Multiple sequence alignment - TraesCS1A01G401800

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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 TraesCS1A01G401800 chr1A 100.000 4639 0 0 1 4639 565291128 565295766 0.000000e+00 8567.0
1 TraesCS1A01G401800 chr1A 100.000 30 0 0 3872 3901 527869938 527869967 6.480000e-04 56.5
2 TraesCS1A01G401800 chr1A 100.000 28 0 0 3876 3903 105176903 105176876 8.000000e-03 52.8
3 TraesCS1A01G401800 chr1D 91.010 1802 72 45 618 2374 470999159 471000915 0.000000e+00 2348.0
4 TraesCS1A01G401800 chr1D 88.914 1326 84 35 2774 4063 471001604 471002902 0.000000e+00 1576.0
5 TraesCS1A01G401800 chr1D 88.906 640 42 13 1 620 470998490 470999120 0.000000e+00 761.0
6 TraesCS1A01G401800 chr1D 90.501 379 16 11 2373 2743 471001165 471001531 2.510000e-132 483.0
7 TraesCS1A01G401800 chr1D 91.525 236 14 2 4401 4636 471003231 471003460 2.080000e-83 320.0
8 TraesCS1A01G401800 chr1D 87.943 141 13 4 4062 4201 471003064 471003201 3.710000e-36 163.0
9 TraesCS1A01G401800 chr1D 83.571 140 20 3 2844 2981 436713123 436712985 1.350000e-25 128.0
10 TraesCS1A01G401800 chr1D 100.000 28 0 0 3876 3903 310696643 310696616 8.000000e-03 52.8
11 TraesCS1A01G401800 chr1B 91.146 1615 71 29 3070 4636 654716508 654718098 0.000000e+00 2124.0
12 TraesCS1A01G401800 chr1B 89.394 1650 84 42 624 2227 654714005 654715609 0.000000e+00 1993.0
13 TraesCS1A01G401800 chr1B 91.723 447 25 5 1 442 654713369 654713808 1.100000e-170 610.0
14 TraesCS1A01G401800 chr1B 88.397 474 30 19 2245 2706 654715676 654716136 8.780000e-152 547.0
15 TraesCS1A01G401800 chr1B 92.446 278 15 1 2706 2977 654716179 654716456 4.350000e-105 392.0
16 TraesCS1A01G401800 chr1B 86.957 138 13 5 2843 2978 669710467 669710333 2.890000e-32 150.0
17 TraesCS1A01G401800 chr1B 93.333 45 3 0 531 575 654713883 654713927 3.000000e-07 67.6
18 TraesCS1A01G401800 chr3A 89.697 165 17 0 3076 3240 455803530 455803366 1.310000e-50 211.0
19 TraesCS1A01G401800 chr3A 92.105 152 8 4 2829 2977 455803811 455803661 1.310000e-50 211.0
20 TraesCS1A01G401800 chr3A 86.232 138 15 4 3077 3212 427333067 427332932 3.740000e-31 147.0
21 TraesCS1A01G401800 chr3A 87.302 126 16 0 2849 2974 427333264 427333139 1.350000e-30 145.0
22 TraesCS1A01G401800 chr3A 100.000 33 0 0 3871 3903 122496204 122496236 1.390000e-05 62.1
23 TraesCS1A01G401800 chr3B 89.634 164 17 0 3076 3239 435959307 435959144 4.700000e-50 209.0
24 TraesCS1A01G401800 chr3B 90.789 152 10 4 2829 2977 435959581 435959431 2.830000e-47 200.0
25 TraesCS1A01G401800 chr3B 87.302 126 16 0 2849 2974 413419084 413419209 1.350000e-30 145.0
26 TraesCS1A01G401800 chr3D 91.447 152 9 4 2829 2977 337974628 337974478 6.080000e-49 206.0
27 TraesCS1A01G401800 chr3D 87.681 138 13 4 3077 3212 308057679 308057544 1.730000e-34 158.0
28 TraesCS1A01G401800 chr6B 100.000 34 0 0 3871 3904 560765045 560765012 3.880000e-06 63.9
29 TraesCS1A01G401800 chr4D 100.000 28 0 0 3876 3903 331146631 331146658 8.000000e-03 52.8


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 TraesCS1A01G401800 chr1A 565291128 565295766 4638 False 8567.000000 8567 100.000000 1 4639 1 chr1A.!!$F2 4638
1 TraesCS1A01G401800 chr1D 470998490 471003460 4970 False 941.833333 2348 89.799833 1 4636 6 chr1D.!!$F1 4635
2 TraesCS1A01G401800 chr1B 654713369 654718098 4729 False 955.600000 2124 91.073167 1 4636 6 chr1B.!!$F1 4635

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
389 391 0.249447 CGACTTGGAGTGTGCACTGA 60.249 55.0 19.41 0.0 42.66 3.41 F
832 925 0.261696 GCTTCCTCTCTCTCCCTCCT 59.738 60.0 0.00 0.0 0.00 3.69 F
2569 3012 0.039798 CGTACACACACGCACCTACT 60.040 55.0 0.00 0.0 34.78 2.57 F
3048 3574 0.458025 GCGGCTAACTGCGTAGAAGT 60.458 55.0 7.78 0.0 44.05 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1340 0.033991 CTCCCTCTTCACCTCCTCGA 60.034 60.0 0.0 0.0 0.0 4.04 R
2797 3303 0.031178 GCCGCCCTGCAATTAATCAG 59.969 55.0 0.0 0.0 0.0 2.90 R
3476 4005 0.038166 TACTGTTCCCCGTCGTACCT 59.962 55.0 0.0 0.0 0.0 3.08 R
3985 4541 0.105760 AGCAAAATCACCACCACCCA 60.106 50.0 0.0 0.0 0.0 4.51 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
138 139 2.906182 GATCCCGCTCGTCATGCACA 62.906 60.000 0.00 0.00 0.00 4.57
