Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold471
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: 181774
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 12838 characters in sequence are not A, C, G, or T
Found at i:5021 original size:28 final size:28
Alignment explanation
Indices: 4962--5023 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
4952 AAAACCTTTT
*
4962 TTTTTTAAAATTTATCGAAATGGGCCAC
1 TTTTTTAAAATTTACCGAAATGGGCCAC
* *
4990 TTTTTTAATTATTTACCGGAATGGGCCA-
1 TTTTTTAA-AATTTACCGAAATGGGCCAC
5018 TTTTTT
1 TTTTTT
5024 GCGAAATCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (28 bp):
TTTTTTAAAATTTACCGAAATGGGCCAC
Found at i:5464 original size:125 final size:126
Alignment explanation
Indices: 5254--5510 Score: 349
Period size: 125 Copynumber: 2.0 Consensus size: 126
5244 CGTTTTTGGT
** * **
5254 CAAATAGTATAAAATCGCTTCTACCAGGATGTTATCAGAAAAAAAAATTGTGAAATCGTGCCCTC
1 CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAAAAAAAAATTGTGAAATCGCACCCTC
* * * *
5319 GTGGATGCGATTTCGGTACAGTTGCTCATGTAAGAAATAATT-TTTTTTGACATTTTCTGAG
66 GTGGACGCGATTTCGCTACAGTTGCTCATGTAAGAAATAATTATTTTTTGAC-GTTTCTAAG
* * *
5380 CAAATAGTATAAAATCGCTGATACTAGGATGCTAT-ATG-AGAAGAAATTGTGAAATCGCACCCT
1 CAAATAGTATAAAATCGCTGATACCAGGATGCTATCA-GAAAAAAAAATTGTGAAATCGCACCCT
* *
5443 CGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTATTTTTTGACGTTTCTAAG
65 CGTGGACGCGATTTCGCTACAGTTGCTCATGTAAGAAATAATTATTTTTTGACGTTTCTAAG
5505 CAAATA
1 CAAATA
5511 ATGTCAAATC
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
125 74 0.64
126 41 0.36
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (126 bp):
CAAATAGTATAAAATCGCTGATACCAGGATGCTATCAGAAAAAAAAATTGTGAAATCGCACCCTC
GTGGACGCGATTTCGCTACAGTTGCTCATGTAAGAAATAATTATTTTTTGACGTTTCTAAG
Found at i:7676 original size:24 final size:24
Alignment explanation
Indices: 7644--7699 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
7634 TGTATGTGAA
*
7644 GGTGTTTGCATTATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
7668 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
*
7692 GGAGTTTG
1 GGTGTTTG
7700 AAAGCCATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.29
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGGCGAC
Found at i:8562 original size:7 final size:7
Alignment explanation
Indices: 8552--8583 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
8542 TTATATACAT
8552 AATACTA
1 AATACTA
8559 AATACTA
1 AATACTA
8566 AATACTA
1 AATACTA
8573 AATACTA
1 AATACTA
8580 AATA
1 AATA
8584 TCAATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:9693 original size:30 final size:31
Alignment explanation
Indices: 9659--9722 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
9649 GCCATTGATG
9659 AAAATAT-AAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
9689 AAAATATAAAAAAATTTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
9720 AAA
1 AAA
9723 TAGAGTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:9705 original size:21 final size:21
Alignment explanation
Indices: 9666--9705 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9656 ATGAAAATAT
* **
9666 AAAAAATTTAAAATTATTTTA
1 AAAAAATATAAAAAAATTTTA
9687 AAAAAATATAAAAAAATTT
1 AAAAAATATAAAAAAATTT
9706 ATAATTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAATATAAAAAAATTTTA
Found at i:23366 original size:340 final size:341
Alignment explanation
Indices: 22734--23415 Score: 1357
Period size: 340 Copynumber: 2.0 Consensus size: 341
22724 ACTTATTTTT
22734 TTATAATTGAATTTAAAATAAAAATAATCGTTAAATTGAAGTTATTAAGCTTAATTAGTAATTTT
1 TTATAATTGAATTTAAAATAAAAATAATCGTTAAATTGAAGTTATTAAGCTTAATTAGTAATTTT
22799 GGATTTTATATCACATATAAACATATTTATAGGTATATTTGGATGTATATATTATTAATAGGCTA
66 GGATTTTATATCACATATAAACATATTTATAGGTATATTTGGATGTATATATTATTAATAGGCTA
22864 GAAACTATTAAACTGTAGATATGTACATAAAAATATTGATAAATCTGAGATGATAAATGGAATAA
131 GAAACTATTAAACTGTAGATATGTACATAAAAATATTGATAAATCTGAGATGATAAATGGAATAA
22929 TTAGAAAGCGTTGAATGTGCGTCAAATAATGAAATGGAGAAAAGAATTATTGAAATAATAATATA
196 TTAGAAAGCGTTGAATGTGCGTCAAATAATGAAATGGAGAAAAGAATTATTGAAATAATAATATA
22994 TGTATCGAATTACTTTAAAGCGTGACAACAATCTACTGCGTTATGTTATTGAATTTCCTTATATC
261 TGTATCGAATTACTTTAAAGCGTGACAACAATCTACTGCGTTATGTTATTGAATTTCCTTATATC
23059 TTTCATATTGGCAAAG
326 TTTCATATTGGCAAAG
23075 TTATAATTGAA-TTAAAATAAAAATAATCGTTAAATTGAAGTTATTAAGCTTAATTAGTAATTTT
1 TTATAATTGAATTTAAAATAAAAATAATCGTTAAATTGAAGTTATTAAGCTTAATTAGTAATTTT
