Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 87 of 133
Found at i:17241123 original size:10 final size:10
Alignment explanation
Indices: 17241108--17241150 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
17241098 GTTGGAGCAT
17241108 ATTATTTATA
1 ATTATTTATA
17241118 ATTATTTATA
1 ATTATTTATA
*
17241128 A-TATAATATA
1 ATTAT-TTATA
*
17241138 ATTAATTATA
1 ATTATTTATA
17241148 ATT
1 ATT
17241151 TAATATTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
9 3 0.11
10 23 0.82
11 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTATTTATA
Found at i:17241139 original size:20 final size:20
Alignment explanation
Indices: 17241114--17241156 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17241104 GCATATTATT
*
17241114 TATAATTATTTATAATATAA
1 TATAATTAATTATAATATAA
*
17241134 TATAATTAATTATAATTTAA
1 TATAATTAATTATAATATAA
17241154 TAT
1 TAT
17241157 TATATAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATAATTAATTATAATATAA
Found at i:17241829 original size:2 final size:2
Alignment explanation
Indices: 17241822--17241873 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
17241812 GTAAGTAAAG
* * *
17241822 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT GT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17241864 AT AT AT AT AT
1 AT AT AT AT AT
17241874 GCTAATTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17242207 original size:13 final size:13
Alignment explanation
Indices: 17242149--17242222 Score: 50
Period size: 13 Copynumber: 6.0 Consensus size: 13
17242139 TATATTTTAT
*
17242149 TATTTATTTAAT-
1 TATTAATTTAATA
17242161 T-TTATATTT-ATA
1 TATTA-ATTTAATA
**
17242173 TATTAATAAAAT-
1 TATTAATTTAATA
17242185 TATT-ATTTAATA
1 TATTAATTTAATA
* * *
17242197 TTTTCATTTAAAA
1 TATTAATTTAATA
17242210 TATTAATTTAATA
1 TATTAATTTAATA
17242223 AAAATATTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
11 9 0.20
12 15 0.33
13 22 0.48
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTAATTTAATA
Found at i:17263880 original size:17 final size:16
Alignment explanation
Indices: 17263840--17263905 Score: 53
Period size: 17 Copynumber: 4.0 Consensus size: 16
17263830 CTTAAAACTT
* *
17263840 AATAGATAGTTACTAA
1 AATAGAAAGTTTCTAA
*
17263856 ATAAAGAAAGTTTCTAA
1 A-ATAGAAAGTTTCTAA
17263873 AATTAGAAAGTTAT-TAA
1 AA-TAGAAAGTT-TCTAA
* *
17263890 AATAAAAAATTTCTAA
1 AATAGAAAGTTTCTAA
17263906 TTCCTAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 1 0.03
16 12 0.30
17 26 0.65
18 1 0.03
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (16 bp):
AATAGAAAGTTTCTAA
Found at i:17266881 original size:18 final size:17
Alignment explanation
Indices: 17266858--17266910 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
17266848 ATTATTCTTA
17266858 TGATATTTGAATAACACG
1 TGATA-TTGAATAACACG
* *
17266876 TGATATT-CATAACATG
1 TGATATTGAATAACACG
*
17266892 TGATACTTGAATAATACG
1 TGATA-TTGAATAACACG
17266910 T
1 T
17266911 TTGTATCGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 12 0.43
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (17 bp):
TGATATTGAATAACACG
Found at i:17266960 original size:21 final size:21
Alignment explanation
Indices: 17266935--17266978 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
17266925 GATCACACAA
*
17266935 TTTTTGCTAATTTTTTTTCCT
1 TTTTTGCTAATTTTTTTACCT
* **
17266956 TTTTTTCTTCTTTTTTTACCT
1 TTTTTGCTAATTTTTTTACCT
17266977 TT
1 TT
17266979 CTTTTTACAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTGCTAATTTTTTTACCT
Found at i:17269961 original size:7 final size:7
Alignment explanation
Indices: 17269949--17270051 Score: 68
Period size: 7 Copynumber: 14.4 Consensus size: 7
17269939 TGCATAATTA
17269949 GTTTAGG
1 GTTTAGG
17269956 GTTTAGGG
1 GTTTA-GG
17269964 GTTTAGATTG
1 GTTTAG---G
*
17269974 CGTTTAAG
1 -GTTTAGG
*
17269982 G-TTAGA
1 GTTTAGG
*
17269988 G-TTATG
1 GTTTAGG
17269994 GTTTAGG
1 GTTTAGG
17270001 GTTTAGG
1 GTTTAGG
17270008 G-TTAGG
1 GTTTAGG
*
17270014 GTCTAGG
1 GTTTAGG
*
17270021 GTTGAGG
1 GTTTAGG
*
17270028 GTTTTGG
1 GTTTAGG
* *
17270035 ATTTAAG
1 GTTTAGG
17270042 GTTTAGG
1 GTTTAGG
17270049 GTT
1 GTT
17270052 AATGATTAGG
Statistics
Matches: 73, Mismatches: 16, Indels: 14
0.71 0.16 0.14
Matches are distributed among these distances:
6 14 0.19
7 45 0.62
8 8 0.11
10 1 0.01
11 5 0.07
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:17270011 original size:20 final size:20
Alignment explanation
Indices: 17269983--17270096 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
17269973 GCGTTTAAGG
*
17269983 TTAGAGTTATGGTTTAGGGT
1 TTAGGGTTATGGTTTAGGGT
* *
17270003 TTAGGGTTAGGGTCTAGGGT
1 TTAGGGTTATGGTTTAGGGT
* * *
17270023 TGAGGGTTTTGGATTTAAGGT
1 TTAGGGTTATGG-TTTAGGGT
*
17270044 TTAGGGTTAAT-GATTAGGGTT
1 TTAGGGTT-ATGGTTTAGGG-T
* **
17270065 TTA-AGTTACAGTTTAGGGT
1 TTAGGGTTATGGTTTAGGGT
17270084 TTA-GGTT-TGGTTT
1 TTAGGGTTATGGTTT
17270097 TTAGATTTGG
Statistics
Matches: 72, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
18 4 0.06
19 8 0.11
20 41 0.57
21 18 0.25
22 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (20 bp):
TTAGGGTTATGGTTTAGGGT
Found at i:17270123 original size:16 final size:16
Alignment explanation
Indices: 17270102--17270134 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17270092 GGTTTTTAGA
17270102 TTTGGGAATTAGGGTT
1 TTTGGGAATTAGGGTT
*
17270118 TTTGGGAATTGGGGTT
1 TTTGGGAATTAGGGTT
17270134 T
1 T
17270135 AGGGTTTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.45
Consensus pattern (16 bp):
TTTGGGAATTAGGGTT
Found at i:17276755 original size:8 final size:8
Alignment explanation
Indices: 17276742--17276780 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
17276732 TATTATTATC
17276742 ATATATAA
1 ATATATAA
17276750 ATATATAA
1 ATATATAA
*
17276758 A-ATAT-C
1 ATATATAA
17276764 ATATATAA
1 ATATATAA
17276772 ATATATAA
1 ATATATAA
17276780 A
1 A
17276781 AATTATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 1 0.04
7 8 0.30
8 18 0.67
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAA
Found at i:17276766 original size:22 final size:22
Alignment explanation
Indices: 17276738--17276781 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17276728 ATTTTATTAT
17276738 TATCATATATAAATATATAAAA
1 TATCATATATAAATATATAAAA
17276760 TATCATATATAAATATATAAAA
1 TATCATATATAAATATATAAAA
17276782 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
TATCATATATAAATATATAAAA
Found at i:17276818 original size:16 final size:16
Alignment explanation
Indices: 17276797--17276828 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17276787 TATTATTATT
17276797 ATATATAAAAATAAAA
1 ATATATAAAAATAAAA
*
17276813 ATATATATAAATAAAA
1 ATATATAAAAATAAAA
17276829 GAAAAGTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATATATAAAAATAAAA
Found at i:17278412 original size:21 final size:21
Alignment explanation
Indices: 17278388--17278429 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17278378 ATCTGTTGGG
17278388 GCTGTAGGATTCCTTGTAGAT
1 GCTGTAGGATTCCTTGTAGAT
17278409 GCTGTAGGATTCCTTGTAGAT
1 GCTGTAGGATTCCTTGTAGAT
17278430 CATGTCACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.29, T:0.38
Consensus pattern (21 bp):
GCTGTAGGATTCCTTGTAGAT
Found at i:17282781 original size:25 final size:25
Alignment explanation
Indices: 17282747--17282797 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17282737 AACGCATGTC
17282747 TTCATTCATGCATCATATATTGCAA
1 TTCATTCATGCATCATATATTGCAA
17282772 TTCATTCATGCATCATATATTGCAA
1 TTCATTCATGCATCATATATTGCAA
17282797 T
1 T
17282798 GTATCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (25 bp):
TTCATTCATGCATCATATATTGCAA
Found at i:17285539 original size:144 final size:141
Alignment explanation
Indices: 17285170--17285576 Score: 394
Period size: 144 Copynumber: 2.8 Consensus size: 141
17285160 GGAAAGTACA
* * * * *
17285170 AAATTACTGAAATGCCCTTTAAGGGGTATTTTCATAATTTGACCTTTATGAGCCCGAATTTTCAT
1 AAATTAC-GAAATACCCTTTAA-GGGTATTTTCATAATTTGACCTTTTTGAGCCTGGATTTTTAT
** * *
17285235 GAAACTTTTTAGATCTTGA-TTCATAATATTTCATGATTTTT-AGTGCATTTGAAATCACATCCA
64 GAAA-TTTTTAGATCTCAATTTCATAATATTTCATAATTTTTGA-TGCATTTAAAATCACAT-CA
*
17285298 TATCCCTAAAAATTTT
126 TATCCCTAAAAATTTG
* * * * * * *
17285314 AAATTACCAGAATACCC-TTAAGGGTATTTTCATAATTTGGCCATTTTGATCGTAGATTTTTGTG
1 AAATTACGA-AATACCCTTTAAGGGTATTTTCATAATTTGACCTTTTTGAGCCTGGATTTTTATG
** * * * *
17285378 AAACTTTCCAAATCTCAATTTCATAATATTTTATAATTTTTGATGCATTTAAAATCGCGGT-AGT
65 AAA-TTTTTAGATCTCAATTTCATAATATTTCATAATTTTTGATGCATTTAAAATCAC-ATCA-T
17285442 A-CCCTAAAAATTATG
127 ATCCCTAAAAATT-TG
* * * *
17285457 AAATTATCGAAATACCCTTTAAGAGTATTTTCGTAATTTGATCTTTTTGAGCTTGGATTTTTATG
1 AAATTA-CGAAATACCCTTTAAGGGTATTTTCATAATTTGACCTTTTTGAGCCTGGATTTTTATG
* * *
17285522 AAATTTTATAGATCTCAATTTTATAATATTTCATAATTTTTGGTG-TTTTAAAATC
65 AAATTTT-TAGATCTCAATTTCATAATATTTCATAATTTTTGATGCATTTAAAATC
17285577 TCATAAATGA
Statistics
Matches: 214, Mismatches: 40, Indels: 19
0.78 0.15 0.07
Matches are distributed among these distances:
142 58 0.27
143 66 0.31
144 90 0.42
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.43
Consensus pattern (141 bp):
AAATTACGAAATACCCTTTAAGGGTATTTTCATAATTTGACCTTTTTGAGCCTGGATTTTTATGA
AATTTTTAGATCTCAATTTCATAATATTTCATAATTTTTGATGCATTTAAAATCACATCATATCC
CTAAAAATTTG
Found at i:17287789 original size:3 final size:3
Alignment explanation
Indices: 17287781--17287853 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
17287771 ACAAGTGTAA
17287781 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
17287829 AAT AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
17287854 GGATGGGATT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17293410 original size:21 final size:21
