Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001448.1 Hibiscus syriacus cultivar Beakdansim tig00002799_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: 1849635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:271057 original size:30 final size:31
Alignment explanation
Indices: 271018--271077 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
271008 ACATGCTGCC
**
271018 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
271049 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
271078 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:273790 original size:19 final size:18
Alignment explanation
Indices: 273768--273814 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
273758 AGTGAATAAT
273768 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
273787 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
273806 AATA-AAGAA
1 AATATAAGAA
273815 AGGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:274261 original size:19 final size:20
Alignment explanation
Indices: 274223--274275 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
274213 GAAACCCCTT
*
274223 TGAAAATACATGATTTTTTTGA
1 TGAAAATACATGA--TTTTTAA
274245 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
274264 TGAAGATACATG
1 TGAAAATACATG
274276 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
22 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:274992 original size:30 final size:31
Alignment explanation
Indices: 274953--275012 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
274943 ACATACTGCC
274953 ATGATATCTAAATG-ATATGCAAACATAATAA
1 ATGATATCTAAA-GCATATGCAAACATAATAA
* *
274984 ATGA-ATCTAAAGCATATGTAAGCATAATA
1 ATGATATCTAAAGCATATGCAAACATAATA
275013 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAGCATATGCAAACATAATAA
Found at i:277806 original size:64 final size:65
Alignment explanation
Indices: 277661--277816 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 65
277651 CGGTACACTA
* * * *
277661 TGAGTGCATCGGTACACTAATTACATTCGATGTTTCAAACAAGCCAGGAGTGCATTGATGCATGG
1 TGAGTGCATCGATACACTAAATGCATTCGATGTTTCAAACAAGCCAGGAGTGCATCGATGCATGG
** * * *
277726 TCTGTGCATC-AGTACACAAAATGCATTCGATGTTTCAATA-AA-TCATGAGTGCATCGATGCAT
1 TGAGTGCATCGA-TACACTAAATGCATTCGATGTTTCAA-ACAAGCCAGGAGTGCATCGATGCAT
*
277788 TG
64 GG
*
277790 TGAGCGCATCGATACACTAAATGCATT
1 TGAGTGCATCGATACACTAAATGCATT
277817 TGAAATAGAG
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
64 39 0.53
65 34 0.46
66 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (65 bp):
TGAGTGCATCGATACACTAAATGCATTCGATGTTTCAAACAAGCCAGGAGTGCATCGATGCATGG
Found at i:279773 original size:23 final size:22
Alignment explanation
Indices: 279741--279811 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 22
279731 CAGCAGAGTA
*
279741 CATCTATGCACATTCAAGGAATG
1 CATCGATGCACATTCAAGG-ATG
* *
279764 CATCGGTGCATC-TTC-ATGATG
1 CATCGATGCA-CATTCAAGGATG
*
279785 TATCGATGCACATTCAAGGCATG
1 CATCGATGCACATTCAAGG-ATG
279808 CATC
1 CATC
279812 AGTACGCTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 14 0.38
22 4 0.11
23 17 0.46
24 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATG
Found at i:280193 original size:94 final size:94
Alignment explanation
Indices: 280032--280220 Score: 369
Period size: 94 Copynumber: 2.0 Consensus size: 94
280022 CAAATAATGC
280032 AATCAAAAGTGTTATTTATAAGCATTTTCCAAAAGCTAATTAAAAGTGCTATAATTATTTTAAAC
1 AATCAAAAGTGTTATTTATAAGCATTTTCCAAAAGCTAATTAAAAGTGCTATAATTATTTTAAAC
280097 ACTAAGTGAAGATAGGTCAGTTAAACCTA
66 ACTAAGTGAAGATAGGTCAGTTAAACCTA
*
280126 AATCAAAAGTGTTATTTATAAGCATTTTCTAAAAGCTAATTAAAAGTGCTATAATTATTTTAAAC
1 AATCAAAAGTGTTATTTATAAGCATTTTCCAAAAGCTAATTAAAAGTGCTATAATTATTTTAAAC
280191 ACTAAGTGAAGATAGGTCAGTTAAACCTA
66 ACTAAGTGAAGATAGGTCAGTTAAACCTA
280220 A
1 A
280221 TTCTCTCATA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 94 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (94 bp):
AATCAAAAGTGTTATTTATAAGCATTTTCCAAAAGCTAATTAAAAGTGCTATAATTATTTTAAAC
ACTAAGTGAAGATAGGTCAGTTAAACCTA
Found at i:289220 original size:27 final size:26
Alignment explanation
Indices: 289180--289230 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
289170 GAGCCTTTAT
289180 ATTTTTTTAATTTTC-TTCTTCTTCCC
1 ATTTTTTTAATTTTCATTC-TCTTCCC
*
289206 ATTTTCTTTCATTTTCATTCTCTTC
1 ATTTT-TTTAATTTTCATTCTCTTC
289231 TTCTTCCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 14 0.64
28 3 0.14
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTTTTAATTTTCATTCTCTTCCC
Found at i:289741 original size:20 final size:21
Alignment explanation
Indices: 289703--289742 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
289693 TCGGAGTTTA
289703 AGTATCAATATTGGGATGAAC
1 AGTATCAATATTGGGATGAAC
*
289724 AGTATGAATATT-GGATGAA
1 AGTATCAATATTGGGATGAA
289743 TTGGGGCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.25, T:0.30
Consensus pattern (21 bp):
AGTATCAATATTGGGATGAAC
Found at i:292256 original size:26 final size:26
Alignment explanation
Indices: 292224--292300 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
292214 TTAATTGAAC
292224 TAAAAGAGCT-AATAAATCT-TTTCTAA
1 TAAAAGAG-TAAATAAATCTCTTT-TAA
292250 TAAAAGAGTAAATAAATCTCTTTTAA
1 TAAAAGAGTAAATAAATCTCTTTTAA
*
292276 TAAAAGA-TGAATTAAATCTCTTTTA
1 TAAAAGAGT-AAATAAATCTCTTTTA
292301 TCTTTATCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
25 2 0.04
26 42 0.89
27 3 0.06
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (26 bp):
TAAAAGAGTAAATAAATCTCTTTTAA
Found at i:295049 original size:18 final size:19
Alignment explanation
Indices: 295028--295065 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
295018 TCGATACTGA
*
295028 CCTT-TCAGTATCGATACC
1 CCTTCTCAGTATCAATACC
295046 CCTTCCTCAGTATCAATACC
1 CCTT-CTCAGTATCAATACC
295066 TCAACTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.37, G:0.08, T:0.32
Consensus pattern (19 bp):
CCTTCTCAGTATCAATACC
Found at i:297169 original size:120 final size:120
Alignment explanation
Indices: 296815--297181 Score: 520
Period size: 120 Copynumber: 3.1 Consensus size: 120
296805 ACACTTATAT
* * *
296815 GATTTAGGTTCGATCTTTGTAGACA-CTGATGTTTGACATAAGGTTCGCAACCCCAAATCTTCAT
1 GATTTAGGTTCGAGCTTTGTACACATCTGATGTTTGACATAAGGTTTGCAACCCCAAATCTTCAT
* * * * *
296879 TAAAGTCATATTAGTACGCTTCCCAGTCCATATCTCATATAGTGTCTTTTAAACC
66 AAAAGACATACTAGGACGCTTCCCAGTCCATATCTCATATAGTGTCTTTTGAACC
*
296934 GATTTAGGTTCGAGCTTTGTACACATCTGATGTTTGATATAAGGTTTGCAACCCCAAATCTTCAT
1 GATTTAGGTTCGAGCTTTGTACACATCTGATGTTTGACATAAGGTTTGCAACCCCAAATCTTCAT
* * *
296999 AAAAGACATACTAGGACACTTCCCAATCCATATCTCATATGGTGTCTTTTGAACC
66 AAAAGACATACTAGGACGCTTCCCAGTCCATATCTCATATAGTGTCTTTTGAACC
* * * * * *
297054 GATTTAGGTTTGAGCTTTGTATACATATGATGTTTGACATAAAGTTTGCAACACCAAATCATCAT
1 GATTTAGGTTCGAGCTTTGTACACATCTGATGTTTGACATAAGGTTTGCAACCCCAAATCTTCAT
* * * *
297119 AAAAGGCGTACTAGGATGCTTCCCAGTCCATATCTCATATAGTGTCTTTTGAACAA
66 AAAAGACATACTAGGACGCTTCCCAGTCCATATCTCATATAGTGTCTTTTGAAC-C
297175 GATTTAG
1 GATTTAG
297182 TGTGAAAGCG
Statistics
Matches: 220, Mismatches: 26, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
119 23 0.10
120 190 0.86
121 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (120 bp):
GATTTAGGTTCGAGCTTTGTACACATCTGATGTTTGACATAAGGTTTGCAACCCCAAATCTTCAT
AAAAGACATACTAGGACGCTTCCCAGTCCATATCTCATATAGTGTCTTTTGAACC
Found at i:299974 original size:16 final size:16
Alignment explanation
Indices: 299945--299977 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
299935 TTGTGTATCA
299945 AACATACGTCGTTACT
1 AACATACGTCGTTACT
299961 AACA-ACGTCTGTTACT
1 AACATACGTC-GTTACT
299977 A
1 A
299978 TAAAAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (16 bp):
AACATACGTCGTTACT
Found at i:304054 original size:20 final size:21
Alignment explanation
Indices: 304009--304062 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
303999 AGTCAGGGTT
*
304009 GTATCAATAACTACCTATAGGA
1 GTATCAAT-ACTACCTATAAGA
*
304031 GTATCAATACTTCC-ATAAGA
1 GTATCAATACTACCTATAAGA
*
304051 GTATCGATACTA
1 GTATCAATACTA
304063 AAGGTTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.54
21 5 0.18
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (21 bp):
GTATCAATACTACCTATAAGA
Found at i:321504 original size:18 final size:19
Alignment explanation
Indices: 321481--321523 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
321471 GTACAAAAAG
321481 AAAGAAAAG-ACAAAAGAA
1 AAAGAAAAGAACAAAAGAA
*
321499 AAAGAAAAGAATAAAAGAA
1 AAAGAAAAGAACAAAAGAA
321518 AAAGAA
1 AAAGAA
321524 TAATTTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAGAAAAGAACAAAAGAA
Found at i:331254 original size:18 final size:18
Alignment explanation
Indices: 331222--331268 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
331212 CTTTCTATCT
*
331222 TTATTT-CATT-TTTTTT
1 TTATTTCCATTATTTTTA
331238 TCTATTTCCATTATTTTTA
1 T-TATTTCCATTATTTTTA
331257 TTATTATCCATT
1 TTATT-TCCATT
331269 TCTTAATTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 8 0.31
19 12 0.46
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATTTCCATTATTTTTA
Found at i:339345 original size:60 final size:60
Alignment explanation
Indices: 339241--339353 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 60
339231 TGGCTAGTTC
* * * *
339241 GGTAAGTTTTCCTGTTCTGGGAAGTTTGGCATTACAGATTGGTCTGGCTGGTGCTGGATT
1 GGTAAGTTTTCCGGTTCTGGGAAGTTCGGCATTACAGATGGGTCTGACTGGTGCTGGATT
* * *
339301 GGTAAGTTTTCCGGTTTTGGGAAGTTCGGCATTGCTGATGGGTCTGACTGGTG
1 GGTAAGTTTTCCGGTTCTGGGAAGTTCGGCATTACAGATGGGTCTGACTGGTG
339354 TGGTTTAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.14, C:0.13, G:0.35, T:0.37
Consensus pattern (60 bp):
GGTAAGTTTTCCGGTTCTGGGAAGTTCGGCATTACAGATGGGTCTGACTGGTGCTGGATT
Found at i:361134 original size:40 final size:41
Alignment explanation
Indices: 361080--361193 Score: 117
Period size: 40 Copynumber: 2.8 Consensus size: 41
361070 CAACATAGTG
* * **
361080 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTCA
1 GTACTGTAGCGGCGTTTTTATACAAACGCCGCAACAGAAT-A
* * *
361122 -TA-TGTAGTGGCGTTTTTCA-ATAAACGCCGCAACCGAATA
1 GTACTGTAGCGGCGTTTTT-ATACAAACGCCGCAACAGAATA
*
361161 GTACTTTAGCGGCGTTTTTATACAAACGCCGCA
1 GTACTGTAGCGGCGTTTTTATACAAACGCCGCA
361194 TAGTATTCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
39 1 0.02
40 30 0.52
41 27 0.47
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (41 bp):
GTACTGTAGCGGCGTTTTTATACAAACGCCGCAACAGAATA
Found at i:361138 original size:81 final size:81
Alignment explanation
Indices: 360998--361193 Score: 223
Period size: 81 Copynumber: 2.4 Consensus size: 81
360988 GAAACAGAGC
* * * * * * *
360998 AGTACTTCAGCGGCATTTTTATACAAATGTCGCAATAGGTTAATCCATAGTGGCATTTTTTCAAT
1 AGTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTAATACATAGTGGCA-TTTTTCAAT
* * * *
361063 GAACTCC-CAACATAGT
65 AAACGCCGCAACAGAAT
* * ** *
361079 GGTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTCATATGTAGTGGCGTTTTTCAATA
1 AGTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTAATACATAGTGGCATTTTTCAATA
*
361144 AACGCCGCAACCGAAT
66 AACGCCGCAACAGAAT
361160 AGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
