Multiple sequence alignment - TraesCS2A01G321100

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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 TraesCS2A01G321100 chr2A 100.000 5367 0 0 1 5367 550703657 550698291 0.000000e+00 9912.0
1 TraesCS2A01G321100 chr2A 88.806 268 21 2 3825 4091 550687942 550688201 2.410000e-83 320.0
2 TraesCS2A01G321100 chr2A 88.148 270 27 2 4087 4355 550690805 550691070 3.120000e-82 316.0
3 TraesCS2A01G321100 chr2A 85.366 82 6 3 4944 5020 116076339 116076419 4.460000e-11 80.5
4 TraesCS2A01G321100 chr2D 92.885 2572 111 42 622 3170 437947157 437949679 0.000000e+00 3670.0
5 TraesCS2A01G321100 chr2D 90.061 1791 119 30 3391 5157 437950447 437952202 0.000000e+00 2266.0
6 TraesCS2A01G321100 chr2D 87.083 1169 82 25 3258 4390 438045439 438046574 0.000000e+00 1258.0
7 TraesCS2A01G321100 chr2D 90.553 561 43 6 3825 4384 437975963 437976514 0.000000e+00 734.0
8 TraesCS2A01G321100 chr2D 83.553 608 55 21 1 597 126977364 126976791 1.320000e-145 527.0
9 TraesCS2A01G321100 chr2D 83.466 502 42 21 1 496 613309541 613309075 3.840000e-116 429.0
10 TraesCS2A01G321100 chr2D 92.308 182 12 1 3177 3358 437950168 437950347 1.920000e-64 257.0
11 TraesCS2A01G321100 chr2D 89.381 113 11 1 5255 5367 437952483 437952594 2.020000e-29 141.0
12 TraesCS2A01G321100 chr2D 83.117 154 17 7 4416 4563 483149150 483149300 1.210000e-26 132.0
13 TraesCS2A01G321100 chr2D 97.059 34 1 0 3367 3400 437950382 437950415 2.090000e-04 58.4
14 TraesCS2A01G321100 chrUn 92.418 2585 124 35 627 3176 276464193 276461646 0.000000e+00 3622.0
15 TraesCS2A01G321100 chrUn 92.418 2585 124 35 627 3176 276526313 276528860 0.000000e+00 3622.0
16 TraesCS2A01G321100 chrUn 92.418 2585 124 35 627 3176 295904990 295907537 0.000000e+00 3622.0
17 TraesCS2A01G321100 chrUn 93.925 1037 53 6 3354 4390 412752369 412753395 0.000000e+00 1557.0
18 TraesCS2A01G321100 chrUn 85.806 310 21 9 4949 5255 325990797 325991086 1.880000e-79 307.0
19 TraesCS2A01G321100 chrUn 85.806 310 21 9 4949 5255 373351281 373350992 1.880000e-79 307.0
20 TraesCS2A01G321100 chrUn 97.727 44 1 0 5212 5255 93030878 93030921 5.760000e-10 76.8
21 TraesCS2A01G321100 chr2B 92.409 909 62 4 3482 4390 514769830 514770731 0.000000e+00 1290.0
22 TraesCS2A01G321100 chr2B 92.637 584 25 6 3825 4390 514681940 514682523 0.000000e+00 824.0
23 TraesCS2A01G321100 chr2B 85.405 185 19 3 3178 3354 514769544 514769728 9.180000e-43 185.0
24 TraesCS2A01G321100 chr2B 84.146 82 7 6 4944 5020 165173858 165173938 2.070000e-09 75.0
25 TraesCS2A01G321100 chr6B 92.437 595 34 8 1 592 5320610 5321196 0.000000e+00 839.0
26 TraesCS2A01G321100 chr6B 87.080 387 42 7 212 597 72373237 72372858 1.070000e-116 431.0
27 TraesCS2A01G321100 chr6B 82.424 165 19 5 5085 5247 9311898 9311742 9.380000e-28 135.0
28 TraesCS2A01G321100 chr3D 93.817 469 26 3 130 596 540129175 540128708 0.000000e+00 702.0
29 TraesCS2A01G321100 chr3D 86.486 185 25 0 1751 1935 405309912 405309728 2.530000e-48 204.0
30 TraesCS2A01G321100 chr3D 97.059 34 1 0 4967 5000 539341443 539341410 2.090000e-04 58.4
31 TraesCS2A01G321100 chr4B 92.144 471 32 5 130 597 664088819 664088351 0.000000e+00 660.0
32 TraesCS2A01G321100 chr4D 85.548 602 43 22 1 593 43674296 43674862 1.660000e-164 590.0
33 TraesCS2A01G321100 chr1B 84.823 593 50 18 1 588 26600240 26599683 1.310000e-155 560.0
34 TraesCS2A01G321100 chr1B 79.481 385 69 6 1569 1948 486971865 486971486 1.150000e-66 265.0
35 TraesCS2A01G321100 chr5A 83.690 607 50 26 1 597 536800113 536799546 1.320000e-145 527.0
36 TraesCS2A01G321100 chr4A 83.195 601 51 26 1 596 444148326 444147771 6.200000e-139 505.0
37 TraesCS2A01G321100 chr4A 81.188 606 63 26 1 596 696091343 696090779 1.770000e-119 440.0
38 TraesCS2A01G321100 chr7A 83.000 600 59 25 1 593 6871448 6872011 2.230000e-138 503.0
39 TraesCS2A01G321100 chr7A 90.719 334 24 6 1 329 634322237 634321906 6.380000e-119 438.0
40 TraesCS2A01G321100 chr7A 83.438 320 39 10 3743 4061 668679532 668679838 8.800000e-73 285.0
41 TraesCS2A01G321100 chr7A 94.118 34 2 0 5216 5249 727768009 727768042 1.000000e-02 52.8
42 TraesCS2A01G321100 chr7B 81.833 600 64 21 1 593 134310396 134310957 3.790000e-126 462.0
43 TraesCS2A01G321100 chr7B 96.491 57 2 0 4122 4178 639285227 639285171 1.590000e-15 95.3
44 TraesCS2A01G321100 chr7B 90.385 52 4 1 5283 5333 110318505 110318454 3.470000e-07 67.6
45 TraesCS2A01G321100 chr1A 80.399 602 58 28 10 593 496124562 496124003 2.330000e-108 403.0
46 TraesCS2A01G321100 chr1A 80.260 385 66 6 1569 1948 462796326 462795947 1.140000e-71 281.0
47 TraesCS2A01G321100 chr1D 80.000 375 64 7 1569 1937 363725747 363725378 3.190000e-67 267.0
48 TraesCS2A01G321100 chr3B 79.605 304 58 4 1634 1935 531212328 531212027 1.170000e-51 215.0
49 TraesCS2A01G321100 chr3B 84.444 180 11 9 5085 5255 439458506 439458335 1.550000e-35 161.0


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 TraesCS2A01G321100 chr2A 550698291 550703657 5366 True 9912.00 9912 100.0000 1 5367 1 chr2A.!!$R1 5366
