Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 54
Found at i:5016678 original size:24 final size:24
Alignment explanation
Indices: 5016642--5016713 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
5016632 CAGAGATATC
*
5016642 AGAAATCAA-AACAGAATTCAAATC
1 AGAAAT-AAGAACAGAATTCAAATA
*
5016666 AGATATAAGAACAGAATTCAAATA
1 AGAAATAAGAACAGAATTCAAATA
* * *
5016690 AGAAATTAGAAAAAAATTCAAATA
1 AGAAATAAGAACAGAATTCAAATA
5016714 TAAAATTAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 39 0.95
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (24 bp):
AGAAATAAGAACAGAATTCAAATA
Found at i:5016719 original size:24 final size:25
Alignment explanation
Indices: 5016680--5016734 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
5016670 ATAAGAACAG
5016680 AATTCAAATAAGAAATTAGA-AAAA
1 AATTCAAATAAGAAATTAGATAAAA
5016704 AATTCAAATATA-AAATTAGATAAAA
1 AATTCAAATA-AGAAATTAGATAAAA
*
5016729 TATTCA
1 AATTCA
5016735 TGTGATTACG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (25 bp):
AATTCAAATAAGAAATTAGATAAAA
Found at i:5022172 original size:32 final size:31
Alignment explanation
Indices: 5022136--5022209 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
5022126 CCCGGAAAAA
5022136 GTCAACGGTCGT-TCAATGACCGGTCAACGCCG
1 GTCAACGGTC-TATCAATG-CCGGTCAACGCCG
* * **
5022168 GTCAAAGTTCTAGTCAATGGTGGTCAACGCCG
1 GTCAACGGTCTA-TCAATGCCGGTCAACGCCG
5022200 GTCAACGGTC
1 GTCAACGGTC
5022210 AACACTGGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.03
32 27 0.79
33 6 0.18
ACGTcount: A:0.23, C:0.27, G:0.28, T:0.22
Consensus pattern (31 bp):
GTCAACGGTCTATCAATGCCGGTCAACGCCG
Found at i:5028282 original size:21 final size:21
Alignment explanation
Indices: 5028240--5028294 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
5028230 AAGGCCTTAT
*
5028240 CCTTTTGATGAAAAGTGATTAA
1 CCTTTTCATG-AAAGTGATTAA
5028262 CCTTTTCATGAAAG-GATTTAA
1 CCTTTTCATGAAAGTGA-TTAA
*
5028283 TCTTTTCATGAA
1 CCTTTTCATGAA
5028295 GAGAATTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 19 0.63
22 9 0.30
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (21 bp):
CCTTTTCATGAAAGTGATTAA
Found at i:5031886 original size:21 final size:21
Alignment explanation
Indices: 5031862--5031901 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5031852 GGGTTAAGAC
*
5031862 CTTTCAATGAAATGACTTAAT
1 CTTTCAATGAAAGGACTTAAT
*
5031883 CTTTCAATTAAAGGACTTA
1 CTTTCAATGAAAGGACTTA
5031902 CCCTTTTGAT
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:0.15, G:0.10, T:0.38
Consensus pattern (21 bp):
CTTTCAATGAAAGGACTTAAT
Found at i:5031907 original size:21 final size:21
Alignment explanation
Indices: 5031860--5031907 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
5031850 AAGGGTTAAG
*
5031860 ACCTTTCAATGAAATGACTTA
1 ACCTTTCAATGAAAGGACTTA
* *
5031881 ATCTTTCAATTAAAGGACTTA
1 ACCTTTCAATGAAAGGACTTA
*
5031902 CCCTTT
1 ACCTTT
5031908 TGATGAAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (21 bp):
ACCTTTCAATGAAAGGACTTA
Found at i:5035746 original size:18 final size:19
Alignment explanation
Indices: 5035725--5035775 Score: 50
Period size: 22 Copynumber: 2.6 Consensus size: 19
5035715 AATTTGAGAT
*
5035725 AATTTCTTATTT-TGACTA
1 AATTTATTATTTGTGACTA
5035743 AATTTATTATGTTTTGTGACTA
1 AATTTATTA---TTTGTGACTA
*
5035765 AATTTGTTATT
1 AATTTATTATT
5035776 GTAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
21 3 0.11
22 14 0.52
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (19 bp):
AATTTATTATTTGTGACTA
Found at i:5037455 original size:23 final size:23
Alignment explanation
Indices: 5037429--5037473 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5037419 CACCACAGCT
*
5037429 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
5037452 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
5037474 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:5037691 original size:149 final size:148
Alignment explanation
Indices: 5037441--5037754 Score: 488
Period size: 149 Copynumber: 2.1 Consensus size: 148
5037431 TATAATTGCA
5037441 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
* * * * * *
5037505 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCACAAATGTT
*
5037570 C-CACAGAATATATATATATC
129 CTCA-AGAATATACATATATC
*
5037590 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCCTAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
5037655 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTCT
66 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCT
* *
5037720 GAAGAATATACATATGTC
131 CAAGAATATACATATATC
5037738 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
5037755 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
148 47 0.31
149 105 0.69
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCT
CAAGAATATACATATATC
Found at i:5039434 original size:64 final size:63
Alignment explanation
Indices: 5039336--5039496 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
5039326 TAATGAAGGT
* * *
5039336 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT--
*
5039399 GG
62 GC
*
5039401 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATGC
* *
5039465 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
5039497 CTTAAACAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATGC
Found at i:5040613 original size:20 final size:21
Alignment explanation
Indices: 5040588--5040626 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5040578 CACATAGACG
*
5040588 TTAACATCA-ATTTTCATCAC
1 TTAACATCATAATTTCATCAC
5040608 TTAACATCATAATTTCATC
1 TTAACATCATAATTTCATC
5040627 TCTAAATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAACATCATAATTTCATCAC
Found at i:5042871 original size:23 final size:23
Alignment explanation
Indices: 5042845--5042889 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5042835 CACCACAGCT
* *
5042845 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
*
5042868 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
5042890 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:5043107 original size:149 final size:148
Alignment explanation
Indices: 5042857--5043170 Score: 488
Period size: 149 Copynumber: 2.1 Consensus size: 148
5042847 TATAATTGCA
5042857 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
* * * * * *
5042921 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCACAAATGTT
*
5042986 CC-ACAGAATATATATATATC
129 CCGA-AGAATATACATATATC
* *
5043006 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCCTAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
5043071 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTCC
66 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCC
*
5043136 GAAGAATATACATATGTC
131 GAAGAATATACATATATC
5043154 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
5043171 CCCTCGACTC
Statistics
Matches: 152, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
148 48 0.32
149 104 0.68
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCC
GAAGAATATACATATATC
Found at i:5044850 original size:64 final size:63
Alignment explanation
Indices: 5044752--5044912 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
5044742 TAATGAAGGT
* * *
5044752 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAAT--
*
5044815 GG
62 GC
*
5044817 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATGC
* *
5044881 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
5044913 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCCATTCGATGTTTTCTATTTAAATGC
Found at i:5047138 original size:29 final size:28
Alignment explanation
Indices: 5047104--5047164 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
5047094 TCCTTTTCTG
*
5047104 ATATTTCTA-AATAAATAAATATTTTATTT
1 ATATTT-TATAATAAATAAATATATT-TTT
* *
5047133 ATATTTTATTATATATAAATATATTTTT
1 ATATTTTATAATAAATAAATATATTTTT
5047161 ATAT
1 ATAT
5047165 AATTATAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATTTTATAATAAATAAATATATTTTT
Found at i:5052848 original size:165 final size:165
Alignment explanation
Indices: 5052576--5052872 Score: 443
Period size: 165 Copynumber: 1.8 Consensus size: 165
5052566 AGGCTGAAGG
*
5052576 GATCCAAGCTCGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGTTATTTGCCATG
1 GATCCAAGCTCGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGCTATTTGCCATG
* * * *
5052641 GGCAGATTTATCAAAAACGGATGATGAAATATCATAACAAGAAAGTACATCCAAGAGAGTTCCAA
66 AGCAGATGTATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCAAGAGAGTTCCAA
5052706 GATGTTGATCTAGTGCTGAAAAAGGAGACTGAATA
131 GATGTTGATCTAGTGCTGAAAAAGGAGACTGAATA
* *** *
5052741 GATCCAAGCTTGATTTGATCAATTAAGTTTTATTGATGAGAATG-TATTGAAAGCTATTTGCCAT
1 GATCCAAGCTCGATTTGATCAATTAAACCTTATTGATGAG-ATGAGATTGAAAGCTATTTGCCAT
* ** **
5052805 GAGCAGATGTATCAGAAGTGGATGATGAAAGATCACAACAAGAAAGTACATCTGAGAGAGTTCCA
65 GAGCAGATGTATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCAAGAGAGTTCCA
5052870 AGA
130 AGA
5052873 GAGCGATCTA
