Multiple sequence alignment - TraesCS5B01G456500

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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 TraesCS5B01G456500 chr5B 100.000 2909 0 0 1 2909 631547927 631550835 0.000000e+00 5373.0
1 TraesCS5B01G456500 chr5B 76.774 1085 187 38 773 1822 531696799 531695745 5.480000e-152 547.0
2 TraesCS5B01G456500 chr5D 90.709 2680 167 47 1 2637 502731123 502733763 0.000000e+00 3494.0
3 TraesCS5B01G456500 chr5D 80.709 762 110 21 2156 2904 423327591 423328328 2.530000e-155 558.0
4 TraesCS5B01G456500 chr5D 80.899 534 79 14 2122 2649 447524466 447523950 1.620000e-107 399.0
5 TraesCS5B01G456500 chr5D 87.372 293 33 3 681 973 502711128 502711416 1.670000e-87 333.0
6 TraesCS5B01G456500 chr5D 93.548 217 10 4 2695 2909 502733759 502733973 1.300000e-83 320.0
7 TraesCS5B01G456500 chr5D 83.966 237 32 5 2122 2354 301101218 301100984 3.770000e-54 222.0
8 TraesCS5B01G456500 chr2D 83.096 1124 145 25 786 1895 569679878 569678786 0.000000e+00 981.0
9 TraesCS5B01G456500 chr2D 83.843 916 121 16 943 1836 569808377 569807467 0.000000e+00 846.0
10 TraesCS5B01G456500 chr2D 81.336 509 62 19 2403 2904 24864742 24864260 1.640000e-102 383.0
11 TraesCS5B01G456500 chr2D 79.459 370 52 16 2433 2794 62055316 62054963 1.040000e-59 241.0
12 TraesCS5B01G456500 chr2D 89.375 160 16 1 787 946 569808897 569808739 1.770000e-47 200.0
13 TraesCS5B01G456500 chr2B 82.578 1125 149 26 786 1895 682192074 682190982 0.000000e+00 948.0
14 TraesCS5B01G456500 chr2B 78.894 796 135 25 2122 2907 797551205 797551977 2.590000e-140 508.0
15 TraesCS5B01G456500 chr7A 86.060 703 93 3 1231 1930 436170353 436169653 0.000000e+00 750.0
16 TraesCS5B01G456500 chr7A 84.181 708 92 8 1232 1930 634326547 634327243 0.000000e+00 669.0
17 TraesCS5B01G456500 chrUn 78.894 796 135 25 2122 2907 275011294 275012066 2.590000e-140 508.0
18 TraesCS5B01G456500 chrUn 78.740 762 123 29 2161 2909 315959339 315958604 9.430000e-130 473.0
19 TraesCS5B01G456500 chr7B 80.462 650 106 14 518 1155 381605850 381605210 7.290000e-131 477.0
20 TraesCS5B01G456500 chr7B 74.377 562 119 22 1235 1782 683107185 683107735 1.760000e-52 217.0
21 TraesCS5B01G456500 chr3A 80.705 539 85 13 2122 2649 130830988 130831518 4.520000e-108 401.0
22 TraesCS5B01G456500 chr3D 84.943 352 44 9 2543 2892 123288517 123288861 5.970000e-92 348.0
23 TraesCS5B01G456500 chr5A 87.251 251 30 2 2122 2370 44969683 44969933 4.740000e-73 285.0
24 TraesCS5B01G456500 chr5A 83.088 136 18 4 2402 2532 476340348 476340483 5.090000e-23 119.0
25 TraesCS5B01G456500 chr5A 92.308 52 2 1 2483 2532 476340491 476340542 4.020000e-09 73.1
26 TraesCS5B01G456500 chr1D 82.428 313 45 5 2224 2532 461385684 461385990 6.180000e-67 265.0
27 TraesCS5B01G456500 chr1D 80.299 335 49 15 2575 2901 472293961 472293636 1.350000e-58 237.0
28 TraesCS5B01G456500 chr6B 80.352 341 52 12 2575 2907 171180627 171180960 8.050000e-61 244.0
