Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 134 of 173
Found at i:40758604 original size:57 final size:57
Alignment explanation
Indices: 40758530--40758654 Score: 178
Period size: 57 Copynumber: 2.2 Consensus size: 57
40758520 TGACAAATTC
* ** *
40758530 TAAACCCTAAACCCTAACCCTTAACTTCGAAACCTTAAACCCTTAACTTAAAAACCA
1 TAAACCTTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCA
* * *
40758587 TAAACCTTAAACTCTAACCCTTAACTTAAAAACCCTAAACCCTTGACTTAAAAACCT
1 TAAACCTTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCA
40758644 TAAACCCTTAA
1 TAAA-CCTTAA
40758655 CTTAACTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
57 54 0.90
58 6 0.10
ACGTcount: A:0.42, C:0.31, G:0.02, T:0.25
Consensus pattern (57 bp):
TAAACCTTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCA
Found at i:40758630 original size:22 final size:22
Alignment explanation
Indices: 40758602--40758659 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
40758592 CTTAAACTCT
40758602 AACCCTTAACTTAAAAACCCTA
1 AACCCTTAACTTAAAAACCCTA
* *
40758624 AACCCTTGACTTAAAAACCTTA
1 AACCCTTAACTTAAAAACCCTA
40758646 AACCCTTAACTTAA
1 AACCCTTAACTTAA
40758660 CTTAAAAACC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.26
Consensus pattern (22 bp):
AACCCTTAACTTAAAAACCCTA
Found at i:40758677 original size:28 final size:28
Alignment explanation
Indices: 40758616--40758688 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
40758606 CTTAACTTAA
*
40758616 AAACCCTAAACCCTTGACTTAAAAACCTT
1 AAACCCTAAA-CCTTAACTTAAAAACCTT
*
40758645 AAACCCTTAA-CTTAACTTAAAAACCCTT
1 AAACCCTAAACCTTAACTTAAAAA-CCTT
*
40758673 TAACCCTAAACCTTAA
1 AAACCCTAAACCTTAA
40758689 ACCCTAACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 12 0.32
28 12 0.32
29 14 0.37
ACGTcount: A:0.42, C:0.30, G:0.01, T:0.26
Consensus pattern (28 bp):
AAACCCTAAACCTTAACTTAAAAACCTT
Found at i:40758691 original size:49 final size:49
Alignment explanation
Indices: 40758581--40758709 Score: 140
Period size: 49 Copynumber: 2.6 Consensus size: 49
40758571 CTTAACTTAA
* *
40758581 AAACCATAAACCTTAAACTC-TAACCCTTAACTTAAAAACCCTAAACCCT
1 AAACCTTAAACCTTAAACCCTTAA-CCTTAACTTAAAAACCCTAAACCCT
** *
40758630 TGA-CTTAAAAACCTTAAACCCTTAA-CTTAACTTAAAAACCCTTTAACCCT
1 AAACCTT--AAACCTTAAACCCTTAACCTTAACTTAAAAACCC-TAAACCCT
*
40758680 AAACCTTAAACCCT-AACCCTTAACCTTAAC
1 AAACCTTAAACCTTAAACCCTTAACCTTAAC
40758710 CCTAACCCTT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
48 11 0.17
49 29 0.44
50 20 0.30
51 6 0.09
ACGTcount: A:0.42, C:0.32, G:0.01, T:0.26
Consensus pattern (49 bp):
AAACCTTAAACCTTAAACCCTTAACCTTAACTTAAAAACCCTAAACCCT
Found at i:40758719 original size:13 final size:13
Alignment explanation
Indices: 40758666--40758718 Score: 63
Period size: 14 Copynumber: 4.0 Consensus size: 13
40758656 TTAACTTAAA
40758666 AACCCTTTAACCCT
1 AACCC-TTAACCCT
*
40758680 AAACCTTAAACCCT
1 AACCCTT-AACCCT
*
40758694 AACCCTTAACCTT
1 AACCCTTAACCCT
40758707 AACCC-TAACCCT
1 AACCCTTAACCCT
40758719 TGACTGGTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.18
13 12 0.35
14 16 0.47
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.25
Consensus pattern (13 bp):
AACCCTTAACCCT
Found at i:40762103 original size:127 final size:127
Alignment explanation
Indices: 40761830--40762401 Score: 862
Period size: 127 Copynumber: 4.5 Consensus size: 127
40761820 CCCAAACATG
* ** *
40761830 CTACTGTAGCAAAAGCGCGTCCACGTGGGCATGATTTCACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
40761895 TTGAAGCG--TTTTTATACTATTTGCTCAGAAATGTCAAGTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
*
40761955 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
40762020 TTGAAGCATTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* *
40762082 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCTATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
40762147 TTGAAGCGTTTTTTTTAATTATTTGCTCAGAAATGTCAAGTCGAAATTATTTCTTCCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* * *
40762209 CTACTGTAGCAAAAGCGCGTCCACGAAGGCGTGATTTCAGAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * *
40762274 TTGACGCGTTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTA-TTTTTGCAGGAC
66 TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
* ** * * * * *
40762335 CTACTGTAGCAAAAGCGCGTACACGTTGGCGCAACTTCAGAAATTCTTCTGATAAAGCATCATGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
40762400 TT
66 TT
40762402 TGATTTTATA
Statistics
Matches: 408, Mismatches: 37, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
125 67 0.16
126 69 0.17
127 272 0.67
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (127 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTTTAAACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTTCCAGGAC
Found at i:40778702 original size:28 final size:33
Alignment explanation
Indices: 40778644--40778708 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 33
40778634 GCATGAGAAT
* *
40778644 TTTTCCTTTTTTTATCTCTCTTGTTCTTTT-CC
1 TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
40778676 TTTT-CTTTCTTT-TCTCTCCT-TTC-TTTCCC
1 TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
40778705 TTTT
1 TTTT
40778709 ATTTTTGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.10
29 9 0.30
30 7 0.23
31 7 0.23
32 4 0.13
ACGTcount: A:0.02, C:0.28, G:0.02, T:0.69
Consensus pattern (33 bp):
TTTTCCTTTCTTTATCTCTCCTGTTCTTTTCCC
Found at i:40784372 original size:21 final size:22
Alignment explanation
Indices: 40784348--40784398 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
40784338 CGTATGGCAC
*
40784348 AATAATTTATTTTTC-TATTTA
1 AATAATTTATTTTTCATAATTA
*
40784369 AAT-ATGTATTTTTCATAATTA
1 AATAATTTATTTTTCATAATTA
*
40784390 ATTAATTTA
1 AATAATTTA
40784399 ATGAATTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (22 bp):
AATAATTTATTTTTCATAATTA
Found at i:40784861 original size:44 final size:44
Alignment explanation
Indices: 40784802--40784892 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
40784792 GTTGAAGCAA
* * *
40784802 AATAAAAGTTGTGATAATTATACATTTAAAAACAATTATATTTT
1 AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
* * *
40784846 AATAGAAGTTATGATAATTACATATTTAAAAATAATTATAATTT
1 AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
40784890 AAT
1 AAT
40784893 TTACAATTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (44 bp):
AATAAAAGTTATGATAATTACACATTTAAAAACAATTATAATTT
Found at i:40804016 original size:31 final size:30
Alignment explanation
Indices: 40803947--40804016 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
40803937 AGGTTTCATT
* *
40803947 TCAGTCACTCAACTTTAGAAAAATAACAAA
1 TCAGTCACTCAACATTACAAAAATAACAAA
* * *
40803977 ACAATCACT-AACATTATCAAAAAGTGACAAA
1 TCAGTCACTCAACATTA-CAAAAA-TAACAAA
40804008 TCAGTCACT
1 TCAGTCACT
40804017 TATTAACATT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 6 0.19
30 12 0.39
31 13 0.42
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (30 bp):
TCAGTCACTCAACATTACAAAAATAACAAA
Found at i:40804078 original size:21 final size:21
Alignment explanation
Indices: 40804052--40804091 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40804042 AATGGGACCA
40804052 CTGATGTGGCAAGTTAACTAG
1 CTGATGTGGCAAGTTAACTAG
*
40804073 CTGATGTGGCCAGTTAACT
1 CTGATGTGGCAAGTTAACT
40804092 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
CTGATGTGGCAAGTTAACTAG
Found at i:40806316 original size:18 final size:18
Alignment explanation
Indices: 40806295--40806330 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40806285 TCACACAAAG
*
40806295 TAAAAAAATATTAAAAAA
1 TAAAAAAATAATAAAAAA
*
40806313 TAAAAAATTAATAAAAAA
1 TAAAAAAATAATAAAAAA
40806331 ATTTAATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAAAAATAATAAAAAA
Found at i:40806690 original size:143 final size:145
Alignment explanation
Indices: 40806499--40806784 Score: 461
Period size: 143 Copynumber: 2.0 Consensus size: 145
40806489 GTAAAAATAT
* *
40806499 AATTTCATCATTTTAATAGTCTCCATCTTTATAATTTTTAAAGGATTAAATTAAAATTTTATCAT
1 AATTTCATCATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
* *
40806564 TTTT-AGGGGGTCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTCAAAGGGCC
66 TTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTCAAAGGGCA
40806628 TAAAT-GAAAATTAC
131 TAAATAGAAAATTAC
*
40806642 AATTTCA-CAATTTTAATAGCCTCTATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCA
1 AATTTCATC-ATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCA
* * * *
40806706 TTTTTAAGGGGGCCAAAGTGTAATTTTATCTTTATTAATTTAAAATTTTAAAAATTTCAAAGGGC
65 TTTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTCAAAGGGC
40806771 ATAAATAGAAAATT
130 ATAAATAGAAAATT
40806785 TTCCATTTTA
Statistics
Matches: 131, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
142 1 0.01
143 64 0.49
144 59 0.45
145 7 0.05
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (145 bp):
AATTTCATCATTTTAATAGCCTCCATCTTTATAATTTTTAAAGGATTAAATCAAAATTTTATCAT
TTTTAAGGGGGCCAAAGTGCAATTGTACCTTTACTAATTTAAAATTTTAAAAATTTCAAAGGGCA
TAAATAGAAAATTAC
Found at i:40807425 original size:11 final size:12
Alignment explanation
Indices: 40807409--40807456 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
40807399 TAAAACATAG
40807409 TTGTATT-TTAT
1 TTGTATTATTAT
40807420 TTGTATTATTAT
1 TTGTATTATTAT
40807432 TAT-TATTATTAT
1 T-TGTATTATTAT
40807444 TAT-TATTATTAT
1 T-TGTATTATTAT
40807456 T
1 T
40807457 ATTATTTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.20
12 27 0.77
13 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (12 bp):
TTGTATTATTAT
Found at i:40807431 original size:3 final size:3
Alignment explanation
Indices: 40807423--40807462 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
40807413 ATTTTATTTG
40807423 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
40807463 TATCTCAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40811948 original size:13 final size:13
Alignment explanation
Indices: 40811930--40811959 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40811920 GCACTAAAAG
*
40811930 ACAACAGAAGCAA
1 ACAACAGAAACAA
40811943 ACAACAGAAACAA
1 ACAACAGAAACAA
40811956 ACAA
1 ACAA
40811960 AAACAATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.23, G:0.10, T:0.00
Consensus pattern (13 bp):
ACAACAGAAACAA
Found at i:40812908 original size:12 final size:12
Alignment explanation
Indices: 40812888--40812920 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40812878 ATAAAAAAAC
40812888 ATTTTATTTAAT
1 ATTTTATTTAAT
*
40812900 ATTTCATTTAAT
1 ATTTTATTTAAT
40812912 -TTTTATTTA
1 ATTTTATTTA
40812921 TTTACTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTATTTAAT
Found at i:40813582 original size:41 final size:40
Alignment explanation
Indices: 40813530--40813621 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