Alignment explanation
Indices: 17293386--17293426 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17293376 AGACGTAGAT
17293386 TGGTTTTGAAAAATGGCATTC
1 TGGTTTTGAAAAATGGCATTC
* *
17293407 TGGTTTTGGAACATGGCATT
1 TGGTTTTGAAAAATGGCATT
17293427 TTAGGTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (21 bp):
TGGTTTTGAAAAATGGCATTC
Found at i:17304841 original size:10 final size:10
Alignment explanation
Indices: 17304826--17304861 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
17304816 TTTTATCCGT
17304826 TTTGACCAAA
1 TTTGACCAAA
*
17304836 TTTGACCAAT
1 TTTGACCAAA
*
17304846 TTTGATCAAA
1 TTTGACCAAA
17304856 TTTGAC
1 TTTGAC
17304862 TAAGTTTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (10 bp):
TTTGACCAAA
Found at i:17309627 original size:39 final size:39
Alignment explanation
Indices: 17309560--17309712 Score: 183
Period size: 39 Copynumber: 3.9 Consensus size: 39
17309550 TAGTGACGTG
17309560 CCTTC-ATTTTGAAGGAGCTTTAAATTTTAAAGTTGTAC
1 CCTTCAATTTTGAAGGAGCTTTAAATTTTAAAGTTGTAC
* *
17309598 CCCTCAATTTTGAAGGAGAC-TTAATTTTTAAAG-TG-AC
1 CCTTCAATTTTGAAGGAG-CTTTAAATTTTAAAGTTGTAC
17309635 ATACCTTC-ATTTTGAAGGAGCTTTAAATTTTAAAGTTGTAC
1 ---CCTTCAATTTTGAAGGAGCTTTAAATTTTAAAGTTGTAC
* *
17309676 CCTTCAGTTTTGAAGGAG-TCTTAATTTTTAAAGTTGT
1 CCTTCAATTTTGAAGGAGCT-TTAAATTTTAAAGTTGT
17309713 GTGCCTCTGT
Statistics
Matches: 99, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
37 2 0.02
38 13 0.13
39 75 0.76
40 7 0.07
41 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (39 bp):
CCTTCAATTTTGAAGGAGCTTTAAATTTTAAAGTTGTAC
Found at i:17309642 original size:78 final size:78
Alignment explanation
Indices: 17309520--17309709 Score: 281
Period size: 78 Copynumber: 2.4 Consensus size: 78
17309510 AAGCTATGCG
* * * * * * *
17309520 CCTCCATTTTGAAGAAGCCCTTAATTCTTATAGTGACGTGCCTTCATTTTGAAGGAGCTTTAAAT
1 CCTCAATTTTGAAGGAG-ACTTAATTTTTAAAGTGACATACCTTCATTTTGAAGGAGCTTTAAAT
17309585 TTTAAAGTTGTACC
65 TTTAAAGTTGTACC
17309599 CCTCAATTTTGAAGGAGACTTAATTTTTAAAGTGACATACCTTCATTTTGAAGGAGCTTTAAATT
1 CCTCAATTTTGAAGGAGACTTAATTTTTAAAGTGACATACCTTCATTTTGAAGGAGCTTTAAATT
17309664 TTAAAGTTGTACC
66 TTAAAGTTGTACC
* * *
17309677 CTTCAGTTTTGAAGGAGTCTTAATTTTTAAAGT
1 CCTCAATTTTGAAGGAGACTTAATTTTTAAAGT
17309710 TGTGTGCCTC
Statistics
Matches: 101, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 86 0.85
79 15 0.15
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (78 bp):
CCTCAATTTTGAAGGAGACTTAATTTTTAAAGTGACATACCTTCATTTTGAAGGAGCTTTAAATT
TTAAAGTTGTACC
Found at i:17311989 original size:17 final size:16
Alignment explanation
Indices: 17311967--17312001 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17311957 TAAATTGATG
17311967 AACTATAAGCAAATATA
1 AACTATAAGCAAA-ATA
*
17311984 AACTATAATCAAAATA
1 AACTATAAGCAAAATA
17312000 AA
1 AA
17312002 GAGATAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (16 bp):
AACTATAAGCAAAATA
Found at i:17318766 original size:17 final size:16
Alignment explanation
Indices: 17318744--17318778 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17318734 TAAATTGATG
17318744 AACTATAAGCAAATATA
1 AACTATAAGCAAA-ATA
*
17318761 AACTATAATCAAAATA
1 AACTATAAGCAAAATA
17318777 AA
1 AA
17318779 AAGATAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (16 bp):
AACTATAAGCAAAATA
Found at i:17319753 original size:131 final size:131
Alignment explanation
Indices: 17319519--17319780 Score: 515
Period size: 131 Copynumber: 2.0 Consensus size: 131
17319509 TTTGATAATT
*
17319519 TCTTGAGTTATACAAATCCAAATCAAAAATTGTTTAAAGATTTAGAAACTAGACTTAAAGGGCTT
1 TCTTGAGTTATACAAATCCAAATAAAAAATTGTTTAAAGATTTAGAAACTAGACTTAAAGGGCTT
17319584 TCTATCCATATAAAATTCATCTCCTAATTCATTGTATACTAATTATAGTGAATTTTCAAAACTAC
66 TCTATCCATATAAAATTCATCTCCTAATTCATTGTATACTAATTATAGTGAATTTTCAAAACTAC
17319649 C
131 C
17319650 TCTTGAGTTATACAAATCCAAATAAAAAATTGTTTAAAGATTTAGAAACTAGACTTAAAGGGCTT
1 TCTTGAGTTATACAAATCCAAATAAAAAATTGTTTAAAGATTTAGAAACTAGACTTAAAGGGCTT
17319715 TCTATCCATATAAAATTCATCTCCTAATTCATTGTATACTAATTATAGTGAATTTTCAAAACTAC
66 TCTATCCATATAAAATTCATCTCCTAATTCATTGTATACTAATTATAGTGAATTTTCAAAACTAC
17319780 C
131 C
17319781 CCTCGTGCAG
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
131 130 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (131 bp):
TCTTGAGTTATACAAATCCAAATAAAAAATTGTTTAAAGATTTAGAAACTAGACTTAAAGGGCTT
TCTATCCATATAAAATTCATCTCCTAATTCATTGTATACTAATTATAGTGAATTTTCAAAACTAC
C
Found at i:17323139 original size:16 final size:16
Alignment explanation
Indices: 17323118--17323151 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17323108 AGGATAATGA
17323118 AGCTTTGTTATTAGGT
1 AGCTTTGTTATTAGGT
17323134 AGCTTTGTTATTAGGT
1 AGCTTTGTTATTAGGT
17323150 AG
1 AG
17323152 ACCCTTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (16 bp):
AGCTTTGTTATTAGGT
Found at i:17327344 original size:117 final size:117
Alignment explanation
Indices: 17327130--17327350 Score: 354
Period size: 117 Copynumber: 1.9 Consensus size: 117
17327120 AAATAAATAT
17327130 TAGTAATATTTGAAATAAAAAATATTTTGGAAAAAGTTTTGAATTTTGAAAAAATTTATTTAGTA
1 TAGTAATATTTGAAATAAAAAATATTTTGGAAAAAGTTTTGAATTTTGAAAAAATTTATTTAGTA
* *
17327195 CATGACTCTTATAATATATTATTTTGGCACTAAATAATAAATCTAGTGATTC
66 CATAACTCTTATAATATATTATTTTGGCACTAAAAAATAAATCTAGTGATTC
* * *
17327247 TAGTGATATTTGAAATGAAAAATATTTTGG-AAAAGATTTTGGATTTTGAAAAAATTTATTTAGT
1 TAGTAATATTTGAAATAAAAAATATTTTGGAAAAAG-TTTTGAATTTTGAAAAAATTTATTTAGT
* * *
17327311 ACATAATTCTTATGATATATTATTTTGGTACTAAAAAATA
65 ACATAACTCTTATAATATATTATTTTGGCACTAAAAAATA
17327351 TTATGTCTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 5 0.05
117 90 0.95
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.42
Consensus pattern (117 bp):
TAGTAATATTTGAAATAAAAAATATTTTGGAAAAAGTTTTGAATTTTGAAAAAATTTATTTAGTA
CATAACTCTTATAATATATTATTTTGGCACTAAAAAATAAATCTAGTGATTC
Found at i:17328569 original size:188 final size:190
Alignment explanation
Indices: 17328280--17328648 Score: 519
Period size: 188 Copynumber: 1.9 Consensus size: 190
17328270 AAGCACCAAA
* * * *
17328280 AAGCCTTACCTTTTTTCTCTCAAAAATTCAAGAGCATTCTAAAGAATCAAACTTTAATTCTTCCC
1 AAGCCTTACCTTCTTTCTCTCAAAAATTCAAAAGCATTCTAAAAAATAAAACTTTAATTCTTCCC
* * * * *
17328345 ATTCTTGTATCCAAATTATATTTGTTCTTTATTTATCATTCTTTGTAC-A-TAGGCAAACATCCA
66 ATTCTTGTATCCAAATCATATTGGTTCTTCATTTATCATTCTTTGCACTATTAGGCAAACACCCA
** * * * *
17328408 ACCTTAGTGAGATTATTTAGTTTTCAAAAACACTTGTCTTTCATTTGAGTTTGCAAAAAC
131 ACAGTAATGAGATTATTTAGTTTGCAAAAACACTTGTCTCTAATTTGAGTTTGCAAAAAC
* *
17328468 AAGCCTTACCTTCTTTCTTTCAAAAATTCAAAAGCATTCTAAAAAATAAAACTTTAATTCTTCCT
1 AAGCCTTACCTTCTTTCTCTCAAAAATTCAAAAGCATTCTAAAAAATAAAACTTTAATTCTTCCC
17328533 ATTCTT-TCATCCAAATCATATTGGTTCTTCATTTATCATTCTTTGCACTTAATTAGGCAAACAC
66 ATTCTTGT-ATCCAAATCATATTGGTTCTTCATTTATCATTCTTTGCAC-T-ATTAGGCAAACAC
* *
17328597 CCAACAGTAATGAGGTTATTTAGTTTGCAAAAGCACTTGTCTCTAATTTGAG
128 CCAACAGTAATGAGATTATTTAGTTTGCAAAAACACTTGTCTCTAATTTGAG
17328649 ATTGTGGGTT
Statistics
Matches: 157, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
187 1 0.01
188 101 0.64
191 1 0.01
192 54 0.34
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (190 bp):
AAGCCTTACCTTCTTTCTCTCAAAAATTCAAAAGCATTCTAAAAAATAAAACTTTAATTCTTCCC
ATTCTTGTATCCAAATCATATTGGTTCTTCATTTATCATTCTTTGCACTATTAGGCAAACACCCA
ACAGTAATGAGATTATTTAGTTTGCAAAAACACTTGTCTCTAATTTGAGTTTGCAAAAAC
Found at i:17332869 original size:370 final size:371
Alignment explanation
Indices: 17332100--17333042 Score: 1295
Period size: 370 Copynumber: 2.5 Consensus size: 371
17332090 GTCATACTAG
* * * *
17332100 TGTCACAGACCTAATAAGGAGTCCTGAAT-CTCACATCGAACATAATAGGAGGGTCACTGGGGTA
1 TGTCACGGATCTAATAAGGAGTCTTGAATCCT-ACATCAAACATAATAGGAGGGTCACTGGGGTA
* * * * *
17332164 TAAAAAGGTTCACACCACCTCTTCCTTGTGAGGCACCTTTTGTAGGACAAAACCATGAGGCTAGG
65 TAAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAAG
* * * * *
17332229 GGGGTCAGAGCAGACAATATCTCACAAGGGTGTGAACCGTGGCAGGTAGGATGATCTGGGACGTC
130 GGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGTAGGCTGATCTGAGACGTC
* * ** * * *
17332294 GGATGAGTAGATGCCCGGGTCCTGGAGCTGCACGGGTTTGGAGCTTAAGTTTTGACCTGTGACAA
195 GGATGAGTGGATGCCCGGGTCCTAGAGCCACACGGGTTTGGAGCTTAAGTCTCGACCCGTGACAA
* * * *
17332359 GTGGTATCAATGCCAGCCCTAAATCGTTCGATCCACGCCAAGCACCTCGAAGGAGGTAGGCAAGG
260 GTGGTATCAAAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAAGAAGGTAAGCAAGG
** * *
17332424 TGGCCAGCCTCCGTGACGAGGGTGTCACGAGGTTGGGTGGGAGAGAA
325 TGGCCAGCCTCCGTGACGAGGACGTCACAAGGTTGGATGGGAGAGAA
* *
17332471 TGTCACGGATCTAATAAGGAGTCTTGAATCCTACATCAAATATAATAGAAGGGTCACTGGGGTAT
1 TGTCACGGATCTAATAAGGAGTCTTGAATCCTACATCAAACATAATAGGAGGGTCACTGGGGTAT
* *
17332536 AATAGGGTTCACACCACCTCTTCCTTGTGAGACGCCTTTTGTAGGACAAAACCGTGAGGCCAAGG
66 AAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAAGG
* * *
17332601 AGGCCAGAGCGGACAATACCTCACAAGGATGTGAACCGTGGCAGGTAGGCTGATCTGAGACGCCG
131 GGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGTAGGCTGATCTGAGACGTCG
* *
17332666 GATGAGTGGA-GCTCGGGTCCTAGAGCCACGCGGGTTTGGAGCTTAAGTCTCGACCCGTGACAAG
196 GATGAGTGGATGCCCGGGTCCTAGAGCCACACGGGTTTGGAGCTTAAGTCTCGACCCGTGACAAG
* * *
17332730 TGGTATCAAAGCCAGCCCTAAACCGTTCGATCCACGCCCAGCACCTTG-AGAAAGGTAAGCAGGG
261 TGGTATCAAAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAAG-AAGGTAAGCAAGG
* *
17332794 TGGTCAGCCTCCGTGACGAGGACGTCACAAGGTTGGATGGGGGAGAA
325 TGGCCAGCCTCCGTGACGAGGACGTCACAAGGTTGGATGGGAGAGAA
* * * * *
17332841 TGTCATGGA-CTTAATAAAGAGTCTTGAATCCTATATCAAACATAATAGGAGGGTCATTGGGATA
1 TGTCACGGATC-TAATAAGGAGTCTTGAATCCTACATCAAACATAATAGGAGGGTCACTGGGGTA
* * * *
17332905 TAAAAGGGTTCACACTACCACTTCCTTGTGAGGCGCCTTTTGTAGGATAAAATCGTGAGGCC-AG
65 TAAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAAG
* * * * *
