Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004845.1 Hibiscus syriacus cultivar Beakdansim tig00010926_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 163978
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:508 original size:21 final size:21
Alignment explanation
Indices: 470--509 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
460 TTTATTCATA
* * *
470 AAAACAAATTGGACAAATCAG
1 AAAACAAATAGAAAAAATCAG
491 AAAACAAATAGAAAAAATC
1 AAAACAAATAGAAAAAATC
510 TAGCTTATAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAACAAATAGAAAAAATCAG
Found at i:1298 original size:115 final size:114
Alignment explanation
Indices: 1127--1334 Score: 326
Period size: 115 Copynumber: 1.8 Consensus size: 114
1117 GAGAGCTATA
* * *
1127 TATAGCAAATCTCATCGTCAAAGGCTGGACTATAAAATTTCAGAAAATATATCGAGAAGCAAATG
1 TATAGCAAATCTCATCGTCAAAGGCTGGACCATAAAATTCCAGAAAATATACCGAGAAGCAAATG
1192 TCGCAGCGAATTTTATATTCAAAGATGGAATGACTACTATACTTGAGAGG
66 TCGCAGCGAATTTTATA-TCAAAGATGGAATGACTACTATACTTGAGAGG
** * *
1242 TATAGCAAATCTCATCGTCAAAGGCTGGACCATGGAGTTCCAGAAAGTATACCGAGAAGCAAATG
1 TATAGCAAATCTCATCGTCAAAGGCTGGACCATAAAATTCCAGAAAATATACCGAGAAGCAAATG
* *
1307 TCGCAGCGGATTTTATATCCAAGATGGA
66 TCGCAGCGAATTTTATATCAAAGATGGA
1335 CTCCGCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
114 10 0.12
115 74 0.88
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (114 bp):
TATAGCAAATCTCATCGTCAAAGGCTGGACCATAAAATTCCAGAAAATATACCGAGAAGCAAATG
TCGCAGCGAATTTTATATCAAAGATGGAATGACTACTATACTTGAGAGG
Found at i:1449 original size:130 final size:130
Alignment explanation
Indices: 1214--1494 Score: 393
Period size: 130 Copynumber: 2.2 Consensus size: 130
1204 TTATATTCAA
* * *
1214 AGATGGAATGACTACTATACTTGAGAGGTATAGCAAATCTCATCGTCAAAGGCTGGACCATGGAG
1 AGATGGAATGACTACCATACTTGAGAGCTATAGCAAATCTCATCGTCAAAGGCTGGACCATAGAG
* * *
1279 TTCCAGAAAGTATACCGAGAAGCAAATGTCGCAGCGGATTTTATATCCAAGATGGACTCCGCATT
66 TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACAGATTTTATATCCAAGATGGACTCCGCATT
* * * * *
1344 AGATGGAATGAGTACCATACTTGAGAGCTGTTGTAATTCTCATCGTCAAAGGCTGGACCATAGAG
1 AGATGGAATGACTACCATACTTGAGAGCTATAGCAAATCTCATCGTCAAAGGCTGGACCATAGAG
* * *
1409 TTCCAGAAAGTATACCGAGAAGTAAATGCCGCAACAGATTTTATATCCAAGATGAACTTCC-CAC
66 TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACAGATTTTATATCCAAGATGGAC-TCCGCAT
1473 T
130 T
* * *
1474 ATATGGAATGCCTACTATACT
1 AGATGGAATGACTACCATACT
1495 CTCGGCATAC
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 129 0.98
131 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (130 bp):
AGATGGAATGACTACCATACTTGAGAGCTATAGCAAATCTCATCGTCAAAGGCTGGACCATAGAG
TTCCAGAAAGTATACCGAGAAGCAAATGCCGCAACAGATTTTATATCCAAGATGGACTCCGCATT
Found at i:8799 original size:45 final size:45
Alignment explanation
Indices: 8721--8937 Score: 290
Period size: 45 Copynumber: 4.8 Consensus size: 45
8711 CCAAGTGGGG
*
8721 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACTGCCAATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* * * * *
8766 CTATGCTTGATGAGAGTCATTCCAAAAATGCTGCACAGCCAAGGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* * * *
8811 CTATACCTGATGATAGTCATTCCGAAAAGGTTGCGCAGCCGATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* ** *
8856 CTATACCTGATGATAGTCATTTTGAAAAGGCTGCACAACCAATGA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
* *
8901 CTATACCTGATGTGAGTCATTCTGAAAAGGCTGCACA
1 CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACA
8938 ACCAGAAAGA
Statistics
Matches: 148, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 148 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (45 bp):
CTATACCTGATGAGAGTCATTCCGAAAAGGCTGCACAGCCAATGA
Found at i:39164 original size:7 final size:7
Alignment explanation
Indices: 39152--39354 Score: 406
Period size: 7 Copynumber: 29.0 Consensus size: 7
39142 TTCCCGACTT
39152 GCTTCTA
1 GCTTCTA
39159 GCTTCTA
1 GCTTCTA
39166 GCTTCTA
1 GCTTCTA
39173 GCTTCTA
1 GCTTCTA
39180 GCTTCTA
1 GCTTCTA
39187 GCTTCTA
1 GCTTCTA
39194 GCTTCTA
1 GCTTCTA
39201 GCTTCTA
1 GCTTCTA
39208 GCTTCTA
1 GCTTCTA
39215 GCTTCTA
1 GCTTCTA
39222 GCTTCTA
1 GCTTCTA
39229 GCTTCTA
1 GCTTCTA
39236 GCTTCTA
1 GCTTCTA
39243 GCTTCTA
1 GCTTCTA
39250 GCTTCTA
1 GCTTCTA
39257 GCTTCTA
1 GCTTCTA
39264 GCTTCTA
1 GCTTCTA
39271 GCTTCTA
1 GCTTCTA
39278 GCTTCTA
1 GCTTCTA
39285 GCTTCTA
1 GCTTCTA
39292 GCTTCTA
1 GCTTCTA
39299 GCTTCTA
1 GCTTCTA
39306 GCTTCTA
1 GCTTCTA
39313 GCTTCTA
1 GCTTCTA
39320 GCTTCTA
1 GCTTCTA
39327 GCTTCTA
1 GCTTCTA
39334 GCTTCTA
1 GCTTCTA
39341 GCTTCTA
1 GCTTCTA
39348 GCTTCTA
1 GCTTCTA
39355 AGCCATCTAC
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 196 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (7 bp):
GCTTCTA
Found at i:39457 original size:7 final size:7
Alignment explanation
Indices: 39445--39540 Score: 192
Period size: 7 Copynumber: 13.7 Consensus size: 7
39435 TTCCTGACTT
39445 GCTTCTA
1 GCTTCTA
39452 GCTTCTA
1 GCTTCTA
39459 GCTTCTA
1 GCTTCTA
39466 GCTTCTA
1 GCTTCTA
39473 GCTTCTA
1 GCTTCTA
39480 GCTTCTA
1 GCTTCTA
39487 GCTTCTA
1 GCTTCTA
39494 GCTTCTA
1 GCTTCTA
39501 GCTTCTA
1 GCTTCTA
39508 GCTTCTA
1 GCTTCTA
39515 GCTTCTA
1 GCTTCTA
39522 GCTTCTA
1 GCTTCTA
39529 GCTTCTA
1 GCTTCTA
39536 GCTTC
1 GCTTC
39541 GATTCAGTGT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 89 1.00
ACGTcount: A:0.14, C:0.29, G:0.15, T:0.43
Consensus pattern (7 bp):
GCTTCTA
Found at i:58530 original size:14 final size:14
Alignment explanation
Indices: 58511--58538 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
58501 ATCATAACAA
