Multiple sequence alignment - TraesCS7A01G309900

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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 TraesCS7A01G309900 chr7A 100.000 4400 0 0 1 4400 438167456 438171855 0.000000e+00 8126.0
1 TraesCS7A01G309900 chr7A 94.355 372 19 1 47 416 692315404 692315033 1.780000e-158 569.0
2 TraesCS7A01G309900 chr7A 89.116 147 12 1 3769 3915 344681255 344681397 3.500000e-41 180.0
3 TraesCS7A01G309900 chr7A 95.000 40 2 0 662 701 692315033 692314994 3.670000e-06 63.9
4 TraesCS7A01G309900 chr7D 92.088 2692 173 20 870 3541 388021605 388024276 0.000000e+00 3755.0
5 TraesCS7A01G309900 chr7D 87.671 219 22 4 1894 2110 387346130 387346345 2.630000e-62 250.0
6 TraesCS7A01G309900 chr7D 93.333 150 10 0 4251 4400 434909928 434909779 5.730000e-54 222.0
7 TraesCS7A01G309900 chr7D 92.667 150 11 0 4251 4400 23555724 23555575 2.660000e-52 217.0
8 TraesCS7A01G309900 chr7D 90.517 116 9 2 725 840 387925774 387925887 7.620000e-33 152.0
9 TraesCS7A01G309900 chr7B 90.770 2026 136 30 803 2810 383502056 383504048 0.000000e+00 2658.0
10 TraesCS7A01G309900 chr7B 89.571 652 50 11 2859 3494 383504220 383504869 0.000000e+00 811.0
11 TraesCS7A01G309900 chr7B 79.260 622 113 14 2108 2725 403563939 403563330 1.890000e-113 420.0
12 TraesCS7A01G309900 chr7B 79.479 614 108 15 2118 2725 407940584 407939983 1.890000e-113 420.0
13 TraesCS7A01G309900 chr7B 79.119 613 111 15 2118 2725 403729781 403729181 1.470000e-109 407.0
14 TraesCS7A01G309900 chr7B 78.630 613 113 15 2118 2725 408111520 408110921 1.480000e-104 390.0
15 TraesCS7A01G309900 chr7B 87.879 99 12 0 3819 3917 356690167 356690265 2.780000e-22 117.0
16 TraesCS7A01G309900 chr7B 77.540 187 40 2 1212 1397 403732324 403732139 1.290000e-20 111.0
17 TraesCS7A01G309900 chr7B 78.571 168 34 2 1212 1378 407943167 407943001 4.650000e-20 110.0
18 TraesCS7A01G309900 chr7B 92.105 76 6 0 1511 1586 403732001 403731926 1.670000e-19 108.0
19 TraesCS7A01G309900 chr7B 90.789 76 7 0 1511 1586 407942844 407942769 7.790000e-18 102.0
20 TraesCS7A01G309900 chr7B 90.789 76 7 0 1511 1586 408113781 408113706 7.790000e-18 102.0
21 TraesCS7A01G309900 chr7B 77.143 175 38 2 1212 1385 403566477 403566304 2.800000e-17 100.0
22 TraesCS7A01G309900 chr7B 84.848 99 9 6 3599 3696 383505120 383505213 1.300000e-15 95.3
23 TraesCS7A01G309900 chr5B 90.870 1150 98 5 1894 3039 674737981 674736835 0.000000e+00 1535.0
24 TraesCS7A01G309900 chr5B 90.379 634 53 6 2034 2664 674746729 674746101 0.000000e+00 826.0
25 TraesCS7A01G309900 chr5B 88.663 344 35 3 2660 3000 674738651 674738309 2.450000e-112 416.0
26 TraesCS7A01G309900 chr5B 90.541 296 25 2 3955 4248 605523725 605523431 5.340000e-104 388.0
27 TraesCS7A01G309900 chr2D 87.665 681 71 9 45 724 406696115 406696783 0.000000e+00 780.0
28 TraesCS7A01G309900 chr2D 90.873 252 23 0 415 666 541547288 541547539 5.450000e-89 339.0
29 TraesCS7A01G309900 chr2D 87.215 219 23 4 1894 2110 486374001 486373786 1.220000e-60 244.0
30 TraesCS7A01G309900 chr2D 92.000 150 12 0 4251 4400 647130789 647130640 1.240000e-50 211.0
31 TraesCS7A01G309900 chr3A 87.164 483 32 12 3769 4249 377486567 377486113 5.040000e-144 521.0
32 TraesCS7A01G309900 chr3A 90.909 363 31 2 47 408 691315052 691315413 1.840000e-133 486.0
33 TraesCS7A01G309900 chr3A 90.345 290 26 1 3962 4249 614236890 614236601 3.210000e-101 379.0
34 TraesCS7A01G309900 chr3A 88.015 267 31 1 403 669 300127741 300127476 9.190000e-82 315.0
35 TraesCS7A01G309900 chr3A 95.312 64 3 0 662 725 636159927 636159864 7.790000e-18 102.0
36 TraesCS7A01G309900 chr4D 91.328 369 26 5 44 408 337089858 337089492 2.360000e-137 499.0
37 TraesCS7A01G309900 chr4D 80.257 623 101 19 2118 2724 84777176 84776560 2.410000e-122 449.0
38 TraesCS7A01G309900 chr4D 87.215 219 23 4 1894 2110 502962181 502961966 1.220000e-60 244.0
39 TraesCS7A01G309900 chr4D 94.667 75 4 0 1511 1585 84779018 84778944 2.780000e-22 117.0
40 TraesCS7A01G309900 chr5A 90.054 372 33 4 40 408 613719563 613719193 3.080000e-131 479.0
41 TraesCS7A01G309900 chr5A 89.589 365 33 3 47 408 524767480 524767118 4.010000e-125 459.0
42 TraesCS7A01G309900 chr5A 92.000 150 12 0 4251 4400 398719540 398719391 1.240000e-50 211.0
43 TraesCS7A01G309900 chr5A 92.000 150 12 0 4251 4400 616101835 616101686 1.240000e-50 211.0
44 TraesCS7A01G309900 chr5A 91.935 62 5 0 662 723 613719185 613719124 2.180000e-13 87.9
45 TraesCS7A01G309900 chr5A 95.918 49 2 0 662 710 12407419 12407467 3.650000e-11 80.5
46 TraesCS7A01G309900 chr6B 90.164 366 33 3 45 408 364747606 364747242 1.430000e-129 473.0
47 TraesCS7A01G309900 chr6B 89.835 364 34 3 46 408 4419471 4419110 8.620000e-127 464.0
48 TraesCS7A01G309900 chr5D 89.779 362 36 1 47 408 530821549 530821909 3.100000e-126 462.0
49 TraesCS7A01G309900 chr5D 90.351 228 21 1 2698 2925 327294974 327294748 9.250000e-77 298.0
50 TraesCS7A01G309900 chr5D 87.671 219 22 4 1894 2110 133274562 133274347 2.630000e-62 250.0
51 TraesCS7A01G309900 chr5D 87.671 219 22 4 1894 2110 324711994 324712209 2.630000e-62 250.0
52 TraesCS7A01G309900 chr5D 87.215 219 23 4 1894 2110 46641596 46641381 1.220000e-60 244.0
53 TraesCS7A01G309900 chr6A 92.617 298 20 1 3953 4248 13749476 13749773 1.130000e-115 427.0
54 TraesCS7A01G309900 chr6A 90.690 290 24 2 3962 4249 34187469 34187181 2.480000e-102 383.0
55 TraesCS7A01G309900 chr6A 89.773 176 17 1 3769 3943 13749320 13749495 1.590000e-54 224.0
56 TraesCS7A01G309900 chr6A 92.667 150 11 0 4251 4400 13749820 13749969 2.660000e-52 217.0
