Multiple sequence alignment - TraesCS7A01G315200

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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 TraesCS7A01G315200 chr7A 100.000 3919 0 0 1 3919 449337366 449333448 0.000000e+00 7238
1 TraesCS7A01G315200 chr7A 84.971 173 13 8 2768 2931 193577959 193578127 3.130000e-36 163
2 TraesCS7A01G315200 chr7A 78.601 243 21 12 3623 3841 449326841 449326606 8.840000e-27 132
3 TraesCS7A01G315200 chr7D 93.519 3163 131 26 287 3439 395878170 395875072 0.000000e+00 4638
4 TraesCS7A01G315200 chr7D 90.455 440 27 4 3488 3919 395875001 395874569 2.040000e-157 566
5 TraesCS7A01G315200 chr7D 91.777 377 30 1 1656 2032 403215682 403215307 1.250000e-144 523
6 TraesCS7A01G315200 chr7D 90.957 188 11 5 1 185 395878390 395878206 8.410000e-62 248
7 TraesCS7A01G315200 chr7D 86.207 174 11 8 2767 2931 403215318 403215149 4.020000e-40 176
8 TraesCS7A01G315200 chr7B 92.557 2875 128 48 652 3484 395591779 395588949 0.000000e+00 4045
9 TraesCS7A01G315200 chr7B 89.269 643 42 10 1 639 395606018 395605399 0.000000e+00 780
10 TraesCS7A01G315200 chr7B 88.764 445 31 8 3485 3919 395588916 395588481 9.650000e-146 527
11 TraesCS7A01G315200 chr7B 79.386 228 26 10 3630 3843 395416445 395416225 1.470000e-29 141
12 TraesCS7A01G315200 chr3D 93.103 377 25 1 1656 2032 281330671 281330296 5.720000e-153 551
13 TraesCS7A01G315200 chr3D 91.803 366 29 1 1656 2021 187441 187077 3.490000e-140 508
14 TraesCS7A01G315200 chr3D 86.207 174 11 8 2767 2931 281330307 281330138 4.020000e-40 176
15 TraesCS7A01G315200 chr4A 92.162 370 29 0 1656 2025 599904472 599904103 1.250000e-144 523
16 TraesCS7A01G315200 chr4A 86.207 174 11 8 2767 2931 599904107 599903938 4.020000e-40 176
17 TraesCS7A01G315200 chr2A 90.957 376 33 1 1650 2025 426711502 426711876 4.520000e-139 505
18 TraesCS7A01G315200 chr2A 84.483 174 14 8 2767 2931 426711872 426712041 4.050000e-35 159
19 TraesCS7A01G315200 chr2A 84.393 173 14 8 2768 2931 734549464 734549632 1.460000e-34 158
20 TraesCS7A01G315200 chr5A 92.749 331 22 2 1656 1985 426932058 426931729 9.850000e-131 477
21 TraesCS7A01G315200 chr1A 91.541 331 26 2 1656 1985 244510684 244510355 4.620000e-124 455
22 TraesCS7A01G315200 chr5D 85.057 174 13 8 2767 2931 119466356 119466187 8.710000e-37 165


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 TraesCS7A01G315200 chr7A 449333448 449337366 3918 True 7238.000000 7238 100.000000 1 3919 1 chr7A.!!$R2 3918
1 TraesCS7A01G315200 chr7D 395874569 395878390 3821 True 1817.333333 4638 91.643667 1 3919 3 chr7D.!!$R1 3918
2 TraesCS7A01G315200 chr7D 403215149 403215682 533 True 349.500000 523 88.992000 1656 2931 2 chr7D.!!$R2 1275
3 TraesCS7A01G315200 chr7B 395588481 395591779 3298 True 2286.000000 4045 90.660500 652 3919 2 chr7B.!!$R3 3267
4 TraesCS7A01G315200 chr7B 395605399 395606018 619 True 780.000000 780 89.269000 1 639 1 chr7B.!!$R2 638
