Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 56
Found at i:3561920 original size:42 final size:42
Alignment explanation
Indices: 3561853--3562031 Score: 304
Period size: 42 Copynumber: 4.3 Consensus size: 42
3561843 TATATTCGCA
* * *
3561853 TTGCGAGAGTCCAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
3561895 TTGCGATAGTCGATGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
3561937 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
3561979 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
3562021 TTGCGATAGTC
1 TTGCGATAGTC
3562032 CAAAATCGCA
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 128 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:3561959 original size:84 final size:84
Alignment explanation
Indices: 3561828--3562034 Score: 312
Period size: 84 Copynumber: 2.5 Consensus size: 84
3561818 GCTTCGACTA
* * *
3561828 TCGCATTGCGATTTA-T--ATATTCGCATTGCGAGAGTCCAAGTTTGCGTTGCGATTTATTCCAA
1 TCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAA
*
3561890 GTTCGTTGCGATAGTCGATGT
64 GTTCGTTGCGATAGTCGAAGT
*
3561911 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGT
3561976 TCGTTGCGATAGTCGAAGT
66 TCGTTGCGATAGTCGAAGT
* *
3561995 TCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
3562035 AATCGCAACG
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
83 15 0.13
84 92 0.81
86 6 0.05
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (84 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGT
TCGTTGCGATAGTCGAAGT
Found at i:3562796 original size:21 final size:21
Alignment explanation
Indices: 3562772--3562864 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
3562762 TGCGATTTTG
3562772 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
*
3562793 GACTATCGCAATGCGAA-TAT-
1 GACTATCGCAACGCGAACT-TC
* * *
3562813 GTA-AATCGCAATGCGAACTTG
1 G-ACTATCGCAACGCGAACTTC
*
3562834 GACTATCGCAACGTGAACTTC
1 GACTATCGCAACGCGAACTTC
3562855 GACTATCGCA
1 GACTATCGCA
3562865 TTGCGATTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:3562884 original size:62 final size:63
Alignment explanation
Indices: 3562761--3562954 Score: 195
Period size: 62 Copynumber: 3.1 Consensus size: 63
3562751 CCACCAGTCG
* *
3562761 TTGCGAT-TTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGC
1 TTGCGATACTTGGACTATCGCAACGCGAACTTCGACTATCGCATTGCG-AT-T-TACATATTCGC
3562822 A
63 A
* *
3562823 ATGCGA-ACTTGGACTATCGCAACGTGAACTTCGACTATCGCATTGCGATTTACATATTCGCA
1 TTGCGATACTTGGACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCA
* *** * ** *
3562885 TTGCGATAGTCCAAGT-TCGCATTGCGATA-GTCGACTATCGCATTGCGATTTACATATTCGCA
1 TTGCGATACTTGGACTATCGCAACGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCA
3562947 TTGCGATA
1 TTGCGATA
3562955 GTCCAAGTTC
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.02
60 2 0.02
61 3 0.03
62 100 0.89
63 5 0.04
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (63 bp):
TTGCGATACTTGGACTATCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCA
Found at i:3562905 original size:21 final size:21
Alignment explanation
Indices: 3562879--3562967 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 21
3562869 GATTTACATA
3562879 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
3562900 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
3562920 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
3562941 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
3562962 TTCGCA
1 TTCGCA
3562968 AGTTCGCATT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
20 17 0.30
21 39 0.68
22 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3562993 original size:21 final size:21
Alignment explanation
Indices: 3562966--3563106 Score: 164
Period size: 21 Copynumber: 6.8 Consensus size: 21
3562956 TCCAAGTTCG
3562966 CAAGTTCGCATTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTC
* *
3562987 GAAGTTCGCGTTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTC
3563008 CAAGTTCGCATTGCGATAGT-
1 CAAGTTCGCATTGCGATAGTC
* * *
3563028 C-GGCTATCGCATTGCGAT-TTA
1 CAAG-T-TCGCATTGCGATAGTC
3563049 CATA-TTCGCATTGCGATAGTC
1 CA-AGTTCGCATTGCGATAGTC
3563070 CAAGTTCGCATTGCGATAGTC
1 CAAGTTCGCATTGCGATAGTC
* *
3563091 CAAGTTTGCGTTGCGA
1 CAAGTTCGCATTGCGA
3563107 ATCTGGAAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.01
20 16 0.16
21 85 0.83
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
CAAGTTCGCATTGCGATAGTC
Found at i:3563779 original size:3 final size:3
Alignment explanation
Indices: 3563768--3563811 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
3563758 AAGATAAAAA
*
3563768 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT A
3563812 TTTTTATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 28 0.76
4 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3564298 original size:3 final size:3
Alignment explanation
Indices: 3564290--3564358 Score: 120
Period size: 3 Copynumber: 22.7 Consensus size: 3
3564280 AGTCTCAAAT
*
3564290 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3564338 ATA ATAA ATA ATA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA AT
3564359 CTGAAGTGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 60 0.95
4 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3564907 original size:16 final size:16
Alignment explanation
Indices: 3564871--3564907 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3564861 TGACAAATAA
*
3564871 CATTCGATCCAAATTG
1 CATTTGATCCAAATTG
3564887 CATTTGATCCAAATTG
1 CATTTGATCCAAATTG
3564903 CATTT
1 CATTT
3564908 AATGTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (16 bp):
CATTTGATCCAAATTG
Found at i:3566047 original size:15 final size:15
Alignment explanation
Indices: 3566024--3566053 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3566014 GTTAGGTGTT
3566024 TTGAAAACTTTATCC
1 TTGAAAACTTTATCC
*
3566039 TTGACAACTTTATCC
1 TTGAAAACTTTATCC
3566054 ATGCAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (15 bp):
TTGAAAACTTTATCC
Found at i:3566162 original size:17 final size:18
Alignment explanation
Indices: 3566126--3566170 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
3566116 TTTATGAGGA
*
3566126 AATTGGAATCTTTGCAGG
1 AATTGGAATCTGTGCAGG
3566144 AATTGGAATCTGT-CAGG
1 AATTGGAATCTGTGCAGG
3566161 AATTGGAATC
1 AATTGGAATC
3566171 CAATTCCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (18 bp):
AATTGGAATCTGTGCAGG
Found at i:3566828 original size:37 final size:38
Alignment explanation
Indices: 3566742--3566835 Score: 136
Period size: 38 Copynumber: 2.5 Consensus size: 38
3566732 TTTTTACCCT
3566742 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACCCGAATATCACACTTAAAA
* * *
3566781 AAACCTGACCCGACTCGACCCGAATATCACTCTT-AAA
1 AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
*
3566818 AAACCCGACCCAACCCGA
1 AAACCCGACCCGACCCGA
3566836 ATATATGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
37 18 0.37
38 25 0.51
39 6 0.12
ACGTcount: A:0.38, C:0.39, G:0.11, T:0.12
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:3567055 original size:270 final size:267
Alignment explanation
Indices: 3566560--3567156 Score: 746
Period size: 270 Copynumber: 2.2 Consensus size: 267
3566550 ATTTTTATTC
* * * *
3566560 AATATATGAATTAGAAACTCGACCAGACACGACACAAAATAATAAAAATATTATTTTTATTCAAT
1 AATATATGAATTAGAAACCCGACCCG--A--AC-CGAAATAATAAAAATATTATTTTTATTCAAA
* * * *
3566625 AAAAACATTGACTTAATTGAAAAAAAAATTATATATAGAGGGGTATTATTGTAATTATTTATAAA
61 AAAAACAGTGACTTAATTGAAAAAAAAATTATATATAGAAGGGTATTATTATAATTATTCATAAA
* * *
3566690 TATATAAGGTAAAATTATATATTTTTTTCGGGTCGTCTAGTTTTTTTACCCTAAACCCGAACCCG
126 TATATAAGGTAAAATTATATATTATTTTCGGGTCGGCTAG-TTTTTCACCCTAAACCCGAACCCG
* * ** *
3566755 ACCCGACCCGAATATCACACTTAAAAAAACCTGACCCGACTCGACCCGAATATCACTCTT-AAAA
190 ACCAGACCCGAATATCACACTTAAAAAAACCT-ACCCGACCCGACCAAAATA-AACT-TTCAAAA
3566819 AACCCGACCCAACCCG
252 AACCCGACCCAACCCG
*
3566835 AATATATGAATTAGAAATCCGACCCGAACCGAAATAATAAAAA-ATTATTTTTATTCAAAAAAAA
1 AATATATGAATTAGAAACCCGACCCGAACCGAAATAATAAAAATATTATTTTTATTCAAAAAAAA
* * *
3566899 TAGTGACTTAATTGAAAATATATATATATATATATAGAAGGGTATTATTATAATTATTCCTAAAT
66 CAGTGACTTAATTGAAAA-A-A-AAAT-TATATATAGAAGGGTATTATTATAATTATTCATAAAT
* *
3566964 ATATAAGGTAAAATTATATA-TATTTTCGGGTCGGGTA-TTTTTCACCCTAAACCCGAACTCGAC
127 ATATAAGGTAAAATTATATATTATTTTCGGGTCGGCTAGTTTTTCACCCTAAACCCGAACCCGAC
* *** *
3567027 CAGACCCGAATATCACACTTAAAAAAACCTACCCGACCCGACCAAAATAAAGTTTCATCTAACCT
192 CAGACCCGAATATCACACTTAAAAAAACCTACCCGACCCGACCAAAATAAACTTTCAAAAAACCC
*
3567092 GACCCGACCCG
257 GACCCAACCCG
3567103 AATATATGAATTAGAAACCCGACCCGAA---ATAATAA-AAAAATA--ATTTTTATTCAA
1 AATATATGAATTAGAAACCCGACCCGAACCGA-AATAATAAAAATATTATTTTTATTCAA
3567157 TATATAAATA
Statistics
Matches: 286, Mismatches: 29, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
264 12 0.04
265 6 0.02
266 6 0.02
267 2 0.01
268 44 0.15
269 52 0.18
270 67 0.23
271 3 0.01
272 17 0.06
273 54 0.19
275 23 0.08
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.29
Consensus pattern (267 bp):
AATATATGAATTAGAAACCCGACCCGAACCGAAATAATAAAAATATTATTTTTATTCAAAAAAAA
CAGTGACTTAATTGAAAAAAAAATTATATATAGAAGGGTATTATTATAATTATTCATAAATATAT
