Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 72 of 198
Found at i:22546606 original size:25 final size:25
Alignment explanation
Indices: 22546577--22546626 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
22546567 AATTGTACTA
22546577 AATTGTAACAAATTGATAATTTTAC
1 AATTGTAACAAATTGATAATTTTAC
22546602 AATTGTAACAAATTGATAATTTTAC
1 AATTGTAACAAATTGATAATTTTAC
22546627 TATCATTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTGTAACAAATTGATAATTTTAC
Found at i:22561903 original size:17 final size:16
Alignment explanation
Indices: 22561869--22561900 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22561859 AATTGGGTTG
*
22561869 AAAAAATTATTTAATT
1 AAAAAATTAGTTAATT
22561885 AAAAAATTAGTTAATT
1 AAAAAATTAGTTAATT
22561901 TAATTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AAAAAATTAGTTAATT
Found at i:22563586 original size:20 final size:20
Alignment explanation
Indices: 22563561--22563600 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
22563551 GTGATCTTGA
22563561 GTAGAAGTAGACTTGTATTG
1 GTAGAAGTAGACTTGTATTG
*
22563581 GTAGAAGTGGACTTGTATTG
1 GTAGAAGTAGACTTGTATTG
22563601 ATACAACTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.35
Consensus pattern (20 bp):
GTAGAAGTAGACTTGTATTG
Found at i:22566642 original size:16 final size:16
Alignment explanation
Indices: 22566621--22566665 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
22566611 TACTTTTTAA
*
22566621 AATAATTTTAATTTTT
1 AATAATTTTAAATTTT
22566637 AATAATTTTATAAATTTT
1 AATAA-TTT-TAAATTTT
22566655 AA-AATTTTAAA
1 AATAATTTTAAA
22566666 AATTTAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 5 0.19
18 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATTTTAAATTTT
Found at i:22566659 original size:8 final size:8
Alignment explanation
Indices: 22566624--22566672 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
22566614 TTTTTAAAAT
22566624 AATTTT-A
1 AATTTTAA
*
22566631 ATTTTTAA
1 AATTTTAA
22566639 TAATTTTATA
1 -AATTTTA-A
22566649 AATTTTAA
1 AATTTTAA
22566657 AATTTTAA
1 AATTTTAA
*
22566665 AAATTTAA
1 AATTTTAA
22566673 TTCTTGACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
7 5 0.14
8 17 0.47
9 13 0.36
10 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AATTTTAA
Found at i:22566662 original size:17 final size:17
Alignment explanation
Indices: 22566615--22566670 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
22566605 TTTTTATACT
*
22566615 TTTTAAAATAATTT-TAAT
1 TTTTAAAAT--TTTATAAA
22566633 TTTTAATAATTTTATAAA
1 TTTTAA-AATTTTATAAA
*
22566651 TTTTAAAATTTTAAAAA
1 TTTTAAAATTTTATAAA
22566668 TTT
1 TTT
22566671 AATTCTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 16 0.47
18 15 0.44
19 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAAATTTTATAAA
Found at i:22571008 original size:25 final size:25
Alignment explanation
Indices: 22570980--22571031 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
22570970 AACAACAATC
* *
22570980 CATGTAAATCATGTAACTTTTAAAT
1 CATGTAAATCATATAACATTTAAAT
*
22571005 CATGTAAATCATATAACATTTATAT
1 CATGTAAATCATATAACATTTAAAT
22571030 CA
1 CA
22571032 ATTTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (25 bp):
CATGTAAATCATATAACATTTAAAT
Found at i:22571327 original size:23 final size:23
Alignment explanation
Indices: 22571295--22571363 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
22571285 CGAGCTGAAT
* * *
22571295 AAACGATAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
*
22571318 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
22571341 AAACGGTAAGCT-CATACGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
22571364 TGGTGAGTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 3 0.08
23 37 0.93
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:22577944 original size:20 final size:21
Alignment explanation
Indices: 22577898--22577941 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
22577888 ACACATAATG
22577898 TTTCCATTCTAAAATAAACAT
1 TTTCCATTCTAAAATAAACAT
22577919 TTTCCATTCTAAAATAAACAT
1 TTTCCATTCTAAAATAAACAT
22577940 TT
1 TT
22577942 CCAACTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTCCATTCTAAAATAAACAT
Found at i:22578352 original size:25 final size:25
Alignment explanation
Indices: 22578324--22578375 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
22578314 AACAACAATC
* *
22578324 CATGTAAATCATGTAACTTTTAAAT
1 CATGTAAATCATATAACATTTAAAT
*
22578349 CATGTAAATCATATAACATTTATAT
1 CATGTAAATCATATAACATTTAAAT
22578374 CA
1 CA
22578376 AAATTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (25 bp):
CATGTAAATCATATAACATTTAAAT
Found at i:22578667 original size:23 final size:23
Alignment explanation
Indices: 22578640--22578708 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
22578630 CGAGCTAAAT
* *
22578640 AAACGGTAAGCTCTATTGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
*
22578663 AAACGGTAAGCTCCGTAGAGCTG
1 AAACGGTAAGCTCCATAGAGCTG
22578686 AAACGGTAAGCT-CATACGAGCTG
1 AAACGGTAAGCTCCATA-GAGCTG
22578709 TGGTGAGTCC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 3 0.07
23 38 0.93
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCCATAGAGCTG
Found at i:22584362 original size:25 final size:25
Alignment explanation
Indices: 22584323--22584394 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
22584313 TAGGCCCATT
* *
22584323 TTCACAGCTCGTGTGAGCATACTAA
1 TTCACAGCTCATGTGAGCATACCAA
* *
22584348 TTTACAGCTCATGTGAGCATACCGA
1 TTCACAGCTCATGTGAGCATACCAA
22584373 TTCACAGCTCATGTGAGCATAC
1 TTCACAGCTCATGTGAGCATAC
22584395 ATGTACAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (25 bp):
TTCACAGCTCATGTGAGCATACCAA
Found at i:22584874 original size:22 final size:22
Alignment explanation
Indices: 22584846--22584953 Score: 144
Period size: 22 Copynumber: 4.9 Consensus size: 22
22584836 TTTATTGTTC
*
22584846 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
22584868 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
22584890 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
22584912 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
22584934 AAACATGAGAGCTTAGTACG
1 AAACATGAGAGCTTAGTACG
22584954 GTTGTTGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:22598425 original size:22 final size:21
Alignment explanation
Indices: 22598400--22598443 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
22598390 TGATAAACTT
22598400 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
22598422 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
22598443 T
1 T
22598444 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:22600012 original size:12 final size:11
Alignment explanation
Indices: 22599987--22600024 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
22599977 GAACATGATG
22599987 AATTTTA-ATT
1 AATTTTATATT
22599997 AATTTTATAGTT
1 AATTTTATA-TT
22600009 AATTTT-TATT
1 AATTTTATATT
22600019 AATTTT
1 AATTTT
22600025 GACTATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (11 bp):
AATTTTATATT
Found at i:22600264 original size:14 final size:15
Alignment explanation
Indices: 22600243--22600285 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
22600233 AAAAAAAGGG
*
22600243 TCTAGTTGAACCGCA
1 TCTAGTTGAACCGAA
22600258 T-TAGTTGAACCGAA
1 TCTAGTTGAACCGAA
22600272 TCTAG-TGAACCGAA
1 TCTAGTTGAACCGAA
22600286 CCAGCCACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (15 bp):
TCTAGTTGAACCGAA
Found at i:22603951 original size:12 final size:12
Alignment explanation
Indices: 22603925--22603957 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22603915 TAGTTTAGGT
22603925 TTAG-TTTTC-C
1 TTAGCTTTTCTC
22603935 TTAGCTTTTCTC
1 TTAGCTTTTCTC
22603947 TTAGCTTTTCT
1 TTAGCTTTTCT
22603958 TCCTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 4 0.19
11 5 0.24
12 12 0.57
ACGTcount: A:0.09, C:0.21, G:0.09, T:0.61
Consensus pattern (12 bp):
TTAGCTTTTCTC
Found at i:22606514 original size:23 final size:23
Alignment explanation
Indices: 22606470--22606514 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
22606460 GATTTAATCA
*
22606470 CAATATAATCACATATTAACATT
1 CAATATAATCACAAATTAACATT
*
22606493 CAATTTAATCA-AAATTATACAT
1 CAATATAATCACAAATTA-ACAT
22606515 AATACAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (23 bp):
CAATATAATCACAAATTAACATT
Found at i:22606600 original size:17 final size:16
Alignment explanation
Indices: 22606571--22606605 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
22606561 AGTTCAGGGG
22606571 CATTTTTATAATTTTC
1 CATTTTTATAATTTTC
*
22606587 CATTTTTCTCAATTTTC
1 CATTTTTAT-AATTTTC
22606604 CA
1 CA
22606606 CCTGATCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (16 bp):
CATTTTTATAATTTTC
Found at i:22610009 original size:3 final size:3
Alignment explanation
Indices: 22610001--22610031 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
22609991 ATTTTTAATA
22610001 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22610032 GTAAGATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22610227 original size:23 final size:23
Alignment explanation
Indices: 22610181--22610229 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
22610171 GAAATAAAAT
*
22610181 ACCTAACCCGAAATACTAACTAA
1 ACCTAACCCGAAATACCAACTAA
* * *
22610204 ACCTAACCCGAATTACCCATTAA
1 ACCTAACCCGAAATACCAACTAA
22610227 ACC
1 ACC
22610230 CTAGCCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.35, G:0.04, T:0.18
Consensus pattern (23 bp):
ACCTAACCCGAAATACCAACTAA
