Multiple sequence alignment - TraesCS3D01G187200

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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 TraesCS3D01G187200 chr3D 100.000 4358 0 0 1 4358 173626221 173621864 0.000000e+00 8048.0
1 TraesCS3D01G187200 chr3D 79.437 817 130 23 1147 1956 173606893 173606108 1.070000e-150 544.0
2 TraesCS3D01G187200 chr3D 86.321 212 29 0 2104 2315 173605998 173605787 9.430000e-57 231.0
3 TraesCS3D01G187200 chr3D 82.353 187 32 1 2108 2293 174046486 174046300 1.250000e-35 161.0
4 TraesCS3D01G187200 chr3D 98.039 51 1 0 2684 2734 157099399 157099349 6.000000e-14 89.8
5 TraesCS3D01G187200 chr1D 98.085 940 16 2 2 939 308191415 308192354 0.000000e+00 1635.0
6 TraesCS3D01G187200 chr1D 91.919 99 6 2 3685 3782 411517707 411517804 2.110000e-28 137.0
7 TraesCS3D01G187200 chr2D 97.140 944 24 3 2 943 136354802 136355744 0.000000e+00 1591.0
8 TraesCS3D01G187200 chr2D 91.759 631 38 6 323 949 107840835 107840215 0.000000e+00 865.0
9 TraesCS3D01G187200 chr2D 85.016 634 67 18 1 631 626710779 626711387 1.720000e-173 619.0
10 TraesCS3D01G187200 chr2D 84.772 637 61 24 1 631 626747558 626748164 1.340000e-169 606.0
11 TraesCS3D01G187200 chr2D 88.793 232 24 2 710 939 626711391 626711622 2.570000e-72 283.0
12 TraesCS3D01G187200 chr2D 86.638 232 29 2 710 939 626748168 626748399 5.590000e-64 255.0
13 TraesCS3D01G187200 chr2D 82.022 89 12 2 2643 2728 473096452 473096365 6.050000e-09 73.1
14 TraesCS3D01G187200 chr4B 96.379 939 32 2 2 939 527323941 527323004 0.000000e+00 1544.0
15 TraesCS3D01G187200 chr2B 94.569 939 33 3 2 939 39737904 39738825 0.000000e+00 1435.0
16 TraesCS3D01G187200 chr3A 92.894 971 39 10 2726 3694 212110291 212109349 0.000000e+00 1384.0
17 TraesCS3D01G187200 chr3A 93.875 898 40 7 1123 2016 212111793 212110907 0.000000e+00 1339.0
18 TraesCS3D01G187200 chr3A 93.929 593 22 6 2086 2667 212110902 212110313 0.000000e+00 883.0
19 TraesCS3D01G187200 chr3A 92.383 512 38 1 3847 4358 212108884 212108374 0.000000e+00 728.0
20 TraesCS3D01G187200 chr3A 77.063 1430 223 59 1126 2518 211957793 211956432 0.000000e+00 726.0
21 TraesCS3D01G187200 chr3A 80.952 189 35 1 2108 2295 212703055 212702867 9.760000e-32 148.0
22 TraesCS3D01G187200 chr3A 100.000 34 0 0 4325 4358 212108101 212108068 3.640000e-06 63.9
23 TraesCS3D01G187200 chr3B 91.581 974 48 17 1000 1951 252560064 252559103 0.000000e+00 1314.0
24 TraesCS3D01G187200 chr3B 92.483 745 36 9 2613 3341 252558432 252557692 0.000000e+00 1048.0
25 TraesCS3D01G187200 chr3B 92.015 551 22 9 2086 2615 252559074 252558525 0.000000e+00 754.0
26 TraesCS3D01G187200 chr3B 78.941 850 127 25 1123 1956 252347274 252346461 8.300000e-147 531.0
27 TraesCS3D01G187200 chr3B 87.234 94 12 0 2200 2293 252795838 252795745 1.660000e-19 108.0
28 TraesCS3D01G187200 chr5B 86.002 943 80 22 1 939 533770160 533769266 0.000000e+00 963.0
29 TraesCS3D01G187200 chr5B 91.837 98 7 1 3684 3780 661300481 661300384 7.600000e-28 135.0
30 TraesCS3D01G187200 chr5B 90.385 104 7 3 3676 3778 33626953 33627054 2.730000e-27 134.0
31 TraesCS3D01G187200 chr5B 82.022 89 13 3 2643 2728 176590545 176590633 6.050000e-09 73.1
32 TraesCS3D01G187200 chr5A 84.746 590 56 18 75 651 554353891 554353323 1.060000e-155 560.0
33 TraesCS3D01G187200 chr5A 89.298 299 23 5 643 939 554350793 554350502 2.480000e-97 366.0
34 TraesCS3D01G187200 chr5A 98.039 51 1 0 2681 2731 533944238 533944288 6.000000e-14 89.8
35 TraesCS3D01G187200 chr7D 91.753 291 21 3 651 939 298811216 298810927 6.790000e-108 401.0
36 TraesCS3D01G187200 chr6D 94.681 94 5 0 3692 3785 129438578 129438485 3.510000e-31 147.0
37 TraesCS3D01G187200 chr6D 92.079 101 3 5 3680 3775 149721765 149721665 2.110000e-28 137.0
38 TraesCS3D01G187200 chr4D 95.556 90 4 0 3687 3776 62484741 62484652 1.260000e-30 145.0
39 TraesCS3D01G187200 chr4D 94.624 93 4 1 3691 3782 190532992 190533084 4.540000e-30 143.0
40 TraesCS3D01G187200 chr4D 83.529 85 11 2 2643 2726 320044176 320044258 4.670000e-10 76.8
41 TraesCS3D01G187200 chr5D 94.565 92 4 1 3690 3780 225253272 225253181 1.630000e-29 141.0
42 TraesCS3D01G187200 chr5D 98.039 51 1 0 2681 2731 420277180 420277230 6.000000e-14 89.8
43 TraesCS3D01G187200 chr1B 94.565 92 4 1 3692 3782 27294475 27294384 1.630000e-29 141.0
44 TraesCS3D01G187200 chr7A 88.235 68 7 1 496 563 460757336 460757270 3.610000e-11 80.5
45 TraesCS3D01G187200 chr7A 83.146 89 12 2 2644 2729 8236009 8236097 1.300000e-10 78.7
46 TraesCS3D01G187200 chr7A 83.333 84 11 3 2646 2726 623742187 623742104 1.680000e-09 75.0


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 TraesCS3D01G187200 chr3D 173621864 173626221 4357 True 8048.000000 8048 100.000000 1 4358 1 chr3D.!!$R2 4357
1 TraesCS3D01G187200 chr3D 173605787 173606893 1106 True 387.500000 544 82.879000 1147 2315 2 chr3D.!!$R4 1168
2 TraesCS3D01G187200 chr1D 308191415 308192354 939 False 1635.000000 1635 98.085000 2 939 1 chr1D.!!$F1 937
3 TraesCS3D01G187200 chr2D 136354802 136355744 942 False 1591.000000 1591 97.140000 2 943 1 chr2D.!!$F1 941
4 TraesCS3D01G187200 chr2D 107840215 107840835 620 True 865.000000 865 91.759000 323 949 1 chr2D.!!$R1 626
5 TraesCS3D01G187200 chr2D 626710779 626711622 843 False 451.000000 619 86.904500 1 939 2 chr2D.!!$F2 938
