Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold7
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: 6555642
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 349864 characters in sequence are not A, C, G, or T
File 32 of 37
Found at i:5549710 original size:24 final size:20
Alignment explanation
Indices: 5549591--5549695 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
5549581 AAAAAGATAG
* *
5549591 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGAAA
*
5549611 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
5549631 AATGTATCGATACGTTTAGGTAAAAGAGAA
1 AATGTATCGATAC----A--T---TGA-AA
5549661 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
5549681 AATGTATCGATACAT
1 AATGTATCGATACAT
5549696 CTGGGTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
20 46 0.67
21 2 0.03
24 2 0.03
26 2 0.03
29 2 0.03
30 15 0.22
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:5550885 original size:32 final size:32
Alignment explanation
Indices: 5550849--5550918 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
5550839 GACTTGCATA
* *
5550849 GGCTTTAAAAAAAGGTGCCACTAACTTATGTG
1 GGCTTTAAAAAAAGGTACCACCAACTTATGTG
* * * * *
5550881 GGCTTTGAAAAGAGTTACCACCGACTTGTGTG
1 GGCTTTAAAAAAAGGTACCACCAACTTATGTG
5550913 GGCTTT
1 GGCTTT
5550919 GAAAGGGTGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (32 bp):
GGCTTTAAAAAAAGGTACCACCAACTTATGTG
Found at i:5551257 original size:197 final size:196
Alignment explanation
Indices: 5550860--5551434 Score: 702
Period size: 197 Copynumber: 2.9 Consensus size: 196
5550850 GCTTTAAAAA
* * *
5550860 AAGG-TGCCACTAACTTATGTGGGCTTTGAAAAGAGTTACCACCGACTTGTGTGGGCTTTGAAAG
1 AAGGATGCCACTGAC-T-TGTGGGCTTTGAAAAGA--TACCACTGAC-T-TGTGGGCTTTGAAAA
* * * * * *
5550924 GGTGCCACTGACTTGTGGGTTTTGAGAAGGATGCCACTGACTTATGGGCGTTGAAAGGATGCCAC
60 GATGCCACTAACTTGTGGGCTTTGA-AAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCAC
* * * * *
5550989 TGACTTATGGGCTTTGAAAAGATGCCATTGACTTATAGGCTTTAAAAAGATGCCACTAACTTGTA
124 TGACTTGT-GGCTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTAACTTATA
5551054 GGCTTTGAG
188 GGCTTTGAG
* *
5551063 AAGGATGCCATTGACTTGTGAGCTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGATGCC
1 AAGGATGCCACTGACTTGTGGGCTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGATGCC
** * *
5551128 ACTAACTAATGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAAAGGATGACACTGACTTG
66 ACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* * * * * *
5551193 TGAGCTTTGAAGAGATGCCACTAACTTGTGGGCTTTGAAAAGATGCCATTGACTTATGGGCTTTG
131 TG-GCTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTAACTTATAGGCTTTG
5551258 AG
195 AG
*** * * *
5551260 AAGGATGCCACTGACTTGTGGGCTTTGAGGGGATGCCATTGACTTGTGGGCTTTGAAGAGATGCC
1 AAGGATGCCACTGACTTGTGGGCTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGATGCC
* * * * *
5551325 CCTAACTTGTGGGCTTTGAAGAGATGCCTCTGACCTGTGGGCTTTGAAAAGATGCCACTGACTTG
66 ACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
* *
5551390 TGGTTTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAGAGATG
131 TGG-CTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGATG
5551435 AATGTTGTAG
Statistics
Matches: 321, Mismatches: 48, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
196 2 0.01
197 246 0.77
198 34 0.11
199 1 0.00
200 9 0.03
202 16 0.05
203 5 0.02
204 8 0.02
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (196 bp):
AAGGATGCCACTGACTTGTGGGCTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAGATGCC
ACTAACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTG
TGGCTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTAACTTATAGGCTTTGA
G
Found at i:5551433 original size:28 final size:28
Alignment explanation
Indices: 5550858--5551434 Score: 641
Period size: 28 Copynumber: 20.3 Consensus size: 28
5550848 AGGCTTTAAA
* *
5550858 AAAAGGTGCCACTAACTTATGTGGGCTTTG
1 AAAAGATGCCACTGAC-T-TGTGGGCTTTG
* *
5550888 AAAAGAGTTACCACCGACTTGTGTGGGCTTTG
1 AAAAGA--TGCCACTGAC-T-TGTGGGCTTTG
* * *
5550920 AAAGGGTGCCACTGACTTGTGGGTTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
5550948 AGAAGGATGCCACTGACTTATGGGCGTTG
1 A-AAAGATGCCACTGACTTGTGGGCTTTG
* *
5550977 AAAGGATGCCACTGACTTATGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * * *
5551005 AAAAGATGCCATTGACTTATAGGCTTTA
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
5551033 AAAAGATGCCACTAACTTGTAGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
5551061 AGAAGGATGCCATTGACTTGTGAGCTTTG
1 A-AAAGATGCCACTGACTTGTGGGCTTTG
*
5551090 AAAAGATACCACTGACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* **
5551118 AAAAGATGCCACTAACTAATGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
5551146 AAAAGATGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
5551174 AAAGGATGACACTGACTTGTGAGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
5551202 AAGAGATGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* *
5551230 AAAAGATGCCATTGACTTATGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
5551258 AGAAGGATGCCACTGACTTGTGGGCTTTG
1 A-AAAGATGCCACTGACTTGTGGGCTTTG
*** *
5551287 AGGGGATGCCATTGACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
5551315 AAGAGATGCCCCTAACTTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
5551343 AAGAGATGCCTCTGACCTGTGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
**
5551371 AAAAGATGCCACTGACTTGTGGTTTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
5551399 AAAAGATGCCACTGACTTATGGGCTTTG
1 AAAAGATGCCACTGACTTGTGGGCTTTG
*
5551427 AAGAGATG
1 AAAAGATG
5551435 AATGTTGTAG
Statistics
Matches: 468, Mismatches: 74, Indels: 12
0.84 0.13 0.02
Matches are distributed among these distances:
28 358 0.76
29 73 0.16
30 13 0.03
32 24 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (28 bp):
AAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:5552105 original size:19 final size:19
Alignment explanation
Indices: 5552081--5552148 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
5552071 AATTCAACAA
5552081 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
5552100 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
5552115 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
5552132 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
5552149 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:5552120 original size:13 final size:13
Alignment explanation
Indices: 5552102--5552126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5552092 ACATAAGTTT
5552102 TGTATCGATACAA
1 TGTATCGATACAA
5552115 TGTATCGATACA
1 TGTATCGATACA
5552127 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5552124 original size:32 final size:32
Alignment explanation
Indices: 5552083--5552145 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5552073 TTCAACAATT
*
5552083 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
5552115 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
5552146 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:5552206 original size:13 final size:13
Alignment explanation
Indices: 5552188--5552213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5552178 CATTTTTCTG
5552188 TGTATCGATACAT
1 TGTATCGATACAT
5552201 TGTATCGATACAT
1 TGTATCGATACAT
5552214 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5552210 original size:33 final size:33
Alignment explanation
Indices: 5552168--5552234 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5552158 GCCAAGGAAA
***
5552168 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
5552201 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
5552234 T
1 T
5552235 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:5554706 original size:54 final size:50
Alignment explanation
Indices: 5554582--5554970 Score: 159
Period size: 51 Copynumber: 7.4 Consensus size: 50
5554572 CTCAATTCTC
* * * * *
5554582 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAACACAAATTTT
*
5554632 CTATAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATCTCC---AAAACA-CAAATTTT
* ***
5554687 CACAATCGGGGATACTCCAAC-CCTG-TTAATCATCGGGGATACTCC--AACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCC-GATT--T--T-----AT-CTCCAAAACACAAAT-TTT
** * * * * ** *
5554745 C-TGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAACA-CAAATTTT
* * * * *
5554793 CATAATCGGGGATACTCCAACCCCGGTTTTAT-TGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATCT-CCAAAACAC-AAATTTT
* * * *
5554844 CCACAATCGGGGATACTCCAACCCCAGA-TTTATTTTCAAAACACCAATTTTT
1 -CACAATCGGGGATACTCCAACTCC-GATTTTATCTCCAAAACA-CAAATTTT
* * *
5554896 C-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCCAACTCCGATTTTATCTCC-AAAACA-CAAATTTT
* *
5554950 CATAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
5554971 CTCGTTGTCT
Statistics
Matches: 266, Mismatches: 36, Indels: 72
0.71 0.10 0.19
Matches are distributed among these distances:
46 3 0.01
47 2 0.01
48 6 0.02
49 4 0.02
50 3 0.01
51 67 0.25
52 61 0.23
53 35 0.13
54 41 0.15
55 24 0.09
56 3 0.01
57 4 0.02
58 7 0.03
62 2 0.01
63 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAACACAAATTTT
Found at i:5554721 original size:27 final size:28
Alignment explanation
Indices: 5554691--5554766 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
5554681 AATTTTCACA
*
5554691 ATCGGGGATACTCCAACCCTGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
5554718 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
5554746 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
5554767 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:5554929 original size:53 final size:52
Alignment explanation
Indices: 5554585--5554971 Score: 265
Period size: 52 Copynumber: 7.4 Consensus size: 52
5554575 AATTCTCCAC
* * * * *
5554585 AATCGGGGATATTCCAACTCCGATTTTATTTTC-AAGACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTC-AT
* * * *
5554636 AATCGGGGATACTCCAACTCCGATTTTATCTCCAAAAAAACACCAAATTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAAACACCAATTTTTCAT
* * * *** * *
5554690 AATCGGGGATACTCCAACCCTG--TTAATCATCGGGGATACTCCAACCCCGTTATTTC-T
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAA-----TT-TTTCAT
* * * ***
5554747 GA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCAT
* * * * *