1 AGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
361194 TAGTATTCAT
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
80 14 0.15
81 82 0.85
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (81 bp):
AGTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTAATACATAGTGGCATTTTTCAATA
AACGCCGCAACAGAAT
Found at i:361188 original size:41 final size:42
Alignment explanation
Indices: 361080--361382 Score: 150
Period size: 41 Copynumber: 7.5 Consensus size: 42
361070 CAACATAGTG
* **
361080 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAAGAGGGTCA
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAACAGAATCA
* * * *
361122 -TA-TGTAGTGGCGTTTTTCA-ATAAACGCCGCAACCGAAT-A
1 GTACTTTAGCGGCGTTTTT-ATACAAACGCCGCAACAGAATCA
* *
361161 GTACTTTAGCGGCGTTTTTATACAAACGCCGC-ATAGTATTCA
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAACAG-AATCA
* ** * * *
361203 -T-CTATATTGGCGTTTATTCA-ACAAACGCTGCAATAGAGT-A
1 GTACTTTAGCGGCGTTT-TT-ATACAAACGCCGCAACAGAATCA
* * * * * *
361243 GTACTTTAGCGGCGGTTAT-TACAAATGCCGCTATAGACTC-
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAACAGAATCA
* * * * * * ** *
361283 TTACTTTAGTGGCGTTTTTAGAAAAACACCGCTATGGACTC-
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCAACAGAATCA
* * *
361324 GTACTTTAGTGGCGTTTTTATACAAACGCTGCTAA-AGACT-A
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGC-AACAGAATCA
*
361365 GTACTTTAG-TGCGTTTTT
1 GTACTTTAGCGGCGTTTTT
361383 GTTTACAGAC
Statistics
Matches: 201, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
39 1 0.00
40 82 0.41
41 101 0.50
42 17 0.08
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (42 bp):
GTACTTTAGCGGCGTTTTTATACAAACGCCGCAACAGAATCA
Found at i:361214 original size:81 final size:80
Alignment explanation
Indices: 361080--361352 Score: 264
Period size: 81 Copynumber: 3.4 Consensus size: 80
361070 CAACATAGTG
* * * *
361080 GTACTTTAGCGGCGTTTTTATACAAACGCCGCA-AGAGGGTCATATGTAGTGGCGTTTTTCAATA
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCATAGA--CTCATCTATAGTGGCGTTTTTCAAAA
**
361144 AACGCCGCAACCGAATA
64 AACGCCGCAATAGAATA
* * *
361161 GTACTTTAGCGGCGTTTTTATACAAACGCCGCATAGTATTCATCTATATTGGCGTTTATTCAACA
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGCATAG-ACTCATCTATAGTGGCGTTT-TTCAAAA
* *
361226 AACGCTGCAATAGAGTA
64 AACGCCGCAATAGAATA
* * * * *
361243 GTACTTTAGCGGCGGTTAT-TACAAATGCCGCTATAGACTCTTACTTTAGTGGCGTTTTT-AGAA
1 GTACTTTAGCGGCGTTTTTATACAAACGCCGC-ATAGACTCAT-CTATAGTGGCGTTTTTCA-AA
* * * * *
361306 AAACACCGCTATGGACTC
63 AAACGCCGCAATAGAATA
*
361324 GTACTTTAGTGGCGTTTTTATACAAACGC
1 GTACTTTAGCGGCGTTTTTATACAAACGC
361353 TGCTAAAGAC
Statistics
Matches: 158, Mismatches: 27, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
80 1 0.01
81 94 0.59
82 62 0.39
83 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (80 bp):
GTACTTTAGCGGCGTTTTTATACAAACGCCGCATAGACTCATCTATAGTGGCGTTTTTCAAAAAA
CGCCGCAATAGAATA
Found at i:361425 original size:42 final size:42
Alignment explanation
Indices: 361319--361490 Score: 170
Period size: 42 Copynumber: 4.1 Consensus size: 42
361309 CACCGCTATG
* * **
361319 GACTCGTACTTTAGTGGCG-TTTT-TATACAAACGCTGCTAAA
1 GACTAGTACTTTAGT-GCGTTTTTGTTTACAAACGCCACTAAA
*
361360 GACTAGTACTTTAGTGCGTTTTTGTTTACAGACGCCACTAAA
1 GACTAGTACTTTAGTGCGTTTTTGTTTACAAACGCCACTAAA
* * * *
361402 GACTGGTATTTTGGTAGCG-TTTTGTTTACAAACGCCGCTAAA
1 GACTAGTACTTTAGT-GCGTTTTTGTTTACAAACGCCACTAAA
* * * * *
361444 TACTAATACTTTAGTGACGTTTTTGTTTACCAACACCGCTAAA
1 GACTAGTACTTTAGTG-CGTTTTTGTTTACAAACGCCACTAAA
361487 GACT
1 GACT
361491 CTTGTGTTTG
Statistics
Matches: 108, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
40 3 0.03
41 19 0.18
42 59 0.55
43 27 0.25
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (42 bp):
GACTAGTACTTTAGTGCGTTTTTGTTTACAAACGCCACTAAA
Found at i:361443 original size:84 final size:84
Alignment explanation
Indices: 361335--361490 Score: 226
Period size: 84 Copynumber: 1.9 Consensus size: 84
361325 TACTTTAGTG
* * *
361335 GCGTTTTTATACAAACGCTGCTAAAGACTAGTACTTTAGTG-CGTTTTTGTTTA-CAGACGCCAC
1 GCGTTTTTATACAAACGCCGCTAAAGACTAATACTTTAGTGACGTTTTTGTTTACCA-ACACCAC
361398 TAAAGACTGGTATTTTGGTA
65 TAAAGACTGGTATTTTGGTA
* * *
361418 GCGTTTTGTTTACAAACGCCGCTAAATACTAATACTTTAGTGACGTTTTTGTTTACCAACACCGC
1 GCGTTTT-TATACAAACGCCGCTAAAGACTAATACTTTAGTGACGTTTTTGTTTACCAACACCAC
361483 TAAAGACT
65 TAAAGACT
361491 CTTGTGTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
83 7 0.11
84 30 0.47
85 25 0.39
86 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (84 bp):
GCGTTTTTATACAAACGCCGCTAAAGACTAATACTTTAGTGACGTTTTTGTTTACCAACACCACT
AAAGACTGGTATTTTGGTA
Found at i:363155 original size:29 final size:28
Alignment explanation
Indices: 363121--363203 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
363111 ATTAAATGAC
*
363121 CAAAATATAAATTTTTAAAGTTTAGTGA
1 CAAAATATAAATTTTTAAAGTTTAGGGA
**
363149 TCAAAATATAAACTTTAAAAAAGTTTAGGGA
1 -CAAAATATAAA-TTT-TTAAAGTTTAGGGA
*
363180 CTAAATGAT-AATTTTTAAAAGTTT
1 CAAAAT-ATAAATTTTT-AAAGTTT
363204 TCATTGACGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
29 21 0.48
30 10 0.23
31 13 0.30
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (28 bp):
CAAAATATAAATTTTTAAAGTTTAGGGA
Found at i:364777 original size:24 final size:24
Alignment explanation
Indices: 364745--364792 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
364735 ATGCATGAAA
364745 TTGTACATAGATGTTTTATACATC
1 TTGTACATAGATGTTTTATACATC
*
364769 TTGTACATAGATTTTTTATACATC
1 TTGTACATAGATGTTTTATACATC
364793 ATCAGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.48
Consensus pattern (24 bp):
TTGTACATAGATGTTTTATACATC
Found at i:365171 original size:59 final size:59
Alignment explanation
Indices: 365072--365205 Score: 178
Period size: 59 Copynumber: 2.3 Consensus size: 59
365062 CAACAGGCTG
* * ** *
365072 CATATTCGGGATTACACTAAAGGATACTTAGTGTATATGGTCGACACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGGATACCTAGTACAGATGGTCGACACGACCTTATGTGT
* * * *
365131 CATATTTGGGATTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGATTGCACTAAAGGATACCTAGTACAGATGGTCGACACGACCTTATGTGT
*
365190 CATACTCGGGATTGCA
1 CATATTCGGGATTGCA
365206 TTACGGTGCA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (59 bp):
CATATTCGGGATTGCACTAAAGGATACCTAGTACAGATGGTCGACACGACCTTATGTGT
Found at i:365337 original size:45 final size:45
Alignment explanation
Indices: 365280--365432 Score: 279
Period size: 45 Copynumber: 3.4 Consensus size: 45
365270 ATGGTTTATG
*
365280 GTATATTGGTAAAATAAGCTTACGAGCTTATGAGATAAATGGTAA
1 GTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAA
*
365325 GTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGATAA
1 GTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAA
*
365370 GTATATTGGTAAAATAAGCTTATGAGCTTATGGGATAAATGGTAA
1 GTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAA
365415 GTATATTGGTAAAATAAG
1 GTATATTGGTAAAATAAG
365433 AAATTTTATA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 104 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (45 bp):
GTATATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAA
Found at i:367742 original size:21 final size:20
Alignment explanation
Indices: 367724--367847 Score: 87
Period size: 21 Copynumber: 6.1 Consensus size: 20
367714 CTAGAAAATG
367724 AAGAAGAA-AAAAATAAAAACA
1 AAGAAGAAGAAAAA-AAAAA-A
* *
367745 AA-AAAAACAAAAAAGAAAAA
1 AAGAAGAAGAAAAAA-AAAAA
367765 AAGAA-AAGAATAAAACAAAAA
1 AAGAAGAAGAA-AAAA-AAAAA
* * *
367786 AAGAAAAAGAAGAAAACAAA
1 AAGAAGAAGAAAAAAAAAAA
*
367806 AAGAAAGAAGAAAAGAAAAAA
1 AAG-AAGAAGAAAAAAAAAAA
*
367827 AAG--GTAGAAAAAAAGAAAA
1 AAGAAGAAGAAAAAAA-AAAA
367846 AA
1 AA
367848 ATATGAGAAG
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
18 9 0.11
19 6 0.07
20 19 0.22
21 46 0.54
22 5 0.06
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.02
Consensus pattern (20 bp):
AAGAAGAAGAAAAAAAAAAA
Found at i:367835 original size:18 final size:16
Alignment explanation
Indices: 367724--367846 Score: 97
Period size: 18 Copynumber: 7.1 Consensus size: 16
367714 CTAGAAAATG
367724 AAGAAGAAAAAAATAAA
1 AAGAAGAAAAAAA-AAA
*
367741 AACAA-AAAAAACAAAA
1 AAGAAGAAAAAA-AAAA
367757 AAGAA-AAAAAGAAAAGA
1 AAGAAGAAAAA-AAAA-A
* *
367774 ATAAAACAAAAAAAGAAA
1 A-AGAAGAAAAAAA-AAA
367792 AAGAAGAAAACAAAAAGA
1 AAGAAGAAAA-AAAAA-A
367810 AAGAAGAAAAGAAAAAA
1 AAGAAGAAAA-AAAAAA
*
367827 AAGGTAGAAAAAAAGAAA
1 AA-GAAGAAAAAAA-AAA
367845 AA
1 AA
367847 AATATGAGAA
Statistics
Matches: 89, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
16 21 0.24
17 23 0.26
18 38 0.43
19 7 0.08
ACGTcount: A:0.81, C:0.03, G:0.13, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAAAAAAAA
Found at i:367848 original size:1 final size:1
Alignment explanation
Indices: 367730--367828 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
367720 AATGAAGAAG
* * * * * * * * * *
367730 AAAAAAATAAAAACAAAAAAAACAAAAAAGAAAAAAAGAAAAGAATAAAACAAAAAAAGAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
367795 AAGAAAACAAAAAGAAAGAAGAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
367829 GGTAGAAAAA
Statistics
Matches: 66, Mismatches: 32, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (1 bp):
A
Found at i:367848 original size:8 final size:8
Alignment explanation
Indices: 367727--367827 Score: 79
Period size: 8 Copynumber: 13.2 Consensus size: 8
367717 GAAAATGAAG
367727 AAGAAAAA
1 AAGAAAAA
*
367735 AATAAAAA
1 AAGAAAAA
*
367743 CA-AAAAA
1 AAGAAAAA
*
367750 AA-CAAAA
1 AAGAAAAA
367757 AAGAAAAA
1 AAGAAAAA
367765 AAG---AA
1 AAGAAAAA
*
367770 AAGAATAA
1 AAGAAAAA
*
367778 AACAAAAA
1 AAGAAAAA
367786 AAGAAAAA
1 AAGAAAAA
*
367794 GAAGAAAAC
1 -AAGAAAAA
*
367803 AA-AAAGA
1 AAGAAAAA
*
367810 AAGAAGAA
1 AAGAAAAA
367818 AAGAAAAA
1 AAGAAAAA
367826 AA
1 AA
367828 AGGTAGAAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
5 5 0.07
7 17 0.23
8 44 0.60
9 7 0.10
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:367848 original size:21 final size:21
Alignment explanation
Indices: 367730--367827 Score: 64
Period size: 20 Copynumber: 4.9 Consensus size: 21
367720 AATGAAGAAG
* *
367730 AAAAAAATAAA-AACAAAA-A
1 AAAAAAAGAAAGAAAAAAAGA
*
367749 AAACAAA-AAAGAAAAAAAGA
1 AAAAAAAGAAAGAAAAAAAGA
* *
367769 AAAGAATA-AAACAAAAAAAGA
1 AAA-AAAAGAAAGAAAAAAAGA
* *
367790 AAAAGAAGAAA-ACAAAAAGA
1 AAAAAAAGAAAGAAAAAAAGA
* *
367810 AAGAAGA-AAAGAAAAAAA
1 AAAAAAAGAAAGAAAAAAA
367828 AGGTAGAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
18 3 0.05
19 15 0.24
20 24 0.39
21 20 0.32
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAGAAAAAAAGA
Found at i:371392 original size:24 final size:24
Alignment explanation
Indices: 371365--371413 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
371355 TGCATGACAT
*
371365 TGTACATTGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
371389 TGTATATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
371413 T
1 T
371414 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:371611 original size:57 final size:58
Alignment explanation
Indices: 371542--371663 Score: 183
Period size: 58 Copynumber: 2.1 Consensus size: 58
