Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 125 of 373
Found at i:41019822 original size:24 final size:24
Alignment explanation
Indices: 41019791--41019836 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
41019781 AATTTATCAG
**
41019791 AAAGGGCTTTGCC-CCAGTTATTA
1 AAAGGGCTAGGCCTCCAGTTATTA
41019814 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTAGGCCTCCAGTTAT
41019837 ATGATAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 7 0.37
25 8 0.42
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
AAAGGGCTAGGCCTCCAGTTATTA
Found at i:41020016 original size:42 final size:42
Alignment explanation
Indices: 41019957--41020048 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
41019947 TAGTCTCCCC
* ** ** *
41019957 AAATGGGCTTGCATACATTTATTGGTATTTCATGTGATACTG
1 AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTG
*
41019999 AAATGGGCGTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTG
41020041 AAATGGGC
1 AAATGGGC
41020049 CTAAAGGCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (42 bp):
AAATGGGCGTGCATACATCCATTGACATTACATGTGATACTG
Found at i:41022415 original size:27 final size:27
Alignment explanation
Indices: 41022385--41022476 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
41022375 ATTACCAAAG
* *
41022385 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTAAAAAATTACTATTT
* *
41022412 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTAAAAAATTACTATTT
* *
41022439 TACCCTCGATTTAAAAAATTATTGTTT
1 TACCCTCGATTTAAAAAATTACTATTT
41022466 TACCCTCGATT
1 TACCCTCGATT
41022477 GTGAAATTAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTAAAAAATTACTATTT
Found at i:41022542 original size:27 final size:27
Alignment explanation
Indices: 41022508--41022631 Score: 119
Period size: 27 Copynumber: 4.6 Consensus size: 27
41022498 TATAGGGTAG
41022508 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
41022535 AATAACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
** *
41022562 AATTACCGTAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
41022589 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
41022616 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
41022632 TTGACTTTCT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 5 0.06
27 68 0.88
28 4 0.05
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:41022619 original size:54 final size:54
Alignment explanation
Indices: 41022528--41022688 Score: 144
Period size: 54 Copynumber: 2.9 Consensus size: 54
41022518 ATACCCCTAG
* *** * *
41022528 TTTGTAAAATAACCAAAATACCACTGGTTTGTGAAATTACCGTAATACCCTCAA
1 TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAA
* * * *
41022582 TTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGAC
1 TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCC-TCAA
* * * * * *
41022637 TTTCTAAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 TTTGT-AAAATAACCA-AAATACCACTGATTTACAAAATTACAGAAATACCCT
41022689 TGGTTTGTAG
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
54 42 0.48
55 8 0.09
56 38 0.43
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (54 bp):
TTTGTAAAATAACCAAAATACCACTGATTTACAAAATTACAGAAATACCCTCAA
Found at i:41022682 original size:27 final size:27
Alignment explanation
Indices: 41022587--41022694 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
41022577 CTCAATTTGT
** * *
41022587 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
41022614 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
41022641 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
41022670 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
41022695 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:41023597 original size:25 final size:26
Alignment explanation
Indices: 41023563--41023632 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 26
41023553 AGGAAGTGCT
* *
41023563 AAAAGGGCTCCGCCCCAGTTTA-CCG
1 AAAAGGGCTCTGCCCCAGTTTATCAG
*
41023588 AAAAGGGCTCTGCCCTAGTTTATCAG
1 AAAAGGGCTCTGCCCCAGTTTATCAG
*
41023614 AAAA-GGCTTTGCCCCAGTT
1 AAAAGGGCTCTGCCCCAGTT
41023633 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 33 0.85
26 6 0.15
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (26 bp):
AAAAGGGCTCTGCCCCAGTTTATCAG
Found at i:41026847 original size:40 final size:40
Alignment explanation
Indices: 41026749--41027011 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
41026739 TCCTCGTTCA
* * * * *
41026749 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41026788 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41026828 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
41026868 AATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41026908 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41026948 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
41026988 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41027012 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41034793 original size:40 final size:40
Alignment explanation
Indices: 41034695--41034950 Score: 320
Period size: 40 Copynumber: 6.4 Consensus size: 40
41034685 TCCTCGTTCA
* * * * *
41034695 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
41034734 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41034774 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
41034814 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
41034854 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
41034894 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
*
41034934 AAAGCCTTCGGGACTTA
1 AATGCCTTCGGGACTTA
41034951 GCCGGACAGC
Statistics
Matches: 195, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.19
40 150 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:41040723 original size:28 final size:28
Alignment explanation
Indices: 41040683--41040741 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
41040673 TACTAGTGTA
41040683 ATTGCATTGATTGATCCTAGTTCGACTC
1 ATTGCATTGATTGATCCTAGTTCGACTC
*
41040711 ATTGCATTGATTGATCCTGGTTCGACTC
1 ATTGCATTGATTGATCCTAGTTCGACTC
41040739 ATT
1 ATT
41040742 CTTATGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (28 bp):
ATTGCATTGATTGATCCTAGTTCGACTC
Found at i:41050998 original size:22 final size:22
Alignment explanation
Indices: 41050957--41051000 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41050947 ATAGAAAAAC
**
41050957 CCAGAATAAAGAAATTCAAGAT
1 CCAGAATAAAGAAACCCAAGAT
*
41050979 CCAGGATAAAGAAACCCAAGAT
1 CCAGAATAAAGAAACCCAAGAT
41051001 ACGATACTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (22 bp):
CCAGAATAAAGAAACCCAAGAT
Found at i:41054013 original size:47 final size:48
Alignment explanation
Indices: 41053935--41054067 Score: 150
Period size: 46 Copynumber: 2.8 Consensus size: 48
41053925 GTAACCCGCC
* *
41053935 CATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCC-AGTTACAT
* * * *
41053984 C-TCA-TGAACTCGGTCTCAACTCAATGAGTTCGGA---CATTTGCAT
1 CATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCAGTTACAT
*
41054027 CTATAAGTGAACTCGGACTCAACTTAATGAGTTCGGATGCC
1 C-ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCC
41054068 CAAATATCCC
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
43 7 0.10
44 1 0.01
45 2 0.03
46 28 0.41
47 27 0.39
48 2 0.03
49 2 0.03
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (48 bp):
CATAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCAGTTACAT
Found at i:41058619 original size:54 final size:54
Alignment explanation
Indices: 41058546--41058653 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
41058536 GAATTGAAAG
*
41058546 ATCAAATTGAGTAGAACGTAGGAAATGAGCACGATTGTTTGATGATGAATTGAT
1 ATCAAATTGAGTAGAACGTAGGAAATGAGCACGATCGTTTGATGATGAATTGAT
41058600 ATCAAATTGAGTAGAACGTAGGAAATGAGCACGATCGTTTGATGATGAATTGAT
1 ATCAAATTGAGTAGAACGTAGGAAATGAGCACGATCGTTTGATGATGAATTGAT
41058654 GGATAAGACC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (54 bp):
ATCAAATTGAGTAGAACGTAGGAAATGAGCACGATCGTTTGATGATGAATTGAT
Found at i:41059185 original size:20 final size:20
Alignment explanation
Indices: 41059139--41059185 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41059129 AGCTCGTTTC
*
41059139 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
41059159 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
41059179 CAGCTCA
1 CAGCTCA
41059186 ATCTTAACCC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:41060728 original size:9 final size:9
Alignment explanation
Indices: 41060714--41060749 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
41060704 AGAAGTGAGC
41060714 AAAAAAAGAA
1 AAAAAAAG-A
41060724 AAAAAAAGA
1 AAAAAAAGA
41060733 AAAAAAAGA
1 AAAAAAAGA
41060742 ACAAAAAA
1 A-AAAAAA
41060750 AAGAAGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 11 0.44
10 14 0.56
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:41060729 original size:10 final size:10
Alignment explanation
Indices: 41060714--41060750 Score: 58
Period size: 9 Copynumber: 3.7 Consensus size: 10
41060704 AGAAGTGAGC
41060714 AAAAAAAGAA
1 AAAAAAAGAA
41060724 AAAAAAAG-A
1 AAAAAAAGAA
41060733 AAAAAAAGAA
1 AAAAAAAGAA
41060743 CAAAAAAA
1 -AAAAAAA
41060751 AGAAGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.36
10 9 0.36
11 7 0.28
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:41060752 original size:12 final size:12
Alignment explanation
Indices: 41060722--41060754 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41060712 GCAAAAAAAG
*
41060722 AAAAAAA-AAGA
1 AAAAAAAGAACA
41060733 AAAAAAAGAACA
1 AAAAAAAGAACA
41060745 AAAAAAAGAA
1 AAAAAAAGAA
41060755 GTGAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAACA
Found at i:41060760 original size:26 final size:24
Alignment explanation
Indices: 41060696--41060761 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 24
41060686 AAGTTGAAAT
*
41060696 AAAAAAAAAGAAGTGAGCAAAAAAAG
1 AAAAAAAAAGAAGTGA--AAAAAAAA
*
41060722 AAAAAAAAAGAA---AAAAAAGAA
1 AAAAAAAAAGAAGTGAAAAAAAAA
*
41060743 CAAAAAAAAGAAGTGAAAA
1 AAAAAAAAAGAAGTGAAAA
41060762 GTCTTGCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 17 0.50
23 1 0.03
24 4 0.12
26 12 0.35
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (24 bp):
AAAAAAAAAGAAGTGAAAAAAAAA
Found at i:41063636 original size:20 final size:20
Alignment explanation
Indices: 41063589--41063627 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41063579 TAGCTCGTTT
*
41063589 CCAGCTCACTCGAGCTCAAG
1 CCAGCTCACTCAAGCTCAAG
* *
41063609 CCAACTCATTCAAGCTCAA
1 CCAGCTCACTCAAGCTCAA
41063628 TTCAGCTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.13, T:0.18
Consensus pattern (20 bp):
CCAGCTCACTCAAGCTCAAG
Found at i:41068940 original size:22 final size:22
Alignment explanation