5554796 AATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTT-CAT
* *
5554848 AATCGGGGATACTCCAACCCCAGA-TTTATTTTC-AAAACACCAATTTTTCCTTT
1 AATCGGGGATACTCCAACCCC-GATTTTATTTCCAAAAACACCAATTTTT-C-AT
* *
5554901 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCAT
*
5554953 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
5554972 TCGTTGTCTC
Statistics
Matches: 264, Mismatches: 48, Indels: 47
0.74 0.13 0.13
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 3 0.01
51 64 0.24
52 74 0.28
53 35 0.13
54 46 0.17
55 22 0.08
56 2 0.01
57 6 0.02
58 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCAT
Found at i:5554963 original size:105 final size:103
Alignment explanation
Indices: 5554751--5554971 Score: 266
Period size: 105 Copynumber: 2.1 Consensus size: 103
5554741 ATTTCTGAGG
* ***
5554751 GGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
* * * * *
5554816 CGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG
66 CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
* *
5554854 GGATACTCCAACCCCAGA-TTTATTTTCAAAACACCAATTTTTCCTTTAATCGGGGATACTCCAA
1 GGATACTCCAACCCC-GACTTTATTTCCAAAACACCAATTTTT-C-ATAATCGGGGATACTCCAA
* * *
5554918 CTCCGATTTTATTTCCAAAAATACCAATTTTT-CATAATCGA
63 CCCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA
5554959 GGATACTCCAACC
1 GGATACTCCAACC
5554972 TCGTTGTCTC
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
103 34 0.34
104 3 0.03
105 47 0.47
106 16 0.16
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.33
Consensus pattern (103 bp):
GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:5555047 original size:263 final size:262
Alignment explanation
Indices: 5554580--5555080 Score: 740
Period size: 263 Copynumber: 1.9 Consensus size: 262
5554570 TTCTCAATTC
* * * *
5554580 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
5554645 TACTCCAACTCCGATTTTATCTCCAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATCTCC-AAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCC
* * *
5554710 TGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATT
130 TGTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* *
5554775 TCCAAAATATTGATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
195 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
5554840 TTT
260 TTT
*
5554843 TCCACAATCGGGGATACTCCAACCCCAGA-TTTATTTTCAAAACACCAATTTTTCCTTTAATCGG
1 TCCACAATCGGGGATACTCCAACCCC-GATTTTATTTTCAAAACACCAA-TTTT-CTATAATCGG
* * * *
5554907 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTTTTCATAATCGAGGATACTCCAA-
63 GGATACTCCAACTCCGATTTTATCTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
** * *
5554970 CCTCGTTGTCTCATCGGGGATACTCCAA-CCCATTACTTCCGAGGGGATACTCCGACCCCGGCTT
128 CCT-GTT-AATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTT
*
5555034 TATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
191 TATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
5555081 TTATTTTCGA
Statistics
Matches: 213, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
262 3 0.01
263 151 0.71
264 24 0.11
265 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATCTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCT
GTTAATCATCGGGGATACTCCAACCCCATTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:5562106 original size:13 final size:13
Alignment explanation
Indices: 5562088--5562113 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5562078 TACAGCAAGT
5562088 ATGTATCGATACA
1 ATGTATCGATACA
5562101 ATGTATCGATACA
1 ATGTATCGATACA
5562114 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5564373 original size:21 final size:21
Alignment explanation
Indices: 5564340--5564384 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5564330 TTGCAAGTTG
*
5564340 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5564362 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5564382 AAA
1 AAA
5564385 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5566208 original size:15 final size:15
Alignment explanation
Indices: 5566188--5566218 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5566178 TAAAAATGTC
*
5566188 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
5566203 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
5566218 C
1 C
5566219 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:5568316 original size:13 final size:13
Alignment explanation
Indices: 5568298--5568336 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5568288 CATTTTTTCT
5568298 TTGTATCGATACA
1 TTGTATCGATACA
5568311 TTGTATCGATACA
1 TTGTATCGATACA
5568324 TTGTATCGATACA
1 TTGTATCGATACA
5568337 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5570898 original size:13 final size:13
Alignment explanation
Indices: 5570880--5570905 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5570870 TACAGCAAGT
5570880 ATGTATCGATACA
1 ATGTATCGATACA
5570893 ATGTATCGATACA
1 ATGTATCGATACA
5570906 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5571830 original size:17 final size:17
Alignment explanation
Indices: 5571808--5571841 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5571798 CAGAGGTAAG
*
5571808 AAGGAAGGCAAAGTCAA
1 AAGGAAGCCAAAGTCAA
*
5571825 AAGGAAGCCACAGTCAA
1 AAGGAAGCCAAAGTCAA
5571842 GAATCGATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.18, G:0.26, T:0.06
Consensus pattern (17 bp):
AAGGAAGCCAAAGTCAA
Found at i:5577512 original size:14 final size:13
Alignment explanation
Indices: 5577489--5577542 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
5577479 CCTTCTCTTC
5577489 AAAAAAAAAAGCA
1 AAAAAAAAAAGCA
5577502 AAAAGAAAAAAG-A
1 AAAA-AAAAAAGCA
5577515 AAAAAACAAAA-CA
1 AAAAAA-AAAAGCA
5577528 AAAAAACAAAA-CA
1 AAAAAA-AAAAGCA
5577541 AA
1 AA
5577543 GTAAAAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.05
13 29 0.76
14 7 0.18
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGCA
Found at i:5577517 original size:13 final size:12
Alignment explanation
Indices: 5577489--5577566 Score: 57
Period size: 13 Copynumber: 6.1 Consensus size: 12
5577479 CCTTCTCTTC
5577489 AAAAAAAAAAGCA
1 AAAAAAAAAAG-A
5577502 AAAAGAAAAAAGA
1 AAAA-AAAAAAGA
*
5577515 AAAAAACAAAACA
1 AAAAAA-AAAAGA
*
5577528 AAAAAACAAAACA
1 AAAAAA-AAAAGA
** *
5577541 AAGTAAAAGAGA
1 AAAAAAAAAAGA
*
5577553 GAAAAGAAAAAGA
1 -AAAAAAAAAAGA
5577566 A
1 A
5577567 CCTGCTTAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
12 7 0.13
13 39 0.74
14 7 0.13
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:5578693 original size:60 final size:59
Alignment explanation
Indices: 5578535--5579465 Score: 946
Period size: 60 Copynumber: 16.3 Consensus size: 59
5578525 TCTTTTTAGC
* * **
5578535 CCTCAAAGAGCATGATGCCTTTTCCTTTTAAAGCCCACAAAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
*
5578595 CCTCAAAGAGCAAGA--CAC----CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGATGC-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGT
*
5578650 CCTTAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGT
*
5578710 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGT
* **
5578770 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
* * **
5578829 CCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
* * *
5578888 CCTCAAAGAGCATGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* * * *
5578949 CCCCAAAGAGTAGGACG-C----CTTTTAAAGCCCACACAAATTGGTGGCATTTTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* * * **
5579004 CCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
* *
5579063 CCTCAAAGAG-AGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT-AGT
1 CCTCAAAGAGCA-GGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* * ** *
5579122 CCTCAAATAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTAATGGCACCTTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* * ** *
5579183 CCCCAAAGAGCAGGA--CC---CCTTTCGAAGCCCACACAAGTTGGTGGAATTTTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
* * **
5579238 CCCCAAAGAGCAGGA--CC---CCTTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
**
5579293 CCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGG------CA-T
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
5579340 CCTCAAAGAGCAGGA--CAC----CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CCTCAAAGAGCAGGATGC-CTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGT
** * * *
5579395 CCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACGAGTTAGTGGCACTTTTTAGT
1 CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGT
5579450 CCTCAAAGAGCAGGAT
1 CCTCAAAGAGCAGGAT
5579466 ACGCTTTATT
Statistics
Matches: 762, Mismatches: 64, Indels: 95
0.83 0.07 0.10
Matches are distributed among these distances:
43 1 0.00
45 1 0.00
46 1 0.00
47 37 0.05
48 2 0.00
54 31 0.04
55 229 0.30
56 15 0.02
57 4 0.01
58 1 0.00
59 169 0.22
60 234 0.31
61 37 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (59 bp):
CCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGT
Found at i:5578992 original size:234 final size:231
Alignment explanation
Indices: 5578527--5579465 Score: 1124
Period size: 234 Copynumber: 4.1 Consensus size: 231
5578517 CTCCTTTCTC
* * *
5578527 TTTTT-AGCCCTCAAAGAGCATGATGCCTTTTCCTTTTAAAGCCCACAAAAGTTGGTGGCACCTT
1 TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-CTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * **
5578591 CAGTCCTCAAAGAGCAAGAC-AC---CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
65 CAGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCC
* * * *
5578652 TTAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAA
129 TCAAAGAGCAGGATGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCCCAAA
5578717 GAGCAGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
193 GAGCAGGACGCC-TTTC----AAAGCCCACACAAGTTGGTGGCA
* *
5578761 TTTTCCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
5578826 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCT
66 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
*
5578891 CAAAGAGCATGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
130 CAAAGAGCAGGATGCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCCCAAA
* * *
5578956 GAGTAGGACGCCTTTTAAAGCCCACACAAATTGGTGGCA
193 GAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
