Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 56 of 144
Found at i:17277772 original size:29 final size:30
Alignment explanation
Indices: 17277678--17277772 Score: 135
Period size: 30 Copynumber: 3.2 Consensus size: 30
17277668 GGCCGAAACA
*
17277678 TAATTTT-GAGAAAGTTTAGATGTCAAAATG
1 TAATTTTAGAGAAAGTTTAG-GGTCAAAATG
17277708 TAA-TTTAGAGAAAGTTTAGGGTCAAAATG
1 TAATTTTAGAGAAAGTTTAGGGTCAAAATG
17277737 TAATTTTAGA-AAAGTTTAAGGGTCAAAATG
1 TAATTTTAGAGAAAGTTT-AGGGTCAAAATG
17277767 -AATTTT
1 TAATTTT
17277773 TTTAAAAAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
29 28 0.46
30 33 0.54
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.36
Consensus pattern (30 bp):
TAATTTTAGAGAAAGTTTAGGGTCAAAATG
Found at i:17278046 original size:75 final size:77
Alignment explanation
Indices: 17277950--17278105 Score: 235
Period size: 76 Copynumber: 2.1 Consensus size: 77
17277940 AGAAATCGAG
*
17277950 AATAGCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTAAAAAAAA
1 AATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAA
17278014 CAGAAATTGAAA
66 CAGAAATTGAAA
* * ***
17278026 AATACCTCGGCGTGTG-CCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTCAAAAA
1 AATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAA
*
17278090 CAGAATTTGAAA
66 CAGAAATTGAAA
17278102 AATA
1 AATA
17278106 ATTTGTGAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 35 0.49
76 37 0.51
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (77 bp):
AATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAAAAAA
CAGAAATTGAAA
Found at i:17278961 original size:1 final size:1
Alignment explanation
Indices: 17278957--17279019 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
17278947 TTTTTCCTTC
* * * * * * *
17278957 TTTTTTCTTTTTTTTTGTTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17279020 AGGCATAATA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:17278963 original size:11 final size:9
Alignment explanation
Indices: 17278947--17279012 Score: 75
Period size: 8 Copynumber: 7.4 Consensus size: 9
17278937 TTCATCTTGA
*
17278947 TTTTTCCTT
1 TTTTTTCTT
17278956 CTTTTTTCTTT
1 -TTTTTTC-TT
*
17278967 TTTTTTGTT
1 TTTTTTCTT
17278976 TTTTTTC-T
1 TTTTTTCTT
17278984 TTTTTTC-T
1 TTTTTTCTT
17278992 TTTTTTC-T
1 TTTTTTCTT
17279000 TTTTTTCTT
1 TTTTTTCTT
17279009 TTTT
1 TTTT
17279013 CTTTTTTAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
8 24 0.47
9 13 0.25
10 12 0.24
11 2 0.04
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:17278970 original size:8 final size:8
Alignment explanation
Indices: 17278954--17279019 Score: 89
Period size: 8 Copynumber: 8.1 Consensus size: 8
17278944 TGATTTTTCC
17278954 TTCTTTTT
1 TTCTTTTT
*
17278962 TCTTTTTTT
1 T-TCTTTTT
*
17278971 TTGTTTTTT
1 TT-CTTTTT
17278980 TTCTTTTT
1 TTCTTTTT
17278988 TTCTTTTT
1 TTCTTTTT
17278996 TTCTTTTT
1 TTCTTTTT
17279004 TTC-TTTT
1 TTCTTTTT
17279011 TTCTTTTT
1 TTCTTTTT
17279019 T
1 T
17279020 AGGCATAATA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
7 7 0.13
8 31 0.58
9 15 0.28
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.88
Consensus pattern (8 bp):
TTCTTTTT
Found at i:17278977 original size:16 final size:15
Alignment explanation
Indices: 17278947--17279019 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
17278937 TTCATCTTGA
* *
17278947 TTTTTCCTTCTTTTT
1 TTTTTTCTTTTTTTT
* *
17278962 TCTTTT-TTTTTGTT
1 TTTTTTCTTTTTTTT
17278976 TTTTTTCTTTTTTTCT
1 TTTTTTCTTTTTTT-T
*
17278992 TTTTTTCTTTTTTTC
1 TTTTTTCTTTTTTTT
17279007 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
17279020 AGGCATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
14 11 0.22
15 23 0.47
16 15 0.31
ACGTcount: A:0.00, C:0.12, G:0.01, T:0.86
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:17279712 original size:44 final size:44
Alignment explanation
Indices: 17279649--17279737 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
17279639 TTCTTTCATC
*
17279649 ATCTTATTGTTTAAATTTAAAGTATTATCTGAAATAATTTTCTT
1 ATCTTATTGTTCAAATTTAAAGTATTATCTGAAATAATTTTCTT
*
17279693 ATCTTGTTGTTCAAATTTAAAGTATTATCTGAAATAATTTTCTT
1 ATCTTATTGTTCAAATTTAAAGTATTATCTGAAATAATTTTCTT
17279737 A
1 A
17279738 GGCAAACTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (44 bp):
ATCTTATTGTTCAAATTTAAAGTATTATCTGAAATAATTTTCTT
Found at i:17283022 original size:4 final size:4
Alignment explanation
Indices: 17283013--17283049 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
17283003 ATGCACATGC
*
17283013 AATG AATG AACG AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG A
17283050 TAAATGTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22
Consensus pattern (4 bp):
AATG
Found at i:17284782 original size:35 final size:34
Alignment explanation
Indices: 17284735--17284841 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 34
17284725 AAACGATTTT
*
17284735 TTTTGAAAACACGAAAAAATTTTAAAACACTAGAA
1 TTTTAAAAACACG-AAAAATTTTAAAACACTAGAA
* * * * *
17284770 TTTTAGAGACACGAAAATTTTTGAAACACGAGAA
1 TTTTAAAAACACGAAAAATTTTAAAACACTAGAA
17284804 TTGTTAAAAACACGAAAAATTTTGAAAA-A-TAGAA
1 TT-TTAAAAACACGAAAAATTTT-AAAACACTAGAA
17284838 TTTT
1 TTTT
17284842 TTTGAAAACA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.03
34 26 0.44
35 28 0.47
36 3 0.05
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (34 bp):
TTTTAAAAACACGAAAAATTTTAAAACACTAGAA
Found at i:17284788 original size:17 final size:17
Alignment explanation
Indices: 17284750--17284830 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
17284740 AAAACACGAA
*
17284750 AAAATTTTA-AAACACT
1 AAAATTTTAGAAACACG
* *
17284766 AGAATTTTAGAGACACG
1 AAAATTTTAGAAACACG
*
17284783 AAAATTTTTGAAACACG
1 AAAATTTTAGAAACACG
* *
17284800 AGAATTGTTAAAAACACG
1 AAAATT-TTAGAAACACG
17284818 AAAAATTTT-GAAA
1 -AAAATTTTAGAAA
17284831 AATAGAATTT
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
16 8 0.16
17 27 0.53
18 11 0.22
19 5 0.10
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (17 bp):
AAAATTTTAGAAACACG
Found at i:17284844 original size:18 final size:20
Alignment explanation
Indices: 17284823--17284861 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
17284813 ACACGAAAAA
17284823 TTTTGAAAA-AT-AGAATTT
1 TTTTGAAAACATGAGAATTT
17284841 TTTTGAAAACATGAGAATTT
1 TTTTGAAAACATGAGAATTT
17284861 T
1 T
17284862 GAAAAACGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 2 0.11
20 8 0.42
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (20 bp):
TTTTGAAAACATGAGAATTT
Found at i:17285064 original size:21 final size:21
Alignment explanation
Indices: 17285035--17285125 Score: 90
Period size: 19 Copynumber: 4.7 Consensus size: 21
17285025 ATTTAGTGTC
*
17285035 AAATATTTTTTGAAACACGAG
1 AAATTTTTTTTGAAACACGAG
17285056 AAATTTTTTTTGAAAACACGA-
1 AAATTTTTTTTG-AAACACGAG
*
17285077 AAA----TTTCGAAACACGAG
1 AAATTTTTTTTGAAACACGAG
*
17285094 -AATTTTTTTTGAAA-AC-AC
1 AAATTTTTTTTGAAACACGAG
17285112 AAATTTTTTTTGAA
1 AAATTTTTTTTGAA
17285126 TATTTCTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
16 10 0.17
17 4 0.07
18 1 0.02
19 15 0.25
20 7 0.12
21 14 0.24
22 8 0.14
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (21 bp):
AAATTTTTTTTGAAACACGAG
Found at i:17285263 original size:5 final size:5
Alignment explanation
Indices: 17285249--17285282 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
17285239 AAATTATTTA
*
17285249 AAATA AAATT AAATT GAAATT AAATT AAATT AAA
1 AAATT AAATT AAATT -AAATT AAATT AAATT AAA
17285283 AATATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (5 bp):
AAATT
Found at i:17285273 original size:16 final size:16
Alignment explanation
Indices: 17285249--17285279 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17285239 AAATTATTTA
17285249 AAATAAAATTAAATTG
1 AAATAAAATTAAATTG
*
17285265 AAATTAAATTAAATT
1 AAATAAAATTAAATT
17285280 AAAAATATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATAAAATTAAATTG
Found at i:17285778 original size:4 final size:4
Alignment explanation
Indices: 17285758--17285803 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
17285748 AAAAAATTAT
*
17285758 TTTC TTT- TTTC -TTC TTTC TTTC -TTC TTTC -TTC TTCC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
17285802 TT
1 TT
17285804 CCCCGATCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
3 12 0.33
4 24 0.67
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:17285781 original size:18 final size:18
Alignment explanation
Indices: 17285758--17285800 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17285748 AAAAAATTAT
*
17285758 TTTCTTTTTTCTTCTTTC
1 TTTCTTTTTTCTTCTTCC
*
17285776 TTTCTTCTTTCTTCTTCC
1 TTTCTTTTTTCTTCTTCC
17285794 TTTCTTT
1 TTTCTTT
17285801 CTTCCCCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTCTTTTTTCTTCTTCC
Found at i:17287439 original size:247 final size:246
Alignment explanation
Indices: 17287003--17287487 Score: 961
Period size: 247 Copynumber: 2.0 Consensus size: 246
17286993 AGGCGGTAGA
17287003 CTTCTTCAACTTAGTGCCCATGTGTTTGAATAGTTCCTGCTAAAAGTGGCTCATGAATATTTTGT
1 CTTCTTCAACTTAGTGCCCATGTGTTTGAATAGTTCCTGCTAAAAGTGGCTCATGAATATTTTGT
17287068 CCTGATCGGTAACAATAGACTCAGGGATGCCGTGTAGTTTATATACATGAGTGAGGTACTCTTGA
66 CCTGATCGGTAACAATAGACTCAGGGATGCCGTGTAGTTTATATACATGAGTGAGGTACTCTTGA
17287133 GCCACTGTAAGAGCAGTATAAGGGTGAGCCAATGCTAAAAAATGGCCATATTTGGTTAAGCGATC
131 GCCACTGTAAGAGCAGTATAAGGGTGAGCCAATGCTAAAAAATGGCCATATTTGGTTAAGCGATC
17287198 AACCACCACAAGGACCGTTGACTTCCCGTGCGAGAGTGGCAGGGGGTCCCC
196 AACCACCACAAGGACCGTTGACTTCCCGTGCGAGAGTGGCAGGGGGTCCCC
17287249 NCTTCTTCAACTTAGTGCCCATGTGTTTGAATAGTTCCTGCTAAAAGTGGCTCATGAATATTTTG
1 -CTTCTTCAACTTAGTGCCCATGTGTTTGAATAGTTCCTGCTAAAAGTGGCTCATGAATATTTTG
17287314 TCCTGATCGGTAACAATAGACTCAGGGATGCCGTGTAGTTTATATACATGAGTGAGGTACTCTTG
65 TCCTGATCGGTAACAATAGACTCAGGGATGCCGTGTAGTTTATATACATGAGTGAGGTACTCTTG
17287379 AGCCACTGTAAGAGCAGTATAAGGGTGAGCCAATGCTAAAAAATGGCCATATTTGGTTAAGCGAT
130 AGCCACTGTAAGAGCAGTATAAGGGTGAGCCAATGCTAAAAAATGGCCATATTTGGTTAAGCGAT
17287444 CAACCACCACAAGGACCGTTGACTTCCCGTGCGAGAGTGGCAGG
195 CAACCACCACAAGGACCGTTGACTTCCCGTGCGAGAGTGGCAGG
17287488 CCTTCCACAA
Statistics
Matches: 238, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
247 238 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (246 bp):
CTTCTTCAACTTAGTGCCCATGTGTTTGAATAGTTCCTGCTAAAAGTGGCTCATGAATATTTTGT
CCTGATCGGTAACAATAGACTCAGGGATGCCGTGTAGTTTATATACATGAGTGAGGTACTCTTGA
GCCACTGTAAGAGCAGTATAAGGGTGAGCCAATGCTAAAAAATGGCCATATTTGGTTAAGCGATC
AACCACCACAAGGACCGTTGACTTCCCGTGCGAGAGTGGCAGGGGGTCCCC
Found at i:17291411 original size:10 final size:10
Alignment explanation
Indices: 17291390--17291424 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
17291380 ACATTTCCCC
17291390 CTTTTTTC-T
1 CTTTTTTCTT
17291399 CTTTTTTCTT
1 CTTTTTTCTT
*
17291409 CTTTTTTTTT
1 CTTTTTTCTT
17291419 CTTTTT
1 CTTTTT
17291425 GCTTACGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:17291414 original size:20 final size:20
