Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 45 of 62
Found at i:10526774 original size:2 final size:2
Alignment explanation
Indices: 10526732--10526761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10526722 GATACGCGCC
10526732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10526762 GGCGTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10529659 original size:21 final size:21
Alignment explanation
Indices: 10529629--10529669 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10529619 AGTGCCCAAC
* *
10529629 AATAATAAAATTGATAGAAAA
1 AATAACAAAATTAATAGAAAA
10529650 AATAACAAAATTAATAGAAA
1 AATAACAAAATTAATAGAAA
10529670 TAATTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (21 bp):
AATAACAAAATTAATAGAAAA
Found at i:10530518 original size:2 final size:2
Alignment explanation
Indices: 10530511--10530546 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10530501 TAATATGAAA
10530511 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
10530547 CTTATACGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10533522 original size:18 final size:18
Alignment explanation
Indices: 10533499--10533534 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10533489 TAATTATGTG
10533499 TTTAGTTTACAATTATGA
1 TTTAGTTTACAATTATGA
10533517 TTTAGTTTACAATTATGA
1 TTTAGTTTACAATTATGA
10533535 CTGTAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTAGTTTACAATTATGA
Found at i:10533974 original size:22 final size:24
Alignment explanation
Indices: 10533949--10534009 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
10533939 TTGTCACCTT
*
10533949 ATCCCTAAATTCTTAAAC-TT-AA
1 ATCCCTAAAATCTTAAACATTCAA
10533971 ATCCCTAAAATCTTAAACATTCAA
1 ATCCCTAAAATCTTAAACATTCAA
*
10533995 ATCTCTAAAAATCTT
1 ATCCCT-AAAATCTT
10534010 TTAAATCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 17 0.50
23 2 0.06
24 7 0.21
25 8 0.24
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (24 bp):
ATCCCTAAAATCTTAAACATTCAA
Found at i:10534187 original size:11 final size:12
Alignment explanation
Indices: 10534156--10534193 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
10534146 GGGTTAGGAT
10534156 ATTTTTTTTAAA
1 ATTTTTTTTAAA
10534168 ATTTTTTTTAAA
1 ATTTTTTTTAAA
*
10534180 TTTTTTTTTAAA
1 ATTTTTTTTAAA
10534192 AT
1 AT
10534194 AAAAAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTTTTAAA
Found at i:10534955 original size:3 final size:3
Alignment explanation
Indices: 10534947--10534971 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10534937 ATTCATATTA
10534947 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
10534972 TAATCAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:10538558 original size:283 final size:285
Alignment explanation
Indices: 10538051--10538618 Score: 1122
Period size: 283 Copynumber: 2.0 Consensus size: 285
10538041 ATGCAGTATT
10538051 ATAACCAAGTAGGACGTTAAGACACCCGATAAGACTGCCTATGGTTTTGTAAATGAGAAACAGAA
1 ATAACCAAGTAGGACGTTAAGACACCCGATAAGACTGCCTATGGTTTTGTAAATGAGAAACAGAA
10538116 GAAGGTAAAGAAGAAACATATTGTAATGAAGGAGACAGAGGAACATCTGTTGAGGCTAAAGGAGG
66 GAAGGTAAAGAAGAAACATATTGTAATGAAGGAGACAGAGGAACATCTGTTGAGGCTAAAGGAGG
10538181 AACATAATTCTACTGAGAAGAAATAGGGTCAAAAGAATGAGAAGAAATAACCAGAAATTCAAAAT
131 AACATAATTCTACTGAGAAGAAATAGGGTCAAAAGAATGAGAAGAAATAACCAGAAATTCAAAAT
10538246 CAGGAATACATTGTGGAGAGGGGAAAATAGGAGTATGACTAGAAGAAACAAAATGAAAGGG-AAC
196 CAGGAATACATTGTGGAGAGGGGAAAATAGGAGTATGACTAGAAGAAACAAAATGAAAGGGAAAC
10538310 ACAGCTTCATG-AAAATGACATCAC
261 ACAGCTTCATGAAAAATGACATCAC
10538334 ATAACCAAGTAGGACGTTAAGACACCCGATAAGACTGCCTATGGTTTTGTAAATGAGAAACAGAA
1 ATAACCAAGTAGGACGTTAAGACACCCGATAAGACTGCCTATGGTTTTGTAAATGAGAAACAGAA
10538399 GAAGGTAAAGAAGAAACATATTGTAATGAAGGAGACAGAGGAACATCTGTTGAGGCTAAAGGAGG
66 GAAGGTAAAGAAGAAACATATTGTAATGAAGGAGACAGAGGAACATCTGTTGAGGCTAAAGGAGG
10538464 AACATAATTCTACTGAGAAGAAATAGGGTCAAAAGAATGAGAAGAAATAACCAGAAATTCAAAAT
131 AACATAATTCTACTGAGAAGAAATAGGGTCAAAAGAATGAGAAGAAATAACCAGAAATTCAAAAT
10538529 CAGGAATACATTGTGGAGAGGGGAAAATAGGAGTATGACTAGAAGAAACAAAATGAAAGGGAAAC
196 CAGGAATACATTGTGGAGAGGGGAAAATAGGAGTATGACTAGAAGAAACAAAATGAAAGGGAAAC
10538594 ACAGCTTCATGAAAAATGACATCAC
261 ACAGCTTCATGAAAAATGACATCAC
10538619 GATTGACAAA
Statistics
Matches: 283, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
283 256 0.90
284 14 0.05
285 13 0.05
ACGTcount: A:0.46, C:0.12, G:0.24, T:0.18
Consensus pattern (285 bp):
ATAACCAAGTAGGACGTTAAGACACCCGATAAGACTGCCTATGGTTTTGTAAATGAGAAACAGAA
GAAGGTAAAGAAGAAACATATTGTAATGAAGGAGACAGAGGAACATCTGTTGAGGCTAAAGGAGG
AACATAATTCTACTGAGAAGAAATAGGGTCAAAAGAATGAGAAGAAATAACCAGAAATTCAAAAT
CAGGAATACATTGTGGAGAGGGGAAAATAGGAGTATGACTAGAAGAAACAAAATGAAAGGGAAAC
ACAGCTTCATGAAAAATGACATCAC
Found at i:10542912 original size:21 final size:21
Alignment explanation
Indices: 10542886--10542981 Score: 165
Period size: 21 Copynumber: 4.6 Consensus size: 21
10542876 ATTTCCAGAT
*
10542886 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTGGACTA
*
10542907 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
10542928 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
10542949 TCGCAACGCGAACTTGGACTA
1 TCGCAACGCGAACTTGGACTA
*
10542970 TCGCAATGCGAA
1 TCGCAACGCGAA
10542982 TATGTAAATC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (21 bp):
TCGCAACGCGAACTTGGACTA
Found at i:10542994 original size:20 final size:20
Alignment explanation
Indices: 10542969--10543061 Score: 136
Period size: 20 Copynumber: 4.6 Consensus size: 20
10542959 AACTTGGACT
10542969 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
10542989 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
10543010 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
10543030 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
10543050 ATCGCAATGCGA
1 ATCGCAATGCGA
10543062 TAGTCGAAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
18 2 0.03
19 3 0.05
20 44 0.67
21 12 0.18
22 3 0.05
23 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:10543015 original size:21 final size:20
Alignment explanation
Indices: 10542900--10543068 Score: 77
Period size: 21 Copynumber: 8.2 Consensus size: 20
10542890 AACGCGAACT
10542900 TCGACTATCGCAATGCGA-A
1 TCGACTATCGCAATGCGATA
* *
10542919 CTTGGACTATCGCAACGCGA-A
1 --TCGACTATCGCAATGCGATA
* *
10542940 CTTGGACTATCGCAACGCGA-A
1 --TCGACTATCGCAATGCGATA
*
10542961 CTTGGACTATCGCAATGCGAATA
1 --TCGACTATCGCAATGCG-ATA
*
10542984 T-GTA-AATCGCAATGCGATA
1 TCG-ACTATCGCAATGCGATA
10543003 GTCGACTATCGCAATGCGAATA
1 -TCGACTATCGCAATGCG-ATA
*
10543025 T-GTA-AATCGCAATGCGAATA
1 TCG-ACTATCGCAATGCG-ATA
*
10543045 T-GTA-AATCGCAATGCGATA
1 TCG-ACTATCGCAATGCGATA
10543064 GTCGA
1 -TCGA
10543069 AGTTCGCGTT
Statistics
Matches: 132, Mismatches: 6, Indels: 21
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.05
20 48 0.36
21 73 0.55
22 4 0.03
23 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (20 bp):
TCGACTATCGCAATGCGATA
Found at i:10543116 original size:41 final size:41
Alignment explanation
Indices: 10543071--10543173 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 41
10543061 ATAGTCGAAG
*
10543071 TTCGCGTTGCGATAGT-CAACTATCACATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAACT-TCACATTGCGATTTACATA
* * *
10543112 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAA
1 TTCGCATTGCGATAGTCCAACTTCACATTGCGATTTA---CATA
10543156 TTCG--TTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
10543174 AATCGCAACG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
41 29 0.54
42 18 0.33
44 7 0.13
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCCAACTTCACATTGCGATTTACATA
Found at i:10543138 original size:21 final size:21
Alignment explanation
Indices: 10543051--10543173 Score: 94
Period size: 21 Copynumber: 5.9 Consensus size: 21
10543041 AATATGTAAA
* *
10543051 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
10543072 TCGCGTTGCGATAGT-CAACT
1 TCGCATTGCGATAGTCCAAGT
* * *
10543092 ATCACATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
10543113 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
10543134 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAGT
10543157 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
10543174 AATCGCAACG
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
19 7 0.09
20 16 0.20
21 47 0.57
22 1 0.01
23 11 0.13
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:10543273 original size:6 final size:6
Alignment explanation
Indices: 10543262--10543294 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
10543252 AGACACGTAT
10543262 GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
10543295 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:10543971 original size:21 final size:20
Alignment explanation
Indices: 10543910--10544024 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 20
10543900 CGTTGCGATT
10543910 TTGGACTATCGCAAT--GAA
1 TTGGACTATCGCAATGCGAA
* * *
10543928 TTTGGAATAAATCACAACGCGAA
1 -TTGGACT--ATCGCAATGCGAA
10543951 CTTGGACTATCGCAATGCGAA
1 -TTGGACTATCGCAATGCGAA
* *
10543972 TATGTA-AATCGCAATGCGATA
1 T-TGGACTATCGCAATGCGA-A
* * *
10543993 GTCGACTATCGTAATGCGAA
1 TTGGACTATCGCAATGCGAA
*
10544013 CTTCGACTATCG
1 -TTGGACTATCG
10544025 TATTGCGATT
Statistics
Matches: 73, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
19 6 0.08
20 16 0.22
21 42 0.58
23 9 0.12
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGGACTATCGCAATGCGAA
Found at i:10544090 original size:21 final size:21
Alignment explanation
Indices: 10544041--10544114 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
10544031 GATTTACATA
*
10544041 TTCGCATTACGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
10544062 TT-GCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
10544082 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
10544103 TTCGCGTTGCGA
1 TTCGCATTGCGA
10544115 ATCTGGAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 19 0.39
21 30 0.61
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:10546181 original size:26 final size:26
Alignment explanation
Indices: 10546152--10546209 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
10546142 AATATTATTA
10546152 TGAATTATTTTAATTTTGTACACCTT
1 TGAATTATTTTAATTTTGTACACCTT
10546178 TGAATTATTTTAATTTTGTACACCTT
1 TGAATTATTTTAATTTTGTACACCTT
10546204 TGAATT
1 TGAATT
10546210 TATTAATGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.53
Consensus pattern (26 bp):
TGAATTATTTTAATTTTGTACACCTT
Found at i:10550833 original size:21 final size:21
Alignment explanation