1 TraesCS2A01G321100 chr2A 550687942 550691070 3128 False 318.00 320 88.4770 3825 4355 2 chr2A.!!$F2 530
2 TraesCS2A01G321100 chr2D 437947157 437952594 5437 False 1278.48 3670 92.3388 622 5367 5 chr2D.!!$F4 4745
3 TraesCS2A01G321100 chr2D 438045439 438046574 1135 False 1258.00 1258 87.0830 3258 4390 1 chr2D.!!$F2 1132
4 TraesCS2A01G321100 chr2D 437975963 437976514 551 False 734.00 734 90.5530 3825 4384 1 chr2D.!!$F1 559
5 TraesCS2A01G321100 chr2D 126976791 126977364 573 True 527.00 527 83.5530 1 597 1 chr2D.!!$R1 596
6 TraesCS2A01G321100 chrUn 276461646 276464193 2547 True 3622.00 3622 92.4180 627 3176 1 chrUn.!!$R1 2549
7 TraesCS2A01G321100 chrUn 276526313 276528860 2547 False 3622.00 3622 92.4180 627 3176 1 chrUn.!!$F2 2549
8 TraesCS2A01G321100 chrUn 295904990 295907537 2547 False 3622.00 3622 92.4180 627 3176 1 chrUn.!!$F3 2549
9 TraesCS2A01G321100 chrUn 412752369 412753395 1026 False 1557.00 1557 93.9250 3354 4390 1 chrUn.!!$F5 1036
10 TraesCS2A01G321100 chr2B 514681940 514682523 583 False 824.00 824 92.6370 3825 4390 1 chr2B.!!$F2 565
11 TraesCS2A01G321100 chr2B 514769544 514770731 1187 False 737.50 1290 88.9070 3178 4390 2 chr2B.!!$F3 1212
12 TraesCS2A01G321100 chr6B 5320610 5321196 586 False 839.00 839 92.4370 1 592 1 chr6B.!!$F1 591
13 TraesCS2A01G321100 chr4D 43674296 43674862 566 False 590.00 590 85.5480 1 593 1 chr4D.!!$F1 592
14 TraesCS2A01G321100 chr1B 26599683 26600240 557 True 560.00 560 84.8230 1 588 1 chr1B.!!$R1 587
15 TraesCS2A01G321100 chr5A 536799546 536800113 567 True 527.00 527 83.6900 1 597 1 chr5A.!!$R1 596
16 TraesCS2A01G321100 chr4A 444147771 444148326 555 True 505.00 505 83.1950 1 596 1 chr4A.!!$R1 595
17 TraesCS2A01G321100 chr4A 696090779 696091343 564 True 440.00 440 81.1880 1 596 1 chr4A.!!$R2 595
18 TraesCS2A01G321100 chr7A 6871448 6872011 563 False 503.00 503 83.0000 1 593 1 chr7A.!!$F1 592
19 TraesCS2A01G321100 chr7B 134310396 134310957 561 False 462.00 462 81.8330 1 593 1 chr7B.!!$F1 592
20 TraesCS2A01G321100 chr1A 496124003 496124562 559 True 403.00 403 80.3990 10 593 1 chr1A.!!$R2 583

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
661 736 0.030908 GGAGTACCTTCTCGATGGCG 59.969 60.0 0.00 0.00 35.52 5.69 F
770 845 0.161235 CGGCGAGAGATACGTACGAG 59.839 60.0 24.41 3.66 36.22 4.18 F
1341 1441 0.460109 TCTTCGCCATGGACATCGTG 60.460 55.0 18.40 7.32 0.00 4.35 F
2618 2734 0.035630 GAGCAGGCAAGTCTGTCCAT 60.036 55.0 3.39 0.00 37.12 3.41 F
3325 3932 0.249868 TGCCAGAGGTATATGTGCGC 60.250 55.0 0.00 0.00 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2288 0.249657 GCGAGATGCTGGACCTAAGG 60.250 60.0 0.0 0.0 41.73 2.69 R
2184 2289 0.461548 TGCGAGATGCTGGACCTAAG 59.538 55.0 0.0 0.0 46.63 2.18 R
3297 3904 0.106708 TACCTCTGGCATTCGCATCC 59.893 55.0 0.0 0.0 41.24 3.51 R
4235 7566 0.101219 GTTATTACCCTCGTCGCCGT 59.899 55.0 0.0 0.0 35.01 5.68 R
5198 8550 0.186630 AAACTAACACCACCCCACCC 59.813 55.0 0.0 0.0 0.00 4.61 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
236 273 7.760437 AGACTGAAGTTTCCGTACTCTAATAC 58.240 38.462 0.00 0.00 0.00 1.89
269 317 8.479313 ACATGTATACATTTACACACACTCAG 57.521 34.615 15.85 2.52 35.04 3.35
280 328 2.880268 CACACACTCAGCATCTGGAAAA 59.120 45.455 0.00 0.00 31.51 2.29
294 344 6.961554 GCATCTGGAAAATACACGTAAAGAAG 59.038 38.462 0.00 0.00 0.00 2.85
346 406 7.867445 AATAAAATCGTACAGGTGCAAAAAG 57.133 32.000 0.00 0.00 0.00 2.27
372 434 1.794512 CAAACCCATGGGAAAAAGCG 58.205 50.000 38.07 13.50 38.96 4.68
396 458 2.116125 AAACAGCCCAGCCCAGTC 59.884 61.111 0.00 0.00 0.00 3.51
458 520 5.186198 CCCAAAATAGGAGTCAGTCGAATT 58.814 41.667 0.00 0.00 0.00 2.17
462 524 6.969828 AAATAGGAGTCAGTCGAATTCAAC 57.030 37.500 6.22 0.00 0.00 3.18
597 672 7.279758 AGCTGACTGAAATCTAGCTAAAATGAC 59.720 37.037 0.00 0.00 42.45 3.06
598 673 7.065085 GCTGACTGAAATCTAGCTAAAATGACA 59.935 37.037 0.00 0.00 0.00 3.58
599 674 8.846943 TGACTGAAATCTAGCTAAAATGACAA 57.153 30.769 0.00 0.00 0.00 3.18
600 675 9.453572 TGACTGAAATCTAGCTAAAATGACAAT 57.546 29.630 0.00 0.00 0.00 2.71
609 684 9.607988 TCTAGCTAAAATGACAATTAATTCGGA 57.392 29.630 0.00 0.00 0.00 4.55
611 686 8.911247 AGCTAAAATGACAATTAATTCGGAAC 57.089 30.769 0.00 0.00 0.00 3.62
652 727 4.095211 AGTGGGAAACTAGGAGTACCTTC 58.905 47.826 0.00 0.00 45.36 3.46
654 729 4.160065 GTGGGAAACTAGGAGTACCTTCTC 59.840 50.000 0.00 0.00 45.36 2.87
661 736 0.030908 GGAGTACCTTCTCGATGGCG 59.969 60.000 0.00 0.00 35.52 5.69
739 814 2.656651 CTCCCTGCGCTCGATTCG 60.657 66.667 9.73 0.00 0.00 3.34
740 815 3.417275 CTCCCTGCGCTCGATTCGT 62.417 63.158 9.73 0.00 0.00 3.85
741 816 2.509336 CCCTGCGCTCGATTCGTT 60.509 61.111 9.73 0.00 0.00 3.85
742 817 2.517450 CCCTGCGCTCGATTCGTTC 61.517 63.158 9.73 0.00 0.00 3.95
761 836 2.374830 CTGGATTGCCGGCGAGAGAT 62.375 60.000 23.38 10.49 36.79 2.75
765 840 1.735376 ATTGCCGGCGAGAGATACGT 61.735 55.000 23.38 0.00 0.00 3.57
766 841 1.096967 TTGCCGGCGAGAGATACGTA 61.097 55.000 23.90 0.00 0.00 3.57
