Multiple sequence alignment - TraesCS7D01G356300

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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 TraesCS7D01G356300 chr7D 100.000 2402 0 0 1 2402 459746478 459748879 0.000000e+00 4436.0
1 TraesCS7D01G356300 chr7D 93.307 254 17 0 2149 2402 459785670 459785923 2.250000e-100 375.0
2 TraesCS7D01G356300 chr7D 79.597 397 61 13 1 379 459466010 459466404 1.420000e-67 267.0
3 TraesCS7D01G356300 chr7A 93.357 1144 37 15 412 1538 539852833 539851712 0.000000e+00 1655.0
4 TraesCS7D01G356300 chr7A 95.186 457 14 3 1536 1988 539851654 539851202 0.000000e+00 715.0
5 TraesCS7D01G356300 chr7A 93.734 383 22 1 1 383 539853208 539852828 7.450000e-160 573.0
6 TraesCS7D01G356300 chr7A 92.727 385 14 3 2028 2402 539851043 539850663 5.840000e-151 544.0
7 TraesCS7D01G356300 chr7A 80.952 378 55 10 1 361 540755947 540755570 1.410000e-72 283.0
8 TraesCS7D01G356300 chr7A 86.192 239 23 4 2153 2391 539931580 539931352 1.430000e-62 250.0
9 TraesCS7D01G356300 chr7A 79.016 386 65 12 1 374 540771834 540771453 1.430000e-62 250.0
10 TraesCS7D01G356300 chr7A 82.212 208 24 9 1013 1210 540202097 540201893 1.480000e-37 167.0
11 TraesCS7D01G356300 chr7B 93.585 265 17 0 2124 2388 481852490 481852754 1.730000e-106 396.0
12 TraesCS7D01G356300 chr7B 95.833 216 9 0 2187 2402 482074009 482074224 1.370000e-92 350.0
13 TraesCS7D01G356300 chr7B 85.000 340 26 8 1809 2123 481851733 481852072 2.980000e-84 322.0
14 TraesCS7D01G356300 chr7B 80.206 389 58 12 1 372 481617635 481618021 8.460000e-70 274.0
15 TraesCS7D01G356300 chr7B 89.247 93 7 1 1118 1210 481843720 481843809 1.950000e-21 113.0
16 TraesCS7D01G356300 chr6D 87.500 72 4 3 1687 1754 291149781 291149711 7.120000e-11 78.7
17 TraesCS7D01G356300 chr6D 97.368 38 1 0 1410 1447 422507189 422507152 5.540000e-07 65.8
18 TraesCS7D01G356300 chr6A 89.062 64 6 1 1687 1750 611567687 611567749 7.120000e-11 78.7
19 TraesCS7D01G356300 chr3D 86.765 68 9 0 1687 1754 477251697 477251764 2.560000e-10 76.8
20 TraesCS7D01G356300 chr6B 82.558 86 12 3 1672 1754 135505591 135505676 3.310000e-09 73.1
21 TraesCS7D01G356300 chr6B 88.000 50 4 2 1410 1458 637751088 637751040 9.270000e-05 58.4
22 TraesCS7D01G356300 chr2A 85.135 74 8 3 1687 1757 654916479 654916406 3.310000e-09 73.1
23 TraesCS7D01G356300 chr5B 83.544 79 10 3 1677 1754 664376027 664376103 1.190000e-08 71.3
24 TraesCS7D01G356300 chr4D 90.741 54 3 2 1407 1459 337756085 337756137 1.190000e-08 71.3
25 TraesCS7D01G356300 chr4B 83.544 79 10 2 1671 1749 269174070 269174145 1.190000e-08 71.3
26 TraesCS7D01G356300 chr4B 81.395 86 13 2 1672 1754 12501301 12501386 1.540000e-07 67.6