5578995 TTTTTCAGTCCTCAAAGAGCGGGACGCATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
5579060 AGTCCTCAAAGAG-AGGGATGCCTTTTCTTTTAAAGCCCACCCAAGTTGGTGGCACCTTTAGTCC
66 AGTCCTCAAAGAGCA-GGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCC
* **
5579124 TCAAATAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTAATGGCACCTTTCAGTCCCCAA
129 TCAAAGAGCAGGATGCTTTTTCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCCCAA
* * *
5579189 AGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGAA
192 AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * ** **
5579229 TTTTTCAGTCCCCAAAGAGCAGGA--CC---CCTTTCGAAGCCCACACAAGTTGGTGGCATTTTT
1 TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTT
*
5579289 CAGTCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGG------CA-TCCT
65 CAGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCT
** * *
5579343 CAAAGAGCAGGA--C---ACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAG
130 CAAAGAGCAGGATGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCCCAAAG
* * *
5579403 AGCAGGACACCTTTCAAAGCCCACACGAGTTAGTGGCA
194 AGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
5579441 CTTTTT-AGTCCTCAAAGAGCAGGAT
1 -TTTTTCAGTCCTCAAAGAGCAGGAT
5579466 ACGCTTTATT
Statistics
Matches: 633, Mismatches: 58, Indels: 49
0.86 0.08 0.07
Matches are distributed among these distances:
211 3 0.00
212 82 0.13
213 10 0.02
216 1 0.00
218 15 0.02
219 1 0.00
225 20 0.03
229 30 0.05
230 21 0.03
231 1 0.00
232 1 0.00
233 1 0.00
234 315 0.50
235 24 0.04
238 32 0.05
239 72 0.11
240 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (231 bp):
TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
AAAGAGCAGGATGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCCCAAAGAG
CAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:5579001 original size:55 final size:56
Alignment explanation
Indices: 5578559--5579464 Score: 841
Period size: 55 Copynumber: 15.9 Consensus size: 56
5578549 ATGCCTTTTC
* ** * *
5578559 CTTTTAAAGCCCACAAAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAAGACAC-
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
* * *
5578613 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG-C---T
5578673 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTC-AGTCCTCAAAGAGCAGGACG-C---T
* * *
5578733 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG-C---T
**
5578793 CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACG-C---T
* ** * *
5578852 CTTTTAAAGCCCACCCAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCATGATGCTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGC----T
** * *
5578911 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGGACGC-
1 CTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
* *
5578967 CTTTTAAAGCCCACACAAATTGGTGGCATTTTTCAGTCCTCAAAGAGCGGGACGCATTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGC----T
** *
5579027 CTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAG-AGGGATGCCTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCA-GGACG-C---T
* ** * *
5579086 CTTTTAAAGCCCACCCAAGTTGGTGGCACCTTT-AGTCCTCAAATAGCAGGATGCTTTTT
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGC----T
** ** * *
5579145 CTTTTCAAAGCCCACACAAGTTAATGGCACCTTTCAGTCCCCAAAGAGCAGGAC-CC
1 CTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
** * * *
5579201 CTTTCGAAGCCCACACAAGTTGGTGGAATTTTTCAGTCCCCAAAGAGCAGGAC-CC
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
** *
5579256 CTTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACAC-
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
* *
5579311 CTTTCAAAGCCCACACAAGTTGGTGG-------CA-TCCTCAAAGAGCAGGACAC-
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
* *
5579358 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC-
1 CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
* * *
5579413 CTTTCAAAGCCCACACGAGTTAGTGGCACTTTTT-AGTCCTCAAAGAGCAGGA
1 CTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGA
5579465 TACGCTTTAT
Statistics
Matches: 755, Mismatches: 64, Indels: 65
0.85 0.07 0.07
Matches are distributed among these distances:
47 44 0.06
48 2 0.00
54 29 0.04
55 244 0.32
56 15 0.02
58 2 0.00
59 166 0.22
60 212 0.28
61 41 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (56 bp):
CTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGCT
Found at i:5579361 original size:47 final size:48
Alignment explanation
Indices: 5579289--5579440 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
5579279 TGGCATTTTT
5579289 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
*
5579337 CA-TCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGG
1 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
* *
5579384 CATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTAGTGG
1 -------CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
5579439 CA
1 CA
5579441 CTTTTTAGTC
Statistics
Matches: 92, Mismatches: 4, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
47 44 0.48
48 4 0.04
54 2 0.02
55 42 0.46
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (48 bp):
CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG
Found at i:5579417 original size:102 final size:102
Alignment explanation
Indices: 5579241--5579440 Score: 346
Period size: 102 Copynumber: 2.0 Consensus size: 102
5579231 TTTCAGTCCC
* * *
5579241 CAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
*
5579306 GACACCTTTCAAAGCCCACACAAGTTGGTGGCATCCT
66 GACACCTTTCAAAGCCCACACAAGTTAGTGGCATCCT
*
5579343 CAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
1 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
*
5579408 GACACCTTTCAAAGCCCACACGAGTTAGTGGCA
66 GACACCTTTCAAAGCCCACACAAGTTAGTGGCA
5579441 CTTTTTAGTC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (102 bp):
CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
GACACCTTTCAAAGCCCACACAAGTTAGTGGCATCCT
Found at i:5580286 original size:19 final size:19
Alignment explanation
Indices: 5580262--5580329 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
5580252 AATTCAAAAA
5580262 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
5580281 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
5580296 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
5580313 ATTATATCGATACATAA
1 TTTGTATCGATACATAA
5580330 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:5580300 original size:32 final size:32
Alignment explanation
Indices: 5580264--5580326 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
5580254 TTCAAAAATT
* *
5580264 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTATATCGATACAA
5580296 TGTATCGATACATAAGTATTATATCGATACA
1 TGTATCGATACATAAGTATTATATCGATACA
5580327 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTATATCGATACAA
Found at i:5580301 original size:13 final size:13
Alignment explanation
Indices: 5580283--5580307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5580273 ACATAAGTTT
5580283 TGTATCGATACAA
1 TGTATCGATACAA
5580296 TGTATCGATACA
1 TGTATCGATACA
5580308 TAAGTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5580387 original size:13 final size:13
Alignment explanation
Indices: 5580369--5580394 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5580359 CATTTTTCTG
5580369 TGTATCGATACAT
1 TGTATCGATACAT
5580382 TGTATCGATACAT
1 TGTATCGATACAT
5580395 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5580406 original size:33 final size:33
Alignment explanation
Indices: 5580349--5580415 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
5580339 GCCAAGGAAA
***
5580349 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
5580382 TGTATCGATACATGGATCTTTGTATCTATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
5580415 T
1 T
5580416 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:5582810 original size:51 final size:53
Alignment explanation
Indices: 5582754--5583139 Score: 240
Period size: 51 Copynumber: 7.3 Consensus size: 53
5582744 AATTCTCCAC
* * *
5582754 AATCGGGGATATTCCAACTCCGATTTTATTTTC-AAGACACTAA-TTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAACTTTTCTAT
* ** * *
5582805 AATCGGGGATACTCCAACTCCGATTTTATCTCCCAAAAAACACTAAATTTTC-AC
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTTC-AAAAACACTAACTTTTCTAT
* ** * * * * *
5582859 AATCGGGGATACTCCAACCCCG--TTAATCATCGGAGATACTCCAACCCCGTTATT-TCT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTC--AAAAACACTAA---C-TT-TTCTAT
* * * * * *
5582916 GA--GGGGATACTCCAACCCCGACTTTA-TTTCCAAAATATTAATTTTTC-AT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAACTTTTCTAT
* * * * * *
5582965 AATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAACTTTTCTAT
* * * *
5583017 AATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTTTCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAA-CTTTTCTAT
* * * * * *
5583070 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTC-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAACTTTTCTAT
*
5583122 AATCGAGGATACTCCAAC
1 AATCGGGGATACTCCAAC
5583140 TTCGTTGTCT
Statistics
Matches: 264, Mismatches: 51, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
49 4 0.02
50 2 0.01
51 68 0.26
52 68 0.26
53 45 0.17
54 44 0.17
55 23 0.09
56 4 0.02
57 6 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAAACACTAACTTTTCTAT
Found at i:5582933 original size:28 final size:27
Alignment explanation
Indices: 5582863--5582935 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
5582853 TTTCACAATC
*
5582863 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
* *
5582890 GGAGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
5582918 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
5582936 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:5583043 original size:52 final size:50
Alignment explanation
Indices: 5582751--5583139 Score: 232
Period size: 52 Copynumber: 7.4 Consensus size: 50
5582741 CTCAATTCTC
* * * * *
5582751 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAA-TTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
* * * * *
5582801 CTATAATCGGGGATACTCCAACTCCGATTTTATCTCCCAAAAAACACTAAATTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTAT-T--C-TAAAACACCAATTTTT