5 TraesCS7A01G315200 chr3D 281330138 281330671 533 True 363.500000 551 89.655000 1656 2931 2 chr3D.!!$R2 1275
6 TraesCS7A01G315200 chr4A 599903938 599904472 534 True 349.500000 523 89.184500 1656 2931 2 chr4A.!!$R1 1275
7 TraesCS7A01G315200 chr2A 426711502 426712041 539 False 332.000000 505 87.720000 1650 2931 2 chr2A.!!$F2 1281

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
268 315 0.110486 ATTCCACCCTGCTGTTTCGT 59.890 50.0 0.00 0.0 0.00 3.85 F
1083 1168 0.107945 CCGGCCAAGAAGAGGAAGAG 60.108 60.0 2.24 0.0 0.00 2.85 F
1085 1170 0.393673 GGCCAAGAAGAGGAAGAGGC 60.394 60.0 0.00 0.0 39.86 4.70 F
2701 2814 0.259938 ACCTGGGCCTGATCAAATCC 59.740 55.0 12.58 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1249 0.623324 CCTTGGGGGTGTCCATCCTA 60.623 60.0 0.00 0.0 36.58 2.94 R
2517 2630 0.250234 CTCCCTCACGGCTTCAATGA 59.750 55.0 0.00 0.0 0.00 2.57 R
2791 2904 0.321671 TCCTCAGCCACTGTACAAGC 59.678 55.0 0.00 0.2 32.61 4.01 R
3708 3914 0.035739 GGGAACGGCCAAAGAGTACA 59.964 55.0 2.24 0.0 38.95 2.90 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
17 18 2.994688 CGCGCGAAATGACGATCA 59.005 55.556 28.94 0.00 35.09 2.92
18 19 1.084666 CGCGCGAAATGACGATCAG 60.085 57.895 28.94 0.00 35.09 2.90
43 45 1.537202 CTCCGTCCTGCTTCCTTTTTG 59.463 52.381 0.00 0.00 0.00 2.44
53 55 2.459934 CTTCCTTTTTGTGCGTTGGAC 58.540 47.619 0.00 0.00 0.00 4.02
202 208 4.767255 CAGGCACAGGGACGGCTC 62.767 72.222 0.00 0.00 35.55 4.70
259 306 3.262420 CGTACAGAGAAATTCCACCCTG 58.738 50.000 0.00 0.00 0.00 4.45
268 315 0.110486 ATTCCACCCTGCTGTTTCGT 59.890 50.000 0.00 0.00 0.00 3.85
271 318 0.310854 CCACCCTGCTGTTTCGTTTC 59.689 55.000 0.00 0.00 0.00 2.78
276 323 3.181490 ACCCTGCTGTTTCGTTTCTTTTC 60.181 43.478 0.00 0.00 0.00 2.29
277 324 3.035942 CCTGCTGTTTCGTTTCTTTTCG 58.964 45.455 0.00 0.00 0.00 3.46
278 325 2.446282 TGCTGTTTCGTTTCTTTTCGC 58.554 42.857 0.00 0.00 0.00 4.70
279 326 1.443176 GCTGTTTCGTTTCTTTTCGCG 59.557 47.619 0.00 0.00 0.00 5.87
280 327 2.848002 GCTGTTTCGTTTCTTTTCGCGA 60.848 45.455 3.71 3.71 0.00 5.87
282 329 2.604011 TGTTTCGTTTCTTTTCGCGAGA 59.396 40.909 9.59 0.43 34.78 4.04
328 375 4.554134 GCTCGTTAACCTGTTTCTCCAAAC 60.554 45.833 0.00 0.00 42.16 2.93
384 435 4.002982 GAGATACTTGTGTGCATTGTGGA 58.997 43.478 0.00 0.00 0.00 4.02
385 436 4.005650 AGATACTTGTGTGCATTGTGGAG 58.994 43.478 0.00 0.00 0.00 3.86
386 437 2.057137 ACTTGTGTGCATTGTGGAGT 57.943 45.000 0.00 0.00 0.00 3.85
387 438 3.207265 ACTTGTGTGCATTGTGGAGTA 57.793 42.857 0.00 0.00 0.00 2.59
388 439 2.878406 ACTTGTGTGCATTGTGGAGTAC 59.122 45.455 0.00 0.00 0.00 2.73
389 440 2.928801 TGTGTGCATTGTGGAGTACT 57.071 45.000 0.00 0.00 0.00 2.73
390 441 4.202315 ACTTGTGTGCATTGTGGAGTACTA 60.202 41.667 0.00 0.00 0.00 1.82
391 442 3.659786 TGTGTGCATTGTGGAGTACTAC 58.340 45.455 0.00 0.00 0.00 2.73
473 528 0.747852 TTCGGGCCACAAGGAAAAAC 59.252 50.000 4.39 0.00 36.89 2.43
475 530 0.750249 CGGGCCACAAGGAAAAACTT 59.250 50.000 4.39 0.00 36.89 2.66
