Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold436
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: 700632
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:285419 original size:17 final size:17
Alignment explanation
Indices: 285397--285429 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
285387 ATCTGTGGTT
285397 TTGGTTT-TTGTCAAAAA
1 TTGGTTTATT-TCAAAAA
285414 TTGGTTTATTTCAAAA
1 TTGGTTTATTTCAAAA
285430 TCCAAGCCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (17 bp):
TTGGTTTATTTCAAAAA
Found at i:287015 original size:15 final size:16
Alignment explanation
Indices: 286992--287024 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
286982 AAGGGGGAGA
*
286992 AATTTTTTAAGCATTT
1 AATTTTTAAAGCATTT
287008 AATTTTTAAAGCATTT
1 AATTTTTAAAGCATTT
287024 A
1 A
287025 TTATTTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
AATTTTTAAAGCATTT
Found at i:287707 original size:13 final size:13
Alignment explanation
Indices: 287689--287719 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
287679 TGATACATAG
*
287689 TACATTGTATCGA
1 TACATTATATCGA
287702 TACATTATATCGA
1 TACATTATATCGA
287715 TACAT
1 TACAT
287720 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:290365 original size:19 final size:20
Alignment explanation
Indices: 290331--290375 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
290321 GCATTAGCAT
*
290331 ATATTTTTCTAAATTT-TAA
1 ATATTTTTATAAATTTCTAA
*
290350 ATATTTTTATATATTTCCTAA
1 ATATTTTTATAAATTT-CTAA
290371 ATATT
1 ATATT
290376 AAAATTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTTTATAAATTTCTAA
Found at i:291089 original size:38 final size:36
Alignment explanation
Indices: 291038--291148 Score: 111
Period size: 37 Copynumber: 3.0 Consensus size: 36
291028 TAGAAACCGG
*
291038 TTTCAACCGTGCCACCAGTTAAGAATAGT-GATTTTT
1 TTTCAACTGTGCCACCAGTTAAGAATAGTAG-TTTTT
*
291074 ATTTCGAACTGTGCCACC-GATAAGAATAGTAGTTTTT
1 -TTTC-AACTGTGCCACCAGTTAAGAATAGTAGTTTTT
* *
291111 GTTCTAAATCGTGCCACCAGATT-AGAATAGTAGTTTTT
1 TTTC-AACT-GTGCCACCAG-TTAAGAATAGTAGTTTTT
291149 GTTCTAACCT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
36 6 0.10
37 28 0.44
38 28 0.44
39 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (36 bp):
TTTCAACTGTGCCACCAGTTAAGAATAGTAGTTTTT
Found at i:291149 original size:38 final size:38
Alignment explanation
Indices: 291045--291155 Score: 131
Period size: 38 Copynumber: 2.9 Consensus size: 38
291035 CGGTTTCAAC
* * *
291045 CGTGCCACCAG-TTAAGAATAGT-GATTTTTATTTCGAACT
1 CGTGCCACCAGATT-AGAATAGTAG-TTTTT-GTTCTAAAT
*
291084 -GTGCCACC-GATAAGAATAGTAGTTTTTGTTCTAAAT
1 CGTGCCACCAGATTAGAATAGTAGTTTTTGTTCTAAAT
291120 CGTGCCACCAGATTAGAATAGTAGTTTTTGTTCTAA
1 CGTGCCACCAGATTAGAATAGTAGTTTTTGTTCTAA
291156 CCTATACCAC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
36 6 0.10
37 22 0.35
38 35 0.56
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (38 bp):
CGTGCCACCAGATTAGAATAGTAGTTTTTGTTCTAAAT
Found at i:292762 original size:157 final size:156
Alignment explanation
Indices: 292288--292867 Score: 652
Period size: 157 Copynumber: 3.7 Consensus size: 156
292278 GCCCCAAACC
* * *
292288 TAATTAAAACACAAAATTAAACATCAAA-AGAATCAAAATCAACATATAAAGCACATCC-CAAGT
1 TAATTAAAACACAAAATTAAACATCAAAGAG-ATCAAAATCAACATACAAAACACATCCAAAAGT
* * *** *
292351 TACAAGGAAGATTCAGCCAAGTACTTTTAACCTTAGAACAAAATTTTCGAATAAACTTGTTACAC
65 TACAAGGAAGATTCAGCCAAGTACTTTTAGCCTTAGAACAAAATTTTCAAATAAACTCCCTAAAC
* * * *
292416 TTTTTAATTTTGCAAATTAATCCTTACC
130 -TTTTAAATTTACAAATTAATTCTTACA
* ** *
292444 TAATTAAAACACAAAATTAAACATTC-AAGAGATCAAAATCAGCATACAAAACACATTTAAGAGT
1 TAATTAAAACACAAAATTAAACA-TCAAAGAGATCAAAATCAACATACAAAACACATCCAAAAGT
* * * ** *
292508 TACAAGGGAGGTTCGGTTAAGTAC-TTTGGCCTTAGAACAAAATTTTCAAATAAAC-CCCTTAAA
65 TACAAGGAAGATTCAGCCAAGTACTTTTAGCCTTAGAACAAAATTTTCAAATAAACTCCC-TAAA
292571 CTTTCTAAATTTACAAATTAATTCTTACA
129 CTTT-TAAATTTACAAATTAATTCTTACA
* ** * ** *
292600 CAATTAAAATGCAAAATTAAGCATCAAAGAGATGGAAATCAACATCCAAAACACATCCAAAAGTT
1 TAATTAAAACACAAAATTAAACATCAAAGAGATCAAAATCAACATACAAAACACATCCAAAAGTT
* *
292665 ACAAGGAAGTTTTAGCCAAGTACTTTTAGCCTTAGAACAAAATTTTCAAATAAACTCCCTAAACA
66 ACAAGGAAGATTCAGCCAAGTACTTTTAGCCTTAGAACAAAATTTTCAAATAAACTCCCTAAAC-
*
292730 TTTTAAATTTACAAATTAGTTCTTACA
130 TTTTAAATTTACAAATTAATTCTTACA
* * * * * *
292757 TAATTAAAACACAAAATCAAACATTAAAGAAATCAAAATCAGCATTCAAAACACAACCAAAAGTT
1 TAATTAAAACACAAAATTAAACATCAAAGAGATCAAAATCAACATACAAAACACATCCAAAAGTT
* * **
292822 ACAAGAAAGATTC-GACCAAGTAAC-TGTAGCCTCGGAACAAAATTTT
66 ACAAGGAAGATTCAG-CCAAGT-ACTTTTAGCCTTAGAACAAAATTTT
292868 TAGTATTTAC
Statistics
Matches: 353, Mismatches: 60, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
155 5 0.01
156 168 0.48
157 172 0.49
158 8 0.02
ACGTcount: A:0.46, C:0.18, G:0.09, T:0.27
Consensus pattern (156 bp):
TAATTAAAACACAAAATTAAACATCAAAGAGATCAAAATCAACATACAAAACACATCCAAAAGTT
ACAAGGAAGATTCAGCCAAGTACTTTTAGCCTTAGAACAAAATTTTCAAATAAACTCCCTAAACT
TTTAAATTTACAAATTAATTCTTACA
Found at i:293852 original size:21 final size:21
Alignment explanation
Indices: 293826--293882 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
293816 AAAAAATCCA
293826 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
293847 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
293868 AATGTATCGATACAT
1 AATGTATCGATACAT
293883 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:293962 original size:19 final size:19
Alignment explanation
Indices: 293938--294005 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
293928 AATTCAACAA
293938 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
293957 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
293972 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
293989 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
294006 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:293977 original size:13 final size:13
Alignment explanation
Indices: 293959--293983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293949 ACATAAGTTT
293959 TGTATCGATACAA
1 TGTATCGATACAA
293972 TGTATCGATACA
1 TGTATCGATACA
293984 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:293981 original size:32 final size:32
Alignment explanation
Indices: 293940--294002 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
293930 TTCAACAATT
*
293940 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
293972 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
294003 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:294063 original size:13 final size:13
Alignment explanation
Indices: 294045--294070 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
294035 CATTTTTCTG
294045 TGTATCGATACAT
1 TGTATCGATACAT
294058 TGTATCGATACAT
1 TGTATCGATACAT
294071 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:294067 original size:33 final size:33
Alignment explanation
Indices: 294025--294091 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
294015 GCCAAGGAAA
***
294025 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
294058 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
294091 T
1 T
294092 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:296609 original size:28 final size:27
Alignment explanation
Indices: 296542--296610 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
296532 CTTCACAATC
**
296542 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
296569 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
296597 GGGGATACTCCAAC
1 GGGGATACTCCAAC
296611 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:296655 original size:107 final size:105
Alignment explanation
Indices: 296488--296880 Score: 339
Period size: 107 Copynumber: 3.7 Consensus size: 105
296478 TTCTATAATC
*
296488 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTT-C-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
296553 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
63 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* * *
296597 GGGGATACTCCAACTCCGGTTTTATTTCTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATTTCAAAAACACCAATTTTT-CACAATCGGGGATACTCCAA
*** * ** * * * ** * *
296662 TCTTGGTTTTATTTTC---AAAACGCCAATTTTCCTTTAAT-C--
65 -CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCCGA
* *
296701 GGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
296766 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* ** * * * *** * * *
296809 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
296874 CCCGTTA
66 CCCGTTA
296881 TTTTCGAAGG
Statistics
Matches: 222, Mismatches: 48, Indels: 30
0.74 0.16 0.10
Matches are distributed among these distances:
102 2 0.01
103 6 0.03
104 47 0.21
105 18 0.08
106 18 0.08
107 71 0.32
108 29 0.13
109 31 0.14
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTTCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:296670 original size:52 final size:52
Alignment explanation
Indices: 296428--296766 Score: 200
Period size: 52 Copynumber: 6.4 Consensus size: 52
296418 TTATCAATTC
* * * *
296428 TCCACAATCGGGGATATTCCAACCCCGATTTTATTT-TCAAAACACTAA-TTT
1 TCCACAATCGGGGATACTCCAACTCCGGTTTTATTTCT-AAAACACCAATTTT
* * * * *
296479 TCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCT
1 TCCACAATCGGGGATACTCCAACTCCGGTTTTATTT-C-TAAAACACCAATTT-T
* * * ** **
296534 T-CACAATCGGGGATACTCCAAC-CCCGTTAATCATCGGGGATACTCCAAC-CCCGTTATT
1 TCCACAATCGGGGATACTCCAACTCCGGTT--TTAT------TTCTAAAACACCAATT-TT
* *
296592 T-C-CGA--GGGGATACTCCAACTCCGGTTTTATTTCTAAAACACTAATTTT
1 TCCACAATCGGGGATACTCCAACTCCGGTTTTATTTCTAAAACACCAATTTT
* *
296640 TCCACAATCGGGGATACTCCAA-TCTTGGTTTTATTT-TCAAAACGCCAA-TTT
1 TCCACAATCGGGGATACTCCAACTC-CGGTTTTATTTCT-AAAACACCAATTTT
** * * *
296691 TCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTT
1 TCC-ACAATCGGGGATACTCCAACTCCGGTTTTA-TTTCTAAAACACCAATTTT
*
296745 T-CACAATCGAGGATACTCCAAC
1 TCCACAATCGGGGATACTCCAAC
296767 CTCGTTATTT
Statistics
Matches: 219, Mismatches: 42, Indels: 53
0.70 0.13 0.17
Matches are distributed among these distances:
48 9 0.04
49 4 0.02
50 2 0.01
51 40 0.18
52 71 0.32
53 27 0.12
54 27 0.12
55 19 0.09
56 5 0.02
57 2 0.01
58 7 0.03
59 4 0.02
60 1 0.00
61 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
TCCACAATCGGGGATACTCCAACTCCGGTTTTATTTCTAAAACACCAATTTT
Found at i:296750 original size:104 final size:103
Alignment explanation
