Multiple sequence alignment - TraesCS2B01G328000

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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 TraesCS2B01G328000 chr2B 100.000 4084 0 0 1 4084 470063174 470059091 0.000000e+00 7542.0
1 TraesCS2B01G328000 chr2B 97.222 72 1 1 3459 3530 470059676 470059606 1.990000e-23 121.0
2 TraesCS2B01G328000 chr2B 97.222 72 1 1 3499 3569 470059716 470059645 1.990000e-23 121.0
3 TraesCS2B01G328000 chr2B 92.208 77 4 1 1580 1654 392896280 392896204 1.550000e-19 108.0
4 TraesCS2B01G328000 chr2B 92.208 77 4 1 1580 1654 392896205 392896281 1.550000e-19 108.0
5 TraesCS2B01G328000 chr2B 91.026 78 4 2 1580 1654 38398976 38398899 7.220000e-18 102.0
6 TraesCS2B01G328000 chr2B 90.566 53 2 3 1530 1580 21778137 21778086 2.630000e-07 67.6
7 TraesCS2B01G328000 chr2B 90.196 51 3 1 1532 1580 392896828 392896878 9.480000e-07 65.8
8 TraesCS2B01G328000 chr2B 81.818 77 10 4 1535 1607 492619736 492619660 1.230000e-05 62.1
9 TraesCS2B01G328000 chr2A 96.611 1564 36 6 1 1551 534629138 534627579 0.000000e+00 2579.0
10 TraesCS2B01G328000 chr2A 94.981 1056 49 3 1653 2708 534627580 534626529 0.000000e+00 1653.0
11 TraesCS2B01G328000 chr2A 94.965 715 28 4 2778 3492 534626427 534625721 0.000000e+00 1114.0
12 TraesCS2B01G328000 chr2A 88.760 516 29 7 3547 4046 534625739 534625237 4.520000e-169 604.0
13 TraesCS2B01G328000 chr2A 91.071 56 1 4 1528 1580 119279357 119279411 5.660000e-09 73.1
14 TraesCS2B01G328000 chr2D 96.652 1374 31 6 189 1551 396665421 396664052 0.000000e+00 2268.0
15 TraesCS2B01G328000 chr2D 92.979 1054 64 6 1653 2705 396664053 396663009 0.000000e+00 1528.0
16 TraesCS2B01G328000 chr2D 90.000 580 20 18 2949 3491 396662946 396662368 0.000000e+00 715.0
17 TraesCS2B01G328000 chr2D 93.886 458 27 1 3589 4046 396662321 396661865 0.000000e+00 689.0
18 TraesCS2B01G328000 chr2D 96.335 191 7 0 1 191 396666906 396666716 8.520000e-82 315.0
19 TraesCS2B01G328000 chr2D 87.500 96 6 4 1568 1659 643870684 643870591 5.580000e-19 106.0
20 TraesCS2B01G328000 chr3A 87.466 367 41 4 2308 2674 293042622 293042261 6.310000e-113 418.0
21 TraesCS2B01G328000 chr6B 86.921 367 43 2 2308 2674 356796099 356795738 1.370000e-109 407.0
22 TraesCS2B01G328000 chr6B 91.667 48 4 0 1533 1580 644808880 644808927 2.630000e-07 67.6
23 TraesCS2B01G328000 chr5B 86.921 367 39 3 2308 2674 179796405 179796048 1.770000e-108 403.0
24 TraesCS2B01G328000 chr5B 88.372 86 6 4 1580 1664 397951792 397951710 2.600000e-17 100.0
25 TraesCS2B01G328000 chr5B 89.394 66 6 1 1602 1667 2570480 2570416 9.410000e-12 82.4
26 TraesCS2B01G328000 chr5B 93.617 47 1 2 1536 1580 482199768 482199722 7.320000e-08 69.4
27 TraesCS2B01G328000 chr5B 87.719 57 5 1 2707 2763 100015926 100015872 9.480000e-07 65.8
28 TraesCS2B01G328000 chr1B 85.831 367 43 3 2308 2674 87188017 87188374 8.280000e-102 381.0
29 TraesCS2B01G328000 chr1B 83.186 339 30 7 2337 2675 10841076 10840765 6.680000e-73 285.0
30 TraesCS2B01G328000 chr1B 91.026 78 4 2 1580 1654 687182004 687182081 7.220000e-18 102.0
31 TraesCS2B01G328000 chr1B 94.737 57 2 1 1605 1661 502107183 502107128 2.020000e-13 87.9
32 TraesCS2B01G328000 chr1B 91.667 48 2 2 1534 1580 616902658 616902612 9.480000e-07 65.8
33 TraesCS2B01G328000 chr1B 86.885 61 3 5 1524 1580 194357334 194357275 3.410000e-06 63.9
34 TraesCS2B01G328000 chr5A 92.593 81 4 2 1580 1658 676482242 676482162 9.280000e-22 115.0
35 TraesCS2B01G328000 chr5A 90.909 77 5 2 1580 1655 562406392 562406467 7.220000e-18 102.0
36 TraesCS2B01G328000 chr3B 88.636 88 6 4 1576 1661 826657451 826657366 2.010000e-18 104.0
37 TraesCS2B01G328000 chr3B 87.952 83 6 2 1580 1658 321594222 321594140 1.210000e-15 95.3
38 TraesCS2B01G328000 chr7B 90.000 80 3 2 1580 1659 63780369 63780443 9.340000e-17 99.0
39 TraesCS2B01G328000 chrUn 91.935 62 5 0 2701 2762 86630781 86630720 2.020000e-13 87.9
40 TraesCS2B01G328000 chrUn 90.196 51 1 4 1530 1580 23714997 23715043 3.410000e-06 63.9
41 TraesCS2B01G328000 chr5D 88.889 72 4 3 1612 1681 460390497 460390566 7.270000e-13 86.1
42 TraesCS2B01G328000 chr5D 90.196 51 3 2 1531 1580 409447940 409447989 9.480000e-07 65.8
43 TraesCS2B01G328000 chr7D 100.000 34 0 0 1547 1580 54967186 54967153 3.410000e-06 63.9
44 TraesCS2B01G328000 chr4D 86.441 59 5 2 1551 1607 300788842 300788899 1.230000e-05 62.1


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 TraesCS2B01G328000 chr2B 470059091 470063174 4083 True 2594.666667 7542 98.14800 1 4084 3 chr2B.!!$R5 4083
1 TraesCS2B01G328000 chr2A 534625237 534629138 3901 True 1487.500000 2579 93.82925 1 4046 4 chr2A.!!$R1 4045
2 TraesCS2B01G328000 chr2D 396661865 396666906 5041 True 1103.000000 2268 93.97040 1 4046 5 chr2D.!!$R2 4045

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
108 109 1.277273 CTTCTGGAGTGGCAGACATGA 59.723 52.381 0.00 0.0 0.0 3.07 F
1566 2877 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.0 0.0 3.46 F