Found at i:22613277 original size:5 final size:5
Alignment explanation
Indices: 22613267--22613292 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
22613257 GTAAGCTAAA
22613267 CGCAC CGCAC CGCAC CGCAC CGCAC C
1 CGCAC CGCAC CGCAC CGCAC CGCAC C
22613293 CAATTGTCCA
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:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CGCAC
Found at i:22616667 original size:89 final size:88
Alignment explanation
Indices: 22616516--22616689 Score: 312
Period size: 89 Copynumber: 2.0 Consensus size: 88
22616506 TAGCTCTTGA
* *
22616516 TCAAAAATGAATTGTAATAGAGAGTATTTATAACTTATTGGCTTGATGCGTACAACACGTAAATT
1 TCAAAAATGAATTATAATAGAGAGTATTTATAACTTATTGGCTTGATGCATACAACACGTAAATT
22616581 AACATAATTTCATGTTGAAAAAGG
66 AACATAATTTCATGTT-AAAAAGG
*
22616605 TCAAAAATGAATTATAATGGAGAGTATTTATAACTTATTGGCTTGATGCATACAACACGTAAATT
1 TCAAAAATGAATTATAATAGAGAGTATTTATAACTTATTGGCTTGATGCATACAACACGTAAATT
22616670 AACATAATTTCATGTTAAAA
66 AACATAATTTCATGTTAAAA
22616690 GAGGAAGTTT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
88 4 0.05
89 78 0.95
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (88 bp):
TCAAAAATGAATTATAATAGAGAGTATTTATAACTTATTGGCTTGATGCATACAACACGTAAATT
AACATAATTTCATGTTAAAAAGG
Found at i:22620919 original size:23 final size:23
Alignment explanation
Indices: 22620893--22620954 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
22620883 TAAAAAATTT
* *
22620893 AAAATATATATTATTTATTATAA
1 AAAATATATATTATTAAATATAA
* * * *
22620916 AAAACATAAAATATTAAATATTA
1 AAAATATATATTATTAAATATAA
*
22620939 AAAATATATATAATTA
1 AAAATATATATTATTA
22620955 CATTATAACT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATATATATTATTAAATATAA
Found at i:22624065 original size:19 final size:18
Alignment explanation
Indices: 22624034--22624086 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
22624024 ATATAAGTCT
22624034 AAAAAAT-AAAATAAAAC
1 AAAAAATGAAAATAAAAC
** *
22624051 AACTAATGAAAAATAAAAG
1 AAAAAATG-AAAATAAAAC
22624070 AAAAAATGAAAATAAAA
1 AAAAAATGAAAATAAAA
22624087 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 15 0.52
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (18 bp):
AAAAAATGAAAATAAAAC
Found at i:22624087 original size:19 final size:19
Alignment explanation
Indices: 22624034--22624092 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
22624024 ATATAAGTCT
22624034 AAAAAAT-AAAAT-AAAAC
1 AAAAAATGAAAATAAAAAC
** *
22624051 AACTAATGAAAA-ATAAAAG
1 AAAAAATGAAAATA-AAAAC
*
22624070 AAAAAATGAAAATAAAAAT
1 AAAAAATGAAAATAAAAAC
22624089 AAAA
1 AAAA
22624093 TAATTAAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
17 5 0.16
18 4 0.12
19 22 0.69
20 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAATGAAAATAAAAAC
Found at i:22626103 original size:25 final size:27
Alignment explanation
Indices: 22626048--22626104 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
22626038 TTGGAAGAGG
22626048 AAAATTTGGAGAAGAACATCAAAAATA
1 AAAATTTGGAGAAGAACATCAAAAATA
22626075 AAAATTTGGAGAGAGAA-A-C-AAAATA
1 AAAATTTGGAGA-AGAACATCAAAAATA
22626100 AAAAT
1 AAAAT
22626105 AAAAATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.38
26 1 0.03
27 13 0.45
28 4 0.14
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAATTTGGAGAAGAACATCAAAAATA
Found at i:22633126 original size:6 final size:6
Alignment explanation
Indices: 22633103--22633146 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
22633093 AAATTGAATG
* *
22633103 TAAAAA TTAAAT TAAAAA TAAAAA TATTAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA
22633147 AATTGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
6 26 0.81
8 6 0.19
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (6 bp):
TAAAAA
Found at i:22633133 original size:20 final size:19
Alignment explanation
Indices: 22633104--22633147 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
22633094 AATTGAATGT
*
22633104 AAAAATTAAATTAAAAATA
1 AAAAATTAAAATAAAAATA
22633123 AAAATATTAAAATAAAAATA
1 AAAA-ATTAAAATAAAAATA
22633143 AAAAA
1 AAAAA
22633148 ATTGCCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATTAAAATAAAAATA
Found at i:22633148 original size:14 final size:14
Alignment explanation
Indices: 22633116--22633149 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
22633106 AAATTAAATT
*
22633116 AAAAATAAAAATAT
1 AAAAATAAAAATAA
*
22633130 TAAAATAAAAATAA
1 AAAAATAAAAATAA
22633144 AAAAAT
1 AAAAAT
22633150 TGCCAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:22636816 original size:24 final size:24
Alignment explanation
Indices: 22636795--22636844 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
22636785 AATCAATGTC
*
22636795 AAATATATTATGCTAACAAATGCT
1 AAATATATTATACTAACAAATGCT
* *
22636819 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAACAAATGCT
22636843 AA
1 AA
22636845 TTCTTCTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.34
Consensus pattern (24 bp):
AAATATATTATACTAACAAATGCT
Found at i:22645874 original size:14 final size:13
Alignment explanation
Indices: 22645844--22645882 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
22645834 ATGAAGAGCT
*
22645844 TAATAATAACA-A
1 TAATAATAATACA
22645856 TAATAATATATACA
1 TAATAATA-ATACA
22645870 TAATAATAATACA
1 TAATAATAATACA
22645883 AAAAGGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 8 0.33
13 7 0.29
14 9 0.38
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAATACA
Found at i:22647873 original size:12 final size:12
Alignment explanation
Indices: 22647856--22647880 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22647846 GGTGTTCATT
22647856 CGGTTAACCGAC
1 CGGTTAACCGAC
22647868 CGGTTAACCGAC
1 CGGTTAACCGAC
22647880 C
1 C
22647881 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:22648078 original size:27 final size:27
Alignment explanation
Indices: 22648041--22648126 Score: 136
Period size: 27 Copynumber: 3.2 Consensus size: 27
22648031 TTTTGGTTAA
*
22648041 AAATTAACCGAATTACCCGAATTAACC
1 AAATTACCCGAATTACCCGAATTAACC
22648068 AAATTACCCGAATTACCCGAATTAACC
1 AAATTACCCGAATTACCCGAATTAACC
* * *
22648095 GAATTACCCGAATTAACCAAATTAACC
1 AAATTACCCGAATTACCCGAATTAACC
22648122 AAATT
1 AAATT
22648127 GAATCACTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (27 bp):
AAATTACCCGAATTACCCGAATTAACC
Found at i:22648117 original size:9 final size:9
Alignment explanation
Indices: 22648042--22648126 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
22648032 TTTGGTTAAA
22648042 AATTAACCG
1 AATTAACCG
*
22648051 AATTACCCG
1 AATTAACCG
*
22648060 AATTAACCA
1 AATTAACCG
*
22648069 AATTACCCG
1 AATTAACCG
*
22648078 AATTACCCG
1 AATTAACCG
22648087 AATTAACCG
1 AATTAACCG
*
22648096 AATTACCCG
1 AATTAACCG
*
22648105 AATTAACCA
1 AATTAACCG
*
22648114 AATTAACCA
1 AATTAACCG
22648123 AATT
1 AATT
22648127 GAATCACTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:22648790 original size:33 final size:35
Alignment explanation
Indices: 22648735--22648802 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
22648725 ATTCTATAGT
* *
22648735 TTTTAATTATGTCTTGATCATTAAGTG-TTTGCATC
1 TTTTAATTATGACATGA-CATTAAGTGTTTTGCATC
*
22648770 TTTTAATTATGACATG-CATTATGTGTTTTGCAT
1 TTTTAATTATGACATGACATTAAGTGTTTTGCAT
22648803 TAAATAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 8 0.28
34 7 0.24
35 14 0.48
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (35 bp):
TTTTAATTATGACATGACATTAAGTGTTTTGCATC
Found at i:22648953 original size:49 final size:52
Alignment explanation
Indices: 22648886--22648992 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 52
22648876 TGTTAGTTAA
* *
22648886 AGTTTGCATCATTAAATTAAGTCATGCA-TTAAGTAACTTATTTGTTCATTT
1 AGTTTACATCATTAAATTAAGTCATGCATTTAAGCAACTTATTTGTTCATTT
* * *
22648937 AGTTTACATC-TT-AATTAAGTCTTGCATTTAAGCATCTTGTTTGTTCATTT
1 AGTTTACATCATTAAATTAAGTCATGCATTTAAGCAACTTATTTGTTCATTT
22648987 AGTTTA
1 AGTTTA
22648993 AAGCATGAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 13 0.26
50 28 0.56
51 9 0.18
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (52 bp):
AGTTTACATCATTAAATTAAGTCATGCATTTAAGCAACTTATTTGTTCATTT
Found at i:22653728 original size:18 final size:18
Alignment explanation
Indices: 22653705--22653742 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
22653695 CTAGACTTAA
*
22653705 TATAGCTGAACTTTGTTT
1 TATAGCTCAACTTTGTTT
22653723 TATAGCTCAACTTTGTTT
1 TATAGCTCAACTTTGTTT
22653741 TA
1 TA
22653743 CTTGCTCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (18 bp):
TATAGCTCAACTTTGTTT
Found at i:22658021 original size:6 final size:6
Alignment explanation
Indices: 22658005--22658059 Score: 92
Period size: 6 Copynumber: 9.0 Consensus size: 6
22657995 CTAGAGATTG
*
22658005 AAAACT AAAAACT AAAACT AAAACT AAAACT AAAACT AAAATT AAAACT
1 AAAACT -AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT AAAACT
22658054 AAAACT
1 AAAACT
22658060 GCAATTGCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
6 40 0.87
7 6 0.13
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAACT
Found at i:22665817 original size:6 final size:6
Alignment explanation
Indices: 22665808--22665844 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
22665798 CATGGCCATG
*
22665808 GCCACA GCCACA GCCACA GCCACA GCCACG GCCACA G
1 GCCACA GCCACA GCCACA GCCACA GCCACA GCCACA G
22665845 TCGTGGCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.30, C:0.49, G:0.22, T:0.00
Consensus pattern (6 bp):
GCCACA
Found at i:22667780 original size:172 final size:172
Alignment explanation
