Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 79 of 82
Found at i:29757685 original size:13 final size:13
Alignment explanation
Indices: 29757667--29757691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29757657 ACTTGAGAGC
29757667 TTCTCTCTCTAAA
1 TTCTCTCTCTAAA
29757680 TTCTCTCTCTAA
1 TTCTCTCTCTAA
29757692 TTATCTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCTCTCTCTAAA
Found at i:29758791 original size:28 final size:29
Alignment explanation
Indices: 29758748--29758810 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
29758738 GACATGTAAT
*
29758748 AATTTTTTTATCATGACATATAACAATAA
1 AATTTTTTAATCATGACATATAACAATAA
** * *
29758777 AATTTTTTAAT-ATGATGTGTAACAATTA
1 AATTTTTTAATCATGACATATAACAATAA
29758805 AATTTT
1 AATTTT
29758811 CAACTAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (29 bp):
AATTTTTTAATCATGACATATAACAATAA
Found at i:29774312 original size:1 final size:1
Alignment explanation
Indices: 29774308--29774354 Score: 58
Period size: 1 Copynumber: 47.0 Consensus size: 1
29774298 ATAACAAGGA
* * * *
29774308 CCCCCCCACCCCCCCCCACCCCCCCCCCCCCCGCCCCCCCACCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
29774355 TTCCTTCAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.06, C:0.91, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:29774337 original size:23 final size:23
Alignment explanation
Indices: 29774308--29774354 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
29774298 ATAACAAGGA
*
29774308 CCCCCCCACC-CCCCCCCACCCC
1 CCCCCCCCCCGCCCCCCCACCCC
29774330 CCCCCCCCCCGCCCCCCCACCCC
1 CCCCCCCCCCGCCCCCCCACCCC
29774353 CC
1 CC
29774355 TTCCTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.06, C:0.91, G:0.02, T:0.00
Consensus pattern (23 bp):
CCCCCCCCCCGCCCCCCCACCCC
Found at i:29784985 original size:33 final size:33
Alignment explanation
Indices: 29784947--29785012 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
29784937 ATTTTTTAAT
*
29784947 ATATTAGACTGACATTGTCAATTTCGGAAAGTA
1 ATATTAGACTGACATTGTCAATTTCGAAAAGTA
29784980 ATATTAGACTGACATTGTCAATTTCGAAAAGTA
1 ATATTAGACTGACATTGTCAATTTCGAAAAGTA
29785013 TAAAAACTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (33 bp):
ATATTAGACTGACATTGTCAATTTCGAAAAGTA
Found at i:29785280 original size:29 final size:29
Alignment explanation
Indices: 29785248--29785303 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
29785238 TTTAATTTAA
*
29785248 AATTAA-AATATATAAATTTAATTAAATAC
1 AATTAATAA-ATAAAAATTTAATTAAATAC
*
29785277 AATTAATAAATAAAAATTTATTTAAAT
1 AATTAATAAATAAAAATTTAATTAAAT
29785304 TTTCTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (29 bp):
AATTAATAAATAAAAATTTAATTAAATAC
Found at i:29792760 original size:12 final size:12
Alignment explanation
Indices: 29792729--29792782 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
29792719 AGCAGCTACT
29792729 GCAACAACAAG-A
1 GCAACAAC-AGCA
*
29792741 ACAACAACAGCA
1 GCAACAACAGCA
*
29792753 GCAGCAACAGCA
1 GCAACAACAGCA
* *
29792765 GCAACAGCAACA
1 GCAACAACAGCA
29792777 GCAACA
1 GCAACA
29792783 GTTACAGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 2 0.06
12 33 0.94
ACGTcount: A:0.52, C:0.31, G:0.17, T:0.00
Consensus pattern (12 bp):
GCAACAACAGCA
Found at i:29792777 original size:15 final size:15
Alignment explanation
Indices: 29792742--29792779 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
29792732 ACAACAAGAA
* *
29792742 CAACAACAGCAGCAG
1 CAACAGCAGCAACAG
29792757 CAACAGCAGCAACAG
1 CAACAGCAGCAACAG
29792772 CAACAGCA
1 CAACAGCA
29792780 ACAGTTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.34, G:0.18, T:0.00
Consensus pattern (15 bp):
CAACAGCAGCAACAG
Found at i:29820737 original size:15 final size:16
Alignment explanation
Indices: 29820717--29820750 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
29820707 AAATGAAATA
*
29820717 TTTAAATAATTTT-TT
1 TTTAAAAAATTTTATT
29820732 TTTAAAAAATTTTATT
1 TTTAAAAAATTTTATT
29820748 TTT
1 TTT
29820751 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAAAAAATTTTATT
Found at i:29820807 original size:14 final size:13
Alignment explanation
Indices: 29820728--29820818 Score: 60
Period size: 14 Copynumber: 6.8 Consensus size: 13
29820718 TTAAATAATT
*
29820728 TTTTTTTAAAAAA
1 TTTTTTTAATAAA
** *
29820741 TTTTATTTTTTTAA
1 TTTT-TTTAATAAA
*
29820755 TTTTTTGAAATATAA
1 TTTTTT-TAATA-AA
*
29820770 ATTTTTTAATTAAA
1 TTTTTTTAA-TAAA
*
29820784 TTTTTATAATCAAA
1 TTTTTTTAAT-AAA
29820798 TTTTTTTAAT--A
1 TTTTTTTAATAAA
29820809 TTTTTTTAAT
1 TTTTTTTAAT
29820819 TGATAATATG
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
11 11 0.18
13 7 0.12
14 33 0.55
15 9 0.15
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (13 bp):
TTTTTTTAATAAA
Found at i:29821541 original size:16 final size:16
Alignment explanation
Indices: 29821514--29821556 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
29821504 TTTTATTAAT
29821514 TATTTTTT-ATTTTTA
1 TATTTTTTAATTTTTA
29821529 TATTTTTTAATTTTTA
1 TATTTTTTAATTTTTA
29821545 TATATTTTTAAT
1 TAT-TTTTTAAT
29821557 ATAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.31
16 10 0.38
17 8 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTTAATTTTTA
Found at i:29821550 original size:26 final size:27
Alignment explanation
Indices: 29821503--29821574 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
29821493 AGAACAAATA
*
29821503 ATTTTATTAATTATTTTTTATTTTTAT
1 ATTTTATTAATTATTTTATATTTTTAT
29821530 ATTTT-TTAATT-TTTATATATTTTTA-
1 ATTTTATTAATTATTT-TATATTTTTAT
* * *
29821555 ATATAATTAATTATATTATA
1 ATTTTATTAATTATTTTATA
29821575 ATTATTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 6 0.16
26 25 0.66
27 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTATTAATTATTTTATATTTTTAT
Found at i:29821591 original size:17 final size:19
Alignment explanation
Indices: 29821569--29821607 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
29821559 AATTAATTAT
29821569 ATTAT-AATTATT-TTAAA
1 ATTATAAATTATTGTTAAA
*
29821586 ATTATAAATTTTTGTTAAA
1 ATTATAAATTATTGTTAAA
29821605 ATT
1 ATT
29821608 GAGACCTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATTATAAATTATTGTTAAA
Found at i:29828832 original size:2 final size:2
Alignment explanation
Indices: 29828825--29828871 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
29828815 ACAAGCATGC
* * *
29828825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AG AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29828867 AT AT A
1 AT AT A
29828872 CCTCCAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:29838974 original size:27 final size:27
Alignment explanation
Indices: 29838938--29838991 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
29838928 GACCTTGAGA
*
29838938 AAATAATTTTAAGTAAATAAATGGTAG
1 AAATAATTTTAAATAAATAAATGGTAG
*
29838965 AAATAATTTTAAATAAATAGATGGTAG
1 AAATAATTTTAAATAAATAAATGGTAG
29838992 TGTCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (27 bp):
AAATAATTTTAAATAAATAAATGGTAG
Found at i:29850031 original size:7 final size:7
Alignment explanation
Indices: 29850019--29850044 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29850009 TTTTTAGTAA
29850019 AAATTTT
1 AAATTTT
29850026 AAATTTT
1 AAATTTT
29850033 AAATTTT
1 AAATTTT
29850040 AAATT
1 AAATT
29850045 AAAAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:29852037 original size:16 final size:16
Alignment explanation
Indices: 29852018--29852048 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29852008 TCAAAAAAAT
29852018 TATAATTTAAAAATTA
1 TATAATTTAAAAATTA
*
29852034 TATAATTTGAAAATT
1 TATAATTTAAAAATT
29852049 TGTTTGAATC
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATAATTTAAAAATTA
Found at i:29854165 original size:14 final size:16
Alignment explanation
