Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 88 of 143
Found at i:27634890 original size:21 final size:21
Alignment explanation
Indices: 27634847--27634893 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
27634837 ACGAGCCACC
* *
27634847 GCAATACTTTACTCGACCCGG
1 GCAATACTCTACTCCACCCGG
* *
27634868 GCAATACTCTACTCCTCCTGG
1 GCAATACTCTACTCCACCCGG
27634889 GCAAT
1 GCAAT
27634894 TGGACCCTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (21 bp):
GCAATACTCTACTCCACCCGG
Found at i:27638185 original size:17 final size:15
Alignment explanation
Indices: 27638151--27638190 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
27638141 AACACATTAC
*
27638151 CTTTCTTTTCTTCTT
1 CTTTCTTTTCTCCTT
27638166 CTTTCTTTCCTCTCCTT
1 CTTTCTTT--TCTCCTT
27638183 CTTTCTTT
1 CTTTCTTT
27638191 ATTTCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
17 14 0.64
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (15 bp):
CTTTCTTTTCTCCTT
Found at i:27638849 original size:17 final size:17
Alignment explanation
Indices: 27638827--27638862 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
27638817 TATGATTATA
27638827 TTATAATATAATATAAT
1 TTATAATATAATATAAT
* *
27638844 TTATAATTTAATTTAAT
1 TTATAATATAATATAAT
27638861 TT
1 TT
27638863 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATAATATAATATAAT
Found at i:27639195 original size:22 final size:20
Alignment explanation
Indices: 27639167--27639225 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
27639157 CAGTAAATGA
27639167 TTTTAAAATTATTAAAATTATT
1 TTTTAAAA-TA-TAAAATTATT
27639189 TTTTAAAA-ATATAAA-TA-T
1 TTTTAAAATATA-AAATTATT
27639207 TTTT-AAATATAAAATTATT
1 TTTTAAAATATAAAATTATT
27639226 AAAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
17 6 0.18
18 10 0.30
19 5 0.15
20 4 0.12
22 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATATAAAATTATT
Found at i:27639211 original size:18 final size:18
Alignment explanation
Indices: 27639188--27639246 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 18
27639178 TTAAAATTAT
27639188 TTTTTAAAAATATAAATA
1 TTTTTAAAAATATAAATA
27639206 TTTTT--AAATATAAA-A
1 TTTTTAAAAATATAAATA
* *
27639221 TTATTAAAATTATTAAATA
1 TTTTTAAAAATA-TAAATA
*
27639240 ATTTTAA
1 TTTTTAA
27639247 TTTTCAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 5 0.15
16 9 0.27
17 4 0.12
18 9 0.27
19 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAATATAAATA
Found at i:27643994 original size:24 final size:24
Alignment explanation
Indices: 27643967--27644023 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
27643957 TAGCCAACAT
*
27643967 GAGCCCAGAATGATTAGCTCTTAC
1 GAGCCCAGAATAATTAGCTCTTAC
27643991 GAGCCCAGAATAATTAGCTCTTAC
1 GAGCCCAGAATAATTAGCTCTTAC
*
27644015 AAGCCCAGA
1 GAGCCCAGA
27644024 TAGAGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (24 bp):
GAGCCCAGAATAATTAGCTCTTAC
Found at i:27646267 original size:30 final size:32
Alignment explanation
Indices: 27646221--27646286 Score: 91
Period size: 30 Copynumber: 2.1 Consensus size: 32
27646211 CCCTAATTTT
*
27646221 AATTTGAAGGACTAAATTGATAAATTTT-TAG
1 AATTTGAAGGACTAAATTCATAAATTTTGTAG
* *
27646252 AATTT-AAGGGCTAAATTCATCAATTTTGTAG
1 AATTTGAAGGACTAAATTCATAAATTTTGTAG
27646283 AATT
1 AATT
27646287 GGGGACTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (32 bp):
AATTTGAAGGACTAAATTCATAAATTTTGTAG
Found at i:27647113 original size:19 final size:20
Alignment explanation
Indices: 27647089--27647128 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27647079 GATCGTTGAC
*
27647089 CGTTGACTA-TTGATTTTTT
1 CGTTGACTAGTTGACTTTTT
27647108 CGTTGACTAGTTGACTTTTT
1 CGTTGACTAGTTGACTTTTT
27647128 C
1 C
27647129 TAGAAAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (20 bp):
CGTTGACTAGTTGACTTTTT
Found at i:27648986 original size:30 final size:30
Alignment explanation
Indices: 27648947--27649116 Score: 132
Period size: 30 Copynumber: 5.7 Consensus size: 30
27648937 AAATGAAATC
* *
27648947 TTGGAAAGTTTGGGGGCCAAATTCAAATTT
1 TTGGAAAGTTCGGGGGTCAAATTCAAATTT
* *
27648977 TTGGGAAGTTCGAGGGTCAAATGT-AAATTT
1 TTGGAAAGTTCGGGGGTCAAAT-TCAAATTT
* *
27649007 TTGGAAAGTTCGGGGGTCAAATCCAATTTT
1 TTGGAAAGTTCGGGGGTCAAATTCAAATTT
* **
27649037 TTGGGAAGTTC-GACGTCAAA-TCTAAATTT
1 TTGGAAAGTTCGGGGGTCAAATTC-AAATTT
* * * * *
27649066 TAGGGAAGTTTGAGGGTCAAATAT-GAATTT
1 TTGGAAAGTTCGGGGGTCAAAT-TCAAATTT
* **
27649096 TTGAAAAGTTCAAGGGTCAAA
1 TTGGAAAGTTCGGGGGTCAAA
27649117 ACATAATTTT
Statistics
Matches: 110, Mismatches: 24, Indels: 12
0.75 0.16 0.08
Matches are distributed among these distances:
28 1 0.01
29 21 0.19
30 86 0.78
31 1 0.01
32 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (30 bp):
TTGGAAAGTTCGGGGGTCAAATTCAAATTT
Found at i:27649064 original size:59 final size:60
Alignment explanation
Indices: 27648947--27649087 Score: 194
Period size: 60 Copynumber: 2.4 Consensus size: 60
27648937 AAATGAAATC
* * * *
27648947 TTGGAAAGTTTGGGGGCCAAATTCAAATTTTTGGGAAGTTCGAGGGTCAAATGTAAATTT
1 TTGGAAAGTTTGGGGGTCAAATCCAAATTTTTGGGAAGTTCGAGCGTCAAATCTAAATTT
* *
27649007 TTGGAAAGTTCGGGGGTCAAATCCAATTTTTTGGGAAGTTCGA-CGTCAAATCTAAATTT
1 TTGGAAAGTTTGGGGGTCAAATCCAAATTTTTGGGAAGTTCGAGCGTCAAATCTAAATTT
* * *
27649066 TAGGGAAGTTTGAGGGTCAAAT
1 TTGGAAAGTTTGGGGGTCAAAT
27649088 ATGAATTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 32 0.45
60 39 0.55
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (60 bp):
TTGGAAAGTTTGGGGGTCAAATCCAAATTTTTGGGAAGTTCGAGCGTCAAATCTAAATTT
Found at i:27649106 original size:59 final size:59
Alignment explanation
Indices: 27648949--27649087 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 59
27648939 ATGAAATCTT
* * * * * * *
27648949 GGAAAGTTTGGGGGCCAAATTCAAATTTTTGGGAAGTTCGAGGGTCAAATGTAAATTTTT
1 GGAAAGTTCGAGGGTCAAA-TCCAATTTTTGGGAAGTTCGAGCGTCAAATCTAAATTTTA
*
27649009 GGAAAGTTCGGGGGTCAAATCCAATTTTTTGGGAAGTTCGA-CGTCAAATCTAAATTTTA
1 GGAAAGTTCGAGGGTCAAATCCAA-TTTTTGGGAAGTTCGAGCGTCAAATCTAAATTTTA
* *
27649068 GGGAAGTTTGAGGGTCAAAT
1 GGAAAGTTCGAGGGTCAAAT
27649088 ATGAATTTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 36 0.52
60 33 0.48
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (59 bp):
GGAAAGTTCGAGGGTCAAATCCAATTTTTGGGAAGTTCGAGCGTCAAATCTAAATTTTA
Found at i:27649125 original size:30 final size:30
Alignment explanation
Indices: 27649078--27649155 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
27649068 GGGAAGTTTG
* *
27649078 AGGGTC-AAATATGAATTTTTGAA-AAGTTCA
1 AGGGTCAAAACAT-AATTTTCGAATAA-TTCA
*
27649108 AGGGTCAAAACATAATTTTCGAATAATTTA
1 AGGGTCAAAACATAATTTTCGAATAATTCA
*
27649138 AGGGTTAAAACATAATTT
1 AGGGTCAAAACATAATTT
27649156 CTAAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
AGGGTCAAAACATAATTTTCGAATAATTCA
Found at i:27649163 original size:30 final size:30
Alignment explanation
Indices: 27649107--27649163 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27649097 TGAAAAGTTC
*
27649107 AAGGGTCAAAACATAATTTTCGAATAATTT
1 AAGGGTCAAAACATAATTTTCAAATAATTT
*
27649137 AAGGGTTAAAACATAA-TTTCTAAATAA
1 AAGGGTCAAAACATAATTTTC-AAATAA
27649164 AATATGGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (30 bp):
AAGGGTCAAAACATAATTTTCAAATAATTT
Found at i:27651099 original size:122 final size:122
Alignment explanation
Indices: 27650805--27651101 Score: 366
Period size: 122 Copynumber: 2.4 Consensus size: 122
27650795 TGGTGTTGTA
* *
27650805 GCTTCA-TATTTTGTTCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGTTTGACCCA
1 GCTTCATTATTTTGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTCTGACCCA
* * ** * * * *
27650869 TTTCTCTATATCTCATCAGGAAGATAAGGTTTTGAAGTTTCACTCAAATTGAGCTTT
66 CTTCTCTATATCTAATCAAAAAGATAAGGGTTTAAAGTTTCAATCAAATTGAGCTTC
* * *
27650926 GCTTCATTATTTTAG-TCTACTTCTCTGTATTTCATCAGGAAAATGACCGCTTCGTTGTCTGACC
1 GCTTCATTATTTT-GTTC-ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTCTGACC
* * *
27650990 CACTTCTCTGTATCTAATCAAAAAGAT-GGGGTTTAAAGTTTCAATCACATTGAGCTTC
64 CACTTCTCTATATCTAATCAAAAAGATAAGGGTTTAAAGTTTCAATCAAATTGAGCTTC
* * * *
27651048 GCTTCATTGTTTTGGTTCACTTTTCTGCATCTCATCAGGAAGATGATCGCTTCA
1 GCTTCATTATTTT-GTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCA
27651102 CCACTTTGAT
Statistics
Matches: 148, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
121 6 0.04
122 76 0.51
123 66 0.45
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (122 bp):
GCTTCATTATTTTGTTCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGTCTGACCCA
CTTCTCTATATCTAATCAAAAAGATAAGGGTTTAAAGTTTCAATCAAATTGAGCTTC
Found at i:27651301 original size:76 final size:76
Alignment explanation
Indices: 27651162--27651340 Score: 234
Period size: 76 Copynumber: 2.4 Consensus size: 76
27651152 ATTTTAAGCC
* * **
27651162 ACTTCTCTGTATCTCATCAAGAAGATG-GGGTTTGAAGTTTCACTTGCATTGAGCTTCACTTCAT
1 ACTTCTCTATATCTCATCAAGAAGATGAGGATTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
* *
27651226 TGTTTTGGTCT
66 TATTTGGGTCT
* * **
27651237 ACTTCTATATATCTCATCAGGAAGATGAGGATTTGAAGTTTCACTCACATTGAGCTTCGTTTCAT
1 ACTTCTCTATATCTCATCAAGAAGATGAGGATTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
*
27651302 TATTTGGGTTT
66 TATTTGGGTCT
* *
27651313 ACATCTCTATATCTCATCAAGAAAATGA
1 ACTTCTCTATATCTCATCAAGAAGATGA
27651341 CCACTTCACC
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 24 0.27
76 64 0.73
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (76 bp):
