.00 0.00 35.63 3.72
5120 5296 9.640963 GTAATCACATGTACTCCCTATATTGTC 57.359 37.037 0.00 0.00 0.00 3.18
5206 5465 4.082081 TGAAAAAGCAGCTTGGATACCATG 60.082 41.667 8.88 0.00 31.53 3.66
5239 5498 4.610007 GCAGAATGTTCATACATAGCGCAG 60.610 45.833 11.47 0.64 44.14 5.18
5617 5877 1.417145 TGCCTTCTTGCTGCCATTTTT 59.583 42.857 0.00 0.00 0.00 1.94
5658 5920 1.991813 TGGTTCATGGATGGTCAAGGA 59.008 47.619 0.00 0.00 0.00 3.36
6340 6603 6.183360 GGATTCTCAATGGAATTTTGGAGGAG 60.183 42.308 0.00 0.00 36.24 3.69
6446 6709 9.241919 TCATTTGCACTAGATTTCATAGGAAAA 57.758 29.630 6.65 0.00 45.52 2.29
6489 6752 7.272037 TCTTTGAAAGAATCCTACGCTTTTT 57.728 32.000 4.94 0.00 33.83 1.94
6606 7107 6.748332 GCCCCTATATGCTTAACTGATCCTTT 60.748 42.308 0.00 0.00 0.00 3.11
6665 7166 9.643652 GATCAAATTAACTAGAAAGAATCTGCG 57.356 33.333 0.00 0.00 39.30 5.18
6699 7200 0.108585 AAAGAACAGGAAGCGCCTCA 59.891 50.000 8.52 0.00 46.97 3.86
6725 7226 4.044426 GGATTTGGCTTCATAACGATTGC 58.956 43.478 0.00 0.00 0.00 3.56
6864 7365 8.912988 CCTTTTGCCAAGAATCCTATAATGTAA 58.087 33.333 0.00 0.00 0.00 2.41
6888 7389 6.830873 AATATATGAGCAGCCTTGGATTTC 57.169 37.500 0.00 0.00 0.00 2.17
7001 7502 2.223021 CGCACCATGTAGTATGCACAAC 60.223 50.000 0.00 0.00 37.97 3.32
7014 7515 7.969536 AGTATGCACAACATAACATATCCTC 57.030 36.000 0.00 0.00 42.88 3.71
7051 7552 6.306356 CCAGTCTTTGCTTTTCGAATATGTTG 59.694 38.462 0.00 0.00 0.00 3.33
7079 7580 5.240844 TCAGACTCATTCTAGTTGTCGTTCA 59.759 40.000 0.00 0.00 31.12 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.026052 GTTTCAGGGGATTTCCATGTCAT 58.974 43.478 0.00 0.00 46.65 3.06
1 2 3.181424 TGTTTCAGGGGATTTCCATGTCA 60.181 43.478 0.00 0.00 46.65 3.58
2 3 3.193479 GTGTTTCAGGGGATTTCCATGTC 59.807 47.826 0.00 0.00 46.65 3.06
5 6 3.541242 TGTGTTTCAGGGGATTTCCAT 57.459 42.857 0.00 0.00 37.91 3.41
6 7 3.320610 TTGTGTTTCAGGGGATTTCCA 57.679 42.857 0.00 0.00 37.91 3.53
7 8 4.100963 AGTTTTGTGTTTCAGGGGATTTCC 59.899 41.667 0.00 0.00 0.00 3.13
8 9 5.276461 AGTTTTGTGTTTCAGGGGATTTC 57.724 39.130 0.00 0.00 0.00 2.17
9 10 6.800072 TTAGTTTTGTGTTTCAGGGGATTT 57.200 33.333 0.00 0.00 0.00 2.17
10 11 6.800072 TTTAGTTTTGTGTTTCAGGGGATT 57.200 33.333 0.00 0.00 0.00 3.01
