Multiple sequence alignment - TraesCS7A01G174500

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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 TraesCS7A01G174500 chr7A 100.000 3472 0 0 1 3472 128407141 128403670 0.000000e+00 6412.0
1 TraesCS7A01G174500 chr7A 83.261 920 145 5 1578 2489 128510815 128509897 0.000000e+00 837.0
2 TraesCS7A01G174500 chr7A 89.286 364 37 2 1024 1387 128511408 128511047 4.090000e-124 455.0
3 TraesCS7A01G174500 chr7A 86.842 152 20 0 3321 3472 594411995 594412146 1.660000e-38 171.0
4 TraesCS7A01G174500 chr7A 94.737 95 2 3 1406 1497 699348421 699348327 1.000000e-30 145.0
5 TraesCS7A01G174500 chr7D 94.467 1735 87 5 1495 3228 127650510 127648784 0.000000e+00 2663.0
6 TraesCS7A01G174500 chr7D 92.143 1260 89 8 1495 2749 127682657 127681403 0.000000e+00 1770.0
7 TraesCS7A01G174500 chr7D 90.898 802 50 5 619 1419 127683432 127682653 0.000000e+00 1055.0
8 TraesCS7A01G174500 chr7D 91.447 760 42 6 619 1374 127652288 127651548 0.000000e+00 1022.0
9 TraesCS7A01G174500 chr7D 82.632 927 149 7 1574 2489 127737137 127736212 0.000000e+00 809.0
10 TraesCS7A01G174500 chr7D 82.556 900 146 9 1597 2489 127732908 127732013 0.000000e+00 782.0
11 TraesCS7A01G174500 chr7D 81.568 727 128 4 1768 2489 127730475 127729750 2.310000e-166 595.0
12 TraesCS7A01G174500 chr7D 89.218 371 38 2 1024 1394 127766143 127765775 2.440000e-126 462.0
13 TraesCS7A01G174500 chr7D 89.101 367 39 1 1028 1394 127753626 127753261 4.090000e-124 455.0
14 TraesCS7A01G174500 chr7D 88.068 352 41 1 1028 1379 127700365 127700015 1.930000e-112 416.0
15 TraesCS7A01G174500 chr7D 92.424 198 15 0 3275 3472 127648785 127648588 2.040000e-72 283.0
16 TraesCS7A01G174500 chr7D 82.857 175 28 2 3152 3325 27384703 27384876 4.640000e-34 156.0
17 TraesCS7A01G174500 chr7D 81.579 152 28 0 3321 3472 162199813 162199662 3.640000e-25 126.0
18 TraesCS7A01G174500 chr7B 89.663 1780 165 12 1495 3266 89542557 89540789 0.000000e+00 2250.0
19 TraesCS7A01G174500 chr7B 91.879 825 37 9 604 1419 89543356 89542553 0.000000e+00 1125.0
20 TraesCS7A01G174500 chr7B 83.680 913 142 6 1578 2486 89560579 89559670 0.000000e+00 854.0
21 TraesCS7A01G174500 chr7B 83.206 917 145 7 1580 2489 89656871 89655957 0.000000e+00 832.0
22 TraesCS7A01G174500 chr7B 90.110 364 34 2 1024 1387 89657523 89657162 4.060000e-129 472.0
23 TraesCS7A01G174500 chr7B 88.636 352 38 2 1028 1379 89561042 89560693 8.910000e-116 427.0
24 TraesCS7A01G174500 chr6D 90.538 539 47 4 12 548 103031738 103031202 0.000000e+00 710.0
25 TraesCS7A01G174500 chr6D 84.868 152 23 0 3321 3472 91039994 91040145 1.670000e-33 154.0
26 TraesCS7A01G174500 chr6D 92.233 103 2 5 1400 1498 452466996 452467096 1.300000e-29 141.0
27 TraesCS7A01G174500 chr6D 81.333 150 26 2 3323 3472 341154537 341154684 1.690000e-23 121.0
28 TraesCS7A01G174500 chr6D 81.081 148 26 2 3325 3472 357352931 357352786 2.190000e-22 117.0
29 TraesCS7A01G174500 chr6D 80.405 148 27 2 3325 3472 321770931 321771076 1.020000e-20 111.0
30 TraesCS7A01G174500 chr6D 80.672 119 21 2 3322 3440 456505710 456505826 1.330000e-14 91.6
31 TraesCS7A01G174500 chr6D 86.301 73 9 1 3393 3465 363614286 363614215 1.030000e-10 78.7
32 TraesCS7A01G174500 chr6A 90.018 551 52 2 1 548 422818775 422819325 0.000000e+00 710.0
33 TraesCS7A01G174500 chr1B 90.092 545 50 4 9 552 540147224 540147765 0.000000e+00 704.0
34 TraesCS7A01G174500 chr1B 84.768 151 20 2 3322 3472 604328141 604327994 7.760000e-32 148.0
35 TraesCS7A01G174500 chr2D 89.818 550 51 5 1 548 382182627 382182081 0.000000e+00 701.0
36 TraesCS7A01G174500 chr2D 89.455 550 55 3 1 548 515071887 515072435 0.000000e+00 691.0
