Multiple sequence alignment - TraesCS7D01G194300

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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 TraesCS7D01G194300 chr7D 100.000 3002 0 0 1 3002 151015077 151012076 0.000000e+00 5544
1 TraesCS7D01G194300 chr7D 80.503 795 146 8 2189 2977 453167034 453167825 4.280000e-168 601
2 TraesCS7D01G194300 chr7D 82.927 533 71 12 113 629 91823952 91824480 2.110000e-126 462
3 TraesCS7D01G194300 chr7D 79.641 167 26 7 1094 1256 381003260 381003098 2.450000e-21 113
4 TraesCS7D01G194300 chr4B 90.617 810 63 11 1 800 403037240 403036434 0.000000e+00 1062
5 TraesCS7D01G194300 chr4B 83.225 614 89 6 1478 2078 403050391 403049779 4.370000e-153 551
6 TraesCS7D01G194300 chr4B 81.465 669 83 23 788 1443 403036419 403035779 7.420000e-141 510
7 TraesCS7D01G194300 chr7B 89.100 789 68 12 21 800 113133211 113132432 0.000000e+00 965
8 TraesCS7D01G194300 chr7B 80.278 791 135 17 2198 2975 534508894 534508112 7.220000e-161 577
9 TraesCS7D01G194300 chr7B 78.057 875 174 16 2139 3002 721591880 721592747 1.220000e-148 536
10 TraesCS7D01G194300 chr7B 81.614 669 82 23 788 1443 113132417 113131777 1.600000e-142 516
11 TraesCS7D01G194300 chr7B 81.887 530 78 15 114 629 42753662 42753137 5.950000e-117 431
12 TraesCS7D01G194300 chr7B 75.621 644 114 32 797 1415 113143902 113143277 2.280000e-71 279
13 TraesCS7D01G194300 chr2D 82.416 745 115 14 2238 2974 524046405 524047141 1.170000e-178 636
14 TraesCS7D01G194300 chr7A 80.303 792 139 15 2221 3001 661297691 661296906 1.550000e-162 582
15 TraesCS7D01G194300 chr7A 84.013 613 86 7 1478 2078 150905372 150904760 2.010000e-161 579
16 TraesCS7D01G194300 chr7A 82.163 527 79 10 114 629 93530293 93530815 3.550000e-119 438
17 TraesCS7D01G194300 chr7A 75.542 646 106 33 790 1413 150910967 150910352 1.370000e-68 270
18 TraesCS7D01G194300 chr3D 81.818 682 118 6 2139 2815 48050683 48051363 4.340000e-158 568
19 TraesCS7D01G194300 chr3D 78.256 814 156 14 2139 2937 32626177 32626984 1.240000e-138 503
20 TraesCS7D01G194300 chr3B 81.402 699 117 10 2283 2976 101291443 101290753 2.610000e-155 558
21 TraesCS7D01G194300 chr3B 83.877 521 71 8 114 623 82823896 82823378 4.500000e-133 484
22 TraesCS7D01G194300 chr2B 80.374 749 134 13 2139 2878 704289716 704288972 9.400000e-155 556
23 TraesCS7D01G194300 chr2B 75.652 460 70 17 2484 2924 93343465 93343029 1.100000e-44 191
24 TraesCS7D01G194300 chr3A 82.707 532 75 8 115 634 158163326 158163852 9.810000e-125 457
25 TraesCS7D01G194300 chr3A 82.659 519 69 15 114 620 734747579 734748088 9.880000e-120 440
26 TraesCS7D01G194300 chr5A 82.364 533 74 13 115 632 563059421 563059948 2.120000e-121 446


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 TraesCS7D01G194300 chr7D 151012076 151015077 3001 True 5544.0 5544 100.000 1 3002 1 chr7D.!!$R1 3001
1 TraesCS7D01G194300 chr7D 453167034 453167825 791 False 601.0 601 80.503 2189 2977 1 chr7D.!!$F2 788
2 TraesCS7D01G194300 chr7D 91823952 91824480 528 False 462.0 462 82.927 113 629 1 chr7D.!!$F1 516
3 TraesCS7D01G194300 chr4B 403035779 403037240 1461 True 786.0 1062 86.041 1 1443 2 chr4B.!!$R2 1442
4 TraesCS7D01G194300 chr4B 403049779 403050391 612 True 551.0 551 83.225 1478 2078 1 chr4B.!!$R1 600
5 TraesCS7D01G194300 chr7B 113131777 113133211 1434 True 740.5 965 85.357 21 1443 2 chr7B.!!$R4 1422
6 TraesCS7D01G194300 chr7B 534508112 534508894 782 True 577.0 577 80.278 2198 2975 1 chr7B.!!$R3 777
7 TraesCS7D01G194300 chr7B 721591880 721592747 867 False 536.0 536 78.057 2139 3002 1 chr7B.!!$F1 863
8 TraesCS7D01G194300 chr7B 42753137 42753662 525 True 431.0 431 81.887 114 629 1 chr7B.!!$R1 515
9 TraesCS7D01G194300 chr7B 113143277 113143902 625 True 279.0 279 75.621 797 1415 1 chr7B.!!$R2 618
10 TraesCS7D01G194300 chr2D 524046405 524047141 736 False 636.0 636 82.416 2238 2974 1 chr2D.!!$F1 736
11 TraesCS7D01G194300 chr7A 661296906 661297691 785 True 582.0 582 80.303 2221 3001 1 chr7A.!!$R3 780
12 TraesCS7D01G194300 chr7A 150904760 150905372 612 True 579.0 579 84.013 1478 2078 1 chr7A.!!$R1 600
13 TraesCS7D01G194300 chr7A 93530293 93530815 522 False 438.0 438 82.163 114 629 1 chr7A.!!$F1 515
14 TraesCS7D01G194300 chr7A 150910352 150910967 615 True 270.0 270 75.542 790 1413 1 chr7A.!!$R2 623
15 TraesCS7D01G194300 chr3D 48050683 48051363 680 False 568.0 568 81.818 2139 2815 1 chr3D.!!$F2 676
16 TraesCS7D01G194300 chr3D 32626177 32626984 807 False 503.0 503 78.256 2139 2937 1 chr3D.!!$F1 798
17 TraesCS7D01G194300 chr3B 101290753 101291443 690 True 558.0 558 81.402 2283 2976 1 chr3B.!!$R2 693
18 TraesCS7D01G194300 chr3B 82823378 82823896 518 True 484.0 484 83.877 114 623 1 chr3B.!!$R1 509
19 TraesCS7D01G194300 chr2B 704288972 704289716 744 True 556.0 556 80.374 2139 2878 1 chr2B.!!$R2 739
20 TraesCS7D01G194300 chr3A 158163326 158163852 526 False 457.0 457 82.707 115 634 1 chr3A.!!$F1 519
21 TraesCS7D01G194300 chr3A 734747579 734748088 509 False 440.0 440 82.659 114 620 1 chr3A.!!$F2 506
22 TraesCS7D01G194300 chr5A 563059421 563059948 527 False 446.0 446 82.364 115 632 1 chr5A.!!$F1 517

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
233 242 0.464735 TTCTGTCCCGGTGGTGTTTG 60.465 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2108 0.033601 TGAGTTGGGTGTTTGCTGGT 60.034 50.0 0.0 0.0 0.0 4.0 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