541 596 6.091713 CGGTCAAATTTTAGTTACAGGATCGT 59.908 38.462 0.00 0.00 0.00 3.73
553 608 0.461548 AGGATCGTGACGCATCATGT 59.538 50.000 15.44 0.00 41.84 3.21
561 616 4.570369 TCGTGACGCATCATGTGATATTTT 59.430 37.500 4.86 0.00 41.84 1.82
574 629 9.685276 TCATGTGATATTTTTACTCCATTCACT 57.315 29.630 0.00 0.00 34.72 3.41
598 653 9.463443 ACTTAGAAAACTGTTAAAATGTCATGC 57.537 29.630 0.00 0.00 0.00 4.06
715 772 2.642154 TGGTTAAGCGGGACTCAAAA 57.358 45.000 0.00 0.00 0.00 2.44
732 794 5.021033 TCAAAAGGAATTTGCAAGCAAGA 57.979 34.783 7.60 0.51 46.53 3.02
740 806 5.476614 GAATTTGCAAGCAAGAGAAGGAAT 58.523 37.500 7.60 0.00 37.24 3.01
869 948 0.897863 CCAATTCCAGTTCCCCGCAA 60.898 55.000 0.00 0.00 0.00 4.85
886 965 1.795162 GCAATCCAATTCGAACCAGCG 60.795 52.381 0.00 0.00 0.00 5.18
887 966 1.737236 CAATCCAATTCGAACCAGCGA 59.263 47.619 0.00 0.00 38.72 4.93
888 967 1.656652 ATCCAATTCGAACCAGCGAG 58.343 50.000 0.00 0.00 41.79 5.03
889 968 1.019278 TCCAATTCGAACCAGCGAGC 61.019 55.000 0.00 0.00 41.79 5.03
1010 1089 1.134560 CCCCTCGCTCGCTTATATACC 59.865 57.143 0.00 0.00 0.00 2.73
1011 1090 1.816835 CCCTCGCTCGCTTATATACCA 59.183 52.381 0.00 0.00 0.00 3.25
1021 1103 0.604578 TTATATACCAGCCGGACCGC 59.395 55.000 5.05 4.11 35.59 5.68
1032 1114 2.434774 GGACCGCCCTTTGGTTCT 59.565 61.111 0.00 0.00 40.63 3.01
1076 1158 1.846124 AAGTCCCCGGCCAAGAAGA 60.846 57.895 2.24 0.00 0.00 2.87
1077 1162 1.842381 AAGTCCCCGGCCAAGAAGAG 61.842 60.000 2.24 0.00 0.00 2.85
1083 1168 0.107945 CCGGCCAAGAAGAGGAAGAG 60.108 60.000 2.24 0.00 0.00 2.85
1084 1169 0.107945 CGGCCAAGAAGAGGAAGAGG 60.108 60.000 2.24 0.00 0.00 3.69
1085 1170 0.393673 GGCCAAGAAGAGGAAGAGGC 60.394 60.000 0.00 0.00 39.86 4.70
1164 1249 2.159366 CGAGTACGAGAAGCTGGTCATT 60.159 50.000 0.00 0.00 42.66 2.57
1284 1371 2.114411 GGCGGGTTCTTGGTTGGA 59.886 61.111 0.00 0.00 0.00 3.53
1288 1375 1.595093 CGGGTTCTTGGTTGGATGCC 61.595 60.000 0.00 0.00 0.00 4.40
1296 1383 1.456331 GGTTGGATGCCTGGATGGG 60.456 63.158 0.00 0.00 36.00 4.00
1299 1386 1.517538 TTGGATGCCTGGATGGGGTT 61.518 55.000 0.00 0.00 36.00 4.11
1308 1395 3.026694 CCTGGATGGGGTTCTCATTTTC 58.973 50.000 0.00 0.00 0.00 2.29
1317 1404 3.486383 GGTTCTCATTTTCCTGTGGTGA 58.514 45.455 0.00 0.00 0.00 4.02
1318 1405 3.253432 GGTTCTCATTTTCCTGTGGTGAC 59.747 47.826 0.00 0.00 0.00 3.67
1395 1482 4.131088 GCGGACCTCGACCTGTCC 62.131 72.222 12.07 12.07 46.15 4.02
1581 1689 5.911838 GGCAGCATTTCTTATTCGATTTCTC 59.088 40.000 0.00 0.00 0.00 2.87
1582 1690 5.911838 GCAGCATTTCTTATTCGATTTCTCC 59.088 40.000 0.00 0.00 0.00 3.71
1583 1691 6.238593 GCAGCATTTCTTATTCGATTTCTCCT 60.239 38.462 0.00 0.00 0.00 3.69
1654 1762 2.806237 CTCGAGGGGCTAACGGTC 59.194 66.667 3.91 0.00 0.00 4.79
2029 2138 0.677842 GGTACTCTGTGGTCACCGTT 59.322 55.000 0.00 0.00 0.00 4.44
2038 2147 2.110213 GTCACCGTTCAGTGCCCA 59.890 61.111 0.00 0.00 37.68 5.36
2226 2335 2.629656 AATGCCTGCAAGACGCCAC 61.630 57.895 0.00 0.00 41.33 5.01
