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 54 of 62
Found at i:12766920 original size:23 final size:22
Alignment explanation
Indices: 12766868--12766928 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
12766858 ACATTTTATA
*
12766868 TGGCACTTCGGTGCAATTCTAC
1 TGGCACTTCGGTGCAACTCTAC
* *
12766890 TCGCCACTACGGTGCAACTCTAC
1 T-GGCACTTCGGTGCAACTCTAC
12766913 GTGGCACTTCGGTGCA
1 -TGGCACTTCGGTGCA
12766929 TTTATCGGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.26
Consensus pattern (22 bp):
TGGCACTTCGGTGCAACTCTAC
Found at i:12771922 original size:23 final size:23
Alignment explanation
Indices: 12771888--12771948 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
12771878 ATATTTTATA
*
12771888 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAACTCTACG
*
12771911 TGGCACTACGGTGCAACTCTACG
1 TGGCACTTCGGTGCAACTCTACG
12771934 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
12771949 TTTATCGGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAACTCTACG
Found at i:12774907 original size:23 final size:23
Alignment explanation
Indices: 12774852--12774900 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
12774842 CCATAATACT
12774852 CTTATAATCCTTTCATATTTACC
1 CTTATAATCCTTTCATATTTACC
12774875 CTTATAATCCTTTCATATTTACC
1 CTTATAATCCTTTCATATTTACC
12774898 CTT
1 CTT
12774901 TTTATCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (23 bp):
CTTATAATCCTTTCATATTTACC
Found at i:12779103 original size:23 final size:23
Alignment explanation
Indices: 12779044--12779096 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
12779034 ATTACCATAA
12779044 TACCCTTATAATCCTTTCATATT
1 TACCCTTATAATCCTTTCATATT
12779067 TACCCTTATAATCCTTTCATATT
1 TACCCTTATAATCCTTTCATATT
12779090 TACCCTT
1 TACCCTT
12779097 TTTATCCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (23 bp):
TACCCTTATAATCCTTTCATATT
Found at i:12780196 original size:2 final size:2
Alignment explanation
Indices: 12780184--12780216 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12780174 ATTTTCAAGA
*
12780184 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12780217 CATACGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12782003 original size:16 final size:18
Alignment explanation
Indices: 12781984--12782019 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
12781974 GGTGATTAAC
12781984 TCTTTTATGT-A-TTACA
1 TCTTTTATGTCATTTACA
12782000 TC-TTTATGTCATTTACA
1 TCTTTTATGTCATTTACA
12782017 TCT
1 TCT
12782020 AGAATAGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (18 bp):
TCTTTTATGTCATTTACA
Found at i:12782007 original size:15 final size:17
Alignment explanation
Indices: 12781987--12782019 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12781977 GATTAACTCT
12781987 TTTATGT-A-TTACATC
1 TTTATGTCATTTACATC
12782002 TTTATGTCATTTACATC
1 TTTATGTCATTTACATC
12782019 T
1 T
12782020 AGAATAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.55
Consensus pattern (17 bp):
TTTATGTCATTTACATC
Found at i:12784985 original size:32 final size:32
Alignment explanation
Indices: 12784935--12785000 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
12784925 GATCACAAAT
*
12784935 TTAAAATTTAAGAGTCTAACG-TTATCGATCCG
1 TTAAAATTTAAGACTCTAACGTTTAT-GATCCG
* * *
12784967 TTAAAATTTTAGTCTCTAAGGTTTATGATCCG
1 TTAAAATTTAAGACTCTAACGTTTATGATCCG
12784999 TT
1 TT
12785001 CGATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (32 bp):
TTAAAATTTAAGACTCTAACGTTTATGATCCG
Found at i:12787343 original size:20 final size:20
Alignment explanation
Indices: 12787318--12787355 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12787308 TAATTTTGAT
12787318 TAAAATGATTCTTATTTAGA
1 TAAAATGATTCTTATTTAGA
* *
12787338 TAAAATTATTTTTATTTA
1 TAAAATGATTCTTATTTA
12787356 AATGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TAAAATGATTCTTATTTAGA
Found at i:12789255 original size:3 final size:3
Alignment explanation
Indices: 12789247--12789325 Score: 83
Period size: 3 Copynumber: 27.0 Consensus size: 3
12789237 AATTGTTAAA
* *
12789247 ATT ATT ATT ATT AATT ATT ATT ATT -TA ATT ATT ACT A-T ATT ATT
1 ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
12789291 ATT ATT ATT ATT ATT ATG GTT ATT TTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12789326 TCTTTTATAG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 5 0.08
3 55 0.87
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:12791748 original size:10 final size:10
Alignment explanation
Indices: 12791733--12791773 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
12791723 TTTTGTGTGT
12791733 TGTTCGTTTA
1 TGTTCGTTTA
12791743 TGTTCGTTTA
1 TGTTCGTTTA
12791753 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
12791766 TGTTCGTT
1 TGTTCGTT
12791774 CGTTCGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 18 0.64
13 10 0.36
ACGTcount: A:0.07, C:0.10, G:0.22, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:12791880 original size:16 final size:16
Alignment explanation
Indices: 12791855--12791887 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12791845 AAAAAAAAAT
12791855 TGTTCCTTTATGTTCG
1 TGTTCCTTTATGTTCG
*
12791871 TGTTCGTTTATGTTCG
1 TGTTCCTTTATGTTCG
12791887 T
1 T
12791888 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCCTTTATGTTCG
Found at i:12791967 original size:30 final size:30
Alignment explanation
Indices: 12791931--12791996 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
12791921 CCGTTCGTGT
12791931 GCGTTCGGTTCGTTTACAGGTCTATTTGAC
1 GCGTTCGGTTCGTTTACAGGTCTATTTGAC
*
12791961 GCGTTCGGTTCGTTTATAGGTCTATTTGAC
1 GCGTTCGGTTCGTTTACAGGTCTATTTGAC
12791991 GCGTTC
1 GCGTTC
12791997 AATTGTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.12, C:0.20, G:0.27, T:0.41
Consensus pattern (30 bp):
GCGTTCGGTTCGTTTACAGGTCTATTTGAC
Found at i:12792008 original size:30 final size:30
Alignment explanation
Indices: 12791939--12792008 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
12791929 GTGCGTTCGG
* **
12791939 TTCGTTTACAGGTCTATTTGACGCGTTCGG
1 TTCGTTTATAGGTCTATTTGACGCGTTCAA
12791969 TTCGTTTATAGGTCTATTTGACGCGTTCAA
1 TTCGTTTATAGGTCTATTTGACGCGTTCAA
12791999 TT-GTATTATA
1 TTCGT-TTATA
12792009 CTTTTAGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 2 0.06
30 34 0.94
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (30 bp):
TTCGTTTATAGGTCTATTTGACGCGTTCAA
Found at i:12792924 original size:16 final size:16
Alignment explanation
Indices: 12792905--12792935 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12792895 ATATTATATA
12792905 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
12792921 ATATTATGAATTATT
1 ATATAATGAATTATT
12792936 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:12798777 original size:10 final size:10
Alignment explanation
Indices: 12798741--12798784 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
12798731 AAATTTTGGA
12798741 TTTTTTG-TT
1 TTTTTTGTTT
**
12798750 TTTTTTGCCT
1 TTTTTTGTTT
12798760 TTTTTTGTTT
1 TTTTTTGTTT
12798770 TTTTTTGTTT
1 TTTTTTGTTT
12798780 TTTTT
1 TTTTT
12798785 AAAAAATAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
9 7 0.23
10 24 0.77
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:12802383 original size:13 final size:13
Alignment explanation
Indices: 12802365--12802394 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12802355 ATTTCATTGC
12802365 TTTAATTTTATAT
1 TTTAATTTTATAT
*
12802378 TTTAATTTTATTT
1 TTTAATTTTATAT
12802391 TTTA
1 TTTA
12802395 CCCTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTAATTTTATAT
Found at i:12803813 original size:40 final size:40
Alignment explanation
Indices: 12803726--12803897 Score: 127
Period size: 40 Copynumber: 4.2 Consensus size: 40
12803716 TAACTTTACC
*
12803726 GGCGTTTCTTTACAAACGTCGCAATAAAGTTCATCTATAGT
1 GGCGTTT-TTTACAAACGCCGCAATAAAGTTCATCTATAGT
*
12803767 GGCGTTTTTTGACAAACGCCGCAAT--AGATCTATCTATAGT
1 GGCGTTTTTT-ACAAACGCCGCAATAAAGTTC-ATCTATAGT
* * * * *
12803807 GGCGTTTTTTCAATAAACGCCACAACATA-TT-AGTACTTTAGT
1 GGCGTTTTTT--ACAAACGCCGCAATAAAGTTCA-T-CTATAGT
* * * * * * *
12803849 GGTGTTTTATATAAACACCTCAATAGAGTTCACCTATAGT
1 GGCGTTTTTTACAAACGCCGCAATAAAGTTCATCTATAGT
12803889 GGCGTTTTT
1 GGCGTTTTT
12803898 CAATAAACAC
Statistics
Matches: 104, Mismatches: 18, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
39 4 0.04
40 49 0.47
41 34 0.33
42 16 0.15
43 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (40 bp):
GGCGTTTTTTACAAACGCCGCAATAAAGTTCATCTATAGT
Found at i:12804063 original size:83 final size:83
Alignment explanation
Indices: 12803800--12804070 Score: 269
Period size: 83 Copynumber: 3.3 Consensus size: 83
12803790 ATAGATCTAT
* * * * * *
12803800 CTATAGTGGCGTTTTTTCAATAAACGCCACAACATATTAGTACTTTAGTGGT-GTTTTATATAAA
1 CTATAGTGGCGTTTTTTCAATAAACACCATAACAAATTAGAACTTTAGCGGTATTTTTATATAAA
* * *
12803864 CACCTCAATAGAGTTCAC
66 CACCACAATAGATTTAAC
** * *
12803882 CTATAGTGGCG-TTTTTCAATAAACACTGTAACAAATGAGAACTTTAGCGGCATTTTTATATAAA
1 CTATAGTGGCGTTTTTTCAATAAACACCATAACAAATTAGAACTTTAGCGGTATTTTTATATAAA
** *
12803946 TGCCACAATAGGTTTAAC
66 CACCACAATAGATTTAAC
* * * * *
12803964 CTATAGTGACATTTTTTCAATAAACACCATAATAAATTAGAACTTTAACGGTATTTTTATACAAA
1 CTATAGTGGCGTTTTTTCAATAAACACCATAACAAATTAGAACTTTAGCGGTATTTTTATATAAA
* *
12804029 CACCGCAATA-ATATTTAC
66 CACCACAATAGAT-TTAAC
* * * *
12804047 CTGTAGTAGCGCTTTTTAAATAAA
1 CTATAGTGGCGTTTTTTCAATAAA
12804071 TGCCGCAATA
Statistics
Matches: 150, Mismatches: 36, Indels: 5
0.79 0.19 0.03
Matches are distributed among these distances:
81 31 0.21
82 44 0.29
83 75 0.50
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (83 bp):
CTATAGTGGCGTTTTTTCAATAAACACCATAACAAATTAGAACTTTAGCGGTATTTTTATATAAA
CACCACAATAGATTTAAC
Found at i:12807787 original size:43 final size:42
Alignment explanation
Indices: 12807720--12808003 Score: 300
Period size: 43 Copynumber: 6.6 Consensus size: 42
12807710 TTATATTAAC
* * * * *
12807720 AAACGCCGTTATAGATTTGACTTTTTACGGTGTTT-TTCCAAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCC-AA
* * *
12807762 AAATGCCACTATAGATCTGACCTTTTGAGGCGTTTGTATCCAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAA
* * * *
12807805 AAACGCCGCTACAGATATGACCTTTTGCGGCATTTGTATACAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAA
** **
12807848 AAGTGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTAAACAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAA
* *
12807891 AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCCAA
1 AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAA
**
12807933 AAACGCCGCTATAGATCTAGACCTTTTGCGGCGTTTGTTTAAAA
1 AAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTG-TTCCAA
* *