11 12 6.382859 AGTTTTAGTTTTGTGTTTCAGGGGAT 59.617 34.615 0.00 0.00 0.00 3.85
12 13 5.717654 AGTTTTAGTTTTGTGTTTCAGGGGA 59.282 36.000 0.00 0.00 0.00 4.81
13 14 5.972935 AGTTTTAGTTTTGTGTTTCAGGGG 58.027 37.500 0.00 0.00 0.00 4.79
14 15 6.626302 TGAGTTTTAGTTTTGTGTTTCAGGG 58.374 36.000 0.00 0.00 0.00 4.45
15 16 6.751888 CCTGAGTTTTAGTTTTGTGTTTCAGG 59.248 38.462 0.00 0.00 41.17 3.86
16 17 7.484959 GTCCTGAGTTTTAGTTTTGTGTTTCAG 59.515 37.037 0.00 0.00 0.00 3.02
17 18 7.175990 AGTCCTGAGTTTTAGTTTTGTGTTTCA 59.824 33.333 0.00 0.00 0.00 2.69
18 19 7.535997 AGTCCTGAGTTTTAGTTTTGTGTTTC 58.464 34.615 0.00 0.00 0.00 2.78
19 20 7.462571 AGTCCTGAGTTTTAGTTTTGTGTTT 57.537 32.000 0.00 0.00 0.00 2.83
38 39 2.554785 CCCGAGGTATCCGAATAGTCCT 60.555 54.545 0.00 0.00 0.00 3.85
245 246 2.290260 TGATTTCTGCGGGAACTGTGAT 60.290 45.455 0.00 0.00 36.83 3.06
252 253 1.739035 CGCTACTGATTTCTGCGGGAA 60.739 52.381 0.00 0.00 42.46 3.97
272 273 1.266718 TGTTCTTGTGAAAGCATCCGC 59.733 47.619 0.00 0.00 33.52 5.54
276 277 5.779529 ATTGTCTGTTCTTGTGAAAGCAT 57.220 34.783 0.00 0.00 33.52 3.79
283 284 3.734231 ACGTCGTATTGTCTGTTCTTGTG 59.266 43.478 0.00 0.00 0.00 3.33
284 285 3.973657 ACGTCGTATTGTCTGTTCTTGT 58.026 40.909 0.00 0.00 0.00 3.16
285 286 3.364023 GGACGTCGTATTGTCTGTTCTTG 59.636 47.826 9.92 0.00 35.45 3.02
288 289 3.213249 AGGACGTCGTATTGTCTGTTC 57.787 47.619 9.40 0.00 35.45 3.18
291 292 3.242673 GGTCTAGGACGTCGTATTGTCTG 60.243 52.174 17.54 6.10 35.45 3.51
293 294 2.941720 AGGTCTAGGACGTCGTATTGTC 59.058 50.000 17.54 8.61 32.65 3.18
295 296 5.450171 CATAAGGTCTAGGACGTCGTATTG 58.550 45.833 17.54 8.10 32.65 1.90
296 297 4.518211 CCATAAGGTCTAGGACGTCGTATT 59.482 45.833 17.54 11.63 32.65 1.89
298 299 3.470709 CCATAAGGTCTAGGACGTCGTA 58.529 50.000 16.44 16.44 32.65 3.43
310 311 4.711178 CGTCCTCGAGCACCATAAGGTC 62.711 59.091 6.99 0.00 42.67 3.85
322 360 2.751913 CCGAGACCACGTCCTCGAG 61.752 68.421 24.36 5.13 36.28 4.04
466 516 0.105964 TGGGAGAAGGAGATCCGGAG 60.106 60.000 11.34 0.00 42.08 4.63
469 522 1.617850 CAGATGGGAGAAGGAGATCCG 59.382 57.143 0.00 0.00 42.08 4.18
533 586 2.474032 GGTTTCTCGCTGTAATCGTTGC 60.474 50.000 0.00 0.00 0.00 4.17
534 587 2.222508 CGGTTTCTCGCTGTAATCGTTG 60.223 50.000 0.00 0.00 0.00 4.10