37 TraesCS7A01G174500 chr2D 94.565 92 1 4 1415 1503 455242713 455242623 4.670000e-29 139.0
38 TraesCS7A01G174500 chr2D 82.667 150 24 2 3321 3469 83825414 83825562 7.820000e-27 132.0
39 TraesCS7A01G174500 chr2D 82.353 153 21 5 3322 3472 144999562 144999710 1.010000e-25 128.0
40 TraesCS7A01G174500 chr1D 89.636 550 53 3 1 548 38524358 38523811 0.000000e+00 697.0
41 TraesCS7A01G174500 chr1D 89.636 550 53 4 1 548 418310122 418309575 0.000000e+00 697.0
42 TraesCS7A01G174500 chr1D 82.000 150 25 2 3321 3469 28180675 28180823 3.640000e-25 126.0
43 TraesCS7A01G174500 chr1D 80.255 157 29 2 3316 3472 371547628 371547782 2.190000e-22 117.0
44 TraesCS7A01G174500 chrUn 89.474 551 53 5 1 549 104791481 104792028 0.000000e+00 691.0
45 TraesCS7A01G174500 chrUn 81.513 119 19 3 3322 3440 92181414 92181529 1.030000e-15 95.3
46 TraesCS7A01G174500 chrUn 86.076 79 7 4 3362 3440 92181588 92181662 7.990000e-12 82.4
47 TraesCS7A01G174500 chrUn 87.500 72 7 2 3369 3440 92181727 92181796 7.990000e-12 82.4
48 TraesCS7A01G174500 chr3B 89.331 553 55 3 1 549 462092428 462092980 0.000000e+00 691.0
49 TraesCS7A01G174500 chr4D 85.526 152 19 3 3321 3471 507758536 507758685 4.640000e-34 156.0
50 TraesCS7A01G174500 chr4D 85.517 145 20 1 3326 3469 28845166 28845022 2.160000e-32 150.0
51 TraesCS7A01G174500 chr4D 82.550 149 22 3 3324 3472 439728651 439728507 1.010000e-25 128.0
52 TraesCS7A01G174500 chr4D 80.667 150 25 3 3324 3472 502023202 502023056 2.830000e-21 113.0
53 TraesCS7A01G174500 chr4D 87.778 90 11 0 3383 3472 495616597 495616508 4.740000e-19 106.0
54 TraesCS7A01G174500 chr4D 79.470 151 30 1 3322 3472 499735356 499735505 4.740000e-19 106.0
55 TraesCS7A01G174500 chr5D 85.135 148 22 0 3325 3472 404474025 404474172 6.000000e-33 152.0
56 TraesCS7A01G174500 chr5D 82.119 151 23 4 3322 3472 33077002 33077148 3.640000e-25 126.0
57 TraesCS7A01G174500 chr3D 84.868 152 19 4 3322 3472 40737248 40737100 2.160000e-32 150.0
58 TraesCS7A01G174500 chr3D 83.553 152 25 0 3321 3472 438630063 438630214 3.610000e-30 143.0
59 TraesCS7A01G174500 chr3D 97.468 79 2 0 1415 1493 142089846 142089768 6.040000e-28 135.0
60 TraesCS7A01G174500 chr2A 84.106 151 23 1 3322 3472 431073206 431073057 1.000000e-30 145.0
61 TraesCS7A01G174500 chr4A 96.591 88 0 3 1413 1497 742452807 742452720 3.610000e-30 143.0
62 TraesCS7A01G174500 chr4A 84.106 151 19 4 3322 3472 2178547 2178692 1.300000e-29 141.0
63 TraesCS7A01G174500 chr4A 95.506 89 3 1 1402 1489 603501355 603501443 1.300000e-29 141.0
64 TraesCS7A01G174500 chr5A 95.556 90 1 3 1414 1500 680978076 680978165 1.300000e-29 141.0
65 TraesCS7A01G174500 chr5B 94.565 92 1 4 1415 1502 664669497 664669406 4.670000e-29 139.0
66 TraesCS7A01G174500 chr2B 92.708 96 4 2 1400 1493 185800366 185800272 6.040000e-28 135.0
67 TraesCS7A01G174500 chr4B 81.818 165 25 5 3161 3324 87889679 87889519 2.170000e-27 134.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G174500 chr7A 128403670 128407141 3471 True 6412.000000 6412 100.000000 1 3472 1 chr7A.!!$R1 3471
1 TraesCS7A01G174500 chr7A 128509897 128511408 1511 True 646.000000 837 86.273500 1024 2489 2 chr7A.!!$R3 1465
2 TraesCS7A01G174500 chr7D 127681403 127683432 2029 True 1412.500000 1770 91.520500 619 2749 2 chr7D.!!$R6 2130
3 TraesCS7A01G174500 chr7D 127648588 127652288 3700 True 1322.666667 2663 92.779333 619 3472 3 chr7D.!!$R5 2853
4 TraesCS7A01G174500 chr7D 127729750 127737137 7387 True 728.666667 809 82.252000 1574 2489 3 chr7D.!!$R7 915
5 TraesCS7A01G174500 chr7B 89540789 89543356 2567 True 1687.500000 2250 90.771000 604 3266 2 chr7B.!!$R1 2662
