Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 30 of 171
Found at i:13704519 original size:58 final size:57
Alignment explanation
Indices: 13704430--13704606 Score: 196
Period size: 56 Copynumber: 3.1 Consensus size: 57
13704420 TAATTTTAAA
* * * *
13704430 TTTTTAAATCTGGAAAAGGTGATATAGGCCATTGAGTGGTAAACAATCAAAAAAATATT
1 TTTTTAAATTTGAAAAAGGTGATGTA-GCCATTG-GTGGCAAACAATCAAAAAAATATT
* * * * *
13704489 TTTTTTAATTTGAAAAAAGTGATGTAGCCATTGGGTGACAAAC-ACCCAAAAAAT-TT
1 TTTTTAAATTTGAAAAAGGTGATGTAGCCATT-GGTGGCAAACAATCAAAAAAATATT
* * *
13704545 TTTTTAAATTTGAGAAAGGTGGTGTAGACCATTGGTGGCAAACACTCAAAAAAATATT
1 TTTTTAAATTTGAAAAAGGTGATGTAG-CCATTGGTGGCAAACAATCAAAAAAATATT
13704603 TTTT
1 TTTT
13704607 ATTCGTATTT
Statistics
Matches: 97, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
56 34 0.35
57 22 0.23
58 19 0.20
59 22 0.23
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (57 bp):
TTTTTAAATTTGAAAAAGGTGATGTAGCCATTGGTGGCAAACAATCAAAAAAATATT
Found at i:13718229 original size:12 final size:11
Alignment explanation
Indices: 13718212--13718241 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
13718202 GTAGTCCGTG
13718212 TTTTTTTGTTT
1 TTTTTTTGTTT
13718223 TTTTTTTGTTT
1 TTTTTTTGTTT
13718234 TCTTTTTT
1 T-TTTTTT
13718242 AGTTAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:13739440 original size:10 final size:10
Alignment explanation
Indices: 13739425--13739449 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13739415 CTATTAAAAC
13739425 AACAACCCCA
1 AACAACCCCA
13739435 AACAACCCCA
1 AACAACCCCA
13739445 AACAA
1 AACAA
13739450 GCACAACACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.44, G:0.00, T:0.00
Consensus pattern (10 bp):
AACAACCCCA
Found at i:13749630 original size:2 final size:2
Alignment explanation
Indices: 13749623--13749672 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
13749613 TTAAAAGTAA
13749623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13749665 AT AT AT AT
1 AT AT AT AT
13749673 CATTTGGTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13754163 original size:29 final size:29
Alignment explanation
Indices: 13754130--13754191 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
13754120 GCATTTATAA
13754130 TATCTATATACACACTTATATATGCACCC
1 TATCTATATACACACTTATATATGCACCC
13754159 TATCTATATACACACTTATATATGCACCC
1 TATCTATATACACACTTATATATGCACCC
13754188 TATC
1 TATC
13754192 CCTAAGTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
TATCTATATACACACTTATATATGCACCC
Found at i:13761680 original size:23 final size:23
Alignment explanation
Indices: 13761637--13761690 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
13761627 GAAATTAAAT
* *
13761637 TATAATTTTTACCATGATAAAAG
1 TATAATTTTTACAAAGATAAAAG
* *
13761660 TATAATTTTTA-AAAGATTAAAT
1 TATAATTTTTACAAAGATAAAAG
*
13761682 TAAAATTTT
1 TATAATTTT
13761691 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (23 bp):
TATAATTTTTACAAAGATAAAAG
Found at i:13761688 original size:22 final size:23
Alignment explanation
Indices: 13761630--13761690 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
13761620 GGAGGTCGAA
* *
13761630 ATTAAATTATAATTTTTACCATG
1 ATTAAATTATAATTTTTACAAAG
* *
13761653 ATAAAAGTATAATTTTTA-AAAG
1 ATTAAATTATAATTTTTACAAAG
*
13761675 ATTAAATTAAAATTTT
1 ATTAAATTATAATTTT
13761691 ATTATTTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (23 bp):
ATTAAATTATAATTTTTACAAAG
Found at i:13762485 original size:19 final size:21
Alignment explanation
Indices: 13762461--13762502 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13762451 TTCGATTTAA
13762461 AAAATTTG-A-TAAAAATTTT
1 AAAATTTGAATTAAAAATTTT
*
13762480 AAAATTTGAATTAAATATTTT
1 AAAATTTGAATTAAAAATTTT
13762501 AA
1 AA
13762503 GTTATTTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
AAAATTTGAATTAAAAATTTT
Found at i:13777840 original size:15 final size:16
Alignment explanation
Indices: 13777810--13777841 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13777800 CTCAACTCCA
13777810 TATTTTTTAGTGTAGT
1 TATTTTTTAGTGTAGT
13777826 TATTTTTTAGT-TAGT
1 TATTTTTTAGTGTAGT
13777841 T
1 T
13777842 TAGTCAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.66
Consensus pattern (16 bp):
TATTTTTTAGTGTAGT
Found at i:13786810 original size:14 final size:15
Alignment explanation
Indices: 13786775--13786808 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13786765 AATTTAAGAG
* *
13786775 AAAAATGAATATTGT
1 AAAAATAAATATTCT
13786790 AAAAATAAATATTCT
1 AAAAATAAATATTCT
13786805 AAAA
1 AAAA
13786809 TATTAGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (15 bp):
AAAAATAAATATTCT
Found at i:13819096 original size:23 final size:23
Alignment explanation
Indices: 13819069--13819186 Score: 159
Period size: 23 Copynumber: 5.0 Consensus size: 23
13819059 CTAGCGCGCG
13819069 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
* *
13819092 CTCTGTTTAGCAC-GTCTCGTGCT
1 CTCTGATTAGCACTGTGT-GTGCT
13819115 CTCTGTTATTAGCACTGTGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCT
13819140 CTCTGATTAGCACT-TCGTGTGCT
1 CTCTGATTAGCACTGT-GTGTGCT
*
13819163 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTGTGTGTGCT
13819186 C
1 C
13819187 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.05
23 60 0.71
24 1 0.01
25 17 0.20
26 3 0.04
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (23 bp):
CTCTGATTAGCACTGTGTGTGCT
Found at i:13819135 original size:48 final size:46
Alignment explanation
Indices: 13819069--13819186 Score: 175
Period size: 48 Copynumber: 2.5 Consensus size: 46
13819059 CTAGCGCGCG
*
13819069 CTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGTGCT
1 CTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGT-GTGCT
*
13819115 CTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCGTGTGCT
1 CTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGTGCT
*
13819163 CTCTGATTAGCACTTTGTGTGCTC
1 CTCTGATTAGCACTGTGTGTGCTC
13819187 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
46 23 0.35
48 42 0.64
49 1 0.02
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (46 bp):
CTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACGTCGTGTGCT
Found at i:13819215 original size:39 final size:39
Alignment explanation
Indices: 13819151--13819225 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
13819141 TCTGATTAGC
*
13819151 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
13819190 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
13819226 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:13819220 original size:23 final size:23
Alignment explanation
Indices: 13819185--13819278 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
13819175 CTTTGTGTGC
*
13819185 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
13819208 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
13819231 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
13819256 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
13819278 T
1 T
13819279 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:13820724 original size:23 final size:23
