Multiple sequence alignment - TraesCS7B01G103500

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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 TraesCS7B01G103500 chr7B 100.000 3532 0 0 1 3532 118975006 118978537 0.000000e+00 6523.0
1 TraesCS7B01G103500 chr7B 100.000 1787 0 0 3753 5539 118978758 118980544 0.000000e+00 3301.0
2 TraesCS7B01G103500 chr7B 95.037 806 16 2 1 782 32327147 32327952 0.000000e+00 1245.0
3 TraesCS7B01G103500 chr7B 94.431 808 20 3 1 784 701323298 701324104 0.000000e+00 1219.0
4 TraesCS7B01G103500 chr7B 92.617 596 18 2 1 570 380059367 380059962 0.000000e+00 833.0
5 TraesCS7B01G103500 chr7B 88.235 136 15 1 1278 1412 579561210 579561075 1.600000e-35 161.0
6 TraesCS7B01G103500 chr7B 93.976 83 3 2 4292 4373 701408191 701408272 2.100000e-24 124.0
7 TraesCS7B01G103500 chr7B 96.000 50 2 0 4223 4272 1283828 1283779 1.280000e-11 82.4
8 TraesCS7B01G103500 chr7B 94.340 53 2 1 4213 4265 747110352 747110301 4.600000e-11 80.5
9 TraesCS7B01G103500 chr7B 91.667 48 3 1 4022 4068 749533680 749533633 1.290000e-06 65.8
10 TraesCS7B01G103500 chr7B 100.000 33 0 0 4018 4050 656276030 656275998 1.670000e-05 62.1
11 TraesCS7B01G103500 chr7D 93.310 1734 101 9 1493 3214 156684772 156686502 0.000000e+00 2545.0
12 TraesCS7B01G103500 chr7D 96.532 894 18 6 4363 5248 156687429 156688317 0.000000e+00 1467.0
13 TraesCS7B01G103500 chr7D 92.391 644 15 2 782 1415 156684086 156684705 0.000000e+00 887.0
14 TraesCS7B01G103500 chr7D 95.279 466 17 5 3762 4226 156686971 156687432 0.000000e+00 734.0
15 TraesCS7B01G103500 chr7D 96.233 292 11 0 5248 5539 156688346 156688637 3.880000e-131 479.0
16 TraesCS7B01G103500 chr7D 94.737 285 11 2 3213 3495 156686584 156686866 1.830000e-119 440.0
17 TraesCS7B01G103500 chr7D 91.228 57 4 1 4017 4072 633508590 633508534 5.950000e-10 76.8
18 TraesCS7B01G103500 chr7D 92.453 53 3 1 4017 4068 633507104 633507052 2.140000e-09 75.0
19 TraesCS7B01G103500 chr7A 92.746 1737 107 13 1493 3214 211638156 211639888 0.000000e+00 2492.0
20 TraesCS7B01G103500 chr7A 90.373 966 60 18 4292 5248 211640855 211641796 0.000000e+00 1238.0
21 TraesCS7B01G103500 chr7A 95.039 645 21 2 782 1415 211637433 211638077 0.000000e+00 1003.0
22 TraesCS7B01G103500 chr7A 89.038 520 41 10 3762 4267 211640370 211640887 1.010000e-176 630.0
23 TraesCS7B01G103500 chr7A 95.205 292 14 0 5248 5539 211641825 211642116 3.910000e-126 462.0
24 TraesCS7B01G103500 chr7A 90.411 292 19 2 3213 3495 211639975 211640266 5.240000e-100 375.0
25 TraesCS7B01G103500 chr7A 91.071 56 4 1 4014 4068 733624896 733624951 2.140000e-09 75.0
26 TraesCS7B01G103500 chr7A 100.000 33 0 0 4018 4050 676347105 676347073 1.670000e-05 62.1
27 TraesCS7B01G103500 chr5B 95.545 808 12 2 1 784 527498888 527498081 0.000000e+00 1271.0
28 TraesCS7B01G103500 chr5B 94.575 811 20 2 1 787 467125666 467124856 0.000000e+00 1232.0
29 TraesCS7B01G103500 chr5B 94.431 808 25 9 1 788 127704007 127703200 0.000000e+00 1225.0
30 TraesCS7B01G103500 chr5B 93.936 808 19 4 1 784 315933306 315934107 0.000000e+00 1194.0
31 TraesCS7B01G103500 chr5B 93.812 808 17 3 1 784 670703209 670704007 0.000000e+00 1184.0
32 TraesCS7B01G103500 chr5B 93.317 808 29 2 1 785 315194867 315194062 0.000000e+00 1170.0
33 TraesCS7B01G103500 chr5B 92.593 81 5 1 4292 4372 134923392 134923471 1.260000e-21 115.0
34 TraesCS7B01G103500 chr4B 95.303 809 13 3 1 784 491803670 491804478 0.000000e+00 1260.0
35 TraesCS7B01G103500 chr4B 95.191 811 14 3 1 787 445267933 445267124 0.000000e+00 1258.0
36 TraesCS7B01G103500 chr4B 94.932 809 16 3 1 785 447793160 447793967 0.000000e+00 1243.0
37 TraesCS7B01G103500 chr4B 92.857 84 6 0 4292 4375 192792757 192792840 7.540000e-24 122.0
38 TraesCS7B01G103500 chr4B 92.982 57 3 1 3757 3813 191087080 191087135 1.280000e-11 82.4
39 TraesCS7B01G103500 chr6B 95.056 809 16 2 1 785 644391273 644390465 0.000000e+00 1251.0
40 TraesCS7B01G103500 chr6B 92.481 133 10 0 1278 1410 601874130 601874262 2.040000e-44 191.0
41 TraesCS7B01G103500 chr6B 85.294 136 19 1 1278 1412 663291303 663291438 7.480000e-29 139.0
42 TraesCS7B01G103500 chr6B 93.220 59 3 1 1132 1190 601873964 601874021 9.890000e-13 86.1
43 TraesCS7B01G103500 chr6B 96.078 51 2 0 4223 4273 632889535 632889485 3.560000e-12 84.2
44 TraesCS7B01G103500 chr6B 92.453 53 4 0 4217 4269 552761565 552761617 5.950000e-10 76.8
45 TraesCS7B01G103500 chr2B 94.828 812 18 2 1 788 433081309 433080498 0.000000e+00 1245.0
46 TraesCS7B01G103500 chr1B 94.894 803 17 2 1 779 484911021 484910219 0.000000e+00 1234.0
47 TraesCS7B01G103500 chr1B 88.971 136 14 1 1278 1412 177477854 177477719 3.430000e-37 167.0
