Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002705.1 Hibiscus syriacus cultivar Beakdansim tig00005582_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: 469953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:228450 original size:15 final size:14
Alignment explanation
Indices: 228415--228457 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
228405 TTCTGGAAAG
228415 TCGAGTCAACTCGA
1 TCGAGTCAACTCGA
228429 TCGAGTCAACTC-A
1 TCGAGTCAACTCGA
228442 TACCGAGTCAACTCGA
1 T--CGAGTCAACTCGA
228458 ATAGGTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.08
14 12 0.46
15 11 0.42
16 1 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (14 bp):
TCGAGTCAACTCGA
Found at i:228572 original size:22 final size:22
Alignment explanation
Indices: 228544--228586 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
228534 CCTGCCCAGA
228544 GTTGACT-TTGACCTTTGATTGC
1 GTTGACTATTGA-CTTTGATTGC
228566 GTTGACTATTGACTTTGATTG
1 GTTGACTATTGACTTTGATTG
228587 AAAAGTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.16, C:0.14, G:0.23, T:0.47
Consensus pattern (22 bp):
GTTGACTATTGACTTTGATTGC
Found at i:230982 original size:14 final size:14
Alignment explanation
Indices: 230963--230991 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
230953 ACGGTCAACG
230963 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
230977 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
230991 G
1 G
230992 ACCGGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:230998 original size:9 final size:9
Alignment explanation
Indices: 230986--231055 Score: 68
Period size: 9 Copynumber: 7.3 Consensus size: 9
230976 AGTCGGGTCG
*
230986 GGTCAGACC
1 GGTCAAACC
230995 GGTCAAACC
1 GGTCAAACC
*
231004 GGTTCGAACC
1 GG-TCAAACC
*
231014 GGTCGAAACT
1 GGTC-AAACC
231024 GGTCAAACC
1 GGTCAAACC
*
231033 GGTTGAAAACC
1 GG-T-CAAACC
231044 GGTCAAACC
1 GGTCAAACC
231053 GGT
1 GGT
231056 TTCCAGCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 26 0.52
10 17 0.34
11 7 0.14
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:231016 original size:19 final size:19
Alignment explanation
Indices: 230986--231055 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 19
230976 AGTCGGGTCG
*
230986 GGTCAGACCGGTC-AAACC
1 GGTCAAACCGGTCGAAACC
* *
231004 GGTTCGAACCGGTCGAAACT
1 GG-TCAAACCGGTCGAAACC
*
231024 GGTCAAACCGGTTGAAAACC
1 GGTCAAACCGGTCG-AAACC
231044 GGTCAAACCGGT
1 GGTCAAACCGGT
231056 TTCCAGCCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 2 0.05
19 19 0.44
20 22 0.51
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGTCGAAACC
Found at i:231051 original size:29 final size:28
Alignment explanation
Indices: 230986--231055 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
230976 AGTCGGGTCG
*
230986 GGTCAGACCGGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTCAAACCGGTTCGAACC
*
231014 GGTCGAAACTGGTCAAACCGGTT-GAAAACC
1 GGTC-AAACCGGTCAAACCGGTTCG--AACC
231044 GGTCAAACCGGT
1 GGTCAAACCGGT
231056 TTCCAGCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 23 0.64
30 8 0.22
ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16
Consensus pattern (28 bp):
GGTCAAACCGGTCAAACCGGTTCGAACC
Found at i:238225 original size:19 final size:18
Alignment explanation
Indices: 238203--238274 Score: 56
Period size: 19 Copynumber: 3.7 Consensus size: 18
238193 ATCAGTTCAG
238203 ACCGGTCAAACCGATTCGA
1 ACCGGTCAAACCG-TTCGA
* * *
238222 ACCGGTCGAAATCGGTCAA
1 ACCGGTC-AAACCGTTCGA
238241 ACCGGTCAGAACCGGTT-GAAA
1 ACCGGTCA-AACC-GTTCG--A
238262 ACCGGTCAAACCG
1 ACCGGTCAAACCG
238275 GTTTCCAGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 21 0.50
20 11 0.26
21 9 0.21
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (18 bp):
ACCGGTCAAACCGTTCGA
Found at i:238237 original size:10 final size:9
Alignment explanation
Indices: 238221--238276 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
238211 AACCGATTCG
238221 AACCGGTCGA
1 AACCGGTC-A
*
238231 AATCGGTCA
1 AACCGGTCA
238240 AACCGGTCA
1 AACCGGTCA
*
238249 GAACCGGTTGAA
1 -AACCGG-T-CA
238261 AACCGGTCA
1 AACCGGTCA
238270 AACCGGT
1 AACCGGT
238277 TTCCAGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 17 0.44
10 14 0.36
11 7 0.18
12 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.27, T:0.14
Consensus pattern (9 bp):
AACCGGTCA
Found at i:238239 original size:29 final size:30
Alignment explanation
Indices: 238203--238276 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
238193 ATCAGTTCAG
*
238203 ACCGGTCAAACCGATTC-GAACCGGTCG-AA
1 ACCGGTCAAACCG-GTCAGAACCGGTCGAAA
* *
238232 ATCGGTCAAACCGGTCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTCAGAACCGGTCGAAA
238262 ACCGGTCAAACCGGT
1 ACCGGTCAAACCGGT
238277 TTCCAGCCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 2 0.05
29 21 0.54
30 16 0.41
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (30 bp):
ACCGGTCAAACCGGTCAGAACCGGTCGAAA
Found at i:238275 original size:20 final size:21
Alignment explanation
Indices: 238239--238277 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
238229 GAAATCGGTC
238239 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
238260 AAACCGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
238278 TCCAGCCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.15
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:242936 original size:14 final size:14
Alignment explanation
Indices: 242917--242963 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
242907 TTTCATTAAT
242917 ATATTATTAAAATA
1 ATATTATTAAAATA
*
242931 ATATTAATTAAATTA
1 ATATT-ATTAAAATA
* *
242946 AAATT-TTAAAATT
1 ATATTATTAAAATA
242959 ATATT
1 ATATT
242964 GAAATAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 10 0.37
14 5 0.19
15 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATTATTAAAATA
Found at i:242976 original size:28 final size:27
Alignment explanation
Indices: 242923--243005 Score: 76
Period size: 28 Copynumber: 2.9 Consensus size: 27
242913 TAATATATTA
* * *
242923 TTAAAATAATATTAATTAAATTAAAATT
1 TTAAAATTATATTAAATAAA-AAAAATT
242951 TTAAAATTATATTGAAATAAAAAAAATT
1 TTAAAATTATATT-AAATAAAAAAAATT
* *
242979 TCCCAAAATTATAATTAAATTAAAAAA
1 T--TAAAATTAT-ATTAAATAAAAAAA
243006 GTATTCCCTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 19 0.41
29 6 0.13
30 18 0.39
31 3 0.07
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (27 bp):
TTAAAATTATATTAAATAAAAAAAATT
Found at i:245155 original size:20 final size:20
Alignment explanation
Indices: 245132--245177 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
245122 ATTTTTTACC
245132 TTTTAGTTTTAT-TAAGTAAA
1 TTTTA-TTTTATATAAGTAAA
* *
245152 TTTTATTTTATATAATTATA
1 TTTTATTTTATATAAGTAAA
245172 TTTTAT
1 TTTTAT
245178 AAAACTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTATTTTATATAAGTAAA
Found at i:250350 original size:166 final size:168
Alignment explanation
Indices: 250027--250354 Score: 536
Period size: 167 Copynumber: 2.0 Consensus size: 168
250017 TTCGATGAAT
* *
250027 TAAAATCATCATCACAATTTTTTTTTCATCTTATCTCATTTTATCCAATCAAACTTTTTTTAAAA
1 TAAAATCATCATCACAATTTTTTTTTCATATTATCTCATTTTATCCAATCAAACTATTTTTAAAA
* * * *
250092 TTAACTCAAAAATTATAAATTCAAATGTGAGTTTTAAAATCTTTTTCCATCGAATTAACGTTATT
66 TGAACTCAAAAATTATAAATTCAAATATGAGTTTTAAAATATTTTTCCATCGAATTAACATTATT
* *
250157 CATTTTTCAGTTAATTTCAAATGAAATATATTGTGTAC
131 CATTGTTCAATTAATTTCAAATGAAATATATTGTGTAC
*
250195 TAAAATCGTCATCACAATTTTTTTTTTCATATT-TCTCATTTTATCCAATCAAAC-ATTTTTAAA
1 TAAAATCATCATCACAA-TTTTTTTTTCATATTATCTCATTTTATCCAATCAAACTATTTTTAAA
*
250258 ATGAACTCAAAAATTATAAATTCAAATATGAGTTTTAAAATATTTTT-CATCGAATTAATATTAT
65 ATGAACTCAAAAATTATAAATTCAAATATGAGTTTTAAAATATTTTTCCATCGAATTAACATTAT
250322 TCATTGTTCAATTAATTTCAAATGAAATATATT
130 TCATTGTTCAATTAATTTCAAATGAAATATATT
250355 ATGTGCACTA
Statistics
Matches: 149, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
166 46 0.31
167 52 0.35
168 37 0.25
169 14 0.09
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.45
Consensus pattern (168 bp):
TAAAATCATCATCACAATTTTTTTTTCATATTATCTCATTTTATCCAATCAAACTATTTTTAAAA
TGAACTCAAAAATTATAAATTCAAATATGAGTTTTAAAATATTTTTCCATCGAATTAACATTATT
CATTGTTCAATTAATTTCAAATGAAATATATTGTGTAC
Found at i:254548 original size:7 final size:7
Alignment explanation
Indices: 254533--254564 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
254523 ACTACCAGTC
*
254533 TTCTCAT
1 TTCTTAT
254540 TTCTTAT
1 TTCTTAT
254547 TTCTTAT
1 TTCTTAT
254554 TTCTTAT
1 TTCTTAT
254561 TTCT
1 TTCT
254565 GTTTGTACGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (7 bp):
TTCTTAT
Found at i:257914 original size:32 final size:33
Alignment explanation
Indices: 257837--257914 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 33
257827 TAAAACAAAT
* *
257837 AAAA-ATAATAAATATATAATACTAAGTAAAAA
1 AAAATATAATATATACATAATACTAAGTAAAAA
* * *
257869 AAAATA-AAGATATACATGATATTAAG-AAAAA
1 AAAATATAATATATACATAATACTAAGTAAAAA
*
257900 AATATATAATATATA
1 AAAATATAATATATA
257915 TAAATAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
31 10 0.27
32 26 0.70
33 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (33 bp):
AAAATATAATATATACATAATACTAAGTAAAAA
Found at i:258084 original size:20 final size:17
Alignment explanation
Indices: 258061--258101 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 17
258051 AGATATACAT
258061 AATAAAAATAATATAATATA
1 AATAAAAAT--TATAAT-TA
258081 AATAAAAATTATAATTA
1 AATAAAAATTATAATTA
258098 AATA
1 AATA
258102 TATATATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.29
18 6 0.29
20 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAAAAATTATAATTA
Found at i:259802 original size:106 final size:104
Alignment explanation
Indices: 259507--260019 Score: 513
Period size: 106 Copynumber: 5.0 Consensus size: 104
259497 TATTGTTCCA
* *