23139 GGATTTTATATCACATATAAACATATTTATAGGTATATTTGGATGTATATATTATTAATAGGCTA
66 GGATTTTATATCACATATAAACATATTTATAGGTATATTTGGATGTATATATTATTAATAGGCTA
23204 GAAACTATTAAACTGTAGATATGTACATAAAAATATTGATAAATCTGAGATGATAAATGGAATAA
131 GAAACTATTAAACTGTAGATATGTACATAAAAATATTGATAAATCTGAGATGATAAATGGAATAA
23269 TTAGAAAGCGTTGAATGTGCGTCAAATAATGAAATGGAGAAAAGAATTATTGAAATAATAATATA
196 TTAGAAAGCGTTGAATGTGCGTCAAATAATGAAATGGAGAAAAGAATTATTGAAATAATAATATA
23334 TGTATCGAATTACTTTAAAGCGTGACAACAATCTACTGCGTTATGTTATTGAATTTCCTTATATC
261 TGTATCGAATTACTTTAAAGCGTGACAACAATCTACTGCGTTATGTTATTGAATTTCCTTATATC
23399 TTTCATATTGGCAAAG
326 TTTCATATTGGCAAAG
23415 T
1 T
23416 ACAAATAAAA
Statistics
Matches: 341, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
340 330 0.97
341 11 0.03
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.37
Consensus pattern (341 bp):
TTATAATTGAATTTAAAATAAAAATAATCGTTAAATTGAAGTTATTAAGCTTAATTAGTAATTTT
GGATTTTATATCACATATAAACATATTTATAGGTATATTTGGATGTATATATTATTAATAGGCTA
GAAACTATTAAACTGTAGATATGTACATAAAAATATTGATAAATCTGAGATGATAAATGGAATAA
TTAGAAAGCGTTGAATGTGCGTCAAATAATGAAATGGAGAAAAGAATTATTGAAATAATAATATA
TGTATCGAATTACTTTAAAGCGTGACAACAATCTACTGCGTTATGTTATTGAATTTCCTTATATC
TTTCATATTGGCAAAG
Found at i:30753 original size:12 final size:12
Alignment explanation
Indices: 30736--30763 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30726 TCATTCTAAT
30736 TTCAAGTTTAAA
1 TTCAAGTTTAAA
30748 TTCAAGTTTAAA
1 TTCAAGTTTAAA
30760 TTCA
1 TTCA
30764 TACTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (12 bp):
TTCAAGTTTAAA
Found at i:30915 original size:20 final size:20
Alignment explanation
Indices: 30890--30928 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30880 TCTCCTCACC
* *
30890 AACCACTAATCACATCATAG
1 AACCACCAATCACACCATAG
30910 AACCACCAATCACACCATA
1 AACCACCAATCACACCATA
30929 CATCAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.36, G:0.03, T:0.15
Consensus pattern (20 bp):
AACCACCAATCACACCATAG
Found at i:32398 original size:51 final size:51
Alignment explanation
Indices: 32321--32421 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
32311 AAGAGTCTAA
* *
32321 CATATCCCATGAATGTGTAGTATATAGCTAACACCCCTCCAAACACAACCAG
1 CATATCCCATGAACGTGTAGCATATAGCTAACA-CCCTCCAAACACAACCAG
* *
32373 CATATCCCGTG-ACGTGTAGCATATAGCTAACACCCTTCAAACACAACCA
1 CATATCCCATGAACGTGTAGCATATAGCTAACACCCTCCAAACACAACCA
32422 ATGACTCATA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 16 0.36
51 19 0.42
52 10 0.22
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.21
Consensus pattern (51 bp):
CATATCCCATGAACGTGTAGCATATAGCTAACACCCTCCAAACACAACCAG
Found at i:32786 original size:12 final size:12
Alignment explanation
Indices: 32771--32795 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32761 CTCAATATGC
32771 ATCACATATCAT
1 ATCACATATCAT
32783 ATCACATATCAT
1 ATCACATATCAT
32795 A
1 A
32796 AGCATAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCACATATCAT
Found at i:33959 original size:18 final size:19
Alignment explanation
Indices: 33936--33974 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
33926 TATTTTAAAA
33936 TTTAAAGTAA-TA-TATATT
1 TTTAAA-TAATTATTATATT
33954 TTTAAATAATTATTATATT
1 TTTAAATAATTATTATATT
33973 TT
1 TT
33975 ATTATTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.16
18 8 0.42
19 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTAAATAATTATTATATT
Found at i:42124 original size:94 final size:95
Alignment explanation
Indices: 42004--42194 Score: 375
Period size: 94 Copynumber: 2.0 Consensus size: 95
41994 TAAATAAATA
42004 TTAATAAATCTTAGATTTAAGATTTTGGATGGGTTTAGGGCATCGAATTTAGAGTCTAGGATCTC
1 TTAATAAATCTTAGATTTAAGATTTTGGATGGGTTTAGGGCATCGAATTTAGAGTCTAGGATCTC
42069 AGGTTTAAAATTTAGGGTTTTAGTAATTAT
66 AGGTTTAAAATTTAGGGTTTTAGTAATTAT
42099 TTAATAAATC-TAGATTTAAGATTTTGGATGGGTTTAGGGCATCGAATTTAGAGTCTAGGATCTC
1 TTAATAAATCTTAGATTTAAGATTTTGGATGGGTTTAGGGCATCGAATTTAGAGTCTAGGATCTC
42163 AGGTTTAAAATTTAGGGTTTTAGTAATTAT
66 AGGTTTAAAATTTAGGGTTTTAGTAATTAT
42193 TT
1 TT
42195 CTAATTAATT
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 86 0.90
95 10 0.10
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.41
Consensus pattern (95 bp):
TTAATAAATCTTAGATTTAAGATTTTGGATGGGTTTAGGGCATCGAATTTAGAGTCTAGGATCTC
AGGTTTAAAATTTAGGGTTTTAGTAATTAT
Found at i:43391 original size:13 final size:13
Alignment explanation
