Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397274.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_228.0, 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: 2969030
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 66526 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:1069098 original size:21 final size:21
Alignment explanation
Indices: 1069061--1069100 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1069051 GAAATAGGAT
*
1069061 GGATTTTGGATTTATAGATAA
1 GGATTTTGCATTTATAGATAA
1069082 GGATTTT-CATTTAATAGAT
1 GGATTTTGCATTT-ATAGAT
1069101 TATTTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.45
Consensus pattern (21 bp):
GGATTTTGCATTTATAGATAA
Found at i:1086761 original size:25 final size:27
Alignment explanation
Indices: 1086733--1086787 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
1086723 TTTTTATTTA
1086733 TTAATTATT-AAT-TATAAAAATTAAT
1 TTAATTATTAAATATATAAAAATTAAT
* *
1086758 TTAATTTTTAAATAATATAAAAATTTAT
1 TTAATTATTAAAT-ATATAAAAATTAAT
1086786 TT
1 TT
1086788 GAACATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.32
26 3 0.12
28 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAATTATTAAATATATAAAAATTAAT
Found at i:1096431 original size:12 final size:11
Alignment explanation
Indices: 1096413--1096446 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
1096403 ATTTAGAAGG
1096413 CTCTTCTTCTT
1 CTCTTCTTCTT
1096424 CATCTTCTTCTT
1 C-TCTTCTTCTT
1096436 CTGCTTCTTCT
1 CT-CTTCTTCT
1096447 GAAGATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.03, C:0.35, G:0.03, T:0.59
Consensus pattern (11 bp):
CTCTTCTTCTT
Found at i:1102204 original size:21 final size:19
Alignment explanation
Indices: 1102167--1102213 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1102157 TATTCCTTGC
1102167 TTATTTTTTTTCTTTATCT-
1 TTATTTTTTTTCTTTAT-TA
*
1102186 TTATTTTTATT-TTTATTA
1 TTATTTTTTTTCTTTATTA
1102204 TTATTATTTT
1 TTATT-TTTT
1102214 CGAACCTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 10 0.42
19 13 0.54
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (19 bp):
TTATTTTTTTTCTTTATTA
Found at i:1105242 original size:15 final size:15
Alignment explanation
Indices: 1105222--1105252 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1105212 ACATAAAATA
1105222 ATAAGTGTCATTTTG
1 ATAAGTGTCATTTTG
1105237 ATAAGTGTCATTTTG
1 ATAAGTGTCATTTTG
1105252 A
1 A
1105253 AACTATAATG
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:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
ATAAGTGTCATTTTG
Found at i:1106838 original size:5 final size:5
Alignment explanation
Indices: 1106828--1106853 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1106818 ATAGATTATG
1106828 GAGAA GAGAA GAGAA GAGAA GAGAA G
1 GAGAA GAGAA GAGAA GAGAA GAGAA G
1106854 GAAAAGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:1110211 original size:2 final size:2
Alignment explanation
Indices: 1110206--1110243 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1110196 CACACACTCC
*
1110206 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1110244 CCCTTGATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1122767 original size:46 final size:45
Alignment explanation
Indices: 1122635--1122771 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
1122625 TGACCCTAAG
* * *
1122635 TTAATTATTGTAGAACAATGCACAACTATACCTCA-AAAGACAAATG
1 TTAATTATTGTTGAATAATGCACAACTATA--TCATAAAGACAAATA
* ** *
1122681 TTAATTATTCTT-AATAACACACAACTATACCTCA-AGAGACAAATA
1 TTAATTATTGTTGAATAATGCACAACTATA--TCATAAAGACAAATA
*
1122726 TTAATTATTGTTGTATAATGCACAACTATATCATGAAAGACAAATA
1 TTAATTATTGTTGAATAATGCACAACTATATCAT-AAAGACAAATA
1122772 ATATGAAAAC
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
44 3 0.04
45 39 0.51
46 34 0.45
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (45 bp):
TTAATTATTGTTGAATAATGCACAACTATATCATAAAGACAAATA
Found at i:1128679 original size:16 final size:15
Alignment explanation
Indices: 1128654--1128701 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
1128644 ATTAGATGTT
1128654 AAAATAAAAAATAAAA
1 AAAAT-AAAAATAAAA
1128670 AAAAGTAAAAAGTAAAA
1 AAAA-TAAAAA-TAAAA
1128687 AAAAT-AAAATAAAA
1 AAAATAAAAATAAAA
1128701 A
1 A
1128702 TCATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.20
15 4 0.13
16 10 0.33
17 10 0.33
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.12
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:1128680 original size:17 final size:16
Alignment explanation
Indices: 1128654--1128695 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
1128644 ATTAGATGTT
1128654 AAAATAAAAAATAAAA
1 AAAATAAAAAATAAAA
*
1128670 AAAAGTAAAAAGTAAAA
1 AAAA-TAAAAAATAAAA
1128687 AAAATAAAA
1 AAAATAAAA
1128696 TAAAAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (16 bp):
AAAATAAAAAATAAAA
Found at i:1133939 original size:31 final size:32
Alignment explanation
Indices: 1133878--1134027 Score: 95
Period size: 35 Copynumber: 4.8 Consensus size: 32
1133868 ATGTTATAAT
* * *
1133878 TAAAATAAAATATATAATATGAGAATTTAAAA
1 TAAAATAAAATATATAATATAAAAAATTAAAA
1133910 TAAAATTAAAATA-A-AATATAAAAAATTAAAA
1 TAAAA-TAAAATATATAATATAAAAAATTAAAA
** * *
1133941 T-TTATATAATATA-AGTA-AAAGAAATT-AAA
1 TAAAATAAAATATATAATATAAA-AAATTAAAA
1133970 T----TAAAATATATAATATAAAAAATTATATTAA
1 TAAAATAAAATATATAATATAAAAAATTA-A--AA
* * *
1134001 AAAAATAAAATATATAACATTAAAAAT
1 TAAAATAAAATATATAATATAAAAAAT
1134028 ATATTTAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
26 8 0.09
27 8 0.09
28 3 0.03
29 14 0.15
30 10 0.11
31 17 0.18
32 6 0.06
33 7 0.08
35 20 0.22
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (32 bp):
TAAAATAAAATATATAATATAAAAAATTAAAA
Found at i:1133941 original size:15 final size:15
Alignment explanation
Indices: 1133917--1134030 Score: 55
Period size: 14 Copynumber: 7.9 Consensus size: 15
1133907 AAATAAAATT
1133917 AAAA-TAAAATATAA
1 AAAATTAAAATATAA
* *
1133931 AAAATTAAAATTTAT
1 AAAATTAAAATATAA
* *
1133946 ATAA-TATAAGTA-AA
1 AAAATTA-AAATATAA
1133960 AGAAATT-AAAT-TAA
1 A-AAATTAAAATATAA
* *
1133974 AATA-TATAATATAA
1 AAAATTAAAATATAA
*
1133988 AAAATT-ATAT-TAA
1 AAAATTAAAATATAA
* *
1134001 AAAAATAAAATATAT
1 AAAATTAAAATATAA
*
1134016 AACATTAAAAATATA
1 AAAATT-AAAATATA
1134031 TTTAATAGAT
Statistics
Matches: 71, Mismatches: 18, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
12 1 0.01
13 13 0.18
14 25 0.35
15 23 0.32
16 9 0.13
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAATTAAAATATAA
Found at i:1134003 original size:14 final size:16
Alignment explanation
Indices: 1133972--1134031 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1133962 AAATTAAATT
1133972 AAAATATATAATATAA
1 AAAATATATAATATAA
* *
1133988 AAAATTATATTAAAAAAA
1 AAAA-TATA-TAATATAA
* *
1134006 TAAAATATATAACATTA
1 -AAAATATATAATATAA
1134023 AAAATATAT
1 AAAATATAT
1134032 TTAATAGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 13 0.36
17 9 0.25
18 10 0.28
19 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATATATAATATAA
Found at i:1134010 original size:50 final size:50
Alignment explanation
Indices: 1133912--1134010 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
1133902 ATTTAAAATA
* * * *
1133912 AAATTAAAATAAAATATAAAAAATTAAAATTTATATAATATAAGTAAAAG
1 AAATTAAAATAAAATATAAAAAATAAAAAATTATATAATAAAAATAAAAG
* * *
1133962 AAATTAAATTAAAATATATAATATAAAAAATTATATTAA-AAAAATAAAA
1 AAATTAAAATAAAATATAAAAAATAAAAAATTATA-TAATAAAAATAAAA
1134011 TATATAACAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 38 0.93
51 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (50 bp):
AAATTAAAATAAAATATAAAAAATAAAAAATTATATAATAAAAATAAAAG
Found at i:1134022 original size:28 final size:27
Alignment explanation
Indices: 1133917--1134024 Score: 92
Period size: 28 Copynumber: 3.9 Consensus size: 27
1133907 AAATAAAATT
*
1133917 AAAATAAAATATAAAAAATTAAAATTTAT
1 AAAATAAAATATAAAAAATT-AAA-TTAA
* *
1133946 ATAATATAAGTA-AAAGAAATTAAATTAA
1 AAAATA-AAATATAAA-AAATTAAATTAA
* * *
1133974 AATATATAATATAAAAAATTATATTAAA
1 AAAATAAAATATAAAAAATTAAATT-AA
* *
1134002 AAAATAAAATATATAACATTAAA
1 AAAATAAAATATAAAAAATTAAA
1134025 AATATATTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
27 12 0.19
28 30 0.48
29 11 0.18
30 9 0.15
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAATAAAATATAAAAAATTAAATTAA
Found at i:1134130 original size:18 final size:18
Alignment explanation
Indices: 1134088--1134140 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
1134078 CATTAAATTT
1134088 ATATTTTAATAAA-TAAAA
1 ATATTTTAA-AAATTAAAA
*
1134106 ATAATTTTAAAAATTAATA
1 AT-ATTTTAAAAATTAAAA
*
1134125 ATA-TTTATAAATTAAA
1 ATATTTTAAAAATTAAA
1134141 CGTTACAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.37
18 6 0.20
19 13 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTTTAAAAATTAAAA
Found at i:1134136 original size:17 final size:16