Alignment explanation
Indices: 17291391--17291454 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 20
17291381 CATTTCCCCC
*
17291391 TTTTTTCTCTTTTTTCTTCT
1 TTTTTTCTCTTTTTGCTTCT
*
17291411 TTTTTTTTCTTTTTGCTTACGT
1 TTTTTTCTCTTTTTGCTT-C-T
17291433 TTTTTTCTCTTCTTTGCTTCT
1 TTTTTTCTCTT-TTTGCTTCT
17291454 T
1 T
17291455 GTTTGTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 16 0.42
21 3 0.08
22 12 0.32
23 7 0.18
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTTCTCTTTTTGCTTCT
Found at i:17291795 original size:30 final size:30
Alignment explanation
Indices: 17291750--17291925 Score: 198
Period size: 30 Copynumber: 5.9 Consensus size: 30
17291740 AAATGCAGCA
*
17291750 AAAGTTTTA-GGGTCAAAACATAATTTTGAG
1 AAAG-TTTAGGGGTCAAAATATAATTTTGAG
* * * *
17291780 AAATTTTAGTGGTCAAAATGTAATTTAGAG
1 AAAGTTTAGGGGTCAAAATATAATTTTGAG
*
17291810 AAAGTTTAGGGGTCAAAAATATAATTTAGA-
1 AAAGTTTAGGGGTC-AAAATATAATTTTGAG
** * *
17291840 AAAGTTTAGGGGTTGAAATGTAATTTTGAA
1 AAAGTTTAGGGGTCAAAATATAATTTTGAG
17291870 AAAGTTTAGGGGTCAAAA-ATAATTTT-AG
1 AAAGTTTAGGGGTCAAAATATAATTTTGAG
*
17291898 AAAAGTTTAGGGGTCAAAATACAATTTT
1 -AAAGTTTAGGGGTCAAAATATAATTTT
17291926 TACAAAAATT
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
28 1 0.01
29 41 0.33
30 68 0.55
31 14 0.11
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (30 bp):
AAAGTTTAGGGGTCAAAATATAATTTTGAG
Found at i:17297582 original size:15 final size:15
Alignment explanation
Indices: 17297562--17297592 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17297552 TCTTATAAAT
*
17297562 TTATTAGATAATTTA
1 TTATTAAATAATTTA
17297577 TTATTAAATAATTTA
1 TTATTAAATAATTTA
17297592 T
1 T
17297593 CTCACACAAT
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATTAAATAATTTA
Found at i:17301281 original size:16 final size:17
Alignment explanation
Indices: 17301250--17301283 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17301240 ACTAAGAGAA
17301250 CAAACACAATAAAAAAT
1 CAAACACAATAAAAAAT
*
17301267 CAAATACAA-AAAAAAT
1 CAAACACAATAAAAAAT
17301283 C
1 C
17301284 TAATTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.71, C:0.18, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAACACAATAAAAAAT
Found at i:17308957 original size:132 final size:132
Alignment explanation
Indices: 17308759--17309021 Score: 481
Period size: 132 Copynumber: 2.0 Consensus size: 132
17308749 AGACGGGTTG
* * *
17308759 ATTAGTCAATCTAGCTTGAAGCGGGCTCAAAAGATCAACCGTATAGAGTTTTCGCTATCCTTTGT
1 ATTAGTCAATCTAGCTTGAAGCGGGATCAAAAGATCAACCATATAGAGTTTTCACTATCCTTTGT
17308824 ATGGATTCCCATACATGTATTGCTAAACAAACGGGGGATTGAACAAAAAACGAGTGGATGGTTAG
66 ATGGATTCCCATACATGTATTGCTAAACAAACGGGGGATTGAACAAAAAACGAGTGGATGGTTAG
17308889 GT
131 GT
* *
17308891 ATTAGTCAATCTAGCTTGAAGTGGGATCCAAAGATCAACCATATAGAGTTTTCACTATCCTTTGT
1 ATTAGTCAATCTAGCTTGAAGCGGGATCAAAAGATCAACCATATAGAGTTTTCACTATCCTTTGT
17308956 ATGGATTCCCATACATGTATTGCTAAACAAACGGGGGATTGAACAAAAAACGAGTGGATGGTTAG
66 ATGGATTCCCATACATGTATTGCTAAACAAACGGGGGATTGAACAAAAAACGAGTGGATGGTTAG
17309021 G
131 G
17309022 AACACCAAAA
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 126 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (132 bp):
ATTAGTCAATCTAGCTTGAAGCGGGATCAAAAGATCAACCATATAGAGTTTTCACTATCCTTTGT
ATGGATTCCCATACATGTATTGCTAAACAAACGGGGGATTGAACAAAAAACGAGTGGATGGTTAG
GT
Found at i:17311231 original size:8 final size:8
Alignment explanation
Indices: 17311218--17311243 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17311208 TGTGCTCCTT
17311218 AAGAACTA
1 AAGAACTA
17311226 AAGAACTA
1 AAGAACTA
17311234 AAGAACTA
1 AAGAACTA
17311242 AA
1 AA
17311244 CAAGTGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (8 bp):
AAGAACTA
Found at i:17316513 original size:17 final size:17
Alignment explanation
Indices: 17316491--17316524 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17316481 ATAGATTCGC
*
17316491 TTAGATATACTTAGTAT
1 TTAGATATAATTAGTAT
17316508 TTAGATATAATTAGTAT
1 TTAGATATAATTAGTAT
17316525 AATATACGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (17 bp):
TTAGATATAATTAGTAT
Found at i:17323390 original size:27 final size:27
Alignment explanation
Indices: 17323309--17323451 Score: 144
Period size: 27 Copynumber: 5.2 Consensus size: 27
17323299 AAAGTTTTTC
*
17323309 AATCTATAAATAAGGGCAAAATTGTAA
1 AATCTAAAAATAAGGGCAAAATTGTAA
* *
17323336 AATATAAAAATATATAGGCAAAATTGTAA
1 AATCTAAAAATA-A-GGGCAAAATTGTAA
* * *
17323365 AATCTTAAAATAGGGGCAAAACTGTAA
1 AATCTAAAAATAAGGGCAAAATTGTAA
* * * *
17323392 AATCTAAAGAACAAAGGTAAAATTGTAT
1 AATCTAAA-AATAAGGGCAAAATTGTAA
*
17323420 AATCTAAAAACT-AGGGGAAAATTGTAA
1 AATCTAAAAA-TAAGGGCAAAATTGTAA
17323447 AATCT
1 AATCT
17323452 GAAGAACAAA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
27 48 0.52
28 22 0.24
29 23 0.25
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (27 bp):
AATCTAAAAATAAGGGCAAAATTGTAA
Found at i:17323423 original size:28 final size:28
Alignment explanation
Indices: 17323320--17323486 Score: 117
Period size: 28 Copynumber: 6.0 Consensus size: 28
17323310 ATCTATAAAT
* *
17323320 AAGGGCAAAATTGTAAAATATAAA-AATA
1 AAGGG-AAAATTGTAAAATCTAAAGAACA
* * *
17323348 TATAGGCAAAATTGTAAAATCTTAA-AA-T
1 -A-AGGGAAAATTGTAAAATCTAAAGAACA
* *
17323376 AGGGGCAAAACTGTAAAATCTAAAGAACA
1 AAGGG-AAAATTGTAAAATCTAAAGAACA
* * *
17323405 AAGGTAAAATTGTATAATCTAAA-AACT
1 AAGGGAAAATTGTAAAATCTAAAGAACA
* *
17323432 AGGGGAAAATTGTAAAATCTGAAGAACA
1 AAGGGAAAATTGTAAAATCTAAAGAACA
* * * * *
17323460 AAAGCAAAACTATAAAATTTAAAGAAC
1 AAGGGAAAATTGTAAAATCTAAAGAAC
17323487 GTGAGCAATA
Statistics
Matches: 107, Mismatches: 26, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
26 2 0.02
27 39 0.36
28 41 0.38
29 22 0.21
30 3 0.03
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.22
Consensus pattern (28 bp):
AAGGGAAAATTGTAAAATCTAAAGAACA
Found at i:17323435 original size:56 final size:55
Alignment explanation
Indices: 17323309--17323482 Score: 190
Period size: 55 Copynumber: 3.1 Consensus size: 55
17323299 AAAGTTTTTC
* * * *
17323309 AATCTATAAATAAGGGCAAAATTGTAAAATATAAA-AATATATAGGCAAAATTGTAA
1 AATCTAAAAATAGGGGCAAAATTGTAAAATCTAAAGAACA-A-AGGCAAAATTGTAA
* * * *
17323365 AATCTTAAAATAGGGGCAAAACTGTAAAATCTAAAGAACAAAGGTAAAATTGTAT
1 AATCTAAAAATAGGGGCAAAATTGTAAAATCTAAAGAACAAAGGCAAAATTGTAA
* * * *
17323420 AATCTAAAAACTAGGGG-AAAATTGTAAAATCTGAAGAACAAAAGCAAAACTATAA
1 AATCTAAAAA-TAGGGGCAAAATTGTAAAATCTAAAGAACAAAGGCAAAATTGTAA
*
17323475 AATTTAAA
1 AATCTAAA
17323483 GAACGTGAGC
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
55 59 0.60
56 37 0.37
57 3 0.03
ACGTcount: A:0.55, C:0.08, G:0.14, T:0.24
Consensus pattern (55 bp):
AATCTAAAAATAGGGGCAAAATTGTAAAATCTAAAGAACAAAGGCAAAATTGTAA
Found at i:17331373 original size:242 final size:232
Alignment explanation
Indices: 17330965--17331837 Score: 638
Period size: 242 Copynumber: 3.8 Consensus size: 232
17330955 AATACATACA
* * * * * *
17330965 TAACTATTATTATAATATAGATCATAATAAATGATATAGTGTTACCTGATATTGTAATGTTTAGT
1 TAACTATTATTATAATATAGATCATAATAAATGAGATAGTATTACATGATATTATAATATTTAAT
* * * *
17331030 CATCGATGCATATATGTAAACTATTAATATATATTATATGATATGATATAGTAGGAGGGCTAAGT
66 AATCGATGCATATATATAAACTATTAATATATATTATATGATATAATATAGTAGGAGGGCTAAAT
* * **
17331095 TTTAAATGTACGGAAACTATAGGGACTTAAAGCATATTTCAATTAGTATAATAATAAACAATAAT
131 TTCAAATGTACGCAAACTATAGGGACTTAAAGCATATTTCAACCAGTATAATAATAAACAATAAT
17331160 ATATAATAAGTAATATATAATGTACTACTATTATTTG
196 ATATAATAAGTAATATATAATGTACTACTATTATTTG
* *
17331197 TAACTATTATTATAATATAGATTATAATAAATGAGATAGTATTACATGCTATTATAATATTTAAT
1 TAACTATTATTATAATATAGATCATAATAAATGAGATAGTATTACATGATATTATAATATTTAAT
**
17331262 AATTTATGCGTATATATATAAACTATTAATATATGATATGATATAGCATTATATAATATAGTAGG
66 AATCGATGC--ATATATATAAACTATTAATATAT-AT-T-ATAT-G----ATATAATATAGTAGG
* * * *
17331327 AGGGTTAAATTTCAAATGTTC-CAATAGTATAGGGACTTAGAGCATATTTCAACCAGTATAATAA
121 AGGGCTAAATTTCAAATGTACGCAA-ACTATAGGGACTTAAAGCATATTTCAACCAGTATAATAA
* *
17331391 TAAACAATAATATATAATATA-TAATA-AT-ATGTA--A-TATGTA-ATA
185 TAAACAATAATATATAATA-AGTAATATATAATGTACTACTAT-TATTTG
* * * * * * * *
17331434 T-A-TAATA-TATAATGTA-CT-ACTATTATAT-ATA-ACTATT--ATTATATTAT-ATATTATA
1 TAACTATTATTATAATATAGATCA-TAATAAATGAGATAGTATTACATGATATTATAATATT-TA
** ** * * * *
17331489 ATAAAAGATATAATATATTATATACTATATGATATGATA-TAGCATTATATAATATAGTAGGAGG
64 ATAATCGAT-GCATATA-TATAAACTAT-TAATAT-ATATTA-TATGATATAATATAGTAGGAGG
* * * * *
17331553 GTTAACTTTCAAATGTACGAAAAATATAGGGACTTAAAACATATTTCAA-C-------TAAT---
124 GCTAAATTTCAAATGTACGCAAACTATAGGGACTTAAAGCATATTTCAACCAGTATAATAATAAA
* *
17331607 --ATAATA-ATAAT---TAATATATAATGTACTACTATTATATA
189 CAATAATATATAATAAGTAATATATAATGTACTACTATTATTTG
* * * * *
17331645 TAACTATTATTATATTATAGATTACAATAAAAT-ATATAGTATTACATGATATTATAAT-GTTAA
1 TAACTATTATTATAATATAGATCATAAT-AAATGAGATAGTATTACATGATATTATAATATTTAA
* * * * * * *
17331708 TATTTGATGC--ATATATAAACTATTAATACATTATATAGCATTATATAATATAGTAGAAGTGCT
65 TAATCGATGCATATATATAAACTATTAATATA-TAT-TA-TATGATATAATATAGTAGGAGGGCT
* * * * * * * * *
17331771 AACTTTCAAATGTATGAAAAGTATAGGGATTTAGAGCATATTTCAACAAGTATCATAATAATCAA
127 AAATTTCAAATGTACGCAAACTATAGGGACTTAAAGCATATTTCAACCAGTATAATAATAAACAA
17331836 TA
192 TA
17331838 TACAATGTAC
Statistics
Matches: 513, Mismatches: 75, Indels: 110
0.73 0.11 0.16
Matches are distributed among these distances:
206 5 0.01
207 2 0.00
208 5 0.01
209 5 0.01
210 9 0.02
211 7 0.01
212 2 0.00
213 10 0.02
214 16 0.03
215 76 0.15
216 7 0.01
217 5 0.01
218 8 0.02
219 10 0.02
220 2 0.00
222 1 0.00
223 62 0.12
224 2 0.00
227 1 0.00
228 16 0.03
229 25 0.05
230 6 0.01
231 7 0.01
232 66 0.13
233 7 0.01
234 30 0.06
235 6 0.01
236 2 0.00
237 9 0.02
238 4 0.01
240 5 0.01
241 4 0.01
242 90 0.18
243 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (232 bp):
TAACTATTATTATAATATAGATCATAATAAATGAGATAGTATTACATGATATTATAATATTTAAT
AATCGATGCATATATATAAACTATTAATATATATTATATGATATAATATAGTAGGAGGGCTAAAT
TTCAAATGTACGCAAACTATAGGGACTTAAAGCATATTTCAACCAGTATAATAATAAACAATAAT
ATATAATAAGTAATATATAATGTACTACTATTATTTG
Found at i:17331407 original size:7 final size:7
Alignment explanation
Indices: 17331397--17331544 Score: 77
Period size: 7 Copynumber: 20.1 Consensus size: 7
17331387 ATAATAAACA
17331397 ATAATAT
1 ATAATAT
17331404 ATAATAT
1 ATAATAT
17331411 ATAATAAT
1 ATAAT-AT
17331419 ATGTAATAT
1 A--TAATAT
*
17331428 GTAATAT
1 ATAATAT
17331435 ATAATAT
1 ATAATAT
*
17331442 ATAATGT
1 ATAATAT
*
17331449 ACTACTAT
1 A-TAATAT
17331457 -T-ATAT
1 ATAATAT
17331462 ATAACTAT
1 ATAA-TAT
*
17331470 -TATTAT
1 ATAATAT
*
17331476 ATTATAT
1 ATAATAT
*
17331483 ATTATAAT
1 ATAAT-AT
* *
17331491 AAAAGAT
1 ATAATAT
17331498 ATAATAT
1 ATAATAT
*
17331505 ATTATAT
1 ATAATAT
17331512 ACTATATGAT
1 A-TA-AT-AT
*
17331522 ATGATAT
1 ATAATAT
* *
17331529 AGCATTAT
1 A-TAATAT
17331537 ATAATAT
1 ATAATAT
17331544 A
1 A
17331545 GTAGGAGGGT
Statistics
Matches: 106, Mismatches: 22, Indels: 26