2488 3799 0.037734 AATTCCCTTCACCGGTGTCC 59.962 55.000 32.74 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 3339 0.032813 AGCCTGTATTGCCAAGCCAT 60.033 50.0 0.00 0.0 0.00 4.40 R
3017 4380 0.458260 GCATCATCATGTTGCTGCCA 59.542 50.0 17.79 0.0 39.34 4.92 R
3859 5281 0.249398 CGGACTTGTGGGAGGGTAAG 59.751 60.0 0.00 0.0 0.00 2.34 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
108 109 1.277273 CTTCTGGAGTGGCAGACATGA 59.723 52.381 0.00 0.00 0.00 3.07
282 1585 1.338020 CCAGACTCTTTTGGTTGGTGC 59.662 52.381 0.00 0.00 0.00 5.01
301 1604 5.584649 TGGTGCTGGAATTCTATAAAAGACG 59.415 40.000 5.23 0.00 32.51 4.18
336 1639 9.495572 AAAACCAAGTGAACAAAACAAAATAGA 57.504 25.926 0.00 0.00 0.00 1.98
356 1659 9.448438 AAATAGATTGCATGACACTTAACAGTA 57.552 29.630 0.00 0.00 0.00 2.74
357 1660 9.448438 AATAGATTGCATGACACTTAACAGTAA 57.552 29.630 0.00 0.00 0.00 2.24
383 1686 3.616219 TGTAGTGTTGGCTTCACACTTT 58.384 40.909 18.47 3.63 41.36 2.66
395 1698 3.889196 TCACACTTTGAATTGTACGGC 57.111 42.857 0.00 0.00 0.00 5.68
398 1701 2.946329 ACACTTTGAATTGTACGGCACA 59.054 40.909 0.00 0.00 34.51 4.57
418 1721 7.010091 CGGCACACATTTCTTTTAAAACTCTTT 59.990 33.333 0.00 0.00 0.00 2.52
568 1871 7.110155 TCTGACCTTTCAAACTAGAACAAAGT 58.890 34.615 0.00 0.00 0.00 2.66
674 1978 1.477553 CATGGGGCAGTACAAGCAAT 58.522 50.000 11.68 1.06 0.00 3.56
687 1991 9.612620 GCAGTACAAGCAATATGGATTTTATAC 57.387 33.333 5.55 0.00 0.00 1.47
778 2082 3.806625 ACTTTGTGAATTGCAACAGCT 57.193 38.095 0.00 0.00 0.00 4.24
1355 2659 1.344763 AGTAGCGAGCAGAACAAACCT 59.655 47.619 0.00 0.00 0.00 3.50
1380 2691 4.474651 AGGTCAGGATCACATGGTTTATCA 59.525 41.667 0.00 0.00 0.00 2.15
1434 2745 9.110617 CAAAGCTATGCATTCGAAATACATTAG 57.889 33.333 3.54 10.79 0.00 1.73
1515 2826 0.179192 TTTGTTCATCAGCGCGCATC 60.179 50.000 35.10 11.65 0.00 3.91
1534 2845 7.359181 CGCGCATCAATCTTGAGTTACATTATA 60.359 37.037 8.75 0.00 41.08 0.98
1560 2871 7.902920 TTTACATAATTACTACTCCCTCCGT 57.097 36.000 0.00 0.00 0.00 4.69
1561 2872 7.516198 TTACATAATTACTACTCCCTCCGTC 57.484 40.000 0.00 0.00 0.00 4.79
1562 2873 4.831710 ACATAATTACTACTCCCTCCGTCC 59.168 45.833 0.00 0.00 0.00 4.79
1563 2874 1.978454 ATTACTACTCCCTCCGTCCG 58.022 55.000 0.00 0.00 0.00 4.79
1564 2875 0.911769 TTACTACTCCCTCCGTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
1565 2876 0.911769 TACTACTCCCTCCGTCCGAA 59.088 55.000 0.00 0.00 0.00 4.30
1566 2877 0.038744 ACTACTCCCTCCGTCCGAAA 59.961 55.000 0.00 0.00 0.00 3.46
1567 2878 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
1568 2879 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
1569 2880 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1570 2881 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1571 2882 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1572 2883 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1573 2884 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1574 2885 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1575 2886 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1576 2887 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1577 2888 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1578 2889 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1579 2890 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1580 2891 4.201685 CCGTCCGAAAATACTTGTCATCAC 60.202 45.833 0.00 0.00 0.00 3.06
1581 2892 4.625742 CGTCCGAAAATACTTGTCATCACT 59.374 41.667 0.00 0.00 0.00 3.41
1582 2893 5.220228 CGTCCGAAAATACTTGTCATCACTC 60.220 44.000 0.00 0.00 0.00 3.51
1583 2894 5.063564 GTCCGAAAATACTTGTCATCACTCC 59.936 44.000 0.00 0.00 0.00 3.85
1584 2895 4.332819 CCGAAAATACTTGTCATCACTCCC 59.667 45.833 0.00 0.00 0.00 4.30
1585 2896 5.178797 CGAAAATACTTGTCATCACTCCCT 58.821 41.667 0.00 0.00 0.00 4.20
1586 2897 5.292101 CGAAAATACTTGTCATCACTCCCTC 59.708 44.000 0.00 0.00 0.00 4.30
1587 2898 4.762289 AATACTTGTCATCACTCCCTCC 57.238 45.455 0.00 0.00 0.00 4.30
1588 2899 0.898320 ACTTGTCATCACTCCCTCCG 59.102 55.000 0.00 0.00 0.00 4.63
1589 2900 0.898320 CTTGTCATCACTCCCTCCGT 59.102 55.000 0.00 0.00 0.00 4.69
1590 2901 0.895530 TTGTCATCACTCCCTCCGTC 59.104 55.000 0.00 0.00 0.00 4.79
1591 2902 0.970937 TGTCATCACTCCCTCCGTCC 60.971 60.000 0.00 0.00 0.00 4.79
1592 2903 1.753078 TCATCACTCCCTCCGTCCG 60.753 63.158 0.00 0.00 0.00 4.79
1593 2904 1.753078 CATCACTCCCTCCGTCCGA 60.753 63.158 0.00 0.00 0.00 4.55
1594 2905 1.000019 ATCACTCCCTCCGTCCGAA 60.000 57.895 0.00 0.00 0.00 4.30
1595 2906 0.613853 ATCACTCCCTCCGTCCGAAA 60.614 55.000 0.00 0.00 0.00 3.46
1596 2907 0.828762 TCACTCCCTCCGTCCGAAAA 60.829 55.000 0.00 0.00 0.00 2.29
1597 2908 0.249398 CACTCCCTCCGTCCGAAAAT 59.751 55.000 0.00 0.00 0.00 1.82
1598 2909 1.479323 CACTCCCTCCGTCCGAAAATA 59.521 52.381 0.00 0.00 0.00 1.40