Alignment explanation
Indices: 1134105--1134139 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1134095 AATAAATAAA
1134105 AATAATTTTAAAAATT
1 AATAATTTTAAAAATT
*
1134121 AATAATATTTATAAATT
1 AATAAT-TTTAAAAATT
1134138 AA
1 AA
1134140 ACGTTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATTTTAAAAATT
Found at i:1146956 original size:31 final size:30
Alignment explanation
Indices: 1146918--1146979 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
1146908 AACCAAACTG
*
1146918 TTTACAGAGCAAAATCAAAAAGTACATACTA
1 TTTACAGAGCAAAACCAAAAAGTACAT-CTA
*
1146949 TTTACAGAGCAAAACCAAAAATTACATCTA
1 TTTACAGAGCAAAACCAAAAAGTACATCTA
1146979 T
1 T
1146980 ATGCACATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (30 bp):
TTTACAGAGCAAAACCAAAAAGTACATCTA
Found at i:1147970 original size:31 final size:30
Alignment explanation
Indices: 1147909--1147998 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
1147899 AATAAAGTCA
* * * * *
1147909 TTATATTTTAATTAT-ATTTAATTAAGTTT
1 TTATATTTTTATTTTAAATTAAATAAATTT
* *
1147938 TTATATTTTTTATTTTGAGTTAAATAAATTT
1 TTATA-TTTTTATTTTAAATTAAATAAATTT
1147969 TTATATTTTTATTTTAAATTAAATAAATTT
1 TTATATTTTTATTTTAAATTAAATAAATTT
1147999 AAAAATTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.10
30 31 0.60
31 16 0.31
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (30 bp):
TTATATTTTTATTTTAAATTAAATAAATTT
Found at i:1150030 original size:6 final size:6
Alignment explanation
Indices: 1150016--1150045 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1150006 AAGATTTGAC
*
1150016 AGGCTG AGGCAG AGGCAG AGGCAG AGGCAG
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCAG
1150046 TGGAAGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.50, T:0.03
Consensus pattern (6 bp):
AGGCAG
Found at i:1151869 original size:4 final size:4
Alignment explanation
Indices: 1151860--1151886 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1151850 ATATTATCCC
1151860 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1151887 ATTATATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1154222 original size:21 final size:21
Alignment explanation
Indices: 1154174--1154223 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1154164 AAAAATCGTG
*
1154174 CTCCCCCCACCCCTCCCCCTC
1 CTCCCTCCACCCCTCCCCCTC
* * * *
1154195 ATGCCTCCACCCCTTCCTCTC
1 CTCCCTCCACCCCTCCCCCTC
1154216 CTCCCTCC
1 CTCCCTCC
1154224 CTATGCCGCC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.70, G:0.02, T:0.22
Consensus pattern (21 bp):
CTCCCTCCACCCCTCCCCCTC
Found at i:1154236 original size:31 final size:31
Alignment explanation
Indices: 1154190--1154248 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1154180 CCACCCCTCC
*
1154190 CCCTCATGCCTCCACCCCTTCCTCTCCTCCCT
1 CCCTCATGCCGCCACCCCTTCCTC-CCTCCCT
1154222 CCCT-ATGCCGCCACCCCTTCCTCCCTC
1 CCCTCATGCCGCCACCCCTTCCTCCCTC
1154249 ATCCCTCGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 18 0.69
32 4 0.15
ACGTcount: A:0.07, C:0.63, G:0.05, T:0.25
Consensus pattern (31 bp):
CCCTCATGCCGCCACCCCTTCCTCCCTCCCT
Found at i:1169863 original size:8 final size:7
Alignment explanation
Indices: 1169835--1169860 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1169825 TATACTTTCA
1169835 TTTAATT
1 TTTAATT
1169842 TTTAATT
1 TTTAATT
1169849 TTTAATT
1 TTTAATT
1169856 TTTAA
1 TTTAA
1169861 ATTATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:1169868 original size:15 final size:14
Alignment explanation
Indices: 1169836--1169869 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1169826 ATACTTTCAT
*
1169836 TTAATTTTTAATTT
1 TTAATTTTTAATTA
1169850 TTAATTTTTAAATTA
1 TTAATTTTT-AATTA
1169865 TTAAT
1 TTAAT
1169870 ATAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTAATTTTTAATTA
Found at i:1173616 original size:23 final size:23
Alignment explanation
Indices: 1173501--1173619 Score: 114
Period size: 23 Copynumber: 5.2 Consensus size: 23
1173491 TTACTCGAAA
* *
1173501 GTTTCAAAGATTGTT-TCCATGAG
1 GTTTCAAAAATTGTTACCCA-GAG
* * *
1173524 GTTTTAAAAGTTGTTACCCAAAG
1 GTTTCAAAAATTGTTACCCAGAG
* * *
1173547 ATTTCAAAAATTGTTACTCGGAG
1 GTTTCAAAAATTGTTACCCAGAG
* * *
1173570 ATTTTAAAAATTATTACCCAGAG
1 GTTTCAAAAATTGTTACCCAGAG
*
1173593 GTTTCAAAAATTGTTATCCAGAG
1 GTTTCAAAAATTGTTACCCAGAG
1173616 GTTT
1 GTTT
1173620 TGAAAATAGT
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
23 73 0.96
24 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (23 bp):
GTTTCAAAAATTGTTACCCAGAG
Found at i:1173625 original size:23 final size:23
Alignment explanation
Indices: 1173521--1173740 Score: 115
Period size: 23 Copynumber: 9.7 Consensus size: 23
1173511 TTGTTTCCAT
*
1173521 GAGGTTTTAAAAGTTGTTACCCA
1 GAGGTTTTAAAAATTGTTACCCA
* * * * *
1173544 AAGATTTCAAAAATTGTTACTCG
1 GAGGTTTTAAAAATTGTTACCCA
* *
1173567 GAGATTTTAAAAATTATTACCCA
1 GAGGTTTTAAAAATTGTTACCCA
* *
1173590 GAGGTTTCAAAAATTGTTATCCA
1 GAGGTTTTAAAAATTGTTACCCA
* * * *
1173613 GAGGTTTTGAAAATAG-TA-TCT
1 GAGGTTTTAAAAATTGTTACCCA
* * * * *
1173634 GAAGGATTTGAAGATAGTTACCTA
1 G-AGGTTTTAAAAATTGTTACCCA
* * * * * *
1173658 GAGG-CTTAAAGATGGTTTCTCT
1 GAGGTTTTAAAAATTGTTACCCA
* *
1173680 GAGGTTTTAAAGATTGTTA-CCT
1 GAGGTTTTAAAAATTGTTACCCA
* *
1173702 GAAGGTTTCAAAAATTATTACCCA
1 G-AGGTTTTAAAAATTGTTACCCA
* *
1173726 AAGGTTTTAAGAATT
1 GAGGTTTTAAAAATT
1173741 ATTATCTAGA
Statistics
Matches: 148, Mismatches: 43, Indels: 12
0.73 0.21 0.06
Matches are distributed among these distances:
21 2 0.01
22 33 0.22
23 110 0.74
24 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (23 bp):
GAGGTTTTAAAAATTGTTACCCA
Found at i:1173626 original size:46 final size:45
Alignment explanation
Indices: 1173501--1173626 Score: 139
Period size: 46 Copynumber: 2.7 Consensus size: 45
1173491 TTACTCGAAA
* *
1173501 GTTTCAAAGATTGTT-TCCATGAGGTTTTAAAAGTTGTTACCCAAAG
1 GTTTCAAAAATTGTTATCCA-GAGGTTTTAAAA-TTATTACCCAAAG
* * * *
1173547 ATTTCAAAAATTGTTA-CTCGGAGATTTTAAAAATTATTACCCAGAG
1 GTTTCAAAAATTGTTATC-CAGAGGTTTT-AAAATTATTACCCAAAG
1173593 GTTTCAAAAATTGTTATCCAGAGGTTTTGAAAAT
1 GTTTCAAAAATTGTTATCCAGAGGTTTT-AAAAT
1173627 AGTATCTGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
46 60 0.91
47 6 0.09
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (45 bp):
GTTTCAAAAATTGTTATCCAGAGGTTTTAAAATTATTACCCAAAG
Found at i:1173669 original size:22 final size:22
Alignment explanation
Indices: 1173644--1173703 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1173634 GAAGGATTTG
1173644 AAGATAGTTACCTAGAGG-CTTA
1 AAGATAGTTACCT-GAGGTCTTA
* * *
1173666 AAGATGGTTTCTCTGAGGTTTTA
1 AAGATAGTTAC-CTGAGGTCTTA
*
1173689 AAGATTGTTACCTGA
1 AAGATAGTTACCTGA
1173704 AGGTTTCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 17 0.55
23 14 0.45
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (22 bp):
AAGATAGTTACCTGAGGTCTTA
Found at i:1174870 original size:15 final size:15
Alignment explanation
Indices: 1174850--1174887 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1174840 TTCTTTAAAA
1174850 AAGTCAAATCTTGCG
1 AAGTCAAATCTTGCG
1174865 AAGTCAAATCTTGCG
1 AAGTCAAATCTTGCG
1174880 AAGTCAAA
1 AAGTCAAA
1174888 GTCAATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (15 bp):
AAGTCAAATCTTGCG
Found at i:1175700 original size:14 final size:14
Alignment explanation
Indices: 1175681--1175719 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
1175671 ATTGATCATC
1175681 AAATATCATTCTTA
1 AAATATCATTCTTA
1175695 AAATATCATTCTTA
1 AAATATCATTCTTA
1175709 AAATATCATTC
1 AAATATCATTC
1175720 AAGCAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATCATTCTTA
Found at i:1180115 original size:18 final size:19
Alignment explanation
Indices: 1180085--1180121 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1180075 CTTTTCTCAA
1180085 TTTATATTATTA-TTATTT
1 TTTATATTATTATTTATTT
1180103 TTTAT-TTATTTATTTATTT
1 TTTATATTA-TTATTTATTT
1180122 CAATTCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 8 0.47
19 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATATTATTATTTATTT
Found at i:1181813 original size:30 final size:30
Alignment explanation
Indices: 1181779--1181838 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1181769 AATCAATCAC
*
1181779 GAGTTTATTTGA-TTCAAAATAAAAATATAA
1 GAGTTTATTT-ACCTCAAAATAAAAATATAA
*
1181809 GAGTTTATTTACCTCAAAATAAAACTATAA
1 GAGTTTATTTACCTCAAAATAAAAATATAA
1181839 AGACTTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (30 bp):
GAGTTTATTTACCTCAAAATAAAAATATAA
Found at i:1183395 original size:20 final size:21
Alignment explanation
Indices: 1183357--1183396 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1183347 TTTAGCGATG
* *
1183357 TATTTTAAAAAATTCTTAAAC
1 TATTGTAAAAAAGTCTTAAAC
1183378 TATTGTAAAAAAGT-TTAAA
1 TATTGTAAAAAAGTCTTAAA
1183397 TGAATTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TATTGTAAAAAAGTCTTAAAC