0.69 0.14 0.17
Matches are distributed among these distances:
5 3 0.03
6 5 0.05
7 65 0.61
8 21 0.20
9 5 0.05
10 7 0.07
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:17331409 original size:17 final size:17
Alignment explanation
Indices: 17331387--17331426 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17331377 AACCAGTATA
17331387 ATAATAAACAATAATAT
1 ATAATAAACAATAATAT
* *
17331404 ATAATATATAATAATAT
1 ATAATAAACAATAATAT
*
17331421 GTAATA
1 ATAATA
17331427 TGTAATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAAACAATAATAT
Found at i:17331416 original size:24 final size:24
Alignment explanation
Indices: 17331387--17331445 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
17331377 AACCAGTATA
17331387 ATAATAA-ACAATAATATATAATAT
1 ATAATAATA-AATAATATATAATAT
** *
17331411 ATAATAATATGTAATATGTAATAT
1 ATAATAATAAATAATATATAATAT
17331435 ATAATATATAA
1 ATAATA-ATAA
17331446 TGTACTACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (24 bp):
ATAATAATAAATAATATATAATAT
Found at i:17331798 original size:215 final size:214
Alignment explanation
Indices: 17331156--17331947 Score: 641
Period size: 215 Copynumber: 3.6 Consensus size: 214
17331146 TAATAAACAA
* * * *
17331156 TAATAT-ATAATAAGTAATATATAATGTACTACTATTATTTGTAACTATTATTATAATATAGATT
1 TAATATAATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTATATTATAGATT
* * *
17331220 ATAAT-AAATGAGATAGTATTACATGCTATTATAATATTTAATAATTT-ATGCGTATATATATAA
66 ACAATAAAAT-ATATAGTATTACATGATATTAT-A-ATTTAAT-ATTTGATGC----ATATATAA
* *
17331283 ACTATTAATATATGATATGATATAGCATTATATAATATAGTAGGAGGGTTAAATTTCAAATGT-T
123 ACTATT-A-ATA-CAT-T-ATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAATGTAT
* *
17331347 CCAATAGTATAGGGACTTAGAGCATATTTCAAC
183 -GAAAAGTATAGGGACTTAGAGCATATTTCAAC
* * * * * *
17331380 CAGTATAATAATAAACAATAATATATAATATA-TA--ATAATATGTAA-TATGTAATATATAATA
1 TAATATAATAAT--A-ATTAATATATAATGTACTACTATTATATATAACTAT-T-AT-TAT-AT-
* ** * * *** **
17331441 TATA-ATGTACTACTATTATATATAACTATT--ATTATATTATATATTATAATAAAAGATATAAT
58 TATAGAT-TAC-AATAAAATATAT-AGTATTACATGATATTATA-ATT-TAATATTTGAT-GCAT
* *
17331503 ATATTATATACTA-T-ATGATATGATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAA
117 ATA-TA-A-ACTATTAAT-ACATTATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAA
* * * *
17331566 TGTACGAAAAATATAGGGACTTAAAACATATTTCAAC
178 TGTATGAAAAGTATAGGGACTTAGAGCATATTTCAAC
17331603 TAATATAATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTATATTATAGATT
1 TAATATAATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTATATTATAGATT
17331668 ACAATAAAATATATAGTATTACATGATATTATAATGTTAATATTTGATGCATATATAAACTATTA
66 ACAATAAAATATATAGTATTACATGATATTATAAT-TTAATATTTGATGCATATATAAACTATTA
* * *
17331733 ATACATTATATAGCATTATATAATATAGTAGAAGTGCTAACTTTCAAATGTATGAAAAGTATAGG
130 ATACATTATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAATGTATGAAAAGTATAGG
*
17331798 GATTTAGAGCATATTTCAAC
195 GACTTAGAGCATATTTCAAC
* * *
17331818 -AAGTATCATAATAATCAATATACAATGTACTACTA-T-TAT-T-A-TATTA-TAGT-TTATA-A
1 TAA-TATAATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTA-TATTATAGA
* * *
17331874 -T---A-AAAATATATAGTATTATATGATATTGTACGTTTAATCA-TTGATGCATATATATAAAC
64 TTACAATAAAATATATAGTATTACATGATATTATA-ATTTAAT-ATTTGATGC--ATATATAAAC
*
17331933 TATTAATATATTATA
125 TATTAATACATTATA
17331948 CATTATGTGA
Statistics
Matches: 469, Mismatches: 62, Indels: 93
0.75 0.10 0.15
Matches are distributed among these distances:
203 38 0.08
204 3 0.01
205 24 0.05
207 1 0.00
208 1 0.00
209 7 0.01
210 6 0.01
211 1 0.00
212 1 0.00
213 3 0.01
214 7 0.01
215 104 0.22
216 4 0.01
217 10 0.02
218 19 0.04
219 18 0.04
220 18 0.04
221 6 0.01
222 2 0.00
223 90 0.19
224 10 0.02
225 19 0.04
226 8 0.02
227 8 0.02
228 25 0.05
229 24 0.05
230 5 0.01
231 7 0.01
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (214 bp):
TAATATAATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTATATTATAGATT
ACAATAAAATATATAGTATTACATGATATTATAATTTAATATTTGATGCATATATAAACTATTAA
TACATTATATAGCATTATATAATATAGTAGGAGGGTTAACTTTCAAATGTATGAAAAGTATAGGG
ACTTAGAGCATATTTCAAC
Found at i:17332144 original size:15 final size:15
Alignment explanation
Indices: 17332124--17332153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17332114 AATACATTTT
17332124 ATAAGTATTAATATA
1 ATAAGTATTAATATA
*
17332139 ATAAGTATTATTATA
1 ATAAGTATTAATATA
17332154 TTATAGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
ATAAGTATTAATATA
Found at i:17333968 original size:26 final size:27
Alignment explanation
Indices: 17333916--17333968 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
17333906 GGGACTTAAC
* *
17333916 ATTTTAAATATTTTTAATTGAATTTGAT
1 ATTTTAAATA-TTTTAATTAAAATTGAT
17333944 ATTTTAAATA-TTTAATTAAAATTGA
1 ATTTTAAATATTTTAATTAAAATTGA
17333969 CATGTGTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
28 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (27 bp):
ATTTTAAATATTTTAATTAAAATTGAT
Found at i:17335194 original size:31 final size:29
Alignment explanation
Indices: 17335126--17335197 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
17335116 CTCAGGTTAT
* * *
17335126 ATTTTAGTCACTTATGTTTGAAATGTTAC
1 ATTTTAGTCACTTACGTTTCAAATGTAAC
* *
17335155 GTTTTAGTCACTTACGTTATCACATTGTAAC
1 ATTTTAGTCACTTACGTT-TCA-AATGTAAC
17335186 ATTTTAGTCACT
1 ATTTTAGTCACT
17335198 GAGCCGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 16 0.46
30 2 0.06
31 17 0.49
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.46
Consensus pattern (29 bp):
ATTTTAGTCACTTACGTTTCAAATGTAAC
Found at i:17337973 original size:33 final size:33
Alignment explanation
Indices: 17337926--17337999 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
17337916 CGAGGGAAAA
*
17337926 ATCAATTTATCCTTTTTAATTTATTTTATTTCT
1 ATCATTTTATCCTTTTTAATTTATTTTATTTCT
* *
17337959 ATCATTTTATCCTTTTTAATTTCTTTTATTTTT
1 ATCATTTTATCCTTTTTAATTTATTTTATTTCT
17337992 ATCATTTT
1 ATCATTTT
17338000 TAAAATTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66
Consensus pattern (33 bp):
ATCATTTTATCCTTTTTAATTTATTTTATTTCT
Found at i:17342574 original size:45 final size:45
Alignment explanation
Indices: 17342510--17342765 Score: 180
Period size: 45 Copynumber: 5.8 Consensus size: 45
17342500 TTGGCTTTAA
*
17342510 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCAT-CTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATGCTT-AG
* **
17342555 TCTGC-CTCACTGCAACTTCA-GGAGGATAGGACTTGCTTTGCTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCCATGCTTAG
*
17342600 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAG--ATG--T-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATGCTTAG
* * * * * * *
17342640 TTCTGCT-CTCTACAACTTCAGAGAGGTAAGA--T-CCAAGGTTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCC-ATG-CTTAG
* * ** * *
17342684 TCCGCTCCACTGCAACTTCAAGGAGATAAGA-TTATC-GGCTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATGC-TTAG
*
17342728 CCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCA
17342766 ATTTCAAAAT
Statistics
Matches: 165, Mismatches: 27, Indels: 37
0.72 0.12 0.16
Matches are distributed among these distances:
40 23 0.14
41 7 0.04
43 8 0.05
44 57 0.35
45 62 0.38
46 8 0.05
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATGCTTAG
Found at i:17342702 original size:44 final size:44
Alignment explanation
Indices: 17342601--17342758 Score: 123
Period size: 44 Copynumber: 3.7 Consensus size: 44
17342591 TTTGCTTAGT
* * * ***
17342601 CTGCTCCACTGCAACTTCAGGGAGATAAGA-C-TA-GATGTGTT
1 CTGCTCCACTGCAACTTCAGAGAGATAAGATCATAGGCTTTAAC
* * * *
17342642 CTGCT-CTCTACAACTTCAGAGAGGTAAGATCCA-AGGTTTTAATC
1 CTGCTCCACTGCAACTTCAGAGAGATAAGAT-CATAGGCTTTAA-C
* *
17342686 C-GCTCCACTGCAACTTCA-AGGAGATAAGATTATCGGCTTTAAC
1 CTGCTCCACTGCAACTTCAGA-GAGATAAGATCATAGGCTTTAAC
*
17342729 CTGCTCCACTGCAACTTCAGGGAGATAAGA
1 CTGCTCCACTGCAACTTCAGAGAGATAAGA
17342759 CTTGCCAATT
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
40 20 0.22
41 5 0.05
42 2 0.02
43 10 0.11
44 54 0.59
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGAGAGATAAGATCATAGGCTTTAAC
Found at i:17345283 original size:98 final size:98
Alignment explanation
Indices: 17345114--17345310 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
17345104 TTGCAATAAA
*
17345114 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
17345179 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
* *
17345212 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* *
17345277 CCTTTAGAATCTCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
17345310 A
1 A
17345311 TGATTTTAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGAAATATTTCCTTT
Found at i:17345538 original size:75 final size:70
Alignment explanation
Indices: 17345450--17345594 Score: 236
Period size: 75 Copynumber: 2.0 Consensus size: 70
17345440 TTTAAAAATC
17345450 GAGTAAAAAATGTAATGTTATGCTACATTAAATATATAATGCAATAATAAATACTACGATAGCAT
1 GAGTAAAAAATGTAATGTTATGCTACATTAAATATATAATGC---AA-AAATACTACGATAGCAT
17345515 AGAAATAAT
62 AGAAATAAT
*
17345524 GAGTAAAAAAATGTAATGTTATGCTACATTAAATATATAATGCAACAATACTACGATAGCATAGA
1 GAGT-AAAAAATGTAATGTTATGCTACATTAAATATATAATGCAAAAATACTACGATAGCATAGA
17345589 AATAAT
65 AATAAT
17345595 ACAAATATAT
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
71 25 0.36
72 2 0.03
74 4 0.06
75 38 0.55
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (70 bp):
GAGTAAAAAATGTAATGTTATGCTACATTAAATATATAATGCAAAAATACTACGATAGCATAGAA
ATAAT
Found at i:17347132 original size:30 final size:30
Alignment explanation
Indices: 17347098--17347160 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
17347088 ATTTATTTTA
*
17347098 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
*
17347128 TTGTTAACTTTGTTATTATTTTAGAGACAT
1 TTGTTAACTTTGTTATTATTTTAAAGACAT
17347158 TTG
1 TTG
17347161 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.56
Consensus pattern (30 bp):
TTGTTAACTTTGTTATTATTTTAAAGACAT
Found at i:17347306 original size:12 final size:12
Alignment explanation
Indices: 17347285--17347318 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
17347275 ATATATTTTT
*
17347285 AAAATTATATAA
1 AAAATAATATAA
17347297 AAAATAATATAA
1 AAAATAATATAA
*
17347309 AAATTAATAT
1 AAAATAATAT
17347319 GGGCAGGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:17349156 original size:8 final size:8
Alignment explanation
Indices: 17349143--17349173 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17349133 AACTATTTTA
17349143 ATTAAAAT
1 ATTAAAAT
17349151 ATTAAAAT
1 ATTAAAAT
17349159 ATTAAAAT
1 ATTAAAAT
*
17349167 AATAAAA
1 ATTAAAA
17349174 AAACACACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
ATTAAAAT
Found at i:17349940 original size:12 final size:12
Alignment explanation
Indices: 17349925--17349966 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
17349915 CTATAAAAAT
17349925 ATTTTTATTAAA
1 ATTTTTATTAAA