Indices: 296430--296767 Score: 308
Period size: 104 Copynumber: 3.2 Consensus size: 103
296420 ATCAATTCTC
* * * *
296430 CACAATCGGGGATATTCCAACCCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
* *
296494 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTTC-AAAAACACCAATTT-TT
* * ** * * * ** * *
296535 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGGGGATACTCCAACCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C--
* * *
296597 GGGGATACTCCAACTCCGGTTTTA-TTTCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTT
** *
296641 CCACAATCGGGGATACTCCAATCTTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
296706 TACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTT
*
296746 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
296768 TCGTTATTTC
Statistics
Matches: 180, Mismatches: 39, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
103 7 0.04
104 45 0.25
105 39 0.22
106 17 0.09
107 34 0.19
108 10 0.06
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTT
Found at i:296786 original size:28 final size:28
Alignment explanation
Indices: 296750--296826 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
296740 ATTTTTCACA
* * *
296750 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
296778 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
296806 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
296827 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:296795 original size:212 final size:212
Alignment explanation
Indices: 296425--296877 Score: 651
Period size: 212 Copynumber: 2.1 Consensus size: 212
296415 AGTTTATCAA
* *
296425 TTCTCCACAATCGGGGATATTCCAACCCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
* *
296490 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
296555 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTT
131 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
*
296620 ATTTCTAAAACACTAAT
196 ATTCCTAAAACACTAAT
* * ** * * *
296637 TTTTCCACAATCGGGGATACTCCAATCTTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCG
* *
296702 GGGATACTCCAACTCCGATTTTATTTTC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCA
65 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCA
* *
296765 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT
130 ACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCT
* * *
296830 TTATTCCTAAAATATTGAT
194 TTATTCCTAAAACACTAAT
* *
296849 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATCGGGGATACTCCAACCCCG
296878 TTATTTTCGA
Statistics
Matches: 211, Mismatches: 28, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
211 48 0.23
212 129 0.61
213 34 0.16
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
ATTCCTAAAACACTAAT
Found at i:296959 original size:80 final size:79
Alignment explanation
Indices: 296780--296983 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
296770 GTTATTTCAT
* * * *
296780 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCTAAAATAT
* * *
296845 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** **
296859 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCTAAAAT-A
296924 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
296939 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
296984 TGTTATTATC
Statistics
Matches: 104, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 56 0.54
80 48 0.46
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCTAAAATAT
CGATTTCTCACAAC
Found at i:297011 original size:80 final size:76
Alignment explanation
Indices: 296780--297014 Score: 209
Period size: 80 Copynumber: 2.9 Consensus size: 76
296770 GTTATTTCAT
* * * * *
296780 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCC-GTTTTATTCC-AAAACAT
* *
296845 TGATTTCTCATAAT
63 TGATTTCTCACAAC
* * * * * *
296859 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCCG---TTTTATTCCAAAACA
*
296924 TCGATTTCTCACAAC
62 TTGATTTCTCACAAC
* * *
296939 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCTGTTATTATCTCCAAAACAT
1 CGGGGATACTCCAACCCCGTTATTTTCAAGGG-ATACTCCAACCCCGTT-TTAT-TCCAAAACAT
*
297004 TAAATTTCTCA
63 T-GATTTCTCA
297015 TTGGGAAATA
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 53 0.43
80 59 0.48
81 6 0.05
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.31
Consensus pattern (76 bp):
CGGGGATACTCCAACCCCGTTATTTTCAAGGGATACTCCAACCCCGTTTTATTCCAAAACATTGA
TTTCTCACAAC
Found at i:304284 original size:53 final size:52
Alignment explanation
Indices: 304164--304504 Score: 189
Period size: 52 Copynumber: 6.5 Consensus size: 52
304154 AGTTTATCAA
* * *
304164 TTCTCCACAATC-GGGATATTCCAACCCCGATTTTATTTTCAAAACACTAAGT
1 TTCT-CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAGT
* * *
304216 TTCT-ATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAA-T
1 TTCTCACAATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAAGT
* * ** * *
304268 TTCTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTCACAATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAA----GT
* * * * * *
304325 TATTTC-CGA--GGGGATACTCCAACTCCGGTTTTATTTCTAAAACACTAA-T
1 T-TCTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAGT
* * ** * * * *
304374 TTTTCCACAATCGGGGATACTCCAATCTTGGTTTTATTTTCAAAACGCCAATT
1 TTCT-CACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAGT
** * * * *
304427 TTC-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAATACCAAAT
1 TTCTC-ACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAGT
* *
304479 TTTTCACAATCGAGGATACTCCAACC
1 TTCTCACAATCGGGGATACTCCAACC
304505 TCGTTATTTC
Statistics
Matches: 217, Mismatches: 50, Indels: 44
0.70 0.16 0.14
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 7 0.03
51 29 0.13
52 105 0.48
53 34 0.16
54 6 0.03
55 17 0.08
56 2 0.01
57 8 0.04
58 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
TTCTCACAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAGT
Found at i:304291 original size:104 final size:102
Alignment explanation
Indices: 304164--304509 Score: 265
Period size: 104 Copynumber: 3.3 Consensus size: 102
304154 AGTTTATCAA
* *
304164 TTCTCCACAATC-GGGATATTCCAACCCCGATTTTATTTTCAAAACACTAAGTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCG-TTTTATTTTCAAAACACCAAGTTTCT-TAATCGG
* *
304228 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
64 GGATACTCCAACTCCGATTTTATTT-CAAAAAACACAAAT
* ** * * *
304268 TTCT-CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAACCCCGTTAT-TT
1 TTCTCCACAATCGGGGATACTCCAACCCCGTTTTATTTTC---AAAACACCAA----GTT-TCTT
**** * * *
304330 CCGAGGGGATACTCCAACTCCGGTTTTATTTC-TAAAACACTAAT
58 AATCGGGGATACTCCAACTCCGATTTTATTTCAAAAAACACAAAT
* *** * *
304374 TTTTCCACAATCGGGGATACTCCAATCTTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCG
1 TTCTCCACAATCGGGGATACTCCAA-CCCCGTTTTATTTTCAAAACACCAAGTTT-C-TTAATCG
*
304439 GGGATACTCCAACTCCGATTTTATTTTCAAAATAC-CAAAT
63 GGGATACTCCAACTCCGATTTTA-TTTCAAAAAACACAAAT
* * *
304479 TT-TTCACAATCGAGGATACTCCAACCTCGTT
1 TTCTCCACAATCGGGGATACTCCAACCCCGTT
304510 ATTTCATCGG
Statistics
Matches: 186, Mismatches: 39, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
101 1 0.01
102 8 0.04
103 12 0.06
104 65 0.35
105 16 0.09
106 24 0.13
107 21 0.11
108 28 0.15
109 10 0.05
110 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (102 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGTTTTATTTTCAAAACACCAAGTTTCTTAATCGGGG
ATACTCCAACTCCGATTTTATTTCAAAAAACACAAAT
Found at i:304346 original size:28 final size:27
Alignment explanation
Indices: 304279--304347 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
304269 TCTCACAATC
**
304279 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
304306 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
304334 GGGGATACTCCAAC
1 GGGGATACTCCAAC
304348 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:304407 original size:52 final size:52
Alignment explanation
Indices: 304334--304503 Score: 195
Period size: 52 Copynumber: 3.3 Consensus size: 52
304324 TTATTTCCGA
*
304334 GGGGATACTCCAACTCCGGTTTTA-TTTCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTTC-AAAACACAAATTTTTCCACAATC
* * * **
304386 GGGGATACTCCAA-TCTTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTC-CGGTTTTATTTTCAAAACACAAATTTTTCC-ACAATC
* *
304438 GGGGATACTCCAACTCCGATTTTATTTTCAAAATACCAAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTTCAAAACA-CAAATTTTTCCACAATC
*
304490 GAGGATACTCCAAC
1 GGGGATACTCCAAC
304504 CTCGTTATTT
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
51 8 0.08
52 77 0.78
53 10 0.10
54 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATTTTCAAAACACAAATTTTTCCACAATC
Found at i:304523 original size:28 final size:28
Alignment explanation
Indices: 304487--304563 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
304477 ATTTTTCACA
* * *
304487 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
304515 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
304543 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
304564 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:304695 original size:82 final size:78
Alignment explanation
Indices: 304517--304721 Score: 225
Period size: 82 Copynumber: 2.6 Consensus size: 78
304507 GTTATTTCAT
* * *
304517 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAATATT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATATT
* *
304582 GATTTCTCATAAT
66 GATTTCTCACAAC
* * ** * *
304595 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTCT-AATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCTAAAT-A
304659 TTCACGATTTCTCACAAC
64 TT---GATTTCTCACAAC
* *
304677 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
304722 TGTTATTATC
Statistics
Matches: 106, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
78 45 0.42
79 10 0.09
81 5 0.05
82 46 0.43
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATATT
GATTTCTCACAAC
Found at i:317129 original size:8 final size:8
Alignment explanation
Indices: 317128--317174 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
317118 AAAAAGCAAA
317128 AAAAAAAGC
1 AAAAAAA-C
317137 AAAAAAA-
1 AAAAAAAC
317144 AAACAAAAC
1 AAA-AAAAC
317153 AAAAAAAC
1 AAAAAAAC
*
317161 AAAACAAAG
1 AAAA-AAAC
317170 AAAAA
1 AAAAA
317175 GAGAGAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
7 3 0.09
8 14 0.41
9 17 0.50
