Multiple sequence alignment - TraesCS3D01G516000

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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 TraesCS3D01G516000 chr3D 100.000 4128 0 0 1 4128 599262623 599266750 0.000000e+00 7624.0
1 TraesCS3D01G516000 chr3D 91.398 1953 133 18 1884 3827 599197160 599195234 0.000000e+00 2643.0
2 TraesCS3D01G516000 chr3D 84.291 592 41 24 854 1419 599198448 599197883 7.860000e-147 531.0
3 TraesCS3D01G516000 chr3D 90.763 249 13 4 1628 1876 599197465 599197227 1.430000e-84 324.0
4 TraesCS3D01G516000 chr3D 86.538 260 24 5 3870 4128 599179164 599178915 4.060000e-70 276.0
5 TraesCS3D01G516000 chr3D 83.851 161 15 7 1458 1612 599197608 599197453 4.300000e-30 143.0
6 TraesCS3D01G516000 chr3D 84.733 131 4 11 596 710 599198932 599198802 2.610000e-22 117.0
7 TraesCS3D01G516000 chr3A 95.893 2873 66 15 1260 4128 729311752 729314576 0.000000e+00 4604.0
8 TraesCS3D01G516000 chr3A 94.006 1952 86 14 1884 3827 729407499 729405571 0.000000e+00 2928.0
9 TraesCS3D01G516000 chr3A 92.366 655 41 7 6 654 729310197 729310848 0.000000e+00 924.0
10 TraesCS3D01G516000 chr3A 93.062 418 3 5 854 1256 729311307 729311713 4.600000e-164 588.0
11 TraesCS3D01G516000 chr3A 81.008 595 62 31 720 1296 729421582 729421021 3.810000e-115 425.0
12 TraesCS3D01G516000 chr3A 92.369 249 11 2 1628 1876 729407830 729407590 8.490000e-92 348.0
13 TraesCS3D01G516000 chr3A 82.888 374 39 13 343 700 729421919 729421555 3.100000e-81 313.0
14 TraesCS3D01G516000 chr3A 88.506 261 23 6 3870 4128 729394065 729393810 4.010000e-80 309.0
15 TraesCS3D01G516000 chr3A 86.829 205 22 3 1404 1607 654399440 654399640 1.490000e-54 224.0
16 TraesCS3D01G516000 chr3A 92.593 108 1 1 693 793 729311182 729311289 9.250000e-32 148.0
17 TraesCS3D01G516000 chr3A 98.361 61 1 0 1359 1419 729408300 729408240 1.570000e-19 108.0
18 TraesCS3D01G516000 chr3B 98.454 647 9 1 2026 2671 807175766 807176412 0.000000e+00 1138.0
19 TraesCS3D01G516000 chr3B 82.051 156 23 5 1404 1557 684051453 684051605 1.200000e-25 128.0
20 TraesCS3D01G516000 chr3B 86.486 74 10 0 1424 1497 684045246 684045319 9.510000e-12 82.4
21 TraesCS3D01G516000 chr7B 88.235 731 31 11 1200 1918 38467412 38466725 0.000000e+00 822.0
22 TraesCS3D01G516000 chr6B 87.179 195 22 1 1413 1607 232864520 232864711 6.950000e-53 219.0
23 TraesCS3D01G516000 chr6B 82.383 193 28 3 1418 1607 693932929 693933118 3.300000e-36 163.0
24 TraesCS3D01G516000 chr5B 86.154 195 24 1 1413 1607 380670489 380670298 1.500000e-49 207.0
25 TraesCS3D01G516000 chr6D 83.902 205 28 3 1404 1607 456422332 456422532 1.510000e-44 191.0
26 TraesCS3D01G516000 chr6A 77.885 208 19 14 1404 1607 603098301 603098485 2.030000e-18 104.0


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 TraesCS3D01G516000 chr3D 599262623 599266750 4127 False 7624.0 7624 100.0000 1 4128 1 chr3D.!!$F1 4127