57 TraesCS7A01G309900 chr1D 90.909 297 27 0 3953 4249 232351990 232352286 2.470000e-107 399.0
58 TraesCS7A01G309900 chr3B 90.268 298 25 3 3955 4249 754990538 754990242 1.920000e-103 387.0
59 TraesCS7A01G309900 chr3B 88.973 263 27 2 405 666 662489091 662488830 1.530000e-84 324.0
60 TraesCS7A01G309900 chr3D 90.722 291 24 2 3962 4249 197997806 197998096 6.900000e-103 385.0
61 TraesCS7A01G309900 chr3D 89.272 261 28 0 406 666 269465759 269465499 1.180000e-85 327.0
62 TraesCS7A01G309900 chr3D 88.258 264 31 0 403 666 200267475 200267738 2.550000e-82 316.0
63 TraesCS7A01G309900 chr3D 92.667 150 11 0 4251 4400 66882051 66882200 2.660000e-52 217.0
64 TraesCS7A01G309900 chr3D 92.000 150 12 0 4251 4400 136759327 136759178 1.240000e-50 211.0
65 TraesCS7A01G309900 chr3D 85.926 135 18 1 3810 3943 601621134 601621268 4.590000e-30 143.0
66 TraesCS7A01G309900 chr1B 89.577 307 27 4 3947 4249 588427101 588427406 6.900000e-103 385.0
67 TraesCS7A01G309900 chr6D 89.615 260 25 2 403 662 38212460 38212717 3.280000e-86 329.0
68 TraesCS7A01G309900 chr6D 90.385 156 15 0 4245 4400 450630211 450630366 5.770000e-49 206.0
69 TraesCS7A01G309900 chr2B 90.650 246 23 0 416 661 135101660 135101415 1.180000e-85 327.0
70 TraesCS7A01G309900 chr4A 88.679 265 28 2 403 667 615435020 615435282 5.490000e-84 322.0
71 TraesCS7A01G309900 chr4A 87.552 241 29 1 2698 2938 708848116 708847877 1.210000e-70 278.0
72 TraesCS7A01G309900 chr4A 92.105 76 6 0 1511 1586 497909027 497908952 1.670000e-19 108.0
73 TraesCS7A01G309900 chrUn 88.506 174 18 2 3772 3943 336577332 336577159 4.460000e-50 209.0
74 TraesCS7A01G309900 chr4B 93.590 78 5 0 1508 1585 121590715 121590792 2.780000e-22 117.0


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 TraesCS7A01G309900 chr7A 438167456 438171855 4399 False 8126.000000 8126 100.000000 1 4400 1 chr7A.!!$F2 4399
1 TraesCS7A01G309900 chr7D 388021605 388024276 2671 False 3755.000000 3755 92.088000 870 3541 1 chr7D.!!$F3 2671
2 TraesCS7A01G309900 chr7B 383502056 383505213 3157 False 1188.100000 2658 88.396333 803 3696 3 chr7B.!!$F2 2893
3 TraesCS7A01G309900 chr7B 403563330 403566477 3147 True 260.000000 420 78.201500 1212 2725 2 chr7B.!!$R1 1513
4 TraesCS7A01G309900 chr7B 408110921 408113781 2860 True 246.000000 390 84.709500 1511 2725 2 chr7B.!!$R4 1214
5 TraesCS7A01G309900 chr7B 407939983 407943167 3184 True 210.666667 420 82.946333 1212 2725 3 chr7B.!!$R3 1513
6 TraesCS7A01G309900 chr7B 403729181 403732324 3143 True 208.666667 407 82.921333 1212 2725 3 chr7B.!!$R2 1513
7 TraesCS7A01G309900 chr5B 674736835 674738651 1816 True 975.500000 1535 89.766500 1894 3039 2 chr5B.!!$R3 1145
8 TraesCS7A01G309900 chr5B 674746101 674746729 628 True 826.000000 826 90.379000 2034 2664 1 chr5B.!!$R2 630
9 TraesCS7A01G309900 chr2D 406696115 406696783 668 False 780.000000 780 87.665000 45 724 1 chr2D.!!$F1 679
10 TraesCS7A01G309900 chr4D 84776560 84779018 2458 True 283.000000 449 87.462000 1511 2724 2 chr4D.!!$R3 1213
11 TraesCS7A01G309900 chr6A 13749320 13749969 649 False 289.333333 427 91.685667 3769 4400 3 chr6A.!!$F1 631

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
35 36 0.184692 TCTTGGTGTTGTGGCCATCA 59.815 50.0 9.72 6.28 34.37 3.07 F
1112 1116 0.178992 CTCATCCTCTCGCCTCTCCT 60.179 60.0 0.00 0.00 0.00 3.69 F
1483 1514 0.098025 TTGATTCCGCCGCGAATTTC 59.902 50.0 15.93 6.21 32.56 2.17 F
3096 5698 1.729586 TGGTTCTTCCTACCACAGCT 58.270 50.0 0.00 0.00 40.65 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1463 0.098728 CGCGGCGGAATCAAAAGAAT 59.901 50.000 15.84 0.00 0.00 2.40 R
2133 4537 1.166531 GGAGCACCAACCTGTGTGTC 61.167 60.000 0.00 0.00 38.52 3.67 R
3249 5852 1.001631 TGATTCCTCCTCGGGCTCA 59.998 57.895 0.00 0.00 0.00 4.26 R
4351 7149 2.789779 GCCCGTATGCAAACATGTTACG 60.790 50.000 19.19 19.19 37.04 3.18 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
30 31 4.782019 TCATATTTCTTGGTGTTGTGGC 57.218 40.909 0.00 0.00 0.00 5.01
32 33 1.786937 ATTTCTTGGTGTTGTGGCCA 58.213 45.000 0.00 0.00 0.00 5.36
33 34 1.786937 TTTCTTGGTGTTGTGGCCAT 58.213 45.000 9.72 0.00 34.37 4.40
34 35 1.327303 TTCTTGGTGTTGTGGCCATC 58.673 50.000 9.72 3.12 34.37 3.51
35 36 0.184692 TCTTGGTGTTGTGGCCATCA 59.815 50.000 9.72 6.28 34.37 3.07
38 39 4.172625 GTGTTGTGGCCATCACCA 57.827 55.556 9.72 4.98 45.48 4.17
41 42 1.067635 GTGTTGTGGCCATCACCAATC 60.068 52.381 9.72 4.29 45.48 2.67
42 43 1.203038 TGTTGTGGCCATCACCAATCT 60.203 47.619 9.72 0.00 45.48 2.40
43 44 2.040947 TGTTGTGGCCATCACCAATCTA 59.959 45.455 9.72 0.00 45.48 1.98
49 50 5.073554 TGTGGCCATCACCAATCTATAATCT 59.926 40.000 9.72 0.00 45.48 2.40
104 105 8.677148 TTCTAATTCTATCAACATACAAGCCC 57.323 34.615 0.00 0.00 0.00 5.19
106 107 8.150945 TCTAATTCTATCAACATACAAGCCCTC 58.849 37.037 0.00 0.00 0.00 4.30
124 125 0.320683 TCCACCTCATCAAGTGTGCG 60.321 55.000 0.00 0.00 31.88 5.34
206 207 4.634184 ATTCTCTCAACATGCAAGCATC 57.366 40.909 4.24 0.00 33.90 3.91
216 217 0.895100 TGCAAGCATCCCACTTCACC 60.895 55.000 0.00 0.00 0.00 4.02
217 218 1.926511 GCAAGCATCCCACTTCACCG 61.927 60.000 0.00 0.00 0.00 4.94
222 223 1.609580 GCATCCCACTTCACCGTACAA 60.610 52.381 0.00 0.00 0.00 2.41
225 226 4.703897 CATCCCACTTCACCGTACAATAT 58.296 43.478 0.00 0.00 0.00 1.28
226 227 4.829872 TCCCACTTCACCGTACAATATT 57.170 40.909 0.00 0.00 0.00 1.28
229 230 6.005198 TCCCACTTCACCGTACAATATTTTT 58.995 36.000 0.00 0.00 0.00 1.94
230 231 7.166851 TCCCACTTCACCGTACAATATTTTTA 58.833 34.615 0.00 0.00 0.00 1.52
268 270 8.764287 GCAAACCATACCAATATGCTTATTTTC 58.236 33.333 2.22 0.00 37.46 2.29
