Multiple sequence alignment - TraesCS1D01G411400

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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 TraesCS1D01G411400 chr1D 100.000 6826 0 0 919 7744 472904316 472911141 0.000000e+00 12606.0
1 TraesCS1D01G411400 chr1D 93.047 791 46 4 5394 6175 472914794 472915584 0.000000e+00 1147.0
2 TraesCS1D01G411400 chr1D 100.000 594 0 0 1 594 472903398 472903991 0.000000e+00 1098.0
3 TraesCS1D01G411400 chr1D 84.989 926 97 20 3802 4716 472913240 472914134 0.000000e+00 902.0
4 TraesCS1D01G411400 chr1D 92.193 602 39 6 4796 5396 472914134 472914728 0.000000e+00 845.0
5 TraesCS1D01G411400 chr1D 86.747 581 64 5 3022 3596 435293767 435293194 1.100000e-177 634.0
6 TraesCS1D01G411400 chr1D 82.768 708 69 24 4950 5632 472915922 472916601 4.030000e-162 582.0
7 TraesCS1D01G411400 chr1D 83.305 587 62 19 4150 4733 435284413 435283860 6.930000e-140 508.0
8 TraesCS1D01G411400 chr1D 85.833 240 18 10 228 452 103741452 103741214 2.790000e-59 241.0
9 TraesCS1D01G411400 chr1D 85.833 240 18 9 228 454 384847863 384848099 2.790000e-59 241.0
10 TraesCS1D01G411400 chr1D 84.390 205 29 3 7542 7744 212706329 212706126 1.700000e-46 198.0
11 TraesCS1D01G411400 chr1D 98.571 70 1 0 1966 2035 472905333 472905402 2.930000e-24 124.0
12 TraesCS1D01G411400 chr1D 98.571 70 1 0 1936 2005 472905363 472905432 2.930000e-24 124.0
13 TraesCS1D01G411400 chr1D 90.909 55 2 3 4729 4783 74276253 74276304 3.880000e-08 71.3
14 TraesCS1D01G411400 chr1A 96.199 5814 159 24 1966 7744 566635455 566641241 0.000000e+00 9455.0
15 TraesCS1D01G411400 chr1A 92.026 1091 53 18 919 2005 566634464 566635524 0.000000e+00 1502.0
16 TraesCS1D01G411400 chr1A 92.803 792 47 5 5394 6175 566647209 566648000 0.000000e+00 1138.0
17 TraesCS1D01G411400 chr1A 90.973 565 39 8 4837 5396 566646564 566647121 0.000000e+00 750.0
18 TraesCS1D01G411400 chr1A 82.203 590 62 26 4150 4733 532795919 532795367 1.180000e-127 468.0
19 TraesCS1D01G411400 chr1A 95.633 229 10 0 1 229 548224404 548224632 1.230000e-97 368.0
20 TraesCS1D01G411400 chr1A 89.017 173 17 2 283 454 566633658 566633829 6.090000e-51 213.0
21 TraesCS1D01G411400 chr1A 92.593 135 9 1 460 594 566634309 566634442 7.930000e-45 193.0
22 TraesCS1D01G411400 chr1A 81.068 206 24 8 1051 1245 532810346 532810145 4.840000e-32 150.0
23 TraesCS1D01G411400 chr1A 94.118 51 0 3 4733 4783 469589990 469589943 3.000000e-09 75.0
24 TraesCS1D01G411400 chr1B 95.692 2530 75 13 5221 7744 657408944 657411445 0.000000e+00 4037.0
25 TraesCS1D01G411400 chr1B 97.862 2292 43 5 2424 4711 657405967 657408256 0.000000e+00 3956.0
26 TraesCS1D01G411400 chr1B 85.220 1157 128 20 4770 5909 588514722 588513592 0.000000e+00 1149.0
27 TraesCS1D01G411400 chr1B 92.269 789 48 7 5394 6170 657415193 657415980 0.000000e+00 1107.0
28 TraesCS1D01G411400 chr1B 98.227 564 10 0 4659 5222 657408257 657408820 0.000000e+00 987.0
29 TraesCS1D01G411400 chr1B 95.866 508 20 1 1498 2005 657404987 657405493 0.000000e+00 821.0
30 TraesCS1D01G411400 chr1B 90.033 602 46 9 4796 5396 657414522 657415110 0.000000e+00 767.0
31 TraesCS1D01G411400 chr1B 93.164 512 26 6 997 1500 657404439 657404949 0.000000e+00 743.0
32 TraesCS1D01G411400 chr1B 95.699 465 14 4 1966 2426 657405424 657405886 0.000000e+00 743.0
33 TraesCS1D01G411400 chr1B 89.027 565 56 2 3022 3583 588516297 588515736 0.000000e+00 695.0
34 TraesCS1D01G411400 chr1B 81.290 465 53 21 4150 4610 588515215 588514781 5.750000e-91 346.0
35 TraesCS1D01G411400 chr1B 91.463 82 5 2 919 1000 657404331 657404410 2.280000e-20 111.0
36 TraesCS1D01G411400 chr4A 83.466 1760 133 70 2999 4733 605665774 605664148 0.000000e+00 1493.0
37 TraesCS1D01G411400 chr4A 84.186 215 18 11 229 432 516937774 516937983 2.200000e-45 195.0
38 TraesCS1D01G411400 chr4A 82.857 140 16 8 1070 1201 605667945 605667806 1.370000e-22 119.0
39 TraesCS1D01G411400 chr5D 83.526 1123 121 28 4770 5854 557180743 557179647 0.000000e+00 990.0
40 TraesCS1D01G411400 chr5D 84.909 550 37 21 3550 4093 557181715 557181206 1.490000e-141 514.0
41 TraesCS1D01G411400 chr5D 84.127 315 31 9 2428 2740 557182531 557182234 3.540000e-73 287.0
42 TraesCS1D01G411400 chr5D 87.500 232 11 5 230 454 364664977 364665197 1.290000e-62 252.0
43 TraesCS1D01G411400 chr5D 81.333 300 48 8 7448 7741 481477417 481477714 3.610000e-58 237.0
44 TraesCS1D01G411400 chr5D 84.434 212 27 5 7538 7744 124345970 124346180 3.660000e-48 204.0
45 TraesCS1D01G411400 chr5D 84.444 135 15 6 1073 1201 557184065 557183931 2.270000e-25 128.0
46 TraesCS1D01G411400 chr5D 95.918 49 1 1 4735 4783 410508136 410508183 2.320000e-10 78.7
47 TraesCS1D01G411400 chr5B 82.443 1179 143 34 4767 5893 709424375 709425541 0.000000e+00 972.0
48 TraesCS1D01G411400 chr5B 89.238 446 39 9 4144 4584 709423886 709424327 4.080000e-152 549.0
49 TraesCS1D01G411400 chr5B 83.669 496 32 21 3550 4036 709423383 709423838 9.290000e-114 422.0
50 TraesCS1D01G411400 chr5B 90.357 280 27 0 2999 3278 709423084 709423363 1.230000e-97 368.0
51 TraesCS1D01G411400 chr7B 88.504 809 69 13 2995 3794 253699102 253698309 0.000000e+00 957.0