40813520 CGTTTGGATA
* * *
40813530 AAAATGCCGCTAAAGATCGAGCA-TGAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAGATCGAG-ATTGAGAGGCGCTTTATGG
*
40813570 CAAAACGCCGCTAAAGATCGAGATTTAGAGGCGCTTTATGG
1 -AAAACGCCGCTAAAGATCGAGATTGAGAGGCGCTTTATGG
40813611 AAAACGCCGCT
1 AAAACGCCGCT
40813622 TAAAATAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 12 0.26
41 34 0.74
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (40 bp):
AAAACGCCGCTAAAGATCGAGATTGAGAGGCGCTTTATGG
Found at i:40813765 original size:41 final size:41
Alignment explanation
Indices: 40813704--40813941 Score: 354
Period size: 41 Copynumber: 5.8 Consensus size: 41
40813694 CTTTTGGAGA
*
40813704 TTTAGCGGCGTTTTTAG-GAAAGCGCCGCTAATGCCCAGGGC
1 TTTAGCGGCGTTTTT-GTGAAAGCGCCGCTAATGCCCAGGCC
40813745 TTTAGCGGCGTTTTTCG-GAAAGCGCCGCTAATGCCCAGGCC
1 TTTAGCGGCGTTTTT-GTGAAAGCGCCGCTAATGCCCAGGCC
*
40813786 TTTAGCGGCGTTTTTGTGAAAGTGCCGCTAATGCCCCAGGCC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATG-CCCAGGCC
* *
40813828 TTTAGTGGCGTTTTTGTGAAAGCGCCGCTAATGTCCAGGCC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
* * *
40813869 TTTAGCGGCGTTTTTGTGAAAGCGCCGCCAATGCCTAGGGC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
* *
40813910 TTTAGCAGCGTTTTTGGGAAAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAAT
40813942 AATGCTCAGG
Statistics
Matches: 181, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 1 0.01
41 141 0.78
42 39 0.22
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGCC
Found at i:40813856 original size:83 final size:81
Alignment explanation
Indices: 40813704--40813941 Score: 361
Period size: 83 Copynumber: 2.9 Consensus size: 81
40813694 CTTTTGGAGA
40813704 TTTAGCGGCGTTTTTAG-GAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTTCGGAAAGC
1 TTTAGCGGCGTTTTT-GTGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTT-GGAAAGC
40813768 GCCGCTAATGCCCAGGCC
64 GCCGCTAATGCCCAGGCC
* * *
40813786 TTTAGCGGCGTTTTTGTGAAAGTGCCGCTAATGCCCCAGGCCTTTAGTGGCGTTTTTGTGAAAGC
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATG-CCCAGGGCTTTAGCGGCGTTTTTG-GAAAGC
*
40813851 GCCGCTAATGTCCAGGCC
64 GCCGCTAATGCCCAGGCC
* * *
40813869 TTTAGCGGCGTTTTTGTGAAAGCGCCGCCAATGCCTAGGGCTTTAGCAGCGTTTTTGGGAAAGCG
1 TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTT-GGAAAGCG
40813934 CCGCTAAT
65 CCGCTAAT
40813942 AATGCTCAGG
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
81 1 0.01
82 65 0.46
83 76 0.54
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (81 bp):
TTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTTGGAAAGCGC
CGCTAATGCCCAGGCC
Found at i:40813924 original size:124 final size:124
Alignment explanation
Indices: 40813704--40813941 Score: 363
Period size: 124 Copynumber: 1.9 Consensus size: 124
40813694 CTTTTGGAGA
*
40813704 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGGCTTTAGCGGCGTTTTTCGGAAAGCG
1 TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTCGGAAAGCG
* * * *
40813769 CCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTGTGAAAGTGCCGCTAATGCCCCAGGCC
66 CCGCCAATGCCCAGGCCTTTAGCAGCGTTTTTGGGAAAGCGCCGCTAATGCCCCAGGCC
* *
40813828 TTTAGTGGCGTTTTT-GTGAAAGCGCCGCTAATGTCCAGGCCTTTAGCGGCGTTTTT-GTGAAAG
1 TTTAGCGGCGTTTTTAG-GAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTCG-GAAAG
* *
40813891 CGCCGCCAATGCCTAGGGCTTTAGCAGCGTTTTTGGGAAAGCGCCGCTAAT
64 CGCCGCCAATGCCCAGGCCTTTAGCAGCGTTTTTGGGAAAGCGCCGCTAAT
40813942 AATGCTCAGG
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
123 2 0.02
124 101 0.98
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (124 bp):
TTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATGCCCAGGCCTTTAGCGGCGTTTTTCGGAAAGCG
CCGCCAATGCCCAGGCCTTTAGCAGCGTTTTTGGGAAAGCGCCGCTAATGCCCCAGGCC
Found at i:40814132 original size:66 final size:66
Alignment explanation
Indices: 40814061--40814194 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
40814051 ATTTATATAT
40814061 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
40814126 C
66 C
*
40814127 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTTAAAATATTGAATTAATTATCA
1 TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
40814192 C
66 C
40814193 TA
1 TA
40814195 TAGTTTAGGG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (66 bp):
TAAATAATTTCTTATATAATCGTAAAAGAGATAGTATTAATTTGAAAATATTGAATTAATTATCA
C
Found at i:40814726 original size:20 final size:19
Alignment explanation
Indices: 40814701--40814772 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
40814691 TTTTTCGTGA
40814701 TTTAAAATTTTAAAATCAAT
1 TTTAAAATTTTAAAAT-AAT
* **
40814721 TTTAAAATATTTTAAATTTT
1 TTTAAAAT-TTTAAAATAAT
40814741 TTTAGAAATTTTAAAA-AGAT
1 TTTA-AAATTTTAAAATA-AT
*
40814761 TTTAAACTTTTA
1 TTTAAAATTTTA
40814773 TTTTTATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 7 0.17
20 24 0.57
21 11 0.26
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAAAATTTTAAAATAAT
Found at i:40814734 original size:10 final size:10
Alignment explanation
Indices: 40814707--40814766 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
40814697 GTGATTTAAA
40814707 ATTTTAAAAT
1 ATTTTAAAAT
40814717 CAATTTTAAAAT
1 --ATTTTAAAAT
*
40814729 ATTTTAAATT
1 ATTTTAAAAT
*
40814739 TTTTTAGAAAT
1 ATTTTA-AAAT
* *
40814750 -TTTAAAAAG
1 ATTTTAAAAT
40814759 ATTTTAAA
1 ATTTTAAA
40814767 CTTTTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
9 3 0.08
10 24 0.60
11 3 0.08
12 10 0.25
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:40815330 original size:42 final size:42
Alignment explanation
Indices: 40815269--40815617 Score: 479
Period size: 42 Copynumber: 8.3 Consensus size: 42
40815259 GATATGTTTT
* *
40815269 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* * *
40815311 TAGCGGCGTTTATGGGAAAAGCGCCGCTGAAGGTCTGCTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* *
40815353 TAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
* *
40815395 TAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTGATATA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
* * * *
40815438 TAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCTTGAGCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
40815481 TAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGATCTA
*
40815523 TAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGATCTA
* * *
40815565 TAGCGGCGTTT-TTGGAAAAGCGCCGTTAAAGGTCATGACCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-TGATCTA
40815607 TAGCGGCGTTT
1 TAGCGGCGTTT
40815618 ATGTTTATTT
Statistics
Matches: 279, Mismatches: 24, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
41 4 0.01
42 215 0.77
43 60 0.22
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (42 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTGATCTA
Found at i:40815552 original size:169 final size:169
Alignment explanation
Indices: 40815269--40815617 Score: 488
Period size: 169 Copynumber: 2.1 Consensus size: 169
40815259 GATATGTTTT
* * **
40815269 TAGCGGCGTTTGTGTGAAAAGCGCCGCTAAAGGTCTGTTCTATAGCGGCGTTTATGGGAAAAGCG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCTGAGCTATAGCGGCGTTTATGGGAAAAGCG
* * * *
40815334 CCGCTGAAGGTCTGCTCTATAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CTGTTCTATAG
66 CCGCTAAAGGTCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAG
* * *
40815398 CGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTGATATA
131 CGGCGTTT-TGGGAAAAGCGCCGCTAAAGGTCATGACATA
* * *
40815438 TAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCTTGAGCTATAGCGGCGTTTGTGGG-AAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC-TGAGCTATAGCGGCGTTTATGGGAAAAGC
*
40815502 GCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCCTGATCTAT
65 GCCGCTAAAGGT-CTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTAT
* * *
40815566 AGCGGCGTTTTTGGAAAAGCGCCGTTAAAGGTCATGACCTA
129 AGCGGCGTTTTGGGAAAAGCGCCGCTAAAGGTCATGACATA
40815607 TAGCGGCGTTT
1 TAGCGGCGTTT
40815618 ATGTTTATTT
Statistics
Matches: 158, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
169 98 0.62
170 60 0.38
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (169 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCTGAGCTATAGCGGCGTTTATGGGAAAAGCG
CCGCTAAAGGTCTGATCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTATAG
CGGCGTTTTGGGAAAAGCGCCGCTAAAGGTCATGACATA
Found at i:40816565 original size:42 final size:42
Alignment explanation
Indices: 40816465--40816575 Score: 190
Period size: 42 Copynumber: 2.7 Consensus size: 42
40816455 TGGCGTAAAA
*
40816465 CCTGCTAGGCTCA-AGCCTGATAAAAACTCACCAGCACTAGG
1 CCTGCTAGGCTTATAGCCTGATAAAAACTCACCAGCACTAGG
*
40816506 -CTGCTAGGCTTATAGCCTGATAAAAACTCACCGGCACTAGG
1 CCTGCTAGGCTTATAGCCTGATAAAAACTCACCAGCACTAGG
40816547 CCTGCTAGGCTTATAGCCTGATAAAAACT
1 CCTGCTAGGCTTATAGCCTGATAAAAACT
40816576 GATACATAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
40 11 0.17
41 27 0.41
42 28 0.42
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.22
Consensus pattern (42 bp):
CCTGCTAGGCTTATAGCCTGATAAAAACTCACCAGCACTAGG
Found at i:40819225 original size:19 final size:20
Alignment explanation
Indices: 40819154--40819228 Score: 61
Period size: 19 Copynumber: 3.9 Consensus size: 20
40819144 TAATTATTTA
*
40819154 TATTTAATCATATAATAAAT
1 TATTTAATCATTTAATAAAT
*
40819174 TA-TTAATACAATTAATACAAT
1 TATTTAAT-CATTTAATA-AAT
*
40819195 T-TATT-AT-TTTTAATAAAT
1 TAT-TTAATCATTTAATAAAT
40819213 TATTTAAT-ATTTAATA
1 TATTTAATCATTTAATA
40819229 TTTATTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
18 6 0.14
19 21 0.48
20 9 0.20
21 6 0.14
22 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTAATCATTTAATAAAT
Found at i:40822274 original size:42 final size:42
Alignment explanation
Indices: 40822228--40822307 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
40822218 AGAATTTCGA
*
40822228 TATATGATTACGTGTAACAC-CATGTCTGGGACATTGGCGTTG
1 TATATGATTACGTGTAACACAC-TGTCTGGGACAGTGGCGTTG
* *
40822270 TATATGATTTCGTGTAAGACACTGTCTGGGACAGTGGC
1 TATATGATTACGTGTAACACACTGTCTGGGACAGTGGC
40822308 ATCAATATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (42 bp):
TATATGATTACGTGTAACACACTGTCTGGGACAGTGGCGTTG
Found at i:40828598 original size:18 final size:18
Alignment explanation
Indices: 40828569--40828620 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
40828559 AGCAAGAAAC
40828569 TTGAGTTGAGCTCGCATCCT
1 TTGA-TTGAGCTCGCA-CCT
*
40828589 TTGA-TGAGCTCGCACTT
1 TTGATTGAGCTCGCACCT
40828606 TTGATTGAGCTCGCA
1 TTGATTGAGCTCGCA
40828621 AATGTAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 6 0.20
18 20 0.67
20 4 0.13
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (18 bp):
TTGATTGAGCTCGCACCT
Found at i:40835946 original size:15 final size:15
Alignment explanation