48 TraesCS7B01G103500 chr6A 80.000 295 38 16 1132 1410 547822149 547822438 1.220000e-46 198.0
49 TraesCS7B01G103500 chr6A 92.683 82 6 0 4292 4373 190660424 190660343 9.750000e-23 119.0
50 TraesCS7B01G103500 chr6A 92.683 82 6 0 4292 4373 190738347 190738266 9.750000e-23 119.0
51 TraesCS7B01G103500 chr6D 90.000 150 12 3 1278 1425 401301256 401301404 2.040000e-44 191.0
52 TraesCS7B01G103500 chr6D 94.545 55 3 0 1136 1190 401301116 401301170 9.890000e-13 86.1
53 TraesCS7B01G103500 chr5D 90.909 88 8 0 4292 4379 532592534 532592447 9.750000e-23 119.0
54 TraesCS7B01G103500 chr5D 96.000 50 2 0 4223 4272 494775530 494775481 1.280000e-11 82.4
55 TraesCS7B01G103500 chr5D 90.164 61 6 0 4007 4067 276289727 276289667 4.600000e-11 80.5
56 TraesCS7B01G103500 chr2D 91.011 89 6 2 4292 4378 534925539 534925451 9.750000e-23 119.0
57 TraesCS7B01G103500 chr2D 90.000 90 8 1 4292 4380 79051082 79050993 1.260000e-21 115.0
58 TraesCS7B01G103500 chr2D 97.872 47 1 0 4223 4269 528081701 528081747 1.280000e-11 82.4
59 TraesCS7B01G103500 chr1D 98.039 51 1 0 4223 4273 302256709 302256659 7.640000e-14 89.8
60 TraesCS7B01G103500 chr3A 96.000 50 2 0 4223 4272 551729079 551729030 1.280000e-11 82.4
61 TraesCS7B01G103500 chr3D 91.837 49 3 1 3765 3813 156240579 156240626 3.580000e-07 67.6
62 TraesCS7B01G103500 chr3B 91.489 47 3 1 3762 3807 731499416 731499462 4.630000e-06 63.9


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 TraesCS7B01G103500 chr7B 118975006 118980544 5538 False 4912.000000 6523 100.000000 1 5539 2 chr7B.!!$F5 5538
1 TraesCS7B01G103500 chr7B 32327147 32327952 805 False 1245.000000 1245 95.037000 1 782 1 chr7B.!!$F1 781
2 TraesCS7B01G103500 chr7B 701323298 701324104 806 False 1219.000000 1219 94.431000 1 784 1 chr7B.!!$F3 783
3 TraesCS7B01G103500 chr7B 380059367 380059962 595 False 833.000000 833 92.617000 1 570 1 chr7B.!!$F2 569
4 TraesCS7B01G103500 chr7D 156684086 156688637 4551 False 1092.000000 2545 94.747000 782 5539 6 chr7D.!!$F1 4757
5 TraesCS7B01G103500 chr7A 211637433 211642116 4683 False 1033.333333 2492 92.135333 782 5539 6 chr7A.!!$F2 4757
6 TraesCS7B01G103500 chr5B 527498081 527498888 807 True 1271.000000 1271 95.545000 1 784 1 chr5B.!!$R4 783
7 TraesCS7B01G103500 chr5B 467124856 467125666 810 True 1232.000000 1232 94.575000 1 787 1 chr5B.!!$R3 786
8 TraesCS7B01G103500 chr5B 127703200 127704007 807 True 1225.000000 1225 94.431000 1 788 1 chr5B.!!$R1 787
9 TraesCS7B01G103500 chr5B 315933306 315934107 801 False 1194.000000 1194 93.936000 1 784 1 chr5B.!!$F2 783
10 TraesCS7B01G103500 chr5B 670703209 670704007 798 False 1184.000000 1184 93.812000 1 784 1 chr5B.!!$F3 783
11 TraesCS7B01G103500 chr5B 315194062 315194867 805 True 1170.000000 1170 93.317000 1 785 1 chr5B.!!$R2 784
12 TraesCS7B01G103500 chr4B 491803670 491804478 808 False 1260.000000 1260 95.303000 1 784 1 chr4B.!!$F4 783
13 TraesCS7B01G103500 chr4B 445267124 445267933 809 True 1258.000000 1258 95.191000 1 787 1 chr4B.!!$R1 786
14 TraesCS7B01G103500 chr4B 447793160 447793967 807 False 1243.000000 1243 94.932000 1 785 1 chr4B.!!$F3 784
15 TraesCS7B01G103500 chr6B 644390465 644391273 808 True 1251.000000 1251 95.056000 1 785 1 chr6B.!!$R2 784
16 TraesCS7B01G103500 chr2B 433080498 433081309 811 True 1245.000000 1245 94.828000 1 788 1 chr2B.!!$R1 787
17 TraesCS7B01G103500 chr1B 484910219 484911021 802 True 1234.000000 1234 94.894000 1 779 1 chr1B.!!$R2 778

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
43 44 1.137086 TGCTCTTCGATAGTTGGCTCC 59.863 52.381 0.00 0.0 37.40 4.70 F
999 1043 1.608336 ACCTCGACATCCACCGGAA 60.608 57.895 9.46 0.0 34.34 4.30 F
1450 1495 0.178990 GCCTTCCCCACAAGACACTT 60.179 55.000 0.00 0.0 0.00 3.16 F
2028 2107 0.179097 CGAGAAGCTTAGCCAGTCCC 60.179 60.000 0.00 0.0 0.00 4.46 F
2740 2822 1.134340 ACTGTCACGGTTGCTTTACCA 60.134 47.619 0.00 0.0 38.12 3.25 F
3358 3534 1.177401 GCCCCTTTGCTTTGAGTAGG 58.823 55.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1056 1100 0.032017 GCAGGTAAGGAGGAGGAGGA 60.032 60.000 0.0 0.0 0.00 3.71 R
2009 2088 0.179097 GGGACTGGCTAAGCTTCTCG 60.179 60.000 0.0 0.0 0.00 4.04 R
3015 3097 1.390463 GACGGAATGAAACAGCGAGAC 59.610 52.381 0.0 0.0 0.00 3.36 R
3754 3952 0.032416 CTCCTTCCTCCCCGTCCTTA 60.032 60.000 0.0 0.0 0.00 2.69 R
3760 3958 0.033011 TCTCTTCTCCTTCCTCCCCG 60.033 60.000 0.0 0.0 0.00 5.73 R
4646 4861 0.242017 GCGAAATGAGCCTTTGTGCT 59.758 50.000 0.0 0.0 46.37 4.40 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
43 44 1.137086 TGCTCTTCGATAGTTGGCTCC 59.863 52.381 0.00 0.00 37.40 4.70
415 439 7.878477 ATTCTTCGTTACAGAATCGTTACAA 57.122 32.000 0.00 0.00 36.42 2.41
499 523 4.156008 GGGCAACTCAATTCTTCGTTACAT 59.844 41.667 0.00 0.00 0.00 2.29