AAGGTAAAATTATATATTATTTTCGGGTCGGCTAGTTTTTCACCCTAAACCCGAACCCGACCAGA
CCCGAATATCACACTTAAAAAAACCTACCCGACCCGACCAAAATAAACTTTCAAAAAACCCGACC
CAACCCG
Found at i:3568858 original size:22 final size:22
Alignment explanation
Indices: 3568814--3568858 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3568804 CACTAGTTAT
*
3568814 TATATATGATTATTATCATGAA
1 TATATATGATTATTATCACGAA
*
3568836 TATATATGATGT-TTATTACGAA
1 TATATATGAT-TATTATCACGAA
3568858 T
1 T
3568859 GTTATTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (22 bp):
TATATATGATTATTATCACGAA
Found at i:3569153 original size:86 final size:81
Alignment explanation
Indices: 3569009--3569162 Score: 184
Period size: 86 Copynumber: 1.8 Consensus size: 81
3568999 TCAGATTATC
* * * * *
3569009 ACTAAAGGATACCTAGTGCAGCACTAAAGGATACCTAGTGTATATGGTGGGCATGACCTTATGTG
1 ACTAAAGGATACCTAGTGCAGCACTAAAGGATACCTAGAGTAGATGGTGGACACGACCTCATGTG
3569074 TCAAATTCAAGATCGT
66 TCAAATTCAAGATCGT
*
3569090 ACTAAAGGATACCTAGTGCGGGTCAGTACTAAAGGATACCTAGAGCT-GATGGTGGACACGACCT
1 ACTAAAGGATACCTAGT----G-CAGCACTAAAGGATACCTAGAG-TAGATGGTGGACACGACCT
*
3569154 CCTGTGTCA
60 CATGTGTCA
3569163 TATCGGTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
81 17 0.28
85 1 0.02
86 41 0.68
87 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (81 bp):
ACTAAAGGATACCTAGTGCAGCACTAAAGGATACCTAGAGTAGATGGTGGACACGACCTCATGTG
TCAAATTCAAGATCGT
Found at i:3574872 original size:8 final size:8
Alignment explanation
Indices: 3574837--3574874 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
3574827 TTATTTCACT
3574837 TATATGT-
1 TATATGTA
3574844 TATAT-TA
1 TATATGTA
*
3574851 TATATATA
1 TATATGTA
3574859 TATATGTA
1 TATATGTA
3574867 TATATGTA
1 TATATGTA
3574875 CACATTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (8 bp):
TATATGTA
Found at i:3575209 original size:18 final size:19
Alignment explanation
Indices: 3575185--3575229 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3575175 TTTACTTCTT
3575185 TATTATTATATTTATTTAC
1 TATTATTATATTTATTTAC
* *
3575204 -ATTATT-TATTTTTTTTC
1 TATTATTATATTTATTTAC
3575221 TATTATTAT
1 TATTATTAT
3575230 TATATTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 9 0.41
18 12 0.55
19 1 0.05
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATTATATTTATTTAC
Found at i:3575237 original size:18 final size:18
Alignment explanation
Indices: 3575180--3575238 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
3575170 ATTTCTTTAC
3575180 TTCT-TTATTATTATATT
1 TTCTATTATTATTATATT
* *
3575197 TATTTACATTATTTATT-TTTT
1 T-TCT--ATTA-TTATTATATT
3575218 TTCTATTATTATTATATT
1 TTCTATTATTATTATATT
3575236 TTC
1 TTC
3575239 CCTCCCTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
17 6 0.19
18 12 0.38
20 2 0.06
21 7 0.22
22 5 0.16
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTCTATTATTATTATATT
Found at i:3575255 original size:286 final size:279
Alignment explanation
Indices: 3574698--3575207 Score: 911
Period size: 286 Copynumber: 1.8 Consensus size: 279
3574688 TCTTTCATTT
*
3574698 TAGTCCTTTCTCGGGATATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTGTATATAT
1 TAGTCCTTTCTCGGGATATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATAT
3574763 TTTATATTATTATTAGTTTTTTTTTTTTTTTACACATTCGTATATATTTATTATTAGTATATTAT
66 TTTATATTATTATTAG--TTTTTTTTTTTTTACACATTCGTATATATTTATTATTAGTATATTAT
3574828 TATTTCACTTATATGTTATATTATATATATATATATGTATATATGTACACATTTTGTATTTTACC
129 TATTTCACTTATATG---T-TTATATATATATATA-GTATATATGTACACATTTTGTATTTTACC
*
3574893 CTATTTGTTTACTTCTTTATTATTATATTTATTTACATTAGTTTTAATTATCTTTTTATATTACA
189 CTATTTCTTTACTTCTTTATTATTATATTTATTTACATTAGTTTTAATTATCTTTTTATATTACA
3574958 TTATAATATTTATATATATTTTATAC
254 TTATAATATTTATATATATTTTATAC
3574984 TAGTCCTTTCTCGGGATATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATAT
1 TAGTCCTTTCTCGGGATATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATAT
3575049 TTTATATTATTATTAG-TTTTTTTTTTTTACACATTCGTATATATTTATTATTAGTATATTATTA
66 TTTATATTATTATTAGTTTTTTTTTTTTTACACATTCGTATATATTTATTATTAGTATATTATTA
3575113 TTTCACTTATATG-TTATAT-TATATATA-TATATATGTACACATTTTGTATTTTACCCTATTTC
131 TTTCACTTATATGTTTATATATATATATAGTATATATGTACACATTTTGTATTTTACCCTATTTC
3575175 TTTACTTCTTTATTATTATATTTATTTACATTA
196 TTTACTTCTTTATTATTATATTTATTTACATTA
3575208 TTTATTTTTT
Statistics
Matches: 222, Mismatches: 2, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
275 67 0.30
277 8 0.04
278 6 0.03
283 61 0.27
286 80 0.36
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (279 bp):
TAGTCCTTTCTCGGGATATTAGTTTTAATTATCTTTTTATATTACATTATAATATTTATATATAT
TTTATATTATTATTAGTTTTTTTTTTTTTACACATTCGTATATATTTATTATTAGTATATTATTA
TTTCACTTATATGTTTATATATATATATAGTATATATGTACACATTTTGTATTTTACCCTATTTC
TTTACTTCTTTATTATTATATTTATTTACATTAGTTTTAATTATCTTTTTATATTACATTATAAT
ATTTATATATATTTTATAC
Found at i:3575398 original size:12 final size:13
Alignment explanation
Indices: 3575363--3575400 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3575353 TATATATATA
*
3575363 TATTTTCTTATTT
1 TATTTTATTATTT
3575376 TATTTTCATTATTT
1 TATTTT-ATTATTT
3575390 T-TTTTATTATT
1 TATTTTATTATT
3575401 AGTTTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 10 0.43
14 7 0.30
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:3585974 original size:1 final size:1
Alignment explanation
Indices: 3585968--3585997 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3585958 TCTTAAGTTG
3585968 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3585998 CGTTTAGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3586585 original size:1 final size:1
Alignment explanation
Indices: 3586579--3586605 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3586569 GAGCATCTTC
3586579 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
3586606 TCATCAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3586971 original size:105 final size:105
Alignment explanation
Indices: 3586789--3587774 Score: 1667
Period size: 105 Copynumber: 9.4 Consensus size: 105
3586779 CAGGTTTCAC
*
3586789 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
3586854 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
3586894 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
3586959 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
3586999 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
3587064 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
3587104 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
*
3587169 GACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* *
3587209 TCAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
3587274 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
3587314 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACATAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* *
3587379 TACGAAGGGACCGCTGGTTGTCAACAAACATTTTTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
3587419 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
3587484 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* *
3587524 TCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGTAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
3587589 GACGAAGGGACCGCTGGTTGTCAACAAACA-TT-TC-A-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* * ** * * **
3587625 TCAGAGTCAATTTCAACTTCACAGCGAAGGATATTATACTCGAGACAGCACAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
* ** * * *
3587690 AACGAAGGGATGGCTGGTTGTCAACAAATAATTTCCCGATT
66 GACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATT
* *
3587731 CCAGAGCCAATTTCAACTTCACAACGGAGGATATTGGAC-CCAGA
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
3587775 ACAATACTAC
Statistics
Matches: 838, Mismatches: 38, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
101 81 0.10
102 2 0.00
103 4 0.00
104 3 0.00
105 714 0.85
106 34 0.04
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:3590041 original size:18 final size:18
Alignment explanation
Indices: 3589993--3590042 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
3589983 TTTACTTCTT
3589993 TATTATTATATTTATTTAC
1 TATTATTATATTT-TTTAC
*
3590012 -ATTATT-TATTTTTTTC
1 TATTATTATATTTTTTAC
3590028 TATTATTATATTTTT
1 TATTATTATATTTTT
3590043 CCCTCCCTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
18 13 0.46
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTATATTTTTTAC
Found at i:3590203 original size:12 final size:13
Alignment explanation
Indices: 3590168--3590205 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3590158 TATATATATA
*
3590168 TATTTTCTTATTT
1 TATTTTATTATTT
3590181 TATTTTCATTATTT
1 TATTTT-ATTATTT
3590195 T-TTTTATTATT
1 TATTTTATTATT
3590206 AGTTTACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 10 0.43
14 7 0.30
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTATTT
Found at i:3590291 original size:27 final size:26
Alignment explanation
Indices: 3590258--3590317 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
3590248 TTTAGTTTTA
*
3590258 TTTATTTATTACTATTATATATATCTT
1 TTTATTT-TTACCATTATATATATCTT
* * *
3590285 TTTATTTTTCCCATTGTTTATATCTT
1 TTTATTTTTACCATTATATATATCTT
3590311 TATTATT
1 T-TTATT