276 278 6.597672 ACCAATATGCTTATTTTCGTCACTGA 59.402 34.615 2.22 0.00 0.00 3.41
289 291 9.817809 ATTTTCGTCACTGAACATATGTAGTAT 57.182 29.630 9.21 0.00 0.00 2.12
340 342 3.056607 CCTAAAGGTTGTGAAATGCCCTG 60.057 47.826 0.00 0.00 0.00 4.45
350 352 4.771577 TGTGAAATGCCCTGATTTACACAT 59.228 37.500 0.00 0.00 33.41 3.21
368 370 8.896320 TTACACATAATGCAAGTACGGAATAT 57.104 30.769 0.00 0.00 0.00 1.28
426 428 9.604626 GATCTTTTATTGCATACTAGTCAATGC 57.395 33.333 19.50 19.50 46.92 3.56
451 453 4.247794 CATGCAATGCACGTTAATTTGG 57.752 40.909 11.23 0.00 43.04 3.28
458 460 6.970043 GCAATGCACGTTAATTTGGAAGTATA 59.030 34.615 0.00 0.00 0.00 1.47
471 473 7.637631 TTTGGAAGTATATTAAGTGCATGCA 57.362 32.000 18.46 18.46 0.00 3.96
580 582 4.318404 GCGCTTGATATTGAAGCAGTCTAC 60.318 45.833 16.44 0.00 45.15 2.59
587 589 3.902261 TTGAAGCAGTCTACGTCGTTA 57.098 42.857 1.78 0.00 0.00 3.18
599 601 5.451662 GTCTACGTCGTTAGATTGACATGAC 59.548 44.000 1.78 0.00 34.78 3.06
602 604 5.946298 ACGTCGTTAGATTGACATGACTTA 58.054 37.500 0.00 0.00 34.78 2.24
623 625 7.458397 ACTTAATGGCCGAGATTAATTGGATA 58.542 34.615 7.09 0.00 0.00 2.59
626 628 5.241403 TGGCCGAGATTAATTGGATATGT 57.759 39.130 0.00 0.00 0.00 2.29
633 635 7.094634 CCGAGATTAATTGGATATGTCCCTTTG 60.095 40.741 5.98 0.00 44.41 2.77
634 636 7.661437 CGAGATTAATTGGATATGTCCCTTTGA 59.339 37.037 5.98 0.00 44.41 2.69
652 654 9.457436 TCCCTTTGAGTCTTTTTATATTGGTAC 57.543 33.333 0.00 0.00 0.00 3.34
741 743 8.625467 ACCTAGTTCTCCTAATTAAATCCTGT 57.375 34.615 0.00 0.00 0.00 4.00
742 744 8.487028 ACCTAGTTCTCCTAATTAAATCCTGTG 58.513 37.037 0.00 0.00 0.00 3.66
743 745 8.487028 CCTAGTTCTCCTAATTAAATCCTGTGT 58.513 37.037 0.00 0.00 0.00 3.72
746 748 9.892130 AGTTCTCCTAATTAAATCCTGTGTAAG 57.108 33.333 0.00 0.00 0.00 2.34
747 749 9.886132 GTTCTCCTAATTAAATCCTGTGTAAGA 57.114 33.333 0.00 0.00 0.00 2.10
749 751 9.268282 TCTCCTAATTAAATCCTGTGTAAGAGT 57.732 33.333 0.00 0.00 0.00 3.24
750 752 9.319143 CTCCTAATTAAATCCTGTGTAAGAGTG 57.681 37.037 0.00 0.00 0.00 3.51
751 753 8.822805 TCCTAATTAAATCCTGTGTAAGAGTGT 58.177 33.333 0.00 0.00 0.00 3.55
752 754 9.099454 CCTAATTAAATCCTGTGTAAGAGTGTC 57.901 37.037 0.00 0.00 0.00 3.67
753 755 9.877178 CTAATTAAATCCTGTGTAAGAGTGTCT 57.123 33.333 0.00 0.00 0.00 3.41
754 756 8.779354 AATTAAATCCTGTGTAAGAGTGTCTC 57.221 34.615 0.00 0.00 0.00 3.36
755 757 7.540474 TTAAATCCTGTGTAAGAGTGTCTCT 57.460 36.000 0.00 0.00 43.37 3.10
757 759 5.652994 ATCCTGTGTAAGAGTGTCTCTTC 57.347 43.478 14.10 8.09 46.42 2.87
758 760 3.827302 TCCTGTGTAAGAGTGTCTCTTCC 59.173 47.826 14.10 5.41 46.42 3.46
759 761 3.829601 CCTGTGTAAGAGTGTCTCTTCCT 59.170 47.826 14.10 0.00 46.42 3.36
760 762 4.282195 CCTGTGTAAGAGTGTCTCTTCCTT 59.718 45.833 14.10 0.00 46.42 3.36
761 763 5.455056 TGTGTAAGAGTGTCTCTTCCTTC 57.545 43.478 14.10 6.27 46.42 3.46
762 764 5.141182 TGTGTAAGAGTGTCTCTTCCTTCT 58.859 41.667 14.10 0.00 46.42 2.85
763 765 6.304624 TGTGTAAGAGTGTCTCTTCCTTCTA 58.695 40.000 14.10 0.00 46.42 2.10
764 766 6.776116 TGTGTAAGAGTGTCTCTTCCTTCTAA 59.224 38.462 14.10 0.00 46.42 2.10
765 767 7.085746 GTGTAAGAGTGTCTCTTCCTTCTAAC 58.914 42.308 14.10 7.16 46.42 2.34
766 768 6.776116 TGTAAGAGTGTCTCTTCCTTCTAACA 59.224 38.462 14.10 9.24 46.42 2.41
767 769 5.715434 AGAGTGTCTCTTCCTTCTAACAC 57.285 43.478 0.00 0.00 37.60 3.32
768 770 5.836358 AAGAGTGTCTCTTCCTTCTAACACT 59.164 40.000 5.71 5.71 46.42 3.55
769 771 5.242838 AGAGTGTCTCTTCCTTCTAACACTG 59.757 44.000 10.38 0.00 45.25 3.66
770 772 5.141182 AGTGTCTCTTCCTTCTAACACTGA 58.859 41.667 5.25 0.00 44.02 3.41
771 773 5.598830 AGTGTCTCTTCCTTCTAACACTGAA 59.401 40.000 5.25 0.00 44.02 3.02
772 774 5.692654 GTGTCTCTTCCTTCTAACACTGAAC 59.307 44.000 0.00 0.00 35.35 3.18
773 775 4.918583 GTCTCTTCCTTCTAACACTGAACG 59.081 45.833 0.00 0.00 0.00 3.95
774 776 3.650139 TCTTCCTTCTAACACTGAACGC 58.350 45.455 0.00 0.00 0.00 4.84
775 777 2.450609 TCCTTCTAACACTGAACGCC 57.549 50.000 0.00 0.00 0.00 5.68
776 778 1.689813 TCCTTCTAACACTGAACGCCA 59.310 47.619 0.00 0.00 0.00 5.69
777 779 2.103432 TCCTTCTAACACTGAACGCCAA 59.897 45.455 0.00 0.00 0.00 4.52
778 780 2.875933 CCTTCTAACACTGAACGCCAAA 59.124 45.455 0.00 0.00 0.00 3.28
779 781 3.502211 CCTTCTAACACTGAACGCCAAAT 59.498 43.478 0.00 0.00 0.00 2.32
780 782 4.466828 CTTCTAACACTGAACGCCAAATG 58.533 43.478 0.00 0.00 0.00 2.32
781 783 2.225491 TCTAACACTGAACGCCAAATGC 59.775 45.455 0.00 0.00 0.00 3.56
782 784 0.743688 AACACTGAACGCCAAATGCA 59.256 45.000 0.00 0.00 41.33 3.96
783 785 0.961019 ACACTGAACGCCAAATGCAT 59.039 45.000 0.00 0.00 41.33 3.96
784 786 1.068333 ACACTGAACGCCAAATGCATC 60.068 47.619 0.00 0.00 41.33 3.91
785 787 1.200716 CACTGAACGCCAAATGCATCT 59.799 47.619 0.00 0.00 41.33 2.90
786 788 1.470098 ACTGAACGCCAAATGCATCTC 59.530 47.619 0.00 0.00 41.33 2.75
787 789 0.447406 TGAACGCCAAATGCATCTCG 59.553 50.000 0.00 4.00 41.33 4.04
788 790 0.863119 GAACGCCAAATGCATCTCGC 60.863 55.000 0.00 0.28 41.33 5.03
789 791 1.308069 AACGCCAAATGCATCTCGCT 61.308 50.000 0.00 0.00 43.06 4.93
790 792 0.461870 ACGCCAAATGCATCTCGCTA 60.462 50.000 0.00 0.00 43.06 4.26
791 793 0.234106 CGCCAAATGCATCTCGCTAG 59.766 55.000 0.00 0.00 43.06 3.42
792 794 1.303309 GCCAAATGCATCTCGCTAGT 58.697 50.000 0.00 0.00 43.06 2.57
793 795 1.672881 GCCAAATGCATCTCGCTAGTT 59.327 47.619 0.00 0.00 43.06 2.24
794 796 2.098117 GCCAAATGCATCTCGCTAGTTT 59.902 45.455 0.00 0.00 43.06 2.66
795 797 3.428045 GCCAAATGCATCTCGCTAGTTTT 60.428 43.478 0.00 0.00 43.06 2.43
796 798 4.737054 CCAAATGCATCTCGCTAGTTTTT 58.263 39.130 0.00 0.00 43.06 1.94
832 834 3.268023 AGGGGTAAATTCTTCTCGCTG 57.732 47.619 0.00 0.00 0.00 5.18