73 75 5.968676 ATGATTTAGTGTAGGCCAAGGTA 57.031 39.130 5.01 0.00 0.00 3.08
76 78 2.934263 TAGTGTAGGCCAAGGTAGGT 57.066 50.000 5.01 0.00 0.00 3.08
78 80 0.540454 GTGTAGGCCAAGGTAGGTCC 59.460 60.000 5.01 0.00 32.23 4.46
98 100 2.556114 CCTCTTTTTGTCTGGGCTCCAT 60.556 50.000 0.00 0.00 30.82 3.41
161 164 2.269940 AGGGTTTATGTCCTGCTCAGT 58.730 47.619 0.00 0.00 31.11 3.41
184 193 4.500116 GGCGGCACCGACTCTCTC 62.500 72.222 14.43 0.00 45.30 3.20
233 242 0.464735 TTCTGTCCCGGTGGTGTTTG 60.465 55.000 0.00 0.00 0.00 2.93
437 450 2.297895 ATGGGGCCTTAGCACGACA 61.298 57.895 0.84 0.00 46.55 4.35
440 453 2.388232 GGGCCTTAGCACGACAACG 61.388 63.158 0.84 0.00 42.56 4.10
473 486 2.089201 ACTACAATAAGGTTTGCCCGC 58.911 47.619 0.00 0.00 38.74 6.13
562 589 7.186804 GTGGTCTACGAATTTGGATGTATTTG 58.813 38.462 0.00 0.00 0.00 2.32
564 591 7.065324 TGGTCTACGAATTTGGATGTATTTGTC 59.935 37.037 0.00 0.00 32.19 3.18
584 612 8.882415 TTTGTCTACTTCTCGTATTCTTTGTT 57.118 30.769 0.00 0.00 0.00 2.83
636 664 9.771534 TGAAAGTTTTCCTTGAAAAGAAAAAGA 57.228 25.926 2.42 0.00 45.77 2.52
705 733 7.206687 TGGCTACAAAACTTGATTTTAGTTGG 58.793 34.615 0.00 0.00 38.50 3.77
913 974 4.617530 GCGTCTCCGTTTGGCATATATAGA 60.618 45.833 0.00 0.00 36.15 1.98
919 980 7.764443 TCTCCGTTTGGCATATATAGAATTAGC 59.236 37.037 0.00 0.00 34.14 3.09
932 997 1.666189 GAATTAGCGAGGAACTGTGGC 59.334 52.381 0.00 0.00 41.55 5.01
944 1009 3.449018 GGAACTGTGGCTTATCTCTCTCA 59.551 47.826 0.00 0.00 0.00 3.27
945 1010 4.081420 GGAACTGTGGCTTATCTCTCTCAA 60.081 45.833 0.00 0.00 0.00 3.02
946 1011 5.396213 GGAACTGTGGCTTATCTCTCTCAAT 60.396 44.000 0.00 0.00 0.00 2.57
947 1012 5.275067 ACTGTGGCTTATCTCTCTCAATC 57.725 43.478 0.00 0.00 0.00 2.67
948 1013 4.961730 ACTGTGGCTTATCTCTCTCAATCT 59.038 41.667 0.00 0.00 0.00 2.40
949 1014 5.068987 ACTGTGGCTTATCTCTCTCAATCTC 59.931 44.000 0.00 0.00 0.00 2.75
950 1015 5.207354 TGTGGCTTATCTCTCTCAATCTCT 58.793 41.667 0.00 0.00 0.00 3.10
951 1016 5.301551 TGTGGCTTATCTCTCTCAATCTCTC 59.698 44.000 0.00 0.00 0.00 3.20
968 1033 5.831702 TCTCTCCTGTATAAACGAGAACC 57.168 43.478 0.00 0.00 0.00 3.62
982 1047 1.531578 GAGAACCGCACTTCCTTTGAC 59.468 52.381 0.00 0.00 0.00 3.18
983 1048 1.134220 AGAACCGCACTTCCTTTGACA 60.134 47.619 0.00 0.00 0.00 3.58
986 1051 1.515521 CCGCACTTCCTTTGACACCC 61.516 60.000 0.00 0.00 0.00 4.61
987 1052 0.535102 CGCACTTCCTTTGACACCCT 60.535 55.000 0.00 0.00 0.00 4.34
988 1053 1.239347 GCACTTCCTTTGACACCCTC 58.761 55.000 0.00 0.00 0.00 4.30
989 1054 1.202818 GCACTTCCTTTGACACCCTCT 60.203 52.381 0.00 0.00 0.00 3.69
990 1055 2.498167 CACTTCCTTTGACACCCTCTG 58.502 52.381 0.00 0.00 0.00 3.35
991 1056 1.421646 ACTTCCTTTGACACCCTCTGG 59.578 52.381 0.00 0.00 37.80 3.86
1024 1089 4.785453 CAGCACCCTCCGCTTCCC 62.785 72.222 0.00 0.00 37.72 3.97
1045 1110 2.438614 TCCTCGAGGAGCCTCACG 60.439 66.667 30.49 1.27 42.86 4.35
1048 1113 2.438614 TCGAGGAGCCTCACGGAG 60.439 66.667 16.23 0.26 42.86 4.63
1064 1144 1.674221 CGGAGTGCTGAAGAAAGGGAG 60.674 57.143 0.00 0.00 0.00 4.30
1067 1147 0.962855 GTGCTGAAGAAAGGGAGGGC 60.963 60.000 0.00 0.00 0.00 5.19
1068 1148 1.379176 GCTGAAGAAAGGGAGGGCC 60.379 63.158 0.00 0.00 0.00 5.80
1076 1156 0.776080 AAAGGGAGGGCCAAAGAGGA 60.776 55.000 6.18 0.00 41.22 3.71
1082 1162 1.616628 GGGCCAAAGAGGAGGAGGA 60.617 63.158 4.39 0.00 41.22 3.71
1084 1164 1.631071 GGCCAAAGAGGAGGAGGAGG 61.631 65.000 0.00 0.00 41.22 4.30
1085 1165 0.618968 GCCAAAGAGGAGGAGGAGGA 60.619 60.000 0.00 0.00 41.22 3.71
1138 1218 4.025401 CGTTGCTGGCCGTGTTCC 62.025 66.667 0.00 0.00 0.00 3.62
1139 1219 2.904866 GTTGCTGGCCGTGTTCCA 60.905 61.111 0.00 0.00 0.00 3.53
1142 1222 2.904866 GCTGGCCGTGTTCCACAA 60.905 61.111 0.00 0.00 33.40 3.33
1158 1238 0.615331 ACAAGCTGGACCACATCGAT 59.385 50.000 0.00 0.00 0.00 3.59
1167 1247 2.628178 GGACCACATCGATATCCTCACA 59.372 50.000 0.00 0.00 0.00 3.58
1252 1332 0.436150 CATCGATATGCGCTTCCACG 59.564 55.000 9.73 9.39 40.61 4.94
1253 1333 0.032130 ATCGATATGCGCTTCCACGT 59.968 50.000 9.73 0.00 40.61 4.49
1261 1341 3.774702 GCTTCCACGTCGCCGAAC 61.775 66.667 0.00 0.00 37.88 3.95
1262 1342 2.355363 CTTCCACGTCGCCGAACA 60.355 61.111 0.00 0.00 37.88 3.18
1263 1343 1.952133 CTTCCACGTCGCCGAACAA 60.952 57.895 0.00 0.00 37.88 2.83
1268 1348 1.446618 ACGTCGCCGAACAATACCC 60.447 57.895 0.00 0.00 37.88 3.69
1269 1349 1.153706 CGTCGCCGAACAATACCCT 60.154 57.895 0.00 0.00 35.63 4.34
1270 1350 1.418342 CGTCGCCGAACAATACCCTG 61.418 60.000 0.00 0.00 35.63 4.45
1271 1351 1.087771 GTCGCCGAACAATACCCTGG 61.088 60.000 0.00 0.00 0.00 4.45
1296 1385 2.235898 ACTCTTTGAGATGGTGAGAGCC 59.764 50.000 1.25 0.00 37.87 4.70
1305 1394 2.725312 GGTGAGAGCCGCCATGAGA 61.725 63.158 0.00 0.00 44.82 3.27
1308 1397 4.521062 AGAGCCGCCATGAGACGC 62.521 66.667 0.00 0.00 0.00 5.19
1336 1425 4.021925 GGTGCGAGGCCTTCTGGT 62.022 66.667 6.77 0.00 35.27 4.00
1344 1433 4.021925 GCCTTCTGGTGCGAGGGT 62.022 66.667 0.00 0.00 33.06 4.34
1345 1434 2.046892 CCTTCTGGTGCGAGGGTG 60.047 66.667 0.00 0.00 0.00 4.61
1347 1436 1.371183 CTTCTGGTGCGAGGGTGAA 59.629 57.895 0.00 0.00 0.00 3.18
1348 1437 0.036010 CTTCTGGTGCGAGGGTGAAT 60.036 55.000 0.00 0.00 0.00 2.57
1351 1440 0.036010 CTGGTGCGAGGGTGAATTCT 60.036 55.000 7.05 0.00 0.00 2.40
1356 1445 1.066858 TGCGAGGGTGAATTCTCAGAC 60.067 52.381 7.05 0.00 30.14 3.51
