Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001827.1 Hibiscus syriacus cultivar Beakdansim tig00003695_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62958
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Found at i:634 original size:2 final size:2
Alignment explanation
Indices: 627--670 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
617 CATATCAGTG
627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
669 AT
1 AT
671 TTGTTAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:821 original size:13 final size:13
Alignment explanation
Indices: 803--829 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
793 CAGTGATTAC
803 TATATCATCAACA
1 TATATCATCAACA
816 TATATCATCAACA
1 TATATCATCAACA
829 T
1 T
830 GACCTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (13 bp):
TATATCATCAACA
Found at i:1678 original size:33 final size:33
Alignment explanation
Indices: 1598--1740 Score: 155
Period size: 32 Copynumber: 4.4 Consensus size: 33
1588 GGGGGATTGA
* * *
1598 AGTGACTGAAGTGGAGATGGAGTTTGAGATGGT
1 AGTGATTGAAGTGGAGATGGAATATGAGATGGT
*
1631 AGTGA-TGAAGTGGAGATGTAATATGAGATGGT
1 AGTGATTGAAGTGGAGATGGAATATGAGATGGT
*
1663 AGTGATTGAAGTGGAGATGGAATATGAGACGGT
1 AGTGATTGAAGTGGAGATGGAATATGAGATGGT
* * * * * **
1696 GGT-AATGAAGTGAAGATGGATTATAAGATAAT
1 AGTGATTGAAGTGGAGATGGAATATGAGATGGT
*
1728 TGTGATTGAAGTG
1 AGTGATTGAAGTG
1741 ATTGCAGTAG
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 53 0.57
33 40 0.43
ACGTcount: A:0.34, C:0.01, G:0.37, T:0.28
Consensus pattern (33 bp):
AGTGATTGAAGTGGAGATGGAATATGAGATGGT
Found at i:1679 original size:65 final size:65
Alignment explanation
Indices: 1598--1740 Score: 169
Period size: 65 Copynumber: 2.2 Consensus size: 65
1588 GGGGGATTGA
* * * * * * * * **
1598 AGTGACTGAAGTGGAGATGGAGTTTGAGATGGTAGTGATGAAGTGGAGATGTAATATGAGATGGT
1 AGTGATTGAAGTGGAGATGGAATATGAGACGGTAGTAATGAAGTGAAGATGGAATATAAGATAAT
* *
1663 AGTGATTGAAGTGGAGATGGAATATGAGACGGTGGTAATGAAGTGAAGATGGATTATAAGATAAT
1 AGTGATTGAAGTGGAGATGGAATATGAGACGGTAGTAATGAAGTGAAGATGGAATATAAGATAAT
*
1728 TGTGATTGAAGTG
1 AGTGATTGAAGTG
1741 ATTGCAGTAG
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.34, C:0.01, G:0.37, T:0.28
Consensus pattern (65 bp):
AGTGATTGAAGTGGAGATGGAATATGAGACGGTAGTAATGAAGTGAAGATGGAATATAAGATAAT
Found at i:1815 original size:42 final size:42
Alignment explanation
Indices: 1756--1892 Score: 138
Period size: 42 Copynumber: 3.3 Consensus size: 42
1746 AGTAGAGGAT
* *
1756 TATGAGTTTG-TGATGATGAAAGTGATTGAATTGGAGATGGA
1 TATGAGATTGATGGTGATGAAAGTGATTGAATTGGAGATGGA
* *
1797 GTATGAGATT-ATGGTGATGAAAGTGATTGAAGTGTAGATGGA
1 -TATGAGATTGATGGTGATGAAAGTGATTGAATTGGAGATGGA
* ** * * *
1839 TATGAG-TTGGTGGTGATGAAAGACATTGACTTAGAGATGAAA
1 TATGAGATTGATGGTGATGAAAGTGATTGAATTGGAGATG-GA
1881 TATGAGA-TGATG
1 TATGAGATTGATG
1893 ATGAAGCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.03
41 29 0.37
42 47 0.60
ACGTcount: A:0.34, C:0.01, G:0.34, T:0.31
Consensus pattern (42 bp):
TATGAGATTGATGGTGATGAAAGTGATTGAATTGGAGATGGA
Found at i:1859 original size:83 final size:81
Alignment explanation
Indices: 1709--1888 Score: 193
Period size: 83 Copynumber: 2.2 Consensus size: 81
1699 AATGAAGTGA
* * * * *
1709 AGATGGATTATAAGATAATTGTGATTGAAGTGATTGCAGTAGAGGATTATGAGTTTGTGATGATG
1 AGATGGAATATGAGATAATGGTGATTGAAGTGATTGAAGTAGAGGATTATGAGTTGGTGATGATG
** *
1774 AAAGTGATTGAATTGG
66 AAAGACATTGAATTAG
* * *
1790 AGATGGAGTATGAGATTATGGTGA-TGAAAGTGATTGAAGTGTAGATGGA-TATGAGTTGGTGGT
1 AGATGGAATATGAGATAATGGTGATTG-AAGTGATTGAA--GTAGA-GGATTATGAGTTGGTGAT
*