1 TraesCS3D01G516000 chr3D 599195234 599198932 3698 True 751.6 2643 87.0072 596 3827 5 chr3D.!!$R2 3231
2 TraesCS3D01G516000 chr3A 729310197 729314576 4379 False 1566.0 4604 93.4785 6 4128 4 chr3A.!!$F2 4122
3 TraesCS3D01G516000 chr3A 729405571 729408300 2729 True 1128.0 2928 94.9120 1359 3827 3 chr3A.!!$R2 2468
4 TraesCS3D01G516000 chr3A 729421021 729421919 898 True 369.0 425 81.9480 343 1296 2 chr3A.!!$R3 953
5 TraesCS3D01G516000 chr3B 807175766 807176412 646 False 1138.0 1138 98.4540 2026 2671 1 chr3B.!!$F3 645
6 TraesCS3D01G516000 chr7B 38466725 38467412 687 True 822.0 822 88.2350 1200 1918 1 chr7B.!!$R1 718

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
848 1482 0.179059 TGACTGCTTGCTTTCGGTCA 60.179 50.000 9.25 9.25 43.87 4.02 F
849 1483 0.514691 GACTGCTTGCTTTCGGTCAG 59.485 55.000 6.71 0.00 38.22 3.51 F
1351 2071 1.005037 CGTAGTGCCTGTGCCTCAA 60.005 57.895 0.00 0.00 36.33 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 3469 0.468226 TGTCCATTCATACGCCTCCC 59.532 55.000 0.00 0.0 0.00 4.30 R
2683 3787 1.669115 CAGAACCACCACAGCGGAG 60.669 63.158 0.00 0.0 38.63 4.63 R
3285 4390 2.515523 CTCCTCCTTGGGCATGCG 60.516 66.667 12.44 0.0 36.20 4.73 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
19 20 1.447838 ATGCGTGGACGATGTGGTC 60.448 57.895 2.73 0.00 43.02 4.02
37 38 3.243636 TGGTCGTGAAAACTAGACAGTCC 60.244 47.826 0.00 0.00 35.49 3.85
39 40 3.982058 GTCGTGAAAACTAGACAGTCCAG 59.018 47.826 0.00 0.00 32.29 3.86
41 42 4.823442 TCGTGAAAACTAGACAGTCCAGTA 59.177 41.667 1.69 0.00 32.29 2.74
69 70 4.904251 TGGGGAAACATTCAAAAATCTCCA 59.096 37.500 0.00 0.00 0.00 3.86
79 80 8.316214 ACATTCAAAAATCTCCAAGCATACAAT 58.684 29.630 0.00 0.00 0.00 2.71
141 142 1.129437 GACAAACTGCTCGGCTTCATC 59.871 52.381 0.00 0.00 0.00 2.92
152 153 2.894765 TCGGCTTCATCGTATCCCATAA 59.105 45.455 0.00 0.00 0.00 1.90
157 158 4.932200 GCTTCATCGTATCCCATAAAGGAG 59.068 45.833 0.00 0.00 39.95 3.69
158 159 5.482908 CTTCATCGTATCCCATAAAGGAGG 58.517 45.833 0.00 0.00 39.95 4.30
183 185 5.640189 AGCAAATCCTGACAAGATCAAAG 57.360 39.130 0.00 0.00 36.69 2.77
189 191 2.486982 CCTGACAAGATCAAAGCACTGG 59.513 50.000 0.00 0.00 36.69 4.00
204 206 1.066858 CACTGGCACGATTAGAGGTGT 60.067 52.381 0.00 0.00 36.54 4.16
209 211 2.263077 GCACGATTAGAGGTGTCAGTG 58.737 52.381 0.00 0.00 36.54 3.66
211 213 3.429547 GCACGATTAGAGGTGTCAGTGAT 60.430 47.826 0.00 0.00 36.54 3.06
286 288 2.393646 CGGAGAGGGGAAAGAAGATCT 58.606 52.381 0.00 0.00 0.00 2.75
294 296 3.430513 GGGGAAAGAAGATCTACGGTCAC 60.431 52.174 0.00 0.00 0.00 3.67
307 309 2.100631 GGTCACGATTGCCCACGAG 61.101 63.158 0.00 0.00 0.00 4.18
358 360 1.089481 TCGCACGGCCAGAATCATTC 61.089 55.000 2.24 0.00 0.00 2.67