17332969 GGGGCCAAAGCGGACAATACCTCACAAGGGTGTGAACCGTGACAAGTAGGCTAATCT-AGGATGT
130 GGGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGTAGGCTGATCTGA-GACGT
17333033 CGGATGAGTG
194 CGGATGAGTG
17333043 AATGTCTGAG
Statistics
Matches: 504, Mismatches: 64, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
368 1 0.00
369 69 0.14
370 252 0.50
371 180 0.36
372 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (371 bp):
TGTCACGGATCTAATAAGGAGTCTTGAATCCTACATCAAACATAATAGGAGGGTCACTGGGGTAT
AAAAGGGTTCACACCACCTCTTCCTTGTGAGGCGCCTTTTGTAGGACAAAACCGTGAGGCCAAGG
GGGCCAGAGCGGACAATACCTCACAAGGGTGTGAACCGTGGCAGGTAGGCTGATCTGAGACGTCG
GATGAGTGGATGCCCGGGTCCTAGAGCCACACGGGTTTGGAGCTTAAGTCTCGACCCGTGACAAG
TGGTATCAAAGCCAGCCCTAAACCGTTCGATCCACGCCAAGCACCTCGAAGAAGGTAAGCAAGGT
GGCCAGCCTCCGTGACGAGGACGTCACAAGGTTGGATGGGAGAGAA
Found at i:17335234 original size:18 final size:18
Alignment explanation
Indices: 17335211--17335246 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
17335201 CCTATTCTCA
17335211 ATTAAAAAT-TAAATAATT
1 ATTAAAAATATAAA-AATT
17335229 ATTAAAAATATAAAAATT
1 ATTAAAAATATAAAAATT
17335247 CAATTTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAAAAATATAAAAATT
Found at i:17336064 original size:21 final size:21
Alignment explanation
Indices: 17336040--17336088 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
17336030 CATCTTTATT
17336040 ATTTTTAT-TTATTTTAATTTG
1 ATTTTTATCTT-TTTTAATTTG
*
17336061 ATTTTTATCTTTTTTATTTTG
1 ATTTTTATCTTTTTTAATTTG
17336082 ATTTTTA
1 ATTTTTA
17336089 CCTCATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (21 bp):
ATTTTTATCTTTTTTAATTTG
Found at i:17336097 original size:32 final size:31
Alignment explanation
Indices: 17336061--17336149 Score: 126
Period size: 31 Copynumber: 2.8 Consensus size: 31
17336051 TTTTAATTTG
17336061 ATTTTTATCTTTTTTATTTTGATTTTTACCTC
1 ATTTTTAT-TTTTTTATTTTGATTTTTACCTC
* * *
17336093 ATTTTTATTTTATTATTTTAATTTTTATCTC
1 ATTTTTATTTTTTTATTTTGATTTTTACCTC
17336124 ATCTTTTA-TTTTTTATTTTGATTTTT
1 AT-TTTTATTTTTTTATTTTGATTTTT
17336150 TTGCTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
31 38 0.75
32 13 0.25
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (31 bp):
ATTTTTATTTTTTTATTTTGATTTTTACCTC
Found at i:17336100 original size:62 final size:62
Alignment explanation
Indices: 17336029--17336149 Score: 149
Period size: 62 Copynumber: 2.0 Consensus size: 62
17336019 CCCTTTGTTT
* * *
17336029 TCATCTTTATTATTTTTA-TTT-ATTTTAATTTGAT-TTTTATCTTTTTTATTTTGATTTTTACC
1 TCATCTTTATT-TTATTATTTTAATTTTAATCTCATCTTTTA--TTTTTTATTTTGATTTTTACC
* *
17336091 TCATTTTTATTTTATTATTTTAATTTTTATCTCATCTTTTATTTTTTATTTTGATTTTT
1 TCATCTTTATTTTATTATTTTAATTTTAATCTCATCTTTTATTTTTTATTTTGATTTTT
17336150 TTGCTTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 5 0.10
62 31 0.61
63 10 0.20
64 5 0.10
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.71
Consensus pattern (62 bp):
TCATCTTTATTTTATTATTTTAATTTTAATCTCATCTTTTATTTTTTATTTTGATTTTTACC
Found at i:17337637 original size:26 final size:25
Alignment explanation
Indices: 17337598--17337649 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
17337588 AAGAGTTTTC
*
17337598 TTCAATTTAGTGGATTAAAGCCTTGG
1 TTCAATTTAATGGATTAAA-CCTTGG
17337624 TTCAATTTAATGGATTAAACCTTGG
1 TTCAATTTAATGGATTAAACCTTGG
17337649 T
1 T
17337650 GTGGACAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (25 bp):
TTCAATTTAATGGATTAAACCTTGG
Found at i:17338507 original size:21 final size:20
Alignment explanation
Indices: 17338465--17338507 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
17338455 TGAATTTTTG
*
17338465 GAAAAAGAAAATTTTGATTT
1 GAAAAAGAAAATTTTGAGTT
17338485 GAAAAAG-AAATTTGATGAGTT
1 GAAAAAGAAAATTT--TGAGTT
17338506 GA
1 GA
17338508 TGAATGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
21 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.30
Consensus pattern (20 bp):
GAAAAAGAAAATTTTGAGTT
Found at i:17341331 original size:17 final size:18
Alignment explanation
Indices: 17341309--17341351 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
17341299 TGATGAGAAT
17341309 ATATTT-TTAACGCATGA
1 ATATTTGTTAACGCATGA
*
17341326 ATATTTGGTTAATGCATGA
1 ATATTT-GTTAACGCATGA
*
17341345 ATCTTTG
1 ATATTTG
17341352 AACATGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.44
Consensus pattern (18 bp):
ATATTTGTTAACGCATGA
Found at i:17341337 original size:19 final size:19
Alignment explanation
Indices: 17341315--17341351 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17341305 GAATATATTT
17341315 TTAACGCATGAATATTTGG
1 TTAACGCATGAATATTTGG
* *
17341334 TTAATGCATGAATCTTTG
1 TTAACGCATGAATATTTG
17341352 AACATGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (19 bp):
TTAACGCATGAATATTTGG
Found at i:17342682 original size:41 final size:44
Alignment explanation
Indices: 17342635--17342729 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 44
17342625 TGCTTGATAT
* *
17342635 ACATATGTT-C-T-TGTGTGTGCTTAATT-TTATTATATGCTTTG
1 ACATATGTTGCATATGTGTATGCTTAATTGTTA-TATATGCTTTA
* *
17342676 ACATATGTATGCATATGTTTATGCTTAATTGTTATATTTGCTTTA
1 ACATATGT-TGCATATGTGTATGCTTAATTGTTATATATGCTTTA
17342721 ACATATGTT
1 ACATATGTT
17342730 TGTTGAGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
41 8 0.18
42 1 0.02
43 1 0.02
44 2 0.04
45 30 0.67
46 3 0.07
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (44 bp):
ACATATGTTGCATATGTGTATGCTTAATTGTTATATATGCTTTA
Found at i:17343361 original size:21 final size:21
Alignment explanation
Indices: 17343335--17343374 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17343325 TTGAAGAATG
*
17343335 GATCGATTGGATATTCAACAA
1 GATCGATTGGATATACAACAA
*
17343356 GATCGATTGGGTATACAAC
1 GATCGATTGGATATACAAC
17343375 CAGAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GATCGATTGGATATACAACAA
Found at i:17344222 original size:23 final size:23
Alignment explanation
Indices: 17344192--17344240 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
17344182 TTTATTCGAT
17344192 TACCATCTACATCTAAAAGCTAA
1 TACCATCTACATCTAAAAGCTAA
*
17344215 TACCATCTATATCTAAAAGCTAA
1 TACCATCTACATCTAAAAGCTAA
17344238 TAC
1 TAC
17344241 ATCATACCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.24, G:0.04, T:0.29
Consensus pattern (23 bp):
TACCATCTACATCTAAAAGCTAA
Found at i:17348040 original size:102 final size:101
Alignment explanation
Indices: 17347872--17348055 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 101
17347862 TTATGACATG
*
17347872 TATTCCTACTTTTTGACAAGTCAACCTTTTTTACACAGTTGATATGGAGTCAATAAATGGTGAAA
1 TATTCCTACTTTTTAACAAGTCAACCTTTTTTACACAGTTGATATGGAGTCAATAAATGGTGAAA
17347937 TAGTGTTTCACCAAGGTTTAAACAGGCCCTGACACA
66 TAGTGTTTCACCAAGGTTTAAACAGGCCCTGACACA
*
17347973 TATTCCTACTTTTTAACGAGTCAACCTTTTTATACACA-TTCGATATGGAGTCAATAAATGGTGA
1 TATTCCTACTTTTTAACAAGTCAACCTTTTT-TACACAGTT-GATATGGAGTCAATAAATGGTGA
*
17348037 AATAGTGTTTCACGAAGGT
64 AATAGTGTTTCACCAAGGT
17348056 CAATTGATAG
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
101 31 0.40
102 47 0.60
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (101 bp):
TATTCCTACTTTTTAACAAGTCAACCTTTTTTACACAGTTGATATGGAGTCAATAAATGGTGAAA
TAGTGTTTCACCAAGGTTTAAACAGGCCCTGACACA
Found at i:17351537 original size:20 final size:20
Alignment explanation
Indices: 17351503--17351542 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17351493 TGATTTTGGG
* * *
17351503 TTATTTTAGATTCAATTTAT
1 TTATTTTAAAATCAAATTAT
17351523 TTATTTTAAAATCAAATTAT
1 TTATTTTAAAATCAAATTAT
17351543 ACAAAATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTTTAAAATCAAATTAT
Found at i:17357336 original size:39 final size:40
Alignment explanation
Indices: 17357269--17357358 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 40
17357259 TGTGGACTTT
* * * * *
17357269 GAGCATGGAGGATCTGGTCGGATGTTTTGGACTTG-AAAC
1 GAGCTTGGAGAATCTAGTCGGATATTTTGGACATGAAAAC
* *
17357308 GAGCTTGGAGAATCTAGTTGGATATTTTGGACATGAAAAG
1 GAGCTTGGAGAATCTAGTCGGATATTTTGGACATGAAAAC
17357348 GAG-TTGGAGAA
1 GAGCTTGGAGAA
17357359 GTGTTTGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 37 0.86
40 6 0.14
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.28
Consensus pattern (40 bp):
GAGCTTGGAGAATCTAGTCGGATATTTTGGACATGAAAAC
Found at i:17364096 original size:10 final size:9
Alignment explanation
Indices: 17364068--17364100 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
17364058 CCAATATATA
17364068 AAATTAATT
1 AAATTAATT
17364077 -AATTAATT
1 AAATTAATT
17364085 AAATTAAATT
1 AAATT-AATT
17364095 AAATTA
1 AAATTA
17364101 GTGTTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTAATT
Found at i:17365217 original size:25 final size:25
Alignment explanation
Indices: 17365161--17365211 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
17365151 AGTTTGGAGG
*
17365161 TGATGTGAACTTGTAATGGTGATGA
1 TGATGTGAACTTGTAATGGTAATGA
17365186 TGATGTGAACTTGTAATGGTAATGA
1 TGATGTGAACTTGTAATGGTAATGA
17365211 T
1 T
17365212 AGTGTGGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.37
Consensus pattern (25 bp):
TGATGTGAACTTGTAATGGTAATGA
Found at i:17367723 original size:18 final size:19
Alignment explanation
Indices: 17367683--17367725 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
17367673 AAAATTCAAA
*
17367683 AAAAATCTAAAATATTTTT
1 AAAAATCTAAAATATTTTG
17367702 AAAAATCTAAAATA-TTTG
1 AAAAATCTAAAATATTTTG
17367720 AAAAAT
1 AAAAAT
17367726 ATATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAAATCTAAAATATTTTG
Found at i:17367818 original size:19 final size:19
Alignment explanation
Indices: 17367796--17367836 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17367786 AAATTTTAAT
17367796 AAAAAATCCAAAAAATTCA
1 AAAAAATCCAAAAAATTCA
** *
17367815 AAAAAATTTAAAAAATTTA
1 AAAAAATCCAAAAAATTCA