3590318 ACCACCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATTTTTACCATTATATATATCTT
Found at i:3594240 original size:6 final size:6
Alignment explanation
Indices: 3594229--3594255 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3594219 GAATTTAGTA
3594229 TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT
3594256 TATAACTCAA
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:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:3594370 original size:33 final size:34
Alignment explanation
Indices: 3594333--3594405 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 34
3594323 ATAAAGTAAG
**
3594333 ATGTATTAAA-ATA-TAAATGATTCATACATTTAA
1 ATGTATTAAATATATTAAAT-ATAAATACATTTAA
*
3594366 ATGTA-TAAATATATTTAATATAAATACATTTAA
1 ATGTATTAAATATATTAAATATAAATACATTTAA
*
3594399 ATATATT
1 ATGTATT
3594406 TTTATTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
32 4 0.12
33 24 0.73
34 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (34 bp):
ATGTATTAAATATATTAAATATAAATACATTTAA
Found at i:3594389 original size:15 final size:16
Alignment explanation
Indices: 3594356--3594403 Score: 62
Period size: 15 Copynumber: 2.9 Consensus size: 16
3594346 TAAATGATTC
3594356 ATACATTTAAATGTATAA
1 ATACATTTAAA--TATAA
*
3594374 ATATATTT-AATATAA
1 ATACATTTAAATATAA
3594389 ATACATTTAAATATA
1 ATACATTTAAATATA
3594404 TTTTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 6 0.22
17 2 0.07
18 7 0.26
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (16 bp):
ATACATTTAAATATAA
Found at i:3594421 original size:24 final size:25
Alignment explanation
Indices: 3594371--3594423 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
3594361 TTTAAATGTA
3594371 TAAATATATTTAATATAAATACATT
1 TAAATATATTTAATATAAATACATT
* **
3594396 TAAATATATTT-TTATTTATACATT
1 TAAATATATTTAATATAAATACATT
3594420 TAAA
1 TAAA
3594424 AATAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATATATTTAATATAAATACATT
Found at i:3594597 original size:22 final size:22
Alignment explanation
Indices: 3594567--3594611 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
3594557 AAATTTGAAG
3594567 AAAAAATATTAAAT-TT-AATTT
1 AAAAAATA-TAAATCTTAAATTT
3594588 AAAAATATATAAATCTTAAATTT
1 AAAAA-ATATAAATCTTAAATTT
3594611 A
1 A
3594612 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAAATATAAATCTTAAATTT
Found at i:3595312 original size:41 final size:42
Alignment explanation
Indices: 3595214--3595452 Score: 237
Period size: 41 Copynumber: 5.8 Consensus size: 42
3595204 GTTTCCAGAT
**
3595214 TCGCAATGCGATTTTGGACTATCGCAATGCG-ATA-GTCGACTA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGT--ACTA
*
3595256 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACTA
*
3595297 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACTA
* * *
3595338 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACT-TGGACTA
1 TCGCAATGCGA-ACTTGGACTATCGCAATGCGAA-TATGTACTA
* * *
3595380 TCGCAATGCGAA-TACGTA-AATCGCAATGCG-ATA-GTCGACTA
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT--ACTA
* *
3595421 TCGCAATGCGAACTTCGACTATCGCATTGCGA
1 TCGCAATGCGAACTTGGACTATCGCAATGCGA
3595453 TTTACATATT
Statistics
Matches: 167, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 103 0.62
42 56 0.34
43 3 0.02
44 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTACTA
Found at i:3595341 original size:103 final size:103
Alignment explanation
Indices: 3595234--3595432 Score: 355
Period size: 103 Copynumber: 1.9 Consensus size: 103
3595224 ATTTTGGACT
*
3595234 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATC
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATACGTAAATC
* *
3595299 GCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
66 GCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
3595337 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATACGTAAATC
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATACGTAAATC
3595402 GCAATGCGATAGTCGACTATCGCAATGCGAA
66 GCAATGCGATAGTCGACTATCGCAATGCGAA
3595433 CTTCGACTAT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 91 0.99
104 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.23
Consensus pattern (103 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATACGTAAATC
GCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:3595362 original size:62 final size:62
Alignment explanation
Indices: 3595214--3595493 Score: 315
Period size: 62 Copynumber: 4.5 Consensus size: 62
3595204 GTTTCCAGAT
** * * * *
3595214 TCGCAATGCGATTTTGGACTATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGA-ACTTCGACTATCGCAATGCGAA-TTGTACAA
* *
3595277 TCGCAATGCGAATA-T-GTA-AATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-AA
1 TCGCAATGCG-ATAGTCG-ACTATCGCAATGCGAACTTCGACTATCGCAATGCGAAT-TGTACAA
* *
3595338 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATACGTA-AA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAAT-TGTACAA
*
3595400 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCATTGCG-ATT-TACATA
1 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATTGTACA-A
* *
3595461 TTCGCATTGCGATAGTCGACTATCGCATTGCGA
1 -TCGCAATGCGATAGTCGACTATCGCAATGCGA
3595494 TAGTCCAAAA
Statistics
Matches: 194, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
59 2 0.01
60 4 0.02
61 18 0.09
62 156 0.80
63 12 0.06
64 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (62 bp):
TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAATTGTACAA
Found at i:3595466 original size:41 final size:41
Alignment explanation
Indices: 3595214--3595495 Score: 221
Period size: 41 Copynumber: 6.8 Consensus size: 41
3595204 GTTTCCAGAT
* *
3595214 TCGCAATGCGATTTTGGACTATCGCAATGCGATA-GT-CGACTA
1 TCGCAATGCGA-ATTCGACTATCGCAATGCGATATGTAC-A-TA
*
3595256 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A
1 TCGCAATGCGAA-TTCGACTATCGCAATGCG-ATATGTACATA
*
3595297 TCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A
1 TCGCAATGCGAA-TTCGACTATCGCAATGCG-ATATGTACATA
* *
3595338 TCGCAATGCGATAGTCGACTATCGCAATGCGA-ACTTGGAC-TA
1 TCGCAATGCGA-ATTCGACTATCGCAATGCGATA--TGTACATA
* *
3595380 TCGCAATGCGAATACGTA-AATCGCAATGCGATA-GT-CGACTA
1 TCGCAATGCGAATTCG-ACTATCGCAATGCGATATGTAC-A-TA
*
3595421 TCGCAATGCGAACTTCGACTATCGCATTGCGAT-T-TACATA
1 TCGCAATGCGAA-TTCGACTATCGCAATGCGATATGTACATA
* * *
3595461 TTCGCATTGCGATAGTCGACTATCGCATTGCGATA
1 -TCGCAATGCGA-ATTCGACTATCGCAATGCGATA
3595496 GTCCAAAATC
Statistics
Matches: 206, Mismatches: 13, Indels: 42
0.79 0.05 0.16
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 3 0.01
41 133 0.65
42 61 0.30
43 4 0.02
44 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAATTCGACTATCGCAATGCGATATGTACATA
Found at i:3595488 original size:21 final size:21
Alignment explanation
Indices: 3595214--3595519 Score: 203
Period size: 21 Copynumber: 14.8 Consensus size: 21
3595204 GTTTCCAGAT
** *
3595214 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATAGTCGACTA
3595235 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
* *
3595256 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
3595277 TCGCAATGCGAATA-T-GTA-AA
1 TCGCAATGCG-ATAGTCG-ACTA
* *
3595297 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
3595318 TCGCAATGCGAATA-T-GTA-AA
1 TCGCAATGCG-ATAGTCG-ACTA
3595338 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
* *
3595359 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
3595380 TCGCAATGCGA-A-TACGTA-AA
1 TCGCAATGCGATAGT-CG-ACTA
3595400 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
*
3595421 TCGCAATGCGA-ACTTCGACTA
1 TCGCAATGCGATA-GTCGACTA
* *
3595442 TCGCATTGCGAT--T-TACATA
1 TCGCAATGCGATAGTCGAC-TA
*
3595461 TTCGCATTGCGATAGTCGACTA
1 -TCGCAATGCGATAGTCGACTA
* * **
3595483 TCGCATTGCGATAGTCCAAAA
1 TCGCAATGCGATAGTCGACTA
*
3595504 TCGCATTGCGATAGTC
1 TCGCAATGCGATAGTC
3595520 CAAAAGCGCA
Statistics
Matches: 237, Mismatches: 21, Indels: 54
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.01
19 8 0.03
20 57 0.24
21 159 0.67
22 6 0.03
23 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGACTA
Found at i:3595520 original size:21 final size:21
Alignment explanation
Indices: 3595462--3595529 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
3595452 ATTTACATAT
* **
3595462 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
3595483 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
3595504 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
*
3595525 GCGCA
1 TCGCA
3595530 ACGACTGGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:3595623 original size:6 final size:6
Alignment explanation
Indices: 3595612--3595655 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
3595602 GACACGTATT
3595612 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
3595656 TGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3596184 original size:6 final size:6
Alignment explanation
Indices: 3596163--3596202 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
3596153 TCTCGTCTCG
3596163 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3596203 ACGTGTCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:3596407 original size:21 final size:21
Alignment explanation