Indices: 22667371--22667849 Score: 683
Period size: 172 Copynumber: 2.8 Consensus size: 172
22667361 ATTTCGAAGT
* ** * *
22667371 GGTCGTTTGCTACAAATTGGTAGGGTGTTCCATTTTTGTAATTTATTATGTTTTTTGGATTATTG
1 GGTCGTTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTG
* * * **
22667436 GGGTAAAAAGGTCAAGAAACAGTGTATGGTACAACATTTTTACCTAGGTAATATTAAAAAAATAA
66 GGGTAAATAGGTCAAGAAACGGTGTATGGTACAACAATTTTACCTAAATAATA-T-AAAAAATAA
** * * *
22667501 TTAAATACGGAAATGGGTAACCTTACAAATTAAGTACTGAAATG
129 TTAAATACAAAAATGGGCAACCGTACAAATTAAGTACCGAAATG
* * *
22667545 GATCGTTTGTTACAAATTGGTA-GGTGACCCATTTTGGTATTTTATTATTATTTTTTAGATTATT
1 GGTCGTTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTA-TGTTTTTTGGATTATT
*
22667609 GGGGTAAATAGGTCAAGAAACGGTGTATGGTACAATAATTTTACCTAAATAATATAAAAAATAAT
65 GGGGTAAATAGGTCAAGAAACGGTGTATGGTACAACAATTTTACCTAAATAATATAAAAAATAAT
*
22667674 TAAATACAAAAATGGGCAACCGTACAGATTAAGTACCGAAATG
130 TAAATACAAAAATGGGCAACCGTACAAATTAAGTACCGAAATG
*
22667717 GGTCATTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTG
1 GGTCGTTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTG
* * * * *
22667782 GGGTAAATAGGTCAAGACACGATATATGATACAACAATTTTACTTAAATAATATAAAAAA-AATT
66 GGGTAAATAGGTCAAGAAACGGTGTATGGTACAACAATTTTACCTAAATAATATAAAAAATAATT
22667846 AAAT
131 AAAT
22667850 GGACGACATT
Statistics
Matches: 273, Mismatches: 30, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
171 8 0.03
172 136 0.50
173 47 0.17
174 82 0.30
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (172 bp):
GGTCGTTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTG
GGGTAAATAGGTCAAGAAACGGTGTATGGTACAACAATTTTACCTAAATAATATAAAAAATAATT
AAATACAAAAATGGGCAACCGTACAAATTAAGTACCGAAATG
Found at i:22670516 original size:74 final size:73
Alignment explanation
Indices: 22670355--22670517 Score: 263
Period size: 74 Copynumber: 2.2 Consensus size: 73
22670345 AATAATATAA
22670355 AAAAACCCTAAAATTAATAACTGAAATGACAAAAAAGTCATTACATAAATACAAACTTGACTATT
1 AAAAACCCTAAAATTAATAACTGAAATGACAAAAAAGTCATTACATAAATACAAACTTGACTATT
22670420 TAAATTGC
66 TAAATTGC
** * * *
22670428 AAAAACCCTAAAAATTAATAACTGAAATGGGAAAAAAGTCATTATATAACTACAAAGTTGACTAT
1 AAAAACCCT-AAAATTAATAACTGAAATGACAAAAAAGTCATTACATAAATACAAACTTGACTAT
22670493 TTAAATTGC
65 TTAAATTGC
22670502 AAAAACCCCTAAAATT
1 AAAAA-CCCTAAAATT
22670518 GATGGTTTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
73 9 0.11
74 70 0.84
75 4 0.05
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.26
Consensus pattern (73 bp):
AAAAACCCTAAAATTAATAACTGAAATGACAAAAAAGTCATTACATAAATACAAACTTGACTATT
TAAATTGC
Found at i:22670710 original size:33 final size:33
Alignment explanation
Indices: 22670666--22670735 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
22670656 ATGCCATTGA
* * *
22670666 TACTGCGGTGGATATGGGCCGGGAGAAGTGGAG
1 TACTGCAGTGGATACGAGCCGGGAGAAGTGGAG
* *
22670699 TACTGCAGTGGATACGAGCCGGTAGGAGTGGAG
1 TACTGCAGTGGATACGAGCCGGGAGAAGTGGAG
22670732 TACT
1 TACT
22670736 AAGGTGGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.43, T:0.20
Consensus pattern (33 bp):
TACTGCAGTGGATACGAGCCGGGAGAAGTGGAG
Found at i:22674941 original size:15 final size:14
Alignment explanation
Indices: 22674907--22674947 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
22674897 ACATTTCAAT
22674907 AAATC-AATAAAAA
1 AAATCAAATAAAAA
*
22674920 AATTCAAATAAATAA
1 AAATCAAATAAA-AA
22674935 AAATCAAATAAAA
1 AAATCAAATAAAA
22674948 TTACATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 13 0.54
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATCAAATAAAAA
Found at i:22674962 original size:15 final size:16
Alignment explanation
Indices: 22674944--22674978 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
22674934 AAAATCAAAT
22674944 AAAATTACATTA-TAA
1 AAAATTACATTACTAA
22674959 AAAATTACATTACTAA
1 AAAATTACATTACTAA
22674975 AAAA
1 AAAA
22674979 ATCACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACATTACTAA
Found at i:22675248 original size:106 final size:104
Alignment explanation
Indices: 22674953--22675466 Score: 660
Period size: 106 Copynumber: 4.9 Consensus size: 104
22674943 TAAAATTACA
* *
22674953 TTATAAAAAATTACATTACTAAAAAAATCACAAAAATACTAAACTAAACACTAACAATTTATAAC
1 TTATAAAAATTTACATTACTAAAAAAATCA-AAAAATACTAAACTAAACACTAAAAATTTATAAC
* *
22675018 TTAATCATAAATTACAAACAAAATAACTAT--AATT-TTT
65 CTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
* * * * *
22675055 TTAAAAAAAAATAAAAATTTACATTACT-AAAAAATTACAAAACACTAAACTAAACACTAACAGT
1 TT--------ATAAAAATTTACATTACTAAAAAAATCAAAAAATACTAAACTAAACACTAAAAAT
* *
22675119 TTGTAACCTAATCATAAATTACTAACAAAACAACTATAAAATTATTT
58 TTATAACCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
* *
22675166 TTTTTAAAATTTACATTACTAAAAAAAATCAAAAAATACTAAACTAAACACTAAAAATTTTATAA
1 TTATAAAAATTTACATTACT-AAAAAAATCAAAAAATACTAAACTAAACACTAAAAA-TTTATAA
22675231 CCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
64 CCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
* *
22675272 TTTTAAAAATTTACATTACTAAAAAAAATAAAAAAATACTAAACTAAACACTAAAAATTTTATAA
1 TTATAAAAATTTACATTACT-AAAAAAATCAAAAAATACTAAACTAAACACTAAAAA-TTTATAA
22675337 CCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
64 CCTAATCATAAATTACTAACAAAATAACTATAAAATTATTT
** * * * ** * *
22675378 AAAAAAAAAATTACATTACT-AAAAAATCACAAAGCACTAAACTAAAAACTAACAATTTATAACC
1 TTATAAAAATTTACATTACTAAAAAAATCAAAAAATACTAAACTAAACACTAAAAATTTATAACC
22675442 TAATCATAAATTACTAACAAAATAA
66 TAATCATAAATTACTAACAAAATAA
22675467 TTTTACATTA
Statistics
Matches: 367, Mismatches: 31, Indels: 27
0.86 0.07 0.06
Matches are distributed among these distances:
102 2 0.01
103 50 0.14
104 29 0.08
105 30 0.08
106 165 0.45
108 57 0.16
109 8 0.02
110 21 0.06
111 5 0.01
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (104 bp):
TTATAAAAATTTACATTACTAAAAAAATCAAAAAATACTAAACTAAACACTAAAAATTTATAACC
TAATCATAAATTACTAACAAAATAACTATAAAATTATTT
Found at i:22675429 original size:74 final size:80
Alignment explanation
Indices: 22675379--22675546 Score: 212
Period size: 81 Copynumber: 2.1 Consensus size: 80
22675369 AAATTATTTA
* * * *
22675379 AAAAAAAAATTACATTACTAAAAAATCACAAAGCACTAAACTAAAAACTAACAATTTATAACCTA
1 AAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAA-TAATAACCTA
22675444 ATCATAAATTACTAAC
65 ATCATAAATTACTAAC
** * * * *
22675460 AAAATAATTTTACATTAATAAAAAATCACAAAACACTAAACTGAACAC-AACAATTTATAACATA
1 AAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAA-TAATAACCTA
*
22675524 ATCCTAAATTACTAAC
65 ATCATAAATTACTAAC
22675540 AAAATAA
1 AAAATAA
22675547 TTTTAAAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 37 0.47
81 41 0.53
ACGTcount: A:0.58, C:0.17, G:0.01, T:0.24
Consensus pattern (80 bp):
AAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAATAATAACCTAA
TCATAAATTACTAAC
Found at i:22675451 original size:81 final size:81
Alignment explanation
Indices: 22675366--22675546 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 81
22675356 CAAAATAACT
* * *
22675366 ATAAAATTATTTAA-AAAA-AAAATTACATTACTAAAAAATCACAAAGCACTAAACTAAAAACTA
1 ATAAAATTA-CTAACAAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAAC-A
*
22675429 ACAATTTATAACCTAATC
64 ACAATTTATAACATAATC
** * *
22675447 AT-AAATTACTAACAAAATAATTTTACATTAATAAAAAATCACAAAACACTAAACTGAACACAAC
1 ATAAAATTACTAACAAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAACAAC
22675511 AATTTATAACATAATC
66 AATTTATAACATAATC
*
22675527 CT-AAATTACTAACAAAATAA
1 ATAAAATTACTAACAAAATAA
22675547 TTTTAAAATA
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
79 3 0.03
80 47 0.53
81 39 0.44
ACGTcount: A:0.57, C:0.15, G:0.01, T:0.26
Consensus pattern (81 bp):
ATAAAATTACTAACAAAATAAAATTACATTAATAAAAAATCACAAAACACTAAACTAAAAACAAC
AATTTATAACATAATC
Found at i:22675526 original size:80 final size:81
Alignment explanation
Indices: 22675388--22675551 Score: 267
Period size: 80 Copynumber: 2.0 Consensus size: 81
22675378 AAAAAAAAAA
* * *
22675388 TTACATTACTAAAAAATCACAAAGCACTAAACTAAAAACTAACAATTTATAACCTAATCATAAAT
1 TTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAATTTATAACATAATCATAAAT
22675453 TACTAACAAAATAATT
66 TACTAACAAAATAATT
* * *
22675469 TTACATTAATAAAAAATCACAAAACACTAAACTGAACAC-AACAATTTATAACATAATCCTAAAT
1 TTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAATTTATAACATAATCATAAAT
22675533 TACTAACAAAATAATT
66 TACTAACAAAATAATT
22675549 TTA
1 TTA
22675552 AAATAATTAT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 42 0.55
81 35 0.45
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.27
Consensus pattern (81 bp):
TTACATTAATAAAAAATCACAAAACACTAAACTAAAAACTAACAATTTATAACATAATCATAAAT
TACTAACAAAATAATT
Found at i:22675741 original size:14 final size:14
Alignment explanation
Indices: 22675707--22675750 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
22675697 AATACATACC
22675707 TTTTTT-TTCTTCCT
1 TTTTTTCTTCTT-CT
*
22675721 TTCTTTCTTCTTCT
1 TTTTTTCTTCTTCT
*
22675735 TTTTTTCTTCTCCT
1 TTTTTTCTTCTTCT
22675749 TT
1 TT
22675751 CTCTCCTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTTCTTCTTCT
Found at i:22675759 original size:23 final size:26
Alignment explanation
Indices: 22675708--22675764 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 26
22675698 ATACATACCT
* *
22675708 TTTTTTTCTTCCTTTCTTTCTTCTTC
1 TTTTTTTCTTCCTTCCTTTCTTCTCC
22675734 TTTTTTTCTT-C-TCCTTTC-TCTCC
1 TTTTTTTCTTCCTTCCTTTCTTCTCC
*
22675757 TTTCTTTC
1 TTTTTTTC
22675765 CCTCTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.39
24 6 0.21
25 1 0.04
26 10 0.36