1358 1447 2.612972 GCGAGGGTGAATTCTCAGACAA 60.613 50.000 7.05 0.00 30.14 3.18
1359 1448 3.866651 CGAGGGTGAATTCTCAGACAAT 58.133 45.455 7.05 0.00 30.14 2.71
1360 1449 3.620374 CGAGGGTGAATTCTCAGACAATG 59.380 47.826 7.05 0.00 30.14 2.82
1362 1451 4.583871 AGGGTGAATTCTCAGACAATGTC 58.416 43.478 5.02 5.02 30.14 3.06
1363 1452 4.288105 AGGGTGAATTCTCAGACAATGTCT 59.712 41.667 10.56 10.56 44.44 3.41
1365 1454 5.106396 GGGTGAATTCTCAGACAATGTCTTG 60.106 44.000 13.99 9.73 41.37 3.02
1377 1466 1.645710 ATGTCTTGTCCCTTCTCGGT 58.354 50.000 0.00 0.00 0.00 4.69
1380 1469 1.550976 GTCTTGTCCCTTCTCGGTGAT 59.449 52.381 0.00 0.00 0.00 3.06
1419 1510 9.912634 CTTGCTTGTTTATCCTATTTTTCTCAA 57.087 29.630 0.00 0.00 0.00 3.02
1421 1512 9.691362 TGCTTGTTTATCCTATTTTTCTCAAAC 57.309 29.630 0.00 0.00 0.00 2.93
1431 1522 9.801873 TCCTATTTTTCTCAAACAAAAACTCTG 57.198 29.630 0.00 0.00 35.95 3.35
1432 1523 9.801873 CCTATTTTTCTCAAACAAAAACTCTGA 57.198 29.630 0.00 0.00 35.95 3.27
1440 1531 8.405531 TCTCAAACAAAAACTCTGATTTACTGG 58.594 33.333 0.00 0.00 0.00 4.00
1443 1534 6.463995 ACAAAAACTCTGATTTACTGGCAA 57.536 33.333 0.00 0.00 0.00 4.52
1444 1535 7.054491 ACAAAAACTCTGATTTACTGGCAAT 57.946 32.000 0.00 0.00 0.00 3.56
1445 1536 7.500141 ACAAAAACTCTGATTTACTGGCAATT 58.500 30.769 0.00 0.00 0.00 2.32
1446 1537 7.986889 ACAAAAACTCTGATTTACTGGCAATTT 59.013 29.630 0.00 0.00 0.00 1.82
1447 1538 8.490355 CAAAAACTCTGATTTACTGGCAATTTC 58.510 33.333 0.00 0.00 0.00 2.17
1448 1539 7.530426 AAACTCTGATTTACTGGCAATTTCT 57.470 32.000 0.00 0.00 0.00 2.52
1449 1540 7.530426 AACTCTGATTTACTGGCAATTTCTT 57.470 32.000 0.00 0.00 0.00 2.52
1450 1541 7.530426 ACTCTGATTTACTGGCAATTTCTTT 57.470 32.000 0.00 0.00 0.00 2.52
1451 1542 7.955918 ACTCTGATTTACTGGCAATTTCTTTT 58.044 30.769 0.00 0.00 0.00 2.27
1452 1543 9.077885 ACTCTGATTTACTGGCAATTTCTTTTA 57.922 29.630 0.00 0.00 0.00 1.52
1453 1544 9.346725 CTCTGATTTACTGGCAATTTCTTTTAC 57.653 33.333 0.00 0.00 0.00 2.01
1454 1545 8.855110 TCTGATTTACTGGCAATTTCTTTTACA 58.145 29.630 0.00 0.00 0.00 2.41
1455 1546 9.643693 CTGATTTACTGGCAATTTCTTTTACAT 57.356 29.630 0.00 0.00 0.00 2.29
1456 1547 9.638239 TGATTTACTGGCAATTTCTTTTACATC 57.362 29.630 0.00 0.00 0.00 3.06
1457 1548 9.087424 GATTTACTGGCAATTTCTTTTACATCC 57.913 33.333 0.00 0.00 0.00 3.51
1458 1549 7.775053 TTACTGGCAATTTCTTTTACATCCT 57.225 32.000 0.00 0.00 0.00 3.24
1459 1550 6.670695 ACTGGCAATTTCTTTTACATCCTT 57.329 33.333 0.00 0.00 0.00 3.36
1460 1551 7.775053 ACTGGCAATTTCTTTTACATCCTTA 57.225 32.000 0.00 0.00 0.00 2.69
1461 1552 8.189119 ACTGGCAATTTCTTTTACATCCTTAA 57.811 30.769 0.00 0.00 0.00 1.85
1462 1553 8.088365 ACTGGCAATTTCTTTTACATCCTTAAC 58.912 33.333 0.00 0.00 0.00 2.01
1463 1554 8.189119 TGGCAATTTCTTTTACATCCTTAACT 57.811 30.769 0.00 0.00 0.00 2.24
1464 1555 8.646900 TGGCAATTTCTTTTACATCCTTAACTT 58.353 29.630 0.00 0.00 0.00 2.66
1465 1556 9.489084 GGCAATTTCTTTTACATCCTTAACTTT 57.511 29.630 0.00 0.00 0.00 2.66
1475 1566 9.906660 TTTACATCCTTAACTTTATTTGCTGTG 57.093 29.630 0.00 0.00 0.00 3.66
1476 1567 7.524717 ACATCCTTAACTTTATTTGCTGTGT 57.475 32.000 0.00 0.00 0.00 3.72
1485 1576 4.715523 TTGCTGTGTAGGGCGCCC 62.716 66.667 39.29 39.29 0.00 6.13
1524 1615 2.654749 TCATCGGGTGCGATGATATC 57.345 50.000 3.52 0.00 46.46 1.63
1546 1637 2.083774 TGGATTCGACATTCAAGGTGC 58.916 47.619 0.00 0.00 0.00 5.01
1564 1655 0.804989 GCTGATCACAAAGTTCCCCG 59.195 55.000 0.00 0.00 0.00 5.73
1568 1659 0.179004 ATCACAAAGTTCCCCGTGCA 60.179 50.000 0.00 0.00 0.00 4.57
1569 1660 0.394488 TCACAAAGTTCCCCGTGCAA 60.394 50.000 0.00 0.00 0.00 4.08
1578 1669 1.672356 CCCCGTGCAAGAGGAGTTG 60.672 63.158 0.00 0.00 0.00 3.16
1584 1675 0.035881 TGCAAGAGGAGTTGGAGCTG 59.964 55.000 0.00 0.00 0.00 4.24
1594 1685 2.945668 GAGTTGGAGCTGTCAAACTGTT 59.054 45.455 0.61 0.00 45.63 3.16
1595 1686 2.684881 AGTTGGAGCTGTCAAACTGTTG 59.315 45.455 0.00 0.00 44.20 3.33
1605 1696 1.680735 TCAAACTGTTGGCATCGCTTT 59.319 42.857 0.00 0.00 35.29 3.51
1609 1700 0.109597 CTGTTGGCATCGCTTTCCAC 60.110 55.000 0.00 0.00 0.00 4.02
1610 1701 1.154225 GTTGGCATCGCTTTCCACG 60.154 57.895 0.00 0.00 0.00 4.94
1611 1702 2.976840 TTGGCATCGCTTTCCACGC 61.977 57.895 0.00 0.00 0.00 5.34
1617 1708 1.568612 ATCGCTTTCCACGCACACTG 61.569 55.000 0.00 0.00 0.00 3.66
1662 1753 0.885879 TCCTGAAGCGCTTTCGACTA 59.114 50.000 25.84 5.45 38.71 2.59
1681 1772 4.168883 ACTAAGCCAAAGGTCCTTCTACT 58.831 43.478 4.10 0.00 0.00 2.57
1682 1773 3.704800 AAGCCAAAGGTCCTTCTACTC 57.295 47.619 4.10 0.00 0.00 2.59
1683 1774 2.621070 AGCCAAAGGTCCTTCTACTCA 58.379 47.619 4.10 0.00 0.00 3.41
1684 1775 2.303311 AGCCAAAGGTCCTTCTACTCAC 59.697 50.000 4.10 0.00 0.00 3.51
1685 1776 2.615747 GCCAAAGGTCCTTCTACTCACC 60.616 54.545 4.10 0.00 0.00 4.02
1689 1780 3.544698 AGGTCCTTCTACTCACCAAGA 57.455 47.619 0.00 0.00 0.00 3.02
1730 1827 1.070275 CTATGATGCCGGAGCTGCA 59.930 57.895 5.05 2.27 43.97 4.41
1818 1915 3.211045 GCTCCTAGAGTCTCTCGACATT 58.789 50.000 5.39 0.00 42.73 2.71
1821 1918 2.032377 CCTAGAGTCTCTCGACATTCGC 60.032 54.545 5.39 0.00 42.73 4.70
1851 1948 3.703286 CATGTTTGCATGGACGATGAT 57.297 42.857 1.05 0.00 46.47 2.45
1867 1964 4.156556 ACGATGATATGCAAGCAAAGTGTT 59.843 37.500 0.00 0.00 0.00 3.32
1875 1972 4.144297 TGCAAGCAAAGTGTTCTAGGATT 58.856 39.130 0.00 0.00 0.00 3.01