363 365 1.004745 ACGGCCAGAATCATTCACCTT 59.995 47.619 2.24 0.00 0.00 3.50
370 372 5.198965 CCAGAATCATTCACCTTTCCTGAT 58.801 41.667 0.00 0.00 0.00 2.90
378 380 5.592587 TTCACCTTTCCTGATTTTCCCTA 57.407 39.130 0.00 0.00 0.00 3.53
452 455 1.676529 CGAGAACGCCCAATCTCTCTA 59.323 52.381 0.00 0.00 39.92 2.43
454 457 3.648009 GAGAACGCCCAATCTCTCTATG 58.352 50.000 0.00 0.00 39.18 2.23
468 471 5.296748 TCTCTCTATGTCTCTCTCATCGTG 58.703 45.833 0.00 0.00 0.00 4.35
501 504 2.022195 CCACTCTCATTGGCAATGGAG 58.978 52.381 33.38 33.38 39.75 3.86
643 656 3.457012 AGAGTACTAGAGTGACTCCTCCC 59.543 52.174 9.33 0.00 40.44 4.30
657 687 0.938192 CCTCCCTACCCTCTCCTCTT 59.062 60.000 0.00 0.00 0.00 2.85
658 688 1.292546 CCTCCCTACCCTCTCCTCTTT 59.707 57.143 0.00 0.00 0.00 2.52
659 689 2.518834 CCTCCCTACCCTCTCCTCTTTA 59.481 54.545 0.00 0.00 0.00 1.85
660 690 3.143168 CCTCCCTACCCTCTCCTCTTTAT 59.857 52.174 0.00 0.00 0.00 1.40
661 691 4.357399 CCTCCCTACCCTCTCCTCTTTATA 59.643 50.000 0.00 0.00 0.00 0.98
662 692 5.326900 CTCCCTACCCTCTCCTCTTTATAC 58.673 50.000 0.00 0.00 0.00 1.47
663 693 4.107636 TCCCTACCCTCTCCTCTTTATACC 59.892 50.000 0.00 0.00 0.00 2.73
664 694 4.108287 CCCTACCCTCTCCTCTTTATACCT 59.892 50.000 0.00 0.00 0.00 3.08
665 695 5.326900 CCTACCCTCTCCTCTTTATACCTC 58.673 50.000 0.00 0.00 0.00 3.85
666 696 5.075344 CCTACCCTCTCCTCTTTATACCTCT 59.925 48.000 0.00 0.00 0.00 3.69
667 697 5.069518 ACCCTCTCCTCTTTATACCTCTC 57.930 47.826 0.00 0.00 0.00 3.20
668 698 4.735020 ACCCTCTCCTCTTTATACCTCTCT 59.265 45.833 0.00 0.00 0.00 3.10
669 699 5.163023 ACCCTCTCCTCTTTATACCTCTCTC 60.163 48.000 0.00 0.00 0.00 3.20
670 700 5.321927 CCTCTCCTCTTTATACCTCTCTCC 58.678 50.000 0.00 0.00 0.00 3.71
671 701 5.321927 CTCTCCTCTTTATACCTCTCTCCC 58.678 50.000 0.00 0.00 0.00 4.30
672 702 4.106663 TCTCCTCTTTATACCTCTCTCCCC 59.893 50.000 0.00 0.00 0.00 4.81
673 703 3.158676 CCTCTTTATACCTCTCTCCCCG 58.841 54.545 0.00 0.00 0.00 5.73
674 704 3.158676 CTCTTTATACCTCTCTCCCCGG 58.841 54.545 0.00 0.00 0.00 5.73
675 705 2.517127 TCTTTATACCTCTCTCCCCGGT 59.483 50.000 0.00 0.00 34.86 5.28
676 706 3.052338 TCTTTATACCTCTCTCCCCGGTT 60.052 47.826 0.00 0.00 32.36 4.44
677 707 3.409804 TTATACCTCTCTCCCCGGTTT 57.590 47.619 0.00 0.00 32.36 3.27
678 708 1.790818 ATACCTCTCTCCCCGGTTTC 58.209 55.000 0.00 0.00 32.36 2.78
679 709 0.325016 TACCTCTCTCCCCGGTTTCC 60.325 60.000 0.00 0.00 32.36 3.13
680 710 2.368011 CCTCTCTCCCCGGTTTCCC 61.368 68.421 0.00 0.00 0.00 3.97
690 720 2.954611 GGTTTCCCGTTGCAGCTC 59.045 61.111 0.00 0.00 0.00 4.09
691 721 2.556287 GTTTCCCGTTGCAGCTCG 59.444 61.111 0.00 0.00 0.00 5.03
789 1102 0.615850 CTTTCTCAGTCCCTCCCCAC 59.384 60.000 0.00 0.00 0.00 4.61
790 1103 0.193574 TTTCTCAGTCCCTCCCCACT 59.806 55.000 0.00 0.00 0.00 4.00
791 1104 0.545309 TTCTCAGTCCCTCCCCACTG 60.545 60.000 0.00 0.00 41.32 3.66