Found at i:1184806 original size:30 final size:28
Alignment explanation
Indices: 1184770--1184848 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 28
1184760 ATCATTTGTT
*
1184770 AATAATAAAAATTTATTTCATTTAAAATAA
1 AATAATAAAAATTTATTTAATTT--AATAA
* * * *
1184800 AATAATAATAACTTAATTGAATTTGATAA
1 AATAATAA-AAATTTATTTAATTTAATAA
*
1184829 AAGAATAAAAATTTATTTAA
1 AATAATAAAAATTTATTTAA
1184849 AATTTTTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 9 0.23
29 11 0.28
30 8 0.21
31 11 0.28
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.38
Consensus pattern (28 bp):
AATAATAAAAATTTATTTAATTTAATAA
Found at i:1185518 original size:21 final size:21
Alignment explanation
Indices: 1185492--1185537 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1185482 AATATAAAAA
*
1185492 AAATAAATTT-TTAGTTTTTTT
1 AAATAAATTTATAAG-TTTTTT
1185513 AAAT-AATTTATAAGTTTTTT
1 AAATAAATTTATAAGTTTTTT
1185533 AAATA
1 AAATA
1185538 TTATCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
AAATAAATTTATAAGTTTTTT
Found at i:1186654 original size:18 final size:17
Alignment explanation
Indices: 1186606--1186660 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 17
1186596 GAATTTTGAT
1186606 AAATATTATATTAATTATAA
1 AAATA-TATA-TAATTA-AA
1186626 AAAT-T-TATAATTAAA
1 AAATATATATAATTAAA
1186641 AAATAATATATAATTTAAA
1 AAAT-ATATATAA-TTAAA
1186660 A
1 A
1186661 TTAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 3 0.10
18 6 0.19
19 6 0.19
20 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATATATAATTAAA
Found at i:1194104 original size:15 final size:15
Alignment explanation
Indices: 1194084--1194113 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1194074 GATTGGGGTA
1194084 CATGGAAAGCAAGGT
1 CATGGAAAGCAAGGT
1194099 CATGGAAAGCAAGGT
1 CATGGAAAGCAAGGT
1194114 TTCCTACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (15 bp):
CATGGAAAGCAAGGT
Found at i:1194401 original size:19 final size:19
Alignment explanation
Indices: 1194365--1194400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1194355 ATGCTCAAAT
1194365 AAATTCTTAAATTATTTTA
1 AAATTCTTAAATTATTTTA
*
1194384 AAATTTTTAAA-TATTTT
1 AAATTCTTAAATTATTTT
1194401 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATTCTTAAATTATTTTA
Found at i:1194442 original size:21 final size:21
Alignment explanation
Indices: 1194418--1194459 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1194408 TTATTATATT
1194418 TAATTAATT-TTTTATAATTAA
1 TAATTAATTATTTT-TAATTAA
1194439 TAATTAATTATTTTTAATTAA
1 TAATTAATTATTTTTAATTAA
1194460 AAGATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAATTAATTATTTTTAATTAA
Found at i:1195252 original size:20 final size:21
Alignment explanation
Indices: 1195214--1195253 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1195204 GCATTTCACT
1195214 TACATTAATTCTGTTAATTAC
1 TACATTAATTCTGTTAATTAC
*
1195235 TACATTAA-TCTTTTAATTA
1 TACATTAATTCTGTTAATTA
1195254 TTCAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (21 bp):
TACATTAATTCTGTTAATTAC
Found at i:1199970 original size:20 final size:19
Alignment explanation
Indices: 1199945--1199983 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1199935 TATATTTAAT
1199945 TTAATACTTATTAAAATTTA
1 TTAATACTT-TTAAAATTTA
*
1199965 TTAATACTTTTAAATTTTA
1 TTAATACTTTTAAAATTTA
1199984 AATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATACTTTTAAAATTTA
Found at i:1200577 original size:3 final size:3
Alignment explanation
Indices: 1200569--1200596 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1200559 AAGACGATTG
1200569 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1200597 TATATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1211991 original size:67 final size:67
Alignment explanation
Indices: 1211912--1212044 Score: 248
Period size: 67 Copynumber: 2.0 Consensus size: 67
1211902 ATGCGGCTTG
* *
1211912 TTCTGGTGTCTTATAATCTTTTTCCTTGAACGGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
1 TTCTGGTGTCTTATAAACTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
1211977 CA
66 CA
1211979 TTCTGGTGTCTTATAAACTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
1 TTCTGGTGTCTTATAAACTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
1212044 C
66 C
1212045 GTGCGCAGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (67 bp):
TTCTGGTGTCTTATAAACTTTTTCCTTGAACAGGGTTTGCAGGAAAGTTATCTAGATTTCAAGAT
CA
Found at i:1217495 original size:20 final size:19
Alignment explanation
Indices: 1217453--1217495 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1217443 TAGTAGAATC
* *
1217453 TAAAAAAATATTTAATTAT
1 TAAAAAAATATCTAATTAG
*
1217472 TAAAAATATATCTAATTTAG
1 TAAAAAAATATCTAA-TTAG
1217492 TAAA
1 TAAA
1217496 TGAGGATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAAAAATATCTAATTAG
Found at i:1218346 original size:52 final size:52
Alignment explanation
Indices: 1218289--1218395 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
1218279 TCAATCTTTA
1218289 ACTATCTCCTACAAAACTCTTACCTTCTTTACTTGCTGCACAGATTTTCCTT
1 ACTATCTCCTACAAAACTCTTACCTTCTTTACTTGCTGCACAGATTTTCCTT
1218341 ACTATCTCCTACAAAACTCTTACCTTCTTTACTTGCTGCACAGATTTTCCTT
1 ACTATCTCCTACAAAACTCTTACCTTCTTTACTTGCTGCACAGATTTTCCTT
1218393 ACT
1 ACT
1218396 TCTGTTCTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.23, C:0.31, G:0.06, T:0.40
Consensus pattern (52 bp):
ACTATCTCCTACAAAACTCTTACCTTCTTTACTTGCTGCACAGATTTTCCTT
Found at i:1226537 original size:6 final size:7
Alignment explanation
Indices: 1226515--1226543 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1226505 TGATGCAAGT
1226515 AAAGCAA
1 AAAGCAA
1226522 AAAGCAA
1 AAAGCAA
1226529 AAAGC-A
1 AAAGCAA
1226535 AAAGCAA
1 AAAGCAA
1226542 AA
1 AA
1226544 CTATATTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGCAA
Found at i:1226539 original size:13 final size:14
Alignment explanation
Indices: 1226515--1226543 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1226505 TGATGCAAGT
1226515 AAAGCAAAAAGCAA
1 AAAGCAAAAAGCAA
1226529 AAAGC-AAAAGCAA
1 AAAGCAAAAAGCAA
1226542 AA
1 AA
1226544 CTATATTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAGCAAAAAGCAA
Found at i:1230310 original size:19 final size:19
Alignment explanation
Indices: 1230282--1230335 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 19
1230272 TATAAAATGT
* *
1230282 TATAAGTATATATAATTTG
1 TATAAATATATATAATTTA
*
1230301 TATAAATATAT-T-ATATA
1 TATAAATATATATAATTTA
*
1230318 TATACATATATATAATTT
1 TATAAATATATATAATTT
1230336 TATGTATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 13 0.46
18 2 0.07
19 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
TATAAATATATATAATTTA
Found at i:1230668 original size:5 final size:5
Alignment explanation
Indices: 1230645--1230798 Score: 79
Period size: 5 Copynumber: 30.4 Consensus size: 5
1230635 ATGTTATAAT
* * *
1230645 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAGAA TCAAAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA T--AAAA
* ** * **
1230692 TTAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAGG
1 -TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA
* *
1230738 TAAAA TAAAA TAAAA TAAAA T-AAA TAAAA TAAAA -AATA TATTAA -AAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
1230786 TAAAAA TAAAA TA
1 T-AAAA TAAAA TA
1230799 TATAAGATTA
Statistics
Matches: 115, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
4 18 0.16
5 73 0.63
6 19 0.17
7 2 0.02
8 3 0.03
ACGTcount: A:0.71, C:0.01, G:0.02, T:0.27
Consensus pattern (5 bp):
TAAAA
Found at i:1230676 original size:24 final size:25
Alignment explanation
Indices: 1230649--1230960 Score: 116
Period size: 26 Copynumber: 12.1 Consensus size: 25
1230639 TATAATTAAA
*
1230649 ATAA-AAAATATTAAAATAAAATAT
1 ATAATAAAATATAAAAATAAAATAT
1230673 ATAATATAAGA-ATCAAAAATTAAAATA-
1 ATAATA-AA-ATAT-AAAAA-TAAAATAT
*
1230700 A-AATAAAATATAAAAAATTAAAATTT
1 ATAATAAAATAT-AAAAA-TAAAATAT
*
1230726 AT-ATAATATAGGT-AAAATAAAATA-
1 ATAATAAAATA--TAAAAATAAAATAT
* *
1230750 A-AATAAAATAAATAAAATAAAAAAT
1 ATAATAAAATATA-AAAATAAAATAT
* *
1230775 ATATTAAAAAATAAAAATAAAATAT
1 ATAATAAAATATAAAAATAAAATAT
* **
1230800 ATAAGATTATAATAATAAATAAAA-AT
1 ATAATAAAAT-ATAA-AAATAAAATAT
*
1230826 AAAATATATGACAT-TAAAAATAAAA-A-
1 ATAATA-A--A-ATATAAAAATAAAATAT
* * *
1230852 A-AATAAATATATGACATTAAAA-AT
1 ATAATAAA-ATATAAAAATAAAATAT
* * *
1230876 ATATTTAAGATATGATATTATATAAAA-ATT
1 ATA-ATAA-A-AT-ATA-AAAATAAAATA-T
*
1230906 AATAATAAAAAATAAAAAATAAAATATT
1 -ATAATAAAATAT-AAAAATAAAATA-T
1230934 ATAATAATAA-ATAAAAATAAAATAT
1 ATAATAA-AATATAAAAATAAAATAT
1230959 AT
1 AT
1230961 GACATTAAAA
Statistics
Matches: 220, Mismatches: 35, Indels: 65
0.69 0.11 0.20
Matches are distributed among these distances:
22 3 0.01
23 9 0.04
24 25 0.11
25 48 0.22
26 54 0.25
27 45 0.20
28 20 0.09
29 7 0.03
30 6 0.03
31 3 0.01
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (25 bp):
