Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008103.1 Hibiscus syriacus cultivar Beakdansim tig00110633_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1996589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1080427 original size:22 final size:22
Alignment explanation
Indices: 1080384--1080428 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1080374 CTGGTATCGA
* *
1080384 TACCTTACCATGGTATCAATAC
1 TACCATACCATGGTACCAATAC
* *
1080406 TACCATACTATGGTACCGATAC
1 TACCATACCATGGTACCAATAC
1080428 T
1 T
1080429 CCCTTCTAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (22 bp):
TACCATACCATGGTACCAATAC
Found at i:1080472 original size:93 final size:94
Alignment explanation
Indices: 1080317--1080503 Score: 243
Period size: 93 Copynumber: 2.0 Consensus size: 94
1080307 CTATACTTCT
* * * *
1080317 ATACTATGGTATCGATACCCCCTACCGGTATCGGTACCAATCTTAGGTTCGATGTGCCTGGTATC
1 ATACTATGGTACCGATACCCCCTACCAGTATCGATACCAATCTTAGATTCGATGTGCCTGGTATC
*
1080382 GATA-CCTTACCATGGTATCAATACTACC
66 GATACCCTTACAATGGTATCAATACTACC
* * * *
1080410 ATACTATGGTACCGATACTCCCTTCTAGTATCGATACCAAT-TTAGATTCGATGTTGCTTGGTAT
1 ATACTATGGTACCGATACCCCCTACCAGTATCGATACCAATCTTAGATTCGATG-TGCCTGGTAT
* * *
1080474 CGATACCCTTATAATGGTATCGATGCTACC
65 CGATACCCTTACAATGGTATCAATACTACC
1080504 TCATCGATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
92 11 0.14
93 49 0.61
94 20 0.25
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (94 bp):
ATACTATGGTACCGATACCCCCTACCAGTATCGATACCAATCTTAGATTCGATGTGCCTGGTATC
GATACCCTTACAATGGTATCAATACTACC
Found at i:1083889 original size:17 final size:18
Alignment explanation
Indices: 1083867--1083902 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1083857 TTTTTACTAC
1083867 TTTAACAC-TTTCTAGAT
1 TTTAACACATTTCTAGAT
1083884 TTTAACACAATTTCTAGAT
1 TTTAACAC-ATTTCTAGAT
1083903 CACGAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
19 9 0.53
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTAACACATTTCTAGAT
Found at i:1087155 original size:54 final size:56
Alignment explanation
Indices: 1087095--1087200 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
1087085 TGCAACCTAA
* *
1087095 GAAATTCATAA-GAGTTTATGAATTTCCGTATT-GCACTATGTGTGTAACCCCCAC
1 GAAATTCATAATGAGTTTATGAATTTCCATATTGGCACTATGTGTGAAACCCCCAC
*
1087149 GAAATTCATAATGAGTTTATGAATTTTCATATTGGCACTATGTGTGAAACCC
1 GAAATTCATAATGAGTTTATGAATTTCCATATTGGCACTATGTGTGAAACCC
1087201 AGTACTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 11 0.23
55 19 0.40
56 17 0.36
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (56 bp):
GAAATTCATAATGAGTTTATGAATTTCCATATTGGCACTATGTGTGAAACCCCCAC
Found at i:1087239 original size:51 final size:53
Alignment explanation
Indices: 1087075--1087247 Score: 169
Period size: 51 Copynumber: 3.3 Consensus size: 53
1087065 TGTCGAATGA
* * *
1087075 GCACTATGTGTGCA-ACCTAAGAAATTCATAA-GAGTTTATGAATTTCCGTATT
1 GCACTATGTGTGAACACCCACGAAATTCATAATGAGTTTATGAATTT-CGTATT
* *
1087127 GCACTATGTGTGTAACCCCCACGAAATTCATAATGAGTTTATGAATTTTCATATT
1 GCACTATGTGTG-AACACCCACGAAATTCATAATGAGTTTATGAA-TTTCGTATT
* * *
1087182 GGCACTATGTGTGAA-ACCCA-GTACTT-AT-ATGATTTTATGAATTATCGTATT
1 -GCACTATGTGTGAACACCCACGAAATTCATAATGAGTTTATGAATT-TCGTATT
*
1087233 GACACTAAGTGTGAA
1 G-CACTATGTGTGAA
1087248 GAAACCATGG
Statistics
Matches: 103, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
50 3 0.03
51 30 0.29
52 14 0.14
53 5 0.05
54 18 0.17
55 18 0.17
56 15 0.15
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (53 bp):
GCACTATGTGTGAACACCCACGAAATTCATAATGAGTTTATGAATTTCGTATT
Found at i:1093869 original size:55 final size:55
Alignment explanation
Indices: 1093777--1093931 Score: 188
Period size: 55 Copynumber: 2.8 Consensus size: 55
1093767 TACTGAATGA
* ** *
1093777 GCACTATATGTGCAA-CCTA-AGAAATTCATAACAAGTTTATGAATTTTCGTATTG
1 GCACTATATGTGCAACCCCACA-AAATTCATAATGAGTTTATGAATTTTCATATTG
* *
1093831 GCACTATGTGTTCAACCCCACAAAATTCATAATGAGTTTATGAATTTTCATATTG
1 GCACTATATGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTTCATATTG
*** * *
1093886 GCACTATATGTGCAACCCCATGTACTTTATAATGAGTTTATGAATT
1 GCACTATATGTGCAACCCCACAAAATTCATAATGAGTTTATGAATT
1093932 ATTGTATCGG
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
54 13 0.15
55 72 0.84
56 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (55 bp):
GCACTATATGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTTCATATTG
Found at i:1093953 original size:55 final size:55
Alignment explanation
Indices: 1093798--1093954 Score: 174
Period size: 55 Copynumber: 2.9 Consensus size: 55
1093788 GCAACCTAAG
** * *
1093798 AAATTCATAACAAGTTTATGAATTTTCGTATTGGCACTATGTGTTCAACCCCACA
1 AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTAAGTGTGCAACCCCACA
* **
1093853 AAATTCATAATGAGTTTATGAATTTTCATATTGGCACTATA-TGTGCAACCCCATG
1 AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTA-AGTGTGCAACCCCACA
* * * * *
1093908 TACTTTATAATGAGTTTATGAATTATT-GTATCGGTACTAAGTGTGCA
1 AAATTCATAATGAGTTTATGAATT-TTCGTATTGGCACTAAGTGTGCA
1093955 GAAACCATGG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 1 0.01
55 83 0.97
56 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (55 bp):
AAATTCATAATGAGTTTATGAATTTTCGTATTGGCACTAAGTGTGCAACCCCACA
Found at i:1099180 original size:18 final size:18
Alignment explanation
Indices: 1099157--1099200 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1099147 TCAATTCCAT
1099157 AAACCCTAATATGAACAC
1 AAACCCTAATATGAACAC
*
1099175 AAACCCTTATATGAACAC
1 AAACCCTAATATGAACAC
1099193 AAACCCTA
1 AAACCCTA
1099201 GAATCTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.18
Consensus pattern (18 bp):
AAACCCTAATATGAACAC
Found at i:1101036 original size:102 final size:102
Alignment explanation
Indices: 1100851--1101162 Score: 286
Period size: 95 Copynumber: 3.1 Consensus size: 102
1100841 AGCAAATATC
* * * *
1100851 AAAATTTATCTCAGTTGAGATGATTTTTTCTTAAAATAAATTTCATCTCGCTTGAGACAATTTTC
1 AAAATTTATCTCACTTGAGATG-GTTTTTCTTAAAATCAATTTCATCTCGCTTGAGACAAGTTTC
* * * * *
1100916 CCTTGAAATAAAAATTTG-AATTTTGTTGACTTGAAACA
65 CCTTAAAACAAAAATTTGAAATTGT-TTCACTCGAAACA
* *** * *
1100954 AAAATTTATCTCACTTGAGATGGTTTCTT-TTAAAATCAATTTCGTCTTTTTTGAGGC-GGTTTC
1 AAAATTTATCTCACTTGAGATGGTTT-TTCTTAAAATCAATTTCATCTCGCTTGAGACAAGTTTC
*
1101017 CCTTAAAACACAAATTTTGAAATTGTTTCACTCGAAACA
65 CCTTAAAACA-AAAATTTGAAATTGTTTCACTCGAAACA
* *
1101056 AAAATTTA--TCACTTGAGATGGTTTTTCTTAAAATCAA-TT--T-T-GCTTGAGA-TAGTTCCC
1 AAAATTTATCTCACTTGAGATGGTTTTTCTTAAAATCAATTTCATCTCGCTTGAGACAAGTTTCC
** * * * *
1101113 CTTGGAACACATATTTTGAAATTGTTTCACTTGAAACG
66 CTTAAAACA-AAAATTTGAAATTGTTTCACTCGAAACA
1101151 AAAATTTATCTC
1 AAAATTTATCTC
1101163 TTCTTAGATA
Statistics
Matches: 176, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
95 51 0.29
96 1 0.01
97 3 0.02
99 4 0.02
100 26 0.15
101 12 0.07
102 51 0.29
103 28 0.16
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (102 bp):
AAAATTTATCTCACTTGAGATGGTTTTTCTTAAAATCAATTTCATCTCGCTTGAGACAAGTTTCC
CTTAAAACAAAAATTTGAAATTGTTTCACTCGAAACA
Found at i:1104066 original size:21 final size:21
Alignment explanation
Indices: 1104032--1104071 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1104022 TGTTGTATAT
*
1104032 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTAGGGATGATTTTGG
1104052 AGCCGTTTAGGGATGATTTT
1 AGCCG-TTAGGGATGATTTT
1104072 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTAGGGATGATTTTGG
Found at i:1104213 original size:20 final size:20
Alignment explanation
Indices: 1104184--1104236 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1104174 GCAGCCTTCG
* *
1104184 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGCAGGA
*
1104204 TGCATCGATGCAGAGCAGGA
1 TGCATCGATGCACAGCAGGA
1104224 TGCATCGATGCAC
1 TGCATCGATGCAC
1104237 TAAGTGCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1104281 original size:20 final size:21
Alignment explanation
Indices: 1104256--1104313 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
1104246 TCGAAATGGA
1104256 GTGCATGGATGCACTA-CATG
1 GTGCATGGATGCACTAGCATG
** *
1104276 GTGCATCCATGCACTAGTGGATG
1 GTGCATGGATGCACTA--GCATG
1104299 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1104314 TTGACACCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.47
23 16 0.53
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (21 bp):
GTGCATGGATGCACTAGCATG
Found at i:1104560 original size:21 final size:21
Alignment explanation
Indices: 1104536--1104575 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1104526 ATGTTTAATG
1104536 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1104557 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1104576 CCAATTGTTT
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:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1107537 original size:20 final size:22
Alignment explanation
Indices: 1107512--1107551 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1107502 TGTTGTATAT
1107512 AGCCA-TTGGGGATG-TTTTGG
1 AGCCATTTGGGGATGATTTTGG
1107532 AGCCATTTGGGGATGATTTT
1 AGCCATTTGGGGATGATTTT
1107552 TCTATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AGCCATTTGGGGATGATTTTGG
Found at i:1107693 original size:20 final size:20
Alignment explanation
Indices: 1107664--1107736 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
1107654 GCAGTCTTAG
* *
1107664 TGCATGGATGCATAGCAAGA
1 TGCATCGATGCACAGCAAGA
1107684 TGCATCGATGCACAGCAAGA
1 TGCATCGATGCACAGCAAGA
1107704 TGCATCGATGCACAGCAAGA
1 TGCATCGATGCACAGCAAGA
1107724 TGCATCGATGCAC
1 TGCATCGATGCAC
1107737 TAAGTGCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAAGA
Found at i:1107804 original size:43 final size:42
Alignment explanation
Indices: 1107753--1107855 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 42
1107743 CATTCGAAAT
*
1107753 GGAGTGCATGGATGCACTGCATG-GTCCATCGATGCACTAGT-
1 GGAGTGCATGGATGCACTGCAGGAGTCCATCGATGCACT-GTA
* * *
1107794 GGTAGGTGCATGGATGCACTGTAGGAGTGCATGGATGCACTGTA
1 GG-A-GTGCATGGATGCACTGCAGGAGTCCATCGATGCACTGTA
1107838 GGAGTGCATGGATGCACT
1 GGAGTGCATGGATGCACT
1107856 TTGACACCCT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
41 2 0.04
42 16 0.30
43 21 0.39
44 15 0.28
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.24
Consensus pattern (42 bp):
GGAGTGCATGGATGCACTGCAGGAGTCCATCGATGCACTGTA
Found at i:1107825 original size:21 final size:21
Alignment explanation
Indices: 1107753--1107855 Score: 129
Period size: 21 Copynumber: 4.9 Consensus size: 21
1107743 CATTCGAAAT
*
1107753 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGTA
* * *
1107774 TG-GTCCATCGATGCACTAGT-
1 GGAGTGCATGGATGCACT-GTA
1107794 GGTAGGTGCATGGATGCACTGTA
1 GG-A-GTGCATGGATGCACTGTA
1107817 GGAGTGCATGGATGCACTGTA
1 GGAGTGCATGGATGCACTGTA
1107838 GGAGTGCATGGATGCACT
1 GGAGTGCATGGATGCACT
1107856 TTGACACCCT
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
20 14 0.20
21 38 0.54
22 3 0.04
23 15 0.21
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
GGAGTGCATGGATGCACTGTA
Found at i:1109681 original size:21 final size:21
Alignment explanation
Indices: 1109655--1109697 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1109645 GTAGCAGTAT
*
1109655 TGTAGCAGGGTGTCGGTTCCC
1 TGTAGCAGGGTATCGGTTCCC
1109676 TGTAGCAGGGTATCGGTTCCC
1 TGTAGCAGGGTATCGGTTCCC
1109697 T
1 T
1109698 ATCAGCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.12, C:0.23, G:0.35, T:0.30
Consensus pattern (21 bp):
TGTAGCAGGGTATCGGTTCCC
Found at i:1109756 original size:22 final size:22
Alignment explanation
Indices: 1109728--1109771 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1109718 TAACATTTGG
*
1109728 TACTGTTCAGGGTATTGTTCAT
1 TACTGTTCACGGTATTGTTCAT
1109750 TACTGTTCACGGTATTGTTCAT
1 TACTGTTCACGGTATTGTTCAT
1109772 ATCGTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.20, T:0.45
Consensus pattern (22 bp):
TACTGTTCACGGTATTGTTCAT
Found at i:1110059 original size:63 final size:63
Alignment explanation
Indices: 1109981--1110105 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
1109971 AAAACTTTTG
*
1109981 GGTATATCATGCGTTAGGTCCTCCATTTCCAGTGTACTTCATGCTTTTGTCACCAAAATAAAT
1 GGTAAATCATGCGTTAGGTCCTCCATTTCCAGTGTACTTCATGCTTTTGTCACCAAAATAAAT
*
1110044 GGTAAATCATGCGTTAGGTCCTCCATTTCCAGTGTACTTCATGTTTTTGTCACCAAAATAAA
1 GGTAAATCATGCGTTAGGTCCTCCATTTCCAGTGTACTTCATGCTTTTGTCACCAAAATAAA
1110106 GGATTAATCG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (63 bp):
GGTAAATCATGCGTTAGGTCCTCCATTTCCAGTGTACTTCATGCTTTTGTCACCAAAATAAAT
Found at i:1113034 original size:44 final size:43
Alignment explanation
Indices: 1112925--1113228 Score: 272
Period size: 44 Copynumber: 7.1 Consensus size: 43
1112915 GTGGGATTGG
* ** * *
1112925 AAAAATTAGGGGTCTCAATTATAAAGGTAAAAAGTGAGATT-G
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATTAA
* * *
1112967 AAAAATTAGGGGCTTCAACTATAAATATAAAAAGTGAGATTGAA
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATT-AA
* ** *
1113011 AAAAATTAGGGGCCTCAATTATAAATGTAAAAAGTGGGATTGAC
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATT-AA