ACTTCTCTATATCTCATCAAGAAGATGAGGATTTGAAGTTTCACTCACATTGAGCTTCACTTCAT
TATTTGGGTCT
Found at i:27651469 original size:48 final size:48
Alignment explanation
Indices: 27651414--27651508 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
27651404 ACATTGAGCT
** * * * * *
27651414 TCGCTTCATTATTTTGGTTCACTTCTTTGTATCTCATGAGGAAAATGA
1 TCGCTTCACCATTTTGATCCACTTCTCTATATCTCATCAGGAAAATGA
27651462 TCGCTTCACCATTTTGATCCACTTCTCTATATCTCATCAGGAAAATG
1 TCGCTTCACCATTTTGATCCACTTCTCTATATCTCATCAGGAAAATG
27651509 GGGATTTGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (48 bp):
TCGCTTCACCATTTTGATCCACTTCTCTATATCTCATCAGGAAAATGA
Found at i:27651548 original size:124 final size:124
Alignment explanation
Indices: 27651228--27651667 Score: 616
Period size: 124 Copynumber: 3.6 Consensus size: 124
27651218 CACTTCATTG
* * * *
27651228 TTTTGGTCTACTTCTATATATCTCATCAGGAAGATGAGGATTTGAAGTTTCACTCACATTGAGCT
1 TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGAGGATTTGAAGTTTCACTCACATTGAGCT
* * * * * * *
27651293 TCGTTTCATTATTTGGGTTTACATCTCTATATCTCATCAAGAAAATGACCACTTCACCA
66 TCGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCACCA
* * *
27651352 TTTTGATCCACTT-T-TGTATCTCATTAGG-AAGTGAGGATTTGAAGTTTCACTCACATTGAGCT
1 TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGAGGATTTGAAGTTTCACTCACATTGAGCT
* * *
27651414 TCGCTTCATTATTTTGGTTCACTTCTTTGTATCTCATGAGGAAAATGATCGCTTCACCA
66 TCGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCACCA
*
27651473 TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGGGGATTTGAAGTTTCACTCACATTGAGCT
1 TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGAGGATTTGAAGTTTCACTCACATTGAGCT
* * * *
27651538 TCACTTCATTATTTTGGTTCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATCA
66 TCGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCACCA
* * * * *
27651597 TTTTTATCCACTTCTCTGTATCTCATCAGGAAAATGGGGATTTGAAATTTCACTCACATTGAGAT
1 TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGAGGATTTGAAGTTTCACTCACATTGAGCT
27651662 TCGCTT
66 TCGCTT
27651668 GATTTGAAGT
Statistics
Matches: 282, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
121 94 0.33
122 13 0.05
123 13 0.05
124 162 0.57
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (124 bp):
TTTTGATCCACTTCTCTATATCTCATCAGGAAAATGAGGATTTGAAGTTTCACTCACATTGAGCT
TCGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCAGGAAAATGACCGCTTCACCA
Found at i:27651681 original size:33 final size:33
Alignment explanation
Indices: 27651635--27651700 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
27651625 GGAAAATGGG
27651635 GATTTGAAATTTCACTCACATTGAGATTCGCTT
1 GATTTGAAATTTCACTCACATTGAGATTCGCTT
*
27651668 GATTTGAAGTTTCACTCACATTGAGATTCGCTT
1 GATTTGAAATTTCACTCACATTGAGATTCGCTT
27651701 CATTATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (33 bp):
GATTTGAAATTTCACTCACATTGAGATTCGCTT
Found at i:27651797 original size:157 final size:157
Alignment explanation
Indices: 27651511--27651824 Score: 520
Period size: 157 Copynumber: 2.0 Consensus size: 157
27651501 GGAAAATGGG
* *
27651511 GATTTGAAGTTTCACTCACATTGAGCTTCACTTCATTATTTTGGTTCACTTCTCTGTATCTCATT
1 GATTTGAAGTTTCACTCACATTGAGATTCACTTCATTATTTTGGTTCACTTCTCTGTATCTCATC
* * * * * *
27651576 AGGAAGATGACCGCTTCATCATTTTTATCCACTTCTCTGTATCTCATCAGGAAAATGGGGATTTG
66 AGGAAAATAACCGCTTAACCATTTTGATCCACTTCTCTCTATCTCATCAGGAAAATGGGGATTTG
27651641 AAATTTCACTCACATTGAGATTCGCTT
131 AAATTTCACTCACATTGAGATTCGCTT
*
27651668 GATTTGAAGTTTCACTCACATTGAGATTCGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATC
1 GATTTGAAGTTTCACTCACATTGAGATTCACTTCATTATTTTGGTTCACTTCTCTGTATCTCATC
*
27651733 AGGAAAATAACCGCTTAACCATTTTGATCCACTTCTCTCTATCTCATCAGGAAGATGGGGATTTG
66 AGGAAAATAACCGCTTAACCATTTTGATCCACTTCTCTCTATCTCATCAGGAAAATGGGGATTTG
* *
27651798 AAGTTTCACTCACATTGAGCTTCGCTT
131 AAATTTCACTCACATTGAGATTCGCTT
27651825 CTTGTAAAGC
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (157 bp):
GATTTGAAGTTTCACTCACATTGAGATTCACTTCATTATTTTGGTTCACTTCTCTGTATCTCATC
AGGAAAATAACCGCTTAACCATTTTGATCCACTTCTCTCTATCTCATCAGGAAAATGGGGATTTG
AAATTTCACTCACATTGAGATTCGCTT
Found at i:27652589 original size:43 final size:40
Alignment explanation
Indices: 27652501--27652618 Score: 131
Period size: 43 Copynumber: 3.0 Consensus size: 40
27652491 TTTGGTTTCA
*
27652501 AGACGCCCTTTGTGGGTTTTTATCTTGA----TTTTTTTT
1 AGACGCCCTTTGTGGGTTTTTATCTCGATCCTTTTTTTTT
*
27652537 AGACTCCCTTTGCT-GGTTTTCT-TCTCGATCTCTTTTTTTTT
1 AGACGCCCTTTG-TGGGTTTT-TATCTCGATC-CTTTTTTTTT
27652578 CGAGACGCCCTTTGTGGGTTTTTATCTCGATCCTTTTTTTT
1 --AGACGCCCTTTGTGGGTTTTTATCTCGATCCTTTTTTTT
27652619 AGGTAAAATA
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
36 22 0.32
37 2 0.03
41 8 0.12
42 11 0.16
43 25 0.37
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.53
Consensus pattern (40 bp):
AGACGCCCTTTGTGGGTTTTTATCTCGATCCTTTTTTTTT
Found at i:27658367 original size:23 final size:23
Alignment explanation
Indices: 27658283--27658478 Score: 132
Period size: 23 Copynumber: 8.4 Consensus size: 23
27658273 TACGGAACAA
* * *
27658283 AAACGGAGAGTAC-CTAAGTACT
1 AAACGGAGAGCACACAAAGTGCT
*
27658305 AAACGGAGAGCATA-AAAGTGCT
1 AAACGGAGAGCACACAAAGTGCT
* * *
27658327 GGGTAACAGAGAGCACACTAAGTGCT
1 ---AAACGGAGAGCACACAAAGTGCT
* * *
27658353 AAACTGAGAGTACACAAAGTACT
1 AAACGGAGAGCACACAAAGTGCT
* *
27658376 AATCGGAGAGCACACGAAGTGCT
1 AAACGGAGAGCACACAAAGTGCT
* *
27658399 AATCGAAGAGCACACGAAA-TGCT
1 AAACGGAGAGCACAC-AAAGTGCT
* *
27658422 AATA-AGAGAGCACACGAAGTGCT
1 AA-ACGGAGAGCACACAAAGTGCT
*
27658445 AATAACGGAGAGCACGA-AATGTGCT
1 -A-AACGGAGAGCAC-ACAAAGTGCT
27658470 AAACGGAGA
1 AAACGGAGA
27658479 ACGCGCTAAG
Statistics
Matches: 135, Mismatches: 27, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
22 19 0.14
23 77 0.57
24 5 0.04
25 26 0.19
26 8 0.06
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (23 bp):
AAACGGAGAGCACACAAAGTGCT
Found at i:27658461 original size:69 final size:70
Alignment explanation
Indices: 27658336--27658471 Score: 154
Period size: 69 Copynumber: 1.9 Consensus size: 70
27658326 TGGGTAACAG
* * * *
27658336 AGAGCACACTAAGTGCTAAACTGAGAGTACACAAAGTACTAATCGGAGAGCACACG-AA-GTGCT
1 AGAGCACACGAAATGCTAAACAGAGAGCACACAAAGTACTAATCGGAGAG-ACACGAAATGTGCT
27658399 AATCGA
65 AATCGA
* *
27658405 AGAGCACACGAAATGCTAATA-AGAGAGCACACGAAGTGCTAATAACGGAGAG-CACGAAATGTG
1 AGAGCACACGAAATGCTAA-ACAGAGAGCACACAAAGTACTAAT--CGGAGAGACACGAAATGTG
27658468 CTAA
63 CTAA
27658472 ACGGAGAACG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
69 39 0.70
70 3 0.05
71 14 0.25
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (70 bp):
AGAGCACACGAAATGCTAAACAGAGAGCACACAAAGTACTAATCGGAGAGACACGAAATGTGCTA
ATCGA
Found at i:27659359 original size:24 final size:24
Alignment explanation
Indices: 27659343--27659417 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
27659333 AGTTTGACTC
27659343 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
*
27659367 AAACAAATAAA-CGTAGTTTAATTG
1 AAACAAATAAATAG-AGTTTAATTG
*
27659391 AAACAATTAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTTAATTG
27659415 AAA
1 AAA
27659418 GATTATTTCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
23 1 0.02
24 44 0.96
25 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.29
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTTAATTG
Found at i:27666455 original size:18 final size:18
Alignment explanation
Indices: 27666423--27666461 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27666413 TGGATTTTTA
* *
27666423 TAAAATAATAAAAATACG
1 TAAAATAAGAAAAATAAG
*
27666441 TAAAATAAGAGAAATAAG
1 TAAAATAAGAAAAATAAG
27666459 TAA
1 TAA
27666462 GACAAAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (18 bp):
TAAAATAAGAAAAATAAG
Found at i:27669700 original size:13 final size:13
Alignment explanation
Indices: 27669682--27669707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27669672 CACCACAAAC
27669682 CCTTCCTAACCAT
1 CCTTCCTAACCAT
27669695 CCTTCCTAACCAT
1 CCTTCCTAACCAT
27669708 TAACCCCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (13 bp):
CCTTCCTAACCAT
Found at i:27673331 original size:2 final size:2
Alignment explanation
Indices: 27673324--27673367 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
27673314 AATAAGGCCT
27673324 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27673366 GA
1 GA
27673368 ATGTTGGGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27675579 original size:38 final size:39
Alignment explanation
Indices: 27675537--27675622 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 39
27675527 AAAAGGTTGG
** * *
27675537 ATCTCGTTATATTACCTGATAATTTGCAAC-AATGCTAA
1 ATCTCGTTATATTACCAAAGAATCTGCAACAAATGCTAA
* *
27675575 ATCTCATTTTATTACCAAAGAATCTGCAACAAATGCTAA
1 ATCTCGTTATATTACCAAAGAATCTGCAACAAATGCTAA
27675614 ATCTCGTTA
1 ATCTCGTTA
27675623 AAATCTATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 24 0.62
39 15 0.38
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (39 bp):
ATCTCGTTATATTACCAAAGAATCTGCAACAAATGCTAA
Found at i:27680167 original size:6 final size:6
Alignment explanation
Indices: 27680156--27680190 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
27680146 AGGTTTCCAA
*
27680156 AAATGG AAATGG AAATGA AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
27680191 ATCAATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:27680178 original size:18 final size:18
