Multiple sequence alignment - TraesCS7A01G182300

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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 TraesCS7A01G182300 chr7A 100.000 2725 0 0 1 2725 137454339 137451615 0.000000e+00 5033.0
1 TraesCS7A01G182300 chr7A 100.000 58 0 0 2979 3036 137451361 137451304 1.150000e-19 108.0
2 TraesCS7A01G182300 chr7A 90.411 73 7 0 555 627 501077689 501077617 2.490000e-16 97.1
3 TraesCS7A01G182300 chr7B 90.758 2164 88 36 615 2725 101498027 101495923 0.000000e+00 2785.0
4 TraesCS7A01G182300 chr7B 92.710 535 34 5 1 534 101498569 101498039 0.000000e+00 767.0
5 TraesCS7A01G182300 chr7B 88.312 77 7 2 541 617 117192092 117192166 1.160000e-14 91.6
6 TraesCS7A01G182300 chr7D 93.705 1795 60 8 948 2725 137293728 137291970 0.000000e+00 2639.0
7 TraesCS7A01G182300 chr7D 93.097 536 34 3 1 534 137294758 137294224 0.000000e+00 782.0
8 TraesCS7A01G182300 chr7D 91.000 200 14 4 615 812 137294217 137294020 1.790000e-67 267.0
9 TraesCS7A01G182300 chr5B 96.825 63 2 0 555 617 322277269 322277207 4.140000e-19 106.0
10 TraesCS7A01G182300 chr6B 92.000 75 5 1 555 628 680166584 680166510 1.490000e-18 104.0
11 TraesCS7A01G182300 chr6B 96.774 62 1 1 555 616 123500538 123500598 5.360000e-18 102.0
12 TraesCS7A01G182300 chr3B 96.774 62 2 0 555 616 798306142 798306081 1.490000e-18 104.0
13 TraesCS7A01G182300 chr1B 96.825 63 1 1 555 617 121848589 121848650 1.490000e-18 104.0
14 TraesCS7A01G182300 chr4D 95.312 64 2 1 555 618 449455640 449455702 1.930000e-17 100.0
15 TraesCS7A01G182300 chr6A 90.411 73 6 1 555 627 27342955 27342884 8.960000e-16 95.3


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 TraesCS7A01G182300 chr7A 137451304 137454339 3035 True 2570.500000 5033 100.000000 1 3036 2 chr7A.!!$R2 3035
1 TraesCS7A01G182300 chr7B 101495923 101498569 2646 True 1776.000000 2785 91.734000 1 2725 2 chr7B.!!$R1 2724
2 TraesCS7A01G182300 chr7D 137291970 137294758 2788 True 1229.333333 2639 92.600667 1 2725 3 chr7D.!!$R1 2724

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
306 308 0.812811 CCCATGATCCACGTGCTCAG 60.813 60.0 19.5 13.18 34.47 3.35 F
1264 1437 0.423544 AGGTCTTTCAGGGGGAGGAT 59.576 55.0 0.0 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1633 0.110678 TCCATCCTCCTAGCGACGAT 59.889 55.0 0.0 0.0 0.0 3.73 R
2991 3204 0.309302 CCGCTCTCTATGTCACGAGG 59.691 60.0 0.0 0.0 0.0 4.63 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
89 90 1.977854 TGACTTGCCCTACAGTGTCAT 59.022 47.619 0.00 0.00 38.10 3.06
95 96 2.292267 GCCCTACAGTGTCATTGGATG 58.708 52.381 0.00 0.00 0.00 3.51
204 205 2.417933 CCTCCTTTCTGTCGCTTGATTG 59.582 50.000 0.00 0.00 0.00 2.67
238 239 2.247358 TGGATACTAGCATGGCGATCA 58.753 47.619 0.00 0.00 37.61 2.92
306 308 0.812811 CCCATGATCCACGTGCTCAG 60.813 60.000 19.50 13.18 34.47 3.35