Indices: 29854146--29854184 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
29854136 AAACCAAAAA
*
29854146 AAAAAAAAAG-AAA-G
1 AAAAAAAAAGCAAACC
29854160 AAAAAAAAAGCAAACC
1 AAAAAAAAAGCAAACC
29854176 AAAAAAAAA
1 AAAAAAAAA
29854185 AACATTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 3 0.14
16 9 0.41
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGCAAACC
Found at i:29854179 original size:15 final size:14
Alignment explanation
Indices: 29854146--29854188 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
29854136 AAACCAAAAA
*
29854146 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAC
29854160 AAAAAAAAAGCAAAC
1 AAAAAAAAAG-AAAC
*
29854175 CAAAAAAAA-AAAC
1 AAAAAAAAAGAAAC
29854188 A
1 A
29854189 TTTCGTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.16
14 10 0.40
15 11 0.44
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAC
Found at i:29855361 original size:21 final size:21
Alignment explanation
Indices: 29855328--29855367 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29855318 ATTCTAGTTT
** *
29855328 TGGTTTTTTTTTTTTAACAAA
1 TGGTTTTAGTTTTTGAACAAA
29855349 TGGTTTTAGTTTTTGAACA
1 TGGTTTTAGTTTTTGAACA
29855368 GTATTCCTTT
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:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (21 bp):
TGGTTTTAGTTTTTGAACAAA
Found at i:29859958 original size:2 final size:2
Alignment explanation
Indices: 29859951--29859997 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
29859941 TAAGAGGAAG
29859951 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29859991 AT AT AT A
1 AT AT AT A
29859998 CTGTGGCTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29861391 original size:2 final size:2
Alignment explanation
Indices: 29861384--29861440 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
29861374 GTANAAATGC
*
29861384 TA TA TA TA TA TA TA TA TA TA T- TA TA CA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29861424 TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
29861441 GAGGCATAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29862675 original size:31 final size:30
Alignment explanation
Indices: 29862604--29862681 Score: 77
Period size: 31 Copynumber: 2.5 Consensus size: 30
29862594 TTTGGGAGAC
*
29862604 AAAATTATAAAATTTTTAAAAAAATAAAAAT
1 AAAATTATAAAA-TTTTAAAAAAACAAAAAT
* **
29862635 AAAAATATAAAATTTTAAATCAAAACAAGGA-
1 AAAATTATAAAATTTTAAA--AAAACAAAAAT
*
29862666 AAAATTATAAACTTTT
1 AAAATTATAAAATTTT
29862682 GGGGGGGCGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 7 0.18
31 25 0.64
32 7 0.18
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAATTATAAAATTTTAAAAAAACAAAAAT
Found at i:29864867 original size:13 final size:13
Alignment explanation
Indices: 29864849--29864873 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29864839 ATTATATATT
29864849 TTTAAAATAATTC
1 TTTAAAATAATTC
29864862 TTTAAAATAATT
1 TTTAAAATAATT
29864874 AATACAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAAATAATTC
Found at i:29865452 original size:28 final size:29
Alignment explanation
Indices: 29865421--29865479 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
29865411 TTATTAATTC
*
29865421 TATATATCATA-TTTAACTATTTA-TATTT
1 TATACATCATAGTTTAA-TATTTAGTATTT
*
29865449 TATACATTATAGTTTAATATTTAGTATTT
1 TATACATCATAGTTTAATATTTAGTATTT
29865478 TA
1 TA
29865480 AGTTTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
TATACATCATAGTTTAATATTTAGTATTT
Found at i:29872915 original size:105 final size:105
Alignment explanation
Indices: 29872610--29872915 Score: 445
Period size: 105 Copynumber: 2.9 Consensus size: 105
29872600 ATTATCCCTC
* *
29872610 TTCTGAAGAGACCTCTCT-CCTTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAATTTG
1 TTCTGAAGAAACCTCTCTGCC-TTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTG
** * * *
29872674 CCCCTCCAGACCCAACAGTTGCCCCTGAAAACGCAGTCAAT
65 CCCCTTGAGACCCAACAGTTGCCCATGGAAACACAGTCAAT
* *
29872715 TTCTGAAAAAACCTCTCTGCCTTCAGACTCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
1 TTCTGAAGAAACCTCTCTGCCTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
* * *
29872780 CCCTTGAGACCCAACATTTGCCCATTGAAACACAGTCATT
66 CCCTTGAGACCCAACAGTTGCCCATGGAAACACAGTCAAT
*
29872820 TTCTGAAGAAACCTCTCTGCCTTCAGAAT-TCGAGTTTCCTCAAGATTCTGAAGACACCAGTTTG
1 TTCTGAAGAAACCTCTCTGCCTTCAGAATCT-GAATTTCCTCAAGATTCTGAAGACACCAGTTTG
* *
29872884 GCCCTTGAGACCCAACAGTTGGCCATGGAAAC
65 CCCCTTGAGACCCAACAGTTGCCCATGGAAAC
29872916 TGATTCACAT
Statistics
Matches: 180, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
104 1 0.01
105 177 0.98
106 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (105 bp):
TTCTGAAGAAACCTCTCTGCCTTCAGAATCTGAATTTCCTCAAGATTCTGAAGACACCAGTTTGC
CCCTTGAGACCCAACAGTTGCCCATGGAAACACAGTCAAT
Found at i:29886471 original size:25 final size:25
Alignment explanation
Indices: 29886417--29886472 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
29886407 ATTTTTAATT
* *
29886417 TTTAAATTTATTTATTAATAACATA
1 TTTATATTTATTCATTAATAACATA
* *
29886442 ATTATATTTAATTCATTCATAA-ATA
1 TTTATATTT-ATTCATTAATAACATA
29886467 TTTATA
1 TTTATA
29886473 CACAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATATTTATTCATTAATAACATA
Found at i:29894097 original size:70 final size:70
Alignment explanation
Indices: 29893984--29894123 Score: 253
Period size: 70 Copynumber: 2.0 Consensus size: 70
29893974 AAGAAAGCCC
* * *
29893984 AGAAGATGCATATAGATAATTTGGTATTCAAGTGACTGAAGCAAGGAGCAAGGCAATAAGATTGA
1 AGAAGATACATATAAATAATTTGGTATTCAAGCGACTGAAGCAAGGAGCAAGGCAATAAGATTGA
29894049 GATGA
66 GATGA
29894054 AGAAGATACATATAAATAATTTGGTATTCAAGCGACTGAAGCAAGGAGCAAGGCAATAAGATTGA
1 AGAAGATACATATAAATAATTTGGTATTCAAGCGACTGAAGCAAGGAGCAAGGCAATAAGATTGA
29894119 GATGA
66 GATGA
29894124 GTTTGTTGGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (70 bp):
AGAAGATACATATAAATAATTTGGTATTCAAGCGACTGAAGCAAGGAGCAAGGCAATAAGATTGA
GATGA
Found at i:29895641 original size:6 final size:6
Alignment explanation
Indices: 29895630--29895656 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29895620 ACCTCGATCC
29895630 CGGATT CGGATT CGGATT CGGATT CGG
1 CGGATT CGGATT CGGATT CGGATT CGG
29895657 GTCGGTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.30
Consensus pattern (6 bp):
CGGATT
Found at i:29896182 original size:17 final size:17
Alignment explanation
Indices: 29896158--29896195 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
29896148 CAAAATAAAC
29896158 ATTT-ATTTTTCAAATTT
1 ATTTAATTTTT-AAATTT
29896175 -TTTAATTTTTAAATTT
1 ATTTAATTTTTAAATTT
29896191 ATTTA
1 ATTTA
29896196 TTAATGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTAATTTTTAAATTT
Found at i:29896183 original size:16 final size:17
Alignment explanation
Indices: 29896158--29896195 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29896148 CAAAATAAAC
*
29896158 ATTTATTTTTCAAATTT
1 ATTTAATTTTCAAATTT
*
29896175 -TTTAATTTTTAAATTT
1 ATTTAATTTTCAAATTT
29896191 ATTTA
1 ATTTA
29896196 TTAATGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTAATTTTCAAATTT
Found at i:29898764 original size:96 final size:96
Alignment explanation
Indices: 29898633--29898827 Score: 300
Period size: 96 Copynumber: 2.0 Consensus size: 96
29898623 TCCAATGCAT
* * **
29898633 TCAAAGTTGAAAAGCCGAAGGAATATTGAAAAAGTTAAGTAGTTTCCATAAAACAAACGTATCAT
1 TCAAAGTTGAAAAGCCAAAAGAATATTGAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
*
29898698 CCTGCTCTACCACCTCTCACCCTAGCATCAC
66 CCTGCACTACCACCTCTCACCCTAGCATCAC
* * * *
29898729 TCAAAGTTGAAAGGCCAAAAGAATATTTAATAAGTTGAGTAGTTTCCATAAAACAAAAATATCAT
1 TCAAAGTTGAAAAGCCAAAAGAATATTGAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
*
29898794 CCTGCACTACCACCTCTCACCCTTGCATCAC
66 CCTGCACTACCACCTCTCACCCTAGCATCAC