17367834 AAA
1 AAA
17367837 TTTTAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAAATCCAAAAAATTCA
Found at i:17367935 original size:21 final size:21
Alignment explanation
Indices: 17367867--17367935 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
17367857 TCTTAAAATT
**
17367867 AAAAAAAT-TAAAAAATTGAAA
1 AAAAAAATCT-AAAAATTTTAA
** **
17367888 ATAATAAAATCTAAACTTTTTTG
1 A-AA-AAAATCTAAAAATTTTAA
17367911 AAAAAAATCTAAAAATTTTAA
1 AAAAAAATCTAAAAATTTTAA
17367932 AAAA
1 AAAA
17367936 TTATAATTTT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
21 19 0.54
22 4 0.11
23 11 0.31
24 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (21 bp):
AAAAAAATCTAAAAATTTTAA
Found at i:17367953 original size:20 final size:21
Alignment explanation
Indices: 17367926--17367970 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
17367916 AATCTAAAAA
*
17367926 TTTTAAAAAA-T-TATAATTT
1 TTTTAAAAAACTGTAAAATTT
17367945 TTTTAAAAAAACTGTAAAATTT
1 TTTT-AAAAAACTGTAAAATTT
17367967 TTTT
1 TTTT
17367971 TTAATTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 6 0.27
21 1 0.05
22 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTAAAAAACTGTAAAATTT
Found at i:17368035 original size:20 final size:20
Alignment explanation
Indices: 17368012--17368068 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
17368002 ATGTTACAAT
*
17368012 TTTTTTATATATTTTATGAA
1 TTTTTTAGATATTTTATGAA
* *
17368032 TTTTTTAGATTTTTTTTGAA
1 TTTTTTAGATATTTTATGAA
* *
17368052 TTTTTAAGATTTTTTAT
1 TTTTTTAGATATTTTAT
17368069 TGAAATTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (20 bp):
TTTTTTAGATATTTTATGAA
Found at i:17368065 original size:21 final size:20
Alignment explanation
Indices: 17368023--17368096 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
17368013 TTTTTATATA
* *
17368023 TTTTATGAATTTTTTAGATT
1 TTTTTTGAATTTTTAAGATT
17368043 TTTTTTGAATTTTTAAGATT
1 TTTTTTGAATTTTTAAGATT
*
17368063 TTTTATTGAAATTTTAAG--T
1 TTTT-TTGAATTTTTAAGATT
*
17368082 TCTTTT-AATTTTTAA
1 TTTTTTGAATTTTTAA
17368097 TTTTTCAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
17 8 0.17
18 2 0.04
19 4 0.08
20 22 0.46
21 12 0.25
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTTGAATTTTTAAGATT
Found at i:17371998 original size:40 final size:40
Alignment explanation
Indices: 17371920--17371998 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
17371910 CTTAATTTAA
* * *
17371920 AAAATAAAATAAATAAATAAAACAAAAAAAGAATAAAAAG
1 AAAAGAAAATAAACAAATAAAACAAAAAAACAATAAAAAG
* *
17371960 AAAAGAAAATAAACAAATAAAAACCAAAACACAA-AAAAA
1 AAAAGAAAATAAACAAAT-AAAACAAAAAAACAATAAAAA
17371999 TTATAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 21 0.64
41 12 0.36
ACGTcount: A:0.80, C:0.08, G:0.04, T:0.09
Consensus pattern (40 bp):
AAAAGAAAATAAACAAATAAAACAAAAAAACAATAAAAAG
Found at i:17372908 original size:3 final size:3
Alignment explanation
Indices: 17372902--17372933 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
17372892 TAAAGAGGAA
17372902 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17372934 GAGAATTGTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17378321 original size:14 final size:15
Alignment explanation
Indices: 17378302--17378331 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17378292 CTAGAACTAT
17378302 TAACAATGTAT-TAA
1 TAACAATGTATGTAA
17378316 TAACAATGTATGTAA
1 TAACAATGTATGTAA
17378331 T
1 T
17378332 GAATATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (15 bp):
TAACAATGTATGTAA
Found at i:17380669 original size:30 final size:30
Alignment explanation
Indices: 17380635--17380755 Score: 109
Period size: 30 Copynumber: 4.0 Consensus size: 30
17380625 AAGAGCTTAA
*
17380635 GAATTTTGATATCCAAGCTTGAAAGCTTGG
1 GAATTTTGACATCCAAGCTTGAAAGCTTGG
* * * *
17380665 GAATTTTGACATCTAAGCTTGAGAGTTTAG
1 GAATTTTGACATCCAAGCTTGAAAGCTTGG
** * * *
17380695 GAACATTGACATCCAAGCTTGAGAGTTTGA
1 GAATTTTGACATCCAAGCTTGAAAGCTTGG
** *
17380725 GAATTTCAATATCCAAGC-TGAAGAGCTTGG
1 GAATTTTGACATCCAAGCTTGAA-AGCTTGG
17380755 G
1 G
17380756 GGCTTTAACA
Statistics
Matches: 72, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
29 3 0.04
30 69 0.96
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (30 bp):
GAATTTTGACATCCAAGCTTGAAAGCTTGG
Found at i:17382817 original size:13 final size:13
Alignment explanation
Indices: 17382792--17382828 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
17382782 CAACAAAATG
17382792 AATAAAATAAAAA
1 AATAAAATAAAAA
* *
17382805 AATCAAATCAAAA
1 AATAAAATAAAAA
17382818 AATAAAATAAA
1 AATAAAATAAA
17382829 GATGGGAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAAA
Found at i:17383673 original size:5 final size:5
Alignment explanation
Indices: 17383660--17383725 Score: 54
Period size: 5 Copynumber: 14.0 Consensus size: 5
17383650 TGTGTGAATT
*
17383660 GAAACA GAAAA GAAAA G--AA GAAAA G-AAA GAAAA GGAAAA GGAAA G--AA
1 GAAA-A GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA -GAAAA GAAAA GAAAA
*
17383707 GAAAA GAAAA -AAAA CAAAA
1 GAAAA GAAAA GAAAA GAAAA
17383726 AGATAATAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
3 6 0.12
4 8 0.15
5 29 0.56
6 9 0.17
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:17383704 original size:28 final size:28
Alignment explanation
Indices: 17383666--17383720 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
17383656 AATTGAAACA
*
17383666 GAAAAGAAAAGAAGAAAAGAAAGAAAAG
1 GAAAAGAAAAGAAGAAAAGAAAAAAAAG
*
17383694 GAAAAGGAAAGAAGAAAAGAAAAAAAA
1 GAAAAGAAAAGAAGAAAAGAAAAAAAA
17383721 CAAAAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (28 bp):
GAAAAGAAAAGAAGAAAAGAAAAAAAAG
Found at i:17383705 original size:16 final size:16
Alignment explanation
Indices: 17383668--17383716 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
17383658 TTGAAACAGA
17383668 AAAGAAAAGAAGAAAAG
1 AAAGAAAAG-AGAAAAG
17383685 AAAGAAAAG-GAAAAGG
1 AAAGAAAAGAGAAAA-G
*
17383701 AAAGAAGAAAAGAAAA
1 AAAGAA-AAGAGAAAA
17383717 AAAACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 11 0.39
18 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAGAAAAG
Found at i:17383726 original size:28 final size:28
Alignment explanation
Indices: 17383661--17383728 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
17383651 GTGTGAATTG
*
17383661 AAACAGAAAAGAAAAGAAGAAAAGAAAGA
1 AAACA-AAAAGAAAAGAAGAAAAGAAAAA
** *
17383690 AAAGGAAAAGGAAAGAAGAAAAGAAAAA
1 AAACAAAAAGAAAAGAAGAAAAGAAAAA
17383718 AAACAAAAAGA
1 AAACAAAAAGA
17383729 TAATAATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 29 0.91
29 3 0.09
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (28 bp):
AAACAAAAAGAAAAGAAGAAAAGAAAAA
Found at i:17383734 original size:3 final size:3
Alignment explanation
Indices: 17383728--17383805 Score: 149
Period size: 3 Copynumber: 26.3 Consensus size: 3
17383718 AAACAAAAAG
17383728 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17383775 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17383806 CAGTGACATT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17384248 original size:115 final size:114
Alignment explanation
Indices: 17384106--17384719 Score: 450
Period size: 115 Copynumber: 5.4 Consensus size: 114
17384096 CAAAATTACA
* * * *
17384106 AGTCAAAATGAA-CTGACTAGGACCGAGTCAAAGTAAAAAATGATCGAGATGAAACCACGAATCA
1 AGTCAAAATGAAGC-GACCAGGACCGAGTCAAGGTAAAAAATGA-CGAGACGAAACCATGAATCA
** *
17384170 TAAGAAATGAGATAGACTAAGCCAAGATAAAGTGACTAGGACAAAACCACG
64 TAAGAAATGATCTAGACTAAGCCAAGATAAAGTGACTAGGACAAAACCATG
* * * * *
17384221 AGTCAAAATGAAGCGACCGGGATCGAGTCTAGGTAAAAAATGACTGGGACGAAACCATGTATCAT
1 AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAATGAC-GAGACGAAACCATGAATCAT
* * * * * * * * **
17384286 AAGAAGTGATTTAGATTGAGCCAAGATCATGTGA-TCGAGACGAAACTTTG
65 AAGAAATGATCTAGACTAAGCCAAGATAAAGTGACTAG-GACAAAACCATG
* * * ** * *
17384336 AGTCAAAATGAAGCGACCAGGACTGAGTCTAGATTGAAAATGACCAGGACGAAGCCATGAATCAT
1 AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAATGACGA-GACGAAACCATGAATCAT
* * * ** **
17384401 AAGAAATGATTTAGAC-AGAGCTAAGATTAAGT-ACCGGGATGAAACCATG
65 AAGAAATGATCTAGACTA-AGCCAAGATAAAGTGACTAGGACAAAACCATG
* * * ** * * ** * *
17384450 AGTCAAAATGATGCGACCAAG-CCTAGTCAAGGTCGAGAATGACCAAGATAAAACCATAAATTAT
1 AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAATGA-CGAGACGAAACCATGAATCAT
*
17384514 AAGAAATGATCTAGACTAAGCCAAGATCAAA-TGACCAGGACAAAACCATG
65 AAGAAATGATCTAGACTAAGCCAAGAT-AAAGTGACTAGGACAAAACCATG
* * ** * * * * * *
17384564 AGTCAAAATAAAGTGACCAAAATCGAGTCGAGGTCAAGAATTATC-AGAACAAAACCATGAATCA
1 AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAATGA-CGAG-ACGAAACCATGAATCA
* * * * * **
17384628 TAAGAAATGATCTGGATTAAGCCAAAATCAAGTGACTGGGATGAAACCATG
64 TAAGAAATGATCTAGACTAAGCCAAGATAAAGTGACTAGGACAAAACCATG
* * * * * *
17384679 AGTCAAAATGAAGTGATCAGAATCGAGTCGAGGTCAAAAAT
1 AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAAT
17384720 AAATGACTGA
Statistics
Matches: 399, Mismatches: 87, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
113 52 0.13
114 72 0.18
115 274 0.69
116 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.18
Consensus pattern (114 bp):
AGTCAAAATGAAGCGACCAGGACCGAGTCAAGGTAAAAAATGACGAGACGAAACCATGAATCATA
AGAAATGATCTAGACTAAGCCAAGATAAAGTGACTAGGACAAAACCATG
Found at i:17385488 original size:60 final size:60
Alignment explanation
Indices: 17385418--17385532 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
17385408 TCTTTGGATC
* * * ***
17385418 CAAGCCACCTTTTTGGTTTTTTAACTTGAACTTTTTCTTTTTGTTCTTTTTTTTTAGGTT
1 CAAGCCACCTTTTCGGGTTTTCAACTTGAACTCCCTCTTTTTGTTCTTTTTTTTTAGGTT
* *
17385478 CAAGCTACCTTTTCGGGTTTTCAACTTGAACTCCCTCTTTTTTTTCTTTTTTTTT
1 CAAGCCACCTTTTCGGGTTTTCAACTTGAACTCCCTCTTTTTGTTCTTTTTTTTT
