Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004737.1 Hibiscus syriacus cultivar Beakdansim tig00010696_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: 105883
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3719 original size:22 final size:22
Alignment explanation
Indices: 3694--3751 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
3684 GGATCGCTTC
3694 GGTACGATGTACCATATAAATT
1 GGTACGATGTACCATATAAATT
3716 GGTACGATGTACCATATAAATT
1 GGTACGATGTACCATATAAATT
3738 GGTACGATGTACCA
1 GGTACGATGTACCA
3752 GTTTCTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (22 bp):
GGTACGATGTACCATATAAATT
Found at i:15621 original size:15 final size:14
Alignment explanation
Indices: 15598--15664 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
15588 TATCATTAAA
*
15598 TTAATTTATAAAAAT
1 TTAAATTAT-AAAAT
15613 TTAAATTATAAAAT
1 TTAAATTATAAAAT
* * *
15627 ATAAAATATATAAT
1 TTAAATTATAAAAT
15641 TATAAATTAGTTAAAAAT
1 T-TAAATTA--T-AAAAT
15659 TTAAAT
1 TTAAAT
15665 GTAATTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
14 16 0.39
15 14 0.34
17 6 0.15
18 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
TTAAATTATAAAAT
Found at i:16109 original size:17 final size:17
Alignment explanation
Indices: 16064--16119 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
16054 GAATGAATTG
*
16064 AAATAATATT-TTTATT
1 AAATAATTTTATTTATT
*
16080 AATATGATATTTATTTATT
1 AA-ATAAT-TTTATTTATT
16099 AAATAATTTTATATT-TT
1 AAATAATTTTAT-TTATT
16116 AAAT
1 AAAT
16120 TTGTACAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 2 0.06
17 15 0.45
18 8 0.24
19 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATAATTTTATTTATT
Found at i:19903 original size:35 final size:35
Alignment explanation
Indices: 19857--19957 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 35
19847 AACACAGTCA
**
19857 TCAATTACATTCTAAACCCCAAAATCCAAAATGTT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* * *
19892 TCAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* * *
19927 TCAATTACATGCTCAACCCC-AAATTCAAAAT
1 TCAATTACATTCTAAACCCCAAAATCCAAAAT
19958 CCATTCTCAA
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
34 8 0.15
35 47 0.85
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:23893 original size:6 final size:7
Alignment explanation
Indices: 23877--23904 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
23867 TTGAAATTTA
23877 TTTTAAT
1 TTTTAAT
23884 TTTTAAT
1 TTTTAAT
23891 TTTTAAT
1 TTTTAAT
23898 TTTTAAT
1 TTTTAAT
23905 AAAAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTAAT
Found at i:25470 original size:23 final size:23
Alignment explanation
Indices: 25403--25471 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
25393 CACCACAGCT
* *
25403 CGTATAATTGCACCGAAGTGCAA
1 CGTAGAATTGCACCGAAGTGCCA
* *
25426 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
25449 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
25472 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:28899 original size:14 final size:16
Alignment explanation
Indices: 28868--28905 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
28858 AATACTATCG
28868 ATAATATTTCTAAAAT
1 ATAATATTTCTAAAAT
*
28884 ATAAT-TTT-TAAGAT
1 ATAATATTTCTAAAAT
28898 ATAATATT
1 ATAATATT
28906 AATAATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 10 0.50
15 5 0.25
16 5 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAATATTTCTAAAAT
Found at i:33590 original size:14 final size:14
Alignment explanation
Indices: 33571--33598 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33561 TAACAGACTT
33571 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
33585 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
33599 TGGTATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:35417 original size:51 final size:51
Alignment explanation
Indices: 35358--35458 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
35348 TCAGGGAGAG
* * * *
35358 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCAATATTTATTTACAACCTATT
35409 AGTTACAAGGAATTTCAACCTGTTCAAACCAATATTTATTTACAACCTAT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCAATATTTATTTACAACCTAT
35459 CCTTTCCTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCAATATTTATTTACAACCTATT
Found at i:37705 original size:14 final size:14
Alignment explanation
Indices: 37686--37713 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37676 TAACAGACTT
37686 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
37700 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
37714 ACATCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:38511 original size:26 final size:26
Alignment explanation
Indices: 38475--38530 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
38465 TGAGCAAAGT