1853 GATGAAAGACATTGACTTAG
62 GATGAAAGACATTGAATTAG
*
1873 AGATGAAATATGAGAT
1 AGATGGAATATGAGAT
1889 GATGATGAAG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
80 2 0.02
81 30 0.37
83 47 0.57
84 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (81 bp):
AGATGGAATATGAGATAATGGTGATTGAAGTGATTGAAGTAGAGGATTATGAGTTGGTGATGATG
AAAGACATTGAATTAG
Found at i:1867 original size:41 final size:41
Alignment explanation
Indices: 1747--1860 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 41
1737 AGTGATTGCA
* * *
1747 GTAGA-GGATTATGAGTTTGTGATGATGAAAGTGATTGAATT
1 GTAGATGGAGTATGAG-TTGTGGTGATGAAAGTGATTGAAGT
* *
1788 GGAGATGGAGTATGAGATTATGGTGATGAAAGTGATTGAAGT
1 GTAGATGGAGTATGAG-TTGTGGTGATGAAAGTGATTGAAGT
1830 GTAGATGGA-TATGAGTTGGTGGTGATGAAAG
1 GTAGATGGAGTATGAGTT-GTGGTGATGAAAG
1861 ACATTGACTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 22 0.35
42 39 0.62
ACGTcount: A:0.32, C:0.00, G:0.37, T:0.32
Consensus pattern (41 bp):
GTAGATGGAGTATGAGTTGTGGTGATGAAAGTGATTGAAGT
Found at i:16434 original size:30 final size:30
Alignment explanation
Indices: 16400--16458 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
16390 ACACCTAACT
16400 TTTGAAAATTACCCTTTTGGTCCCTAAACA
1 TTTGAAAATTACCCTTTTGGTCCCTAAACA
*
16430 TTTGAAAATTACCCTTTTGGTCCTTAAAC
1 TTTGAAAATTACCCTTTTGGTCCCTAAAC
16459 TTTTCCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (30 bp):
TTTGAAAATTACCCTTTTGGTCCCTAAACA
Found at i:17506 original size:47 final size:45
Alignment explanation
Indices: 17415--17510 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 45
17405 AAGCCACCTG
17415 TTGTTAAAAATCTAACAAAGGAGTGACGTGTTAGTTAACAGGAAT
1 TTGTTAAAAATCTAACAAAGGAGTGACGTGTTAGTTAACAGGAAT
17460 TTGTTAAAAATCTAACAAA-GAGTGACAACGTGTTAGTTAACAGGAAT
1 TTGTTAAAAATCTAACAAAGGAGTG---ACGTGTTAGTTAACAGGAAT
17507 TTGT
1 TTGT
17511 ACATTTACAC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
44 5 0.10
45 19 0.40
47 24 0.50
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
TTGTTAAAAATCTAACAAAGGAGTGACGTGTTAGTTAACAGGAAT
Found at i:19022 original size:3 final size:3
Alignment explanation
Indices: 19014--19047 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19004 TGTCATTAAC
*
19014 TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
19048 CAACTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21083 original size:29 final size:28
Alignment explanation
Indices: 21040--21108 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
21030 GTAAAAGATT
*
21040 AAATACTTTAAGTACCT-ATTTTGATTAAA
1 AAATAATTTAAGTA-CTGATTTTGA-TAAA
*
21069 AAATAATTTAGGTACTGATTTTGATAAA
1 AAATAATTTAAGTACTGATTTTGATAAA
21097 AAA-AA-TTAAGTA
1 AAATAATTTAAGTA
21109 ATTAAACGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.17
27 2 0.06
28 9 0.25
29 19 0.53
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (28 bp):
AAATAATTTAAGTACTGATTTTGATAAA
Found at i:21163 original size:22 final size:22
Alignment explanation
Indices: 21131--21173 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21121 ACATGTCATA
21131 ATTTTTGTGATATTATAAGAAC
1 ATTTTTGTGATATTATAAGAAC
*
21153 ATTTTTTTGATATTATAAGAA
1 ATTTTTGTGATATTATAAGAA
21174 TATTAATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTTTGTGATATTATAAGAAC
Found at i:21605 original size:28 final size:29
Alignment explanation
Indices: 21541--21617 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 29
21531 AAAATTTCAT
* *
21541 ATATTAGTTTTAAATAAAATAAAATTTAA
1 ATATTAATTTTAAATAAAATAAAATCTAA
* * * *
21570 ATGTTAATTTTAAA-AATATTAAATCTAG
1 ATATTAATTTTAAATAAAATAAAATCTAA