17385533 TTTTAGAGTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.13, C:0.19, G:0.10, T:0.57
Consensus pattern (60 bp):
CAAGCCACCTTTTCGGGTTTTCAACTTGAACTCCCTCTTTTTGTTCTTTTTTTTTAGGTT
Found at i:17392567 original size:16 final size:16
Alignment explanation
Indices: 17392546--17392576 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17392536 CAAATGCATG
17392546 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
17392562 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
17392577 TATTTACCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:17396042 original size:14 final size:14
Alignment explanation
Indices: 17396019--17396051 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17396009 AAGAAAATGG
17396019 TTTTTTTATT-TTT
1 TTTTTTTATTATTT
17396032 TTTTATTTATTATTT
1 TTTT-TTTATTATTT
17396047 TTTTT
1 TTTTT
17396052 GAAAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 7 0.39
15 7 0.39
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTATTATTT
Found at i:17396130 original size:13 final size:12
Alignment explanation
Indices: 17396104--17396141 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
17396094 CAACAAAATG
17396104 AATAAAATAAAA
1 AATAAAATAAAA
*
17396116 AATCAAATCAAAA
1 AATAAAAT-AAAA
17396129 AATAAAATAAAA
1 AATAAAATAAAA
17396141 A
1 A
17396142 TGGGAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:17396593 original size:19 final size:19
Alignment explanation
Indices: 17396569--17396606 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
17396559 TAGAAAAGCC
17396569 CAGATTTCT-TCAAAATTTT
1 CAGATTTCTCTC-AAATTTT
17396588 CAGATTTCTCTCAAATTTT
1 CAGATTTCTCTCAAATTTT
17396607 GTCTTGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.47
Consensus pattern (19 bp):
CAGATTTCTCTCAAATTTT
Found at i:17396998 original size:18 final size:19
Alignment explanation
Indices: 17396975--17397012 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
17396965 ATTGGAATAG
17396975 AAAAGGAAAA-AAGAAAAA
1 AAAAGGAAAAGAAGAAAAA
17396993 AAAAGGAAAAGAAGAAAAA
1 AAAAGGAAAAGAAGAAAAA
17397012 A
1 A
17397013 TGAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGGAAAAGAAGAAAAA
Found at i:17397002 original size:16 final size:16
Alignment explanation
Indices: 17396983--17397018 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17396973 AGAAAAGGAA
17396983 AAAAGAAAAAAAAAGG
1 AAAAGAAAAAAAAAGG
* *
17396999 AAAAGAAGAAAAAATG
1 AAAAGAAAAAAAAAGG
17397015 AAAA
1 AAAA
17397019 TAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAAAAAAGG
Found at i:17397023 original size:3 final size:3
Alignment explanation
Indices: 17397017--17397110 Score: 126
Period size: 3 Copynumber: 32.7 Consensus size: 3
17397007 AAAAAATGAA
17397017 AAT AAT AAT AAAT AAT AAT AAT -AT AAT -AT AAT AAT -AT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
17397060 AGT AAT -AT AAC AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17397106 AAT AA
1 AAT AA
17397111 CAATGACATT
Statistics
Matches: 81, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
2 10 0.12
3 68 0.84
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17397093 original size:37 final size:35
Alignment explanation
Indices: 17397017--17397103 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 35
17397007 AAAAAATGAA
*
17397017 AATAATAATA-AATAATAATAATATAATATAATAAT
1 AATAATAATATAAT-ATAACAATATAATATAATAAT
17397052 -ATAATAATAGTAATATAACAATATAATAATAATAAT
1 AATAATAATA-TAATATAACAATATAAT-ATAATAAT
17397088 AATAATAATAATAATA
1 AATAATAAT-ATAATA
17397104 ATAATAACAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
34 9 0.20
35 12 0.26
36 11 0.24
37 13 0.28
38 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (35 bp):
AATAATAATATAATATAACAATATAATATAATAAT
Found at i:17397109 original size:43 final size:40
Alignment explanation
Indices: 17397018--17397109 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 40
17397008 AAAAATGAAA
*
17397018 ATAATAATAA-ATAATAATAATATAATATAATAATAT-A-
1 ATAATAATAATATAACAATAATATAATATAATAATATAAT
*
17397055 ATAATAGTAATATAACAAT-ATAATAATAATAATAATAATAAT
1 ATAATAATAATATAACAATAAT-ATAAT-ATAATAAT-ATAAT
17397097 AATAATAATAATA
1 -ATAATAATAATA
17397110 ACAATGACAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
37 11 0.24
38 12 0.27
39 8 0.18
40 2 0.04
41 1 0.02
43 11 0.24
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (40 bp):
ATAATAATAATATAACAATAATATAATATAATAATATAAT
Found at i:17398554 original size:34 final size:35
Alignment explanation
Indices: 17398505--17398571 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
17398495 ATGTTGGTGT
17398505 TGAGTTATGAATTGCAAAGTTAAGTTAAATTGGGAG
1 TGAGTTA-GAATTGCAAAGTTAAGTTAAATTGGGAG
17398541 TGAGTTA-AATTGCAAAGTTAAGTTAAATTGG
1 TGAGTTAGAATTGCAAAGTTAAGTTAAATTGG
17398572 CTTTTCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 24 0.77
36 7 0.23
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (35 bp):
TGAGTTAGAATTGCAAAGTTAAGTTAAATTGGGAG
Found at i:17398566 original size:18 final size:18
Alignment explanation
Indices: 17398514--17398570 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
17398504 TTGAGTTATG
17398514 AATTGCAAAGTTAAGTTA
1 AATTGCAAAGTTAAGTTA
** *
17398532 AATTG-GGAG-TGAGTTA
1 AATTGCAAAGTTAAGTTA
17398548 AATTGCAAAGTTAAGTTA
1 AATTGCAAAGTTAAGTTA
17398566 AATTG
1 AATTG
17398571 GCTTTTCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 11 0.35
17 4 0.13
18 16 0.52
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (18 bp):
AATTGCAAAGTTAAGTTA
Found at i:17399086 original size:60 final size:61
Alignment explanation
Indices: 17399025--17399143 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 61
17399015 TTAGAAATAT
* * **
17399025 TTTCT-TATTTTAAATTTCT-AAATTCTCCATCATTTAGGCCTGTTTAGAAAT-TTTTTTTA
1 TTTCTATATTTTAAATTTCTAAAATT-TCCACCATTTAGGACAATTTAGAAATATTTTTTTA
* * * *
17399084 TTTCTATTTTTTATATTTTTAAAATTTTCACCATTTAGGACAATTTAGAAATATTTTTTT
1 TTTCTATATTTTAAATTTCTAAAATTTCCACCATTTAGGACAATTTAGAAATATTTTTTT
17399144 TCAGAATTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
59 5 0.10
60 32 0.65
61 12 0.24
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (61 bp):
TTTCTATATTTTAAATTTCTAAAATTTCCACCATTTAGGACAATTTAGAAATATTTTTTTA
Found at i:17399168 original size:111 final size:114
Alignment explanation
Indices: 17398999--17399207 Score: 300
Period size: 111 Copynumber: 1.9 Consensus size: 114
17398989 CTAATTATTC
* * *
17398999 CACCATTTAAGCCAAATTAGAAATATTTTCTTATTTTAAATTTCTAAATTCTCCATCATTTAGGC
1 CACCATTTAAGACAAATTAGAAATATTTTCTTATTTCAAATTTCTAAATTCTCAATCATTTAGGC
* *
17399064 CTGTTTAGAAATTTTTTTTATTTC-TATTTTTTATATTTTTAAAATTTT
66 CTATTTAGAAATTCTTTTTATTTCTTATTTTTTATATTTTTAAAATTTT
* * * *
17399112 CACCATTTAGGACAATTTAGAAATA-TTT-TT-TTTCAGAATTTCTAAATTTTCAATCATTTGGG
1 CACCATTTAAGACAAATTAGAAATATTTTCTTATTTCA-AATTTCTAAATTCTCAATCATTTAGG
17399174 CCTATTTAGAAATTCTTTTTATTTCTTATTTTTT
65 CCTATTTAGAAATTCTTTTTATTTCTTATTTTTT
17399208 TTGGAAAGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
110 4 0.05
111 48 0.56
112 11 0.13
113 22 0.26
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (114 bp):
CACCATTTAAGACAAATTAGAAATATTTTCTTATTTCAAATTTCTAAATTCTCAATCATTTAGGC
CTATTTAGAAATTCTTTTTATTTCTTATTTTTTATATTTTTAAAATTTT
Found at i:17400189 original size:13 final size:12
Alignment explanation
Indices: 17400171--17400242 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 12
17400161 AAACACCCAT
17400171 TTTTTTTCTTGTG
1 TTTTTTT-TTGTG
*
17400184 TTTTTTTTTTTG
1 TTTTTTTTTGTG
* *
17400196 TTTCTCTTATGTG
1 TTT-TTTTTTGTG
17400209 TTTTTCTTTTGTTG
1 TTTTT-TTTTG-TG
17400223 TTTTGTTCTTCTGTG
1 TTTT-TT-TT-TGTG
17400238 TTTTT
1 TTTTT
17400243 GTGTCAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
12 8 0.17
13 20 0.43
14 8 0.17
15 9 0.19
16 2 0.04
ACGTcount: A:0.01, C:0.08, G:0.14, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGTG
Found at i:17400212 original size:23 final size:23
Alignment explanation
Indices: 17400170--17400221 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
17400160 TAAACACCCA
* *
17400170 TTTT-TTTTCTTGTGT-TTTTTT
1 TTTTGTTTTCTTATGTGTTTTTC
17400191 TTTTGTTTCTCTTATGTGTTTTTC
1 TTTTGTTT-TCTTATGTGTTTTTC
17400215 TTTTGTT
1 TTTTGTT
17400222 GTTTTGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 3 0.12
23 7 0.27
24 12 0.46
ACGTcount: A:0.02, C:0.08, G:0.12, T:0.79
Consensus pattern (23 bp):
TTTTGTTTTCTTATGTGTTTTTC
Found at i:17400479 original size:17 final size:15
Alignment explanation
Indices: 17400429--17400479 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 15
17400419 CTAAAAAACT
17400429 AATAATAAATCTAATAA
1 AATAATAAATC-AA-AA
17400446 AATAA-AAATACAAAA
1 AATAATAAAT-CAAAA
17400461 AATAGATAAATCAACAA
1 AATA-ATAAATCAA-AA
17400478 AA
1 AA
17400480 AAATGAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.20
16 10 0.33
17 14 0.47
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.20
Consensus pattern (15 bp):
AATAATAAATCAAAA
Found at i:17401312 original size:13 final size:13
Alignment explanation
Indices: 17401294--17401318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17401284 TTTTTCCTCT
17401294 TTTTTATTTTTCA
1 TTTTTATTTTTCA
17401307 TTTTTATTTTTC
1 TTTTTATTTTTC
17401319 CTCTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTCA
Found at i:17401334 original size:31 final size:31
Alignment explanation
Indices: 17401273--17401335 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 31
17401263 TCTCTTATTC
17401273 TCATTTTTCATTTTTTCCTCTTTTTTATTTT
1 TCATTTTTCATTTTTTCCTCTTTTTTATTTT
17401304 TCATTTTT-A-TTTTTCCTCTTTCTTTCATTTT
1 TCATTTTTCATTTTTTCCTCTTT-TTT-ATTTT
17401335 T
1 T
17401336 TCACCCATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 14 0.47