1599 2910 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1600 2911 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1601 2912 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1602 2913 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1603 2914 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1604 2915 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1605 2916 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1606 2917 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1607 2918 4.571919 TCCGTCCGAAAATACTTGTCATT 58.428 39.130 0.00 0.00 0.00 2.57
1608 2919 5.722263 TCCGTCCGAAAATACTTGTCATTA 58.278 37.500 0.00 0.00 0.00 1.90
1609 2920 6.342906 TCCGTCCGAAAATACTTGTCATTAT 58.657 36.000 0.00 0.00 0.00 1.28
1610 2921 7.490840 TCCGTCCGAAAATACTTGTCATTATA 58.509 34.615 0.00 0.00 0.00 0.98
1611 2922 8.145767 TCCGTCCGAAAATACTTGTCATTATAT 58.854 33.333 0.00 0.00 0.00 0.86
1612 2923 8.770828 CCGTCCGAAAATACTTGTCATTATATT 58.229 33.333 0.00 0.00 0.00 1.28
1640 2951 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1641 2952 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1642 2953 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1643 2954 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1644 2955 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1645 2956 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1646 2957 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1647 2958 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1648 2959 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1649 2960 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1650 2961 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1651 2962 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1652 2963 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1653 2964 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
1702 3013 1.952296 CTATTGAGGTGCTGGCATTCC 59.048 52.381 0.00 0.00 0.00 3.01
1883 3194 6.341316 ACTTATGCTTGAATGACGACATACT 58.659 36.000 0.00 0.00 35.50 2.12
1901 3212 2.723273 ACTTACCCTTTGTGCTATGCC 58.277 47.619 0.00 0.00 0.00 4.40
1902 3213 2.041081 ACTTACCCTTTGTGCTATGCCA 59.959 45.455 0.00 0.00 0.00 4.92
1906 3217 3.707316 ACCCTTTGTGCTATGCCAATTA 58.293 40.909 0.00 0.00 0.00 1.40
1953 3264 7.389330 ACAATTATCTTTCGTGATACACCAACA 59.611 33.333 0.00 0.00 0.00 3.33
1975 3286 9.853555 CAACAGTTTACTATTGGCATCAAATTA 57.146 29.630 0.00 0.00 36.36 1.40
2032 3343 3.526931 TGAGAAGTAGTAGCACATGGC 57.473 47.619 0.00 0.00 45.30 4.40
2052 3363 1.066605 CTTGGCAATACAGGCTGATGC 59.933 52.381 23.66 24.75 36.31 3.91
2086 3397 4.952335 ACTGGCAAGATTCCATTAGAAAGG 59.048 41.667 0.00 0.00 38.21 3.11
2090 3401 6.101997 GGCAAGATTCCATTAGAAAGGTTTG 58.898 40.000 0.00 0.00 38.21 2.93
2220 3531 4.461431 ACATGAATCTCAATGAGCTGCAAA 59.539 37.500 5.18 0.00 0.00 3.68
2291 3602 9.207868 ACAAAAGTAAGCTATATCTCCTTCTCT 57.792 33.333 0.00 0.00 0.00 3.10
2352 3663 1.377994 CTGCCCCTTTCTGCTGAGT 59.622 57.895 0.00 0.00 0.00 3.41
2399 3710 2.027745 TGAGATGCTCAAGACCAAGGTC 60.028 50.000 11.29 11.29 37.57 3.85
2488 3799 0.037734 AATTCCCTTCACCGGTGTCC 59.962 55.000 32.74 0.00 0.00 4.02
2521 3832 2.819608 TGTTTTGCAGGAAGGCATACTC 59.180 45.455 0.00 0.00 44.48 2.59
2739 4102 8.234136 TCCGTGTCTAGATAAATGTAAGACAT 57.766 34.615 6.74 0.00 41.31 3.06
2751 4114 4.846779 TGTAAGACATGCTTTTTGGGAC 57.153 40.909 7.53 1.23 38.05 4.46
2752 4115 4.211125 TGTAAGACATGCTTTTTGGGACA 58.789 39.130 7.53 3.35 38.05 4.02
2758 4121 0.850100 TGCTTTTTGGGACAGAGGGA 59.150 50.000 0.00 0.00 42.39 4.20
2759 4122 1.202927 TGCTTTTTGGGACAGAGGGAG 60.203 52.381 0.00 0.00 42.39 4.30
2760 4123 1.202940 GCTTTTTGGGACAGAGGGAGT 60.203 52.381 0.00 0.00 42.39 3.85
2761 4124 2.039879 GCTTTTTGGGACAGAGGGAGTA 59.960 50.000 0.00 0.00 42.39 2.59
2762 4125 3.870299 GCTTTTTGGGACAGAGGGAGTAG 60.870 52.174 0.00 0.00 42.39 2.57
2763 4126 3.269592 TTTTGGGACAGAGGGAGTAGA 57.730 47.619 0.00 0.00 42.39 2.59
2764 4127 3.269592 TTTGGGACAGAGGGAGTAGAA 57.730 47.619 0.00 0.00 42.39 2.10
2765 4128 3.269592 TTGGGACAGAGGGAGTAGAAA 57.730 47.619 0.00 0.00 42.39 2.52
2766 4129 3.269592 TGGGACAGAGGGAGTAGAAAA 57.730 47.619 0.00 0.00 0.00 2.29
2767 4130 3.803340 TGGGACAGAGGGAGTAGAAAAT 58.197 45.455 0.00 0.00 0.00 1.82
2768 4131 4.955335 TGGGACAGAGGGAGTAGAAAATA 58.045 43.478 0.00 0.00 0.00 1.40
2769 4132 5.538877 TGGGACAGAGGGAGTAGAAAATAT 58.461 41.667 0.00 0.00 0.00 1.28
2770 4133 5.970640 TGGGACAGAGGGAGTAGAAAATATT 59.029 40.000 0.00 0.00 0.00 1.28
2771 4134 7.136885 TGGGACAGAGGGAGTAGAAAATATTA 58.863 38.462 0.00 0.00 0.00 0.98
2772 4135 7.794683 TGGGACAGAGGGAGTAGAAAATATTAT 59.205 37.037 0.00 0.00 0.00 1.28
2773 4136 8.661345 GGGACAGAGGGAGTAGAAAATATTATT 58.339 37.037 0.00 0.00 0.00 1.40
2774 4137 9.495572 GGACAGAGGGAGTAGAAAATATTATTG 57.504 37.037 0.00 0.00 0.00 1.90
2775 4138 8.910351 ACAGAGGGAGTAGAAAATATTATTGC 57.090 34.615 0.00 0.00 0.00 3.56
2776 4139 8.718656 ACAGAGGGAGTAGAAAATATTATTGCT 58.281 33.333 0.00 0.00 0.00 3.91
2863 4226 0.773644 AGGGATGCAAGTGGTTCAGT 59.226 50.000 0.00 0.00 0.00 3.41