6 TraesCS7A01G174500 chr7B 89655957 89657523 1566 True 652.000000 832 86.658000 1024 2489 2 chr7B.!!$R3 1465
7 TraesCS7A01G174500 chr7B 89559670 89561042 1372 True 640.500000 854 86.158000 1028 2486 2 chr7B.!!$R2 1458
8 TraesCS7A01G174500 chr6D 103031202 103031738 536 True 710.000000 710 90.538000 12 548 1 chr6D.!!$R1 536
9 TraesCS7A01G174500 chr6A 422818775 422819325 550 False 710.000000 710 90.018000 1 548 1 chr6A.!!$F1 547
10 TraesCS7A01G174500 chr1B 540147224 540147765 541 False 704.000000 704 90.092000 9 552 1 chr1B.!!$F1 543
11 TraesCS7A01G174500 chr2D 382182081 382182627 546 True 701.000000 701 89.818000 1 548 1 chr2D.!!$R1 547
12 TraesCS7A01G174500 chr2D 515071887 515072435 548 False 691.000000 691 89.455000 1 548 1 chr2D.!!$F3 547
13 TraesCS7A01G174500 chr1D 38523811 38524358 547 True 697.000000 697 89.636000 1 548 1 chr1D.!!$R1 547
14 TraesCS7A01G174500 chr1D 418309575 418310122 547 True 697.000000 697 89.636000 1 548 1 chr1D.!!$R2 547
15 TraesCS7A01G174500 chrUn 104791481 104792028 547 False 691.000000 691 89.474000 1 549 1 chrUn.!!$F1 548
16 TraesCS7A01G174500 chr3B 462092428 462092980 552 False 691.000000 691 89.331000 1 549 1 chr3B.!!$F1 548

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
991 1014 0.531974 CCGTATATTGCACCACCGCT 60.532 55.0 0.00 0.0 0.0 5.52 F
1750 4609 0.107214 GGAATGTCATTGAGGCGGGA 60.107 55.0 1.88 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 4777 0.246635 ACGGAGACAACCTGATTCCG 59.753 55.0 16.32 16.32 45.2 4.30 R
3355 8496 0.249953 TCGTAAAAGGCAAGCGGACA 60.250 50.0 0.00 0.00 0.0 4.02 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
69 70 1.065410 TGGCCTTTGGGTCAGAGGAA 61.065 55.000 3.32 0.00 43.05 3.36
155 156 4.876107 ACGCAAACCGATCAAGAATAGATT 59.124 37.500 0.00 0.00 41.02 2.40
175 176 6.716284 AGATTGGAAAACCAAAAAGAAACCA 58.284 32.000 5.79 0.00 33.20 3.67
177 178 8.490311 AGATTGGAAAACCAAAAAGAAACCATA 58.510 29.630 5.79 0.00 33.20 2.74
201 203 1.987855 AAGATGACCGGCGGGAGAA 60.988 57.895 31.78 12.78 36.97 2.87
218 220 3.332919 GAGAAAGAAAACCCCGGAGTAC 58.667 50.000 0.73 0.00 0.00 2.73
314 316 3.071837 TGGCGGCGGTCATGTAGA 61.072 61.111 9.78 0.00 0.00 2.59
369 371 1.218854 GGCGACGGCTAGGGTTTAA 59.781 57.895 15.00 0.00 39.81 1.52
402 404 8.589701 TTGCGATAGATACCATATTAGAAGGA 57.410 34.615 0.00 0.00 39.76 3.36
430 436 4.895668 AGGTTGGTGGAATAGTTCGTTA 57.104 40.909 0.00 0.00 0.00 3.18
513 523 5.793817 ACAAGCCAAAACAAATCCTAATCC 58.206 37.500 0.00 0.00 0.00 3.01
590 601 7.969536 AAACATCTTTATATGATGAGACGGG 57.030 36.000 17.70 0.00 42.68 5.28
592 603 5.046304 ACATCTTTATATGATGAGACGGGGG 60.046 44.000 17.70 0.00 42.68 5.40
593 604 4.747583 TCTTTATATGATGAGACGGGGGA 58.252 43.478 0.00 0.00 0.00 4.81
595 606 2.704190 ATATGATGAGACGGGGGAGT 57.296 50.000 0.00 0.00 0.00 3.85
596 607 3.827817 ATATGATGAGACGGGGGAGTA 57.172 47.619 0.00 0.00 0.00 2.59
597 608 2.002505 ATGATGAGACGGGGGAGTAG 57.997 55.000 0.00 0.00 0.00 2.57
598 609 0.755698 TGATGAGACGGGGGAGTAGC 60.756 60.000 0.00 0.00 0.00 3.58
600 611 0.851469 ATGAGACGGGGGAGTAGCTA 59.149 55.000 0.00 0.00 0.00 3.32
601 612 0.851469 TGAGACGGGGGAGTAGCTAT 59.149 55.000 0.00 0.00 0.00 2.97
602 613 1.202903 TGAGACGGGGGAGTAGCTATC 60.203 57.143 0.00 0.00 0.00 2.08
603 614 0.851469 AGACGGGGGAGTAGCTATCA 59.149 55.000 0.00 0.00 0.00 2.15
604 615 1.429687 AGACGGGGGAGTAGCTATCAT 59.570 52.381 0.00 0.00 0.00 2.45
607 618 1.202582 CGGGGGAGTAGCTATCATTCG 59.797 57.143 0.00 0.00 0.00 3.34
608 619 2.249139 GGGGGAGTAGCTATCATTCGT 58.751 52.381 0.00 0.00 0.00 3.85
609 620 3.428532 GGGGGAGTAGCTATCATTCGTA 58.571 50.000 0.00 0.00 0.00 3.43