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (31 bp):
TCATTTTTCATTTTTTCCTCTTTTTTATTTT
Found at i:17401704 original size:11 final size:11
Alignment explanation
Indices: 17401688--17401728 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
17401678 CTTTTATTTG
17401688 TTTTTCTTTCT
1 TTTTTCTTTCT
17401699 TTTTTC-TTCT
1 TTTTTCTTTCT
*
17401709 TTTTT-TTTTT
1 TTTTTCTTTCT
17401719 TTTTTGCTTT
1 TTTTT-CTTT
17401729 GAGACCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 17 0.65
11 6 0.23
12 3 0.12
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:17401711 original size:19 final size:19
Alignment explanation
Indices: 17401664--17401720 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
17401654 GTGGCATTCA
*
17401664 TTTC-TCTTTTCTCTCTTT
1 TTTCTTCTTTTCTTTCTTT
17401682 TATT-TGT-TTTTCTTTCTTT
1 T-TTCT-TCTTTTCTTTCTTT
17401701 TTTCTTCTTTT-TTT-TTT
1 TTTCTTCTTTTCTTTCTTT
17401718 TTT
1 TTT
17401721 TTTGCTTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 19 0.58
20 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTCTTCTTTTCTTTCTTT
Found at i:17401717 original size:14 final size:14
Alignment explanation
Indices: 17401670--17401717 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
17401660 TTCATTTCTC
17401670 TTTTCTCTCTTTTATT
1 TTTTCT-TCTTTT-TT
*
17401686 TGTTT-TTCTTTCTT
1 T-TTTCTTCTTTTTT
17401700 TTTTCTTCTTTTTT
1 TTTTCTTCTTTTTT
17401714 TTTT
1 TTTT
17401718 TTTTTTGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 15 0.54
15 5 0.18
16 2 0.07
17 3 0.11
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:17401728 original size:28 final size:30
Alignment explanation
Indices: 17401664--17401728 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
17401654 GTGGCATTCA
*
17401664 TTTCTCTTTTCTCTCTTTTATTTGTTTTTC
1 TTTCTTTTTTCTCTCTTTTATTTGTTTTTC
*
17401694 TTTCTTTTTTCT-TCTTTT-TTT-TTTTTT
1 TTTCTTTTTTCTCTCTTTTATTTGTTTTTC
17401721 TTTGCTTT
1 TTT-CTTT
17401729 GAGACCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.25
28 7 0.22
29 6 0.19
30 11 0.34
ACGTcount: A:0.02, C:0.15, G:0.03, T:0.80
Consensus pattern (30 bp):
TTTCTTTTTTCTCTCTTTTATTTGTTTTTC
Found at i:17407436 original size:51 final size:51
Alignment explanation
Indices: 17407357--17407455 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
17407347 TATTTATTTA
* * * * *
17407357 TTCTTTTTGGATTTTTAAATTTTTCACCATTTGGGTCAATTTAGAAATATT
1 TTCTTTTTGAATTTCTAAAATTTCCACCATTTGGGCCAATTTAGAAATATT
*
17407408 TTCTTTTTGAATTTCTAAAATTTCCACCATTTGGGCCTATTTAGAAAT
1 TTCTTTTTGAATTTCTAAAATTTCCACCATTTGGGCCAATTTAGAAAT
17407456 TCTTTTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.49
Consensus pattern (51 bp):
TTCTTTTTGAATTTCTAAAATTTCCACCATTTGGGCCAATTTAGAAATATT
Found at i:17407948 original size:17 final size:17
Alignment explanation
Indices: 17407926--17407958 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17407916 AAAATAAATT
17407926 ATAAAAACAAAA-GAAAA
1 ATAAAAA-AAAATGAAAA
17407943 ATAAAAAAAAATGAAA
1 ATAAAAAAAAATGAAA
17407959 TGGCTAGGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
ATAAAAAAAAATGAAAA
Found at i:17408758 original size:24 final size:22
Alignment explanation
Indices: 17408711--17408766 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
17408701 CTAACAAAAA
* *
17408711 ATAAAAAAAAGAAAAAATATAG
1 ATAAAAAAATGAAAAAATAAAG
17408733 ATAAAAAAATGAAAAAGATCAAAG
1 ATAAAAAAATGAAAAA-AT-AAAG
*
17408757 ATAAATAAAT
1 ATAAAAAAAT
17408767 AAATTAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
24 12 0.41
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (22 bp):
ATAAAAAAATGAAAAAATAAAG
Found at i:17408833 original size:18 final size:18
Alignment explanation
Indices: 17408794--17408827 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17408784 AAGATAAAAC
*
17408794 AAAAAAATGAAAATAGTG
1 AAAAAAATGAAAATAATG
17408812 AAAAAAAT-AAAATAAT
1 AAAAAAATGAAAATAAT
17408828 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (18 bp):
AAAAAAATGAAAATAATG
Found at i:17412170 original size:14 final size:15
Alignment explanation
Indices: 17412141--17412191 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
17412131 CCAAAATTTG
*
17412141 AAACCCTAAATTCCT
1 AAACCCTAAATCCCT
17412156 AAACCCT-AATCCCT
1 AAACCCTAAATCCCT
* *
17412170 -AATCCTAAAT-CTT
1 AAACCCTAAATCCCT
17412183 AAACCCTAA
1 AAACCCTAA
17412192 CCTTAACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 7 0.23
14 16 0.53
15 7 0.23
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.25
Consensus pattern (15 bp):
AAACCCTAAATCCCT
Found at i:17412336 original size:18 final size:18
Alignment explanation
Indices: 17412313--17412375 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
17412303 TACATTATTA
17412313 CATGCATTCATATATTGT
1 CATGCATTCATATATTGT
*
17412331 CATGCATCCATACT-TTGT
1 CATGCATTCATA-TATTGT
* *
17412349 TATTCA-T-ATTATATTGT
1 CATGCATTCA-TATATTGT
17412366 CATGCATTCA
1 CATGCATTCA
17412376 CCATGTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
16 2 0.06
17 10 0.29
18 20 0.59
19 2 0.06
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (18 bp):
CATGCATTCATATATTGT
Found at i:17414340 original size:3 final size:3
Alignment explanation
Indices: 17414332--17414365 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17414322 AAGCAAAAGA
*
17414332 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17414366 CTACTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17417219 original size:52 final size:51
Alignment explanation
Indices: 17417103--17417258 Score: 190
Period size: 52 Copynumber: 3.0 Consensus size: 51
17417093 TGGACAAGAA
*
17417103 GACTTACAAAAGAAGAATTCTAAG-AGAAAGAAGATTCTTAA-AGGTAAGTTT
1 GACTTACAAAAGAAGAATTCTAAGAAGAGAG-A-ATTCTTAATAGGTAAGTTT
* *
17417154 GACTTGCAAAAGAATAATTCTAAGAAGAGATGAATTCTTAATAGGTAAGTTT
1 GACTTACAAAAGAAGAATTCTAAGAAGAGA-GAATTCTTAATAGGTAAGTTT
* * * * *
17417206 GACTTACAGAAGAAGAATTTTAAGAGGAGAGAGATTTTTAATAGGCAAGTTT
1 GACTTACAAAAGAAGAATTCTAAGAAGAGAGA-ATTCTTAATAGGTAAGTTT
17417258 G
1 G
17417259 TATGGTTATA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
51 32 0.35
52 58 0.64
53 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (51 bp):
GACTTACAAAAGAAGAATTCTAAGAAGAGAGAATTCTTAATAGGTAAGTTT
Found at i:17417880 original size:25 final size:25
Alignment explanation
Indices: 17417790--17417889 Score: 112
Period size: 25 Copynumber: 4.0 Consensus size: 25
17417780 AAGTGGTATC
* *
17417790 AGAGCTGAAGGTTCAAAACGTGAGA
1 AGAGCTGAAGGTTCAAGACGTGGGA
* * * *
17417815 AGAGTTGAAGATTCAA-ATGTGGAA
1 AGAGCTGAAGGTTCAAGACGTGGGA
**
17417839 AGAGCCAAAGGTTCAAGACGTGGGA
1 AGAGCTGAAGGTTCAAGACGTGGGA
*
17417864 AGAGCTGAAGGTTCAAGATGTGGGA
1 AGAGCTGAAGGTTCAAGACGTGGGA
17417889 A
1 A
17417890 AAACATGGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
24 17 0.28
25 43 0.72
ACGTcount: A:0.38, C:0.10, G:0.34, T:0.18
Consensus pattern (25 bp):
AGAGCTGAAGGTTCAAGACGTGGGA
Found at i:17423241 original size:2 final size:2
Alignment explanation
Indices: 17423234--17423260 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17423224 AAGATTTCAT
17423234 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 T
17423261 CTTTAAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17437855 original size:29 final size:28
Alignment explanation
Indices: 17437811--17437869 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
17437801 AAATTAAATA
** *
17437811 TTATATTTTGATTTTGTTATTTATTAAT
1 TTATATTTTGATTTTGAAATTTAATAAT
17437839 TTATAATTTT-ATATTTGAAATTTAATAAT
1 TTAT-ATTTTGAT-TTTGAAATTTAATAAT
17437868 TT
1 TT
17437870 TTTTATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TTATATTTTGATTTTGAAATTTAATAAT
Found at i:17437938 original size:14 final size:15
Alignment explanation
Indices: 17437911--17437943 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17437901 ATTCTTTTGC
17437911 TATTAAATTAATTTT
1 TATTAAATTAATTTT
*
17437926 TATT-AATTTATTTT
1 TATTAAATTAATTTT
17437940 TATT
1 TATT
17437944 TTTGTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTAAATTAATTTT
Found at i:17441977 original size:134 final size:133
Alignment explanation
Indices: 17441752--17442202 Score: 553
Period size: 134 Copynumber: 3.4 Consensus size: 133
17441742 AACCGTTAAA
* * * *
17441752 TTAGTTGTGTTTTTATGAGAAAAATGTCATTACTTTGGTGGCATTTGTAACTGAAAACATCGCTA
1 TTAGTGGTATTTTTATGAGAAAAATGCCATTGCTTTGGTGGCATTTGTAACTGAAAACATCGCTA
** * * * * *
17441817 CTTTAGAGGTGTTTATATCTGTAAATGCCTTTATATTAACGATTTTTATATCTTTGAGAGGCCAC
66 CTTTAGAGGCATTTGTATCTGAAAATGCCTTTATATTAACG-TATTTATATCTTTGAGACGCCGC
*
17441882 TATT
130 TAAT
* * *
17441886 TTAGTGATATTTTTATGAGAAAAATGCCATTGCTTTGGTGGCATTTGTAATTGAAAACACCGCTA
1 TTAGTGGTATTTTTATGAGAAAAATGCCATTGCTTTGGTGGCATTTGTAACTGAAAACATCGCTA
* * * *
17441951 CTTTAGAGGCATTTGTATATGAAAATGCCTTTATAGTAACTGTGTTTATATCTTTGAGACGCTGC
66 CTTTAGAGGCATTTGTATCTGAAAATGCCTTTATATTAAC-GTATTTATATCTTTGAGACGCCGC
17442016 TAAT
130 TAAT
* * * ** *
17442020 TTAGTGGCATTTTTATGAGAAAAATAG-CGTTGCTTTGGTGGCGTTTGTAACTGAAAATGTCACT
1 TTAGTGGTATTTTTATGAGAAAAAT-GCCATTGCTTTGGTGGCATTTGTAACTGAAAACATCGCT
* * * *
17442084 ACTTTAGAAGCATTTGTATCTGAAAATGTCTTTATATTAACGGCATTTATATCTTTTAGACGCCG
65 ACTTTAGAGGCATTTGTATCTGAAAATGCCTTTATATTAAC-GTATTTATATCTTTGAGACGCCG
17442149 CTAAT
129 CTAAT
* * * * *
17442154 TTAGTGGTATTTTTTTAAGAAAAATGCTATTGCTTTGGTAGCGTTTGTA
1 TTAGTGGTATTTTTATGAGAAAAATGCCATTGCTTTGGTGGCATTTGTA
17442203 TAAAAAATAT
Statistics
Matches: 272, Mismatches: 42, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
133 1 0.00
134 269 0.99
135 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (133 bp):
TTAGTGGTATTTTTATGAGAAAAATGCCATTGCTTTGGTGGCATTTGTAACTGAAAACATCGCTA
CTTTAGAGGCATTTGTATCTGAAAATGCCTTTATATTAACGTATTTATATCTTTGAGACGCCGCT