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTTTTTCTTCCTTCCTTTCTTCTCC
Found at i:22675785 original size:37 final size:35
Alignment explanation
Indices: 22675712--22675779 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
22675702 ATACCTTTTT
*
22675712 TTTCTTCCTTTCTTTCTTCTTCTTTTTTTCTTCTCC
1 TTTCTTCCTTTCTTTC-TCCTCTTTTTTTCTTCTCC
22675748 TTTCTCTCCTTTCTTTC-CCTCTTTTTTTCTTC
1 TTTCT-TCCTTTCTTTCTCCTCTTTTTTTCTTC
22675780 ACTCCTGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 14 0.47
36 5 0.17
37 11 0.37
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (35 bp):
TTTCTTCCTTTCTTTCTCCTCTTTTTTTCTTCTCC
Found at i:22676920 original size:20 final size:19
Alignment explanation
Indices: 22676879--22676959 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 19
22676869 AAAAGAGGGA
*
22676879 AAGAAAGGAGAGAAAAGAG
1 AAGAAAAGAGAGAAAAGAG
22676898 AAGAAAAGA-AGAAGAAGAGG
1 AAGAAAAGAGAGAA-AAGA-G
*
22676918 AAGAAGAA-AGAAAGAAAGA-
1 AAGAA-AAGAGAGA-AAAGAG
*
22676937 AAG-AAAGAAAG-AAAGA-
1 AAGAAAAGAGAGAAAAGAG
22676953 AAGAAAA
1 AAGAAAA
22676960 AATGTATGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
16 8 0.16
17 5 0.10
18 7 0.14
19 15 0.29
20 7 0.14
21 8 0.16
22 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAGAAAAGAGAGAAAAGAG
Found at i:22676930 original size:4 final size:4
Alignment explanation
Indices: 22676877--22676958 Score: 80
Period size: 4 Copynumber: 20.0 Consensus size: 4
22676867 AAAAAAGAGG
* *
22676877 GAAA GAAA GGAGA GAAAA GAGAA GAAA -AGAA G-AA GAAGA GGAA G-AA
1 GAAA GAAA -GAAA G-AAA GA-AA GAAA GA-AA GAAA GAA-A GAAA GAAA
22676923 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
22676959 AAATGTATGC
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
3 7 0.10
4 47 0.70
5 13 0.19
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:22677190 original size:101 final size:100
Alignment explanation
Indices: 22677085--22677416 Score: 389
Period size: 101 Copynumber: 3.4 Consensus size: 100
22677075 ATGGTTTAAT
* *
22677085 TTTTTTA-TGAATGCAAATTTTTTATAATTATTTTAAAATTATTCTGTTAGTAATTTGA-GATTA
1 TTTTTTAGT-AATGTAAATTTTTTATAATTATTTT-AAATTATTTTGTTAGTAATTT-ATGATTA
** *
22677148 TATTATAAATTGTT-GGGTTTAGTTTAGTGTTTTGTGA
63 GGTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
* * * *
22677185 TTTTTTTATTAATGTAAA---ATTAT--TT-TGTT-AATTATTTTGTTAGTAATTTATGGTTAGG
1 -TTTTTTAGTAATGTAAATTTTTTATAATTATTTTAAATTATTTTGTTAGTAATTTATGATTAGG
22677243 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
65 TTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
* * * *
22677279 TTTTTTAGTAATGT-AATTTTTTAAAAATAATTTTATAGTTATTTTGTTAGCAATTTATGATTAG
1 TTTTTTAGTAATGTAAATTTTTT-ATAATTATTTTA-AATTATTTTGTTAGTAATTTATGATTAG
22677343 GTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
64 GTTATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
*
22677380 TTTTTTAGTAATGTAAAATTTTTATAATGTAATTTTA
1 TTTTTTAGTAATGTAAATTTTTTATAAT-T-ATTTTA
22677417 TTTGATTTTT
Statistics
Matches: 197, Mismatches: 19, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
92 3 0.02
93 48 0.24
94 22 0.11
95 5 0.03
96 3 0.02
98 5 0.03
99 3 0.02
101 94 0.48
102 8 0.04
103 6 0.03
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (100 bp):
TTTTTTAGTAATGTAAATTTTTTATAATTATTTTAAATTATTTTGTTAGTAATTTATGATTAGGT
TATAAATTGTTAGTGTTTAGTTTAGTGTTTTGTGA
Found at i:22677219 original size:12 final size:12
Alignment explanation
Indices: 22677202--22677226 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22677192 ATTAATGTAA
22677202 AATTATTTTGTT
1 AATTATTTTGTT
22677214 AATTATTTTGTT
1 AATTATTTTGTT
22677226 A
1 A
22677227 GTAATTTATG
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (12 bp):
AATTATTTTGTT
Found at i:22679423 original size:33 final size:33
Alignment explanation
Indices: 22679379--22679569 Score: 170
Period size: 33 Copynumber: 5.8 Consensus size: 33
22679369 CAGCCTACTA
*
22679379 CCACCTCAGTACTCCACTCCTCCCGACTCGTAT
1 CCACCTCAGTACTCCACTCCTCCCGGCTCGTAT
* *
22679412 CCACCTTAGTACTCCACTCCTCCCGGCTTGTAT
1 CCACCTCAGTACTCCACTCCTCCCGGCTCGTAT
** * * * *
22679445 CCACAACAATACTCCACTCTTCCTGGCTTGTAT
1 CCACCTCAGTACTCCACTCCTCCCGGCTCGTAT
* * * ** *
22679478 CCACCTAAGCACTCCACTCATCTTGGC-CTATAT
1 CCACCTCAGTACTCCACTCCTCCCGGCTC-GTAT
* * * *
22679511 CCACAGT-GGTACTCCACTCCTTCCGGCCCGTAT
1 CCAC-CTCAGTACTCCACTCCTCCCGGCTCGTAT
*
22679544 CCACCACAGTACTCCACTCCTCCCGG
1 CCACCTCAGTACTCCACTCCTCCCGG
22679570 TTCAAGTTCA
Statistics
Matches: 124, Mismatches: 30, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
33 122 0.98
34 2 0.02
ACGTcount: A:0.19, C:0.43, G:0.12, T:0.26
Consensus pattern (33 bp):
CCACCTCAGTACTCCACTCCTCCCGGCTCGTAT
Found at i:22679852 original size:73 final size:73
Alignment explanation
Indices: 22679728--22679889 Score: 245
Period size: 73 Copynumber: 2.2 Consensus size: 73
22679718 TCAAACCATC
* * *
22679728 AATTTTAGGGGGTTTTGCAATTTAAATAGTCAACTTTGTATTTATGTAATGACTTTTTTGTC-AT
1 AATTTTA-GGGTTTTTGCAATTTAAATAGTCAACTTTGCATTTATGCAATGACTTTTTT-TCTAT
*
22679792 TTCAGTTATT
64 TTAAGTTATT
*
22679802 AATTTTAGGGTTTTTGCAATTTAAATAGTCAAGTTTGCATTTATGCAATGACTTTTTTTCTATTT
1 AATTTTAGGGTTTTTGCAATTTAAATAGTCAACTTTGCATTTATGCAATGACTTTTTTTCTATTT
*
22679867 AAGTTGTT
66 AAGTTATT
22679875 AATTTTAGGGTTTTT
1 AATTTTAGGGTTTTT
22679890 TTGTATTATT
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
72 2 0.02
73 72 0.89
74 7 0.09
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.51
Consensus pattern (73 bp):
AATTTTAGGGTTTTTGCAATTTAAATAGTCAACTTTGCATTTATGCAATGACTTTTTTTCTATTT
AAGTTATT
Found at i:22682989 original size:18 final size:19
Alignment explanation
Indices: 22682966--22683001 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
22682956 TATCCTTCTT
22682966 TTTGTTCTCCTT-TCTTTC
1 TTTGTTCTCCTTATCTTTC
22682984 TTTGTTCTCCTTATCTTT
1 TTTGTTCTCCTTATCTTT
22683002 TTCCTTCTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.03, C:0.25, G:0.06, T:0.67
Consensus pattern (19 bp):
TTTGTTCTCCTTATCTTTC
Found at i:22683270 original size:18 final size:19
Alignment explanation
Indices: 22683233--22683274 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
22683223 AGGCATCGCT
22683233 AATAAAATAATATTAAAAA
1 AATAAAATAATATTAAAAA
*
22683252 AATAAAA-ATTATTATAAAA
1 AATAAAATAATATTA-AAAA
22683271 AATA
1 AATA
22683275 GGTGGTGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAATAATATTAAAAA
Found at i:22683677 original size:28 final size:27
Alignment explanation
Indices: 22683614--22683677 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
22683604 AACCAACAAT
* * *
22683614 TTATTCTTGTAATTAATTTTTTTTCTA
1 TTATTTTTGTAATTAATTATTTTTATA
* *
22683641 TTACATTTTGTAATTAATTAATTTTTATC
1 TTA-TTTTTGTAATTAATT-ATTTTTATA
22683670 TTATTTTT
1 TTATTTTT
22683678 ATAAAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
27 3 0.10
28 17 0.59
29 9 0.31
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (27 bp):
TTATTTTTGTAATTAATTATTTTTATA
Found at i:22687475 original size:44 final size:44
Alignment explanation
Indices: 22687420--22688278 Score: 367
Period size: 44 Copynumber: 19.3 Consensus size: 44
22687410 GTTGCAAACT
* * * * *
22687420 CAGGGAGGCAAGGTTGGTGTCTTTGATTTGCTTCGCTGTTAGCA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * ***
22687464 CAGGAAGGCAAGATTTGCTATC-TTCAGTCTGCTCCGCTGTCAACC
1 CAGGAAGGCAAGA-TTGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* * ** * * *
22687509 CAGGGAGGCATGGCTGGTGTCTTCGATCTGCTTTGCTGGCAGTA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * ***
22687553 CAGGAAGGCAAGATCTGCTATC-TTCAGTCTGCTCCACTGTTAACC
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** *
22687598 CAGGGAGGCAAGGCTGGTGT-TTTCGATCTGCTTCGCTGTTAGTA
1 CAGGAAGGCAAGATTGGTGTCTTT-GATCTGCTTCGCTGTCAGTA
* * * * *
22687642 CAGGAAGGCAAGATCTGCTATC-TTCAGTCTTCTCCGCTGTCAGTA
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* * * *
22687687 CAGGGAGGCAAGACTGGTGTCTTCGATCTGCTTCACTGTCAGTA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * ***
22687731 CAGGAAGGCAAGATCTGCTATC-TTCAGTCTGCTCCACTATCAACC
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** *
22687776 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * * ***
22687820 TAGGAAGGCAAGATCTGCT-ACCTTCAGTCTACTCCGCTGTCAACC
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** *
22687865 CAGGGAA-GCGAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTA
1 CA-GGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * ***
22687909 TAGGAAGGCAATATCTGCTATC-TTCAGTCTGCTTCGCTGTTAACC
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** *
22687954 CAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * *
22687998 AAGGAAGGCAAGATCTGCTATC-TTCAGTCTTCTTTGCTGTCAGTA
1 CAGGAAGGCAAGAT-TGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
** *
22688043 CAAGG-AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCAGTA
1 C-AGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * *
22688087 CAGGAAGGAAAGATTTGCTATC-TTCAGTCTGCTCCGCTGTCA-AA
1 CAGGAAGGCAAGA-TTGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** * *
22688131 CTAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTATCAGTA
1 C-AGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
* * * * * * * * ***
22688176 TAGGAAGGCAATATTTGCTATC-TTCAGTATGCTCCGTTGTCAACC
1 CAGGAAGGCAAGA-TTGGTGTCTTTGA-TCTGCTTCGCTGTCAGTA
* ** * * *
22688221 CAGGGAGGCAAGGCTGGTGTCTTTGACCTGCTTCACTGTTAGTA
1 CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
22688265 CAGGAAGGCAAGAT
1 CAGGAAGGCAAGAT
22688279 CCGCTATCTT