767 842 1.082235 GCCGGCGAGAGATACGTAC 60.082 63.158 12.58 0.00 0.00 3.67
768 843 1.203563 CCGGCGAGAGATACGTACG 59.796 63.158 15.01 15.01 34.92 3.67
769 844 1.217585 CCGGCGAGAGATACGTACGA 61.218 60.000 24.41 6.04 36.22 3.43
770 845 0.161235 CGGCGAGAGATACGTACGAG 59.839 60.000 24.41 3.66 36.22 4.18
772 847 1.192090 GGCGAGAGATACGTACGAGAC 59.808 57.143 24.41 11.80 0.00 3.36
774 849 1.451278 CGAGAGATACGTACGAGACCG 59.549 57.143 24.41 11.31 42.50 4.79
775 850 2.736978 GAGAGATACGTACGAGACCGA 58.263 52.381 24.41 0.00 39.50 4.69
776 851 2.725723 GAGAGATACGTACGAGACCGAG 59.274 54.545 24.41 0.00 39.50 4.63
777 852 1.192090 GAGATACGTACGAGACCGAGC 59.808 57.143 24.41 2.45 39.50 5.03
818 905 3.200593 CTGCTGCACCGATCTGCC 61.201 66.667 0.00 0.00 36.21 4.85
840 927 2.097036 GCCTAAATAAAGCAACCCGGT 58.903 47.619 0.00 0.00 0.00 5.28
923 1010 2.283821 GGAAACCCTGGGCATGCA 60.284 61.111 21.36 0.00 0.00 3.96
945 1033 4.505217 GTCGCCGTCGCATGCAAG 62.505 66.667 19.57 7.78 35.26 4.01
993 1081 4.702081 CGGCCGATCGATCCGACC 62.702 72.222 31.28 16.05 45.53 4.79
994 1082 4.702081 GGCCGATCGATCCGACCG 62.702 72.222 18.66 8.09 43.10 4.79
995 1083 3.657059 GCCGATCGATCCGACCGA 61.657 66.667 18.66 0.00 46.76 4.69
996 1084 2.979197 GCCGATCGATCCGACCGAT 61.979 63.158 18.66 0.00 46.76 4.18
997 1085 1.134901 CCGATCGATCCGACCGATC 59.865 63.158 18.66 14.31 46.76 3.69
1000 1088 2.715536 ATCGATCCGACCGATCACA 58.284 52.632 0.00 0.00 46.85 3.58
1001 1089 1.248486 ATCGATCCGACCGATCACAT 58.752 50.000 0.00 0.00 46.85 3.21
1005 1093 1.338337 GATCCGACCGATCACATGACT 59.662 52.381 0.00 0.00 45.92 3.41
1016 1104 1.071299 ACATGACTGACAGGCGCAA 59.929 52.632 10.83 0.00 33.22 4.85
1021 1109 1.975363 GACTGACAGGCGCAAGATGC 61.975 60.000 10.83 0.00 40.69 3.91
1081 1169 1.733399 GTCCAGTCCAGCGTCGAAC 60.733 63.158 0.00 0.00 0.00 3.95
1111 1208 4.717629 TCAGCGTCTTCACGGCGG 62.718 66.667 13.24 0.00 46.80 6.13
1191 1291 2.984623 GTGTCCCCTTACGACCCC 59.015 66.667 0.00 0.00 0.00 4.95
1211 1311 3.065306 CTACCGGCTGTGGGACAA 58.935 61.111 0.00 0.00 44.16 3.18
1216 1316 1.369692 CGGCTGTGGGACAACTACA 59.630 57.895 0.00 0.00 44.16 2.74
1341 1441 0.460109 TCTTCGCCATGGACATCGTG 60.460 55.000 18.40 7.32 0.00 4.35
1620 1720 2.811317 CGGTGCTCCAAGCTCGTC 60.811 66.667 5.52 0.00 42.97 4.20
1733 1833 2.267351 CCATGCCGCAGTTCCACAA 61.267 57.895 0.00 0.00 0.00 3.33
1741 1841 0.880278 GCAGTTCCACAACGAGAGCA 60.880 55.000 0.00 0.00 37.61 4.26
1974 2074 2.634940 AGCTGCAACCTCTCTCTTGTTA 59.365 45.455 1.02 0.00 0.00 2.41
1978 2078 5.486526 CTGCAACCTCTCTCTTGTTAAGAT 58.513 41.667 0.00 0.00 36.82 2.40
2051 2156 2.892425 GACAAGATCCAGGCGGCG 60.892 66.667 0.51 0.51 0.00 6.46
2326 2434 8.095937 TCTAACAAAGATGATGATGATGATGC 57.904 34.615 0.00 0.00 0.00 3.91
2330 2438 6.946009 ACAAAGATGATGATGATGATGCCATA 59.054 34.615 0.00 0.00 32.09 2.74
2333 2441 5.880887 AGATGATGATGATGATGCCATACAC 59.119 40.000 0.00 0.00 32.09 2.90
2352 2468 2.029649 CACTGGGGAATTTGCTCAACTG 60.030 50.000 0.00 0.00 0.00 3.16
2368 2484 1.370900 CTGGTTTCTGCTGCGCAAC 60.371 57.895 13.05 7.98 38.41 4.17
2385 2501 0.535102 AACTGCTTGGGAAGGTGTCG 60.535 55.000 0.00 0.00 0.00 4.35
2460 2576 1.810412 GCGCCCTCGGATTTCTACATT 60.810 52.381 0.00 0.00 35.95 2.71
2533 2649 4.041740 CGATCCTCGGTTATCTTCAACA 57.958 45.455 0.00 0.00 36.00 3.33
2561 2677 2.512286 ATCCATGTGAGTGGCGCG 60.512 61.111 0.00 0.00 39.19 6.86
2618 2734 0.035630 GAGCAGGCAAGTCTGTCCAT 60.036 55.000 3.39 0.00 37.12 3.41
2624 2740 1.281899 GCAAGTCTGTCCATCTACGC 58.718 55.000 0.00 0.00 0.00 4.42
2625 2741 1.134965 GCAAGTCTGTCCATCTACGCT 60.135 52.381 0.00 0.00 0.00 5.07
2639 2755 5.278266 CCATCTACGCTTTGTTCCTTTTTCA 60.278 40.000 0.00 0.00 0.00 2.69
2641 2757 7.361713 CCATCTACGCTTTGTTCCTTTTTCATA 60.362 37.037 0.00 0.00 0.00 2.15
2643 2759 5.508200 ACGCTTTGTTCCTTTTTCATACA 57.492 34.783 0.00 0.00 0.00 2.29
2644 2760 5.519722 ACGCTTTGTTCCTTTTTCATACAG 58.480 37.500 0.00 0.00 0.00 2.74
2645 2761 4.382754 CGCTTTGTTCCTTTTTCATACAGC 59.617 41.667 0.00 0.00 0.00 4.40
2825 2945 1.004918 CGCCGACTTCCTCAAGGTT 60.005 57.895 0.00 0.00 33.37 3.50
2943 3063 4.041723 GGGACGACAACACTGAATTTTTG 58.958 43.478 0.00 0.00 0.00 2.44
3063 3188 2.089201 CAGCTTGATCTGCCAATCACA 58.911 47.619 7.48 0.00 35.44 3.58
3129 3254 4.845580 CTGAAGCGCGGCCTGGAT 62.846 66.667 8.83 0.00 0.00 3.41
3170 3295 1.017701 GGCCGTACAGCACTGGTAAC 61.018 60.000 3.01 0.00 34.19 2.50
3186 3793 6.088883 CACTGGTAACCACGAATTAATTTTGC 59.911 38.462 1.43 0.00 0.00 3.68
3196 3803 6.640499 CACGAATTAATTTTGCTTCTCAACCA 59.360 34.615 1.43 0.00 33.73 3.67
3297 3904 1.926511 GCCTGTTGGAGAATGGTGCG 61.927 60.000 0.00 0.00 34.57 5.34
3320 3927 3.044235 TGCGAATGCCAGAGGTATATG 57.956 47.619 0.00 0.00 41.78 1.78
3323 3930 2.738846 CGAATGCCAGAGGTATATGTGC 59.261 50.000 0.00 0.00 0.00 4.57
3325 3932 0.249868 TGCCAGAGGTATATGTGCGC 60.250 55.000 0.00 0.00 0.00 6.09
3345 3960 6.639279 GTGCGCCTAAAAGTTTTGAAAATCTA 59.361 34.615 11.18 0.00 0.00 1.98