Indices: 40835926--40835972 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
40835916 GATTTAATGT
40835926 TTAGGGGTTATAGGG
1 TTAGGGGTTATAGGG
40835941 TTAGGGGTT-TAAGGG
1 TTAGGGGTTAT-AGGG
**
40835956 TTAGACGTTAT-GGG
1 TTAGGGGTTATAGGG
40835970 TTA
1 TTA
40835973 AGAGTTAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 7 0.25
15 20 0.71
16 1 0.04
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.36
Consensus pattern (15 bp):
TTAGGGGTTATAGGG
Found at i:40835979 original size:21 final size:22
Alignment explanation
Indices: 40835940--40835980 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40835930 GGGTTATAGG
*
40835940 GTTAGGGGTTTAAGGGTTAGAC
1 GTTAGGGGTTTAAGAGTTAGAC
*
40835962 GTTATGGG-TTAAGAGTTAG
1 GTTAGGGGTTTAAGAGTTAG
40835981 GGATTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.39, T:0.34
Consensus pattern (22 bp):
GTTAGGGGTTTAAGAGTTAGAC
Found at i:40836365 original size:284 final size:285
Alignment explanation
Indices: 40835941--40836680 Score: 915
Period size: 284 Copynumber: 2.5 Consensus size: 285
40835931 GGTTATAGGG
* * *
40835941 TTAGGGGTTTAAGGGTTAGACGTTATGGGTTAAGAGTTAGGGATTTAGGGTTTAGGGATTCAGGG
1 TTAGGGGTTAAAGGGTTAGA-GTTAGGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGATTCAGGG
* * *
40836006 ATCGAGTTAGGATTTTGGGCATTTCGATTAA--A--TTTTTAATATATATTTTAAATATGTTCTT
65 GTCGAGTTAGGATTTTGGG--TTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTT
* * *
40836067 ATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTGGTTTAGGGTATATGATTTAT
128 ATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATACGATTAAT
* *
40836132 TTAAGATTTAAGGCCGGTTTAGAAGTTCATATTTTAAGGTTTAGGGAGTATGGGTTTA-GGA-A-
193 TTAAGATTTAAGGCCAGTTTAGAAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATAT
40836194 T-TATGGTTTAAGGGTTGGGATTTAAGGT
258 TGTATGGTTTAA-GGTTGGGATTTAAGGT
* * * * *
40836222 TTAGGGGTTAAAGGGTTAGATGTTTA-GGGTTAGACACATTAGGGGTTAAAGG-TTAGGGATTTA
1 TTAGGGGTTAAAGGGTTAGA-G-TTAGGGGTTA-AGA-GTTAGGGATTTAAGGTTTAGGGATTCA
* * *
40836285 GGGGTCGGGTTAGGGTTTTGGGTTTAGATTAATTATTTTTTTAATTTATATTTTTAATATGTTCT
62 GGGGTCGAGTTAGGATTTTGGGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCT
* *
40836350 TATGTAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGTTATACGATTAA
127 TATATAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATACGATTAA
* * *
40836415 TTTAATATTTAAGGCCAGTTTAGGAGTTTATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATT
192 TTTAAGATTTAAGGCCAGTTTAGAAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGA--
40836480 TGGATTAGGGACTATGGTTTAAGGTTGGGATTTAAGGT
255 T--ATT---G--TATGGTTTAAGGTTGGGATTTAAGGT
* * *
40836518 TTAGGGGTTAGGGTTTAGGGGTTAGACATTAGGGGTTAAGAGTTAGGGATTTAAGGTTTATGGAT
1 TTAGGGGTTA------AAGGGTTAGA-GTTAGGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGAT
* * * *
40836583 TCAGGGGCCGAGTTAAGATTTTGAGTTAAGATTAATTATTTTTTTAATTTATATTTTAAATATGT
59 TCAGGGGTCGAGTTAGGATTTTGGGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGT
40836648 TCTTATATAATTGTAAAAGAGATAATAATAAAT
124 TCTTATATAATTGTAAAAGAGATAATAATAAAT
40836681 CAAATATACT
Statistics
Matches: 390, Mismatches: 41, Indels: 36
0.84 0.09 0.08
Matches are distributed among these distances:
280 9 0.02
281 26 0.07
282 35 0.09
283 11 0.03
284 140 0.36
285 3 0.01
290 1 0.00
291 1 0.00
296 26 0.07
297 10 0.03
300 12 0.03
301 101 0.26
302 15 0.04
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (285 bp):
TTAGGGGTTAAAGGGTTAGAGTTAGGGGTTAAGAGTTAGGGATTTAAGGTTTAGGGATTCAGGGG
TCGAGTTAGGATTTTGGGTTTAGATTAATTATTTTTTTAATTTATATTTTAAATATGTTCTTATA
TAATTGTAAAAGAGATAATAATAAATTTGTTTAGGGTTTTTAGTTTAGGGTATACGATTAATTTA
AGATTTAAGGCCAGTTTAGAAGTTCATATTTTAAGGTTTAGGGAGTATGGATTTAGGGATATTGT
ATGGTTTAAGGTTGGGATTTAAGGT
Found at i:40836485 original size:14 final size:15
Alignment explanation
Indices: 40836455--40836500 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
40836445 TATTTTAAGG
40836455 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
40836470 TTTAGGGA-TTTGGA
1 TTTAGGGAGTATGGA
*
40836484 -TTAGGGACTATGG-
1 TTTAGGGAGTATGGA
40836497 TTTA
1 TTTA
40836501 AGGTTGGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 7 0.26
14 12 0.44
15 8 0.30
ACGTcount: A:0.24, C:0.02, G:0.35, T:0.39
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:40836534 original size:14 final size:14
Alignment explanation
Indices: 40836515--40836542 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40836505 TGGGATTTAA
40836515 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
40836529 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
40836543 ACATTAGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (14 bp):
GGTTTAGGGGTTAG
Found at i:40836563 original size:14 final size:13
Alignment explanation
Indices: 40836518--40836565 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
40836508 GATTTAAGGT
*
40836518 TTAGGGGTTAGGG
1 TTAGGGGTTAGAG
*
40836531 TTTAGGGGTTAGACA
1 -TTAGGGGTTAGA-G
40836546 TTAGGGGTTAAGAG
1 TTAGGGGTT-AGAG
40836560 TTAGGG
1 TTAGGG
40836566 ATTTAAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 26 0.90
15 3 0.10
ACGTcount: A:0.23, C:0.02, G:0.44, T:0.31
Consensus pattern (13 bp):
TTAGGGGTTAGAG
Found at i:40837230 original size:175 final size:177
Alignment explanation
Indices: 40837039--40837390 Score: 663
Period size: 175 Copynumber: 2.0 Consensus size: 177
40837029 ATTATTTAAT
40837039 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
*
40837104 CAATATTTATTTTGAGAGTACTT-GG-TTTTTTTATTTTGCAAACAATAAATCAATTTATAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAA
40837167 ACAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 ACAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
* *
40837214 TTGGATAATTCTAACTTAATAATTAATTATAGCCATTTTATCATTTGTTTTCTTATTAAAATATA
1 TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
40837279 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAA
66 CAATATTTATTTTGAGAGTACTTGGGTTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAA
40837344 ACAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
131 ACAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
40837391 AAATGAAATA
Statistics
Matches: 172, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
175 86 0.50
176 2 0.01
177 84 0.49
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (177 bp):
TTGGATAATTCTAACTTAATAATTAATTACAACCATTTTATCATTTGTTTTCTTATTAAAATATA
CAATATTTATTTTGAGAGTACTTGGGTTTTTTTTATTTTGCAAAAAATAAATCAATTTATAAAAA
ACAAAATAAAAAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCA
Found at i:40837694 original size:40 final size:41
Alignment explanation
Indices: 40837650--40837727 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 41
40837640 AATTTTTTGT
40837650 GGCG-TTTCTATGAAAAACGCCGCA-AAAGATAAA-CAATAGC
1 GGCGTTTTCTAT-AAAAACGCCGCACAAA-ATAAATCAATAGC
*
40837690 GGCGTTTTTTATAAAAACGCCGCACAAAATAAATCAAT
1 GGCGTTTTCTATAAAAACGCCGCACAAAATAAATCAAT
40837728 TTTTAGCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
40 21 0.62
41 13 0.38
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (41 bp):
GGCGTTTTCTATAAAAACGCCGCACAAAATAAATCAATAGC
Found at i:40837942 original size:75 final size:75
Alignment explanation
Indices: 40837807--40838006 Score: 284
Period size: 75 Copynumber: 2.7 Consensus size: 75
40837797 TTCTTTGCAA
*
40837807 AAAAATAAATCAA--T-TAATAAA-AAAATAAAAAAACTTTTAGCATAGCAAAACGACGTAATCT
1 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAAA-TTTTAGCAT-----AACGACGTAATCT
40837868 TATTCAAGATGAAGCG
60 TATTCAAGATGAAGCG
*
40837884 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGCATAACGACGTAATCTTGTTCA
1 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGCATAACGACGTAATCTTATTCA
40837949 AGATGAAGCG
66 AGATGAAGCG
*
40837959 AAAAATAAATCAATTTATAAAAAACAAAAT-AAAAAATTTTAACATAAC
1 AAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGCATAAC
40838007 AAAACGGCGT
Statistics
Matches: 116, Mismatches: 3, Indels: 11
0.89 0.02 0.08
Matches are distributed among these distances:
74 17 0.15
75 58 0.50
77 13 0.11
79 1 0.01
80 15 0.13
81 12 0.10
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.24
Consensus pattern (75 bp):
AAAAATAAATCAATTTATAAAAAACAAAATAAAAAAATTTTAGCATAACGACGTAATCTTATTCA
AGATGAAGCG
Found at i:40840948 original size:120 final size:120
Alignment explanation
Indices: 40840799--40841102 Score: 495
Period size: 120 Copynumber: 2.5 Consensus size: 120
40840789 TTATTAGTTA
** * * *
40840799 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* *
40840863 AAATTT-TCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
65 -AATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
40840919 TAATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
1 TAATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
*
40840984 CTTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
66 ATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
*
40841039 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TAATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40841103 TAAATATGAT
Statistics
Matches: 173, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
119 4 0.02
120 167 0.97
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (120 bp):
TAATTATTAAAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
ATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
Found at i:40840970 original size:15 final size:15
Alignment explanation
Indices: 40840935--40840976 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40840925 TTAAAAATTT
*
40840935 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40840949 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40840963 TATTTAATAATAAT
1 TATTTAATTATAAT
40840977 TATGTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40841068 original size:61 final size:60
Alignment explanation
Indices: 40840883--40841070 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 60
40840873 TTATAGTATC
40840883 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATT-AAAATTTTATTAAATT
* * * * * * * * * *
40840944 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTACTTTATATTTTA-CAGTATC
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATTA-TTAAAATTTTATTA-AATT
40841003 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAA-AATTTTATTAAATT
40841064 ATATATT
1 ATATATT
40841071 TTAATTATAA
Statistics
Matches: 95, Mismatches: 20, Indels: 24
0.68 0.14 0.17
Matches are distributed among these distances:
57 11 0.12
58 7 0.07
59 20 0.21
60 13 0.14
61 26 0.27
62 7 0.07
63 11 0.12
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAATTTTATTAAATT
Found at i:40841085 original size:16 final size:16
Alignment explanation
Indices: 40841064--40841105 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40841054 TTATTAAATT