21598 ATATTAATTTATAAATAAAA
1 ATATTAATTT-TAAATAAAA
21618 ATTTGTTTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
28 19 0.50
29 16 0.42
30 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (29 bp):
ATATTAATTTTAAATAAAATAAAATCTAA
Found at i:22815 original size:139 final size:139
Alignment explanation
Indices: 22565--22817 Score: 463
Period size: 139 Copynumber: 1.8 Consensus size: 139
22555 GATATTACTA
*
22565 TGTACACTTAAATCCCGAAGATTCGAGTGTCACACGGAATTAATAAAGTAACTAACAAATTTTTT
1 TGTACACTTAAATCCCGAAGATTCGAGTGTCACACGGAATTAATAAAGTAACAAACAAATTTTTT
22630 ATTGAAATCATTTTGAACTTTTAAAGCGTTTATTCTAAGTATGAAAACAGAGAATAACATGGATT
66 ATTGAAATCATTTTGAACTTTTAAAGCGTTTATTCTAAGTATGAAAACAGAGAATAACATGGATT
22695 AGTTGACTT
131 AGTTGACTT
* *
22704 TGTACACTTAAATCCCGAAGATTCGAGTGTCACATGGAATTAATAAAGTGAA-AAACAATTTTTT
1 TGTACACTTAAATCCCGAAGATTCGAGTGTCACACGGAATTAATAAAGT-AACAAACAAATTTTT
22768 TATTGAAATCATTTTGAACTTTTAAAGCGTTTATTCTAAGTATGAAAACA
65 TATTGAAATCATTTTGAACTTTTAAAGCGTTTATTCTAAGTATGAAAACA
22818 TAATACTTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
139 108 0.98
140 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (139 bp):
TGTACACTTAAATCCCGAAGATTCGAGTGTCACACGGAATTAATAAAGTAACAAACAAATTTTTT
ATTGAAATCATTTTGAACTTTTAAAGCGTTTATTCTAAGTATGAAAACAGAGAATAACATGGATT
AGTTGACTT
Found at i:24375 original size:21 final size:21
Alignment explanation
Indices: 24351--24395 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
24341 TCTTATATGG
*
24351 ATACCAATTCATCTAGTATAA
1 ATACCAATTCATATAGTATAA
*
24372 ATACCAATTCATATAGTATCA
1 ATACCAATTCATATAGTATAA
24393 ATA
1 ATA
24396 TTGACACTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (21 bp):
ATACCAATTCATATAGTATAA
Found at i:25455 original size:21 final size:22
Alignment explanation
Indices: 25429--25472 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25419 CGAGTCAAAG
25429 ATGCACCTAAGTG-C-TTACCAC
1 ATGCA-CTAAGTGTCATTACCAC
*
25450 ATGCACTGAGTGTCATTACCAC
1 ATGCACTAAGTGTCATTACCAC
25472 A
1 A
25473 ATGCTGCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.25
Consensus pattern (22 bp):
ATGCACTAAGTGTCATTACCAC
Found at i:28172 original size:69 final size:67
Alignment explanation
Indices: 27967--28223 Score: 239
Period size: 69 Copynumber: 3.8 Consensus size: 67
27957 TAGGAATTGT
* * * * *
27967 TCACCCGGAATAAATATGATTAGATGCTCTCGTGCGAGTTACCCTGATCCTTCGGGGCATCCGT-
1 TCACCCGGAATAAATATGATTAGGTGCTCTCGTGTGAGTCACCCTAATCCTTTGGGGC-TCCGTC
*
28031 GTG
65 GAG
* * * * *
28034 TCACCCGGAATAAATATAATTAGGTACT-TCTGTGTAAGTCACCCTAATCGTTTGGAGCTCCCGT
1 TCACCCGGAATAAATATGATTAGGTGCTCTC-GTGTGAGTCACCCTAATCCTTTGGGGCT-CCGT
28098 GCGAG
64 -CGAG
* * * *
28103 TCACCCAGAATAAATATGATTAGGTGCTCTAGTGTGAGTCACCGTAATCCTTTGGGGCTCTTGTA
1 TCACCCGGAATAAATATGATTAGGTGCTCTCGTGTGAGTCACCCTAATCCTTTGGGGCTC-CGT-
28168 CGAG
64 CGAG
** * * * * * *
28172 TCACTTGAAATAAATATGATTAGTTTCTCCCGTCTGAGTCACCGTAATCCTT
1 TCACCCGGAATAAATATGATTAGGTGCTCTCGTGTGAGTCACCCTAATCCTT
28224 CAAGGCTATC
Statistics
Matches: 154, Mismatches: 30, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
66 3 0.02
67 49 0.32
68 1 0.01
69 100 0.65
70 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (67 bp):
TCACCCGGAATAAATATGATTAGGTGCTCTCGTGTGAGTCACCCTAATCCTTTGGGGCTCCGTCG
AG
Found at i:28253 original size:69 final size:69
Alignment explanation
Indices: 28110--28262 Score: 164
Period size: 69 Copynumber: 2.2 Consensus size: 69
28100 GAGTCACCCA
* * *** * *
28110 GAATAAATATGATTAGGTGCTCTAGTGTGAGTCACCGTAATCCTTTGGGGCTCTTGTACGAGTCA
1 GAATAAATATGATTAGGTGCTCCAGTCTGAGTCACCGTAATCCTTCAAGGCTATCGTACGAGTCA