3400 4082 9.899226 GAATTAGTATCAAATTAGGATGTTGGC 57.101 33.333 3.45 0.00 0.00 4.52
3702 4386 2.725312 GCGCTGATCCTGACAGGGA 61.725 63.158 21.56 8.73 46.37 4.20
3831 4515 2.436292 CTCGTCGACGGAGGAGGT 60.436 66.667 35.05 0.00 46.45 3.85
3921 4605 4.487412 CAGCGGTACCGTCGGGTC 62.487 72.222 33.34 16.84 46.01 4.46
3924 4608 4.166011 CGGTACCGTCGGGTCGTC 62.166 72.222 26.39 0.81 46.01 4.20
3925 4609 4.166011 GGTACCGTCGGGTCGTCG 62.166 72.222 17.28 0.59 46.01 5.12
3926 4610 3.423154 GTACCGTCGGGTCGTCGT 61.423 66.667 17.28 0.00 46.01 4.34
3927 4611 3.118454 TACCGTCGGGTCGTCGTC 61.118 66.667 17.28 0.00 46.01 4.20
4051 4765 3.338126 CTCCTCGTCGTTCCACGGG 62.338 68.421 0.00 0.00 42.81 5.28
4160 7491 2.266055 CTGAACAGGGACGGAGCC 59.734 66.667 0.00 0.00 0.00 4.70
4235 7566 0.326927 GGGGAACAGATTCGGGTTCA 59.673 55.000 19.14 0.00 43.96 3.18
4395 7726 1.274728 CCGATGCATTGGTTGGGAAAA 59.725 47.619 23.23 0.00 0.00 2.29
4396 7727 2.289320 CCGATGCATTGGTTGGGAAAAA 60.289 45.455 23.23 0.00 0.00 1.94
4397 7728 3.598299 CGATGCATTGGTTGGGAAAAAT 58.402 40.909 5.98 0.00 0.00 1.82
4398 7729 4.002316 CGATGCATTGGTTGGGAAAAATT 58.998 39.130 5.98 0.00 0.00 1.82
4401 7732 5.296151 TGCATTGGTTGGGAAAAATTACA 57.704 34.783 0.00 0.00 0.00 2.41
4402 7733 5.059833 TGCATTGGTTGGGAAAAATTACAC 58.940 37.500 0.00 0.00 0.00 2.90
4403 7734 5.163258 TGCATTGGTTGGGAAAAATTACACT 60.163 36.000 0.00 0.00 0.00 3.55
4404 7735 5.762711 GCATTGGTTGGGAAAAATTACACTT 59.237 36.000 0.00 0.00 0.00 3.16
4405 7736 6.293353 GCATTGGTTGGGAAAAATTACACTTG 60.293 38.462 0.00 0.00 0.00 3.16
4406 7737 5.283457 TGGTTGGGAAAAATTACACTTGG 57.717 39.130 0.00 0.00 0.00 3.61
4409 7740 5.756347 GGTTGGGAAAAATTACACTTGGAAC 59.244 40.000 0.00 0.00 0.00 3.62
4425 7756 4.062677 TGGAACCTGGTTGTATATACGC 57.937 45.455 18.42 0.00 0.00 4.42
4426 7757 3.707611 TGGAACCTGGTTGTATATACGCT 59.292 43.478 18.42 0.00 0.00 5.07
4427 7758 4.202182 TGGAACCTGGTTGTATATACGCTC 60.202 45.833 18.42 0.00 0.00 5.03
4428 7759 4.038883 GGAACCTGGTTGTATATACGCTCT 59.961 45.833 18.42 0.00 0.00 4.09
4429 7760 5.242393 GGAACCTGGTTGTATATACGCTCTA 59.758 44.000 18.42 0.00 0.00 2.43
4430 7761 6.071503 GGAACCTGGTTGTATATACGCTCTAT 60.072 42.308 18.42 0.00 0.00 1.98
4431 7762 7.121759 GGAACCTGGTTGTATATACGCTCTATA 59.878 40.741 18.42 0.00 0.00 1.31
4432 7763 7.388460 ACCTGGTTGTATATACGCTCTATAC 57.612 40.000 8.33 3.80 34.19 1.47
4433 7764 6.093219 ACCTGGTTGTATATACGCTCTATACG 59.907 42.308 8.33 0.00 35.65 3.06
4434 7765 6.426980 TGGTTGTATATACGCTCTATACGG 57.573 41.667 8.33 0.00 35.65 4.02
4435 7766 6.172630 TGGTTGTATATACGCTCTATACGGA 58.827 40.000 8.33 0.00 35.65 4.69
4436 7767 6.314648 TGGTTGTATATACGCTCTATACGGAG 59.685 42.308 8.33 0.00 35.65 4.63
4437 7768 6.536582 GGTTGTATATACGCTCTATACGGAGA 59.463 42.308 8.33 0.00 35.65 3.71
4509 7843 4.489679 AAATCTGACTTTCTTTCGCACC 57.510 40.909 0.00 0.00 0.00 5.01
4518 7852 7.324935 TGACTTTCTTTCGCACCAGTATATAA 58.675 34.615 0.00 0.00 0.00 0.98
4543 7877 5.847670 TTTCACAAAAAGAAAACCCAACG 57.152 34.783 0.00 0.00 32.47 4.10
4544 7878 3.254892 TCACAAAAAGAAAACCCAACGC 58.745 40.909 0.00 0.00 0.00 4.84
4553 7887 1.308998 AAACCCAACGCTGACTTCAG 58.691 50.000 1.56 1.56 46.40 3.02
4569 7903 5.833131 TGACTTCAGGGCTAAAAATTTGTCT 59.167 36.000 0.00 0.00 0.00 3.41
4571 7905 7.124573 ACTTCAGGGCTAAAAATTTGTCTTT 57.875 32.000 0.00 0.00 0.00 2.52
4572 7906 6.986231 ACTTCAGGGCTAAAAATTTGTCTTTG 59.014 34.615 0.00 0.00 0.00 2.77
4599 7933 7.841956 TGAAAACAAGTCAAAGGTGGATTTTA 58.158 30.769 0.00 0.00 0.00 1.52
4604 7938 9.679661 AACAAGTCAAAGGTGGATTTTATTTTT 57.320 25.926 0.00 0.00 0.00 1.94
4613 7947 6.939730 AGGTGGATTTTATTTTTGCGGAATTT 59.060 30.769 0.00 0.00 0.00 1.82
4626 7960 5.957842 TGCGGAATTTTTCTCACAAGTAT 57.042 34.783 0.00 0.00 0.00 2.12
4640 7974 7.861629 TCTCACAAGTATAATGGAAGGTCAAT 58.138 34.615 0.00 0.00 0.00 2.57
4733 8068 5.310451 TGTAGATACACCAAGGAACCAAAC 58.690 41.667 0.00 0.00 0.00 2.93
4737 8072 0.666374 CACCAAGGAACCAAACGTCC 59.334 55.000 0.00 0.00 0.00 4.79
4739 8074 1.281656 CAAGGAACCAAACGTCCGC 59.718 57.895 0.00 0.00 0.00 5.54
4789 8124 7.961325 GATCTTTCAAAAATGATCCGAAGAC 57.039 36.000 0.00 0.00 38.89 3.01
4790 8125 6.875948 TCTTTCAAAAATGATCCGAAGACA 57.124 33.333 0.00 0.00 0.00 3.41
4791 8126 7.270757 TCTTTCAAAAATGATCCGAAGACAA 57.729 32.000 0.00 0.00 0.00 3.18
4792 8127 7.885297 TCTTTCAAAAATGATCCGAAGACAAT 58.115 30.769 0.00 0.00 0.00 2.71
4793 8128 9.008965 TCTTTCAAAAATGATCCGAAGACAATA 57.991 29.630 0.00 0.00 0.00 1.90
4794 8129 8.964420 TTTCAAAAATGATCCGAAGACAATAC 57.036 30.769 0.00 0.00 0.00 1.89
4795 8130 7.680442 TCAAAAATGATCCGAAGACAATACA 57.320 32.000 0.00 0.00 0.00 2.29
4830 8165 8.334734 AGGAAGATAATATGGATTGCATAGCTT 58.665 33.333 4.17 5.04 0.00 3.74
4849 8184 3.359033 CTTTGGCTGGAAATCTGATCCA 58.641 45.455 0.40 0.40 44.58 3.41
4889 8224 6.208988 TCTACAACTTACAGCATCTACTGG 57.791 41.667 0.00 0.00 42.21 4.00
4898 8233 2.035704 CAGCATCTACTGGCAGACCTAG 59.964 54.545 23.66 12.71 36.63 3.02
4905 8240 1.912043 ACTGGCAGACCTAGCAAATCT 59.088 47.619 23.66 0.00 36.63 2.40