247 249 1.052124 TGGTCTGAACGGGTTGACCT 61.052 55.000 17.05 0.00 46.50 3.85
298 300 2.272146 GTGGCCGTCATCCATGGT 59.728 61.111 12.58 0.00 35.81 3.55
371 373 2.159435 GCCTTGCCCAGTGTTAATTACG 60.159 50.000 0.00 0.00 0.00 3.18
389 391 0.249447 CGACTTGGAGTGTGCACTGA 60.249 55.000 19.41 0.00 42.66 3.41
390 392 1.606480 CGACTTGGAGTGTGCACTGAT 60.606 52.381 19.41 3.35 42.66 2.90
391 393 1.802960 GACTTGGAGTGTGCACTGATG 59.197 52.381 19.41 4.50 42.66 3.07
435 453 1.611491 GTCGCCTCCCAACAAATTTGA 59.389 47.619 24.64 0.68 0.00 2.69
438 456 2.607771 CGCCTCCCAACAAATTTGACTG 60.608 50.000 24.64 18.56 0.00 3.51
444 462 6.024552 TCCCAACAAATTTGACTGCTAATC 57.975 37.500 24.64 0.00 0.00 1.75
445 463 5.774690 TCCCAACAAATTTGACTGCTAATCT 59.225 36.000 24.64 0.00 0.00 2.40
446 464 6.267471 TCCCAACAAATTTGACTGCTAATCTT 59.733 34.615 24.64 1.56 0.00 2.40
447 465 6.930722 CCCAACAAATTTGACTGCTAATCTTT 59.069 34.615 24.64 1.05 0.00 2.52
448 466 8.087750 CCCAACAAATTTGACTGCTAATCTTTA 58.912 33.333 24.64 0.00 0.00 1.85
449 467 9.643693 CCAACAAATTTGACTGCTAATCTTTAT 57.356 29.630 24.64 0.00 0.00 1.40
458 476 9.691362 TTGACTGCTAATCTTTATTTGTTTTCC 57.309 29.630 0.00 0.00 0.00 3.13
519 548 5.898061 CGTGGTGAACTAAAAACTACGTTTC 59.102 40.000 0.00 0.00 41.89 2.78
523 552 8.767085 TGGTGAACTAAAAACTACGTTTCATAG 58.233 33.333 0.00 9.09 34.43 2.23
533 562 4.933400 ACTACGTTTCATAGCGGTTGAATT 59.067 37.500 0.00 0.00 33.37 2.17
537 566 5.163893 ACGTTTCATAGCGGTTGAATTAGTG 60.164 40.000 11.21 5.15 33.37 2.74
542 571 6.112734 TCATAGCGGTTGAATTAGTGACATT 58.887 36.000 0.00 0.00 0.00 2.71
596 644 2.165319 AAAACTAGCACGTGAGACCC 57.835 50.000 22.23 0.00 0.00 4.46
597 645 0.320697 AAACTAGCACGTGAGACCCC 59.679 55.000 22.23 0.00 0.00 4.95
666 755 5.952347 AGTTAAGTAGAACCATTCCGGAT 57.048 39.130 4.15 0.00 38.63 4.18
705 794 6.294508 CCCCGCAAGAAGAAAGAAATAAAGAA 60.295 38.462 0.00 0.00 43.02 2.52
787 880 2.158682 ACACAATCACACACTAGCCCAA 60.159 45.455 0.00 0.00 0.00 4.12
832 925 0.261696 GCTTCCTCTCTCTCCCTCCT 59.738 60.000 0.00 0.00 0.00 3.69
855 949 1.843376 CCCTCACACACACCCCTCT 60.843 63.158 0.00 0.00 0.00 3.69
856 950 1.674057 CCTCACACACACCCCTCTC 59.326 63.158 0.00 0.00 0.00 3.20
858 952 0.833834 CTCACACACACCCCTCTCCT 60.834 60.000 0.00 0.00 0.00 3.69
859 953 0.832135 TCACACACACCCCTCTCCTC 60.832 60.000 0.00 0.00 0.00 3.71
860 954 1.536662 ACACACACCCCTCTCCTCC 60.537 63.158 0.00 0.00 0.00 4.30
861 955 2.122954 ACACACCCCTCTCCTCCC 59.877 66.667 0.00 0.00 0.00 4.30
862 956 2.689034 CACACCCCTCTCCTCCCC 60.689 72.222 0.00 0.00 0.00 4.81
863 957 2.876858 ACACCCCTCTCCTCCCCT 60.877 66.667 0.00 0.00 0.00 4.79
983 1079 0.530288 GCTCCAGCTCCGATCTATCC 59.470 60.000 0.00 0.00 38.21 2.59
987 1083 2.042297 TCCAGCTCCGATCTATCCATCT 59.958 50.000 0.00 0.00 0.00 2.90
989 1085 3.380004 CCAGCTCCGATCTATCCATCTAC 59.620 52.174 0.00 0.00 0.00 2.59
1179 1287 2.207924 GCCGGGGATGGACTACGAT 61.208 63.158 2.18 0.00 0.00 3.73
1185 1293 0.660595 GGATGGACTACGATGACGCG 60.661 60.000 3.53 3.53 43.96 6.01
1438 1546 3.537297 GCGACGACGAGAGCAAGC 61.537 66.667 12.29 0.00 42.66 4.01
1504 1620 8.246180 GGTAAGATCTGATTTGATTTCTTGCAA 58.754 33.333 0.00 0.00 0.00 4.08
1514 1630 9.650371 GATTTGATTTCTTGCAAAAACTTTACC 57.350 29.630 0.00 0.00 37.52 2.85
1517 1633 7.551585 TGATTTCTTGCAAAAACTTTACCTGA 58.448 30.769 0.00 0.00 0.00 3.86
1518 1634 8.203485 TGATTTCTTGCAAAAACTTTACCTGAT 58.797 29.630 0.00 0.00 0.00 2.90
1531 1647 5.416952 ACTTTACCTGATTGATCTTGGCTTG 59.583 40.000 0.00 0.00 0.00 4.01
1541 1657 4.096681 TGATCTTGGCTTGGAGTTCTAGA 58.903 43.478 0.00 0.00 0.00 2.43
1544 1660 4.096681 TCTTGGCTTGGAGTTCTAGATCA 58.903 43.478 3.70 0.00 0.00 2.92
1545 1661 4.161189 TCTTGGCTTGGAGTTCTAGATCAG 59.839 45.833 3.70 0.00 0.00 2.90
1546 1662 3.713003 TGGCTTGGAGTTCTAGATCAGA 58.287 45.455 3.70 0.00 0.00 3.27
1576 1704 3.881688 AGGTTGATTGATCTGCATACAGC 59.118 43.478 0.00 0.00 44.10 4.40
1648 1777 3.001838 TCACGTTCGATTGTTCTTGTTGG 59.998 43.478 0.00 0.00 0.00 3.77
1653 1782 4.002906 TCGATTGTTCTTGTTGGTAGCT 57.997 40.909 0.00 0.00 0.00 3.32
1654 1783 4.385825 TCGATTGTTCTTGTTGGTAGCTT 58.614 39.130 0.00 0.00 0.00 3.74
1655 1784 4.213270 TCGATTGTTCTTGTTGGTAGCTTG 59.787 41.667 0.00 0.00 0.00 4.01