Indices: 43373--43400 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
43363 GGATAGTCAA
43373 TTTTATTAAATAT
1 TTTTATTAAATAT
43386 TTTTATTAAATAT
1 TTTTATTAAATAT
43399 TT
1 TT
43401 AAGGAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTATTAAATAT
Found at i:43420 original size:69 final size:69
Alignment explanation
Indices: 43309--43447 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
43299 CATCGAGATC
*
43309 TTAAATATTTTTATTAAATATTTAAGGAGTTATATTGTAGATGACTTGAAGTTTGGATAGTCAAT
1 TTAAATATTTTTATTAAATATTTAAGGAGTTATATTGTAGATGACTTGAAGTTTGAATAGTCAAT
43374 TTTA
66 TTTA
43378 TTAAATATTTTTATTAAATATTTAAGGAGTTATATTGTAGATGACTTGAAGTTTGAATAGTCAAT
1 TTAAATATTTTTATTAAATATTTAAGGAGTTATATTGTAGATGACTTGAAGTTTGAATAGTCAAT
43443 TTTA
66 TTTA
43447 T
1 T
43448 CGAATTAGTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (69 bp):
TTAAATATTTTTATTAAATATTTAAGGAGTTATATTGTAGATGACTTGAAGTTTGAATAGTCAAT
TTTA
Found at i:46357 original size:12 final size:12
Alignment explanation
Indices: 46340--46364 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46330 TGCATGCCGA
46340 CATTGGTAACAG
1 CATTGGTAACAG
46352 CATTGGTAACAG
1 CATTGGTAACAG
46364 C
1 C
46365 TTTTTTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (12 bp):
CATTGGTAACAG
Found at i:51872 original size:3 final size:3
Alignment explanation
Indices: 51864--51891 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
51854 TCGAAAAAAC
51864 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
51892 ATGGTCTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52848 original size:74 final size:74
Alignment explanation
Indices: 52763--52926 Score: 328
Period size: 74 Copynumber: 2.2 Consensus size: 74
52753 AAAATTTTAT
52763 ATTTTTATATATTTTTAAATTATTTAAAATTATGTTTATTTTTTAAAATTTGAAGGCTTTTTTAA
1 ATTTTTATATATTTTTAAATTATTTAAAATTATGTTTATTTTTTAAAATTTGAAGGCTTTTTTAA
52828 TTTTTCACA
66 TTTTTCACA
52837 ATTTTTATATATTTTTAAATTATTTAAAATTATGTTTATTTTTTAAAATTTGAAGGCTTTTTTAA
1 ATTTTTATATATTTTTAAATTATTTAAAATTATGTTTATTTTTTAAAATTTGAAGGCTTTTTTAA
52902 TTTTTCACA
66 TTTTTCACA
52911 ATTTTTATATATTTTT
1 ATTTTTATATATTTTT
52927 TGAAAATACA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 90 1.00
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (74 bp):
ATTTTTATATATTTTTAAATTATTTAAAATTATGTTTATTTTTTAAAATTTGAAGGCTTTTTTAA
TTTTTCACA
Found at i:54539 original size:19 final size:19
Alignment explanation
Indices: 54494--54542 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
54484 CTGACATGTA
* * * *
54494 AAGTGCATACTGGCGCTCG
1 AAGTGCATCCTGGCACACC
*
54513 AAGCGCATCCTGGCACACC
1 AAGTGCATCCTGGCACACC
54532 AAGTGCATCCT
1 AAGTGCATCCT
54543 AGAGCGTAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGTGCATCCTGGCACACC
Found at i:66505 original size:17 final size:17
Alignment explanation
Indices: 66485--66524 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
66475 CTTCATCCAA
* *
66485 AAAGAGTTGCCTCGCCC
1 AAAGAGTAGCCTCACCC
*
66502 AAAGAGTAGCCTTACCC
1 AAAGAGTAGCCTCACCC
66519 AAAGAG
1 AAAGAG
66525 GTACCTAGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (17 bp):
AAAGAGTAGCCTCACCC
Found at i:70465 original size:12 final size:13
Alignment explanation
Indices: 70437--70469 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
70427 TTGTGTTTAA
70437 AAATAACATACAAT
1 AAATAA-ATACAAT
70451 AAATAAATA-AAT
1 AAATAAATACAAT
70463 AAATAAA
1 AAATAAA
70470 CCCACATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 3 0.16
14 6 0.32
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAATACAAT
Found at i:72496 original size:43 final size:42
Alignment explanation
Indices: 72443--72562 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
72433 TCCGAGGTGT
* *
72443 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATATGA
1 GATTACGTGTAAGACCATGTCTGGGACA-TGGCATAGATATGA
* * * *
72486 GATTGCGTGTAAGACCCTGTCCGGGACAGTGGCATAGATATGT
1 GATTACGTGTAAGACCATGTCTGGGACA-TGGCATAGATATGA
* * * * *
72529 GATAACCTATAAGACCATATCTGGGATATGGCAT
1 GATTACGTGTAAGACCATGTCTGGGACATGGCAT
72563 TGTATGTGAT
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 6 0.10
43 57 0.90
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATGGCATAGATATGA
Found at i:73365 original size:139 final size:140
Alignment explanation
Indices: 73103--73382 Score: 537
Period size: 139 Copynumber: 2.0 Consensus size: 140
73093 TTCATTTTGG
73103 GAAGTATGTTTCATGGTTATATGTTTTGGTTTTAGCAATGAGGTAAATGATGAATATATATTGAT