29 TraesCS5B01G456500 chr6D 79.942 344 50 16 2571 2907 89154141 89154472 4.850000e-58 235.0
30 TraesCS5B01G456500 chr4B 77.316 313 63 8 1235 1543 55704959 55705267 8.280000e-41 178.0
31 TraesCS5B01G456500 chr4D 76.282 312 68 6 1235 1543 38304741 38305049 8.340000e-36 161.0


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 TraesCS5B01G456500 chr5B 631547927 631550835 2908 False 5373 5373 100.0000 1 2909 1 chr5B.!!$F1 2908
1 TraesCS5B01G456500 chr5B 531695745 531696799 1054 True 547 547 76.7740 773 1822 1 chr5B.!!$R1 1049
2 TraesCS5B01G456500 chr5D 502731123 502733973 2850 False 1907 3494 92.1285 1 2909 2 chr5D.!!$F3 2908
3 TraesCS5B01G456500 chr5D 423327591 423328328 737 False 558 558 80.7090 2156 2904 1 chr5D.!!$F1 748
4 TraesCS5B01G456500 chr5D 447523950 447524466 516 True 399 399 80.8990 2122 2649 1 chr5D.!!$R2 527
5 TraesCS5B01G456500 chr2D 569678786 569679878 1092 True 981 981 83.0960 786 1895 1 chr2D.!!$R3 1109
6 TraesCS5B01G456500 chr2D 569807467 569808897 1430 True 523 846 86.6090 787 1836 2 chr2D.!!$R4 1049
7 TraesCS5B01G456500 chr2B 682190982 682192074 1092 True 948 948 82.5780 786 1895 1 chr2B.!!$R1 1109
8 TraesCS5B01G456500 chr2B 797551205 797551977 772 False 508 508 78.8940 2122 2907 1 chr2B.!!$F1 785
9 TraesCS5B01G456500 chr7A 436169653 436170353 700 True 750 750 86.0600 1231 1930 1 chr7A.!!$R1 699
10 TraesCS5B01G456500 chr7A 634326547 634327243 696 False 669 669 84.1810 1232 1930 1 chr7A.!!$F1 698
11 TraesCS5B01G456500 chrUn 275011294 275012066 772 False 508 508 78.8940 2122 2907 1 chrUn.!!$F1 785
12 TraesCS5B01G456500 chrUn 315958604 315959339 735 True 473 473 78.7400 2161 2909 1 chrUn.!!$R1 748
13 TraesCS5B01G456500 chr7B 381605210 381605850 640 True 477 477 80.4620 518 1155 1 chr7B.!!$R1 637
14 TraesCS5B01G456500 chr7B 683107185 683107735 550 False 217 217 74.3770 1235 1782 1 chr7B.!!$F1 547
15 TraesCS5B01G456500 chr3A 130830988 130831518 530 False 401 401 80.7050 2122 2649 1 chr3A.!!$F1 527

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
202 203 0.037326 GGCATGTTCAGTGTCCTCGA 60.037 55.0 0.0 0.0 0.00 4.04 F
503 531 0.098200 GCGTGAATTTAACCTCGCCC 59.902 55.0 0.0 0.0 38.16 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 2110 0.940126 CTGCAGCTTGTCAAACTCGT 59.060 50.000 0.0 0.0 0.0 4.18 R
2469 2962 1.561542 GAGTGAGGATGGATGGTGGTT 59.438 52.381 0.0 0.0 0.0 3.67 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
28 29 4.060038 GCACACCACCATGGCTGC 62.060 66.667 13.04 7.40 42.67 5.25
35 36 2.038329 ACCATGGCTGCCTGCAAT 59.962 55.556 21.03 1.29 45.15 3.56
59 60 3.085443 AGAATCCGTATCTTGCTCGTG 57.915 47.619 0.00 0.00 0.00 4.35
119 120 3.865929 CTCCGTCAACTGCAGCGGT 62.866 63.158 23.94 0.00 44.07 5.68
202 203 0.037326 GGCATGTTCAGTGTCCTCGA 60.037 55.000 0.00 0.00 0.00 4.04
203 204 1.071605 GCATGTTCAGTGTCCTCGAC 58.928 55.000 0.00 0.00 0.00 4.20
269 270 4.314440 GTCGCCCCAGCAGTCACA 62.314 66.667 0.00 0.00 39.83 3.58