* * * *
5582856 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGAGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATTTTAT--TC-TA-AAACACCAA-----TT-TTT
** * * * **
5582914 C-TGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACCAATTTTT
* * *
5582962 CATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACCAATTTTT
* *
5583013 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTT
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAA-TTTTT
** * * *
5583066 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTT
*
5583119 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
5583140 TTCGTTGTCT
Statistics
Matches: 269, Mismatches: 43, Indels: 52
0.74 0.12 0.14
Matches are distributed among these distances:
48 4 0.01
49 4 0.01
50 3 0.01
51 68 0.25
52 70 0.26
53 38 0.14
54 46 0.17
55 24 0.09
56 2 0.01
57 5 0.02
58 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTT
Found at i:5583132 original size:105 final size:103
Alignment explanation
Indices: 5582920--5583139 Score: 280
Period size: 105 Copynumber: 2.1 Consensus size: 103
5582910 ATTTCTGAGG
* **
5582920 GGATACTCCAACCCCGACTTTATTTCCAAAATATTAATTTTTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
* * * * *
5582985 CGGTTTTATTGCTAAAACACTAATTTTTCCACAATCGG
66 CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
** * *
5583023 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTTCTTTAATCGGGGATACTCCAAC
1 GGATACTCCAACCCCGACTTTATTTCCAAAACACCAA-TTTTTC-ATAATCGGGGATACTCCAAC
* *
5583088 TCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATCGA
64 CCCGATTTTA-TTCCAAAAACACCAATTTTTCCACAATCGA
5583128 GGATACTCCAAC
1 GGATACTCCAAC
5583140 TTCGTTGTCT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
103 31 0.31
104 6 0.06
105 47 0.47
106 16 0.16
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.33
Consensus pattern (103 bp):
GGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTTCATAATCGGGGATACTCCAACCC
CGATTTTATTCCAAAAACACCAATTTTTCCACAATCGA
Found at i:5583218 original size:264 final size:263
Alignment explanation
Indices: 5582749--5583250 Score: 751
Period size: 264 Copynumber: 1.9 Consensus size: 263
5582739 TTCTCAATTC
* * * *
5582749 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
5582814 TACTCCAACTCCGATTTTATCTCCCAAAAAACACTAAATTTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATCTCCCAAAAAACACTAAATTTTCACAATCGAGGATACTCCAACCC
*
5582879 CGTTAATCATCGGAGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTAATCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
*
5582944 TCCAAAATATTAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
196 TCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
5583009 TTT
261 TTT
* *
5583012 TCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTTTCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA--TTTTCTATAATCGGG
* *
5583077 GATACTCCAACTCCGATTTTAT-TTCCAAAAATAC-C-AATTTTTCACAATCGAGGATACTCCAA
64 GATACTCCAACTCCGATTTTATCTCCCAAAAA-ACACTAAATTTTCACAATCGAGGATACTCCAA
** ** * * *
5583139 CTTCGTTGTCTCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCGACCCCGGCTT
128 CCCCGTT-AATCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTT
* *
5583204 TA-TTCCAAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
192 TATTTCC-AAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCG
5583251 CTATTTTCAA
Statistics
Matches: 214, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
263 77 0.36
264 99 0.46
265 38 0.18
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (263 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATCTCCCAAAAAACACTAAATTTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
TCCAAAATATTAATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
TTT
Found at i:5591147 original size:15 final size:15
Alignment explanation
Indices: 5591105--5591152 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
5591095 GTCGTGTATC
5591105 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
5591120 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
5591135 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
5591150 GAT
1 GAT
5591153 TTGGCAGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (15 bp):
GATGATTTTGTGGTG
Found at i:5599008 original size:20 final size:20
Alignment explanation
Indices: 5598982--5599036 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
5598972 AAAAAGACAG
* *
5598982 AATGTATTGATACATTAATA
1 AATGTATCGATACATTAAAA
*
5599002 CATGTATCGATACATTAAAA
1 AATGTATCGATACATTAAAA
5599022 AATGTATCGATACAT
1 AATGTATCGATACAT
5599037 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTAAAA
Found at i:5599064 original size:70 final size:71
Alignment explanation
Indices: 5598932--5599087 Score: 228
Period size: 71 Copynumber: 2.2 Consensus size: 71
5598922 TTTTAACTAG
* ** * *
5598932 ATGTATCAATACATCGAAAAATGTATCGATATATCTGGGTAAAAAGACAGAATGTATTGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
*
5598997 T-AATAC
66 TGAA-AA
5599003 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGT-AAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
5599067 TGAAAA
66 TGAAAA
5599073 AT-TATCGATACATTA
1 ATGTATCGATACATTA
5599088 GGGTAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
69 13 0.17
70 27 0.35
71 38 0.49
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
TGAAAA
Found at i:5600364 original size:20 final size:20
Alignment explanation
Indices: 5600339--5600377 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5600329 AGATATAATT
*
5600339 AGTGAATTTATTGACACATA
1 AGTGAATGTATTGACACATA
*
5600359 AGTGAATGTATTGATACAT
1 AGTGAATGTATTGACACAT
5600378 GTCTCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTGAATGTATTGACACATA
Found at i:5601563 original size:22 final size:22
Alignment explanation
Indices: 5601521--5601563 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
5601511 GAGAAGTTCA
* *
5601521 AATGTTTTTCAAGTAATAAATC
1 AATGTTTTTAAAATAATAAATC
5601543 AATGTTTTTTAAAATAA-AAAT
1 AATG-TTTTTAAAATAATAAAT
5601564 ACTTAGCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (22 bp):
AATGTTTTTAAAATAATAAATC
Found at i:5614513 original size:32 final size:30
Alignment explanation
Indices: 5614477--5614535 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
5614467 GAAATAAAAT
5614477 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
5614509 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
5614536 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:5615028 original size:20 final size:20
Alignment explanation
Indices: 5615003--5615054 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5614993 GTCAACCTTA
5615003 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACCT
5615023 ATGTATCGATACAAATACCT
1 ATGTATCGATACAAATACCT
5615043 ATGTATCGATAC
1 ATGTATCGATAC
5615055 TTTGATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAATACCT
Found at i:5619255 original size:48 final size:49
Alignment explanation
Indices: 5619182--5619343 Score: 145
Period size: 48 Copynumber: 3.4 Consensus size: 49
5619172 ATTGATACAT
* * * ** *
5619182 ATGAACAAGGTATTGATACATCTGGGTTTTTCCA-AATGTATGGATACA
1 ATGAATAATGTATCGATACATCTGGGTTTTTCCAGAATGTATCAATAAA
* *
5619230 ATGCAA-AATGTATCTATACATCTGGG-TTTTCTAGAATGTATCAATAAA
1 ATG-AATAATGTATCGATACATCTGGGTTTTTCCAGAATGTATCAATAAA
* * * *
5619278 ATGAATAATGTATCGATACACCTGGG--TTTCCAGATTGCATCAATACA
1 ATGAATAATGTATCGATACATCTGGGTTTTTCCAGAATGTATCAATAAA
* * *
5619325 ATTACTAATGTATTGATAC
1 ATGAATAATGTATCGATAC
5619344 TTCCACTATT
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
47 41 0.43
48 52 0.55
49 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (49 bp):
ATGAATAATGTATCGATACATCTGGGTTTTTCCAGAATGTATCAATAAA
Found at i:5622444 original size:13 final size:13
Alignment explanation
Indices: 5622426--5622450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5622416 ACCAAGATCA
5622426 TGTATCGATACAG
1 TGTATCGATACAG
5622439 TGTATCGATACA
1 TGTATCGATACA
5622451 AGGCAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:5625417 original size:20 final size:21
Alignment explanation
Indices: 5625387--5625426 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
5625377 TCTGGGTTTT
5625387 TTCAGATGTATCGATACATTA
1 TTCAGATGTATCGATACATTA
5625408 TTCA-ATGTATCGATACATT
1 TTCAGATGTATCGATACATT
5625427 CTGGAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCAGATGTATCGATACATTA
Found at i:5629853 original size:12 final size:12
Alignment explanation
Indices: 5629819--5629854 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5629809 TCTGAGTCAA
*
5629819 CTTCATCATCAT
1 CTTCATCATCTT
*
5629831 CATCATCATCTT
1 CTTCATCATCTT
5629843 CTTCATCATCTT
1 CTTCATCATCTT
5629855 TGATGGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTCATCATCTT
Found at i:5631522 original size:20 final size:19
Alignment explanation
Indices: 5631515--5631565 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
5631505 CAATTGAGTG
*
5631515 TGTATCGAAACAATGAACA
1 TGTATCGATACAATGAACA
*
5631534 TGTATCGATACAAAGCATA-A
1 TGTATCGATACAATG-A-ACA
5631554 TGTATCGATACA
1 TGTATCGATACA
5631566 TCTGGATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.46
20 14 0.50
21 1 0.04
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (19 bp):
TGTATCGATACAATGAACA
Found at i:5631964 original size:22 final size:22
Alignment explanation
Indices: 5631927--5631983 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
5631917 ATTATAACTT
*
5631927 CCCTTTAAAAAA--TTTTCTCC
1 CCCTTAAAAAAATTTTTTCTCC
5631947 CCCTTAAAAAAATTTTTTCTCC
1 CCCTTAAAAAAATTTTTTCTCC
* *
5631969 CTCTTAATAAAATTT
1 CCCTTAAAAAAATTT
5631984 CTTCCCTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 11 0.34
22 21 0.66
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (22 bp):
CCCTTAAAAAAATTTTTTCTCC
Found at i:5631989 original size:20 final size:20
Alignment explanation
Indices: 5631926--5632000 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
5631916 AATTATAACT
5631926 TCCCT-TTAAAAAATTT-TC
1 TCCCTCTTAAAAAATTTCTC
* *
5631944 TCCCCCTTAAAAAAATTTTTTC
1 TCCCTCTT-AAAAAA-TTTCTC
5631966 TCCCTCTTAATAAAATTTCT-
1 TCCCTCTTAA-AAAATTTCTC
*
5631986 TCCCTTTTAAAAAAT
1 TCCCTCTTAAAAAAT
5632001 AAAATCTCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