58511 AATTATATAACTAT
1 AATTATATAACTAT
58525 AATTATATAACTAT
1 AATTATATAACTAT
58539 TTTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:58572 original size:24 final size:25
Alignment explanation
Indices: 58545--58591 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
58535 CTATTTTTTC
58545 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
58569 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
58592 TTTTTTGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:63537 original size:22 final size:22
Alignment explanation
Indices: 63512--63575 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
63502 AATATTAAAT
*
63512 ATAATAAATAATATTATTTATC
1 ATAATAAATAATATTATTTATA
* *
63534 ATAA-AACTTAATATT-TTTAAA
1 ATAATAA-ATAATATTATTTATA
*
63555 ATATTAAAATAAT-TTATTTAT
1 ATAAT-AAATAATATTATTTAT
63576 TATTAACTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 11 0.34
22 19 0.59
23 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATAAATAATATTATTTATA
Found at i:69185 original size:15 final size:14
Alignment explanation
Indices: 69151--69193 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
69141 TAGCAAAAAA
*
69151 AAATTAATAATATT
1 AAATAAATAATATT
69165 AAATAAATAATAATT
1 AAATAAATAAT-ATT
* *
69180 ATATAAATATTATT
1 AAATAAATAATATT
69194 TTAATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATAAATAATATT
Found at i:69207 original size:30 final size:31
Alignment explanation
Indices: 69151--69238 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 31
69141 TAGCAAAAAA
* *
69151 AAATTAATAATATTAAATAAATAATAATTATAT
1 AAATAAAT-ATATT-AATAAAAAATAATTATAT
* * *
69184 AAAT-ATTATTTTAATAAAAAATAA-TATTT
1 AAATAAATATATTAATAAAAAATAATTATAT
*
69213 ACATAAATATATTAATAAAAAATAAT
1 AAATAAATATATTAATAAAAAATAAT
69239 AACTATTTAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
29 7 0.15
30 29 0.63
31 4 0.09
32 2 0.04
33 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
AAATAAATATATTAATAAAAAATAATTATAT
Found at i:69220 original size:15 final size:14
Alignment explanation
Indices: 69156--69236 Score: 58
Period size: 15 Copynumber: 5.5 Consensus size: 14
69146 AAAAAAAATT
*
69156 AATAATATTAAATA
1 AATAATATTTAATA
*
69170 AATAATAATTATATA
1 AATAATATTTA-ATA
*
69185 AATATTATTTTAATAAAA
1 AATAATA-TTTAAT---A
69203 AATAATATTTACATA
1 AATAATATTTA-ATA
69218 AAT-ATA-TTAATA
1 AATAATATTTAATA
*
69230 AAAAATA
1 AATAATA
69237 ATAACTATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
12 5 0.09
13 6 0.11
14 12 0.22
15 15 0.28
16 3 0.06
17 4 0.07
18 9 0.17
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATATTTAATA
Found at i:69239 original size:30 final size:32
Alignment explanation
Indices: 69164--69240 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 32
69154 TTAATAATAT
*
69164 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
69198 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
69228 TAAAAAATAATAA
1 TAAAAAATAATAA
69241 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 16 0.40
32 2 0.05
33 18 0.45
34 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:69254 original size:33 final size:32
Alignment explanation
Indices: 69164--69254 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 32
69154 TTAATAATAT
* * * *
69164 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAA-TATTTAAAAAATATATTAA
*
69198 T--AAAA-AATAATATTTACATAAATATATTAA
1 TAAAAAATAATAATATTTA-AAAAATATATTAA
69228 TAAAAAATAATAACTATTTAAAAAATA
1 TAAAAAATAATAA-TATTTAAAAAATA
69255 CTAACATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
29 5 0.11
30 15 0.33
31 3 0.07
32 5 0.11
33 11 0.24
34 7 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (32 bp):
TAAAAAATAATAATATTTAAAAAATATATTAA
Found at i:80859 original size:13 final size:13
Alignment explanation
Indices: 80841--80869 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
80831 GCTTGTCAAC
80841 GGTCAACGGGTCT
1 GGTCAACGGGTCT
80854 GGTCAACGGGTCT
1 GGTCAACGGGTCT
80867 GGT
1 GGT
80870 TATGACCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.41, T:0.24
Consensus pattern (13 bp):
GGTCAACGGGTCT
Found at i:85766 original size:3 final size:3
Alignment explanation
Indices: 85758--85784 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
85748 GAATTGGGTT
85758 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
85785 GACGAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:86138 original size:91 final size:91
Alignment explanation
Indices: 85983--86167 Score: 370
Period size: 91 Copynumber: 2.0 Consensus size: 91
85973 ATTGATTGGA
85983 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
1 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
86048 CTTGCTGCGTTTTAATGTCTCACCAT
66 CTTGCTGCGTTTTAATGTCTCACCAT
86074 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
1 GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
86139 CTTGCTGCGTTTTAATGTCTCACCAT
66 CTTGCTGCGTTTTAATGTCTCACCAT
86165 GCA
1 GCA
86168 GGGACCTGGA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 94 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (91 bp):
GCATATGCTCCTTTTTCATCCAAGGCTGGAAAGGTATGGCTGTTTTGAAGGTAGGTTAGTCTTAT
CTTGCTGCGTTTTAATGTCTCACCAT
Found at i:87389 original size:31 final size:31
Alignment explanation
Indices: 87354--87428 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
87344 TAAAAAAATA
*
87354 TAATATTTGAGT-ACTTTTGTTTTTATTTAAT
1 TAATATTTG-GTCACTTTCGTTTTTATTTAAT
*
87385 TAATATTTGGTCACTTTCGTTTTTATTTAAG
1 TAATATTTGGTCACTTTCGTTTTTATTTAAT
* *
87416 TAAGATATGGTCA
1 TAATATTTGGTCA