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:317133 original size:12 final size:12
Alignment explanation
Indices: 317112--317164 Score: 72
Period size: 12 Copynumber: 4.3 Consensus size: 12
317102 CTTCTCTTCA
317112 AAAAAGAAAAAGC
1 AAAAA-AAAAAGC
317125 AAAAAAAAAAGC
1 AAAAAAAAAAGC
317137 AAAAAAAAAA-C
1 AAAAAAAAAAGC
*
317148 AAAACAAAAAAAC
1 AAAA-AAAAAAGC
317161 AAAA
1 AAAA
317165 CAAAGAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.13
12 23 0.61
13 10 0.26
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGC
Found at i:317134 original size:18 final size:16
Alignment explanation
Indices: 317111--317174 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
317101 CCTTCTCTTC
317111 AAAAAAGAAAAAGCAAAA
1 AAAAAAGAAAAA--AAAA
317129 AAAAAAGCAAAAAAAAA
1 AAAAAAG-AAAAAAAAA
* *
317146 ACAAAACAAAAAAACAA
1 AAAAAAGAAAAAAA-AA
*
317163 AACAAAGAAAAA
1 AAAAAAGAAAAA
317175 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.18
17 20 0.51
18 7 0.18
19 5 0.13
ACGTcount: A:0.84, C:0.09, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:317168 original size:13 final size:12
Alignment explanation
Indices: 317110--317164 Score: 67
Period size: 13 Copynumber: 4.4 Consensus size: 12
317100 ACCTTCTCTT
317110 CAAAAAAGAAAAA
1 CAAAAAA-AAAAA
*
317123 GCAAAAAAAAAAG
1 -CAAAAAAAAAAA
317136 C-AAAAAAAAAA
1 CAAAAAAAAAAA
317147 CAAAACAAAAAAA
1 CAAAA-AAAAAAA
317160 CAAAA
1 CAAAA
317165 CAAAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.27
12 4 0.11
13 16 0.43
14 7 0.19
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:318351 original size:59 final size:59
Alignment explanation
Indices: 318190--319503 Score: 1632
Period size: 59 Copynumber: 22.8 Consensus size: 59
318180 TTTCCTTTTA
* ** * * *
318190 AAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACACATTTTCTCTT
** ** *
318250 AAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318310 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
*
318369 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318428 AAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACAC--CTT-TC--
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318482 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
*
318541 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318600 AAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACAC--CTT-TC--
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318654 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
*
318713 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318772 AAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACAC--CTT-TC--
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318826 AAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACAC--CTT-TC--
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* * * *
318880 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318939 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
318998 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
319057 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC-GAGACGCCTTTTCT-TT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAG-GACACATTTTCTCTT
*
319115 CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACAC--CTT-TC--
1 -AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* ** ** * * *
319171 AAAGCCCATACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGGGGGACTGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGAC-ACATTTTCTCTT
* ** * *
319232 AAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* * *
319291 CAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACAC-----CTTTT
1 -AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* ** *
319347 AAAGCCCACACAAATTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGACAC-----CTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* *
319402 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGC--CTT-TC--
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
* * * * *
319457 AAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGA
319504 TATACTTTAT
Statistics
Matches: 1142, Mismatches: 76, Indels: 77
0.88 0.06 0.06
Matches are distributed among these distances:
54 196 0.17
55 170 0.15
56 20 0.02
57 14 0.01
58 7 0.01
59 549 0.48
60 144 0.13
61 42 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (59 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACATTTTCTCTT
Found at i:318534 original size:172 final size:172
Alignment explanation
Indices: 318190--319503 Score: 1879
Period size: 172 Copynumber: 7.6 Consensus size: 172
318180 TTTCCTTTTA
* ** *
318190 AAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGC
** ***
318255 CCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTCTTAAAGCCCACA
65 CCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGA--CACCTT-TC--AAAGCCCACA
318320 CAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
124 CAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
*
318369 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCC
*
318434 CACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
66 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
318499 GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
131 GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
*
318541 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCC
*
318606 CACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
66 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
318671 GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
131 GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
*
318713 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCC
*
318778 CACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
66 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
* * *
318843 GTGGCACCTTCAATCCTCAAAGAGCAGGACAC--CTT-TC--
131 GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
* *
318880 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCC
* *
318945 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACA
66 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACA
* *
319010 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTT
126 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
319057 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGC-GAGACGCCTTTTCT-TTCAAAG
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAG-GACGCCTTTTCTCTT-AAAG
*
319120 CCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCATACAAG
64 CCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
** * * * *
319185 TTGGTGGCATTTTTCAGTCCTCAAAGAGGGGGACTGCCTTTTCTTTT
128 TTGGTGGCA-CCTTCAGTCCTCAAAGAGCGGGAC-ACTTTTTCTCTT
* * * *
319232 AAAGCCCACCCAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTT-AAAGC
* * * *
319297 CCACACAAGTTGGTGGCACCTTTTAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAAT
65 CCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGT
** * *
319362 TGGTGGCATTTTCCAGTCCTTAAAGAGCAGGACAC-----CTCTT
129 TGGTGGCACCTT-CAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
319402 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TT-TC--AAAGC
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGC
* * * * *
319462 CCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
65 CCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGA
319504 TATACTTTAT
Statistics
Matches: 1061, Mismatches: 54, Indels: 54
0.91 0.05 0.05
Matches are distributed among these distances:
165 41 0.04
167 103 0.10
168 1 0.00
169 4 0.00
170 30 0.03
171 23 0.02
172 442 0.42
173 26 0.02
174 25 0.02
175 70 0.07
176 97 0.09
177 96 0.09
178 79 0.07
179 24 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (172 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTCTTAAAGCC
CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTG
GTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTT
Found at i:318719 original size:231 final size:229
Alignment explanation
Indices: 318190--319503 Score: 1741
Period size: 231 Copynumber: 5.7 Consensus size: 229
318180 TTTCCTTTTA
* ** * *
318190 AAAGCCCCCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGC
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGAC-AC-TTTCTCTTAAAGC
** ** *
318255 CCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTCTTAAAGCCCACA
63 CCACACAAGTTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACA
* *
318320 CAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTTAAAGCCCACACAAGTT
127 CAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTT
318385 GGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTC
192 GGTGGCACCTTCAGTCCTCAAAGAGCAGGACACC--TT-TC
* *
318426 TTAAAGCCCACACAAGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACCTT-TC--AAAGCC
1 --AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACTTTCTCTTAAAGCC
* *
318488 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTTAAAGCCCACACA
64 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACA
318553 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTTGG
129 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTTGG
*
318618 TGGCACCTTCAATCCTCAAAGAGCAGGACACCTTTC
194 TGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTC
*
318654 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACTTTTTCTCTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACAC--TTTCTCTTAAAGCC
318719 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACA
64 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACA
*
318784 AGTTGGTGGCACCTTCAATCCTCAAAGAGCAGGACACC--TT-TC--AAAGCCCACACAAGTTGG
129 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTTGG
*
318844 TGGCACCTTCAATCCTCAAAGAGCAGGACACCTTTC
194 TGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTC
* * *
318880 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCC
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGAC-AC-TTTCTCTTAAAGCC
* * *
318945 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACA
64 CACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACA
* * *
319010 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGG
129 AGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTTGG
*
319075 TGGCACCTTCAGTCCTCAAAGAGC-GAGACGCCTTTTCTTTC
194 TGGCACCTTCAGTCCTCAAAGAGCAG-GAC-AC----CTTTC
*
319116 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTT-TC--AAAGCCC