Statistics
Matches: 558, Mismatches: 222, Indels: 70
0.66 0.26 0.08
Matches are distributed among these distances:
43 7 0.01
44 277 0.50
45 267 0.48
46 7 0.01
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (44 bp):
CAGGAAGGCAAGATTGGTGTCTTTGATCTGCTTCGCTGTCAGTA
Found at i:22687493 original size:89 final size:89
Alignment explanation
Indices: 22687344--22688290 Score: 1311
Period size: 89 Copynumber: 10.6 Consensus size: 89
22687334 GGAGACAGAA
* * * * * * * *
22687344 CTGGTATCTTCGATCTGCTTTGCTGTCAATACAGGAAGGCAAGATTTGTTATTTTTAGTCTGTTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
22687409 CGTTG-CAAACTCAGGGAGGCAAGG
66 CGCTGTC-AACCCAGGGAGGCAAGG
* * * * * *
22687433 TTGGTGTCTTTGATTTGCTTCGCTGTTAGCACAGGAAGGCAAGATTTGCTATCTTCAGTCTGCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
*
22687498 CGCTGTCAACCCAGGGAGGCATGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* *
22687522 CTGGTGTCTTCGATCTGCTTTGCTGGCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
22687587 CACTGTTAACCCAGGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * *
22687611 CTGGTGTTTTCGATCTGCTTCGCTGTTAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTTCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
*** *
22687676 CGCTGTCAGTACAGGGAGGCAAGA
66 CGCTGTCAACCCAGGGAGGCAAGG
*
22687700 CTGGTGTCTTCGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
22687765 CACTATCAACCCAGGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * *
22687789 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTATAGGAAGGCAAGATCTGCTACCTTCAGTCTACTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
22687854 CGCTGTCAACCCAGGGAAGCGAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * *
22687878 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTATAGGAAGGCAATATCTGCTATCTTCAGTCTGCTT
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
*
22687943 CGCTGTTAACCCAGGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * *
22687967 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTAAAGGAAGGCAAGATCTGCTATCTTCAGTCTTCTT
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *** *
22688032 TGCTGTCAGTACAAGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* *
22688056 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGAAAGATTTGCTATCTTCAGTCTGCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
* *
22688121 CGCTGTCAAACTAGGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * * * *
22688145 CTGGTGTCTTCGATCTGCTTCGCTATCAGTATAGGAAGGCAATATTTGCTATCTTCAGTATGCTC
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
*
22688210 CGTTGTCAACCCAGGGAGGCAAGG
66 CGCTGTCAACCCAGGGAGGCAAGG
* * * * *
22688234 CTGGTGTCTTTGACCTGCTTCACTGTTAGTACAGGAAGGCAAGATCCGCTATCTTCA
1 CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
22688291 CTGATCTGTT
Statistics
Matches: 758, Mismatches: 99, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
89 757 1.00
90 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (89 bp):
CTGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTC
CGCTGTCAACCCAGGGAGGCAAGG
Found at i:22690140 original size:13 final size:12
Alignment explanation
Indices: 22690101--22690160 Score: 52
Period size: 13 Copynumber: 4.9 Consensus size: 12
22690091 CCTGTAGAGG
22690101 TTTTTG-TTTGT
1 TTTTTGTTTTGT
* *
22690112 TTTTTGTTCCTAT
1 TTTTTGTT-TTGT
22690125 TTTTTGCTTTTGT
1 TTTTTG-TTTTGT
22690138 TTTTTGTTTT-T
1 TTTTTGTTTTGT
*
22690149 TTGTTTTTTTTG
1 TT-TTTGTTTTG
22690161 ATCGAATCTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 9 0.23
12 12 0.31
13 16 0.41
14 2 0.05
ACGTcount: A:0.02, C:0.05, G:0.13, T:0.80
Consensus pattern (12 bp):
TTTTTGTTTTGT
Found at i:22696792 original size:8 final size:9
Alignment explanation
Indices: 22696770--22696860 Score: 58
Period size: 9 Copynumber: 9.1 Consensus size: 9
22696760 GCCCATTTTT
22696770 ATTTTAAAA
1 ATTTTAAAA
22696779 ATTTTAAAA
1 ATTTTAAAA
*
22696788 ATTTAAAAAAA
1 ATTT--TAAAA
22696799 GTATTTTAAAAA
1 --ATTTT-AAAA
22696811 TATTTTTAAAA
1 -A-TTTTAAAA
22696822 TATTTTTAAAA
1 -A-TTTTAAAA
22696833 TATTTT-AAA
1 -ATTTTAAAA
**
22696842 ATTAAAAAA
1 ATTTTAAAA
22696851 ATTTTAAAA
1 ATTTTAAAA
22696860 A
1 A
22696861 AGTATGTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
8 3 0.04
9 27 0.39
10 4 0.06
11 23 0.33
12 8 0.12
13 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:22696809 original size:11 final size:11
Alignment explanation
Indices: 22696795--22696843 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
22696785 AAAATTTAAA
*
22696795 AAAAGTATTTTA
1 AAAA-TATTTTT
22696807 AAAATATTTTT
1 AAAATATTTTT
22696818 AAAATATTTTT
1 AAAATATTTTT
22696829 AAAATA-TTTT
1 AAAATATTTTT
22696839 AAAAT
1 AAAAT
22696844 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
10 9 0.25
11 23 0.64
12 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
AAAATATTTTT
Found at i:22696825 original size:22 final size:22
Alignment explanation
Indices: 22696771--22696843 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
22696761 CCCATTTTTA
22696771 TTTTAAAA-ATTTTAAAAAT-T
1 TTTTAAAATATTTTAAAAATAT
***
22696791 TAAAAAAAGTATTTTAAAAATAT
1 TTTTAAAA-TATTTTAAAAATAT
*
22696814 TTTTAAAATATTTTTAAAATA-
1 TTTTAAAATATTTTAAAAATAT
22696835 TTTTAAAAT
1 TTTTAAAAT
22696844 TAAAAAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 5 0.12
21 9 0.21
22 23 0.53
23 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
TTTTAAAATATTTTAAAAATAT
Found at i:22696859 original size:10 final size:10
Alignment explanation
Indices: 22696770--22696882 Score: 65
Period size: 11 Copynumber: 10.9 Consensus size: 10
22696760 GCCCATTTTT
22696770 ATTTT-AAAA
1 ATTTTAAAAA
22696779 ATTTT-AAAA
1 ATTTTAAAAA
*
22696788 ATTTAAAAAAA
1 ATTT-TAAAAA
22696799 GTATTTTAAAAA
1 --ATTTTAAAAA
22696811 TATTTTTAAAATA
1 -A-TTTTAAAA-A
* *
22696824 TTTTTAAAAT
1 ATTTTAAAAA
22696834 ATTTT--AAA
1 ATTTTAAAAA
*
22696842 A-TTAAAAAA
1 ATTTTAAAAA
22696851 ATTTTAAAAA
1 ATTTTAAAAA
*
22696861 AGTATGTAAAAA
1 A-T-TTTAAAAA
22696873 TATTTTAAAA
1 -ATTTTAAAA
22696883 TTAAAAAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
7 2 0.02
8 3 0.04
9 17 0.21
10 12 0.15
11 21 0.26
12 21 0.26
13 6 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:22702026 original size:15 final size:16
Alignment explanation
Indices: 22702006--22702036 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22701996 TCCTTGTAAC
22702006 TTGTTTG-AATTTTTT
1 TTGTTTGAAATTTTTT
22702021 TTGTTTGAAATTTTTT
1 TTGTTTGAAATTTTTT
22702037 ATCTATAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (16 bp):
TTGTTTGAAATTTTTT
Found at i:22704447 original size:9 final size:10
Alignment explanation
Indices: 22704420--22704445 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
22704410 GTAGGTTCGT
22704420 AAAAAAATTG
1 AAAAAAATTG
22704430 AAAAAAATTG
1 AAAAAAATTG
22704440 AAAAAA
1 AAAAAA
22704446 TTTCGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:22705324 original size:18 final size:19
Alignment explanation
Indices: 22705296--22705350 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
22705286 ATGAAAAGGA
22705296 AAAAGAGATTGAAAAAGATG
1 AAAAGA-ATTGAAAAAGATG
* *
22705316 ATAA-AATTGAAAGAGA-G
1 AAAAGAATTGAAAAAGATG
*
22705333 AAAAGAATCGAAAAAGAT
1 AAAAGAATTGAAAAAGAT
22705351 TGTGAAAAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.14
18 20 0.71
19 1 0.04
20 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.15
Consensus pattern (19 bp):
AAAAGAATTGAAAAAGATG
Found at i:22709620 original size:51 final size:50
Alignment explanation
Indices: 22709544--22709734 Score: 203
Period size: 51 Copynumber: 3.8 Consensus size: 50
22709534 CCGGTTCATA
* *
22709544 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATAAATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTAAA-G
* * *
22709595 TAGTAGCCTACACATAGTACTACACACGTGATCGA--AGCTATCCGGT-ACG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTAAAG
* * *
22709644 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACAAG
1 --TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTA-AAG
*
22709696 TAGTAGCCTGTACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
22709735 TTCACTTTCA
Statistics
Matches: 116, Mismatches: 14, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
49 5 0.04
50 39 0.34
51 67 0.58
52 4 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTAAAG
Found at i:22709750 original size:101 final size:102
Alignment explanation
Indices: 22709534--22709726 Score: 266
Period size: 102 Copynumber: 1.9 Consensus size: 102
22709524 ATTAATGATA
* *
22709534 CCGGTTCATATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATAAATGTAGT
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATAAATGTAGT
*
22709599 AGCCTACACATAGTACTACACACGTGATCGAAGCTAT
66 AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
* * * *
22709636 CCGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACAA-GTA
1 CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATA-AATGTA
**
22709698 GTAGCCTGTACATAGTACTACACACGTGA
64 GTAGCCTACACATAGTACTACACACGTGA
22709727 CCATCACTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
101 35 0.43
102 42 0.52
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CCGGTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATAAATGTAGT
AGCCTACACATAGTACTACACACGTGATCCAAGCTAT
Found at i:22713430 original size:40 final size:41
Alignment explanation
Indices: 22713386--22713542 Score: 149
Period size: 41 Copynumber: 3.8 Consensus size: 41