87429 TTGAGGGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (31 bp):
TAATATTTGGTCACTTTCGTTTTTATTTAAT
Found at i:92583 original size:21 final size:20
Alignment explanation
Indices: 92544--92581 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
92534 AGATTATGCA
92544 GGGGGTACAGATTCCCCCTG
1 GGGGGTACAGATTCCCCCTG
92564 GGGGGTATC-GATTCCCCC
1 GGGGGTA-CAGATTCCCCC
92582 CTAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGTACAGATTCCCCCTG
Found at i:92743 original size:23 final size:23
Alignment explanation
Indices: 92713--92759 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
92703 AACAAGTTTT
92713 GGAATAATCAAAGGATTAGGATC
1 GGAATAATCAAAGGATTAGGATC
*
92736 GGAATAATCAAATGATTAGGATC
1 GGAATAATCAAAGGATTAGGATC
92759 G
1 G
92760 AATCAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (23 bp):
GGAATAATCAAAGGATTAGGATC
Found at i:92765 original size:19 final size:21
Alignment explanation
Indices: 92718--92767 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
92708 GTTTTGGAAT
*
92718 AATCAAAGGATTAGGATCGGAA
1 AATCAAATGATTAGGATCGG-A
92740 TAATCAAATGATTAGGATC-G-
1 -AATCAAATGATTAGGATCGGA
92760 AATCAAAT
1 AATCAAAT
92768 CAAGGCTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
22 1 0.04
23 17 0.65
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCAAATGATTAGGATCGGA
Found at i:93386 original size:2 final size:2
Alignment explanation
Indices: 93379--93426 Score: 87
Period size: 2 Copynumber: 23.5 Consensus size: 2
93369 GTGATGAAAC
93379 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93421 GAT AT A
1 -AT AT A
93427 ATAATAAGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 43 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94140 original size:18 final size:18
Alignment explanation
Indices: 94107--94147 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
94097 TATGCTTATA
*
94107 TGAT-ATAAATGAATTAG
1 TGATAATAAATGAATTAC
94124 TGATAATAATATG-ATTAC
1 TGATAATAA-ATGAATTAC
94142 TGATAA
1 TGATAA
94148 ATATGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 14 0.67
19 3 0.14
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (18 bp):
TGATAATAAATGAATTAC
Found at i:94618 original size:21 final size:22
Alignment explanation
Indices: 94592--94634 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
94582 GTAGTAGTAG
*
94592 TGTAGC-AGGGTATCGGTTCCC
1 TGTAGCAAGGGAATCGGTTCCC
94613 TGTAGCAAGGGAATCGGTTCCC
1 TGTAGCAAGGGAATCGGTTCCC
94635 CTATTACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.19, C:0.23, G:0.33, T:0.26
Consensus pattern (22 bp):
TGTAGCAAGGGAATCGGTTCCC
Found at i:94980 original size:16 final size:15
Alignment explanation
Indices: 94959--95006 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
94949 GTGGGAAGTG
94959 AAGAAAAGTGAAGAGA
1 AAGAAAAGTGAAGA-A
94975 AAG-AAA--GAAGAA
1 AAGAAAAGTGAAGAA
94987 AA-AAAAGTGAAGCAA
1 AAGAAAAGTGAAG-AA
95002 AAGAA
1 AAGAA
95007 GATGGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 6 0.22
13 5 0.19
14 4 0.15
15 7 0.26
16 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.25, T:0.04
Consensus pattern (15 bp):
AAGAAAAGTGAAGAA
Found at i:98957 original size:23 final size:22
Alignment explanation
Indices: 98922--98967 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
98912 AAACATAAAT
* *
98922 AAAAAAGATATAGTTATAGTAC
1 AAAAAAGACATAGTTAAAGTAC
98944 AAAAAAGTACATAGTTAAAGTAC
1 AAAAAAG-ACATAGTTAAAGTAC
98967 A
1 A
98968 TAATATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.24
Consensus pattern (22 bp):
AAAAAAGACATAGTTAAAGTAC
Found at i:100147 original size:28 final size:29
Alignment explanation
Indices: 100115--100174 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
100105 AACATACTCT
* * *
100115 TATTTTTTTAATATTTGTTATTAAGGA-C
1 TATTTTTTAAATACTAGTTATTAAGGAGC
*
100143 TATTTTTTAAATACTAGTTATTATGGAGC
1 TATTTTTTAAATACTAGTTATTAAGGAGC
100172 TAT
1 TAT
100175 CCTTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (29 bp):
TATTTTTTAAATACTAGTTATTAAGGAGC
Found at i:100930 original size:26 final size:26
Alignment explanation
Indices: 100884--100938 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
100874 TTTATAATTT
* *
100884 TTATTATAATTTTTTATTTAATAAA-A
1 TTATTATAATTTATTAATTAA-AAATA
100910 TTATATATAA-TTATTAATTAAAAATA
1 TTAT-TATAATTTATTAATTAAAAATA
100936 TTA
1 TTA
100939 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 3 0.12
26 17 0.68
27 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATTATAATTTATTAATTAAAAATA
Found at i:103310 original size:74 final size:74
Alignment explanation
Indices: 103220--103370 Score: 230
Period size: 74 Copynumber: 2.0 Consensus size: 74
103210 GTTTGCGTAA
** * * *
103220 AAATTTTAGACTTGTTTTAAATATTGGTCGGGTTTGGATTTCATAATTGTTCATATTTATAATTA
1 AAATTTTAGACTTGTTTTAAATATTAATCGGGTTTGGACTTCATAATAGTCCATATTTATAATTA
*
103285 TAATAAATG
66 TAATAAACG
* *
103294 AAATTTTAGGCTTGTTTTAAATATTAATCGGGTTTGGGCTTCATAATAGTCCATATTTATAATTA
1 AAATTTTAGACTTGTTTTAAATATTAATCGGGTTTGGACTTCATAATAGTCCATATTTATAATTA
103359 TAATAAACG
66 TAATAAACG
103368 AAA
1 AAA
103371 AATATTTAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (74 bp):
AAATTTTAGACTTGTTTTAAATATTAATCGGGTTTGGACTTCATAATAGTCCATATTTATAATTA
TAATAAACG
Found at i:105948 original size:12 final size:12
Alignment explanation
Indices: 105931--105955 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
105921 CTCAAAATAA
105931 TTTTCAGGAATT
1 TTTTCAGGAATT
105943 TTTTCAGGAATT
1 TTTTCAGGAATT
105955 T
1 T
105956 AGCACTGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTTCAGGAATT
Found at i:109529 original size:29 final size:29
Alignment explanation
Indices: 109495--109578 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
109485 AATTTATCTG
109495 AATAATTCTGTTTTGATAATTATTCTTAA
1 AATAATTCTGTTTTGATAATTATTCTTAA
* ** *
109524 AATAA-TCT-TTCT-ATTTTTA-TCTT-G
1 AATAATTCTGTTTTGATAATTATTCTTAA
* *
109548 AGTAATTCCGTTTTGATAATTATTTCTTAA
1 AATAATTCTGTTTTGATAATTA-TTCTTAA
109578 A
1 A
109579 CTTGTATCAC
Statistics
Matches: 39, Mismatches: 10, Indels: 11
0.65 0.17 0.18
Matches are distributed among these distances:
24 4 0.10
25 6 0.15
26 8 0.21
27 8 0.21
28 3 0.08
29 9 0.23
30 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (29 bp):
AATAATTCTGTTTTGATAATTATTCTTAA
Found at i:130838 original size:14 final size:13
Alignment explanation
Indices: 130818--130885 Score: 59
Period size: 14 Copynumber: 5.0 Consensus size: 13
130808 TATATATTAT
130818 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
130831 ACAGAAGAAGAAAAA
1 A-AGAAGAA-AAAAA
*
130846 AAAAAG-AAAAAA
1 AAGAAGAAAAAAA
*
130858 AAGAA-AATGAAAACG
1 AAGAAGAA--AAAA-A
130873 AAGAAGAAAAAAA
1 AAGAAGAAAAAAA
130886 TGAAAATGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
12 10 0.23
13 2 0.05
14 19 0.43
15 11 0.25
16 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.01
Consensus pattern (13 bp):
AAGAAGAAAAAAA
Found at i:130855 original size:27 final size:28
Alignment explanation
Indices: 130825--130935 Score: 79
Period size: 27 Copynumber: 3.9 Consensus size: 28
130815 TATAAGAAGA
130825 AAAAAAACAGA-AGAAGAAAAAAAAAAG
1 AAAAAAACAGAGAGAAGAAAAAAAAAAG
* *
130852 AAAAAAA-AGA-A-AATGAAAACGAAGAAG
1 AAAAAAACAGAGAGAA-GAAAA-AAAAAAG
* * *
130879 AAAAAAATGAAAATGAGAAAGAAAAGAAAAAG
1 AAAAAAA--CAGA-GAG-AAGAAAAAAAAAAG
*
130911 AAAAAAAC-GAGAGATGAAAAAAAAA
1 AAAAAAACAGAGAGAAGAAAAAAAAA
130936 TGAGAGACTA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
25 2 0.03
26 9 0.13
27 29 0.43
28 3 0.04
29 1 0.01
30 2 0.03
32 14 0.21
33 5 0.07
34 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.04
Consensus pattern (28 bp):
AAAAAAACAGAGAGAAGAAAAAAAAAAG
Found at i:130869 original size:6 final size:5
Alignment explanation
Indices: 130821--130914 Score: 66
Period size: 5 Copynumber: 17.4 Consensus size: 5
130811 ATATTATAAG
* *
130821 AAGAA AAAAA ACAGAA GAAGAAA AAAAA AAGAA AA-AA AAGAA AATGAA
1 AAGAA AAGAA A-AGAA -AAG-AA AAGAA AAGAA AAGAA AAGAA AA-GAA
*
130869 AACGAA GAAGAA AA-AA ATGAA AATGAGA AAGAA AAGAAA AAGAA AA
1 AA-GAA -AAGAA AAGAA AAGAA AA-GA-A AAGAA AAG-AA AAGAA AA
130915 AAACGAGAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
4 7 0.10
5 30 0.42
6 27 0.38
7 8 0.11
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:130897 original size:20 final size:22
Alignment explanation
Indices: 130861--130903 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
130851 GAAAAAAAAG
130861 AAAATGAAAACGAAG-AAGAAA
1 AAAATGAAAACGAAGAAAGAAA
*
130882 AAAATGAAAATG-AGAAAGAAA
1 AAAATGAAAACGAAGAAAGAAA
130903 A
1 A
130904 GAAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (22 bp):
AAAATGAAAACGAAGAAAGAAA
Found at i:130915 original size:6 final size:6
Alignment explanation
Indices: 130821--130915 Score: 58
Period size: 6 Copynumber: 16.3 Consensus size: 6
130811 ATATTATAAG
* *
130821 AAGAAA AA-AAA CAGAAG AAGAAA AA-AAA AAG--A AA-AAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * * * *
130864 ATGAAA ACGAAGA AGAAAAA AATGAAA ATGAGA AAG-AA AAGAAA AAGAAA
1 AAGAAA AAGAA-A A-AGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA
130914 AA
1 AA
130916 AACGAGAGAT
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
4 3 0.04
5 16 0.24
6 38 0.57
7 8 0.12
8 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:130936 original size:44 final size:43
Alignment explanation
Indices: 130825--130940 Score: 107
Period size: 44 Copynumber: 2.7 Consensus size: 43
130815 TATAAGAAGA
*
130825 AAAAAAAC-AGAAGAAGAAAAAAAAA--AGAAAAAAAAGAAAATG
1 AAAAAAACGAG-AG-AGAAAAAAAAATGAGAAAAAAAAGAAAAAG
* * *
130867 AAAACGAA-GA-AGAAAAAAATGAAAATGAGAAAGAAAAGAAAAAG
1 AAAA-AAACGAGAGAGAAAAA--AAAATGAGAAAAAAAAGAAAAAG
130911 AAAAAAACGAGAGATGAAAAAAAAATGAGA
1 AAAAAAACGAGAGA-GAAAAAAAAATGAGA
130941 GACTAAAGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
40 6 0.10
41 2 0.03
42 8 0.14
43 5 0.08
44 30 0.51
45 3 0.05
46 5 0.08
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.04
Consensus pattern (43 bp):
AAAAAAACGAGAGAGAAAAAAAAATGAGAAAAAAAAGAAAAAG
Found at i:134547 original size:40 final size:40
Alignment explanation
Indices: 134492--134573 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
134482 TGCAAGTTTA
134492 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
134532 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
134572 TA
1 TA
134574 GCACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:134779 original size:48 final size:45
Alignment explanation
Indices: 134677--134803 Score: 157
Period size: 48 Copynumber: 2.8 Consensus size: 45
134667 GTAACCATGC
* * * *
134677 AAATAAGTTTATGAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
* *
134721 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATT-GGAA
*
134769 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
134804 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
44 21 0.29
46 12 0.17
47 13 0.18
48 26 0.36
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:135568 original size:21 final size:21
Alignment explanation
Indices: 135543--135582 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
135533 TTTATTTTCA
135543 TAATAAATTT-TATACTAAAAG
