Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 82 of 89
Found at i:19621475 original size:20 final size:20
Alignment explanation
Indices: 19621447--19621503 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
19621437 TAATACTGAC
19621447 CCTTT-AGTATCGATACCAA
1 CCTTTGAGTATCGATACCAA
*
19621466 CCTTTGAGTAGCGATACCAA
1 CCTTTGAGTATCGATACCAA
19621486 CCTCTTG-GTATCGATACC
1 CCT-TTGAGTATCGATACC
19621504 GACTGACTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 26 0.76
21 3 0.09
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (20 bp):
CCTTTGAGTATCGATACCAA
Found at i:19637812 original size:31 final size:30
Alignment explanation
Indices: 19637755--19637831 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
19637745 GTTAGTCAAG
* *
19637755 TTTGCATTCAAATAATGCAAAGTATGTCATA
1 TTTGCATTC-AATAAAGCAAAGTATGTCAGA
* *
19637786 TTTGCATTCAGATAAAGTACAA-TATGTCAGG
1 TTTGCATTCA-ATAAAGCA-AAGTATGTCAGA
*
19637817 TTTACATTCAATAAA
1 TTTGCATTCAATAAA
19637832 TGCACAGGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 6 0.15
31 31 0.79
32 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (30 bp):
TTTGCATTCAATAAAGCAAAGTATGTCAGA
Found at i:19654115 original size:15 final size:15
Alignment explanation
Indices: 19654095--19654126 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19654085 TTCAATGTTG
*
19654095 TATCAAAATTTCCTT
1 TATCAAAACTTCCTT
19654110 TATCAAAACTTCCTT
1 TATCAAAACTTCCTT
19654125 TA
1 TA
19654127 CGAACCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.44
Consensus pattern (15 bp):
TATCAAAACTTCCTT
Found at i:19658870 original size:50 final size:50
Alignment explanation
Indices: 19658795--19658894 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
19658785 CATAGGAAAT
19658795 GATATACCTAGTTTATAGTCTGTTAAGACTTGGTTAAGTAGTTGTTTTTC
1 GATATACCTAGTTTATAGTCTGTTAAGACTTGGTTAAGTAGTTGTTTTTC
19658845 GATATACCTAGTTTATAGTCTGTTAAGACTTGGTTAAGTAGTTGTTTTTC
1 GATATACCTAGTTTATAGTCTGTTAAGACTTGGTTAAGTAGTTGTTTTTC
19658895 TATGAAATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (50 bp):
GATATACCTAGTTTATAGTCTGTTAAGACTTGGTTAAGTAGTTGTTTTTC
Found at i:19662835 original size:247 final size:247
Alignment explanation
Indices: 19662399--19662892 Score: 988
Period size: 247 Copynumber: 2.0 Consensus size: 247
19662389 TTTGTAAATG
19662399 TTATGTGACATCTTTGACTCGTATTCGGGGATGGATATGGGAAATGAGTGTTACATAAACCATAA
1 TTATGTGACATCTTTGACTCGTATTCGGGGATGGATATGGGAAATGAGTGTTACATAAACCATAA
19662464 CGTGTCGAAAAAGGGAGCCTTCTTGTTTGTAAAACTTTTTTATTGCTTTATAATATTTTTATCAT
66 CGTGTCGAAAAAGGGAGCCTTCTTGTTTGTAAAACTTTTTTATTGCTTTATAATATTTTTATCAT
19662529 GTGGGTTTTAGAACATTGAGAACAATTTTTGGTTTAAGTGTGGGGGAGATGAATGAATTTTGTTG
131 GTGGGTTTTAGAACATTGAGAACAATTTTTGGTTTAAGTGTGGGGGAGATGAATGAATTTTGTTG
19662594 CTTACTTGTTGAACAGAGGAATGTAAAATATTAATTTAATTCTTGTTGATGA
196 CTTACTTGTTGAACAGAGGAATGTAAAATATTAATTTAATTCTTGTTGATGA
19662646 TTATGTGACATCTTTGACTCGTATTCGGGGATGGATATGGGAAATGAGTGTTACATAAACCATAA
1 TTATGTGACATCTTTGACTCGTATTCGGGGATGGATATGGGAAATGAGTGTTACATAAACCATAA
19662711 CGTGTCGAAAAAGGGAGCCTTCTTGTTTGTAAAACTTTTTTATTGCTTTATAATATTTTTATCAT
66 CGTGTCGAAAAAGGGAGCCTTCTTGTTTGTAAAACTTTTTTATTGCTTTATAATATTTTTATCAT
19662776 GTGGGTTTTAGAACATTGAGAACAATTTTTGGTTTAAGTGTGGGGGAGATGAATGAATTTTGTTG
131 GTGGGTTTTAGAACATTGAGAACAATTTTTGGTTTAAGTGTGGGGGAGATGAATGAATTTTGTTG
19662841 CTTACTTGTTGAACAGAGGAATGTAAAATATTAATTTAATTCTTGTTGATGA
196 CTTACTTGTTGAACAGAGGAATGTAAAATATTAATTTAATTCTTGTTGATGA
19662893 CTTAGAAATA
Statistics
Matches: 247, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 247 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (247 bp):
TTATGTGACATCTTTGACTCGTATTCGGGGATGGATATGGGAAATGAGTGTTACATAAACCATAA
CGTGTCGAAAAAGGGAGCCTTCTTGTTTGTAAAACTTTTTTATTGCTTTATAATATTTTTATCAT
GTGGGTTTTAGAACATTGAGAACAATTTTTGGTTTAAGTGTGGGGGAGATGAATGAATTTTGTTG
CTTACTTGTTGAACAGAGGAATGTAAAATATTAATTTAATTCTTGTTGATGA
Found at i:19665608 original size:82 final size:81
Alignment explanation
Indices: 19665433--19665836 Score: 512
Period size: 81 Copynumber: 5.0 Consensus size: 81
19665423 CCTTTCCTCT
* * * * * *
19665433 AAAGGAATTTAACCTTTCGTCTAACTTA-TATTATTAGCACATTTCTGCCAAATACACAGTTAGG
1 AAAGGCATTTAACCTTTCATCTAAC-TAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGG
19665497 CATTTAATCTTTTACCC
65 CATTTAATCTTTTACCC
* * *
19665514 AAAGGCATTTAACCTTTCATCTAGCTAGCATGATTGGCACATTTCTGCTAAATGCACAATTAGGG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTA-GG
*
19665579 AATTTAATCTTTTACCC
65 CATTTAATCTTTTACCC
* *
19665596 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCATC-TTTCTACAAAATGCACAGTT-GG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCA-CATTTCTGCCAAATGCACAGTTAGG
* *
19665659 CATGTAATCTTTTACTC
65 CATTTAATCTTTTACCC
* * * *
19665676 AAAGACATTTAACATTTTATCTAACTAACATGATTGGCATC-TTTCTGCCAAATGCACAGTTAGG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCA-CATTTCTGCCAAATGCACAGTTAGG
* *
19665740 CATTTAATATTTTACTC
65 CATTTAATCTTTTACCC
* *
19665757 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCA-ACTTTCTGCCCAATGTACAGTTAGG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACA-TTTCTGCCAAATGCACAGTTAGG
*
19665821 TATTTAAATCTTTTAC
65 CATTT-AATCTTTTAC
19665837 TCATAATATC
Statistics
Matches: 283, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
80 73 0.26
81 127 0.45
82 82 0.29
83 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (81 bp):
AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGC
ATTTAATCTTTTACCC
Found at i:19666228 original size:20 final size:21
Alignment explanation
Indices: 19666203--19666256 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
19666193 TGGCTCAATA
19666203 GTATCGATAGC-C-ATACTATG
1 GTATCGATA-CTCTATACTATG
19666223 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCTATACTATG
*
19666245 GTACCGATACTC
1 GTATCGATACTC
19666257 CCTTTCAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 3 0.10
22 17 0.57
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCTATACTATG
Found at i:19670619 original size:54 final size:53
Alignment explanation
Indices: 19670561--19670881 Score: 358
Period size: 54 Copynumber: 5.9 Consensus size: 53
19670551 CTATACAGAA
* *
19670561 ATTCATCTACTCATGATGAATTCTGT-GAGTTTCACACATAGTGCCTGTACGGTG
1 ATTCATCAACTCATGATGAATT-TGTGGA-TTTCACACATAGTGCATGTACGGTG
* * *
19670615 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACAAAGTGCTTGTACGATG
1 ATTCATCAACTCATGATGAATTT-GTGGATTT-CACACATAGTGCATGTACGGTG
* * * *
19670670 ATTCATCAACCCATGATGAATTCTGTGGATTACACATATAGTGCATGTACGGTC
1 ATTCATCAACTCATGATGAATT-TGTGGATTTCACACATAGTGCATGTACGGTG
* * * * *
19670724 ATTCATCAACTCATAATGAATTTCGTGGATTACACATATAGTGCAGGAACGGTG
1 ATTCATCAACTCATGATGAATTT-GTGGATTTCACACATAGTGCATGTACGGTG
* * *
19670778 ATTCATCAACTCATTATGAATTATGTGGATTTTCACACAAAGTGTC-TGTACGATG
1 ATTCATCAACTCATGATGAATT-TGTGGA-TTTCACACATAGTG-CATGTACGGTG
* * *
19670833 ATTCATCAACTCATGATGAATTTCGTGGATTGCACATATAGTGTATGTA
1 ATTCATCAACTCATGATGAATTT-GTGGATTTCACACATAGTGCATGTA
19670882 GTACACATAA
Statistics
Matches: 229, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.01
54 132 0.58
55 93 0.41
56 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (53 bp):
ATTCATCAACTCATGATGAATTTGTGGATTTCACACATAGTGCATGTACGGTG
Found at i:19670831 original size:163 final size:163
Alignment explanation
Indices: 19670561--19670881 Score: 454
Period size: 163 Copynumber: 2.0 Consensus size: 163
19670551 CTATACAGAA
* * * ** *
19670561 ATTCATCTACTCATGATGAATTCTGTGAGTTTCACACATAGTGCCTGTACGGTGATTCATCAACT
1 ATTCATCAACTCATAATGAATTCTGTGAGTTACACACATAGTGCAGGAACGGTGATTCATCAACT
19670626 CATGATGAATTTCGTGGATTTGCACACAAAGTGCTTGTACGATGATTCATCAACCCATGATGAA-
66 CATGATGAATTTCGTGGATTTGCACACAAAGTGCTTGTACGATGATTCATCAACCCATGATGAAT
19670690 TTCTGTGGATTACACATATAGTGCATGTACGGTC
131 TTC-GTGGATTACACATATAGTGCATGTACGGTC
*
19670724 ATTCATCAACTCATAATGAATT-TCGTG-GATTACACATATAGTGCAGGAACGGTGATTCATCAA
1 ATTCATCAACTCATAATGAATTCT-GTGAG-TTACACACATAGTGCAGGAACGGTGATTCATCAA
* * *
19670787 CTCATTATGAATTAT-GTGGATTTTCACACAAAGTG-TCTGTACGATGATTCATCAACTCATGAT
64 CTCATGATGAATT-TCGTGGATTTGCACACAAAGTGCT-TGTACGATGATTCATCAACCCATGAT
* *
19670850 GAATTTCGTGGATTGCACATATAGTGTATGTA
127 GAATTTCGTGGATTACACATATAGTGCATGTA
19670882 GTACACATAA
Statistics
Matches: 141, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
162 3 0.02
163 134 0.95
164 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (163 bp):
ATTCATCAACTCATAATGAATTCTGTGAGTTACACACATAGTGCAGGAACGGTGATTCATCAACT
CATGATGAATTTCGTGGATTTGCACACAAAGTGCTTGTACGATGATTCATCAACCCATGATGAAT
TTCGTGGATTACACATATAGTGCATGTACGGTC
Found at i:19670869 original size:109 final size:107
Alignment explanation
Indices: 19670561--19670875 Score: 416
Period size: 109 Copynumber: 2.9 Consensus size: 107
19670551 CTATACAGAA
*
19670561 ATTCATCTACTCATGATGAATTCTGT-GAGTTTCACACATAGTGCCTGTACGGTGATTCATCAAC
1 ATTCATCAACTCATGATGAATTCTGTGGA-TTTCACACATAGTG-CTGTACGGTGATTCATCAAC
* * ** *
19670625 TCATGATGAATTTCGTGGATTTGCACACAAAGTGCTTGTACGATG
64 TCATGATGAATTTCGTGGA-TTGCACATATAGTGCAGGAACGATG
* * * *
19670670 ATTCATCAACCCATGATGAATTCTGTGGATTACACATATAGTGCATGTACGGTCATTCATCAACT
1 ATTCATCAACTCATGATGAATTCTGTGGATTTCACACATAGTGC-TGTACGGTGATTCATCAACT
* * *
19670735 CATAATGAATTTCGTGGATTACACATATAGTGCAGGAACGGTG
65 CATGATGAATTTCGTGGATTGCACATATAGTGCAGGAACGATG
* * * *
19670778 ATTCATCAACTCATTATGAATTATGTGGATTTTCACACAAAGTGTCTGTACGATGATTCATCAAC
1 ATTCATCAACTCATGATGAATTCTGTGGA-TTTCACACATAGTG-CTGTACGGTGATTCATCAAC
19670843 TCATGATGAATTTCGTGGATTGCACATATAGTG
64 TCATGATGAATTTCGTGGATTGCACATATAGTG
19670876 TATGTAGTAC
Statistics
Matches: 179, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
108 45 0.25
109 131 0.73
110 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (107 bp):
ATTCATCAACTCATGATGAATTCTGTGGATTTCACACATAGTGCTGTACGGTGATTCATCAACTC
ATGATGAATTTCGTGGATTGCACATATAGTGCAGGAACGATG
Found at i:19671505 original size:242 final size:243
Alignment explanation
Indices: 19671080--19671566 Score: 967
Period size: 242 Copynumber: 2.0 Consensus size: 243
19671070 TCAAGCATCC
19671080 ATAAAAACATGTATCATACCCAAAGTTAGAATATTTCCTAACCATTATACTTAAACAATACTCAA
1 ATAAAAACATGTATCATACCCAAAGTTAGAATATTTCCTAACCATTATACTTAAACAATACTCAA
19671145 AAGAACATATCATTAACTTTCTATACTTTAATCAGTCTATTTTAACATTTCTGGCTCCATAGTAT
66 AAGAACATATCATTAACTTTCTATACTTTAATCAGTCTATTTTAACATTTCTGGCTCCATAGTAT
19671210 CGATACTACTACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCGGGTATCGAT
131 CGATACTACTACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCGGGTATCGAT
19671275 ACC-AAAATAGGTTCAATGTTGCCTAGTATTGATACCCTTACCATGGT
196 ACCAAAAATAGGTTCAATGTTGCCTAGTATTGATACCCTTACCATGGT
19671322 ATAAAAACATGTATCATACCCAAAGTTAGAATATTTCCTAACCATTATACTTAAACAATACTCAA
1 ATAAAAACATGTATCATACCCAAAGTTAGAATATTTCCTAACCATTATACTTAAACAATACTCAA
19671387 AAGAACATATCATTAACTTTCTATACTTTAATCAGTCTATTTTAACATTTCTGGCTCCATAGTAT