22713376 TGTGATTCGA
* ** *
22713386 AATAGCTTCGGCTATTTATGGCACTTAGTGTGCA-TTTGGG
1 AATAGCTTCGGCTATATATGGCACTTAGTGTGCAGACTGAG
* *
22713426 AATAGCTTTGGCTATATATGGCACTTAGTGTGTGAGACTGAG
1 AATAGCTTCGGCTATATATGGCACTTAGTGTG-CAGACTGAG
* * * *
22713468 -ATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGA-TTAT
1 AATAGCTTCGGCTATATATGGCACTTAGTGTGC-AGACTGAG
* * *
22713508 AATAGCTTCGGCTATACGATGGTATTTAGTGTGCA
1 AATAGCTTCGGCTATA-TATGGCACTTAGTGTGCA
22713543 AAACATTGAG
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
40 32 0.34
41 47 0.49
42 16 0.17
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.34
Consensus pattern (41 bp):
AATAGCTTCGGCTATATATGGCACTTAGTGTGCAGACTGAG
Found at i:22725730 original size:27 final size:27
Alignment explanation
Indices: 22725700--22725830 Score: 163
Period size: 27 Copynumber: 4.9 Consensus size: 27
22725690 TAAATTATCG
* **
22725700 AAATACCCCCATAGATTAAAATGACCA
1 AAATACCCCTATAGGGTAAAATGACCA
* * **
22725727 AAATACCCCTATAGGGTAAGATAACTG
1 AAATACCCCTATAGGGTAAAATGACCA
* *
22725754 AAATACGCCTATAGGGTAAAATGACTA
1 AAATACCCCTATAGGGTAAAATGACCA
*
22725781 AAATACCCATATAGGGTAAAATGACCA
1 AAATACCCCTATAGGGTAAAATGACCA
*
22725808 AAATACCCCCATAGGGTAAAATG
1 AAATACCCCTATAGGGTAAAATG
22725831 GGTGTTATAC
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 88 1.00
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAAAATGACCA
Found at i:22726267 original size:27 final size:27
Alignment explanation
Indices: 22726182--22726272 Score: 114
Period size: 28 Copynumber: 3.4 Consensus size: 27
22726172 ATGGCACTGT
*
22726182 ACTGTTACTGTATTGGCTAAGGCCCAC
1 ACTGTTACTGTATGGGCTAAGGCCCAC
* * *
22726209 ACTATTACTGCATTGGGCTAAGGCTCAC
1 ACTGTTACTGTA-TGGGCTAAGGCCCAC
22726237 ACTGTTACTGTATCGGGCT-AGGCCCAC
1 ACTGTTACTGTAT-GGGCTAAGGCCCAC
22726264 ACTG-TACTG
1 ACTGTTACTG
22726273 ATACTGAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
26 5 0.09
27 22 0.40
28 28 0.51
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (27 bp):
ACTGTTACTGTATGGGCTAAGGCCCAC
Found at i:22726287 original size:32 final size:34
Alignment explanation
Indices: 22726237--22726306 Score: 81
Period size: 32 Copynumber: 2.1 Consensus size: 34
22726227 TAAGGCTCAC
* * *
22726237 ACTGTTACTGTATCGGGCT-AGGCCCACACTG-T
1 ACTGATACTGAATAGGGCTCAGGCCCACACTGTT
* *
22726269 ACTGATACTGAATAGGGCTCGGGCCCAGACTGTT
1 ACTGATACTGAATAGGGCTCAGGCCCACACTGTT
22726303 ACTG
1 ACTG
22726307 CATGTTGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 16 0.52
33 10 0.32
34 5 0.16
ACGTcount: A:0.21, C:0.26, G:0.27, T:0.26
Consensus pattern (34 bp):
ACTGATACTGAATAGGGCTCAGGCCCACACTGTT
Found at i:22727111 original size:17 final size:16
Alignment explanation
Indices: 22727084--22727116 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
22727074 TAGTTAGACT
22727084 AAACTGAGACTGTAGG
1 AAACTGAGACTGTAGG
22727100 AAACTGGAGACTGTAGG
1 AAACT-GAGACTGTAGG
22727117 GAGACTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (16 bp):
AAACTGAGACTGTAGG
Found at i:22733579 original size:23 final size:23
Alignment explanation
Indices: 22733546--22733643 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
22733536 ATAAGTGCCA
22733546 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
22733569 CACTGATATGTAGCCGTAA-CTAC
1 CACTGAAATGTAGCCG-AAGCTAC
*
22733592 CACTGAAATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
22733615 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
22733638 CACTGA
1 CACTGA
22733644 TCAATAACAC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
22 1 0.01
23 66 0.96
24 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:22735678 original size:27 final size:27
Alignment explanation
Indices: 22735562--22735666 Score: 129
Period size: 27 Copynumber: 3.9 Consensus size: 27
22735552 AATAAATGAT
* * * *
22735562 CGAAATGCCCCTATAGAGTAAAATTAC
1 CGAAATACCCCCATAGGGTAAAATAAC
* * * * *
22735589 TGAAATGCCCCTATAGGGTAAGATGAC
1 CGAAATACCCCCATAGGGTAAAATAAC
22735616 CGAAATACCCCCATAGGGTAAAATAAC
1 CGAAATACCCCCATAGGGTAAAATAAC
22735643 CGAAATACCCCCATAGGGTAAAAT
1 CGAAATACCCCCATAGGGTAAAAT
22735667 GAGTGTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (27 bp):
CGAAATACCCCCATAGGGTAAAATAAC
Found at i:22735678 original size:54 final size:54
Alignment explanation
Indices: 22735555--22735668 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
22735545 AGCTGTCAAT
* * * * * * *
22735555 AAATGATCGAAATGCCCCTATAGAGTAAAATTACTGAAATGCCCCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGAGTAAAATAACCGAAATACCCCCATAGGGTA
* *
22735609 AGATGACCGAAATACCCCCATAGGGTAAAATAACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGAGTAAAATAACCGAAATACCCCCATAGGGTA
22735663 AAATGA
1 AAATGA
22735669 GTGTTATACC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (54 bp):
AAATGACCGAAATACCCCCATAGAGTAAAATAACCGAAATACCCCCATAGGGTA
Found at i:22735912 original size:26 final size:26
Alignment explanation
Indices: 22735859--22735913 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
22735849 TTTGCCACAT
* *
22735859 ATACTGTTACTGGCAGCTTCACTGCG
1 ATACTATTACTGGCAGCTTCACTACG
* **
22735885 ATACTATTATTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTCACTACG
22735911 ATA
1 ATA
22735914 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTCACTACG
Found at i:22736089 original size:28 final size:28
Alignment explanation
Indices: 22736016--22736107 Score: 107
Period size: 28 Copynumber: 3.4 Consensus size: 28
22736006 ATGGCACTGT
* *
22736016 ACTGTTACTATATTGGGATAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
22736044 ACTATTACTGCATTGGGCTAAGGCTCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* *
22736072 ACTGTTACTGTATCGGGCT-AGGCCCAT
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
22736099 ACTG-TACTG
1 ACTGTTACTG
22736108 ATACTGAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 5 0.09
27 10 0.19
28 39 0.72
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:22757715 original size:41 final size:41
Alignment explanation
Indices: 22757658--22757742 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
22757648 TTTAAAATTG
*
22757658 TTTCAAAAGTTTCTAAGAGTTCAAAGTAGATATTCAAAGTT
1 TTTCAAAAGTTTCTAAGAGTTCAAAGTAGATAGTCAAAGTT
22757699 TTTCAAAAGTTTCTAAGAGTTCAAAGTAGATAGTCAAAGTT
1 TTTCAAAAGTTTCTAAGAGTTCAAAGTAGATAGTCAAAGTT
22757740 TTT
1 TTT
22757743 ATCTCTTAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (41 bp):
TTTCAAAAGTTTCTAAGAGTTCAAAGTAGATAGTCAAAGTT
Found at i:22762853 original size:25 final size:25
Alignment explanation
Indices: 22762825--22762877 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
22762815 ATCTTCCTGT
* *
22762825 TATTTAGCTCTTATGAGCATCCCGA
1 TATTTAGCTCTCACGAGCATCCCGA
* * *
22762850 TATTTGGTTCTCACGAGCATTCCGA
1 TATTTAGCTCTCACGAGCATCCCGA
22762875 TAT
1 TAT
22762878 CTGGATCTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
TATTTAGCTCTCACGAGCATCCCGA
Found at i:22762886 original size:25 final size:25
Alignment explanation
Indices: 22762839--22762901 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
22762829 TAGCTCTTAT
* * *
22762839 GAGCATCCCGATATTTGGTTCTCAC
1 GAGCATTCCGATATCTGGATCTCAC
**
22762864 GAGCATTCCGATATCTGGATCTCTT
1 GAGCATTCCGATATCTGGATCTCAC
*
22762889 GAGCTTTCCGATA
1 GAGCATTCCGATA
22762902 AATGGCTCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (25 bp):
GAGCATTCCGATATCTGGATCTCAC
Found at i:22771696 original size:2 final size:2
Alignment explanation
Indices: 22771689--22771719 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22771679 AAGAAATTGA
22771689 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
22771720 TTCCTATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22773160 original size:5 final size:5
Alignment explanation
Indices: 22773150--22773174 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22773140 GGTAAGTTCG
22773150 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
22773175 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:22773373 original size:45 final size:45
Alignment explanation
Indices: 22773277--22773421 Score: 152
Period size: 45 Copynumber: 3.2 Consensus size: 45
22773267 ATCAAACGAG
*
22773277 TAAGACCATAGTTGAAAGACACTAACTATGGCACTATACCGGAAATAAA
1 TAAGACCATAGTTGAAAGACA-T---TATGGCACTATACCAGAAATAAA
* * *
22773326 TAAGACCATAGTTGAAGGACATTATGGCACTATACTAG-AATCGAA
1 TAAGACCATAGTTGAAAGACATTATGGCACTATACCAGAAAT-AAA
* **
22773371 TAAGACCATAGTTGAAAGACACTATGGCA-TCATGTCAG-AATAAA
1 TAAGACCATAGTTGAAAGACATTATGGCACT-ATACCAGAAATAAA
22773415 TAAGACC
1 TAAGACC
22773422 GGGGATGAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
44 13 0.15
45 50 0.60
48 1 0.01
49 20 0.24
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACATTATGGCACTATACCAGAAATAAA
Found at i:22776543 original size:15 final size:15
Alignment explanation
Indices: 22776523--22776552 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22776513 AATTGGATTA
*
22776523 AGAAAATTATTTAAT
1 AGAAAATTAATTAAT
22776538 AGAAAATTAATTAAT
1 AGAAAATTAATTAAT
22776553 TTAATAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AGAAAATTAATTAAT
Found at i:22780023 original size:7 final size:7
Alignment explanation
Indices: 22780006--22780034 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
22779996 TTCAACAAGC
22780006 AAAAT-A
1 AAAATAA
22780012 AAAATAA
1 AAAATAA
22780019 AAAATAA
1 AAAATAA
22780026 AAAATAA
1 AAAATAA
22780033 AA
1 AA
22780035 GAAGAAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAATAA
Found at i:22780129 original size:1 final size:1
Alignment explanation
Indices: 22780123--22780147 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22780113 TTGGATAAAC
22780123 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
22780148 GTTTCCCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:22788562 original size:33 final size:33
Alignment explanation
Indices: 22788520--22788587 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
22788510 GGAGGGGTAA
22788520 GTATGAGATTCCATCTATTCGGGTAATAGAGCT
1 GTATGAGATTCCATCTATTCGGGTAATAGAGCT
22788553 GTATGAGATTCCATCTATTCGGGTAATAGAGCT
1 GTATGAGATTCCATCTATTCGGGTAATAGAGCT
22788586 GT
1 GT
22788588 TCAGGAGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (33 bp):
GTATGAGATTCCATCTATTCGGGTAATAGAGCT
Found at i:22791255 original size:93 final size:93
Alignment explanation
Indices: 22791137--22791349 Score: 329
Period size: 93 Copynumber: 2.3 Consensus size: 93
22791127 AGCCTTGTTA
*
22791137 TCTTTAGCTTTACTGATCTTCTTCTTGTTCTTCTTCTCGGTTTTCTCTTCGACAACTTCCGGAAT
1 TCTTTAGCTTTACTGATCTTCTTCTTGTTCTTCTTCTCGGTTTTCTCTTCGACAACTTCCGAAAT
** *
22791202 TTGTGAATCCC-TTGGAGGTTCAACAGAT
66 TAATGAA-CCCTTTGGACGTTCAACAGAT
* * * *
22791230 TCTTCAGCTTTACTGATCTTTTTCTTGTTCTTCTTCTCTGTTTTCTCTTGGACAACTTCCGAAAT
1 TCTTTAGCTTTACTGATCTTCTTCTTGTTCTTCTTCTCGGTTTTCTCTTCGACAACTTCCGAAAT
22791295 TAATGAACCCTTTGGACGTTCAACAGAT
66 TAATGAACCCTTTGGACGTTCAACAGAT
*
22791323 TCTTTAGCTTTGCTGATCTTCTTCTTG
1 TCTTTAGCTTTACTGATCTTCTTCTTG
22791350 GTTTTCTCTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
92 3 0.03
93 105 0.97
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (93 bp):
TCTTTAGCTTTACTGATCTTCTTCTTGTTCTTCTTCTCGGTTTTCTCTTCGACAACTTCCGAAAT
TAATGAACCCTTTGGACGTTCAACAGAT
Found at i:22800222 original size:69 final size:69
Alignment explanation
Indices: 22799967--22800564 Score: 470
Period size: 69 Copynumber: 8.7 Consensus size: 69
22799957 ACAACATTTA
* * * *
22799967 TGTCATATTAAGGCTC-TCGGGATAAAAATCACAGCCTCCAACACAGTTAGCGAGAGCAAAGCTC
1 TGTCATATTAAGGCTCGT-AGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTC
*
22800031 CCAAC
65 CCAGC
* * * ** * * *
22800036 TATCTTATTAAGGCTCGTAGG-TGAAGAGCCATAGCCT-TCAACACAGTTAGTGAGAGTAAAGCT
1 TGTCATATTAAGGCTCGTAGGAT-AAAAATCACAGCCTCT-AACATAGTTAGTGAGAGCAAAGCT
22800099 CCCAGC
64 CCCAGC
* * * * * * *
22800105 TGTCATATTAAGGCTTGTAGG-TGAAGAGTTATAGTCT-TCAACACAGTTAGTGAGAGCAAAGCT
1 TGTCATATTAAGGCTCGTAGGAT-AAAAATCACAGCCTCT-AACATAGTTAGTGAGAGCAAAGCT
22800168 CCCAGC
64 CCCAGC
* * * ** * *
22800174 TGTTATATTAAGGCTCGTAAGATAAAAATCACAGCCTCTAATATAGTTAGCAAGAGTAAAGTTCC
1 TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTCC
*
22800239 CAGTT
66 CAG-C
* * * * *
22800244 TGTCATATTAAAGCTCGTAGGATAAAAA-CTGCAGTCTCTAATATAGCTAGTGAGAGCAAAGCTC
1 TGTCATATTAAGGCTCGTAGGATAAAAATC-ACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTC
*
22800308 CCAAC
65 CCAGC
** * * * * * * *
22800313 TGTCATATTAAAACTCGCAGGATAAAAACCACAACCTCCAACATAGTTAGCGAAAGCAAAGCTCT
1 TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTCC
22800378 CAGC
66 CAGC
* * * ** * * *
22800382 AGTCATACTAAGGCTCGCAGGATAAAAATCGTAGCCTCCAATATAGTTAGTGAGAGTAAAGCTCC
1 TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTCC
*
22800447 CAAC
66 CAGC
* * **** * * * * *
22800451 TGTCATATTAAGGCTCGTAGGATATAAACCGTTTCTTCCAACACAGTTAGCGAGAGCAAAACTCC
1 TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTCC
*
22800516 CAAC
66 CAGC
* * * * *
22800520 TGCCATACTAAGGCTCGCAGGATAAAGATCACAGCCTCCAACATA
1 TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATA
22800565 ATTTACGAGA
Statistics
Matches: 425, Mismatches: 96, Indels: 16
0.79 0.18 0.03
Matches are distributed among these distances:
68 1 0.00
69 365 0.86
70 59 0.14
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (69 bp):
TGTCATATTAAGGCTCGTAGGATAAAAATCACAGCCTCTAACATAGTTAGTGAGAGCAAAGCTCC
CAGC
Found at i:22800556 original size:138 final size:138
Alignment explanation
Indices: 22799967--22800562 Score: 559
Period size: 138 Copynumber: 4.3 Consensus size: 138
22799957 ACAACATTTA
* * *
22799967 TGTCATATTAAGGCTCTCGGGATAAAAATCACAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCC
1 TGTCATATTAAGGCTCGCAGGATAAAAATCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCC
* * * * * * * * *
22800032 CAACTATCTTATTAAGGCTCGTAGG-TGAAGAGCCATAGCCTTCAACACAGTTAGTGAGAGTAAA
66 CAACTGTCATATTAAGGCTCGTAGGAT-AAAAACCACAACCTCCAACACAGTTAGCGAGAGCAAA
22800096 GCTCCCAGC
130 GCTCCCAGC
* * * * * * * *
22800105 TGTCATATTAAGGCTTGTAGG-TGAAGAGTTATAGTCTTCAACACAGTTAGTGAGAGCAAAGCTC
1 TGTCATATTAAGGCTCGCAGGAT-AAAAATCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTC
* * * * * * * * * *
22800169 CCAGCTGTTATATTAAGGCTCGTAAGATAAAAATCACAGCCTCTAATATAGTTAGCAAGAGTAAA
65 CCAACTGTCATATTAAGGCTCGTAGGATAAAAACCACAACCTCCAACACAGTTAGCGAGAGCAAA
* *
22800234 GTTCCCAGTT
130 GCTCCCAG-C
* * * * * * * *
22800244 TGTCATATTAAAGCTCGTAGGATAAAAA-CTGCAGTCTCTAATATAGCTAGTGAGAGCAAAGCTC
1 TGTCATATTAAGGCTCGCAGGATAAAAATC-ACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTC
** * * *
22800308 CCAACTGTCATATTAAAACTCGCAGGATAAAAACCACAACCTCCAACATAGTTAGCGAAAGCAAA
65 CCAACTGTCATATTAAGGCTCGTAGGATAAAAACCACAACCTCCAACACAGTTAGCGAGAGCAAA
*
22800373 GCTCTCAGC
130 GCTCCCAGC
* * ** * * *
22800382 AGTCATACTAAGGCTCGCAGGATAAAAATCGTAGCCTCCAATATAGTTAGTGAGAGTAAAGCTCC
1 TGTCATATTAAGGCTCGCAGGATAAAAATCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCC
* **** * *
22800447 CAACTGTCATATTAAGGCTCGTAGGATATAAACCGTTTCTTCCAACACAGTTAGCGAGAGCAAAA
66 CAACTGTCATATTAAGGCTCGTAGGATAAAAACCACAACCTCCAACACAGTTAGCGAGAGCAAAG
*
22800512 CTCCCAAC
131 CTCCCAGC
* * *
22800520 TGCCATACTAAGGCTCGCAGGATAAAGATCACAGCCTCCAACA
1 TGTCATATTAAGGCTCGCAGGATAAAAATCACAGCCTCCAACA
22800563 TAATTTACGA
Statistics
Matches: 367, Mismatches: 85, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
137 1 0.00
138 256 0.70
139 109 0.30
140 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (138 bp):
TGTCATATTAAGGCTCGCAGGATAAAAATCACAGCCTCCAACACAGTTAGTGAGAGCAAAGCTCC
CAACTGTCATATTAAGGCTCGTAGGATAAAAACCACAACCTCCAACACAGTTAGCGAGAGCAAAG
CTCCCAGC
Found at i:22804565 original size:3 final size:3
Alignment explanation
Indices: 22804559--22804593 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
22804549 TTCCCCTTTC
* *
22804559 TCT TCT TCT TCT TCT TTT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
22804594 CCAACAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:22805018 original size:23 final size:24
Alignment explanation
Indices: 22804974--22805019 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
22804964 GACGCCAATT
*
22804974 TTGTTTTATGAATCATATATATTA
1 TTGTTTTATGAATAATATATATTA
22804998 TTGTTTTATGAA-AATATATATT
1 TTGTTTTATGAATAATATATATT
22805020 GCAATTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (24 bp):
TTGTTTTATGAATAATATATATTA
Found at i:22805270 original size:9 final size:9
Alignment explanation
Indices: 22805256--22805286 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22805246 GTTAAACGAA
22805256 TCGAGTTAT
1 TCGAGTTAT
*
22805265 TCGAGTTAA
1 TCGAGTTAT
22805274 TCGAGTTAT
1 TCGAGTTAT
22805283 TCGA
1 TCGA
22805287 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:22805357 original size:9 final size:9
Alignment explanation
Indices: 22805340--22805376 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
22805330 TGAGTTTTCG
22805340 AATTCGAAT
1 AATTCGAAT
*
22805349 AACTCGAAT
1 AATTCGAAT
22805358 AATTCGAAT
1 AATTCGAAT
22805367 AATTCGAAT
1 AATTCGAAT
22805376 A
1 A
22805377 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:22807008 original size:9 final size:9
Alignment explanation
Indices: 22806994--22807034 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
22806984 TTTGGTTAAA
22806994 AATTACCCG
1 AATTACCCG
22807003 AATTACCCG
1 AATTACCCG
*
22807012 AATTACCTG
1 AATTACCCG
*
22807021 AATTAACCG
1 AATTACCCG
22807030 AATTA
1 AATTA
22807035 ACCAAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:22807035 original size:9 final size:9
Alignment explanation
Indices: 22806994--22807042 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
22806984 TTTGGTTAAA
*
22806994 AATTACCCG
1 AATTAACCG
*
22807003 AATTACCCG
1 AATTAACCG
22807012 AATT-ACCTG
1 AATTAACC-G
22807021 AATTAACCG
1 AATTAACCG
*
22807030 AATTAACCA
1 AATTAACCG
22807039 AATT
1 AATT
22807043 GTATCACTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 2 0.06
9 31 0.86
10 3 0.08
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:22811026 original size:38 final size:39
Alignment explanation
Indices: 22810951--22811027 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
22810941 TGGTGAAAAG
22810951 ATAAAAAAAATTGAAAAAGTTACATCAACATAAAACTAAT
1 ATAAAAAAAATTGAAAAAGTTACATCAACAT-AAACTAAT
*
22810991 ATAAAAAAATTTGAAAAAGTTACATCAACAT-AACTAA
1 ATAAAAAAAATTGAAAAAGTTACATCAACATAAACTAA
22811028 CTTCCCAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 6 0.17
40 30 0.83
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.23
Consensus pattern (39 bp):
ATAAAAAAAATTGAAAAAGTTACATCAACATAAACTAAT
Found at i:22812653 original size:14 final size:14
Alignment explanation
Indices: 22812634--22812666 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22812624 TGTTTGACTA
*
22812634 AAAATGGTTTCTGG
1 AAAATGATTTCTGG
22812648 AAAATGATTTCTGG
1 AAAATGATTTCTGG
22812662 AAAAT
1 AAAAT
22812667 AAATTACTTT
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:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:22813105 original size:46 final size:46