6 TraesCS3D01G187200 chr2D 626747558 626748399 841 False 430.500000 606 85.705000 1 939 2 chr2D.!!$F3 938
7 TraesCS3D01G187200 chr4B 527323004 527323941 937 True 1544.000000 1544 96.379000 2 939 1 chr4B.!!$R1 937
8 TraesCS3D01G187200 chr2B 39737904 39738825 921 False 1435.000000 1435 94.569000 2 939 1 chr2B.!!$F1 937
9 TraesCS3D01G187200 chr3A 212108068 212111793 3725 True 879.580000 1384 94.616200 1123 4358 5 chr3A.!!$R3 3235
10 TraesCS3D01G187200 chr3A 211956432 211957793 1361 True 726.000000 726 77.063000 1126 2518 1 chr3A.!!$R1 1392
11 TraesCS3D01G187200 chr3B 252557692 252560064 2372 True 1038.666667 1314 92.026333 1000 3341 3 chr3B.!!$R3 2341
12 TraesCS3D01G187200 chr3B 252346461 252347274 813 True 531.000000 531 78.941000 1123 1956 1 chr3B.!!$R1 833
13 TraesCS3D01G187200 chr5B 533769266 533770160 894 True 963.000000 963 86.002000 1 939 1 chr5B.!!$R1 938
14 TraesCS3D01G187200 chr5A 554350502 554353891 3389 True 463.000000 560 87.022000 75 939 2 chr5A.!!$R1 864

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
977 3538 0.308684 CGCATCGTAGCCCGTAGTAA 59.691 55.0 0.00 0.00 37.94 2.24 F
1092 3669 0.033781 GCAGCTCCCACAAATTTGCA 59.966 50.0 18.12 0.00 0.00 4.08 F
1097 3674 0.033781 TCCCACAAATTTGCAGCAGC 59.966 50.0 18.12 0.00 42.57 5.25 F
2079 4700 0.391793 GCTCACTTAGGTGGGTCAGC 60.392 60.0 6.73 3.83 45.21 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 4488 0.107643 TGTGAACGCTGACAATGGGA 59.892 50.0 0.00 0.00 0.00 4.37 R
2069 4690 0.685097 TGAAGTACAGCTGACCCACC 59.315 55.0 23.35 5.32 0.00 4.61 R
2992 5762 1.073177 GCATGTTGCAGCACCATTTC 58.927 50.0 5.00 0.00 44.26 2.17 R
4075 7241 1.055040 GGCATCTCCATAGCAGACCT 58.945 55.0 0.00 0.00 34.01 3.85 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
196 200 2.280628 CGAGAATAAGCTTGGGACACC 58.719 52.381 9.86 0.00 39.29 4.16
917 3478 2.094234 ACAAAAATTAGATGGCCCGTGC 60.094 45.455 0.00 0.00 0.00 5.34
939 3500 2.357327 ACGCACGAGCATTGTACTAA 57.643 45.000 5.50 0.00 42.27 2.24
945 3506 6.036735 ACGCACGAGCATTGTACTAATTTATT 59.963 34.615 5.50 0.00 42.27 1.40
969 3530 5.779806 AATCATTTATACGCATCGTAGCC 57.220 39.130 5.34 0.00 45.45 3.93
970 3531 3.581755 TCATTTATACGCATCGTAGCCC 58.418 45.455 5.34 0.00 45.45 5.19
971 3532 2.054687 TTTATACGCATCGTAGCCCG 57.945 50.000 5.34 0.00 45.45 6.13
972 3533 0.953727 TTATACGCATCGTAGCCCGT 59.046 50.000 5.34 0.00 45.45 5.28
973 3534 1.807139 TATACGCATCGTAGCCCGTA 58.193 50.000 5.34 0.00 45.45 4.02
974 3535 0.520404 ATACGCATCGTAGCCCGTAG 59.480 55.000 5.34 0.00 45.45 3.51
975 3536 0.815213 TACGCATCGTAGCCCGTAGT 60.815 55.000 0.00 0.00 41.54 2.73
976 3537 0.815213 ACGCATCGTAGCCCGTAGTA 60.815 55.000 0.00 0.00 38.73 1.82
977 3538 0.308684 CGCATCGTAGCCCGTAGTAA 59.691 55.000 0.00 0.00 37.94 2.24
978 3539 1.068748 CGCATCGTAGCCCGTAGTAAT 60.069 52.381 0.00 0.00 37.94 1.89
979 3540 2.593257 GCATCGTAGCCCGTAGTAATC 58.407 52.381 0.00 0.00 37.94 1.75
980 3541 2.847901 CATCGTAGCCCGTAGTAATCG 58.152 52.381 0.00 0.00 37.94 3.34
981 3542 0.588252 TCGTAGCCCGTAGTAATCGC 59.412 55.000 0.00 0.00 37.94 4.58
982 3543 0.308684 CGTAGCCCGTAGTAATCGCA 59.691 55.000 0.00 0.00 0.00 5.10
983 3544 1.763634 GTAGCCCGTAGTAATCGCAC 58.236 55.000 0.00 0.00 0.00 5.34
984 3545 0.308684 TAGCCCGTAGTAATCGCACG 59.691 55.000 0.00 0.00 35.50 5.34
987 3548 3.609258 CGTAGTAATCGCACGGGC 58.391 61.111 0.00 0.00 32.19 6.13
998 3559 2.340809 CACGGGCGTTCACTGGTA 59.659 61.111 0.00 0.00 0.00 3.25
1008 3569 3.448686 CGTTCACTGGTATCTCCATGTC 58.551 50.000 0.00 0.00 46.12 3.06
1012 3573 2.032620 ACTGGTATCTCCATGTCGTCC 58.967 52.381 0.00 0.00 46.12 4.79
1016 3577 2.223829 GGTATCTCCATGTCGTCCAGTG 60.224 54.545 0.00 0.00 35.97 3.66
1050 3613 2.694109 GCTGATTACGGAGGGAGTAGTT 59.306 50.000 0.00 0.00 0.00 2.24
1052 3615 3.952323 CTGATTACGGAGGGAGTAGTTGA 59.048 47.826 0.00 0.00 0.00 3.18
1078 3655 0.107456 CCCCACGATTATCAGCAGCT 59.893 55.000 0.00 0.00 0.00 4.24
1079 3656 1.506493 CCCACGATTATCAGCAGCTC 58.494 55.000 0.00 0.00 0.00 4.09
1080 3657 1.506493 CCACGATTATCAGCAGCTCC 58.494 55.000 0.00 0.00 0.00 4.70
1081 3658 1.506493 CACGATTATCAGCAGCTCCC 58.494 55.000 0.00 0.00 0.00 4.30
1082 3659 1.123077 ACGATTATCAGCAGCTCCCA 58.877 50.000 0.00 0.00 0.00 4.37
1083 3660 1.202580 ACGATTATCAGCAGCTCCCAC 60.203 52.381 0.00 0.00 0.00 4.61
1084 3661 1.202568 CGATTATCAGCAGCTCCCACA 60.203 52.381 0.00 0.00 0.00 4.17
1085 3662 2.742856 CGATTATCAGCAGCTCCCACAA 60.743 50.000 0.00 0.00 0.00 3.33
1086 3663 2.877097 TTATCAGCAGCTCCCACAAA 57.123 45.000 0.00 0.00 0.00 2.83
1087 3664 3.370840 TTATCAGCAGCTCCCACAAAT 57.629 42.857 0.00 0.00 0.00 2.32
1088 3665 2.226962 ATCAGCAGCTCCCACAAATT 57.773 45.000 0.00 0.00 0.00 1.82
1089 3666 1.999648 TCAGCAGCTCCCACAAATTT 58.000 45.000 0.00 0.00 0.00 1.82
1090 3667 1.614903 TCAGCAGCTCCCACAAATTTG 59.385 47.619 16.67 16.67 0.00 2.32
1091 3668 0.319405 AGCAGCTCCCACAAATTTGC 59.681 50.000 18.12 2.94 0.00 3.68
1092 3669 0.033781 GCAGCTCCCACAAATTTGCA 59.966 50.000 18.12 0.00 0.00 4.08
1093 3670 1.938016 GCAGCTCCCACAAATTTGCAG 60.938 52.381 18.12 10.74 0.00 4.41
1094 3671 0.319405 AGCTCCCACAAATTTGCAGC 59.681 50.000 18.12 17.94 0.00 5.25
1095 3672 0.033781 GCTCCCACAAATTTGCAGCA 59.966 50.000 18.12 0.00 0.00 4.41