Alignment explanation
Indices: 27680155--27680191 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27680145 TAGGTTTCCA
27680155 AAAATGGAAATGGAAATG
1 AAAATGGAAATGGAAATG
27680173 AAAATGGAAATGGAAATG
1 AAAATGGAAATGGAAATG
27680191 A
1 A
27680192 TCAATTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.27, T:0.16
Consensus pattern (18 bp):
AAAATGGAAATGGAAATG
Found at i:27690726 original size:7 final size:7
Alignment explanation
Indices: 27690716--27690754 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
27690706 GGAAGACCCC
*
27690716 CAAAACC
1 CAAAACT
27690723 CAAAACT
1 CAAAACT
27690730 CAAAACT
1 CAAAACT
27690737 CAAAACT
1 CAAAACT
27690744 CAAAACT
1 CAAAACT
27690751 CAAA
1 CAAA
27690755 TAAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.10
Consensus pattern (7 bp):
CAAAACT
Found at i:27693383 original size:24 final size:25
Alignment explanation
Indices: 27693334--27693385 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
27693324 AATATTCATA
27693334 TTATATTGTTTTAATATTTAATAATT
1 TTATATTGTTTT-ATATTTAATAATT
*
27693360 TTATATT-TTTT-TATTTATTGAATT
1 TTATATTGTTTTATATTTAAT-AATT
27693384 TT
1 TT
27693386 TTATATAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 6 0.25
25 4 0.17
26 7 0.29
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTATATTGTTTTATATTTAATAATT
Found at i:27696164 original size:21 final size:21
Alignment explanation
Indices: 27696114--27696164 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
27696104 CTCGATTGAC
*
27696114 AAATCTCACATTTTTATCTTG
1 AAATCTCATATTTTTATCTTG
*
27696135 AAATCTCATTTTTTTATCTTG
1 AAATCTCATATTTTTATCTTG
27696156 AAATCTCAT
1 AAATCTCAT
27696165 GTTTCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (21 bp):
AAATCTCATATTTTTATCTTG
Found at i:27697333 original size:17 final size:17
Alignment explanation
Indices: 27697311--27697387 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
27697301 AATAAAGATA
27697311 TAAATTTAGTTTTAAA-T
1 TAAATTTA-TTTTAAATT
* *
27697328 TAAATTTATTATGAATT
1 TAAATTTATTTTAAATT
* *
27697345 TAAATTTGTATTAAAATT
1 TAAATTTAT-TTTAAATT
* *
27697363 TGAATTTATTATAAATT
1 TAAATTTATTTTAAATT
27697380 TAAATTTA
1 TAAATTTA
27697388 AAACTAAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
16 5 0.11
17 30 0.64
18 12 0.26
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:27697445 original size:46 final size:46
Alignment explanation
Indices: 27697395--27697486 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
27697385 TTAAAACTAA
* *
27697395 ATTAAATGTCCAAAATCCATTTACAAGCTCGATTGGGCCAAATTTG
1 ATTAAATGTCCAAAATCCATTTACAAGCCCAATTGGGCCAAATTTG
* ** *
27697441 ATTAAATGTCCAAAGTTTATTTACAAGCCCAATTGGGCTAAATTTG
1 ATTAAATGTCCAAAATCCATTTACAAGCCCAATTGGGCCAAATTTG
27697487 GCTAGCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (46 bp):
ATTAAATGTCCAAAATCCATTTACAAGCCCAATTGGGCCAAATTTG
Found at i:27698206 original size:15 final size:15
Alignment explanation
Indices: 27698181--27698221 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
27698171 TTGATAATTT
27698181 TATTAAATATTTATAA
1 TATT-AATATTTATAA
*
27698197 TATTAATATTTTTAA
1 TATTAATATTTATAA
*
27698212 TAATAATATT
1 TATTAATATT
27698222 ATTAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTAATATTTATAA
Found at i:27698215 original size:37 final size:39
Alignment explanation
Indices: 27698156--27698229 Score: 91
Period size: 37 Copynumber: 1.9 Consensus size: 39
27698146 ACATACATTA
*
27698156 ATAATAGTAAATGTTTTGATAAT-T-TTATTAAATATTT
1 ATAATAGTAAATGTTTTAATAATATATTATTAAATATTT
*
27698193 ATAATATTAATAT-TTTTAATAATAATATTATTAAATA
1 ATAATAGTAA-ATGTTTTAATAAT-ATATTATTAAATA
27698230 AAAAAAGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 18 0.58
38 2 0.06
39 1 0.03
40 10 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (39 bp):
ATAATAGTAAATGTTTTAATAATATATTATTAAATATTT
Found at i:27699279 original size:29 final size:28
Alignment explanation
Indices: 27699245--27699330 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 28
27699235 TAAACTATCC
* *
27699245 AAAAATCACATTTTGACCCCAAAACTTT
1 AAAAATTACATTTTGACCCTAAAACTTT
*
27699273 AGAAAATTACATTTTGACCTTAAAACTTCT
1 A-AAAATTACATTTTGACCCTAAAACTT-T
* *
27699303 AAAAATTACATTTTTACCCTTAAACTTT
1 AAAAATTACATTTTGACCCTAAAACTTT
27699331 CCTAAATTCC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.04
29 46 0.92
30 2 0.04
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (28 bp):
AAAAATTACATTTTGACCCTAAAACTTT
Found at i:27699337 original size:29 final size:28
Alignment explanation
Indices: 27699275--27699347 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
27699265 AAAACTTTAG
*
27699275 AAAATTACATTTTGACCTTAAAACTTCT
1 AAAATTACATTTTTACCTTAAAACTTCT
27699303 AAAAATTACATTTTTACCCTT-AAACTTTCCT
1 -AAAATTACATTTTTA-CCTTAAAAC-TT-CT
*
27699334 -AAATTCCATTTTTA
1 AAAATTACATTTTTA
27699348 ACCCCGATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 31 0.79
30 6 0.15
31 2 0.05
ACGTcount: A:0.37, C:0.19, G:0.01, T:0.42
Consensus pattern (28 bp):
AAAATTACATTTTTACCTTAAAACTTCT
Found at i:27699393 original size:29 final size:29
Alignment explanation
Indices: 27699361--27699452 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
27699351 CCGATTTTAC
27699361 CCAAAATTACCATTTTACCCCCAAATCTT
1 CCAAAATTACCATTTTACCCCCAAATCTT
** ** *
27699390 CCAAAATT-CCATTTTGACCCTGATTTCAT
1 CCAAAATTACCATTTT-ACCCCCAAATCTT
* *
27699419 -CAAAATTACTATTTTACCCCTAAA-CTTT
1 CCAAAATTACCATTTTACCCCCAAATC-TT
27699447 CCAAAA
1 CCAAAA
27699453 CCCTATTTTA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.02
28 20 0.42
29 27 0.56
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCCAAATCTT
Found at i:27699397 original size:59 final size:59
Alignment explanation
Indices: 27699304--27699526 Score: 208
Period size: 59 Copynumber: 3.8 Consensus size: 59
27699294 AAAACTTCTA
** * *
27699304 AAAATTA-CATTTTTACCCTTAAACTTTCCTAAATTCCATTTTTAACCCCGATTTTACCC
1 AAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
* * *
27699363 AAAATTACCATTTTACCCCCAAA-TCTTCCAAAATTCCA-TTTTGACCCTGATTTCA-TC
1 AAAATTACCATTTTACCCCCAAACT-TTCCAAAATTCCATTTTTAACCCCGATTTCACCC
* * * * **
27699420 AAAATTACTATTTTACCCCTAAACTTTCCAAAA--CCCTATTTTAACCTCGATTTCACTA
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCAT-TTTTAACCCCGATTTCACCC
* * * *
27699478 AAAATTACCGTTTTACCCCCGAACCTTT-TAAAATCCCATTTTTAACCCC
1 AAAATTACCATTTTACCCCC-AAACTTTCCAAAATTCCATTTTTAACCCC
27699527 AAATTTTCCC
Statistics
Matches: 134, Mismatches: 21, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
55 2 0.01
57 44 0.33
58 38 0.28
59 45 0.34
60 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.03, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
Found at i:27699449 original size:57 final size:57
Alignment explanation
Indices: 27699304--27699496 Score: 196
Period size: 57 Copynumber: 3.3 Consensus size: 57
27699294 AAAACTTCTA
* * * * *
27699304 AAAATTA-CATTTTTACCCTTAAACTTTCCTAAATTCCATTTTTAACCCCGATTTTACCC
1 AAAATTACCA-TTTTACCCCTAAACTTTCCAAAATTCCA-TTTT-ACCCTGATTTCACTC
*
27699363 AAAATTACCATTTTACCCCCAAA-TCTTCCAAAATTCCATTTTGACCCTGATTTCA-TC
1 AAAATTACCATTTTACCCCTAAACT-TTCCAAAATTCCATTTT-ACCCTGATTTCACTC
* * * *
27699420 AAAATTACTATTTTACCCCTAAACTTTCCAAAA-CCCTATTTTAACCTCGATTTCACTA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-ATTTTACCCT-GATTTCACTC
*
27699478 AAAATTACCGTTTTACCCC
1 AAAATTACCATTTTACCCC
27699497 CGAACCTTTT
Statistics
Matches: 114, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
56 6 0.05
57 42 0.37
58 34 0.30
59 30 0.26
60 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTACCCTGATTTCACTC
Found at i:27699511 original size:115 final size:116
Alignment explanation
Indices: 27699304--27699519 Score: 276
Period size: 115 Copynumber: 1.9 Consensus size: 116
27699294 AAAACTTCTA
* ** * *
27699304 AAAATTACATTTTTACCCTTAAACTTTCCTAAATTCCATTTTTAACCCCGATTTTACCCAAAATT
1 AAAATTACATTTTTACCCCTAAACTTTCCTAAAACCCATTTTTAACCCCGATTTCACCAAAAATT
* *
27699369 ACCATTTTACCCCCAAATCTTCCAAAATTCCATTTTGACCCTGATTTCATC
66 ACCATTTTACCCCCAAACCTTCCAAAATCCCATTTTGACCCTGATTTCATC
* *
27699420 AAAATTAC-TATTTTACCCCTAAACTTTCC-AAAACCC-TATTTTAACCTCGATTTCACTAAAAA
1 AAAATTACAT-TTTTACCCCTAAACTTTCCTAAAACCCAT-TTTTAACCCCGATTTCACCAAAAA
* * **
27699482 TTACCGTTTTACCCCCGAACCTTTTAAAATCCCATTTT
64 TTACCATTTTACCCCCAAACCTTCCAAAATCCCATTTT
27699520 TAACCCCAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
114 1 0.01
115 58 0.68
116 26 0.31
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (116 bp):
AAAATTACATTTTTACCCCTAAACTTTCCTAAAACCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCAAACCTTCCAAAATCCCATTTTGACCCTGATTTCATC
Found at i:27701333 original size:22 final size:22
Alignment explanation
Indices: 27701291--27701365 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
27701281 AACAAAACAC
* *
27701291 AAAACCTGCAAC-CCCTCTTGA
1 AAAACCAGCAACACCTTCTTGA
* * *
27701312 AAAACCAGTAGCATCTTCTTGA
1 AAAACCAGCAACACCTTCTTGA
* * *
27701334 AATACCAACAACACCTTCTTGG
1 AAAACCAGCAACACCTTCTTGA
27701356 AAAACCAGCA
1 AAAACCAGCA
27701366 GCCAAGAACC
Statistics
Matches: 40, Mismatches: 13, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 9 0.22
22 31 0.77
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAACCAGCAACACCTTCTTGA
Found at i:27713676 original size:13 final size:13
Alignment explanation
