Multiple sequence alignment - TraesCS6A01G190400

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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 TraesCS6A01G190400 chr6A 100.000 2612 0 0 1 2612 252514094 252516705 0.000000e+00 4824.0
1 TraesCS6A01G190400 chr6A 89.682 1570 143 12 702 2254 252522448 252524015 0.000000e+00 1984.0
2 TraesCS6A01G190400 chr6A 92.424 528 34 3 1 523 252435617 252436143 0.000000e+00 749.0
3 TraesCS6A01G190400 chr6A 76.465 1041 154 68 1476 2460 252345711 252344706 5.060000e-132 481.0
4 TraesCS6A01G190400 chr6A 87.968 374 42 3 703 1076 396908704 396908334 3.090000e-119 438.0
5 TraesCS6A01G190400 chr6A 89.503 181 19 0 524 704 252522191 252522371 2.020000e-56 230.0
6 TraesCS6A01G190400 chr6A 89.167 120 12 1 702 821 39286926 39286808 5.820000e-32 148.0
7 TraesCS6A01G190400 chr6A 84.091 132 16 4 525 652 206268878 206269008 3.530000e-24 122.0
8 TraesCS6A01G190400 chr4A 86.129 930 102 24 1699 2612 200248584 200247666 0.000000e+00 977.0
9 TraesCS6A01G190400 chr4A 84.029 958 121 26 1674 2612 287923078 287924022 0.000000e+00 893.0
10 TraesCS6A01G190400 chr4A 78.947 532 89 20 4 518 392840939 392840414 8.950000e-90 340.0
11 TraesCS6A01G190400 chr4A 79.035 539 77 25 1 524 309770736 309770219 1.160000e-88 337.0
12 TraesCS6A01G190400 chr4A 87.302 126 15 1 702 827 136763930 136763806 2.710000e-30 143.0
13 TraesCS6A01G190400 chr4A 84.058 138 14 6 529 663 386703885 386703753 2.730000e-25 126.0
14 TraesCS6A01G190400 chr4A 85.714 119 9 7 548 663 386727066 386726953 4.570000e-23 119.0
15 TraesCS6A01G190400 chr4A 82.927 123 15 6 540 657 512728948 512728827 3.560000e-19 106.0
16 TraesCS6A01G190400 chr3A 85.592 937 112 19 1683 2612 683303403 683304323 0.000000e+00 961.0
17 TraesCS6A01G190400 chr3A 93.939 528 27 2 1 523 275464212 275464739 0.000000e+00 793.0
18 TraesCS6A01G190400 chr3A 93.762 529 28 3 1 524 275484794 275485322 0.000000e+00 789.0
19 TraesCS6A01G190400 chr3A 81.168 531 78 19 3 523 245745602 245746120 8.700000e-110 407.0
20 TraesCS6A01G190400 chr3A 81.096 529 76 19 6 523 245881592 245882107 4.050000e-108 401.0
21 TraesCS6A01G190400 chr3A 80.718 529 74 17 3 523 220283482 220282974 1.130000e-103 387.0
22 TraesCS6A01G190400 chr3A 79.266 545 75 28 3 523 177775713 177776243 1.920000e-91 346.0
23 TraesCS6A01G190400 chr3A 79.159 547 74 29 3 524 177793069 177793600 2.490000e-90 342.0
24 TraesCS6A01G190400 chr3A 84.858 317 44 4 780 1093 380193240 380192925 1.510000e-82 316.0
25 TraesCS6A01G190400 chr3A 84.227 317 46 4 780 1093 380256360 380256045 3.270000e-79 305.0
26 TraesCS6A01G190400 chr3A 88.415 164 15 4 1401 1561 146485933 146486095 7.380000e-46 195.0
27 TraesCS6A01G190400 chr3A 87.500 104 8 3 521 620 82323879 82323777 5.910000e-22 115.0
28 TraesCS6A01G190400 chr3A 81.022 137 21 4 525 657 619999493 619999358 1.280000e-18 104.0
29 TraesCS6A01G190400 chr3A 85.714 98 11 3 1476 1573 192599446 192599540 1.650000e-17 100.0
30 TraesCS6A01G190400 chr3A 84.000 100 11 5 1476 1573 192571032 192571128 9.950000e-15 91.6
31 TraesCS6A01G190400 chr4B 82.604 983 132 34 1653 2612 575301771 575302737 0.000000e+00 832.0
32 TraesCS6A01G190400 chr1B 82.836 938 124 34 1696 2612 516139911 516138990 0.000000e+00 806.0