270 271 3.555324 TCGCCCCAGCAGTCACAA 61.555 61.111 0.00 0.00 39.83 3.33
271 272 3.052082 CGCCCCAGCAGTCACAAG 61.052 66.667 0.00 0.00 39.83 3.16
272 273 2.674380 GCCCCAGCAGTCACAAGG 60.674 66.667 0.00 0.00 39.53 3.61
284 306 0.390603 TCACAAGGCGTGTAATCCCG 60.391 55.000 5.58 0.00 46.44 5.14
285 307 1.078708 ACAAGGCGTGTAATCCCGG 60.079 57.895 3.68 0.00 39.29 5.73
305 327 1.482621 CCACCGCTGATGTCGATTCG 61.483 60.000 0.00 0.00 0.00 3.34
309 331 1.002792 CCGCTGATGTCGATTCGAGTA 60.003 52.381 9.42 2.13 36.23 2.59
318 340 1.674441 TCGATTCGAGTATTGACGGCT 59.326 47.619 4.29 0.00 0.00 5.52
320 342 2.540973 CGATTCGAGTATTGACGGCTCA 60.541 50.000 0.00 0.00 0.00 4.26
321 343 3.444916 GATTCGAGTATTGACGGCTCAA 58.555 45.455 0.00 0.00 40.77 3.02
323 345 3.079960 TCGAGTATTGACGGCTCAATC 57.920 47.619 13.13 7.65 42.54 2.67
325 347 2.791560 CGAGTATTGACGGCTCAATCAG 59.208 50.000 13.13 3.81 42.54 2.90
326 348 3.489229 CGAGTATTGACGGCTCAATCAGA 60.489 47.826 13.13 0.00 42.54 3.27
340 368 3.772025 TCAATCAGAGAGAAGGGAGAACC 59.228 47.826 0.00 0.00 40.67 3.62
341 369 1.840737 TCAGAGAGAAGGGAGAACCG 58.159 55.000 0.00 0.00 46.96 4.44
354 382 0.463654 AGAACCGTTCAACTGCAGCA 60.464 50.000 15.27 0.00 0.00 4.41
369 397 1.866880 GCAGCAGCAGGTTTTTGTCTG 60.867 52.381 0.00 0.00 41.58 3.51
373 401 2.023673 CAGCAGGTTTTTGTCTGGTCA 58.976 47.619 0.00 0.00 39.36 4.02
376 404 1.681264 CAGGTTTTTGTCTGGTCACCC 59.319 52.381 0.00 0.00 0.00 4.61
377 405 1.286553 AGGTTTTTGTCTGGTCACCCA 59.713 47.619 0.00 0.00 38.87 4.51
386 414 1.228003 TGGTCACCCATTCGCGTTT 60.228 52.632 5.77 0.00 35.17 3.60
387 415 1.231958 TGGTCACCCATTCGCGTTTC 61.232 55.000 5.77 0.00 35.17 2.78
399 427 3.684103 TCGCGTTTCAAGAACAACAAT 57.316 38.095 5.77 0.00 0.00 2.71
408 436 7.297391 GTTTCAAGAACAACAATTTGCAACTT 58.703 30.769 0.00 0.00 36.00 2.66
413 441 3.608796 ACAACAATTTGCAACTTTGGCT 58.391 36.364 19.91 8.47 36.00 4.75
456 484 1.672881 CTGGAAGCTTAGGATTTGGCG 59.327 52.381 0.00 0.00 0.00 5.69
458 486 2.092429 TGGAAGCTTAGGATTTGGCGAT 60.092 45.455 0.00 0.00 0.00 4.58
459 487 2.291741 GGAAGCTTAGGATTTGGCGATG 59.708 50.000 0.00 0.00 0.00 3.84
460 488 1.312815 AGCTTAGGATTTGGCGATGC 58.687 50.000 0.00 0.00 0.00 3.91
463 491 3.077359 GCTTAGGATTTGGCGATGCTAT 58.923 45.455 3.46 0.00 31.30 2.97
465 493 4.093556 GCTTAGGATTTGGCGATGCTATAC 59.906 45.833 3.46 0.00 31.30 1.47
466 494 5.482908 CTTAGGATTTGGCGATGCTATACT 58.517 41.667 3.46 0.00 31.30 2.12
469 497 4.516698 AGGATTTGGCGATGCTATACTTTG 59.483 41.667 0.00 0.00 0.00 2.77
472 500 2.637947 TGGCGATGCTATACTTTGCAA 58.362 42.857 0.00 0.00 42.74 4.08
473 501 3.213506 TGGCGATGCTATACTTTGCAAT 58.786 40.909 0.00 0.00 42.74 3.56
474 502 4.384940 TGGCGATGCTATACTTTGCAATA 58.615 39.130 0.00 0.00 42.74 1.90
476 504 5.049474 TGGCGATGCTATACTTTGCAATAAG 60.049 40.000 0.00 0.00 42.74 1.73
478 506 6.074005 GCGATGCTATACTTTGCAATAAGTC 58.926 40.000 7.05 0.00 42.74 3.01
481 509 4.814234 TGCTATACTTTGCAATAAGTCCGG 59.186 41.667 7.05 0.00 39.08 5.14
