Multiple sequence alignment - TraesCS4A01G139500

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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 TraesCS4A01G139500 chr4A 100.000 6123 0 0 1 6123 211000276 210994154 0.000000e+00 11308.0
1 TraesCS4A01G139500 chr4A 94.764 382 19 1 3681 4062 662252666 662253046 1.470000e-165 593.0
2 TraesCS4A01G139500 chr4B 90.056 3570 147 81 1 3461 273688586 273685116 0.000000e+00 4434.0
3 TraesCS4A01G139500 chr4B 94.786 748 8 13 5201 5923 237055051 237054310 0.000000e+00 1136.0
4 TraesCS4A01G139500 chr4B 96.837 569 16 2 4633 5200 273684572 273684005 0.000000e+00 950.0
5 TraesCS4A01G139500 chr4B 94.195 379 21 1 3684 4062 629468072 629467695 1.480000e-160 577.0
6 TraesCS4A01G139500 chr4B 82.414 580 42 22 1 546 10621674 10622227 9.360000e-123 451.0
7 TraesCS4A01G139500 chr4B 82.414 580 42 19 1 546 565112241 565111688 9.360000e-123 451.0
8 TraesCS4A01G139500 chr4B 90.728 302 18 3 4295 4595 273684852 273684560 1.600000e-105 394.0
9 TraesCS4A01G139500 chr4B 96.020 201 5 1 5923 6123 273684012 273683815 2.130000e-84 324.0
10 TraesCS4A01G139500 chr4B 92.000 225 15 2 4072 4295 273685123 273684901 4.610000e-81 313.0
11 TraesCS4A01G139500 chr4B 94.764 191 9 1 3462 3652 629471650 629471461 4.640000e-76 296.0
12 TraesCS4A01G139500 chr4D 89.213 2503 94 64 1 2387 291736809 291739251 0.000000e+00 2964.0
13 TraesCS4A01G139500 chr4D 96.618 887 29 1 2380 3266 291739575 291740460 0.000000e+00 1471.0
14 TraesCS4A01G139500 chr4D 97.235 651 16 2 4551 5200 291741250 291741899 0.000000e+00 1101.0
15 TraesCS4A01G139500 chr4D 93.274 223 15 0 4295 4517 291741027 291741249 4.580000e-86 329.0
16 TraesCS4A01G139500 chr4D 96.020 201 7 1 5923 6123 291741892 291742091 5.920000e-85 326.0
17 TraesCS4A01G139500 chr4D 96.111 180 6 1 3286 3465 291740587 291740765 6.000000e-75 292.0
18 TraesCS4A01G139500 chr5A 95.687 742 11 11 5199 5925 524327586 524328321 0.000000e+00 1173.0
19 TraesCS4A01G139500 chr7A 96.965 692 8 3 5201 5879 53625381 53626072 0.000000e+00 1149.0
20 TraesCS4A01G139500 chr6B 94.980 737 16 10 5201 5922 442426839 442427569 0.000000e+00 1136.0
21 TraesCS4A01G139500 chr6B 94.267 750 11 14 5200 5923 566539843 566540586 0.000000e+00 1118.0
22 TraesCS4A01G139500 chr6B 94.110 747 13 13 5201 5922 153303975 153303235 0.000000e+00 1107.0
23 TraesCS4A01G139500 chr6B 99.476 382 2 0 3681 4062 416893730 416893349 0.000000e+00 695.0
24 TraesCS4A01G139500 chr6B 96.606 383 11 2 3681 4062 345228685 345228304 8.660000e-178 634.0
25 TraesCS4A01G139500 chr6B 82.414 580 42 19 1 546 160388827 160388274 9.360000e-123 451.0
26 TraesCS4A01G139500 chr6B 100.000 221 0 0 3462 3682 416894011 416893791 5.710000e-110 409.0
27 TraesCS4A01G139500 chr6B 81.750 537 47 22 2 513 387719552 387720062 9.560000e-108 401.0
28 TraesCS4A01G139500 chr6B 91.720 157 5 2 3526 3682 345231748 345231600 1.730000e-50 211.0
29 TraesCS4A01G139500 chr6A 94.400 750 15 11 5200 5922 75914536 75913787 0.000000e+00 1127.0
30 TraesCS4A01G139500 chr3A 94.393 749 11 13 5200 5923 156305596 156304854 0.000000e+00 1122.0
31 TraesCS4A01G139500 chr3A 99.298 570 2 2 3462 4029 639497671 639497102 0.000000e+00 1029.0
32 TraesCS4A01G139500 chr3A 92.054 516 18 9 3461 3954 552628627 552628113 0.000000e+00 704.0
33 TraesCS4A01G139500 chr3A 96.748 123 3 1 3951 4073 552627763 552627642 2.890000e-48 204.0
34 TraesCS4A01G139500 chr2B 93.578 763 16 15 5192 5928 316101333 316100578 0.000000e+00 1107.0
35 TraesCS4A01G139500 chr2B 92.328 756 21 18 5201 5924 23311543 23312293 0.000000e+00 1040.0
36 TraesCS4A01G139500 chr2B 81.207 580 49 18 1 546 29005561 29006114 4.420000e-111 412.0
37 TraesCS4A01G139500 chr2B 100.000 28 0 0 4205 4232 689240091 689240118 1.100000e-02 52.8
38 TraesCS4A01G139500 chr2B 100.000 28 0 0 4205 4232 689257008 689257035 1.100000e-02 52.8
39 TraesCS4A01G139500 chr7B 92.732 743 26 18 5200 5925 559546222 559545491 0.000000e+00 1048.0
40 TraesCS4A01G139500 chr7B 83.240 537 40 19 1 513 718400354 718399844 1.210000e-121 448.0
41 TraesCS4A01G139500 chr7B 81.724 580 46 20 1 546 709129231 709128678 4.390000e-116 429.0
42 TraesCS4A01G139500 chr1B 91.754 764 22 20 5200 5922 143630477 143631240 0.000000e+00 1024.0
43 TraesCS4A01G139500 chr1B 96.931 391 4 1 3681 4071 70323491 70323109 0.000000e+00 649.0
44 TraesCS4A01G139500 chr1B 100.000 221 0 0 3462 3682 70324294 70324074 5.710000e-110 409.0
45 TraesCS4A01G139500 chr5B 99.476 382 2 0 3681 4062 240564366 240564747 0.000000e+00 695.0
46 TraesCS4A01G139500 chr5B 99.524 210 0 1 3473 3682 240561002 240561210 1.250000e-101 381.0
47 TraesCS4A01G139500 chr5B 100.000 29 0 0 4199 4227 680849225 680849253 3.000000e-03 54.7
48 TraesCS4A01G139500 chr5D 87.692 390 38 7 3684 4072 496997983 496997603 4.350000e-121 446.0
49 TraesCS4A01G139500 chr5D 93.220 118 6 2 3460 3576 495962184 495962068 8.160000e-39 172.0