Indices: 3596292--3596577 Score: 125
Period size: 21 Copynumber: 13.8 Consensus size: 21
3596282 TGCAATTTTG
*
3596292 GACTATCGCAATGCGATAGTC
1 GACTATCGCATTGCGATAGTC
*
3596313 GACTATCGCAATGCGAATA-T-
1 GACTATCGCATTGCG-ATAGTC
* *
3596333 GTA-AATCGCAATGCGATAGTC
1 G-ACTATCGCATTGCGATAGTC
*
3596354 GAAGT-TCGCATTGCGATAGTCC
1 G-ACTATCGCATTGCGATAGT-C
* * *
3596376 AAGT-TCACATTGCGATAGTC
1 GACTATCGCATTGCGATAGTC
*
3596396 GACTATCGCATTACGAT--T-
1 GACTATCGCATTGCGATAGTC
* * *
3596414 TACATATTCGCAATGCGAAAGTCC
1 GAC-TA-TCGCATTGCGATAGT-C
* * *
3596438 AAGT-TCGCATTGCAATAGTCC
1 GACTATCGCATTGCGATAGT-C
* * *
3596459 AAGT-TCGCATTGCGA-ACTTC
1 GACTATCGCATTGCGATA-GTC
3596479 GACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATAGTC
*
3596497 TACATATTCGCATTGCGATAGTCC
1 GAC-TA-TCGCATTGCGATAGT-C
* * *
3596521 AAGT-TTGCATTGCGATAGTC
1 GACTATCGCATTGCGATAGTC
*
3596541 GACTATCGCATTGCGATAATC
1 GACTATCGCATTGCGATAGTC
* **
3596562 CAAAATCGCATTGCGA
1 GACTATCGCATTGCGA
3596578 ATCTGGAAAC
Statistics
Matches: 208, Mismatches: 34, Indels: 46
0.72 0.12 0.16
Matches are distributed among these distances:
18 4 0.02
19 9 0.04
20 44 0.21
21 141 0.68
22 6 0.03
23 2 0.01
24 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (21 bp):
GACTATCGCATTGCGATAGTC
Found at i:3596442 original size:83 final size:83
Alignment explanation
Indices: 3596303--3596540 Score: 331
Period size: 83 Copynumber: 2.9 Consensus size: 83
3596293 ACTATCGCAA
* *
3596303 TGCGATAGTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGTTCGCAT
1 TGCGATAGTCGACTATCGCATTGCG-AT-T-TACATATTCGCAATGCGATAGTCCAAGTTCGCAT
3596365 TGCGATAGTCCAAGTTCACAT
63 TGCGATAGTCCAAGTTCACAT
* *
3596386 TGCGATAGTCGACTATCGCATTACGATTTACATATTCGCAATGCGAAAGTCCAAGTTCGCATTGC
1 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGC
* *
3596451 AATAGTCCAAGTTCGCAT
66 GATAGTCCAAGTTCACAT
* * *
3596469 TGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTTGCATTG
1 TGCGATA-GTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCGCATTG
3596533 CGATAGTC
65 CGATAGTC
3596541 GACTATCGCA
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 4 0.03
83 131 0.94
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (83 bp):
TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCGCATTGC
GATAGTCCAAGTTCACAT
Found at i:3596507 original size:62 final size:62
Alignment explanation
Indices: 3596441--3596557 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
3596431 AAAGTCCAAG
*
3596441 TTCGCATTGCAATAGTCCAAGTTCGCATTGCGA-ACTTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATA-GTCGACTATCGCATTGCGATTTACATA
* *
3596503 TTCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCGACTATCGCATTGCGAT
1 TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGAT
3596558 AATCCAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
62 50 0.98
63 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCAATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:3596550 original size:83 final size:83
Alignment explanation
Indices: 3596297--3596577 Score: 329
Period size: 83 Copynumber: 3.4 Consensus size: 83
3596287 TTTTGGACTA
* * *
3596297 TCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGACTATCGCATTGCG-AT-T-TACATATTCGCAATGCGATAGTCCAAGT
*
3596359 TCGCATTGCGATAGTCCAAGT
63 TCGCATTGCGATAGTCCAACT
* * *
3596380 TCACATTGCGATAGTCGACTATCGCATTACGATTTACATATTCGCAATGCGAAAGTCCAAGTTCG
1 TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCG
* *
3596445 CATTGCAATAGTCCAAGT
66 CATTGCGATAGTCCAACT
* * *
3596463 TCGCATTGCGA-ACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTT
1 TCGCATTGCGATA-GTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTC
*
3596527 GCATTGCGATAGT-CGACT
65 GCATTGCGATAGTCCAACT
* * **
3596545 ATCGCATTGCGATAATCCAAAATCGCATTGCGA
1 -TCGCATTGCGATAGTCGACTATCGCATTGCGA
3596578 ATCTGGAAAC
Statistics
Matches: 172, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
80 2 0.01
81 2 0.01
82 7 0.04
83 160 0.93
84 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (83 bp):
TCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCAATGCGATAGTCCAAGTTCG
CATTGCGATAGTCCAACT
Found at i:3599119 original size:22 final size:20
Alignment explanation
Indices: 3599072--3599127 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
3599062 CGTTGAACAG
*
3599072 TGGGGGGAATCGATACCCCC
1 TGGGGGGAATCGGTACCCCC
3599092 TGGGGGGAATCGGTACCCCC
1 TGGGGGGAATCGGTACCCCC
*
3599112 TTATGGGGGAATCGGT
1 -T-GGGGGGAATCGGT
3599128 TCCCTCTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.59
21 1 0.03
22 12 0.38
ACGTcount: A:0.18, C:0.23, G:0.39, T:0.20
Consensus pattern (20 bp):
TGGGGGGAATCGGTACCCCC
Found at i:3601718 original size:22 final size:23
Alignment explanation
Indices: 3601672--3601732 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
3601662 TTCCCCTGTG
3601672 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
3601695 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
3601717 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
3601733 TCTGCACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:3608464 original size:20 final size:20
Alignment explanation
Indices: 3608439--3608478 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3608429 TTCGCTTTGA
*
3608439 ATAAGAACATTATCGATACT
1 ATAAGAACAATATCGATACT
*
3608459 ATAAGAATAATATCGATACT
1 ATAAGAACAATATCGATACT
3608479 CACCCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (20 bp):
ATAAGAACAATATCGATACT
Found at i:3609091 original size:20 final size:20
Alignment explanation
Indices: 3609066--3609105 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3609056 AAGTTTTTAC
3609066 CTTTTGCTTACTATTTAGAA
1 CTTTTGCTTACTATTTAGAA
3609086 CTTTTGCTTACTATTTAGAA
1 CTTTTGCTTACTATTTAGAA
3609106 TAAAGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (20 bp):
CTTTTGCTTACTATTTAGAA
Found at i:3611793 original size:2 final size:2
Alignment explanation
Indices: 3611788--3611821 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3611778 ATTTAGTGAT
*
3611788 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3611822 GATTATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3612846 original size:14 final size:14
Alignment explanation
Indices: 3612827--3612853 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3612817 TTTATATTTA
3612827 ATGTATTTACAAGG
1 ATGTATTTACAAGG
3612841 ATGTATTTACAAG
1 ATGTATTTACAAG
3612854 CTCTTAAGAT
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:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
ATGTATTTACAAGG
Found at i:3620035 original size:24 final size:24
Alignment explanation
Indices: 3619973--3620039 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3619963 GTGACTCTCT
* *
3619973 TGGACAAGATGATGTGGAGTCCAG
1 TGGACAAGATAATGTGGAGTCCAA
*
3619997 T-GAGCAAAATAATGTGGAGTCCAA
1 TGGA-CAAGATAATGTGGAGTCCAA
*
3620021 TGGACAAGATCATGTGGAG
1 TGGACAAGATAATGTGGAG
3620040 CTCAGGATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (24 bp):
TGGACAAGATAATGTGGAGTCCAA
Found at i:3625266 original size:39 final size:39
Alignment explanation
Indices: 3625210--3625334 Score: 214
Period size: 39 Copynumber: 3.2 Consensus size: 39
3625200 AGGATACCTA
*
3625210 GTGCATATGGTGGACACAACCTTATATGTAAGCACTTCG
1 GTGCATATGGTGGACACAACCTTATGTGTAAGCACTTCG
* *
3625249 GTGCATATGGTGCACACAACCTTATGTTTAAGCACTTCG
1 GTGCATATGGTGGACACAACCTTATGTGTAAGCACTTCG
*
3625288 GTGCATATGGTGGACACAACCTTATGTGTAAGCACTACG
1 GTGCATATGGTGGACACAACCTTATGTGTAAGCACTTCG
3625327 GTGCATAT
1 GTGCATAT
3625335 TTTTTACTCG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (39 bp):
GTGCATATGGTGGACACAACCTTATGTGTAAGCACTTCG
Found at i:3627835 original size:14 final size:13
Alignment explanation
Indices: 3627817--3627902 Score: 94
Period size: 12 Copynumber: 7.0 Consensus size: 13
3627807 TTGCCCATTT
3627817 TTTATT-TT-TTA
1 TTTATTATTATTA
3627828 TTTATTATTATTA
1 TTTATTATTATTA
3627841 TTTTATTATTATTA
1 -TTTATTATTATTA
3627855 -TTA-TATTATTA
1 TTTATTATTATTA
*
3627866 -TTATTATTAATA
1 TTTATTATTATTA
**
3627878 AATATTATTATTA
1 TTTATTATTATTA
3627891 -TTATTATTATTA
1 TTTATTATTATTA
3627903 CAGGCCCAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
11 17 0.26
12 23 0.35
13 13 0.20
14 13 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:3627837 original size:3 final size:3
Alignment explanation
Indices: 3627829--3627902 Score: 107
Period size: 3 Copynumber: 25.0 Consensus size: 3
3627819 TATTTTTTAT
3627829 TTA TTA TTA TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
3627876 TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
3627903 CAGGCCCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 4 0.06
3 58 0.91
4 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3627838 original size:17 final size:17
Alignment explanation
Indices: 3627818--3627902 Score: 102
Period size: 17 Copynumber: 5.0 Consensus size: 17
3627808 TGCCCATTTT
3627818 TTATT-TTTTATTTATTA
1 TTATTATTTTA-TTATTA
3627835 TTATTATTTTATTATTA
1 TTATTATTTTATTATTA
*
3627852 TTATTATATTATTATTA
1 TTATTATTTTATTATTA
* * *
3627869 TTATTA-ATAAATATTA
1 TTATTATTTTATTATTA
3627885 TTATTATTATTATTATTA