1877 1974 5.412594 TGCAAGCAAAGTGTTCTAGGATTAG 59.587 40.000 0.00 0.00 0.00 1.73
1902 1999 2.109774 CTGAGGCATCCTGAAGACTCT 58.890 52.381 6.78 0.00 31.76 3.24
1920 2017 7.716799 AGACTCTATGGATGATTATGACCTC 57.283 40.000 0.00 0.00 0.00 3.85
1923 2020 7.244558 ACTCTATGGATGATTATGACCTCTCA 58.755 38.462 0.00 0.00 0.00 3.27
1927 2024 7.997773 ATGGATGATTATGACCTCTCATTTG 57.002 36.000 0.00 0.00 38.21 2.32
1944 2041 8.696043 TCTCATTTGATTATACAATTCCCAGG 57.304 34.615 0.00 0.00 0.00 4.45
1975 2072 6.267817 TGGTCTACTAAACCAATCGAATACG 58.732 40.000 0.00 0.00 43.72 3.06
1981 2078 6.509656 ACTAAACCAATCGAATACGCTATGA 58.490 36.000 0.00 0.00 39.58 2.15
1983 2080 3.318017 ACCAATCGAATACGCTATGAGC 58.682 45.455 0.00 0.00 39.58 4.26
1987 2084 5.154222 CAATCGAATACGCTATGAGCTGTA 58.846 41.667 0.00 1.98 39.60 2.74
1988 2085 4.143194 TCGAATACGCTATGAGCTGTAC 57.857 45.455 0.00 0.00 39.60 2.90
1989 2086 2.903095 CGAATACGCTATGAGCTGTACG 59.097 50.000 0.00 0.00 39.60 3.67
2005 2102 4.872691 GCTGTACGAGTCCTTACTAGTGTA 59.127 45.833 5.39 0.00 41.12 2.90
2006 2103 5.526846 GCTGTACGAGTCCTTACTAGTGTAT 59.473 44.000 5.39 0.00 41.12 2.29
2010 2107 8.206867 TGTACGAGTCCTTACTAGTGTATATGT 58.793 37.037 5.39 0.00 41.12 2.29
2011 2108 9.698309 GTACGAGTCCTTACTAGTGTATATGTA 57.302 37.037 5.39 0.00 41.12 2.29
2012 2109 8.600449 ACGAGTCCTTACTAGTGTATATGTAC 57.400 38.462 5.39 0.00 39.74 2.90
2013 2110 7.659390 ACGAGTCCTTACTAGTGTATATGTACC 59.341 40.741 5.39 0.00 39.74 3.34
2014 2111 7.658982 CGAGTCCTTACTAGTGTATATGTACCA 59.341 40.741 5.39 0.00 35.56 3.25
2015 2112 8.921353 AGTCCTTACTAGTGTATATGTACCAG 57.079 38.462 5.39 0.00 32.84 4.00
2016 2113 7.447853 AGTCCTTACTAGTGTATATGTACCAGC 59.552 40.741 5.39 0.00 32.84 4.85
2017 2114 7.230108 GTCCTTACTAGTGTATATGTACCAGCA 59.770 40.741 5.39 0.00 0.00 4.41
2022 2125 7.039882 ACTAGTGTATATGTACCAGCAAACAC 58.960 38.462 0.00 0.00 36.98 3.32
2026 2129 2.373335 ATGTACCAGCAAACACCCAA 57.627 45.000 0.00 0.00 0.00 4.12
2028 2131 1.064314 TGTACCAGCAAACACCCAACT 60.064 47.619 0.00 0.00 0.00 3.16
2029 2132 1.607148 GTACCAGCAAACACCCAACTC 59.393 52.381 0.00 0.00 0.00 3.01
2036 2139 3.197549 AGCAAACACCCAACTCACATTTT 59.802 39.130 0.00 0.00 0.00 1.82
2037 2140 4.404073 AGCAAACACCCAACTCACATTTTA 59.596 37.500 0.00 0.00 0.00 1.52
2043 2146 6.512297 ACACCCAACTCACATTTTATTTGAC 58.488 36.000 0.00 0.00 0.00 3.18
2054 2157 9.605955 TCACATTTTATTTGACATTCGTGTAAG 57.394 29.630 0.00 0.00 0.00 2.34
2055 2158 8.849490 CACATTTTATTTGACATTCGTGTAAGG 58.151 33.333 0.00 0.00 0.00 2.69
2078 2181 5.197451 GGTGACCCACATTCCATTTGTATA 58.803 41.667 0.00 0.00 35.86 1.47
2079 2182 5.299279 GGTGACCCACATTCCATTTGTATAG 59.701 44.000 0.00 0.00 35.86 1.31
2080 2183 5.885912 GTGACCCACATTCCATTTGTATAGT 59.114 40.000 0.00 0.00 34.08 2.12
2081 2184 7.051623 GTGACCCACATTCCATTTGTATAGTA 58.948 38.462 0.00 0.00 34.08 1.82
2082 2185 7.719633 GTGACCCACATTCCATTTGTATAGTAT 59.280 37.037 0.00 0.00 34.08 2.12
2083 2186 8.939932 TGACCCACATTCCATTTGTATAGTATA 58.060 33.333 0.00 0.00 0.00 1.47
2084 2187 9.959721 GACCCACATTCCATTTGTATAGTATAT 57.040 33.333 0.00 0.00 0.00 0.86
2111 2214 9.618890 AGTACTTGTATTTGTTATGCATCTCAT 57.381 29.630 0.19 0.00 39.17 2.90
2112 2215 9.869844 GTACTTGTATTTGTTATGCATCTCATC 57.130 33.333 0.19 0.00 36.63 2.92
2113 2216 7.934457 ACTTGTATTTGTTATGCATCTCATCC 58.066 34.615 0.19 0.00 36.63 3.51
2114 2217 7.557358 ACTTGTATTTGTTATGCATCTCATCCA 59.443 33.333 0.19 0.00 36.63 3.41
2115 2218 8.467963 TTGTATTTGTTATGCATCTCATCCAT 57.532 30.769 0.19 0.29 36.63 3.41
2116 2219 9.571816 TTGTATTTGTTATGCATCTCATCCATA 57.428 29.630 0.19 0.00 36.63 2.74
2117 2220 9.002600 TGTATTTGTTATGCATCTCATCCATAC 57.997 33.333 0.19 10.62 36.63 2.39
2118 2221 9.002600 GTATTTGTTATGCATCTCATCCATACA 57.997 33.333 0.19 0.00 36.63 2.29
2119 2222 7.500720 TTTGTTATGCATCTCATCCATACAG 57.499 36.000 0.19 0.00 36.63 2.74
2120 2223 4.999311 TGTTATGCATCTCATCCATACAGC 59.001 41.667 0.19 0.00 36.63 4.40
2121 2224 3.782656 ATGCATCTCATCCATACAGCA 57.217 42.857 0.00 0.00 35.03 4.41
2122 2225 3.564053 TGCATCTCATCCATACAGCAA 57.436 42.857 0.00 0.00 0.00 3.91
2123 2226 4.094830 TGCATCTCATCCATACAGCAAT 57.905 40.909 0.00 0.00 0.00 3.56
2124 2227 4.466827 TGCATCTCATCCATACAGCAATT 58.533 39.130 0.00 0.00 0.00 2.32
2125 2228 4.891168 TGCATCTCATCCATACAGCAATTT 59.109 37.500 0.00 0.00 0.00 1.82
2126 2229 6.063404 TGCATCTCATCCATACAGCAATTTA 58.937 36.000 0.00 0.00 0.00 1.40
2127 2230 6.546772 TGCATCTCATCCATACAGCAATTTAA 59.453 34.615 0.00 0.00 0.00 1.52
2128 2231 7.068470 TGCATCTCATCCATACAGCAATTTAAA 59.932 33.333 0.00 0.00 0.00 1.52
2129 2232 7.594015 GCATCTCATCCATACAGCAATTTAAAG 59.406 37.037 0.00 0.00 0.00 1.85
2130 2233 8.627403 CATCTCATCCATACAGCAATTTAAAGT 58.373 33.333 0.00 0.00 0.00 2.66
2131 2234 9.851686 ATCTCATCCATACAGCAATTTAAAGTA 57.148 29.630 0.00 0.00 0.00 2.24
2132 2235 9.679661 TCTCATCCATACAGCAATTTAAAGTAA 57.320 29.630 0.00 0.00 0.00 2.24
2137 2240 9.679661 TCCATACAGCAATTTAAAGTAATCTCA 57.320 29.630 0.00 0.00 0.00 3.27
2157 2260 4.143333 ATCTCCAACGCCGACCCG 62.143 66.667 0.00 0.00 0.00 5.28
2181 2285 1.272425 ACCCCTCGCATCCATTCAAAA 60.272 47.619 0.00 0.00 0.00 2.44
2203 2307 0.878523 CGTTGTCCAGACTGCGGAAA 60.879 55.000 0.00 0.00 33.29 3.13
2208 2312 0.400213 TCCAGACTGCGGAAACCATT 59.600 50.000 0.00 0.00 0.00 3.16
2219 2323 1.950909 GGAAACCATTCAACACGGTCA 59.049 47.619 0.00 0.00 37.29 4.02