371532 TGTGATATTT
* * *
371542 TACCATAAATGTTATTTCGGGTATGAACTGACC-ATTGTTAAATATATGGTTATATGA
1 TACCATGAATGTTATTTCAGGTATGAACTGACCTAATGTTAAATATATGGTTATATGA
* * *
371599 TACCATGAATGTTATTTTAGGTATGAATTGCCCTAATGTTAAATATATGGTTATATGA
1 TACCATGAATGTTATTTCAGGTATGAACTGACCTAATGTTAAATATATGGTTATATGA
371657 TACCATG
1 TACCATG
371664 GATAAATGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 28 0.48
58 30 0.52
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (58 bp):
TACCATGAATGTTATTTCAGGTATGAACTGACCTAATGTTAAATATATGGTTATATGA
Found at i:372013 original size:45 final size:45
Alignment explanation
Indices: 371959--372108 Score: 273
Period size: 45 Copynumber: 3.3 Consensus size: 45
371949 ATTTATGGTG
371959 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
*
372004 TATTGGTAAAATAAGTTTACGAGCTTATGGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
* *
372049 TATTGGTAAAATAAGCTTATGAGCTTTTGGGATAAATGGTAAGTA
1 TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
372094 TATTGGTAAAATAAG
1 TATTGGTAAAATAAG
372109 AAATTTTATA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 101 1.00
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (45 bp):
TATTGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTA
Found at i:374647 original size:19 final size:19
Alignment explanation
Indices: 374622--374670 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
374612 AAATAACTAC
374622 TAAAATTAAAAAAAAT-AA
1 TAAAATTAAAAAAAATAAA
* *
374640 TAAAAATTACAAATAATAAA
1 T-AAAATTAAAAAAAATAAA
374660 TAAAATTAAAA
1 TAAAATTAAAA
374671 TATACAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 22 0.85
20 3 0.12
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAATTAAAAAAAATAAA
Found at i:375608 original size:10 final size:10
Alignment explanation
Indices: 375593--375625 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
375583 TGTTTCAGTG
*
375593 ATTTTGCCTT
1 ATTTTGACTT
375603 ATTTTGACTT
1 ATTTTGACTT
375613 ATTTTGACTT
1 ATTTTGACTT
375623 ATT
1 ATT
375626 GGTGATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (10 bp):
ATTTTGACTT
Found at i:376020 original size:112 final size:112
Alignment explanation
Indices: 375776--376211 Score: 540
Period size: 112 Copynumber: 3.9 Consensus size: 112
375766 ACCCAGGAAA
* * * ** * * *
375776 CATTGAATCAAGGCAGACTTGTTGCATTGTTACTTATGGAATATCAAATCTT-GACAGAGAGAGA
1 CATTGAATCGAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGA-AGAGAGAGA
* *
375840 TATGTTCCGCTTCTTCT--AAGGGAATATCAGATATGGGAAAGTTGATAT
65 TATGTTCCGCTTCTT-TGAAAGGGAATATCAGATATGTGAAAATTGAT-T
375888 -ATTGAATCG-GAGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGAGA
1 CATTGAATCGAG-GTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGAGA
* ** *
375951 TATATTTTGCTTCTTTGAAAGGGAATATCAGATCTGTGAAAATTGATT
65 TATGTTCCGCTTCTTTGAAAGGGAATATCAGATATGTGAAAATTGATT
* *
375999 CATTGAATCGAGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGAT
1 CATTGAATCGAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGAGAT
* * * * * *
376064 TTGTTCCACTTCTTTGAAAGGGAATATCAAATTTGTAAAAATTGATC
66 ATGTTCCGCTTCTTTGAAAGGGAATATCAGATATGTGAAAATTGATT
* * * *
376111 CATTAAATCGAGCTAGACTTGTTCTGCTGCCACTCAGGGAATATCAAATCTTGGAAGAGAGAGAT
1 CATTGAATCGAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGAGAT
* * *
376176 CTGTTCCGCTTCTTTGAAAAGGAATATCATATATGT
66 ATGTTCCGCTTCTTTGAAAGGGAATATCAGATATGT
376212 AGGGGTCGAT
Statistics
Matches: 284, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
110 2 0.01
111 63 0.22
112 218 0.77
113 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (112 bp):
CATTGAATCGAGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGAGAT
ATGTTCCGCTTCTTTGAAAGGGAATATCAGATATGTGAAAATTGATT
Found at i:379011 original size:101 final size:101
Alignment explanation
Indices: 378835--379037 Score: 361
Period size: 101 Copynumber: 2.0 Consensus size: 101
378825 TTTAATGTAT
378835 TACAAGATGTCGTAATACCAGGGATTTCCATCATTTTTCTCTTCTATACTATAGCAATGGGCTGG
1 TACAAGATGTCGTAATACCAGGGATTTCCATCATTTTTCTCTTCTATACTATAGCAATGGGCTGG
378900 ATACCAATAAGCTTGTATCGTAATAGGCATCATGCC
66 ATACCAATAAGCTTGTATCGTAATAGGCATCATGCC
* * *
378936 TACAAGATGTCGTAATACCAGGGATTTCCATCGTTTTTCTCTTTTATGCTATAGCAATGGGCTGG
1 TACAAGATGTCGTAATACCAGGGATTTCCATCATTTTTCTCTTCTATACTATAGCAATGGGCTGG
* *
379001 ATACCCATAAGTTTGTATCGTAATAGGCATCATGCC
66 ATACCAATAAGCTTGTATCGTAATAGGCATCATGCC
379037 T
1 T
379038 GAATATTCAT
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (101 bp):
TACAAGATGTCGTAATACCAGGGATTTCCATCATTTTTCTCTTCTATACTATAGCAATGGGCTGG
ATACCAATAAGCTTGTATCGTAATAGGCATCATGCC
Found at i:384558 original size:21 final size:21
Alignment explanation
Indices: 384529--384570 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
384519 TTCTTCAGAG
* *
384529 GTAATACCAATAGTTGGAGCT
1 GTAACACCAATAGTTGAAGCT
384550 GTAACACCAATAGTTGAAGCT
1 GTAACACCAATAGTTGAAGCT
384571 TTTCCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (21 bp):
GTAACACCAATAGTTGAAGCT
Found at i:396132 original size:13 final size:13
Alignment explanation
Indices: 396114--396170 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
396104 TACGAACAAT
396114 AAATAAACAATAC
1 AAATAAACAATAC
396127 AAATAAACTAATAC
1 AAATAAAC-AATAC
*
396141 ----GAACAAT--
1 AAATAAACAATAC
396148 AAATAAACAATAC
1 AAATAAACAATAC
396161 AAATAAACAA
1 AAATAAACAA
396171 ATACGAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
9 3 0.09
10 3 0.09
11 6 0.17
13 18 0.51
14 5 0.14
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (13 bp):
AAATAAACAATAC
Found at i:396133 original size:17 final size:17
Alignment explanation
Indices: 396111--396167 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
396101 GTTTACGAAC
396111 AATAAATAAACAATACA
1 AATAAATAAACAATACA
*
396128 AATAAACTAATACGA-AC-
1 AATAAA-TAA-ACAATACA
396145 AATAAATAAACAATACA
1 AATAAATAAACAATACA
396162 AATAAA
1 AATAAA
396168 CAAATACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.09
16 5 0.15
17 18 0.53
18 5 0.15
19 3 0.09
ACGTcount: A:0.68, C:0.12, G:0.02, T:0.18
Consensus pattern (17 bp):
AATAAATAAACAATACA
Found at i:396144 original size:34 final size:34
Alignment explanation
Indices: 396104--396179 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
396094 CGAACATGTT
*
396104 TACGAACAATAAATAAACAATACAAATAAACTAA
1 TACGAACAATAAATAAACAATACAAATAAACAAA
396138 TACGAACAATAAATAAACAATACAAATAAACAAA
1 TACGAACAATAAATAAACAATACAAATAAACAAA
396172 TACGAACA
1 TACGAACA
396180 TGATATTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (34 bp):
TACGAACAATAAATAAACAATACAAATAAACAAA
Found at i:396172 original size:21 final size:21
Alignment explanation
Indices: 396125--396173 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
396115 AATAAACAAT
* *
396125 ACAAATAAACTAATACGAACA
1 ACAAATAAACTAATACAAAAA
*
396146 ATAAATAAAC-AATACAAATAA
1 ACAAATAAACTAATACAAA-AA
396167 ACAAATA
1 ACAAATA
396174 CGAACATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (21 bp):
ACAAATAAACTAATACAAAAA
Found at i:399727 original size:18 final size:18
Alignment explanation
Indices: 399696--399731 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
399686 TAAAATTAGG
*
399696 CCTCAGTATCGATACTGA
1 CCTCAATATCGATACTGA
*
399714 CCTCAATATTGATACTGA
1 CCTCAATATCGATACTGA
399732 AACAATGAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (18 bp):
CCTCAATATCGATACTGA
Found at i:403344 original size:14 final size:16
Alignment explanation
Indices: 403325--403356 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
403315 GGATCATATT
403325 CACATA-ATTCA-TCA
1 CACATACATTCATTCA
403339 CACATACATTCATTCA
1 CACATACATTCATTCA
403355 CA
1 CA
403357 TAGATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (16 bp):
CACATACATTCATTCA
Found at i:404329 original size:36 final size:36
Alignment explanation
Indices: 404285--404360 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 36
404275 ATTTTCGGGA
*
404285 TTTTGCTATATTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATATTTGGCAAAATTCGAATAAAGACGAT
*
404321 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATATTTGGCAAAATTCGAATAAAGACGAT
404357 TTTT
1 TTTT
404361 TTTGCTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGCTATATTTGGCAAAATTCGAATAAAGACGAT
Found at i:416309 original size:14 final size:14
Alignment explanation
Indices: 416290--416325 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
416280 GCAAACAATC
416290 TACCTTGTGAGGTT
1 TACCTTGTGAGGTT
416304 TACCTTGTGAGGTT
1 TACCTTGTGAGGTT
*
416318 TTCCTTGT
1 TACCTTGT
416326 AAGTTTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (14 bp):
TACCTTGTGAGGTT
Found at i:418443 original size:21 final size:21
Alignment explanation
Indices: 418418--418459 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
418408 CCAGAATGGG
*
418418 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
418439 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
418460 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:418631 original size:18 final size:19
Alignment explanation
Indices: 418570--418623 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
418560 CTCGGGTTAA
* *
418570 TGTTCAAACAGTGATTTAC
1 TGTTCAAATAGTAATTTAC
418589 TGTTCAAATAGTAATTTAC
1 TGTTCAAATAGTAATTTAC
418608 TGTTCAAATAGTAATT
1 TGTTCAAATAGTAATT
418624 ACTATTCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (19 bp):
TGTTCAAATAGTAATTTAC
Found at i:420044 original size:29 final size:29
Alignment explanation
Indices: 420012--420069 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
420002 AAATTTTGAA
*
420012 TAAATTCAATTAAGTCCAAATA-CATTTTG
1 TAAATTCAATCAAGTCCAAA-ACCATTTTG
420041 TAAATTCAATCAAGTCCAAAACCATTTTG
1 TAAATTCAATCAAGTCCAAAACCATTTTG
420070 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATCAAGTCCAAAACCATTTTG
Found at i:420818 original size:29 final size:30
Alignment explanation
Indices: 420786--420844 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
420776 TAAATTTGAA
420786 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAA-ACCATTTTG
420815 TAAATTCAATTCAAGTCCAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAACCATTTTG
420845 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAACCATTTTG
Found at i:421603 original size:29 final size:31
Alignment explanation
Indices: 421571--421630 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
421561 AAATTTTGAA
*
421571 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
421600 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
421631 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:423029 original size:791 final size:796
Alignment explanation
Indices: 419410--424025 Score: 8428
Period size: 791 Copynumber: 5.9 Consensus size: 796
419400 AAATTTTGTA
419410 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
419475 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
66 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
419540 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
131 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
*
419605 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTAAAC-AAAAA-AACAAACATGTT