29898825 TCA
1 TCA
29898828 TCTCTCATGT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (96 bp):
TCAAAGTTGAAAAGCCAAAAGAATATTGAAAAAGTTAAGTAGTTTCCATAAAACAAAAATATCAT
CCTGCACTACCACCTCTCACCCTAGCATCAC
Found at i:29901696 original size:6 final size:6
Alignment explanation
Indices: 29901685--29901710 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
29901675 TTATGTACAG
29901685 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
29901711 CAAAGCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:29903149 original size:170 final size:170
Alignment explanation
Indices: 29902867--29903194 Score: 476
Period size: 170 Copynumber: 1.9 Consensus size: 170
29902857 GTCATTTTAA
* * * *
29902867 GATATTGATGTAATATGTATGATAATGTAGTGTATTGATATGACATAATGATATAATTATATGAC
1 GATATTGATATAATATGTATGATAATATAGTGTATTGATATGACATAATAATATAATTACATGAC
* * * * *
29902932 AACTAATTATAATTAGTTATAACATTATCTATCAATTTCTTTCGTTATTTTACGATATTGACATT
66 AACTAATTATAAGTAGTTAGAACATCATCTATCAAATTCATTCGTTATTTTACGATATTGACATT
* * * *
29902997 ACATATTGACGTGTTATAATAGATAAGAATATAATATACT
131 ACATATTGACATATCATAATAAATAAGAATATAATATACT
* * * *
29903037 GATATTGATATAATATGTATGATAATATAGTGTATTGATGTGATATGATAATATAATTACATGAT
1 GATATTGATATAATATGTATGATAATATAGTGTATTGATATGACATAATAATATAATTACATGAC
**
29903102 AACTAATTATAAGTAGTTAGAACATCATCTATCAAATTCATTCGTTATTTTACGATATTGATGTT
66 AACTAATTATAAGTAGTTAGAACATCATCTATCAAATTCATTCGTTATTTTACGATATTGACATT
*
29903167 ACATGTTGACATATCATAATAAATAAGA
131 ACATATTGACATATCATAATAAATAAGA
29903195 GCATGATACA
Statistics
Matches: 138, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
170 138 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (170 bp):
GATATTGATATAATATGTATGATAATATAGTGTATTGATATGACATAATAATATAATTACATGAC
AACTAATTATAAGTAGTTAGAACATCATCTATCAAATTCATTCGTTATTTTACGATATTGACATT
ACATATTGACATATCATAATAAATAAGAATATAATATACT
Found at i:29903374 original size:19 final size:19
Alignment explanation
Indices: 29903352--29903393 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
29903342 CAAAAATATT
29903352 TATTTAAA-ATTTTTAAAA
1 TATTTAAAGATTTTTAAAA
29903370 GTATTTAAAGATTTTTAAAA
1 -TATTTAAAGATTTTTAAAA
29903390 TATT
1 TATT
29903394 ATATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATTTAAAGATTTTTAAAA
Found at i:29903574 original size:21 final size:20
Alignment explanation
Indices: 29903534--29903585 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
29903524 TCACCATATG
29903534 TTAATTTAATTAATTTTTTA
1 TTAATTTAATTAATTTTTTA
29903554 TTAATTT-ATTAAGTATTTTTA
1 TTAATTTAATTAA-T-TTTTTA
*
29903575 TTAATGTAATT
1 TTAATTTAATT
29903586 TGTGATACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.18
20 8 0.29
21 12 0.43
22 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTAATTTAATTAATTTTTTA
Found at i:29903608 original size:22 final size:21
Alignment explanation
Indices: 29903583--29903625 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29903573 TATTAATGTA
29903583 ATTTG-TGATACATATGAAAATT
1 ATTTGATGATA-AT-TGAAAATT
*
29903605 ATTTGATTATAATTGAAAATT
1 ATTTGATGATAATTGAAAATT
29903626 TTACTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (21 bp):
ATTTGATGATAATTGAAAATT
Found at i:29918208 original size:2 final size:2
Alignment explanation
Indices: 29918201--29918289 Score: 88
Period size: 2 Copynumber: 43.0 Consensus size: 2
29918191 TTTCATGGGT
* ** *
29918201 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA CA GTA CT TA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA
* **
29918244 CGT GTA CN GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 -GA G-A GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29918288 GA
1 GA
29918290 CAGACTTACG
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
2 70 0.99
3 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.44, T:0.06
Consensus pattern (2 bp):
GA
Found at i:29924184 original size:14 final size:14
Alignment explanation
Indices: 29924165--29924199 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29924155 GCAAAAGAAG
*
29924165 ACAAAAAAACCCAA
1 ACAAAAAAACCAAA
29924179 ACAAAAAAACCAAA
1 ACAAAAAAACCAAA
29924193 ACAAAAA
1 ACAAAAA
29924200 GGTAGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (14 bp):
ACAAAAAAACCAAA
Found at i:29929124 original size:14 final size:13
Alignment explanation
Indices: 29929101--29929143 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
29929091 TAGGGTTCCG
29929101 CTTTTTCTCTTTT
1 CTTTTTCTCTTTT
29929114 CTTTCTTCTCTTTT
1 CTTT-TTCTCTTTT
*
29929128 CTTTAT-TCTTTT
1 CTTTTTCTCTTTT
29929140 CTTT
1 CTTT
29929144 CTTTTTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 13 0.46
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTTTCTCTTTT
Found at i:29953753 original size:16 final size:16
Alignment explanation
Indices: 29953732--29953763 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29953722 TTTATAATAT
29953732 TTTTAAAATATTATTA
1 TTTTAAAATATTATTA
*
29953748 TTTTAAAATTTTATTA
1 TTTTAAAATATTATTA
29953764 AAATTAAGGA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAAAATATTATTA
Found at i:29960686 original size:4 final size:4
Alignment explanation
Indices: 29960677--29960745 Score: 66
Period size: 4 Copynumber: 17.2 Consensus size: 4
29960667 ATGAAATAAC
* * * * * * *
29960677 ATAT ATAT ATAC ATAC ATAC ATAT ATAT ATAT ACAT ACAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
29960725 ATAT ATAT ATAT ATAG ATAT A
1 ATAT ATAT ATAT ATAT ATAT A
29960746 CATGTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (4 bp):
ATAT
Found at i:29960705 original size:22 final size:22
Alignment explanation
Indices: 29960677--29960745 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
29960667 ATGAAATAAC
29960677 ATATATATATACATACATACAT
1 ATATATATATACATACATACAT
29960699 ATATATATATACATACATACAT
1 ATATATATATACATACATACAT
* * * *
29960721 ACATATATATATATATATAGAT
1 ATATATATATACATACATACAT
29960743 ATA
1 ATA
29960746 CATGTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (22 bp):
ATATATATATACATACATACAT
Found at i:29960714 original size:26 final size:26
Alignment explanation
Indices: 29960677--29960735 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
29960667 ATGAAATAAC
*
29960677 ATATATATATACATACATACATATAT
1 ATATATACATACATACATACATATAT
29960703 ATATATACATACATACATACATATAT
1 ATATATACATACATACATACATATAT
29960729 ATATATA
1 ATATATA
29960736 TATAGATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATATACATACATACATACATATAT
Found at i:29983080 original size:10 final size:10
Alignment explanation
Indices: 29983065--29983094 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
29983055 GCAACAAACC
29983065 AATTAATTAA
1 AATTAATTAA
29983075 AATTAATTAA
1 AATTAATTAA
*
29983085 AATCAATTAA
1 AATTAATTAA
29983095 TTATACGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
AATTAATTAA
Found at i:29987934 original size:2 final size:2
Alignment explanation
Indices: 29987927--29987983 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
29987917 ATTGAGCTAA
29987927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29987969 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
29987984 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29988407 original size:2 final size:2
Alignment explanation
Indices: 29988400--29988439 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29988390 TTGTGAAATC
29988400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29988440 TATTTTGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29989614 original size:55 final size:55
Alignment explanation
Indices: 29989527--29989648 Score: 217
Period size: 55 Copynumber: 2.2 Consensus size: 55
29989517 TTATGCCCCC
*
29989527 TCAAACTTTTGGATCCTTTTTTCCAGTCTCCTACTTGCAAGGGCACCAAACCTAT