4906 8241 3.107601 ACTGGCAGACCTAGCAAATCTA 58.892 45.455 23.66 0.00 36.63 1.98
4925 8260 5.290493 TCTAGCTCTTTGAACTTCCACAA 57.710 39.130 0.00 0.00 0.00 3.33
4928 8263 5.859205 AGCTCTTTGAACTTCCACAAAAT 57.141 34.783 0.00 0.00 35.95 1.82
4929 8264 6.959639 AGCTCTTTGAACTTCCACAAAATA 57.040 33.333 0.00 0.00 35.95 1.40
4930 8265 6.739112 AGCTCTTTGAACTTCCACAAAATAC 58.261 36.000 0.00 0.00 35.95 1.89
4933 8268 5.894393 TCTTTGAACTTCCACAAAATACCCA 59.106 36.000 0.00 0.00 35.95 4.51
4934 8269 5.523438 TTGAACTTCCACAAAATACCCAC 57.477 39.130 0.00 0.00 0.00 4.61
4935 8270 4.537751 TGAACTTCCACAAAATACCCACA 58.462 39.130 0.00 0.00 0.00 4.17
4936 8271 4.339814 TGAACTTCCACAAAATACCCACAC 59.660 41.667 0.00 0.00 0.00 3.82
4937 8272 2.882137 ACTTCCACAAAATACCCACACG 59.118 45.455 0.00 0.00 0.00 4.49
4938 8273 2.642154 TCCACAAAATACCCACACGT 57.358 45.000 0.00 0.00 0.00 4.49
4940 8275 4.082665 TCCACAAAATACCCACACGTTA 57.917 40.909 0.00 0.00 0.00 3.18
4941 8276 4.066490 TCCACAAAATACCCACACGTTAG 58.934 43.478 0.00 0.00 0.00 2.34
4957 8309 4.390909 CACGTTAGTCACCCCTTAAATGTC 59.609 45.833 0.00 0.00 0.00 3.06
4958 8310 3.937079 CGTTAGTCACCCCTTAAATGTCC 59.063 47.826 0.00 0.00 0.00 4.02
4993 8345 9.952188 GGTACCTTATTAGCAAATTCTCAAATC 57.048 33.333 4.06 0.00 0.00 2.17
5043 8395 5.122869 TGACCTACGTAGTTCTACATGTCAC 59.877 44.000 19.31 0.00 37.78 3.67
5044 8396 5.251764 ACCTACGTAGTTCTACATGTCACT 58.748 41.667 20.73 6.05 37.78 3.41
5045 8397 6.409704 ACCTACGTAGTTCTACATGTCACTA 58.590 40.000 20.73 5.00 37.78 2.74
5049 8401 4.497674 CGTAGTTCTACATGTCACTAGGCC 60.498 50.000 0.00 0.00 0.00 5.19
5074 8426 5.743636 AAAAATTGGCATGATGTACCAGT 57.256 34.783 0.00 0.00 34.28 4.00
5081 8433 4.067896 GGCATGATGTACCAGTTATGAGG 58.932 47.826 0.00 0.00 0.00 3.86
5092 8444 8.880244 TGTACCAGTTATGAGGAATAATGCTAT 58.120 33.333 0.00 0.00 33.32 2.97
5146 8498 6.446781 AACAAGCTGATGTGGAGAATTATG 57.553 37.500 0.00 0.00 32.81 1.90
5149 8501 6.832384 ACAAGCTGATGTGGAGAATTATGATT 59.168 34.615 0.00 0.00 30.82 2.57
5153 8505 6.712095 GCTGATGTGGAGAATTATGATTGGTA 59.288 38.462 0.00 0.00 0.00 3.25
5154 8506 7.229306 GCTGATGTGGAGAATTATGATTGGTAA 59.771 37.037 0.00 0.00 0.00 2.85
5155 8507 9.293404 CTGATGTGGAGAATTATGATTGGTAAT 57.707 33.333 0.00 0.00 0.00 1.89
5177 8529 0.252696 AAAAAGGGGGATGAAGGGGC 60.253 55.000 0.00 0.00 0.00 5.80
5179 8531 3.928172 AAGGGGGATGAAGGGGCCA 62.928 63.158 4.39 0.00 0.00 5.36
5180 8532 4.143301 GGGGGATGAAGGGGCCAC 62.143 72.222 4.39 0.00 0.00 5.01
5191 8543 2.355115 GGGCCACCCGAGTTGAAT 59.645 61.111 4.39 0.00 32.13 2.57
5192 8544 1.304134 GGGCCACCCGAGTTGAATT 60.304 57.895 4.39 0.00 32.13 2.17
5193 8545 1.595093 GGGCCACCCGAGTTGAATTG 61.595 60.000 4.39 0.00 32.13 2.32
5194 8546 1.595093 GGCCACCCGAGTTGAATTGG 61.595 60.000 0.00 0.00 0.00 3.16
5197 8549 4.337013 CCCGAGTTGAATTGGGGG 57.663 61.111 0.00 0.00 39.96 5.40
5213 8565 2.859971 GGGGGTGGGGTGGTGTTA 60.860 66.667 0.00 0.00 0.00 2.41
5214 8566 2.761160 GGGGTGGGGTGGTGTTAG 59.239 66.667 0.00 0.00 0.00 2.34
5215 8567 2.158130 GGGGTGGGGTGGTGTTAGT 61.158 63.158 0.00 0.00 0.00 2.24
5219 8744 1.133730 GGTGGGGTGGTGTTAGTTTGA 60.134 52.381 0.00 0.00 0.00 2.69
5276 8817 6.328672 AGGTATGAGCTATGGAGAAAGTTCAT 59.671 38.462 6.84 6.84 43.41 2.57
5288 8829 3.247648 AGAAAGTTCATTGTTCGTCACGG 59.752 43.478 0.00 0.00 0.00 4.94
5306 8847 1.336517 CGGAAGTAGCGGTTGAAGACA 60.337 52.381 0.00 0.00 0.00 3.41
5310 8851 3.188159 AGTAGCGGTTGAAGACACAAA 57.812 42.857 0.00 0.00 0.00 2.83
5334 8875 3.432588 CGAGTCGGTCCGCTCACT 61.433 66.667 25.29 16.93 32.65 3.41
5337 8878 4.057428 GTCGGTCCGCTCACTGCT 62.057 66.667 6.34 0.00 40.11 4.24
5342 8883 1.739562 GTCCGCTCACTGCTGAAGG 60.740 63.158 0.00 0.00 36.69 3.46
5348 8889 1.929836 GCTCACTGCTGAAGGTATTCG 59.070 52.381 0.00 0.00 38.34 3.34
5357 8898 4.100035 TGCTGAAGGTATTCGATCTGTCAT 59.900 41.667 0.00 0.00 38.34 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 132 7.859325 TTCTTAAGGGTGATAACAATGCTAC 57.141 36.000 1.85 0.00 0.00 3.58
154 187 7.672983 TTTTTGTGCTAATTGTGTGGAAAAA 57.327 28.000 0.00 0.00 0.00 1.94
269 317 6.417191 TCTTTACGTGTATTTTCCAGATGC 57.583 37.500 0.00 0.00 0.00 3.91
280 328 8.885722 TGAGTTTTGTTTCTTCTTTACGTGTAT 58.114 29.630 0.00 0.00 0.00 2.29
346 406 0.396060 TCCCATGGGTTTGCTTTTGC 59.604 50.000 30.28 0.00 40.36 3.68
396 458 1.508088 GCTGGATTTTCGCTGGTGG 59.492 57.895 0.00 0.00 0.00 4.61
458 520 3.970410 CTGGGCTGGGCTGGTTGA 61.970 66.667 0.00 0.00 0.00 3.18
462 524 3.329889 TGTACTGGGCTGGGCTGG 61.330 66.667 0.00 0.00 0.00 4.85
507 579 4.006780 TGTGCTTTAAGATCTGTGCAGA 57.993 40.909 4.23 4.23 42.37 4.26
515 587 6.127647 TGACCATTGGATTGTGCTTTAAGATC 60.128 38.462 10.37 0.00 0.00 2.75
593 668 4.574828 CCCTCGTTCCGAATTAATTGTCAT 59.425 41.667 5.17 0.00 34.74 3.06
597 672 4.189231 ACTCCCTCGTTCCGAATTAATTG 58.811 43.478 5.17 0.00 34.74 2.32
598 673 4.482952 ACTCCCTCGTTCCGAATTAATT 57.517 40.909 0.00 0.00 34.74 1.40
599 674 4.648307 AGTACTCCCTCGTTCCGAATTAAT 59.352 41.667 0.00 0.00 34.74 1.40