ATAATAAAATATAAAAATAAAATAT
Found at i:1230820 original size:33 final size:33
Alignment explanation
Indices: 1230747--1230967 Score: 150
Period size: 33 Copynumber: 7.0 Consensus size: 33
1230737 GTAAAATAAA
* *
1230747 ATAA-AATAAA-ATAAATAAAATA-A-AA-AAT
1 ATAATAATAAATAAAAATAAAATATATAACATT
* * *
1230775 ATATTAAAAAATAAAAATAAAATATATAAGATT
1 ATAATAATAAATAAAAATAAAATATATAACATT
*
1230808 ATAATAATAAATAAAAATAAAATATATGACATT
1 ATAATAATAAATAAAAATAAAATATATAACATT
*
1230841 A-AA-AATAAA-AAAAAT-AAATATATGACATT
1 ATAATAATAAATAAAAATAAAATATATAACATT
* * * * * *
1230870 A-AA-AATATATTTAAGATATGATATTATATAAAAAT
1 ATAATAATA-A-ATAA-AAAT-AAAATATATAACATT
*
1230905 -TAATAATAAA-AAATAA-AAAATA-A-AATATT
1 ATAATAATAAATAAA-AATAAAATATATAACATT
*
1230934 ATAATAATAAATAAAAATAAAATATATGACATT
1 ATAATAATAAATAAAAATAAAATATATAACATT
1230967 A
1 A
1230968 AAAATATATT
Statistics
Matches: 151, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.02
29 30 0.20
30 31 0.21
31 20 0.13
32 8 0.05
33 43 0.28
35 12 0.08
36 4 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
ATAATAATAAATAAAAATAAAATATATAACATT
Found at i:1230824 original size:39 final size:37
Alignment explanation
Indices: 1230740--1230829 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
1230730 AATATAGGTA
1230740 AAAT-AAAAT-AAAATAAAATAAATAAAATAAAAAAT
1 AAATAAAAATAAAAATAAAATAAATAAAATAAAAAAT
* * * *
1230775 ATATTAAAAAATAAAAATAAAATATATAAGATTATAATAAT
1 A-AAT-AAAAATAAAAATAAAATAAATAA-AATA-AAAAAT
1230816 AAATAAAAATAAAA
1 AAATAAAAATAAAA
1230830 TATATGACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
35 1 0.02
36 2 0.05
38 5 0.11
39 25 0.57
40 5 0.11
41 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (37 bp):
AAATAAAAATAAAAATAAAATAAATAAAATAAAAAAT
Found at i:1230937 original size:27 final size:27
Alignment explanation
Indices: 1230897--1230958 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
1230887 ATGATATTAT
1230897 ATAAAA-ATTAATAATAAAAAATAAAAA
1 ATAAAATATTAATAATAAAAAAT-AAAA
*
1230924 ATAAAATATT-ATAATAATAAATAAAA
1 ATAAAATATTAATAATAAAAAATAAAA
1230950 ATAAAATAT
1 ATAAAATAT
1230959 ATGACATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 13 0.39
27 17 0.52
28 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (27 bp):
ATAAAATATTAATAATAAAAAATAAAA
Found at i:1230939 original size:20 final size:20
Alignment explanation
Indices: 1230890--1230949 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1230880 TTAAGATATG
*
1230890 ATATTAT-ATAAAAATTAATA
1 ATATTATAATAAAAAATAA-A
* *
1230910 ATA-AAAAATAAAAAATAAA
1 ATATTATAATAAAAAATAAA
*
1230929 ATATTATAATAATAAATAAA
1 ATATTATAATAAAAAATAAA
1230949 A
1 A
1230950 ATAAAATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.16
20 27 0.84
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATATTATAATAAAAAATAAA
Found at i:1230970 original size:97 final size:100
Alignment explanation
Indices: 1230808--1231016 Score: 331
Period size: 97 Copynumber: 2.1 Consensus size: 100
1230798 ATATAAGATT
*
1230808 ATAATAATAAAT-AAAAATAAAATATATGACATTAAAAATAAAAAAAATAAATATATGACATTAA
1 ATAATAAAAAATAAAAAATAAAATATATGACATTAAAAATAAAAAAAATAAATATATGACATTAA
*
1230872 AAATATATTTAAGATATGATATTATATAAAAATTA
66 AAATATATTTAAGAGATGATATTATATAAAAATTA
*
1230907 ATAATAAAAAATAAAAAATAAAATAT-T---A-TAATAATAAATAAAAATAAAATATATGACATT
1 ATAATAAAAAATAAAAAATAAAATATATGACATTAAAAATAAA-AAAAAT-AAATATATGACATT
1230967 AAAAATATATTTAAGAGATGATATTATATAAAAATTA
64 AAAAATATATTTAAGAGATGATATTATATAAAAATTA
1231004 ATAATAAAAAATA
1 ATAATAAAAAATA
1231017 TAAATATATT
Statistics
Matches: 104, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
95 9 0.09
96 7 0.07
97 63 0.61
99 12 0.12
100 13 0.12
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (100 bp):
ATAATAAAAAATAAAAAATAAAATATATGACATTAAAAATAAAAAAAATAAATATATGACATTAA
AAATATATTTAAGAGATGATATTATATAAAAATTA
Found at i:1231197 original size:15 final size:15
Alignment explanation
Indices: 1231174--1231217 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
1231164 TGTTATTTTC
1231174 CTTGTAATCACATTA
1 CTTGTAATCACATTA
*
1231189 CTTGCAATCACATTA
1 CTTGTAATCACATTA
1231204 CTTGTAATCACATT
1 CTTGTAATCACATT
1231218 GCATTGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (15 bp):
CTTGTAATCACATTA
Found at i:1232666 original size:22 final size:20
Alignment explanation
Indices: 1232639--1232712 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 20
1232629 AAGATATAAA
1232639 AATAATAAATATTATTTTAATT
1 AATAATAAATA-TA-TTTAATT
* *
1232661 AATAATAATTAGTAATTAATT
1 AATAATAAATA-TATTTAATT
1232682 -ATAA-AAATATATTTAATTT
1 AATAATAAATATATTTAA-TT
1232701 AA-AATAAA-ATAT
1 AATAATAAATATAT
1232713 AAATTTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
18 6 0.14
19 12 0.27
20 8 0.18
21 6 0.14
22 12 0.27
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
AATAATAAATATATTTAATT
Found at i:1232702 original size:23 final size:23
Alignment explanation
Indices: 1232676--1232743 Score: 57
Period size: 25 Copynumber: 2.7 Consensus size: 23
1232666 TAATTAGTAA
1232676 TTAATTATAAAAATATATTTAAT
1 TTAATTATAAAAATATATTTAAT
* *
1232699 TTAA-AATAAAATATAAATTTTTAAT
1 TTAATTATAAAA-AT--ATATTTAAT
1232724 TTAATATAATAAAAAATATA
1 TTAAT-T-AT-AAAAATATA
1232744 AATTATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
22 6 0.18
23 6 0.18
25 12 0.35
26 2 0.06
28 4 0.12
29 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATTATAAAAATATATTTAAT
Found at i:1232764 original size:30 final size:31
Alignment explanation
Indices: 1232692--1232764 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 31
1232682 ATAAAAATAT
1232692 ATTTAATTTAA-AATAAAATATAAATTTTTA
1 ATTTAATTTAATAATAAAATATAAATTTTTA
*
1232722 ATTTAATATAATAA-AAAATATAAATTATTTA
1 ATTTAATTTAATAATAAAATATAAATT-TTTA
*
1232753 ATTT-TTTTAATA
1 ATTTAATTTAATA
1232765 GTTAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.74
31 10 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATTTAATTTAATAATAAAATATAAATTTTTA
Found at i:1235779 original size:167 final size:166
Alignment explanation
Indices: 1235478--1235780 Score: 511
Period size: 167 Copynumber: 1.8 Consensus size: 166
1235468 GGTCAATATA
* *
1235478 TTGACCTGTGTTTAGCTTTCTTTGATTCTGAGTTTTAGTTTGTTTTTTCAAAACTTAAATTTTGA
1 TTGACCTGTGTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTTCCAAAACTTAAATTTTGA
* * *
1235543 GTTTGAAGATGGTCTTGTAAATTTACAGAATGGTAAACAAGGGGGTGGAGGTTGCTTCCCTTTTT
66 GTTTGAAGATGGTCTTGTAAATATACAGAATGATAAACAAGGGGGTGGAGGGTGCTTCCCTTTTT
1235608 CTTTCATTAAAGTTTATCCTCGTAATGATCAACATT
131 CTTTCATTAAAGTTTATCCTCGTAATGATCAACATT
1235644 TTGACCTGTGTTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTTCCAAAACTTAAATTTTG
1 TTGACCTGTG-TTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTTCCAAAACTTAAATTTTG
*
1235709 AGTTTTAAGATGGTCTTGTAAATATACAGAATGATAAACAAGGGGGATGG-GGGTGCTT-CCTTT
65 AGTTTGAAGATGGTCTTGTAAATATACAGAATGATAAACAAGGGGG-TGGAGGGTGCTTCCCTTT
1235772 GTTCTTTCA
129 -TTCTTTCA
1235781 GCTTTAAAAT
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
166 15 0.12
167 110 0.86
168 3 0.02
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (166 bp):
TTGACCTGTGTTTAGCATTCTTTGATTCTGAGTTTTAGTTTGTTTTTCCAAAACTTAAATTTTGA
GTTTGAAGATGGTCTTGTAAATATACAGAATGATAAACAAGGGGGTGGAGGGTGCTTCCCTTTTT
CTTTCATTAAAGTTTATCCTCGTAATGATCAACATT
Found at i:1245061 original size:15 final size:15
Alignment explanation
Indices: 1245041--1245076 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1245031 TTATAGTTAT
1245041 TACATGAATTAAAAC
1 TACATGAATTAAAAC
1245056 TACATGAATTAAAAC
1 TACATGAATTAAAAC
1245071 TACATG
1 TACATG
1245077 TATACGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (15 bp):
TACATGAATTAAAAC
Found at i:1246261 original size:90 final size:90
Alignment explanation
Indices: 1246101--1246284 Score: 278
Period size: 90 Copynumber: 2.0 Consensus size: 90
1246091 CTAATATTTC
* *
1246101 AAGTTTTGGTATTATTTTGTTGTCATCATCTTCAAACTTTAAAAAGATTTCAATAATTGGATTTT
1 AAGTGTTGGTATTATTTTGTTGTCATCATCTCCAAACTTTAAAAAGATTTCAATAATTGGATTTT
* * * *
1246166 GATTTTTGGTTTTAGCAAATCAGGT
66 AATTTTTGGTTGTAACAAATCAAGT
* * * *
1246191 AAGTGTTGGTATTATTTTGTTTTCATCATCTCCAAACTTTAAAAGGATTTCAATGATTGGTTTTT
1 AAGTGTTGGTATTATTTTGTTGTCATCATCTCCAAACTTTAAAAAGATTTCAATAATTGGATTTT
1246256 AATTTTTGGTTGTAACAAATCAAGT
66 AATTTTTGGTTGTAACAAATCAAGT
1246281 AAGT
1 AAGT
1246285 AACTTGATAT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (90 bp):
AAGTGTTGGTATTATTTTGTTGTCATCATCTCCAAACTTTAAAAAGATTTCAATAATTGGATTTT
AATTTTTGGTTGTAACAAATCAAGT
Found at i:1246699 original size:29 final size:29
Alignment explanation
Indices: 1246657--1246725 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 29
1246647 CAAAAGTGAA
* *
1246657 TAACCCACCAAGAAGTGGAAGAATACTTG
1 TAACACACCAAGAAATGGAAGAATACTTG
* * *
1246686 TAACACACTAAGAAATGGATGGATACTTG
1 TAACACACCAAGAAATGGAAGAATACTTG
* *