38475 TTCTGCAAGCTGTCCAACTTAAGCGC
1 TTCTGCAAGCTGTCCAACTTAAGCGC
38501 TTCTGCAAGCTGTCCAACTTAAGCGC
1 TTCTGCAAGCTGTCCAACTTAAGCGC
38527 TTCT
1 TTCT
38531 ACAATTACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (26 bp):
TTCTGCAAGCTGTCCAACTTAAGCGC
Found at i:44482 original size:3 final size:3
Alignment explanation
Indices: 44474--44498 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44464 GAATTGGGTT
44474 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
44499 ATGAATCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:50833 original size:13 final size:13
Alignment explanation
Indices: 50815--50844 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
50805 GATTGCGAAG
50815 AATTAAAAATTTA
1 AATTAAAAATTTA
50828 AATT-AAAATTTA
1 AATTAAAAATTTA
50840 AATTA
1 AATTA
50845 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:52306 original size:26 final size:25
Alignment explanation
Indices: 52262--52310 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
52252 AATAATAATA
52262 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
52288 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
52311 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:52366 original size:38 final size:37
Alignment explanation
Indices: 52324--52660 Score: 178
Period size: 36 Copynumber: 8.8 Consensus size: 37
52314 TTTTTTTAAA
*
52324 AAAAACTATATATTATATATATTTTCAAAATGGTTTTT
1 AAAAACTATATATTATATATATTTTCAAAA-CGTTTTT
* *
52362 AAAAA-T-TATATTATATAAATGTTTTCATAACG-TTTT
1 AAAAACTATATATTATAT--ATATTTTCAAAACGTTTTT
* * *
52398 CAAAAGTATATATTATATATATTTT-AAAACGTTTTA
1 AAAAACTATATATTATATATATTTTCAAAACGTTTTT
**
52434 AAAAACTATATATTATATA-ATTTTCAAAAAATATATTTTCAAAATGGTTTTT
1 AAAAACTATATATTATATATATTTTC----AA-A-A----C--GT----TTTT
* * * * *
52486 AAAAATTATATATTATATAAATGTTTTCATAACG-TTTT
1 AAAAACTATATATTATATATATTTTC--AAAACGTTTTT
* * * *
52524 CAAAAGTATATATTATATATATTTTAAAAACGTTTTC
1 AAAAACTATATATTATATATATTTTCAAAACGTTTTT
*
52561 AAAAACTATATATTATATA-ATTTTCAAAA-ATATTTT
1 AAAAACTATATATTATATATATTTTCAAAACGT-TTTT
* *
52597 AAAAACTATATA--ATACATATTTTCAAAA-ATGTTTT
1 AAAAACTATATATTATATATATTTTCAAAACGT-TTTT
*
52632 --AAACTATATATTATATATGTTTTTCAAAA
1 AAAAACTATATATTATATAT-ATTTTCAAAA
52661 ACAATTTGCA
Statistics
Matches: 235, Mismatches: 35, Indels: 60
0.71 0.11 0.18
Matches are distributed among these distances:
33 10 0.04
34 4 0.02
35 32 0.14
36 82 0.35
37 23 0.10
38 50 0.21
40 2 0.01
41 1 0.00
42 1 0.00
45 1 0.00
46 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 21 0.09
53 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
AAAAACTATATATTATATATATTTTCAAAACGTTTTT
Found at i:52443 original size:25 final size:23
Alignment explanation
Indices: 52414--52496 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 23
52404 TATATATTAT
52414 ATATATTTTAAAACGTTTTAAAAA
1 ATATATTTTAAAA-GTTTTAAAAA
*
52438 ACTATATATTATATAA-TTTTCAAAAA
1 A-TATAT-TT-TAAAAGTTTT-AAAAA
52464 ATATATTTTCAAAATGGTTTTTAAAAA
1 ATATATTTT-AAAA--G-TTTTAAAAA
*
52491 TTATAT
1 ATATAT
52497 ATTATATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
23 1 0.02
24 6 0.13
25 14 0.30
26 8 0.17
27 14 0.30
28 4 0.09
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.45
Consensus pattern (23 bp):
ATATATTTTAAAAGTTTTAAAAA
Found at i:52468 original size:126 final size:127
Alignment explanation
Indices: 52340--52590 Score: 472
Period size: 126 Copynumber: 2.0 Consensus size: 127
52330 TATATATTAT
52340 ATATATTTTCAAAATGGTTTTTAAAAA-T-TATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
52403 GTATATATTATATATATTTT-AAAACGTTTTAAAAAACTATATATTATATAATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTAAAAAACTATATATTATATAATTTTCAAAAA
52464 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
*
52529 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTAAAAAACTATATATTATATAATTTTCAAAAA
52591 TATTTTAAAA
Statistics
Matches: 123, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
124 27 0.22
125 1 0.01
126 55 0.45
127 40 0.33
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGTTTTAAAAAACTATATATTATATAATTTTCAAAAA
Found at i:52473 original size:15 final size:16
Alignment explanation
Indices: 52448--52477 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52438 ACTATATATT
52448 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
52464 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
52478 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:52512 original size:27 final size:25
Alignment explanation
Indices: 52412--52512 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 25
52402 AGTATATATT
* *
52412 ATATATATTTTAAAACGTTTTAAAAA
1 ATATATATTATAAAATGTTTT-AAAA
* *
52438 ACTATATATTATATAAT-TTTCAAAA
1 A-TATATATTATAAAATGTTTTAAAA
*