600 675 4.019174 AGTACTCCCTCGTTCCGAATTAA 58.981 43.478 0.00 0.00 34.74 1.40
601 676 3.624777 AGTACTCCCTCGTTCCGAATTA 58.375 45.455 0.00 0.00 34.74 1.40
602 677 2.454538 AGTACTCCCTCGTTCCGAATT 58.545 47.619 0.00 0.00 34.74 2.17
603 678 2.140839 AGTACTCCCTCGTTCCGAAT 57.859 50.000 0.00 0.00 34.74 3.34
604 679 2.636830 CTAGTACTCCCTCGTTCCGAA 58.363 52.381 0.00 0.00 34.74 4.30
605 680 1.745141 GCTAGTACTCCCTCGTTCCGA 60.745 57.143 0.00 0.00 0.00 4.55
606 681 0.662085 GCTAGTACTCCCTCGTTCCG 59.338 60.000 0.00 0.00 0.00 4.30
607 682 2.055684 AGCTAGTACTCCCTCGTTCC 57.944 55.000 0.00 0.00 0.00 3.62
608 683 3.807553 ACTAGCTAGTACTCCCTCGTTC 58.192 50.000 24.97 0.00 34.13 3.95
609 684 3.929955 ACTAGCTAGTACTCCCTCGTT 57.070 47.619 24.97 0.00 34.13 3.85
610 685 3.966665 ACTACTAGCTAGTACTCCCTCGT 59.033 47.826 26.36 18.39 37.73 4.18
611 686 4.309099 CACTACTAGCTAGTACTCCCTCG 58.691 52.174 26.36 17.82 37.73 4.63
612 687 4.505390 CCCACTACTAGCTAGTACTCCCTC 60.505 54.167 26.36 0.00 37.73 4.30
613 688 3.395273 CCCACTACTAGCTAGTACTCCCT 59.605 52.174 26.36 6.29 37.73 4.20
614 689 3.393941 TCCCACTACTAGCTAGTACTCCC 59.606 52.174 26.36 0.00 37.73 4.30
615 690 4.703379 TCCCACTACTAGCTAGTACTCC 57.297 50.000 26.36 0.00 37.73 3.85
616 691 6.121590 AGTTTCCCACTACTAGCTAGTACTC 58.878 44.000 26.36 11.93 37.73 2.59
617 692 6.077202 AGTTTCCCACTACTAGCTAGTACT 57.923 41.667 26.36 19.43 37.73 2.73
618 693 6.486320 CCTAGTTTCCCACTACTAGCTAGTAC 59.514 46.154 26.36 17.70 41.50 2.73
619 694 6.388100 TCCTAGTTTCCCACTACTAGCTAGTA 59.612 42.308 27.73 27.73 41.50 1.82
620 695 5.193325 TCCTAGTTTCCCACTACTAGCTAGT 59.807 44.000 28.50 28.50 41.50 2.57
739 814 2.435938 TCGCCGGCAATCCAGAAC 60.436 61.111 28.98 0.00 0.00 3.01
740 815 2.125147 CTCGCCGGCAATCCAGAA 60.125 61.111 28.98 0.00 0.00 3.02
741 816 3.074369 TCTCGCCGGCAATCCAGA 61.074 61.111 28.98 15.46 0.00 3.86
742 817 2.374830 ATCTCTCGCCGGCAATCCAG 62.375 60.000 28.98 14.04 0.00 3.86
761 836 0.390340 ACTGCTCGGTCTCGTACGTA 60.390 55.000 16.05 1.79 37.69 3.57
765 840 0.604511 TGTCACTGCTCGGTCTCGTA 60.605 55.000 0.00 0.00 37.69 3.43
766 841 1.897137 TGTCACTGCTCGGTCTCGT 60.897 57.895 0.00 0.00 37.69 4.18
767 842 1.442857 GTGTCACTGCTCGGTCTCG 60.443 63.158 0.00 0.00 37.82 4.04
768 843 0.387878 CAGTGTCACTGCTCGGTCTC 60.388 60.000 19.69 0.00 39.62 3.36
769 844 1.662608 CAGTGTCACTGCTCGGTCT 59.337 57.895 19.69 0.00 39.62 3.85
770 845 4.251760 CAGTGTCACTGCTCGGTC 57.748 61.111 19.69 0.00 39.62 4.79
803 890 3.200593 CAGGCAGATCGGTGCAGC 61.201 66.667 5.64 5.64 45.93 5.25
804 891 3.200593 GCAGGCAGATCGGTGCAG 61.201 66.667 8.97 2.61 45.93 4.41
805 892 4.783621 GGCAGGCAGATCGGTGCA 62.784 66.667 8.97 0.00 45.93 4.57
806 893 2.593468 TTAGGCAGGCAGATCGGTGC 62.593 60.000 0.00 0.00 43.19 5.01
807 894 0.107703 TTTAGGCAGGCAGATCGGTG 60.108 55.000 0.00 0.00 0.00 4.94
808 895 0.839946 ATTTAGGCAGGCAGATCGGT 59.160 50.000 0.00 0.00 0.00 4.69
809 896 2.839486 TATTTAGGCAGGCAGATCGG 57.161 50.000 0.00 0.00 0.00 4.18
810 897 3.058639 GCTTTATTTAGGCAGGCAGATCG 60.059 47.826 0.00 0.00 0.00 3.69
811 898 3.885297 TGCTTTATTTAGGCAGGCAGATC 59.115 43.478 0.00 0.00 0.00 2.75
812 899 3.902218 TGCTTTATTTAGGCAGGCAGAT 58.098 40.909 0.00 0.00 0.00 2.90
813 900 3.364460 TGCTTTATTTAGGCAGGCAGA 57.636 42.857 0.00 0.00 0.00 4.26
818 905 2.099098 CCGGGTTGCTTTATTTAGGCAG 59.901 50.000 0.00 0.00 37.28 4.85
906 993 1.679559 GATGCATGCCCAGGGTTTCC 61.680 60.000 16.68 0.00 0.00 3.13
913 1000 3.945434 GACGCGATGCATGCCCAG 61.945 66.667 15.93 7.13 0.00 4.45
988 1076 0.455815 TCAGTCATGTGATCGGTCGG 59.544 55.000 0.00 0.00 0.00 4.79
990 1078 2.534298 CTGTCAGTCATGTGATCGGTC 58.466 52.381 0.00 0.00 0.00 4.79
991 1079 1.205655 CCTGTCAGTCATGTGATCGGT 59.794 52.381 0.00 0.00 0.00 4.69
992 1080 1.931906 CCTGTCAGTCATGTGATCGG 58.068 55.000 0.00 0.00 0.00 4.18
993 1081 1.284657 GCCTGTCAGTCATGTGATCG 58.715 55.000 0.00 0.00 0.00 3.69
994 1082 1.284657 CGCCTGTCAGTCATGTGATC 58.715 55.000 0.00 0.00 0.00 2.92
995 1083 0.742281 GCGCCTGTCAGTCATGTGAT 60.742 55.000 0.00 0.00 0.00 3.06
996 1084 1.374631 GCGCCTGTCAGTCATGTGA 60.375 57.895 0.00 0.00 0.00 3.58
997 1085 1.229975 TTGCGCCTGTCAGTCATGTG 61.230 55.000 4.18 0.00 0.00 3.21
998 1086 0.952497 CTTGCGCCTGTCAGTCATGT 60.952 55.000 4.18 0.00 0.00 3.21
999 1087 0.671472 TCTTGCGCCTGTCAGTCATG 60.671 55.000 4.18 0.00 0.00 3.07
1000 1088 0.251354 ATCTTGCGCCTGTCAGTCAT 59.749 50.000 4.18 0.00 0.00 3.06
1001 1089 0.671472 CATCTTGCGCCTGTCAGTCA 60.671 55.000 4.18 0.00 0.00 3.41
1005 1093 2.747460 GGCATCTTGCGCCTGTCA 60.747 61.111 4.18 0.00 46.21 3.58
1170 1270 3.266964 TCGTAAGGGGACACGACG 58.733 61.111 0.00 0.00 41.89 5.12
1182 1282 3.140141 CGGTAGCGGGGGTCGTAA 61.140 66.667 6.39 0.00 41.72 3.18
1211 1311 0.452184 CACGAGGCAGACGATGTAGT 59.548 55.000 0.00 0.00 34.70 2.73
1254 1354 0.458716 GGAGGAAGCCGAACTCGAAG 60.459 60.000 0.00 0.00 43.02 3.79
1310 1410 2.019951 GCGAAGAAGGCGTTGACGA 61.020 57.895 7.85 0.00 43.02 4.20