794 1107 2.122954 AGTCCCTCCCCACTGTCC 59.877 66.667 0.00 0.00 0.00 4.02
798 1111 1.207488 TCCCTCCCCACTGTCCATTG 61.207 60.000 0.00 0.00 0.00 2.82
839 1473 0.317603 CTGTGTGCTTGACTGCTTGC 60.318 55.000 0.00 0.00 0.00 4.01
841 1475 0.383231 GTGTGCTTGACTGCTTGCTT 59.617 50.000 0.00 0.00 0.00 3.91
842 1476 1.105457 TGTGCTTGACTGCTTGCTTT 58.895 45.000 0.00 0.00 0.00 3.51
843 1477 1.066002 TGTGCTTGACTGCTTGCTTTC 59.934 47.619 0.00 0.00 0.00 2.62
844 1478 0.308684 TGCTTGACTGCTTGCTTTCG 59.691 50.000 0.00 0.00 0.00 3.46
845 1479 0.386478 GCTTGACTGCTTGCTTTCGG 60.386 55.000 0.00 0.00 0.00 4.30
846 1480 0.947244 CTTGACTGCTTGCTTTCGGT 59.053 50.000 0.00 0.00 0.00 4.69
847 1481 0.944386 TTGACTGCTTGCTTTCGGTC 59.056 50.000 5.18 5.18 38.67 4.79
848 1482 0.179059 TGACTGCTTGCTTTCGGTCA 60.179 50.000 9.25 9.25 43.87 4.02
849 1483 0.514691 GACTGCTTGCTTTCGGTCAG 59.485 55.000 6.71 0.00 38.22 3.51
850 1484 1.208614 CTGCTTGCTTTCGGTCAGC 59.791 57.895 0.00 0.00 37.82 4.26
851 1485 1.509644 CTGCTTGCTTTCGGTCAGCA 61.510 55.000 0.59 0.59 45.73 4.41
909 1543 2.512515 GCGGCCACTCCATCTCAC 60.513 66.667 2.24 0.00 34.01 3.51
972 1616 3.988976 TCATCCACCAAGAAAGAGGAG 57.011 47.619 0.00 0.00 0.00 3.69
1220 1893 2.661537 GTGCAAAACTTGGCGCCC 60.662 61.111 26.77 5.97 34.58 6.13
1221 1894 2.837291 TGCAAAACTTGGCGCCCT 60.837 55.556 26.77 2.62 0.00 5.19
1222 1895 1.529478 TGCAAAACTTGGCGCCCTA 60.529 52.632 26.77 11.47 0.00 3.53
1223 1896 1.212751 GCAAAACTTGGCGCCCTAG 59.787 57.895 26.77 23.09 32.84 3.02
1224 1897 1.883021 CAAAACTTGGCGCCCTAGG 59.117 57.895 26.77 9.48 30.92 3.02
1334 2054 4.093291 AGCAGGAGGAAGCTGCCG 62.093 66.667 4.63 0.00 44.38 5.69
1351 2071 1.005037 CGTAGTGCCTGTGCCTCAA 60.005 57.895 0.00 0.00 36.33 3.02
1447 2395 2.480610 CGGCCAGCGCAATAATGGT 61.481 57.895 11.47 0.00 36.43 3.55
1507 2474 7.505585 TGGTTCAGTTTTGACATTAGGATCTTT 59.494 33.333 0.00 0.00 31.71 2.52
1558 2531 2.210116 TGGTTCAGCTTCGACAGTTTC 58.790 47.619 0.00 0.00 0.00 2.78
1617 2609 1.202615 TGGCATGAGCAGCTAGATCAC 60.203 52.381 0.00 0.00 46.85 3.06
1676 2669 8.658609 CGCATCAATTTCTTGGAATAATGTTTT 58.341 29.630 0.00 0.00 32.95 2.43
1742 2739 6.917533 TCAAACACCTAGTGCTACTAAGTAC 58.082 40.000 0.00 0.00 36.98 2.73
1794 2809 5.858381 CCACAGGCACTTAGTGATATATGT 58.142 41.667 17.40 9.13 34.75 2.29
1795 2810 6.993079 CCACAGGCACTTAGTGATATATGTA 58.007 40.000 17.40 0.00 34.75 2.29
1796 2811 7.441836 CCACAGGCACTTAGTGATATATGTAA 58.558 38.462 17.40 0.00 34.75 2.41
1797 2812 7.600375 CCACAGGCACTTAGTGATATATGTAAG 59.400 40.741 17.40 4.29 34.75 2.34
1798 2813 7.116948 CACAGGCACTTAGTGATATATGTAAGC 59.883 40.741 17.40 0.00 34.75 3.09
1908 3007 6.767524 AAGAGTAGTGAGGTATCAGTTCTG 57.232 41.667 0.00 0.00 36.83 3.02
2365 3469 5.178096 TGATGGTTATATGCTGGGGTATG 57.822 43.478 0.00 0.00 0.00 2.39