* * * * *
1113055 AAAAATTAGGGGTCTCCATTATAAATGTAAAAAAATAAGATTAC
1 AAAAATTAGGGGCCTCAATTATAAATAT-AAAAAGTAAGATTAA
* * * * *
1113099 AAAAATTAGGGGTCTCAATTATAAAGAGAAAAAATAAAATT--
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATTAA
* * * * * *
1113140 AAAAATTAAGGGCCTTAATTATAAAAAGAAAAAATAAAATTAA
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATTAA
** * *
1113183 AAAAATTAAAGACCTCAATTATAAAAATAAAAAGTAAGATTAA
1 AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATTAA
1113226 AAA
1 AAA
1113229 TTTTAAGGCC
Statistics
Matches: 226, Mismatches: 31, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
41 37 0.16
42 36 0.16
43 52 0.23
44 91 0.40
45 10 0.04
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAAATTAGGGGCCTCAATTATAAATATAAAAAGTAAGATTAA
Found at i:1113559 original size:2 final size:2
Alignment explanation
Indices: 1113546--1113575 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1113536 GAACGGAATC
*
1113546 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1113576 GCATGCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1114701 original size:22 final size:22
Alignment explanation
Indices: 1114673--1114722 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1114663 TTAGTTTTTT
1114673 TTTTTTGAAATACTTTTAGGTA
1 TTTTTTGAAATACTTTTAGGTA
*
1114695 TTTTTTGAAATACTTTTAGGTT
1 TTTTTTGAAATACTTTTAGGTA
1114717 TTTTTT
1 TTTTTT
1114723 TATAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (22 bp):
TTTTTTGAAATACTTTTAGGTA
Found at i:1118344 original size:15 final size:15
Alignment explanation
Indices: 1118326--1118374 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1118316 AAGGCTGCAA
1118326 CATCACAAGCACCAT
1 CATCACAAGCACCAT
*** *
1118341 CATCACAAGTTGCAA
1 CATCACAAGCACCAT
1118356 CATCA-AAGCACCAT
1 CATCACAAGCACCAT
1118370 CATCA
1 CATCA
1118375 TCACAAGTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.41, C:0.35, G:0.08, T:0.16
Consensus pattern (15 bp):
CATCACAAGCACCAT
Found at i:1118384 original size:32 final size:30
Alignment explanation
Indices: 1118305--1118374 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1118295 ACAACGATTA
*
1118305 CACCATCATCA-AAGGCTGCAACATCACAAG
1 CACCATCATCACAA-GTTGCAACATCACAAG
1118335 CACCATCATCACAAGTTGCAACATCA-AAG
1 CACCATCATCACAAGTTGCAACATCACAAG
1118364 CACCATCATCA
1 CACCATCATCA
1118375 TCACAAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
29 14 0.37
30 22 0.58
31 2 0.05
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (30 bp):
CACCATCATCACAAGTTGCAACATCACAAG
Found at i:1120917 original size:27 final size:27
Alignment explanation
Indices: 1120887--1120969 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1120877 ACAATATAGT
1120887 ATATGTTCAAAGACTCTCAATTATATG
1 ATATGTTCAAAGACTCTCAATTATATG
* * *
1120914 ATA--TTGAATG-TTCATACAA-TATA-G
1 ATATGTTCAAAGACTC-T-CAATTATATG
*
1120938 AATATGTTCAAAGACTCTCAATCATATG
1 -ATATGTTCAAAGACTCTCAATTATATG
1120966 ATAT
1 ATAT
1120970 TGAATGTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 16
0.64 0.11 0.25
Matches are distributed among these distances:
24 3 0.07
25 13 0.32
26 6 0.15
27 16 0.39
28 3 0.07
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (27 bp):
ATATGTTCAAAGACTCTCAATTATATG
Found at i:1120996 original size:52 final size:52
Alignment explanation
Indices: 1120875--1120983 Score: 200
Period size: 52 Copynumber: 2.1 Consensus size: 52
1120865 GTCTGGGTGA
* *
1120875 ATACAATATAGTATATGTTCAAAGACTCTCAATTATATGATATTGAATGTTC
1 ATACAATATAGAATATGTTCAAAGACTCTCAATCATATGATATTGAATGTTC
1120927 ATACAATATAGAATATGTTCAAAGACTCTCAATCATATGATATTGAATGTTC
1 ATACAATATAGAATATGTTCAAAGACTCTCAATCATATGATATTGAATGTTC
1120979 ATACA
1 ATACA
1120984 CTCCTGCATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (52 bp):
ATACAATATAGAATATGTTCAAAGACTCTCAATCATATGATATTGAATGTTC
Found at i:1122219 original size:2 final size:2
Alignment explanation
Indices: 1122212--1122269 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1122202 GTTAATTGAA
1122212 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1122254 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1122270 GGGTGAAAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1135118 original size:8 final size:8
Alignment explanation
Indices: 1135105--1135210 Score: 63
Period size: 8 Copynumber: 12.8 Consensus size: 8
1135095 AACAAGAAAT
1135105 GAAAAAAA
1 GAAAAAAA
*
1135113 GAAAAAGA
1 GAAAAAAA
1135121 GAAAAATAA
1 GAAAAA-AA
*
1135130 AAAATAAAA
1 GAAA-AAAA
*
1135139 TGATGAAAAA
1 -GA-AAAAAA
*
1135149 GGAAAAAA
1 GAAAAAAA
*
1135157 GAAAAAAT
1 GAAAAAAA
*
1135165 GAAAAAAT
1 GAAAAAAA
1135173 GAAAAAAA
1 GAAAAAAA
*
1135181 TAATAAAAA
1 GAA-AAAAA
*
1135190 -ATAATAAA
1 GA-AAAAAA
*
1135198 -AAAATAA
1 GAAAAAAA
1135205 GAAAAA
1 GAAAAA
1135211 TTAAAAATGG
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
7 4 0.05
8 51 0.67
9 13 0.17
10 7 0.09
11 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1135146 original size:38 final size:39
Alignment explanation
Indices: 1135107--1135269 Score: 105
Period size: 38 Copynumber: 4.3 Consensus size: 39
1135097 CAAGAAATGA
1135107 AAAAAAG-AAAAAGAGAAAAAT-AAAAAAT-AAAATGATG
1 AAAAAAGAAAAAAGA-AAAAATGAAAAAATGAAAATGATG
* **
1135144 AAAAAGGAAAAAAGAAAAAATGAAAAAATGAAAAAAAT-
1 AAAAAAGAAAAAAGAAAAAATGAAAAAATGAAAATGATG
* * *
1135182 AATAAAA-AATAATA-AAAAAATAAGAAAAATTAAAA--ATG
1 AA-AAAAGAA-AAAAGAAAAAATGA-AAAAATGAAAATGATG
* * *
1135220 GAAGAAG--AAATGAAAAAATG-AAAAATGAAAAAATGATG
1 AAAAAAGAAAAAAGAAAAAATGAAAAAATG--AAAATGATG
*
1135258 AAAAAAGGAAAA
1 AAAAAAGAAAAA
1135270 TAAAAGTGGG
Statistics
Matches: 96, Mismatches: 15, Indels: 27
0.70 0.11 0.20
Matches are distributed among these distances:
34 6 0.06
35 2 0.02
36 11 0.11
37 17 0.18
38 35 0.36
39 22 0.23
40 3 0.03
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (39 bp):
AAAAAAGAAAAAAGAAAAAATGAAAAAATGAAAATGATG
Found at i:1135149 original size:30 final size:29
Alignment explanation
Indices: 1135101--1135274 Score: 89
Period size: 27 Copynumber: 6.0 Consensus size: 29
1135091 CTTGAACAAG
*
1135101 AAATGAAAAAAAGAAAAAGAGAAAAATAAA
1 AAAT-AAAAAATGAAAAAGAGAAAAATAAA
* *
1135131 AAATAAAATGATGAAAAAG-GAAAAAAGAAA
1 AAATAAAA-AATGAAAAAGAG-AAAAATAAA
*
1135161 AAATGAAAAAATG-AAAA-A-AATAATAAA
1 AAAT-AAAAAATGAAAAAGAGAAAAATAAA
* *
1135188 AAATAATAAAA--AAATA-AGAAAAATTAA
1 AAATAA-AAAATGAAAAAGAGAAAAATAAA
* * * *
1135215 AAATGGAAGAA-G-AAATGA-AAAAATGAA
1 AAAT-AAAAAATGAAAAAGAGAAAAATAAA
* *
1135242 AAATGAAAAAATGATGAAAAAAGGAAAATAAA
1 AAAT-AAAAAATGA--AAAAGAGAAAAATAAA
1135274 A
1 A
1135275 GTGGGGTTCA
Statistics
Matches: 109, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
26 6 0.06
27 48 0.44
28 3 0.03
29 9 0.08
30 27 0.25
31 8 0.07
32 8 0.07
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (29 bp):
AAATAAAAAATGAAAAAGAGAAAAATAAA
Found at i:1135179 original size:10 final size:9
Alignment explanation
Indices: 1135166--1135217 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
1135156 AGAAAAAATG
*
1135166 AAAAAATGA
1 AAAAAATAA
1135175 AAAAAATAA
1 AAAAAATAA
1135184 TAAAAAATAATA
1 -AAAAAAT-A-A
1135196 AAAAAATAA
1 AAAAAATAA
*
1135205 GAAAAATTAA
1 -AAAAAATAA
1135215 AAA
1 AAA
1135218 TGGAAGAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 12 0.32
10 16 0.43
11 8 0.22
12 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1135188 original size:11 final size:11
Alignment explanation
Indices: 1135174--1135210 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1135164 TGAAAAAATG
1135174 AAAAAAATAAT
1 AAAAAAATAAT
1135185 -AAAAAATAAT
1 AAAAAAATAAT
*
1135195 AAAAAAATAAG
1 AAAAAAATAAT
1135206 AAAAA
1 AAAAA
1135211 TTAAAAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:1135188 original size:18 final size:17
Alignment explanation
Indices: 1135158--1135217 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 17
1135148 AGGAAAAAAG
* *
1135158 AAAAAATGAAAAAATGA
1 AAAAAATAAAAAAATTA
1135175 AAAAAATAATAAAAAATAATA
1 AAAAAAT-A-AAAAAAT--TA
1135196 AAAAAATAAGAAAAATTA
1 AAAAAATAA-AAAAATTA
1135214 AAAA
1 AAAA
1135218 TGGAAGAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
17 7 0.19
18 6 0.17
19 8 0.22
20 7 0.19
21 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAAAAATTA
Found at i:1135240 original size:8 final size:8
Alignment explanation
Indices: 1135227--1135255 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1135217 ATGGAAGAAG
1135227 AAATGAAA
1 AAATGAAA
1135235 AAATG-AA
1 AAATGAAA
1135242 AAATGAAA
1 AAATGAAA
1135250 AAATGA
1 AAATGA
1135256 TGAAAAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (8 bp):
AAATGAAA
Found at i:1135250 original size:6 final size:7
Alignment explanation
Indices: 1135101--1135251 Score: 59
Period size: 7 Copynumber: 21.4 Consensus size: 7
1135091 CTTGAACAAG
1135101 AAATGAAA
1 AAATG-AA
*
1135109 AAAAGAA
1 AAATGAA
*
1135116 AAAGAGAA
1 AAA-TGAA
*
1135124 AAATAAA
1 AAATGAA
1135131 AAAT-AA
1 AAATGAA
1135137 AATGATGAA
1 AA--ATGAA
*
1135146 AAAGGAA
1 AAATGAA
*
1135153 AAAAGAAA
1 AAATG-AA
1135161 AAATGAAA
1 AAATG-AA
1135169 AAATGAA
1 AAATGAA
1135176 AAA--AA
1 AAATGAA
* *
1135181 TAATAAA
1 AAATGAA
1135188 AAAT-AA
1 AAATGAA
1135194 TAAA--AA
1 -AAATGAA
*
1135200 AATAAGAA
1 AA-ATGAA
*
1135208 AAATTAA
1 AAATGAA
1135215 AAATG--
1 AAATGAA
*
1135220 GAA-GAA
1 AAATGAA
1135226 GAAATGAAA
1 -AAATG-AA
1135235 AAATGAA
1 AAATGAA
1135242 AAATGAA
1 AAATGAA
1135249 AAA
1 AAA
1135252 ATGATGAAAA
Statistics
Matches: 114, Mismatches: 13, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
4 1 0.01
5 8 0.07
6 9 0.08
7 53 0.46
8 37 0.32
9 6 0.05
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (7 bp):
AAATGAA
Found at i:1136593 original size:37 final size:37
Alignment explanation
Indices: 1136521--1136606 Score: 113
Period size: 37 Copynumber: 2.3 Consensus size: 37
1136511 TTCGACCTTC
*
1136521 GAAGCAAATCAAACTTAAGGCTTCACGAAAGAGTAGT
1 GAAGCAAATCAAACTTAAGCCTTCACGAAAGAGTAGT
* *
1136558 GAAGCAAAT-AATCTATAAGCCTTTACAGAAA-AGTAGT
1 GAAGCAAATCAAACT-TAAGCCTTCAC-GAAAGAGTAGT
1136595 GAAGCAAATCAA
1 GAAGCAAATCAA
1136607 GATTGTTCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 4 0.09
37 33 0.77
38 6 0.14
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.20
Consensus pattern (37 bp):
GAAGCAAATCAAACTTAAGCCTTCACGAAAGAGTAGT
Found at i:1136947 original size:165 final size:163
Alignment explanation
Indices: 1136605--1137121 Score: 530
Period size: 165 Copynumber: 3.1 Consensus size: 163
1136595 GAAGCAAATC
* * * * * *
1136605 AAGATTGTTCGAGTCCTATACT-CTCTGGAGGAATAGAGAGCAGACACGTTAGTTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCT-TGAACGAATAGGGAGC-GACACGTTTGTTAAAGATTGTT
* * * * ** * * * * *
1136669 CGAGTCTTATACTCTCTGAAGGAATAGAGAACG-ACACGTTAGT-TGAAGATTGTTTGAGTCCTA
64 CGAGTCCTATACTCCCTGAACGAATAGGGAGTGAACCCATT-TTATGAAGATTGTTCGAGTTCTA
* * * ** * *
1136732 TACTCTCTGAATGAATAGGGAGTGGATAC-GTTCATTG
128 TACTCCCTGAACGAATAGGGAG-AGACCCATTTTA-TG
*
1136769 AAGATTGTTCGAGTCTTATACTCCTTGAACAAATAGGGAGCGTACACGTTTGTTAAAGATTGTTC
1 AAGATTGTTCGAGTCTTATACTCCTTGAACGAATAGGGAGCG-ACACGTTTGTTAAAGATTGTTC
*
1136834 GAGTCCTATACTCCCTGAACGAATAGGGAGTGAACCCATTTTATGAAGATTGCTCGAGTTCTATA
65 GAGTCCTATACTCCCTGAACGAATAGGGAGTGAACCCATTTTATGAAGATTGTTCGAGTTCTATA
1136899 CTCCCTGAACGAATAGGGAGAAGACCCATTTTATG
130 CTCCCTGAACGAATAGGGAG-AGACCCATTTTATG
1136934 AAGATTGTTCGAGT-TCTATACTCCTTGAACGAATAGGGAGCGA-ACCAGTTT-TTATAAGATTG
1 AAGATTGTTCGAGTCT-TATACTCCTTGAACGAATAGGGAGCGACA-C-GTTTGTTA-AAGATTG
* * * * *
1136996 TTTGAGTTCTATACTCCCTAAAC-AGATAAGGAGTGAACCCATTTTATGAAGATTTTTCGAGTTC
62 TTCGAGTCCTATACTCCCTGAACGA-ATAGGGAGTGAACCCATTTTATGAAGATTGTTCGAGTTC
* * * *
1137060 TATACTCCTTGAACGAATAGGGAGCGAACCCATTTTTTT
126 TATACTCCCTGAACGAATAGGGAGAG-ACCCATTTTATG
1137099 AAGATTGTTCGAGGTC-TATACTC
1 AAGATTGTTCGA-GTCTTATACTC
1137122 TCTGAAATAA
Statistics
Matches: 302, Mismatches: 38, Indels: 25
0.83 0.10 0.07
Matches are distributed among these distances:
163 2 0.01
164 88 0.29
165 207 0.69
166 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (163 bp):
AAGATTGTTCGAGTCTTATACTCCTTGAACGAATAGGGAGCGACACGTTTGTTAAAGATTGTTCG
AGTCCTATACTCCCTGAACGAATAGGGAGTGAACCCATTTTATGAAGATTGTTCGAGTTCTATAC
TCCCTGAACGAATAGGGAGAGACCCATTTTATG
Found at i:1137137 original size:55 final size:54
Alignment explanation
Indices: 1136605--1137145 Score: 422
Period size: 55 Copynumber: 9.9 Consensus size: 54
1136595 GAAGCAAATC
* * * * * * *
1136605 AAGATTGTTCGAGTCCTATACTCTCTGGAGGAATAGAGAGC-AGACACGTTAGT-TG
1 AAGATTGTTCGAGTTCTATACTC-CTGAACGAATAGGGAGCGA-ACCCATT-TTATG
* * * * * *
1136660 AAGATTGTTCGAG-TCTTATACTCTCTGAAGGAATAGAGAACG-ACACGTTAGT-TG
1 AAGATTGTTCGAGTTC-TATACTC-CTGAACGAATAGGGAGCGAACCCATT-TTATG
* * * * * ** * *
1136714 AAGATTGTTTGAGTCCTATACTCTCTGAATGAATAGGGAGTGGATAC-GTTCATTG
1 AAGATTGTTCGAGTTCTATACTC-CTGAACGAATAGGGAGCGAACCCATTTTA-TG
* * * * *
1136769 AAGATTGTTCGAG-TCTTATACTCCTTGAACAAATAGGGAGCGTACACGTTTGT-TA
1 AAGATTGTTCGAGTTC-TATACTCC-TGAACGAATAGGGAGCGAACCCATTT-TATG