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACTTTCTCTTAAAGCCC
* ** ** * * *
319178 ATACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGGGGGACTGCCTTTTCTTTTAAAGCCCACCC
65 ACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGAC-ACCTTTTCTCTTAAAGCCCACAC
** * *
319243 AAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTT
128 AAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTT-AAAGCCCACACAAGTT
* * *
319308 GGTGGCACCTTTTAGTCCCCAAAGAGCAGGACACCTTTT
192 GGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTC
* ** *
319347 AAAGCCCACACAAATTGGTGGCATTTTCCAGTCCTTAAAGAGCAGGACAC---CTCTTAAAGCCC
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACACTTTCTCTTAAAGCCC
* *
319409 ACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--TT-TC--AAAGCCCACACG
65 ACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACA
* * * *
319469 AGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
129 AGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGA
319504 TATACTTTAT
Statistics
Matches: 980, Mismatches: 67, Indels: 70
0.88 0.06 0.06
Matches are distributed among these distances:
225 22 0.02
226 277 0.28
227 2 0.00
228 10 0.01
229 9 0.01
230 6 0.01
231 373 0.38
232 49 0.05
233 21 0.02
234 66 0.07
235 30 0.03
236 50 0.05
237 41 0.04
238 24 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (229 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACTTTCTCTTAAAGCCCA
CACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAG
TTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACACCTTTTCTCTTAAAGCCCACACAAGTTGGTG
GCACCTTCAGTCCTCAAAGAGCAGGACACCTTTC
Found at i:318876 original size:25 final size:25
Alignment explanation
Indices: 318793--318877 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
318783 AAGTTGGTGG
318793 CACCTTCAATCCTCAAAGAGCAGGA
1 CACCTTCAATCCTCAAAGAGCAGGA
* * * **
318818 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACC-TTC-AA-TCCTCA-AAG-AGCAGGA
318847 CACCTTCAATCCTCAAAGAGCAGGA
1 CACCTTCAATCCTCAAAGAGCAGGA
318872 CACCTT
1 CACCTT
318878 TCAAAGCCCA
Statistics
Matches: 44, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
24 3 0.07
25 13 0.30
26 7 0.16
27 4 0.09
28 7 0.16
29 7 0.16
30 3 0.07
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (25 bp):
CACCTTCAATCCTCAAAGAGCAGGA
Found at i:320257 original size:21 final size:21
Alignment explanation
Indices: 320231--320287 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
320221 AAAAAATCCA
*
320231 AATGTATCGATACATTTGTAC
1 AATGTATCGATACATTTATAC
**
320252 AATGTATCGATACATTTATGG
1 AATGTATCGATACATTTATAC
320273 AATGTATCGATACAT
1 AATGTATCGATACAT
320288 CCTACAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTATAC
Found at i:320297 original size:21 final size:20
Alignment explanation
Indices: 320229--320307 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 20
320219 AAAAAAAATC
*
320229 CAAATGTATCGATACATTTGTA
1 CAAATGTATCGATACA--TCTA
*
320251 C-AATGTATCGATACATTTA
1 CAAATGTATCGATACATCTA
**
320270 TGGAATGTATCGATACATCCTA
1 -CAAATGTATCGATACAT-CTA
*
320292 CAAATGTATCAATACA
1 CAAATGTATCGATACA
320308 GGGTCCCAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
19 3 0.06
21 42 0.88
22 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (20 bp):
CAAATGTATCGATACATCTA
Found at i:320367 original size:19 final size:19
Alignment explanation
Indices: 320343--320410 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
320333 AATTCAACAA
320343 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
320362 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
320377 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
320394 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
320411 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:320382 original size:13 final size:13
Alignment explanation
Indices: 320364--320388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
320354 ACATAAGTTT
320364 TGTATCGATACAA
1 TGTATCGATACAA
320377 TGTATCGATACA
1 TGTATCGATACA
320389 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:320386 original size:32 final size:32
Alignment explanation
Indices: 320345--320407 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
320335 TTCAACAATT
*
320345 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
320377 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
320408 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:320468 original size:13 final size:13
Alignment explanation
Indices: 320450--320475 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320440 CATTTTTCTG
320450 TGTATCGATACAT
1 TGTATCGATACAT
320463 TGTATCGATACAT
1 TGTATCGATACAT
320476 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320472 original size:33 final size:33
Alignment explanation
Indices: 320430--320496 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
320420 GCCAAGGAAA
***
320430 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
320463 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
320496 T
1 T
320497 TAGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:322890 original size:51 final size:53
Alignment explanation
Indices: 322826--323167 Score: 212
Period size: 52 Copynumber: 6.5 Consensus size: 53
322816 AGTTTATCAA
* * * *
322826 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
322877 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
322931 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * *
322989 TAT-TTC-CGA--GGGGATACTCCAACTCCGGTTTTA-TTGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * *
323038 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCAAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
323091 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
323143 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
323168 CTCGTTATTT
Statistics
Matches: 224, Mismatches: 39, Indels: 55
0.70 0.12 0.17
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 6 0.03
51 36 0.16
52 79 0.35
53 34 0.15
54 29 0.13
55 23 0.10
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:323010 original size:28 final size:27
Alignment explanation
Indices: 322943--323011 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
322933 CTTCACAATC
**
322943 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
322970 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
322998 GGGGATACTCCAAC
1 GGGGATACTCCAAC
323012 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:323151 original size:104 final size:103
Alignment explanation
Indices: 322831--323166 Score: 304
Period size: 104 Copynumber: 3.2 Consensus size: 103
322821 ATCAATTCTC
* * * *
322831 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAAACACAAATTTTCCTTTAATCGGGGAT
*
322895 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
65 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * * ** * * * * ** * *
322936 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCGA
1 CACAATCGGGGATACTCCAATCCGGTTTTATTTTC---AAAACACAAATTTTCCTTTA-AT-C--
* * * *
322998 GGGGATACTCCAACTCCGGTTTTA-TTGCTAAAACACTAATTTTT
59 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
323042 CCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCAAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAATCC-GGTTTTATTTTCAAAACACAAATTTTCCTTTAATCGGGGA
*
323107 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
64 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
323147 CACAATCGAGGATACTCCAA
1 CACAATCGGGGATACTCCAA
323167 CCTCGTTATT
Statistics
Matches: 177, Mismatches: 40, Indels: 29
0.72 0.16 0.12
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 38 0.21
106 16 0.09
107 36 0.20
108 9 0.05
109 28 0.16
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (103 bp):
CACAATCGGGGATACTCCAATCCGGTTTTATTTTCAAAACACAAATTTTCCTTTAATCGGGGATA
CTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:323187 original size:28 final size:28
Alignment explanation
Indices: 323151--323227 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
323141 ATTTTTCACA
* * *
323151 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
323179 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
323207 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
323228 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:323196 original size:212 final size:212
Alignment explanation
Indices: 322829--323235 Score: 649
Period size: 212 Copynumber: 1.9 Consensus size: 212
322819 TTATCAATTC
* *
322829 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGGGGA
* *
322894 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
322959 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
323024 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
323041 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCAAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACAAATTTT-CTATAATCGGG
*
323105 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
323168 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
323233 ATT
193 ATT
323236 CCCAAAATAT
Statistics
Matches: 179, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
211 31 0.17
212 113 0.63
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATT
GCTAAAACACTAATTTT
Found at i:323294 original size:107 final size:107
Alignment explanation
Indices: 322889--323306 Score: 303
Period size: 107 Copynumber: 3.9 Consensus size: 107
322879 TTCTATAATC
* * * * *
322889 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * *
322954 AACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
64 AACCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
* ** * * * * * *
322998 GGGGATACTCCAACTCCGGTTTTA-TTGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCT-CACAATCGAGGATACTCCA
* * * ***** * * * ** * *
323062 ATCCTGGT-TTTATTTTCAAAACGCAAATTTTCCTTTA-AT-C--
65 ACCCCGTTATTTATCGGGGATACTCCAA--CCCCGTTACTTCCGA
* * *
323102 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
323167 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAACCCCGTTACTTCCGA
* * *** * * *
323210 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
323274 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAACCCCG
323307 ATTTTTTTTT
Statistics
Matches: 239, Mismatches: 58, Indels: 26
0.74 0.18 0.08
Matches are distributed among these distances:
104 50 0.21
105 23 0.10
106 20 0.08
107 95 0.40
108 29 0.12
109 22 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAACCCCGTTACTTCCGA
Found at i:324427 original size:20 final size:20
Alignment explanation
Indices: 324402--324439 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
324392 TTTCTTAGCC
324402 TTTTTTTTTGTTTTTGCTTT
1 TTTTTTTTTGTTTTTGCTTT
*
324422 TTTTTTTTTTTTTTTGCT
1 TTTTTTTTTGTTTTTGCT
324440 AAGTTTCCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.05, G:0.08, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTGTTTTTGCTTT
Found at i:324433 original size:17 final size:17
Alignment explanation
Indices: 324401--324432 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
324391 TTTTCTTAGC
324401 CTTTTTTTTTGTTTTTG
1 CTTTTTTTTTGTTTTTG
324418 CTTTTTTTTT-TTTTT
1 CTTTTTTTTTGTTTTT
324433 TTTTGCTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (17 bp):
CTTTTTTTTTGTTTTTG
Found at i:325198 original size:154 final size:154
Alignment explanation
Indices: 324897--325318 Score: 406
Period size: 154 Copynumber: 2.7 Consensus size: 154
324887 ATAAAAATGC
* * * * * ** * *
324897 AAAACTCATAAAATAAATTGAATT-TTCATAATCTTATCTAGTATGAATTTATTAAA-AACATTT
1 AAAACTTATAAAATAAATTGAATTCTT-AAAAACTAATCTAATATGAA-TTAAAAAATAATAATT
** * * * * * * *
324960 GATGAATTTTAAAAATTTTAAAATGAGAAAGATCCAACAGAAAAAATTTACAGAGTAGAAAACTC
64 GAAAAATTTTAAAAATTATAAACTTAGAAAAATCCTACTGAAAAAATTTACAGAGTAGAAAAATC
* *
325025 CGTACATTGAAATAGGAAAAA-TTCT
129 CATACATTGAAACAGGAAAAATTTCT
* * * *
325050 AAAACTTATAAAATAAATTGAA-TCTTTTAAAATTGATCTAATTTGAATTAAAAAAATAATAATT
1 AAAACTTATAAAATAAATTGAATTC-TTAAAAACTAATCTAATATGAATT-AAAAAATAATAATT
* * *
325114 GAAAAATTTTAAAAATTATAAACTTAGAAAAATCCTACTGGAGAAATTTACGGAGTAGAAAAATC
64 GAAAAATTTTAAAAATTATAAACTTAGAAAAATCCTACTGAAAAAATTTACAGAGTAGAAAAATC
** *
325179 CATATTTTGGTAACA-GAAAAATTTCT
129 CATACATT-GAAACAGGAAAAATTTCT
* * * *
325205 AAAACTTATAAAATAAATTTAATTCTTAAAAACTAATTTAATATGAATTAAACAATAATATTTGA
1 AAAACTTATAAAATAAATTGAATTCTTAAAAACTAATCTAATATGAATTAAAAAATAATAATTGA
* * * *
325270 AGAATTTTGAAAATTATAAACTTAAAAAAAATCCTACT-AAACAATTTAC
66 AAAATTTTAAAAATTATAAACTT-AGAAAAATCCTACTGAAAAAATTTAC
325319 GAAGTGAAAA
Statistics
Matches: 218, Mismatches: 43, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
152 3 0.01
153 38 0.17
154 114 0.52
155 61 0.28
156 2 0.01
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (154 bp):
AAAACTTATAAAATAAATTGAATTCTTAAAAACTAATCTAATATGAATTAAAAAATAATAATTGA
AAAATTTTAAAAATTATAAACTTAGAAAAATCCTACTGAAAAAATTTACAGAGTAGAAAAATCCA
TACATTGAAACAGGAAAAATTTCT
Found at i:325236 original size:19 final size:20
Alignment explanation
Indices: 325209--325246 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
325199 ATTTCTAAAA
325209 CTTATAAAA-TAAATTTAATT
1 CTTATAAAACT-AATTTAATT
325229 CTTA-AAAACTAATTTAAT
1 CTTATAAAACTAATTTAAT
325247 ATGAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (20 bp):
CTTATAAAACTAATTTAATT
Found at i:325319 original size:154 final size:152
Alignment explanation
Indices: 325040--325329 Score: 388
Period size: 155 Copynumber: 1.9 Consensus size: 152
325030 ATTGAAATAG
* * * *
325040 GAAAAATTCTAAAACTTATAAAATAAATTGAATCTTTTAAAATTGATCTAATTTGAATTAAAAAA
1 GAAAAATTCTAAAACTTATAAAATAAATTGAATCTTTAAAAACTAATCTAATATGAATTAAAAAA
* * *
325105 ATAATAATTGAAAAATTTTAAAAATTATAAACTTAGAAAAATCCTACTGGAGAAATTTACGGAGT
66 ATAATAATTGAAAAATTTTAAAAATTATAAACTTAAAAAAATCCTACT-GAAAAATTTACGAAGT
325170 AGAAAAATCCATATTTTGGTAACA
130 -GAAAAATCCATATTTTGGTAACA
* *
325194 GAAAAATTTCTAAAACTTATAAAATAAATTTAAT-TCTTAAAAACTAATTTAATATGAATT-AAA
1 GAAAAA-TTCTAAAACTTATAAAATAAATTGAATCT-TTAAAAACTAATCTAATATGAATTAAAA
* * * *
325257 CAATAATATTTGAAGAATTTTGAAAATTATAAACTTAAAAAAAATCCTACT-AAACAATTTACGA
64 AAATAATAATTGAAAAATTTTAAAAATTATAAACTT-AAAAAAATCCTACTGAAA-AATTTACGA
325321 AGTGAAAAA
127 AGTGAAAAA
325330 CTTCTGTTAG
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
153 8 0.07
154 53 0.45
155 58 0.49
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (152 bp):
GAAAAATTCTAAAACTTATAAAATAAATTGAATCTTTAAAAACTAATCTAATATGAATTAAAAAA
ATAATAATTGAAAAATTTTAAAAATTATAAACTTAAAAAAATCCTACTGAAAAATTTACGAAGTG
AAAAATCCATATTTTGGTAACA
Found at i:325703 original size:20 final size:20
Alignment explanation
Indices: 325655--325706 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
325645 GTATCGTTAC
* *
325655 AATGTATCAATACATGACTA
1 AATGTATCGATACATGAATA
* *
325675 AATGTATCGATACTTGAATT
1 AATGTATCGATACATGAATA
325695 AATGTATCGATA
1 AATGTATCGATA
325707 TAAGTCATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATGAATA
Found at i:325778 original size:13 final size:13
Alignment explanation
Indices: 325760--325784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325750 ACACACAATA
325760 TGTATCGATACAT
1 TGTATCGATACAT
325773 TGTATCGATACA
1 TGTATCGATACA
325785 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:325781 original size:32 final size:33
Alignment explanation
Indices: 325740--325807 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
325730 GTAGCTAAAT
* *
325740 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCAATACA
*
325772 TTGTATCGATACACCATAAAATGTATCAATACA
1 TTGTATCGATACACCACAAAATGTATCAATACA
325805 TTG
1 TTG
325808 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCAATACA
Found at i:329437 original size:13 final size:13
Alignment explanation
Indices: 329419--329444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329409 CAATTTTTTG
329419 TGTATCGATACAT
1 TGTATCGATACAT
329432 TGTATCGATACAT
1 TGTATCGATACAT
329445 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:330184 original size:21 final size:21
Alignment explanation
Indices: 330143--330186 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
330133 CTCTCCTTTA
* *
330143 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
330164 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
330185 TC
1 TC
330187 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:331868 original size:21 final size:20
Alignment explanation
Indices: 331822--331868 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
331812 TTTGATGCTA
331822 ATTTTGATGAAAAACGAAGT
1 ATTTTGATGAAAAACGAAGT
331842 -TATTTGAAGTGAAAAAC-AAGT
1 AT-TTTG-A-TGAAAAACGAAGT
331863 ATTTTG
1 ATTTTG
331869 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTTGATGAAAAACGAAGT
Found at i:332007 original size:13 final size:13
Alignment explanation
Indices: 331989--332027 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
331979 ATAATCACCC
*
331989 TGTATCGATACAG
1 TGTATCGATACAA
332002 TGTATCGATACAA
1 TGTATCGATACAA
332015 TGTATCGATACAA
1 TGTATCGATACAA
332028 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:332038 original size:20 final size:20
Alignment explanation
Indices: 332013--332091 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
332003 GTATCGATAC
332013 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
332033 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
332058 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
332078 CATGTATCGATACA
1 AATGTATCGATACA
332092 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:334127 original size:15 final size:15
Alignment explanation
Indices: 334107--334137 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
334097 ATTTCGTTTG
*
334107 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
334122 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
334137 G
1 G
334138 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:335970 original size:21 final size:21
Alignment explanation
Indices: 335941--335985 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
335931 AAGTTTTCAT
*
335941 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
335961 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
335983 TTT
1 TTT
335986 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:338348 original size:93 final size:93
Alignment explanation
Indices: 338216--338412 Score: 385
Period size: 93 Copynumber: 2.1 Consensus size: 93
338206 ATCGATACAT
*
338216 TGTATCGACACATACTTGCTGTATCGATACAAGTTTGGCTACTGCCAAGAAATGTATCGATACAT
1 TGTATCGATACATACTTGCTGTATCGATACAAGTTTGGCTACTGCCAAGAAATGTATCGATACAT
338281 CTTTTTCATGTATCGATACATTGCAACA
66 CTTTTTCATGTATCGATACATTGCAACA
338309 TGTATCGATACATACTTGCTGTATCGATACAAGTTTGGCTACTGCCAAGAAATGTATCGATACAT
1 TGTATCGATACATACTTGCTGTATCGATACAAGTTTGGCTACTGCCAAGAAATGTATCGATACAT
338374 CTTTTTCATGTATCGATACATTGCAACA
66 CTTTTTCATGTATCGATACATTGCAACA
338402 TGTATCGATAC
1 TGTATCGATAC
338413 TTTGAATTGT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 103 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (93 bp):
TGTATCGATACATACTTGCTGTATCGATACAAGTTTGGCTACTGCCAAGAAATGTATCGATACAT
CTTTTTCATGTATCGATACATTGCAACA
Found at i:342019 original size:13 final size:13
Alignment explanation
Indices: 342001--342036 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
341991 GCATTCTCTA
*
342001 TATCGATACATTG
1 TATCGATACACTG
342014 TATCGATACACTG
1 TATCGATACACTG
342027 TATCGATACA
1 TATCGATACA
342037 AGGGGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (13 bp):
TATCGATACACTG
Found at i:343900 original size:22 final size:21
Alignment explanation
Indices: 343875--343918 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
343865 CGAAATTGTC
*
343875 AAATTATTTTACTAAGGGGGAG
1 AAATT-TTTGACTAAGGGGGAG
*
343897 AAATTTTTGATTAAGGGGGAG
1 AAATTTTTGACTAAGGGGGAG
343918 A
1 A
343919 GAAAAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (21 bp):
AAATTTTTGACTAAGGGGGAG
Found at i:344574 original size:33 final size:32
Alignment explanation
Indices: 344517--344580 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
344507 CTAAATTTGT
*
344517 ATCGATACACACAATATGTATCGATACATTGC
1 ATCGATACACACAAAATGTATCGATACATTGC
*
344549 ATCGATACACCATAAAATGTATCGATACATTG
1 ATCGATACA-CACAAAATGTATCGATACATTG
344581 GCTTGTAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (32 bp):
ATCGATACACACAAAATGTATCGATACATTGC
Found at i:348364 original size:16 final size:16
Alignment explanation
Indices: 348345--348375 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
348335 TGTTCCGAAT
348345 AACTCTTGTTTAGAAA
1 AACTCTTGTTTAGAAA
*
348361 AACTTTTGTTTAGAA
1 AACTCTTGTTTAGAA
348376 CAGTTGGTGG
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:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (16 bp):
