Multiple sequence alignment - TraesCS2D01G471600

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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 TraesCS2D01G471600 chr2D 100.000 2471 0 0 1 2471 575365182 575367652 0.000000e+00 4564.0
1 TraesCS2D01G471600 chr2D 92.683 41 3 0 1134 1174 621755342 621755302 2.650000e-05 60.2
2 TraesCS2D01G471600 chr2A 87.487 967 55 21 576 1476 713668386 713667420 0.000000e+00 1055.0
3 TraesCS2D01G471600 chr2A 92.970 569 28 4 1519 2085 713667344 713666786 0.000000e+00 819.0
4 TraesCS2D01G471600 chr2A 93.538 325 19 2 2148 2471 713645286 713644963 1.330000e-132 483.0
5 TraesCS2D01G471600 chr2A 82.447 564 47 10 1 548 713669417 713668890 1.740000e-121 446.0
6 TraesCS2D01G471600 chr2A 91.935 124 9 1 2090 2212 713645408 713645285 3.270000e-39 172.0
7 TraesCS2D01G471600 chr2A 83.465 127 16 3 1072 1197 712859585 712859463 2.010000e-21 113.0
8 TraesCS2D01G471600 chr2A 81.022 137 26 0 1032 1168 714045247 714045111 2.600000e-20 110.0
9 TraesCS2D01G471600 chr2A 96.491 57 2 0 2119 2175 713645565 713645509 7.270000e-16 95.3
10 TraesCS2D01G471600 chr5A 79.602 201 32 7 2267 2465 649197126 649197319 4.290000e-28 135.0
11 TraesCS2D01G471600 chr2B 81.102 127 22 2 1072 1197 690666778 690666653 1.560000e-17 100.0
12 TraesCS2D01G471600 chr2B 77.419 124 27 1 1068 1190 693232666 693232543 3.410000e-09 73.1
13 TraesCS2D01G471600 chr7A 74.026 154 37 3 2312 2464 641342874 641343025 2.650000e-05 60.2
14 TraesCS2D01G471600 chr7D 76.786 112 20 5 498 607 53806006 53805899 9.540000e-05 58.4
15 TraesCS2D01G471600 chr4A 84.746 59 8 1 532 590 668697824 668697881 9.540000e-05 58.4
16 TraesCS2D01G471600 chr7B 86.275 51 7 0 2231 2281 432932051 432932001 3.430000e-04 56.5
17 TraesCS2D01G471600 chr4B 100.000 30 0 0 2231 2260 621980642 621980671 3.430000e-04 56.5


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 TraesCS2D01G471600 chr2D 575365182 575367652 2470 False 4564.000000 4564 100.000000 1 2471 1 chr2D.!!$F1 2470
1 TraesCS2D01G471600 chr2A 713666786 713669417 2631 True 773.333333 1055 87.634667 1 2085 3 chr2A.!!$R4 2084
2 TraesCS2D01G471600 chr2A 713644963 713645565 602 True 250.100000 483 93.988000 2090 2471 3 chr2A.!!$R3 381

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
551 567 0.037975 TTGCGAGTTCGGTTAGGTCC 60.038 55.0 3.5 0.0 40.23 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2702 0.03601 CAGGCTTTCGATGAGGTGGT 60.036 55.0 0.0 0.0 0.0 4.16 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
54 55 9.490663 CTTTTCATCTGGCTAATTACGTAAAAG 57.509 33.333 12.81 13.43 0.00 2.27
58 59 9.090692 TCATCTGGCTAATTACGTAAAAGTTAC 57.909 33.333 12.81 8.30 0.00 2.50
128 129 7.462724 CGTTGTGAAAAGGAAAAGAAATGACAC 60.463 37.037 0.00 0.00 0.00 3.67
149 150 3.088532 CGACCCAAAATCCATGGAAGAA 58.911 45.455 20.67 0.00 40.56 2.52
160 161 2.283298 CATGGAAGAACTGGATGTCGG 58.717 52.381 0.00 0.00 0.00 4.79
166 167 1.971357 AGAACTGGATGTCGGAAGTGT 59.029 47.619 0.00 0.00 0.00 3.55
236 240 4.006780 AGCCATGGTCCAATTCAAAAAC 57.993 40.909 14.67 0.00 0.00 2.43
237 241 3.390639 AGCCATGGTCCAATTCAAAAACA 59.609 39.130 14.67 0.00 0.00 2.83
241 245 6.054295 CCATGGTCCAATTCAAAAACAGAAA 58.946 36.000 2.57 0.00 0.00 2.52
258 262 3.928375 CAGAAAACCTACATTTGCCATGC 59.072 43.478 0.00 0.00 0.00 4.06
301 305 0.530288 AATTTCCGCCATTTGGGACG 59.470 50.000 0.00 0.00 40.01 4.79
342 350 3.865011 TTGCCATGCGAATGTACAAAT 57.135 38.095 0.00 0.00 0.00 2.32
345 353 2.853594 GCCATGCGAATGTACAAATGTG 59.146 45.455 0.00 0.00 0.00 3.21
346 354 3.673052 GCCATGCGAATGTACAAATGTGT 60.673 43.478 0.00 0.00 42.09 3.72