2538 3642 1.980844 CATCAGTTCAATTGTGCGTGC 59.019 47.619 5.13 0.00 0.00 5.34
2683 3787 4.577834 AGAGCTATTAGAGGCGTTTCTC 57.422 45.455 0.00 0.00 0.00 2.87
3080 4184 4.709886 TGAATAATCCTGGACTTCGAGTCA 59.290 41.667 0.00 0.00 46.79 3.41
3357 4462 1.351017 GGGTGGGTTTCAGTCTGATCA 59.649 52.381 2.68 0.00 0.00 2.92
3363 4468 4.405680 TGGGTTTCAGTCTGATCATATCGT 59.594 41.667 2.68 0.00 0.00 3.73
3530 4635 6.477253 TGCACCTGGTTATTTCTGTATTGTA 58.523 36.000 0.00 0.00 0.00 2.41
3531 4636 7.116075 TGCACCTGGTTATTTCTGTATTGTAT 58.884 34.615 0.00 0.00 0.00 2.29
3532 4637 7.613801 TGCACCTGGTTATTTCTGTATTGTATT 59.386 33.333 0.00 0.00 0.00 1.89
3533 4638 7.915397 GCACCTGGTTATTTCTGTATTGTATTG 59.085 37.037 0.00 0.00 0.00 1.90
3534 4639 7.915397 CACCTGGTTATTTCTGTATTGTATTGC 59.085 37.037 0.00 0.00 0.00 3.56
3607 4712 4.570772 AGATGGTTTCGATAATGTGTTCCG 59.429 41.667 0.00 0.00 0.00 4.30
3608 4713 3.666274 TGGTTTCGATAATGTGTTCCGT 58.334 40.909 0.00 0.00 0.00 4.69
3689 4794 3.181450 GCACAGGCTTCCATCCTACTTAT 60.181 47.826 0.00 0.00 36.96 1.73
3912 5017 0.806868 CAATCATGAGTGCCAAGCGT 59.193 50.000 10.61 0.00 0.00 5.07
3935 5040 5.643777 GTGAGTAATGTAATGCCACAAGAGT 59.356 40.000 0.00 0.00 30.84 3.24
3975 5080 5.714806 CACCTTGTGGGGTTATGTCTAAAAT 59.285 40.000 0.00 0.00 37.52 1.82
3977 5082 7.394923 CACCTTGTGGGGTTATGTCTAAAATTA 59.605 37.037 0.00 0.00 37.52 1.40
4073 5178 0.250510 TGCCATGGTTAGCACGAACA 60.251 50.000 14.67 0.00 33.08 3.18
4103 5208 1.472480 GCGGTAAAGGTACTACACGGA 59.528 52.381 0.00 0.00 38.49 4.69
4112 5217 7.657023 AAAGGTACTACACGGAAAGATCTAT 57.343 36.000 0.00 0.00 38.49 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.695893 GACCACATCGTCCACGCATG 61.696 60.000 0.00 2.67 39.60 4.06
2 3 2.048597 GACCACATCGTCCACGCA 60.049 61.111 0.00 0.00 39.60 5.24
3 4 3.179265 CGACCACATCGTCCACGC 61.179 66.667 0.00 0.00 46.25 5.34
19 20 3.978687 ACTGGACTGTCTAGTTTTCACG 58.021 45.455 19.55 0.00 34.34 4.35
37 38 6.588719 TTGAATGTTTCCCCAAGATTACTG 57.411 37.500 0.00 0.00 28.47 2.74
39 40 8.846943 ATTTTTGAATGTTTCCCCAAGATTAC 57.153 30.769 0.00 0.00 28.47 1.89
41 42 7.748677 AGATTTTTGAATGTTTCCCCAAGATT 58.251 30.769 0.00 0.00 31.00 2.40
102 103 2.434185 GATGGCGCACCGAAGACA 60.434 61.111 10.83 0.00 39.70 3.41
111 112 2.031919 AGTTTGTCGGATGGCGCA 59.968 55.556 10.83 0.00 0.00 6.09
113 114 1.970917 GAGCAGTTTGTCGGATGGCG 61.971 60.000 0.00 0.00 0.00 5.69
152 153 1.995542 TCAGGATTTGCTTCCCTCCTT 59.004 47.619 0.00 0.00 35.95 3.36
157 158 2.795329 TCTTGTCAGGATTTGCTTCCC 58.205 47.619 0.00 0.00 36.35 3.97
158 159 4.012374 TGATCTTGTCAGGATTTGCTTCC 58.988 43.478 0.00 0.00 35.90 3.46
183 185 0.108138 ACCTCTAATCGTGCCAGTGC 60.108 55.000 0.00 0.00 38.26 4.40
189 191 2.094700 TCACTGACACCTCTAATCGTGC 60.095 50.000 0.00 0.00 33.09 5.34
204 206 5.010112 GGGAAATAGATCTCGTCATCACTGA 59.990 44.000 0.00 0.00 0.00 3.41