Indices: 41068915--41068965 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
41068905 CACTAGGGAC
41068915 TATGTGATCTGAACTCATGAGT-
1 TATGTGATCTGAACTCATGA-TA
* **
41068937 TATGTGGTCTGGGCTCATGATA
1 TATGTGATCTGAACTCATGATA
41068959 TATGTGA
1 TATGTGA
41068966 CACATGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (22 bp):
TATGTGATCTGAACTCATGATA
Found at i:41080858 original size:25 final size:25
Alignment explanation
Indices: 41080820--41080868 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41080810 CTATATTATG
* *
41080820 AAAAATGACTATTTTGCCCCTAGGT
1 AAAAATGACCATTTTACCCCTAGGT
41080845 AAAAATGACCATTTTACCCCTAGG
1 AAAAATGACCATTTTACCCCTAGG
41080869 GTTTAAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (25 bp):
AAAAATGACCATTTTACCCCTAGGT
Found at i:41081075 original size:25 final size:25
Alignment explanation
Indices: 41080998--41081068 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
41080988 GAGGAAGTGC
* * *
41080998 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
41081023 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
41081048 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGC-TTTGCCCCAGTT
41081069 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 30 0.71
26 12 0.29
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:41081081 original size:25 final size:26
Alignment explanation
Indices: 41081008--41081081 Score: 84
Period size: 25 Copynumber: 2.9 Consensus size: 26
41080998 AAAAGGGCTA
*
41081008 TGCCCCAGTTTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
41081033 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
*
41081059 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
41081082 AGGCCACCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.09
25 28 0.65
26 11 0.26
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:41084636 original size:37 final size:37
Alignment explanation
Indices: 41084586--41084664 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
41084576 TTATTACGAA
* *
41084586 GTCTTACCCGGACATAA-TCTCCACACAAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACAAAGTCATCGG
**
41084623 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACAAAGTCATCGG
41084660 GTCTT
1 GTCTT
41084665 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 35 0.95
38 2 0.05
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACAAAGTCATCGG
Found at i:41084861 original size:47 final size:47
Alignment explanation
Indices: 41084783--41085228 Score: 741
Period size: 47 Copynumber: 9.4 Consensus size: 47
41084773 CCCTTCGGGA
* * * * * *
41084783 CTTATCACATTTATGCACTTTCGCATCCATCACGTTGGCCACTT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
***
41084830 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41084877 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41084924 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41084971 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41085018 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41085067 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41085114 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41085161 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41085210 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41085229 GTCTTGGCTG
Statistics
Matches: 378, Mismatches: 16, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
46 2 0.01
47 282 0.75
49 94 0.25
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41085096 original size:143 final size:143
Alignment explanation
Indices: 41084783--41085228 Score: 763
Period size: 143 Copynumber: 3.1 Consensus size: 143
41084773 CCCTTCGGGA
* * * * * * ***
41084783 CTTATCACATTTATGCACTTTCGCATCCATCACGTTGGCCACTT-GGCCCCGTCACATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGCCTTATCACATATATACA
41084847 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCAC
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
*
41084910 ATCGGCTATTAGGC
130 ATCGGCCATTAGGC
41084924 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
41084989 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
41085054 TCGGCCATTAGGC
131 TCGGCCATTAGGC
*
41085067 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
41085132 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
41085197 TCGGCCATTAGGC
131 TCGGCCATTAGGC
41085210 CTTATCACATATATACACT
1 CTTATCACATATATACACT
41085229 GTCTTGGCTG
Statistics
Matches: 291, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
140 2 0.01
141 90 0.31
143 199 0.68
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:41088510 original size:43 final size:42
Alignment explanation
Indices: 41088417--41088588 Score: 148
Period size: 43 Copynumber: 4.0 Consensus size: 42
41088407 GATTACCGAG
* * ** *
41088417 ATATGGTTACATGTAAAACCATGTCTAAGACATTGGCATTGT
1 ATATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
* *
41088459 ATTGTGATTACCTGTAAGACCATGTCTGGGACATTGGCATCGTT
1 A-TATGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-T
* * * * *
41088503 ATATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCAAT
1 ATATGATTACATGTAAGACCATGTCTGGGACATTGGCATC-GT
* * * * * *
41088546 ATGTGATAACATATAAGACCATATCTGGGATA-TGGCATTGT
1 ATATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
41088587 AT
1 AT
41088589 GAGCTTTATG
Statistics
Matches: 104, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
41 3 0.03
42 7 0.07
43 92 0.88
44 2 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (42 bp):
ATATGATTACATGTAAGACCATGTCTGGGACATTGGCATCGT
Found at i:41092010 original size:20 final size:20
Alignment explanation
Indices: 41091981--41092056 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 20
41091971 ATTTTAAATT
*
41091981 CAAGTGAAAATGATTTTAAC
1 CAAGTCAAAATGATTTTAAC
* *
41092001 CAAGTCAAAATGATTTCAAT
1 CAAGTCAAAATGATTTTAAC
*
41092021 CAAGTTC-AAATCATTTT-AC
1 CAAG-TCAAAATGATTTTAAC
41092040 CACA-TCAAAATGATTTT
1 CA-AGTCAAAATGATTTT
41092057 TGAAAAAGTC
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.04
19 12 0.26
20 30 0.65
21 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAC
Found at i:41098609 original size:53 final size:54
Alignment explanation
Indices: 41098501--41098730 Score: 260
Period size: 55 Copynumber: 4.3 Consensus size: 54
41098491 ACTTCTCACT
* * *
41098501 GTCTTACATGGTATCC-T---TT-TGAAACTTACCATTGCCATGTCTCGACATG
1 GTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGACATG
* *
41098550 GTCTTACATGGTATCCTTGCCTTATG-AACTCACCAATGCCATGCCTTGGCATG
1 GTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGACATG
* * *
41098603 GTCTTACATGGGA-CCTTTGCCTTATAGAAACTTATCAATGCCATGTCTTGACATG
1 GTCTTACATGGTATCC-TTGCCTTAT-GAAACTTACCAATGCCATGCCTTGACATG
* * * *
41098658 GTCTTACATGATATCCTTGCCTTA-GAAACCTTACCAATTTCCATGCATTGTCATG
1 GTCTTACATGGTATCCTTGCCTTATGAAA-CTTACCAA-TGCCATGCCTTGACATG
41098713 GTCTTACATGGTATCCTT
1 GTCTTACATGGTATCCTT
41098731 AAAACCTAAT
Statistics
Matches: 152, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
49 16 0.11
50 1 0.01
52 2 0.01
53 49 0.32
54 10 0.07
55 72 0.47
56 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
GTCTTACATGGTATCCTTGCCTTATGAAACTTACCAATGCCATGCCTTGACATG
Found at i:41098667 original size:108 final size:110
Alignment explanation
Indices: 41098521--41098723 Score: 304
Period size: 108 Copynumber: 1.9 Consensus size: 110
41098511 GTATCCTTTT
* *
41098521 GAAACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACC
*
41098584 AA-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
65 AATTGCCATGCATTGGCATGGTCTTACATGGGACCTTTGCCTTATA
* * *
41098629 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
* *
41098694 ATTTCCATGCATTGTCATGGTCTTACATGG
66 ATTGCCATGCATTGGCATGGTCTTACATGG
41098724 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 51 0.61
109 7 0.08
110 25 0.30
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (110 bp):
GAAACTTACCAATGCCATGTCTCGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCA
ATTGCCATGCATTGGCATGGTCTTACATGGGACCTTTGCCTTATA
Found at i:41117308 original size:28 final size:28
Alignment explanation
Indices: 41117270--41117423 Score: 265
Period size: 28 Copynumber: 5.5 Consensus size: 28
41117260 TAAATTGTAC
*
41117270 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
41117298 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
41117326 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41117354 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41117382 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41117409 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41117424 GACTTAATAT
Statistics
Matches: 123, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
27 24 0.20
28 99 0.80
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:41117336 original size:56 final size:55
Alignment explanation
Indices: 41117245--41117423 Score: 268
Period size: 56 Copynumber: 3.2 Consensus size: 55
41117235 GAGATTGGCG
* * * *
41117245 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAG-TTGATTATGTAGCA
*
41117302 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATGTAGCA
*
41117358 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATGTAGCA
*
41117413 CTGAGTGTGCG
1 CTAAGTGTGCG
41117424 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
55 23 0.20
56 75 0.66
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (55 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATGTAGCA
Found at i:41125556 original size:28 final size:28
Alignment explanation
Indices: 41125518--41125671 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
41125508 TAAATTGTAC
*
41125518 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
41125546 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41125574 AGCACTAAGTGTGCGAGTTTAATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41125602 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41125630 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
41125657 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41125672 GACTTAATAT
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 24 0.20
28 97 0.80
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:41125584 original size:56 final size:55
Alignment explanation
Indices: 41125493--41125671 Score: 259
Period size: 56 Copynumber: 3.2 Consensus size: 55
41125483 GAGATTGGCG
* * * *
41125493 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAG-TTGATTATGTAGCA
* *
41125550 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTAATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATGTAGCA
*
41125606 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATGTAGCA
*
41125661 CTGAGTGTGCG
1 CTAAGTGTGCG
41125672 GACTTAATAT
