Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 181 of 189
Found at i:53773968 original size:85 final size:85
Alignment explanation
Indices: 53773875--53774092 Score: 260
Period size: 85 Copynumber: 2.6 Consensus size: 85
53773865 AAAAACATTA
*
53773875 CTATAGAACATGAAATTTAGC-GACGCTTTTCCCAAAAACACCACTAAAGAACATGACATTTAGC
1 CTATAGAACATGAAATTTAGCTG-CGCTTTCCCCAAAAACACCACTAAAGAACATGACATTTAGC
** *
53773939 GGCGCTTTCCCACAAACGCCG
65 AACGCTTTCCCACAAACACCG
** * * *
53773960 CTATAGAACATGATGTTTAGCTGCGCTTTCCCCACAAACGCCACTAAAGAACATGACCTTTAGCA
1 CTATAGAACATGAAATTTAGCTGCGCTTTCCCCAAAAACACCACTAAAGAACATGACATTTAGCA
*
53774025 ACGCTTTTCCACAAACACCG
66 ACGCTTTCCCACAAACACCG
* ** * * *
53774045 CTAAAGAACATGACCTTTCA-TTGCGCTTTCCCCAGAAACACCGCTAAA
1 CTATAGAACATGAAATTT-AGCTGCGCTTTCCCCAAAAACACCACTAAA
53774093 AGTCATGTTA
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
85 112 0.98
86 2 0.02
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.22
Consensus pattern (85 bp):
CTATAGAACATGAAATTTAGCTGCGCTTTCCCCAAAAACACCACTAAAGAACATGACATTTAGCA
ACGCTTTCCCACAAACACCG
Found at i:53774072 original size:42 final size:42
Alignment explanation
Indices: 53773879--53774092 Score: 216
Period size: 42 Copynumber: 5.0 Consensus size: 42
53773869 ACATTACTAT
** * *
53773879 AGAACATGAAATTTAGC-GACGCTTTTCCCAAAAACACCACTAA
1 AGAACATGACCTTTAGCTG-CGC-TTTCCCACAAACACCGCTAA
* * * *
53773922 AGAACATGACATTTAGCGGCGCTTTCCCACAAACGCCGCTAT
1 AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
** * *
53773964 AGAACATGATGTTTAGCTGCGCTTTCCCCACAAACGCCACTAA
1 AGAACATGACCTTTAGCTGCGCTTT-CCCACAAACACCGCTAA
** *
53774007 AGAACATGACCTTTAGCAACGCTTTTCCACAAACACCGCTAA
1 AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
* *
53774049 AGAACATGACCTTTCA-TTGCGCTTTCCCCAGAAACACCGCTAA
1 AGAACATGACCTTT-AGCTGCGCTTT-CCCACAAACACCGCTAA
53774092 A
1 A
53774093 AGTCATGTTA
Statistics
Matches: 145, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
42 72 0.50
43 72 0.50
44 1 0.01
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (42 bp):
AGAACATGACCTTTAGCTGCGCTTTCCCACAAACACCGCTAA
Found at i:53774238 original size:11 final size:13
Alignment explanation
Indices: 53774222--53774255 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
53774212 AATTTTACGG
53774222 AAAAATTTCG-T-
1 AAAAATTTCGTTC
53774233 AAAAATTTCGTTC
1 AAAAATTTCGTTC
53774246 AAAAATTTCG
1 AAAAATTTCG
53774256 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:53775503 original size:103 final size:103
Alignment explanation
Indices: 53775324--53775592 Score: 461
Period size: 103 Copynumber: 2.6 Consensus size: 103
53775314 TATGAAGGGA
*
53775324 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
53775389 AGGGGTTGCTAAGTGCTGATTCCCCG-ATCCATTGGTGG
66 AGGGGTTGCTAAGTGCTGATTCCCCGAAT-CATTGGTGG
*
53775427 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTCAAGGGGGTTGCTAAGTGCTGATTCCCCCA
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
*
53775492 AGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGG
66 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
* *
53775530 TTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAA-GGGGTTGCTAAGTGCTGATTCCCC
1 TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGT-AAAGGGGGTTGCTAAGTGCTGATTCCCC
53775593 GAATCACTGG
Statistics
Matches: 158, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
103 154 0.97
104 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (103 bp):
TTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTAAAGGGGGTTGCTAAGTGCTGATTCCCCCA
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGG
Found at i:53782668 original size:9 final size:9
Alignment explanation
Indices: 53782656--53782721 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
53782646 TGATATATAT
53782656 TTATGTAAG
1 TTATGTAAG
53782665 TTATGTAAG
1 TTATGTAAG
*
53782674 TTATGATATG
1 TTATG-TAAG
* * *
53782684 ATATAT-AT
1 TTATGTAAG
53782692 TTATGT-A-
1 TTATGTAAG
53782699 TTATGTAAG
1 TTATGTAAG
53782708 TTATGTAAG
1 TTATGTAAG
53782717 TTATG
1 TTATG
53782722 ATCCAAAGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 29 0.62
10 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:53782670 original size:36 final size:34
Alignment explanation
Indices: 53782629--53782712 Score: 150
Period size: 36 Copynumber: 2.4 Consensus size: 34
53782619 ATCCAAAGTT
53782629 TTATGTAAGTTATGATATGATATATATTTATGTAA
1 TTATGTAAGTTATGATATGATATATATTTATGT-A
53782664 GTTATGTAAGTTATGATATGATATATATTTATGTA
1 -TTATGTAAGTTATGATATGATATATATTTATGTA
53782699 TTATGTAAGTTATG
1 TTATGTAAGTTATG
53782713 TAAGTTATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
34 14 0.29
35 1 0.02
36 33 0.69
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.49
Consensus pattern (34 bp):
TTATGTAAGTTATGATATGATATATATTTATGTA
Found at i:53782793 original size:13 final size:13
Alignment explanation
Indices: 53782775--53782801 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53782765 TGATTATCAT
53782775 CTTTAAATTTTAA
1 CTTTAAATTTTAA
53782788 CTTTAAATTTTAA
1 CTTTAAATTTTAA
53782801 C
1 C
53782802 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:53785201 original size:22 final size:22
Alignment explanation
Indices: 53785158--53785201 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
53785148 AACATATAAT
*
53785158 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
53785180 TAAA-TAATCTAAAAATTGCAAA
1 TAAATTAATC-AAAAATTACAAA
53785202 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:53787897 original size:31 final size:31
Alignment explanation
Indices: 53787862--53787957 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
53787852 TGTTTGCCCA
53787862 TTTAATTTGATGCACAATTTCATGCAATAAC
1 TTTAATTTGATGCACAATTTCATGCAATAAC
* * ** **
53787893 TTTAATATGTCTG-ATTATGACATGTC-A-AAC
1 TTTAATTTG-ATGCACAATTTCATG-CAATAAC
*
53787923 ATT--TTTGATGCACAATTTCATGCAATAAC
1 TTTAATTTGATGCACAATTTCATGCAATAAC
53787952 TTTAAT
1 TTTAAT
53787958 ATGTCTGATT
Statistics
Matches: 44, Mismatches: 14, Indels: 14
0.61 0.19 0.19
Matches are distributed among these distances:
27 3 0.07
28 11 0.25
29 5 0.11
30 5 0.11
31 17 0.39
32 3 0.07
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (31 bp):
TTTAATTTGATGCACAATTTCATGCAATAAC
Found at i:53787933 original size:59 final size:59
Alignment explanation
Indices: 53787867--53787986 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
53787857 GCCCATTTAA
53787867 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
1 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
*
53787926 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATTACATGTCAAACATT
1 TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
53787985 TT
1 TT
53787987 GTCTAGAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (59 bp):
TTTGATGCACAATTTCATGCAATAACTTTAATATGTCTGATTATGACATGTCAAACATT
Found at i:53800907 original size:26 final size:27
Alignment explanation
Indices: 53800838--53800911 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
53800828 TATTTTCTCG
*
53800838 AAATTTTACTAGGGGTAAAATCATCAA
1 AAATTTTACTAAGGGTAAAATCATCAA
*
53800865 AAATTTTA-TCAAAGGTAAAATCATC-A
1 AAATTTTACT-AAGGGTAAAATCATCAA
53800891 AAATTTTACTAAGGGTAAAAT
1 AAATTTTACTAAGGGTAAAAT
53800912 AGTGATGAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATTTTACTAAGGGTAAAATCATCAA
Found at i:53823895 original size:13 final size:13
Alignment explanation
Indices: 53823877--53823916 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
53823867 TCGACCTAAA
53823877 TAATTACAAA-AGT
1 TAATTACAAATA-T
53823890 TAATTACAAATAT
1 TAATTACAAATAT
*
53823903 TAGTTACAAATAT
1 TAATTACAAATAT
53823916 T
1 T
53823917 TTGTCAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 24 0.96
14 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (13 bp):
TAATTACAAATAT
Found at i:53824336 original size:18 final size:19
Alignment explanation
Indices: 53824300--53824351 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
53824290 TTATTTTAGC
* *
53824300 TAAATTTAAAATTATAAAAA
1 TAAATATAAAAATA-AAAAA
53824320 TAAATA-AAAAATAAAAAA
1 TAAATATAAAAATAAAAAA
*
53824338 TAATTATAAAAATA
1 TAAATATAAAAATA
53824352 TAATTTAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 10 0.36
19 13 0.46
20 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAATATAAAAATAAAAAA
Found at i:53826811 original size:40 final size:42
Alignment explanation
Indices: 53826748--53826864 Score: 143
Period size: 41 Copynumber: 2.9 Consensus size: 42
53826738 TAAAAATTCA
* *
53826748 CGGCGTTTAT-GAGAAAAACGCCGCTATTGTCTTA-CTTTTG
1 CGGCGTTTATGGAGAAAAACGCCGCTATTGCCTTACCTTCTG
*
53826788 CGGTGTTTATGGAGAAAAA-GCCGCTATTGCCTTACCTTCTG
1 CGGCGTTTATGGAGAAAAACGCCGCTATTGCCTTACCTTCTG
* * * *
53826829 CGGCGTTTAT-GAGAGAAACACCACTATTACCTTACC
1 CGGCGTTTATGGAGAAAAACGCCGCTATTGCCTTACC