1 TCAAACATTTGGATCCTTTTTTCCAGTCTCCTACTTGCAAGGGCACCAAACCTAT
* *
29989582 TCAAACATTTGGATCCTTTTTTCCGGTTTCCTACTTGCAAGGGCACCAAACCTAT
1 TCAAACATTTGGATCCTTTTTTCCAGTCTCCTACTTGCAAGGGCACCAAACCTAT
29989637 TCAAACATTTGG
1 TCAAACATTTGG
29989649 CAAAATGGTA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 64 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (55 bp):
TCAAACATTTGGATCCTTTTTTCCAGTCTCCTACTTGCAAGGGCACCAAACCTAT
Found at i:29994149 original size:22 final size:22
Alignment explanation
Indices: 29994121--29994164 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
29994111 TCTTTTAATT
29994121 TTTTAAAATT-ATACAATAATAA
1 TTTTAAAATTAATA-AATAATAA
29994143 TTTTAAAATTAATAAATAATAA
1 TTTTAAAATTAATAAATAATAA
29994165 ATAATGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATTAATAAATAATAA
Found at i:29997842 original size:17 final size:19
Alignment explanation
Indices: 29997801--29997842 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29997791 TATCAAACAA
29997801 TTTGAAGAATAAAATTAAT
1 TTTGAAGAATAAAATTAAT
*
29997820 TATTGAATAA-AAAATT-AT
1 T-TTGAAGAATAAAATTAAT
29997838 TTTGA
1 TTTGA
29997843 GAGCCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 3 0.14
19 7 0.33
20 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (19 bp):
TTTGAAGAATAAAATTAAT
Found at i:30002986 original size:2 final size:2
Alignment explanation
Indices: 30002979--30003006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30002969 TCATTCTCAT
30002979 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
30003007 CCTTTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:30004059 original size:24 final size:24
Alignment explanation
Indices: 30004032--30004081 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
30004022 CGAGGACTGC
*
30004032 TCAACAAGTTTAGAATCGATAGAA
1 TCAACAAGTGTAGAATCGATAGAA
* * *
30004056 TCAAGAAGTGTGGAATCTATAGAA
1 TCAACAAGTGTAGAATCGATAGAA
30004080 TC
1 TC
30004082 TGCAGAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (24 bp):
TCAACAAGTGTAGAATCGATAGAA
Found at i:30006187 original size:27 final size:25
Alignment explanation
Indices: 30006156--30006230 Score: 71
Period size: 27 Copynumber: 2.9 Consensus size: 25
30006146 TTATTAATTA
*
30006156 AAATTTCGAATTTATAAATTACAGTT
1 AAATTTCGAATTTATAAATTACA-TC
** *
30006182 ACAATTTCGATATTT-TAAAAGATATC
1 A-AATTTCGA-ATTTATAAATTACATC
*
30006208 AAATCTCGAATTTATAAATTACA
1 AAATTTCGAATTTATAAATTACA
30006231 AACACGACTA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
24 4 0.11
25 13 0.34
26 3 0.08
27 14 0.37
28 4 0.11
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (25 bp):
AAATTTCGAATTTATAAATTACATC
Found at i:30021675 original size:2 final size:2
Alignment explanation
Indices: 30021668--30021710 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
30021658 NNNNNNNNNN
* *
30021668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30021710 A
1 A
30021711 CAGAGACGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:30024690 original size:14 final size:14
Alignment explanation
Indices: 30024665--30024708 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
30024655 GGGAGGTTAC
30024665 TTTA-AGTTTAGGG
1 TTTACAGTTTAGGG
* *
30024678 TTTAGATTTTAGGG
1 TTTACAGTTTAGGG
30024692 TTTACAGTTTAGGG
1 TTTACAGTTTAGGG
30024706 TTT
1 TTT
30024709 GGTTATGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.50
Consensus pattern (14 bp):
TTTACAGTTTAGGG
Found at i:30033934 original size:3 final size:3
Alignment explanation
Indices: 30033926--30033958 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30033916 CTTTGTGTTT
30033926 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30033959 CCATTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30052039 original size:71 final size:71
Alignment explanation
Indices: 30051951--30052089 Score: 260
Period size: 71 Copynumber: 2.0 Consensus size: 71
30051941 TGTGAAGAGT
30051951 AAAAATACTCCTTTCTATACATTCTATGTAATATTGTTATATGCACTGAATAGATTTTGTTGCCC
1 AAAAATACTCCTTTCTATACATTCTATGTAATATTGTTATATGCACTGAATAGATTTTGTTGCCC
30052016 TTAATG
66 TTAATG
* *
30052022 AAAAATACTCCTTTCTATACATTCTATGTACTGTTGTTATATGCACTGAATAGATTTTGTTGCCC
1 AAAAATACTCCTTTCTATACATTCTATGTAATATTGTTATATGCACTGAATAGATTTTGTTGCCC
30052087 TTA
66 TTA
30052090 TAGTCAATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (71 bp):
AAAAATACTCCTTTCTATACATTCTATGTAATATTGTTATATGCACTGAATAGATTTTGTTGCCC
TTAATG
Found at i:30052262 original size:57 final size:57
Alignment explanation
Indices: 30052162--30052325 Score: 176
Period size: 57 Copynumber: 2.9 Consensus size: 57
30052152 AACTGGGGAC
* *
30052162 AGGGATCGGGG-AGTGAGAGATGATTACCGCTC-CCTCAGGCGATCTAGGTCAATTTCA
1 AGGGATCGGGGCA-TGAGAGATGATTATCGCTCTCC-CAGGCGATCTAGATCAATTTCA
* * * *
30052219 CA-GGATCGGGGCATGAGAGATGACTATCGCTCTACCAGTCGATCTAGATCTATTTCA
1 -AGGGATCGGGGCATGAGAGATGATTATCGCTCTCCCAGGCGATCTAGATCAATTTCA
* *
30052276 AGGGATCATGGGGCA--AAAGATGATTATTGCTCTCCCAGGCGATCTAGATC
1 AGGGATC--GGGGCATGAGAGATGATTATCGCTCTCCCAGGCGATCTAGATC
30052326 TGTTTCACGG
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
56 1 0.01
57 80 0.89
58 3 0.03
59 6 0.07
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (57 bp):
AGGGATCGGGGCATGAGAGATGATTATCGCTCTCCCAGGCGATCTAGATCAATTTCA
Found at i:30067298 original size:15 final size:16
Alignment explanation
Indices: 30067274--30067303 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30067264 TGAAAAATGG
30067274 GGCAATGAAACAGCTT
1 GGCAATGAAACAGCTT
30067290 GGCAA-GAAACAGCT
1 GGCAATGAAACAGCT
30067304 AAAAAAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (16 bp):
GGCAATGAAACAGCTT
Found at i:30073830 original size:2 final size:2
Alignment explanation
Indices: 30073823--30073847 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30073813 CTATTCTTCA
30073823 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
30073848 TTGATCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30078805 original size:24 final size:24
Alignment explanation
Indices: 30078778--30078827 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30078768 TGTTATGGAG
30078778 TAGTTTTGCAACATCAGGTAATGA
1 TAGTTTTGCAACATCAGGTAATGA
30078802 TAGTTTTGCAACATCAGGTAATGA
1 TAGTTTTGCAACATCAGGTAATGA
30078826 TA
1 TA
30078828 CTTGTACAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (24 bp):
TAGTTTTGCAACATCAGGTAATGA
Found at i:30093414 original size:4 final size:4
Alignment explanation
Indices: 30093405--30093429 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30093395 CTTTATAAAA
30093405 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
30093430 GAAAGCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:30108111 original size:51 final size:51
Alignment explanation
Indices: 30108056--30108157 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
30108046 ACACAGAGCA
30108056 AAAAATATTTGCATCACTATAAGTTCAGTAGACTTTACCTAAATGGTTACC
1 AAAAATATTTGCATCACTATAAGTTCAGTAGACTTTACCTAAATGGTTACC
30108107 AAAAATATTTGCATCACTATAAGTTCAGTAGACTTTACCTAAATGGTTACC
1 AAAAATATTTGCATCACTATAAGTTCAGTAGACTTTACCTAAATGGTTACC
30108158 TATAAAAGAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (51 bp):
AAAAATATTTGCATCACTATAAGTTCAGTAGACTTTACCTAAATGGTTACC
Found at i:30111393 original size:72 final size:72
Alignment explanation
Indices: 30111274--30111773 Score: 734
Period size: 72 Copynumber: 6.9 Consensus size: 72
30111264 CCAAAGAAGA
* * * * *
30111274 CTCTGCCTCACGTTCAGAATTAG-TCTCAACCACAGAAGGTGCCTCCACCATGCCTGACTTATCA
1 CTCTGCTTCACATTCAGAATT-GTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCT
30111338 GGACAAGG
65 GGACAAGG
* * * * *
30111346 CTCTGCTTCACATTCAGAATTATTCTCAACCATAACAGGTGCTTCCACCATGCCTGAATTATCCG
1 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
*