Alignment explanation
Indices: 13820698--13820860 Score: 144
Period size: 23 Copynumber: 7.4 Consensus size: 23
13820688 AGTGCTGGGC
*
13820698 AACAGAGAGCACACAAAATGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
13820721 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
13820740 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * * *
13820760 ATCAGAGAGTATACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
13820783 ATCAGAGAGCACA-GAACTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
13820805 ATCAGAGAGCACACACAGTTCTA
1 AACAGAGAGCACACAAAGTGCTA
*
13820828 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
13820851 AACAGAGAGC
1 AACAGAGAGC
13820861 GCGCTAGTGT
Statistics
Matches: 115, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 21 0.18
23 77 0.67
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:13820808 original size:45 final size:46
Alignment explanation
Indices: 13820743--13820860 Score: 132
Period size: 45 Copynumber: 2.6 Consensus size: 46
13820733 ACAAAGTACT
* * * * *
13820743 GAGCACACAAAGTGCTAATCAGAGAGTATACGA-AGTGCTAATCAGA
1 GAGCACACACACTGCTAATCAGAGAGCACAC-ACAGTGCTAAACAGA
* *
13820789 GAGCACAGA-ACTGCTAATCAGAGAGCACACACAGTTCTAAACAGA
1 GAGCACACACACTGCTAATCAGAGAGCACACACAGTGCTAAACAGA
* *
13820834 GAGCACACACAGTGCTAAACAGAGAGC
1 GAGCACACACACTGCTAATCAGAGAGC
13820861 GCGCTAGTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
44 1 0.02
45 37 0.61
46 23 0.38
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (46 bp):
GAGCACACACACTGCTAATCAGAGAGCACACACAGTGCTAAACAGA
Found at i:13821820 original size:33 final size:30
Alignment explanation
Indices: 13821768--13821827 Score: 75
Period size: 33 Copynumber: 1.9 Consensus size: 30
13821758 CACACCTTAA
*
13821768 CTTTCTCCTTTCCTTTTTCTTCAATTTGGT
1 CTTTCTCCTTTCCTCTTTCTTCAATTTGGT
*
13821798 CTTTCTCCTTCTTCCCTCTTTCTTTAATTT
1 CTTTCTCC-T-TT-CCTCTTTCTTCAATTT
13821828 CATACAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 8 0.32
31 1 0.04
32 2 0.08
33 14 0.56
ACGTcount: A:0.07, C:0.30, G:0.03, T:0.60
Consensus pattern (30 bp):
CTTTCTCCTTTCCTCTTTCTTCAATTTGGT
Found at i:13828448 original size:20 final size:21
Alignment explanation
Indices: 13828410--13828449 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13828400 CCCAATTTTC
*
13828410 ATTCTTTTTTACGTTTAAATTT
1 ATTCTTTTATACG-TTAAATTT
13828432 ATTCTTTTATACG-TAAAT
1 ATTCTTTTATACGTTAAAT
13828450 CTAGAGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
22 12 0.71
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTCTTTTATACGTTAAATTT
Found at i:13828977 original size:10 final size:10
Alignment explanation
Indices: 13828958--13829067 Score: 63
Period size: 10 Copynumber: 11.5 Consensus size: 10
13828948 TTTAAAATCA
13828958 ATAAAA-ATT
1 ATAAAATATT
13828967 ATAAAATATT
1 ATAAAATATT
** *
13828977 ATTTAATTTT
1 ATAAAATATT
*
13828987 AATAAAA-AAT
1 -ATAAAATATT
*
13828997 ATAAAATTTT
1 ATAAAATATT
*
13829007 ATAAAA-ATC
1 ATAAAATATT
* * *
13829016 GTAAAAAATA
1 ATAAAATATT
13829026 ATAAAATA-T
1 ATAAAATATT
13829035 ATAGAAATA-T
1 ATA-AAATATT
13829045 A-AAAA-ATT
1 ATAAAATATT
*
13829053 ATAAAATTTT
1 ATAAAATATT
13829063 ATAAA
1 ATAAA
13829068 GTCATAAGAA
Statistics
Matches: 76, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
7 1 0.01
8 5 0.07
9 26 0.34
10 40 0.53
11 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAAAATATT
Found at i:13829058 original size:56 final size:57
Alignment explanation
Indices: 13828988--13829105 Score: 161
Period size: 58 Copynumber: 2.1 Consensus size: 57
13828978 TTTAATTTTA
* * *
13828988 ATAAAAAATATAAAATTTTATAAAAATCGTAA-AAAA-TA-ATAAAATATATAGAAAT
1 ATAAAAAATATAAAATTTTAT-AAAATCATAAGAAAATTATACAAAATATAGAGAAAT
*
13829043 ATAAAAAATTATAAAATTTTATAAAGTCATAAGAAAATTATACAAAATATAGAGAAAT
1 ATAAAAAA-TATAAAATTTTATAAAATCATAAGAAAATTATACAAAATATAGAGAAAT
13829101 ATAAA
1 ATAAA
13829106 TTTAGTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
55 16 0.29
56 17 0.31
57 2 0.04
58 20 0.36
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.29
Consensus pattern (57 bp):
ATAAAAAATATAAAATTTTATAAAATCATAAGAAAATTATACAAAATATAGAGAAAT
Found at i:13829074 original size:28 final size:28
Alignment explanation
Indices: 13828988--13829084 Score: 110
Period size: 28 Copynumber: 3.5 Consensus size: 28
13828978 TTTAATTTTA
13828988 ATAAAAAA-TATAAAATTTTATAAAAATC
1 ATAAAAAATTATAAAATTTTAT-AAAATC
* * *
13829016 GTAAAAAATAATAAAA-TATATAGAAAT-
1 ATAAAAAATTATAAAATTTTATA-AAATC
*
13829043 ATAAAAAATTATAAAATTTTATAAAGTC
1 ATAAAAAATTATAAAATTTTATAAAATC
13829071 ATAAGAAAATTATA
1 ATAA-AAAATTATA
13829085 CAAAATATAG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 18 0.32
28 24 0.42
29 15 0.26
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (28 bp):
ATAAAAAATTATAAAATTTTATAAAATC
Found at i:13829659 original size:88 final size:85
Alignment explanation
Indices: 13829494--13829699 Score: 206
Period size: 87 Copynumber: 2.4 Consensus size: 85
13829484 GAGCAAGGGC
* * *
13829494 TTAATTGTTTTTTTGAAATATTTTGAGTGTCTTTTTTATGCATTTTGGAAGTTCAAATACTAATT
1 TTAATTGTTTTTTTGAAAAAGTTTGAGAGTCTTTTTTATGCATTTTGGAAGTTCAAATACTAATT
**
13829559 GAGTGGGAAAAAATAGGGGT
66 GAGTGACAAAAAATAGGGGT
* * *
13829579 TTAATTGTTTTTTTTTGAAAAAGTTTGAGAGCTTTTTTTTATGCATTTT-GAATGTTTAAGTACT
1 TTAATTG--TTTTTTTGAAAAAGTTTGAGAG-TCTTTTTTATGCATTTTGGAA-GTTCAAATACT
** *
13829643 CAATTGAGT-ACAAAAAA-AAAGAT
62 -AATTGAGTGACAAAAAATAGGGGT
* * *
13829666 TTAATTATTTTTTT-AAAAAATTTGAGTG-CTTTTT
1 TTAATTGTTTTTTTGAAAAAGTTTGAGAGTCTTTTT
13829700 ATACCTTAAG
Statistics
Matches: 101, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
82 5 0.05
84 12 0.12
85 14 0.14
87 31 0.31
88 31 0.31
89 8 0.08
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.47
Consensus pattern (85 bp):
TTAATTGTTTTTTTGAAAAAGTTTGAGAGTCTTTTTTATGCATTTTGGAAGTTCAAATACTAATT
GAGTGACAAAAAATAGGGGT
Found at i:13833814 original size:17 final size:17
Alignment explanation
Indices: 13833792--13833828 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
13833782 TTTTATGCAT
13833792 CCTAGTATGTAACACAG
1 CCTAGTATGTAACACAG
13833809 CCTAGTATGTAACACAG
1 CCTAGTATGTAACACAG
13833826 CCT
1 CCT
13833829 CAGTCCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (17 bp):
CCTAGTATGTAACACAG
Found at i:13839742 original size:29 final size:29
Alignment explanation
Indices: 13839710--13839770 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
13839700 TATTTCGAAC
* *
13839710 AAAAGATTACTAG-CTTTAGATACTAATAA
1 AAAACATT-CTAGACTTGAGATACTAATAA
* *
13839739 AAAACATTTTTGACTTGAGATACTAATAA
1 AAAACATTCTAGACTTGAGATACTAATAA
13839768 AAA
1 AAA
13839771 TTAAAACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 25 0.93
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (29 bp):
AAAACATTCTAGACTTGAGATACTAATAA
Found at i:13849695 original size:24 final size:24
Alignment explanation
Indices: 13849668--13849715 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13849658 CAAAAATATG
*
13849668 AAAGGTTAA-AGAAGATGGAAGGTT
1 AAAGGTTAAGAG-AGATGAAAGGTT
13849692 AAAGGTTAAGAGAGATGAAAGGTT
1 AAAGGTTAAGAGAGATGAAAGGTT