* *
1136824 AAGATTGTTCGAGTCCTATACTCCCTGAACGAATAGGGAGTGAACCCATTTTATG
1 AAGATTGTTCGAGTTCTATACT-CCTGAACGAATAGGGAGCGAACCCATTTTATG
* *
1136879 AAGATTGCTCGAGTTCTATACTCCCTGAACGAATAGGGAG-AAGACCCATTTTATG
1 AAGATTGTTCGAGTTCTATACT-CCTGAACGAATAGGGAGCGA-ACCCATTTTATG
1136934 AAGATTGTTCGAGTTCTATACTCCTTGAACGAATAGGGAGCGAA-CCAGTTTTTAT-
1 AAGATTGTTCGAGTTCTATACTCC-TGAACGAATAGGGAGCGAACCCA--TTTTATG
* * * *
1136989 AAGATTGTTTGAGTTCTATACTCCCTAAAC-AGATAAGGAGTGAACCCATTTTATG
1 AAGATTGTTCGAGTTCTATACT-CCTGAACGA-ATAGGGAGCGAACCCATTTTATG
* * *
1137044 AAGATTTTTCGAGTTCTATACTCCTTGAACGAATAGGGAGCGAACCCATTTTTTT
1 AAGATTGTTCGAGTTCTATACTCC-TGAACGAATAGGGAGCGAACCCATTTTATG
* ** * *
1137099 AAGATTGTTCGAGGTCTATACTCTCTGAAATAAAAGGGAGCGGACCC
1 AAGATTGTTCGAGTTCTATACTC-CTGAACGAATAGGGAGCGAACCC
1137146 GTCCTTCATA
Statistics
Matches: 409, Mismatches: 52, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
54 66 0.16
55 324 0.79
56 19 0.05
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (54 bp):
AAGATTGTTCGAGTTCTATACTCCTGAACGAATAGGGAGCGAACCCATTTTATG
Found at i:1139675 original size:30 final size:31
Alignment explanation
Indices: 1139635--1139694 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1139625 AAATAGATAT
1139635 TTAAAGGGACTAAAATAGCAATAACAAAAAG
1 TTAAAGGGACTAAAATAGCAATAACAAAAAG
* * *
1139666 TTAAA-GGACTAAAATGGTATTAACAAAAA
1 TTAAAGGGACTAAAATAGCAATAACAAAAA
1139695 CCTAATGAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.57, C:0.08, G:0.15, T:0.20
Consensus pattern (31 bp):
TTAAAGGGACTAAAATAGCAATAACAAAAAG
Found at i:1141188 original size:15 final size:16
Alignment explanation
Indices: 1141168--1141200 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1141158 CATGTAAACA
1141168 AATAAAAGTAA-TAAT
1 AATAAAAGTAATTAAT
*
1141183 AATAAAATTAATTAAT
1 AATAAAAGTAATTAAT
1141199 AA
1 AA
1141201 GTAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AATAAAAGTAATTAAT
Found at i:1141226 original size:21 final size:21
Alignment explanation
Indices: 1141180--1141228 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1141170 TAAAAGTAAT
*
1141180 AATAATA-AAATTAATTAATA
1 AATAATATAAATTAATTAAAA
*
1141200 AGTAATATAAATATAA-TAAAA
1 AATAATATAAAT-TAATTAAAA
1141221 AATAATAT
1 AATAATAT
1141229 TATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAATATAAATTAATTAAAA
Found at i:1141769 original size:131 final size:131
Alignment explanation
Indices: 1141520--1141786 Score: 297
Period size: 131 Copynumber: 2.0 Consensus size: 131
1141510 ATCTTTAGGA
* * * * *
1141520 AGGG-TGATAACACGGTTCTTACGCGATGAGGACGGTAGGTTATCTAAGGTTGACGCGGCTCCTA
1 AGGGATGATAACACGGTTCCTACGCGATGAAGACGGTAGGTTATCTAAGGGTGACACGACTCCTA
* * ** * **
1141584 CGTGATGGGGAGGTTTGGTCCGGGGATGACATTATTCCTACGTGATAAAAATGGCAGGCCATCTG
66 CGTGATGAGAAGGTTTGGTCCGGGGATGACACGATTCCTAAGTGATAAAAATGGCAAACCATCTG
1141649 T
131 T
*
1141650 AGGGATGATAACACGGTTCCTACGCGATGAAGACGGCT-GGTTATCTAGGGGTGACACGACTCCT
1 AGGGATGATAACACGGTTCCTACGCGATGAAGACGG-TAGGTTATCTAAGGGTGACACGACTCCT
* * * * * * **
1141714 ACTTGATGAGAAGGTTTGGT-TGATGGATGACACGGTTCTTAAGTGATGAGGATGGCAAACCATC
65 ACGTGATGAGAAGGTTTGGTCCG-GGGATGACACGATTCCTAAGTGATAAAAATGGCAAACCATC
*
1141778 TTT
129 TGT
1141781 AGGGAT
1 AGGGAT
1141787 AATGGTTTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
130 5 0.04
131 106 0.95
132 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (131 bp):
AGGGATGATAACACGGTTCCTACGCGATGAAGACGGTAGGTTATCTAAGGGTGACACGACTCCTA
CGTGATGAGAAGGTTTGGTCCGGGGATGACACGATTCCTAAGTGATAAAAATGGCAAACCATCTG
T
Found at i:1141890 original size:30 final size:29
Alignment explanation
Indices: 1141856--1141943 Score: 113
Period size: 30 Copynumber: 3.0 Consensus size: 29
1141846 GACAAAAATC
* * * *
1141856 GTTTCAAGGGAAACGATCTCAAAGATGTTT
1 GTTTCAAGAGAAACAAACTCAAAGAT-TTG
1141886 GTTTCAAGAGAAACAAACTCAAAGAATTTG
1 GTTTCAAGAGAAACAAACTCAAAG-ATTTG
*
1141916 GTTTAAAGAGAAACAAACTCAAAGATTT
1 GTTTCAAGAGAAACAAACTCAAAGATTT
1141944 TTCTTTGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
29 4 0.08
30 46 0.88
31 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.26
Consensus pattern (29 bp):
GTTTCAAGAGAAACAAACTCAAAGATTTG
Found at i:1141958 original size:29 final size:30
Alignment explanation
Indices: 1141873--1141955 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
1141863 GGGAAACGAT
* *
1141873 CTCAAAGATGTTTGTTTCAAGAGAAACAAA
1 CTCAAAGATTTTTGTTTAAAGAGAAACAAA
* *
1141903 CTCAAAGAATTTGGTTTAAAGAGAAACAAA
1 CTCAAAGATTTTTGTTTAAAGAGAAACAAA
*
1141933 CTCAAAGATTTTTCTTTGAAAGA
1 CTCAAAGATTTTTGTTT-AAAGA
1141956 AACTGTCTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 40 0.89
31 5 0.11
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (30 bp):
CTCAAAGATTTTTGTTTAAAGAGAAACAAA
Found at i:1142431 original size:40 final size:38
Alignment explanation
Indices: 1142366--1142477 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 38
1142356 AAAACTTTTA
*
1142366 TTTTT-AGAAATTGTCTCAAGTGAGACGACACTTTGTT
1 TTTTTAAGAAATTGTCTCAAGCGAGACGACACTTTGTT
* *
1142403 TTTTTAGAGAAAGTTGTCTCAAGCGAGAC-AAAATTTG--
1 TTTTTA-AGAAA-TTGTCTCAAGCGAGACGACACTTTGTT
*
1142440 TTTTTAAGAAAATTGTCTCTAGC--GACGACACTTT-TT
1 TTTTTAAG-AAATTGTCTCAAGCGAGACGACACTTTGTT
1142476 TT
1 TT
1142478 ATTTTTTAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
34 3 0.05
35 5 0.08
36 14 0.23
37 14 0.23
39 11 0.18
40 15 0.24
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.39
Consensus pattern (38 bp):
TTTTTAAGAAATTGTCTCAAGCGAGACGACACTTTGTT
Found at i:1142464 original size:36 final size:36
Alignment explanation
Indices: 1142331--1142469 Score: 111
Period size: 36 Copynumber: 3.7 Consensus size: 36
1142321 CAAAGATTTC
* * **
1142331 TTAAGAAAACTATCTCAAAAGAGACAAAACTTT-TATT
1 TTAAGAAAATTGTCTCAAGCGAGACAAAA-TTTGT-TT
* * * *
1142368 TTTAG-AAATTGTCTCAAGTGAGACGACACTTTGTTTTT
1 TTAAGAAAATTGTCTCAAGCGAGAC-AAAATTTG--TTT
*
1142406 TTAGAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTT
1 TTA-AGAAAATTGTCTCAAGCGAGACAAAATTTGTTT
*
1142443 TTAAGAAAATTGTCTCTAGCGACGACA
1 TTAAGAAAATTGTCTCAAGCGA-GACA
1142470 CTTTTTTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
36 35 0.43
37 16 0.20
38 4 0.05
39 9 0.11
40 17 0.21
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (36 bp):
TTAAGAAAATTGTCTCAAGCGAGACAAAATTTGTTT
Found at i:1142820 original size:4 final size:4
Alignment explanation
Indices: 1142811--1142850 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
1142801 TTCATGTATC
*
1142811 ATGT ATGT ATGT GT-T GATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT ATGT ATGT
1142851 TCTCAATCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 30 0.94
5 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1146346 original size:23 final size:23
Alignment explanation
Indices: 1146320--1146364 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1146310 ATTCAATGCT
1146320 AAACAAT-AATAAATAAAAAAATC
1 AAACAATAAAT-AATAAAAAAATC
* *
1146343 AAACATTAAATGATAAAAAAAT
1 AAACAATAAATAATAAAAAAAT
1146365 ATGATTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (23 bp):
AAACAATAAATAATAAAAAAATC
Found at i:1146805 original size:5 final size:5
Alignment explanation
Indices: 1146795--1146819 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1146785 TTTCGCAAAG
1146795 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
1146820 GATGAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:1147301 original size:30 final size:30
Alignment explanation
Indices: 1147172--1147364 Score: 142
Period size: 30 Copynumber: 6.4 Consensus size: 30
1147162 TTCTAATTAC
* * * *
1147172 AAGGACCAAAATGGAAAAAATAGAAACTTA
1 AAGGACTAAAATAGTAAAAATAGAAATTTA
* * * * *
1147202 ATGGACCAAAATAG-AAAAAGCAAAAACTTA
1 AAGGACTAAAATAGTAAAAA-TAGAAATTTA
* *
1147232 AAGGA-TTAAATAGTAAAAATAGATATTTA
1 AAGGACTAAAATAGTAAAAATAGAAATTTA
* * *
1147261 AAGAGACTAAAATAGCAATAATAGAAAGTTA
1 AAG-GACTAAAATAGTAAAAATAGAAATTTA
* ** * * *
1147292 AAGGACTAAAATGGTATGAACAAAAACTTA
1 AAGGACTAAAATAGTAAAAATAGAAATTTA
1147322 AA-GAGCTAAAATAGTAAAAACT-GAAATTTA
1 AAGGA-CTAAAATAGTAAAAA-TAGAAATTTA
1147352 AAGGACTAAAATA
1 AAGGACTAAAATA
1147365 TGATTAACAT
Statistics
Matches: 127, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
29 22 0.17
30 81 0.64
31 24 0.19
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.20
Consensus pattern (30 bp):
AAGGACTAAAATAGTAAAAATAGAAATTTA
Found at i:1147303 original size:90 final size:90
Alignment explanation
Indices: 1147172--1147364 Score: 221
Period size: 90 Copynumber: 2.1 Consensus size: 90
1147162 TTCTAATTAC
* * * * *
1147172 AAGGACCAAAATGGAAAAAATAGAAACTTAATGGACCAAAATAG-AAAAAGCAAAAACTTAAAG-
1 AAGGACTAAAATAGCAATAATAGAAACTTAAAGGACCAAAATAGTAAAAA-CAAAAACTTAAAGA
* *
1147235 GATTAAATAGTAAAAA-TAGATATTTA
65 GATAAAATAGTAAAAACT-GAAATTTA
* * * **
1147261 AAGAGACTAAAATAGCAATAATAGAAAGTTAAAGGACTAAAATGGTATGAACAAAAACTTAAAGA
1 AAG-GACTAAAATAGCAATAATAGAAACTTAAAGGACCAAAATAGTAAAAACAAAAACTTAAAGA
*
1147326 GCTAAAATAGTAAAAACTGAAATTTA
65 GATAAAATAGTAAAAACTGAAATTTA
1147352 AAGGACTAAAATA
1 AAGGACTAAAATA
1147365 TGATTAACAT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
89 3 0.03
90 56 0.64
91 27 0.31
92 1 0.01
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.20
Consensus pattern (90 bp):
AAGGACTAAAATAGCAATAATAGAAACTTAAAGGACCAAAATAGTAAAAACAAAAACTTAAAGAG
ATAAAATAGTAAAAACTGAAATTTA
Found at i:1151558 original size:19 final size:20
Alignment explanation
Indices: 1151519--1151564 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
1151509 CGATATACCA
1151519 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
1151539 GGTAACAAA-ATGAT-AAACC
1 GGTAA-AAATATGATAAAACC
1151558 GGTAAAA
1 GGTAAAA
1151565 TTAAAAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 10 0.40
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:1153221 original size:15 final size:17
Alignment explanation
Indices: 1153179--1153226 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1153169 TTTTTAACCA
*
1153179 ATATTTATCTAAAATAT
1 ATATTTATATAAAATAT
*
1153196 ATATTTTTATAAAATAT
1 ATATTTATATAAAATAT
1153213 A-ATTATATATAAAA
1 ATATT-TATATAAAA
1153227 AATTAATCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 3 0.11
17 24 0.89
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTATATAAAATAT
Found at i:1154131 original size:15 final size:15
Alignment explanation
Indices: 1154111--1154141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1154101 CAACATATAG
1154111 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1154126 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1154141 A
1 A
1154142 TTTAGAATTA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1155244 original size:15 final size:15
Alignment explanation
Indices: 1155224--1155254 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1155214 TTTCTTCATT
1155224 ACTCTTTACCTTATA
1 ACTCTTTACCTTATA
1155239 ACTCTTTACCTTATA
1 ACTCTTTACCTTATA
1155254 A
1 A
1155255 TATAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
ACTCTTTACCTTATA
Found at i:1155518 original size:2 final size:2
Alignment explanation
Indices: 1155513--1155554 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1155503 TTTTTCATCC
*
1155513 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1155555 CGATCATCCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1157561 original size:35 final size:36
Alignment explanation
Indices: 1157474--1157595 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
1157464 TTATCCTATT
* *
1157474 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
1157509 AACTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATC-ATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
1157546 ATCA-TTTTCAAAGAAACATTTATCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
*
1157581 ACCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
1157596 TTGGTTACCA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
35 35 0.45
36 8 0.10
37 34 0.44
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:1160312 original size:16 final size:16
Alignment explanation
Indices: 1160288--1160321 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1160278 TATCGCCGAC
*
1160288 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1160304 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1160320 CG
1 CG
1160322 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1160788 original size:37 final size:37
Alignment explanation
Indices: 1160729--1160840 Score: 162
Period size: 35 Copynumber: 3.2 Consensus size: 37
1160719 ATCCCATTAT
* *
1160729 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
*
1160765 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
1160801 CA-TTTTCAAAGAAACATTTACCAAAC-TTG-AAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
1160835 CATTTT
1 CATTTT
1160841 AATACTTTCA
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
34 10 0.14
35 27 0.39
36 13 0.19
37 20 0.29
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAAC
Found at i:1161490 original size:28 final size:28
Alignment explanation
Indices: 1161458--1161513 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1161448 CCGAGAGAGA
1161458 GGCTCTCAAGTAGTGGATCAGCGTCTAC
1 GGCTCTCAAGTAGTGGATCAGCGTCTAC
1161486 GGCTCTCAAGTAGTGGATCAGCGTCTAC
1 GGCTCTCAAGTAGTGGATCAGCGTCTAC
1161514 TTGTCTTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.29, T:0.25
Consensus pattern (28 bp):
GGCTCTCAAGTAGTGGATCAGCGTCTAC
Found at i:1161761 original size:20 final size:21
Alignment explanation
Indices: 1161719--1161761 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1161709 GAACCGAGCA
*
1161719 GATGCAATGAACCAGACAACT
1 GATGCAATAAACCAGACAACT
1161740 GATGCAATAAACCAGA-AACT
1 GATGCAATAAACCAGACAACT
1161760 GA
1 GA
1161762 ATTCAGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (21 bp):
GATGCAATAAACCAGACAACT
Found at i:1168431 original size:60 final size:61
Alignment explanation
Indices: 1168255--1168431 Score: 211
Period size: 60 Copynumber: 2.9 Consensus size: 61
1168245 ATGTCCCTAC
* *
1168255 ACTATGACCCTCATTT-TAAATTGGTCCCTAAACTTTTGAACATTCCAATTTCAT-CCTAAA
1 ACTATAACCCTC-TTTCTAAATTAGTCCCTAAACTTTTGAACATTCCAATTTCATCCCTAAA
* * *
1168315 ACTATAACTCC-CATTCTAAATTAGTCCTTAAACTTTTGAACATTCTAATTGT-ATCCCTAAA
1 ACTATAAC-CCTCTTTCTAAATTAGTCCCTAAACTTTTGAACATTCCAATT-TCATCCCTAAA
* * **
1168376 A-TATAACCCTCTTTCTAAATTAATCCCCAAACTTTTGATTATTCCAATTTCATCCC
1 ACTATAACCCTCTTTCTAAATTAGTCCCTAAACTTTTGAACATTCCAATTTCATCCC
1168432 CAAATTCATC
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
59 5 0.05
60 84 0.85
61 10 0.10
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (61 bp):
ACTATAACCCTCTTTCTAAATTAGTCCCTAAACTTTTGAACATTCCAATTTCATCCCTAAA
Found at i:1170066 original size:291 final size:291
Alignment explanation
Indices: 1169535--1170113 Score: 1149
Period size: 291 Copynumber: 2.0 Consensus size: 291
1169525 CCAACAGGCG
1169535 GAGCTACCCAATGGACAGAACGATTGACTTCCACTCTACAGCAAGTCCTCAAAGAAACTTCCCAC
1 GAGCTACCCAATGGACAGAACGATTGACTTCCACTCTACAGCAAGTCCTCAAAGAAACTTCCCAC
1169600 GCTGATGCATTAATTGCCATATGTTTCAATCGTAAACTTTTCTTCCATAATTAAAGGTGACCGAA
66 GCTGATGCATTAATTGCCATATGTTTCAATCGTAAACTTTTCTTCCATAATTAAAGGTGACCGAA
1169665 CAGCGGCTACTGCAAGGATAGTGAATGCACAAACTAAGATAACTATGTGGTAAATGAATTATTAC
131 CAGCGGCTACTGCAAGGATAGTGAATGCACAAACTAAGATAACTATGTGGTAAATGAATTATTAC
*
1169730 TATTTTTTGAATTCGTTCGAGCACCAAGAATGTTAAGGGTATAAGCGTTCAATATCAAATGGTTG
196 TATTTTTTGAATTCGTTCGAGCACCAAGAATGTTAAGGATATAAGCGTTCAATATCAAATGGTTG
1169795 AGAGTTATCTTTAAACATATACTACTTTCTC
261 AGAGTTATCTTTAAACATATACTACTTTCTC
1169826 GAGCTACCCAATGGACAGAACGATTGACTTCCACTCTACAGCAAGTCCTCAAAGAAACTTCCCAC
1 GAGCTACCCAATGGACAGAACGATTGACTTCCACTCTACAGCAAGTCCTCAAAGAAACTTCCCAC
1169891 GCTGATGCATTAATTGCCATATGTTTCAATCGTAAACTTTTCTTCCATAATTAAAGGTGACCGAA
66 GCTGATGCATTAATTGCCATATGTTTCAATCGTAAACTTTTCTTCCATAATTAAAGGTGACCGAA
1169956 CAGCGGCTACTGCAAGGATAGTGAATGCACAAACTAAGATAACTATGTGGTAAATGAATTATTAC
131 CAGCGGCTACTGCAAGGATAGTGAATGCACAAACTAAGATAACTATGTGGTAAATGAATTATTAC
1170021 TATTTTTTGAATTCGTTCGAGCACCAAGAATGTTAAGGATATAAGCGTTCAATATCAAATGGTTG
196 TATTTTTTGAATTCGTTCGAGCACCAAGAATGTTAAGGATATAAGCGTTCAATATCAAATGGTTG
1170086 AGAGTTATCTTTAAACATATACTACTTT
261 AGAGTTATCTTTAAACATATACTACTTT
1170114 GTACTTATCC
Statistics
Matches: 287, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
291 287 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (291 bp):
GAGCTACCCAATGGACAGAACGATTGACTTCCACTCTACAGCAAGTCCTCAAAGAAACTTCCCAC
GCTGATGCATTAATTGCCATATGTTTCAATCGTAAACTTTTCTTCCATAATTAAAGGTGACCGAA
CAGCGGCTACTGCAAGGATAGTGAATGCACAAACTAAGATAACTATGTGGTAAATGAATTATTAC
TATTTTTTGAATTCGTTCGAGCACCAAGAATGTTAAGGATATAAGCGTTCAATATCAAATGGTTG
AGAGTTATCTTTAAACATATACTACTTTCTC
Found at i:1171023 original size:30 final size:28
Alignment explanation
Indices: 1170968--1171023 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 28
1170958 AGTATGATTT
1170968 AAAAAAAATAAAGTTTAGATACTAAAAC
1 AAAAAAAATAAAGTTTAGATACTAAAAC
1170996 AAAACAAAAGTAATAGTTTAG-TACTAAA
1 AAAA-AAAA-TAA-AGTTTAGATACTAAA
1171024 TATGTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 4 0.16
30 10 0.40
31 7 0.28
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (28 bp):
AAAAAAAATAAAGTTTAGATACTAAAAC
Found at i:1171506 original size:22 final size:22
Alignment explanation
Indices: 1171478--1171529 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1171468 TTTTGTCCGG
1171478 ATTTTTATA-TATA-TTATTATTT
1 ATTTTTATATTATATTTA-TA-TT
*
1171500 ATTTTTAAATTATATTTATATT
1 ATTTTTATATTATATTTATATT
1171522 ATTTTTAT
1 ATTTTTAT
1171530 TTTGCAGGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 17 0.65
23 6 0.23
24 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTTATATTATATTTATATT
Found at i:1184566 original size:17 final size:18
Alignment explanation
Indices: 1184544--1184578 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1184534 AATGCTGTTG
*
1184544 GATGTTGTGG-AAATTGA
1 GATGTTATGGAAAATTGA
1184561 GATGTTATGGAAAATTGA
1 GATGTTATGGAAAATTGA
1184579 ATTGTGCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (18 bp):
GATGTTATGGAAAATTGA
Found at i:1186991 original size:520 final size:521
Alignment explanation
Indices: 1185951--1186992 Score: 2077
Period size: 520 Copynumber: 2.0 Consensus size: 521
1185941 TGCTCCTAAA
1185951 TACATCTATATAATCCTATATGAGTTCTTTGACAGTCAATAACTTAAGTGAAAAGGTCTCAAATA
1 TACATCTATATAATCCTATATGAGTTCTTTGACAGTCAATAACTTAAGTGAAAAGGTCTCAAATA
1186016 TGACCTTTTTATGGATTTATCATTTTTCATGATGGACAAATGGTTTCATGATCAAGTAGACTATA
66 TGACCTTTTTATGGATTTATCATTTTTCATGATGGACAAATGGTTTCATGATCAAGTAGACTATA
1186081 ACACAGCTAGGGAATGACATCTTGAGTAAGCTCCGAGAATAATGGAGAGTTCTGCACCCAAAAGA
131 ACACAGCTAGGGAATGACATCTTGAGTAAGCTCCGAGAATAATGGAGAGTTCTGCACCCAAAAGA
1186146 TCGTATGTCTGACGAAGAGCAAAAGAAGATAAGAGATATGAGAGAGAAAATGTCCAAGATGATGG
196 TCGTATGTCTGACGAAGAGCAAAAGAAGATAAGAGATATGAGAGAGAAAATGTCCAAGATGATGG
1186211 ATAAAATAATTGCTTTGGCCAAAGGAAAAGAGACTTCTACAAAAGAAAGGAAAGAGCTCGATGAA
261 ATAAAATAATTGCTTTGGCCAAAGGAAAAGAGACTTCTACAAAAGAAAGGAAAGAGCTCGATGAA
1186276 AATAATCCCACGGTGTCAAATACACAAGGGACAACTTTAGAATAAGATGATCCTAACCAGTCTTA
326 AATAATCCCACGGTGTCAAATACACAAGGGACAACTTTAGAATAAGATGATCCTAACCAGTCTTA
1186341 GAAATCACGCATAATCACCATTCGTATCAACAAGTTGTTTGGAGACACCAAAAAAATGGGGACAA
391 GAAATCACGCATAATCACCATTCGTATCAACAAGTTGTTTGGAGACACCAAAAAAATGGGGACAA
1186406 CTATAAAAGTTAATAAAGATGAAAAGAAGCCATGTAATCAGAACTCGTTGGTATTTGGGAGTATA
456 CTATAAAAGTTAATAAAGATGAAAAGAAGCCATGTAATCAGAACTCGTTGGTATTTGGGAGTATA
1186471 C
521 C
1186472 TACATCTATATAATCCTATATGAGTTCTTTGACAGTCAATAACTTAAGTGAAAAGGTC-CAAATA
1 TACATCTATATAATCCTATATGAGTTCTTTGACAGTCAATAACTTAAGTGAAAAGGTCTCAAATA
1186536 TGACCTTTTTATGGATTTATCATTTTTCATGATGGACAAATGGTTTCATGATCAAGTAGACTATA
66 TGACCTTTTTATGGATTTATCATTTTTCATGATGGACAAATGGTTTCATGATCAAGTAGACTATA
1186601 ACACAGCTAGGGAATGACATCTTGAGTAAGCTCCGAGAATAATGGAGAGTTCTGCACCCAAAAGA
131 ACACAGCTAGGGAATGACATCTTGAGTAAGCTCCGAGAATAATGGAGAGTTCTGCACCCAAAAGA
1186666 TCGTATGTCTGACGAAGAGCAAAAGAAGATAAGAGATATGAGAGAGAAAATGTCCAAGATGATGG
196 TCGTATGTCTGACGAAGAGCAAAAGAAGATAAGAGATATGAGAGAGAAAATGTCCAAGATGATGG
1186731 ATAAAATAATTGCTTTGGCCAAAGGAAAAGAGACTTCTACAAAAGAAAGGAAAGAGCTCGATGAA
261 ATAAAATAATTGCTTTGGCCAAAGGAAAAGAGACTTCTACAAAAGAAAGGAAAGAGCTCGATGAA
1186796 AATAATCCCACGGTGTCAAATACACAAGGGACAACTTTAGAATAAGATGATCCTAACCAGTCTTA
326 AATAATCCCACGGTGTCAAATACACAAGGGACAACTTTAGAATAAGATGATCCTAACCAGTCTTA
1186861 GAAATCACGCATAATCACCATTCGTATCAACAAGTTGTTTGGAGACACCAAAAAAATGGGGACAA
391 GAAATCACGCATAATCACCATTCGTATCAACAAGTTGTTTGGAGACACCAAAAAAATGGGGACAA
1186926 CTATAAAAGTTAATAAAGATGAAAAGAAGCCATGTAATCAGAACTCGTTGGTATTTGGGAGTATA
456 CTATAAAAGTTAATAAAGATGAAAAGAAGCCATGTAATCAGAACTCGTTGGTATTTGGGAGTATA
1186991 C
521 C
1186992 T
1 T
1186993 CCCAACGTCA
Statistics
Matches: 521, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
520 463 0.89
521 58 0.11
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (521 bp):
TACATCTATATAATCCTATATGAGTTCTTTGACAGTCAATAACTTAAGTGAAAAGGTCTCAAATA
TGACCTTTTTATGGATTTATCATTTTTCATGATGGACAAATGGTTTCATGATCAAGTAGACTATA
ACACAGCTAGGGAATGACATCTTGAGTAAGCTCCGAGAATAATGGAGAGTTCTGCACCCAAAAGA
TCGTATGTCTGACGAAGAGCAAAAGAAGATAAGAGATATGAGAGAGAAAATGTCCAAGATGATGG
ATAAAATAATTGCTTTGGCCAAAGGAAAAGAGACTTCTACAAAAGAAAGGAAAGAGCTCGATGAA
AATAATCCCACGGTGTCAAATACACAAGGGACAACTTTAGAATAAGATGATCCTAACCAGTCTTA
GAAATCACGCATAATCACCATTCGTATCAACAAGTTGTTTGGAGACACCAAAAAAATGGGGACAA
CTATAAAAGTTAATAAAGATGAAAAGAAGCCATGTAATCAGAACTCGTTGGTATTTGGGAGTATA
C
Found at i:1190736 original size:129 final size:129
Alignment explanation
Indices: 1190581--1190836 Score: 485
Period size: 129 Copynumber: 2.0 Consensus size: 129
1190571 CATTTTCAAA
*
1190581 ATTGTCTCTATTAAAAGAGTCTGTAAAACTTGAACAAATAAAAGATTTCAGAGAACTGAAATAGA
1 ATTGTCTCTATTAAAAGAGTCAGTAAAACTTGAACAAATAAAAGATTTCAGAGAACTGAAATAGA
*
1190646 AATGTTCCAAAAAGTCTAGCAATTTAATATGCTAGTTGCTTTATTTTGTCTGCATCCACTTAAT
66 AATGTTCCAAAAAGTCTAGCAATTTAATATGCTAGTTGCTTTATTTTGTCTACATCCACTTAAT
1190710 ATTGTCTCTATTAAAAGAGTCAGTAAAACTTGAACAAATAAAAGATTTCAGAGAACTGAAATAGA
1 ATTGTCTCTATTAAAAGAGTCAGTAAAACTTGAACAAATAAAAGATTTCAGAGAACTGAAATAGA
*
1190775 AATGTTCCAAAAAGTCTAGCAATTTAATATGCTAGTTGCTTTATTTTGTCTACGTCCACTTA
66 AATGTTCCAAAAAGTCTAGCAATTTAATATGCTAGTTGCTTTATTTTGTCTACATCCACTTA
1190837 CTATGTCAAG
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 124 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (129 bp):
ATTGTCTCTATTAAAAGAGTCAGTAAAACTTGAACAAATAAAAGATTTCAGAGAACTGAAATAGA
AATGTTCCAAAAAGTCTAGCAATTTAATATGCTAGTTGCTTTATTTTGTCTACATCCACTTAAT
Found at i:1192321 original size:41 final size:42
Alignment explanation
Indices: 1192227--1192326 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
1192217 TAGTAAGTCA
* *
1192227 TTCAGGCCATC-AGTAAGTCTTTCGAGCATGATGCTTAAATCC
1 TTCAGGCCATCTA-TAAGTCTTTCGAGCAAGATGCATAAATCC
* *
1192269 TTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-ATAAATCC
1 TTCAGGCCATCTATAAGTCTTTCGAGCAAGATGCATAAATCC
*
1192310 TTCAAGCCATCTATAAG
1 TTCAGGCCATCTATAAG
1192327 ACCTTCGGGC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 21 0.42
42 28 0.56
43 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (42 bp):
TTCAGGCCATCTATAAGTCTTTCGAGCAAGATGCATAAATCC
Found at i:1192685 original size:259 final size:259
Alignment explanation
Indices: 1192219--1193084 Score: 1090
Period size: 259 Copynumber: 3.3 Consensus size: 259
1192209 TTATTACTTA
* *
1192219 GTAAGTCATTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCTTTCAGACCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
* * ** * *
1192284 AGTCTTTCGAGCAAGATGATAAATCCTTCAAGCCATCTATAAGACCTTCGGGCAGGTTGTTTTCA
66 AGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
* * *
1192349 CATGATTTTCGAAAAATGAGAAAACGATTTCCAAATTTTCTCATTTAAATCTTTTCTAAAAAATG
131 CATGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAAATG
* *
1192414 AAATTATTGAAAAGTAAGAAACTGATTTCCATAGTTTCTTACTTAGTAAACTATTTCCAAAATTG
196 AAATTGTTGAAAAGTAAGAAAGTGATTTCCA-AGTTTCTTACTTAGTAAACTATTTCCAAAATTG
* * * * * * *
1192479 GTAAGTCTTTCAGATCATCACTAAGTATTTCGAGCATAATGATTAAATCCTTTGGGTTATCTATA
1 GTAAGTCTTTCAGACCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
*
1192544 AGCCTTTCGAGAAAGATGATAAGT-CTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
66 AGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
*
1192608 CATGATTTTCGAAAAATGAGAAAACAATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAAATG
131 CATGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAAATG
*
1192673 AAATTGTTGAAAAGTAAGAAAGTGATTTCCAGAGTTTCTTACTTAGTAAACTATTTCCAAAATTA
196 AAATTGTTGAAAAGTAAGAAAGTGATTTCCA-AGTTTCTTACTTAGTAAACTATTTCCAAAATTG
* * * * * *
1192738 GTAAGTCCTTC-GAGCCATCAGTAAGTCTTTCAAGCATGATGGTTAAATCCTACGGGTCTTCTAC
1 GTAAGTCTTTCAGA-CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
**
1192802 AAGCCTTTTAAGCAAGATGATAAGTCCTTCGAGCTATCCATAAGAGCTTCGAGCTATCCATAAGA
65 AAGCCTTTCGAGCAAGATGATAAGTCCTTC--G----------G-G---C---C-ATCCATAAGA
* * * * * *
1192867 CTTTCGGGTAGGATATTTTCACATGATTTTCAAAAAATGAGAAAATGATTTCCAAAGTTACTCAT
110 CCTTCGGGCAGGATGTTTTCACATGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCAT
* *
1192932 TTAAATATTTTCTGAAAAATGAAATTGTTGAAAAGTAAGAAAGTGGTTTCCAAATATTCTTACTT
175 TTAAATATTTTCTGAAAAATGAAATTGTTGAAAAGTAAGAAAGTGATTTCCAAGT-TTCTTACTT
1192997 AGTAAACTATTTCCAAAATTG
239 AGTAAACTATTTCCAAAATTG
* * * * *
1193018 GTGAGTCCTTT-GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCGTTTGGGTCATCTAT
1 GTAAGT-CTTTCAGACCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTAT
1193082 AAG
65 AAG
1193085 TATTTCCCAT
Statistics
Matches: 522, Mismatches: 59, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
258 2 0.00
259 229 0.44
260 81 0.16
262 1 0.00
272 1 0.00
273 1 0.00
276 1 0.00
279 3 0.01
280 199 0.38
281 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (259 bp):
GTAAGTCTTTCAGACCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATA
AGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
CATGATTTTCGAAAAATGAGAAAACGATTTCCAAAGTTTCTCATTTAAATATTTTCTGAAAAATG