998 1042 2.036731 ACCTCGACATCCACCGGA 59.963 61.111 9.46 0.00 35.55 5.14
999 1043 1.608336 ACCTCGACATCCACCGGAA 60.608 57.895 9.46 0.00 34.34 4.30
1224 1268 2.125106 GCTCTCCCGTTTCCGCAT 60.125 61.111 0.00 0.00 0.00 4.73
1225 1269 2.464459 GCTCTCCCGTTTCCGCATG 61.464 63.158 0.00 0.00 0.00 4.06
1415 1460 1.299976 GTCGGGGTGAGCCTTGATT 59.700 57.895 0.00 0.00 34.45 2.57
1416 1461 0.322546 GTCGGGGTGAGCCTTGATTT 60.323 55.000 0.00 0.00 34.45 2.17
1418 1463 1.032114 CGGGGTGAGCCTTGATTTCC 61.032 60.000 0.00 0.00 34.45 3.13
1419 1464 0.332972 GGGGTGAGCCTTGATTTCCT 59.667 55.000 0.00 0.00 34.45 3.36
1420 1465 1.272704 GGGGTGAGCCTTGATTTCCTT 60.273 52.381 0.00 0.00 34.45 3.36
1422 1467 1.203287 GGTGAGCCTTGATTTCCTTGC 59.797 52.381 0.00 0.00 0.00 4.01
1423 1468 1.203287 GTGAGCCTTGATTTCCTTGCC 59.797 52.381 0.00 0.00 0.00 4.52
1424 1469 1.076024 TGAGCCTTGATTTCCTTGCCT 59.924 47.619 0.00 0.00 0.00 4.75
1425 1470 1.475682 GAGCCTTGATTTCCTTGCCTG 59.524 52.381 0.00 0.00 0.00 4.85
1426 1471 0.533951 GCCTTGATTTCCTTGCCTGG 59.466 55.000 0.00 0.00 0.00 4.45
1427 1472 0.533951 CCTTGATTTCCTTGCCTGGC 59.466 55.000 12.87 12.87 0.00 4.85
1428 1473 1.259609 CTTGATTTCCTTGCCTGGCA 58.740 50.000 19.30 19.30 36.47 4.92
1429 1474 1.829222 CTTGATTTCCTTGCCTGGCAT 59.171 47.619 24.03 5.98 38.76 4.40
1430 1475 1.187974 TGATTTCCTTGCCTGGCATG 58.812 50.000 24.03 23.76 38.76 4.06
1442 1487 4.380945 GGCATGGCCTTCCCCACA 62.381 66.667 8.35 0.00 46.69 4.17
1443 1488 2.283821 GCATGGCCTTCCCCACAA 60.284 61.111 3.32 0.00 37.79 3.33
1444 1489 2.353610 GCATGGCCTTCCCCACAAG 61.354 63.158 3.32 0.00 37.79 3.16
1445 1490 1.383799 CATGGCCTTCCCCACAAGA 59.616 57.895 3.32 0.00 37.79 3.02
1446 1491 0.967380 CATGGCCTTCCCCACAAGAC 60.967 60.000 3.32 0.00 37.79 3.01
1447 1492 1.434513 ATGGCCTTCCCCACAAGACA 61.435 55.000 3.32 0.00 37.79 3.41
1448 1493 1.603739 GGCCTTCCCCACAAGACAC 60.604 63.158 0.00 0.00 0.00 3.67
1449 1494 1.456287 GCCTTCCCCACAAGACACT 59.544 57.895 0.00 0.00 0.00 3.55
1450 1495 0.178990 GCCTTCCCCACAAGACACTT 60.179 55.000 0.00 0.00 0.00 3.16
1451 1496 1.073284 GCCTTCCCCACAAGACACTTA 59.927 52.381 0.00 0.00 0.00 2.24
1485 1530 2.616376 TGGCATTCGATTTTACCGATGG 59.384 45.455 0.00 0.00 35.84 3.51
1486 1531 2.604614 GGCATTCGATTTTACCGATGGC 60.605 50.000 1.01 1.01 35.84 4.40
1489 1534 2.702592 TCGATTTTACCGATGGCCTT 57.297 45.000 3.32 0.00 0.00 4.35
1490 1535 2.557317 TCGATTTTACCGATGGCCTTC 58.443 47.619 3.32 6.40 0.00 3.46
1491 1536 1.260561 CGATTTTACCGATGGCCTTCG 59.739 52.381 29.01 29.01 38.83 3.79
1497 1568 1.811266 CCGATGGCCTTCGTGACAG 60.811 63.158 31.81 17.16 37.42 3.51
1499 1570 0.670546 CGATGGCCTTCGTGACAGTT 60.671 55.000 27.97 0.00 34.46 3.16
1557 1628 1.699730 ATCGGTACACATGGATCGGA 58.300 50.000 0.00 0.00 0.00 4.55
1606 1677 0.960364 GCTCAAGGTTTGGATCCGCA 60.960 55.000 7.39 0.00 0.00 5.69
1634 1705 5.301805 TCTGATCTATGCCAATTCTACACGA 59.698 40.000 0.00 0.00 0.00 4.35
1641 1712 9.337396 TCTATGCCAATTCTACACGATTTAATT 57.663 29.630 0.00 0.00 0.00 1.40
1676 1752 4.240881 AGCTGGGCAATTCTCTTCAATA 57.759 40.909 0.00 0.00 0.00 1.90
1680 1756 5.751990 GCTGGGCAATTCTCTTCAATAAATG 59.248 40.000 0.00 0.00 0.00 2.32
1712 1788 4.378616 CGGCAAGTCTTTTACATTGTTTCG 59.621 41.667 0.00 0.00 0.00 3.46
1713 1789 5.516090 GGCAAGTCTTTTACATTGTTTCGA 58.484 37.500 0.00 0.00 0.00 3.71
1743 1819 6.760291 AGAAGATTCTTTAGACCGAAACACT 58.240 36.000 0.00 0.00 32.55 3.55
1745 1821 8.532819 AGAAGATTCTTTAGACCGAAACACTAT 58.467 33.333 0.00 0.00 32.55 2.12
1746 1822 8.705048 AAGATTCTTTAGACCGAAACACTATC 57.295 34.615 0.00 0.00 0.00 2.08
1757 1833 7.987458 AGACCGAAACACTATCATGATTAATGT 59.013 33.333 14.65 12.64 37.56 2.71
1764 1840 9.553064 AACACTATCATGATTAATGTCTTCCTC 57.447 33.333 14.65 0.00 37.56 3.71
1779 1855 1.892209 TCCTCTTTTGTTCTTCCCGC 58.108 50.000 0.00 0.00 0.00 6.13
1797 1873 1.802069 GCTTGTTCAGGAGAGGACAC 58.198 55.000 0.00 0.00 0.00 3.67
1867 1943 6.500684 TGCCAATGTTAGATTTCTTCACTC 57.499 37.500 0.00 0.00 0.00 3.51
1872 1948 8.233190 CCAATGTTAGATTTCTTCACTCTGTTC 58.767 37.037 0.00 0.00 0.00 3.18
1874 1950 7.953158 TGTTAGATTTCTTCACTCTGTTCTG 57.047 36.000 0.00 0.00 0.00 3.02
1879 1955 2.487934 TCTTCACTCTGTTCTGCTTGC 58.512 47.619 0.00 0.00 0.00 4.01
1888 1964 1.960689 TGTTCTGCTTGCCCCTTTTAC 59.039 47.619 0.00 0.00 0.00 2.01
1895 1971 2.364002 GCTTGCCCCTTTTACTTGTGAA 59.636 45.455 0.00 0.00 0.00 3.18
1900 1976 3.006859 GCCCCTTTTACTTGTGAAGCAAT 59.993 43.478 0.00 0.00 36.36 3.56
1902 1978 4.990426 CCCCTTTTACTTGTGAAGCAATTG 59.010 41.667 0.00 0.00 36.36 2.32
1903 1979 5.453198 CCCCTTTTACTTGTGAAGCAATTGT 60.453 40.000 7.40 0.00 36.36 2.71
1904 1980 6.048509 CCCTTTTACTTGTGAAGCAATTGTT 58.951 36.000 7.40 0.00 36.36 2.83