13849716 GAACATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.21
Consensus pattern (24 bp):
AAAGGTTAAGAGAGATGAAAGGTT
Found at i:13853948 original size:14 final size:14
Alignment explanation
Indices: 13853929--13853956 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13853919 CGACAACCAC
13853929 GATTTCTATATTCT
1 GATTTCTATATTCT
13853943 GATTTCTATATTCT
1 GATTTCTATATTCT
13853957 TTTTCACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
GATTTCTATATTCT
Found at i:13856268 original size:25 final size:24
Alignment explanation
Indices: 13856231--13856279 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
13856221 TTTCTTTTAT
13856231 TTATATTATAATAATAATAAAATA
1 TTATATTATAATAATAATAAAATA
* * *
13856255 TTATATTTTAAATAATTATTAAATA
1 TTATATTAT-AATAATAATAAAATA
13856280 ATAACTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATATTATAATAATAATAAAATA
Found at i:13857525 original size:11 final size:11
Alignment explanation
Indices: 13857511--13857586 Score: 53
Period size: 12 Copynumber: 6.6 Consensus size: 11
13857501 TGTTTTTGGT
13857511 TTTTTTTGTTG
1 TTTTTTTGTTG
**
13857522 TTTTGATGTTG
1 TTTTTTTGTTG
** *
13857533 TTTTGGTGATG
1 TTTTTTTGTTG
* *
13857544 CTTTTGTTGTTA
1 -TTTTTTTGTTG
13857556 TTTTTGTTGTTG
1 TTTTT-TTGTTG
*
13857568 TTTTTTCTGTTA
1 TTTTTT-TGTTG
13857580 TTTTTTT
1 TTTTTTT
13857587 ATGCGTTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
11 24 0.46
12 28 0.54
ACGTcount: A:0.05, C:0.03, G:0.20, T:0.72
Consensus pattern (11 bp):
TTTTTTTGTTG
Found at i:13857560 original size:12 final size:12
Alignment explanation
Indices: 13857545--13857584 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
13857535 TTGGTGATGC
13857545 TTTTGTTGTTAT
1 TTTTGTTGTTAT
*
13857557 TTTTGTTGTTGT
1 TTTTGTTGTTAT
13857569 TTTT-TCTGTTAT
1 TTTTGT-TGTTAT
13857581 TTTT
1 TTTT
13857585 TTATGCGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 24 0.96
ACGTcount: A:0.05, C:0.03, G:0.15, T:0.78
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:13870707 original size:28 final size:28
Alignment explanation
Indices: 13870645--13870727 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
13870635 ATTATTATAT
* *
13870645 TAAAATAT-ATTCTTATAATTTTTTAATAA
1 TAAAATATAATT-TTATCA-TTTTTAAAAA
*
13870674 TTAAAT-TAAATTTTATCATTTTTAAAAA
1 TAAAATAT-AATTTTATCATTTTTAAAAA
*
13870702 TAAAATATAATTTTGTCATTTATTAA
1 TAAAATATAATTTTATCATTT-TTAA
13870728 TATACAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
28 27 0.60
29 15 0.33
30 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.51
Consensus pattern (28 bp):
TAAAATATAATTTTATCATTTTTAAAAA
Found at i:13880949 original size:2 final size:2
Alignment explanation
Indices: 13880942--13880967 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13880932 GCTTATTGAG
13880942 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13880968 TGTGTTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13887667 original size:2 final size:2
Alignment explanation
Indices: 13887660--13887695 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13887650 GATAAATCTC
13887660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13887696 GTATGTATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13889240 original size:27 final size:28
Alignment explanation
Indices: 13889183--13889254 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
13889173 TTCAAAAAAG
13889183 AAAAATATCTATTGGTAGATTTGTTCAA
1 AAAAATATCTATTGGTAGATTTGTTCAA
*
13889211 AAAAATATCCATTGGTAGATTTGTTCAA
1 AAAAATATCTATTGGTAGATTTGTTCAA
13889239 AAAAA-ATCTATTGGTA
1 AAAAATATCTATTGGTA
13889255 ACAGTTCTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 10 0.24
28 32 0.76
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (28 bp):
AAAAATATCTATTGGTAGATTTGTTCAA
Found at i:13901792 original size:3 final size:3
Alignment explanation
Indices: 13901784--13901815 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13901774 ACTGGTAACA
13901784 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13901816 ATGTTAAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:13902469 original size:51 final size:51
Alignment explanation
Indices: 13902409--13902510 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
13902399 AAGTTTTACT
13902409 TGACATTGATATGATTATTATAACTGTAAAAATATTATGCCCTGCACTTAA
1 TGACATTGATATGATTATTATAACTGTAAAAATATTATGCCCTGCACTTAA
13902460 TGACATTGATATGATTATTATAACTGTAAAAATATTATGCCCTGCACTTAA
1 TGACATTGATATGATTATTATAACTGTAAAAATATTATGCCCTGCACTTAA
13902511 AACGTAAGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (51 bp):
TGACATTGATATGATTATTATAACTGTAAAAATATTATGCCCTGCACTTAA
Found at i:13902977 original size:16 final size:17
Alignment explanation
Indices: 13902951--13902999 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
13902941 CAAAATTAAT
13902951 AAATTTT-TAATTTA-A
1 AAATTTTATAATTTATA
*
13902966 ATATTTTATAATTTATA
1 AAATTTTATAATTTATA
*
13902983 AAATTTTA-AATTAATA
1 AAATTTTATAATTTATA
13902999 A
1 A
13903000 TGAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 15 0.52
17 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTTTATAATTTATA
Found at i:13903043 original size:25 final size:23
Alignment explanation
Indices: 13903002--13903048 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
13902992 ATTAATAATG
* *
13903002 AAAAAAATTATATTTTAACTTTAT
1 AAAAAAATTAAAATTTAA-TTTAT
13903026 AAAAAATATTAAAATTTAATTTA
1 AAAAAA-ATTAAAATTTAATTTA
13903049 ACCTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAAAATTAAAATTTAATTTAT
Found at i:13903050 original size:30 final size:30
Alignment explanation
Indices: 13903005--13903074 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
13902995 AATAATGAAA
* *
13903005 AAAATTATATTTTAA-CTTTATAAAAAATATT
1 AAAATTATAATTTAACCTTT-T-AAAAATAAT
13903036 AAAATT-TAATTTAACCTTTTAAAAATAAT
1 AAAATTATAATTTAACCTTTTAAAAATAAT
*
13903065 AAAAATATAA
1 AAAATTATAA
13903075 ATTATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 13 0.38
30 11 0.32
31 10 0.29
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTATAATTTAACCTTTTAAAAATAAT
Found at i:13903068 original size:8 final size:8
Alignment explanation
Indices: 13903057--13903117 Score: 54
Period size: 8 Copynumber: 7.6 Consensus size: 8
13903047 TAACCTTTTA
13903057 AAAATAAT
1 AAAATAAT
13903065 AAAA-ATAT
1 AAAATA-AT
* *
13903073 AAATTATT
1 AAAATAAT
13903081 AAAATAAT
1 AAAATAAT
13903089 AAAA-ATAT
1 AAAATA-AT
* *
13903097 AAATTATT
1 AAAATAAT
13903105 AAAATAAT
1 AAAATAAT
13903113 AAAAT
1 AAAAT
13903118 CACATTTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
7 2 0.05
8 37 0.90
9 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
AAAATAAT
Found at i:13903087 original size:24 final size:24
Alignment explanation
Indices: 13903057--13903116 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
13903047 TAACCTTTTA
13903057 AAAATAATAAAAATATAAATTATT
1 AAAATAATAAAAATATAAATTATT
13903081 AAAATAATAAAAATATAAATTATT
1 AAAATAATAAAAATATAAATTATT
13903105 AAAATAATAAAA
1 AAAATAATAAAA
13903117 TCACATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAATAATAAAAATATAAATTATT
Found at i:13909794 original size:6 final size:6
Alignment explanation
Indices: 13909786--13909863 Score: 111
Period size: 6 Copynumber: 13.0 Consensus size: 6
13909776 GCAACATTAA
* * * * *
13909786 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAG TAATAG TAATAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG TAATAG
13909834 TAATAG TAATAG TAATAG TAATAG TAATAG
1 TAATAG TAATAG TAATAG TAATAG TAATAG
13909864 CCACCTAAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (6 bp):
TAATAG
Found at i:13910820 original size:12 final size:12
Alignment explanation
Indices: 13910795--13910830 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
13910785 CTTTCCGGGA
13910795 ATCCTTCTTCTC
1 ATCCTTCTTCTC
* *
13910807 ATCTTTCTTTTC
1 ATCCTTCTTCTC
13910819 ATCCTTCTTCTC
1 ATCCTTCTTCTC
13910831 CTCTTTTGCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (12 bp):
ATCCTTCTTCTC
Found at i:13916524 original size:26 final size:26
Alignment explanation
Indices: 13916464--13916525 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
13916454 AAGCAAAATG
*
13916464 TTTAATTTTTTAAAATATACTTCCAA
1 TTTAATTTTTTAAAATATACTTCAAA
* * * *
13916490 TTTAGATTTTTTAATATTTATTTTAAA
1 TTTA-ATTTTTTAAAATATACTTCAAA
13916517 TTTAATTTT
1 TTTAATTTT
13916526 ACCTTTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTAATTTTTTAAAATATACTTCAAA
Found at i:13919568 original size:24 final size:24
Alignment explanation
Indices: 13919541--13919617 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
13919531 ATGAGTGTTT
13919541 TTTAAGAATGAAATTATATTTGGG
1 TTTAAGAATGAAATTATATTTGGG
* ** *
13919565 TTTAAAAAT-AGTTTATGAGTGTT--T
1 TTTAAGAATGAAATTAT-A-T-TTGGG
13919589 TTTAAGAATGAAATTATATTTGGG
1 TTTAAGAATGAAATTATATTTGGG
13919613 TTTAA
1 TTTAA
13919618 AAATATTTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
24 23 0.59
25 6 0.15
26 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (24 bp):
TTTAAGAATGAAATTATATTTGGG
Found at i:13919568 original size:42 final size:42
Alignment explanation
Indices: 13919499--13919616 Score: 164
Period size: 48 Copynumber: 2.7 Consensus size: 42
13919489 AGAGTTATTA
* *
13919499 TTTAGGAATAAAATTATATTTGGGTTTAGTTTATGAGTGTTT
1 TTTAAGAATGAAATTATATTTGGGTTTAGTTTATGAGTGTTT
13919541 TTTAAGAATGAAATTATATTTGGGTTTAAAAATAGTTTATGAGTGTTT
1 TTTAAGAATGAAATTATATTTGGG-TT-----TAGTTTATGAGTGTTT
13919589 TTTAAGAATGAAATTATATTTGGGTTTA
1 TTTAAGAATGAAATTATATTTGGGTTTA
13919617 AAAATATTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
42 24 0.35
43 2 0.03
47 2 0.03
48 40 0.59
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (42 bp):
TTTAAGAATGAAATTATATTTGGGTTTAGTTTATGAGTGTTT
Found at i:13919596 original size:48 final size:48
Alignment explanation
Indices: 13919525--13919622 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
13919515 TATTTGGGTT
13919525 TAGTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAA
1 TAGTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAA
13919573 TAGTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAA
1 TAGTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAA
13919621 TA
1 TA
13919623 TTTGAGTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (48 bp):
TAGTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGGTTTAAAAA
Found at i:13920524 original size:24 final size:24
Alignment explanation
Indices: 13920497--13920542 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
13920487 TCATTAACTT
*
13920497 TGTTTGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
*
13920521 TGTTCGTGAACATGTTCGATTA
1 TGTTCGTGAACATGTTCAATTA
13920543 AGTTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:13920608 original size:30 final size:29
Alignment explanation
Indices: 13920568--13920626 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
13920558 TTCGTGAGCA
*
13920568 TTAAACAAACGAACATGAACACACATAATT
1 TTAAACAAACGAACATGAACA-AAATAATT
*
13920598 TTAAATAAACGAACATGAACAAAATAATT
1 TTAAACAAACGAACATGAACAAAATAATT
13920627 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (29 bp):
TTAAACAAACGAACATGAACAAAATAATT
Found at i:13928895 original size:27 final size:28
Alignment explanation
Indices: 13928852--13928904 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
13928842 TATAAAAAAA
*
13928852 TTAAAATTACAATTATA-AGAAAATTCT
1 TTAAAATTACAAATATACAGAAAATTCT
*
13928879 TTAAAATTTA-AAATATACATAAAATT
1 TTAAAA-TTACAAATATACAGAAAATT
13928905 GAACCCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAAAATTACAAATATACAGAAAATTCT
Found at i:13931447 original size:23 final size:23
Alignment explanation
Indices: 13931393--13931448 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
13931383 GAACGCTAGC
*
13931393 GCGCTTACTGTTTCGCACTTTGT
1 GCGCTTACTGTTTCGCACTTCGT
*
13931416 GTGCTTACTGTTTCGCACTTCGT
1 GCGCTTACTGTTTCGCACTTCGT
*
13931439 GCGCCTACTG
1 GCGCTTACTG
13931449 ATTTGTGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.09, C:0.29, G:0.23, T:0.39
Consensus pattern (23 bp):
GCGCTTACTGTTTCGCACTTCGT
Found at i:13931493 original size:22 final size:23
Alignment explanation
Indices: 13931465--13931510 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
13931455 GCTATGTGCA
13931465 CCTACT-GATTGCACTGTATGTG
1 CCTACTGGATTGCACTGTATGTG
*
13931487 CCTACTGGATTGCACTGTGTGTG
1 CCTACTGGATTGCACTGTATGTG
13931510 C
1 C
13931511 TTATTGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (23 bp):
CCTACTGGATTGCACTGTATGTG
Found at i:13932312 original size:3 final size:3
Alignment explanation
Indices: 13932304--13932339 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
13932294 TACATCCCAA
13932304 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13932340 GAATAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13933517 original size:14 final size:15
Alignment explanation
Indices: 13933498--13933532 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
13933488 TGGGTTGGAC
*
13933498 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
13933512 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
13933527 TTGGTT
1 TTGGTT
13933533 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:13933530 original size:20 final size:20
Alignment explanation
Indices: 13933507--13933553 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13933497 CTTGGTTCAA
13933507 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
* *
13933527 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
13933547 TTGGTTT
1 TTGGTTT
13933554 AAATGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:13933547 original size:15 final size:15
Alignment explanation
Indices: 13933529--13933558 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13933519 AAATGGGTTT
13933529 GGTTAGGTTTAAATG
1 GGTTAGGTTTAAATG
*
13933544 GGTTTGGTTTAAATG
1 GGTTAGGTTTAAATG
13933559 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTAGGTTTAAATG
Found at i:13939073 original size:3 final size:3
Alignment explanation
Indices: 13939065--13939103 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
13939055 TACATCCCAA