482 510 4.814771 GCTATACTTTGCAATAAGTCCGGT 59.185 41.667 7.05 0.00 39.08 5.28
483 511 5.987347 GCTATACTTTGCAATAAGTCCGGTA 59.013 40.000 7.05 0.00 39.08 4.02
484 512 6.145696 GCTATACTTTGCAATAAGTCCGGTAG 59.854 42.308 7.05 7.47 39.08 3.18
486 514 1.647346 TTGCAATAAGTCCGGTAGCG 58.353 50.000 7.49 7.49 0.00 4.26
487 515 0.533491 TGCAATAAGTCCGGTAGCGT 59.467 50.000 13.99 0.00 0.00 5.07
498 526 2.234414 TCCGGTAGCGTGAATTTAACCT 59.766 45.455 13.99 0.00 0.00 3.50
503 531 0.098200 GCGTGAATTTAACCTCGCCC 59.902 55.000 0.00 0.00 38.16 6.13
504 532 1.444836 CGTGAATTTAACCTCGCCCA 58.555 50.000 0.00 0.00 0.00 5.36
506 534 2.422127 CGTGAATTTAACCTCGCCCAAT 59.578 45.455 0.00 0.00 0.00 3.16
508 536 2.680841 TGAATTTAACCTCGCCCAATCG 59.319 45.455 0.00 0.00 0.00 3.34
509 537 2.702592 ATTTAACCTCGCCCAATCGA 57.297 45.000 0.00 0.00 36.94 3.59
511 539 0.899720 TTAACCTCGCCCAATCGACT 59.100 50.000 0.00 0.00 34.46 4.18
512 540 0.458669 TAACCTCGCCCAATCGACTC 59.541 55.000 0.00 0.00 34.46 3.36
513 541 2.107141 CCTCGCCCAATCGACTCC 59.893 66.667 0.00 0.00 34.46 3.85
514 542 2.107141 CTCGCCCAATCGACTCCC 59.893 66.667 0.00 0.00 34.46 4.30
515 543 2.363795 TCGCCCAATCGACTCCCT 60.364 61.111 0.00 0.00 33.02 4.20
522 550 1.759445 CCAATCGACTCCCTCATCACT 59.241 52.381 0.00 0.00 0.00 3.41
527 555 0.908198 GACTCCCTCATCACTGGCTT 59.092 55.000 0.00 0.00 0.00 4.35
528 556 1.280421 GACTCCCTCATCACTGGCTTT 59.720 52.381 0.00 0.00 0.00 3.51
540 568 0.951040 CTGGCTTTCCGACGAAGCTT 60.951 55.000 17.57 0.00 46.64 3.74
568 596 2.074547 AGATTGTTGTCCGGTACACG 57.925 50.000 0.00 0.00 38.00 4.49
574 602 3.993584 GTCCGGTACACGTGGCCA 61.994 66.667 21.57 0.00 42.24 5.36
638 666 3.723235 ATCGTCGCGGCTGAAGCAT 62.723 57.895 9.90 0.00 44.36 3.79
642 670 3.884350 CGCGGCTGAAGCATGCAT 61.884 61.111 21.98 8.13 44.36 3.96
679 712 0.106619 TTGGTAGGGTTGGTTTGCGT 60.107 50.000 0.00 0.00 0.00 5.24
695 728 4.021925 GTCGTGGCAGCCCTCCTT 62.022 66.667 9.64 0.00 0.00 3.36
707 740 1.144716 CCTCCTTCGCTGCTGCATA 59.855 57.895 16.29 0.00 39.64 3.14
712 745 0.572590 CTTCGCTGCTGCATACGTAC 59.427 55.000 20.02 0.00 39.64 3.67
714 747 2.576893 CGCTGCTGCATACGTACGG 61.577 63.158 21.06 2.64 39.64 4.02
719 752 0.870307 GCTGCATACGTACGGACAGG 60.870 60.000 21.06 5.73 0.00 4.00
720 753 0.870307 CTGCATACGTACGGACAGGC 60.870 60.000 21.06 16.09 0.00 4.85
721 754 1.590792 GCATACGTACGGACAGGCC 60.591 63.158 21.06 0.00 0.00 5.19
755 791 2.892425 GCGGCCATCGAACTGGAG 60.892 66.667 9.29 3.34 42.43 3.86
768 804 3.669036 CTGGAGGACGACGAGCACG 62.669 68.421 0.00 0.76 45.75 5.34
784 820 0.389426 CACGTCCTAACCGAACCTGG 60.389 60.000 0.00 0.00 0.00 4.45
879 915 2.203714 GGAGGATCGGGAGAGGGG 60.204 72.222 0.00 0.00 45.48 4.79
1095 1532 0.463295 TCTACGAGCTAGTGGACGGG 60.463 60.000 8.94 0.00 0.00 5.28
1145 1585 3.074412 CCGACAGATGCTTAACTTGGTT 58.926 45.455 0.00 0.00 0.00 3.67
1228 1686 3.329889 TCTGCCCTCGCCACCATT 61.330 61.111 0.00 0.00 0.00 3.16