Indices: 10550809--10550855 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
10550799 AGTCATTATT
10550809 TGCATTGCATCACTTTGCATC
1 TGCATTGCATCACTTTGCATC
*
10550830 TGCATTGCATCACTTTGCATT
1 TGCATTGCATCACTTTGCATC
10550851 TGCAT
1 TGCAT
10550856 CTTTGCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.15, T:0.40
Consensus pattern (21 bp):
TGCATTGCATCACTTTGCATC
Found at i:10550861 original size:14 final size:14
Alignment explanation
Indices: 10550822--10550869 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
10550812 ATTGCATCAC
10550822 TTTGCATC--TGCA
1 TTTGCATCTTTGCA
10550834 -TTGCATCACTTTGCA
1 TTTGCAT--CTTTGCA
10550849 TTTGCATCTTTGCA
1 TTTGCATCTTTGCA
10550863 TTTGCAT
1 TTTGCAT
10550870 AATCATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.19
13 1 0.03
14 14 0.45
15 4 0.13
16 6 0.19
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.46
Consensus pattern (14 bp):
TTTGCATCTTTGCA
Found at i:10556959 original size:36 final size:36
Alignment explanation
Indices: 10556912--10556985 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
10556902 TTTATCTCAT
* *
10556912 TCAAGATTGTTTTTTCTTGAAATAGAAGATTTTATC
1 TCAAGATTGTTTTTCCTTGAAATAAAAGATTTTATC
*
10556948 TCAAGATTGTTTTTCCTTGAAATAAAATATTTTATC
1 TCAAGATTGTTTTTCCTTGAAATAAAAGATTTTATC
10556984 TC
1 TC
10556986 GCTTGAGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (36 bp):
TCAAGATTGTTTTTCCTTGAAATAAAAGATTTTATC
Found at i:10557105 original size:36 final size:36
Alignment explanation
Indices: 10556976--10557252 Score: 306
Period size: 36 Copynumber: 7.6 Consensus size: 36
10556966 GAAATAAAAT
* * *
10556976 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAAC--AA
* * * *
10557014 GATTTTATCTCGCTTAAGATAGTTTCCCTCGAAACAGAA
1 -ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAAC--AA
* * * *
10557053 GATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAA
1 -ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
*
10557090 ATTTTGTCTCCCTTGAGACGGTTTCCCAT-GAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCC-TCGAAACAA
*
10557126 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
* * *
10557162 ATTTAGTCTCCCTTGAGACAG-TTCCTTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
* * *
10557197 ATTTTGTCTCCCTTGAGACGGGTTCCCTTGAAACAA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
10557233 ATTTTGTCTCCCTTGAGACA
1 ATTTTGTCTCCCTTGAGACA
10557253 ATCTCCCTTG
Statistics
Matches: 219, Mismatches: 16, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
35 33 0.15
36 114 0.52
37 3 0.01
39 69 0.32
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (36 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTCGAAACAA
Found at i:10557211 original size:107 final size:110
Alignment explanation
Indices: 10557015--10557263 Score: 335
Period size: 107 Copynumber: 2.3 Consensus size: 110
10557005 GAAACAAAAG
* * * * * * * *
10557015 ATTTTATCTCGCTTAAGATAGTTTCCCTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAGATTTTATCTCCCTTGAGACAGTTCCT
*
10557080 CTCGAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCATGAAACAA
65 CTCGAAACAAATTTTGTCTCCCTTGAGACGGGTTCCCATGAAACAA
10557126 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAAC-AA-A-TTTAGTCTCCCTTGAGACAGTTCCT
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGATTTTA-TCTCCCTTGAGACAGTTCCT
* *
10557188 -TTGAAACAAATTTTGTCTCCCTTGAGACGGGTTCCCTTGAAACAA
65 CTCGAAACAAATTTTGTCTCCCTTGAGACGGGTTCCCATGAAACAA
* *
10557233 ATTTTGTCTCCCTTGAGACAATCTCCCTTGA
1 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
10557264 GATAATTTCA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
107 75 0.60
108 18 0.15
109 2 0.02
111 29 0.23
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (110 bp):
ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGATTTTATCTCCCTTGAGACAGTTCCTC
TCGAAACAAATTTTGTCTCCCTTGAGACGGGTTCCCATGAAACAA
Found at i:10557271 original size:71 final size:71
Alignment explanation
Indices: 10556976--10557263 Score: 288
Period size: 71 Copynumber: 3.9 Consensus size: 71
10556966 GAAATAAAAT
* * * * * * * * *
10556976 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGCTTAAGATAGTTTCC
1 ATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAAC--AA-ATTTTGTCTCCCTTGAGACAG-TTCC
*
10557041 CTCGAAACAGAA
62 CTTGAAAC--AA
* * * * * * * *
10557053 GATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCA
1 -ATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG-TTCCCT
10557118 TGAAACAA
64 TGAAACAA
* * *
10557126 ATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTAGTCTCCCTTGAGACAGTTCCTTTG
1 ATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCCCTTG
10557191 AAACAA
66 AAACAA
* *
10557197 ATTTTGTCTCCCTTGAGACGGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATCTCCCTT
1 ATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGT-TCCCTT
10557262 GA
65 GA
10557264 GATAATTTCA
Statistics
Matches: 187, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
71 66 0.35
72 57 0.30
73 2 0.01
75 27 0.14
76 2 0.01
78 33 0.18
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (71 bp):
ATTTTGTCTCCCTTGAGACAGGTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCCCTTG
AAACAA
Found at i:10557435 original size:43 final size:43
Alignment explanation
Indices: 10557364--10557866 Score: 387
Period size: 43 Copynumber: 11.6 Consensus size: 43
10557354 GTTTTTGAAG
* * *
10557364 AAGCTTG-A-GACCATCGTGATATGCAGGGGTTTCTTGAGGAC
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
*
10557405 AAGTTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
* * * *
10557448 AAGATTG-AGAAACCATCGTGATATGTAGGGGTTTCTTGATGAT
1 AAGCTTGAAG-GACCATCGTGATATGTAGGGGTTCCTTGATGAC
10557491 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
*
10557534 AAGCTTG-AGGACCATTGTGATATGTAGGGGTTCCTTGATGAC
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
** * * * * * * * *
10557576 AAATTTG-ATGACAAGCTTGAGAAACCATTGTAGGGGTTTCTTTATGAA
1 AAGCTTGAAGGACCA--TCGTG--A-TA-TGTAGGGGTTCCTTGATGAC
*
10557624 AAGC-TGAGGGACCATCGTGATATGTAGGGGTT-CTTGATG--
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
10557663 AAGCTTG-AGGACC-TCGTGATATGTA-GGG-TCCTTGATGAC
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
** *
10557702 AATTTGATGACAAGCTTGAAACCATCGTGATATGTA-GGGTTTCTTGATG--
1 AAGCT--TG--AAG---G--ACCATCGTGATATGTAGGGGTTCCTTGATGAC
* *
10557751 AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAA
1 AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
** *
10557794 AAATTGATGACAAACTTGAGACCA-CGTGATATGTAGGGGTTTCTTGATGA-
1 AAGCT--TG---AA---G-GACCATCGTGATATGTAGGGGTTCCTTGATGAC
*
10557844 AAGCTTGAGGGA-CATCGTGATAT
1 AAGCTTGAAGGACCATCGTGATAT
10557867 AGGGTTTGAT
Statistics
Matches: 376, Mismatches: 46, Indels: 80
0.75 0.09 0.16
Matches are distributed among these distances:
36 1 0.00
37 10 0.03
38 12 0.03
39 12 0.03
40 20 0.05
41 36 0.10
42 59 0.16
43 113 0.30
44 9 0.02
45 5 0.01
46 4 0.01
47 6 0.02
48 26 0.07
49 6 0.02
50 18 0.05
51 34 0.09
52 5 0.01
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (43 bp):
AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGAC
Found at i:10557574 original size:128 final size:128
Alignment explanation
Indices: 10557352--10557792 Score: 484
Period size: 128 Copynumber: 3.4 Consensus size: 128
10557342 CCTGATTTTA
* * * * *
10557352 GGGTTT-TTGAAG-AAGCTTG-A-GACCATCGTGATATGCAGGGGTTTCTTGAGGACAAGTTTGA
1 GGGTTTCTTGATGAAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTG-
10557413 AGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGATTGA-GAAACCATCGTGATATGTAG
65 AGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGATTGATGAAACCATCGTGATATGTAG
10557476 GGGTTTCTTGATGATAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTG
1 GGGTTTCTTGATGA-AAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTG
* * * * *
10557541 AGGACCATTGTGATATGTAGGGGTTCCTTGATGACAA-ATTTGATGACAAGC-TTGAGAAACCAT
65 AGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGA-TTGATGA-AACCATCGTG--A-TA-
10557604 TGTAG
124 TGTAG
* *
10557609 GGGTTTCTTTATGAAAAGC-TGAGGGACCATCGTGATATGTAGGGGTT-CTTGATG--AAGCTTG
1 GGGTTTCTTGATG-AAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTG
10557670 AGGACC-TCGTGATATGTA-GGG-TCCTTGATGACAATTTGA-TGACAAGCTTGAAACCATCGTG
65 AGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA---GATTG---A---TGAAACCATCGTG
10557731 ATATGTA-
121 ATATGTAG
*
10557738 GGGTTTCTTGATG-AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA
1 GGGTTTCTTGATGAAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGA
10557793 AAAATTGATG
Statistics
Matches: 272, Mismatches: 18, Indels: 48
0.80 0.05 0.14
Matches are distributed among these distances:
124 6 0.02
125 5 0.02
126 13 0.05
127 15 0.06
128 82 0.30
129 73 0.27
130 8 0.03
131 10 0.04
132 29 0.11
133 24 0.09
134 7 0.03
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (128 bp):
GGGTTTCTTGATGAAAGCTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGCTTGA
GGACCATCGTGATATGTAGGGGTTCCTTGATGACAAGATTGATGAAACCATCGTGATATGTAG
Found at i:10557685 original size:38 final size:39
Alignment explanation
Indices: 10557604--10557793 Score: 152
Period size: 40 Copynumber: 4.5 Consensus size: 39
10557594 GAGAAACCAT
*
10557604 TGTAGGGGTTTCTTTATGAAAAGCTGAGGGACCATCGTGATA
1 TGTAGGGG-TTCTTGATG--AAGCTGAGGGACCATCGTGATA
10557646 TGTAGGGGTTCTTGATGAAGCTTGA-GGACC-TCGTGATA
1 TGTAGGGGTTCTTGATGAAGC-TGAGGGACCATCGTGATA
* * *
10557684 TGTA-GGGTCCTTGATGACAATTTGATGACAAGCTTGAAACCATCGTGATA
1 TGTAGGGGTTCTTGATG--AA---GCTG---AG---G-GACCATCGTGATA
*
10557734 TGTAGGGTTTCTTGATGAAGCTTGAGGGACCATCGTGATA
1 TGTAGGGGTTCTTGATGAAGC-TGAGGGACCATCGTGATA
10557774 TGTAGGGGTTCCTTGATGAA
1 TGTAGGGGTT-CTTGATGAA
10557794 AAATTGATGA
Statistics
Matches: 121, Mismatches: 9, Indels: 37
0.72 0.05 0.22
Matches are distributed among these distances:
37 11 0.09
38 12 0.10
39 11 0.09
40 24 0.20
41 20 0.17
42 9 0.07
44 3 0.02
46 1 0.01
47 2 0.02
48 1 0.01
49 5 0.04
50 12 0.10
51 10 0.08
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.32
Consensus pattern (39 bp):
TGTAGGGGTTCTTGATGAAGCTGAGGGACCATCGTGATA
Found at i:10557730 original size:50 final size:50
Alignment explanation
Indices: 10557663--10557845 Score: 167
Period size: 51 Copynumber: 3.8 Consensus size: 50
10557653 GTTCTTGATG
*
10557663 AAGCTTGAGGACC-TCGTGATATGTAGGG-TCCTTGATGACAATTTGATGAC
1 AAGCTTGA-GACCATCGTGATATGTAGGGTTCCTTGATGA-AAATTGATGAC
* * **
10557713 AAGCTTGAAACCATCGTGATATGTAGGGTTTCTTGATG-AAGCT--TG--
1 AAGCTTGAGACCATCGTGATATGTAGGGTTCCTTGATGAAAATTGATGAC
10557758 -AG---G-GACCATCGTGATATGTAGGGGTTCCTTGATGAAAAATTGATGAC