66 AAGAACATATCATTAACTTTCTATACTTTAATCAGTCTATTTTAACATTTCTGGCTCCATAGTAT
19671452 CGATACTACTACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCGGGTATCGAT
131 CGATACTACTACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCGGGTATCGAT
19671517 ACCAAAAATAGGTTCAATGTTGCCTAGTATTGATACCCTTACCATGGT
196 ACCAAAAATAGGTTCAATGTTGCCTAGTATTGATACCCTTACCATGGT
19671565 AT
1 AT
19671567 CAATACTACC
Statistics
Matches: 244, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
242 198 0.81
243 46 0.19
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (243 bp):
ATAAAAACATGTATCATACCCAAAGTTAGAATATTTCCTAACCATTATACTTAAACAATACTCAA
AAGAACATATCATTAACTTTCTATACTTTAATCAGTCTATTTTAACATTTCTGGCTCCATAGTAT
CGATACTACTACCCTAGTACCGATACTTCTATACTATGGTACCGATACCCCCTTCGGGTATCGAT
ACCAAAAATAGGTTCAATGTTGCCTAGTATTGATACCCTTACCATGGT
Found at i:19677739 original size:54 final size:54
Alignment explanation
Indices: 19677681--19677973 Score: 388
Period size: 54 Copynumber: 5.4 Consensus size: 54
19677671 TATGGAAATG
* *
19677681 CATCAACTCATGATGAATTCCGTGGGTTTCACACACAGTGCCTGTACGGTGATT
1 CATCAACTCATGATGAATTCCGTGGATTTCACACAAAGTGCCTGTACGGTGATT
* *
19677735 CATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGCTTGTACGGTGATT
1 CATCAACTCATGATGAATTCCGTGGATTT-CACACAAAGTGCCTGTACGGTGATT
* * * * * *
19677790 CATCAACCCATGATGAATTCTGTGGATTGCACATATAGTGCCTGTACGGTAATT
1 CATCAACTCATGATGAATTCCGTGGATTTCACACAAAGTGCCTGTACGGTGATT
* * * * * *
19677844 CATCAACTCATGATGAATTCCGTGGATTGCACATATAGTACATGTACGGTAATT
1 CATCAACTCATGATGAATTCCGTGGATTTCACACAAAGTGCCTGTACGGTGATT
* * * *
19677898 CATCAACTCATGATGAATTCTGTGTATTTGCACACAAAGTGTCTGTATGGTGATT
1 CATCAACTCATGATGAATTCCGTGGATTT-CACACAAAGTGCCTGTACGGTGATT
19677953 CATCAACTCATGATGAATTCC
1 CATCAACTCATGATGAATTCC
19677974 ATTGATTGCA
Statistics
Matches: 212, Mismatches: 25, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
54 124 0.58
55 88 0.42
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (54 bp):
CATCAACTCATGATGAATTCCGTGGATTTCACACAAAGTGCCTGTACGGTGATT
Found at i:19677932 original size:163 final size:163
Alignment explanation
Indices: 19677654--19677998 Score: 496
Period size: 163 Copynumber: 2.1 Consensus size: 163
19677644 TTTATTAGAA
* * * *
19677654 TGCACA-AGTAGTGCCTATATGGAAATGCATCAACTCATGATGAATTCCGTGGGTTTCACACACA
1 TGCACATA-TAGTGCCTGTACGGAAATGCATCAACTCATGATGAATTCCGTGGATTGCACACACA
* * *
19677718 GTGCCTGTACGGTGATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTG-CTTGTA
65 GTACATGTACGGTAATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGTC-TGTA
**
19677782 CGGTGATTCATCAACCCATGATGAATTCTGTGGAT
129 CGGTGATTCATCAACCCATGATGAATTCCATGGAT
* * * *
19677817 TGCACATATAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTCCGTGGATTGCACATATAG
1 TGCACATATAGTGCCTGTACGGAAATGCATCAACTCATGATGAATTCCGTGGATTGCACACACAG
* *
19677882 TACATGTACGGTAATTCATCAACTCATGATGAATTCTGTGTATTTGCACACAAAGTGTCTGTATG
66 TACATGTACGGTAATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGTCTGTACG
* *
19677947 GTGATTCATCAACTCATGATGAATTCCATTGAT
131 GTGATTCATCAACCCATGATGAATTCCATGGAT
*
19677980 TGCACATATAGTGCATGTA
1 TGCACATATAGTGCCTGTA
19677999 GTACACATAG
Statistics
Matches: 162, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
163 160 0.99
164 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (163 bp):
TGCACATATAGTGCCTGTACGGAAATGCATCAACTCATGATGAATTCCGTGGATTGCACACACAG
TACATGTACGGTAATTCATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGTCTGTACG
GTGATTCATCAACCCATGATGAATTCCATGGAT
Found at i:19677986 original size:109 final size:109
Alignment explanation
Indices: 19677681--19677998 Score: 451
Period size: 109 Copynumber: 2.9 Consensus size: 109
19677671 TATGGAAATG
* * *
19677681 CATCAACTCATGATGAATTCCGTGGGTTT-CACACACAGTGCCTGTACGGTGATTCATCAACTCA
1 CATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGCCTGTACGGTGATTCATCAACTCA
* * * * *
19677745 TGATGAATTCTGTGGATTTGCACACAAAGTGCTTGTACGGTGATT
66 TGATGAATTCCGTGGA-TTGCACATATAGTGCATGTACGGTAATT
* * * *
19677790 CATCAACCCATGATGAATTCTGTGGA-TTGCACATATAGTGCCTGTACGGTAATTCATCAACTCA
1 CATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGCCTGTACGGTGATTCATCAACTCA
*
19677854 TGATGAATTCCGTGGATTGCACATATAGTACATGTACGGTAATT
66 TGATGAATTCCGTGGATTGCACATATAGTGCATGTACGGTAATT
* * *
19677898 CATCAACTCATGATGAATTCTGTGTATTTGCACACAAAGTGTCTGTATGGTGATTCATCAACTCA
1 CATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGCCTGTACGGTGATTCATCAACTCA
* *
19677963 TGATGAATTCCATTGATTGCACATATAGTGCATGTA
66 TGATGAATTCCGTGGATTGCACATATAGTGCATGTA
19677999 GTACACATAG
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
108 49 0.26
109 136 0.74
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (109 bp):
CATCAACTCATGATGAATTCTGTGGATTTGCACACAAAGTGCCTGTACGGTGATTCATCAACTCA
TGATGAATTCCGTGGATTGCACATATAGTGCATGTACGGTAATT
Found at i:19685806 original size:21 final size:21
Alignment explanation
Indices: 19685782--19685833 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
19685772 TTGTAGCGAA
*
19685782 CATCTTTCTTGCTATGAGATC
1 CATCTTTCTTGCTATAAGATC
19685803 CATCTTTCTTGCTATAAGATC
1 CATCTTTCTTGCTATAAGATC
*
19685824 CCTCTTTCTT
1 CATCTTTCTT
19685834 TGCAAATACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.27, G:0.10, T:0.46
Consensus pattern (21 bp):
CATCTTTCTTGCTATAAGATC
Found at i:19691529 original size:20 final size:21
Alignment explanation
Indices: 19691504--19691551 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
19691494 TTTATCCGGA
*
19691504 AAAAAATCCGGTCTGGGG-TT
1 AAAAAATCCGGTCAGGGGTTT
19691524 AAAAAATCCGGTCAGGGGTTT
1 AAAAAATCCGGTCAGGGGTTT
19691545 AAAAAAT
1 AAAAAAT
19691552 TGGATGACCG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
AAAAAATCCGGTCAGGGGTTT
Found at i:19693132 original size:36 final size:36
Alignment explanation
Indices: 19693083--19693158 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
19693073 ATTGAGGACG
* *
19693083 AGGATCATTACAGAGATTGTACCGGCAAGCGATACA
1 AGGATCATGACAGAGATTATACCGGCAAGCGATACA
19693119 AGGATCATGACAGAGATTATACCGGCAAGCGATACA
1 AGGATCATGACAGAGATTATACCGGCAAGCGATACA
19693155 AGGA
1 AGGA
19693159 ATAAGTCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.17
Consensus pattern (36 bp):
AGGATCATGACAGAGATTATACCGGCAAGCGATACA
Found at i:19705693 original size:48 final size:48
Alignment explanation
Indices: 19705622--19705718 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
19705612 CTGATTCAAC
19705622 ATGTTGAATGCTATAATCGTGCTAAGTTATTCAATTGAATTTATTCTT
1 ATGTTGAATGCTATAATCGTGCTAAGTTATTCAATTGAATTTATTCTT
19705670 ATGTTGAATGCTATAATCGTGCTAAGTTATTCAATTGAATTTATTCTT
1 ATGTTGAATGCTATAATCGTGCTAAGTTATTCAATTGAATTTATTCTT
19705718 A
1 A
19705719 CTACCTGGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (48 bp):
ATGTTGAATGCTATAATCGTGCTAAGTTATTCAATTGAATTTATTCTT
Found at i:19721043 original size:105 final size:111
Alignment explanation
Indices: 19720908--19721126 Score: 378
Period size: 105 Copynumber: 2.0 Consensus size: 111
19720898 GATATATTTC
19720908 CTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTAC-TATTAAGATATA-TC
1 CTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATTAAGATATATTC
19720971 AAT-ACAGTC-TTATAGAGCAA-CAGTTACGGAGCTTG-TTAGATG
66 AATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGATG
19721013 CTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATATTAAGATATAT
1 CTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTAC--ATATTAAGATATAT
19721078 TCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGATG
64 TCAATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGATG
19721126 C
1 C
19721127 ATCAAAACAA
Statistics
Matches: 106, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
105 49 0.46
108 12 0.11
109 5 0.05
110 6 0.06
111 11 0.10
112 15 0.14
113 8 0.08
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (111 bp):
CTATTATGTAGGAAGGACAAATCCTATCTTAATCATACACACCCACTACATATTAAGATATATTC
AATAACAGTCTTTATAGAGCAACCAGTTACGGAGCTTGTTTAGATG
Found at i:19721406 original size:82 final size:75
Alignment explanation
Indices: 19721251--19721411 Score: 250
Period size: 82 Copynumber: 2.1 Consensus size: 75
19721241 GTCATGGTCG
*
19721251 TCAATCCAAACATTGTCTCTAACAATATATCATGTAAATTCTGCATCTCTATGCAATACAACTCA
1 TCAAACCAAACATTGTCTCTAACAATATATCATGTAAATTCTGCATCTCTATGCAATACAACTCA
19721316 TTGTCATCAA
66 TTGTCATCAA
19721326 TCAAACCAATACATTGTTCTCTAACAATATAATCATGTATCAATTCTGCATCTCTATGTCAATAA
1 TCAAACCAA-ACATTG-TCTCTAACAATAT-ATCATGTA--AATTCTGCATCTCTATG-CAAT-A
19721391 CAACTCATTGTCATCAA
59 CAACTCATTGTCATCAA
19721408 TCAA
1 TCAA
19721412 TAACATGTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
75 8 0.10
76 6 0.08
77 13 0.17
78 8 0.10
80 17 0.22
81 4 0.05
82 22 0.28
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (75 bp):
TCAAACCAAACATTGTCTCTAACAATATATCATGTAAATTCTGCATCTCTATGCAATACAACTCA
TTGTCATCAA
Found at i:19722164 original size:18 final size:19
Alignment explanation
Indices: 19722141--19722190 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
19722131 CAATAATTTT
19722141 AGTATCGATACTCAAGG-G
1 AGTATCGATACTCAAGGAG
* * *
19722159 AGTATCGATTCACAGGGTAG
1 AGTATCGATACTCAAGG-AG
19722179 AGTATCGATACT
1 AGTATCGATACT
19722191 AAGTTATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
20 11 0.44
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
AGTATCGATACTCAAGGAG
Found at i:19727488 original size:20 final size:20
Alignment explanation
Indices: 19727448--19727494 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
19727438 CAATTGGTAC
*
19727448 CGATACCGAAGGGGGAGTAT
1 CGATACCGAAGGGGAAGTAT
19727468 CGATACCGAA-GGGAAGCTAT
1 CGATACCGAAGGGGAAG-TAT
*
19727488 CAATACC
1 CGATACC
19727495 ATTTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.34, C:0.21, G:0.30, T:0.15
Consensus pattern (20 bp):
CGATACCGAAGGGGAAGTAT
Found at i:19727539 original size:35 final size:35
Alignment explanation
Indices: 19727485--19727566 Score: 146
Period size: 35 Copynumber: 2.3 Consensus size: 35
19727475 GAAGGGAAGC
*
19727485 TATCAATACCATTTCAAAATAGAATGCAAAAATGG
1 TATCGATACCATTTCAAAATAGAATGCAAAAATGG
*
19727520 TATCGATACCATTTTAAAATAGAATGCAAAAATGG
1 TATCGATACCATTTCAAAATAGAATGCAAAAATGG
19727555 TATCGATACCAT
1 TATCGATACCAT
19727567 AGCATAGTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (35 bp):
TATCGATACCATTTCAAAATAGAATGCAAAAATGG
Found at i:19727578 original size:19 final size:19
Alignment explanation
Indices: 19727554--19727594 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
19727544 TGCAAAAATG
*
19727554 GTATCGATACCATAGCATA
1 GTATCGATACCATAGAATA
* *
19727573 GTATCGGTACTATAGAATA
1 GTATCGATACCATAGAATA
19727592 GTA
1 GTA
19727595 GTATCAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACCATAGAATA
Found at i:19728071 original size:55 final size:55
Alignment explanation
Indices: 19727960--19728104 Score: 154
Period size: 55 Copynumber: 2.6 Consensus size: 55
