Multiple sequence alignment - TraesCS7A01G182100

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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 TraesCS7A01G182100 chr7A 100.000 3080 0 0 1 3080 136757892 136754813 0.000000e+00 5688.0
1 TraesCS7A01G182100 chr7A 83.775 604 59 17 2478 3080 136467263 136466698 1.260000e-148 536.0
2 TraesCS7A01G182100 chr7A 82.682 358 24 11 2554 2911 136536462 136536143 1.810000e-72 283.0
3 TraesCS7A01G182100 chr7A 91.111 45 3 1 372 415 112977461 112977505 3.320000e-05 60.2
4 TraesCS7A01G182100 chr7A 90.244 41 3 1 379 418 243349061 243349021 6.000000e-03 52.8
5 TraesCS7A01G182100 chr7D 89.776 2631 144 64 497 3080 136892837 136890285 0.000000e+00 3253.0
6 TraesCS7A01G182100 chr7D 88.536 567 43 10 2480 3042 136864581 136864033 0.000000e+00 667.0
7 TraesCS7A01G182100 chr7D 91.262 309 18 4 4 310 136894902 136894601 2.210000e-111 412.0
8 TraesCS7A01G182100 chr7D 81.348 445 35 13 2611 3049 136925095 136925497 4.960000e-83 318.0
9 TraesCS7A01G182100 chr7D 89.888 89 6 1 2832 2920 136794080 136793995 9.030000e-21 111.0
10 TraesCS7A01G182100 chr7B 88.653 1648 107 31 1448 3080 100332692 100331110 0.000000e+00 1934.0
11 TraesCS7A01G182100 chr7B 83.296 904 49 36 465 1319 100333697 100332847 0.000000e+00 739.0
12 TraesCS7A01G182100 chr7B 85.015 327 21 10 4 330 100335852 100335554 1.070000e-79 307.0
13 TraesCS7A01G182100 chr7B 94.737 38 1 1 379 415 490679643 490679680 1.190000e-04 58.4
14 TraesCS7A01G182100 chr5B 87.719 57 4 3 365 419 631892151 631892206 2.560000e-06 63.9
15 TraesCS7A01G182100 chr3D 92.857 42 2 1 379 419 446429882 446429841 3.320000e-05 60.2
16 TraesCS7A01G182100 chr2B 97.143 35 1 0 385 419 787961744 787961710 3.320000e-05 60.2


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 TraesCS7A01G182100 chr7A 136754813 136757892 3079 True 5688.000000 5688 100.000000 1 3080 1 chr7A.!!$R3 3079
1 TraesCS7A01G182100 chr7A 136466698 136467263 565 True 536.000000 536 83.775000 2478 3080 1 chr7A.!!$R1 602
2 TraesCS7A01G182100 chr7D 136890285 136894902 4617 True 1832.500000 3253 90.519000 4 3080 2 chr7D.!!$R3 3076
3 TraesCS7A01G182100 chr7D 136864033 136864581 548 True 667.000000 667 88.536000 2480 3042 1 chr7D.!!$R2 562
4 TraesCS7A01G182100 chr7B 100331110 100335852 4742 True 993.333333 1934 85.654667 4 3080 3 chr7B.!!$R1 3076

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
793 2628 0.387929 TATCCACCGCAGATTCCGAC 59.612 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2438 4388 0.469892 AAGTTCAACAAGGGGGCAGG 60.47 55.0 0.0 0.0 0.0 4.85 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
61 62 2.352651 CAGCATGTTCTTACCATCACCG 59.647 50.000 0.00 0.00 0.00 4.94
69 70 1.195442 TTACCATCACCGTGCCTCCA 61.195 55.000 0.00 0.00 0.00 3.86
76 77 2.361610 CCGTGCCTCCAATGCCTT 60.362 61.111 0.00 0.00 0.00 4.35
163 164 1.845809 GATGCGACGGGATGATTGGC 61.846 60.000 0.00 0.00 0.00 4.52
283 286 2.811317 CGTCTCGCCTGGCTGTTC 60.811 66.667 17.92 4.09 0.00 3.18
346 657 3.552604 GCTCACGCCATAAACTTTTCA 57.447 42.857 0.00 0.00 0.00 2.69
349 660 4.923281 GCTCACGCCATAAACTTTTCAAAT 59.077 37.500 0.00 0.00 0.00 2.32
351 663 6.751888 GCTCACGCCATAAACTTTTCAAATAT 59.248 34.615 0.00 0.00 0.00 1.28
355 667 9.438291 CACGCCATAAACTTTTCAAATATAGAG 57.562 33.333 0.00 0.00 0.00 2.43
356 668 9.391006 ACGCCATAAACTTTTCAAATATAGAGA 57.609 29.630 0.00 0.00 0.00 3.10