259507 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAAATT----G--TTTGTTGACAGT
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAAATTGGAAGTTTTTGTTGACAAT
*
259565 CAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCG
64 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
* * *
259606 AGTCTAATATCCTT--C-GT----TTGAAATTGACTCTG-AA-T-GAA-ATTTTGTTGACAATCA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTTTTGTTGACAATCA
* * * *
259660 GCCTCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTG
66 GCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
* * * * *
259699 GGTCCAATATCCTTCGCTGGGAAGTTGAAATTGGCCCTGAAATTGGGAAGTTATTTATTGACAGT
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAGTT-TTTGTTGACAAT
* * *
259764 CAACCGCCTCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG
64 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
*
259805 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTTTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAG-TTTTTGTTGACAAT
* * * *
259870 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
* * * * * * *
259911 AATCCAATATCCTTCACTGTGAAGTTGAAATTGGTTCTAAAACTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAGTT-TTTGTTGACAAT
* * * * *
259976 CAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
260017 AGT
1 AGT
260020 GGCACGATAT
Statistics
Matches: 348, Mismatches: 44, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
89 1 0.00
90 2 0.01
91 1 0.00
92 13 0.04
93 59 0.17
95 1 0.00
96 3 0.01
99 12 0.03
100 13 0.04
101 2 0.01
102 1 0.00
104 3 0.01
105 3 0.01
106 231 0.66
107 3 0.01
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (104 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAGTTTTTGTTGACAATCA
GCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
Found at i:260799 original size:67 final size:66
Alignment explanation
Indices: 260692--260848 Score: 201
Period size: 67 Copynumber: 2.4 Consensus size: 66
260682 AAGATATCTG
* * * * **
260692 TTGTTTCATGA-AAACGGTCTGAAGGGAAAGAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGA-
260756 TT
65 TT
* *
260758 TGTGTTTCAAGAGAAACTGTCTCAAGGGATACAAAA-TTTGTTTTAGGGGAAATAAATTCAAAGA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGA
260822 TT
65 TT
*
260824 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
260849 AAAGATGAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 23 0.29
66 4 0.05
67 34 0.43
68 19 0.24
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:260868 original size:36 final size:36
Alignment explanation
Indices: 260827--260941 Score: 131
Period size: 36 Copynumber: 3.2 Consensus size: 36
260817 AAAGATTTTG
* *
260827 TTTCAAGGGAAACTGTCTCAAGAAAGATGAAATTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGATGAAATTTA
** *
260863 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGATGAAATTTA
* * * * *
260899 GTTCCAAAAGAAATTGTCTCAAGGGAGATGAAATTTG
1 -TTTCAAGAGAAACTGTCTCAAGAGAGATGAAATTTA
260936 TTTCAA
1 TTTCAA
260942 ATAATTTGTT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 36 0.56
37 28 0.44
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGATGAAATTTA
Found at i:260964 original size:87 final size:86
Alignment explanation
Indices: 260857--261027 Score: 243
Period size: 86 Copynumber: 2.0 Consensus size: 86
260847 AGAAAGATGA
*
260857 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAG
* * *
260922 GGAGATGAAATTTGTTTCAAAT
65 AGAGACGAAATTTATTTCAAAT
* * * * **
260944 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGA
261009 GAGACGAAATTTATTTCAA
66 GAGACGAAATTTATTTCAA
261028 GGGAAATGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 38 0.51
87 36 0.49
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (86 bp):
AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGA
GAGACGAAATTTATTTCAAAT
Found at i:260987 original size:36 final size:36
Alignment explanation
Indices: 260944--261135 Score: 186
Period size: 36 Copynumber: 5.5 Consensus size: 36
260934 TGTTTCAAAT
260944 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
260980 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * *
261016 AATTTATTTCAAGGGAAA-TGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* * * * *
261045 -TTTATATTTCAAGAGAAACTATCTCAAGGGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* *
261081 AATTTCGTTTCAATGGAAACTATCTCAAGAGAGACAA
1 AATTT-GTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
261118 AATTCGTTTCAAGGGAAA
1 AATTTGTTTCAAGGGAAA
261136 TGTTTTCAAT
Statistics
Matches: 127, Mismatches: 17, Indels: 24
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.02
29 16 0.13
30 2 0.02
32 1 0.01
33 1 0.01
34 1 0.01
35 3 0.02
36 68 0.54
37 33 0.26
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:261034 original size:102 final size:101
Alignment explanation
Indices: 260948--261211 Score: 420
Period size: 102 Copynumber: 2.6 Consensus size: 101
260938 TCAAATAATT
* * *
260948 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
261013 CGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
261049 TATTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTCGTTTCAATGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-GTTTCAAGGGAAACTATCTCAAGAGAG
*
261114 ACAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
65 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
261151 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAA-AATTTGTTTCAAGGGAAACTATCTCAAG
261212 CAAGATAAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 33 0.22
102 111 0.75
103 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:261101 original size:37 final size:35
Alignment explanation
Indices: 261051--261131 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 35
261041 AATGTTTATA
*
261051 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTCG
1 TTTCAAG-GAAACTATCTCAAGAGAGACAAAA-TTCG
261088 TTTCAATGGAAACTATCTCAAGAGAGACAAAATTCG
1 TTTCAA-GGAAACTATCTCAAGAGAGACAAAATTCG
261124 TTTCAAGG
1 TTTCAAGG
261132 GAAATGTTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 2 0.05
36 10 0.24
37 29 0.69
38 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (35 bp):
TTTCAAGGAAACTATCTCAAGAGAGACAAAATTCG
Found at i:262920 original size:15 final size:13
Alignment explanation
Indices: 262878--262937 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
262868 TTTCTTCAAA
*
262878 TTTC-CTTTGTTT
1 TTTCTCTTTTTTT
*
262890 TTTCTCTTTTTAT
1 TTTCTCTTTTTTT
**
262903 TTTCTCTTTGCTT
1 TTTCTCTTTTTTT
*
262916 TTT-T-TTTCTTT
1 TTTCTCTTTTTTT
262927 TTTCTCTTTTT
1 TTTCTCTTTTT
262938 GTTCTGATTG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
11 8 0.22
12 6 0.16
13 23 0.62
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:265770 original size:9 final size:9
Alignment explanation
Indices: 265756--265795 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
265746 AATGGAGTAC
265756 AAAAATAAA
1 AAAAATAAA
265765 AAAAATAAA
1 AAAAATAAA
*
265774 ATAAATTAAA
1 A-AAAATAAA
265784 AAAGAATAAA
1 AAA-AATAAA
265794 AA
1 AA
265796 TAATGTGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 12 0.44
10 15 0.56
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:265996 original size:37 final size:36
Alignment explanation
Indices: 265890--266012 Score: 118
Period size: 37 Copynumber: 3.6 Consensus size: 36
265880 GGTATACATG
* *
265890 ATATTAAGAAAA-AAATA-AAATAAAGTAAAAATATA
1 ATATTAAGAAAATATATATAAA-AACGTAAAAATATA
* *
265925 ATA-TATA-TAAATA-A-ATAAAAAC--AAAAATAGA
1 ATATTA-AGAAAATATATATAAAAACGTAAAAATATA
265956 ATATTAAGAAAATATATATAAAAACGTATAAAATATA
1 ATATTAAGAAAATATATATAAAAACGTA-AAAATATA
*
265993 ATATTAAAAAAATATATATA
1 ATATTAAGAAAATATATATA
266013 CATAGTAAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
31 12 0.17
32 7 0.10
33 4 0.06
34 17 0.24
35 5 0.07
36 1 0.01
37 26 0.36
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (36 bp):
ATATTAAGAAAATATATATAAAAACGTAAAAATATA
Found at i:266008 original size:23 final size:21
Alignment explanation
Indices: 265964--266008 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
265954 GAATATTAAG
**
265964 AAAATATATATAAAAACGTAT
1 AAAATATATATAAAAAAATAT
265985 AAAATATAATATTAAAAAAATAT
1 AAAATAT-ATA-TAAAAAAATAT
266008 A
1 A
266009 TATACATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 3 0.15
23 10 0.50
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATATATATAAAAAAATAT
Found at i:266088 original size:20 final size:21
Alignment explanation
Indices: 266051--266090 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
266041 CTATACATAT
**
266051 ATATATATATAATGATATAAG
1 ATATATATATAAAAATATAAG
266072 ATATATA-ATAAAAATATAA
1 ATATATATATAAAAATATAA
266091 ATAAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
ATATATATATAAAAATATAAG
Found at i:275518 original size:27 final size:27
Alignment explanation
Indices: 275451--275521 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
275441 ATTTTTTTAT
*
275451 AAAACATTACATTAAACCCTAAACCAC
1 AAAACATTACATTTAACCCTAAACCAC
*
275478 GAAACATTACATTTAACCCTAAACCAC
1 AAAACATTACATTTAACCCTAAACCAC
275505 AAAACATTACATTTAAC
1 AAAACATTACATTTAAC
275522 AGATAAAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.49, C:0.27, G:0.01, T:0.23
Consensus pattern (27 bp):
AAAACATTACATTTAACCCTAAACCAC
Found at i:278869 original size:65 final size:64
Alignment explanation
Indices: 278736--278895 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
278726 TGCACTAAGA
* *
278736 GTGCATCGATGCATAAAATGCATTCGATATTTTAAAATAGCCTGAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTACATCGATGCATGGATT
** *
278800 GTGCATCGATGCATTTAATGCATTCGATGTTTTCATAAA-ATCCTGAGTACATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AAATAGCCTGAGTACATCGATGCATGGAT
278863 AT
64 -T
278865 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
278896 CAATTTATTC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 31 0.36