196 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
419668 AGTAGCACATGAAATTC-A-ATATCCAAGACTAAAATAC-TTATGCAATACCAATTGTTGAAA-T
261 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
419729 TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCA-
326 TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCAT
419793 TTGAAAATTTTGATATCAA-TGTT--AGAG--------------TAAACCACATGCATAAACATT
391 TTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
419841 C-AATATAGGCC-AAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
456 CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
419904 AATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
521 AATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
419969 TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
586 TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
420034 CATTTTGTAAATTCAA-TCAAGTCC-AAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
651 CATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
420097 TCAACAATCTCCCCC-TTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTCCC
716 TCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTCCC
420161 CCTTAATAAAATATTT
781 CCTTAATAAAATATTT
* *
420177 AATGAAAAAGAGACTAGTCCATTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
420242 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
66 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
420307 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
131 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
420372 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAAC-AAAAATAACAAACATG-T
196 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
420435 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGC-ATA-CAATTGTTGAAATT
261 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
420498 TGATATC-A-ATCAATTGTTAAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCA
326 TGATATCAATATCAATTGTT-AAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCA
420561 TTTGAAAA-TTTGATATCAATTG-TAGAGAGATATCATTTTCATTTAAACCACATGCATAAACAT
390 TTTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACAT
420624 TCAAATATAGGCC-AAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATT-
455 TCAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTA
420687 AAATTAAAATTAAAATTTAATGTTCAAATAGT-AA-TACTA-TCAT-AAAACATTTTTGTGCTC-
520 AAATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCA
420747 --TTT-AATTAAAAGAACTTTGAATT-TTTTTGTAAA-TTTGAATAAATTCAATTAAGTCCAAAT
585 ATTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAAT
420807 ACATTTTGTAAATTCAATTCAAGTCC-AAAACCATTTTGCCTTAAATTGTTATACCG-AACATAG
650 ACATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAG
420870 TTTCAACAATCT--CCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAA--C
715 -TTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTC
420931 CCCCTTAATAAAATATTT
779 CCCCTTAATAAAATATTT
420949 AATGAAAAAGATACTAGTCCC-TTTTCATT-AAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
421012 TTTTTGTTATATC-AAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGCAGTAAGTAGTA
66 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAG-AGTAAGTAGTA
421076 AATTTTACA-TTTAAAAAATCATTTG-AAAATCAAAGCTCCCCCTCAAT-AATACATTCCAAATA
130 AATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATA
421138 AAATTTAGCTTTAAGAAC-AGACACTTAAACAAAATTGAATTTCAACAAAAAAATAAC-AACATG
195 AAATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAAC-AAAAAATAACAAACATG
421201 TTAGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAA
259 TTAGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAA
421266 TTTGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGC
324 TTTGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGC
421331 ATTTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACA
389 ATTTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACA
421396 TTCAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATT
454 TTCAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATT
421461 AAAATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTC
519 AAAATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTC
421526 AATTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAA
584 AATTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAA
421591 TACATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATA-CGAAACATA
649 TACATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATA
421655 GTTCAAC-ATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAA-TGTTTTTGGC-AAAAACTC
714 GTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTC
421717 CCCCTTAAT-AAATATTT
779 CCCCTTAATAAAATATTT
* *
421734 AATGAAAAAGAGACTAGTCCATTTTTCATT-AAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCT-CCCC
421798 CTTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTT-AAA-AACTATGGAGAGTAAGTAGTA
65 CTTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTA
421861 AATTTTACATTTTAAAAAATCA-TTGAAAAATCAAAGCTCCCCCTCAAT-AATACATTCCAAATA
130 AATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATA
421924 AAATTTAGCTTT-AGAA-AAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGT
195 AAATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGT
421987 TAGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAAT
260 TAGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAAT
422052 TTGATATCAATATC-ATTGTT-AAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCA
325 TTGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCA
422115 TTTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACAT
390 TTTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACAT
422180 TCAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATT-
455 TCAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTA
422244 AAATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCA
520 AAATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCA
422309 ATTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAA-TAAGTCC-AAT
585 ATTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAAT
422372 ACATTTTGTAAATTCAATTCAAGTCCAAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATA
650 ACATTTTGTAAATTCAATTCAAGTCC-AAAAACCATTTTGCCTTAAATTGTTATACCGAAACATA
422437 GTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTC
714 GTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTC
422502 CCCCTTAATAAAATATTT
779 CCCCTTAATAAAATATTT
422520 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
422585 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
66 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
422650 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
131 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
422715 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAAC-AACATGTT
196 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
422779 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
261 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
422844 TGATATC-ATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCAT
326 TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCAT
422908 TTG-AAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
391 TTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
422972 CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
456 CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
*
423037 AATTAAAATTAAAATTTAATGTTCTAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
521 AATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
423102 TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCC-AATA
586 TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
423166 CATTTTGTAAATTC-ATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
651 CATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
423230 TCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTCCC
716 TCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTCCC
423295 CCTTAATAAAATATTT
781 CCTTAATAAAATATTT
423311 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
1 AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
423376 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTAT-G-GAGTAAGTAGTAA
66 TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
423439 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
131 ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
423504 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
196 AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
423569 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAA-T
261 AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
*
423633 TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATTAAGTTTTCCAAAAATGCTATGCAT
326 TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCAT
423698 TTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
391 TTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
423763 CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
456 CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
* *
423828 AATTAAAATTAAAATTTAATGTTCTAATA-TAAATTACT-TTCATAAAAACAGTTTTGTGCTCAA
521 AATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
423891 TTTTAAATT-AAAGAAC-TTGAATTA-TTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
586 TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
* *
423953 CATTTTGTAAATTCAATTCAAGTCTAAAAACCATTTTGCCTTAAATTGTTATATCGAAACATAGT
651 CATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
424018 TCAACAAT
716 TCAACAAT
424026 GAGGTTTTAA
Statistics
Matches: 3750, Mismatches: 14, Indels: 149
0.96 0.00 0.04
Matches are distributed among these distances:
766 28 0.01
767 310 0.08
768 158 0.04
769 97 0.03
770 98 0.03
771 61 0.02
772 62 0.02
773 57 0.02
774 145 0.04
775 91 0.02
776 22 0.01
777 8 0.00
778 4 0.00
779 17 0.00
780 46 0.01
781 39 0.01
782 142 0.04
783 231 0.06
784 99 0.03
785 316 0.08
786 295 0.08
787 79 0.02
788 130 0.03
789 201 0.05
790 172 0.05
791 604 0.16
792 213 0.06
793 25 0.01
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (796 bp):
AATGAAAAAGATACTAGTCCCTTTTTCATTAAAAAATTGAATTTTTCAAACTAAACTCCTCCCCC
TTTTTGTTATATCAAAAATAATTCGATCTTTGAAGTTTAAAATAACTATGGAGAGTAAGTAGTAA
ATTTTACATTTTAAAAAATCATTTGAAAAATCAAAGCTCCCCCTCAATAAATACATTCCAAATAA
AATTTAGCTTTAAGAACAAGACACTTAAACAAAATTGAATTTCAACAAAAAATAACAAACATGTT
AGTAGCACATGAAATTCAATATATCCAAGACTAAAATACTTTATGCAATACCAATTGTTGAAATT
TGATATCAATATCAATTGTTAAAATTAAGTGCATATGCATAAAGTTTTCCAAAAATGCTATGCAT
TTGAAAATTTTGATATCAATTGTTAGAGAGATATCATTTTCATTTAAACCACATGCATAAACATT
CAAATATAGGCCAAAAATTAAAATTTATAAAATCAAAGTATTTTGAAATTTAGGCCAAAAATTAA
AATTAAAATTAAAATTTAATGTTCAAATAGTAAATTACTATTCATAAAAACATTTTTGTGCTCAA
TTTTAAATTAAAAGAACTTTGAATTATTTTTGTAAATTTTGAATAAATTCAATTAAGTCCAAATA
CATTTTGTAAATTCAATTCAAGTCCAAAAACCATTTTGCCTTAAATTGTTATACCGAAACATAGT
TCAACAATCTCCCCCTTTTTGATATAACAAAACATTTGAAAAATTGTTTTTGGCAAAAAACTCCC
CCTTAATAAAATATTT
Found at i:423200 original size:30 final size:28
Alignment explanation
Indices: 423145--423202 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
423135 AAATTTTGAA
*