53826865 ATTTGCAGCG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 30 0.45
41 36 0.55
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (42 bp):
CGGCGTTTATGGAGAAAAACGCCGCTATTGCCTTACCTTCTG
Found at i:53835928 original size:42 final size:42
Alignment explanation
Indices: 53835881--53835962 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
53835871 CTGACTTAGG
53835881 TCACACGACCAAGCCACACG-TCCGTGTGTCAGGCCGTGTGTC
1 TCACACGACCAAGCCACACGCT-CGTGTGTCAGGCCGTGTGTC
** *
53835923 TCACACGACCAAGTTACACGCTCGTGTGTCTGGCCGTGTG
1 TCACACGACCAAGCCACACGCTCGTGTGTCAGGCCGTGTG
53835963 GACCTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (42 bp):
TCACACGACCAAGCCACACGCTCGTGTGTCAGGCCGTGTGTC
Found at i:53838573 original size:45 final size:46
Alignment explanation
Indices: 53838501--53838618 Score: 132
Period size: 45 Copynumber: 2.5 Consensus size: 46
53838491 AAAATAATAT
* * **
53838501 TATTTTAATAATTTTAATAATT-AATTTAATTTAATTCTTATCTTG-G
1 TATTTTATTAA-TTTAAT-ATTAAATTTAATCTAATAATTATCTTGAG
53838547 TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTGATAAG
1 TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTG---AG
*
53838596 TATTGTATTAATTTAATATTAAA
1 TATTTTATTAATTTAATATTAAA
53838619 ATGATTAAGT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
44 3 0.05
45 26 0.42
46 10 0.16
49 23 0.37
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (46 bp):
TATTTTATTAATTTAATATTAAATTTAATCTAATAATTATCTTGAG
Found at i:53849566 original size:77 final size:76
Alignment explanation
Indices: 53849402--53849809 Score: 433
Period size: 77 Copynumber: 5.3 Consensus size: 76
53849392 CGAAAAAATT
* * * *
53849402 AGTGAACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAACGAACCGTAAAAATTATAGA-AAC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACA-ACTAC
*
53849466 GATATTAAATCA
65 AATATTAAATCA
* * * *
53849478 AGTGAACTGTTAAAATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGTAAAAATGACAACTGC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAACTAC
*
53849543 GATATTAAATCA
65 AATATTAAATCA
* * * * * * *
53849555 ATTGAATTGTTAAAATATTGAAGGTCGCGATCTTAAATCGAGCGAACCGTAAAAATGACAGCCAC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AACGAACCGTAAAAATGACAACTAC
*
53849620 AATATTAAATCG
65 AATATTAAATCA
** * * * * * * *
53849632 AGCAAACTATTAGAATATCAAAGGTCGCAATCTTAAATTAAGTGGACCGTAAAAATGACAA-TCG
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAA-CGAACCGTAAAAATGACAACT-A
53849696 CAATATTAAATCA
64 CAATATTAAATCA
* * *
53849709 AGCGAACTGCTAGAATATCGAAGGTCGCGATCTTAAAATCAAGCGAACCGTAAAAATGACAACCA
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTT-AAATCAA-CGAACCGTAAAAATGACAACTA
**
53849774 CTGTATTAAATCA
64 CAATATTAAATCA
* *
53849787 AGCGAACTATTAGAATATCGAAG
1 AGTGAACTGTTAGAATATCGAAG
53849810 ATCATGATAG
Statistics
Matches: 278, Mismatches: 48, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
76 39 0.14
77 183 0.66
78 56 0.20
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (76 bp):
AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAACGAACCGTAAAAATGACAACTACA
ATATTAAATCA
Found at i:53849610 original size:40 final size:39
Alignment explanation
Indices: 53849415--53849610 Score: 127
Period size: 40 Copynumber: 5.1 Consensus size: 39
53849405 GAACTGTTAG
53849415 AATATCGAAGGTTGCGATCTTAAATC-AACGAACCGTAAA
1 AATATCGAAGG-TGCGATCTTAAATCAAACGAACCGTAAA
* * * ** * *
53849454 AATTATAGAA---ACGATATTAAATCAAGTGAACTGTTAA
1 AA-TATCGAAGGTGCGATCTTAAATCAAACGAACCGTAAA
* *
53849491 AATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGTAAA
1 AATATCGAAGG-TGCGATCTTAAATCAAACGAACCGTAAA
* * ** ** *
53849531 AATGA-C-AA-CTGCGATATTAAATCAATTGAATTGTTAA
1 AAT-ATCGAAGGTGCGATCTTAAATCAAACGAACCGTAAA
* * *
53849568 AATATTGAAGGTCGCGATCTTAAATCGAGCGAACCGTAAA
1 AATATCGAAGGT-GCGATCTTAAATCAAACGAACCGTAAA
53849608 AAT
1 AAT
53849611 GACAGCCACA
Statistics
Matches: 112, Mismatches: 34, Indels: 21
0.67 0.20 0.13
Matches are distributed among these distances:
36 18 0.16
37 34 0.30
38 2 0.02
39 5 0.04
40 52 0.46
41 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (39 bp):
AATATCGAAGGTGCGATCTTAAATCAAACGAACCGTAAA
Found at i:53849688 original size:154 final size:153
Alignment explanation
Indices: 53849402--53849805 Score: 488
Period size: 154 Copynumber: 2.6 Consensus size: 153
53849392 CGAAAAAATT
* * * * ** *
53849402 AGTGAACTGTTAGAATATCGAAGGTTGCGATCTTAAATCAACGAACCGTAAAAATTATAGAAACG
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAGCGAACCGTAAAAATGACAGCCACA
* * * * * * *
53849467 ATATTAAATCAAGTGAACTGTTAAAATATCGAAGGTTGCGATCTTAAGTCGAACGAACCGTAAAA
66 ATATTAAATCAAGCGAACTATTAGAATATCAAAGGTCGCAATCTTAAATCGAACGAACCGTAAAA
*
53849532 ATGACAA-CTGCGATATTAAATCA
131 ATGACAATC-GCAATATTAAATCA
* * * *
53849555 ATTGAATTGTTAAAATATTGAAGGTCGCGATCTTAAATCGAGCGAACCGTAAAAATGACAGCCAC
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATC-AGCGAACCGTAAAAATGACAGCCAC
* * * * *
53849620 AATATTAAATCGAGCAAACTATTAGAATATCAAAGGTCGCAATCTTAAAT-TAAGTGGACCGTAA
65 AATATTAAATCAAGCGAACTATTAGAATATCAAAGGTCGCAATCTTAAATCGAA-CGAACCGTAA
53849684 AAATGACAATCGCAATATTAAATCA
129 AAATGACAATCGCAATATTAAATCA
* * *
53849709 AGCGAACTGCTAGAATATCGAAGGTCGCGATCTTAAAATCAAGCGAACCGTAAAAATGACAACCA
1 AGTGAACTGTTAGAATATCGAAGGTCGCGATCTT-AAATC-AGCGAACCGTAAAAATGACAGCCA
**
53849774 CTGTATTAAATCAAGCGAACTATTAGAATATC
64 CAATATTAAATCAAGCGAACTATTAGAATATC
53849806 GAAGATCATG
Statistics
Matches: 211, Mismatches: 36, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
153 36 0.17
154 118 0.56
155 57 0.27
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (153 bp):
AGTGAACTGTTAGAATATCGAAGGTCGCGATCTTAAATCAGCGAACCGTAAAAATGACAGCCACA
ATATTAAATCAAGCGAACTATTAGAATATCAAAGGTCGCAATCTTAAATCGAACGAACCGTAAAA
ATGACAATCGCAATATTAAATCA
Found at i:53858496 original size:21 final size:21
Alignment explanation
Indices: 53858460--53858522 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
53858450 TTAAATATAA
* *
53858460 ATTATAAAATTCATAAAAACTT
1 ATTAT-AAATTTATAAAAAATT
53858482 ATTATAAATTTATAAAAAATT
1 ATTATAAATTTATAAAAAATT
* * *
53858503 ATAAAAAATTT-TAGAAAATT
1 ATTATAAATTTATAAAAAATT
53858523 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
20 8 0.22
21 23 0.64
22 5 0.14
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTATAAATTTATAAAAAATT
Found at i:53858501 original size:11 final size:11
Alignment explanation
Indices: 53858465--53858534 Score: 56
Period size: 10 Copynumber: 6.5 Consensus size: 11
53858455 TATAAATTAT
*
53858465 AAAATTCAT-A
1 AAAATTTATAA
* *
53858475 AAAACTTATTA
1 AAAATTTATAA
*
53858486 TAAATTTATAA
1 AAAATTTATAA
53858497 AAAA-TTATAA
1 AAAATTTATAA
*
53858507 AAAATTT-TAG
1 AAAATTTATAA
*
53858517 AAAATTTTTAGA
1 AAAATTTATA-A
53858529 AAAATT
1 AAAATT
53858535 ATTGAAACAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 26 0.54
11 16 0.33
12 6 0.12
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAATTTATAA
Found at i:53858506 original size:10 final size:10
Alignment explanation
Indices: 53858465--53858536 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 10
53858455 TATAAATTAT
53858465 AAAATTCATAA
1 AAAATT-ATAA
* *
53858476 AAACTTATTAT
1 AAAATTA-TAA
*
53858487 AAATTTATAA
1 AAAATTATAA
53858497 AAAATTATAA
1 AAAATTATAA
*
53858507 AAAATTTTAGA
1 AAAATTATA-A
* *
53858518 AAATTTTTAGA
1 AAAATTATA-A
53858529 AAAATTAT
1 AAAATTAT
53858537 TGAAACATCA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
10 20 0.40
11 30 0.60
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAATTATAA
Found at i:53858644 original size:31 final size:30
Alignment explanation
Indices: 53858586--53858652 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
53858576 TATAAATTTT
* *
53858586 TAAAATTTTTAAAAATTACAAATAAGTTAGA
1 TAAAATTTTAAAAAATTACAAAGAAGTT-GA
* *
53858617 TAAAATTATTAAAAAATTA-ATAGAAGTTTA
1 TAAAATT-TTAAAAAATTACAAAGAAGTTGA
53858647 TAAAAT
1 TAAAAT
53858653 AAAAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 7 0.23
31 14 0.45
32 10 0.32
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (30 bp):
TAAAATTTTAAAAAATTACAAAGAAGTTGA
Found at i:53859128 original size:16 final size:17
Alignment explanation
Indices: 53859107--53859148 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
53859097 CGTTTGGTTC
53859107 GCTGTAATAGAATAGA-
1 GCTGTAATAGAATAGAG
*
53859123 GCTGTAATGGAATAGAG
1 GCTGTAATAGAATAGAG
53859140 GC-GTAATAG
1 GCTGTAATAG
53859149 TAATTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (17 bp):
GCTGTAATAGAATAGAG
Found at i:53859583 original size:60 final size:60
Alignment explanation
Indices: 53859515--53859703 Score: 230
Period size: 60 Copynumber: 3.2 Consensus size: 60
53859505 ATTTAATAAA
53859515 AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCAT
* * * * *
53859575 AATATATAATACT-ATAAAATATAATTTAAAATAATTATTATTAAATAT-AATTTA--ATAA--A
1 AATATATAAT-TTAATAAAAT-T--CTTAATATAATTATTCTT--ATATGAATTTACTAAAATCA
