Multiple sequence alignment - TraesCS4A01G117500

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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 TraesCS4A01G117500 chr4A 100.000 4384 0 0 1 4384 143432827 143437210 0.000000e+00 8096.0
1 TraesCS4A01G117500 chr4D 91.857 4470 186 81 1 4346 327440843 327436428 0.000000e+00 6074.0
2 TraesCS4A01G117500 chr4B 92.750 4276 184 51 1 4206 406894458 406890239 0.000000e+00 6063.0
3 TraesCS4A01G117500 chr7B 84.146 82 8 5 4130 4208 605080753 605080674 1.690000e-09 75.0
4 TraesCS4A01G117500 chr7B 89.286 56 4 2 4130 4185 605080099 605080046 7.870000e-08 69.4
5 TraesCS4A01G117500 chr5A 95.556 45 2 0 1810 1854 564438220 564438176 6.080000e-09 73.1
6 TraesCS4A01G117500 chr2A 91.837 49 2 2 4142 4188 81665018 81664970 2.830000e-07 67.6


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 TraesCS4A01G117500 chr4A 143432827 143437210 4383 False 8096 8096 100.000 1 4384 1 chr4A.!!$F1 4383
1 TraesCS4A01G117500 chr4D 327436428 327440843 4415 True 6074 6074 91.857 1 4346 1 chr4D.!!$R1 4345
2 TraesCS4A01G117500 chr4B 406890239 406894458 4219 True 6063 6063 92.750 1 4206 1 chr4B.!!$R1 4205

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
397 409 1.475169 CCTCTCCCATCGCCATGCTA 61.475 60.0 0.00 0.0 0.00 3.49 F
1692 1731 0.802607 GCAGTGCAGTAGCGGTAGTC 60.803 60.0 11.09 0.0 46.23 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2082 0.681733 TGCTCTCGCTGAACTCCTTT 59.318 50.0 0.0 0.0 36.97 3.11 R
3441 3551 0.041312 ACGAAACAGCAACGACATGC 60.041 50.0 0.0 0.0 46.78 4.06 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
33 34 7.426929 AATGATGAATAGATAACCGAGCAAC 57.573 36.000 0.00 0.00 0.00 4.17
156 157 8.017418 ACAAAGTCCACTCCATTTCAATTTTA 57.983 30.769 0.00 0.00 0.00 1.52
394 406 2.281345 GCCTCTCCCATCGCCATG 60.281 66.667 0.00 0.00 0.00 3.66
395 407 2.281345 CCTCTCCCATCGCCATGC 60.281 66.667 0.00 0.00 0.00 4.06
396 408 2.815945 CCTCTCCCATCGCCATGCT 61.816 63.158 0.00 0.00 0.00 3.79
397 409 1.475169 CCTCTCCCATCGCCATGCTA 61.475 60.000 0.00 0.00 0.00 3.49
891 909 7.364522 CTATTTATAGCCCACGTACGTAGTA 57.635 40.000 22.34 10.28 45.11 1.82
1017 1035 2.679837 CGTGATGGATTTGAAGAGGGTG 59.320 50.000 0.00 0.00 0.00 4.61
1174 1192 0.955428 TGGTTCTGACGATGCTTGGC 60.955 55.000 0.00 0.00 0.00 4.52
1327 1346 1.960994 GCAGAACTCGCTTCTTCGGC 61.961 60.000 0.00 0.00 37.08 5.54