1096 3673 1.938016 GCTCCCACAAATTTGCAGCAG 60.938 52.381 18.12 10.13 0.00 4.24
1097 3674 0.033781 TCCCACAAATTTGCAGCAGC 59.966 50.000 18.12 0.00 42.57 5.25
1098 3675 0.952010 CCCACAAATTTGCAGCAGCC 60.952 55.000 18.12 0.00 41.13 4.85
1099 3676 1.286354 CCACAAATTTGCAGCAGCCG 61.286 55.000 18.12 0.00 41.13 5.52
1100 3677 1.665599 ACAAATTTGCAGCAGCCGC 60.666 52.632 18.12 0.00 41.13 6.53
1215 3817 1.199615 CCCCTCTCCTCTTCTTCACC 58.800 60.000 0.00 0.00 0.00 4.02
1510 4121 4.920640 GGTATCGACCTGAATCTCTGAA 57.079 45.455 0.00 0.00 43.16 3.02
1512 4123 4.339814 GGTATCGACCTGAATCTCTGAACT 59.660 45.833 0.00 0.00 43.16 3.01
1514 4125 4.179926 TCGACCTGAATCTCTGAACTTG 57.820 45.455 0.00 0.00 0.00 3.16
1538 4150 1.228831 CACAAATCCCACAGCCCCA 60.229 57.895 0.00 0.00 0.00 4.96
1844 4460 2.161855 TCTGGAATGCAACGAAATGCT 58.838 42.857 12.30 0.00 46.54 3.79
1866 4482 2.364647 GTCGATTCCGGAGACCCTAAAT 59.635 50.000 3.34 0.00 36.24 1.40
1872 4488 0.541863 CGGAGACCCTAAATGGTGCT 59.458 55.000 0.00 0.00 39.24 4.40
1922 4538 1.734707 CGACGGTGACCTCATTGTACC 60.735 57.143 0.00 0.00 0.00 3.34
1928 4544 1.822990 TGACCTCATTGTACCGTCTCC 59.177 52.381 0.00 0.00 0.00 3.71
1949 4570 4.326504 CCCCCTATTTTTGCTTGCATAG 57.673 45.455 0.00 0.00 0.00 2.23
1952 4573 5.362430 CCCCCTATTTTTGCTTGCATAGTTA 59.638 40.000 0.00 0.00 0.00 2.24
1957 4578 9.450807 CCTATTTTTGCTTGCATAGTTACATAC 57.549 33.333 0.00 0.00 0.00 2.39
1982 4603 9.903682 ACTTACATTTGATGATCAACTTCTTTG 57.096 29.630 7.48 2.39 35.89 2.77
2005 4626 6.125719 TGTTTTATAATGGAGCATGCTGGTA 58.874 36.000 28.27 11.39 0.00 3.25
2016 4637 3.130633 GCATGCTGGTACGAATGTATGA 58.869 45.455 11.37 0.00 32.11 2.15
2017 4638 3.185188 GCATGCTGGTACGAATGTATGAG 59.815 47.826 11.37 0.00 32.11 2.90
2018 4639 2.821546 TGCTGGTACGAATGTATGAGC 58.178 47.619 0.00 0.00 37.80 4.26
2020 4641 2.797156 GCTGGTACGAATGTATGAGCTG 59.203 50.000 0.00 0.00 35.95 4.24
2021 4642 3.490933 GCTGGTACGAATGTATGAGCTGA 60.491 47.826 0.00 0.00 35.95 4.26
2022 4643 4.682787 CTGGTACGAATGTATGAGCTGAA 58.317 43.478 0.00 0.00 32.11 3.02
2023 4644 5.276461 TGGTACGAATGTATGAGCTGAAT 57.724 39.130 0.00 0.00 32.11 2.57
2024 4645 6.399639 TGGTACGAATGTATGAGCTGAATA 57.600 37.500 0.00 0.00 32.11 1.75
2026 4647 6.700081 TGGTACGAATGTATGAGCTGAATAAC 59.300 38.462 0.00 0.00 32.11 1.89
2027 4648 6.924060 GGTACGAATGTATGAGCTGAATAACT 59.076 38.462 0.00 0.00 32.11 2.24
2028 4649 8.080417 GGTACGAATGTATGAGCTGAATAACTA 58.920 37.037 0.00 0.00 32.11 2.24
2031 4652 9.547753 ACGAATGTATGAGCTGAATAACTATTT 57.452 29.630 0.00 0.00 0.00 1.40
2039 4660 7.978982 TGAGCTGAATAACTATTTCTCTTTGC 58.021 34.615 0.00 0.00 0.00 3.68
2040 4661 7.826252 TGAGCTGAATAACTATTTCTCTTTGCT 59.174 33.333 0.00 0.00 0.00 3.91
2042 4663 7.281999 AGCTGAATAACTATTTCTCTTTGCTCC 59.718 37.037 0.00 0.00 0.00 4.70
2045 4666 7.606456 TGAATAACTATTTCTCTTTGCTCCGTT 59.394 33.333 0.00 0.00 0.00 4.44
2048 4669 6.002062 ACTATTTCTCTTTGCTCCGTTTTG 57.998 37.500 0.00 0.00 0.00 2.44
2050 4671 3.691049 TTCTCTTTGCTCCGTTTTGTG 57.309 42.857 0.00 0.00 0.00 3.33
2051 4672 2.912771 TCTCTTTGCTCCGTTTTGTGA 58.087 42.857 0.00 0.00 0.00 3.58
2054 4675 5.245531 TCTCTTTGCTCCGTTTTGTGATAT 58.754 37.500 0.00 0.00 0.00 1.63
2055 4676 6.403049 TCTCTTTGCTCCGTTTTGTGATATA 58.597 36.000 0.00 0.00 0.00 0.86
2057 4678 8.201464 TCTCTTTGCTCCGTTTTGTGATATATA 58.799 33.333 0.00 0.00 0.00 0.86
2058 4679 8.902540 TCTTTGCTCCGTTTTGTGATATATAT 57.097 30.769 0.00 0.00 0.00 0.86
2060 4681 9.385902 CTTTGCTCCGTTTTGTGATATATATTG 57.614 33.333 0.00 0.00 0.00 1.90
2064 4685 7.095229 GCTCCGTTTTGTGATATATATTGCTCA 60.095 37.037 0.00 0.00 0.00 4.26
2066 4687 7.931407 TCCGTTTTGTGATATATATTGCTCACT 59.069 33.333 16.96 0.00 38.98 3.41
2067 4688 8.559536 CCGTTTTGTGATATATATTGCTCACTT 58.440 33.333 16.96 0.00 38.98 3.16
2072 4693 9.710900 TTGTGATATATATTGCTCACTTAGGTG 57.289 33.333 16.96 0.00 44.23 4.00
2073 4694 8.314021 TGTGATATATATTGCTCACTTAGGTGG 58.686 37.037 16.96 0.00 43.17 4.61
2074 4695 7.766278 GTGATATATATTGCTCACTTAGGTGGG 59.234 40.741 5.01 2.28 46.13 4.61
2079 4700 0.391793 GCTCACTTAGGTGGGTCAGC 60.392 60.000 6.73 3.83 45.21 4.26
2083 4704 1.899814 CACTTAGGTGGGTCAGCTGTA 59.100 52.381 14.67 0.00 42.42 2.74
2133 4755 1.542915 CTTGCATGACTTTCAGGTGGG 59.457 52.381 0.00 0.00 29.72 4.61
2158 4780 6.856895 ACTTTCTTCAGGAAAAGAAGTTGTG 58.143 36.000 0.00 0.00 43.95 3.33
2484 5124 7.066781 TCAGTCTGGATACCATAGTCATGTAA 58.933 38.462 0.00 0.00 30.82 2.41
2488 5128 8.589338 GTCTGGATACCATAGTCATGTAATCTT 58.411 37.037 0.00 0.00 30.82 2.40
2552 5203 6.742718 GTCTCGCGTAATTAGTAGTGTTAACA 59.257 38.462 5.77 3.59 0.00 2.41
2553 5204 7.271223 GTCTCGCGTAATTAGTAGTGTTAACAA 59.729 37.037 10.51 0.00 0.00 2.83
2554 5205 7.264448 TCGCGTAATTAGTAGTGTTAACAAC 57.736 36.000 10.51 6.08 0.00 3.32
2601 5258 6.484288 TGTGACAGATAATTTCACCAAGGAT 58.516 36.000 5.07 0.00 39.16 3.24
2602 5259 6.599244 TGTGACAGATAATTTCACCAAGGATC 59.401 38.462 5.07 0.00 39.16 3.36
2653 5407 8.066247 AGTTGAACACTAGGTATATACTCCCTT 58.934 37.037 12.54 0.00 31.97 3.95
2654 5408 8.702819 GTTGAACACTAGGTATATACTCCCTTT 58.297 37.037 12.54 0.45 0.00 3.11
2667 5421 8.762481 ATATACTCCCTTTGTCCCAAAATAAC 57.238 34.615 0.00 0.00 0.00 1.89
2668 5422 4.157246 ACTCCCTTTGTCCCAAAATAACC 58.843 43.478 0.00 0.00 0.00 2.85