53859634 -
60 T
53859634 AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCAT
53859694 AATATATAAT
1 AATATATAAT
53859704 ACTATAAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
54 4 0.04
55 6 0.06
56 15 0.14
57 3 0.03
58 2 0.02
59 18 0.17
60 28 0.26
61 2 0.02
62 3 0.03
63 15 0.14
64 6 0.06
65 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATAATTATTCTTATATGAATTTACTAAAATCAT
Found at i:53859604 original size:119 final size:119
Alignment explanation
Indices: 53859360--53859717 Score: 682
Period size: 119 Copynumber: 3.0 Consensus size: 119
53859350 TTAATCATAT
*
53859360 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATA-T
*
53859425 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
53859480 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
53859545 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
53859599 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
53859664 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
66 ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
53859717 T
1 T
53859718 ATATAATCTA
Statistics
Matches: 236, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
118 5 0.02
119 169 0.72
120 62 0.26
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATA
ATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:53860028 original size:15 final size:15
Alignment explanation
Indices: 53860005--53860041 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
53859995 ACACATCAGC
53860005 TTCGCAGTCATAGAA
1 TTCGCAGTCATAGAA
*
53860020 TTCGTAGTCATAGAA
1 TTCGCAGTCATAGAA
53860035 TTCGCAG
1 TTCGCAG
53860042 AAACATCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (15 bp):
TTCGCAGTCATAGAA
Found at i:53860762 original size:49 final size:49
Alignment explanation
Indices: 53860709--53860812 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
53860699 GAAAAAAAAT
* * * *
53860709 AAATTAAAATTAAGTTTAATATCATGAATTAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
53860758 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
53860807 AAATTA
1 AAATTA
53860813 TAACACATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:53864340 original size:19 final size:19
Alignment explanation
Indices: 53864316--53864369 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
53864306 AATCATATCT
53864316 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
53864335 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
53864354 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
53864370 CTTAAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53864365 original size:38 final size:40
Alignment explanation
Indices: 53864293--53864369 Score: 113
Period size: 38 Copynumber: 1.9 Consensus size: 40
53864283 AAATTAAATC
53864293 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATA--TTCTAAGATTGCATATCATA
*
53864335 TCTAAGATTAC-ATATCATA-TCTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATTCTAAGATTGCATATC
53864370 CTTAAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 16 0.47
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (40 bp):
TCTAAGATTACAAAATCATATTCTAAGATTGCATATCATA
Found at i:53864970 original size:45 final size:45
Alignment explanation
Indices: 53864919--53865297 Score: 204
Period size: 44 Copynumber: 8.7 Consensus size: 45
53864909 TTGTTTATTT
* * * *
53864919 AGTCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
*
53864964 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * *
53865009 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * * *
53865051 A-TCTG-TTCTCTACAACTTCAGAGAGATAAGA-TCTATGATT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGAT--TTCTTG
* ** * * * * *
53865093 AATCCACTCCACTGTAACTTCAGGGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
* * * * *
53865137 AATCTGCTCCACTGCAACTTCAGGGAGATAATATTAGA-TGC--G
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
* * * *
53865179 A-TCTGCT-CTCTGCAACTTCAGAGAGATAAGATATGTGA-TT-TT-
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTG
* ** * * * * * *
53865221 AATCCACTCCACTGCGACTTCAGAGAGATAGGA-T-TATTGGCTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTG
*
53865265 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
53865298 TTCGCCATCT
Statistics
Matches: 261, Mismatches: 51, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
39 2 0.01
40 44 0.17
41 13 0.05
42 9 0.03
43 13 0.05
44 102 0.39
45 77 0.30
46 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:53865138 original size:44 final size:44
Alignment explanation
Indices: 53865063--53865299 Score: 227
Period size: 44 Copynumber: 5.5 Consensus size: 44
53865053 CTGTTCTCTA
** **
53865063 CAACTTCAGAGAGATAAGATCTA-TGATTTTAATCCACTCCACTG
1 CAACTTCAGAGAGATAAGAT-TATTGGCTTTAATCTGCTCCACTG
* * *
53865107 TAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTATTGGCTTTAATCTGCTCCACTG
* * * * *
53865151 CAACTTCAGGGAGATAATATTAGAT-GC---GATCTGCT-CTCTG
1 CAACTTCAGAGAGATAAGATTA-TTGGCTTTAATCTGCTCCACTG
** **
53865191 CAACTTCAGAGAGATAAGA-TATGTGATTTTAATCCACTCCACTG
1 CAACTTCAGAGAGATAAGATTAT-TGGCTTTAATCTGCTCCACTG
* *
53865235 CGACTTCAGAGAGATAGGATTATTGGCTTTAATCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTATTGGCTTTAATCTGCTCCACTG
*
53865279 CAACTTCAGGGAGATAAGATT
1 CAACTTCAGAGAGATAAGATT
53865300 CGCCATCTTC
Statistics
Matches: 153, Mismatches: 31, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
39 3 0.02
40 21 0.14
41 7 0.05
43 7 0.05
44 111 0.73
45 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTATTGGCTTTAATCTGCTCCACTG
Found at i:53865161 original size:128 final size:128
Alignment explanation
Indices: 53865011--53865297 Score: 475
Period size: 128 Copynumber: 2.2 Consensus size: 128
53865001 CTTTCTTGGG
* *
53865011 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGTTCTCTACAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTACAACTTCAGAGAG
* * *
53865076 ATAAGATCTATGATTTTAATCCACTCCACTGTAACTTCAGGGAGATAGGATTATTGGCTTTAA
66 ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
* ** *
53865139 TCTGCTCCACTGCAACTTCAGGGAGATAATATTAGATGCGATCTGCTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTACAACTTCAGAGAG
* *
53865204 ATAAGATATGTGATTTTAATCCACTCCACTGCGACTTCAGAGAGATAGGATTATTGGCTTTAA
66 ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
53865267 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
53865298 TTCGCCATCT
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
128 147 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (128 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAGATGCGATCTGCTCTCTACAACTTCAGAGAG
ATAAGATATATGATTTTAATCCACTCCACTGCAACTTCAGAGAGATAGGATTATTGGCTTTAA
Found at i:53865738 original size:44 final size:44
Alignment explanation
Indices: 53865675--53865783 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
53865665 ATTCTACTCC
53865675 ACTGTTGCTCAGGGAGATAGGA-TTCACAATCTTCAACCTATTCT
1 ACTGTTGCTCAGGGAGATAGGACTT-ACAATCTTCAACCTATTCT
*
53865719 ACTGTTGAC-CAGGGAGATAGGACTTACAATCTTCAACCTATTCC
1 ACTGTTG-CTCAGGGAGATAGGACTTACAATCTTCAACCTATTCT
**
53865763 ACTACTG-TCTAGGGAGATAGG
1 ACTGTTGCTC-AGGGAGATAGG
53865784 GCTGGGGTCA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
43 1 0.02
44 54 0.93
45 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
ACTGTTGCTCAGGGAGATAGGACTTACAATCTTCAACCTATTCT
Found at i:53865906 original size:88 final size:88
Alignment explanation
Indices: 53865783--53866446 Score: 958
Period size: 88 Copynumber: 7.6 Consensus size: 88
53865773 AGGGAGATAG
* * * *
53865783 GGCTGGGGTCATCGATTTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
53865848 TCCGCTGCAACCTAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
53865871 GGCTGGTGTCTTCGATCCGGTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
53865936 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
53865959 GG-T-TTGTCTTCGATCTGCTTTC-CTGTCGGTGCAGGAAGGCAAGATCTGCAATTTTTAACTTG
1 GGCTGGTGTCTTCGATCTGC-TTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTG
*
53866021 CTCCGCTGCAACCTAGGGAGGCAA
65 CTCCGCTGCAACCCAGGGAGGCAA
* * * *
53866045 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACATGT
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
53866110 TCCGCTGCAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
53866133 GGCTGGTGTCTTCGATCTGGTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* ***
53866198 TCCGCTACAACCCAAAAAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
53866221 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTG-TAATTTTTAACTTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTG
*
53866285 CTCTGCTGCAACCCAGGGAGGCAA
65 CTCCGCTGCAACCCAGGGAGGCAA
* * *
53866309 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* * *
53866374 TCCACTACAACCCAAGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* * *
53866397 GGTTGGTGTCTTCGAACTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTG
53866447 TTATCTTCAC
Statistics
Matches: 514, Mismatches: 56, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
86 73 0.14
87 9 0.02
88 431 0.84
89 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:53866351 original size:44 final size:44
Alignment explanation
Indices: 53866039--53866353 Score: 115
Period size: 44 Copynumber: 7.2 Consensus size: 44
53866029 CAACCTAGGG
* *
53866039 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAAGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
* * * ** * * ** *
53866083 AGGCAAGATCTGCTAT-TTTTAACATG-TTCCGCTG-CAACCCAAGG
1 AGGCAAG-GCTGGTGTCTTCGATC-TGCTT-CGCTGTCGATGCAAGA
* * * *
53866127 AGGCAAGGCTGGTGTCTTCGATCTGGTTCGTTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
* * * * ** * * * * ** *
53866171 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCT-ACAACCCAAAA
1 AGGCAAG-GCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
* * *
53866215 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGTAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
* * ** * * ** * *
53866259 AGGCAAGATCT-GTAAT-TTTTAACTTGC-TCTGCTG-CAACCCAGGG
1 AGGCAAG-GCTGGT-GTCTTCGATC-TGCTTC-GCTGTCGATGCAAGA
*
53866303 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGTTGTCGATGCAAGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
53866347 AGGCAAG
1 AGGCAAG
53866354 ATCTGCTATT
Statistics
Matches: 175, Mismatches: 80, Indels: 32
0.61 0.28 0.11
Matches are distributed among these distances:
43 37 0.21
44 102 0.58
45 36 0.21
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGATGCAAGA
Found at i:53872884 original size:23 final size:22
Alignment explanation
Indices: 53872826--53872884 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
53872816 AATAAAAATA
*
53872826 AAAACATATGTATAATATATAT
1 AAAACATATATATAATATATAT
* * *
53872848 ATAAGCATACATATACTATATAT
1 A-AAACATATATATAATATATAT
53872871 AAAACAATATATAT
1 AAAAC-ATATATAT
53872885 TACATAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAACATATATATAATATATAT
Found at i:53873417 original size:23 final size:22
Alignment explanation
Indices: 53873374--53873469 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 22
53873364 AAAATGTATC
* *
53873374 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
53873395 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
53873418 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
53873437 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
53873456 TACATATCATATCT
1 TACAAATCATATCT
53873470 AAGATTGCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
19 37 0.57
21 3 0.05
22 15 0.23
23 10 0.15
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:53873434 original size:19 final size:19
Alignment explanation
Indices: 53873410--53873482 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
53873400 AATCATATCT
53873410 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53873429 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
53873448 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
53873467 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
53873483 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53874084 original size:30 final size:29
Alignment explanation
Indices: 53874046--53874108 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
53874036 TAGGTATATG
*
53874046 TATAATTGAGCTAAAATTAAGATTT-CATT
1 TATAATTGAACTAAAATTAA-ATTTACATT
* *
53874075 TATATATTGAATTAAAATTAAATTTATATT
1 TATA-ATTGAACTAAAATTAAATTTACATT
53874105 TATA
1 TATA
53874109 CAATTGCACC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (29 bp):
TATAATTGAACTAAAATTAAATTTACATT
Found at i:53874257 original size:16 final size:16
Alignment explanation
Indices: 53874238--53874271 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53874228 AATACATTGG
53874238 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
53874254 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
53874270 AA
1 AA
53874272 ATATAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:53875829 original size:20 final size:20
Alignment explanation
Indices: 53875804--53875847 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
53875794 CATAGAACAC
53875804 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
53875824 AAAAGAAGGGCCAAGTAGAA
1 AAAAGAAGGGCCAAGTAGAA
53875844 AAAA
1 AAAA
53875848 ATCATCCATA
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:0.59, C:0.09, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAAGAAGGGCCAAGTAGAA
Found at i:53875942 original size:12 final size:12
Alignment explanation
Indices: 53875922--53875951 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53875912 GAGATAAAGG
*
53875922 AAACGCTATATT
1 AAACTCTATATT
53875934 AAACTCTATATT
1 AAACTCTATATT
53875946 AAACTC
1 AAACTC
53875952 AGCAAGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (12 bp):
AAACTCTATATT
Found at i:53877489 original size:32 final size:32
Alignment explanation
Indices: 53877453--53877524 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
53877443 ATTTTTACTT
** *
53877453 AAATAATCAAATAAATTCTCATAAAGTAATAA
1 AAATAATCAAATAAACCCTCATAAAATAATAA
* *
53877485 AAATAATCAATTAAGCCCTCATAAAATAATAA
1 AAATAATCAAATAAACCCTCATAAAATAATAA
53877517 AAA-AATCA
1 AAATAATCA
53877525 CTTAAGTTCG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.60, C:0.12, G:0.03, T:0.25
Consensus pattern (32 bp):
AAATAATCAAATAAACCCTCATAAAATAATAA
Found at i:53877530 original size:31 final size:32
Alignment explanation
Indices: 53877470--53877530 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
53877460 CAAATAAATT
*
53877470 CTCATAAAGTAATAAAAATAATCAATTAAGCC
1 CTCATAAAATAATAAAAATAATCAATTAAGCC
*
53877502 CTCATAAAATAATAAAAA-AATCACTTAAG
1 CTCATAAAATAATAAAAATAATCAATTAAG
53877531 TTCGGATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (32 bp):
CTCATAAAATAATAAAAATAATCAATTAAGCC
Found at i:53877719 original size:13 final size:13
Alignment explanation
Indices: 53877701--53877735 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
53877691 TGATTTTGTG
53877701 AAAATTTCGTTAA
1 AAAATTTCGTTAA
* *
53877714 AAAATTTCATTCA
1 AAAATTTCGTTAA
53877727 AAAATTTCG
1 AAAATTTCG
53877736 AAGTTTGGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (13 bp):
AAAATTTCGTTAA
Found at i:53878913 original size:50 final size:50
Alignment explanation
Indices: 53878805--53879045 Score: 275
Period size: 50 Copynumber: 4.7 Consensus size: 50
53878795 GGTAAAAAGA
* * *
53878805 TCCCATATAAGACCATGTCTAGGACATGGCATTAGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--GAGAGG
*
53878861 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGACGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGG
* * *
53878911 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGATAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGG
** * * * * **
53878961 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGG
* *
53879011 TCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
53879046 TAGTTTAAAA
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
50 123 0.75
52 1 0.01
53 4 0.02
55 2 0.01
56 35 0.21
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGG
Found at i:53886720 original size:19 final size:19
Alignment explanation
Indices: 53886656--53886720 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 19
53886646 CAAAAAATAA
* *
53886656 ATTTTTTTATAAAATGACTT
1 ATTTTTTGA-AAAATAACTT
*
53886676 ATTATTTTGAAAAATAGAAATT
1 ATT-TTTTGAAAAAT--AACTT
*
53886698 ATTTTTTGAAAAATAACTC
1 ATTTTTTGAAAAATAACTT
53886717 ATTT
1 ATTT
53886721 ATAAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 16 0.43
22 6 0.16
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (19 bp):
ATTTTTTGAAAAATAACTT
Found at i:53886846 original size:22 final size:22
Alignment explanation
Indices: 53886794--53886847 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
53886784 ATAATTTTTT
53886794 AATTTTAAT-TAAAAATATTAA
1 AATTTTAATATAAAAATATTAA
*
53886815 AAATTTAATAT-AAAATATTATA
1 AATTTTAATATAAAAATATTA-A
*
53886837 ATTTTTAATAT
1 AATTTTAATAT
53886848 TATTAAACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAATATAAAAATATTAA
Found at i:53894755 original size:27 final size:28
Alignment explanation
Indices: 53894702--53894765 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
53894692 TAACAAATAA
*
53894702 TTTAAAAA-TTATAAAAAAAATTCAAAT
1 TTTAAAAATTTATAAAAAAAATTAAAAT
* *
53894729 TTTAAAAATTTTTAAAAAATA-TAAAAT
1 TTTAAAAATTTATAAAAAAAATTAAAAT
* *
53894756 ATTCAAAATT
1 TTTAAAAATT
53894766 AAAATTAGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTAAAAATTTATAAAAAAAATTAAAAT
Found at i:53895940 original size:14 final size:15
Alignment explanation