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
55 22 0.20
56 74 0.67
57 15 0.14
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (55 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTGATTATGTAGCA
Found at i:41125635 original size:84 final size:83
Alignment explanation
Indices: 41125493--41125671 Score: 270
Period size: 84 Copynumber: 2.1 Consensus size: 83
41125483 GAGATTGGCG
* *
41125493 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGT
1 CTAAGTGTGCGAGTTTAAATTGTA-AGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGT
*
41125558 GCGAGTTTGATTATGTAGCA
65 GCGAG-TTGATTATATAGCA
* *
41125578 CTAAGTGTGCGAGTTTAATTATGT-AGCACTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGT
1 CTAAGTGTGCGAGTTTAAAT-TGTAAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGT
41125642 GCGAGTTGATTATATAGCA
65 GCGAGTTGATTATATAGCA
*
41125661 CTGAGTGTGCG
1 CTAAGTGTGCG
41125672 GACTTAATAT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
83 23 0.26
84 43 0.49
85 18 0.21
86 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (83 bp):
CTAAGTGTGCGAGTTTAAATTGTAAGCACTAAGTGTGCGAGCTTGATTATATAGCACTAAGTGTG
CGAGTTGATTATATAGCA
Found at i:41125684 original size:27 final size:28
Alignment explanation
Indices: 41125493--41125671 Score: 209
Period size: 28 Copynumber: 6.4 Consensus size: 28
41125483 GAGATTGGCG
* * * *
41125493 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTTGAA-TATATAGCA
* * *
41125522 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATATAGCA
* *
41125550 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGAATATATAGCA
*
41125578 CTAAGTGTGCGAGTTT-AATTATGTAGCA
1 CTAAGTGTGCGAGTTTGAA-TATATAGCA
*
41125606 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGAATATATAGCA
*
41125634 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGAATATATAGCA
*
41125661 CTGAGTGTGCG
1 CTAAGTGTGCG
41125672 GACTTAATAT
Statistics
Matches: 136, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
27 25 0.18
28 95 0.70
29 16 0.12
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGAATATATAGCA
Found at i:41129155 original size:27 final size:27
Alignment explanation
Indices: 41129125--41129302 Score: 142
Period size: 27 Copynumber: 6.6 Consensus size: 27
41129115 ATATTGAGCC
* * **
41129125 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* * *
41129152 CGCATACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
41129179 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-AAT
* ** ** *
41129207 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
41129234 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
41129261 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
41129288 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
41129303 GTACAATTTA
Statistics
Matches: 121, Mismatches: 27, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
27 98 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:41137147 original size:27 final size:27
Alignment explanation
Indices: 41137117--41137294 Score: 151
Period size: 27 Copynumber: 6.6 Consensus size: 27
41137107 ATATTGAGCC
* * **
41137117 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
41137144 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
41137171 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-AAT
* ** ** *
41137199 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
41137226 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
41137253 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
41137280 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
41137295 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:41137256 original size:82 final size:81
Alignment explanation
Indices: 41137143--41137293 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
41137133 TATAATCATC
* * * *
41137143 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCACTCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCACCCTT
41137208 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
41137225 TCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
1 TCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTT
41137289 AGTGC
65 AGTGC
41137294 TGTACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 17 0.28
82 44 0.72
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACCCTTA
GTGCCGCATGGTCAAT
Found at i:41163431 original size:27 final size:27
Alignment explanation
Indices: 41163397--41163596 Score: 215
Period size: 27 Copynumber: 7.4 Consensus size: 27
41163387 TGGATAAGTT
*
41163397 GTAGAATTATCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
41163424 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
**
41163451 GTAGAATTATTGAAATACCCCTGT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
41163477 GATAGAATTACCGAAATACCCTTGT-AG
1 G-TAGAATTACCGAAATACCCCTGTAAG
* *
41163504 GATAGAATTACCGAAATACCCTTGTAGG
1 G-TAGAATTACCGAAATACCCCTGTAAG
* * ** *
41163532 GTAGAAATACTGAAATACTGCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
* * **
41163559 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
41163586 GTAAAATTACC
1 GTAGAATTACC
41163597 ATTTTGCCCC
Statistics
Matches: 149, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 145 0.97
28 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:41163473 original size:54 final size:54
Alignment explanation
Indices: 41163397--41163596 Score: 240
Period size: 54 Copynumber: 3.7 Consensus size: 54
41163387 TGGATAAGTT
41163397 GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
* *
41163451 GTAGAATTATTGAAATACCCCTGT-AGGATAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAAGG-TAGAATTACCGAAATACCCCTGTAGG
* * * * * * **
41163505 ATAGAATTACCGAAATACCCTTGTAGGGTAGAAATACTGAAATACTGCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
* * * ** *
41163559 GTAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACC
41163597 ATTTTGCCCC
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 3 0.02
54 121 0.96
55 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (54 bp):
GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGG
Found at i:41163533 original size:81 final size:80
Alignment explanation
Indices: 41163398--41163596 Score: 272
Period size: 81 Copynumber: 2.5 Consensus size: 80
41163388 GGATAAGTTG
* * * *
41163398 TAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATTG
1 TAGAATTACCGAAATACCCTTGT-AGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTG
41163463 AAATACCCCTGTAGGA
65 AAATACCCCTGTAGGA
*
41163479 TAGAATTACCGAAATACCCTTGTAGGATAGAATTACCGAAATACCCTTGTAGGGTAGAAATACTG
1 TAGAATTACCGAAATACCCTTGTAGG-TAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTG
** *
41163544 AAATACTGCTGTAGGG
65 AAATACCCCTGTAGGA
* * *
41163560 TAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 TAGAATTACCGAAATACCCTTGT-AGGTAGAATTACC
41163597 ATTTTGCCCC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
80 3 0.03
81 100 0.95
82 2 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (80 bp):
TAGAATTACCGAAATACCCTTGTAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAAATACTGA
AATACCCCTGTAGGA
Found at i:41164292 original size:27 final size:26
Alignment explanation
Indices: 41164248--41164298 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
41164238 CTCACTGCAA
*
41164248 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
41164275 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
41164299 GGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:41165613 original size:19 final size:19
Alignment explanation
Indices: 41165589--41165663 Score: 100
Period size: 19 Copynumber: 3.9 Consensus size: 19
41165579 TTCATTTAAC
41165589 AAACACATTAAAACACATT
1 AAACACATTAAAACACATT
*
41165608 AAACACATTAATCACACATT
1 AAACACATTAA-AACACATT
*
41165628 AAACTCATTAAAA-ATCATT
1 AAACACATTAAAACA-CATT
41165647 AAACACATT-AAACACAT
1 AAACACATTAAAACACAT
41165664 GTGGCAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
18 7 0.14
19 25 0.51
20 17 0.35
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (19 bp):
AAACACATTAAAACACATT
Found at i:41165626 original size:11 final size:9
Alignment explanation
Indices: 41165589--41165663 Score: 96
Period size: 9 Copynumber: 7.9 Consensus size: 9
41165579 TTCATTTAAC
41165589 AAACACATT
1 AAACACATT
41165598 AAAACACATT
1 -AAACACATT
41165608 AAACACATT
1 AAACACATT
41165617 AATCACACATT
1 AA--ACACATT
*
41165628 AAACTCATT
1 AAACACATT
*
41165637 AAAAATCATT
1 AAACA-CATT
41165647 AAACACATT
1 AAACACATT
41165656 AAACACAT
1 AAACACAT
41165664 GTGGCAATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
9 32 0.55
10 17 0.29
11 9 0.16
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (9 bp):
AAACACATT
Found at i:41165713 original size:34 final size:34
Alignment explanation
Indices: 41165675--41165771 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
41165665 TGGCAATAAA
* * *
41165675 TTATTCCAGCAACTAAATTAACTAAGATAAGCAT
1 TTATTCTAGCAACTCAATTAACTAACATAAGCAT
41165709 TTATTCTAGCAACTCAATTAACTAACATAAGCAT
1 TTATTCTAGCAACTCAATTAACTAACATAAGCAT
41165743 TTATTCTAGCAACTCAATTAA-TAAC-TAAG
1 TTATTCTAGCAACTCAATTAACTAACATAAG
41165772 ATGAGTTCAA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 4 0.07
33 4 0.07
34 52 0.87
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (34 bp):
TTATTCTAGCAACTCAATTAACTAACATAAGCAT
Found at i:41179651 original size:40 final size:40
Alignment explanation
Indices: 41179606--41179797 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
41179596 ATAACCACAA
* * *
41179606 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
41179646 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
41179686 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
41179726 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
41179766 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41179798 CATTCAATGC
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41179690 original size:80 final size:80
Alignment explanation
Indices: 41179577--41179796 Score: 248
Period size: 80 Copynumber: 2.8 Consensus size: 80
41179567 ACCCAAGTTT
* * * * * * * * *
41179577 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
*
41179640 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
41179656 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
* *
41179720 TCACTAGCATAAATGC
65 GCACTAGCACAAATGC
* *
41179736 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
41179797 TCATTCAATG
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 12 0.10
80 98 0.84
81 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC
Found at i:41193006 original size:11 final size:11
Alignment explanation
Indices: 41192992--41193048 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