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
165 113 0.97
166 3 0.03
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (165 bp):
GATCCAAGCTCGATTTGATCAATTAAACCTTATTGATGAGATGAGATTGAAAGCTATTTGCCATG
AGCAGATGTATCAAAAACGGATGATGAAAGATCACAACAAGAAAGTACATCCAAGAGAGTTCCAA
GATGTTGATCTAGTGCTGAAAAAGGAGACTGAATA
Found at i:5053088 original size:9 final size:8
Alignment explanation
Indices: 5053066--5053114 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
5053056 TTATGCTTGA
*
5053066 AAAAAAAT
1 AAAAAAAG
5053074 ATAAAAAATG
1 A-AAAAAA-G
5053084 AAAAAAAAG
1 -AAAAAAAG
5053093 AAAAAAAG
1 AAAAAAAG
5053101 -AAAAAAG
1 AAAAAAAG
5053108 AAAAAAA
1 AAAAAAA
5053115 AATTGAACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 7 0.19
8 15 0.42
9 7 0.19
10 6 0.17
11 1 0.03
ACGTcount: A:0.86, C:0.00, G:0.08, T:0.06
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5053089 original size:17 final size:17
Alignment explanation
Indices: 5053064--5053116 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
5053054 TATTATGCTT
*
5053064 GAAAAAAAATATAAAAAA
1 GAAAAAAAAGA-AAAAAA
5053082 TGAAAAAAAAGAAAAAAA
1 -GAAAAAAAAGAAAAAAA
5053100 GAAAAAAGAA-AAAAAAA
1 GAAAAAA-AAGAAAAAAA
5053117 TTGAACCAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 14 0.44
18 8 0.25
19 10 0.31
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAGAAAAAAA
Found at i:5053096 original size:15 final size:15
Alignment explanation
Indices: 5053086--5053114 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5053076 AAAAAATGAA
5053086 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
5053101 AAAAAAGAAAAAAA
1 AAAAAAGAAAAAAA
5053115 AATTGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:5053115 original size:9 final size:9
Alignment explanation
Indices: 5053064--5053115 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
5053054 TATTATGCTT
5053064 GAAAAAAAA
1 GAAAAAAAA
* *
5053073 TATAAAAAAT
1 GA-AAAAAAA
5053083 GAAAAAAAA
1 GAAAAAAAA
5053092 G-AAAAAAA
1 GAAAAAAAA
5053100 G--AAAAAA
1 GAAAAAAAA
5053107 GAAAAAAAA
1 GAAAAAAAA
5053116 ATTGAACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 7 0.19
8 8 0.22
9 14 0.39
10 7 0.19
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.06
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:5055444 original size:114 final size:114
Alignment explanation
Indices: 5055244--5055463 Score: 368
Period size: 114 Copynumber: 1.9 Consensus size: 114
5055234 CACGTTCTCG
* * *
5055244 TAGTAGAAATAATGAGACCCGATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
5055309 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTAA
*
5055358 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
5055423 GGTAGGAACCCCAGAACCAATCATTGGAATTAAAAGATGAA
66 GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAA
5055464 CTGCATGATC
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTGGAATTAAAAGATGAATTTGCTAA
Found at i:5057989 original size:22 final size:22
Alignment explanation
Indices: 5057963--5058035 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
5057953 ATCTACACTC
5057963 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
5057985 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
5058007 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
5058029 TTCAAAG
1 TTCAAAG
5058036 TTGAAAGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:5058813 original size:168 final size:165
Alignment explanation
Indices: 5058533--5058857 Score: 569
Period size: 168 Copynumber: 2.0 Consensus size: 165
5058523 AGAATGAGCA
5058533 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACGA
* *
5058598 TTTCCATAGTTTCTCATTTTATCCTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTCC
66 TTTCCATAATTTCTCATTTTATCCTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
5058663 TTAGTTTTTTTTTACTTAGTAAACTATTTCCAATAGCC
131 TTAG---TTTTTTACTTAGTAAACTATTTCCAATAGCC
*
5058701 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTGAAAAAAATAATGAGAAAACGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACGA
* *
5058766 TTTCCATAATTTCTCATTTTATCTTTTCTAAAATGAAATTTTTGAAAAGTAAGAAAACGATTTCC
66 TTTCCATAATTTCTCATTTTATCCTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
*
5058831 TTAGTTTTTTACTTATTAAACTATTTC
131 TTAGTTTTTTACTTAGTAAACTATTTC
5058858 GCACATCTGT
Statistics
Matches: 151, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
165 22 0.15
168 129 0.85
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (165 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACGA
TTTCCATAATTTCTCATTTTATCCTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
TTAGTTTTTTACTTAGTAAACTATTTCCAATAGCC
Found at i:5059069 original size:76 final size:76
Alignment explanation
Indices: 5058861--5059072 Score: 406
Period size: 76 Copynumber: 2.8 Consensus size: 76
5058851 CTATTTCGCA
*
5058861 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGACGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5058926 AGCCTTAGGGT
66 AGCCTTAGGGT
*
5058937 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5059002 AGCCTTAGGGT
66 AGCCTTAGGGT
5059013 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTT
5059073 GTTATTTTGA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 133 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:5059358 original size:75 final size:75
Alignment explanation
Indices: 5059197--5059405 Score: 366
Period size: 75 Copynumber: 2.8 Consensus size: 75
5059187 CTATTTCCCA
5059197 CATCTGTAAGTCCTACAGTGCATGATGTTTACAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTT-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5059262 AGCCTTAGGGT
65 AGCCTTAGGGT
* *
5059273 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAGGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTT-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5059337 AGCCTTAGGGT
65 AGCCTTAGGGT
*
5059348 CATCTGTAAGTCCTACAGTGCATGGTGTTTCAAAAAGCCTTCGGGAGCTTTTTGATGT
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATGT
5059406 GTATTTGAAA
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
74 17 0.13
75 63 0.50
76 46 0.37
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (75 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGT
Found at i:5059608 original size:76 final size:76
Alignment explanation
Indices: 5059522--5059714 Score: 327
Period size: 76 Copynumber: 2.6 Consensus size: 76
5059512 TTCCCACATT
* *
5059522 TGTAATTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAAAGCC
5059587 TTAGGGTCATC
66 TTAGGGTCATC
*
5059598 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAAAGCC
5059663 TTAGGGTCATC
66 TTAGGGTCATC
*
5059674 TGTAAGTCCTTCAGTGCATGATGTTT-TCAAAAA-CCTTCGGG
1 TGTAAGTCCTACAGTGCATGATGTTTCT-AAAAAGCCTTCGGG
5059715 TCGTCTGTAA
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
75 8 0.07
76 103 0.93
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
TGTAAGTCCTACAGTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTACAAAGCC
TTAGGGTCATC
Found at i:5059722 original size:46 final size:46
Alignment explanation
Indices: 5059647--5059842 Score: 306
Period size: 46 Copynumber: 4.3 Consensus size: 46
5059637 GGGAGCTTTT
* * *
5059647 TGATGTTTAC-AAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
*
5059692 TGATGTTTTCAAAAACCTTCGGGTCGTCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
5059738 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
* *
5059784 TGATGTTTTC-AAAACTTTCGGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTC-GGGTCATCTGTAAGTCCTTCAGTGCA
*
5059830 TGGTGTTTTCAAA
1 TGATGTTTTCAAA
5059843 CATTTCCATC
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
45 17 0.12
46 121 0.86
47 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
Found at i:5060007 original size:3 final size:3
Alignment explanation
Indices: 5060001--5060054 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
5059991 AATAATAATA
* * * *
5060001 ATT ATT ATT ATT ATT AAT ATT AAT ATT AAT ATT AAT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
5060047 ATTT ATT A
1 A-TT ATT A
5060055 AATATTACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:5060010 original size:6 final size:6
Alignment explanation
Indices: 5059976--5060061 Score: 75
Period size: 6 Copynumber: 13.8 Consensus size: 6
5059966 AATTTAAATT
* * * * *
5059976 TATTAT TATTAA -AATAA TAATAA TAATTAT TATTAT TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA T-ATTAA TATTAA TATTAA TATTAA
*
5060024 TATTAA TATTAA TATTATA TATTATT TATTAAA TATTA
1 TATTAA TATTAA TATTA-A TATTA-A TATT-AA TATTA
5060062 CAAAGCCCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.06
6 45 0.65
7 19 0.28
8 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAA
Found at i:5061245 original size:15 final size:15
Alignment explanation
Indices: 5061227--5061266 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
5061217 AAAAATCCTA