1 AAGCTTGAGACCATCGTGATATGTA-GGGTTCCTTGATG-AAAATTGATGAC
* *
10557805 AAACTTGAGACCA-CGTGATATGTAGGGGTTTCTTGATGAAA
1 AAGCTTGAGACCATCGTGATATGTA-GGGTTCCTTGATGAAA
10557846 GCTTGAGGGA
Statistics
Matches: 109, Mismatches: 10, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
40 16 0.15
41 13 0.12
43 3 0.03
44 2 0.02
45 2 0.02
47 2 0.02
48 1 0.01
49 6 0.06
50 26 0.24
51 33 0.30
52 5 0.05
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (50 bp):
AAGCTTGAGACCATCGTGATATGTAGGGTTCCTTGATGAAAATTGATGAC
Found at i:10557774 original size:218 final size:217
Alignment explanation
Indices: 10557382--10557866 Score: 598
Period size: 218 Copynumber: 2.2 Consensus size: 217
10557372 GACCATCGTG
* * * *
10557382 ATATGCAGGGGTTTCTTGAGGACAAGTTTGAAGGACCATCGTGATATGTAGGGGTTCCTTGATGA
1 ATATGTAGGGGTTTCTTGATGA-AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA
* *
10557447 CAAGATTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGATAAGCTTGAAGGACCATCGTGA
65 -AAGATTGAGAAACCATCGTGATATGTAGGGCTTTCTTGATGACAAGCTTGAA-GACCATCGTGA
*
10557512 TATGTAGGGGTTCCTTGATGACAAGCTTGAGGACCATTGTGATATGTAGGGGTTCCTTGATGACA
128 TATGTAGGGGTTCCTTGATGA-AAGCTTGAGGACCATCGTGATATGTAGGGGTTCCTTGATGA-A
* *
10557577 AATTTGATGACAAGCTTGAGA-AAC-C
191 AAATTGATGACAAACTTGAGACAACGC
*
10557602 AT-TGTAGGGGTTTCTTTATGAAAAGC-TGAGGGACCATCGTGATATGTAGGGGTT-CTTGATG-
1 ATATGTAGGGGTTTCTTGATG-AAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA
* *
10557663 AAGCTTGAG-GACC-TCGTGATATGTAGGGTCCTTGATGACAATTTGATGACAAGCTTGAA-ACC
65 AAGATTGAGAAACCATCGTGATATGTAGGG--CTT--T--C---TTGATGACAAGCTTGAAGACC
*
10557725 ATCGTGATATGTA-GGGTTTCTTGATG-AAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTT
121 ATCGTGATATGTAGGGGTTCCTTGATGAAAGCTTGA-GGACCATCGTGATATGTAGGGGTTCCTT
* *
10557788 GATGAAAAATTGATGACAAACTTGAGACCACGTG
185 GATGAAAAATTGATGACAAACTTGAGACAACG-C
10557822 ATATGTAGGGGTTTCTTGATGAAAGCTTGAGGGA-CATCGTGATAT
1 ATATGTAGGGGTTTCTTGATGAAAGCTTGAGGGACCATCGTGATAT
10557867 AGGGTTTGAT
Statistics
Matches: 233, Mismatches: 16, Indels: 32
0.83 0.06 0.11
Matches are distributed among these distances:
213 15 0.06
214 3 0.01
215 10 0.04
217 36 0.15
218 61 0.26
219 31 0.13
220 37 0.16
221 24 0.10
222 16 0.07
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.30
Consensus pattern (217 bp):
ATATGTAGGGGTTTCTTGATGAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAA
AGATTGAGAAACCATCGTGATATGTAGGGCTTTCTTGATGACAAGCTTGAAGACCATCGTGATAT
GTAGGGGTTCCTTGATGAAAGCTTGAGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAATT
GATGACAAACTTGAGACAACGC
Found at i:10557834 original size:92 final size:91
Alignment explanation
Indices: 10557633--10557890 Score: 365
Period size: 92 Copynumber: 2.9 Consensus size: 91
10557623 AAAGCTGAGG
10557633 GACCATCGTGATATGTAGGGG-TTCTTGATGAAGCTTGA-GGACC-TCGTGATATGTAGGGTCCT
1 GACCATCGTGATATGTAGGGGTTTCTTGATGAAGCTTGAGGGACCATCGTGATATGTAGGGTCCT
* * *
10557695 TGATGACAATTTGATGACAAGCTTGA
66 TGATGAAAAATTGATGACAAACTTGA
*
10557721 AACCATCGTGATATGTA-GGGTTTCTTGATGAAGCTTGAGGGACCATCGTGATATGTAGGGGTTC
1 GACCATCGTGATATGTAGGGGTTTCTTGATGAAGCTTGAGGGACCATCGTGATATGTA-GGG-TC
10557785 CTTGATGAAAAATTGATGACAAACTTGA
64 CTTGATGAAAAATTGATGACAAACTTGA
10557813 GACCA-CGTGATATGTAGGGGTTTCTTGATGAAAGCTTGAGGGA-CATCGTGATA--TAGGGT--
1 GACCATCGTGATATGTAGGGGTTTCTTGATG-AAGCTTGAGGGACCATCGTGATATGTAGGGTCC
*
10557872 TTGATGACAAACTTGATGA
65 TTGATGA-AAAATTGATGA
10557891 ACCTTGAGGG
Statistics
Matches: 156, Mismatches: 6, Indels: 17
0.87 0.03 0.09
Matches are distributed among these distances:
86 7 0.04
87 13 0.08
88 34 0.22
89 8 0.05
90 14 0.09
91 14 0.09
92 54 0.35
93 12 0.08
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (91 bp):
GACCATCGTGATATGTAGGGGTTTCTTGATGAAGCTTGAGGGACCATCGTGATATGTAGGGTCCT
TGATGAAAAATTGATGACAAACTTGA
Found at i:10558035 original size:86 final size:88
Alignment explanation
Indices: 10557926--10558149 Score: 357
Period size: 86 Copynumber: 2.6 Consensus size: 88
10557916 GGTTCCTTGG
10557926 TGACAATTAAGAAATGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGA
1 TGACAATTAAGAAATGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGA
10557991 -CTTCAGTGC-GATG-TTTCAAA
66 CCTTCAGTGCAGATGTTTTCAAA
10558011 TGACAATTAAGAAATTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAG
1 TGACAATTAAGAAA-TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAG
10558076 ACCTTCAGTGCATGATGTTTTCAAA
65 ACCTTCAGTGCA-GATGTTTTCAAA
* * * *
10558101 TGA-ATTTAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTTTAAATCCTT
1 TGACAATTAAGAAA-TGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTT
10558150 TGGGTTATCT
Statistics
Matches: 129, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
85 14 0.11
86 51 0.40
87 9 0.07
89 45 0.35
90 10 0.08
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (88 bp):
TGACAATTAAGAAATGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGA
CCTTCAGTGCAGATGTTTTCAAA
Found at i:10561299 original size:40 final size:41
Alignment explanation
Indices: 10561203--10561309 Score: 103
Period size: 43 Copynumber: 2.6 Consensus size: 41
10561193 TTAGATGCAC
* *
10561203 CATTTTTAATTAACTAAATTAATTATTATTAATTTAAAACT
1 CATTTTAAAATAACTAAATTAATTATTATTAATTTAAAACT
* * *
10561244 CCTTTTAAATCAATAAC-AATTTAATTATTACTT-ATTTAAAATT
1 CATTTT-AA--AATAACTAAATTAATTATTA-TTAATTTAAAACT
*
10561287 CATTTTAAAATAA-TTAATTAATT
1 CATTTTAAAATAACTAAATTAATT
10561310 TAAATCACAT
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
40 12 0.23
41 5 0.09
42 3 0.06
43 26 0.49
44 7 0.13
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (41 bp):
CATTTTAAAATAACTAAATTAATTATTATTAATTTAAAACT
Found at i:10562645 original size:13 final size:14
Alignment explanation
Indices: 10562619--10562647 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10562609 TGATTTTATG
10562619 GTTTCTCTCTAATT
1 GTTTCTCTCTAATT
10562633 GTTTCTC-CTAATT
1 GTTTCTCTCTAATT
10562646 GT
1 GT
10562648 CGCCTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.14, C:0.21, G:0.10, T:0.55
Consensus pattern (14 bp):
GTTTCTCTCTAATT
Found at i:10563924 original size:21 final size:21
Alignment explanation
Indices: 10563894--10564081 Score: 140
Period size: 21 Copynumber: 9.0 Consensus size: 21
10563884 GATTTACATA
*
10563894 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
10563915 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
10563938 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
10563957 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
10563980 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
10563999 TTCGCATTGCAATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
10564022 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
10564041 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
10564064 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
10564082 AATCGCAACG
Statistics
Matches: 132, Mismatches: 21, Indels: 30
0.72 0.11 0.16
Matches are distributed among these distances:
19 33 0.25
21 63 0.48
23 36 0.27
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:10563948 original size:42 final size:42
Alignment explanation
Indices: 10563900--10564081 Score: 301
Period size: 42 Copynumber: 4.3 Consensus size: 42
10563890 CATATTCGCA
*
10563900 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
10563942 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCTAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
10563984 TTGCGATAGTCCAAGTTCGCATTGCAATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
10564026 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
10564068 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
10564082 AATCGCAACG
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 127 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:10564088 original size:84 final size:84
Alignment explanation
Indices: 10563900--10564081 Score: 337
Period size: 84 Copynumber: 2.2 Consensus size: 84
10563890 CATATTCGCA
* *
10563900 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCATTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
*
10563965 GCGATTTATTCTAAATTCG
66 GCGATTTATTCCAAATTCG
10563984 TTGCGATAGTCCAAGTTCGCATTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
1 TTGCGATAGTCCAAGTTCGCATTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
10564049 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
10564068 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
10564082 AATCGCAACG
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCATTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCG
Found at i:10564178 original size:6 final size:6
Alignment explanation
Indices: 10564167--10564231 Score: 109
Period size: 6 Copynumber: 11.3 Consensus size: 6
10564157 GACACGTATT
10564167 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
10564215 ACC-CG ACC-CG ACC-CG AC
1 ACCACG ACCACG ACCACG AC
10564232 GAGACGGCGA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 14 0.24
6 45 0.76
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:10564766 original size:6 final size:5
Alignment explanation
Indices: 10564721--10564762 Score: 66
Period size: 5 Copynumber: 8.0 Consensus size: 5
10564711 TCTCGTCTCA
10564721 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG TGGTCG TGGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG -GGTCG -GGTCG
10564763 TGGTAATACG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.69
6 11 0.31
ACGTcount: A:0.00, C:0.19, G:0.57, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:10564907 original size:42 final size:42
Alignment explanation
Indices: 10564860--10564950 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
10564850 GCGATTTTGG
10564860 ATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACT
* *
10564902 ATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACT
10564944 ATCGCAA
1 ATCGCAA
10564951 TGAGAATATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACT
Found at i:10564926 original size:21 final size:21
Alignment explanation
Indices: 10564860--10564929 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
10564850 GCGATTTTGG
10564860 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
10564881 ATCACAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
10564902 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
10564923 ATCGCAA
1 ATCGCAA
10564930 TGCGAACTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 9 0.24
21 19 0.51
23 9 0.24
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:10564940 original size:23 final size:21