AAATTGTTGAAAAGTAAGAAAGTGATTTCCAAGTTTCTTACTTAGTAAACTATTTCCAAAATTG
Found at i:1192872 original size:20 final size:20
Alignment explanation
Indices: 1192828--1192866 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1192818 ATGATAAGTC
1192828 CTTCGAGCTATCCATAAGAG
1 CTTCGAGCTATCCATAAGAG
1192848 CTTCGAGCTATCCATAAGA
1 CTTCGAGCTATCCATAAGA
1192867 CTTTCGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
CTTCGAGCTATCCATAAGAG
Found at i:1195491 original size:179 final size:178
Alignment explanation
Indices: 1195173--1195534 Score: 437
Period size: 179 Copynumber: 2.0 Consensus size: 178
1195163 ATTTATAGAC
*** *
1195173 ACTTTATGCGTGCACCTCGTTGGGCATTCATTATGGAAAAAAGTATCGACACTTATTTAAAAAGT
1 ACTTTATGCGTGCACCTCGTTGGGCATTCATTATGGAAAAAAGTATCGACAAAAATTCAAAAAGT
* * *
1195238 GTCGATACATTATGTTGACCTATTCTCTCATAAAATCGATATATTTATACCGGTTACATTGTAAA
66 GTCGATACATTATGTTGACCTATTCTCTAATAAAACCGATATAATTATACCGGTTACATTGTAAA
*
1195303 TTTACCTATTACATTATAATTATCGATTTCTATGTTTTTGG-GATCGAT
131 TTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGTG-TCGAT
* * * *
1195351 ACTTTATGCGTGCACCTCGTTTTGGG-ATTCATTTTGGGCAATAAGTATCGACAAAAATTCCACA
1 ACTTTATGCGTGCACCTCG--TTGGGCATTCATTAT-GGAAAAAAGTATCGACAAAAATT-CAAA
* * * * * * *
1195415 AA-TGTCGATACATTATGCTT-ACCTGTTTTGTAAT-TAACCGGTATAATTATACCTGTTATATT
62 AAGTGTCGATACATTATG-TTGACCTATTCTCTAATAAAACCGATATAATTATACCGGTTACATT
* * *
1195477 GTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTTGGTGTCGAT
126 GTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGTGTCGAT
1195530 ACTTT
1 ACTTT
1195535 TATAAAATGT
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
178 19 0.12
179 82 0.53
180 49 0.31
181 6 0.04
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (178 bp):
ACTTTATGCGTGCACCTCGTTGGGCATTCATTATGGAAAAAAGTATCGACAAAAATTCAAAAAGT
GTCGATACATTATGTTGACCTATTCTCTAATAAAACCGATATAATTATACCGGTTACATTGTAAA
TTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGTGTCGAT
Found at i:1198299 original size:19 final size:19
Alignment explanation
Indices: 1198275--1198318 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1198265 ATTCACATAT
1198275 AAAATTATAAATCGTATAC
1 AAAATTATAAATCGTATAC
**
1198294 AAAATTATGTATCGTATAC
1 AAAATTATAAATCGTATAC
1198313 AAAATT
1 AAAATT
1198319 TCCCCTACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Found at i:1200573 original size:198 final size:199
Alignment explanation
Indices: 1199902--1201400 Score: 1867
Period size: 200 Copynumber: 7.5 Consensus size: 199
1199892 AAATATTGAT
* * * * *
1199902 ACAAATTTAAAAAGTGTCGATAC-TTGATGTAGACCTATTTTCTCATAAAATCGATAAATTTATA
1 ACAAATTTAAAAAGTGTCGATACATT-ATGTAGACCTATTTTCTAAT-TAACCGATATATTTCTA
* * *
1199966 CTGGTTACATTGTTAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATA
64 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
1200031 CAATTTTAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGT
129 CAATTTTAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGT
1200096 ATCGAC
194 ATCGAC
* * * *
1200102 ACAAATTTAAAAAAGTGTTGATACATTATGTAAACCTATTTTCAAATTAACCGGTATATTTCTAC
1 ACAAATTT-AAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTAC
* * * * * *
1200167 TGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGATATTTTTTGGATGGATAC
65 CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC
* *
1200232 ACTTTTAAATGTATAGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGTA
130 AATTTTAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGTA
1200297 TCGAC
195 TCGAC
* * * * *
1200302 ATAAATTTTAAAAAGTGTCGATACATTATTTATACCAATTTTCTAATTAACCGGTATATTTCTAC
1 ACAAA-TTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTAC
* * *
1200367 CGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTCAATGTTTTTAGGATCGATAC
65 CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC
* * * * *
1200432 AATTTTAACTGTATCGACACTTTATGCGTGTACCTC-GTTGGTCATTCATTCTGGTCAAAACGTA
130 AATTTTAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGTA
1200496 TCGAC
195 TCGAC
*
1200501 ACAAATTTTAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACC-AGTATATTTCTAC
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGA-TATATTTCTAC
* * *
1200565 CAGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTTGGATCGATAC
65 CGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC
** * * * *
1200630 AATTTTATCTGTATCGACACTTTATGT-GTGCACCTC-GTTGGGCATTCATTCTCGTCAAAACGT
130 AATTTTAAATGTATCGACACTTTAT-TCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGT
1200693 ATCGAC
194 ATCGAC
*
1200699 ACAAATTTAAAAGGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTACC
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTACC
* * * *
1200764 GGTTATATTAG-AAATTTACCTATTATATTATAATTATTGGTTTCGATGTTTTTGGGATTGATAC
66 GGTTACATT-GTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC
** * * * *
1200828 TTTTTATAAATGTATCGACACTTTATTCGTGCACCTTGGTTGGTCATTTAATCTGGACAAAAAAT
130 AATTT-TAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGT
1200893 ATCGAC
194 ATCGAC
* * *
1200899 AC-AATTTAAAAAGTGTCGATATATTATGCAGACCTATTTTCTAATTAACCGATATATATCTACC
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTACC
** * * *
1200963 AATTACATTGGAAATTTACCTATTACGTTATAATTATCTGATTT-GATGTTTTTGGGATCGATAC
66 GGTTACATTGTAAATTTACCTATTACATTATAATTATC-GGTTTCGATGTTTTTGGGATCGATAC
** * * *
1201027 TTTTTATAAATGTATCAACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGATAAAGAGT
130 AATTT-TAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGT
1201092 ATCGAC
194 ATCGAC
* * * * ** **
1201098 ACAATTTTCAAAAGT-TCGATACATTATGTTGACCTATTCTC-ACAGAAAACCGATATATTTAGA
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTA-A-TTAACCGATATATTTCTA
* ** * * *
1201161 TCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGA
64 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
* * ** * * *
1201226 C-TTTTTATATATGTATCGACACTATATGT-GTGCACC-CATTTTGGGCATTCATTCTAGACAAC
129 CAATTTTA-A-ATGTATCGACACTTTAT-TCGTGCACCTC-GGTTGGTCATTCATTCTGGACAAA
*
1201288 AAGAATCGAC
190 AAGTATCGAC
* * * * *
1201298 AC-AATTTAAAAAGTGTAGATACATTATATTGACC-AGTTTTCTAATTAAACCGGTATATATCTA
1 ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTA-TTTTCTAATT-AACCGATATATTTCTA
* *
1201361 CCGGTTACATTGGAAATTTACCTATTACGTTATAATTATC
64 CCGGTTACATTGTAAATTTACCTATTACATTATAATTATC
1201401 TCAATTATTT
Statistics
Matches: 1136, Mismatches: 139, Indels: 48
0.86 0.11 0.04
Matches are distributed among these distances:
198 302 0.27
199 280 0.25
200 516 0.45
201 36 0.03
202 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
ACAAATTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCGATATATTTCTACC
GGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACA
ATTTTAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTGGACAAAAAGTAT
CGAC
Found at i:1204064 original size:90 final size:91
Alignment explanation
Indices: 1203958--1204126 Score: 295
Period size: 92 Copynumber: 1.9 Consensus size: 91
1203948 ATTTAATTTC
* *
1203958 AATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGATTAGGGTAACT
1 AATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAAACCCTAATATGATTAGGGTAACT
1204022 TGGATATAAAAGGATTACTAAATTCT
66 TGGATATAAAAGGATTACTAAATTCT
1204048 AATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAAAACCCTAATATGATTAGGGTAAC
1 AATTAATTAAATATAGATTTAATTAATTTGAAAAAAT-AAAAAACCCTAATATGATTAGGGTAAC
*
1204113 TTGGCTATAAAAGG
65 TTGGATATAAAAGG
1204127 GTGGGTTAGG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
90 36 0.49
92 38 0.51
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (91 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAAAAATAAAAAACCCTAATATGATTAGGGTAACT
TGGATATAAAAGGATTACTAAATTCT
Found at i:1210816 original size:90 final size:91
Alignment explanation
Indices: 1210695--1210873 Score: 306
Period size: 90 Copynumber: 2.0 Consensus size: 91
1210685 TAATCCCGAA
* * *
1210695 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
1210759 TTAGGGTAACTTGGATATAAAAGGAT
66 TTAGGGTAACTTGGATATAAAAGGAT
*
1210785 TATTAAATTCCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
*
1210850 TTAGGGTAACTTGGCTATAAAAGG
66 TTAGGGTAACTTGGATATAAAAGG
1210874 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 45 0.54
91 38 0.46
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (91 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGA
TTAGGGTAACTTGGATATAAAAGGAT
Found at i:1212408 original size:6 final size:6
Alignment explanation
Indices: 1212397--1212458 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
1212387 ACTTGTTTGG
* * *
1212397 ATCATC ATCATC ATCATC ATCATC ATCATC ATCTTC ATCTTC ATCTTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
* *
1212445 ATCGTC ATCTTC AT
1 ATCATC ATCATC AT
1212459 TGACCGCTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.26, C:0.32, G:0.02, T:0.40
Consensus pattern (6 bp):
ATCATC
Found at i:1212414 original size:12 final size:12
Alignment explanation
Indices: 1212397--1212458 Score: 88
Period size: 12 Copynumber: 5.2 Consensus size: 12
1212387 ACTTGTTTGG
*
1212397 ATCATCATCATC
1 ATCATCATCTTC
*
1212409 ATCATCATCATC
1 ATCATCATCTTC
1212421 ATCATCATCTTC
1 ATCATCATCTTC
*
1212433 ATCTTCATCTTC
1 ATCATCATCTTC
*
1212445 ATCGTCATCTTC
1 ATCATCATCTTC
1212457 AT
1 AT
1212459 TGACCGCTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.26, C:0.32, G:0.02, T:0.40
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1214466 original size:201 final size:200
Alignment explanation
Indices: 1213928--1214728 Score: 1275
Period size: 200 Copynumber: 4.0 Consensus size: 200
1213918 ACACATGAAA
1213928 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
1 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
* * *
1213993 TCGATACATTATGTAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTGAAAAA
66 TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCAGTTACATTGAAAAA
* * * *
1214058 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGTGATTGATACGTTTTATAAATGTATC
131 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGTATC
1214123 GACAC
196 GACAC
* *
1214128 TTTATGCGTGCACCTCGTTAGGCATTCATCCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
1 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
*
1214193 TCGATACATTATGTAGACCTATTCTCACATAAAACCGATATATTTATACCAGTTACATTGAAAAA
66 TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCAGTTACATTGAAAAA
* *
1214258 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATTGAGACTTTTTATAAATGTAGC
131 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGTATC
1214323 GACAC
196 GACAC
* * * * * *
1214328 TTTATGCGTGCACCTAGTTTGGGCATTTATTCTTGACAAAAAGTATCGACGCAAATTTCAAAAGT
1 TTTATGCGTGCACCTCG-TTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGT
* *
1214393 GTCGATACATTATGTTA-ACCTATTGTCACATAAAACCGGTATATTTATACCGGTTACATT-ACA
65 GTCGATACATTATG-TAGACCTATTCTCACATAAAACCGGTATATTTATACCAGTTACATTGA-A
1214456 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGT
128 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGT
1214521 -TCGACAC
193 ATCGACAC
* * * *
1214528 TTTATGTGTGCACCCCTTTTGGGCATTCATTCTGGACAAAAAGTATCAACACAAATTCCACAAGT
1 TTTATGCGTGCACCTC-GTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGT
* * * * *
1214593 GTCGATACATTATGTACACCTATTCTCTCATAAAATCGGTATATTTATACCAGTTAGATTGACAA
65 GTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCAGTTACATTGAAAA
*
1214658 ATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATGTAT
130 ATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGTAT
1214723 CGACAC
195 CGACAC
1214729 ATATGTTTAC
Statistics
Matches: 554, Mismatches: 40, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
199 2 0.00
200 383 0.69
201 167 0.30
202 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (200 bp):
TTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCAGTTACATTGAAAAA
TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGTATC
GACAC
Found at i:1214688 original size:401 final size:400
Alignment explanation
Indices: 1213928--1214728 Score: 1293
Period size: 401 Copynumber: 2.0 Consensus size: 400
1213918 ACACATGAAA
* *
1213928 TTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCACAAGTG
1 TTTATGCGTGCACCTAGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCAAAAGTG
* *
1213993 TCGATACATTATGTAGACCTATTCTCTCATAAAACTGGTATATTTATACCGGTTACATTGAAAAA
66 TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTGAAAAA
* * *
1214058 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGTGATTGATACGTTTTATAAATGTATC
131 TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACGTTTTATAAATGTATC
* *
1214123 GACACTTTATGCGTGCACCTCGTTAGGCATTCATCCTGGACAAAAAGTATCGACACAAATTCCAC
196 GACACTTTATGCGTGCACCCCGTTAGGCATTCATCCTGGACAAAAAGTATCAACACAAATTCCAC
*
1214188 AAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATATATTTATACCAGTTACATTG
261 AAGTGTCGATACATTATGTACACCTATTCTCACATAAAACCGATATATTTATACCAGTTACATTG
*
1214253 AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATTGAGACTTTTTATAAAT
326 AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAAT
1214318 GTAGCGACAC
391 GTAGCGACAC
* * * *
1214328 TTTATGCGTGCACCTAGTTTGGGCATTTATTCTTGACAAAAAGTATCGACGCAAATTTCAAAAGT
1 TTTATGCGTGCACCTAG-TTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCAAAAGT
*
1214393 GTCGATACATTATGTTA-ACCTATTGTCACATAAAACCGGTATATTTATACCGGTTACATT-ACA
65 GTCGATACATTATG-TAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTGA-A
*
1214456 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAATGT
128 AAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACGTTTTATAAATGT
* * * *
1214521 -TCGACACTTTATGTGTGCACCCCTTTTGGGCATTCATTCTGGACAAAAAGTATCAACACAAATT
193 ATCGACACTTTATGCGTGCACCCC-GTTAGGCATTCATCCTGGACAAAAAGTATCAACACAAATT
* * * *
1214585 CCACAAGTGTCGATACATTATGTACACCTATTCTCTCATAAAATCGGTATATTTATACCAGTTAG
257 CCACAAGTGTCGATACATTATGTACACCTATTCTCACATAAAACCGATATATTTATACCAGTTAC
* *
1214650 ATTGACAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTTAT
322 ATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTAT
*
1214715 AAATGTATCGACAC
387 AAATGTAGCGACAC
1214729 ATATGTTTAC
Statistics
Matches: 369, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
400 38 0.10
401 329 0.89
402 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (400 bp):
TTTATGCGTGCACCTAGTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTCCAAAAGTG
TCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACATTGAAAAA
TTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACGTTTTATAAATGTATC
GACACTTTATGCGTGCACCCCGTTAGGCATTCATCCTGGACAAAAAGTATCAACACAAATTCCAC
AAGTGTCGATACATTATGTACACCTATTCTCACATAAAACCGATATATTTATACCAGTTACATTG
AAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAGACTTTTTATAAAT
GTAGCGACAC
Found at i:1215201 original size:19 final size:19
Alignment explanation
Indices: 1215176--1215224 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1215166 TTACATTCAC
1215176 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
* *
1215195 CTACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
1215214 ATACAAAATTA
1 ATACAAAATTA
1215225 ACCCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:1216774 original size:18 final size:18
Alignment explanation
Indices: 1216751--1216807 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
1216741 TCCCCCTTAT
1216751 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
1216769 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
* *
1216787 TTCCTCAATCTTTTTTTC
1 TTCCTCCATCTTTTCTTC
1216805 TTC
1 TTC
1216808 ATATTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:1219773 original size:182 final size:182
Alignment explanation
Indices: 1219456--1220117 Score: 983
Period size: 182 Copynumber: 3.7 Consensus size: 182
1219446 TTATTACGCG
* *
1219456 TACTTAT--TAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTCG
1 TACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTGGTCATTTCG
*
1219519 AGACCGATTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
66 AGACCGATTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* *
1219584 AACACTTTATAGGCGCTATTACTGCTTGTCTTTTAAATTCCAAAAGTGTCGA
131 GACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGA
* * * *
1219636 TACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATTTTG
1 TACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTGGTCATTTCG
* * * *
1219701 AGACCGATTTTATCATAATTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAGTATC
66 AGACCGATTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* *
1219766 GACACTTTATTGGCGCTATTACTACTTCTCTTTTAAATTCCAAAAGTGTCGA
131 GACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGA
* * *
1219818 TACTTATAATAAAGTATCAACACTTTCAACATATCCGATAGCACTTTACCGGTTTGGTCATTTTG
1 TACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTGGTCATTTCG
* * * *
1219883 AGATCGGTTTTATCATATTTTTACCTATTATATTGTTATGGGTCGATACATTTTTAAAAAGTATC
66 AGACCGATTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* *
1219948 GACACTTTATTA-GCTCTATTATTGCTTCTCTTTTAAATTCCAAAAGTGTC--
131 GACACTTTA-TAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGA
* * *
1219998 TGCTTATATTAAAGTATCGACACTTTCAACATATTCGATAGCGCTTTACCGGTTTGGTCATTTCG
1 TACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTGGTCATTTCG
* * * * * *
1220063 AGACTGGTTTTGTCATATTTTTACTTGTTATATTGCTATGGATCGATACATTTTT
66 AGACCGATTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTT
1220118 TATTTGTATC
Statistics
Matches: 438, Mismatches: 41, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
180 114 0.26
182 323 0.74
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
TACTTATAATAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTGGTCATTTCG
AGACCGATTTTATCATATTTTTACCTATTATATTGTTATGGATCGATACATTTTTATAAAGTATC
GACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGA
Found at i:1223660 original size:26 final size:26
Alignment explanation
Indices: 1223606--1223695 Score: 117
Period size: 26 Copynumber: 3.3 Consensus size: 26
1223596 CATGGCTCTG
* *
1223606 ATATGATAATATATATAATAATTTCAAAA
1 ATAT-ATAATATATATAGT--TTTTAAAA
1223635 ATATATAATATATATAGTTTTTAAAA
1 ATATATAATATATATAGTTTTTAAAA
* *
1223661 ATATATAGTATATATAGTTTTTTAAA
1 ATATATAATATATATAGTTTTTAAAA
1223687 ATATATAAT
1 ATATATAAT
1223696 TTCAAAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 39 0.70
28 13 0.23
29 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATATAATATATATAGTTTTTAAAA
Found at i:1223746 original size:40 final size:41
Alignment explanation
Indices: 1223644--1223753 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 41
1223634 AATATATAAT
*
1223644 ATATATAGTTTTTAAAAATATATAGTATATATAGTTTTTTAAA
1 ATATATA-TTTTT-AAAATATATAATATATATAGTTTTTTAAA
* *
1223687 ATATATAATTTCAAAATATATAATATATATAG-TTTTTAAA
1 ATATATATTTTTAAAATATATAATATATATAGTTTTTTAAA
*
1223727 AT-TATTTTTTTAAATATATATAATATA
1 ATATATATTTTTAAA-ATATATAATATA
1223754 GTTATTGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 9 0.15
40 22 0.37
41 19 0.32
42 3 0.05
43 7 0.12
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (41 bp):
ATATATATTTTTAAAATATATAATATATATAGTTTTTTAAA
Found at i:1223784 original size:40 final size:37
Alignment explanation
Indices: 1223652--1223788 Score: 132
Period size: 38 Copynumber: 3.5 Consensus size: 37
1223642 ATATATATAG
1223652 TTTTTAAAAATATATAGTATATATAGTTTTTTAAAATATA
1 TTTTTAAAAATATATA-TATATATAG-TTTTTAAAA-ATA
* * *
1223692 TAATTTCAAAATATATAATATATATAGTTTTTAAAATTA
1 T-TTTTAAAAATATAT-ATATATATAGTTTTTAAAAATA
** *
1223731 TTTTTTTAAATATATATA-ATATAGTTATTGAAAACATA
1 TTTTTAAAAATATATATATATATAGTT-TTTAAAA-ATA
* *
1223769 TTTTTGAAAACATATATATA
1 TTTTTAAAAATATATATATA
1223789 GCTTTTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
36 8 0.10
37 9 0.11
38 28 0.35
39 4 0.05
40 10 0.12
41 21 0.26
42 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTTTAAAAATATATATATATATAGTTTTTAAAAATA
Found at i:1223881 original size:7 final size:7
Alignment explanation
Indices: 1223871--1223926 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
1223861 ATAGTATATG
1223871 TATTATT
1 TATTATT
1223878 TATTATT
1 TATTATT
1223885 T-TTATT
1 TATTATT
1223891 T-TATATT
1 TAT-TATT
1223898 TATTA--
1 TATTATT
1223903 TATTACTT
1 TATTA-TT
1223911 TATTATT
1 TATTATT
1223918 TATTTATT
1 TA-TTATT
1223926 T
1 T
1223927 GTTTAACTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.12
6 7 0.16
7 19 0.44
8 12 0.28
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:1223895 original size:27 final size:30
Alignment explanation
Indices: 1223865--1223922 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 30
1223855 ATAAATATAG
1223865 TATATGTATTAT-TTA-TTATT-TTTATTT
1 TATATGTATTATATTACTTATTATTTATTT
*
1223892 TATATTTATTATATTACTTTATTATTTATTT
1 TATATGTATTATATTAC-TTATTATTTATTT
1223923 ATTTGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 11 0.42
28 3 0.12
30 5 0.19
31 7 0.27
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (30 bp):
TATATGTATTATATTACTTATTATTTATTT
Found at i:1223899 original size:20 final size:21
Alignment explanation
Indices: 1223871--1223926 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1223861 ATAGTATATG
*
1223871 TATTATTTATTATTTTTATTT
1 TATTATTTATTATTTTTACTT
*
1223892 TA-TATTTATTA-TATTACTT
1 TATTATTTATTATTTTTACTT
1223911 TATTATTTATTTATTT
1 TATTATTTA-TTATTT
1223927 GTTTAACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.28
20 15 0.52
21 5 0.17
22 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTATTTATTATTTTTACTT
Found at i:1223901 original size:24 final size:23
Alignment explanation
Indices: 1223873--1223926 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1223863 AGTATATGTA
*
1223873 TTATTTATTATTTTTATT-TTATAT
1 TTATTTATTA-CTTTATTATT-TAT
1223897 TTATTATATTACTTTATTATTTAT
1 TTATT-TATTACTTTATTATTTAT
1223921 TTATTT
1 TTATTT
1223927 GTTTAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 19 0.70
25 7 0.26
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTTATTACTTTATTATTTAT
Found at i:1225081 original size:20 final size:21
Alignment explanation
Indices: 1225056--1225094 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1225046 AATTTATTTT
*
1225056 TTTAATA-TTTTTTCTTTTAA
1 TTTAATACCTTTTTCTTTTAA
1225076 TTTAATACCTTTTTCTTTT
1 TTTAATACCTTTTTCTTTT
1225095 GTTTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATACCTTTTTCTTTTAA
Found at i:1225100 original size:21 final size:20
Alignment explanation
Indices: 1225055--1225100 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1225045 CAATTTATTT
*
1225055 TTTTAATATTTTTTCTTTTA
1 TTTTAATACTTTTTCTTTTA
* *
1225075 ATTTAATACCTTTTTCTTTTG
1 TTTTAATA-CTTTTTCTTTTA
1225096 TTTTA
1 TTTTA
1225101 TTTAACATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTAATACTTTTTCTTTTA
Found at i:1226111 original size:17 final size:16
Alignment explanation
Indices: 1226089--1226126 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
1226079 TGGGGTAGGA
1226089 ATTTTTTTATTTCTATT
1 ATTTTTTTATTT-TATT
1226106 ATTTTTTTATTTTATT
1 ATTTTTTTATTTTATT
1226122 -TTTTT
1 ATTTTT
1226127 ACTAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTTTATTTTATT
Found at i:1228350 original size:19 final size:17
Alignment explanation
Indices: 1228326--1228367 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1228316 TCTTGCATCG
1228326 TGCATTTTTGCATATTTTT
1 TGCATTTTT-CAT-TTTTT
1228345 TGCATTTTTCATTTTTT
1 TGCATTTTTCATTTTTT
*
1228362 TACATT
1 TGCATT
1228368 CAAATTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 3 0.14
19 9 0.41
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.64
Consensus pattern (17 bp):
TGCATTTTTCATTTTTT
Found at i:1228804 original size:24 final size:24
Alignment explanation
Indices: 1228740--1228807 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1228730 TCAAGGGGAC
*
1228740 TCATCTGCTACAAAAGAACAAGCT
1 TCATCTGCTACAAAAGCACAAGCT
* **
1228764 TCATCTACTACAAAAGCACAATTT
1 TCATCTGCTACAAAAGCACAAGCT
*
1228788 TCATCTGCTGCAAAAGCACA
1 TCATCTGCTACAAAAGCACA
1228808 TGCCTTTGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (24 bp):
TCATCTGCTACAAAAGCACAAGCT
Found at i:1237377 original size:14 final size:14
Alignment explanation
Indices: 1237358--1237386 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1237348 ATAGTATGAT
1237358 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1237372 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1237386 T
1 T
1237387 AATATATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1237406 original size:30 final size:32
Alignment explanation
Indices: 1237370--1237489 Score: 87
Period size: 30 Copynumber: 3.9 Consensus size: 32
1237360 TTTGAAAACA
1237370 TATTTTTGAAAACATATA-AT-ATATAGTTTT
1 TATTTTTGAAAACATATATATAATATAGTTTT
***
1237400 TATTTTTTTGAACATATATATAATATAG----
1 TATTTTTGAAAACATATATATAATATAGTTTT
* * **
1237428 --TTTTTGAAAACATATAATATAGTTTTTAAATTT
1 TATTTTTGAAAACATAT-ATATA--ATATAGTTTT
1237461 T-TTTTTGAAAACATATATATAATATAGTT
1 TATTTTTGAAAACATATATATAATATAGTT
1237490 CTTGAAAACA
Statistics
Matches: 67, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
26 12 0.18
27 5 0.07
29 3 0.04
30 15 0.22
31 6 0.09
32 6 0.09
33 5 0.07
34 15 0.22
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (32 bp):
TATTTTTGAAAACATATATATAATATAGTTTT
Found at i:1237435 original size:56 final size:57
Alignment explanation
Indices: 1237372--1237502 Score: 187
Period size: 60 Copynumber: 2.3 Consensus size: 57
1237362 TGAAAACATA
1237372 TTTTTGAAAACATATAATATATAGTTTTT-A-TTTTTTTG-AACATATATATAATATAG
1 TTTTTGAAAACATAT-A-ATATAGTTTTTAATTTTTTTTGAAACATATATATAATATAG
1237428 TTTTTGAAAACATATAATATAGTTTTTAAATTTTTTTTTGAAAACATATATATAATATAG
1 TTTTTGAAAACATATAATATAGTTTTT-AA-TTTTTTTTG-AAACATATATATAATATAG
*
1237488 TTCTTGAAAACATAT
1 TTTTTGAAAACATAT
1237503 TTTTGAAAAC
Statistics
Matches: 68, Mismatches: 1, Indels: 8
0.88 0.01 0.10
Matches are distributed among these distances:
54 11 0.16
55 1 0.01
56 16 0.24
58 8 0.12
60 32 0.47
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (57 bp):