5061227 TTATAAAAATTAATT
1 TTATAAAAATTAATT
* *
5061242 TTATATAAATTACTT
1 TTATAAAAATTAATT
*
5061257 TTAGAAAAAT
1 TTATAAAAAT
5061267 AATCATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TTATAAAAATTAATT
Found at i:5061539 original size:25 final size:25
Alignment explanation
Indices: 5061483--5061529 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5061473 TTCTAAATAA
*
5061483 ATAAATATTTATTTATATTTTATAT
1 ATAAATATTTATTTATATATTATAT
5061508 ATAAATATTT-TTTATA-ATTATA
1 ATAAATATTTATTTATATATTATA
5061530 CTTTGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATAAATATTTATTTATATATTATAT
Found at i:5061773 original size:164 final size:165
Alignment explanation
Indices: 5061502--5061832 Score: 603
Period size: 164 Copynumber: 2.0 Consensus size: 165
5061492 TATTTATATT
*
5061502 TTATATATAAATATTTTTTATAATTATACTTTGAAATAATAGGATTATAAATTAAATATATTTTG
1 TTATATATAAATATTTTATATAATTATACTTTGAAATAATAGGATTATAAATTAAATATATTTTG
*
5061567 AACTTTTAAAATTTCCAATAATAGAGACAATTTATAATTAATAAAGTACCAA-TGGGGGTTGTAG
66 AACTTTTAAAATTTCCAATAATAGAGACAATTTATAATTAATAAAGTACCAATTGGGCGTTGTAG
5061631 GGGTGCTAATCCTTCCCTAAACGTAACCGACGACG
131 GGGTGCTAATCCTTCCCTAAACGTAACCGACGACG
5061666 TTATATATAAATA-TTTATATAATTATACTTTGAAATAATAGGATTATAAATTAAATATATTTTT
1 TTATATATAAATATTTTATATAATTATACTTTGAAATAATAGGATTATAAATTAAATATA-TTTT
5061730 GAACTTTTAAAATTTCCAATAATAGAGACAATTTATAATTAATAAAGTACCAATTTTGGGCGTTG
65 GAACTTTTAAAATTTCCAATAATAGAGACAATTTATAATTAATAAAGTACCAA--TTGGGCGTTG
5061795 TAGGGGTGCTAATCCTTCCCTAAACGTAACCGACGACG
128 TAGGGGTGCTAATCCTTCCCTAAACGTAACCGACGACG
5061833 AATCCCTTTT
Statistics
Matches: 161, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
163 45 0.28
164 70 0.43
167 46 0.29
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (165 bp):
TTATATATAAATATTTTATATAATTATACTTTGAAATAATAGGATTATAAATTAAATATATTTTG
AACTTTTAAAATTTCCAATAATAGAGACAATTTATAATTAATAAAGTACCAATTGGGCGTTGTAG
GGGTGCTAATCCTTCCCTAAACGTAACCGACGACG
Found at i:5069990 original size:22 final size:22
Alignment explanation
Indices: 5069962--5070014 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
5069952 GAAAATGCAA
5069962 AAAATGCATATTAATAAGCATG
1 AAAATGCATATTAATAAGCATG
*
5069984 AAAATGCATATTAATATGCATG
1 AAAATGCATATTAATAAGCATG
5070006 AAAATGCAT
1 AAAATGCAT
5070015 CTAATTGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.28
Consensus pattern (22 bp):
AAAATGCATATTAATAAGCATG
Found at i:5076361 original size:16 final size:16
Alignment explanation
Indices: 5076340--5076379 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
5076330 GAAAATCATC
5076340 AACAAACTTTAACATG
1 AACAAACTTTAACATG
5076356 AACAAACTTTAACATG
1 AACAAACTTTAACATG
5076372 AACAAACT
1 AACAAACT
5076380 GAATTTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.20, G:0.05, T:0.23
Consensus pattern (16 bp):
AACAAACTTTAACATG
Found at i:5078110 original size:20 final size:20
Alignment explanation
Indices: 5078085--5078140 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
5078075 CCAAGGACTT
5078085 AGGGATCGATCTTTTAGGGG
1 AGGGATCGATCTTTTAGGGG
5078105 AGGGATCGATCTTTTAGGGG
1 AGGGATCGATCTTTTAGGGG
5078125 AGGGATCGATCCTTTT
1 AGGGATCGAT-CTTTT
5078141 CATGAAGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 30 0.86
21 5 0.14
ACGTcount: A:0.20, C:0.12, G:0.36, T:0.32
Consensus pattern (20 bp):
AGGGATCGATCTTTTAGGGG
Found at i:5081501 original size:36 final size:36
Alignment explanation
Indices: 5081449--5081520 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
5081439 CCCATCTATT
* *
5081449 GACAGTAGAAAATCTCTACTAGTCACAACACATATA
1 GACAATAGAAAATCTCTACTAGTAACAACACATATA
*
5081485 GACAATAGAAAATCTCTACTCGTAACAACACATATA
1 GACAATAGAAAATCTCTACTAGTAACAACACATATA
5081521 CATATCTCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (36 bp):
GACAATAGAAAATCTCTACTAGTAACAACACATATA
Found at i:5091960 original size:43 final size:43
Alignment explanation
Indices: 5091894--5091976 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
5091884 ATCATACATC
* * *
5091894 TCTATAAGGTTGCTGGAGTGTCACATATGCCAAACGACATTTG
1 TCTAAAAGGTTGCTGGAGCGTCACATAGGCCAAACGACATTTG
*
5091937 TCTAAAAGGTTTCTGGAGCGTCACATAGGCCAAACGACAT
1 TCTAAAAGGTTGCTGGAGCGTCACATAGGCCAAACGACAT
5091977 CCGGTGCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTAAAAGGTTGCTGGAGCGTCACATAGGCCAAACGACATTTG
Found at i:5094055 original size:20 final size:21
Alignment explanation
Indices: 5094017--5094055 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5094007 CATCAAAGTC
5094017 TTTGTTGAAGCCATGAAATCT
1 TTTGTTGAAGCCATGAAATCT
*
5094038 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAAGCCATGAAAT
5094056 TCCTGCAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (21 bp):
TTTGTTGAAGCCATGAAATCT
Found at i:5099654 original size:82 final size:82
Alignment explanation
Indices: 5099512--5099686 Score: 242
Period size: 82 Copynumber: 2.1 Consensus size: 82
5099502 ATATCAGTCT
*
5099512 TCATTGCATGTCTCATTGTTAGAACGTGAATAACCTTCAAAAGATGATAAATAAGGCCTTGAATG
1 TCATTGCATGTCTCATTGTTAGAACGTGAATAACCTTCAAAAGATGATAAATAAGACCTTGAATG
* *
5099577 CAAGCTTTGAATGCTTG
66 CAAGCTTTAAATGCATG
* * * ** * *
5099594 TTATTGCATGTCTCCTTGTTAGAACGTGAATAGCCTTCAAAATTTGATGAATAATACCTTGAATG
1 TCATTGCATGTCTCATTGTTAGAACGTGAATAACCTTCAAAAGATGATAAATAAGACCTTGAATG
* *
5099659 GAAGGTTTAAATGCATG
66 CAAGCTTTAAATGCATG
5099676 TCATTGCATGT
1 TCATTGCATGT
5099687 TCCAAGAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (82 bp):
TCATTGCATGTCTCATTGTTAGAACGTGAATAACCTTCAAAAGATGATAAATAAGACCTTGAATG
CAAGCTTTAAATGCATG
Found at i:5106676 original size:3 final size:3
Alignment explanation
Indices: 5106668--5106700 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5106658 AAATCACTAG
*
5106668 TCT TCT TCT TAT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5106701 GCATCACCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5113750 original size:13 final size:13
Alignment explanation
Indices: 5113732--5113758 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5113722 TTACAGACGC
5113732 GCATATGAAGACT
1 GCATATGAAGACT
5113745 GCATATGAAGACT
1 GCATATGAAGACT
5113758 G
1 G
5113759 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:5113778 original size:4 final size:4
Alignment explanation
Indices: 5113769--5113795 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5113759 TTCAACTATG
5113769 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
5113796 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:5119239 original size:21 final size:22
Alignment explanation
Indices: 5119215--5119270 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
5119205 ATCCATCACA
*
5119215 AAAAGGGATCAATCTTTTTA-G
1 AAAAGGGATCAATCCTTTTAGG
* **
5119236 AAAATGGATTGATCCTTTTAGG
1 AAAAGGGATCAATCCTTTTAGG
5119258 AAAAGGGATCAAT
1 AAAAGGGATCAAT
5119271 AATTTTTCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (22 bp):
AAAAGGGATCAATCCTTTTAGG
Found at i:5121845 original size:30 final size:30
Alignment explanation
Indices: 5121788--5121858 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
5121778 GGTTAACTCG
* *
5121788 TTGACTTTGACCGAGTCAACCCATTGACCA
1 TTGACTTTGACAGAGTCAAACCATTGACCA
** *
5121818 TTGACTTTGACAGAGTCAAACTGTTGACCG
1 TTGACTTTGACAGAGTCAAACCATTGACCA
*
5121848 TTGACATTGAC
1 TTGACTTTGAC
5121859 TTTGACAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (30 bp):
TTGACTTTGACAGAGTCAAACCATTGACCA
Found at i:5127184 original size:90 final size:91
Alignment explanation
Indices: 5127029--5127211 Score: 235
Period size: 90 Copynumber: 2.0 Consensus size: 91
5127019 CCTAAGACCT
* * * ** * * *
5127029 TACGGACCTAAGGATACCCTTGGGTAGGCCCATAGGCCTCAAGGTATATCATTAGTTTGATTCCC
1 TACGGACCTAAGAATACCCCTGGGTAGGCCCATAGGCCCCAAGCAATATCATCAGGTTGACTCCC
*
5127094 T-TTGATGTGTTCTTAGGGTAA-CCC
66 TCTTGATGTGTGCTTAGGGTAAGCCC
* *
5127118 TACGGACCTAACGAATACCCCTGGGTAGGCCCATAGGCCCCAAGCAATCTCCTCAGGTTGACTCC
1 TACGGACCTAA-GAATACCCCTGGGTAGGCCCATAGGCCCCAAGCAATATCATCAGGTTGACTCC
*
5127183 CTCTTGTTGTGTGCTTAGGGTAAGCCC
65 CTCTTGATGTGTGCTTAGGGTAAGCCC
5127210 TA
1 TA
5127212 TGGATGCAGT
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
89 11 0.14
90 45 0.57
91 18 0.23
92 5 0.06
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (91 bp):
TACGGACCTAAGAATACCCCTGGGTAGGCCCATAGGCCCCAAGCAATATCATCAGGTTGACTCCC
TCTTGATGTGTGCTTAGGGTAAGCCC
Found at i:5129172 original size:30 final size:30
Alignment explanation
Indices: 5129106--5129173 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
5129096 AGGTCAACTT
* * *
5129106 GTTGACTTTGACTGAGTCAACTCCTTGATC
1 GTTGACTTTGACCGAGTCAACTACTTGACC
* *
5129136 GATGACTTTGACCGAGTCAAAC-AGTTGACC
1 GTTGACTTTGACCGAGTC-AACTACTTGACC
5129166 GTTGACTT
1 GTTGACTT
5129174 CGAATTTGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (30 bp):
GTTGACTTTGACCGAGTCAACTACTTGACC
Found at i:5133113 original size:8 final size:8
Alignment explanation
Indices: 5133100--5133125 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5133090 ATTGAGGATT