535 588 1.990563 CGGTTTCTCGCTGTAATCGTT 59.009 47.619 0.00 0.00 0.00 3.85
553 606 1.852895 GATTTTGTCGATCTCGGTCGG 59.147 52.381 0.00 0.00 41.74 4.79
600 653 0.040692 CGCGATCCGAGGTAATTCGA 60.041 55.000 0.00 0.00 43.03 3.71
618 671 2.582734 AAATCCGGCGGGTTCCTACG 62.583 60.000 26.78 0.00 33.83 3.51
620 673 1.523524 GAAATCCGGCGGGTTCCTA 59.476 57.895 26.78 4.76 33.83 2.94
826 885 2.040412 CCACTAAAAGCCCAGGAAGACT 59.960 50.000 0.00 0.00 0.00 3.24
1073 1134 2.342279 CCGGACGAAGCTGAACCA 59.658 61.111 0.00 0.00 0.00 3.67
1278 1339 3.006217 GCTTCAAAGATTCCAACCAAGCT 59.994 43.478 0.00 0.00 33.68 3.74
1335 1402 4.615588 AATATCCTTAGGCTCTGAGTGC 57.384 45.455 6.53 0.00 0.00 4.40
1336 1403 6.825721 ACAAAAATATCCTTAGGCTCTGAGTG 59.174 38.462 6.53 0.00 0.00 3.51
1337 1404 6.963322 ACAAAAATATCCTTAGGCTCTGAGT 58.037 36.000 6.53 0.00 0.00 3.41
1338 1405 7.872113 AACAAAAATATCCTTAGGCTCTGAG 57.128 36.000 0.00 0.00 0.00 3.35
1339 1406 7.499232 GCTAACAAAAATATCCTTAGGCTCTGA 59.501 37.037 0.00 0.00 0.00 3.27
1340 1407 7.255277 GGCTAACAAAAATATCCTTAGGCTCTG 60.255 40.741 0.00 0.00 37.15 3.35
1344 1411 6.961360 AGGCTAACAAAAATATCCTTAGGC 57.039 37.500 0.00 0.00 39.23 3.93
1366 1433 6.871844 TGAGAAACCATCACAGAATCTCTAG 58.128 40.000 0.00 0.00 34.41 2.43
1369 1436 5.702670 TGTTGAGAAACCATCACAGAATCTC 59.297 40.000 0.00 0.00 34.01 2.75
1373 1440 5.375773 TCATGTTGAGAAACCATCACAGAA 58.624 37.500 0.00 0.00 30.04 3.02
1374 1441 4.971939 TCATGTTGAGAAACCATCACAGA 58.028 39.130 0.00 0.00 30.04 3.41
1375 1442 5.694231 TTCATGTTGAGAAACCATCACAG 57.306 39.130 0.00 0.00 30.04 3.66
1377 1444 6.095377 GGAATTCATGTTGAGAAACCATCAC 58.905 40.000 7.93 0.00 0.00 3.06
1379 1446 6.271488 TGGAATTCATGTTGAGAAACCATC 57.729 37.500 7.93 0.00 33.73 3.51
1380 1447 5.186409 CCTGGAATTCATGTTGAGAAACCAT 59.814 40.000 7.93 0.00 36.08 3.55
1382 1449 4.524328 ACCTGGAATTCATGTTGAGAAACC 59.476 41.667 7.93 0.00 0.00 3.27
1383 1450 5.241506 TGACCTGGAATTCATGTTGAGAAAC 59.758 40.000 7.93 0.00 0.00 2.78
1389 1458 6.930164 TCAAAATTGACCTGGAATTCATGTTG 59.070 34.615 7.93 2.46 31.01 3.33
1399 1468 6.016360 CACTGTACAATCAAAATTGACCTGGA 60.016 38.462 0.00 0.00 44.25 3.86