41192982 TGTTTATCTT
41192992 ATTTATTTTTA
1 ATTTATTTTTA
*
41193003 ATTTTCCTTTTTA
1 A-TTT-ATTTTTA
*
41193016 ATTTTAATTTT-
1 A-TTTATTTTTA
*
41193027 ATTTATTTTTT
1 ATTTATTTTTA
41193038 ATTTATTTTTA
1 ATTTATTTTTA
41193049 TCAATCATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 8 0.21
11 12 0.32
12 7 0.18
13 11 0.29
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTATTTTTA
Found at i:41195185 original size:24 final size:24
Alignment explanation
Indices: 41195135--41195188 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
41195125 AATCGAATTT
*
41195135 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
41195159 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
41195183 GCACAC
1 GCACAC
41195189 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:41197655 original size:5 final size:5
Alignment explanation
Indices: 41197640--41197681 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
41197630 TCTGAGTCCA
41197640 TTTATT TTTAT TTTAT TTTAT TTTAT TTT-T TTTA- TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41197682 CTTAAGACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.24
5 22 0.65
6 4 0.12
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:41207665 original size:3 final size:3
Alignment explanation
Indices: 41207657--41207714 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
41207647 GGCCCAAATG
* * * * * *
41207657 ATT ATT ATT ATT ATT ATT ATC ATT ACT ACT ACT ACT ATT ATT AAAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
41207703 ATT ATT ATT ATT
1 ATT ATT ATT ATT
41207715 CTTACAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:41208073 original size:15 final size:15
Alignment explanation
Indices: 41208053--41208083 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41208043 AAAAGTTATT
41208053 ATTTTTATTTTTAAA
1 ATTTTTATTTTTAAA
41208068 ATTTTTATTTTTAAA
1 ATTTTTATTTTTAAA
41208083 A
1 A
41208084 AGAGAGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTATTTTTAAA
Found at i:41210716 original size:16 final size:16
Alignment explanation
Indices: 41210695--41210745 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
41210685 AAAAGCATGT
*
41210695 GAAAAAGAATTTGAAA
1 GAAAAAGAATATGAAA
41210711 GAAAAAAAGAA-ATGAAA
1 G--AAAAAGAATATGAAA
* *
41210728 GAAAAAGAGTGTGAAA
1 GAAAAAGAATATGAAA
41210744 GA
1 GA
41210746 GAGCAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 6 0.21
18 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
GAAAAAGAATATGAAA
Found at i:41210726 original size:17 final size:18
Alignment explanation
Indices: 41210696--41210733 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
41210686 AAAGCATGTG
*
41210696 AAAAAGAATTTGAAAGAA
1 AAAAAGAATATGAAAGAA
41210714 AAAAAGAA-ATGAAAGAA
1 AAAAAGAATATGAAAGAA
41210731 AAA
1 AAA
41210734 GAGTGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (18 bp):
AAAAAGAATATGAAAGAA
Found at i:41210743 original size:21 final size:20
Alignment explanation
Indices: 41210719--41210776 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
41210709 AAGAAAAAAA
**
41210719 GAAATGAAAGAAAAAGAGTGT
1 GAAA-GAAAGAAAAAGAGAAT
*
41210740 GAAAGAGAGCAAAAAGAGAAT
1 GAAAGAAAG-AAAAAGAGAAT
*
41210761 GAGAGAAAGAAAAAGA
1 GAAAGAAAGAAAAAGA
41210777 ATTTGATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.62, C:0.02, G:0.29, T:0.07
Consensus pattern (20 bp):
GAAAGAAAGAAAAAGAGAAT
Found at i:41210743 original size:33 final size:36
Alignment explanation
Indices: 41210695--41210768 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 36
41210685 AAAAGCATGT
*
41210695 GAAAAAGAATTTGAAAGA-A-AAAAAGA-AATGAAA
1 GAAAAAGAATGTGAAAGAGACAAAAAGAGAATGAAA
* *
41210728 GAAAAAGAGTGTGAAAGAGAGCAAAAAGAGAATGAGA
1 GAAAAAGAATGTGAAAGAGA-CAAAAAGAGAATGAAA
41210765 GAAA
1 GAAA
41210769 GAAAAAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 16 0.47
34 1 0.03
36 7 0.21
37 10 0.29
ACGTcount: A:0.64, C:0.01, G:0.26, T:0.09
Consensus pattern (36 bp):
GAAAAAGAATGTGAAAGAGACAAAAAGAGAATGAAA
Found at i:41214634 original size:80 final size:80
Alignment explanation
Indices: 41214518--41214703 Score: 238
Period size: 80 Copynumber: 2.3 Consensus size: 80
41214508 AGTAACTCAT
* *
41214518 ACAATGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
41214582 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
41214597 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
41214661 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
41214678 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
41214704 CAGCATTCAA
Statistics
Matches: 95, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
79 12 0.13
80 72 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:41214663 original size:40 final size:40
Alignment explanation
Indices: 41214520--41214703 Score: 214
Period size: 40 Copynumber: 4.6 Consensus size: 40
41214510 TAACTCATAC
*
41214520 AATGCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
41214560 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
41214600 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
41214640 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
41214681 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41214704 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
39 9 0.07
40 105 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:41217132 original size:40 final size:40
Alignment explanation
Indices: 41217049--41217268 Score: 259
Period size: 40 Copynumber: 5.5 Consensus size: 40
41217039 ACCCAAGTAT
** * *
41217049 CTTCGGGAT-TTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGG-TCTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
41217087 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
41217127 CTTCGGGACTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41217167 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * * *
41217207 CTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAAGC
1 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
*
41217247 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
41217269 CATTCGAATA
Statistics
Matches: 154, Mismatches: 23, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
37 1 0.01
38 11 0.07
39 16 0.10
40 125 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:41219374 original size:59 final size:59
Alignment explanation
Indices: 41219307--41219423 Score: 207
Period size: 59 Copynumber: 2.0 Consensus size: 59
41219297 AATTCAACTC
*
41219307 GTTTGAGTTAGATTTAGTTGCTCTCCAACTTATTTCTTTTATCATTTTAATAAACTAAT
1 GTTTGAGTTAAATTTAGTTGCTCTCCAACTTATTTCTTTTATCATTTTAATAAACTAAT
* *
41219366 GTTTGAGTTAAATTTAGTTGCTCTCTAGCTTATTTCTTTTATCATTTTAATAAACTAA
1 GTTTGAGTTAAATTTAGTTGCTCTCCAACTTATTTCTTTTATCATTTTAATAAACTAA
41219424 GTATTGGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.50
Consensus pattern (59 bp):
GTTTGAGTTAAATTTAGTTGCTCTCCAACTTATTTCTTTTATCATTTTAATAAACTAAT
Found at i:41221937 original size:46 final size:45
Alignment explanation
Indices: 41221880--41222049 Score: 171
Period size: 46 Copynumber: 3.7 Consensus size: 45
41221870 CATCTCATAT
*
41221880 CCGATGTATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CGTCTCGAGG
* * * * *
41221926 CCGTTGCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACT-GGCTTCGTCTCGAGG
* * * * * *
41221972 TCGATGCCATCTCCCAAACATGATCTTACACTGGCTCTCATAAT-GTGG
1 CCGATG-CATGTCCCAGACATG-TCTTACACTGGCT-TCGT-CTCGAGG
41222020 CCGATGCATGTCCCAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
41222050 AGCTCACACA
Statistics
Matches: 99, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
46 49 0.49
47 31 0.31
48 18 0.18
49 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTTCGTCTCGAGG
Found at i:41225303 original size:53 final size:53
Alignment explanation
Indices: 41225120--41225374 Score: 254
Period size: 55 Copynumber: 4.8 Consensus size: 53
41225110 ATTAGGGTTT
* *
41225120 AAGGATACCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-G-TTCATAAGGC
* * *
41225175 AAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
41225230 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * * *
41225283 AAGGATATCATGTAATACCATGTCGAGACATGGCAATGGTAAGTT--TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCAT-AAGGC
* * *
41225332 AAGGATACCATGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
41225375 GTACCTGTGT
Statistics
Matches: 170, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
49 38 0.22
51 1 0.01
52 8 0.05
53 41 0.24
54 8 0.05
55 70 0.41
56 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:41225326 original size:108 final size:110
Alignment explanation
Indices: 41225127--41225327 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
41225117 TTTAAGGATA
41225127 CCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
*
41225192 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
41225237 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATATCATGTAAT
1 CCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTC-TAAGGCAAGGATATCATGTAAG
* *
41225299 ACCATGTCGAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
41225328 TCAAAAGGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 3 0.04
108 48 0.57
109 7 0.08
110 26 0.31
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGTAATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:41225588 original size:16 final size:16
Alignment explanation
Indices: 41225567--41225597 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41225557 ATAAATTTGA
41225567 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
41225583 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
41225598 AGTGAAGAAG
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:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:41227189 original size:26 final size:26
Alignment explanation
Indices: 41227107--41227220 Score: 111
Period size: 26 Copynumber: 4.4 Consensus size: 26
41227097 AGGATGTACT
*
41227107 TTATCTAGCAGGCCTTGAGTCAGTGA
1 TTATCTAGCAGGCCTTGAGCCAGTGA
* *
41227133 TTATCGAGTAGGCCTTGAGCCAGTGA
1 TTATCTAGCAGGCCTTGAGCCAGTGA
* * * *
41227159 TTATTTAGCAGGCCTTCAGCCGGTGT
1 TTATCTAGCAGGCCTTGAGCCAGTGA
* * * * *
41227185 TTATTTAACAGGTCTTGAGCTAATGA
1 TTATCTAGCAGGCCTTGAGCCAGTGA
*
41227211 TTATTTAGCA
1 TTATCTAGCA
41227221 AGTTGGTGAC
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (26 bp):
TTATCTAGCAGGCCTTGAGCCAGTGA
Found at i:41236597 original size:27 final size:27
Alignment explanation
Indices: 41236542--41236599 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41236532 AAAAATCATC
***
41236542 ACAATTTAGTCACTATTTCATATTTAT
1 ACAATTTAGTCACTATTTCATAAAAAT
41236569 ACAATTTAGTCACTATTTCATAAAAAT
1 ACAATTTAGTCACTATTTCATAAAAAT