343 345 4.195334 GGGCGCCCACCATCTGAT 62.195 66.667 40.73 0.00 35.81 2.90
373 375 2.353208 GGTTTGACTTGTTGCACCACAA 60.353 45.455 4.02 4.02 35.33 3.33
381 383 1.102978 GTTGCACCACAAACAGGAGT 58.897 50.000 0.00 0.00 40.82 3.85
390 392 3.146828 AAACAGGAGTGGGGGTGGC 62.147 63.158 0.00 0.00 0.00 5.01
391 393 4.918360 ACAGGAGTGGGGGTGGCA 62.918 66.667 0.00 0.00 0.00 4.92
394 396 3.721706 GGAGTGGGGGTGGCAGAG 61.722 72.222 0.00 0.00 0.00 3.35
439 441 2.502947 AGGAAAACCTACCCGTATGGAC 59.497 50.000 1.27 0.00 37.49 4.02
453 455 5.054477 CCGTATGGACAATACTACCAAAGG 58.946 45.833 0.00 0.00 39.29 3.11
550 552 8.944212 AAAATCAATAAAAACTACTTCGTCCG 57.056 30.769 0.00 0.00 0.00 4.79
551 553 7.662604 AATCAATAAAAACTACTTCGTCCGT 57.337 32.000 0.00 0.00 0.00 4.69
552 554 6.695292 TCAATAAAAACTACTTCGTCCGTC 57.305 37.500 0.00 0.00 0.00 4.79
553 555 6.449698 TCAATAAAAACTACTTCGTCCGTCT 58.550 36.000 0.00 0.00 0.00 4.18
554 556 6.364165 TCAATAAAAACTACTTCGTCCGTCTG 59.636 38.462 0.00 0.00 0.00 3.51
555 557 3.996150 AAAACTACTTCGTCCGTCTGA 57.004 42.857 0.00 0.00 0.00 3.27
556 558 2.985406 AACTACTTCGTCCGTCTGAC 57.015 50.000 0.00 0.00 40.81 3.51
585 587 8.780846 TTTTTGACTCTAGTGTAGTGTTGAAA 57.219 30.769 0.00 0.00 33.12 2.69
586 588 8.780846 TTTTGACTCTAGTGTAGTGTTGAAAA 57.219 30.769 0.00 0.00 33.12 2.29
587 589 8.780846 TTTGACTCTAGTGTAGTGTTGAAAAA 57.219 30.769 0.00 0.00 33.12 1.94
588 590 7.766219 TGACTCTAGTGTAGTGTTGAAAAAC 57.234 36.000 0.00 0.00 33.12 2.43
589 591 6.474427 TGACTCTAGTGTAGTGTTGAAAAACG 59.526 38.462 0.00 0.00 33.12 3.60
590 592 6.335777 ACTCTAGTGTAGTGTTGAAAAACGT 58.664 36.000 0.00 0.00 0.00 3.99
591 593 6.474751 ACTCTAGTGTAGTGTTGAAAAACGTC 59.525 38.462 0.00 0.00 0.00 4.34
592 594 6.567050 TCTAGTGTAGTGTTGAAAAACGTCT 58.433 36.000 0.00 0.00 0.00 4.18
593 595 7.037438 TCTAGTGTAGTGTTGAAAAACGTCTT 58.963 34.615 0.00 0.00 0.00 3.01
594 596 8.190122 TCTAGTGTAGTGTTGAAAAACGTCTTA 58.810 33.333 0.00 0.00 0.00 2.10
595 597 6.997222 AGTGTAGTGTTGAAAAACGTCTTAC 58.003 36.000 0.00 0.00 0.00 2.34
596 598 6.591062 AGTGTAGTGTTGAAAAACGTCTTACA 59.409 34.615 0.00 0.00 0.00 2.41
597 599 7.279313 AGTGTAGTGTTGAAAAACGTCTTACAT 59.721 33.333 0.00 0.00 0.00 2.29
598 600 7.906527 GTGTAGTGTTGAAAAACGTCTTACATT 59.093 33.333 0.00 0.00 0.00 2.71
599 601 9.096160 TGTAGTGTTGAAAAACGTCTTACATTA 57.904 29.630 0.00 0.00 0.00 1.90
602 604 8.073768 AGTGTTGAAAAACGTCTTACATTATGG 58.926 33.333 0.00 0.00 0.00 2.74
603 605 7.325097 GTGTTGAAAAACGTCTTACATTATGGG 59.675 37.037 0.00 0.00 0.00 4.00
604 606 7.228906 TGTTGAAAAACGTCTTACATTATGGGA 59.771 33.333 0.00 0.00 0.00 4.37
605 607 7.136289 TGAAAAACGTCTTACATTATGGGAC 57.864 36.000 0.00 1.75 0.00 4.46
608 610 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
609 611 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
610 612 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