1454 1525 9.229784 CATGATTAAGCTCACAACAAATATGAC 57.770 33.333 0.00 0.00 0.00 3.06
1477 1548 3.415212 TGTCCAAAAGAGGAAGCTCATG 58.585 45.455 0.00 0.00 39.92 3.07
1492 1563 3.346315 CACCTCTGCAACATATGTCCAA 58.654 45.455 9.23 0.00 0.00 3.53
1518 1589 2.048127 GCGGCGTGGAACTCTTCT 60.048 61.111 9.37 0.00 31.75 2.85
1740 1811 2.837337 CGATGCTAACGCCGAATAAG 57.163 50.000 0.00 0.00 34.43 1.73
1850 1921 0.751643 ACCACACCTCCAACAGTTGC 60.752 55.000 7.88 0.00 0.00 4.17
1964 2036 3.354948 TGTCTGAAACATAGCCATGCT 57.645 42.857 0.00 0.00 36.32 3.79
2064 2138 3.361786 ACTAACTTGCACAACCCAAAGT 58.638 40.909 0.00 0.00 0.00 2.66
2173 2247 5.124457 ACATAACAGAACCTGATCACATTGC 59.876 40.000 0.45 0.00 35.18 3.56
2417 2491 0.729116 GGATGATCAACACTGCACGG 59.271 55.000 0.00 0.00 0.00 4.94
2662 2737 7.212976 TGCCAATGAATAACAGCAAAAGTAAA 58.787 30.769 0.00 0.00 0.00 2.01
2795 2870 3.634910 TCTTTTACCTTTTGCACCAGGAC 59.365 43.478 15.99 0.00 33.90 3.85
2796 2871 3.888930 CTCTTTTACCTTTTGCACCAGGA 59.111 43.478 15.99 0.00 33.90 3.86
2896 3023 1.073897 GGCTGGGGGTGCAGATATC 59.926 63.158 0.00 0.00 0.00 1.63
2906 3033 1.723128 AATATGAGCTGGGCTGGGGG 61.723 60.000 0.00 0.00 39.88 5.40
2968 3108 4.465512 GCTGCACGGTTGGATGCG 62.466 66.667 0.00 0.00 45.13 4.73
3057 3197 8.024145 TGGGAAAAAGCAAGTAAATCCTTTTA 57.976 30.769 0.00 0.00 36.73 1.52
3133 3273 8.141268 ACATGTAACTAAATTGGTTGAACAAGG 58.859 33.333 4.95 2.87 33.23 3.61
3687 3855 7.328737 TCCCGTTTTAGAAATTTGAACCAAAA 58.671 30.769 0.00 0.00 36.90 2.44
3691 3859 9.083080 CATATTCCCGTTTTAGAAATTTGAACC 57.917 33.333 0.00 0.00 0.00 3.62
3758 3929 3.556213 GGCCGTTAGCATCCACATGTATA 60.556 47.826 0.00 0.00 46.50 1.47
3954 4125 3.580022 TCATCGTGGCTATGATCTGGAAT 59.420 43.478 1.10 0.00 30.09 3.01
4037 4208 5.018809 AGTTCATCACCCATGCAAACTAAT 58.981 37.500 0.00 0.00 31.70 1.73
4039 4210 4.009675 GAGTTCATCACCCATGCAAACTA 58.990 43.478 0.00 0.00 31.70 2.24
4140 4314 3.627123 TGGTCATGCTTAAATCGGACATG 59.373 43.478 0.00 0.00 39.53 3.21
4168 4342 4.889832 AGCTTATGCAATAGCTGTTGTC 57.110 40.909 22.26 15.39 42.74 3.18
4354 4529 7.667043 AGCTTTACGAAGTTGAAATATGTCA 57.333 32.000 0.00 0.00 37.78 3.58
4415 4590 1.562475 GAGTAATGGGGTGGCCTGTAA 59.438 52.381 3.32 0.00 0.00 2.41