2234 2343 2.665185 AAGACGCCACAGAACGGC 60.665 61.111 0.00 0.00 46.62 5.68
2271 2384 4.822896 ACTTTCCACGCCAATTTTGTACTA 59.177 37.500 0.00 0.00 0.00 1.82
2272 2385 5.475564 ACTTTCCACGCCAATTTTGTACTAT 59.524 36.000 0.00 0.00 0.00 2.12
2273 2386 4.955925 TCCACGCCAATTTTGTACTATG 57.044 40.909 0.00 0.00 0.00 2.23
2278 2391 4.637091 ACGCCAATTTTGTACTATGGTACC 59.363 41.667 15.88 4.43 45.49 3.34
2287 2400 6.436738 TTGTACTATGGTACCAAACTTCCA 57.563 37.500 20.76 8.92 45.49 3.53
2297 2410 6.183360 TGGTACCAAACTTCCAAAATCTTTCC 60.183 38.462 13.60 0.00 0.00 3.13
2517 2630 4.681978 GGCCGTCCAGCAGAACGT 62.682 66.667 0.00 0.00 0.00 3.99
2701 2814 0.259938 ACCTGGGCCTGATCAAATCC 59.740 55.000 12.58 0.00 0.00 3.01
2721 2834 0.674581 TGCTCATGAGGCAGAAACCG 60.675 55.000 23.89 0.00 34.56 4.44
2724 2837 0.911769 TCATGAGGCAGAAACCGGAT 59.088 50.000 9.46 0.00 33.69 4.18
2753 2866 2.346541 CCAGGCTCTGCTCGTCTGA 61.347 63.158 4.10 0.00 0.00 3.27
2785 2898 1.535462 GGTTCAACGTCCATTCCACAG 59.465 52.381 0.00 0.00 0.00 3.66
2791 2904 1.280982 CGTCCATTCCACAGTCATCG 58.719 55.000 0.00 0.00 0.00 3.84
2830 2943 4.465305 AGGAAGATCCAGGAAAGCAAAATG 59.535 41.667 0.00 0.00 39.61 2.32
3072 3194 3.333804 CTTTGCTTCTCTTCTCCCTGTC 58.666 50.000 0.00 0.00 0.00 3.51
3079 3201 1.204467 CTCTTCTCCCTGTCTGTCTGC 59.796 57.143 0.00 0.00 0.00 4.26
3091 3213 2.749441 GTCTGCCTGCCTTCTGCC 60.749 66.667 0.00 0.00 40.16 4.85
3136 3258 7.117812 GTGATTAGTAGTAACTGCTTTTCTGCA 59.882 37.037 0.00 0.00 41.05 4.41
3213 3335 3.338249 AGGATTCAGACCAAATGTGTCG 58.662 45.455 0.00 0.00 37.80 4.35
3235 3360 5.992829 TCGTAGTGCCACTTTTCTTCAATTA 59.007 36.000 1.02 0.00 0.00 1.40
3236 3361 6.653320 TCGTAGTGCCACTTTTCTTCAATTAT 59.347 34.615 1.02 0.00 0.00 1.28
3237 3362 6.742718 CGTAGTGCCACTTTTCTTCAATTATG 59.257 38.462 1.02 0.00 0.00 1.90
3384 3509 1.745489 CCGTTTGTAGGAGGCTGCC 60.745 63.158 11.65 11.65 0.00 4.85
3438 3563 8.246180 ACAAAATTGCAGAGTATCAAAGTATGG 58.754 33.333 0.00 0.00 37.82 2.74
3443 3568 4.384056 CAGAGTATCAAAGTATGGCCCAG 58.616 47.826 0.00 0.00 37.82 4.45
3452 3577 2.320781 AGTATGGCCCAGCTACTACTG 58.679 52.381 0.00 0.00 37.42 2.74
3472 3597 8.368668 ACTACTGGCCATATTAGAGTGATAAAC 58.631 37.037 18.52 0.00 0.00 2.01
3498 3655 6.344500 AGGAGTGTATCTTGACAAAGCATAG 58.656 40.000 0.00 0.00 33.06 2.23
3499 3656 5.525378 GGAGTGTATCTTGACAAAGCATAGG 59.475 44.000 0.00 0.00 33.06 2.57
3503 3660 6.540189 GTGTATCTTGACAAAGCATAGGATGT 59.460 38.462 0.00 0.00 33.06 3.06
3510 3706 5.414454 TGACAAAGCATAGGATGTGGTAAAC 59.586 40.000 0.00 0.00 0.00 2.01
3536 3732 9.831737 CACAAGAACCAATCAGTAAGAATTTAG 57.168 33.333 0.00 0.00 0.00 1.85
3568 3774 7.639113 TTAATATGCCTAACAGTTTTCCTGG 57.361 36.000 0.00 0.00 46.06 4.45
3570 3776 3.806949 TGCCTAACAGTTTTCCTGGAT 57.193 42.857 0.00 0.00 46.06 3.41
3595 3801 0.034186 TTCCGAAGAGCATGGGCAAT 60.034 50.000 0.00 0.00 44.61 3.56
3599 3805 2.223572 CCGAAGAGCATGGGCAATTAAC 60.224 50.000 0.00 0.00 44.61 2.01