* *
17349937 ATTTTCAAATAAA
1 ATTTT-TATTAAA
17349950 ATTTTTATT-AA
1 ATTTTTATTAAA
17349961 ATTTTT
1 ATTTTT
17349967 TTATTCCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 8 0.32
12 7 0.28
13 10 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTTTTATTAAA
Found at i:17353163 original size:20 final size:20
Alignment explanation
Indices: 17353138--17353183 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17353128 TATTAACTTG
17353138 AAAAAAATA-AAAAAATATT
1 AAAAAAATACAAAAAATATT
*
17353157 AAAAAAATACAGAAAATATT
1 AAAAAAATACAAAAAATATT
*
17353177 AATAAAA
1 AAAAAAA
17353184 CATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAAAATACAAAAAATATT
Found at i:17353605 original size:15 final size:15
Alignment explanation
Indices: 17353585--17353620 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17353575 CATAAAGCTC
17353585 CTTCTTCCATCTTCA
1 CTTCTTCCATCTTCA
*
17353600 CTTCTTCTATCTTCA
1 CTTCTTCCATCTTCA
17353615 CTTCTT
1 CTTCTT
17353621 ATAATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.36, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTCTTCCATCTTCA
Found at i:17354615 original size:11 final size:12
Alignment explanation
Indices: 17354594--17354622 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
17354584 TTTTATTAAG
17354594 TATTTAGTTTAT
1 TATTTAGTTTAT
17354606 TATTTA-TTTAT
1 TATTTAGTTTAT
17354617 TATTTA
1 TATTTA
17354623 AATGTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (12 bp):
TATTTAGTTTAT
Found at i:17363744 original size:12 final size:12
Alignment explanation
Indices: 17363700--17363748 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
17363690 TATGGGCCCT
*
17363700 AAATTATAAATA
1 AAATTATATATA
17363712 AAATTA-ATA-A
1 AAATTATATATA
**
17363722 GTATTAT-TATA
1 AAATTATATATA
17363733 AAATTATATATA
1 AAATTATATATA
17363745 AAAT
1 AAAT
17363749 AATTATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
10 7 0.24
11 8 0.28
12 14 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
AAATTATATATA
Found at i:17365385 original size:129 final size:129
Alignment explanation
Indices: 17365155--17365409 Score: 420
Period size: 129 Copynumber: 2.0 Consensus size: 129
17365145 TTGTAAGATC
* * *
17365155 AATTGGATAAAAAATAATTAGGATAATATTTTAGAATAAAGAGTTGGATTGATCAACTCATGAAG
1 AATTGGATAAAAAATAATTAGGACAATATTTTAGAATAAAGAGTTGGACTAATCAACTCATGAAG
* *
17365220 CAGGCGATTAAACTAGTTGAATTAATTTTCTCTATTTTAAAAAAAATATTTTTATTTTAATATG
66 CAGACCATTAAACTAGTTGAATTAATTTTCTCTATTTTAAAAAAAATATTTTTATTTTAATATG
* *
17365284 AATTGGATAAAAAATAATTAGGACAATATTTTAGAATAAAGAGTTGGACTAATTAACTCATGAAT
1 AATTGGATAAAAAATAATTAGGACAATATTTTAGAATAAAGAGTTGGACTAATCAACTCATGAAG
* * *
17365349 CAGACCATTAAACTAGTTGAATTAATTTTCTCTATTTTTAAATATATATTTTTATTTTAAT
66 CAGACCATTAAACTAGTTGAATTAATTTTCTCTATTTTAAAAAAAATATTTTTATTTTAAT
17365410 TTATTCAATT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 116 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (129 bp):
AATTGGATAAAAAATAATTAGGACAATATTTTAGAATAAAGAGTTGGACTAATCAACTCATGAAG
CAGACCATTAAACTAGTTGAATTAATTTTCTCTATTTTAAAAAAAATATTTTTATTTTAATATG
Found at i:17374313 original size:76 final size:75
Alignment explanation
Indices: 17374188--17374330 Score: 232
Period size: 76 Copynumber: 1.9 Consensus size: 75
17374178 GCTGCTATTC
*
17374188 TAGAATTATGCATATTATTTAATCCGTGGAAGACAAAAGAAAGTGTTTTAGAACTTGTTGCATCT
1 TAGAATTATGCATATTATTTAATCCGTGGAAGACAAAAGAAAGTATTTTAGAACTTGTTGCATCT
17374253 TATAAGGTGT
66 TATAAGGTGT
* * **
17374263 TAGAATTATGCATATTGTATTAATCTGTGGAAGGGAAAAGAAAGTATTTTAGAACTTGTTGCATC
1 TAGAATTATGCATATTAT-TTAATCCGTGGAAGACAAAAGAAAGTATTTTAGAACTTGTTGCATC
17374328 TTA
65 TTA
17374331 AGTTCTTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
75 17 0.27
76 45 0.73
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.36
Consensus pattern (75 bp):
TAGAATTATGCATATTATTTAATCCGTGGAAGACAAAAGAAAGTATTTTAGAACTTGTTGCATCT
TATAAGGTGT
Found at i:17383486 original size:37 final size:37
Alignment explanation
Indices: 17383410--17383496 Score: 88
Period size: 37 Copynumber: 2.3 Consensus size: 37
17383400 GATAATCACT
* *
17383410 TTAATATTAAATTAATAAAATACTATCAAGATAAGTA
1 TTAATTTTAAATTAATAAAATACTATCAAAATAAGTA
* *
17383447 TTAATTTTAATTTAATATTAAAT-CTATTAAAATAA-TA
1 TTAATTTTAAATTAATA--AAATACTATCAAAATAAGTA
*
17383484 TTATTTTTGAAAT
1 TTAATTTT-AAAT
17383497 AGTTAATCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
37 24 0.59
38 13 0.32
39 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (37 bp):
TTAATTTTAAATTAATAAAATACTATCAAAATAAGTA
Found at i:17392996 original size:41 final size:41
Alignment explanation
Indices: 17392948--17393106 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
17392938 GTGAAATTAT
* *
17392948 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
*
17392989 TC-GGACTATACGTCC-AGCAGGCTAAGTGCCGGTGAGTTGAA
1 TCAGG-CTATACG-CCTAGCAGGCTAAGTGCCGGTGAATTGAA
* * *
17393030 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
*
17393071 TCAGGCTATAGGCCTAGCAGGCTAAGTGCCGGTGAA
1 TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAA
17393107 CGGAATTAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.03
41 99 0.94
42 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (41 bp):
TCAGGCTATACGCCTAGCAGGCTAAGTGCCGGTGAATTGAA
Found at i:17393107 original size:41 final size:41
Alignment explanation
Indices: 17392961--17393147 Score: 218
Period size: 41 Copynumber: 4.6 Consensus size: 41
17392951 GACTATACGT
* *
17392961 CTAGCAGGCTAAGTGCCGGTGAATTGAATC-GGACTATACGTC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGG-CTATAAG-C
** *
17393003 C-AGCAGGCTAAGTGCCGGTGAGTTGAATCAGGCTACAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
17393043 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAGGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* * **
17393084 CTAGCAGGCTAAGTGCCGGTGAACGGAATTAAACTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
* *
17393125 CTATCAGG-TGAAGTGCCAGTGAA
1 CTAGCAGGCT-AAGTGCCGGTGAA
17393148 TCTGTTTAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
40 3 0.02
41 122 0.95
42 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:17400378 original size:13 final size:13
Alignment explanation
Indices: 17400360--17400388 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17400350 TTCAACTACT
17400360 CTAGATATATGCA
1 CTAGATATATGCA
17400373 CTAGATATATGCA
1 CTAGATATATGCA
17400386 CTA
1 CTA
17400389 TCTCCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
CTAGATATATGCA
Found at i:17402155 original size:5 final size:5
Alignment explanation
Indices: 17402145--17402174 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
17402135 AATTTAAGTA
17402145 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
17402175 AATGAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:17403157 original size:25 final size:25
Alignment explanation
Indices: 17403106--17403161 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
17403096 ACTTTAGCGC
* * ***
17403106 GCTCTCTGATTATTAGCATGTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
17403131 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
17403156 GCTCTC
1 GCTCTC
17403162 CGTTTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:17403201 original size:22 final size:21
Alignment explanation
Indices: 17403129--17403209 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 21
17403119 TAGCATGTTG
*
17403129 GTGCTCTCTGATTACTAGCACGACA
1 GTGCTCTCTG-TT--TAGCAC-ATA
*
17403154 GTGCTCTCCGTTTAGCACATA
1 GTGCTCTCTGTTTAGCACATA
* *
17403175 TGTGCTCTCTGTTTAGTACTTTA
1 -GTGCTCTCTGTTTAGCAC-ATA
*
17403198 GTGCTCTTTGTT
1 GTGCTCTCTGTT
17403210 CATTAGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 2 0.04
22 33 0.69
23 2 0.04
24 2 0.04
25 9 0.19
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (21 bp):
GTGCTCTCTGTTTAGCACATA
Found at i:17407465 original size:155 final size:155
Alignment explanation
Indices: 17407183--17407499 Score: 625
Period size: 155 Copynumber: 2.0 Consensus size: 155
17407173 AAATTAACCA
17407183 ACATTCATATTATGGAAAAAATATCATTTTGCCCCTATACTTTTGACTTCTTTACAATTTAGTCC
1 ACATTCATATTATGGAAAAAATATCATTTTGCCCCTATACTTTTGACTTCTTTACAATTTAGTCC
17407248 CTAGGCTCGTAAAATGAAATTCATGCAATTTCATACACACCTAAGCCTAGCCAAATTTTATATGT
66 CTAGGCTCGTAAAATGAAATTCATGCAATTTCATACACACCTAAGCCTAGCCAAATTTTATATGT
17407313 GCTTATAGTAGCCCATATATTCCAC
131 GCTTATAGTAGCCCATATATTCCAC
17407338 ACATTCATATTATGGAAAAAATATCATTTTGCCCCTATACTTTTGACTTCTTTACAATTTAGTCC
1 ACATTCATATTATGGAAAAAATATCATTTTGCCCCTATACTTTTGACTTCTTTACAATTTAGTCC
17407403 CTAGGCTCGTAAAATGAAATTCATGCAATTTCATACACACCTAAGCCTAGCCAAATTTTATATGT
66 CTAGGCTCGTAAAATGAAATTCATGCAATTTCATACACACCTAAGCCTAGCCAAATTTTATATGT
17407468 GCTTATAGTAGCCCATATATTCCAC
131 GCTTATAGTAGCCCATATATTCCAC
*
17407493 AAATTCA
1 ACATTCA
17407500 CACATTTACC
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
155 161 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (155 bp):
ACATTCATATTATGGAAAAAATATCATTTTGCCCCTATACTTTTGACTTCTTTACAATTTAGTCC
CTAGGCTCGTAAAATGAAATTCATGCAATTTCATACACACCTAAGCCTAGCCAAATTTTATATGT
GCTTATAGTAGCCCATATATTCCAC
Found at i:17432215 original size:41 final size:41
Alignment explanation
Indices: 17432166--17432274 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 41
17432156 GACTTTAAGT
*
17432166 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
*
17432207 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
17432248 CTAGCAGGCTAAGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
17432275 TTTAAATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 58 0.92
42 5 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:17439914 original size:41 final size:41
Alignment explanation
Indices: 17439865--17439973 Score: 173
Period size: 41 Copynumber: 2.6 Consensus size: 41
17439855 GACTTTAAGT
*
17439865 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
*
17439906 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
17439947 CTAGCAGGCTAAGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
17439974 TTTAAATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
41 58 0.92
42 5 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:17441761 original size:3 final size:3
Alignment explanation
Indices: 17441753--17441784 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17441743 TTAAATAAGC
17441753 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17441785 CAACTCGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17446590 original size:41 final size:41
Alignment explanation
Indices: 17446532--17446610 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
17446522 GAGTATGACG
*
17446532 AACTGTCAAGTGTCTCATGATCCCTTCTGACTTGCACAATC
1 AACTGTCAAGTGCCTCATGATCCCTTCTGACTTGCACAATC
17446573 AACTGTCAAGTGCCTCATGATCCCTTCTGACTTGCACA
1 AACTGTCAAGTGCCTCATGATCCCTTCTGACTTGCACA