Indices: 53895918--53895946 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53895908 TTAGATTAAT
53895918 TTTTATTTAAAATTA
1 TTTTATTTAAAATTA
53895933 TTTT-TTTAAAATTA
1 TTTTATTTAAAATTA
53895947 CATATATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTTAAAATTA
Found at i:53902142 original size:20 final size:20
Alignment explanation
Indices: 53902109--53902147 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
53902099 CTAAACATTT
53902109 ACTTTTTTTCTT-AATTTGG
1 ACTTTTTTTCTTAAATTTGG
*
53902128 ACTTTATTTTGTTAAATTTG
1 ACTTT-TTTTCTTAAATTTG
53902148 ACCTTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (20 bp):
ACTTTTTTTCTTAAATTTGG
Found at i:53902770 original size:13 final size:15
Alignment explanation
Indices: 53902752--53902783 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
53902742 TTTTACTTTA
53902752 AAAAAAT-TAAAT-T
1 AAAAAATATAAATAT
53902765 AAAAAATATAAATAT
1 AAAAAATATAAATAT
53902780 AAAA
1 AAAA
53902784 GAGTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAATATAAATAT
Found at i:53905482 original size:31 final size:31
Alignment explanation
Indices: 53905444--53905509 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
53905434 AATTAAAATA
*
53905444 AAAATTAAAAAAAGTATTT-TAAAAA-TATTTT
1 AAAATTAAAAAAA--ATTTAAAAAAAGTATTTT
53905475 AAAATTAAAAAAAATTTAAAAAAAGTATTTT
1 AAAATTAAAAAAAATTTAAAAAAAGTATTTT
53905506 AAAA
1 AAAA
53905510 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.12
30 5 0.16
31 23 0.72
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
AAAATTAAAAAAAATTTAAAAAAAGTATTTT
Found at i:53905484 original size:17 final size:17
Alignment explanation
Indices: 53905462--53905495 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53905452 AAAAAGTATT
* *
53905462 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
53905479 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
53905496 AAAGTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:53905498 original size:12 final size:12
Alignment explanation
Indices: 53905481--53905520 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
53905471 TTTTAAAATT
53905481 AAAAAAAATTTA
1 AAAAAAAATTTA
* *
53905493 AAAAAAGTATTTT
1 AAAAAA-AATTTA
53905506 AAAAAAAATTTA
1 AAAAAAAATTTA
53905518 AAA
1 AAA
53905521 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAAAAAATTTA
Found at i:53905505 original size:42 final size:42
Alignment explanation
Indices: 53905427--53905549 Score: 178
Period size: 42 Copynumber: 2.9 Consensus size: 42
53905417 TCAAATTTTT
* *
53905427 TTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAATA
1 TTTT-AAAATTAAAA-AAAATTTAAAAAAAGTATTTTAAAAAAA
53905471 TTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAAAA
1 TTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAAAA
* *
53905513 ATTTAAAATT-TAAAAAATTT-AAAAAAGTATTTTAAAA
1 TTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAA
53905550 TTAAAAAATA
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
40 17 0.23
41 9 0.12
42 35 0.47
43 10 0.13
44 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (42 bp):
TTTTAAAATTAAAAAAAATTTAAAAAAAGTATTTTAAAAAAA
Found at i:53905532 original size:28 final size:28
Alignment explanation
Indices: 53905479--53905558 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 28
53905469 TATTTTAAAA
**
53905479 TTAAAAAA-AATTTAAAA--AAAGTATT
1 TTAAAAAAGAATTTAAAATTAAAAAATT
53905504 TTAAAAAA-AATTTAAAATTTAAAAAA-T
1 TTAAAAAAGAATTTAAAA-TTAAAAAATT
*
53905531 TTAAAAAAGTATTTTAAAATTAAAAAAT
1 TTAAAAAAG-AATTTAAAATTAAAAAAT
53905559 AAAAAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 17 0.37
27 9 0.20
28 12 0.26
29 8 0.17
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
TTAAAAAAGAATTTAAAATTAAAAAATT
Found at i:53905538 original size:11 final size:11
Alignment explanation
Indices: 53905475--53905520 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
53905465 AAAATATTTT
53905475 AAAA-TTAAAA
1 AAAATTTAAAA
53905485 AAAATTTAAAA
1 AAAATTTAAAA
53905496 AAAGTATTTTAAAA
1 AAA--A-TTTAAAA
53905510 AAAATTTAAAA
1 AAAATTTAAAA
53905521 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.12
11 16 0.50
12 1 0.03
13 1 0.03
14 10 0.31
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAATTTAAAA
Found at i:53905564 original size:28 final size:30
Alignment explanation
Indices: 53905514--53905573 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
53905504 TTAAAAAAAA
** *
53905514 TTTAAAATTTAAAAAATTTAAAA-AAGTAT
1 TTTAAAATTTAAAAAATAAAAAATAAATAT
53905543 TTTAAAA-TTAAAAAATAAAAAATAAATAT
1 TTTAAAATTTAAAAAATAAAAAATAAATAT
53905572 TT
1 TT
53905574 ATTATTCGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TTTAAAATTTAAAAAATAAAAAATAAATAT
Found at i:53905574 original size:28 final size:28
Alignment explanation
Indices: 53905506--53905574 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
53905496 AAAGTATTTT
**
53905506 AAAAAAA-ATTTAAAATTTAAAAAATTT
1 AAAAAAATATTTAAAATTTAAAAAATAA
*
53905533 AAAAAAGTATTTTAAAA-TTAAAAAATAA
1 AAAAAAATA-TTTAAAATTTAAAAAATAA
53905561 AAAATAAATATTTA
1 AAAA-AAATATTTA
53905575 TTATTCGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 6 0.17
28 18 0.51
29 11 0.31
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAAAATATTTAAAATTTAAAAAATAA
Found at i:53905574 original size:41 final size:41
Alignment explanation
Indices: 53905438--53905568 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 41
53905428 TTTAAAAATT
** *
53905438 AAAATAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAAT-T
1 AAAATAAAAATTAAAAAAAGTATTTT--AAA-ATTAAAAAATAA
* **
53905481 AAAA-AAAATTTAAAAAAAGTATTTTAAAA--AAAATTTAA
1 AAAATAAAAATTAAAAAAAGTATTTTAAAATTAAAAAATAA
** *
53905519 AATTTAAAAAATTTAAAAAAGTATTTTAAAATTAAAAAATAA
1 AAAAT-AAAAATTAAAAAAAGTATTTTAAAATTAAAAAATAA
53905561 AAAATAAA
1 AAAATAAA
53905569 TATTTATTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 12
0.73 0.15 0.13
Matches are distributed among these distances:
37 3 0.04
38 2 0.03
39 1 0.01
40 26 0.38
41 3 0.04
42 30 0.43
43 4 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (41 bp):
AAAATAAAAATTAAAAAAAGTATTTTAAAATTAAAAAATAA
Found at i:53908844 original size:19 final size:19
Alignment explanation
Indices: 53908820--53908857 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53908810 CATCCAAACA
53908820 CTAGAAAAATAAATCATTT
1 CTAGAAAAATAAATCATTT
*
53908839 CTAGAAAAGTAAATCATTT
1 CTAGAAAAATAAATCATTT
53908858 TTCAGAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
CTAGAAAAATAAATCATTT
Found at i:53911843 original size:15 final size:15
Alignment explanation
Indices: 53911815--53911847 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
53911805 TCCAAAAAGT
53911815 AAATCATTTTCTGGA
1 AAATCATTTTCTGGA
53911830 AAAT-ATTTTACTGGA
1 AAATCATTTT-CTGGA
53911845 AAA
1 AAA
53911848 CAAACGGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (15 bp):
AAATCATTTTCTGGA
Found at i:53929405 original size:17 final size:18
Alignment explanation
Indices: 53929373--53929407 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53929363 TAAAAATTTA
*
53929373 TAAAATTTATTTAAAAAG
1 TAAAAATTATTTAAAAAG
53929391 TAAAAATTA-TTAAAAAG
1 TAAAAATTATTTAAAAAG
53929408 GTATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAAAATTATTTAAAAAG
Found at i:53932426 original size:21 final size:19
Alignment explanation
Indices: 53932401--53932442 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
53932391 TATATAATAT
*
53932401 AAAATTTTAGAAATTATTAAA
1 AAAATATTAGAAA-TA-TAAA
53932422 AAAATATTAGAAATATAAA
1 AAAATATTAGAAATATAAA
53932441 AA
1 AA
53932443 TGGTGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAATATTAGAAATATAAA
Found at i:53936273 original size:18 final size:20
Alignment explanation
Indices: 53936252--53936288 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
53936242 GATCATTAAT
53936252 TTGTA-ATTTAAA-AATTTA
1 TTGTAGATTTAAATAATTTA
*
53936270 TTGTAGTTTTAAATAATTT
1 TTGTAGATTTAAATAATTT
53936289 CAAATGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TTGTAGATTTAAATAATTTA
Found at i:53936320 original size:35 final size:31
Alignment explanation
Indices: 53936276--53936355 Score: 81
Period size: 35 Copynumber: 2.5 Consensus size: 31
53936266 TTTATTGTAG
53936276 TTTTA-AATAATTTCAAATGATTTTTATAATTT
1 TTTTATAATAATTTCAAAT-ATTTTTAT-ATTT
* *
53936308 TTATTATTAATAAATTTTACATATTTTTATATTT
1 TT-TTA-TAAT-AATTTCAAATATTTTTATATTT
*
53936342 TTTTATAATCATTT
1 TTTTATAATAATTT
53936356 GAAAAACCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
31 4 0.10
32 6 0.15
33 6 0.15
34 6 0.15
35 11 0.27
36 8 0.20
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (31 bp):
TTTTATAATAATTTCAAATATTTTTATATTT
Found at i:53940163 original size:29 final size:30
Alignment explanation
Indices: 53940111--53940177 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
53940101 TTCTATTTTT
*
53940111 TTTTTTGAATTTTTATAAACTTTTTATATA