AACTCTTGTTTAGAAA
Found at i:349158 original size:17 final size:18
Alignment explanation
Indices: 349136--349169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
349126 ATCACCTTTT
349136 ATGAAA-AATGCATTTGA
1 ATGAAATAATGCATTTGA
*
349153 ATGAAATGATGCATTTG
1 ATGAAATAATGCATTTG
349170 TTAGATGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (18 bp):
ATGAAATAATGCATTTGA
Found at i:351069 original size:2 final size:2
Alignment explanation
Indices: 351062--351086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
351052 CTCCAAGTCC
351062 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
351087 GTACACGCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353566 original size:86 final size:85
Alignment explanation
Indices: 353439--353597 Score: 230
Period size: 86 Copynumber: 1.9 Consensus size: 85
353429 CTTGAATTAG
* ** *
353439 ATTAAATTAATTAAGAGATAAAAAAAAAGTTATCTCTAATTATTTTAAATTAATTAAGAAATCAA
1 ATTAAATTAATTAAGAAATAAAAAAAAAGTTATCTCTAATTAAATTAAATTAATTAAGAAATAAA
353504 TAAATAAATTTTTTAATTTA
66 TAAATAAATTTTTTAATTTA
* *
353524 ATTAAATTAATTAA-AAATAAATAAAAAATTTTATCTTTAATTAAATTAAATTAATTAAGAAATA
1 ATTAAATTAATTAAGAAATAAA-AAAAAA-GTTATCTCTAATTAAATTAAATTAATTAAGAAATA
*
353588 AATATATAAA
64 AATAAATAAA
353598 GGATGTAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 6 0.09
85 20 0.31
86 39 0.60
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (85 bp):
ATTAAATTAATTAAGAAATAAAAAAAAAGTTATCTCTAATTAAATTAAATTAATTAAGAAATAAA
TAAATAAATTTTTTAATTTA
Found at i:357166 original size:2 final size:2
Alignment explanation
Indices: 357159--357183 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
357149 GAAGCCAAGC
357159 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
357184 TTTCTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:357500 original size:13 final size:13
Alignment explanation
Indices: 357482--357508 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
357472 ATTTTTATTT
357482 TATTTATGTTATA
1 TATTTATGTTATA
357495 TATTTATGTTATA
1 TATTTATGTTATA
357508 T
1 T
357509 TGTTTTTGTA
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TATTTATGTTATA
Found at i:358475 original size:19 final size:19
Alignment explanation
Indices: 358444--358480 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
358434 ATCAAAAACG
358444 GTATTTCAAAATAATTTTTT
1 GTATTTCAAAAT-ATTTTTT
358464 GTATTT-AAAATATTTTT
1 GTATTTCAAAATATTTTT
358481 GAGACAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
GTATTTCAAAATATTTTTT
Found at i:358771 original size:92 final size:92
Alignment explanation
Indices: 358538--358774 Score: 332
Period size: 92 Copynumber: 2.6 Consensus size: 92
358528 GTTAAATACT
* * * *
358538 AATGTATTGATACATCTA-GTGAATGTATCGATACATATGGTTGGCAATAACTACAAAATGTTAA
1 AATGTATCGATACAT-TATGTGAATGTATCGATACATATAGTTGGCAGTAGCTACAAAATGTTAA
*
358602 AACCCTTATTTTTACTAATACAAGTGAA
65 AACCCTTATTTTTACCAATACAAGTGAA
* * *
358630 AAAGTATCGATACATAATGTGAATGTATCGATACATATAATTGGCAGTAGCTACAAAATGTTAAA
1 AATGTATCGATACATTATGTGAATGTATCGATACATATAGTTGGCAGTAGCTACAAAATGTTAAA
*
358695 ACCCTTATTTTTACCGATACAAGTGAA
66 ACCCTTATTTTTACCAATACAAGTGAA
* * * * *
358722 AATGTATCGATACATTATATGGATGTATCGATACATTTTGTTGGTAGTAGCTA
1 AATGTATCGATACATTATGTGAATGTATCGATACATATAGTTGGCAGTAGCTA
358775 AACAAATCTT
Statistics
Matches: 127, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
91 1 0.01
92 126 0.99
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (92 bp):
AATGTATCGATACATTATGTGAATGTATCGATACATATAGTTGGCAGTAGCTACAAAATGTTAAA
ACCCTTATTTTTACCAATACAAGTGAA
Found at i:358847 original size:20 final size:20
Alignment explanation
Indices: 358824--358862 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
358814 AAATGTATGG
358824 ATACAATACA-GAATGTATTA
1 ATAC-ATACATGAATGTATTA
*
358844 ATACATCCATGAATGTATT
1 ATACATACATGAATGTATT
358863 GATATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (20 bp):
ATACATACATGAATGTATTA
Found at i:359807 original size:19 final size:20
Alignment explanation
Indices: 359785--359823 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
359775 GTTCATTCCA
*
359785 TAAT-GAGACATCTATTCTT
1 TAATGGAGACAACTATTCTT
*
359804 TAATGGTGACAACTATTCTT
1 TAATGGAGACAACTATTCTT
359824 ATTGGAAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (20 bp):
TAATGGAGACAACTATTCTT
Found at i:363651 original size:19 final size:20
Alignment explanation
Indices: 363610--363657 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
363600 TTTTCTAGAA
363610 TTTTTTCTTATTATCTGCAG
1 TTTTTTCTTATTATCTGCAG
*
363630 TTTTTT-TTATTAT-TTCATG
1 TTTTTTCTTATTATCTGCA-G
363649 TTTTTTCTT
1 TTTTTTCTT
363658 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.71
Consensus pattern (20 bp):
TTTTTTCTTATTATCTGCAG
Found at i:367981 original size:20 final size:20
Alignment explanation
Indices: 367958--368030 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
367948 ACAACTCAAA
367958 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
367978 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
367999 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
368019 GTATCGATACAT
1 GTATCGATACAT
368031 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:368002 original size:21 final size:21
Alignment explanation
Indices: 367976--368051 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
367966 ACATGTTGCA
367976 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
367997 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
368017 ATGTATCGATACAT-AAAAAGG
1 ATGTATCGATACATGAAAAA-G
368038 ATGTATCGATACAT
1 ATGTATCGATACAT
368052 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 14 0.31
21 30 0.67
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:368009 original size:41 final size:41
Alignment explanation
Indices: 367958--368051 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
367948 ACAACTCAAA
367958 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-GAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGGAT
367999 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
368040 GTATCGATACAT
1 GTATCGATACAT
368052 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 5 0.10
41 47 0.90
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
Found at i:368108 original size:13 final size:13
Alignment explanation
Indices: 368090--368115 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
368080 TACAGCAAGT
368090 ATGTATCGATACA
1 ATGTATCGATACA
368103 ATGTATCGATACA
1 ATGTATCGATACA
368116 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:372197 original size:15 final size:15
Alignment explanation
Indices: 372177--372207 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
372167 TAAAAATGTC
*
372177 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
372192 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
372207 C
1 C
372208 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:374003 original size:1 final size:1
Alignment explanation
Indices: 373997--374048 Score: 104
Period size: 1 Copynumber: 52.0 Consensus size: 1
373987 CCTTAATTGT
373997 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
374049 TGAAATCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:374332 original size:20 final size:21
Alignment explanation
Indices: 374254--374331 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
374244 ATGTCCAAAA
*
374254 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
374274 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
374298 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
374319 TGTATCGATACAT
1 TGTATCGATACAT
374332 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:374336 original size:13 final size:13
Alignment explanation
Indices: 374318--374356 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
374308 ACATTTTTTG
374318 TTGTATCGATACA
1 TTGTATCGATACA
374331 TTGTATCGATACA
1 TTGTATCGATACA
*
374344 CTGTATCGATACA
1 TTGTATCGATACA
374357 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:376184 original size:17 final size:17
Alignment explanation
Indices: 376162--376208 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
376152 AATTACTTGA
376162 TTAAGGGGGAGATTTTT
1 TTAAGGGGGAGATTTTT
376179 TTAAGGGGGAGATTTTT
1 TTAAGGGGGAGATTTTT
*
376196 TAAACGGGGGAGA
1 TTAA-GGGGGAGA
376209 CAAAGGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.28, C:0.02, G:0.38, T:0.32
Consensus pattern (17 bp):
TTAAGGGGGAGATTTTT
Found at i:376836 original size:20 final size:20
Alignment explanation
Indices: 376813--376885 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
376803 ACAACTCAAA
376813 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
376833 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
376854 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
376874 GTATCGATACAT
1 GTATCGATACAT
376886 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:376857 original size:21 final size:21
Alignment explanation
Indices: 376831--376906 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
376821 ACATGTTGCA
376831 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
376852 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
376872 ATGTATCGATACAT-AAAAAGG
1 ATGTATCGATACATGAAAAA-G
376893 ATGTATCGATACAT
1 ATGTATCGATACAT
376907 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 14 0.31
21 30 0.67
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:376864 original size:41 final size:41
Alignment explanation
Indices: 376813--376906 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
376803 ACAACTCAAA
376813 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-GAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGGAT
376854 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
376895 GTATCGATACAT
1 GTATCGATACAT
376907 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 5 0.10
41 47 0.90
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
Found at i:376963 original size:13 final size:13
Alignment explanation
Indices: 376945--376970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
376935 TACAGCAAGT
376945 ATGTATCGATACA
1 ATGTATCGATACA
376958 ATGTATCGATACA
1 ATGTATCGATACA
376971 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:379206 original size:5 final size:5