3654 3860 1.086696 GTTTAGCATTGGAGCTGCGA 58.913 50.000 0.00 0.00 46.11 5.10
3656 3862 2.042686 TTAGCATTGGAGCTGCGATT 57.957 45.000 4.99 0.00 46.11 3.34
3657 3863 1.302366 TAGCATTGGAGCTGCGATTG 58.698 50.000 4.99 1.37 46.11 2.67
3658 3864 0.679002 AGCATTGGAGCTGCGATTGT 60.679 50.000 4.99 0.00 44.66 2.71
3669 3875 3.379372 AGCTGCGATTGTTTGCATAGATT 59.621 39.130 0.00 0.00 41.46 2.40
3677 3883 6.415867 CGATTGTTTGCATAGATTGATTCCAC 59.584 38.462 0.00 0.00 0.00 4.02
3705 3911 2.042686 TGTTGACACTGCAAAGAGCT 57.957 45.000 0.00 0.00 45.94 4.09
3706 3912 3.192541 TGTTGACACTGCAAAGAGCTA 57.807 42.857 0.00 0.00 45.94 3.32
3707 3913 2.872245 TGTTGACACTGCAAAGAGCTAC 59.128 45.455 0.00 0.00 45.94 3.58
3708 3914 3.134458 GTTGACACTGCAAAGAGCTACT 58.866 45.455 0.00 0.00 45.94 2.57
3709 3915 2.759191 TGACACTGCAAAGAGCTACTG 58.241 47.619 0.00 0.00 45.94 2.74
3779 3985 5.422331 TCATTCAGGTTAGTCTAGTTCCAGG 59.578 44.000 0.00 0.00 0.00 4.45
3787 3993 6.550108 GGTTAGTCTAGTTCCAGGTCATGATA 59.450 42.308 0.00 0.00 0.00 2.15
3788 3994 7.069578 GGTTAGTCTAGTTCCAGGTCATGATAA 59.930 40.741 0.00 0.00 0.00 1.75
3789 3995 6.723298 AGTCTAGTTCCAGGTCATGATAAG 57.277 41.667 0.00 0.00 0.00 1.73
3847 4053 5.236478 AGTTAACAACTCCAATCAAGTGTCG 59.764 40.000 8.61 0.00 37.02 4.35
3861 4067 2.960819 AGTGTCGACTAACCAAGATGC 58.039 47.619 17.92 0.00 0.00 3.91
3898 4104 1.334960 GCCACGTTGGAATGACAAGTG 60.335 52.381 8.04 0.00 40.96 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.551407 GGACGGAGGGGCCTGATC 61.551 72.222 0.84 0.00 0.00 2.92
35 36 1.133407 GTGTCCAACGCACAAAAAGGA 59.867 47.619 0.00 0.00 36.88 3.36
43 45 2.978010 CCCCTGTGTCCAACGCAC 60.978 66.667 0.00 0.00 33.08 5.34
53 55 4.394712 GACCCGACTGCCCCTGTG 62.395 72.222 0.00 0.00 0.00 3.66
97 99 2.235016 TGCCACTTGTATCACCAAACC 58.765 47.619 0.00 0.00 0.00 3.27
180 186 4.351054 GTCCCTGTGCCTGGGTGG 62.351 72.222 14.10 0.00 42.31 4.61
181 187 4.704833 CGTCCCTGTGCCTGGGTG 62.705 72.222 14.10 7.15 42.31 4.61
185 191 4.767255 GAGCCGTCCCTGTGCCTG 62.767 72.222 0.00 0.00 0.00 4.85
259 306 1.443176 CGCGAAAAGAAACGAAACAGC 59.557 47.619 0.00 0.00 0.00 4.40
268 315 4.210537 AGAAACGATTCTCGCGAAAAGAAA 59.789 37.500 11.33 0.00 42.26 2.52
271 318 3.706994 AGAAACGATTCTCGCGAAAAG 57.293 42.857 11.33 0.00 42.26 2.27
276 323 3.706994 AGAAAAGAAACGATTCTCGCG 57.293 42.857 8.51 0.00 45.19 5.87
277 324 5.270812 AGAAGAAAAGAAACGATTCTCGC 57.729 39.130 8.51 1.80 45.19 5.03
278 325 6.004099 CGAAGAAGAAAAGAAACGATTCTCG 58.996 40.000 8.51 1.45 45.19 4.04
279 326 5.786086 GCGAAGAAGAAAAGAAACGATTCTC 59.214 40.000 8.51 0.00 45.19 2.87
282 329 4.610680 CGGCGAAGAAGAAAAGAAACGATT 60.611 41.667 0.00 0.00 0.00 3.34
283 330 3.120649 CGGCGAAGAAGAAAAGAAACGAT 60.121 43.478 0.00 0.00 0.00 3.73
284 331 2.220133 CGGCGAAGAAGAAAAGAAACGA 59.780 45.455 0.00 0.00 0.00 3.85
285 332 2.560896 CGGCGAAGAAGAAAAGAAACG 58.439 47.619 0.00 0.00 0.00 3.60