Indices: 27713658--27713690 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
27713648 ACACCCCTAG
27713658 TTTGATCCATGAA
1 TTTGATCCATGAA
*
27713671 TTTGATCCATGAG
1 TTTGATCCATGAA
27713684 TTTGATC
1 TTTGATC
27713691 ATCGATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (13 bp):
TTTGATCCATGAA
Found at i:27741490 original size:27 final size:27
Alignment explanation
Indices: 27741460--27741523 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
27741450 AAATGCTTTA
* * *
27741460 TTTTTATAGATTGCCACAAAGGTTTCC
1 TTTTCATAGATTACCACAAAGGCTTCC
*
27741487 TTTTCATATG-TTATCACAAAGGCTTCC
1 TTTTCATA-GATTACCACAAAGGCTTCC
27741514 TTTTCATAGA
1 TTTTCATAGA
27741524 CTGTCGTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 29 0.94
28 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (27 bp):
TTTTCATAGATTACCACAAAGGCTTCC
Found at i:27742967 original size:24 final size:24
Alignment explanation
Indices: 27742935--27743021 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
27742925 GCGCACAAAT
27742935 GAAATGAGGCACTTCGGTGCAATC
1 GAAATGAGGCACTTCGGTGCAATC
27742959 GAAATGAGGCACTTCGGTGCAATC
1 GAAATGAGGCACTTCGGTGCAATC
* *
27742983 GAAATGTGGCACTTCGATGCAA-C
1 GAAATGAGGCACTTCGGTGCAATC
* *
27743006 TAGAATGTGGCACTTC
1 GA-AATGAGGCACTTC
27743022 AATGCAAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 2 0.03
24 57 0.97
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
GAAATGAGGCACTTCGGTGCAATC
Found at i:27747659 original size:2 final size:2
Alignment explanation
Indices: 27747652--27747685 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27747642 GCCATTGCAG
27747652 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
27747686 TATATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:27749057 original size:17 final size:18
Alignment explanation
Indices: 27749035--27749068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27749025 TCGGCATGCA
*
27749035 GCTTTAT-GATGTAAATT
1 GCTTTATAGATGAAAATT
27749052 GCTTTATAGATGAAAAT
1 GCTTTATAGATGAAAAT
27749069 ATTTCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (18 bp):
GCTTTATAGATGAAAATT
Found at i:27769767 original size:14 final size:15
Alignment explanation
Indices: 27769750--27769786 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
27769740 TTCCTTTTAC
27769750 TTTAAAAAA-AT-TCA
1 TTTAAAAAATATAT-A
27769764 TTTAAAAAATATATA
1 TTTAAAAAATATATA
27769779 TTTAAAAA
1 TTTAAAAA
27769787 TAGTCACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 11 0.52
16 1 0.05
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAAAATATATA
Found at i:27769847 original size:20 final size:21
Alignment explanation
Indices: 27769800--27769848 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
27769790 TCACCCTTTA
* *
27769800 TAAAAAATTAATCTATTTTTT
1 TAAAAAATTAATCTATATTCT
*
27769821 TATAAAATTAA-CTATATTCT
1 TAAAAAATTAATCTATATTCT
27769841 TAAAAAAT
1 TAAAAAAT
27769849 AATAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAAATTAATCTATATTCT
Found at i:27781288 original size:13 final size:13
Alignment explanation
Indices: 27781270--27781305 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
27781260 GATACAACTC
**
27781270 TTGGTTCTACCGG
1 TTGGTTCTACCAA
27781283 TTGGTTCTACCAA
1 TTGGTTCTACCAA
27781296 TTGGTTCTAC
1 TTGGTTCTAC
27781306 TGATACAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (13 bp):
TTGGTTCTACCAA
Found at i:27788507 original size:18 final size:19
Alignment explanation
Indices: 27788460--27788507 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
27788450 AACAGTAGTT
*
27788460 TATATAAAATAGATATGTA
1 TATATAAAATAGATATATA
*
27788479 TATATATAATAG-TATATA
1 TATATAAAATAGATATATA
*
27788497 TGTATAAAATA
1 TATATAAAATA
27788508 TACAATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (19 bp):
TATATAAAATAGATATATA
Found at i:27788534 original size:16 final size:16
Alignment explanation
Indices: 27788477--27788537 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
27788467 AATAGATATG
* *
27788477 TATATATATAATAGTA
1 TATATATATAAAAATA
*
27788493 TATATGTAT-AAAATA
1 TATATATATAAAAATA
* *
27788508 TACAATTTATAAAAATA
1 TA-TATATATAAAAATA
*
27788525 TATGTATATAAAA
1 TATATATATAAAA
27788538 TTACTAATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 6 0.17
16 21 0.60
17 8 0.23
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (16 bp):
TATATATATAAAAATA
Found at i:27788758 original size:13 final size:13
Alignment explanation
Indices: 27788740--27788764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27788730 GAAAAAATGG
27788740 TGGAAAGTGGGGT
1 TGGAAAGTGGGGT
27788753 TGGAAAGTGGGG
1 TGGAAAGTGGGG
27788765 ACCGAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.56, T:0.20
Consensus pattern (13 bp):
TGGAAAGTGGGGT
Found at i:27792209 original size:117 final size:116
Alignment explanation
Indices: 27791994--27792336 Score: 476
Period size: 117 Copynumber: 2.9 Consensus size: 116
27791984 TCGGGGGGCG
* *
27791994 AAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATTGGATTTTGGAGAGTTCGAGGGTAAAATGG
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAA-TGGATTTTGAAGAGTTCGAGGGTAAAATGG
* * *
27792058 TAATTTTTGGTAAAATCGAGGTTAAAATGGGATTTTATAAAG-TCTTAAGGTA
65 TAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTAGAAAGTTC-GAAGGTA
* * *
27792110 AAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGATATTTTAAAGAGTTCGAGGGTAAAATGG
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATG-GATTTTGAAGAGTTCGAGGGTAAAATGG
* * **
27792175 TAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTGGAGAGTTCGGGGGTA
65 TAATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTAGAAAGTTCGAAGGTA
*
27792227 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAA-AGTTCGAGGGTAAAATG
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAAT-GGATTTT-GAAGAGTTCGAGGGTAAAATG
* *
27792291 GTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
64 GTAATTTTTGGTAAAATCGGGGTT-AAAATGGGATTTTAGAAAGTT
27792337 TGGGAGTAAA
Statistics
Matches: 203, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
116 11 0.05
117 167 0.82
118 25 0.12
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (116 bp):
AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGATTTTGAAGAGTTCGAGGGTAAAATGGT
AATTTTTGGTAAAATCGGGGTTAAAATGGGATTTTAGAAAGTTCGAAGGTA
Found at i:27792328 original size:30 final size:30
Alignment explanation
Indices: 27791994--27792318 Score: 159
Period size: 30 Copynumber: 11.1 Consensus size: 30
27791984 TCGGGGGGCG
*
27791994 AAATGGTAA-TTTTGGTAAAATCGGGGTTAA
1 AAATGGTAATTTTTGGTGAAATCGGGGTT-A
* **
27792024 AAATTGG--A-TTTTGGAGAGTTCGAGGG-TA
1 AAA-TGGTAATTTTTGGTGAAATCG-GGGTTA
* *
27792052 AAATGGTAATTTTTGGTAAAATCGAGGTTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTA
* * **
27792082 AAATGG-GA-TTTT-AT-AAAGTCTTAAGG-TA
1 AAATGGTAATTTTTGGTGAAA-TC--GGGGTTA
* * *
27792110 AAATGGTAATTTTTGGTAAAATTGAGGTTAA
1 AAATGGTAATTTTTGGTGAAATCGGGGTT-A
* *** **
27792141 AAATGAT-A-TTTTAAAGAGTTCGAGGG-TA
1 AAATGGTAATTTTTGGTGAAATCG-GGGTTA
*
27792169 AAATGGTAATTTTTGGTAAAATCGGGGTTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTA
* * ** *
27792199 AAATGG-GA-TTTTGGAGAGTTCGGGGGTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTA
*
27792227 AAATGGTAATTTTTGGTGAAATCGAGGTTAA
1 AAATGGTAATTTTTGGTGAAATCGGGGTT-A
*
27792258 AAATGG-GA-TTTT-G-GAAAGTTCGAGGG-TA
1 AAATGGTAATTTTTGGTGAAA--TCG-GGGTTA
27792286 AAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAATGGTAATTTTTGGTGAAATCGGGGTTA
27792316 AAA
1 AAA
27792319 ATGGGATTTT
Statistics
Matches: 218, Mismatches: 47, Indels: 60
0.67 0.14 0.18
Matches are distributed among these distances:
26 3 0.01
27 10 0.05
28 52 0.24
29 49 0.22
30 77 0.35
31 20 0.09
32 7 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AAATGGTAATTTTTGGTGAAATCGGGGTTA
Found at i:27792329 original size:29 final size:28
Alignment explanation
Indices: 27792179--27792330 Score: 130
Period size: 28 Copynumber: 5.2 Consensus size: 28
27792169 AAATGGTAAT
*
27792179 TTTTGGTAAAATCGGGGTTAAAATGGGA
1 TTTTGGTGAAATCGGGGTTAAAATGGGA
* ** * *
27792207 TTTTGGAGAGTTCGGGGGTAAAATGGTAA
1 TTTTGGTGAAATCGGGGTTAAAATGG-GA
*
27792236 TTTTTGGTGAAATCGAGGTTAAAAATGGGA
1 -TTTTGGTGAAATCGGGGTT-AAAATGGGA
*
27792266 TTTT-G-GAAAGTTCGAGGG-TAAAATGGTAA
1 TTTTGGTGAAA--TCG-GGGTTAAAATGG-GA
27792295 TTTTTGGTGAAATCGGGGTTAAAAATGGGA
1 -TTTTGGTGAAATCGGGGTT-AAAATGGGA
27792325 TTTTGG
1 TTTTGG
27792331 AAAGTTTGGG
Statistics
Matches: 97, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
27 4 0.04
28 29 0.30
29 19 0.20
30 26 0.27
31 15 0.15
32 4 0.04
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (28 bp):
TTTTGGTGAAATCGGGGTTAAAATGGGA
Found at i:27792346 original size:29 final size:28
Alignment explanation
Indices: 27792190--27792349 Score: 107
Period size: 29 Copynumber: 5.5 Consensus size: 28
27792180 TTTGGTAAAA
* *
27792190 TCGGGGTTAAAATGGGATTTTGGAGAGT
1 TCGGGGTAAAAATGGGATTTTGGAAAGT
*
27792218 TCGGGGGT-AAAATGGTAATTTTTGGTGAAA--
1 TC-GGGGTAAAAATGG-GA-TTTT-G-GAAAGT
*
27792248 TCGAGGTTAAAAATGGGATTTTGGAAAGT
1 TCG-GGGTAAAAATGGGATTTTGGAAAGT
*
27792277 TCGAGGGT-AAAATGGTAATTTTTGGTGAAA--
1 TCG-GGGTAAAAATGG-GA-TTTT-G-GAAAGT
27792307 TCGGGGTTAAAAATGGGATTTTGGAAAGT
1 TCGGGG-TAAAAATGGGATTTTGGAAAGT
*
27792336 TTGGGAGTAAAAAT
1 TCGGG-GTAAAAAT
27792350 ATAATTTCTG
Statistics
Matches: 106, Mismatches: 8, Indels: 35