13939065 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
13939104 GAATAGAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:13940171 original size:14 final size:13
Alignment explanation
Indices: 13940136--13940184 Score: 62
Period size: 14 Copynumber: 3.6 Consensus size: 13
13940126 TTTTCGAAAA
*
13940136 AAAGTTAACGGTC
1 AAAGTCAACGGTC
13940149 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
13940162 AATTGTCAACGGTC
1 AA-AGTCAACGGTC
13940176 AAAAGTCAA
1 -AAAGTCAA
13940185 AGTCAACGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 14 0.45
14 15 0.48
15 2 0.06
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:13940256 original size:14 final size:15
Alignment explanation
Indices: 13940237--13940271 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
13940227 TGGGTTGGAC
*
13940237 TTGGTTC-AATTGGT
1 TTGGTTCAAATGGGT
13940251 TTGGTTCAAATGGGT
1 TTGGTTCAAATGGGT
13940266 TTGGTT
1 TTGGTT
13940272 AGGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.14, C:0.06, G:0.31, T:0.49
Consensus pattern (15 bp):
TTGGTTCAAATGGGT
Found at i:13940269 original size:20 final size:20
Alignment explanation
Indices: 13940246--13940292 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
13940236 CTTGGTTCAA
13940246 TTGGTTTGGTTCAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
* *
13940266 TTGGTTAGGTTTAAATGGGT
1 TTGGTTTGGTTCAAATGGGT
13940286 TTGGTTT
1 TTGGTTT
13940293 AAATGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (20 bp):
TTGGTTTGGTTCAAATGGGT
Found at i:13940286 original size:15 final size:15
Alignment explanation
Indices: 13940268--13940297 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13940258 AAATGGGTTT
13940268 GGTTAGGTTTAAATG
1 GGTTAGGTTTAAATG
*
13940283 GGTTTGGTTTAAATG
1 GGTTAGGTTTAAATG
13940298 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTAGGTTTAAATG
Found at i:13942401 original size:23 final size:21
Alignment explanation
Indices: 13942375--13942432 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
13942365 TTATAATCTA
13942375 TAATATAATAACAGATATTATAT
1 TAATAT-ATAACAGATATTAT-T
*
13942398 TAATACTTATAA-ATATATTATT
1 TAATA--TATAACAGATATTATT
13942420 TCAATATATAACA
1 T-AATATATAACA
13942433 CTACTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 17 0.57
24 4 0.13
25 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
TAATATATAACAGATATTATT
Found at i:13945983 original size:16 final size:16
Alignment explanation
Indices: 13945962--13945998 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
13945952 TAATCACATA
13945962 TGCATTAAATGAATAT
1 TGCATTAAATGAATAT
13945978 TGCATTAAATGAATAT
1 TGCATTAAATGAATAT
13945994 TGCAT
1 TGCAT
13945999 GAATATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (16 bp):
TGCATTAAATGAATAT
Found at i:13946102 original size:41 final size:39
Alignment explanation
Indices: 13946014--13946102 Score: 97
Period size: 41 Copynumber: 2.2 Consensus size: 39
13946004 TTTGGTTGTG
* * *
13946014 AAACGCCGTTAATGTTTTGATTTTAGCGGCGTTTATGAT
1 AAACGTCGCTAATGTTCTGATTTTAGCGGCGTTTATGAT
* * *
13946053 AAAGCGTCGCTAATGTTCTGACTTTTAGCGGTGTTTTTCTAT
1 AAA-CGTCGCTAATGTTCTGA-TTTTAGCGGCGTTTAT-GAT
13946095 AAACGTCG
1 AAACGTCG
13946103 TTATTGTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.07
40 14 0.34
41 19 0.46
42 5 0.12
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (39 bp):
AAACGTCGCTAATGTTCTGATTTTAGCGGCGTTTATGAT
Found at i:13946197 original size:40 final size:39
Alignment explanation
Indices: 13946103--13946208 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 39
13946093 ATAAACGTCG
* * * * *
13946103 TTATTGTTTTACCTTTTGCAGAGTTGATGAAAAAACACCG
1 TTATTG-TTTACTTTTTGCGGCGTTTATGAAAAAACACCA
* *
13946143 CTATTGCTTTACTTTTTGCGGCGTTTATGGAAAAACACCA
1 TTATTG-TTTACTTTTTGCGGCGTTTATGAAAAAACACCA
**
13946183 TTATTGTTTCACTTTTTAAGGCGTTT
1 TTATTGTTT-ACTTTTTGCGGCGTTT
13946209 TCTATCCTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
39 3 0.06
40 51 0.94
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (39 bp):
TTATTGTTTACTTTTTGCGGCGTTTATGAAAAAACACCA
Found at i:13946826 original size:42 final size:43
Alignment explanation
Indices: 13946686--13946825 Score: 219
Period size: 43 Copynumber: 3.3 Consensus size: 43
13946676 CGCTAAAGAT
*
13946686 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
* * *
13946729 AACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTTCCCCACA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
*
13946772 AACGCCGCTAAA-AACATGGTCTTTAGCGGCGCTTTTCCCATA
1 AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
*
13946814 AACGCCACTAAA
1 AACGCCGCTAAA
13946826 ATTAACAAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 37 0.42
43 51 0.58
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
AACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACA
Found at i:13948227 original size:14 final size:14
Alignment explanation
Indices: 13948208--13948238 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
13948198 AAGGAGTCTA
13948208 AATGCCACACACAC
1 AATGCCACACACAC
13948222 AATGCCACACACAC
1 AATGCCACACACAC
13948236 AAT
1 AAT
13948239 CTATCCGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.39, G:0.06, T:0.10
Consensus pattern (14 bp):
AATGCCACACACAC
Found at i:13951445 original size:41 final size:41
Alignment explanation
Indices: 13951397--13951600 Score: 320
Period size: 41 Copynumber: 5.0 Consensus size: 41
13951387 ATTATTACAC
**
13951397 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTT
*
13951438 TGACCTTTAGTGGCG-TTTGCCCATAAGCGCCGCTATTGCTT
1 TGACCTTTAGCGGCGCTTT-CCCATAAGCGCCGCTATTGCTT
*
13951479 TGACCTTTAACGGCGCTTTCCCATAAGCGCCGCTATTGCTT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTT
* *
13951520 TGACCTTTAGCGGCGCTTTCCCATAAACGCCGCTATTGCTA
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTT
* *
13951561 TGATCTTTAGCGGCGCTTTCCCATAAGCACCGCTATTGCT
1 TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCT
13951601 CTACTTTTTG
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.02
41 144 0.96
42 3 0.02
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (41 bp):
TGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTT
Found at i:13955425 original size:30 final size:31
Alignment explanation
Indices: 13955359--13955447 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 31
13955349 GAACTCCGAA
*
13955359 AAATTTAAGTACCAACTTAAGAAAAACTATC
1 AAATTTAAGTACCAACTTAAAAAAAACTATC
*
13955390 AAATTTAGGTACCAA-TTAAAAAAAACATATC
1 AAATTTAAGTACCAACTTAAAAAAAAC-TATC
* * *
13955421 AATTTTAAATACCAAATTAAACAAAAA
1 AAATTTAAGTACCAACTTAAA-AAAAA
13955448 AAGTATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
30 10 0.20
31 30 0.60
32 5 0.10
33 5 0.10
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.26
Consensus pattern (31 bp):
AAATTTAAGTACCAACTTAAAAAAAACTATC
Found at i:13978497 original size:27 final size:29
Alignment explanation
Indices: 13978440--13978499 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
13978430 AAAAAATATC
*
13978440 AATACATTCTAACAATTTCAAAATCTTAT
1 AATACATTCTAACAATTTCAAAATCTAAT
* * *