209 211 3.839293 CCGGGAAATAGATCTCGTCATC 58.161 50.000 0.00 0.00 41.74 2.92
211 213 1.340248 GCCGGGAAATAGATCTCGTCA 59.660 52.381 2.18 0.00 41.74 4.35
266 268 2.393646 AGATCTTCTTTCCCCTCTCCG 58.606 52.381 0.00 0.00 0.00 4.63
294 296 3.853330 CGTGCTCGTGGGCAATCG 61.853 66.667 0.00 0.00 44.18 3.34
321 323 4.404654 CCGGCTGAAGTTTGCGCC 62.405 66.667 4.18 0.00 39.14 6.53
322 324 3.595108 GACCGGCTGAAGTTTGCGC 62.595 63.158 0.00 0.00 0.00 6.09
358 360 5.538433 TGTTTAGGGAAAATCAGGAAAGGTG 59.462 40.000 0.00 0.00 0.00 4.00
363 365 6.369629 TCTTGTGTTTAGGGAAAATCAGGAA 58.630 36.000 0.00 0.00 0.00 3.36
393 396 1.065701 ACGTGCGTGGCATAAAACAAA 59.934 42.857 0.00 0.00 41.91 2.83
396 399 2.598000 TTACGTGCGTGGCATAAAAC 57.402 45.000 7.55 0.00 41.91 2.43
404 407 1.002251 ACCATTTGTTTACGTGCGTGG 60.002 47.619 7.55 0.00 0.00 4.94
452 455 3.820467 GAGATCCACGATGAGAGAGACAT 59.180 47.826 0.00 0.00 0.00 3.06
454 457 3.476552 AGAGATCCACGATGAGAGAGAC 58.523 50.000 0.00 0.00 0.00 3.36
468 471 0.467290 AGAGTGGGCGAGAGAGATCC 60.467 60.000 0.00 0.00 0.00 3.36
501 504 2.025898 GGTACTCTCCCACTACTGCTC 58.974 57.143 0.00 0.00 0.00 4.26
643 656 6.045106 AGAGAGGTATAAAGAGGAGAGGGTAG 59.955 46.154 0.00 0.00 0.00 3.18
657 687 3.303049 GAAACCGGGGAGAGAGGTATAA 58.697 50.000 6.32 0.00 37.26 0.98
658 688 2.425392 GGAAACCGGGGAGAGAGGTATA 60.425 54.545 6.32 0.00 37.26 1.47
659 689 1.691801 GGAAACCGGGGAGAGAGGTAT 60.692 57.143 6.32 0.00 37.26 2.73
660 690 0.325016 GGAAACCGGGGAGAGAGGTA 60.325 60.000 6.32 0.00 37.26 3.08
661 691 1.612739 GGAAACCGGGGAGAGAGGT 60.613 63.158 6.32 0.00 40.50 3.85
662 692 2.368011 GGGAAACCGGGGAGAGAGG 61.368 68.421 6.32 0.00 43.64 3.69
663 693 3.310652 GGGAAACCGGGGAGAGAG 58.689 66.667 6.32 0.00 43.64 3.20
674 704 2.556287 CGAGCTGCAACGGGAAAC 59.444 61.111 1.02 0.00 0.00 2.78
675 705 3.353836 GCGAGCTGCAACGGGAAA 61.354 61.111 17.49 0.00 45.45 3.13
684 714 1.097547 AGAGAGAGAGAGCGAGCTGC 61.098 60.000 0.84 0.00 46.98 5.25
685 715 0.940126 GAGAGAGAGAGAGCGAGCTG 59.060 60.000 0.84 0.00 0.00 4.24
686 716 0.833287 AGAGAGAGAGAGAGCGAGCT 59.167 55.000 0.00 0.00 0.00 4.09
687 717 1.202580 AGAGAGAGAGAGAGAGCGAGC 60.203 57.143 0.00 0.00 0.00 5.03
688 718 2.363680 AGAGAGAGAGAGAGAGAGCGAG 59.636 54.545 0.00 0.00 0.00 5.03
689 719 2.388735 AGAGAGAGAGAGAGAGAGCGA 58.611 52.381 0.00 0.00 0.00 4.93
690 720 2.868583 CAAGAGAGAGAGAGAGAGAGCG 59.131 54.545 0.00 0.00 0.00 5.03
691 721 2.615912 GCAAGAGAGAGAGAGAGAGAGC 59.384 54.545 0.00 0.00 0.00 4.09
764 1077 1.377856 GGGACTGAGAAAGCCTGCC 60.378 63.158 0.00 0.00 0.00 4.85
789 1102 3.025978 AGAGAGAGAGAGCAATGGACAG 58.974 50.000 0.00 0.00 0.00 3.51
790 1103 3.023119 GAGAGAGAGAGAGCAATGGACA 58.977 50.000 0.00 0.00 0.00 4.02
791 1104 3.290710 AGAGAGAGAGAGAGCAATGGAC 58.709 50.000 0.00 0.00 0.00 4.02