611 613 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
612 614 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
613 615 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
619 621 2.128507 GGGACGGAGGGAGTAGCTG 61.129 68.421 0.00 0.00 0.00 4.24
645 647 3.950395 GCTCCATTGCTCCTGATAGTTTT 59.050 43.478 0.00 0.00 0.00 2.43
676 678 2.113860 TGAGAGAATTTTGCTCCGGG 57.886 50.000 0.00 0.00 32.82 5.73
681 683 2.937149 GAGAATTTTGCTCCGGGTAGTC 59.063 50.000 0.00 0.00 0.00 2.59
805 809 1.226128 GAGAAGGAATTGCACGCGC 60.226 57.895 5.73 0.00 39.24 6.86
830 834 1.066858 CCACCGCTTATCTGTCACACT 60.067 52.381 0.00 0.00 0.00 3.55
833 837 4.433615 CACCGCTTATCTGTCACACTTAT 58.566 43.478 0.00 0.00 0.00 1.73
834 838 5.451381 CCACCGCTTATCTGTCACACTTATA 60.451 44.000 0.00 0.00 0.00 0.98
835 839 6.216569 CACCGCTTATCTGTCACACTTATAT 58.783 40.000 0.00 0.00 0.00 0.86
836 840 7.368059 CACCGCTTATCTGTCACACTTATATA 58.632 38.462 0.00 0.00 0.00 0.86
837 841 7.326305 CACCGCTTATCTGTCACACTTATATAC 59.674 40.741 0.00 0.00 0.00 1.47
838 842 6.523546 CCGCTTATCTGTCACACTTATATACG 59.476 42.308 0.00 0.00 0.00 3.06
839 843 6.032565 CGCTTATCTGTCACACTTATATACGC 59.967 42.308 0.00 0.00 0.00 4.42
840 844 7.085116 GCTTATCTGTCACACTTATATACGCT 58.915 38.462 0.00 0.00 0.00 5.07
841 845 7.595502 GCTTATCTGTCACACTTATATACGCTT 59.404 37.037 0.00 0.00 0.00 4.68
892 896 0.872388 AAAATCACGGCGTCTGTTCC 59.128 50.000 10.85 0.00 0.00 3.62
895 899 0.968901 ATCACGGCGTCTGTTCCCTA 60.969 55.000 10.85 0.00 0.00 3.53
1067 1228 2.802816 CAGACGTAATAGCTGATTGGCC 59.197 50.000 0.00 0.00 0.00 5.36
1068 1229 1.792949 GACGTAATAGCTGATTGGCCG 59.207 52.381 0.00 0.85 0.00 6.13
1069 1230 0.512952 CGTAATAGCTGATTGGCCGC 59.487 55.000 0.00 0.00 0.00 6.53
1070 1231 0.512952 GTAATAGCTGATTGGCCGCG 59.487 55.000 0.00 0.00 0.00 6.46
1071 1232 1.227999 TAATAGCTGATTGGCCGCGC 61.228 55.000 0.00 0.00 0.00 6.86
1072 1233 2.947938 AATAGCTGATTGGCCGCGCT 62.948 55.000 5.56 3.70 34.88 5.92
1170 1343 2.589442 GGACGTGAACCGCAACCA 60.589 61.111 0.00 0.00 41.42 3.67
1264 1437 0.423544 AGGTCTTTCAGGGGGAGGAT 59.576 55.000 0.00 0.00 0.00 3.24
1439 1612 4.988716 TCGTGGTCCTGCGGGAGT 62.989 66.667 16.70 0.00 43.12 3.85
1574 1747 1.252215 TATCGTGCAGGAACCCGACA 61.252 55.000 13.87 0.00 31.43 4.35
1583 1756 4.178169 AACCCGACAACGTGCCCA 62.178 61.111 0.00 0.00 37.88 5.36
1801 1977 2.360852 GTGCCAGTGAGCATGCCT 60.361 61.111 15.66 0.77 46.24 4.75
1815 1991 1.417517 CATGCCTAGGATGGTGCACTA 59.582 52.381 17.98 11.97 36.41 2.74
1834 2010 9.096160 GTGCACTAAGATTATATGAGATCATGG 57.904 37.037 10.32 0.00 37.15 3.66
1926 2102 7.551262 ACTCCTTTGTCATTAATATTGTGCGTA 59.449 33.333 0.00 0.00 0.00 4.42
2017 2204 4.437682 ACCAGTTGTTTCATGGAGAGAA 57.562 40.909 0.00 0.00 37.54 2.87
2029 2216 5.687780 TCATGGAGAGAATACATGCATTGT 58.312 37.500 0.00 1.44 41.22 2.71