13978469 AATATATT-TAACATTTTTAAAAT-TAAT
1 AATACATTCTAACAATTTCAAAATCTAAT
13978496 AATA
1 AATA
13978500 ATATATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 7 0.26
28 13 0.48
29 7 0.26
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (29 bp):
AATACATTCTAACAATTTCAAAATCTAAT
Found at i:13980069 original size:59 final size:60
Alignment explanation
Indices: 13979943--13980219 Score: 323
Period size: 61 Copynumber: 4.6 Consensus size: 60
13979933 CTTTTTGTCA
* ** * *
13979943 AGAAAAAAATTTCAAAATTTTGGGGTGTTAGCCATGC-AATGGCCGACACCCCCTTTTTCTCG
1 AGAAAAAAA-TTCAAATTTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCCC-TGTTCTCG
* *
13980005 AG-AAAAAATTCAAATTTTTTTGGTATTGGCCATGC-AATGGCCGACACCTCCTGTTCTCG
1 AGAAAAAAATTCAAATTTTTTTGGTGTTGGCCAT-CAAATGGCCGACACCCCCTGTTCTCG
** *
13980064 AGAAAAAAAAATTC-AATTTTTTT--TGTTGGCCATCAAATGGTAGACACCCTCTGTTCTCG
1 AG--AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCG
*
13980123 AGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCG
1 AG-AAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCG
*
13980184 AGAAAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
1 AG--AAAAAAATTCAAATTTTTTTGGTGTTGGCCAT
13980220 TTTCCTCGGA
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
58 11 0.06
59 49 0.26
60 37 0.19
61 50 0.26
62 44 0.23
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (60 bp):
AGAAAAAAATTCAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCG
Found at i:13980131 original size:61 final size:60
Alignment explanation
Indices: 13979967--13980219 Score: 295
Period size: 59 Copynumber: 4.2 Consensus size: 60
13979957 AAATTTTGGG
* * *
13979967 GTGTTAGCCATGC-AATGGCCGACACCCCCTTTTTCTCGAG---AAAAAATTCAAATTTTTTT
1 GTGTTGGCCAT-CAAATGGCCGACACCCTC-TGTTCTCGAGAAAAAAAAATT-AAATTTTTTT
* *
13980026 GGTATTGGCCATGC-AATGGCCGACA-CCTCCTGTTCTCGAGAAAAAAAAATTCAATTTTTTT
1 -GTGTTGGCCAT-CAAATGGCCGACACCCT-CTGTTCTCGAGAAAAAAAAATTAAATTTTTTT
** *
13980087 -TGTTGGCCATCAAATGGTAGACACCCTCTGTTCTCGAGAAAAAAAATTTAAATTTTTTT
1 GTGTTGGCCATCAAATGGCCGACACCCTCTGTTCTCGAGAAAAAAAAATTAAATTTTTTT
*
13980146 GGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCTCGAGAAAAAAAAATTTAAATTTTTTT
1 -GTGTTGGCCATCAAATGGCCGACACCCTCTGTTCTCGAGAAAAAAAAA-TTAAATTTTTTT
13980208 GGTGTTGGCCAT
1 -GTGTTGGCCAT
13980220 TTTCCTCGGA
Statistics
Matches: 170, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
58 1 0.01
59 59 0.35
60 26 0.15
61 52 0.31
62 32 0.19
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
GTGTTGGCCATCAAATGGCCGACACCCTCTGTTCTCGAGAAAAAAAAATTAAATTTTTTT
Found at i:13980157 original size:120 final size:120
Alignment explanation
Indices: 13979999--13980219 Score: 349
Period size: 120 Copynumber: 1.8 Consensus size: 120
13979989 CACCCCCTTT
*
13979999 TTCTCGAGAAAAAATTCAAATTTTTTTGGTATTGGCCATGC-AATGGCCGACACCTCCTGTTCTC
1 TTCTCGAGAAAAAATTCAAATTTTTTTGGTATTGGCCAT-CAAATGGCCGACACCCCCTGTTCTC
*
13980063 GAGAAAAAAAAA-TTCAATTTTTTT-TGTTGGCCATCAAATGGTAGACACCCTCTG
65 GAGAAAAAAAAATTTAAATTTTTTTGTGTTGGCCATCAAATGGTAGACACCCTCTG
* *
13980117 TTCTCGAGAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCCCTGTTCT
1 TTCTCGAG--AAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTCT
13980182 CGAGAAAAAAAAATTTAAATTTTTTTGGTGTTGGCCAT
64 CGAGAAAAAAAAATTTAAATTTTTTT-GTGTTGGCCAT
13980220 TTTCCTCGGA
Statistics
Matches: 93, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
118 8 0.09
119 1 0.01
120 63 0.68
121 11 0.12
123 10 0.11
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (120 bp):
TTCTCGAGAAAAAATTCAAATTTTTTTGGTATTGGCCATCAAATGGCCGACACCCCCTGTTCTCG
AGAAAAAAAAATTTAAATTTTTTTGTGTTGGCCATCAAATGGTAGACACCCTCTG
Found at i:13981162 original size:30 final size:30
Alignment explanation
Indices: 13981102--13981193 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
13981092 TAATAATTAG
* * ** *
13981102 AATATAAATGAAATTAGAAAGAAAAATTAA
1 AATATAAACGAAATTCGAAATTAAATTTAA
13981132 AATATACAA-GAAATTCGAAATTAAATTTAA
1 AATATA-AACGAAATTCGAAATTAAATTTAA
*
13981162 AATAAAAACGAAATTAC-AAATTAAATTTAA
1 AATATAAACGAAATT-CGAAATTAAATTTAA
13981192 AA
1 AA
13981194 AGTAAAGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.04
30 49 0.91
31 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (30 bp):
AATATAAACGAAATTCGAAATTAAATTTAA
Found at i:13983397 original size:20 final size:20
Alignment explanation
Indices: 13983372--13983409 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
13983362 ATGATGGATG
13983372 AAAGTCGATCAACGGCGGAC
1 AAAGTCGATCAACGGCGGAC
*
13983392 AAAGTCGGTCAACGGCGG
1 AAAGTCGATCAACGGCGG
13983410 TTAACGATTG
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:0.32, C:0.24, G:0.34, T:0.11
Consensus pattern (20 bp):
AAAGTCGATCAACGGCGGAC
Found at i:13983441 original size:20 final size:20
Alignment explanation
Indices: 13983380--13983441 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
13983370 TGAAAGTCGA
* * * *
13983380 TCAACGGCGGACAAAGTCGG
1 TCAACGGCGGTCAACGACTG
* *
13983400 TCAACGGCGGTTAACGATTG
1 TCAACGGCGGTCAACGACTG
* *
13983420 TCAACGGTGGTCAACGGCTG
1 TCAACGGCGGTCAACGACTG
13983440 TC
1 TC
13983442 TCGGGACGTT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.19
Consensus pattern (20 bp):
TCAACGGCGGTCAACGACTG
Found at i:13983739 original size:83 final size:83
Alignment explanation
Indices: 13983600--13985031 Score: 2173
Period size: 83 Copynumber: 17.3 Consensus size: 83
13983590 ATAAATATAA
* **
13983600 ATATGATAAAAATTATAATATAATAAAAAAAATTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13983665 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
* **
13983683 ATATGATAAAAATTGTAAAATAATAAAATTTTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
* *
13983748 TTGTCAAATCAACGCATT
66 TTATCAAATCAACACATT
* *
13983766 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTCAAAGATATAAAATTAAAAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13983831 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
* ***
13983849 ATATGATAAAAATTGTAAAATAATAAATTTTTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13983914 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
* * *
13983932 ATATGATAAAAATTGTAAAATAAT-AAAATTTTTATTTACAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
* *
13983996 TTGTTAAATCAACACATT
66 TTATCAAATCAACACATT
* **
13984014 ATATGATAAAAATTGTAAAATAATAAAATTTTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
* *
13984079 TTGTCAAATGAACACATT
66 TTATCAAATCAACACATT
* *
13984097 ATATGAT-AAAATTGTAATATAAT--AAAATTTTATTTAAAAATATAAAATTAATAAATATTATA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
13984159 TTGTCAAATCAACACATT
66 TTATCAAATCAACACATT
* * *
13984177 ATATTATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAAAAAAT-TTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13984241 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
* *
13984259 ATATGATAAAAATTGTAAAATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
13984324 TTATCAAATCAATACATT
66 TTATCAAATCAACACATT
* *
13984342 ATATGATAAAAATTGTAAAATAAT-AAAATTTTTATTTAAAGATAT-AAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