394 1387 4.866327 AAAAATACCCTTCCGTCCCATA 57.134 40.909 0.00 0.00 0.00 2.74
406 1399 3.120792 CCGTCCCATAATGTAAGACGTG 58.879 50.000 9.63 0.00 46.62 4.49
407 1400 3.429822 CCGTCCCATAATGTAAGACGTGT 60.430 47.826 9.63 0.00 46.62 4.49
409 1402 4.628333 CGTCCCATAATGTAAGACGTGTTT 59.372 41.667 2.22 0.00 43.89 2.83
411 1404 6.311723 GTCCCATAATGTAAGACGTGTTTTG 58.688 40.000 2.22 0.00 0.00 2.44
412 1405 6.148150 GTCCCATAATGTAAGACGTGTTTTGA 59.852 38.462 2.22 0.00 0.00 2.69
413 1406 6.148150 TCCCATAATGTAAGACGTGTTTTGAC 59.852 38.462 2.22 0.00 0.00 3.18
416 1409 8.020819 CCATAATGTAAGACGTGTTTTGACATT 58.979 33.333 21.50 21.50 38.95 2.71
420 1413 4.461992 AAGACGTGTTTTGACATTACGG 57.538 40.909 0.00 0.00 38.92 4.02
421 1414 2.803956 AGACGTGTTTTGACATTACGGG 59.196 45.455 0.00 0.00 38.92 5.28
422 1415 2.801679 GACGTGTTTTGACATTACGGGA 59.198 45.455 0.00 0.00 38.92 5.14
423 1416 2.545106 ACGTGTTTTGACATTACGGGAC 59.455 45.455 0.00 0.00 38.92 4.46
438 1431 0.957362 GGGACGGAGGGAGTATTACG 59.043 60.000 0.00 0.00 0.00 3.18
439 1432 1.685148 GGACGGAGGGAGTATTACGT 58.315 55.000 0.00 0.00 37.26 3.57
441 1434 2.292267 GACGGAGGGAGTATTACGTGA 58.708 52.381 0.00 0.00 34.43 4.35
442 1435 2.290093 GACGGAGGGAGTATTACGTGAG 59.710 54.545 0.00 0.00 34.43 3.51
443 1436 1.607628 CGGAGGGAGTATTACGTGAGG 59.392 57.143 0.00 0.00 0.00 3.86
444 1437 1.962100 GGAGGGAGTATTACGTGAGGG 59.038 57.143 0.00 0.00 0.00 4.30
445 1438 2.423947 GGAGGGAGTATTACGTGAGGGA 60.424 54.545 0.00 0.00 0.00 4.20
446 1439 3.294214 GAGGGAGTATTACGTGAGGGAA 58.706 50.000 0.00 0.00 0.00 3.97
447 1440 3.896272 GAGGGAGTATTACGTGAGGGAAT 59.104 47.826 0.00 0.00 0.00 3.01
448 1441 3.641906 AGGGAGTATTACGTGAGGGAATG 59.358 47.826 0.00 0.00 0.00 2.67
449 1442 3.387050 GGGAGTATTACGTGAGGGAATGT 59.613 47.826 0.00 0.00 0.00 2.71
450 1443 4.141779 GGGAGTATTACGTGAGGGAATGTT 60.142 45.833 0.00 0.00 0.00 2.71
456 2177 9.106070 AGTATTACGTGAGGGAATGTTAATTTC 57.894 33.333 0.00 0.00 0.00 2.17
461 2182 7.368059 ACGTGAGGGAATGTTAATTTCTTTTC 58.632 34.615 0.00 0.00 0.00 2.29
462 2183 6.523201 CGTGAGGGAATGTTAATTTCTTTTCG 59.477 38.462 0.00 0.00 0.00 3.46
469 2190 3.189702 TGTTAATTTCTTTTCGGCGAGGG 59.810 43.478 10.46 4.59 0.00 4.30
483 2267 1.402852 GCGAGGGGAAAATGTGCTTTC 60.403 52.381 0.00 0.00 35.04 2.62
495 2279 1.346395 TGTGCTTTCCATACCGACAGT 59.654 47.619 0.00 0.00 0.00 3.55
504 2300 0.397254 ATACCGACAGTGGAGGAGGG 60.397 60.000 12.33 0.00 0.00 4.30
527 2323 1.899814 AGGAAGACGGTTGATGCTACA 59.100 47.619 0.00 0.00 0.00 2.74
528 2324 2.093973 AGGAAGACGGTTGATGCTACAG 60.094 50.000 0.00 0.00 0.00 2.74
530 2326 2.949451 AGACGGTTGATGCTACAGAG 57.051 50.000 0.00 0.00 0.00 3.35
531 2327 2.447443 AGACGGTTGATGCTACAGAGA 58.553 47.619 0.00 0.00 0.00 3.10
532 2328 2.425312 AGACGGTTGATGCTACAGAGAG 59.575 50.000 0.00 0.00 0.00 3.20
533 2329 1.478510 ACGGTTGATGCTACAGAGAGG 59.521 52.381 0.00 0.00 0.00 3.69
534 2330 1.202463 CGGTTGATGCTACAGAGAGGG 60.202 57.143 0.00 0.00 0.00 4.30
535 2331 1.474143 GGTTGATGCTACAGAGAGGGC 60.474 57.143 0.00 0.00 0.00 5.19
536 2332 0.461548 TTGATGCTACAGAGAGGGCG 59.538 55.000 0.00 0.00 0.00 6.13
545 2351 1.689582 AGAGAGGGCGGTAAAGGGG 60.690 63.158 0.00 0.00 0.00 4.79
552 2358 2.673687 CGGTAAAGGGGCCGCAAA 60.674 61.111 23.39 3.44 41.53 3.68
555 2361 1.153647 GTAAAGGGGCCGCAAATGC 60.154 57.895 23.39 7.18 37.78 3.56
569 2375 2.256174 CAAATGCAACAGAATCCAGCG 58.744 47.619 0.00 0.00 0.00 5.18