50 TraesCS4A01G139500 chr3B 81.928 581 44 26 1 546 16180161 16180715 9.430000e-118 435.0
51 TraesCS4A01G139500 chr3B 93.162 117 6 1 3461 3577 84606017 84605903 2.930000e-38 171.0
52 TraesCS4A01G139500 chr7D 88.285 239 12 7 5698 5923 106371742 106371977 7.820000e-69 272.0
53 TraesCS4A01G139500 chr7D 79.585 289 40 10 3791 4075 251366379 251366652 8.100000e-44 189.0
54 TraesCS4A01G139500 chr6D 100.000 28 0 0 4205 4232 30060818 30060791 1.100000e-02 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G139500 chr4A 210994154 211000276 6122 True 11308.0 11308 100.000000 1 6123 1 chr4A.!!$R1 6122
1 TraesCS4A01G139500 chr4B 273683815 273688586 4771 True 1283.0 4434 93.128200 1 6123 5 chr4B.!!$R3 6122
2 TraesCS4A01G139500 chr4B 237054310 237055051 741 True 1136.0 1136 94.786000 5201 5923 1 chr4B.!!$R1 722
3 TraesCS4A01G139500 chr4B 10621674 10622227 553 False 451.0 451 82.414000 1 546 1 chr4B.!!$F1 545
4 TraesCS4A01G139500 chr4B 565111688 565112241 553 True 451.0 451 82.414000 1 546 1 chr4B.!!$R2 545
5 TraesCS4A01G139500 chr4B 629467695 629471650 3955 True 436.5 577 94.479500 3462 4062 2 chr4B.!!$R4 600
6 TraesCS4A01G139500 chr4D 291736809 291742091 5282 False 1080.5 2964 94.745167 1 6123 6 chr4D.!!$F1 6122
7 TraesCS4A01G139500 chr5A 524327586 524328321 735 False 1173.0 1173 95.687000 5199 5925 1 chr5A.!!$F1 726
8 TraesCS4A01G139500 chr7A 53625381 53626072 691 False 1149.0 1149 96.965000 5201 5879 1 chr7A.!!$F1 678
9 TraesCS4A01G139500 chr6B 442426839 442427569 730 False 1136.0 1136 94.980000 5201 5922 1 chr6B.!!$F2 721
10 TraesCS4A01G139500 chr6B 566539843 566540586 743 False 1118.0 1118 94.267000 5200 5923 1 chr6B.!!$F3 723
11 TraesCS4A01G139500 chr6B 153303235 153303975 740 True 1107.0 1107 94.110000 5201 5922 1 chr6B.!!$R1 721
12 TraesCS4A01G139500 chr6B 416893349 416894011 662 True 552.0 695 99.738000 3462 4062 2 chr6B.!!$R4 600
13 TraesCS4A01G139500 chr6B 160388274 160388827 553 True 451.0 451 82.414000 1 546 1 chr6B.!!$R2 545
14 TraesCS4A01G139500 chr6B 345228304 345231748 3444 True 422.5 634 94.163000 3526 4062 2 chr6B.!!$R3 536
15 TraesCS4A01G139500 chr6B 387719552 387720062 510 False 401.0 401 81.750000 2 513 1 chr6B.!!$F1 511
16 TraesCS4A01G139500 chr6A 75913787 75914536 749 True 1127.0 1127 94.400000 5200 5922 1 chr6A.!!$R1 722
17 TraesCS4A01G139500 chr3A 156304854 156305596 742 True 1122.0 1122 94.393000 5200 5923 1 chr3A.!!$R1 723
18 TraesCS4A01G139500 chr3A 639497102 639497671 569 True 1029.0 1029 99.298000 3462 4029 1 chr3A.!!$R2 567
19 TraesCS4A01G139500 chr3A 552627642 552628627 985 True 454.0 704 94.401000 3461 4073 2 chr3A.!!$R3 612
20 TraesCS4A01G139500 chr2B 316100578 316101333 755 True 1107.0 1107 93.578000 5192 5928 1 chr2B.!!$R1 736
21 TraesCS4A01G139500 chr2B 23311543 23312293 750 False 1040.0 1040 92.328000 5201 5924 1 chr2B.!!$F1 723
22 TraesCS4A01G139500 chr2B 29005561 29006114 553 False 412.0 412 81.207000 1 546 1 chr2B.!!$F2 545
23 TraesCS4A01G139500 chr7B 559545491 559546222 731 True 1048.0 1048 92.732000 5200 5925 1 chr7B.!!$R1 725
24 TraesCS4A01G139500 chr7B 718399844 718400354 510 True 448.0 448 83.240000 1 513 1 chr7B.!!$R3 512
25 TraesCS4A01G139500 chr7B 709128678 709129231 553 True 429.0 429 81.724000 1 546 1 chr7B.!!$R2 545
26 TraesCS4A01G139500 chr1B 143630477 143631240 763 False 1024.0 1024 91.754000 5200 5922 1 chr1B.!!$F1 722
27 TraesCS4A01G139500 chr1B 70323109 70324294 1185 True 529.0 649 98.465500 3462 4071 2 chr1B.!!$R1 609
28 TraesCS4A01G139500 chr5B 240561002 240564747 3745 False 538.0 695 99.500000 3473 4062 2 chr5B.!!$F2 589
29 TraesCS4A01G139500 chr3B 16180161 16180715 554 False 435.0 435 81.928000 1 546 1 chr3B.!!$F1 545

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
124 126 0.304705 GATTAAGCACGCATCCACCG 59.695 55.000 0.00 0.0 0.00 4.94 F
125 127 0.392461 ATTAAGCACGCATCCACCGT 60.392 50.000 0.00 0.0 39.91 4.83 F
1417 1559 0.388520 CGAGTTCGTCATCCACTGCA 60.389 55.000 0.00 0.0 34.11 4.41 F
2538 3030 0.032813 CCCATGACCCATGAGGCTTT 60.033 55.000 8.38 0.0 43.81 3.51 F
2738 3230 0.962356 CTGCACCATCACCAGTTCCC 60.962 60.000 0.00 0.0 0.00 3.97 F
4126 8458 1.007964 TGCACATTGGTTTTCGCGG 60.008 52.632 6.13 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1417 1559 0.908910 TGGGAACATGTACCGCTGAT 59.091 50.000 13.12 0.00 33.40 2.90 R
1441 1583 1.075600 GAGGGAGACAGGGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30 R
2924 3420 1.673920 GACCTCACAAAAGCGGTCAAA 59.326 47.619 0.00 0.00 44.11 2.69 R
3923 7900 1.686110 CTTAGGCGTCCTGGAGGGT 60.686 63.158 17.33 0.00 34.61 4.34 R
4322 8706 3.154827 ACATGTGGTCCCGAAAGATTT 57.845 42.857 0.00 0.00 0.00 2.17 R
5879 10364 0.651551 AGTCGCGACTACTCATCGAC 59.348 55.000 38.67 9.13 46.72 4.20 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