1 GAAGTATGTTTCATGGTTATATGTTTTGGTTTTAGCAATGAGGTAAATGATGAATATATATTGAT
73168 TGAGTATTGGTTATTTTGGTACGATTCTATATGGTTGATTAAATGCTAAAGTTACATATTTTATG
66 TGAGTATTGGTTATTTTGGTACGATTCTATATGGTTGATTAAATGCTAAAGTTACATATTTTATG
73233 TAATTATATT
131 TAATTATATT
73243 GAAGTATGTTT-ATGGTTATATGTTTTGGTTTTAGCAATGAGGTAAATGATGAATATATATTGAT
1 GAAGTATGTTTCATGGTTATATGTTTTGGTTTTAGCAATGAGGTAAATGATGAATATATATTGAT
73307 TGAGTATTGGTTATTTTGGTACGATTCCT-TATGGTTGATTAAATGCTAAAGTTACATATTTTAT
66 TGAGTATTGGTTATTTTGGTACGATT-CTATATGGTTGATTAAATGCTAAAGTTACATATTTTAT
73371 GTAATTATATT
130 GTAATTATATT
73382 G
1 G
73383 GTTAATTTAT
Statistics
Matches: 139, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
139 126 0.91
140 13 0.09
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (140 bp):
GAAGTATGTTTCATGGTTATATGTTTTGGTTTTAGCAATGAGGTAAATGATGAATATATATTGAT
TGAGTATTGGTTATTTTGGTACGATTCTATATGGTTGATTAAATGCTAAAGTTACATATTTTATG
TAATTATATT
Found at i:90250 original size:56 final size:56
Alignment explanation
Indices: 90164--90277 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
90154 TTACAAAAAA
90164 AAAAAAAAAAGGAAATCTAATGGAGGCTTCTTAGAAATATAAACACATACATACTG
1 AAAAAAAAAAGGAAATCTAATGGAGGCTTCTTAGAAATATAAACACATACATACTG
*
90220 AAAAAAAAAAGGTAATCTAATGGAGGCTTCTTAGAAATATAAACACATACATACTG
1 AAAAAAAAAAGGAAATCTAATGGAGGCTTCTTAGAAATATAAACACATACATACTG
90276 AA
1 AA
90278 CAATTCCAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.22
Consensus pattern (56 bp):
AAAAAAAAAAGGAAATCTAATGGAGGCTTCTTAGAAATATAAACACATACATACTG
Found at i:97121 original size:13 final size:14
Alignment explanation
Indices: 97103--97134 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
97093 TTTAAGATTA
97103 AATTAATAAA-AAT
1 AATTAATAAATAAT
97116 AATTAATAAATAAT
1 AATTAATAAATAAT
97130 -ATTAA
1 AATTAA
97135 CAATTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAATAAATAAT
Found at i:98342 original size:3 final size:3
Alignment explanation
Indices: 98334--98416 Score: 130
Period size: 3 Copynumber: 27.3 Consensus size: 3
98324 ACTTGATTTC
*
98334 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
98382 TAT TAT TCT TAT TAT TAT TAT ATAG TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT T
98417 CTTACATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
3 71 0.97
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:98549 original size:16 final size:16
Alignment explanation
Indices: 98528--98558 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
98518 TCTTAGTTTC
98528 TATGTACATATATACG
1 TATGTACATATATACG
*
98544 TATGTACATTTATAC
1 TATGTACATATATAC
98559 TTTTATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
TATGTACATATATACG
Found at i:99753 original size:27 final size:27
Alignment explanation
Indices: 99730--99782 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
99720 TGTTATAACT
99730 TTTTTTTATTTACCAAAAAATATATAA
1 TTTTTTTATTTACCAAAAAATATATAA
*
99757 TTTTTTTATTTACCAAAATATATATA
1 TTTTTTTATTTACCAAAAAATATATA
99783 TAAAAAACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTTTTATTTACCAAAAAATATATAA
Found at i:99857 original size:27 final size:27
Alignment explanation
Indices: 99817--99869 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
99807 ACTCCCTGGG
*
99817 TGGAGGGAAGCAGGTTGGCGGCACCAA
1 TGGAGGGAACCAGGTTGGCGGCACCAA
99844 TGGAGGGAACCAGGTTGGCGGCACCA
1 TGGAGGGAACCAGGTTGGCGGCACCA
99870 CCCTTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.43, T:0.11
Consensus pattern (27 bp):
TGGAGGGAACCAGGTTGGCGGCACCAA
Found at i:99939 original size:18 final size:17
Alignment explanation
Indices: 99916--100066 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 17
99906 GAAGGAGAGG
99916 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
99934 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
99951 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
99967 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
99985 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
100005 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
100023 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
100044 GAGAA-AAA-AAAAAGAA
1 G-GAAGAAAGAAAAAGAA
*
100060 AGAAGAA
1 GGAAGAA
100067 GAAGAGGGAA
Statistics
Matches: 106, Mismatches: 15, Indels: 26
0.72 0.10 0.18
Matches are distributed among these distances:
15 12 0.11
16 10 0.09
17 7 0.07
18 28 0.26
19 26 0.25
20 16 0.15