19727950 TAAGTGAGCA
* * *
19727960 AAAACTTAAGAAATTTCATACTATGTGTATGGA-TTTCTATATGGGCAATTGGTGTGC
1 AAAAC-TAAGAAA-TTCATACTAAGTGTATGAATTTTCTATA-GGGCAATTGATGTGC
*
19728017 AAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATA-GGCACTAT-ATGTGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTTC-TATAGGGCAAT-TGATGTGC
* * *
19728072 GAAA-TAATAAATTCATACCAAGTGTATGAATTT
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTT
19728105 CCCTATGAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
54 27 0.35
55 30 0.38
56 12 0.15
57 9 0.12
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTTCTATAGGGCAATTGATGTGC
Found at i:19728123 original size:54 final size:55
Alignment explanation
Indices: 19728012--19728124 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 55
19728002 GGGCAATTGG
* * * * *
19728012 TGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGCACTATA
1 TGTGCAAAACTAAGAAATTCATACCAAGTGTATGAATTTCCCTATAGGAAATATA
* * *
19728067 TGTGCGAAA-TAATAAATTCATACCAAGTGTATGAATTTCCCTAT-GAGAAATGTA
1 TGTGCAAAACTAAGAAATTCATACCAAGTGTATGAATTTCCCTATAG-GAAATATA
19728121 TGTG
1 TGTG
19728125 AAATTATCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.02
54 40 0.82
55 8 0.16
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (55 bp):
TGTGCAAAACTAAGAAATTCATACCAAGTGTATGAATTTCCCTATAGGAAATATA
Found at i:19728424 original size:68 final size:68
Alignment explanation
Indices: 19728326--19728899 Score: 842
Period size: 68 Copynumber: 8.4 Consensus size: 68
19728316 AAGATTATAT
* * * * ** * *
19728326 GCCTAACTATGCAGTTGACAAAAAGATGTCAATTATAACATTTAGATGAAACGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728391 GAG
66 GAG
* * *
19728394 GCCTAACTGTGCATTTGAGAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAGGGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728459 GAG
66 GAG
* * ** * *
19728462 GCCTAACTGTGCATTTGACAAAAAAGTACCAATTATGCCAGTTAGATGAAAGGCTATGTTCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728527 GAG
66 GAG
* * * *
19728530 GCCTAACTATGCATTTGACAGAAAGGTGTTAATTATGCCAATTAGGTGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728595 GAG
66 GAG
* * * *
19728598 GCCTAAATGTGCATTTGACAGAAAGGTGTCAATTATACCAATTAGATGAAAGGCTAAGCGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728663 GAG
66 GAG
*
19728666 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
19728731 CAG
66 GAG
* *
19728734 ACCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728799 GAG
66 GAG
* * * *
19728802 GCCTACCTATGCATTTAACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
19728867 GAG
66 GAG
*
19728870 GCCTAAATGTGCATTTGACAGAAAGGTGTC
1 GCCTAACTGTGCATTTGACAGAAAGGTGTC
19728900 TTAAATACCG
Statistics
Matches: 451, Mismatches: 55, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 451 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (68 bp):
GCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:19729171 original size:81 final size:81
Alignment explanation
Indices: 19728900--19729162 Score: 384
Period size: 81 Copynumber: 3.2 Consensus size: 81
19728890 GAAAGGTGTC
*
19728900 TTAAATACCGTTGAGTAAAAGAATAATGGCCGAACTGTGCATTTGGCAGAAA-GATGTTATTTAT
1 TTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGCAGAAATG-TGTTATTTAT
* *
19728964 GCTAGTTAGATGAACGG
65 GCCAATTAGATGAACGG
* * * * *
19728981 TTAAATATCGTTTAGTAAAAGAATAATGGTCTAACTGTGCATTTGGTAGAAATGTGTCATTTATG
1 TTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGCAGAAATGTGTTATTTATG
*
19729046 TCAATTAGATGAACGG
66 CCAATTAGATGAACGG
* *
19729062 TTAAATACCATTGAGTAAAAGAATAATGGCCTAACTATGCATTTGGCAGAAATGTGTTATTTATG
1 TTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGCAGAAATGTGTTATTTATG
*
19729127 CCAATTAGATGAATGG
66 CCAATTAGATGAACGG
* *
19729143 TTAAACACTGTTGAGTAAAA
1 TTAAATACCGTTGAGTAAAA
19729163 CATGAATGGT
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
81 159 0.99
82 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
TTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCATTTGGCAGAAATGTGTTATTTATG
CCAATTAGATGAACGG
Found at i:19729200 original size:29 final size:29
Alignment explanation
Indices: 19729135--19729191 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
19729125 TGCCAATTAG
* *
19729135 ATGAATGGTTAAACACTGTTGAGTAAAAC
1 ATGAATGGTTAAACACCGGTGAGTAAAAC
*
19729164 ATGAATGGTTAAATACCGGTGAGTAAAA
1 ATGAATGGTTAAACACCGGTGAGTAAAA
19729192 GAGTAATGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (29 bp):
ATGAATGGTTAAACACCGGTGAGTAAAAC
Found at i:19729272 original size:110 final size:110
Alignment explanation
Indices: 19729054--19729257 Score: 248
Period size: 110 Copynumber: 1.9 Consensus size: 110
19729044 TGTCAATTAG
* * * **
19729054 ATGAACGGTTAAATACCATTGAGTAAAAGAATAATGGCCTAACTATGCATTTGGCAGAAATGTGT
1 ATGAACGGTTAAATACCAGTGAGTAAAAGAATAATGGACTAACTATGCATTTGACAGAAAAATGT
* ** * *
19729119 TATTTATGCCAATTAGATGAATGGTTAAACACTGTTGAGTAAAAC
66 CAAATATGCCAATTAGATGAAAGGCTAAACACTGTTGAGTAAAAC
* * * ** *
19729164 ATGAATGGTTAAATACCGGTGAGTAAAAGAGTAATGGACTAGTTGTGCATTTGACAGAAAAATGT
1 ATGAACGGTTAAATACCAGTGAGTAAAAGAATAATGGACTAACTATGCATTTGACAGAAAAATGT
19729229 CAAATATG-CAAGTTAGATGAAAGGCTAAA
66 CAAATATGCCAA-TTAGATGAAAGGCTAAA
19729258 TACCTTTGGG
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
109 3 0.04
110 74 0.96
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (110 bp):
ATGAACGGTTAAATACCAGTGAGTAAAAGAATAATGGACTAACTATGCATTTGACAGAAAAATGT
CAAATATGCCAATTAGATGAAAGGCTAAACACTGTTGAGTAAAAC
Found at i:19731295 original size:21 final size:20
Alignment explanation
Indices: 19731267--19731305 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
19731257 CACTGTAGGA
*
19731267 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
19731287 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
19731306 GACCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:19732854 original size:102 final size:102
Alignment explanation
Indices: 19732678--19732876 Score: 344
Period size: 102 Copynumber: 2.0 Consensus size: 102
19732668 AAAAACCAAG
* *
19732678 ACTACACAACCAATCCGAAAACGAAGAATATACAAACACCAACATTAATAAAAATGGAAGCAAAT
1 ACTACACAACCAATCCCAAAACGAAGAATATAAAAACACCAACATTAATAAAAATGGAAGCAAAT
19732743 TAATCACTTCCAATCAGAGACATCAAAAACAACAAAC
66 TAATCACTTCCAATCAGAGACATCAAAAACAACAAAC
* * *
19732780 ACTACACAACCAATCCCAAAACGAAGAATATAAAAACGCCAATATTAATAAAAGTGGAAGCAAAT
1 ACTACACAACCAATCCCAAAACGAAGAATATAAAAACACCAACATTAATAAAAATGGAAGCAAAT
*
19732845 TAATCACTTCCAATCAGAGACTTCAAAAACAA
66 TAATCACTTCCAATCAGAGACATCAAAAACAA
19732877 AGCTTCACAC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.53, C:0.23, G:0.09, T:0.16
Consensus pattern (102 bp):
ACTACACAACCAATCCCAAAACGAAGAATATAAAAACACCAACATTAATAAAAATGGAAGCAAAT
TAATCACTTCCAATCAGAGACATCAAAAACAACAAAC
Found at i:19734272 original size:24 final size:23
Alignment explanation
Indices: 19734245--19734295 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
19734235 ACTTAATTCG
19734245 TAATTAAT-AATAAATTAAAAATCC
1 TAATTAATAAAT-AATT-AAAATCC
*
19734269 TAA-TAATAAATAATTTAAATCC
1 TAATTAATAAATAATTAAAATCC
19734291 TAATT
1 TAATT
19734296 GAAATTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (23 bp):
TAATTAATAAATAATTAAAATCC
Found at i:19741341 original size:183 final size:184
Alignment explanation
Indices: 19741033--19741394 Score: 701
Period size: 183 Copynumber: 2.0 Consensus size: 184
19741023 CACTGATATG
19741033 TTGTTCTTGAAATTCTCCATGTTCAATATTTCTACCCTTCCCTTTCTTTAAGAGAAATTCTCCTT
1 TTGTTCTTGAAATTCTCCATGTTCAATATTTCTACCCTTCCCTTTCTTTAAGAGAAATTCTCCTT
19741098 CGAGAAAAACTCTCGTTCGAGAAACAAACACTTTGTTCTCGTTAGGGTTGAAGAAATAATATCCC
66 CGAGAAAAACTCTCGTTCGAGAAACAAACACTTTGTTCTCGTTAGGGTTGAAGAAATAATATCCC
19741163 TTAG-TTC-TTAGGATATCCTACAAATATACACTAATGAGATTTAAGTTCGAGTT
131 TTAGTTTCTTTAGGATATCCTACAAATATACACTAATGAGA-TTAAGTTCGAGTT
19741216 TTGTTCTTGAAATTCTCCATGTTCAATATTTCTACCCTTCCCTTTCTTTAAGAGAAATTCTCCTT
1 TTGTTCTTGAAATTCTCCATGTTCAATATTTCTACCCTTCCCTTTCTTTAAGAGAAATTCTCCTT
19741281 CGAGAAAAACTCTCGTTCGAGAAACAAACACTTTGTTCTCGTTAGGGTTGAAGAAATAATATCCC
66 CGAGAAAAACTCTCGTTCGAGAAACAAACACTTTGTTCTCGTTAGGGTTGAAGAAATAATATCCC
19741346 TTAGTTTCTTTAGGATATCCTACAAATATACACTAATGAGATTAAGTTC
131 TTAGTTTCTTTAGGATATCCTACAAATATACACTAATGAGATTAAGTTC
19741395 TTTTGAACCG
Statistics
Matches: 177, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
183 134 0.76
184 11 0.06
185 32 0.18
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (184 bp):
TTGTTCTTGAAATTCTCCATGTTCAATATTTCTACCCTTCCCTTTCTTTAAGAGAAATTCTCCTT
CGAGAAAAACTCTCGTTCGAGAAACAAACACTTTGTTCTCGTTAGGGTTGAAGAAATAATATCCC
TTAGTTTCTTTAGGATATCCTACAAATATACACTAATGAGATTAAGTTCGAGTT
Found at i:19744531 original size:77 final size:79
Alignment explanation
Indices: 19744438--19744584 Score: 217
Period size: 77 Copynumber: 1.9 Consensus size: 79
19744428 AATTAAAATG
*
19744438 TTATTTAATTAATTCAAATTAAATATCCATT-AAAGACTTATAATCTAAATTACAATCT-TTAAC
1 TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTGTTAAC
19744501 GTTTATTTAAACTC
66 GTTTATTTAAACTC
* * * * * *
19744515 TTATTTAATTATTTCAAATTAAATATCGATTAAAAGAGTTGTAATCAAAATTACATTCTGTTAAT
1 TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTGTTAAC
19744580 GTTTA
66 GTTTA
19744585 CTTACTATAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 29 0.48
78 23 0.38
79 9 0.15
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATCCATTAAAAGACTTATAATCAAAATTACAATCTGTTAAC
GTTTATTTAAACTC
Found at i:19747803 original size:61 final size:61
Alignment explanation
Indices: 19747691--19747808 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
19747681 AAGCTTACGA
* * *
19747691 TCTAGTGTTGATCCGAATATGACATATAAGGTCGTGCTCACCACATACACTAGGTTTATAG
1 TCTAGTGTTGATCCGAATATGACACATAAGGTCGTGCCCACCACATACACTAAGTTTATAG
* * * * *
19747752 TCTAGTGTTGATCCGAATATGACACATATGGTTGTTCCCACCACCTGCACTAAGTTT
1 TCTAGTGTTGATCCGAATATGACACATAAGGTCGTGCCCACCACATACACTAAGTTT
19747809 CCTTGCACAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (61 bp):
TCTAGTGTTGATCCGAATATGACACATAAGGTCGTGCCCACCACATACACTAAGTTTATAG
Found at i:19747985 original size:2 final size:2
Alignment explanation
Indices: 19747978--19748019 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
19747968 CCCAAATAAC
19747978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19748020 GCATAATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19751706 original size:31 final size:30
Alignment explanation
Indices: 19751648--19751709 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
19751638 AATTACCATT
* **
19751648 AAACCAAGACACCTATCCTTATTATCTTCC
1 AAACCAAGACACCTAACCTTACCATCTTCC
19751678 AAACCAAGACACCTAAACCTTACCATCTTCC
1 AAACCAAGACACCT-AACCTTACCATCTTCC
19751709 A
1 A
19751710 TAAGTCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.24
Consensus pattern (30 bp):
AAACCAAGACACCTAACCTTACCATCTTCC
Found at i:19757233 original size:19 final size:20