1405 1424 2.586079 CGCCACATCGATTCGGCT 60.586 61.111 25.05 0.00 42.59 5.52
1416 1435 1.135083 CGATTCGGCTCACAGGTTAGT 60.135 52.381 0.00 0.00 0.00 2.24
1430 1452 6.666546 TCACAGGTTAGTGCCTAAATACTACT 59.333 38.462 0.00 0.00 39.35 2.57
1431 1453 6.979238 CACAGGTTAGTGCCTAAATACTACTC 59.021 42.308 0.00 0.00 37.04 2.59
1451 1480 7.819900 ACTACTCCTGTGTTTAGTGATTCAATC 59.180 37.037 0.00 0.00 0.00 2.67
1459 1488 7.714813 TGTGTTTAGTGATTCAATCTTCTGTGA 59.285 33.333 0.00 0.00 0.00 3.58
1460 1489 8.559536 GTGTTTAGTGATTCAATCTTCTGTGAA 58.440 33.333 0.00 0.00 38.09 3.18
1464 1493 5.704515 AGTGATTCAATCTTCTGTGAACAGG 59.295 40.000 10.45 0.00 43.91 4.00
1478 1507 4.826733 TGTGAACAGGTACATGCTTCATTT 59.173 37.500 20.32 4.27 0.00 2.32
1488 1520 7.173907 AGGTACATGCTTCATTTACATGCTATC 59.826 37.037 0.00 0.00 43.96 2.08
1502 1534 8.771521 TTACATGCTATCCAAGGTTACTACTA 57.228 34.615 0.00 0.00 0.00 1.82
1504 1536 7.727181 ACATGCTATCCAAGGTTACTACTAAG 58.273 38.462 0.00 0.00 0.00 2.18
1505 1537 6.158023 TGCTATCCAAGGTTACTACTAAGC 57.842 41.667 0.00 0.00 0.00 3.09
1506 1538 5.659525 TGCTATCCAAGGTTACTACTAAGCA 59.340 40.000 0.00 0.00 33.46 3.91
1507 1539 5.984323 GCTATCCAAGGTTACTACTAAGCAC 59.016 44.000 0.00 0.00 33.46 4.40
1508 1540 6.183360 GCTATCCAAGGTTACTACTAAGCACT 60.183 42.308 0.00 0.00 33.46 4.40
1509 1541 7.014038 GCTATCCAAGGTTACTACTAAGCACTA 59.986 40.741 0.00 0.00 33.46 2.74
1510 1542 6.521151 TCCAAGGTTACTACTAAGCACTAC 57.479 41.667 0.00 0.00 33.46 2.73
1515 1553 5.526846 AGGTTACTACTAAGCACTACTAGCG 59.473 44.000 0.00 0.00 37.01 4.26
1522 1560 6.636562 ACTAAGCACTACTAGCGACAATAT 57.363 37.500 0.00 0.00 37.01 1.28
1527 1565 7.215719 AGCACTACTAGCGACAATATTATGA 57.784 36.000 0.00 0.00 37.01 2.15
1550 1588 8.242729 TGAAGCAGATATAACTCTGAAGATCA 57.757 34.615 7.41 3.38 44.48 2.92
1578 1617 9.766277 TTTCACTGTTGAATTTGCAATTTTAAC 57.234 25.926 23.90 23.90 41.50 2.01
1579 1618 8.484641 TCACTGTTGAATTTGCAATTTTAACA 57.515 26.923 27.97 27.97 0.00 2.41
1587 1626 8.660373 TGAATTTGCAATTTTAACAAAGTCGTT 58.340 25.926 0.00 0.00 46.03 3.85
1588 1627 8.819152 AATTTGCAATTTTAACAAAGTCGTTG 57.181 26.923 0.00 0.00 43.43 4.10
1593 1632 6.904543 GCAATTTTAACAAAGTCGTTGCAAAT 59.095 30.769 0.00 0.00 41.31 2.32
1634 1673 5.007682 ACTACCCGTAATGCTGTTGAAAAT 58.992 37.500 0.00 0.00 0.00 1.82
1649 1688 7.489574 TGTTGAAAATCCTTTAAATTGCCAC 57.510 32.000 0.00 0.00 0.00 5.01