Alignment explanation
Indices: 10564860--10564941 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
10564850 GCGATTTTGG
*
10564860 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* * *
10564881 ATCACAATGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
10564902 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
10564923 ATCGCAATGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
10564942 CTATCGCAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
19 9 0.20
21 19 0.41
23 18 0.39
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:10564947 original size:21 final size:21
Alignment explanation
Indices: 10564885--10564952 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
10564875 GAATAAATCA
*
10564885 CAATGCGAACTTCGACTATCG
1 CAATGCGAACTTGGACTATCG
* *
10564906 CAA--CGAATTTGGAATAAATCG
1 CAATGCGAACTTGGACT--ATCG
10564927 CAATGCGAACTTGGACTATCG
1 CAATGCGAACTTGGACTATCG
10564948 CAATG
1 CAATG
10564953 AGAATATGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 9 0.24
21 19 0.50
23 10 0.26
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (21 bp):
CAATGCGAACTTGGACTATCG
Found at i:10565018 original size:21 final size:21
Alignment explanation
Indices: 10564994--10565076 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 21
10564984 TTTGGAATAA
10564994 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
10565015 AT-----CGC-AA-TTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
10565029 ATCGTAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* *
10565050 ATCGCAATGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
10565071 ATCGCA
1 ATCGCA
10565077 TTGCAATTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
14 9 0.17
15 2 0.04
16 3 0.06
19 3 0.06
20 2 0.04
21 33 0.63
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:10565194 original size:21 final size:21
Alignment explanation
Indices: 10565091--10565191 Score: 166
Period size: 21 Copynumber: 4.8 Consensus size: 21
10565081 AATTTACATA
10565091 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
10565112 TTTGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
10565133 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
10565154 TTCGCATTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
10565175 TTCGCGTTGCGATAGTC
1 TTCGCATTGCGATAGTC
10565192 GAATTTGGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:10565229 original size:21 final size:21
Alignment explanation
Indices: 10565205--10565279 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
10565195 TTTGGAATAA
* *
10565205 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTGGACT
10565226 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
10565247 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTGGACT
*
10565268 ATCGCATTGCGA
1 ATCGCAATGCGA
10565280 TTTACATATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGGACT
Found at i:10565239 original size:176 final size:176
Alignment explanation
Indices: 10565029--10565359 Score: 517
Period size: 176 Copynumber: 1.9 Consensus size: 176
10565019 CAATTCGACT
* * * *
10565029 ATCGTAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGCATTGC-AA-TT-TACATA
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGAC-TA
* *
10565091 TTCGCATTGCGATAGTCCA-AGTTTGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
65 -TCGCATTGCGAT-GTACATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
*
10565155 TCGCATTGTGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAA
127 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAA
10565205 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTAT
1 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTAT
*
10565270 CGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGC
66 CGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGC
*
10565335 ATTGCGATAGTCGAAGTTTGCGTTG
131 ATTGCGATAGTCGAAGTTCGCGTTG
10565360 TGAATCTGGA
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
176 121 0.85
177 15 0.11
178 4 0.03
179 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (176 bp):
ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTAT
CGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGC
ATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAATAA
Found at i:10565314 original size:21 final size:21
Alignment explanation
Indices: 10565288--10565352 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
10565278 GATTTACATA
10565288 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
10565309 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
10565330 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
10565351 TT
1 TT
10565353 TGCGTTGTGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:10567045 original size:46 final size:45
Alignment explanation
Indices: 10566926--10567030 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 45
10566916 TGCACTAAGG
*
10566926 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAGCCTGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGA
* *
10566971 GTGCATCAATGGATAAAATGCATTCGATGTTTTCATAA-AAACCTGA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGA
10567017 GTGCATCGATGCAT
1 GTGCATCGATGCAT
10567031 GGAAGTGCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 27 0.51
46 24 0.45
47 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (45 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGA
Found at i:10567092 original size:20 final size:20
Alignment explanation
Indices: 10567067--10567104 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10567057 TTCGAAATGG
10567067 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
10567087 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
10567105 CCTTCACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:10575600 original size:46 final size:46
Alignment explanation
Indices: 10575533--10575651 Score: 229
Period size: 46 Copynumber: 2.6 Consensus size: 46
10575523 TGCATGGTCT
10575533 GTGCATCGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGA
10575579 GTGCATCGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGA
*
10575625 GTGCATCGATGCATAAAATGAATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
10575652 AATGGTGAGT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTTATAAAAACCTGA
Found at i:10575606 original size:64 final size:63
Alignment explanation
Indices: 10575473--10575607 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 63
10575463 CTAAGGGTGT
* * ****
10575473 ATCGATGTATAAAATGCATTTGATGTTTCAAACAAACCTGAGTGCATCGATGCATGGTCTGTGC
1 ATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCAT-GAAAATGC
*
10575537 ATCGATGCATAAAATGCATTCGATGTTTTTATAA-AAACCTGAGTGCATCGATGCAT-AAAATGC
1 ATCGATGCATAAAATGCATTCGATG-TTTCA-AACAAACCTGAGTGCATCGATGCATGAAAATGC
10575600 ATTCGATG
1 A-TCGATG
10575608 TTTTTATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
63 4 0.07
64 29 0.48
65 26 0.43
66 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (63 bp):
ATCGATGCATAAAATGCATTCGATGTTTCAAACAAACCTGAGTGCATCGATGCATGAAAATGC
Found at i:10576066 original size:2 final size:2
Alignment explanation
Indices: 10576061--10576094 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
10576051 TTTTCGAGCA
10576061 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10576095 TTACACAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:10577725 original size:33 final size:30
Alignment explanation
Indices: 10577687--10577746 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 30
10577677 TCCCTACATA
10577687 TTTAATTCTTATATTTTAATTTATATTTTTTTG
1 TTTAATTCTTA-ATTTTAA-TTAT-TTTTTTTG
10577720 TTTAATTCTTAATTTTAATTATTTTTT
1 TTTAATTCTTAATTTTAATTATTTTTT
10577747 ATTTGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 5 0.19
31 4 0.15
32 7 0.26
33 11 0.41
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTAATTCTTAATTTTAATTATTTTTTTTG
Found at i:10581837 original size:22 final size:21
Alignment explanation
Indices: 10581792--10581872 Score: 110
Period size: 22 Copynumber: 3.8 Consensus size: 21
10581782 TAGACGATAT
*
10581792 AGAAAATAAA-AAATAAAAGAG
1 AGAAAATAAAGAAA-AAGAGAG
10581813 AGAAAATAAAGAAAGAAGAGAG
1 AGAAAATAAAGAAA-AAGAGAG
10581835 AGAAAATAAAGAAAAAGAGAG
1 AGAAAATAAAGAAAAAGAGAG
*
10581856 AGAAAAGAAAGCAAAAA
1 AGAAAATAAAG-AAAAA
10581873 AATGAAGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.49
22 28 0.51
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (21 bp):
AGAAAATAAAGAAAAAGAGAG
Found at i:10581872 original size:11 final size:10
Alignment explanation
Indices: 10581806--10581891 Score: 52
Period size: 11 Copynumber: 8.4 Consensus size: 10
10581796 AATAAAAAAT
*
10581806 AAAAGAGAG-
1 AAAAGAAAGA
*
10581815 AAAATAAAGA
1 AAAAGAAAGA
*
10581825 AAGAAGAGAGA
1 AA-AAGAAAGA
*
10581836 GAAAATAAAGA
1 -AAAAGAAAGA
*
10581847 AAAAGAGAGA
1 AAAAGAAAGA
10581857 GAAAAGAAAGCA
1 -AAAAGAAAG-A
*
10581869 AAAA-AATGA
1 AAAAGAAAGA
10581878 AGAAAGAAA-A
1 A-AAAGAAAGA
10581888 AAAA
1 AAAA
10581892 ATAAAATACT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
9 12 0.20
10 18 0.31
11 26 0.44
12 3 0.05
ACGTcount: A:0.73, C:0.01, G:0.22, T:0.03
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:10581882 original size:43 final size:43
Alignment explanation
Indices: 10581792--10581897 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 43
10581782 TAGACGATAT
* *
10581792 AGAAAATAAAAAATAAAAGAGAGAAAATAAAGAAAGAAGAGAG
1 AGAAAATAAAAAATAAAAGAGAGAAAAGAAAGAAAGAAAAGAG
*
10581835 AGAAAATAAAGAAA-AAGAGAGAGAAAAGAAAGCAAA-AAAATGA-
1 AGAAAATAAA-AAATAAAAGAGAGAAAAGAAAG-AAAGAAAA-GAG
*
10581878 AGAAAGAAAAAAAAATAAAA
1 AG-AA-AATAAAAAATAAAA
10581898 TACTTCAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
43 31 0.60
44 13 0.25
45 8 0.15
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.06
Consensus pattern (43 bp):
AGAAAATAAAAAATAAAAGAGAGAAAAGAAAGAAAGAAAAGAG
Found at i:10581897 original size:26 final size:25
Alignment explanation
Indices: 10581837--10581897 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
10581827 GAAGAGAGAG
* *
10581837 AAAATAAAGAAAAAGAGAGAGAAAAG
1 AAAATAAA-AAAAAGAGAAAGAAAAA
** *
10581863 AAAGCAAAAAAATGAAGAAAGAAAAA
1 AAAATAAAAAAAAG-AGAAAGAAAAA
10581889 AAAATAAAA
1 AAAATAAAA
10581898 TACTTCAAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAATAAAAAAAAGAGAAAGAAAAA
Found at i:10582681 original size:28 final size:28
Alignment explanation
Indices: 10582616--10582683 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
10582606 CAAAGAAACC
10582616 AACCTGAAACACATTACCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
* *
10582644 AACCTAAAACACATTAGCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
**
10582672 AATTTGAAACAC
1 AACCTGAAACAC
10582684 TCTACTTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.43, C:0.31, G:0.04, T:0.22
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAATT
Found at i:10584084 original size:54 final size:54
Alignment explanation
Indices: 10583981--10584632 Score: 793
Period size: 54 Copynumber: 12.1 Consensus size: 54
10583971 CCAAACAATA
* * * * *
10583981 TGATGTCTTCTAATGAATTTT-AAAGAAGTTAAGCCTGAA-TTTCAGGGGTTTAT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCT-AATTTTTAGGGGTTTCT
**
10584034 TGATGTTTTCAAATGAATTTTGAAAGAATATAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
*
10584088 TGATGTCTTT-AAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAAGGGTTTCT
1 TGATGT-TTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* *
10584142 TGATATTTTCATATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * *
10584196 TAATGTCTTCAAATGAATTTTTAAAGAAGCTAAGCCTAA-TTTTAGGGGTTTAT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
10584249 TAATGTTTT-GAATGAATTTTGAAGGAAGCTAAGCCTAATTTTTA-GGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * *
10584301 TGTTGTTTTCAAATGAATGTTT-AAAGGAA-CTAAGCTTGATTTTTAGGGGTTTAT
1 TGATGTTTTCAAATGAAT-TTTGAAA-GAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
10584355 TGATGTCTTCAAATAAATTTTGAAATAAGCTAAG-CTAAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCT-AATTTTTAGGGGTTTCT
* *
10584409 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCTTAATTTTTATGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * *
10584463 TGATGTTTTCAAATGAACGTTT-AAAGGAGCTAAGCCTAATTTTTAAGGGTTTTT
1 TGATGTTTTCAAATGAA-TTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * *
10584517 TGATGCTTTCAAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGAGGATTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * *
10584571 TAATGATTACTTAAAATGAATTTTTAAAGAAGCTAAGCCTAATTTTTAAGGTTTTCT
1 TGATG-TT--TTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
10584628 TGATG
1 TGATG
10584633 ATAACTGTAA
Statistics
Matches: 514, Mismatches: 67, Indels: 32
0.84 0.11 0.05
Matches are distributed among these distances:
52 40 0.08
53 82 0.16
54 341 0.66
55 8 0.02
57 43 0.08
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:10585385 original size:18 final size:18
Alignment explanation
Indices: 10585362--10585399 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
10585352 CCAGGAAGAG
10585362 AATGAAGACTGCTCTAGC
1 AATGAAGACTGCTCTAGC
*
10585380 AATGAAGACTGCTCTTGC
1 AATGAAGACTGCTCTAGC
10585398 AA
1 AA
10585400 CCATTCTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (18 bp):
AATGAAGACTGCTCTAGC
Found at i:10585620 original size:37 final size:37
Alignment explanation
Indices: 10585554--10585637 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
10585544 TATTTTGTCC
*
10585554 TTCTTAGGATCGTTTCTCTGGAAATTCATTTGAGTCA
1 TTCTTAGGATCGTTTCTCTAGAAATTCATTTGAGTCA
* *
10585591 TTCTTAGGA-CTGTTTGTCTAG-AATGTCATTTGAGTCC
1 TTCTTAGGATC-GTTTCTCTAGAAAT-TCATTTGAGTCA
10585628 TTCTTAGGAT
1 TTCTTAGGAT
10585638 TGTCTCCCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 4 0.10
37 37 0.90
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (37 bp):
TTCTTAGGATCGTTTCTCTAGAAATTCATTTGAGTCA
Found at i:10585806 original size:14 final size:14
Alignment explanation
Indices: 10585787--10585820 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
10585777 ACGAAAACTT
10585787 AGCAAAGATAAAGA
1 AGCAAAGATAAAGA
10585801 AGCAAAGATAAAGA
1 AGCAAAGATAAAGA
10585815 AGCAAA
1 AGCAAA
10585821 TATTTATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.09, G:0.21, T:0.06
Consensus pattern (14 bp):
AGCAAAGATAAAGA
Found at i:10586788 original size:2 final size:2
Alignment explanation
Indices: 10586783--10586821 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10586773 TTTTTTGAGC
10586783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10586822 TTACATAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10589286 original size:50 final size:50
Alignment explanation
Indices: 10589227--10589327 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
10589217 CTAAGGCAAT
* **
10589227 GTTCACTTATTATGAAGTCAATAGTATATCTCCTGCAAGTATGCTCAGGG
1 GTTCACTTATTAGGAAGTCAATAGTATATCTCCCACAAGTATGCTCAGGG
*
10589277 GTTCACTTATTAGGGAGTCAATAGTATATCTCCCACAAGTATGCTCAGGG
1 GTTCACTTATTAGGAAGTCAATAGTATATCTCCCACAAGTATGCTCAGGG
10589327 G
1 G
10589328 GTGACTACTA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (50 bp):
GTTCACTTATTAGGAAGTCAATAGTATATCTCCCACAAGTATGCTCAGGG
Found at i:10598998 original size:27 final size:27
Alignment explanation
Indices: 10598958--10599010 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
10598948 AACTAAATAA
*
10598958 AAAGAAAAATAAATAAATAAATAAATC
1 AAAGAAAAATAAATAAATAAAAAAATC
*
10598985 AAAGAAGAAA-AAATATATAAAAAAAT
1 AAAGAA-AAATAAATAAATAAAAAAAT
10599011 GTTACATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (27 bp):
AAAGAAAAATAAATAAATAAAAAAATC
Found at i:10599025 original size:16 final size:17
Alignment explanation
Indices: 10598999--10599030 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
10598989 AAGAAAAAAT
10598999 ATATAAAAAAATGTTAC
1 ATATAAAAAAATGTTAC
10599016 ATAT-AAAAAATGTTA
1 ATATAAAAAAATGTTA
10599031 AAAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATAAAAAAATGTTAC
Found at i:10600840 original size:38 final size:37
Alignment explanation
Indices: 10600705--10601186 Score: 345
Period size: 38 Copynumber: 13.0 Consensus size: 37
10600695 TAATAAAATA
* *
10600705 ATATATTTTCAAAAATATTTCCCAAAACTATATA-AT
1 ATATATTTTCAAAAATATTTTCAAAAACTATATATAT
*
10600741 ATATATATTTCAAAAATATTTT--AAAACTATATATTTT
1 ATATAT-TTTCAAAAATATTTTCAAAAACTATATA-TAT
* * *
10600778 ATACTTTTTTAAAAAATGTTTTCAAAAACTATATATTAT
1 ATA-TATTTTCAAAAATATTTTCAAAAACTATATA-TAT
* *
10600817 ATATGTTTTCAAAAATATTTTCAAAAACTTTATAATAT
1 ATATATTTTCAAAAATATTTTCAAAAACTATAT-ATAT
* *
10600855 ATATATTTT-TAAAATGTTTTCAAAAACTAT-TATAT
1 ATATATTTTCAAAAATATTTTCAAAAACTATATATAT
* *
10600890 ATATATATT-AAAAA-A-ATTCAAAAACTATATATTAT
1 ATATATTTTCAAAAATATTTTCAAAAACTATATA-TAT
* *
10600925 TTATATTTTC-AAAATGTTTTC-AAAACTATATA-AT
1 ATATATTTTCAAAAATATTTTCAAAAACTATATATAT
* ***
10600959 ATATATTTTCGAATACCGTTTTC-AAAACTATATGATAT
1 ATATATTTTC-AAAAATATTTTCAAAAACTATAT-ATAT
***
10600997 ATATATTTTCGAATACCGA-TTTCAAAATTA-TATATATAT
1 ATATATTTTC-AA-AAATATTTTCAAAA--ACTATATATAT
**
10601036 ATATATTTTTGAAAATCATTTTC-AAAACTATATAATAT
1 ATATATTTTCAAAAAT-ATTTTCAAAAACTATAT-ATAT
* ** * ** *
10601074 ATATATTTTTGAAAACCGATTTTTAAAAAAAAGCATAT-T
1 ATATA-TTTTCAAAA-ATATTTTCAAAAACTA-TATATAT
* *
10601113 ATATGTTTTCAAAAACCATTTTCAAAAA--ATCATATAT
1 ATATATTTTCAAAAA-TATTTTCAAAAACTAT-ATATAT
* *
10601150 -CATATTTTCAAAAATATTTTCAAAAATTATACTATAT
1 ATATATTTTCAAAAATATTTTCAAAAACTATA-TATAT
10601187 TAATAATAAA
Statistics
Matches: 360, Mismatches: 52, Indels: 67
0.75 0.11 0.14
Matches are distributed among these distances:
33 12 0.03
34 13 0.04
35 52 0.14
36 55 0.15
37 67 0.19
38 90 0.25
39 56 0.16
40 12 0.03
41 3 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (37 bp):
ATATATTTTCAAAAATATTTTCAAAAACTATATATAT
Found at i:10601058 original size:77 final size:76
Alignment explanation
Indices: 10600733--10601163 Score: 245
Period size: 77 Copynumber: 5.8 Consensus size: 76
10600723 TTCCCAAAAC
** * * ** **
10600733 TATATAATATATATATTTC-AAAAATATTTT-AAAACTATATATTTTATACT-TTTTTAAAAAAT
1 TATATAATATATAT-TTTCGAAAACCATTTTCAAAACTATATAATATATA-TATTTTCGAAAACC
* *
10600795 GTTTTCAAAAACTA
64 GATTTC-AAAATTA
* * ** * * *
10600809 TATATTATATATGTTTTC-AAAAATATTTTCAAAAACTTTATAATATATATATTTT-TAAAA-TG
1 TATATAATATATATTTTCGAAAACCATTTTC-AAAACTATATAATATATATATTTTCGAAAACCG
* *
10600871 TTTTCAAAAACTA
65 ATTTC-AAAATTA
* ** * * *
10600884 T-TAT-ATATATATATT--AAAA--AAATTCAAAAACTATATATTATTTATATTTTC-AAAA-TG
1 TATATAATATATATTTTCGAAAACCATTTTC-AAAACTATATAATATATATATTTTCGAAAACCG
* *
10600941 TTTTCAAAA--C
65 ATTTCAAAATTA
* * * *
10600951 TATATAATATATATTTTCGAATACCGTTTTCAAAACTATATGATATATATATTTTCGAATACCGA
1 TATATAATATATATTTTCGAAAACCATTTTCAAAACTATATAATATATATATTTTCGAAAACCGA
10601016 TTTCAAAATTA
66 TTTCAAAATTA
* * *
10601027 TATATATATATATATTTTTGAAAATCATTTTCAAAACTATATAATATATATATTTTTGAAAACCG
1 TATATA-ATATATATTTTCGAAAACCATTTTCAAAACTATATAATATATATATTTTCGAAAACCG
* *
10601092 ATTTTTAAAA-AA
65 A-TTTCAAAATTA
* * * * * * *
10601104 AAGCATATTATATGTTTTCAAAAACCATTTTCAAAA--A-ATCATATATCATATTTTCAAAAA
1 TA-TATAATATATATTTTCGAAAACCATTTTCAAAACTATATAATATAT-ATATTTTCGAAAA
10601164 TATTTTCAAA
Statistics
Matches: 292, Mismatches: 45, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
67 1 0.00
68 3 0.01
69 14 0.05
70 37 0.13
71 3 0.01
72 26 0.09
73 15 0.05
74 20 0.07
75 43 0.15
76 23 0.08
77 97 0.33
78 10 0.03
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (76 bp):
TATATAATATATATTTTCGAAAACCATTTTCAAAACTATATAATATATATATTTTCGAAAACCGA
TTTCAAAATTA
Found at i:10601168 original size:12 final size:12
Alignment explanation
Indices: 10601151--10601176 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10601141 ATCATATATC
10601151 ATATTTTCAAAA
1 ATATTTTCAAAA
10601163 ATATTTTCAAAA
1 ATATTTTCAAAA
10601175 AT
1 AT
10601177 TATACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:10601169 original size:35 final size:36
Alignment explanation
Indices: 10601073--10601175 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 36
10601063 CTATATAATA
** *
10601073 TATATATTTTTGAAAACCGATTTTTAAAAAAAAGCATAT
1 TATATATTTTCAAAAACC-A-TTTT-CAAAAAAGCATAT
* *
10601112 TATATGTTTTCAAAAACCATTTTCAAAAAATCATA-
1 TATATATTTTCAAAAACCATTTTCAAAAAAGCATAT
*
10601147 TATCATATTTTCAAAAA-TATTTTCAAAAA
1 TAT-ATATTTTCAAAAACCATTTTCAAAAA
10601176 TTATACTATA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 14 0.25
36 22 0.39
37 4 0.07
38 1 0.02
39 15 0.27
ACGTcount: A:0.47, C:0.11, G:0.04, T:0.39
Consensus pattern (36 bp):
TATATATTTTCAAAAACCATTTTCAAAAAAGCATAT
Found at i:10603151 original size:85 final size:85
Alignment explanation
Indices: 10603062--10603471 Score: 448
Period size: 85 Copynumber: 4.8 Consensus size: 85
10603052 CAGATAGATT
* *
10603062 TTCTCGACTTAAGTTATGCTGTAAATTTGATATG-CGCTTGAGCTGAATGTAATCGAAGC-CGAA
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTC-CTTGAGCTGAATGTAATCGAA-CTCGAA
* *
10603125 GGTTTTTGTTGACAGATAGCCC
64 GGTTTTGGTTGACAGATAACCC
* * * * * *
10603147 TTCTCGCCTTGAGCTATGTTATAAATTTGATATGTCATTGAGTTGAATGTAATCGAACTCGAAGA