124 126 0.304705 GATTAAGCACGCATCCACCG 59.695 55.000 0.00 0.00 0.00 4.94
125 127 0.392461 ATTAAGCACGCATCCACCGT 60.392 50.000 0.00 0.00 39.91 4.83
139 141 1.470632 CCACCGTTGCAAAACACACAT 60.471 47.619 0.00 0.00 0.00 3.21
140 142 2.223595 CCACCGTTGCAAAACACACATA 60.224 45.455 0.00 0.00 0.00 2.29
141 143 3.042189 CACCGTTGCAAAACACACATAG 58.958 45.455 0.00 0.00 0.00 2.23
170 172 3.758755 AAGAGAGTGTGCATGAGACAA 57.241 42.857 0.00 0.00 0.00 3.18
271 292 3.281727 TGGCAGAAGAAACAGTTGAGT 57.718 42.857 0.00 0.00 0.00 3.41
324 345 1.833630 TGCTAGAGGACATGGGAAGTG 59.166 52.381 0.00 0.00 0.00 3.16
336 375 1.004918 GGAAGTGGGTCGTGTCCAG 60.005 63.158 0.00 0.00 34.56 3.86
346 385 1.476891 GTCGTGTCCAGGAATCTAGCA 59.523 52.381 0.00 0.00 0.00 3.49
368 413 7.246311 AGCAACATCAACAGAAATTCTTATCG 58.754 34.615 0.00 0.00 0.00 2.92
379 424 7.881232 ACAGAAATTCTTATCGACCCTAACAAA 59.119 33.333 0.00 0.00 0.00 2.83
380 425 8.175716 CAGAAATTCTTATCGACCCTAACAAAC 58.824 37.037 0.00 0.00 0.00 2.93
381 426 7.881232 AGAAATTCTTATCGACCCTAACAAACA 59.119 33.333 0.00 0.00 0.00 2.83
382 427 7.611213 AATTCTTATCGACCCTAACAAACAG 57.389 36.000 0.00 0.00 0.00 3.16
410 455 6.238759 GGCAGGAATCGATTGCTACTTAATTT 60.239 38.462 28.64 4.28 36.24 1.82
411 456 7.041372 GGCAGGAATCGATTGCTACTTAATTTA 60.041 37.037 28.64 0.00 36.24 1.40
468 515 1.722011 CGCTTAACCACGAATCCAGT 58.278 50.000 0.00 0.00 0.00 4.00
521 579 3.988517 GACGAAACTATGCATACTAGGCC 59.011 47.826 1.16 0.00 0.00 5.19
565 623 5.667888 GCACTACGGCGCTAACAATAATATG 60.668 44.000 6.90 0.00 0.00 1.78
593 656 3.245519 GGTGACAAGAAGAAGACGTGAAC 59.754 47.826 0.00 0.00 0.00 3.18
616 679 1.541233 GCAGGATGGGAACGAATCGAT 60.541 52.381 10.55 0.00 35.86 3.59
622 685 3.046968 TGGGAACGAATCGATGAACAA 57.953 42.857 10.55 0.00 0.00 2.83
627 690 1.394917 ACGAATCGATGAACAAGCAGC 59.605 47.619 10.55 0.00 0.00 5.25
632 695 0.455633 CGATGAACAAGCAGCAAGGC 60.456 55.000 0.00 0.00 0.00 4.35
661 724 4.820897 ACAAGATCGAGCAACAGATTACA 58.179 39.130 2.38 0.00 0.00 2.41
671 734 3.691609 GCAACAGATTACAGAAAGGAGGG 59.308 47.826 0.00 0.00 0.00 4.30
672 735 4.807643 GCAACAGATTACAGAAAGGAGGGT 60.808 45.833 0.00 0.00 0.00 4.34
673 736 4.559862 ACAGATTACAGAAAGGAGGGTG 57.440 45.455 0.00 0.00 0.00 4.61
674 737 3.264450 ACAGATTACAGAAAGGAGGGTGG 59.736 47.826 0.00 0.00 0.00 4.61
675 738 2.239907 AGATTACAGAAAGGAGGGTGGC 59.760 50.000 0.00 0.00 0.00 5.01
676 739 1.742308 TTACAGAAAGGAGGGTGGCT 58.258 50.000 0.00 0.00 0.00 4.75
677 740 0.984230 TACAGAAAGGAGGGTGGCTG 59.016 55.000 0.00 0.00 0.00 4.85
678 741 1.001641 CAGAAAGGAGGGTGGCTGG 60.002 63.158 0.00 0.00 0.00 4.85
679 742 2.234296 AGAAAGGAGGGTGGCTGGG 61.234 63.158 0.00 0.00 0.00 4.45
680 743 3.268032 AAAGGAGGGTGGCTGGGG 61.268 66.667 0.00 0.00 0.00 4.96
681 744 3.829311 AAAGGAGGGTGGCTGGGGA 62.829 63.158 0.00 0.00 0.00 4.81
682 745 4.748798 AGGAGGGTGGCTGGGGAG 62.749 72.222 0.00 0.00 0.00 4.30
723 787 4.701765 CACCTTGATCTCTTGGATTCGAT 58.298 43.478 0.00 0.00 34.33 3.59
786 852 2.839098 CAAGGGTGTGTGAGGCCT 59.161 61.111 3.86 3.86 0.00 5.19
787 853 1.151450 CAAGGGTGTGTGAGGCCTT 59.849 57.895 6.77 0.00 0.00 4.35
790 856 1.136329 AGGGTGTGTGAGGCCTTGAT 61.136 55.000 6.77 0.00 0.00 2.57
922 1023 3.883744 CTCCAAAGCCCACGTCGCT 62.884 63.158 0.74 0.74 38.53 4.93
931 1032 2.657237 CACGTCGCTCCCTCCTTT 59.343 61.111 0.00 0.00 0.00 3.11
957 1063 4.150454 CCTCCCGCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
958 1064 2.520741 CTCCCGCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
961 1067 2.430610 CCCGCTCCTCCTCCTCTTG 61.431 68.421 0.00 0.00 0.00 3.02
966 1072 0.689412 CTCCTCCTCCTCTTGTCCCC 60.689 65.000 0.00 0.00 0.00 4.81
990 1096 2.907917 CCGAAACCCCCAAACGCA 60.908 61.111 0.00 0.00 0.00 5.24
991 1097 2.333581 CGAAACCCCCAAACGCAC 59.666 61.111 0.00 0.00 0.00 5.34
992 1098 2.333581 GAAACCCCCAAACGCACG 59.666 61.111 0.00 0.00 0.00 5.34
993 1099 3.202216 GAAACCCCCAAACGCACGG 62.202 63.158 0.00 0.00 0.00 4.94
1131 1239 4.767255 CTCCTCGCAGCCCACACC 62.767 72.222 0.00 0.00 0.00 4.16
1164 1283 1.011968 CGGCGGTTCTCACGATTTCA 61.012 55.000 0.00 0.00 0.00 2.69
1166 1285 1.737793 GGCGGTTCTCACGATTTCAAT 59.262 47.619 0.00 0.00 0.00 2.57
1167 1286 2.223044 GGCGGTTCTCACGATTTCAATC 60.223 50.000 0.00 0.00 0.00 2.67
1168 1287 2.673368 GCGGTTCTCACGATTTCAATCT 59.327 45.455 0.00 0.00 33.24 2.40
1371 1513 2.048127 GACCGCCTCAACGCTTCT 60.048 61.111 0.00 0.00 0.00 2.85
1417 1559 0.388520 CGAGTTCGTCATCCACTGCA 60.389 55.000 0.00 0.00 34.11 4.41
1441 1583 1.076995 GGTACATGTTCCCAGCCCC 60.077 63.158 10.29 0.00 0.00 5.80
1452 1594 4.748798 CAGCCCCTCCCTCCCTGT 62.749 72.222 0.00 0.00 0.00 4.00
1453 1595 4.423209 AGCCCCTCCCTCCCTGTC 62.423 72.222 0.00 0.00 0.00 3.51
1454 1596 4.423209 GCCCCTCCCTCCCTGTCT 62.423 72.222 0.00 0.00 0.00 3.41
1558 1710 1.672737 CGCCAATTTTGCTCTTTCCCC 60.673 52.381 0.00 0.00 0.00 4.81