1 TTTTTTGAATTTTTATAAACTTTTAATATA
* *
53940141 TTTTTTGAATTTTTA-AAAGTTTTAATTTA
1 TTTTTTGAATTTTTATAAACTTTTAATATA
*
53940170 TTTGTTGA
1 TTTTTTGA
53940178 TGACACATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTTTGAATTTTTATAAACTTTTAATATA
Found at i:53942557 original size:6 final size:6
Alignment explanation
Indices: 53942546--53942571 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53942536 GCAGTTTTGC
53942546 TTTCTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT
53942572 GACACTAGGA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:53943554 original size:16 final size:17
Alignment explanation
Indices: 53943525--53943559 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
53943515 TAAAATAATA
53943525 TAATATATTAATTATAT
1 TAATATATTAATTATAT
*
53943542 TAATA-ATTTATTATAT
1 TAATATATTAATTATAT
53943558 TA
1 TA
53943560 TTAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATATTAATTATAT
Found at i:53943566 original size:20 final size:20
Alignment explanation
Indices: 53943519--53943566 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
53943509 ATTTATTAAA
53943519 ATAATATAATATATTAATTAT
1 ATAA-ATAATATATTAATTAT
* *
53943540 ATTAATAATTTATTATATTAT
1 ATAAATAATATATTA-ATTAT
53943561 -TAAATA
1 ATAAATA
53943567 TAAACAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAATAATATATTAATTAT
Found at i:53943626 original size:21 final size:22
Alignment explanation
Indices: 53943594--53943635 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
53943584 ATATTTAATA
53943594 ATATTAAATATTATAATATTTG
1 ATATTAAATATTATAATATTTG
*
53943616 ATATT-AATATTTTAATATTT
1 ATATTAAATATTATAATATTT
53943636 TTAGAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATATTAAATATTATAATATTTG
Found at i:53946333 original size:19 final size:19
Alignment explanation
Indices: 53946309--53946346 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
53946299 GGCGAGAGTG
53946309 GATGTTATTAAATCCATCA
1 GATGTTATTAAATCCATCA
*
53946328 GATGTTATTGAATCCATCA
1 GATGTTATTAAATCCATCA
53946347 CCACTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (19 bp):
GATGTTATTAAATCCATCA
Found at i:53950434 original size:17 final size:18
Alignment explanation
Indices: 53950414--53950447 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53950404 TAATTAATTT
53950414 TTTA-TATTTTTTAAATC
1 TTTATTATTTTTTAAATC
53950431 TTTATTATTTTTTAAAT
1 TTTATTATTTTTTAAAT
53950448 AATTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTATTATTTTTTAAATC
Found at i:53951091 original size:5 final size:5
Alignment explanation
Indices: 53951081--53951107 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
53951071 ACAAGATTAC
53951081 ATCAA ATCAA ATCAA ATCAA ATCAA AT
1 ATCAA ATCAA ATCAA ATCAA ATCAA AT
53951108 TTTTACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (5 bp):
ATCAA
Found at i:53954355 original size:5 final size:5
Alignment explanation
Indices: 53954345--53954416 Score: 144
Period size: 5 Copynumber: 14.4 Consensus size: 5
53954335 AATTATTTTC
53954345 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
53954395 ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT AT
53954417 GATCAACCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 67 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:53956050 original size:17 final size:17
Alignment explanation
Indices: 53956010--53956043 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53956000 CATTATGAAA
53956010 TGTAATTAAATTTGAGC
1 TGTAATTAAATTTGAGC
53956027 TGTAATTAAATTTGAGC
1 TGTAATTAAATTTGAGC
53956044 CTTAATTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (17 bp):
TGTAATTAAATTTGAGC
Found at i:53959663 original size:3 final size:3
Alignment explanation
Indices: 53959657--53959682 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
53959647 CACCAAATAA
53959657 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
53959683 AACCTAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53960169 original size:15 final size:16
Alignment explanation
Indices: 53960141--53960170 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53960131 GTTGGACTAA
53960141 ATTGAATATGAGTTAT
1 ATTGAATATGAGTTAT
53960157 ATTGAAT-TGAGTTA
1 ATTGAATATGAGTTA
53960171 AATTCATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
ATTGAATATGAGTTAT
Found at i:53960524 original size:25 final size:24
Alignment explanation
Indices: 53960486--53960568 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
53960476 CACAACTTAT
*
53960486 ATGAGCTTCTCGTTATACAGCTCGC
1 ATGAGCTTCCCGTTAT-CAGCTCGC
* *
53960511 ATGAGCTTCCCGTTACTCAGGTCGT
1 ATGAGCTTCCCGTTA-TCAGCTCGC
*
53960536 ATGAGCTTCCCGTTATTCAGCTCGG
1 ATGAGCTTCCCGTTA-TCAGCTCGC
*
53960561 AAGAGCTT
1 ATGAGCTT
53960569 ATTGTTTACA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (24 bp):
ATGAGCTTCCCGTTATCAGCTCGC
Found at i:53964289 original size:3 final size:3
Alignment explanation
Indices: 53964281--53964322 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
53964271 AGTTTCAACT
53964281 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
53964323 GATTTCAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:53965862 original size:7 final size:7
Alignment explanation
Indices: 53965850--53965885 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
53965840 TACTCTTCTC
53965850 AAATTTA
1 AAATTTA
53965857 AAATTTA
1 AAATTTA
53965864 AAATTTA
1 AAATTTA
53965871 AAATTTA
1 AAATTTA
53965878 AAATTTA
1 AAATTTA
53965885 A
1 A
53965886 TCTCTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAATTTA
Found at i:53966678 original size:24 final size:26
Alignment explanation
Indices: 53966640--53966705 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
53966630 TACTATTATC
*
53966640 ATTATTTATT-TTTATGTTATTCAT-A
1 ATTATTTATTACTTATGTTATT-ATAA
53966665 A-TATTT-TTACTTATG-TATTATAA
1 ATTATTTATTACTTATGTTATTATAA
53966688 ATTATTTATTAC-TATGTT
1 ATTATTTATTACTTATGTT
53966706 TACCTCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.06
23 8 0.23
24 19 0.54
25 6 0.17
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (26 bp):
ATTATTTATTACTTATGTTATTATAA
Found at i:53967038 original size:45 final size:41
Alignment explanation
Indices: 53966987--53967075 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 41
53966977 ATTTGCTCCT
53966987 AAAATACTACAAAACAAAATTA-AAATAATTTGTATAATTCCATGA
1 AAAATACTACAAAACAAAA--AGAAA-AA--TGTATAATTCCATGA
*
53967032 AAAATACTACAAAGCAAAAAGAAAAATGTATAATTCCATGA
1 AAAATACTACAAAACAAAAAGAAAAATGTATAATTCCATGA
53967073 AAA
1 AAA
53967076 GCCCCTGTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
41 18 0.43
43 3 0.07
44 3 0.07
45 18 0.43
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.24
Consensus pattern (41 bp):
AAAATACTACAAAACAAAAAGAAAAATGTATAATTCCATGA
Found at i:53970977 original size:16 final size:16
Alignment explanation
Indices: 53970952--53970987 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
53970942 CATCAACAAA
53970952 TTTTTTTATATAT-AT
1 TTTTTTTATATATAAT
53970967 TTTTCTTTATATATAAT
1 TTTT-TTTATATATAAT
53970984 TTTT
1 TTTT
53970988 ATATGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 9 0.47
17 6 0.32
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTATATATAAT
Found at i:53973618 original size:85 final size:86
Alignment explanation
Indices: 53973464--53973624 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 86
53973454 TAGTTGCCCA
* *
53973464 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCGAATATGTTGTGCACTCACAACAAGTGACAA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
*
53973529 TAACTGTAAATATGTGGTTCG
66 TAACTGCAAATATGTGGTTCG
* * *
53973550 TCCAC-AAACCCAGTGGCAGTTTGTTTAATCTG-AAACCATGTTGTGCACTCATAACAAGTGGCA
1 TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAA-CATGTTGTGCACTCACAACAAGTGACA
*
53973613 GTAACTGCAAAT
65 ATAACTGCAAAT
53973625 GTTTTTATCT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 2 0.03
85 60 0.90
86 5 0.07
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (86 bp):
TCCACAAAACCCAGTGACAGTTTGTTTAATCTGCAAACATGTTGTGCACTCACAACAAGTGACAA
TAACTGCAAATATGTGGTTCG
Found at i:53975601 original size:29 final size:30
Alignment explanation
Indices: 53975534--53975611 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
53975524 AAACTATATT
*
53975534 TTAGGAGCTCAATTGATTGCCAACTTTCAA
1 TTAGGGGCTCAATTGATTGCCAACTTTCAA
** *
53975564 TTAATGGCTCAATTGATTG-CAATTTTCAA
1 TTAGGGGCTCAATTGATTGCCAACTTTCAA
*
53975593 TTAGGGGCTTAATTGATTG
1 TTAGGGGCTCAATTGATTG
53975612 TATTCTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (30 bp):
TTAGGGGCTCAATTGATTGCCAACTTTCAA
Found at i:53981064 original size:19 final size:20
Alignment explanation
Indices: 53981018--53981067 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53981008 AAACTTAAAA
** *
53981018 TTAAAAAATAATAATATTTT