5133100 AAATTGTA
1 AAATTGTA
5133108 AAATTGTA
1 AAATTGTA
5133116 AAATTGTA
1 AAATTGTA
5133124 AA
1 AA
5133126 GTTAGTAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (8 bp):
AAATTGTA
Found at i:5133851 original size:15 final size:14
Alignment explanation
Indices: 5133823--5133878 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
5133813 TCCTCCGAGC
*
5133823 CGACAGAGTCAACT
1 CGACTGAGTCAACT
*
5133837 CGCACTGAGTTAACT
1 CG-ACTGAGTCAACT
*
5133852 CGACTAAGTCAACT
1 CGACTGAGTCAACT
5133866 C-ACT-AGGTCAACT
1 CGACTGA-GTCAACT
5133879 AGTTGACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.03
13 10 0.28
14 13 0.36
15 12 0.33
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (14 bp):
CGACTGAGTCAACT
Found at i:5133875 original size:13 final size:14
Alignment explanation
Indices: 5133829--5133878 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
5133819 GAGCCGACAG
*
5133829 AGTCAACTCGCACTG
1 AGTCAACTCG-ACTA
*
5133844 AGTTAACTCGACTA
1 AGTCAACTCGACTA
5133858 AGTCAACTC-ACTA
1 AGTCAACTCGACTA
*
5133871 GGTCAACT
1 AGTCAACT
5133879 AGTTGACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 11 0.35
14 11 0.35
15 9 0.29
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (14 bp):
AGTCAACTCGACTA
Found at i:5138579 original size:17 final size:17
Alignment explanation
Indices: 5138557--5138610 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
5138547 CTCGTTGACT
5138557 TTGACCAAATCAACCCG
1 TTGACCAAATCAACCCG
** *
5138574 TTGACC--ATTGA--CT
1 TTGACCAAATCAACCCG
5138587 TTGACCAAATCAACCCG
1 TTGACCAAATCAACCCG
5138604 TTGACCA
1 TTGACCA
5138611 TTGACTTTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
13 7 0.26
15 6 0.22
17 14 0.52
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (17 bp):
TTGACCAAATCAACCCG
Found at i:5138647 original size:30 final size:30
Alignment explanation
Indices: 5138551--5138622 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
5138541 GGTCAACTCG
5138551 TTGACTTTGACCAAATCAACCCGTTGACCA
1 TTGACTTTGACCAAATCAACCCGTTGACCA
5138581 TTGACTTTGACCAAATCAACCCGTTGACCA
1 TTGACTTTGACCAAATCAACCCGTTGACCA
5138611 TTGACTTTGACC
1 TTGACTTTGACC
5138623 GAGTCGAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (30 bp):
TTGACTTTGACCAAATCAACCCGTTGACCA
Found at i:5141248 original size:90 final size:90
Alignment explanation
Indices: 5141096--5141269 Score: 262
Period size: 90 Copynumber: 1.9 Consensus size: 90
5141086 AAGACCTTGC
* * * **
5141096 GGACCTAAGGATACCCTTGGTTAGGCCCATAGGCACCAATGTATATCCTTAGGTTGGTTCCC-TT
1 GGACCTAAGGATACCCTTGGGTAGGCCCATAGGCACCAAGGAATATCCTTAGGTTGACTCCCTTT
*
5141160 TGTTGTGTACTTAGGGTAACCCTAT
66 TGCTGTGTACTTAGGGTAACCCTAT
5141185 GGACCTAAGGAATACCCTTGGGTAGGCCCATAGGTC-CCAAGGAATATCCTTAGGTTGACTCCCT
1 GGACCTAAGG-ATACCCTTGGGTAGGCCCATAGG-CACCAAGGAATATCCTTAGGTTGACTCCCT
5141249 TTTGCTGTGTACTTAGGGTAA
64 TTTGCTGTGTACTTAGGGTAA
5141270 GGCCTACGGA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
89 10 0.13
90 45 0.59
91 21 0.28
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (90 bp):
GGACCTAAGGATACCCTTGGGTAGGCCCATAGGCACCAAGGAATATCCTTAGGTTGACTCCCTTT
TGCTGTGTACTTAGGGTAACCCTAT
Found at i:5144978 original size:17 final size:17
Alignment explanation
Indices: 5144956--5144989 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5144946 CATCGAAAAA
5144956 CATAAAAAATGACTTTT
1 CATAAAAAATGACTTTT
**
5144973 CATAAAATTTGACTTTT
1 CATAAAAAATGACTTTT
5144990 TGGTTAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
CATAAAAAATGACTTTT
Found at i:5149351 original size:31 final size:30
Alignment explanation
Indices: 5149310--5149382 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
5149300 GCAAAAGAAA
5149310 AAAATAACATAAATTGAAAGTACAAGAAAAT
1 AAAATAACATAAATTGAAA-TACAAGAAAAT
* * ** *
5149341 AAAATCACATACATTGAAATATTATAAAAT
1 AAAATAACATAAATTGAAATACAAGAAAAT
*
5149371 AAAATTACATAA
1 AAAATAACATAA
5149383 GTAATGGTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (30 bp):
AAAATAACATAAATTGAAATACAAGAAAAT
Found at i:5152766 original size:36 final size:36
Alignment explanation
Indices: 5152722--5152826 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
5152712 CATATCACAT
* ** *
5152722 ATTACATTAAGGAGATAAGAACAATGAACTTTACAC
1 ATTACATTAAGGAGATAAAAACAAAAAACCTTACAC
*
5152758 ATTACATTAAGGATATAAAAACAAAAAACCTTACAC
1 ATTACATTAAGGAGATAAAAACAAAAAACCTTACAC
* *
5152794 ATTACGTTAAGGAGATAAAAACAACAAACCTTA
1 ATTACATTAAGGAGATAAAAACAAAAAACCTTA
5152827 AACACCATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.23
Consensus pattern (36 bp):
ATTACATTAAGGAGATAAAAACAAAAAACCTTACAC
Found at i:5156769 original size:18 final size:18
Alignment explanation
Indices: 5156746--5156784 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5156736 ACCGTTCACA
5156746 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
5156764 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
5156782 ACC
1 ACC
5156785 ACTGCTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5157920 original size:13 final size:13
Alignment explanation
Indices: 5157919--5157948 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5157909 CCGTTGACCC
5157919 GACCCGACCCGTT
1 GACCCGACCCGTT
*
5157932 GACTCGACCCGTT
1 GACCCGACCCGTT
5157945 GACC
1 GACC
5157949 GTTGACCGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5157923 original size:18 final size:18
Alignment explanation
Indices: 5157897--5157942 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5157887 ACCGGTCACA
*
5157897 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
5157915 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
5157933 ACTCGACCCG
1 ACCCGACCCG
5157943 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5159613 original size:24 final size:24
Alignment explanation
Indices: 5159495--5159610 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
5159485 TTCGATTTGA
5159495 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
5159519 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
5159543 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
5159567 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
5159591 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
5159611 CTGATTTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5161812 original size:13 final size:13
Alignment explanation
Indices: 5161811--5161840 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5161801 CCGTTGACCC
5161811 GACCCGACCCGTT
1 GACCCGACCCGTT
*
5161824 GACTCGACCCGTT
1 GACCCGACCCGTT
5161837 GACC
1 GACC
5161841 GTTGACCGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:5161815 original size:18 final size:18
Alignment explanation
Indices: 5161789--5161834 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5161779 ACCGGTCACA
*
5161789 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
5161807 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
5161825 ACTCGACCCG
1 ACCCGACCCG
5161835 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:5163416 original size:24 final size:24
Alignment explanation
Indices: 5163389--5163504 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
5163379 TTCGATTTGA
5163389 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
5163413 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
5163437 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
5163461 ATTCTGATCTGATACTTGACCTGT
1 ATTCTGATCTGATACTTGACATGG
* * *
5163485 ATTTTTATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
5163505 CTGATTTATG
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:5163521 original size:24 final size:24
Alignment explanation
Indices: 5163446--5163511 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
5163436 GATTCTGATC
* * * * *
5163446 TGATACTTGACTTGGATTCTGATC
1 TGATACTTGACCTGTATTTTTATA
5163470 TGATACTTGACCTGTATTTTTATA
1 TGATACTTGACCTGTATTTTTATA
5163494 TGATACTTGACCTG-ATTT
1 TGATACTTGACCTGTATTT
5163512 ATGTTTTGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 4 0.11
24 33 0.89
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (24 bp):
TGATACTTGACCTGTATTTTTATA
Found at i:5165595 original size:23 final size:22
Alignment explanation
Indices: 5165554--5165614 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
5165544 TATTTCTAAA
5165554 ATTATTTTAAATTTATTAATGATTTT
1 ATTATTTT--ATTT-TTAAT-ATTTT
5165580 ATTATTTTATTTTTAATATTTT
1 ATTATTTTATTTTTAATATTTT
*
5165602 -TAAATTTTATTTT
1 AT-TATTTTATTTT
5165615 AGATTATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.03
22 15 0.45
23 5 0.15
24 4 0.12
26 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTTTATTTTTAATATTTT
Found at i:5165667 original size:27 final size:28
Alignment explanation
Indices: 5165610--5165676 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
5165600 TTTAAATTTT
*
5165610 ATTTTAGATTATATAATATGAATTTATAA
1 ATTTTATATT-TATAATATGAATTTATAA
* *
5165639 ATTTTATATTTATATTATGTA-TTATAA