12807977 AAATGCCGCTATAGATCTTGACTTTTT
1 AAACGCCGCTATAGATC-TGACCTTTT
12808004 TGCGACATTT
Statistics
Matches: 204, Mismatches: 33, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
42 47 0.23
43 126 0.62
44 30 0.15
45 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAA
Found at i:12807912 original size:129 final size:130
Alignment explanation
Indices: 12807760--12808003 Score: 357
Period size: 129 Copynumber: 1.9 Consensus size: 130
12807750 TGTTTTTCCA
* * *
12807760 AAAAATGCCACTATAGATCTGACCTTTTGAGGCGTTTGTATCCAAAAACGCCGCTACAGATAT-G
1 AAAAACGCCACTATAGATATGACCTTTTGAGGCATTTGT-TCCAAAAACGCCGCTACAGATATAG
* *
12807824 ACCTTTTGCGGCATTTGTATACAAAAGTGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTAAA
65 ACCTTTTGCGGCATTTGTATAAAAAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTAAA
12807888 C
130 C
* * * *
12807889 AAAAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTAGA
1 AAAAACGCCACTATAGATATGACCTTTTGAGGCATTTGTTCCAAAAACGCCGCTACAGATATAGA
* * *
12807954 CCTTTTGCGGCGTTTGTTTAAAAAAATGCCGCTATAGATCTTGACTTTTT
66 CCTTTTGCGGCATTTGTATAAAAAAATGCCGCTATAGATCTTGACCTTTT
12808004 TGCGACATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
128 21 0.21
129 72 0.71
130 8 0.08
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (130 bp):
AAAAACGCCACTATAGATATGACCTTTTGAGGCATTTGTTCCAAAAACGCCGCTACAGATATAGA
CCTTTTGCGGCATTTGTATAAAAAAATGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTAAAC
Found at i:12808002 original size:86 final size:85
Alignment explanation
Indices: 12807720--12807992 Score: 343
Period size: 86 Copynumber: 3.2 Consensus size: 85
12807710 TTATATTAAC
* * * * ** *
12807720 AAACGCCGTTATAGATTTGACTTTTTACGGTGTTT-TTCCAAAAAATGCCACTATAGATCTGACC
1 AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCC-AAAAATGCCGCTATAGATCTGACC
* * **
12807784 TTTTGAGGCGTTTGTATCCAA
65 TTTTGCGGCGTTTGTTTAAAA
* * *
12807805 AAACGCCGCTACAGATATGACCTTTTGCGGCATTTGTATACAAAAGTGCCGCTATAGATCTGACC
1 AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGT-TCCAAAAATGCCGCTATAGATCTGACC
*
12807870 TTTTGCGGCGTTTG-TAAACAA
65 TTTTGCGGCGTTTGTTTAA-AA
*
12807891 AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAGATCTAGACC
1 AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAATGCCGCTATAGATCT-GACC
12807956 TTTTGCGGCGTTTGTTTAAAA
65 TTTTGCGGCGTTTGTTTAAAA
*
12807977 AAATGCCGCTATAGAT
1 AAACGCCGCTATAGAT
12807993 CTTGACTTTT
Statistics
Matches: 162, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
85 48 0.30
86 109 0.67
87 5 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (85 bp):
AAACGCCGCTATAGATATGACCTTTTGCGGCATTTGTTCCAAAAATGCCGCTATAGATCTGACCT
TTTGCGGCGTTTGTTTAAAA
Found at i:12808318 original size:147 final size:147
Alignment explanation
Indices: 12808051--12808344 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
12808041 TACCGGCGCT
12808051 TCTTGCGACATTTTTACTATCGCCGCGAGTGCTTTTAGCAGCACTTACAAACGTCGATATAGGAC
1 TCTTGCGACATTTTTACTATCGCCGCGAGTGCTTTTAGCAGCACTTACAAACGTCGATATAGGAC
12808116 TACAAAAACGTCGTTAAAAGTCTATTTTGCTGTAGTGCACACTTGACATCATGATGGACAAACAT
66 TACAAAAACGTCGTTAAAAGTCTATTTTGCTGTAGTGCACACTTGACATCATGATGGACAAACAT
12808181 TCATTTTCATTACTATG
131 TCATTTTCATTACTATG
12808198 TCTTGCGACATTTTTACTATCGCCGCGAGTGCTTTTAGCAGCACTTACAAACGTCGATATAGGAC
1 TCTTGCGACATTTTTACTATCGCCGCGAGTGCTTTTAGCAGCACTTACAAACGTCGATATAGGAC
12808263 TACAAAAACGTCGTTAAAAGTCTATTTTGCTGTAGTGCACACTTGACATCATGATGGACAAACAT
66 TACAAAAACGTCGTTAAAAGTCTATTTTGCTGTAGTGCACACTTGACATCATGATGGACAAACAT
12808328 TCATTTTCATTACTATG
131 TCATTTTCATTACTATG
12808345 CTATTTATAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (147 bp):
TCTTGCGACATTTTTACTATCGCCGCGAGTGCTTTTAGCAGCACTTACAAACGTCGATATAGGAC
TACAAAAACGTCGTTAAAAGTCTATTTTGCTGTAGTGCACACTTGACATCATGATGGACAAACAT
TCATTTTCATTACTATG
Found at i:12809290 original size:91 final size:91
Alignment explanation
Indices: 12809135--12809318 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
12809125 TATTTTCCAT
12809135 TCAATATTCATTTTGCTTTCAAGAACACCATTTGTACTCAATTTTATTCATCTTTGAGTGTTCTT
1 TCAATATTCATTTTGCTTTCAAGAACACCATTTGTACTCAATTTTATTCATCTTTGAGTGTTCTT
12809200 TTCTTGTTCTAGAATTGTGCAAACAA
66 TTCTTGTTCTAGAATTGTGCAAACAA
12809226 TCAATATTCATTTTGCTTTCAAGAACACCATTTGTACTCAATTTTATTCATCTTTGAGTGTTCTT
1 TCAATATTCATTTTGCTTTCAAGAACACCATTTGTACTCAATTTTATTCATCTTTGAGTGTTCTT
12809291 TTCTTGTTCTAGAATTGTGCAAACAA
66 TTCTTGTTCTAGAATTGTGCAAACAA
12809317 TC
1 TC
12809319 TACCTTGTGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (91 bp):
TCAATATTCATTTTGCTTTCAAGAACACCATTTGTACTCAATTTTATTCATCTTTGAGTGTTCTT
TTCTTGTTCTAGAATTGTGCAAACAA
Found at i:12818537 original size:290 final size:290
Alignment explanation
Indices: 12818017--12818598 Score: 1128
Period size: 290 Copynumber: 2.0 Consensus size: 290
12818007 ATTGGTTCTT
*
12818017 AAACTTTTGTATATTTTAATATCATCTATAAATTATAACTCTAATTCTAAATTAATCCTTAAACT
1 AAACTTTTGAATATTTTAATATCATCTATAAATTATAACTCTAATTCTAAATTAATCCTTAAACT
12818082 TTTGAACATTCTATTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCTAAACTTTTGAAT
66 TTTGAACATTCTATTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCTAAACTTTTGAAT
12818147 ATTCCAATTTCATTTCCACATACATCCAAATGTGTAATTAGTTTTGGCCATAATTTAACCTAAAT
131 ATTCCAATTTCATTTCCACATACATCCAAATGTGTAATTAGTTTTGGCCATAATTTAACCTAAAT
12818212 TTTGTTTTTCAAACATTTAAAAATATAATTTGGCCTAACGATTTCATTAACAAGAGATGTGATAA
196 TTTGTTTTTCAAACATTTAAAAATATAATTTGGCCTAACGATTTCATTAACAAGAGATGTGATAA
*
12818277 ATATATACGTATAGCCTGGGATGAAATTGG
261 ATATATACGTATAACCTGGGATGAAATTGG
12818307 AAACTTTTGAATATTTTAATATCATCTATAAATTATAACTCTAATTCTAAATTAATCCTTAAACT
1 AAACTTTTGAATATTTTAATATCATCTATAAATTATAACTCTAATTCTAAATTAATCCTTAAACT
12818372 TTTGAACATTCTATTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCTAAACTTTTGAAT
66 TTTGAACATTCTATTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCTAAACTTTTGAAT
*
12818437 ATTCCAATTTCATTTCCACATACATCCAAATGTGTAATTAGTTTTGGCCATAATTTAACCTAAGT
131 ATTCCAATTTCATTTCCACATACATCCAAATGTGTAATTAGTTTTGGCCATAATTTAACCTAAAT
*
12818502 TTTGTTTTTCAAACATTTAAAAATATAATTTGGCCTACCGATTTCATTAACAAGAGATGTGATAA
196 TTTGTTTTTCAAACATTTAAAAATATAATTTGGCCTAACGATTTCATTAACAAGAGATGTGATAA
12818567 ATATATACGTATAACCTGGGATGAAATTGG
261 ATATATACGTATAACCTGGGATGAAATTGG
12818597 AA
1 AA
12818599 TATTTAAAAA
Statistics
Matches: 288, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
290 288 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (290 bp):
AAACTTTTGAATATTTTAATATCATCTATAAATTATAACTCTAATTCTAAATTAATCCTTAAACT
TTTGAACATTCTATTCATCCCTAAACTATGACCCTCTTTCTAAATTGGTCCCTAAACTTTTGAAT
ATTCCAATTTCATTTCCACATACATCCAAATGTGTAATTAGTTTTGGCCATAATTTAACCTAAAT
TTTGTTTTTCAAACATTTAAAAATATAATTTGGCCTAACGATTTCATTAACAAGAGATGTGATAA
ATATATACGTATAACCTGGGATGAAATTGG
Found at i:12818688 original size:60 final size:61
Alignment explanation
Indices: 12818584--12818728 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 61
12818574 CGTATAACCT
* * ** *
12818584 GGGATGAAATTGGAATATTTAAAAAGTTTGGGGACCAATTTAGAATGAAAGTTATAGTTTA
1 GGGATAAAATTGAAATATTTAAAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAGGTTA
* * *
12818645 GGGATAAAATTGAAATA-TTCAAAAGTTTAAGGACTAATTTAGAATGATAGTTATAGGTTA
1 GGGATAAAATTGAAATATTTAAAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAGGTTA
*
12818705 GGGATAAAATT-AAAGCATTTAAAA
1 GGGATAAAATTGAAA-TATTTAAAA
12818729 TTTTATGGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
59 3 0.04
60 49 0.68
61 20 0.28
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.32
Consensus pattern (61 bp):
GGGATAAAATTGAAATATTTAAAAAGTTTAAGGACCAATTTAGAATGAAAGTTATAGGTTA
Found at i:12819397 original size:31 final size:33
Alignment explanation
Indices: 12819355--12819417 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
12819345 AATCAAGTAT
12819355 AAATATTAAAGTAAAAGAAAA-ATTAAATTAAG
1 AAATATTAAAGTAAAAGAAAACATTAAATTAAG
* *
12819387 AAATA-TAAAGTAATAGAAAACTTTAAATTAA
1 AAATATTAAAGTAAAAGAAAACATTAAATTAA
12819418 AAGGATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (33 bp):
AAATATTAAAGTAAAAGAAAACATTAAATTAAG
Found at i:12820437 original size:10 final size:10
Alignment explanation
Indices: 12820415--12820486 Score: 78
Period size: 10 Copynumber: 7.2 Consensus size: 10
12820405 ACCAAACAAA
12820415 AATAAAA-AT
1 AATAAAATAT
12820424 AATAAAATAT
1 AATAAAATAT
12820434 AATAAAAATATAT
1 AAT--AAA-ATAT
12820447 AATAAAA-AT
1 AATAAAATAT
12820456 AA-AAAATAT
1 AATAAAATAT
*
12820465 AATATAATAT
1 AATAAAATAT
*
12820475 AATATAATAT
1 AATAAAATAT
12820485 AA
1 AA
12820487 AATATAAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 11
0.82 0.01 0.16
Matches are distributed among these distances:
8 4 0.07
9 15 0.27
10 24 0.43
11 3 0.05
12 3 0.05
13 7 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAAATAT
Found at i:12820525 original size:42 final size:42
Alignment explanation
Indices: 12820418--12820536 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
12820408 AAACAAAAAT
* * *
12820418 AAAA-ATAATAAAATATAATA-AAAAT-ATATAATAAAAATAA
1 AAAATATAATATAATATAATATAATATAAAAT-ATAAAAATAA
12820458 AAAATATAATATAATATAATATAATATAAAATATAAAAATAA
1 AAAATATAATATAATATAATATAATATAAAATATAAAAATAA
* * *
12820500 AAAA-ATAATATTAATGTAATGTAATATATAATA-AAAA
1 AAAATATAATA-TAATATAATATAATATAAAATATAAAA
12820537 CTATATAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
40 4 0.06
41 25 0.36
42 37 0.54
43 3 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (42 bp):
AAAATATAATATAATATAATATAATATAAAATATAAAAATAA
Found at i:12820525 original size:47 final size:47
Alignment explanation
Indices: 12820412--12820546 Score: 138
Period size: 46 Copynumber: 2.9 Consensus size: 47
12820402 GGGACCAAAC
* *
12820412 AAAAATA-AAAATAATAAAATATAATA-AAAATATATAATAAAAATA
1 AAAAATATAATATAATATAATATAATATAAAATATATAATAAAAATA
12820457 AAAAATATAATATAATATAATATAATATAAAATATA-AA-AATAAA-A
1 AAAAATATAATATAATATAATATAATATAAAATATATAATAA-AAATA
* *
12820502 AAATAATATTAATGTAATGTAATAT-ATAATAAAAACTATATAATA
1 AAA-AATA-TAATATAATATAATATAAT-AT-AAAA-TATATAATA
12820547 TTATATTTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
45 13 0.17
46 28 0.37
47 24 0.32
48 4 0.05
49 4 0.05
50 2 0.03
51 1 0.01
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (47 bp):
AAAAATATAATATAATATAATATAATATAAAATATATAATAAAAATA
Found at i:12820553 original size:42 final size:40
Alignment explanation
Indices: 12820412--12820536 Score: 132
Period size: 41 Copynumber: 3.1 Consensus size: 40
12820402 GGGACCAAAC
* *
12820412 AAAAAT-AAAA-ATAATA-AAATATAATAAAAATATATAAT
1 AAAAATAAAAATATAATATTAATATAAT-ATAATATATAAT
*
12820450 AAAAATAAAAAATATAATA-TAATATAATATAATATAAAATAT
1 AAAAAT-AAAAATATAATATTAATATAATATAATAT-ATA-AT
* * *
12820492 AAAAATAAAAAAATAATATTAATGTAATGTAATATATAAT