2246 2350 3.342627 CTGTGGCGCGGTTCGAAA 61.343 61.111 8.83 0.00 41.67 3.46
2266 2370 0.031585 GTGTTTTCTCCCGCAAACCC 59.968 55.000 0.00 0.00 32.76 4.11
2313 2423 4.363990 CAGACCGCTGTCACGCCT 62.364 66.667 11.07 0.00 44.33 5.52
2314 2424 3.616721 AGACCGCTGTCACGCCTT 61.617 61.111 11.07 0.00 44.33 4.35
2320 2430 1.347817 CGCTGTCACGCCTTCTTCTC 61.348 60.000 0.00 0.00 0.00 2.87
2326 2436 0.600255 CACGCCTTCTTCTCACCGTT 60.600 55.000 0.00 0.00 0.00 4.44
2342 2452 2.167662 CCGTTCTAGCCCACCAAAATT 58.832 47.619 0.00 0.00 0.00 1.82
2354 2465 1.507742 ACCAAAATTCCCCCACCTCTT 59.492 47.619 0.00 0.00 0.00 2.85
2545 2661 1.135315 CTGCATTCAAACGCCTCCG 59.865 57.895 0.00 0.00 41.14 4.63
2580 2697 1.926108 AGCTGAGAAACCTACTCCGT 58.074 50.000 0.00 0.00 33.95 4.69
2585 2702 0.886563 AGAAACCTACTCCGTCCACG 59.113 55.000 0.00 0.00 39.44 4.94
2641 2762 0.326522 TCAGGCAAGCTCCTCCCATA 60.327 55.000 0.00 0.00 33.25 2.74
2646 2767 1.207791 CAAGCTCCTCCCATACACCT 58.792 55.000 0.00 0.00 0.00 4.00
2674 2796 3.461773 CGAGGCCAGACGTGGGAT 61.462 66.667 5.01 0.00 45.17 3.85
2730 2857 5.259632 CTCCTTCCATCATTTTCTCCACTT 58.740 41.667 0.00 0.00 0.00 3.16
2841 2972 2.922503 TCGCTGCTCCACCTTCCA 60.923 61.111 0.00 0.00 0.00 3.53
2849 2982 1.961180 CTCCACCTTCCACCCTAGCG 61.961 65.000 0.00 0.00 0.00 4.26
2865 2998 3.036084 CGCGACGGAGCAAGTTGT 61.036 61.111 0.00 0.00 36.85 3.32
2894 3027 2.616330 CGGCGTGTGGTTCAGCAAT 61.616 57.895 0.00 0.00 0.00 3.56
2896 3029 0.031994 GGCGTGTGGTTCAGCAATTT 59.968 50.000 0.00 0.00 0.00 1.82
2900 3033 1.117994 TGTGGTTCAGCAATTTGCCA 58.882 45.000 17.51 5.54 46.52 4.92
2918 3051 1.679139 CACTCCAAGCCAACTCACAA 58.321 50.000 0.00 0.00 0.00 3.33
2950 3083 0.329261 TTGCTCAAGGCTGGCATAGT 59.671 50.000 3.38 0.00 42.39 2.12
2990 3126 1.079197 ATCGTTGCTGCCATCGACA 60.079 52.632 11.57 0.00 43.50 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 75 1.202940 GCCCAGACAAAAAGAGGACCT 60.203 52.381 0.00 0.00 0.00 3.85
76 78 1.073923 GGAGCCCAGACAAAAAGAGGA 59.926 52.381 0.00 0.00 0.00 3.71
78 80 2.276732 TGGAGCCCAGACAAAAAGAG 57.723 50.000 0.00 0.00 0.00 2.85
98 100 6.395780 TCTAAAAACAGGGGATATGGTGAA 57.604 37.500 0.00 0.00 0.00 3.18
148 151 2.236223 CTCGCCACTGAGCAGGACAT 62.236 60.000 2.20 0.00 0.00 3.06
184 193 3.181439 GGGGAGGACCTTATTCCATCTTG 60.181 52.174 0.00 0.00 38.25 3.02
233 242 1.369448 CGCTCTCCGACGATGCTAC 60.369 63.158 0.00 0.00 40.02 3.58
437 450 3.388162 TGTAGTAGACAGTCGGCACGTT 61.388 50.000 0.00 0.00 43.17 3.99
440 453 3.505464 ATTGTAGTAGACAGTCGGCAC 57.495 47.619 0.00 0.00 39.88 5.01
473 486 1.173444 CGTCATCGTCCCTCCCTAGG 61.173 65.000 0.06 0.06 43.25 3.02
562 589 9.276397 GTAGAACAAAGAATACGAGAAGTAGAC 57.724 37.037 0.00 0.00 38.94 2.59
564 591 8.460428 AGGTAGAACAAAGAATACGAGAAGTAG 58.540 37.037 0.00 0.00 38.94 2.57
662 690 6.491745 TGTAGCCAATCTTTTATGGTTGTCAA 59.508 34.615 0.00 0.00 39.00 3.18
705 733 5.371526 TGATCAAGCCATCAGGATAACTTC 58.628 41.667 0.00 0.00 36.89 3.01
710 738 3.413846 GCTGATCAAGCCATCAGGATA 57.586 47.619 15.98 0.00 46.95 2.59
778 806 6.731292 TTATCTCATTCTTGTAGCCAGCTA 57.269 37.500 0.00 0.00 0.00 3.32
808 862 4.040765 TCTGCTCAGAAAGTGACGTTCAC 61.041 47.826 13.39 9.30 39.96 3.18
913 974 1.279271 AGCCACAGTTCCTCGCTAATT 59.721 47.619 0.00 0.00 0.00 1.40
919 980 2.428890 AGAGATAAGCCACAGTTCCTCG 59.571 50.000 0.00 0.00 0.00 4.63
932 997 8.868522 ATACAGGAGAGATTGAGAGAGATAAG 57.131 38.462 0.00 0.00 0.00 1.73
944 1009 6.459848 CGGTTCTCGTTTATACAGGAGAGATT 60.460 42.308 10.31 0.00 38.57 2.40
945 1010 5.008811 CGGTTCTCGTTTATACAGGAGAGAT 59.991 44.000 10.31 0.00 38.57 2.75
946 1011 4.334759 CGGTTCTCGTTTATACAGGAGAGA 59.665 45.833 10.31 1.39 38.57 3.10
947 1012 4.599047 CGGTTCTCGTTTATACAGGAGAG 58.401 47.826 10.31 0.00 38.57 3.20
948 1013 3.181493 GCGGTTCTCGTTTATACAGGAGA 60.181 47.826 7.11 7.11 41.72 3.71
949 1014 3.114065 GCGGTTCTCGTTTATACAGGAG 58.886 50.000 2.78 2.78 41.72 3.69
950 1015 2.492881 TGCGGTTCTCGTTTATACAGGA 59.507 45.455 0.00 0.00 41.72 3.86
951 1016 2.601763 GTGCGGTTCTCGTTTATACAGG 59.398 50.000 0.00 0.00 41.72 4.00
968 1033 0.535102 AGGGTGTCAAAGGAAGTGCG 60.535 55.000 0.00 0.00 0.00 5.34
986 1051 1.381928 GGCCATGACATGCACCAGAG 61.382 60.000 16.76 2.09 0.00 3.35
987 1052 1.378911 GGCCATGACATGCACCAGA 60.379 57.895 16.76 0.00 0.00 3.86
988 1053 2.767445 CGGCCATGACATGCACCAG 61.767 63.158 19.86 11.91 0.00 4.00
989 1054 2.751036 CGGCCATGACATGCACCA 60.751 61.111 19.86 0.00 0.00 4.17
990 1055 4.197498 GCGGCCATGACATGCACC 62.197 66.667 10.10 11.96 0.00 5.01
991 1056 3.405592 CTGCGGCCATGACATGCAC 62.406 63.158 10.10 4.18 0.00 4.57
993 1058 4.564116 GCTGCGGCCATGACATGC 62.564 66.667 6.12 5.70 0.00 4.06
994 1059 3.135457 TGCTGCGGCCATGACATG 61.135 61.111 16.57 8.56 37.74 3.21
995 1060 3.136123 GTGCTGCGGCCATGACAT 61.136 61.111 16.57 0.00 37.74 3.06
1043 1108 0.035458 CCCTTTCTTCAGCACTCCGT 59.965 55.000 0.00 0.00 0.00 4.69
1045 1110 1.339535 CCTCCCTTTCTTCAGCACTCC 60.340 57.143 0.00 0.00 0.00 3.85
1048 1113 0.962855 GCCCTCCCTTTCTTCAGCAC 60.963 60.000 0.00 0.00 0.00 4.40
1054 1119 1.076187 CTCTTTGGCCCTCCCTTTCTT 59.924 52.381 0.00 0.00 0.00 2.52
1059 1139 1.617839 CTCCTCTTTGGCCCTCCCT 60.618 63.158 0.00 0.00 35.26 4.20
1064 1144 1.616628 TCCTCCTCCTCTTTGGCCC 60.617 63.158 0.00 0.00 35.26 5.80
1067 1147 1.494960 CTCCTCCTCCTCCTCTTTGG 58.505 60.000 0.00 0.00 37.10 3.28