698 2518 2.744352 ATTGGGAGAGAGAAATGCCC 57.256 50.000 0.00 0.00 39.29 5.36
743 2563 0.933097 CCCATGAAGTCAGAATCGCG 59.067 55.000 0.00 0.00 0.00 5.87
766 2601 1.927569 CTGACGAGGAGGGAGGGAGA 61.928 65.000 0.00 0.00 0.00 3.71
779 2614 3.385115 GGAGGGAGAGGAAAAGTATCCA 58.615 50.000 0.00 0.00 42.27 3.41
793 2628 0.387929 TATCCACCGCAGATTCCGAC 59.612 55.000 0.00 0.00 0.00 4.79
794 2629 2.629050 ATCCACCGCAGATTCCGACG 62.629 60.000 0.00 0.00 0.00 5.12
819 2654 3.641454 GGCCCGGATCCCCTGATC 61.641 72.222 0.73 0.00 45.61 2.92
861 2702 2.024590 CTTAACTACCCCCGCCCTCG 62.025 65.000 0.00 0.00 0.00 4.63
875 2716 4.544689 CTCGCTCGCCAGACGGAG 62.545 72.222 0.00 0.00 43.89 4.63
894 2735 2.612251 CTCCCTCCTCCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
895 2736 3.036959 TCCCTCCTCCCTCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
896 2737 3.039526 CCCTCCTCCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
937 2778 4.067512 TCCCTCTCAGCTCGGCCT 62.068 66.667 0.00 0.00 0.00 5.19
938 2779 3.535962 CCCTCTCAGCTCGGCCTC 61.536 72.222 0.00 0.00 0.00 4.70
939 2780 2.441901 CCTCTCAGCTCGGCCTCT 60.442 66.667 0.00 0.00 0.00 3.69
940 2781 2.489275 CCTCTCAGCTCGGCCTCTC 61.489 68.421 0.00 0.00 0.00 3.20
941 2782 2.441164 TCTCAGCTCGGCCTCTCC 60.441 66.667 0.00 0.00 0.00 3.71
942 2783 3.535962 CTCAGCTCGGCCTCTCCC 61.536 72.222 0.00 0.00 0.00 4.30
990 2834 2.686106 GTGGAACCTAGGCGGGGA 60.686 66.667 9.30 0.00 36.97 4.81
992 2836 3.162154 GGAACCTAGGCGGGGAGG 61.162 72.222 9.30 1.50 38.92 4.30
993 2837 3.162154 GAACCTAGGCGGGGAGGG 61.162 72.222 9.30 0.00 37.14 4.30
994 2838 4.817909 AACCTAGGCGGGGAGGGG 62.818 72.222 9.30 0.00 37.14 4.79
1038 2882 2.743928 CACCGGAACAGCAGCTCC 60.744 66.667 9.46 0.00 0.00 4.70
1182 3038 3.672295 CTTCCAGAGGCGCCACTCC 62.672 68.421 31.54 14.54 38.26 3.85
1311 3167 4.404654 CCTGCCGCGGCTTGTTTC 62.405 66.667 45.79 20.24 42.51 2.78
1319 3175 2.361230 GGCTTGTTTCCCCTCCGG 60.361 66.667 0.00 0.00 0.00 5.14
1324 3249 1.710996 TTGTTTCCCCTCCGGCTTCA 61.711 55.000 0.00 0.00 0.00 3.02
1346 3272 4.794248 TCATCTTCCGTGAAATATTGCG 57.206 40.909 0.00 0.00 0.00 4.85
1352 3278 4.702247 TCCGTGAAATATTGCGTAATCG 57.298 40.909 0.69 0.00 40.37 3.34
1383 3312 2.631418 TGAGACGTGAAGATCGAACC 57.369 50.000 0.00 0.00 0.00 3.62
1387 3316 3.576648 AGACGTGAAGATCGAACCTTTC 58.423 45.455 0.00 0.00 0.00 2.62
1401 3332 4.938226 CGAACCTTTCTTTTCCTAGAGCAT 59.062 41.667 0.00 0.00 0.00 3.79
1420 3351 6.019881 AGAGCATTTTTGCTTTGTTTTACGTC 60.020 34.615 1.51 0.00 46.36 4.34
1423 3356 7.043656 AGCATTTTTGCTTTGTTTTACGTCTAC 60.044 33.333 0.00 0.00 43.52 2.59
1436 3369 7.118680 TGTTTTACGTCTACCAGATTTGATTCC 59.881 37.037 0.00 0.00 0.00 3.01
1440 3373 4.504461 CGTCTACCAGATTTGATTCCTTCG 59.496 45.833 0.00 0.00 0.00 3.79
1450 3383 1.135867 GATTCCTTCGCGCTGATCTC 58.864 55.000 5.56 0.00 0.00 2.75
1458 3391 0.531532 CGCGCTGATCTCTGGGATTT 60.532 55.000 5.56 0.00 34.33 2.17
1471 3404 3.019564 CTGGGATTTGAGGTTGATGGTC 58.980 50.000 0.00 0.00 0.00 4.02
1480 3413 7.395190 TTTGAGGTTGATGGTCAATCTAATG 57.605 36.000 5.51 0.00 46.96 1.90
1485 3418 5.126061 GGTTGATGGTCAATCTAATGTTGCT 59.874 40.000 0.00 0.00 38.79 3.91
1514 3447 8.262227 TCTTATTCCGGCTCTATGTTTTTAGAA 58.738 33.333 0.00 0.00 0.00 2.10
1515 3448 6.927294 ATTCCGGCTCTATGTTTTTAGAAG 57.073 37.500 0.00 0.00 0.00 2.85
1519 3452 7.788026 TCCGGCTCTATGTTTTTAGAAGAATA 58.212 34.615 0.00 0.00 0.00 1.75