1 TTAAAAAATAATAATACGTC
*
53981038 TTATAAAA-AATAATACGTC
1 TTAAAAAATAATAATACGTC
53981057 TTAAAAAATAA
1 TTAAAAAATAA
53981068 AAGAGTGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
TTAAAAAATAATAATACGTC
Found at i:53982275 original size:61 final size:60
Alignment explanation
Indices: 53982147--53982280 Score: 173
Period size: 61 Copynumber: 2.2 Consensus size: 60
53982137 TATTAAATTG
* * *
53982147 TATAATAAATAATTTAATTATATTTTAATATAATTATTATTAAATAAAATTTAATAACAA
1 TATAATATATAATTTAATAACATTTTAATATAATTATTATTAAATAAAATTTAATAACAA
* * *
53982207 TAAAATATATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TTAATAA-TA
1 TATAATATATAATTTAATAACATT-TTAATATAATTATTATT-AAATA-AAATTTAATAACAA
53982268 TATAATATATAAT
1 TATAATATATAAT
53982281 ATTAGAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 20 0.31
61 30 0.47
62 12 0.19
63 2 0.03
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (60 bp):
TATAATATATAATTTAATAACATTTTAATATAATTATTATTAAATAAAATTTAATAACAA
Found at i:53986348 original size:50 final size:50
Alignment explanation
Indices: 53986233--53986476 Score: 299
Period size: 50 Copynumber: 4.7 Consensus size: 50
53986223 GATAATAACA
* * ** * *
53986233 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
53986284 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
53986334 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
53986384 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
*
53986439 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
53986477 TCTTTTACCC
Statistics
Matches: 167, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 94 0.56
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 35 0.21
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:53986419 original size:100 final size:105
Alignment explanation
Indices: 53986232--53986478 Score: 360
Period size: 100 Copynumber: 2.4 Consensus size: 105
53986222 TGATAATAAC
** * *
53986232 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
* *
53986297 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
53986334 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTCTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
53986397 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
53986439 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATC
53986479 TTTTACCCAA
Statistics
Matches: 129, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
100 50 0.39
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 36 0.28
107 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATCTCGGTGCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:53986590 original size:13 final size:13
Alignment explanation
Indices: 53986574--53986605 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
53986564 TGCTTGATCA
*
53986574 TCATCAAATAAAT
1 TCATAAAATAAAT
53986587 TCATAAAATAAAT
1 TCATAAAATAAAT
53986600 TCATAA
1 TCATAA
53986606 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:53986852 original size:30 final size:30
Alignment explanation
Indices: 53986817--53986874 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
53986807 CCTCGACTCT
*
53986817 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
53986847 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
53986875 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:53998567 original size:90 final size:89
Alignment explanation
Indices: 53998368--53998583 Score: 240
Period size: 90 Copynumber: 2.4 Consensus size: 89
53998358 CATCTTACCC
* * * * * *
53998368 GAAATGAGAAAGACTATAGTTGAAAGATACTATGATATTAAATCGGAATGAATAAGACTATAGTT
1 GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGAACGAATAAGACCATAGTT
53998433 GAAAGATACTACGGCACTAAACTG
66 GAAAGATACTACGGCACTAAACTG
* * * *
53998457 GAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCATTAAATCTGATACGAATAAGACCATAGT
1 GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGA-ACGAATAAGACCATAGT
* * *
53998522 TGAAAGATATTATGGCA-T-CACATG
65 TGAAAGATACTACGGCACTAAAC-TG
* *
53998546 GATAATGAT-CAATACCATAGTTGAAAGATACTGTGACA
1 GA-AATG-TGCAAGACCATAGTTGAAAGATACTATGACA
53998584 CTACTTCGGA
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
88 2 0.02
89 45 0.42
90 58 0.55
91 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (89 bp):
GAAATGTGCAAGACCATAGTTGAAAGATACTATGACATTAAATCGGAACGAATAAGACCATAGTT
GAAAGATACTACGGCACTAAACTG
Found at i:53998608 original size:45 final size:45
Alignment explanation
Indices: 53998368--53998613 Score: 198
Period size: 45 Copynumber: 5.5 Consensus size: 45
53998358 CATCTTACCC
* ** * *
53998368 GAAATGAGA-AAGACTATAGTTGAAAGATACTATGATATTAAATCG
1 GAAATGA-ATAAGACCATAGTTGAAAGATACTATGGCACTACATCG
* * *
53998413 G-AATGAATAAGACTATAGTTGAAAGATACTACGGCACTA-AACTG
1 GAAATGAATAAGACCATAGTTGAAAGATACTATGGCACTACATC-G
** * * * *
53998457 GAAATGTGTAAGACCGTAGTTGAAAGATACTATGGCATTAAATCT
1 GAAATGAATAAGACCATAGTTGAAAGATACTATGGCACTACATCG
* * *
53998502 GATACGAATAAGACCATAGTTGAAAGATATTATGGCA-TCACAT-G
1 GAAATGAATAAGACCATAGTTGAAAGATACTATGGCACT-ACATCG
* * * *
53998546 GATAATG-ATCAATACCATAGTTGAAAGATACTGTGACACTACTTCG
1 GA-AATGAAT-AAGACCATAGTTGAAAGATACTATGGCACTACATCG
* *
53998592 GAAATGCATAAGACCATGGTTG
1 GAAATGAATAAGACCATAGTTG
53998614 GAATATATCA
Statistics
Matches: 161, Mismatches: 30, Indels: 20
0.76 0.14 0.09
Matches are distributed among these distances:
43 3 0.02
44 39 0.24
45 111 0.69
46 8 0.05
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.26
Consensus pattern (45 bp):
GAAATGAATAAGACCATAGTTGAAAGATACTATGGCACTACATCG
Found at i:54003360 original size:16 final size:16
Alignment explanation
Indices: 54003339--54003372 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54003329 TGTGACTTTC
54003339 AAAAATCCAATCTTCA
1 AAAAATCCAATCTTCA
54003355 AAAAATCCAATCTTCA
1 AAAAATCCAATCTTCA
54003371 AA
1 AA
54003373 GGGAAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATCCAATCTTCA
Found at i:54003744 original size:36 final size:36
Alignment explanation
Indices: 54003696--54003766 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
54003686 ATCAAGGGCT
*
54003696 ACAATTAAAAGCTGTATACAATTTGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
* *
54003732 ACAATTAGAAGCTGTATACAATTAGAACTTTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
54003767 TTACATAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:54003754 original size:17 final size:17
Alignment explanation
Indices: 54003695--54003758 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
54003685 CATCAAGGGC
*
54003695 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
* *
54003712 TACAATTTGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
54003731 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
54003748 TACAATTAGAA
1 TACAATTAGAA
54003759 CTTTAAGATT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
16 3 0.08
17 20 0.56
19 10 0.28
20 3 0.08
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:54007017 original size:19 final size:19
Alignment explanation
Indices: 54006981--54007017 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
54006971 CACATGTCAT
*
54006981 GTATCACTATCTAGTCCAC
1 GTATCACTATCTAATCCAC
*
54007000 GTATCACTATTTAATCCA
1 GTATCACTATCTAATCCA
54007018 TGTTAGTTTT
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:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (19 bp):
GTATCACTATCTAATCCAC
Found at i:54014615 original size:42 final size:43
Alignment explanation
Indices: 54014569--54014674 Score: 146
Period size: 42 Copynumber: 2.5 Consensus size: 43
54014559 GGAAACCTGC
* *
54014569 AAGGGTTAAACGGAAGCTCATAAA-AGCTGAA-TGAAAACCCAT
1 AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTG-AAACCCAG
*
54014611 AAGGGTTAAACTGCAGCTCA-AAATAGCTGAACTGAAACCCAG
1 AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCAG
*
54014653 AAGGGTTAAACTGAAACTCATA
1 AAGGGTTAAACTGAAGCTCATA
54014675 TGAGATAACT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.05
42 50 0.89
43 3 0.05
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (43 bp):
AAGGGTTAAACTGAAGCTCATAAATAGCTGAACTGAAACCCAG
Found at i:54014686 original size:20 final size:20
Alignment explanation
Indices: 54014661--54014702 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54014651 AGAAGGGTTA
54014661 AACTGAAACTCAT-ATGAGAT
1 AACTGAAACTCATGA-GAGAT
*
54014681 AACTGAAGCTCATGAGAGAT
1 AACTGAAACTCATGAGAGAT
54014701 AA
1 AA
54014703 ACGGAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (20 bp):
AACTGAAACTCATGAGAGAT
Found at i:54017107 original size:20 final size:20
Alignment explanation
Indices: 54017074--54017123 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
54017064 GTTGATGAGA
* * *
54017074 AAAAAATAATTATAAGTTAT
1 AAAAATTAAATATAAATTAT
*
54017094 AAAAATTAAATATAAATTTT
1 AAAAATTAAATATAAATTAT
*
54017114 AAAAGTTAAA
1 AAAAATTAAA