1733 1885 2.510238 GATCTCACGCGCCTGCTT 60.510 61.111 5.73 0.00 39.65 3.91
1767 1919 4.079850 CGCTGCAGGAGCTCACCT 62.080 66.667 17.12 1.26 46.64 4.00
1779 1931 0.817654 GCTCACCTTTATTGCCACCC 59.182 55.000 0.00 0.00 0.00 4.61
1813 1965 3.643978 GCCTGGCGTCGATGATGC 61.644 66.667 9.31 2.41 43.13 3.91
2170 2328 8.971073 TCTCTCCTTTGAAATGGGAAATTAATC 58.029 33.333 0.00 0.00 0.00 1.75
2205 2363 5.475564 TGCCTTTAACCAAGTCAAGGAATAC 59.524 40.000 8.99 0.00 38.52 1.89
2236 2394 8.391075 TGTAAAAGTAGAAATGGTTTCAGGAG 57.609 34.615 5.36 0.00 42.10 3.69
2274 2432 2.229302 GTCCTCACTTGTAGTCGAGCTT 59.771 50.000 0.00 0.00 0.00 3.74
2517 3009 4.846779 TTGGTTATGTTTTCTGACTGGC 57.153 40.909 0.00 0.00 0.00 4.85
2538 3030 0.032813 CCCATGACCCATGAGGCTTT 60.033 55.000 8.38 0.00 43.81 3.51
2539 3031 1.215173 CCCATGACCCATGAGGCTTTA 59.785 52.381 8.38 0.00 43.81 1.85
2591 3083 5.762825 CAAGATTTGGAATCGATGATGGT 57.237 39.130 0.00 0.00 0.00 3.55
2663 3155 4.216042 TCACAACTAAATGATGGCAGTGTG 59.784 41.667 0.00 0.00 0.00 3.82
2738 3230 0.962356 CTGCACCATCACCAGTTCCC 60.962 60.000 0.00 0.00 0.00 3.97
2835 3327 3.733443 CCATCGATATGGTCACACTCA 57.267 47.619 0.00 0.00 46.68 3.41
2868 3360 3.580895 TCCTACACTGAACTATGCACCAA 59.419 43.478 0.00 0.00 0.00 3.67
2884 3380 5.932455 TGCACCAATATGATCTGATGAGAA 58.068 37.500 0.00 0.00 0.00 2.87
2885 3381 5.761726 TGCACCAATATGATCTGATGAGAAC 59.238 40.000 0.00 0.00 0.00 3.01
2909 3405 3.111038 GGCCAAAGCGCCTGTATC 58.889 61.111 2.29 0.00 46.10 2.24
2924 3420 4.581824 GCCTGTATCAAACATCATGACCAT 59.418 41.667 0.00 0.00 37.50 3.55
2931 3427 4.082841 TCAAACATCATGACCATTTGACCG 60.083 41.667 19.47 3.34 35.05 4.79
3031 3527 8.485976 AGAAAGTTCCTTTGATCTCTTAATCG 57.514 34.615 0.00 0.00 33.49 3.34
3141 3637 1.098050 GCAGAAAATCGTGCCCAGAT 58.902 50.000 0.00 0.00 33.29 2.90
3166 3662 4.499183 AGAGAAATGGAAGAGCTAACGTG 58.501 43.478 0.00 0.00 0.00 4.49
3389 3992 5.818136 TCAAATTAGCTAATCAGGCACAC 57.182 39.130 19.11 0.00 0.00 3.82
3407 4010 4.757149 GCACACTAACAGAAGTCATTTCCT 59.243 41.667 0.00 0.00 36.40 3.36
3420 4023 5.337788 AGTCATTTCCTTGTCCTCTCTAGT 58.662 41.667 0.00 0.00 0.00 2.57
3421 4024 6.494952 AGTCATTTCCTTGTCCTCTCTAGTA 58.505 40.000 0.00 0.00 0.00 1.82
3424 4027 7.923878 GTCATTTCCTTGTCCTCTCTAGTAATC 59.076 40.741 0.00 0.00 0.00 1.75
4073 8404 2.542595 CGACGCTTTACAAACAGAGGTT 59.457 45.455 0.00 0.00 39.43 3.50
4074 8405 3.603857 CGACGCTTTACAAACAGAGGTTG 60.604 47.826 0.00 0.00 37.30 3.77
4075 8406 2.616842 ACGCTTTACAAACAGAGGTTGG 59.383 45.455 0.00 0.00 37.30 3.77
4076 8407 2.031157 CGCTTTACAAACAGAGGTTGGG 60.031 50.000 0.00 0.00 37.30 4.12
4077 8408 3.219281 GCTTTACAAACAGAGGTTGGGA 58.781 45.455 0.00 0.00 37.30 4.37
4078 8409 3.826729 GCTTTACAAACAGAGGTTGGGAT 59.173 43.478 0.00 0.00 37.30 3.85
4126 8458 1.007964 TGCACATTGGTTTTCGCGG 60.008 52.632 6.13 0.00 0.00 6.46
4133 8465 1.600023 TTGGTTTTCGCGGAAGTCAT 58.400 45.000 6.13 0.00 0.00 3.06
4257 8592 4.804108 TGATTTGGCGTTTTAGATGTTGG 58.196 39.130 0.00 0.00 0.00 3.77
4264 8599 6.383415 TGGCGTTTTAGATGTTGGTATTTTC 58.617 36.000 0.00 0.00 0.00 2.29
4271 8606 9.681062 TTTTAGATGTTGGTATTTTCCCTCTAG 57.319 33.333 0.00 0.00 0.00 2.43
4314 8698 1.435256 ACCACTATACCAGCATCCCC 58.565 55.000 0.00 0.00 0.00 4.81
4315 8699 1.345009 ACCACTATACCAGCATCCCCA 60.345 52.381 0.00 0.00 0.00 4.96
4322 8706 0.409092 ACCAGCATCCCCAAACATGA 59.591 50.000 0.00 0.00 0.00 3.07
4372 8756 0.588252 CACAGACAAACCCTCGCTTG 59.412 55.000 0.00 0.00 0.00 4.01
4390 8774 4.612943 GCTTGACTAACCTATCTTCCTCG 58.387 47.826 0.00 0.00 0.00 4.63
4421 8805 3.132467 GGGTATCTACTCCGTTTCAGCTT 59.868 47.826 0.00 0.00 0.00 3.74
4434 8818 4.911610 CGTTTCAGCTTGTTCAAACCATAG 59.088 41.667 0.00 0.00 0.00 2.23
4473 8857 6.431198 TTTGAACTTGTGTTAGGAGTGAAC 57.569 37.500 0.00 0.00 36.39 3.18
4540 8924 6.785191 ACGCTGATAAATAGTGTTCCAATTG 58.215 36.000 0.00 0.00 35.50 2.32
4545 8929 9.177608 CTGATAAATAGTGTTCCAATTGGAGAA 57.822 33.333 25.69 15.89 46.36 2.87
4583 8967 5.677319 ATAAGATGTCGAGTCCAAAAGGA 57.323 39.130 0.00 0.00 0.00 3.36
4584 8968 4.351874 AAGATGTCGAGTCCAAAAGGAA 57.648 40.909 0.00 0.00 0.00 3.36
4585 8969 4.351874 AGATGTCGAGTCCAAAAGGAAA 57.648 40.909 0.00 0.00 0.00 3.13
4586 8970 4.911390 AGATGTCGAGTCCAAAAGGAAAT 58.089 39.130 0.00 0.00 0.00 2.17
4587 8971 4.938226 AGATGTCGAGTCCAAAAGGAAATC 59.062 41.667 0.00 0.00 0.00 2.17
4588 8972 4.079980 TGTCGAGTCCAAAAGGAAATCA 57.920 40.909 0.00 0.00 0.00 2.57
4589 8973 4.651778 TGTCGAGTCCAAAAGGAAATCAT 58.348 39.130 0.00 0.00 0.00 2.45
4590 8974 4.695455 TGTCGAGTCCAAAAGGAAATCATC 59.305 41.667 0.00 0.00 0.00 2.92
4591 8975 4.938226 GTCGAGTCCAAAAGGAAATCATCT 59.062 41.667 0.00 0.00 0.00 2.90
4592 8976 5.412904 GTCGAGTCCAAAAGGAAATCATCTT 59.587 40.000 0.00 0.00 0.00 2.40
4593 8977 5.412594 TCGAGTCCAAAAGGAAATCATCTTG 59.587 40.000 0.00 0.00 0.00 3.02
4594 8978 5.182001 CGAGTCCAAAAGGAAATCATCTTGT 59.818 40.000 0.00 0.00 0.00 3.16