27 TraesCS7D01G356300 chr4A 87.273 55 5 1 1393 1447 704184796 704184848 7.170000e-06 62.1
28 TraesCS7D01G356300 chr4A 87.273 55 5 1 1393 1447 704211704 704211756 7.170000e-06 62.1
29 TraesCS7D01G356300 chr4A 87.273 55 5 1 1393 1447 704238584 704238636 7.170000e-06 62.1
30 TraesCS7D01G356300 chr2B 85.484 62 5 3 1399 1459 786549308 786549250 7.170000e-06 62.1
31 TraesCS7D01G356300 chr5A 85.455 55 6 1 1393 1447 480561385 480561437 3.340000e-04 56.5


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 TraesCS7D01G356300 chr7D 459746478 459748879 2401 False 4436.00 4436 100.0000 1 2402 1 chr7D.!!$F2 2401
1 TraesCS7D01G356300 chr7A 539850663 539853208 2545 True 871.75 1655 93.7510 1 2402 4 chr7A.!!$R5 2401
2 TraesCS7D01G356300 chr7B 481851733 481852754 1021 False 359.00 396 89.2925 1809 2388 2 chr7B.!!$F4 579

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
76 77 0.108424 CCGAGAGCCAGGACTTGAAG 60.108 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1464 0.247736 ACTCTGATGACTTGCCGGTC 59.752 55.0 1.9 0.0 36.81 4.79 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
49 50 2.685388 GCTCCATGAAGCTAAAACTCCC 59.315 50.000 0.00 0.00 39.27 4.30
76 77 0.108424 CCGAGAGCCAGGACTTGAAG 60.108 60.000 0.00 0.00 0.00 3.02
82 83 1.143684 AGCCAGGACTTGAAGCAAAGA 59.856 47.619 0.00 0.00 0.00 2.52
110 111 7.201821 GGGATTGTCTATCATTTTCGGTTTCAT 60.202 37.037 0.00 0.00 34.77 2.57
116 117 3.070748 TCATTTTCGGTTTCATCGCAGA 58.929 40.909 0.00 0.00 45.75 4.26
126 127 2.174363 TCATCGCAGATGGCTAATGG 57.826 50.000 15.33 0.00 45.12 3.16
187 188 1.675552 AACCTGGAAACAAGACACCG 58.324 50.000 0.00 0.00 42.06 4.94
193 194 2.105821 TGGAAACAAGACACCGGAAGAT 59.894 45.455 9.46 0.00 37.44 2.40
257 258 9.442047 CTCTGATTTGTAAGAGGATGTTTAAGT 57.558 33.333 0.00 0.00 0.00 2.24
279 280 6.923670 AGTACTCAACTATGGAGAGGGATAA 58.076 40.000 0.00 0.00 36.36 1.75
294 295 4.100373 AGGGATAATAGCTAAGCCCTCTG 58.900 47.826 14.44 0.00 42.02 3.35
306 307 0.538287 GCCCTCTGGACAGCAACTTT 60.538 55.000 0.00 0.00 0.00 2.66
307 308 1.242076 CCCTCTGGACAGCAACTTTG 58.758 55.000 0.00 0.00 0.00 2.77
319 320 1.000274 GCAACTTTGCGGTCAAGGATT 60.000 47.619 0.00 0.00 45.11 3.01
343 344 0.464373 CGGTGGGAACTGGGATGATG 60.464 60.000 0.00 0.00 0.00 3.07
351 352 0.179037 ACTGGGATGATGCATGACCG 60.179 55.000 2.46 0.59 0.00 4.79
389 390 6.642707 CCAGATTTGGGTTTGTAACTTGTA 57.357 37.500 0.00 0.00 41.05 2.41
390 391 7.045126 CCAGATTTGGGTTTGTAACTTGTAA 57.955 36.000 0.00 0.00 41.05 2.41
391 392 7.145323 CCAGATTTGGGTTTGTAACTTGTAAG 58.855 38.462 0.00 0.00 41.05 2.34
392 393 7.201875 CCAGATTTGGGTTTGTAACTTGTAAGT 60.202 37.037 0.00 0.00 41.05 2.24