1246715 TCACCCACCAA
1 TAACACACCAA
1246726 AAGTGAATGG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (29 bp):
TAACACACCAAGAAATGGAAGAATACTTG
Found at i:1251055 original size:19 final size:19
Alignment explanation
Indices: 1251031--1251068 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1251021 GATTTTCTTA
1251031 CTTCCTCTAAATACTTTTT
1 CTTCCTCTAAATACTTTTT
*
1251050 CTTCCTCTAAATGCTTTTT
1 CTTCCTCTAAATACTTTTT
1251069 TTTTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.03, T:0.53
Consensus pattern (19 bp):
CTTCCTCTAAATACTTTTT
Found at i:1257882 original size:4 final size:4
Alignment explanation
Indices: 1257873--1257905 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1257863 ATCAAAAGGA
1257873 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
1257906 GAAGGGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1259611 original size:31 final size:31
Alignment explanation
Indices: 1259571--1259634 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1259561 AGCATCGTAA
* * * *
1259571 CCCATTTCATATGCCTTGTTAGTATTTGGTG
1 CCCACTTCATATGCCATATTAGTATATGGTG
*
1259602 CCCACTTCATATGTCATATTAGTATATGGTG
1 CCCACTTCATATGCCATATTAGTATATGGTG
1259633 CC
1 CC
1259635 ACGTCAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (31 bp):
CCCACTTCATATGCCATATTAGTATATGGTG
Found at i:1263833 original size:30 final size:30
Alignment explanation
Indices: 1263797--1263861 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
1263787 AATTAAGTAC
*
1263797 TTATATTTTTATTTTGAACT-AAATATATTT
1 TTATATTTTTATTTT-AACTCAAATAAATTT
*
1263827 TTATATTTTTATTTTAAGTCAAATAAATTT
1 TTATATTTTTATTTTAACTCAAATAAATTT
1263857 TTATA
1 TTATA
1263862 ATTAATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (30 bp):
TTATATTTTTATTTTAACTCAAATAAATTT
Found at i:1264596 original size:21 final size:21
Alignment explanation
Indices: 1264570--1264619 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
1264560 AATTGTTGGC
1264570 ATATTTTTAAAATAAAAAATT
1 ATATTTTTAAAATAAAAAATT
*
1264591 ATATTTTT-AATTAAAAAATT
1 ATATTTTTAAAATAAAAAATT
*
1264611 ATCTTTTTA
1 ATATTTTTA
1264620 TATTGTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTTTAAAATAAAAAATT
Found at i:1290214 original size:25 final size:24
Alignment explanation
Indices: 1290181--1290255 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
1290171 TATATATTAC
1290181 AAAA-AATTAATATTTTAAATTTA
1 AAAATAATTAATATTTTAAATTTA
*
1290204 AAAAGTAATTAAAATTATTAATATTTA
1 AAAA-TAATTAATATT-TTAA-ATTTA
**
1290231 ATCATAA-TAATA-TTTAAATTATA
1 AAAATAATTAATATTTTAAATT-TA
1290254 AA
1 AA
1290256 TTAAATATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
22 3 0.07
23 11 0.26
24 1 0.02
25 13 0.31
26 7 0.17
27 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (24 bp):
AAAATAATTAATATTTTAAATTTA
Found at i:1293954 original size:22 final size:23
Alignment explanation
Indices: 1293916--1293961 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1293906 ATTTTTTTCA
1293916 ATTTATATTATTATATT-TATTT
1 ATTTATATTATTATATTCTATTT
*
1293938 ATTTATA-TATTTCTATTCTATTT
1 ATTTATATTA-TTATATTCTATTT
1293961 A
1 A
1293962 CTCATATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 2 0.10
22 13 0.62
23 6 0.29
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTATATTATTATATTCTATTT
Found at i:1294126 original size:21 final size:21
Alignment explanation
Indices: 1294088--1294128 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1294078 TGATATTCGT
* *
1294088 TTTTCTATTATATGAATTTTA
1 TTTTCTATGATATAAATTTTA
*
1294109 TTTTCTATGATTTAAATTTT
1 TTTTCTATGATATAAATTTT
1294129 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTCTATGATATAAATTTTA
Found at i:1296847 original size:40 final size:39
Alignment explanation
Indices: 1296792--1296874 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 39
1296782 CTTTATGATC
* *
1296792 AAAAGATGAGTTAAGGAAAAAAAAGGAA-AAAAAGAAAGAG
1 AAAAGACGAGATAAGG-AAAAAAAGGAACAAAAAGAAAG-G
* *
1296832 AAAAGACGAGATAAGGAAAAAAGGGAACCAAAAGAAAGG
1 AAAAGACGAGATAAGGAAAAAAAGGAACAAAAAGAAAGG
1296871 AAAA
1 AAAA
1296875 ATAATTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 15 0.39
40 23 0.61
ACGTcount: A:0.66, C:0.04, G:0.25, T:0.05
Consensus pattern (39 bp):
AAAAGACGAGATAAGGAAAAAAAGGAACAAAAAGAAAGG
Found at i:1296935 original size:31 final size:32
Alignment explanation
Indices: 1296871--1296936 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1296861 AAAAGAAAGG
*
1296871 AAAAATAATTCCAAAATTTGAGCTAAGGAAAA
1 AAAAATAATTCCAAAATATGAGCTAAGGAAAA
1296903 AAAAATAATTCCAAAATATGAGCTAAGGAAAA
1 AAAAATAATTCCAAAATATGAGCTAAGGAAAA
1296935 AA
1 AA
1296937 CATAAACGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (32 bp):
AAAAATAATTCCAAAATATGAGCTAAGGAAAA
Found at i:1296991 original size:42 final size:41
Alignment explanation
Indices: 1296898--1296991 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
1296888 TTGAGCTAAG
*
1296898 GAAAAAAAAATAATTCCAAAATATGAGCTAAGGAAAAAACA
1 GAAAAAAAAATAATGCCAAAATATGAGCTAAGGAAAAAACA
* * * * * **
1296939 TAAACGAAAAATGATGCTAAAATTTGAGCTAAGGAAAGAATGA
1 GAAA-AAAAAATAATGCCAAAATATGAGCTAAGGAAA-AAACA
1296982 GAAAAAAAAA
1 GAAAAAAAAA
1296992 GAAAAAAAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
41 3 0.07
42 32 0.78
43 6 0.15
ACGTcount: A:0.61, C:0.07, G:0.16, T:0.16
Consensus pattern (41 bp):
GAAAAAAAAATAATGCCAAAATATGAGCTAAGGAAAAAACA
Found at i:1298218 original size:25 final size:25
Alignment explanation
Indices: 1298180--1298227 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1298170 ATTAACAATA
*
1298180 AAATAAAATAACATAGTA-AAATAAG
1 AAATAAAAGAACATA-TATAAATAAG
*
1298205 AAATAAAAGCACATATATAAATA
1 AAATAAAAGAACATATATAAATA
1298228 TTAATTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (25 bp):
AAATAAAAGAACATATATAAATAAG
Found at i:1298555 original size:28 final size:27
Alignment explanation
Indices: 1298523--1298624 Score: 91
Period size: 28 Copynumber: 3.7 Consensus size: 27
1298513 TTATAAATTT
*
1298523 TTAATATTTTAAATATAAAATAATGATA
1 TTAATATTTTAAATAT-AAATAATCATA
* *
1298551 TTAATATTTTAATTATAAATTATTC-TA
1 TTAATATTTTAAATATAAA-TAATCATA
* **
1298578 TTCTATAAGTTAAA-ATAAATAATCATA
1 TT-AATATTTTAAATATAAATAATCATA
* *
1298605 TTAAAATTTTAAATAAAAAT
1 TTAATATTTTAAATATAAAT
1298625 TTAGTAATGT
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
26 11 0.19
27 21 0.37
28 25 0.44
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
TTAATATTTTAAATATAAATAATCATA
Found at i:1298579 original size:27 final size:28
Alignment explanation
Indices: 1298523--1298624 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 28
1298513 TTATAAATTT
1298523 TTAATATTTTAAATATAAAATAATGATA
1 TTAATATTTTAAATATAAAATAATGATA
* * **
1298551 TTAATATTTTAATTAT-AAATTATTCTA
1 TTAATATTTTAAATATAAAATAATGATA
* ** *
1298578 TTCTATAAGTTAAA-AT-AAATAATCATA
1 TT-AATATTTTAAATATAAAATAATGATA
*
1298605 TTAAAATTTTAAATA-AAAAT
1 TTAATATTTTAAATATAAAAT
1298625 TTAGTAATGT
Statistics
Matches: 56, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
26 7 0.12
27 27 0.48
28 22 0.39
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (28 bp):
TTAATATTTTAAATATAAAATAATGATA
Found at i:1300269 original size:24 final size:24
Alignment explanation
Indices: 1300237--1300286 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1300227 CGCTGGGCTT
* *
1300237 TTCTGATCTCTTCAACTGTTGCCA
1 TTCTAATCTCTTCAACTGTCGCCA
1300261 TTCTAATCTCTTCAACTGTCGCCA
1 TTCTAATCTCTTCAACTGTCGCCA
1300285 TT
1 TT
1300287 GCCGCTGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.30, G:0.10, T:0.42
Consensus pattern (24 bp):
TTCTAATCTCTTCAACTGTCGCCA
Found at i:1300982 original size:19 final size:19
Alignment explanation
Indices: 1300955--1300993 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1300945 TTGGAGCCTA
1300955 ATGAAGAAGAATTAAAGTG
1 ATGAAGAAGAATTAAAGTG
*
1300974 ATGAGGAAGAATTAAAGTG
1 ATGAAGAAGAATTAAAGTG
1300993 A
1 A
1300994 AGCAATCGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (19 bp):
ATGAAGAAGAATTAAAGTG
Found at i:1311587 original size:12 final size:12
Alignment explanation
Indices: 1311570--1311594 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1311560 ATCATTCAGA
1311570 CCATTCAAGAAT
1 CCATTCAAGAAT
1311582 CCATTCAAGAAT
1 CCATTCAAGAAT
1311594 C
1 C
1311595 TGAATACCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (12 bp):
CCATTCAAGAAT
Found at i:1312320 original size:16 final size:16
Alignment explanation
Indices: 1312286--1312331 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1312276 GAAACCAAAA
*
1312286 TTTAGATTTTGATTCT
1 TTTAGATTTTTATTCT
* *
1312302 TTTGGATTTTTATTTT
1 TTTAGATTTTTATTCT
*
1312318 TTTATATTTTTATT
1 TTTAGATTTTTATT
1312332 AAATCCAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (16 bp):
TTTAGATTTTTATTCT
Found at i:1313675 original size:68 final size:67
Alignment explanation