4595 8979 6.371548 CGAGTCCAAAAGGAAATCATCTTGTA 59.628 38.462 0.00 0.00 0.00 2.41
4596 8980 7.413438 CGAGTCCAAAAGGAAATCATCTTGTAG 60.413 40.741 0.00 0.00 0.00 2.74
4597 8981 7.461749 AGTCCAAAAGGAAATCATCTTGTAGA 58.538 34.615 0.00 0.00 0.00 2.59
4598 8982 7.609532 AGTCCAAAAGGAAATCATCTTGTAGAG 59.390 37.037 0.00 0.00 0.00 2.43
4599 8983 7.607991 GTCCAAAAGGAAATCATCTTGTAGAGA 59.392 37.037 0.00 0.00 39.13 3.10
4600 8984 7.607991 TCCAAAAGGAAATCATCTTGTAGAGAC 59.392 37.037 0.00 0.00 37.17 3.36
4601 8985 7.609532 CCAAAAGGAAATCATCTTGTAGAGACT 59.390 37.037 0.00 0.00 37.17 3.24
4602 8986 8.663911 CAAAAGGAAATCATCTTGTAGAGACTC 58.336 37.037 0.00 0.00 37.17 3.36
4603 8987 7.487822 AAGGAAATCATCTTGTAGAGACTCA 57.512 36.000 5.02 0.00 37.17 3.41
4604 8988 7.111247 AGGAAATCATCTTGTAGAGACTCAG 57.889 40.000 5.02 0.00 37.17 3.35
4605 8989 6.667414 AGGAAATCATCTTGTAGAGACTCAGT 59.333 38.462 5.02 0.00 37.17 3.41
4606 8990 7.836685 AGGAAATCATCTTGTAGAGACTCAGTA 59.163 37.037 5.02 0.00 37.17 2.74
4607 8991 8.134895 GGAAATCATCTTGTAGAGACTCAGTAG 58.865 40.741 5.02 0.00 37.17 2.57
4608 8992 8.815565 AAATCATCTTGTAGAGACTCAGTAGA 57.184 34.615 5.02 2.54 37.17 2.59
4610 8994 7.189079 TCATCTTGTAGAGACTCAGTAGAGA 57.811 40.000 5.02 2.11 44.99 3.10
4611 8995 7.625469 TCATCTTGTAGAGACTCAGTAGAGAA 58.375 38.462 5.02 0.00 44.99 2.87
4612 8996 8.271458 TCATCTTGTAGAGACTCAGTAGAGAAT 58.729 37.037 5.02 0.00 44.99 2.40
4613 8997 7.857734 TCTTGTAGAGACTCAGTAGAGAATG 57.142 40.000 5.02 0.00 44.98 2.67
4614 8998 7.625469 TCTTGTAGAGACTCAGTAGAGAATGA 58.375 38.462 5.02 0.00 44.98 2.57
4615 8999 8.271458 TCTTGTAGAGACTCAGTAGAGAATGAT 58.729 37.037 5.02 0.00 44.98 2.45
4616 9000 8.815565 TTGTAGAGACTCAGTAGAGAATGATT 57.184 34.615 5.02 0.00 44.98 2.57
4617 9001 9.907229 TTGTAGAGACTCAGTAGAGAATGATTA 57.093 33.333 5.02 0.00 44.98 1.75
4618 9002 9.332502 TGTAGAGACTCAGTAGAGAATGATTAC 57.667 37.037 5.02 0.00 44.98 1.89
4619 9003 9.555727 GTAGAGACTCAGTAGAGAATGATTACT 57.444 37.037 5.02 0.00 44.98 2.24
4620 9004 8.450578 AGAGACTCAGTAGAGAATGATTACTG 57.549 38.462 5.02 4.87 44.98 2.74
4621 9005 8.271458 AGAGACTCAGTAGAGAATGATTACTGA 58.729 37.037 5.02 11.68 46.54 3.41
4622 9006 8.220755 AGACTCAGTAGAGAATGATTACTGAC 57.779 38.462 8.94 2.68 44.89 3.51
4623 9007 7.011950 AGACTCAGTAGAGAATGATTACTGACG 59.988 40.741 8.94 8.32 44.89 4.35
4624 9008 6.824196 ACTCAGTAGAGAATGATTACTGACGA 59.176 38.462 8.94 0.00 44.89 4.20
4625 9009 7.337184 ACTCAGTAGAGAATGATTACTGACGAA 59.663 37.037 8.94 0.00 44.89 3.85
4626 9010 7.698628 TCAGTAGAGAATGATTACTGACGAAG 58.301 38.462 8.94 0.00 44.89 3.79
4627 9011 6.416455 CAGTAGAGAATGATTACTGACGAAGC 59.584 42.308 5.22 0.00 44.36 3.86
4628 9012 5.330455 AGAGAATGATTACTGACGAAGCA 57.670 39.130 0.00 0.00 0.00 3.91
4629 9013 5.724328 AGAGAATGATTACTGACGAAGCAA 58.276 37.500 0.00 0.00 0.00 3.91
4630 9014 6.344500 AGAGAATGATTACTGACGAAGCAAT 58.656 36.000 0.00 0.00 0.00 3.56
4631 9015 6.478344 AGAGAATGATTACTGACGAAGCAATC 59.522 38.462 0.00 0.00 38.63 2.67
4647 9080 7.120579 ACGAAGCAATCAAATACATCTGGTTAA 59.879 33.333 0.00 0.00 0.00 2.01
4660 9093 7.100458 ACATCTGGTTAATGCAATTAGTTCC 57.900 36.000 0.00 0.00 40.40 3.62
4755 9188 8.522003 TGTCAACATATTTGATGTTAATGCAGT 58.478 29.630 2.78 0.00 39.94 4.40
4834 9267 6.567602 ATTTCTGCTATCCTACTTCTGGTT 57.432 37.500 0.00 0.00 0.00 3.67
4913 9346 2.093394 GGAAGAGCCTCCTGGTTAACTC 60.093 54.545 5.42 0.00 35.27 3.01
4918 9351 1.135333 GCCTCCTGGTTAACTCTCTCG 59.865 57.143 5.42 0.00 35.27 4.04
4921 9354 0.179134 CCTGGTTAACTCTCTCGGCG 60.179 60.000 0.00 0.00 0.00 6.46
4934 9368 0.389391 CTCGGCGACACCCATAGAAT 59.611 55.000 4.99 0.00 33.26 2.40
4990 9425 3.195396 TCAGCTGACTGCCTTTTTGTTTT 59.805 39.130 13.74 0.00 44.10 2.43
5176 9611 0.983467 TCCAGCCAACTGCATAGTGA 59.017 50.000 0.00 0.00 43.02 3.41
5192 9627 8.599055 TGCATAGTGAATGAGCTAGAAATTAG 57.401 34.615 0.00 0.00 37.86 1.73
5193 9628 8.206867 TGCATAGTGAATGAGCTAGAAATTAGT 58.793 33.333 0.00 0.00 37.86 2.24
5194 9629 8.707839 GCATAGTGAATGAGCTAGAAATTAGTC 58.292 37.037 0.00 0.00 37.86 2.59
5195 9630 8.910666 CATAGTGAATGAGCTAGAAATTAGTCG 58.089 37.037 0.00 0.00 37.86 4.18
5196 9631 7.101652 AGTGAATGAGCTAGAAATTAGTCGA 57.898 36.000 0.00 0.00 0.00 4.20
5197 9632 7.548097 AGTGAATGAGCTAGAAATTAGTCGAA 58.452 34.615 0.00 0.00 0.00 3.71
5369 9804 2.520020 AGCAGCAGCAGCAACCAA 60.520 55.556 12.92 0.00 45.49 3.67
5379 9814 1.151810 AGCAACCAAGGGAGGAGGA 60.152 57.895 0.00 0.00 0.00 3.71
5770 10245 1.954362 GAGTGCTCCAGATCCAGCGT 61.954 60.000 4.85 0.00 38.59 5.07
5880 10365 3.637273 GTCGGCCCTGGAACTGGT 61.637 66.667 0.00 0.00 46.69 4.00
5881 10366 3.319198 TCGGCCCTGGAACTGGTC 61.319 66.667 0.00 0.00 46.69 4.02
5882 10367 4.760047 CGGCCCTGGAACTGGTCG 62.760 72.222 0.00 0.00 46.69 4.79
5883 10368 3.319198 GGCCCTGGAACTGGTCGA 61.319 66.667 0.00 0.00 46.69 4.20
5884 10369 2.670148 GGCCCTGGAACTGGTCGAT 61.670 63.158 0.00 0.00 46.69 3.59