65 52 0.60
66 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTACATCGATGCATGGATT
Found at i:278934 original size:65 final size:63
Alignment explanation
Indices: 278736--278937 Score: 221
Period size: 65 Copynumber: 3.1 Consensus size: 63
278726 TGCACTAAGA
* * * *
278736 GTGCATCGATGCATAAAATGCATTCGATATTTTAAAATAGCCTGAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGAT-GTTCAATATATCCTGAGTGCATCGATGCATGGATT
** * *
278800 GTGCATCGATGCATTTAATGCATTCGATGTTTTC-ATAAAATCCTGAGTACATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATG--TTCAAT-ATATCCTGAGTGCATCGATGCATGGAT
278863 AT
63 -T
* *
278865 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATTCAATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAATATA-TC-CTGAGTGCATCGATGCATGGATT
278929 GGTGCATCG
1 -GTGCATCG
278938 GTACACTCTT
Statistics
Matches: 115, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
63 4 0.03
64 48 0.42
65 63 0.55
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAATATATCCTGAGTGCATCGATGCATGGATT
Found at i:280045 original size:21 final size:21
Alignment explanation
Indices: 280011--280054 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
280001 CCGGAGGAGG
* *
280011 AGGAGGAGCACGTGAAGAGCT
1 AGGAGCAGCACGTGAAGAACT
*
280032 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGTGAAGAACT
280053 AG
1 AG
280055 CTCCCGGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.39, T:0.11
Consensus pattern (21 bp):
AGGAGCAGCACGTGAAGAACT
Found at i:292865 original size:23 final size:22
Alignment explanation
Indices: 292834--292918 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 22
292824 ATTTTTGTGC
292834 ATAGAGTATCGATACCGCCTTTGA
1 ATAG-GTATCGATACC-CCTTTGA
*
292858 ATAGGTATTGATA-CCC-TTGCA
1 ATAGGTATCGATACCCCTTTG-A
* * *
292879 ATAAGTATCAATACCATCTTTGA
1 ATAGGTATCGATACC-CCTTTGA
292902 ATAGGTATCGATACCCC
1 ATAGGTATCGATACCCC
292919 CTGATGGCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.06
21 13 0.27
22 3 0.06
23 23 0.47
24 7 0.14
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (22 bp):
ATAGGTATCGATACCCCTTTGA
Found at i:295019 original size:19 final size:19
Alignment explanation
Indices: 294995--295065 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
294985 AATAGTCTGA
294995 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
295014 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
295033 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
295052 GTGCATCGATGCAT
1 GTGCATCGATGCAT
295066 TAAATGTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGATT
Found at i:295103 original size:65 final size:64
Alignment explanation
Indices: 295033--295189 Score: 194
Period size: 65 Copynumber: 2.4 Consensus size: 64
295023 TGCATGGATT
* * *
295033 GTGCATCGATGCATGGATTGTGCATCGATGCATTAAATGTATTCGATGTTTTC-ATAAAATC-CT
1 GTGCATCGATGCATGGATTGTGCATCGATGCATAAAATGCATTCGATG--TTCAATAAAATCAAT
295096 G
64 G
** *
295097 AGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCATTCGATGTTCAATTTATTCAAT
1 -GTGCATCGATGCATGGAT-TGTGCATCGATGCATAAAATGCATTCGATGTTCAATAAAATCAAT
295161 G
64 G
295162 GTGCATCGATGCATGGATTGGTGCATCG
1 GTGCATCGATGCATGGATT-GTGCATCG
295190 GTACACTCTT
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
63 3 0.04
64 23 0.28
65 55 0.68
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATGGATTGTGCATCGATGCATAAAATGCATTCGATGTTCAATAAAATCAATG
Found at i:301813 original size:21 final size:21
Alignment explanation
Indices: 301774--301830 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
301764 TGGTAAAGCG
301774 CTACCGGTTTTG-T-TTTTTT
1 CTACCGGTTTTGTTATTTTTT
301793 CTACCGGTTTTGTTATTTTTT
1 CTACCGGTTTTGTTATTTTTT
* *
301814 CTATCGATTTTGTTATT
1 CTACCGGTTTTGTTATT
301831 GTTGGGCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.35
20 1 0.03
21 21 0.62
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.61
Consensus pattern (21 bp):
CTACCGGTTTTGTTATTTTTT
Found at i:307366 original size:31 final size:31
Alignment explanation
Indices: 307331--307409 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
307321 GGGCCGTAGG
*
307331 GCCTACCTAAGAATACATCTTAGGGCCACA-A
1 GCCTACCTAAGAAT-CATCTCAGGGCCACAGA
** * *
307362 GCCTACCCGAGAATGATCTCAGGGCCGCAGA
1 GCCTACCTAAGAATCATCTCAGGGCCACAGA
*
307393 GCCTACCTAAGATTCAT
1 GCCTACCTAAGAATCAT
307410 TAGGTCCATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (31 bp):
GCCTACCTAAGAATCATCTCAGGGCCACAGA
Found at i:310237 original size:19 final size:18
Alignment explanation
Indices: 310209--310248 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
310199 GCCGGTCAAC
*
310209 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
310227 GGTCAAACGGGTCGGGTCG
1 GGTC-AACGGGTCGGGTCG
310246 GGT
1 GGT
310249 TGTAACTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:310829 original size:87 final size:87
Alignment explanation
Indices: 310683--310857 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
310673 CAGAGAGGAA
310683 TTATGAGCATTTTCTGCAGAAAAATAAAGAGAAAATAACCTCAGTGACCAAAATGTCTTATAATA
1 TTATGAGCATTTTCTGCAGAAAAATAAAGAGAAAATAACCTCAGTGACCAAAATGTCTTATAATA
310748 TACGATTTTAATCAACTTTTTT
66 TACGATTTTAATCAACTTTTTT
310770 TTATGAGCATTTTCTGCAGAAAAATAAAGAGAAAATAACCTCAGTGACCAAAATGTCTTATAATA
1 TTATGAGCATTTTCTGCAGAAAAATAAAGAGAAAATAACCTCAGTGACCAAAATGTCTTATAATA
310835 TACGATTTTAATCAACTTTTTT
66 TACGATTTTAATCAACTTTTTT
310857 T
1 T
310858 GGATTTATCA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (87 bp):
TTATGAGCATTTTCTGCAGAAAAATAAAGAGAAAATAACCTCAGTGACCAAAATGTCTTATAATA
TACGATTTTAATCAACTTTTTT
Found at i:311095 original size:20 final size:20
Alignment explanation
Indices: 310961--311209 Score: 234
Period size: 20 Copynumber: 12.3 Consensus size: 20
310951 GATTCTGACT
* **
310961 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTACGTA
* * *
310981 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTACGT-A
* *
311003 ATCGCAATGCGA-ATACGTAA
1 ATCGCATTGCGATTTACGT-A
* * * *
311023 ATCGCAATGCGAATTAGGAAA
1 ATCGCATTGCGATTTACG-TA
* *
311044 ATCGCAATACGA-TTACGTA
1 ATCGCATTGCGATTTACGTA
*
311063 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
311083 ATCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
*
311103 ATCGTATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
*
311123 TTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACGTA
* * *
311143 TTCGCATTGCGATTTTCCTA
1 ATCGCATTGCGATTTACGTA
311163 ATTCGCATTGCGATTTACGTA
1 A-TCGCATTGCGATTTACGTA
*
311184 TTCGCATTGCGATTTA-GTAA
1 ATCGCATTGCGATTTACGT-A
311204 ATCGCA
1 ATCGCA
311210 ACGAGATTCT
Statistics
Matches: 194, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.06
20 124 0.64
21 56 0.29
22 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATTTACGTA
Found at i:311247 original size:81 final size:81
Alignment explanation
Indices: 311084--311250 Score: 180
Period size: 81 Copynumber: 2.1 Consensus size: 81
311074 ATTTACGTAA
* * ** *
311084 TCGCATTGCGATTTACGTAATCGTATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATTTACGTATTCGCA
* * * *
311149 TTGCGATTTTCCTAAT
66 ATACGAATTTCCAAAT
*
311165 TCGCATTGCGATTTACGTATTCGCATTGCGATTTA-GTAAATCGCAACGAGATTCTGAC-TA-TC
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGT-AATCGCAACGAGATT-T-ACGTATTC
311227 GCAATACTGAATTT-CAAAT
63 GCAATAC-GAATTTCCAAAT
311246 TCGCA
1 TCGCA
311251 ACTCGATTTC
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
80 2 0.03
81 60 0.83
82 8 0.11
83 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (81 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCAACGAGATTTACGTATTCGCA
ATACGAATTTCCAAAT
Found at i:312090 original size:24 final size:24
Alignment explanation
Indices: 312063--312116 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
312053 GTATTCGAAA
312063 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
312087 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
312111 TTTGAT
1 TTTGAT
312117 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:314654 original size:20 final size:19
Alignment explanation
Indices: 314626--314680 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
314616 CAATCATCTT
*
314626 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
314646 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
314665 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
314681 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:314668 original size:19 final size:20
Alignment explanation
Indices: 314587--314680 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
314577 GGCATTCATT
*
314587 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
314607 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
314628 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
314648 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
314667 TGAAAATCGCAACG
1 TGACTATCGCAACG
314681 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:314699 original size:33 final size:33
Alignment explanation
Indices: 314653--314746 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
314643 GGAAATGACT
*
314653 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
314686 ATCGCAATACGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
*
314719 ATCACAA-AGCGAAATGAAAATCGCAACG
1 ATCGCAATA-CGAAATGAAAATCGCAACG
314747 CGAATTTCGT
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATACGAAATGAAAATCGCAACGAGAGA
Found at i:314709 original size:19 final size:19
Alignment explanation
Indices: 314653--314711 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
314643 GGAAATGACT
*
314653 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
314672 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
314686 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
314705 ATCGCAA
1 ATCGCAA
314712 CGAGGGAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 8 0.25