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
10603212 TTTTGGTTGACAGATAACCC
66 TTTTGGTTGACAGATAACCC
* * * *
10603232 TTCTCGCCTTGAGTTATGTTGCAAATGTGATATGTCCTTGAGCTGAATGTAATCGATCTCGAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* *
10603297 TTTTGGTTGATAGATAATCC
66 TTTTGGTTGACAGATAACCC
* * * * **
10603317 TTATCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGTTGAATGTAATTGAATTTAAAGG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
* * *
10603382 TTATGGTTGAGAGATAGCCC
66 TTTTGGTTGACAGATAACCC
* ** * * ** * * * *
10603402 TTATTTCATTGAGCTATGCTGCGAATTTGATATGCCCTAT-AGCTAAATGGAATCAAACTCGAAG
1 TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCT-TGAGCTGAATGTAATCGAACTCGAAG
10603466 GTTTTG
65 GTTTTG
10603472 ATATGCCCTA
Statistics
Matches: 272, Mismatches: 50, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
84 1 0.00
85 269 0.99
86 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (85 bp):
TTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG
TTTTGGTTGACAGATAACCC
Found at i:10605160 original size:99 final size:99
Alignment explanation
Indices: 10604988--10605194 Score: 301
Period size: 99 Copynumber: 2.1 Consensus size: 99
10604978 GGACAACTCA
* * * * *
10604988 ATATTATAATCACCTTTATCACGCTAGTTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCACGCTAGCTAAATCTAATACATAAAGCCAGAGCATTTAACCAATT
*
10605053 GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
10605087 ATATTATAATCACCTTTATCAGGCTAGCTAAATCTAATACATAAAGCCAGAG-AGTTTAACCAAT
1 ATATTATAATCACCTTTATCACGCTAGCTAAATCTAATACATAAAGCCAGAGCA-TTTAACCAAT
** *
10605151 TGCTCTAGAGGGACCGCTCAAGCTTTATTGTATAT
65 TGCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
10605186 AT-TTATAAT
1 ATATTATAAT
10605195 ATGGGTATAC
Statistics
Matches: 97, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
98 8 0.08
99 89 0.92
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCACGCTAGCTAAATCTAATACATAAAGCCAGAGCATTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:10608779 original size:20 final size:20
Alignment explanation
Indices: 10608746--10608804 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 20
10608736 AACATTGAAT
*
10608746 AAAAATTAACTAAATAAAAAG
1 AAAAA-TAAATAAATAAAAAG
10608767 AAAAATAAATAAAT-AAAAG
1 AAAAATAAATAAATAAAAAG
10608786 AAGAAA-AAATAAATAAAAA
1 AA-AAATAAATAAATAAAAA
10608805 ATGTTACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 15 0.43
20 15 0.43
21 5 0.14
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAAATAAATAAATAAAAAG
Found at i:10610532 original size:9 final size:8
Alignment explanation
Indices: 10610518--10610592 Score: 71
Period size: 9 Copynumber: 8.5 Consensus size: 8
10610508 CCGAAAATGA
10610518 AATAAAATT
1 AATAAAA-T
10610527 AATAAAAT
1 AATAAAAT
10610535 AA-AACATAT
1 AATAA-A-AT
10610544 AATAAAAAT
1 AAT-AAAAT
10610553 AATAATAAT
1 AATAA-AAT
10610562 AATAATAAT
1 AATAA-AAT
10610571 AATAATAAT
1 AATAA-AAT
10610580 AATAATAAT
1 AATAA-AAT
10610589 AATA
1 AATA
10610593 TATTTTCAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
7 2 0.03
8 6 0.10
9 50 0.82
10 1 0.02
11 2 0.03
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:10610549 original size:12 final size:12
Alignment explanation
Indices: 10610527--10610592 Score: 82
Period size: 12 Copynumber: 5.6 Consensus size: 12
10610517 AAATAAAATT
10610527 AATAA-AATAAA
1 AATAATAATAAA
10610538 ACAT-ATAATAAA
1 A-ATAATAATAAA
*
10610550 AATAATAATAAT
1 AATAATAATAAA
*
10610562 AATAATAATAAT
1 AATAATAATAAA
*
10610574 AATAATAATAAT
1 AATAATAATAAA
10610586 AATAATA
1 AATAATA
10610593 TATTTTCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
11 4 0.08
12 47 0.92
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:10610556 original size:3 final size:3
Alignment explanation
Indices: 10610542--10610592 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
10610532 AATAAAACAT
*
10610542 ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10610590 ATA
1 ATA
10610593 TATTTTCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:10610768 original size:74 final size:75
Alignment explanation
Indices: 10610618--10610939 Score: 364
Period size: 74 Copynumber: 4.3 Consensus size: 75
10610608 TTCCCAAAAC
*
10610618 TATATA-ATATATGTTTTTCAAAAATATATT--AAAACTATATATTATATATTTTTTAAAAATGT
1 TATATATATATATG-TTTTCAAAAATATTTTCAAAAACTATATA--ATATATTTTTT-AAAATGT
* *
10610680 TTTCAAAAA--CTA
62 TTTAAAAAAGTTTA
10610692 TATAT-TATATATGTTTTCAAAAATATTTTCAAAAACTATATAATATATTTTTTAAAATGTTTTA
1 TATATATATATATGTTTTCAAAAATATTTTCAAAAACTATATAATATATTTTTTAAAATGTTTTA
10610756 AAAAAGTTTA
66 AAAAAGTTTA
10610766 TAT-TATATATATGTTTTCAAAAATATTTTCAAAAACTATATAATATATTTTTTTAAAATGTTTT
1 TATATATATATATGTTTTCAAAAATATTTTCAAAAACTATATAATATA-TTTTTTAAAATGTTTT
10610830 AAAAAAGTTTA
65 AAAAAAGTTTA
* *
10610841 TATTATATATATAT-ATTT--AAAATGTTTTCAAAAACTATATATTATATATATATTTTTTAAAA
1 TA-TATATATATATGTTTTCAAAAATATTTTCAAAAAC----TA-TATA-ATATATTTTTTAAAA
* * *
10610903 TGTTTT-CAAAACTATA
59 TGTTTTAAAAAAGTTTA
*
10610919 TA-ATATATATAT-TTTTGAAAA
1 TATATATATATATGTTTTCAAAA
10610940 CCGATTTTTA
Statistics
Matches: 222, Mismatches: 9, Indels: 30
0.85 0.03 0.11
Matches are distributed among these distances:
72 15 0.07
73 27 0.12
74 75 0.34
75 40 0.18
76 17 0.08
77 9 0.04
78 14 0.06
79 20 0.09
80 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (75 bp):
TATATATATATATGTTTTCAAAAATATTTTCAAAAACTATATAATATATTTTTTAAAATGTTTTA
AAAAAGTTTA
Found at i:10610860 original size:39 final size:37
Alignment explanation
Indices: 10610648--10610939 Score: 328
Period size: 37 Copynumber: 7.8 Consensus size: 37
10610638 AAAATATATT
10610648 AAAACTATATATTATATAT-TTTTTAAAAATGTTTTCA
1 AAAACTATATATTATATATATTTTT-AAAATGTTTTCA
* * *
10610685 AAAACTATATATTATATATGTTTTCAAAAATATTTTCA
1 AAAACTATATATTATATATATTTT-TAAAATGTTTTCA
*
10610723 AAAACTATATA--ATATAT-TTTTTAAAATGTTTTAA
1 AAAACTATATATTATATATATTTTTAAAATGTTTTCA
* * *
10610757 AAAAGTTTATATTATATATATGTTTTCAAAAATATTTTCA
1 AAAACTATATATTATATATAT-TTTT--AAAATGTTTTCA
* *
10610797 AAAACTATATA--ATATATTTTTTTAAAATGTTTTAA
1 AAAACTATATATTATATATATTTTTAAAATGTTTTCA
* *
10610832 AAAAGTTTATATTATATATATATATTTAAAATGTTTTCA
1 AAAACTATATATTATATATAT-T-TTTAAAATGTTTTCA
10610871 AAAACTATATATTATATATATATTTTTTAAAATGTTTTC-
1 AAAACTATATA-T-TATATATA-TTTTTAAAATGTTTTCA
*
10610910 AAAACTATATAATATATATATTTTTGAAAA
1 AAAACTATATATTATATATATTTTT-AAAA
10610940 CCGATTTTTA
Statistics
Matches: 218, Mismatches: 21, Indels: 32
0.80 0.08 0.12
Matches are distributed among these distances:
34 19 0.09
35 23 0.11
36 17 0.08
37 43 0.20
38 38 0.17
39 34 0.16
40 34 0.16
41 9 0.04
42 1 0.00
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.47
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTTAAAATGTTTTCA
Found at i:10612108 original size:2 final size:2
Alignment explanation
Indices: 10612101--10612126 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10612091 TATTTTCTAA
10612101 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
10612127 GTAATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10613373 original size:20 final size:21
Alignment explanation
Indices: 10613339--10613390 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
10613329 GTGAATAAAA
10613339 TGTA-AATTTTAAAAACTTTG
1 TGTACAATTTTAAAAACTTTG
10613359 TGTACAATTTTAAAAACTTTG
1 TGTACAATTTTAAAAACTTTG
10613380 TGTACAATTTT
1 TGTACAATTTT
10613391 GAAATAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (21 bp):
TGTACAATTTTAAAAACTTTG
Found at i:10614310 original size:19 final size:19
Alignment explanation
Indices: 10614259--10614312 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
10614249 AATTGAAAAA
*
10614259 GGGTATTGATACC-CAAGCT
1 GGGTATCGATACCAC-AGCT
*
10614278 TGGTATCGATACCACAGCT
1 GGGTATCGATACCACAGCT
10614297 GGGTATCGATACCACA
1 GGGTATCGATACCACA
10614313 ACAAGGGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (19 bp):
GGGTATCGATACCACAGCT
Found at i:10615050 original size:22 final size:22
Alignment explanation
Indices: 10615022--10615066 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
10615012 AGTCGAGAGT
*
10615022 TACATAGGTCCTTCGGGATATA
1 TACATAGGTCCTTCGGGACATA
10615044 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
10615066 T
1 T
10615067 TTCACATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:10621237 original size:24 final size:24
Alignment explanation
Indices: 10621161--10621241 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
10621151 TTTCGATTTA
* *
10621161 AATTCTGTTCTGATATCTGATATG
1 AATTATGTTCTGATATCTGATCTG
* * * *
10621185 AAATATGCTCTG-TTTCCTGACCTG
1 AATTATGTTCTGATAT-CTGATCTG
* *
10621209 GATTATGTTCTGATATATGATCTG
1 AATTATGTTCTGATATCTGATCTG
10621233 AATTATGTT
1 AATTATGTT
10621242 TTGTTTTATG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (24 bp):
AATTATGTTCTGATATCTGATCTG
Found at i:10624622 original size:33 final size:33
Alignment explanation
Indices: 10624585--10624651 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
10624575 TTAAATAATA
*
10624585 AGATCAGACGGAATAAAATGATTGAAATACCCT
1 AGATCAAACGGAATAAAATGATTGAAATACCCT
*
10624618 AGATCAAACGGAATGAAATGATTGAAATACCCT
1 AGATCAAACGGAATAAAATGATTGAAATACCCT
10624651 A
1 A
10624652 TATCTGTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (33 bp):
AGATCAAACGGAATAAAATGATTGAAATACCCT
Found at i:10629636 original size:18 final size:18
Alignment explanation
Indices: 10629607--10629708 Score: 141
Period size: 18 Copynumber: 5.7 Consensus size: 18
10629597 GTAGAATTTA
*
10629607 TCCCGTAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
10629625 TCCTGAAGGACCACTGTG
1 TCCCGAAGGACCACTATG
10629643 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* * *
10629661 TCCCAAATGAACACTATG
1 TCCCGAAGGACCACTATG
*
10629679 TCCCGAATGACCACTATG
1 TCCCGAAGGACCACTATG
10629697 TCCCGAAGGACC
1 TCCCGAAGGACC
10629709 GCGTAGACCC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.27, C:0.32, G:0.21, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:10632214 original size:91 final size:91
Alignment explanation
Indices: 10632054--10632365 Score: 491
Period size: 91 Copynumber: 3.4 Consensus size: 91
10632044 AGGTTGAACA
* *
10632054 AGTTATTCTCATTATGAACTCTCCACTGGAAATGTTGA-GCCAAGGTTGAACAAGTTCTTCTCAT
1 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATG-CAAGGTTGAACAAGTTCTTCTCAT
*
10632118 TATGAACTTCTTCTCCCTTGTTGGATG
65 TATGAACTTCTTCTCCCTCGTTGGATG
* ** * * *
10632145 AGTTCTTCTCATTATGAACTCTCTTCTAGAAATGTTGATGCAAGTTTGAACAAGTTATTCTCATT
1 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATT
*
10632210 ATGAACTTCTTCTCCCTCGCTGGATG
66 ATGAACTTCTTCTCCCTCGTTGGATG
*
10632236 AGTTCTTCTCATTATGAACTCCCCACTGAAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATT
*
10632301 ATAAACTTCTTCTCCCTCGTTGGATG
66 ATGAACTTCTTCTCCCTCGTTGGATG
*
10632327 AGTTCTTCTCATTATGAACTCCCTACTGGAAATGTTGAT
1 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGAT
10632366 TAGTTTATCC
Statistics
Matches: 201, Mismatches: 19, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
91 200 1.00
92 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTTCTCCCTCGTTGGATG
Found at i:10632463 original size:14 final size:14
Alignment explanation
Indices: 10632442--10632476 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
10632432 TTGAAGTACC
10632442 CAAAGGTATTGATT
1 CAAAGGTATTGATT
*
10632456 CGAAGGTATTGATT
1 CAAAGGTATTGATT
10632470 CAAAGGT
1 CAAAGGT
10632477 CTTCGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (14 bp):
CAAAGGTATTGATT
Found at i:10633107 original size:129 final size:130
Alignment explanation
Indices: 10632877--10633135 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
10632867 ATCGGCTAGA
10632877 GCCTACTCCAAAATTAGAACGACAACTTGTCTTCAAGCAATCATTCTCTTTTTTAGAAGAGTAAT
1 GCCTACTCCAAAATTAGAACGACAACTTGTCTTCAAGCAATCATTCTCTTTTTTAGAAGAGTAAT
10632942 ATGATCAGCTCGTGTCAAATTGTCTTTTCTTTTCTCTTGTTTTTGTTTC-TCATGAAAATCTTAG
66 ATGATCAGCTCGTGTCAAATTGTCTTTTCTTTTCTCTTGTTTTTGTTTCTTCATGAAAATCTTAG
10633006 GCCTACTCCAAAATTAGAACGACAACTTGTCTTCAAGCAATCATTCTCTTTTTTAGAAGAGTAAT
1 GCCTACTCCAAAATTAGAACGACAACTTGTCTTCAAGCAATCATTCTCTTTTTTAGAAGAGTAAT
10633071 ATGATCAGCTCGTGTCAAATTGTCTTTTCTTTTCTCTTGTTTTTGTTTCTTCATGAAAATCTTAG
66 ATGATCAGCTCGTGTCAAATTGTCTTTTCTTTTCTCTTGTTTTTGTTTCTTCATGAAAATCTTAG
10633136 AAATAATGCT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 114 0.88
130 15 0.12
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.41
Consensus pattern (130 bp):
GCCTACTCCAAAATTAGAACGACAACTTGTCTTCAAGCAATCATTCTCTTTTTTAGAAGAGTAAT
ATGATCAGCTCGTGTCAAATTGTCTTTTCTTTTCTCTTGTTTTTGTTTCTTCATGAAAATCTTAG
Found at i:10634572 original size:5 final size:5
Alignment explanation
Indices: 10634558--10634606 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
10634548 TTTCTCTCCT
* *
10634558 TTTTC TTTTTC TTTTT TTTTC TTTTT TTTTC -TTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
10634607 TTGTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
4 4 0.11
5 29 0.76
6 5 0.13
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTTTC
Found at i:10634576 original size:10 final size:10
Alignment explanation
Indices: 10634558--10634730 Score: 100
Period size: 11 Copynumber: 16.2 Consensus size: 10
10634548 TTTCTCTCCT
10634558 TTTTCTTTTTC
1 TTTT-TTTTTC
10634569 TTTTTTTTTC
1 TTTTTTTTTC
10634579 TTTTTTTTTC
1 TTTTTTTTTC
*
10634589 -TTTCTTTTC
1 TTTTTTTTTC
10634598 TTTTCTTTTT-
1 TTTT-TTTTTC
*
10634608 TGTTTTTTTCC
1 T-TTTTTTTTC
*
10634619 TTCTTTTTTTG
1 TT-TTTTTTTC
*
10634630 TTTTTTTGTTT
1 TTTTTTT-TTC
10634641 TTTCTATTTTTC
1 TTT-T-TTTTTC
10634653 TATTTTTCTTT-
1 T-TTTTT-TTTC
*
10634664 TTCTTTATTTC
1 TT-TTTTTTTC
* *
10634675 TCTCTTTTTC
1 TTTTTTTTTC
* *
10634685 TCTCTTTTTC
1 TTTTTTTTTC
* *
10634695 TGTCTTTTCTC
1 T-TTTTTTTTC
10634706 TTTTTTTATTTC
1 -TTTTTT-TTTC
10634718 TTTTTCTTTTC
1 TTTTT-TTTTC
10634729 TT
1 TT
10634731 CTCTTCAAAA
Statistics
Matches: 129, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.06
10 51 0.40
11 52 0.40
12 13 0.10
13 5 0.04
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:10634588 original size:20 final size:20
Alignment explanation
Indices: 10634558--10634730 Score: 100
Period size: 21 Copynumber: 8.1 Consensus size: 20
10634548 TTTCTCTCCT
10634558 TTTTCTTTTTCTTTTTTTTTC
1 TTTT-TTTTTCTTTTTTTTTC
*
10634579 TTTTTTTTTC-TTTCTTTTC
1 TTTTTTTTTCTTTTTTTTTC
*
10634598 TTTTCTTTTT-TGTTTTTTTCC
1 TTTT-TTTTTCT-TTTTTTTTC
* *
10634619 TTCTTTTTTTGTTTTTTTGTTT
1 TT-TTTTTTTCTTTTTTT-TTC
10634641 TTTCTATTTTTCTATTTTTCTTT-
1 TTT-T-TTTTTCT-TTTTT-TTTC
* * *
10634664 TTCTTTATTTCTCTCTTTTTC
1 TT-TTTTTTTCTTTTTTTTTC
* * * *
10634685 TCTCTTTTTCTGTCTTTTCTC
1 TTTTTTTTTCT-TTTTTTTTC
10634706 TTTTTTTATTTCTTTTTCTTTTC
1 -TTTTTT-TTTCTTTTT-TTTTC
10634729 TT
1 TT
10634731 CTCTTCAAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 31
0.69 0.12 0.19
Matches are distributed among these distances:
19 12 0.10
20 21 0.18
21 34 0.29
22 22 0.19
23 18 0.16
24 8 0.07
25 1 0.01
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTTTTTC
Found at i:10634601 original size:67 final size:64
Alignment explanation
Indices: 10634537--10634735 Score: 178
Period size: 67 Copynumber: 3.0 Consensus size: 64
10634527 CCCCTTTTAA
*
10634537 TTTTTTCCTTTTTTCTCTCCTTTTTCTTTTTCTTTTTTTTTCTTTTTTTTTCTTTCTTTTCTTTT
1 TTTTTTCCTTTTTTCTCT-CTTTTTCTTTTTCTTTTTTTTT-TTTATTTTTCTTTCTTTTCTTTT
10634602 C
64 C
** * *
10634603 TTTTTTGTTTTTTTC-CTTCTTTTT-TTGTTT-TTTTGTTTTTTCTATTTTTCTAT-TTTTCTTT
1 TTTTTTCCTTTTTTCTC-TCTTTTTCTT-TTTCTTTT-TTTTTTTTATTTTTCTTTCTTTTC-TT
10634664 TTC
62 TTC
*
10634667 TTTATTTCTCTCTTTTTCTCTCTTTTTC--TGTCTTTTCTCTTTTTTTATTTCTT-TTTCTTTTC
1 TTT-TTTC-CT-TTTTTCTCTCTTTTTCTTTTTCTTTT-T-TTTTTTTATTT-TTCTTTCTTTTC
*
10634729 TTCTC
60 TTTTC
10634734 TT
1 TT
10634736 CAAAACAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
63 5 0.05
64 24 0.22
65 20 0.19
66 20 0.19
67 31 0.29
68 8 0.07
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (64 bp):
TTTTTTCCTTTTTTCTCTCTTTTTCTTTTTCTTTTTTTTTTTTATTTTTCTTTCTTTTCTTTTC
Found at i:10634650 original size:8 final size:8
Alignment explanation
Indices: 10634639--10634716 Score: 52
Period size: 8 Copynumber: 9.4 Consensus size: 8
10634629 GTTTTTTTGT
10634639 TTTTTCTA
1 TTTTTCTA
10634647 TTTTTCTA
1 TTTTTCTA
10634655 TTTTTCT-
1 TTTTTCTA
*
10634662 TTTTCTTTA
1 TTTT-TCTA
10634671 TTTCTCTCT-
1 TTT-T-TCTA
*
10634680 TTTTCTCTC
1 TTTT-TCTA
*
10634689 TTTTTCTG
1 TTTTTCTA
*
10634697 TCTTTTCTC
1 T-TTTTCTA
*
10634706 TTTTTTTA
1 TTTTTCTA
10634714 TTT
1 TTT
10634717 CTTTTTCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
7 4 0.07
8 34 0.58
9 17 0.29
10 4 0.07
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (8 bp):
TTTTTCTA
Found at i:10634659 original size:1 final size:1
Alignment explanation
Indices: 10634557--10634643 Score: 57
Period size: 1 Copynumber: 87.0 Consensus size: 1
10634547 TTTTCTCTCC
* * * * * * * * ** *
10634557 TTTTTCTTTTTCTTTTTTTTTCTTTTTTTTTCTTTCTTTTCTTTTCTTTTTTGTTTTTTTCCTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
10634622 TTTTTTTGTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTT
10634644 CTATTTTTCT
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.85
Consensus pattern (1 bp):
T
Found at i:10634681 original size:57 final size:54
Alignment explanation
Indices: 10634569--10634734 Score: 144
Period size: 57 Copynumber: 3.0 Consensus size: 54
10634559 TTTCTTTTTC
* *
10634569 TTTTTTTTTCTTT-TTTTTTCTTTCTTTTCTTTTCTT-TTTTGT-TTTTTTC-CTTCT
1 TTTTTTTTTTTTTGTTTTTTCTAT-TTTTCTTTT-TTCTTTT-TCTTTTTTCTC-TCT
10634623 TTTTTTGTTTTTTTGTTTTTTCTATTTTTCTATTTTTCTTTTTCTTTATTTCTCTCT
1 TTTTTT-TTTTTTTGTTTTTTCTATTTTTCT-TTTTTCTTTTTCTTT-TTTCTCTCT
* * * *
10634680 TTTTCTCTCTTTTTCTGTCTTTTCTCTTTTT-TTATTTCTTTTTCTTTTCTTCTCT
1 TTTT-T-T-TTTTTTTGTTTTTTCTATTTTTCTTTTTTCTTTTTCTTTT-TTCTCT
10634735 TCAAAACAAA
Statistics
Matches: 95, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
54 6 0.06
55 15 0.16
56 20 0.21
57 31 0.33
58 3 0.03
59 20 0.21
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.79
Consensus pattern (54 bp):
TTTTTTTTTTTTTGTTTTTTCTATTTTTCTTTTTTCTTTTTCTTTTTTCTCTCT
Found at i:10641042 original size:22 final size:22
Alignment explanation
Indices: 10641017--10641094 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
10641007 TTGAGGGTAT
10641017 AGTGGTCCTTCGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
*
10641039 AGTGGTCCTTTGGGACGTATCC
1 AGTGGTCCTTCGGGACGTATCC
10641061 AGTGGTCCTTCGGGAC--AT--
1 AGTGGTCCTTCGGGACGTATCC
10641079 AGTGGTCCTTCGGGAC
1 AGTGGTCCTTCGGGAC
10641095 AAATACTGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
18 16 0.30
20 2 0.04
22 36 0.67
ACGTcount: A:0.14, C:0.24, G:0.33, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATCC
Found at i:10647974 original size:22 final size:21
Alignment explanation
Indices: 10647949--10648022 Score: 91
Period size: 22 Copynumber: 3.6 Consensus size: 21
10647939 GGGTATAGTT
*
10647949 GTCCTTCGGGACGTATCCAGTA
1 GTCCTTCGGGAC-TATCCAGTG
10647971 GTCCTTCGGGAC-AT--AGTG
1 GTCCTTCGGGACTATCCAGTG
*
10647989 GTCTTTCGGGACATATCCAGTG
1 GTCCTTCGGGAC-TATCCAGTG
10648011 GTCCTTCGGGAC
1 GTCCTTCGGGAC
10648023 CTAGTGGTCC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 14 0.31
20 4 0.09
22 27 0.60
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
GTCCTTCGGGACTATCCAGTG
Found at i:10647998 original size:18 final size:18
Alignment explanation
Indices: 10647943--10648041 Score: 81
Period size: 22 Copynumber: 5.1 Consensus size: 18
10647933 AGTCGAGGGT
*
10647943 ATAGTTGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
*
10647961 GTATCCAGTAGTCCTTCGGGAC
1 --AT--AGTGGTCCTTCGGGAC
*
10647983 ATAGTGGTCTTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
10648001 ATATCCAGTGGTCCTTCGGGAC
1 --AT--AGTGGTCCTTCGGGAC
* *
10648023 CTAGTGGTCCTTCGAGAC
1 ATAGTGGTCCTTCGGGAC
10648041 A
1 A
10648042 AATACTGAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
18 29 0.44
20 7 0.11
22 30 0.45
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:10647998 original size:40 final size:40
Alignment explanation
Indices: 10647943--10648041 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
10647933 AGTCGAGGGT
* *
10647943 ATAGTTGTCCTTCGGGACGTATCCAGTAGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGACATATCCAGTAGTCCTTCGGGAC
* *
10647983 ATAGTGGTCTTTCGGGACATATCCAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGACATATCCAGTAGTCCTTCGGGAC
* *
10648023 CTAGTGGTCCTTCGAGACA
1 ATAGTGGTCCTTCGGGACA
10648042 AATACTGAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.29
Consensus pattern (40 bp):
ATAGTGGTCCTTCGGGACATATCCAGTAGTCCTTCGGGAC
Found at i:10649832 original size:21 final size:21
Alignment explanation
Indices: 10649806--10649847 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
10649796 ATTTGAATAT
*
10649806 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
10649827 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
10649848 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:10650173 original size:35 final size:33
Alignment explanation