Alignment explanation
Indices: 19757205--19757245 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
19757195 TTGAATTTTA
*
19757205 CATTGCAGG-TACCGATACC
1 CATTGAAGGATACCGATACC
19757224 CATTGAAGGTATACCGATACC
1 CATTGAAGG-ATACCGATACC
19757245 C
1 C
19757246 CACACTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (20 bp):
CATTGAAGGATACCGATACC
Found at i:19762812 original size:21 final size:23
Alignment explanation
Indices: 19762783--19762839 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
19762773 TGTGCACCAG
19762783 GTATCGATACCC-C-TTCAACGT
1 GTATCGATACCCTCTTTCAACGT
* * *
19762804 GTATTGATACCCTCTTTGAATGT
1 GTATCGATACCCTCTTTCAACGT
19762827 GTATCGATACCCT
1 GTATCGATACCCT
19762840 ATAAGGGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.37
22 1 0.03
23 18 0.60
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (23 bp):
GTATCGATACCCTCTTTCAACGT
Found at i:19764677 original size:19 final size:20
Alignment explanation
Indices: 19764631--19764679 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
19764621 TAATAAAGGG
19764631 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
19764651 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
19764670 AATAAAATAA
1 AATAAAATAA
19764680 ATAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:19765135 original size:19 final size:21
Alignment explanation
Indices: 19765092--19765142 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19765082 GAAACCCCTT
19765092 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
19765113 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
19765132 TGAAGATACAT
1 TGAAAATACAT
19765143 TCTCTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:19766072 original size:30 final size:31
Alignment explanation
Indices: 19766031--19766090 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
19766021 ACATGTTGCC
**
19766031 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
19766062 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
19766091 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:19767349 original size:74 final size:74
Alignment explanation
Indices: 19767263--19767422 Score: 250
Period size: 74 Copynumber: 2.2 Consensus size: 74
19767253 TTAAATAGGG
* *
19767263 AGGTACCGATACCCCTATGCCAATTTTGGCTCTGAGAAAAACAGAATGCCAAATGGGTATCGATA
1 AGGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCGATA
19767328 -CCCCTTATA
66 CCCCCTTA-A
* *
19767337 AGGTACCGATACCCCTATGCCAATTTTGGTTCCGAGAAAAACAGAATGCCCAATGGGTACCGATA
1 AGGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCGATA
*
19767402 CCCCCTTAG
66 CCCCCTTAA
*
19767411 AGGTACTGATAC
1 AGGTACCGATAC
19767423 ATCTAGTCAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 72 0.91
75 7 0.09
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (74 bp):
AGGTACCGATACCCCTATGCCAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCGATA
CCCCCTTAA
Found at i:19769132 original size:20 final size:20
Alignment explanation
Indices: 19769104--19769141 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19769094 ACTCATAGTC
*
19769104 AGTATCGATATTGTTCTTTA
1 AGTACCGATATTGTTCTTTA
19769124 AGTACCGATATTGTTCTT
1 AGTACCGATATTGTTCTT
19769142 GCAACCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (20 bp):
AGTACCGATATTGTTCTTTA
Found at i:19773033 original size:13 final size:13
Alignment explanation
Indices: 19773017--19773049 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
19773007 AATGGGTAAT
19773017 TTTGAAAACTAAG-
1 TTTGAAAAC-AAGA
19773030 TTTGAAAACAAGA
1 TTTGAAAACAAGA
19773043 TTTGAAA
1 TTTGAAA
19773050 TTCAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.30
Consensus pattern (13 bp):
TTTGAAAACAAGA
Found at i:19773516 original size:20 final size:21
Alignment explanation
Indices: 19773491--19773548 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
19773481 CAGACCCCGT
*
19773491 GGGGGGTATCGATTCCCT-AC
1 GGGGGGTATCGATTCCCTGAA
* *
19773511 GGGGGGAATCGGTTCCCCTGAA
1 GGGGGGTATCGATT-CCCTGAA
*
19773533 AGGGGGTATCGATTCC
1 GGGGGGTATCGATTCC
19773549 TCCTGCACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 12 0.40
21 6 0.20
22 12 0.40
ACGTcount: A:0.17, C:0.22, G:0.38, T:0.22
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCTGAA
Found at i:19781224 original size:17 final size:17
Alignment explanation
Indices: 19781202--19781244 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
19781192 AAAATTCTAG
19781202 TATACTAAAATGGTACT
1 TATACTAAAATGGTACT
19781219 TATACTAAAATGGTACT
1 TATACTAAAATGGTACT
*
19781236 GATACTAAA
1 TATACTAAA
19781245 TACAATATTG
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:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (17 bp):
TATACTAAAATGGTACT
Found at i:19785713 original size:84 final size:84
Alignment explanation
Indices: 19785611--19785778 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
19785601 ATCGATCAAA
19785611 TCTTTCACATCTTATCACCTCCATGGAAATAAAAACTCTATTAGATTTGACCTATAAAGAGGAAT
1 TCTTTCACATCTTATCACCTCCATGGAAATAAAAACTCTATTAGATTTGACCTATAAAGAGGAAT
19785676 CGATTGAGATCTTGTCTTG
66 CGATTGAGATCTTGTCTTG
19785695 TCTTTCACATCTTATCACCTCCATGGAAATAAAAACTCTATTAGATTTGACCTATAAAGAGGAAT
1 TCTTTCACATCTTATCACCTCCATGGAAATAAAAACTCTATTAGATTTGACCTATAAAGAGGAAT
19785760 CGATTGAGATCTTGTCTTG
66 CGATTGAGATCTTGTCTTG
19785779 AGAAGTCAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (84 bp):
TCTTTCACATCTTATCACCTCCATGGAAATAAAAACTCTATTAGATTTGACCTATAAAGAGGAAT
CGATTGAGATCTTGTCTTG
Found at i:19804788 original size:15 final size:17
Alignment explanation
Indices: 19804746--19804791 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
19804736 CGATCTTTTC
19804746 TAGAATTTGAAAATATA
1 TAGAATTTGAAAATATA
*
19804763 TA-AAATT-AAAATA-A
1 TAGAATTTGAAAATATA
19804777 -AGAATTTGAAAATAT
1 TAGAATTTGAAAATAT
19804792 GATCTACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
13 1 0.04
14 5 0.21
15 12 0.50
16 4 0.17
17 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
TAGAATTTGAAAATATA
Found at i:19810497 original size:18 final size:18
Alignment explanation
Indices: 19810474--19810533 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
19810464 TTGAGTCATC
*
19810474 GGATGCTCCACAGCATTG
1 GGATGCTCCATAGCATTG
19810492 GGATGCTCCATAGCATTG
1 GGATGCTCCATAGCATTG
*
19810510 GGATGATCCATAGCATTG
1 GGATGCTCCATAGCATTG
*
19810528 GAATGC
1 GGATGC
19810534 CACAACATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (18 bp):
GGATGCTCCATAGCATTG
Found at i:19817200 original size:46 final size:46
Alignment explanation
Indices: 19817143--19817234 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
19817133 TTTAGATGTT
19817143 TTTGAGGTTGTAGAATCATTTTCAAGCATGATTGATATTTAAAATC
1 TTTGAGGTTGTAGAATCATTTTCAAGCATGATTGATATTTAAAATC
19817189 TTTGAGGTTGTAGAATCATTTTCAAGCATGATTGATATTTAAAATC
1 TTTGAGGTTGTAGAATCATTTTCAAGCATGATTGATATTTAAAATC
19817235 ACTTGTACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (46 bp):
TTTGAGGTTGTAGAATCATTTTCAAGCATGATTGATATTTAAAATC
Found at i:19822020 original size:90 final size:90
Alignment explanation
Indices: 19821864--19822041 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
19821854 CCTAACACAC
* * * *
19821864 CCTTTTATAGCCAAGTTACCCTAGTGATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
19821929 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
19821954 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATTTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
19822019 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
19822042 TTTGGGATAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:19833429 original size:9 final size:9
Alignment explanation
Indices: 19833412--19833443 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
19833402 CCACCTATTA
*
19833412 CCCAGTTGG
1 CCCAATTGG
19833421 CCCAATTGG
1 CCCAATTGG
19833430 CCCAATTGG
1 CCCAATTGG
19833439 CCCAA
1 CCCAA
19833444 CACATGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.19
Consensus pattern (9 bp):
CCCAATTGG
Found at i:19835953 original size:31 final size:30
Alignment explanation
Indices: 19835877--19835954 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
19835867 AGTCAGTTAC
*
19835877 GTTAGGGACCATATTACAAATGGAATAAAT
1 GTTAGGGACCATATTGCAAATGGAATAAAT
*
19835907 GTTGGGGGACCATATTGCAAAT-GAACTAAAT
1 GTT-AGGGACCATATTGCAAATGGAA-TAAAT
*
19835938 GTTAGAGGACTATATTG
1 GTTAG-GGACCATATTG
19835955 TAAGTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (30 bp):
GTTAGGGACCATATTGCAAATGGAATAAAT
Found at i:19837163 original size:16 final size:15
Alignment explanation
Indices: 19837119--19837163 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
19837109 CAAATTAAAA
19837119 TATTCAATTTTATATT
1 TATTCAATTTT-TATT
* *
19837135 AATTTAATTTTTATT
1 TATTCAATTTTTATT
19837150 TATTCAATTCTTTA
1 TATTCAATT-TTTA
19837164 AATTTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTCAATTTTTATT
Found at i:19837168 original size:24 final size:26
Alignment explanation
Indices: 19837140--19837199 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 26
19837130 ATATTAATTT
19837140 AATTTTTATTTATTC-AATT-CTTTA
1 AATTTTTATTTATTCTAATTCCTTTA
**
19837164 AA--TTTATTTATTCTTTTTCCTTTA
1 AATTTTTATTTATTCTAATTCCTTTA
19837188 AATTGTTTATTT
1 AATT-TTTATTT
19837200 TAGTTAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
22 11 0.38
23 2 0.07
24 9 0.31
27 7 0.24
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (26 bp):
AATTTTTATTTATTCTAATTCCTTTA
Found at i:19845172 original size:26 final size:27
Alignment explanation
Indices: 19845143--19845196 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
19845133 TGCATTGATG
19845143 TTTTCATAATTTTACCCT-TAAGGGTA
1 TTTTCATAATTTTACCCTATAAGGGTA
*
19845169 TTTTCATAATTTTACCTTATAAGGGTA
1 TTTTCATAATTTTACCCTATAAGGGTA
19845196 T
1 T
19845197 GGTTGTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (27 bp):
TTTTCATAATTTTACCCTATAAGGGTA
Found at i:19847898 original size:68 final size:68
Alignment explanation
Indices: 19847814--19847950 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
19847804 GACAACAATG
19847814 ATAAACAGTAAGATTGATGTCATTGTCTATCAATAAAAAAAATGAAGAAAGAGATCTCATCAAAA
1 ATAAACAGTAAGATTGATGTCATTGTCTATCAATAAAAAAAATGAAGAAAGAGATCTCATCAAAA
19847879 AAA
66 AAA
19847882 ATAAACAGTAAGATTGATGTCATTGTCTATCAATAAAAAAAATGAAGAAAGAGATCTCATCAAAA
1 ATAAACAGTAAGATTGATGTCATTGTCTATCAATAAAAAAAATGAAGAAAGAGATCTCATCAAAA
19847947 AAA
66 AAA
19847950 A
1 A
19847951 ATATCTATAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (68 bp):
ATAAACAGTAAGATTGATGTCATTGTCTATCAATAAAAAAAATGAAGAAAGAGATCTCATCAAAA
AAA
Found at i:19854692 original size:8 final size:8
Alignment explanation
Indices: 19854675--19854733 Score: 59
Period size: 8 Copynumber: 7.6 Consensus size: 8
19854665 AAAACCATTT
*
19854675 CATACATA
1 CATATATA
*
19854683 CATATGTA
1 CATATATA