2671 5425 5.966684 TCCCTTTGTCCCAAAATAACCTTA 58.033 37.500 0.00 0.00 0.00 2.69
2672 5426 6.566914 TCCCTTTGTCCCAAAATAACCTTAT 58.433 36.000 0.00 0.00 0.00 1.73
2673 5427 7.020009 TCCCTTTGTCCCAAAATAACCTTATT 58.980 34.615 0.00 0.00 34.98 1.40
2676 5430 9.567776 CCTTTGTCCCAAAATAACCTTATTTTT 57.432 29.630 11.45 0.00 45.89 1.94
2678 5432 8.910351 TTGTCCCAAAATAACCTTATTTTTGG 57.090 30.769 18.79 18.79 45.89 3.28
2679 5433 7.454225 TGTCCCAAAATAACCTTATTTTTGGG 58.546 34.615 27.78 27.78 45.89 4.12
2683 5437 8.955388 CCCAAAATAACCTTATTTTTGGGAATG 58.045 33.333 28.96 10.96 45.89 2.67
2699 5469 4.634004 TGGGAATGTTGTACTAAATCAGCG 59.366 41.667 0.00 0.00 0.00 5.18
2832 5602 6.157820 TCCATAACTCATACCCTTTGATCACA 59.842 38.462 0.00 0.00 0.00 3.58
2850 5620 4.340617 TCACAATATTTTGACAGGACCCC 58.659 43.478 2.69 0.00 36.64 4.95
2943 5713 5.296780 GGCATTTCAAGTATGTGCTTAGCTA 59.703 40.000 5.60 0.00 36.15 3.32
3073 5843 3.969312 TGTATCATCAGGCATCTCCAAGA 59.031 43.478 0.00 0.00 37.29 3.02
3292 6062 3.071874 TGGATGGTGGTGATTCTGTTC 57.928 47.619 0.00 0.00 0.00 3.18
3309 6079 6.403333 TCTGTTCGTTGTTATATGCTTGTC 57.597 37.500 0.00 0.00 0.00 3.18
3379 6149 5.391416 GCTCTTTTAGAGACCTGAACAATGC 60.391 44.000 7.85 0.00 45.07 3.56
3472 6243 2.632377 CATGTATTGGGCTTGACGAGT 58.368 47.619 0.00 0.00 0.00 4.18
3507 6278 3.487563 CCGAAGGCACTATTGTTTTCC 57.512 47.619 0.00 0.00 46.14 3.13
3508 6279 2.817258 CCGAAGGCACTATTGTTTTCCA 59.183 45.455 0.00 0.00 46.14 3.53
3509 6280 3.365969 CCGAAGGCACTATTGTTTTCCAC 60.366 47.826 0.00 0.00 46.14 4.02
3510 6281 3.365969 CGAAGGCACTATTGTTTTCCACC 60.366 47.826 0.00 0.00 38.49 4.61
3511 6282 3.237268 AGGCACTATTGTTTTCCACCA 57.763 42.857 0.00 0.00 36.02 4.17
3512 6283 3.778265 AGGCACTATTGTTTTCCACCAT 58.222 40.909 0.00 0.00 36.02 3.55
3513 6284 4.159557 AGGCACTATTGTTTTCCACCATT 58.840 39.130 0.00 0.00 36.02 3.16
3514 6285 4.021192 AGGCACTATTGTTTTCCACCATTG 60.021 41.667 0.00 0.00 36.02 2.82
3519 6290 8.247562 GCACTATTGTTTTCCACCATTGTAATA 58.752 33.333 0.00 0.00 0.00 0.98
3525 6296 8.821686 TGTTTTCCACCATTGTAATATCATCT 57.178 30.769 0.00 0.00 0.00 2.90
3526 6297 9.253832 TGTTTTCCACCATTGTAATATCATCTT 57.746 29.630 0.00 0.00 0.00 2.40
3529 6300 7.822161 TCCACCATTGTAATATCATCTTTGG 57.178 36.000 0.00 0.00 0.00 3.28
3530 6301 7.353525 TCCACCATTGTAATATCATCTTTGGT 58.646 34.615 0.00 0.00 35.41 3.67
3531 6302 8.498575 TCCACCATTGTAATATCATCTTTGGTA 58.501 33.333 0.00 0.00 33.38 3.25
3532 6303 9.300681 CCACCATTGTAATATCATCTTTGGTAT 57.699 33.333 0.00 0.00 33.38 2.73
3539 6310 9.387397 TGTAATATCATCTTTGGTATAGTCCCA 57.613 33.333 0.00 0.00 28.76 4.37
3546 6317 8.540388 TCATCTTTGGTATAGTCCCATATAAGC 58.460 37.037 0.00 0.00 0.00 3.09
3573 6344 5.488341 AGTATGGACTGTATGGTGTTTGTC 58.512 41.667 0.00 0.00 33.41 3.18
3585 6356 2.097466 GGTGTTTGTCGCATAATGAGGG 59.903 50.000 0.00 0.00 0.00 4.30
3586 6357 2.097466 GTGTTTGTCGCATAATGAGGGG 59.903 50.000 0.00 0.00 0.00 4.79
3588 6359 0.465460 TTGTCGCATAATGAGGGGCC 60.465 55.000 0.00 0.00 0.00 5.80
3589 6360 1.961277 GTCGCATAATGAGGGGCCG 60.961 63.158 0.00 0.00 0.00 6.13
3591 6362 1.227823 CGCATAATGAGGGGCCGAA 60.228 57.895 0.00 0.00 0.00 4.30
3593 6364 1.172812 GCATAATGAGGGGCCGAACC 61.173 60.000 0.00 0.00 37.93 3.62
3594 6365 0.474184 CATAATGAGGGGCCGAACCT 59.526 55.000 0.00 0.00 42.18 3.50
3664 6435 5.603596 TCACTACCAAACAAATCTACGTGT 58.396 37.500 0.00 0.00 0.00 4.49
3666 6437 7.208777 TCACTACCAAACAAATCTACGTGTAA 58.791 34.615 0.00 0.00 0.00 2.41
3704 6475 9.628500 ATTTTATGTATTTTACTCCCTCTGTCC 57.372 33.333 0.00 0.00 0.00 4.02
3705 6476 5.632034 ATGTATTTTACTCCCTCTGTCCC 57.368 43.478 0.00 0.00 0.00 4.46
3706 6477 4.431378 TGTATTTTACTCCCTCTGTCCCA 58.569 43.478 0.00 0.00 0.00 4.37
3707 6478 4.847512 TGTATTTTACTCCCTCTGTCCCAA 59.152 41.667 0.00 0.00 0.00 4.12
3708 6479 5.311121 TGTATTTTACTCCCTCTGTCCCAAA 59.689 40.000 0.00 0.00 0.00 3.28
3709 6480 4.799715 TTTTACTCCCTCTGTCCCAAAA 57.200 40.909 0.00 0.00 0.00 2.44
3710 6481 5.333566 TTTTACTCCCTCTGTCCCAAAAT 57.666 39.130 0.00 0.00 0.00 1.82
3711 6482 6.457159 TTTTACTCCCTCTGTCCCAAAATA 57.543 37.500 0.00 0.00 0.00 1.40
3712 6483 6.652205 TTTACTCCCTCTGTCCCAAAATAT 57.348 37.500 0.00 0.00 0.00 1.28
3713 6484 7.758820 TTTACTCCCTCTGTCCCAAAATATA 57.241 36.000 0.00 0.00 0.00 0.86
3714 6485 7.758820 TTACTCCCTCTGTCCCAAAATATAA 57.241 36.000 0.00 0.00 0.00 0.98
3715 6486 6.253946 ACTCCCTCTGTCCCAAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
3716 6487 5.970640 ACTCCCTCTGTCCCAAAATATAAGA 59.029 40.000 0.00 0.00 0.00 2.10
3717 6488 6.447084 ACTCCCTCTGTCCCAAAATATAAGAA 59.553 38.462 0.00 0.00 0.00 2.52
3718 6489 6.659824 TCCCTCTGTCCCAAAATATAAGAAC 58.340 40.000 0.00 0.00 0.00 3.01
3719 6490 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
3720 6491 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
3721 6492 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
3722 6493 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
3723 6494 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
3724 6495 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
3754 6525 9.971922 ACTACACTAGTGTAAAAACGTTCTTAT 57.028 29.630 30.31 6.91 44.47 1.73
3769 6540 9.688592 AAACGTTCTTATATTATAGGACGAAGG 57.311 33.333 15.69 11.19 44.28 3.46