15 2 0.06
16 3 0.09
17 2 0.06
18 2 0.06
19 15 0.47
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:314749 original size:19 final size:18
Alignment explanation
Indices: 314633--314750 Score: 63
Period size: 19 Copynumber: 6.7 Consensus size: 18
314623 CTTAATGTCT
**
314633 ATCGCAACGCGGAAATGACT
1 ATCGCAA-GC-GAAATGAAA
314653 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
314672 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
314686 ATCGCAATACGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
314705 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
*
314719 ATCACAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
314738 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
314751 TTTCGTTTTG
Statistics
Matches: 76, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
14 16 0.21
15 4 0.05
16 4 0.05
17 4 0.05
18 4 0.05
19 35 0.46
20 9 0.12
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:314768 original size:19 final size:19
Alignment explanation
Indices: 314746--314797 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
314736 AAATCGCAAC
* * *
314746 GCGAATTTCGTTTTGCGTT
1 GCGATTTTCATTTCGCGTT
314765 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
314784 GCGATTTTCATTTC
1 GCGATTTTCATTTC
314798 ACATTTCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:314807 original size:19 final size:19
Alignment explanation
Indices: 314763--314807 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
314753 TCGTTTTGCG
* *
314763 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCACA
314782 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
314801 TTTCGAT
1 TTGCGAT
314808 AGTCATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:314933 original size:14 final size:14
Alignment explanation
Indices: 314914--314950 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
314904 TATCAATTAA
314914 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
314928 ACAAATCATCTTTT
1 ACAAATCAACTTTT
314942 ACAAATCAA
1 ACAAATCAA
314951 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:316324 original size:21 final size:20
Alignment explanation
Indices: 316300--316360 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
316290 GTGAATCGGG
*
316300 CTCTTGAATGGTGAGAGGGAC
1 CTCTTGAACGGTGAGAGGG-C
* * *
316321 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGAGAG-GGC
*
316342 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGAGAGGG
316361 GACTCTCGAG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGAGAGGGC
Found at i:318793 original size:19 final size:19
Alignment explanation
Indices: 318729--318841 Score: 128
Period size: 20 Copynumber: 6.1 Consensus size: 19
318719 TCTTTTGGTT
*
318729 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
318748 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
318768 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
318788 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
318805 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
318821 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
318840 GA
1 GA
318842 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 30 0.38
20 31 0.39
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:318820 original size:33 final size:36
Alignment explanation
Indices: 318737--318836 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 36
318727 TTGAAATGAA
*
318737 AATCGCAACGAGAGAATGAAAATCGCAACGCGGAAATG
1 AATCGCAACGCGA-AATGAAAATCGCAAC-CGGAAATG
*
318775 ACTATCGCAACGCGAAATGAAAATCGCAA-C-GAGA-G
1 A--ATCGCAACGCGAAATGAAAATCGCAACCGGAAATG
318810 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
318837 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
33 26 0.45
35 2 0.03
36 3 0.05
37 1 0.02
38 1 0.02
39 14 0.24
40 11 0.19
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (36 bp):
AATCGCAACGCGAAATGAAAATCGCAACCGGAAATG
Found at i:318932 original size:20 final size:20
Alignment explanation
Indices: 318868--318958 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
318858 CGATTATATC
* *
318868 GTTGTGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
*
318887 GTTGCGATTTTCATTTCTCTT
1 GTTGCGATTTTCATTT-TCGT
**
318908 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
*
318928 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
*
318948 GTTGTGATTTT
1 GTTGCGATTTT
318959 AAGTTTAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.20
20 32 0.53
21 16 0.27
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:319555 original size:21 final size:21
Alignment explanation
Indices: 319513--319684 Score: 174
Period size: 20 Copynumber: 8.4 Consensus size: 21
319503 AGTCAGATTT
*
319513 GCATTGCGATTTACGT-ATTC
1 GCATTGCGATTTACCTAATTC
*
319533 GCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACCTAATTC
*
319554 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACCTAATTC
** *
319574 GTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACCTAATTC
*
319595 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACCTAATTC
** *
319615 GTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACCTAATTC
*
319636 GCATTGCGATTTACGTAA-TC
1 GCATTGCGATTTACCTAATTC
* * **
319656 GCGTTGTGATTTATGT-ATTC
1 GCATTGCGATTTACCTAATTC
319676 GCATTGCGA
1 GCATTGCGA
319685 ATTAAGAAAA
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
19 1 0.01
20 70 0.57
21 52 0.42
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (21 bp):
GCATTGCGATTTACCTAATTC
Found at i:319565 original size:41 final size:41
Alignment explanation
Indices: 319513--319684 Score: 267
Period size: 41 Copynumber: 4.2 Consensus size: 41
319503 AGTCAGATTT
* *
319513 GCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCGTTGCGATTTTCCTAATTC
*
319554 GCATTGCGATTTACGTAATCGTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCGTTGCGATTTTCCTAATTC
*
319595 GCATTGCGATTTACGTAATCGTGTTGCGATTTTCCTAATTC
1 GCATTGCGATTTACGTAATCGCGTTGCGATTTTCCTAATTC
* *
319636 GCATTGCGATTTACGTAATCGCGTTGTGATTTAT-GT-ATTC
1 GCATTGCGATTTACGTAATCGCGTTGCGATTT-TCCTAATTC
319676 GCATTGCGA
1 GCATTGCGA
319685 ATTAAGAAAA
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 13 0.10
41 110 0.89
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (41 bp):
GCATTGCGATTTACGTAATCGCGTTGCGATTTTCCTAATTC
Found at i:336365 original size:21 final size:21
Alignment explanation
Indices: 336339--336378 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
336329 CCGGTTTTGC
*
336339 CGGTTTTTAGCCGGTTCATCT
1 CGGTTTTCAGCCGGTTCATCT
*
336360 CGGTTTTCAGTCGGTTCAT
1 CGGTTTTCAGCCGGTTCAT
336379 TGCCAGCCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.25, T:0.42
Consensus pattern (21 bp):
CGGTTTTCAGCCGGTTCATCT
Found at i:339542 original size:13 final size:14
Alignment explanation
Indices: 339514--339544 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
339504 GTTGTAGGGG
339514 AAATGGAGACAGAA
1 AAATGGAGACAGAA
339528 AAATGGAGA-AGAA
1 AAATGGAGACAGAA
339541 AAAT
1 AAAT
339545 AGTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.26, T:0.10
Consensus pattern (14 bp):
AAATGGAGACAGAA
Found at i:344910 original size:16 final size:17
Alignment explanation
Indices: 344888--344926 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
344878 GAAAGACTGA
*
344888 AAAAATG-TTACAAAAT
1 AAAAATGATTAAAAAAT
*
344904 TAAAATGATTAAAAAAT
1 AAAAATGATTAAAAAAT
344921 AAAAAT
1 AAAAAT
344927 AATAAAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAAATGATTAAAAAAT
Found at i:346651 original size:31 final size:31
Alignment explanation
Indices: 346613--346680 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
346603 ATCCCACTAG
346613 ATTTTATAAACGATACAAATGTTGATTTATT
1 ATTTTATAAACGATACAAATGTTGATTTATT
346644 ATTTTATAAACGATACAAATGTTGATTTATT
1 ATTTTATAAACGATACAAATGTTGATTTATT
346675 ATTTTA
1 ATTTTA
346681 GGTTTAATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (31 bp):
ATTTTATAAACGATACAAATGTTGATTTATT
Found at i:347242 original size:5 final size:5
Alignment explanation
Indices: 347234--347293 Score: 84
Period size: 5 Copynumber: 12.0 Consensus size: 5
347224 TAACTTAGCT
* * *
347234 TTTTC TTTTC TGTTC TTTTC TTTTC TTTTC TTTTC TTTTC GTTTC GTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
*
347284 GTTTC TTTTC
1 TTTTC TTTTC
347294 GTGCTTAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.73
Consensus pattern (5 bp):
TTTTC
Found at i:348680 original size:14 final size:14
Alignment explanation
Indices: 348661--348691 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
348651 ATTATTTAAA
348661 TTATTTGAATTTAT
1 TTATTTGAATTTAT
*
348675 TTATTTGAATTTGT
1 TTATTTGAATTTAT
348689 TTA
1 TTA
348692 AATAATTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.65
Consensus pattern (14 bp):
TTATTTGAATTTAT
Found at i:350641 original size:22 final size:22
Alignment explanation
Indices: 350616--350679 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
350606 CACGCTGAAT
350616 GTTGAACGGTTCAACATTCAGC
1 GTTGAACGGTTCAACATTCAGC
350638 GTTGAACGGTTCAACATTCAGC
1 GTTGAACGGTTCAACATTCAGC
*
350660 GTTGAATGGTTC--CATTCAGC
1 GTTGAACGGTTCAACATTCAGC
350680 AGTAAACAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 8 0.20
22 33 0.80
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (22 bp):
GTTGAACGGTTCAACATTCAGC
Found at i:352501 original size:16 final size:16
Alignment explanation
Indices: 352480--352511 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
352470 AAGGGAAATT
352480 CATCATGTCGATATGA
1 CATCATGTCGATATGA
352496 CATCATGTCGATATGA
1 CATCATGTCGATATGA
352512 TGAGTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (16 bp):
CATCATGTCGATATGA
Found at i:353054 original size:18 final size:18
Alignment explanation
Indices: 353027--353066 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