393 394 8.842280 CAGATTTGGGTTTGTAACTTGTAAGTA 58.158 33.333 0.00 0.00 38.57 2.24
394 395 9.063615 AGATTTGGGTTTGTAACTTGTAAGTAG 57.936 33.333 0.00 0.00 38.57 2.57
395 396 8.756486 ATTTGGGTTTGTAACTTGTAAGTAGT 57.244 30.769 0.00 0.00 38.57 2.73
396 397 7.556733 TTGGGTTTGTAACTTGTAAGTAGTG 57.443 36.000 0.00 0.00 38.57 2.74
397 398 6.056884 TGGGTTTGTAACTTGTAAGTAGTGG 58.943 40.000 0.00 0.00 38.57 4.00
398 399 6.057533 GGGTTTGTAACTTGTAAGTAGTGGT 58.942 40.000 0.00 0.00 38.57 4.16
399 400 6.543465 GGGTTTGTAACTTGTAAGTAGTGGTT 59.457 38.462 0.00 0.00 38.57 3.67
400 401 7.254898 GGGTTTGTAACTTGTAAGTAGTGGTTC 60.255 40.741 0.00 0.00 38.57 3.62
401 402 7.280652 GGTTTGTAACTTGTAAGTAGTGGTTCA 59.719 37.037 0.00 0.00 38.57 3.18
402 403 8.667463 GTTTGTAACTTGTAAGTAGTGGTTCAA 58.333 33.333 0.00 0.00 38.57 2.69
403 404 8.428186 TTGTAACTTGTAAGTAGTGGTTCAAG 57.572 34.615 0.00 0.00 38.57 3.02
404 405 6.480981 TGTAACTTGTAAGTAGTGGTTCAAGC 59.519 38.462 0.00 0.00 38.57 4.01
405 406 5.291905 ACTTGTAAGTAGTGGTTCAAGCT 57.708 39.130 0.00 0.00 37.52 3.74
406 407 5.298347 ACTTGTAAGTAGTGGTTCAAGCTC 58.702 41.667 0.00 0.00 37.52 4.09
407 408 4.267349 TGTAAGTAGTGGTTCAAGCTCC 57.733 45.455 0.00 0.00 0.00 4.70
408 409 2.861147 AAGTAGTGGTTCAAGCTCCC 57.139 50.000 0.00 0.00 0.00 4.30
409 410 0.984995 AGTAGTGGTTCAAGCTCCCC 59.015 55.000 0.00 0.00 0.00 4.81
410 411 0.690762 GTAGTGGTTCAAGCTCCCCA 59.309 55.000 0.00 0.00 0.00 4.96
411 412 0.690762 TAGTGGTTCAAGCTCCCCAC 59.309 55.000 13.34 13.34 46.17 4.61
412 413 1.456287 GTGGTTCAAGCTCCCCACT 59.544 57.895 13.74 0.00 43.21 4.00
413 414 0.178990 GTGGTTCAAGCTCCCCACTT 60.179 55.000 13.74 0.00 43.21 3.16
414 415 0.178992 TGGTTCAAGCTCCCCACTTG 60.179 55.000 0.00 0.00 44.76 3.16
415 416 0.178990 GGTTCAAGCTCCCCACTTGT 60.179 55.000 3.67 0.00 43.97 3.16
416 417 1.073284 GGTTCAAGCTCCCCACTTGTA 59.927 52.381 3.67 0.00 43.97 2.41
417 418 2.427506 GTTCAAGCTCCCCACTTGTAG 58.572 52.381 3.67 0.00 43.97 2.74
418 419 2.024176 TCAAGCTCCCCACTTGTAGA 57.976 50.000 3.67 0.00 43.97 2.59
419 420 2.334977 TCAAGCTCCCCACTTGTAGAA 58.665 47.619 3.67 0.00 43.97 2.10
420 421 2.912956 TCAAGCTCCCCACTTGTAGAAT 59.087 45.455 3.67 0.00 43.97 2.40
421 422 4.101114 TCAAGCTCCCCACTTGTAGAATA 58.899 43.478 3.67 0.00 43.97 1.75
422 423 4.721776 TCAAGCTCCCCACTTGTAGAATAT 59.278 41.667 3.67 0.00 43.97 1.28
423 424 5.191722 TCAAGCTCCCCACTTGTAGAATATT 59.808 40.000 3.67 0.00 43.97 1.28
424 425 6.385759 TCAAGCTCCCCACTTGTAGAATATTA 59.614 38.462 3.67 0.00 43.97 0.98
425 426 6.176014 AGCTCCCCACTTGTAGAATATTAC 57.824 41.667 0.00 0.00 0.00 1.89
426 427 5.905913 AGCTCCCCACTTGTAGAATATTACT 59.094 40.000 0.00 0.00 0.00 2.24
427 428 7.073854 AGCTCCCCACTTGTAGAATATTACTA 58.926 38.462 0.00 0.00 0.00 1.82