2031 2218 4.454678 TGGAGAGAATACATGCATTGTCC 58.545 43.478 11.24 0.00 39.87 4.02
2053 2244 6.313905 GTCCAAAAGAGAAAGATATGCTCGAA 59.686 38.462 0.00 0.00 33.98 3.71
2076 2267 4.775780 ACTAGGGTTCTAATGTGCAGTACA 59.224 41.667 0.00 0.00 44.87 2.90
2077 2268 8.529053 GAACTAGGGTTCTAATGTGCAGTACAC 61.529 44.444 0.00 0.00 46.54 2.90
2095 2286 4.370364 ACACTGCACTAAACTTTTGTGG 57.630 40.909 15.12 5.08 32.85 4.17
2122 2313 5.241662 AGTACTCTTTGTGATCAGAAAGGC 58.758 41.667 33.02 23.30 40.73 4.35
2240 2431 3.467226 GCAGTGGCTAGGGCGGTA 61.467 66.667 0.00 0.00 39.81 4.02
2241 2432 3.026431 GCAGTGGCTAGGGCGGTAA 62.026 63.158 0.00 0.00 39.81 2.85
2242 2433 1.830145 CAGTGGCTAGGGCGGTAAT 59.170 57.895 0.00 0.00 39.81 1.89
2291 2482 0.801067 CTCCGGCCGAGAAACTTACG 60.801 60.000 30.73 5.39 41.63 3.18
2329 2542 5.968582 TCGCTCACAATGAGAGAGAAAACAA 60.969 40.000 11.79 0.00 45.93 2.83
2475 2688 1.722464 CAGATTTTGGTTGCATGCACG 59.278 47.619 22.58 0.00 0.00 5.34
2525 2738 1.741770 GCTAGACAACTGTGGCCCG 60.742 63.158 0.00 0.00 30.22 6.13
2540 2753 1.592223 CCCGTCTCGAAGCTTCCTT 59.408 57.895 20.62 0.00 0.00 3.36
2554 2767 2.031682 GCTTCCTTATGGCTTATGTGCG 60.032 50.000 0.00 0.00 0.00 5.34
2627 2840 6.312399 TCTGAAACATGGTGTGATTTGTAC 57.688 37.500 0.00 0.00 0.00 2.90
2642 2855 7.276878 TGTGATTTGTACAGTGTATAATGGTCG 59.723 37.037 12.58 0.00 0.00 4.79
2643 2856 6.759356 TGATTTGTACAGTGTATAATGGTCGG 59.241 38.462 12.58 0.00 0.00 4.79
2664 2877 8.443937 GGTCGGAGAATAAATATTTGCATCTAC 58.556 37.037 11.05 10.38 39.69 2.59
3008 3221 3.784701 TTTCCTCGTGACATAGAGAGC 57.215 47.619 11.15 0.00 36.65 4.09
3009 3222 1.300481 TCCTCGTGACATAGAGAGCG 58.700 55.000 11.15 0.00 36.65 5.03
3010 3223 0.309302 CCTCGTGACATAGAGAGCGG 59.691 60.000 11.15 0.00 36.65 5.52
3011 3224 1.018148 CTCGTGACATAGAGAGCGGT 58.982 55.000 5.30 0.00 36.65 5.68
3012 3225 1.402259 CTCGTGACATAGAGAGCGGTT 59.598 52.381 5.30 0.00 36.65 4.44
3013 3226 1.400846 TCGTGACATAGAGAGCGGTTC 59.599 52.381 0.00 0.00 0.00 3.62
3014 3227 1.534175 CGTGACATAGAGAGCGGTTCC 60.534 57.143 0.00 0.00 0.00 3.62
3015 3228 1.751924 GTGACATAGAGAGCGGTTCCT 59.248 52.381 0.00 0.00 0.00 3.36
3016 3229 2.166664 GTGACATAGAGAGCGGTTCCTT 59.833 50.000 0.00 0.00 0.00 3.36
3017 3230 3.380637 GTGACATAGAGAGCGGTTCCTTA 59.619 47.826 0.00 0.00 0.00 2.69
3018 3231 4.038162 GTGACATAGAGAGCGGTTCCTTAT 59.962 45.833 0.00 0.00 0.00 1.73
3019 3232 4.649674 TGACATAGAGAGCGGTTCCTTATT 59.350 41.667 0.00 0.00 0.00 1.40
3020 3233 5.831525 TGACATAGAGAGCGGTTCCTTATTA 59.168 40.000 0.00 0.00 0.00 0.98
3021 3234 6.493802 TGACATAGAGAGCGGTTCCTTATTAT 59.506 38.462 0.00 0.00 0.00 1.28
3022 3235 6.692486 ACATAGAGAGCGGTTCCTTATTATG 58.308 40.000 0.00 0.00 0.00 1.90
3023 3236 3.996480 AGAGAGCGGTTCCTTATTATGC 58.004 45.455 0.00 0.00 0.00 3.14
3024 3237 2.731976 GAGAGCGGTTCCTTATTATGCG 59.268 50.000 0.00 0.00 0.00 4.73