1692 1731 0.802607 GCAGTGCAGTAGCGGTAGTC 60.803 60.000 11.09 0.00 46.23 2.59
1752 1797 4.034858 GGCCGAAAGTGTTAAGTTATAGGC 59.965 45.833 0.00 0.00 34.49 3.93
1770 1815 1.889170 GGCTCCTTCCTGTTTTTCTGG 59.111 52.381 0.00 0.00 36.63 3.86
1824 1869 3.060602 ACTTCAGTTAAAGACGAGCAGC 58.939 45.455 0.00 0.00 0.00 5.25
1992 2037 0.832135 TGAAGGTGGAGCTCCTCGTT 60.832 55.000 32.03 32.03 39.41 3.85
1995 2040 0.968393 AGGTGGAGCTCCTCGTTCTC 60.968 60.000 32.28 15.72 36.82 2.87
2037 2082 2.664851 CGCCTTGAGCACACCGAA 60.665 61.111 0.00 0.00 44.04 4.30
2129 2174 2.815647 GCTCGAGAAAGGCGTGGG 60.816 66.667 18.75 0.00 0.00 4.61
2163 2208 1.996798 TCTCCTTCACGGACAACTCT 58.003 50.000 0.00 0.00 36.69 3.24
2253 2298 1.378250 GCAGGAGGCTGTCAGCAAT 60.378 57.895 25.68 13.92 44.75 3.56
2298 2343 5.153513 CGTGGTGAAGGTTTGTGATTATTG 58.846 41.667 0.00 0.00 0.00 1.90
2375 2424 7.085052 GTCTAACTGACTGGTTGAACTTTTT 57.915 36.000 0.00 0.00 42.21 1.94
2376 2425 8.205131 GTCTAACTGACTGGTTGAACTTTTTA 57.795 34.615 0.00 0.00 42.21 1.52
2377 2426 8.121086 GTCTAACTGACTGGTTGAACTTTTTAC 58.879 37.037 0.00 0.00 42.21 2.01
2385 2434 7.312899 ACTGGTTGAACTTTTTACTTTCAGTG 58.687 34.615 0.00 0.00 31.11 3.66
2454 2503 2.094700 GGAAAAGATTGGGAAAGACGGC 60.095 50.000 0.00 0.00 0.00 5.68
2557 2606 2.263540 GCGGCGTAAGAACCTGGA 59.736 61.111 9.37 0.00 43.02 3.86
2568 2617 1.777272 AGAACCTGGACTGCCTCTTTT 59.223 47.619 0.00 0.00 34.31 2.27
2569 2618 2.175715 AGAACCTGGACTGCCTCTTTTT 59.824 45.455 0.00 0.00 34.31 1.94
2827 2896 1.666553 CACCGCAACGCAGAAGGTA 60.667 57.895 0.00 0.00 33.30 3.08
2828 2897 1.666872 ACCGCAACGCAGAAGGTAC 60.667 57.895 0.00 0.00 32.76 3.34
2830 2899 1.626654 CCGCAACGCAGAAGGTACTG 61.627 60.000 0.00 0.00 40.86 2.74
2844 2927 2.038557 AGGTACTGCACTTCATTTCGGT 59.961 45.455 0.00 0.00 37.18 4.69
2846 2929 2.550830 ACTGCACTTCATTTCGGTCT 57.449 45.000 0.00 0.00 0.00 3.85
2848 2931 2.146342 CTGCACTTCATTTCGGTCTGT 58.854 47.619 0.00 0.00 0.00 3.41
2850 2933 1.873591 GCACTTCATTTCGGTCTGTGT 59.126 47.619 0.00 0.00 0.00 3.72
2865 2955 5.622233 CGGTCTGTGTCTCTCATGAACAATA 60.622 44.000 0.31 0.00 0.00 1.90
2866 2956 6.344500 GGTCTGTGTCTCTCATGAACAATAT 58.656 40.000 0.31 0.00 0.00 1.28
3392 3491 1.012086 CGAGGTTGTGATCCATGCAG 58.988 55.000 0.00 0.00 0.00 4.41
3393 3492 1.405933 CGAGGTTGTGATCCATGCAGA 60.406 52.381 0.00 0.00 0.00 4.26
3394 3493 2.286872 GAGGTTGTGATCCATGCAGAG 58.713 52.381 0.00 0.00 0.00 3.35