33 TraesCS6A01G190400 chr1B 82.678 941 126 34 1693 2612 450484562 450485486 0.000000e+00 800.0
34 TraesCS6A01G190400 chr1B 80.347 173 24 7 521 692 582702899 582703062 3.530000e-24 122.0
35 TraesCS6A01G190400 chr5B 81.903 967 134 35 1672 2612 459234482 459235433 0.000000e+00 778.0
36 TraesCS6A01G190400 chr5B 100.000 32 0 0 661 692 274391153 274391184 2.810000e-05 60.2
37 TraesCS6A01G190400 chr3B 81.598 989 137 39 1653 2612 274913392 274912420 0.000000e+00 776.0
38 TraesCS6A01G190400 chr7A 87.218 399 49 2 703 1101 428310767 428310371 1.100000e-123 453.0
39 TraesCS6A01G190400 chr7A 86.816 402 47 4 703 1101 428319001 428318603 6.630000e-121 444.0
40 TraesCS6A01G190400 chr7A 80.000 550 65 31 1 523 245380448 245380979 5.310000e-97 364.0
41 TraesCS6A01G190400 chr7A 89.444 180 18 1 3 181 165207276 165207097 2.620000e-55 226.0
42 TraesCS6A01G190400 chr7A 87.302 126 15 1 702 827 139414044 139414168 2.710000e-30 143.0
43 TraesCS6A01G190400 chr2A 81.733 531 78 15 3 523 335222720 335223241 2.400000e-115 425.0
44 TraesCS6A01G190400 chr2A 78.022 546 79 32 3 523 285373544 285374073 3.270000e-79 305.0
45 TraesCS6A01G190400 chr2A 85.000 100 9 6 1476 1573 122400208 122400113 2.140000e-16 97.1
46 TraesCS6A01G190400 chr5A 85.467 289 40 2 785 1072 453312939 453313226 1.520000e-77 300.0
47 TraesCS6A01G190400 chr5A 85.366 287 39 3 785 1070 75570255 75570539 7.070000e-76 294.0
48 TraesCS6A01G190400 chr5A 83.077 130 18 4 527 655 205548532 205548406 5.910000e-22 115.0
49 TraesCS6A01G190400 chr5A 83.486 109 14 4 548 655 205515281 205515176 5.950000e-17 99.0
50 TraesCS6A01G190400 chr5A 95.833 48 2 0 1582 1629 335640543 335640496 7.750000e-11 78.7
51 TraesCS6A01G190400 chr1A 83.706 313 46 5 785 1093 127119795 127120106 9.140000e-75 291.0
52 TraesCS6A01G190400 chr1A 87.500 120 14 1 702 821 125824775 125824657 1.260000e-28 137.0
53 TraesCS6A01G190400 chr1A 89.796 98 8 2 1476 1573 226901743 226901648 9.820000e-25 124.0
54 TraesCS6A01G190400 chr2D 89.216 102 8 2 1472 1573 289146955 289146857 9.820000e-25 124.0
55 TraesCS6A01G190400 chr2D 89.474 57 1 4 1386 1441 256532999 256533051 1.680000e-07 67.6
56 TraesCS6A01G190400 chr4D 89.091 55 3 3 1399 1452 311401856 311401908 6.030000e-07 65.8
57 TraesCS6A01G190400 chr4D 93.182 44 2 1 1399 1442 311409881 311409923 2.170000e-06 63.9
58 TraesCS6A01G190400 chr4D 87.719 57 2 4 1386 1441 331625692 331625744 7.810000e-06 62.1
59 TraesCS6A01G190400 chr6D 93.023 43 2 1 1399 1441 273692133 273692092 7.810000e-06 62.1
60 TraesCS6A01G190400 chr6D 93.023 43 2 1 1399 1441 273700304 273700263 7.810000e-06 62.1
61 TraesCS6A01G190400 chr6D 86.207 58 3 4 1386 1442 116189208 116189261 1.010000e-04 58.4


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 TraesCS6A01G190400 chr6A 252514094 252516705 2611 False 4824 4824 100.0000 1 2612 1 chr6A.!!$F3 2611
1 TraesCS6A01G190400 chr6A 252522191 252524015 1824 False 1107 1984 89.5925 524 2254 2 chr6A.!!$F4 1730
2 TraesCS6A01G190400 chr6A 252435617 252436143 526 False 749 749 92.4240 1 523 1 chr6A.!!$F2 522
3 TraesCS6A01G190400 chr6A 252344706 252345711 1005 True 481 481 76.4650 1476 2460 1 chr6A.!!$R2 984
4 TraesCS6A01G190400 chr4A 200247666 200248584 918 True 977 977 86.1290 1699 2612 1 chr4A.!!$R2 913