52 TraesCS1D01G411400 chr7B 88.774 775 71 9 5218 5985 253696277 253695512 0.000000e+00 935.0
53 TraesCS1D01G411400 chr7B 87.789 778 82 9 5218 5985 718359772 718358998 0.000000e+00 898.0
54 TraesCS1D01G411400 chr7B 87.669 592 55 11 2428 3004 253699986 253699398 0.000000e+00 673.0
55 TraesCS1D01G411400 chr7B 85.400 637 86 6 2428 3060 744662757 744662124 0.000000e+00 654.0
56 TraesCS1D01G411400 chr7B 85.333 150 19 3 997 1143 253707670 253707521 1.350000e-32 152.0
57 TraesCS1D01G411400 chr7B 81.000 100 11 4 5123 5221 718359943 718359851 1.080000e-08 73.1
58 TraesCS1D01G411400 chr7A 88.235 816 70 13 2995 3805 316021383 316020589 0.000000e+00 952.0
59 TraesCS1D01G411400 chr7A 88.114 774 77 8 5219 5985 316017587 316016822 0.000000e+00 905.0
60 TraesCS1D01G411400 chr7A 85.359 683 79 9 3326 3998 717086781 717087452 0.000000e+00 688.0
61 TraesCS1D01G411400 chr7A 87.458 590 60 7 2428 3004 316022267 316021679 0.000000e+00 667.0
62 TraesCS1D01G411400 chr7A 86.610 590 62 11 2425 3004 717085597 717086179 3.050000e-178 636.0
63 TraesCS1D01G411400 chr7A 84.646 495 60 14 4255 4739 316020495 316020007 5.440000e-131 479.0
64 TraesCS1D01G411400 chr7A 87.814 279 25 8 4770 5046 717087820 717088091 1.250000e-82 318.0
65 TraesCS1D01G411400 chr7A 88.827 179 19 1 2003 2181 735710683 735710860 1.310000e-52 219.0
66 TraesCS1D01G411400 chr7A 90.667 150 12 1 1996 2145 316024093 316023946 1.700000e-46 198.0
67 TraesCS1D01G411400 chr7A 87.333 150 17 1 1996 2145 717083251 717083398 3.720000e-38 171.0
68 TraesCS1D01G411400 chr7A 85.065 154 19 3 997 1147 316031219 316031067 3.740000e-33 154.0
69 TraesCS1D01G411400 chr7A 97.500 40 1 0 1966 2005 717083251 717083290 1.390000e-07 69.4
70 TraesCS1D01G411400 chr7D 88.127 817 72 14 2995 3802 279740947 279741747 0.000000e+00 948.0
71 TraesCS1D01G411400 chr7D 88.250 783 75 10 5212 5985 279743826 279744600 0.000000e+00 920.0
72 TraesCS1D01G411400 chr7D 85.505 683 72 12 3326 3998 621644858 621645523 0.000000e+00 688.0
73 TraesCS1D01G411400 chr7D 87.858 593 55 8 2425 3004 279740063 279740651 0.000000e+00 680.0
74 TraesCS1D01G411400 chr7D 86.455 598 68 7 2413 3004 621643669 621644259 1.820000e-180 643.0
75 TraesCS1D01G411400 chr7D 85.000 640 86 8 2428 3060 633055919 633055283 6.550000e-180 641.0
76 TraesCS1D01G411400 chr7D 84.444 495 61 14 4255 4739 279741844 279742332 2.530000e-129 473.0
77 TraesCS1D01G411400 chr7D 92.557 309 16 4 2995 3296 621644558 621644866 3.320000e-118 436.0
78 TraesCS1D01G411400 chr7D 96.053 228 9 0 1 228 63275952 63276179 9.490000e-99 372.0
79 TraesCS1D01G411400 chr7D 84.507 213 25 7 7538 7744 192030594 192030384 3.660000e-48 204.0
80 TraesCS1D01G411400 chr7D 88.667 150 14 3 1996 2145 279738697 279738843 6.170000e-41 180.0
81 TraesCS1D01G411400 chr7D 86.667 150 17 3 997 1143 279731367 279731516 6.220000e-36 163.0
82 TraesCS1D01G411400 chr7D 95.349 43 2 0 5178 5220 621646323 621646365 1.390000e-07 69.4
83 TraesCS1D01G411400 chr2D 96.610 236 8 0 1 236 534762898 534762663 7.280000e-105 392.0
84 TraesCS1D01G411400 chr2D 96.070 229 9 0 1 229 101695964 101695736 2.640000e-99 374.0
85 TraesCS1D01G411400 chr2D 96.491 228 5 1 1 228 533321280 533321056 2.640000e-99 374.0
86 TraesCS1D01G411400 chr2D 85.377 212 25 5 7538 7744 6375091 6375301 1.690000e-51 215.0
87 TraesCS1D01G411400 chr2D 85.377 212 25 5 7538 7744 6397529 6397739 1.690000e-51 215.0
88 TraesCS1D01G411400 chr2D 92.308 52 3 1 4734 4784 30747338 30747287 1.080000e-08 73.1
89 TraesCS1D01G411400 chr4D 96.460 226 8 0 4 229 482523963 482523738 2.640000e-99 374.0
90 TraesCS1D01G411400 chr4D 96.053 228 8 1 1 228 490861171 490861397 3.410000e-98 370.0
91 TraesCS1D01G411400 chr4D 84.906 212 26 5 7538 7744 112054567 112054777 7.870000e-50 209.0
92 TraesCS1D01G411400 chr4D 84.348 230 15 10 232 454 151981461 151981246 1.020000e-48 206.0
93 TraesCS1D01G411400 chr6D 96.053 228 9 0 1 228 429303589 429303816 9.490000e-99 372.0
94 TraesCS1D01G411400 chr6D 79.498 239 31 12 228 454 56208239 56208471 3.740000e-33 154.0
95 TraesCS1D01G411400 chr3D 95.614 228 10 0 1 228 483197358 483197131 4.420000e-97 366.0
96 TraesCS1D01G411400 chr3D 92.593 54 0 4 4730 4783 101551363 101551314 3.000000e-09 75.0
97 TraesCS1D01G411400 chr3A 84.716 229 22 5 231 452 683683518 683683296 4.710000e-52 217.0
98 TraesCS1D01G411400 chr3A 79.747 237 32 12 229 454 431863474 431863705 2.890000e-34 158.0
99 TraesCS1D01G411400 chr3B 82.427 239 27 12 228 454 451069713 451069478 2.200000e-45 195.0
100 TraesCS1D01G411400 chr3B 94.000 50 0 3 4734 4783 242162967 242163013 1.080000e-08 73.1
101 TraesCS1D01G411400 chr2A 79.747 237 31 11 229 454 25350808 25351038 1.040000e-33 156.0
102 TraesCS1D01G411400 chrUn 87.023 131 15 1 1996 2124 31227518 31227648 6.260000e-31 147.0
103 TraesCS1D01G411400 chr6B 94.231 52 2 1 4733 4783 712185952 712186003 2.320000e-10 78.7
104 TraesCS1D01G411400 chr5A 87.234 47 5 1 201 247 401495551 401495506 1.400000e-02 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 TraesCS1D01G411400 chr1D 472903398 472911141 7743 False 6852.000000 12606 100.000000 1 7744 2 chr1D.!!$F3 7743