1551 3484 4.410555 ACTTGGGGCTTTAATTTGGTTGAA 59.589 37.500 0.00 0.00 0.00 2.69
1552 3485 5.104318 ACTTGGGGCTTTAATTTGGTTGAAA 60.104 36.000 0.00 0.00 0.00 2.69
1563 3496 8.934507 TTAATTTGGTTGAAAGAAACGAACAT 57.065 26.923 0.00 0.00 29.01 2.71
1587 3520 0.841961 TTGATCTGATGGCCTCCTGG 59.158 55.000 3.32 0.00 0.00 4.45
1591 3524 0.620556 TCTGATGGCCTCCTGGTTTC 59.379 55.000 3.32 0.00 35.27 2.78
1623 3556 8.500773 AGCAACAATCAAATGCAATAAAAGAAG 58.499 29.630 0.00 0.00 42.45 2.85
1624 3557 8.497554 GCAACAATCAAATGCAATAAAAGAAGA 58.502 29.630 0.00 0.00 39.81 2.87
1629 3562 8.638685 ATCAAATGCAATAAAAGAAGAATCGG 57.361 30.769 0.00 0.00 0.00 4.18
1633 3566 5.160641 TGCAATAAAAGAAGAATCGGTTGC 58.839 37.500 0.00 0.00 39.69 4.17
1657 3596 6.418057 TTTTAGTTGTTGCATTTCTCCCAT 57.582 33.333 0.00 0.00 0.00 4.00
1701 3642 5.958955 TCAATTTGTGTGTGTGATGACAAA 58.041 33.333 0.00 0.00 41.27 2.83
1780 3728 6.043590 ACAACCTCTGCATCATTCATAGGATA 59.956 38.462 0.00 0.00 33.52 2.59
1782 3730 6.887013 ACCTCTGCATCATTCATAGGATATC 58.113 40.000 0.00 0.00 33.52 1.63
1796 3744 2.164338 GGATATCGAGTGGGTCTCCTC 58.836 57.143 0.00 0.00 39.84 3.71
1797 3745 2.164338 GATATCGAGTGGGTCTCCTCC 58.836 57.143 0.00 0.00 39.84 4.30
1798 3746 1.223501 TATCGAGTGGGTCTCCTCCT 58.776 55.000 0.00 0.00 39.84 3.69
1813 3761 5.183522 GTCTCCTCCTACCTCCAATAATACG 59.816 48.000 0.00 0.00 0.00 3.06
1814 3762 3.830755 TCCTCCTACCTCCAATAATACGC 59.169 47.826 0.00 0.00 0.00 4.42
1882 3830 3.312421 ACTGCCGATTAATTGATGGAACG 59.688 43.478 4.10 0.00 0.00 3.95
1919 3867 4.526970 ACCAATGATCACCGAGCTTAATT 58.473 39.130 0.00 0.00 0.00 1.40
1920 3868 5.680619 ACCAATGATCACCGAGCTTAATTA 58.319 37.500 0.00 0.00 0.00 1.40
1921 3869 6.119536 ACCAATGATCACCGAGCTTAATTAA 58.880 36.000 0.00 0.00 0.00 1.40
1922 3870 6.038271 ACCAATGATCACCGAGCTTAATTAAC 59.962 38.462 0.00 0.00 0.00 2.01
1925 3873 6.844696 TGATCACCGAGCTTAATTAACATC 57.155 37.500 0.00 0.00 0.00 3.06
2010 3958 1.216710 CCTGGACGAGCTCAAGGAC 59.783 63.158 15.40 0.00 0.00 3.85
2090 4038 2.353607 CGCCTAGCATCGACCGAC 60.354 66.667 0.00 0.00 0.00 4.79
2096 4044 4.492160 GCATCGACCGACGGAGCA 62.492 66.667 23.38 3.14 42.82 4.26
2107 4056 1.457303 CGACGGAGCAAAAGAACAGAG 59.543 52.381 0.00 0.00 0.00 3.35
2240 4189 3.266772 AGGTTGTGAGCCAGGATTAATGA 59.733 43.478 0.00 0.00 0.00 2.57
2278 4227 2.100197 GGAATTGGGGCTAGGTGAAAC 58.900 52.381 0.00 0.00 0.00 2.78
2326 4276 1.376424 CAGGTGTGCCGAGCAGAAT 60.376 57.895 0.00 0.00 40.08 2.40
2437 4387 4.070716 CAGCTCTCCAAGTTGTCTGAAAT 58.929 43.478 1.45 0.00 31.96 2.17
2438 4388 4.153835 CAGCTCTCCAAGTTGTCTGAAATC 59.846 45.833 1.45 0.00 31.96 2.17
2442 4392 3.149196 TCCAAGTTGTCTGAAATCCTGC 58.851 45.455 1.45 0.00 0.00 4.85
2512 4463 6.003326 TGACAGAGCAGATATTTCCACAAAA 58.997 36.000 0.00 0.00 0.00 2.44
2513 4464 6.149973 TGACAGAGCAGATATTTCCACAAAAG 59.850 38.462 0.00 0.00 0.00 2.27
2515 4466 5.012239 AGAGCAGATATTTCCACAAAAGCA 58.988 37.500 0.00 0.00 0.00 3.91
2559 4518 2.799126 TCACCATTAACCTTGGCGAT 57.201 45.000 0.00 0.00 37.81 4.58
2675 4638 5.999600 TGACATGTGGGATGATTATGCTAAG 59.000 40.000 1.15 0.00 0.00 2.18
2802 4766 3.365820 GCATGAAGCAACAACATGTTAGC 59.634 43.478 11.53 15.15 38.77 3.09
2821 4785 6.095580 TGTTAGCAGAATCTCACAGGTAGTAG 59.904 42.308 0.00 0.00 0.00 2.57
2857 4824 3.279434 GGCTTACTAAATCTGGTGGTGG 58.721 50.000 0.00 0.00 0.00 4.61
2858 4825 3.308188 GGCTTACTAAATCTGGTGGTGGT 60.308 47.826 0.00 0.00 0.00 4.16