0.71 0.05 0.23
Matches are distributed among these distances:
27 8 0.08
28 18 0.17
29 37 0.35
30 20 0.19
31 16 0.15
32 7 0.07
ACGTcount: A:0.32, C:0.03, G:0.33, T:0.32
Consensus pattern (28 bp):
TCGGGGTAAAAATGGGATTTTGGAAAGT
Found at i:27792356 original size:59 final size:59
Alignment explanation
Indices: 27791994--27792336 Score: 480
Period size: 59 Copynumber: 5.9 Consensus size: 59
27791984 TCGGGGGGCG
* * *
27791994 AAATGGTAA-TTTTGGTAAAATCGGGGTTAAAAATTGGATTTTGGAGAGTTCGAGGGTA
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
** * *
27792052 AAATGGTAATTTTTGGTAAAATCGAGGTT-AAAATGGGATTTTATAAAG-TCTTAAGGTA
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTC-GAGGGTA
* ** *
27792110 AAATGGTAATTTTTGGTAAAATTGAGGTTAAAAATGATATTTT-AAAGAGTTCGAGGGTA
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAA-AGTTCGAGGGTA
* * *
27792169 AAATGGTAATTTTTGGTAAAATCGGGGTT-AAAATGGGATTTTGGAGAGTTCGGGGGTA
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
*
27792227 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
* *
27792286 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTT
1 AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTT
27792337 TGGGAGTAAA
Statistics
Matches: 253, Mismatches: 25, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.01
58 108 0.43
59 141 0.56
60 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
AAATGGTAATTTTTGGTAAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTA
Found at i:27794181 original size:28 final size:29
Alignment explanation
Indices: 27794121--27794181 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
27794111 CTAAATGTAT
* *
27794121 TTAAATTTAAAACAGAATTTAAATTTAAA
1 TTAAATTTAAAACAGAATTCAAACTTAAA
**
27794150 -TAAATTTAAAA-TTAATTCAAACTTAAA
1 TTAAATTTAAAACAGAATTCAAACTTAAA
27794177 TTAAA
1 TTAAA
27794182 ATCCAAGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (29 bp):
TTAAATTTAAAACAGAATTCAAACTTAAA
Found at i:27794854 original size:200 final size:200
Alignment explanation
Indices: 27794496--27795227 Score: 1106
Period size: 200 Copynumber: 3.7 Consensus size: 200
27794486 TTCATTGATC
* * * * * **
27794496 TGGTCTTCTTCTCTGTGTCTCATTAGGAAGATGACCGCGATC-ATCTGTTTTAATTCGCTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGC-CTCGCT-TGTTTCGATTCGCTTCTCT
* * * * *
27794560 GGATCGCCTCAGGAAGATGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTA
64 GGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
* * * * * *
27794625 TTGCTTCTACCTACTTCTCAGTATCTCATCAGGAAGTTGGGTTCGAAGATTTGCTCGCGTTGAGC
129 TTGCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGC
* *
27794690 GCTGAGC
194 GTTGAGT
* *
27794697 TAGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGATTCGCTTCTCTGG
* *
27794762 ATCTCTTCAGGAAGATGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
*
27794827 GCTTCAACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
131 GCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
27794892 TGAGT
196 TGAGT
*
27794897 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGCTTCGCTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGATTCGCTTCTCTGG
*
27794962 ATCTCCTCAAGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * * *
27795027 GCTTCGACCTGATTCTCGGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCAT
131 GCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
27795092 TGAGT
196 TGAGT
* * *
27795097 TGGTATTCTTTTTTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGATTCACTTCTCTGG
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGATTCGCTTCTCTGG
* * *
27795162 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTTTGTGTCTCATCAGGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
27795227 G
131 G
27795228 GTGGTAATCT
Statistics
Matches: 490, Mismatches: 40, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
200 455 0.93
201 35 0.07
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTCGATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
GCTTCAACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTGGCTCGTGTTGAGCGT
TGAGT
Found at i:27808933 original size:30 final size:30
Alignment explanation
Indices: 27808886--27808945 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
27808876 AACTAATAAA
**
27808886 AATAAAATTATATTTTAATTTTTTAAAAAT
1 AATAAAATTATATTTTAATCATTTAAAAAT
*
27808916 AATAAAATTTTGA-TTTAATCATTTAAAAAT
1 AATAAAATTAT-ATTTTAATCATTTAAAAAT
27808946 TATATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
AATAAAATTATATTTTAATCATTTAAAAAT
Found at i:27825939 original size:19 final size:18
Alignment explanation
Indices: 27825895--27825940 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
27825885 AAGTTAAACA
* * *
27825895 AATCGAGTTATTTGAGTT
1 AATCGAATTATTCGAGTC
27825913 AATCGAATTATTCGAGTC
1 AATCGAATTATTCGAGTC
27825931 AACTCGAATT
1 AA-TCGAATT
27825941 TTTTTTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
AATCGAATTATTCGAGTC
Found at i:27827570 original size:13 final size:12
Alignment explanation
Indices: 27827555--27827601 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
27827545 AAAAAACTAA
27827555 AAAAAGAAAGAC
1 AAAAAGAAAGAC
27827567 AAAAAGAAA-AC
1 AAAAAGAAAGAC
27827578 TAAAAAAAGAAAGAC
1 ---AAAAAGAAAGAC
*
27827593 GAAAAGAAA
1 AAAAAGAAA
27827602 ACTAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 2 0.07
12 17 0.57
14 9 0.30
15 2 0.07
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAGAC
Found at i:27827576 original size:26 final size:26
Alignment explanation
Indices: 27827542--27827613 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
27827532 CAATCAAATG
27827542 AAAAA-AAAACTAAAAAAAGAAAGAC
1 AAAAAGAAAACTAAAAAAAGAAAGAC
27827567 AAAAAGAAAACTAAAAAAAGAAAGAC
1 AAAAAGAAAACTAAAAAAAGAAAGAC
* *
27827593 GAAAAGAAAACTAAGAAAAGA
1 AAAAAGAAAACTAAAAAAAGA
27827614 GAGGAGATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 5 0.11
26 39 0.89
ACGTcount: A:0.76, C:0.07, G:0.12, T:0.04
Consensus pattern (26 bp):
AAAAAGAAAACTAAAAAAAGAAAGAC
Found at i:27827610 original size:14 final size:14
Alignment explanation
Indices: 27827541--27827613 Score: 59
Period size: 14 Copynumber: 5.5 Consensus size: 14
27827531 ACAATCAAAT
*
27827541 GAAAAAAAAACTAA
1 GAAAAGAAAACTAA
*
27827555 AAAAAGAAAGAC--A
1 GAAAAGAAA-ACTAA
27827568 -AAAAGAAAACTAA
1 GAAAAGAAAACTAA
*
27827581 AAAAAGAAAGAC---
1 GAAAAGAAA-ACTAA
27827593 GAAAAGAAAACTAA
1 GAAAAGAAAACTAA
27827607 GAAAAGA
1 GAAAAGA
27827614 GAGGAGATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
11 4 0.08
12 16 0.33
13 2 0.04
14 22 0.46
15 4 0.08
ACGTcount: A:0.75, C:0.07, G:0.14, T:0.04
Consensus pattern (14 bp):
GAAAAGAAAACTAA
Found at i:27834170 original size:16 final size:16
Alignment explanation
Indices: 27834147--27834218 Score: 126
Period size: 16 Copynumber: 4.5 Consensus size: 16
27834137 TGTTTGGTTC
27834147 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
27834163 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
27834179 ACTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
27834195 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
27834211 GCTGTAAT
1 GCTGTAAT
27834219 CAGTAATTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.38, C:0.06, G:0.31, T:0.26
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:27834291 original size:44 final size:46
Alignment explanation
Indices: 27834204--27834292 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
27834194 AGCTGTAATG
* *
27834204 GAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGATTGGAATA
1 GAATAGAGCTGTAATCAATAATTCAATTGTTTGGTTGAATGGAATA
*
27834250 GAATAGAGCTGTAAT-AAT-ATTC-TTGTGTTTGGTTGAATGGAAT
1 GAATAGAGCTGTAATCAATAATTCAAT-TGTTTGGTTGAATGGAAT
27834293 GATGCTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 21 0.54
45 2 0.05
46 15 0.38
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (46 bp):
GAATAGAGCTGTAATCAATAATTCAATTGTTTGGTTGAATGGAATA
Found at i:27834457 original size:58 final size:56
Alignment explanation
Indices: 27834388--27834533 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
27834378 AATTTTAATG
*
27834388 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATACTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-CTTTAACATA
* *
27834446 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATCTTTAACATA
*
27834504 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
27834534 TATAATATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.54
59 16 0.20
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATCTTTAACATA
Found at i:27837769 original size:31 final size:31
Alignment explanation
Indices: 27837714--27837792 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
27837704 TAACATAGGT
* *
27837714 ACTTATTTAACTACAA-A-AATAATTTAAGA
1 ACTTATTTAAATAAAATATAATAATTTAAGA
27837743 ACTTATTTAAATAAAATATAATAATTTAAGA
1 ACTTATTTAAATAAAATATAATAATTTAAGA
*
27837774 ACTTATTTAAATAATATAT
1 ACTTATTTAAATAAAATAT
27837793 TAGCCATTGG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 14 0.31
30 1 0.02
31 30 0.67
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (31 bp):
ACTTATTTAAATAAAATATAATAATTTAAGA
Found at i:27838093 original size:10 final size:10
Alignment explanation
Indices: 27838066--27838096 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
27838056 ATCAGCAAAA
27838066 TTCACATAAT