5 TraesCS6A01G190400 chr4A 287923078 287924022 944 False 893 893 84.0290 1674 2612 1 chr4A.!!$F1 938
6 TraesCS6A01G190400 chr4A 392840414 392840939 525 True 340 340 78.9470 4 518 1 chr4A.!!$R6 514
7 TraesCS6A01G190400 chr4A 309770219 309770736 517 True 337 337 79.0350 1 524 1 chr4A.!!$R3 523
8 TraesCS6A01G190400 chr3A 683303403 683304323 920 False 961 961 85.5920 1683 2612 1 chr3A.!!$F10 929
9 TraesCS6A01G190400 chr3A 275464212 275464739 527 False 793 793 93.9390 1 523 1 chr3A.!!$F8 522
10 TraesCS6A01G190400 chr3A 275484794 275485322 528 False 789 789 93.7620 1 524 1 chr3A.!!$F9 523
11 TraesCS6A01G190400 chr3A 245745602 245746120 518 False 407 407 81.1680 3 523 1 chr3A.!!$F6 520
12 TraesCS6A01G190400 chr3A 245881592 245882107 515 False 401 401 81.0960 6 523 1 chr3A.!!$F7 517
13 TraesCS6A01G190400 chr3A 220282974 220283482 508 True 387 387 80.7180 3 523 1 chr3A.!!$R2 520
14 TraesCS6A01G190400 chr3A 177775713 177776243 530 False 346 346 79.2660 3 523 1 chr3A.!!$F2 520
15 TraesCS6A01G190400 chr3A 177793069 177793600 531 False 342 342 79.1590 3 524 1 chr3A.!!$F3 521
16 TraesCS6A01G190400 chr4B 575301771 575302737 966 False 832 832 82.6040 1653 2612 1 chr4B.!!$F1 959
17 TraesCS6A01G190400 chr1B 516138990 516139911 921 True 806 806 82.8360 1696 2612 1 chr1B.!!$R1 916
18 TraesCS6A01G190400 chr1B 450484562 450485486 924 False 800 800 82.6780 1693 2612 1 chr1B.!!$F1 919
19 TraesCS6A01G190400 chr5B 459234482 459235433 951 False 778 778 81.9030 1672 2612 1 chr5B.!!$F2 940
20 TraesCS6A01G190400 chr3B 274912420 274913392 972 True 776 776 81.5980 1653 2612 1 chr3B.!!$R1 959
21 TraesCS6A01G190400 chr7A 245380448 245380979 531 False 364 364 80.0000 1 523 1 chr7A.!!$F2 522
22 TraesCS6A01G190400 chr2A 335222720 335223241 521 False 425 425 81.7330 3 523 1 chr2A.!!$F2 520
23 TraesCS6A01G190400 chr2A 285373544 285374073 529 False 305 305 78.0220 3 523 1 chr2A.!!$F1 520

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
800 929 0.170561 CGTGGTACTTGGAGTCTCCG 59.829 60.0 14.34 3.39 40.17 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2484 1.964223 GGTGCCATCCTTAGATCTCGA 59.036 52.381 0.0 0.0 0.0 4.04 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
40 42 6.895782 TGGTATGGACAATTTTAGAGGTAGG 58.104 40.000 0.00 0.00 0.00 3.18
95 97 2.629336 TGCATTTTTGAACCCAACCC 57.371 45.000 0.00 0.00 30.88 4.11
129 133 0.486879 AGGTGAAATTTGGCTGGGGA 59.513 50.000 0.00 0.00 0.00 4.81
204 214 6.017192 GGCTAAATTGTGTTTCTTGCCAAAAT 60.017 34.615 0.00 0.00 37.91 1.82
233 260 1.062810 AGGTGTAGGGATGAGGAGGAC 60.063 57.143 0.00 0.00 0.00 3.85
277 305 4.244862 GGTCAAGCCACAAAATAACATGG 58.755 43.478 0.00 0.00 37.17 3.66
317 353 3.657398 TGGTGAGGATGAGAATGCAAT 57.343 42.857 0.00 0.00 0.00 3.56
529 579 1.553248 TCTGGGGTGTTACAGATTCGG 59.447 52.381 0.00 0.00 38.71 4.30
533 583 2.093128 GGGGTGTTACAGATTCGGACAT 60.093 50.000 0.00 0.00 0.00 3.06
534 584 3.133362 GGGGTGTTACAGATTCGGACATA 59.867 47.826 0.00 0.00 0.00 2.29
542 592 4.517285 ACAGATTCGGACATAGTGCAAAT 58.483 39.130 0.00 0.00 0.00 2.32
544 594 6.112734 ACAGATTCGGACATAGTGCAAATAA 58.887 36.000 0.00 0.00 0.00 1.40
557 607 5.638133 AGTGCAAATAAGGGCATCTCATAT 58.362 37.500 0.00 0.00 42.75 1.78