1068 1148 1.007721 TCCTCCTCCTCCTCCTCTTTG 59.992 57.143 0.00 0.00 0.00 2.77
1076 1156 3.024356 TCGCCTCCTCCTCCTCCT 61.024 66.667 0.00 0.00 0.00 3.69
1082 1162 3.351885 AGTCCCTCGCCTCCTCCT 61.352 66.667 0.00 0.00 0.00 3.69
1084 1164 3.151022 CCAGTCCCTCGCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1085 1165 4.787280 CCCAGTCCCTCGCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1121 1201 4.025401 GGAACACGGCCAGCAACG 62.025 66.667 2.24 0.00 0.00 4.10
1138 1218 0.320683 TCGATGTGGTCCAGCTTGTG 60.321 55.000 0.00 0.00 0.00 3.33
1139 1219 0.615331 ATCGATGTGGTCCAGCTTGT 59.385 50.000 0.00 0.00 0.00 3.16
1142 1222 1.620819 GGATATCGATGTGGTCCAGCT 59.379 52.381 8.54 0.00 0.00 4.24
1158 1238 1.760875 GTCGGGCCCTGTGAGGATA 60.761 63.158 22.43 0.00 37.67 2.59
1167 1247 4.033776 CACACCATGTCGGGCCCT 62.034 66.667 22.43 0.00 40.22 5.19
1204 1284 3.461773 CTCGGGCTCGTCCATGGT 61.462 66.667 12.58 0.00 37.69 3.55
1252 1332 1.087771 CCAGGGTATTGTTCGGCGAC 61.088 60.000 10.16 5.76 0.00 5.19
1253 1333 1.219664 CCAGGGTATTGTTCGGCGA 59.780 57.895 4.99 4.99 0.00 5.54
1268 1348 2.840651 ACCATCTCAAAGAGTACCCCAG 59.159 50.000 0.00 0.00 0.00 4.45
1269 1349 2.571653 CACCATCTCAAAGAGTACCCCA 59.428 50.000 0.00 0.00 0.00 4.96
1270 1350 2.838202 TCACCATCTCAAAGAGTACCCC 59.162 50.000 0.00 0.00 0.00 4.95
1271 1351 3.769844 TCTCACCATCTCAAAGAGTACCC 59.230 47.826 0.00 0.00 0.00 3.69
1274 1354 3.449018 GGCTCTCACCATCTCAAAGAGTA 59.551 47.826 0.00 0.00 36.64 2.59
1276 1356 2.738000 CGGCTCTCACCATCTCAAAGAG 60.738 54.545 0.00 0.00 37.20 2.85
1277 1357 1.205655 CGGCTCTCACCATCTCAAAGA 59.794 52.381 0.00 0.00 0.00 2.52
1279 1359 0.391661 GCGGCTCTCACCATCTCAAA 60.392 55.000 0.00 0.00 0.00 2.69
1296 1385 3.857854 GCACTGCGTCTCATGGCG 61.858 66.667 0.00 0.00 0.00 5.69
1336 1425 1.066858 GTCTGAGAATTCACCCTCGCA 60.067 52.381 8.44 0.00 32.30 5.10
1356 1445 2.289694 ACCGAGAAGGGACAAGACATTG 60.290 50.000 0.00 0.00 46.96 2.82
1358 1447 1.276421 CACCGAGAAGGGACAAGACAT 59.724 52.381 0.00 0.00 46.96 3.06
1359 1448 0.679505 CACCGAGAAGGGACAAGACA 59.320 55.000 0.00 0.00 46.96 3.41
1360 1449 0.966920 TCACCGAGAAGGGACAAGAC 59.033 55.000 0.00 0.00 46.96 3.01
1362 1451 2.009042 GCATCACCGAGAAGGGACAAG 61.009 57.143 0.00 0.00 46.96 3.16
1363 1452 0.036388 GCATCACCGAGAAGGGACAA 60.036 55.000 0.00 0.00 46.96 3.18
1365 1454 1.519455 CGCATCACCGAGAAGGGAC 60.519 63.158 0.00 0.00 46.96 4.46
1371 1460 1.037579 ATCCTCACGCATCACCGAGA 61.038 55.000 0.00 0.00 0.00 4.04
1377 1466 1.739466 GCAAGAAATCCTCACGCATCA 59.261 47.619 0.00 0.00 0.00 3.07
1380 1469 1.536766 CAAGCAAGAAATCCTCACGCA 59.463 47.619 0.00 0.00 0.00 5.24
1414 1503 8.405531 CCAGTAAATCAGAGTTTTTGTTTGAGA 58.594 33.333 0.00 0.00 0.00 3.27
1416 1507 6.978080 GCCAGTAAATCAGAGTTTTTGTTTGA 59.022 34.615 0.00 0.00 0.00 2.69
1419 1510 6.463995 TGCCAGTAAATCAGAGTTTTTGTT 57.536 33.333 0.00 0.00 0.00 2.83
1421 1512 7.951530 AATTGCCAGTAAATCAGAGTTTTTG 57.048 32.000 0.00 0.00 0.00 2.44
1424 1515 7.530426 AGAAATTGCCAGTAAATCAGAGTTT 57.470 32.000 0.00 0.00 0.00 2.66
1426 1517 7.530426 AAAGAAATTGCCAGTAAATCAGAGT 57.470 32.000 0.00 0.00 0.00 3.24
1427 1518 9.346725 GTAAAAGAAATTGCCAGTAAATCAGAG 57.653 33.333 0.00 0.00 0.00 3.35
1428 1519 8.855110 TGTAAAAGAAATTGCCAGTAAATCAGA 58.145 29.630 0.00 0.00 0.00 3.27
1431 1522 9.087424 GGATGTAAAAGAAATTGCCAGTAAATC 57.913 33.333 0.00 0.00 0.00 2.17
1432 1523 8.815912 AGGATGTAAAAGAAATTGCCAGTAAAT 58.184 29.630 0.00 0.00 0.00 1.40
1449 1540 9.906660 CACAGCAAATAAAGTTAAGGATGTAAA 57.093 29.630 0.00 0.00 0.00 2.01
1450 1541 9.073475 ACACAGCAAATAAAGTTAAGGATGTAA 57.927 29.630 0.00 0.00 0.00 2.41
1451 1542 8.630054 ACACAGCAAATAAAGTTAAGGATGTA 57.370 30.769 0.00 0.00 0.00 2.29
1452 1543 7.524717 ACACAGCAAATAAAGTTAAGGATGT 57.475 32.000 0.00 0.00 0.00 3.06
1453 1544 8.184192 CCTACACAGCAAATAAAGTTAAGGATG 58.816 37.037 0.00 0.00 0.00 3.51
1454 1545 7.339466 CCCTACACAGCAAATAAAGTTAAGGAT 59.661 37.037 0.00 0.00 0.00 3.24
1455 1546 6.657541 CCCTACACAGCAAATAAAGTTAAGGA 59.342 38.462 0.00 0.00 0.00 3.36
1456 1547 6.625081 GCCCTACACAGCAAATAAAGTTAAGG 60.625 42.308 0.00 0.00 0.00 2.69
1457 1548 6.322491 GCCCTACACAGCAAATAAAGTTAAG 58.678 40.000 0.00 0.00 0.00 1.85
1458 1549 5.106475 CGCCCTACACAGCAAATAAAGTTAA 60.106 40.000 0.00 0.00 0.00 2.01
1459 1550 4.393680 CGCCCTACACAGCAAATAAAGTTA 59.606 41.667 0.00 0.00 0.00 2.24
1460 1551 3.190535 CGCCCTACACAGCAAATAAAGTT 59.809 43.478 0.00 0.00 0.00 2.66
1461 1552 2.747446 CGCCCTACACAGCAAATAAAGT 59.253 45.455 0.00 0.00 0.00 2.66
1462 1553 2.477863 GCGCCCTACACAGCAAATAAAG 60.478 50.000 0.00 0.00 0.00 1.85
1463 1554 1.470890 GCGCCCTACACAGCAAATAAA 59.529 47.619 0.00 0.00 0.00 1.40
1464 1555 1.091537 GCGCCCTACACAGCAAATAA 58.908 50.000 0.00 0.00 0.00 1.40
1465 1556 0.746563 GGCGCCCTACACAGCAAATA 60.747 55.000 18.11 0.00 0.00 1.40
1466 1557 2.046285 GGCGCCCTACACAGCAAAT 61.046 57.895 18.11 0.00 0.00 2.32
1467 1558 2.671619 GGCGCCCTACACAGCAAA 60.672 61.111 18.11 0.00 0.00 3.68
1468 1559 4.715523 GGGCGCCCTACACAGCAA 62.716 66.667 38.76 0.00 0.00 3.91
1485 1576 3.186119 GAGTCGAAGGCTCTTCAATGAG 58.814 50.000 13.24 0.00 40.46 2.90
1516 1607 5.863935 TGAATGTCGAATCCACGATATCATC 59.136 40.000 3.12 0.00 41.61 2.92
1521 1612 4.142026 ACCTTGAATGTCGAATCCACGATA 60.142 41.667 0.00 0.00 43.93 2.92