1 TTATTATT-TTATTATTA
3627903 CAGGCCCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 14 0.24
17 33 0.56
18 12 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTATTTTATTATTA
Found at i:3627895 original size:28 final size:28
Alignment explanation
Indices: 3627829--3627902 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
3627819 TATTTTTTAT
* *
3627829 TTATTATTATTATT-TTATT-ATTATTA
1 TTATTATTATTATTATTATTAATAAATA
3627855 TTA-TATTATTATTATTATTAATAAATA
1 TTATTATTATTATTATTATTAATAAATA
3627882 TTATTATTATTATTATTATTA
1 TTATTATTATTATTATTATTA
3627903 CAGGCCCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.23
26 8 0.19
27 8 0.19
28 17 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTATTATTATTATTATTATTAATAAATA
Found at i:3630115 original size:24 final size:21
Alignment explanation
Indices: 3630069--3630125 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 21
3630059 TGTCATGAAA
3630069 GTATCGATA-CTTCTCTTGTG
1 GTATCGATACCTTCTCTTGTG
3630089 GTATCGATACCTCTCTTACTTGTG
1 GTATCGATACCT-TC-T-CTTGTG
3630113 GTATCGATACCTT
1 GTATCGATACCTT
3630126 AAGAATAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.27
21 2 0.06
22 2 0.06
23 2 0.06
24 18 0.55
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (21 bp):
GTATCGATACCTTCTCTTGTG
Found at i:3630596 original size:32 final size:32
Alignment explanation
Indices: 3630550--3630622 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
3630540 GTAGAAAAAA
*
3630550 TAACAAAACCGATAGCGTTTTACCGGTTTTGT
1 TAACAAAACCGATAGCGCTTTACCGGTTTTGT
** *
3630582 TAACAAAATTGATAGCGCTTTACCGGTTTTTT
1 TAACAAAACCGATAGCGCTTTACCGGTTTTGT
3630614 TAACAAAAC
1 TAACAAAAC
3630623 GTGTAAAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
TAACAAAACCGATAGCGCTTTACCGGTTTTGT
Found at i:3631647 original size:15 final size:15
Alignment explanation
Indices: 3631627--3631655 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3631617 TTTATCTCCA
3631627 AATAAAATATTAAAT
1 AATAAAATATTAAAT
3631642 AATAAAATATTAAA
1 AATAAAATATTAAA
3631656 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAATATTAAAT
Found at i:3636118 original size:35 final size:35
Alignment explanation
Indices: 3636070--3636284 Score: 331
Period size: 35 Copynumber: 6.1 Consensus size: 35
3636060 AAGGTGAATG
** *
3636070 AAGTCGAACGGAAGGAAATATCCCACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
* * *
3636105 AAGTCGAATGGAAGGAAGCATCGACACTTTTGATTT
1 AAGTCGAACGGAAGGAAGCATCG-CACTTTCGATTC
*
3636141 AAGTCGAACGAAAGGAAGCATCGCACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
3636176 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
* *
3636211 AAGTCGAACGGAAGGAGGCATCGTACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
*
3636246 AAGTCGAACGGAAGGAGGCATCGCACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
3636281 AAGT
1 AAGT
3636285 GTTCATCTTT
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
35 134 0.81
36 31 0.19
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (35 bp):
AAGTCGAACGGAAGGAAGCATCGCACTTTCGATTC
Found at i:3638800 original size:2 final size:2
Alignment explanation
Indices: 3638793--3638832 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3638783 GGATCATGTC
3638793 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
3638833 GGATACACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3640418 original size:35 final size:36
Alignment explanation
Indices: 3640370--3640451 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 36
3640360 TGAAATCATT
*
3640370 AAAAAAATAATTTAATATTAAAATCATAATCATAAG
1 AAAAAAATAATTTAAGATTAAAATCATAATCATAAG
* * *
3640406 AAAAAAAT-ATTTAAGATTCAAATTATAATCATTAAT
1 AAAAAAATAATTTAAGATTAAAATCATAATCA-TAAG
*
3640442 AAATAAATAA
1 AAAAAAATAA
3640452 ATATAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 20 0.51
36 18 0.46
37 1 0.03
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (36 bp):
AAAAAAATAATTTAAGATTAAAATCATAATCATAAG
Found at i:3640609 original size:7 final size:7
Alignment explanation
Indices: 3640597--3640622 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3640587 TATCATTAAC
3640597 TATAATA
1 TATAATA
3640604 TATAATA
1 TATAATA
3640611 TATAATA
1 TATAATA
3640618 TATAA
1 TATAA
3640623 AAAATATTTT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAATA
Found at i:3642964 original size:23 final size:23
Alignment explanation
Indices: 3642931--3642998 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3642921 AACCTTATAT
*
3642931 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* *
3642954 GGCA-TTACGGTGCAATTCTACGT
1 GGCACTT-CGGTGCATTTCTACGC
*
3642977 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3642999 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 2 0.05
23 34 0.89
24 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3645526 original size:28 final size:28
Alignment explanation
Indices: 3645465--3645558 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
3645455 AGAAATACAA
* * * **
3645465 TTATTGTAATTTATAAAAAAATTGTATT
1 TTATTGTAATTTATAAAACATTTTTCCT
3645493 TTATTGTAATTTATAAAACATTTTTCCT
1 TTATTGTAATTTATAAAACATTTTTCCT
* * *
3645521 TAATTGTAAATTT-CAAACCATTTTGTCCT
1 TTATTGT-AATTTATAAAACATTTT-TCCT
3645550 TTATTGTAA
1 TTATTGTAA
3645559 ATTCCAATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 40 0.73
29 15 0.27
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (28 bp):
TTATTGTAATTTATAAAACATTTTTCCT
Found at i:3645606 original size:30 final size:30
Alignment explanation
Indices: 3645507--3645627 Score: 131
Period size: 29 Copynumber: 4.1 Consensus size: 30
3645497 TGTAATTTAT
* *
3645507 AAAACATTTT-TCCTTAATTGTAAATTTCAA
1 AAAAC-TTTTGTCCTTTATTGTAAATTCCAA
**
3645537 ACCA-TTTTGTCCTTTATTGTAAATTCC-A
1 AAAACTTTTGTCCTTTATTGTAAATTCCAA
* * *
3645565 ATAAGTTTTGTCCTTTATTTTAAATTCCAA
1 AAAACTTTTGTCCTTTATTGTAAATTCCAA
* *
3645595 AAAACTTTTGTCCTTTTTTATAAATTCCAA
1 AAAACTTTTGTCCTTTATTGTAAATTCCAA
3645625 AAA
1 AAA
3645628 GTTTTATCCT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.09
29 38 0.49
30 32 0.42
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (30 bp):
AAAACTTTTGTCCTTTATTGTAAATTCCAA
Found at i:3645637 original size:29 final size:28
Alignment explanation
Indices: 3645541--3645638 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
3645531 TTTCAAACCA
* *
3645541 TTTTGTCCTTTATTGTAAATTCCAATAAG
1 TTTTGTCCTTT-TTTTAAATTCCAAAAAG
*
3645570 TTTTGTCCTTTATTTTAAATTCCAAAAAAC
1 TTTTGTCCTTT-TTTTAAATTCC-AAAAAG
3645600 TTTTGTCCTTTTTTATAAATTCCAAAAAG
1 TTTTGTCCTTTTTT-TAAATTCCAAAAAG
*
3645629 TTTTATCCTT
1 TTTTGTCCTT
3645639 CATGGGTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
29 39 0.63
30 23 0.37
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (28 bp):
TTTTGTCCTTTTTTTAAATTCCAAAAAG
Found at i:3650115 original size:3 final size:3
Alignment explanation
Indices: 3650101--3650196 Score: 68
Period size: 3 Copynumber: 32.0 Consensus size: 3
3650091 TTTTGCACGT
* * * * * * * * *
3650101 TTA TTT TTA TTA TTA GTG TAA TTA TTG TAA TTA TTA TAA TTG TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3650149 TTA TTA TTA TTA TTA -TA TTT TTA TTA TTA TTAA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
3650194 TTA
1 TTA
3650197 CATATTACAT
Statistics
Matches: 67, Mismatches: 24, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
2 2 0.03
3 63 0.94
4 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3650134 original size:9 final size:9
Alignment explanation
Indices: 3650119--3650196 Score: 77
Period size: 9 Copynumber: 8.7 Consensus size: 9
3650109 ATTATTAGTG
*
3650119 TAATTATTG
1 TAATTATTA
3650128 TAATTATTA
1 TAATTATTA
*
3650137 TAATTGTTA
1 TAATTATTA
3650146 TAATTATTA
1 TAATTATTA
*
3650155 TTATTATTA
1 TAATTATTA
*
3650164 T-ATTTTTA
1 TAATTATTA
*
3650172 TTATTATTAA
1 TAATTATT-A
*
3650182 TAAATATTA
1 TAATTATTA
*
3650191 TTATTA
1 TAATTA
3650197 CATATTACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
8 7 0.12
9 43 0.75
10 7 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TAATTATTA
Found at i:3650731 original size:31 final size:31
Alignment explanation
Indices: 3650696--3650757 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3650686 ATCAACTTAG
*
3650696 TGTATAAAGGTGTGCACCAAGCATCAGTGCC
1 TGTATAAAGGTGTGCACCAAACATCAGTGCC
3650727 TGTATAAAGGTGTGCACCAAACATCAGTGCC
1 TGTATAAAGGTGTGCACCAAACATCAGTGCC
3650758 AACTTAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.23
Consensus pattern (31 bp):
TGTATAAAGGTGTGCACCAAACATCAGTGCC
Found at i:3670448 original size:31 final size:32
Alignment explanation
Indices: 3670395--3670454 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 32
3670385 TCCATAGGCG
*
3670395 TAGCTGAATCTTAATTGTCTTACCCAGCTGAA
1 TAGCTGAACCTTAATTGTCTTACCCAGCTGAA
3670427 TAGCTGAACCTTAA-TGTCTTACCCAGCT
1 TAGCTGAACCTTAATTGTCTTACCCAGCT
3670455 TTCAGGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (32 bp):
TAGCTGAACCTTAATTGTCTTACCCAGCTGAA
Found at i:3685725 original size:266 final size:263
Alignment explanation
Indices: 3685235--3685735 Score: 754
Period size: 264 Copynumber: 1.9 Consensus size: 263
3685225 ACCCGGCCCA