3770 6541 7.824672 ACGTTCTTATATTATAGGACGAAGGG 58.175 38.462 15.69 5.28 44.28 3.95
3771 6542 7.667219 ACGTTCTTATATTATAGGACGAAGGGA 59.333 37.037 15.69 0.00 44.28 4.20
3772 6543 8.182881 CGTTCTTATATTATAGGACGAAGGGAG 58.817 40.741 7.03 0.00 44.28 4.30
3773 6544 9.022884 GTTCTTATATTATAGGACGAAGGGAGT 57.977 37.037 0.00 0.00 0.00 3.85
3775 6546 9.678260 TCTTATATTATAGGACGAAGGGAGTAC 57.322 37.037 0.00 0.00 0.00 2.73
3776 6547 9.683870 CTTATATTATAGGACGAAGGGAGTACT 57.316 37.037 0.00 0.00 36.60 2.73
3780 6551 7.573968 TTATAGGACGAAGGGAGTACTAAAC 57.426 40.000 0.00 0.00 38.40 2.01
3781 6552 3.771216 AGGACGAAGGGAGTACTAAACA 58.229 45.455 0.00 0.00 29.47 2.83
3782 6553 3.509184 AGGACGAAGGGAGTACTAAACAC 59.491 47.826 0.00 0.00 29.47 3.32
3783 6554 3.496155 GACGAAGGGAGTACTAAACACG 58.504 50.000 0.00 2.60 0.00 4.49
3784 6555 2.887152 ACGAAGGGAGTACTAAACACGT 59.113 45.455 0.00 3.26 0.00 4.49
3795 6566 7.375017 GGAGTACTAAACACGTTTGACATTTTG 59.625 37.037 5.42 0.00 34.23 2.44
3801 6572 2.035009 CACGTTTGACATTTTGCAACCG 60.035 45.455 0.00 0.00 36.25 4.44
3827 6598 9.638300 GAGTGTCTTATTTATGAACTAATTGCG 57.362 33.333 0.00 0.00 0.00 4.85
3829 6600 7.376072 GTGTCTTATTTATGAACTAATTGCGCC 59.624 37.037 4.18 0.00 0.00 6.53
3830 6601 7.282224 TGTCTTATTTATGAACTAATTGCGCCT 59.718 33.333 4.18 0.00 0.00 5.52
3864 7030 2.106332 CCGCCGCTACTACAAGGG 59.894 66.667 0.00 0.00 0.00 3.95
3874 7040 0.340208 ACTACAAGGGAGCTAGGCCT 59.660 55.000 11.78 11.78 0.00 5.19
3903 7069 2.681064 CCAGGGGCAATGGTGGTG 60.681 66.667 0.00 0.00 32.85 4.17
3910 7076 1.290009 GCAATGGTGGTGCAAGGTC 59.710 57.895 0.00 0.00 41.80 3.85
3996 7162 3.138884 TGCTACAAAAGGCACATCTCA 57.861 42.857 0.00 0.00 33.23 3.27
4014 7180 1.072806 TCACAATGCTGCAAGAGGAGT 59.927 47.619 6.36 0.00 35.34 3.85
4027 7193 0.798776 GAGGAGTGTTGCAACATCGG 59.201 55.000 33.16 0.00 41.59 4.18
4030 7196 1.514678 GAGTGTTGCAACATCGGCCA 61.515 55.000 33.16 7.58 41.59 5.36
4079 7245 3.515286 TCGATGGCGACCGAGGTC 61.515 66.667 12.07 12.07 42.51 3.85
4087 7253 1.360551 CGACCGAGGTCTGCTATGG 59.639 63.158 18.85 0.00 42.54 2.74
4117 7283 2.040012 ACGACTACAGTGAAGGAGGAGA 59.960 50.000 0.00 0.00 0.00 3.71
4119 7285 2.425668 GACTACAGTGAAGGAGGAGAGC 59.574 54.545 0.00 0.00 0.00 4.09
4120 7286 2.225142 ACTACAGTGAAGGAGGAGAGCA 60.225 50.000 0.00 0.00 0.00 4.26
4128 7294 1.649321 AGGAGGAGAGCAATGTGTGA 58.351 50.000 0.00 0.00 0.00 3.58
4188 7354 4.369182 GACGATGTCTGTTACAATAGGGG 58.631 47.826 0.00 0.00 42.70 4.79
4189 7355 3.134081 ACGATGTCTGTTACAATAGGGGG 59.866 47.826 0.00 0.00 42.70 5.40
4192 7358 2.498481 TGTCTGTTACAATAGGGGGTCG 59.502 50.000 0.00 0.00 34.29 4.79
4230 7396 0.179936 GAGCAGGGATGAGGGTTCAG 59.820 60.000 0.00 0.00 36.61 3.02
4251 7417 0.608856 ACATCACCCATTGCTCGCAA 60.609 50.000 6.80 6.80 40.47 4.85
4296 7462 1.930908 GACTGCAGCATCACCCTTGC 61.931 60.000 15.27 0.00 40.45 4.01
4313 7479 1.356624 GCTGTAATGTGGGCATCGC 59.643 57.895 0.00 0.00 33.50 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
196 200 1.221840 CCCTCTTCACCCATCCACG 59.778 63.158 0.00 0.00 0.00 4.94
893 3454 4.625311 CACGGGCCATCTAATTTTTGTTTC 59.375 41.667 4.39 0.00 0.00 2.78
945 3506 6.311935 GGGCTACGATGCGTATAAATGATTAA 59.688 38.462 0.00 0.00 41.53 1.40
949 3510 3.581755 GGGCTACGATGCGTATAAATGA 58.418 45.455 0.00 0.00 41.53 2.57
950 3511 3.991605 GGGCTACGATGCGTATAAATG 57.008 47.619 0.00 0.00 41.53 2.32
964 3525 1.763634 GTGCGATTACTACGGGCTAC 58.236 55.000 0.00 0.00 0.00 3.58
965 3526 0.308684 CGTGCGATTACTACGGGCTA 59.691 55.000 0.00 0.00 34.43 3.93
966 3527 1.065273 CGTGCGATTACTACGGGCT 59.935 57.895 0.00 0.00 34.43 5.19
967 3528 3.609258 CGTGCGATTACTACGGGC 58.391 61.111 0.00 0.00 34.43 6.13
970 3531 3.609258 GCCCGTGCGATTACTACG 58.391 61.111 0.00 0.00 37.55 3.51
980 3541 3.869473 TACCAGTGAACGCCCGTGC 62.869 63.158 0.00 0.00 0.00 5.34
981 3542 1.079405 ATACCAGTGAACGCCCGTG 60.079 57.895 0.00 0.00 0.00 4.94
982 3543 1.217244 GATACCAGTGAACGCCCGT 59.783 57.895 0.00 0.00 0.00 5.28
983 3544 0.527817 GAGATACCAGTGAACGCCCG 60.528 60.000 0.00 0.00 0.00 6.13
984 3545 0.179081 GGAGATACCAGTGAACGCCC 60.179 60.000 0.00 0.00 38.79 6.13
985 3546 0.535335 TGGAGATACCAGTGAACGCC 59.465 55.000 0.00 0.00 44.64 5.68
995 3556 2.032620 ACTGGACGACATGGAGATACC 58.967 52.381 0.00 0.00 39.54 2.73
996 3557 2.223829 CCACTGGACGACATGGAGATAC 60.224 54.545 0.00 0.00 32.69 2.24
997 3558 2.031870 CCACTGGACGACATGGAGATA 58.968 52.381 0.00 0.00 32.69 1.98
998 3559 0.826715 CCACTGGACGACATGGAGAT 59.173 55.000 0.00 0.00 32.69 2.75
1008 3569 2.736721 CAATGACAAGTACCACTGGACG 59.263 50.000 0.71 0.00 0.00 4.79
1012 3573 3.402110 TCAGCAATGACAAGTACCACTG 58.598 45.455 0.00 0.00 0.00 3.66
1016 3577 4.034048 CCGTAATCAGCAATGACAAGTACC 59.966 45.833 0.00 0.00 0.00 3.34
1050 3613 2.832643 TAATCGTGGGGAGGTAGTCA 57.167 50.000 0.00 0.00 0.00 3.41
1052 3615 3.231818 CTGATAATCGTGGGGAGGTAGT 58.768 50.000 0.00 0.00 0.00 2.73
1057 3620 1.875576 GCTGCTGATAATCGTGGGGAG 60.876 57.143 0.00 0.00 0.00 4.30
1058 3621 0.106708 GCTGCTGATAATCGTGGGGA 59.893 55.000 0.00 0.00 0.00 4.81
1059 3622 0.107456 AGCTGCTGATAATCGTGGGG 59.893 55.000 0.00 0.00 0.00 4.96
1060 3623 1.506493 GAGCTGCTGATAATCGTGGG 58.494 55.000 7.01 0.00 0.00 4.61