2859 4826 3.689649 GCTTACTAAATCTGGTGGTGGTG 59.310 47.826 0.00 0.00 0.00 4.17
2865 4832 0.250901 ATCTGGTGGTGGTGCTTGAC 60.251 55.000 0.00 0.00 0.00 3.18
2938 4909 0.178992 CCCCAAAACCTGAGACAGCA 60.179 55.000 0.00 0.00 0.00 4.41
2950 4921 4.118410 CTGAGACAGCAGCTCGATTAAAT 58.882 43.478 0.00 0.00 35.15 1.40
3021 5008 0.671472 TCTGATGCTTGTGACAGCGG 60.671 55.000 0.00 0.00 43.37 5.52
3024 5011 1.002366 GATGCTTGTGACAGCGGTAG 58.998 55.000 0.00 0.00 43.37 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 2.769617 CAGCAAGTTACCGCGACG 59.230 61.111 8.23 0.00 0.00 5.12
42 43 2.095853 CACGGTGATGGTAAGAACATGC 59.904 50.000 0.74 0.00 0.00 4.06
154 155 1.595382 CCTCCGGTCGCCAATCATC 60.595 63.158 0.00 0.00 0.00 2.92
163 164 1.654954 ATTGACGTCTCCTCCGGTCG 61.655 60.000 17.92 1.01 0.00 4.79
200 201 3.235481 TCGGGGAACACGCCAAGA 61.235 61.111 0.00 0.00 36.59 3.02
330 333 9.391006 TCTCTATATTTGAAAAGTTTATGGCGT 57.609 29.630 0.00 0.00 0.00 5.68
375 941 4.167307 ACATTATGGGACGGAAGGGTATTT 59.833 41.667 0.00 0.00 0.00 1.40
379 945 1.591768 ACATTATGGGACGGAAGGGT 58.408 50.000 0.00 0.00 0.00 4.34
381 947 4.377897 GTCTTACATTATGGGACGGAAGG 58.622 47.826 0.00 0.00 0.00 3.46
387 953 6.148150 TCAAAACACGTCTTACATTATGGGAC 59.852 38.462 0.00 1.75 0.00 4.46
388 954 6.148150 GTCAAAACACGTCTTACATTATGGGA 59.852 38.462 0.00 0.00 0.00 4.37
389 955 6.072948 TGTCAAAACACGTCTTACATTATGGG 60.073 38.462 0.00 0.00 0.00 4.00
390 956 6.893759 TGTCAAAACACGTCTTACATTATGG 58.106 36.000 0.00 0.00 0.00 2.74
391 957 8.948853 AATGTCAAAACACGTCTTACATTATG 57.051 30.769 2.52 0.00 38.48 1.90
394 1387 7.067116 CGTAATGTCAAAACACGTCTTACATT 58.933 34.615 7.86 7.86 38.48 2.71
406 1399 2.414138 CTCCGTCCCGTAATGTCAAAAC 59.586 50.000 0.00 0.00 0.00 2.43
407 1400 2.613474 CCTCCGTCCCGTAATGTCAAAA 60.613 50.000 0.00 0.00 0.00 2.44
409 1402 0.533491 CCTCCGTCCCGTAATGTCAA 59.467 55.000 0.00 0.00 0.00 3.18
411 1404 1.039233 TCCCTCCGTCCCGTAATGTC 61.039 60.000 0.00 0.00 0.00 3.06
412 1405 1.000739 TCCCTCCGTCCCGTAATGT 59.999 57.895 0.00 0.00 0.00 2.71
413 1406 1.041447 ACTCCCTCCGTCCCGTAATG 61.041 60.000 0.00 0.00 0.00 1.90
416 1409 0.552848 AATACTCCCTCCGTCCCGTA 59.447 55.000 0.00 0.00 0.00 4.02
417 1410 0.552848 TAATACTCCCTCCGTCCCGT 59.447 55.000 0.00 0.00 0.00 5.28
420 1413 1.336125 CACGTAATACTCCCTCCGTCC 59.664 57.143 0.00 0.00 0.00 4.79
421 1414 2.290093 CTCACGTAATACTCCCTCCGTC 59.710 54.545 0.00 0.00 0.00 4.79
422 1415 2.295885 CTCACGTAATACTCCCTCCGT 58.704 52.381 0.00 0.00 0.00 4.69
423 1416 1.607628 CCTCACGTAATACTCCCTCCG 59.392 57.143 0.00 0.00 0.00 4.63
425 1418 2.941480 TCCCTCACGTAATACTCCCTC 58.059 52.381 0.00 0.00 0.00 4.30
426 1419 3.393426 TTCCCTCACGTAATACTCCCT 57.607 47.619 0.00 0.00 0.00 4.20
427 1420 3.387050 ACATTCCCTCACGTAATACTCCC 59.613 47.826 0.00 0.00 0.00 4.30
428 1421 4.667519 ACATTCCCTCACGTAATACTCC 57.332 45.455 0.00 0.00 0.00 3.85
429 1422 8.658499 AATTAACATTCCCTCACGTAATACTC 57.342 34.615 0.00 0.00 0.00 2.59
430 1423 9.106070 GAAATTAACATTCCCTCACGTAATACT 57.894 33.333 0.00 0.00 0.00 2.12
431 1424 9.106070 AGAAATTAACATTCCCTCACGTAATAC 57.894 33.333 0.00 0.00 0.00 1.89
432 1425 9.675464 AAGAAATTAACATTCCCTCACGTAATA 57.325 29.630 0.00 0.00 0.00 0.98
433 1426 8.575649 AAGAAATTAACATTCCCTCACGTAAT 57.424 30.769 0.00 0.00 0.00 1.89
434 1427 7.989416 AAGAAATTAACATTCCCTCACGTAA 57.011 32.000 0.00 0.00 0.00 3.18