3025 3238 2.364324 AGAGCGGTTCCTTATTATGCGA 59.636 45.455 0.00 0.00 0.00 5.10
3026 3239 2.475487 GAGCGGTTCCTTATTATGCGAC 59.525 50.000 0.00 0.00 0.00 5.19
3027 3240 2.102588 AGCGGTTCCTTATTATGCGACT 59.897 45.455 0.00 0.00 0.00 4.18
3028 3241 2.475487 GCGGTTCCTTATTATGCGACTC 59.525 50.000 0.00 0.00 0.00 3.36
3029 3242 3.799232 GCGGTTCCTTATTATGCGACTCT 60.799 47.826 0.00 0.00 0.00 3.24
3030 3243 3.982058 CGGTTCCTTATTATGCGACTCTC 59.018 47.826 0.00 0.00 0.00 3.20
3031 3244 3.982058 GGTTCCTTATTATGCGACTCTCG 59.018 47.826 0.00 0.00 43.89 4.04
3032 3245 4.261489 GGTTCCTTATTATGCGACTCTCGA 60.261 45.833 0.00 0.00 43.74 4.04
3033 3246 4.485024 TCCTTATTATGCGACTCTCGAC 57.515 45.455 0.00 0.00 43.74 4.20
3034 3247 4.135306 TCCTTATTATGCGACTCTCGACT 58.865 43.478 0.00 0.00 43.74 4.18
3035 3248 4.213694 TCCTTATTATGCGACTCTCGACTC 59.786 45.833 0.00 0.00 43.74 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.297427 AGGTAAGAGGGTTAGGGCTAAT 57.703 45.455 0.00 0.00 0.00 1.73
77 78 4.186926 CTGACATCCAATGACACTGTAGG 58.813 47.826 0.00 0.00 31.98 3.18
89 90 6.373005 TGAAAATCCTAGACTGACATCCAA 57.627 37.500 0.00 0.00 0.00 3.53
95 96 8.364142 ACTGCTATATGAAAATCCTAGACTGAC 58.636 37.037 0.00 0.00 0.00 3.51
238 239 1.032794 TGGCTCAGCGTTATCGATCT 58.967 50.000 0.00 0.00 39.71 2.75
251 252 5.931294 TGGTACGGAATAATTTATGGCTCA 58.069 37.500 0.00 0.00 0.00 4.26
337 339 4.288105 AGTCAAACCTCTTCCACATCAGAT 59.712 41.667 0.00 0.00 0.00 2.90
343 345 3.644966 ACAAGTCAAACCTCTTCCACA 57.355 42.857 0.00 0.00 0.00 4.17
373 375 3.580319 GCCACCCCCACTCCTGTT 61.580 66.667 0.00 0.00 0.00 3.16
381 383 2.589157 CGTTACTCTGCCACCCCCA 61.589 63.158 0.00 0.00 0.00 4.96
390 392 0.249073 CCGATGAGGCCGTTACTCTG 60.249 60.000 0.00 0.00 35.98 3.35
391 393 0.395311 TCCGATGAGGCCGTTACTCT 60.395 55.000 0.00 0.00 40.77 3.24
394 396 4.732106 CTCCGATGAGGCCGTTAC 57.268 61.111 0.00 0.00 40.77 2.50
405 407 0.044244 TTTTCCTCCCCTCCTCCGAT 59.956 55.000 0.00 0.00 0.00 4.18
560 562 8.780846 TTTCAACACTACACTAGAGTCAAAAA 57.219 30.769 0.00 0.00 0.00 1.94
561 563 8.780846 TTTTCAACACTACACTAGAGTCAAAA 57.219 30.769 0.00 0.00 0.00 2.44
562 564 8.662141 GTTTTTCAACACTACACTAGAGTCAAA 58.338 33.333 0.00 0.00 32.54 2.69
563 565 7.009815 CGTTTTTCAACACTACACTAGAGTCAA 59.990 37.037 0.00 0.00 32.54 3.18
564 566 6.474427 CGTTTTTCAACACTACACTAGAGTCA 59.526 38.462 0.00 0.00 32.54 3.41
565 567 6.474751 ACGTTTTTCAACACTACACTAGAGTC 59.525 38.462 0.00 0.00 32.54 3.36
566 568 6.335777 ACGTTTTTCAACACTACACTAGAGT 58.664 36.000 0.00 0.00 32.54 3.24
567 569 6.696148 AGACGTTTTTCAACACTACACTAGAG 59.304 38.462 0.00 0.00 32.54 2.43
568 570 6.567050 AGACGTTTTTCAACACTACACTAGA 58.433 36.000 0.00 0.00 32.54 2.43
569 571 6.823678 AGACGTTTTTCAACACTACACTAG 57.176 37.500 0.00 0.00 32.54 2.57
570 572 7.758980 TGTAAGACGTTTTTCAACACTACACTA 59.241 33.333 0.00 0.00 32.54 2.74