1905 1981 6.018832 CCCTTTTACTTGTGAAGCAATTGTTG 60.019 38.462 7.40 0.00 36.36 3.33
1926 2005 5.437289 TGTGTTGCTGATAAAAGAAGTGG 57.563 39.130 0.00 0.00 0.00 4.00
1928 2007 3.255642 TGTTGCTGATAAAAGAAGTGGCC 59.744 43.478 0.00 0.00 0.00 5.36
1942 2021 0.817654 GTGGCCTTTCTTATGGTGGC 59.182 55.000 3.32 0.00 42.56 5.01
1985 2064 3.131396 AGACGACGATGATAAATTGGGC 58.869 45.455 0.00 0.00 0.00 5.36
1994 2073 3.489355 TGATAAATTGGGCGATGCAGAT 58.511 40.909 0.00 0.00 0.00 2.90
2003 2082 2.592861 GATGCAGATGGGGACGCC 60.593 66.667 0.53 0.53 0.00 5.68
2027 2106 0.808060 GCGAGAAGCTTAGCCAGTCC 60.808 60.000 0.00 0.00 44.04 3.85
2028 2107 0.179097 CGAGAAGCTTAGCCAGTCCC 60.179 60.000 0.00 0.00 0.00 4.46
2030 2109 1.138069 GAGAAGCTTAGCCAGTCCCTC 59.862 57.143 0.00 0.00 0.00 4.30
2051 2130 3.118629 TCGACAATGCTTCTGATAAGCCT 60.119 43.478 7.23 0.00 42.36 4.58
2052 2131 4.099419 TCGACAATGCTTCTGATAAGCCTA 59.901 41.667 7.23 0.00 42.36 3.93
2055 2134 4.572389 ACAATGCTTCTGATAAGCCTAACG 59.428 41.667 7.23 0.00 42.36 3.18
2056 2135 3.887621 TGCTTCTGATAAGCCTAACGT 57.112 42.857 7.23 0.00 42.36 3.99
2057 2136 3.521560 TGCTTCTGATAAGCCTAACGTG 58.478 45.455 7.23 0.00 42.36 4.49
2069 2148 3.197579 TAACGTGCCCATGTGCCCA 62.198 57.895 0.00 0.00 0.00 5.36
2085 2164 1.625818 GCCCACCTAGATCTGGTATGG 59.374 57.143 15.85 15.85 35.80 2.74
2096 2175 4.845225 AGATCTGGTATGGCTGATCAATCT 59.155 41.667 0.00 0.00 38.13 2.40
2103 2182 6.327365 TGGTATGGCTGATCAATCTCTTTCTA 59.673 38.462 0.00 0.00 0.00 2.10
2108 2187 7.114754 TGGCTGATCAATCTCTTTCTAATTGT 58.885 34.615 0.00 0.00 33.22 2.71
2139 2218 3.499918 GCCTAGTGACCATCATGTTATGC 59.500 47.826 0.00 0.00 0.00 3.14
2140 2219 4.707105 CCTAGTGACCATCATGTTATGCA 58.293 43.478 0.00 0.00 0.00 3.96
2172 2253 3.887621 TCTGGTGCCACATTAGTAGAC 57.112 47.619 0.00 0.00 0.00 2.59
2305 2387 3.252458 GCTTGTCCTTCGTGGTTAATTGT 59.748 43.478 0.00 0.00 37.07 2.71
2414 2496 5.683509 GCAATATGAGAAGTCAGTACCTGCT 60.684 44.000 0.00 0.00 35.66 4.24
2450 2532 2.213499 GGGATCCATTGCTTAGTCGTG 58.787 52.381 15.23 0.00 0.00 4.35
2639 2721 5.606348 TTCTTAGCATGGTTGGTTTTGTT 57.394 34.783 1.12 0.00 34.79 2.83
2740 2822 1.134340 ACTGTCACGGTTGCTTTACCA 60.134 47.619 0.00 0.00 38.12 3.25
2744 2826 1.202830 TCACGGTTGCTTTACCACCAT 60.203 47.619 0.00 0.00 38.12 3.55
2991 3073 3.705579 CAGACAGTGAGGGAGAATGAGAT 59.294 47.826 0.00 0.00 0.00 2.75
3015 3097 4.550076 AGAACATTCAAGACTGGGAGAG 57.450 45.455 0.00 0.00 0.00 3.20
3052 3134 2.482721 CCGTCCACAGTACCAAAATCAC 59.517 50.000 0.00 0.00 0.00 3.06
3068 3150 6.866248 CCAAAATCACGGTAAGCTAAACATTT 59.134 34.615 0.00 0.00 0.00 2.32
3070 3152 7.448748 AAATCACGGTAAGCTAAACATTTCT 57.551 32.000 0.00 0.00 0.00 2.52
3087 3169 8.831715 AACATTTCTCCCACATGTTTATTTTC 57.168 30.769 0.00 0.00 37.79 2.29
3148 3230 5.678583 TGGAATTTTGTTTTGAGATGCCAA 58.321 33.333 0.00 0.00 0.00 4.52
3152 3234 7.592164 GGAATTTTGTTTTGAGATGCCAATTTG 59.408 33.333 0.00 0.00 0.00 2.32
3154 3236 4.686191 TGTTTTGAGATGCCAATTTGGT 57.314 36.364 16.62 0.00 40.46 3.67
3193 3279 3.419943 TGGATGCATTGAAGTGCTTGTA 58.580 40.909 0.00 0.00 45.27 2.41
3255 3429 2.307496 TGGCCACTTCACATCCAAAT 57.693 45.000 0.00 0.00 0.00 2.32
3321 3497 7.428183 CAGGACAATGAATTTTATACGGTTTCG 59.572 37.037 0.00 0.00 43.02 3.46
3358 3534 1.177401 GCCCCTTTGCTTTGAGTAGG 58.823 55.000 0.00 0.00 0.00 3.18
3404 3580 6.531240 CACCTGTTTGTATTTATGCATTGACC 59.469 38.462 3.54 0.00 0.00 4.02
3430 3606 5.856126 ACACGTATGTAAACACATTCCAG 57.144 39.130 0.00 0.00 37.26 3.86
3818 4016 0.978146 CTGACAGGTGGGACTAGGGG 60.978 65.000 0.00 0.00 0.00 4.79
3839 4037 0.258774 AGTCTTTGCCACACCAACCT 59.741 50.000 0.00 0.00 0.00 3.50
3846 4044 1.166531 GCCACACCAACCTGACAGAC 61.167 60.000 3.32 0.00 0.00 3.51
3897 4095 0.103937 GCGCTAAGCCTCAGATCAGT 59.896 55.000 0.00 0.00 40.81 3.41
3905 4103 4.226427 AGCCTCAGATCAGTGCAATTTA 57.774 40.909 0.00 0.00 0.00 1.40
4074 4281 6.933514 TCTCTTTATCCCAAAAGGCAATTT 57.066 33.333 0.00 0.00 37.13 1.82
4113 4328 6.306987 ACTTTCACAACCATACCAGAAATCT 58.693 36.000 0.00 0.00 0.00 2.40
4198 4413 9.599866 CAAGTGGTTGTATAGTTTCTCATGATA 57.400 33.333 0.00 0.00 0.00 2.15
4240 4455 5.884322 TCTACAGTACTCCCTCTGTAAACA 58.116 41.667 0.00 0.00 43.49 2.83
4241 4456 6.309357 TCTACAGTACTCCCTCTGTAAACAA 58.691 40.000 0.00 0.00 43.49 2.83
4242 4457 5.881923 ACAGTACTCCCTCTGTAAACAAA 57.118 39.130 0.00 0.00 42.13 2.83
4243 4458 6.435292 ACAGTACTCCCTCTGTAAACAAAT 57.565 37.500 0.00 0.00 42.13 2.32
4244 4459 7.549147 ACAGTACTCCCTCTGTAAACAAATA 57.451 36.000 0.00 0.00 42.13 1.40
4245 4460 8.147244 ACAGTACTCCCTCTGTAAACAAATAT 57.853 34.615 0.00 0.00 42.13 1.28
4246 4461 9.263446 ACAGTACTCCCTCTGTAAACAAATATA 57.737 33.333 0.00 0.00 42.13 0.86