611 622 4.142138 GGGGGAGTAGCTATCATTCGTATG 60.142 50.000 0.00 0.00 0.00 2.39
639 650 3.487574 CGCTAGAGTTGCTATAGTGTTGC 59.512 47.826 0.84 0.00 33.00 4.17
815 837 9.269453 GTCACACCAAACTTCTAGTACTTTATT 57.731 33.333 0.00 0.00 0.00 1.40
932 955 5.835113 AGAAACAGAGCAAACAAAGCTTA 57.165 34.783 0.00 0.00 43.58 3.09
934 957 4.574599 AACAGAGCAAACAAAGCTTAGG 57.425 40.909 0.00 0.00 43.58 2.69
935 958 3.555966 ACAGAGCAAACAAAGCTTAGGT 58.444 40.909 0.00 0.00 43.58 3.08
936 959 3.316308 ACAGAGCAAACAAAGCTTAGGTG 59.684 43.478 0.00 0.00 43.58 4.00
937 960 2.294512 AGAGCAAACAAAGCTTAGGTGC 59.705 45.455 0.00 7.78 43.58 5.01
938 961 1.001378 AGCAAACAAAGCTTAGGTGCG 60.001 47.619 0.00 0.00 39.87 5.34
939 962 1.408422 CAAACAAAGCTTAGGTGCGC 58.592 50.000 0.00 0.00 38.13 6.09
940 963 1.001378 CAAACAAAGCTTAGGTGCGCT 60.001 47.619 9.73 0.00 38.30 5.92
989 1012 1.202486 ACTCCGTATATTGCACCACCG 60.202 52.381 0.00 0.00 0.00 4.94
991 1014 0.531974 CCGTATATTGCACCACCGCT 60.532 55.000 0.00 0.00 0.00 5.52
992 1015 1.295792 CGTATATTGCACCACCGCTT 58.704 50.000 0.00 0.00 0.00 4.68
993 1016 1.260561 CGTATATTGCACCACCGCTTC 59.739 52.381 0.00 0.00 0.00 3.86
994 1017 2.285083 GTATATTGCACCACCGCTTCA 58.715 47.619 0.00 0.00 0.00 3.02
995 1018 2.057137 ATATTGCACCACCGCTTCAT 57.943 45.000 0.00 0.00 0.00 2.57
996 1019 2.700722 TATTGCACCACCGCTTCATA 57.299 45.000 0.00 0.00 0.00 2.15
1287 1310 2.203195 ACGCAGCAGCAGGTCAAA 60.203 55.556 0.82 0.00 42.27 2.69
1318 1341 0.740868 CATCGTTGATGCCGTCCACT 60.741 55.000 0.00 0.00 33.17 4.00
1319 1342 0.460284 ATCGTTGATGCCGTCCACTC 60.460 55.000 0.00 0.00 0.00 3.51
1335 1358 1.743252 CTCCAAGGGCGCTCTGTTC 60.743 63.158 12.52 0.00 0.00 3.18
1419 2439 7.502177 CATTTTGTGCTGATGAATTGTACTC 57.498 36.000 0.00 0.00 0.00 2.59
1420 2440 5.627499 TTTGTGCTGATGAATTGTACTCC 57.373 39.130 0.00 0.00 0.00 3.85
1421 2441 3.609853 TGTGCTGATGAATTGTACTCCC 58.390 45.455 0.00 0.00 0.00 4.30
1422 2442 3.264193 TGTGCTGATGAATTGTACTCCCT 59.736 43.478 0.00 0.00 0.00 4.20
1423 2443 3.873952 GTGCTGATGAATTGTACTCCCTC 59.126 47.826 0.00 0.00 0.00 4.30
1424 2444 3.118261 TGCTGATGAATTGTACTCCCTCC 60.118 47.826 0.00 0.00 0.00 4.30
1425 2445 3.722147 CTGATGAATTGTACTCCCTCCG 58.278 50.000 0.00 0.00 0.00 4.63
1428 2448 4.712829 TGATGAATTGTACTCCCTCCGTAA 59.287 41.667 0.00 0.00 0.00 3.18
1430 2450 4.824289 TGAATTGTACTCCCTCCGTAAAC 58.176 43.478 0.00 0.00 0.00 2.01
1431 2451 4.529377 TGAATTGTACTCCCTCCGTAAACT 59.471 41.667 0.00 0.00 0.00 2.66
1432 2452 5.716228 TGAATTGTACTCCCTCCGTAAACTA 59.284 40.000 0.00 0.00 0.00 2.24
1434 2454 6.803366 ATTGTACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
1436 2456 7.902920 TTGTACTCCCTCCGTAAACTAATAT 57.097 36.000 0.00 0.00 0.00 1.28
1437 2457 8.995027 TTGTACTCCCTCCGTAAACTAATATA 57.005 34.615 0.00 0.00 0.00 0.86
1438 2458 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
1439 2459 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
1440 2460 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1443 2463 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1445 2465 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1446 2466 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1447 2467 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1448 2468 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1449 2469 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1463 2483 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
1464 2484 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
1466 2486 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
1467 2487 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