447 448 8.675705 TTACTACTAATATTGTGTGCATGCAT 57.324 30.769 25.64 10.06 0.00 3.96
448 449 7.194607 ACTACTAATATTGTGTGCATGCATC 57.805 36.000 25.64 19.65 0.00 3.91
449 450 6.994496 ACTACTAATATTGTGTGCATGCATCT 59.006 34.615 25.64 9.42 0.00 2.90
450 451 6.068473 ACTAATATTGTGTGCATGCATCTG 57.932 37.500 25.64 7.71 0.00 2.90
451 452 4.316205 AATATTGTGTGCATGCATCTGG 57.684 40.909 25.64 0.00 0.00 3.86
452 453 1.842052 ATTGTGTGCATGCATCTGGA 58.158 45.000 25.64 9.79 0.00 3.86
453 454 1.842052 TTGTGTGCATGCATCTGGAT 58.158 45.000 25.64 0.00 0.00 3.41
482 483 4.213482 ACGCTAACAGATTTGACCTTTCAC 59.787 41.667 0.00 0.00 0.00 3.18
485 486 6.145535 GCTAACAGATTTGACCTTTCACTTG 58.854 40.000 0.00 0.00 0.00 3.16
522 523 1.153086 GCAGGTCGATGCCTCCAAT 60.153 57.895 0.00 0.00 40.43 3.16
525 526 0.467384 AGGTCGATGCCTCCAATCTG 59.533 55.000 0.00 0.00 32.39 2.90
526 527 1.162800 GGTCGATGCCTCCAATCTGC 61.163 60.000 0.00 0.00 0.00 4.26
527 528 0.179062 GTCGATGCCTCCAATCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
694 697 5.169992 TCCTGATATCGGAATGCATGAAT 57.830 39.130 13.42 0.00 0.00 2.57
696 699 6.343703 TCCTGATATCGGAATGCATGAATAG 58.656 40.000 13.42 0.00 0.00 1.73
697 700 6.070596 TCCTGATATCGGAATGCATGAATAGT 60.071 38.462 13.42 0.00 0.00 2.12
698 701 7.124147 TCCTGATATCGGAATGCATGAATAGTA 59.876 37.037 13.42 0.00 0.00 1.82
699 702 7.223582 CCTGATATCGGAATGCATGAATAGTAC 59.776 40.741 13.42 0.00 0.00 2.73
700 703 7.041721 TGATATCGGAATGCATGAATAGTACC 58.958 38.462 0.00 0.00 0.00 3.34
701 704 4.002906 TCGGAATGCATGAATAGTACCC 57.997 45.455 0.00 0.00 0.00 3.69
702 705 3.389656 TCGGAATGCATGAATAGTACCCA 59.610 43.478 0.00 0.00 0.00 4.51
703 706 4.041567 TCGGAATGCATGAATAGTACCCAT 59.958 41.667 0.00 0.00 0.00 4.00
704 707 5.247337 TCGGAATGCATGAATAGTACCCATA 59.753 40.000 0.00 0.00 0.00 2.74
705 708 5.351465 CGGAATGCATGAATAGTACCCATAC 59.649 44.000 0.00 0.00 0.00 2.39
706 709 6.237901 GGAATGCATGAATAGTACCCATACA 58.762 40.000 0.00 0.00 33.30 2.29
707 710 6.372659 GGAATGCATGAATAGTACCCATACAG 59.627 42.308 0.00 0.00 33.30 2.74
736 739 3.325870 CAACTTAGACTGAACGGCATGA 58.674 45.455 0.00 0.00 0.00 3.07
761 764 0.370273 GGCTGAAGTATGAACGCACG 59.630 55.000 0.00 0.00 0.00 5.34
766 769 2.984471 TGAAGTATGAACGCACGTCTTC 59.016 45.455 12.15 12.15 33.24 2.87
844 847 2.224646 GGAATCATTGGGAGAGGTAGCC 60.225 54.545 0.00 0.00 0.00 3.93
845 848 1.439543 ATCATTGGGAGAGGTAGCCC 58.560 55.000 0.00 0.00 44.93 5.19
864 867 1.658686 CTCTAGGCGCCTCGTTGACT 61.659 60.000 36.73 9.44 0.00 3.41
866 869 1.078759 CTAGGCGCCTCGTTGACTTG 61.079 60.000 36.73 3.22 0.00 3.16
963 966 2.333926 TCATTTCGACGCAACCACTAG 58.666 47.619 0.00 0.00 0.00 2.57