1 TAAT-AATTTATATACTAAAAG
135564 TAATAATTTATATACTAAA
1 TAATAATTTATATACTAAA
135583 CGTGTAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (21 bp):
TAATAATTTATATACTAAAAG
Found at i:137725 original size:6 final size:6
Alignment explanation
Indices: 137660--137721 Score: 115
Period size: 6 Copynumber: 10.3 Consensus size: 6
137650 TCCGTACGTT
137660 TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA
1 TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA TGTGAA
*
137708 TGTGAA TGAGAA TG
1 TGTGAA TGTGAA TG
137722 AGAAAGCCGT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (6 bp):
TGTGAA
Found at i:139751 original size:21 final size:20
Alignment explanation
Indices: 139700--139751 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
139690 TTTTCCCAAT
*
139700 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
139720 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
139741 TCGCAATGCGA
1 TCGCAATGCGA
139752 TACTGACTAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:139768 original size:20 final size:20
Alignment explanation
Indices: 139740--139793 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
139730 AATTGGGAAA
*
139740 ATCGCAATGCGATACTGACT
1 ATCGTAATGCGATACTGACT
*
139760 ATCGTAATGCGATACTTACT
1 ATCGTAATGCGATACTGACT
139780 ATCGTAATGCGATA
1 ATCGTAATGCGATA
139794 ATACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGTAATGCGATACTGACT
Found at i:139804 original size:61 final size:61
Alignment explanation
Indices: 139737--139874 Score: 159
Period size: 61 Copynumber: 2.3 Consensus size: 61
139727 GCGAATTGGG
* * ** * *
139737 AAAATCGCAATGCGATACTGACTATCGTAATGCGATACTTACTATCGTAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACCGACTATCGCAACGCGATAATAC
* * * * * *
139798 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCCGATTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACCGACTATCGCAACGCGATAATAC
*
139859 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
139875 TTTCAAAGCG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACCGACTATCGCAACGCGATAATAC
Found at i:139827 original size:20 final size:20
Alignment explanation
Indices: 139802--139854 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
139792 TAATACAAAA
* *
139802 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACCGACTT
* *
139822 TCGCAACGCGATTCCGATTT
1 TCGCAACGCGATACCGACTT
139842 TCGCAACGCGATA
1 TCGCAACGCGATA
139855 ATACATAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACCGACTT
Found at i:140387 original size:20 final size:20
Alignment explanation
Indices: 140328--140391 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
140318 GTGATTTTAG
*
140328 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
140348 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
140368 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
140388 TTTC
1 TTTC
140392 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:140582 original size:25 final size:24
Alignment explanation
Indices: 140528--140582 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
140518 TGTTTATTAT
* *
140528 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
140552 TAGTTTTTGGTATAT-TTAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
140578 TGTTT
1 TGTTT
140583 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:141725 original size:18 final size:18
Alignment explanation
Indices: 141704--141748 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
141694 TCCACTTCGG
*
141704 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
141722 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
141740 GAGCCATCA
1 GAGCCATCA
141749 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:142284 original size:19 final size:20
Alignment explanation
Indices: 142241--142285 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
142231 CACAACACGA
142241 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
142261 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
142280 AAATGA
1 AAATGA
142286 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:142291 original size:19 final size:19
Alignment explanation
Indices: 142249--142364 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
142239 GAAAATGACT
***
142249 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
142269 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
142288 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
142302 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
142320 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
142334 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
142353 ATCGCAATGCGA
1 ATCGCAATGCGA
142365 TTTGTGTTTC
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
14 20 0.26
15 1 0.01
16 6 0.08
17 2 0.03
18 11 0.14
19 27 0.35
20 10 0.13
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:142304 original size:14 final size:14
Alignment explanation
Indices: 142285--142342 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
142275 ATGCGAAATG
142285 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
142299 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
142315 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
142331 AAAATCGCAACG
1 AAAATCGCAACG
142343 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:142327 original size:32 final size:33
Alignment explanation
Indices: 142269--142359 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
142259 GGAAATGGCT
142269 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