41236596 ACAA
1 ACAA
41236600 ATTCATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (27 bp):
ACAATTTAGTCACTATTTCATAAAAAT
Found at i:41238189 original size:41 final size:41
Alignment explanation
Indices: 41238109--41238195 Score: 122
Period size: 41 Copynumber: 2.1 Consensus size: 41
41238099 AATTGTTGTA
* * *
41238109 TGAATTGCACATAAGTGCCCCTGTTTGTACTTTGATACCCT
1 TGAATTCCACATAAGTGCCCCTGTTTGTACTTAGATACCCC
*
41238150 TGAATTCCACATACGTGCCCCTGTTTGTACTTCAG-TACCCC
1 TGAATTCCACATAAGTGCCCCTGTTTGTACTT-AGATACCCC
41238191 TGAAT
1 TGAAT
41238196 GTAGATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (41 bp):
TGAATTCCACATAAGTGCCCCTGTTTGTACTTAGATACCCC
Found at i:41241789 original size:33 final size:33
Alignment explanation
Indices: 41241747--41241815 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
41241737 CGTATCTGGG
*
41241747 ATATGGCATCTATATGAGACTTCGTGTAAGACC
1 ATATGGCATCGATATGAGACTTCGTGTAAGACC
*
41241780 ATATGGCATCGATATGAGACTTCGTGTAATACC
1 ATATGGCATCGATATGAGACTTCGTGTAAGACC
41241813 ATA
1 ATA
41241816 GCTGGGCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (33 bp):
ATATGGCATCGATATGAGACTTCGTGTAAGACC
Found at i:41251522 original size:27 final size:28
Alignment explanation
Indices: 41251468--41251524 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 28
41251458 ATGGTGAGAA
41251468 AGTTTATGTACATGTATATATATATGAAC
1 AGTTTATGTACATG-ATATATATATGAAC
*
41251497 AGTTTATGTATATG-TATATATATGAAC
1 AGTTTATGTACATGATATATATATGAAC
41251524 A
1 A
41251525 TATGATAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 14 0.52
29 13 0.48
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (28 bp):
AGTTTATGTACATGATATATATATGAAC
Found at i:41254875 original size:15 final size:15
Alignment explanation
Indices: 41254855--41254900 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
41254845 ATTATGATAT
41254855 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
41254870 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
* * *
41254885 TTTATCATAGATTTC
1 TGTATCTTGGATTTC
41254900 T
1 T
41254901 TTGTTCTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (15 bp):
TGTATCTTGGATTTC
Found at i:41261946 original size:63 final size:63
Alignment explanation
Indices: 41261847--41261970 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
41261837 TGAGCTGAAC
* * * **
41261847 GATAGTGTGATGGTGCTCCGACTAATTCCAACCTTCATGAACTTCTGAGCACTATAAAACATG
1 GATAGTGTGATGGTGCTACGACTAATTCCAAACTTCACGAACTTCCAAGCACTATAAAACATG
* *
41261910 GATAGTGTGATGGTGCTATGACTAATTCCAAACTTCACGAGCTTCCAAGCACTATAAAACA
1 GATAGTGTGATGGTGCTACGACTAATTCCAAACTTCACGAACTTCCAAGCACTATAAAACA
41261971 GAGGAAAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (63 bp):
GATAGTGTGATGGTGCTACGACTAATTCCAAACTTCACGAACTTCCAAGCACTATAAAACATG
Found at i:41272023 original size:37 final size:37
Alignment explanation
Indices: 41271973--41272051 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41271963 TTATTACGAA
* * *
41271973 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41272010 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41272047 GTCTT
1 GTCTT
41272052 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41272329 original size:47 final size:47
Alignment explanation
Indices: 41272169--41272440 Score: 463
Period size: 47 Copynumber: 5.7 Consensus size: 47
41272159 GCCCTTCGGG
*
41272169 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
41272219 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCATATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATC--ACATATATAC
41272268 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
41272315 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41272362 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
41272409 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
41272441 ATACTATCAT
Statistics
Matches: 215, Mismatches: 5, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
47 133 0.62
49 77 0.36
50 4 0.02
51 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:41272378 original size:25 final size:25
Alignment explanation
Indices: 41272302--41272380 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
41272292 ATTAGGCCTT
41272302 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
**** ***
41272327 ATCACAT-CGGCCA-TTAGGCATT-
1 ATCACATATATACACTTTCACATTC
41272349 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
41272374 ATCACAT
1 ATCACAT
41272381 CGGCCATTAG
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 14 0.38
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:41277119 original size:21 final size:21
Alignment explanation
Indices: 41277095--41277136 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
41277085 GTCTAGGTTG
41277095 GACTACTTCAGGAGGTCTTTC
1 GACTACTTCAGGAGGTCTTTC
41277116 GACTACTTCAGGAGGTCTTTC
1 GACTACTTCAGGAGGTCTTTC
41277137 ACATTGCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (21 bp):
GACTACTTCAGGAGGTCTTTC
Found at i:41285018 original size:40 final size:40
Alignment explanation
Indices: 41284954--41285065 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
41284944 GACTATGTTT
* *
41284954 GGCACTAAGTGTGCATTTCAAAATAGCTTTGGCTCTAAAT-A
1 GGCACTAAGTGTGCAATTCAAAATAGC-TTCGC-CTAAATGA
* *
41284995 -GCACTAAGTGTGCAAATT-GAAATAGCTTCGCCTATATGA
1 GGCACTAAGTGTGC-AATTCAAAATAGCTTCGCCTAAATGA
* * *
41285034 GGCACTAAGTGTGCGATACCAAGATAGCTTCG
1 GGCACTAAGTGTGCAAT-TCAAAATAGCTTCG
41285066 GTTTATTGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
38 5 0.09
39 7 0.12
40 33 0.57
41 13 0.22
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (40 bp):
GGCACTAAGTGTGCAATTCAAAATAGCTTCGCCTAAATGA
Found at i:41287872 original size:30 final size:30
Alignment explanation
Indices: 41287838--41287906 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
41287828 ATGCGTATAG
41287838 CCATGTGTCACACACAGTTGAGACACACGC
1 CCATGTGTCACACACAGTTGAGACACACGC
* *
41287868 CCATGTGTCATACACGGTTGAGACACACGC
1 CCATGTGTCACACACAGTTGAGACACACGC
*
41287898 CCGTGTGTC
1 CCATGTGTC
41287907 TACTCATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (30 bp):
CCATGTGTCACACACAGTTGAGACACACGC
Found at i:41291579 original size:20 final size:21
Alignment explanation
Indices: 41291540--41291579 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41291530 GTTATAATGA
*
41291540 CCACACGGGCGTGTTGCCCTT
1 CCACACGGGCATGTTGCCCTT
*
41291561 CCACATGGGCATG-TGCCCT
1 CCACACGGGCATGTTGCCCT
41291580 GTTTCATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.23
Consensus pattern (21 bp):
CCACACGGGCATGTTGCCCTT
Found at i:41304668 original size:165 final size:166
Alignment explanation
Indices: 41304358--41304789 Score: 532
Period size: 171 Copynumber: 2.6 Consensus size: 166
41304348 AGGGTGTTCC
* * * *
41304358 ATTTTT-GTAATTTATTATGTTTTTTGGATTATTAGGGTAAAAAGGTCAAGAAAT-AGTGTATAG
1 ATTTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTAAATAGGTCAAGAAATGA-TGTATGG
* * * ** *
41304421 TACAACATTTTTACCTAGGTAATATTAAAAAAATAATTAAATACGGAAATGGGTAACCTTACAAA
65 TACAACAATTTTACCTA---AATAATATAAAAATAATTAAATACAAAAATGGGCAACCTTACAAA
* *
41304486 TTAAGTACCGAAATGGGTCGGTTGTTACAAATTGGTA-CG
127 CTAAGTACCGAAATGGGTCAGTTGTTACAAATTGGTAGCG
* *
41304525 ATTTTTGGTATTTTATTAAGTTTTTTGGATTATTGGGGTAAATAGGTTAAGAAATGATGTATGGT
1 ATTTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTAAATAGGTCAAGAAATGATGTATGGT
*
41304590 ACAATAATTTTACCTAAATAATATAAAAATAATTAAATACAAAAATGGGCAACCTTACAAACTAA
66 ACAACAATTTTACCTAAATAATATAAAAATAATTAAATACAAAAATGGGCAACCTTACAAACTAA
* * *
41304655 GTGCCGAAATGGGTCATTTGTTACAAATTGGTAGGGTG
131 GTACCGAAATGGGTCAGTTGTTACAAATTGGTA--GCG
* * *
41304693 ACCCATTTTGGTATTTTATTATGTTTTTTGAATTATTGGGGTAAATAGGTCAAGACACA-G-TAT
1 A---TTTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTAAATAGGTCAAGA-A-ATGATGT
*
41304756 ATGGTACAACAATTTTACTTAAATAATATAAAAA
61 ATGGTACAACAATTTTACCTAAATAATATAAAAA
41304790 AAATATTAAA
Statistics
Matches: 230, Mismatches: 25, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
165 73 0.32
167 6 0.03
168 66 0.29
169 1 0.00
171 81 0.35
172 2 0.01
173 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (166 bp):
ATTTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTAAATAGGTCAAGAAATGATGTATGGT
ACAACAATTTTACCTAAATAATATAAAAATAATTAAATACAAAAATGGGCAACCTTACAAACTAA
GTACCGAAATGGGTCAGTTGTTACAAATTGGTAGCG
Found at i:41304781 original size:171 final size:169
Alignment explanation
Indices: 41304332--41304871 Score: 609
Period size: 165 Copynumber: 3.2 Consensus size: 169
41304322 GAAGAGGCCG
* ** * * *
41304332 TTTGCTACAAATTGGTAGGGTGTTCCATTTTTGTAATTTATTATGTTTTTTGGATTATTAGGGTA
1 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTA
* * * * *
41304397 AAAAGGTCAAGAAATAGTGTATAGTACAACATTTTTACCTAGGTAATATTAAAAAAATAATTAAA
66 AATAGGTCAAG-AA-AGTGTATGGTACAACAATTTTACCTA---AATAATATAAAAATAATTAAA
** * *
41304462 TACGGAAATGGGTAACCTTACAAATTAAGTACCGAAATGGGTCG
126 TACAAAAATGGGCAACCTTACAAATTAAGTACCGAAATGGGTCA
* * * *
41304506 GTTGTTACAAATTGGTA---CGA---TTTTTGGTATTTTATTAAGTTTTTTGGATTATTGGGGTA
1 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTA
* *
41304565 AATAGGTTAAGAAATGATGTATGGTACAATAATTTTACCTAAATAATATAAAAATAATTAAATAC
66 AATAGGTCAAGAAA-G-TGTATGGTACAACAATTTTACCTAAATAATATAAAAATAATTAAATAC
* *
41304630 AAAAATGGGCAACCTTACAAACTAAGTGCCGAAATGGGTCA
129 AAAAATGGGCAACCTTACAAATTAAGTACCGAAATGGGTCA
*
41304671 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGAATTATTGGGGTA
1 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTA
* *
41304736 AATAGGTCAAGACACAGTATATGGTACAACAATTTTACTTAAATAATAT--AAA-AA--AAATA-
66 AATAGGTCAAGA-A-AGTGTATGGTACAACAATTTTACCTAAATAATATAAAAATAATTAAATAC
** * * * ** *
41304795 TTAAATGGACGACATTACAAATTAAGTATTGAAATGGTTCA
129 AAAAATGGGCAACCTTACAAATTAAGTACCGAAATGGGTCA
41304836 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTAT
1 TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTAT
41304872 ATATCTGTCA
Statistics
Matches: 315, Mismatches: 41, Indels: 29
0.82 0.11 0.08
Matches are distributed among these distances:
165 140 0.44
166 6 0.02
167 3 0.01
168 68 0.22
169 3 0.01
171 77 0.24
172 2 0.01
173 1 0.00
174 15 0.05
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (169 bp):
TTTGTTACAAATTGGTAGGGTGACCCATTTTGGTATTTTATTATGTTTTTTGGATTATTGGGGTA
AATAGGTCAAGAAAGTGTATGGTACAACAATTTTACCTAAATAATATAAAAATAATTAAATACAA
AAATGGGCAACCTTACAAATTAAGTACCGAAATGGGTCA
Found at i:41314496 original size:40 final size:40
Alignment explanation
Indices: 41314415--41314674 Score: 366
Period size: 40 Copynumber: 6.6 Consensus size: 40
41314405 AAACCAAGTA
** * **
41314415 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTTAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
41314454 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