21 6 0.06
22 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:99949 original size:10 final size:10
Alignment explanation
Indices: 99918--99989 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
99908 AGGAGAGGGG
*
99918 AAGAAGAAGA
1 AAGAAAAAGA
99928 AAGAAAGGAAGA
1 AAGAAA--AAGA
99940 AAGAAAAAGA
1 AAGAAAAAGA
* *
99950 AGGAAAAGGA
1 AAGAAAAAGA
99960 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
99974 AAGAAAAAGA
1 AAGAAAAAGA
*
99984 AGGAAA
1 AAGAAA
99990 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:99949 original size:22 final size:23
Alignment explanation
Indices: 99918--100019 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
99908 AGGAGAGGGG
*
99918 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
99940 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
99962 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
99988 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
100012 AAGAAAAA
1 AAGAAAAA
100020 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:99976 original size:28 final size:28
Alignment explanation
Indices: 99921--100000 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
99911 AGAGGGGAAG
99921 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
99946 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
99980 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
100001 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:99994 original size:38 final size:38
Alignment explanation
Indices: 99936--100093 Score: 172
Period size: 38 Copynumber: 4.3 Consensus size: 38
99926 GAAAGAAAGG
99936 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
99970 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* *
100008 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
* * *
100046 GAA-AAA-AAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGG-
1 -AAGAAAGAAAAAG-AAGGA-AAGAAAAGGAAAGGAGAGGA
100083 AA-AAAGAAAAA
1 AAGAAAGAAAAA
100094 AAAAAGGTAA
Statistics
Matches: 107, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
34 15 0.14
35 1 0.01
36 5 0.05
37 10 0.09
38 61 0.57
39 15 0.14
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:99996 original size:10 final size:10
Alignment explanation
Indices: 99938--100038 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
99928 AAGAAAGGAA
*
99938 GAAAGAAAAA
1 GAAAGAAAAG
*
99948 GAAGGAAAAG
1 GAAAGAAAAG
* *
99958 GAAAGGAGAG
1 GAAAGAAAAG
99968 GAAAG-AAA-
1 GAAAGAAAAG
99976 GAAA-AAGAAG
1 GAAAGAA-AAG
99986 GAAAGAAAAG
1 GAAAGAAAAG
***
99996 GAAAGGGGAG
1 GAAAGAAAAG
100006 GAAAG-AAA-
1 GAAAGAAAAG
100014 GAAA-AATAAG
1 GAAAGAA-AAG
100024 GAAAGAAAAG
1 GAAAGAAAAG
100034 GAAAG
1 GAAAG
100039 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 7 0.10
10 51 0.71
11 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:100625 original size:19 final size:18
Alignment explanation
Indices: 100585--100635 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
100575 AAAATATATA
**
100585 TAATATTTTGGTATTTTT
1 TAATATTTTATTATTTTT
100603 TAATATTTTATTATTTTT
1 TAATATTTTATTATTTTT
*
100621 GTAATGTTTTATTAT
1 -TAATATTTTATTAT
100636 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTT
Found at i:100660 original size:13 final size:13
Alignment explanation
Indices: 100642--100667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
100632 TTATGGGTTT
100642 TATAAAAAAATAA
1 TATAAAAAAATAA
100655 TATAAAAAAATAA
1 TATAAAAAAATAA
100668 AAAATTACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:100714 original size:27 final size:27
Alignment explanation
Indices: 100672--100744 Score: 128
Period size: 27 Copynumber: 2.7 Consensus size: 27
100662 AAATAAAAAA
100672 TTACCAAAATATTATAAAATTTTTTTAT
1 TTACCAAAATA-TATAAAATTTTTTTAT
*
100700 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATAAAATTTTTTTAT
100727 TTACCAAAATATATAAAA
1 TTACCAAAATATATAAAA
100745 AAAAGTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 32 0.74
28 11 0.26
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (27 bp):
TTACCAAAATATATAAAATTTTTTTAT
Found at i:100763 original size:14 final size:12
Alignment explanation
Indices: 100741--100784 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 12
100731 CAAAATATAT
100741 AAAAAAAAGTAAA
1 AAAAAAAAG-AAA
100754 AAACAAAAAGAATA
1 AAA-AAAAAGAA-A
100768 AAAAAAAAGGAAA
1 AAAAAAAA-GAAA
100781 AAAA
1 AAAA