1078 3655 0.033781 GCTGCTGCAAATTTGTGGGA 59.966 50.000 19.03 11.98 39.41 4.37
1079 3656 0.952010 GGCTGCTGCAAATTTGTGGG 60.952 55.000 19.03 10.51 41.91 4.61
1080 3657 1.286354 CGGCTGCTGCAAATTTGTGG 61.286 55.000 19.03 12.72 41.91 4.17
1081 3658 1.893168 GCGGCTGCTGCAAATTTGTG 61.893 55.000 27.51 13.10 41.91 3.33
1082 3659 1.665599 GCGGCTGCTGCAAATTTGT 60.666 52.632 27.51 0.00 41.91 2.83
1083 3660 2.385091 GGCGGCTGCTGCAAATTTG 61.385 57.895 32.12 14.03 42.25 2.32
1084 3661 2.047939 GGCGGCTGCTGCAAATTT 60.048 55.556 32.12 0.00 42.25 1.82
1085 3662 4.424566 CGGCGGCTGCTGCAAATT 62.425 61.111 32.12 0.00 41.39 1.82
1495 4106 3.923461 CGACAAGTTCAGAGATTCAGGTC 59.077 47.826 0.00 0.00 0.00 3.85
1498 4109 3.923461 GGACGACAAGTTCAGAGATTCAG 59.077 47.826 0.00 0.00 0.00 3.02
1501 4112 3.069586 TGTGGACGACAAGTTCAGAGATT 59.930 43.478 0.00 0.00 39.46 2.40
1502 4113 2.628178 TGTGGACGACAAGTTCAGAGAT 59.372 45.455 0.00 0.00 39.46 2.75
1507 4118 2.875933 GGATTTGTGGACGACAAGTTCA 59.124 45.455 3.17 0.00 45.43 3.18
1509 4120 2.227194 GGGATTTGTGGACGACAAGTT 58.773 47.619 3.17 0.00 45.43 2.66
1510 4121 1.142060 TGGGATTTGTGGACGACAAGT 59.858 47.619 3.17 0.56 45.43 3.16
1512 4123 1.134068 TGTGGGATTTGTGGACGACAA 60.134 47.619 0.00 0.00 43.11 3.18
1514 4125 1.156736 CTGTGGGATTTGTGGACGAC 58.843 55.000 0.00 0.00 0.00 4.34
1538 4150 3.760684 AGGTCGATACTGGTCGTAAAAGT 59.239 43.478 0.00 0.00 42.07 2.66
1844 4460 0.256752 TAGGGTCTCCGGAATCGACA 59.743 55.000 20.32 1.63 39.00 4.35
1872 4488 0.107643 TGTGAACGCTGACAATGGGA 59.892 50.000 0.00 0.00 0.00 4.37
1928 4544 3.706086 ACTATGCAAGCAAAAATAGGGGG 59.294 43.478 0.00 0.00 0.00 5.40
1940 4561 9.438291 CAAATGTAAGTATGTAACTATGCAAGC 57.562 33.333 0.00 0.00 37.50 4.01
1957 4578 9.903682 ACAAAGAAGTTGATCATCAAATGTAAG 57.096 29.630 0.29 0.00 38.22 2.34
1979 4600 6.070881 ACCAGCATGCTCCATTATAAAACAAA 60.071 34.615 19.68 0.00 31.97 2.83
1981 4602 4.955450 ACCAGCATGCTCCATTATAAAACA 59.045 37.500 19.68 0.00 31.97 2.83
1982 4603 5.520376 ACCAGCATGCTCCATTATAAAAC 57.480 39.130 19.68 0.00 31.97 2.43
2005 4626 9.547753 AAATAGTTATTCAGCTCATACATTCGT 57.452 29.630 0.00 0.00 0.00 3.85
2016 4637 7.281999 GGAGCAAAGAGAAATAGTTATTCAGCT 59.718 37.037 0.00 0.00 0.00 4.24
2017 4638 7.413644 GGAGCAAAGAGAAATAGTTATTCAGC 58.586 38.462 0.00 0.00 0.00 4.26
2018 4639 7.278868 ACGGAGCAAAGAGAAATAGTTATTCAG 59.721 37.037 0.00 0.00 0.00 3.02
2020 4641 7.541122 ACGGAGCAAAGAGAAATAGTTATTC 57.459 36.000 0.00 0.00 0.00 1.75
2021 4642 7.923414 AACGGAGCAAAGAGAAATAGTTATT 57.077 32.000 0.00 0.00 0.00 1.40
2022 4643 7.923414 AAACGGAGCAAAGAGAAATAGTTAT 57.077 32.000 0.00 0.00 0.00 1.89
2023 4644 7.227910 ACAAAACGGAGCAAAGAGAAATAGTTA 59.772 33.333 0.00 0.00 0.00 2.24
2024 4645 6.039382 ACAAAACGGAGCAAAGAGAAATAGTT 59.961 34.615 0.00 0.00 0.00 2.24
2026 4647 5.853282 CACAAAACGGAGCAAAGAGAAATAG 59.147 40.000 0.00 0.00 0.00 1.73
2027 4648 5.529430 TCACAAAACGGAGCAAAGAGAAATA 59.471 36.000 0.00 0.00 0.00 1.40
2028 4649 4.338118 TCACAAAACGGAGCAAAGAGAAAT 59.662 37.500 0.00 0.00 0.00 2.17
2030 4651 3.275143 TCACAAAACGGAGCAAAGAGAA 58.725 40.909 0.00 0.00 0.00 2.87
2031 4652 2.912771 TCACAAAACGGAGCAAAGAGA 58.087 42.857 0.00 0.00 0.00 3.10
2034 4655 9.385902 CAATATATATCACAAAACGGAGCAAAG 57.614 33.333 0.00 0.00 0.00 2.77
2035 4656 7.860373 GCAATATATATCACAAAACGGAGCAAA 59.140 33.333 0.00 0.00 0.00 3.68
2036 4657 7.228507 AGCAATATATATCACAAAACGGAGCAA 59.771 33.333 0.00 0.00 0.00 3.91
2038 4659 7.095229 TGAGCAATATATATCACAAAACGGAGC 60.095 37.037 0.00 0.00 0.00 4.70
2039 4660 8.223769 GTGAGCAATATATATCACAAAACGGAG 58.776 37.037 15.56 0.00 41.32 4.63
2040 4661 7.931407 AGTGAGCAATATATATCACAAAACGGA 59.069 33.333 19.69 0.00 43.55 4.69
2064 4685 1.900486 GTACAGCTGACCCACCTAAGT 59.100 52.381 23.35 0.00 0.00 2.24
2066 4687 2.320681 AGTACAGCTGACCCACCTAA 57.679 50.000 23.35 0.00 0.00 2.69
2067 4688 2.176889 GAAGTACAGCTGACCCACCTA 58.823 52.381 23.35 0.00 0.00 3.08
2068 4689 0.977395 GAAGTACAGCTGACCCACCT 59.023 55.000 23.35 2.05 0.00 4.00
2069 4690 0.685097 TGAAGTACAGCTGACCCACC 59.315 55.000 23.35 5.32 0.00 4.61
2070 4691 1.618837 TCTGAAGTACAGCTGACCCAC 59.381 52.381 23.35 12.10 45.38 4.61
2071 4692 2.009681 TCTGAAGTACAGCTGACCCA 57.990 50.000 23.35 13.07 45.38 4.51
2072 4693 3.067833 GTTTCTGAAGTACAGCTGACCC 58.932 50.000 23.35 7.33 45.38 4.46
2073 4694 3.728845 TGTTTCTGAAGTACAGCTGACC 58.271 45.455 23.35 10.08 45.38 4.02
2074 4695 5.931441 AATGTTTCTGAAGTACAGCTGAC 57.069 39.130 23.35 14.11 45.38 3.51
2133 4755 6.969473 CACAACTTCTTTTCCTGAAGAAAGTC 59.031 38.462 10.00 0.00 45.11 3.01
2158 4780 4.646945 TCATCGATGCTAGGAAGGATATCC 59.353 45.833 20.81 14.41 39.96 2.59
2374 5001 9.184523 TGCACTTATTTTTGGTTAGCTACATAT 57.815 29.630 0.00 0.00 0.00 1.78
2484 5124 5.703130 GCTGGAAGTAGACAACTCAAAAGAT 59.297 40.000 0.00 0.00 37.50 2.40
2488 5128 4.689612 AGCTGGAAGTAGACAACTCAAA 57.310 40.909 0.00 0.00 37.50 2.69
2552 5203 6.155666 ACTGCAAGGTAAAAACTGCCTAGTT 61.156 40.000 0.00 0.00 43.97 2.24
2553 5204 3.821033 CTGCAAGGTAAAAACTGCCTAGT 59.179 43.478 0.00 0.00 39.67 2.57
2554 5205 3.821033 ACTGCAAGGTAAAAACTGCCTAG 59.179 43.478 0.00 0.00 39.67 3.02
2601 5258 8.234136 ACTCCTATGTAATACAAGACATTCGA 57.766 34.615 0.00 0.00 37.47 3.71