423145 TAAATTCAATTAAGTCCAATACATTTTG
1 TAAATTCAATTAAGTCCAAAACATTTTG
423173 TAAATTC-ATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCC-AAAA-CATTTTG
423203 CCTTAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 3 0.12
28 13 0.50
29 3 0.12
30 7 0.27
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (28 bp):
TAAATTCAATTAAGTCCAAAACATTTTG
Found at i:423965 original size:29 final size:31
Alignment explanation
Indices: 423931--423990 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
423921 AAATTTTGAA
*
423931 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
423960 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
423991 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:425945 original size:78 final size:78
Alignment explanation
Indices: 425848--426003 Score: 312
Period size: 78 Copynumber: 2.0 Consensus size: 78
425838 AATCTACTGT
425848 AGGTACTAGATGGGTATTTAGGAATAAGCTTGATGAAAGTGGTAATATAGTGAGAAACAAGGCTA
1 AGGTACTAGATGGGTATTTAGGAATAAGCTTGATGAAAGTGGTAATATAGTGAGAAACAAGGCTA
425913 GACTTGTTGCTCA
66 GACTTGTTGCTCA
425926 AGGTACTAGATGGGTATTTAGGAATAAGCTTGATGAAAGTGGTAATATAGTGAGAAACAAGGCTA
1 AGGTACTAGATGGGTATTTAGGAATAAGCTTGATGAAAGTGGTAATATAGTGAGAAACAAGGCTA
425991 GACTTGTTGCTCA
66 GACTTGTTGCTCA
426004 GAGGGCATAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.35, C:0.09, G:0.28, T:0.28
Consensus pattern (78 bp):
AGGTACTAGATGGGTATTTAGGAATAAGCTTGATGAAAGTGGTAATATAGTGAGAAACAAGGCTA
GACTTGTTGCTCA
Found at i:427598 original size:24 final size:23
Alignment explanation
Indices: 427571--427621 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
427561 AGAATTGATA
427571 CCCTCTTAAAGGGGAACCGATTCC
1 CCCT-TTAAAGGGGAACCGATTCC
*
427595 CCCTTTGAAGGGGAACCGATTCC
1 CCCTTTAAAGGGGAACCGATTCC
427618 CCCT
1 CCCT
427622 GGAGGGAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.22, C:0.35, G:0.22, T:0.22
Consensus pattern (23 bp):
CCCTTTAAAGGGGAACCGATTCC
Found at i:440978 original size:27 final size:27
Alignment explanation
Indices: 440940--440993 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
440930 ACACACGATC
440940 GATCATCATTTGGGATTTCAAAGCTGA
1 GATCATCATTTGGGATTTCAAAGCTGA
440967 GATCATCATTTGGGATTTCAAAGCTGA
1 GATCATCATTTGGGATTTCAAAGCTGA
440994 AACTATCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (27 bp):
GATCATCATTTGGGATTTCAAAGCTGA
Found at i:443963 original size:21 final size:21
Alignment explanation
Indices: 443937--443988 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
443927 GAGACCCGAA
* *
443937 TATCGATATTCTACGAATATG
1 TATCGATACTCTACAAATATG
443958 TATCGATACTCTACAAATATG
1 TATCGATACTCTACAAATATG
443979 TATCGATACT
1 TATCGATACT
443989 ACCCTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (21 bp):
TATCGATACTCTACAAATATG
Found at i:456510 original size:26 final size:27
Alignment explanation
Indices: 456447--456511 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
456437 AAGAATCAAC
*
456447 AAATCTCTTCTAATATAATAGAAAAAT
1 AAATCTCTTTTAATATAATAGAAAAAT
* * *
456474 AAATCTTTTTTAATA-AA-AGAGGAATT
1 AAATCTCTTTTAATATAATAGA-AAAAT
456500 AAATCTCTTTTA
1 AAATCTCTTTTA
456512 TCTTTATCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 3 0.09
26 16 0.50
27 13 0.41
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (27 bp):
AAATCTCTTTTAATATAATAGAAAAAT
Found at i:458034 original size:18 final size:18
Alignment explanation
Indices: 458013--458047 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
458003 AATTAAATAA
*
458013 ATAAAGACTAAAATAAAT
1 ATAAAAACTAAAATAAAT
*
458031 ATAAAAATTAAAATAAA
1 ATAAAAACTAAAATAAA
458048 AGGAAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
ATAAAAACTAAAATAAAT
Found at i:462043 original size:26 final size:25
Alignment explanation
Indices: 462014--462072 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
462004 TGAAAGAGCT
462014 AATAAATATATTCT-AATAAAAGAGGA
1 AATAAATATATT-TGAATAAAAGA-GA
* *
462040 AATAAATGTCTTTGAATAAAAGAGA
1 AATAAATATATTTGAATAAAAGAGA
462065 AATTAAAT
1 AA-TAAAT
462073 CTTTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.29
Consensus pattern (25 bp):
AATAAATATATTTGAATAAAAGAGA
Found at i:475813 original size:21 final size:21
Alignment explanation
Indices: 475787--475836 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
475777 TGATATGTTG
*
475787 CTCTCTCTAC-TTCTGTTGCTT
1 CTCTCTCTACTTTC-GCTGCTT
* *
475808 CTCTCTTTGCTTTCGCTGCTT
1 CTCTCTCTACTTTCGCTGCTT
475829 CTCTCTCT
1 CTCTCTCT
475837 GCCTCGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.02, C:0.36, G:0.10, T:0.52
Consensus pattern (21 bp):
CTCTCTCTACTTTCGCTGCTT
Found at i:478378 original size:24 final size:24
Alignment explanation
Indices: 478351--478485 Score: 101
Period size: 24 Copynumber: 5.6 Consensus size: 24
478341 TATATCAAAA
* * *
478351 ATCAAATCATAATTCACGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
478375 ATCATATCAAAATCCAAGTCAAAT
1 ATCAAATCAAAATCCAAGTCAAGT
* *
478399 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
** * *
478423 ATCGGATCAGAATCCATGTC-AGAT
1 ATCAAATCAAAATCCAAGTCAAG-T
* * **
478447 ATCAGATCAGAATCCTTGTCAAGT
1 ATCAAATCAAAATCCAAGTCAAGT
*
478471 ATCAGATCATAAATC
1 ATCAAATCA-AAATC
478486 AAATCGAAAA
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 87 0.92
25 6 0.06
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAAATCAAAATCCAAGTCAAGT
Found at i:478420 original size:48 final size:48
Alignment explanation
Indices: 478345--478485 Score: 165
Period size: 48 Copynumber: 2.9 Consensus size: 48
478335 AATGGATATA
* * * * * *
478345 TCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAAG
1 TCAAATATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
* * *
478393 TCAAATATCAGATCAGAATCCAAGTCAAGTATCGGATCAGAATCCATG
1 TCAAATATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
* **
478441 TCAGATATCAGATCAGAATCCTTGTCAAGTATCAGATCATAAATC
1 TCAAATATCAGATCAGAATCCAAGTCAAGTATCAGATCA-AAATC
478486 AAATCGAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 74 0.95
49 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.26
Consensus pattern (48 bp):
TCAAATATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
Found at i:483017 original size:24 final size:24
Alignment explanation
Indices: 483007--483121 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
482997 CATAATTCAC
* *
483007 GTCAAGTATCATATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
483031 GTCAAATATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
483055 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
483079 GTC-AGATATCAAATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
483103 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
483122 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:483059 original size:48 final size:48
Alignment explanation
Indices: 482984--483124 Score: 183
Period size: 48 Copynumber: 2.9 Consensus size: 48
482974 AATGGATATA
* * * * *
482984 TCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAAG
1 TCAAATATCAAATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
* * *
483032 TCAAATATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATG
1 TCAAATATCAAATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
* *
483080 TCAGATATCAAATCAGAATCCATGTCAAGTATCAGATCAGAAATC
1 TCAAATATCAAATCAGAATCCAAGTCAAGTATCAGATCA-AAATC
483125 AAATCGAAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
48 76 0.95
49 4 0.05
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (48 bp):
TCAAATATCAAATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAAG
Found at i:483138 original size:72 final size:71
Alignment explanation
Indices: 482987--483138 Score: 164
Period size: 72 Copynumber: 2.1 Consensus size: 71
482977 GGATATATCA
* * * *
482987 AAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAAGTCAAATATCAGATCAGAATC
1 AAAATCAGATCAGAATCCACGTCAAGTATCAAATCAAAATCCAAGTCAAATATCAGATCAGAATC
*
483052 CAAGTC
66 CAAATC
* * * * *
483058 AAGTATCAGATCAGAATCCATGTC-AGATATCAAATCAGAATCCATGTCAAGTATCAGATCAGAA
1 AA-AATCAGATCAGAATCCACGTCAAG-TATCAAATCAAAATCCAAGTCAAATATCAGATCAG-A
483122 AT-CAAATC
63 ATCCAAATC
483130 GAAAATCAG
1 -AAAATCAG
483139 GTAAAATATT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
71 4 0.06
72 57 0.86
73 5 0.08
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (71 bp):
AAAATCAGATCAGAATCCACGTCAAGTATCAAATCAAAATCCAAGTCAAATATCAGATCAGAATC
CAAATC
Found at i:485523 original size:18 final size:18
Alignment explanation
Indices: 485472--485528 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
485462 AGTCAATGGT
*
485472 TCGGGTCAACGGGTCAGG
1 TCGGGTCAACGGGTCGGG
485490 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACGGGTCGGG
*
485508 TCGGGTCAACGGGTCGCG
1 TCGGGTCAACGGGTCGGG
485526 TCG
1 TCG
485529 TGTTGTAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.12, C:0.25, G:0.46, T:0.18
Consensus pattern (18 bp):
TCGGGTCAACGGGTCGGG
Found at i:491047 original size:2 final size:2
Alignment explanation
Indices: 491042--491081 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
491032 CGTGTGTGCT
491042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
491082 CTAGCATAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:492955 original size:41 final size:40
Alignment explanation
Indices: 492887--493000 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 40
492877 AAGATAGGCA
492887 ATAGCGGCGTTTATAATAAAAATGCCACTAAAGGACA-GAACT
1 ATAGCGGCGTTTAT-A-AAAAATGCCACTAAAGGACATG-ACT
* * *
492929 ATTGCGGCGTTTATTAAAAAATGCCACCAAAGTACATGACT
1 ATAGCGGCGTTTA-TAAAAAATGCCACTAAAGGACATGACT
*
492970 ATAGCGGCATTTGA-AACAAAATGCCACTAAA
1 ATAGCGGCGTTT-ATAA-AAAATGCCACTAAA
493001 CTACAAGTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
40 2 0.03
41 44 0.71
42 15 0.24
43 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (40 bp):
ATAGCGGCGTTTATAAAAAATGCCACTAAAGGACATGACT
Found at i:493013 original size:41 final size:41
Alignment explanation
Indices: 492946--493023 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
492936 CGTTTATTAA
* *
492946 AAAATGCCACCAAAGTACATGACTATAGCGGCATTTGAAAC
1 AAAATGCCACCAAACTACAAGACTATAGCGGCATTTGAAAC
* * *
492987 AAAATGCCACTAAACTACAAGTCTATAGTGGCATTTG
1 AAAATGCCACCAAACTACAAGACTATAGCGGCATTTG
493024 TTCACAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATGCCACCAAACTACAAGACTATAGCGGCATTTGAAAC
Found at i:501983 original size:41 final size:41
Alignment explanation
Indices: 501876--502026 Score: 142
Period size: 41 Copynumber: 3.7 Consensus size: 41
501866 AGTTCGATCT
* * *
501876 TGGCAGCATGTACTAATTCACAATTCAATTCAATTCAATCA
1 TGGCAGCATGCAATAATTCACCATTCAATTCAATTCAATCA
* * * * * * *
501917 TGACAACATGTAATAGTTAAACATTCGATTCAATTCAATCA
1 TGGCAGCATGCAATAATTCACCATTCAATTCAATTCAATCA
* * *
501958 TGGCAGCATGCAATACTTCACCATTCAACTT-GATTCGATCA
1 TGGCAGCATGCAATAATTCACCATTCAA-TTCAATTCAATCA
* * *
501999 TGGAATCATACAATAATTCACCATTCAA
1 TGGCAGCATGCAATAATTCACCATTCAA
502027 CTTGATTTGA
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
41 86 0.98
42 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (41 bp):
TGGCAGCATGCAATAATTCACCATTCAATTCAATTCAATCA