17446611 GTTTATTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (41 bp):
AACTGTCAAGTGCCTCATGATCCCTTCTGACTTGCACAATC
Found at i:17479228 original size:13 final size:14
Alignment explanation
Indices: 17479195--17479225 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17479185 TGTTTAACTA
*
17479195 AAAATGATTTTTGG
1 AAAATGATTTATGG
17479209 AAAATGATTTATGG
1 AAAATGATTTATGG
17479223 AAA
1 AAA
17479226 TGACTTACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (14 bp):
AAAATGATTTATGG
Found at i:17479794 original size:16 final size:16
Alignment explanation
Indices: 17479763--17479799 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
17479753 ATGCGAAGAA
17479763 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
17479779 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
17479795 TATTA
1 TATTA
17479800 AAATAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:17485683 original size:24 final size:24
Alignment explanation
Indices: 17485629--17485707 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
17485619 GTTCCTGGAC
*
17485629 TCGTGGTTGTCCCTGTTGGAGGAG
1 TCGTGGTTGTCCCAGTTGGAGGAG
*
17485653 TTGTGGTTGTCCCAGTTGGAGGAG
1 TCGTGGTTGTCCCAGTTGGAGGAG
* * ** *
17485677 TCATGGTAGGGCCAGTCGGAGGAG
1 TCGTGGTTGTCCCAGTTGGAGGAG
17485701 TCGTGGT
1 TCGTGGT
17485708 AGGGCCGGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.29
Consensus pattern (24 bp):
TCGTGGTTGTCCCAGTTGGAGGAG
Found at i:17485721 original size:24 final size:24
Alignment explanation
Indices: 17485664--17485713 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
17485654 TGTGGTTGTC
*
17485664 CCAGTTGGAGGAGTCATGGTAGGG
1 CCAGTCGGAGGAGTCATGGTAGGG
*
17485688 CCAGTCGGAGGAGTCGTGGTAGGG
1 CCAGTCGGAGGAGTCATGGTAGGG
17485712 CC
1 CC
17485714 GGTGGGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.46, T:0.18
Consensus pattern (24 bp):
CCAGTCGGAGGAGTCATGGTAGGG
Found at i:17485760 original size:27 final size:27
Alignment explanation
Indices: 17485724--17485797 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
17485714 GGTGGGAGCT
17485724 GGATTTGTGTCCGGTAATGTTGGAGTC
1 GGATTTGTGTCCGGTAATGTTGGAGTC
* * *
17485751 GGATTGGTGTCTGGTAATGTTGGAGTT
1 GGATTTGTGTCCGGTAATGTTGGAGTC
*
17485778 GGATTTGTGTCCGGTGATGT
1 GGATTTGTGTCCGGTAATGT
17485798 CGGGGTAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.14, C:0.08, G:0.39, T:0.39
Consensus pattern (27 bp):
GGATTTGTGTCCGGTAATGTTGGAGTC
Found at i:17488994 original size:22 final size:22
Alignment explanation
Indices: 17488963--17489005 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17488953 TTTATAGTTG
*
17488963 AGTGATAAAAAAATCATAATTA
1 AGTGACAAAAAAATCATAATTA
17488985 AGTGACAAAAAAATCATAATT
1 AGTGACAAAAAAATCATAATT
17489006 CAGTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (22 bp):
AGTGACAAAAAAATCATAATTA
Found at i:17489013 original size:19 final size:19
Alignment explanation
Indices: 17488968--17489014 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
17488958 AGTTGAGTGA
17488968 TAAAAAAATCATAATTAAG
1 TAAAAAAATCATAATTAAG
*
17488987 TGACAAAAAAATCATAATTCAG
1 T---AAAAAAATCATAATTAAG
17489009 TAAAAA
1 TAAAAA
17489015 TTTAAATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.25
22 18 0.75
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (19 bp):
TAAAAAAATCATAATTAAG
Found at i:17490207 original size:19 final size:19
Alignment explanation
Indices: 17490175--17490222 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
17490165 GCTTGGAGCT
**
17490175 TATTTTAACCTTTATAGTAA
1 TATTTTAATTTTTATA-TAA
*
17490195 T-TTTTAATTTTTATATTA
1 TATTTTAATTTTTATATAA
17490213 TATTTTAATT
1 TATTTTAATT
17490223 GTTTTTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 20 0.83
20 1 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTTAATTTTTATATAA
Found at i:17490233 original size:20 final size:19
Alignment explanation
Indices: 17490196--17490236 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
17490186 TTATAGTAAT
17490196 TTTTAATTTTTATATTATA
1 TTTTAATTTTTATATTATA
* *
17490215 TTTTAATTGTTTTTCTTATA
1 TTTTAATT-TTTATATTATA
17490235 TT
1 TT
17490237 ATCCGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTAATTTTTATATTATA
Found at i:17492700 original size:162 final size:159
Alignment explanation
Indices: 17492463--17492764 Score: 435
Period size: 162 Copynumber: 1.9 Consensus size: 159
17492453 AACCCCTTTT
* *
17492463 TGAACAAGCAAACAACTCCAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTACATTATTT
1 TGAACAAGCAAACAACTCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTACATGATTT
* * ** * * *
17492528 TACGTGTAAACAATCAGATCAGATGAAATATTAAGAAAGCATTAACAGAAATGAAAAACAAAG-T
66 TACATGTAAACAATCAGATCAAACAAAATATTAAGAAAGCACTAACACAAACG-AAAACAAAGTT
17492592 CAAAAACAATACATCCAAGGAAAACCCTCTA
130 C-AAAACAATACATCCAAGGAAAACCCTCTA
* * *
17492623 TGAACAAGCAAACAACCTTCAAAATTCTCAAATCTAATGACTTGATTGATTTAAATCTACATGAT
1 TGAACAAGCAAACAA-C-TCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTACATGAT
* *
17492688 TTTACATGTAAACAATCAGATCAAACAAAATGTTAAGAAAGCACTAACACAAACGAAAACAATGT
64 TTTACATGTAAACAATCAGATCAAACAAAATATTAAGAAAGCACTAACACAAACGAAAACAAAGT
17492753 TCAAAACAATAC
129 TCAAAACAATAC
17492765 TGTTGACGGG
Statistics
Matches: 125, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
160 15 0.12
161 19 0.15
162 91 0.73
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (159 bp):
TGAACAAGCAAACAACTCAAAATTCTCAAATCTAATGACTTGATTAACTTAAACCTACATGATTT
TACATGTAAACAATCAGATCAAACAAAATATTAAGAAAGCACTAACACAAACGAAAACAAAGTTC
AAAACAATACATCCAAGGAAAACCCTCTA
Found at i:17495224 original size:5 final size:5
Alignment explanation
Indices: 17495214--17495240 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17495204 GAGCAACCGT
17495214 AAAGA AAAGA AAAGA AAAGA AAAGA AA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AA
17495241 TATCTCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:17497143 original size:4 final size:4
Alignment explanation
Indices: 17497134--17497164 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
17497124 AAAAAATACT
17497134 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
17497165 TAAATAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:17498392 original size:16 final size:16
Alignment explanation
Indices: 17498371--17498410 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
17498361 CGTTTGGTTC
*
17498371 GCTGTAATTGAATAGA
1 GCTGTAATGGAATAGA
17498387 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
17498403 GCTGTAAT
1 GCTGTAAT
17498411 AGTAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:17498443 original size:45 final size:44
Alignment explanation
Indices: 17498392--17498484 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
17498382 ATAGAGCTGT
* * *
17498392 AATGGAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGT-ATTC-ATGTGTTTAGTTGAATGG
*
17498437 AATGGAATAAAACTGTAATAGTATTCTTGTGTTTAGTTGAATGG
1 AATGGAATAAAACTGTAATAGTATTCATGTGTTTAGTTGAATGG
17498481 AATG
1 AATG
17498485 ATTTTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.51
45 20 0.47
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAAAACTGTAATAGTATTCATGTGTTTAGTTGAATGG
Found at i:17498706 original size:56 final size:56
Alignment explanation
Indices: 17498591--17498719 Score: 145
Period size: 56 Copynumber: 2.3 Consensus size: 56
17498581 AATAAAATTA
* * *
17498591 TTAATATAAATAATAAATAATTTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATTTAATAAAATTTTAAAATAATTATTATT-AATATAAT
* *
17498649 TTAATAAAA-AATATATAATTTAATAAAATTCTTAAAATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATTTAATAAAATT-TTAAAATAATTATTATTAATAT-AAT
* *
17498705 TTACTAAAATCATAA
1 TTAATAAAATAATAA
17498720 TATATAATAG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
55 4 0.07
56 29 0.48
57 21 0.35
58 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATTTAATAAAATTTTAAAATAATTATTATTAATATAAT
Found at i:17499213 original size:43 final size:43
Alignment explanation
Indices: 17499158--17499246 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
17499148 CAATTCAACT
*
17499158 TTTATTTTTTCCATTTCAATTGTTGGAAACTCCATCATTCACG
1 TTTATTTTTTCCATTTCAATTGTTAGAAACTCCATCATTCACG
17499201 TTTATTTTTTCCATTTCAATTGTTAGAAACTCCATCATTCACG
1 TTTATTTTTTCCATTTCAATTGTTAGAAACTCCATCATTCACG
17499244 TTT
1 TTT
17499247 GTTGTCCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.08, T:0.48
Consensus pattern (43 bp):
TTTATTTTTTCCATTTCAATTGTTAGAAACTCCATCATTCACG
Found at i:17502291 original size:44 final size:44
Alignment explanation
Indices: 17502243--17502767 Score: 329
Period size: 44 Copynumber: 11.6 Consensus size: 44
17502233 TTCAATCTAT
* * *
17502243 TCCACTGCAATTTCAGGGAGATTAGACTTATAGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
* * * **
17502287 TCCACTGCAACTTCAGGGAGATGAGATTTGTAATTTTTCGTTTTAATCTAT
1 TCCACTGCAACTTCAGGGAGAT-A-A---G--ATTTATAGCTTTAATCTGC
* * * * * * *
17502338 TCTACTACAACTTTAGGGAAATAAGATATGTAGCCTTT-ATCTGA
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAG-CTTTAATCTGC
* * * * *
17502382 TGCACTGCAACTTTAGGGAGATAAAATTTGTAACTTATAGCTTCAATCTGT
1 TCCACTGCAACTTCAGGGAGAT--AA---G--ATTTATAGCTTTAATCTGC
* * * * * *
17502433 TCCACTGTAACTTCAGGGAAATGAGATTTGTAACTTTAATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
* * *
17502477 TCCACTGCAACTTCAGGGAGATCAGGTTTATAACTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
* * * * * *
17502521 TCTACTGCAACTTCAGAGAGATAAGATTCACTATCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTA-TAGCTTTAATCTGC
* * * * * * *
17502566 TCCACTGCAACTTTAGGAAGATGAGATTTGTAACTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
* * * *
17502610 TCCACTGCGACTTCAGGGAGATAAGATTTGT-GTTTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTT-AATCTGC
* * * * * * * *
17502654 TCCACTGCAATTTCAAGGAGATAATATTAACATCTTCAATCTAC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
* * * **
17502698 TCCATTGCAACCTCAGGGAG--AAGATTTGTTTCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
*
17502740 TTCACTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
17502768 CGCGACGATG
Statistics
Matches: 369, Mismatches: 91, Indels: 42
0.74 0.18 0.08
Matches are distributed among these distances:
42 32 0.09
43 2 0.01
44 224 0.61
45 39 0.11
46 5 0.01
49 4 0.01
50 4 0.01
51 59 0.16
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTGC
Found at i:17502430 original size:95 final size:94
Alignment explanation
Indices: 17502231--17502763 Score: 290
Period size: 95 Copynumber: 5.8 Consensus size: 94
17502221 TATATGTGTT
* * *
17502231 GCTTCAATCTATTCCACTGCAA-TTTCAGGGAGATTAGACTTATAGCTTTAATCTGCTCCACTGC
1 GCTTCAATCTATTCCACTGCAACTTT-AGGGAAATAAGA-TTGTAGCTTTAATCTGCTCCACTGC
* * * * *
17502295 AACTTCAGGGAGATGAGATTTGTAATTTTTC
64 AACTTCAGGGAGATAAAATTTGTAACTTATA
* * * * * *
17502326 GTTTTAATCTATTCTACTACAACTTTAGGGAAATAAGATATGTAGCCTTT-ATCTGATGCACTGC