AAT
Found at i:17450930 original size:173 final size:173
Alignment explanation
Indices: 17450601--17450930 Score: 391
Period size: 173 Copynumber: 1.9 Consensus size: 173
17450591 CACGGTAATT
* * * * *
17450601 GAAGGTGTATATTCAAGAAAAATGCCTTTAATAATTTCTTTTAAATTTTGTAGATAATTAATGAA
1 GAAGGTGTATATTCAAGAAAAAAGCCTTTAATAATTTCTTTTAAACTTAGTACATAATTAATAAA
* ** * *
17450666 GGCATTTTTAGATAAAAATCATCGTCAATAATTTCCTCTAAAAAGTTTTTAGGATTATTAAAGGT
66 GGCATTTTTAGATAAAAATCATCCTCAATAATTTCCTCTAAAAAAATTTTAGAATTACTAAAGGT
* *
17450731 GTCTTCTACTGGAAAATACCTTTAATATACCAGTACGATTATA
131 GTCTTCTACTGCAAAAAACCTTTAATATACCAGTACGATTATA
* * *
17450774 GAAGGTGTTTATTCTAGAAAAAAGCCTTTAATAATTTC-TTTAAACTTAGTACATAATTACTAAA
1 GAAGGTGTATATTCAAGAAAAAAGCCTTTAATAATTTCTTTTAAACTTAGTACATAATTAATAAA
* * * *
17450838 TGCGTTTGTTA-ATAACACA-CA-CCTCTAATAATTTCCCTTTAAAAAAATTTTAGAATTACT-A
66 GGCATTT-TTAGATAA-AAATCATCCTC-AATAATTT-CCTCTAAAAAAATTTTAGAATTACTAA
* *
17450899 AGGTGTCTTTTACTGACAAAAAACTTTTAATA
127 AGGTGTCTTCTACTG-CAAAAAACCTTTAATA
17450931 AATAAATTTT
Statistics
Matches: 131, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
171 3 0.02
172 55 0.42
173 73 0.56
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (173 bp):
GAAGGTGTATATTCAAGAAAAAAGCCTTTAATAATTTCTTTTAAACTTAGTACATAATTAATAAA
GGCATTTTTAGATAAAAATCATCCTCAATAATTTCCTCTAAAAAAATTTTAGAATTACTAAAGGT
GTCTTCTACTGCAAAAAACCTTTAATATACCAGTACGATTATA
Found at i:17451143 original size:485 final size:482
Alignment explanation
Indices: 17450514--17451590 Score: 1404
Period size: 485 Copynumber: 2.2 Consensus size: 482
17450504 AATAAACGCA
* * * * * *
17450514 TTCTAAATTTTGTTAGGATTATTAAAAGCGTTTTCTACTGCAAAAAAACTTTCAATATATAGCTA
1 TTCTAAAATTTGTTGGGATTATTAAAGGCGTCTTCTACTGC-AAAAATCCTTCAATATA-AGCTA
* *
17450579 TACAAATTTTAACACGGTAATTGAAGGTGTATATTCAAGAAAAATGCCTTTAATAATTTCTTTTA
64 TACAAATTTTAACACGGTAATTGAAGGCGTATATTCAAGAAAAATGCATTTAATAATTTCTTTTA
*
17450644 AATTTTGTAGATAATTAATGAAGGCATTTTTAGATAAAAA-T-CATCGTCAATAATTTCCTCTAA
129 AATTTTGTAGATAATTAATGAAGACATTTTTAGATAAAAACTCCAT--T-AATAATTTCCTCTAA
* * * * * *
17450707 AAAGTTTTTAGGATTATTAAAGGTGTCTTCTACTGGAAAATACCTTTAATATACCAGTACGATTA
191 AAAATTTTTAGGATTATTAAAAGCGTCTTCTACTGGAAAACACCTTCAATATACCACTACGATTA
***
17450772 TAGAAGGTGTTTAT-TCTAGAAAAAAGCCTTTAATAATT-TCTTTAAACTTAGTACATAATTACT
256 TAGAAAACGTTTATCT-TAGAAAAAAGCCTTTAATAATTCT-TTTAAACTTAGTACATAATTACT
* * *
17450835 AAATGCGTTTGTTAATAACACACACCTCT-AATAATTTCCCTTTAAAAAAATTTTAGAATTACT-
319 AAAGGCGTTTGTTAATAACACAC-CCTCTCAATAATTTCCC-TCAAAAAAATTTTAAAATTACTA
* * *
17450898 AAGGTGTCTTT-TACTGACAAAAAACTTTTAATAAATAAATTTTAAATTATCTTCATAAAAATTG
382 AAGGCGT-TTTCTACTGAC-AAAAACCTTCAATAAATAAATTTTAAATTATCTTCATAAAAATTG
*
17450962 AAGGCGTTTCTTTAGAATAAACGCCTTCAATAATTTT-C
445 AAGGCGTTTCTTTAGAATAAACGCATTCAAT-ATTTTCC
*
17451000 TTCTAAAATTTGTTGGGATTGTTAAAGGCGTCTTCTACTGCAAAAATCCTTCAATATACAGCTAT
1 TTCTAAAATTTGTTGGGATTATTAAAGGCGTCTTCTACTGCAAAAATCCTTCAATATA-AGCTAT
*
17451065 ACAAATTTTAACATGGTAATTGAAGGCGTATATTCAAGAAAAATGCATTTAATAA-TTCTTTTTA
65 ACAAATTTTAACACGGTAATTGAAGGCGTATATTCAAGAAAAATGCATTTAATAATTTC-TTTTA
* * **
17451129 AATTTTGTAGATAATTAGTGAATACATTTTTAGATAAAAACTGCCATTAATAATTTTTTCTAAAA
129 AATTTTGTAGATAATTAATGAAGACATTTTTAGATAAAAACT-CCATTAATAATTTCCTCTAAAA
* * * *
17451194 AATTTTTAGGATTATTAAAAGCGTCTTCTATTGGAAAACGCCTTCAATATACCACTATGGTTATA
193 AATTTTTAGGATTATTAAAAGCGTCTTCTACTGGAAAACACCTTCAATATACCACTACGATTATA
* * *
17451259 GAAAACGTTTATCTTAGAGAAACGCCTTTAATAATTCTTTTAAACTTAGTACATAATTACTGAAG
258 GAAAACGTTTATCTTAGAAAAAAGCCTTTAATAATTCTTTTAAACTTAGTACATAATTACTAAAG
* * * *
17451324 GCGTTTGTTAATAACACACGCTTTCAATAATTTTCCTCAAAAAAATTTTAAAATTATTAAAGGCG
323 GCGTTTGTTAATAACACACCCTCTCAATAATTTCCCTCAAAAAAATTTTAAAATTACTAAAGGCG
**
17451389 TTTTCTACTGACAAACGCCTTCAATAAATAAATTTTAAATTATCTTCATAAAAATTGAAGGCGTT
388 TTTTCTACTGACAAAAACCTTCAATAAATAAATTTTAAATTATCTTCATAAAAATTGAAGGCGTT
*
17451454 TCTTTATAATAAACGCATTCAATATTTTCC
453 TCTTTAGAATAAACGCATTCAATATTTTCC
* ** * *
17451484 TTCTAGAATTTGTTGAAATTATTAAAGGCCTCTTCTACT--ATAAAATGCCTTCAATATAATGCC
1 TTCTAAAATTTGTTGGGATTATTAAAGGCGTCTTCTACTGCA-AAAAT-CCTTCAATATAA-GCT
* * * * *
17451547 ACACAAATATTAACACGGTTAA-TAAAGGCATATATTTAAGAAAA
63 ATACAAATTTTAACACGG-TAATTGAAGGCGTATATTCAAGAAAA
17451591 CATCTTTTAT
Statistics
Matches: 519, Mismatches: 58, Indels: 30
0.86 0.10 0.05
Matches are distributed among these distances:
482 1 0.00
483 11 0.02
484 180 0.35
485 284 0.55
486 40 0.08
488 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.37
Consensus pattern (482 bp):
TTCTAAAATTTGTTGGGATTATTAAAGGCGTCTTCTACTGCAAAAATCCTTCAATATAAGCTATA
CAAATTTTAACACGGTAATTGAAGGCGTATATTCAAGAAAAATGCATTTAATAATTTCTTTTAAA
TTTTGTAGATAATTAATGAAGACATTTTTAGATAAAAACTCCATTAATAATTTCCTCTAAAAAAT
TTTTAGGATTATTAAAAGCGTCTTCTACTGGAAAACACCTTCAATATACCACTACGATTATAGAA
AACGTTTATCTTAGAAAAAAGCCTTTAATAATTCTTTTAAACTTAGTACATAATTACTAAAGGCG
TTTGTTAATAACACACCCTCTCAATAATTTCCCTCAAAAAAATTTTAAAATTACTAAAGGCGTTT
TCTACTGACAAAAACCTTCAATAAATAAATTTTAAATTATCTTCATAAAAATTGAAGGCGTTTCT
TTAGAATAAACGCATTCAATATTTTCC
Found at i:17452836 original size:28 final size:28
Alignment explanation
Indices: 17452805--17452858 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
17452795 GCTGAATGGT
*
17452805 TTGCTGAACCTTATTGTATGATATTGTA
1 TTGCTGAACCGTATTGTATGATATTGTA
* **
17452833 TTGCTTAATGGTATTGTATGATATTG
1 TTGCTGAACCGTATTGTATGATATTG
17452859 GAAGGCTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.48
Consensus pattern (28 bp):
TTGCTGAACCGTATTGTATGATATTGTA
Found at i:17452895 original size:80 final size:79
Alignment explanation
Indices: 17452757--17452972 Score: 315
Period size: 80 Copynumber: 2.7 Consensus size: 79
17452747 ATTTTTTTTA
* * *
17452757 CTGAATGGTATTGAATGATATTGGGGGCTGAATTATATGCTGAATGGTTTGCTGAACCTTATTGT
1 CTGAATGGTATTGTATGATATTGGGGGCTGAATCATATGCTGAATGGTTTGCTAAACCTTATTGT
17452822 ATGATATTGTATTG
66 ATGATATTGTATTG
* * * * *
17452836 CTTAATGGTATTGTATGATATTGGAAGGCTGAATCATATGTTGAATGATTTACTAAACCTTATTG
1 CTGAATGGTATTGTATGATATTGG-GGGCTGAATCATATGCTGAATGGTTTGCTAAACCTTATTG
* *
17452901 TCTGATATTGTTTTG
65 TATGATATTGTATTG
*
17452916 CTGAATGGTTTTGTATGATATTAGGGGGCTGAATCATATGCTGAATGGTTTGCTAAA
1 CTGAATGGTATTGTATGATATT-GGGGGCTGAATCATATGCTGAATGGTTTGCTAAA
17452973 TGGTATTTCT
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
79 22 0.18
80 95 0.80
81 2 0.02
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (79 bp):
CTGAATGGTATTGTATGATATTGGGGGCTGAATCATATGCTGAATGGTTTGCTAAACCTTATTGT
ATGATATTGTATTG
Found at i:17456150 original size:18 final size:18
Alignment explanation
Indices: 17456124--17456166 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
17456114 ATTATCAGTT
*
17456124 TTAAATTTAGATGTGTGG
1 TTAATTTTAGATGTGTGG
17456142 TTAATTTTAGATGTGTGG
1 TTAATTTTAGATGTGTGG
17456160 TTAATTT
1 TTAATTT
17456167 ATTGAAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (18 bp):
TTAATTTTAGATGTGTGG
Found at i:17457691 original size:6 final size:6
Alignment explanation
Indices: 17457680--17457717 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
17457670 TGAATGACCC
*
17457680 TTTTCT TTTTCT TTTTC- TTTT-T TTTTCT TTTTAT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
17457718 TATTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 8 0.28
6 21 0.72
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTCT
Found at i:17457706 original size:16 final size:16
Alignment explanation
Indices: 17457679--17457718 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
17457669 GTGAATGACC
17457679 CTTTTCTTTTTCTTTTT
1 CTTTT-TTTTTCTTTTT
17457696 CTTTTTTTTTCTTTTT
1 CTTTTTTTTTCTTTTT
*
17457712 ATTTTTT
1 CTTTTTT
17457719 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (16 bp):
CTTTTTTTTTCTTTTT
Found at i:17457723 original size:12 final size:12
Alignment explanation
Indices: 17457691--17457770 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
17457681 TTTCTTTTTC
*
17457691 TTTTTCTTTT-T
1 TTTTTATTTTAT
17457702 TTTTCT-TTTTAT
1 TTTT-TATTTTAT
*
17457714 TTTTTATTTTAA
1 TTTTTATTTTAT
*
17457726 TTTTGATTTTAT
1 TTTTTATTTTAT
17457738 TTATTT-TGTGTTGA-
1 TT-TTTAT-T-TT-AT
*
17457752 TTTTTATGTTAT
1 TTTTTATTTTAT
17457764 TTTTTAT
1 TTTTTAT
17457771 ATTTTGTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
11 10 0.18
12 33 0.60
13 6 0.11
14 5 0.09
15 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:17457740 original size:21 final size:21
Alignment explanation
Indices: 17457716--17457766 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
17457706 CTTTTTATTT
*
17457716 TTTATTTTAATTTTGA-TTTTA
1 TTTATTTT-ATGTTGATTTTTA
*
17457737 TTTATTTTGTGTTGATTTTTA
1 TTTATTTTATGTTGATTTTTA
17457758 TGTTATTTT
1 T-TTATTTT
17457767 TTATATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 14 0.54
22 7 0.27
ACGTcount: A:0.18, C:0.00, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTATTTTATGTTGATTTTTA
Found at i:17457797 original size:3 final size:3
Alignment explanation
Indices: 17457783--17457827 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
17457773 TTTGTTATGA
* *
17457783 TAT TAT TGT TAT TAT TAT TAT TAT TAT TGT TAT T-T TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17457828 CTAGTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17458070 original size:23 final size:20
Alignment explanation
Indices: 17458027--17458073 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
17458017 TTTTGCCAAA
*
17458027 AAATAAAATTAAAAAAAGAT
1 AAATAAAATAAAAAAAAGAT
17458047 AAATAAAATAAAAGGAAAATGAT
1 AAATAAAATAAAA--AAAA-GAT
17458070 AAAT
1 AAAT
17458074 TATATAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 12 0.52
22 4 0.17
23 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAAAAAGAT
Found at i:17458241 original size:11 final size:11
Alignment explanation
Indices: 17458227--17458264 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
17458217 ATTAAACAAT
17458227 ATAAAATAATA
1 ATAAAATAATA
*
17458238 ATAAAATAAAA
1 ATAAAATAATA
*
17458249 ATGAAATAATA
1 ATAAAATAATA
17458260 ATAAA
1 ATAAA
17458265 TGATATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:17461436 original size:18 final size:18
Alignment explanation
Indices: 17461415--17461449 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17461405 ATTATAAATA
*
17461415 ATATTTTAATAATTTTTT
1 ATATATTAATAATTTTTT
*
17461433 ATATATTATTAATTTTT
1 ATATATTAATAATTTTT
17461450 ACAATAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATATTAATAATTTTTT
Found at i:17462615 original size:21 final size:19
Alignment explanation
Indices: 17462591--17462629 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
17462581 TATGATTAAA
17462591 AAATAAAAATTAAAAAAACAC
1 AAAT-AAAA-TAAAAAAACAC
*
17462612 AAATACAATAAAAAAACA
1 AAATAAAATAAAAAAACA
17462630 AATGACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 3 0.18
21 4 0.24
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAAATAAAAAAACAC
Found at i:17475089 original size:61 final size:58
Alignment explanation
Indices: 17475014--17475227 Score: 203
Period size: 62 Copynumber: 3.5 Consensus size: 58
17475004 TGTCTGGCCA
*
17475014 AAAATGCCTTCAATAATCCATAAAAAAATTTGCAAGAGATTATTGAAAGCATTTTTGGCT
1 AAAATGCCTTCAATAATCCATAAAAAAATTTGCAAG-GATTATT-AAAGCATTTTTAGCT
* * **
17475074 GAAAACGCCTTCAATAATCCATACAAAAAATTTTGGAAGGGATTATTAAATGTGTTTTTAGCT
1 -AAAATGCCTTCAATAATCCATA-AAAAAA-TTTGCAA-GGATTATTAAA-GCATTTTTAGCT
* ** * * *
17475137 AGAAATGCCTTCAATAACCCATTCAACATTTTGTACAGGATTATTCAAAGCATTTTCTAGCT
1 A-AAATGCCTTCAATAATCCATAAAAAAATTTGCA-AGGATTATT-AAAGCATTTT-TAGCT
* *
17475199 AAAAATACCTTCATTAATCCATAAAAAAA
1 -AAAATGCCTTCAATAATCCATAAAAAAA
17475228 CATTTAGTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
61 39 0.32
62 42 0.34
63 41 0.33
64 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (58 bp):
AAAATGCCTTCAATAATCCATAAAAAAATTTGCAAGGATTATTAAAGCATTTTTAGCT
Found at i:17475147 original size:63 final size:62
Alignment explanation
Indices: 17475015--17475227 Score: 211
Period size: 63 Copynumber: 3.4 Consensus size: 62
17475005 GTCTGGCCAA
* * *
17475015 AAATGCCTTCAATAATCCATAAAAAAA-TTTGCAAGAGATTATTGAAAGCATTTTTGGCT-G
1 AAATGCCTTCAATAATCCATAAAAAAATTTTGCAAGGGATTATTCAAAGCATTTTTAGCTAG
* * **
17475075 AAAACGCCTTCAATAATCCATACAAAAAATTTTGGAAGGGATTATT-AAATGTGTTTTTAGCTAG
1 -AAATGCCTTCAATAATCCATA-AAAAAATTTTGCAAGGGATTATTCAAA-GCATTTTTAGCTAG
* ** * * *
17475139 AAATGCCTTCAATAACCCAT-TCAACATTTTGTACA-GGATTATTCAAAGCATTTTCTAGCTAA
1 AAATGCCTTCAATAATCCATAAAAAAATTTTGCA-AGGGATTATTCAAAGCATTTT-TAGCTAG
* *
17475201 AAATACCTTCATTAATCCATAAAAAAA
1 AAATGCCTTCAATAATCCATAAAAAAA
17475228 CATTTAGTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
61 42 0.34
62 36 0.29
63 44 0.36
64 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (62 bp):
AAATGCCTTCAATAATCCATAAAAAAATTTTGCAAGGGATTATTCAAAGCATTTTTAGCTAG
Found at i:17475300 original size:35 final size:35
Alignment explanation
Indices: 17475249--17475320 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
17475239 GTTATATATG
* * *
17475249 TGAAGTCAGTTGTAAGTTTATGC-CTATAAAACATT
1 TGAAGTCAGCTATAAGTTTATGCTC-AGAAAACATT
17475284 TGAAGTCAGCTATAAGTTTATGCTCAGAAAACATT
1 TGAAGTCAGCTATAAGTTTATGCTCAGAAAACATT
17475319 TG
1 TG
17475321 GTTTATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (35 bp):
TGAAGTCAGCTATAAGTTTATGCTCAGAAAACATT
Found at i:17479043 original size:63 final size:61
Alignment explanation
Indices: 17478944--17479095 Score: 155
Period size: 63 Copynumber: 2.4 Consensus size: 61
17478934 AAATGATCAA
* * * * * *
17478944 TGAAGGC-TTTTTACCAAAAAAATACCTTTAATAATCCCCTCCAATTTTTTATCAAGAGATTAT
1 TGAAGGCATTTTTA--ACAAAAATGCCTTTAACAATCCCCTCCAAATTTTTA-AAAAAGATTAT
*
17479007 TGAAGGCATTTTTAACTAAAAATGCCTTTAACAATCCCCTTCAAATTTTTAAAAAAGATTAT
1 TGAAGGCATTTTTAAC-AAAAATGCCTTTAACAATCCCCTCCAAATTTTTAAAAAAGATTAT
* **
17479069 TAAAGATATTTTCTAA-AAAAATGCCTT
1 TGAAGGCATTTT-TAACAAAAATGCCTT
17479096 CAAGTAATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
61 11 0.14
62 19 0.25
63 40 0.53
64 6 0.08
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.36
Consensus pattern (61 bp):
TGAAGGCATTTTTAACAAAAATGCCTTTAACAATCCCCTCCAAATTTTTAAAAAAGATTAT
Found at i:17479129 original size:62 final size:63
Alignment explanation
Indices: 17479054--17479232 Score: 177
Period size: 63 Copynumber: 2.8 Consensus size: 63
17479044 CCTTCAAATT
** * * *
17479054 TTTAAAAAAGATTATTAAAGATATTTTCTAAAAAAATGCCTTCAAGTAATTTCTTTTA-AAAAA
1 TTTAAAAGGGATTATTAAAGATATTTTCTAAAAAAATACCTTCAA-TAATTTCCTTGATAAAAA
* * * * *
17479117 TTT-TAGGGGATTATTGAAGGTATTTT-TAGTTAAAAATACCTTCAATAA-TTCCTTGATAAAAA
1 TTTAAAAGGGATTATTAAAGATATTTTCTA--AAAAAATACCTTCAATAATTTCCTTGATAAAAA
*
17479179 TTTAAAAGGGATAATTAAAGATATTTTCTATAAACAAAATACCTTCAATAATTT
1 TTTAAAAGGGATTATTAAAGATATTTTC--TAAA-AAAATACCTTCAATAATTT
17479233 TTAAAAAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
61 8 0.09
62 28 0.31
63 34 0.37
64 1 0.01
65 16 0.18
66 4 0.04
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (63 bp):
TTTAAAAGGGATTATTAAAGATATTTTCTAAAAAAATACCTTCAATAATTTCCTTGATAAAAA
Found at i:17479441 original size:62 final size:61
Alignment explanation
Indices: 17479323--17479503 Score: 172
Period size: 62 Copynumber: 3.0 Consensus size: 61
17479313 CCAAAAAAAT
* * * * * * *
17479323 ACCTTGAATAA-TT-TTTTAAAAAGTTTAAAAGGGTTATTGAAG-GTGTTTTCTTCAAAATAC
1 ACCTTCAATAATTTCTTTTAAAAAATTTTAAAGGATTATTAAAGCAT-TTTT-TACAAAATAC
* *
17479383 ACCTTCAATAATTT-TTTTAAAAAATTTTTAGGAGATTATTAAAGGCATTTTTTACAAAATAC
1 ACCTTCAATAATTTCTTTTAAAAAATTTTAAAG-GATTATTAAA-GCATTTTTTACAAAATAC
* * * *
17479445 TCCTTCAATAATTTCTTTTATAAAATTTTAAAGGATTATTGAAGTATTTTTTACTAAAA
1 ACCTTCAATAATTTCTTTTAAAAAATTTTAAAGGATTATTAAAGCATTTTTTAC-AAAA
17479504 ATGCTTAAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
60 10 0.10
61 26 0.26
62 43 0.43
63 20 0.20
64 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (61 bp):
ACCTTCAATAATTTCTTTTAAAAAATTTTAAAGGATTATTAAAGCATTTTTTACAAAATAC
Found at i:17486548 original size:161 final size:160
Alignment explanation
Indices: 17485903--17486609 Score: 430
Period size: 161 Copynumber: 4.5 Consensus size: 160
17485893 TAATAATTTT
* * * * * *
17485903 GATAGTTTCAATACATGATATTAAAC-TTATCCAAATTATTGAACTTAGTTTTC-TTAGTTGATA
1 GATAGCTTCAATACATGATATTAAACTTTAT-CGAATGATTGAACTTGGTTTCCATGA-TTGATA
* * * * * * * * **
17485966 TGTATGAAAAAGTTATTGTTTACATCTATTTAGGACATTTTGTGCCATTAATAAATAAAAATACA
64 TATGTGAAAAAGTTGTTGTTAACATTTATTTAGGATATTTTATGCCGTTAA-AAGGAAAAATACA
* * ** *
17486031 AATTTGGACCA-GTTGTTCTATTGT-AAGAGTTTG
128 AATTT-GACAATATTAATCTATT-TCAACAGTTTG
* * * * **
17486064 GATAGCTCCAACATATGATATTAAAC-TTATCCAAATGATTGAACTTATTTTTCACA-G-TT-A-
1 GATAGCTTCAATACATGATATTAAACTTTAT-CGAATGATTGAACTT-GGTTTC-CATGATTGAT
* * ** * * * * * * *
17486124 ATATGCATGAAAAAGTTATTGTTTATGTATGTTTAAGACT-TTTTGTGCTGTTAAGAGGCAAACA
63 ATATG--TGAAAAAGTTGTTGTTAACATTTATTTAGGA-TATTTTATGCCGTTAAAAGG-AAAAA
* **** ** * *
17486188 TGCAAATTTGTTGTTATTGTTCTATTTTAACAATTTG
124 TACAAATTTGACAATATTAATCTATTTCAACAGTTTG
* * * * * * ** *
17486225 CATAACTTCAATACATG--A-T-AA-TTGA---AATAATTGACCTTGGTTTTCACAATTGATATG
1 GATAGCTTCAATACATGATATTAAACTTTATCGAATGATTGAACTTGGTTTCCATGATTGATATA
* *** * * * * * *
17486282 TGTGAAAAAGCTAACGTTTACGTCTATTTTGGATATTTTATGCTGTTAAAAGGCAAAATACAAAT
66 TGTGAAAAAGTTGTTGTTAACATTTATTTAGGATATTTTATGCCGTTAAAAGGAAAAATACAAAT
* * ** *
17486347 TTGATAATGTTGTTCTATTTTAACAGTTTG
131 TTGACAATATTAATCTATTTCAACAGTTTG
*
17486377 GATAGCTTCAATACATGATATTAAA-TTTGATCGAATGATTGAACTTGGTTTCTA-GAGTTGATA
1 GATAGCTTCAATACATGATATTAAACTTT-ATCGAATGATTGAACTTGGTTTCCATGA-TTGATA
17486440 TATGTGAAAAAGTTGTTGTTAACATTTATTTAGGACTATTTT-TGCCGTTAAAAGGAAAAAATAC
64 TATGTGAAAAAGTTGTTGTTAACATTTATTTAGGA-TATTTTATGCCGTTAAAAGG-AAAAATAC
* *
17486504 AAATTTGCCACTATTAATCTATTTCAACAGTTTG
127 AAATTTGACAATATTAATCTATTTCAACAGTTTG
* * *
17486538 GATGGCTTCAATACATGATATTAAACTTTTTCGAATGATTGAACTTGGTTTCCATGATTGATATT
1 GATAGCTTCAATACATGATATTAAACTTTATCGAATGATTGAACTTGGTTTCCATGATTGATATA
17486603 TGTGAAA
66 TGTGAAA
17486610 GGCCCAAATG
Statistics
Matches: 426, Mismatches: 92, Indels: 56
0.74 0.16 0.10
Matches are distributed among these distances:
151 2 0.00
152 53 0.12
153 52 0.12
154 2 0.00
155 5 0.01
156 4 0.01
157 5 0.01
158 1 0.00
159 5 0.01
160 65 0.15
161 223 0.52
162 8 0.02
163 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (160 bp):
GATAGCTTCAATACATGATATTAAACTTTATCGAATGATTGAACTTGGTTTCCATGATTGATATA
TGTGAAAAAGTTGTTGTTAACATTTATTTAGGATATTTTATGCCGTTAAAAGGAAAAATACAAAT
TTGACAATATTAATCTATTTCAACAGTTTG
Found at i:17488287 original size:14 final size:14
Alignment explanation
Indices: 17488268--17488295 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17488258 TCTAAACCCC
17488268 TATAGTGATTACAT
1 TATAGTGATTACAT
17488282 TATAGTGATTACAT
1 TATAGTGATTACAT
17488296 GAGACTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TATAGTGATTACAT
Found at i:17490348 original size:29 final size:29
Alignment explanation
Indices: 17490278--17490349 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
17490268 TCACTTTACA
* * * *
17490278 TAAATAAATTTTTATATTTTAATTGTATT
1 TAAATAAATTTTAATATTTGAATTGCATC
17490307 TAAATAAGA-TTTAATA-TTGAATTTGCATC
1 TAAATAA-ATTTTAATATTTGAA-TTGCATC
17490336 TAAATAAATTTTAA
1 TAAATAAATTTTAA
17490350 CCTTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 5 0.14
29 30 0.83
30 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (29 bp):
TAAATAAATTTTAATATTTGAATTGCATC
Done.