286 333 2.031944 AGCGGCGAAGAAGAAAAGAAAC 60.032 45.455 12.98 0.00 0.00 2.78
287 334 2.218603 AGCGGCGAAGAAGAAAAGAAA 58.781 42.857 12.98 0.00 0.00 2.52
288 335 1.798813 GAGCGGCGAAGAAGAAAAGAA 59.201 47.619 12.98 0.00 0.00 2.52
289 336 1.429463 GAGCGGCGAAGAAGAAAAGA 58.571 50.000 12.98 0.00 0.00 2.52
290 337 0.093705 CGAGCGGCGAAGAAGAAAAG 59.906 55.000 12.98 0.00 44.57 2.27
291 338 0.599204 ACGAGCGGCGAAGAAGAAAA 60.599 50.000 12.98 0.00 44.57 2.29
292 339 0.599204 AACGAGCGGCGAAGAAGAAA 60.599 50.000 12.98 0.00 44.57 2.52
295 342 0.365859 GTTAACGAGCGGCGAAGAAG 59.634 55.000 12.98 0.00 44.57 2.85
298 345 1.445582 AGGTTAACGAGCGGCGAAG 60.446 57.895 12.98 2.60 44.57 3.79
340 387 8.786826 TCTCTTCTTTGACAACTCTAAACAAA 57.213 30.769 0.00 0.00 0.00 2.83
341 388 8.964476 ATCTCTTCTTTGACAACTCTAAACAA 57.036 30.769 0.00 0.00 0.00 2.83
342 389 9.477484 GTATCTCTTCTTTGACAACTCTAAACA 57.523 33.333 0.00 0.00 0.00 2.83
343 390 9.699703 AGTATCTCTTCTTTGACAACTCTAAAC 57.300 33.333 0.00 0.00 0.00 2.01
347 394 7.655328 CACAAGTATCTCTTCTTTGACAACTCT 59.345 37.037 0.00 0.00 33.63 3.24
482 537 1.623811 TGTTCCTGGAGAAGTACAGCC 59.376 52.381 0.00 0.00 34.29 4.85
489 544 4.453819 GTCACATTCTTGTTCCTGGAGAAG 59.546 45.833 10.02 10.02 34.29 2.85
541 596 7.254761 GGAGTAAAAATATCACATGATGCGTCA 60.255 37.037 11.83 11.83 39.04 4.35
561 616 8.974060 AACAGTTTTCTAAGTGAATGGAGTAA 57.026 30.769 0.00 0.00 37.97 2.24
572 627 9.463443 GCATGACATTTTAACAGTTTTCTAAGT 57.537 29.630 0.00 0.00 0.00 2.24
574 629 7.114247 GCGCATGACATTTTAACAGTTTTCTAA 59.886 33.333 0.30 0.00 0.00 2.10
577 632 5.174761 TGCGCATGACATTTTAACAGTTTTC 59.825 36.000 5.66 0.00 0.00 2.29
578 633 5.046529 TGCGCATGACATTTTAACAGTTTT 58.953 33.333 5.66 0.00 0.00 2.43
593 648 5.512753 ACCACAATTATATTTGCGCATGA 57.487 34.783 12.75 3.07 0.00 3.07
596 651 3.623510 TCGACCACAATTATATTTGCGCA 59.376 39.130 5.66 5.66 0.00 6.09
597 652 4.203950 TCGACCACAATTATATTTGCGC 57.796 40.909 0.00 0.00 0.00 6.09
598 653 4.772434 CCTCGACCACAATTATATTTGCG 58.228 43.478 7.17 3.88 0.00 4.85
610 665 1.262417 TATGAACAGCCTCGACCACA 58.738 50.000 0.00 0.00 0.00 4.17
647 702 4.036498 GTGTTCTGCTTACGCTCCTATAGA 59.964 45.833 0.00 0.00 36.97 1.98
648 703 4.291783 GTGTTCTGCTTACGCTCCTATAG 58.708 47.826 0.00 0.00 36.97 1.31
715 772 3.257624 CCTTCTCTTGCTTGCAAATTCCT 59.742 43.478 9.39 0.00 0.00 3.36
732 794 0.036010 CACGTGGAGGCATTCCTTCT 60.036 55.000 7.95 0.00 46.92 2.85
869 948 1.656652 CTCGCTGGTTCGAATTGGAT 58.343 50.000 0.00 0.00 38.08 3.41
886 965 2.328099 CCCTTGGCTGTTGTCGCTC 61.328 63.158 0.00 0.00 0.00 5.03
887 966 2.281761 CCCTTGGCTGTTGTCGCT 60.282 61.111 0.00 0.00 0.00 4.93
888 967 3.365265 CCCCTTGGCTGTTGTCGC 61.365 66.667 0.00 0.00 0.00 5.19
889 968 1.228124 TTCCCCTTGGCTGTTGTCG 60.228 57.895 0.00 0.00 0.00 4.35
940 1019 2.674220 GGAGTGGAGGAGCTTGGGG 61.674 68.421 0.00 0.00 0.00 4.96
989 1068 2.089980 GTATATAAGCGAGCGAGGGGA 58.910 52.381 0.00 0.00 0.00 4.81