2880 4243 4.737855 TCAGTACTTTGCATCCCTCTAC 57.262 45.455 0.00 0.00 0.00 2.59
2893 4256 3.752665 TCCCTCTACGCTGGTATTCTAG 58.247 50.000 0.00 0.00 0.00 2.43
3017 4380 0.616111 AGAGCGGGATTCTGGACACT 60.616 55.000 0.00 0.00 0.00 3.55
3066 4429 0.250234 CTTCCAGCGAACCATGGAGA 59.750 55.000 21.47 0.16 46.01 3.71
3070 4433 0.247460 CAGCGAACCATGGAGAGTGA 59.753 55.000 21.47 0.00 0.00 3.41
3071 4434 0.247736 AGCGAACCATGGAGAGTGAC 59.752 55.000 21.47 0.62 0.00 3.67
3109 4472 6.316390 CCTAAACAACCAACCTATCAAGCTAG 59.684 42.308 0.00 0.00 0.00 3.42
3197 4560 5.127845 TGCCACTTCATGTTGTAAAAAGGAA 59.872 36.000 0.00 0.00 30.28 3.36
3230 4593 2.868583 GCATCTGTCGATGTACATGCTT 59.131 45.455 14.43 0.00 46.96 3.91
3268 4661 8.712103 AGATTCATCATCTTTCAGATTGGACTA 58.288 33.333 0.00 0.00 39.47 2.59
3295 4688 2.355756 AGATTGCATGATGTTACCGCAC 59.644 45.455 0.00 0.00 31.10 5.34
3310 4703 1.676967 GCACTTTCCCCTCCAGCTG 60.677 63.158 6.78 6.78 0.00 4.24
3342 4735 2.159407 GGAGTACTCGTGTAGCCTGAAC 60.159 54.545 16.56 0.00 0.00 3.18
3427 4820 2.862536 CGTCTCATAGCCTTGTGTGATG 59.137 50.000 0.00 0.00 0.00 3.07
3433 4826 1.888215 AGCCTTGTGTGATGTGTCTG 58.112 50.000 0.00 0.00 0.00 3.51
3478 4878 8.340618 AGTACAAACAAAATCTGCATCTGTAT 57.659 30.769 0.00 0.00 0.00 2.29
3479 4879 8.454106 AGTACAAACAAAATCTGCATCTGTATC 58.546 33.333 0.00 0.00 0.00 2.24
3480 4880 7.458409 ACAAACAAAATCTGCATCTGTATCT 57.542 32.000 0.00 0.00 0.00 1.98
3481 4881 7.310664 ACAAACAAAATCTGCATCTGTATCTG 58.689 34.615 0.00 0.00 0.00 2.90
3482 4882 7.040201 ACAAACAAAATCTGCATCTGTATCTGT 60.040 33.333 0.00 0.00 0.00 3.41
3483 4883 8.453320 CAAACAAAATCTGCATCTGTATCTGTA 58.547 33.333 0.00 0.00 0.00 2.74
3484 4884 8.743085 AACAAAATCTGCATCTGTATCTGTAT 57.257 30.769 0.00 0.00 0.00 2.29
3485 4885 8.375608 ACAAAATCTGCATCTGTATCTGTATC 57.624 34.615 0.00 0.00 0.00 2.24
3486 4886 8.209584 ACAAAATCTGCATCTGTATCTGTATCT 58.790 33.333 0.00 0.00 0.00 1.98
3487 4887 8.496751 CAAAATCTGCATCTGTATCTGTATCTG 58.503 37.037 0.00 0.00 0.00 2.90
3488 4888 6.914654 ATCTGCATCTGTATCTGTATCTGT 57.085 37.500 0.00 0.00 0.00 3.41
3489 4889 8.414629 AATCTGCATCTGTATCTGTATCTGTA 57.585 34.615 0.00 0.00 0.00 2.74
3490 4890 8.592529 ATCTGCATCTGTATCTGTATCTGTAT 57.407 34.615 0.00 0.00 0.00 2.29
3491 4891 8.049655 TCTGCATCTGTATCTGTATCTGTATC 57.950 38.462 0.00 0.00 0.00 2.24
3492 4892 7.121907 TCTGCATCTGTATCTGTATCTGTATCC 59.878 40.741 0.00 0.00 0.00 2.59
3493 4893 6.153510 TGCATCTGTATCTGTATCTGTATCCC 59.846 42.308 0.00 0.00 0.00 3.85
3494 4894 6.379703 GCATCTGTATCTGTATCTGTATCCCT 59.620 42.308 0.00 0.00 0.00 4.20
3495 4895 7.416213 GCATCTGTATCTGTATCTGTATCCCTC 60.416 44.444 0.00 0.00 0.00 4.30
3496 4896 7.091533 TCTGTATCTGTATCTGTATCCCTCA 57.908 40.000 0.00 0.00 0.00 3.86
3497 4897 7.526918 TCTGTATCTGTATCTGTATCCCTCAA 58.473 38.462 0.00 0.00 0.00 3.02
3498 4898 8.004801 TCTGTATCTGTATCTGTATCCCTCAAA 58.995 37.037 0.00 0.00 0.00 2.69
3499 4899 8.547481 TGTATCTGTATCTGTATCCCTCAAAA 57.453 34.615 0.00 0.00 0.00 2.44
3500 4900 8.988060 TGTATCTGTATCTGTATCCCTCAAAAA 58.012 33.333 0.00 0.00 0.00 1.94
3527 4927 8.604640 AAAATCTGCATCTGTATCTGTATCTG 57.395 34.615 0.00 0.00 0.00 2.90
3528 4928 6.914654 ATCTGCATCTGTATCTGTATCTGT 57.085 37.500 0.00 0.00 0.00 3.41
3529 4929 8.414629 AATCTGCATCTGTATCTGTATCTGTA 57.585 34.615 0.00 0.00 0.00 2.74
3530 4930 8.592529 ATCTGCATCTGTATCTGTATCTGTAT 57.407 34.615 0.00 0.00 0.00 2.29
3531 4931 8.049655 TCTGCATCTGTATCTGTATCTGTATC 57.950 38.462 0.00 0.00 0.00 2.24
3532 4932 7.121907 TCTGCATCTGTATCTGTATCTGTATCC 59.878 40.741 0.00 0.00 0.00 2.59
3533 4933 6.153510 TGCATCTGTATCTGTATCTGTATCCC 59.846 42.308 0.00 0.00 0.00 3.85
3534 4934 6.379703 GCATCTGTATCTGTATCTGTATCCCT 59.620 42.308 0.00 0.00 0.00 4.20
3535 4935 7.416213 GCATCTGTATCTGTATCTGTATCCCTC 60.416 44.444 0.00 0.00 0.00 4.30
3536 4936 7.091533 TCTGTATCTGTATCTGTATCCCTCA 57.908 40.000 0.00 0.00 0.00 3.86
3537 4937 7.526918 TCTGTATCTGTATCTGTATCCCTCAA 58.473 38.462 0.00 0.00 0.00 3.02
3538 4938 8.004801 TCTGTATCTGTATCTGTATCCCTCAAA 58.995 37.037 0.00 0.00 0.00 2.69
3539 4939 8.547481 TGTATCTGTATCTGTATCCCTCAAAA 57.453 34.615 0.00 0.00 0.00 2.44
3540 4940 8.988060 TGTATCTGTATCTGTATCCCTCAAAAA 58.012 33.333 0.00 0.00 0.00 1.94
3624 5046 6.097356 GCAGATTGCAATATGGTTGATATGG 58.903 40.000 29.64 6.31 44.26 2.74
3639 5061 7.092623 TGGTTGATATGGTATAACTCTGGTTGT 60.093 37.037 0.00 0.00 36.92 3.32
3640 5062 7.441458 GGTTGATATGGTATAACTCTGGTTGTC 59.559 40.741 0.00 0.00 36.92 3.18
3659 5081 2.924290 GTCGTGCTGATTAGAGAACCAC 59.076 50.000 0.00 0.00 0.00 4.16
3667 5089 4.430007 TGATTAGAGAACCACCGAAATCG 58.570 43.478 0.00 0.00 39.44 3.34
3706 5128 4.571984 TGATTTCGACATATGTTGCTCCAG 59.428 41.667 17.10 1.38 0.00 3.86
3767 5189 5.712152 ACAGTTTGCAGCTAGCTAAAAAT 57.288 34.783 18.86 16.72 45.94 1.82
3781 5203 5.610398 AGCTAAAAATGTGTTCCAAAAGGG 58.390 37.500 0.00 0.00 38.37 3.95