100785 TCACACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.54
14 13 0.46
ACGTcount: A:0.84, C:0.02, G:0.09, T:0.05
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:103715 original size:15 final size:14
Alignment explanation
Indices: 103675--103703 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
103665 TTTTTGTATC
103675 AATTTAATTATTCT
1 AATTTAATTATTCT
103689 AATTTAATTATTCT
1 AATTTAATTATTCT
103703 A
1 A
103704 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:103868 original size:20 final size:20
Alignment explanation
Indices: 103843--103904 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
103833 CTTATTTTTC
*
103843 TTTCTTTCCTCCCTTTTCCT
1 TTTCTTTCCTCTCTTTTCCT
*
103863 TTTCTTTCCT-TCTTTTTC-
1 TTTCTTTCCTCTCTTTTCCT
*
103881 TTTCTTTCCTCTCATTTCCT
1 TTTCTTTCCTCTCTTTTCCT
103901 TTTC
1 TTTC
103905 CTTCTTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.28
19 12 0.33
20 14 0.39
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCTTTCCTCTCTTTTCCT
Found at i:103919 original size:10 final size:10
Alignment explanation
Indices: 103837--103938 Score: 55
Period size: 10 Copynumber: 9.8 Consensus size: 10
103827 AAATGCCTTA
103837 TTTTTCTTTC
1 TTTTTCTTTC
* **
103847 -TTTCCTCCC
1 TTTTTCTTTC
*
103856 TTTTCCTTT-
1 TTTTTCTTTC
* *
103865 TCTTTCCTTC
1 TTTTTCTTTC
103875 TTTTTCTTTC
1 TTTTTCTTTC
103885 TTTCCTCTCATTTC
1 TTT--T-TC-TTTC
* *
103899 CTTTTCCTTC
1 TTTTTCTTTC
103909 TTTTTCTTTC
1 TTTTTCTTTC
103919 TTCCTTTCTTTC
1 TT--TTTCTTTC
*
103931 TTCTTCTT
1 TTTTTCTT
103939 CCCCTCTCCT
Statistics
Matches: 69, Mismatches: 15, Indels: 16
0.69 0.15 0.16
Matches are distributed among these distances:
9 12 0.17
10 35 0.51
11 2 0.03
12 12 0.17
13 2 0.03
14 6 0.09
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:103926 original size:38 final size:38
Alignment explanation
Indices: 103832--103926 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
103822 ATTCCAAATG
* * *
103832 CCTTATTTTTCTTTCTTTCCTCCCTTTTCCTTTTCTTT
1 CCTTCTTTTTCTTTCTTTCCTCCCATTTCCTTTTCCTT
*
103870 CCTTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTT
1 CCTTCTTTTTCTTTCTTTCCTCCCATTTCCTTTTCCTT
* *
103908 -CTTTTTCTTTCTTCCTTTC
1 CCTTCTT-TTTCTTTCTTTC
103927 TTTCTTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
37 5 0.10
38 45 0.90
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (38 bp):
CCTTCTTTTTCTTTCTTTCCTCCCATTTCCTTTTCCTT
Found at i:103936 original size:28 final size:29
Alignment explanation
Indices: 103857--103938 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 29
103847 TTTCCTCCCT
103857 TTTCCTTTTCTTTC--CTTCTTTTTCTTTC
1 TTTCC-TTTCTTTCTTCTTCTTTTTCTTTC
*
103885 TTTCCTCTCATTTCCTTTTCCTTCTTTTTCTTTC
1 TTTCCTTTC-TTT-C--TT-CTTCTTTTTCTTTC
103919 -TTCCTTTCTTTCTTCTTCTT
1 TTTCCTTTCTTTCTTCTTCTT
103939 CCCCTCTCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
27 3 0.07
28 14 0.31
29 3 0.07
31 1 0.02
32 3 0.07
33 7 0.16
34 14 0.31
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTCCTTTCTTTCTTCTTCTTTTTCTTTC
Found at i:103937 original size:18 final size:17
Alignment explanation
Indices: 103832--103940 Score: 80
Period size: 18 Copynumber: 6.1 Consensus size: 17
103822 ATTCCAAATG
*
103832 CCTTATTTTTCTTTCTTT
1 CCTTCTTTTTCTTTC-TT
* *
103850 CCTCCCTTTTCCTTTTCTTT
1 CCT-TCTTTTTC-TTTC-TT
103870 CCTTCTTTTTCTTTCTTT
1 CCTTCTTTTTCTTTC-TT
* *
103888 CC-TCTCATTTCCTT-TT
1 CCTTCT-TTTTCTTTCTT
103904 CCTTCTTTTTCTTTCTT
1 CCTTCTTTTTCTTTCTT
103921 CCTTTCTTTCTTC-TTCTT
1 CC-TTCTTT-TTCTTTCTT
103939 CC
1 CC
103941 CCTCTCCTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.13
17 10 0.13
18 31 0.41
19 14 0.19
20 10 0.13
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (17 bp):
CCTTCTTTTTCTTTCTT
Found at i:104025 original size:27 final size:27
Alignment explanation
Indices: 103987--104067 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
103977 AATTCAAGGG
*
103987 TGGTGCCGCCAACCTGGTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
****
104014 TGGTGCCGCCAACCTGCTTCCCTTGTT
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
*
104041 TGGTGCCGCCAACCTACTTCCCTCCAC
1 TGGTGCCGCCAACCTGCTTCCCTCCAC
104068 CTAGGGAGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACCTGCTTCCCTCCAC
Found at i:104126 original size:16 final size:15
Alignment explanation
Indices: 104093--104131 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
104083 ATCAGTTCAG
104093 GTTTTTTTTTCTTCT