18 4 0.08
19 7 0.15
20 15 0.31
21 9 0.19
22 13 0.27
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
TCCCTCTTAAAAAATTTCTC
Found at i:5639857 original size:79 final size:80
Alignment explanation
Indices: 5639718--5639868 Score: 216
Period size: 79 Copynumber: 1.9 Consensus size: 80
5639708 TTTTATTTCC
* * *
5639718 GAGGGGATACTCCAACCCCAATTTTTATTCCCAAAACAACGATTTTTCACAATTGAGGATACTCT
1 GAGGGGATACTCCAACCCCAAGTTTTATTCCCAAAACAACAATTTTCCACAATTGAGGATACTCT
5639783 AACCCCGTTATTTTT
66 AACCCCGTTATTTTT
* * * *
5639798 GAGGGGATACTCCAA-CCCTAGTTTTATTTCCAAAACACCAATTTTCCAGC-ATTGGGGATACTC
1 GAGGGGATACTCCAACCCCAAGTTTTATTCCCAAAACAACAATTTTCCA-CAATTGAGGATACTC
5639861 TAACCCCG
65 TAACCCCG
5639869 ATTTTATTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
79 47 0.75
80 16 0.25
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (80 bp):
GAGGGGATACTCCAACCCCAAGTTTTATTCCCAAAACAACAATTTTCCACAATTGAGGATACTCT
AACCCCGTTATTTTT
Found at i:5639941 original size:50 final size:51
Alignment explanation
Indices: 5639800--5639968 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
5639790 TTATTTTTGA
* * *
5639800 GGGGATACTCCAA-CCCTAGTTTTATTTCCAAAACACCAATTTTCCAGCATT
1 GGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACCAATTTTCCACCATC
* *
5639851 GGGGATACTCTAACCCCGATTTTATTTCGAAAACACCAATTTTCCACCATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACCATC
* * * * *
5639902 GGGGATA-TCCAACCCCGATTTTATTCCCAGAACATCAATTTTCTACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACCATC
* *
5639952 AGGGATACTCAAACCCC
1 GGGGATACTCCAACCCC
5639969 ATTATTTTTG
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 42 0.41
51 56 0.55
52 4 0.04
ACGTcount: A:0.30, C:0.29, G:0.12, T:0.28
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACCATC
Found at i:5640344 original size:23 final size:22
Alignment explanation
Indices: 5640313--5640361 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
5640303 CGTCCCTACT
**
5640313 TTTTATGTATTTTTGTGCATTTA
1 TTTTATGTAAGTTTGT-CATTTA
* *
5640336 TTTTGTGTAAGTTTGTCTTTTA
1 TTTTATGTAAGTTTGTCATTTA
5640358 TTTT
1 TTTT
5640362 CTTTGTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTTATGTAAGTTTGTCATTTA
Found at i:5641873 original size:32 final size:33
Alignment explanation
Indices: 5641808--5641875 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
5641798 ACACAAATCA
*
5641808 AATACAAAGAGCTTTCAAAGAATAACAATAATG
1 AATACAAAGAGCTTTCAAAGAATAACAACAATG
5641841 AATACAAAGAGCTTTCAAAGAA-AACAACAATG
1 AATACAAAGAGCTTTCAAAGAATAACAACAATG
5641873 AAT
1 AAT
5641876 GTAAAAGCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.35
33 22 0.65
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.19
Consensus pattern (33 bp):
AATACAAAGAGCTTTCAAAGAATAACAACAATG
Found at i:5642192 original size:19 final size:19
Alignment explanation
Indices: 5642147--5642200 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
5642137 GTTAGGCATA
*
5642147 ATGTATCGATACAATTCTTC
1 ATGTATCGATAC-ATTCTCC
*
5642167 ATGTATCGATACATTGTCC
1 ATGTATCGATACATTCTCC
*
5642186 CTGTATCGATACATT
1 ATGTATCGATACATT
5642201 TGAGTTAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTCTCC
Found at i:5642272 original size:19 final size:19
Alignment explanation
Indices: 5642227--5642282 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
5642217 TTGCCACTTT
*
5642227 CATGTATTGATACAATTGAG
1 CATGTATTGATACAA-TGAA
*
5642247 TATGTATTGATACAATGAA
1 CATGTATTGATACAATGAA
*
5642266 CATGTATCGATACAATG
1 CATGTATTGATACAATG
5642283 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATTGATACAATGAA
Found at i:5642285 original size:13 final size:13
Alignment explanation
Indices: 5642267--5642293 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5642257 TACAATGAAC
5642267 ATGTATCGATACA
1 ATGTATCGATACA
5642280 ATGTATCGATACA
1 ATGTATCGATACA
5642293 A
1 A
5642294 AGCATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5646607 original size:52 final size:52
Alignment explanation
Indices: 5646522--5646646 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
5646512 ATATGAAAAG
* *
5646522 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
5646574 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
5646626 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
5646647 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:5646659 original size:52 final size:51
Alignment explanation
Indices: 5646522--5646666 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
5646512 ATATGAAAAG
*
5646522 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
5646574 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
5646626 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
5646667 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:5646673 original size:13 final size:13
Alignment explanation
Indices: 5646655--5646679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5646645 CAAAGATCAG
5646655 TGTATCGATACAA
1 TGTATCGATACAA
5646668 TGTATCGATACA
1 TGTATCGATACA
5646680 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5648315 original size:13 final size:13
Alignment explanation
Indices: 5648292--5648328 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5648282 ATAGTAACCC
*
5648292 ATGTATTGATACA
1 ATGTATCGATACA
*
5648305 TTGTATCGATACA
1 ATGTATCGATACA
5648318 ATGTATCGATA
1 ATGTATCGATA
5648329 TAAAGAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5653111 original size:13 final size:13
Alignment explanation
Indices: 5653093--5653119 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5653083 ACATTATTCT
5653093 TTGTATCGATACA
1 TTGTATCGATACA
5653106 TTGTATCGATACA
1 TTGTATCGATACA
5653119 T
1 T
5653120 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5653137 original size:32 final size:33
Alignment explanation
Indices: 5653074--5653138 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
5653064 CTCACCCAGA
* *
5653074 TGTATCGATACATTATTCTTTGTATCGATACAT
1 TGTATCGATACATTATTCATTGTATCAATACAT
*
5653107 TGTATCGATACA-TGTTCATTGTATCAATACAT
1 TGTATCGATACATTATTCATTGTATCAATACAT
5653139 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATTATTCATTGTATCAATACAT
Found at i:5653149 original size:20 final size:19
Alignment explanation
Indices: 5653103--5653159 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5653093 TTGTATCGAT
*
5653103 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
5653122 TCATTGTATCAATACATGG
1 ACATTGTATCGATACATGG
5653141 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
5653160 AAATTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:5653419 original size:33 final size:33
Alignment explanation
Indices: 5653376--5653444 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
5653366 GCACCACTGT
*
5653376 TTGTATCGATACATGGTACAAT-GTATCGATACA
1 TTGTATCGATACATGAT-CAATAGTATCGATACA
* *
5653409 TTGTTTCGATACATGATGAATAGTATCGATACA
1 TTGTATCGATACATGATCAATAGTATCGATACA
5653442 TTG
1 TTG
5653445 CTTGTAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATCAATAGTATCGATACA
Found at i:5662113 original size:13 final size:13
Alignment explanation
Indices: 5662095--5662121 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5662085 ACATTATTCT
5662095 TTGTATCGATACA
1 TTGTATCGATACA
5662108 TTGTATCGATACA
1 TTGTATCGATACA
5662121 T
1 T
5662122 GAAATTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5662188 original size:13 final size:13
Alignment explanation
Indices: 5662167--5662219 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
5662157 CGATACATGG
*
5662167 TACAATGTATCGA
1 TACATTGTATCGA
5662180 TACATTGTATCGA
1 TACATTGTATCGA
5662193 TACA-TG-AT-G-
1 TACATTGTATCGA
5662202 -A-ATTGTATCGA
1 TACATTGTATCGA
5662213 TACATTG
1 TACATTG
5662220 CTTGTAGCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5662188 original size:33 final size:33
Alignment explanation
Indices: 5662151--5662219 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
5662141 CTACCACTGT
*
5662151 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
5662184 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
5662217 TTG
1 TTG
5662220 CTTGTAGCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:5662429 original size:13 final size:13
Alignment explanation
Indices: 5662408--5662460 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
5662398 CGATACATGG
*
5662408 TACAATGTATCGA
1 TACATTGTATCGA
5662421 TACATTGTATCGA
1 TACATTGTATCGA
5662434 TACA-TG-AT-G-
1 TACATTGTATCGA
5662443 -A-ATTGTATCGA
1 TACATTGTATCGA
5662454 TACATTG
1 TACATTG
5662461 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:5662434 original size:33 final size:33
Alignment explanation
Indices: 5662392--5662460 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
5662382 GCACCACTGT
*
5662392 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
5662425 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
5662458 TTG
1 TTG
5662461 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:5662566 original size:241 final size:241
Alignment explanation
Indices: 5662143--5662624 Score: 883
Period size: 241 Copynumber: 2.0 Consensus size: 241
5662133 TAGCTACCCT
5662143 ACCACTGTTTGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGATGAATTGT
1 ACCACTGTTTGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGATGAATTGT
* * * *
5662208 ATCGATACATTGCTTGTAGCGGCTATAAACGGCTATAATTTCAAATCAATGTATCGATACTTTAT
66 ATCGATACATTGCTTGTAACAGCTATAAACGGCTATAATTTCAAATCAATATATCGATACATTAT
5662273 GAATTGTATCAATACATGGCTACGGGAATGCATTGAAACAAGCACCAAACAAGCTTACAACGACT
131 GAATTGTATCAATACATGGCTACGGGAATGCATTGAAACAAGCACCAAACAAGCTTACAACGACT
*
5662338 AGAAACACAATCATTTAACCTCCAACGGATATGTCAGCATTCAAGC
196 AGAAACACAATCATTCAACCTCCAACGGATATGTCAGCATTCAAGC
5662384 ACCACTGTTTGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGATGAATTGT
1 ACCACTGTTTGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGATGAATTGT
*
5662449 ATCGATACATTGCTTGTAACAGCTATAAATGGCTATAATTTCAAATCAATATATCGATACATTAT
66 ATCGATACATTGCTTGTAACAGCTATAAACGGCTATAATTTCAAATCAATATATCGATACATTAT
* * *
5662514 GAATTGTATCGATACATGGCTATGGGAATGCATTGAAACAAGCACCAAACAAGCTTACAACGGCT
131 GAATTGTATCAATACATGGCTACGGGAATGCATTGAAACAAGCACCAAACAAGCTTACAACGACT