3838 5260 3.287867 TTCATCCTGATTCCTGGAAGC 57.712 47.619 17.46 17.46 42.56 3.86
3848 5270 0.906756 TCCTGGAAGCTAGCTGTGCT 60.907 55.000 20.16 1.15 43.32 4.40
3859 5281 3.138798 CTGTGCTGCTGGGATGCC 61.139 66.667 0.00 0.00 0.00 4.40
3870 5292 1.696314 GGGATGCCTTACCCTCCCA 60.696 63.158 0.00 0.00 45.66 4.37
3871 5293 1.532238 GGATGCCTTACCCTCCCAC 59.468 63.158 0.00 0.00 0.00 4.61
3872 5294 1.279025 GGATGCCTTACCCTCCCACA 61.279 60.000 0.00 0.00 0.00 4.17
3873 5295 0.623723 GATGCCTTACCCTCCCACAA 59.376 55.000 0.00 0.00 0.00 3.33
3874 5296 0.625849 ATGCCTTACCCTCCCACAAG 59.374 55.000 0.00 0.00 0.00 3.16
3875 5297 0.770557 TGCCTTACCCTCCCACAAGT 60.771 55.000 0.00 0.00 0.00 3.16
3876 5298 0.035343 GCCTTACCCTCCCACAAGTC 60.035 60.000 0.00 0.00 0.00 3.01
3877 5299 0.618981 CCTTACCCTCCCACAAGTCC 59.381 60.000 0.00 0.00 0.00 3.85
3878 5300 0.249398 CTTACCCTCCCACAAGTCCG 59.751 60.000 0.00 0.00 0.00 4.79
3879 5301 0.178926 TTACCCTCCCACAAGTCCGA 60.179 55.000 0.00 0.00 0.00 4.55
3880 5302 0.042131 TACCCTCCCACAAGTCCGAT 59.958 55.000 0.00 0.00 0.00 4.18
3881 5303 1.265454 ACCCTCCCACAAGTCCGATC 61.265 60.000 0.00 0.00 0.00 3.69
3953 5387 1.252904 TTGGCTGGCCTTTCATCTGC 61.253 55.000 13.05 0.00 36.94 4.26
4037 5471 6.474140 TTCATCAGCATAAGCATTCCAAAT 57.526 33.333 0.00 0.00 45.49 2.32
4039 5473 7.585579 TCATCAGCATAAGCATTCCAAATAA 57.414 32.000 0.00 0.00 45.49 1.40
4040 5474 7.428020 TCATCAGCATAAGCATTCCAAATAAC 58.572 34.615 0.00 0.00 45.49 1.89
4042 5476 6.798482 TCAGCATAAGCATTCCAAATAACAG 58.202 36.000 0.00 0.00 45.49 3.16
4045 5479 7.760794 CAGCATAAGCATTCCAAATAACAGAAA 59.239 33.333 0.00 0.00 45.49 2.52
4046 5480 7.977853 AGCATAAGCATTCCAAATAACAGAAAG 59.022 33.333 0.00 0.00 45.49 2.62
4047 5481 7.761249 GCATAAGCATTCCAAATAACAGAAAGT 59.239 33.333 0.00 0.00 41.58 2.66
4057 5491 9.226606 TCCAAATAACAGAAAGTAATAGTGTGG 57.773 33.333 0.00 0.00 0.00 4.17
4058 5492 9.226606 CCAAATAACAGAAAGTAATAGTGTGGA 57.773 33.333 0.00 0.00 0.00 4.02
4063 5497 7.964604 ACAGAAAGTAATAGTGTGGAAGTTC 57.035 36.000 0.00 0.00 0.00 3.01
4064 5498 7.506114 ACAGAAAGTAATAGTGTGGAAGTTCA 58.494 34.615 5.01 0.00 0.00 3.18
4065 5499 8.157476 ACAGAAAGTAATAGTGTGGAAGTTCAT 58.843 33.333 5.01 0.00 0.00 2.57
4066 5500 9.003658 CAGAAAGTAATAGTGTGGAAGTTCATT 57.996 33.333 5.01 0.00 0.00 2.57
4067 5501 9.574516 AGAAAGTAATAGTGTGGAAGTTCATTT 57.425 29.630 5.01 0.00 0.00 2.32
4068 5502 9.612620 GAAAGTAATAGTGTGGAAGTTCATTTG 57.387 33.333 5.01 0.00 0.00 2.32
4069 5503 7.145932 AGTAATAGTGTGGAAGTTCATTTGC 57.854 36.000 5.01 0.00 0.00 3.68
4070 5504 6.942576 AGTAATAGTGTGGAAGTTCATTTGCT 59.057 34.615 5.01 0.00 0.00 3.91
4071 5505 5.886960 ATAGTGTGGAAGTTCATTTGCTC 57.113 39.130 5.01 0.00 0.00 4.26
4072 5506 2.887152 AGTGTGGAAGTTCATTTGCTCC 59.113 45.455 5.01 0.00 0.00 4.70
4073 5507 2.887152 GTGTGGAAGTTCATTTGCTCCT 59.113 45.455 5.01 0.00 0.00 3.69
4074 5508 3.057946 GTGTGGAAGTTCATTTGCTCCTC 60.058 47.826 5.01 0.00 0.00 3.71
4075 5509 3.181440 TGTGGAAGTTCATTTGCTCCTCT 60.181 43.478 5.01 0.00 0.00 3.69
4076 5510 4.041567 TGTGGAAGTTCATTTGCTCCTCTA 59.958 41.667 5.01 0.00 0.00 2.43
4077 5511 4.393371 GTGGAAGTTCATTTGCTCCTCTAC 59.607 45.833 5.01 0.00 0.00 2.59
4078 5512 3.942115 GGAAGTTCATTTGCTCCTCTACC 59.058 47.826 5.01 0.00 0.00 3.18
4079 5513 4.323868 GGAAGTTCATTTGCTCCTCTACCT 60.324 45.833 5.01 0.00 0.00 3.08
4080 5514 4.479786 AGTTCATTTGCTCCTCTACCTC 57.520 45.455 0.00 0.00 0.00 3.85
4081 5515 4.100373 AGTTCATTTGCTCCTCTACCTCT 58.900 43.478 0.00 0.00 0.00 3.69
4082 5516 4.534103 AGTTCATTTGCTCCTCTACCTCTT 59.466 41.667 0.00 0.00 0.00 2.85
4083 5517 4.744795 TCATTTGCTCCTCTACCTCTTC 57.255 45.455 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.001487 CATGCACAACTGGAGCGAAAA 60.001 47.619 0.00 0.00 0.00 2.29
46 47 0.169894 GCAAGAAGCTTGCAGTAGGC 59.830 55.000 22.99 0.00 44.34 3.93
58 59 9.483062 CAAATACGAGAAGAATAAAGCAAGAAG 57.517 33.333 0.00 0.00 0.00 2.85
108 109 5.643777 GTGCACTTAGTAGATCCAAACATGT 59.356 40.000 10.32 0.00 0.00 3.21
176 177 8.486210 ACCTGCTGATAATCTAATCACAGTTAA 58.514 33.333 0.00 0.00 35.51 2.01
282 1585 7.265673 TGACTCCGTCTTTTATAGAATTCCAG 58.734 38.462 0.65 0.00 33.81 3.86
301 1604 4.338118 TGTTCACTTGGTTTTCATGACTCC 59.662 41.667 0.00 0.00 0.00 3.85
336 1639 7.711846 TGTTTTACTGTTAAGTGTCATGCAAT 58.288 30.769 0.00 0.00 37.19 3.56
383 1686 3.818210 AGAAATGTGTGCCGTACAATTCA 59.182 39.130 12.46 0.00 41.89 2.57
418 1721 7.336176 ACACGCGATATATTCTACAATCCTCTA 59.664 37.037 15.93 0.00 0.00 2.43
458 1761 5.991606 CCGCCATCTGACTAAAGAATGATAA 59.008 40.000 0.00 0.00 0.00 1.75
459 1762 5.541845 CCGCCATCTGACTAAAGAATGATA 58.458 41.667 0.00 0.00 0.00 2.15
568 1871 7.717875 AGGCATTTACACTTTACACTGTTAAGA 59.282 33.333 13.56 0.00 0.00 2.10
623 1927 3.386932 AGTGGCCCATGATTACAATGT 57.613 42.857 0.00 0.00 0.00 2.71
778 2082 5.432645 TGTGGAAGAGTCAAACAACACATA 58.567 37.500 0.00 0.00 33.23 2.29
1107 2411 6.018016 CACCGATATCAGCATCACATAAAACA 60.018 38.462 3.12 0.00 0.00 2.83