577 627 7.452562 TCATATAACACACATGCATATGGTCT 58.547 34.615 10.24 0.00 38.66 3.85
581 631 3.118775 ACACACATGCATATGGTCTACGT 60.119 43.478 10.24 0.00 38.66 3.57
625 675 3.509442 TCCAAGGGTGCATTTTCAGAAT 58.491 40.909 0.00 0.00 0.00 2.40
645 695 1.067142 TGATTCGAGTTCGTTGAGGGG 60.067 52.381 1.07 0.00 40.80 4.79
659 709 1.132977 TGAGGGGAGTAGTGGTTCACA 60.133 52.381 0.78 0.00 36.74 3.58
661 711 2.572104 GAGGGGAGTAGTGGTTCACATT 59.428 50.000 0.78 0.00 36.74 2.71
666 716 3.056749 GGAGTAGTGGTTCACATTCTCGT 60.057 47.826 0.78 0.00 36.74 4.18
674 724 4.021456 TGGTTCACATTCTCGTGATGTAGT 60.021 41.667 0.00 0.00 45.03 2.73
692 742 5.845103 TGTAGTGGAAGTAATTGTTCACGA 58.155 37.500 0.00 0.00 0.00 4.35
694 744 4.699637 AGTGGAAGTAATTGTTCACGACA 58.300 39.130 0.00 0.00 36.19 4.35
699 749 2.671396 AGTAATTGTTCACGACATCGGC 59.329 45.455 6.21 0.00 44.95 5.54
706 835 0.388520 TCACGACATCGGCAGTTCTG 60.389 55.000 6.21 0.00 44.95 3.02
716 845 1.920574 CGGCAGTTCTGTAGATGTTCG 59.079 52.381 1.78 0.00 0.00 3.95
762 891 3.506455 TCGAAGAGGAACTTGACGAATCT 59.494 43.478 0.00 0.00 41.55 2.40
780 909 2.257207 TCTGAATCCCTTCGGAGTTGT 58.743 47.619 0.00 0.00 43.12 3.32
782 911 1.067142 TGAATCCCTTCGGAGTTGTCG 60.067 52.381 0.00 0.00 43.12 4.35
793 922 1.342174 GGAGTTGTCGTGGTACTTGGA 59.658 52.381 0.00 0.00 0.00 3.53
800 929 0.170561 CGTGGTACTTGGAGTCTCCG 59.829 60.000 14.34 3.39 40.17 4.63
821 950 1.921230 GACTTGCCGATCTCGTTCTTC 59.079 52.381 0.00 0.00 37.74 2.87
823 952 0.606096 TTGCCGATCTCGTTCTTCCA 59.394 50.000 0.00 0.00 37.74 3.53
827 956 1.269166 CGATCTCGTTCTTCCAACGG 58.731 55.000 7.01 0.00 43.24 4.44
828 957 1.135489 CGATCTCGTTCTTCCAACGGA 60.135 52.381 7.01 4.29 43.24 4.69
859 988 1.433534 GTTCAGAGAGGAACTTGCCG 58.566 55.000 0.00 0.00 41.55 5.69
894 1023 3.449227 TCGGGCGTCGATCTTGCT 61.449 61.111 0.00 0.00 43.74 3.91
895 1024 3.257561 CGGGCGTCGATCTTGCTG 61.258 66.667 0.00 0.00 42.43 4.41
896 1025 3.567797 GGGCGTCGATCTTGCTGC 61.568 66.667 0.00 0.00 0.00 5.25
927 1056 1.138047 GCGAACCCACGTAGTCGATG 61.138 60.000 11.93 0.00 41.61 3.84
931 1060 0.389426 ACCCACGTAGTCGATGTTGC 60.389 55.000 0.00 0.00 41.61 4.17
932 1061 1.082117 CCCACGTAGTCGATGTTGCC 61.082 60.000 0.00 0.00 41.61 4.52
938 1067 2.041966 GTAGTCGATGTTGCCGTATCG 58.958 52.381 7.11 7.11 45.49 2.92
949 1078 1.063649 CCGTATCGAGTGGTCGTGG 59.936 63.158 0.00 0.00 46.85 4.94
958 1087 0.468585 AGTGGTCGTGGAGGTACACA 60.469 55.000 0.00 0.00 41.38 3.72
967 1096 3.015327 GTGGAGGTACACAGTCGTAGAT 58.985 50.000 0.00 0.00 39.22 1.98
973 1102 5.191426 AGGTACACAGTCGTAGATGTACAT 58.809 41.667 8.43 8.43 46.00 2.29
1001 1130 6.784473 TCATCATAGAGGTACTTGACATCCAT 59.216 38.462 0.00 0.00 41.55 3.41
1095 1224 4.742201 GCGGACGGCAGAGCAAGA 62.742 66.667 0.00 0.00 42.87 3.02
1101 1230 2.105466 CGGCAGAGCAAGAAGGAGC 61.105 63.158 0.00 0.00 0.00 4.70
1107 1236 3.130160 GCAAGAAGGAGCCCTGCG 61.130 66.667 0.00 0.00 33.44 5.18
1137 1266 2.031674 GCAAAGCACTGGCCTGGTTT 62.032 55.000 14.52 14.52 41.44 3.27
1140 1269 1.109323 AAGCACTGGCCTGGTTTGTC 61.109 55.000 14.82 0.80 42.56 3.18
1146 1275 1.098712 TGGCCTGGTTTGTCGTTGTC 61.099 55.000 3.32 0.00 0.00 3.18
1151 1280 0.108281 TGGTTTGTCGTTGTCACCGA 60.108 50.000 0.00 0.00 0.00 4.69
1153 1282 1.193874 GGTTTGTCGTTGTCACCGATC 59.806 52.381 0.00 0.00 36.62 3.69