833 835 2.572104 AGGGGTAAATTCTTCTCGCTGT 59.428 45.455 0.00 0.00 0.00 4.40
834 836 3.009143 AGGGGTAAATTCTTCTCGCTGTT 59.991 43.478 0.00 0.00 0.00 3.16
878 882 4.933330 TCGCTAGTAAGGCAGAATAGTTG 58.067 43.478 0.00 0.00 0.00 3.16
932 936 2.617308 CCATCCATTCTGTAAGCAGCTG 59.383 50.000 10.11 10.11 42.29 4.24
978 982 2.196997 ATCGCAACCCTAGCCAAGCA 62.197 55.000 0.00 0.00 0.00 3.91
980 984 2.690778 GCAACCCTAGCCAAGCACG 61.691 63.158 0.00 0.00 0.00 5.34
986 990 1.153289 CTAGCCAAGCACGAGCCAT 60.153 57.895 0.00 0.00 43.56 4.40
1019 1023 4.398319 CAGCTATAAATACCCAACCCCTG 58.602 47.826 0.00 0.00 0.00 4.45
1111 1115 1.178534 CCTCATCCTCTCGCCTCTCC 61.179 65.000 0.00 0.00 0.00 3.71
1112 1116 0.178992 CTCATCCTCTCGCCTCTCCT 60.179 60.000 0.00 0.00 0.00 3.69
1115 1119 1.360393 ATCCTCTCGCCTCTCCTCCT 61.360 60.000 0.00 0.00 0.00 3.69
1117 1121 1.225983 CTCTCGCCTCTCCTCCTCA 59.774 63.158 0.00 0.00 0.00 3.86
1129 1133 5.046304 CCTCTCCTCCTCAACACAGATTTAA 60.046 44.000 0.00 0.00 0.00 1.52
1138 1142 8.593679 TCCTCAACACAGATTTAACAATCTAGA 58.406 33.333 0.00 0.00 46.44 2.43
1155 1159 3.753070 GAGTTAGCGCCTCCGTCCG 62.753 68.421 2.29 0.00 36.67 4.79
1169 1173 1.062845 GTCCGTCTCGTAGCTGCTC 59.937 63.158 4.91 0.00 0.00 4.26
1170 1174 1.376812 TCCGTCTCGTAGCTGCTCA 60.377 57.895 4.91 0.00 0.00 4.26
1391 1395 1.666011 GTGCACTCGGAGAAGACCA 59.334 57.895 12.86 0.00 34.09 4.02
1483 1514 0.098025 TTGATTCCGCCGCGAATTTC 59.902 50.000 15.93 6.21 32.56 2.17
1504 1535 3.056821 TCGTGCTGAAATATATCCTCCGG 60.057 47.826 0.00 0.00 0.00 5.14
1506 1537 4.246458 GTGCTGAAATATATCCTCCGGTC 58.754 47.826 0.00 0.00 0.00 4.79
1612 1643 2.446848 CGGATCTGCCATGTCCCCT 61.447 63.158 0.00 0.00 35.94 4.79
1688 2759 7.122138 AGAGATATATCCTACGTCCGTGATA 57.878 40.000 9.18 2.82 0.00 2.15
1760 2861 4.553330 ATTCCTGTATTTGACGACACCT 57.447 40.909 0.00 0.00 0.00 4.00
1837 3123 4.094739 TGAATCAGTATGTCGCACAAATGG 59.905 41.667 0.00 0.00 37.40 3.16
1848 3680 5.297278 TGTCGCACAAATGGTAGTTAAGTTT 59.703 36.000 0.00 0.00 0.00 2.66
1849 3681 5.623673 GTCGCACAAATGGTAGTTAAGTTTG 59.376 40.000 0.00 0.00 36.23 2.93
1867 3700 6.991485 AGTTTGACAAATGTTAATGAAGCG 57.009 33.333 3.49 0.00 0.00 4.68
1869 3702 5.697473 TTGACAAATGTTAATGAAGCGGA 57.303 34.783 0.00 0.00 0.00 5.54
1877 3710 4.075682 TGTTAATGAAGCGGAACCATTGA 58.924 39.130 0.00 0.00 33.21 2.57
1938 4338 5.161358 GTGCAATTTAGTTGTTTCCTAGCC 58.839 41.667 0.00 0.00 40.07 3.93
1953 4353 5.276461 TCCTAGCCACAAGTATGTATGTG 57.724 43.478 0.00 0.00 45.06 3.21
2128 4531 7.173907 ACATCTGAGGTTAATTCTTGTCTTGTG 59.826 37.037 0.00 0.00 0.00 3.33
2133 4537 7.973388 TGAGGTTAATTCTTGTCTTGTGTTTTG 59.027 33.333 0.00 0.00 0.00 2.44
2293 4740 6.772770 TGATGCTTTTGTTTCAATCACATG 57.227 33.333 0.00 0.00 0.00 3.21
2298 4745 8.659925 TGCTTTTGTTTCAATCACATGTTATT 57.340 26.923 0.00 0.00 0.00 1.40
2390 4852 5.307196 GGAAATTACTATCCCAGTGGAGCTA 59.693 44.000 11.95 0.00 46.08 3.32
2399 4861 3.587061 TCCCAGTGGAGCTAATCAAGAAA 59.413 43.478 11.95 0.00 35.03 2.52
2558 5020 2.158623 AGACCTGATGGACAAGTTTGCA 60.159 45.455 0.00 0.00 37.04 4.08
2810 5273 4.341806 TGTCTTGAACAATGGCATGAACTT 59.658 37.500 0.00 0.00 34.03 2.66
2815 5281 4.341806 TGAACAATGGCATGAACTTTCTGT 59.658 37.500 0.00 0.00 0.00 3.41
2855 5321 5.521735 GTCATGTGTTGAGCTACTTATCAGG 59.478 44.000 0.00 0.00 34.17 3.86
2894 5481 8.472007 TTTTCTAACCAATTCTGGAGCTTAAA 57.528 30.769 0.00 0.00 46.92 1.52
2925 5513 9.120538 GATATTTTTGGATTGTGTTAGCCTCTA 57.879 33.333 0.00 0.00 0.00 2.43
2926 5514 7.775053 ATTTTTGGATTGTGTTAGCCTCTAA 57.225 32.000 0.00 0.00 0.00 2.10
2927 5515 7.775053 TTTTTGGATTGTGTTAGCCTCTAAT 57.225 32.000 0.00 0.00 0.00 1.73
2948 5537 8.832735 TCTAATTGTCCCCTTAGTGTAATCTTT 58.167 33.333 0.00 0.00 0.00 2.52
2962 5551 7.220030 AGTGTAATCTTTCAGTGTGTGAGATT 58.780 34.615 13.38 13.38 36.21 2.40
3007 5609 7.038088 TGGTATAATACATGACATGCCATCTCT 60.038 37.037 15.49 0.00 29.55 3.10
3044 5646 8.058667 TGTTTCATCATATTCATGAGCAACTT 57.941 30.769 0.00 0.00 44.30 2.66
3071 5673 6.878317 TCATTGTTAGCTAAGCTAGTCATGT 58.122 36.000 6.38 0.00 42.34 3.21
3074 5676 6.280855 TGTTAGCTAAGCTAGTCATGTTCA 57.719 37.500 6.38 0.00 42.34 3.18
3090 5692 4.015872 TGTTCACATGGTTCTTCCTACC 57.984 45.455 0.00 0.00 37.07 3.18
3096 5698 1.729586 TGGTTCTTCCTACCACAGCT 58.270 50.000 0.00 0.00 40.65 4.24
3165 5768 1.832167 TTTTGCTGTGCAGGACCCC 60.832 57.895 1.11 0.00 40.61 4.95
3204 5807 4.411981 CCTGCTGCTGCTGCCTCT 62.412 66.667 25.44 0.00 40.48 3.69
3249 5852 3.383223 CAAGGAGGAGGAGAAGAAGGAT 58.617 50.000 0.00 0.00 0.00 3.24
3315 5918 1.201647 GACGACTAAGCTGTGTGCCTA 59.798 52.381 0.00 0.00 44.23 3.93
3316 5919 1.825474 ACGACTAAGCTGTGTGCCTAT 59.175 47.619 0.00 0.00 44.23 2.57
3335 5938 2.396590 TCTTCATAAAGCCGTGTCCC 57.603 50.000 0.00 0.00 32.18 4.46
3338 5941 0.322322 TCATAAAGCCGTGTCCCGTT 59.678 50.000 0.00 0.00 33.66 4.44
3383 5988 9.052759 TGAACACTAAAGTTTTTCAGTCCTATC 57.947 33.333 0.00 0.00 0.00 2.08
3474 6079 9.208022 TCATGCACTTAGTTACTTATATGCATC 57.792 33.333 17.19 0.00 46.67 3.91
3475 6080 9.212641 CATGCACTTAGTTACTTATATGCATCT 57.787 33.333 17.19 0.00 46.67 2.90
3494 6100 2.029200 TCTCTCTGCTTGTGCTTCTCTG 60.029 50.000 0.00 0.00 40.48 3.35
3495 6101 0.797542 CTCTGCTTGTGCTTCTCTGC 59.202 55.000 0.00 0.00 40.48 4.26
3497 6103 0.517755 CTGCTTGTGCTTCTCTGCTG 59.482 55.000 0.00 0.00 40.48 4.41
3499 6105 0.237761 GCTTGTGCTTCTCTGCTGTG 59.762 55.000 0.00 0.00 36.03 3.66
3507 6124 3.181466 TGCTTCTCTGCTGTGTTTCACTA 60.181 43.478 1.72 0.00 35.11 2.74