28175 CTTG
66 CTTG
* * * * * *
28179 AAATAAATATGATTAGTTTCTCCCGTCTGAGTCACCGTAATCCTTCAAGGCTATCGTACTAGTTA
1 GAATAAATATGATTAGGTGCTCCAGTCTGAGTCACCGTAATCCTTCAAGGCTATCGTACGAGTCA
28244 -TCTG
66 CT-TG
*
28248 GAATAATTATGATTA
1 GAATAAATATGATTA
28263 AAATTAGTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
68 1 0.01
69 67 0.99
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (69 bp):
GAATAAATATGATTAGGTGCTCCAGTCTGAGTCACCGTAATCCTTCAAGGCTATCGTACGAGTCA
CTTG
Found at i:29806 original size:7 final size:7
Alignment explanation
Indices: 29794--29877 Score: 152
Period size: 7 Copynumber: 12.1 Consensus size: 7
29784 CTTTAGAAGG
29794 GAAAGAA
1 GAAAGAA
29801 GAAAGAA
1 GAAAGAA
29808 GAAAGAA
1 GAAAGAA
29815 GAAAGAA
1 GAAAGAA
*
29822 GAAACAA
1 GAAAGAA
29829 GAAAGAA
1 GAAAGAA
29836 GAAAGAA
1 GAAAGAA
29843 GAAAGAA
1 GAAAGAA
29850 GAAAGAA
1 GAAAGAA
29857 GAAAGAA
1 GAAAGAA
29864 GAAAGAA
1 GAAAGAA
29871 G-AAGAA
1 GAAAGAA
29877 G
1 G
29878 GGAAAAACCT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
6 6 0.08
7 69 0.92
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAAGAA
Found at i:35956 original size:65 final size:65
Alignment explanation
Indices: 35885--36008 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 65
35875 CCCATTCAAC
* * ** *
35885 AGGTACCGATACCCTCTCAAACGAAAAGAATTACAGAATGTAATGAGGGTACCGATACCCCAGTT
1 AGGTACCGATACCCTCTCAAACGAAAAAAATAACAGAATACAATAAGGGTACCGATACCCCAGTT
* ** *
35950 AGGTACCGATGCCCTCTTGAACGAAAAAAATAACAGAATACAGTAAGGGTACCGATACC
1 AGGTACCGATACCCTCTCAAACGAAAAAAATAACAGAATACAATAAGGGTACCGATACC
36009 TCATAGGGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
65 50 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (65 bp):
AGGTACCGATACCCTCTCAAACGAAAAAAATAACAGAATACAATAAGGGTACCGATACCCCAGTT
Found at i:36739 original size:2 final size:2
Alignment explanation
Indices: 36732--36763 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
36722 CATATAAGTG
36732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36764 TTTTTTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37291 original size:30 final size:30
Alignment explanation
Indices: 37255--37311 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
37245 AGAGTCGAGG
* *
37255 GTTACCTATGTCCTTCGGGACATATGGGCA
1 GTTACCTATGTCATTCGGAACATATGGGCA
*
37285 GTTACCTATGTTATTCGGAACATATGG
1 GTTACCTATGTCATTCGGAACATATGG
37312 ATAGAGGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (30 bp):
GTTACCTATGTCATTCGGAACATATGGGCA
Found at i:37355 original size:22 final size:22
Alignment explanation
Indices: 37328--37374 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
37318 GACCCTCGAT
*
37328 ACATATACAGTGGTGCTTCGGG
1 ACATATACAGTGGTCCTTCGGG
*
37350 ACATATATAGTGGTCCTTCGGG
1 ACATATACAGTGGTCCTTCGGG
37372 ACA
1 ACA
37375 AATAGATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (22 bp):
ACATATACAGTGGTCCTTCGGG
Found at i:41728 original size:2 final size:2
Alignment explanation
Indices: 41721--41768 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
41711 CATAGAAGTG
41721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41763 AT AT AT
1 AT AT AT
41769 TCAAGTATGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42382 original size:22 final size:22
Alignment explanation
Indices: 42313--42393 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
42303 ATATTGATAG
* *
42313 TGGTCCCTCGGGACATATACAA
1 TGGTCCTTCGAGACATATACAA
* *
42335 TGGTCATTCGAGAAATATACAA
1 TGGTCCTTCGAGACATATACAA
* *
42357 TGGTCCTTCGAGACATATATAG
1 TGGTCCTTCGAGACATATACAA
*