1155 1284 1.279527 TTGTCGTTGTCACCGATCGC 61.280 55.000 10.32 0.00 36.62 4.58
1158 1287 2.774951 CGTTGTCACCGATCGCGAC 61.775 63.158 22.09 22.09 40.82 5.19
1160 1289 1.076533 GTTGTCACCGATCGCGACAT 61.077 55.000 28.18 0.00 39.29 3.06
1162 1291 1.064296 GTCACCGATCGCGACATCT 59.936 57.895 23.26 0.00 40.82 2.90
1167 1296 1.951130 CGATCGCGACATCTTGGGG 60.951 63.158 12.93 0.00 40.82 4.96
1190 1319 1.381327 GGAGGGACGTCATGGAGGA 60.381 63.158 18.91 0.00 0.00 3.71
1221 1359 3.003763 AGGTCGAGGCAGGGGTTC 61.004 66.667 0.00 0.00 0.00 3.62
1222 1360 3.319198 GGTCGAGGCAGGGGTTCA 61.319 66.667 0.00 0.00 0.00 3.18
1261 1399 2.442272 ATGGCGGCCTCTACTCGT 60.442 61.111 21.46 0.00 0.00 4.18
1263 1401 3.138798 GGCGGCCTCTACTCGTCA 61.139 66.667 12.87 0.00 0.00 4.35
1268 1406 1.062845 GCCTCTACTCGTCAGCGTC 59.937 63.158 0.00 0.00 39.49 5.19
1275 1413 3.384014 CTCGTCAGCGTCGGAGGAC 62.384 68.421 1.18 0.00 39.89 3.85
1288 1426 2.156343 GGAGGACGATATTGTGGAGC 57.844 55.000 0.00 0.00 0.00 4.70
1292 1430 1.202580 GGACGATATTGTGGAGCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
1294 1432 1.208052 ACGATATTGTGGAGCAGCTGT 59.792 47.619 16.64 1.59 0.00 4.40
1299 1437 3.054503 GTGGAGCAGCTGTGGCAG 61.055 66.667 16.64 0.00 41.70 4.85
1315 1453 3.710722 AGAGCAGCTTGGGGACGG 61.711 66.667 0.00 0.00 0.00 4.79
1359 1497 4.479993 GGCACGAGGGCTCTGCAT 62.480 66.667 0.00 0.00 39.42 3.96
1360 1498 3.200593 GCACGAGGGCTCTGCATG 61.201 66.667 0.00 0.00 35.40 4.06
1364 1502 4.891037 GAGGGCTCTGCATGGGGC 62.891 72.222 0.00 0.00 45.13 5.80
1376 1514 3.642741 ATGGGGCGAGGAGGAGGTT 62.643 63.158 0.00 0.00 0.00 3.50
1385 1523 2.034221 GAGGAGGTTGGGGTGCAC 59.966 66.667 8.80 8.80 0.00 4.57
1514 1652 2.684735 GGGAGGACGAGAGGGAGT 59.315 66.667 0.00 0.00 0.00 3.85
1523 1661 0.612174 CGAGAGGGAGTGGGTGAGAA 60.612 60.000 0.00 0.00 0.00 2.87
1573 1711 1.306296 GGCTGGGGTTTAGATGGCA 59.694 57.895 0.00 0.00 0.00 4.92
1615 1778 1.146485 CAGATGGGCTGCTGAGAGG 59.854 63.158 0.00 0.00 37.90 3.69
1621 1784 3.715097 GCTGCTGAGAGGCCCAGT 61.715 66.667 0.00 0.00 34.29 4.00
1860 2035 2.561858 ACTAGGACGGGTTTGAGAAGTC 59.438 50.000 0.00 0.00 0.00 3.01
1864 2039 1.343465 GACGGGTTTGAGAAGTCTCCA 59.657 52.381 5.88 0.00 42.20 3.86
1869 2044 4.278419 CGGGTTTGAGAAGTCTCCAAAAAT 59.722 41.667 5.88 0.00 42.20 1.82
1918 2098 4.003648 AGTGGCGAAAGAATTTACAGGAG 58.996 43.478 0.00 0.00 39.27 3.69
2077 2268 5.123820 TCACCATGTGAATTTCCTTCGATTC 59.876 40.000 0.00 0.00 39.78 2.52
2218 2419 3.188460 CACGACAAAACTCGGAATCCATT 59.812 43.478 0.00 0.00 38.02 3.16
2260 2461 1.691195 TTGGGGCGTCACAACTCTCA 61.691 55.000 0.00 0.00 0.00 3.27
2283 2484 4.590918 TCCACTTACAAGAGATCTCGACT 58.409 43.478 16.97 5.79 34.09 4.18
2336 2541 6.589135 ACGGAAGAAGAAGAAGAGGTAAAAA 58.411 36.000 0.00 0.00 0.00 1.94
2374 2583 3.951680 ACGAGTGAAACCAATGAACCTTT 59.048 39.130 0.00 0.00 37.80 3.11
2415 2626 9.996554 TGAAAGAAGAATACAACATAGTTGAGA 57.003 29.630 15.99 4.64 0.00 3.27
2432 2644 5.011943 AGTTGAGAGAAATTGAGAGCACTCT 59.988 40.000 12.54 0.00 42.99 3.24
2448 2661 5.930135 AGCACTCTGGTAGAAAAGAGAAAA 58.070 37.500 6.69 0.00 42.15 2.29
2487 2700 4.329462 CCTTGGAGGTTGTAGAGCTATC 57.671 50.000 0.00 0.00 35.91 2.08
2521 2735 6.976925 GCATAATGGACAAGAAGGAATTGAAG 59.023 38.462 0.00 0.00 0.00 3.02