1660 1789 4.335315 TGTTCTTGTTGGTAGCTTGTTGAG 59.665 41.667 0.00 0.00 0.00 3.02
1662 1791 4.523083 TCTTGTTGGTAGCTTGTTGAGTT 58.477 39.130 0.00 0.00 0.00 3.01
1732 1866 5.844516 CCCCTTTCCACTGGATAATACTAGA 59.155 44.000 0.00 0.00 0.00 2.43
1831 1966 6.785488 TTTAATTAGATCTACCATGCAGCG 57.215 37.500 0.67 0.00 0.00 5.18
1834 1969 0.105593 AGATCTACCATGCAGCGTGG 59.894 55.000 29.36 29.36 45.34 4.94
1864 1999 6.439636 TCGATCCTTTCCATTCCATTCTAT 57.560 37.500 0.00 0.00 0.00 1.98
1865 2000 7.553504 TCGATCCTTTCCATTCCATTCTATA 57.446 36.000 0.00 0.00 0.00 1.31
1966 2101 8.762426 GGTCCTAGATCGAATACAAAATTGTAC 58.238 37.037 8.09 0.00 45.47 2.90
1979 2114 7.069877 ACAAAATTGTACTAGTACCACTGGA 57.930 36.000 26.41 7.40 40.16 3.86
1988 2123 3.857157 AGTACCACTGGAGCAAAAAGA 57.143 42.857 0.71 0.00 0.00 2.52
1993 2128 2.288030 CCACTGGAGCAAAAAGAGCTTG 60.288 50.000 0.00 0.00 43.58 4.01
1995 2130 3.067180 CACTGGAGCAAAAAGAGCTTGAA 59.933 43.478 0.00 0.00 43.58 2.69
2040 2175 3.665745 AGGTTGATGAATGGTTGTTGC 57.334 42.857 0.00 0.00 0.00 4.17
2049 2184 6.265876 TGATGAATGGTTGTTGCTGCATATAT 59.734 34.615 1.84 0.00 0.00 0.86
2050 2185 7.447853 TGATGAATGGTTGTTGCTGCATATATA 59.552 33.333 1.84 0.00 0.00 0.86
2075 2210 3.255642 TGCCCACAGCTTTTTGATTAGAC 59.744 43.478 0.00 0.00 44.23 2.59
2076 2211 3.367395 GCCCACAGCTTTTTGATTAGACC 60.367 47.826 0.00 0.00 38.99 3.85
2077 2212 3.119849 CCCACAGCTTTTTGATTAGACCG 60.120 47.826 0.00 0.00 0.00 4.79
2191 2330 4.495184 GCGTCCTTGTTAATTAATCCACCG 60.495 45.833 0.31 2.25 0.00 4.94
2281 2469 8.439964 TGATCCATCAACCATCAGATATCTAA 57.560 34.615 4.54 0.00 33.08 2.10
2282 2470 8.537858 TGATCCATCAACCATCAGATATCTAAG 58.462 37.037 4.54 0.00 33.08 2.18
2283 2471 6.705302 TCCATCAACCATCAGATATCTAAGC 58.295 40.000 4.54 0.00 0.00 3.09
2284 2472 6.499699 TCCATCAACCATCAGATATCTAAGCT 59.500 38.462 4.54 0.00 0.00 3.74
2285 2473 7.675619 TCCATCAACCATCAGATATCTAAGCTA 59.324 37.037 4.54 0.00 0.00 3.32
2286 2474 7.763528 CCATCAACCATCAGATATCTAAGCTAC 59.236 40.741 4.54 0.00 0.00 3.58
2287 2475 8.530311 CATCAACCATCAGATATCTAAGCTACT 58.470 37.037 4.54 0.00 0.00 2.57
2289 2477 9.588096 TCAACCATCAGATATCTAAGCTACTAA 57.412 33.333 4.54 0.00 0.00 2.24
2290 2478 9.632807 CAACCATCAGATATCTAAGCTACTAAC 57.367 37.037 4.54 0.00 0.00 2.34
2291 2479 8.046294 ACCATCAGATATCTAAGCTACTAACG 57.954 38.462 4.54 0.00 0.00 3.18
2292 2480 6.970043 CCATCAGATATCTAAGCTACTAACGC 59.030 42.308 4.54 0.00 0.00 4.84
2293 2481 6.497785 TCAGATATCTAAGCTACTAACGCC 57.502 41.667 4.54 0.00 0.00 5.68
2294 2482 5.121925 TCAGATATCTAAGCTACTAACGCCG 59.878 44.000 4.54 0.00 0.00 6.46
2295 2483 5.121925 CAGATATCTAAGCTACTAACGCCGA 59.878 44.000 4.54 0.00 0.00 5.54
2296 2484 5.881443 AGATATCTAAGCTACTAACGCCGAT 59.119 40.000 2.53 0.00 0.00 4.18
2297 2485 3.892918 TCTAAGCTACTAACGCCGATC 57.107 47.619 0.00 0.00 0.00 3.69
2298 2486 3.208594 TCTAAGCTACTAACGCCGATCA 58.791 45.455 0.00 0.00 0.00 2.92
2300 2488 1.390565 AGCTACTAACGCCGATCACT 58.609 50.000 0.00 0.00 0.00 3.41
2301 2489 1.749634 AGCTACTAACGCCGATCACTT 59.250 47.619 0.00 0.00 0.00 3.16
2302 2490 1.852895 GCTACTAACGCCGATCACTTG 59.147 52.381 0.00 0.00 0.00 3.16
2303 2491 2.479049 GCTACTAACGCCGATCACTTGA 60.479 50.000 0.00 0.00 0.00 3.02
2306 2494 2.159366 ACTAACGCCGATCACTTGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
2307 2495 0.603569 AACGCCGATCACTTGAGAGT 59.396 50.000 0.00 0.00 36.25 3.24
2396 2837 5.522824 CCATACAAGCATGATGGATCGATAG 59.477 44.000 12.31 0.00 42.41 2.08
2429 2870 9.519191 CCATCCATATCCATGAGTACAAATAAA 57.481 33.333 0.00 0.00 33.67 1.40
2470 2911 8.144155 AGTAGTAGCAAACAAAAGAGAAAGAC 57.856 34.615 0.00 0.00 0.00 3.01
2502 2943 3.071312 TGGTGTACGGTGTGAACCTAAAT 59.929 43.478 0.00 0.00 0.00 1.40
2503 2944 3.681417 GGTGTACGGTGTGAACCTAAATC 59.319 47.826 0.00 0.00 0.00 2.17
2504 2945 4.309099 GTGTACGGTGTGAACCTAAATCA 58.691 43.478 0.00 0.00 0.00 2.57
2569 3012 0.039798 CGTACACACACGCACCTACT 60.040 55.000 0.00 0.00 34.78 2.57
2708 3160 3.286329 TGTGATGCACAATGGCTAGAT 57.714 42.857 0.00 0.00 41.69 1.98
2709 3161 3.208594 TGTGATGCACAATGGCTAGATC 58.791 45.455 0.00 0.00 41.69 2.75
2710 3162 3.208594 GTGATGCACAATGGCTAGATCA 58.791 45.455 0.00 0.00 34.08 2.92