3395 3494 0.737219 GGTTGTGATCCATGCAGAGC 59.263 55.000 0.00 0.00 0.00 4.09
3398 3497 0.179702 TGTGATCCATGCAGAGCCTC 59.820 55.000 0.00 0.00 0.00 4.70
3399 3498 0.879400 GTGATCCATGCAGAGCCTCG 60.879 60.000 0.00 0.00 0.00 4.63
3402 3501 1.117749 ATCCATGCAGAGCCTCGCTA 61.118 55.000 9.33 0.00 39.88 4.26
3452 3562 1.340465 CGTACTCGCATGTCGTTGC 59.660 57.895 8.91 0.00 39.67 4.17
3482 3592 0.966875 GTTGGGGTGATGCATGCAGA 60.967 55.000 26.69 12.36 0.00 4.26
3483 3593 0.681887 TTGGGGTGATGCATGCAGAG 60.682 55.000 26.69 0.00 0.00 3.35
3638 3752 4.301628 GTGCTTGCTGCTTGACTTTATTT 58.698 39.130 0.00 0.00 43.37 1.40
3760 3874 0.393944 TCTCAGCGTACGGAGGACAT 60.394 55.000 18.39 0.00 38.50 3.06
3814 3930 3.802418 GACCACAACGGACGTGCCT 62.802 63.158 0.00 0.00 38.63 4.75
3819 3935 1.135199 CACAACGGACGTGCCTATACT 60.135 52.381 0.00 0.00 0.00 2.12
3867 3984 4.778415 CTCTCGTCCACGTGCCCG 62.778 72.222 10.91 14.12 40.80 6.13
3878 3995 0.396139 ACGTGCCCGAGGTAATCCTA 60.396 55.000 0.00 0.00 45.24 2.94
3880 3997 1.137479 CGTGCCCGAGGTAATCCTAAA 59.863 52.381 0.00 0.00 45.24 1.85
3882 3999 3.743269 CGTGCCCGAGGTAATCCTAAAAT 60.743 47.826 0.00 0.00 45.24 1.82
3883 4000 4.204799 GTGCCCGAGGTAATCCTAAAATT 58.795 43.478 0.00 0.00 45.24 1.82
3884 4001 5.370679 GTGCCCGAGGTAATCCTAAAATTA 58.629 41.667 0.00 0.00 45.24 1.40
3900 4017 9.232882 TCCTAAAATTATTAAGCTCCCTAGGAA 57.767 33.333 11.48 0.00 30.73 3.36
3912 4029 4.570933 GCTCCCTAGGAATAGAGGCATAGA 60.571 50.000 11.48 0.00 0.00 1.98
3926 4043 3.118445 AGGCATAGAAGAGCTCCAAAGTC 60.118 47.826 10.93 0.46 0.00 3.01
3930 4047 5.064579 GCATAGAAGAGCTCCAAAGTCTTTC 59.935 44.000 10.93 5.03 30.55 2.62
3931 4048 4.972751 AGAAGAGCTCCAAAGTCTTTCT 57.027 40.909 10.93 7.42 30.55 2.52
3932 4049 5.303259 AGAAGAGCTCCAAAGTCTTTCTT 57.697 39.130 10.93 0.00 38.10 2.52
3933 4050 6.426646 AGAAGAGCTCCAAAGTCTTTCTTA 57.573 37.500 10.93 0.00 35.02 2.10
3945 4063 3.583526 AGTCTTTCTTAGAAGTGGACCCC 59.416 47.826 15.43 0.00 33.81 4.95
3971 4089 3.971305 TGTAAGGGTATGGTAGGGTCATG 59.029 47.826 0.00 0.00 0.00 3.07
3977 4095 0.346932 ATGGTAGGGTCATGGGTCCT 59.653 55.000 0.00 0.18 34.85 3.85
3992 4110 1.409064 GGTCCTGCATGACAGTATCGA 59.591 52.381 21.49 0.00 45.68 3.59
3995 4113 4.122776 GTCCTGCATGACAGTATCGAAAT 58.877 43.478 16.22 0.00 45.68 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 3.551890 CCGGTTACTGAACGAATGATGAG 59.448 47.826 0.00 0.00 36.32 2.90