1 TraesCS1D01G411400 chr1D 472913240 472916601 3361 False 869.000000 1147 88.249250 3802 6175 4 chr1D.!!$F5 2373
2 TraesCS1D01G411400 chr1D 435293194 435293767 573 True 634.000000 634 86.747000 3022 3596 1 chr1D.!!$R4 574
3 TraesCS1D01G411400 chr1D 435283860 435284413 553 True 508.000000 508 83.305000 4150 4733 1 chr1D.!!$R3 583
4 TraesCS1D01G411400 chr1A 566633658 566641241 7583 False 2840.750000 9455 92.458750 283 7744 4 chr1A.!!$F2 7461
5 TraesCS1D01G411400 chr1A 566646564 566648000 1436 False 944.000000 1138 91.888000 4837 6175 2 chr1A.!!$F3 1338
6 TraesCS1D01G411400 chr1A 532795367 532795919 552 True 468.000000 468 82.203000 4150 4733 1 chr1A.!!$R2 583
7 TraesCS1D01G411400 chr1B 657404331 657415980 11649 False 1474.666667 4037 94.475000 919 7744 9 chr1B.!!$F1 6825
8 TraesCS1D01G411400 chr1B 588513592 588516297 2705 True 730.000000 1149 85.179000 3022 5909 3 chr1B.!!$R1 2887
9 TraesCS1D01G411400 chr4A 605664148 605667945 3797 True 806.000000 1493 83.161500 1070 4733 2 chr4A.!!$R1 3663
10 TraesCS1D01G411400 chr5D 557179647 557184065 4418 True 479.750000 990 84.251500 1073 5854 4 chr5D.!!$R1 4781
11 TraesCS1D01G411400 chr5B 709423084 709425541 2457 False 577.750000 972 86.426750 2999 5893 4 chr5B.!!$F1 2894
12 TraesCS1D01G411400 chr7B 253695512 253699986 4474 True 855.000000 957 88.315667 2428 5985 3 chr7B.!!$R3 3557
13 TraesCS1D01G411400 chr7B 744662124 744662757 633 True 654.000000 654 85.400000 2428 3060 1 chr7B.!!$R2 632
14 TraesCS1D01G411400 chr7B 718358998 718359943 945 True 485.550000 898 84.394500 5123 5985 2 chr7B.!!$R4 862
15 TraesCS1D01G411400 chr7A 316016822 316024093 7271 True 640.200000 952 87.824000 1996 5985 5 chr7A.!!$R2 3989
16 TraesCS1D01G411400 chr7A 717083251 717088091 4840 False 376.480000 688 88.923200 1966 5046 5 chr7A.!!$F2 3080
17 TraesCS1D01G411400 chr7D 633055283 633055919 636 True 641.000000 641 85.000000 2428 3060 1 chr7D.!!$R2 632
18 TraesCS1D01G411400 chr7D 279738697 279744600 5903 False 640.200000 948 87.469200 1996 5985 5 chr7D.!!$F3 3989
19 TraesCS1D01G411400 chr7D 621643669 621646365 2696 False 459.100000 688 89.966500 2413 5220 4 chr7D.!!$F4 2807

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
148 149 0.039798 TCGGAAAAGTCTCACGACCG 60.040 55.000 0.00 0.00 41.16 4.79 F
307 308 0.180406 AAAGATAATCGGGCCGTGCT 59.820 50.000 27.32 13.76 0.00 4.40 F
989 1465 0.390860 CACTCCACCTCCATCGATCC 59.609 60.000 0.00 0.00 0.00 3.36 F
1678 2947 0.527113 TATCCTCGACCGTGCGAAAA 59.473 50.000 0.00 0.00 40.13 2.29 F
2588 6635 0.597568 TGCAGAACGCCTTCATTTGG 59.402 50.000 0.00 0.00 41.33 3.28 F
4258 8841 3.587797 TGCCCTAAGTACGACTCAAAG 57.412 47.619 0.00 0.00 0.00 2.77 F
5025 9718 0.698818 AGTGGCCCCTAGAACAAAGG 59.301 55.000 0.00 0.00 0.00 3.11 F
6629 21553 1.414866 TTACTGTGGTGGCTGAGGCA 61.415 55.000 3.93 3.93 40.87 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 2476 0.179156 TTTCGCACGGTCGAGGATAC 60.179 55.000 0.00 0.0 39.82 2.24 R
2242 3903 0.912487 AAGGCGGATTACCCCAGTCA 60.912 55.000 0.00 0.0 0.00 3.41 R
2322 3988 1.673009 GAACAACCCAATCCGGCGA 60.673 57.895 9.30 0.0 0.00 5.54 R
3353 7836 1.601412 GCTGTGGTTGCTGAGCTTTTC 60.601 52.381 5.83 0.0 0.00 2.29 R
4454 9044 0.249398 ATCCACCGTAGTTCAGGCAC 59.751 55.000 0.00 0.0 0.00 5.01 R
5576 13920 1.581934 TGCTGTAGCTTCACACACAC 58.418 50.000 5.38 0.0 42.66 3.82 R
6641 21565 1.966451 GTCCTGCCCAACTTGGTCG 60.966 63.158 7.06 0.0 35.17 4.79 R
7619 22561 0.460722 TCGTCACGAGAAACCCAACA 59.539 50.000 0.00 0.0 0.00 3.33 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
67 68 6.381498 AAAAAGGAAAAACCAGAAAGGGAA 57.619 33.333 0.00 0.00 43.89 3.97
68 69 6.381498 AAAAGGAAAAACCAGAAAGGGAAA 57.619 33.333 0.00 0.00 43.89 3.13
69 70 5.353394 AAGGAAAAACCAGAAAGGGAAAC 57.647 39.130 0.00 0.00 43.89 2.78
70 71 4.067972 GGAAAAACCAGAAAGGGAAACC 57.932 45.455 0.00 0.00 45.19 3.27
112 113 4.799473 CCATGCGCGCGACAAGTG 62.799 66.667 37.18 23.72 0.00 3.16
113 114 4.075910 CATGCGCGCGACAAGTGT 62.076 61.111 37.18 12.87 0.00 3.55
114 115 3.777925 ATGCGCGCGACAAGTGTC 61.778 61.111 37.18 13.89 41.47 3.67
137 138 3.876300 CGGAGCACCTCGGAAAAG 58.124 61.111 0.00 0.00 33.52 2.27
138 139 1.004918 CGGAGCACCTCGGAAAAGT 60.005 57.895 0.00 0.00 33.52 2.66
139 140 1.014564 CGGAGCACCTCGGAAAAGTC 61.015 60.000 0.00 0.00 33.52 3.01
140 141 0.321996 GGAGCACCTCGGAAAAGTCT 59.678 55.000 0.00 0.00 0.00 3.24
141 142 1.673329 GGAGCACCTCGGAAAAGTCTC 60.673 57.143 0.00 0.00 0.00 3.36
142 143 1.000955 GAGCACCTCGGAAAAGTCTCA 59.999 52.381 0.00 0.00 0.00 3.27
143 144 1.149148 GCACCTCGGAAAAGTCTCAC 58.851 55.000 0.00 0.00 0.00 3.51
144 145 1.419374 CACCTCGGAAAAGTCTCACG 58.581 55.000 0.00 0.00 0.00 4.35
145 146 1.000607 CACCTCGGAAAAGTCTCACGA 60.001 52.381 0.00 0.00 0.00 4.35
146 147 1.000496 ACCTCGGAAAAGTCTCACGAC 60.000 52.381 0.00 0.00 40.54 4.34
147 148 1.669211 CCTCGGAAAAGTCTCACGACC 60.669 57.143 0.00 0.00 41.16 4.79
148 149 0.039798 TCGGAAAAGTCTCACGACCG 60.040 55.000 0.00 0.00 41.16 4.79
149 150 1.615107 CGGAAAAGTCTCACGACCGC 61.615 60.000 0.00 0.00 41.16 5.68
150 151 0.319641 GGAAAAGTCTCACGACCGCT 60.320 55.000 0.00 0.00 41.16 5.52
151 152 1.061485 GAAAAGTCTCACGACCGCTC 58.939 55.000 0.00 0.00 41.16 5.03