2711 3163 3.628942 GTGATGCACAATGGCTAGATCAA 59.371 43.478 0.00 0.00 34.08 2.57
2712 3164 4.277672 GTGATGCACAATGGCTAGATCAAT 59.722 41.667 0.00 0.00 34.08 2.57
2713 3165 4.517832 TGATGCACAATGGCTAGATCAATC 59.482 41.667 0.00 0.00 34.04 2.67
2714 3166 2.874086 TGCACAATGGCTAGATCAATCG 59.126 45.455 0.00 0.00 34.04 3.34
2725 3225 4.790140 GCTAGATCAATCGTTTGCTTTGTG 59.210 41.667 0.00 0.00 32.61 3.33
2794 3300 5.301045 AGTTGTATAAGATTGACCGATCGGA 59.699 40.000 39.55 19.09 38.96 4.55
2797 3303 1.941325 AAGATTGACCGATCGGAAGC 58.059 50.000 39.55 25.95 38.96 3.86
2904 3410 0.951040 CCAAGAGCGAGGTTGACCAC 60.951 60.000 2.56 0.00 38.89 4.16
2981 3487 4.957684 CCTTCCCAAGGTACCTACATAG 57.042 50.000 16.67 9.16 43.95 2.23
2982 3488 4.296056 CCTTCCCAAGGTACCTACATAGT 58.704 47.826 16.67 0.00 43.95 2.12
2983 3489 5.461327 CCTTCCCAAGGTACCTACATAGTA 58.539 45.833 16.67 0.00 43.95 1.82
2985 3491 5.739143 TCCCAAGGTACCTACATAGTACT 57.261 43.478 16.67 0.00 40.01 2.73
2986 3492 5.699143 TCCCAAGGTACCTACATAGTACTC 58.301 45.833 16.67 0.00 40.01 2.59
2987 3493 4.831710 CCCAAGGTACCTACATAGTACTCC 59.168 50.000 16.67 0.00 40.01 3.85
2990 3496 5.739143 AGGTACCTACATAGTACTCCCAA 57.261 43.478 14.41 0.00 40.01 4.12
2991 3497 6.096164 AGGTACCTACATAGTACTCCCAAA 57.904 41.667 14.41 0.00 40.01 3.28
3015 3523 3.431766 GGATTAGGGTTACGATGCACAGT 60.432 47.826 0.00 0.00 0.00 3.55
3032 3558 2.153945 GTGCGATGTTTGCATGCGG 61.154 57.895 14.09 0.00 45.34 5.69
3047 3573 2.288969 GCGGCTAACTGCGTAGAAG 58.711 57.895 7.78 5.42 44.05 2.85
3048 3574 0.458025 GCGGCTAACTGCGTAGAAGT 60.458 55.000 7.78 0.00 44.05 3.01
3049 3575 1.269166 CGGCTAACTGCGTAGAAGTG 58.731 55.000 7.78 0.00 44.05 3.16
3050 3576 1.000145 GGCTAACTGCGTAGAAGTGC 59.000 55.000 7.78 5.83 44.05 4.40
3051 3577 1.000145 GCTAACTGCGTAGAAGTGCC 59.000 55.000 7.78 0.00 0.00 5.01
3052 3578 1.641577 CTAACTGCGTAGAAGTGCCC 58.358 55.000 7.78 0.00 0.00 5.36
3055 3581 3.296709 CTGCGTAGAAGTGCCCGGT 62.297 63.158 0.00 0.00 0.00 5.28
3056 3582 2.813908 GCGTAGAAGTGCCCGGTG 60.814 66.667 0.00 0.00 0.00 4.94
3057 3583 2.813908 CGTAGAAGTGCCCGGTGC 60.814 66.667 0.00 4.04 41.77 5.01
3197 3723 4.060667 CACACCCACCCCATCCCC 62.061 72.222 0.00 0.00 0.00 4.81
3624 4165 2.878406 AGCGACAACAGCAATAACAACT 59.122 40.909 0.00 0.00 37.01 3.16
3674 4218 1.708993 TTCCAGCTTGCCCTGACAGT 61.709 55.000 0.93 0.00 34.77 3.55
3684 4228 0.105593 CCCTGACAGTGATCCATCGG 59.894 60.000 0.00 0.00 0.00 4.18
3704 4250 3.134127 GATTCGGCGCCCTTTGCT 61.134 61.111 23.46 0.00 38.05 3.91
3705 4251 2.676471 ATTCGGCGCCCTTTGCTT 60.676 55.556 23.46 0.00 38.05 3.91
3706 4252 2.872337 GATTCGGCGCCCTTTGCTTG 62.872 60.000 23.46 3.72 38.05 4.01
3709 4255 2.622011 CGGCGCCCTTTGCTTGTTA 61.622 57.895 23.46 0.00 38.05 2.41
3786 4335 7.255555 CGATGAGGATATGATCTAGCTTAGCAT 60.256 40.741 7.07 0.00 0.00 3.79
3852 4404 4.501921 GCATGTTAGCGTAGTGTTAGTACC 59.498 45.833 0.00 0.00 0.00 3.34
3962 4518 4.762765 ACTTGGAGCCGTATCTATCTAGTG 59.237 45.833 0.00 0.00 0.00 2.74
3966 4522 4.635324 GGAGCCGTATCTATCTAGTGGTAC 59.365 50.000 0.00 0.00 0.00 3.34
3972 4528 7.364232 GCCGTATCTATCTAGTGGTACTACCTA 60.364 44.444 5.65 0.00 39.58 3.08
3976 4532 7.927683 TCTATCTAGTGGTACTACCTACTGT 57.072 40.000 5.65 0.00 39.58 3.55
3980 4536 8.789767 ATCTAGTGGTACTACCTACTGTACTA 57.210 38.462 5.65 9.27 39.58 1.82
3981 4537 8.012957 TCTAGTGGTACTACCTACTGTACTAC 57.987 42.308 5.65 10.37 45.30 2.73
3984 4540 6.644347 GTGGTACTACCTACTGTACTACTGA 58.356 44.000 6.79 0.00 43.24 3.41
3985 4541 7.278875 GTGGTACTACCTACTGTACTACTGAT 58.721 42.308 6.79 0.00 43.24 2.90
3986 4542 7.226325 GTGGTACTACCTACTGTACTACTGATG 59.774 44.444 6.79 0.00 43.24 3.07
3987 4543 6.709846 GGTACTACCTACTGTACTACTGATGG 59.290 46.154 0.00 4.54 39.04 3.51
4010 4571 2.562298 TGGTGGTGATTTTGCTTGATCC 59.438 45.455 0.00 0.00 0.00 3.36
4036 4597 2.286772 CCGTTTCCTTGACTTTGAACCG 60.287 50.000 0.00 0.00 0.00 4.44
4049 4611 7.857569 TGACTTTGAACCGAGTACAAAATTAG 58.142 34.615 0.00 0.00 34.03 1.73
4075 4800 7.121315 GGTGATGCTTAATAACTTTCAAGGACT 59.879 37.037 0.00 0.00 0.00 3.85
4076 4801 7.965107 GTGATGCTTAATAACTTTCAAGGACTG 59.035 37.037 0.00 0.00 0.00 3.51
4077 4802 6.254281 TGCTTAATAACTTTCAAGGACTGC 57.746 37.500 0.00 0.00 0.00 4.40