1524 1615 2.094258 CACCTTGAATGTCGAATCCACG 59.906 50.000 0.00 0.00 0.00 4.94
1530 1621 2.542020 TCAGCACCTTGAATGTCGAA 57.458 45.000 0.00 0.00 0.00 3.71
1546 1637 1.806542 CACGGGGAACTTTGTGATCAG 59.193 52.381 0.00 0.00 34.29 2.90
1564 1655 0.036022 AGCTCCAACTCCTCTTGCAC 59.964 55.000 0.00 0.00 0.00 4.57
1568 1659 1.722034 TGACAGCTCCAACTCCTCTT 58.278 50.000 0.00 0.00 0.00 2.85
1569 1660 1.722034 TTGACAGCTCCAACTCCTCT 58.278 50.000 0.00 0.00 0.00 3.69
1578 1669 0.312102 GCCAACAGTTTGACAGCTCC 59.688 55.000 0.00 0.00 34.24 4.70
1584 1675 0.593128 AGCGATGCCAACAGTTTGAC 59.407 50.000 0.00 0.00 34.24 3.18
1594 1685 3.430862 GCGTGGAAAGCGATGCCA 61.431 61.111 0.00 0.00 0.00 4.92
1605 1696 0.753867 TAACTTCCAGTGTGCGTGGA 59.246 50.000 0.00 0.00 42.62 4.02
1609 1700 2.550978 CCCTATAACTTCCAGTGTGCG 58.449 52.381 0.00 0.00 0.00 5.34
1610 1701 2.504175 TCCCCTATAACTTCCAGTGTGC 59.496 50.000 0.00 0.00 0.00 4.57
1611 1702 4.708177 CATCCCCTATAACTTCCAGTGTG 58.292 47.826 0.00 0.00 0.00 3.82
1617 1708 2.553247 GCAGGCATCCCCTATAACTTCC 60.553 54.545 0.00 0.00 44.09 3.46
1623 1714 4.250699 GGGCAGGCATCCCCTATA 57.749 61.111 0.00 0.00 44.09 1.31
1644 1735 1.656095 CTTAGTCGAAAGCGCTTCAGG 59.344 52.381 25.24 15.36 37.46 3.86
1662 1753 2.979678 TGAGTAGAAGGACCTTTGGCTT 59.020 45.455 8.49 0.00 0.00 4.35
1683 1774 0.469917 CACTGTCACCCACTCTTGGT 59.530 55.000 0.00 0.00 42.10 3.67
1684 1775 0.886490 GCACTGTCACCCACTCTTGG 60.886 60.000 0.00 0.00 43.50 3.61
1685 1776 0.179048 TGCACTGTCACCCACTCTTG 60.179 55.000 0.00 0.00 0.00 3.02
1689 1780 2.111878 GCTGCACTGTCACCCACT 59.888 61.111 0.00 0.00 0.00 4.00
1692 1783 2.034687 ATGGCTGCACTGTCACCC 59.965 61.111 0.50 0.00 0.00 4.61
1694 1785 2.986306 GCCATGGCTGCACTGTCAC 61.986 63.158 29.98 0.00 38.26 3.67
1713 1804 1.070275 CTGCAGCTCCGGCATCATA 59.930 57.895 0.00 0.00 41.06 2.15
1743 1840 3.259064 GTTGGTGAGCGAATTAGCAGTA 58.741 45.455 13.26 0.00 40.15 2.74
1791 1888 1.452145 GAGACTCTAGGAGCGGGCAG 61.452 65.000 0.00 0.00 32.04 4.85
1851 1948 4.905429 TCCTAGAACACTTTGCTTGCATA 58.095 39.130 0.00 0.00 0.00 3.14
1867 1964 3.463704 TGCCTCAGAGTCCTAATCCTAGA 59.536 47.826 0.00 0.00 0.00 2.43
1875 1972 1.570979 TCAGGATGCCTCAGAGTCCTA 59.429 52.381 7.59 0.00 39.01 2.94
1877 1974 1.138661 CTTCAGGATGCCTCAGAGTCC 59.861 57.143 0.00 0.00 34.76 3.85
1902 1999 8.883302 TCAAATGAGAGGTCATAATCATCCATA 58.117 33.333 0.00 0.00 43.04 2.74
1920 2017 7.373493 GCCTGGGAATTGTATAATCAAATGAG 58.627 38.462 0.00 0.00 0.00 2.90
1923 2020 6.142498 TGGCCTGGGAATTGTATAATCAAAT 58.858 36.000 3.32 0.00 0.00 2.32
1927 2024 4.082026 GCATGGCCTGGGAATTGTATAATC 60.082 45.833 3.32 0.00 0.00 1.75
1960 2057 4.211374 GCTCATAGCGTATTCGATTGGTTT 59.789 41.667 0.00 0.00 39.71 3.27
1975 2072 1.950909 AGGACTCGTACAGCTCATAGC 59.049 52.381 0.00 0.00 42.84 2.97
1981 2078 3.940221 CACTAGTAAGGACTCGTACAGCT 59.060 47.826 0.00 0.00 37.10 4.24
1983 2080 8.710551 CATATACACTAGTAAGGACTCGTACAG 58.289 40.741 0.00 0.00 37.10 2.74
1987 2084 7.659390 GGTACATATACACTAGTAAGGACTCGT 59.341 40.741 0.00 0.00 33.39 4.18
1988 2085 7.658982 TGGTACATATACACTAGTAAGGACTCG 59.341 40.741 0.00 0.00 33.39 4.18
1989 2086 8.915057 TGGTACATATACACTAGTAAGGACTC 57.085 38.462 0.00 0.00 33.39 3.36
2005 2102 3.730215 TGGGTGTTTGCTGGTACATAT 57.270 42.857 0.00 0.00 38.20 1.78
2006 2103 3.150767 GTTGGGTGTTTGCTGGTACATA 58.849 45.455 0.00 0.00 38.20 2.29
2010 2107 1.213182 TGAGTTGGGTGTTTGCTGGTA 59.787 47.619 0.00 0.00 0.00 3.25
2011 2108 0.033601 TGAGTTGGGTGTTTGCTGGT 60.034 50.000 0.00 0.00 0.00 4.00
2012 2109 0.385390 GTGAGTTGGGTGTTTGCTGG 59.615 55.000 0.00 0.00 0.00 4.85
2013 2110 1.102154 TGTGAGTTGGGTGTTTGCTG 58.898 50.000 0.00 0.00 0.00 4.41
2014 2111 2.071778 ATGTGAGTTGGGTGTTTGCT 57.928 45.000 0.00 0.00 0.00 3.91
2015 2112 2.888834 AATGTGAGTTGGGTGTTTGC 57.111 45.000 0.00 0.00 0.00 3.68
2016 2113 7.493971 TCAAATAAAATGTGAGTTGGGTGTTTG 59.506 33.333 0.00 0.00 0.00 2.93
2017 2114 7.494298 GTCAAATAAAATGTGAGTTGGGTGTTT 59.506 33.333 0.00 0.00 0.00 2.83
2022 2125 7.062138 CGAATGTCAAATAAAATGTGAGTTGGG 59.938 37.037 0.00 0.00 0.00 4.12
2026 2129 7.648142 ACACGAATGTCAAATAAAATGTGAGT 58.352 30.769 0.00 0.00 31.55 3.41
2028 2131 9.605955 CTTACACGAATGTCAAATAAAATGTGA 57.394 29.630 0.00 0.00 40.48 3.58
2029 2132 8.849490 CCTTACACGAATGTCAAATAAAATGTG 58.151 33.333 0.00 0.00 40.48 3.21
2036 2139 5.640357 GTCACCCTTACACGAATGTCAAATA 59.360 40.000 0.00 0.00 40.48 1.40
2037 2140 4.454504 GTCACCCTTACACGAATGTCAAAT 59.545 41.667 0.00 0.00 40.48 2.32
2043 2146 1.002659 TGGGTCACCCTTACACGAATG 59.997 52.381 16.04 0.00 45.70 2.67
2054 2157 1.550072 CAAATGGAATGTGGGTCACCC 59.450 52.381 5.63 5.63 45.71 4.61
2055 2158 2.247358 ACAAATGGAATGTGGGTCACC 58.753 47.619 0.00 0.00 35.22 4.02
2085 2188 9.618890 ATGAGATGCATAACAAATACAAGTACT 57.381 29.630 0.00 0.00 34.82 2.73
2086 2189 9.869844 GATGAGATGCATAACAAATACAAGTAC 57.130 33.333 0.00 0.00 37.34 2.73
2087 2190 9.056005 GGATGAGATGCATAACAAATACAAGTA 57.944 33.333 0.00 0.00 37.34 2.24
2088 2191 7.557358 TGGATGAGATGCATAACAAATACAAGT 59.443 33.333 0.00 0.00 37.34 3.16
2089 2192 7.933396 TGGATGAGATGCATAACAAATACAAG 58.067 34.615 0.00 0.00 37.34 3.16
2090 2193 7.878547 TGGATGAGATGCATAACAAATACAA 57.121 32.000 0.00 0.00 37.34 2.41
2091 2194 9.002600 GTATGGATGAGATGCATAACAAATACA 57.997 33.333 0.00 0.00 43.67 2.29