1 AAAAATAAAAATATAATATTAATATAATATAATATATAAT
12820532 AAAAA
1 AAAAA
12820537 CTATATAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
38 6 0.08
40 17 0.23
41 29 0.39
42 22 0.30
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (40 bp):
AAAAATAAAAATATAATATTAATATAATATAATATATAAT
Found at i:12820684 original size:69 final size:68
Alignment explanation
Indices: 12820563--12820691 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 68
12820553 TTTCAAAAAT
* *
12820563 AATATGTTTTCAGAAATTATATATTATATATGTTTCCAAAAATATTTTAAAAACTATATACGTTT
1 AATATGTTTTCAGAAA-TATATATTATATATGTTTCCAAAAACATTTAAAAAACTATATACGTTT
12820628 TAAA
65 TAAA
* *
12820632 AATATGTTTTCA-AAA-CTATATTATATATGTTTTCAAAAACCATTCTAAAAAAACTATATA
1 AATATGTTTTCAGAAATATATATTATATATGTTTCCAAAAA-CATT-T-AAAAAACTATATA
12820692 TTATATGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
66 22 0.42
67 3 0.06
68 4 0.08
69 24 0.45
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (68 bp):
AATATGTTTTCAGAAATATATATTATATATGTTTCCAAAAACATTTAAAAAACTATATACGTTTT
AAA
Found at i:12820685 original size:38 final size:37
Alignment explanation
Indices: 12820643--12820733 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 37
12820633 ATATGTTTTC
12820643 AAAACTATATTATATATGTTTTCAAAAACCA-TTCTAAA
1 AAAACTATA-TATATATGTTTT-AAAAACCATTTCTAAA
** *
12820681 AAAACTATATATTATATGTTTTAAAAATTATTTTTAAA
1 AAAACTATATA-TATATGTTTTAAAAACCATTTCTAAA
12820719 AGAAACTATATATAT
1 A-AAACTATATATAT
12820734 TATACATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 8 0.17
38 29 0.62
39 10 0.21
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (37 bp):
AAAACTATATATATATGTTTTAAAAACCATTTCTAAA
Found at i:12820809 original size:35 final size:35
Alignment explanation
Indices: 12820643--12820876 Score: 186
Period size: 35 Copynumber: 6.5 Consensus size: 35
12820633 ATATGTTTTC
*
12820643 AAAACTATAT-TATATATGTTTTCAAAAACCATTCTAAA
1 AAAACTATATAT-TATACGTTTTC-AAAACCATT-T-AA
* * **
12820681 AAAACTATATATTATATGTTTTAAAAATTATTTTTAAA
1 AAAACTATATATTATACGTTTTCAAAACCA--TTT-AA
* * **
12820719 AGAAACTATATATATTATACATTTTTAAAATTATTT-A
1 A-AAAC--TATATATTATACGTTTTCAAAACCATTTAA
* *
12820756 AAAA-TATATACTATACGTTTTCAAAACCGTTTAA
1 AAAACTATATATTATACGTTTTCAAAACCATTTAA
* * *
12820790 AAAACTATTTATTATACGTTTTCAAAACCGTTTTA
1 AAAACTATATATTATACGTTTTCAAAACCATTTAA
* * ** *
12820825 AAAATTATACATTATGTGTTTTCAAAACCATTTTA
1 AAAACTATATATTATACGTTTTCAAAACCATTTAA
12820860 AAAACTATATATTATAC
1 AAAACTATATATTATAC
12820877 ATTTGTTTAA
Statistics
Matches: 163, Mismatches: 25, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
33 22 0.13
34 5 0.03
35 69 0.42
36 3 0.02
37 7 0.04
38 25 0.15
39 10 0.06
41 22 0.13
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (35 bp):
AAAACTATATATTATACGTTTTCAAAACCATTTAA
Found at i:12827871 original size:45 final size:45
Alignment explanation
Indices: 12827820--12828015 Score: 234
Period size: 45 Copynumber: 4.4 Consensus size: 45
12827810 CATACAAGTG
* *
12827820 CATTATCAGCATG-AAAGGATGCTATAGTTGAAATGTATATGGGTA
1 CATTATCAACA-GAAAAGTATGCTATAGTTGAAATGTATATGGGTA
*
12827865 CATTATCAACAGAAAAGTAAGC-ACTAGTTGAAATGTATATGGGTA
1 CATTATCAACAGAAAAGTATGCTA-TAGTTGAAATGTATATGGGTA
* * *
12827910 CATTATCAACAGTAAAGTATACTATAGTTGGAATGTATATGGGTA
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* * * * * *
12827955 CATCATCAACAGAAAAGTATGTTATTGTTGAGATGCATATGGGTG
1 CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
* *
12828000 CATTATTAACATAAAA
1 CATTATCAACAGAAAA
12828016 ATATATTACG
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.02
45 126 0.98
46 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (45 bp):
CATTATCAACAGAAAAGTATGCTATAGTTGAAATGTATATGGGTA
Found at i:12828633 original size:10 final size:10
Alignment explanation
Indices: 12828618--12828649 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12828608 CTTATATGGC
12828618 ATGTAATTAA
1 ATGTAATTAA
12828628 ATGTAATTAA
1 ATGTAATTAA
*
12828638 ATGTAATAAA
1 ATGTAATTAA
12828648 AT
1 AT
12828650 ATTTTGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (10 bp):
ATGTAATTAA
Found at i:12830498 original size:21 final size:21
Alignment explanation
Indices: 12830472--12830538 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
12830462 ATTCTGACTA
*
12830472 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCTAAT
*
12830493 TCGCGTTGCGATTTTTCTAAT
1 TCGCGTTGCGATTTTCCTAAT
**
12830514 TCGCAATGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCTAAT
12830535 TCGC
1 TCGC
12830539 AATGCGAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCTAAT
Found at i:12830539 original size:21 final size:20
Alignment explanation
Indices: 12830509--12830627 Score: 148
Period size: 20 Copynumber: 5.9 Consensus size: 20
12830499 TGCGATTTTT
* * *
12830509 CTAATTCGCAATGCGATTTTC
1 CTAAATCGCAATGCGA-ATAC
*
12830530 CTAATTCGCAATGCGAATAC
1 CTAAATCGCAATGCGAATAC
*
12830550 GTAAATCGCAATGCGAATAC
1 CTAAATCGCAATGCGAATAC
*
12830570 GTAAATCGCAATGCGAATAC
1 CTAAATCGCAATGCGAATAC
*
12830590 CTAAATCGCAATGCGAATAT
1 CTAAATCGCAATGCGAATAC
* *
12830610 GTAAATCGCAACGCGAAT
1 CTAAATCGCAATGCGAAT
12830628 CTGACTATCG
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
20 74 0.82
21 16 0.18
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
CTAAATCGCAATGCGAATAC
Found at i:12830560 original size:20 final size:20
Alignment explanation
Indices: 12830535--12830627 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
12830525 TTTTCCTAAT
12830535 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
12830555 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
12830575 TCGCAATGCGAATACCTAAA
1 TCGCAATGCGAATACGTAAA
*
12830595 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
12830615 TCGCAACGCGAAT
1 TCGCAATGCGAAT
12830628 CTGACTATCG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:12830637 original size:20 final size:20
Alignment explanation
Indices: 12830614--12830696 Score: 139
Period size: 20 Copynumber: 4.2 Consensus size: 20
12830604 GAATATGTAA
* *
12830614 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
12830634 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
12830654 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
12830674 ATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
12830694 ATC
1 ATC
12830697 ACAATACTGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:12830638 original size:40 final size:40
Alignment explanation
Indices: 12830554--12830685 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
12830544 GAATACGTAA
* * * *
12830554 ATCGCAATGCGAATACGTAAATCGCAATGCGAATACCT-A-A
1 ATCGCAACGCGAATATGTAAATCGCAACGCGAAT--CTGACT
*
12830594 ATCGCAATGCGAATATGTAAATCGCAACGCGAATCTGACT
1 ATCGCAACGCGAATATGTAAATCGCAACGCGAATCTGACT
* * * * * *
12830634 ATCGCAACGAGATTCTG-ACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGAATATGTA-AATCGCAACGCGAATCTGACT
12830674 ATCGCAACGCGA
1 ATCGCAACGCGA
12830686 TTCTGACTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.03
39 2 0.03
40 74 0.95
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (40 bp):
ATCGCAACGCGAATATGTAAATCGCAACGCGAATCTGACT
Found at i:12830640 original size:60 final size:61
Alignment explanation
Indices: 12830514--12830627 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 61
12830504 TTTTTCTAAT
* * * *
12830514 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAATACGTAAA
*
12830575 TCGCAATGCGA-ATACCTAAATCGCAATGCGAATATGTAAATCGCAACGCGAAT
1 TCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAAT
12830628 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 37 0.77
61 11 0.23
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (61 bp):
TCGCAATGCGATATACCTAAATCGCAATGCGAATACGTAAATCGCAACGCGAATACGTAAA
Found at i:12831551 original size:24 final size:24
Alignment explanation
Indices: 12831518--12831570 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
12831508 TATTCGAAAC
*
12831518 TTGATCTTGGTCAATACCCGGACT
1 TTGATATTGGTCAATACCCGGACT
* *
12831542 TTGATATTGGTCAATACTCGGATT
1 TTGATATTGGTCAATACCCGGACT
12831566 TTGAT
1 TTGAT
12831571 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (24 bp):
TTGATATTGGTCAATACCCGGACT
Found at i:12834010 original size:20 final size:20
Alignment explanation
Indices: 12833985--12834055 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
12833975 GACATTCATT
12833985 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCAGAA-A
*
12834005 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACGCAGAAA
*
12834025 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCAGAAA
12834045 TGACTATCGCA
1 TGACTATCGCA
12834056 TTGCGATTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 44 0.94
21 3 0.06
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCAGAAA
Found at i:12834075 original size:14 final size:14
Alignment explanation
Indices: 12834056--12834109 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
12834046 GACTATCGCA
12834056 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
12834070 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
12834087 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
12834103 TTGCGAT
1 TTGCGAT
12834110 AGTCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:12834093 original size:33 final size:34
Alignment explanation
Indices: 12834051--12834129 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 34
12834041 GAAATGACTA
**
12834051 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-TT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
12834084 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
*
12834118 TCGCGTTGCGAT
1 TCGCATTGCGAT
12834130 AGTCTGGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 29 0.69
34 13 0.31
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
Found at i:12834254 original size:14 final size:14
Alignment explanation
Indices: 12834235--12834271 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12834225 CATCAATTAA
12834235 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
12834249 ACAAATCATCTTTT
1 ACAAATCAACATTT
12834263 ACAAATCAA
1 ACAAATCAA
12834272 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:12835751 original size:21 final size:21
Alignment explanation
Indices: 12835727--12835783 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
12835717 GGATGATAGG
12835727 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGATAGGGGA
12835748 GGCCTCTTGAACGATAGGGGA
1 GGCCTCTTGAACGATAGGGGA
12835769 GGCCTCTTGAACGAT
1 GGCCTCTTGAACGAT
12835784 GACAGATGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.35, T:0.21
Consensus pattern (21 bp):
GGCCTCTTGAACGATAGGGGA
Found at i:12835755 original size:42 final size:42