794 1107 4.458397 AGAGAGAGAGAGAGAGAGCAATG 58.542 47.826 0.00 0.00 0.00 2.82
798 1111 2.435805 TGGAGAGAGAGAGAGAGAGAGC 59.564 54.545 0.00 0.00 0.00 4.09
839 1473 1.572085 CCTGCTGTGCTGACCGAAAG 61.572 60.000 0.00 0.00 0.00 2.62
841 1475 2.031012 CCTGCTGTGCTGACCGAA 59.969 61.111 0.00 0.00 0.00 4.30
842 1476 4.687215 GCCTGCTGTGCTGACCGA 62.687 66.667 0.00 0.00 0.00 4.69
843 1477 4.694233 AGCCTGCTGTGCTGACCG 62.694 66.667 5.92 0.00 37.76 4.79
844 1478 1.860484 GAAAGCCTGCTGTGCTGACC 61.860 60.000 7.20 0.00 39.48 4.02
845 1479 1.578423 GAAAGCCTGCTGTGCTGAC 59.422 57.895 7.20 2.73 39.48 3.51
846 1480 1.601759 GGAAAGCCTGCTGTGCTGA 60.602 57.895 7.20 0.00 39.48 4.26
847 1481 2.633509 GGGAAAGCCTGCTGTGCTG 61.634 63.158 0.69 0.00 39.48 4.41
848 1482 2.282745 GGGAAAGCCTGCTGTGCT 60.283 61.111 0.69 1.64 41.89 4.40
849 1483 3.376918 GGGGAAAGCCTGCTGTGC 61.377 66.667 0.00 0.00 0.00 4.57
850 1484 2.115910 TGGGGAAAGCCTGCTGTG 59.884 61.111 0.00 0.00 0.00 3.66
851 1485 2.116125 GTGGGGAAAGCCTGCTGT 59.884 61.111 0.00 0.00 0.00 4.40
852 1486 2.677875 GGTGGGGAAAGCCTGCTG 60.678 66.667 0.00 0.00 0.00 4.41
909 1543 2.283966 ACGAGGTGGGAGTGGGAG 60.284 66.667 0.00 0.00 0.00 4.30
972 1616 1.673665 CACAGCAGAGACAAGGGGC 60.674 63.158 0.00 0.00 0.00 5.80
1080 1729 4.477975 GTCACCTCCTCGACGCCG 62.478 72.222 0.00 0.00 37.07 6.46
1220 1893 1.072648 AGCGTCCTAGTCCTAGCCTAG 59.927 57.143 7.41 7.41 33.23 3.02
1221 1894 1.138568 AGCGTCCTAGTCCTAGCCTA 58.861 55.000 0.00 0.00 31.95 3.93
1222 1895 0.466555 CAGCGTCCTAGTCCTAGCCT 60.467 60.000 0.00 0.00 31.95 4.58
1223 1896 2.034607 CAGCGTCCTAGTCCTAGCC 58.965 63.158 0.00 0.00 31.95 3.93
1224 1897 1.104577 AGCAGCGTCCTAGTCCTAGC 61.105 60.000 0.00 0.00 31.95 3.42
1334 2054 0.955919 GGTTGAGGCACAGGCACTAC 60.956 60.000 0.00 0.00 43.71 2.73
1351 2071 2.034066 CACGGGGCAATGACAGGT 59.966 61.111 0.00 0.00 0.00 4.00
1437 2385 7.553881 TTCAGACTAAAGCTACCATTATTGC 57.446 36.000 0.00 0.00 0.00 3.56
1447 2395 5.871524 CAGAGCAACATTCAGACTAAAGCTA 59.128 40.000 0.00 0.00 0.00 3.32
1676 2669 7.394816 AGGTAAATGTAAGCTAGCAGAAAGAA 58.605 34.615 18.83 0.00 0.00 2.52
1678 2671 6.818644 TGAGGTAAATGTAAGCTAGCAGAAAG 59.181 38.462 18.83 0.00 0.00 2.62
1742 2739 3.181503 GCATACACTCATCAAGCAACTGG 60.182 47.826 0.00 0.00 0.00 4.00
1781 2796 7.812669 CCGATGTGTGCTTACATATATCACTAA 59.187 37.037 6.42 0.00 41.15 2.24
1782 2797 7.039993 ACCGATGTGTGCTTACATATATCACTA 60.040 37.037 6.42 0.00 41.15 2.74
1783 2798 6.159293 CCGATGTGTGCTTACATATATCACT 58.841 40.000 6.42 0.00 41.15 3.41
1784 2799 5.926542 ACCGATGTGTGCTTACATATATCAC 59.073 40.000 6.42 0.00 41.15 3.06
1785 2800 6.096673 ACCGATGTGTGCTTACATATATCA 57.903 37.500 6.42 0.00 41.15 2.15
1786 2801 7.170828 TGAAACCGATGTGTGCTTACATATATC 59.829 37.037 6.42 0.00 41.15 1.63