1 TTCACATAAT
27838076 TTCAACATAAT
1 TTC-ACATAAT
27838087 TTCACATAAT
1 TTCACATAAT
27838097 CTCAGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (10 bp):
TTCACATAAT
Found at i:27841564 original size:23 final size:22
Alignment explanation
Indices: 27841507--27841578 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
27841497 TATATTGCTG
* *
27841507 TTTTGATGCTG-TTTTTTACTG
1 TTTTGGTGCTGTTTTTTTACTA
* *
27841528 TTTTGGTTGTTGTTTTTATTATTA
1 TTTTGG-TGCTGTTTTT-TTACTA
27841552 TTTTGGTGCTGTTTTTTTTACTA
1 TTTTGGTGCTG-TTTTTTTACTA
27841575 TTTT
1 TTTT
27841579 ATTTTTTACC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 5 0.12
22 4 0.10
23 17 0.41
24 15 0.37
ACGTcount: A:0.10, C:0.06, G:0.17, T:0.68
Consensus pattern (22 bp):
TTTTGGTGCTGTTTTTTTACTA
Found at i:27841571 original size:26 final size:24
Alignment explanation
Indices: 27841528--27841576 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
27841518 TTTTTTACTG
*
27841528 TTTTGGTTGTTGTTTTTATTATTA
1 TTTTGGTTGTTGTTTTTACTATTA
*
27841552 TTTTGGTGCTGTTTTTTTTACTATT
1 TTTTGGT--TGTTGTTTTTACTATT
27841577 TTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (24 bp):
TTTTGGTTGTTGTTTTTACTATTA
Found at i:27841605 original size:20 final size:20
Alignment explanation
Indices: 27841580--27841619 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
27841570 TACTATTTTA
27841580 TTTTTTACCGTTTCGATGCT
1 TTTTTTACCGTTTCGATGCT
* *
27841600 TTTTTTACTGTTTTGATGCT
1 TTTTTTACCGTTTCGATGCT
27841620 GTTATTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.60
Consensus pattern (20 bp):
TTTTTTACCGTTTCGATGCT
Found at i:27841637 original size:15 final size:15
Alignment explanation
Indices: 27841627--27841682 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
27841617 GCTGTTATTT
27841627 TTGTTATTGTTTTTG
1 TTGTTATTGTTTTTG
27841642 TTGTTATT-TTTGTTG
1 TTGTTATTGTTT-TTG
* *
27841657 CAATTTTTGTTGTTTTTG
1 ---TTGTTATTGTTTTTG
27841675 TTGTTATT
1 TTGTTATT
27841683 TTGCTGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 3 0.09
15 17 0.53
18 9 0.28
19 3 0.09
ACGTcount: A:0.09, C:0.02, G:0.18, T:0.71
Consensus pattern (15 bp):
TTGTTATTGTTTTTG
Found at i:27841646 original size:24 final size:24
Alignment explanation
Indices: 27841599--27841724 Score: 102
Period size: 24 Copynumber: 5.4 Consensus size: 24
27841589 GTTTCGATGC
*
27841599 TTTTT-TTACTGTTTTGATGCTGTTA
1 TTTTTGTTACTGTTTT--TGTTGTTA
*
27841624 TTTTTGTTATTGTTTTTGTTGTTA
1 TTTTTGTTACTGTTTTTGTTGTTA
* **
27841648 TTTTTGTTGCAATTTTTGTTGTT-
1 TTTTTGTTACTGTTTTTGTTGTTA
*
27841671 TTTGTTGTTA----TTTTGCTGTTA
1 TTT-TTGTTACTGTTTTTGTTGTTA
* * *
27841692 TTTTTATTGCTGTTTTGGTTGTTA
1 TTTTTGTTACTGTTTTTGTTGTTA
27841716 TTTTTGTTA
1 TTTTTGTTA
27841725 TTTTGATGTT
Statistics
Matches: 80, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
20 13 0.16
21 3 0.04
23 3 0.04
24 47 0.59
25 5 0.06
26 9 0.11
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.69
Consensus pattern (24 bp):
TTTTTGTTACTGTTTTTGTTGTTA
Found at i:27841684 original size:12 final size:12
Alignment explanation
Indices: 27841619--27841723 Score: 101
Period size: 12 Copynumber: 9.1 Consensus size: 12
27841609 GTTTTGATGC
27841619 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
27841631 TATTGTTTTTGT
1 TGTTATTTTTGT
27841643 TGTTATTTTTGT
1 TGTTATTTTTGT
**
27841655 TGCAATTTTTGT
1 TGTTATTTTTGT
27841667 TG---TTTTTGT
1 TGTTATTTTTGT
*
27841676 TGTTA-TTTTGC
1 TGTTATTTTTGT
*
27841687 TGTTATTTTTAT
1 TGTTATTTTTGT
* * *
27841699 TGCTGTTTTGGT
1 TGTTATTTTTGT
27841711 TGTTATTTTTGT
1 TGTTATTTTTGT
27841723 T
1 T
27841724 ATTTTGATGT
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
9 9 0.12
11 10 0.14
12 54 0.74
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:27841694 original size:44 final size:44
Alignment explanation
Indices: 27841619--27841742 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
27841609 GTTTTGATGC
* * * * *
27841619 TGTTATTTTTGTTATTGTTTTTGTTGTTATTTTTGTTGCAATTTT
1 TGTTGTTTTTGTTGTT-ATTTTGATGTTATTTTTATTGCAATTTT
* **
27841664 TGTTGTTTTTGTTGTTATTTTGCTGTTATTTTTATTGCTGTTTT
1 TGTTGTTTTTGTTGTTATTTTGATGTTATTTTTATTGCAATTTT
*
27841708 GGTTGTTATTT-TTGTTATTTTGATGTTATTTTTAT
1 TGTTGTT-TTTGTTGTTATTTTGATGTTATTTTTAT
27841743 GCGTTTTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 52 0.75
45 17 0.25
ACGTcount: A:0.10, C:0.02, G:0.17, T:0.70
Consensus pattern (44 bp):
TGTTGTTTTTGTTGTTATTTTGATGTTATTTTTATTGCAATTTT
Found at i:27842311 original size:20 final size:20
Alignment explanation
Indices: 27842283--27842330 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
27842273 CTGCTGCTAG
*
27842283 TTTTGTTTCACTTACAACAC
1 TTTTTTTTCACTTACAACAC
*
27842303 TTTTTTTTCACTTACAACTC
1 TTTTTTTTCACTTACAACAC
27842323 TCTTTTTT
1 T-TTTTTT
27842331 GAAAACTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.19, C:0.23, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTTTTTCACTTACAACAC
Found at i:27842547 original size:26 final size:26
Alignment explanation
Indices: 27842493--27842563 Score: 126
Period size: 26 Copynumber: 2.8 Consensus size: 26
27842483 AGATTTGACC
27842493 CTTGATCTTTCACCTACT-AAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
*
27842518 CTTGATCTTTCATCTACTAAAAAACT
1 CTTGATCTTTCACCTACTAAAAAACT
27842544 CTTGATCTTTCACCTACTAA
1 CTTGATCTTTCACCTACTAA
27842564 CTACTAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
25 17 0.40
26 26 0.60
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (26 bp):
CTTGATCTTTCACCTACTAAAAAACT
Found at i:27846918 original size:26 final size:25
Alignment explanation
Indices: 27846864--27846934 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
27846854 AGATTTGACC
*
27846864 CTTGACCTTTCACCTACTAAAAACT
1 CTTGATCTTTCACCTACTAAAAACT
* *
27846889 CTTGATCTTTCATCTATTAAAAAACT
1 CTTGATCTTTCACCTACT-AAAAACT
27846915 CTTGATCTTTCACCTACTAA
1 CTTGATCTTTCACCTACTAA
27846935 CTACTAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.43
26 23 0.57
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (25 bp):
CTTGATCTTTCACCTACTAAAAACT
Found at i:27851588 original size:24 final size:24
Alignment explanation
Indices: 27851552--27851604 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
27851542 CTGCTGCTAG
*
27851552 TTTTGTTTCTCACTTACAACACTA
1 TTTTTTTTCTCACTTACAACACTA
* * * *
27851576 TTTTTTTTTTCACTTTCAACTCTC
1 TTTTTTTTCTCACTTACAACACTA
27851600 TTTTT
1 TTTTT
27851605 CAGCTCACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTTTTTCTCACTTACAACACTA
Found at i:27852691 original size:29 final size:31
Alignment explanation
Indices: 27852657--27852734 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 31
27852647 ATAGCGTTTA
*
27852657 TGATAATTATGTAATTTTCA-AAAG-TTAGG
1 TGATAATTATGTAATTTTAACAAAGTTTAGG
**
27852686 TGATAAAAATGTAATTTTAATCAAAGTTTAGG
1 TGATAATTATGTAATTTTAA-CAAAGTTTAGG
27852718 -GATAATTAATGTAATTT
1 TGATAATT-ATGTAATTT
27852735 ACCCTAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 17 0.43
31 9 0.22
32 14 0.35
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (31 bp):
TGATAATTATGTAATTTTAACAAAGTTTAGG
Found at i:27852717 original size:32 final size:29
Alignment explanation
Indices: 27852665--27852734 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
27852655 TATGATAATT
*
27852665 ATGTAATTTTCAAAAGTTAGGTGATAA-AA
1 ATGTAATTTTAAAAAGTTAGG-GATAATAA
*
27852694 ATGTAATTTTAATCAAAGTTTAGGGATAATTA
1 ATGTAATTTTAA--AAAG-TTAGGGATAATAA
27852726 ATGTAATTT
1 ATGTAATTT
27852735 ACCCTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 11 0.31
31 9 0.26
32 15 0.43
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.40
Consensus pattern (29 bp):
ATGTAATTTTAAAAAGTTAGGGATAATAA
Found at i:27854198 original size:20 final size:22
Alignment explanation
Indices: 27854167--27854209 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
27854157 CGATCTGAAA
*
27854167 CACGATTTTTTTTCAA-TTTTC
1 CACGATTTTTTTTAAAGTTTTC
27854188 CACGA-TTTTTTTAAAGTTTTC
1 CACGATTTTTTTTAAAGTTTTC
27854209 C
1 C
27854210 GAATTATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (22 bp):
CACGATTTTTTTTAAAGTTTTC
Found at i:27863881 original size:23 final size:23
Alignment explanation
Indices: 27863855--27863927 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
27863845 AATAACAACC
* *
27863855 AAAACAGCAGCAAAAATAAAAAA
1 AAAACAGAAACAAAAATAAAAAA
* *
27863878 AAAATAGAAACAAAAATAACAATA
1 AAAACAGAAACAAAAATAA-AAAA
* *
27863902 AAAACAGTACCAAAATAGTAAAAAA
1 AAAACAGAAACAAAA-A-TAAAAAA
27863927 A
1 A
27863928 TAGCACCAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 16 0.41
24 15 0.38
25 5 0.13
26 3 0.08
ACGTcount: A:0.73, C:0.11, G:0.07, T:0.10
Consensus pattern (23 bp):
AAAACAGAAACAAAAATAAAAAA
Found at i:27863906 original size:47 final size:45
Alignment explanation
Indices: 27863843--27863953 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 45
27863833 CCAAACAATC
*
27863843 AAAATAACAACCAAAACAGCAGCAAAAATAAAAAAAAAATAGAAACA
1 AAAATAACAATCAAAACAGCA-CAAAAATAAAAAAAAAATAG-AACA
* * * ** * *
27863890 AAAATAACAATAAAAACAGTACCAAAATAGTAAAAAAATAGCACC
1 AAAATAACAATCAAAACAGCACAAAAATAAAAAAAAAATAGAACA
*
27863935 AAAACAACAATCAAAACAG
1 AAAATAACAATCAAAACAG
27863954 TAAAAACATA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 19 0.35
46 17 0.31
47 18 0.33
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.09