5887 10383 0.176680 CCCTGGAACTGGTCGATGAG 59.823 60.000 0.00 0.00 46.69 2.90
6002 10501 2.194201 TTGTTTACCCAGCACCTAGC 57.806 50.000 0.00 0.00 46.19 3.42
6040 10539 7.920151 TGTGGCTATTTCATTGTTGCATAATAC 59.080 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 112 3.049674 CAACGGTGGATGCGTGCT 61.050 61.111 0.00 0.00 0.00 4.40
124 126 4.970003 GTCTGACTATGTGTGTTTTGCAAC 59.030 41.667 0.00 0.00 0.00 4.17
125 127 4.881273 AGTCTGACTATGTGTGTTTTGCAA 59.119 37.500 8.91 0.00 0.00 4.08
139 141 5.070685 TGCACACTCTCTTTAGTCTGACTA 58.929 41.667 13.34 13.34 0.00 2.59
140 142 3.891977 TGCACACTCTCTTTAGTCTGACT 59.108 43.478 15.57 15.57 0.00 3.41
141 143 4.244425 TGCACACTCTCTTTAGTCTGAC 57.756 45.455 0.00 0.00 0.00 3.51
170 172 0.472352 TACGTCCCCAGGAAGTGGTT 60.472 55.000 11.78 0.00 46.37 3.67
260 281 5.414454 TGCTTAGTTTGTGACTCAACTGTTT 59.586 36.000 9.95 0.00 39.86 2.83
261 282 4.941263 TGCTTAGTTTGTGACTCAACTGTT 59.059 37.500 9.95 0.00 39.86 3.16
271 292 4.415881 TCCTCTTGTGCTTAGTTTGTGA 57.584 40.909 0.00 0.00 0.00 3.58
305 326 1.139853 CCACTTCCCATGTCCTCTAGC 59.860 57.143 0.00 0.00 0.00 3.42
306 327 1.765314 CCCACTTCCCATGTCCTCTAG 59.235 57.143 0.00 0.00 0.00 2.43
307 328 1.080498 ACCCACTTCCCATGTCCTCTA 59.920 52.381 0.00 0.00 0.00 2.43
308 329 0.178861 ACCCACTTCCCATGTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
313 334 1.374947 CACGACCCACTTCCCATGT 59.625 57.895 0.00 0.00 0.00 3.21
324 345 1.409427 CTAGATTCCTGGACACGACCC 59.591 57.143 0.00 0.00 0.00 4.46
336 375 6.500684 TTTCTGTTGATGTTGCTAGATTCC 57.499 37.500 0.00 0.00 0.00 3.01
346 385 7.148239 GGGTCGATAAGAATTTCTGTTGATGTT 60.148 37.037 0.00 0.00 0.00 2.71
368 413 2.749621 CTGCCATCTGTTTGTTAGGGTC 59.250 50.000 0.00 0.00 0.00 4.46
379 424 2.569059 CAATCGATTCCTGCCATCTGT 58.431 47.619 7.92 0.00 0.00 3.41
380 425 1.266175 GCAATCGATTCCTGCCATCTG 59.734 52.381 7.92 0.00 0.00 2.90
381 426 1.142465 AGCAATCGATTCCTGCCATCT 59.858 47.619 15.23 0.00 36.73 2.90
382 427 1.602311 AGCAATCGATTCCTGCCATC 58.398 50.000 15.23 0.00 36.73 3.51
414 459 8.909923 TGTCTCAGATCCTGTTATTATTTCGTA 58.090 33.333 0.00 0.00 32.61 3.43
415 460 7.707035 GTGTCTCAGATCCTGTTATTATTTCGT 59.293 37.037 0.00 0.00 32.61 3.85
416 461 7.706607 TGTGTCTCAGATCCTGTTATTATTTCG 59.293 37.037 0.00 0.00 32.61 3.46
417 462 8.948631 TGTGTCTCAGATCCTGTTATTATTTC 57.051 34.615 0.00 0.00 32.61 2.17
521 579 2.809665 GCTTGGTCAGGATCTATGGCTG 60.810 54.545 0.00 0.00 0.00 4.85
565 623 3.002759 GTCTTCTTCTTGTCACCAAGTGC 59.997 47.826 2.69 0.00 46.70 4.40
593 656 0.744414 ATTCGTTCCCATCCTGCGTG 60.744 55.000 0.00 0.00 0.00 5.34
616 679 2.554636 CCGCCTTGCTGCTTGTTCA 61.555 57.895 0.00 0.00 0.00 3.18
622 685 1.450312 GTATGTCCGCCTTGCTGCT 60.450 57.895 0.00 0.00 0.00 4.24
627 690 1.860950 CGATCTTGTATGTCCGCCTTG 59.139 52.381 0.00 0.00 0.00 3.61
632 695 2.492019 TGCTCGATCTTGTATGTCCG 57.508 50.000 0.00 0.00 0.00 4.79
661 724 2.234296 CCCAGCCACCCTCCTTTCT 61.234 63.158 0.00 0.00 0.00 2.52
675 738 4.421554 TCTGCCTCCCCTCCCCAG 62.422 72.222 0.00 0.00 0.00 4.45
676 739 4.421554 CTCTGCCTCCCCTCCCCA 62.422 72.222 0.00 0.00 0.00 4.96
677 740 4.095400 TCTCTGCCTCCCCTCCCC 62.095 72.222 0.00 0.00 0.00 4.81
678 741 2.445654 CTCTCTGCCTCCCCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
679 742 2.445654 CCTCTCTGCCTCCCCTCC 60.446 72.222 0.00 0.00 0.00 4.30
680 743 2.445654 CCCTCTCTGCCTCCCCTC 60.446 72.222 0.00 0.00 0.00 4.30
681 744 2.955246 TCCCTCTCTGCCTCCCCT 60.955 66.667 0.00 0.00 0.00 4.79
682 745 2.766229 GTCCCTCTCTGCCTCCCC 60.766 72.222 0.00 0.00 0.00 4.81
683 746 3.151022 CGTCCCTCTCTGCCTCCC 61.151 72.222 0.00 0.00 0.00 4.30
684 747 3.844090 GCGTCCCTCTCTGCCTCC 61.844 72.222 0.00 0.00 0.00 4.30
685 748 3.071206 TGCGTCCCTCTCTGCCTC 61.071 66.667 0.00 0.00 0.00 4.70
686 749 3.386237 GTGCGTCCCTCTCTGCCT 61.386 66.667 0.00 0.00 0.00 4.75
786 852 2.878406 GCCGCTCCTGCTATAAAATCAA 59.122 45.455 0.00 0.00 36.97 2.57
787 853 2.494059 GCCGCTCCTGCTATAAAATCA 58.506 47.619 0.00 0.00 36.97 2.57
790 856 0.544223 TGGCCGCTCCTGCTATAAAA 59.456 50.000 0.00 0.00 36.97 1.52
868 937 3.058160 CACGGCCCAAGGAGCAAG 61.058 66.667 0.00 0.00 0.00 4.01
869 938 4.659172 CCACGGCCCAAGGAGCAA 62.659 66.667 0.00 0.00 0.00 3.91
892 993 1.616994 GCTTTGGAGTATTGGGCTGGT 60.617 52.381 0.00 0.00 0.00 4.00
922 1023 0.402887 GGGAAAACGGAAAGGAGGGA 59.597 55.000 0.00 0.00 0.00 4.20
931 1032 2.926242 AGCGGGAGGGAAAACGGA 60.926 61.111 0.00 0.00 0.00 4.69
961 1067 1.904865 GTTTCGGGGGTTTGGGGAC 60.905 63.158 0.00 0.00 0.00 4.46
966 1072 2.602267 GGGGGTTTCGGGGGTTTG 60.602 66.667 0.00 0.00 0.00 2.93
992 1098 4.437587 ACAGCTCCATGGCCTGCC 62.438 66.667 23.97 0.00 0.00 4.85
993 1099 2.827642 GACAGCTCCATGGCCTGC 60.828 66.667 23.97 19.19 0.00 4.85
1122 1230 2.036256 GAATGGCAGGTGTGGGCT 59.964 61.111 0.00 0.00 0.00 5.19
1131 1239 2.825836 GCCGGTGAGGAATGGCAG 60.826 66.667 1.90 0.00 46.76 4.85