156 157 1.381872 CCTGTGGGGAGACGAGGAT 60.382 63.158 0.00 0.00 37.23 3.24
376 388 3.933722 ATGGCGATGGGAGAGGCG 61.934 66.667 0.00 0.00 0.00 5.52
377 389 2.281345 CATGGCGATGGGAGAGGC 60.281 66.667 0.00 0.00 0.00 4.70
378 390 1.475169 TAGCATGGCGATGGGAGAGG 61.475 60.000 10.93 0.00 0.00 3.69
433 445 1.151668 GTGCATGGCTGGATATCGAC 58.848 55.000 0.00 0.00 0.00 4.20
1017 1035 1.142748 CTCCTCCACGATGTCCAGC 59.857 63.158 0.00 0.00 0.00 4.85
1259 1277 1.126846 CTTACAACTCGGCGCAGAAAG 59.873 52.381 12.27 8.05 0.00 2.62
1269 1287 5.177511 TGAAGAGAAATGTGCTTACAACTCG 59.822 40.000 0.00 0.00 0.00 4.18
1351 1370 2.746362 CACTTCTTCCTGCACCTGAATC 59.254 50.000 0.00 0.00 0.00 2.52
1416 1435 6.368779 AAACACAGGAGTAGTATTTAGGCA 57.631 37.500 0.00 0.00 0.00 4.75
1430 1452 7.388776 CAGAAGATTGAATCACTAAACACAGGA 59.611 37.037 8.03 0.00 0.00 3.86
1431 1453 7.173907 ACAGAAGATTGAATCACTAAACACAGG 59.826 37.037 8.03 0.00 0.00 4.00
1451 1480 3.668447 AGCATGTACCTGTTCACAGAAG 58.332 45.455 8.61 0.00 46.59 2.85
1459 1488 6.625740 GCATGTAAATGAAGCATGTACCTGTT 60.626 38.462 0.00 0.00 41.27 3.16
1460 1489 5.163622 GCATGTAAATGAAGCATGTACCTGT 60.164 40.000 0.00 0.00 41.27 4.00
1464 1493 7.041167 TGGATAGCATGTAAATGAAGCATGTAC 60.041 37.037 0.00 0.00 41.27 2.90
1478 1507 8.771521 TTAGTAGTAACCTTGGATAGCATGTA 57.228 34.615 0.00 0.00 0.00 2.29
1488 1520 6.527057 AGTAGTGCTTAGTAGTAACCTTGG 57.473 41.667 0.00 0.00 0.00 3.61
1502 1534 7.658261 TCATAATATTGTCGCTAGTAGTGCTT 58.342 34.615 5.81 0.00 0.00 3.91
1504 1536 7.410942 GCTTCATAATATTGTCGCTAGTAGTGC 60.411 40.741 5.81 2.50 0.00 4.40
1505 1537 7.595130 TGCTTCATAATATTGTCGCTAGTAGTG 59.405 37.037 4.22 4.22 0.00 2.74
1506 1538 7.658261 TGCTTCATAATATTGTCGCTAGTAGT 58.342 34.615 0.00 0.00 0.00 2.73
1507 1539 8.023706 TCTGCTTCATAATATTGTCGCTAGTAG 58.976 37.037 0.00 0.00 0.00 2.57
1508 1540 7.882179 TCTGCTTCATAATATTGTCGCTAGTA 58.118 34.615 0.00 0.00 0.00 1.82
1509 1541 6.749139 TCTGCTTCATAATATTGTCGCTAGT 58.251 36.000 0.00 0.00 0.00 2.57
1510 1542 7.824704 ATCTGCTTCATAATATTGTCGCTAG 57.175 36.000 0.00 0.00 0.00 3.42
1560 1599 8.660373 ACGACTTTGTTAAAATTGCAAATTCAA 58.340 25.926 1.71 0.00 33.97 2.69
1576 1615 7.540745 GTCCATATTATTTGCAACGACTTTGTT 59.459 33.333 0.00 0.00 37.54 2.83
1577 1616 7.027161 GTCCATATTATTTGCAACGACTTTGT 58.973 34.615 0.00 0.00 37.54 2.83
1578 1617 6.472163 GGTCCATATTATTTGCAACGACTTTG 59.528 38.462 0.00 0.00 38.37 2.77