362 377 8.553459 ACAAATGTGTACCAATGTTTCAAAAA 57.447 26.923 0.00 0.00 35.72 1.94
397 413 2.110213 GAATATGGGTGGCGGCGA 59.890 61.111 12.98 0.00 0.00 5.54
412 428 4.452733 CGACGGGAAGGGCTGGTC 62.453 72.222 0.00 0.00 0.00 4.02
413 429 4.452733 GACGGGAAGGGCTGGTCG 62.453 72.222 0.00 0.00 0.00 4.79
416 432 4.475135 GGGAAGGGCTGGTCGCTC 62.475 72.222 0.00 0.00 40.36 5.03
417 433 4.821589 GGAAGGGCTGGTCGCTCG 62.822 72.222 0.00 0.00 46.47 5.03
418 434 4.821589 GAAGGGCTGGTCGCTCGG 62.822 72.222 0.00 0.00 46.47 4.63
433 449 4.465446 CGGGAGGGAGAGAGGGCA 62.465 72.222 0.00 0.00 0.00 5.36
441 457 0.545646 GGAGAGAGGGCAGCTGAAAT 59.454 55.000 20.43 0.39 0.00 2.17
450 466 6.010219 AGAGGGCAGCTGAAATTTTTACTTA 58.990 36.000 20.43 0.00 0.00 2.24
453 469 4.558860 GGCAGCTGAAATTTTTACTTAGCG 59.441 41.667 20.43 0.00 35.04 4.26
455 471 5.153513 CAGCTGAAATTTTTACTTAGCGCA 58.846 37.500 8.42 0.00 35.04 6.09
476 492 4.474113 CAGCCGAGGTCGAGTATATTTAC 58.526 47.826 0.00 0.00 43.02 2.01
482 498 5.105834 AGGTCGAGTATATTTACGAGTGC 57.894 43.478 0.00 0.00 35.52 4.40
485 501 5.505324 GGTCGAGTATATTTACGAGTGCTGT 60.505 44.000 0.00 0.00 35.52 4.40
491 507 7.101054 AGTATATTTACGAGTGCTGTTGGAAA 58.899 34.615 0.00 0.00 33.32 3.13
493 509 5.705609 ATTTACGAGTGCTGTTGGAAATT 57.294 34.783 0.00 0.00 0.00 1.82
526 542 2.994578 GAGGACAAACTTTACTCCGCTC 59.005 50.000 0.00 0.00 0.00 5.03
548 564 0.794473 GGTTTGCGAGTTCGGTTAGG 59.206 55.000 3.50 0.00 40.23 2.69
549 565 1.505425 GTTTGCGAGTTCGGTTAGGT 58.495 50.000 3.50 0.00 40.23 3.08
551 567 0.037975 TTGCGAGTTCGGTTAGGTCC 60.038 55.000 3.50 0.00 40.23 4.46
558 574 4.821177 CGGTTAGGTCCGGTTAGC 57.179 61.111 0.00 0.00 45.88 3.09
559 575 1.142531 CGGTTAGGTCCGGTTAGCC 59.857 63.158 0.00 3.89 45.88 3.93
560 576 1.606885 CGGTTAGGTCCGGTTAGCCA 61.607 60.000 0.00 0.00 45.88 4.75
561 577 0.107993 GGTTAGGTCCGGTTAGCCAC 60.108 60.000 0.00 0.00 34.09 5.01
562 578 0.459063 GTTAGGTCCGGTTAGCCACG 60.459 60.000 0.00 0.00 34.09 4.94
568 584 1.929169 GTCCGGTTAGCCACGTATTTC 59.071 52.381 0.00 0.00 34.09 2.17
584 600 5.595952 ACGTATTTCCCTCTACTAACCGATT 59.404 40.000 0.00 0.00 0.00 3.34
585 601 6.772716 ACGTATTTCCCTCTACTAACCGATTA 59.227 38.462 0.00 0.00 0.00 1.75
586 602 7.449704 ACGTATTTCCCTCTACTAACCGATTAT 59.550 37.037 0.00 0.00 0.00 1.28
587 603 8.950210 CGTATTTCCCTCTACTAACCGATTATA 58.050 37.037 0.00 0.00 0.00 0.98
592 1095 4.954826 CCTCTACTAACCGATTATAGGGGG 59.045 50.000 0.00 0.00 30.88 5.40
594 1097 5.969086 TCTACTAACCGATTATAGGGGGTT 58.031 41.667 8.05 8.05 44.49 4.11
597 1100 2.201523 ACCGATTATAGGGGGTTGGT 57.798 50.000 0.00 0.00 0.00 3.67
602 1105 4.020485 CCGATTATAGGGGGTTGGTTAGAG 60.020 50.000 0.00 0.00 0.00 2.43
608 1111 1.631898 GGGGGTTGGTTAGAGTTGCTA 59.368 52.381 0.00 0.00 0.00 3.49
628 1131 2.467566 TAAGGGCCTTCGAGTTGTTC 57.532 50.000 24.77 0.00 0.00 3.18
631 1134 0.534203 GGGCCTTCGAGTTGTTCACA 60.534 55.000 0.84 0.00 0.00 3.58
658 1161 7.426456 CGAAATTGTACAATACTGCAATCAGAC 59.574 37.037 21.07 0.00 42.95 3.51
672 1175 4.025979 GCAATCAGACCTATAACGTTTCCG 60.026 45.833 5.91 0.00 40.83 4.30
714 1242 1.298413 ATACGCGCGTGTCTAGCTG 60.298 57.895 42.78 7.98 0.00 4.24
747 1275 4.554723 CGTGAGTTTAAAAGGGAAGCAGTG 60.555 45.833 0.00 0.00 0.00 3.66
780 1326 3.194861 GCGTGCCCTTTTTCTTTTCTTT 58.805 40.909 0.00 0.00 0.00 2.52
827 1378 1.373748 GTACACGTGTCACCGGCAT 60.374 57.895 27.16 0.00 0.00 4.40
837 1388 1.401552 GTCACCGGCATGTACGTAGTA 59.598 52.381 0.00 0.00 45.11 1.82
897 1461 9.044646 TGGTATCCTCCTAGTATAGTACTGTAG 57.955 40.741 5.39 1.45 39.81 2.74
906 1470 7.598493 CCTAGTATAGTACTGTAGTCCGTTCTC 59.402 44.444 10.00 0.00 39.81 2.87