1 ATTTTATATTTATAATATGAATTTATAA
*
5165666 ATTTTTTATTT
1 ATTTTATATTT
5165677 TTAAATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 16 0.47
28 9 0.26
29 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTATATTTATAATATGAATTTATAA
Found at i:5165669 original size:35 final size:34
Alignment explanation
Indices: 5165597--5165669 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
5165587 TATTTTTAAT
* *
5165597 ATTTTTAAATTTTATTTTAGATTATATAATATGA
1 ATTTATAAATTTTATTTTAGATTATATAATATAA
* * *
5165631 ATTTATAAATTTTATATTTATATTATGTATTATAA
1 ATTTATAAATTTTAT-TTTAGATTATATAATATAA
5165666 ATTT
1 ATTT
5165670 TTTATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (34 bp):
ATTTATAAATTTTATTTTAGATTATATAATATAA
Found at i:5166970 original size:16 final size:17
Alignment explanation
Indices: 5166951--5166991 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
5166941 TTTCCAATGT
5166951 TTTGTTTT-TTATTT-TC
1 TTTGTTTTATT-TTTCTC
5166967 TTTGATTTTATTTTTCTC
1 TTTG-TTTTATTTTTCTC
5166985 TTTGTTT
1 TTTGTTT
5166992 GCTTGCATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTGTTTTATTTTTCTC
Found at i:5169562 original size:31 final size:31
Alignment explanation
Indices: 5169488--5169656 Score: 209
Period size: 31 Copynumber: 5.5 Consensus size: 31
5169478 TCAAATAAGG
* * *
5169488 TTTATAAACATTTATTCAAATATAAAT-ATA
1 TTTACAAACATTCATTCAAATAGAAATAATA
* * *
5169518 TTTATAAAAATTCATTCAAATATAAATAATA
1 TTTACAAACATTCATTCAAATAGAAATAATA
* *
5169549 TTTACAGACATTCATTCAAATGGAAA-AATA
1 TTTACAAACATTCATTCAAATAGAAATAATA
* *
5169579 TTTAC-AACATTCATTCAAATAGAAATAGTG
1 TTTACAAACATTCATTCAAATAGAAATAATA
*
5169609 TTTGCAAACATTCATTCAAATAGAAATAAATA
1 TTTACAAACATTCATTCAAATAGAAAT-AATA
5169641 TTTACAAACATTCATT
1 TTTACAAACATTCATT
5169657 ATAGTATAAA
Statistics
Matches: 120, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
29 18 0.15
30 40 0.33
31 45 0.38
32 17 0.14
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (31 bp):
TTTACAAACATTCATTCAAATAGAAATAATA
Found at i:5169620 original size:60 final size:60
Alignment explanation
Indices: 5169488--5169656 Score: 187
Period size: 60 Copynumber: 2.8 Consensus size: 60
5169478 TCAAATAAGG
* * * * * *
5169488 TTTATAAACATTTATTCAAAT-ATAAATATATTTATAAAAATTCATTCAAATATAAATAATA
1 TTTACAAACATTCATTCAAATGA-AAAAATATTTA-CAACATTCATTCAAATAGAAATAATA
* * * *
5169549 TTTACAGACATTCATTCAAATGGAAAAATATTTACAACATTCATTCAAATAGAAATAGTG
1 TTTACAAACATTCATTCAAATGAAAAAATATTTACAACATTCATTCAAATAGAAATAATA
*
5169609 TTTGCAAACATTCATTCAAATAGAAATAAATATTTACAAACATTCATT
1 TTTACAAACATTCATTCAAAT-GAAA-AAATATTTAC-AACATTCATT
5169657 ATAGTATAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
60 40 0.44
61 31 0.34
62 10 0.11
63 10 0.11
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (60 bp):
TTTACAAACATTCATTCAAATGAAAAAATATTTACAACATTCATTCAAATAGAAATAATA
Found at i:5171175 original size:20 final size:21
Alignment explanation
Indices: 5171147--5171187 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
5171137 TCAAACTTAA
*
5171147 TCCTAAAAAATAAAAGATAAT
1 TCCTAAAAAACAAAAGATAAT
5171168 TCCT-AAAAACAAAAGATAAT
1 TCCTAAAAAACAAAAGATAAT
5171188 CTTGATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (21 bp):
TCCTAAAAAACAAAAGATAAT
Found at i:5173813 original size:24 final size:25
Alignment explanation
Indices: 5173767--5173814 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5173757 ATAAAATACA
5173767 ATAAATTCCAGAGCATAAGAAAATC
1 ATAAATTCCAGAGCATAAGAAAATC
*
5173792 ATAAATATCC-GAGTAT-AGAAAAT
1 ATAAAT-TCCAGAGCATAAGAAAAT
5173815 GGGGAGCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 11 0.52
26 3 0.14
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.23
Consensus pattern (25 bp):
ATAAATTCCAGAGCATAAGAAAATC
Found at i:5186522 original size:16 final size:16
Alignment explanation
Indices: 5186501--5186544 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
5186491 CAACCAATGA
*
5186501 TAAAAAAATAAAAACAG
1 TAAAAAAA-CAAAACAG
*
5186518 TAAAAAAACAACACAG
1 TAAAAAAACAAAACAG
5186534 TAAAAAAACAA
1 TAAAAAAACAA
5186545 CATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.75, C:0.11, G:0.05, T:0.09
Consensus pattern (16 bp):
TAAAAAAACAAAACAG
Found at i:5186545 original size:16 final size:16
Alignment explanation
Indices: 5186514--5186546 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5186504 AAAAATAAAA
5186514 ACAGTAAAAAAACAAC
1 ACAGTAAAAAAACAAC
5186530 ACAGTAAAAAAACAAC
1 ACAGTAAAAAAACAAC
5186546 A
1 A
5186547 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (16 bp):
ACAGTAAAAAAACAAC
Found at i:5186561 original size:12 final size:12
Alignment explanation
Indices: 5186546--5186578 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5186536 AAAAAACAAC
5186546 ATAAAATAAAAT
1 ATAAAATAAAAT
5186558 AT-AAATATAAAT
1 ATAAAATA-AAAT
5186570 ATAAAATAA
1 ATAAAATAA
5186579 GTACAAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.26
12 9 0.47
13 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
ATAAAATAAAAT
Found at i:5188454 original size:39 final size:39
Alignment explanation
Indices: 5188400--5188497 Score: 178
Period size: 39 Copynumber: 2.5 Consensus size: 39
5188390 AGGTTGAACA
*
5188400 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
5188439 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
*
5188478 AGGTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
5188498 CTCCACTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATG
Found at i:5188457 original size:91 final size:91
Alignment explanation
Indices: 5188293--5188458 Score: 260
Period size: 91 Copynumber: 1.8 Consensus size: 91
5188283 TGATGGAATC
* * * * *
5188293 GAGCTAAGGTTAAAGAAGTTCTTCTCATTATGAACTTTTTCTCTCTCATTGGATGAGTTCTTTTC
1 GAGCCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTC
*
5188358 ATTTTGAACTCTCCACTGGAAATATT
66 ATTATGAACTCTCCACTGGAAATATT
* *
5188384 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTC
1 GAGCCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTC
5188449 ATTATGAACT
66 ATTATGAACT
5188459 TCTTCTCCCT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 67 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (91 bp):
GAGCCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTC
ATTATGAACTCTCCACTGGAAATATT
Found at i:5188534 original size:91 final size:91
Alignment explanation
Indices: 5188439--5188874 Score: 745
Period size: 91 Copynumber: 4.8 Consensus size: 91
5188429 TCGTTGGATG
* *
5188439 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
5188504 TAGAAATGTTGAGCCAAGGTTGAACA
66 TAGAAATGTTGAGCCAAGGTTGAACA
* *
5188530 AGTTCTTGTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
5188595 TAGAAATGTTGAGCCAAGGTTGAACA
66 TAGAAATGTTGAGCCAAGGTTGAACA
* *
5188621 AGTTCTTTTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
* *
5188686 TGGAAATTTTGAGCCAAGGTTGAACA
66 TAGAAATGTTGAGCCAAGGTTGAACA
5188712 AGTTCTTCTCATTATGAA---CTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
*
5188774 TAGAAATGTTGAGCCAAGGTTGAATA
66 TAGAAATGTTGAGCCAAGGTTGAACA
*
5188800 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCTA-
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
5188864 TAGGAAATGTT
66 TA-GAAATGTT
5188875 AATTGATTTA
Statistics
Matches: 326, Mismatches: 15, Indels: 8
0.93 0.04 0.02
Matches are distributed among these distances:
88 84 0.26
90 2 0.01
91 240 0.74
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
TAGAAATGTTGAGCCAAGGTTGAACA
Found at i:5188542 original size:130 final size:130
Alignment explanation
Indices: 5188309--5188588 Score: 488
Period size: 130 Copynumber: 2.2 Consensus size: 130
5188299 AGGTTAAAGA
* * * * *
5188309 AGTTCTTCTCATTATGAACTTTTTCTCTCTCATTGGATGAGTTCTTTTCATTTTGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
*
5188374 TGGAAATATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TAGAAATATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
5188439 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
* *
5188504 TAGAAATGTTGAGCCAAGGTTGAACAAGTTCTTGTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TAGAAATATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
5188569 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
5188589 CCCCACTAGA
Statistics
Matches: 142, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 142 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (130 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
TAGAAATATTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATG
Found at i:5188826 original size:179 final size:180
Alignment explanation
Indices: 5188439--5188874 Score: 741
Period size: 179 Copynumber: 2.4 Consensus size: 180
5188429 TCGTTGGATG
* *
5188439 AGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGGTCTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
*
5188504 TAGAAATGTTGAGCCAAGGTTGAACAAGTTCTTGTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TAGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTCCCTCGTTGGATG
5188569 AGTTCTTCTCATTATGAACTCCCCACTAGAAATGTTGAGCCAAGGTTGAACA
129 AGTTCTTCTCATTATGAACTCCCCACTAGAAATGTTGAGCCAAGGTTGAACA
* *
5188621 AGTTCTTTTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTTTTCTCATTATGAACTCTCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
* *
5188686 TGGAAATTTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAA-CTTCTCCCTCGTTGGATGAG
66 TAGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAATCTTCTCCCTCGTTGGATGAG
* *
5188750 TTCTTCTCATTATGAACTCTCCACTAGAAATGTTGAGCCAAGGTTGAATA
131 TTCTTCTCATTATGAACTCCCCACTAGAAATGTTGAGCCAAGGTTGAACA
*
5188800 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCTA-
1 AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
5188864 TAGGAAATGTT
66 TA-GAAATGTT
5188875 AATTGATTTA
Statistics
Matches: 239, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
178 1 0.00
179 136 0.57
182 102 0.43
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (180 bp):
AGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
TAGAAATGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAATCTTCTCCCTCGTTGGATGAG
TTCTTCTCATTATGAACTCCCCACTAGAAATGTTGAGCCAAGGTTGAACA
Found at i:5189667 original size:54 final size:56
Alignment explanation
Indices: 5189601--5189707 Score: 146
Period size: 54 Copynumber: 1.9 Consensus size: 56
5189591 AGCTTCTTCA
* ** *
5189601 AAAAGATTCATTTACAGTCATCAAGAAACCCC-TAAAATTAGGCTTAGTTTCTTTC
1 AAAAGATTCATTTAAAAACATCAAGAAACCCCTTAAAATCAGGCTTAGTTTCTTTC
* *
5189656 AAAA-ATTCATTTAAAAACATCATGAAACCCCTTAAAATCAGGTTTAGTTTCT
1 AAAAGATTCATTTAAAAACATCAAGAAACCCCTTAAAATCAGGCTTAGTTTCT
5189708 AAAAATCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 23 0.51
55 22 0.49
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (56 bp):
AAAAGATTCATTTAAAAACATCAAGAAACCCCTTAAAATCAGGCTTAGTTTCTTTC
Found at i:5189704 original size:55 final size:56
Alignment explanation
Indices: 5189588--5189707 Score: 147
Period size: 55 Copynumber: 2.2 Consensus size: 56
5189578 CCTTCATAAA
* * ** *
5189588 TTTAGCTTC-TTCAAAAAGATTCATTTACAGTCATCAAGAAACCCCTAAAATTAGG
1 TTTAGTTTCTTTCAAAAAGATTCATTTAAAAACATCAAGAAACCCCTAAAATCAGG
* *
5189643 CTTAGTTTCTTTC-AAAA-ATTCATTTAAAAACATCATGAAACCCCTTAAAATCAGG
1 TTTAGTTTCTTTCAAAAAGATTCATTTAAAAACATCAAGAAACCCC-TAAAATCAGG
5189698 TTTAGTTTCT
1 TTTAGTTTCT
5189708 AAAAATCTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
54 23 0.42
55 29 0.53
56 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (56 bp):
TTTAGTTTCTTTCAAAAAGATTCATTTAAAAACATCAAGAAACCCCTAAAATCAGG
Found at i:5190397 original size:52 final size:55
Alignment explanation
Indices: 5190284--5190417 Score: 168
Period size: 52 Copynumber: 2.4 Consensus size: 55
5190274 AGTTTTCGAG
*
5190284 GAACCCCCTAAAAATTAGGCTTAGCTTCCTTTTAAAAACTCTTTGAAATCTATCATCAA
1 GAACCCCCTAAAAATTAGGCTTAGC-T-CTTCTAAAAACTCTTTGAAA--TATCATCAA
*
5190343 GAACCCCCTGAAAATTAGGCTTAG-T-TTCTAAAAACTCATTTGAAA-A-CATCAA
1 GAACCCCCTAAAAATTAGGCTTAGCTCTTCTAAAAACTC-TTTGAAATATCATCAA
*
5190395 GAAACCCCTAAAAATTAGGCTTA
1 GAACCCCCTAAAAATTAGGCTTA
5190418 TATTCTTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
52 27 0.39
53 1 0.01
55 11 0.16
56 7 0.10
57 1 0.01
59 23 0.33
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.28
Consensus pattern (55 bp):
GAACCCCCTAAAAATTAGGCTTAGCTCTTCTAAAAACTCTTTGAAATATCATCAA
Found at i:5191813 original size:28 final size:28
Alignment explanation
Indices: 5191740--5191814 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 28
5191730 TTCCTTGGGA
* *
5191740 AGGTAATGTGTTTCAGGCTAATTTGGGG
1 AGGTAATGTGTTTCAGGTTAATTTAGGG
* *
5191768 AAGTAATGTATTTCAGGTTAATTTAGGG
1 AGGTAATGTGTTTCAGGTTAATTTAGGG
* * *
5191796 TGGTATTGTGTTTTAGGTT
1 AGGTAATGTGTTTCAGGTT
5191815 GGTTCTTTGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.04, G:0.31, T:0.43
Consensus pattern (28 bp):
AGGTAATGTGTTTCAGGTTAATTTAGGG
Found at i:5192499 original size:10 final size:10
Alignment explanation
Indices: 5192484--5192552 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 10
5192474 CATTTTATCA
5192484 TTTTTCTTTT
1 TTTTTCTTTT
*
5192494 TTTTTCATGTT
1 TTTTTC-TTTT
*
5192505 TTTTTCTCTT
1 TTTTTCTTTT
**
5192515 ACTTTC-TTT
1 TTTTTCTTTT
*
5192524 TTTTTCTTTC
1 TTTTTCTTTT
5192534 TTTTTC-TTT
1 TTTTTCTTTT
*
5192543 TCTTTCTTTT
1 TTTTTCTTTT
5192553 CCTTTTATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 13 0.28
10 24 0.52
11 9 0.20
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:5192526 original size:17 final size:16
Alignment explanation
Indices: 5192503--5192545 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5192493 TTTTTTCATG
5192503 TTTTTTTCTCTTACTT
1 TTTTTTTCTCTTACTT
* *
5192519 TCTTTTTTTTCTTTCTT
1 T-TTTTTTCTCTTACTT
5192536 TTTCTTTTCT
1 TTT-TTTTCT
5192546 TTCTTTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTCTTACTT
Found at i:5192539 original size:19 final size:19
Alignment explanation
Indices: 5192484--5192551 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
5192474 CATTTTATCA
*
5192484 TTTTTCTTTTTTTTTCATGTT
1 TTTTTCTTTCTTTTTC-T-TT
5192505 TTTTTC--TCTTACTTTCTTT
1 TTTTTCTTTCTT--TTTCTTT
5192524 TTTTTCTTTCTTTTTCTTT
1 TTTTTCTTTCTTTTTCTTT
*
5192543 TCTTTCTTT
1 TTTTTCTTT
5192552 TCCTTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 26 0.63
20 1 0.02
21 14 0.34
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTCTTTTTCTTT
Found at i:5192553 original size:9 final size:9
Alignment explanation
Indices: 5192503--5192553 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
5192493 TTTTTTCATG
5192503 TTTT-TTTC
1 TTTTCTTTC
*
5192511 TCTTACTTTC
1 T-TTTCTTTC
*
5192521 TTTTTTTTC
1 TTTTCTTTC
*
5192530 TTTCTTTTTC
1 TTT-TCTTTC
5192540 TTTTCTTTC
1 TTTTCTTTC
5192549 TTTTC
1 TTTTC
5192554 CTTTTATTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.03
9 21 0.58
10 14 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:5192557 original size:15 final size:14
Alignment explanation
Indices: 5192486--5192558 Score: 67
Period size: 15 Copynumber: 4.9 Consensus size: 14
5192476 TTTTATCATT
*
5192486 TTTCTTTTTTTTTC
1 TTTCTTTTCTTTTC
* *
5192500 ATGTTTTTTTCTCTTAC
1 -T-TTCTTTTCT-TTTC
5192517 TTTCTTTT-TTTTC
1 TTTCTTTTCTTTTC
5192530 TTTCTTTTTCTTTTC
1 TTTC-TTTTCTTTTC
5192545 TTTCTTTTCCTTTT
1 TTTCTTTT-CTTTT
5192559 ATTCTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 7 0.15
14 9 0.19
15 21 0.44
16 8 0.17
17 3 0.06
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:5203703 original size:29 final size:29
Alignment explanation
Indices: 5203671--5203793 Score: 110
Period size: 29 Copynumber: 4.3 Consensus size: 29
5203661 CTTTTTAAAA
*
5203671 TAATTACCAAAATAGCACCCTTTTCGAAT
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
** *
5203700 TAATTCCCAAAATAGCACCAATTTCAAAT
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
* * *** *
5203729 TAATTCCCAGAATATC-TTTTTTTTGAA-
1 TAATTCCCAAAATAGCACCCTTTTCGAAT
*
5203756 -AATTACCAAAATAGCA-CCTATTTCGAAT
1 TAATTCCCAAAATAGCACCCT-TTTCGAAT
5203784 TAATTCCCAA
1 TAATTCCCAA
5203794 CCAAAATAGT
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
26 13 0.18
27 6 0.08
28 5 0.07
29 47 0.66
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCCTTTTCGAAT
Found at i:5203800 original size:33 final size:33
Alignment explanation
Indices: 5203760--5203825 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
5203750 TTTGAAAATT
* ***
5203760 ACCAAAATAGCACCTATTTCGAATTAATTCCCA
1 ACCAAAATAGCACCAAAACCGAATTAATTCCCA
*
5203793 ACCAAAATAGTACCAAAACCGAATTAATTCCCA
1 ACCAAAATAGCACCAAAACCGAATTAATTCCCA
5203826 GAATAGTACC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.23
Consensus pattern (33 bp):
ACCAAAATAGCACCAAAACCGAATTAATTCCCA
Found at i:5203877 original size:8 final size:8
Alignment explanation
Indices: 5203836--5203921 Score: 71
Period size: 8 Copynumber: 11.5 Consensus size: 8
5203826 GAATAGTACC
5203836 GGTCAAC-
1 GGTCAACG
5203843 GGTCAAC-
1 GGTCAACG
5203850 GGTCAACG
1 GGTCAACG
*
5203858 GGTCGAGTCG
1 GGTC-A-ACG
5203868 GGTCAACG
1 GGTCAACG
5203876 GGT---CG
1 GGTCAACG
5203881 GGTCAACG
1 GGTCAACG
*
5203889 GGTAAACG
1 GGTCAACG
5203897 GGT---CG
1 GGTCAACG
5203902 GGTCAACG
1 GGTCAACG
*
5203910 GGTAAACG
1 GGTCAACG
5203918 GGTC
1 GGTC
5203922 GTGACCGGTC
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
5 10 0.15
7 14 0.22
8 33 0.51
9 2 0.03
10 6 0.09
ACGTcount: A:0.22, C:0.22, G:0.41, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:5203882 original size:13 final size:13
Alignment explanation
Indices: 5203864--5203891 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5203854 AACGGGTCGA
5203864 GTCGGGTCAACGG
1 GTCGGGTCAACGG
5203877 GTCGGGTCAACGG
1 GTCGGGTCAACGG
5203890 GT
1 GT
5203892 AAACGGGTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.18
Consensus pattern (13 bp):
GTCGGGTCAACGG
Found at i:5211036 original size:84 final size:85
Alignment explanation