1556 2576 7.810759 CGGTTTATTTGTGGCTACTAATTTTGT 59.189 33.333 14.32 0.00 34.75 2.83
1559 2579 4.513198 TTGTGGCTACTAATTTTGTGCC 57.487 40.909 0.64 13.31 40.62 5.01
1567 2588 5.800438 GCTACTAATTTTGTGCCTTGCTTAC 59.200 40.000 0.00 0.00 0.00 2.34
1723 4582 2.819422 TCGTAGACGATTTCAGACGG 57.181 50.000 0.00 0.00 44.22 4.79
1750 4609 0.107214 GGAATGTCATTGAGGCGGGA 60.107 55.000 1.88 0.00 0.00 5.14
1762 4621 1.887707 GGCGGGATTCGATGGTGTC 60.888 63.158 0.00 0.00 42.43 3.67
1918 4777 2.871427 GATTGGCGCGGATCGTGTC 61.871 63.158 8.83 0.00 42.53 3.67
1942 4801 0.391597 TCAGGTTGTCTCCGTTCACC 59.608 55.000 0.00 0.00 0.00 4.02
2052 4911 1.406069 CCACATGGTAGAGCCTCACAC 60.406 57.143 0.00 0.00 38.35 3.82
2081 4940 1.348696 TGGATGGTCGCATGCAGATAT 59.651 47.619 19.57 13.40 0.00 1.63
2266 7387 3.010420 GCTAGATGTCCCCTTGAACAAC 58.990 50.000 0.00 0.00 0.00 3.32
2375 7500 7.287696 AGTTCATTCACCCAACTTCAATTACTT 59.712 33.333 0.00 0.00 0.00 2.24
2562 7699 8.485578 TTTAGTACAAGGGTGGATTCAAATTT 57.514 30.769 0.00 0.00 0.00 1.82
2596 7733 6.861065 TGAAAATAAACCCGAGAGATATGC 57.139 37.500 0.00 0.00 0.00 3.14
2605 7742 2.320367 CGAGAGATATGCGGTTGTAGC 58.680 52.381 0.00 0.00 0.00 3.58
2706 7844 6.855667 TCCATATTCATTGGGATTGATCACT 58.144 36.000 0.00 0.00 34.85 3.41
2709 7847 7.309012 CCATATTCATTGGGATTGATCACTGAC 60.309 40.741 0.00 0.00 0.00 3.51
2732 7872 1.766864 GGTAGAGGAAGGAGGGGCC 60.767 68.421 0.00 0.00 0.00 5.80
2791 7931 0.532196 GTAGCGACACCAATAGGGCC 60.532 60.000 0.00 0.00 42.05 5.80
2817 7957 6.043127 TCTCGATTCCCATATTTCTTCCATCA 59.957 38.462 0.00 0.00 0.00 3.07
2828 7968 8.781196 CATATTTCTTCCATCACTCGATCAATT 58.219 33.333 0.00 0.00 0.00 2.32
2867 8007 5.998454 TGCATTGCTTAGCTAGAAATCTC 57.002 39.130 10.49 0.00 28.86 2.75
2868 8008 5.678583 TGCATTGCTTAGCTAGAAATCTCT 58.321 37.500 10.49 0.00 28.86 3.10
2905 8045 7.026562 CGTAGCTATACATCTTCTCATCTTGG 58.973 42.308 0.00 0.00 31.76 3.61
2911 8051 4.305524 ACATCTTCTCATCTTGGGAGGAT 58.694 43.478 0.00 0.00 43.43 3.24
3034 8175 5.123820 CGAGCCTCTGATACCAATTGAAAAA 59.876 40.000 7.12 0.00 0.00 1.94
3146 8287 3.263170 TGAGCCTAACAATTGCTACTCCA 59.737 43.478 5.05 0.00 34.99 3.86
3227 8368 3.325135 TGAAGGAGAAGGAGAAACTGGAC 59.675 47.826 0.00 0.00 0.00 4.02
3228 8369 2.261729 AGGAGAAGGAGAAACTGGACC 58.738 52.381 0.00 0.00 0.00 4.46
3244 8385 1.407025 GGACCGGTCCTCCTTCAAATC 60.407 57.143 40.89 14.29 46.16 2.17
3249 8390 3.412386 CGGTCCTCCTTCAAATCAAAGT 58.588 45.455 0.00 0.00 0.00 2.66
3250 8391 3.821033 CGGTCCTCCTTCAAATCAAAGTT 59.179 43.478 0.00 0.00 0.00 2.66
3252 8393 4.218635 GGTCCTCCTTCAAATCAAAGTTCC 59.781 45.833 0.00 0.00 0.00 3.62
3253 8394 4.827284 GTCCTCCTTCAAATCAAAGTTCCA 59.173 41.667 0.00 0.00 0.00 3.53
3258 8399 7.386025 CCTCCTTCAAATCAAAGTTCCAATTTC 59.614 37.037 0.00 0.00 0.00 2.17
3272 8413 7.975750 AGTTCCAATTTCTCTCTTATAAACGC 58.024 34.615 0.00 0.00 0.00 4.84
3273 8414 7.606456 AGTTCCAATTTCTCTCTTATAAACGCA 59.394 33.333 0.00 0.00 0.00 5.24
3274 8415 7.915293 TCCAATTTCTCTCTTATAAACGCAA 57.085 32.000 0.00 0.00 0.00 4.85
3280 8421 8.492673 TTTCTCTCTTATAAACGCAACATCAT 57.507 30.769 0.00 0.00 0.00 2.45
3286 8427 7.811653 TCTTATAAACGCAACATCATTCACAA 58.188 30.769 0.00 0.00 0.00 3.33
3289 8430 3.272439 ACGCAACATCATTCACAACAG 57.728 42.857 0.00 0.00 0.00 3.16
3347 8488 1.671054 CCGGATGTTCGCAACCAGT 60.671 57.895 0.00 0.00 39.72 4.00
3351 8492 1.732259 GGATGTTCGCAACCAGTACTG 59.268 52.381 16.34 16.34 39.55 2.74
3355 8496 0.386476 TTCGCAACCAGTACTGACGT 59.614 50.000 24.68 11.56 0.00 4.34
3356 8497 0.318360 TCGCAACCAGTACTGACGTG 60.318 55.000 24.68 17.84 0.00 4.49
3388 8529 1.100510 TTACGATAGCGCAGTCCACT 58.899 50.000 11.47 0.00 42.48 4.00