2526 2740 2.554032 ACAAGAAGGAATTGAAGCCACG 59.446 45.455 0.00 0.00 0.00 4.94
2528 2742 0.171231 GAAGGAATTGAAGCCACGCC 59.829 55.000 0.00 0.00 0.00 5.68
2563 2777 7.751768 AGATAAACAAGGAACAAGGAAGAAG 57.248 36.000 0.00 0.00 0.00 2.85
2583 2797 8.627208 AAGAAGAAATTCAAATAGCACTCTGA 57.373 30.769 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 69 5.055812 GGGTTCAAAAATGCATCAAGTTCA 58.944 37.500 0.00 0.00 0.00 3.18
68 70 5.055812 TGGGTTCAAAAATGCATCAAGTTC 58.944 37.500 0.00 0.00 0.00 3.01
204 214 1.702699 TCCCTACACCTCTCCCCTTA 58.297 55.000 0.00 0.00 0.00 2.69
233 260 3.243401 CCATGTGTGATCCATGCATGAAG 60.243 47.826 28.31 12.34 39.21 3.02
277 305 2.049077 TGCGCATTGTGTGTTTCATC 57.951 45.000 5.66 0.00 0.00 2.92
317 353 4.145052 TGTTGTGTGGTGTTTATGCCATA 58.855 39.130 0.00 0.00 37.09 2.74
529 579 4.823989 AGATGCCCTTATTTGCACTATGTC 59.176 41.667 0.00 0.00 40.88 3.06
533 583 4.502105 TGAGATGCCCTTATTTGCACTA 57.498 40.909 0.00 0.00 40.88 2.74
534 584 3.370840 TGAGATGCCCTTATTTGCACT 57.629 42.857 0.00 0.00 40.88 4.40
542 592 6.493189 TGTGTGTTATATGAGATGCCCTTA 57.507 37.500 0.00 0.00 0.00 2.69
544 594 5.311265 CATGTGTGTTATATGAGATGCCCT 58.689 41.667 0.00 0.00 30.08 5.19
557 607 5.047188 CGTAGACCATATGCATGTGTGTTA 58.953 41.667 20.40 7.96 0.00 2.41
625 675 1.067142 CCCCTCAACGAACTCGAATCA 60.067 52.381 6.05 0.00 43.02 2.57
627 677 1.204941 CTCCCCTCAACGAACTCGAAT 59.795 52.381 6.05 0.00 43.02 3.34
630 680 1.132643 CTACTCCCCTCAACGAACTCG 59.867 57.143 0.00 0.00 46.33 4.18
645 695 3.921021 CACGAGAATGTGAACCACTACTC 59.079 47.826 0.00 0.00 42.55 2.59
659 709 6.525578 TTACTTCCACTACATCACGAGAAT 57.474 37.500 0.00 0.00 0.00 2.40
661 711 6.071560 ACAATTACTTCCACTACATCACGAGA 60.072 38.462 0.00 0.00 0.00 4.04
666 716 6.367695 CGTGAACAATTACTTCCACTACATCA 59.632 38.462 0.00 0.00 0.00 3.07
674 724 4.387559 CGATGTCGTGAACAATTACTTCCA 59.612 41.667 0.00 0.00 42.37 3.53
692 742 2.497675 ACATCTACAGAACTGCCGATGT 59.502 45.455 22.01 22.01 43.04 3.06
694 744 3.735208 CGAACATCTACAGAACTGCCGAT 60.735 47.826 1.46 1.92 0.00 4.18
699 749 2.271800 GCCCGAACATCTACAGAACTG 58.728 52.381 0.00 0.00 0.00 3.16
706 835 2.960129 CGCCGCCCGAACATCTAC 60.960 66.667 0.00 0.00 40.02 2.59
716 845 4.519437 GTACCACTACCGCCGCCC 62.519 72.222 0.00 0.00 0.00 6.13
752 881 3.521560 CGAAGGGATTCAGATTCGTCAA 58.478 45.455 8.24 0.00 39.62 3.18
775 904 2.035576 GACTCCAAGTACCACGACAACT 59.964 50.000 0.00 0.00 0.00 3.16
780 909 1.542492 GGAGACTCCAAGTACCACGA 58.458 55.000 17.10 0.00 36.28 4.35
782 911 0.531200 CCGGAGACTCCAAGTACCAC 59.469 60.000 21.49 0.00 35.91 4.16
800 929 0.173708 AGAACGAGATCGGCAAGTCC 59.826 55.000 7.22 0.00 44.95 3.85
821 950 2.436417 ACCATGAATGACTTCCGTTGG 58.564 47.619 0.00 0.00 33.98 3.77
823 952 3.750371 TGAACCATGAATGACTTCCGTT 58.250 40.909 0.00 0.00 0.00 4.44
827 956 4.874966 CCTCTCTGAACCATGAATGACTTC 59.125 45.833 0.00 0.00 0.00 3.01
828 957 4.533707 TCCTCTCTGAACCATGAATGACTT 59.466 41.667 0.00 0.00 0.00 3.01
833 962 5.251764 CAAGTTCCTCTCTGAACCATGAAT 58.748 41.667 0.00 0.00 44.55 2.57
835 964 3.557898 GCAAGTTCCTCTCTGAACCATGA 60.558 47.826 0.00 0.00 44.55 3.07
859 988 2.343544 CCGAACGACTTCATACCGAAAC 59.656 50.000 0.00 0.00 31.71 2.78
887 1016 0.995024 AAGTACCCCAGCAGCAAGAT 59.005 50.000 0.00 0.00 0.00 2.40