970 973 0.889306 ACGCAACCACTAGAGACTCC 59.111 55.000 0.00 0.00 0.00 3.85
995 998 1.209504 CGGTCTCCATTCCTTTGCCTA 59.790 52.381 0.00 0.00 0.00 3.93
1001 1004 4.413520 TCTCCATTCCTTTGCCTAGCTAAT 59.586 41.667 0.00 0.00 0.00 1.73
1066 1069 3.518998 CCCTGCTGCTGCTCATGC 61.519 66.667 17.00 1.02 40.48 4.06
1225 1228 7.326789 CGCACTCAATTGTGATTTCTAAACATT 59.673 33.333 14.16 0.00 40.12 2.71
1306 1309 2.775911 TCCTGATCTTGCAGTTCCTG 57.224 50.000 0.00 0.00 34.06 3.86
1375 1378 5.393569 CCTGGAACTATGGATATAGACGCTG 60.394 48.000 1.62 0.00 38.88 5.18
1452 1455 2.409064 TCCCACTGTCCTCAAGGTTA 57.591 50.000 0.00 0.00 36.34 2.85
1571 1649 2.493278 GGTTACTGCCGTGTTACCTCTA 59.507 50.000 0.00 0.00 36.87 2.43
1591 1669 6.041409 CCTCTATGGACATGTAATCTCAGTGT 59.959 42.308 0.00 0.00 38.35 3.55
1596 1674 4.327357 GGACATGTAATCTCAGTGTTGTCG 59.673 45.833 0.00 0.00 34.51 4.35
1625 1703 5.160607 TGATCTTTGTACCGTTCCAATCT 57.839 39.130 0.00 0.00 0.00 2.40
1729 1811 9.903185 GCGTTTAGATCTTTATAAGAAACACTC 57.097 33.333 0.00 0.00 41.63 3.51
1752 1834 8.218488 ACTCTTAAATTTCTTTACAGAGGGTGT 58.782 33.333 0.00 0.00 43.86 4.16
1753 1835 9.720769 CTCTTAAATTTCTTTACAGAGGGTGTA 57.279 33.333 0.00 0.00 40.94 2.90
1765 1847 4.941263 ACAGAGGGTGTACGTACGTTATTA 59.059 41.667 27.92 5.17 37.75 0.98
1936 2021 7.645340 GGGATTGATACGACTTGAATGAATTTG 59.355 37.037 0.00 0.00 0.00 2.32
2004 2145 3.318275 TGTTCCGAGACTGGCTATACATC 59.682 47.826 0.00 0.00 0.00 3.06
2020 2161 7.226918 GGCTATACATCTATCTAGACATGCGTA 59.773 40.741 0.00 0.00 34.72 4.42
2021 2162 8.779303 GCTATACATCTATCTAGACATGCGTAT 58.221 37.037 0.00 3.17 34.72 3.06
2067 2292 1.070786 GTTTCAGTCCGCCAGTGGA 59.929 57.895 15.20 0.00 35.04 4.02
2221 2873 1.269988 TGCTTCTAGATGCAGGATCGC 60.270 52.381 24.97 4.47 36.70 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 6.705863 AATGATAGACAATCCCTTCTTTGC 57.294 37.500 0.00 0.00 33.22 3.68
82 83 5.755849 ACCGAAAATGATAGACAATCCCTT 58.244 37.500 0.00 0.00 33.22 3.95
116 117 1.831286 GCTGCCTGCCATTAGCCAT 60.831 57.895 0.00 0.00 42.71 4.40
143 144 1.691196 TGGTTTCTGTGCCTCTTTGG 58.309 50.000 0.00 0.00 39.35 3.28
154 155 4.464069 TCCAGGTTTTGTTTGGTTTCTG 57.536 40.909 0.00 0.00 33.65 3.02
187 188 5.063817 GCAAACAATAACAATGGCATCTTCC 59.936 40.000 0.00 0.00 0.00 3.46
193 194 3.323115 TCCTGCAAACAATAACAATGGCA 59.677 39.130 0.00 0.00 0.00 4.92
257 258 7.616150 GCTATTATCCCTCTCCATAGTTGAGTA 59.384 40.741 0.00 0.00 0.00 2.59
279 280 2.324541 CTGTCCAGAGGGCTTAGCTAT 58.675 52.381 3.59 0.00 0.00 2.97
294 295 3.432186 ACCGCAAAGTTGCTGTCC 58.568 55.556 13.75 0.00 46.41 4.02
306 307 1.472552 CCGTATCAATCCTTGACCGCA 60.473 52.381 0.00 0.00 43.48 5.69