3438 8579 2.675772 ACCCTGTCGACGACCTCC 60.676 66.667 24.33 0.63 0.00 4.30
3453 8594 3.989698 CTCCACAGCGGCTACCACG 62.990 68.421 0.26 0.00 33.14 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.112412 GGCCTTTCCTCTGACCCAAA 59.888 55.000 0.00 0.00 0.00 3.28
56 57 1.767692 GGCCTTTCCTCTGACCCAA 59.232 57.895 0.00 0.00 0.00 4.12
57 58 2.592993 CGGCCTTTCCTCTGACCCA 61.593 63.158 0.00 0.00 0.00 4.51
201 203 3.921257 CGTACTCCGGGGTTTTCTT 57.079 52.632 15.04 0.00 0.00 2.52
218 220 0.037232 AGAGTCTTTTTCCCGAGCCG 60.037 55.000 0.00 0.00 0.00 5.52
393 395 6.241645 CACCAACCTTTCTCTTCCTTCTAAT 58.758 40.000 0.00 0.00 0.00 1.73
402 404 5.584551 ACTATTCCACCAACCTTTCTCTT 57.415 39.130 0.00 0.00 0.00 2.85
408 410 3.782656 ACGAACTATTCCACCAACCTT 57.217 42.857 0.00 0.00 0.00 3.50
430 436 2.831333 CTCACGAGGCTCAAGCAATAT 58.169 47.619 15.95 0.00 44.36 1.28
564 575 8.840321 CCCGTCTCATCATATAAAGATGTTTTT 58.160 33.333 14.57 0.00 42.63 1.94
565 576 7.445402 CCCCGTCTCATCATATAAAGATGTTTT 59.555 37.037 14.57 0.00 42.63 2.43
567 578 6.467677 CCCCGTCTCATCATATAAAGATGTT 58.532 40.000 14.57 0.00 42.63 2.71
569 580 5.187772 TCCCCCGTCTCATCATATAAAGATG 59.812 44.000 10.68 10.68 43.25 2.90
570 581 5.342017 TCCCCCGTCTCATCATATAAAGAT 58.658 41.667 0.00 0.00 0.00 2.40
571 582 4.747583 TCCCCCGTCTCATCATATAAAGA 58.252 43.478 0.00 0.00 0.00 2.52
572 583 4.528596 ACTCCCCCGTCTCATCATATAAAG 59.471 45.833 0.00 0.00 0.00 1.85
573 584 4.489737 ACTCCCCCGTCTCATCATATAAA 58.510 43.478 0.00 0.00 0.00 1.40
574 585 4.127918 ACTCCCCCGTCTCATCATATAA 57.872 45.455 0.00 0.00 0.00 0.98
575 586 3.827817 ACTCCCCCGTCTCATCATATA 57.172 47.619 0.00 0.00 0.00 0.86
577 588 2.818216 GCTACTCCCCCGTCTCATCATA 60.818 54.545 0.00 0.00 0.00 2.15
578 589 2.002505 CTACTCCCCCGTCTCATCAT 57.997 55.000 0.00 0.00 0.00 2.45
579 590 0.755698 GCTACTCCCCCGTCTCATCA 60.756 60.000 0.00 0.00 0.00 3.07
580 591 0.468400 AGCTACTCCCCCGTCTCATC 60.468 60.000 0.00 0.00 0.00 2.92
582 593 0.851469 ATAGCTACTCCCCCGTCTCA 59.149 55.000 0.00 0.00 0.00 3.27
583 594 1.202903 TGATAGCTACTCCCCCGTCTC 60.203 57.143 0.00 0.00 0.00 3.36
584 595 0.851469 TGATAGCTACTCCCCCGTCT 59.149 55.000 0.00 0.00 0.00 4.18
586 597 2.249139 GAATGATAGCTACTCCCCCGT 58.751 52.381 0.00 0.00 0.00 5.28
587 598 1.202582 CGAATGATAGCTACTCCCCCG 59.797 57.143 0.00 0.00 0.00 5.73
589 600 4.142138 CCATACGAATGATAGCTACTCCCC 60.142 50.000 0.00 0.00 34.84 4.81
590 601 4.678309 GCCATACGAATGATAGCTACTCCC 60.678 50.000 0.00 0.00 34.84 4.30
592 603 4.425520 GGCCATACGAATGATAGCTACTC 58.574 47.826 0.00 0.00 34.84 2.59
593 604 3.195825 GGGCCATACGAATGATAGCTACT 59.804 47.826 4.39 0.00 34.84 2.57
595 606 2.500098 GGGGCCATACGAATGATAGCTA 59.500 50.000 4.39 0.00 34.84 3.32
596 607 1.279271 GGGGCCATACGAATGATAGCT 59.721 52.381 4.39 0.00 34.84 3.32
597 608 1.679032 GGGGGCCATACGAATGATAGC 60.679 57.143 4.39 0.00 34.84 2.97
598 609 1.405526 CGGGGGCCATACGAATGATAG 60.406 57.143 4.39 0.00 34.84 2.08
600 611 1.374947 CGGGGGCCATACGAATGAT 59.625 57.895 4.39 0.00 34.84 2.45
601 612 2.825982 CGGGGGCCATACGAATGA 59.174 61.111 4.39 0.00 34.84 2.57
602 613 2.107041 TAGCGGGGGCCATACGAATG 62.107 60.000 16.90 0.00 0.00 2.67
603 614 1.827399 CTAGCGGGGGCCATACGAAT 61.827 60.000 16.90 7.93 0.00 3.34
604 615 2.444329 TAGCGGGGGCCATACGAA 60.444 61.111 16.90 3.00 0.00 3.85
607 618 1.408453 AACTCTAGCGGGGGCCATAC 61.408 60.000 4.39 0.00 0.00 2.39
608 619 1.074775 AACTCTAGCGGGGGCCATA 60.075 57.895 4.39 0.00 0.00 2.74
609 620 2.366972 AACTCTAGCGGGGGCCAT 60.367 61.111 4.39 0.00 0.00 4.40
611 622 4.858680 GCAACTCTAGCGGGGGCC 62.859 72.222 0.00 0.00 0.00 5.80
722 744 0.171007 AGCGTGTGCATAATGGCAAC 59.829 50.000 0.00 0.00 46.93 4.17