52463 A-ATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAAT-G-TTTTAAAA
52490 ATTATATATTATATAAATGTTTT
1 A-TATATATTATA-AAATGTTTT
52513 CATAACGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
23 8 0.14
24 4 0.07
25 5 0.08
26 4 0.07
27 24 0.41
28 2 0.03
29 12 0.20
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
ATATATATTATAAAATGTTTTAAAA
Found at i:52674 original size:71 final size:69
Alignment explanation
Indices: 52532--52682 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 69
52522 TTCAAAAGTA
* * * *
52532 TATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAATATTTT
1 TATATAATACATATTTTAAAAACGTTTT--AAAACTATATATTATATAATTTTCAAAAACAATTT
52597 AAAAAC
64 AAAAAC
* *
52603 TATATAATACATATTTTCAAAAATGTTTT-AAACTATATATTATATATGTTTTTCAAAAACAATT
1 TATATAATACATATTTT-AAAAACGTTTTAAAACTATATATTATATA--ATTTTCAAAAACAATT
**
52667 TGCAAAC
63 TAAAAAC
*
52674 TGTATAATA
1 TATATAATA
52683 TATGTGTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
69 17 0.25
71 41 0.60
72 10 0.15
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (69 bp):
TATATAATACATATTTTAAAAACGTTTTAAAACTATATATTATATAATTTTCAAAAACAATTTAA
AAAC
Found at i:53468 original size:165 final size:165
Alignment explanation
Indices: 53275--54359 Score: 1474
Period size: 165 Copynumber: 6.6 Consensus size: 165
53265 AAGTTGAATA
* *
53275 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
53340 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
53405 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
53440 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
53505 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
53570 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
53605 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
53670 CCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
53735 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
53770 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
53835 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
* * * * * *
53896 CTATGCTGCAAATGGTGTG-CCTTGGAGCTGAGCG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
* * * * * * * * * * *
53930 TAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTT
1 TAATCGAACTCGAGGGTCTTTG---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * * * * * * *
53995 ATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC-TTTGGT---AGATAGCCCTTCTCGAC
63 GTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTTGGTCACAGATAACCCTTCTAGCC
* * * * * * *
54055 TTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCG
126 TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
* * * * * * * *
54094 TAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCTGGCCTTGAGCTAAGCTGCAAATGGTG
1 TAATCGAACTCGAGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * * *
54159 TGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAATAGATAACCCTTCTAGCCTTG
64 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTG
* * *
54223 AGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
129 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
** *
54260 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
54325 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
54360 GGTGGCAGGT
Statistics
Matches: 833, Mismatches: 73, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
160 30 0.04
161 35 0.04
162 31 0.04
163 72 0.09
164 179 0.21
165 455 0.55
166 31 0.04
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:53831 original size:246 final size:244
Alignment explanation
Indices: 53275--54400 Score: 1479
Period size: 246 Copynumber: 4.6 Consensus size: 244
53265 AAGTTGAATA
* *
53275 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
53340 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTGAG
* * * * * * *** *
53405 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTG---GCAGA
127 CTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGA
* * * * * * * * *
53467 TAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCG
191 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
* * * * * * * *
53520 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCGAGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * * * ** *
53585 TGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
62 TGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTGA
** * *
53650 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTCACAG
126 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAG
* *
53715 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
190 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
*
53770 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
53835 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTGAGCTAT
*