4251 4466 8.957466 ACTCCCTCTGTAAACAAATATAAAAGC 58.043 33.333 0.00 0.00 0.00 3.51
4252 4467 7.981142 TCCCTCTGTAAACAAATATAAAAGCG 58.019 34.615 0.00 0.00 0.00 4.68
4253 4468 7.608761 TCCCTCTGTAAACAAATATAAAAGCGT 59.391 33.333 0.00 0.00 0.00 5.07
4254 4469 8.241367 CCCTCTGTAAACAAATATAAAAGCGTT 58.759 33.333 0.00 0.00 0.00 4.84
4255 4470 9.620660 CCTCTGTAAACAAATATAAAAGCGTTT 57.379 29.630 2.53 2.53 0.00 3.60
4271 4486 7.448748 AAAGCGTTTAGATCACTAAAATGGT 57.551 32.000 0.00 0.00 45.97 3.55
4272 4487 7.448748 AAGCGTTTAGATCACTAAAATGGTT 57.551 32.000 0.00 4.88 45.97 3.67
4273 4488 7.448748 AGCGTTTAGATCACTAAAATGGTTT 57.551 32.000 0.00 0.00 45.97 3.27
4274 4489 8.556213 AGCGTTTAGATCACTAAAATGGTTTA 57.444 30.769 0.00 0.00 45.97 2.01
4278 4493 9.239551 GTTTAGATCACTAAAATGGTTTAGGGT 57.760 33.333 8.03 0.00 46.67 4.34
4279 4494 9.816787 TTTAGATCACTAAAATGGTTTAGGGTT 57.183 29.630 8.03 1.16 46.67 4.11
4280 4495 9.816787 TTAGATCACTAAAATGGTTTAGGGTTT 57.183 29.630 8.03 0.00 46.67 3.27
4282 4497 9.462606 AGATCACTAAAATGGTTTAGGGTTTAG 57.537 33.333 8.03 0.00 46.67 1.85
4283 4498 8.589701 ATCACTAAAATGGTTTAGGGTTTAGG 57.410 34.615 8.03 0.00 46.67 2.69
4284 4499 6.949463 TCACTAAAATGGTTTAGGGTTTAGGG 59.051 38.462 8.03 0.00 46.67 3.53
4285 4500 7.422799 TCACTAAAATGGTTTAGGGTTTAGGGT 60.423 37.037 8.03 0.00 46.67 4.34
4286 4501 7.786046 CTAAAATGGTTTAGGGTTTAGGGTT 57.214 36.000 0.00 0.00 41.71 4.11
4287 4502 8.197592 CTAAAATGGTTTAGGGTTTAGGGTTT 57.802 34.615 0.00 0.00 41.71 3.27
4288 4503 9.311676 CTAAAATGGTTTAGGGTTTAGGGTTTA 57.688 33.333 0.00 0.00 41.71 2.01
4289 4504 7.786046 AAATGGTTTAGGGTTTAGGGTTTAG 57.214 36.000 0.00 0.00 0.00 1.85
4290 4505 5.259627 TGGTTTAGGGTTTAGGGTTTAGG 57.740 43.478 0.00 0.00 0.00 2.69
4291 4506 4.044444 TGGTTTAGGGTTTAGGGTTTAGGG 59.956 45.833 0.00 0.00 0.00 3.53
4292 4507 4.044571 GGTTTAGGGTTTAGGGTTTAGGGT 59.955 45.833 0.00 0.00 0.00 4.34
4293 4508 5.252863 GGTTTAGGGTTTAGGGTTTAGGGTA 59.747 44.000 0.00 0.00 0.00 3.69
4294 4509 6.240438 GGTTTAGGGTTTAGGGTTTAGGGTAA 60.240 42.308 0.00 0.00 0.00 2.85
4295 4510 7.237982 GTTTAGGGTTTAGGGTTTAGGGTAAA 58.762 38.462 0.00 0.00 0.00 2.01
4296 4511 5.525454 AGGGTTTAGGGTTTAGGGTAAAG 57.475 43.478 0.00 0.00 0.00 1.85
4297 4512 5.172483 AGGGTTTAGGGTTTAGGGTAAAGA 58.828 41.667 0.00 0.00 0.00 2.52
4308 4523 9.064706 GGGTTTAGGGTAAAGAAATATAAGAGC 57.935 37.037 0.00 0.00 0.00 4.09
4356 4571 9.439500 ACCTAAACGCTCTTATATTTGTTTACA 57.561 29.630 0.00 0.00 32.41 2.41
4526 4741 3.387050 GGTACTTGGATCTTACACGGGAT 59.613 47.826 0.00 0.00 0.00 3.85
4529 4744 2.882927 TGGATCTTACACGGGATTCG 57.117 50.000 0.00 0.00 45.88 3.34
4610 4825 0.460987 CAACTCATCTGCCGAGGACC 60.461 60.000 0.00 0.00 34.66 4.46
4646 4861 6.693466 TCGACCTGTACAAGATGTCATAAAA 58.307 36.000 0.00 0.00 0.00 1.52
4647 4862 6.811665 TCGACCTGTACAAGATGTCATAAAAG 59.188 38.462 0.00 0.00 0.00 2.27
4731 4946 6.748333 AATGATACACTTGACTGTCCATTG 57.252 37.500 5.17 1.57 31.61 2.82
4827 5046 4.127171 TGTCTCCAGCAAAGTGTTACTTC 58.873 43.478 0.00 0.00 37.47 3.01
4852 5071 4.832266 CAGCTGTATAAGAGAGGAGATGGT 59.168 45.833 5.25 0.00 0.00 3.55
4855 5074 5.303078 GCTGTATAAGAGAGGAGATGGTTGA 59.697 44.000 0.00 0.00 0.00 3.18
4937 5156 6.791887 TTTCAGTCAGCTTTGATGAGTTAG 57.208 37.500 0.00 0.00 0.00 2.34
4984 5205 4.301072 AAACCTTGACAGGCTATGCTAA 57.699 40.909 0.00 0.00 45.56 3.09
5056 5277 6.286240 TGCATCTGAGTACTACAACAAGAT 57.714 37.500 0.00 0.00 0.00 2.40
5082 5303 6.119536 TGGGCTGTTAGATAAAATGTGGTAG 58.880 40.000 0.00 0.00 0.00 3.18
5083 5304 6.120220 GGGCTGTTAGATAAAATGTGGTAGT 58.880 40.000 0.00 0.00 0.00 2.73
5084 5305 7.092802 TGGGCTGTTAGATAAAATGTGGTAGTA 60.093 37.037 0.00 0.00 0.00 1.82
5101 5322 7.834881 TGGTAGTACCAGGATTGACTTATAG 57.165 40.000 18.45 0.00 44.79 1.31
5164 5390 6.956202 TGCCAAAATTCACAAATTCCAAAT 57.044 29.167 0.00 0.00 33.93 2.32
5254 5509 2.416547 GTCTGCAGTAATCGCAACACAT 59.583 45.455 14.67 0.00 39.30 3.21
5263 5518 7.243487 CAGTAATCGCAACACATCAACTAAAT 58.757 34.615 0.00 0.00 0.00 1.40
5370 5625 5.415701 TCACATGGTTCTTTCAATAAGAGGC 59.584 40.000 0.00 0.00 0.00 4.70
5463 5718 4.267928 CCACAACAGTTACTAATAGCGAGC 59.732 45.833 0.00 0.00 0.00 5.03
5467 5722 3.700038 ACAGTTACTAATAGCGAGCCACT 59.300 43.478 0.00 0.00 0.00 4.00
5473 5728 0.176680 AATAGCGAGCCACTGACAGG 59.823 55.000 7.51 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
461 485 2.762459 CCCTGGCGGTAGGCTGTA 60.762 66.667 0.00 0.00 44.18 2.74
499 523 4.157289 GGTCCTGTCTCAGTGTAACGATTA 59.843 45.833 0.00 0.00 45.86 1.75
695 727 5.975693 TCGAAATTTGACCCTTTTGCTAT 57.024 34.783 0.00 0.00 0.00 2.97
971 1015 1.829222 GATGTCGAGGTGGAAAGGGTA 59.171 52.381 0.00 0.00 0.00 3.69