353017 AAAAATCTTA
353027 TTTA-TTTATAAATATAT
1 TTTATTTTATAAATATAT
353044 TTTATTTTATAAATATAT
1 TTTATTTTATAAATATAT
*
353062 ATTAT
1 TTTAT
353067 GAGGTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATTTTATAAATATAT
Found at i:354018 original size:53 final size:53
Alignment explanation
Indices: 353957--354127 Score: 319
Period size: 53 Copynumber: 3.3 Consensus size: 53
353947 CATTCCAAAG
353957 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
354010 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
*
354063 CCTACTGATAAATTTTCACCTAGGTCTATGCCTGCTGTTTTTGTAGG--ATTC
1 CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
354114 CCTACTGATAAATT
1 CCTACTGATAAATT
354128 CTTTTCAACC
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
51 18 0.15
53 99 0.85
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (53 bp):
CCTACTGATAAATTTTCACCTAGGTCTGTGCCTGCTGTTTTTGTAGGATATTC
Found at i:360404 original size:115 final size:113
Alignment explanation
Indices: 360178--360413 Score: 391
Period size: 115 Copynumber: 2.0 Consensus size: 113
360168 TTTGGTTGCC
*
360178 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGCTATAGAGTAAGACAAAGC
1 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
360243 AAAATTTTCCAAATCTTACATCACATTTACTGGCAATAAATGAATGAGCA
66 AAAATTTTCCAAATCTTACATCACATTTACTGGCAAT-AA-GAATGAGCA
360293 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
1 TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAG-
360358 AACAAAACTTTTCCAAATCTTACATCACATTTACTGGCAATAAATGAATGAGCA
65 --CAAAA-TTTTCCAAATCTTACATCACATTTACTGGCAAT-AA-GAATGAGCA
360412 TG
1 TG
360414 ATCTTCCATG
Statistics
Matches: 116, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
115 63 0.54
118 5 0.04
119 48 0.41
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (113 bp):
TGCCAATATTTCACAAATCACGAATCAGAAGTAATGTAGCCACATGATATAGAGTAAGACAAAGC
AAAATTTTCCAAATCTTACATCACATTTACTGGCAATAAGAATGAGCA
Found at i:362450 original size:135 final size:135
Alignment explanation
Indices: 362208--362472 Score: 530
Period size: 135 Copynumber: 2.0 Consensus size: 135
362198 ACTTGACAGC
362208 TACTGATTAAAATAAACCCATCATTATAATTTATATATGTATATCCATTTACTAATCATACTTAT
1 TACTGATTAAAATAAACCCATCATTATAATTTATATATGTATATCCATTTACTAATCATACTTAT
362273 AATTGGTAATTAACCATGTATCAAAGACATGTCAAATTCCAAGACTAATCAATATAATAAATTAA
66 AATTGGTAATTAACCATGTATCAAAGACATGTCAAATTCCAAGACTAATCAATATAATAAATTAA
362338 CCATT
131 CCATT
362343 TACTGATTAAAATAAACCCATCATTATAATTTATATATGTATATCCATTTACTAATCATACTTAT
1 TACTGATTAAAATAAACCCATCATTATAATTTATATATGTATATCCATTTACTAATCATACTTAT
362408 AATTGGTAATTAACCATGTATCAAAGACATGTCAAATTCCAAGACTAATCAATATAATAAATTAA
66 AATTGGTAATTAACCATGTATCAAAGACATGTCAAATTCCAAGACTAATCAATATAATAAATTAA
362473 ATACCAGGTA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
135 130 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (135 bp):
TACTGATTAAAATAAACCCATCATTATAATTTATATATGTATATCCATTTACTAATCATACTTAT
AATTGGTAATTAACCATGTATCAAAGACATGTCAAATTCCAAGACTAATCAATATAATAAATTAA
CCATT
Found at i:370757 original size:85 final size:85
Alignment explanation
Indices: 370498--370757 Score: 378
Period size: 85 Copynumber: 3.1 Consensus size: 85
370488 ACCCGATATG
* * * * *
370498 ATTTCATTTGAAATTTTTGGCCATCTAAAAGTTTTAGATATTTAAAATAGTGATCCCTGTACCAT
1 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCCTGTACGAT
370563 TGAAAATATTACATATCCGA
66 TGAAAATATTACATATCCGA
* * * *
370583 ATTTGATTTGAAAATTTTGGGTATCTAAACA-TTTTGGATATTTAAAATAGTGATCCATATACGA
1 ATTTTATTTGAAAATTTTGGGCATCTAAA-AGTTTTGGATATTTAAAATAGTGATCCCTGTACGA
* *
370647 TTGAAATTATTACATATCCAA
65 TTGAAAATATTACATATCCGA
*
370668 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCCTGTAAGAT
1 ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCCTGTACGAT
* *
370733 TAAAAATATTACATATTCGA
66 TGAAAATATTACATATCCGA
370753 ATTTT
1 ATTTT
370758 TAGATTGAGT
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
84 1 0.01
85 152 0.99
86 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (85 bp):
ATTTTATTTGAAAATTTTGGGCATCTAAAAGTTTTGGATATTTAAAATAGTGATCCCTGTACGAT
TGAAAATATTACATATCCGA
Found at i:371867 original size:21 final size:21
Alignment explanation
Indices: 371843--371882 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
371833 AAAAATTAAT
* *
371843 TAAAACATTATTTTTTTTACC
1 TAAAACATTAATCTTTTTACC
371864 TAAAACATTAATCTTTTTA
1 TAAAACATTAATCTTTTTA
371883 ATATTTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAACATTAATCTTTTTACC
Found at i:375806 original size:3 final size:3
Alignment explanation
Indices: 375798--375828 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
375788 TAATGGGAAT
375798 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
375829 GTTTCTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:381153 original size:21 final size:21
Alignment explanation
Indices: 381129--381171 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
381119 TTCAAGCTAC
381129 ATAATTATTTCACATTGGTTT
1 ATAATTATTTCACATTGGTTT
*
381150 ATAATTATTTCGCATTGGTTT
1 ATAATTATTTCACATTGGTTT
381171 A
1 A
381172 AGAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (21 bp):
ATAATTATTTCACATTGGTTT
Found at i:381536 original size:21 final size:21
Alignment explanation
Indices: 381510--381552 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
381500 TTAGAAACTC
*
381510 TAATGTCTTCCCCTGATCTGA
1 TAATGTCTTCCCCTGACCTGA
381531 TAATGTCTTCCCCTGACCTGA
1 TAATGTCTTCCCCTGACCTGA
381552 T
1 T
381553 CGAAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (21 bp):
TAATGTCTTCCCCTGACCTGA
Found at i:383134 original size:15 final size:15
Alignment explanation
Indices: 383116--383145 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
383106 GGTTAAGGAC
*
383116 GAGAGAGTTAAGAGG
1 GAGAGAGTCAAGAGG
383131 GAGAGAGTCAAGAGG
1 GAGAGAGTCAAGAGG
383146 TTGGAGAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.47, T:0.10
Consensus pattern (15 bp):
GAGAGAGTCAAGAGG
Found at i:385790 original size:17 final size:17
Alignment explanation
Indices: 385770--385804 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
385760 AAAAGTAAAA
*
385770 TTTATCGGATATATTTT
1 TTTATCAGATATATTTT
385787 TTTATCAGATATATTTT
1 TTTATCAGATATATTTT
385804 T
1 T
385805 ATTTATGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (17 bp):
TTTATCAGATATATTTT
Found at i:385809 original size:19 final size:18
Alignment explanation
Indices: 385769--385810 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
385759 AAAAAGTAAA
*
385769 ATTTATCGGATATATTTT
1 ATTTATCAGATATATTTT
385787 -TTTATCAGATATATTTTT
1 ATTTATCAGATATA-TTTT
385805 ATTTAT
1 ATTTAT
385811 GTCACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (18 bp):
ATTTATCAGATATATTTT
Found at i:386041 original size:21 final size:21
Alignment explanation
Indices: 386015--386081 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
386005 AGGTCGAAAA
*
386015 AATATTTTAAATATTATTATT
1 AATATTTTAAATATTAATATT
* * *
386036 AGTATTTTTATTATTAATATT
1 AATATTTTAAATATTAATATT
386057 AATA--TT-AATATTAATATT
1 AATATTTTAAATATTAATATT
386075 AATATTT
1 AATATTT
386082 CTTTATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 15 0.39
19 2 0.05
20 1 0.03
21 20 0.53
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
AATATTTTAAATATTAATATT
Found at i:386056 original size:6 final size:6
Alignment explanation
Indices: 386047--386080 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
386037 GTATTTTTAT
386047 TATTAA TATTAA TATTAA TATTAA TATTAA TATT
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATT
386081 TCTTTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:388883 original size:111 final size:112
Alignment explanation
Indices: 388633--388982 Score: 540
Period size: 112 Copynumber: 3.1 Consensus size: 112
388623 GATACTTATA
** * * **
388633 ATAAAGTATCGACACTATCAACATATCTAGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
388698 TTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGATGCATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
388745 ATAAAGTATCAACACTATCAACATATCCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
388810 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
388856 ATAAAGTATCGGCACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
388921 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
388968 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
388983 AAACCGACAA
Statistics
Matches: 216, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
111 103 0.48
112 113 0.52
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.44
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:394470 original size:127 final size:127
Alignment explanation
Indices: 394241--394768 Score: 871
Period size: 127 Copynumber: 4.2 Consensus size: 127
394231 GTACTATTCA
*
394241 CGTGAATGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
394306 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
394368 CGTGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAACATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
*
394433 TATTATGTCACTTATGTCCCCTGGGAACTATTAATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
394495 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATATTATCATTGCTC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
394560 TATTATGTCACTTATGT-CCCTCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCT-GGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
394622 TGTGAAGGCGCGTTCCCGGGGGCGCACATTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
* * * *
394687 TATTATGTCACTTATGTCCCCTGAGAACTATTTATGTCAATACCTACTATTTCTTAGGGGA-
66 TATTATGTCACTTATGTCCCCTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* * *
394748 CTTTAAAGCGCGTTCCCGGGG
1 CGTGAAGGCGCGTTCCCGGGG
394769 AACTATAGAT
Statistics