941 1509 9.461312 AAAACAGCTTACAAATATAGATGACCA 57.539 29.630 0.00 0.00 0.00 4.02
948 1516 8.974060 TTACAAATATAGATGACCAGGTTTCC 57.026 34.615 0.00 0.00 0.00 3.13
984 1552 4.986708 TTTGCCCTTGGTCCGCCC 62.987 66.667 0.00 0.00 0.00 6.13
1009 1578 3.242011 ACTTGATTTGCCATGGGAAACT 58.758 40.909 30.92 20.17 38.20 2.66
1017 1586 1.089920 CCATGGGAAACTTCAGCTCG 58.910 55.000 2.85 0.00 0.00 5.03
1019 1588 1.466167 CATGGGAAACTTCAGCTCGTG 59.534 52.381 0.00 0.00 0.00 4.35
1050 1619 1.511464 GACGTCGTCGAGATGCGTT 60.511 57.895 10.05 0.00 39.47 4.84
1140 1709 1.266989 GGCAACTGTGTAAGCTCCAAC 59.733 52.381 0.00 0.00 0.00 3.77
1174 1743 1.218047 GGCTACGACTGGTGCATCA 59.782 57.895 0.00 0.00 0.00 3.07
1181 1750 3.149196 ACGACTGGTGCATCAATTTCTT 58.851 40.909 0.00 0.00 0.00 2.52
1190 1759 2.478539 GCATCAATTTCTTCCCTGACGC 60.479 50.000 0.00 0.00 0.00 5.19
1194 1763 2.005971 ATTTCTTCCCTGACGCGTAC 57.994 50.000 13.97 6.75 0.00 3.67
1195 1764 0.675083 TTTCTTCCCTGACGCGTACA 59.325 50.000 13.97 11.56 0.00 2.90
1196 1765 0.242825 TTCTTCCCTGACGCGTACAG 59.757 55.000 23.28 23.28 35.43 2.74
1201 1770 2.258591 CTGACGCGTACAGTGGCT 59.741 61.111 13.97 0.00 39.67 4.75
1202 1771 2.049526 TGACGCGTACAGTGGCTG 60.050 61.111 13.97 0.00 39.67 4.85
1203 1772 3.479269 GACGCGTACAGTGGCTGC 61.479 66.667 13.97 0.00 34.92 5.25
1208 1777 3.041940 GTACAGTGGCTGCGCGTT 61.042 61.111 8.43 0.00 34.37 4.84
1253 1822 4.473520 CAAGGAGCCGGGCGTGAT 62.474 66.667 14.39 0.00 0.00 3.06
1269 1838 0.320683 TGATGGTGAAGTCCACGCTG 60.321 55.000 0.00 0.00 46.62 5.18
1392 1961 1.633432 TGGGAAGATCGGGTGATTGTT 59.367 47.619 0.00 0.00 34.09 2.83
1395 1964 2.939103 GGAAGATCGGGTGATTGTTGAG 59.061 50.000 0.00 0.00 34.09 3.02
1400 1969 3.040147 TCGGGTGATTGTTGAGAAGTC 57.960 47.619 0.00 0.00 0.00 3.01
1401 1970 2.632996 TCGGGTGATTGTTGAGAAGTCT 59.367 45.455 0.00 0.00 0.00 3.24
1409 1978 3.751479 TGTTGAGAAGTCTAAGCTGCA 57.249 42.857 1.02 0.00 0.00 4.41
1412 1981 1.066573 TGAGAAGTCTAAGCTGCAGGC 60.067 52.381 17.12 7.98 42.19 4.85
1476 2045 2.209838 ACACCGTCGCATAGAAGATG 57.790 50.000 0.00 0.00 0.00 2.90
1477 2046 0.855349 CACCGTCGCATAGAAGATGC 59.145 55.000 0.00 0.00 41.35 3.91
1483 2052 2.938354 GCATAGAAGATGCGGCCAT 58.062 52.632 2.24 0.00 35.17 4.40
1490 2059 4.223800 GATGCGGCCATCAACAGA 57.776 55.556 2.24 0.00 45.75 3.41
1492 2061 1.718757 GATGCGGCCATCAACAGACC 61.719 60.000 2.24 0.00 45.75 3.85
1493 2062 2.045926 GCGGCCATCAACAGACCT 60.046 61.111 2.24 0.00 0.00 3.85
1495 2064 0.811616 GCGGCCATCAACAGACCTAG 60.812 60.000 2.24 0.00 0.00 3.02
1496 2065 0.537188 CGGCCATCAACAGACCTAGT 59.463 55.000 2.24 0.00 0.00 2.57
1498 2067 1.471676 GGCCATCAACAGACCTAGTCG 60.472 57.143 0.00 0.00 37.67 4.18
1499 2068 1.476891 GCCATCAACAGACCTAGTCGA 59.523 52.381 0.00 0.00 37.67 4.20
1500 2069 2.101582 GCCATCAACAGACCTAGTCGAT 59.898 50.000 0.00 0.00 37.67 3.59
1501 2070 3.430929 GCCATCAACAGACCTAGTCGATT 60.431 47.826 0.00 0.00 37.67 3.34
1502 2071 4.115516 CCATCAACAGACCTAGTCGATTG 58.884 47.826 0.00 7.35 37.67 2.67
1503 2072 3.868757 TCAACAGACCTAGTCGATTGG 57.131 47.619 11.56 0.00 37.67 3.16
1504 2073 3.427573 TCAACAGACCTAGTCGATTGGA 58.572 45.455 8.04 0.00 37.67 3.53
1505 2074 3.830178 TCAACAGACCTAGTCGATTGGAA 59.170 43.478 8.04 0.00 37.67 3.53
1506 2075 4.466370 TCAACAGACCTAGTCGATTGGAAT 59.534 41.667 8.04 0.00 37.67 3.01
1507 2076 5.046591 TCAACAGACCTAGTCGATTGGAATT 60.047 40.000 8.04 0.00 37.67 2.17
1508 2077 6.153851 TCAACAGACCTAGTCGATTGGAATTA 59.846 38.462 8.04 0.00 37.67 1.40
1510 2079 7.125792 ACAGACCTAGTCGATTGGAATTAAT 57.874 36.000 8.04 0.00 37.67 1.40