307 308 1.217882 CCGTATCAATCCTTGACCGC 58.782 55.000 0.00 0.00 43.48 5.68
315 316 2.561569 CAGTTCCCACCGTATCAATCC 58.438 52.381 0.00 0.00 0.00 3.01
319 320 0.252330 TCCCAGTTCCCACCGTATCA 60.252 55.000 0.00 0.00 0.00 2.15
358 359 4.226168 ACAAACCCAAATCTGGTCCAAAAA 59.774 37.500 0.00 0.00 41.72 1.94
374 375 6.057533 ACCACTACTTACAAGTTACAAACCC 58.942 40.000 0.00 0.00 40.37 4.11
377 378 8.789825 TTGAACCACTACTTACAAGTTACAAA 57.210 30.769 0.00 0.00 40.37 2.83
383 384 5.291905 AGCTTGAACCACTACTTACAAGT 57.708 39.130 0.00 0.00 42.91 3.16
384 385 4.691216 GGAGCTTGAACCACTACTTACAAG 59.309 45.833 0.00 0.00 38.07 3.16
385 386 4.504340 GGGAGCTTGAACCACTACTTACAA 60.504 45.833 0.00 0.00 0.00 2.41
387 388 3.597255 GGGAGCTTGAACCACTACTTAC 58.403 50.000 0.00 0.00 0.00 2.34
389 390 1.351350 GGGGAGCTTGAACCACTACTT 59.649 52.381 0.00 0.00 0.00 2.24
390 391 0.984995 GGGGAGCTTGAACCACTACT 59.015 55.000 0.00 0.00 0.00 2.57
391 392 0.690762 TGGGGAGCTTGAACCACTAC 59.309 55.000 0.00 0.00 0.00 2.73
392 393 3.173852 TGGGGAGCTTGAACCACTA 57.826 52.632 0.00 0.00 0.00 2.74
393 394 4.002006 TGGGGAGCTTGAACCACT 57.998 55.556 0.00 0.00 0.00 4.00
394 395 4.081050 GTGGGGAGCTTGAACCAC 57.919 61.111 12.28 12.28 45.56 4.16
395 396 0.178992 CAAGTGGGGAGCTTGAACCA 60.179 55.000 0.00 0.00 44.29 3.67
396 397 0.178990 ACAAGTGGGGAGCTTGAACC 60.179 55.000 11.37 0.00 44.29 3.62
397 398 2.038557 TCTACAAGTGGGGAGCTTGAAC 59.961 50.000 11.37 0.00 44.29 3.18
398 399 2.334977 TCTACAAGTGGGGAGCTTGAA 58.665 47.619 11.37 0.00 44.29 2.69
399 400 2.024176 TCTACAAGTGGGGAGCTTGA 57.976 50.000 11.37 0.00 44.29 3.02
400 401 2.859165 TTCTACAAGTGGGGAGCTTG 57.141 50.000 3.81 3.81 46.23 4.01
401 402 5.717119 AATATTCTACAAGTGGGGAGCTT 57.283 39.130 0.00 0.00 0.00 3.74
402 403 5.905913 AGTAATATTCTACAAGTGGGGAGCT 59.094 40.000 0.00 0.00 0.00 4.09
403 404 6.176014 AGTAATATTCTACAAGTGGGGAGC 57.824 41.667 0.00 0.00 0.00 4.70
404 405 8.480133 AGTAGTAATATTCTACAAGTGGGGAG 57.520 38.462 18.85 0.00 39.86 4.30
405 406 9.940974 TTAGTAGTAATATTCTACAAGTGGGGA 57.059 33.333 18.85 0.00 39.86 4.81
420 421 9.771534 TGCATGCACACAATATTAGTAGTAATA 57.228 29.630 18.46 11.56 35.90 0.98
421 422 8.675705 TGCATGCACACAATATTAGTAGTAAT 57.324 30.769 18.46 7.91 33.25 1.89
422 423 8.675705 ATGCATGCACACAATATTAGTAGTAA 57.324 30.769 25.37 0.00 0.00 2.24
423 424 8.150296 AGATGCATGCACACAATATTAGTAGTA 58.850 33.333 25.37 0.00 0.00 1.82
424 425 6.994496 AGATGCATGCACACAATATTAGTAGT 59.006 34.615 25.37 0.00 0.00 2.73
425 426 7.295930 CAGATGCATGCACACAATATTAGTAG 58.704 38.462 25.37 0.00 0.00 2.57
426 427 6.205270 CCAGATGCATGCACACAATATTAGTA 59.795 38.462 25.37 0.00 0.00 1.82
427 428 5.009310 CCAGATGCATGCACACAATATTAGT 59.991 40.000 25.37 1.30 0.00 2.24