893 1022 2.436646 CGCCAAGTACCCCAGCAG 60.437 66.667 0.00 0.00 0.00 4.24
894 1023 2.521451 TTCGCCAAGTACCCCAGCA 61.521 57.895 0.00 0.00 0.00 4.41
895 1024 2.038837 GTTCGCCAAGTACCCCAGC 61.039 63.158 0.00 0.00 0.00 4.85
896 1025 1.376812 GGTTCGCCAAGTACCCCAG 60.377 63.158 0.00 0.00 34.59 4.45
916 1045 0.804364 TACGGCAACATCGACTACGT 59.196 50.000 0.00 0.00 40.69 3.57
927 1056 1.138047 CGACCACTCGATACGGCAAC 61.138 60.000 0.00 0.00 43.06 4.17
931 1060 1.063649 CCACGACCACTCGATACGG 59.936 63.158 0.00 0.00 43.06 4.02
932 1061 0.027716 CTCCACGACCACTCGATACG 59.972 60.000 0.00 0.00 43.06 3.06
938 1067 0.243095 GTGTACCTCCACGACCACTC 59.757 60.000 0.00 0.00 0.00 3.51
946 1075 2.430465 TCTACGACTGTGTACCTCCAC 58.570 52.381 0.00 0.00 35.86 4.02
949 1078 4.633126 TGTACATCTACGACTGTGTACCTC 59.367 45.833 16.78 0.00 43.76 3.85
958 1087 4.887655 TGATGACCATGTACATCTACGACT 59.112 41.667 21.44 0.00 42.05 4.18
967 1096 6.373759 AGTACCTCTATGATGACCATGTACA 58.626 40.000 0.00 0.00 35.26 2.90
973 1102 5.269189 TGTCAAGTACCTCTATGATGACCA 58.731 41.667 0.00 0.00 35.91 4.02
1087 1216 1.989620 CAGGGCTCCTTCTTGCTCT 59.010 57.895 0.00 0.00 41.22 4.09
1091 1220 1.743252 GTCGCAGGGCTCCTTCTTG 60.743 63.158 0.00 0.00 0.00 3.02
1107 1236 3.435186 GCTTTGCTGAGCCCCGTC 61.435 66.667 0.23 0.00 36.66 4.79
1121 1250 1.076044 ACAAACCAGGCCAGTGCTT 60.076 52.632 5.01 0.00 37.74 3.91
1137 1266 1.731613 GCGATCGGTGACAACGACA 60.732 57.895 19.50 0.00 43.78 4.35
1140 1269 2.503158 TCGCGATCGGTGACAACG 60.503 61.111 18.30 6.54 36.13 4.10
1146 1275 1.482621 CCAAGATGTCGCGATCGGTG 61.483 60.000 14.06 10.42 36.13 4.94
1151 1280 2.203070 GCCCCAAGATGTCGCGAT 60.203 61.111 14.06 0.00 0.00 4.58
1153 1282 3.499737 GTGCCCCAAGATGTCGCG 61.500 66.667 0.00 0.00 0.00 5.87
1155 1284 2.819595 CGGTGCCCCAAGATGTCG 60.820 66.667 0.00 0.00 0.00 4.35
1158 1287 2.124570 CTCCGGTGCCCCAAGATG 60.125 66.667 0.00 0.00 0.00 2.90
1167 1296 3.771160 ATGACGTCCCTCCGGTGC 61.771 66.667 14.12 0.00 0.00 5.01
1190 1319 4.393778 ACCTCCACCGGATCCCGT 62.394 66.667 9.46 2.41 46.80 5.28
1192 1321 3.537874 CGACCTCCACCGGATCCC 61.538 72.222 9.46 0.00 0.00 3.85
1213 1351 1.601171 CCTCTGCTCTGAACCCCTG 59.399 63.158 0.00 0.00 0.00 4.45
1221 1359 1.067749 CCATCTCGCCTCTGCTCTG 59.932 63.158 0.00 0.00 34.43 3.35
1222 1360 2.795110 GCCATCTCGCCTCTGCTCT 61.795 63.158 0.00 0.00 34.43 4.09
1243 1381 2.336809 CGAGTAGAGGCCGCCATC 59.663 66.667 13.15 6.47 0.00 3.51
1244 1382 2.442272 ACGAGTAGAGGCCGCCAT 60.442 61.111 13.15 1.89 0.00 4.40
1245 1383 3.138798 GACGAGTAGAGGCCGCCA 61.139 66.667 13.15 0.00 0.00 5.69
1249 1387 2.325666 GACGCTGACGAGTAGAGGCC 62.326 65.000 0.00 0.00 43.93 5.19
1268 1406 1.603172 GCTCCACAATATCGTCCTCCG 60.603 57.143 0.00 0.00 38.13 4.63
1275 1413 1.596260 CACAGCTGCTCCACAATATCG 59.404 52.381 15.27 0.00 0.00 2.92
1279 1417 1.975407 GCCACAGCTGCTCCACAAT 60.975 57.895 15.27 0.00 35.50 2.71
1280 1418 2.595463 GCCACAGCTGCTCCACAA 60.595 61.111 15.27 0.00 35.50 3.33
1292 1430 2.281970 CCAAGCTGCTCTGCCACA 60.282 61.111 1.00 0.00 0.00 4.17
1294 1432 4.355720 CCCCAAGCTGCTCTGCCA 62.356 66.667 1.00 0.00 0.00 4.92
1299 1437 4.021925 ACCGTCCCCAAGCTGCTC 62.022 66.667 1.00 0.00 0.00 4.26
1346 1484 4.559063 CCCCATGCAGAGCCCTCG 62.559 72.222 0.00 0.00 34.09 4.63