152 153 0.319641 AAAAGTCTCACGACCGCTCC 60.320 55.000 0.00 0.00 41.16 4.70
153 154 2.473664 AAAGTCTCACGACCGCTCCG 62.474 60.000 0.00 0.00 41.16 4.63
166 167 3.767230 CTCCGCGCGTGACACTTG 61.767 66.667 29.95 10.76 0.00 3.16
192 193 3.145551 GGAGCGCTCCCCGACTAA 61.146 66.667 40.99 0.00 43.94 2.24
193 194 2.499827 GGAGCGCTCCCCGACTAAT 61.500 63.158 40.99 0.00 43.94 1.73
194 195 1.007154 GAGCGCTCCCCGACTAATC 60.007 63.158 27.22 0.00 40.02 1.75
203 204 2.613486 CGACTAATCGTTGCGGCG 59.387 61.111 0.51 0.51 43.66 6.46
204 205 1.870458 CGACTAATCGTTGCGGCGA 60.870 57.895 12.98 4.94 43.66 5.54
205 206 1.798368 CGACTAATCGTTGCGGCGAG 61.798 60.000 12.98 0.00 44.43 5.03
206 207 2.078958 GACTAATCGTTGCGGCGAGC 62.079 60.000 12.98 0.00 44.43 5.03
216 217 4.880537 CGGCGAGCGCTCCTCAAT 62.881 66.667 30.66 0.00 40.78 2.57
217 218 2.512515 GGCGAGCGCTCCTCAATT 60.513 61.111 30.66 0.00 40.78 2.32
218 219 1.227263 GGCGAGCGCTCCTCAATTA 60.227 57.895 30.66 0.00 40.78 1.40
219 220 1.218230 GGCGAGCGCTCCTCAATTAG 61.218 60.000 30.66 15.35 40.78 1.73
220 221 0.528684 GCGAGCGCTCCTCAATTAGT 60.529 55.000 30.66 0.00 40.78 2.24
221 222 1.203928 CGAGCGCTCCTCAATTAGTG 58.796 55.000 30.66 9.45 40.78 2.74
222 223 1.202302 CGAGCGCTCCTCAATTAGTGA 60.202 52.381 30.66 0.00 40.78 3.41
223 224 2.544694 CGAGCGCTCCTCAATTAGTGAT 60.545 50.000 30.66 0.00 40.78 3.06
224 225 3.462021 GAGCGCTCCTCAATTAGTGATT 58.538 45.455 27.22 0.00 40.45 2.57
225 226 3.873952 GAGCGCTCCTCAATTAGTGATTT 59.126 43.478 27.22 0.00 40.45 2.17
226 227 3.873952 AGCGCTCCTCAATTAGTGATTTC 59.126 43.478 2.64 0.00 35.07 2.17
227 228 3.302740 GCGCTCCTCAATTAGTGATTTCG 60.303 47.826 0.00 0.00 35.07 3.46
228 229 3.246226 CGCTCCTCAATTAGTGATTTCGG 59.754 47.826 0.00 0.00 35.07 4.30
229 230 3.002759 GCTCCTCAATTAGTGATTTCGGC 59.997 47.826 0.00 0.00 35.07 5.54
230 231 3.194861 TCCTCAATTAGTGATTTCGGCG 58.805 45.455 0.00 0.00 35.07 6.46
231 232 2.936498 CCTCAATTAGTGATTTCGGCGT 59.064 45.455 6.85 0.00 35.07 5.68
232 233 3.374058 CCTCAATTAGTGATTTCGGCGTT 59.626 43.478 6.85 0.00 35.07 4.84
233 234 4.142687 CCTCAATTAGTGATTTCGGCGTTT 60.143 41.667 6.85 0.00 35.07 3.60
234 235 5.365403 TCAATTAGTGATTTCGGCGTTTT 57.635 34.783 6.85 0.00 0.00 2.43
235 236 5.764131 TCAATTAGTGATTTCGGCGTTTTT 58.236 33.333 6.85 0.00 0.00 1.94
236 237 6.900189 TCAATTAGTGATTTCGGCGTTTTTA 58.100 32.000 6.85 0.00 0.00 1.52
237 238 7.018826 TCAATTAGTGATTTCGGCGTTTTTAG 58.981 34.615 6.85 0.00 0.00 1.85
238 239 3.197434 AGTGATTTCGGCGTTTTTAGC 57.803 42.857 6.85 0.00 0.00 3.09
251 252 6.864560 GCGTTTTTAGCCTATTTTTACCTG 57.135 37.500 0.00 0.00 0.00 4.00
252 253 6.384224 GCGTTTTTAGCCTATTTTTACCTGT 58.616 36.000 0.00 0.00 0.00 4.00
253 254 6.864685 GCGTTTTTAGCCTATTTTTACCTGTT 59.135 34.615 0.00 0.00 0.00 3.16
254 255 7.148869 GCGTTTTTAGCCTATTTTTACCTGTTG 60.149 37.037 0.00 0.00 0.00 3.33
255 256 7.327518 CGTTTTTAGCCTATTTTTACCTGTTGG 59.672 37.037 0.00 0.00 39.83 3.77
256 257 6.844097 TTTAGCCTATTTTTACCTGTTGGG 57.156 37.500 0.00 0.00 41.89 4.12
257 258 3.096852 AGCCTATTTTTACCTGTTGGGC 58.903 45.455 0.00 0.00 39.10 5.36
258 259 2.167693 GCCTATTTTTACCTGTTGGGCC 59.832 50.000 0.00 0.00 39.10 5.80
259 260 3.436243 CCTATTTTTACCTGTTGGGCCA 58.564 45.455 0.00 0.00 39.10 5.36
260 261 4.030216 CCTATTTTTACCTGTTGGGCCAT 58.970 43.478 7.26 0.00 39.10 4.40
261 262 5.205056 CCTATTTTTACCTGTTGGGCCATA 58.795 41.667 7.26 0.00 39.10 2.74
262 263 5.838521 CCTATTTTTACCTGTTGGGCCATAT 59.161 40.000 7.26 0.00 39.10 1.78
263 264 7.007723 CCTATTTTTACCTGTTGGGCCATATA 58.992 38.462 7.26 0.00 39.10 0.86
264 265 6.976934 ATTTTTACCTGTTGGGCCATATAG 57.023 37.500 7.26 6.12 39.10 1.31
265 266 5.718801 TTTTACCTGTTGGGCCATATAGA 57.281 39.130 7.26 0.00 39.10 1.98
266 267 5.922960 TTTACCTGTTGGGCCATATAGAT 57.077 39.130 7.26 0.00 39.10 1.98
267 268 7.395525 TTTTACCTGTTGGGCCATATAGATA 57.604 36.000 7.26 0.00 39.10 1.98
268 269 6.620877 TTACCTGTTGGGCCATATAGATAG 57.379 41.667 7.26 0.00 39.10 2.08
269 270 4.763355 ACCTGTTGGGCCATATAGATAGA 58.237 43.478 7.26 0.00 39.10 1.98
270 271 4.780021 ACCTGTTGGGCCATATAGATAGAG 59.220 45.833 7.26 0.00 39.10 2.43
271 272 5.026121 CCTGTTGGGCCATATAGATAGAGA 58.974 45.833 7.26 0.00 0.00 3.10
272 273 5.664908 CCTGTTGGGCCATATAGATAGAGAT 59.335 44.000 7.26 0.00 0.00 2.75
273 274 6.841229 CCTGTTGGGCCATATAGATAGAGATA 59.159 42.308 7.26 0.00 0.00 1.98
274 275 7.512058 CCTGTTGGGCCATATAGATAGAGATAT 59.488 40.741 7.26 0.00 0.00 1.63
275 276 9.593565 CTGTTGGGCCATATAGATAGAGATATA 57.406 37.037 7.26 0.00 0.00 0.86
307 308 0.180406 AAAGATAATCGGGCCGTGCT 59.820 50.000 27.32 13.76 0.00 4.40
308 309 0.532862 AAGATAATCGGGCCGTGCTG 60.533 55.000 27.32 0.00 0.00 4.41
389 390 2.753849 TTTAGCCGGTGCCATGCC 60.754 61.111 1.90 0.00 38.69 4.40
537 1013 6.128336 CCTGAATTCATGTGTCAGTTTCTCTC 60.128 42.308 8.96 0.00 37.64 3.20
544 1020 3.118261 TGTGTCAGTTTCTCTCTTGGCTT 60.118 43.478 0.00 0.00 0.00 4.35
550 1026 2.469274 TTCTCTCTTGGCTTCTGCAG 57.531 50.000 7.63 7.63 41.91 4.41
571 1047 2.767394 GTTTCTTCTACCTCTCCCCTCC 59.233 54.545 0.00 0.00 0.00 4.30
946 1422 5.328565 TCTGTCTCTCTCTCTTTGGATTGA 58.671 41.667 0.00 0.00 0.00 2.57