53900 GCTGCAAATGGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACC
131 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACC
*
53965 CTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
196 CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
** * *
54014 TAATCGAACTTAAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
54079 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCTGGCCTTGAGCT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT--TGGCAGATAGCCCTTCTCGACTTGAGCT
* * *
54144 AAGCTGCAAATGGTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAATAGATAA
129 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
*
54209 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
194 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
** *
54260 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
54325 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCT-GACCTTGAGC
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT--TGGCAGATAGCCCTTCTCGA-CTTGAGC
*
54389 TAAGCTGCAAAT
128 TATGCTGCAAAT
54401 AGTTTGTTTA
Statistics
Matches: 794, Mismatches: 74, Indels: 25
0.89 0.08 0.03
Matches are distributed among these distances:
244 156 0.20
245 148 0.19
246 355 0.45
249 82 0.10
250 53 0.07
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.29
Consensus pattern (244 bp):
TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTGAGCTAT
GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACC
CTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTG
Found at i:59374 original size:13 final size:13
Alignment explanation
Indices: 59356--59385 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
59346 GATTGCGAAG
59356 AATTAAAAATTTA
1 AATTAAAAATTTA
59369 AATT-AAAATTTA
1 AATTAAAAATTTA
59381 AATTA
1 AATTA
59386 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:59965 original size:22 final size:22
Alignment explanation
Indices: 59935--59988 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
59925 CGGTGTAGCC
59935 CCGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
59957 CTGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
59979 CCGGCGGCCG
1 CCGGCCGCCG
59989 GGCCAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.04, C:0.48, G:0.31, T:0.17
Consensus pattern (22 bp):
CCGGCCGCCGCTCTCAGTCGCT
Found at i:60720 original size:11 final size:10
Alignment explanation
Indices: 60704--60753 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 10
60694 GACCCTGCAC
60704 AAAAATAAAT
1 AAAAATAAAT
60714 GAAAAATAAAT
1 -AAAAATAAAT
60725 AAATTAA-AAAT
1 AAA--AATAAAT
60736 AAAAATAAAT
1 AAAAATAAAT
*
60746 AATAATAA
1 AAAAATAA
60754 TATATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
9 2 0.06
10 14 0.40
11 17 0.49
12 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:60726 original size:15 final size:15
Alignment explanation
Indices: 60706--60738 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
60696 CCCTGCACAA
60706 AAATAAATGAAAAAT
1 AAATAAATGAAAAAT
*
60721 AAATAAATTAAAAAT
1 AAATAAATGAAAAAT
60736 AAA
1 AAA
60739 AATAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAATGAAAAAT
Found at i:60828 original size:41 final size:42
Alignment explanation
Indices: 60771--60853 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
60761 AAACGTTTTC
* *
60771 AAAAACATATAATATATAAATTTTTAAAATGTTTTTTTAAAAA
1 AAAAACATATAATATATAAATTTTCAAAATG-GTTTTTAAAAA
*
60814 AAAAAC-TAT-ATATATATATTTTCAAAATGGTTTTTAAAAA
1 AAAAACATATAATATATAAATTTTCAAAATGGTTTTTAAAAA
60854 TTATATTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 10 0.27
41 18 0.49
42 3 0.08
43 6 0.16
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (42 bp):
AAAAACATATAATATATAAATTTTCAAAATGGTTTTTAAAAA
Found at i:60864 original size:36 final size:34
Alignment explanation
Indices: 60814--60948 Score: 139
Period size: 35 Copynumber: 3.8 Consensus size: 34
60804 TTTTTAAAAA
* *
60814 AAAAACTATATATATATATTTTCAAAATGGTTTTT
1 AAAAACTATATATATATATTTTCAAAA-CGTTTTC
* * *
60849 AAAAATTATATTATATAAATGTTTTCATAACGTTTTC
1 AAAAACTATA-TATAT--ATATTTTCAAAACGTTTTC
60886 AAAAGTA-TATATTATATATATTTT-AAAACGTTTTC
1 AAAA--ACTATA-TATATATATTTTCAAAACGTTTTC
60921 AAAAACTATATATATATAATTTTCAAAA
1 AAAAACTATATATATAT-ATTTTCAAAA
60949 ATATATTTCA
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
33 8 0.09
34 9 0.11
35 27 0.32
36 11 0.13
37 9 0.11
38 20 0.24
39 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (34 bp):
AAAAACTATATATATATATTTTCAAAACGTTTTC
Found at i:61000 original size:122 final size:123
Alignment explanation
Indices: 60827--61084 Score: 459
Period size: 122 Copynumber: 2.1 Consensus size: 123
60817 AACTATATAT
60827 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATA-TTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