3508 6125 3.809832 GCTTCTCTGCTGTGTTTCACTAA 59.190 43.478 1.72 0.00 35.11 2.24
3513 6130 6.578944 TCTCTGCTGTGTTTCACTAAGTTAA 58.421 36.000 1.72 0.00 35.11 2.01
3548 6233 5.036737 GCTTGTTTATCGATGTTTGGGATG 58.963 41.667 8.54 0.00 0.00 3.51
3553 6238 0.617935 TCGATGTTTGGGATGGAGCA 59.382 50.000 0.00 0.00 0.00 4.26
3566 6251 1.675641 GGAGCACTGATTTGGCCGT 60.676 57.895 0.00 0.00 0.00 5.68
3573 6258 0.457035 CTGATTTGGCCGTTGGATGG 59.543 55.000 0.00 0.00 0.00 3.51
3579 6264 2.408835 GCCGTTGGATGGAATGCG 59.591 61.111 0.00 0.00 37.56 4.73
3581 6266 2.114670 CCGTTGGATGGAATGCGCT 61.115 57.895 9.73 0.00 37.56 5.92
3582 6267 1.656818 CCGTTGGATGGAATGCGCTT 61.657 55.000 9.73 0.00 37.56 4.68
3585 6270 2.033299 CGTTGGATGGAATGCGCTTATT 59.967 45.455 9.73 0.00 37.56 1.40
3586 6271 3.489059 CGTTGGATGGAATGCGCTTATTT 60.489 43.478 9.73 0.00 37.56 1.40
3589 6274 2.796593 GGATGGAATGCGCTTATTTTGC 59.203 45.455 9.73 0.67 0.00 3.68
3590 6275 2.292103 TGGAATGCGCTTATTTTGCC 57.708 45.000 9.73 0.00 0.00 4.52
3592 6277 1.202245 GGAATGCGCTTATTTTGCCGA 60.202 47.619 9.73 0.00 0.00 5.54
3595 6347 1.090728 TGCGCTTATTTTGCCGATGA 58.909 45.000 9.73 0.00 0.00 2.92
3597 6349 1.202132 GCGCTTATTTTGCCGATGACA 60.202 47.619 0.00 0.00 0.00 3.58
3607 6359 2.597455 TGCCGATGACATCAGATCCTA 58.403 47.619 15.58 0.00 0.00 2.94
3608 6360 2.560105 TGCCGATGACATCAGATCCTAG 59.440 50.000 15.58 0.00 0.00 3.02
3609 6361 2.673610 GCCGATGACATCAGATCCTAGC 60.674 54.545 15.58 3.19 0.00 3.42
3613 6365 1.611006 TGACATCAGATCCTAGCGAGC 59.389 52.381 0.00 0.00 0.00 5.03
3617 6369 0.886938 TCAGATCCTAGCGAGCTCGG 60.887 60.000 35.10 19.74 34.05 4.63
3637 6389 3.157252 GCCAGCCTCCGGATCAGA 61.157 66.667 3.57 0.00 0.00 3.27
3639 6391 2.049627 GCCAGCCTCCGGATCAGATT 62.050 60.000 3.57 0.00 0.00 2.40
3653 6405 2.672996 GATTGCACTGGGCCGTGT 60.673 61.111 22.92 12.16 43.89 4.49
3696 6448 4.383861 CTGGGTGCTGCTGCTCGA 62.384 66.667 17.00 5.73 40.48 4.04
3697 6449 4.383861 TGGGTGCTGCTGCTCGAG 62.384 66.667 17.00 8.45 40.48 4.04
3717 6469 4.389576 GGTCGCGGCTTGTGCTTG 62.390 66.667 11.94 0.00 39.59 4.01
3735 6487 4.986531 CGCGCGTTGACGGTTGTG 62.987 66.667 24.19 0.00 40.23 3.33
3736 6488 3.932313 GCGCGTTGACGGTTGTGT 61.932 61.111 8.43 0.00 40.23 3.72
3737 6489 2.053465 CGCGTTGACGGTTGTGTG 60.053 61.111 0.00 0.00 40.23 3.82
3738 6490 2.326550 GCGTTGACGGTTGTGTGG 59.673 61.111 5.62 0.00 40.23 4.17
3739 6491 3.018973 CGTTGACGGTTGTGTGGG 58.981 61.111 0.00 0.00 35.37 4.61
3740 6492 2.539338 CGTTGACGGTTGTGTGGGG 61.539 63.158 0.00 0.00 35.37 4.96
3741 6493 1.452470 GTTGACGGTTGTGTGGGGT 60.452 57.895 0.00 0.00 0.00 4.95
3742 6494 1.153127 TTGACGGTTGTGTGGGGTC 60.153 57.895 0.00 0.00 0.00 4.46
3743 6495 1.911702 TTGACGGTTGTGTGGGGTCA 61.912 55.000 0.00 0.00 35.97 4.02
3744 6496 1.597027 GACGGTTGTGTGGGGTCAG 60.597 63.158 0.00 0.00 0.00 3.51
3745 6497 2.319890 GACGGTTGTGTGGGGTCAGT 62.320 60.000 0.00 0.00 0.00 3.41
3746 6498 1.597027 CGGTTGTGTGGGGTCAGTC 60.597 63.158 0.00 0.00 0.00 3.51
3747 6499 1.228154 GGTTGTGTGGGGTCAGTCC 60.228 63.158 0.00 0.00 0.00 3.85
3748 6500 1.705997 GGTTGTGTGGGGTCAGTCCT 61.706 60.000 0.00 0.00 36.25 3.85
3749 6501 0.535102 GTTGTGTGGGGTCAGTCCTG 60.535 60.000 0.00 0.00 36.25 3.86
3750 6502 2.032681 GTGTGGGGTCAGTCCTGC 59.967 66.667 0.00 0.00 36.25 4.85
3751 6503 2.447572 TGTGGGGTCAGTCCTGCA 60.448 61.111 0.00 0.00 36.25 4.41
3752 6504 2.032681 GTGGGGTCAGTCCTGCAC 59.967 66.667 0.00 0.00 36.25 4.57
3753 6505 2.447572 TGGGGTCAGTCCTGCACA 60.448 61.111 0.00 0.00 36.25 4.57
3754 6506 2.348998 GGGGTCAGTCCTGCACAG 59.651 66.667 0.00 0.00 36.25 3.66
3767 6519 4.320456 CACAGGCAGGTCGCTGGT 62.320 66.667 0.00 0.00 41.91 4.00
3770 6522 1.741770 CAGGCAGGTCGCTGGTAAC 60.742 63.158 0.00 0.00 41.91 2.50
3775 6527 2.125269 GGTCGCTGGTAACCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
3796 6548 5.934625 GCATACAACATTACATAGGGAGGAG 59.065 44.000 0.00 0.00 0.00 3.69
3897 6649 4.601857 TGGAATAGTCTCCTCCAAAAACCT 59.398 41.667 1.14 0.00 36.30 3.50
3902 6654 2.623416 GTCTCCTCCAAAAACCTTGTGG 59.377 50.000 0.00 0.00 39.83 4.17
3904 6656 1.047801 CCTCCAAAAACCTTGTGGGG 58.952 55.000 0.00 0.00 40.03 4.96
3917 6669 4.045334 ACCTTGTGGGGAAAATATGAGGAA 59.955 41.667 0.00 0.00 40.03 3.36
3920 6672 6.838612 CCTTGTGGGGAAAATATGAGGAATAA 59.161 38.462 0.00 0.00 0.00 1.40
3924 6676 8.506921 TGTGGGGAAAATATGAGGAATAATGTA 58.493 33.333 0.00 0.00 0.00 2.29
3925 6677 9.014297 GTGGGGAAAATATGAGGAATAATGTAG 57.986 37.037 0.00 0.00 0.00 2.74
3926 6678 8.170061 TGGGGAAAATATGAGGAATAATGTAGG 58.830 37.037 0.00 0.00 0.00 3.18
3927 6679 8.170730 GGGGAAAATATGAGGAATAATGTAGGT 58.829 37.037 0.00 0.00 0.00 3.08
3987 6739 3.593442 AACTCATTCAAACCCTGTGGA 57.407 42.857 0.00 0.00 34.81 4.02
4094 6846 8.780249 GGGCAATAAATATGTCGTGTATACTTT 58.220 33.333 4.17 0.00 0.00 2.66
4096 6848 9.512287 GCAATAAATATGTCGTGTATACTTTCG 57.488 33.333 4.17 6.85 0.00 3.46
4108 6860 4.934602 TGTATACTTTCGTAAAAACCCCGG 59.065 41.667 4.17 0.00 0.00 5.73
4198 6952 9.436957 GAATCTGTAAAGTAAACTCATCAAGGA 57.563 33.333 0.00 0.00 0.00 3.36
4248 7002 7.884877 TGAACATGAACAATTCAGGAAGATACT 59.115 33.333 9.95 0.00 43.68 2.12
4249 7003 8.641498 AACATGAACAATTCAGGAAGATACTT 57.359 30.769 9.95 0.00 43.68 2.24
4269 7067 5.650543 ACTTTGAACACATTTCTGGAACAC 58.349 37.500 0.00 0.00 0.00 3.32
4287 7085 2.224818 ACACAGAAGTCGGTAGAGACCT 60.225 50.000 0.00 0.00 44.46 3.85
4304 7102 6.719301 AGAGACCTGATGAACAAATCAATCT 58.281 36.000 0.00 0.00 42.54 2.40
4367 7165 7.975750 TGCTTATTACGTAACATGTTTGCATA 58.024 30.769 17.78 7.46 33.30 3.14