789 811 8.828688 ATAAAGTACTAGAAGTTTGGTGTGAC 57.171 34.615 0.00 0.00 0.00 3.67
872 895 1.859703 CTGCTCGAATGATGCTCTGTC 59.140 52.381 0.00 0.00 0.00 3.51
932 955 2.555199 GAATCTATGACAAGCGCACCT 58.445 47.619 11.47 0.00 0.00 4.00
934 957 2.279741 TGGAATCTATGACAAGCGCAC 58.720 47.619 11.47 0.00 0.00 5.34
935 958 2.689553 TGGAATCTATGACAAGCGCA 57.310 45.000 11.47 0.00 0.00 6.09
936 959 2.156504 CGATGGAATCTATGACAAGCGC 59.843 50.000 0.00 0.00 42.58 5.92
937 960 2.156504 GCGATGGAATCTATGACAAGCG 59.843 50.000 0.00 0.00 42.58 4.68
938 961 3.133691 TGCGATGGAATCTATGACAAGC 58.866 45.455 0.00 0.00 42.58 4.01
939 962 5.063186 GCTATGCGATGGAATCTATGACAAG 59.937 44.000 0.00 0.00 42.58 3.16
940 963 4.931601 GCTATGCGATGGAATCTATGACAA 59.068 41.667 0.00 0.00 42.58 3.18
991 1014 2.099098 TGCTTCGATCGACAGCTATGAA 59.901 45.455 32.38 20.07 33.07 2.57
992 1015 1.676006 TGCTTCGATCGACAGCTATGA 59.324 47.619 32.38 20.31 33.07 2.15
993 1016 1.783711 GTGCTTCGATCGACAGCTATG 59.216 52.381 32.38 15.99 33.07 2.23
994 1017 1.405463 TGTGCTTCGATCGACAGCTAT 59.595 47.619 32.38 0.00 33.07 2.97
995 1018 0.808755 TGTGCTTCGATCGACAGCTA 59.191 50.000 32.38 24.55 33.07 3.32
996 1019 0.174389 ATGTGCTTCGATCGACAGCT 59.826 50.000 32.38 20.55 33.07 4.24
1318 1341 1.768684 AAGAACAGAGCGCCCTTGGA 61.769 55.000 2.29 0.00 0.00 3.53
1319 1342 1.301677 GAAGAACAGAGCGCCCTTGG 61.302 60.000 2.29 0.00 0.00 3.61
1357 1380 0.685097 CCGTTTGAGGAGACCCTTCA 59.315 55.000 0.00 0.00 44.53 3.02
1404 2424 3.133003 ACGGAGGGAGTACAATTCATCAG 59.867 47.826 0.00 0.00 0.00 2.90
1419 2439 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1420 2440 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1421 2441 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1422 2442 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1423 2443 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1437 2457 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
1438 2458 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
1439 2459 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
1440 2460 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
1480 2500 8.465201 CGGTACTCAGTACTTCCTTAAACTAAT 58.535 37.037 14.75 0.00 38.85 1.73
1481 2501 7.448469 ACGGTACTCAGTACTTCCTTAAACTAA 59.552 37.037 14.75 0.00 38.85 2.24
1482 2502 6.942576 ACGGTACTCAGTACTTCCTTAAACTA 59.057 38.462 14.75 0.00 38.85 2.24
1483 2503 5.772169 ACGGTACTCAGTACTTCCTTAAACT 59.228 40.000 14.75 0.00 38.85 2.66
1484 2504 5.860716 CACGGTACTCAGTACTTCCTTAAAC 59.139 44.000 14.75 0.00 38.85 2.01
1485 2505 5.769662 TCACGGTACTCAGTACTTCCTTAAA 59.230 40.000 14.75 0.00 38.85 1.52
1486 2506 5.182001 GTCACGGTACTCAGTACTTCCTTAA 59.818 44.000 14.75 0.00 38.85 1.85
1487 2507 4.697352 GTCACGGTACTCAGTACTTCCTTA 59.303 45.833 14.75 0.00 38.85 2.69
1488 2508 3.505293 GTCACGGTACTCAGTACTTCCTT 59.495 47.826 14.75 0.00 38.85 3.36
1489 2509 3.080319 GTCACGGTACTCAGTACTTCCT 58.920 50.000 14.75 0.00 38.85 3.36
1491 2511 4.494350 TTGTCACGGTACTCAGTACTTC 57.506 45.455 14.75 0.00 38.85 3.01
1492 2512 5.464030 AATTGTCACGGTACTCAGTACTT 57.536 39.130 14.75 0.00 38.85 2.24
1493 2513 5.464030 AAATTGTCACGGTACTCAGTACT 57.536 39.130 14.75 0.00 38.85 2.73
1494 2514 6.535274 AAAAATTGTCACGGTACTCAGTAC 57.465 37.500 6.40 6.40 38.19 2.73
1532 2552 8.432359 GCACAAAATTAGTAGCCACAAATAAAC 58.568 33.333 0.00 0.00 0.00 2.01
1556 2576 2.112087 TGCGGTGTAAGCAAGGCA 59.888 55.556 0.00 0.00 42.18 4.75
1567 2588 4.226761 GGAACTCTGTTTTATTTGCGGTG 58.773 43.478 0.00 0.00 0.00 4.94
1723 4582 1.819632 AATGACATTCCGAGCGGCC 60.820 57.895 3.59 0.00 34.68 6.13