Alignment explanation
Indices: 12835657--12835784 Score: 118
Period size: 42 Copynumber: 3.0 Consensus size: 42
12835647 TCTAGAATGT
* * *
12835657 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGA
* ** *
12835699 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
* **
12835741 TAGGG-GAGGCCTCTTGAACGAT-AGGGGAGGCCTCTTGAACGA
1 T-GGGAGAGGACTCTTGAACGATGACAGG-GGCCTCTTGAACGA
12835783 TG
1 TG
12835785 ACAGATGAGT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
41 4 0.06
42 61 0.86
43 6 0.08
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGA
Found at i:12836289 original size:20 final size:20
Alignment explanation
Indices: 12836266--12836410 Score: 133
Period size: 20 Copynumber: 7.5 Consensus size: 20
12836256 GAAACTTAAA
*
12836266 ATCGCAACGGGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
12836286 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
12836306 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
12836326 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
12836340 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
12836362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
12836382 ATTGCAATGC-AAATTTGACT
1 ATCGCAACGCGAAA-ATGACT
12836402 ATCGCAACG
1 ATCGCAACG
12836411 AGAGAATCGC
Statistics
Matches: 104, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
14 7 0.07
16 2 0.02
17 1 0.01
18 4 0.04
19 5 0.05
20 78 0.75
22 7 0.07
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:12836365 original size:76 final size:76
Alignment explanation
Indices: 12836276--12836426 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 76
12836266 ATCGCAACGG
* *
12836276 GAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAGAGAA
1 GAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAATTTGACTATCGCAACGAGAGAA
12836341 TCGCAATGCGC
66 TCGCAATGCGC
*
12836352 GAAAATGACTATCGCAACGCGAAAATGACTATTGCAATGCAAATTTGACTATCGCAACGAGAGAA
1 GAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAATTTGACTATCGCAACGAGAGAA
12836417 TCGCAATGCG
66 TCGCAATGCG
12836427 ATTTTCATTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.20
Consensus pattern (76 bp):
GAAAATGACTATCGCAACGCGAAAATGACTATCGCAATGCAAATTTGACTATCGCAACGAGAGAA
TCGCAATGCGC
Found at i:12836480 original size:20 final size:20
Alignment explanation
Indices: 12836453--12836572 Score: 123
Period size: 20 Copynumber: 5.6 Consensus size: 20
12836443 GCGATTCTTT
12836453 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
12836473 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
12836493 CGTTGCGATTTTGTTGTTGCGATTTTCT
1 CGTTGCGA-----TAG-T-C-ATTTTCG
*
12836521 CGTTGAGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
12836541 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
12836561 CATTGCGATAGT
1 CGTTGCGATAGT
12836573 AAACTATTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
20 62 0.75
21 1 0.01
22 1 0.01
23 2 0.02
25 2 0.02
26 1 0.01
27 1 0.01
28 13 0.16
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:12836525 original size:14 final size:14
Alignment explanation
Indices: 12836486--12836525 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12836476 TGCGATAGTC
*
12836486 ATTTTCGCGTTGCG
1 ATTTTCTCGTTGCG
* *
12836500 ATTTTGTTGTTGCG
1 ATTTTCTCGTTGCG
12836514 ATTTTCTCGTTG
1 ATTTTCTCGTTG
12836526 AGATAGTCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.07, C:0.15, G:0.25, T:0.53
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:12836537 original size:68 final size:68
Alignment explanation
Indices: 12836441--12836569 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 68
12836431 TCATTTCACA
* *
12836441 TTGCGATTCTTTCGTTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCGTTGCGATTTTG
1 TTGCGATTCTTTCGTTGAGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTTTG
12836506 TTG
66 TTG
*
12836509 TTGCGATT-TTCTCGTTGAGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATTCTT-TCGTTGAGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGAT
12836570 AGTAAACTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 2 0.04
68 55 0.96
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (68 bp):
TTGCGATTCTTTCGTTGAGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCGATTTTG
TTG
Found at i:12838472 original size:20 final size:20
Alignment explanation
Indices: 12838449--12838645 Score: 89
Period size: 20 Copynumber: 10.6 Consensus size: 20
12838439 TCTGAAACTT
*
12838449 AAAAGCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
12838469 AAAATCGTAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
12838489 ACTATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * * **
12838509 ACTATCGGAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
12838529 ACTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
*
12838545 --AATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
12838562 AAAATCACAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
12838582 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
12838602 ACTATCGC-A-ACG-CAA-G
1 AAAATCGCAACACGAAAATG
12838618 --AATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
12838635 AAAATCGCAAC
1 AAAATCGCAAC
12838646 GACAGAATCA
Statistics
Matches: 135, Mismatches: 31, Indels: 23
0.71 0.16 0.12
Matches are distributed among these distances:
14 10 0.07
15 2 0.01
16 11 0.08
17 2 0.01
18 4 0.03
19 21 0.16
20 85 0.63
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:12838509 original size:40 final size:40
Alignment explanation
Indices: 12838454--12838539 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
12838444 AACTTAAAAG
*
12838454 CGCAACACGAAAATGAAAATCGTAACACGAAAATGACTAT
1 CGCAACACGAAAATGAAAATCGGAACACGAAAATGACTAT
** * **
12838494 CGCAACACGAAAATGACTATCGGAACGCGAATTTGACTAT
1 CGCAACACGAAAATGAAAATCGGAACACGAAAATGACTAT
12838534 CGCAAC
1 CGCAAC
12838540 GCAAGAATCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.16
Consensus pattern (40 bp):
CGCAACACGAAAATGAAAATCGGAACACGAAAATGACTAT
Found at i:12838594 original size:73 final size:73
Alignment explanation
Indices: 12838471--12838645 Score: 278
Period size: 73 Copynumber: 2.4 Consensus size: 73
12838461 CGAAAATGAA
* ** * *
12838471 AATCGTAACACGAAAATGACTATCGCAACACGAAAATGACTATCGGAACGCGAATTTGACTATCG
1 AATCGCAACACG-AAATGAAAATCACAACACGAAAATGACTATCGCAACGCGAATTTGACTATCG
12838536 CAACGCAAG
65 CAACGCAAG
*
12838545 AATCGCAACGCGAAATGAAAATCACAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGC
1 AATCGCAACACGAAATGAAAATCACAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGC
12838610 AACGCAAG
66 AACGCAAG
*
12838618 AATCGCAACACGAAATGAAAATCGCAAC
1 AATCGCAACACGAAATGAAAATCACAAC
12838646 GACAGAATCA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
73 83 0.89
74 10 0.11
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (73 bp):
AATCGCAACACGAAATGAAAATCACAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGC
AACGCAAG
Found at i:12839019 original size:22 final size:22
Alignment explanation
Indices: 12838994--12839043 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
12838984 ATTTAGCCGA
* *
12838994 AGATGGATACTGATATCGTTGG
1 AGATGGAGACTGATATCGTCGG
* *
12839016 AGATGGGGACTGATTTCGTCGG
1 AGATGGAGACTGATATCGTCGG
12839038 AGATGG
1 AGATGG
12839044 GGACGAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.38, T:0.28
Consensus pattern (22 bp):
AGATGGAGACTGATATCGTCGG
Found at i:12839044 original size:22 final size:22
Alignment explanation
Indices: 12839002--12839047 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
12838992 GAAGATGGAT
*
12839002 ACTGATATCGTTGGAGATGGGG
1 ACTGATATCGTCGGAGATGGGG
*
12839024 ACTGATTTCGTCGGAGATGGGG
1 ACTGATATCGTCGGAGATGGGG
12839046 AC
1 AC
12839048 GAATGTCGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.39, T:0.26
Consensus pattern (22 bp):
ACTGATATCGTCGGAGATGGGG
Found at i:12839297 original size:21 final size:21
Alignment explanation
Indices: 12839273--12839318 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
12839263 TATTCGCATT
12839273 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
12839294 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
12839315 GCGA
1 GCGA
12839319 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:12841682 original size:2 final size:2
Alignment explanation
Indices: 12841675--12841710 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
12841665 GGTATCGTCC
12841675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
12841711 ATTATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12841896 original size:10 final size:10
Alignment explanation
Indices: 12841881--12841911 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
12841871 CATTTAATAA
12841881 AAAATATTTT
1 AAAATATTTT
12841891 AAAATATTTT
1 AAAATATTTT
12841901 AAAATATTTT
1 AAAATATTTT
12841911 A
1 A
12841912 TTTTAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAAATATTTT
Found at i:12843128 original size:30 final size:31
Alignment explanation
Indices: 12843065--12843145 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
12843055 TTTAAGGATC
* * *
12843065 AAATTGATATTTTATTTATAGTTTTGAGGTT
1 AAATTAATATTTTATTTAAAGTTTAGAGGTT
*
12843096 AAATTAGTATTTTATTTAAAGTTTAG-GGTT
1 AAATTAATATTTTATTTAAAGTTTAGAGGTT
* *
12843126 AAATTAATATTCTATCTAAA
1 AAATTAATATTTTATTTAAA
12843146 ACTTAAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.49
Consensus pattern (31 bp):
AAATTAATATTTTATTTAAAGTTTAGAGGTT
Found at i:12846958 original size:21 final size:21
Alignment explanation
Indices: 12846932--12846971 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12846922 CAGAACCCCA
*
12846932 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
12846953 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
12846972 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:12847006 original size:20 final size:21
Alignment explanation
Indices: 12846952--12847014 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
12846942 GATTCCCCTG
12846952 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
12846976 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
12846996 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
12847015 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:12854986 original size:46 final size:44
Alignment explanation
Indices: 12854929--12855126 Score: 139
Period size: 46 Copynumber: 4.4 Consensus size: 44
12854919 TTCATTGAGA
* *
12854929 GCATCCATTCATACTTATACTGCACCATTATGCATTTTCATTTATG
1 GCATCCTTTCATACCTATA-TGCACCATTATGCA-TTTCATTTATG
* * * * *
12854975 GCATTCTTTCATGCCAATATTGCACCCA-TATGCATTTCAATAATG
1 GCATCCTTTCATACCTATA-TGCA-CCATTATGCATTTCATTTATG