989 1465 0.390860 CACTCCACCTCCATCGATCC 59.609 60.000 0.00 0.00 0.00 3.36
1201 1716 4.883585 TGATTTGATCTGATTTCCCCTTCG 59.116 41.667 0.00 0.00 0.00 3.79
1205 1720 4.286707 TGATCTGATTTCCCCTTCGTCTA 58.713 43.478 0.00 0.00 0.00 2.59
1272 1792 1.880340 CCATCTGACGAGCCGCTTC 60.880 63.158 0.00 0.00 0.00 3.86
1346 1866 0.881159 CCCGTCGTCGATCTAGCTCT 60.881 60.000 2.98 0.00 39.71 4.09
1405 1952 4.510167 AATCCCGTCTGATTTGAATCCT 57.490 40.909 1.56 0.00 34.50 3.24
1406 1953 5.630415 AATCCCGTCTGATTTGAATCCTA 57.370 39.130 1.56 0.00 34.50 2.94
1501 2298 8.068380 GGCAAACCATTCTATTCGTACTATTTC 58.932 37.037 0.00 0.00 35.26 2.17
1533 2351 2.476185 GCATTGTGCGTGTAGAATGGAC 60.476 50.000 9.24 0.00 36.70 4.02
1567 2385 3.382865 TCATCTGCCAGTATCTGTGTCTC 59.617 47.826 0.00 0.00 0.00 3.36
1678 2947 0.527113 TATCCTCGACCGTGCGAAAA 59.473 50.000 0.00 0.00 40.13 2.29
1679 2948 0.736325 ATCCTCGACCGTGCGAAAAG 60.736 55.000 0.00 0.00 40.13 2.27
1733 3002 8.148351 TGAGCCACTATCAGTAATTTGGTATAC 58.852 37.037 0.00 0.00 0.00 1.47
1994 3265 4.845387 CATCAAGTGCTGAGATTATGTGC 58.155 43.478 0.00 0.00 37.52 4.57
2054 3325 2.661176 TAAATCACCCTCCACCCTCT 57.339 50.000 0.00 0.00 0.00 3.69
2083 3354 7.869429 AGCATAATGTATAAGCTTTTTGCATCC 59.131 33.333 3.20 0.00 45.94 3.51
2199 3856 8.842358 TGGTTTTTCTGTTAGTATGGTAGAAG 57.158 34.615 0.00 0.00 0.00 2.85
2322 3988 8.511126 AGAATATTTTATTGACCCCTGGTACAT 58.489 33.333 0.00 0.00 38.20 2.29
2542 6581 2.446435 TGCCAGTCCTTTAATTGCTCC 58.554 47.619 0.00 0.00 0.00 4.70
2588 6635 0.597568 TGCAGAACGCCTTCATTTGG 59.402 50.000 0.00 0.00 41.33 3.28
2624 6673 3.848726 CTTTCAACACTTTGTGTGCCTT 58.151 40.909 4.01 0.00 46.79 4.35
2900 7038 9.205719 CATTCCACAAAACACAATGAATAATGA 57.794 29.630 0.00 0.00 0.00 2.57
3213 7675 7.360113 TCAGATGTTGAACCAGCAGTATATA 57.640 36.000 0.00 0.00 31.34 0.86
3321 7804 4.846779 TTTTGGAACTGTGCCTAATGTC 57.153 40.909 6.34 0.00 0.00 3.06
4217 8790 7.682741 GCACAGATGGCATGTTTTAGATACAAT 60.683 37.037 3.81 0.00 0.00 2.71
4258 8841 3.587797 TGCCCTAAGTACGACTCAAAG 57.412 47.619 0.00 0.00 0.00 2.77
4425 9012 5.470047 AGTGGTGTGAAGTTAGTCCTAAG 57.530 43.478 0.00 0.00 0.00 2.18
4675 9283 6.737720 AGCTGACCATATTGATCTTCTGTA 57.262 37.500 0.00 0.00 0.00 2.74
4711 9372 2.942804 TCACAAGTTCTCCAATTGCCA 58.057 42.857 0.00 0.00 0.00 4.92
4737 9402 5.163663 TGCATTCCATCCTACGATGTTTTTC 60.164 40.000 0.00 0.00 43.87 2.29
4985 9678 0.827507 TTGGCACTCCCTTTCTTGGC 60.828 55.000 0.00 0.00 35.19 4.52
5025 9718 0.698818 AGTGGCCCCTAGAACAAAGG 59.301 55.000 0.00 0.00 0.00 3.11
5460 13792 5.283457 ACCATGGTCTATTAGCTGTTCTC 57.717 43.478 13.00 0.00 0.00 2.87
5687 14031 4.637977 TGTTGGAGCGCATATTACAAATGA 59.362 37.500 11.47 0.00 0.00 2.57
6175 20625 2.689691 GGGGGCTGGCCTATTCACA 61.690 63.158 20.47 0.00 36.10 3.58
6444 21368 9.103861 ACTAGGAACTACGTCTTGTAACTATAC 57.896 37.037 0.00 0.00 41.75 1.47
6451 21375 4.643784 ACGTCTTGTAACTATACTGGGAGG 59.356 45.833 0.00 0.00 32.98 4.30
6569 21493 2.370189 AGAATCAAATCCCTAGGCCTCG 59.630 50.000 9.68 1.43 0.00 4.63
6629 21553 1.414866 TTACTGTGGTGGCTGAGGCA 61.415 55.000 3.93 3.93 40.87 4.75
6632 21556 2.359230 GTGGTGGCTGAGGCAGAC 60.359 66.667 9.68 5.60 40.49 3.51
6662 21586 2.113139 CAAGTTGGGCAGGACCGT 59.887 61.111 0.00 0.00 40.62 4.83
6706 21630 2.523168 TGTGACTGGCGAGGGTGA 60.523 61.111 0.00 0.00 0.00 4.02
6708 21632 3.680786 TGACTGGCGAGGGTGACG 61.681 66.667 0.00 0.00 0.00 4.35
6802 21726 1.065418 CCTGTGTGGCCTAGGGTTAAG 60.065 57.143 11.72 0.00 0.00 1.85
6844 21768 4.041075 GGTGTTGTGGGGGTTGATTTAATT 59.959 41.667 0.00 0.00 0.00 1.40
6875 21799 5.733620 ATTAAGTGGAGTGAACTTACCGA 57.266 39.130 0.00 0.00 39.28 4.69
6883 21807 4.312443 GAGTGAACTTACCGATGGTTGAA 58.688 43.478 0.00 0.00 37.09 2.69
6897 21821 4.081322 TGGTTGAAGGGTCTAACAGTTC 57.919 45.455 0.00 0.00 0.00 3.01
6939 21878 4.039124 CCAGCCAATGGTTGTTTTCTAAGT 59.961 41.667 14.91 0.00 44.91 2.24
6948 21887 4.928601 GTTGTTTTCTAAGTCCCACAACC 58.071 43.478 0.00 0.00 38.60 3.77
6949 21888 4.237976 TGTTTTCTAAGTCCCACAACCA 57.762 40.909 0.00 0.00 0.00 3.67
6998 21937 8.865590 ACAATATCATAAAACCATAAAACGCC 57.134 30.769 0.00 0.00 0.00 5.68
7021 21960 5.513441 CCAAAACCCAAAATACCCTAAACCC 60.513 44.000 0.00 0.00 0.00 4.11
7128 22067 2.937799 TCGTCATATTTTAACCGCCACC 59.062 45.455 0.00 0.00 0.00 4.61
7129 22068 2.032426 CGTCATATTTTAACCGCCACCC 59.968 50.000 0.00 0.00 0.00 4.61
7197 22136 1.746517 CGGGTGGGTAGCATAGACC 59.253 63.158 0.00 0.00 36.12 3.85
7218 22157 2.601763 CGCCACTCGTAACTCAATTACC 59.398 50.000 0.00 0.00 40.22 2.85
7243 22182 2.829384 GGGAGGGCCAACACACTCA 61.829 63.158 6.18 0.00 35.15 3.41
7245 22184 1.600916 GAGGGCCAACACACTCACC 60.601 63.158 6.18 0.00 0.00 4.02
7253 22192 2.224523 CCAACACACTCACCACTGGTAT 60.225 50.000 0.00 0.00 32.11 2.73
7259 22198 2.813754 CACTCACCACTGGTATGTTTGG 59.186 50.000 0.00 0.00 32.11 3.28
7264 22203 1.619432 CCACTGGTATGTTTGGCCCAT 60.619 52.381 0.00 0.00 0.00 4.00
7287 22226 5.162637 TGGCTAATCTGGGACCATAATACT 58.837 41.667 0.00 0.00 0.00 2.12
7330 22269 6.435430 TGCAATTAAGCAGTATTGTCGATT 57.565 33.333 0.00 0.00 40.11 3.34
7359 22300 5.448654 TCATTATTTTGGACATGGCTAGCT 58.551 37.500 15.72 0.00 0.00 3.32