*
19854691 CATATACA
1 CATATATA
*
19854699 TATATATA
1 CATATATA
19854707 CATATATA
1 CATATATA
19854715 C--ATATA
1 CATATATA
19854721 CATATATA
1 CATATATA
*
19854729 TATAT
1 CATAT
19854734 TCATAAATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 6 0.15
8 35 0.85
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (8 bp):
CATATATA
Found at i:19854700 original size:6 final size:6
Alignment explanation
Indices: 19854689--19854732 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
19854679 CATACATATG
* * * *
19854689 TACATA TACATA TATATA CATATA TACATA TACATA TATATA TA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TA
19854733 TTCATAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (6 bp):
TACATA
Found at i:19854707 original size:24 final size:24
Alignment explanation
Indices: 19854680--19854730 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
19854670 CATTTCATAC
*
19854680 ATACATATGTACATATACATATAT
1 ATACATATATACATATACATATAT
19854704 ATACATATATACATATACATATAT
1 ATACATATATACATATACATATAT
19854728 ATA
1 ATA
19854731 TATTCATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (24 bp):
ATACATATATACATATACATATAT
Found at i:19854713 original size:18 final size:18
Alignment explanation
Indices: 19854692--19854732 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19854682 ACATATGTAC
*
19854692 ATATACATATATATACAT
1 ATATACATATACATACAT
*
19854710 ATATACATATACATATAT
1 ATATACATATACATACAT
19854728 ATATA
1 ATATA
19854733 TTCATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATACATATACATACAT
Found at i:19854726 original size:14 final size:14
Alignment explanation
Indices: 19854680--19854744 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
19854670 CATTTCATAC
*
19854680 ATACATATGTACAT
1 ATACATATATACAT
19854694 ATAC--ATAT--AT
1 ATACATATATACAT
19854704 ATACATATATACAT
1 ATACATATATACAT
*
19854718 ATACATATATATAT
1 ATACATATATACAT
* *
19854732 ATTCATAAATACA
1 ATACATATATACA
19854745 ATTATAACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 6 0.14
12 7 0.17
14 29 0.69
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (14 bp):
ATACATATATACAT
Found at i:19863689 original size:18 final size:18
Alignment explanation
Indices: 19863668--19863708 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
19863658 AGGCATTTGA
19863668 TCCTCTGGAT-GTGCTTGT
1 TCCTCT-GATCGTGCTTGT
*
19863686 TCCTCTGCTCGTGCTTGT
1 TCCTCTGATCGTGCTTGT
19863704 TCCTC
1 TCCTC
19863709 GTGCTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.02, C:0.32, G:0.22, T:0.44
Consensus pattern (18 bp):
TCCTCTGATCGTGCTTGT
Found at i:19863723 original size:18 final size:19
Alignment explanation
Indices: 19863678--19863728 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
19863668 TCCTCTGGAT
*
19863678 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
19863696 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
19863714 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
19863729 CGGAGTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:19865216 original size:22 final size:22
Alignment explanation
Indices: 19865185--19865245 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
19865175 CAAAACCCCA
19865185 GGGGGTATCGGTTCCCTTCAAG
1 GGGGGTATCGGTTCCCTTCAAG
*
19865207 GGGGGAATCGGTTCCCTTCAAG
1 GGGGGTATCGGTTCCCTTCAAG
*
19865229 GGGGGTATCGATTCCCT
1 GGGGGTATCGGTTCCCT
19865246 CTGCACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.15, C:0.23, G:0.36, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGGTTCCCTTCAAG
Found at i:19885702 original size:20 final size:20
Alignment explanation
Indices: 19885650--19885741 Score: 76
Period size: 20 Copynumber: 4.4 Consensus size: 20
19885640 ACCTACCCTA
19885650 TTGACTTTGACCCGACTTGAATCG
1 TTGACTTTGA-CCG--TT-AATCG
* *
19885674 TTAACTTTGACCGTTAATTG
1 TTGACTTTGACCGTTAATCG
** *
19885694 TTGACTTTGACTATTGATCG
1 TTGACTTTGACCGTTAATCG
* * *
19885714 TTGACTTTGATCGTTGACCG
1 TTGACTTTGACCGTTAATCG
19885734 TTGACTTT
1 TTGACTTT
19885742 TTTAAGACCT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 43 0.75
21 2 0.04
23 3 0.05
24 9 0.16
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGACTTTGACCGTTAATCG
Found at i:19885723 original size:13 final size:14
Alignment explanation
Indices: 19885700--19885731 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
19885690 ATTGTTGACT
19885700 TTGACTATTGATCG
1 TTGACTATTGATCG
19885714 TTGACT-TTGATCG
1 TTGACTATTGATCG
19885727 TTGAC
1 TTGAC
19885732 CGTTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGACTATTGATCG
Found at i:19886336 original size:28 final size:28
Alignment explanation
Indices: 19886252--19886330 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
19886242 GCATCATTCA
* *
19886252 TGATTCTGCATGGGCATAGTCCCCGTCC
1 TGATTCTACATGGGCTTAGTCCCCGTCC
* *
19886280 TGATTCTTCATGGGTTTAGTCCCCGTCC
1 TGATTCTACATGGGCTTAGTCCCCGTCC
19886308 TGATTCTACATGGGCTTAG-CCCC
1 TGATTCTACATGGGCTTAGTCCCC
19886331 TATCCTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 4 0.09
28 42 0.91
ACGTcount: A:0.14, C:0.30, G:0.23, T:0.33
Consensus pattern (28 bp):
TGATTCTACATGGGCTTAGTCCCCGTCC
Found at i:19886382 original size:30 final size:30
Alignment explanation
Indices: 19886356--19886449 Score: 93
Period size: 30 Copynumber: 3.1 Consensus size: 30
19886346 GAGGACCTTT
*
19886356 TTCCCCGTCTTAATTCTACATGGGACCTCG
1 TTCCCCGTCTTAATTCTACATGGGACCTCA
* * * *
19886386 TTCCCTGTCATGATTCTGA-ATAGGACCTCA
1 TTCCCCGTCTTAATTCT-ACATGGGACCTCA
* *
19886416 TTCCCCGT-TCTAATTTTACATGGGACCTCG
1 TTCCCCGTCT-TAATTCTACATGGGACCTCA
19886446 TTCC
1 TTCC
19886450 TTGTTATGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 1 0.02
30 48 0.96
31 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (30 bp):
TTCCCCGTCTTAATTCTACATGGGACCTCA
Found at i:19886422 original size:60 final size:60
Alignment explanation
Indices: 19886342--19886458 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
19886332 ATCCTAATTT
**
19886342 TGAAGAGGACCTTTTTCCCCG-TCTTAATTCTACATGGGACCTCGTTCCCTGTCATGATTC
1 TGAAGAGGACCTCATTCCCCGTTC-TAATTCTACATGGGACCTCGTTCCCTGTCATGATTC
* * * *
19886402 TGAATAGGACCTCATTCCCCGTTCTAATTTTACATGGGACCTCGTTCCTTGTTATGA
1 TGAAGAGGACCTCATTCCCCGTTCTAATTCTACATGGGACCTCGTTCCCTGTCATGA
19886459 CATCTGCATG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 48 0.96
61 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (60 bp):
TGAAGAGGACCTCATTCCCCGTTCTAATTCTACATGGGACCTCGTTCCCTGTCATGATTC
Found at i:19886482 original size:30 final size:30
Alignment explanation
Indices: 19886446--19886528 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
19886436 TGGGACCTCG
19886446 TTCCTTGTTATGACATCTGCATGAAATAAA
1 TTCCTTGTTATGACATCTGCATGAAATAAA
* * *
19886476 TTCCTTGTTCTGACATCAGCATGAGATAAA
1 TTCCTTGTTATGACATCTGCATGAAATAAA
*
19886506 TTCCTTGTTTTGACATCTGCATG
1 TTCCTTGTTATGACATCTGCATG
19886529 GGATTATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (30 bp):
TTCCTTGTTATGACATCTGCATGAAATAAA
Found at i:19889611 original size:17 final size:17
Alignment explanation
Indices: 19889586--19889619 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
19889576 CATTGACTTT
19889586 GACCGGACCCATTGACC
1 GACCGGACCCATTGACC
*
19889603 GACCTGACCCATTGACC
1 GACCGGACCCATTGACC
19889620 ATTGAGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.41, G:0.21, T:0.15
Consensus pattern (17 bp):
GACCGGACCCATTGACC
Found at i:19889656 original size:20 final size:20
Alignment explanation
Indices: 19889614--19889659 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
19889604 ACCTGACCCA
*
19889614 TTGACCATTGAGCTTGAATG
1 TTGACCATTGAGCTTGAACG
*
19889634 TTGACCATTGA-CTTTGACCG
1 TTGACCATTGAGC-TTGAACG
19889654 TTGACC
1 TTGACC
19889660 TCTATCCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGACCATTGAGCTTGAACG
Found at i:19890207 original size:28 final size:27
Alignment explanation
Indices: 19890134--19890231 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
19890124 GTATCATTCA
* *
19890134 TGATTCTACATGGGCTTAGTCCTCCTCT
1 TGATTCTATATGGGCTTAGTCC-CCTCC
* * **
19890162 TGATTTTGTATGCTCTTAGTCCCCGTCC
1 TGATTCTATATGGGCTTAGTCCCC-TCC
* * **
19890190 TGATTCTGTATGGGCTTAATCCTTATCC
1 TGATTCTATATGGGCTTAGTCC-CCTCC
19890218 TGATTCTATATGGG
1 TGATTCTATATGGG
19890232 GCCTCATTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 2 0.04
28 53 0.96
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (27 bp):
TGATTCTATATGGGCTTAGTCCCCTCC
Found at i:19890254 original size:30 final size:29
Alignment explanation
Indices: 19890211--19890295 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 29
19890201 GGGCTTAATC
* * *
19890211 CTTATCCTGATTCTATATGGGGCCTCATTT
1 CTTATCCTAATTCT-GATGGGACCTCATTT
* *
19890241 CTTATCTTAATTCTGATGGGACCTCATTC
1 CTTATCCTAATTCTGATGGGACCTCATTT
** * *
19890270 CCCATCCTCATTCTACATGGGACCTC
1 CTTATCCTAATTCT-GATGGGACCTC
19890296 GTTTTCCGTT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.19, C:0.29, G:0.14, T:0.38
Consensus pattern (29 bp):
CTTATCCTAATTCTGATGGGACCTCATTT
Found at i:19890337 original size:30 final size:31
Alignment explanation
Indices: 19890303--19890379 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
19890293 CTCGTTTTCC
* *
19890303 GTTCTCACATCTTCATGAG-ACAAATTCCCA
1 GTTCTGACATCTACATGAGAACAAATTCCCA
* * *
19890333 GTTCTGACATCTGCAT-AGAATAAATTCCCT
1 GTTCTGACATCTACATGAGAACAAATTCCCA
19890363 GTTCTGACATCTACATG
1 GTTCTGACATCTACATG
19890380 TGATTATATC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (31 bp):
GTTCTGACATCTACATGAGAACAAATTCCCA
Found at i:19891435 original size:27 final size:27
Alignment explanation
Indices: 19891403--19891459 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
19891393 AACGTGGTAG
19891403 TTTCTATAAGGTCTAGTCAGCAACAAT
1 TTTCTATAAGGTCTAGTCAGCAACAAT
*
19891430 TTTCTATAAGGTCTAGTCAGCAACAGT
1 TTTCTATAAGGTCTAGTCAGCAACAAT
19891457 TTT
1 TTT
19891460 TTAGAACATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (27 bp):
TTTCTATAAGGTCTAGTCAGCAACAAT
Found at i:19891471 original size:27 final size:27
Alignment explanation
Indices: 19891414--19891477 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
19891404 TTCTATAAGG
* **
19891414 TCTAGTCAGCAACAATTTTCTATAAGG
1 TCTAGTCAGCAACAATTTTCTAGAACA
* *
19891441 TCTAGTCAGCAACAGTTTTTTAGAACA
1 TCTAGTCAGCAACAATTTTCTAGAACA
*
19891468 TCTATTCAGC
1 TCTAGTCAGC
19891478 GCCTTCTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (27 bp):
TCTAGTCAGCAACAATTTTCTAGAACA
Found at i:19893874 original size:24 final size:24
Alignment explanation
Indices: 19893825--19893874 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
19893815 TGATTTCTAA
**
19893825 AATTTTAAATTCTAAAATTCAAAT
1 AATTTTAAATTCTAAAATAAAAAT
*
19893849 AATTTTAAATT-TTAAATAAAATAT
1 AATTTTAAATTCTAAAATAAAA-AT
19893873 AA
1 AA