13984405 TTATTAAATCAACACATT
66 TTATCAAATCAACACATT
* *
13984423 ATATAATAAAAATTGTAATATAATAAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGT
1 ATATGATAAAAATTGTAATATAAT-AAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGT
* *
13984488 ATTGTCAAATCAGCACATT
65 ATTATCAAATCAACACATT
*
13984507 ATATGATAAAAATTGTAATATAAT-AAAAATATTTATTTAAAGATATAAAATTAATAAATATTAT
1 ATATGATAAAAATTGTAATATAATAAAAAAT-TTTATTTAAAGATATAAAATTAATAAATATTGT
*
13984571 ATTGTCAAATCAACACATT
65 ATTATCAAATCAACACATT
* *
13984590 ATATTATAAAAATTGTAATATAATAAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
13984655 TTATCAAATCAGCACATT
66 TTATCAAATCAACACATT
*
13984673 ATATGATAAAAATTATAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13984738 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
*
13984756 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
13984821 TTGTCAAATCAACACATT
66 TTATCAAATCAACACATT
* * *
13984839 ATATTATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTATA
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
13984904 TTATCAAATCAACACATT
66 TTATCAAATCAACACATT
* * * * *
13984922 ATATGATAAAAATTGTAATATAATAATAAGTTGTACTTT-AA-ATATGAAAATTTGATAAATAAT
1 ATATGATAAAAATTGTAATATAATAAAAAATTTTA-TTTAAAGATAT-AAAA-TTAATAAATATT
* * * *
13984985 GTATTGTCAAATTAATACAAT
63 GTATTATCAAATCAACACATT
* * * *
13985006 ATTTAACATAAATTGTAATATAATAA
1 ATATGATAAAAATTGTAATATAATAA
13985032 CTATCTTTTT
Statistics
Matches: 1244, Mismatches: 92, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
80 58 0.05
81 72 0.06
82 197 0.16
83 805 0.65
84 112 0.09
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (83 bp):
ATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
TTATCAAATCAACACATT
Found at i:13989287 original size:41 final size:41
Alignment explanation
Indices: 13989241--13989331 Score: 123
Period size: 41 Copynumber: 2.2 Consensus size: 41
13989231 GAAATAAATA
*
13989241 ATAAAAGTTGAACAGTACCTGA-TCAATGATTGGTGT-AAAC
1 ATAAAAGTTGAACAGCA-CTGAGTCAATGATTGGTGTCAAAC
* *
13989281 AGTAAAAGTTGAACAGCACTTAGTCAATGATTGGTGTCAGAC
1 A-TAAAAGTTGAACAGCACTGAGTCAATGATTGGTGTCAAAC
13989323 ATAAAAGTT
1 ATAAAAGTT
13989332 TGTGTTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
40 4 0.09
41 37 0.82
42 4 0.09
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (41 bp):
ATAAAAGTTGAACAGCACTGAGTCAATGATTGGTGTCAAAC
Found at i:13989604 original size:57 final size:57
Alignment explanation
Indices: 13989534--13989647 Score: 126
Period size: 57 Copynumber: 2.0 Consensus size: 57
13989524 TAAGTGTCGA
* * * *
13989534 CCATGCAATTGTCGATA-CTCTCTTTTCTAG-AGAAAAAATTTCAAAATTTTTTTATTGG
1 CCATGCAAATGTCGACACCCCT-TTTTCTAGAAAAAAAAATTT--AAATTTTTTTATTGG
* *
13989592 CCAT-CAAATGTCGACACCCCTTTTTCTCGAAAAAAAAATTTAAATTTTTTTTTTGG
1 CCATGCAAATGTCGACACCCCTTTTTCTAGAAAAAAAAATTTAAATTTTTTTATTGG
13989648 TGTCGACCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
56 14 0.29
57 17 0.35
58 17 0.35
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (57 bp):
CCATGCAAATGTCGACACCCCTTTTTCTAGAAAAAAAAATTTAAATTTTTTTATTGG
Found at i:13989910 original size:17 final size:17
Alignment explanation
Indices: 13989888--13989922 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
13989878 TGTTTCTCTT
13989888 AAAATAACAAGAAAATG
1 AAAATAACAAGAAAATG
13989905 AAAATAACAAGAAAATG
1 AAAATAACAAGAAAATG
13989922 A
1 A
13989923 GAGTGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.71, C:0.06, G:0.11, T:0.11
Consensus pattern (17 bp):
AAAATAACAAGAAAATG
Found at i:13990034 original size:31 final size:31
Alignment explanation
Indices: 13989992--13990051 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
13989982 TACAATCGAA
* *
13989992 TTTCGGGGTTGAGCTATATACTGTCATGTAT
1 TTTCGGAGTTGAACTATATACTGTCATGTAT
*
13990023 TTTCGGAGTTGAATTATATACTGTCATGT
1 TTTCGGAGTTGAACTATATACTGTCATGT
13990052 GAAGCGGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (31 bp):
TTTCGGAGTTGAACTATATACTGTCATGTAT
Found at i:13991436 original size:21 final size:20
Alignment explanation
Indices: 13991389--13991436 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
13991379 CGATGTCTCG
*
13991389 ATTTTATATTTTTTTAAATT
1 ATTTTTTATTTTTTTAAATT
* *
13991409 TTATTTTTATTTTTTTCTAATT
1 AT-TTTTTATTTTTTT-AAATT
13991431 ATTTTT
1 ATTTTT
13991437 CAATTTTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTTTATTTTTTTAAATT
Found at i:13992503 original size:30 final size:30
Alignment explanation
Indices: 13992469--13992564 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
13992459 CCCCTTTACT
*
13992469 TTTTAAATTTAATTT-GTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTCG-AATTTC-TTGTATA
13992499 TTTTAAATTTAATTTCGAATTTCTTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
* ** * *
13992529 TTTTAATTTTTCTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCGAATTTCTTGTATA
13992559 TTTTAA
1 TTTTAA
13992565 TTATTATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.03
30 55 0.95
31 1 0.02
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTCGAATTTCTTGTATA
Found at i:13993581 original size:59 final size:57
Alignment explanation
Indices: 13993403--13993718 Score: 175
Period size: 59 Copynumber: 5.5 Consensus size: 57
13993393 CCAACACAAA
*
13993403 AAAAATTTACAATTTTTTTATCCGAGAAAAAGGGG-TGTCGGCCATGCAATGGCCAACACCC
1 AAAAATTT--AATTTTTTT-T-CGAG-AAAAGGGGATGTCGGCCATGCAATGGCCAACTCCC
* * * ** * *
13993464 AAAAATGTAATTTTTTTT--A-AATA-GGGAGTGTCGGCTATTTAATGGCTAACAT-CA
1 AAAAATTTAATTTTTTTTCGAGAAAAGGGGA-TGTCGGCCATGCAATGGCCAAC-TCCC
*
13993518 AAAAATTTGAATTTTTTTCTCGAGAAAAGGGGATGTCGACCATGCAATGGCCAACTCCC
1 AAAAATTT-AATTTTTTT-TCGAGAAAAGGGGATGTCGGCCATGCAATGGCCAACTCCC
** * * * * *** * **
13993577 AAAAATGCAATTTTTATTT-TA-AATAGGGGGTGTCGGTCATTTGATGGCCAACACAAA
1 AAAAATTTAATTTTT-TTTCGAGAAAAGGGGATGTCGGCCATGCAATGGCCAACTC-CC
* *** *
13993634 AAAAATTTAAAATTTTTTTATCGAGAAATGAGGG-TGTCGGCCATTTGATGGCCAACACCC
1 AAAAATTT--AATTTTTTT-TCGAGAAAAG-GGGATGTCGGCCATGCAATGGCCAACTCCC
* *
13993694 AAAAATGTAA-TTTTTTTAGAGAAAA
1 AAAAATTTAATTTTTTTTCGAGAAAA
13993719 TGGAGTGTCG
Statistics
Matches: 197, Mismatches: 40, Indels: 41
0.71 0.14 0.15
Matches are distributed among these distances:
52 3 0.02
53 3 0.02
54 26 0.13
55 10 0.05
56 33 0.17
57 13 0.07
58 15 0.08
59 46 0.23
60 12 0.06
61 33 0.17
62 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (57 bp):
AAAAATTTAATTTTTTTTCGAGAAAAGGGGATGTCGGCCATGCAATGGCCAACTCCC
Found at i:13993688 original size:117 final size:115
Alignment explanation
Indices: 13993374--13993710 Score: 418
Period size: 117 Copynumber: 2.9 Consensus size: 115
13993364 AGGAGGAGTT
* * *
13993374 AGTGTCGTCTA-TTACATGGCCAACACAAAAAAAATTTACAATTTTTTTATCCGAGAAAAAGGGG
1 AGTGTCGGCTATTTA-ATGGCCAACACAAAAAAAATTTAAAATTTTTTTAT-CGAGAAAGA-GGG
13993438 TGTCGGCCATGCAATGGCCAACACCCAAAAATGTAA-TTTTTTTTAAATAGGG
63 TGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTAAATAGGG
* * *
13993490 AGTGTCGGCTATTTAATGGCTAACATC--AAAAAATTT-GAATTTTTTTCTCGAGAAA-AGGGGA
1 AGTGTCGGCTATTTAATGGCCAACA-CAAAAAAAATTTAAAATTTTTTTATCGAGAAAGA-GGG-
* * *
13993551 TGTCGACCATGCAATGGCCAACTCCCAAAAATGCAATTTTTATTTTAAATAGGG