Found at i:502027 original size:41 final size:41
Alignment explanation
Indices: 501949--502048 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
501939 ATTCGATTCA
* * * *
501949 ATTCAATCATGGCAGCATGCAATACTTCACCATTCAACTTG
1 ATTCGATCATGGAAGCATACAATAATTCACCATTCAACTTG
*
501990 ATTCGATCATGGAATCATACAATAATTCACCATTCAACTTG
1 ATTCGATCATGGAAGCATACAATAATTCACCATTCAACTTG
* *
502031 ATTTGATCATGGTAGCAT
1 ATTCGATCATGGAAGCAT
502049 GCATTTACTC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (41 bp):
ATTCGATCATGGAAGCATACAATAATTCACCATTCAACTTG
Found at i:507212 original size:39 final size:39
Alignment explanation
Indices: 507178--507253 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
507168 ACTAGGATGT
*
507178 TTCCCAGTCCATATTTCATATCGTGTCTTTCTAGGACAC
1 TTCCCAGTCCATATCTCATATCGTGTCTTTCTAGGACAC
* * *
507217 TTCTCAGTCCATATCTCATATGGTTTCTTT-T-GGACAC
1 TTCCCAGTCCATATCTCATATCGTGTCTTTCTAGGACAC
507254 GATTTAGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 6 0.18
38 1 0.03
39 26 0.79
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (39 bp):
TTCCCAGTCCATATCTCATATCGTGTCTTTCTAGGACAC
Found at i:508305 original size:49 final size:49
Alignment explanation
Indices: 508227--508365 Score: 226
Period size: 49 Copynumber: 2.8 Consensus size: 49
508217 TTCATGTTGA
*
508227 TTTATAAATTACCTCCACTATTTTATTCAAAATTTAAAAATAGGCATTTC
1 TTTACAAATTA-CTCCACTATTTTATTCAAAATTTAAAAATAGGCATTTC
* *
508277 TTTACAAATTACTCCACTATTTTATTCAAAATTTATAAATAGGTATTTC
1 TTTACAAATTACTCCACTATTTTATTCAAAATTTAAAAATAGGCATTTC
508326 TTTACAAATTACTCCCACTATTTTATTCAAAA-TTAAAAAT
1 TTTACAAATTACT-CCACTATTTTATTCAAAATTTAAAAAT
508366 CCTCATGTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
49 56 0.67
50 28 0.33
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (49 bp):
TTTACAAATTACTCCACTATTTTATTCAAAATTTAAAAATAGGCATTTC
Found at i:510252 original size:17 final size:17
Alignment explanation
Indices: 510222--510255 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
510212 TCGTGACCAA
510222 CTTTTATCTATTATATC
1 CTTTTATCTATTATATC
* *
510239 CTTTTGTCTTTTATATC
1 CTTTTATCTATTATATC
510256 TAGAATAGGC
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:0.18, C:0.18, G:0.03, T:0.62
Consensus pattern (17 bp):
CTTTTATCTATTATATC
Found at i:513765 original size:77 final size:79
Alignment explanation
Indices: 513676--513834 Score: 191
Period size: 77 Copynumber: 2.0 Consensus size: 79
513666 TTCGAATTAA
* *
513676 TTAAATTATTATTTAATTAATT-CAAATTAAATACCCAT-TAAAGACTTATAATTC-GAATTACA
1 TTAAACTATTATTTAATT-ATTCCAAATTAAATACCCATGAAAAGACTTATAA-TCAGAATTACA
513738 CTC-TTTAACGTTTAT
64 CTCTTTTAACGTTTAT
* * * * * *
513753 TTAAACTATTATTTAATTATTCCTAATTAAATATCCATGAAAAGAGTTGTAATCATAATTACATT
1 TTAAACTATTATTTAATTATTCCAAATTAAATACCCATGAAAAGACTTATAATCAGAATTACACT
*
513818 CTTTTAATGTTTAT
66 CTTTTAACGTTTAT
513832 TTA
1 TTA
513835 CTATATCTGG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
76 3 0.04
77 33 0.48
78 19 0.28
79 14 0.20
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (79 bp):
TTAAACTATTATTTAATTATTCCAAATTAAATACCCATGAAAAGACTTATAATCAGAATTACACT
CTTTTAACGTTTAT
Found at i:521152 original size:15 final size:16
Alignment explanation
Indices: 521125--521156 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
521115 TTGGGATAAT
521125 TAAAATCATATGTATA
1 TAAAATCATATGTATA
521141 TAAAAT-ATATGTATA
1 TAAAATCATATGTATA
521156 T
1 T
521157 TAACTCTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (16 bp):
TAAAATCATATGTATA
Found at i:523101 original size:20 final size:23
Alignment explanation
Indices: 523074--523132 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
523064 TTCGTAAGAT
*
523074 TACTTTGTGTACT-TGG-AGTA-
1 TACTTTGTGTACTATGGCAATAG
*
523094 TTCTTTGTGTACTATGGCAATAG
1 TACTTTGTGTACTATGGCAATAG
523117 TACTTTGTGTACTATG
1 TACTTTGTGTACTATG
523133 ACACTTTGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.36
21 3 0.09
22 3 0.09
23 15 0.45
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.46
Consensus pattern (23 bp):
TACTTTGTGTACTATGGCAATAG
Found at i:525002 original size:339 final size:339
Alignment explanation
Indices: 524382--525059 Score: 1320
Period size: 339 Copynumber: 2.0 Consensus size: 339
524372 AAGTTGGATG
*
524382 GAGATGTGTCTTTACTTCGAGGATCAGCTCGAGTGTGGTGGACAAACACTACTATGTATGCACTG
1 GAGATGTGTCTTTACTTCGAGGATCAGCTCGAGTGTGGTGGACAAACACTACTATGTATGCACCG
524447 CCTAAGCAAGTGACCTGGTAGTTCTTTCAAGGTGAATTTAAGAACAAGTAAAATGATGAACAATT
66 CCTAAGCAAGTGACCTGGTAGTTCTTTCAAGGTGAATTTAAGAACAAGTAAAATGATGAACAATT
*
524512 TATGCGGGCGATGCTACTGAAGTTTCTTAATTTGAAACAAGGAGATCGAATAATACATGAGTACA
131 TATGCGGGCGATGCTACTGAAGTTTCTTAATTTGAAACAAGGAGATCGAACAATACATGAGTACA
524577 AAGTTGAGTATAACAAGCTAAGTCGTTTTGCTATTGAAGTAGTTCCCAATGATAAGGCTCGACGT
196 AAGTTGAGTATAACAAGCTAAGTCGTTTTGCTATTGAAGTAGTTCCCAATGATAAGGCTCGACGT
524642 GATTGGTTCATCAAGGGATTGTCATAAACCGAGCTAAGGTCATCAAAAGAGCTCAAGATGAGACT
261 GATTGGTTCATCAAGGGATTGTCATAAACCGAGCTAAGGTCATCAAAAGAGCTCAAGATGAGACT
524707 TTAACATTGAAGCA
326 TTAACATTGAAGCA
524721 GAGATGTGTCTTTACTTCGAGGATCAGCTCGAGTGTGGTGGACAAACACTACTATGTATGCACCG
1 GAGATGTGTCTTTACTTCGAGGATCAGCTCGAGTGTGGTGGACAAACACTACTATGTATGCACCG
524786 CCTAAGCAAGTGACCTGGTAGTTCTTTCAAGGTGAATTTAAGAACAAGTAAAATGATGAACAATT
66 CCTAAGCAAGTGACCTGGTAGTTCTTTCAAGGTGAATTTAAGAACAAGTAAAATGATGAACAATT
524851 TATGCGGGCGATGCTACTGAAGTTTCTTAATTTGAAACAAGGAGATCGAACAATACATGAGTACA
131 TATGCGGGCGATGCTACTGAAGTTTCTTAATTTGAAACAAGGAGATCGAACAATACATGAGTACA
* *
524916 AGGTTGAGTATAACAAGCTAAGTCTTTTTGCTATTGAAGTAGTTCCCAATGATAAGGCTCGACGT
196 AAGTTGAGTATAACAAGCTAAGTCGTTTTGCTATTGAAGTAGTTCCCAATGATAAGGCTCGACGT
524981 GATTGGTTCATCAAGGGATTGTCATAAACCGAGCTAAGGTCATCAAAAGAGCTCAAGATGAGACT
261 GATTGGTTCATCAAGGGATTGTCATAAACCGAGCTAAGGTCATCAAAAGAGCTCAAGATGAGACT
525046 TTAACATTGAAGCA
326 TTAACATTGAAGCA
525060 AGGTATGCAG
Statistics
Matches: 335, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
339 335 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (339 bp):
GAGATGTGTCTTTACTTCGAGGATCAGCTCGAGTGTGGTGGACAAACACTACTATGTATGCACCG
CCTAAGCAAGTGACCTGGTAGTTCTTTCAAGGTGAATTTAAGAACAAGTAAAATGATGAACAATT
TATGCGGGCGATGCTACTGAAGTTTCTTAATTTGAAACAAGGAGATCGAACAATACATGAGTACA
AAGTTGAGTATAACAAGCTAAGTCGTTTTGCTATTGAAGTAGTTCCCAATGATAAGGCTCGACGT
GATTGGTTCATCAAGGGATTGTCATAAACCGAGCTAAGGTCATCAAAAGAGCTCAAGATGAGACT
TTAACATTGAAGCA
Found at i:527681 original size:18 final size:19
Alignment explanation
Indices: 527646--527682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
527636 CACGGAATGT
527646 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
527666 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
527683 GAATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:527861 original size:37 final size:37
Alignment explanation
Indices: 527827--527896 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
527817 TACAAATTGT
527827 AAAATATTT-TATATATTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATATATTTCTTTAAAAAATTAAATTC
* * *
527863 ATAATATTTATATATATTTTTTTACAAAATTAAA
1 AAAATATTTATATATATTTCTTTAAAAAATTAAA
527897 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 8 0.27
37 22 0.73
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AAAATATTTATATATATTTCTTTAAAAAATTAAATTC
Found at i:531145 original size:13 final size:13
Alignment explanation
Indices: 531123--531170 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 13
531113 ACCTTGAATG
531123 TTTTTATAAAAGTA
1 TTTTTAT-AAAGTA
531137 TTTTT-TAAAGTA
1 TTTTTATAAAGTA
*
531149 -TTTGA-AAA-TA
1 TTTTTATAAAGTA
531159 TTTTTATAAAGT
1 TTTTTATAAAGT
531171 TTATGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
10 2 0.07
11 10 0.36
12 9 0.32
13 2 0.07
14 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTTTTATAAAGTA
Found at i:531163 original size:23 final size:24
Alignment explanation
Indices: 531136--531188 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
531126 TTATAAAAGT
531136 ATTTTT-TAAAGTATT-TGAAAAT-
1 ATTTTTATAAAGT-TTATGAAAATG
531158 ATTTTTATAAAGTTTATGAAAATG
1 ATTTTTATAAAGTTTATGAAAATG
531182 ATTTTTA
1 ATTTTTA
531189 CGAATGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.29
23 13 0.46
24 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTTTATAAAGTTTATGAAAATG
Found at i:531488 original size:21 final size:21
Alignment explanation
Indices: 531463--531540 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
531453 TTCGTAAGAG
*
531463 TACTTTGTGTACTTGGAGTAT
1 TACTTTGTGTACTTGGAGTAA
*
531484 TACTTTGTGTACTATGGCAAG-AG
1 TACTTTGTGTACT-TGG--AGTAA
* *
531507 TACTTTGTGTATTTGTAGTAA
1 TACTTTGTGTACTTGGAGTAA
*
531528 TACTTTATGTACT
1 TACTTTGTGTACT
531541 ATGGCACTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.04
21 25 0.53
22 5 0.11
23 13 0.28
24 2 0.04
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (21 bp):
TACTTTGTGTACTTGGAGTAA
Found at i:531508 original size:44 final size:44
Alignment explanation
Indices: 531458--531546 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
531448 GGATTTTCGT
* *
531458 AAGAGTACTTTGTGTACTTGGAGTATTACTTTGTGTACTATGGC
1 AAGAGTACTTTGTGTACTTGGAGTAATACTTTATGTACTATGGC
* *
531502 AAGAGTACTTTGTGTATTTGTAGTAATACTTTATGTACTATGGC
1 AAGAGTACTTTGTGTACTTGGAGTAATACTTTATGTACTATGGC
531546 A
1 A
531547 CTTTGTGTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (44 bp):
AAGAGTACTTTGTGTACTTGGAGTAATACTTTATGTACTATGGC
Found at i:540599 original size:76 final size:78
Alignment explanation
Indices: 540506--540659 Score: 192
Period size: 76 Copynumber: 2.0 Consensus size: 78
540496 TTCGAATTAA
**
540506 TAAAATTCTCATTTAATTAATT-CAAATTAAATAT-ACATTAAAGAC-TTATAATCTGAATTACA
1 TAAAATTCTCATTTAATT-ATTCCAAATTAAATATCA-ATTAAA-ACGTTATAATCAAAATTACA
540568 -ATTTTAATGTTTATT
63 TATTTTAATGTTTATT
*
540583 TAAAA-TCTTATTTAATTATTCCAAATTAAATATCAATTAAAACTGTTATAATCAAAATTACATT
1 TAAAATTCTCATTTAATTATTCCAAATTAAATATCAATTAAAAC-GTTATAATCAAAATTACA-T
*
540647 CTTTTAATGTTTA
64 ATTTTAATGTTTA
540660 CTTACTTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
75 5 0.07
76 29 0.43
77 21 0.31
79 12 0.18
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (78 bp):
TAAAATTCTCATTTAATTATTCCAAATTAAATATCAATTAAAACGTTATAATCAAAATTACATAT
TTTAATGTTTATT
Found at i:543530 original size:291 final size:291
Alignment explanation
Indices: 543006--543579 Score: 1085
Period size: 291 Copynumber: 2.0 Consensus size: 291
542996 ATAATGCATG
*
543006 TTTTATGTAATCTTAGTTGTTATTATTTCTAGTTGTTCTCACTTGTAGTTCTATCTGCTGATATA
1 TTTTATGTAATCCTAGTTGTTATTATTTCTAGTTGTTCTCACTTGTAGTTCTATCTGCTGATATA
543071 CTGATGTTATTAGGCCCTTCGAGCTTAATCCCTTGATCTTTGGATTACTTATCCCAAACTATCTG
66 CTGATGTTATTAGGCCCTTCGAGCTTAATCCCTTGATCTTTGGATTACTTATCCCAAACTATCTG
* *
543136 TCGATACTGATATTATCCCTTTAGTATCGATCCTAAACCCCGAGTATAGGTACCCACTTGTTGGT
131 TCGATACCGATATTATCCCTTTAGTATCGATACTAAACCCCGAGTATAGGTACCCACTTGTTGGT
* *
543201 ATTGATACCTACTGGCTGATATGGCTGATTTAGGAAATGTAGTATTGATACTCTTGGCTGCATCG
196 ATTGATACCTACTAGCTGATATGGCTGATTTAGGAAATGTAGTATTGATACTCTTGGCTACATCG
543266 ATACCAAAATTAGGTTCGATGTTATGGTTGA
261 ATACCAAAATTAGGTTCGATGTTATGGTTGA
543297 TTTTATGTAATCCTAGTTGTTATTATTTCTAGTTGTTCTCACTTGTAGTTCTATCTGCTGATATA