5662579 AGAAACACAATCATTCAACCTCCAACGGATATGTCAGCATTCAAGC
196 AGAAACACAATCATTCAACCTCCAACGGATATGTCAGCATTCAAGC
5662625 TTATAAATTT
Statistics
Matches: 232, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
241 232 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (241 bp):
ACCACTGTTTGTATCGATACATGGTACAATGTATCGATACATTGTATCGATACATGATGAATTGT
ATCGATACATTGCTTGTAACAGCTATAAACGGCTATAATTTCAAATCAATATATCGATACATTAT
GAATTGTATCAATACATGGCTACGGGAATGCATTGAAACAAGCACCAAACAAGCTTACAACGACT
AGAAACACAATCATTCAACCTCCAACGGATATGTCAGCATTCAAGC
Found at i:5664966 original size:20 final size:19
Alignment explanation
Indices: 5664940--5664995 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
5664930 CTGCTACTTT
* *
5664940 CATGTATCGATGCAATTGAG
1 CATGTATCGATACAA-TGAA
* *
5664960 TATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
*
5664979 CATGTATCGATATAATG
1 CATGTATCGATACAATG
5664996 TATCGATACA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:5667441 original size:13 final size:13
Alignment explanation
Indices: 5667423--5667448 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5667413 GGATTTTTTG
5667423 TGTATCGATACAT
1 TGTATCGATACAT
5667436 TGTATCGATACAT
1 TGTATCGATACAT
5667449 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5669522 original size:21 final size:20
Alignment explanation
Indices: 5669493--5669535 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5669483 GGCTAGTATG
* *
5669493 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCAACCT
*
5669514 GGGAGTGCCGGTCGCAACCT
1 GGGACTGCCGGTCGCAACCT
5669534 GG
1 GG
5669536 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.30, G:0.42, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCAACCT
Found at i:5672059 original size:15 final size:15
Alignment explanation
Indices: 5672039--5672069 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5672029 ATTTCGTTTG
*
5672039 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
5672054 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
5672069 G
1 G
5672070 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:5676045 original size:13 final size:13
Alignment explanation
Indices: 5676027--5676052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5676017 ATATTTTTTG
5676027 TGTATCGATACAT
1 TGTATCGATACAT
5676040 TGTATCGATACAT
1 TGTATCGATACAT
5676053 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5676063 original size:32 final size:33
Alignment explanation
Indices: 5676006--5676070 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
5675996 TACAAGCCAA
5676006 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
5676040 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
5676071 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:5676064 original size:19 final size:19
Alignment explanation
Indices: 5676006--5676070 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
5675996 TACAAGCCAA
5676006 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
5676027 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
5676040 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
5676059 TGTATCGATACA
1 TGTATCGATACA
5676071 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:5676770 original size:21 final size:21
Alignment explanation
Indices: 5676741--5676798 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
5676731 TTCTAGTTGC
* *
5676741 AATTTATTTCTTTTCTCCTCT
1 AATTCATTTATTTTCTCCTCT
**
5676762 AATTCATTTATTTTCTTTTCT
1 AATTCATTTATTTTCTCCTCT
* *
5676783 AATTCGTTTAATTTCT
1 AATTCATTTATTTTCT
5676799 TTTCAAGAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTCATTTATTTTCTCCTCT
Found at i:5676799 original size:21 final size:21
Alignment explanation
Indices: 5676759--5676802 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5676749 TCTTTTCTCC
*
5676759 TCTAATTCATTTATTTTCTTT
1 TCTAATTCATTTAATTTCTTT
*
5676780 TCTAATTCGTTTAATTTCTTT
1 TCTAATTCATTTAATTTCTTT
5676801 TC
1 TC
5676803 AAGAACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.02, T:0.64
Consensus pattern (21 bp):
TCTAATTCATTTAATTTCTTT
Found at i:5679953 original size:15 final size:16
Alignment explanation
Indices: 5679930--5679970 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
5679920 CTTTTCTAGG
5679930 TCAACAATTTTC-TTT
1 TCAACAATTTTCATTT
*
5679945 TCAAGAA-TTTCATTT
1 TCAACAATTTTCATTT
5679960 TCAACAATTTT
1 TCAACAATTTT
5679971 TTATTTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.32, C:0.17, G:0.02, T:0.49
Consensus pattern (16 bp):
TCAACAATTTTCATTT
Found at i:5680066 original size:48 final size:48
Alignment explanation
Indices: 5679995--5680093 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
5679985 CCTTCAATTT
5679995 TAAAATTATCTTCTTATGCCTTAGGTTCATGGAATCAAATT-TTAATGC
1 TAAAATTATCTTCTTATGCCTTAGGTTCATGGAATCAAATTCTT-ATGC
*
5680043 TAAAATTATCTTCTTATGCCTTAGGTTCATGGATTCAAATTCTTATGC
1 TAAAATTATCTTCTTATGCCTTAGGTTCATGGAATCAAATTCTTATGC
5680091 TAA
1 TAA
5680094 TTCTTCAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (48 bp):
TAAAATTATCTTCTTATGCCTTAGGTTCATGGAATCAAATTCTTATGC
Found at i:5682205 original size:32 final size:33
Alignment explanation
Indices: 5682162--5682223 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
5682152 ACAATTCGTT
* **
5682162 GTGTATCGATACCAAG-ATCATGTATCGATATA
1 GTGTATCGATACAAAGTAAAATGTATCGATATA
*
5682194 GTGTATTGATACAAAGTAAAATGTATCGAT
1 GTGTATCGATACAAAGTAAAATGTATCGAT
5682224 TCTTCTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 14 0.56
33 11 0.44
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (33 bp):
GTGTATCGATACAAAGTAAAATGTATCGATATA
Found at i:5682238 original size:20 final size:22
Alignment explanation
Indices: 5682215--5682257 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5682205 CAAAGTAAAA
*
5682215 TGTATCGATTC-TTCT-GGGTT
1 TGTATCGATACTTTCTAGGGTT
5682235 TGTATCGATACTTTCTAGGGTT
1 TGTATCGATACTTTCTAGGGTT
5682257 T
1 T
5682258 TAACCTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (22 bp):
TGTATCGATACTTTCTAGGGTT
Found at i:5683988 original size:26 final size:26
Alignment explanation
Indices: 5683959--5684008 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5683949 TTGTCAAATT
** *
5683959 TTAAACATTTTTTATTTATATATACA
1 TTAAACATTCATTAATTATATATACA
*
5683985 TTAAATATTCATTAATTATATATA
1 TTAAACATTCATTAATTATATATA
5684009 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAACATTCATTAATTATATATACA
Found at i:5693206 original size:22 final size:21
Alignment explanation
Indices: 5693139--5693212 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
5693129 AAGTTTTTGT
**
5693139 TTTTCTTAGCTAATTC-TTTA
1 TTTTCTTTTCTAATTCATTTA
* *
5693159 TTTTCTTTT-TGCAACTCATTAA
1 TTTTCTTTTCT--AATTCATTTA
5693181 TTTTCTTTTCTAATTCATTTA
1 TTTTCTTTTCTAATTCATTTA
*
5693202 CTTTTTTTTTC
1 -TTTTCTTTTC
5693213 AAGAAGATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 12 0.29
22 21 0.50
23 1 0.02
ACGTcount: A:0.18, C:0.16, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTCTTTTCTAATTCATTTA
Found at i:5693210 original size:21 final size:22
Alignment explanation
Indices: 5693138--5693210 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 22
5693128 CAAGTTTTTG
* *
5693138 TTTTTCTTAGCTAATTC-TTTAT
1 TTTTT-TTTGCTAATTCATTTAA
*
5693160 TTTCTTTTTGC-AACTCA-TTAA
1 TTT-TTTTTGCTAATTCATTTAA
*
5693181 TTTTCTTTT-CTAATTCATTTAC
1 TTTT-TTTTGCTAATTCATTTAA
5693203 TTTTTTTT
1 TTTTTTTT
5693211 TCAAGAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.05
21 23 0.56
22 14 0.34
23 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTTTTTTGCTAATTCATTTAA
Found at i:5695782 original size:13 final size:13
Alignment explanation
Indices: 5695764--5695789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5695754 ACATAAGTGT
5695764 TGTATCGATACAA
1 TGTATCGATACAA
5695777 TGTATCGATACAA
1 TGTATCGATACAA
5695790 AGCCATCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5702312 original size:37 final size:38
Alignment explanation
Indices: 5702237--5702340 Score: 115
Period size: 37 Copynumber: 2.8 Consensus size: 38
5702227 ACTTTAAAAC
* *** *
5702237 TTTGCCAAAATAATGT-CAAAAG-TTGAAAATCCTCAT
1 TTTGCCAAAATAAAGTCCAAAAGCCCAAAAACCCTCAT
* *
5702273 TTTTCCAAAATAAAGTTCAAAAGCCCAAAAACCCT-AT
1 TTTGCCAAAATAAAGTCCAAAAGCCCAAAAACCCTCAT
*
5702310 TTTGCCAAAATAAAGTCCAAAAGCCTAAAAA
1 TTTGCCAAAATAAAGTCCAAAAGCCCAAAAA
5702341 TAATATGGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
36 14 0.25
37 36 0.63
38 7 0.12
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (38 bp):
TTTGCCAAAATAAAGTCCAAAAGCCCAAAAACCCTCAT
Found at i:5704245 original size:21 final size:22
Alignment explanation
Indices: 5704221--5704267 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5704211 TTCTACTTTG
*
5704221 AACTAAT-AGGATTTTCAATTA
1 AACTAATAAAGATTTTCAATTA
**
5704242 AACTTTTAAAGATTTTCAATTA
1 AACTAATAAAGATTTTCAATTA
5704264 AACT
1 AACT
5704268 TTTTCTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
AACTAATAAAGATTTTCAATTA
Found at i:5705196 original size:20 final size:21
Alignment explanation
Indices: 5705151--5705206 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
5705141 ATAAAACAAA
*
5705151 AGAAATAGAGAAGGAAAAAAGT
1 AGAAATA-AGAAAGAAAAAAGT
5705173 -GAAATAAGAAAGAAAAAA-T
1 AGAAATAAGAAAGAAAAAAGT
* *
5705192 AGAAAAAAAAAAGAA
1 AGAAATAAGAAAGAA
5705207 CTTTCATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 23 0.77
21 6 0.20
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (21 bp):
AGAAATAAGAAAGAAAAAAGT
Found at i:5706100 original size:57 final size:57
Alignment explanation
Indices: 5706029--5706348 Score: 351
Period size: 57 Copynumber: 5.6 Consensus size: 57
5706019 TTATCTAGGT
* * *
5706029 TATTTAACATAATCTAAGACCATTTTAGTAATTTTTATAATTTTAGAGTAATTTAAG
1 TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGAGTTATTTAAG
* * * *
5706086 TATTTAACAAAATCTAGGGTCATTTTAGTAATTTTTATCATTTTAG-GTTTATTTAGG
1 TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGAG-TTATTTAAG
* *
5706143 TTATTTAACATAATCTAAGGCCATTTTAGTAA-TTTTATAATTTTAGAGTAATTTAAG
1 -TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGAGTTATTTAAG
* * * * * *
5706200 TATTTAACAAAATCTAGGGTCATTTCAGTAATTTTTATCATTTTAGGGTTATTTAGG
1 TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGAGTTATTTAAG
* * ** * *
5706257 TTATTTAACATAATATAAGGTCATTTTAGTAATTTCAATCATTTTA-AGGTTTTTTATG
1 -TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGA-GTTATTTAAG
* * *
5706315 T-TATTAACATAACCTAAGACCATTTTAGCAATTT
1 TAT-TTAACATAATCTAAGGCCATTTTAGTAATTT
5706349 ACGTCATTTT
Statistics
Matches: 221, Mismatches: 35, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
56 29 0.13
57 116 0.52
58 76 0.34
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (57 bp):
TATTTAACATAATCTAAGGCCATTTTAGTAATTTTTATCATTTTAGAGTTATTTAAG
Found at i:5706213 original size:114 final size:114
Alignment explanation
Indices: 5706008--5706291 Score: 487
Period size: 114 Copynumber: 2.5 Consensus size: 114
5705998 GTAACATTTG
* * *
5706008 CATTCTTAAGGTTATCTAGGTTATTTAACATAATCTAAGACCATTTTAGTAATTTTTATAATTTT
1 CATT-TTAGGGTTATTTAGGTTATTTAACATAATCTAAGGCCATTTTAGTAA-TTTTATAATTTT
*
5706073 AGAGTAATTTAAGTATTTAACAAAATCTAGGGTCATTTTAGTAATTTTTAT
64 AGAGTAATTTAAGTATTTAACAAAATCTAGGGTCATTTCAGTAATTTTTAT
*
5706124 CATTTTAGGTTTATTTAGGTTATTTAACATAATCTAAGGCCATTTTAGTAATTTTATAATTTTAG
1 CATTTTAGGGTTATTTAGGTTATTTAACATAATCTAAGGCCATTTTAGTAATTTTATAATTTTAG
5706189 AGTAATTTAAGTATTTAACAAAATCTAGGGTCATTTCAGTAATTTTTAT
66 AGTAATTTAAGTATTTAACAAAATCTAGGGTCATTTCAGTAATTTTTAT
* *
5706238 CATTTTAGGGTTATTTAGGTTATTTAACATAATATAAGGTCATTTTAGTAATTT
1 CATTTTAGGGTTATTTAGGTTATTTAACATAATCTAAGGCCATTTTAGTAATTT
5706292 CAATCATTTT
Statistics
Matches: 160, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
114 113 0.71
115 43 0.27
116 4 0.03
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (114 bp):
CATTTTAGGGTTATTTAGGTTATTTAACATAATCTAAGGCCATTTTAGTAATTTTATAATTTTAG
AGTAATTTAAGTATTTAACAAAATCTAGGGTCATTTCAGTAATTTTTAT
Found at i:5706224 original size:28 final size:28
Alignment explanation
Indices: 5706079--5706229 Score: 74
Period size: 28 Copynumber: 5.3 Consensus size: 28
5706069 TTTTAGAGTA
5706079 ATTTAAGTATTTAACAAAATCTAGGGTC
1 ATTTAAGTATTTAACAAAATCTAGGGTC
* * * * * *
5706107 ATTTTAGTAATTTTTATC--ATTTTAGGTTT
1 ATTTAAGT-A--TTTAACAAAATCTAGGGTC
* * * *
5706136 ATTTAGGTTATTTAACATAATCTAAGGCC
1 ATTTAAG-TATTTAACAAAATCTAGGGTC
* * * * * * *
5706165 ATTTTAGTAATTTTA-TAATTTTAGAGTA
1 ATTTAAGT-ATTTAACAAAATCTAGGGTC
5706193 ATTTAAGTATTTAACAAAATCTAGGGTC
1 ATTTAAGTATTTAACAAAATCTAGGGTC
*
5706221 ATTTCAGTA
1 ATTTAAGTA
5706230 ATTTTTATCA
Statistics
Matches: 81, Mismatches: 34, Indels: 16
0.62 0.26 0.12
Matches are distributed among these distances:
27 10 0.12
28 36 0.44
29 29 0.36
30 1 0.01
31 5 0.06
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
ATTTAAGTATTTAACAAAATCTAGGGTC
Found at i:5706356 original size:57 final size:58
Alignment explanation
Indices: 5706008--5706411 Score: 217
Period size: 57 Copynumber: 7.0 Consensus size: 58
5705998 GTAACATTTG
* * **
5706008 CATTCTTAAGGTTATCTAGGTTATTTAACATAATC-TAAGACCATTTTAGTAATTTTTAT
1 CATT-TTAAGGTTATTTAGGTTATTTAACATAA-CATAAGACCATTTTAGCAATTTCAAT
* * * * * ** * **
5706067 AATTTT-AGAGTAATTTAAG-TATTTAACAAAATC-TAGGGTCATTTTAGTAATTTTTAT
1 CATTTTAAG-GTTATTTAGGTTATTTAACATAA-CATAAGACCATTTTAGCAATTTCAAT
* * *
5706124 CATTTT-AGGTTTATTTAGGTTATTTAACATAATC-TAAGGCCATTTTAGTAATTT-TAT
1 CATTTTAAGG-TTATTTAGGTTATTTAACATAA-CATAAGACCATTTTAGCAATTTCAAT
* * * * * ** * * **
5706181 AATTTT-AGAGTAATTTAAG-TATTTAACAAAATC-TAGGGTCATTTCAGTAATTTTTAT
1 CATTTTAAG-GTTATTTAGGTTATTTAACATAA-CATAAGACCATTTTAGCAATTTCAAT
* * ** *
5706238 CATTTTAGGGTTATTTAGGTTATTTAACATAATATAAGGTCATTTTAGTAATTTCAAT
1 CATTTTAAGGTTATTTAGGTTATTTAACATAACATAAGACCATTTTAGCAATTTCAAT
* * * *
5706296 CATTTTAAGGTTTTTTATGTTA-TTAACATAACCTAAGACCATTTTAGCAATTT-ACGT
1 CATTTTAAGGTTATTTAGGTTATTTAACATAACATAAGACCATTTTAGCAATTTCA-AT
* * ** * *
5706353 CATTTT-AGGTCTGTCTAGGTTAATTTAACAT-ATTTAAG-TCATTTTAGCAATTTCCAT
1 CATTTTAAGGT-TATTTAGGTT-ATTTAACATAACATAAGACCATTTTAGCAATTTCAAT
5706410 CA
1 CA
5706412 AGTTAGGATT
Statistics
Matches: 284, Mismatches: 48, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
56 36 0.13
57 140 0.49
58 98 0.35
59 10 0.04
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (58 bp):
CATTTTAAGGTTATTTAGGTTATTTAACATAACATAAGACCATTTTAGCAATTTCAAT
Found at i:5708207 original size:92 final size:93
Alignment explanation
Indices: 5708062--5708239 Score: 241
Period size: 92 Copynumber: 1.9 Consensus size: 93
5708052 TATTTTCATG
* * * * * *
5708062 TGTATTGATACAAATGAGGGTTTCAGGATTTCTTTAGCTACTGCCAACCAGATGTGTCGATACAT
1 TGTATCGATAAAAATAAGGGTTTCAAGACTTCTTTAGCTACTGCCAACCAGATGTATCGATACAT
*
5708127 TCACATAATATATTGATACATTTTTACT
66 TCACAAAATATATTGATACATTTTTACT
* * * * *
5708155 TGTATCGATAAAAATAAGGGTTTCAATACTTC-TTAGCTACTGTCAACTAGATGTATTGTTACAT
1 TGTATCGATAAAAATAAGGGTTTCAAGACTTCTTTAGCTACTGCCAACCAGATGTATCGATACAT
5708219 TCACAAAATATATTGATACAT
66 TCACAAAATATATTGATACAT
5708240 GCAATCTTGA
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
92 47 0.64
93 26 0.36
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (93 bp):
TGTATCGATAAAAATAAGGGTTTCAAGACTTCTTTAGCTACTGCCAACCAGATGTATCGATACAT
TCACAAAATATATTGATACATTTTTACT
Found at i:5715381 original size:13 final size:13
Alignment explanation
Indices: 5715363--5715388 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5715353 CAATTTTTGG
5715363 TGTATCGATACAT
1 TGTATCGATACAT
5715376 TGTATCGATACAT
1 TGTATCGATACAT
5715389 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5715400 original size:32 final size:33
Alignment explanation
Indices: 5715343--5715406 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
5715333 TACAAGCCAA
**
5715343 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
5715376 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
5715407 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:5715413 original size:19 final size:18
Alignment explanation
Indices: 5715343--5715413 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
5715333 TACAAGCCAA
5715343 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
5715363 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
5715376 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
5715395 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
5715414 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:5717507 original size:21 final size:20
Alignment explanation
Indices: 5717478--5717516 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5717468 AGCTAGTGTG
*
5717478 GGGACTGCCCGGTTGCGACTT
1 GGGACTG-CCGGTCGCGACTT
*
5717499 GGGAGTGCCGGTCGCGAC
1 GGGACTGCCGGTCGCGAC
5717517 CTGGTGGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.10, C:0.28, G:0.44, T:0.18
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACTT
Found at i:5724149 original size:13 final size:13
Alignment explanation
Indices: 5724131--5724156 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5724121 TACAAGGTAA
5724131 TGTATCGATACAT
1 TGTATCGATACAT
5724144 TGTATCGATACAT
1 TGTATCGATACAT
5724157 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5725039 original size:20 final size:22
Alignment explanation
Indices: 5725014--5725058 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
5725004 GCAGCTACCT
*
5725014 CCAGGTCACGATT-GGC-ACTC
1 CCAGGTCACAATTGGGCAACTC
5725034 CCAGGTCACAATTGGGCAACTC
1 CCAGGTCACAATTGGGCAACTC
5725056 CCA
1 CCA
5725059 CACCCACTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.55
21 3 0.14
22 7 0.32
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.18
Consensus pattern (22 bp):
CCAGGTCACAATTGGGCAACTC
Found at i:5725841 original size:256 final size:257
Alignment explanation
Indices: 5725386--5725894 Score: 948
Period size: 256 Copynumber: 2.0 Consensus size: 257
5725376 CAGTTCGTGA
* *
5725386 GAACCTTGTTCGGGCTTTCCTCAGTAATGCTCGTCTCGAGCATAATGATAGCAAGGAAGTTGTTG
1 GAACCTTGTTCGGGCTTTCCTCAGTAACGCTCGTCTCAAGCATAATGATAGCAAGGAAGTTGTTG
*
5725451 CAATTCATTCCTACCTCATGGGTCAAGACTTGATCCTTACCCCCTCCATTTTAGCCGATGCACTA
66 CAATTCATTCCTACCTCATGGGTCAAGACTTGATCCTTACCCCCTCCATTTTAGCCAATGCACTA
*
5725516 AACATGTCGTATGAGGGAGAGATCAAAAAGGGGACGGCTCCTCGAAACACTAGAGTTCCCCTAAA
131 AACATGTCGTATGAGGGAGAGATCAAAAAGGGGACGACTCCTCGAAACACTAGAGTTCCCCTAAA
5725581 TAAAGCCACTCGCCTTCCACCTCATGA-TACCTTCACCTTCTCATAACCCACATCGTTACCT
196 TAAAGCCACTCGCCTTCCACCTCATGATTACCTTCACCTTCTCATAACCCACATCGTTACCT
5725642 GAACCTTGTTCGGGCTTTCCTCAGTAACGCTCGTCTCAAGCATAATGATAGCAAGGAAGTTGTTG
1 GAACCTTGTTCGGGCTTTCCTCAGTAACGCTCGTCTCAAGCATAATGATAGCAAGGAAGTTGTTG
5725707 CAATTCATTCCTACCTCATGGGTCAAGACTTGATCCTTACCCCCTCCATTTTAGCCAATGCACTA
66 CAATTCATTCCTACCTCATGGGTCAAGACTTGATCCTTACCCCCTCCATTTTAGCCAATGCACTA
5725772 AACATGTCGTATGAGGGAGAGATCAAAAAGGGGACGACTCCTCGAAACACTAGAGTTCCCCTAAA
131 AACATGTCGTATGAGGGAGAGATCAAAAAGGGGACGACTCCTCGAAACACTAGAGTTCCCCTAAA
5725837 TAAAGCCACTCGCCTTCCACCTCATGATCGTTACCTTCACCTTCTCATAACCCACATC
196 TAAAGCCACTCGCCTTCCACCTCATGA---TTACCTTCACCTTCTCATAACCCACATC
5725895 TTCCGACCGT
Statistics
Matches: 245, Mismatches: 4, Indels: 4
0.97 0.02 0.02
Matches are distributed among these distances:
256 218 0.89
260 27 0.11
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (257 bp):
GAACCTTGTTCGGGCTTTCCTCAGTAACGCTCGTCTCAAGCATAATGATAGCAAGGAAGTTGTTG
CAATTCATTCCTACCTCATGGGTCAAGACTTGATCCTTACCCCCTCCATTTTAGCCAATGCACTA
AACATGTCGTATGAGGGAGAGATCAAAAAGGGGACGACTCCTCGAAACACTAGAGTTCCCCTAAA
TAAAGCCACTCGCCTTCCACCTCATGATTACCTTCACCTTCTCATAACCCACATCGTTACCT
Found at i:5727373 original size:13 final size:13
Alignment explanation
Indices: 5727355--5727379 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5727345 CGTTATGCTT
5727355 TGTATCGATACAA
1 TGTATCGATACAA
5727368 TGTATCGATACA
1 TGTATCGATACA
5727380 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5727419 original size:20 final size:20
Alignment explanation
Indices: 5727364--5727420 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
5727354 TTGTATCGAT
*
5727364 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* * **
5727383 TC-ATTATATAAATACATGG
1 ACAATTGTATCGATACATGG
5727402 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
5727421 AAATTGGTAG
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 13 0.48
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:5729583 original size:97 final size:96
Alignment explanation
Indices: 5729334--5729572 Score: 334
Period size: 97 Copynumber: 2.5 Consensus size: 96