60892 ATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATA-TATATAATTTTCAAAA
65 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
*
60949 ATATATTTCAAAATGGTTTTTAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATATTTCAAAATGGTTTTTAAAAAT-TATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
61014 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
65 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
*
61073 ATAT-TTTAAAAA
1 ATATATTTCAAAA
61085 CTATATAATA
Statistics
Matches: 131, Mismatches: 2, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
121 21 0.16
122 60 0.46
123 30 0.23
124 20 0.15
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (123 bp):
ATATATTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGTA
TATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
Found at i:61017 original size:36 final size:36
Alignment explanation
Indices: 60964--61131 Score: 126
Period size: 36 Copynumber: 4.6 Consensus size: 36
60954 TTTCAAAATG
* * * * *
60964 GTTTTTAAAATTATATATTATATAAATGTTTTCATAAC
1 GTTTTCAAAAGTATATA-T-TATAAATATTTTAAAAAC
*
61002 GTTTTCAAAAGTATATATTATATATATTTTAAAAAC
1 GTTTTCAAAAGTATATATTATAAATATTTTAAAAAC
* * *
61038 GTTTTCAAAAACTATATATTATATAAT-TTTCAAAAAT
1 GTTTTC-AAAAGTATATATTATA-AATATTTTAAAAAC
* * * * * *
61075 ATTTTAAAAACTATATAATATACATATTTTCAAAAAT
1 GTTTTCAAAAGTATATATTATAAATATTTT-AAAAAC
*
61112 GTTTT--AAACTATATATTATA
1 GTTTTCAAAAGTATATATTATA
61132 TATGTATTTT
Statistics
Matches: 109, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
35 16 0.15
36 38 0.35
37 38 0.35
38 17 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
GTTTTCAAAAGTATATATTATAAATATTTTAAAAAC
Found at i:61073 original size:37 final size:36
Alignment explanation
Indices: 60949--61148 Score: 185
Period size: 37 Copynumber: 5.4 Consensus size: 36
60939 ATTTTCAAAA
** *
60949 ATATA-TTTCAAAATGGTTTTTAAAATTATATATTAT
1 ATATATTTTCAAAAACG-TTTTAAAACTATATATTAT
* * *
60985 ATAAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 AT--ATATTTTCAAAAACGTTTT-AAAACTATATATTAT
61023 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT--AAAACTATATATTAT
** *
61060 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTT-AAAACTATATATTAT
* *
61096 ACATATTTTCAAAAATGTTTT-AAACTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAACTATATATTAT
61131 ATATGTATTTTCAAAAAC
1 ATA--TATTTTCAAAAAC
61149 AATTTGCAAA
Statistics
Matches: 137, Mismatches: 17, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
35 15 0.11
36 39 0.28
37 58 0.42
38 21 0.15
39 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATTTTCAAAAACGTTTTAAAACTATATATTAT
Found at i:61160 original size:74 final size:71
Alignment explanation
Indices: 60966--61170 Score: 189
Period size: 74 Copynumber: 2.8 Consensus size: 71
60956 TCAAAATGGT
* * ** * * * *
60966 TTTTAAAATTATATATTATATAAATGTTTTC-ATAACGTTTTCAAAAGTATATATTATATATATT
1 TTTTAAAACTATATATTATAT-AA--TTTTCAAAAACAATTTAAAAACTATATAATATACATATT
61030 TTAAAAACG
63 TTAAAAACG
* *
61039 TTTTCAAAAACTATATATTATATAATTTTCAAAAATATTTTAAAAACTATATAATATACATATTT
1 TTTT--AAAACTATATATTATATAATTTTCAAAAACAATTTAAAAACTATATAATATACATATTT
*
61104 TCAAAAATG
64 T-AAAAACG
** *
61113 TTTT-AAACTATATATTATATATGTATTTTCAAAAACAATTTGCAAACTGTATAATATA
1 TTTTAAAACTATATATTATATA---ATTTTCAAAAACAATTTAAAAACTATATAATATA
61171 TATGTGTATA
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
71 17 0.15
72 5 0.05
73 32 0.29
74 41 0.37
75 16 0.14
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (71 bp):
TTTTAAAACTATATATTATATAATTTTCAAAAACAATTTAAAAACTATATAATATACATATTTTA
AAAACG
Found at i:61170 original size:37 final size:34
Alignment explanation
Indices: 61045--61171 Score: 101
Period size: 37 Copynumber: 3.5 Consensus size: 34
61035 AACGTTTTCA
* * *
61045 AAAACTATATATTATATAATTTTCAAAAATATTTT
1 AAAACTATATAATATATTATTTTCAAAAA-AATTT
* **
61080 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATA-TTATTTTCAAAAAAATTT
*
61116 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATAT-TATTTTCAAAAA-AATTT
* *
61154 GCAAACTGTATAATATAT
1 -AAAACTATATAATATAT
61172 ATGTGTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
35 10 0.14
36 18 0.24
37 34 0.46
38 3 0.04
39 9 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAACTATATAATATATTATTTTCAAAAAAATTT
Found at i:63346 original size:15 final size:17
Alignment explanation
Indices: 63307--63348 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
63297 TAATAATAAT
63307 AATAAAAATATATAAAC
1 AATAAAAATATATAAAC
63324 AAGT-AAAAT-TA-AAAC
1 AA-TAAAAATATATAAAC
63339 AATAAAAATA
1 AATAAAAATA
63349 CAATTAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.05
15 11 0.50
16 2 0.09
17 7 0.32
18 1 0.05
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (17 bp):
AATAAAAATATATAAAC
Found at i:64660 original size:2 final size:2