*
40841064 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40841080 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40841095 AT-TATGTTTAA
1 ATATAT-TTTAA
40841106 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40841090 original size:15 final size:15
Alignment explanation
Indices: 40841055--40841096 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40841045 TTAAGAATTT
*
40841055 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40841069 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40841083 TATTTAATAATAAT
1 TATTTAATTATAAT
40841097 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40841246 original size:157 final size:157
Alignment explanation
Indices: 40841039--40841355 Score: 546
Period size: 157 Copynumber: 2.0 Consensus size: 157
40841029 ATAAGAATAT
*
40841039 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
40841104 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
40841169 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
40841196 TAATTA-TAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTT
1 TAATTATTAAGAATTTTATTAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTT
*
40841260 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATCA
65 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
* *
40841325 ATAATCATTTACCAAAACAATTTTATGC
130 ATAATAATTTACCAAAACAAATTTATGC
40841353 TAA
1 TAA
40841356 GGGTATTCTA
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
156 25 0.17
157 126 0.83
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:40843689 original size:23 final size:23
Alignment explanation
Indices: 40843662--40843709 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
40843652 CTCCAACTAT
40843662 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
40843685 CAAAACAGATCACTCCACCATCC
1 CAAAACAGATCACTCCACCATCC
40843708 CA
1 CA
40843710 CGTCAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.44, G:0.04, T:0.12
Consensus pattern (23 bp):
CAAAACAGATCACTCCACCATCC
Found at i:40845645 original size:42 final size:43
Alignment explanation
Indices: 40845539--40845694 Score: 154
Period size: 42 Copynumber: 3.7 Consensus size: 43
40845529 TAGAAGTGCT
* * *
40845539 GCTAAATGTCATGACCTTTAGCGGCGTTT-TCAGAAAAGCGCC
1 GCTAAAGGTCATGACCTTTAGCGGCGTTTGTCGGGAAAGCGCC
* * ** * * * *
40845581 ACTAAAAGTCATGGTCTATAGCGGCGTTTTTCGGG-AGGCGTC
1 GCTAAAGGTCATGACCTTTAGCGGCGTTTGTCGGGAAAGCGCC
* * * **
40845623 GCTAAAGGTCATGACTTTTAGCGGCATTTGTGGGGAAATTGCC
1 GCTAAAGGTCATGACCTTTAGCGGCGTTTGTCGGGAAAGCGCC
40845666 GCTAAAGGTCATGACCTTTAGCGGCGTTT
1 GCTAAAGGTCATGACCTTTAGCGGCGTTT
40845695 ATTTTAAGAA
Statistics
Matches: 88, Mismatches: 24, Indels: 3
0.77 0.21 0.03
Matches are distributed among these distances:
42 55 0.62
43 33 0.38
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (43 bp):
GCTAAAGGTCATGACCTTTAGCGGCGTTTGTCGGGAAAGCGCC
Found at i:40847058 original size:2 final size:2
Alignment explanation
Indices: 40847051--40847081 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
40847041 TATGTTTCTG
40847051 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
40847082 GTTTTGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40852678 original size:50 final size:51
Alignment explanation
Indices: 40852591--40852696 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 51
40852581 TGTATATATT
*
40852591 TTTAAAATATAAAAGAAATAATAAATTTTAAAATACA-TTTATCTAAAAAA
1 TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
* * * *
40852641 TTTAAAATATTACAA-AAATAA-AAAATTTAAATTTACATCTTTTTCTAAATAA
1 TTTAAAATA-TAAAAGAAATAATAAAATTTAAA-ATACA-CTTTATCTAAAAAA
40852693 TTTA
1 TTTA
40852697 CAAACAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
49 9 0.19
50 19 0.40
51 4 0.09
52 15 0.32
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.39
Consensus pattern (51 bp):
TTTAAAATATAAAAGAAATAATAAAATTTAAAATACACTTTATCTAAAAAA
Found at i:40852968 original size:16 final size:16
Alignment explanation
Indices: 40852947--40852979 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
40852937 ACAAATTTAC
40852947 TGAGTTTTTGAGGTTA
1 TGAGTTTTTGAGGTTA
*
40852963 TGAGTTTTTGAGTTTA
1 TGAGTTTTTGAGGTTA
40852979 T
1 T
40852980 CAAAATCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (16 bp):
TGAGTTTTTGAGGTTA
Found at i:40853052 original size:16 final size:17
Alignment explanation
Indices: 40853028--40853061 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40853018 ATTATATGTG
40853028 TTTAAATATAA-TTATA
1 TTTAAATATAATTTATA
*
40853044 TTTATATATAATTTATA
1 TTTAAATATAATTTATA
40853061 T
1 T
40853062 GTATTTTAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATATAATTTATA
Found at i:40861176 original size:12 final size:11
Alignment explanation
Indices: 40861159--40861219 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 11
40861149 AACAAATCAT
40861159 CTCTCATATTTC
1 CTCTCA-ATTTC
40861171 CTCTCAA-TTC
1 CTCTCAATTTC
40861181 CTCTCAATTTC
1 CTCTCAATTTC
*
40861192 CT-TCCAAAATT-
1 CTCT-C-AATTTC
40861203 CTCTCAATTTC
1 CTCTCAATTTC
40861214 CT-TCAA
1 CTCTCAA
40861220 AAATTCTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 19 0.45
11 12 0.29
12 11 0.26
ACGTcount: A:0.23, C:0.34, G:0.00, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40861206 original size:22 final size:22
Alignment explanation
Indices: 40861176--40861231 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
40861166 ATTTCCTCTC
*
40861176 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCAAA
40861199 AATTCTCTCAATTTCCTTCAAA
1 AATTCTCTCAATTTCCTTCAAA
40861221 AATTCTCTCAA
1 AATTCTCTCAA
40861232 ATCCATATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCAAA
Found at i:40862421 original size:7 final size:7
Alignment explanation
Indices: 40862411--40862435 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40862401 ATTCGATTGA
40862411 TATTTAG
1 TATTTAG
40862418 TATTTAG
1 TATTTAG
40862425 TATTTAG
1 TATTTAG
40862432 TATT
1 TATT
40862436 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:40863110 original size:18 final size:18
Alignment explanation
Indices: 40863084--40863120 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40863074 AGGTACGTTT
*
40863084 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
40863102 CCTAACCCTTATATGTAC
1 CCTAACCCTTATATGTAC
40863120 C
1 C
40863121 ATTTTCCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.35, G:0.08, T:0.32
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:40863387 original size:9 final size:9
Alignment explanation
Indices: 40863348--40863387 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
40863338 CGTCCTAAGT
40863348 CCGGAAGAA
1 CCGGAAGAA
*
40863357 CCAGAAGAA
1 CCGGAAGAA
*
40863366 CCGAAAGAA
1 CCGGAAGAA
40863375 CCGGAAGAA
1 CCGGAAGAA
40863384 CCGG
1 CCGG
40863388 GTTTCATACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.45, C:0.25, G:0.30, T:0.00
Consensus pattern (9 bp):
CCGGAAGAA
Found at i:40863733 original size:23 final size:23
Alignment explanation
Indices: 40863704--40864552 Score: 754
Period size: 23 Copynumber: 34.7 Consensus size: 23
40863694 TTTGATGTAA
*
40863704 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAATTTAAT
*** *
40863727 CCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40863750 TAAAAACCCTAACGTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40863773 TAAAAACTCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40863796 TAAAAACCCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
*
40863820 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
40863846 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40863869 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
40863898 TAAAAACCCTAAAACCTTAA-TTAA-
1 TAAAAACCCT--AACC-TAATTTAAT
*
40863922 -AAACCCTAACCTTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
*
40863948 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40863971 TATAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40863994 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40864017 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
* * *
40864040 TAAAAATCATAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40864063 TAAAAATCCTAAACTCTTAA-TTAA-
1 TAAAAACCCT-AAC-C-TAATTTAAT
40864087 -AAACCCTAACCCTAACCTAATTTAAT
1 TAAA----AACCCTAACCTAATTTAAT
40864113 TAAAAACCCTAACCCTAACCAAATTTAAT
1 TAAAAACCCTAA-CCT-----AATTTAAT
* *
40864142 TAAAAACTCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40864165 TAAAAACCCTAAACC---CTTAAT
1 TAAAAACCCT-AACCTAATTTAAT
40864186 TAAAAACCCTAATCTTAACATAATTTAAT
1 TAAAAACCCTAA-C----C-TAATTTAAT
*
40864215 TAAAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAATTTAAT
40864238 TAAAAACCCTAACATTAGCCTAATTTAAT
1 TAAAAACCCT---A--A-CCTAATTTAAT
40864267 TAAAAACCCTAACCTAACCTAATTTAAT
1 TAAAAA--C---CCTAACCTAATTTAAT
*
40864295 TAAAAACCCTAATCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40864318 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40864341 TAAAAACCCTAGCCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40864364 TAAAAACTCTAAACCCTTAA-TTAA-
1 TAAAAACCCT-AA-CC-TAATTTAAT
* *
40864388 AAACTCAAACCTTAACCTAATTTAAT
1 TAA---AAACCCTAACCTAATTTAAT
40864414 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
40864437 TAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAA--C---CC-TAACCTAATTTAAT
40864466 TAAAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCTAATTTAAT
*
40864489 TAAAAACCCTAACCTAATTTAAAC
1 TAAAAACCCTAACCTAATTT-AAT
***
40864513 CCTAAACCCTAAACCGTAATTTAAT
1 TAAAAACCCT-AACC-TAATTTAAT
40864538 TAAAAACCCTAACCT
1 TAAAAACCCTAACCT
40864553 TAACATAATG
Statistics
Matches: 693, Mismatches: 53, Indels: 160
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.00
21 16 0.02
23 383 0.55
24 43 0.06
25 66 0.10
26 29 0.04
27 31 0.04
28 26 0.04
29 92 0.13
31 2 0.00
34 3 0.00
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTTAAT
Found at i:40863840 original size:50 final size:49
Alignment explanation
Indices: 40863704--40864031 Score: 317
Period size: 50 Copynumber: 6.7 Consensus size: 49
40863694 TTTGATGTAA
* * *
40863704 TAAAAACCCTAA-CC-TAATT--TAACCCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCCTTAATTAAAAACCCT-AACCTTAACCTAATTTAAT
**
40863750 TAAAAACCCTAACGTAATTTAATTAAAAA--CT---C-TAACCTAATTTAAT
1 TAAAAACCCTAAC---CCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
40863796 TAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAACCCT-AACCCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
*
40863846 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAACCCTAACC---CTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
*
40863898 TAAAAACCCTAAAACCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