Matches: 374, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
126 21 0.06
127 349 0.93
128 4 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTTATGTCCCCTGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:395268 original size:33 final size:33
Alignment explanation
Indices: 395171--395276 Score: 140
Period size: 34 Copynumber: 3.2 Consensus size: 33
395161 TTAAGTTGAA
* * *
395171 TTTAATGTTAAATTTTGAATACTATAATTTATAT
1 TTTAATTTTAAA-TTTCAATACTATAATTTGTAT
* * *
395205 TTTAAATTTAAATTTCAAATAATATTATTTGTAT
1 TTTAATTTTAAATTTC-AATACTATAATTTGTAT
395239 TTTAATTTTAAATTTCAATACTATAATTTGTAT
1 TTTAATTTTAAATTTCAATACTATAATTTGTAT
395272 TTTAA
1 TTTAA
395277 AAATATTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 23 0.37
34 39 0.63
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (33 bp):
TTTAATTTTAAATTTCAATACTATAATTTGTAT
Found at i:395855 original size:21 final size:21
Alignment explanation
Indices: 395788--395858 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
395778 TATGGTATAA
* *
395788 AACCCTGCGAGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
395809 AA-CCTGGCGGACTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
395830 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
395851 AACCCTGC
1 AACCCTGC
395859 AGAGATGACA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:397690 original size:23 final size:22
Alignment explanation
Indices: 397662--397719 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
397652 TTTAAATAAA
*
397662 TAATAATTATATAAATATTATTT
1 TAATAATTATATAAATAATA-TT
*
397685 TAATAA--A-AAAAATAATATT
1 TAATAATTATATAAATAATATT
397704 TATATAATTATATAAA
1 TA-ATAATTATATAAA
397720 ATATAATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 1 0.04
22 1 0.04
23 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAATTATATAAATAATATT
Found at i:400160 original size:29 final size:31
Alignment explanation
Indices: 400049--400171 Score: 178
Period size: 31 Copynumber: 4.0 Consensus size: 31
400039 CCCGAAGGAC
* ** *
400049 CAGTCCATAGGTCCATAAGAACCTAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
400080 CAGTCCATATGTCCCGAATAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
400111 CAGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
*
400142 CAGT-C-TATGTCCTGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAT
400171 C
1 C
400172 CTCGACTCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
29 24 0.28
30 1 0.01
31 60 0.71
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAT
Found at i:404089 original size:20 final size:19
Alignment explanation
Indices: 404023--404092 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
404013 AAAATATTTT
*
404023 TATGAATAGTACTATACTA
1 TATGAATAGTACGATACTA
* *
404042 TATGAACAGTGCCGATACTA
1 TATGAATAGT-ACGATACTA
*
404062 TA-GAAATAGTATCGATACTG
1 TATG-AATAGTA-CGATACTA
404082 TATGAATAGTA
1 TATGAATAGTA
404093 ATGAACAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.24
20 30 0.73
21 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (19 bp):
TATGAATAGTACGATACTA
Found at i:404745 original size:31 final size:30
Alignment explanation
Indices: 404703--404809 Score: 144
Period size: 31 Copynumber: 3.5 Consensus size: 30
404693 ATAGGTCCAT
*
404703 AAGAACCTAGGTAATCAGTCTATATGTCCCA
1 AAGAACATAGGTAATCAGTC-ATATGTCCCA
**
404734 AAGAACATAGGTAATCAGTCCATATGTCCTT
1 AAGAACATAGGTAATCAGT-CATATGTCCCA
* *
404765 AAGAACATAGGTAATCAGTC-CATGTCCCG
1 AAGAACATAGGTAATCAGTCATATGTCCCA
404794 AAGAACATAGGTAATC
1 AAGAACATAGGTAATC
404810 CTCGACTCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
29 22 0.32
30 1 0.01
31 45 0.65
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (30 bp):
AAGAACATAGGTAATCAGTCATATGTCCCA
Found at i:410639 original size:148 final size:147
Alignment explanation
Indices: 410277--411011 Score: 940
Period size: 148 Copynumber: 5.0 Consensus size: 147
410267 TTTTCAGAGA
* * * *
410277 TGAGTTGACATTTCACTGAAACGTTGCTGAAGATGATTGACGGGGCACTAAAAAGTTG-T---AT
1 TGAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCAT
* * * * *
410338 TTTCTAGCATCCTGCATTATTAATGGCCCGTTCTAAAGAGTATTAATGGCTCGTTTTGACATTTT
66 TTTCTGGCATCCTGCATTATTAATGGCCAGTTCTGAAGAGTATTAATGGCCCATTTTGACATTTT
*
410403 CGGGCATGGTACATTAT
131 CGGGCATGGTGCATTAT
* * * *
410420 TGAGATAACATTTCACTAAAAAGTTACTGAAGATGATTGATGAGGCACTGAAAAGTTGCTGGCAT
1 TGAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCAT
* * *
410485 TTTCTGGCATCTTGCATTATTAATGGCCAGTTATGAAGAGTATTAATGACCCATTTTGACATTTT
66 TTTCTGGCATCCTGCATTATTAATGGCCAGTTCTGAAGAGTATTAATGGCCCATTTTGACATTTT
410550 CGGGCATGGTGCATTAT
131 CGGGCATGGTGCATTAT
* * *
410567 TAGAGATGACATTTCATTGAAAAGTTGATGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCA
1 T-GAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCA
* * * * * ** * *
410632 TTTTCTGGTACCCTGTATTGTTATTGGATATTTCTAAAGAGTATTAATGGCCCATTTTGACATTT
65 TTTTCTGGCATCCTGCATTATTAATGGCCAGTTCTGAAGAGTATTAATGGCCCATTTTGACATTT
** *
410697 TCAAGCACGGTGCATTAT
130 TCGGGCATGGTGCATTAT
* * * * * * *
410715 TGAGATAACATTTAAGTGTAAAGTTGCTGAAGATGATTGATGAGGCACTGAAAATTTGCTGGAAT
1 TGAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCAT
* ** * *
410780 TTTCTAGCATCCTGCATTATTAATAACCCGTTCTGAAGAGTATTAATGGCGCATTTTGACATTTT
66 TTTCTGGCATCCTGCATTATTAATGGCCAGTTCTGAAGAGTATTAATGGCCCATTTTGACATTTT
410845 CGGGCATGGTGCATTAT
131 CGGGCATGGTGCATTAT
* *
410862 TAAAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCA
1 T-GAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCA
* * * *
410927 TTTTCTGGCACCCTGCATTGTTAATGGTCCA-TTCTGAAGAGTATTTAATGGCTCGTTTTGACAT
65 TTTTCTGGCATCCTGCATTATTAATGG-CCAGTTCTGAAGAGTA-TTAATGGCCCATTTTGACAT
*
410991 TTTCAGGCATGGTGCATTAT
128 TTTCGGGCATGGTGCATTAT
411011 T
1 T
411012 CATTTGACTT
Statistics
Matches: 501, Mismatches: 83, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
143 50 0.10
144 1 0.00
147 197 0.39
148 213 0.43
149 40 0.08
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (147 bp):
TGAGATGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGCTGGCAT
TTTCTGGCATCCTGCATTATTAATGGCCAGTTCTGAAGAGTATTAATGGCCCATTTTGACATTTT
CGGGCATGGTGCATTAT
Found at i:410819 original size:295 final size:293
Alignment explanation
Indices: 410282--411011 Score: 1045
Period size: 295 Copynumber: 2.5 Consensus size: 293
410272 AGAGATGAGT
* * *
410282 TGACATTTCACTGAAACGTTGCTGAAGATGATTGACGGGGCACTAAAAAGTTG-T---ATTTTCT
1 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
* * * ** *
410343 AGCATCCTGCATTATTAATGGCCCGTTCTAAAGAGTATTAATGGCTCGTTTTGACATTTTCGGGC
66 GGCACCCTGCATTGTTAATGG--TATTCTAAAGAGTATTAATGGCTCGTTTTGACATTTTCAGGC
* *
410408 ATGGTACATTATTGAGATAACATTTCACTAAAAAGTTACTGAAGATGATTGATGAGGCACTGAAA
129 ATGGTGCATTATTGAGATAACATTTAACTAAAAAGTTACTGAAGATGATTGATGAGGCACTGAAA
* * * **
410473 AGTTGCTGGCATTTTCTGGCATCTTGCATTATTAATGGCCAGTTATGAAGAGTATTAATGACCCA
194 AGTTGCTGGAATTTTCTAGCATCCTGCATTATTAATAACCAGTTATGAAGAGTATTAATGACCCA
*
410538 TTTTGACATTTTCGGGCATGGTGCATTATTAGAGA
259 TTTTGACATTTTCGGGCATGGTGCATTATTAAAGA
* *
410573 TGACATTTCATTGAAAAGTTGATGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
1 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
* * * * * *
410638 GGTACCCTGTATTGTTATTGGATATTTCTAAAGAGTATTAATGGCCCATTTTGACATTTTCAAGC
66 GGCACCCTGCATTGTTAATGG-TA-TTCTAAAGAGTATTAATGGCTCGTTTTGACATTTTCAGGC
* * ** *
410703 ACGGTGCATTATTGAGATAACATTTAAGTGTAAAGTTGCTGAAGATGATTGATGAGGCACTGAAA
129 ATGGTGCATTATTGAGATAACATTTAACTAAAAAGTTACTGAAGATGATTGATGAGGCACTGAAA
* * * * *
410768 ATTTGCTGGAATTTTCTAGCATCCTGCATTATTAATAACCCGTTCTGAAGAGTATTAATGGCGCA
194 AGTTGCTGGAATTTTCTAGCATCCTGCATTATTAATAACCAGTTATGAAGAGTATTAATGACCCA
410833 TTTTGACATTTTCGGGCATGGTGCATTATTAAAGA
259 TTTTGACATTTTCGGGCATGGTGCATTATTAAAGA
410868 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
1 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
*
410933 GGCACCCTGCATTGTTAATGGTCCATTCTGAAGAGTATTTAATGGCTCGTTTTGACATTTTCAGG
66 GGCACCCTGCATTGTTAATGGT--ATTCTAAAGAGTA-TTAATGGCTCGTTTTGACATTTTCAGG
410998 CATGGTGCATTATT
128 CATGGTGCATTATT
411012 CATTTGACTT
Statistics
Matches: 385, Mismatches: 46, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
291 48 0.12
292 1 0.00
294 1 0.00
295 297 0.77
296 38 0.10
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (293 bp):
TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGGCATTTTCT
GGCACCCTGCATTGTTAATGGTATTCTAAAGAGTATTAATGGCTCGTTTTGACATTTTCAGGCAT
GGTGCATTATTGAGATAACATTTAACTAAAAAGTTACTGAAGATGATTGATGAGGCACTGAAAAG
TTGCTGGAATTTTCTAGCATCCTGCATTATTAATAACCAGTTATGAAGAGTATTAATGACCCATT
TTGACATTTTCGGGCATGGTGCATTATTAAAGA
Found at i:418068 original size:21 final size:21
Alignment explanation
Indices: 418042--418081 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
418032 CCCCCTTTGA
*
418042 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
418063 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
418082 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:423456 original size:28 final size:28
Alignment explanation
Indices: 423424--423487 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
423414 CAATAACCAT
*
423424 ATATTTAACTAAACTCAAATTTATACAC
1 ATATTTAACTAAACTCAAATTAATACAC
*
423452 ATATTTAACTAAACTCAAATTAATACAT
1 ATATTTAACTAAACTCAAATTAATACAC
423480 ATATTTAA
1 ATATTTAA
423488 AACATTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATTTAACTAAACTCAAATTAATACAC
Found at i:433317 original size:16 final size:17
Alignment explanation
Indices: 433281--433323 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
433271 GATAGTACAC
433281 AATATATGAA-ATTTATA
1 AATATAT-AATATTTATA
433298 AATATATAATATTT-TA
1 AATATATAATATTTATA
433314 AATATA-AATA
1 AATATATAATA
433324 CTAAAAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 10 0.40
17 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATATATAATATTTATA
Found at i:437825 original size:41 final size:40