1512 2081 8.701895 ACAGACCTAGTCGATTGGAATTAATTA 58.298 33.333 0.00 0.00 37.67 1.40
1513 2082 9.712305 CAGACCTAGTCGATTGGAATTAATTAT 57.288 33.333 0.00 0.00 37.67 1.28
1514 2083 9.712305 AGACCTAGTCGATTGGAATTAATTATG 57.288 33.333 0.00 0.00 37.67 1.90
1515 2084 8.848474 ACCTAGTCGATTGGAATTAATTATGG 57.152 34.615 0.00 0.00 0.00 2.74
1517 2086 8.936864 CCTAGTCGATTGGAATTAATTATGGTC 58.063 37.037 0.00 0.00 0.00 4.02
1528 2130 7.044314 GGAATTAATTATGGTCGTTGCTTTTCG 60.044 37.037 0.00 0.00 0.00 3.46
1565 2167 9.830975 AATAAAACATGGCTTTTGTAGACTTTT 57.169 25.926 0.00 0.00 30.89 2.27
1569 2171 9.908152 AAACATGGCTTTTGTAGACTTTTATAC 57.092 29.630 0.00 0.00 30.89 1.47
1570 2172 7.748847 ACATGGCTTTTGTAGACTTTTATACG 58.251 34.615 0.00 0.00 30.89 3.06
1620 2224 4.797471 TGCAATCAAAGCTGTGTATGTTC 58.203 39.130 3.21 0.00 0.00 3.18
1661 2265 5.824429 TGTATCCCTAGTTTACGTTGATCG 58.176 41.667 0.00 0.00 46.00 3.69
1677 2281 3.785486 TGATCGCACTTTCATCCTACAG 58.215 45.455 0.00 0.00 0.00 2.74
1740 2344 7.458397 TGGTTGAATCTTGTAACCTTGATACT 58.542 34.615 0.00 0.00 43.28 2.12
1810 2414 5.011023 AGCAAGGTTGGATTTAGTTTTCAGG 59.989 40.000 0.00 0.00 0.00 3.86
1811 2415 5.010617 GCAAGGTTGGATTTAGTTTTCAGGA 59.989 40.000 0.00 0.00 0.00 3.86
1879 2483 1.598701 GCAGGGGTCACATCTTTGCC 61.599 60.000 0.00 0.00 0.00 4.52
1908 2512 1.739338 CTATTGGAGGCTCGCCGAGT 61.739 60.000 16.50 0.00 41.95 4.18
1921 2525 1.531149 CGCCGAGTTTATTATGGGCTG 59.469 52.381 0.00 0.00 38.39 4.85
1960 2564 2.337583 TCGGCAAGAAGAACGATTCTG 58.662 47.619 0.00 0.00 39.47 3.02
2025 2629 3.384146 AGCCAGTGACATGATGAGTAGAG 59.616 47.826 0.00 0.00 0.00 2.43
2092 2696 8.969260 ATTTATCTCAACATGTCATCTTAGCA 57.031 30.769 0.00 0.00 0.00 3.49
2093 2697 8.791327 TTTATCTCAACATGTCATCTTAGCAA 57.209 30.769 0.00 0.00 0.00 3.91
2098 2702 7.823799 TCTCAACATGTCATCTTAGCAAACATA 59.176 33.333 0.00 0.00 0.00 2.29
2099 2703 7.751732 TCAACATGTCATCTTAGCAAACATAC 58.248 34.615 0.00 0.00 0.00 2.39
2107 2711 5.435686 TCTTAGCAAACATACCACCTCAT 57.564 39.130 0.00 0.00 0.00 2.90
2109 2713 2.632377 AGCAAACATACCACCTCATCG 58.368 47.619 0.00 0.00 0.00 3.84
2113 2717 4.437390 GCAAACATACCACCTCATCGAAAG 60.437 45.833 0.00 0.00 0.00 2.62
2116 2720 1.568504 TACCACCTCATCGAAAGCCT 58.431 50.000 0.00 0.00 0.00 4.58
2117 2721 0.036010 ACCACCTCATCGAAAGCCTG 60.036 55.000 0.00 0.00 0.00 4.85
2182 2850 5.362556 ACACATGTCATCTTAGCAAACAC 57.637 39.130 0.00 0.00 0.00 3.32
2200 2868 1.021968 ACGTCACCTCAACAAAAGCC 58.978 50.000 0.00 0.00 0.00 4.35
2214 2882 2.496871 CAAAAGCCCACCTCAATATGCA 59.503 45.455 0.00 0.00 0.00 3.96
2219 2887 1.958579 CCCACCTCAATATGCATGGTG 59.041 52.381 20.86 20.86 45.42 4.17
2267 2936 1.303155 TCAACATGCACGCATCCCA 60.303 52.632 0.44 0.00 33.90 4.37
2279 2948 1.070601 CGCATCCCATGTCACCTCATA 59.929 52.381 0.00 0.00 0.00 2.15
2283 2952 4.940046 GCATCCCATGTCACCTCATATAAG 59.060 45.833 0.00 0.00 0.00 1.73
2298 2967 6.073447 TCATATAAGGTCCACCACAACATT 57.927 37.500 0.00 0.00 38.89 2.71
2320 2989 8.353684 ACATTTATGTGAACACGTTTTCCATTA 58.646 29.630 17.59 10.20 40.03 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.939132 AGCCAGATGAAAAGTTATGATCAG 57.061 37.500 0.09 0.00 0.00 2.90
66 67 7.687103 CTTAGGGTAATGCTACACCTAAGAAGG 60.687 44.444 19.05 0.00 46.62 3.46
128 129 2.722094 TCTTCCATGGATTTTGGGTCG 58.278 47.619 17.06 0.00 34.85 4.79
149 150 2.832129 ACATACACTTCCGACATCCAGT 59.168 45.455 0.00 0.00 0.00 4.00
210 214 6.371595 TTTGAATTGGACCATGGCTAAATT 57.628 33.333 13.04 14.53 0.00 1.82
211 215 6.371595 TTTTGAATTGGACCATGGCTAAAT 57.628 33.333 13.04 6.10 0.00 1.40