2602 5259 9.613957 CTACTCCTATGTAATACAAGACATTCG 57.386 37.037 0.00 0.00 37.47 3.34
2671 5425 9.927668 CTGATTTAGTACAACATTCCCAAAAAT 57.072 29.630 0.00 0.00 0.00 1.82
2672 5426 7.870445 GCTGATTTAGTACAACATTCCCAAAAA 59.130 33.333 0.00 0.00 0.00 1.94
2673 5427 7.375053 GCTGATTTAGTACAACATTCCCAAAA 58.625 34.615 0.00 0.00 0.00 2.44
2675 5429 5.123186 CGCTGATTTAGTACAACATTCCCAA 59.877 40.000 0.00 0.00 0.00 4.12
2676 5430 4.634004 CGCTGATTTAGTACAACATTCCCA 59.366 41.667 0.00 0.00 0.00 4.37
2677 5431 4.873827 TCGCTGATTTAGTACAACATTCCC 59.126 41.667 0.00 0.00 0.00 3.97
2678 5432 5.350365 TGTCGCTGATTTAGTACAACATTCC 59.650 40.000 0.00 0.00 0.00 3.01
2679 5433 6.090898 AGTGTCGCTGATTTAGTACAACATTC 59.909 38.462 0.00 0.00 0.00 2.67
2681 5435 5.479306 AGTGTCGCTGATTTAGTACAACAT 58.521 37.500 0.00 0.00 0.00 2.71
2683 5437 5.840940 AAGTGTCGCTGATTTAGTACAAC 57.159 39.130 0.00 0.00 0.00 3.32
2699 5469 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
2832 5602 3.732048 ACGGGGTCCTGTCAAAATATT 57.268 42.857 0.00 0.00 0.00 1.28
2850 5620 4.868171 ACACAATGTATACTGCCAGTAACG 59.132 41.667 8.93 0.00 33.89 3.18
2992 5762 1.073177 GCATGTTGCAGCACCATTTC 58.927 50.000 5.00 0.00 44.26 2.17
3073 5843 2.546899 TGCAGGTATAGTGTTCCACCT 58.453 47.619 0.00 0.00 42.17 4.00
3269 6039 3.157087 ACAGAATCACCACCATCCAAAC 58.843 45.455 0.00 0.00 0.00 2.93
3292 6062 5.163992 ACTGTTCGACAAGCATATAACAACG 60.164 40.000 0.00 0.00 0.00 4.10
3309 6079 4.000988 ACCCATAAGCAGTTAACTGTTCG 58.999 43.478 30.90 18.88 45.45 3.95
3361 6131 2.354704 CGGGCATTGTTCAGGTCTCTAA 60.355 50.000 0.00 0.00 0.00 2.10
3379 6149 2.551912 GGTATCCGCAATTGCCGGG 61.552 63.158 28.70 23.14 37.91 5.73
3472 6243 1.879380 CTTCGGCAAGTTGGATGTCAA 59.121 47.619 4.75 0.00 0.00 3.18
3500 6271 8.821686 AGATGATATTACAATGGTGGAAAACA 57.178 30.769 0.00 0.00 28.98 2.83
3503 6274 8.694540 CCAAAGATGATATTACAATGGTGGAAA 58.305 33.333 0.00 0.00 28.98 3.13
3505 6276 7.353525 ACCAAAGATGATATTACAATGGTGGA 58.646 34.615 0.00 0.00 0.00 4.02
3506 6277 7.587037 ACCAAAGATGATATTACAATGGTGG 57.413 36.000 0.00 0.00 0.00 4.61
3513 6284 9.387397 TGGGACTATACCAAAGATGATATTACA 57.613 33.333 0.00 0.00 34.44 2.41
3520 6291 8.540388 GCTTATATGGGACTATACCAAAGATGA 58.460 37.037 0.00 0.00 42.17 2.92
3521 6292 8.321353 TGCTTATATGGGACTATACCAAAGATG 58.679 37.037 0.00 0.00 42.17 2.90
3522 6293 8.449423 TGCTTATATGGGACTATACCAAAGAT 57.551 34.615 0.00 0.00 42.17 2.40
3523 6294 7.038302 CCTGCTTATATGGGACTATACCAAAGA 60.038 40.741 0.00 0.00 42.17 2.52
3524 6295 7.038302 TCCTGCTTATATGGGACTATACCAAAG 60.038 40.741 0.00 0.00 42.17 2.77
3525 6296 6.790461 TCCTGCTTATATGGGACTATACCAAA 59.210 38.462 0.00 0.00 42.17 3.28
3526 6297 6.327781 TCCTGCTTATATGGGACTATACCAA 58.672 40.000 0.00 0.00 42.17 3.67
3527 6298 5.910931 TCCTGCTTATATGGGACTATACCA 58.089 41.667 0.00 0.00 43.22 3.25
3528 6299 5.958987 ACTCCTGCTTATATGGGACTATACC 59.041 44.000 0.00 0.00 0.00 2.73
3529 6300 8.634444 CATACTCCTGCTTATATGGGACTATAC 58.366 40.741 0.00 0.00 0.00 1.47
3530 6301 7.785028 CCATACTCCTGCTTATATGGGACTATA 59.215 40.741 0.00 0.00 40.23 1.31
3531 6302 6.613271 CCATACTCCTGCTTATATGGGACTAT 59.387 42.308 0.00 0.00 40.23 2.12
3532 6303 5.958380 CCATACTCCTGCTTATATGGGACTA 59.042 44.000 0.00 0.00 40.23 2.59
3533 6304 4.780021 CCATACTCCTGCTTATATGGGACT 59.220 45.833 0.00 0.00 40.23 3.85
3534 6305 4.777896 TCCATACTCCTGCTTATATGGGAC 59.222 45.833 8.81 0.00 42.92 4.46
3535 6306 4.777896 GTCCATACTCCTGCTTATATGGGA 59.222 45.833 8.81 0.00 42.92 4.37
3536 6307 4.780021 AGTCCATACTCCTGCTTATATGGG 59.220 45.833 8.81 0.00 42.92 4.00
3537 6308 5.247110 ACAGTCCATACTCCTGCTTATATGG 59.753 44.000 3.21 3.21 43.70 2.74
3538 6309 6.352016 ACAGTCCATACTCCTGCTTATATG 57.648 41.667 0.00 0.00 31.97 1.78
3539 6310 7.124901 CCATACAGTCCATACTCCTGCTTATAT 59.875 40.741 0.00 0.00 31.97 0.86
3540 6311 6.437477 CCATACAGTCCATACTCCTGCTTATA 59.563 42.308 0.00 0.00 31.97 0.98
3541 6312 5.247110 CCATACAGTCCATACTCCTGCTTAT 59.753 44.000 0.00 0.00 31.97 1.73
3542 6313 4.588951 CCATACAGTCCATACTCCTGCTTA 59.411 45.833 0.00 0.00 31.97 3.09
3543 6314 3.389329 CCATACAGTCCATACTCCTGCTT 59.611 47.826 0.00 0.00 31.97 3.91
3544 6315 2.968574 CCATACAGTCCATACTCCTGCT 59.031 50.000 0.00 0.00 31.97 4.24
3545 6316 2.700897 ACCATACAGTCCATACTCCTGC 59.299 50.000 0.00 0.00 31.97 4.85
3546 6317 3.706594 ACACCATACAGTCCATACTCCTG 59.293 47.826 0.00 0.00 31.97 3.86
3573 6344 1.227823 TTCGGCCCCTCATTATGCG 60.228 57.895 0.00 0.00 0.00 4.73
3635 6406 6.808008 AGATTTGTTTGGTAGTGAGACATG 57.192 37.500 0.00 0.00 0.00 3.21
3694 6465 6.631766 CGTTCTTATATTTTGGGACAGAGGGA 60.632 42.308 0.00 0.00 42.39 4.20
3695 6466 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
3696 6467 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
3697 6468 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
3698 6469 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
3728 6499 9.971922 ATAAGAACGTTTTTACACTAGTGTAGT 57.028 29.630 29.34 22.10 45.57 2.73
3743 6514 9.688592 CCTTCGTCCTATAATATAAGAACGTTT 57.311 33.333 0.46 0.00 0.00 3.60
3744 6515 8.302438 CCCTTCGTCCTATAATATAAGAACGTT 58.698 37.037 0.00 0.00 0.00 3.99
3745 6516 7.667219 TCCCTTCGTCCTATAATATAAGAACGT 59.333 37.037 7.91 0.00 0.00 3.99
3746 6517 8.048534 TCCCTTCGTCCTATAATATAAGAACG 57.951 38.462 0.00 0.00 0.00 3.95