1 TTTTATGTAATCCTAGTTGTTATTATTTCTAGTTGTTCTCACTTGTAGTTCTATCTGCTGATATA
*
543362 CTGATGTTATTGGGCCCTTCGAGCTTAATCCCTTGATCTTTGGATTACTTATCCCAAACTATCTG
66 CTGATGTTATTAGGCCCTTCGAGCTTAATCCCTTGATCTTTGGATTACTTATCCCAAACTATCTG
*
543427 TCGATACCGATATTATCCCTTTAGTATCGATACTGAACCCCGAGTATAGGTACCCACTTGTTGGT
131 TCGATACCGATATTATCCCTTTAGTATCGATACTAAACCCCGAGTATAGGTACCCACTTGTTGGT
543492 ATTGATACCTACTAGCTGATATGGCTGATTTAGGAAATGTAGTATTGATACTCTTGGCTACATCG
196 ATTGATACCTACTAGCTGATATGGCTGATTTAGGAAATGTAGTATTGATACTCTTGGCTACATCG
543557 ATACCAAAATTAGGTTCGATGTT
261 ATACCAAAATTAGGTTCGATGTT
543580 TTAAAAAAAC
Statistics
Matches: 276, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 276 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (291 bp):
TTTTATGTAATCCTAGTTGTTATTATTTCTAGTTGTTCTCACTTGTAGTTCTATCTGCTGATATA
CTGATGTTATTAGGCCCTTCGAGCTTAATCCCTTGATCTTTGGATTACTTATCCCAAACTATCTG
TCGATACCGATATTATCCCTTTAGTATCGATACTAAACCCCGAGTATAGGTACCCACTTGTTGGT
ATTGATACCTACTAGCTGATATGGCTGATTTAGGAAATGTAGTATTGATACTCTTGGCTACATCG
ATACCAAAATTAGGTTCGATGTTATGGTTGA
Found at i:544361 original size:23 final size:23
Alignment explanation
Indices: 544325--544442 Score: 127
Period size: 23 Copynumber: 5.1 Consensus size: 23
544315 TTGCTCACAT
544325 AATTTTCACCGAAGTG-CCACATAG
1 AATTTTC-CCGAAG-GACCACATAG
*
544349 AATTTTTCCGAAGGACCACATA-
1 AATTTTCCCGAAGGACCACATAG
*
544371 AATATATCCCGAAGGACCACATAG
1 AAT-TTTCCCGAAGGACCACATAG
544395 -ATTTGTCCCGAAGGACCACATAG
1 AATTT-TCCCGAAGGACCACATAG
* *
544418 -TTTTGTCCCAAAGGACCACATAG
1 AATTT-TCCCGAAGGACCACATAG
544441 AA
1 AA
544443 CCCTCGATTC
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.06
23 71 0.87
24 6 0.07
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (23 bp):
AATTTTCCCGAAGGACCACATAG
Found at i:549982 original size:2 final size:2
Alignment explanation
Indices: 549975--550001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
549965 AGCTTAATAA
549975 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
550002 GCCTTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:550298 original size:15 final size:15
Alignment explanation
Indices: 550274--550314 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
550264 TAAAAATAAA
550274 TAATATTATTAA-TTT
1 TAATA-TATTAATTTT
550289 TAATGATATTAATTTT
1 TAAT-ATATTAATTTT
550305 TAATATATTA
1 TAATATATTA
550315 GATCCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TAATATATTAATTTT
Found at i:553821 original size:65 final size:64
Alignment explanation
Indices: 553740--553916 Score: 207
Period size: 65 Copynumber: 2.7 Consensus size: 64
553730 GAGACAAAAC
* * *
553740 TTTGTTTCTAGAGAAACTGTCTCAAGGAAGATG-AAATTTGTTTCAAGGGATACAGATCCAAGGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGG-AGAGGAAAATTTGTTTCAAGGGA-ACAGATCCAAGGA
553804 T
64 T
* *
553805 TTTGTTTCAAGGGAAACTGTCTCAA-GAGAGGCAAAATTTGTTTCAAGGGAATAGATTCAAGGAT
1 TTTGTTTCAAGGGAAACTGTCTCAAGGAGAGG-AAAATTTGTTTCAAGGGAACAGATCCAAGGAT
* * * *
553869 TTTGTTTCAAGGAAAACTATCTCAA-GAGAGACAAAACTTGGTTTCAAG
1 TTTGTTTCAAGGGAAACTGTCTCAAGGAGAG-GAAAA-TTTGTTTCAAG
553917 AGAAACTCTC
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
63 4 0.04
64 45 0.45
65 50 0.51
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (64 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGGAGAGGAAAATTTGTTTCAAGGGAACAGATCCAAGGAT
Found at i:553894 original size:64 final size:65
Alignment explanation
Indices: 553773--553916 Score: 218
Period size: 64 Copynumber: 2.2 Consensus size: 65
553763 AAGGAAGATG
* * *
553773 AAATTTGTTTCAAGGGATACAGATCCAAGGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGGCA
1 AAATTTGTTTCAAGGGATACAGATCCAAGGATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACA
* *
553838 AAATTTGTTTCAAGGGA-ATAGATTCAAGGATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACA
1 AAATTTGTTTCAAGGGATACAGATCCAAGGATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACA
*
553902 AAACTTGGTTTCAAG
1 AAA-TTTGTTTCAAG
553917 AGAAACTCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
64 45 0.62
65 27 0.38
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (65 bp):
AAATTTGTTTCAAGGGATACAGATCCAAGGATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACA
Found at i:553921 original size:166 final size:166
Alignment explanation
Indices: 553640--554088 Score: 521
Period size: 166 Copynumber: 2.7 Consensus size: 166
553630 AAGGATAATG
* * ** * * *
553640 GTTTCAAGAGAAACCGTCTCAAGATAGACAAAACATATTTCAAGGGAAACA-ATCTCAAAGGTTG
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGGAACAGAT-TCAAAGATT-
* * * *
553704 GTGTTTCAAGGGAAA-TCGTCTCAAGAGAGACAAAACTTTGTTTCTAGAGAAACTGTCTCAAGGA
64 TTGTTTCAAGGAAAACT-GTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTCTCTCAAGGA
* * * *
553768 AGATGAAATTTGTTTCAAGGGATACAGATCCAAGGATTTT
128 AGA-CAAATTTGTTTAAAGGGAAACAGATCCAAAGATTTT
* * * *
553808 GTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATTTGTTTCAA-GGGAATAGATTCAAGGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGGAACAGATTCAAAGATTTT
* * *
553872 GTTTCAAGGAAAACTATCTCAAGAGAGACAAAACTTGGTTTCAAGAGAAACTCTCTCAAGGGAGA
66 GTTTCAAGGAAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTCTCTCAAGGAAGA
* * *
553937 CAATTTTTTTTAAAGGGAAACAGATTCAAAGATTTT
131 CAAATTTGTTTAAAGGGAAACAGATCCAAAGATTTT
* * * * *
553973 GTTTCAAGAGAAACTGTCTCAAGGGAGATAAACTTTGTTTCAAGGGGAACATATTCAAATATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGGAACAGATTCAAAGATTTT
* *
554038 GGTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAAC
66 -GTTTCAAGGA-AAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAAC
554089 AGATTCAAAG
Statistics
Matches: 238, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
165 67 0.28
166 92 0.39
167 41 0.17
168 38 0.16
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.28
Consensus pattern (166 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGGAACAGATTCAAAGATTTT
GTTTCAAGGAAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTCTCTCAAGGAAGA
CAAATTTGTTTAAAGGGAAACAGATCCAAAGATTTT
Found at i:553922 original size:101 final size:100
Alignment explanation
Indices: 553808--554311 Score: 270
Period size: 100 Copynumber: 5.1 Consensus size: 100
553798 CAAGGATTTT
* * * * * *
553808 GTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATTTGTTTCAAGGG-AATAGATTCAAGGATTTT
1 GTTTCAAGAGAAACTCTCTCAAGAGAGAC-AAATTTGTTTAAAGGGAAACAGATTCAAAGATTTT
553872 GTTTCAAG-GAAAACTATCTCAAGAGAGACAAAACTTG
65 GTTTCAAGAG-AAACTATCTCAAGAGAGA-AAAACTTG
* * *
553909 GTTTCAAGAGAAACTCTCTCAAGGGAGACAATTTTTTTTAAAGGGAAACAGATTCAAAGATTTTG
1 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAATTTGTTTAAAGGGAAACAGATTCAAAGATTTTG
* * * *
553974 TTTCAAGAGAAACTGTCTCAAGGGAGATAAACTTT
66 TTTCAAGAGAAACTATCTCAAGAGAGAAAAACTTG
* * * * * * * *
554009 GTTTCAAGGGGAACATAT-TC---A-A-A-TATTTTGGTTTCAAGAGAAACTG-TCTCAAGGGAG
1 GTTTCAAGAGAAAC-TCTCTCAAGAGAGACAAATTT-GTTTAAAGGGAAACAGAT-TCAA---AG
* * * **
554066 ACAAAATTTGTTTCAAGGGAAACAGAT-TC-A-A-AG---ATTTTG
60 ----ATTTTGTTTCAAGAGAAAC-TATCTCAAGAGAGAAAAACTTG
* * * * * *
554105 GTTTCGATAGAAATTGTCTCAAGAGAGACAAACTTTGTTTCAAGGGAAACATATTCAAAGATTTT
1 GTTTCAAGAGAAACTCTCTCAAGAGAGACAAA-TTTGTTTAAAGGGAAACAGATTCAAAGATTTT
* * *
554170 GGTTTCAAGA-AAACTGTCTCAAGAGAG-ACAACTTT
65 -GTTTCAAGAGAAACTATCTCAAGAGAGAAAAACTTG
* * *
554205 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGG----AGA--CAAA-A-TTT
1 GTTTCAAGAGAAACTCTCTCAAGAGAGAC-AAATTTGTTTAAAGGGAAACAGATTCAAAGATTTT
* * * * *
554262 GTTTCAAGGGAAACTGTCTCAAGGGAGAAAAAATTT
65 GTTTCAAGAGAAACTATCTCAAGAGAGAAAAACTTG
*
554298 GTTTCAAGGGAAAC
1 GTTTCAAGAGAAAC
554312 AGCTTCAACG
Statistics
Matches: 313, Mismatches: 58, Indels: 72
0.71 0.13 0.16
Matches are distributed among these distances:
91 8 0.03
92 19 0.06
93 20 0.06
94 11 0.04
95 29 0.09
96 26 0.08
97 1 0.00
98 4 0.01
99 5 0.02
100 75 0.24
101 72 0.23
102 38 0.12
103 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (100 bp):
GTTTCAAGAGAAACTCTCTCAAGAGAGACAAATTTGTTTAAAGGGAAACAGATTCAAAGATTTTG
TTTCAAGAGAAACTATCTCAAGAGAGAAAAACTTG
Found at i:554051 original size:66 final size:65
Alignment explanation
Indices: 553906--554218 Score: 432
Period size: 66 Copynumber: 4.8 Consensus size: 65
553896 GAGACAAAAC
* * * * *
553906 TTGGTTTCAAGAGAAACTCTCTCAAGGGAGACAATTTTTTTTAAAGGGAAACAGATTCAAAGATT
1 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGAAAACTTTGTTTCAAGGGAAACAGATTCAAAGATT
* * *
553971 TT-GTTTCAAGAGAAACTGTCTCAAGGGAGATAAACTTTGTTTCAAGGGGAACATATTCAAATAT
1 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAACTTTGTTTCAAGGGAAACAGATTCAAAGAT
554035 T
65 T
*
554036 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATTCAAAGAT
1 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAACTTTGTTTCAAGGGAAACAGATTCAAAGAT
554101 T
65 T
* * * * *
554102 TTGGTTTCGATAGAAATTGTCTCAAGAGAGACAAACTTTGTTTCAAGGGAAACATATTCAAAGAT
1 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAACTTTGTTTCAAGGGAAACAGATTCAAAGAT
554167 T
65 T
* * *
554168 TTGGTTTCAAGA-AAACTGTCTCAAGAGAGACAACTTTGTTTCAAGAGAAAC
1 TTGGTTTCAAGAGAAACTGTCTCAAGGGAGAAAACTTTGTTTCAAGGGAAAC
554219 TGTCTCAAGG
Statistics
Matches: 222, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
64 46 0.21
65 48 0.22
66 128 0.58
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGGTTTCAAGAGAAACTGTCTCAAGGGAGAAAACTTTGTTTCAAGGGAAACAGATTCAAAGATT
Found at i:554249 original size:21 final size:21
Alignment explanation
Indices: 554223--554308 Score: 103
Period size: 21 Copynumber: 4.4 Consensus size: 21
554213 AGAAACTGTC
554223 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
554244 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
554265 TCAA-GG-G---AAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
*
554280 TCAAGGGAGAAAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
554301 TCAAGGGA
1 TCAAGGGA
554309 AACAGCTTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
15 7 0.13
16 5 0.09
17 1 0.02
19 1 0.02
20 5 0.09
21 36 0.65
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:554275 original size:57 final size:57
Alignment explanation
Indices: 554188--554371 Score: 217
Period size: 57 Copynumber: 3.1 Consensus size: 57
554178 GAAAACTGTC
* * *
554188 TCAAGAGAGAC-AACTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
*
554244 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
* * *
554301 TCAAGGGAAACAGCTTCAACGATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTTGT
1 TCAAGGGAGACA-----AA--A-TTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA-TTTGT
554366 T
57 T
554367 TCAAG
1 TCAAG
554372 AGAAACTGTC
Statistics
Matches: 110, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
56 10 0.09
57 53 0.48
62 2 0.02
64 1 0.01
65 33 0.30
66 11 0.10
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (57 bp):
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
Found at i:554295 original size:36 final size:36
Alignment explanation
Indices: 554244--554407 Score: 164
Period size: 36 Copynumber: 4.7 Consensus size: 36
554234 AAAATTTGTT
*
554244 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTC
*
554280 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAG-C