Indices: 10650128--10650200 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
10650118 CCTTTTGTAA
* * *
10650128 AGGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
10650163 AGGGAAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
10650196 AGGGA
1 AGGGA
10650201 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 11 0.32
34 1 0.03
35 22 0.65
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (33 bp):
AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:10651521 original size:20 final size:20
Alignment explanation
Indices: 10651478--10651527 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
10651468 AAGATAATTT
10651478 AATTTTG-AAATCAAAAGTTG
1 AATTTTGAAAATCAAAAG-TG
10651498 -ATTTTGAAAATCAAAA-TG
1 AATTTTGAAAATCAAAAGTG
10651516 AAATTTTGAAAA
1 -AATTTTGAAAA
10651528 ATAATTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 6 0.22
20 19 0.70
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (20 bp):
AATTTTGAAAATCAAAAGTG
Found at i:10652995 original size:21 final size:21
Alignment explanation
Indices: 10652969--10653046 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
10652959 ATCAGATTGT
10652969 CCAGGGGGTACAGATTCTCCC
1 CCAGGGGGTACAGATTCTCCC
10652990 CCAGGGGGTATC-GA-T-T-CC
1 CCAGGGGGTA-CAGATTCTCCC
* * *
10653008 CC---GAGAACAGATTCCCCC
1 CCAGGGGGTACAGATTCTCCC
10653026 CCAGGGGGTACAGATTC-CCC
1 CCAGGGGGTACAGATTCTCCC
10653046 C
1 C
10653047 TGCATGGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 17
0.67 0.08 0.26
Matches are distributed among these distances:
14 1 0.02
15 5 0.11
16 1 0.02
18 8 0.18
19 1 0.02
20 5 0.11
21 22 0.50
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.27, T:0.17
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCTCCC
Found at i:10653261 original size:21 final size:21
Alignment explanation
Indices: 10653228--10653267 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
10653218 TTTTTGCAGA
*
10653228 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
10653250 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
10653268 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:10653525 original size:35 final size:33
Alignment explanation
Indices: 10653480--10653552 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
10653470 CCTTTTGTAA
* * *
10653480 AGGGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
10653515 AGGGAAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
10653548 AGGGA
1 AGGGA
10653553 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 11 0.32
34 1 0.03
35 22 0.65
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (33 bp):
AGGGAAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:10654195 original size:22 final size:23
Alignment explanation
Indices: 10654171--10654213 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10654161 TTAATAAATC
*
10654171 AAATTATAATAATTAAAATAACA
1 AAATCATAATAATTAAAATAACA
*
10654194 AAATCATAA-AATAAAAATAA
1 AAATCATAATAATTAAAATAA
10654214 AATAAACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (23 bp):
AAATCATAATAATTAAAATAACA
Found at i:10654223 original size:22 final size:23
Alignment explanation
Indices: 10654176--10654223 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
10654166 AAATCAAATT
* *
10654176 ATAATAATTAAAATAACAAAATC
1 ATAATAATAAAAATAACAAAAAC
10654199 ATAA-AATAAAAATAA-AATAAAC
1 ATAATAATAAAAATAACAA-AAAC
10654221 ATA
1 ATA
10654224 CATTCAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.73
23 4 0.18
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAATAATAAAAATAACAAAAAC
Found at i:10655665 original size:3 final size:3
Alignment explanation
Indices: 10655657--10655712 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
10655647 GTTTGGGTTG
* * * * * *
10655657 TAA TAA TAA TAT TAT TTA TAA TAA TAT TAA AAA TAA TAA TCA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10655705 TAA TAA TA
1 TAA TAA TA
10655713 TAGTTATAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:10655692 original size:15 final size:15
Alignment explanation
Indices: 10655657--10655713 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
10655647 GTTTGGGTTG
*
10655657 TAATAATAATATTAT
1 TAATAATAATATTAA
*
10655672 TTATAATAATATTAA
1 TAATAATAATATTAA
*
10655687 AAATAATAATCA-TAA
1 TAATAATAAT-ATTAA
10655702 TAATAATAATAT
1 TAATAATAATAT
10655714 AGTTATAGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATAATAATATTAA
Found at i:10657342 original size:59 final size:59
Alignment explanation
Indices: 10657223--10657355 Score: 157
Period size: 59 Copynumber: 2.2 Consensus size: 59
10657213 GTCAATTGAT
* *
10657223 CATTTTGTAACTTTTAATAGTCAATGGACTCAACAAAGCAATATCATATAGTCGGAAGAC
1 CATTTTGTAACTTTCAATAGTCAA-GGACTCAACAAAGCAACATCATATAGTCGGAAGAC
* *
10657283 CATTTTGTAACTTTCAATAGTC-GGAGACTCAACAAATCAACACTC-TATAGTC-GAGAGAC
1 CATTTTGTAACTTTCAATAGTCAAG-GACTCAACAAAGCAACA-TCATATAGTCGGA-AGAC
10657342 CATTTGTGT-ACTTT
1 CATTT-TGTAACTTT
10657356 ACCCCAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
58 3 0.05
59 36 0.55
60 26 0.40
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (59 bp):
CATTTTGTAACTTTCAATAGTCAAGGACTCAACAAAGCAACATCATATAGTCGGAAGAC
Found at i:10658393 original size:29 final size:29
Alignment explanation
Indices: 10658359--10658416 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
10658349 AAAATTTTAG
10658359 AAGGGCC-AAATT-GAATTTCTTTTAAATTT
1 AAGGGCCAAAATTAGAA--TCTTTTAAATTT
10658388 AAGGGCCAAAATTAGAATCTTTTAAATTT
1 AAGGGCCAAAATTAGAATCTTTTAAATTT
10658417 TGGAGGGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 19 0.70
30 5 0.19
31 3 0.11
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
AAGGGCCAAAATTAGAATCTTTTAAATTT
Found at i:10658937 original size:15 final size:15
Alignment explanation
Indices: 10658919--10658949 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10658909 ATCCAGCCAA
*
10658919 AGTTAATATTCGATT
1 AGTTAATATACGATT
10658934 AGTTAATATACGATT
1 AGTTAATATACGATT
10658949 A
1 A
10658950 ACACTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (15 bp):
AGTTAATATACGATT
Found at i:10660845 original size:15 final size:15
Alignment explanation
Indices: 10660827--10660857 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10660817 AAATTCTAAA
10660827 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
10660842 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
10660857 T
1 T
10660858 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:10664188 original size:24 final size:24
Alignment explanation
Indices: 10664171--10664282 Score: 152
Period size: 24 Copynumber: 4.7 Consensus size: 24
10664161 ATCATAACAT
*
10664171 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAG
* *
10664195 AATCTAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
* *
10664219 AATCCAGTTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
* *
10664243 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
10664267 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
10664283 TATAATAGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 79 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:10664254 original size:48 final size:48
Alignment explanation
Indices: 10664171--10664282 Score: 170
Period size: 48 Copynumber: 2.3 Consensus size: 48
10664161 ATCATAACAT
*
10664171 AATCCAGGTCAAGTATCAGATCAAAATCTAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCCGATCAG
* * * *
10664219 AATCCAGTTCAAGTATCCGATCAGAATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCCGATCAG
*
10664267 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
10664283 TATAATAGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (48 bp):
AATCCAGGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCCGATCAG
Found at i:10666777 original size:18 final size:18
Alignment explanation
Indices: 10666754--10666796 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
10666744 ATGGTCAACA
10666754 GTCGGGTCAACGGGTCAG
1 GTCGGGTCAACGGGTCAG
*
10666772 GTCGGGTCAACGGGTCGG
1 GTCGGGTCAACGGGTCAG
10666790 GTCGGGT
1 GTCGGGT
10666797 TATAACCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.21, G:0.49, T:0.19
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCAG
Found at i:10667922 original size:2 final size:2
Alignment explanation
Indices: 10667915--10667947 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10667905 TTTACATTCT
10667915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10667948 GACCTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10675397 original size:19 final size:19
Alignment explanation
Indices: 10675350--10675403 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
10675340 TTTGTTATGT
*
10675350 TTATAATATTAATTAT-AA
1 TTATAATATTATTTATAAA
* *
10675368 TT-T-TTAATATTTATAAA
1 TTATAATATTATTTATAAA
*
10675385 TTATAATATTATTTTTAAA
1 TTATAATATTATTTATAAA
10675404 ATTTTTAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 3 0.11
19 11 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAATATTATTTATAAA
Found at i:10675398 original size:28 final size:28
Alignment explanation
Indices: 10675349--10675415 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
10675339 TTTTGTTATG
* *
10675349 TTTATAATATTAATTATAATTTTTAATA
1 TTTATAATATTAAATATAATTTTTAAAA
*
10675377 TTTATAA-ATTATAATATTATTTTTAAAA
1 TTTATAATATTA-AATATAATTTTTAAAA
*
10675405 TTTTTAATATT
1 TTTATAATATT
10675416 TAAACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 4 0.12
28 26 0.79
29 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTATAATATTAAATATAATTTTTAAAA
Found at i:10675413 original size:37 final size:36
Alignment explanation
Indices: 10675350--10675434 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 36
10675340 TTTGTTATGT
* *
10675350 TTATAATATTA--ATTATAATTTTTAATATTTATAAA
1 TTATAATATTATTTTTAAAATTTTTAATATTTA-AAA
*
10675385 TTATAATATTATTTTTAAAATTTTTAATATTTAAAC
1 TTATAATATTATTTTTAAAATTTTTAATATTTAAAA
* *
10675421 TAATAATATCATTT
1 TTATAATATTATTT
10675435 AGATTCTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 11 0.26
36 14 0.33
37 18 0.42
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (36 bp):
TTATAATATTATTTTTAAAATTTTTAATATTTAAAA
Found at i:10675472 original size:12 final size:12
Alignment explanation
Indices: 10675443--10675476 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
10675433 TTAGATTCTT
10675443 TTATATATTTTAG
1 TTATATA-TTTAG
*
10675456 TTATATATTTCG
1 TTATATATTTAG
10675468 TTATATATT
1 TTATATATT
10675477 GTCCGTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (12 bp):
TTATATATTTAG
Done.