Alignment explanation
Indices: 437780--437872 Score: 93
Period size: 41 Copynumber: 2.3 Consensus size: 40
437770 AAGTGTTCTA
* *
437780 TAGCGGCGTTTTTA-GGCTAAACGCCACAAAATTTAAACATG
1 TAGCGGCGTTTTTACAGCCAAACGCCACAAAA-TTAAAC-TG
* * *
437821 TAGC-G-GTTTTTACTATCCAAACGCCACAAAATTATACTT
1 TAGCGGCGTTTTTAC-AGCCAAACGCCACAAAATTAAACTG
437860 TAGCGGCGTTTTT
1 TAGCGGCGTTTTT
437873 CCAACAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
39 12 0.28
40 7 0.16
41 24 0.56
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (40 bp):
TAGCGGCGTTTTTACAGCCAAACGCCACAAAATTAAACTG
Found at i:437907 original size:42 final size:41
Alignment explanation
Indices: 437858--437995 Score: 111
Period size: 42 Copynumber: 3.3 Consensus size: 41
437848 AAAATTATAC
*
437858 TTTAGCGGCGTTTTTCCAACAAACGCCGCAATAGAGTGGTAA
1 TTTAGCGGCGTTTTTCCAA-AAACGCCGCAATAGAGTAGTAA
* * * * * *
437900 TTTAGCGGCGTTTATAGCTAAAAA-GCCGAAATAAATTTGT--
1 TTTAGCGGCGTTT-T-TCCAAAAACGCCGCAATAGAGTAGTAA
* * *
437940 TTACAGTGGCGTTTTTTCAATAAACGCCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTTTCCAA-AAACGCCGCAATAGAGTAGTAA
*
437983 TTTAACGGCGTTT
1 TTTAGCGGCGTTT
437996 GTATAAAAAC
Statistics
Matches: 71, Mismatches: 18, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
39 2 0.03
40 6 0.08
41 21 0.30
42 33 0.46
43 6 0.08
44 3 0.04
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTCCAAAAACGCCGCAATAGAGTAGTAA
Found at i:438626 original size:22 final size:22
Alignment explanation
Indices: 438598--438646 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
438588 ATGTTTTTCT
438598 GCTTTCGAATA-GAAAAATAATA
1 GCTTTCGAATATG-AAAATAATA
*
438620 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATATGAAAATAATA
438642 GCTTT
1 GCTTT
438647 TTAAAACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATATGAAAATAATA
Found at i:439520 original size:73 final size:73
Alignment explanation
Indices: 439401--439550 Score: 275
Period size: 73 Copynumber: 2.1 Consensus size: 73
439391 AAGTGAACAA
*
439401 TATGGTGAAGACTTTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTAATT-TGTTGTTAAG
1 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGT-ATTCTGTTGTTAAG
439465 TATTAATTT
65 TATTAATTT
439474 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
1 TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
439539 ATTAATTT
66 ATTAATTT
439547 TATG
1 TATG
439551 CATCACTTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 3 0.04
73 72 0.96
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (73 bp):
TATGGTGAAGACTGTTTATGCATAACTTTAATGTTTCTAAATTTTAATGTATTCTGTTGTTAAGT
ATTAATTT
Found at i:439984 original size:90 final size:86
Alignment explanation
Indices: 439809--440138 Score: 257
Period size: 90 Copynumber: 3.8 Consensus size: 86
439799 TTTAGCTGCA
* * * * *
439809 TTTTTATACAAACGCCGTAATAGGTGTAATCTATAGTGGCATTTTAATACCAAACGCCGTAAAAT
1 TTTTTATA-AAAAGCCGCAATAGGTGTAATCTATAGTGGC-GTTT-ATAACAAACGCCGCAAAAT
*** * *
439874 ATTTATACAAAAGTGGCATTTTTAG
63 ATTTATACTTTAGCGACATTTTT-G
*
439899 TTTTTATAAAAATGCCGCAATAGGTGTAATCTATAGTGGCGTTTGGATAAAAAACGCCGCAAAAT
1 TTTTTATAAAAA-GCCGCAATAGGTGTAATCTATAGTGGCGTTT--ATAACAAACGCCGCAAAAT
439964 ATTTATACTTTAGCGACATTTTTG
63 ATTTATACTTTAGCGACATTTTTG
* * * * *
439988 ---TT-CAAACA-CCGCAATAGGTTTGATATATATAGTGGCGTTATTTCAACAAACGCCGCAAAA
1 TTTTTATAAAAAGCCGCAATAGGTGT-A-ATCTATAGTGGCGTT-TAT-AACAAACGCCGCAAAA
*
440048 TATTTATACTTTAGCGGC---TTT-
62 TATTTATACTTTAGCGACATTTTTG
* * * * * * * *
440069 TTTGTATAAACA-CCGTAATAGGTATAATATATAGTGACGTTTTTAACAAACGCCGTAAAATATT
1 TTTTTATAAAAAGCCGCAATAGGTGTAATCTATAGTGGCGTTTATAACAAACGCCGCAAAATATT
*
440133 TGTACT
66 TATACT
440139 CTAATGGCAT
Statistics
Matches: 204, Mismatches: 26, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
81 24 0.12
82 6 0.03
83 26 0.13
84 4 0.02
85 66 0.32
86 3 0.01
89 7 0.03
90 68 0.33
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (86 bp):
TTTTTATAAAAAGCCGCAATAGGTGTAATCTATAGTGGCGTTTATAACAAACGCCGCAAAATATT
TATACTTTAGCGACATTTTTG
Found at i:440047 original size:85 final size:81
Alignment explanation
Indices: 439786--440138 Score: 278
Period size: 85 Copynumber: 4.2 Consensus size: 81
439776 AAATGTCGCA
* * * * * * * * *
439786 AAAATATTTGTACTTTAGCTG-CATTTTTATACAAACGCCGTAATAGGTGTAATCTATAGTGGCA
1 AAAATATTTATACTTTAGC-GACATTTTTGTATAAACACCGCAATAGGTATAATATATAGTGACG
* *
439850 TTTTAATACCAAACGCCGT
65 TTTT--TAACAAACGCCGC
*** * * * * *
439869 AAAATATTTATACAAAAGTGGCATTTTTAGTTTTTATAAAAATGCCGCAATAGGTGTAATCTATA
1 AAAATATTTATACTTTAGCGACATTTTT-G----TATAAACA--CCGCAATAGGTATAATATATA
* * *
439934 GTGGCGTTTGGATAAAAAACGCCGC
59 GTGACGTTT--TTAACAAACGCCGC
* *
439959 AAAATATTTATACTTTAGCGACATTTTTGT-TCAAACACCGCAATAGGTTTGATATATATAGTGG
1 AAAATATTTATACTTTAGCGACATTTTTGTAT-AAACACCGCAATAGGTAT-A-ATATATAGTGA
440023 CGTTATTTCAACAAACGCCGC
63 CGTT-TTT-AACAAACGCCGC
* * *
440044 AAAATATTTATACTTTAGCGGCTTTTTTGTATAAACACCGTAATAGGTATAATATATAGTGACGT
1 AAAATATTTATACTTTAGCGACATTTTTGTATAAACACCGCAATAGGTATAATATATAGTGACGT
*
440109 TTTTAACAAACGCCGT
66 TTTTAACAAACGCCGC
*
440125 AAAATATTTGTACT
1 AAAATATTTATACT
440139 CTAATGGCAT
Statistics
Matches: 222, Mismatches: 32, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
81 24 0.11
82 4 0.02
83 47 0.21
84 4 0.02
85 74 0.33
86 2 0.01
88 5 0.02
89 1 0.00
90 61 0.27
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (81 bp):
AAAATATTTATACTTTAGCGACATTTTTGTATAAACACCGCAATAGGTATAATATATAGTGACGT
TTTTAACAAACGCCGC
Found at i:445458 original size:42 final size:41
Alignment explanation
Indices: 445411--445580 Score: 156
Period size: 42 Copynumber: 4.1 Consensus size: 41
445401 GTTTTTTAAC
445411 AAACGCCGTAATAGAATGGTAAATTAGTGGCGTTTATACCAA
1 AAACGCCGTAATAG-ATGGTAAATTAGTGGCGTTTATACCAA
*
445453 AAACGCCGCAATAGAT--TAATATATAGTGGCGTTT-TAGCC-A
1 AAACGCCGTAATAGATGGTAA-AT-TAGTGGCGTTTATA-CCAA
* *
445493 AAACGCCGTAATAGATCGGTAAATTAGCT-GTGTTTATACCAC
1 AAACGCCGTAATAGAT-GGTAAATTAG-TGGCGTTTATACCAA
* * *
445535 AAACACCGTAATAGAT--TACACATATAGTGGCGTTTATTCCTA
1 AAACGCCGTAATAGATGGTA-A-AT-TAGTGGCGTTTATACCAA
445577 AAAC
1 AAAC
445581 ACTACAATAG
Statistics
Matches: 106, Mismatches: 9, Indels: 26
0.75 0.06 0.18
Matches are distributed among these distances:
39 5 0.05
40 21 0.20
41 28 0.26
42 49 0.46
43 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (41 bp):
AAACGCCGTAATAGATGGTAAATTAGTGGCGTTTATACCAA
Found at i:445497 original size:82 final size:83
Alignment explanation
Indices: 445411--445569 Score: 234
Period size: 82 Copynumber: 1.9 Consensus size: 83
445401 GTTTTTTAAC
* *
445411 AAACGCCGTAATAGAAT-GGTAAATTAG-TGGCGTTTATACCAAAAACGCCGCAATAGATTA-AT
1 AAACGCCGTAATAG-ATCGGTAAATTAGCT-GCGTTTATACCAAAAACACCGCAATAGATTACAC
445473 ATATAGTGGCGTTTTAGCCA
64 ATATAGTGGCGTTTTAGCCA
* * *
445493 AAACGCCGTAATAGATCGGTAAATTAGCTGTGTTTATACCACAAACACCGTAATAGATTACACAT
1 AAACGCCGTAATAGATCGGTAAATTAGCTGCGTTTATACCAAAAACACCGCAATAGATTACACAT
445558 ATAGTGGCGTTT
66 ATAGTGGCGTTT
445570 ATTCCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 2 0.03
82 51 0.74
83 16 0.23
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (83 bp):
AAACGCCGTAATAGATCGGTAAATTAGCTGCGTTTATACCAAAAACACCGCAATAGATTACACAT
ATAGTGGCGTTTTAGCCA
Found at i:445604 original size:42 final size:40
Alignment explanation
Indices: 445577--445664 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
445567 TTTATTCCTA
*
445577 AAACACTACAATAGTGATAATAAATAGTGGCGTTTTTAGAT
1 AAACACCAC-ATAGTGATAATAAATAGTGGCGTTTTTAGAT
* * *
445618 AAACACCACATAGTGTTAATTAATAGTGGCGTTTTTAGAA
1 AAACACCACATAGTGATAATAAATAGTGGCGTTTTTAGAT
445658 AAACACC
1 AAACACC
445665 GCAATAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 35 0.81
41 8 0.19
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.30
Consensus pattern (40 bp):
AAACACCACATAGTGATAATAAATAGTGGCGTTTTTAGAT
Found at i:445643 original size:40 final size:41
Alignment explanation
Indices: 445558--445735 Score: 153
Period size: 41 Copynumber: 4.3 Consensus size: 41
445548 GATTACACAT
*** * *
445558 ATAGTGGCGTTTATTCCTAAAACACTACAATAGTGATAATAA
1 ATAGTGGCGTTT-TTAGAAAAACACCACAATAGTGTTAATAA
* *
445600 ATAGTGGCGTTTTTAGATAAACACCAC-ATAGTGTTAATTA
1 ATAGTGGCGTTTTTAGAAAAACACCACAATAGTGTTAATAA
* * *
445640 ATAGTGGCGTTTTTAGAAAAACACCGCAATAGTTTTAATCA
1 ATAGTGGCGTTTTTAGAAAAACACCACAATAGTGTTAATAA
* ** ** * * *
445681 ATAATGGTATTTTTTTAACAAACGCCACAATAGT-ATAATCA
1 ATAGTGGCGTTTTTAGAA-AAACACCACAATAGTGTTAATAA
*
445722 ATAGTGGTGTTTTT
1 ATAGTGGCGTTTTT
445736 TTGTATAAAC
Statistics
Matches: 113, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 36 0.32
41 52 0.46
42 25 0.22
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (41 bp):
ATAGTGGCGTTTTTAGAAAAACACCACAATAGTGTTAATAA
Found at i:447179 original size:42 final size:42
Alignment explanation
Indices: 447130--447226 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
447120 GTTTGTTACC
* *
447130 AAACGCCGCTAA-AAAATTGTACTTTAGTGGCGTTTTTG-ACAT
1 AAACGCCGC-AATAAAATTGTAATTTAGTGGCATTTTTGTA-AT
* *
447172 AAACGCCGCAATAGAGTTGTAATTTAGTGGCATTTTTGTAAT
1 AAACGCCGCAATAAAATTGTAATTTAGTGGCATTTTTGTAAT
**
447214 AAACATCGCAATA
1 AAACGCCGCAATA
447227 GTATGCCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.94
43 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (42 bp):
AAACGCCGCAATAAAATTGTAATTTAGTGGCATTTTTGTAAT
Found at i:447227 original size:42 final size:42
Alignment explanation
Indices: 447146--447227 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
447136 CGCTAAAAAA
* * *
447146 TTGTACTTTAGTGGCGTTTTTGACATAAACGCCGCAATAGAG
1 TTGTAATTTAGTGGCATTTTTGACATAAACACCGCAATAGAG
*
447188 TTGTAATTTAGTGGCATTTTTGTA-ATAAACATCGCAATAG
1 TTGTAATTTAGTGGCATTTTTG-ACATAAACACCGCAATAG
447228 TATGCCCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 34 0.97
43 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (42 bp):
TTGTAATTTAGTGGCATTTTTGACATAAACACCGCAATAGAG