1053 1097 0.105401 GGTAAGGAGGAGGAGGAGGG 60.105 65.000 0.00 0.00 0.00 4.30
1056 1100 0.032017 GCAGGTAAGGAGGAGGAGGA 60.032 60.000 0.00 0.00 0.00 3.71
1224 1268 1.083080 CGAAATGCACAACGCGTCA 60.083 52.632 14.44 6.50 46.97 4.35
1225 1269 2.417553 GCGAAATGCACAACGCGTC 61.418 57.895 14.44 0.00 46.97 5.19
1410 1455 1.551430 CATGCCAGGCAAGGAAATCAA 59.449 47.619 20.84 0.00 43.62 2.57
1426 1471 2.283821 TTGTGGGGAAGGCCATGC 60.284 61.111 5.01 0.00 35.15 4.06
1427 1472 0.967380 GTCTTGTGGGGAAGGCCATG 60.967 60.000 5.01 0.00 35.15 3.66
1428 1473 1.384191 GTCTTGTGGGGAAGGCCAT 59.616 57.895 5.01 0.00 35.15 4.40
1429 1474 2.081787 TGTCTTGTGGGGAAGGCCA 61.082 57.895 5.01 0.00 35.15 5.36
1430 1475 1.603739 GTGTCTTGTGGGGAAGGCC 60.604 63.158 0.00 0.00 0.00 5.19
1431 1476 0.178990 AAGTGTCTTGTGGGGAAGGC 60.179 55.000 0.00 0.00 0.00 4.35
1432 1477 3.721087 ATAAGTGTCTTGTGGGGAAGG 57.279 47.619 0.00 0.00 0.00 3.46
1433 1478 6.405278 AAAAATAAGTGTCTTGTGGGGAAG 57.595 37.500 0.00 0.00 0.00 3.46
1458 1503 2.919666 AAAATCGAATGCCAAGGACG 57.080 45.000 0.00 0.00 0.00 4.79
1470 1515 2.557317 GAAGGCCATCGGTAAAATCGA 58.443 47.619 5.01 0.00 41.04 3.59
1485 1530 1.261619 CTCAACAACTGTCACGAAGGC 59.738 52.381 0.00 0.00 0.00 4.35
1486 1531 1.261619 GCTCAACAACTGTCACGAAGG 59.738 52.381 0.00 0.00 0.00 3.46
1489 1534 2.135139 GATGCTCAACAACTGTCACGA 58.865 47.619 0.00 0.00 0.00 4.35
1490 1535 1.866601 TGATGCTCAACAACTGTCACG 59.133 47.619 0.00 0.00 0.00 4.35
1491 1536 2.348872 CGTGATGCTCAACAACTGTCAC 60.349 50.000 0.00 0.00 33.15 3.67
1497 1568 0.867746 TCTGCGTGATGCTCAACAAC 59.132 50.000 0.00 0.00 46.63 3.32
1499 1570 1.733912 GAATCTGCGTGATGCTCAACA 59.266 47.619 0.00 0.00 46.63 3.33
1587 1658 0.960364 TGCGGATCCAAACCTTGAGC 60.960 55.000 13.41 3.99 0.00 4.26
1606 1677 9.664332 GTGTAGAATTGGCATAGATCAGAATAT 57.336 33.333 0.00 0.00 0.00 1.28
1641 1712 7.896383 ATTGCCCAGCTAATTAAGAACAATA 57.104 32.000 0.00 0.00 0.00 1.90
1676 1752 5.200368 AGACTTGCCGTTTTCATTCATTT 57.800 34.783 0.00 0.00 0.00 2.32
1680 1756 5.974751 TGTAAAAGACTTGCCGTTTTCATTC 59.025 36.000 0.00 0.00 0.00 2.67
1689 1765 4.378616 CGAAACAATGTAAAAGACTTGCCG 59.621 41.667 0.00 0.00 0.00 5.69
1720 1796 8.705048 ATAGTGTTTCGGTCTAAAGAATCTTC 57.295 34.615 0.00 0.00 0.00 2.87
1721 1797 8.311836 TGATAGTGTTTCGGTCTAAAGAATCTT 58.688 33.333 0.00 0.00 0.00 2.40
1725 1801 7.608153 TCATGATAGTGTTTCGGTCTAAAGAA 58.392 34.615 0.00 0.00 0.00 2.52
1727 1803 8.425577 AATCATGATAGTGTTTCGGTCTAAAG 57.574 34.615 9.04 0.00 0.00 1.85
1732 1808 8.142994 ACATTAATCATGATAGTGTTTCGGTC 57.857 34.615 9.04 0.00 36.24 4.79
1734 1810 8.370493 AGACATTAATCATGATAGTGTTTCGG 57.630 34.615 9.04 0.00 36.24 4.30
1735 1811 9.855361 GAAGACATTAATCATGATAGTGTTTCG 57.145 33.333 9.04 0.00 36.24 3.46
1740 1816 9.775854 AAGAGGAAGACATTAATCATGATAGTG 57.224 33.333 9.04 10.47 36.24 2.74
1745 1821 8.868522 ACAAAAGAGGAAGACATTAATCATGA 57.131 30.769 0.00 0.00 36.24 3.07
1746 1822 9.565213 GAACAAAAGAGGAAGACATTAATCATG 57.435 33.333 0.00 0.00 39.07 3.07
1757 1833 3.740115 CGGGAAGAACAAAAGAGGAAGA 58.260 45.455 0.00 0.00 0.00 2.87
1764 1840 3.181491 TGAACAAGCGGGAAGAACAAAAG 60.181 43.478 0.00 0.00 0.00 2.27
1779 1855 2.630098 TCAGTGTCCTCTCCTGAACAAG 59.370 50.000 0.00 0.00 32.55 3.16
1797 1873 4.828939 AGCTAATCCAGACATCTCTCTCAG 59.171 45.833 0.00 0.00 0.00 3.35
1836 1912 3.632643 TCTAACATTGGCAGCAGATGA 57.367 42.857 12.71 0.00 0.00 2.92
1867 1943 1.043022 AAAAGGGGCAAGCAGAACAG 58.957 50.000 0.00 0.00 0.00 3.16
1872 1948 1.963515 ACAAGTAAAAGGGGCAAGCAG 59.036 47.619 0.00 0.00 0.00 4.24
1874 1950 1.960689 TCACAAGTAAAAGGGGCAAGC 59.039 47.619 0.00 0.00 0.00 4.01
1879 1955 4.871933 ATTGCTTCACAAGTAAAAGGGG 57.128 40.909 0.00 0.00 42.87 4.79
1888 1964 4.492895 GCAACACAACAATTGCTTCACAAG 60.493 41.667 5.05 0.00 46.21 3.16
1900 1976 6.751425 CACTTCTTTTATCAGCAACACAACAA 59.249 34.615 0.00 0.00 0.00 2.83
1902 1978 5.687285 CCACTTCTTTTATCAGCAACACAAC 59.313 40.000 0.00 0.00 0.00 3.32
1903 1979 5.735922 GCCACTTCTTTTATCAGCAACACAA 60.736 40.000 0.00 0.00 0.00 3.33
1904 1980 4.261572 GCCACTTCTTTTATCAGCAACACA 60.262 41.667 0.00 0.00 0.00 3.72
1905 1981 4.229876 GCCACTTCTTTTATCAGCAACAC 58.770 43.478 0.00 0.00 0.00 3.32
1926 2005 1.474077 CACAGCCACCATAAGAAAGGC 59.526 52.381 0.00 0.00 45.54 4.35
1928 2007 3.441572 CCTTCACAGCCACCATAAGAAAG 59.558 47.826 0.00 0.00 0.00 2.62
1942 2021 0.243907 ATCGTCCGACACCTTCACAG 59.756 55.000 0.00 0.00 0.00 3.66
1985 2064 2.969238 GCGTCCCCATCTGCATCG 60.969 66.667 0.00 0.00 0.00 3.84
2009 2088 0.179097 GGGACTGGCTAAGCTTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
2027 2106 3.247173 GCTTATCAGAAGCATTGTCGAGG 59.753 47.826 0.00 0.00 42.56 4.63