1341 1441 2.095252 GGCGACGAAGAAGGTGAGC 61.095 63.158 0.00 0.00 0.00 4.26
1389 1489 4.143333 ATCTTGGCGGGGTCGTCG 62.143 66.667 0.00 0.00 45.11 5.12
1695 1795 2.570135 GAGATGCTGATCCAGGTTTCC 58.430 52.381 0.00 0.00 31.21 3.13
1698 1798 1.588239 TGGAGATGCTGATCCAGGTT 58.412 50.000 0.88 0.00 40.70 3.50
1733 1833 1.298859 GCGGTTCCAAATGCTCTCGT 61.299 55.000 0.00 0.00 0.00 4.18
1741 1841 1.303091 GCCACGTAGCGGTTCCAAAT 61.303 55.000 0.00 0.00 28.63 2.32
2183 2288 0.249657 GCGAGATGCTGGACCTAAGG 60.250 60.000 0.00 0.00 41.73 2.69
2184 2289 0.461548 TGCGAGATGCTGGACCTAAG 59.538 55.000 0.00 0.00 46.63 2.18
2186 2291 1.676678 GGTGCGAGATGCTGGACCTA 61.677 60.000 0.00 0.00 46.63 3.08
2309 2414 5.880887 GTGTATGGCATCATCATCATCATCT 59.119 40.000 1.65 0.00 34.96 2.90
2310 2415 5.880887 AGTGTATGGCATCATCATCATCATC 59.119 40.000 1.65 0.00 34.96 2.92
2311 2416 5.648092 CAGTGTATGGCATCATCATCATCAT 59.352 40.000 1.65 0.00 34.96 2.45
2312 2417 5.001232 CAGTGTATGGCATCATCATCATCA 58.999 41.667 1.65 0.00 34.96 3.07
2330 2438 1.963515 GTTGAGCAAATTCCCCAGTGT 59.036 47.619 0.00 0.00 0.00 3.55
2333 2441 1.547372 CCAGTTGAGCAAATTCCCCAG 59.453 52.381 0.00 0.00 0.00 4.45
2368 2484 1.672356 CCGACACCTTCCCAAGCAG 60.672 63.158 0.00 0.00 0.00 4.24
2385 2501 1.008309 GTACTCGGCGCTCATCTCC 60.008 63.158 7.64 0.00 0.00 3.71
2533 2649 3.118482 ACTCACATGGATCAGCGAGAAAT 60.118 43.478 0.00 0.00 0.00 2.17
2592 2708 2.281970 CTTGCCTGCTCTGCACCA 60.282 61.111 0.00 0.00 38.72 4.17
2618 2734 6.483974 TGTATGAAAAAGGAACAAAGCGTAGA 59.516 34.615 0.00 0.00 0.00 2.59
2624 2740 5.403466 GCTGCTGTATGAAAAAGGAACAAAG 59.597 40.000 0.00 0.00 0.00 2.77
2625 2741 5.068987 AGCTGCTGTATGAAAAAGGAACAAA 59.931 36.000 0.00 0.00 0.00 2.83
2715 2835 0.936764 CCGATCTCGCCGATGACTTG 60.937 60.000 0.00 0.00 38.18 3.16
3129 3254 3.013921 GCAGTTATCGGTTTCATTGGGA 58.986 45.455 0.00 0.00 0.00 4.37
3170 3295 6.089417 GGTTGAGAAGCAAAATTAATTCGTGG 59.911 38.462 0.10 0.00 38.44 4.94
3186 3793 5.106673 GGACCGTTAATTTCTGGTTGAGAAG 60.107 44.000 0.00 0.00 41.86 2.85
3196 3803 7.645058 ATCAAATCATGGACCGTTAATTTCT 57.355 32.000 0.00 0.00 0.00 2.52
3255 3862 2.486636 TAACGCACTGCTCACTCCCG 62.487 60.000 0.00 0.00 0.00 5.14
3297 3904 0.106708 TACCTCTGGCATTCGCATCC 59.893 55.000 0.00 0.00 41.24 3.51
3320 3927 5.462068 AGATTTTCAAAACTTTTAGGCGCAC 59.538 36.000 10.83 0.00 0.00 5.34
3323 3930 6.308041 GCCTAGATTTTCAAAACTTTTAGGCG 59.692 38.462 14.87 0.00 33.40 5.52
3325 3932 9.541143 TTTGCCTAGATTTTCAAAACTTTTAGG 57.459 29.630 0.00 6.50 0.00 2.69
3400 4082 1.638133 CTTCTGGATCTGCACGTCAG 58.362 55.000 8.24 8.24 44.21 3.51
3461 4143 4.935495 CAGCACCTGCACCACGGT 62.935 66.667 0.00 0.00 45.16 4.83
3649 4333 1.450312 CCTGACCATCCTGGCGTTC 60.450 63.158 0.00 0.00 42.67 3.95
3754 4438 1.264020 GCGAACAGTTGCTGAATGTCA 59.736 47.619 2.91 0.00 35.18 3.58
3889 4573 4.463879 CTGGGCGGCAGGACTCTG 62.464 72.222 12.47 0.00 43.64 3.35
4160 7491 2.164865 AACACGAGCAGCCTCCTCTG 62.165 60.000 0.00 0.00 34.49 3.35
4235 7566 0.101219 GTTATTACCCTCGTCGCCGT 59.899 55.000 0.00 0.00 35.01 5.68
4395 7726 4.542697 ACAACCAGGTTCCAAGTGTAATT 58.457 39.130 0.12 0.00 0.00 1.40
4396 7727 4.178956 ACAACCAGGTTCCAAGTGTAAT 57.821 40.909 0.12 0.00 0.00 1.89
4397 7728 3.655615 ACAACCAGGTTCCAAGTGTAA 57.344 42.857 0.12 0.00 0.00 2.41
4398 7729 4.986054 ATACAACCAGGTTCCAAGTGTA 57.014 40.909 0.12 1.66 0.00 2.90
4401 7732 5.667466 CGTATATACAACCAGGTTCCAAGT 58.333 41.667 13.22 0.00 0.00 3.16
4402 7733 4.510340 GCGTATATACAACCAGGTTCCAAG 59.490 45.833 13.22 0.00 0.00 3.61
4403 7734 4.162698 AGCGTATATACAACCAGGTTCCAA 59.837 41.667 13.22 0.00 0.00 3.53
4404 7735 3.707611 AGCGTATATACAACCAGGTTCCA 59.292 43.478 13.22 0.00 0.00 3.53
4405 7736 4.038883 AGAGCGTATATACAACCAGGTTCC 59.961 45.833 13.22 0.00 0.00 3.62
4406 7737 5.197682 AGAGCGTATATACAACCAGGTTC 57.802 43.478 13.22 3.42 0.00 3.62
4409 7740 6.457934 CCGTATAGAGCGTATATACAACCAGG 60.458 46.154 13.22 0.00 36.37 4.45
4484 7815 7.084486 GGTGCGAAAGAAAGTCAGATTTATTT 58.916 34.615 0.00 0.00 36.56 1.40
4485 7816 6.206634 TGGTGCGAAAGAAAGTCAGATTTATT 59.793 34.615 0.00 0.00 0.00 1.40
4487 7818 5.060506 TGGTGCGAAAGAAAGTCAGATTTA 58.939 37.500 0.00 0.00 0.00 1.40
4490 7821 3.070018 CTGGTGCGAAAGAAAGTCAGAT 58.930 45.455 0.00 0.00 0.00 2.90
4491 7822 2.158957 ACTGGTGCGAAAGAAAGTCAGA 60.159 45.455 0.00 0.00 0.00 3.27
4492 7823 2.213499 ACTGGTGCGAAAGAAAGTCAG 58.787 47.619 0.00 0.00 0.00 3.51
4504 7838 8.903570 TTTGTGAAAATTTATATACTGGTGCG 57.096 30.769 0.00 0.00 0.00 5.34
4518 7852 7.301789 CGTTGGGTTTTCTTTTTGTGAAAATT 58.698 30.769 5.20 0.00 42.76 1.82
4533 7867 1.676006 CTGAAGTCAGCGTTGGGTTTT 59.324 47.619 0.00 0.00 37.15 2.43
4537 7871 1.672356 CCCTGAAGTCAGCGTTGGG 60.672 63.158 2.59 0.00 42.47 4.12
4543 7877 4.790765 AATTTTTAGCCCTGAAGTCAGC 57.209 40.909 2.59 0.00 42.47 4.26
4544 7878 6.015940 AGACAAATTTTTAGCCCTGAAGTCAG 60.016 38.462 1.05 1.05 43.40 3.51
4553 7887 7.546778 TTCAACAAAGACAAATTTTTAGCCC 57.453 32.000 0.00 0.00 0.00 5.19