Alignment explanation
Indices: 22813038--22813139 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
22813028 TATTACAAAT
* * **
22813038 TAGTAGTATACCACATGATAACTACAATATTTTCTAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAATATCATCTAAGTGCATAAC
22813084 TAGTATTACACCACATGATAACTACAATATCATCTAAGTGCATAAC
1 TAGTATTACACCACATGATAACTACAATATCATCTAAGTGCATAAC
*
22813130 TAATATTACA
1 TAGTATTACA
22813140 AATTAATAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (46 bp):
TAGTATTACACCACATGATAACTACAATATCATCTAAGTGCATAAC
Found at i:22813265 original size:19 final size:19
Alignment explanation
Indices: 22813238--22813274 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
22813228 GTCCAAGTGC
*
22813238 ATAACTAGTATTACACCAT
1 ATAACTAGTACTACACCAT
*
22813257 ATAATTAGTACTACACCA
1 ATAACTAGTACTACACCA
22813275 CATTAAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (19 bp):
ATAACTAGTACTACACCAT
Found at i:22814264 original size:32 final size:32
Alignment explanation
Indices: 22814223--22814283 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
22814213 TGTCAATCAT
22814223 TTCAATATCCAACAAGC-TTAAAACATAATAAG
1 TTCAATATCCAACAA-CTTTAAAACATAATAAG
22814255 TTCAATATCCAACAACTTTAAAACATAAT
1 TTCAATATCCAACAACTTTAAAACATAAT
22814284 TTCAAAATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAACTTTAAAACATAATAAG
Found at i:22814293 original size:29 final size:29
Alignment explanation
Indices: 22814221--22814295 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 29
22814211 ATTGTCAATC
22814221 ATTTCAATATCCAACAAGCTTAAAACATA
1 ATTTCAATATCCAACAAGCTTAAAACATA
22814250 ATAAGTTCAATATCCAACAA-CTTTAAAACATA
1 AT---TTCAATATCCAACAAGC-TTAAAACATA
*
22814282 ATTTCAAAATCCAA
1 ATTTCAATATCCAA
22814296 TAAACTAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
29 13 0.32
31 1 0.02
32 27 0.66
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (29 bp):
ATTTCAATATCCAACAAGCTTAAAACATA
Found at i:22814304 original size:21 final size:21
Alignment explanation
Indices: 22814275--22814317 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
22814265 AACAACTTTA
22814275 AAACATAATTTCAAAATCCAAT
1 AAACATAATTTCAAAAT-CAAT
*
22814297 AAAC-TAATTTCAATATCAAT
1 AAACATAATTTCAAAATCAAT
22814317 A
1 A
22814318 TCTAACCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.30
Consensus pattern (21 bp):
AAACATAATTTCAAAATCAAT
Found at i:22815712 original size:4 final size:4
Alignment explanation
Indices: 22815703--22815729 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
22815693 GGATCAAAGG
22815703 ACAA ACAA ACAA ACAA ACAA ACAA ACA
1 ACAA ACAA ACAA ACAA ACAA ACAA ACA
22815730 GAAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:22823391 original size:23 final size:23
Alignment explanation
Indices: 22823369--22823441 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
22823359 TTTTTATTAT
22823369 TGTGA-TATATGCTTAAATGTTA
1 TGTGACTATATGCTTAAATGTTA
22823391 TGTGACTATATG-----A-G-TA
1 TGTGACTATATGCTTAAATGTTA
22823407 TTGTGA-TATATGCTTAAATGTTA
1 -TGTGACTATATGCTTAAATGTTA
*
22823430 TGTGATTATATG
1 TGTGACTATATG
22823442 AGTGTTGTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 19
0.68 0.00 0.32
Matches are distributed among these distances:
16 8 0.20
17 6 0.15
18 1 0.02
21 1 0.02
22 11 0.27
23 14 0.34
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.45
Consensus pattern (23 bp):
TGTGACTATATGCTTAAATGTTA
Found at i:22823394 original size:22 final size:22
Alignment explanation
Indices: 22823369--22823474 Score: 76
Period size: 22 Copynumber: 5.3 Consensus size: 22
22823359 TTTTTATTAT
22823369 TGTGATATATGCTTAAATGTTA
1 TGTGATATATGCTTAAATGTTA
22823391 TGTGACTATATG-----A-G-TA
1 TGTGA-TATATGCTTAAATGTTA
22823407 TTGTGATATATGCTTAAATGTTA
1 -TGTGATATATGCTTAAATGTTA
*
22823430 TGTGATTATATG----AGTG-T-
1 TGTGA-TATATGCTTAAATGTTA
*
22823447 TGTGATATATTCTTAAATGTTA
1 TGTGATATATGCTTAAATGTTA
22823469 TGTGAT
1 TGTGAT
22823475 TACATGTGTA
Statistics
Matches: 65, Mismatches: 3, Indels: 32
0.65 0.03 0.32
Matches are distributed among these distances:
16 13 0.20
17 11 0.17
18 2 0.03
19 3 0.05
20 3 0.05
21 2 0.03
22 17 0.26
23 14 0.22
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (22 bp):
TGTGATATATGCTTAAATGTTA
Found at i:22823420 original size:39 final size:39
Alignment explanation
Indices: 22823366--22823502 Score: 211
Period size: 39 Copynumber: 3.5 Consensus size: 39
22823356 GTTTTTTTAT
*
22823366 TATTGTGATATATGCTTAAATGTTATGTGACTATATGAG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
22823405 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
* * * *
22823444 TGTTGTGATATATTCTTAAATGTTATGTGATTACATGTG
1 TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
* *
22823483 TAATGTGATATATGGTTAAA
1 TATTGTGATATATGCTTAAA
22823503 AGTGAATATG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.45
Consensus pattern (39 bp):
TATTGTGATATATGCTTAAATGTTATGTGATTATATGAG
Found at i:22835159 original size:42 final size:42
Alignment explanation
Indices: 22835102--22835199 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
22835092 GCAGATTCTT
* * * * *
22835102 CACAACTCGTCTGAGCAGCGTCGTGTAGCTAATATTCTAACC
1 CACAGCTCGTGTGAGCAACATCGTGTAGCTAACATTCTAACC
22835144 CACAGCTCGTGTGAGCAACATCGTGTAGCTAACATTCTAACC
1 CACAGCTCGTGTGAGCAACATCGTGTAGCTAACATTCTAACC
*
22835186 CACAGCTTGTGTGA
1 CACAGCTCGTGTGA
22835200 ATAGGCCCAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (42 bp):
CACAGCTCGTGTGAGCAACATCGTGTAGCTAACATTCTAACC
Found at i:22837088 original size:23 final size:23
Alignment explanation
Indices: 22837059--22837175 Score: 173
Period size: 23 Copynumber: 5.1 Consensus size: 23
22837049 GTGTCACACA
22837059 GAAATGTAGCCGAAGCTACCACT
1 GAAATGTAGCCGAAGCTACCACT
*
22837082 GATATGTAGCCGTAA-CTACCACT
1 GAAATGTAGCCG-AAGCTACCACT
*
22837105 GAAATGTAGCCGTAGCTACCACT
1 GAAATGTAGCCGAAGCTACCACT
*
22837128 GAAATGTAGCCGAAGCTACCGCT
1 GAAATGTAGCCGAAGCTACCACT
* *
22837151 AAAATGAAGCCGAAGCTACCACT
1 GAAATGTAGCCGAAGCTACCACT
22837174 GA
1 GA
22837176 TCAATAACAC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
22 1 0.01
23 80 0.96
24 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (23 bp):
GAAATGTAGCCGAAGCTACCACT
Found at i:22860576 original size:23 final size:23
Alignment explanation
Indices: 22860515--22860584 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
22860505 TCATTAACAT
* *
22860515 TGTTCAGAAACATGTTCAATTATA
1 TGTTCATAAACATGTTCGATTA-A
* *
22860539 TGTTCATAAAGATGTTCGTTTAA
1 TGTTCATAAACATGTTCGATTAA
* *
22860562 TGTTCGTGAACATGTTCGATTAA
1 TGTTCATAAACATGTTCGATTAA
22860585 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (23 bp):
TGTTCATAAACATGTTCGATTAA
Found at i:22883963 original size:60 final size:60
Alignment explanation
Indices: 22883890--22884009 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
22883880 GTATGAGATG
22883890 AATATTGTTCGTTTACATGACGTACTAGCTAGGTAAACGTCATGCATATAGACACATATT
1 AATATTGTTCGTTTACATGACGTACTAGCTAGGTAAACGTCATGCATATAGACACATATT
22883950 AATATTGTTCGTTTACATGACGTACTAGCTAGGTAAACGTCATGCATATAGACACATATT
1 AATATTGTTCGTTTACATGACGTACTAGCTAGGTAAACGTCATGCATATAGACACATATT
22884010 CTCCTCTAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
AATATTGTTCGTTTACATGACGTACTAGCTAGGTAAACGTCATGCATATAGACACATATT
Found at i:22887268 original size:46 final size:46
Alignment explanation
Indices: 22887206--22887390 Score: 257
Period size: 46 Copynumber: 4.0 Consensus size: 46
22887196 ACATTGCTAT
* *
22887206 AACTCAGTATGGTTTTCTTCAC-GAAAATACCATACCTACTTTTCAC
1 AACTAAGTATGGTTTTCTTCACTG-AAACACCATACCTACTTTTCAC
* * *
22887252 AACTAAGTATGTTTTTCTTCACTGAAGCACCATACCTACATTTCAC
1 AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
22887298 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* * *
22887344 AACTCAA-TATGGTTTTCTTCATTGAAATACCATACCTACGTTTCAC
1 AACT-AAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
22887390 A
1 A
22887391 CTTTTCCATG
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
46 122 0.98
47 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTAAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:22887363 original size:92 final size:92
Alignment explanation
Indices: 22887206--22887390 Score: 284
Period size: 92 Copynumber: 2.0 Consensus size: 92
22887196 ACATTGCTAT
* *
22887206 AACTCAGTATGGTTTTCTTCACGAAAATACCATACCTACTTTTCACAACTAAGTATGTTTTTCTT
1 AACTCAGTATGGTTTTCTTCACGAAAACACCATACCTACTTTTCACAACTAAGTATGGTTTTCTT
*
22887271 CACTGAAGCACCATACCTACATTTCAC
66 CACTGAAACACCATACCTACATTTCAC
22887298 AACTCAGTATGGTTTTCTTCACTG-AAACACCATACCTACTTTTCACAACTCAA-TATGGTTTTC
1 AACTCAGTATGGTTTTCTTCAC-GAAAACACCATACCTACTTTTCACAACT-AAGTATGGTTTTC
* * *
22887361 TTCATTGAAATACCATACCTACGTTTCAC
64 TTCACTGAAACACCATACCTACATTTCAC
22887390 A
1 A
22887391 CTTTTCCATG
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
92 82 0.96
93 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (92 bp):
AACTCAGTATGGTTTTCTTCACGAAAACACCATACCTACTTTTCACAACTAAGTATGGTTTTCTT
CACTGAAACACCATACCTACATTTCAC
Found at i:22888646 original size:16 final size:17
Alignment explanation
Indices: 22888600--22888647 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
22888590 AAATTCTTTT
*
22888600 TAAATCAGAAAATTCAA
1 TAAATCACAAAATTCAA
*
22888617 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
22888634 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
22888648 TTCTAAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Done.