222 226 7.762159 TGTAGGTTTTCTGTTTTTGAATTGGAC 59.238 33.333 0.00 0.00 0.00 4.02
236 240 3.928375 GCATGGCAAATGTAGGTTTTCTG 59.072 43.478 0.00 0.00 0.00 3.02
237 241 3.367292 CGCATGGCAAATGTAGGTTTTCT 60.367 43.478 0.00 0.00 0.00 2.52
241 245 1.832883 TCGCATGGCAAATGTAGGTT 58.167 45.000 0.00 0.00 0.00 3.50
272 276 9.500785 CCCAAATGGCGGAAATTTTTATATAAT 57.499 29.630 0.00 0.00 0.00 1.28
273 277 8.705594 TCCCAAATGGCGGAAATTTTTATATAA 58.294 29.630 0.00 0.00 0.00 0.98
274 278 8.145122 GTCCCAAATGGCGGAAATTTTTATATA 58.855 33.333 0.00 0.00 0.00 0.86
275 279 6.989759 GTCCCAAATGGCGGAAATTTTTATAT 59.010 34.615 0.00 0.00 0.00 0.86
276 280 6.342111 GTCCCAAATGGCGGAAATTTTTATA 58.658 36.000 0.00 0.00 0.00 0.98
277 281 5.182487 GTCCCAAATGGCGGAAATTTTTAT 58.818 37.500 0.00 0.00 0.00 1.40
278 282 4.570930 GTCCCAAATGGCGGAAATTTTTA 58.429 39.130 0.00 0.00 0.00 1.52
279 283 3.407698 GTCCCAAATGGCGGAAATTTTT 58.592 40.909 0.00 0.00 0.00 1.94
280 284 2.611722 CGTCCCAAATGGCGGAAATTTT 60.612 45.455 0.00 0.00 32.29 1.82
281 285 1.067213 CGTCCCAAATGGCGGAAATTT 60.067 47.619 0.00 0.00 32.29 1.82
282 286 0.530288 CGTCCCAAATGGCGGAAATT 59.470 50.000 0.00 0.00 32.29 1.82
283 287 1.944234 GCGTCCCAAATGGCGGAAAT 61.944 55.000 0.00 0.00 35.18 2.17
284 288 2.631580 GCGTCCCAAATGGCGGAAA 61.632 57.895 0.00 0.00 35.18 3.13
285 289 3.059386 GCGTCCCAAATGGCGGAA 61.059 61.111 0.00 0.00 35.18 4.30
367 382 4.649218 CACCCATATTCCCACTTTTTAGGG 59.351 45.833 0.00 0.00 46.90 3.53
368 383 4.649218 CCACCCATATTCCCACTTTTTAGG 59.351 45.833 0.00 0.00 0.00 2.69
409 425 4.816984 TCTCCCTCCCGAGCGACC 62.817 72.222 0.00 0.00 0.00 4.79
410 426 3.213402 CTCTCCCTCCCGAGCGAC 61.213 72.222 0.00 0.00 0.00 5.19
411 427 3.408099 CTCTCTCCCTCCCGAGCGA 62.408 68.421 0.00 0.00 0.00 4.93
412 428 2.904866 CTCTCTCCCTCCCGAGCG 60.905 72.222 0.00 0.00 0.00 5.03
413 429 2.520741 CCTCTCTCCCTCCCGAGC 60.521 72.222 0.00 0.00 0.00 5.03
414 430 2.197324 CCCTCTCTCCCTCCCGAG 59.803 72.222 0.00 0.00 0.00 4.63
415 431 4.144727 GCCCTCTCTCCCTCCCGA 62.145 72.222 0.00 0.00 0.00 5.14
416 432 4.465446 TGCCCTCTCTCCCTCCCG 62.465 72.222 0.00 0.00 0.00 5.14
417 433 2.445654 CTGCCCTCTCTCCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
418 434 3.160748 GCTGCCCTCTCTCCCTCC 61.161 72.222 0.00 0.00 0.00 4.30
419 435 2.042025 AGCTGCCCTCTCTCCCTC 60.042 66.667 0.00 0.00 0.00 4.30
420 436 2.365370 CAGCTGCCCTCTCTCCCT 60.365 66.667 0.00 0.00 0.00 4.20
421 437 1.557269 TTTCAGCTGCCCTCTCTCCC 61.557 60.000 9.47 0.00 0.00 4.30
422 438 0.545646 ATTTCAGCTGCCCTCTCTCC 59.454 55.000 9.47 0.00 0.00 3.71
423 439 2.416680 AATTTCAGCTGCCCTCTCTC 57.583 50.000 9.47 0.00 0.00 3.20
424 440 2.895242 AAATTTCAGCTGCCCTCTCT 57.105 45.000 9.47 0.00 0.00 3.10
425 441 3.949842 AAAAATTTCAGCTGCCCTCTC 57.050 42.857 9.47 0.00 0.00 3.20
426 442 4.411013 AGTAAAAATTTCAGCTGCCCTCT 58.589 39.130 9.47 0.00 0.00 3.69
433 449 5.371115 TGCGCTAAGTAAAAATTTCAGCT 57.629 34.783 9.73 0.00 0.00 4.24
441 457 1.730064 CTCGGCTGCGCTAAGTAAAAA 59.270 47.619 9.73 0.00 0.00 1.94
453 469 0.882474 ATATACTCGACCTCGGCTGC 59.118 55.000 0.00 0.00 40.29 5.25
455 471 3.188048 CGTAAATATACTCGACCTCGGCT 59.812 47.826 0.00 0.00 40.29 5.52
459 475 5.049543 AGCACTCGTAAATATACTCGACCTC 60.050 44.000 0.00 0.00 0.00 3.85
465 481 6.270815 TCCAACAGCACTCGTAAATATACTC 58.729 40.000 0.00 0.00 0.00 2.59
476 492 3.490526 CCAAAAATTTCCAACAGCACTCG 59.509 43.478 0.00 0.00 0.00 4.18
482 498 2.142319 CCGGCCAAAAATTTCCAACAG 58.858 47.619 2.24 0.00 0.00 3.16
485 501 1.346068 CCTCCGGCCAAAAATTTCCAA 59.654 47.619 2.24 0.00 0.00 3.53
491 507 0.323451 GTCCTCCTCCGGCCAAAAAT 60.323 55.000 2.24 0.00 0.00 1.82