1859 2341 2.572290 TGTGTCTGACGAGAACTCTGA 58.428 47.619 2.98 0.00 0.00 3.27
1992 2480 7.148255 GGTTAGATTGTCATTGTCACTTGCATA 60.148 37.037 0.00 0.00 0.00 3.14
2017 2505 1.206132 CGGTCACCTTGGTGCAGTATA 59.794 52.381 14.49 0.00 0.00 1.47
2018 2506 2.158957 CGGTCACCTTGGTGCAGTATAT 60.159 50.000 14.49 0.00 0.00 0.86
2019 2507 3.069016 CGGTCACCTTGGTGCAGTATATA 59.931 47.826 14.49 0.00 0.00 0.86
2020 2508 4.262463 CGGTCACCTTGGTGCAGTATATAT 60.262 45.833 14.49 0.00 0.00 0.86
2183 2671 4.208632 CCATCTCCGTGGCAGTTC 57.791 61.111 0.00 0.00 31.43 3.01
2188 2676 1.874019 CTCCGTGGCAGTTCGATCG 60.874 63.158 9.36 9.36 0.00 3.69
2209 2697 3.750130 CGGATTTGAATGAGATGGCTAGG 59.250 47.826 0.00 0.00 0.00 3.02
2219 2708 3.513119 TGAGATGGCTAGGAGCACATATC 59.487 47.826 13.21 13.21 44.75 1.63
2221 2710 4.102598 AGATGGCTAGGAGCACATATCAT 58.897 43.478 0.21 0.00 44.75 2.45
2222 2711 3.690475 TGGCTAGGAGCACATATCATG 57.310 47.619 0.21 0.00 44.75 3.07
2323 2814 4.154347 CCTCGAGAGCAGCCACCC 62.154 72.222 15.71 0.00 0.00 4.61
2423 2916 2.597217 CCCCGTTGTGCACCACAT 60.597 61.111 19.87 0.00 44.16 3.21
2439 2932 1.299089 CATATGTCGCCGAGCACGA 60.299 57.895 4.70 0.00 42.66 4.35
2469 2962 4.745751 CGGTTGTCGGCCGCCTAA 62.746 66.667 23.51 12.47 42.82 2.69
2481 2974 0.106719 CCGCCTAAACCACCATCCAT 60.107 55.000 0.00 0.00 0.00 3.41
2486 2979 2.509548 CCTAAACCACCATCCATCCTCA 59.490 50.000 0.00 0.00 0.00 3.86
2490 2983 1.206878 CCACCATCCATCCTCACTCA 58.793 55.000 0.00 0.00 0.00 3.41
2491 2984 1.773052 CCACCATCCATCCTCACTCAT 59.227 52.381 0.00 0.00 0.00 2.90
2493 2986 2.053244 ACCATCCATCCTCACTCATCC 58.947 52.381 0.00 0.00 0.00 3.51
2494 2987 2.336891 CCATCCATCCTCACTCATCCT 58.663 52.381 0.00 0.00 0.00 3.24
2511 3008 5.028802 TCATCCTCTCTTCTCACCTTCATT 58.971 41.667 0.00 0.00 0.00 2.57
2637 3136 2.177518 ACCCACCCTCTCTCCTCCA 61.178 63.158 0.00 0.00 0.00 3.86
2657 3159 1.212441 ACCCTCTTCTCTATCGACGGT 59.788 52.381 0.00 0.00 0.00 4.83
2658 3160 2.437281 ACCCTCTTCTCTATCGACGGTA 59.563 50.000 0.00 0.00 0.00 4.02
2713 3216 3.669036 CTCCGCTCGACACCGACAG 62.669 68.421 0.00 0.00 40.30 3.51
2747 3267 3.066621 GTCCACTTTTGCAACATCACTGA 59.933 43.478 0.00 0.00 0.00 3.41
2795 3315 6.970613 ACAAGACCGATGTTACAAAAGAAAAC 59.029 34.615 0.00 0.00 0.00 2.43
2809 3329 5.405935 AAAGAAAACTGCACAAAGACCTT 57.594 34.783 0.00 0.00 0.00 3.50
2840 3361 4.900635 AAAAAGCCGCAACCATATCTAG 57.099 40.909 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 0.813184 ACGGATTCTTGCATTGCAGG 59.187 50.000 14.13 14.13 40.61 4.85
59 60 1.212229 GTAGGAGGCGCCGTATAGC 59.788 63.158 23.20 7.51 43.43 2.97
93 94 2.201022 AGTTGACGGAGAGTGCGGT 61.201 57.895 0.00 0.00 34.75 5.68
202 203 0.036875 GCTAGAGCACCAACCCAAGT 59.963 55.000 0.00 0.00 41.59 3.16
203 204 2.859992 GCTAGAGCACCAACCCAAG 58.140 57.895 0.00 0.00 41.59 3.61
256 257 2.674380 GCCTTGTGACTGCTGGGG 60.674 66.667 0.00 0.00 0.00 4.96
269 270 2.124860 GCCGGGATTACACGCCTT 60.125 61.111 2.18 0.00 42.08 4.35