1 TAAAAACCCT-AACCCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
* ** *
40863948 TAAAAACCCT-AGCC-TAATTTAATTA---TAAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCCTTAA-TTAAAAACCCT-AACCTTAACCTAATTTAAT
*
40863994 TAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCT
1 TAAAAACCCTAACC---CTTAATTAAAAACCCTAACCT
40864032 AATTTAATTA
Statistics
Matches: 236, Mismatches: 18, Indels: 50
0.78 0.06 0.16
Matches are distributed among these distances:
44 11 0.05
45 1 0.00
46 65 0.28
47 9 0.04
48 8 0.03
49 5 0.02
50 73 0.31
51 10 0.04
52 48 0.20
53 6 0.03
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (49 bp):
TAAAAACCCTAACCCTTAATTAAAAACCCTAACCTTAACCTAATTTAAT
Found at i:40863845 original size:29 final size:29
Alignment explanation
Indices: 40863812--40863909 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
40863802 CCCTAAACCC
40863812 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
40863841 TTAATTAAAAA--C---CC-TAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
40863864 TTAATTAAAAACCCTAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTTAACCTAAT
40863893 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
40863910 AACCTTAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
23 20 0.32
24 2 0.03
25 1 0.02
27 1 0.02
28 2 0.03
29 37 0.59
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (29 bp):
TTAATTAAAAACCCTAACCTTAACCTAAT
Found at i:40863935 original size:102 final size:98
Alignment explanation
Indices: 40863724--40864552 Score: 632
Period size: 102 Copynumber: 8.4 Consensus size: 98
40863714 AACCTAATTT
* *
40863724 AACCCTAAACCCTAACCTAAATTAATTAAAAACCCTAACGTAATTTAATTAAAAACT--CTAACC
1 AACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCTAACC
*
40863787 TAATTTAATTAAAAACCCTAAACCCTTAATTAAA
65 TAATTTAATTAAAAACCCTAAAACCTTAATTAAA
*
40863821 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAA--CT-ACC-TA
40863886 ACCTAATTTAATTAAAAACCCTAAAACCTTAATTAAA
62 ACCTAATTTAATTAAAAACCCTAAAACCTTAATTAAA
* * *
40863923 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTATAAAC--CCTAACCT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCTAACCT
40863986 AATTTAATTAAAAACCCT--AACC-TAATTTAATTA
66 AATTTAATTAAAAACCCTAAAACCTTAA-TTAA--A
* * * *
40864019 AA----AACCCTAACCTAATTTAATTAAAAATCATAGCCTAATTTAATTAAAAA-T-CCTAAACT
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCTAACCT
*
40864078 --CTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAA
66 AATTTAATTAAAAACCCTAA----AACC----TTAATTAAA
* * *
40864117 AACCCTAACCCTAACCAAATTTAATTAAAAACTCTAGCCTAATTTAATTAAAAAC--CCTAAACC
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCT-AACC
* *
40864180 ---CTTAATTAAAAACCCTAATCTTAA-CATAATTTAATTA
65 TAATTTAATTAAAAACCCTAA----AACCTTAA-TTAA--A
*
40864217 AA----AACCCTAACCTAAATTAATTAAAAACCCTAACATTAGCCTAATTTAATTAAAAACCCTA
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCT---A--A-CCTAATTTAATTAAAAA--CT-
*
40864278 ACCTAACCTAATTTAATTAAAAACCCT--AATC-TAATTTAATTA
57 ACCTAACCTAATTTAATTAAAAACCCTAAAACCTTAA-TTAA--A
*
40864320 AA----AACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAACT--CTAAACC
1 AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCT-AACC
* * *
40864379 ---CTTAATTAAAAA--CTCAAACCTTAACCTAATTTA
65 TAATTTAATTAAAAACCCTAAAACCTTAA-TTAA---A
*****
40864412 ATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAAC--CC
1 AACCCTAACCCTAACCTAATTTAATTAAAAA--C---CC-TAACCTAATTTAATTAAAAACTACC
*
40864475 TAACCTAATTTAATTAAAAACCCT--AACC-TAATT-TA
60 TAACCTAATTTAATTAAAAACCCTAAAACCTTAATTAAA
40864510 AACCCTAAACCCTAAACCGTAATTTAATTAAAAACCCTAACCT
1 AACCCT-AACCCT-AACC-TAATTTAATTAAAAACCCTAACCT
40864553 TAACATAATG
Statistics
Matches: 622, Mismatches: 41, Indels: 140
0.77 0.05 0.17
Matches are distributed among these distances:
88 2 0.00
90 29 0.05
91 6 0.01
92 57 0.09
93 7 0.01
94 8 0.01
95 8 0.01
96 129 0.21
97 28 0.05
98 12 0.02
99 8 0.01
100 13 0.02
101 26 0.04
102 199 0.32
103 49 0.08
104 17 0.03
106 6 0.01
107 3 0.00
109 15 0.02
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (98 bp):
AACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACTACCTAACCT
AATTTAATTAAAAACCCTAAAACCTTAATTAAA
Found at i:40863978 original size:125 final size:123
Alignment explanation
Indices: 40863827--40864503 Score: 549
Period size: 125 Copynumber: 5.5 Consensus size: 123
40863817 TAAAAACCCT
*
40863827 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAA
40863892 TTTAATTAAAAACCCTAAAACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA
66 TTTAATTAAAAACCCTAAAACCTTAATTAAAAACCCTAA-C-TAACCTAATTTAATTAAA
* *
40863952 AACCCTAGCCTAATTTAATTATAAACCCTAACCTAATTTAATTAAAAA--C---CC-TAACCTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAA
* * *
40864011 TTTAATTAAAAACCCTAACCTAA-TTTAATTAAAAA---TCA-TAGCCTAATTTAATTAAA
66 TTTAATTAAAAACCCTAA---AACCTTAATTAAAAACCCTAACTAACCTAATTTAATTAAA
* *
40864067 AATCCTAAACTCTTAA-TTAA--AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT
1 AACCCT-AAC-C-TAATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAACCTT
* * * * *
40864129 AACCAAATTTAATTAAAAACTCTAGCCTAA-TTTAATTAAAAACCCT-A--AACC---CTTAATT
59 AACCTAATTTAATTAAAAACCCTA---AAACCTTAATTAAAAACCCTAACTAACCTAATTTAATT
40864187 AAA
121 AAA
* *
40864190 AACCCTAATCTTAACATAATTTAATTAAAAACCCTAACCTAAATTAATTAAAAACCCTAACATTA
1 AACCCTAA-C----C-TAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTA
*
40864255 GCCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAA-T---CTAATTTA
60 ACCTAATTTAATTAAAAACCCTAA---AACC----TTAATTAAAAACCCTAACTAACCTAATTTA
40864316 ATTAAA
118 ATTAAA
* * *
40864322 AACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAACTCTAAACCCTTAA-TT
1 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTTAACCT
* * * * *
40864386 AA--AAACT-CAAACCTTAACCTAA-TTTAATTAAAAA-CC---CTAACCTAATTTAATTAAA
64 AATTTAATTAAAAACCCTAA---AACCTTAATTAAAAACCCTAACTAACCTAATTTAATTAAA
40864441 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCT
1 AA--C---CC-TAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCT
40864504 AATTTAAACC
Statistics
Matches: 459, Mismatches: 39, Indels: 110
0.75 0.06 0.18
Matches are distributed among these distances:
115 24 0.05
116 3 0.01
117 5 0.01
118 7 0.02
119 78 0.17
120 2 0.00
121 13 0.03
122 4 0.01
123 19 0.04
124 19 0.04
125 185 0.40
126 46 0.10
127 11 0.02
128 5 0.01
129 4 0.01
130 15 0.03
131 2 0.00
132 17 0.04
ACGTcount: A:0.47, C:0.22, G:0.01, T:0.30
Consensus pattern (123 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAA
TTTAATTAAAAACCCTAAAACCTTAATTAAAAACCCTAACTAACCTAATTTAATTAAA
Found at i:40864185 original size:267 final size:264
Alignment explanation
Indices: 40863707--40864552 Score: 966
Period size: 267 Copynumber: 3.1 Consensus size: 264
40863697 GATGTAATAA
**** * *
40863707 AAACCCT-AACCTAATTTAACCCTAAACCCTAACCTAAATTAATTAAAAACCCTAACGTAATTTA
1 AAACCCTAAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
*
40863771 ATTAAAAACTCTAACCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTTAAC
66 ATTAAAAA-TCTAACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAACC-TAAC
40863836 CTAATTTAATTAAAAACCCTAA-CCT----AATTTAATTAAAAACCCTAACCTTAACCTAATTTA
129 CTAATTTAATTAAAAACCCTAACCCTAACCAATTTAATTAAAAA--CT---C-TAACCTAATTTA
*
40863896 ATTAAAAACCCTAAAACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAGC
188 ATTAAAAACCCT-AAACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAC
40863961 CTAATTTAATTAT
252 CTAATTTAATTAT
40863974 AAACCCT-AACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
1 AAACCCTAAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
* *
40864038 ATTAAAAATCATAGCCTAATTTAATTAAAAATCCTAAACTCTTAATTAAAAACCCTAACCCTAAC
66 ATTAAAAATC-TAACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAA-CCTAAC
*
40864103 CTAATTTAATTAAAAACCCTAACCCTAACCAAATTTAATTAAAAACTCTAGCCTAATTTAATTAA
129 CTAATTTAATTAAAAACCCTAACCCTAACC-AATTTAATTAAAAACTCTAACCTAATTTAATTAA
* * *
40864168 AAACCCTAAACCCTTAATTAAAAACCCTAATCTTAACATAATTTAATTAAAAACCCTAACCTAAA
193 AAACCCTAAA-CCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAAT
*
40864233 TTAATTAA
257 TTAATTAT
40864241 AAACCCTAACATTAGCCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTA
1 AAACCCT-A-A--A-CCTAATTTAATTAAAAA--C---CCTAACCTAATTTAATTAAAAACCCTA
* * ** *
40864306 ATCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAAC
56 ACCTAATTTAATTAAAAA-TCTAACCTAATTTAATTAAAAACCCTAAACT--CTTAATTAAAAAC
* * * * * *
40864371 TCT-A---AACC---CTTAATTAAAAACTCAAACCTTAACCTAATTTAATTAAAAACCCTAACCT
118 CCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACC-AATTTAATTAAAAACTCTAACCT
* ***** *
40864429 AATTTAATTAAAAACCCT-AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAA
182 AATTTAATTAAAAACCCTAAACCTTAA-TTAA---AAACCCTAACCTTAACCTAATTTAATTAAA
***
40864493 AACCCTAACCTAATTTAAACCCT
243 AACCCTAACCTAATTT-AATTAT
40864516 AAACCCTAAACCGTAATTTAATTAAAAACCCTAACCT
1 AAACCCTAAACC-TAATTTAATTAAAAACCCTAACCT
40864553 TAACATAATG
Statistics
Matches: 506, Mismatches: 44, Indels: 59
0.83 0.07 0.10
Matches are distributed among these distances:
266 13 0.03
267 223 0.44
268 6 0.01
269 1 0.00
270 9 0.02
271 23 0.05
272 62 0.12
273 32 0.06
274 38 0.08
275 14 0.03
278 69 0.14
279 2 0.00
280 14 0.03
ACGTcount: A:0.47, C:0.23, G:0.01, T:0.30
Consensus pattern (264 bp):
AAACCCTAAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTA
ATTAAAAATCTAACCTAATTTAATTAAAAACCCTAAACTCTTAATTAAAAACCCTAACCTAACCT
AATTTAATTAAAAACCCTAACCCTAACCAATTTAATTAAAAACTCTAACCTAATTTAATTAAAAA
CCCTAAACCTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA
TTAT
Found at i:40864402 original size:19 final size:21
Alignment explanation
Indices: 40864359--40864402 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40864349 CTAGCCTAAT
40864359 TTAATTAAAAACTCTAAACCC
1 TTAATTAAAAACTCTAAACCC
40864380 TTAATTAAAAACTC-AAA-CC
1 TTAATTAAAAACTCTAAACCC
40864399 TTAA
1 TTAA
40864403 CCTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 3 0.13
21 14 0.61
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (21 bp):
TTAATTAAAAACTCTAAACCC
Found at i:40864690 original size:116 final size:116
Alignment explanation
Indices: 40864555--40864775 Score: 381
Period size: 116 Copynumber: 1.9 Consensus size: 116
40864545 CCTAACCTTA
* *
40864555 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAA-TAATAATTTTACATAATTT
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAA-AAATTAATAATTGTACATAATTT
*
40864619 GATAATTTTACTAACCATTAATACAATTTTTTGACTTAATAATTTTACATTC
65 GATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
*
40864671 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTATATAATTTG
1 ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
*
40864736 ATAATTTTCCTAACCATTAATACAATTTTTTGACGTAATA
66 ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATA
40864776 CAATTTATCA
Statistics
Matches: 99, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 3 0.03
116 96 0.97
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
ACATAATGTTAGATTTGGAAAAATGTTTTGACTGATACTAAAAATTAATAATTGTACATAATTTG
ATAATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTC
Found at i:40868102 original size:126 final size:125
Alignment explanation
Indices: 40867807--40868158 Score: 539
Period size: 126 Copynumber: 2.8 Consensus size: 125
40867797 CCCAAACATG
* *
40867807 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
* * *
40867872 TAGAAGCAATTTTATATTATTTGCTTAGAAACGTC-AAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* * *
40867931 CTACTGTAGCAAAAGA-GCG-CTGACGAGGCCGCGATTTCACAAATTCTTATCAAATAACATCCT
1 CTACTGTAGCAAAA-ACGCGTC-CACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCT
*
40867994 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCCATGAC
64 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
* *
40868057 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCATAAATTCTTCTCAAATACCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
**
40868122 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
40868159 CTCGAAATTA
Statistics
Matches: 206, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
123 1 0.00
124 89 0.43
125 7 0.03
126 108 0.52
127 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (125 bp):
CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAACATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:40877545 original size:2 final size:2
Alignment explanation
Indices: 40877538--40877574 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40877528 ACATGCATCT
40877538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40877575 GGGCAGAGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40882846 original size:25 final size:26
Alignment explanation
Indices: 40882809--40882858 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
40882799 GTTGTAAATT
40882809 GGAAAAATATCTTCAG-AAATTTTCC
1 GGAAAAATATCTTCAGAAAATTTTCC
* * *
40882834 GGAACAATCTCTTTAGAAAATTTTC
1 GGAAAAATATCTTCAGAAAATTTTC
40882859 TCTCTATAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (26 bp):
GGAAAAATATCTTCAGAAAATTTTCC
Found at i:40887496 original size:29 final size:30
Alignment explanation
Indices: 40887453--40887511 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
40887443 GTTTTTACAC
*
40887453 TTTCACAATCATTTTATTTCCTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
* * *
40887483 TTTCACCA-CATTTTCTTACTTCTTAATCG
1 TTTCACAATCATTTTATTACCTCTTAATCG
40887512 GCTCCCTAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTCACAATCATTTTATTACCTCTTAATCG
Found at i:40894984 original size:19 final size:19
Alignment explanation
Indices: 40894957--40894995 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
40894947 TGATTTGTTT
*
40894957 TAAGCTTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
40894976 TAAGATTTATCTACCTAAA
1 TAAGATTTATCTACCTAAA
40894995 T
1 T
40894996 GACTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAGATTTATCTACCTAAA
Found at i:40897409 original size:27 final size:27
Alignment explanation
Indices: 40897358--40897415 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
40897348 GTAATTAATC
** * *
40897358 AAGAGTTATATCTTTTGGTTATTGATA
1 AAGAGTTATATCACTTGATTATTGACA
*
40897385 AAGAGTTATATCACTTGATTTTTGACA
1 AAGAGTTATATCACTTGATTATTGACA
40897412 AAGA
1 AAGA
40897416 ACTATAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (27 bp):
AAGAGTTATATCACTTGATTATTGACA
Found at i:40899771 original size:11 final size:11
Alignment explanation
Indices: 40899748--40899794 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
40899738 AACAAATCCT
40899748 CTCTCATATTTC
1 CTCTCA-ATTTC
40899760 CTCTCAATTTC
1 CTCTCAATTTC
* *
40899771 CTTTCAATTTT
1 CTCTCAATTTC
40899782 CTCTCAATTTC
1 CTCTCAATTTC
40899793 CT
1 CT
40899795 TCCAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.17, C:0.32, G:0.00, T:0.51
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:40899805 original size:22 final size:22
Alignment explanation
Indices: 40899760--40899806 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
40899750 CTCATATTTC
* **
40899760 CTCTCAATTTCCTTTCAATTTT
1 CTCTCAATTTCCTTCCAAAATT
40899782 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
40899804 CTC
1 CTC
40899807 ATAAATCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:40899829 original size:51 final size:51
Alignment explanation
Indices: 40899772--40899897 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
40899762 CTCAATTTCC
* * *
40899772 TTTCAATTTTCTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTC-TCAAACCCATATTTAA
* *
40899823 TTTCAATTTCCTCTCAAATTCATTCCAAAAATCTCTCAAACCCATATTTAA
1 TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
*
40899874 TTTCAATTTGCTCTCAATTTCCTT
1 TTTCAATTTCCTCTCAATTTCCTT
40899898 TTTTTAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.30, C:0.25, G:0.01, T:0.44
Consensus pattern (51 bp):
TTTCAATTTCCTCTCAATTTCCTTCCAAAAATCTCTCAAACCCATATTTAA
Found at i:40902168 original size:25 final size:25
Alignment explanation
Indices: 40902135--40902248 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
40902125 TTTAAATTTA
*
40902135 TTATTTGATGTATTAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
40902160 TTATTTGATGTAATACACATAGAAAGT
1 TTATTTGATGTAATA-AAATAG-AAGT
* ** *
40902187 TT-TTCGA-GT--T-ATTTTG-A-T
1 TTATTTGATGTAATAAAATAGAAGT
40902205 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
40902231 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
40902249 ACCCTAACCT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
18 1 0.01
19 3 0.04
20 4 0.06
21 5 0.07
23 2 0.03
24 3 0.04
25 35 0.51
26 10 0.14
27 6 0.09
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:40902290 original size:29 final size:29
Alignment explanation
Indices: 40902248--40903008 Score: 1000
Period size: 29 Copynumber: 25.4 Consensus size: 29
40902238 ATGTAATAAA
*
40902248 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902277 AACCCTAACATAACCTAATTAAAGACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *****
40902306 AACCCTAACCCTAACCTTAACCTAACCTAATTAAA
1 AACCCTAA-CATAACC-TAA-TTAA---AAACCCT
*
40902341 AACCCTAACCCTAACTTAACATAATTAAAAACCCT
1 AACCCTAA--C--A--TAACCTAATTAAAAACCCT
*
40902376 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40902405 AACCTTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* * *
40902434 AACCCTAACCTAACTTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40902463 AAGCCTAACATAACTTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
**
40902492 AACCCTAACCCAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40902521 AACCCTAACCTAGCCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40902550 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40902579 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40902608 AACCCTAACCTAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902637 AACCCATAACATAACCTAATTAAAAACCCA
1 AACCC-TAACATAACCTAATTAAAAACCCT
*
40902667 AACCCTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902696 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902725 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
40902754 AACCCTAACCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAA-C--A--TAACCTAATTAAAAACCCT
40902788 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902817 AACCCTAACTTAACCTAACCTAATTAAAAACCTT
1 AACCCTAAC---A--TAACCTAATTAAAAACCCT
40902851 AACCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902880 AACCCTAACCTAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
* *
40902909 AACCTTAACATAACCTAATTAAAAACCCA
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902938 AACCCTAACATAACATAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902967 ACCCCTAACATAACCTAATTAAAAACCCT
1 AACCCTAACATAACCTAATTAAAAACCCT
*
40902996 AGCCCTAACATAA
1 AACCCTAACATAA
40903009 TAATTTTACA
Statistics
Matches: 657, Mismatches: 53, Indels: 44
0.87 0.07 0.06
Matches are distributed among these distances:
29 526 0.80
30 35 0.05
31 5 0.01
32 4 0.01
33 2 0.00
34 54 0.08
35 19 0.03
36 2 0.00
38 3 0.00
39 3 0.00
40 4 0.01
ACGTcount: A:0.47, C:0.32, G:0.01, T:0.21
Consensus pattern (29 bp):
AACCCTAACATAACCTAATTAAAAACCCT
Found at i:40902316 original size:41 final size:41
Alignment explanation
Indices: 40902271--40902355 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
40902261 CCTAATTAAA
*
40902271 AACCCTAACCCTAACATAACCTAATTAAAGACCCTAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCT
* *
40902312 AACCCTAACCTTAACCTAACCTAATTAAAAACCCTAACCCT
1 AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCT
40902353 AAC
1 AAC
40902356 TTAACATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.20
Consensus pattern (41 bp):
AACCCTAACCCTAACATAACCTAATTAAAAACCCTAACCCT
Found at i:40902331 original size:11 final size:12
Alignment explanation
Indices: 40902301--40902333 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40902291 CTAATTAAAG
*
40902301 ACCCTAACCCTA
1 ACCCTAACCTTA
40902313 ACCCTAACCTTA
1 ACCCTAACCTTA
40902325 A-CCTAACCT
1 ACCCTAACCT
40902334 AATTAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.33, C:0.45, G:0.00, T:0.21
Consensus pattern (12 bp):
ACCCTAACCTTA
Found at i:40902355 original size:70 final size:69
Alignment explanation
Indices: 40902248--40902391 Score: 243
Period size: 70 Copynumber: 2.1 Consensus size: 69
40902238 ATGTAATAAA
* * *
40902248 AACCCTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACCTAATTAAAGACCCTAACCCTA
1 AACCTTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACATAATTAAAAACCCTAACCCTA
40902313 ACCCT
66 A-CCT
*
40902318 AACCTTAACCTAACCTAATTAAAAACCCTAACCCTAACTTAACATAATTAAAAACCCTAACCCTA
1 AACCTTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACATAATTAAAAACCCTAACCCTA
40902383 ACCT
66 ACCT
40902387 AACCT
1 AACCT
40902392 AATTAAAAAC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
69 8 0.11
70 62 0.89
ACGTcount: A:0.44, C:0.34, G:0.01, T:0.22
Consensus pattern (69 bp):
AACCTTAACCTAACCTAATTAAAAACCCTAACCCTAACATAACATAATTAAAAACCCTAACCCTA
ACCT
Found at i:40902407 original size:18 final size:18
Alignment explanation
Indices: 40902384--40902437 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
40902374 CTAACCCTAA
40902384 CCTAACCTAATTAAAAAC
1 CCTAACCTAATTAAAAAC
40902402 CCTAACC---TT---AA-
1 CCTAACCTAATTAAAAAC
40902413 CCTAACCTAATTAAAAAC
1 CCTAACCTAATTAAAAAC
40902431 CCTAACC
1 CCTAACC
40902438 CTAACCTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
14 2 0.07
15 2 0.07
17 2 0.07
18 14 0.48
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (18 bp):