435 1428 7.989416 AAAGAAATTAACATTCCCTCACGTA 57.011 32.000 0.00 0.00 0.00 3.57
436 1429 6.894339 AAAGAAATTAACATTCCCTCACGT 57.106 33.333 0.00 0.00 0.00 4.49
437 1430 6.523201 CGAAAAGAAATTAACATTCCCTCACG 59.477 38.462 0.44 0.00 0.00 4.35
438 1431 6.806739 CCGAAAAGAAATTAACATTCCCTCAC 59.193 38.462 0.00 0.00 0.00 3.51
439 1432 6.571537 GCCGAAAAGAAATTAACATTCCCTCA 60.572 38.462 0.00 0.00 0.00 3.86
441 1434 5.621329 CGCCGAAAAGAAATTAACATTCCCT 60.621 40.000 0.00 0.00 0.00 4.20
442 1435 4.561213 CGCCGAAAAGAAATTAACATTCCC 59.439 41.667 0.00 0.00 0.00 3.97
443 1436 5.395642 TCGCCGAAAAGAAATTAACATTCC 58.604 37.500 0.00 0.00 0.00 3.01
444 1437 5.511729 CCTCGCCGAAAAGAAATTAACATTC 59.488 40.000 0.00 0.00 0.00 2.67
445 1438 5.399013 CCTCGCCGAAAAGAAATTAACATT 58.601 37.500 0.00 0.00 0.00 2.71
446 1439 4.142469 CCCTCGCCGAAAAGAAATTAACAT 60.142 41.667 0.00 0.00 0.00 2.71
447 1440 3.189702 CCCTCGCCGAAAAGAAATTAACA 59.810 43.478 0.00 0.00 0.00 2.41
448 1441 3.427098 CCCCTCGCCGAAAAGAAATTAAC 60.427 47.826 0.00 0.00 0.00 2.01
449 1442 2.750712 CCCCTCGCCGAAAAGAAATTAA 59.249 45.455 0.00 0.00 0.00 1.40
450 1443 2.027007 TCCCCTCGCCGAAAAGAAATTA 60.027 45.455 0.00 0.00 0.00 1.40
456 2177 1.135402 CATTTTCCCCTCGCCGAAAAG 60.135 52.381 0.00 0.00 40.31 2.27
461 2182 3.051392 GCACATTTTCCCCTCGCCG 62.051 63.158 0.00 0.00 0.00 6.46
462 2183 1.250840 AAGCACATTTTCCCCTCGCC 61.251 55.000 0.00 0.00 0.00 5.54
483 2267 0.747255 CTCCTCCACTGTCGGTATGG 59.253 60.000 0.00 0.00 34.58 2.74
489 2273 3.077556 CCCCCTCCTCCACTGTCG 61.078 72.222 0.00 0.00 0.00 4.35
495 2279 1.866997 TCTTCCTCCCCCTCCTCCA 60.867 63.158 0.00 0.00 0.00 3.86
504 2300 0.744771 GCATCAACCGTCTTCCTCCC 60.745 60.000 0.00 0.00 0.00 4.30
527 2323 1.689582 CCCCTTTACCGCCCTCTCT 60.690 63.158 0.00 0.00 0.00 3.10
528 2324 2.908796 CCCCTTTACCGCCCTCTC 59.091 66.667 0.00 0.00 0.00 3.20
530 2326 4.501285 GGCCCCTTTACCGCCCTC 62.501 72.222 0.00 0.00 36.63 4.30
536 2332 1.515487 CATTTGCGGCCCCTTTACC 59.485 57.895 0.00 0.00 0.00 2.85
545 2351 0.994263 GATTCTGTTGCATTTGCGGC 59.006 50.000 0.00 0.00 45.83 6.53
552 2358 1.825090 TTCGCTGGATTCTGTTGCAT 58.175 45.000 0.00 0.00 0.00 3.96
555 2361 1.536766 TGCTTTCGCTGGATTCTGTTG 59.463 47.619 0.00 0.00 36.97 3.33
569 2375 5.218139 CAACACAAGGAAGAATCTGCTTTC 58.782 41.667 0.00 0.00 0.00 2.62
577 2383 1.537202 GCTCGCAACACAAGGAAGAAT 59.463 47.619 0.00 0.00 0.00 2.40
675 2495 4.956075 GGGCATTTCTCTCTCCCAATTTAA 59.044 41.667 0.00 0.00 36.96 1.52
682 2502 0.105778 CTCGGGCATTTCTCTCTCCC 59.894 60.000 0.00 0.00 0.00 4.30
721 2541 0.659957 GATTCTGACTTCATGGGCGC 59.340 55.000 0.00 0.00 0.00 6.53
743 2563 1.316706 CCTCCCTCCTCGTCAGTGAC 61.317 65.000 13.56 13.56 0.00 3.67
766 2601 1.906574 TCTGCGGTGGATACTTTTCCT 59.093 47.619 0.00 0.00 36.68 3.36
779 2614 2.423898 ATCCGTCGGAATCTGCGGT 61.424 57.895 19.76 0.00 44.07 5.68
794 2629 4.315941 GATCCGGGCCGTCCATCC 62.316 72.222 26.32 3.73 34.36 3.51
795 2630 4.315941 GGATCCGGGCCGTCCATC 62.316 72.222 25.75 21.24 34.36 3.51
815 2650 4.815973 CGGGGTGGGAGGGGATCA 62.816 72.222 0.00 0.00 0.00 2.92
866 2707 3.151022 GAGGGAGGCTCCGTCTGG 61.151 72.222 36.83 0.00 45.36 3.86
870 2711 4.467107 GGAGGAGGGAGGCTCCGT 62.467 72.222 27.68 27.68 45.24 4.69
872 2713 3.767044 GAGGGAGGAGGGAGGCTCC 62.767 73.684 25.80 25.80 41.15 4.70
873 2714 2.123033 GAGGGAGGAGGGAGGCTC 60.123 72.222 5.78 5.78 0.00 4.70
874 2715 3.773154 GGAGGGAGGAGGGAGGCT 61.773 72.222 0.00 0.00 0.00 4.58