1021 1103 2.335712 GCTCCGCAGAACCAAAGGG 61.336 63.158 0.00 0.00 41.29 3.95
1057 1139 1.675641 CTTCTTGGCCGGGGACTTG 60.676 63.158 2.18 0.00 0.00 3.16
1069 1151 1.736612 GCTGCCTCTTCCTCTTCTTG 58.263 55.000 0.00 0.00 0.00 3.02
1110 1195 3.004946 TCTGCTGCAGCCTGCCTA 61.005 61.111 34.64 14.99 44.23 3.93
1164 1249 0.623324 CCTTGGGGGTGTCCATCCTA 60.623 60.000 0.00 0.00 36.58 2.94
1284 1371 0.920763 TGAGAACCCCATCCAGGCAT 60.921 55.000 0.00 0.00 35.39 4.40
1288 1375 3.026694 GGAAAATGAGAACCCCATCCAG 58.973 50.000 0.00 0.00 0.00 3.86
1296 1383 3.253432 GTCACCACAGGAAAATGAGAACC 59.747 47.826 0.00 0.00 0.00 3.62
1299 1386 3.136443 ACAGTCACCACAGGAAAATGAGA 59.864 43.478 0.00 0.00 0.00 3.27
1308 1395 1.168407 CCTGCAACAGTCACCACAGG 61.168 60.000 0.00 0.00 38.81 4.00
1317 1404 1.595382 GCTGTCGACCTGCAACAGT 60.595 57.895 20.81 0.68 41.90 3.55
1318 1405 2.661566 CGCTGTCGACCTGCAACAG 61.662 63.158 23.75 10.51 42.59 3.16
1395 1482 3.118112 AGGAGATGTAGGCCTTGTTGATG 60.118 47.826 12.58 0.00 0.00 3.07
1515 1602 4.393834 GCCAGGAAAGAGAGAAAGTTTCT 58.606 43.478 18.05 18.05 44.21 2.52
1549 1657 2.315720 AGAAATGCTGCCCCTTTCTT 57.684 45.000 13.07 2.85 36.14 2.52
1550 1658 2.315720 AAGAAATGCTGCCCCTTTCT 57.684 45.000 13.07 13.07 40.10 2.52
1581 1689 1.542492 AGACTGCAGCCAAATCAAGG 58.458 50.000 15.27 0.00 0.00 3.61
1582 1690 3.002042 CGATAGACTGCAGCCAAATCAAG 59.998 47.826 15.27 0.00 39.76 3.02
1583 1691 2.938451 CGATAGACTGCAGCCAAATCAA 59.062 45.455 15.27 0.00 39.76 2.57
2017 2126 1.522806 GCACTGAACGGTGACCACA 60.523 57.895 16.58 0.00 39.34 4.17
2047 2156 1.665544 CGACGTCGTACAGCAGCTTG 61.666 60.000 29.08 0.00 34.11 4.01
2131 2240 1.142097 GTAGAACTCCTGCCTCGCC 59.858 63.158 0.00 0.00 0.00 5.54
2226 2335 1.328680 CCTCAAATGATCGCCGTTCTG 59.671 52.381 0.00 0.00 0.00 3.02
2234 2343 4.032900 CGTGGAAAGTACCTCAAATGATCG 59.967 45.833 0.00 0.00 0.00 3.69
2271 2384 6.994421 AAGATTTTGGAAGTTTGGTACCAT 57.006 33.333 17.17 0.00 32.31 3.55
2272 2385 6.183360 GGAAAGATTTTGGAAGTTTGGTACCA 60.183 38.462 11.60 11.60 0.00 3.25
2273 2386 6.220930 GGAAAGATTTTGGAAGTTTGGTACC 58.779 40.000 4.43 4.43 0.00 3.34
2278 2391 6.991531 TGAATGGGAAAGATTTTGGAAGTTTG 59.008 34.615 0.00 0.00 0.00 2.93
2517 2630 0.250234 CTCCCTCACGGCTTCAATGA 59.750 55.000 0.00 0.00 0.00 2.57
2638 2751 2.494918 CCGAGGTAGAACAGCCCG 59.505 66.667 0.00 0.00 0.00 6.13
2721 2834 1.202698 AGCCTGGCTTGATCGTTATCC 60.203 52.381 17.22 0.00 33.89 2.59
2724 2837 1.134699 CAGAGCCTGGCTTGATCGTTA 60.135 52.381 24.26 0.00 39.88 3.18
2785 2898 0.721718 GCCACTGTACAAGCGATGAC 59.278 55.000 0.00 0.00 0.00 3.06
2791 2904 0.321671 TCCTCAGCCACTGTACAAGC 59.678 55.000 0.00 0.20 32.61 4.01
2830 2943 2.768344 TTCCTGATCCCGGCCCTC 60.768 66.667 0.00 0.00 0.00 4.30
2946 3068 1.815003 ACTACACACCGGCACTAGTAC 59.185 52.381 0.00 0.00 0.00 2.73
2947 3069 1.814394 CACTACACACCGGCACTAGTA 59.186 52.381 0.00 0.00 0.00 1.82
2948 3070 0.601558 CACTACACACCGGCACTAGT 59.398 55.000 0.00 0.00 0.00 2.57