TTTTTGAAAACATATAATATAGTTTTTAATTTTTTTTGAAACATATATATAATATAG
Found at i:1237439 original size:26 final size:26
Alignment explanation
Indices: 1237410--1237502 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 26
1237400 TATTTTTTTG
1237410 AACATATATATAATATAGTTTTTGAA
1 AACATATATATAATATAGTTTTTGAA
* **
1237436 AACATATAATATAGTTTTTAAATTTTTTTTTGAA
1 AACATAT-ATATA------ATA-TAGTTTTTGAA
*
1237470 AACATATATATAATATAGTTCTTGAA
1 AACATATATATAATATAGTTTTTGAA
1237496 AACATAT
1 AACATAT
1237503 TTTTGAAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
26 22 0.42
27 7 0.13
33 7 0.13
34 16 0.31
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (26 bp):
AACATATATATAATATAGTTTTTGAA
Found at i:1237514 original size:40 final size:38
Alignment explanation
Indices: 1237428--1237576 Score: 120
Period size: 34 Copynumber: 4.0 Consensus size: 38
1237418 TATAATATAG
* ** *
1237428 TTTTTGAAAAC---ATATAATATAGTTTT-TAAATTTT
1 TTTTTGAAAACTATATATAATATAGTTTTGAAAACATA
1237462 TTTTTGAAAACATATATATAATATAGTTCTTGAAAACATA
1 TTTTTGAAAAC-TATATATAATATAGTT-TTGAAAACATA
*
1237502 TTTTTGAAAAC---ATAT-ATATAGCTTTTAAAAACA-A
1 TTTTTGAAAACTATATATAATATAG-TTTTGAAAACATA
*
1237536 TTTTTGAAAACGTATATA-ATATATAATTTTTGAAAACATA
1 TTTTTGAAAAC-TATATATA-ATAT-AGTTTTGAAAACATA
1237576 T
1 T
1237577 CATAGTTTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
34 23 0.25
35 14 0.15
36 6 0.06
38 16 0.17
39 16 0.17
40 18 0.19
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (38 bp):
TTTTTGAAAACTATATATAATATAGTTTTGAAAACATA
Found at i:1237540 original size:74 final size:74
Alignment explanation
Indices: 1237428--1237576 Score: 194
Period size: 74 Copynumber: 2.0 Consensus size: 74
1237418 TATAATATAG
* **** *
1237428 TTTTTGAAAACATATAATATAGTTTTTAAATTTTTTTTTGAAAACATATAT-ATAATATAGTTCT
1 TTTTTGAAAACATATAATATAGTTTTAAAAACAATTTTTGAAAACATATATAAT-ATATAATTCT
1237492 TGAAAACATA
65 TGAAAACATA
* *
1237502 TTTTTGAAAACATAT-ATATAGCTTTTAAAAACAATTTTTGAAAACGTATATAATATATAATTTT
1 TTTTTGAAAACATATAATATAG-TTTTAAAAACAATTTTTGAAAACATATATAATATATAATTCT
1237566 TGAAAACATA
65 TGAAAACATA
1237576 T
1 T
1237577 CATAGTTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
73 6 0.09
74 57 0.88
75 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (74 bp):
TTTTTGAAAACATATAATATAGTTTTAAAAACAATTTTTGAAAACATATATAATATATAATTCTT
GAAAACATA
Found at i:1237628 original size:18 final size:17
Alignment explanation
Indices: 1237600--1237634 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1237590 ATAAATATAG
*
1237600 TATATGTATTATTTATT
1 TATATGTATTACTTATT
1237617 TATATAGTATTACTTATT
1 TATAT-GTATTACTTATT
1237635 ATTTTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TATATGTATTACTTATT
Found at i:1237785 original size:34 final size:34
Alignment explanation
Indices: 1237741--1237824 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 34
1237731 AACTAAACAA
*
1237741 GTAGGTCTGATCCAACAAGCAAGCCCGACTAGGG
1 GTAGGCCTGATCCAACAAGCAAGCCCGACTAGGG
* *
1237775 GTAGGCCTGATCCAGCAAGCAAGTCCGACTAGGG
1 GTAGGCCTGATCCAACAAGCAAGCCCGACTAGGG
*
1237809 GTAGGCCTGACCCAAC
1 GTAGGCCTGATCCAAC
1237825 CCAATAAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.27, C:0.29, G:0.30, T:0.14
Consensus pattern (34 bp):
GTAGGCCTGATCCAACAAGCAAGCCCGACTAGGG
Found at i:1238160 original size:11 final size:11
Alignment explanation
Indices: 1238141--1238174 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1238131 TAGCAAGCAG
1238141 CCAAGCAAAAA
1 CCAAGCAAAAA
*
1238152 CCGAGCAAAAAA
1 CCAAGC-AAAAA
1238164 CCAAGCAAAAA
1 CCAAGCAAAAA
1238175 TATTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.62, C:0.26, G:0.12, T:0.00
Consensus pattern (11 bp):
CCAAGCAAAAA
Found at i:1238162 original size:12 final size:12
Alignment explanation
Indices: 1238141--1238174 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1238131 TAGCAAGCAG
1238141 CCAAGC-AAAAA
1 CCAAGCAAAAAA
*
1238152 CCGAGCAAAAAA
1 CCAAGCAAAAAA
1238164 CCAAGCAAAAA
1 CCAAGCAAAAA
1238175 TATTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.62, C:0.26, G:0.12, T:0.00
Consensus pattern (12 bp):
CCAAGCAAAAAA
Found at i:1238877 original size:21 final size:22
Alignment explanation
Indices: 1238837--1238883 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
1238827 TTAATCTTTT
* *
1238837 TTTAATATTTGTTTTCTTTTAA
1 TTTAATACTTGTTTTATTTTAA
*
1238859 TTTAATACTT-TTTTATTTTAT
1 TTTAATACTTGTTTTATTTTAA
1238880 TTTA
1 TTTA
1238884 TTTAACGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTAATACTTGTTTTATTTTAA
Found at i:1245469 original size:17 final size:18
Alignment explanation
Indices: 1245441--1245474 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1245431 GTTTGACGTA
1245441 TTTATAAAAATATAATTT
1 TTTATAAAAATATAATTT
1245459 TTTAT-AAAATATAATT
1 TTTATAAAAATATAATT
1245475 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATAAAAATATAATTT
Found at i:1245481 original size:15 final size:16
Alignment explanation
Indices: 1245440--1245487 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1245430 AGTTTGACGT
1245440 ATTTATA-AAAATATA
1 ATTTATATAAAATATA
*
1245455 ATTTTTTATAAAATATA
1 A-TTTATATAAAATATA
*
1245472 A-TTATATAAAAAATA
1 ATTTATATAAAATATA
1245487 A
1 A
1245488 AATAAACCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.50
16 5 0.18
17 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTATATAAAATATA
Found at i:1245484 original size:17 final size:17
Alignment explanation
Indices: 1245446--1245486 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1245436 ACGTATTTAT
* *
1245446 AAAAATATAATTTTTTA
1 AAAAATATAATTATATA
*
1245463 TAAAATATAATTATATA
1 AAAAATATAATTATATA
1245480 AAAAATA
1 AAAAATA
1245487 AAATAAACCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATATAATTATATA
Found at i:1245666 original size:14 final size:14
Alignment explanation
Indices: 1245649--1245678 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1245639 CAAGAAATGT
1245649 AATTCATTTTCCAG
1 AATTCATTTTCCAG
1245663 AATTCATTTTCCAG
1 AATTCATTTTCCAG
1245677 AA
1 AA
1245679 AATGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (14 bp):
AATTCATTTTCCAG
Found at i:1251554 original size:225 final size:223
Alignment explanation
Indices: 1250843--1251540 Score: 961
Period size: 225 Copynumber: 3.1 Consensus size: 223
1250833 AATATAAACG
* * *
1250843 ATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAACACTTATG
1 ATAACATAACC-GTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
* * * * * ** *
1250908 TAACGTAATAGGTAGTGCCTTTTTAAAGCATACGAGGCTTTAGAAATTTGATGATAACAAAATAG
65 TAACGTAATAGATAGCGCCTTTTTAAAGCTTATGGGGCTTTA-AAATCCGACGATAACAAAATAG
* ** *
1250973 GTTAATTACTTGATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAACATTATCAAAG
129 GTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAAG
1251038 TTTAAGCTGATGGAGCCTTAGGAATCCGACA
194 TTTAAGCTGATGGAGCCTTA-GAATCCGACA
* * *
1251069 ATAGCATAATCGATAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
1 ATAACATAACCGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
* *
1251134 AACGTAATA-AGTAGCGCCTTTTTAAAGCTGATGGGGCTTTGGAAATCCGACGATAACAAAATAG
66 AACGTAATAGA-TAGCGCCTTTTTAAAGCTTATGGGGCTTT-AAAATCCGACGATAACAAAATAG
* * * *
1251198 GTTAACTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAATGCCTAAAATGTTACCAAAC
129 GTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAAG
*
1251263 TTTAAGCTGAT-GAGGCCTTAGATATCTGACA
194 TTTAAGCTGATGGA-GCCTTAGA-ATCCGACA
*
1251294 ATAACATAACCGATTAATTACTGGAAACATTATCAATCATAATAACATATTAGGTAGCGCTTATG
1 ATAACATAACCG-TTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATG
* * *
1251359 TAACGTAATAGATAGCACATTATTAAAGCTTATGGGG-TCTTAAAATCCGACGATAACAAAATAG
65 TAACGTAATAGATAGCGCCTTTTTAAAGCTTATGGGGCT-TTAAAATCCGACGATAACAAAATAG
* * *
1251423 GTTAATTACTTAATTTGTTATCAATATTATCAACATATTAGGTAACGCCTAAAATGTCAACAAAG
129 GTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAAG
* * *
1251488 ATTAAGCTGATGGAGTCTTAGTAATCCGACG
194 TTTAAGCTGATGGAGCCTTAG-AATCCGACA
1251519 ATAACATAACCAGTTAATTACT
1 ATAACATAACC-GTTAATTACT
1251541 TGATTTGTTA
Statistics
Matches: 418, Mismatches: 44, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
224 4 0.01
225 317 0.76
226 96 0.23
227 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (223 bp):
ATAACATAACCGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTATGT
AACGTAATAGATAGCGCCTTTTTAAAGCTTATGGGGCTTTAAAATCCGACGATAACAAAATAGGT
TAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAAAGTT
TAAGCTGATGGAGCCTTAGAATCCGACA
Found at i:1252067 original size:212 final size:214
Alignment explanation
Indices: 1251699--1252091 Score: 673
Period size: 212 Copynumber: 1.8 Consensus size: 214
1251689 TATATGTATA
1251699 TGTGTGTGTATCGATACATTTTACATGCAGATTGTTTAAGCCTTAATGTGGAATTAACCAAAGTT
1 TGTGTGTGTATCGATACATTTTACATGCAGATTGTTTAAGCCTTAATGTGGAATTAACCAAAGTT
* * * * *
1251764 TAAGCTGATGGAGCCTTTGGAATTCGACGATAACGTAACCGATTAATTACTTGATTTGTTATCAA
66 AAAGCTGATGGAGCCTTTAGAATCCAACGATAACATAACCGATTAATTACTTGATTTGTTATCAA
1251829 GCTTTATCAACATATTACCATGTACATTGTTTACGCATATTATCATCATACCGATCGAAATTATA
131 GCTTTATCAACATATTACCATGTACATTGTTTACGCATATTATCATCATACCGATCGAAATTATA
1251894 AGTATGGAAAATATATGCG
196 AGTATGGAAAATATATGCG
* *
1251913 TGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTAAGCCTTTATGTGGAATTAACCAAAGTT
1 TGTGTGTGTATCGATACATTTTACATGCAGATTGTTTAAGCCTTAATGTGGAATTAACCAAAGTT
* *
1251978 AAAGCTGATTGAGCC-TTAGAA-CCAACGATAACATAACCGGTTAATTACTTGATTTGTTATCAA
66 AAAGCTGATGGAGCCTTTAGAATCCAACGATAACATAACCGATTAATTACTTGATTTGTTATCAA
* *
1252041 GCTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATAC
131 GCTTTATCAACATATTACCATGTACATTGTTTACGCATATTATCATCATAC
1252092 TGATTGACTT
Statistics
Matches: 168, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
212 87 0.52
213 5 0.03
214 76 0.45
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (214 bp):
TGTGTGTGTATCGATACATTTTACATGCAGATTGTTTAAGCCTTAATGTGGAATTAACCAAAGTT
AAAGCTGATGGAGCCTTTAGAATCCAACGATAACATAACCGATTAATTACTTGATTTGTTATCAA
GCTTTATCAACATATTACCATGTACATTGTTTACGCATATTATCATCATACCGATCGAAATTATA
AGTATGGAAAATATATGCG
Found at i:1252196 original size:14 final size:14
Alignment explanation
Indices: 1252177--1252203 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1252167 AAAATATATA
1252177 TGTGTGTGTGTTTG
1 TGTGTGTGTGTTTG
1252191 TGTGTGTGTGTTT
1 TGTGTGTGTGTTT
1252204 AGATACATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (14 bp):
TGTGTGTGTGTTTG
Found at i:1252687 original size:280 final size:280
Alignment explanation
Indices: 1251912--1252895 Score: 1536
Period size: 282 Copynumber: 3.5 Consensus size: 280
1251902 AAATATATGC
*
1251912 GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTAAGCCTTTATGTGGAATTAACCAAAGT
1 GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
*
1251977 TAAAGCTGATTGAGCCTTAGAACCAACGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
66 TAAAGCTGATTGAGCCTTAGAACCGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
*
1252042 CTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAACT
131 CTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAACA
* * * *
1252107 GTTTTCATTGGAAATTAGTCTATTACTTTAAAGTAATATGTTTTGAAATTATAAGTATGGAAAAT
196 GTTTTCATTGGAAATTAATATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATGGAAAAT
* * *
1252172 ATATATGTGTGTGTGTTTGT
261 ATATATATATGTGTGTGTGT
* * * *
1252192 GTGTGTGTGTTTAGATACATTTTACGTGCAGATTATTTGAGCCTTTATGTGGAATTAACAAAAGT
1 GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
* * * * *
1252257 TAAAGCTGATGGAGCTTTAGGAATCCGACGATAACATAATCGGTTAATTATTTGATTTTTTATCA
66 TAAAGCTGATTGAGCCTTA-GAA-CCGACGATAACATAACCGGTTAATTACTTGATTTGTTATCA
* * *
1252322 AGCTTTATCAACATATTACCATGTACATTGTTTACGCTTATTATCATGATACCGATTGACTTTAA
129 AGCTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAA
*
1252387 CAGTTTTCATTGGAAATTAATATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATGGAAA
194 CAGTTTTCATTGGAAATTAATATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATGGAAA
1252452 ATATATATATATGTGTGTGTGT
259 ATATATATATATGTGTGTGTGT
*
1252474 GTGTGTGTGTATCGATACATTTTATGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
1 GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
* * *
1252539 TAAAGCTAATTGAGCCTTAGAACCGACGATAACATAACCAGTTAATTAATTGATTTGTTATCAAG
66 TAAAGCTGATTGAGCCTTAGAACCGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
*
1252604 CTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAACC
131 CTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAACA
* *
1252669 GTTTTCATTGGAAATTAATTTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATGAAATAT
196 GTTTTCATTGGAAATTAATATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATG-GA-A-
*
1252734 ATATCTATATATATATATGTGTGTGT
258 A-A--TATATATATATGTGTGTGTGT
* * *
1252760 GTGTGTGTGTGTGGATACATTTTACGTGCAGATAGTTTGAGCCTTTATGTGGAATTAACCAAAGT
1 GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
* * ** **
1252825 TAAAGTTGATTGAGCCTTAGAACAGAAAATAACATAACTTGTTAATTACTTGATTTGTTATCAAG