1787 2802 6.989759 TGAAACCGATGTGTGCTTACATATAT 59.010 34.615 6.42 0.00 41.15 0.86
1788 2803 6.342111 TGAAACCGATGTGTGCTTACATATA 58.658 36.000 6.42 0.00 41.15 0.86
1789 2804 5.182487 TGAAACCGATGTGTGCTTACATAT 58.818 37.500 6.42 0.00 41.15 1.78
1790 2805 4.570930 TGAAACCGATGTGTGCTTACATA 58.429 39.130 6.42 0.00 41.15 2.29
1791 2806 3.407698 TGAAACCGATGTGTGCTTACAT 58.592 40.909 6.17 6.17 43.61 2.29
1792 2807 2.839975 TGAAACCGATGTGTGCTTACA 58.160 42.857 0.00 0.00 34.63 2.41
1793 2808 3.889196 TTGAAACCGATGTGTGCTTAC 57.111 42.857 0.00 0.00 0.00 2.34
1794 2809 4.902443 TTTTGAAACCGATGTGTGCTTA 57.098 36.364 0.00 0.00 0.00 3.09
1795 2810 3.791973 TTTTGAAACCGATGTGTGCTT 57.208 38.095 0.00 0.00 0.00 3.91
1796 2811 4.320608 AATTTTGAAACCGATGTGTGCT 57.679 36.364 0.00 0.00 0.00 4.40
1797 2812 5.006165 TGAAAATTTTGAAACCGATGTGTGC 59.994 36.000 8.47 0.00 0.00 4.57
1798 2813 6.580963 TGAAAATTTTGAAACCGATGTGTG 57.419 33.333 8.47 0.00 0.00 3.82
1908 3007 7.970061 TGATGTAAAGATGATTAGCAACAAAGC 59.030 33.333 0.00 0.00 0.00 3.51
2314 3418 6.042552 TCCCTAAAGATGATCTGAATCCTCAC 59.957 42.308 0.00 0.00 31.12 3.51
2365 3469 0.468226 TGTCCATTCATACGCCTCCC 59.532 55.000 0.00 0.00 0.00 4.30
2538 3642 6.158598 AGCAATGGTTTGTTAAGCACATAAG 58.841 36.000 0.00 0.00 43.84 1.73
2683 3787 1.669115 CAGAACCACCACAGCGGAG 60.669 63.158 0.00 0.00 38.63 4.63
2756 3860 3.875727 AGATCTGATGGTGCTTCATTTCG 59.124 43.478 0.00 0.00 0.00 3.46
3283 4388 4.431131 CCTCCTTGGGCATGCGGT 62.431 66.667 12.44 0.00 0.00 5.68
3285 4390 2.515523 CTCCTCCTTGGGCATGCG 60.516 66.667 12.44 0.00 36.20 4.73
3357 4462 2.534349 GACAATTGACACGCGACGATAT 59.466 45.455 15.93 0.00 0.00 1.63
3363 4468 1.525197 GACTTGACAATTGACACGCGA 59.475 47.619 15.93 0.00 0.00 5.87
3607 4712 7.166804 GGACATACACAACACAACACATAAAAC 59.833 37.037 0.00 0.00 0.00 2.43
3608 4713 7.197017 GGACATACACAACACAACACATAAAA 58.803 34.615 0.00 0.00 0.00 1.52
3729 4834 4.525874 TCCAGATAATGATCGATCAGCAGT 59.474 41.667 30.11 18.25 40.64 4.40
3731 4836 4.620097 GCTCCAGATAATGATCGATCAGCA 60.620 45.833 30.11 21.01 40.64 4.41
3732 4837 3.864583 GCTCCAGATAATGATCGATCAGC 59.135 47.826 30.11 20.87 40.64 4.26
3912 5017 5.804639 ACTCTTGTGGCATTACATTACTCA 58.195 37.500 0.00 0.00 0.00 3.41
3935 5040 7.519032 CACAAGGTGGGTAAAAAGAAGATTA 57.481 36.000 0.00 0.00 0.00 1.75
3975 5080 9.806203 ATTTGCGATTTTCATTGATCAAGATAA 57.194 25.926 14.54 12.08 0.00 1.75
3977 5082 8.195436 AGATTTGCGATTTTCATTGATCAAGAT 58.805 29.630 14.54 2.97 0.00 2.40
4031 5136 6.463049 GCAAGCTGATGTAGTAGAATTAGGGA 60.463 42.308 0.00 0.00 0.00 4.20
4038 5143 4.445453 CATGGCAAGCTGATGTAGTAGAA 58.555 43.478 0.00 0.00 0.00 2.10
4042 5147 1.283029 ACCATGGCAAGCTGATGTAGT 59.717 47.619 13.04 0.00 0.00 2.73
4073 5178 3.926058 ACCTTTACCGCCATATTCAGT 57.074 42.857 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.