7371 22312 4.207281 CTAGCTAGCGCCCGTGCA 62.207 66.667 8.05 0.00 37.32 4.57
7545 22486 2.563179 ACTACGATCCTATCCCACATGC 59.437 50.000 0.00 0.00 0.00 4.06
7619 22561 4.039245 TCGGAACTCAGATCTGTTTTCACT 59.961 41.667 26.38 9.36 0.00 3.41
7621 22563 5.059833 GGAACTCAGATCTGTTTTCACTGT 58.940 41.667 26.38 12.67 0.00 3.55
7631 22573 4.398044 TCTGTTTTCACTGTTGGGTTTCTC 59.602 41.667 0.00 0.00 0.00 2.87
7633 22575 2.702592 TTCACTGTTGGGTTTCTCGT 57.297 45.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 6.381498 TTCCCTTTCTGGTTTTTCCTTTTT 57.619 33.333 0.00 0.00 37.07 1.94
45 46 6.177610 GTTTCCCTTTCTGGTTTTTCCTTTT 58.822 36.000 0.00 0.00 37.07 2.27
46 47 5.338871 GGTTTCCCTTTCTGGTTTTTCCTTT 60.339 40.000 0.00 0.00 37.07 3.11
47 48 4.163458 GGTTTCCCTTTCTGGTTTTTCCTT 59.837 41.667 0.00 0.00 37.07 3.36
48 49 3.709653 GGTTTCCCTTTCTGGTTTTTCCT 59.290 43.478 0.00 0.00 37.07 3.36
49 50 3.491964 CGGTTTCCCTTTCTGGTTTTTCC 60.492 47.826 0.00 0.00 0.00 3.13
50 51 3.491964 CCGGTTTCCCTTTCTGGTTTTTC 60.492 47.826 0.00 0.00 0.00 2.29
51 52 2.432874 CCGGTTTCCCTTTCTGGTTTTT 59.567 45.455 0.00 0.00 0.00 1.94
52 53 2.036387 CCGGTTTCCCTTTCTGGTTTT 58.964 47.619 0.00 0.00 0.00 2.43
53 54 1.215924 TCCGGTTTCCCTTTCTGGTTT 59.784 47.619 0.00 0.00 0.00 3.27
54 55 0.848053 TCCGGTTTCCCTTTCTGGTT 59.152 50.000 0.00 0.00 0.00 3.67
55 56 0.848053 TTCCGGTTTCCCTTTCTGGT 59.152 50.000 0.00 0.00 0.00 4.00
56 57 1.611977 GTTTCCGGTTTCCCTTTCTGG 59.388 52.381 0.00 0.00 0.00 3.86
57 58 1.611977 GGTTTCCGGTTTCCCTTTCTG 59.388 52.381 0.00 0.00 0.00 3.02
58 59 1.816572 CGGTTTCCGGTTTCCCTTTCT 60.817 52.381 0.00 0.00 44.15 2.52
59 60 0.594602 CGGTTTCCGGTTTCCCTTTC 59.405 55.000 0.00 0.00 44.15 2.62
60 61 2.723231 CGGTTTCCGGTTTCCCTTT 58.277 52.632 0.00 0.00 44.15 3.11
61 62 4.486887 CGGTTTCCGGTTTCCCTT 57.513 55.556 0.00 0.00 44.15 3.95
71 72 0.321830 TCCCGTGATTTCCGGTTTCC 60.322 55.000 0.00 0.00 43.98 3.13
72 73 1.084289 CTCCCGTGATTTCCGGTTTC 58.916 55.000 0.00 0.00 43.98 2.78
73 74 0.688487 TCTCCCGTGATTTCCGGTTT 59.312 50.000 0.00 0.00 43.98 3.27
74 75 0.036671 GTCTCCCGTGATTTCCGGTT 60.037 55.000 0.00 0.00 43.98 4.44
75 76 1.595357 GTCTCCCGTGATTTCCGGT 59.405 57.895 0.00 0.00 43.98 5.28
76 77 1.518572 CGTCTCCCGTGATTTCCGG 60.519 63.158 0.00 0.00 45.07 5.14
77 78 2.165301 GCGTCTCCCGTGATTTCCG 61.165 63.158 0.00 0.00 39.32 4.30
78 79 1.814169 GGCGTCTCCCGTGATTTCC 60.814 63.158 0.00 0.00 39.32 3.13
79 80 0.462047 ATGGCGTCTCCCGTGATTTC 60.462 55.000 0.00 0.00 39.32 2.17
80 81 0.744414 CATGGCGTCTCCCGTGATTT 60.744 55.000 0.00 0.00 43.20 2.17
81 82 1.153369 CATGGCGTCTCCCGTGATT 60.153 57.895 0.00 0.00 43.20 2.57
82 83 2.501128 CATGGCGTCTCCCGTGAT 59.499 61.111 0.00 0.00 43.20 3.06
83 84 4.451150 GCATGGCGTCTCCCGTGA 62.451 66.667 4.67 0.00 43.20 4.35
95 96 4.799473 CACTTGTCGCGCGCATGG 62.799 66.667 32.61 21.28 0.00 3.66
96 97 3.964729 GACACTTGTCGCGCGCATG 62.965 63.158 32.61 26.74 35.12 4.06
97 98 3.777925 GACACTTGTCGCGCGCAT 61.778 61.111 32.61 11.22 35.12 4.73
119 120 2.358247 TTTTCCGAGGTGCTCCGC 60.358 61.111 0.00 0.00 39.05 5.54
120 121 1.004918 ACTTTTCCGAGGTGCTCCG 60.005 57.895 0.00 0.00 39.05 4.63
121 122 0.321996 AGACTTTTCCGAGGTGCTCC 59.678 55.000 0.00 0.00 0.00 4.70
122 123 1.000955 TGAGACTTTTCCGAGGTGCTC 59.999 52.381 0.00 0.00 0.00 4.26
123 124 1.048601 TGAGACTTTTCCGAGGTGCT 58.951 50.000 0.00 0.00 0.00 4.40
124 125 1.149148 GTGAGACTTTTCCGAGGTGC 58.851 55.000 0.00 0.00 0.00 5.01
125 126 1.000607 TCGTGAGACTTTTCCGAGGTG 60.001 52.381 0.00 0.00 33.31 4.00
126 127 1.325355 TCGTGAGACTTTTCCGAGGT 58.675 50.000 0.00 0.00 33.31 3.85
149 150 3.767230 CAAGTGTCACGCGCGGAG 61.767 66.667 35.22 25.44 0.00 4.63
176 177 1.007154 GATTAGTCGGGGAGCGCTC 60.007 63.158 29.38 29.38 0.00 5.03
177 178 2.846652 CGATTAGTCGGGGAGCGCT 61.847 63.158 11.27 11.27 44.00 5.92
178 179 2.354773 CGATTAGTCGGGGAGCGC 60.355 66.667 0.00 0.00 44.00 5.92
187 188 1.917921 CTCGCCGCAACGATTAGTC 59.082 57.895 0.00 0.00 42.02 2.59
188 189 2.165301 GCTCGCCGCAACGATTAGT 61.165 57.895 0.00 0.00 42.02 2.24
189 190 2.621000 GCTCGCCGCAACGATTAG 59.379 61.111 0.00 0.00 42.02 1.73
190 191 3.251763 CGCTCGCCGCAACGATTA 61.252 61.111 0.00 0.00 42.02 1.75
199 200 2.954020 TAATTGAGGAGCGCTCGCCG 62.954 60.000 29.81 0.00 43.17 6.46
200 201 1.218230 CTAATTGAGGAGCGCTCGCC 61.218 60.000 29.81 23.00 43.17 5.54
201 202 0.528684 ACTAATTGAGGAGCGCTCGC 60.529 55.000 29.81 23.71 42.33 5.03
202 203 1.202302 TCACTAATTGAGGAGCGCTCG 60.202 52.381 29.81 16.23 0.00 5.03
203 204 2.586258 TCACTAATTGAGGAGCGCTC 57.414 50.000 29.38 29.38 0.00 5.03
204 205 3.550437 AATCACTAATTGAGGAGCGCT 57.450 42.857 11.27 11.27 37.77 5.92
205 206 3.302740 CGAAATCACTAATTGAGGAGCGC 60.303 47.826 0.00 0.00 37.77 5.92
206 207 3.246226 CCGAAATCACTAATTGAGGAGCG 59.754 47.826 0.00 0.00 37.77 5.03
207 208 3.002759 GCCGAAATCACTAATTGAGGAGC 59.997 47.826 0.00 0.00 37.77 4.70
208 209 3.246226 CGCCGAAATCACTAATTGAGGAG 59.754 47.826 0.00 0.00 37.77 3.69
209 210 3.194861 CGCCGAAATCACTAATTGAGGA 58.805 45.455 0.00 0.00 37.77 3.71
210 211 2.936498 ACGCCGAAATCACTAATTGAGG 59.064 45.455 0.00 0.00 37.77 3.86
211 212 4.600012 AACGCCGAAATCACTAATTGAG 57.400 40.909 0.00 0.00 37.77 3.02