4078 4803 5.767665 TGCTTAATAACTTTCAAGGACTGCA 59.232 36.000 0.00 0.00 0.00 4.41
4079 4804 6.434028 TGCTTAATAACTTTCAAGGACTGCAT 59.566 34.615 0.00 0.00 0.00 3.96
4080 4805 6.749118 GCTTAATAACTTTCAAGGACTGCATG 59.251 38.462 0.00 0.00 0.00 4.06
4081 4806 4.708726 ATAACTTTCAAGGACTGCATGC 57.291 40.909 11.82 11.82 0.00 4.06
4082 4807 1.985473 ACTTTCAAGGACTGCATGCA 58.015 45.000 21.29 21.29 0.00 3.96
4194 4927 1.141019 GGACGATGCTCTTGCGGTA 59.859 57.895 0.00 0.00 43.34 4.02
4239 4973 7.829378 ATCGGTACAGAAAGTTAGTTGATTC 57.171 36.000 0.00 0.00 0.00 2.52
4247 4981 4.946160 AAGTTAGTTGATTCATGGGGGA 57.054 40.909 0.00 0.00 0.00 4.81
4248 4982 4.510167 AGTTAGTTGATTCATGGGGGAG 57.490 45.455 0.00 0.00 0.00 4.30
4251 4987 3.659183 AGTTGATTCATGGGGGAGAAG 57.341 47.619 0.00 0.00 0.00 2.85
4255 4991 3.133665 TGATTCATGGGGGAGAAGGAAT 58.866 45.455 0.00 0.00 0.00 3.01
4268 5004 1.887198 GAAGGAATCGATCGAGGGCTA 59.113 52.381 23.84 0.00 0.00 3.93
4341 5077 0.512952 GAAGTGCAGCAACGTACTGG 59.487 55.000 17.40 3.17 35.62 4.00
4342 5078 0.884704 AAGTGCAGCAACGTACTGGG 60.885 55.000 17.40 0.00 35.62 4.45
4536 5277 2.764128 TGGGAGAGACCATCGGGC 60.764 66.667 0.00 0.00 41.20 6.13
4617 5364 5.222870 ACAGAAGGGATGAGACTATTGGAT 58.777 41.667 0.00 0.00 0.00 3.41
4637 5384 3.153369 TGCTAGGGTCAAAAGCATTGA 57.847 42.857 1.23 1.23 41.15 2.57
4638 5385 3.495331 TGCTAGGGTCAAAAGCATTGAA 58.505 40.909 6.54 0.00 41.15 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.227276 CGATCACGAGGGGAGGGG 61.227 72.222 0.00 0.00 42.66 4.79
90 91 1.747145 CGATGCTGATCTCAGGGCT 59.253 57.895 9.15 0.00 43.94 5.19
97 98 2.419198 GCCGTCCGATGCTGATCT 59.581 61.111 0.00 0.00 0.00 2.75
127 128 2.738139 CGCCACTGTGCATGACGA 60.738 61.111 1.29 0.00 0.00 4.20
298 300 0.251033 TCCTCTTCCCGACGAGTCAA 60.251 55.000 0.00 0.00 0.00 3.18
350 352 2.159435 CGTAATTAACACTGGGCAAGGC 60.159 50.000 0.00 0.00 0.00 4.35
352 354 4.000988 AGTCGTAATTAACACTGGGCAAG 58.999 43.478 0.00 0.00 0.00 4.01
353 355 4.010667 AGTCGTAATTAACACTGGGCAA 57.989 40.909 0.00 0.00 0.00 4.52
354 356 3.688694 AGTCGTAATTAACACTGGGCA 57.311 42.857 0.00 0.00 0.00 5.36
355 357 3.126343 CCAAGTCGTAATTAACACTGGGC 59.874 47.826 5.80 0.00 29.28 5.36
365 367 2.806244 GTGCACACTCCAAGTCGTAATT 59.194 45.455 13.17 0.00 0.00 1.40
371 373 1.802960 CATCAGTGCACACTCCAAGTC 59.197 52.381 21.04 0.00 40.20 3.01
389 391 2.434336 TGAAGAACGGGTAGCATAGCAT 59.566 45.455 0.00 0.00 41.82 3.79
390 392 1.828595 TGAAGAACGGGTAGCATAGCA 59.171 47.619 0.00 0.00 41.82 3.49
391 393 2.202566 GTGAAGAACGGGTAGCATAGC 58.797 52.381 0.00 0.00 38.62 2.97
392 394 2.167693 TGGTGAAGAACGGGTAGCATAG 59.832 50.000 0.00 0.00 0.00 2.23
393 395 2.181125 TGGTGAAGAACGGGTAGCATA 58.819 47.619 0.00 0.00 0.00 3.14
394 396 0.981183 TGGTGAAGAACGGGTAGCAT 59.019 50.000 0.00 0.00 0.00 3.79
463 481 9.807921 TGAAACCTAGAGGAATATTTCAGTTTT 57.192 29.630 1.60 0.00 33.96 2.43
467 496 7.500227 TGCATGAAACCTAGAGGAATATTTCAG 59.500 37.037 14.07 9.39 38.77 3.02
519 548 5.991328 ATGTCACTAATTCAACCGCTATG 57.009 39.130 0.00 0.00 0.00 2.23
523 552 3.369756 TCGAATGTCACTAATTCAACCGC 59.630 43.478 0.00 0.00 34.34 5.68
533 562 7.040755 ACCAATTCAAAATGTCGAATGTCACTA 60.041 33.333 0.00 0.00 32.27 2.74
537 566 8.514136 TTTACCAATTCAAAATGTCGAATGTC 57.486 30.769 0.00 0.00 32.27 3.06
542 571 7.045126 AGGTTTTACCAATTCAAAATGTCGA 57.955 32.000 0.00 0.00 41.95 4.20
596 644 2.664916 CACACTTGCTCGGATTTTTGG 58.335 47.619 0.00 0.00 0.00 3.28
597 645 2.053627 GCACACTTGCTCGGATTTTTG 58.946 47.619 0.00 0.00 46.17 2.44
705 794 1.615384 GCATGGTCAAGGCCTTCTTCT 60.615 52.381 17.29 0.00 32.41 2.85
787 880 0.961358 AGCACGACGAGTAGAAGGCT 60.961 55.000 0.00 0.00 0.00 4.58
823 916 0.851332 TGAGGGTCTGAGGAGGGAGA 60.851 60.000 0.00 0.00 0.00 3.71
832 925 1.407656 GGGTGTGTGTGAGGGTCTGA 61.408 60.000 0.00 0.00 0.00 3.27
855 949 2.614013 GGGAAGGCAAGGGGAGGA 60.614 66.667 0.00 0.00 0.00 3.71
856 950 3.744155 GGGGAAGGCAAGGGGAGG 61.744 72.222 0.00 0.00 0.00 4.30
858 952 4.301662 AGGGGGAAGGCAAGGGGA 62.302 66.667 0.00 0.00 0.00 4.81
859 953 3.744155 GAGGGGGAAGGCAAGGGG 61.744 72.222 0.00 0.00 0.00 4.79
860 954 3.744155 GGAGGGGGAAGGCAAGGG 61.744 72.222 0.00 0.00 0.00 3.95
861 955 2.941025 TGGAGGGGGAAGGCAAGG 60.941 66.667 0.00 0.00 0.00 3.61