1 TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTC
* * *
554315 TTCAA---CG----ATTTTGTTTCAAGGGAAACTATC
1 -TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTC
* * *
554345 TCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTC
1 TCAAGGGAGA-AAAAATTTGTTTCAAGGGAAACTGTC
**
554382 TCAAGGGAGACGAAATTTGTTTCAAG
1 TCAAGGGAGAAAAAATTTGTTTCAAG
554408 CAAAACATAT
Statistics
Matches: 104, Mismatches: 14, Indels: 20
0.75 0.10 0.14
Matches are distributed among these distances:
29 22 0.21
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 49 0.47
37 29 0.28
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (36 bp):
TCAAGGGAGAAAAAATTTGTTTCAAGGGAAACTGTC
Found at i:554377 original size:37 final size:36
Alignment explanation
Indices: 554324--554407 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 36
554314 CTTCAACGAT
*
554324 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
* * *
554360 CTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
554397 TTTGTTTCAAG
1 TTTGTTTCAAG
554408 CAAAACATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 11 0.26
37 32 0.74
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
Found at i:554377 original size:102 final size:101
Alignment explanation
Indices: 554244--554471 Score: 314
Period size: 102 Copynumber: 2.2 Consensus size: 101
554234 AAAATTTGTT
* * **
554244 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGA
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGCAA
* *
554309 AACAGCTTCAACGATTTTGTTTCAAGGGAAACTATC
66 AACAGATTCAAAGATTTTGTTTCAAGGGAAACTATC
**
554345 TCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGCA
1 TCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGCA
* * *
554410 AAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTA
65 AAACAGATTCAAAGATTTTGTTTCAAGGGAAACTATC
* *
554447 TTAATG-GAGACAAAGTTTGTTTCAA
1 TCAA-GAGAGACAAAATTTGTTTCAA
554472 AGGAAATATA
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
101 24 0.21
102 87 0.78
103 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (101 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGCAA
AACAGATTCAAAGATTTTGTTTCAAGGGAAACTATC
Found at i:554466 original size:65 final size:65
Alignment explanation
Indices: 554361--554507 Score: 199
Period size: 65 Copynumber: 2.2 Consensus size: 65
554351 GAGACAAAAC
*
554361 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTGTTTC-AAGCAAAACATATTCAAAGA
1 TTTGTTTCAAGAGAAACTGTATCAAGGGAGACGAAATTTGTTTCAAAG-AAAACATATTCAAAGA
554425 T
65 T
* * * * *
554426 TTTGTTTCAAGGGAAACTGTATTAATGGAGAC-AAAGTTTGTTTCAAAGGAAATATATTCAAAGA
1 TTTGTTTCAAGAGAAACTGTATCAAGGGAGACGAAA-TTTGTTTCAAAGAAAACATATTCAAAGA
554490 T
65 T
554491 TTTGGTTTCAAGAGAAA
1 TTT-GTTTCAAGAGAAA
554508 AAATTTCAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
64 3 0.04
65 54 0.75
66 15 0.21
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (65 bp):
TTTGTTTCAAGAGAAACTGTATCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAAGAT
Found at i:562989 original size:60 final size:60
Alignment explanation
Indices: 562890--563002 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
562880 GGCTAGTTCA
* * *
562890 GTAAGTTTTTCGGTTCTGGGAAGTATGGCATTGCAGATTAGTCTGGCTGGTGTTGGATCG
1 GTAAGTTTTTCGATTCTGGGAAGTATGACATTGCAGATTAGTATGGCTGGTGTTGGATCG
**
562950 GTAAG-TTTTCTGATTCTGGGAAGT-TCGACATTGTTGATTAGTATGGCTGGTGT
1 GTAAGTTTTTC-GATTCTGGGAAGTAT-GACATTGCAGATTAGTATGGCTGGTGT
563003 GGTTTAGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 6 0.13
60 40 0.87
ACGTcount: A:0.18, C:0.11, G:0.33, T:0.39
Consensus pattern (60 bp):
GTAAGTTTTTCGATTCTGGGAAGTATGACATTGCAGATTAGTATGGCTGGTGTTGGATCG
Found at i:564702 original size:23 final size:23
Alignment explanation
Indices: 564657--564760 Score: 122
Period size: 23 Copynumber: 4.5 Consensus size: 23
564647 TGTAGTGTAG
* * * *
564657 AAACAGTGTTTTCCGGCTCTGGT
1 AAACAGAGTTTTCTGACACTGGT
*
564680 AAGA-AGAGTTTTAC-GACAATGGT
1 AA-ACAGAGTTTT-CTGACACTGGT
564703 AAACAGAGTTTTCTGACACTGGT
1 AAACAGAGTTTTCTGACACTGGT
564726 AAACAGAGTTTTCTGACACTGGT
1 AAACAGAGTTTTCTGACACTGGT
*
564749 AAACAAAGTTTT
1 AAACAGAGTTTT
564761 TCGGTTTTGG
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.03
23 67 0.94
24 2 0.03
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (23 bp):
AAACAGAGTTTTCTGACACTGGT
Found at i:568337 original size:17 final size:16
Alignment explanation
Indices: 568308--568349 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
568298 GAAAATAAGG
568308 ATTGAAAGAAATGAAA
1 ATTGAAAGAAATGAAA
*
568324 ATTGATAAGGAATG-AA
1 ATTGA-AAGAAATGAAA
*
568340 ATGGAAAGAA
1 ATTGAAAGAA
568350 TTGATATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.18
16 11 0.50
17 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (16 bp):
ATTGAAAGAAATGAAA
Found at i:568530 original size:35 final size:35
Alignment explanation
Indices: 568490--568601 Score: 188
Period size: 35 Copynumber: 3.2 Consensus size: 35
568480 AAGGGAATTA
*
568490 TGATGATATAGGCATGAAATGGTGATAGAAGATGG
1 TGATGATATAGGCATGAAATGGTGATGGAAGATGG
*
568525 TGATGATATAGGCATGCAATGGTGATGGAAGATGG
1 TGATGATATAGGCATGAAATGGTGATGGAAGATGG
*
568560 TGATGATATAGGCGTGAAAATGGTGATGGAAGATGG
1 TGATGATATAGGCATG-AAATGGTGATGGAAGATGG
568596 TGATGA
1 TGATGA
568602 ACAGATAGTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 48 0.67
36 24 0.33
ACGTcount: A:0.34, C:0.04, G:0.37, T:0.26
Consensus pattern (35 bp):
TGATGATATAGGCATGAAATGGTGATGGAAGATGG
Found at i:568561 original size:13 final size:13
Alignment explanation
Indices: 568543--568600 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
568533 TAGGCATGCA
568543 ATGGTGATGGAAG
1 ATGGTGATGGAAG
*
568556 ATGGTGAT-G-AT
1 ATGGTGATGGAAG
* *
568567 ATAGGCG-T-GAAA
1 AT-GGTGATGGAAG
568579 ATGGTGATGGAAG
1 ATGGTGATGGAAG
568592 ATGGTGATG
1 ATGGTGATG
568601 AACAGATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 8 0.22
12 8 0.22
13 20 0.56
ACGTcount: A:0.31, C:0.02, G:0.41, T:0.26
Consensus pattern (13 bp):
ATGGTGATGGAAG
Found at i:568983 original size:19 final size:20
Alignment explanation
Indices: 568936--568986 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
568926 GAAACCCATT
**
568936 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
568956 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
568975 TGAAGATACATG
1 TGAAAATACATG
568987 CTCTTGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:573735 original size:13 final size:13
Alignment explanation
Indices: 573719--573775 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
573709 GTTCAATGCA
*
573719 CGTCATAAATGAG
1 CGTCATAAATGTG
*
573732 CGTCAAAAATGTG
1 CGTCATAAATGTG
*
573745 C--CATAAATGCG
1 CGTCATAAATGTG
*
573756 TGTCATAAATGTG
1 CGTCATAAATGTG
573769 CGTCATA
1 CGTCATA
573776 GATTTATGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 8 0.23
13 27 0.77
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:573753 original size:24 final size:24
Alignment explanation
Indices: 573722--573769 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
573712 CAATGCACGT
573722 CATAAATGAGCGTCAAAAATGTGC
1 CATAAATGAGCGTCAAAAATGTGC
* * *
573746 CATAAATGCGTGTCATAAATGTGC
1 CATAAATGAGCGTCAAAAATGTGC
573770 GTCATAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (24 bp):
CATAAATGAGCGTCAAAAATGTGC
Found at i:574974 original size:24 final size:24
Alignment explanation
Indices: 574930--574976 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
574920 ACGGACACAA
* **
574930 CTCTTGGCACTTCAAGTGACGTTT
1 CTCTTGGAACTTCAAAAGACGTTT
574954 CTCTTGGAACTTCAAAAGACGTT
1 CTCTTGGAACTTCAAAAGACGTT
574977 ATCTTTGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (24 bp):
CTCTTGGAACTTCAAAAGACGTTT
Found at i:574992 original size:24 final size:24
Alignment explanation
Indices: 574947--574992 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
574937 CACTTCAAGT
* *
574947 GACGTTTCTCTTGGAACTTCAAAA
1 GACGTTTCTCTTGAAACATCAAAA
574971 GACGTTATCT-TTGAAACATCAA
1 GACGTT-TCTCTTGAAACATCAA
574993 GAGATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (24 bp):
GACGTTTCTCTTGAAACATCAAAA
Found at i:576345 original size:20 final size:19
Alignment explanation
Indices: 576318--576357 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
576308 TGTAGGATTC
*
576318 TTTTCTT-TTGCTTTTG-T
1 TTTTCTTCTTTCTTTTGCT
576335 TTTTCTTCTTTCTTTTGCT
1 TTTTCTTCTTTCTTTTGCT
576354 TTTT
1 TTTT
576358 GTTGCAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (19 bp):
TTTTCTTCTTTCTTTTGCT
Found at i:576769 original size:35 final size:35
Alignment explanation
Indices: 576724--576833 Score: 166
Period size: 35 Copynumber: 3.1 Consensus size: 35
576714 TGGTAAGGGA
576724 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* * * *
576759 ATGGTGATGATACAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
*
576794 ATGGTGATGATATAGGCGTGAAAATGGTGATTGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATAGAAG
576830 ATGG
1 ATGG
576834 GGATCAACAG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 49 0.74
36 17 0.26
ACGTcount: A:0.33, C:0.05, G:0.37, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:577228 original size:19 final size:20
Alignment explanation
Indices: 577181--577231 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
577171 GAAACCCCTT
**
577181 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTAAA
577201 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
577220 TGAAGATACATG
1 TGAAAATACATG
577232 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:583496 original size:21 final size:21
Alignment explanation
Indices: 583449--583496 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
583439 CTACTATACT
*
583449 CGCAATAGCGCCCGCTATGGC
1 CGCAATAGCGCCCGCTATGAC
* * *
583470 CACAATAGCGTCCGTTATGAC
1 CGCAATAGCGCCCGCTATGAC
583491 CGCAAT
1 CGCAAT
583497 CGAGGTAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (21 bp):
CGCAATAGCGCCCGCTATGAC
Found at i:585938 original size:20 final size:21
Alignment explanation
Indices: 585910--585949 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
585900 ATCCAATTTC
585910 TTGTCAAGCA-AAATTGAATA
1 TTGTCAAGCACAAATTGAATA
*
585930 TTGTGAAGCACAAATTGAAT
1 TTGTCAAGCACAAATTGAAT
585950 TCTCTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (21 bp):
TTGTCAAGCACAAATTGAATA
Found at i:586760 original size:42 final size:43
Alignment explanation
Indices: 586707--586834 Score: 190
Period size: 42 Copynumber: 3.0 Consensus size: 43
586697 GTTGATTTTA
*
586707 TTTAGACTTATTGAGACTTATTAGTGTTATGGTGTTATTTATT
1 TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATT
* *
586750 TTTA-ACTTATTGAGACATAATAGTGTTCTGGTGTTATTTA-T
1 TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATT
*
586791 TTTAGACTTATTGAGACTTAAT-GATGTTATGGTGTTTTTTATT
1 TTTAGACTTATTGAGACTTAATAG-TGTTATGGTGTTATTTATT
586834 T
1 T
586835 ACTTGCTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.08
42 64 0.84
43 6 0.08
ACGTcount: A:0.24, C:0.05, G:0.18, T:0.52
Consensus pattern (43 bp):
TTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTATTTATT
Done.