Found at i:456388 original size:43 final size:43
Alignment explanation
Indices: 456233--456478 Score: 188
Period size: 43 Copynumber: 5.9 Consensus size: 43
456223 TGTTTTTGCT
* * * **
456233 AAAAACGCCGCAAAACATCAATACCTACTGCGGCGTTTGT-GG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTA
* * * * * *
456275 GAAAACGCCACAAAACATCAACACCTACTGCGACG-TT-TCAGA
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTC-TA
*
456317 GAAAAATGCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTA
1 -AAAAACGCCGCTAAACATCA-ACACCTATTGCGGCGTTTGTCTA
* * * * *
456361 AAAAACGCCGCTAAATATCAACACCTATTACGGCATTTTTCTG
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTA
* * *
456404 ACAAAC-ACGCTAAATATCAACACCTATTGCGGCGTTTG--T-
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTA
* * *
456443 --GAACGCCGCTAAATATCAATACCTATTGCGGCGTTT
1 AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTT
456479 TTTAACAAAA
Statistics
Matches: 170, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
37 3 0.02
38 29 0.17
40 2 0.01
41 2 0.01
42 61 0.36
43 67 0.39
44 4 0.02
45 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAACATCAACACCTATTGCGGCGTTTGTCTA
Found at i:456467 original size:38 final size:38
Alignment explanation
Indices: 456324--456478 Score: 141
Period size: 38 Copynumber: 3.8 Consensus size: 38
456314 AGAGAAAAAT
* *
456324 GCCGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTAAAAAAC
1 GCCGCTAAATATCA-ACACCTATTGCGGCGTTTG--T---GAAC
* * * *
456367 GCCGCTAAATATCAACACCTATTACGGCATTTTTCTGACAA
1 GCCGCTAAATATCAACACCTATTGCGGC--GTTTGTGA-AC
*
456408 ACACGCTAAATATCAACACCTATTGCGGCGTTTGTGAAC
1 GC-CGCTAAATATCAACACCTATTGCGGCGTTTGTGAAC
*
456447 GCCGCTAAATATCAATACCTATTGCGGCGTTT
1 GCCGCTAAATATCAACACCTATTGCGGCGTTT
456479 TTTAACAAAA
Statistics
Matches: 94, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
38 29 0.31
39 2 0.02
40 7 0.07
41 2 0.02
42 26 0.28
43 25 0.27
45 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (38 bp):
GCCGCTAAATATCAACACCTATTGCGGCGTTTGTGAAC
Found at i:457004 original size:20 final size:20
Alignment explanation
Indices: 456979--457037 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
456969 AAATATCCTA
456979 TAGCACTATAAAT-AAATAAT
1 TAGCACTATAAATAAAAT-AT
456999 TAGCACTATAAATAAAATAT
1 TAGCACTATAAATAAAATAT
457019 TAGCACTA-AGAATAAAATA
1 TAGCACTATA-AATAAAATA
457038 AAATGAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.86
21 4 0.11
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (20 bp):
TAGCACTATAAATAAAATAT
Found at i:457669 original size:29 final size:28
Alignment explanation
Indices: 457630--457759 Score: 106
Period size: 29 Copynumber: 4.5 Consensus size: 28
457620 GTAAGTGCTG
457630 TTTTCGTAATTATTTTTAAAAAG-GTACTAC
1 TTTT-GTAATTATTTTTAAAAAGTG-A-TAC
* *
457660 TTTTGTAATTATTTTTACAACAGTGATAG
1 TTTTGTAATTATTTTTA-AAAAGTGATAC
* *
457689 TTTGGTAATTATTTTTAAAACAATGATA-
1 TTTTGTAATTATTTTTAAAA-AGTGATAC
**
457717 TTTTGGTAATTATTTAAAAAAAGGTGATA-
1 TTTT-GTAATTATTTTTAAAAA-GTGATAC
457746 TTTTCGTAA-TATTT
1 TTTT-GTAATTATTT
457760 GACTTTGGCA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
28 11 0.13
29 64 0.75
30 9 0.11
31 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (28 bp):
TTTTGTAATTATTTTTAAAAAGTGATAC
Found at i:461290 original size:20 final size:20
Alignment explanation
Indices: 461265--461323 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
461255 AAATATCCTA
461265 TAGCACTATAAAT-AAATAAT
1 TAGCACTATAAATAAAAT-AT
461285 TAGCACTATAAATAAAATAT
1 TAGCACTATAAATAAAATAT
461305 TAGCACTA-AGAATAAAATA
1 TAGCACTATA-AATAAAATA
461324 AAATGAAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.86
21 4 0.11
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (20 bp):
TAGCACTATAAATAAAATAT
Found at i:461941 original size:29 final size:28
Alignment explanation
Indices: 461907--462045 Score: 145
Period size: 29 Copynumber: 4.8 Consensus size: 28
461897 TAATTTAGGT
*
461907 AAGTGCTATTTTCGTAATTATTTTTAAA
1 AAGTGATATTTTCGTAATTATTTTTAAA
* *
461935 AAGGTGCTACTTTCGTAATTATTTTTACAA
1 AA-GTGATATTTTCGTAATTATTTTTA-AA
* * *
461965 CAGTGATAGTTTGGTAATTATTTTTAAA
1 AAGTGATATTTTCGTAATTATTTTTAAA
* * *
461993 ACAATGATATTTTGGTAATTATTTTAAAAA
1 A-AGTGATATTTTCGTAATTATTTT-TAAA
462023 AAGGTGATATTTTCGTAA-TATTT
1 AA-GTGATATTTTCGTAATTATTT
462046 GACTTTGGCA
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
28 4 0.04
29 71 0.75
30 20 0.21
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (28 bp):
AAGTGATATTTTCGTAATTATTTTTAAA
Found at i:461975 original size:86 final size:86
Alignment explanation
Indices: 461839--462045 Score: 204
Period size: 86 Copynumber: 2.4 Consensus size: 86
461829 ATTATGGGAA
* * * * *
461839 TATTTTT-AAAAGTGTGCTAGTTTCGTTAATATGTTTAAAATAATGTTAGTTTTGTAATTA-ATT
1 TATTTTTAAAAAG-GTGCTACTTTCG-TAATATTTTTAAAACAATGATAGTTTGGTAATTATATT
** * *
461902 TAGGTA-AGTGCTATTTTCGTAAT
64 TA-AAACAATGATATTTTCGTAAT
* * *
461925 TATTTTTAAAAAGGTGCTACTTTCGTAATTATTTTTACAACAGTGATAGTTTGGTAATTATTTTT
1 TATTTTTAAAAAGGTGCTACTTTCGTAA-TATTTTTAAAACAATGATAGTTTGGTAATTATATTT
*
461990 AAAACAATGATATTTTGGTAAT
65 AAAACAATGATATTTTCGTAAT
* * *
462012 TATTTTAAAAAAAGGTGATATTTTCGTAATATTT
1 TATTTT-TAAAAAGGTGCTACTTTCGTAATATTT
462046 GACTTTGGCA
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
85 3 0.03
86 44 0.44
87 34 0.34
88 19 0.19
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.47
Consensus pattern (86 bp):
TATTTTTAAAAAGGTGCTACTTTCGTAATATTTTTAAAACAATGATAGTTTGGTAATTATATTTA
AAACAATGATATTTTCGTAAT
Found at i:464425 original size:21 final size:21
Alignment explanation
Indices: 464374--464426 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
464364 ATTATGACTA
464374 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
464395 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
464416 TCGCAATGCGA
1 TCGCAATGCGA
464427 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:464459 original size:21 final size:20
Alignment explanation
Indices: 464416--464462 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
464406 TTTTCCCAAT
*
464416 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
464436 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
464457 TCGCAA
1 TCGCAA
464463 CGTGATACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:464480 original size:41 final size:41
Alignment explanation
Indices: 464453--464591 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
464443 GCGAATTTGG
*
464453 AAAATCGCAACGTGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
464494 AAAATCGCAACGCGATACTGACTTTCGCAACTCGATACT-T
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
** * * * *
464534 AATTTCGCAACTCAAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGC-GATACTGACTATCGCAACGCGATAATAC
* *
464576 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
464592 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
40 10 0.13
41 59 0.77
42 8 0.10
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:464481 original size:20 final size:20
Alignment explanation
Indices: 464456--464571 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
464446 AATTTGGAAA
*
464456 ATCGCAACGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
464476 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
464497 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
464517 TTCGCAACTCGATACTTAAT
1 ATCGCAACGCGATACTGACT
* * *
464537 TTCGCAACTCAAATACTGACT
1 ATCGCAACGC-GATACTGACT
* *
464558 TTCGCAACGAGATA
1 ATCGCAACGCGATA
464572 ATACATAATC
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.56
21 30 0.39
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:465088 original size:19 final size:20
Alignment explanation
Indices: 465066--465113 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
465056 TTTATTCTCT
465066 CGTTGCGATAGTCA-ATTCG
1 CGTTGCGATAGTCATATTCG
* *
465085 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATAGTCATATTCG
*
465105 TGTTGCGAT
1 CGTTGCGAT
465114 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:465109 original size:20 final size:20
Alignment explanation
Indices: 465066--465123 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
465056 TTTATTCTCT
* *
465066 CGTTGCGATAGTCA-ATTCG
1 CGTTGCGATTGTCATTTTCG
465085 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
465105 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
465124 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.38
20 21 0.62
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:466459 original size:18 final size:18
Alignment explanation
Indices: 466438--466485 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
466428 TCCACTTTGG
466438 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
466456 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
466474 GAGCCATCACCT
1 GAGCCATCACCT
466486 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:467045 original size:20 final size:20
Alignment explanation
Indices: 467020--467065 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
467010 TAGTTTACTT
467020 TCGCAACACGAAAAT-GACTA
1 TCGCAACACGAAAATCG-CTA
* *
467040 TCGCAACGCGGAAATCGCTA
1 TCGCAACACGAAAATCGCTA
467060 TCGCAA
1 TCGCAA
467066 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.28, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATCGCTA
Found at i:467136 original size:14 final size:14
Alignment explanation
Indices: 467117--467173 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
467107 GTGTTTCGCG
467117 TTGCGATTTTGTCA
1 TTGCGATTTTGTCA
*
467131 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTT--TGT--CA
*
467150 TTGCGATTTTGTCG
1 TTGCGATTTTGTCA
467164 TTGCGATTTT
1 TTGCGATTTT
467174 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 8 0.23
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCA
Done.