4380 7178 2.720659 TGCATACGGGCAACACAAA 58.279 47.368 0.00 0.00 41.65 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.906867 CCACAACACCAAGAAATATGAAGATAT 58.093 33.333 0.00 0.00 0.00 1.63
5 6 6.350445 GCCACAACACCAAGAAATATGAAGAT 60.350 38.462 0.00 0.00 0.00 2.40
6 7 5.048083 GCCACAACACCAAGAAATATGAAGA 60.048 40.000 0.00 0.00 0.00 2.87
7 8 5.163513 GCCACAACACCAAGAAATATGAAG 58.836 41.667 0.00 0.00 0.00 3.02
8 9 4.021544 GGCCACAACACCAAGAAATATGAA 60.022 41.667 0.00 0.00 0.00 2.57
10 11 3.257873 TGGCCACAACACCAAGAAATATG 59.742 43.478 0.00 0.00 31.46 1.78
11 12 3.505386 TGGCCACAACACCAAGAAATAT 58.495 40.909 0.00 0.00 31.46 1.28
12 13 2.950781 TGGCCACAACACCAAGAAATA 58.049 42.857 0.00 0.00 31.46 1.40
13 14 1.786937 TGGCCACAACACCAAGAAAT 58.213 45.000 0.00 0.00 31.46 2.17
14 15 1.686052 GATGGCCACAACACCAAGAAA 59.314 47.619 8.16 0.00 39.96 2.52
15 16 1.327303 GATGGCCACAACACCAAGAA 58.673 50.000 8.16 0.00 39.96 2.52
16 17 0.184692 TGATGGCCACAACACCAAGA 59.815 50.000 8.16 0.00 39.96 3.02
17 18 0.314935 GTGATGGCCACAACACCAAG 59.685 55.000 21.50 0.00 42.56 3.61
18 19 2.424474 GTGATGGCCACAACACCAA 58.576 52.632 21.50 0.00 42.56 3.67
19 20 4.172625 GTGATGGCCACAACACCA 57.827 55.556 21.50 6.90 42.56 4.17
26 27 5.564550 AGATTATAGATTGGTGATGGCCAC 58.435 41.667 8.16 2.36 44.95 5.01
27 28 5.848286 AGATTATAGATTGGTGATGGCCA 57.152 39.130 8.56 8.56 36.62 5.36
78 79 9.120538 GGGCTTGTATGTTGATAGAATTAGAAA 57.879 33.333 0.00 0.00 0.00 2.52
81 82 7.389053 GGAGGGCTTGTATGTTGATAGAATTAG 59.611 40.741 0.00 0.00 0.00 1.73
89 90 2.357154 GGTGGAGGGCTTGTATGTTGAT 60.357 50.000 0.00 0.00 0.00 2.57
97 98 0.842030 TGATGAGGTGGAGGGCTTGT 60.842 55.000 0.00 0.00 0.00 3.16
104 105 1.446907 GCACACTTGATGAGGTGGAG 58.553 55.000 0.00 0.00 37.72 3.86
106 107 0.320683 TCGCACACTTGATGAGGTGG 60.321 55.000 0.00 0.00 37.72 4.61
124 125 7.502120 AATATTGTTAGTGGATGCTGATGTC 57.498 36.000 0.00 0.00 0.00 3.06
185 186 3.380637 GGATGCTTGCATGTTGAGAGAAT 59.619 43.478 13.18 0.00 0.00 2.40
206 207 5.890424 AAAATATTGTACGGTGAAGTGGG 57.110 39.130 0.00 0.00 0.00 4.61
216 217 8.967218 CATGGGCTGAAATAAAAATATTGTACG 58.033 33.333 0.00 0.00 0.00 3.67
217 218 8.764287 GCATGGGCTGAAATAAAAATATTGTAC 58.236 33.333 0.00 0.00 36.96 2.90
222 223 7.282901 GGTTTGCATGGGCTGAAATAAAAATAT 59.717 33.333 0.00 0.00 41.91 1.28
225 226 4.759183 GGTTTGCATGGGCTGAAATAAAAA 59.241 37.500 0.00 0.00 41.91 1.94
226 227 4.202398 TGGTTTGCATGGGCTGAAATAAAA 60.202 37.500 0.00 0.00 41.91 1.52
229 230 2.533916 TGGTTTGCATGGGCTGAAATA 58.466 42.857 0.00 0.00 41.91 1.40
230 231 1.350071 TGGTTTGCATGGGCTGAAAT 58.650 45.000 0.00 0.00 41.91 2.17
312 314 6.379386 GCATTTCACAACCTTTAGGAAGTAC 58.621 40.000 2.06 0.00 38.94 2.73
340 342 7.241663 TCCGTACTTGCATTATGTGTAAATC 57.758 36.000 0.00 0.00 31.83 2.17
409 411 4.749976 TGTACGCATTGACTAGTATGCAA 58.250 39.130 23.76 13.01 45.73 4.08
520 522 5.631512 GCGTGTAGTTAATTTCATGCCAAAA 59.368 36.000 9.69 0.00 37.00 2.44
525 527 6.192137 CGTTTAGCGTGTAGTTAATTTCATGC 59.808 38.462 12.08 12.08 41.37 4.06
559 561 4.806247 ACGTAGACTGCTTCAATATCAAGC 59.194 41.667 10.98 10.98 45.59 4.01
562 564 4.095932 ACGACGTAGACTGCTTCAATATCA 59.904 41.667 0.00 0.00 0.00 2.15
565 567 4.430137 AACGACGTAGACTGCTTCAATA 57.570 40.909 0.00 0.00 0.00 1.90
580 582 6.864560 TTAAGTCATGTCAATCTAACGACG 57.135 37.500 0.00 0.00 34.78 5.12
587 589 3.879295 CGGCCATTAAGTCATGTCAATCT 59.121 43.478 2.24 0.00 0.00 2.40
599 601 6.824305 ATCCAATTAATCTCGGCCATTAAG 57.176 37.500 2.24 0.00 30.94 1.85
602 604 6.248433 ACATATCCAATTAATCTCGGCCATT 58.752 36.000 2.24 0.00 0.00 3.16
623 625 8.971073 CCAATATAAAAAGACTCAAAGGGACAT 58.029 33.333 0.00 0.00 0.00 3.06
626 628 9.457436 GTACCAATATAAAAAGACTCAAAGGGA 57.543 33.333 0.00 0.00 0.00 4.20
683 685 3.181505 CGCGTTGCTGTGGGAATATAAAA 60.182 43.478 0.00 0.00 0.00 1.52
688 690 2.395360 GCGCGTTGCTGTGGGAATA 61.395 57.895 8.43 0.00 41.73 1.75
695 697 4.973055 TTACCCGCGCGTTGCTGT 62.973 61.111 29.95 18.43 43.27 4.40
698 700 0.858548 GTAATTTACCCGCGCGTTGC 60.859 55.000 29.95 14.71 41.47 4.17
724 726 9.319143 CACTCTTACACAGGATTTAATTAGGAG 57.681 37.037 0.00 0.00 0.00 3.69
725 727 8.822805 ACACTCTTACACAGGATTTAATTAGGA 58.177 33.333 0.00 0.00 0.00 2.94
726 728 9.099454 GACACTCTTACACAGGATTTAATTAGG 57.901 37.037 0.00 0.00 0.00 2.69
727 729 9.877178 AGACACTCTTACACAGGATTTAATTAG 57.123 33.333 0.00 0.00 0.00 1.73
728 730 9.871238 GAGACACTCTTACACAGGATTTAATTA 57.129 33.333 0.00 0.00 0.00 1.40
729 731 8.598041 AGAGACACTCTTACACAGGATTTAATT 58.402 33.333 0.00 0.00 37.60 1.40
730 732 8.140112 AGAGACACTCTTACACAGGATTTAAT 57.860 34.615 0.00 0.00 37.60 1.40
731 733 7.540474 AGAGACACTCTTACACAGGATTTAA 57.460 36.000 0.00 0.00 37.60 1.52
745 747 5.242838 CAGTGTTAGAAGGAAGAGACACTCT 59.757 44.000 4.15 0.00 44.02 3.24
746 748 5.241949 TCAGTGTTAGAAGGAAGAGACACTC 59.758 44.000 4.15 0.00 44.02 3.51
747 749 5.141182 TCAGTGTTAGAAGGAAGAGACACT 58.859 41.667 1.44 1.44 46.01 3.55
748 750 5.455056 TCAGTGTTAGAAGGAAGAGACAC 57.545 43.478 0.00 0.00 38.06 3.67
749 751 5.507482 CGTTCAGTGTTAGAAGGAAGAGACA 60.507 44.000 0.00 0.00 33.89 3.41
750 752 4.918583 CGTTCAGTGTTAGAAGGAAGAGAC 59.081 45.833 0.00 0.00 33.89 3.36
751 753 4.558898 GCGTTCAGTGTTAGAAGGAAGAGA 60.559 45.833 0.00 0.00 33.89 3.10
752 754 3.675698 GCGTTCAGTGTTAGAAGGAAGAG 59.324 47.826 0.00 0.00 33.89 2.85
753 755 3.554337 GGCGTTCAGTGTTAGAAGGAAGA 60.554 47.826 0.00 0.00 33.89 2.87
754 756 2.737252 GGCGTTCAGTGTTAGAAGGAAG 59.263 50.000 0.00 0.00 33.89 3.46
755 757 2.103432 TGGCGTTCAGTGTTAGAAGGAA 59.897 45.455 0.00 0.00 33.89 3.36