4453 4628 5.649395 AGCAAAAGCAATATCACTTAGCTCA 59.351 36.000 0.00 0.00 34.31 4.26
4514 4689 2.907696 TCGTGGTCCTAAAATGGGAAGA 59.092 45.455 0.00 0.00 34.35 2.87
4518 4693 1.339631 TGCTCGTGGTCCTAAAATGGG 60.340 52.381 0.00 0.00 0.00 4.00
4649 4824 6.433847 TTGTTCATAGGGACAGAAAGAAGA 57.566 37.500 0.00 0.00 0.00 2.87
4974 5150 5.890419 ACGAAGCTAGGGTTAGTGTTACTAT 59.110 40.000 0.00 0.00 29.64 2.12
5012 5188 8.651391 TGTAATTAGAGAAGACAAACGTGAAA 57.349 30.769 0.00 0.00 0.00 2.69
5129 5388 5.132144 TCCCCCTGTCTCAAAATATAAGACC 59.868 44.000 0.00 0.00 38.91 3.85
5206 5465 4.241590 TGAACATTCTGCATCAACAACC 57.758 40.909 0.00 0.00 0.00 3.77
5617 5877 2.130272 TACATGCGCATGGGGTTAAA 57.870 45.000 43.46 22.28 42.91 1.52
5620 5880 0.746063 CAATACATGCGCATGGGGTT 59.254 50.000 43.46 32.48 42.91 4.11
5658 5920 9.300681 CCCTTACAAATATGGATATGTTCACAT 57.699 33.333 0.00 0.00 40.22 3.21
5738 6000 7.225931 AGTGTTAATTTTAAGCAAGTGACGAGA 59.774 33.333 0.00 0.00 0.00 4.04
5835 6098 2.293122 GCCAACAGCAATAAGTGACACA 59.707 45.455 8.59 0.00 42.97 3.72
6446 6709 2.922283 AGAGGTTGGAGTGGATGGAAAT 59.078 45.455 0.00 0.00 0.00 2.17
6489 6752 8.278729 TGTAATGATGTTTGATTGTGCATAGA 57.721 30.769 0.00 0.00 0.00 1.98
6606 7107 7.571080 AAACAAGGGTATTTGAACTACGAAA 57.429 32.000 0.00 0.00 0.00 3.46
6665 7166 6.258507 TCCTGTTCTTTTAACGGTTAACACTC 59.741 38.462 12.62 4.54 0.00 3.51
6699 7200 5.913137 TCGTTATGAAGCCAAATCCATTT 57.087 34.783 0.00 0.00 0.00 2.32
6725 7226 1.135199 CAAGCATGCACAAAGCCCTAG 60.135 52.381 21.98 0.00 44.83 3.02
6864 7365 7.008941 AGAAATCCAAGGCTGCTCATATATTT 58.991 34.615 0.00 0.00 0.00 1.40
6888 7389 9.613428 TCAACTAAAATATTGATGGGTGTAGAG 57.387 33.333 0.00 0.00 29.89 2.43
6981 7482 2.746904 TGTTGTGCATACTACATGGTGC 59.253 45.455 0.00 0.10 37.57 5.01
7001 7502 7.094463 GGAAGCAAATCAGGAGGATATGTTATG 60.094 40.741 0.00 0.00 34.28 1.90
7014 7515 3.613432 GCAAAGACTGGAAGCAAATCAGG 60.613 47.826 0.00 0.00 37.60 3.86
7051 7552 6.183360 ACGACAACTAGAATGAGTCTGATCTC 60.183 42.308 0.00 1.79 37.12 2.75
7106 7607 2.806945 ACATGACCGTCCCATCATTT 57.193 45.000 0.00 0.00 33.18 2.32


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

AutoCloner maintained by Alex Coulton.