571 573 6.591062 TGTAAGACGTTTTTCAACACTACACT 59.409 34.615 0.00 0.00 32.54 3.55
572 574 6.764094 TGTAAGACGTTTTTCAACACTACAC 58.236 36.000 0.00 0.00 32.54 2.90
573 575 6.964741 TGTAAGACGTTTTTCAACACTACA 57.035 33.333 0.00 0.00 32.54 2.74
576 578 8.073768 CCATAATGTAAGACGTTTTTCAACACT 58.926 33.333 2.36 0.00 32.54 3.55
577 579 7.325097 CCCATAATGTAAGACGTTTTTCAACAC 59.675 37.037 2.36 0.00 32.54 3.32
578 580 7.228906 TCCCATAATGTAAGACGTTTTTCAACA 59.771 33.333 2.36 0.00 32.54 3.33
579 581 7.536281 GTCCCATAATGTAAGACGTTTTTCAAC 59.464 37.037 2.36 0.00 0.00 3.18
580 582 7.571613 CGTCCCATAATGTAAGACGTTTTTCAA 60.572 37.037 2.36 0.00 43.89 2.69
581 583 6.128499 CGTCCCATAATGTAAGACGTTTTTCA 60.128 38.462 0.00 0.00 43.89 2.69
582 584 6.245724 CGTCCCATAATGTAAGACGTTTTTC 58.754 40.000 0.00 0.00 43.89 2.29
583 585 5.122711 CCGTCCCATAATGTAAGACGTTTTT 59.877 40.000 9.63 0.00 46.62 1.94
584 586 4.632688 CCGTCCCATAATGTAAGACGTTTT 59.367 41.667 9.63 0.00 46.62 2.43
585 587 4.081531 TCCGTCCCATAATGTAAGACGTTT 60.082 41.667 9.63 0.00 46.62 3.60
586 588 3.448301 TCCGTCCCATAATGTAAGACGTT 59.552 43.478 9.63 0.00 46.62 3.99
587 589 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
589 591 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
590 592 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
591 593 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
592 594 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
593 595 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
594 596 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
595 597 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
596 598 2.890814 CTACTCCCTCCGTCCCATAAT 58.109 52.381 0.00 0.00 0.00 1.28
597 599 1.756690 GCTACTCCCTCCGTCCCATAA 60.757 57.143 0.00 0.00 0.00 1.90
598 600 0.178970 GCTACTCCCTCCGTCCCATA 60.179 60.000 0.00 0.00 0.00 2.74
599 601 1.457831 GCTACTCCCTCCGTCCCAT 60.458 63.158 0.00 0.00 0.00 4.00
600 602 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
601 603 2.128507 CAGCTACTCCCTCCGTCCC 61.129 68.421 0.00 0.00 0.00 4.46
602 604 1.380112 ACAGCTACTCCCTCCGTCC 60.380 63.158 0.00 0.00 0.00 4.79
603 605 0.966370 ACACAGCTACTCCCTCCGTC 60.966 60.000 0.00 0.00 0.00 4.79
604 606 1.076906 ACACAGCTACTCCCTCCGT 59.923 57.895 0.00 0.00 0.00 4.69
605 607 1.513158 CACACAGCTACTCCCTCCG 59.487 63.158 0.00 0.00 0.00 4.63
606 608 1.219393 GCACACAGCTACTCCCTCC 59.781 63.158 0.00 0.00 41.15 4.30
607 609 4.921834 GCACACAGCTACTCCCTC 57.078 61.111 0.00 0.00 41.15 4.30
619 621 0.321919 TCAGGAGCAATGGAGCACAC 60.322 55.000 0.00 0.00 36.85 3.82
661 663 2.572104 AGACTACCCGGAGCAAAATTCT 59.428 45.455 0.73 0.00 0.00 2.40
689 693 5.383476 CAGCTATCAGGATCAAATTCCCTT 58.617 41.667 0.00 0.00 36.35 3.95
700 704 1.073474 TGCCCCCAGCTATCAGGAT 60.073 57.895 0.00 0.00 44.23 3.24
756 760 3.029074 CGATTTTAATGTACAGCTGCGC 58.971 45.455 15.27 0.00 0.00 6.09