1 GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGAT-TGTAG-CTTTAATCTGCTCCACTGC
*
17502390 AACTTTAGGGAGATAAAATTTGTAACTTATA
64 AACTTCAGGGAGATAAAATTTGTAACTTATA
* * * * * *
17502421 GCTTCAATCTGTTCCACTGTAACTTCAGGGAAATGAGATTTGTAACTTTAATTTGCTCCACTGCA
1 GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGA-TTGTAGCTTTAATCTGCTCCACTGCA
* *
17502486 ACTTCAGGGAGAT--CA--GGT---TTATA
65 ACTTCAGGGAGATAAAATTTGTAACTTATA
* * ** * * * * * * * *
17502509 ACTTTAATCTGCTCTACTGCAACTTCAGAGAGATAAGATTCACTATCTTCAATCTACTCCACTGC
1 GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGATT--GTAGCTTTAATCTGCTCCACTGC
* * * *
17502574 AACTTTAGGAAGATGAGATTTG-----TA-A
64 AACTTCAGGGAGATAAAATTTGTAACTTATA
* * * * * *
17502599 -CTTCAATCTACTCCACTGCGACTTCAGGGAGATAAGATTTGT-GTTTTCAATCTACTCCACTGC
1 GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGA-TTGTAGCTTT-AATCTGCTCCACTGC
* * *
17502662 AATTTCAAGGAGAT--AATAT-TAAC--AT-
64 AACTTCAGGGAGATAAAATTTGTAACTTATA
* * * * * ** *
17502687 -CTTCAATCTACTCCATTGCAACCTCAGGG--AGAAGATTTGTTTCTTTAATCTGCTTCACTGCA
1 GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGA-TTGTAGCTTTAATCTGCTCCACTGCA
17502749 ACTTCAGGGAGATAA
65 ACTTCAGGGAGATAA
17502764 GATTCGCGAC
Statistics
Matches: 345, Mismatches: 72, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
86 38 0.11
87 7 0.02
88 88 0.26
89 62 0.18
90 3 0.01
91 5 0.01
93 2 0.01
94 5 0.01
95 127 0.37
96 8 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (94 bp):
GCTTCAATCTATTCCACTGCAACTTTAGGGAAATAAGATTGTAGCTTTAATCTGCTCCACTGCAA
CTTCAGGGAGATAAAATTTGTAACTTATA
Found at i:17502613 original size:133 final size:132
Alignment explanation
Indices: 17502422--17502767 Score: 405
Period size: 133 Copynumber: 2.6 Consensus size: 132
17502412 TAACTTATAG
** * *
17502422 CTTCAATCTGTTCCACTGTAACTTCAGGGAA-ATGAGATTTGTAACTTTAATTTGCTCCACTGCA
1 CTTCAATCTACTCCACTGCAACTTCA-GGAAGATGAGATTTGTAACTTTAATCTGCTCCACTGCA
* * * *
17502486 ACTTCAGGGAGATCAGGTTTATAACTTT-AATCTGCTCTACTGCAACTTC-AGAGAGATAAGATT
65 ACTTCAGGGAGATAAGATTTAT-ACTTTCAATCTACTCCACTGCAACTTCAAG-GAGATAAGATT
*
17502549 CACTAT
128 AAC-AT
* * * *
17502555 CTTCAATCTACTCCACTGCAACTTTAGGAAGATGAGATTTGTAACTTCAATCTACTCCACTGCGA
1 CTTCAATCTACTCCACTGCAACTTCAGGAAGATGAGATTTGTAACTTTAATCTGCTCCACTGCAA
* ** * *
17502620 CTTCAGGGAGATAAGATTTGTGTTTTCAATCTACTCCACTGCAATTTCAAGGAGATAATATTAAC
66 CTTCAGGGAGATAAGATTTATACTTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGATTAAC
17502685 AT
131 AT
* * * ** *
17502687 CTTCAATCTACTCCATTGCAACCTCAGGGAGA--AGATTTGTTTCTTTAATCTGCTTCACTGCAA
1 CTTCAATCTACTCCACTGCAACTTCAGGAAGATGAGATTTGTAACTTTAATCTGCTCCACTGCAA
17502750 CTTCAGGGAGATAAGATT
66 CTTCAGGGAGATAAGATT
17502768 CGCGACGATG
Statistics
Matches: 182, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
130 43 0.24
132 37 0.20
133 100 0.55
134 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (132 bp):
CTTCAATCTACTCCACTGCAACTTCAGGAAGATGAGATTTGTAACTTTAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATTTATACTTTCAATCTACTCCACTGCAACTTCAAGGAGATAAGATTAAC
AT
Found at i:17505394 original size:90 final size:89
Alignment explanation
Indices: 17505238--17505448 Score: 269
Period size: 90 Copynumber: 2.4 Consensus size: 89
17505228 TATTACAAAC
** * * * * * *
17505238 CTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTAGCTTTAATATGCTCTACTGCCACTTCAGA
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAGATTTAATATGCCCTACTACAACTTCAGA
17505303 GAGATAAGACTCGCTATCTTCAATT
66 GAGATAAGACTCGCTATCTTCAA-T
* * * *
17505328 TTGCTCCACTACAGCTTTAGGGAGATAAGATTTGTAGATTTAATCTGCCCTACTACAACTTTAGA
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAGATTTAATATGCCCTACTACAACTTCAGA
* * *
17505393 GAGATAAGATTTGCTATTTTCAAT
66 GAGATAAGACTCGCTATCTTCAAT
*
17505417 CTGCTCCACTACAATTTTAGGGAGATAAGATT
1 CTGCTCCACTACAACTTTAGGGAGATAAGATT
17505449 AGTTCTTCAA
Statistics
Matches: 103, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
89 30 0.29
90 73 0.71
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (89 bp):
CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTAGATTTAATATGCCCTACTACAACTTCAGA
GAGATAAGACTCGCTATCTTCAAT
Found at i:17505475 original size:43 final size:44
Alignment explanation
Indices: 17505238--17505493 Score: 203
Period size: 44 Copynumber: 5.8 Consensus size: 44
17505228 TATTACAAAC
** * * * *
17505238 CTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTAGCTTTAAT
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTATCTTCAAT
* * * * * * * *
17505282 ATGCTCTACTGCCACTTCAGAGAGATAAGACTCGCTATCTTCAATT
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTG-TATCTTCAA-T
* * ** *
17505328 TTGCTCCACTACAGCTTTAGGGAGATAAGATTTGTAGATTTAAT
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTATCTTCAAT
* *
17505372 CTGC-CCTACTACAACTTTAGAGAGATAAGATTTGCTATTTTCAAT
1 CTGCTCC-ACTACAACTTTAGGGAGATAAGATTTG-TATCTTCAAT
* *
17505417 CTGCTCCACTACAATTTTAGGGAGATAAGATTAGT-TCTTCAAT
1 CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTATCTTCAAT
* * * *
17505460 TTTCTCCACTGCAA-TTTAAGGGATATAAGATTTG
1 CTGCTCCACTACAACTTT-AGGGAGATAAGATTTG
17505494 CCATGGTGAC
Statistics
Matches: 169, Mismatches: 37, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
42 3 0.02
43 34 0.20
44 56 0.33
45 48 0.28
46 28 0.17
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (44 bp):
CTGCTCCACTACAACTTTAGGGAGATAAGATTTGTATCTTCAAT
Found at i:17508430 original size:29 final size:30
Alignment explanation
Indices: 17508372--17508430 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
17508362 CAAAGCAATA
*
17508372 CATGAACTTTAGTTTAATGTGCAATTTTATT
1 CATGAACTTTAGTTT-ATGTGCAATGTTATT
17508403 CATGAACTTT-GATTT-TGTGCAATGTTAT
1 CATGAACTTTAG-TTTATGTGCAATGTTAT
17508431 ACATAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 12 0.46
30 1 0.04
31 13 0.50
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (30 bp):
CATGAACTTTAGTTTATGTGCAATGTTATT
Found at i:17509355 original size:179 final size:179
Alignment explanation
Indices: 17509039--17509378 Score: 491
Period size: 179 Copynumber: 1.9 Consensus size: 179
17509029 ACTACTGGAC
** *
17509039 GCACATTTTACATCGAATATATTGATGAGCGTTAGGCACAAATTATACTTCGGTCGTTTCGATGA
1 GCACATTTTACATCGAATATACCGATGAGCGTTAGGCACAAATTATACTTCGATCGTTTCGATGA
** * * *
17509104 GGCACTGACTGCCAGATTGACATGATGGTTGGATGATTCGTGTATCTGTCCTTGGTTCGTGCCCA
66 GGCACTGACTGCCAGATTGACATGATGGTCAGATGATCCGTGTATCCGTCCTTGGTCCGTGCCCA
* * *
17509169 TCTAATAGGGGTTGTAAAATGTAAACTGGCTGCCCAATAACTGTTGGGA
131 ACTAATAGGGGTTATAAAACGTAAACTGGCTGCCCAATAACTGTTGGGA
* * * *
17509218 GCACATTTTACATTGGATATACCGATGAGTGTTAGGTACAAATTATACTTCGATCGTTTCGATGA
1 GCACATTTTACATCGAATATACCGATGAGCGTTAGGCACAAATTATACTTCGATCGTTTCGATGA
* * * * * *
17509283 GGCACTGACTGTCAGATTGGCTTGGTTGTCAGATGATCCGTGTATCCGTCCTTGGTCCGTGTCCA
66 GGCACTGACTGCCAGATTGACATGATGGTCAGATGATCCGTGTATCCGTCCTTGGTCCGTGCCCA
17509348 ACTAATAGGGGTTATAAAACGTAAACTGGCT
131 ACTAATAGGGGTTATAAAACGTAAACTGGCT
17509379 TAACAGTTAT
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
179 140 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (179 bp):
GCACATTTTACATCGAATATACCGATGAGCGTTAGGCACAAATTATACTTCGATCGTTTCGATGA
GGCACTGACTGCCAGATTGACATGATGGTCAGATGATCCGTGTATCCGTCCTTGGTCCGTGCCCA
ACTAATAGGGGTTATAAAACGTAAACTGGCTGCCCAATAACTGTTGGGA
Found at i:17510082 original size:21 final size:21
Alignment explanation
Indices: 17510049--17510088 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17510039 TCAAAGGTTA
*
17510049 TAAGCAAATTAAAAAATAAGC
1 TAAGCAAAATAAAAAATAAGC
* *
17510070 TAAGTAAAATAAAGAATAA
1 TAAGCAAAATAAAAAATAA
17510089 CAAAATGTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.05, G:0.10, T:0.20
Consensus pattern (21 bp):
TAAGCAAAATAAAAAATAAGC
Found at i:17512647 original size:3 final size:3
Alignment explanation
Indices: 17512639--17512677 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
17512629 ATGTAATTCT
17512639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17512678 AATATGATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17513897 original size:20 final size:21
Alignment explanation
Indices: 17513859--17513900 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17513849 ATACTCAATC
*
17513859 ACAAAAAATAAAGACAACAAG
1 ACAAAAAAGAAAGACAACAAG
17513880 ACAAAAAAGAAAGA-AACAAG
1 ACAAAAAAGAAAGACAACAAG
17513900 A
1 A
17513901 TGCGGTCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.74, C:0.12, G:0.12, T:0.02
Consensus pattern (21 bp):
ACAAAAAAGAAAGACAACAAG
Found at i:17522754 original size:25 final size:25
Alignment explanation
Indices: 17522634--17522799 Score: 92
Period size: 25 Copynumber: 6.8 Consensus size: 25
17522624 TATGATATGA
* *
17522634 CATTCTGATT-TGATAATGAAATGT
1 CATTCTGATTATAATAATAAAATGT
* * * *
17522658 TATTCTTATTTTAATGAAT-AAATAT
1 CATTCTGATTATAAT-AATAAAATGT
* * *
17522683 CA-TCTTGATTCTGAAT-ATGATATGT
1 CATTC-TGATTAT-AATAATAAAATGT
* * *
17522708 CGTTTTGATT-TGATAATAAAATGT
1 CATTCTGATTATAATAATAAAATGT
* * *
17522732 CACTCTGATTCTAATAATCAAATGT
1 CATTCTGATTATAATAATAAAATGT
* * *
17522757 CATTCCGATTATGATAATGAAATGT
1 CATTCTGATTATAATAATAAAATGT
*
17522782 TATTCTGATTATAA-AATA
1 CATTCTGATTATAATAATA
17522800 TGAAAATGGT
Statistics
Matches: 106, Mismatches: 28, Indels: 16
0.71 0.19 0.11
Matches are distributed among these distances:
23 2 0.02
24 30 0.28
25 67 0.63
26 7 0.07
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (25 bp):
CATTCTGATTATAATAATAAAATGT
Found at i:17522791 original size:74 final size:74
Alignment explanation
Indices: 17522624--17522791 Score: 162
Period size: 74 Copynumber: 2.3 Consensus size: 74
17522614 TTAAGTAAAT
* * * * * * * *
17522624 TATGATATGACATTCTGATTTGATAATGAAATGTTATTCTTATTTTAATGAATAAATATCATCTT
1 TATGAAATGTCATTCTGATTTGATAATAAAATGTCACTCTGATTCTAATGAATAAATATCATCTC
*
17522689 GATTCTGAA
66 GATTATGAA
* * * *
17522698 TATGATATGTCGTTTTGATTTGATAATAAAATGTCACTCTGATTCTAAT-AATCAAATGTCAT-T
1 TATGAAATGTCATTCTGATTTGATAATAAAATGTCACTCTGATTCTAATGAAT-AAATATCATCT
17522761 CCGATTATG-A
65 -CGATTATGAA
*
17522771 TAATGAAATGTTATTCTGATT
1 T-ATGAAATGTCATTCTGATT
17522792 ATAAAATATG
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
73 6 0.08
74 70 0.92
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (74 bp):
TATGAAATGTCATTCTGATTTGATAATAAAATGTCACTCTGATTCTAATGAATAAATATCATCTC
GATTATGAA
Found at i:17524765 original size:87 final size:87
Alignment explanation
Indices: 17524592--17524875 Score: 347
Period size: 87 Copynumber: 3.3 Consensus size: 87
17524582 GCACAGACAT
** ** ** * * *
17524592 GTTACAGTTTAAACTGATAGATCAGATAATAGTATGCAATAAAGCT-ACGTACATA-CGATACAG
1 GTTACAG-TTAAACTGCCAGATCAGATAATAGTACACAGCAAAGCTGACATACA-AGTGGTACAG
* *
17524655 TGTGGTAAACCGCTATACTGATAA
64 TGAGGTAAACCGCTATACCGATAA
*
17524679 GTTACAATTAAACTGCCAGATCAGATAATAGTACACAGCAAAGCTGACATACAAGTGGTACAGTG
1 GTTACAGTTAAACTGCCAGATCAGATAATAGTACACAGCAAAGCTGACATACAAGTGGTACAGTG
*
17524744 CGGTAAACCGCTATACCGATAA
66 AGGTAAACCGCTATACCGATAA