Consensus pattern (45 bp):
AAAATAACAATCAAAACAGCACAAAAATAAAAAAAAAATAGAACA
Found at i:27863950 original size:34 final size:34
Alignment explanation
Indices: 27863912--27864013 Score: 125
Period size: 34 Copynumber: 3.0 Consensus size: 34
27863902 AAAACAGTAC
27863912 CAAAATAGTAAAAAAATAGCACCAAAACAACAAT
1 CAAAATAGTAAAAAAATAGCACCAAAACAACAAT
* * *
27863946 CAAAACAGTAAAAACATAACACCAAAACAACAA-
1 CAAAATAGTAAAAAAATAGCACCAAAACAACAAT
* * * *
27863979 AAAAATAGCAACCAAAACAGCACCAAAACAACAAT
1 CAAAATAGTAA-AAAAATAGCACCAAAACAACAAT
27864014 ATAATTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
33 8 0.14
34 48 0.86
ACGTcount: A:0.65, C:0.23, G:0.05, T:0.08
Consensus pattern (34 bp):
CAAAATAGTAAAAAAATAGCACCAAAACAACAAT
Found at i:27863973 original size:22 final size:23
Alignment explanation
Indices: 27863935--27864000 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
27863925 AAATAGCACC
* * *
27863935 AAAACAACAATCAAAACAGTAAA
1 AAAATAACAACCAAAACAGCAAA
* *
27863958 AACATAAC-ACCAAAACAACAAA
1 AAAATAACAACCAAAACAGCAAA
*
27863980 AAAATAGCAACCAAAACAGCA
1 AAAATAACAACCAAAACAGCA
27864001 CCAAAACAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.50
23 17 0.50
ACGTcount: A:0.67, C:0.23, G:0.05, T:0.06
Consensus pattern (23 bp):
AAAATAACAACCAAAACAGCAAA
Found at i:27866974 original size:16 final size:19
Alignment explanation
Indices: 27866955--27866994 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
27866945 AAATTTTTTA
27866955 TTTTTTATAA-AT-TA-AT
1 TTTTTTATAATATATATAT
27866971 TTTTTTATAATATATATAT
1 TTTTTTATAATATATATAT
27866990 TTTTT
1 TTTTT
27866995 ATTTCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 2 0.10
18 2 0.10
19 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATAATATATATAT
Found at i:27867220 original size:33 final size:33
Alignment explanation
Indices: 27867180--27867264 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
27867170 TGAAAAAATT
27867180 AATATTTTCTAATGTTT-AGATGAATCTATATAA
1 AATATTTTCTAATGTTTGA-ATGAATCTATATAA
* * *
27867213 AATATTTTCTGATGTTTGAATGAATCTGTGTAA
1 AATATTTTCTAATGTTTGAATGAATCTATATAA
**
27867246 AATATTTTCTGGTGTTTGA
1 AATATTTTCTAATGTTTGA
27867265 CAGATTTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 46 0.98
34 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (33 bp):
AATATTTTCTAATGTTTGAATGAATCTATATAA
Found at i:27870314 original size:7 final size:7
Alignment explanation
Indices: 27870274--27870314 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
27870264 AAATCGGAAC
27870274 GAAGGAG
1 GAAGGAG
27870281 GAA-GAG
1 GAAGGAG
*
27870287 GAAGGGG
1 GAAGGAG
27870294 GAAGG-G
1 GAAGGAG
27870300 GAAGGGAG
1 GAA-GGAG
27870308 GAAGGAG
1 GAAGGAG
27870315 AAGAGAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
6 10 0.33
7 16 0.53
8 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (7 bp):
GAAGGAG
Found at i:27873220 original size:27 final size:27
Alignment explanation
Indices: 27873177--27873266 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
27873167 TTGTTTCAGA
**
27873177 TTTTAAGGGACTTAAAAAATAATCAAC
1 TTTTAAGGGACAAAAAAAATAATCAAC
* **
27873204 TTTTAAGGGACAAAAAAAA-ATTCAGT
1 TTTTAAGGGACAAAAAAAATAATCAAC
* *
27873230 TTTTAAGGAGTCCAAAAAAATATTTATCAAC
1 TTTTAAGG-G-ACAAAAAAA-A-TAATCAAC
27873261 TTTTAA
1 TTTTAA
27873267 AAGGCTTAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 12 0.25
27 18 0.38
28 8 0.17
29 1 0.02
31 9 0.19
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (27 bp):
TTTTAAGGGACAAAAAAAATAATCAAC
Found at i:27873233 original size:26 final size:27
Alignment explanation
Indices: 27873171--27873237 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
27873161 TTAAATTTGT
*
27873171 TTCAGATTTTAAGGGACTTAAAAAATAA
1 TTCAGATTTTAAGGGAC-TAAAAAAAAA
27873199 -TCA-ACTTTTAAGGGAC-AAAAAAAAA
1 TTCAGA-TTTTAAGGGACTAAAAAAAAA
*
27873224 TTCAGTTTTTAAGG
1 TTCAGATTTTAAGG
27873238 AGTCCAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
25 8 0.24
26 12 0.35
27 14 0.41
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (27 bp):
TTCAGATTTTAAGGGACTAAAAAAAAA
Found at i:27874753 original size:27 final size:27
Alignment explanation
Indices: 27874715--27874831 Score: 182
Period size: 27 Copynumber: 4.3 Consensus size: 27
27874705 GTATAAATGG
27874715 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
27874742 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
27874769 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
** *
27874796 GTGGTGCCTTTCT-ATCAGGTGGCACCA
1 GTGGTGCCTACCTGA-CAGGCGGCACCA
27874823 GTGGTGCCT
1 GTGGTGCCT
27874832 TTCTATCAGG
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:27874832 original size:27 final size:27
Alignment explanation
Indices: 27874715--27874849 Score: 175
Period size: 27 Copynumber: 5.0 Consensus size: 27
27874705 GTATAAATGG
27874715 GTGGTGCCTACCTGA-CAGGCGGCACCA
1 GTGGTGCCTACCT-ATCAGGCGGCACCA
27874742 GTGGTGCCTACCTGA-CAGGCGGCACCA
1 GTGGTGCCTACCT-ATCAGGCGGCACCA
*
27874769 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
** *
27874796 GTGGTGCCTTTCTATCAGGTGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
** *
27874823 GTGGTGCCTTTCTATCAGGTGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
27874850 ACTCGTATTT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTATCAGGCGGCACCA
Found at i:27875120 original size:57 final size:55
Alignment explanation
Indices: 27875006--27875136 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
27874996 AAAAATTAAA
* * *
27875006 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
27875061 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
27875118 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
27875137 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:27875240 original size:27 final size:27
Alignment explanation
Indices: 27875202--27875289 Score: 176
Period size: 27 Copynumber: 3.3 Consensus size: 27
27875192 TTTTACAAGA
27875202 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACTGGGTAGGCGGCACTAGT
27875229 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACTGGGTAGGCGGCACTAGT
27875256 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACTGGGTAGGCGGCACTAGT
27875283 GGTGCCT
1 GGTGCCT
27875290 TTGTCAATGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.14, C:0.23, G:0.41, T:0.23
Consensus pattern (27 bp):
GGTGCCTACTGGGTAGGCGGCACTAGT
Found at i:27875359 original size:25 final size:25
Alignment explanation
Indices: 27875324--27875373 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
27875314 CAGATCTGTT
27875324 TAACAGCAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
*
27875349 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
27875374 AGGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGCAAATTTTTGAAGAAGGAA
Found at i:27875421 original size:26 final size:26
Alignment explanation
Indices: 27875364--27875421 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
27875354 GTAAATTTTT
* * *
27875364 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
27875390 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
27875416 GCAGAA
1 GAAGAA
27875422 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:27878222 original size:28 final size:28
Alignment explanation
Indices: 27878169--27878226 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
27878159 CATTTTTCTG
*
27878169 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
27878197 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
27878225 TT
1 TT
27878227 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:27878267 original size:26 final size:26
Alignment explanation
Indices: 27878218--27878267 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
27878208 TCTATTTAAA
* *
27878218 TTTGAATTTATTTAATAGTTTTTATG
1 TTTGAATTAATTTAATAGTGTTTATG
27878244 TTTGAATTAATTTAATTAG-GTTTA
1 TTTGAATTAATTTAA-TAGTGTTTA
27878268 GCAAATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (26 bp):
TTTGAATTAATTTAATAGTGTTTATG
Found at i:27878344 original size:6 final size:6
Alignment explanation
Indices: 27878333--27878391 Score: 93
Period size: 6 Copynumber: 9.8 Consensus size: 6
27878323 ATATTTGCAT
*
27878333 ACATAA ACATAA ATA-AGA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATA-A ACATAA ACATAA ACATAA ACATAA ACATAA
27878381 ACATAA ACATA
1 ACATAA ACATA
27878392 TTTAATGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 1 0.02
6 47 0.96
7 1 0.02
ACGTcount: A:0.66, C:0.15, G:0.02, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:27878833 original size:6 final size:6
Alignment explanation
Indices: 27878824--27878850 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
27878814 CTGCGACTGC
27878824 GGCTCA GGCTCA GGCTCA GGCTCA GGC
1 GGCTCA GGCTCA GGCTCA GGCTCA GGC
27878851 GGCTGAAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (6 bp):
GGCTCA
Found at i:27880816 original size:17 final size:16
Alignment explanation
Indices: 27880784--27880815 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27880774 TTTTTTTTTA
27880784 AAAATATTTAATATAT
1 AAAATATTTAATATAT
27880800 AAAATATTTAA-ATAT
1 AAAATATTTAATATAT
27880815 A
1 A
27880816 TCAATTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:27881424 original size:27 final size:27
Alignment explanation
Indices: 27881411--27881472 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