4571 7905 4.524714 TCCACCTTTGACTTGTTTTCAACA 59.475 37.500 0.00 0.00 40.21 3.33
4572 7906 5.066968 TCCACCTTTGACTTGTTTTCAAC 57.933 39.130 0.00 0.00 35.77 3.18
4591 7925 9.061435 AGAAAAATTCCGCAAAAATAAAATCCA 57.939 25.926 0.00 0.00 0.00 3.41
4599 7933 6.538381 ACTTGTGAGAAAAATTCCGCAAAAAT 59.462 30.769 0.00 0.00 33.33 1.82
4604 7938 5.957842 ATACTTGTGAGAAAAATTCCGCA 57.042 34.783 0.00 0.00 0.00 5.69
4613 7947 7.685481 TGACCTTCCATTATACTTGTGAGAAA 58.315 34.615 0.00 0.00 0.00 2.52
4719 8054 0.816421 CGGACGTTTGGTTCCTTGGT 60.816 55.000 0.00 0.00 0.00 3.67
4722 8057 2.248835 CGCGGACGTTTGGTTCCTT 61.249 57.895 0.00 0.00 33.53 3.36
4737 8072 1.635844 TACAACCAATGCTAGACGCG 58.364 50.000 3.53 3.53 43.27 6.01
4739 8074 8.443160 CCAATATATTACAACCAATGCTAGACG 58.557 37.037 0.00 0.00 0.00 4.18
4744 8079 9.592196 AAGATCCAATATATTACAACCAATGCT 57.408 29.630 0.00 0.00 0.00 3.79
4781 8116 9.358406 TCCTATAAGTATTGTATTGTCTTCGGA 57.642 33.333 0.00 0.00 0.00 4.55
4782 8117 9.976511 TTCCTATAAGTATTGTATTGTCTTCGG 57.023 33.333 0.00 0.00 0.00 4.30
4830 8165 2.726821 GTGGATCAGATTTCCAGCCAA 58.273 47.619 0.00 0.00 43.78 4.52
4835 8170 3.184628 AGACAGGTGGATCAGATTTCCA 58.815 45.455 0.00 0.00 40.96 3.53
4842 8177 3.692257 AAGTCAAGACAGGTGGATCAG 57.308 47.619 2.72 0.00 0.00 2.90
4849 8184 7.736893 AGTTGTAGAAATAAGTCAAGACAGGT 58.263 34.615 2.72 0.00 0.00 4.00
4879 8214 1.270041 GCTAGGTCTGCCAGTAGATGC 60.270 57.143 0.00 0.00 37.19 3.91
4887 8222 2.158900 GCTAGATTTGCTAGGTCTGCCA 60.159 50.000 0.00 0.00 45.55 4.92
4898 8233 5.182001 TGGAAGTTCAAAGAGCTAGATTTGC 59.818 40.000 5.01 2.51 36.55 3.68
4905 8240 6.959639 ATTTTGTGGAAGTTCAAAGAGCTA 57.040 33.333 5.01 0.00 35.47 3.32
4906 8241 5.859205 ATTTTGTGGAAGTTCAAAGAGCT 57.141 34.783 5.01 0.00 35.47 4.09
4925 8260 3.557686 GGGTGACTAACGTGTGGGTATTT 60.558 47.826 0.00 0.00 0.00 1.40
4928 8263 0.968405 GGGTGACTAACGTGTGGGTA 59.032 55.000 0.00 0.00 0.00 3.69
4929 8264 1.750297 GGGTGACTAACGTGTGGGT 59.250 57.895 0.00 0.00 0.00 4.51
4930 8265 1.004200 GGGGTGACTAACGTGTGGG 60.004 63.158 0.00 0.00 0.00 4.61
4933 8268 4.202388 ACATTTAAGGGGTGACTAACGTGT 60.202 41.667 0.00 0.00 0.00 4.49
4934 8269 4.320870 ACATTTAAGGGGTGACTAACGTG 58.679 43.478 0.00 0.00 0.00 4.49
4935 8270 4.564199 GGACATTTAAGGGGTGACTAACGT 60.564 45.833 0.00 0.00 0.00 3.99
4936 8271 3.937079 GGACATTTAAGGGGTGACTAACG 59.063 47.826 0.00 0.00 0.00 3.18
4937 8272 3.937079 CGGACATTTAAGGGGTGACTAAC 59.063 47.826 0.00 0.00 0.00 2.34
4938 8273 3.583966 ACGGACATTTAAGGGGTGACTAA 59.416 43.478 0.00 0.00 0.00 2.24
4940 8275 1.982958 ACGGACATTTAAGGGGTGACT 59.017 47.619 0.00 0.00 0.00 3.41
4941 8276 2.081462 CACGGACATTTAAGGGGTGAC 58.919 52.381 0.00 0.00 0.00 3.67
5011 8363 8.796475 TGTAGAACTACGTAGGTCATTTTAACT 58.204 33.333 35.43 18.71 42.47 2.24
5020 8372 5.353678 AGTGACATGTAGAACTACGTAGGTC 59.646 44.000 29.40 29.40 40.33 3.85
5060 8412 4.960938 TCCTCATAACTGGTACATCATGC 58.039 43.478 0.00 0.00 38.20 4.06
5158 8510 0.252696 GCCCCTTCATCCCCCTTTTT 60.253 55.000 0.00 0.00 0.00 1.94
5161 8513 3.029981 GGCCCCTTCATCCCCCTT 61.030 66.667 0.00 0.00 0.00 3.95
5174 8526 1.304134 AATTCAACTCGGGTGGCCC 60.304 57.895 0.00 0.00 41.09 5.80
5175 8527 1.595093 CCAATTCAACTCGGGTGGCC 61.595 60.000 0.00 0.00 0.00 5.36
5176 8528 1.595093 CCCAATTCAACTCGGGTGGC 61.595 60.000 0.00 0.00 33.67 5.01
5177 8529 0.965363 CCCCAATTCAACTCGGGTGG 60.965 60.000 0.00 0.00 36.92 4.61
5179 8531 1.382629 CCCCCAATTCAACTCGGGT 59.617 57.895 0.00 0.00 36.92 5.28
5180 8532 4.337013 CCCCCAATTCAACTCGGG 57.663 61.111 0.00 0.00 38.52 5.14
5196 8548 2.859971 TAACACCACCCCACCCCC 60.860 66.667 0.00 0.00 0.00 5.40
5197 8549 1.722110 AACTAACACCACCCCACCCC 61.722 60.000 0.00 0.00 0.00 4.95
5198 8550 0.186630 AAACTAACACCACCCCACCC 59.813 55.000 0.00 0.00 0.00 4.61
5199 8551 1.133730 TCAAACTAACACCACCCCACC 60.134 52.381 0.00 0.00 0.00 4.61
5200 8552 2.351706 TCAAACTAACACCACCCCAC 57.648 50.000 0.00 0.00 0.00 4.61
5201 8553 3.383698 TTTCAAACTAACACCACCCCA 57.616 42.857 0.00 0.00 0.00 4.96
5202 8554 3.702548 ACTTTTCAAACTAACACCACCCC 59.297 43.478 0.00 0.00 0.00 4.95
5203 8555 4.994907 ACTTTTCAAACTAACACCACCC 57.005 40.909 0.00 0.00 0.00 4.61
5204 8556 7.541162 ACTTAACTTTTCAAACTAACACCACC 58.459 34.615 0.00 0.00 0.00 4.61
5276 8817 1.774639 GCTACTTCCGTGACGAACAA 58.225 50.000 6.54 0.00 0.00 2.83
5288 8829 2.750948 TGTGTCTTCAACCGCTACTTC 58.249 47.619 0.00 0.00 0.00 3.01
5295 8836 3.980646 TCCATTTTGTGTCTTCAACCG 57.019 42.857 0.00 0.00 0.00 4.44
5306 8847 2.618053 GACCGACTCGATCCATTTTGT 58.382 47.619 0.00 0.00 0.00 2.83
5310 8851 1.734137 CGGACCGACTCGATCCATT 59.266 57.895 12.55 0.00 32.35 3.16
5328 8869 1.929836 CGAATACCTTCAGCAGTGAGC 59.070 52.381 0.00 0.00 46.19 4.26
5334 8875 3.447229 TGACAGATCGAATACCTTCAGCA 59.553 43.478 0.00 0.00 0.00 4.41
5337 8878 5.359756 CCAATGACAGATCGAATACCTTCA 58.640 41.667 0.00 0.00 0.00 3.02
5342 8883 3.733337 AGGCCAATGACAGATCGAATAC 58.267 45.455 5.01 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.