1579 1618 6.377146 AGGTCCATATTATTTGCAACGACTTT 59.623 34.615 0.00 0.00 0.00 2.66
1593 1632 8.117956 ACGGGTAGTATATTCAGGTCCATATTA 58.882 37.037 0.00 0.00 0.00 0.98
1616 1655 4.701956 AGGATTTTCAACAGCATTACGG 57.298 40.909 0.00 0.00 0.00 4.02
1634 1673 5.867903 CCATATGGTGGCAATTTAAAGGA 57.132 39.130 14.09 0.00 42.12 3.36
1649 1688 6.978080 GCCTAATGTTTGTAACAACCATATGG 59.022 38.462 20.68 20.68 45.86 2.74
1692 1731 6.154534 AGCAGCCCTATAAAGTTTAAAAAGGG 59.845 38.462 24.06 24.06 44.24 3.95
1752 1797 2.868899 AGCCAGAAAAACAGGAAGGAG 58.131 47.619 0.00 0.00 0.00 3.69
1770 1815 6.129053 AGTAATGCAGAGCAGAAATTTAGC 57.871 37.500 6.93 6.93 43.65 3.09
1824 1869 4.022935 TGGAACTGCAGCTTGTATCTTTTG 60.023 41.667 15.27 0.00 0.00 2.44
1992 2037 1.081641 GTTGAAGTCGCCGTCGAGA 60.082 57.895 0.00 0.00 46.46 4.04
1995 2040 4.117372 GCGTTGAAGTCGCCGTCG 62.117 66.667 0.00 0.00 46.61 5.12
2037 2082 0.681733 TGCTCTCGCTGAACTCCTTT 59.318 50.000 0.00 0.00 36.97 3.11
2129 2174 1.587613 GAGATGTCGCGGACAGAGC 60.588 63.158 6.13 3.94 46.04 4.09
2163 2208 2.165357 TCCTGCTTCTGATCCAGCTA 57.835 50.000 9.37 0.00 36.92 3.32
2377 2426 5.334414 GGTGATGCTTCTTGTACACTGAAAG 60.334 44.000 0.00 0.00 42.29 2.62
2385 2434 2.237392 AGGAGGGTGATGCTTCTTGTAC 59.763 50.000 0.88 0.00 0.00 2.90
2436 2485 1.165270 CGCCGTCTTTCCCAATCTTT 58.835 50.000 0.00 0.00 0.00 2.52
2454 2503 1.660333 GCGAGCTTCTTGTGGAAAACG 60.660 52.381 0.00 0.00 33.07 3.60
2827 2896 2.146342 CAGACCGAAATGAAGTGCAGT 58.854 47.619 0.00 0.00 0.00 4.40
2828 2897 2.096069 CACAGACCGAAATGAAGTGCAG 60.096 50.000 0.00 0.00 0.00 4.41
2830 2899 1.873591 ACACAGACCGAAATGAAGTGC 59.126 47.619 0.00 0.00 0.00 4.40
2844 2927 6.815142 CACATATTGTTCATGAGAGACACAGA 59.185 38.462 0.00 0.00 0.00 3.41
2846 2929 5.876460 CCACATATTGTTCATGAGAGACACA 59.124 40.000 0.00 0.00 0.00 3.72
2848 2931 6.298441 TCCACATATTGTTCATGAGAGACA 57.702 37.500 0.00 0.00 0.00 3.41
2850 2933 6.183360 ACGATCCACATATTGTTCATGAGAGA 60.183 38.462 0.00 0.00 0.00 3.10
2865 2955 5.870433 TGTTATGTTTACGAACGATCCACAT 59.130 36.000 0.14 6.33 38.65 3.21
2866 2956 5.228665 TGTTATGTTTACGAACGATCCACA 58.771 37.500 0.14 0.00 38.65 4.17
3247 3346 2.931105 TATGGTGGTGGCGGTGGT 60.931 61.111 0.00 0.00 0.00 4.16
3248 3347 2.124736 CTATGGTGGTGGCGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
3249 3348 2.824041 GCTATGGTGGTGGCGGTG 60.824 66.667 0.00 0.00 0.00 4.94