30111411 GACAGGG
66 GACAAGG
30111418 CTCTGCTTCACATTCAGAATTGTT-TGCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCT
1 CTCTGCTTCACATTCAGAATTGTTCT-CAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCT
30111482 GGACAAGG
65 GGACAAGG
* * *
30111490 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCTTCTATCATGCCTGACTTATCTG
1 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
30111555 GACAAGG
66 GACAAGG
* * * **
30111562 CTCTGCTTCACATTCAGGATTGTCCTCAACCATAGCAGGTGCCTCCATCACACCTGACTTATCTG
1 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
* *
30111627 GAAAAGA
66 GACAAGG
*
30111634 CTCTGCTTCACATTCGGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
1 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
30111699 GACAAGG
66 GACAAGG
* ** *
30111706 CTCTGCTTCACATTCAGAATTGCTCTCAACCATAGCAGGTGTGTCCACCGTGCCTGACTTATCTG
1 CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
30111771 GAC
66 GAC
30111774 CAATGGTAAT
Statistics
Matches: 385, Mismatches: 40, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
71 1 0.00
72 383 0.99
73 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (72 bp):
CTCTGCTTCACATTCAGAATTGTTCTCAACCATAGCAGGTGCCTCCACCATGCCTGACTTATCTG
GACAAGG
Found at i:30146497 original size:30 final size:30
Alignment explanation
Indices: 30146461--30146521 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
30146451 AGCCATAATT
**
30146461 TAACAGATTGTGTTCAATTT-TCTTTTATTA
1 TAACAGATCATGTTCAATTTCT-TTTTATTA
*
30146491 TAACAGATCATGTTCGATTTCTTTTTATTA
1 TAACAGATCATGTTCAATTTCTTTTTATTA
30146521 T
1 T
30146522 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (30 bp):
TAACAGATCATGTTCAATTTCTTTTTATTA
Found at i:30152667 original size:19 final size:21
Alignment explanation
Indices: 30152644--30152689 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
30152634 TTTTTTATTT
*
30152644 TTTAAATAAA-AAATTATATA
1 TTTAAATAAATAAATTAAATA
30152664 -TT-AATAAATAAATTAAATA
1 TTTAAATAAATAAATTAAATA
30152683 TTTAAAT
1 TTTAAAT
30152690 GTAAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 6 0.27
19 11 0.50
20 2 0.09
21 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTAAATAAATAAATTAAATA
Found at i:30152999 original size:15 final size:17
Alignment explanation
Indices: 30152969--30153000 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
30152959 TTACAAATCT
30152969 TAAAATAAATATTATGA
1 TAAAATAAATATTATGA
30152986 TAAAA-AAA-ATTATGA
1 TAAAATAAATATTATGA
30153001 CAAAGAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAAATAAATATTATGA
Found at i:30154023 original size:17 final size:17
Alignment explanation
Indices: 30154001--30154037 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30153991 AGAATCTCTT
*
30154001 ATTAAAATAATTATTTA
1 ATTAAAATAATTATATA
*
30154018 ATTAAAATTATTATATA
1 ATTAAAATAATTATATA
30154035 ATT
1 ATT
30154038 TAGTTCGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAAATAATTATATA
Found at i:30156579 original size:30 final size:30
Alignment explanation
Indices: 30156536--30156649 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
30156526 TAAAATAAAT
*
30156536 AAAATTGTATTGAAACTAATTATTAAACAA
1 AAAATTATATTGAAACTAATTATTAAACAA
* * *
30156566 AAAATTATTTTGAAACCATTAAAAATATATAAAATAAA
1 AAAATTATATTGAAA-C--T---AAT-TATTAAA-CAA
*
30156604 TAAAATTGTATTGAAACTAATTATTAAACAA
1 -AAAATTATATTGAAACTAATTATTAAACAA
*
30156635 AAAATTATTTTGAAA
1 AAAATTATATTGAAA
30156650 GCCATTAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
30 26 0.40
31 3 0.05
32 6 0.09
33 4 0.06
36 4 0.06
37 6 0.09
38 3 0.05
39 13 0.20
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (30 bp):
AAAATTATATTGAAACTAATTATTAAACAA
Found at i:30156677 original size:70 final size:70
Alignment explanation
Indices: 30156478--30156689 Score: 399
Period size: 70 Copynumber: 3.0 Consensus size: 70
30156468 TTGAAGAATA
*
30156478 AAACTAATTATTAAATAAAAAATTATTTTGAAAGCCATTAAAAATATATAAAATAAATAAAATTG
1 AAACTAATTATTAAACAAAAAATTATTTTGAAAGCCATTAAAAATATATAAAATAAATAAAATTG
30156543 TATTG
66 TATTG
30156548 AAACTAATTATTAAACAAAAAATTATTTTGAAA-CCATTAAAAATATATAAAATAAATAAAATTG
1 AAACTAATTATTAAACAAAAAATTATTTTGAAAGCCATTAAAAATATATAAAATAAATAAAATTG
30156612 TATTG
66 TATTG
*
30156617 AAACTAATTATTAAACAAAAAATTATTTTGAAAGCCATTAAAAATATATATAATAAATAAAATTG
1 AAACTAATTATTAAACAAAAAATTATTTTGAAAGCCATTAAAAATATATAAAATAAATAAAATTG
30156682 TATTG
66 TATTG
30156687 AAA
1 AAA
30156690 GAAATATAAT
Statistics
Matches: 139, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
69 69 0.50
70 70 0.50
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (70 bp):
AAACTAATTATTAAACAAAAAATTATTTTGAAAGCCATTAAAAATATATAAAATAAATAAAATTG
TATTG
Found at i:30158312 original size:109 final size:108
Alignment explanation
Indices: 30158192--30158392 Score: 255
Period size: 109 Copynumber: 1.8 Consensus size: 108
30158182 TAAATAAAAT
* * *
30158192 TTAATTCAATAAATAATATTATTTAATTTTAAAAGT-TTAAATTAATTAAT-TACTAATAAATTT
1 TTAATTAAATAAATAATAATATTTAA-TTTAAAAATATTAAATTAATT-ATGTACTAAT-AA-TT
*
30158255 AT-TAAATAGTGTAATTAATCAAATAAAATAATATGTTAGTCAACAA
62 ATCTAAATAATGTAATTAATCAAATAAAATAATATGTTAGTCAACAA
* * *
30158301 TTAATTAAATAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTTATGTATTAATAATTATC
1 TTAATTAAATAAATAATAATATTTAATTTAAAAAT-ATTAAATTAATTATGTACTAATAATTATC
* *
30158366 TAAATAATTTAATTAATTAAATAAAAT
65 TAAATAATGTAATTAATCAAATAAAAT
30158393 TTAATTAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
108 12 0.15
109 51 0.65
110 16 0.20
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (108 bp):
TTAATTAAATAAATAATAATATTTAATTTAAAAATATTAAATTAATTATGTACTAATAATTATCT
AAATAATGTAATTAATCAAATAAAATAATATGTTAGTCAACAA
Found at i:30158380 original size:17 final size:17
Alignment explanation
Indices: 30158358--30158399 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
30158348 TATGTATTAA
30158358 TAATTATCTAAAT-AATT
1 TAATTAT-TAAATAAATT
30158375 TAATTAATTAAATAAAATT
1 TAATT-ATTAAAT-AAATT
30158394 TAATTA
1 TAATTA
30158400 AATAAGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.45
18 3 0.14
19 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTATTAAATAAATT
Found at i:30158451 original size:92 final size:93
Alignment explanation
Indices: 30158301--30158483 Score: 219
Period size: 92 Copynumber: 2.0 Consensus size: 93
30158291 TAGTCAACAA
* * *
30158301 TTAATTAAATAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTTATGTATTAATAA-TT-A
1 TTAATTAAATAAGTAATAATATTTAATTTAAAAACAATCAAATTAGTTATGTACTAATAACTTAA
** *
30158364 TCTAAATAATTTAATTAATTAAATAAAAT
66 T-TAAATAATACAATTAATAAAATAAAAT
* * * * *
30158393 TTAATTAAATAAGTAATATTATTTACTTT-TAAACAATCAAATTAATTTGTGTACTAATAACTTA
1 TTAATTAAATAAGTAATAATATTTAATTTAAAAACAATCAAATT-AGTTATGTACTAATAACTTA
*
30158457 ATTAAATAGTACAATTAATAAAATAAA
65 ATTAAATAATACAATTAATAAAATAAA
30158484 TTAATGTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
91 11 0.14
92 40 0.53
93 23 0.30
94 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (93 bp):
TTAATTAAATAAGTAATAATATTTAATTTAAAAACAATCAAATTAGTTATGTACTAATAACTTAA
TTAAATAATACAATTAATAAAATAAAAT
Found at i:30158477 original size:25 final size:24
Alignment explanation
Indices: 30158447--30158510 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
30158437 ATTTGTGTAC
30158447 TAATAACTTAATTAAATAGTA-CAAT
1 TAATAA-TTAATTAAAT-GTATCAAT
* *
30158472 TAATAAAATAAATT-AATGTATTAAT
1 TAAT--AATTAATTAAATGTATCAAT
30158497 TAATAATTAATTAA
1 TAATAATTAATTAA
30158511 TTAAGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 7 0.22
24 4 0.12
25 14 0.44
26 5 0.16
27 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (24 bp):
TAATAATTAATTAAATGTATCAAT
Found at i:30158483 original size:202 final size:203
Alignment explanation
Indices: 30158107--30158548 Score: 604