1 GTTTTTTTTTCTTCT
* *
104108 GTTTTTTATTTTTTTT
1 GTTTTTT-TTTCTTCT
104124 GTTTTTTT
1 GTTTTTTT
104132 ATATATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.03, C:0.05, G:0.08, T:0.85
Consensus pattern (15 bp):
GTTTTTTTTTCTTCT
Found at i:104188 original size:27 final size:26
Alignment explanation
Indices: 104130--104188 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
104120 TTTTGTTTTT
*
104130 TTATATATTTTGGTAAATAAAAAAAT
1 TTATATATTTTGGTAAATAAAAAAAG
104156 TATATATATTTTGGTAAATAAAAAAAAG
1 T-TATATATTTTGGTAAAT-AAAAAAAG
104184 TTATA
1 TTATA
104189 ACATTTTAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 21 0.70
28 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAG
Found at i:104194 original size:28 final size:27
Alignment explanation
Indices: 104131--104200 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
104121 TTTGTTTTTT
*
104131 TATATATTTTGGTAAATAAAAAAATTA
1 TATACATTTTGGTAAATAAAAAAATTA
*
104158 TATATATTTTGGTAAATAAAAAAAAGTTA
1 TATACATTTTGGTAAAT-AAAAAAA-TTA
*
104187 TA-ACATTTTAGTAA
1 TATACATTTTGGTAA
104201 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
27 17 0.44
28 17 0.44
29 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (27 bp):
TATACATTTTGGTAAATAAAAAAATTA
Found at i:104576 original size:2 final size:2
Alignment explanation
Indices: 104569--104603 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
104559 CATTAGCTTA
*
104569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
104604 GATAGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105298 original size:31 final size:29
Alignment explanation
Indices: 105260--105337 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
105250 CTAACGGCTC
*
105260 AGTGACTAAAATGTTACAACGTGAAAACATA
1 AGTGACTAAAATGTAAC-A-GTGAAAACATA
* * **
105291 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAGTGAAAACATA
105320 AGTGACTAAAATGTAACA
1 AGTGACTAAAATGTAACA
105338 TGAGCCAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 25 0.61
30 1 0.02
31 15 0.37
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAGTGAAAACATA
Found at i:109512 original size:28 final size:28
Alignment explanation
Indices: 109481--109537 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
109471 ATATCAATTA
109481 TAGGTAAGTATACATACGCTCTATTAAC
1 TAGGTAAGTATACATACGCTCTATTAAC
109509 TAGGTAAGTATACATACGCTCTATTAAC
1 TAGGTAAGTATACATACGCTCTATTAAC
109537 T
1 T
109538 TGAATTCTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (28 bp):
TAGGTAAGTATACATACGCTCTATTAAC
Found at i:110732 original size:35 final size:37
Alignment explanation
Indices: 110669--110738 Score: 126
Period size: 36 Copynumber: 1.9 Consensus size: 37
110659 AATATAGCTT
110669 CCAGTGTCATGATTTCTTTTAAGTTTTGTA-AATTAA
1 CCAGTGTCATGATTTCTTTTAAGTTTTGTATAATTAA
110705 CCAGTGTCATGATTTC-TTTAAGTTTTGTATAATT
1 CCAGTGTCATGATTTCTTTTAAGTTTTGTATAATT
110739 TAGTTGTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (37 bp):
CCAGTGTCATGATTTCTTTTAAGTTTTGTATAATTAA
Found at i:114275 original size:5 final size:5
Alignment explanation
Indices: 114265--114290 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
114255 ATAGCTAGAA
114265 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
114291 TAGGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:122093 original size:2 final size:2
Alignment explanation
Indices: 122086--122119 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
122076 TTGTAGTGGC
122086 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
122120 TTTGATTGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:130607 original size:16 final size:16
Alignment explanation
Indices: 130581--130622 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
130571 AAGAGTTTTG
*
130581 AATTTAAGTTGAACTA
1 AATTGAAGTTGAACTA
*
130597 TATTGAAGTTGAACTA
1 AATTGAAGTTGAACTA
*
130613 AATTTAAGTT
1 AATTGAAGTT
130623 TTGAATTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (16 bp):
AATTGAAGTTGAACTA
Found at i:134988 original size:18 final size:18
Alignment explanation
Indices: 134967--135002 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
134957 GAAATTATAA
*
134967 AAAAAATTAAAAAAAGTT
1 AAAAAATAAAAAAAAGTT
*
134985 AAAAACTAAAAAAAAGTT
1 AAAAAATAAAAAAAAGTT
135003 CAAGTTTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAAAATAAAAAAAAGTT
Found at i:135625 original size:18 final size:18
Alignment explanation