3685235 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAATATATAT
1 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAATATATAT
*
3685300 ATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTC
66 ATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTC
*
3685365 GGGTCGAGTATTTTTCACCCTAAACCATAACCCGACCCGAATATCACTTAAAAAAACCGACCCGA
131 GGGTC-AGTATTTTTCACCCTAAACCAGAACCCGACCCGAATATCACTTAAAAAAA-C-ACCCGA
*
3685430 CCCGACCAAAATAAAATTTCACTCGACCCGACCCGAATATATAAATTAGATATCCAACCCGACCC
193 CCCGACCAAAATAAAATTTCACCCGACCCGACCCGAATATATAAATTAGATATCCAACCCGACCC
3685495 GACCTG
258 GACCTG
3685501 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAA-A-AGTA
1 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAATATA-TA
*
3685563 TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGG
65 TATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTTTCGGG
*
3685628 TCGGGT-A-T-TTTTT-ACCCTAAACCCGAACTCGACCGACCCGAATATCACACTT-AAAAAA-A
129 TCGGGTCAGTATTTTTCACCCTAAACCAGAA--C--CCGACCCGAATAT--CACTTAAAAAAACA
* *
3685687 -CTGACCCGACCAAAATAAAGTTTCACCCGACCCGACCCGAGATA-ATAAA
188 CCCGACCCGACCAAAATAAAATTTCACCCGACCCGACCCGA-ATATATAAA
3685736 AAAATATTTT
Statistics
Matches: 219, Mismatches: 7, Indels: 23
0.88 0.03 0.09
Matches are distributed among these distances:
260 12 0.05
261 47 0.21
262 6 0.03
263 2 0.01
264 71 0.32
265 24 0.11
266 57 0.26
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (263 bp):
ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAATATATAT
ATATAAAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTCGGGTC
GGGTCAGTATTTTTCACCCTAAACCAGAACCCGACCCGAATATCACTTAAAAAAACACCCGACCC
GACCAAAATAAAATTTCACCCGACCCGACCCGAATATATAAATTAGATATCCAACCCGACCCGAC
CTG
Found at i:3688736 original size:18 final size:18
Alignment explanation
Indices: 3688713--3688753 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3688703 CTCGGGGAGA
3688713 GATATCAGGTTTTGGCAT
1 GATATCAGGTTTTGGCAT
3688731 GATATCAGGTTTTGGCAT
1 GATATCAGGTTTTGGCAT
3688749 GATAT
1 GATAT
3688754 TTGGCTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (18 bp):
GATATCAGGTTTTGGCAT
Found at i:3693907 original size:38 final size:38
Alignment explanation
Indices: 3693856--3693933 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
3693846 AAGAATGTTA
3693856 TCCAAAGATGCTTTTCAATTCTCACAATAGGAATTGAG
1 TCCAAAGATGCTTTTCAATTCTCACAATAGGAATTGAG
3693894 TCCAAAGATGCTTTTCAATTCTCACAATAGGAATTGAG
1 TCCAAAGATGCTTTTCAATTCTCACAATAGGAATTGAG
3693932 TC
1 TC
3693934 ATCAAAAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (38 bp):
TCCAAAGATGCTTTTCAATTCTCACAATAGGAATTGAG
Found at i:3695792 original size:15 final size:16
Alignment explanation
Indices: 3695764--3695795 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3695754 ATAAATGATA
3695764 ATAAAAAATGAAGATG
1 ATAAAAAATGAAGATG
3695780 ATAAAAAAT-AAGATG
1 ATAAAAAATGAAGATG
3695795 A
1 A
3695796 AATTAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (16 bp):
ATAAAAAATGAAGATG
Found at i:3696520 original size:17 final size:17
Alignment explanation
Indices: 3696498--3696535 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
3696488 ATAGTCAGAA
3696498 AAAGAGGATTTTTAATT
1 AAAGAGGATTTTTAATT
3696515 AAAGAGGATTTTTAATT
1 AAAGAGGATTTTTAATT
3696532 AAAG
1 AAAG
3696536 GACAATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (17 bp):
AAAGAGGATTTTTAATT
Found at i:3697219 original size:20 final size:21
Alignment explanation
Indices: 3697190--3697248 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
3697180 TTTCCAGTCA
3697190 GGAG-AAAGGATCGATCCCTT
1 GGAGAAAAGGATCGATCCCTT
* *
3697210 TGA-AAAAGGATGGAT-CCTT
1 GGAGAAAAGGATCGATCCCTT
3697229 GGAGAAAAGGATCGATCCCT
1 GGAGAAAAGGATCGATCCCT
3697249 CAAAAGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 23 0.72
21 3 0.09
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (21 bp):
GGAGAAAAGGATCGATCCCTT
Found at i:3702683 original size:24 final size:24
Alignment explanation
Indices: 3702655--3702703 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3702645 CTTTGGGAGA
*
3702655 AATGATCCATCCCTTTTCAAAATG
1 AATGATCCACCCCTTTTCAAAATG
*
3702679 AATGATCGACCCCTTTTCAAAATG
1 AATGATCCACCCCTTTTCAAAATG
3702703 A
1 A
3702704 CCGATCCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.31
Consensus pattern (24 bp):
AATGATCCACCCCTTTTCAAAATG
Found at i:3703901 original size:45 final size:44
Alignment explanation
Indices: 3703761--3703893 Score: 162
Period size: 45 Copynumber: 3.0 Consensus size: 44
3703751 GTTGATTCTG
* * *
3703761 TGTGATCCAGACCTAGCCTAAGGTA-TTGGGAGGTGTTGATGTTA
1 TGTGACCCAGACCTCGCCTAAGATACTTGGGA-GTGTTGATGTTA
* * *
3703805 TGTGACCCAGACCTCGCCTGAGATACTTGGGTAGTGCTGATGCTA
1 TGTGACCCAGACCTCGCCTAAGATACTTGGG-AGTGTTGATGTTA
3703850 TGTGACCC-GAACCTCGCCTAAGATACTTGGGAGATGTTGATGTT
1 TGTGACCCAG-ACCTCGCCTAAGATACTTGGGAG-TGTTGATGTT
3703894 GTATGACCTA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
44 24 0.32
45 51 0.67
46 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (44 bp):
TGTGACCCAGACCTCGCCTAAGATACTTGGGAGTGTTGATGTTA
Found at i:3705871 original size:26 final size:24
Alignment explanation
Indices: 3705841--3705898 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
3705831 CAATATACAG
3705841 ATAAAAAATAATAACATAGTTACGTA
1 ATAAAAAATAATAA-ATAGTTA-GTA
* * *
3705867 ATAAAAAA-ATTTAATATTTAGTA
1 ATAAAAAATAATAAATAGTTAGTA
3705890 ATAAAAAAT
1 ATAAAAAAT
3705899 TTAATTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 11 0.39
24 6 0.21
25 3 0.11
26 8 0.29
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.31
Consensus pattern (24 bp):
ATAAAAAATAATAAATAGTTAGTA
Found at i:3708163 original size:22 final size:22
Alignment explanation
Indices: 3708135--3708186 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
3708125 ACGGAATGTA
* *
3708135 AGATTATTAGCGAGAATAAAAG
1 AGATTATCAGCAAGAATAAAAG
*
3708157 AGATTATCAGTAAGAAT-AAA-
1 AGATTATCAGCAAGAATAAAAG
3708177 AGATTATCAG
1 AGATTATCAG
3708187 AGAATAGAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 10 0.37
21 3 0.11
22 14 0.52
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (22 bp):
AGATTATCAGCAAGAATAAAAG
Found at i:3710740 original size:21 final size:21
Alignment explanation
Indices: 3710700--3710742 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3710690 AAAAAACAGA
*
3710700 AAAATTAAAAATAGTCAAAAT
1 AAAATTAAAAATAATCAAAAT
*
3710721 AAAATTGAAAAATAATAAAAAT
1 AAAATT-AAAAATAATCAAAAT
3710743 GGGTTGTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAATTAAAAATAATCAAAAT
Found at i:3711265 original size:21 final size:21
Alignment explanation
Indices: 3711239--3711290 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3711229 AGTGAGTTTG
**
3711239 GGATCGATCCCTTTATCAAAA
1 GGATCGATCCCTCGATCAAAA
*
3711260 GGATCGATCCCTCGATGAAAA
1 GGATCGATCCCTCGATCAAAA
*
3711281 TGATCGATCC
1 GGATCGATCC
3711291 TTTCCCTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
GGATCGATCCCTCGATCAAAA
Found at i:3715069 original size:23 final size:21
Alignment explanation
Indices: 3715020--3715101 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
3715010 CCAGAACCCC
* **
3715020 AGGGGGGTATCGATTCCCCTGT
1 AGGGGGG-ATCGGTTCCCCTCA
*
3715042 GGGGGGGATCGGTTCCCCTTCAA
1 AGGGGGGATCGGTTCCCC-TC-A
*
3715065 AGGGGGAATCGGTT-CCCTCA
1 AGGGGGGATCGGTTCCCCTCA
* *
3715085 TGGGGGGATCGATTCCC
1 AGGGGGGATCGGTTCCC
3715102 TCTGCACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
20 12 0.25
21 14 0.29
22 10 0.21
23 12 0.25
ACGTcount: A:0.15, C:0.24, G:0.38, T:0.23
Consensus pattern (21 bp):
AGGGGGGATCGGTTCCCCTCA
Found at i:3715095 original size:20 final size:21
Alignment explanation
Indices: 3715043--3715103 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
3715033 TTCCCCTGTG
3715043 GGGGGGATCGGTTCCCCTTCAAA
1 GGGGGGATCGGTT-CCC-TCAAA
* *
3715066 GGGGGAATCGGTTCCCTC-AT
1 GGGGGGATCGGTTCCCTCAAA
*
3715086 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
3715104 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 12 0.35
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:3719193 original size:16 final size:16
Alignment explanation
Indices: 3719172--3719203 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3719162 TTTCCAAGTC
3719172 TGTTTTAGCTTTCAAA
1 TGTTTTAGCTTTCAAA
3719188 TGTTTTAGCTTTCAAA
1 TGTTTTAGCTTTCAAA
3719204 AGAAGATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
TGTTTTAGCTTTCAAA
Found at i:3722522 original size:15 final size:16
Alignment explanation
Indices: 3722491--3722525 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3722481 GCTTTCAAAA
*
3722491 TTGAAAAATGAACATT
1 TTGAAAAATGAAAATT
3722507 TTGAAAAA-GAAAATT
1 TTGAAAAATGAAAATT
3722522 TTGA
1 TTGA
3722526 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.31
Consensus pattern (16 bp):
TTGAAAAATGAAAATT
Found at i:3725442 original size:31 final size:31
Alignment explanation
Indices: 3725407--3725465 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
3725397 CCAGATACTA
*
3725407 GTCAGTTATGCATTCAGATAATGCATAGTGT
1 GTCAGGTATGCATTCAGATAATGCATAGTGT
* *
3725438 GTCAGGTATGTATTTAGATAATGCATAG
1 GTCAGGTATGCATTCAGATAATGCATAG