270 271 4.171103 GGCCGGGATTACACGCCT 62.171 66.667 2.18 0.00 42.08 5.52
271 272 4.476752 TGGCCGGGATTACACGCC 62.477 66.667 2.18 0.00 42.08 5.68
272 273 3.199891 GTGGCCGGGATTACACGC 61.200 66.667 2.18 0.00 42.08 5.34
284 306 3.740128 ATCGACATCAGCGGTGGCC 62.740 63.158 15.67 0.00 41.24 5.36
285 307 1.766143 GAATCGACATCAGCGGTGGC 61.766 60.000 15.67 1.41 40.37 5.01
291 313 4.147306 GTCAATACTCGAATCGACATCAGC 59.853 45.833 0.00 0.00 0.00 4.26
299 321 2.044860 GAGCCGTCAATACTCGAATCG 58.955 52.381 0.00 0.00 0.00 3.34
318 340 3.772025 GGTTCTCCCTTCTCTCTGATTGA 59.228 47.826 0.00 0.00 0.00 2.57
320 342 2.763448 CGGTTCTCCCTTCTCTCTGATT 59.237 50.000 0.00 0.00 0.00 2.57
321 343 2.291930 ACGGTTCTCCCTTCTCTCTGAT 60.292 50.000 0.00 0.00 0.00 2.90
323 345 1.551452 ACGGTTCTCCCTTCTCTCTG 58.449 55.000 0.00 0.00 0.00 3.35
325 347 1.893801 TGAACGGTTCTCCCTTCTCTC 59.106 52.381 20.53 0.00 32.53 3.20
326 348 2.011122 TGAACGGTTCTCCCTTCTCT 57.989 50.000 20.53 0.00 32.53 3.10
328 350 2.047830 AGTTGAACGGTTCTCCCTTCT 58.952 47.619 20.53 7.91 32.53 2.85
332 354 0.534203 TGCAGTTGAACGGTTCTCCC 60.534 55.000 20.53 9.11 0.00 4.30
340 368 3.024784 TGCTGCTGCAGTTGAACG 58.975 55.556 28.50 5.00 45.31 3.95
354 382 2.024414 GTGACCAGACAAAAACCTGCT 58.976 47.619 0.00 0.00 0.00 4.24
373 401 1.265905 GTTCTTGAAACGCGAATGGGT 59.734 47.619 15.93 0.00 44.11 4.51
376 404 3.358775 TGTTGTTCTTGAAACGCGAATG 58.641 40.909 15.93 0.00 0.00 2.67
377 405 3.684103 TGTTGTTCTTGAAACGCGAAT 57.316 38.095 15.93 0.00 0.00 3.34
386 414 6.128336 CCAAAGTTGCAAATTGTTGTTCTTGA 60.128 34.615 13.56 0.00 37.06 3.02
387 415 6.022821 CCAAAGTTGCAAATTGTTGTTCTTG 58.977 36.000 13.56 4.90 37.06 3.02
399 427 7.014230 AGAGTAATTTCTAGCCAAAGTTGCAAA 59.986 33.333 0.00 0.00 0.00 3.68
408 436 4.288626 ACCACCAGAGTAATTTCTAGCCAA 59.711 41.667 0.00 0.00 0.00 4.52
413 441 5.248477 AGCAGAACCACCAGAGTAATTTCTA 59.752 40.000 0.00 0.00 0.00 2.10
443 471 5.482908 AGTATAGCATCGCCAAATCCTAAG 58.517 41.667 0.00 0.00 0.00 2.18
446 474 4.357918 AAGTATAGCATCGCCAAATCCT 57.642 40.909 0.00 0.00 0.00 3.24
450 478 3.013219 TGCAAAGTATAGCATCGCCAAA 58.987 40.909 0.00 0.00 35.51 3.28
453 481 3.904136 ATTGCAAAGTATAGCATCGCC 57.096 42.857 1.71 0.00 40.94 5.54
454 482 5.990408 ACTTATTGCAAAGTATAGCATCGC 58.010 37.500 1.71 0.00 40.94 4.58
455 483 6.593978 GGACTTATTGCAAAGTATAGCATCG 58.406 40.000 1.71 0.00 39.78 3.84
456 484 6.347725 CCGGACTTATTGCAAAGTATAGCATC 60.348 42.308 1.71 0.00 39.78 3.91
458 486 4.814234 CCGGACTTATTGCAAAGTATAGCA 59.186 41.667 1.71 0.00 39.78 3.49
459 487 4.814771 ACCGGACTTATTGCAAAGTATAGC 59.185 41.667 9.46 0.00 39.78 2.97
460 488 6.145696 GCTACCGGACTTATTGCAAAGTATAG 59.854 42.308 9.46 5.36 39.78 1.31
463 491 4.186159 GCTACCGGACTTATTGCAAAGTA 58.814 43.478 9.46 0.00 39.78 2.24
465 493 2.030457 CGCTACCGGACTTATTGCAAAG 59.970 50.000 9.46 0.00 0.00 2.77
466 494 2.004017 CGCTACCGGACTTATTGCAAA 58.996 47.619 9.46 0.00 0.00 3.68