Period size: 202 Copynumber: 2.2 Consensus size: 203
30158097 CTCTTGACAT
*
30158107 TAAGTAATAA-ATTTAATTTTTAAAATAATTAAATTAGTTAATGTATTAATAATTTATATAAATA
1 TAAGTAATAATATTTAA-TTTAAAAATAATTAAATTAGTTAATGTATTAATAATTTATATAAATA
* * * * *
30158171 GTTTAATTGATTAAATAAAATTTAATTCAATAAATAATATTATTTAATTTTAAAAGTTTAAATTA
65 ATTTAATTAATTAAATAAAATTTAATTAAATAAATAATATTATTTAATTTTAAAAGATCAAATTA
* ** * * *
30158236 ATTAATTACTAATAAATTTATTAAATAGTGTAATTAATCAAATAAAATAATATGTTAGTCAACAA
130 ATTAATTACTAATAAATTAATTAAATAGTACAATTAATAAAATAAAATAATATATTAATCAACAA
30158301 TTAATTAAA
195 TTAATTAAA
*
30158310 TAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTT-ATGTATTAATAA-TTATCTAAATAA
1 TAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTTAATGTATTAATAATTTATATAAATAA
* *
30158373 TTTAATTAATTAAATAAAATTTAATTAAATAAGTAATATTATTTACTTTTAAACA-ATCAAATTA
66 TTTAATTAATTAAATAAAATTTAATTAAATAAATAATATTATTTAATTTTAAA-AGATCAAATTA
** * * * * *
30158437 ATTTGTGTACTAATAACTTAATTAAATAGTACAATTAATAAAATAAATTAATGTATTAATTAATA
130 ATTAAT-TACTAATAAATTAATTAAATAGTACAATTAATAAAATAAAATAATATATTAATCAACA
*
30158502 ATTAATTAAT
194 ATTAATTAAA
*
30158512 TAAGTAATAATATTTAATTTAAAAAATAATTTAATTA
1 TAAGTAATAATATTTAATTT-AAAAATAATTAAATTA
30158549 ATAAAAGTAA
Statistics
Matches: 211, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
201 70 0.33
202 89 0.42
203 46 0.22
204 6 0.03
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (203 bp):
TAAGTAATAATATTTAATTTAAAAATAATTAAATTAGTTAATGTATTAATAATTTATATAAATAA
TTTAATTAATTAAATAAAATTTAATTAAATAAATAATATTATTTAATTTTAAAAGATCAAATTAA
TTAATTACTAATAAATTAATTAAATAGTACAATTAATAAAATAAAATAATATATTAATCAACAAT
TAATTAAA
Found at i:30158506 original size:19 final size:19
Alignment explanation
Indices: 30158482--30158550 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
30158472 TAATAAAATA
*
30158482 AATTAATGT-ATTAATTAAT
1 AATTAAT-TAATTAAGTAAT
30158501 AATTAATTAATTAAGTAAT
1 AATTAATTAATTAAGTAAT
* **
30158520 AA-TATTTAATTTAAAAAAT
1 AATTAATTAA-TTAAGTAAT
30158539 AATTTAATTAAT
1 AA-TTAATTAAT
30158551 AAAAGTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 7 0.17
19 27 0.66
20 1 0.02
21 6 0.15
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTAATTAATTAAGTAAT
Found at i:30158560 original size:22 final size:22
Alignment explanation
Indices: 30158535--30158586 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
30158525 TTAATTTAAA
30158535 AAATAATTTA-ATTAATAAAAGT
1 AAATAATTTATATTAA-AAAAGT
*
30158557 AAATACATTTATATTAAAAATGT
1 AAATA-ATTTATATTAAAAAAGT
*
30158580 ATATAAT
1 AAATAAT
30158587 AGTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 14 0.54
24 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AAATAATTTATATTAAAAAAGT
Found at i:30159337 original size:27 final size:27
Alignment explanation
Indices: 30159307--30159358 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
30159297 AAATAATTAA
30159307 ATTAGTTAATGTATTAATAATTTATAT
1 ATTAGTTAATGTATTAATAATTTATAT
30159334 ATTAGTTAATGTATTAATAATTTAT
1 ATTAGTTAATGTATTAATAATTTAT
30159359 TTAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (27 bp):
ATTAGTTAATGTATTAATAATTTATAT
Found at i:30160925 original size:2 final size:2
Alignment explanation
Indices: 30160918--30160942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30160908 TAACTAGTAC
30160918 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30160943 TACTTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30165489 original size:4 final size:4
Alignment explanation
Indices: 30165482--30165507 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30165472 TTTTTTTTCA
30165482 AAAG AAAG AAAG AAAG AAAG AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AA
30165508 CGATATTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:30168111 original size:26 final size:25
Alignment explanation
Indices: 30168061--30168123 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
30168051 TTTGATTAAA
30168061 ATAAAAATATAAAAATTTAAGTAAATAT
1 ATAAAAA-AT-AAAATTTAAGTAAAT-T
30168089 ATAAAAAATAAAATTT-AGTTAAATT
1 ATAAAAAATAAAATTTAAG-TAAATT
*
30168114 AAAAAAAATA
1 ATAAAAAATA
30168124 TTTTAGGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 12 0.36
26 12 0.36
27 2 0.06
28 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (25 bp):
ATAAAAAATAAAATTTAAGTAAATT
Found at i:30168503 original size:19 final size:19
Alignment explanation
Indices: 30168479--30168517 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30168469 CTCGATAGAT
30168479 AGTTAAAGGCAACATGGTG
1 AGTTAAAGGCAACATGGTG
30168498 AGTTAAAGGCAACATGGTG
1 AGTTAAAGGCAACATGGTG
30168517 A
1 A
30168518 TGATTCCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTTAAAGGCAACATGGTG
Found at i:30169165 original size:10 final size:10
Alignment explanation
Indices: 30169150--30169176 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
30169140 TAATCTTCAT
30169150 TTTCATTTTC
1 TTTCATTTTC
30169160 TTTCATTTTC
1 TTTCATTTTC
30169170 TTTCATT
1 TTTCATT
30169177 GAATCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTCATTTTC
Found at i:30169686 original size:2 final size:2
Alignment explanation
Indices: 30169679--30169706 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30169669 ATCTGTAAAC
30169679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30169707 TACTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30174556 original size:16 final size:17
Alignment explanation
Indices: 30174519--30174561 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
30174509 ACCCAAAAGC
30174519 AAAAAATAAACATACGAAT
1 AAAAAA-AAACATAC-AAT
30174538 AAAAAAAAACATA-AAT
1 AAAAAAAAACATACAAT
30174554 AAATAAAA
1 AAA-AAAA
30174562 TCAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.26
17 4 0.17
18 7 0.30
19 6 0.26
ACGTcount: A:0.77, C:0.07, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAAAAAAACATACAAT
Found at i:30174932 original size:19 final size:19
Alignment explanation
Indices: 30174888--30174932 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
30174878 AGATTCATTT
* *
30174888 CTGGACTTCTTTGGATAGA
1 CTGGACTTCTGTGGAAAGA
* *
30174907 ATAGACTTCTGTGGAAAGA
1 CTGGACTTCTGTGGAAAGA
30174926 CTGGACT
1 CTGGACT
30174933 CCTATGGATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (19 bp):
CTGGACTTCTGTGGAAAGA
Found at i:30177063 original size:31 final size:32
Alignment explanation
Indices: 30177001--30177079 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
30176991 CTTTTTTTTC
30177001 TTCTTCTTTATTTTTTTATTATTTTACTTCCTCA
1 TTCTTC-TTATTTTTTTATTATTTTA-TTCCTCA
**
30177035 TTCTTCTTATTTTTTTACTT-TTTT-TTCCTTT
1 TTCTTCTTATTTTTTTA-TTATTTTATTCCTCA
30177066 TTC-TCTT-TTTTTTT
1 TTCTTCTTATTTTTTT
30177080 CTCCCTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 7 0.17
30 4 0.10
31 8 0.19
33 15 0.36
34 8 0.19
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (32 bp):
TTCTTCTTATTTTTTTATTATTTTATTCCTCA
Found at i:30186311 original size:16 final size:17
Alignment explanation
Indices: 30186290--30186322 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30186280 TTATACAATG
30186290 GTTAAAT-ATATAAATA
1 GTTAAATAATATAAATA
30186306 GTTAAATAATATAAATA
1 GTTAAATAATATAAATA
30186323 AAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
GTTAAATAATATAAATA
Found at i:30193918 original size:2 final size:2
Alignment explanation
Indices: 30193911--30193936 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30193901 GTTTATGCTT
30193911 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
30193937 AGCCATTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:30200168 original size:9 final size:9
Alignment explanation
Indices: 30200156--30200203 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
30200146 TTTAATCGTA
*
30200156 TTAAACATG