756 758 1.689813 TGGCGTTCAGTGTTAGAAGGA 59.310 47.619 0.00 0.00 33.89 3.36
757 759 2.163818 TGGCGTTCAGTGTTAGAAGG 57.836 50.000 0.00 0.00 34.84 3.46
758 760 4.466828 CATTTGGCGTTCAGTGTTAGAAG 58.533 43.478 0.00 0.00 0.00 2.85
759 761 3.304391 GCATTTGGCGTTCAGTGTTAGAA 60.304 43.478 0.00 0.00 0.00 2.10
760 762 2.225491 GCATTTGGCGTTCAGTGTTAGA 59.775 45.455 0.00 0.00 0.00 2.10
761 763 2.584791 GCATTTGGCGTTCAGTGTTAG 58.415 47.619 0.00 0.00 0.00 2.34
762 764 2.697431 GCATTTGGCGTTCAGTGTTA 57.303 45.000 0.00 0.00 0.00 2.41
763 765 3.568093 GCATTTGGCGTTCAGTGTT 57.432 47.368 0.00 0.00 0.00 3.32
806 808 6.890268 AGCGAGAAGAATTTACCCCTAAAAAT 59.110 34.615 0.00 0.00 0.00 1.82
811 813 3.773119 ACAGCGAGAAGAATTTACCCCTA 59.227 43.478 0.00 0.00 0.00 3.53
814 816 5.372547 AAAACAGCGAGAAGAATTTACCC 57.627 39.130 0.00 0.00 0.00 3.69
954 958 2.182842 GCTAGGGTTGCGATGCTGG 61.183 63.158 0.00 0.00 0.00 4.85
978 982 2.202866 CCAGTGTCCTATGGCTCGT 58.797 57.895 0.00 0.00 0.00 4.18
986 990 5.011738 GGTATTTATAGCTGCCAGTGTCCTA 59.988 44.000 0.00 0.00 0.00 2.94
1019 1023 2.180432 AACCTAGGGTTTCGTTGCTC 57.820 50.000 14.81 0.00 44.33 4.26
1129 1133 2.362717 GGAGGCGCTAACTCTAGATTGT 59.637 50.000 7.64 0.00 35.34 2.71
1138 1142 3.823330 CGGACGGAGGCGCTAACT 61.823 66.667 7.64 0.00 0.00 2.24
1155 1159 1.268999 CCATCTGAGCAGCTACGAGAC 60.269 57.143 0.00 0.00 0.00 3.36
1169 1173 1.539929 GGTCCTCTTGATCGCCATCTG 60.540 57.143 0.00 0.00 0.00 2.90
1170 1174 0.755686 GGTCCTCTTGATCGCCATCT 59.244 55.000 0.00 0.00 0.00 2.90
1457 1462 1.827578 GCGGCGGAATCAAAAGAATC 58.172 50.000 9.78 0.00 0.00 2.52
1458 1463 0.098728 CGCGGCGGAATCAAAAGAAT 59.901 50.000 15.84 0.00 0.00 2.40
1504 1535 1.673923 GGCCAACGTTACCCTACAGAC 60.674 57.143 0.00 0.00 0.00 3.51
1506 1537 0.611714 AGGCCAACGTTACCCTACAG 59.388 55.000 15.13 0.00 0.00 2.74
1633 1768 3.565482 CGCACTATAAACCAGCAATCCAT 59.435 43.478 0.00 0.00 0.00 3.41
1688 2759 9.464714 CTACATTTCTAGCGATACATGTTACTT 57.535 33.333 2.30 0.00 0.00 2.24
1809 2910 4.934602 TGTGCGACATACTGATTCATCAAA 59.065 37.500 0.00 0.00 36.18 2.69
1848 3680 5.457140 GTTCCGCTTCATTAACATTTGTCA 58.543 37.500 0.00 0.00 0.00 3.58
1849 3681 4.857037 GGTTCCGCTTCATTAACATTTGTC 59.143 41.667 0.00 0.00 0.00 3.18
1867 3700 8.378172 TGAGTCGATAATAATTCAATGGTTCC 57.622 34.615 0.00 0.00 0.00 3.62
1869 3702 9.613428 TTCTGAGTCGATAATAATTCAATGGTT 57.387 29.630 0.00 0.00 0.00 3.67
1877 3710 6.148480 GGCAGCATTCTGAGTCGATAATAATT 59.852 38.462 0.00 0.00 42.95 1.40
1897 3730 2.518949 CACACATAAACGAATGGCAGC 58.481 47.619 0.00 0.00 0.00 5.25
1907 4307 8.272866 GGAAACAACTAAATTGCACACATAAAC 58.727 33.333 0.00 0.00 42.62 2.01
1938 4338 7.672983 AGGAACTTTCACATACATACTTGTG 57.327 36.000 0.00 0.00 39.61 3.33
2128 4531 2.874849 CACCAACCTGTGTGTCAAAAC 58.125 47.619 0.00 0.00 0.00 2.43
2133 4537 1.166531 GGAGCACCAACCTGTGTGTC 61.167 60.000 0.00 0.00 38.52 3.67
2255 4702 7.275560 ACAAAAGCATCAACTGAAAAGTGTTAC 59.724 33.333 0.00 0.00 0.00 2.50
2298 4745 8.500753 ACAAGACAACACAATTAGAACTTGTA 57.499 30.769 0.00 0.00 41.84 2.41
2310 4757 4.013728 AGCACCTAAACAAGACAACACAA 58.986 39.130 0.00 0.00 0.00 3.33
2390 4852 3.891366 CCACCTTGTCACCTTTCTTGATT 59.109 43.478 0.00 0.00 0.00 2.57
2399 4861 2.529744 GGAGCCCACCTTGTCACCT 61.530 63.158 0.00 0.00 0.00 4.00
2558 5020 5.676137 AGGCAACCATGGAAACACCAGAT 62.676 47.826 21.47 0.00 46.53 2.90
2855 5321 7.672983 TGGTTAGAAAAGAACAGATGACATC 57.327 36.000 7.39 7.39 0.00 3.06
2894 5481 9.423061 GCTAACACAATCCAAAAATATCACTTT 57.577 29.630 0.00 0.00 0.00 2.66
2904 5492 7.232534 ACAATTAGAGGCTAACACAATCCAAAA 59.767 33.333 0.00 0.00 0.00 2.44
2925 5513 7.466804 TGAAAGATTACACTAAGGGGACAATT 58.533 34.615 0.00 0.00 0.00 2.32
2926 5514 7.027874 TGAAAGATTACACTAAGGGGACAAT 57.972 36.000 0.00 0.00 0.00 2.71
2927 5515 6.043938 ACTGAAAGATTACACTAAGGGGACAA 59.956 38.462 0.00 0.00 37.43 3.18
2948 5537 7.624360 ACTAAAAACAAATCTCACACACTGA 57.376 32.000 0.00 0.00 0.00 3.41
3007 5609 4.224991 TGATGAAACATCTGCCAGATCA 57.775 40.909 3.68 0.82 31.32 2.92
3017 5619 8.350722 AGTTGCTCATGAATATGATGAAACATC 58.649 33.333 0.00 4.98 42.19 3.06
3044 5646 7.112452 TGACTAGCTTAGCTAACAATGATGA 57.888 36.000 15.23 0.00 40.82 2.92
3090 5692 5.886992 TGCATGATTCAGAATTAAGCTGTG 58.113 37.500 14.19 0.37 34.98 3.66
3096 5698 8.479689 ACATGGAAATGCATGATTCAGAATTAA 58.520 29.630 19.83 0.00 33.38 1.40
3140 5743 1.280066 CTGCACAGCAAAACAACACC 58.720 50.000 0.00 0.00 38.41 4.16
3228 5831 2.826488 TCCTTCTTCTCCTCCTCCTTG 58.174 52.381 0.00 0.00 0.00 3.61
3249 5852 1.001631 TGATTCCTCCTCGGGCTCA 59.998 57.895 0.00 0.00 0.00 4.26
3315 5918 2.741878 CGGGACACGGCTTTATGAAGAT 60.742 50.000 0.58 0.00 39.42 2.40
3316 5919 1.404986 CGGGACACGGCTTTATGAAGA 60.405 52.381 0.58 0.00 39.42 2.87
3335 5938 3.765026 ACACTAAACAAAACTGGCAACG 58.235 40.909 0.00 0.00 42.51 4.10
3338 5941 5.164954 GTTCAACACTAAACAAAACTGGCA 58.835 37.500 0.00 0.00 0.00 4.92
3429 6034 6.763610 TGCATGACATAACGTTACCATATTCA 59.236 34.615 10.81 7.36 0.00 2.57
3437 6042 6.642683 ACTAAGTGCATGACATAACGTTAC 57.357 37.500 10.81 0.00 0.00 2.50
3474 6079 2.339418 CAGAGAAGCACAAGCAGAGAG 58.661 52.381 0.00 0.00 45.49 3.20
3475 6080 1.607509 GCAGAGAAGCACAAGCAGAGA 60.608 52.381 0.00 0.00 45.49 3.10
3548 6233 1.244019 AACGGCCAAATCAGTGCTCC 61.244 55.000 2.24 0.00 0.00 4.70
3553 6238 1.176527 CATCCAACGGCCAAATCAGT 58.823 50.000 2.24 0.00 0.00 3.41
3566 6251 4.431809 CAAAATAAGCGCATTCCATCCAA 58.568 39.130 11.47 0.00 0.00 3.53
3573 6258 2.187351 TCGGCAAAATAAGCGCATTC 57.813 45.000 11.47 0.00 0.00 2.67
3579 6264 4.035558 TCTGATGTCATCGGCAAAATAAGC 59.964 41.667 15.78 0.00 35.60 3.09