875 2716 3.767044 GAGGAGGGAGGAGGGAGGC 62.767 73.684 0.00 0.00 0.00 4.70
881 2722 2.018086 AGGAGGGAGGAGGGAGGAG 61.018 68.421 0.00 0.00 0.00 3.69
882 2723 2.015726 GAGGAGGGAGGAGGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
895 2736 3.781770 GATGGCGAGTGGCGAGGAG 62.782 68.421 0.00 0.00 44.92 3.69
896 2737 3.838271 GATGGCGAGTGGCGAGGA 61.838 66.667 0.00 0.00 44.92 3.71
937 2778 2.691779 GGAGTCGGAGAGGGGGAGA 61.692 68.421 0.00 0.00 36.95 3.71
938 2779 2.123640 GGAGTCGGAGAGGGGGAG 60.124 72.222 0.00 0.00 36.95 4.30
939 2780 4.124943 CGGAGTCGGAGAGGGGGA 62.125 72.222 0.00 0.00 36.95 4.81
940 2781 4.444081 ACGGAGTCGGAGAGGGGG 62.444 72.222 4.48 0.00 29.74 5.40
987 2831 3.493303 GTCATCCCTGCCCCTCCC 61.493 72.222 0.00 0.00 0.00 4.30
990 2834 3.083997 GTCGTCATCCCTGCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
993 2837 4.148825 AGCGTCGTCATCCCTGCC 62.149 66.667 0.00 0.00 0.00 4.85
994 2838 2.887568 CAGCGTCGTCATCCCTGC 60.888 66.667 0.00 0.00 0.00 4.85
995 2839 2.202797 CCAGCGTCGTCATCCCTG 60.203 66.667 0.00 0.00 0.00 4.45
996 2840 3.461773 CCCAGCGTCGTCATCCCT 61.462 66.667 0.00 0.00 0.00 4.20
997 2841 4.530857 CCCCAGCGTCGTCATCCC 62.531 72.222 0.00 0.00 0.00 3.85
998 2842 2.907897 CTTCCCCAGCGTCGTCATCC 62.908 65.000 0.00 0.00 0.00 3.51
1319 3175 4.889832 ATTTCACGGAAGATGATGAAGC 57.110 40.909 0.00 0.00 32.90 3.86
1324 3249 4.816385 ACGCAATATTTCACGGAAGATGAT 59.184 37.500 7.09 0.00 0.00 2.45
1346 3272 2.279741 TCATGGCAGCAGAACGATTAC 58.720 47.619 0.00 0.00 0.00 1.89
1352 3278 0.671781 ACGTCTCATGGCAGCAGAAC 60.672 55.000 0.00 0.00 0.00 3.01
1383 3312 7.150640 AGCAAAAATGCTCTAGGAAAAGAAAG 58.849 34.615 0.00 0.00 42.12 2.62
1387 3316 6.703165 ACAAAGCAAAAATGCTCTAGGAAAAG 59.297 34.615 3.50 0.00 45.54 2.27
1401 3332 6.618811 TGGTAGACGTAAAACAAAGCAAAAA 58.381 32.000 0.00 0.00 0.00 1.94
1420 3351 3.246226 CGCGAAGGAATCAAATCTGGTAG 59.754 47.826 0.00 0.00 0.00 3.18
1423 3356 1.268234 GCGCGAAGGAATCAAATCTGG 60.268 52.381 12.10 0.00 0.00 3.86
1436 3369 1.591059 CCCAGAGATCAGCGCGAAG 60.591 63.158 12.10 0.00 0.00 3.79
1440 3373 0.942962 CAAATCCCAGAGATCAGCGC 59.057 55.000 0.00 0.00 32.47 5.92
1450 3383 3.019564 GACCATCAACCTCAAATCCCAG 58.980 50.000 0.00 0.00 0.00 4.45
1458 3391 6.065976 ACATTAGATTGACCATCAACCTCA 57.934 37.500 0.00 0.00 39.45 3.86
1471 3404 8.066595 CGGAATAAGAAGAGCAACATTAGATTG 58.933 37.037 0.00 0.00 0.00 2.67
1480 3413 2.609916 GAGCCGGAATAAGAAGAGCAAC 59.390 50.000 5.05 0.00 0.00 4.17
1485 3418 5.871396 AACATAGAGCCGGAATAAGAAGA 57.129 39.130 5.05 0.00 0.00 2.87
1514 3447 5.086621 AGCCCCAAGTCACAAAATTATTCT 58.913 37.500 0.00 0.00 0.00 2.40
1515 3448 5.405935 AGCCCCAAGTCACAAAATTATTC 57.594 39.130 0.00 0.00 0.00 1.75
1519 3452 5.622346 TTAAAGCCCCAAGTCACAAAATT 57.378 34.783 0.00 0.00 0.00 1.82
1551 3484 2.489971 TCAAGCCGATGTTCGTTTCTT 58.510 42.857 0.00 0.00 38.40 2.52
1552 3485 2.163818 TCAAGCCGATGTTCGTTTCT 57.836 45.000 0.00 0.00 38.40 2.52
1563 3496 1.146930 GGCCATCAGATCAAGCCGA 59.853 57.895 0.00 0.00 33.18 5.54
1587 3520 1.266718 TGATTGTTGCTCTGCCGAAAC 59.733 47.619 0.00 0.00 0.00 2.78
1591 3524 2.256174 CATTTGATTGTTGCTCTGCCG 58.744 47.619 0.00 0.00 0.00 5.69
1623 3556 4.148174 GCAACAACTAAAAGCAACCGATTC 59.852 41.667 0.00 0.00 0.00 2.52
1624 3557 4.048504 GCAACAACTAAAAGCAACCGATT 58.951 39.130 0.00 0.00 0.00 3.34
1625 3558 3.067461 TGCAACAACTAAAAGCAACCGAT 59.933 39.130 0.00 0.00 31.42 4.18