1351 1493 4.719369 AGCGTTGAGGCGGTCGAC 62.719 66.667 7.13 7.13 38.22 4.20
1371 1513 2.851045 GCTTGGGGGTTTGGGAGA 59.149 61.111 0.00 0.00 0.00 3.71
1417 1559 0.908910 TGGGAACATGTACCGCTGAT 59.091 50.000 13.12 0.00 33.40 2.90
1441 1583 1.075600 GAGGGAGACAGGGAGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
1514 1656 3.746889 CAGGGAAAATGCGCGCCA 61.747 61.111 30.77 17.39 0.00 5.69
1558 1710 3.025866 GCTCAGAGCGGCAAATTTG 57.974 52.632 14.03 14.03 0.00 2.32
1646 1798 2.502080 GTCTGCACGTCGGACTCG 60.502 66.667 15.45 0.00 45.52 4.18
1718 1870 2.738521 GAAAGCAGGCGCGTGAGA 60.739 61.111 32.39 0.00 45.49 3.27
1733 1885 1.351017 AGCGAGGACTGGAAATTGGAA 59.649 47.619 0.00 0.00 0.00 3.53
1767 1919 1.257055 GCAGGCTGGGTGGCAATAAA 61.257 55.000 17.64 0.00 44.55 1.40
1779 1931 4.034258 CAACCGTGCAGCAGGCTG 62.034 66.667 16.68 16.68 45.15 4.85
1940 2094 4.336433 CGTAGTCATCTGCAATTCCCAAAT 59.664 41.667 0.00 0.00 0.00 2.32
2139 2297 6.387192 TCCCATTTCAAAGGAGAGATTACA 57.613 37.500 0.00 0.00 0.00 2.41
2145 2303 7.917505 CGATTAATTTCCCATTTCAAAGGAGAG 59.082 37.037 0.00 0.00 0.00 3.20
2170 2328 5.379732 TGGTTAAAGGCAAATAAGTTCCG 57.620 39.130 0.00 0.00 0.00 4.30
2236 2394 5.577164 GTGAGGACACACACATACAGTTATC 59.423 44.000 0.00 0.00 45.32 1.75
2299 2457 5.394115 CCCTTGTGTTGTTTTAGAAAGCAGT 60.394 40.000 0.00 0.00 30.82 4.40
2538 3030 4.701651 CAGGACAGGTCTGCAATTCAAATA 59.298 41.667 0.00 0.00 0.00 1.40
2539 3031 3.508793 CAGGACAGGTCTGCAATTCAAAT 59.491 43.478 0.00 0.00 0.00 2.32
2580 3072 8.511604 AAATTAGAACTTGAACCATCATCGAT 57.488 30.769 0.00 0.00 34.96 3.59
2591 3083 9.706691 AGAGTTACATCGAAATTAGAACTTGAA 57.293 29.630 0.00 0.00 0.00 2.69
2663 3155 2.124942 GTAGGTGGCTGCTGAGGC 60.125 66.667 0.00 0.00 45.19 4.70
2738 3230 6.898041 TCTTGTATGGTTTGAGACATTTTCG 58.102 36.000 0.00 0.00 0.00 3.46
2835 3327 2.025981 TCAGTGTAGGAATGCATGCCTT 60.026 45.455 31.74 15.42 35.73 4.35
2868 3360 6.445475 CGTGTCTGTTCTCATCAGATCATAT 58.555 40.000 0.00 0.00 42.63 1.78
2884 3380 2.972505 CGCTTTGGCCGTGTCTGT 60.973 61.111 0.00 0.00 34.44 3.41
2885 3381 4.389576 GCGCTTTGGCCGTGTCTG 62.390 66.667 0.00 0.00 34.44 3.51
2909 3405 4.168014 CGGTCAAATGGTCATGATGTTTG 58.832 43.478 17.40 17.40 0.00 2.93
2924 3420 1.673920 GACCTCACAAAAGCGGTCAAA 59.326 47.619 0.00 0.00 44.11 2.69
2931 3427 3.565482 TCTGACATTGACCTCACAAAAGC 59.435 43.478 0.00 0.00 33.44 3.51
3031 3527 3.601443 AGATGAACAGGACAGTGCTAC 57.399 47.619 0.00 0.00 0.00 3.58
3141 3637 4.382040 CGTTAGCTCTTCCATTTCTCTCCA 60.382 45.833 0.00 0.00 0.00 3.86
3166 3662 2.082231 AGCACTGATGTGTCATTCAGC 58.918 47.619 13.05 4.58 45.44 4.26
3389 3992 6.234177 AGGACAAGGAAATGACTTCTGTTAG 58.766 40.000 0.00 0.00 34.17 2.34
3407 4010 5.761205 AGCTCAGATTACTAGAGAGGACAA 58.239 41.667 0.00 0.00 0.00 3.18
3424 4027 8.279970 AGCATATCTCAACTATACTAGCTCAG 57.720 38.462 0.00 0.00 0.00 3.35
3923 7900 1.686110 CTTAGGCGTCCTGGAGGGT 60.686 63.158 17.33 0.00 34.61 4.34
4073 8404 3.975312 ACGGTGGGTGTATTATAATCCCA 59.025 43.478 16.05 16.05 44.76 4.37
4074 8405 4.564199 GGACGGTGGGTGTATTATAATCCC 60.564 50.000 12.02 12.02 38.68 3.85
4075 8406 4.564199 GGGACGGTGGGTGTATTATAATCC 60.564 50.000 0.00 0.00 0.00 3.01
4076 8407 4.040706 TGGGACGGTGGGTGTATTATAATC 59.959 45.833 0.00 0.00 0.00 1.75
4077 8408 3.975312 TGGGACGGTGGGTGTATTATAAT 59.025 43.478 2.97 2.97 0.00 1.28
4078 8409 3.382278 TGGGACGGTGGGTGTATTATAA 58.618 45.455 0.00 0.00 0.00 0.98
4091 8422 3.644265 TGTGCACTATATTATGGGACGGT 59.356 43.478 19.41 0.00 0.00 4.83
4126 8458 6.253512 GGTCAAAGTTTGTGAACAATGACTTC 59.746 38.462 19.34 7.79 44.44 3.01
4216 8551 9.459640 CCAAATCAATGTCATTAGATTCATCAC 57.540 33.333 16.69 0.00 30.87 3.06
4232 8567 6.183360 CCAACATCTAAAACGCCAAATCAATG 60.183 38.462 0.00 0.00 0.00 2.82
4257 8592 6.295719 TGACCAAGTCTAGAGGGAAAATAC 57.704 41.667 11.05 0.00 33.15 1.89
4264 8599 4.625607 AACTTTGACCAAGTCTAGAGGG 57.374 45.455 0.00 0.00 45.77 4.30
4271 8606 7.699391 GGTAAACTTGTAAACTTTGACCAAGTC 59.301 37.037 12.60 0.00 45.77 3.01
4314 8698 4.022416 TGGTCCCGAAAGATTTCATGTTTG 60.022 41.667 6.16 0.00 37.01 2.93
4315 8699 4.022329 GTGGTCCCGAAAGATTTCATGTTT 60.022 41.667 6.16 0.00 37.01 2.83
4322 8706 3.154827 ACATGTGGTCCCGAAAGATTT 57.845 42.857 0.00 0.00 0.00 2.17
4372 8756 4.463070 ACTCCGAGGAAGATAGGTTAGTC 58.537 47.826 0.00 0.00 0.00 2.59
4390 8774 3.181468 CGGAGTAGATACCCCAAAACTCC 60.181 52.174 8.87 8.87 46.18 3.85
4412 8796 4.681483 GCTATGGTTTGAACAAGCTGAAAC 59.319 41.667 0.00 0.00 31.84 2.78
4421 8805 7.232534 ACCTTAAAAGATGCTATGGTTTGAACA 59.767 33.333 0.00 0.00 0.00 3.18
4434 8818 9.476202 ACAAGTTCAAATTACCTTAAAAGATGC 57.524 29.630 0.00 0.00 0.00 3.91
4496 8880 7.388224 TCAGCGTATCTCCTACAAATAGAGTAG 59.612 40.741 0.00 0.00 38.89 2.57
4540 8924 9.396022 TCTTATATCAAAAGTCACCATTTCTCC 57.604 33.333 0.00 0.00 0.00 3.71