212 213 5.365403 AAAACGCCGAAATCACTAATTGA 57.635 34.783 0.00 0.00 39.11 2.57
213 214 6.237201 GCTAAAAACGCCGAAATCACTAATTG 60.237 38.462 0.00 0.00 0.00 2.32
214 215 5.798434 GCTAAAAACGCCGAAATCACTAATT 59.202 36.000 0.00 0.00 0.00 1.40
215 216 5.329493 GCTAAAAACGCCGAAATCACTAAT 58.671 37.500 0.00 0.00 0.00 1.73
216 217 4.378666 GGCTAAAAACGCCGAAATCACTAA 60.379 41.667 0.00 0.00 37.87 2.24
217 218 3.125658 GGCTAAAAACGCCGAAATCACTA 59.874 43.478 0.00 0.00 37.87 2.74
218 219 2.095415 GGCTAAAAACGCCGAAATCACT 60.095 45.455 0.00 0.00 37.87 3.41
219 220 2.247637 GGCTAAAAACGCCGAAATCAC 58.752 47.619 0.00 0.00 37.87 3.06
220 221 2.622546 GGCTAAAAACGCCGAAATCA 57.377 45.000 0.00 0.00 37.87 2.57
228 229 6.384224 ACAGGTAAAAATAGGCTAAAAACGC 58.616 36.000 0.00 0.00 0.00 4.84
229 230 7.327518 CCAACAGGTAAAAATAGGCTAAAAACG 59.672 37.037 0.00 0.00 0.00 3.60
230 231 7.601130 CCCAACAGGTAAAAATAGGCTAAAAAC 59.399 37.037 0.00 0.00 0.00 2.43
231 232 7.672240 CCCAACAGGTAAAAATAGGCTAAAAA 58.328 34.615 0.00 0.00 0.00 1.94
232 233 6.295405 GCCCAACAGGTAAAAATAGGCTAAAA 60.295 38.462 0.00 0.00 38.26 1.52
233 234 5.186215 GCCCAACAGGTAAAAATAGGCTAAA 59.814 40.000 0.00 0.00 38.26 1.85
234 235 4.707934 GCCCAACAGGTAAAAATAGGCTAA 59.292 41.667 0.00 0.00 38.26 3.09
235 236 4.274978 GCCCAACAGGTAAAAATAGGCTA 58.725 43.478 0.00 0.00 38.26 3.93
236 237 3.096852 GCCCAACAGGTAAAAATAGGCT 58.903 45.455 0.00 0.00 38.26 4.58
237 238 2.167693 GGCCCAACAGGTAAAAATAGGC 59.832 50.000 0.00 0.00 38.26 3.93
238 239 3.436243 TGGCCCAACAGGTAAAAATAGG 58.564 45.455 0.00 0.00 38.26 2.57
239 240 6.976934 ATATGGCCCAACAGGTAAAAATAG 57.023 37.500 0.00 0.00 38.26 1.73
240 241 7.817440 TCTATATGGCCCAACAGGTAAAAATA 58.183 34.615 0.00 0.00 38.26 1.40
241 242 6.678547 TCTATATGGCCCAACAGGTAAAAAT 58.321 36.000 0.00 0.00 38.26 1.82
242 243 6.080969 TCTATATGGCCCAACAGGTAAAAA 57.919 37.500 0.00 0.00 38.26 1.94
243 244 5.718801 TCTATATGGCCCAACAGGTAAAA 57.281 39.130 0.00 0.00 38.26 1.52
244 245 5.922960 ATCTATATGGCCCAACAGGTAAA 57.077 39.130 0.00 0.00 38.26 2.01
245 246 6.327781 TCTATCTATATGGCCCAACAGGTAA 58.672 40.000 0.00 0.00 38.26 2.85
246 247 5.910931 TCTATCTATATGGCCCAACAGGTA 58.089 41.667 0.00 0.00 38.26 3.08
247 248 4.763355 TCTATCTATATGGCCCAACAGGT 58.237 43.478 0.00 0.00 38.26 4.00
248 249 5.026121 TCTCTATCTATATGGCCCAACAGG 58.974 45.833 0.00 0.00 39.47 4.00
249 250 6.805016 ATCTCTATCTATATGGCCCAACAG 57.195 41.667 0.00 0.00 0.00 3.16
371 372 2.489751 GCATGGCACCGGCTAAAC 59.510 61.111 0.00 0.00 40.87 2.01
454 456 2.983592 CCGGCTCACAAACCCCAC 60.984 66.667 0.00 0.00 0.00 4.61
455 457 3.494254 ACCGGCTCACAAACCCCA 61.494 61.111 0.00 0.00 0.00 4.96
458 460 1.358759 CAACACCGGCTCACAAACC 59.641 57.895 0.00 0.00 0.00 3.27
459 461 0.248458 CACAACACCGGCTCACAAAC 60.248 55.000 0.00 0.00 0.00 2.93
460 462 1.380403 CCACAACACCGGCTCACAAA 61.380 55.000 0.00 0.00 0.00 2.83
485 961 1.830145 CCCTTACAGATGGTCCCCG 59.170 63.158 0.00 0.00 0.00 5.73
505 981 4.023279 TGACACATGAATTCAGGGTTTTCG 60.023 41.667 22.84 9.84 30.95 3.46
537 1013 2.883386 AGAAGAAACTGCAGAAGCCAAG 59.117 45.455 23.35 0.00 41.13 3.61
544 1020 3.511934 GGAGAGGTAGAAGAAACTGCAGA 59.488 47.826 23.35 0.00 0.00 4.26
550 1026 2.767394 GGAGGGGAGAGGTAGAAGAAAC 59.233 54.545 0.00 0.00 0.00 2.78
571 1047 2.697644 AGATTGCAGGGGAGGGGG 60.698 66.667 0.00 0.00 0.00 5.40
918 1394 3.652057 AAGAGAGAGAGACAGAGAGGG 57.348 52.381 0.00 0.00 0.00 4.30
919 1395 3.696051 CCAAAGAGAGAGAGACAGAGAGG 59.304 52.174 0.00 0.00 0.00 3.69
920 1396 4.588899 TCCAAAGAGAGAGAGACAGAGAG 58.411 47.826 0.00 0.00 0.00 3.20
921 1397 4.649267 TCCAAAGAGAGAGAGACAGAGA 57.351 45.455 0.00 0.00 0.00 3.10
922 1398 5.418524 TCAATCCAAAGAGAGAGAGACAGAG 59.581 44.000 0.00 0.00 0.00 3.35
923 1399 5.328565 TCAATCCAAAGAGAGAGAGACAGA 58.671 41.667 0.00 0.00 0.00 3.41
924 1400 5.657826 TCAATCCAAAGAGAGAGAGACAG 57.342 43.478 0.00 0.00 0.00 3.51
925 1401 6.425210 TTTCAATCCAAAGAGAGAGAGACA 57.575 37.500 0.00 0.00 0.00 3.41
926 1402 7.158021 TCTTTTCAATCCAAAGAGAGAGAGAC 58.842 38.462 0.00 0.00 35.71 3.36
927 1403 7.308450 TCTTTTCAATCCAAAGAGAGAGAGA 57.692 36.000 0.00 0.00 35.71 3.10
928 1404 7.877097 TCTTCTTTTCAATCCAAAGAGAGAGAG 59.123 37.037 0.00 0.00 40.51 3.20
946 1422 4.040461 TCACGACCCAATCTCTCTTCTTTT 59.960 41.667 0.00 0.00 0.00 2.27
989 1465 1.476007 GGGATCCATGGTCTCGAGGG 61.476 65.000 15.23 5.40 0.00 4.30
1327 1847 0.881159 AGAGCTAGATCGACGACGGG 60.881 60.000 7.55 0.00 40.21 5.28
1405 1952 9.031537 TGTTCAGAGTTAATGGAGTGATAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
1406 1953 7.907389 TGTTCAGAGTTAATGGAGTGATAAGT 58.093 34.615 0.00 0.00 0.00 2.24
1463 2017 1.281867 TGGTTTGCCCTAGGTGATCAG 59.718 52.381 8.29 0.00 0.00 2.90
1510 2307 2.508867 CATTCTACACGCACAATGCAC 58.491 47.619 1.20 0.00 45.36 4.57
1533 2351 3.870274 TGGCAGATGATTCTTCAGAGTG 58.130 45.455 2.77 0.00 34.73 3.51
1658 2476 0.179156 TTTCGCACGGTCGAGGATAC 60.179 55.000 0.00 0.00 39.82 2.24
1679 2948 9.487026 AACCAACAGTTCTTGTGTGATTAGCAC 62.487 40.741 0.00 0.00 40.51 4.40
2054 3325 8.249638 TGCAAAAAGCTTATACATTATGCTGAA 58.750 29.630 0.00 0.00 45.94 3.02
2083 3354 2.135139 ACGTACACATGACACAAGCTG 58.865 47.619 0.00 0.00 0.00 4.24