Alignment explanation
Indices: 64653--64680 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
64643 TTGTATTTAT
64653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64681 ATAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64696 original size:9 final size:9
Alignment explanation
Indices: 64673--64732 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
64663 TATATATATA
64673 TATATATAAT
1 TATA-ATAAT
*
64683 AATAATAAT
1 TATAATAAT
*
64692 TATAATTAT
1 TATAATAAT
64701 TAT--T-AT
1 TATAATAAT
* *
64707 AATAATTAT
1 TATAATAAT
64716 TATAATAAT
1 TATAATAAT
64725 TATAATAA
1 TATAATAA
64733 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 4 0.10
7 1 0.02
8 1 0.02
9 32 0.78
10 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TATAATAAT
Found at i:64696 original size:12 final size:12
Alignment explanation
Indices: 64681--64732 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
64671 TATATATATA
*
64681 ATAATAATAATT
1 ATAATAATTATT
*
64693 ATAATTATTATT
1 ATAATAATTATT
64705 ATAATAATTATT
1 ATAATAATTATT
*
64717 ATAATAATTATA
1 ATAATAATTATT
64729 ATAA
1 ATAA
64733 ATAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:65111 original size:124 final size:120
Alignment explanation
Indices: 64893--65173 Score: 354
Period size: 124 Copynumber: 2.3 Consensus size: 120
64883 CCTTCTCTTT
* * * * *
64893 CTTCAGATAAGTTCTTCTCATTATGAACTTTCCACTGG---GGATGATGTTGACCTATTTCCTTC
1 CTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGATGATGCTAACCTATTTCCTTA
* *
64955 TGTGATAGAGTCATTCAAAAGATTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTC
65 TGTGATAGAATCATACAAAAGATTGAATAAGCTCTTCTCATTATGAA---CTT-TTTCTC
** * *
65015 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGTTTGATGCTAATCTATTTGCTTAT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATTTCCTTAT
* * * *
65080 GTGATAGAATTATACAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTT
66 GTGATAGAATCATACAAAAGATTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
65135 CTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAA
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
65174 AACTGATCCA
Statistics
Matches: 141, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
119 11 0.08
120 33 0.23
121 8 0.06
122 30 0.21
124 59 0.42
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (120 bp):
CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACCTATTTCCTTAT
GTGATAGAATCATACAAAAGATTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
Found at i:65314 original size:113 final size:113
Alignment explanation
Indices: 64987--65696 Score: 738
Period size: 113 Copynumber: 6.2 Consensus size: 113
64977 TTGAATAAGC
* * ****
64987 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * * * **
65052 AAAGTTTGATGCTAATCTATTTGCTTATGTGATAGAA-TTATA-CAAAAGGTTGAATAAGC
66 -AA-----ATGCTGATCCA--T-C--AAGTGAT-GAATTTA-AGCAAAAAGTTGAACAAAT
* *
65111 TCTTCTCATTGTGAAC-T-TT-TT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTC--TCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACTG
** * *
65170 GAAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAAT
65 GAAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
65219 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * *
65284 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 AAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
* * *
65332 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTATGAACTCGAAC
* * * * * * *
65397 TGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAAT
63 TGGAAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
** *
65448 TCTTCTCATTATGGTCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * *
65513 TAATGCTGATCCATTGAA-TGATGAATTCAAGCAAAAAGTTGAACAAGT
66 AAATGCTGATCCA-TCAAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
* * *
65561 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGGTGAGTTCTTCTCATTATGAACTCTAACTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * * * *
65626 TACTGCTGTTCCA-CTGAGTGATGAATTTAAGCAAAAAGTTGAACAAGT
66 AAATGCTGATCCATC-AAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
*
65674 TCTTCTCATTATGAACTTTTTCT
1 TCTTCTCATTATGAACTTCTTCT
65697 GGAAAAGCTG
Statistics
Matches: 514, Mismatches: 57, Indels: 41
0.84 0.09 0.07
Matches are distributed among these distances:
107 3 0.01
108 36 0.07
109 1 0.00
110 3 0.01
111 5 0.01
112 32 0.06
113 273 0.53
114 4 0.01
115 1 0.00
116 98 0.19
118 2 0.00
119 5 0.01
120 30 0.06
121 3 0.01
122 2 0.00
123 1 0.00
124 15 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
AAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAAT
Found at i:65474 original size:229 final size:227
Alignment explanation
Indices: 65111--65696 Score: 769