862 956 2.234296 AGTGGAGGGGGAAGGCAAG 61.234 63.158 0.00 0.00 0.00 4.01
863 957 2.121506 AGTGGAGGGGGAAGGCAA 60.122 61.111 0.00 0.00 0.00 4.52
967 1063 2.455557 AGATGGATAGATCGGAGCTGG 58.544 52.381 5.94 0.00 0.00 4.85
968 1064 3.380004 GGTAGATGGATAGATCGGAGCTG 59.620 52.174 5.94 0.00 0.00 4.24
969 1065 3.626222 GGGTAGATGGATAGATCGGAGCT 60.626 52.174 0.00 0.00 0.00 4.09
970 1066 2.691011 GGGTAGATGGATAGATCGGAGC 59.309 54.545 0.00 0.00 0.00 4.70
972 1068 4.537751 GATGGGTAGATGGATAGATCGGA 58.462 47.826 0.00 0.00 0.00 4.55
976 1072 5.222870 GGATGGATGGGTAGATGGATAGAT 58.777 45.833 0.00 0.00 0.00 1.98
977 1073 4.047135 TGGATGGATGGGTAGATGGATAGA 59.953 45.833 0.00 0.00 0.00 1.98
978 1074 4.365368 TGGATGGATGGGTAGATGGATAG 58.635 47.826 0.00 0.00 0.00 2.08
979 1075 4.434369 TGGATGGATGGGTAGATGGATA 57.566 45.455 0.00 0.00 0.00 2.59
980 1076 3.296399 TGGATGGATGGGTAGATGGAT 57.704 47.619 0.00 0.00 0.00 3.41
981 1077 2.813338 TGGATGGATGGGTAGATGGA 57.187 50.000 0.00 0.00 0.00 3.41
982 1078 2.646297 ACATGGATGGATGGGTAGATGG 59.354 50.000 0.00 0.00 0.00 3.51
983 1079 3.618263 CGACATGGATGGATGGGTAGATG 60.618 52.174 0.00 0.00 0.00 2.90
987 1083 1.055849 CCGACATGGATGGATGGGTA 58.944 55.000 0.00 0.00 42.00 3.69
989 1085 1.073722 CCCGACATGGATGGATGGG 59.926 63.158 0.00 0.00 42.00 4.00
1134 1242 0.735287 GGTAGTCGGCGAAGAACCAC 60.735 60.000 23.70 8.61 0.00 4.16
1185 1293 1.084370 CGATGAAGTCCCTGGCGAAC 61.084 60.000 0.00 0.00 0.00 3.95
1232 1340 0.033991 CTCCCTCTTCACCTCCTCGA 60.034 60.000 0.00 0.00 0.00 4.04
1275 1383 3.898509 GGCACAACAACAGCGCCA 61.899 61.111 2.29 0.00 42.50 5.69
1458 1566 1.543429 CCTTTCTTGGTCTTGTCCGCT 60.543 52.381 0.00 0.00 0.00 5.52
1504 1620 6.494835 AGCCAAGATCAATCAGGTAAAGTTTT 59.505 34.615 0.00 0.00 0.00 2.43
1514 1630 3.618351 ACTCCAAGCCAAGATCAATCAG 58.382 45.455 0.00 0.00 0.00 2.90
1517 1633 4.313020 AGAACTCCAAGCCAAGATCAAT 57.687 40.909 0.00 0.00 0.00 2.57
1518 1634 3.795688 AGAACTCCAAGCCAAGATCAA 57.204 42.857 0.00 0.00 0.00 2.57
1531 1647 7.110155 CCTCTAGGTATCTGATCTAGAACTCC 58.890 46.154 13.80 1.19 38.96 3.85
1566 1694 4.033702 CACTGAAGTGTATGCTGTATGCAG 59.966 45.833 6.42 6.42 46.75 4.41
1648 1777 5.294552 AGTGAAGAACAACTCAACAAGCTAC 59.705 40.000 0.00 0.00 0.00 3.58
1653 1782 5.296780 GGATCAGTGAAGAACAACTCAACAA 59.703 40.000 0.00 0.00 0.00 2.83
1654 1783 4.816385 GGATCAGTGAAGAACAACTCAACA 59.184 41.667 0.00 0.00 0.00 3.33
1655 1784 4.816385 TGGATCAGTGAAGAACAACTCAAC 59.184 41.667 0.00 0.00 0.00 3.18
1660 1789 8.424274 AAAATTTTGGATCAGTGAAGAACAAC 57.576 30.769 1.75 0.00 0.00 3.32
1662 1791 7.147759 TGGAAAATTTTGGATCAGTGAAGAACA 60.148 33.333 8.47 0.00 0.00 3.18
1742 1876 9.769677 AGCTATATATCTGGTATGAACTGGTTA 57.230 33.333 0.00 0.00 0.00 2.85
1831 1966 2.678336 GGAAAGGATCGAACACATCCAC 59.322 50.000 4.88 0.00 42.28 4.02
1834 1969 4.035675 GGAATGGAAAGGATCGAACACATC 59.964 45.833 0.00 0.00 0.00 3.06
1864 1999 6.688637 TTGACCGAATAGAAGACGAGATTA 57.311 37.500 0.00 0.00 0.00 1.75
1865 2000 5.578005 TTGACCGAATAGAAGACGAGATT 57.422 39.130 0.00 0.00 0.00 2.40
1966 2101 4.894784 TCTTTTTGCTCCAGTGGTACTAG 58.105 43.478 9.54 0.00 0.00 2.57
1969 2104 2.226674 GCTCTTTTTGCTCCAGTGGTAC 59.773 50.000 9.54 3.02 0.00 3.34
1973 2108 2.620115 TCAAGCTCTTTTTGCTCCAGTG 59.380 45.455 0.00 0.00 40.22 3.66
1979 2114 5.221322 CCCTAAAGTTCAAGCTCTTTTTGCT 60.221 40.000 3.72 0.00 43.32 3.91
1988 2123 3.764237 TCGAACCCTAAAGTTCAAGCT 57.236 42.857 5.38 0.00 45.27 3.74
1993 2128 3.619038 CAGCTGATCGAACCCTAAAGTTC 59.381 47.826 8.42 0.00 42.25 3.01
1995 2130 2.678190 GCAGCTGATCGAACCCTAAAGT 60.678 50.000 20.43 0.00 0.00 2.66
2049 2184 7.013274 GTCTAATCAAAAAGCTGTGGGCATATA 59.987 37.037 0.00 0.00 44.79 0.86
2050 2185 5.893255 TCTAATCAAAAAGCTGTGGGCATAT 59.107 36.000 0.00 0.00 44.79 1.78
2075 2210 5.886960 ATCATGAAAGGAAGAAAAGACGG 57.113 39.130 0.00 0.00 0.00 4.79
2076 2211 7.588512 AGAAATCATGAAAGGAAGAAAAGACG 58.411 34.615 0.00 0.00 0.00 4.18
2077 2212 9.404348 GAAGAAATCATGAAAGGAAGAAAAGAC 57.596 33.333 0.00 0.00 0.00 3.01
2227 2366 5.971493 AGTATCTTTAGGACCTAGCCAGAT 58.029 41.667 17.67 17.67 0.00 2.90
2268 2456 6.970043 GGCGTTAGTAGCTTAGATATCTGATG 59.030 42.308 15.79 6.33 34.52 3.07