493 509 1.710996 TTGTCCTCCTCCGGCCAAAA 61.711 55.000 2.24 0.00 0.00 2.44
510 526 2.856091 CGTGAGCGGAGTAAAGTTTG 57.144 50.000 0.00 0.00 0.00 2.93
526 542 1.768112 AACCGAACTCGCAAACCGTG 61.768 55.000 0.00 0.00 38.18 4.94
548 564 1.929169 GAAATACGTGGCTAACCGGAC 59.071 52.381 9.46 0.00 39.70 4.79
549 565 1.134729 GGAAATACGTGGCTAACCGGA 60.135 52.381 9.46 0.00 39.70 5.14
551 567 1.134610 AGGGAAATACGTGGCTAACCG 60.135 52.381 0.00 0.00 39.70 4.44
552 568 2.169978 AGAGGGAAATACGTGGCTAACC 59.830 50.000 0.00 0.00 0.00 2.85
553 569 3.538634 AGAGGGAAATACGTGGCTAAC 57.461 47.619 0.00 0.00 0.00 2.34
554 570 4.284178 AGTAGAGGGAAATACGTGGCTAA 58.716 43.478 0.00 0.00 0.00 3.09
555 571 3.907221 AGTAGAGGGAAATACGTGGCTA 58.093 45.455 0.00 0.00 0.00 3.93
556 572 2.748388 AGTAGAGGGAAATACGTGGCT 58.252 47.619 0.00 0.00 0.00 4.75
557 573 4.366586 GTTAGTAGAGGGAAATACGTGGC 58.633 47.826 0.00 0.00 0.00 5.01
558 574 4.498682 CGGTTAGTAGAGGGAAATACGTGG 60.499 50.000 0.00 0.00 0.00 4.94
559 575 4.336433 TCGGTTAGTAGAGGGAAATACGTG 59.664 45.833 0.00 0.00 0.00 4.49
560 576 4.526970 TCGGTTAGTAGAGGGAAATACGT 58.473 43.478 0.00 0.00 0.00 3.57
561 577 5.702349 ATCGGTTAGTAGAGGGAAATACG 57.298 43.478 0.00 0.00 0.00 3.06
568 584 4.954826 CCCCTATAATCGGTTAGTAGAGGG 59.045 50.000 15.70 15.70 40.78 4.30
584 600 3.457012 GCAACTCTAACCAACCCCCTATA 59.543 47.826 0.00 0.00 0.00 1.31
585 601 2.241430 GCAACTCTAACCAACCCCCTAT 59.759 50.000 0.00 0.00 0.00 2.57
586 602 1.631898 GCAACTCTAACCAACCCCCTA 59.368 52.381 0.00 0.00 0.00 3.53
587 603 0.404426 GCAACTCTAACCAACCCCCT 59.596 55.000 0.00 0.00 0.00 4.79
588 604 0.404426 AGCAACTCTAACCAACCCCC 59.596 55.000 0.00 0.00 0.00 5.40
592 1095 4.575236 GCCCTTATAGCAACTCTAACCAAC 59.425 45.833 0.00 0.00 0.00 3.77
594 1097 3.135895 GGCCCTTATAGCAACTCTAACCA 59.864 47.826 0.00 0.00 0.00 3.67
597 1100 4.202223 CGAAGGCCCTTATAGCAACTCTAA 60.202 45.833 0.00 0.00 0.00 2.10
602 1105 2.158943 ACTCGAAGGCCCTTATAGCAAC 60.159 50.000 0.00 0.00 0.00 4.17
608 1111 2.304761 TGAACAACTCGAAGGCCCTTAT 59.695 45.455 0.00 0.00 0.00 1.73
628 1131 5.684850 TGCAGTATTGTACAATTTCGTGTG 58.315 37.500 25.31 14.22 32.75 3.82
631 1134 7.119116 TCTGATTGCAGTATTGTACAATTTCGT 59.881 33.333 25.31 5.15 42.84 3.85
714 1242 2.476534 TAAACTCACGTCGCCGGACC 62.477 60.000 5.05 0.00 40.17 4.46
747 1275 4.629115 GCACGCACACAACCCAGC 62.629 66.667 0.00 0.00 0.00 4.85
780 1326 7.201574 GCACACACTATCGTATCCATGTAAAAA 60.202 37.037 0.00 0.00 0.00 1.94
827 1378 6.036083 GTCCAAGATAACTCGTACTACGTACA 59.964 42.308 8.42 0.00 43.14 2.90
837 1388 2.427453 AGCATCGTCCAAGATAACTCGT 59.573 45.455 0.00 0.00 0.00 4.18
840 1391 3.034635 AGGAGCATCGTCCAAGATAACT 58.965 45.455 0.00 0.00 39.34 2.24
847 1409 1.112113 GGAGTAGGAGCATCGTCCAA 58.888 55.000 0.00 0.00 39.34 3.53
906 1470 5.418310 TTGTAAGCTGTTTTCTCGAAAGG 57.582 39.130 0.00 0.00 0.00 3.11
941 1509 0.402121 GGTGAGCTCCAAGGAAACCT 59.598 55.000 12.15 0.00 33.87 3.50
948 1516 2.743928 GCACGGGTGAGCTCCAAG 60.744 66.667 12.15 2.62 0.00 3.61
984 1552 1.066002 CCCATGGCAAATCAAGTAGCG 59.934 52.381 6.09 0.00 0.00 4.26
1017 1586 4.083862 GTCTCCCCTCCGCACCAC 62.084 72.222 0.00 0.00 0.00 4.16
1028 1597 1.352404 CATCTCGACGACGTCTCCC 59.648 63.158 24.36 0.21 40.69 4.30
1050 1619 3.751246 CCCGTCGCGGTCTTGGTA 61.751 66.667 6.13 0.00 46.80 3.25
1071 1640 3.042887 GTTTGTCACCTCGAATTTGTGC 58.957 45.455 0.00 0.00 0.00 4.57
1125 1694 1.865865 ACGTGTTGGAGCTTACACAG 58.134 50.000 20.51 16.40 43.69 3.66
1126 1695 2.206750 GAACGTGTTGGAGCTTACACA 58.793 47.619 20.51 8.15 43.69 3.72
1127 1696 2.206750 TGAACGTGTTGGAGCTTACAC 58.793 47.619 14.29 14.29 40.89 2.90