1355 2659 1.956869 ACCATGTGATCCTGACCTCA 58.043 50.000 0.00 0.00 0.00 3.86
1396 2707 4.082081 TGCATAGCTTTGCAGTGCTATTTT 60.082 37.500 25.36 9.59 46.55 1.82
1434 2745 9.801873 AAATGACCATGCAGTATTTAATACAAC 57.198 29.630 16.23 8.66 38.21 3.32
1493 2804 0.179192 GCGCGCTGATGAACAAATCA 60.179 50.000 26.67 0.00 43.67 2.57
1534 2845 8.931568 ACGGAGGGAGTAGTAATTATGTAAAAT 58.068 33.333 0.00 0.00 0.00 1.82
1537 2848 6.491403 GGACGGAGGGAGTAGTAATTATGTAA 59.509 42.308 0.00 0.00 0.00 2.41
1538 2849 6.006449 GGACGGAGGGAGTAGTAATTATGTA 58.994 44.000 0.00 0.00 0.00 2.29
1551 2862 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1552 2863 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1553 2864 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1554 2865 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1555 2866 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1556 2867 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1557 2868 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1558 2869 4.625742 AGTGATGACAAGTATTTTCGGACG 59.374 41.667 0.00 0.00 0.00 4.79
1559 2870 5.063564 GGAGTGATGACAAGTATTTTCGGAC 59.936 44.000 0.00 0.00 0.00 4.79
1560 2871 5.175859 GGAGTGATGACAAGTATTTTCGGA 58.824 41.667 0.00 0.00 0.00 4.55
1561 2872 4.332819 GGGAGTGATGACAAGTATTTTCGG 59.667 45.833 0.00 0.00 0.00 4.30
1562 2873 5.178797 AGGGAGTGATGACAAGTATTTTCG 58.821 41.667 0.00 0.00 0.00 3.46
1563 2874 5.586643 GGAGGGAGTGATGACAAGTATTTTC 59.413 44.000 0.00 0.00 0.00 2.29
1564 2875 5.501156 GGAGGGAGTGATGACAAGTATTTT 58.499 41.667 0.00 0.00 0.00 1.82
1565 2876 4.383118 CGGAGGGAGTGATGACAAGTATTT 60.383 45.833 0.00 0.00 0.00 1.40
1566 2877 3.133003 CGGAGGGAGTGATGACAAGTATT 59.867 47.826 0.00 0.00 0.00 1.89
1567 2878 2.695666 CGGAGGGAGTGATGACAAGTAT 59.304 50.000 0.00 0.00 0.00 2.12
1568 2879 2.100197 CGGAGGGAGTGATGACAAGTA 58.900 52.381 0.00 0.00 0.00 2.24
1569 2880 0.898320 CGGAGGGAGTGATGACAAGT 59.102 55.000 0.00 0.00 0.00 3.16
1570 2881 0.898320 ACGGAGGGAGTGATGACAAG 59.102 55.000 0.00 0.00 0.00 3.16
1571 2882 0.895530 GACGGAGGGAGTGATGACAA 59.104 55.000 0.00 0.00 0.00 3.18
1572 2883 0.970937 GGACGGAGGGAGTGATGACA 60.971 60.000 0.00 0.00 0.00 3.58
1573 2884 1.817209 GGACGGAGGGAGTGATGAC 59.183 63.158 0.00 0.00 0.00 3.06
1574 2885 1.753078 CGGACGGAGGGAGTGATGA 60.753 63.158 0.00 0.00 0.00 2.92
1575 2886 1.320344 TTCGGACGGAGGGAGTGATG 61.320 60.000 0.00 0.00 0.00 3.07
1576 2887 0.613853 TTTCGGACGGAGGGAGTGAT 60.614 55.000 0.00 0.00 0.00 3.06
1577 2888 0.828762 TTTTCGGACGGAGGGAGTGA 60.829 55.000 0.00 0.00 0.00 3.41
1578 2889 0.249398 ATTTTCGGACGGAGGGAGTG 59.751 55.000 0.00 0.00 0.00 3.51
1579 2890 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
1580 2891 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
1581 2892 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
1582 2893 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1583 2894 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
1584 2895 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1585 2896 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1586 2897 4.939509 AATGACAAGTATTTTCGGACGG 57.060 40.909 0.00 0.00 0.00 4.79
1615 2926 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1616 2927 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1617 2928 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1618 2929 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1619 2930 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1620 2931 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1621 2932 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1622 2933 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1623 2934 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1624 2935 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1625 2936 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
1626 2937 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1627 2938 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
1628 2939 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
1629 2940 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
1630 2941 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1631 2942 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1632 2943 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1633 2944 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
1634 2945 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
1635 2946 1.631405 TTACTCCCTCCGTCCGAAAA 58.369 50.000 0.00 0.00 0.00 2.29
1636 2947 1.856629 ATTACTCCCTCCGTCCGAAA 58.143 50.000 0.00 0.00 0.00 3.46
1637 2948 2.734755 TATTACTCCCTCCGTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
1638 2949 2.511659 CATATTACTCCCTCCGTCCGA 58.488 52.381 0.00 0.00 0.00 4.55
1639 2950 1.067776 GCATATTACTCCCTCCGTCCG 60.068 57.143 0.00 0.00 0.00 4.79
1640 2951 1.968493 TGCATATTACTCCCTCCGTCC 59.032 52.381 0.00 0.00 0.00 4.79