1762 4621 0.873312 CATGTGCTCCGTGGATCTCG 60.873 60.000 0.00 0.00 0.00 4.04
1918 4777 0.246635 ACGGAGACAACCTGATTCCG 59.753 55.000 16.32 16.32 45.20 4.30
1942 4801 2.809446 TCGAAGCAATCCATGTAGTCG 58.191 47.619 0.00 0.00 33.10 4.18
2266 7387 1.486211 AGAAGGTGGACCGGTCATAG 58.514 55.000 34.40 0.00 42.08 2.23
2375 7500 7.787028 TGCATACTACATAAGTGAACCACATA 58.213 34.615 0.00 0.00 39.39 2.29
2540 7677 6.994421 AAAATTTGAATCCACCCTTGTACT 57.006 33.333 0.00 0.00 0.00 2.73
2562 7699 9.255304 CTCGGGTTTATTTTCAAAATGAAGAAA 57.745 29.630 5.56 0.00 37.70 2.52
2583 7720 0.389391 ACAACCGCATATCTCTCGGG 59.611 55.000 4.89 0.00 46.78 5.14
2596 7733 4.155099 TGAAACCATTACATGCTACAACCG 59.845 41.667 0.00 0.00 0.00 4.44
2605 7742 6.748333 ATGAGTGAGTGAAACCATTACATG 57.252 37.500 0.00 0.00 37.80 3.21
2619 7756 7.756395 ATGAGAACAATTTGAATGAGTGAGT 57.244 32.000 2.79 0.00 0.00 3.41
2706 7844 1.918262 TCCTTCCTCTACCTACCGTCA 59.082 52.381 0.00 0.00 0.00 4.35
2709 7847 1.479021 CCCTCCTTCCTCTACCTACCG 60.479 61.905 0.00 0.00 0.00 4.02
2791 7931 5.858381 TGGAAGAAATATGGGAATCGAGAG 58.142 41.667 0.00 0.00 0.00 3.20
2817 7957 9.778993 CAATGTTCAAGAAATAATTGATCGAGT 57.221 29.630 0.00 0.00 36.60 4.18
2828 7968 7.324935 AGCAATGCATCAATGTTCAAGAAATA 58.675 30.769 8.35 0.00 0.00 1.40
2905 8045 1.097547 CAATGGTCGGTGCATCCTCC 61.098 60.000 0.00 0.00 0.00 4.30
3034 8175 6.636454 ATCCTCTCTAGGTCTATCTCGATT 57.364 41.667 0.00 0.00 44.09 3.34
3227 8368 2.489938 TTGATTTGAAGGAGGACCGG 57.510 50.000 0.00 0.00 41.83 5.28
3228 8369 3.412386 ACTTTGATTTGAAGGAGGACCG 58.588 45.455 0.00 0.00 41.83 4.79
3249 8390 7.915293 TGCGTTTATAAGAGAGAAATTGGAA 57.085 32.000 0.00 0.00 0.00 3.53
3250 8391 7.389330 TGTTGCGTTTATAAGAGAGAAATTGGA 59.611 33.333 0.00 0.00 0.00 3.53
3252 8393 9.214953 GATGTTGCGTTTATAAGAGAGAAATTG 57.785 33.333 0.00 0.00 0.00 2.32
3253 8394 8.946085 TGATGTTGCGTTTATAAGAGAGAAATT 58.054 29.630 0.00 0.00 0.00 1.82
3258 8399 7.848051 GTGAATGATGTTGCGTTTATAAGAGAG 59.152 37.037 0.00 0.00 0.00 3.20
3266 8407 5.175090 TGTTGTGAATGATGTTGCGTTTA 57.825 34.783 0.00 0.00 0.00 2.01
3267 8408 4.039151 TGTTGTGAATGATGTTGCGTTT 57.961 36.364 0.00 0.00 0.00 3.60
3268 8409 3.066621 ACTGTTGTGAATGATGTTGCGTT 59.933 39.130 0.00 0.00 0.00 4.84
3269 8410 2.618241 ACTGTTGTGAATGATGTTGCGT 59.382 40.909 0.00 0.00 0.00 5.24
3270 8411 3.272439 ACTGTTGTGAATGATGTTGCG 57.728 42.857 0.00 0.00 0.00 4.85
3271 8412 6.437928 TCTTAACTGTTGTGAATGATGTTGC 58.562 36.000 2.69 0.00 0.00 4.17
3272 8413 8.291740 TCATCTTAACTGTTGTGAATGATGTTG 58.708 33.333 2.69 0.00 32.53 3.33
3273 8414 8.394971 TCATCTTAACTGTTGTGAATGATGTT 57.605 30.769 2.69 0.00 32.53 2.71
3274 8415 7.984422 TCATCTTAACTGTTGTGAATGATGT 57.016 32.000 2.69 0.00 32.53 3.06
3280 8421 7.984422 ATGACATCATCTTAACTGTTGTGAA 57.016 32.000 2.69 0.00 29.15 3.18
3286 8427 8.798859 AGCTAAAATGACATCATCTTAACTGT 57.201 30.769 0.00 0.00 35.10 3.55
3334 8475 1.860676 GTCAGTACTGGTTGCGAACA 58.139 50.000 22.48 0.00 0.00 3.18
3335 8476 0.782384 CGTCAGTACTGGTTGCGAAC 59.218 55.000 22.48 10.36 0.00 3.95
3347 8488 1.372499 GCAAGCGGACACGTCAGTA 60.372 57.895 0.00 0.00 43.45 2.74
3351 8492 1.782028 AAAAGGCAAGCGGACACGTC 61.782 55.000 0.00 0.00 43.45 4.34
3355 8496 0.249953 TCGTAAAAGGCAAGCGGACA 60.250 50.000 0.00 0.00 0.00 4.02
3356 8497 1.084289 ATCGTAAAAGGCAAGCGGAC 58.916 50.000 0.00 0.00 0.00 4.79
3388 8529 1.122632 TGGGTACAAACGGCTCCAGA 61.123 55.000 0.00 0.00 0.00 3.86
3447 8588 0.832983 AACACCTGTAGGGCGTGGTA 60.833 55.000 2.53 0.00 40.27 3.25
3453 8594 1.079336 GACCGAACACCTGTAGGGC 60.079 63.158 2.53 0.00 40.27 5.19


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

AutoCloner maintained by Alex Coulton.