42379 TGGTCCTTCGGGACA
1 TGGTCCTTCGAGACA
42394 AATGCATAGG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (22 bp):
TGGTCCTTCGAGACATATACAA
Found at i:45786 original size:13 final size:13
Alignment explanation
Indices: 45768--45809 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
45758 CTTTCACAAA
45768 TGCTTAGACAGGT
1 TGCTTAGACAGGT
* *
45781 TGCTTAAACAGAT
1 TGCTTAGACAGGT
*
45794 TGCCTAGACAGGT
1 TGCTTAGACAGGT
45807 TGC
1 TGC
45810 CTTCCTATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (13 bp):
TGCTTAGACAGGT
Found at i:51336 original size:16 final size:16
Alignment explanation
Indices: 51294--51336 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
51284 TGACTTGATC
*
51294 TGATATTTACTTAACT
1 TGATATTTACCTAACT
51310 TGATATTTACCTAACT
1 TGATATTTACCTAACT
51326 T-ATATATTACC
1 TGATAT-TTACC
51337 ATTGATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.33, C:0.16, G:0.05, T:0.47
Consensus pattern (16 bp):
TGATATTTACCTAACT
Found at i:51488 original size:14 final size:14
Alignment explanation
Indices: 51469--51501 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
51459 TATTATATTA
51469 ATTATGATTCTTAT
1 ATTATGATTCTTAT
51483 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
51497 GTTAT
1 ATTAT
51502 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:52175 original size:15 final size:15
Alignment explanation
Indices: 52138--52176 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
52128 TAATAGTTGC
*
52138 ATTGCATATCATATA
1 ATTGCATATCAAATA
* *
52153 GTTTCATATCAAATA
1 ATTGCATATCAAATA
52168 ATTGCATAT
1 ATTGCATAT
52177 TATATTTGAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTGCATATCAAATA
Found at i:52194 original size:27 final size:29
Alignment explanation
Indices: 52138--52197 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
52128 TAATAGTTGC
52138 ATTGCATATCATATAGTTTCATATCAAATA
1 ATTGCATAT-ATATAGTTTCATATCAAATA
* *
52168 ATTGCATAT-TATA-TTTGATATTAAATA
1 ATTGCATATATATAGTTTCATATCAAATA
52195 ATT
1 ATT
52198 AGTATGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 15 0.54
28 4 0.14
30 9 0.32
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (29 bp):
ATTGCATATATATAGTTTCATATCAAATA
Found at i:52991 original size:16 final size:16
Alignment explanation
Indices: 52970--53018 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
52960 TAAATATCAA
52970 ATATAATATATAGTTT
1 ATATAATATATAGTTT
52986 ATATAA-ACTATAGTTT
1 ATATAATA-TATAGTTT
*
53002 -T-T-ATATATAGTTC
1 ATATAATATATAGTTT
53015 ATAT
1 ATAT
53019 TAATTAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 3 0.11
16 14 0.50
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (16 bp):
ATATAATATATAGTTT
Found at i:53033 original size:29 final size:30
Alignment explanation
Indices: 52973--53043 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
52963 ATATCAAATA
*
52973 TAATATATAGTTTATATAAACTATAGT-TT
1 TAATATATAGTTCATATAAACTATAGTATT
* * *
53002 TTATATATAGTTCATATTAATTA-ATGTATT
1 TAATATATAGTTCATATAAACTATA-GTATT
53032 TAACTATATAGT
1 TAA-TATATAGT
53044 ATTCATACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.03
29 21 0.62
30 4 0.12
31 8 0.24
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (30 bp):
TAATATATAGTTCATATAAACTATAGTATT
Found at i:53087 original size:15 final size:15
Alignment explanation
Indices: 53072--53106 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53062 TACTTTGAAT
53072 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
53086 TTATATAAGTATAAA
1 TTATATAAGTATAAA
*
53101 CTATAT
1 TTATAT