2199 3856 6.583912 TGCTATCTTCGTACTTAACATTGC 57.416 37.500 0.00 0.00 0.00 3.56
2242 3903 0.912487 AAGGCGGATTACCCCAGTCA 60.912 55.000 0.00 0.00 0.00 3.41
2322 3988 1.673009 GAACAACCCAATCCGGCGA 60.673 57.895 9.30 0.00 0.00 5.54
2588 6635 6.024049 GTGTTGAAAGCAGCATATTACAGAC 58.976 40.000 0.00 0.00 37.57 3.51
2624 6673 6.597562 ACAATACTTCCTGTGGAACTGTAAA 58.402 36.000 0.00 0.00 36.71 2.01
2900 7038 2.519302 AAGTGCCTTGCGCCAAGT 60.519 55.556 4.18 0.00 39.58 3.16
3213 7675 3.222173 TGTTGTGGCTGATACAAAGGT 57.778 42.857 0.00 0.00 39.50 3.50
3353 7836 1.601412 GCTGTGGTTGCTGAGCTTTTC 60.601 52.381 5.83 0.00 0.00 2.29
3701 8192 9.471702 AAGATTGACATAAGAACATGGAGAAAT 57.528 29.630 0.00 0.00 0.00 2.17
4258 8841 8.638685 AGCATCACATTAATTTCATAAACTGC 57.361 30.769 0.00 0.00 0.00 4.40
4425 9012 4.992951 AGATTGAAATGCAGTTTTGAAGCC 59.007 37.500 0.00 0.00 0.00 4.35
4454 9044 0.249398 ATCCACCGTAGTTCAGGCAC 59.751 55.000 0.00 0.00 0.00 5.01
4614 9220 2.599659 GCACAGTAGCATTTTTCCAGC 58.400 47.619 0.00 0.00 0.00 4.85
4675 9283 7.823799 AGAACTTGTGAACCAAATCAAACAATT 59.176 29.630 0.00 0.00 31.20 2.32
4711 9372 3.117491 CATCGTAGGATGGAATGCAGT 57.883 47.619 16.08 0.00 45.15 4.40
4985 9678 6.090898 CCACTGTCTACGAATTTTAGGAAGTG 59.909 42.308 15.33 15.33 34.02 3.16
5025 9718 2.996631 AGATCAGGGCAATCTCAACAC 58.003 47.619 0.00 0.00 0.00 3.32
5411 13739 6.433716 TGTCATCAAGTCAGAAAATATGGCAA 59.566 34.615 0.00 0.00 0.00 4.52
5576 13920 1.581934 TGCTGTAGCTTCACACACAC 58.418 50.000 5.38 0.00 42.66 3.82
5687 14031 6.266558 TGGACACTACTTTTACCAATTTGCAT 59.733 34.615 0.00 0.00 0.00 3.96
6081 20529 5.903010 ACATATTACCAGTGTCAGGATACCA 59.097 40.000 0.00 0.00 37.17 3.25
6175 20625 3.557054 CCACTAGTGTGCCACATACAAGT 60.557 47.826 21.18 0.00 42.54 3.16
6364 21287 6.874134 CCTAGGTAGTTGGATGCATGTATAAC 59.126 42.308 2.46 3.93 0.00 1.89
6444 21368 9.976776 TGATTAGTTCTAGTATATACCTCCCAG 57.023 37.037 9.32 0.53 0.00 4.45
6569 21493 6.600822 TCCCTGTTGATCAGAAATTCAATCTC 59.399 38.462 0.00 0.00 46.27 2.75
6640 21564 3.365265 CCTGCCCAACTTGGTCGC 61.365 66.667 7.06 4.77 35.17 5.19
6641 21565 1.966451 GTCCTGCCCAACTTGGTCG 60.966 63.158 7.06 0.00 35.17 4.79
6646 21570 2.113139 CACGGTCCTGCCCAACTT 59.887 61.111 0.00 0.00 0.00 2.66
6689 21613 2.523168 TCACCCTCGCCAGTCACA 60.523 61.111 0.00 0.00 0.00 3.58
6706 21630 2.972505 CCTTGCTTGCACGGTCGT 60.973 61.111 9.60 0.00 0.00 4.34
6708 21632 4.389576 CGCCTTGCTTGCACGGTC 62.390 66.667 17.38 10.07 0.00 4.79
6802 21726 2.027469 ACCTCCGGTAAGTTCATTCCAC 60.027 50.000 0.00 0.00 32.11 4.02
6863 21787 3.435671 CCTTCAACCATCGGTAAGTTCAC 59.564 47.826 0.00 0.00 33.12 3.18
6875 21799 4.652822 GAACTGTTAGACCCTTCAACCAT 58.347 43.478 0.00 0.00 0.00 3.55
6883 21807 2.610438 TACCCGAACTGTTAGACCCT 57.390 50.000 2.01 0.00 0.00 4.34
6897 21821 3.559069 TGGTCCTGTCTACTATTACCCG 58.441 50.000 0.00 0.00 0.00 5.28
6939 21878 5.059833 GCAAAAACAATATTGGTTGTGGGA 58.940 37.500 29.31 0.00 42.16 4.37
6948 21887 9.771915 GTATGGGAAATTGCAAAAACAATATTG 57.228 29.630 14.01 14.01 39.32 1.90
6949 21888 9.512588 TGTATGGGAAATTGCAAAAACAATATT 57.487 25.926 1.71 0.00 39.32 1.28
6998 21937 5.513441 GGGGTTTAGGGTATTTTGGGTTTTG 60.513 44.000 0.00 0.00 0.00 2.44
7077 22016 7.218773 CCACTGATACTTTACAAATCAATTGCG 59.781 37.037 0.00 0.00 43.13 4.85
7128 22067 5.631512 GCTAATATCTGAGCTCAAACTACGG 59.368 44.000 18.85 4.10 35.73 4.02
7129 22068 5.631512 GGCTAATATCTGAGCTCAAACTACG 59.368 44.000 18.85 4.89 38.79 3.51
7179 22118 1.746517 GGTCTATGCTACCCACCCG 59.253 63.158 0.00 0.00 0.00 5.28
7184 22123 1.069258 GTGGCGGTCTATGCTACCC 59.931 63.158 0.00 0.00 37.81 3.69
7197 22136 2.601763 GGTAATTGAGTTACGAGTGGCG 59.398 50.000 0.00 0.00 42.95 5.69
7218 22157 3.579302 TTGGCCCTCCCACCACTG 61.579 66.667 0.00 0.00 45.34 3.66
7228 22167 2.382770 TGGTGAGTGTGTTGGCCCT 61.383 57.895 0.00 0.00 0.00 5.19
7243 22182 0.251608 GGGCCAAACATACCAGTGGT 60.252 55.000 20.91 20.91 40.16 4.16
7245 22184 1.477700 CATGGGCCAAACATACCAGTG 59.522 52.381 11.89 0.00 36.27 3.66
7264 22203 5.162637 AGTATTATGGTCCCAGATTAGCCA 58.837 41.667 0.00 0.00 0.00 4.75
7287 22226 3.307906 ACTTCGCACCCGCCACTA 61.308 61.111 0.00 0.00 33.11 2.74
7330 22269 4.161942 CCATGTCCAAAATAATGAGGCCAA 59.838 41.667 5.01 0.00 0.00 4.52
7359 22300 1.451207 AATGAATGCACGGGCGCTA 60.451 52.632 4.58 0.00 45.35 4.26
7367 22308 0.174162 GTCAGCCCCAATGAATGCAC 59.826 55.000 0.00 0.00 0.00 4.57
7370 22311 1.019673 CTCGTCAGCCCCAATGAATG 58.980 55.000 0.00 0.00 0.00 2.67
7371 22312 0.749454 GCTCGTCAGCCCCAATGAAT 60.749 55.000 0.00 0.00 40.14 2.57
7498 22439 3.655276 TCCTTGTAAGGTGAAGACGTC 57.345 47.619 7.70 7.70 46.54 4.34
7575 22516 6.256321 TCCGACGTAGAACCAAAAATTATAGC 59.744 38.462 0.00 0.00 0.00 2.97
7588 22529 3.374678 AGATCTGAGTTCCGACGTAGAAC 59.625 47.826 18.62 18.62 43.22 3.01
7592 22533 2.708051 ACAGATCTGAGTTCCGACGTA 58.292 47.619 29.27 0.00 0.00 3.57
7619 22561 0.460722 TCGTCACGAGAAACCCAACA 59.539 50.000 0.00 0.00 0.00 3.33
7688 22630 0.485099 TACCACCCAAAGTTGCCCAT 59.515 50.000 0.00 0.00 0.00 4.00
7693 22635 2.231235 GCCTCAATACCACCCAAAGTTG 59.769 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.