142302 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
142334 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
142360 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:142395 original size:14 final size:14
Alignment explanation
Indices: 142376--142433 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
142366 TTGTGTTTCG
142376 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
142390 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
142406 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
142422 CGTTGCGATTTT
1 CGTTGCGATTTT
142434 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:142448 original size:19 final size:19
Alignment explanation
Indices: 142392--142491 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
142382 GATTTTGTCG
142392 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
142410 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
142424 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
142443 TTGCGATAGCCATTTCGCG
1 TTGCGATTTTCATTTCGCA
** *
142462 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
142482 TTGCGATTTT
1 TTGCGATTTT
142492 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 9 0.13
19 26 0.39
20 15 0.22
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:142468 original size:38 final size:33
Alignment explanation
Indices: 142371--142449 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
142361 GCGATTTGTG
*
142371 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
142403 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
142436 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
142450 AGCCATTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:142480 original size:20 final size:19
Alignment explanation
Indices: 142422--142488 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
142412 GCGATTTTGT
**
142422 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
142441 CATTGCGATAGCCATTTCG
1 CGTTGCGATAGTCATTTCG
142460 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
142480 CGTTGCGAT
1 CGTTGCGAT
142489 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:142498 original size:20 final size:20
Alignment explanation
Indices: 142436--142513 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 20
142426 GCGATTTTCA
* **
142436 TTTCGCATTGCGATAGCCA-
1 TTTCGCGTTGCGATAGTAAG
* *
142455 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
142475 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
* *
142495 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGATAGTAA
142514 ACTATTCTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 17 0.35
20 31 0.65
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:144375 original size:14 final size:14
Alignment explanation
Indices: 144334--144375 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
144324 GATTGTTTAA
*
144334 TTGATTTGTAAAAG
1 TTGATTTGTAAATG
*
144348 ATGATTTGTAAATG
1 TTGATTTGTAAATG
*
144362 TTGATTTGTTAATG
1 TTGATTTGTAAATG
144376 ATGTGTACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
TTGATTTGTAAATG
Found at i:144545 original size:19 final size:19
Alignment explanation
Indices: 144493--144538 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
144483 GCAACGAGAG
144493 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
144512 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
144531 AATCGCAA
1 AATCGCAA
144539 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:144607 original size:19 final size:20
Alignment explanation
Indices: 144583--144632 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
144573 GCGATTTTGT
144583 CGTTGCGATAGCCA-TTTCA
1 CGTTGCGATAGCCATTTTCA
*
144602 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCA
144622 CGTTGCGATAG
1 CGTTGCGATAG
144633 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:145866 original size:24 final size:24
Alignment explanation
Indices: 145839--145892 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
145829 AGTATTCGAA
*
145839 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
145863 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
145887 TTTGAT
1 TTTGAT
145893 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:148399 original size:33 final size:33
Alignment explanation
Indices: 148357--148481 Score: 198
Period size: 33 Copynumber: 3.8 Consensus size: 33
148347 GGAAATTACT
148357 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
148390 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
148422 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
148456 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
148482 TGCGAATTTA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:148464 original size:66 final size:66
Alignment explanation
Indices: 148358--148490 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
148348 GAAATTACTA
*
148358 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
148423 T
66 T
* *
148424 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAATGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
148489 T
66 T
148490 T
1 T
148491 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:148498 original size:19 final size:19
Alignment explanation
Indices: 148357--148487 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
148347 GGAAATTACT
148357 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
148376 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
148390 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