54017124 AGTTTAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAAATTAAATATAAATTAT
Found at i:54024086 original size:29 final size:30
Alignment explanation
Indices: 54024044--54024121 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
54024034 ATTAAGAATA
*
54024044 CAATCAATTAAGCCCCTAATTGAAAATT-G
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
** *
54024073 CAATCAATTGAGCCATTAATTGAAAGTTGG
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
*
54024103 CAATCAATTGAGCTCCTAA
1 CAATCAATTGAGCCCCTAA
54024122 AATATAGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (30 bp):
CAATCAATTGAGCCCCTAATTGAAAATTGG
Found at i:54028542 original size:13 final size:14
Alignment explanation
Indices: 54028519--54028547 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54028509 TGTGGTATGG
54028519 TAAATTATAATATT
1 TAAATTATAATATT
54028533 TAAA-TATAATATT
1 TAAATTATAATATT
54028546 TA
1 TA
54028548 TAATCACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAAATTATAATATT
Found at i:54039914 original size:60 final size:58
Alignment explanation
Indices: 54039848--54039978 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 58
54039838 ATTTTCTAAT
* * *
54039848 ATTATATATTATA-TATTATT-AATTCATATTTTAAT-ATAATTATATTAAGAATGTTATTAA
1 ATTATATATTATATTATTATTAAATT--T-TATTAATAATAATTATATTAA-AATATAATT-A
* *
54039908 ATTATATATTTTATTGTTATTAAATTTTATTAATAATAATTATATTAAAATATAATTA
1 ATTATATATTATATTATTATTAAATTTTATTAATAATAATTATATTAAAATATAATTA
*
54039966 ATTATTTATTATA
1 ATTATATATTATA
54039979 CAATTTAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
58 12 0.20
59 13 0.21
60 26 0.43
61 6 0.10
62 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
ATTATATATTATATTATTATTAAATTTTATTAATAATAATTATATTAAAATATAATTA
Found at i:54046529 original size:29 final size:30
Alignment explanation
Indices: 54046487--54046564 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
54046477 ATTAAGAATA
*
54046487 CAATCAATTAAGCCCCTAATTGAAAATT-G
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
** *
54046516 CAATCAATTGAGCCATTAATTGAAAGTTGG
1 CAATCAATTGAGCCCCTAATTGAAAATTGG
*
54046546 CAATCAATTGAGCTCCTAA
1 CAATCAATTGAGCCCCTAA
54046565 AATATAGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (30 bp):
CAATCAATTGAGCCCCTAATTGAAAATTGG
Found at i:54048622 original size:85 final size:86
Alignment explanation
Indices: 54048473--54048633 Score: 236
Period size: 85 Copynumber: 1.9 Consensus size: 86
54048463 AGATAAAAAC
* * *
54048473 ATTTGCAGTTACTGCCACTTGTTATGAGTGCACAACATGGTTTCAGATTAAACAAACTGCCACTG
1 ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTG
54048538 GG-TTTGTGGACGAACCACAT
66 GGTTTTGTGGACGAACCACAT
* * * *
54048558 ATTTACAGTTATTGTCACTTGTTGTGAGTGCACAACAT-ATTCGCAGATTAAACAAACTGTCACT
1 ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATT-GCAGATTAAACAAACTGCCACT
54048622 GGGTTTTGTGGA
65 GGGTTTTGTGGA
54048634 TGGGCAACTA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 2 0.03
85 57 0.85
86 8 0.12
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (86 bp):
ATTTACAGTTACTGCCACTTGTTATGAGTGCACAACATGATTGCAGATTAAACAAACTGCCACTG
GGTTTTGTGGACGAACCACAT
Found at i:54051135 original size:16 final size:16
Alignment explanation
Indices: 54051110--54051145 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
54051100 TTTAACATAT
54051110 AAAAATTATATATAAA
1 AAAAATTATATATAAA
54051126 GAAAAA-TATATATAAA
1 -AAAAATTATATATAAA
54051142 AAAA
1 AAAA
54051146 TTTGTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (16 bp):
AAAAATTATATATAAA
Found at i:54055175 original size:18 final size:19
Alignment explanation
Indices: 54055149--54055185 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
54055139 TTATTATATC
54055149 TTATCATTTT-TTAGATTAA
1 TTATCATTTTATT-GATTAA
54055168 TTAT-ATTTTATTGATTAA
1 TTATCATTTTATTGATTAA
54055186 ATACCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATCATTTTATTGATTAA
Found at i:54055445 original size:24 final size:26
Alignment explanation
Indices: 54055393--54055458 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
54055383 TATAGAGGTA
54055393 AACAT-AGTAATAAATAATTTATAAT
1 AACATAAGTAATAAATAATTTATAAT
54055418 -ACATAAGTAA-AAAT-A-TTATGAAT
1 AACATAAGTAATAAATAATTTAT-AAT
*
54055441 AACATAA-AAATAAATAAT
1 AACATAAGTAATAAATAAT
54055459 GATAATAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
22 4 0.12
23 6 0.18
24 18 0.53
25 6 0.18
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (26 bp):
AACATAAGTAATAAATAATTTATAAT
Found at i:54056222 original size:7 final size:7
Alignment explanation
Indices: 54056212--54056247 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
54056202 AATATAAAGA
54056212 TTAAATT
1 TTAAATT
54056219 TTAAATT
1 TTAAATT
54056226 TTAAATT
1 TTAAATT
54056233 TTAAATT
1 TTAAATT
54056240 TTAAATT
1 TTAAATT
54056247 T
1 T
54056248 GAGAAGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTAAATT
Found at i:54056230 original size:21 final size:21
Alignment explanation
Indices: 54056206--54056247 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
54056196 AATAAAAATA
54056206 TAAAGATTAAATTTTAAATTT
1 TAAAGATTAAATTTTAAATTT
**
54056227 TAAATTTTAAATTTTAAATTT
1 TAAAGATTAAATTTTAAATTT
54056248 GAGAAGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAAGATTAAATTTTAAATTT
Found at i:54057788 original size:3 final size:3
Alignment explanation
Indices: 54057780--54057821 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
54057770 TGTTGAAATC
54057780 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
54057822 AGTTGAAACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:54062432 original size:77 final size:77
Alignment explanation
Indices: 54062304--54062459 Score: 242
Period size: 77 Copynumber: 2.0 Consensus size: 77
54062294 ATATAATTTA
* * *
54062304 ATTTTATCAATGAAGCCTTGGTTGTGTTTACAAGGTTAAGGCCCTCAAACTTTCATAGTCTATAT
1 ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTCAAACTTTCATAGTCTATAT
54062369 TTGAGGCTCGCC
66 TTGAGGCTCGCC
* *
54062381 ATTTTATCAATGATGCATTAGTTGTGTTTACAAGATTAAGGCCC-CGTAACTTTCATAGTCTATA
1 ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTC-AAACTTTCATAGTCTATA
*
54062445 TTTGAGTCTCGCC
65 TTTGAGGCTCGCC
54062458 AT
1 AT
54062460 GCACAAATGA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 71 0.99
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (77 bp):
ATTTTATCAATGAAGCATTAGTTGTGTTTACAAGATTAAGGCCCTCAAACTTTCATAGTCTATAT
TTGAGGCTCGCC
Found at i:54073485 original size:11 final size:11
Alignment explanation
Indices: 54073454--54073497 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
54073444 TAAAATGTCT
*
54073454 TAATAAAATAT
1 TAATAAAATAA
*
54073465 TATCTAAAATAA
1 TA-ATAAAATAA
54073477 TAATAAAATAA
1 TAATAAAATAA
54073488 TAATAAAATA
1 TAATAAAATA
54073498 TCACCAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:54084920 original size:12 final size:12
Alignment explanation
Indices: 54084901--54084930 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54084891 AAAGGAAATA
54084901 GAAATGGGAATG
1 GAAATGGGAATG
*
54084913 GGAATGGGAATG
1 GAAATGGGAATG
54084925 GAAATG
1 GAAATG
54084931 ATCCATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (12 bp):
GAAATGGGAATG
Found at i:54096106 original size:53 final size:52
Alignment explanation
Indices: 54096020--54096174 Score: 181
Period size: 53 Copynumber: 3.0 Consensus size: 52
54096010 AAAAAAGTTT
54096020 TTGGGGTTTGGAGGAAGTAAAAGTTTTGA-GAGAAAGCAAAAGGAAAAAAAAA
1 TTGGGGTTTGG-GGAAGTAAAAGTTTTGAGGAGAAAGCAAAAGGAAAAAAAAA
* * ***
54096072 TTGGGAGTTTGGGGAAGTAAAAGTTTTAAGGAGAAAGTAAAAGG-AAAAATTT
1 TTGGG-GTTTGGGGAAGTAAAAGTTTTGAGGAGAAAGCAAAAGGAAAAAAAAA
* * *
54096124 TTAGGGGTTTGGGGGAAGTAAAACTTTTGAGG-GAAATCAAAAAGAAAAAAA
1 TT-GGGGTTT-GGGGAAGTAAAAGTTTTGAGGAGAAAGCAAAAGGAAAAAAA
54096175 GTTTTTGGGG
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
52 41 0.47
53 46 0.53
ACGTcount: A:0.45, C:0.02, G:0.30, T:0.23
Consensus pattern (52 bp):
TTGGGGTTTGGGGAAGTAAAAGTTTTGAGGAGAAAGCAAAAGGAAAAAAAAA
Found at i:54097679 original size:15 final size:16
Alignment explanation
Indices: 54097659--54097704 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
54097649 AAAATATCAA
54097659 TTAAAA-ATATAATTT
1 TTAAAATATATAATTT
* *
54097674 TTAAAATTTATTATTT
1 TTAAAATATATAATTT
54097690 TTAAAATAGTATAAT
1 TTAAAATA-TATAAT
54097705 GGGTTTTTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAAAATATATAATTT
Found at i:54098904 original size:21 final size:21
Alignment explanation
Indices: 54098846--54098907 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
54098836 ATTTGTATAG
* *
54098846 TATTTTTAAGTTATTTAAAAT
1 TATTTTGAATTTATTTAAAAT
* ** *
54098867 GATTATTGAATAAATTTAAATT
1 TATT-TTGAATTTATTTAAAAT
54098889 TATTTTGAATTTATTTAAA
1 TATTTTGAATTTATTTAAA
54098908 GTTAATTATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (21 bp):
TATTTTGAATTTATTTAAAAT
Done.