3581 6266 5.239306 GGATCTGATGTCATCGGCAAAATAA 59.761 40.000 15.78 0.00 35.60 1.40
3582 6267 4.756642 GGATCTGATGTCATCGGCAAAATA 59.243 41.667 15.78 0.00 35.60 1.40
3585 6270 2.171237 AGGATCTGATGTCATCGGCAAA 59.829 45.455 15.78 0.79 35.60 3.68
3586 6271 1.764723 AGGATCTGATGTCATCGGCAA 59.235 47.619 15.78 1.49 35.60 4.52
3589 6274 2.415224 CGCTAGGATCTGATGTCATCGG 60.415 54.545 14.62 14.62 36.99 4.18
3590 6275 2.485814 TCGCTAGGATCTGATGTCATCG 59.514 50.000 8.29 3.74 0.00 3.84
3592 6277 2.230992 GCTCGCTAGGATCTGATGTCAT 59.769 50.000 0.00 0.00 0.00 3.06
3595 6347 1.885887 GAGCTCGCTAGGATCTGATGT 59.114 52.381 0.00 0.00 0.00 3.06
3597 6349 1.164411 CGAGCTCGCTAGGATCTGAT 58.836 55.000 25.07 0.00 0.00 2.90
3627 6379 0.178767 CCAGTGCAATCTGATCCGGA 59.821 55.000 6.61 6.61 37.61 5.14
3629 6381 1.442526 GCCCAGTGCAATCTGATCCG 61.443 60.000 5.92 0.00 40.77 4.18
3635 6387 2.360350 CACGGCCCAGTGCAATCT 60.360 61.111 0.00 0.00 43.89 2.40
3637 6389 2.985282 CACACGGCCCAGTGCAAT 60.985 61.111 10.38 0.00 45.45 3.56
3653 6405 1.449782 CCATACATGCCTACGCCCA 59.550 57.895 0.00 0.00 0.00 5.36
3659 6411 1.985159 GGTCCATCCCATACATGCCTA 59.015 52.381 0.00 0.00 0.00 3.93
3662 6414 1.546323 CCAGGTCCATCCCATACATGC 60.546 57.143 0.00 0.00 36.75 4.06
3663 6415 1.074405 CCCAGGTCCATCCCATACATG 59.926 57.143 0.00 0.00 36.75 3.21
3664 6416 1.346465 ACCCAGGTCCATCCCATACAT 60.346 52.381 0.00 0.00 36.75 2.29
3665 6417 0.045623 ACCCAGGTCCATCCCATACA 59.954 55.000 0.00 0.00 36.75 2.29
3700 6452 4.389576 CAAGCACAAGCCGCGACC 62.390 66.667 8.23 0.00 43.56 4.79
3718 6470 4.986531 CACAACCGTCAACGCGCG 62.987 66.667 30.96 30.96 38.18 6.86
3719 6471 3.932313 ACACAACCGTCAACGCGC 61.932 61.111 5.73 0.00 38.18 6.86
3720 6472 2.053465 CACACAACCGTCAACGCG 60.053 61.111 3.53 3.53 38.18 6.01
3721 6473 2.326550 CCACACAACCGTCAACGC 59.673 61.111 0.00 0.00 38.18 4.84
3722 6474 2.539338 CCCCACACAACCGTCAACG 61.539 63.158 0.00 0.00 39.44 4.10
3723 6475 1.441732 GACCCCACACAACCGTCAAC 61.442 60.000 0.00 0.00 0.00 3.18
3724 6476 1.153127 GACCCCACACAACCGTCAA 60.153 57.895 0.00 0.00 0.00 3.18
3725 6477 2.318519 CTGACCCCACACAACCGTCA 62.319 60.000 0.00 0.00 32.78 4.35
3726 6478 1.597027 CTGACCCCACACAACCGTC 60.597 63.158 0.00 0.00 0.00 4.79
3727 6479 2.319890 GACTGACCCCACACAACCGT 62.320 60.000 0.00 0.00 0.00 4.83
3728 6480 1.597027 GACTGACCCCACACAACCG 60.597 63.158 0.00 0.00 0.00 4.44
3729 6481 1.228154 GGACTGACCCCACACAACC 60.228 63.158 0.00 0.00 0.00 3.77
3730 6482 0.535102 CAGGACTGACCCCACACAAC 60.535 60.000 0.00 0.00 40.05 3.32
3731 6483 1.836391 CAGGACTGACCCCACACAA 59.164 57.895 0.00 0.00 40.05 3.33
3732 6484 2.818169 GCAGGACTGACCCCACACA 61.818 63.158 3.00 0.00 40.05 3.72
3733 6485 2.032681 GCAGGACTGACCCCACAC 59.967 66.667 3.00 0.00 40.05 3.82
3734 6486 2.447572 TGCAGGACTGACCCCACA 60.448 61.111 3.00 0.00 40.05 4.17
3735 6487 2.032681 GTGCAGGACTGACCCCAC 59.967 66.667 3.00 0.00 40.05 4.61
3736 6488 2.447572 TGTGCAGGACTGACCCCA 60.448 61.111 3.00 0.00 40.05 4.96
3737 6489 2.348998 CTGTGCAGGACTGACCCC 59.651 66.667 3.00 0.00 40.05 4.95
3762 6514 1.444836 TGTTGTATGCGGTTACCAGC 58.555 50.000 1.13 6.74 0.00 4.85
3763 6515 4.632251 TGTAATGTTGTATGCGGTTACCAG 59.368 41.667 1.13 0.00 0.00 4.00
3764 6516 4.576879 TGTAATGTTGTATGCGGTTACCA 58.423 39.130 1.13 0.00 0.00 3.25
3765 6517 5.744666 ATGTAATGTTGTATGCGGTTACC 57.255 39.130 0.00 0.00 0.00 2.85
3766 6518 6.073440 CCCTATGTAATGTTGTATGCGGTTAC 60.073 42.308 0.00 0.00 0.00 2.50
3767 6519 5.992829 CCCTATGTAATGTTGTATGCGGTTA 59.007 40.000 0.00 0.00 0.00 2.85
3770 6522 4.637276 TCCCTATGTAATGTTGTATGCGG 58.363 43.478 0.00 0.00 0.00 5.69
3775 6527 7.127405 TGTACTCCTCCCTATGTAATGTTGTA 58.873 38.462 0.00 0.00 0.00 2.41
3828 6580 8.437575 ACAAGGAAGAATTAAGGAGAGTGTTAA 58.562 33.333 0.00 0.00 0.00 2.01
3837 6589 5.642063 CGCAAGTACAAGGAAGAATTAAGGA 59.358 40.000 0.00 0.00 0.00 3.36
3840 6592 7.389330 TCAATCGCAAGTACAAGGAAGAATTAA 59.611 33.333 0.00 0.00 39.48 1.40
3845 6597 4.265904 TCAATCGCAAGTACAAGGAAGA 57.734 40.909 0.00 0.00 39.48 2.87
3897 6649 7.843760 ACATTATTCCTCATATTTTCCCCACAA 59.156 33.333 0.00 0.00 0.00 3.33
3959 6711 6.326323 ACAGGGTTTGAATGAGTTTTACCAAT 59.674 34.615 0.00 0.00 0.00 3.16
3972 6724 6.556874 TCCTTATTTTTCCACAGGGTTTGAAT 59.443 34.615 0.00 0.00 34.93 2.57
3974 6726 5.459505 TCCTTATTTTTCCACAGGGTTTGA 58.540 37.500 0.00 0.00 34.93 2.69
4094 6846 4.796314 CCACCGGGGTTTTTACGA 57.204 55.556 6.32 0.00 0.00 3.43
4108 6860 4.825085 TGTCATACTTTCTGTTTTCCCCAC 59.175 41.667 0.00 0.00 0.00 4.61
4175 6929 9.621629 TTTTCCTTGATGAGTTTACTTTACAGA 57.378 29.630 0.00 0.00 0.00 3.41
4218 6972 7.922278 TCTTCCTGAATTGTTCATGTTCAAAAG 59.078 33.333 8.71 9.09 39.30 2.27
4219 6973 7.780064 TCTTCCTGAATTGTTCATGTTCAAAA 58.220 30.769 8.71 1.89 39.30 2.44
4220 6974 7.345422 TCTTCCTGAATTGTTCATGTTCAAA 57.655 32.000 8.71 0.00 39.30 2.69
4228 6982 8.567948 GTTCAAAGTATCTTCCTGAATTGTTCA 58.432 33.333 0.00 0.00 38.17 3.18
4232 6986 7.874940 TGTGTTCAAAGTATCTTCCTGAATTG 58.125 34.615 0.00 0.00 0.00 2.32
4248 7002 5.649557 CTGTGTTCCAGAAATGTGTTCAAA 58.350 37.500 0.00 0.00 44.49 2.69
4249 7003 5.247507 CTGTGTTCCAGAAATGTGTTCAA 57.752 39.130 0.00 0.00 44.49 2.69
4276 7074 7.070180 TTGATTTGTTCATCAGGTCTCTACCG 61.070 42.308 0.00 0.00 41.78 4.02
4304 7102 8.735692 TGCATATCTTGTAAGTCAAATCATGA 57.264 30.769 0.00 0.00 35.48 3.07
4351 7149 2.789779 GCCCGTATGCAAACATGTTACG 60.790 50.000 19.19 19.19 37.04 3.18


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

AutoCloner maintained by Alex Coulton.