66 TAAAGCTGATTGAGCCTTAGAACCGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
1252890 CTTTAT
131 CTTTAT
1252896 GTGGAATTAA
Statistics
Matches: 641, Mismatches: 55, Indels: 10
0.91 0.08 0.01
Matches are distributed among these distances:
280 234 0.37
281 7 0.01
282 254 0.40
283 1 0.00
284 1 0.00
286 144 0.22
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (280 bp):
GTGTGTGTGTATCGATACATTTTACGTGCAGATTGTTTGAGCCTTTATGTGGAATTAACCAAAGT
TAAAGCTGATTGAGCCTTAGAACCGACGATAACATAACCGGTTAATTACTTGATTTGTTATCAAG
CTTTATCAACATATTACCATGTACATTGTTTATGCATATTATCATGATACTGATTGACTTTAACA
GTTTTCATTGGAAATTAATATATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATGGAAAAT
ATATATATATGTGTGTGTGT
Found at i:1255711 original size:447 final size:444
Alignment explanation
Indices: 1254802--1255734 Score: 1285
Period size: 447 Copynumber: 2.1 Consensus size: 444
1254792 CTGCTTTGTC
*
1254802 ATATTGTCATGTTC-A-ACATGCGT-ATTAGGTATCGATACTTCATGCGTGCATCTAGTTTGGGA
1 ATATTGTCATGTTCGATACATGTGTCA-TAGGTATCGATACTT-ATGCGTGCATCTAGTTTGGGA
* *
1254864 AGCATACTGGATAAAAAGTATCGATACATAAACAAAAAGTATCGATACTTTATGTTAACGTATTT
64 AGCATACTGGAAAAAAAGTATCGATACACAAACAAAAAGTATCGATACTTTATGTTAACGTATTT
1254929 TGTCATTAAACCAGTATATTTTTACCGCTTACATTGCAAATTTACATATTACTTTAAAGTAATCA
129 TGTCATTAAACCAGTATATTTTTACCGCTTACATTGCAAATTTACATATTACTTTAAAGTAATCA
* * * *
1254994 GTTTCGAAGTTTTAAGAATCGATATTTTTCATAAGTGTATCGATATTTATAGGCACAATTATTGA
194 GTTTCAAAGTTTTAAGAATCGATACTTTTCATAAGTGTAACGATATTTATAGGCACAATTATGGA
*
1255059 AACTGATTTTGTCAATTTTCAACCTGTTATATTATTTATATTTAATCGATACCATTACCCTTACC
259 AACAGATTTTGTCAATTTTCAACCTGTTATATTATTTATATTTAATCGATACCATTACCCTTACC
* * * *
1255124 GAAATGTCAATACTTTTGTGTAAGGTATCGATACTTTCGAGATGTTTCGTTTTTTTGTAAACCGG
324 GAAATATCAATACTTTTGTGTAAGGTATCGATACTTTCGAGAAGTTTCGATTTTGTGTAAACCGG
* * *
1255189 TAGCGCTTTACCGGTTTTGTCATATTGAAACCAGTTTTGCCAATTTTTAACTTGTT
389 TAGCGCTTTACCGGTTTTGGCATATTGAAACCAGTTTTGCCAATTTTCAACATGTT
*
1255245 ATATTGTCATGTATCGATACATGTGTCATAGGTATTGATACGTTAT-CTGTGCATCTAGTTTGGG
1 ATATTGTCATGT-TCGATACATGTGTCATAGGTATCGATAC-TTATGC-GTGCATCTAGTTTGGG
* * *
1255309 AATCATACTGGACAAAAAAGTATCGATACACACACAAAAAGTATTGATACTTTATGTTAACGTAT
63 AAGCATACTGGA-AAAAAAGTATCGATACACAAACAAAAAGTATCGATACTTTATGTTAACGTAT
* *
1255374 TTTGTCATTAAACC-GATATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTAAAGTAA
127 TTTGTCATTAAACCAG-TATATTTTTACCGCTTACATTGCAAATTTACATATTACTTTAAAGTAA
* * * *
1255438 T-ATTTTTCAAAGTTTTAAGAATTGATACTTTTCTTACGTGTAACGATACTTTATAAGTG-A-AA
191 TCA-GTTTCAAAGTTTTAAGAATCGATACTTTTCATAAGTGTAACGATA-TTTAT-AG-GCACAA
* * *
1255500 TTATGGAAACCAG-TTTTGTCGATTTTGAACCTGTTATGTTATTTATATTTAATCGATACCATTA
252 TTATGGAAA-CAGATTTTGTCAATTTTCAACCTGTTATATTATTTATATTTAATCGATACCATTA
* * * * *
1255564 CCCTTACCGAAGTATCGATACTTTTGTGTAAGGTTTTGATACTTTTGAGAAGTTTC-ATTTTGTG
316 CCCTTACCGAAATATCAATACTTTTGTGTAAGGTATCGATACTTTCGAGAAGTTTCGATTTTGTG
* * * *** *
1255628 TAAATCGGTATCTCTTTACC-GTTATTGGCATATTGAAATTGGTTTTGTCAATTTTCAACATGTT
381 TAAACCGGTAGCGCTTTACCGGTT-TTGGCATATTGAAACCAGTTTTGCCAATTTTCAACATGTT
* *
1255692 ATATTGTCATGTCTCGATACATGTTTCTTAGGTATCGATACTT
1 ATATTGTCATGT-TCGATACATGTGTCATAGGTATCGATACTT
1255735 TATAGGCGCA
Statistics
Matches: 432, Mismatches: 44, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
443 12 0.03
444 2 0.00
445 2 0.00
446 55 0.13
447 243 0.56
448 112 0.26
449 5 0.01
450 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (444 bp):
ATATTGTCATGTTCGATACATGTGTCATAGGTATCGATACTTATGCGTGCATCTAGTTTGGGAAG
CATACTGGAAAAAAAGTATCGATACACAAACAAAAAGTATCGATACTTTATGTTAACGTATTTTG
TCATTAAACCAGTATATTTTTACCGCTTACATTGCAAATTTACATATTACTTTAAAGTAATCAGT
TTCAAAGTTTTAAGAATCGATACTTTTCATAAGTGTAACGATATTTATAGGCACAATTATGGAAA
CAGATTTTGTCAATTTTCAACCTGTTATATTATTTATATTTAATCGATACCATTACCCTTACCGA
AATATCAATACTTTTGTGTAAGGTATCGATACTTTCGAGAAGTTTCGATTTTGTGTAAACCGGTA
GCGCTTTACCGGTTTTGGCATATTGAAACCAGTTTTGCCAATTTTCAACATGTT
Found at i:1260292 original size:121 final size:120
Alignment explanation
Indices: 1260077--1260300 Score: 281
Period size: 121 Copynumber: 1.9 Consensus size: 120
1260067 TCGTAATAGG
* * * * *
1260077 TTTCAAAGTTTTAAGAATCGATACTTTAATATGTATATTGATACTTTCTGCGTGCATCTCGTTTA
1 TTTCAAAGTTTTAAGAATCGATACTTTAATACGTATATCGATACTTTCTGCGTGCATATAGTATA
* * *
1260142 GGAAGCATATTGGACAACGAATATCGATACAAATACAACAATTTATAGTAATTTA
66 GGAAGCATACTAGACAACAAATATCGATACAAATACAACAATTTATAGTAATTTA
* * *
1260197 TTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTGCGTGCATATAGTAT
1 TTTCAAAGTTTTAAGAATCGATACTT-TAATACGTATATCGATACTTTCTGCGTGCATATAGTAT
* * *
1260262 -GTTAAGCATACTAGACAA-AAAGTATTGATACACATACAA
65 AG-GAAGCATACTAGACAACAAA-TATCGATACAAATACAA
1260301 AAATCATCGA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
120 28 0.32
121 59 0.68
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (120 bp):
TTTCAAAGTTTTAAGAATCGATACTTTAATACGTATATCGATACTTTCTGCGTGCATATAGTATA
GGAAGCATACTAGACAACAAATATCGATACAAATACAACAATTTATAGTAATTTA
Found at i:1260738 original size:200 final size:200
Alignment explanation
Indices: 1260183--1261391 Score: 1547
Period size: 200 Copynumber: 6.1 Consensus size: 200
1260173 AATACAACAA
*
1260183 TTTATAGTAATTTA-TTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCT
1 TTTATAGTAA-TCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCT
* * * *
1260247 GCGTGCATATAGTATGTTAAGCATACTAGACAAAAAGTATTGATACACATACAAAAA-TCATCGA
65 GCGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGT-ATCGA
* * * *
1260311 TACTTTATGTTTACGTATTTTGTCATTAAACCGATATATTTTTACTATTTATATTGTAAATTTAC
129 TACTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTAC
*
1260376 GTATTA-
194 CTATTAC
* * *
1260382 TATTATAGTAATCGGTTTTGAAGTTTTAAGAATCGATACTT-TAATACGTGTATCGATACTTTCT
1 T-TTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCT
* * * * * *
1260446 GCGTGAATCTCGTTTGGGAAGCATACTGGACAAAAATTATCGATACAAATACAACAAA-TATCGA
65 GCGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAA-AAAGTATCGA
* * *
1260510 TACTTTATGTTTACGTATTTTGTCATTAAATCGGTATATTTTTACCGTTTACATTGTAAATTTAC
129 TACTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTAC
* *
1260575 ATATTAT
194 CTATTAC
* *
1260582 TTTATAGTAATCGGTTTCGAAGTTTTAAGAATCGATACTTATCATATGTGTATCGATACTTTCTG
1 TTTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* *
1260647 CGTGCATCTAGTATGTGAAGCATACTGGATAAAAAGTATCGATACACATACAAAAAGTATTGATA
66 CGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATA
* * *
1260712 CTTTATGTTTACATATTTTGTCATTAAATCGGTATAGTTTTACCACTTACATTGTAAATTTACCT
131 CTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTACCT
*
1260777 ATTAT
196 ATTAC
* * *
1260782 TTTATAGTAATAAGTTTAGAAGTTTTAAGAATCGATATTTATCATACGTGTATCGATACTTTCTG
1 TTTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* *
1260847 CGTCCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATATAAAAAGTATCGATA
66 CGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATA
* * *
1260912 CTTTATATTTACGTATTTTGTCATTAAACCGGTATATGTTTACC-TCTTACATTGTAAATTTACC
131 CTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCAT-TTACATTGTAAATTTACC
1260976 TATTAC
195 TATTAC
* * *
1260982 TTTATAGTAATCAATTTCGAAGTTTTAAGAATCGATACTTGTCATACGTGTATCAATACTTTCTG
1 TTTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* * * * *
1261047 CGTGCATCTAATTTGTGAAGCATACTAGATCAATAA-TATCGATACTCATACAAAAAGTAGT-GA
66 CGTGCATCTAGTATGTGAAGCATACTGGA-CAAAAAGTATCGATACACATACAAAAAGTA-TCGA
* * * * * * ** * *
1261110 TACTTTATG-TCAAAGTATCTTGTCATTAAACTGGTATCTTTTTATCGCTAACATAGTAAATTTA
129 TACTTTATGTTTACA-TATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTA
1261174 -CTATTAC
193 CCTATTAC
* * ** * * * *
1261181 TTTAAATTAATCAGTTTTAAAGTTTTAAGAATCGATACTTTTTATATGTGTATCGATACTTTTTG
1 TTTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* * * * * * * * * *
1261246 TGTGCATCTCGTTTGGGAAGCATATTGGACAAAAAGTTTCGATACATATACAAAATGGATCGAAA
66 CGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATA
* * *
1261311 CTTTATGTTTACACATTTTGTCATTAAACCGGTATATTTTTACCTTTTACATTTTAAATTTACCT
131 CTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTACCT
*
1261376 ATAAC
196 ATTAC
*
1261381 TTTAAAGTAAT
1 TTTATAGTAAT
1261392 AAATCTTGAA
Statistics
Matches: 881, Mismatches: 114, Indels: 29
0.86 0.11 0.03
Matches are distributed among these distances:
198 6 0.01
199 333 0.38
200 536 0.61
201 6 0.01
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (200 bp):
TTTATAGTAATCAGTTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
CGTGCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATA
CTTTATGTTTACATATTTTGTCATTAAACCGGTATATTTTTACCATTTACATTGTAAATTTACCT
ATTAC
Found at i:1261320 original size:599 final size:598
Alignment explanation
Indices: 1260183--1261393 Score: 1673
Period size: 599 Copynumber: 2.0 Consensus size: 598
1260173 AATACAACAA
* *
1260183 TTTATAGTAATTTATTTCGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
1 TTTATAGTAA-TAATTTAGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* * *
1260248 CGTGCATATAGTATGTTAAGCATACTAGACAAAAAGTATTGATACACATACAAAAATCATCGATA
65 CGTCCATATAGTATGTGAAGCATACTAGACAAAAAGTATCGATACACATACAAAAATCATCGATA
* * * * *
1260313 CTTTATGTTTACGTATTTTGTCATTAAACCGATATATTTTTACTATTTATATTGTAAATTTACGT
130 CTTTATATTTACGTATTTTGTCATTAAACCGATATATGTTTACTACTTACATTGTAAATTTACCT
** * *
1260378 ATTATATTATAGTAATCGGTTTTGAAGTTTTAAGAATCGATACTTTAATACGTGTATCGATACTT
195 ATTATATTATAGTAATCAATTTCGAAGTTTTAAGAATCGATACTTTAATACGTGTATCAATACTT
** *
1260443 TCTGCGTGAATCTCGTTTGGGAAGCATACTGGACAAAAATTATCGATACAAATACAACAAATATC
260 TCTGCGTGAATCTAATTTGGGAAGCATACTAGACAAAAATTATCGATACAAATACAACAAATATC
** * * * * *
1260508 GATACTTTATGTTTACGTATTTTGTCATTAAATCGGTATATTTTTACCGTTTACATTGTAAATTT
325 GATACTTTATGTCAAAGTATCTTGTCATTAAATCGGTATATTTTTACCGCTAACATAGTAAATTT
* * * *
1260573 ACATATTATTTTATAGTAATCGGTTTCGAAGTTTTAAGAATCGATACTTATCATATGTGTATCGA
390 ACATATTACTTTAAAGTAATCAGTTTCAAAGTTTTAAGAATCGATACTTATCATATGTGTATCGA
* *
1260638 TACTTTCTGCGTGCATCTAGTATGTGAAGCATACTGGATAAAAAGTATCGATACACATACAAAAA
455 TACTTTCTGCGTGCATCTAGTATGGGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAA
* * * * *
1260703 GTATTGATACTTTATGTTTACATATTTTGTCATTAAATCGGTATAGTTTTACCACTTACATTGTA
520 GGATCGAAACTTTATGTTTACACATTTTGTCATTAAACCGGTATAGTTTTACCACTTACATTGTA
* *
1260768 AATTTACCTATTAT
585 AATTTACCTATAAC
*
1260782 TTTATAGTAATAAGTTTAGAAGTTTTAAGAATCGATATTTATCATACGTGTATCGATACTTTCTG
1 TTTATAGTAATAA-TTTAGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTG
* * *
1260847 CGTCCATCTAGTATGTGAAGCATACTGGACAAAAAGTATCGATACACATATAAAAAGT-ATCGAT
65 CGTCCATATAGTATGTGAAGCATACTAGACAAAAAGTATCGATACACATACAAAAA-TCATCGAT
*
1260911 ACTTTATATTTACGTATTTTGTCATTAAACCGGTATATGTTTACCT-CTTACATTGTAAATTTAC
129 ACTTTATATTTACGTATTTTGTCATTAAACCGATATATGTTTA-CTACTTACATTGTAAATTTAC
*
1260975 CTATTACT-TTATAGTAATCAATTTCGAAGTTTTAAGAATCGATACTTGTCATACGTGTATCAAT
193 CTATTA-TATTATAGTAATCAATTTCGAAGTTTTAAGAATCGATACTT-TAATACGTGTATCAAT
* * * **
1261039 ACTTTCTGCGTGCATCTAATTTGTGAAGCATACTAGATCAATAA-TATCGATACTCATACAA-AA
256 ACTTTCTGCGTGAATCTAATTTGGGAAGCATACTAGA-CAAAAATTATCGATACAAATACAACAA
* *
1261102 AGTAGT-GATACTTTATGTCAAAGTATCTTGTCATTAAA-CTGGTATCTTTTTATCGCTAACATA
320 A-TA-TCGATACTTTATGTCAAAGTATCTTGTCATTAAATC-GGTATATTTTTACCGCTAACATA
* * * *
1261165 GTAAATTTAC-TATTACTTTAAATTAATCAGTTTTAAAGTTTTAAGAATCGATACTTTTTATATG
382 GTAAATTTACATATTACTTTAAAGTAATCAGTTTCAAAGTTTTAAGAATCGATACTTATCATATG
* * * * * * *
1261229 TGTATCGATACTTTTTGTGTGCATCTCGTTTGGGAAGCATATTGGACAAAAAGTTTCGATACATA
447 TGTATCGATACTTTCTGCGTGCATCTAGTATGGGAAGCATACTGGACAAAAAGTATCGATACACA
* * **
1261294 TACAAAATGGATCGAAACTTTATGTTTACACATTTTGTCATTAAACCGGTATATTTTTACCTTTT
512 TACAAAAAGGATCGAAACTTTATGTTTACACATTTTGTCATTAAACCGGTATAGTTTTACCACTT
*
1261359 ACATTTTAAATTTACCTATAAC
577 ACATTGTAAATTTACCTATAAC
*
1261381 TTTAAAGTAATAA
1 TTTATAGTAATAA
1261394 ATCTTGAATT
Statistics
Matches: 536, Mismatches: 67, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
598 2 0.00
599 405 0.76
600 123 0.23
601 6 0.01
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (598 bp):
TTTATAGTAATAATTTAGAAGTTTTAAGAATCGATACTTATCATACGTGTATCGATACTTTCTGC
GTCCATATAGTATGTGAAGCATACTAGACAAAAAGTATCGATACACATACAAAAATCATCGATAC
TTTATATTTACGTATTTTGTCATTAAACCGATATATGTTTACTACTTACATTGTAAATTTACCTA
TTATATTATAGTAATCAATTTCGAAGTTTTAAGAATCGATACTTTAATACGTGTATCAATACTTT
CTGCGTGAATCTAATTTGGGAAGCATACTAGACAAAAATTATCGATACAAATACAACAAATATCG
ATACTTTATGTCAAAGTATCTTGTCATTAAATCGGTATATTTTTACCGCTAACATAGTAAATTTA
CATATTACTTTAAAGTAATCAGTTTCAAAGTTTTAAGAATCGATACTTATCATATGTGTATCGAT
ACTTTCTGCGTGCATCTAGTATGGGAAGCATACTGGACAAAAAGTATCGATACACATACAAAAAG
GATCGAAACTTTATGTTTACACATTTTGTCATTAAACCGGTATAGTTTTACCACTTACATTGTAA
ATTTACCTATAAC
Found at i:1264024 original size:19 final size:18
Alignment explanation
Indices: 1263983--1264031 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
1263973 TTGCTCATCT
* *
1263983 CATACATAATTTCATTCA
1 CATACAAAATTTAATTCA
*
1264001 TATACAAAATTATAATTCA
1 CATACAAAATT-TAATTCA
1264020 CATACAAAATTT
1 CATACAAAATTT
1264032 GGCTTACATC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (18 bp):
CATACAAAATTTAATTCA
Done.