1162 1731 3.119352 GGGAAGAAATTGATGCACCAGTC 60.119 47.826 0.00 0.00 0.00 3.51
1174 1743 2.289195 TGTACGCGTCAGGGAAGAAATT 60.289 45.455 18.63 0.00 0.00 1.82
1181 1750 2.632544 CCACTGTACGCGTCAGGGA 61.633 63.158 29.97 8.39 38.46 4.20
1203 1772 3.630148 CATAGGCAGGCGAACGCG 61.630 66.667 3.53 3.53 43.06 6.01
1208 1777 0.975556 TTGGAGACATAGGCAGGCGA 60.976 55.000 0.00 0.00 42.32 5.54
1214 1783 1.473434 CCGTTCCTTGGAGACATAGGC 60.473 57.143 0.00 0.00 42.32 3.93
1245 1814 1.745489 GGACTTCACCATCACGCCC 60.745 63.158 0.00 0.00 0.00 6.13
1253 1822 1.367471 CTCAGCGTGGACTTCACCA 59.633 57.895 0.00 0.00 43.23 4.17
1257 1826 0.793250 GAAAGCTCAGCGTGGACTTC 59.207 55.000 0.00 0.00 0.00 3.01
1269 1838 1.448717 GTCGCTCCCCAGAAAGCTC 60.449 63.158 0.00 0.00 36.35 4.09
1392 1961 1.066573 GCCTGCAGCTTAGACTTCTCA 60.067 52.381 8.66 0.00 38.99 3.27
1412 1981 4.994471 TGGTGCAGCAGCCGTCAG 62.994 66.667 21.74 0.00 41.13 3.51
1418 1987 2.360852 ACCTGATGGTGCAGCAGC 60.361 61.111 26.22 26.22 45.18 5.25
1476 2045 0.811616 CTAGGTCTGTTGATGGCCGC 60.812 60.000 0.00 0.00 0.00 6.53
1477 2046 0.537188 ACTAGGTCTGTTGATGGCCG 59.463 55.000 0.00 0.00 0.00 6.13
1478 2047 1.471676 CGACTAGGTCTGTTGATGGCC 60.472 57.143 0.00 0.00 0.00 5.36
1479 2048 1.476891 TCGACTAGGTCTGTTGATGGC 59.523 52.381 0.00 0.00 0.00 4.40
1481 2050 4.115516 CCAATCGACTAGGTCTGTTGATG 58.884 47.826 0.00 0.00 38.25 3.07
1483 2052 3.427573 TCCAATCGACTAGGTCTGTTGA 58.572 45.455 0.00 0.00 31.27 3.18
1485 2054 5.422214 AATTCCAATCGACTAGGTCTGTT 57.578 39.130 0.00 0.00 0.00 3.16
1487 2056 9.712305 ATAATTAATTCCAATCGACTAGGTCTG 57.288 33.333 3.39 0.00 0.00 3.51
1488 2057 9.712305 CATAATTAATTCCAATCGACTAGGTCT 57.288 33.333 3.39 0.00 0.00 3.85
1489 2058 8.936864 CCATAATTAATTCCAATCGACTAGGTC 58.063 37.037 3.39 0.00 0.00 3.85
1490 2059 8.437575 ACCATAATTAATTCCAATCGACTAGGT 58.562 33.333 3.39 0.00 0.00 3.08
1492 2061 8.648097 CGACCATAATTAATTCCAATCGACTAG 58.352 37.037 3.39 0.00 0.00 2.57
1493 2062 8.145767 ACGACCATAATTAATTCCAATCGACTA 58.854 33.333 21.75 0.00 0.00 2.59
1495 2064 7.186021 ACGACCATAATTAATTCCAATCGAC 57.814 36.000 21.75 1.38 0.00 4.20
1496 2065 7.635423 CAACGACCATAATTAATTCCAATCGA 58.365 34.615 21.75 0.00 0.00 3.59
1498 2067 7.425606 AGCAACGACCATAATTAATTCCAATC 58.574 34.615 3.39 0.00 0.00 2.67
1499 2068 7.346751 AGCAACGACCATAATTAATTCCAAT 57.653 32.000 3.39 0.00 0.00 3.16
1500 2069 6.767524 AGCAACGACCATAATTAATTCCAA 57.232 33.333 3.39 0.00 0.00 3.53
1501 2070 6.767524 AAGCAACGACCATAATTAATTCCA 57.232 33.333 3.39 0.00 0.00 3.53
1502 2071 7.044314 CGAAAAGCAACGACCATAATTAATTCC 60.044 37.037 3.39 0.00 0.00 3.01
1503 2072 7.694784 TCGAAAAGCAACGACCATAATTAATTC 59.305 33.333 3.39 0.00 33.62 2.17
1504 2073 7.531716 TCGAAAAGCAACGACCATAATTAATT 58.468 30.769 5.89 5.89 33.62 1.40
1505 2074 7.079182 TCGAAAAGCAACGACCATAATTAAT 57.921 32.000 0.00 0.00 33.62 1.40
1506 2075 6.483385 TCGAAAAGCAACGACCATAATTAA 57.517 33.333 0.00 0.00 33.62 1.40
1507 2076 6.671614 ATCGAAAAGCAACGACCATAATTA 57.328 33.333 0.00 0.00 41.17 1.40
1508 2077 5.560966 ATCGAAAAGCAACGACCATAATT 57.439 34.783 0.00 0.00 41.17 1.40
1510 2079 5.150683 CAAATCGAAAAGCAACGACCATAA 58.849 37.500 0.00 0.00 41.17 1.90
1512 2081 3.564511 CAAATCGAAAAGCAACGACCAT 58.435 40.909 0.00 0.00 41.17 3.55
1513 2082 2.856720 GCAAATCGAAAAGCAACGACCA 60.857 45.455 0.00 0.00 41.17 4.02
1514 2083 1.713932 GCAAATCGAAAAGCAACGACC 59.286 47.619 0.00 0.00 41.17 4.79
1515 2084 2.650608 AGCAAATCGAAAAGCAACGAC 58.349 42.857 8.68 0.00 41.17 4.34
1517 2086 2.788786 ACAAGCAAATCGAAAAGCAACG 59.211 40.909 8.68 0.00 0.00 4.10