2281 2469 1.390565 AGTGATCGGCGTTAGTAGCT 58.609 50.000 6.85 0.00 34.52 3.32
2282 2470 1.852895 CAAGTGATCGGCGTTAGTAGC 59.147 52.381 6.85 0.00 0.00 3.58
2283 2471 3.064958 TCTCAAGTGATCGGCGTTAGTAG 59.935 47.826 6.85 0.00 0.00 2.57
2284 2472 3.011818 TCTCAAGTGATCGGCGTTAGTA 58.988 45.455 6.85 0.00 0.00 1.82
2285 2473 1.816835 TCTCAAGTGATCGGCGTTAGT 59.183 47.619 6.85 0.00 0.00 2.24
2286 2474 2.159366 ACTCTCAAGTGATCGGCGTTAG 60.159 50.000 6.85 0.00 33.32 2.34
2287 2475 1.816835 ACTCTCAAGTGATCGGCGTTA 59.183 47.619 6.85 0.00 33.32 3.18
2289 2477 0.603569 AACTCTCAAGTGATCGGCGT 59.396 50.000 6.85 0.00 35.36 5.68
2290 2478 1.272781 GAACTCTCAAGTGATCGGCG 58.727 55.000 0.00 0.00 35.36 6.46
2291 2479 2.370281 TGAACTCTCAAGTGATCGGC 57.630 50.000 0.00 0.00 35.36 5.54
2292 2480 5.409520 TGAAAATGAACTCTCAAGTGATCGG 59.590 40.000 0.00 0.00 35.36 4.18
2293 2481 6.471976 TGAAAATGAACTCTCAAGTGATCG 57.528 37.500 0.00 0.00 35.36 3.69
2294 2482 7.120285 TCCATGAAAATGAACTCTCAAGTGATC 59.880 37.037 0.00 0.00 35.36 2.92
2295 2483 6.944290 TCCATGAAAATGAACTCTCAAGTGAT 59.056 34.615 0.00 0.00 35.36 3.06
2296 2484 6.298361 TCCATGAAAATGAACTCTCAAGTGA 58.702 36.000 0.00 0.00 35.36 3.41
2297 2485 6.564709 TCCATGAAAATGAACTCTCAAGTG 57.435 37.500 0.00 0.00 35.36 3.16
2298 2486 7.587037 TTTCCATGAAAATGAACTCTCAAGT 57.413 32.000 0.00 0.00 37.32 3.16
2396 2837 4.346730 TCATGGATATGGATGGATTTGGC 58.653 43.478 0.00 0.00 34.97 4.52
2450 2891 5.299279 CCTGGTCTTTCTCTTTTGTTTGCTA 59.701 40.000 0.00 0.00 0.00 3.49
2452 2893 4.363138 CCTGGTCTTTCTCTTTTGTTTGC 58.637 43.478 0.00 0.00 0.00 3.68
2453 2894 4.098501 AGCCTGGTCTTTCTCTTTTGTTTG 59.901 41.667 0.00 0.00 0.00 2.93
2454 2895 4.281657 AGCCTGGTCTTTCTCTTTTGTTT 58.718 39.130 0.00 0.00 0.00 2.83
2455 2896 3.903467 AGCCTGGTCTTTCTCTTTTGTT 58.097 40.909 0.00 0.00 0.00 2.83
2456 2897 3.584733 AGCCTGGTCTTTCTCTTTTGT 57.415 42.857 0.00 0.00 0.00 2.83
2457 2898 4.646572 ACTAGCCTGGTCTTTCTCTTTTG 58.353 43.478 0.00 0.00 0.00 2.44
2458 2899 4.984146 ACTAGCCTGGTCTTTCTCTTTT 57.016 40.909 0.00 0.00 0.00 2.27
2459 2900 4.505742 CCAACTAGCCTGGTCTTTCTCTTT 60.506 45.833 3.68 0.00 0.00 2.52
2462 2903 2.303311 ACCAACTAGCCTGGTCTTTCTC 59.697 50.000 10.64 0.00 44.05 2.87
2470 2911 0.108329 CCGTACACCAACTAGCCTGG 60.108 60.000 9.44 9.44 40.05 4.45
2504 2945 2.621526 CTGCATGCATACACACATGGAT 59.378 45.455 22.97 0.00 42.62 3.41
2553 2994 1.958579 TCTAAGTAGGTGCGTGTGTGT 59.041 47.619 0.00 0.00 0.00 3.72
2554 2995 2.287970 TGTCTAAGTAGGTGCGTGTGTG 60.288 50.000 0.00 0.00 0.00 3.82
2561 3002 6.069684 ACGTATACATGTCTAAGTAGGTGC 57.930 41.667 0.00 0.00 0.00 5.01
2569 3012 6.292865 GGCTGTACGTACGTATACATGTCTAA 60.293 42.308 29.05 3.12 31.10 2.10
2700 3152 3.266510 AGCAAACGATTGATCTAGCCA 57.733 42.857 9.88 0.00 38.94 4.75
2706 3158 3.959609 GCACAAAGCAAACGATTGATC 57.040 42.857 9.88 0.00 44.79 2.92
2725 3225 6.385033 AGAAATCAAATCAAAGTGCACTAGC 58.615 36.000 22.01 0.00 42.57 3.42
2761 3267 8.448615 GGTCAATCTTATACAACTTGTAACCAC 58.551 37.037 5.73 0.00 36.31 4.16
2794 3300 1.406539 CGCCCTGCAATTAATCAGCTT 59.593 47.619 12.38 0.00 0.00 3.74
2797 3303 0.031178 GCCGCCCTGCAATTAATCAG 59.969 55.000 0.00 0.00 0.00 2.90
2835 3341 1.916206 GCTTCTCCCCCTTGACCCTC 61.916 65.000 0.00 0.00 0.00 4.30
2837 3343 2.677848 GCTTCTCCCCCTTGACCC 59.322 66.667 0.00 0.00 0.00 4.46
2904 3410 3.584052 CGGTAGCCGTCCTCGAGG 61.584 72.222 26.32 26.32 42.73 4.63
2987 3493 4.023193 GCATCGTAACCCTAATCCATTTGG 60.023 45.833 0.00 0.00 33.33 3.28
2990 3496 4.134563 GTGCATCGTAACCCTAATCCATT 58.865 43.478 0.00 0.00 0.00 3.16
2991 3497 3.135712 TGTGCATCGTAACCCTAATCCAT 59.864 43.478 0.00 0.00 0.00 3.41
3015 3523 2.178769 CCGCATGCAAACATCGCA 59.821 55.556 19.57 0.00 44.94 5.10
3022 3530 1.212490 GCAGTTAGCCGCATGCAAA 59.788 52.632 19.57 3.04 44.83 3.68
3032 3558 1.000145 GGCACTTCTACGCAGTTAGC 59.000 55.000 0.00 0.00 37.78 3.09
3049 3575 2.028925 CAAAAGGTTGCACCGGGC 59.971 61.111 6.32 7.25 44.90 6.13
3050 3576 1.184970 ATCCAAAAGGTTGCACCGGG 61.185 55.000 6.32 0.00 44.90 5.73
3051 3577 0.038343 CATCCAAAAGGTTGCACCGG 60.038 55.000 0.00 0.00 44.90 5.28
3052 3578 0.958091 TCATCCAAAAGGTTGCACCG 59.042 50.000 0.00 0.00 44.90 4.94
3055 3581 3.368635 GCATCATCATCCAAAAGGTTGCA 60.369 43.478 0.00 0.00 33.01 4.08