148409 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
148423 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
148442 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
148456 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
148475 ATCGCAATGCGAA
1 ATCGCAATGCGAA
148488 TTTAATTTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 40 0.47
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:148529 original size:33 final size:33
Alignment explanation
Indices: 148482--148564 Score: 148
Period size: 33 Copynumber: 2.5 Consensus size: 33
148472 AAAATCGCAA
* *
148482 TGCGAATTTAATTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
148515 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
148548 TGCGATTTTCATTTCGC
1 TGCGATTTTCATTTCGC
148565 ATTGTGATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTACGATTCTCTCGT
Found at i:148698 original size:14 final size:14
Alignment explanation
Indices: 148679--148715 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
148669 CATCAATTAA
148679 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
148693 ACAAATCACCTTTT
1 ACAAATCAACTTTT
148707 ACAAATCAA
1 ACAAATCAA
148716 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:150129 original size:42 final size:41
Alignment explanation
Indices: 150070--150276 Score: 166
Period size: 42 Copynumber: 4.9 Consensus size: 41
150060 GTGAATCGGG
* *
150070 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * * *
150112 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGA
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
150154 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
150196 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
150238 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGT
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGT
150277 CGAGTCGGGC
Statistics
Matches: 126, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:150136 original size:21 final size:21
Alignment explanation
Indices: 150070--150220 Score: 67
Period size: 21 Copynumber: 7.2 Consensus size: 21
150060 GTGAATCGGG
*
150070 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
150090 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
150112 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* **
150133 CTCTCG-A-GGAATGATAGGGGA
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
150154 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
150175 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
150196 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
150217 CTCT
1 CTCT
150221 CGAGGAATGA
Statistics
Matches: 88, Mismatches: 35, Indels: 14
0.64 0.26 0.10
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 76 0.86
22 6 0.07
23 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:150211 original size:84 final size:84
Alignment explanation
Indices: 150100--150276 Score: 345
Period size: 84 Copynumber: 2.1 Consensus size: 84
150090 CCTCTTCAAC
150100 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
150165 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
150184 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
150249 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
150268 GATGACAGT
1 GATGACAGT
150277 CGAGTCGGGC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 92 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGACTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:150674 original size:91 final size:93
Alignment explanation
Indices: 150497--150675 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 93
150487 TCAAACTTTC
*
150497 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
*
150562 ATTGGCAGCAACCGAATAAATTTACTTA
66 ATTGGCAGAAACCGAATAAATTTACTTA
*
150590 AACCAAAAGACAAAATAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-TTTAGCA
1 AACCAAAAGAC-AAA-AAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
150651 GTATTGGCAGAAACCGAATAAATTT
64 GAATTGGCAGAAACCGAATAAATTT
150676 TCTAAGCAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
91 30 0.38
92 1 0.01
93 14 0.17
94 7 0.09
95 28 0.35
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (93 bp):
AACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
ATTGGCAGAAACCGAATAAATTTACTTA
Found at i:152435 original size:33 final size:33
Alignment explanation
Indices: 152378--152476 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
152368 ACGAGATAAT
152378 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
152412 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
152445 GATAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
152477 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:152470 original size:19 final size:19
Alignment explanation
Indices: 152353--152498 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
152343 TCTTTTGGTT
* *
152353 GAAATGAAAATCACAACGA
1 GAAATGAAAATCGCAACGC
*
152372 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
152392 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
152410 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
152426 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
152443 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
152459 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
152478 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
152497 GA
1 GA
152499 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.43
20 26 0.26
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:152510 original size:19 final size:19