2028 2107 3.247173 GGCTTATCAGAAGCATTGTCGAG 59.753 47.826 6.32 0.00 44.71 4.04
2030 2109 3.201290 AGGCTTATCAGAAGCATTGTCG 58.799 45.455 6.32 0.00 44.71 4.35
2051 2130 2.360600 GGGCACATGGGCACGTTA 60.361 61.111 23.88 0.00 45.66 3.18
2052 2131 4.594854 TGGGCACATGGGCACGTT 62.595 61.111 23.88 0.00 45.66 3.99
2055 2134 3.280938 TAGGTGGGCACATGGGCAC 62.281 63.158 23.88 20.93 45.66 5.01
2056 2135 2.938243 TAGGTGGGCACATGGGCA 60.938 61.111 23.88 0.00 45.66 5.36
2057 2136 1.999634 ATCTAGGTGGGCACATGGGC 62.000 60.000 12.85 12.85 42.44 5.36
2069 2148 3.619900 TCAGCCATACCAGATCTAGGT 57.380 47.619 17.41 17.41 43.14 3.08
2071 2150 5.735285 TTGATCAGCCATACCAGATCTAG 57.265 43.478 0.00 0.00 38.13 2.43
2085 2164 9.852091 AAAACAATTAGAAAGAGATTGATCAGC 57.148 29.630 0.00 0.00 35.36 4.26
2096 2175 5.068987 AGGCACAGCAAAACAATTAGAAAGA 59.931 36.000 0.00 0.00 0.00 2.52
2103 2182 3.636300 TCACTAGGCACAGCAAAACAATT 59.364 39.130 0.00 0.00 0.00 2.32
2108 2187 1.133945 TGGTCACTAGGCACAGCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
2140 2219 1.956477 GGCACCAGAAACACATTCAGT 59.044 47.619 0.00 0.00 40.72 3.41
2172 2253 2.035632 AGCGACTTCTCCTTCCTATGG 58.964 52.381 0.00 0.00 0.00 2.74
2205 2286 4.022503 AGGAAGAGCTTGACAAAATTCTGC 60.023 41.667 0.00 0.00 0.00 4.26
2214 2295 1.423584 TGGTGAGGAAGAGCTTGACA 58.576 50.000 0.00 0.00 0.00 3.58
2305 2387 5.159273 TGTGCCAGTAGTGAATCACATTA 57.841 39.130 16.38 0.00 36.74 1.90
2450 2532 6.095377 CAGTTGGATAGAAAATTCTGTTGCC 58.905 40.000 5.93 0.00 38.19 4.52
2459 2541 9.178758 GTAATGAGTTCCAGTTGGATAGAAAAT 57.821 33.333 0.93 0.00 44.98 1.82
2639 2721 2.423185 CCTGCTGTGTCTGAAACAAACA 59.577 45.455 1.76 3.07 40.31 2.83
2740 2822 5.012561 GCTAGACATAATCTTCCTGGATGGT 59.987 44.000 9.46 0.00 39.04 3.55
2744 2826 5.899547 TCTTGCTAGACATAATCTTCCTGGA 59.100 40.000 0.00 0.00 39.04 3.86
2991 3073 4.347876 TCTCCCAGTCTTGAATGTTCTTCA 59.652 41.667 0.00 0.00 0.00 3.02
3015 3097 1.390463 GACGGAATGAAACAGCGAGAC 59.610 52.381 0.00 0.00 0.00 3.36
3052 3134 4.094442 GTGGGAGAAATGTTTAGCTTACCG 59.906 45.833 0.00 0.00 0.00 4.02
3068 3150 7.458397 ACTGTAGAAAATAAACATGTGGGAGA 58.542 34.615 0.00 0.00 0.00 3.71
3070 3152 9.575868 TTAACTGTAGAAAATAAACATGTGGGA 57.424 29.630 0.00 0.00 0.00 4.37
3105 3187 4.518970 TCCATCCAGTGCAGTTTTCTAAAC 59.481 41.667 0.00 0.00 0.00 2.01
3117 3199 5.055812 TCAAAACAAAATTCCATCCAGTGC 58.944 37.500 0.00 0.00 0.00 4.40
3154 3236 5.674525 CATCCAGTGCAAAGAGGTAGATAA 58.325 41.667 0.00 0.00 0.00 1.75
3255 3429 8.403236 CAGTTTCTTCTTGATCATGCATATCAA 58.597 33.333 20.61 20.61 40.21 2.57
3326 3502 4.767409 AGCAAAGGGGCTAAACTTCTAAAG 59.233 41.667 0.00 0.00 43.70 1.85
3347 3523 2.541762 CGCTAGAATGCCTACTCAAAGC 59.458 50.000 0.00 0.00 0.00 3.51
3358 3534 2.989422 ACAAACAACCGCTAGAATGC 57.011 45.000 0.00 0.00 0.00 3.56
3404 3580 5.786574 GGAATGTGTTTACATACGTGTTTCG 59.213 40.000 0.00 0.00 46.54 3.46
3430 3606 7.175641 ACCAAATGCTATTAATGTCAGCTATCC 59.824 37.037 9.51 0.00 36.26 2.59
3752 3950 1.335882 CCTTCCTCCCCGTCCTTACC 61.336 65.000 0.00 0.00 0.00 2.85
3753 3951 0.325016 TCCTTCCTCCCCGTCCTTAC 60.325 60.000 0.00 0.00 0.00 2.34
3754 3952 0.032416 CTCCTTCCTCCCCGTCCTTA 60.032 60.000 0.00 0.00 0.00 2.69
3755 3953 1.306226 CTCCTTCCTCCCCGTCCTT 60.306 63.158 0.00 0.00 0.00 3.36
3756 3954 1.812113 TTCTCCTTCCTCCCCGTCCT 61.812 60.000 0.00 0.00 0.00 3.85
3757 3955 1.305887 TTCTCCTTCCTCCCCGTCC 60.306 63.158 0.00 0.00 0.00 4.79
3758 3956 0.324460 TCTTCTCCTTCCTCCCCGTC 60.324 60.000 0.00 0.00 0.00 4.79
3759 3957 0.324830 CTCTTCTCCTTCCTCCCCGT 60.325 60.000 0.00 0.00 0.00 5.28
3760 3958 0.033011 TCTCTTCTCCTTCCTCCCCG 60.033 60.000 0.00 0.00 0.00 5.73
3818 4016 1.607148 GGTTGGTGTGGCAAAGACTAC 59.393 52.381 0.00 0.00 0.00 2.73
3839 4037 2.920912 GGTGGGACCCGTCTGTCA 60.921 66.667 5.91 0.00 36.97 3.58
3880 4078 1.134580 TGCACTGATCTGAGGCTTAGC 60.135 52.381 6.60 0.00 0.00 3.09
3897 4095 2.166664 GGCCGGTTGGTAATAAATTGCA 59.833 45.455 1.90 0.00 37.67 4.08
3905 4103 2.167662 CTTTTGAGGCCGGTTGGTAAT 58.832 47.619 1.90 0.00 37.67 1.89
4079 4286 1.338020 GTTGTGAAAGTTCAGCCCCTG 59.662 52.381 0.00 0.00 37.98 4.45
4084 4298 3.568007 TGGTATGGTTGTGAAAGTTCAGC 59.432 43.478 0.00 0.00 37.98 4.26
4085 4299 5.063204 TCTGGTATGGTTGTGAAAGTTCAG 58.937 41.667 0.00 0.00 37.98 3.02
4217 4432 5.884322 TGTTTACAGAGGGAGTACTGTAGA 58.116 41.667 0.00 0.00 45.83 2.59
4218 4433 6.585695 TTGTTTACAGAGGGAGTACTGTAG 57.414 41.667 0.00 0.00 45.83 2.74
4245 4460 9.005777 ACCATTTTAGTGATCTAAACGCTTTTA 57.994 29.630 0.00 0.00 43.20 1.52
4246 4461 7.882179 ACCATTTTAGTGATCTAAACGCTTTT 58.118 30.769 0.00 0.00 43.20 2.27
4247 4462 7.448748 ACCATTTTAGTGATCTAAACGCTTT 57.551 32.000 0.00 0.00 43.20 3.51