757 761 3.607439 CCGATTTTAATGTACAGCTGCG 58.393 45.455 15.27 4.24 0.00 5.18
758 762 3.363178 GCCGATTTTAATGTACAGCTGC 58.637 45.455 15.27 0.00 0.00 5.25
805 809 0.469917 ACAGATAAGCGGTGGATGGG 59.530 55.000 0.00 0.00 0.00 4.00
814 818 6.032565 GCGTATATAAGTGTGACAGATAAGCG 59.967 42.308 0.00 0.00 0.00 4.68
833 837 8.365647 CCCCTTCTTTCTCTTATTAAGCGTATA 58.634 37.037 0.00 0.00 0.00 1.47
834 838 7.217906 CCCCTTCTTTCTCTTATTAAGCGTAT 58.782 38.462 0.00 0.00 0.00 3.06
835 839 6.407752 CCCCCTTCTTTCTCTTATTAAGCGTA 60.408 42.308 0.00 0.00 0.00 4.42
836 840 5.429130 CCCCTTCTTTCTCTTATTAAGCGT 58.571 41.667 0.00 0.00 0.00 5.07
837 841 4.816925 CCCCCTTCTTTCTCTTATTAAGCG 59.183 45.833 0.00 0.00 0.00 4.68
981 1142 0.460987 GAGGTTCTGTGGAGATGCGG 60.461 60.000 0.00 0.00 0.00 5.69
1052 1213 1.227999 GCGCGGCCAATCAGCTATTA 61.228 55.000 8.83 0.00 33.54 0.98
1084 1245 1.948635 GAAGAGCATCGCGGAGAGC 60.949 63.158 6.13 5.52 42.67 4.09
1085 1246 1.656875 CGAAGAGCATCGCGGAGAG 60.657 63.158 6.13 0.00 42.67 3.20
1086 1247 2.409243 CGAAGAGCATCGCGGAGA 59.591 61.111 6.13 0.00 42.67 3.71
1253 1426 3.496160 CCAGCCATCCTCCCCCTG 61.496 72.222 0.00 0.00 0.00 4.45
1460 1633 0.110678 TCCATCCTCCTAGCGACGAT 59.889 55.000 0.00 0.00 0.00 3.73
1468 1641 2.520982 CGGCCGTCCATCCTCCTA 60.521 66.667 19.50 0.00 0.00 2.94
1583 1756 1.215655 GCTTCTGCGTCGTCTGTGTT 61.216 55.000 0.00 0.00 0.00 3.32
1663 1839 4.969196 ACAGTGGCTGGCACGTCG 62.969 66.667 25.76 20.33 35.51 5.12
1801 1977 8.664669 TCATATAATCTTAGTGCACCATCCTA 57.335 34.615 14.63 0.00 0.00 2.94
1815 1991 9.552695 TCTGGTACCATGATCTCATATAATCTT 57.447 33.333 16.75 0.00 34.26 2.40
1834 2010 3.081804 CAAATGACTTGGGGTCTGGTAC 58.918 50.000 0.00 0.00 44.74 3.34
1838 2014 3.423539 TCTCAAATGACTTGGGGTCTG 57.576 47.619 0.00 0.00 44.74 3.51
1926 2102 7.718753 CCAAAGATGGCTACAGATAATTCTTCT 59.281 37.037 0.00 0.00 40.58 2.85
1935 2111 6.296662 TTCTTTCTCCAAAGATGGCTACAGAT 60.297 38.462 0.00 0.00 46.05 2.90
2017 2204 6.839124 TTCTCTTTTGGACAATGCATGTAT 57.161 33.333 0.00 0.00 44.12 2.29
2029 2216 5.977635 TCGAGCATATCTTTCTCTTTTGGA 58.022 37.500 0.00 0.00 0.00 3.53
2031 2218 7.301068 AGTTCGAGCATATCTTTCTCTTTTG 57.699 36.000 1.01 0.00 0.00 2.44
2053 2244 4.775780 TGTACTGCACATTAGAACCCTAGT 59.224 41.667 0.00 0.00 30.04 2.57
2076 2267 3.064820 CGACCACAAAAGTTTAGTGCAGT 59.935 43.478 0.00 0.00 32.09 4.40
2077 2268 3.311322 TCGACCACAAAAGTTTAGTGCAG 59.689 43.478 0.00 0.00 32.09 4.41
2080 2271 5.751990 AGTACTCGACCACAAAAGTTTAGTG 59.248 40.000 0.00 0.00 0.00 2.74
2095 2286 5.298197 TCTGATCACAAAGAGTACTCGAC 57.702 43.478 17.07 4.89 34.09 4.20
2239 2430 5.001232 GCAACAGACTGGTGGAGTTAATTA 58.999 41.667 21.80 0.00 35.13 1.40
2240 2431 3.821033 GCAACAGACTGGTGGAGTTAATT 59.179 43.478 21.80 0.00 35.13 1.40
2241 2432 3.073062 AGCAACAGACTGGTGGAGTTAAT 59.927 43.478 21.80 0.00 35.13 1.40