Alignment explanation
Indices: 152494--152540 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
152484 AAAATCGCAA
*
152494 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
152513 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
152532 TGCGATTTT
1 TGCGATTTT
152541 CATTCTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:153081 original size:20 final size:20
Alignment explanation
Indices: 153056--153108 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
153046 GCGCTATGTA
153056 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
153076 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
153096 TATCTCGTTGCGA
1 AATCGCGTTGCGA
153109 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:153145 original size:20 final size:20
Alignment explanation
Indices: 153117--153170 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
153107 GATTTTGTAT
*
153117 TATCTCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
153137 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
153157 TATCGCATTGCGAT
1 TATCGCATTGCGAT
153171 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:153189 original size:61 final size:61
Alignment explanation
Indices: 153057--153191 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
153047 CGCTATGTAA
* * * * * ** *
153057 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
153118 ATCTCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
153180 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
153192 TTACTTATTC
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
61 57 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:153281 original size:21 final size:21
Alignment explanation
Indices: 153241--153281 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
153231 ACTGTAGACC
** *
153241 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATACAACT
153262 ATCGCAACGCGAAATACAAC
1 ATCGCAACGCGAAATACAAC
153282 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATACAACT
Found at i:154561 original size:29 final size:29
Alignment explanation
Indices: 154520--154578 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
154510 AATTTTTCGT
* *
154520 GGACTAAATTGAAATTTTAATTAAATTTG
1 GGACCAAAATGAAATTTTAATTAAATTTG
*
154549 GGACCAAAATGAAATTTTGATTAAATTTG
1 GGACCAAAATGAAATTTTAATTAAATTTG
154578 G
1 G
154579 ATCTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (29 bp):
GGACCAAAATGAAATTTTAATTAAATTTG
Found at i:156642 original size:23 final size:23
Alignment explanation
Indices: 156616--156660 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
156606 CACCACATCT
*
156616 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
156639 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
156661 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:157053 original size:14 final size:14
Alignment explanation
Indices: 157034--157061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
157024 AACTTGTAAT
157034 TCACGTATCACATA
1 TCACGTATCACATA
157048 TCACGTATCACATA
1 TCACGTATCACATA
157062 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:157316 original size:2 final size:2
Alignment explanation
Indices: 157309--157343 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
157299 TTGTTTTCAC
*
157309 AT AT AT AT TT CAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
157344 TCTCAAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:158225 original size:21 final size:21
Alignment explanation
Indices: 158201--158245 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
158191 TGTTGTTCGT
* *
158201 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
158222 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
158243 TTG
1 TTG
158246 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:161394 original size:23 final size:23
Alignment explanation
Indices: 161368--161412 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
161358 CACCACAGCT
*
161368 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
161391 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
161413 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:161630 original size:149 final size:149
Alignment explanation
Indices: 161380--161694 Score: 569
Period size: 149 Copynumber: 2.1 Consensus size: 149
161370 TATAATTGCA
161380 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTA
161444 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
161509 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
**
161529 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
161594 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
161659 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
161678 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
161695 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAAAAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:161814 original size:14 final size:14
Alignment explanation
Indices: 161795--161822 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
161785 AACTTGTAAT
161795 TCACGTATCACATA
1 TCACGTATCACATA
161809 TCACGTATCACATA
1 TCACGTATCACATA
161823 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:162978 original size:21 final size:21
Alignment explanation
Indices: 162954--162998 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
162944 TGTTGTTCGT
* *
162954 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
162975 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
162996 TTG
1 TTG
162999 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.