41314494 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCGCAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41314534 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* *
41314574 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41314614 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC-AATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41314653 CCTTCGGG-CTTAGCCCGATTAT
1 CCTTCGGGACTTAGCCCGGTTAT
41314675 CAATCCGAAT
Statistics
Matches: 203, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
38 12 0.06
39 25 0.12
40 166 0.82
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:41322589 original size:37 final size:38
Alignment explanation
Indices: 41322548--41322731 Score: 252
Period size: 37 Copynumber: 4.9 Consensus size: 38
41322538 CGGAATAGCT
*
41322548 ACTCGCTCAAATGCCTTCGGACTTA-CCCGTTATAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGTTATAGTA
* * *
41322585 ACTCGCACAATTGCCTTGGGACTTAGCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGTTATAGTA
*
41322623 ACT-GCACAATTGCCTTCGGACTT-G-CCGTTATAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCCGTTATAGTA
*
41322658 ACTCGCAC-AATGCCTTCGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGACTTAGCCC-GTTATAGTA
41322696 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 ACTCGCACAAATGCCTTC-GGACTTAGCCC-GTTAT
41322732 CAATCCGAAT
Statistics
Matches: 131, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
35 27 0.21
36 6 0.05
37 43 0.33
38 30 0.23
39 9 0.07
40 16 0.12
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (38 bp):
ACTCGCACAAATGCCTTCGGACTTAGCCCGTTATAGTA
Found at i:41322713 original size:74 final size:75
Alignment explanation
Indices: 41322524--41322731 Score: 273
Period size: 74 Copynumber: 2.8 Consensus size: 75
41322514 AAACCAAGTA
** *
41322524 CCTTCGGGTTTAGCCGGA-ATAGCT-ACTCGCTCAAATGCCTTCGGACTTACCCGTTATAGTAAC
1 CCTTCGGACTTAGCCGGATATAG-TAACTCGCACAAATGCCTTCGGACTTACCCGTTATAGTAAC
41322587 TCGCACAATTG
65 TCGCACAATTG
* * * *
41322598 CCTTGGGACTTAGCCGGTTATAGTAACT-GCACAATTGCCTTCGGACTT-GCCGTTATAGTAACT
1 CCTTCGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTACCCGTTATAGTAACT
41322661 CGCACAA-TG
66 CGCACAATTG
41322670 CCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CCTTCGGACTTAG-CCGGATATAGTAACTCGCACAAATGCCTTC-GGACTTA-CCC-GTTAT
41322732 CAATCCGAAT
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
72 14 0.12
73 35 0.30
74 46 0.40
75 13 0.11
77 2 0.02
78 5 0.04
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (75 bp):
CCTTCGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTACCCGTTATAGTAACT
CGCACAATTG
Found at i:41338668 original size:27 final size:27
Alignment explanation
Indices: 41338638--41338815 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
41338628 ATATCGAGTC
* * * *
41338638 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
41338665 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41338692 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
41338720 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
41338747 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
41338774 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
41338801 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41338816 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:41338777 original size:82 final size:81
Alignment explanation
Indices: 41338659--41338814 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
41338649 TGCTATATAA
*
41338659 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41338724 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
41338741 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41338805 CACTTAGTGC
65 CACTTAGTGC
41338815 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41344163 original size:46 final size:45
Alignment explanation
Indices: 41344027--41344246 Score: 187
Period size: 47 Copynumber: 4.7 Consensus size: 45
41344017 GGTAAGGTGT
* * * *
41344027 CGATGCCATGTCCTAGACATGGTCTTACACTGGCTCATATTTCAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT--TATCTCGAGC
* *
41344074 CGATGCCATGTCCCCGACATGGTCTTACACTGACTATCATCTCGTAGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCT-T-ATCTCG-AGC
41344122 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTAGGTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTA--TCTCGA-GC
* * * *
41344168 CGATG-CATGTCCCGGACAT-GTCTTACACTAGCCCTTGTCTCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACT-G-GCTTATCTCGA-GC
** * *
41344214 TAATGCCATGTCCCAAACATGGTCCTACACTGG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGG
41344247 TTCTCATAAT
Statistics
Matches: 145, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 60 0.41
47 63 0.43
48 19 0.13
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTTATCTCGAGC
Found at i:41349164 original size:17 final size:18
Alignment explanation
Indices: 41349119--41349164 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
41349109 TTTGACTCGA
*
41349119 TTTTTGATGATTTCTAGG
1 TTTTTGATGATTTCTACG
*
41349137 TTTTTGATGATTTTTACG
1 TTTTTGATGATTTCTACG
41349155 TTTTTG-TGAT
1 TTTTTGATGAT
41349165 CGTTGCTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.15, C:0.04, G:0.20, T:0.61
Consensus pattern (18 bp):
TTTTTGATGATTTCTACG
Found at i:41356455 original size:21 final size:20
Alignment explanation
Indices: 41356431--41356471 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
41356421 ACTTGTTTCA
41356431 CTATCAACAACCATTCAAAAT
1 CTATCAACAACCA-TCAAAAT
* *
41356452 CTATCATCAATCATCAAAAT
1 CTATCAACAACCATCAAAAT
41356472 TCATTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
CTATCAACAACCATCAAAAT
Found at i:41374075 original size:53 final size:53
Alignment explanation
Indices: 41374008--41374114 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 53
41373998 GGTTATGATA
* *
41374008 GGAAGAAAACCATATCATGTAAGA-CTGTAACTAGTGGATTATGGCATCATATG
1 GGAAGAAAACCATATCATGCAAGATCAG-AACTAGTGGATTATGGCATCATATG
* * * * *
41374061 GGAAGAAGATCATATCATGCAAGATCAGAATTGGTGGGTTATGGCATCATATG
1 GGAAGAAAACCATATCATGCAAGATCAGAACTAGTGGATTATGGCATCATATG
41374114 G
1 G
41374115 AGAAATTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
53 44 0.96
54 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (53 bp):
GGAAGAAAACCATATCATGCAAGATCAGAACTAGTGGATTATGGCATCATATG
Found at i:41374303 original size:28 final size:28
Alignment explanation
Indices: 41374263--41374447 Score: 82
Period size: 28 Copynumber: 6.5 Consensus size: 28
41374253 ACTAGATGTA
41374263 AAGGACAA-CCTTTGTGGCAAAACTCTAG
1 AAGGA-AAGCCTTTGTGGCAAAACTCTAG
**
41374291 AAGGAAAGCCTTTGTGGCGAGTA-T-T-G
1 AAGGAAAGCCTTTGTGGC-AAAACTCTAG
* **
41374317 AATGTAAAATATGCCTTTGTGGTGAAACTCTAG
1 AA-G--GAA-A-GCCTTTGTGGCAAAACTCTAG
* * * *
41374350 AAAGACAAGCCTTTGTGAC-AACCTCTATTT
1 AAGGA-AAGCCTTTGTGGCAAAACTCTA--G
*
41374380 AA-GAACGCCTTTGTGG-AAAA-TCTATG
1 AAGGAAAGCCTTTGTGGCAAAACTCTA-G
*
41374406 AAAGGAAAGCCTTTGTGGCAAATCTCT-G
1 -AAGGAAAGCCTTTGTGGCAAAACTCTAG
*
41374434 AAAGGAAAGTCTTT
1 -AAGGAAAGCCTTT
41374448 AGGACGATCT
Statistics
Matches: 119, Mismatches: 20, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
26 4 0.03
27 10 0.08
28 62 0.52
29 18 0.15
30 9 0.08
31 12 0.10
32 1 0.01
33 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (28 bp):
AAGGAAAGCCTTTGTGGCAAAACTCTAG
Found at i:41374403 original size:27 final size:28
Alignment explanation
Indices: 41374386--41374447 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
41374376 ATTTAAGAAC
41374386 GCCTTTGTGGAAAATCTATGAAAGGAAA
1 GCCTTTGTGGAAAATCTATGAAAGGAAA
* *
41374414 GCCTTTGTGGCAAATCTCTGAAAGGAAA
1 GCCTTTGTGGAAAATCTATGAAAGGAAA
*
41374442 GTCTTT
1 GCCTTT
41374448 AGGACGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (28 bp):
GCCTTTGTGGAAAATCTATGAAAGGAAA
Found at i:41374757 original size:23 final size:23
Alignment explanation
Indices: 41374731--41374775 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
41374721 GAGATAATGT
41374731 ATGGACAAGTAGAATAAACTAAA
1 ATGGACAAGTAGAATAAACTAAA
41374754 ATGGACAAGTAGAATAAACTAA
1 ATGGACAAGTAGAATAAACTAA
41374776 GTATCCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (23 bp):
ATGGACAAGTAGAATAAACTAAA
Found at i:41376730 original size:27 final size:28
Alignment explanation
Indices: 41376691--41376834 Score: 113
Period size: 27 Copynumber: 5.2 Consensus size: 28
41376681 TCAGAAAGGC
* *
41376691 ATTCTTTTTAAAGTTCGCAACAAAGGT-T
1 ATTC-TTTCAAAGTTCGCAATAAAGGTCT
* *
41376719 ATTCTTTCAAAGGTCGCCATAAA-GTCT
1 ATTCTTTCAAAGTTCGCAATAAAGGTCT
* * *
41376746 ATTCTTTTAGAGTTTGCCAA-AAAGGTCT
1 ATTCTTTCAAAGTTCG-CAATAAAGGTCT
* *
41376774 ATTCTTTCAGAGTTCATC-ATAAAGG-CT
1 ATTCTTTCAAAGTTC-GCAATAAAGGTCT
*
41376801 ATTCTTTCAAAGTTCATC-ATAAA-GTCT
1 ATTCTTTCAAAGTTC-GCAATAAAGGTCT
41376828 ATTCTTT
1 ATTCTTT
41376835 TAGAGTACGC
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
26 3 0.03
27 65 0.67
28 29 0.30
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (28 bp):
ATTCTTTCAAAGTTCGCAATAAAGGTCT
Found at i:41376848 original size:27 final size:27
Alignment explanation
Indices: 41376718--41376887 Score: 160
Period size: 27 Copynumber: 6.3 Consensus size: 27
41376708 CAACAAAGGT
* *
41376718 TATTCTTTCAAAGGTCGCCATAAAGTC
1 TATTCTTTCAGAGTTCGCCATAAAGTC
* * *
41376745 TATTCTTTTAGAGTTTGCCAAAAAGGTC
1 TATTCTTTCAGAGTTCGCCATAAA-GTC
** *
41376773 TATTCTTTCAGAGTTCATCATAAAGGC
1 TATTCTTTCAGAGTTCGCCATAAAGTC
* **
41376800 TATTCTTTCAAAGTTCATCATAAAGTC
1 TATTCTTTCAGAGTTCGCCATAAAGTC
* * *
41376827 TATTCTTTTAGAGTACGCCATAAAGAC
1 TATTCTTTCAGAGTTCGCCATAAAGTC
* * * * *
41376854 TATTCATTAAGAGTTTGCCATAGAGGC
1 TATTCTTTCAGAGTTCGCCATAAAGTC
41376881 TATTCTT
1 TATTCTT
41376888 AGTTGTCATG
Statistics
Matches: 116, Mismatches: 26, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
27 94 0.81
28 22 0.19
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (27 bp):
TATTCTTTCAGAGTTCGCCATAAAGTC
Found at i:41377268 original size:13 final size:13
Alignment explanation
Indices: 41377250--41377275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41377240 ATATTATAAT
41377250 TATTTTATGTTAA
1 TATTTTATGTTAA
41377263 TATTTTATGTTAA
1 TATTTTATGTTAA
41377276 AAATAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:41378697 original size:40 final size:40
Alignment explanation
Indices: 41378649--41378814 Score: 237
Period size: 40 Copynumber: 4.2 Consensus size: 40
41378639 GGACTAAGAT
* *
41378649 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATCTGTGCGAGTGACTATATCCGGGCTAAGTC
* *
41378689 CCGAAGGCATCTGTGCTAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATCTGTGCGAGTGACTATATCCGGGCTAAGTC
*
41378729 CCGAAGGCATCTGTGCGAGTTACTATATCCGGGCTAAGTC