Indices: 1313519--1313757 Score: 228
Period size: 68 Copynumber: 3.5 Consensus size: 67
1313509 CATGTTTGGT
* * * *
1313519 ATGATGAATACCAT-ACGATTCAAGTATATGATGTAAATTTCATATACCATATGAGATGATTAAA
1 ATGATGAATGCCATGA-GATT-ATGTATATGATGTAAA-TTCATATACTATATGAGATGATTAAG
1313583 TATGC
63 TATGC
* * * * * *
1313588 ATGATGTATACCATAAGATTGTGTATATGATGTAAACTTCATATACTATATAAGGTGATTAAGTA
1 ATGATGAATGCCATGAGATTATGTATATGATGTAAA-TTCATATACTATATGAGATGATTAAGTA
1313653 TGC
65 TGC
* * * * * * * * *
1313656 ATGATAAATGCTAGGAGATTATATATATGATATATATTCCATATACTACATGAGATGATTGAGAA
1 ATGATGAATGCCATGAGATTATGTATATGATGTAAATT-CATATACTATATGAGATGATTAAGTA
**
1313721 AAC
65 TGC
*
1313724 GTGATGAATGCCATGAGATTATGTATATGATGTA
1 ATGATGAATGCCATGAGATTATGTATATGATGTA
1313758 TTTTTCATGT
Statistics
Matches: 137, Mismatches: 31, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
67 2 0.01
68 117 0.85
69 17 0.12
70 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (67 bp):
ATGATGAATGCCATGAGATTATGTATATGATGTAAATTCATATACTATATGAGATGATTAAGTAT
GC
Found at i:1324834 original size:21 final size:21
Alignment explanation
Indices: 1324797--1324836 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1324787 TTTTTCTTTA
*
1324797 TCAAATCGAATTGGATTGAGT
1 TCAAATCGAATTAGATTGAGT
1324818 TCAAATGCGAA-TAGATTGA
1 TCAAAT-CGAATTAGATTGA
1324837 TCATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (21 bp):
TCAAATCGAATTAGATTGAGT
Found at i:1344103 original size:15 final size:14
Alignment explanation
Indices: 1344085--1344120 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1344075 GAATATAAAA
1344085 TAATAAATAATAATT
1 TAATAAATAATAA-T
*
1344100 TAATTAATAATAAT
1 TAATAAATAATAAT
1344114 TAATAAA
1 TAATAAA
1344121 GTATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAAATAATAAT
Found at i:1344128 original size:22 final size:22
Alignment explanation
Indices: 1344083--1344129 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1344073 GTGAATATAA
**
1344083 AATAATAAATAATAATTTAATT
1 AATAATAAATAATAAAGTAATT
* *
1344105 AATAATAATTAATAAAGTATTT
1 AATAATAAATAATAAAGTAATT
1344127 AAT
1 AAT
1344130 TTAAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAATAAATAATAAAGTAATT
Found at i:1344164 original size:26 final size:27
Alignment explanation
Indices: 1344083--1344168 Score: 92
Period size: 26 Copynumber: 3.3 Consensus size: 27
1344073 GTGAATATAA
*
1344083 AATAATAAAT-AATA-ATTTAATTAAT
1 AATAATAAATAAAAATATTTAATTAAT
* *
1344108 AATAATTAAT-AAAGTATTTAATTTAA-
1 AATAATAAATAAAAATATTTAA-TTAAT
1344134 AATAA-AAATAAAAATATTTAATTAAT
1 AATAATAAATAAAAATATTTAATTAAT
*
1344160 TATAATAAA
1 AATAATAAA
1344169 AGAATAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 18 0.36
26 25 0.50
27 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
AATAATAAATAAAAATATTTAATTAAT
Found at i:1365145 original size:22 final size:21
Alignment explanation
Indices: 1365099--1365165 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
1365089 TATATTATGT
*
1365099 TATTATTTATTATAATATTAAA
1 TATTATTTA-TATAATAATAAA
1365121 TATTATTTATA-AATAAATAATA
1 TATTATTTATATAAT-AATAA-A
* *
1365143 TATTTTTTATGATAAAAATAAA
1 TATTATTTAT-ATAATAATAAA
1365165 T
1 T
1365166 TGATTCAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.08
21 6 0.16
22 21 0.55
23 6 0.16
24 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TATTATTTATATAATAATAAA
Found at i:1365457 original size:20 final size:20
Alignment explanation
Indices: 1365412--1365449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1365402 TCTATATATC
* *
1365412 ATTTTAAAAATTGATTTTAA
1 ATTTTAAAAAATAATTTTAA
1365432 ATTTTAAAAAATAATTTT
1 ATTTTAAAAAATAATTTT
1365450 TATTTTTAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTTAAAAAATAATTTTAA
Found at i:1365881 original size:42 final size:39
Alignment explanation
Indices: 1365857--1365964 Score: 129
Period size: 39 Copynumber: 2.9 Consensus size: 39
1365847 TATTTTGTAT
1365857 TACAAAATTATAATAAATTGAAAACAAACTATTTCCTAA
1 TACAAAATTATAATAAATTGAAAACAAACTATTTCCTAA
*
1365896 TACAAAATTATAATAAA-TGAAAA-ATTAAATATTTCCTAA
1 TACAAAATTATAATAAATTGAAAACA--AACTATTTCCTAA
* *
1365935 TA-TAAA--ATAAT-AATGGAAAACAAACTATTT
1 TACAAAATTATAATAAATTGAAAACAAACTATTT
1365965 TCATTATTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
35 9 0.15
36 10 0.16
37 2 0.03
38 9 0.15
39 31 0.51
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (39 bp):
TACAAAATTATAATAAATTGAAAACAAACTATTTCCTAA
Found at i:1366095 original size:39 final size:38
Alignment explanation
Indices: 1365962--1366356 Score: 292
Period size: 39 Copynumber: 10.4 Consensus size: 38
1365952 AAACAAACTA
* * * *
1365962 TTTT-CATTATTATAATTTTGTATAAGGAAATAATTTA
1 TTTTCCATTATTATAATTTTATATTAGGAAATAGTTTG
** *
1365999 TTTTCCATTA-T-T-ATTTTATATT-GAGAAACGGTTTAA
1 TTTTCCATTATTATAATTTTATATTAG-GAAATAGTTT-G
* *
1366035 TTTACCATGA-T-T-ATTTTATATTAGGAAATAGTTTG
1 TTTTCCATTATTATAATTTTATATTAGGAAATAGTTTG
** * *
1366070 TTTTCCCATTATTATAATTTTATATTAAAAAATAATTTA
1 TTTT-CCATTATTATAATTTTATATTAGGAAATAGTTTG
* * **
1366109 TTTTCCATTTATTATAGTTTTGTAACAGGAAATAGTTTG
1 TTTTCCA-TTATTATAATTTTATATTAGGAAATAGTTTG
* * *
1366148 TTTTCCATTTATTATAATTTTGTATTAGAAAATAATTTG
1 TTTTCCA-TTATTATAATTTTATATTAGGAAATAGTTTG
* * *
1366187 TTATCCCATTATTATAATTTTGTATCAGGAAATAGTTTG
1 TT-TTCCATTATTATAATTTTATATTAGGAAATAGTTTG
* * * *
1366226 TTTTCCATTTACTATAATTTTGTATTAGCAAATA-TTTT
1 TTTTCCA-TTATTATAATTTTATATTAGGAAATAGTTTG
* * *
1366264 TTTTTCATCA-T-T-ATTTTATATTAGGAAATAGTCTG
1 TTTTCCATTATTATAATTTTATATTAGGAAATAGTTTG
** * * *
1366299 TTTTCTCATTATTATAATTGCATATTAGGAACTATTTTA
1 TTTTC-CATTATTATAATTTTATATTAGGAAATAGTTTG
*
1366338 TTTTCTTATTGATTATAAT
1 TTTTC-CATT-ATTATAAT
1366357 AATGGGTTTA
Statistics
Matches: 288, Mismatches: 53, Indels: 31
0.77 0.14 0.08
Matches are distributed among these distances:
34 17 0.06
35 25 0.09
36 40 0.14
37 10 0.03
38 23 0.08
39 161 0.56
40 12 0.04
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (38 bp):
TTTTCCATTATTATAATTTTATATTAGGAAATAGTTTG
Found at i:1366259 original size:117 final size:111
Alignment explanation
Indices: 1365966--1366317 Score: 336
Period size: 117 Copynumber: 3.1 Consensus size: 111
1365956 AAACTATTTT
* *
1365966 CATTATTATAATTTTGTATAAGGAAATAATTTATTTTCCA-TTAT-T-ATTTTATATTGAGAAAC
1 CATTATTATAATTTTGTATAAGGAAATAATTTATTTTCCATTTATATAATTTTGTATT-AGAAAT
* * * * *
1366028 GGTTTAATTTACCATGATTATTTTATATTAGGAAATAGTTTGTTTTCC
65 AGTTT-ATTTTCCATGATTATTTTATATTAGAAAATAATTTGTTATCC
* * * **
1366076 CATTATTATAATTTTATATTAA-AAAATAATTTATTTTCCATTTATTATAGTTTTGTAACAGGAA
1 CATTATTATAATTTTGTA-TAAGGAAATAATTTATTTTCCATTTA-TATAATTTTGTATTA-GAA
* * *
1366140 ATAGTTTGTTTTCCATTTATTATAATTTTGTATTAGAAAATAATTTGTTATCC
63 ATAGTTTATTTTCCA-TGA-T-T-ATTTTATATTAGAAAATAATTTGTTATCC
* * *
1366193 CATTATTATAATTTTGTATCAGGAAATAGTTTGTTTTCCATTTACTATAATTTTGTATTAGCAAA
1 CATTATTATAATTTTGTATAAGGAAATAATTTATTTTCCATTTA-TATAATTTTGTATTAG-AAA
* * * * * * * *
1366258 TA-TTTTTTTTTCATCATTATTTTATATTAGGAAATAGTCTGTTTTCT
64 TAGTTTATTTTCCATGATTATTTTATATTAGAAAATAATTTGTTATCC
1366305 CATTATTATAATT
1 CATTATTATAATT
1366318 GCATATTAGG
Statistics
Matches: 197, Mismatches: 33, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
110 34 0.17
111 6 0.03
112 37 0.19
113 9 0.05
114 17 0.09
115 3 0.02
116 13 0.07
117 78 0.40
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (111 bp):
CATTATTATAATTTTGTATAAGGAAATAATTTATTTTCCATTTATATAATTTTGTATTAGAAATA
GTTTATTTTCCATGATTATTTTATATTAGAAAATAATTTGTTATCC
Found at i:1366286 original size:34 final size:33
Alignment explanation
Indices: 1366242--1366311 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
1366232 ATTTACTATA
* * * *
1366242 ATTTTGTATTAGCAAATATTTTTTTTTCATCATT
1 ATTTTATATTAGCAAATAGTCTGTTTTC-TCATT
*
1366276 ATTTTATATTAGGAAATAGTCTGTTTTCTCATT
1 ATTTTATATTAGCAAATAGTCTGTTTTCTCATT
1366309 ATT
1 ATT
1366312 ATAATTGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 8 0.26
34 23 0.74
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56
Consensus pattern (33 bp):
ATTTTATATTAGCAAATAGTCTGTTTTCTCATT
Found at i:1367616 original size:33 final size:35
Alignment explanation
Indices: 1367579--1367643 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 35
1367569 ACATAATATT
* *
1367579 TCCTAATATAAAATAATAAT-AGAAAA-AAATAAC
1 TCCTAAAATAAAATAAAAATAAGAAAACAAATAAC
1367612 TCCTAAAATAAAATAAAAATAAGAAAACAAAT
1 TCCTAAAATAAAATAAAAATAAGAAAACAAAT
1367644 TATTATTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 18 0.64
34 6 0.21
35 4 0.14
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (35 bp):
TCCTAAAATAAAATAAAAATAAGAAAACAAATAAC
Found at i:1367690 original size:39 final size:39
Alignment explanation
Indices: 1367647--1367748 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 39
1367637 AACAAATTAT
* *
1367647 TATTTTGTACTACAAAATTATAATAAATCAAAAACAAAC
1 TATTTTCTAATACAAAATTATAATAAATCAAAAACAAAC