Period size: 229 Copynumber: 2.6 Consensus size: 227
65101 TTGAATAAGC
*
65111 TCTTCTCATTGTGAAC-T-TT-TT-CTTCTTCA-GATGAGTTCTTCTCATTATGAACT-T-CTCT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGATGAGTTCTTCTCATTATGAACTCTAC-CT
** * *
65169 GGAAAAACTGATCCATCAAGTGATGGATTTGAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA
65 GGAAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA
65234 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCA-T
130 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATT
* ** *
65298 CAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
195 CAA-TGATGAATTCAAGCAAAAAGTTGAACAAAT
*
65332 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTATGAACTCTACC
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG--GATGAGTTCTTCTCATTATGAACTCTACC
* * * * * * * *
65397 TGGCAATGTTAATCCATCAAATAATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGG
64 TGGAAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGA
* * * *
65462 TCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTGGTAATGCTGATCCAT
129 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCAT
* *
65527 TGAATGATGAATTCAAGCAAAAAGTTGAACAAGT
194 TCAATGATGAATTCAAGCAAAAAGTTGAACAAAT
* *
65561 TCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGG-TGAGTTCTTCTCATTATGAACTCTAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGATGAGTTCTTCTCATTATGAACTCTACCTG
* * * * *
65625 GTACTGCTGTTCCA-CTGAGTGATGAATTTAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA
66 GAAATGCTGATCCATC-AAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAA
*
65689 CTTTTTCT
130 CTTCTTCT
65697 GGAAAAGCTG
Statistics
Matches: 313, Mismatches: 41, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
221 14 0.04
222 1 0.00
223 2 0.01
224 2 0.01
225 9 0.03
226 84 0.27
227 1 0.00
228 24 0.08
229 172 0.55
230 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (227 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAATGCTGATCCATCAAGTGATGAATTTAAGCAAAAAGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTGATCCATTC
AATGATGAATTCAAGCAAAAAGTTGAACAAAT
Found at i:65685 original size:73 final size:73
Alignment explanation
Indices: 65598--65761 Score: 195
Period size: 73 Copynumber: 2.2 Consensus size: 73
65588 TCTTTAGGTG
* ** * * *
65598 AGTTCTTCTCATTATGAACTCTAACTGGTACTGCTGTTCCACT-GAGTGATGAATTTAAGCAAAA
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCA-TAAAATGATGAATTTAAGCAAAA
65662 AGTTGAACA
65 AGTTGAACA
* ** * * *
65671 AGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATAAAATGATGGATTTGAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATAAAATGATGAATTTAAGCAAAAA
65736 GTTGAACA
66 GTTGAACA
*
65744 AATTCTTCTCATTATGAA
1 AGTTCTTCTCATTATGAA
65762 TTTCTTCTTC
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
72 1 0.01
73 76 0.99
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCTAACTGGAAAAGCTGATCCATAAAATGATGAATTTAAGCAAAAA
GTTGAACA
Found at i:67658 original size:19 final size:19
Alignment explanation
Indices: 67624--67681 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 19
67614 CTTTAACTTA
67624 TTTCAAAATTATAAATTGAAT
1 TTTCAAAA--ATAAATTGAAT
67645 TTTCAAAAATAAATTGAA-
1 TTTCAAAAATAAATTGAAT
*
67663 TCTC--AAATAAATTGAAT
1 TTTCAAAAATAAATTGAAT
67680 TT
1 TT
67682 GGAATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 12 0.35
17 1 0.03
18 3 0.09
19 10 0.29
21 8 0.24
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (19 bp):
TTTCAAAAATAAATTGAAT
Found at i:68031 original size:1 final size:1
Alignment explanation
Indices: 68020--68100 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
68010 CTTGACACCC
* * * * * * * * * *
68020 TTTTTTCTTTTTTCTTTTTTCTTTTTTTCTTTCTTCTCTTTTCTTTCTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
68085 TCTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTT
68101 GTTCTTTTCT
Statistics
Matches: 56, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:68031 original size:7 final size:7
Alignment explanation
Indices: 68019--68110 Score: 94
Period size: 7 Copynumber: 12.3 Consensus size: 7
68009 TCTTGACACC
68019 CTTTTTT
1 CTTTTTT
68026 CTTTTTT
1 CTTTTTT
68033 CTTTTTT
1 CTTTTTT
68040 CTTTTTTT
1 C-TTTTTT
*
68048 CTTTCTT
1 CTTTTTT
*
68055 CTCTTTT
1 CTTTTTT
68062 CTTTCTTT
1 CTTT-TTT
*
68070 TTTTTTT
1 CTTTTTT
68077 CTTTTTTTT
1 C--TTTTTT
68086 CTTTTTTT
1 C-TTTTTT
68094 CTTTTTT
1 CTTTTTT
*
68101 GTTCTTTT
1 CTT-TTTT
68109 CT
1 CT
68111 CTTCAAGCAT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
7 39 0.54
8 26 0.36
9 7 0.10
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.83
Consensus pattern (7 bp):
CTTTTTT
Found at i:68039 original size:9 final size:9
Alignment explanation
Indices: 68034--68108 Score: 82
Period size: 9 Copynumber: 8.2 Consensus size: 9
68024 TTCTTTTTTC