1 CCGAAGGCATCTGTGCGAGTGACTATATCCGGGCTAAGTC
* *
41378769 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATCTGTGCGAG-TGACTATATCCGGGCTAAGTC
*
41378808 CTGAAGG
1 CCGAAGG
41378815 TACTTGGGTT
Statistics
Matches: 118, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
39 14 0.12
40 103 0.87
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATCTGTGCGAGTGACTATATCCGGGCTAAGTC
Found at i:41381862 original size:61 final size:61
Alignment explanation
Indices: 41381791--41381905 Score: 221
Period size: 61 Copynumber: 1.9 Consensus size: 61
41381781 TTTCTCAAAA
41381791 GTAATACTTTTTCTTTCTTTCATTTTCTTTTATTACATTAATATCCCATAAAATGACAATG
1 GTAATACTTTTTCTTTCTTTCATTTTCTTTTATTACATTAATATCCCATAAAATGACAATG
*
41381852 GTAATGCTTTTTCTTTCTTTCATTTTCTTTTATTACATTAATATCCCATAAAAT
1 GTAATACTTTTTCTTTCTTTCATTTTCTTTTATTACATTAATATCCCATAAAAT
41381906 TACTCAAATA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (61 bp):
GTAATACTTTTTCTTTCTTTCATTTTCTTTTATTACATTAATATCCCATAAAATGACAATG
Found at i:41388283 original size:47 final size:47
Alignment explanation
Indices: 41388212--41388943 Score: 1140
Period size: 47 Copynumber: 15.6 Consensus size: 47
41388202 CCCTTCGGGA
* * * *
41388212 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTT-GGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
*
41388259 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388306 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388353 CTTATCACATATATACACTTTCACATTCAT--C-T----C-TTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388392 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41388439 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41388486 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41388535 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41388582 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388631 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41388678 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388727 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
41388774 CTTATCACATATATACACTTTCACATTCATCACATCGGCTGTTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41388821 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41388870 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41388917 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
41388944 TATTCAAATA
Statistics
Matches: 633, Mismatches: 35, Indels: 34
0.90 0.05 0.05
Matches are distributed among these distances:
39 36 0.06
40 1 0.00
41 1 0.00
42 1 0.00
44 1 0.00
45 1 0.00
46 3 0.00
47 415 0.66
49 174 0.27
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41388516 original size:96 final size:94
Alignment explanation
Indices: 41388386--41388943 Score: 909
Period size: 96 Copynumber: 5.9 Consensus size: 94
41388376 CATTCATCTC
41388386 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
*
41388451 ATACACTTTCACATTCATCACATCAGCCA
66 ATACACTTTCACATTCATCACATCGGCCA
* * *
41388480 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGACCTTATCACAT
1 TTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
41388545 ATATACACTTTCACATTCATCACATCGGCTA
64 ATATACACTTTCACATTCATCACATCGGCCA
* * *
41388576 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGTCTTATCACAT
1 TTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
41388641 ATATACACTTTCACATTCATCACATCGGCCA
64 ATATACACTTTCACATTCATCACATCGGCCA
* *
41388672 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 TTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
41388737 ATATACACTTTCACATTCATCACATCGGCCA
64 ATATACACTTTCACATTCATCACATCGGCCA
**
41388768 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTGTTAGGCCTTATCACATAT
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--AT
*
41388833 ATATACACTTTCACATTCATCACATTGGCCA
64 ATATACACTTTCACATTCATCACATCGGCCA
* *
41388864 TTCGGCCTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATAT
1 TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
41388929 ATACACTTTCACATT
66 ATACACTTTCACATT
41388944 TATTCAAATA
Statistics
Matches: 442, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 76 0.17
96 366 0.83
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (94 bp):
TTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAT
ATACACTTTCACATTCATCACATCGGCCA
Found at i:41388561 original size:143 final size:142
Alignment explanation
Indices: 41388386--41388943 Score: 913
Period size: 143 Copynumber: 3.9 Consensus size: 142
41388376 CATTCATCTC
41388386 TTAGGCCTTATCAC-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
1 TTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
41388450 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATATACACTTTCACATT
66 TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCAC--ATATATACACTTTCACATT
*
41388515 CATCACATTGGCCA
129 CATCACATCGGCCA
* * *
41388529 TTCGACCTTATCAC-ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATA
1 TTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--A
** * *
41388593 TATATACACTTTCACATTCATCACATTGGCCATTCGGTCTTATCACATATATACACTTTCACATT
64 TATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATT
41388658 CATCACATCGGCCA
129 CATCACATCGGCCA
* *
41388672 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 TTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
*
41388737 ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTC
65 ATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATTC
**
41388802 ATCACATCGGCTG
130 ATCACATCGGCCA
* *
41388815 TTAGGCCTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACAT
1 TTAGGCCTTATCACA-ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
41388880 ATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATT
65 ATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATT
41388944 TATTCAAATA
Statistics
Matches: 392, Mismatches: 19, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
143 305 0.78
145 87 0.22
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (142 bp):
TTAGGCCTTATCACAATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA
TATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACACTTTCACATTCA
TCACATCGGCCA
Found at i:41395139 original size:21 final size:22
Alignment explanation
Indices: 41395095--41395143 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
41395085 TGGTGAATGT
* *
41395095 ATGAGATTTTGAATGATTGTTG
1 ATGAGATTTTGAAAGATTGATG
*
41395117 ATGA-ATTTTGAAAGCTTGATG
1 ATGAGATTTTGAAAGATTGATG
41395138 AT-AGAT
1 ATGAGAT
41395144 ATTAAAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.24, T:0.41
Consensus pattern (22 bp):
ATGAGATTTTGAAAGATTGATG
Found at i:41395761 original size:43 final size:43
Alignment explanation
Indices: 41395713--41395871 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
41395703 GGTTGCTGAG
*
41395713 TTGTGATTACATGTAAGACCATGCCTGGGACATTGGCATTGTA
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
* * *
41395756 TTGTGAATACGTGTAAGACCATGTCTGGGACATTGGCATCTTTA
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT-TGTA
* * * * * * * *
41395800 TT-CGATTTCATGTAAAACCCTGTCTAGGATAGTGGCATCG-A
1 TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
* *
41395841 TATGTGATAACATGTAAGACCATATCTGGGA
1 T-TGTGATTACATGTAAGACCATGTCTGGGA
41395872 TATGGCGTAA
Statistics
Matches: 91, Mismatches: 22, Indels: 6
0.76 0.18 0.05
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 83 0.91
44 5 0.05
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
TTGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
Found at i:41397229 original size:17 final size:17
Alignment explanation
Indices: 41397207--41397249 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
41397197 TTTACCCGTG
41397207 TGGGGCCCACAAGCCCA
1 TGGGGCCCACAAGCCCA
*
41397224 TGGGGCCCACAAGCCCG
1 TGGGGCCCACAAGCCCA
41397241 TGGGGCCCA
1 TGGGGCCCA
41397250 TTCCGGCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.40, G:0.35, T:0.07
Consensus pattern (17 bp):
TGGGGCCCACAAGCCCA
Found at i:41400932 original size:8 final size:8
Alignment explanation
Indices: 41400919--41401085 Score: 50
Period size: 8 Copynumber: 21.5 Consensus size: 8
41400909 TAAAATGTAA
41400919 AATAATAT
1 AATAATAT
41400927 AATAATAT
1 AATAATAT
*
41400935 AAAAATAT
1 AATAATAT
41400943 -ATAA-AT
1 AATAATAT
* *
41400949 -ATTATGT
1 AATAATAT
* *
41400956 GATAA-AA
1 AATAATAT
41400963 ACATAATAT
1 A-ATAATAT
41400972 AATAA-AT
1 AATAATAT
*
41400979 AATAA-GT
1 AATAATAT
*
41400986 AATGATAT
1 AATAATAT
* ** *
41400994 -GTGTTAA
1 AATAATAT
41401001 AAT-ATAT
1 AATAATAT
*
41401008 ATTAATAT
1 AATAATAT
* *
41401016 GATAATAG
1 AATAATAT
*
41401024 AAAAATAT
1 AATAATAT
41401032 GAAGTAATAT
1 -AA-TAATAT
41401042 AAT-ATAAT
1 AATAAT-AT
41401050 AA-AATAT
1 AATAATAT
41401057 AAGTAA-AT
1 AA-TAATAT
* *
41401065 AATTATAA
1 AATAATAT
41401073 AATATATAT
1 AATA-ATAT
41401082 AATA
1 AATA
41401086 CGTATATTCA
Statistics
Matches: 114, Mismatches: 30, Indels: 29
0.66 0.17 0.17
Matches are distributed among these distances:
6 5 0.04
7 32 0.28
8 57 0.50
9 15 0.13
10 5 0.04
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.34
Consensus pattern (8 bp):
AATAATAT
Found at i:41403218 original size:206 final size:206
Alignment explanation
Indices: 41402864--41403412 Score: 798
Period size: 206 Copynumber: 2.7 Consensus size: 206
41402854 CTTCTTTGAT
* ** *
41402864 TTGTTCTCTAACAATACGGAGATGCCAAATCATCTTAGATTTGCTTT-AGCGTAAGCACGCGAAA
1 TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTG-TTTCAGCGTAAGCACGTGAAA
* * * *
41402928 ACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACAATGATACCAAACCATCTTGGATCT
65 GCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCT
* * ** * *
41402993 GCTTCAGTTTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGC-CTTCCGTCGAATATGGAGAT
130 GCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTC-TCCGTCGAATATGGAGAC
41403057 GCCAAACTTCGAC
194 GCCAAACTTCGAC
*
41403070 TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGACTTGTTTCAGCGTAAGCACGTGAAAG
1 TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGTTTCAGCGTAAGCACGTGAAAG
* * * *
41403135 CTAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACATAAGGATGCCAAATCATCTTGGATCT
66 CCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCT
*
41403199 GCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCTGTCGAATATGGAGACG
130 GCTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATATGGAGACG
* *
41403264 CCAAACTTTGAT
195 CCAAACTTCGAC
* *
41403276 TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGAAAG
1 TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGTTTCAGCGTAAGCACGTGAAAG
* * *
41403341 CCAAATTAGCTATGTCTTTGATTTGTTCTTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTT
66 CCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATC-T
41403406 GCTTCAG
130 GCTTCAG
41403413 CCCGATTTGC
Statistics
Matches: 306, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
205 4 0.01
206 292 0.95
207 10 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (206 bp):
TTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGTTTCAGCGTAAGCACGTGAAAG
CCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGGATCTG
CTTCAGTATAAACATCTGAAGGCCAGATCTGCTATGTATCTGCTCTCCGTCGAATATGGAGACGC
CAAACTTCGAC
Found at i:41404304 original size:1 final size:1
Alignment explanation
Indices: 41404300--41404375 Score: 116
Period size: 1 Copynumber: 76.0 Consensus size: 1
41404290 TCCTCTTCTC
* * * *
41404300 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTATTTTCTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41404365 TTTTTTTTTTT
1 TTTTTTTTTTT
41404376 GATTTTCGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.01, C:0.01, G:0.03, T:0.95
Consensus pattern (1 bp):
T
Found at i:41415327 original size:21 final size:22
Alignment explanation
Indices: 41415294--41415337 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
41415284 ATAAGATAAT
*
41415294 AAACATATTTAA-TAATACATGA
1 AAACATATGTAATTAATA-ATGA
41415316 AAACATA-GTAATTAATAATGA
1 AAACATATGTAATTAATAATGA
41415337 A
1 A
41415338 TTTTGAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAACATATGTAATTAATAATGA
Found at i:41415682 original size:25 final size:22
Alignment explanation
Indices: 41415641--41415698 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
41415631 ATGGTAATAG
41415641 AAAAATATGAAGTAATATAATATA
1 AAAAATAT-AAGTAATA-AATATA
*
41415665 ATAAAATATAAGTAAATAATTATA
1 A-AAAATATAAGT-AATAAATATA
*
41415689 AAATATATAA
1 AAAAATATAA
41415699 TACGTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 8 0.27
24 11 0.37
25 11 0.37
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAATATAAGTAATAAATATA
Found at i:41415696 original size:23 final size:22
Alignment explanation
Indices: 41415635--41415698 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 22
41415625 ATTAATATGG
*
41415635 TAATAGAAAAATATGAAGTAATA
1 TAATATAAAAATAT-AAGTAATA
41415658 TAATATAATAAAATATAAGTAA-A
1 TAATAT-A-AAAATATAAGTAATA
41415681 TAATTATAAAATATATAA
1 TAA-TATAAAA-ATATAA
41415699 TACGTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 3 0.08
23 16 0.44
24 10 0.28
25 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (22 bp):
TAATATAAAAATATAAGTAATA
Found at i:41420949 original size:49 final size:49
Alignment explanation
Indices: 41420875--41420975 Score: 184
Period size: 49 Copynumber: 2.1 Consensus size: 49
41420865 CCCGGAGAAA
*
41420875 GCAAAGTTTTGTTTAGAGAATACCATCAGAGTGTTTAATGAATTGTCGT
1 GCAAAGTTTTGTTTAGAGAACACCATCAGAGTGTTTAATGAATTGTCGT
*
41420924 GCAAAGTTTTGTTTAGAGAACACCATCAGAGTGTTTGATGAATTGTCGT
1 GCAAAGTTTTGTTTAGAGAACACCATCAGAGTGTTTAATGAATTGTCGT
41420973 GCA
1 GCA
41420976 CGCCTGAGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.35
Consensus pattern (49 bp):
GCAAAGTTTTGTTTAGAGAACACCATCAGAGTGTTTAATGAATTGTCGT
Found at i:41427374 original size:27 final size:27
Alignment explanation
Indices: 41427351--41427536 Score: 230
Period size: 27 Copynumber: 6.9 Consensus size: 27
41427341 ATTGATTTGT
* *
41427351 AGAATTACCATTTTACCCTCGATTTAT
1 AGAATTACCGTTTTACCCTCGATTTAC
*
41427378 AGAATTACCGTTTCACCCTCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* * *
41427405 AAAATTACCGTTTCACCCTCGATTTAT
1 AGAATTACCGTTTTACCCTCGATTTAC
* *
41427432 AGAATTACCATTTCACCCTCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
*
41427459 AGAATTACCGTTTTACCATCGATTTAC
1 AGAATTACCGTTTTACCCTCGATTTAC
* **
41427486 AAAATTACTATTTTACCCTC-AGTTTAC
1 AGAATTACCGTTTTACCCTCGA-TTTAC
* *
41427513 AAAATTACCGTTTTACCCTTGATT
1 AGAATTACCGTTTTACCCTCGATT
41427537 GTGAAATTAC
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (27 bp):
AGAATTACCGTTTTACCCTCGATTTAC
Found at i:41427411 original size:54 final size:54
Alignment explanation
Indices: 41427353--41427536 Score: 262
Period size: 54 Copynumber: 3.4 Consensus size: 54
41427343 TGATTTGTAG
* *
41427353 AATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAA
* *
41427407 AATTACCGTTTCACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAA
* * * * *
41427461 AATTACCGTTTTACCATCGATTTACAAAATTACTATTTTACCCTC-AGTTTACAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGA-TTTACAA
*
41427515 AATTACCGTTTTACCCTTGATT
1 AATTACCGTTTTACCCTCGATT
41427537 GTGAAATTAC
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 115 0.99
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAA
Found at i:41427504 original size:81 final size:81
Alignment explanation
Indices: 41427344--41427536 Score: 262
Period size: 81 Copynumber: 2.4 Consensus size: 81
41427334 AAATGCCATT
* * *
41427344 GATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCGTTTCACCCTCGATTTACAAAA
1 GATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCATCGATTTACAAAA
*
41427409 TTACCGTTTCACCCTC
66 TTACCATTTCACCCTC
* *
41427425 GATTTATAGAATTACCATTTCACCCTCGATTTACAGAATTACCGTTTTACCATCGATTTACAAAA
1 GATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCATCGATTTACAAAA
* *
41427490 TTACTATTTTACCCTC
66 TTACCATTTCACCCTC
* * * *
41427506 -AGTTTACAAAATTACCGTTTTACCCTTGATT
1 GA-TTTATAGAATTACCATTTTACCCTCGATT
41427537 GTGAAATTAC
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
80 1 0.01
81 97 0.99
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (81 bp):
GATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTCACCATCGATTTACAAAA
TTACCATTTCACCCTC
Found at i:41427595 original size:27 final size:27
Alignment explanation
Indices: 41427564--41427637 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
41427554 CCCCTGTAGG
*
41427564 ATAAAATTACCAATATACTCC-TTGTTT
1 ATAAAATTACCAAAATAC-CCTTTGTTT
* *
41427591 GTAAAATTACTAAAATACCCTTTGTTT
1 ATAAAATTACCAAAATACCCTTTGTTT
*
41427618 ATAAAATTACCGAAATACCC
1 ATAAAATTACCAAAATACCC
41427638 CTGTAGGGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (27 bp):
ATAAAATTACCAAAATACCCTTTGTTT
Found at i:41427622 original size:54 final size:52
Alignment explanation
Indices: 41427507--41427637 Score: 129
Period size: 54 Copynumber: 2.5 Consensus size: 52
41427497 TTTACCCTCA
* ** * * *
41427507 GTTTACAAAATTACCGTTTTACCCTTGATTGTGAAATTACTGAAATACCCCT
1 GTTTATAAAATTACCAATATACCCTTGATTGTAAAATTACTAAAATACCCCT
** * *
41427559 GTAGGATAAAATTACCAATATACTCCTTGTTTGTAAAATTACTAAAATACCCTTT
1 GT-TTATAAAATTACCAATATAC-CCTTGATTGTAAAATTACTAAAATACCC-CT
41427614 GTTTATAAAATTACCGAA-ATACCC
1 GTTTATAAAATTACC-AATATACCC
41427638 CTGTAGGGTA
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
52 2 0.03
53 16 0.25
54 40 0.63
55 5 0.08
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (52 bp):
GTTTATAAAATTACCAATATACCCTTGATTGTAAAATTACTAAAATACCCCT
Found at i:41427652 original size:27 final size:27
Alignment explanation
Indices: 41427622--41427842 Score: 302
Period size: 27 Copynumber: 8.3 Consensus size: 27
41427612 TTGTTTATAA
41427622 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41427649 AATTATCGTAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
41427676 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41427703 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
41427730 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
41427757 AATTACTGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
41427784 AATT-CTAAAATACCCTTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
41427810 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
41427836 AATTACC
1 AATTACC
41427843 ATTTTGTCCC
Statistics
Matches: 173, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 39 0.23
27 134 0.77
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:41427653 original size:54 final size:54
Alignment explanation
Indices: 41427541--41427842 Score: 294
Period size: 54 Copynumber: 5.6 Consensus size: 54
41427531 TTGATTGTGA
* * * ** *
41427541 AATTACTGAAATACCCCTGTAGGATAAAATTACC-AATATACTCCTTGT-TTGTAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAA-ATAC-CCCTGTAGGGTAG
* * *** *
41427595 AATTACTAAAATACCCTTTGT-TTATAAAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCC-CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
*
41427649 AATTA-TCGTAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
*
41427703 AATTA-TCGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* ** * *
41427757 AATTACTGGAATACCCCTGTAGGGTAGAATT-CTAAAATACCCTTGTAGGGTGG
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * * *
41427810 AATTACCGAGATA-CCTTGTGGGGTAAAATTACC
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACC
41427843 ATTTTGTCCC
Statistics
Matches: 213, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
52 14 0.07
53 39 0.18
54 154 0.72
55 6 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (54 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:41427680 original size:81 final size:81
Alignment explanation
Indices: 41427540--41427816 Score: 281
Period size: 81 Copynumber: 3.4 Consensus size: 81
41427530 CTTGATTGTG
* * * * * ** * *
41427540 AAATTACTGAAATACCCCTGTAGGATAAAATTACCAATATACTCCTTGT-TTGTAAAATTACTAA
1 AAATTACCGAAATACCCCTGTAGGGTAGAATTACCAAAATAC-CCCTGTAGGGTAGAATTACTGA
* **
41427604 AATACCCTTTGT-TTATA
65 AATACCC-CTGTAGGATA
* ** *
41427621 AAATTACCGAAATACCCCTGTAGGGTAGAATTATCGTAATACCCCTGTAGGGTAGAATTACCGAA
1 AAATTACCGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTGAA
*
41427686 ATACCCCTGTAGGGTA
66 ATACCCCTGTAGGATA
* * *
41427702 GAATTATCGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTGGA
1 AAATTACCGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTGAA
*
41427767 ATACCCCTGTAGGGTA
66 ATACCCCTGTAGGATA
* ** * *
41427783 GAATT-CTAAAATACCCTTGTAGGGTGGAATTACC
1 AAATTACCGAAATACCCCTGTAGGGTAGAATTACC
41427817 GAGATACCTT
Statistics
Matches: 165, Mismatches: 29, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
80 32 0.19
81 133 0.81
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (81 bp):
AAATTACCGAAATACCCCTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACTGAA
ATACCCCTGTAGGATA
Found at i:41428320 original size:22 final size:21
Alignment explanation
Indices: 41428271--41428339 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
41428261 AAGCCTTCTA
* *
41428271 ATTATGGCTTTGTGTCAACCT
1 ATTATGGCTCTGTGCCAACCT
*
41428292 ACATATGGCTCTGTGCCAACCT
1 A-TTATGGCTCTGTGCCAACCT
*
41428314 GATTATGGCTGTGTGCCAACCGT
1 -ATTATGGCTCTGTGCCAACC-T
41428337 ATT
1 ATT
41428340 TGCCTAAGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 37 0.93
23 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (21 bp):
ATTATGGCTCTGTGCCAACCT
Done.