1357 1495 3.554342 CCTCCTCCTCGCCCCATG 61.554 72.222 0.00 0.00 0.00 3.66
1358 1496 3.642741 AACCTCCTCCTCGCCCCAT 62.643 63.158 0.00 0.00 0.00 4.00
1359 1497 4.332543 AACCTCCTCCTCGCCCCA 62.333 66.667 0.00 0.00 0.00 4.96
1360 1498 3.787001 CAACCTCCTCCTCGCCCC 61.787 72.222 0.00 0.00 0.00 5.80
1364 1502 2.284699 ACCCCAACCTCCTCCTCG 60.285 66.667 0.00 0.00 0.00 4.63
1412 1550 2.598985 CCCTCTCCTCGATCCCCG 60.599 72.222 0.00 0.00 40.25 5.73
1420 1558 3.460478 ATCCCCTCGCCCTCTCCTC 62.460 68.421 0.00 0.00 0.00 3.71
1457 1595 3.722295 GCACGTTGCTAGCGCCAA 61.722 61.111 10.77 0.00 40.96 4.52
1478 1616 4.752879 CTACCGCCACCACCCACG 62.753 72.222 0.00 0.00 0.00 4.94
1514 1652 0.545309 CTGACCCCTCTTCTCACCCA 60.545 60.000 0.00 0.00 0.00 4.51
1523 1661 1.827492 AACCCTAGGCTGACCCCTCT 61.827 60.000 2.05 0.00 36.41 3.69
1573 1711 1.151677 TCCCTAAGGCCCAACCACT 60.152 57.895 0.00 0.00 43.14 4.00
1598 1761 2.744243 GCCTCTCAGCAGCCCATCT 61.744 63.158 0.00 0.00 0.00 2.90
1621 1784 1.978580 GAGAGGGAGAGAACAACCCAA 59.021 52.381 0.00 0.00 45.43 4.12
1669 1832 6.102663 TCTTCTCTCTATTTCTTTTCTGCGG 58.897 40.000 0.00 0.00 0.00 5.69
1670 1833 7.588143 TTCTTCTCTCTATTTCTTTTCTGCG 57.412 36.000 0.00 0.00 0.00 5.18
1860 2035 7.014230 TCCACCTAAAGTCTCAAATTTTTGGAG 59.986 37.037 3.38 0.00 38.66 3.86
1864 2039 6.551227 AGCTCCACCTAAAGTCTCAAATTTTT 59.449 34.615 0.00 0.00 0.00 1.94
1869 2044 3.306088 CGAGCTCCACCTAAAGTCTCAAA 60.306 47.826 8.47 0.00 0.00 2.69
2070 2261 6.602803 TGGATCTTTGATCCATTTGAATCGAA 59.397 34.615 21.32 0.00 42.81 3.71
2111 2303 6.255020 GCCATCATGTCTTTAATCTTTGCAAG 59.745 38.462 0.00 0.00 0.00 4.01
2218 2419 2.124983 GCGCTCCAGATGCCTTCA 60.125 61.111 0.00 0.00 0.00 3.02
2260 2461 5.197451 AGTCGAGATCTCTTGTAAGTGGAT 58.803 41.667 20.26 0.00 0.00 3.41
2283 2484 1.964223 GGTGCCATCCTTAGATCTCGA 59.036 52.381 0.00 0.00 0.00 4.04
2292 2493 3.411517 CTCCCCGGTGCCATCCTT 61.412 66.667 0.00 0.00 0.00 3.36
2336 2541 4.335315 TCACTCGTTTGTCAAGAAGCAATT 59.665 37.500 0.00 0.00 0.00 2.32
2338 2543 3.266636 TCACTCGTTTGTCAAGAAGCAA 58.733 40.909 0.00 0.00 0.00 3.91
2339 2544 2.899976 TCACTCGTTTGTCAAGAAGCA 58.100 42.857 0.00 0.00 0.00 3.91
2374 2583 8.801882 TTCTTCTTTCAAGTTTTCAACCTCTA 57.198 30.769 0.00 0.00 0.00 2.43
2407 2618 6.210385 AGAGTGCTCTCAATTTCTCTCAACTA 59.790 38.462 17.51 0.00 42.66 2.24
2414 2625 3.936564 ACCAGAGTGCTCTCAATTTCTC 58.063 45.455 17.51 0.00 42.66 2.87
2415 2626 4.774726 TCTACCAGAGTGCTCTCAATTTCT 59.225 41.667 17.51 0.00 42.66 2.52
2448 2661 3.312736 AGGTTGACATGGTGTTCCTTT 57.687 42.857 0.00 0.00 34.23 3.11
2478 2691 6.575162 TTATGCTCGTCATTGATAGCTCTA 57.425 37.500 18.91 11.23 36.63 2.43
2480 2693 5.063186 CCATTATGCTCGTCATTGATAGCTC 59.937 44.000 18.91 0.00 36.63 4.09
2487 2700 4.571984 TCTTGTCCATTATGCTCGTCATTG 59.428 41.667 0.00 0.00 36.63 2.82
2526 2740 2.287909 TGTTTATCTTGTTGCAACCGGC 60.288 45.455 26.14 2.21 45.13 6.13
2528 2742 3.980775 CCTTGTTTATCTTGTTGCAACCG 59.019 43.478 26.14 16.97 0.00 4.44
2534 2748 7.038154 TCCTTGTTCCTTGTTTATCTTGTTG 57.962 36.000 0.00 0.00 0.00 3.33
2563 2777 9.630098 TTTCAATCAGAGTGCTATTTGAATTTC 57.370 29.630 0.00 0.00 35.70 2.17
2583 2797 6.889301 TCAAGTCTTGCATCTCTTTTCAAT 57.111 33.333 7.78 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.