1 TTAAACGTG
*
30200165 TTAATCGTG
1 TTAAACGTG
**
30200174 TTAAATATG
1 TTAAACGTG
*
30200183 TTAATCGTG
1 TTAAACGTG
30200192 TTAAACGTG
1 TTAAACGTG
30200201 TTA
1 TTA
30200204 TTAATCGTGT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (9 bp):
TTAAACGTG
Found at i:30200170 original size:18 final size:18
Alignment explanation
Indices: 30200147--30200203 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
30200137 ATATTTTTAT
*
30200147 TTAATCGTATTAAACATG
1 TTAATCGTGTTAAACATG
*
30200165 TTAATCGTGTTAAATATG
1 TTAATCGTGTTAAACATG
*
30200183 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACATG
30200201 TTA
1 TTA
30200204 TTAATCGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (18 bp):
TTAATCGTGTTAAACATG
Found at i:30212115 original size:2 final size:2
Alignment explanation
Indices: 30212108--30212133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30212098 AACCAAAATA
30212108 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
30212134 GATAGACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30214074 original size:21 final size:21
Alignment explanation
Indices: 30214050--30214101 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
30214040 GGGGCCACCA
* *
30214050 GGAGGGCCTCCGGGGGGTCCT
1 GGAGGGCCACCAGGGGGTCCT
*
30214071 GGAGGGCCACCAGGTGGTCCT
1 GGAGGGCCACCAGGGGGTCCT
*
30214092 GGCGGGCCAC
1 GGAGGGCCAC
30214102 TAAAAGGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.31, G:0.48, T:0.12
Consensus pattern (21 bp):
GGAGGGCCACCAGGGGGTCCT
Found at i:30214116 original size:30 final size:30
Alignment explanation
Indices: 30214080--30214144 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
30214070 TGGAGGGCCA
* *
30214080 CCAGGTGGTCCTGGCGGGCCACTAAAAGGT
1 CCAGGTGGTCCCGGCGGGCCACCAAAAGGT
*
30214110 CCAGGTGGTCCCGGCTGGCCACCAAAAGGT
1 CCAGGTGGTCCCGGCGGGCCACCAAAAGGT
30214140 CCAGG
1 CCAGG
30214145 CGGACCACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.14
Consensus pattern (30 bp):
CCAGGTGGTCCCGGCGGGCCACCAAAAGGT
Found at i:30214160 original size:21 final size:21
Alignment explanation
Indices: 30214110--30214164 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
30214100 ACTAAAAGGT
* *
30214110 CCAGGTGGTCCCGGCTGGCCA
1 CCAGGAGGTCCAGGCTGGCCA
**
30214131 CCAAAAGGTCCAGGC-GGACCA
1 CCAGGAGGTCCAGGCTGG-CCA
30214152 CCAGGAGGTCCAG
1 CCAGGAGGTCCAG
30214165 CATAAGGTGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.22, C:0.35, G:0.35, T:0.09
Consensus pattern (21 bp):
CCAGGAGGTCCAGGCTGGCCA
Found at i:30216772 original size:2 final size:2
Alignment explanation
Indices: 30216765--30216812 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
30216755 CAAGTGATAT
* *
30216765 TG TG TG TG TG CG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
30216807 TG TG TG
1 TG TG TG
30216813 AGAGAGAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.50, T:0.46
Consensus pattern (2 bp):
TG
Found at i:30235754 original size:32 final size:32
Alignment explanation
Indices: 30235718--30235783 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
30235708 TCCATTGCAT
30235718 AAACATTATTGATAACAACTTTCTCATGAAAG
1 AAACATTATTGATAACAACTTTCTCATGAAAG
30235750 AAACATTATTGATAACAACTTTCTCATGAAAG
1 AAACATTATTGATAACAACTTTCTCATGAAAG
30235782 AA
1 AA
30235784 TACAGGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (32 bp):
AAACATTATTGATAACAACTTTCTCATGAAAG
Found at i:30239134 original size:14 final size:14
Alignment explanation
Indices: 30239115--30239144 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
30239105 CTGCATTAGA
30239115 TTTTTAGCTTTCTC
1 TTTTTAGCTTTCTC
30239129 TTTTTAGCTTTCTC
1 TTTTTAGCTTTCTC
30239143 TT
1 TT
30239145 ATGATGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTTTAGCTTTCTC
Found at i:30244300 original size:25 final size:25
Alignment explanation
Indices: 30244272--30244351 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 25
30244262 ACCCTAATCT
30244272 TTAATAAAATAATTTCTTTTGTATA
1 TTAATAAAATAATTTCTTTTGTATA
* * * *
30244297 TTAA-AAGTATCATTTTCAAATAT-TAT-
1 TTAATAA-AAT-AATTTC--TTTTGTATA
*
30244323 TTAATAAAATAATTTTTTTTGTATA
1 TTAATAAAATAATTTCTTTTGTATA
30244348 TTAA
1 TTAA
30244352 AAGAAAAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 14
0.63 0.15 0.23
Matches are distributed among these distances:
23 2 0.05
24 5 0.13
25 14 0.36
26 11 0.28
27 5 0.13
28 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (25 bp):
TTAATAAAATAATTTCTTTTGTATA
Found at i:30244705 original size:17 final size:18
Alignment explanation
Indices: 30244678--30244711 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
30244668 ATACCTACCA
*
30244678 TTCCTTTTTCCTTCTTCC
1 TTCCTTTTTCCCTCTTCC
30244696 TTCC-TTTTCCCTCTTC
1 TTCCTTTTTCCCTCTTC
30244712 GATTTCTCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTTTTTCCCTCTTCC
Found at i:30247819 original size:2 final size:2
Alignment explanation
Indices: 30247812--30247837 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30247802 CTTATAATTT
30247812 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
30247838 CTTGTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30248288 original size:29 final size:29
Alignment explanation
Indices: 30248209--30248314 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 29
30248199 TTAAAAAAAT
* *
30248209 TTAAATAAGTTCTCATATTTTTA--TTACG
1 TTAAATAAGTTTTTATATTTTTATTTTA-G
* *
30248237 TTCAATCAAGTTTTGATATTTTTATTTTGAG
1 TTAAAT-AAGTTTTTATATTTTTATTTT-AG
*
30248268 TTAAATAAGTTTTTATATTTTTATTTTAAA
1 TTAAATAAGTTTTTATATTTTTATTTT-AG
* *
30248298 TCAAATAAGCTTTTATA
1 TTAAATAAGTTTTTATA
30248315 ACTAATAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 5 0.08
29 15 0.23
30 36 0.55
31 8 0.12
32 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.53
Consensus pattern (29 bp):
TTAAATAAGTTTTTATATTTTTATTTTAG
Found at i:30248749 original size:32 final size:32
Alignment explanation
Indices: 30248713--30248775 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
30248703 TTAATATCTT
30248713 ATAATTGATAATAATGTGACATGTTGATATAC
1 ATAATTGATAATAATGTGACATGTTGATATAC
* *
30248745 ATAATTGATGATGATGTGACATGTTGATATA
1 ATAATTGATAATAATGTGACATGTTGATATA
30248776 ATATTTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (32 bp):
ATAATTGATAATAATGTGACATGTTGATATAC
Found at i:30250039 original size:2 final size:2
Alignment explanation
Indices: 30250032--30250183 Score: 147
Period size: 2 Copynumber: 77.5 Consensus size: 2
30250022 ATAGAATCTT
30250032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
30250074 TA TA TA NTA -A TGA -A TT TGA AA GA TA T- TA T- TA TCC TA TT TA
1 TA TA TA -TA TA T-A TA TA T-A TA TA TA TA TA TA TA T-A TA TA TA
* * *
30250114 -A TA GA -A TC T- TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30250153 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30250184 GCGCTGCCGT
Statistics
Matches: 127, Mismatches: 12, Indels: 22
0.79 0.07 0.14
Matches are distributed among these distances:
1 7 0.06
2 116 0.91
3 4 0.03
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30251934 original size:6 final size:6
Alignment explanation
Indices: 30251925--30251963 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
30251915 TTTTTATTTT
* * *
30251925 TTTAAA TTTATA TTTAAA TTTAAA TTTATA TTTATA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
30251964 TATTTACTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TTTAAA
Found at i:30251940 original size:12 final size:12
Alignment explanation
Indices: 30251925--30251963 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
30251915 TTTTTATTTT
30251925 TTTAAATTTATA
1 TTTAAATTTATA
*
30251937 TTTAAATTTAAA
1 TTTAAATTTATA
*
30251949 TTTATATTTATA
1 TTTAAATTTATA
30251961 TTT
1 TTT