4545 8929 8.830580 CGACATCTTATATCAAAAGTCACCATT 58.169 33.333 0.00 0.00 0.00 3.16
4583 8967 8.815565 TCTACTGAGTCTCTACAAGATGATTT 57.184 34.615 0.65 0.00 36.11 2.17
4584 8968 8.271458 TCTCTACTGAGTCTCTACAAGATGATT 58.729 37.037 0.65 0.00 40.98 2.57
4585 8969 7.801104 TCTCTACTGAGTCTCTACAAGATGAT 58.199 38.462 0.65 0.00 40.98 2.45
4586 8970 7.189079 TCTCTACTGAGTCTCTACAAGATGA 57.811 40.000 0.65 0.00 40.98 2.92
4587 8971 7.857734 TTCTCTACTGAGTCTCTACAAGATG 57.142 40.000 0.65 0.00 40.98 2.90
4588 8972 8.271458 TCATTCTCTACTGAGTCTCTACAAGAT 58.729 37.037 0.65 0.00 40.98 2.40
4589 8973 7.625469 TCATTCTCTACTGAGTCTCTACAAGA 58.375 38.462 0.65 0.00 40.98 3.02
4590 8974 7.857734 TCATTCTCTACTGAGTCTCTACAAG 57.142 40.000 0.65 0.00 40.98 3.16
4591 8975 8.815565 AATCATTCTCTACTGAGTCTCTACAA 57.184 34.615 0.65 0.00 40.98 2.41
4592 8976 9.332502 GTAATCATTCTCTACTGAGTCTCTACA 57.667 37.037 0.65 0.00 40.98 2.74
4593 8977 9.555727 AGTAATCATTCTCTACTGAGTCTCTAC 57.444 37.037 0.65 0.00 40.98 2.59
4594 8978 9.554395 CAGTAATCATTCTCTACTGAGTCTCTA 57.446 37.037 0.65 0.00 43.40 2.43
4595 8979 8.271458 TCAGTAATCATTCTCTACTGAGTCTCT 58.729 37.037 6.99 0.00 44.05 3.10
4596 8980 8.445275 TCAGTAATCATTCTCTACTGAGTCTC 57.555 38.462 6.99 0.00 44.05 3.36
4601 8985 7.625828 TTCGTCAGTAATCATTCTCTACTGA 57.374 36.000 6.99 6.99 45.75 3.41
4602 8986 6.416455 GCTTCGTCAGTAATCATTCTCTACTG 59.584 42.308 2.71 2.71 42.51 2.74
4603 8987 6.095580 TGCTTCGTCAGTAATCATTCTCTACT 59.904 38.462 0.00 0.00 0.00 2.57
4604 8988 6.266323 TGCTTCGTCAGTAATCATTCTCTAC 58.734 40.000 0.00 0.00 0.00 2.59
4605 8989 6.451064 TGCTTCGTCAGTAATCATTCTCTA 57.549 37.500 0.00 0.00 0.00 2.43
4606 8990 5.330455 TGCTTCGTCAGTAATCATTCTCT 57.670 39.130 0.00 0.00 0.00 3.10
4607 8991 6.595772 ATTGCTTCGTCAGTAATCATTCTC 57.404 37.500 0.00 0.00 32.67 2.87
4614 8998 7.609760 TGTATTTGATTGCTTCGTCAGTAAT 57.390 32.000 1.53 1.53 40.30 1.89
4615 8999 7.549134 AGATGTATTTGATTGCTTCGTCAGTAA 59.451 33.333 0.00 0.00 0.00 2.24
4616 9000 7.010460 CAGATGTATTTGATTGCTTCGTCAGTA 59.990 37.037 0.00 0.00 0.00 2.74
4617 9001 5.877012 AGATGTATTTGATTGCTTCGTCAGT 59.123 36.000 0.00 0.00 0.00 3.41
4618 9002 6.190264 CAGATGTATTTGATTGCTTCGTCAG 58.810 40.000 0.00 0.00 0.00 3.51
4619 9003 5.065090 CCAGATGTATTTGATTGCTTCGTCA 59.935 40.000 0.00 0.00 0.00 4.35
4620 9004 5.065218 ACCAGATGTATTTGATTGCTTCGTC 59.935 40.000 0.00 0.00 0.00 4.20
4621 9005 4.943705 ACCAGATGTATTTGATTGCTTCGT 59.056 37.500 0.00 0.00 0.00 3.85
4622 9006 5.490139 ACCAGATGTATTTGATTGCTTCG 57.510 39.130 0.00 0.00 0.00 3.79
4623 9007 9.241317 CATTAACCAGATGTATTTGATTGCTTC 57.759 33.333 0.00 0.00 0.00 3.86
4624 9008 7.707893 GCATTAACCAGATGTATTTGATTGCTT 59.292 33.333 0.00 0.00 0.00 3.91
4625 9009 7.147863 TGCATTAACCAGATGTATTTGATTGCT 60.148 33.333 0.00 0.00 0.00 3.91
4626 9010 6.979817 TGCATTAACCAGATGTATTTGATTGC 59.020 34.615 0.00 0.00 0.00 3.56
4627 9011 8.929827 TTGCATTAACCAGATGTATTTGATTG 57.070 30.769 0.00 0.00 0.00 2.67
4660 9093 9.838339 ATGATTCTTTTAGTGGAGTTGGTATAG 57.162 33.333 0.00 0.00 0.00 1.31
4913 9346 1.101635 TCTATGGGTGTCGCCGAGAG 61.102 60.000 2.87 2.87 35.90 3.20
4918 9351 2.325583 TGAATTCTATGGGTGTCGCC 57.674 50.000 7.05 0.00 0.00 5.54
4921 9354 5.581126 TGCATTTGAATTCTATGGGTGTC 57.419 39.130 17.26 6.22 0.00 3.67
4979 9413 6.589907 ACAACTTCTGTAGCAAAACAAAAAGG 59.410 34.615 0.00 0.00 36.10 3.11
4990 9425 3.552132 TCAACCACAACTTCTGTAGCA 57.448 42.857 0.00 0.00 36.10 3.49
5176 9611 7.548097 TGACTTCGACTAATTTCTAGCTCATT 58.452 34.615 0.00 0.00 0.00 2.57
5192 9627 4.898488 CGACTCAAAAACATTGACTTCGAC 59.102 41.667 9.98 0.00 33.79 4.20
5193 9628 4.806775 TCGACTCAAAAACATTGACTTCGA 59.193 37.500 12.57 12.57 36.41 3.71
5194 9629 5.078153 TCGACTCAAAAACATTGACTTCG 57.922 39.130 9.53 9.53 33.50 3.79
5195 9630 6.658831 TCATCGACTCAAAAACATTGACTTC 58.341 36.000 0.00 0.00 0.00 3.01
5196 9631 6.260936 ACTCATCGACTCAAAAACATTGACTT 59.739 34.615 0.00 0.00 0.00 3.01
5197 9632 5.760253 ACTCATCGACTCAAAAACATTGACT 59.240 36.000 0.00 0.00 0.00 3.41
5369 9804 1.938596 TGCTCCTCTCCTCCTCCCT 60.939 63.158 0.00 0.00 0.00 4.20
5379 9814 2.888447 GCTGGTGGTGTGCTCCTCT 61.888 63.158 0.00 0.00 0.00 3.69
5879 10364 0.651551 AGTCGCGACTACTCATCGAC 59.348 55.000 38.67 9.13 46.72 4.20
5880 10365 2.125685 CTAGTCGCGACTACTCATCGA 58.874 52.381 37.98 21.69 42.25 3.59
5881 10366 1.859703 ACTAGTCGCGACTACTCATCG 59.140 52.381 37.98 29.34 42.54 3.84
5882 10367 2.097299 CGACTAGTCGCGACTACTCATC 60.097 54.545 37.98 29.07 46.50 2.92
5883 10368 1.859703 CGACTAGTCGCGACTACTCAT 59.140 52.381 37.98 25.23 46.50 2.90
5884 10369 1.275505 CGACTAGTCGCGACTACTCA 58.724 55.000 37.98 24.10 46.50 3.41
6002 10501 5.647658 TGAAATAGCCACACCTGAATACAAG 59.352 40.000 0.00 0.00 0.00 3.16
6040 10539 5.536554 ACAAGTCGCATTAATGTTCTCTG 57.463 39.130 16.61 11.11 0.00 3.35


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

AutoCloner maintained by Alex Coulton.