CCTAACCTAATTAAAAAC
Found at i:40903066 original size:55 final size:55
Alignment explanation
Indices: 40903006--40903162 Score: 305
Period size: 55 Copynumber: 2.9 Consensus size: 55
40902996 AGCCCTAACA
40903006 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
40903061 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
*
40903116 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAATACAATT
1 TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATT
40903163 ATCAATTAAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 101 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (55 bp):
TAATAATTTTACATAATTTGATAATTTTACTAACAATTAACACAATTTTTGGACT
Found at i:40906408 original size:124 final size:123
Alignment explanation
Indices: 40906188--40906537 Score: 540
Period size: 124 Copynumber: 2.8 Consensus size: 123
40906178 CCCAAACTTG
*
40906188 CTACTGTAGCAAAATCACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCTTGG
1 CTACTGTAGCAAAAT-ACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
40906253 TAGAAGCGATTTTATACTTTTTGCTCAGAAACATCAAAAAAAAAAATTTCTTACATGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAATTTCTTACATGAC
* *
40906312 CTACTATAGCAAAATATCGTCCACGAGGGTGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATA-CGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* **
40906377 TAGAAGCGATTTTATACTATTTGCTCAGAAACTTCAAAAAAAATTATTTCTTACATGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAATTTCTTACATGAC
* * * *
40906436 CTAATGTAGCAAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAAT-ACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
40906501 TAGATGCGATTTTATACTATTTGAC-CAGAAACGTCAA
65 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAA
40906538 CTCGAAATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
123 1 0.00
124 206 0.99
125 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (123 bp):
CTACTGTAGCAAAATACGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGT
AGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAAAAATTTCTTACATGAC
Found at i:40909572 original size:30 final size:30
Alignment explanation
Indices: 40909536--40909596 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
40909526 GAATTTCAAG
40909536 AAAAACACCCAAAACACCATTGGTTTTGTC
1 AAAAACACCCAAAACACCATTGGTTTTGTC
40909566 AAAAACACCCAAAACACCATTGGTTTTGTC
1 AAAAACACCCAAAACACCATTGGTTTTGTC
40909596 A
1 A
40909597 TCTCTCAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (30 bp):
AAAAACACCCAAAACACCATTGGTTTTGTC
Found at i:40916810 original size:42 final size:42
Alignment explanation
Indices: 40916764--40916894 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
40916754 GCCTGAAGGC
* * *
40916764 TGAACAGAAGCTCATGAGAGCTAAACGGAAACCTATAAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
** * *
40916806 TGAACAGAAGCTTGTAAGAGCTGAACGAAAACCCATAAGAGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
* * * * * *
40916848 TTAACTGAAGCTCAAAAGAGTTGAATGGAAACCCATTAGGGT
1 TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
40916890 TGAAC
1 TGAAC
40916895 GAAAACTCAT
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.19
Consensus pattern (42 bp):
TGAACAGAAGCTCATAAGAGCTGAACGGAAACCCATAAGGGT
Found at i:40916830 original size:21 final size:21
Alignment explanation
Indices: 40916749--40916831 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
40916739 ACATCGTTTT
*
40916749 CAGAAGCCT-GAAG-GCTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
40916768 CAGAAG-CTCATGAGAGCTAAA
1 CAGAAGCCT-ATAAGAGCTGAA
* * * *
40916789 CGGAAACCTATAAGGGTTGAA
1 CAGAAGCCTATAAGAGCTGAA
* *
40916810 CAGAAGCTTGTAAGAGCTGAA
1 CAGAAGCCTATAAGAGCTGAA
40916831 C
1 C
40916832 GAAAACCCAT
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
18 2 0.04
19 6 0.13
20 2 0.04
21 33 0.73
22 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.16
Consensus pattern (21 bp):
CAGAAGCCTATAAGAGCTGAA
Found at i:40920889 original size:13 final size:13
Alignment explanation
Indices: 40920871--40920896 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40920861 TGATTTATAT
40920871 GTGTGAAAATTTC
1 GTGTGAAAATTTC
40920884 GTGTGAAAATTTC
1 GTGTGAAAATTTC
40920897 ATCGTTTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:40928095 original size:42 final size:43
Alignment explanation
Indices: 40927978--40928147 Score: 134
Period size: 43 Copynumber: 3.9 Consensus size: 43
40927968 CAGGATTCTA
* * *
40927978 ATATGAGTTATCGTGTAAGACCACGTCTGGGAC-GTTAGCGTCGAT
1 ATATGA-TT-TCGTGTAAGACCATGTCTGGGACAG-TGGCATCGAT
* *
40928023 TTGA-GATTTACGTGTAAGATCATGTCTGGGACA-TCGGCATCG-T
1 AT-ATGATTT-CGTGTAAGACCATGTCTGGGACAGT-GGCATCGAT
* * *
40928066 ATATGATTTCGTGTAAGACCCTGTTTGGGACAGTGGCATTGAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* * * *
40928109 ATTTGATTACATGTAAGACCACGTCTGGGAC-GTTGGCAT
1 ATATGATTTCGTGTAAGACCATGTCTGGGACAG-TGGCAT
40928148 TGTAAGAGCT
Statistics
Matches: 101, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 28 0.28
43 42 0.42
44 27 0.27
45 3 0.03
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
ATATGATTTCGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:40932820 original size:24 final size:24
Alignment explanation
Indices: 40932787--40932833 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40932777 AAGGGGTAAC
* *
40932787 AAGAAGATGAAATGTTAAAGGTTA
1 AAGAAGATGAAAGGTGAAAGGTTA
*
40932811 AAGAATATGAAAGGTGAAAGGTT
1 AAGAAGATGAAAGGTGAAAGGTT
40932834 GAACATCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTA
Found at i:40936781 original size:3 final size:3
Alignment explanation
Indices: 40936773--40936799 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
40936763 ATTAATTTTG
40936773 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
40936800 AATTCTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40942275 original size:14 final size:14
Alignment explanation
Indices: 40942252--40942287 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
40942242 TGGTTGTAAA
* *
40942252 TGGACTTTGGGCTT
1 TGGACATTGGGCAT
40942266 TGGACATTGGGCAT
1 TGGACATTGGGCAT
40942280 TGGACATT
1 TGGACATT
40942288 TATTTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.36
Consensus pattern (14 bp):
TGGACATTGGGCAT
Found at i:40943836 original size:24 final size:24
Alignment explanation
Indices: 40943791--40943854 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
40943781 GAGTTACAAG
* *
40943791 AAGATGAAAGGTTAAAGGTTAAAA
1 AAGATGAAAGGTGAAAGCTTAAAA
* **
40943815 AAGATGAAAGGTGGAAGCTTAAGG
1 AAGATGAAAGGTGAAAGCTTAAAA
*
40943839 GAGATGAAAGGTGAAA
1 AAGATGAAAGGTGAAA
40943855 AGTTGATCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGATGAAAGGTGAAAGCTTAAAA
Found at i:40944045 original size:29 final size:29
Alignment explanation
Indices: 40943979--40944045 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
40943969 TTATCAAAAC
40943979 TACACATGAACTTTGATTCAATATGCAATT
1 TACACATGAACTTTGATT-AATATGCAATT
* * *
40944009 TGATACATGAAGTTTGATT-TTATGCAATT
1 T-ACACATGAACTTTGATTAATATGCAATT
40944038 ATACACAT
1 -TACACAT
40944046 TAAACTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
29 14 0.45
30 2 0.06
31 15 0.48
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (29 bp):
TACACATGAACTTTGATTAATATGCAATT
Found at i:40948168 original size:51 final size:51
Alignment explanation
Indices: 40948092--40948194 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
40948082 TGAATTGCAT
*
40948092 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAGAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
* *
40948143 CGAGTGTAGGCTTGAGGAACACGAACCAAGTCACAAGAAAAAAACAATCTA
1 CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
40948194 C
1 C
40948195 TTACTTTTAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (51 bp):
CGAGTGTAGGCTTAAGCAACACGAACCAAGTCACAAGAAAAAAACAATCTA
Found at i:40951095 original size:17 final size:17
Alignment explanation
Indices: 40951073--40951106 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40951063 TCCTTCTCTT
* *
40951073 TTTCTCTTTTTTTTTTG
1 TTTCTCATTTTTCTTTG
40951090 TTTCTCATTTTTCTTTG
1 TTTCTCATTTTTCTTTG
40951107 CTTAAGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTCTCATTTTTCTTTG
Found at i:40951238 original size:112 final size:114
Alignment explanation
Indices: 40951097--40951303 Score: 285
Period size: 112 Copynumber: 1.8 Consensus size: 114
40951087 TTGTTTCTCA
** * *
40951097 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGATGCGAAGAGAGATGACAACCAAGCACCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAGAGATGACAACCAAACACCCCA
*
40951162 -CCCTGGTTACTCAGCCCAACATACTCCTAATTTATTATATTTATATATG
66 TCCC-GGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* * * *
40951211 TTTTT-TTT-CTTAAGAATATATTGAACCTTTTGACATAAAGAGAGATGACAGCCAAACAGCCCA
1 TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAGAGATGACAACCAAACACCCCA
* *
40951274 TCCCGGTTACTCAGCCTAACACATTCCTAA
66 TCCCGGTTACTCAGCCCAACACACTCCTAA
40951304 AATTTTTTTG
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
112 70 0.86
113 6 0.07
114 5 0.06
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (114 bp):
TTTTTCTTTGCTTAAGAATATATTAAACCTTTTGACACAAAGAGAGATGACAACCAAACACCCCA
TCCCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:40952471 original size:25 final size:27
Alignment explanation
Indices: 40952446--40952511 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 27
40952436 TCCAAACAAA
40952446 ATAAAGTAATAAATAAT-AAAAT-AAA
1 ATAAAGTAATAAATAATAAAAATAAAA
*
40952471 ATAAA-TAAATAAAAAATAAAAATAAAA
1 ATAAAGT-AATAAATAATAAAAATAAAA
40952498 ATAAAG-AA-AAATAA
1 ATAAAGTAATAAATAA
40952512 AAACTGGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 1 0.03
25 19 0.54
26 7 0.20
27 8 0.23
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (27 bp):
ATAAAGTAATAAATAATAAAAATAAAA
Found at i:40952474 original size:13 final size:13
Alignment explanation
Indices: 40952456--40952497 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
40952446 ATAAAGTAAT
40952456 AAATAATAAAATA
1 AAATAATAAAATA
40952469 AAATAA-ATAAATA
1 AAATAATA-AAATA
40952482 AAA-AATAAAAATA
1 AAATAAT-AAAATA
40952495 AAA
1 AAA
40952498 ATAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 22 0.85
14 1 0.04
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
AAATAATAAAATA
Found at i:40952475 original size:17 final size:17
Alignment explanation
Indices: 40952453--40952502 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
40952443 AAAATAAAGT
40952453 AATAAATAATAAAATAA
1 AATAAATAATAAAATAA
*
40952470 AATAAATAA-ATAA-AA
1 AATAAATAATAAAATAA
40952485 AATAAA-AATAAAAATAA
1 AATAAATAAT-AAAATAA
40952502 A
1 A
40952503 GAAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 2 0.07
15 8 0.29
16 6 0.21