30251964 TATTTACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAATTTATA
Found at i:30251946 original size:18 final size:18
Alignment explanation
Indices: 30251925--30251963 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
30251915 TTTTTATTTT
30251925 TTTAAATTTATATTTAAA
1 TTTAAATTTATATTTAAA
*
30251943 TTTAAATTTATATTTATA
1 TTTAAATTTATATTTAAA
30251961 TTT
1 TTT
30251964 TATTTACTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAATTTATATTTAAA
Found at i:30252077 original size:27 final size:27
Alignment explanation
Indices: 30252045--30252106 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
30252035 TTTTTTATTA
30252045 TGTCATATATAAATTCTATATTCTACT
1 TGTCATATATAAATTCTATATTCTACT
* * * *
30252072 TGTCATATGTGAGTTTTATATTCTACT
1 TGTCATATATAAATTCTATATTCTACT
*
30252099 TATCATAT
1 TGTCATAT
30252107 TCTTCTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (27 bp):
TGTCATATATAAATTCTATATTCTACT
Found at i:30268861 original size:21 final size:21
Alignment explanation
Indices: 30268837--30268893 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
30268827 TGTGAATCTG
30268837 GCTGAAGAGACAAAAGAAAAA
1 GCTGAAGAGACAAAAGAAAAA
* ***
30268858 GCTGTAGACGA-AAAAGAATCG
1 GCTGAAGA-GACAAAAGAAAAA
*
30268879 GCTCAAGAGACAAAA
1 GCTGAAGAGACAAAA
30268894 ATACAAGCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.53, C:0.14, G:0.25, T:0.09
Consensus pattern (21 bp):
GCTGAAGAGACAAAAGAAAAA
Found at i:30269036 original size:42 final size:42
Alignment explanation
Indices: 30269011--30269095 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
30269001 AGAAGATATC
*
30269011 GTGGAGGGT-AAAAACCTGGCTGAAGATGCAAAAGAACAAACT
1 GTGGAGGGTGAAAAA-CTGGCTGAAGAAGCAAAAGAACAAACT
* *
30269053 GTGGAGGGTGAAAAACTGGCTGAA-AAGAAAACAGAAGAAACT
1 GTGGAGGGTGAAAAACTGGCTGAAGAAGCAAA-AGAACAAACT
30269095 G
1 G
30269096 CAAATGGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 5 0.13
42 28 0.74
43 5 0.13
ACGTcount: A:0.45, C:0.12, G:0.31, T:0.13
Consensus pattern (42 bp):
GTGGAGGGTGAAAAACTGGCTGAAGAAGCAAAAGAACAAACT
Found at i:30273672 original size:96 final size:95
Alignment explanation
Indices: 30273524--30273810 Score: 346
Period size: 96 Copynumber: 3.0 Consensus size: 95
30273514 AATGTAAACC
* * * * * *
30273524 TGGCTGAAGAGGA-AAAAGAAAAAACTGTGGAGGAAA-AAGAATTGGCTCAAGAGACAAAAATAG
1 TGGCTGAAGA-GACCAAAGAAGAAACTGTGCAGGAAATAATACTT-GCTGAAGAGACAAAAA-AG
* *
30273587 AAGCCAAAGAAGAAATTGTGGAGGATAAAAAAT
63 AAGCTAAAGAAGATATTGTGGAGGATAAAAAAT
*
30273620 TGGCTGAAGAGACCAAAGAAGAAACAGTGCAGGAAATAATACTTGCTGAAGAGACAAAAGAAGAA
1 TGGCTGAAGAGACCAAAGAAGAAACTGTGCAGGAAATAATACTTGCTGAAGAGACAAAA-AAGAA
* *
30273685 GCTAAAGAAGATATCGTGGAGGATAAAATAT
65 GCTAAAGAAGATATTGTGGAGGATAAAAAAT
* * * *
30273716 TTGATGAAGAGACCCAAGAAGAAACTGTGCAGGAAATAATACTTCCTGAAGAGACAAAAAGAAGA
1 TGGCTGAAGAGACCAAAGAAGAAACTGTGCAGGAAATAATACTTGCTGAAGAGAC-AAAA-AAGA
*
30273781 AGCTAAAGAAGGTATCT-TGGAGGATAAAAA
64 AGCTAAAGAAGATAT-TGTGGAGGATAAAAA
30273811 CCAGGCTGAA
Statistics
Matches: 167, Mismatches: 19, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
95 2 0.01
96 124 0.74
97 41 0.25
ACGTcount: A:0.49, C:0.10, G:0.26, T:0.15
Consensus pattern (95 bp):
TGGCTGAAGAGACCAAAGAAGAAACTGTGCAGGAAATAATACTTGCTGAAGAGACAAAAAAGAAG
CTAAAGAAGATATTGTGGAGGATAAAAAAT
Found at i:30273693 original size:54 final size:52
Alignment explanation
Indices: 30273634--30273791 Score: 124
Period size: 54 Copynumber: 3.1 Consensus size: 52
30273624 TGAAGAGACC
30273634 AAAGAAGAAACAGTGCAGGAAATAATACTTGCTGAAGAGACAAAAGAAGAAGCT
1 AAAGAAGAAAC-GTGCAGGAAATAATACTT-CTGAAGAGACAAAAGAAGAAGCT
* * * *
30273688 AAAGAAGATATCGTGGAGGATAA-AATA-TT-TG-A-TG----AAG-AG-A-CC
1 AAAGAAGA-AACGTGCAGGA-AATAATACTTCTGAAGAGACAAAAGAAGAAGCT
*
30273730 CAAGAAGAAACTGTGCAGGAAATAATACTTCCTGAAGAGACAAAAAGAAGAAGCT
1 AAAGAAGAAAC-GTGCAGGAAATAATACTT-CTGAAGAGAC-AAAAGAAGAAGCT
30273785 AAAGAAG
1 AAAGAAG
30273792 GTATCTTGGA
Statistics
Matches: 77, Mismatches: 10, Indels: 33
0.64 0.08 0.28
Matches are distributed among these distances:
41 4 0.05
42 19 0.25
43 3 0.04
44 2 0.03
45 5 0.06
46 1 0.01
47 1 0.01
49 1 0.01
50 1 0.01
51 2 0.03
52 3 0.04
53 4 0.05
54 20 0.26
55 11 0.14
ACGTcount: A:0.50, C:0.11, G:0.24, T:0.15
Consensus pattern (52 bp):
AAAGAAGAAACGTGCAGGAAATAATACTTCTGAAGAGACAAAAGAAGAAGCT
Found at i:30279744 original size:13 final size:14
Alignment explanation
Indices: 30279716--30279745 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
30279706 AACTCACACT
30279716 TTTTTTATTTATTC
1 TTTTTTATTTATTC
30279730 TTTTTTATTTA-TC
1 TTTTTTATTTATTC
30279743 TTT
1 TTT
30279746 GTGGAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTATTC
Found at i:30284813 original size:20 final size:20
Alignment explanation
Indices: 30284788--30284831 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
30284778 ATATCTATAC
30284788 GTCCAAATAATATTAACCAT
1 GTCCAAATAATATTAACCAT
30284808 GTCCAAATAATATTAACCAT
1 GTCCAAATAATATTAACCAT
30284828 GTCC
1 GTCC
30284832 TGACAACGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.30
Consensus pattern (20 bp):
GTCCAAATAATATTAACCAT
Found at i:30286016 original size:12 final size:12
Alignment explanation
Indices: 30285996--30286027 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
30285986 ATATAAATAA
*
30285996 TTTTAAATAATT
1 TTTTTAATAATT
30286008 TTTTTAATAATT
1 TTTTTAATAATT
30286020 TTTTTAAT
1 TTTTTAAT
30286028 TTTATAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTTAATAATT
Found at i:30286217 original size:23 final size:24
Alignment explanation
Indices: 30286155--30286224 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
30286145 TTTATATATG
*
30286155 TTATTTATATTA-AATT-TTATTA
1 TTATTTATGTTATAATTATTATTA
*
30286177 -TATTTGATGTTATTATTATTATTA
1 TTATTT-ATGTTATAATTATTATTA
*
30286201 TTATTT-TGTTATAATTATTTTTA
1 TTATTTATGTTATAATTATTATTA
30286224 T
1 T
30286225 AATTATAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 19 0.47
24 6 0.15
25 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTATTTATGTTATAATTATTATTA
Found at i:30286318 original size:18 final size:18
Alignment explanation
Indices: 30286281--30286319 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
30286271 ATATTTTTAT
*
30286281 TTAATCGTGTTAAACGTG
1 TTAATCGTGTTAAACATG
* *
30286299 TTAATCTTGTTAAATATG
1 TTAATCGTGTTAAACATG
30286317 TTA
1 TTA
30286320 TTGATAGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (18 bp):
TTAATCGTGTTAAACATG
Found at i:30287717 original size:14 final size:14
Alignment explanation
Indices: 30287698--30287724 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30287688 CAAAAATAAT
30287698 TAATTAACTAAAAC
1 TAATTAACTAAAAC
30287712 TAATTAACTAAAA
1 TAATTAACTAAAA
30287725 TTTAAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (14 bp):
TAATTAACTAAAAC
Found at i:30288847 original size:21 final size:20
Alignment explanation
Indices: 30288823--30288861 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30288813 AAAACTAATA
30288823 AATAATAATCAAATTAAAAAG
1 AATAA-AATCAAATTAAAAAG
*
30288844 AATAACATCAAATTAAAA
1 AATAAAATCAAATTAAAA
30288862 TAACTCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (20 bp):
AATAAAATCAAATTAAAAAG
Found at i:30292280 original size:32 final size:34
Alignment explanation
Indices: 30292244--30292313 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
30292234 ATTTAAAATT
*
30292244 TTAAAA-TAAAATATTTAATAAAATTTT-TTTTA
1 TTAAAATTAAAAAATTTAATAAAATTTTATTTTA
* *
30292276 TTAAAATTAAAAAATTTAATAAATTTTTATTTTT
1 TTAAAATTAAAAAATTTAATAAAATTTTATTTTA
30292310 TTAA
1 TTAA
30292314 TTTTTTGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 6 0.18
33 19 0.58
34 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TTAAAATTAAAAAATTTAATAAAATTTTATTTTA
Done.