Indices: 5210934--5211099 Score: 228
Period size: 84 Copynumber: 2.0 Consensus size: 85
5210924 CAATAACCTT
* * * * ***
5210934 TTTTTTTAAATAATTACCAAAATAGCACCCT-TTTCGAATTAATTCTCAAAATAGCACCAATTTC
1 TTTTTTGAAATAATTACCAAAATAACA-CCTATTTCGAATTAATTCCCAAAATAACACCAAAACC
5210998 GAATTAATTCCCAGAATATCA
65 GAATTAATTCCCAGAATATCA
* *
5211019 TTTTTTGAAA-AATTACCAAAATAACACCTATTTCGAATTAATTCCCAAAATAATACCAAAACCT
1 TTTTTTGAAATAATTACCAAAATAACACCTATTTCGAATTAATTCCCAAAATAACACCAAAACCG
5211083 AATTAATTCCCAGAATA
66 AATTAATTCCCAGAATA
5211100 GCACCGGTCA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
83 3 0.04
84 59 0.83
85 9 0.13
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (85 bp):
TTTTTTGAAATAATTACCAAAATAACACCTATTTCGAATTAATTCCCAAAATAACACCAAAACCG
AATTAATTCCCAGAATATCA
Found at i:5211071 original size:29 final size:29
Alignment explanation
Indices: 5210944--5211071 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 29
5210934 TTTTTTTAAA
* *
5210944 TAATTACCAAAATAGCACCCT-TTTCGAAT
1 TAATTCCCAAAATAACA-CCTATTTCGAAT
* * *
5210973 TAATTCTCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAAAATAACACCTATTTCGAAT
* * * *
5211002 TAATTCCCAGAATATCA--TTTTTTGAA-
1 TAATTCCCAAAATAACACCTATTTCGAAT
* *
5211028 AAATTACCAAAATAACACCTATTTCGAAT
1 TAATTCCCAAAATAACACCTATTTCGAAT
5211057 TAATTCCCAAAATAA
1 TAATTCCCAAAATAA
5211072 TACCAAAACC
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
26 13 0.17
27 6 0.08
28 9 0.12
29 50 0.64
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.32
Consensus pattern (29 bp):
TAATTCCCAAAATAACACCTATTTCGAAT
Found at i:5211158 original size:8 final size:8
Alignment explanation
Indices: 5211145--5211186 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
5211135 ACGGTCGGAT
5211145 CGGGTAAA
1 CGGGTAAA
5211153 CGGGTAAA
1 CGGGTAAA
5211161 CGGGT---
1 CGGGTAAA
*
5211166 CGGGTCAA
1 CGGGTAAA
5211174 CGGGTAAA
1 CGGGTAAA
5211182 CGGGT
1 CGGGT
5211187 CGTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
5 5 0.17
8 25 0.83
ACGTcount: A:0.26, C:0.17, G:0.43, T:0.14
Consensus pattern (8 bp):
CGGGTAAA
Found at i:5211170 original size:21 final size:21
Alignment explanation
Indices: 5211144--5211188 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5211134 AACGGTCGGA
5211144 TCGGGTAAACGGGTAAACGGG
1 TCGGGTAAACGGGTAAACGGG
*
5211165 TCGGGTCAACGGGTAAACGGG
1 TCGGGTAAACGGGTAAACGGG
5211186 TCG
1 TCG
5211189 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.42, T:0.16
Consensus pattern (21 bp):
TCGGGTAAACGGGTAAACGGG
Found at i:5213027 original size:7 final size:7
Alignment explanation
Indices: 5213015--5213086 Score: 54
Period size: 7 Copynumber: 10.3 Consensus size: 7
5213005 GTAGTTGTTA
5213015 AAACCCT
1 AAACCCT
5213022 AAACCCT
1 AAACCCT
**
5213029 AAACATT
1 AAACCCT
**
5213036 AAACTAT
1 AAACCCT
5213043 AAACCCT
1 AAACCCT
***
5213050 AAATATT
1 AAACCCT
**
5213057 AAACTTT
1 AAACCCT
5213064 AAACCCT
1 AAACCCT
*
5213071 AAACACT
1 AAACCCT
5213078 AAACCCT
1 AAACCCT
5213085 AA
1 AA
5213087 CCATTCTCCC
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:5213045 original size:21 final size:21
Alignment explanation
Indices: 5213021--5213081 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
5213011 GTTAAAACCC
5213021 TAAACCCTAAACATTAAACTA
1 TAAACCCTAAACATTAAACTA
* *
5213042 TAAACCCTAAATATTAAACTT
1 TAAACCCTAAACATTAAACTA
*
5213063 TAAACCCTAAACACTAAAC
1 TAAACCCTAAACATTAAAC
5213082 CCTAACCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACATTAAACTA
Found at i:5213273 original size:7 final size:7
Alignment explanation
Indices: 5213255--5213299 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
5213245 TTATCTTGTA
5213255 TTAAGAGT
1 TTAAG-GT
5213263 TTAAGGT
1 TTAAGGT
5213270 TTAAGGT
1 TTAAGGT
*
5213277 TTAAGAT
1 TTAAGGT
*
5213284 TTAGGGT
1 TTAAGGT
*
5213291 TTAGGGT
1 TTAAGGT
5213298 TT
1 TT
5213300 TCAACAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (7 bp):
TTAAGGT
Found at i:5213291 original size:21 final size:22
Alignment explanation
Indices: 5213255--5213299 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
5213245 TTATCTTGTA
5213255 TTAAGAGTTTAAGGTTTAAGGT
1 TTAAGAGTTTAAGGTTTAAGGT
* *
5213277 TTAAGA-TTTAGGGTTTAGGGT
1 TTAAGAGTTTAAGGTTTAAGGT
5213298 TT
1 TT
5213300 TCAACAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (22 bp):
TTAAGAGTTTAAGGTTTAAGGT
Found at i:5213743 original size:16 final size:16
Alignment explanation
Indices: 5213719--5213749 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5213709 GGGAGCGCAT
5213719 ACTAGTTATAAATTCA
1 ACTAGTTATAAATTCA
*
5213735 ACTATTTATAAATTC
1 ACTAGTTATAAATTC
5213750 GATTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
ACTAGTTATAAATTCA
Found at i:5217717 original size:15 final size:15
Alignment explanation
Indices: 5217699--5217729 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5217689 AAATTCTAAC
5217699 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
5217714 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
5217729 T
1 T
5217730 CTATCTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:5220254 original size:15 final size:15
Alignment explanation
Indices: 5220217--5220254 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5220207 ATAATTATTT
*
5220217 AAAA-AATTAAATAA
1 AAAATAATTTAATAA
5220231 AAAAT-ATTTAATAA
1 AAAATAATTTAATAA
5220245 AAAATAATTT
1 AAAATAATTT
5220255 TTTATATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATAATTTAATAA
Found at i:5220457 original size:14 final size:14
Alignment explanation
Indices: 5220440--5220467 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5220430 ATCATAACAA
5220440 AATTATATAACTAT
1 AATTATATAACTAT
5220454 AATTATATAACTAT
1 AATTATATAACTAT
5220468 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:5227676 original size:2 final size:2
Alignment explanation
Indices: 5227669--5227733 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
5227659 CCCCCAACTC
5227669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5227711 AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
5227734 GCATTGAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 61 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5228412 original size:60 final size:60
Alignment explanation
Indices: 5228313--5228428 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
5228303 ACCTTTGAAC
*
5228313 ACTTGAATTCATTAACCCATCTAATGATCTTAATGGTTAAAGAGTATATTTATCTTCAAT
1 ACTTGAATTCATTAACCCATCTAATGATCTTAATAGTTAAAGAGTATATTTATCTTCAAT
* * * * *
5228373 ACTTGAGTTCATTAATCCATCTAATGATCTTAGTAGTTAAAGAGTGTATTTCTCTT
1 ACTTGAATTCATTAACCCATCTAATGATCTTAATAGTTAAAGAGTATATTTATCTT
5228429 TTAAAAGTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (60 bp):
ACTTGAATTCATTAACCCATCTAATGATCTTAATAGTTAAAGAGTATATTTATCTTCAAT
Found at i:5231507 original size:33 final size:33
Alignment explanation
Indices: 5231470--5231542 Score: 146
Period size: 33 Copynumber: 2.2 Consensus size: 33
5231460 TTATTGCATT
5231470 ACAACTTCACATATACAAGAACAATTTTGTATA
1 ACAACTTCACATATACAAGAACAATTTTGTATA
5231503 ACAACTTCACATATACAAGAACAATTTTGTATA
1 ACAACTTCACATATACAAGAACAATTTTGTATA
5231536 ACAACTT
1 ACAACTT
5231543 AACAAATAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.30
Consensus pattern (33 bp):
ACAACTTCACATATACAAGAACAATTTTGTATA
Found at i:5232734 original size:33 final size:33
Alignment explanation
Indices: 5232696--5232761 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
5232686 GACTAACATT
*
5232696 TCCAATGTTACAATATTAGGTGTTTAGACTGAA
1 TCCAATGTTACAATATTAGATGTTTAGACTGAA
*
5232729 TCCAATGTTACAATATTAGATGTTTGGACTGAA
1 TCCAATGTTACAATATTAGATGTTTAGACTGAA
5232762 ACGGCCGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TCCAATGTTACAATATTAGATGTTTAGACTGAA
Found at i:5238056 original size:71 final size:71
Alignment explanation
Indices: 5237926--5238061 Score: 173
Period size: 71 Copynumber: 1.9 Consensus size: 71
5237916 GTCTCTACAG
* * * * * *
5237926 GTTCATCTCAATCAAACTGGTAATTCCTTATATAAGTTTATATCGATCGAACTGTTAATTGCTTA
1 GTTCAACTCAATCAAACTGGCAATTCCTTATATAAGTTCAGATCGATCGAACTGGTAATTCCTTA
5237991 TGACAT
66 TGACAT
* * * **
5237997 GTTCAACTCAGTCAAATTGGCAATTCCTTATATAGGTTCAGATCGATCGAGTTGGTAATTCCTTA
1 GTTCAACTCAATCAAACTGGCAATTCCTTATATAAGTTCAGATCGATCGAACTGGTAATTCCTTA
5238062 CGGATCTAAG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (71 bp):
GTTCAACTCAATCAAACTGGCAATTCCTTATATAAGTTCAGATCGATCGAACTGGTAATTCCTTA
TGACAT
Found at i:5238057 original size:35 final size:34
Alignment explanation
Indices: 5237943--5238061 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 34
5237933 TCAATCAAAC
* *
5237943 TGGTAATTCCTTATATAAGTTTATATCGATCGAAC
1 TGGTAATTCCTTATATAAGTTCA-ATCGATCGAAT
* * * * *
5237978 TGTTAATTGCTTATGACATGTTCAACTC-AGTCAAAT
1 TGGTAATTCCTTAT-ATAAGTTCAA-TCGA-TCGAAT
* * *
5238014 TGGCAATTCCTTATATAGGTTCAGATCGATCGAGT
1 TGGTAATTCCTTATATAAGTTCA-ATCGATCGAAT
5238049 TGGTAATTCCTTA