447 448 3.007506 TCTGTTAGCGTCCAAAATCCAGA 59.992 43.478 0.00 0.00 0.00 3.86
448 449 3.334691 TCTGTTAGCGTCCAAAATCCAG 58.665 45.455 0.00 0.00 0.00 3.86
449 450 3.410631 TCTGTTAGCGTCCAAAATCCA 57.589 42.857 0.00 0.00 0.00 3.41
450 451 4.965119 AATCTGTTAGCGTCCAAAATCC 57.035 40.909 0.00 0.00 0.00 3.01
451 452 5.795441 GTCAAATCTGTTAGCGTCCAAAATC 59.205 40.000 0.00 0.00 0.00 2.17
452 453 5.335661 GGTCAAATCTGTTAGCGTCCAAAAT 60.336 40.000 0.00 0.00 0.00 1.82
453 454 4.023536 GGTCAAATCTGTTAGCGTCCAAAA 60.024 41.667 0.00 0.00 0.00 2.44
482 483 0.321122 GGCTGTCCCTGTCTGACAAG 60.321 60.000 12.16 5.66 41.85 3.16
509 510 0.105593 GAGCAGATTGGAGGCATCGA 59.894 55.000 0.00 0.00 0.00 3.59
522 523 2.229543 GGACAATTGCAATGTGAGCAGA 59.770 45.455 13.82 0.00 43.75 4.26
525 526 1.273048 TGGGACAATTGCAATGTGAGC 59.727 47.619 13.82 10.41 31.92 4.26
526 527 2.673043 GCTGGGACAATTGCAATGTGAG 60.673 50.000 13.82 6.31 38.70 3.51
527 528 1.273048 GCTGGGACAATTGCAATGTGA 59.727 47.619 13.82 0.11 38.70 3.58
649 652 0.458669 TCAAATCTCGCCGAGGTACC 59.541 55.000 15.08 2.73 0.00 3.34
650 653 1.135199 TGTCAAATCTCGCCGAGGTAC 60.135 52.381 15.08 2.86 0.00 3.34
694 697 5.069518 TGCCTGTATCTGTATGGGTACTA 57.930 43.478 0.00 0.00 0.00 1.82
696 699 4.101119 AGTTGCCTGTATCTGTATGGGTAC 59.899 45.833 0.00 0.00 0.00 3.34
697 700 4.295201 AGTTGCCTGTATCTGTATGGGTA 58.705 43.478 0.00 0.00 0.00 3.69
698 701 3.115390 AGTTGCCTGTATCTGTATGGGT 58.885 45.455 0.00 0.00 0.00 4.51
699 702 3.845781 AGTTGCCTGTATCTGTATGGG 57.154 47.619 0.00 0.00 0.00 4.00
700 703 5.986135 GTCTAAGTTGCCTGTATCTGTATGG 59.014 44.000 0.00 0.00 0.00 2.74
701 704 6.699204 CAGTCTAAGTTGCCTGTATCTGTATG 59.301 42.308 0.00 0.00 0.00 2.39
702 705 6.607600 TCAGTCTAAGTTGCCTGTATCTGTAT 59.392 38.462 0.00 0.00 0.00 2.29
703 706 5.949952 TCAGTCTAAGTTGCCTGTATCTGTA 59.050 40.000 0.00 0.00 0.00 2.74
704 707 4.772624 TCAGTCTAAGTTGCCTGTATCTGT 59.227 41.667 0.00 0.00 0.00 3.41
705 708 5.330455 TCAGTCTAAGTTGCCTGTATCTG 57.670 43.478 0.00 0.00 0.00 2.90
706 709 5.622460 CGTTCAGTCTAAGTTGCCTGTATCT 60.622 44.000 0.00 0.00 0.00 1.98
707 710 4.563184 CGTTCAGTCTAAGTTGCCTGTATC 59.437 45.833 0.00 0.00 0.00 2.24
723 726 1.473965 CCAGCTATCATGCCGTTCAGT 60.474 52.381 0.00 0.00 0.00 3.41
725 728 0.815213 GCCAGCTATCATGCCGTTCA 60.815 55.000 0.00 0.00 0.00 3.18
736 739 3.722147 CGTTCATACTTCAGCCAGCTAT 58.278 45.455 0.00 0.00 0.00 2.97
776 779 8.792633 CATCAAAGGTAGGAAAGTAAATGACAA 58.207 33.333 0.00 0.00 0.00 3.18
844 847 2.105128 CAACGAGGCGCCTAGAGG 59.895 66.667 38.60 25.82 38.53 3.69
845 848 1.226717 GTCAACGAGGCGCCTAGAG 60.227 63.158 38.60 28.77 0.00 2.43