19893875 ATAAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTTTAAATTCTAAAATAAAAAT
Found at i:19899068 original size:11 final size:11
Alignment explanation
Indices: 19899052--19899076 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19899042 TTTGTGCTCA
19899052 AATTCACTTAT
1 AATTCACTTAT
19899063 AATTCACTTAT
1 AATTCACTTAT
19899074 AAT
1 AAT
19899077 AGGTACTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTCACTTAT
Found at i:19899178 original size:17 final size:16
Alignment explanation
Indices: 19899151--19899183 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
19899141 TATTCATTAT
19899151 AATAAAATTTAAATAA
1 AATAAAATTTAAATAA
19899167 AATAATAATTTAAATAA
1 AATAA-AATTTAAATAA
19899184 TTGAATTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATTTAAATAA
Found at i:19899315 original size:3 final size:3
Alignment explanation
Indices: 19899307--19899365 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
19899297 ATAGTATCAT
19899307 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19899355 TAA TAA TAA TA
1 TAA TAA TAA TA
19899366 CCATAAACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19899802 original size:5 final size:5
Alignment explanation
Indices: 19899787--19899900 Score: 183
Period size: 5 Copynumber: 22.8 Consensus size: 5
19899777 TATATACAAC
* * *
19899787 TTTCA TATCA TTTCA TATCA TTTCA TTTCA TTTCA TTTCA TTTCA TATCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
* *
19899837 TTTCA TGTCA TTTCA TATCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
19899887 TTTCA TTTCA TTTC
1 TTTCA TTTCA TTTC
19899901 TAGACAGACG
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 99 1.00
ACGTcount: A:0.23, C:0.20, G:0.01, T:0.56
Consensus pattern (5 bp):
TTTCA
Found at i:19909675 original size:21 final size:21
Alignment explanation
Indices: 19909650--19909692 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19909640 CATAATAAGT
19909650 TTATAAGAGGATTTATGGATG
1 TTATAAGAGGATTTATGGATG
19909671 TTATAAGAGGATTTATGGATG
1 TTATAAGAGGATTTATGGATG
19909692 T
1 T
19909693 AAGTTAGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.40
Consensus pattern (21 bp):
TTATAAGAGGATTTATGGATG
Found at i:19910354 original size:750 final size:749
Alignment explanation
Indices: 19908910--19910403 Score: 2774
Period size: 750 Copynumber: 2.0 Consensus size: 749
19908900 GTTCTTTGGA
19908910 GATTTTGGATGTTATAAGAGGATTTATGGATGTAAGTTAGTTGGATTAAGTAATGATGAGTTTAA
1 GATTTTGGATGTTATAAGAGGATTTATGGATGTAAGTTAGTTGGATTAAGTAATGATGAGTTTAA
* *
19908975 TGGTATGGTCGGGGATGAAAGTAAGAGATTTAGGCGAAAATGTGGTAAAAAGCAAAGAAAAATAT
66 TGGTATGGTCAGGGATGAAAGTAAGAGATTTAGGCGAAAATATGGTAAAAAGCAAAGAAAAATAT
19909040 GTAAAATACGGGTAACAATATCGGTACTGGAAGAACAATACCGATACTATAGGATTAAATTTGAG
131 GTAAAATACGGGTAACAATATCGGTACTGGAAGAACAATACCGATACTATAGGATTAAATTTGAG
19909105 GAAAAATGATAAACACGACGAACAATATCGATACTTATGCAAGTGGTATCGATACTGAAGTGGGG
196 GAAAAATGATAAACACGACGAACAATATCGATACTTATGCAAGTGGTATCGATACTGAAGTGGGG
19909170 GTATCGATACCAAGAGAGAAATATCGATTGAAAAATGGATTCCAGAATGTGAAAATGGTATCGGT
261 GTATCGATACCAAGAGAGAAATATCGATTGAAAAATGGATTCCAGAATGTGAAAATGGTATCGGT
*
19909235 AATGAAGGGAGTATCAATACCATAGTATAGAAGTATCGATACCATAAAAGGGGTACCGATACTAA
326 AATGAAGGGAGTATCAATACCATAGTATAGAAGTATCGATACCATAAAAGGGATACCGATACTAA
*
19909300 TCAGCCTGAAATTTTAAGTTAGGATGAATTTTAATAGAATTCGAAAATGGTAGTACTTTTGAGTA
391 TCAGCCTGAAATTTTAAGTTAGGATGAATTTTAATAGAATTCAAAAATGGTAGTACTTTTGAGTA
19909365 TTATTTTATATAAATGTTAGAAAGTATACTAACATTTGTATTGTATGTGTGATTATGGATGCTTG
456 TTATTTTATATAAATGTTAGAAAGTATACTAACATTTGTATTGTATGTGTGATTATGGATGCTTG
* *
19909430 TGTAGATCGTAACCAAGCTCATGAATCAAGCAAGAAAAAGAACAATGATAAAGTTGTCGAATAAT
521 TGTAAATCGTAACCAAGCTAATGAATCAAGCAAGAAAAAGAACAATGATAAAGTTGTCGAATAAT
* *
19909495 CGGACATTAGTAAGGCATAATAGTGAGGATTACTAGGTGAGTGCATTGATCATGTACTTATATGT
586 CGGACATCAGTAAGGCATAATAGTGAGGATTACCAGGTGAGTGCATTGATCATGTACTTATATGT
19909560 TATGATAGTCATAGATGCATTTTCCTTAATATATGTATTGCATTTACCGAATGAGCACTATTTGT
651 TATGATAGTCATAGATGCATTTTCCTTAATATATGTATTGCATTTACCGAATGAGCACTATTTGT
19909625 GCAACCTAAGAAATTCATAATAAGTTTATAAGAG
716 GCAACCTAAGAAATTCATAATAAGTTTATAAGAG
19909659 GATTTATGGATGTTATAAGAGGATTTATGGATGTAAGTTAGTTGGATTAAGTAATGATGAGTTTA
1 GATTT-TGGATGTTATAAGAGGATTTATGGATGTAAGTTAGTTGGATTAAGTAATGATGAGTTTA
*
19909724 ATGGTATGGTCAGGGATGAAAGTAAGAGATTTAGGCGAAAATATGGTAAAAAGCAAAGAAAAATT
65 ATGGTATGGTCAGGGATGAAAGTAAGAGATTTAGGCGAAAATATGGTAAAAAGCAAAGAAAAATA
* **
19909789 TGTAAAATATGGGTAACGGTATCGGTACTGGAAGAACAATACCGATACTATAGGATTAAATTTGA
130 TGTAAAATACGGGTAACAATATCGGTACTGGAAGAACAATACCGATACTATAGGATTAAATTTGA
*
19909854 GGAAAAATGATAAACACGACGAACAATATCGATACTTATGCAAGTGGTATCGGTACTGAAGTGGG
195 GGAAAAATGATAAACACGACGAACAATATCGATACTTATGCAAGTGGTATCGATACTGAAGTGGG
19909919 GGTATCGATACCAAGAG-GAAGATATCGATTGAAAAATGGATTCCAGAATGTGAAAATGGTATCG
260 GGTATCGATACCAAGAGAGAA-ATATCGATTGAAAAATGGATTCCAGAATGTGAAAATGGTATCG
*
19909983 GTAATGAAGGGAGTATCAATACTATAGTATAGAAGTATCGATACCATAAAAGGGATACCGATACT
324 GTAATGAAGGGAGTATCAATACCATAGTATAGAAGTATCGATACCATAAAAGGGATACCGATACT
*
19910048 AATCAGCCTGAAATTTTAATTTAGGATGAATTTTAATAGAATTCAAAAATGGTAGTACTTTTGAG
389 AATCAGCCTGAAATTTTAAGTTAGGATGAATTTTAATAGAATTCAAAAATGGTAGTACTTTTGAG
* *
19910113 TATTCTTTTGTATAAATGTTAGAAAGTATACTAACATTTGTATTGTATGTGTGATTATGGATGCT
454 TATTATTTTATATAAATGTTAGAAAGTATACTAACATTTGTATTGTATGTGTGATTATGGATGCT
*
19910178 TGTGTAAATCGTAACCAAGCTAATGAATCAAGCAAGAAAAAGAGCAATGATAAAGTTGTCGAATA
519 TGTGTAAATCGTAACCAAGCTAATGAATCAAGCAAGAAAAAGAACAATGATAAAGTTGTCGAATA
*
19910243 ATCGGACATCAGTAAGGCATAATTGTGAGGATTACCAGGTGAGTGCATTGATCATGTACTTATAT
584 ATCGGACATCAGTAAGGCATAATAGTGAGGATTACCAGGTGAGTGCATTGATCATGTACTTATAT
* *
19910308 GTTATGATAGTCATAGATGCATTTTGCTTAATATATGTATTGCATTTATCGAATGAGCACTATTT
649 GTTATGATAGTCATAGATGCATTTTCCTTAATATATGTATTGCATTTACCGAATGAGCACTATTT
19910373 GTGCAACCTAAGAAATTCATAATAAGTTTAT
714 GTGCAACCTAAGAAATTCATAATAAGTTTAT
19910404 GAATTTCCGT
Statistics
Matches: 722, Mismatches: 21, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
749 8 0.01
750 714 0.99
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (749 bp):
GATTTTGGATGTTATAAGAGGATTTATGGATGTAAGTTAGTTGGATTAAGTAATGATGAGTTTAA
TGGTATGGTCAGGGATGAAAGTAAGAGATTTAGGCGAAAATATGGTAAAAAGCAAAGAAAAATAT
GTAAAATACGGGTAACAATATCGGTACTGGAAGAACAATACCGATACTATAGGATTAAATTTGAG
GAAAAATGATAAACACGACGAACAATATCGATACTTATGCAAGTGGTATCGATACTGAAGTGGGG
GTATCGATACCAAGAGAGAAATATCGATTGAAAAATGGATTCCAGAATGTGAAAATGGTATCGGT
AATGAAGGGAGTATCAATACCATAGTATAGAAGTATCGATACCATAAAAGGGATACCGATACTAA
TCAGCCTGAAATTTTAAGTTAGGATGAATTTTAATAGAATTCAAAAATGGTAGTACTTTTGAGTA
TTATTTTATATAAATGTTAGAAAGTATACTAACATTTGTATTGTATGTGTGATTATGGATGCTTG
TGTAAATCGTAACCAAGCTAATGAATCAAGCAAGAAAAAGAACAATGATAAAGTTGTCGAATAAT
CGGACATCAGTAAGGCATAATAGTGAGGATTACCAGGTGAGTGCATTGATCATGTACTTATATGT
TATGATAGTCATAGATGCATTTTCCTTAATATATGTATTGCATTTACCGAATGAGCACTATTTGT
GCAACCTAAGAAATTCATAATAAGTTTATAAGAG
Found at i:19910526 original size:55 final size:55
Alignment explanation
Indices: 19910364--19910862 Score: 553
Period size: 55 Copynumber: 9.3 Consensus size: 55
19910354 TATCGAATGA
* * *
19910364 GCACTATTTGTGCAACCT-A-AGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTCACA-AAATTCATAATGAGTTTATGAATTTCTGTATTG
* *
19910418 ACACTATGTGTGCAACCT-A-AGAAATTCATAATAAGTTTATGAATTT-TCGTATTG
1 GCACTATGTGTGCAACCTCACA-AAATTCATAATGAGTTTATGAATTTCT-GTATTG
* *
19910472 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGCTTATGAATTTCTATATTG
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
*
19910527 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
*
19910582 GCACTATGTGTGCAACCTCACAAAATTCTTAATGAGTTTATGAATTTCTGTATTG
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
* * *
19910637 GCACTCTGTGTGCAACCTCACGAAATTCATAATGAGTTTATGAATTT-TCATATTG
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCT-GTATTG
* * * * * * *
19910692 GAACTATATGTTCAACCTCACGAAATTCATAATGACTTTATGAACTTCCG---T-
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
* * * *
19910743 --A-T-TG-GTGCAACCTCACGAAATTCATAACGATTTTATGAATTTTTGTATTG
1 GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
* * ** * * *
19910793 GTACTATGTGTACAATCC-CACGTAATTCATAATGAGTTTGTGAATTACTGTATCG
1 GCACTATGTGTGCAA-CCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
* *
19910848 GCACTACGCGTGCAA
1 GCACTATGTGTGCAA
19910863 AGCCATGGAA
Statistics
Matches: 386, Mismatches: 43, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
46 35 0.09
47 1 0.00
48 1 0.00
49 2 0.01
52 2 0.01
53 1 0.00
54 70 0.18
55 270 0.70
56 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (55 bp):
GCACTATGTGTGCAACCTCACAAAATTCATAATGAGTTTATGAATTTCTGTATTG
Found at i:19910821 original size:101 final size:101
Alignment explanation
Indices: 19910646--19910836 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 101
19910636 GGCACTCTGT
* *
19910646 GTGCAACCTCACGAAATTCATAATGAGTTTATGAATTTTCATATTGGAACTATATGTTCAACCTC
1 GTGCAACCTCACGAAATTCATAACGAGTTTATGAATTTTCATATTGGAACTATATGTACAACCTC
19910711 ACGAAATTCATAATGACTTTATGAACTTCCGTATTG
66 ACGAAATTCATAATGACTTTATGAACTTCCGTATTG
* ** * *
19910747 GTGCAACCTCACGAAATTCATAACGATTTTATGAATTTTTGTATTGGTACTATGTGTACAATCC-
1 GTGCAACCTCACGAAATTCATAACGAGTTTATGAATTTTCATATTGGAACTATATGTACAA-CCT
* * *
19910811 CACGTAATTCATAATGAGTTTGTGAA
65 CACGAAATTCATAATGACTTTATGAA
19910837 TTACTGTATC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 77 0.97
102 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (101 bp):
GTGCAACCTCACGAAATTCATAACGAGTTTATGAATTTTCATATTGGAACTATATGTACAACCTC
ACGAAATTCATAATGACTTTATGAACTTCCGTATTG
Found at i:19917332 original size:49 final size:49
Alignment explanation
Indices: 19917243--19917434 Score: 278
Period size: 49 Copynumber: 3.9 Consensus size: 49
19917233 GAATACCATG
* * *
19917243 AGTGGCACCTTTTATGTCGATAATGTACTGTTATGCATTTAATTTTCATT
1 AGTGGCACCTTTTATGCCGA-AATGCACCGTTATGCATTTAATTTTCATT
* * * *
19917293 AGTGACACCTTTTATGCCGAAATGCATCATTATGCATTTAACTATT-ATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAA-TTTTCATT
*
19917342 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
*
19917391 AGTGGCACCTTTTATACCGAAATGCACCGTTATGCATTTAATTT
1 AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTT
19917435 GGCAACATCG
Statistics
Matches: 126, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
48 2 0.02
49 103 0.82
50 21 0.17
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (49 bp):
AGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAATTTTCATT
Found at i:19919714 original size:54 final size:54
Alignment explanation
Indices: 19919632--19919744 Score: 199
Period size: 54 Copynumber: 2.1 Consensus size: 54
19919622 TACTGAATGA
*
19919632 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTG
*
19919686 GCACTATGTGTGCAACCTATGAAATTCATAATAAGTTTATGAATTTCCATATTG
1 GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTG
*
19919740 ACACT
1 GCACT