Alignment explanation
Indices: 379163--379187 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
379153 TGGGAAAGAT
379163 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
379188 TTCAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:379320 original size:28 final size:28
Alignment explanation
Indices: 379284--379360 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
379274 AGTTTTCACA
379284 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
* *
379312 ATCGGGGATACTCTAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
379340 -T-GAGGTGATACTCCAACCCCG
1 ATCG-GG-GATACTCCAACCCCG
379361 GCTTTATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 39 0.91
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:379452 original size:51 final size:51
Alignment explanation
Indices: 379346--379461 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
379336 TTTCTGAGGT
379346 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCAGA
1 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCAGA
* * * ** *
379397 GATACTTCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCATAATTGGG
1 GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCAGA
379448 GATACTCCAACCCC
1 GATACTCCAACCCC
379462 ATTATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCAGA
Found at i:383757 original size:31 final size:31
Alignment explanation
Indices: 383722--383798 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
383712 TACATTGAAT
* * * *
383722 AATGTATCGATGCATCTGGGTAAAAAGAGAG
1 AATGTATCGATACATCTAGGTAAAAAGACAA
383753 AATGTATCGATACATCTAGGTAAAAAGACAA
1 AATGTATCGATACATCTAGGTAAAAAGACAA
383784 AATGTATCGATACAT
1 AATGTATCGATACAT
383799 TACATGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.25
Consensus pattern (31 bp):
AATGTATCGATACATCTAGGTAAAAAGACAA
Found at i:383807 original size:17 final size:17
Alignment explanation
Indices: 383785--383817 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
383775 AAAAGACAAA
383785 ATGTATCGATACATTAC
1 ATGTATCGATACATTAC
383802 ATGTATCGATACATTA
1 ATGTATCGATACATTA
383818 TATCTGGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (17 bp):
ATGTATCGATACATTAC
Found at i:383971 original size:20 final size:20
Alignment explanation
Indices: 383946--383998 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
383936 TCCCAAATGT
383946 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
383966 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
*
383986 TAATGTATCGATA
1 AAATGTATCGATA
383999 TATTTCCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Found at i:384043 original size:13 final size:13
Alignment explanation
Indices: 384027--384054 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
384017 TAGGGCAGCT
384027 TTGTATCGATACA
1 TTGTATCGATACA
384040 TTGTATCGATACA
1 TTGTATCGATACA
384053 TT
1 TT
384055 TACTATTTGT
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:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:385367 original size:19 final size:20
Alignment explanation
Indices: 385324--385375 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
385314 GTCAAAACCC
*
385324 ATGTCTCGATACAATAAATA
1 ATGTATCGATACAATAAATA
*
385344 ATGTATCGATACAATAGA-A
1 ATGTATCGATACAATAAATA
385363 ATGTATCGATACA
1 ATGTATCGATACA
385376 TTTTCCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAATAAATA
Found at i:385918 original size:24 final size:24
Alignment explanation
Indices: 385891--385938 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
385881 ATAGTTATTA
*
385891 TCGAG-GATACTCCAACCCTATTTT
1 TCGAGAGACACTCC-ACCCTATTTT
385915 TCGAGAAGACACTCCACCCTATTT
1 TCGAG-AGACACTCCACCCTATTT
385939 GTTAAGCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.29
Consensus pattern (24 bp):
TCGAGAGACACTCCACCCTATTTT
Found at i:386054 original size:96 final size:97
Alignment explanation
Indices: 385954--386132 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 97
385944 GCTCATCAAG
* * ** *
385954 ATTTAAATATTATTTTTGCTTAAATTGTTATCATCAGGGATGCTCCAACCCC-ATCATCCGAGGG
1 ATTTAAATATTATTTTTGCTTAAATTGTCATCATCAGGAACACTCCAACCCCAATCATCCGAAGG
* *
386018 GATACTCCAGCCCTATTTTCAAACTCGTTAAC
66 GACACTCCAGCCCCATTTTCAAACTCGTTAAC
* *
386050 ATTTAAATCTTATTTTTGCTTAAATTGTCATCATCAGGAACACTCCAACCCCAATCCTCCGAAGG
1 ATTTAAATATTATTTTTGCTTAAATTGTCATCATCAGGAACACTCCAACCCCAATCATCCGAAGG
*
386115 GACACTCCATCCCCATTT
66 GACACTCCAGCCCCATTT
386133 GTAACCAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
96 47 0.65
97 25 0.35
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (97 bp):
ATTTAAATATTATTTTTGCTTAAATTGTCATCATCAGGAACACTCCAACCCCAATCATCCGAAGG
GACACTCCAGCCCCATTTTCAAACTCGTTAAC
Found at i:392976 original size:80 final size:80
Alignment explanation
Indices: 392814--393135 Score: 327
Period size: 80 Copynumber: 4.0 Consensus size: 80
392804 TCAAAAAGGG
* * * * *
392814 TACTCTAACTTCGTTTTTACTTCCTAAACATTGAATGTTTCA-CCTCTGGG-ATACTCCAACCCC
1 TACTCCAACCTCGTTTTTACTTCCAAAACATTGAATTTTTCATCTTC-GGGAATACTCCAACCCC
* *
392877 ATCATCTTCT-AGGCGA
65 ACCATC-TCTGAGGGGA
* ***
392893 TACTCCAACCTCGTTTTTACTTTCAAAACACCAAATTTTTCATCTTCGGGAATACTCCAACCCCA
1 TACTCCAACCTCGTTTTTACTTCCAAAACATTGAATTTTTCATCTTCGGGAATACTCCAACCCCA
392958 CCATCTCTGAGGGGA
66 CCATCTCTGAGGGGA
** * *
392973 TACTCCAACCTAATTTTTACTTCCAAAACATTGAATTTTTCAT-TTCTAGGCATACTCCAACCCC
1 TACTCCAACCTCGTTTTTACTTCCAAAACATTGAATTTTTCATCTTC-GGGAATACTCCAACCCC
**
393037 ACCATCT-TCGAACGGA
65 ACCATCTCT-GAGGGGA
* * * *
393053 TGCTCTAACC-CTGTTTTTACTTCCAAAAACATTGAATTTTTCATCTTGGGGGATACTCCAA-CC
1 TACTCCAACCTC-GTTTTTACTTCC-AAAACATTGAATTTTTCATCTTCGGGAATACTCCAACCC
* *
393116 C-CCATCTCCGAGAGGA
64 CACCATCTCTGAGGGGA
393132 TACT
1 TACT
393136 TTAACCTTAT
Statistics
Matches: 202, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
79 58 0.29
80 112 0.55
81 30 0.15
82 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.11, T:0.33
Consensus pattern (80 bp):
TACTCCAACCTCGTTTTTACTTCCAAAACATTGAATTTTTCATCTTCGGGAATACTCCAACCCCA
CCATCTCTGAGGGGA
Found at i:393121 original size:159 final size:160
Alignment explanation
Indices: 392827--393155 Score: 398
Period size: 160 Copynumber: 2.1 Consensus size: 160
392817 TCTAACTTCG
* * * * *
392827 TTTTTACTTCCTAAACATTGAATGTTTCACCTCTGGGATACTCCAACCCCATCATCTTCTAGGCG
1 TTTTTACTTCCAAAACATTGAATGTTTCACCTCTGGCATACTCCAACCCCACCATCTTCAACGCG
*
392892 ATACTCCAACCTCGTTTTTACTTTCAAAACACCAAATTTTTCATCTTCGGGAATACTCCAACCCC
66 ATACTCCAACCTCGTTTTTACTTCCAAAACACCAAATTTTTCATCTTCGGGAATACTCCAACCCC
* *
392957 ACCATCTCTGAGGGGATACTCCAACC-TAA
131 ACCATCTCCGAGAGGATACTCCAACCTTAA
* **
392986 TTTTTACTTCCAAAACATTGAATTTTTCATTTCTAGGCATACTCCAACCCCACCATCTTCGAACG
1 TTTTTACTTCCAAAACATTGAATGTTTCACCTCT-GGCATACTCCAACCCCACCATCTTC-AACG
* * *** * *
393051 -GATGCTCTAACC-CTGTTTTTACTTCCAAAAACATTGAATTTTTCATCTTGGGGGATACTCCAA
64 CGATACTCCAACCTC-GTTTTTACTTCC-AAAACACCAAATTTTTCATCTTCGGGAATACTCCAA
** *
393114 -CCC-CCATCTCCGAGAGGATACTTTAACCTTAT
127 CCCCACCATCTCCGAGAGGATACTCCAACCTTAA
393146 TTTTTACTTC
1 TTTTTACTTC
393156 TACAATACCG
Statistics
Matches: 144, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
159 52 0.36
160 59 0.41
161 33 0.23
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (160 bp):
TTTTTACTTCCAAAACATTGAATGTTTCACCTCTGGCATACTCCAACCCCACCATCTTCAACGCG
ATACTCCAACCTCGTTTTTACTTCCAAAACACCAAATTTTTCATCTTCGGGAATACTCCAACCCC
ACCATCTCCGAGAGGATACTCCAACCTTAA
Found at i:398553 original size:20 final size:20
Alignment explanation
Indices: 398510--398555 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
398500 AAATCTTTTG
398510 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
398531 CAAATTACTTAGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
398551 CAAAA
1 CAAAA
398556 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:399415 original size:13 final size:13
Alignment explanation
Indices: 399397--399422 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
399387 TACAGCAAGT
399397 ATGTATCGATACA
1 ATGTATCGATACA
399410 ATGTATCGATACA
1 ATGTATCGATACA
399423 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:401681 original size:21 final size:21
Alignment explanation
Indices: 401643--401687 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
401633 TTGCAAGTTG
*
401643 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
401665 AAATAATGAA-TTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
401685 AAA
1 AAA
401688 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:403511 original size:15 final size:15
Alignment explanation
Indices: 403491--403521 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
403481 TAAAAATGTC
*
403491 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
403506 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
403521 C
1 C
403522 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:405581 original size:13 final size:13
Alignment explanation
Indices: 405563--405600 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
405553 GGAAATTCTA
*
405563 TGTATCGATACAT
1 TGTATCGATACAC
405576 TGTATCGATACAC
1 TGTATCGATACAC
405589 TGTATCGATACA
1 TGTATCGATACA
405601 GTGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:405745 original size:21 final size:21
Alignment explanation
Indices: 405721--405767 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
405711 AAATCCTTTG
405721 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
405742 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
405762 CAAAAT
1 CAAAAT
405768 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:405764 original size:20 final size:19
Alignment explanation
Indices: 405723--405765 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
405713 ATCCTTTGCA
405723 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
405743 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
405763 AAA
1 AAA
405766 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:408126 original size:13 final size:13
Alignment explanation
Indices: 408108--408133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
408098 TACAGCAAGT
408108 ATGTATCGATACA
1 ATGTATCGATACA
408121 ATGTATCGATACA
1 ATGTATCGATACA
408134 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:410707 original size:132 final size:132
Alignment explanation
Indices: 410540--410805 Score: 523
Period size: 132 Copynumber: 2.0 Consensus size: 132