* ** *
1367686 TATTTCCTAATACAAAATTATAATAAATGGAAAACTAAC
1 TATTTTCTAATACAAAATTATAATAAATCAAAAACAAAC
* * *
1367725 TATTTTCTAGTATAAAATAATAAT
1 TATTTTCTAATACAAAATTATAAT
1367749 GGAAAATAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (39 bp):
TATTTTCTAATACAAAATTATAATAAATCAAAAACAAAC
Found at i:1367869 original size:36 final size:35
Alignment explanation
Indices: 1367770--1367884 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 35
1367760 TATTTTTATT
* * * * *
1367770 ATTATAATTTTGTATCAGGAAATAGTTT-ATTTTCT
1 ATTATTATTTTATATTA-GAAATAGTTTGATTTACC
1367805 ATTATTATTTTATATTAGAAA-ACGGTTTGATTTACC
1 ATTATTATTTTATATTAGAAATA--GTTTGATTTACC
* *
1367841 ATTGTTATTTTATATTACGAAATAGTTTG-TTTTCGC
1 ATTATTATTTTATATTA-GAAATAGTTTGATTTAC-C
1367877 ATTATTAT
1 ATTATTAT
1367885 AATTTTGTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
33 1 0.02
34 4 0.06
35 22 0.33
36 34 0.52
37 4 0.06
38 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.51
Consensus pattern (35 bp):
ATTATTATTTTATATTAGAAATAGTTTGATTTACC
Found at i:1367896 original size:39 final size:38
Alignment explanation
Indices: 1367767--1368234 Score: 395
Period size: 39 Copynumber: 12.3 Consensus size: 38
1367757 AACTATTTTT
* *
1367767 ATTATTATAATTTTGTATCAGGAAATAGTTTATTTT-C
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
* * * ** *
1367804 --TATTATTATTTTATATTAGAAAACGGTTTGATTTACC
1 ATTATTATAATTTTGTATTAGGAAATAGTTTG-TTTTCC
* * *
1367841 ATT-GT-T-ATTTTATATTACGAAATAGTTTGTTTTCGC
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTC-C
* *
1367877 ATTATTATAATTTTGTATTAAGAAATAATTTGTTTTCC
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
* * *
1367915 ATTTATTATAGTTTTGTATCAGGAAATAGTTTGTTTTTC
1 A-TTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
** *
1367954 ATTTATTATAATTTTGTATTAAAAAATAATTTGTTATTCC
1 A-TTATTATAATTTTGTATTAGGAAATAGTTTGTT-TTCC
*
1367994 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCT
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
* **
1368032 ATTTATTATAA-TTTATATTAACAAATAGTTT-TTTTCATC
1 A-TTATTATAATTTTGTATTAGGAAATAGTTTGTTTTC--C
* ** * *
1368071 ATTATTTTATATTAGGAAATTAGGAAATAGTTGGTTTTCC
1 ATTATTATA-ATTTTG-TATTAGGAAATAGTTTGTTTTCC
**
1368111 ATTTATTATAATTTTGTATTAACAAATAGTTT-TTTT-C
1 A-TTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
* * *
1368148 ATCA-T-T-ATTTTATATTAAGAAATAGTTTGTTTTCCC
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTT-CC
* * *
1368184 ATTATTATAATTGTATATTAGGAAATCGTTTGTTTTCC
1 ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
1368222 TATTAATTATAAT
1 -ATT-ATTATAAT
1368235 AATGGGTTTA
Statistics
Matches: 346, Mismatches: 59, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
33 20 0.06
34 5 0.01
35 28 0.08
36 32 0.09
37 11 0.03
38 39 0.11
39 168 0.49
40 19 0.05
41 19 0.05
42 5 0.01
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (38 bp):
ATTATTATAATTTTGTATTAGGAAATAGTTTGTTTTCC
Found at i:1368080 original size:33 final size:33
Alignment explanation
Indices: 1368016--1368189 Score: 98
Period size: 33 Copynumber: 4.7 Consensus size: 33
1368006 TTGTATTAGG
*
1368016 AAATAGTTTGTTTTCTATTTATTATAATTTATATTAAC
1 AAATAGTTT-TTTTC-A-TCATTAT--TTTATATTAAC
*
1368054 AAATAGTTTTTTTCATCATTATTTTATATTAGGAAATTAGG
1 AAATAGTTTTTTTCATCATTATTTTATATT-----A--A-C
* * *
1368095 AAATAGTTGGTTTTCCATTTATTATAATTTTGTATTAAC
1 AAATAGTT--TTTTTCA-TCA-T-T-ATTTTATATTAAC
*
1368134 AAATAGTTTTTTTCATCATTATTTTATATTAAG
1 AAATAGTTTTTTTCATCATTATTTTATATTAAC
*
1368167 AAATAGTTTGTTTTC-CCATTATT
1 AAATAGTTT-TTTTCATCATTATT
1368190 ATAATTGTAT
Statistics
Matches: 110, Mismatches: 11, Indels: 35
0.71 0.07 0.22
Matches are distributed among these distances:
33 35 0.32
34 6 0.05
35 7 0.06
36 3 0.03
37 11 0.10
38 10 0.09
39 8 0.07
40 2 0.02
41 8 0.07
42 1 0.01
43 6 0.05
44 2 0.02
45 1 0.01
46 1 0.01
47 9 0.08
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (33 bp):
AAATAGTTTTTTTCATCATTATTTTATATTAAC
Found at i:1368099 original size:41 final size:41
Alignment explanation
Indices: 1368048--1368170 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 41
1368038 TATAATTTAT
*
1368048 ATTAACAAATAGTTTTTTTCATCATTATTTTATATTAGGAA
1 ATTAACAAATAGTTTTTTTCATCATTATTTTATATTAAGAA
** * * ** *
1368089 ATTAGGAAATAGTTGGTTTTC--CATT-TATTATAATTTTG-T
1 ATTAACAAATAGTT-TTTTTCATCATTATTTTAT-ATTAAGAA
1368128 ATTAACAAATAGTTTTTTTCATCATTATTTTATATTAAGAA
1 ATTAACAAATAGTTTTTTTCATCATTATTTTATATTAAGAA
1368169 AT
1 AT
1368171 AGTTTGTTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
38 5 0.08
39 17 0.27
40 16 0.26
41 19 0.31
42 5 0.08
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.50
Consensus pattern (41 bp):
ATTAACAAATAGTTTTTTTCATCATTATTTTATATTAAGAA
Found at i:1369562 original size:42 final size:39
Alignment explanation
Indices: 1369540--1369630 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
1369530 TTTTGTACTG
1369540 CAAAATTATAATAAATCGAAAACAAACTATTTTTTAATA
1 CAAAATTATAATAAATCGAAAACAAACTATTTTTTAATA
* ** **
1369579 CAAAATTATAATAAATGGAAAATTAACTATTTCCTAATA
1 CAAAATTATAATAAATCGAAAACAAACTATTTTTTAATA
* *
1369618 TAAAATAATAATA
1 CAAAATTATAATA
1369631 GAAAATAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (39 bp):
CAAAATTATAATAAATCGAAAACAAACTATTTTTTAATA
Found at i:1369571 original size:39 final size:39
Alignment explanation
Indices: 1369528--1369630 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
1369518 AACAAATTAT
* *
1369528 TATTTTGTACTGCAAAATTATAATAAATCGAAAACAAAC
1 TATTTTGTAATACAAAATTATAATAAATCGAAAACAAAC
* * **
1369567 TATTTTTTAATACAAAATTATAATAAATGGAAAATTAAC
1 TATTTTGTAATACAAAATTATAATAAATCGAAAACAAAC
** * *
1369606 TATTTCCTAATATAAAATAATAATA
1 TATTTTGTAATACAAAATTATAATA
1369631 GAAAATAAAC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (39 bp):
TATTTTGTAATACAAAATTATAATAAATCGAAAACAAAC
Found at i:1369730 original size:36 final size:36
Alignment explanation
Indices: 1369651--1369900 Score: 154
Period size: 36 Copynumber: 6.8 Consensus size: 36
1369641 TATTTTCATT
* * * *
1369651 ATTATAATTTTGTATAAGGAAATAGTTT-ATTTTCC
1 ATTATTATTTTATATTAGGAAATAGTTTGATTTACC
* *
1369686 ATTATTATTTTATATTGGGAAATGGTTTGATTTACC
1 ATTATTATTTTATATTAGGAAATAGTTTGATTTACC
* * *
1369722 ATTATTATTTTATATTAGGAAATAGTTCGTTTTCCC
1 ATTATTATTTTATATTAGGAAATAGTTTGATTTACC
* *
1369758 ATTATTATAATTT-TGAATTAAGAAAT-GATTTG-TTTTCC
1 ATTATTAT--TTTAT--ATTAGGAAATAG-TTTGATTTACC
* * ** *
1369796 AATTATTATACTTTTGTATTAGCAAATAGTTTTTTTTATC
1 -ATTA-T-TA-TTTTATATTAGGAAATAGTTTGATTTACC
* * *
1369836 ATTA-T-TTTT-TATTAGAAAATAGTTTGTTTTCCC
1 ATTATTATTTTATATTAGGAAATAGTTTGATTTACC
* *
1369869 ATTATTATAATTGCATATTAGGAAATAATTTG
1 ATTATTAT--TT-TATATTAGGAAATAGTTTG
1369901 TTTTGCTATT
Statistics
Matches: 170, Mismatches: 26, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
33 24 0.14
34 5 0.03
35 24 0.14
36 46 0.27
37 3 0.02
38 9 0.05
39 46 0.27
40 9 0.05
41 3 0.02
42 1 0.01
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (36 bp):
ATTATTATTTTATATTAGGAAATAGTTTGATTTACC
Found at i:1369765 original size:39 final size:39
Alignment explanation
Indices: 1369647--1369904 Score: 188
Period size: 39 Copynumber: 6.9 Consensus size: 39
1369637 AAACTATTTT
* * * *
1369647 CATTATTATAATTTTGTATAAGGAAATAGTTTATTTT-C
1 CATTATTATTATTTTATATTAGGAAATAGTTTGTTTTCC
* * * *
1369685 C---ATTATTATTTTATATTGGGAAATGGTTTGATTTAC
1 CATTATTATTATTTTATATTAGGAAATAGTTTGTTTTCC
*
1369721 C---ATTATTATTTTATATTAGGAAATAGTTCGTTTTCC
1 CATTATTATTATTTTATATTAGGAAATAGTTTGTTTTCC
* *
1369757 CATTATTATAATTTTGA-ATTAAGAAAT-GATTTGTTTTCC
1 CATTATTATTATTTT-ATATTAGGAAATAG-TTTGTTTTCC
* * *
1369796 AATTATTA-TACTTTTGTATTAGCAAATAG-TT-TTTT--
1 CATTATTATTA-TTTTATATTAGGAAATAGTTTGTTTTCC
* * *
1369831 --TTATCATTATTTTTTATTAGAAAATAGTTTGTTTTCC
1 CATTATTATTATTTTATATTAGGAAATAGTTTGTTTTCC
* ** *
1369868 CATTATTATAATTGCATATTAGGAAATAATTTGTTTT
1 CATTATTATTATTTTATATTAGGAAATAGTTTGTTTT
1369905 GCTATTGATT
Statistics
Matches: 174, Mismatches: 30, Indels: 31
0.74 0.13 0.13
Matches are distributed among these distances:
33 21 0.12
34 4 0.02
35 30 0.17
36 33 0.19
37 4 0.02
38 5 0.03
39 75 0.43
40 2 0.01
ACGTcount: A:0.31, C:0.07, G:0.11, T:0.51
Consensus pattern (39 bp):
CATTATTATTATTTTATATTAGGAAATAGTTTGTTTTCC
Found at i:1369849 original size:33 final size:33
Alignment explanation
Indices: 1369807--1369874 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
1369797 ATTATTATAC
* * *
1369807 TTTTGTATTAGCAAATAGTTTTTTTTATCATTA
1 TTTTGTATTAGAAAATAGTTTGTTTTACCATTA
* *
1369840 TTTTTTATTAGAAAATAGTTTGTTTTCCCATTA
1 TTTTGTATTAGAAAATAGTTTGTTTTACCATTA
1369873 TT
1 TT
1369875 ATAATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.57
Consensus pattern (33 bp):
TTTTGTATTAGAAAATAGTTTGTTTTACCATTA
Found at i:1372051 original size:17 final size:16
Alignment explanation
Indices: 1372029--1372060 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1372019 GAAAAAAGGA