1641 2952 3.746045 TTGCATATTACTCCCTCCGTC 57.254 47.619 0.00 0.00 0.00 4.79
1642 2953 3.454812 ACTTTGCATATTACTCCCTCCGT 59.545 43.478 0.00 0.00 0.00 4.69
1643 2954 4.073293 ACTTTGCATATTACTCCCTCCG 57.927 45.455 0.00 0.00 0.00 4.63
1644 2955 6.592870 AGTAACTTTGCATATTACTCCCTCC 58.407 40.000 10.45 0.00 34.77 4.30
1645 2956 7.988028 AGAAGTAACTTTGCATATTACTCCCTC 59.012 37.037 14.62 10.53 38.01 4.30
1646 2957 7.862675 AGAAGTAACTTTGCATATTACTCCCT 58.137 34.615 14.62 12.46 38.01 4.20
1647 2958 9.043079 GTAGAAGTAACTTTGCATATTACTCCC 57.957 37.037 14.62 11.06 38.01 4.30
1648 2959 9.595823 TGTAGAAGTAACTTTGCATATTACTCC 57.404 33.333 14.62 6.03 38.01 3.85
1679 2990 3.589951 ATGCCAGCACCTCAATAGAAT 57.410 42.857 0.00 0.00 0.00 2.40
1702 3013 4.749099 GCTGTATTACCTGCAATGAGAGAG 59.251 45.833 0.00 0.00 0.00 3.20
1808 3119 4.828939 AGAAGACATGAAATTGCTTCACCA 59.171 37.500 0.00 0.00 46.80 4.17
1848 3159 9.462174 TCATTCAAGCATAAGTTAACAAAGTTG 57.538 29.630 8.61 4.10 0.00 3.16
1854 3165 6.425417 TGTCGTCATTCAAGCATAAGTTAACA 59.575 34.615 8.61 0.00 0.00 2.41
1883 3194 2.889170 TGGCATAGCACAAAGGGTAA 57.111 45.000 0.00 0.00 0.00 2.85
1901 3212 9.243105 TCCTTTTTAATGGACTCTTCCTAATTG 57.757 33.333 0.00 0.00 43.31 2.32
1902 3213 9.244292 GTCCTTTTTAATGGACTCTTCCTAATT 57.756 33.333 16.24 0.00 45.10 1.40
1932 3243 6.032956 ACTGTTGGTGTATCACGAAAGATA 57.967 37.500 0.00 0.00 34.23 1.98
2011 3322 3.861840 GCCATGTGCTACTACTTCTCAA 58.138 45.455 0.00 0.00 36.87 3.02
2028 3339 0.032813 AGCCTGTATTGCCAAGCCAT 60.033 50.000 0.00 0.00 0.00 4.40
2032 3343 1.066605 GCATCAGCCTGTATTGCCAAG 59.933 52.381 5.98 0.00 33.58 3.61
2035 3346 0.950116 GAGCATCAGCCTGTATTGCC 59.050 55.000 11.48 3.19 43.56 4.52
2037 3348 2.336945 TGGAGCATCAGCCTGTATTG 57.663 50.000 0.00 0.00 43.56 1.90
2052 3363 6.547141 TGGAATCTTGCCAGTTTAATATGGAG 59.453 38.462 9.98 1.21 39.02 3.86
2135 3446 9.109393 GGATGTGCTTACTTTTATCAATCAGTA 57.891 33.333 0.00 0.00 0.00 2.74
2147 3458 2.756760 CCTGCATGGATGTGCTTACTTT 59.243 45.455 0.00 0.00 45.27 2.66
2220 3531 2.715763 TCAAGGTTACTCTCCAGGGT 57.284 50.000 0.00 0.00 0.00 4.34
2291 3602 5.826586 TCTGAAAAGATTTTAGTTTGCGCA 58.173 33.333 5.66 5.66 0.00 6.09
2352 3663 7.218314 TCTCCCTAGATATGATCTGCATCTA 57.782 40.000 0.00 3.26 40.51 1.98
2399 3710 3.757745 ATAAAATTTCGTGTGGAGCCG 57.242 42.857 0.00 0.00 0.00 5.52
2439 3750 5.180117 GCTCATCTTTCTACAAGCAAGTTCA 59.820 40.000 0.00 0.00 0.00 3.18
2488 3799 2.891112 TGCAAAACAGAGGCACAAAAG 58.109 42.857 0.00 0.00 31.58 2.27
2521 3832 2.372264 AGTATGTCATTGGCAGCCTTG 58.628 47.619 14.15 10.72 0.00 3.61
2677 3989 5.808366 TTCATATAGTCGATTTCCCTGCT 57.192 39.130 0.00 0.00 0.00 4.24
2678 3990 7.324178 ACTATTCATATAGTCGATTTCCCTGC 58.676 38.462 0.00 0.00 42.61 4.85
2711 4023 8.136165 GTCTTACATTTATCTAGACACGGATGT 58.864 37.037 0.00 4.65 43.71 3.06
2726 4089 7.014711 TGTCCCAAAAAGCATGTCTTACATTTA 59.985 33.333 0.00 0.00 36.53 1.40
2731 4094 4.518970 TCTGTCCCAAAAAGCATGTCTTAC 59.481 41.667 0.00 0.00 33.88 2.34
2739 4102 0.850100 TCCCTCTGTCCCAAAAAGCA 59.150 50.000 0.00 0.00 0.00 3.91
2751 4114 8.997323 CAGCAATAATATTTTCTACTCCCTCTG 58.003 37.037 0.00 0.00 0.00 3.35
2752 4115 8.160106 CCAGCAATAATATTTTCTACTCCCTCT 58.840 37.037 0.00 0.00 0.00 3.69
2797 4160 3.254166 GCCAGCAAATATGTAGGTCCATG 59.746 47.826 0.00 0.00 0.00 3.66
2824 4187 5.191722 TCCCTGAAGCATATCCAAAACTACT 59.808 40.000 0.00 0.00 0.00 2.57
2834 4197 3.252701 CACTTGCATCCCTGAAGCATATC 59.747 47.826 0.00 0.00 36.19 1.63
2843 4206 1.171308 CTGAACCACTTGCATCCCTG 58.829 55.000 0.00 0.00 0.00 4.45
2863 4226 2.108168 AGCGTAGAGGGATGCAAAGTA 58.892 47.619 0.00 0.00 33.52 2.24
2880 4243 4.041740 TGCACTAACTAGAATACCAGCG 57.958 45.455 0.00 0.00 0.00 5.18
3017 4380 0.458260 GCATCATCATGTTGCTGCCA 59.542 50.000 17.79 0.00 39.34 4.92
3066 4429 7.173722 TGTTTAGGCTAGAAGTAGTAGTCACT 58.826 38.462 0.00 0.00 38.91 3.41
3070 4433 6.723052 TGGTTGTTTAGGCTAGAAGTAGTAGT 59.277 38.462 0.00 0.00 0.00 2.73
3071 4434 7.166691 TGGTTGTTTAGGCTAGAAGTAGTAG 57.833 40.000 0.00 0.00 0.00 2.57
3109 4472 2.668550 AAACCCGAACTGGCGAGC 60.669 61.111 0.00 0.00 35.87 5.03
3197 4560 4.825422 TCGACAGATGCTGATCTTCTTTT 58.175 39.130 0.82 0.00 36.75 2.27
3295 4688 1.301293 GGTCAGCTGGAGGGGAAAG 59.699 63.158 15.13 0.00 0.00 2.62
3310 4703 1.950909 CGAGTACTCCTCTCCATGGTC 59.049 57.143 17.23 0.00 38.11 4.02
3342 4735 3.568853 AGATAACTTGGATAGGTCGGTCG 59.431 47.826 0.00 0.00 0.00 4.79
3501 4901 9.053840 CAGATACAGATACAGATGCAGATTTTT 57.946 33.333 0.00 0.00 0.00 1.94
3502 4902 8.209584 ACAGATACAGATACAGATGCAGATTTT 58.790 33.333 0.00 0.00 0.00 1.82
3503 4903 7.733969 ACAGATACAGATACAGATGCAGATTT 58.266 34.615 0.00 0.00 0.00 2.17
3504 4904 7.300556 ACAGATACAGATACAGATGCAGATT 57.699 36.000 0.00 0.00 0.00 2.40
3505 4905 6.914654 ACAGATACAGATACAGATGCAGAT 57.085 37.500 0.00 0.00 0.00 2.90
3506 4906 7.121907 GGATACAGATACAGATACAGATGCAGA 59.878 40.741 0.00 0.00 0.00 4.26