Indices: 135597--135631 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
135587 TTTCAGAAAA
135597 TGAAAAGCCAACAGAACAT
1 TGAAAAGCCAACA-AACAT
135616 TGAAAA-CCAACAAACA
1 TGAAAAGCCAACAAACA
135632 AGTAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (18 bp):
TGAAAAGCCAACAAACAT
Found at i:137394 original size:25 final size:25
Alignment explanation
Indices: 137360--137411 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
137350 CCCAGCATAA
137360 ATGCATAACTTGAAGTACTCTTTCT
1 ATGCATAACTTGAAGTACTCTTTCT
*
137385 ATGCATAACTTGAAGTGCTCTTTCT
1 ATGCATAACTTGAAGTACTCTTTCT
137410 AT
1 AT
137412 CATCTCGATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (25 bp):
ATGCATAACTTGAAGTACTCTTTCT
Found at i:145222 original size:29 final size:29
Alignment explanation
Indices: 145180--145239 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
145170 ATGAGTATGT
145180 CTAAATGGGTGTTCGAAGGTGGTTGAAAA
1 CTAAATGGGTGTTCGAAGGTGGTTGAAAA
145209 CTAAATGGGTGTTCGAAGGTGGTTGAAAA
1 CTAAATGGGTGTTCGAAGGTGGTTGAAAA
145238 CT
1 CT
145240 CGCAACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.08, G:0.33, T:0.28
Consensus pattern (29 bp):
CTAAATGGGTGTTCGAAGGTGGTTGAAAA
Found at i:151176 original size:20 final size:20
Alignment explanation
Indices: 151148--151186 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
151138 TGTAGAGTTT
*
151148 ATTGTTGAAAATTTTATATA
1 ATTGATGAAAATTTTATATA
*
151168 ATTGATGAATATTTTATAT
1 ATTGATGAAAATTTTATAT
151187 TTAAAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
ATTGATGAAAATTTTATATA
Found at i:159014 original size:29 final size:29
Alignment explanation
Indices: 158977--159033 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
158967 CACCTTGACA
* * *
158977 TGAATTCTCAATGAACAAGTTCTTCATCG
1 TGAACTCTCAACGAACAAGTTCTCCATCG
159006 TGAACTCTCAACGAACAAGTTCTCCATC
1 TGAACTCTCAACGAACAAGTTCTCCATC
159034 TTTTCCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (29 bp):
TGAACTCTCAACGAACAAGTTCTCCATCG
Found at i:159653 original size:26 final size:27
Alignment explanation
Indices: 159610--159662 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
159600 CTTTCCAATG
159610 TTTTTTACCGAGATTTTCCATATATCT
1 TTTTTTACCGAGATTTTCCATATATCT
* * *
159637 TTTTTTATCGGGA-TTTCCATGTATCT
1 TTTTTTACCGAGATTTTCCATATATCT
159663 GCTAACTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (27 bp):
TTTTTTACCGAGATTTTCCATATATCT
Found at i:172579 original size:17 final size:17
Alignment explanation
Indices: 172554--172599 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
172544 AAAATTATGA
* *
172554 GAAATTACAAATAATTAT
1 GAAA-TACAAAAAATTAC
172572 GAAATACAAAAAATTAC
1 GAAATACAAAAAATTAC
*
172589 GAGATACAAAA
1 GAAATACAAAA
172600 TTTTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (17 bp):
GAAATACAAAAAATTAC
Found at i:173232 original size:91 final size:91
Alignment explanation
Indices: 173115--173298 Score: 309
Period size: 91 Copynumber: 2.0 Consensus size: 91
173105 TATTTTAACT
* *
173115 CATTCAAGATTTTAATTACATGCAAGTTGGTCCCTCTCTAATCAATTTTAA-CAATTTTAATCGA
1 CATTCAAGATTTTAATTACATGCAAGTTGGTCCCTCTCTAATCAATTTTAATC-A-GTGAATCGA
173179 AAATTTATAATAATTTGCACTTTTAGTC
64 AAATTTATAATAATTTGCACTTTTAGTC
173207 CATTCAAGA-TTTAATTACATGCAAGTTGGTCCCTCTCTAATCAATTTTAATTCAGTGAATCGAA
1 CATTCAAGATTTTAATTACATGCAAGTTGGTCCCTCTCTAATCAATTTTAA-TCAGTGAATCGAA
173271 AATTTATAATAATTTGCACTTTTAGTC
65 AATTTATAATAATTTGCACTTTTAGTC
173298 C
1 C
173299 TATTTTTTTT
Statistics
Matches: 88, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
91 77 0.88
92 10 0.11
93 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (91 bp):
CATTCAAGATTTTAATTACATGCAAGTTGGTCCCTCTCTAATCAATTTTAATCAGTGAATCGAAA
ATTTATAATAATTTGCACTTTTAGTC
Found at i:179963 original size:56 final size:56
Alignment explanation
Indices: 179858--179963 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
179848 CCATATACGA
* * * *
179858 AAATTTAATTAATTCTAATTAAATAAGTTAATAAAAAGTTATATGCTTAAATAGAC
1 AAATTTAATTAATTCTAATTAAATAAATGAATAAAAAATCATATGCTTAAATAGAC
179914 AAATTTAATTAATTCTAAAATTAAATAAATGAATAAAAAATCA-AT-CTTAA
1 AAATTTAATTAATTCT--AATTAAATAAATGAATAAAAAATCATATGCTTAA
179964 CCCCTCTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 21 0.48
57 2 0.05
58 21 0.48
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.36
Consensus pattern (56 bp):
AAATTTAATTAATTCTAATTAAATAAATGAATAAAAAATCATATGCTTAAATAGAC
Done.