3747 6518 9.022884 ACTCCCTTCGTCCTATAATATAAGAAC 57.977 37.037 0.00 0.00 0.00 3.01
3749 6520 9.678260 GTACTCCCTTCGTCCTATAATATAAGA 57.322 37.037 0.00 0.00 0.00 2.10
3750 6521 9.683870 AGTACTCCCTTCGTCCTATAATATAAG 57.316 37.037 0.00 0.00 0.00 1.73
3754 6525 9.289782 GTTTAGTACTCCCTTCGTCCTATAATA 57.710 37.037 0.00 0.00 0.00 0.98
3755 6526 7.781693 TGTTTAGTACTCCCTTCGTCCTATAAT 59.218 37.037 0.00 0.00 0.00 1.28
3756 6527 7.067494 GTGTTTAGTACTCCCTTCGTCCTATAA 59.933 40.741 0.00 0.00 0.00 0.98
3757 6528 6.543831 GTGTTTAGTACTCCCTTCGTCCTATA 59.456 42.308 0.00 0.00 0.00 1.31
3758 6529 5.359292 GTGTTTAGTACTCCCTTCGTCCTAT 59.641 44.000 0.00 0.00 0.00 2.57
3759 6530 4.702131 GTGTTTAGTACTCCCTTCGTCCTA 59.298 45.833 0.00 0.00 0.00 2.94
3760 6531 3.509184 GTGTTTAGTACTCCCTTCGTCCT 59.491 47.826 0.00 0.00 0.00 3.85
3761 6532 3.671702 CGTGTTTAGTACTCCCTTCGTCC 60.672 52.174 0.00 0.00 0.00 4.79
3762 6533 3.057946 ACGTGTTTAGTACTCCCTTCGTC 60.058 47.826 0.00 0.00 0.00 4.20
3763 6534 2.887152 ACGTGTTTAGTACTCCCTTCGT 59.113 45.455 0.00 4.12 0.00 3.85
3764 6535 3.565905 ACGTGTTTAGTACTCCCTTCG 57.434 47.619 0.00 3.46 0.00 3.79
3765 6536 5.176406 GTCAAACGTGTTTAGTACTCCCTTC 59.824 44.000 0.00 0.00 0.00 3.46
3766 6537 5.052481 GTCAAACGTGTTTAGTACTCCCTT 58.948 41.667 0.00 0.00 0.00 3.95
3767 6538 4.099881 TGTCAAACGTGTTTAGTACTCCCT 59.900 41.667 0.00 0.00 0.00 4.20
3768 6539 4.370917 TGTCAAACGTGTTTAGTACTCCC 58.629 43.478 0.00 0.00 0.00 4.30
3769 6540 6.535274 AATGTCAAACGTGTTTAGTACTCC 57.465 37.500 0.00 0.00 0.00 3.85
3770 6541 7.097168 GCAAAATGTCAAACGTGTTTAGTACTC 60.097 37.037 0.00 0.00 0.00 2.59
3771 6542 6.689669 GCAAAATGTCAAACGTGTTTAGTACT 59.310 34.615 0.00 0.00 0.00 2.73
3772 6543 6.469595 TGCAAAATGTCAAACGTGTTTAGTAC 59.530 34.615 0.00 0.00 0.00 2.73
3773 6544 6.552629 TGCAAAATGTCAAACGTGTTTAGTA 58.447 32.000 0.00 0.00 0.00 1.82
3774 6545 5.403246 TGCAAAATGTCAAACGTGTTTAGT 58.597 33.333 0.00 0.00 0.00 2.24
3775 6546 5.940603 TGCAAAATGTCAAACGTGTTTAG 57.059 34.783 0.00 0.00 0.00 1.85
3776 6547 5.062308 GGTTGCAAAATGTCAAACGTGTTTA 59.938 36.000 0.00 0.00 0.00 2.01
3777 6548 4.143009 GGTTGCAAAATGTCAAACGTGTTT 60.143 37.500 0.00 0.00 0.00 2.83
3778 6549 3.369451 GGTTGCAAAATGTCAAACGTGTT 59.631 39.130 0.00 0.00 0.00 3.32
3779 6550 2.926838 GGTTGCAAAATGTCAAACGTGT 59.073 40.909 0.00 0.00 0.00 4.49
3780 6551 2.035009 CGGTTGCAAAATGTCAAACGTG 60.035 45.455 0.00 0.00 45.25 4.49
3781 6552 2.189342 CGGTTGCAAAATGTCAAACGT 58.811 42.857 0.00 0.00 45.25 3.99
3782 6553 2.901454 CGGTTGCAAAATGTCAAACG 57.099 45.000 0.00 9.33 45.08 3.60
3783 6554 3.242712 CACTCGGTTGCAAAATGTCAAAC 59.757 43.478 0.00 0.00 0.00 2.93
3784 6555 3.119316 ACACTCGGTTGCAAAATGTCAAA 60.119 39.130 0.00 0.00 0.00 2.69
3795 6566 6.092259 AGTTCATAAATAAGACACTCGGTTGC 59.908 38.462 0.00 0.00 0.00 4.17
3801 6572 9.638300 CGCAATTAGTTCATAAATAAGACACTC 57.362 33.333 0.00 0.00 0.00 3.51
3864 7030 1.551452 ATGGTATCGAGGCCTAGCTC 58.449 55.000 4.42 0.00 0.00 4.09
3874 7040 1.192146 GCCCCTGGCTATGGTATCGA 61.192 60.000 0.00 0.00 46.69 3.59
3901 7067 2.639286 CTGTTGCCGACCTTGCAC 59.361 61.111 0.00 0.00 38.72 4.57
3903 7069 3.365265 CCCTGTTGCCGACCTTGC 61.365 66.667 0.00 0.00 0.00 4.01
3981 7147 2.991190 GCATTGTGAGATGTGCCTTTTG 59.009 45.455 0.00 0.00 0.00 2.44
3985 7151 1.460504 CAGCATTGTGAGATGTGCCT 58.539 50.000 0.00 0.00 38.31 4.75
3993 7159 1.738350 CTCCTCTTGCAGCATTGTGAG 59.262 52.381 0.00 2.24 0.00 3.51
3996 7162 1.202855 ACACTCCTCTTGCAGCATTGT 60.203 47.619 0.00 0.00 0.00 2.71
4014 7180 1.825622 TGTGGCCGATGTTGCAACA 60.826 52.632 32.78 32.78 40.29 3.33
4027 7193 1.873591 CTCCTTACAACTGTGTGTGGC 59.126 52.381 6.07 0.00 38.82 5.01
4030 7196 3.938963 CACAACTCCTTACAACTGTGTGT 59.061 43.478 0.00 2.24 38.82 3.72
4075 7241 1.055040 GGCATCTCCATAGCAGACCT 58.945 55.000 0.00 0.00 34.01 3.85
4079 7245 1.202568 TCGTTGGCATCTCCATAGCAG 60.203 52.381 0.00 0.00 46.04 4.24
4087 7253 2.094700 TCACTGTAGTCGTTGGCATCTC 60.095 50.000 0.00 0.00 0.00 2.75
4097 7263 2.680841 CTCTCCTCCTTCACTGTAGTCG 59.319 54.545 0.00 0.00 0.00 4.18
4103 7269 2.027377 ACATTGCTCTCCTCCTTCACTG 60.027 50.000 0.00 0.00 0.00 3.66
4117 7283 2.097036 CCCATCACATCACACATTGCT 58.903 47.619 0.00 0.00 0.00 3.91
4119 7285 1.819903 TGCCCATCACATCACACATTG 59.180 47.619 0.00 0.00 0.00 2.82
4120 7286 2.097036 CTGCCCATCACATCACACATT 58.903 47.619 0.00 0.00 0.00 2.71
4128 7294 0.754217 GCATCCACTGCCCATCACAT 60.754 55.000 0.00 0.00 45.66 3.21
4168 7334 3.134081 ACCCCCTATTGTAACAGACATCG 59.866 47.826 0.00 0.00 38.07 3.84
4188 7354 4.329545 TTGCAGCACCCCTCGACC 62.330 66.667 0.00 0.00 0.00 4.79
4189 7355 2.743928 CTTGCAGCACCCCTCGAC 60.744 66.667 0.00 0.00 0.00 4.20
4230 7396 0.099436 GCGAGCAATGGGTGATGTTC 59.901 55.000 0.00 0.00 0.00 3.18
4242 7408 0.673333 ATCGGTGATGTTGCGAGCAA 60.673 50.000 6.39 6.39 0.00 3.91
4263 7429 0.036732 GCAGTCACATGACCTCCCAA 59.963 55.000 8.41 0.00 45.85 4.12
4265 7431 0.392193 CTGCAGTCACATGACCTCCC 60.392 60.000 5.25 0.00 45.85 4.30
4296 7462 2.024918 GGCGATGCCCACATTACAG 58.975 57.895 0.00 0.00 44.06 2.74
4323 7489 0.392060 ATGCTGCAACTCGATGAGCA 60.392 50.000 6.36 12.39 43.46 4.26


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

AutoCloner maintained by Alex Coulton.