* * *
17524766 GTTATAGTTAAACTGCCAGATCATATAATAGTACGCAGCAAAGCTGACATACAAGTGGTACAGTG
1 GTTACAGTTAAACTGCCAGATCAGATAATAGTACACAGCAAAGCTGACATACAAGTGGTACAGTG
* * *
17524831 AGGTAAACCACTGTAACGATAA
66 AGGTAAACCGCTATACCGATAA
**
17524853 GTCGCAGTTAAACTGCCAGATCA
1 GTTACAGTTAAACTGCCAGATCA
17524876 AATCAGAATA
Statistics
Matches: 172, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
86 33 0.19
87 139 0.81
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (87 bp):
GTTACAGTTAAACTGCCAGATCAGATAATAGTACACAGCAAAGCTGACATACAAGTGGTACAGTG
AGGTAAACCGCTATACCGATAA
Found at i:17531421 original size:18 final size:19
Alignment explanation
Indices: 17531393--17531431 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
17531383 AGTGAAATTT
17531393 ATTTGAAAATCCCAGAAGG
1 ATTTGAAAATCCCAGAAGG
*
17531412 ATTT-AAAATCCCTGAAGG
1 ATTTGAAAATCCCAGAAGG
17531430 AT
1 AT
17531432 ATAGAGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
ATTTGAAAATCCCAGAAGG
Found at i:17532956 original size:22 final size:22
Alignment explanation
Indices: 17532931--17532973 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17532921 AACTTAATTC
*
17532931 ACATTTATTCATTGAATGTAAT
1 ACATTTATTAATTGAATGTAAT
17532953 ACATTTATTAATTGAATGTAA
1 ACATTTATTAATTGAATGTAA
17532974 ATGAGCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (22 bp):
ACATTTATTAATTGAATGTAAT
Found at i:17533832 original size:22 final size:22
Alignment explanation
Indices: 17533803--17533865 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
17533793 GCAACCATGA
17533803 AGCAGCCCCATACCTCCACTAC
1 AGCAGCCCCATACCTCCACTAC
* *
17533825 AGCGGCCCCATACCCCCACTAC
1 AGCAGCCCCATACCTCCACTAC
*
17533847 AGCAGTCCCATACCTCCAC
1 AGCAGCCCCATACCTCCAC
17533866 AGCCCTCGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.51, G:0.11, T:0.13
Consensus pattern (22 bp):
AGCAGCCCCATACCTCCACTAC
Found at i:17538423 original size:2 final size:2
Alignment explanation
Indices: 17538416--17538446 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17538406 TATGTTACTT
17538416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17538447 TTGATTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17539218 original size:23 final size:25
Alignment explanation
Indices: 17539173--17539218 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
17539163 AAATTAAAAT
**
17539173 ATATTTTTATATTATTTTTAATTTA
1 ATATTTTTATATTATTTAAAATTTA
17539198 ATATTTTTAT-TTA-TTAAAATT
1 ATATTTTTATATTATTTAAAATT
17539219 ATATATATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 3 0.16
25 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
ATATTTTTATATTATTTAAAATTTA
Found at i:17539224 original size:23 final size:25
Alignment explanation
Indices: 17539171--17539224 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
17539161 AAAAATTAAA
**
17539171 ATATATTTTTATATTATTTTTAATT
1 ATATATTTTTATATTATTTAAAATT
17539196 -TAATATTTTTAT-TTA-TTAAAATT
1 AT-ATATTTTTATATTATTTAAAATT
17539219 ATATAT
1 ATATAT
17539225 ATAGTCATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
ATATATTTTTATATTATTTAAAATT
Found at i:17540109 original size:92 final size:92
Alignment explanation
Indices: 17539952--17540135 Score: 341
Period size: 92 Copynumber: 2.0 Consensus size: 92
17539942 TTATATCTTC
* *
17539952 TTCTTTTTTACACAATACTTAGAACTACGTATAGTCTCTCCAATTCATAAGTAGGAGGATAATGC
1 TTCTTTTTTACACAATACTTAGAACTACGCATAGTCTCTCCAATTCATAAGTAGGAAGATAATGC
*
17540017 GCTTTAGCGCACTTGAACTTGCATTCT
66 GCTTTAGCGCACTTAAACTTGCATTCT
17540044 TTCTTTTTTACACAATACTTAGAACTACGCATAGTCTCTCCAATTCATAAGTAGGAAGATAATGC
1 TTCTTTTTTACACAATACTTAGAACTACGCATAGTCTCTCCAATTCATAAGTAGGAAGATAATGC
17540109 GCTTTAGCGCACTTAAACTTGCATTCT
66 GCTTTAGCGCACTTAAACTTGCATTCT
17540136 CCTATATTAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (92 bp):
TTCTTTTTTACACAATACTTAGAACTACGCATAGTCTCTCCAATTCATAAGTAGGAAGATAATGC
GCTTTAGCGCACTTAAACTTGCATTCT
Found at i:17542985 original size:29 final size:30
Alignment explanation
Indices: 17542944--17543000 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
17542934 GTAATTTGTG
17542944 AAAATCAAAAC-AAATTAAAATTTCATGTCT
1 AAAATCAAAACAAAATTAAAATTT-ATGTCT
*
17542974 AAAATC-ACACAAAATTAAAATTTATGT
1 AAAATCAAAACAAAATTAAAATTTATGT
17543001 ATGACATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.30
Consensus pattern (30 bp):
AAAATCAAAACAAAATTAAAATTTATGTCT
Found at i:17546393 original size:31 final size:31
Alignment explanation
Indices: 17546353--17546414 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
17546343 GTTATAAATG
*
17546353 ATCATTAAATTATTCGAAAGTTTTCATTTAA
1 ATCACTAAATTATTCGAAAGTTTTCATTTAA
*
17546384 ATCACTAAATTATTCGAAAGTTTTTATTTAA
1 ATCACTAAATTATTCGAAAGTTTTCATTTAA
17546415 GTCATTGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (31 bp):
ATCACTAAATTATTCGAAAGTTTTCATTTAA
Found at i:17546812 original size:31 final size:31
Alignment explanation
Indices: 17546777--17546843 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
17546767 TTTAAAGTTG
* * **
17546777 AGTGATCGAAACGTAAATTTACTAATAATTT
1 AGTGATCAAAACATAAACATACTAATAATTT
* *
17546808 AGTGATTAAAACATAAACATACTAATAGTTT
1 AGTGATCAAAACATAAACATACTAATAATTT
17546839 AGTGA
1 AGTGA
17546844 CCTTGGATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (31 bp):
AGTGATCAAAACATAAACATACTAATAATTT
Found at i:17547880 original size:36 final size:36
Alignment explanation
Indices: 17547840--17547910 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
17547830 AACGCCATGT
17547840 TTTAATTATATTGCTACCAAGTGAGTATTTTTTTTA
1 TTTAATTATATTGCTACCAAGTGAGTATTTTTTTTA
17547876 TTTAATTATATTGCTACCAAGTGAGTATTTTTTTT
1 TTTAATTATATTGCTACCAAGTGAGTATTTTTTTT
17547911 TACTCCAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (36 bp):
TTTAATTATATTGCTACCAAGTGAGTATTTTTTTTA
Found at i:17549522 original size:96 final size:96
Alignment explanation
Indices: 17549346--17549597 Score: 294
Period size: 96 Copynumber: 2.6 Consensus size: 96
17549336 AAAAGCAGTA
* * * *
17549346 GAGTTCAGTTGGTTGTTCGGTAGGGATGCAGGAGAGTTCCCAGAATTGTTCACGGAACTAGTACT
1 GAGTTCAGTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAACTAGTACA
** **
17549411 GAACTGGGTTGGGCTGTTAAAACTGG-AAGAG
66 GAACTGACTCAGGCTGTTAAAACTGGCAA-AG
** *
17549442 GAGTTTGGTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAATTAG-A-A
1 GAGTTCAGTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAACTAGTACA
*
17549505 GAGATTGCACTCAGGCTGTTAAAACTGGCAAAG
66 GA-ACTG-ACTCAGGCTGTTAAAACTGGCAAAG
* * * * * *
17549538 GAGTTCAGTTCGCTGTTTGGTAGGGATGCAGGAGGATTCCCGGTATTGTTCACCGAACTA
1 GAGTTCAGTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAACTA
17549598 CTGGAACCAC
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
94 2 0.02
95 4 0.03
96 124 0.94
97 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (96 bp):
GAGTTCAGTTGGCTGTTCGGTAGGGATGCAGGAGGGTTCCCAGAATTGTTCACAGAACTAGTACA
GAACTGACTCAGGCTGTTAAAACTGGCAAAG
Found at i:17551555 original size:232 final size:233
Alignment explanation
Indices: 17551029--17551699 Score: 790
Period size: 232 Copynumber: 2.8 Consensus size: 233
17551019 TTATACAATG
* * * * * **
17551029 ACATCAAATATGCAGAAAGACGTTCAGTAACTTCAACACC-TCAAAAAATTATATTTCATTGTTC
1 ACATCAAATATCCAGAAAGACATTCAGTAACTTCAACACCTTC-ATAGATCATATCCCATTGTTC
* * *
17551093 AACTTCATTCACTTTCACAATCAAACAAATGAGAAAGATGTAAATTTTTTTTCCTATGTTGTTCC
65 --C-T--TT-ACTTTCACAATCAAATAAATG-GGAAGATGTAAA--TATTTTCCTATGTTGTTCC
*
17551158 GACTACTCGTTTTTCTTTTTAAGTAACCCTATCCAACACATTTTCAAAGGAGATATGATCCTCTA
121 GACTATTCGTTTTTC-TTTT-A-TAACCCTATCCAACACATTTTCAAAGGAGATATGATCCTCTA
* * * *
17551223 ACAAAGAGCACCCACCGGTAGATCATAAATAAACGAATAGCTTATTACCAG
183 ACAAAGAGCACCCACCGGTAGATCATAAATAAACAAAAAACTTATTACCAA
* * * * *
17551274 CCATTAAATATTCAGAAA-ATCATTCAATAACTTCAACACCTTAATAGATCATATCCCATTGTTC
1 ACATCAAATATCCAGAAAGA-CATTCAGTAACTTCAACACCTTCATAGATCATATCCCATTGTTC
* * * **
17551338 CTTTACTTTCACAACCAAATAAATGGGAAGATGTAACTATTTTCCTGTGTTGTTTTGACTATTCG
65 CTTTACTTTCACAATCAAATAAATGGGAAGATGTAAATATTTTCCTATGTTGTTCCGACTATTCG
* *
17551403 TTTTTCTTTT-TAACCCTATCCAACACATTTCCAAAGGAGATATGATCCTCTAACAAAGGGCACC
130 TTTTTCTTTTATAACCCTATCCAACACATTTTCAAAGGAGATATGATCCTCTAACAAAGAGCACC
* * *
17551467 TATCGGTAGATCATAAATAAATAAAAAACTTATTACCAA
195 CACCGGTAGATCATAAATAAACAAAAAACTTATTACCAA
* *
17551506 ACATCAAATATCCAGAAAGACATTCAGCAACTTCAACACCTTCATAGATCATATCCCATTGTTCA
1 ACATCAAATATCCAGAAAGACATTCAGTAACTTCAACACCTTCATAGATCATATCCCATTGTTCC
* *
17551571 TTAACTTTCACAATCAAATAAATGAGAAGATGTAAATATTTTTCCTATGTTGTTCCGACTATTCA
66 TTTACTTTCACAATCAAATAAATGGGAAGATGTAAATA-TTTTCCTATGTTGTTCCGACTATTC-
* * *
17551636 TTTTTTTTTCTTTTAAAGTACCCTTATACAACACATTTTCAAAGGAGATATGATCCTCTAACAA
129 ---GTTTTTCTTTTATA--ACCC-TATCCAACACATTTTCAAAGGAGATATGATCCTCTAACAA
17551700 CCTTCCAAAT
Statistics
Matches: 367, Mismatches: 47, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
232 174 0.47
233 23 0.06
235 4 0.01
236 29 0.08
237 10 0.03
238 11 0.03
239 19 0.05
240 6 0.02
241 38 0.10
242 1 0.00
243 1 0.00
244 1 0.00
245 49 0.13
246 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (233 bp):
ACATCAAATATCCAGAAAGACATTCAGTAACTTCAACACCTTCATAGATCATATCCCATTGTTCC
TTTACTTTCACAATCAAATAAATGGGAAGATGTAAATATTTTCCTATGTTGTTCCGACTATTCGT
TTTTCTTTTATAACCCTATCCAACACATTTTCAAAGGAGATATGATCCTCTAACAAAGAGCACCC
ACCGGTAGATCATAAATAAACAAAAAACTTATTACCAA
Found at i:17551845 original size:63 final size:58
Alignment explanation
Indices: 17551705--17551855 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 58
17551695 AACAACCTTC
* * * ** *
17551705 CAAATACACGAAAAGAACATAAATGCATCAGCCAAGAATCTATAGGCGAACTTAGACT
1 CAAATACGCGAAAAGAACATAAATGTATCAGCCAAGAACCTATAGGCGAACACACACT
* * **
17551763 CAAATACGCGAAGATAACATAAATGTATCAGCCATTTATACCTATAGGCGACACACACACGCT
1 CAAATACGCGAAAAGAACATAAATGTATCAGCCA-AGA-ACCTATAGGCGA-ACACACA--CT
*
17551826 CAAATACGCGAAAAGAACATAGATGTATCA
1 CAAATACGCGAAAAGAACATAAATGTATCA
17551856 ACTCCGTATA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 30 0.40
59 1 0.01
60 11 0.15
61 4 0.05
63 29 0.39
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (58 bp):
CAAATACGCGAAAAGAACATAAATGTATCAGCCAAGAACCTATAGGCGAACACACACT
Found at i:17551871 original size:63 final size:63
Alignment explanation
Indices: 17551705--17551885 Score: 167
Period size: 63 Copynumber: 3.0 Consensus size: 63
17551695 AACAACCTTC
* * * * * ** *
17551705 CAAATACACGAAAAGAACATAAATGCATCAGCCAAG-A-ATCTATAGGCGA-ACTTAGA--CT
1 CAAATACGCGAAAAGAACATAAATGTATCAACCACGTATACCTATAGGCGACACACACACGCT
* * * **
17551763 CAAATACGCGAAGATAACATAAATGTATCAGCCATTTATACCTATAGGCGACACACACACGCT
1 CAAATACGCGAAAAGAACATAAATGTATCAACCACGTATACCTATAGGCGACACACACACGCT
* * *
17551826 CAAATACGCGAAAAGAACATAGATGTATCAACTC-CGTATATCTATAGGCGACACTCACAC
1 CAAATACGCGAAAAGAACATAAATGTATCAAC-CACGTATACCTATAGGCGACACACACAC
17551886 TCAAATCCGA
Statistics
Matches: 99, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
58 30 0.30
59 1 0.01