864 867 6.293516 GCATTTGGAAATCAGAAATGTTGCAA 60.294 34.615 0.00 0.00 38.69 4.08
866 869 5.179742 TGCATTTGGAAATCAGAAATGTTGC 59.820 36.000 13.95 0.00 38.69 4.17
918 921 2.697654 GATCTGTGATATGGCTGCCTC 58.302 52.381 21.03 9.87 0.00 4.70
970 973 0.818296 AAGGAATGGAGACCGAGACG 59.182 55.000 0.00 0.00 0.00 4.18
995 998 1.078955 CATCCCCATCCCCATTAGCT 58.921 55.000 0.00 0.00 0.00 3.32
1001 1004 3.428664 GTGCCATCCCCATCCCCA 61.429 66.667 0.00 0.00 0.00 4.96
1066 1069 2.360350 ATGTGGCTTCCTGTGCGG 60.360 61.111 0.00 0.00 0.00 5.69
1142 1145 1.221840 GCAGGATCAGAAGCCGGAA 59.778 57.895 5.05 0.00 35.54 4.30
1150 1153 1.219124 GCTGAACGGCAGGATCAGA 59.781 57.895 20.42 0.00 45.03 3.27
1225 1228 0.750249 TCGCAAGTCACAGGAACTCA 59.250 50.000 0.00 0.00 35.01 3.41
1251 1254 2.083774 TGATCAGGATGTGTTTTCGGC 58.916 47.619 0.00 0.00 37.40 5.54
1255 1258 6.966534 AACTTTCTGATCAGGATGTGTTTT 57.033 33.333 22.42 4.68 37.40 2.43
1319 1322 1.080434 GGACCATCGCGGCTAGATC 60.080 63.158 6.13 0.00 39.03 2.75
1375 1378 0.673956 GTCTTCTTGCCGGGGTCTTC 60.674 60.000 2.18 0.00 0.00 2.87
1459 1462 0.904865 TCTGATGACTTGCCGGTCCT 60.905 55.000 1.90 0.00 35.54 3.85
1460 1463 0.460987 CTCTGATGACTTGCCGGTCC 60.461 60.000 1.90 0.00 35.54 4.46
1461 1464 0.247736 ACTCTGATGACTTGCCGGTC 59.752 55.000 1.90 0.00 36.81 4.79
1571 1649 5.809001 ACAACACTGAGATTACATGTCCAT 58.191 37.500 0.00 0.00 0.00 3.41
1591 1669 7.760794 ACGGTACAAAGATCAATAATACGACAA 59.239 33.333 0.00 0.00 0.00 3.18
1596 1674 8.428186 TGGAACGGTACAAAGATCAATAATAC 57.572 34.615 0.00 0.00 0.00 1.89
1625 1703 5.297278 ACGCACACCTTTATTTGTTGAAGTA 59.703 36.000 0.00 0.00 0.00 2.24
1729 1811 8.440833 CGTACACCCTCTGTAAAGAAATTTAAG 58.559 37.037 0.00 0.00 37.09 1.85
1733 1815 5.861727 ACGTACACCCTCTGTAAAGAAATT 58.138 37.500 0.00 0.00 37.09 1.82
1743 1825 4.361451 AATAACGTACGTACACCCTCTG 57.639 45.455 23.12 9.42 0.00 3.35
1748 1830 7.113027 GCAAAGATTAATAACGTACGTACACC 58.887 38.462 23.12 7.53 0.00 4.16
1752 1834 6.336566 TGGGCAAAGATTAATAACGTACGTA 58.663 36.000 23.12 10.51 0.00 3.57
1753 1835 5.177326 TGGGCAAAGATTAATAACGTACGT 58.823 37.500 16.72 16.72 0.00 3.57
1765 1847 5.727434 CTTAAGAGCAATTGGGCAAAGATT 58.273 37.500 7.72 0.00 35.83 2.40
1936 2021 0.386985 GACCGACGACTGACTCCAAC 60.387 60.000 0.00 0.00 0.00 3.77
2004 2145 8.454894 AGTATGTCAATACGCATGTCTAGATAG 58.545 37.037 0.00 0.00 43.03 2.08
2020 2161 7.224753 CGAGTGCCAAATAAGTAGTATGTCAAT 59.775 37.037 0.00 0.00 0.00 2.57
2021 2162 6.533723 CGAGTGCCAAATAAGTAGTATGTCAA 59.466 38.462 0.00 0.00 0.00 3.18
2273 2925 1.894756 GGCAAGCACACCGTTGGTA 60.895 57.895 0.00 0.00 32.11 3.25
2318 2971 3.113745 GCGTTCATGCCCATCCAG 58.886 61.111 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.