3072 3194 2.039405 GCAGAAGGCAGGCAGACAG 61.039 63.158 0.00 0.00 43.97 3.51
3091 3213 2.047844 CAGGGGCAGACAGACACG 60.048 66.667 0.00 0.00 29.09 4.49
3136 3258 2.094390 GGTGCAGCACATCATCAACAAT 60.094 45.455 26.78 0.00 35.86 2.71
3185 3307 6.316390 CACATTTGGTCTGAATCCTAGGTAAC 59.684 42.308 9.08 1.95 0.00 2.50
3187 3309 5.487488 ACACATTTGGTCTGAATCCTAGGTA 59.513 40.000 9.08 0.00 0.00 3.08
3213 3335 7.029563 CCATAATTGAAGAAAAGTGGCACTAC 58.970 38.462 22.37 14.99 0.00 2.73
3235 3360 0.538057 CACAGCAACTCCACCACCAT 60.538 55.000 0.00 0.00 0.00 3.55
3236 3361 1.152984 CACAGCAACTCCACCACCA 60.153 57.895 0.00 0.00 0.00 4.17
3237 3362 2.555547 GCACAGCAACTCCACCACC 61.556 63.158 0.00 0.00 0.00 4.61
3443 3568 5.477291 TCACTCTAATATGGCCAGTAGTAGC 59.523 44.000 13.05 0.00 0.00 3.58
3452 3577 5.869888 CCTCGTTTATCACTCTAATATGGCC 59.130 44.000 0.00 0.00 0.00 5.36
3472 3597 3.614616 GCTTTGTCAAGATACACTCCTCG 59.385 47.826 0.00 0.00 30.57 4.63
3503 3660 5.197451 ACTGATTGGTTCTTGTGTTTACCA 58.803 37.500 0.00 0.00 38.82 3.25
3510 3706 9.831737 CTAAATTCTTACTGATTGGTTCTTGTG 57.168 33.333 0.00 0.00 0.00 3.33
3522 3718 9.618890 ATTAATCTGCTGCTAAATTCTTACTGA 57.381 29.630 0.00 0.00 0.00 3.41
3536 3732 5.471456 ACTGTTAGGCATATTAATCTGCTGC 59.529 40.000 21.08 12.59 38.45 5.25
3568 3774 1.115467 TGCTCTTCGGAAGGAGGATC 58.885 55.000 17.19 3.22 37.31 3.36
3570 3776 0.826715 CATGCTCTTCGGAAGGAGGA 59.173 55.000 17.19 13.88 37.31 3.71
3595 3801 5.136828 TCAGGAGCAACCAAATTCAGTTAA 58.863 37.500 2.96 0.00 42.04 2.01
3599 3805 4.796038 AATCAGGAGCAACCAAATTCAG 57.204 40.909 2.96 0.00 42.04 3.02
3628 3834 4.006319 AGCTCCAATGCTAAACTCAGTTC 58.994 43.478 0.00 0.00 42.10 3.01
3654 3860 7.414222 AGTGGAATCAATCTATGCAAACAAT 57.586 32.000 0.00 0.00 0.00 2.71
3656 3862 7.112122 ACTAGTGGAATCAATCTATGCAAACA 58.888 34.615 0.00 0.00 0.00 2.83
3657 3863 7.280876 TGACTAGTGGAATCAATCTATGCAAAC 59.719 37.037 0.00 0.00 0.00 2.93
3658 3864 7.337938 TGACTAGTGGAATCAATCTATGCAAA 58.662 34.615 0.00 0.00 0.00 3.68
3701 3907 2.735762 CGGCCAAAGAGTACAGTAGCTC 60.736 54.545 2.24 3.28 0.00 4.09
3705 3911 2.028748 GGAACGGCCAAAGAGTACAGTA 60.029 50.000 2.24 0.00 36.34 2.74
3706 3912 1.270678 GGAACGGCCAAAGAGTACAGT 60.271 52.381 2.24 0.00 36.34 3.55
3707 3913 1.439679 GGAACGGCCAAAGAGTACAG 58.560 55.000 2.24 0.00 36.34 2.74
3708 3914 0.035739 GGGAACGGCCAAAGAGTACA 59.964 55.000 2.24 0.00 38.95 2.90
3709 3915 0.035739 TGGGAACGGCCAAAGAGTAC 59.964 55.000 2.24 0.00 38.95 2.73
3779 3985 4.805719 TGTCACGCTGATTCTTATCATGAC 59.194 41.667 0.00 10.95 42.87 3.06
3787 3993 4.067896 ACAAAGATGTCACGCTGATTCTT 58.932 39.130 8.75 8.75 33.41 2.52
3788 3994 3.668447 ACAAAGATGTCACGCTGATTCT 58.332 40.909 0.00 0.00 33.41 2.40
3847 4053 3.247006 TCTTCCGCATCTTGGTTAGTC 57.753 47.619 0.00 0.00 0.00 2.59
3861 4067 2.032550 GTGGCATCATCAACATCTTCCG 59.967 50.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.