68034 TTTTTTC-T
1 TTTTTTCTT
68042 TTTTTTCTT
1 TTTTTTCTT
* *
68051 TCTTCTCTT
1 TTTTTTCTT
*
68060 TTCTTTCTTTT
1 TT-TTT-TCTT
68071 TTTTTTCTT
1 TTTTTTCTT
68080 TTTTTTC-T
1 TTTTTTCTT
68088 TTTTTTCTT
1 TTTTTTCTT
68097 TTTTGTTCTT
1 TTTT-TTCTT
68107 TT
1 TT
68109 CTCTTCAAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
8 15 0.27
9 24 0.43
10 12 0.21
11 5 0.09
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:68045 original size:15 final size:15
Alignment explanation
Indices: 68019--68110 Score: 109
Period size: 15 Copynumber: 6.1 Consensus size: 15
68009 TCTTGACACC
68019 CTTTTTTC-TTTTTT
1 CTTTTTTCTTTTTTT
68033 CTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
68048 CTTTCTTCTCTTTTCTTT
1 CTTT-TT-TCTTTT-TTT
*
68066 CTTTTTT-TTTTCTT
1 CTTTTTTCTTTTTTT
68080 -TTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
* *
68094 CTTTTTTGTTCTTTT
1 CTTTTTTCTTTTTTT
68109 CT
1 CT
68111 CTTCAAGCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
13 6 0.09
14 16 0.24
15 28 0.41
16 3 0.04
17 8 0.12
18 7 0.10
ACGTcount: A:0.00, C:0.16, G:0.01, T:0.83
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:80951 original size:13 final size:13
Alignment explanation
Indices: 80933--80970 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
80923 TTTGGGCTTG
80933 TATTTAT-TATTAT
1 TATTTATATA-TAT
80946 TATTTATATATAT
1 TATTTATATATAT
*
80959 TATATATATATA
1 TATTTATATATA
80971 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTTATATATAT
Found at i:80976 original size:3 final size:3
Alignment explanation
Indices: 80968--81025 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
80958 TTATATATAT
* * * *
80968 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATT ATT ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
81016 ATA ATA ATA A
1 ATA ATA ATA A
81026 ATAAATAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:89155 original size:25 final size:26
Alignment explanation
Indices: 89126--89184 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 26
89116 AACTCAAAAT
*
89126 AGATATAATTTAAGTATCTAA-TAAA
1 AGATATAATTTAAATATCTAATTAAA
*
89151 AG--ATAATTTAAATATTTAATTAAA
1 AGATATAATTTAAATATCTAATTAAA
89175 A-ATATAATTT
1 AGATATAATTT
89185 GAGAAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 15 0.52
24 5 0.17
25 9 0.31
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (26 bp):
AGATATAATTTAAATATCTAATTAAA
Found at i:94127 original size:14 final size:14
Alignment explanation
Indices: 94108--94138 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
94098 AACGAATGTA
94108 AACGAACACAAACG
1 AACGAACACAAACG
*
94122 AACGAACATAAACG
1 AACGAACACAAACG
94136 AAC
1 AAC
94139 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:94813 original size:19 final size:19
Alignment explanation
Indices: 94776--94814 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
94766 TAACCTTTTT
*
94776 TTAGAACATAAGATGTTTA
1 TTAGAACATAAGATCTTTA
* *
94795 TTAGAAGATAATATCTTTA
1 TTAGAACATAAGATCTTTA
94814 T
1 T
94815 ATTATTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (19 bp):
TTAGAACATAAGATCTTTA
Found at i:101724 original size:60 final size:60
Alignment explanation
Indices: 101623--101788 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 60
101613 AATTATATTT
* * * * * * **
101623 TTCATTTTAAATTAATCTCTAAACTTTTGAATATTCTAATTTCATTCTCAATCTATGATTC
1 TTCATTCTAAATTAATCTTTAAACTTTTAAATATTCCAATTTCATCCTCAACCTAT-AACC
*
101684 TT-ATTCTAAATTAATATTTAAACTTTTAAATATTCCAATTTCATCCTCAACCTATAACC
1 TTCATTCTAAATTAATCTTTAAACTTTTAAATATTCCAATTTCATCCTCAACCTATAACC
** * * *
101743 TTCATTCTAAATTGGTCCTCAAACTTTTAAATATTACAATTTCATC
1 TTCATTCTAAATTAATCTTTAAACTTTTAAATATTCCAATTTCATC
101789 TCCAAATTCA
Statistics
Matches: 89, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 4 0.04
60 83 0.93
61 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (60 bp):
TTCATTCTAAATTAATCTTTAAACTTTTAAATATTCCAATTTCATCCTCAACCTATAACC
Found at i:103966 original size:24 final size:25
Alignment explanation
Indices: 103931--103987 Score: 91
Period size: 24 Copynumber: 2.3 Consensus size: 25
103921 GCCTTATTTT
103931 TTAA-TTTTGTTTAATTAATG-ATA
1 TTAATTTTTGTTTAATTAATGAATA
103954 TTAATTTTTGTTTAATTAATGATATA
1 TTAATTTTTGTTTAATTAATGA-ATA
103980 TTAATTTT
1 TTAATTTT
103988 AATAGTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 4 0.13
24 16 0.52
26 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (25 bp):
TTAATTTTTGTTTAATTAATGAATA
Found at i:104494 original size:13 final size:13
Alignment explanation
Indices: 104476--104500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104466 AATATATTCC
104476 ATTAAATTGATTA
1 ATTAAATTGATTA
104489 ATTAAATTGATT
1 ATTAAATTGATT
104501 TGTTATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTAAATTGATTA
Done.