1629 3562 6.292328 GGAGAAATGCAACAACTAAAAGCAAC 60.292 38.462 0.00 0.00 38.85 4.17
1633 3566 5.841810 TGGGAGAAATGCAACAACTAAAAG 58.158 37.500 0.00 0.00 0.00 2.27
1657 3596 2.433444 TCCTTCTTCCCCTCCAAAGA 57.567 50.000 0.00 0.00 0.00 2.52
1733 3674 1.025113 CAGAGTGCACAGCTGGATGG 61.025 60.000 24.14 5.63 0.00 3.51
1780 3728 1.133730 GTAGGAGGAGACCCACTCGAT 60.134 57.143 0.00 0.00 45.76 3.59
1782 3730 0.752376 GGTAGGAGGAGACCCACTCG 60.752 65.000 0.00 0.00 45.76 4.18
1796 3744 3.070446 TGGTGCGTATTATTGGAGGTAGG 59.930 47.826 0.00 0.00 0.00 3.18
1797 3745 4.056050 GTGGTGCGTATTATTGGAGGTAG 58.944 47.826 0.00 0.00 0.00 3.18
1798 3746 3.707611 AGTGGTGCGTATTATTGGAGGTA 59.292 43.478 0.00 0.00 0.00 3.08
1813 3761 2.980233 GTGGCCTGTGAGTGGTGC 60.980 66.667 3.32 0.00 0.00 5.01
1814 3762 1.598962 CTGTGGCCTGTGAGTGGTG 60.599 63.158 3.32 0.00 0.00 4.17
1861 3809 3.312421 ACGTTCCATCAATTAATCGGCAG 59.688 43.478 0.00 0.00 0.00 4.85
1865 3813 3.064682 TGGCACGTTCCATCAATTAATCG 59.935 43.478 1.63 0.00 0.00 3.34
1882 3830 3.505680 TCATTGGTTGTTGTAGATGGCAC 59.494 43.478 0.00 0.00 0.00 5.01
1891 3839 2.813754 CTCGGTGATCATTGGTTGTTGT 59.186 45.455 0.00 0.00 0.00 3.32
1892 3840 2.414559 GCTCGGTGATCATTGGTTGTTG 60.415 50.000 0.00 0.00 0.00 3.33
1893 3841 1.812571 GCTCGGTGATCATTGGTTGTT 59.187 47.619 0.00 0.00 0.00 2.83
2010 3958 2.680913 CGCCGGGAAGCACTTCTTG 61.681 63.158 2.18 3.50 39.45 3.02
2090 4038 3.181526 CGATTCTCTGTTCTTTTGCTCCG 60.182 47.826 0.00 0.00 0.00 4.63
2096 4044 3.058914 CGCCAACGATTCTCTGTTCTTTT 60.059 43.478 0.00 0.00 43.93 2.27
2107 4056 1.143183 TAGAGGGCGCCAACGATTC 59.857 57.895 30.85 14.67 43.93 2.52
2181 4130 5.730550 ACACAACAACACGACATATAGGAT 58.269 37.500 0.00 0.00 0.00 3.24
2182 4131 5.142061 ACACAACAACACGACATATAGGA 57.858 39.130 0.00 0.00 0.00 2.94
2198 4147 3.313526 CCTGAGCCAGCAATATACACAAC 59.686 47.826 0.00 0.00 0.00 3.32
2240 4189 6.131961 CAATTCCAATCTCTACATCCCCTTT 58.868 40.000 0.00 0.00 0.00 3.11
2415 4365 2.827800 TCAGACAACTTGGAGAGCTG 57.172 50.000 0.00 0.00 0.00 4.24
2437 4387 1.152830 GTTCAACAAGGGGGCAGGA 59.847 57.895 0.00 0.00 0.00 3.86
2438 4388 0.469892 AAGTTCAACAAGGGGGCAGG 60.470 55.000 0.00 0.00 0.00 4.85
2442 4392 5.304357 ACATTTTAGAAGTTCAACAAGGGGG 59.696 40.000 5.50 0.00 0.00 5.40
2522 4475 0.614697 GAAATTCCTGGTGGGGTGGG 60.615 60.000 0.00 0.00 35.33 4.61
2527 4482 2.236489 ATGGTGAAATTCCTGGTGGG 57.764 50.000 0.00 0.00 0.00 4.61
2675 4638 9.274065 CTTAGTCAAGGTCAATAATAAAAACGC 57.726 33.333 0.00 0.00 0.00 4.84
2712 4675 3.324993 ACCAAGTGCCAAATAATTTGCG 58.675 40.909 0.00 0.00 39.31 4.85
2802 4766 8.145316 GTAGTACTACTACCTGTGAGATTCTG 57.855 42.308 23.17 0.00 43.96 3.02
2821 4785 8.738645 TTTAGTAAGCCACTAGTAGGTAGTAC 57.261 38.462 1.45 0.00 40.27 2.73
2857 4824 1.673665 CTGGGCTCTGGTCAAGCAC 60.674 63.158 0.00 0.00 43.67 4.40
2858 4825 2.752358 CTGGGCTCTGGTCAAGCA 59.248 61.111 0.00 0.00 41.66 3.91
2859 4826 2.749441 GCTGGGCTCTGGTCAAGC 60.749 66.667 0.00 0.00 39.09 4.01
2865 4832 0.106819 ATTTAGCAGCTGGGCTCTGG 60.107 55.000 17.12 0.00 44.54 3.86
2938 4909 7.329717 GCAGTAGCAGTATAATTTAATCGAGCT 59.670 37.037 0.00 0.00 41.58 4.09
3021 5008 3.380637 TCCTCTGCTGGATACGTTTCTAC 59.619 47.826 5.97 0.00 42.51 2.59
3024 5011 2.427453 TCTCCTCTGCTGGATACGTTTC 59.573 50.000 0.00 0.00 42.51 2.78


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

AutoCloner maintained by Alex Coulton.