* * * * * *
12855020 GTATCCTTTCATGCCGATAATGTACC-TATATGTATTTTATTTATG
1 GCATCCTTTCATACCTAT-ATGCACCAT-TATGCATTTCATTTATG
* * * * * *
12855065 GCATCATTTCATTACCTTTTATACGCTATTATTCATTTCATTTATG
1 GCATCCTTTCA-TACC-TATATGCACCATTATGCATTTCATTTATG
12855111 GCATCCTTTCATACCT
1 GCATCCTTTCATACCT
12855127 TTTATACAAT
Statistics
Matches: 116, Mismatches: 29, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
44 3 0.03
45 53 0.46
46 55 0.47
47 5 0.04
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (44 bp):
GCATCCTTTCATACCTATATGCACCATTATGCATTTCATTTATG
Found at i:12855051 original size:45 final size:45
Alignment explanation
Indices: 12854949--12855076 Score: 114
Period size: 45 Copynumber: 2.8 Consensus size: 45
12854939 ATACTTATAC
* * * *
12854949 TGCA-CCATTATGCATTTTCATTTATGGCATTCTTTCATGCCAATAT
1 TGCACCCA-TATGCA-TTTCAATAATGGCATCCTTTCATGCCAATAA
* *
12854995 TGCACCCATATGCATTTCAATAATGGTATCCTTTCATGCCGATAA
1 TGCACCCATATGCATTTCAATAATGGCATCCTTTCATGCCAATAA
* * * * * * *
12855040 TGTACCTATATGTATTTTATTTATGGCATCATTTCAT
1 TGCACCCATATGCATTTCAATAATGGCATCCTTTCAT
12855077 TACCTTTTAT
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
45 54 0.81
46 10 0.15
47 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (45 bp):
TGCACCCATATGCATTTCAATAATGGCATCCTTTCATGCCAATAA
Found at i:12855250 original size:68 final size:68
Alignment explanation
Indices: 12855170--12855303 Score: 223
Period size: 68 Copynumber: 2.0 Consensus size: 68
12855160 TCATTTACTT
* * * *
12855170 AAAGGCATTTAGCCTTTCATCTGACTAGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTAGAATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
12855235 CTC
66 CTC
*
12855238 AAAGGCACTTAGCCTTTCATCTAACTGGAATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTAGAATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
12855303 C
66 C
12855304 ATTAATCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (68 bp):
AAAGGCACTTAGCCTTTCATCTAACTAGAATAATTGACACCTTTCTGTCAAATACACAGCTAGGC
CTC
Found at i:12855726 original size:54 final size:54
Alignment explanation
Indices: 12855642--12856700 Score: 1372
Period size: 54 Copynumber: 19.9 Consensus size: 54
12855632 TGCCTGTACA
* * * * * *
12855642 GTTATTCATCAAC-TCATGATGAATTCCGTGAATTGCATAATTAGTACCGAAACG
1 GTTATTCATCCACAT-AGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * * *
12855696 GTTATTCATCCATATAGGATAAATTTCGTGAAATGCACATTTAGTGCCGAAACA
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * * *
12855750 ATTATTCATCAACATATGATGAATTCCGTGATATGCACACTTAGTGTCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* *
12855804 ATTATTTATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * *
12855858 GTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTAAGTACCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
*
12855912 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACATTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * * *
12855966 GTTATTCATCCACATATGATGGATTTCGTGACATGTACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * * **
12856020 ATTATTAATCCACATAGGATGAATTCCGTGAATTACACACTTAGTATCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* *
12856074 GTTATTCATCCACATAGGATGAATTTCGTGAAATGCACACTTAGTGTCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
** *
12856128 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTATCGAAAAG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * *
12856182 GTTATTCATCAACATATGATGAATTCCGTGAAATACACACTTAGTGTCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* *
12856236 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTTCCGAAATG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
*
12856290 GTTATTCATCCACATA-G--G-ATTCCGTGAAATGCACACTTAGTGCTGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * **
12856340 GTTATTCATACACTTAGGATGAATTTTGTGAAATGCACACTTAGT---G--A--
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
**
12856387 -TTATTCATCCACATAGGATGAATTTTGTGAAATGCACACTTAGTGCCGAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* ** * *
12856440 GTTATTCATCAACATAGGATGAATTCCGTGAAACACACACTTAGTGTCAAAACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* ** *
12856494 GTTATTCATCCACATAGGATGAATTCCATGAAATGCACACTTAGTGTTGAAATG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * **
12856548 GTTATTCATCCATATAGGATGAATTCCGTGAAATGCAAACTTAGTGAAG-AACG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * * *
12856601 GTTATTCATCCACATAGGATGAATTCTGTGAAACGCACACTTAGTGCTGAAATG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
* * *
12856655 GTTATTCATCCACATCGGATAAATTCCATGAAATGCACACTTAGTG
1 GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTG
12856701 TCTATTTGGT
Statistics
Matches: 879, Mismatches: 112, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
46 42 0.05
49 2 0.00
50 43 0.05
51 4 0.00
53 48 0.05
54 739 0.84
55 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (54 bp):
GTTATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGCCGAAACG
Found at i:12856379 original size:27 final size:27
Alignment explanation
Indices: 12856349--12856429 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 27
12856339 GGTTATTCAT
12856349 ACACTTAGGATGAATTTTGTGAAATGC
1 ACACTTAGGATGAATTTTGTGAAATGC
* *
12856376 ACACTTA-G-TG-ATTAT-T--CAT-C
1 ACACTTAGGATGAATTTTGTGAAATGC
*
12856396 -CACATAGGATGAATTTTGTGAAATGC
1 ACACTTAGGATGAATTTTGTGAAATGC
12856422 ACACTTAG
1 ACACTTAG
12856430 TGCCGAAACG
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
19 5 0.12
20 2 0.05
21 4 0.10
22 4 0.10
23 2 0.05
24 4 0.10
25 4 0.10
26 2 0.05
27 13 0.32
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
ACACTTAGGATGAATTTTGTGAAATGC
Found at i:12861001 original size:44 final size:45
Alignment explanation
Indices: 12860929--12861014 Score: 138
Period size: 44 Copynumber: 1.9 Consensus size: 45
12860919 TTCCATACCA
*
12860929 ATAATGCACCCATATGCATTTCAATTATGGTATCCTTTCATGTCG
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGTCG
* *
12860974 ATAATG-ACCCATATGCATTTTATTTATGGCATCCTTTCATG
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
12861015 CCTTTTATAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 32 0.84
45 6 0.16
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGTCG
Found at i:12861173 original size:67 final size:68
Alignment explanation
Indices: 12861061--12861193 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 68
12861051 TCTTTTACTT
* * * * * *
12861061 AAAGGCATTTAGCCTTTCATCTAATTGGCATAATTGACATCTTTCTGTCAAATGCACAGCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATAAAATACACAGCTAGGC
12861126 CTC
66 CTC
* *
12861129 AAAGGCACTTAGTCTTTCATCTAACT-GCATAATTGACACCTTTCTATAAAATACATAGCTAGGC
1 AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATAAAATACACAGCTAGGC
12861193 C
66 C
12861194 ATTAATCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
67 34 0.60
68 23 0.40
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
AAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATAAAATACACAGCTAGGC
CTC
Found at i:12861534 original size:55 final size:54
Alignment explanation
Indices: 12861475--12861579 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 54
12861465 GTAATGCCTA
* *
12861475 TACGG-TAGTTCATAAACTCATGATGAATTCCGTGGATTTGCACACATAGTGTCTG
1 TACGGTTA-TTCAAAAACTCATGATGAATTCCGT-GAATTGCACACATAGTGTCTG
*
12861530 TACGGTTATTCAAAAACTCATGATGAATTCCGTGAATTGCACACTTAGTG
1 TACGGTTATTCAAAAACTCATGATGAATTCCGTGAATTGCACACATAGTG
12861580 CCGAAATGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
54 15 0.33
55 29 0.63
56 2 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (54 bp):
TACGGTTATTCAAAAACTCATGATGAATTCCGTGAATTGCACACATAGTGTCTG
Found at i:12861594 original size:54 final size:54
Alignment explanation
Indices: 12861551--12862510 Score: 1338
Period size: 54 Copynumber: 17.9 Consensus size: 54
12861541 AAAAACTCAT
* * *
12861551 GATGAATTCCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCCACATAT
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* **
12861605 GATGAATTCCGTGAAATGCACGCTTAGTGCCGAAACAATTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
12861659 GATGAATTCCGTGAAATGCACACTTAGTGTCGAAATGATTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * *
12861713 AATGAATTCCGTGAAATACACACTTAGTGCCGAAATGGTTCTTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* *
12861767 GATGAATTCCGTGAAATGCACACTTAATGCTGAAACGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
12861821 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAAAGATTATTCATCCACGTAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
*
12861875 GATGAATTCCATGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
12861929 GATGAATTCCTTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCAACATAA
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * ** * *
12861983 GATGAATTTCGTGAAATGCACACATAGTGATGAAATGGTTATTCATCCATATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* *
12862037 GATGAATTCCGTGAAATGCACACTTAGTACCGAAACGGTTATTAATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
*
12862091 GATGAATTCCGTGAAATGAACACTTAGTGCCGAAACGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * ** *
12862145 GATGAATTCCGTGAAATGCATACTTACTATCGAAAAGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * ** *
12862199 GATGAATTCCGTGAAATGCACATTTAATGCTTAAATGGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
** * *
12862253 GATGAATTTTGTGAAATGCACACTTAGTGCGGAAACGTTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * *
12862307 GATAAATTCTC-TTAAATGCACAATTAGTGCCGAAACGGTTATTCAT---C-TA-
1 GATGAATTC-CGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * * * *
12862356 CATGAATTCCGTGAAATGCACACTTAGTACCAAAACGGTTATTAATCCATATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* * **
12862410 GATGAATTTCGTGAAATGCATACTTAGTGCCGAAATAGTTATTCATCCACATAG
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
* *
12862464 GATGAATTCCGTGAAATGCACACTTAGTGTCGAAATGGTTATTCATC
1 GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATC
12862511 TTCAGTGAAA
Statistics
Matches: 796, Mismatches: 103, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
48 1 0.00
49 37 0.05
50 2 0.00
51 1 0.00
53 2 0.00
54 753 0.95
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
GATGAATTCCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAG
Found at i:12864229 original size:200 final size:199
Alignment explanation
Indices: 12863904--12864495 Score: 706
Period size: 199 Copynumber: 3.0 Consensus size: 199
12863894 CATGTGTATA
** * ** * *
12863904 GATACTTGATGGTTACGTATATTATCGTTATACCAGTAGATTTTTACCGTTT-TCATTGTAAATT
1 GATACTTGATATTTACGCATATTATCAATATATCGGTAGATTTTTACCGTTTAT-ATTGTAAATT
* * * *