3392 3491 1.226831 GTCACAGCTAGCGAGGCTC 60.227 63.158 9.55 3.87 40.44 4.70
3393 3492 0.394488 TAGTCACAGCTAGCGAGGCT 60.394 55.000 9.55 12.29 43.41 4.58
3394 3493 0.456221 TTAGTCACAGCTAGCGAGGC 59.544 55.000 9.55 4.80 0.00 4.70
3395 3494 1.746220 AGTTAGTCACAGCTAGCGAGG 59.254 52.381 9.55 5.80 0.00 4.63
3398 3497 2.520979 GACAGTTAGTCACAGCTAGCG 58.479 52.381 9.55 7.05 46.77 4.26
3441 3551 0.041312 ACGAAACAGCAACGACATGC 60.041 50.000 0.00 0.00 46.78 4.06
3452 3562 1.152839 ACCCCAACCCACGAAACAG 60.153 57.895 0.00 0.00 0.00 3.16
3482 3592 6.628644 ACCTACTTTTATTGCCTTCTCTCT 57.371 37.500 0.00 0.00 0.00 3.10
3483 3593 6.480651 GCTACCTACTTTTATTGCCTTCTCTC 59.519 42.308 0.00 0.00 0.00 3.20
3602 3712 2.159310 GCAAGCACCTTTTACACACACA 60.159 45.455 0.00 0.00 0.00 3.72
3603 3713 2.099098 AGCAAGCACCTTTTACACACAC 59.901 45.455 0.00 0.00 0.00 3.82
3638 3752 3.515502 TGGGAAAAATTGACACACAACCA 59.484 39.130 0.00 0.00 41.52 3.67
3737 3851 0.809385 CCTCCGTACGCTGAGAAAGA 59.191 55.000 19.26 5.05 0.00 2.52
3814 3930 3.374745 GCCGTACGCTAAAGCAAGTATA 58.625 45.455 10.49 0.00 42.21 1.47
3819 3935 3.465753 CGCCGTACGCTAAAGCAA 58.534 55.556 10.49 0.00 42.21 3.91
3842 3959 1.621301 CGTGGACGAGAGCAAAGCTG 61.621 60.000 0.00 0.00 39.68 4.24
3880 3997 9.052365 CCTCTATTCCTAGGGAGCTTAATAATT 57.948 37.037 9.46 0.00 31.21 1.40
3882 3999 6.440965 GCCTCTATTCCTAGGGAGCTTAATAA 59.559 42.308 9.46 0.00 33.17 1.40
3883 4000 5.958987 GCCTCTATTCCTAGGGAGCTTAATA 59.041 44.000 9.46 3.69 33.17 0.98
3884 4001 4.780554 GCCTCTATTCCTAGGGAGCTTAAT 59.219 45.833 9.46 2.59 33.17 1.40
3898 4015 4.526262 TGGAGCTCTTCTATGCCTCTATTC 59.474 45.833 14.64 0.00 0.00 1.75
3900 4017 4.125124 TGGAGCTCTTCTATGCCTCTAT 57.875 45.455 14.64 0.00 0.00 1.98
3912 4029 6.426646 TCTAAGAAAGACTTTGGAGCTCTT 57.573 37.500 14.64 4.14 39.72 2.85
3945 4063 3.714798 ACCCTACCATACCCTTACATGTG 59.285 47.826 9.11 0.00 0.00 3.21
3958 4076 0.346932 AGGACCCATGACCCTACCAT 59.653 55.000 0.00 0.00 0.00 3.55
3960 4078 1.984288 GCAGGACCCATGACCCTACC 61.984 65.000 0.00 0.00 0.00 3.18
3977 4095 3.871006 GTGGATTTCGATACTGTCATGCA 59.129 43.478 0.00 0.00 0.00 3.96
3992 4110 6.564557 AATGCTTTAATGGGATGTGGATTT 57.435 33.333 0.00 0.00 0.00 2.17
3995 4113 7.487822 TTAAAATGCTTTAATGGGATGTGGA 57.512 32.000 0.00 0.00 33.09 4.02
4137 4259 9.645059 CTCATGAACAGTCTTTTAGAACTCATA 57.355 33.333 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.