3507 4907 7.257003 GGATACAGATACAGATACAGATGCAG 58.743 42.308 0.00 0.00 0.00 4.41
3508 4908 6.153510 GGGATACAGATACAGATACAGATGCA 59.846 42.308 0.00 0.00 39.74 3.96
3509 4909 6.379703 AGGGATACAGATACAGATACAGATGC 59.620 42.308 0.00 0.00 39.74 3.91
3510 4910 7.613411 TGAGGGATACAGATACAGATACAGATG 59.387 40.741 0.00 0.00 39.74 2.90
3511 4911 7.703755 TGAGGGATACAGATACAGATACAGAT 58.296 38.462 0.00 0.00 39.74 2.90
3512 4912 7.091533 TGAGGGATACAGATACAGATACAGA 57.908 40.000 0.00 0.00 39.74 3.41
3513 4913 7.767250 TTGAGGGATACAGATACAGATACAG 57.233 40.000 0.00 0.00 39.74 2.74
3514 4914 8.547481 TTTTGAGGGATACAGATACAGATACA 57.453 34.615 0.00 0.00 39.74 2.29
3541 4941 7.826252 ACAGATACAGATACAGATGCAGTTTTT 59.174 33.333 0.00 0.00 0.00 1.94
3542 4942 7.334090 ACAGATACAGATACAGATGCAGTTTT 58.666 34.615 0.00 0.00 0.00 2.43
3543 4943 6.882656 ACAGATACAGATACAGATGCAGTTT 58.117 36.000 0.00 0.00 0.00 2.66
3544 4944 6.477053 ACAGATACAGATACAGATGCAGTT 57.523 37.500 0.00 0.00 0.00 3.16
3545 4945 6.547510 TGTACAGATACAGATACAGATGCAGT 59.452 38.462 0.00 0.00 36.34 4.40
3546 4946 6.974965 TGTACAGATACAGATACAGATGCAG 58.025 40.000 0.00 0.00 36.34 4.41
3547 4947 6.959639 TGTACAGATACAGATACAGATGCA 57.040 37.500 0.00 0.00 36.34 3.96
3548 4948 6.364706 GCTTGTACAGATACAGATACAGATGC 59.635 42.308 0.00 0.00 42.29 3.91
3549 4949 7.656412 AGCTTGTACAGATACAGATACAGATG 58.344 38.462 0.00 0.00 42.29 2.90
3550 4950 7.831691 AGCTTGTACAGATACAGATACAGAT 57.168 36.000 0.00 0.00 42.29 2.90
3616 5038 7.147794 ACGACAACCAGAGTTATACCATATCAA 60.148 37.037 0.00 0.00 33.27 2.57
3624 5046 3.612860 CAGCACGACAACCAGAGTTATAC 59.387 47.826 0.00 0.00 33.27 1.47
3639 5061 2.094182 GGTGGTTCTCTAATCAGCACGA 60.094 50.000 0.00 0.00 42.56 4.35
3640 5062 2.271800 GGTGGTTCTCTAATCAGCACG 58.728 52.381 0.00 0.00 42.56 5.34
3659 5081 1.394917 CAGGAAACTCTGCGATTTCGG 59.605 52.381 1.75 0.00 40.21 4.30
3667 5089 4.436584 CGAAATCATGTCAGGAAACTCTGC 60.437 45.833 0.00 0.00 40.21 4.26
3706 5128 4.604043 CGCATGTTCGTATCGATCTTTCAC 60.604 45.833 0.00 0.00 35.23 3.18
3781 5203 9.129209 GCCAAATGTGAACTTATTACTTCTTTC 57.871 33.333 0.00 0.00 0.00 2.62
3784 5206 7.665559 TCTGCCAAATGTGAACTTATTACTTCT 59.334 33.333 0.00 0.00 0.00 2.85
3789 5211 6.563422 GCATCTGCCAAATGTGAACTTATTA 58.437 36.000 0.00 0.00 34.31 0.98
3792 5214 4.439305 GCATCTGCCAAATGTGAACTTA 57.561 40.909 0.00 0.00 34.31 2.24
3838 5260 0.814410 CATCCCAGCAGCACAGCTAG 60.814 60.000 0.00 0.00 44.54 3.42
3848 5270 1.619363 AGGGTAAGGCATCCCAGCA 60.619 57.895 12.72 0.00 45.64 4.41
3859 5281 0.249398 CGGACTTGTGGGAGGGTAAG 59.751 60.000 0.00 0.00 0.00 2.34
3877 5299 1.927174 GTTCAACATGACCCGAGATCG 59.073 52.381 0.00 0.00 39.44 3.69
3878 5300 2.932614 CTGTTCAACATGACCCGAGATC 59.067 50.000 0.00 0.00 0.00 2.75
3879 5301 2.936993 GCTGTTCAACATGACCCGAGAT 60.937 50.000 0.00 0.00 0.00 2.75
3880 5302 1.608025 GCTGTTCAACATGACCCGAGA 60.608 52.381 0.00 0.00 0.00 4.04
3881 5303 0.798776 GCTGTTCAACATGACCCGAG 59.201 55.000 0.00 0.00 0.00 4.63
3885 5307 1.068748 CAGCTGCTGTTCAACATGACC 60.069 52.381 21.21 0.00 0.00 4.02
3953 5387 2.122768 AGGAAGGCCTCTAATCTGGTG 58.877 52.381 5.23 0.00 42.19 4.17
4037 5471 9.485206 GAACTTCCACACTATTACTTTCTGTTA 57.515 33.333 0.00 0.00 0.00 2.41
4039 5473 7.506114 TGAACTTCCACACTATTACTTTCTGT 58.494 34.615 0.00 0.00 0.00 3.41
4040 5474 7.962964 TGAACTTCCACACTATTACTTTCTG 57.037 36.000 0.00 0.00 0.00 3.02
4042 5476 9.612620 CAAATGAACTTCCACACTATTACTTTC 57.387 33.333 0.00 0.00 0.00 2.62
4045 5479 6.942576 AGCAAATGAACTTCCACACTATTACT 59.057 34.615 0.00 0.00 0.00 2.24
4046 5480 7.145932 AGCAAATGAACTTCCACACTATTAC 57.854 36.000 0.00 0.00 0.00 1.89
4047 5481 6.374333 GGAGCAAATGAACTTCCACACTATTA 59.626 38.462 0.00 0.00 0.00 0.98
4048 5482 5.183904 GGAGCAAATGAACTTCCACACTATT 59.816 40.000 0.00 0.00 0.00 1.73
4049 5483 4.702131 GGAGCAAATGAACTTCCACACTAT 59.298 41.667 0.00 0.00 0.00 2.12
4050 5484 4.072131 GGAGCAAATGAACTTCCACACTA 58.928 43.478 0.00 0.00 0.00 2.74
4051 5485 2.887152 GGAGCAAATGAACTTCCACACT 59.113 45.455 0.00 0.00 0.00 3.55
4052 5486 2.887152 AGGAGCAAATGAACTTCCACAC 59.113 45.455 0.00 0.00 0.00 3.82
4053 5487 3.149196 GAGGAGCAAATGAACTTCCACA 58.851 45.455 0.00 0.00 0.00 4.17
4054 5488 3.416156 AGAGGAGCAAATGAACTTCCAC 58.584 45.455 0.00 0.00 0.00 4.02
4055 5489 3.795688 AGAGGAGCAAATGAACTTCCA 57.204 42.857 0.00 0.00 0.00 3.53
4056 5490 3.942115 GGTAGAGGAGCAAATGAACTTCC 59.058 47.826 0.00 0.00 0.00 3.46
4057 5491 4.837972 AGGTAGAGGAGCAAATGAACTTC 58.162 43.478 0.00 0.00 0.00 3.01
4058 5492 4.534103 AGAGGTAGAGGAGCAAATGAACTT 59.466 41.667 0.00 0.00 0.00 2.66
4059 5493 4.100373 AGAGGTAGAGGAGCAAATGAACT 58.900 43.478 0.00 0.00 0.00 3.01
4060 5494 4.479786 AGAGGTAGAGGAGCAAATGAAC 57.520 45.455 0.00 0.00 0.00 3.18
4061 5495 5.091261 GAAGAGGTAGAGGAGCAAATGAA 57.909 43.478 0.00 0.00 0.00 2.57
4062 5496 4.744795 GAAGAGGTAGAGGAGCAAATGA 57.255 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.