3725466 GATTACCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (31 bp):
GTCAGGTATGCATTCAGATAATGCATAGTGT
Found at i:3733874 original size:11 final size:11
Alignment explanation
Indices: 3733860--3733885 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3733850 CAATTTCATT
3733860 TTTTTTCATCA
1 TTTTTTCATCA
3733871 TTTTTTCATCA
1 TTTTTTCATCA
3733882 TTTT
1 TTTT
3733886 CTAGAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTCATCA
Found at i:3737684 original size:24 final size:24
Alignment explanation
Indices: 3737674--3737791 Score: 121
Period size: 24 Copynumber: 4.9 Consensus size: 24
3737664 CATAATTCAC
*
3737674 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAAAATCCAA
* *
3737698 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAAAATCCAA
* *
3737722 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCATATCAAAATCCAA
* * * *
3737746 GT-TAGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAAAATCCAA
*
3737770 GTCAAGTATCAGATCAGAAATC
1 GTCAAGTATCATATCA-AAATC
3737792 AAATTGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
23 2 0.02
24 74 0.90
25 6 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAAAATCCAA
Found at i:3737743 original size:48 final size:48
Alignment explanation
Indices: 3737674--3737788 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
3737664 CATAATTCAC
*
3737674 GTCAAGTATCATATCAAAATCCAGGTCAAG-TATCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAGGT-AAGATATCAGATCAGAATCCAA
* * *
3737722 GTCAAGTATCATATCAGAATCCATGTTAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAGGTAAGATATCAGATCAGAATCCAA
*
3737770 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
3737789 ATCAAATTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 2 0.03
48 59 0.97
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAATCCAGGTAAGATATCAGATCAGAATCCAA
Found at i:3737805 original size:48 final size:48
Alignment explanation
Indices: 3737705--3737805 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
3737695 CAGGTCAAGT
* * * *
3737705 ATCAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCATGTTAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCAATGTGAGAA
*
3737753 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAATCAAAT-TGA-AA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATC-AATGTGAGAA
3737801 ATCAG
1 ATCAG
3737806 GTAAAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
48 38 0.83
49 6 0.13
50 2 0.04
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCAATGTGAGAA
Found at i:3740308 original size:13 final size:13
Alignment explanation
Indices: 3740290--3740331 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
3740280 ACGGTCAATA
3740290 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3740303 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
3740316 GATCAACGGGTTG
1 GGTCAACGGGTCG
3740329 GGT
1 GGT
3740332 TGGGTTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.45, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3740386 original size:21 final size:21
Alignment explanation
Indices: 3740348--3740387 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3740338 ATGACCGGTC
**
3740348 AAACCGGTCAAATGGGTTACA
1 AAACCGGTCAAACCGGTTACA
3740369 AAACCGGTCAAACCGGTTA
1 AAACCGGTCAAACCGGTTA
3740388 TTTTTTCTTC
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:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (21 bp):
AAACCGGTCAAACCGGTTACA
Found at i:3747221 original size:33 final size:32
Alignment explanation
Indices: 3747183--3747263 Score: 76
Period size: 33 Copynumber: 2.4 Consensus size: 32
3747173 TCCGTATCTT
*
3747183 TTCTAATTTACTTTGATTATTATTTT-TATTTTA
1 TTCTAATTTACTTTG-TT-TTATTTTAGATTTTA
* *
3747216 TTCTAAATTAATTTTGTTTTATTTTAGATTTTA
1 TTCT-AATTTACTTTGTTTTATTTTAGATTTTA
3747249 TGTCT-ATGTTACTTT
1 T-TCTAAT-TTACTTT
3747264 TTCATATATG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
32 9 0.23
33 18 0.46
34 12 0.31
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.64
Consensus pattern (32 bp):
TTCTAATTTACTTTGTTTTATTTTAGATTTTA
Found at i:3752927 original size:72 final size:71
Alignment explanation
Indices: 3752847--3753076 Score: 319
Period size: 72 Copynumber: 3.2 Consensus size: 71
3752837 TCCATCACAT
3752847 TTGAGATATTTTCCCTTGAAAACTTTT-GTCTCA-TACGAGACAGTCTCTCTCGAAATAAAAATT
1 TTGAGATATTTTCCCTTGAAAA-TTTTCGTCTCACTAC-AGACAGTCTCTCTCGAAA-AAAAATT
3752910 TCATCTCCC
63 TCATCTCCC
*
3752919 TTGAGATATTTTCCCTTGAAAATTTTCGTCTCACT-CAAGACAG-CGTCTCTTGAAACAAAAATT
1 TTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTAC-AGACAGTC-TCTCTCGAAA-AAAAATT
3752982 TCATCTCCC
63 TCATCTCCC
* * *
3752991 TTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTTA-AGACAGTTTCTCTCGAAACAAAATTGC
1 TTGAGATATTTTCCCTTGAAAATTTTCGTCTCAC-TACAGACAGTCTCTCTCGAAAAAAAATTTC
3753055 ATCTCCC
65 ATCTCCC
3753062 TTGAGATA-TTTCCCT
1 TTGAGATATTTTCCCT
3753077 AGATATTTCC
Statistics
Matches: 145, Mismatches: 7, Indels: 14
0.87 0.04 0.08
Matches are distributed among these distances:
70 7 0.05
71 27 0.19
72 109 0.75
73 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (71 bp):
TTGAGATATTTTCCCTTGAAAATTTTCGTCTCACTACAGACAGTCTCTCTCGAAAAAAAATTTCA
TCTCCC
Found at i:3753011 original size:38 final size:38
Alignment explanation
Indices: 3752892--3753230 Score: 140
Period size: 34 Copynumber: 9.3 Consensus size: 38
3752882 CGAGACAGTC
* *
3752892 TCTCTCGAAATAAAAATTTCATCTCCCTTGAGATATTT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* * * * ** * ***
3752930 TCCCTTG----AAAATTTTCGTCTCACTCAAGACAGCG
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
3752964 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* * * * * * *
3753002 TCCCTTG----AAAATTTTCGTCTCACTTAAGACAGTT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* *
3753036 TCTCTCGAAAC-AAAATTGCATCTCCCTTGAGATA-TT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* * * ** ** * * *
3753072 TCCCTAGATATTTCCCTTGAAATTTTTTCTCGCTCGAGATAGTT
1 TCTCTTGA-A----AC-AAAAATTTCATCTCCCTTGAGATATTT
*
3753116 TCTCTTGAAACAAAAATTTCAACTCCC-TGAGATATTT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* * *
3753153 TCCCTTG--A-AAAAATTTCA-----CTTGAGACAATT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
* * * *
3753183 TCTCTTAAAACCAAAATTTCATCTCACTTAAGATATTT
1 TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
3753221 TCTCTTGAAA
1 TCTCTTGAAA
3753231 AATTTCGTCT
Statistics
Matches: 210, Mismatches: 66, Indels: 50
0.64 0.20 0.15
Matches are distributed among these distances:
29 1 0.00
30 13 0.06
32 1 0.00
33 9 0.04
34 60 0.29
35 1 0.00
36 8 0.04
37 32 0.15
38 57 0.27
39 1 0.00
41 1 0.00
43 18 0.09
44 8 0.04
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (38 bp):
TCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTT
Found at i:3753126 original size:80 final size:84
Alignment explanation
Indices: 3752994--3753157 Score: 212
Period size: 80 Copynumber: 2.0 Consensus size: 84
3752984 ATCTCCCTTG
* *
3752994 AGATATTTTCCCTTGAAAATTTTCGTCTCACTTAAGACAGTTTCTCTCGAAAC-AAAATTGCATC
1 AGATATTTTCCCTTGAAAATTTTCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTGCAAC
3753058 TCCCTTGAGATA-TTTCCCT
66 TCCC-TGAGATATTTTCCCT
* * * * * *
3753077 AGATA-TTTCCCTTG-AAATTTT-TTCTCGCTCGAGATAGTTTCTCTTGAAACAAAAATTTCAAC
1 AGATATTTTCCCTTGAAAATTTTCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTGCAAC
3753139 TCCCTGAGATATTTTCCCT
66 TCCCTGAGATATTTTCCCT
3753158 TGAAAAAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 30 0.42
81 27 0.38
82 9 0.13
83 5 0.07
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.38
Consensus pattern (84 bp):
AGATATTTTCCCTTGAAAATTTTCGTCTCACTCAAGACAGTTTCTCTCGAAACAAAAATTGCAAC
TCCCTGAGATATTTTCCCT
Found at i:3760825 original size:21 final size:19
Alignment explanation
Indices: 3760792--3760847 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
3760782 TACTACTAGC
*
3760792 ACAGTATCGATACTTCTTCA
1 ACAGTACCGATACTTCTT-A
*
3760812 ATAGGTACCGATACTATTCTTA
1 ACA-GTACCGATAC--TTCTTA
3760834 ACAGTACCGATACT
1 ACAGTACCGATACT
3760848 CCTTGAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.03
20 2 0.07
21 19 0.63
22 3 0.10
23 5 0.17
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (19 bp):
ACAGTACCGATACTTCTTA
Found at i:3763097 original size:18 final size:18
Alignment explanation
Indices: 3763074--3763108 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3763064 ATCAAAATCA
* *
3763074 ATTTTTGAAAATAAAATG
1 ATTTTTCAAAAGAAAATG
3763092 ATTTTTCAAAAGAAAAT
1 ATTTTTCAAAAGAAAAT
3763109 CTTAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (18 bp):
ATTTTTCAAAAGAAAATG
Found at i:3770380 original size:27 final size:27
Alignment explanation
Indices: 3770348--3770404 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3770338 ACTCAAACTC
3770348 AAACTCAAATCTGTCTTATTACATCTA
1 AAACTCAAATCTGTCTTATTACATCTA
3770375 AAACTCAAATCTGTCTTATTACATCTA
1 AAACTCAAATCTGTCTTATTACATCTA
3770402 AAA
1 AAA
3770405 TAATAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (27 bp):
AAACTCAAATCTGTCTTATTACATCTA
Found at i:3774829 original size:37 final size:37
Alignment explanation