12863968 AACCTATTACTTTACAGTAATAGGTTTTAAAATTATAAGTATCGATACTTTATATATGTGTATCG
65 TACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACTTTATACATGTGTATCG
* * * *
12864033 ATACATTTTGTGTATAAATTGTTTGAGAAGCATACTGGAATAAAAATATCGATACTTATATAGAC
130 ATAC-TTTTGTGTACAAATTGTTTGAGAAGCATACTGGAATAAAAGTATAGATACTTATATAAAC
12864098 AATATT
194 AATATT
* *
12864104 GATACTTGGTATTTACGCATATTATCAATATATCGGTAGACTTTTACCGTTTATATTGTAAATTT
1 GATACTTGATATTTACGCATATTATCAATATATCGGTAGATTTTTACCGTTTATATTGTAAATTT
* * * *
12864169 ACCAATAACTTTAAAGTAATTGGTTTCAAAATT-TCACGTATCGATACTTTATACATGTGTATCG
66 ACCTATTACTTTAAAGTAATAGGTTTCAAAATTAT-AAGTATCGATACTTTATACATGTGTATCG
* * * * * *
12864233 ATACTTTGTGAGTGCAAATTG-TTGAGAAGCATACTGGACTAAAAGTATAGATACCTATACAAAT
130 ATACTTT-TGTGTACAAATTGTTTGAGAAGCATACTGGAATAAAAGTATAGATACTTATATAAAC
*
12864297 ATTATT
194 AATATT
* * * * *
12864303 GATACTTGATGTTTATGCTTATTAT-AATTAAATCGGTAGATTTTTACCGTTTACATTGTAAATT
1 GATACTTGATATTTACGCATATTATCAA-TATATCGGTAGATTTTTACCGTTTATATTGTAAATT
** * * * *
12864367 TATGTATTACTTTATAGTAATAGGTGTCAAAATTATAAGTATCGATACTTTGTACATGTGTATTG
65 TACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACTTTATACATGTGTATCG
* * * *
12864432 ATACTTTTTTGCATACAAATTGTTTGAGATGCATACTAGAATAAAAGTATTGATACTTATATAA
130 ATACTTTTGTG--TACAAATTGTTTGAGAAGCATACTGGAATAAAAGTATAGATACTTATATAA
12864496 TAAGTATGAC
Statistics
Matches: 330, Mismatches: 54, Indels: 15
0.83 0.14 0.04
Matches are distributed among these distances:
198 4 0.01
199 159 0.48
200 131 0.40
201 36 0.11
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (199 bp):
GATACTTGATATTTACGCATATTATCAATATATCGGTAGATTTTTACCGTTTATATTGTAAATTT
ACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGATACTTTATACATGTGTATCGA
TACTTTTGTGTACAAATTGTTTGAGAAGCATACTGGAATAAAAGTATAGATACTTATATAAACAA
TATT
Found at i:12865709 original size:17 final size:17
Alignment explanation
Indices: 12865687--12865722 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12865677 AAAACAAGAT
12865687 ATTTGAAATTAGTTTTA
1 ATTTGAAATTAGTTTTA
12865704 ATTTGAAATTAGTTTTA
1 ATTTGAAATTAGTTTTA
12865721 AT
1 AT
12865723 GTCGGTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (17 bp):
ATTTGAAATTAGTTTTA
Found at i:12867812 original size:23 final size:23
Alignment explanation
Indices: 12867759--12867827 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
12867749 CACCACAACT
*
12867759 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * * **
12867782 AGTGGAATTGCACCGGAGTGCGG
1 CGTAGAATTGCACCGAAGTGCCA
* * *
12867805 CGTAGAATTACACAGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
12867828 TATAATAATG
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:12868489 original size:56 final size:55
Alignment explanation
Indices: 12868385--12868490 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 55
12868375 CATAAATCAT
* * * *
12868385 ATTCGATGTTTGTATTTAATGTGGTGCATCGATGCACTCTTTATGCATCGATGGC
1 ATTCGATGTTTGTATTTAAAGTAGTGCATCGATGCACTCATGATGCATCGATGGC
12868440 ATTCGATGTTTGTATTTTAAAAG-AGTGCATCGATGCACTTCATGA-GCATCG
1 ATTCGATGTTTGTA-TTT-AAAGTAGTGCATCGATGCAC-TCATGATGCATCG
12868491 GTACACCTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
55 14 0.32
56 23 0.52
57 7 0.16
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.38
Consensus pattern (55 bp):
ATTCGATGTTTGTATTTAAAGTAGTGCATCGATGCACTCATGATGCATCGATGGC
Found at i:12870525 original size:16 final size:17
Alignment explanation
Indices: 12870487--12870532 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
12870477 TGTTTATGAG
*
12870487 GGAACTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
12870505 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
12870521 GGAATTGGAATC
1 GGAATTGGAATC
12870533 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:12870599 original size:14 final size:14
Alignment explanation
Indices: 12870580--12870608 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12870570 TGGAATCCAA
12870580 TTCCATATTCTGTT
1 TTCCATATTCTGTT
12870594 TTCCATATTCTGTT
1 TTCCATATTCTGTT
12870608 T
1 T
12870609 GGTTCGCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.59
Consensus pattern (14 bp):
TTCCATATTCTGTT
Found at i:12871556 original size:221 final size:219
Alignment explanation
Indices: 12871169--12871682 Score: 813
Period size: 221 Copynumber: 2.4 Consensus size: 219
12871159 AAATCCGACT
* *
12871169 CGACTCGACCCGAATATCACACTT-AAAAAACCTGACCCGACCCGAACAAAATAAAGTTTCATCC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
*
12871233 GACCCGACCCGAATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAATTATT
66 GACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATT
*
12871298 TTTATTTAATAAAAACAGTGATTTAATCCGACCCGACCTGAATTATATATATTTT-GGAGTCGGT
131 TTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGG-GTCGGT
*
12871362 -CTGGTTTTTTCACACTAAACCCGAA
195 CCCGGTTTTTTCACACTAAACCCG-A
*
12871387 CCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAACTTTCAT
1 --CGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCAT
* *
12871452 CCGACCCTACCCGAATATATGAATTAGAAATCCAACCCGACCTGACCCGAAATAATAAAAAATTA
64 CCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTA
* *
12871517 TTTTTATTTAATAAAAACAGTGACTTAATCTGACCCGACCTGAATTATATATATTTTCGGTTCGG
129 TTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGG
* *
12871582 TCCCGTTTTTTTCACCCTAAACCCGA
194 TCCCGGTTTTTTCACACTAAACCCGA
* * * *
12871608 --ACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACTCGACCAAAATAAAGTTTCACCC
1 CGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
12871671 GACCCGACCCGA
66 GACCCGACCCGA
12871683 CCCGACCCAA
Statistics
Matches: 273, Mismatches: 18, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
217 69 0.25
220 23 0.08
221 159 0.58
222 22 0.08
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.24
Consensus pattern (219 bp):
CGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
GACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATT
TTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTC
CCGGTTTTTTCACACTAAACCCGA
Found at i:12876163 original size:23 final size:23
Alignment explanation
Indices: 12876136--12876199 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
12876126 CATCTCATAT
*
12876136 AATTGCACCAAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
12876159 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
12876182 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
12876200 TATAATAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:12881312 original size:20 final size:20
Alignment explanation
Indices: 12881287--12881339 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
12881277 ATCTTTTTAC
12881287 CGATTTTGTCAAATTGAAAT
1 CGATTTTGTCAAATTGAAAT
12881307 CGATTTTGTCAAATTGAAAT
1 CGATTTTGTCAAATTGAAAT
12881327 CGATTTTGTCAAA
1 CGATTTTGTCAAA
12881340 CTTCAACCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (20 bp):
CGATTTTGTCAAATTGAAAT
Found at i:12881508 original size:220 final size:215
Alignment explanation
Indices: 12881115--12881522 Score: 482
Period size: 220 Copynumber: 1.9 Consensus size: 215
12881105 GCTTTACCGG
* * *
12881115 TTTTGTCAAATTTCAACATGTTATATTGTCATGTAGATACATGTGTCTAAGGTATCGATACTTTA
1 TTTTGTCAAACTTCAACATGTTATATTATCATGTAGATACATGTGTCTAAGGTATCAATACTTTA
* *
12881180 TAGGCGCTATTATTGCACTTCTTTTAAATTCCTAAAATACCGATACTTTGGTGGATATACTTATA
66 TAGACGCTATTATTGCACTTCTTTTAAATTCCTAAAATACCGATACTTTGGTAGATATACTTATA
** * *
12881245 AAAGTGTCGATACAAATGTCAACTATTCTGGTATCTTTTTACCGATTTTGTCAAATTGAAATCGA
131 AAAGTGTCGATACAAATGTCAACTATTCCAGTAGCTCTTTACCGATTTTGTCAAATTGAAATCGA
12881310 TTTTGTCAAATTGAAATCGA
196 TTTTGTCAAATTGAAATCGA
* *
12881330 TTTTGTCAAACTTCAACCTGTTATATTATCATGTATCGATACATGTGTGTAAGGTATCAATACTT
1 TTTTGTCAAACTTCAACATGTTATATTATCATGTA--GATACATGTGTCTAAGGTATCAATACTT
** * * * * * * * *
12881395 T-TGAGACATTTTCCTTTTTTCATTTCTTTTAAATTCCTACAGTATCGATACTTTGGTATATATA
64 TAT-AGAC--GCT-ATTATTGCACTTCTTTTAAATTCCTAAAATACCGATACTTTGGTAGATATA
* * * *
12881459 TTTATACACA-TAG-CGATACAAATTTCAA-TAATTCCAGTAGCTCTTTACCGGTTTTGTCAAAT
125 CTTATA-AAAGT-GTCGATACAAATGTCAACT-ATTCCAGTAGCTCTTTACCGATTTTGTCAAAT
12881521 TG
187 TG
12881523 TAATAGGATT
Statistics
Matches: 159, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
215 32 0.20
216 1 0.01
217 30 0.19
219 2 0.01
220 91 0.57
221 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.41
Consensus pattern (215 bp):
TTTTGTCAAACTTCAACATGTTATATTATCATGTAGATACATGTGTCTAAGGTATCAATACTTTA
TAGACGCTATTATTGCACTTCTTTTAAATTCCTAAAATACCGATACTTTGGTAGATATACTTATA
AAAGTGTCGATACAAATGTCAACTATTCCAGTAGCTCTTTACCGATTTTGTCAAATTGAAATCGA
TTTTGTCAAATTGAAATCGA
Found at i:12881924 original size:20 final size:20
Alignment explanation
Indices: 12881830--12882198 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
12881820 GATTTTCCAT
* ** *
12881830 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
12881850 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
12881870 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12881890 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
12881910 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
12881930 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12881950 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12881970 AATCGCAACGCGTATCCTTA
1 AATCGCAACGCGTATCCGTA
* *
12881990 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
12882010 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12882030 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
12882050 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12882070 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
12882090 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
12882110 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
12882130 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
12882150 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
12882170 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
12882190 AATCACAAC
1 AATCGCAAC
12882199 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:12882910 original size:24 final size:24
Alignment explanation
Indices: 12882871--12882917 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
12882861 AAATTTGGTC
12882871 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
12882895 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
12882918 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:12883109 original size:12 final size:12
Alignment explanation
Indices: 12883092--12883116 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12883082 ATATAATCCT
12883092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12883104 GAAGAAGAAAAA