5729324 TTGAAAAATA
* *
5729334 GGGTTGGAGTATCCCCTCGGAGGAATGGGTTGGAATGTCCCCGATGATGACAATTTAAGTGAGAA
1 GGGTTGGAGTATCCCCTTGGAGGAATGGGTTGGAATGTCCTCGATGATGACAATTTAAGTGAGAA
* *
5729399 TAAAATTTAAAATTTGATGTGTTTAAAAGCG
66 TAAAATTTAAAATTTGAGGTGTGTAAAAGCG
* * * *
5729430 AGGTTGGACTATCCCCTTGGAGGAATGGGGTTGAAATGTCCTCGATGGTGACAATTTAAGTGAGA
1 GGGTTGGAGTATCCCCTTGGAGGAAT-GGGTTGGAATGTCCTCGATGATGACAATTTAAGTGAGA
* *
5729495 ATAAGATTTAAACTTTGAGGTGTGTAAAAGCG
65 ATAAAATTTAAAATTTGAGGTGTGTAAAAGCG
* * * *
5729527 GGGTTAGAGTATCCCCTTGGAGAAATAGGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCCCTTGGAGGAAT-GGGTTGGAATGTCCTCGAT
5729573 AAATAAAATT
Statistics
Matches: 124, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
96 23 0.19
97 101 0.81
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (96 bp):
GGGTTGGAGTATCCCCTTGGAGGAATGGGTTGGAATGTCCTCGATGATGACAATTTAAGTGAGAA
TAAAATTTAAAATTTGAGGTGTGTAAAAGCG
Found at i:5731311 original size:11 final size:10
Alignment explanation
Indices: 5731282--5731333 Score: 59
Period size: 11 Copynumber: 4.9 Consensus size: 10
5731272 TACCTCTTTA
*
5731282 TTTCTATTTC
1 TTTCTTTTTC
5731292 TTCTCTCTTTTC
1 TT-TCT-TTTTC
*
5731304 TTTCTCTTTTT
1 TTTCT-TTTTC
5731315 TTTCTTTTTC
1 TTTCTTTTTC
5731325 TTTCTTTTT
1 TTTCTTTTT
5731334 TTTAGTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 15 0.41
11 16 0.43
12 6 0.16
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:5731319 original size:15 final size:16
Alignment explanation
Indices: 5731299--5731333 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5731289 TTCTTCTCTC
5731299 TTTTCTTTCTCTTT-T
1 TTTTCTTTCTCTTTCT
*
5731314 TTTTCTTTTTCTTTCT
1 TTTTCTTTCTCTTTCT
5731330 TTTT
1 TTTT
5731334 TTTAGTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTCTCTTTCT
Found at i:5732721 original size:32 final size:31
Alignment explanation
Indices: 5732680--5732803 Score: 116
Period size: 32 Copynumber: 4.0 Consensus size: 31
5732670 AATGCCACAA
*
5732680 ACTTATGTGGGCTTT-GAAAGGGGTTGCCATCG
1 ACTTGTGTGGGCTTTAGAAA-GGGTTGCCA-CG
*
5732712 ACTTGTGTGGACTTTAGAAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAGAAAGGGTTGCCA-CG
* *
5732744 ACTTGTGTGGTCTTTAGAGAAGGG-TGCCACTA
1 ACTTGTGTGGGCTTTAGA-AAGGGTTGCCAC-G
*
5732776 AC-T-TGTGGGCTTT-GAAA-GGATGCCACG
1 ACTTGTGTGGGCTTTAGAAAGGGTTGCCACG
5732803 A
1 A
5732804 AGTTGTCGAC
Statistics
Matches: 81, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.04
28 8 0.10
29 2 0.02
30 9 0.11
31 2 0.02
32 48 0.59
33 9 0.11
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTAGAAAGGGTTGCCACG
Found at i:5732799 original size:28 final size:28
Alignment explanation
Indices: 5732671--5733258 Score: 394
Period size: 28 Copynumber: 20.1 Consensus size: 28
5732661 TTTGAAAAAA
*
5732671 ATGCCACAAACTTATGTGGGCTTTGAAAGGGG
1 ATGCCACTAAC-T-TGTGGGCTTTGAAA--GG
* *
5732703 TTGCCA-TCGACTTGTGTGGACTTTAGAAAGGG
1 ATGCCACT-AACTTGTG-GG-CTTT-GAAA-GG
* **
5732735 TTGCCACCGACTTGTGTGGTCTTTAGAGAAGG
1 ATGCCACTAACTTGTG-GG-CTTT-GA-AAGG
*
5732767 GTGCCACTAACTTGTGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* * * * *
5732795 ATGCCACGAAGTTGTCGAC-TTAAAAGGG
1 ATGCCACTAACTTGTGGGCTTTGAAA-GG
* *
5732823 ATGCCACTAACTTGTAGACTTTGAAAAAGG
1 ATGCCACTAACTTGTGGGCTTTG--AAAGG
* * * * *
5732853 -TGCCACTGATTTGTTGGATTTGAAAAAAAAAG
1 ATGCCACTAACTTGTGGGCTTTG-----AAAGG
** *
5732885 ATGCCACTAACTTGTGGATTTTTGAAAAG
1 ATGCCACTAACTTGTGG-GCTTTGAAAGG
* * * *
5732914 ATGCCACTAACTTATAGACTTTGAGAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* * * *
5732942 ATGCCGCTGACTTATGGGATTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* *
5732970 ATGCCACTGACTTGGGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* *
5732998 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* * * *
5733026 GTGCCACTGACCTATGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* * *
5733054 GTGCCACTGACTTGTGGGCTTTGGAAAAG
1 ATGCCACTAACTTGTGGGCTTT-GAAAGG
* **
5733083 -TGCCACCGATTTGTGTGGGCTTTGAAAAGG
1 ATGCCA-CTAACT-TGTGGGCTTTG-AAAGG
* *
5733113 -TACCACTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
*
5733140 ATGCCACTAACTTATGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* *
5733168 ATGCCATTGACTTGTGGGCTTTGAAAGG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* *
5733196 ATGCCACTAACTTGTGGACTTTGAAAAG
1 ATGCCACTAACTTGTGGGCTTTGAAAGG
* **
5733224 ATGCTACTGATTTGTGTGGGCTTTGAGAAGG
1 ATGCCACT-AACT-TGTGGGCTTTGA-AAGG
5733255 ATGC
1 ATGC
5733259 TGTTAGGATC
Statistics
Matches: 456, Mismatches: 77, Indels: 47
0.79 0.13 0.08
Matches are distributed among these distances:
27 10 0.02
28 257 0.56
29 53 0.12
30 39 0.09
31 15 0.03
32 59 0.13
33 19 0.04
34 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
ATGCCACTAACTTGTGGGCTTTGAAAGG
Found at i:5732866 original size:29 final size:29
Alignment explanation
Indices: 5732824--5732879 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5732814 TTAAAAGGGA
5732824 TGCCACTAACTTG-TAGACTTTGAAAAAGG
1 TGCCACTAACTTGTTAGA-TTTGAAAAAGG
* * *
5732853 TGCCACTGATTTGTTGGATTTGAAAAA
1 TGCCACTAACTTGTTAGATTTGAAAAA
5732880 AAAAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.32
Consensus pattern (29 bp):
TGCCACTAACTTGTTAGATTTGAAAAAGG
Found at i:5733131 original size:142 final size:143
Alignment explanation
Indices: 5732905--5733256 Score: 435
Period size: 142 Copynumber: 2.5 Consensus size: 143
5732895 CTTGTGGATT
* * * * * * * * * *
5732905 TTTGAAAAGATGCCACTAACTTATAGACTTTGAGAGGATGCCGCTGA-CT-TATGGGATTTG-AA
1 TTTGAAAGGATGCCACTAACTTGTGGACTTTGAAAAGATGCCACCGATTTGTGTGGGCTTTGAAA
* * * * *
5732967 AGGATGCCACTGACTTGGGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCA
66 AGGATACCACTGACTTGGGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCA
5733032 CTGACCTATGGGC
131 CTGACCTATGGGC
* * *
5733045 TTTGAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAG-TGCCACCGATTTGTGTGGGCTTTGAA
1 TTTGAAAGGATGCCACTAACTTGTGGACTTT-GAAAAGATGCCACCGATTTGTGTGGGCTTTGAA
*
5733109 AAGG-TACCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCC
65 AAGGATACCACTGACTTGGGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCC
* * *
5733173 ATTGACTTGTGGGC
130 ACTGACCTATGGGC
* * *
5733187 TTTGAAAGGATGCCACTAACTTGTGGACTTTGAAAAGATGCTACTGATTTGTGTGGGCTTTGAGA
1 TTTGAAAGGATGCCACTAACTTGTGGACTTTGAAAAGATGCCACCGATTTGTGTGGGCTTTGAAA
5733252 AGGAT
66 AGGAT
5733257 GCTGTTAGGA
Statistics
Matches: 178, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
140 32 0.18
141 11 0.06
142 129 0.72
143 6 0.03
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (143 bp):
TTTGAAAGGATGCCACTAACTTGTGGACTTTGAAAAGATGCCACCGATTTGTGTGGGCTTTGAAA
AGGATACCACTGACTTGGGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCA
CTGACCTATGGGC
Found at i:5733659 original size:13 final size:13
Alignment explanation
Indices: 5733641--5733666 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5733631 TACAGCAAGT
5733641 ATGTATCGATACA
1 ATGTATCGATACA
5733654 ATGTATCGATACA
1 ATGTATCGATACA
5733667 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5735913 original size:21 final size:21
Alignment explanation
Indices: 5735880--5735924 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5735870 TTGCAAGTTG
*
5735880 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
5735902 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
5735922 AAA
1 AAA
5735925 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:5739851 original size:20 final size:20
Alignment explanation
Indices: 5739772--5739851 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
5739762 AATGTCCAAA
*
5739772 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
5739792 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
5739817 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
5739837 TTGTATCGATACATT
1 ATGTATCGATACATT
5739852 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:5739855 original size:13 final size:13
Alignment explanation
Indices: 5739837--5739875 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
5739827 ACATTTTTCT
5739837 TTGTATCGATACA
1 TTGTATCGATACA
5739850 TTGTATCGATACA
1 TTGTATCGATACA
5739863 TTGTATCGATACA
1 TTGTATCGATACA
5739876 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5742429 original size:13 final size:13
Alignment explanation
Indices: 5742411--5742436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5742401 TACAGCAAGT
5742411 ATGTATCGATACA
1 ATGTATCGATACA
5742424 ATGTATCGATACA
1 ATGTATCGATACA
5742437 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5743217 original size:28 final size:28
Alignment explanation
Indices: 5743185--5743351 Score: 185
Period size: 28 Copynumber: 5.9 Consensus size: 28
5743175 TAAGCTTTCA
*
5743185 GATGCCATTGACTTGTGGGC-TTGAGAAG
1 GATGCCACTGACTTGTGGGCTTTGA-AAG
*
5743213 GATGCCACTGACTTGTGAGCTTTGAAAG
1 GATGCCACTGACTTGTGGGCTTTGAAAG
* * **
5743241 GATGCCATTAACTTGTGGTTTTTTG-AAG
1 GATGCCACTGACTTGTGG-GCTTTGAAAG
* * *
5743269 AGATGCTACTGACTTATAGGCTTTGAAAG
1 -GATGCCACTGACTTGTGGGCTTTGAAAG
*
5743298 GATGCCACTAACTTGTGGGCTTTGAAAG
1 GATGCCACTGACTTGTGGGCTTTGAAAG
* *
5743326 GATGCCACTGACCTATGGGCTTTGAA
1 GATGCCACTGACTTGTGGGCTTTGAA
5743352 GAGATGAACA
Statistics
Matches: 114, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
28 90 0.79
29 24 0.21
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (28 bp):
GATGCCACTGACTTGTGGGCTTTGAAAG
Found at i:5743348 original size:56 final size:56
Alignment explanation
Indices: 5743185--5743351 Score: 212
Period size: 56 Copynumber: 3.0 Consensus size: 56
5743175 TAAGCTTTCA
* * *
5743185 GATGCCATTGACTTGTGGGC-TTGAGAAGGATGCCACTGACTTGTGAGCTTTGAAAG
1 GATGCCATTAACTTGTGGGCTTTGA-AAGGATGCCACTGACTTATGGGCTTTGAAAG
** * *
5743241 GATGCCATTAACTTGTGGTTTTTTG-AAGAGATGCTACTGACTTATAGGCTTTGAAAG
1 GATGCCATTAACTTGTGG-GCTTTGAAAG-GATGCCACTGACTTATGGGCTTTGAAAG
* *
5743298 GATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACCTATGGGCTTTGAA
1 GATGCCATTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAA
5743352 GAGATGAACA
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
56 47 0.50
57 44 0.47
58 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (56 bp):
GATGCCATTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAG
Done.