1372029 AATAATAAATAATAAAC
1 AATAATAAAT-ATAAAC
1372046 AATAATAAATATAAA
1 AATAATAAATATAAA
1372061 TAAAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
AATAATAAATATAAAC
Found at i:1375868 original size:14 final size:14
Alignment explanation
Indices: 1375849--1375880 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1375839 TTTTTATAAT
1375849 TAATAATTAATTAA
1 TAATAATTAATTAA
1375863 TAATAATTAATTAA
1 TAATAATTAATTAA
1375877 -AATA
1 TAATA
1375881 TTTTTTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATAATTAATTAA
Found at i:1380146 original size:28 final size:27
Alignment explanation
Indices: 1380088--1380153 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
1380078 TATTTGAGAT
*
1380088 ATAATATTTTATCATAAATTTGTGATGA
1 ATAA-ATTTTATCATAAATTTATGATGA
*
1380116 ATACTAATTTTAT-ATAAATTTAATTAT-A
1 ATA--AATTTTATCATAAATTT-ATGATGA
1380144 ATAAATTTTA
1 ATAAATTTTA
1380154 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
26 7 0.21
28 15 0.45
29 10 0.30
30 1 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
ATAAATTTTATCATAAATTTATGATGA
Found at i:1381818 original size:2 final size:2
Alignment explanation
Indices: 1381811--1381840 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1381801 ATTATTAATA
1381811 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1381841 ACATAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1382042 original size:13 final size:13
Alignment explanation
Indices: 1382024--1382048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1382014 TCCAAATAAA
1382024 TTAAAAATATTTT
1 TTAAAAATATTTT
1382037 TTAAAAATATTT
1 TTAAAAATATTT
1382049 GGTTTTAAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAAAATATTTT
Found at i:1384233 original size:120 final size:118
Alignment explanation
Indices: 1384011--1384247 Score: 339
Period size: 120 Copynumber: 2.0 Consensus size: 118
1384001 TGTAAAGATG
* * * *
1384011 GGGGAACAAACACAAATGTCTAGATGAAATGTAATTGACCTCATCAGTATTATTAAGTCGTATGG
1 GGGGAACAAACACAAATGTCGAGAAGAAATGTAATCGACCTCATCAGTATTATTAAGTCATATGG
* *
1384076 TAATCTCAAATCTCAGCCTCATTGACCTGTCCATGTTTTTTTTGGTTAGTTTT
66 CAATCTCAAATCTCAGCCCCATTGACCTGTCCATGTTTTTTTTGGTTAGTTTT
* * * *
1384129 GGGGAACAAACACACAAATGTCGAGAAGAAATGTGATCGACTTCCTTAGTATTATTAAGTCATAT
1 GGGGAAC-AA-ACACAAATGTCGAGAAGAAATGTAATCGACCTCATCAGTATTATTAAGTCATAT
* * *
1384194 GGCGATCTCAAATCTCTGCCCCATTGACCTTTCCATGTTTTTTTTGGTTAGTTT
64 GGCAATCTCAAATCTCAGCCCCATTGACCTGTCCATGTTTTTTTTGGTTAGTTT
1384248 CAGTTTTTCT
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
118 7 0.07
119 2 0.02
120 95 0.91
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (118 bp):
GGGGAACAAACACAAATGTCGAGAAGAAATGTAATCGACCTCATCAGTATTATTAAGTCATATGG
CAATCTCAAATCTCAGCCCCATTGACCTGTCCATGTTTTTTTTGGTTAGTTTT
Found at i:1399862 original size:89 final size:88
Alignment explanation
Indices: 1399728--1399896 Score: 248
Period size: 89 Copynumber: 1.9 Consensus size: 88
1399718 AAATAATACC
*
1399728 TTGTAAATGGGTACAATTAATCAAAAAGTTATTGCATTAAGAAGAGAAAGGAAAAGAAAATACTA
1 TTGTAAATGGGTACAATTAATCAAAAAGTTATTGCATTAACAAGAGAAAGGAAAAG-AAATACTA
*
1399793 TACCTATAAAACATTGATATCATT
65 TACCAATAAAACATTGATATCATT
** * * * * *
1399817 TTGTAAATGGGTACAATTAATCCCAAATTTCTTGTATTGACAAGAGAAAGGAAAAGAAATATTAT
1 TTGTAAATGGGTACAATTAATCAAAAAGTTATTGCATTAACAAGAGAAAGGAAAAGAAATACTAT
1399882 ACCAATAAAACATTG
66 ACCAATAAAACATTG
1399897 GTACCAATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 22 0.31
89 49 0.69
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (88 bp):
TTGTAAATGGGTACAATTAATCAAAAAGTTATTGCATTAACAAGAGAAAGGAAAAGAAATACTAT
ACCAATAAAACATTGATATCATT
Found at i:1400037 original size:21 final size:22
Alignment explanation
Indices: 1399997--1400038 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1399987 ATCATTAGTC
* *
1399997 ATAAAATTTTATTTAATTTAAA
1 ATAAAATTATATTGAATTTAAA
1400019 ATAAAATTATA-TGAATTTAA
1 ATAAAATTATATTGAATTTAA
1400039 TTGAATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAAATTATATTGAATTTAAA
Found at i:1400606 original size:89 final size:88
Alignment explanation
Indices: 1400495--1400753 Score: 331
Period size: 89 Copynumber: 2.9 Consensus size: 88
1400485 TAAATAATAT
* * * * *
1400495 CTCGTAAATAGGTACAATTAATCAAAAAGTTCTTCTATTAAGAAGAAAAAGGAAAAGAAAATACT
1 CTCGTAAATGGGTACAATTAATCGAAAA-TTCTTATATTAACAAGAGAAAGGAAAAGAAAATACT
*
1400560 ATACCTATAAAACATTGATATCAT
65 ATACCTATAAAACATTGATATCAC
* * * * * * *
1400584 TTTGTAAGTGGGTACAATTAATCGGAAATTTCTTATATTGATAAGAGAAAGGAAAAAAAAATACT
1 CTCGTAAATGGGTACAATTAATC-GAAAATTCTTATATTAACAAGAGAAAGGAAAAGAAAATACT
* *
1400649 ATACCAATAAAACATTGGTATCAC
65 ATACCTATAAAACATTGATATCAC
1400673 CTCGTAAATGGGTACAATTAATTCCGAAAATTCTTGA-ATTAACAAGAGAAAGGAAAAGAAAATA
1 CTCGTAAATGGGTACAATTAA-T-CGAAAATTCTT-ATATTAACAAGAGAAAGGAAAAGAAAATA
1400737 CTATACCTATAAAACAT
63 CTATACCTATAAAACAT
1400754 CGGTATAATT
Statistics
Matches: 144, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
89 89 0.62
90 53 0.37
91 2 0.01
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (88 bp):
CTCGTAAATGGGTACAATTAATCGAAAATTCTTATATTAACAAGAGAAAGGAAAAGAAAATACTA
TACCTATAAAACATTGATATCAC
Found at i:1409590 original size:89 final size:88
Alignment explanation
Indices: 1409479--1409736 Score: 338
Period size: 89 Copynumber: 2.9 Consensus size: 88
1409469 TAAATAATAT
* * * * *
1409479 CTCGTAAATAGGTACAATTAATCAAAAAGTTCTTCTATTAAGAAGAAAAAGGAAAAGAAAATACT
1 CTCGTAAATGGGTACAATTAATCGAAAA-TTCTTATATTAACAAGAGAAAGGAAAAGAAAATACT
*
1409544 ATACCTATAAAACATTGATATCAT
65 ATACCTATAAAACATTGATATCAC
* * * * * * *
1409568 TTTGTAAGTGGGTACAATTAATCGGAAATTTCTTATATTGATAAGAGAAAGGAAAAAAAAATACT
1 CTCGTAAATGGGTACAATTAATC-GAAAATTCTTATATTAACAAGAGAAAGGAAAAGAAAATACT
* *
1409633 ATACCAATAAAACATTGGTATCAC
65 ATACCTATAAAACATTGATATCAC
1409657 CTCGTAAATGGGTACAATTAATCCGAAAATTCTTGA-ATTAACAAGAGAAAGGAAAAGAAAATAC
1 CTCGTAAATGGGTACAATTAAT-CGAAAATTCTT-ATATTAACAAGAGAAAGGAAAAGAAAATAC
1409721 TATACCTATAAAACAT
64 TATACCTATAAAACAT
1409737 CGGTATAATT
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
89 139 0.97
90 5 0.03
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.27
Consensus pattern (88 bp):
CTCGTAAATGGGTACAATTAATCGAAAATTCTTATATTAACAAGAGAAAGGAAAAGAAAATACTA
TACCTATAAAACATTGATATCAC
Found at i:1447180 original size:6 final size:6
Alignment explanation
Indices: 1447171--1447197 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1447161 GACTTAGACT
1447171 TTGGGG TTGGGG TTGGGG TTGGGG TTG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTG
1447198 ACGTAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (6 bp):
TTGGGG
Found at i:1451050 original size:17 final size:17
Alignment explanation
Indices: 1451028--1451079 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1451018 GATATTTTTT
1451028 GCAATGAGGGGAATTCA
1 GCAATGAGGGGAATTCA
*
1451045 GCAATGAGGGTGGA---A
1 GCAATGAGGG-GAATTCA
1451060 GCAATGAGGGGAATTCA
1 GCAATGAGGGGAATTCA
1451077 GCA
1 GCA
1451080 GCACAAGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
17 14 0.48
18 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.38, T:0.15
Consensus pattern (17 bp):
GCAATGAGGGGAATTCA
Found at i:1467744 original size:59 final size:59
Alignment explanation
Indices: 1467652--1467766 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
1467642 AACAAGAGCT
* * * *
1467652 TCATATTTTTTCATGCATTGACGTCTTCTGCCACTACAATTTATCTGACACGGCAGTTG
1 TCATAATTTTCCATGCATTGACGTCTTCTGCCACTACAACTTATCTGACAAGGCAGTTG
* * *
1467711 TCATAATTTTCCATGTATTGATGTCTTCTGCCACTACAGCTTATCTGACAAGGCAG
1 TCATAATTTTCCATGCATTGACGTCTTCTGCCACTACAACTTATCTGACAAGGCAG
1467767 CCGTCATGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (59 bp):
TCATAATTTTCCATGCATTGACGTCTTCTGCCACTACAACTTATCTGACAAGGCAGTTG
Found at i:1469747 original size:33 final size:33
Alignment explanation
Indices: 1469705--1469769 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1469695 ATCTTTTAGA
1469705 GAGAAGGGTCACTTT-TGACTATATCATAACTTG
1 GAGAAGGGTCA-TTTGTGACTATATCATAACTTG
1469738 GAGAAGGGTCATTTGTGACTATATCATAACTT
1 GAGAAGGGTCATTTGTGACTATATCATAACTT
1469770 AACTTGATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (33 bp):
GAGAAGGGTCATTTGTGACTATATCATAACTTG
Found at i:1473155 original size:3 final size:3
Alignment explanation
Indices: 1473147--1473175 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1473137 TCATCAATTA
1473147 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1473176 TAATAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1475504 original size:11 final size:11
Alignment explanation
Indices: 1475488--1475512 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1475478 GATACTAACA
1475488 TGACATTAATG
1 TGACATTAATG
1475499 TGACATTAATG
1 TGACATTAATG
1475510 TGA
1 TGA
1475513 AAAGTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (11 bp):
TGACATTAATG
Done.