1 TGGTAATTCCTTA
5238062 CGGATCTAAG
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
35 39 0.61
36 25 0.39
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (34 bp):
TGGTAATTCCTTATATAAGTTCAATCGATCGAAT
Found at i:5240512 original size:19 final size:19
Alignment explanation
Indices: 5240490--5240556 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
5240480 AAATTTAATT
5240490 AAAATAACAAATACTAATAA
1 AAAATAA-AAATACTAATAA
*
5240510 AAAATAAAAATAGTAA-AA
1 AAAATAAAAATACTAATAA
* * *
5240528 AACAACATAAATAACCAAT-A
1 AA-AATAAAAAT-ACTAATAA
5240548 AAAATAAAA
1 AAAATAAAA
5240557 TCAGTACAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
18 4 0.11
19 20 0.54
20 13 0.35
ACGTcount: A:0.73, C:0.09, G:0.01, T:0.16
Consensus pattern (19 bp):
AAAATAAAAATACTAATAA
Found at i:5242438 original size:22 final size:22
Alignment explanation
Indices: 5242411--5242477 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
5242401 TATGAACTTT
5242411 TTCTCACTCGTTGGATGAGTTC
1 TTCTCACTCGTTGGATGAGTTC
* *
5242433 TTCTCA----TT--ATGAACTTT
1 TTCTCACTCGTTGGATG-AGTTC
5242450 TTCTCACTCGTTGGATGAGTTC
1 TTCTCACTCGTTGGATGAGTTC
5242472 TTCTCA
1 TTCTCA
5242478 TTATGAACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 2 0.06
21 2 0.06
22 15 0.44
23 3 0.09
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.45
Consensus pattern (22 bp):
TTCTCACTCGTTGGATGAGTTC
Found at i:5242443 original size:39 final size:39
Alignment explanation
Indices: 5242389--5242486 Score: 187
Period size: 39 Copynumber: 2.5 Consensus size: 39
5242379 AGGTTGAACA
*
5242389 AGTTCTTCTCGTTATGAACTTTTTCTCACTCGTTGGATG
1 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATG
5242428 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATG
1 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATG
5242467 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
5242487 CCCTACTGGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.46
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATG
Found at i:5242467 original size:23 final size:23
Alignment explanation
Indices: 5242402--5242467 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 23
5242392 TCTTCTCGTT
5242402 ATGAACTTTTTCTCACTCGTTGG
1 ATGAACTTTTTCTCACTCGTTGG
* *
5242425 ATG-AGTTCTTCTCA----TT--
1 ATGAACTTTTTCTCACTCGTTGG
5242441 ATGAACTTTTTCTCACTCGTTGG
1 ATGAACTTTTTCTCACTCGTTGG
5242464 ATGA
1 ATGA
5242468 GTTCTTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 3 0.09
17 9 0.28
18 2 0.06
21 2 0.06
22 9 0.28
23 7 0.22
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (23 bp):
ATGAACTTTTTCTCACTCGTTGG
Found at i:5242534 original size:130 final size:130
Alignment explanation
Indices: 5242298--5242576 Score: 461
Period size: 130 Copynumber: 2.2 Consensus size: 130
5242288 AGGTTGAACA
* * * * *
5242298 AGTTCTTATCATTATGAACTTTTTCTCTCTCGTCGGATGAGTTTTTCTCATTATGAACTCCTTGC
1 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTCGGATGAGTTCTTCTCATTATGAACTCCCTAC
* * *
5242363 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCGTTATGAACTTTTTCTCACTCGTTGGATG
66 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCTCATTATGAACTTCTTCTCACTCGTTGGATG
*
5242428 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCTAC
1 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTCGGATGAGTTCTTCTCATTATGAACTCCCTAC
*
5242493 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCTCATTATGAACTTCTTCTCACTCGTTGGATG
5242558 AG-TCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
5242577 CCCCACTGGA
Statistics
Matches: 139, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
129 17 0.12
130 122 0.88
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (130 bp):
AGTTCTTCTCATTATGAACTTTTTCTCACTCGTCGGATGAGTTCTTCTCATTATGAACTCCCTAC
TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCTCATTATGAACTTCTTCTCACTCGTTGGATG
Found at i:5242661 original size:181 final size:182
Alignment explanation
Indices: 5242428--5242777 Score: 567
Period size: 181 Copynumber: 1.9 Consensus size: 182
5242418 TCGTTGGATG
* * * *
5242428 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCTAC
1 AGTTCTTCTCATAATAAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
* * * *
5242493 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCTCATTATGAACTTCTTCTCCCTCGTTGGATG
66 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCCCATTATGAACTTCATCTCACTCGTCGGATG
5242558 AG-TCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAAGTTGAACA
131 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAAGTTGAACA
* *
5242609 AGTTCTTCTCATAATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCGC
1 AGTTCTTCTCATAATAAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
* *
5242674 TGGAAATGTTGATGCAAGGTTGAGCAAGTTCTTCCCATTATGAACTTCATCTCACTCGTCGGATG
66 TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCCCATTATGAACTTCATCTCACTCGTCGGATG
* *
5242739 AGTTCTTCTCATTATGAACTCCCTACTGGAAATTTTGAT
131 AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGAT
5242778 TGGTTTATTA
Statistics
Matches: 154, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
181 120 0.78
182 34 0.22
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (182 bp):
AGTTCTTCTCATAATAAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
TGGAAATGTTGATGCAAGGTTGAACAAGTTCTGCCCATTATGAACTTCATCTCACTCGTCGGATG
AGTTCTTCTCATTATGAACTCCCCACTGGAAATGTTGATGCAAAGTTGAACA
Found at i:5242702 original size:91 final size:91
Alignment explanation
Indices: 5242428--5242777 Score: 558
Period size: 91 Copynumber: 3.9 Consensus size: 91
5242418 TCGTTGGATG
* *
5242428 AGTTCTTCTCATTATGAACTTTTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCTAC
1 AGTTCTTCTCATTATGAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
5242493 TGGAAATGTTGATGCAAGGTTGAACA
66 TGGAAATGTTGATGCAAGGTTGAACA
* *
5242519 AGTTCTGCTCATTATGAACTTCTTCTCCCTCGTTGGATGAG-TCTTCTCATTATGAACTCCCCAC
1 AGTTCTTCTCATTATGAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
*
5242583 TGGAAATGTTGATGCAAAGTTGAACA
66 TGGAAATGTTGATGCAAGGTTGAACA
* * * *
5242609 AGTTCTTCTCATAATAAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCGC
1 AGTTCTTCTCATTATGAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
*
5242674 TGGAAATGTTGATGCAAGGTTGAGCA
66 TGGAAATGTTGATGCAAGGTTGAACA
* * * *
5242700 AGTTCTTCCCATTATGAACTTCATCTCACTCGTCGGATGAGTTCTTCTCATTATGAACTCCCTAC
1 AGTTCTTCTCATTATGAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
*
5242765 TGGAAATTTTGAT
66 TGGAAATGTTGAT
5242778 TGGTTTATTA
Statistics
Matches: 238, Mismatches: 20, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
90 85 0.36
91 153 0.64
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTTCTTCTCACTCGTTGGATGAGTTCTTCTCATTATGAACTCCCCAC
TGGAAATGTTGATGCAAGGTTGAACA
Found at i:5244764 original size:10 final size:9
Alignment explanation
Indices: 5244751--5244861 Score: 68
Period size: 9 Copynumber: 11.9 Consensus size: 9
5244741 TTCAAAAATT
5244751 TTCTCTTTTC
1 TTCT-TTTTC
5244761 TTC-TTTT-
1 TTCTTTTTC
5244768 TTCTATTTTC
1 TTCT-TTTTC
*
5244778 TTCTTTTTT
1 TTCTTTTTC
*
5244787 TTCTTTTTT
1 TTCTTTTTC
5244796 TTCTTATTT-
1 TTCTT-TTTC
5244805 TTCTTATTT-
1 TTCTT-TTTC
5244814 TTCTTATTTC
1 TTCTT-TTTC
* *
5244824 TTATTTCTTAT
1 TTCTTT-TT-C
*
5244835 TTCTTTCTTT
1 TTCTTT-TTC
5244845 TTCTTTTTC
1 TTCTTTTTC
*
5244854 TACTTTTT
1 TTCTTTTT
5244862 GTCTTTTTTC
Statistics
Matches: 88, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
7 3 0.03
8 4 0.05
9 50 0.57
10 23 0.26
11 8 0.09
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:5244787 original size:18 final size:17
Alignment explanation
Indices: 5244749--5244849 Score: 91
Period size: 18 Copynumber: 5.8 Consensus size: 17
5244739 CTTTCAAAAA
5244749 TTTTCTCTTTTCTTC-TT
1 TTTTCT-TTTTCTTCTTT
5244766 TTTTCTATTTTCTTCTTTT
1 TTTTCT-TTTTCTTC-TTT
*
5244785 TTTTCTTTTTTTTCTTAT
1 TTTTCTTTTTCTTCTT-T
5244803 TTTTCTTATTT-TTC-TT
1 TTTTCTT-TTTCTTCTTT
* *
5244819 ATTTCTTATTTCTTATTT
1 TTTTCTT-TTTCTTCTTT
*
5244837 CTTTCTTTTTCTT
1 TTTTCTTTTTCTT
5244850 TTTCTACTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
16 11 0.15
17 25 0.34
18 26 0.36
19 11 0.15
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTCTTTTTCTTCTTT
Found at i:5244816 original size:9 final size:9
Alignment explanation
Indices: 5244756--5244849 Score: 74
Period size: 9 Copynumber: 10.8 Consensus size: 9
5244746 AAATTTTCTC
*
5244756 TTTTCTTCT
1 TTTTCTTAT
5244765 TTTT-TCTATT
1 TTTTCT-TA-T
*
5244775 TTCTTCTTTT
1 TT-TTCTTAT
*
5244785 TTTTCTTTT
1 TTTTCTTAT
5244794 TTTTCTTAT
1 TTTTCTTAT
5244803 TTTTCTTAT
1 TTTTCTTAT
5244812 TTTTCTTA-
1 TTTTCTTAT
5244820 -TTTCTTA-
1 TTTTCTTAT
5244827 -TTTCTTAT
1 TTTTCTTAT
* *
5244835 TTCT-TTCT
1 TTTTCTTAT
5244843 TTTTCTT
1 TTTTCTT
5244850 TTTCTACTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
7 14 0.19
8 7 0.10
9 41 0.57
10 6 0.08
11 3 0.04
12 1 0.01
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTTAT
Done.