1 GAAGAAGAAAAA
12883116 G
1 G
12883117 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:12885444 original size:19 final size:19
Alignment explanation
Indices: 12885422--12885747 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
12885412 CGGAAAATAC
*
12885422 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12885441 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
12885455 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
12885475 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12885489 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885508 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12885527 AATCGCAAT--G--A-GAG
1 AATCGCAATGCGAAATGAA
12885541 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885560 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12885579 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
12885593 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
12885612 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
12885631 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
12885650 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885669 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885688 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
12885702 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885721 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
12885740 AATCGCAA
1 AATCGCAA
12885748 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 51 0.19
15 3 0.01
16 12 0.04
17 11 0.04
18 4 0.01
19 175 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:12885509 original size:33 final size:34
Alignment explanation
Indices: 12885422--12885747 Score: 328
Period size: 33 Copynumber: 9.2 Consensus size: 34
12885412 CGGAAAATAC
* *
12885422 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
12885455 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
12885489 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
* *
12885527 AATCGCAATGAGAGAATCG-CAAT-GCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACGATGAA
*
12885560 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
12885593 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
12885631 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
12885669 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
12885701 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
12885740 AATCGCAA
1 AATCGCAA
12885748 CGAGATAATC
Statistics
Matches: 253, Mismatches: 14, Indels: 47
0.81 0.04 0.15
Matches are distributed among these distances:
31 1 0.00
32 10 0.04
33 101 0.40
34 31 0.12
35 7 0.03
36 2 0.01
37 3 0.01
38 87 0.34
39 10 0.04
40 1 0.00
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:12885683 original size:161 final size:157
Alignment explanation
Indices: 12885450--12885769 Score: 543
Period size: 161 Copynumber: 2.0 Consensus size: 157
12885440 AAATCCCAAC
*
12885450 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
* *
12885515 ATGCGAAATGAAAATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
12885580 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
12885607 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
12885671 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
12885736 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
12885768 AT
1 AT
12885770 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 119 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:12885785 original size:52 final size:52
Alignment explanation
Indices: 12885450--12885769 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
12885440 AAATCCCAAC
12885450 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
12885503 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
12885555 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
12885607 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
12885664 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
12885716 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
12885768 AT
1 AT
12885770 TATAAACGCA
Statistics
Matches: 253, Mismatches: 9, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 182 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:12885885 original size:19 final size:19
Alignment explanation
Indices: 12885776--12885877 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
12885766 AAATTATAAA
12885776 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12885795 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
12885815 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
*
12885831 CG--TTGTGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12885848 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
12885867 CGCATTGCGAT
1 CGCATTGCGAT
12885878 AGTCATTTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 35 0.48
20 19 0.26
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:12886003 original size:14 final size:14
Alignment explanation
Indices: 12885984--12886020 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12885974 CATCAATTAC
12885984 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
12885998 ACAAATCATCTTTT
1 ACAAATCAACTTTT
12886012 ACAAATCAA
1 ACAAATCAA
12886021 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:12886032 original size:12 final size:12
Alignment explanation
Indices: 12886015--12886087 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
12886005 ATCTTTTACA
12886015 AATCAATTAAAC
1 AATCAATTAAAC
*
12886027 AATCAA--AAATTG
1 AATCAATTAAA--C
**
12886039 AATCAACTTTTAC
1 AATCAA-TTAAAC
12886052 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
12886065 AATCAA-AAAAC
1 AATCAATTAAAC
12886076 AATCAATTAAAC
1 AATCAATTAAAC
12886088 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:12886049 original size:38 final size:38
Alignment explanation
Indices: 12886001--12886073 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
12885991 AACTTTTACA
*
12886001 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
12886039 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
12886074 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:12887966 original size:14 final size:14
Alignment explanation
Indices: 12887947--12888003 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
12887937 GCGAAATGAA
*
12887947 AATCGCAACGACAG
1 AATCGCAACGAAAG
12887961 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
12887978 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
12887994 AATCGCAACG
1 AATCGCAACG
12888004 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:12887974 original size:33 final size:33
Alignment explanation
Indices: 12887928--12888020 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
12887918 GAGAAACCAA
*
12887928 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
12887961 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
12887994 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
12888021 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:12887985 original size:19 final size:19
Alignment explanation
Indices: 12887891--12888025 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
12887881 TAGTTTACTT
* *
12887891 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
12887911 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
12887930 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
12887949 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
12887963 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
12887982 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
12887996 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
12888015 TCGCAATGCGA
1 TCGCAACGCGA
12888026 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 16 0.17
16 11 0.12
17 11 0.12
19 46 0.48
20 11 0.12
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:12888043 original size:19 final size:19
Alignment explanation
Indices: 12888021--12888149 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
12888011 AAAATCGCAA
12888021 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
12888040 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
12888054 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
12888073 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
12888087 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
12888106 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
12888125 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
12888145 TGCGA
1 TGCGA
12888150 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:12888063 original size:33 final size:33
Alignment explanation
Indices: 12888021--12888112 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
12888011 AAAATCGCAA
12888021 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
12888054 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
12888087 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
12888113 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:12888352 original size:93 final size:93
Alignment explanation
Indices: 12888193--12888850 Score: 1293
Period size: 93 Copynumber: 7.1 Consensus size: 93
12888183 TTGAATGGAT
12888193 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888258 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888286 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888351 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888379 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888443 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888471 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888536 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888564 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
12888629 AGTTTAGCAGAATTGGTAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888657 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888721 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888749 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888814 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
12888842 AAATTTACT
1 AAATTTACT
12888851 AAGCAATCTA
Statistics
Matches: 561, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 183 0.33
93 378 0.67
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:12888506 original size:185 final size:186
Alignment explanation
Indices: 12888193--12888850 Score: 1293
Period size: 185 Copynumber: 3.5 Consensus size: 186
12888183 TTGAATGGAT
12888193 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888258 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
12888323 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