17 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAATAATAAAATAA
Found at i:40952479 original size:21 final size:20
Alignment explanation
Indices: 40952443--40952496 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
40952433 ATATCCAAAC
*
40952443 AAAATAAAGT-AATAAATAA
1 AAAATAAAATAAATAAATAA
40952462 TAAAATAAAATAAATAAATAA
1 -AAAATAAAATAAATAAATAA
40952483 AAAATAAAAATAAA
1 AAAAT-AAAATAAA
40952497 AATAAAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATAAAATAAATAAATAA
Found at i:40952508 original size:17 final size:16
Alignment explanation
Indices: 40952453--40952514 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
40952443 AAAATAAAGT
*
40952453 AATAAATAATAAAATAA
1 AATAAA-AATAAAAAAA
40952470 AAT--AAATAAATAAAA
1 AATAAAAATAAA-AAAA
*
40952485 AATAAAAATAAAAATA
1 AATAAAAATAAAAAAA
*
40952501 AAGAAAAATAAAAA
1 AATAAAAATAAAAA
40952515 CTGGGTTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 6 0.15
15 7 0.18
16 16 0.41
17 10 0.26
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AATAAAAATAAAAAAA
Found at i:40956197 original size:14 final size:15
Alignment explanation
Indices: 40956176--40956220 Score: 76
Period size: 14 Copynumber: 3.1 Consensus size: 15
40956166 TTTCTGACAG
40956176 AATAATGACATGAGA
1 AATAATGACATGAGA
40956191 AAT-ATGACATGAG-
1 AATAATGACATGAGA
40956204 AATAATGACATGAGA
1 AATAATGACATGAGA
40956219 AA
1 AA
40956221 GATGTGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.11
14 20 0.71
15 5 0.18
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (15 bp):
AATAATGACATGAGA
Found at i:40956628 original size:27 final size:28
Alignment explanation
Indices: 40956573--40956643 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
40956563 CAATATTTTA
* * *
40956573 TAATTTAA-TCAAT-TATTTAATTGATT
1 TAATTTAACCCAATATATTTAATTAAAT
40956599 TAATTTAACCCAATATATTTAA-TAAAT
1 TAATTTAACCCAATATATTTAATTAAAT
40956626 TAATTTAACCCAATATAT
1 TAATTTAACCCAATATAT
40956644 AATTTAATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 8 0.20
27 25 0.62
28 7 0.17
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (28 bp):
TAATTTAACCCAATATATTTAATTAAAT
Found at i:40961288 original size:23 final size:23
Alignment explanation
Indices: 40961245--40961289 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
40961235 TATTTGTTTT
* *
40961245 ATATTTAAATATTATTTTTAATA
1 ATATTTAAATATTAATATTAATA
40961268 ATATTTAAATATTAATATTAAT
1 ATATTTAAATATTAATATTAAT
40961290 TTATACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTAAATATTAATATTAATA
Found at i:40966259 original size:3 final size:3
Alignment explanation
Indices: 40966251--40966276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40966241 AATGGAGAGA
40966251 AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AG
40966277 AATATATATG
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:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:40967299 original size:25 final size:25
Alignment explanation
Indices: 40967265--40967312 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
40967255 CATAAATGCA
40967265 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATATAG
*
40967290 GCTCTTTATGAGCTTCCTGATAT
1 GCTCTTTATGAGCGTCCTGATAT
40967313 GACTCACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTTATGAGCGTCCTGATATAG
Found at i:40977824 original size:14 final size:14
Alignment explanation
Indices: 40977755--40977831 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
40977745 ACTTTTTTGT
40977755 AAAT-ATATTTTTA
1 AAATAATATTTTTA
* *
40977768 GAA-AATAATTTTAA
1 AAATAAT-ATTTTTA
*
40977782 AAATAATATATATTATT
1 AAATAATAT-T-TT-TA
*
40977799 AAAT-TTATTTTTTA
1 AAATAATA-TTTTTA
40977813 AAATAATATTTTTA
1 AAATAATATTTTTA
40977827 AAATA
1 AAATA
40977832 TTTTATTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
13 4 0.08
14 26 0.54
15 8 0.17
16 5 0.10
17 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (14 bp):
AAATAATATTTTTA
Found at i:40978571 original size:30 final size:30
Alignment explanation
Indices: 40978532--40978588 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
40978522 TTTTATAAAT
40978532 AATTAATATTT-AT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
*
40978562 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
40978589 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 4 0.17
32 2 0.08
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:40987539 original size:27 final size:28
Alignment explanation
Indices: 40987491--40987558 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
40987481 AAAAATATTA
* **
40987491 AAAAATATTTTTTAATTTTTTTTACTTTT
1 AAAAATA-ATTTTAATGATTTTTACTTTT
* *
40987520 -GAAATAATTTTAATGATTTTTATTTTT
1 AAAAATAATTTTAATGATTTTTACTTTT
40987547 AAAAATAATTTT
1 AAAAATAATTTT
40987559 TATTTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
AAAAATAATTTTAATGATTTTTACTTTT
Found at i:40987539 original size:28 final size:27
Alignment explanation
Indices: 40987521--40987571 Score: 61
Period size: 25 Copynumber: 1.9 Consensus size: 27
40987511 TTTACTTTTG
*
40987521 AAATAATTTTAATGATTTTTATTTTTAA
1 AAATAATTTTAAT-ATTTTTACTTTTAA
*
40987549 AAATAATTTT--TATTTTTATTTTT
1 AAATAATTTTAATATTTTTACTTTT
40987572 TATTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
28 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
AAATAATTTTAATATTTTTACTTTTAA
Found at i:40987569 original size:12 final size:12
Alignment explanation
Indices: 40987552--40987591 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
40987542 TTTTTAAAAA
40987552 TAATTTTTATTTT
1 TAATTTTTA-TTT
*
40987565 TATTTTTTATTT
1 TAATTTTTATTT
*
40987577 TAATTTTAATTT
1 TAATTTTTATTT
40987589 TAA
1 TAA
40987592 AAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:40987572 original size:27 final size:28
Alignment explanation
Indices: 40987491--40987572 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 28
40987481 AAAAATATTA
*
40987491 AAAAATATTTTTTAATTTTT-TTTACTTTT
1 AAAAATAATTTTTAATTTTTATTT--TTTT
* *
40987520 -GAAATAA-TTTTAATGATTTT-TATTTTT
1 AAAAATAATTTTTAAT--TTTTATTTTTTT
40987547 AAAAATAATTTTT-ATTTTTATTTTTT
1 AAAAATAATTTTTAATTTTTATTTTTT
40987573 ATTTTAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
26 4 0.09
27 16 0.37
28 13 0.30
29 10 0.23
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (28 bp):
AAAAATAATTTTTAATTTTTATTTTTTT
Found at i:40988395 original size:52 final size:53
Alignment explanation
Indices: 40988317--40988426 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 53
40988307 AATGCTTGAA
* *
40988317 ATTTGTCGTCCGAAGGTTGAGTGCTAGTAATTAATTTGTTTTCAAACTT-ATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
*
40988369 ATTTGTCCTCCTAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
1 ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
*
40988422 GTTTG
1 ATTTG
40988427 CTTGCTCGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 46 0.87
53 7 0.13
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (53 bp):
ATTTGTCCTCCGAAGGTTGAGTGCTAGCAATTAATTTGTTTTCAAACTTCATC
Found at i:41000539 original size:87 final size:87
Alignment explanation
Indices: 41000393--41000567 Score: 314
Period size: 87 Copynumber: 2.0 Consensus size: 87
41000383 AATTTAGTAT
41000393 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
* *
41000458 GTTAATTATTAACTTAAAAATC
66 GTCAATAATTAACTTAAAAATC
41000480 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
1 TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
* *
41000545 GTCACTAATTAACTTAAACATC
66 GTCAATAATTAACTTAAAAATC
41000567 T
1 T
41000568 TAACCACTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (87 bp):
TACAAAACTGAGCTTTCTCCCATGCTCATTGCTTCGTCTCCTTTCTGACTGTCCATTATATATAT
GTCAATAATTAACTTAAAAATC
Found at i:41000727 original size:15 final size:15
Alignment explanation
Indices: 41000707--41000737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41000697 ACAAGAGTTG
*
41000707 AAATAAAATAATAAA
1 AAATAAAAAAATAAA
41000722 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
41000737 A
1 A
41000738 GGTGAAGAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:41003743 original size:2 final size:2
Alignment explanation
Indices: 41003736--41003767 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
41003726 TTTTAACAAA
41003736 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41003768 GGACATCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41011963 original size:14 final size:14
Alignment explanation
Indices: 41011944--41011970 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41011934 CATAAATGAT
41011944 AAAATTTTCACACG
1 AAAATTTTCACACG
41011958 AAAATTTTCACAC
1 AAAATTTTCACAC
41011971 ATATCACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (14 bp):
AAAATTTTCACACG
Found at i:41015825 original size:9 final size:9
Alignment explanation
Indices: 41015811--41015845 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
41015801 ATTATTTTAG
41015811 AAAATTTTT
1 AAAATTTTT
*
41015820 AAAA-TTTA
1 AAAATTTTT
41015828 AAAATTTTT
1 AAAATTTTT
41015837 AAAATTTTT
1 AAAATTTTT
41015846 TTGAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AAAATTTTT
Found at i:41015833 original size:17 final size:18
Alignment explanation
Indices: 41015806--41015843 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
41015796 AAATTATTAT
41015806 TTTAGAAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
41015824 TTTA-AAAATTTTTAAAA
1 TTTAGAAAATTTTTAAAA
41015841 TTT
1 TTT
41015844 TTTTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTAGAAAATTTTTAAAA
Found at i:41015870 original size:28 final size:29
Alignment explanation
Indices: 41015814--41015877 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
41015804 ATTTTAGAAA
* *
41015814 ATTTTTAAAATTTAAAAATTTTTAAAATT
1 ATTTTTGAAATTAAAAAATTTTTAAAATT
*
41015843 -TTTTTGAAATTAAAAAATTATTT-TAATT
1 ATTTTTGAAATTAAAAAATT-TTTAAAATT
41015871 ATTTTTG
1 ATTTTTG
41015878 TATTTTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTTTTGAAATTAAAAAATTTTTAAAATT
Found at i:41019252 original size:15 final size:15
Alignment explanation
Indices: 41019232--41019267 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
41019222 GTGTAAGTAA
41019232 AAATTTATTACTTAC
1 AAATTTATTACTTAC
41019247 AAATTTATTACTTAC
1 AAATTTATTACTTAC
41019262 AAATTT
1 AAATTT
41019268 CTTTACACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTATTACTTAC
Found at i:41019485 original size:16 final size:16
Alignment explanation
Indices: 41019457--41019495 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
41019447 TTTTACTAAT
41019457 ATTATAA-TTTTCATC
1 ATTATAATTTTTCATC
41019472 ATTATAATTTTTCATC
1 ATTATAATTTTTCATC
41019488 ATTATAAT
1 ATTATAAT
41019496 ATCAAGGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTATAATTTTTCATC
Done.