1528 2130 7.832503 AGCCATGTTTTATTACAAGCAAATC 57.167 32.000 0.00 0.00 35.18 2.17
1588 2190 9.123902 ACACAGCTTTGATTGCATATAAAGATA 57.876 29.630 6.92 0.00 33.18 1.98
1605 2209 1.806542 CTGCGGAACATACACAGCTTT 59.193 47.619 0.00 0.00 0.00 3.51
1620 2224 1.978617 AAAAGTGGCCATCCTGCGG 60.979 57.895 9.72 0.00 0.00 5.69
1661 2265 2.813754 TGCAACTGTAGGATGAAAGTGC 59.186 45.455 0.00 0.00 0.00 4.40
1704 2308 5.992217 ACAAGATTCAACCAAGTCTACAGAC 59.008 40.000 0.91 0.91 45.08 3.51
1705 2309 6.174720 ACAAGATTCAACCAAGTCTACAGA 57.825 37.500 0.00 0.00 0.00 3.41
1717 2321 7.094805 TGCAGTATCAAGGTTACAAGATTCAAC 60.095 37.037 0.00 0.00 0.00 3.18
1719 2323 6.472016 TGCAGTATCAAGGTTACAAGATTCA 58.528 36.000 0.00 0.00 0.00 2.57
1722 2326 9.113838 CTTTATGCAGTATCAAGGTTACAAGAT 57.886 33.333 0.00 0.00 0.00 2.40
1740 2344 5.121768 GTCTAGTTCTTTTCGGCTTTATGCA 59.878 40.000 0.00 0.00 45.15 3.96
1810 2414 8.760980 AGAGAGGGAATAGTATATACATGCTC 57.239 38.462 15.18 5.56 0.00 4.26
1811 2415 9.554053 AAAGAGAGGGAATAGTATATACATGCT 57.446 33.333 15.18 0.00 0.00 3.79
1843 2447 7.557719 TGACCCCTGCAATTTTGATTTTAAAAA 59.442 29.630 4.44 0.00 33.67 1.94
1847 2451 5.070981 TGTGACCCCTGCAATTTTGATTTTA 59.929 36.000 0.00 0.00 0.00 1.52
1865 2469 1.523758 AACTCGGCAAAGATGTGACC 58.476 50.000 0.00 0.00 0.00 4.02
1879 2483 1.571919 CCTCCAATAGCCGAAACTCG 58.428 55.000 0.00 0.00 40.07 4.18
1892 2496 1.537814 TAAACTCGGCGAGCCTCCAA 61.538 55.000 34.76 13.13 32.04 3.53
1935 2539 1.864711 TCGTTCTTCTTGCCGAGTTTG 59.135 47.619 0.00 0.00 0.00 2.93
1936 2540 2.234300 TCGTTCTTCTTGCCGAGTTT 57.766 45.000 0.00 0.00 0.00 2.66
1942 2546 2.427506 ACCAGAATCGTTCTTCTTGCC 58.572 47.619 0.00 0.00 38.11 4.52
1947 2551 3.807622 TGACACAACCAGAATCGTTCTTC 59.192 43.478 0.00 0.00 38.11 2.87
2078 2682 6.458751 GGTGGTATGTTTGCTAAGATGACATG 60.459 42.308 0.82 0.00 33.42 3.21
2085 2689 4.901197 TGAGGTGGTATGTTTGCTAAGA 57.099 40.909 0.00 0.00 0.00 2.10
2086 2690 4.271049 CGATGAGGTGGTATGTTTGCTAAG 59.729 45.833 0.00 0.00 0.00 2.18
2087 2691 4.081365 TCGATGAGGTGGTATGTTTGCTAA 60.081 41.667 0.00 0.00 0.00 3.09
2088 2692 3.449377 TCGATGAGGTGGTATGTTTGCTA 59.551 43.478 0.00 0.00 0.00 3.49
2089 2693 2.236146 TCGATGAGGTGGTATGTTTGCT 59.764 45.455 0.00 0.00 0.00 3.91
2090 2694 2.627945 TCGATGAGGTGGTATGTTTGC 58.372 47.619 0.00 0.00 0.00 3.68
2091 2695 4.437390 GCTTTCGATGAGGTGGTATGTTTG 60.437 45.833 0.00 0.00 0.00 2.93
2092 2696 3.689649 GCTTTCGATGAGGTGGTATGTTT 59.310 43.478 0.00 0.00 0.00 2.83
2093 2697 3.270877 GCTTTCGATGAGGTGGTATGTT 58.729 45.455 0.00 0.00 0.00 2.71
2098 2702 0.036010 CAGGCTTTCGATGAGGTGGT 60.036 55.000 0.00 0.00 0.00 4.16
2099 2703 1.372087 GCAGGCTTTCGATGAGGTGG 61.372 60.000 0.00 0.00 0.00 4.61
2107 2711 1.942657 GCATATTGAGCAGGCTTTCGA 59.057 47.619 0.00 0.00 0.00 3.71
2109 2713 3.552273 CCATGCATATTGAGCAGGCTTTC 60.552 47.826 0.00 0.00 46.36 2.62
2113 2717 1.268899 GACCATGCATATTGAGCAGGC 59.731 52.381 0.00 0.00 46.36 4.85
2117 2721 8.048534 ACTAATAATGACCATGCATATTGAGC 57.951 34.615 0.00 0.00 0.00 4.26
2176 2844 3.479505 TTTGTTGAGGTGACGTGTTTG 57.520 42.857 0.00 0.00 0.00 2.93
2182 2850 0.310854 GGGCTTTTGTTGAGGTGACG 59.689 55.000 0.00 0.00 0.00 4.35
2260 2929 2.936919 TATGAGGTGACATGGGATGC 57.063 50.000 0.00 0.00 0.00 3.91
2279 2948 6.152661 CACATAAATGTTGTGGTGGACCTTAT 59.847 38.462 0.00 0.00 40.60 1.73
2283 2952 3.823873 TCACATAAATGTTGTGGTGGACC 59.176 43.478 4.18 0.00 43.67 4.46
2290 2959 6.804534 AAACGTGTTCACATAAATGTTGTG 57.195 33.333 0.00 0.00 44.62 3.33


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

AutoCloner maintained by Alex Coulton.