4248 4463 7.448748 AACCATTTTAGTGATCTAAACGCTT 57.551 32.000 0.00 0.00 43.20 4.68
4249 4464 7.448748 AAACCATTTTAGTGATCTAAACGCT 57.551 32.000 0.00 0.00 43.20 5.07
4250 4465 7.908601 CCTAAACCATTTTAGTGATCTAAACGC 59.091 37.037 0.00 0.00 43.20 4.84
4251 4466 8.395633 CCCTAAACCATTTTAGTGATCTAAACG 58.604 37.037 0.00 0.00 43.20 3.60
4252 4467 9.239551 ACCCTAAACCATTTTAGTGATCTAAAC 57.760 33.333 0.00 0.00 43.20 2.01
4253 4468 9.816787 AACCCTAAACCATTTTAGTGATCTAAA 57.183 29.630 0.00 0.00 41.90 1.85
4254 4469 9.816787 AAACCCTAAACCATTTTAGTGATCTAA 57.183 29.630 0.00 0.00 41.90 2.10
4256 4471 9.462606 CTAAACCCTAAACCATTTTAGTGATCT 57.537 33.333 0.00 0.00 41.90 2.75
4257 4472 8.683615 CCTAAACCCTAAACCATTTTAGTGATC 58.316 37.037 4.02 0.00 41.90 2.92
4258 4473 7.618117 CCCTAAACCCTAAACCATTTTAGTGAT 59.382 37.037 4.02 0.00 41.90 3.06
4259 4474 6.949463 CCCTAAACCCTAAACCATTTTAGTGA 59.051 38.462 4.02 0.00 41.90 3.41
4260 4475 6.722590 ACCCTAAACCCTAAACCATTTTAGTG 59.277 38.462 4.02 0.00 41.90 2.74
4261 4476 6.866621 ACCCTAAACCCTAAACCATTTTAGT 58.133 36.000 4.02 0.00 41.90 2.24
4262 4477 7.786046 AACCCTAAACCCTAAACCATTTTAG 57.214 36.000 0.00 0.00 42.75 1.85
4263 4478 9.311676 CTAAACCCTAAACCCTAAACCATTTTA 57.688 33.333 0.00 0.00 0.00 1.52
4264 4479 7.236019 CCTAAACCCTAAACCCTAAACCATTTT 59.764 37.037 0.00 0.00 0.00 1.82
4265 4480 6.727231 CCTAAACCCTAAACCCTAAACCATTT 59.273 38.462 0.00 0.00 0.00 2.32
4266 4481 6.258354 CCTAAACCCTAAACCCTAAACCATT 58.742 40.000 0.00 0.00 0.00 3.16
4267 4482 5.281874 CCCTAAACCCTAAACCCTAAACCAT 60.282 44.000 0.00 0.00 0.00 3.55
4268 4483 4.044444 CCCTAAACCCTAAACCCTAAACCA 59.956 45.833 0.00 0.00 0.00 3.67
4269 4484 4.044571 ACCCTAAACCCTAAACCCTAAACC 59.955 45.833 0.00 0.00 0.00 3.27
4270 4485 5.261040 ACCCTAAACCCTAAACCCTAAAC 57.739 43.478 0.00 0.00 0.00 2.01
4271 4486 7.296868 TCTTTACCCTAAACCCTAAACCCTAAA 59.703 37.037 0.00 0.00 0.00 1.85
4272 4487 6.797031 TCTTTACCCTAAACCCTAAACCCTAA 59.203 38.462 0.00 0.00 0.00 2.69
4273 4488 6.338397 TCTTTACCCTAAACCCTAAACCCTA 58.662 40.000 0.00 0.00 0.00 3.53
4274 4489 5.172483 TCTTTACCCTAAACCCTAAACCCT 58.828 41.667 0.00 0.00 0.00 4.34
4275 4490 5.519183 TCTTTACCCTAAACCCTAAACCC 57.481 43.478 0.00 0.00 0.00 4.11
4276 4491 9.705103 ATATTTCTTTACCCTAAACCCTAAACC 57.295 33.333 0.00 0.00 0.00 3.27
4282 4497 9.064706 GCTCTTATATTTCTTTACCCTAAACCC 57.935 37.037 0.00 0.00 0.00 4.11
4283 4498 8.771766 CGCTCTTATATTTCTTTACCCTAAACC 58.228 37.037 0.00 0.00 0.00 3.27
4284 4499 9.322773 ACGCTCTTATATTTCTTTACCCTAAAC 57.677 33.333 0.00 0.00 0.00 2.01
4285 4500 9.895138 AACGCTCTTATATTTCTTTACCCTAAA 57.105 29.630 0.00 0.00 0.00 1.85
4286 4501 9.895138 AAACGCTCTTATATTTCTTTACCCTAA 57.105 29.630 0.00 0.00 0.00 2.69
4288 4503 9.543783 CTAAACGCTCTTATATTTCTTTACCCT 57.456 33.333 0.00 0.00 0.00 4.34
4289 4504 9.538508 TCTAAACGCTCTTATATTTCTTTACCC 57.461 33.333 0.00 0.00 0.00 3.69
4331 4546 9.916397 CTGTAAACAAATATAAGAGCGTTTAGG 57.084 33.333 0.00 0.00 31.53 2.69
4338 4553 9.384764 ACTCCTTCTGTAAACAAATATAAGAGC 57.615 33.333 0.00 0.00 0.00 4.09
4349 4564 9.895138 AGTTAAAAGTTACTCCTTCTGTAAACA 57.105 29.630 0.00 0.00 32.58 2.83
4356 4571 7.686434 TGGCATAGTTAAAAGTTACTCCTTCT 58.314 34.615 0.00 0.00 0.00 2.85
4359 4574 8.879427 AAATGGCATAGTTAAAAGTTACTCCT 57.121 30.769 0.00 0.00 0.00 3.69
4526 4741 2.187958 ACCATCCTTCATGAGGTCGAA 58.812 47.619 3.93 0.00 46.39 3.71
4529 4744 5.104259 ACTAAACCATCCTTCATGAGGTC 57.896 43.478 3.93 0.00 46.39 3.85
4610 4825 4.401519 TGTACAGGTCGAATCCTTTCTAGG 59.598 45.833 0.00 0.00 43.46 3.02
4646 4861 0.242017 GCGAAATGAGCCTTTGTGCT 59.758 50.000 0.00 0.00 46.37 4.40
4647 4862 2.729378 GCGAAATGAGCCTTTGTGC 58.271 52.632 0.00 0.00 0.00 4.57
4827 5046 2.881513 TCTCCTCTCTTATACAGCTGCG 59.118 50.000 15.27 0.00 0.00 5.18
4852 5071 3.312404 GCCTCAGCTGTTGTCTCAA 57.688 52.632 14.67 0.00 35.50 3.02
5056 5277 5.192927 CCACATTTTATCTAACAGCCCAGA 58.807 41.667 0.00 0.00 0.00 3.86
5082 5303 6.980416 ACTCCTATAAGTCAATCCTGGTAC 57.020 41.667 0.00 0.00 0.00 3.34
5101 5322 3.963129 TGTGGGTATGGAAAATGACTCC 58.037 45.455 0.00 0.00 0.00 3.85
5164 5390 2.434336 ACAGTAGCTTGGACACAACTCA 59.566 45.455 0.00 0.00 32.14 3.41
5254 5509 7.231317 GGATATTCCATGCTTCCATTTAGTTGA 59.769 37.037 0.00 0.00 36.28 3.18
5286 5541 9.241919 TGGCTTCTAAATATCTGTTTCATTGAA 57.758 29.630 0.00 0.00 0.00 2.69
5370 5625 9.163899 CCATAATTCAGAGGATATCATCAAGTG 57.836 37.037 18.86 9.08 0.00 3.16
5463 5718 1.160137 GCACTTTAGCCTGTCAGTGG 58.840 55.000 0.00 0.00 37.67 4.00
5467 5722 2.928801 TGAAGCACTTTAGCCTGTCA 57.071 45.000 0.00 0.00 34.23 3.58
5473 5728 2.732282 GCCCGAAATGAAGCACTTTAGC 60.732 50.000 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.