2092 2195 9.002600 TGTATGGATGAGATGCATAACAAATAC 57.997 33.333 0.00 12.24 43.67 1.89
2093 2196 9.223099 CTGTATGGATGAGATGCATAACAAATA 57.777 33.333 0.00 1.50 43.67 1.40
2094 2197 7.309012 GCTGTATGGATGAGATGCATAACAAAT 60.309 37.037 0.00 2.37 43.67 2.32
2095 2198 6.016860 GCTGTATGGATGAGATGCATAACAAA 60.017 38.462 0.00 0.00 43.67 2.83
2096 2199 5.471116 GCTGTATGGATGAGATGCATAACAA 59.529 40.000 0.00 0.00 43.67 2.83
2097 2200 4.999311 GCTGTATGGATGAGATGCATAACA 59.001 41.667 0.00 3.19 43.67 2.41
2098 2201 4.999311 TGCTGTATGGATGAGATGCATAAC 59.001 41.667 0.00 0.00 43.67 1.89
2099 2202 5.231702 TGCTGTATGGATGAGATGCATAA 57.768 39.130 0.00 0.00 43.67 1.90
2100 2203 4.895668 TGCTGTATGGATGAGATGCATA 57.104 40.909 0.00 0.00 41.74 3.14
2101 2204 3.782656 TGCTGTATGGATGAGATGCAT 57.217 42.857 0.00 0.00 43.97 3.96
2102 2205 3.564053 TTGCTGTATGGATGAGATGCA 57.436 42.857 0.00 0.00 34.26 3.96
2103 2206 5.449107 AAATTGCTGTATGGATGAGATGC 57.551 39.130 0.00 0.00 0.00 3.91
2104 2207 8.627403 ACTTTAAATTGCTGTATGGATGAGATG 58.373 33.333 0.00 0.00 0.00 2.90
2105 2208 8.757982 ACTTTAAATTGCTGTATGGATGAGAT 57.242 30.769 0.00 0.00 0.00 2.75
2106 2209 9.679661 TTACTTTAAATTGCTGTATGGATGAGA 57.320 29.630 0.00 0.00 0.00 3.27
2111 2214 9.679661 TGAGATTACTTTAAATTGCTGTATGGA 57.320 29.630 0.00 0.00 0.00 3.41
2112 2215 9.941664 CTGAGATTACTTTAAATTGCTGTATGG 57.058 33.333 0.00 0.00 0.00 2.74
2113 2216 9.443283 GCTGAGATTACTTTAAATTGCTGTATG 57.557 33.333 0.00 0.00 0.00 2.39
2114 2217 9.177608 TGCTGAGATTACTTTAAATTGCTGTAT 57.822 29.630 0.00 0.00 0.00 2.29
2115 2218 8.560355 TGCTGAGATTACTTTAAATTGCTGTA 57.440 30.769 0.00 0.00 0.00 2.74
2116 2219 7.452880 TGCTGAGATTACTTTAAATTGCTGT 57.547 32.000 0.00 0.00 0.00 4.40
2117 2220 8.404000 AGATGCTGAGATTACTTTAAATTGCTG 58.596 33.333 0.00 0.00 0.00 4.41
2118 2221 8.517062 AGATGCTGAGATTACTTTAAATTGCT 57.483 30.769 0.00 0.00 0.00 3.91
2119 2222 7.859875 GGAGATGCTGAGATTACTTTAAATTGC 59.140 37.037 0.00 0.00 0.00 3.56
2120 2223 8.896744 TGGAGATGCTGAGATTACTTTAAATTG 58.103 33.333 0.00 0.00 0.00 2.32
2121 2224 9.466497 TTGGAGATGCTGAGATTACTTTAAATT 57.534 29.630 0.00 0.00 0.00 1.82
2122 2225 8.897752 GTTGGAGATGCTGAGATTACTTTAAAT 58.102 33.333 0.00 0.00 0.00 1.40
2123 2226 7.064609 CGTTGGAGATGCTGAGATTACTTTAAA 59.935 37.037 0.00 0.00 0.00 1.52
2124 2227 6.535150 CGTTGGAGATGCTGAGATTACTTTAA 59.465 38.462 0.00 0.00 0.00 1.52
2125 2228 6.042777 CGTTGGAGATGCTGAGATTACTTTA 58.957 40.000 0.00 0.00 0.00 1.85
2126 2229 4.872691 CGTTGGAGATGCTGAGATTACTTT 59.127 41.667 0.00 0.00 0.00 2.66
2127 2230 4.437239 CGTTGGAGATGCTGAGATTACTT 58.563 43.478 0.00 0.00 0.00 2.24
2128 2231 3.739519 GCGTTGGAGATGCTGAGATTACT 60.740 47.826 0.00 0.00 37.30 2.24
2129 2232 2.541762 GCGTTGGAGATGCTGAGATTAC 59.458 50.000 0.00 0.00 37.30 1.89
2130 2233 2.483714 GGCGTTGGAGATGCTGAGATTA 60.484 50.000 0.00 0.00 40.27 1.75
2131 2234 1.661341 GCGTTGGAGATGCTGAGATT 58.339 50.000 0.00 0.00 37.30 2.40
2132 2235 0.179062 GGCGTTGGAGATGCTGAGAT 60.179 55.000 0.00 0.00 40.27 2.75
2133 2236 1.219124 GGCGTTGGAGATGCTGAGA 59.781 57.895 0.00 0.00 40.27 3.27
2134 2237 3.805267 GGCGTTGGAGATGCTGAG 58.195 61.111 0.00 0.00 40.27 3.35
2136 2239 2.125552 TCGGCGTTGGAGATGCTG 60.126 61.111 6.85 0.00 46.16 4.41
2137 2240 2.125512 GTCGGCGTTGGAGATGCT 60.126 61.111 6.85 0.00 40.27 3.79
2157 2260 1.322538 AATGGATGCGAGGGGTTTGC 61.323 55.000 0.00 0.00 36.67 3.68
2164 2267 1.795162 GCGTTTTGAATGGATGCGAGG 60.795 52.381 0.00 0.00 0.00 4.63
2166 2269 3.692998 GCGTTTTGAATGGATGCGA 57.307 47.368 0.00 0.00 0.00 5.10
2181 2285 2.661866 GCAGTCTGGACAACGCGT 60.662 61.111 5.58 5.58 0.00 6.01
2208 2312 1.546923 ACCGATACATGACCGTGTTGA 59.453 47.619 0.00 0.00 33.62 3.18
2219 2323 1.227263 GCGCCACAGACCGATACAT 60.227 57.895 0.00 0.00 0.00 2.29
2266 2370 3.981211 CAAACCCCTCATGTTTGTCTTG 58.019 45.455 7.51 0.00 44.67 3.02
2313 2423 1.549170 GGGCTAGAACGGTGAGAAGAA 59.451 52.381 0.00 0.00 0.00 2.52
2314 2424 1.183549 GGGCTAGAACGGTGAGAAGA 58.816 55.000 0.00 0.00 0.00 2.87
2320 2430 0.250553 TTTGGTGGGCTAGAACGGTG 60.251 55.000 0.00 0.00 0.00 4.94
2326 2436 1.006639 GGGGAATTTTGGTGGGCTAGA 59.993 52.381 0.00 0.00 0.00 2.43
2447 2562 0.917533 AATGGCAGAGGCAGTGAGAT 59.082 50.000 0.00 0.00 42.43 2.75
2498 2613 3.358707 GTTTAGCCGGGCGTGCAA 61.359 61.111 14.39 3.87 0.00 4.08
2545 2661 1.135402 CAGCTTCCATGCGGGTTTAAC 60.135 52.381 0.00 0.00 38.11 2.01
2580 2697 0.460109 CTCATGAACGGATGCGTGGA 60.460 55.000 14.66 8.17 0.00 4.02
2641 2762 4.259356 GGCCTCGTTTAAATAGAAGGTGT 58.741 43.478 0.00 0.00 0.00 4.16
2646 2767 4.178540 CGTCTGGCCTCGTTTAAATAGAA 58.821 43.478 3.32 0.00 0.00 2.10
2674 2796 1.066605 GGCGGAGTAGTGCGATTCTTA 59.933 52.381 16.30 0.00 40.58 2.10
2686 2808 1.602888 GATAGGGAGCGGCGGAGTA 60.603 63.158 9.78 0.00 0.00 2.59
2730 2857 0.108567 TCGTCGGATGCCATCGAAAA 60.109 50.000 0.00 0.00 37.14 2.29
2849 2982 2.853914 GACAACTTGCTCCGTCGC 59.146 61.111 0.00 0.00 0.00 5.19
2894 3027 4.695014 TTGGCTTGGAGTGGCAAA 57.305 50.000 0.00 0.00 44.87 3.68
2896 3029 1.228245 GAGTTGGCTTGGAGTGGCA 60.228 57.895 0.00 0.00 38.22 4.92
2900 3033 2.301346 CTTTGTGAGTTGGCTTGGAGT 58.699 47.619 0.00 0.00 0.00 3.85
2937 3070 1.619363 TCCCCACTATGCCAGCCTT 60.619 57.895 0.00 0.00 0.00 4.35
2950 3083 4.365111 GTGCCACCATGCTCCCCA 62.365 66.667 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.