19919745 GTATTGGCAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (54 bp):
GCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTG
Found at i:19925796 original size:11 final size:10
Alignment explanation
Indices: 19925766--19925811 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
19925756 ACGGGTCGTG
19925766 ACCGGTC-AA
1 ACCGGTCAAA
19925775 ACCGGTCAAA
1 ACCGGTCAAA
19925785 ACCGGTTCAAA
1 ACCGG-TCAAA
19925796 ACCGGTCAAA
1 ACCGGTCAAA
19925806 ACCGGT
1 ACCGGT
19925812 TTCCAGCGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.20
10 18 0.51
11 10 0.29
ACGTcount: A:0.35, C:0.30, G:0.22, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:19925799 original size:21 final size:20
Alignment explanation
Indices: 19925766--19925812 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
19925756 ACGGGTCGTG
19925766 ACCGG-TCAAACCGGTCAAA
1 ACCGGTTCAAACCGGTCAAA
19925785 ACCGGTTCAAAACCGGTCAAA
1 ACCGGTTC-AAACCGGTCAAA
19925806 ACCGGTT
1 ACCGGTT
19925813 TCCAGCGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.19
20 2 0.08
21 19 0.73
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (20 bp):
ACCGGTTCAAACCGGTCAAA
Found at i:19933900 original size:60 final size:59
Alignment explanation
Indices: 19933825--19933998 Score: 215
Period size: 60 Copynumber: 2.9 Consensus size: 59
19933815 CAAAACAAGA
* *
19933825 ATCCATAAGAACTTACCCTAGACCCCTAGGATCCAAGAGTCCAATAT-GAATGATACAGGC
1 ATCCATAA-AACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGGAA-GATACAGGC
* * ** *
19933885 ATCCATAAATACTTACCCTAGAACACTAGGAACTGTGAGTCCAATATGGAAGATACATGC
1 ATCCATAAA-ACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGGAAGATACAGGC
* * *
19933945 ATCCATAAGGACTTACCCTAGACCACTAGGATCTAGGAGTCCAATATAGAAGAT
1 ATCCATAA-AACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGGAAGAT
19933999 TAAAACAGAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 94 0.96
61 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (59 bp):
ATCCATAAAACTTACCCTAGACCACTAGGATCTAAGAGTCCAATATGGAAGATACAGGC
Found at i:19934332 original size:24 final size:24
Alignment explanation
Indices: 19934287--19934333 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19934277 CACAAGGAAT
*
19934287 ATAAAATAGGACATGTTGAGAAAC
1 ATAAAATAGGACATGTTCAGAAAC
19934311 ATAAAATAGGACTAT-TTCAGAAA
1 ATAAAATAGGAC-ATGTTCAGAAA
19934334 AATTAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (24 bp):
ATAAAATAGGACATGTTCAGAAAC
Found at i:19935638 original size:23 final size:23
Alignment explanation
Indices: 19935612--19935656 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19935602 TGTTTTAATA
19935612 TTATTTTCATTTT-TTATATTTAT
1 TTATTTTCATTTTCTT-TATTTAT
*
19935635 TTATTTTTATTTTCTTTATTTA
1 TTATTTTCATTTTCTTTATTTA
19935657 GGTAACACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTATTTTCATTTTCTTTATTTAT
Found at i:19935652 original size:15 final size:16
Alignment explanation
Indices: 19935585--19935655 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 16
19935575 GGGGCAACCC
19935585 ATTTTTATAGTTTATTT
1 ATTTTTATA-TTTATTT
19935602 -TGTTTTA-ATATTATTTT
1 AT-TTTTATAT-TTA-TTT
19935619 CATTTTTTATATTTATTT
1 -A-TTTTTATATTTATTT
*
19935637 ATTTTTAT-TTTCTTT
1 ATTTTTATATTTATTT
19935652 ATTT
1 ATTT
19935656 AGGTAACACT
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
15 11 0.24
16 12 0.26
17 9 0.20
18 3 0.07
19 8 0.17
20 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTTTATATTTATTT
Found at i:19938477 original size:21 final size:21
Alignment explanation
Indices: 19938449--19938540 Score: 68
Period size: 22 Copynumber: 4.4 Consensus size: 21
19938439 AAATAATAAT
19938449 AATA-ATAATATATTATTCAA
1 AATATATAATATATTATTCAA
*
19938469 AATATATAATATATATTTTCAA
1 AATATATAATATAT-TATTCAA
* *
19938491 TAAAACCAT-ATATATT-TT-AA
1 -AATA-TATAATATATTATTCAA
*
19938511 ATTATATAATATA-TATTTCAAA
1 AATATATAATATATTA-TTC-AA
19938533 AATATATA
1 AATATATA
19938541 TGCTCTCAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
18 3 0.05
19 7 0.12
20 8 0.14
21 11 0.20
22 16 0.29
23 9 0.16
24 2 0.04
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATATAATATATTATTCAA
Found at i:19939798 original size:159 final size:159
Alignment explanation
Indices: 19939509--19939826 Score: 627
Period size: 159 Copynumber: 2.0 Consensus size: 159
19939499 TGGACGTAGA
*
19939509 CTTTGTTTGAGAAAGTCGAACCCCTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGTAAAAGC
1 CTTTGTTTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGTAAAAGC
19939574 TTCCACAAAAATTTTAATTGCCAATTCACCCCCCTCTTGGCCGATTCCGTCAATCGATTAACTCA
66 TTCCACAAAAATTTTAATTGCCAATTCACCCCCCTCTTGGCCGATTCCGTCAATCGATTAACTCA
19939639 ACAATTGGCATCAGAGCCTAACTCATTTG
131 ACAATTGGCATCAGAGCCTAACTCATTTG
19939668 CTTTGTTTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGTAAAAGC
1 CTTTGTTTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGTAAAAGC
19939733 TTCCACAAAAATTTTAATTGCCAATTCACCCCCCTCTTGGCCGATTCCGTCAATCGATTAACTCA
66 TTCCACAAAAATTTTAATTGCCAATTCACCCCCCTCTTGGCCGATTCCGTCAATCGATTAACTCA
19939798 ACAATTGGCATCAGAGCCTAACTCATTTG
131 ACAATTGGCATCAGAGCCTAACTCATTTG
19939827 AAGGTTTAAT
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
159 158 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (159 bp):
CTTTGTTTGAGAAAGTCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGTAAAAGC
TTCCACAAAAATTTTAATTGCCAATTCACCCCCCTCTTGGCCGATTCCGTCAATCGATTAACTCA
ACAATTGGCATCAGAGCCTAACTCATTTG
Found at i:19941022 original size:20 final size:20
Alignment explanation
Indices: 19940993--19941032 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19940983 TATGAGAAAT
*
19940993 TGTTTTAAAATAT-AAAATGA
1 TGTTTCAAAAT-TGAAAATGA
19941013 TGTTTCAAAATTGAAAATGA
1 TGTTTCAAAATTGAAAATGA
19941033 AAAAACTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
TGTTTCAAAATTGAAAATGA
Found at i:19955662 original size:36 final size:37
Alignment explanation
Indices: 19955578--19955663 Score: 156
Period size: 37 Copynumber: 2.4 Consensus size: 37
19955568 AAACTGAATG
19955578 AAACAGTTTGTAATGGGGGTTATTTTTCATATTGAAA
1 AAACAGTTTGTAATGGGGGTTATTTTTCATATTGAAA
*
19955615 AAATAGTTTGTAATGGGGGTTATTTTTCATATTGAAA
1 AAACAGTTTGTAATGGGGGTTATTTTTCATATTGAAA
19955652 AAACAG-TTGTAA
1 AAACAGTTTGTAA
19955664 ATAAGGATTG
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 6 0.13
37 41 0.87
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (37 bp):
AAACAGTTTGTAATGGGGGTTATTTTTCATATTGAAA
Found at i:19962961 original size:99 final size:99
Alignment explanation
Indices: 19962850--19963032 Score: 287
Period size: 99 Copynumber: 1.8 Consensus size: 99
19962840 ATATTATATG
** * * **
19962850 TATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATG-GTCATGCTTTATGGATAA
1 TATACAATAAAGCTCAAATTGTCCCTCTAGAGCAATTAGTTAAATGCCCCA-GCTTTATGGATAA
*
19962914 GATTCAGCTAGCCTGATAAATGTGATTATAATTTA
65 GATTCAACTAGCCTGATAAATGTGATTATAATTTA
19962949 TATACAATAAAGCTCAAATTGTCCCTCTAGAGCAATTAGTTAAATGCCCCAGCTTTATGGATAAG
1 TATACAATAAAGCTCAAATTGTCCCTCTAGAGCAATTAGTTAAATGCCCCAGCTTTATGGATAAG
19963014 ATTCAACTAGCCTGATAAA
66 ATTCAACTAGCCTGATAAA
19963033 GGCAAATTAC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
99 74 0.97
100 2 0.03
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (99 bp):
TATACAATAAAGCTCAAATTGTCCCTCTAGAGCAATTAGTTAAATGCCCCAGCTTTATGGATAAG
ATTCAACTAGCCTGATAAATGTGATTATAATTTA
Found at i:19965046 original size:37 final size:37
Alignment explanation
Indices: 19965003--19965109 Score: 196
Period size: 37 Copynumber: 2.9 Consensus size: 37
19964993 CCTCTGGGCC
19965003 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATA
*
19965040 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATTA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATA
*
19965077 ATCTTAAGCCTTCACGGAAAAGTAGTGAAGCAA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
19965110 GCCATTAGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATA
Found at i:19965139 original size:193 final size:186
Alignment explanation
Indices: 19964818--19965228 Score: 601
Period size: 193 Copynumber: 2.2 Consensus size: 186
19964808 GGGCAAGTTA
*
19964818 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGC-AAATCAATCTTAAGCCTTCACAATGAATCAAAT
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCAATCTTAAGCCTTCACAATGAAGCAAAT
* * *
19964882 TAATCTTAATCCTTCATGGAAAAGTAGTGAAGCAAGCCATCAATAAGCCTTTCGAGCATGATGAT
66 TAATCTTAAGCCTTCACGGAAAAGTAGTGAAGCAAGCCATCAATAAGCCTTCCGAGCATGATGAT
* * * *
19964947 TAAATTATTCGGGTCATCTGTCAGCCTTCCAAGCAAGTTGATAAGTCCTCTGGGCC
131 TAAATCATTCGGGTCAGCCGTCAGCCTTCCAAGCAAGATGATAAGTCCTCTGGGCC
19965003 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAAT-AATCTTAAGCCTTCACGGAAGAGTAGTG
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCAATCTTAAGCCTTCAC-----A--A-TG
* * *
19965067 AAGCAAATTAATCTTAAGCCTTCACGGAAAAGTAGTGAAGCAAGCCATTAGTTAGCCTTCCGAGC
58 AAGCAAATTAATCTTAAGCCTTCACGGAAAAGTAGTGAAGCAAGCCATCAATAAGCCTTCCGAGC
*
19965132 ATGATGATTAAATCATTCGGGTCAGCCGTCAGCCTTCCGAGCAAGATGATAAGTCCTCTGGGCC
123 ATGATGATTAAATCATTCGGGTCAGCCGTCAGCCTTCCAAGCAAGATGATAAGTCCTCTGGGCC
* **
19965196 ATTTTAAGCCTTCACAAAAGAGTAGTGAAGCAA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
19965229 GCCATCAGTA
Statistics
Matches: 202, Mismatches: 15, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
185 47 0.23
186 4 0.02
190 1 0.00
192 1 0.00
193 149 0.74
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (186 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAAATCAATCTTAAGCCTTCACAATGAAGCAAAT
TAATCTTAAGCCTTCACGGAAAAGTAGTGAAGCAAGCCATCAATAAGCCTTCCGAGCATGATGAT
TAAATCATTCGGGTCAGCCGTCAGCCTTCCAAGCAAGATGATAAGTCCTCTGGGCC
Found at i:19965292 original size:119 final size:119
Alignment explanation
Indices: 19965077--19965343 Score: 401
Period size: 119 Copynumber: 2.2 Consensus size: 119
19965067 AAGCAAATTA
* *
19965077 ATCTTAAGCCTTCACGGAAA-AGTAGTGAAGCAAGCCATTAGTTAGCCTTCCGAGCATGATGATT
1 ATCTTAAGCCTTCAC-GAAAGAGTAGTGAAGCAAGCCATCAGTAAGCCTTCCGAGCATGATGATT
* *
19965141 AAATCATTCGGGTCAGCCGTCAGCCTTCCGAGCAAGATGATAAGTCCTCTGGGCC
65 AAATCATTCGGGTCAGCCGTAAGCCTTCCGAGCAAGATGATAAGTCCTCTGGGAC
* *
19965196 ATTTTAAGCCTTCACAAAAGAGTAGTGAAGCAAGCCATCAGTAAGCCTTCCGAGCATGATGATTA
1 ATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAGCCATCAGTAAGCCTTCCGAGCATGATGATTA
* * * * * *
19965261 AATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAAGTTCTCTGGGAT
66 AATCATTCGGGTCAGCCGTAAGCCTTCCGAGCAAGATGATAAGTCCTCTGGGAC
*
19965315 ATCTTAAGCCTTCACGGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACGAAAGAGTAGTGAA
19965344 ACAAATCAAG
Statistics
Matches: 132, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
118 3 0.02
119 129 0.98
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (119 bp):
ATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAGCCATCAGTAAGCCTTCCGAGCATGATGATTA
AATCATTCGGGTCAGCCGTAAGCCTTCCGAGCAAGATGATAAGTCCTCTGGGAC