53107 TATATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:53105 original size:27 final size:27
Alignment explanation
Indices: 53075--53172 Score: 117
Period size: 27 Copynumber: 3.7 Consensus size: 27
53065 TTTGAATTTA
* *
53075 TATAGTATAAATTATATAAGTATAAAC
1 TATAGTATATATTATATAAATATAAAC
* *
53102 TATATTATATATTATATAAATATCAAC
1 TATAGTATATATTATATAAATATAAAC
* **
53129 TATAATATATAGCATATAAATATAAAC
1 TATAGTATATATTATATAAATATAAAC
*
53156 TATAGTTTATA-TATATA
1 TATAGTATATATTATATA
53173 GTTTATACTA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
26 5 0.08
27 55 0.92
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (27 bp):
TATAGTATATATTATATAAATATAAAC
Found at i:53172 original size:13 final size:14
Alignment explanation
Indices: 53156--53186 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
53146 AAATATAAAC
53156 TATAGTTTATA-TA
1 TATAGTTTATACTA
53169 TATAGTTTATACTA
1 TATAGTTTATACTA
53183 TATA
1 TATA
53187 AATAGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (14 bp):
TATAGTTTATACTA
Found at i:53199 original size:20 final size:18
Alignment explanation
Indices: 53163--53197 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53153 AACTATAGTT
*
53163 TATATATATAGTTTATAC
1 TATATAAATAGTTTATAC
53181 TATATAAATAGTTTATA
1 TATATAAATAGTTTATA
53198 TAGTTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
TATATAAATAGTTTATAC
Found at i:53366 original size:29 final size:30
Alignment explanation
Indices: 53311--53385 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
53301 TATATAGTTT
* * *
53311 TTATATATAGTTCATATGTAAATTATATA-
1 TTATATATAGTTTATATATAAAGTATATAC
**
53340 TTATATATAGTTTATATATGTAGTATATAC
1 TTATATATAGTTTATATATAAAGTATATAC
*
53370 TATATAAATAGTTTAT
1 T-TATATATAGTTTAT
53386 TAATTAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 24 0.63
30 1 0.03
31 13 0.34
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (30 bp):
TTATATATAGTTTATATATAAAGTATATAC
Found at i:53414 original size:15 final size:15
Alignment explanation
Indices: 53394--53427 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53384 ATTAATTAAT
53394 GTATTCA-ACTATATA
1 GTATTCATAC-ATATA
53409 GTATTCATACATATA
1 GTATTCATACATATA
53424 GTAT
1 GTAT
53428 ATATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (15 bp):
GTATTCATACATATA
Found at i:53454 original size:15 final size:15
Alignment explanation
Indices: 53439--53473 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53429 TATTTTGAAT
53439 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
53453 TTATATAAGTATAAA
1 TTATATAAGTATAAA
*
53468 CTATAT
1 TTATAT
53474 TATATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:53569 original size:18 final size:17
Alignment explanation
Indices: 53528--53737 Score: 67
Period size: 18 Copynumber: 11.7 Consensus size: 17
53518 TCAACCATAG
53528 TATATAGTTTATATATA
1 TATATAGTTTATATATA
*
53545 AACTATAGTTTATATAGTTTA
1 TA-TATAGTTTATATA---TA
* *
53566 TATATAGTTCATAT-GA
1 TATATAGTTTATATATA
*
53582 -A-A-A--CTATATAGTA
1 TATATAGTTTATATA-TA
53595 TATATAGTTTATATACATAA
1 TATATAGTTTATAT--AT-A
* *
53615 TATATAGTATATAAATA
1 TATATAGTTTATATATA
*
53632 TCAACTATAGTATATAGTATA
1 T--A-TATAGTTTATA-TATA
* ** *
53653 TAAATA-TCAACTATAATT
1 TATATAGTTTA-TAT-ATA
53671 TATATAGTTTATATATA
1 TATATAGTTTATATATA
53688 TAGTATA-TACTGTATATATA
1 TA-TATAGT--T-TATATATA
* *
53708 TATGTAGTATATACTATA
1 TATATAGTTTATA-TATA
*
53726 TAAATAGTTTAT
1 TATATAGTTTAT
53738 TAATTAATGT
Statistics
Matches: 142, Mismatches: 24, Indels: 53
0.65 0.11 0.24
Matches are distributed among these distances:
11 4 0.03
13 2 0.01
14 2 0.01
15 2 0.01
16 2 0.01
17 15 0.11
18 52 0.37
19 9 0.06
20 47 0.33
21 7 0.05
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (17 bp):
TATATAGTTTATATATA
Found at i:53570 original size:38 final size:39
Alignment explanation
Indices: 53528--53609 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
53518 TCAACCATAG
* *
53528 TATATAGTTTATAT-ATAAAC-TATAGTTTATATAGTTTA
1 TATATAGTTCATATGA-AAACATATAGTATATATAGTTTA
53566 TATATAGTTCATATGAAAACTATATAGTATATATAGTTTA
1 TATATAGTTCATATGAAAAC-ATATAGTATATATAGTTTA
53606 TATA
1 TATA
53610 CATAATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 17 0.44
39 1 0.03
40 21 0.54
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (39 bp):
TATATAGTTCATATGAAAACATATAGTATATATAGTTTA
Found at i:53579 original size:9 final size:9
Alignment explanation
Indices: 53528--53569 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
53518 TCAACCATAG
53528 TATATAGTT
1 TATATAGTT
*
53537 TATATA-TA
1 TATATAGTT
*
53545 AACTATAGTT
1 TA-TATAGTT
53555 TATATAGTT
1 TATATAGTT
53564 TATATA
1 TATATA
53570 TAGTTCATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 23 0.85
10 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.50
Consensus pattern (9 bp):
TATATAGTT
Found at i:53609 original size:20 final size:20
Alignment explanation
Indices: 53528--53927 Score: 86
Period size: 20 Copynumber: 20.1 Consensus size: 20
53518 TCAACCATAG
53528 TATATAGT-T-TATA-TATA
1 TATATAGTATATATAGTATA
* * *
53545 AACTATAGTTTATATAGTTTA
1 TA-TATAGTATATATAGTATA
* *
53566 TATATAGT-TCATAT-GAAAA
1 TATATAGTAT-ATATAGTATA
*
53585 CTATATAGTATATATAGTTTA
1 -TATATAGTATATATAGTATA
*
53606 TATACA-TAATATATAGTATA
1 TATATAGT-ATATATAGTATA
* *
53626 TA-A-A-TAT-CA-ACTATA
1 TATATAGTATATATAGTATA
*
53641 GTATATAGTATATA-AATATCA
1 -TATATAGTATATATAGTAT-A
* *
53662 -ACTATAATTTATATAGTTTATA
1 TA-TATAGTATATATAG--TATA
53684 TATATAGTATATACT-GTATA
1 TATATAGTATATA-TAGTATA
*
53704 TATATATGTAGTATATACTATA
1 TATATA-GTA-TATATAGTATA
* * *
53726 TAAATAGTTTAT-TAAT-TA
1 TATATAGTATATATAGTATA
* *
53744 -ATGTATTCAACTATATAGTATTCA
1 TATATAGT--A-TATATAGTA-T-A
* * *
53768 TAAATATAGTATATACTTTGAATT
1 T--ATATAGTATATA--TAGTATA
53792 TATATAGTATA-A-A-T-TA
1 TATATAGTATATATAGTATA
*
53808 TATA-AGTATA-A-ACTATA
1 TATATAGTATATATAGTATA
*
53825 TTATATAGTATATA-AATATCA
1 -TATATAGTATATATAGTAT-A
* *
53846 -ACTATAGTATATAGT-TTTTA
1 TA-TATAGTATATA-TAGTATA
*
53866 TATATAGT-TCATAT-GTAAA
1 TATATAGTAT-ATATAGTATA
*
53885 CTATATAGTATATATAGTTTA
1 -TATATAGTATATATAGTATA
*
53906 TATAT-GTAGTATATACTATA
1 TATATAGTA-TATATAGTATA
53926 TA
1 TA
53928 AACAGTTTAT
Statistics
Matches: 285, Mismatches: 47, Indels: 99
0.66 0.11 0.23
Matches are distributed among these distances:
15 13 0.05
16 9 0.03
17 10 0.04
18 15 0.05
19 27 0.09
20 128 0.45
21 27 0.09
22 34 0.12
23 6 0.02
24 6 0.02
25 2 0.01
26 3 0.01
27 5 0.02
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (20 bp):
TATATAGTATATATAGTATA
Found at i:53674 original size:27 final size:27
Alignment explanation
Indices: 53454--53688 Score: 174
Period size: 27 Copynumber: 8.4 Consensus size: 27
53444 TAGTATAAAT
* * *
53454 TATATAAGTATAAACTATATTATATAG
1 TATATAAATATCAACTATAATATATAG
*
53481 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATCAACTATAATATATAG
* *
53508 TATATAAATATCAACCATAGTATATAG
1 TATATAAATATCAACTATAATATATAG
* * *
53535 T-T-TATATATAAACTATAGTTTATATAG
1 TATATAAATATCAACTATA--ATATATAG
* * *
53562 TTTATATATAGTTCATA-TGAAAACTATATAG
1 TATATAAATA--TCA-ACT-ATAA-TATATAG
*
53593 TATATATAGTTTAT-ATAC-ATAATATATAG