12888379 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888443 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
12888508 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
12888564 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
12888629 AGTTTAGCAGAATTGGTAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
12888694 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
12888749 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888814 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
12888851 AAGCAATCTA
Statistics
Matches: 469, Mismatches: 2, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
185 339 0.72
186 130 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:12888690 original size:278 final size:278
Alignment explanation
Indices: 12888193--12888850 Score: 1307
Period size: 278 Copynumber: 2.4 Consensus size: 278
12888183 TTGAATGGAT
12888193 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888258 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
12888323 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
12888388 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
12888453 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
12888471 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888536 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
12888601 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGTAGCAACCGAACAAATTTACT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
12888666 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
196 TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
12888731 AATTGGCAGCAACCGAAC
261 AATTGGCAGCAACCGAAC
12888749 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
12888814 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
12888851 AAGCAATCTA
Statistics
Matches: 379, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 379 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
TTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGCAG
AATTGGCAGCAACCGAAC
Found at i:12890575 original size:14 final size:14
Alignment explanation
Indices: 12890556--12890645 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
12890546 TTGAAATGAA
12890556 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12890570 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
12890587 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
12890603 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
12890622 AATCGCAACGAGAG
1 AATCGCAACGAGAG
12890636 AATCGCAACG
1 AATCGCAACG
12890646 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:12890593 original size:33 final size:33
Alignment explanation
Indices: 12890548--12890662 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
12890538 TCTTTTGGTT
12890548 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
12890581 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
12890614 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
12890647 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
12890663 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:12890594 original size:19 final size:18
Alignment explanation
Indices: 12890555--12890667 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
12890545 GTTGAAATGA
12890555 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
12890570 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
12890587 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
12890603 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
12890620 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
12890636 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
12890653 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
12890668 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:12890698 original size:14 final size:14
Alignment explanation
Indices: 12890679--12890733 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
12890669 TTTGGTTTCG
12890679 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
12890693 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
12890712 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
12890726 CGTTGCGA
1 CGTTGCGA
12890734 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:12890711 original size:33 final size:33
Alignment explanation
Indices: 12890663--12890733 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
12890653 AAAATCGCAA
**
12890663 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
12890696 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
12890729 TGCGA
1 TGCGA
12890734 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:12890741 original size:33 final size:33
Alignment explanation
Indices: 12890674--12890755 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
12890664 GCGATTTTGG
***
12890674 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
12890707 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
12890740 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
12890756 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:12890760 original size:20 final size:20
Alignment explanation
Indices: 12890686--12890774 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
12890676 TCGCGTTGCG
12890686 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
12890706 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
12890719 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
12890739 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
12890759 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
12890775 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:12890896 original size:33 final size:33
Alignment explanation
Indices: 12890854--12890924 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
12890844 AATACTAACT
*
12890854 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
12890887 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
12890920 TGAAA
1 TGAAA
12890925 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:12891158 original size:22 final size:22
Alignment explanation
Indices: 12891106--12891160 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
12891096 TGGTTGTGAG
**
12891106 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
12891128 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
12891150 GGATTTCTTCG
1 GGATTTCTTCG
12891161 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:12891331 original size:20 final size:20
Alignment explanation
Indices: 12891306--12891499 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
12891296 CTTTAAATAT
12891306 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
12891326 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
12891348 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
12891367 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
12891387 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
12891407 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
12891427 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
12891447 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
12891467 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
12891487 CGCGTTGCGATTT
1 CGCGTTGCGATTT
12891500 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:12891493 original size:60 final size:60
Alignment explanation
Indices: 12891306--12891499 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
12891296 CTTTAAATAT
**
12891306 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
12891367 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
12891427 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
12891487 CGCGTTGCGATTT
1 CGCGTTGCGATTT
12891500 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:12891516 original size:21 final size:20
Alignment explanation
Indices: 12891492--12891568 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
12891482 ATATTCGCGT
12891492 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
12891513 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
12891533 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
12891555 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
12891569 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:12891579 original size:20 final size:20
Alignment explanation
Indices: 12891554--12891605 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
12891544 AAGAATCGCG
*
12891554 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
12891574 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
12891594 TTGCGATTCTGG
1 TTGCGATTCTGG
12891606 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:12895168 original size:16 final size:16
Alignment explanation
Indices: 12895147--12895183 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
12895137 AGACTTATTA
12895147 AAAAAATAAGAAAAAT
1 AAAAAATAAGAAAAAT
* *
12895163 AAAAAATAATAATAAT
1 AAAAAATAAGAAAAAT
12895179 AAAAA
1 AAAAA
12895184 TATCAGCGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAATAAGAAAAAT
Found at i:12897630 original size:16 final size:17
Alignment explanation
Indices: 12897609--12897643 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12897599 TTGAAAATCT
12897609 AAATATAAT-TTAATTA
1 AAATATAATATTAATTA
*
12897625 AAATATAATATTTATTA
1 AAATATAATATTAATTA
12897642 AA
1 AA
12897644 CATTAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATAATATTAATTA
Found at i:12898035 original size:15 final size:15
Alignment explanation
Indices: 12897980--12898057 Score: 86
Period size: 15 Copynumber: 5.2 Consensus size: 15
12897970 TCTCCGTTTA
*
12897980 TATTATTATATGTAT
1 TATTATTATATATAT
* *
12897995 TATTAAT-TATACAT
1 TATTATTATATATAT
*
12898009 TATTACTTATATATTT
1 TATTA-TTATATATAT
* *
12898025 TTTTATTATATACAT
1 TATTATTATATATAT
12898040 TATTATTATATATAT
1 TATTATTATATATAT
12898055 TAT
1 TAT
12898058 AATATTAGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
14 10 0.20
15 31 0.62
16 9 0.18
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (15 bp):
TATTATTATATATAT
Found at i:12898063 original size:17 final size:17
Alignment explanation
Indices: 12898028--12898088 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 17
12898018 TATATTTTTT
*
12898028 TATTATATACATTAT--
1 TATTATATATATTATAA
12898043 TATTATATATATTATAA
1 TATTATATATATTATAA
12898060 TATTAGTAT-TATTAAATAA
1 TATTA-TATATATT--ATAA
*
12898079 TATTACATAT
1 TATTATATAT
12898089 GACCCGGAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 14 0.37
17 9 0.24
18 5 0.13
19 10 0.26
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (17 bp):
TATTATATATATTATAA
Done.