Found at i:19973418 original size:61 final size:61
Alignment explanation
Indices: 19973292--19973410 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
19973282 CAAGGACACA
* * * *
19973292 TAGTGTAGGTGGTGGGCACAACCTTATGTGTCATATCCGGATCAGTACTAGAGTGTAAACC
1 TAGTGTAGGTAGTGGGCACAACCTTATGTGTCATATCCGAATCAGCACTAGAGCGTAAACC
**
19973353 TAGTGTAGGTAGTGGGCATGACCTTATGTGTCATATCCGAATC-GACACTAGAGCGTAA
1 TAGTGTAGGTAGTGGGCACAACCTTATGTGTCATATCCGAATCAG-CACTAGAGCGTAA
19973411 GATTAGTGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 1 0.02
61 50 0.98
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.28
Consensus pattern (61 bp):
TAGTGTAGGTAGTGGGCACAACCTTATGTGTCATATCCGAATCAGCACTAGAGCGTAAACC
Found at i:19978028 original size:21 final size:22
Alignment explanation
Indices: 19977980--19978032 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
19977970 CAATGAATTT
* *
19977980 ATAAATTAGTTGAAAATTTAAAG
1 ATAAATTA-TTCAAAATTAAAAG
*
19978003 GTAAATTATTCAAAA-TAAAAG
1 ATAAATTATTCAAAATTAAAAG
19978024 ATAAATTAT
1 ATAAATTAT
19978033 AGTAATGGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 13 0.50
22 6 0.23
23 7 0.27
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (22 bp):
ATAAATTATTCAAAATTAAAAG
Found at i:19979098 original size:21 final size:22
Alignment explanation
Indices: 19979072--19979123 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
19979062 GATCACTGAT
* *
19979072 ATAATTTACCTTTTATTTTA-A
1 ATAATTTACCTTTAAATTTACA
19979093 ATAATTTACCTTTAAATTTACA
1 ATAATTTACCTTTAAATTTACA
19979115 ACTAATTTA
1 A-TAATTTA
19979124 TAATTATACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 18 0.67
22 2 0.07
23 7 0.26
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTTACCTTTAAATTTACA
Found at i:19984865 original size:3 final size:3
Alignment explanation
Indices: 19984857--19984882 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19984847 CCCTACAATA
19984857 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
19984883 CAACCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19984985 original size:26 final size:25
Alignment explanation
Indices: 19984948--19985176 Score: 105
Period size: 24 Copynumber: 9.9 Consensus size: 25
19984938 TTATTTTCAA
19984948 ATTATA-ATATATGTTTTCTAAAACT
1 ATTATATATATAT-TTTTCTAAAACT
*
19984973 ATTATATATATA---TT-TATAA-T
1 ATTATATATATATTTTTCTAAAACT
* * *
19984993 -TCAAACTATATA-TTTTATAAAACT
1 ATTATA-TATATATTTTTCTAAAACT
*
19985017 A-TATATATATATATTTC-AAAACT
1 ATTATATATATATTTTTCTAAAACT
*
19985040 A-TACTATATATATGTTTT-TCAAA--
1 ATTA-TATATATAT-TTTTCTAAAACT
*
19985063 ATTATATATTTA-TTTTC-AAAACT
1 ATTATATATATATTTTTCTAAAACT
*
19985086 ATACTATATTTATATTTTTC-AAAACT
1 AT--TATATATATATTTTTCTAAAACT
*
19985112 A-TACTATACATATTTTT-TAAAAC-
1 ATTA-TATATATATTTTTCTAAAACT
19985135 --TATATAT-TA-TTTTC-AAAACT
1 ATTATATATATATTTTTCTAAAACT
** *
19985155 ATGCTATATACATTTTTC-AAAA
1 ATTATATATATATTTTTCTAAAA
19985177 TATAACAAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 53
0.68 0.09 0.23
Matches are distributed among these distances:
19 12 0.08
20 9 0.06
21 15 0.09
22 11 0.07
23 32 0.20
24 42 0.27
25 20 0.13
26 17 0.11
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (25 bp):
ATTATATATATATTTTTCTAAAACT
Found at i:19985088 original size:69 final size:67
Alignment explanation
Indices: 19984917--19985180 Score: 266
Period size: 67 Copynumber: 4.0 Consensus size: 67
19984907 ATTATATATC
*
19984917 TATATA-TTTTT-AATACTATAT-TTATTTTC-AAA-T-TATA-ATATATGTTTTCTAAAACTAT
1 TATATATTTTTTCAAAACTATATATTATTTTCAAAACTATATATATATAT-TTTTC-AAAACTA-
19984975 TA-TA
63 TACTA
* *
19984979 TATATATTTATAATTC-AAACTATATATT-TTAT-AAAACTATATATATATATATTTCAAAACTA
1 TATATATTT-T--TTCAAAACTATATATTATTTTCAAAACTATATATATATATTTTTCAAAACTA
19985041 TACTA
63 TACTA
*
19985046 TATATATGTTTTTCAAAATTATATATTTATTTTCAAAACTATACTATATTTATATTTTTCAAAAC
1 TATATAT-TTTTTCAAAACTATATA-TTATTTTCAAAACTATA-TATA--TATATTTTTCAAAAC
19985111 TATACTA
61 TATACTA
* * *
19985118 TACATATTTTTT-AAAACTATATATTATTTTCAAAACTATGCTATATACATTTTTCAAAA-TATA
1 TATATATTTTTTCAAAACTATATATTATTTTCAAAACTAT-ATATATATATTTTTCAAAACTATA
19985181 ACAAAACAAA
Statistics
Matches: 172, Mismatches: 10, Indels: 36
0.79 0.05 0.17
Matches are distributed among these distances:
62 6 0.03
63 2 0.01
64 1 0.01
65 3 0.02
66 31 0.18
67 35 0.20
68 13 0.08
69 35 0.20
70 14 0.08
71 5 0.03
72 27 0.16
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.48
Consensus pattern (67 bp):
TATATATTTTTTCAAAACTATATATTATTTTCAAAACTATATATATATATTTTTCAAAACTATAC
TA
Found at i:19985094 original size:115 final size:112
Alignment explanation
Indices: 19984941--19985181 Score: 262
Period size: 115 Copynumber: 2.1 Consensus size: 112
19984931 ACTATATTTA
* **
19984941 TTTTC-AAATTATAATATATGTTTTCTAAAACTATTATATATATATTTAT-AATTC-AAACTAT-
1 TTTTCAAAATTATAATATATATTTTCTAAAACTATTATATATATATTTATCAAAACTAAACTATA
*
19985002 ATATTTTATAAAACTATATATATATATATTTCAAAACTATACTATATATATGT
66 ATATTTTATAAAAC--TATATAT-TAT-TTTCAAAACTATACTATATACA--T
* * * *
19985055 TTTTCAAAATTAT-ATATTTATTTTC-AAAACTATACTATATTTATATTTTTCAAAACTATACTA
1 TTTTCAAAATTATAATATATATTTTCTAAAACTAT--TATATATATATTTATCAAAACTAAACTA
* *
19985118 TACATATTTTTTAAAACTATATATTATTTTCAAAACTATGCTATATACAT
64 TA-ATATTTTATAAAACTATATATTATTTTCAAAACTATACTATATACAT
19985168 TTTTCAAAA-TATAA
1 TTTTCAAAATTATAA
19985182 CAAAACAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 17
0.80 0.07 0.12
Matches are distributed among these distances:
112 3 0.03
113 19 0.17
114 15 0.14
115 40 0.37
116 6 0.06
117 13 0.12
119 13 0.12
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (112 bp):
TTTTCAAAATTATAATATATATTTTCTAAAACTATTATATATATATTTATCAAAACTAAACTATA
ATATTTTATAAAACTATATATTATTTTCAAAACTATACTATATACAT
Found at i:19985104 original size:46 final size:47
Alignment explanation
Indices: 19984999--19985126 Score: 161
Period size: 46 Copynumber: 2.7 Consensus size: 47
19984989 TAATTCAAAC
19984999 TATATATTTTAT-AAAACTATATATATATATATTTCAAAACTATACTATA
1 TATATATTTT-TCAAAA-T-TATATATATATATTTCAAAACTATACTATA
* *
19985048 TATATGTTTTTCAAAATTATATATTTAT-TTTCAAAACTATACTATA
1 TATATATTTTTCAAAATTATATATATATATTTCAAAACTATACTATA
* * *
19985094 TTTATATTTTTCAAAACTATACTATACATATTT
1 TATATATTTTTCAAAATTATA-TATATATATTT
19985127 TTTAAAACTA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
46 36 0.52
47 15 0.22
48 5 0.07
49 13 0.19
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.48
Consensus pattern (47 bp):
TATATATTTTTCAAAATTATATATATATATTTCAAAACTATACTATA
Found at i:19985171 original size:24 final size:23
Alignment explanation
Indices: 19984999--19985176 Score: 156
Period size: 24 Copynumber: 7.7 Consensus size: 23
19984989 TAATTCAAAC
*
19984999 TATATATTTTAT-AAAACTATATA
1 TATATATTTT-TCAAAACTATCTA
*
19985022 TATATATATTTCAAAACTATACTA
1 TATATATTTTTCAAAACTAT-CTA
*
19985046 TATATATGTTTTTCAAAA-T-TATA
1 TATATA--TTTTTCAAAACTATCTA
*
19985069 TATTTA-TTTTCAAAACTATACTA
1 TATATATTTTTCAAAACTAT-CTA
19985092 TATTTATATTTTTCAAAACTATACTA
1 TA--TATATTTTTCAAAACTAT-CTA
* *
19985118 TACATATTTTTTAAAACTA--TA
1 TATATATTTTTCAAAACTATCTA
19985139 TAT-TA-TTTTCAAAACTATGCTA
1 TATATATTTTTCAAAACTAT-CTA
*
19985161 TATACATTTTTCAAAA
1 TATATATTTTTCAAAA
19985177 TATAACAAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 29
0.76 0.07 0.17
Matches are distributed among these distances:
19 11 0.09
20 11 0.09
21 5 0.04
22 7 0.05
23 29 0.23
24 33 0.26
25 4 0.03
26 28 0.22
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (23 bp):
TATATATTTTTCAAAACTATCTA
Found at i:19985202 original size:15 final size:16
Alignment explanation
Indices: 19985173--19985206 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19985163 TACATTTTTC
19985173 AAAATATAACAAAACA
1 AAAATATAACAAAACA
*
19985189 AAAATA-AACTAAACA
1 AAAATATAACAAAACA
19985204 AAA
1 AAA
19985207 GGAAACTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATATAACAAAACA
Found at i:19988332 original size:18 final size:17
Alignment explanation
Indices: 19988278--19988326 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
19988268 TTAGACCCTT
* *
19988278 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
19988296 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
19988314 AGTGCATTCGATG
1 AGTGCA-TCGATG
19988327 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:19988384 original size:64 final size:63
Alignment explanation
Indices: 19988298--19988507 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 63
19988288 TGCACTAAGA
* *
19988298 GTGCATCGATGCATCAAGTGCATTCGATGTTTC-AAAATAGCCAGAGTGCATCGATGCATGGCT-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCGAAAAT--CCACAGTGCATCGATGCATGG-TA
19988361 G
63 G
* * * *
19988362 GTGTATCGATGCATCAAATGCATTCGATGTTTTCGTAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCG-AAAATCCACAGTGCATCGATGCATGGTAG
* * **
19988427 GTGCATCGATGCATAAAATGCATTCGATG-TTC-AATTTAATTCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCGAA---AATCCACAGTGCATCGATGCATGG-T
*
19988490 TG
62 AG
*
19988492 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
19988508 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
61 2 0.02
63 3 0.02
64 47 0.39
65 64 0.53
67 5 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCGAAAATCCACAGTGCATCGATGCATGGTAG
Found at i:19997126 original size:65 final size:65
Alignment explanation
Indices: 19996993--19997152 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
19996983 TGCACTAAGA
* * *
19996993 GTGCATCGATGCATCAAGTGCGTTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
19997057 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
19997120 AT
65 -G
* *
19997122 GTGCATCGATGCATGAAATGAATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
19997153 CAATTTAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.33
65 53 0.63
66 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:20001540 original size:20 final size:22
Alignment explanation
Indices: 20001466--20001548 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
20001456 CAGAACCCCA
* **
20001466 GGGGGGTATCGATTCCC-CTGT
1 GGGGGGAATCGATTCCCTCAAT
*
20001487 GGGGGGAATCGGTTCCCCTTCAA-
1 GGGGGGAATCGATT-CCC-TCAAT
*
20001510 AGGGGGAATCGATTCCCTC-AT
1 GGGGGGAATCGATTCCCTCAAT
20001531 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
20001549 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
20 13 0.25
21 19 0.37
22 6 0.12
23 12 0.24
24 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTCAAT
Found at i:20014136 original size:19 final size:19
Alignment explanation
Indices: 20014112--20014148 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20014102 CTTGAGTTAC
20014112 CAGTCATCTAAGCCTTTAT
1 CAGTCATCTAAGCCTTTAT
20014131 CAGTCATCTAAGCCTTTA
1 CAGTCATCTAAGCCTTTA
20014149 CCATTCGCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (19 bp):
CAGTCATCTAAGCCTTTAT
Done.