410530 AATAAATTTT
*
410540 GTACCAAATGATTTTTGATTCACCAAATGTTTTCTAGTTAAGTACAAATGTTTTCAAGGCTTAAA
1 GTACCAAATGATTTTTGATTCACCAAACGTTTTCTAGTTAAGTACAAATGTTTTCAAGGCTTAAA
410605 ATGATTGATTTTTAAGTTAAATTATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTA
66 ATGATTGATTTTTAAGTTAAATTATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTA
410670 AG
131 AG
410672 GTACCAAATGATTTTTGATTCACCAAACGTTTTCTAGTTAAGTACAAATGTTTTCAAGGCTTAAA
1 GTACCAAATGATTTTTGATTCACCAAACGTTTTCTAGTTAAGTACAAATGTTTTCAAGGCTTAAA
410737 ATGATTGATTTTTAAGTTAAATTATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTA
66 ATGATTGATTTTTAAGTTAAATTATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTA
410802 AG
131 AG
410804 GT
1 GT
410806 TGACTTAGGA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (132 bp):
GTACCAAATGATTTTTGATTCACCAAACGTTTTCTAGTTAAGTACAAATGTTTTCAAGGCTTAAA
ATGATTGATTTTTAAGTTAAATTATATCAAAGTATCGATACATAGGTATTTGTATCGATACATTA
AG
Found at i:410890 original size:20 final size:20
Alignment explanation
Indices: 410833--410913 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 20
410823 GTCAAAACCC
*
410833 TTAAAA-GTATCGATACACAG
1 TTAAAATGTATCGATACA-TG
*
410853 TTCAAA-GTATCGATACATG
1 TTAAAATGTATCGATACATG
*
410872 TTGAAATGTATCGATACATG
1 TTAAAATGTATCGATACATG
**
410892 AAAAAGATGTATCGATACATG
1 TTAAA-ATGTATCGATACATG
410913 T
1 T
410914 CATTGGGATT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.12
20 31 0.60
21 15 0.29
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
TTAAAATGTATCGATACATG
Found at i:410967 original size:19 final size:19
Alignment explanation
Indices: 410943--411007 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
410933 TAGCCAAACT
410943 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
410962 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
410975 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
410996 TGTATCGATACA
1 TGTATCGATACA
411008 TTGGCCTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:410979 original size:13 final size:13
Alignment explanation
Indices: 410961--410986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
410951 TACACAAAAT
410961 ATGTATCGATACA
1 ATGTATCGATACA
410974 ATGTATCGATACA
1 ATGTATCGATACA
410987 CAAAAAATAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:410984 original size:32 final size:33
Alignment explanation
Indices: 410943--411007 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
410933 TAGCCAAACT
410943 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
410975 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
411008 TTGGCCTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:412781 original size:164 final size:165
Alignment explanation
Indices: 412400--412798 Score: 384
Period size: 166 Copynumber: 2.4 Consensus size: 165
412390 AATTTTCATG
* * * **
412400 GGTTT-AAGATTTTTAAAATTAATCAAATATTATTATTTATTTCATATTAAATCAATTTTCAAAT
1 GGTTTCAA-ATTTTTAAAATTCATCAAATATTACTATTAAACTCATATTAAATCAATTTTCAAAT
* * **
412464 ATTCATTCATTTTCATTAGTTTTTGAATTTTTCCTTGAAATTCTCTTATTTTCGAAATATGGAAT
65 ATTCATTCATTTTCATTAGTTTTTGAATTTTTCCTTGAAATTCTCCTATTTTCGAAAAACCGAAT
* *
412529 TTTCTAATTCGTAAATTTTTCACGGGGGATTTTTCTT
130 TTTCTAATTCATAAATTTTTCAC-GAGGATTTTTCTT
* * * * *
412566 GGTTTCTAATTTTTAAAATTCATCAAATGTTACTATTTAATTCATATTAAATCATTTTTCAAA-A
1 GGTTTCAAATTTTTAAAATTCATCAAATATTACTATTAAACTCATATTAAATCAATTTTCAAATA
* * * * *
412630 GTTCATTCATTTTCATTCA-TTTTT-CATTTTTTCTTGAAATTTTCCTATTTT-TAAAAACCGAG
66 -TTCATTCATTTTCATT-AGTTTTTGAATTTTTCCTTGAAATTCTCCTATTTTCGAAAAACCGAA
* * *
412692 TTTTCTACTTTATAAATGTTTTTGA-GAGGATTTTTCTT
129 TTTTCTAATTCATAAA--TTTTTCACGAGGATTTTTCTT
* * * * *
412730 GGTTT-AAATTTTTTTAAATTCATCTAATATT-GTCATTAAACTC-TCATTAAATTAATTTTGAA
1 GGTTTCAAA-TTTTTAAAATTCATCAAATATTACT-ATTAAACTCAT-ATTAAATCAATTTTCAA
*
412792 AAATTCA
63 ATATTCA
412799 AATTATTTCT
Statistics
Matches: 194, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
163 4 0.02
164 81 0.42
165 25 0.13
166 82 0.42
167 2 0.01
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (165 bp):
GGTTTCAAATTTTTAAAATTCATCAAATATTACTATTAAACTCATATTAAATCAATTTTCAAATA
TTCATTCATTTTCATTAGTTTTTGAATTTTTCCTTGAAATTCTCCTATTTTCGAAAAACCGAATT
TTCTAATTCATAAATTTTTCACGAGGATTTTTCTT
Found at i:413343 original size:11 final size:10
Alignment explanation
Indices: 413309--413347 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
413299 CAAAAAAGGG
*
413309 AGAAAAAAAG
1 AGAAAAAAAA
413319 AGAAAGAAAAA
1 AGAAA-AAAAA
413330 AGAAAAAAACA
1 AGAAAAAAA-A
413341 AGAAAAA
1 AGAAAAA
413348 TAGCAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:415905 original size:165 final size:163
Alignment explanation
Indices: 415625--416552 Score: 487
Period size: 167 Copynumber: 5.6 Consensus size: 163
415615 TTCAAGCATC
* * * ** * *
415625 AAAATTCTTCAAATATTATCATTTAAATCCCATTAAATCAATT-TCAAAAAATTCTTTTTATTTT
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATC-ATTCT-AAAAAATT-TATTCATTTT
* * * * *
415689 -TTGAGTTATTG-A-TTTTCTTTTGGAATTCCTTTTGTTTTC-AAATTACGGTGTTTTCTTCTCC
63 CATAAGTT-TTGAATTTTTC-TTTGAAATGCCTATT-TTTTCGAAA-TACGGTGTTTTCTTCTCC
* * *
415750 ATAAAATTTTTCGAAAGGA-TTTTCATGGGTTTAAAATTTTT
124 ATAAAATTTTTCGAGAGGATTTTTC-TGAGTTTTAAA-TTTT
* ** *
415791 ACAATTCAAAAAATATTTTTATTTAATTCATATT-AATCAGTTCTAAAAAATTTATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCA-TTCTAAAAAATTTATTCATTTTCA
* * * *
415855 TAAATTTTTTAATTTTTTCTTTGAAAT-TCTCTTTTTTCGAAATACGGTGTTTTCTAT-T-CAGT
65 T-AAGTTTTGAA-TTTTTCTTTGAAATGCCTATTTTTTCGAAATACGGTGTTTTCT-TCTCCA-T
* * *
415917 -AAATTCTTTTGAGAGGATTTTTCTTAGTTTTCAATTTT
126 AAAATT-TTTCGAGAGGATTTTTCTGAGTTTTAAATTTT
* * * * *
415955 AAAATTCATCAAATATCATCATTTGATTCATATTAAATCATTTTTAAAAAATTAATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCA-TTCTAAAAAATTTATTCATTTTCA
* * * * * *
416020 TAAGTTTTGGATTTTTCTTTGAAATGCCTATTTTTTTGAAAAATC-GAGTTTTCTACTCCGTAAA
65 TAAGTTTTGAATTTTTCTTTGAAATGCCTATTTTTTCGAAATA-CGGTGTTTTCTTCTCCATAAA
* * ** *
416084 TTTTTTCGGGAGGATTTTTCTTGTTTTTTTAATTTT
129 ATTTTTCGAGAGGATTTTTC-TGAGTTTTAAATTTT
* *
416120 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCATTCTTCAAAATTTTATTCATTTTCA
1 AAAATTCATCAAATATTATTATTTAATTCATATTAAATCATTC-TAAAAAATTTATTCATTTTCA
* * ** * * * **** * * *
416185 TGAGTTTGTGAATTGTTTCCTTT-AAATTCCCCTTCTTCCAAAATATAAAGTTTTCTACT-CTTT
65 TAAGTTT-TGAATT-TTT-CTTTGAAATGCCTATTTTTTCGAAATACGGTGTTTTCTTCTCCATA
* * * * **
416248 AATTTTTTTGGGGGAGATTTTTCTTG-GTTTTTATTTTTT
127 AAATTTTTCGAGAG-GATTTTTC-TGAG-TTTTAAATTTT
* * * * ***
416287 AAAATTCATCAAATATCACTATTT-ATATCAAATTAAATAAATT-TACAAAAATCCCTTCATTTT
1 AAAATTCATCAAATATTATTATTTAAT-TCATATTAAAT-CATTCTA-AAAAATTTATTCATTTT
* * * * * * * * * ** *
416350 CTTGAGTTTTTGGATTTTTTCCTTT-AGATTCC-ATTGTTTCCAAAAAATGAAGTTTTCTACTCC
63 CATAAG-TTTT-GAATTTTT-CTTTGAAATGCCTATT-TTTTCGAAATACGGTGTTTTCTTCTCC
* * *
416413 ATAAATTTTTTC-AGGGGGATTTTTCTTG-GTTTTTAATTTTT
124 ATAAAATTTTTCGA-GAGGATTTTTC-TGAG-TTTTAAATTTT
* * * * * * * * *
416454 AAAATTCCTAAAATATCATTATTT-ATTCCATAATAAATCATTTTTCAAAAATTAATTAATTTTT
1 AAAATTCATCAAATATTATTATTTAATT-CATATTAAATCA-TTCTAAAAAATTTATTCATTTTC
* * *
416518 ATGAGTTTTGTATTTTTCTTTGAAATCCCTATTTT
64 ATAAGTTTTGAATTTTTCTTTGAAATGCCTATTTT
416553 CTTGAAAAAT
Statistics
Matches: 607, Mismatches: 116, Indels: 79
0.76 0.14 0.10
Matches are distributed among these distances:
163 14 0.02
164 98 0.16
165 172 0.28
166 76 0.13
167 214 0.35
168 33 0.05
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (163 bp):
AAAATTCATCAAATATTATTATTTAATTCATATTAAATCATTCTAAAAAATTTATTCATTTTCAT
AAGTTTTGAATTTTTCTTTGAAATGCCTATTTTTTCGAAATACGGTGTTTTCTTCTCCATAAAAT
TTTTCGAGAGGATTTTTCTGAGTTTTAAATTTT
Found at i:416300 original size:167 final size:164
Alignment explanation
Indices: 415786--416600 Score: 654
Period size: 167 Copynumber: 4.9 Consensus size: 164
415776 GGGTTTAAAA
* ** ** * *
415786 TTTTTACAATTCAAAAAATATTTTTATTTAATTCATATT-AATCAGTTC-TAAAAAATTTATTCA
1 TTTTTAAAATTCATCAAATATCATTATTT-ATTCATATTAAATCA-TTCTTCAAAAATTAATTCA
* * * * * * * * ** *
415849 TTTTCATAAATTTTTTAATTTTTTCTTTGAAATTCTCTTTTTTCGAAATACGGTGTTTTCTATTC
64 TTTTCATGAGTTTTTGAATTTTTCCTTTGAAATTCCCTTTTTCCAAAATATGAAGTTTTCTACTC
* * * * *
415914 AGTAAATTCTTTTGAGAGGATTTTTCTTAGTTTTCA-
129 A-TAAATTTTTTTGGGGGGATTTTTCTTGGTTTTTAT
* * * *
415950 ATTTTAAAATTCATCAAATATCATCATTTGATTCATATTAAATCATTTTTAAAAAATTAATTCAT
1 TTTTTAAAATTCATCAAATATCATTATTT-ATTCATATTAAATCATTCTTCAAAAATTAATTCAT
* * * * **
416015 TTTCATAAG-TTTTGGATTTTT-CTTTGAAATGCCTATTTTTTTGAAAA-ATCG-AGTTTTCTAC
65 TTTCATGAGTTTTTGAATTTTTCCTTTGAAATTCC--CTTTTTCCAAAATAT-GAAGTTTTCTAC
* * *
416076 TCCGTAAATTTTTTCGGGAGGATTTTTCTT-GTTTTT-T
127 T-CATAAATTTTTTTGGGGGGATTTTTCTTGGTTTTTAT
* * *
416113 TAATTTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATCATTCTTCAAAATTTTATTC
1 T--TTTTAAAATTCATCAAATATCATTATTT-ATTCATATTAAATCATTCTTCAAAAATTAATTC
* * *
416178 ATTTTCATGAGTTTGTGAATTGTTTCCTTT-AAATTCCCCTTCTTCCAAAATATAAAGTTTTCTA
63 ATTTTCATGAGTTTTTGAATT-TTTCCTTTGAAATT-CCCTTTTTCCAAAATATGAAGTTTTCTA
* *
416242 CTCTTTAATTTTTTTGGGGGAGATTTTTCTTGGTTTTTAT
126 CTCATAAATTTTTTTGGGGG-GATTTTTCTTGGTTTTTAT
* * * * ***
416282 TTTTTAAAATTCATCAAATATCACTATTTATATCAAATTAAATAAATT-TACAAAAATCCCTTCA
1 TTTTTAAAATTCATCAAATATCATTATTTAT-TCATATTAAAT-CATTCTTCAAAAATTAATTCA
* * * * *
416346 TTTTCTTGAGTTTTTGGATTTTTTCCTTT-AGATTCCATTGTTTCCAAAAAATGAAGTTTTCTAC
64 TTTTCATGAGTTTTT-GAATTTTTCCTTTGAAATTCCCTT-TTTCCAAAATATGAAGTTTTCTAC
** *
416410 TCCATAAATTTTTTCAGGGGGATTTTTCTTGGTTTTTAA
127 T-CATAAATTTTTTTGGGGGGATTTTTCTTGGTTTTTAT
* * * * *
416449 TTTTTAAAATTCCTAAAATATCATTATTTATTCCATAATAAATCATTTTTCAAAAATTAATTAAT
1 TTTTTAAAATTCATCAAATATCATTATTTATT-CATATTAAATCATTCTTCAAAAATTAATTCAT
* * * * * *
416514 TTTTATGAG-TTTTGTATTTTT-CTTTGAAA-TCCCTATTTTCTTGAAAA-ATCAAGATTTCTAT
65 TTTCATGAGTTTTTGAATTTTTCCTTTGAAATTCCCT-TTTTC--CAAAATATGAAGTTTTCTAC
* *
416575 TCCAGAAATATTTTTGGGGGGATTTT
127 T-CATAAATTTTTTTGGGGGGATTTT
416601 CTTCGGTCTA
Statistics
Matches: 528, Mismatches: 94, Indels: 57
0.78 0.14 0.08
Matches are distributed among these distances:
163 15 0.03
164 88 0.17
165 146 0.28
166 47 0.09
167 197 0.37
168 33 0.06
169 2 0.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (164 bp):
TTTTTAAAATTCATCAAATATCATTATTTATTCATATTAAATCATTCTTCAAAAATTAATTCATT
TTCATGAGTTTTTGAATTTTTCCTTTGAAATTCCCTTTTTCCAAAATATGAAGTTTTCTACTCAT
AAATTTTTTTGGGGGGATTTTTCTTGGTTTTTAT
Done.