27881401 CTGGTAGGTT
27881411 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
27881438 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
27881465 GGCACCAC
1 GGCACCAC
27881473 CCAAAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.10
Consensus pattern (27 bp):
GGCACCACTGGTGCCGCCTACCAGACA
Found at i:27884146 original size:108 final size:107
Alignment explanation
Indices: 27883952--27884162 Score: 368
Period size: 108 Copynumber: 2.0 Consensus size: 107
27883942 AAAGTAATAA
* **
27883952 GAGACTACATTTTTACTTTGATAGTTTTAGGATGATTATTTTGAAAGACGTTTTTTATGTACCTA
1 GAGACTACATTTTTACTTTGATAGTTTTAAGATGATTATTTCAAAAGACGTTTTTTATGTACCTA
* *
27884017 ATTTTAGGAGGAATTTAATTTTAGTTGCGTGTTTATTTCAAG
66 ATTTTAGGAGGAACTTAATTTTAGTTGAGTGTTTATTTCAAG
27884059 GAGACGTACATTTTTACTTTGATAGTTTTAAGATGATTATTTCAAAAGACGTTTTTTATGTACCT
1 GAGAC-TACATTTTTACTTTGATAGTTTTAAGATGATTATTTCAAAAGACGTTTTTTATGTACCT
27884124 AATTTTAGGAGGAACTTAATTTTAGTTGAGTGTTTATTT
65 AATTTTAGGAGGAACTTAATTTTAGTTGAGTGTTTATTT
27884163 TAAGATGGTT
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 5 0.05
108 93 0.95
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (107 bp):
GAGACTACATTTTTACTTTGATAGTTTTAAGATGATTATTTCAAAAGACGTTTTTTATGTACCTA
ATTTTAGGAGGAACTTAATTTTAGTTGAGTGTTTATTTCAAG
Found at i:27898979 original size:6 final size:6
Alignment explanation
Indices: 27898971--27899007 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
27898961 TTGAGGTTGA
*
27898971 GGCTGA GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG G
1 GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG GGCTGG G
27899008 ATAATAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.03, C:0.16, G:0.65, T:0.16
Consensus pattern (6 bp):
GGCTGG
Found at i:27898986 original size:12 final size:12
Alignment explanation
Indices: 27898953--27899007 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
27898943 ATTGTGAAAC
*
27898953 GGCTGGGGTTGA
1 GGCTGGGGCTGA
* *
27898965 GGTTGAGGCTGA
1 GGCTGGGGCTGA
*
27898977 GGCTGGGGCTGG
1 GGCTGGGGCTGA
*
27898989 GGCTGGGGCTGG
1 GGCTGGGGCTGA
27899001 GGCTGGG
1 GGCTGGG
27899008 ATAATAGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.05, C:0.13, G:0.62, T:0.20
Consensus pattern (12 bp):
GGCTGGGGCTGA
Found at i:27900607 original size:40 final size:40
Alignment explanation
Indices: 27900552--27900643 Score: 175
Period size: 40 Copynumber: 2.3 Consensus size: 40
27900542 ATGGGCCTAG
*
27900552 TCAAGTTAGACAGTTAGGATCGGGTTTTGGATGTTCAAGC
1 TCAAGCTAGACAGTTAGGATCGGGTTTTGGATGTTCAAGC
27900592 TCAAGCTAGACAGTTAGGATCGGGTTTTGGATGTTCAAGC
1 TCAAGCTAGACAGTTAGGATCGGGTTTTGGATGTTCAAGC
27900632 TCAAGCTAGACA
1 TCAAGCTAGACA
27900644 TGCATTTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (40 bp):
TCAAGCTAGACAGTTAGGATCGGGTTTTGGATGTTCAAGC
Found at i:27901331 original size:12 final size:12
Alignment explanation
Indices: 27901314--27901340 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27901304 ATTATTTTTG
27901314 AAAATAAAAAAA
1 AAAATAAAAAAA
27901326 AAAATAAAAAAA
1 AAAATAAAAAAA
27901338 AAA
1 AAA
27901341 TAGAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAATAAAAAAA
Found at i:27902856 original size:21 final size:20
Alignment explanation
Indices: 27902824--27902862 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
27902814 TTAAAATTTT
* *
27902824 AAAAAATTAAAAATTATTAA
1 AAAAAATAAAAAAATATTAA
27902844 AAAAACATAAAAAAATATT
1 AAAAA-ATAAAAAAATATT
27902863 TGTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAAAAAAATATTAA
Found at i:27904544 original size:40 final size:40
Alignment explanation
Indices: 27904469--27904570 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
27904459 TTTGGAAAGA
* * ** *
27904469 AAACGCCGCAAAAGGTAAATCAATAGCGGTATTTTTCGAT
1 AAACGCCGCAAAAGGTAAAGCAATAACGACATTTTTAGAT
* *
27904509 AAAC-CTCGCAAAAGGTAAAGCAATAACGACGTTTTTATAT
1 AAACGC-CGCAAAAGGTAAAGCAATAACGACATTTTTAGAT
*
27904549 AAACGCCGCCAAAGGTAAAGCA
1 AAACGCCGCAAAAGGTAAAGCA
27904571 GTAGCGACCT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
39 1 0.02
40 50 0.96
41 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAATAACGACATTTTTAGAT
Found at i:27904677 original size:41 final size:41
Alignment explanation
Indices: 27904576--27904678 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
27904566 AAGCAGTAGC
*
27904576 GACCTTTGGCGGCGTTTATAGAAAAAGCATCGCTAATGCTCT
1 GACCTTTAGCGGCGTTTAT-GAAAAAGCATCGCTAATGCTCT
* * ** * *
27904618 GA-CTTTAGTGGCGCTTATGGGAAAGCGTCGTTAATGCTCT
1 GACCTTTAGCGGCGTTTATGAAAAAGCATCGCTAATGCTCT
27904658 GACCTTTAGCGGCGTTTATGA
1 GACCTTTAGCGGCGTTTATGA
27904679 TGAAGCGTCG
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 20 0.40
41 28 0.56
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (41 bp):
GACCTTTAGCGGCGTTTATGAAAAAGCATCGCTAATGCTCT
Found at i:27904685 original size:41 final size:41
Alignment explanation
Indices: 27904576--27904694 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
27904566 AAGCAGTAGC
* * *
27904576 GACCTTTGGCGGCGTTTATAGAAAAAGCATCGCTAATGCTCT
1 GACCTTTAGCGGCGTTTAT-GAAGAAGCGTCGCTAATGCTCT
* * * *
27904618 GA-CTTTAGTGGCGCTTATG-GGAAAGCGTCGTTAATGCTCT
1 GACCTTTAGCGGCGTTTATGAAG-AAGCGTCGCTAATGCTCT
* *
27904658 GACCTTTAGCGGCGTTTATGATGAAGCGTCGCAAATG
1 GACCTTTAGCGGCGTTTATGAAGAAGCGTCGCTAATG
27904695 GCAGGGCATT
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
40 19 0.31
41 40 0.65
42 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (41 bp):
GACCTTTAGCGGCGTTTATGAAGAAGCGTCGCTAATGCTCT
Found at i:27904978 original size:41 final size:41
Alignment explanation
Indices: 27904781--27904978 Score: 173
Period size: 41 Copynumber: 4.8 Consensus size: 41
27904771 TAAGGATATG
* * *
27904781 GGCATTAGCGGCGCTTTAC-CATAAGTGTCACTAAAGGTCAG
1 GGCATTAGCGGCGCTTT-CTCATAAGCGTCGCTAAAGGTCAA
* * * * *
27904822 GGTATTAGCGGTGCTTTTTCATAAGCGTCGCTAAAGATTAA
1 GGCATTAGCGGCGCTTTCTCATAAGCGTCGCTAAAGGTCAA
* * * * ** ** * *
27904863 GGCATTAGCGGTGCTTTTTTACAAGCACCATTAGAGGTCAG
1 GGCATTAGCGGCGCTTTCTCATAAGCGTCGCTAAAGGTCAA
* * *
27904904 GGCATTAGCGGCGCTTTCCCACAAGCGTTGCTAAAGGTCAA
1 GGCATTAGCGGCGCTTTCTCATAAGCGTCGCTAAAGGTCAA
* *
27904945 GGCATTAGCGGCGCTTTCTCATAAACGCCGCTAA
1 GGCATTAGCGGCGCTTTCTCATAAGCGTCGCTAA
27904979 TGCCCTGATC
Statistics
Matches: 121, Mismatches: 35, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
41 121 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (41 bp):
GGCATTAGCGGCGCTTTCTCATAAGCGTCGCTAAAGGTCAA
Found at i:27905095 original size:10 final size:10
Alignment explanation
Indices: 27905060--27905108 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
27905050 AAACGCCATT
*
27905060 AATTTAATTA
1 AATTAAATTA
*
27905070 AATTATA-TA
1 AATTAAATTA
*
27905079 TATTAAATTA
1 AATTAAATTA
27905089 AATTAAATTA
1 AATTAAATTA
27905099 AATT-AATTA
1 AATTAAATTA
27905108 A
1 A
27905109 TACTTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 13 0.39
10 20 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AATTAAATTA
Found at i:27905106 original size:19 final size:19
Alignment explanation
Indices: 27905057--27905108 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
27905047 CATAAACGCC
* *
27905057 ATTAATTTAATTAAATTAT
1 ATTAAATTAATTAAATTAA
*
27905076 A-TATATTAAATTAAATTAA
1 ATTAAATT-AATTAAATTAA
27905095 ATTAAATTAATTAA
1 ATTAAATTAATTAA
27905109 TACTTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 4 0.15
19 18 0.67
20 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAATTAATTAAATTAA
Found at i:27905866 original size:168 final size:168
Alignment explanation
Indices: 27905588--27905919 Score: 511
Period size: 168 Copynumber: 2.0 Consensus size: 168
27905578 AGCAGCTGGA
** *
27905588 ACAGTAACAATGAAAATGGTGCCCTCTTTACTGAGATTATATGAACAAATGCCCGAACCTAAATA
1 ACAGTAACAATGAAAATGGCACCCTCTTTACTGAGATTACATGAACAAATGCCCGAACCTAAATA
* ** *
27905653 TGTTATTGCTATGGGCGCGTGTAGAATTGTAGGAGGGATGTTCAGTATTGATTCTTATAGTACTG
66 TGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAGTACTG
* *
27905718 TTCGGGGGGTCAATAAGCTAATTCCCGTGGATGTCTAT
131 TTCGGGGGATCAATAAACTAATTCCCGTGGATGTCTAT
* * *
27905756 ACAGTAACAATGAAAATGGCACCCTTTTTAGTGAGATTACATGAACAAATGCCCGAACCTCAATA
1 ACAGTAACAATGAAAATGGCACCCTCTTTACTGAGATTACATGAACAAATGCCCGAACCTAAATA
* *
27905821 TGTTATTGCTATGGGCGCGTGTACAATTACAGGATGGATGTTCAGTACTGATTCTTATAGTCCTG
66 TGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAGTACTG
** *
27905886 TTCGGGGGATGGATAAACTAATTTCCGTGGATGT
131 TTCGGGGGATCAATAAACTAATTCCCGTGGATGT
27905920 TTATTTGTCG
Statistics
Matches: 147, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
168 147 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (168 bp):
ACAGTAACAATGAAAATGGCACCCTCTTTACTGAGATTACATGAACAAATGCCCGAACCTAAATA
TGTTATTGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAGTACTG
TTCGGGGGATCAATAAACTAATTCCCGTGGATGTCTAT
Found at i:27906153 original size:19 final size:18
Alignment explanation
Indices: 27906100--27906153 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
27906090 TTCTAAATCG
27906100 AAATATATTAATATAAATAT
1 AAATATATTAAT-T-AATAT
* *
27906120 AAAAATATAATATTAATAT
1 AAATATATTA-ATTAATAT
27906139 AAATATTATTAATTA
1 AAATA-TATTAATTA
27906154 CTTAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 13 0.46
20 13 0.46
21 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATATTAATTAATAT
Done.