2242 2433 2.438021 AGCAACAGACTGGTGGAGTTAA 59.562 45.455 21.80 0.00 35.13 2.01
2312 2503 6.367149 TCATCGACTTGTTTTCTCTCTCATTG 59.633 38.462 0.00 0.00 0.00 2.82
2329 2542 1.544691 AGTAACGGCTTGTCATCGACT 59.455 47.619 0.00 0.00 33.15 4.18
2525 2738 2.159028 AGCCATAAGGAAGCTTCGAGAC 60.159 50.000 19.91 6.36 36.89 3.36
2578 2791 5.132897 TCAAGCCCATGTTTAATGTGTTC 57.867 39.130 0.00 0.00 0.00 3.18
2627 2840 8.833231 ATTTATTCTCCGACCATTATACACTG 57.167 34.615 0.00 0.00 0.00 3.66
2682 2895 2.439507 TCTTTGGCCATCATAGACTCCC 59.560 50.000 6.09 0.00 30.32 4.30
2986 3199 4.495422 GCTCTCTATGTCACGAGGAAAAA 58.505 43.478 0.00 0.00 0.00 1.94
2987 3200 3.427638 CGCTCTCTATGTCACGAGGAAAA 60.428 47.826 0.00 0.00 0.00 2.29
2988 3201 2.097629 CGCTCTCTATGTCACGAGGAAA 59.902 50.000 0.00 0.00 0.00 3.13
2989 3202 1.671328 CGCTCTCTATGTCACGAGGAA 59.329 52.381 0.00 0.00 0.00 3.36
2990 3203 1.300481 CGCTCTCTATGTCACGAGGA 58.700 55.000 0.00 0.00 0.00 3.71
2991 3204 0.309302 CCGCTCTCTATGTCACGAGG 59.691 60.000 0.00 0.00 0.00 4.63
2992 3205 1.018148 ACCGCTCTCTATGTCACGAG 58.982 55.000 0.00 0.00 0.00 4.18
2993 3206 1.400846 GAACCGCTCTCTATGTCACGA 59.599 52.381 0.00 0.00 0.00 4.35
2994 3207 1.534175 GGAACCGCTCTCTATGTCACG 60.534 57.143 0.00 0.00 0.00 4.35
2995 3208 1.751924 AGGAACCGCTCTCTATGTCAC 59.248 52.381 0.00 0.00 0.00 3.67
2996 3209 2.145397 AGGAACCGCTCTCTATGTCA 57.855 50.000 0.00 0.00 0.00 3.58
2997 3210 4.857509 ATAAGGAACCGCTCTCTATGTC 57.142 45.455 0.00 0.00 0.00 3.06
2998 3211 6.692486 CATAATAAGGAACCGCTCTCTATGT 58.308 40.000 0.00 0.00 0.00 2.29
2999 3212 5.578727 GCATAATAAGGAACCGCTCTCTATG 59.421 44.000 0.00 0.00 0.00 2.23
3000 3213 5.622460 CGCATAATAAGGAACCGCTCTCTAT 60.622 44.000 0.00 0.00 0.00 1.98
3001 3214 4.321008 CGCATAATAAGGAACCGCTCTCTA 60.321 45.833 0.00 0.00 0.00 2.43
3002 3215 3.553096 CGCATAATAAGGAACCGCTCTCT 60.553 47.826 0.00 0.00 0.00 3.10
3003 3216 2.731976 CGCATAATAAGGAACCGCTCTC 59.268 50.000 0.00 0.00 0.00 3.20
3004 3217 2.364324 TCGCATAATAAGGAACCGCTCT 59.636 45.455 0.00 0.00 0.00 4.09
3005 3218 2.475487 GTCGCATAATAAGGAACCGCTC 59.525 50.000 0.00 0.00 0.00 5.03
3006 3219 2.102588 AGTCGCATAATAAGGAACCGCT 59.897 45.455 0.00 0.00 0.00 5.52
3007 3220 2.475487 GAGTCGCATAATAAGGAACCGC 59.525 50.000 0.00 0.00 0.00 5.68
3008 3221 3.978687 AGAGTCGCATAATAAGGAACCG 58.021 45.455 0.00 0.00 0.00 4.44
3009 3222 3.982058 CGAGAGTCGCATAATAAGGAACC 59.018 47.826 0.00 0.00 31.14 3.62
3010 3223 4.676018 GTCGAGAGTCGCATAATAAGGAAC 59.324 45.833 0.00 0.00 40.21 3.62
3011 3224 4.579340 AGTCGAGAGTCGCATAATAAGGAA 59.421 41.667 0.00 0.00 40.21 3.36
3012 3225 4.135306 AGTCGAGAGTCGCATAATAAGGA 58.865 43.478 0.00 0.00 40.21 3.36
3013 3226 4.468643 GAGTCGAGAGTCGCATAATAAGG 58.531 47.826 0.00 0.00 40.21 2.69


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

AutoCloner maintained by Alex Coulton.