Indices: 3774756--3774830 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
3774746 GTTAGAAAAT
* *
3774756 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
3774793 ATTTATATAATTTTTTTTATAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
3774830 A
1 A
3774831 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:3775375 original size:31 final size:32
Alignment explanation
Indices: 3775340--3775399 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
3775330 AGTTTTTAAA
3775340 AAAATTAAAAGTTTAGGTACTAAA-ACATGCC
1 AAAATTAAAAGTTTAGGTACTAAACACATGCC
* * *
3775371 AAAATTGATAGTTTAGGTATTAAACACAT
1 AAAATTAAAAGTTTAGGTACTAAACACAT
3775400 TAAGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (32 bp):
AAAATTAAAAGTTTAGGTACTAAACACATGCC
Found at i:3777475 original size:47 final size:47
Alignment explanation
Indices: 3777421--3777514 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
3777411 TCATTGCATG
*
3777421 ACACATAATTGTATTGTTACAACATTATCATGTTTAAAGCTACCATT
1 ACACATAATTGTATTGTTACAACATTATCATGTTGAAAGCTACCATT
3777468 ACACATAATTGTATTGTTACAACATTATCATGTTGAAAGCTACCATT
1 ACACATAATTGTATTGTTACAACATTATCATGTTGAAAGCTACCATT
3777515 TGACATCAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (47 bp):
ACACATAATTGTATTGTTACAACATTATCATGTTGAAAGCTACCATT
Found at i:3778474 original size:13 final size:13
Alignment explanation
Indices: 3778456--3778480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3778446 CGTGGAATGA
3778456 ACTTGCTAAAAAG
1 ACTTGCTAAAAAG
3778469 ACTTGCTAAAAA
1 ACTTGCTAAAAA
3778481 CTTTTTACTT
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:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
ACTTGCTAAAAAG
Found at i:3785034 original size:22 final size:22
Alignment explanation
Indices: 3784963--3785037 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 22
3784953 AATTTCCATA
*
3784963 GCACTGGTACTAAAGTGCC-TC
1 GCACTGATACTAAAGTGCCTTC
**
3784984 AGCACTGATA-TAGAAGTGTATTC
1 -GCACTGATACTA-AAGTGCCTTC
**
3785007 ATACTGATACTAAAGTGCCTTC
1 GCACTGATACTAAAGTGCCTTC
3785029 GCACTGATA
1 GCACTGATA
3785038 AGAGAATATC
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 2 0.05
22 35 0.85
23 4 0.10
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (22 bp):
GCACTGATACTAAAGTGCCTTC
Found at i:3799057 original size:17 final size:18
Alignment explanation
Indices: 3799035--3799068 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3799025 TCTTTAAGGT
3799035 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
3799052 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
3799069 TATTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:3799100 original size:29 final size:30
Alignment explanation
Indices: 3799035--3799105 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
3799025 TCTTTAAGGT
3799035 ATATTTTA-TT-ATATTTAATATTTTGTTA
1 ATATTTTATTTAATATTTAATATTTTGTTA
*
3799063 GTATTTTATTTAACTATTTAA-ATTTT-TTA
1 ATATTTTATTTAA-TATTTAATATTTTGTTA
3799092 ATATTTTATTTAAT
1 ATATTTTATTTAAT
3799106 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 6 0.16
31 7 0.18
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (30 bp):
ATATTTTATTTAATATTTAATATTTTGTTA
Found at i:3801325 original size:13 final size:13
Alignment explanation
Indices: 3801307--3801331 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3801297 TTTTTGGACT
3801307 TTTTGTTAATTTA
1 TTTTGTTAATTTA
3801320 TTTTGTTAATTT
1 TTTTGTTAATTT
3801332 TGTTTATTAC
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:3803106 original size:11 final size:11
Alignment explanation
Indices: 3803090--3803114 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3803080 ACCAACTTGG
3803090 AAGTTCATTGT
1 AAGTTCATTGT
3803101 AAGTTCATTGT
1 AAGTTCATTGT
3803112 AAG
1 AAG
3803115 ATGCATCGCA
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (11 bp):
AAGTTCATTGT
Found at i:3809356 original size:29 final size:29
Alignment explanation
Indices: 3809314--3809375 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
3809304 CATCTTCCAC
*
3809314 CCTTGTCTGGACGTACGCCCAGCTACCAG
1 CCTTGTCTGCACGTACGCCCAGCTACCAG
* *
3809343 CCTTTTCTGCACGTACGCCCAGCTGCCAG
1 CCTTGTCTGCACGTACGCCCAGCTACCAG
3809372 CCTT
1 CCTT
3809376 CCAGAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.15, C:0.40, G:0.21, T:0.24
Consensus pattern (29 bp):
CCTTGTCTGCACGTACGCCCAGCTACCAG
Found at i:3816399 original size:14 final size:14
Alignment explanation
Indices: 3816382--3816408 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3816372 TTTTTGCCAA
3816382 GGCATTTTCATATT
1 GGCATTTTCATATT
3816396 GGCATTTTCATAT
1 GGCATTTTCATAT
3816409 CGACCCCTTG
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:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (14 bp):
GGCATTTTCATATT
Found at i:3821001 original size:23 final size:23
Alignment explanation
Indices: 3820944--3821001 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
3820934 TTTGATTTCG
* *
3820944 CTACA-CTCAATTTATTTTGCCA
1 CTACATCTCCATTCATTTTGCCA
* * *
3820966 ATACATTTTCATTCATTTTGCCA
1 CTACATCTCCATTCATTTTGCCA
3820989 CTACATCTCCATT
1 CTACATCTCCATT
3821002 TTGTTTTACA
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.26, C:0.28, G:0.03, T:0.43
Consensus pattern (23 bp):
CTACATCTCCATTCATTTTGCCA
Found at i:3823053 original size:21 final size:20
Alignment explanation
Indices: 3823020--3823059 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3823010 TGATCTAAAA
*
3823020 ACTTGGTGAAAATATCAATT
1 ACTTGATGAAAATATCAATT
3823040 ACTTGATGCAAAATATCAAT
1 ACTTGATG-AAAATATCAAT
3823060 ATATTCTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
ACTTGATGAAAATATCAATT
Found at i:3827995 original size:17 final size:17
Alignment explanation
Indices: 3827973--3828035 Score: 108
Period size: 17 Copynumber: 3.7 Consensus size: 17
3827963 AATATATATA
*
3827973 AATATTGTACAATTTGT
1 AATATTTTACAATTTGT
3827990 AATATTTTACAATTTGT
1 AATATTTTACAATTTGT
3828007 AATATTTTACAATTTGT
1 AATATTTTACAATTTGT
*
3828024 AATATTATACAA
1 AATATTTTACAA
3828036 ATATATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (17 bp):
AATATTTTACAATTTGT
Found at i:3828170 original size:24 final size:24
Alignment explanation
Indices: 3828138--3828183 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3828128 ACCAAACACA
3828138 AAATACAACATTCTCAATAATCCT
1 AAATACAACATTCTCAATAATCCT
*
3828162 AAATACAACATTCTCAGTAATC
1 AAATACAACATTCTCAATAATC
3828184 ATATTCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATACAACATTCTCAATAATCCT
Found at i:3841120 original size:22 final size:20
Alignment explanation
Indices: 3841064--3841121 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
3841054 ATATGAAATC
3841064 TATGTCCCGAAGGA-CGTCA
1 TATGTCCCGAAGGACCGTCA
* *
3841083 TCTGTGCCCCTAAGGACCTGTTCA
1 TATGT--CCCGAAGGACC-G-TCA
3841107 TATGTCCCGAAGGAC
1 TATGTCCCGAAGGAC
3841122 ATAGGTAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.13
21 8 0.27
22 10 0.33
23 1 0.03
24 7 0.23
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (20 bp):
TATGTCCCGAAGGACCGTCA
Found at i:3855403 original size:41 final size:43
Alignment explanation
Indices: 3855340--3855420 Score: 121
Period size: 41 Copynumber: 1.9 Consensus size: 43
3855330 AAGTCTTTCG
* *
3855340 AGCATGATGATGAAATCCTTCGGGTCATCTATAA-ACCTTTAA
1 AGCAAGATGATGAAATCCTTCGGGTCATCCATAAGACCTTTAA
*
3855382 AGCAAGATGAT-AAGTCCTTCGGGTCATCCATAAGACCTT
1 AGCAAGATGATGAAATCCTTCGGGTCATCCATAAGACCTT
3855421 CGGGTAGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
AGCAAGATGATGAAATCCTTCGGGTCATCCATAAGACCTTTAA
Found at i:3855552 original size:20 final size:20
Alignment explanation
Indices: 3855527--3855599 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
3855517 TTGCACTTAG
3855527 TAAGTCCTTCGGGCCATCAA
1 TAAGTCCTTCGGGCCATCAA
* * *
3855547 TAAGTCTTTCGAG-CATGATGA
1 TAAGTCCTTCGGGCCATCA--A
*
3855568 TGAAGTCCTTCGGGCCATCAG
1 T-AAGTCCTTCGGGCCATCAA
*
3855589 TAAGTCTTTCG
1 TAAGTCCTTCG
3855600 AGCATGATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.10
20 20 0.49
21 3 0.07
22 10 0.24
23 4 0.10
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (20 bp):
TAAGTCCTTCGGGCCATCAA
Found at i:3855573 original size:22 final size:21
Alignment explanation
Indices: 3855546--3855610 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 21
3855536 CGGGCCATCA
3855546 ATAAGTCTTTCGAGCATGATG
1 ATAAGTCTTTCGAGCATGATG
* * *
3855567 ATGAAGTCCTTCGGGCCATCA-G
1 AT-AAGTCTTTCGAG-CATGATG
3855589 -TAAGTCTTTCGAGCATGATG
1 ATAAGTCTTTCGAGCATGATG
3855609 AT
1 AT
3855611 TAAATCCTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.12
20 11 0.32
21 4 0.12
22 11 0.32
23 4 0.12
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (21 bp):
ATAAGTCTTTCGAGCATGATG
Found at i:3855587 original size:42 final size:42
Alignment explanation
Indices: 3855528--3855619 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
3855518 TGCACTTAGT
3855528 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
* *
3855570 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
*
3855612 AAATCCTT
1 AAGTCCTT
3855620 AGGGTAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATG
Done.