469 497 0.928229 CACGCTACCGGACTTATTGC 59.072 55.000 9.46 0.00 39.22 3.56
472 500 3.814005 AATTCACGCTACCGGACTTAT 57.186 42.857 9.46 0.00 39.22 1.73
473 501 3.598019 AAATTCACGCTACCGGACTTA 57.402 42.857 9.46 0.00 39.22 2.24
474 502 2.467566 AAATTCACGCTACCGGACTT 57.532 45.000 9.46 0.00 39.22 3.01
476 504 2.349580 GGTTAAATTCACGCTACCGGAC 59.650 50.000 9.46 0.00 39.22 4.79
478 506 2.606272 GAGGTTAAATTCACGCTACCGG 59.394 50.000 0.00 0.00 39.22 5.28
481 509 2.030091 GGCGAGGTTAAATTCACGCTAC 59.970 50.000 0.00 0.00 44.31 3.58
482 510 2.273557 GGCGAGGTTAAATTCACGCTA 58.726 47.619 0.00 0.00 44.31 4.26
483 511 1.084289 GGCGAGGTTAAATTCACGCT 58.916 50.000 0.00 0.00 44.31 5.07
484 512 0.098200 GGGCGAGGTTAAATTCACGC 59.902 55.000 0.00 0.00 44.18 5.34
486 514 3.486875 CGATTGGGCGAGGTTAAATTCAC 60.487 47.826 0.00 0.00 0.00 3.18
487 515 2.680841 CGATTGGGCGAGGTTAAATTCA 59.319 45.455 0.00 0.00 0.00 2.57
498 526 2.363795 AGGGAGTCGATTGGGCGA 60.364 61.111 0.00 0.00 38.07 5.54
503 531 2.482664 CCAGTGATGAGGGAGTCGATTG 60.483 54.545 0.00 0.00 0.00 2.67
504 532 1.759445 CCAGTGATGAGGGAGTCGATT 59.241 52.381 0.00 0.00 0.00 3.34
506 534 1.323271 GCCAGTGATGAGGGAGTCGA 61.323 60.000 0.00 0.00 0.00 4.20
508 536 0.908198 AAGCCAGTGATGAGGGAGTC 59.092 55.000 0.00 0.00 0.00 3.36
509 537 1.280421 GAAAGCCAGTGATGAGGGAGT 59.720 52.381 0.00 0.00 0.00 3.85
511 539 0.620556 GGAAAGCCAGTGATGAGGGA 59.379 55.000 0.00 0.00 0.00 4.20
512 540 0.745845 CGGAAAGCCAGTGATGAGGG 60.746 60.000 0.00 0.00 0.00 4.30
513 541 0.250234 TCGGAAAGCCAGTGATGAGG 59.750 55.000 0.00 0.00 0.00 3.86
514 542 1.363744 GTCGGAAAGCCAGTGATGAG 58.636 55.000 0.00 0.00 0.00 2.90
515 543 0.389817 CGTCGGAAAGCCAGTGATGA 60.390 55.000 0.00 0.00 0.00 2.92
522 550 1.070786 AAGCTTCGTCGGAAAGCCA 59.929 52.632 13.35 0.00 31.09 4.75
527 555 2.358247 GCCCAAGCTTCGTCGGAA 60.358 61.111 0.00 0.00 35.50 4.30
528 556 4.735132 CGCCCAAGCTTCGTCGGA 62.735 66.667 0.00 0.00 36.60 4.55
540 568 1.573829 GACAACAATCTTCGCGCCCA 61.574 55.000 0.00 0.00 0.00 5.36
568 596 3.691744 CTCGTCGCTCTCTGGCCAC 62.692 68.421 0.00 0.00 0.00 5.01
574 602 0.523966 CTGTTTCCTCGTCGCTCTCT 59.476 55.000 0.00 0.00 0.00 3.10
638 666 2.379634 CGAAACGGCGACAGATGCA 61.380 57.895 16.62 0.00 0.00 3.96
679 712 3.706373 GAAGGAGGGCTGCCACGA 61.706 66.667 22.05 0.00 0.00 4.35
692 725 0.527600 TACGTATGCAGCAGCGAAGG 60.528 55.000 23.59 8.14 46.23 3.46
695 728 1.585261 CGTACGTATGCAGCAGCGA 60.585 57.895 23.59 8.86 46.23 4.93
737 770 4.467084 TCCAGTTCGATGGCCGCC 62.467 66.667 1.04 1.04 40.41 6.13
741 774 1.519455 CGTCCTCCAGTTCGATGGC 60.519 63.158 0.00 0.00 40.41 4.40
768 804 1.078637 GCCCAGGTTCGGTTAGGAC 60.079 63.158 0.00 0.00 0.00 3.85
771 807 1.221021 GGAGCCCAGGTTCGGTTAG 59.779 63.158 0.00 0.00 0.00 2.34
857 893 0.605319 CTCTCCCGATCCTCCTCTCG 60.605 65.000 0.00 0.00 34.73 4.04
879 915 2.996734 TACACCGGACCGAACCCC 60.997 66.667 17.49 0.00 0.00 4.95
963 1379 3.864983 AAACTCCCGGAGCCCCTGA 62.865 63.158 14.86 0.00 32.04 3.86