3056 3582 3.192466 GCATCATCATCCAAAAGGTTGC 58.808 45.455 0.00 0.00 33.01 4.17
3057 3583 4.430007 CTGCATCATCATCCAAAAGGTTG 58.570 43.478 0.00 0.00 34.25 3.77
3059 3585 3.028850 CCTGCATCATCATCCAAAAGGT 58.971 45.455 0.00 0.00 0.00 3.50
3060 3586 3.293337 TCCTGCATCATCATCCAAAAGG 58.707 45.455 0.00 0.00 0.00 3.11
3061 3587 3.243434 GCTCCTGCATCATCATCCAAAAG 60.243 47.826 0.00 0.00 39.41 2.27
3062 3588 2.691526 GCTCCTGCATCATCATCCAAAA 59.308 45.455 0.00 0.00 39.41 2.44
3063 3589 2.092049 AGCTCCTGCATCATCATCCAAA 60.092 45.455 0.00 0.00 42.74 3.28
3064 3590 1.493446 AGCTCCTGCATCATCATCCAA 59.507 47.619 0.00 0.00 42.74 3.53
3065 3591 1.137697 AGCTCCTGCATCATCATCCA 58.862 50.000 0.00 0.00 42.74 3.41
3066 3592 2.302445 AGTAGCTCCTGCATCATCATCC 59.698 50.000 0.00 0.00 42.74 3.51
3067 3593 3.681593 AGTAGCTCCTGCATCATCATC 57.318 47.619 0.00 0.00 42.74 2.92
3068 3594 3.260380 GGTAGTAGCTCCTGCATCATCAT 59.740 47.826 0.00 0.00 42.74 2.45
3069 3595 2.630098 GGTAGTAGCTCCTGCATCATCA 59.370 50.000 0.00 0.00 42.74 3.07
3070 3596 2.352225 CGGTAGTAGCTCCTGCATCATC 60.352 54.545 0.00 0.00 42.74 2.92
3071 3597 1.615883 CGGTAGTAGCTCCTGCATCAT 59.384 52.381 0.00 0.00 42.74 2.45
3072 3598 1.032794 CGGTAGTAGCTCCTGCATCA 58.967 55.000 0.00 0.00 42.74 3.07
3476 4005 0.038166 TACTGTTCCCCGTCGTACCT 59.962 55.000 0.00 0.00 0.00 3.08
3542 4074 1.517832 GTAGTCCTGCGCCATCAGT 59.482 57.895 4.18 0.00 32.32 3.41
3624 4165 0.461870 CTCGATCAATGGCGGTTGGA 60.462 55.000 0.00 0.00 0.00 3.53
3674 4218 0.313987 CCGAATCGACCGATGGATCA 59.686 55.000 3.36 0.00 34.70 2.92
3684 4228 2.818274 AAAGGGCGCCGAATCGAC 60.818 61.111 22.54 4.09 36.59 4.20
3769 4318 5.620879 CGTGCTGATGCTAAGCTAGATCATA 60.621 44.000 0.00 0.00 41.42 2.15
3771 4320 3.551659 CGTGCTGATGCTAAGCTAGATCA 60.552 47.826 0.00 0.00 41.42 2.92
3786 4335 1.683707 AGCATCCTCTCCGTGCTGA 60.684 57.895 0.00 0.00 46.60 4.26
3852 4404 6.195244 GCATGCATAATTTACAACGACTCTTG 59.805 38.462 14.21 0.00 0.00 3.02
3894 4446 1.790755 TCAATCAGGTACACACGCAC 58.209 50.000 0.00 0.00 0.00 5.34
3943 4495 3.688235 ACCACTAGATAGATACGGCTCC 58.312 50.000 0.00 0.00 0.00 4.70
3966 4522 5.531659 CACCCATCAGTAGTACAGTAGGTAG 59.468 48.000 2.52 0.00 31.13 3.18
3972 4528 2.832129 CACCACCCATCAGTAGTACAGT 59.168 50.000 2.52 0.00 0.00 3.55
3976 4532 2.184533 CACCACCACCCATCAGTAGTA 58.815 52.381 0.00 0.00 0.00 1.82
3980 4536 1.075601 AATCACCACCACCCATCAGT 58.924 50.000 0.00 0.00 0.00 3.41
3981 4537 2.220653 AAATCACCACCACCCATCAG 57.779 50.000 0.00 0.00 0.00 2.90
3984 4540 0.975887 GCAAAATCACCACCACCCAT 59.024 50.000 0.00 0.00 0.00 4.00
3985 4541 0.105760 AGCAAAATCACCACCACCCA 60.106 50.000 0.00 0.00 0.00 4.51
3986 4542 1.047801 AAGCAAAATCACCACCACCC 58.952 50.000 0.00 0.00 0.00 4.61
3987 4543 1.686052 TCAAGCAAAATCACCACCACC 59.314 47.619 0.00 0.00 0.00 4.61
4010 4571 3.625764 TCAAAGTCAAGGAAACGGAACAG 59.374 43.478 0.00 0.00 0.00 3.16
4049 4611 7.121315 AGTCCTTGAAAGTTATTAAGCATCACC 59.879 37.037 0.00 0.00 0.00 4.02
4063 4625 1.985473 TGCATGCAGTCCTTGAAAGT 58.015 45.000 18.46 0.00 0.00 2.66
4194 4927 1.177895 TGCATTGCATGGACCAACGT 61.178 50.000 7.38 0.00 31.71 3.99
4239 4973 1.131638 TCGATTCCTTCTCCCCCATG 58.868 55.000 0.00 0.00 0.00 3.66
4247 4981 0.676736 GCCCTCGATCGATTCCTTCT 59.323 55.000 19.78 0.00 0.00 2.85
4248 4982 0.676736 AGCCCTCGATCGATTCCTTC 59.323 55.000 19.78 5.19 0.00 3.46
4251 4987 0.109039 GCTAGCCCTCGATCGATTCC 60.109 60.000 19.78 9.42 0.00 3.01
4255 4991 0.109913 TTAGGCTAGCCCTCGATCGA 59.890 55.000 30.42 18.32 44.96 3.59
4268 5004 3.347216 ACGTGAGATGCAAAATTAGGCT 58.653 40.909 0.00 0.00 0.00 4.58
4334 5070 1.065701 CTTGATCGAGGTCCCAGTACG 59.934 57.143 1.50 0.00 0.00 3.67
4341 5077 3.215975 ACTAGTAGCTTGATCGAGGTCC 58.784 50.000 17.96 7.29 0.00 4.46
4342 5078 3.251487 GGACTAGTAGCTTGATCGAGGTC 59.749 52.174 17.96 11.22 0.00 3.85
4548 5289 3.849911 TGCAATCACACACTACTAGCTC 58.150 45.455 0.00 0.00 0.00 4.09
4554 5301 3.181516 GCTAGCTTGCAATCACACACTAC 60.182 47.826 15.53 0.00 0.00 2.73
4596 5343 4.041444 GCATCCAATAGTCTCATCCCTTCT 59.959 45.833 0.00 0.00 0.00 2.85
4604 5351 3.898123 GACCCTAGCATCCAATAGTCTCA 59.102 47.826 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.