60 11 0.11
61 4 0.04
63 52 0.53
64 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (63 bp):
CAAATACGCGAAAAGAACATAAATGTATCAACCACGTATACCTATAGGCGACACACACACGCT
Found at i:17557740 original size:15 final size:15
Alignment explanation
Indices: 17557708--17557737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17557698 CACGTGTCTC
17557708 TATTTTTTATATATT
1 TATTTTTTATATATT
17557723 TATTTTTTA-ATATT
1 TATTTTTTATATATT
17557737 T
1 T
17557738 TATATATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTTATATATT
Found at i:17559618 original size:13 final size:15
Alignment explanation
Indices: 17559585--17559620 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
17559575 TATACCTTAC
17559585 ATATAATTTATTTAAT
1 ATATAATTTATTT-AT
*
17559601 ATATAATTTTTTTAT
1 ATATAATTTATTTAT
17559616 ATATA
1 ATATA
17559621 CGCATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATAATTTATTTAT
Found at i:17559619 original size:15 final size:16
Alignment explanation
Indices: 17559585--17559620 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
17559575 TATACCTTAC
17559585 ATATAATTTATTTAAT
1 ATATAATTTATTTAAT
*
17559601 ATATAATTT-TTTTAT
1 ATATAATTTATTTAAT
17559616 ATATA
1 ATATA
17559621 CGCATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATAATTTATTTAAT
Found at i:17560154 original size:108 final size:107
Alignment explanation
Indices: 17559945--17560484 Score: 764
Period size: 108 Copynumber: 5.0 Consensus size: 107
17559935 AAAAAAAAGG
* *
17559945 AAAATATTTCAAAAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTATT
1 AAAAT-TTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
*
17560010 GGGTTTCTATTTCTCGTTCGACCAAATGACTC-AATATCCTTTTCA
64 GGGTTTCGATTTCTCGTTCGACCAAATG-C-CAAATATCCTTTTCA
17560055 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
17560120 GTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-A
66 GTTTCGATTTCTCGTTCGACCAAAT-GCCAAATATCCTTTTCA
* *
17560162 AAAACTTTTTAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
1 AAAA--TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
*
17560227 GGGTTTCGATTTCTCGTTCCACCAAATGACTC-AATATCCTTTTCA
64 GGGTTTCGATTTCTCGTTCGACCAAATG-C-CAAATATCCTTTTCA
* *
17560272 AAACTTTTCAAAATAAGGAAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
1 AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
* *
17560337 GTTTCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAA
66 GTTTCGATTTCTCGTTCGACCAAAT-GCCAAATATCCTTTTCA
* * * * *
17560380 AAAACTTTTCAAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCT
1 AAAA-TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT
* * *
17560445 GGGTTTCGATTTCACGTT-TAGCCAAATTGCTAAATATCCT
64 GGGTTTCGATTTCTCGTTCGA-CCAAA-TGCCAAATATCCT
17560485 CTTGAATTTT
Statistics
Matches: 395, Mismatches: 22, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
107 6 0.02
108 189 0.48
109 107 0.27
110 92 0.23
111 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (107 bp):
AAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGG
GTTTCGATTTCTCGTTCGACCAAATGCCAAATATCCTTTTCA
Found at i:17560330 original size:217 final size:218
Alignment explanation
Indices: 17559951--17560462 Score: 891
Period size: 217 Copynumber: 2.4 Consensus size: 218
17559941 AAGGAAAATA
* * *
17559951 TTTCAAAAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTATTGGGTTT
1 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* * *
17560016 CTATTTCTCGTTCGACCAAATGACTCAATATCCTTTTCAAAAATTTTCAAAATAAGGCAATATTT
66 CGATTTCTCGTTCCACCAAATGACTCAATATCCTTTTCAAAAATTTTCAAAATAAGGAAATATTT
17560081 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATA
131 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATA
17560146 GCCAAATATCCTTTT-AAAAACT
196 GCCAAATATCCTTTTAAAAAACT
*
17560168 TTTTAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
17560233 CGATTTCTCGTTCCACCAAATGACTCAATATCCTTTTCAAAACTTTTCAAAATAAGGAAATATTT
66 CGATTTCTCGTTCCACCAAATGACTCAATATCCTTTTCAAAAATTTTCAAAATAAGGAAATATTT
17560298 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATA
131 TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATA
*
17560363 GCTAAATATCCTTTTAAAAAACT
196 GCCAAATATCCTTTTAAAAAACT
* * * *
17560386 TTTCAAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAACATGCCCTAAGGTGCTGGGTTT
1 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
*
17560451 CGATTTCACGTT
66 CGATTTCTCGTT
17560463 TAGCCAAATT
Statistics
Matches: 279, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
217 201 0.72
218 78 0.28
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (218 bp):
TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
CGATTTCTCGTTCCACCAAATGACTCAATATCCTTTTCAAAAATTTTCAAAATAAGGAAATATTT
TGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCGACCAAATA
GCCAAATATCCTTTTAAAAAACT
Found at i:17572262 original size:44 final size:44
Alignment explanation
Indices: 17572165--17572263 Score: 103
Period size: 44 Copynumber: 2.2 Consensus size: 44
17572155 AAGAATTTCA
* **
17572165 GATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 GATCTTATCTCCCGGAGATTACAGCGGAGCAGATTGAAAATAGT
* * * *
17572209 AATCCTATCTCCCGGAGATTACAGTGGAGCGGATT-AAAATAAAG-
1 GATCTTATCTCCCGGAGATTACAGCGGAGCAGATTGAAAAT--AGT
17572253 GATCTTATCTC
1 GATCTTATCTC
17572264 TCTGAAGTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
43 3 0.07
44 39 0.89
45 2 0.05
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
GATCTTATCTCCCGGAGATTACAGCGGAGCAGATTGAAAATAGT
Found at i:17574908 original size:110 final size:108
Alignment explanation
Indices: 17574534--17574958 Score: 658
Period size: 108 Copynumber: 3.9 Consensus size: 108
17574524 AAGGAAAATA
* *
17574534 TTTCAAAATAAGGCAATATGTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTATTGGGTTTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
*
17574599 GATTTCTCGTTCGACCAAAT-GACTCAATATCCTTTTCAAAAA-T
66 GATTTCTCGTTCGACCAAATAG-CTAAATATCCTTTT-AAAAACT
* *
17574642 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCTTAAGGTATTGGGTTTC
1 TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
*
17574707 GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAACT
66 GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
*
17574750 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
1 TTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
17574815 CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAAACT
65 CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTT-AAAAACT
* * *
17574860 TTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAACGTGCCCTAAGGTGCTGGGTTT
1 TTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* * *
17574925 CGATTTCACGTT-TAGCCAAATTGCTAAATATCCT
65 CGATTTCTCGTTCGA-CCAAATAGCTAAATATCCT
17574959 CTTGAATTTT
Statistics
Matches: 299, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
107 5 0.02
108 100 0.33
109 95 0.32
110 99 0.33
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTC
GATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACT
Found at i:17575617 original size:89 final size:90
Alignment explanation
Indices: 17575447--17575619 Score: 278
Period size: 90 Copynumber: 1.9 Consensus size: 90
17575437 AATTAAGTCT
* * *
17575447 TTTTTTTCCACTCATTTGGGTACTTGAACTTTCAAAATGCATCAAAAAAGCTCTCAAACCTTTTT
1 TTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAAACTTTTT
17575512 CAAAAAAAGCAATTAAGCCCCTACC
66 CAAAAAAAGCAATTAAGCCCCTACC
*
17575537 TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAATA-CCCT-AAAACTTTT
1 TTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAA-AGCCCTCAAAACTTTT
*
17575600 TCAAGAAAAGCAATTAAGCC
65 TCAAAAAAAGCAATTAAGCC
17575620 TATGCTTTTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
89 27 0.35
90 49 0.64
91 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (90 bp):
TTTTTTTCCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAAGCCCTCAAAACTTTTT
CAAAAAAAGCAATTAAGCCCCTACC
Found at i:17575749 original size:19 final size:19
Alignment explanation
Indices: 17575727--17575777 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
17575717 TAATAATTAG
17575727 AAAAAATATAAAAATCGTA
1 AAAAAATATAAAAATCGTA
* * *
17575746 AAAATATAAAAAAATTGTA
1 AAAAAATATAAAAATCGTA
*
17575765 AAAAATTATAAAA
1 AAAAAATATAAAA
17575778 TATATAGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAAATATAAAAATCGTA
Found at i:17575758 original size:47 final size:46
Alignment explanation
Indices: 17575700--17575813 Score: 111
Period size: 47 Copynumber: 2.4 Consensus size: 46
17575690 ATAAAAATTC
* * * *
17575700 AAATATTAAAAATTTATTAATAATTAGAAAAAATATAAAAATCGTAA
1 AAATATAAAAAATTTATAAAAAATTAGAAAAAATATAAAAAT-ATAA
* * * * *
17575747 AAATATAAAAAAATTGTAAAAAATTATAAAATATATAGAAATATAA
1 AAATATAAAAAATTTATAAAAAATTAGAAAAAATATAAAAATATAA
* *
17575793 AAAAATATAAAATTTTATAAA
1 AAATATA-AAAAATTTATAAA
17575814 TTATACAAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
46 9 0.17
47 44 0.83
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (46 bp):
AAATATAAAAAATTTATAAAAAATTAGAAAAAATATAAAAATATAA
Found at i:17575771 original size:10 final size:10
Alignment explanation
Indices: 17575706--17575804 Score: 50
Period size: 10 Copynumber: 10.5 Consensus size: 10
17575696 ATTCAAATAT
*
17575706 TAAAAATTTA
1 TAAAAAATTA
* *
17575716 TTAATAATTA
1 TAAAAAATTA
*
17575726 GAAAAAA-TA
1 TAAAAAATTA
**
17575735 T-AAAAATCG
1 TAAAAAATTA
17575744 T-AAAAA-TA
1 TAAAAAATTA
*
17575752 TAAAAAAATTG
1 T-AAAAAATTA
17575763 TAAAAAATTA
1 TAAAAAATTA
*
17575773 TAAAATA-TA
1 TAAAAAATTA
*
17575782 T-AGAAA-TA
1 TAAAAAATTA
*
17575790 TAAAAAAATA
1 TAAAAAATTA
17575800 TAAAA
1 TAAAA
17575805 TTTTATAAAT
Statistics
Matches: 66, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
8 12 0.18
9 15 0.23
10 37 0.56
11 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:17575777 original size:28 final size:27
Alignment explanation
Indices: 17575727--17575805 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
17575717 TAATAATTAG
**
17575727 AAAAAATATAAAAATCGTA-AAAATATA
1 AAAAAATATAAAAA-AATATAAAATATA
* *
17575754 AAAAAATTGTAAAAAATTATAAAATATA
1 AAAAAA-TATAAAAAAATATAAAATATA
* *
17575782 TAGAAATATAAAAAAATATAAAAT
1 AAAAAATATAAAAAAATATAAAAT
17575806 TTTATAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAAAATATAAAAAAATATAAAATATA
Found at i:17575818 original size:27 final size:26
Alignment explanation
Indices: 17575757--17575841 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
17575747 AAATATAAAA
* *
17575757 AAATTGTAAAAAATTATAAAATATAT
1 AAATTATAAAAAAATATAAAATATAT
* *
17575783 AGAAATATAAAAAAATATAAAATTTTAT
1 A-AATTATAAAAAAATATAAAA-TATAT
* * *
17575811 AAATTAT-ACAAAATGTAAAGAAATAT
1 AAATTATAAAAAAATATAAA-ATATAT
17575837 AAATT
1 AAATT
17575842 TTGTAAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
26 19 0.40
27 23 0.49
28 5 0.11
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (26 bp):
AAATTATAAAAAAATATAAAATATAT
Done.