1228 1686 2.860971 GCGCGATATTGTACCTGCAGTA 60.861 50.000 12.10 2.40 0.00 2.74
1646 2110 0.940126 CTGCAGCTTGTCAAACTCGT 59.060 50.000 0.00 0.00 0.00 4.18
1766 2233 4.347453 CAAGCACCGGCAACCTGC 62.347 66.667 0.00 2.92 44.61 4.85
1859 2341 9.903682 CAGTTTCAGTTGATTCATTCAAGTAAT 57.096 29.630 0.00 0.00 44.50 1.89
2017 2505 4.394729 ACGGCGAACCATTTATCCAATAT 58.605 39.130 16.62 0.00 34.57 1.28
2018 2506 3.811083 ACGGCGAACCATTTATCCAATA 58.189 40.909 16.62 0.00 34.57 1.90
2019 2507 2.650322 ACGGCGAACCATTTATCCAAT 58.350 42.857 16.62 0.00 34.57 3.16
2020 2508 2.116827 ACGGCGAACCATTTATCCAA 57.883 45.000 16.62 0.00 34.57 3.53
2179 2667 5.011090 TCTCATTCAAATCCGATCGAACT 57.989 39.130 18.66 0.00 0.00 3.01
2183 2671 3.120408 GCCATCTCATTCAAATCCGATCG 60.120 47.826 8.51 8.51 0.00 3.69
2188 2676 4.978099 TCCTAGCCATCTCATTCAAATCC 58.022 43.478 0.00 0.00 0.00 3.01
2209 2697 7.545362 AAACAAGTCTACATGATATGTGCTC 57.455 36.000 0.00 0.00 44.60 4.26
2219 2708 6.264832 TCAGTTGCAAAAACAAGTCTACATG 58.735 36.000 0.00 0.00 30.73 3.21
2221 2710 5.414454 ACTCAGTTGCAAAAACAAGTCTACA 59.586 36.000 0.00 0.00 30.73 2.74
2222 2711 5.739161 CACTCAGTTGCAAAAACAAGTCTAC 59.261 40.000 0.00 0.00 30.73 2.59
2323 2814 2.045926 CTTTGGAGGAGCACGGGG 60.046 66.667 0.00 0.00 0.00 5.73
2387 2878 3.423154 GCTTGGTGGTCGGCGAAG 61.423 66.667 12.92 5.24 0.00 3.79
2388 2879 4.243008 TGCTTGGTGGTCGGCGAA 62.243 61.111 12.92 0.00 0.00 4.70
2394 2885 3.785122 AACGGGGTGCTTGGTGGTC 62.785 63.158 0.00 0.00 0.00 4.02
2423 2916 2.407616 CTCGTGCTCGGCGACATA 59.592 61.111 4.99 1.92 37.69 2.29
2468 2961 1.995542 AGTGAGGATGGATGGTGGTTT 59.004 47.619 0.00 0.00 0.00 3.27
2469 2962 1.561542 GAGTGAGGATGGATGGTGGTT 59.438 52.381 0.00 0.00 0.00 3.67
2481 2974 3.268072 TGAGAAGAGAGGATGAGTGAGGA 59.732 47.826 0.00 0.00 0.00 3.71
2486 2979 3.756082 AGGTGAGAAGAGAGGATGAGT 57.244 47.619 0.00 0.00 0.00 3.41
2490 2983 5.028802 TGAATGAAGGTGAGAAGAGAGGAT 58.971 41.667 0.00 0.00 0.00 3.24
2491 2984 4.420206 TGAATGAAGGTGAGAAGAGAGGA 58.580 43.478 0.00 0.00 0.00 3.71
2493 2986 5.410067 GTCTGAATGAAGGTGAGAAGAGAG 58.590 45.833 0.00 0.00 0.00 3.20
2494 2987 4.221703 GGTCTGAATGAAGGTGAGAAGAGA 59.778 45.833 0.00 0.00 0.00 3.10
2584 3081 2.507102 CAATCGCGACGGCTGAGT 60.507 61.111 12.93 0.00 36.88 3.41
2598 3095 4.778143 GGTGGAGCGGCCGACAAT 62.778 66.667 33.48 11.34 40.66 2.71
2657 3159 1.515954 GTAGCAGCAAGAGCGGGTA 59.484 57.895 0.00 0.00 44.63 3.69
2666 3168 0.323302 TTCATCACCGGTAGCAGCAA 59.677 50.000 6.87 0.00 0.00 3.91
2779 3299 7.816995 TCTTTGTGCAGTTTTCTTTTGTAACAT 59.183 29.630 0.00 0.00 0.00 2.71
2784 3304 4.929211 GGTCTTTGTGCAGTTTTCTTTTGT 59.071 37.500 0.00 0.00 0.00 2.83
2832 3353 8.905702 GCGATTTATTTTTGCAACCTAGATATG 58.094 33.333 0.00 0.00 0.00 1.78
2851 3372 3.472652 ACAGAGGTTGTGTTGCGATTTA 58.527 40.909 0.00 0.00 38.99 1.40


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

AutoCloner maintained by Alex Coulton.