1 TATATA-A--ATATCA-ACTATAATATATAG
*
53622 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATCAACTATAATATATAG
53649 TATATAAATATCAACTATAATTTATATAG
1 TATATAAATATCAACTATAA--TATATAG
* *
53678 TTTATATATAT
1 TATATAAATAT
53689 AGTATATACT
Statistics
Matches: 171, Mismatches: 20, Indels: 32
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.07
26 6 0.04
27 89 0.52
28 2 0.01
29 35 0.20
30 3 0.02
31 18 0.11
32 4 0.02
34 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.42
Consensus pattern (27 bp):
TATATAAATATCAACTATAATATATAG
Found at i:53715 original size:24 final size:24
Alignment explanation
Indices: 53586--53727 Score: 80
Period size: 24 Copynumber: 5.8 Consensus size: 24
53576 ATATGAAAAC
53586 TATATAGTATATA-TAGT-T-TATA
1 TATATAGTATATACTA-TATATATA
* * * *
53608 TACATAATATATAGTATATAAATA
1 TATATAGTATATACTATATATATA
* *
53632 TCAACTATAGTATATAGTATATAAATA
1 T--A-TATAGTATATACTATATATATA
* *
53659 TCA-ACTA-TAATTTA-TATAGTTTATA
1 T-ATA-TAGT-ATATACTATA-TATATA
*
53684 TATATAGTATATACTGTATATATA
1 TATATAGTATATACTATATATATA
*
53708 TATGTAGTATATACTATATA
1 TATATAGTATATACTATATA
53728 AATAGTTTAT
Statistics
Matches: 94, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
22 12 0.13
23 3 0.03
24 40 0.43
25 16 0.17
26 2 0.02
27 21 0.22
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (24 bp):
TATATAGTATATACTATATATATA
Found at i:53806 original size:15 final size:15
Alignment explanation
Indices: 53791--53825 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
53781 TACTTTGAAT
53791 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
53805 TTATATAAGTATAAA
1 TTATATAAGTATAAA
*
53820 CTATAT
1 TTATAT
53826 TATATAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:53870 original size:27 final size:27
Alignment explanation
Indices: 53794--53860 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
53784 TTTGAATTTA
* * * *
53794 TATAGTATAAATTATATAAGTATAAAC
1 TATAGTATATAGTATATAAATATCAAC
*
53821 TATATTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
53848 TATAGTATATAGT
1 TATAGTATATAGT
53861 TTTTATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.40
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:53915 original size:13 final size:13
Alignment explanation
Indices: 53821--53927 Score: 51
Period size: 13 Copynumber: 7.9 Consensus size: 13
53811 AAGTATAAAC
53821 TATAT-TATATAG
1 TATATATATATAG
*
53833 TATATAAATATCA-
1 TATATATATAT-AG
53846 -ACTATAGTATATAG
1 TA-TATA-TATATAG
* *
53860 TTTTTATATATAG
1 TATATATATATAG
* *
53873 TTCATATGTAAACTA-
1 -T-ATATATATA-TAG
53888 TATAGTATATATAG
1 TATA-TATATATAG
* *
53902 TTTATATATGTAG
1 TATATATATATAG
53915 TATATACTATATA
1 TATATA-TATATA
53928 AACAGTTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
12 6 0.09
13 34 0.49
14 22 0.32
15 5 0.07
16 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (13 bp):
TATATATATATAG
Found at i:62511 original size:7 final size:7
Alignment explanation
Indices: 62482--62570 Score: 56
Period size: 7 Copynumber: 12.1 Consensus size: 7
62472 TTAATATAGA
62482 TTTTCTT
1 TTTTCTT
*
62489 TCTTCTT
1 TTTTCTT
*
62496 TCTTCTT
1 TTTTCTT
62503 TTTTCTT
1 TTTTCTT
*
62510 TTTTAATT
1 TTTT-CTT
62518 ATTATT-TT
1 -TT-TTCTT
*
62526 TATTC-T
1 TTTTCTT
*
62532 TTCTCTT
1 TTTTCTT
*
62539 TTTCCTT
1 TTTTCTT
62546 TTTTCTCT
1 TTTTCT-T
62554 TTTTCTAT
1 TTTTCT-T
62562 TTCTTCTT
1 TT-TTCTT
62570 T
1 T
62571 CACTTATTCT
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
6 6 0.09
7 35 0.54
8 16 0.25
9 6 0.09
10 2 0.03
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTT
Done.