63 TGTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTT-TTTTAAATAGGG
* *
13993605 GGTGTCGG-TCATTTGATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCGAGAAATGAGGGT
1 AGTGTCGGCT-ATTTAATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCGAGAAA-GAGGGT
***
13993669 GTCGGCCATTTGATGGCCAACACCCAAAAATGTAATTTTTTT
64 GTCGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTT
13993711 AGAGAAAATG
Statistics
Matches: 192, Mismatches: 18, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
112 5 0.03
113 40 0.21
114 16 0.08
115 41 0.21
116 30 0.16
117 56 0.29
118 3 0.02
119 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (115 bp):
AGTGTCGGCTATTTAATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCGAGAAAGAGGGTGT
CGGCCATGCAATGGCCAACACCCAAAAATGTAATTTTTTTTTAAATAGGG
Found at i:13993727 original size:117 final size:112
Alignment explanation
Indices: 13993389--13993768 Score: 415
Period size: 117 Copynumber: 3.3 Consensus size: 112
13993379 CGTCTATTAC
* *
13993389 ATGGCCAACACAAAAAAAATTTACAATTTTTTTATCCGAGAAAAAGGGGTGTCGGCCATGCAATG
1 ATGGCCAACAC-AAAAAAATTTAGAATTTTTTTAT-CGAGAAAGA-GGGTGTCGGCCATGCAATG
*
13993454 GCCAACACCCAAAAATGTAATTTTTTTTAAATAGGGAGTGTCGGCTATTTA
63 GCCAACACCCAAAAATGTAATTTTTTTTAAATAGGGAGTGTCGGC-ATTTG
* * *
13993505 ATGGCTAACATC-AAAAAATTT-GAATTTTTTTCTCGAGAAA-AGGGGATGTCGACCATGCAATG
1 ATGGCCAACA-CAAAAAAATTTAGAATTTTTTTATCGAGAAAGA-GGG-TGTCGGCCATGCAATG
* * *
13993567 GCCAACTCCCAAAAATGCAATTTTTATTTTAAATAGGGGGTGTCGGTCATTTG
63 GCCAACACCCAAAAATGTAA-TTTT-TTTTAAATAGGGAGTGTCGG-CATTTG
* ***
13993620 ATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCGAGAAATGAGGGTGTCGGCCATTTGATGG
1 ATGGCCAACAC-AAAAAAATTTAGAATTTTTTTATCGAGAAA-GAGGGTGTCGGCCATGCAATGG
* * * *
13993685 CCAACACCCAAAAATGTAATTTTTTTAGAGAAAATGGAGTGTCGACCATTTG
64 CCAACACCCAAAAATGTAATTTTTTT-TA-AATAGGGAGTGTCG-GCATTTG
* * * *
13993737 ATGACCAATACCAAAAAATTTTGAATTTTTTT
1 ATGGCCAACACAAAAAAATTTAGAATTTTTTT
13993769 CTCAAAAAGA
Statistics
Matches: 224, Mismatches: 27, Indels: 26
0.81 0.10 0.09
Matches are distributed among these distances:
112 5 0.02
113 40 0.18
114 15 0.07
115 44 0.20
116 42 0.19
117 74 0.33
118 3 0.01
119 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (112 bp):
ATGGCCAACACAAAAAAATTTAGAATTTTTTTATCGAGAAAGAGGGTGTCGGCCATGCAATGGCC
AACACCCAAAAATGTAATTTTTTTTAAATAGGGAGTGTCGGCATTTG
Found at i:13993734 original size:56 final size:56
Alignment explanation
Indices: 13993389--13993755 Score: 236
Period size: 56 Copynumber: 6.3 Consensus size: 56
13993379 CGTCTATTAC
* * * ***
13993389 ATGGCCAACACAAAAAAAATTTACAATTTTTTTATCCGAGAAAAAGGGGTGTCGGCCATGCA
1 ATGGCCAACAC-CAAAAAATGT--AATTTTTTTA---GAGAAAAGGGGGTGTCGGCCATTTG
* * * * * *
13993451 ATGGCCAACACCCAAAAATGTAATTTTTTT-TA-AATAGGGAGTGTCGGCTATTTA
1 ATGGCCAACACCAAAAAATGTAATTTTTTTAGAGAAAAGGGGGTGTCGGCCATTTG
* * * * * * ***
13993505 ATGGCTAACATCAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGATGTCGACCATGCA
1 ATGGCCAACACCAAAAAATGT-AA-TTTTTT-TAGAGAAAAGGGGGTGTCGGCCATTTG
* * * ** * *
13993564 ATGGCCAACTCCCAAAAATGCAATTTTTATTTTA-AATAGGGGGTGTCGGTCATTTG
1 ATGGCCAACACCAAAAAATGTAATTTTT-TTAGAGAAAAGGGGGTGTCGGCCATTTG
* * * *
13993620 ATGGCCAACACAAAAAAAATTTAAAATTTTTTTATCGAGAAATGAGGGTGTCGGCCATTTG
1 ATGGCCAACAC-CAAAAAATGT--AATTTTTTTA--GAGAAAAGGGGGTGTCGGCCATTTG
* * * *
13993681 ATGGCCAACACCCAAAAATGTAATTTTTTTAGAGAAAATGGAGTGTCGACCATTTG
1 ATGGCCAACACCAAAAAATGTAATTTTTTTAGAGAAAAGGGGGTGTCGGCCATTTG
* *
13993737 ATGACCAATACCAAAAAAT
1 ATGGCCAACACCAAAAAAT
13993756 TTTGAATTTT
Statistics
Matches: 234, Mismatches: 59, Indels: 30
0.72 0.18 0.09
Matches are distributed among these distances:
54 33 0.14
55 3 0.01
56 67 0.29
57 14 0.06
58 16 0.07
59 46 0.20
60 8 0.03
61 36 0.15
62 11 0.05
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (56 bp):
ATGGCCAACACCAAAAAATGTAATTTTTTTAGAGAAAAGGGGGTGTCGGCCATTTG
Found at i:13995070 original size:62 final size:61
Alignment explanation
Indices: 13994838--13995196 Score: 314
Period size: 61 Copynumber: 6.0 Consensus size: 61
13994828 AAAAATTTGG
* * * ** **
13994838 GGTGTTGGCCATGC-AATGCCCGACA-CCCCTTTT-TTGTCAAAAAAA-TTCAAAATTTTTT
1 GGTGTTGGCCAT-CAAATGGCAGACACCCCCTTTTCTCGAGAAAAAAATTTCAATTTTTTTT
* * * * *
13994896 GGTGTTGGCCATCAAATAGCCGACA-CTCCTTTTCCTCGA-AAAAAAATTAC-A--TTTTTG
1 GGTGTTGGCCATCAAATGGCAGACACCCCCTTTT-CTCGAGAAAAAAATTTCAATTTTTTTT
* *** *
13994953 GGTGTTGGTCATTGCATGG-ACGACACCCCCTTTTATCGAGAAAAAAA-TTCAAATTTTTTTT
1 GGTGTTGGCCATCAAATGGCA-GACACCCCCTTTTCTCGAGAAAAAAATTTC-AATTTTTTTT
* *
13995014 TGTGTTGGCCATCAAATGGCAGACACCTCCTATTTCTCGAGAAAAAAATTTCAATTTTTTTT
1 GGTGTTGGCCATCAAATGGCAGACACCCCCT-TTTCTCGAGAAAAAAATTTCAATTTTTTTT
* * *
13995076 AGTGTTGGCTATCAAATGGTCA-ACACCCCCTTTTCTCGAGAAAAAAATTTTAATTTTTTTT
1 GGTGTTGGCCATCAAATGG-CAGACACCCCCTTTTCTCGAGAAAAAAATTTCAATTTTTTTT
* * * * * *
13995137 CGTGTTGACAATCAAATGGCCGACAACCCCTTTTCTCGAGAAAAAAA--TCAAATTTTTTT
1 GGTGTTGGCCATCAAATGGCAGACACCCCCTTTTCTCGAGAAAAAAATTTCAATTTTTTTT
13995196 G
1 G
13995197 ATGTCAGTCA
Statistics
Matches: 249, Mismatches: 36, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
57 30 0.12
58 42 0.17
59 19 0.08
60 5 0.02
61 97 0.39
62 51 0.20
63 5 0.02
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (61 bp):
GGTGTTGGCCATCAAATGGCAGACACCCCCTTTTCTCGAGAAAAAAATTTCAATTTTTTTT
Found at i:13995115 original size:123 final size:119
Alignment explanation
Indices: 13994876--13995193 Score: 358
Period size: 123 Copynumber: 2.7 Consensus size: 119
13994866 CTTTTTTGTC
* * *
13994876 AAAAAAATTCAAA-ATTTTTTGGTGTTGGCCATCAAATAGCCGACA-CTCCTTTTCCTCGA-AAA
1 AAAAAAATTCAAATTTTTTTTCGTGTTGGCCATCAAATGGCCGACACCTCCTTTT-CTCGAGAAA
* *** *
13994938 AAAATTACATTTTTGGGTGTTGGTCATTGCATGGACGACACCCCCTTTTATCGAG
65 AAAATTACATTTTTGAGTGTTGGTCATCAAATGGACAACACCCCCTTTTATCGAG
* *
13994993 AAAAAAATTCAAATTTTTTTTTGTGTTGGCCATCAAATGGCAGACACCTCCTATTTCTCGAGAAA
1 AAAAAAATTCAAATTTTTTTTCGTGTTGGCCATCAAATGGCCGACACCTCCT-TTTCTCGAGAAA
* * * *
13995058 AAAATTTCAATTTTTTTTAGTGTTGG-CTATCAAATGGTCAACACCCCCTTTTCTCGAG
65 AAAATTAC-A--TTTTTGAGTGTTGGTC-ATCAAATGGACAACACCCCCTTTTATCGAG
** * *
13995116 AAAAAAATTTTAATTTTTTTTCGTGTTGACAATCAAATGGCCGACAACC-CCTTTTCTCGAGAAA
1 AAAAAAATTCAAATTTTTTTTCGTGTTGGCCATCAAATGGCCGAC-ACCTCCTTTTCTCGAGAAA
* *
13995180 AAAATCAAATTTTT
65 AAAATTACATTTTT
13995194 TTGATGTCAG
Statistics
Matches: 170, Mismatches: 22, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
117 13 0.08
118 28 0.16
119 15 0.09
120 13 0.08
121 2 0.01
122 18 0.11
123 78 0.46
124 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (119 bp):
AAAAAAATTCAAATTTTTTTTCGTGTTGGCCATCAAATGGCCGACACCTCCTTTTCTCGAGAAAA
AAATTACATTTTTGAGTGTTGGTCATCAAATGGACAACACCCCCTTTTATCGAG
Found at i:13995348 original size:61 final size:55
Alignment explanation
Indices: 13995280--13995462 Score: 199
Period size: 61 Copynumber: 3.1 Consensus size: 55
13995270 CCTATTTCAA
* *
13995280 AAAAAATTGCATCTTTTTTTCTATAGAAAAAGAGGTGTCGGCCATTTGATGGTCAACAC
1 AAAAAATTGCA--ATTTTTTCT-T-GAAAAAGGGGTGTCGGCCATTTGATGGTCAACAC
* *
13995339 GAGAAAAATTTGAAAATTTTTTCTTGAGAAAAGGGAGTGTCAGCCATTTGATGGTCAACACC
1 -A-AAAAA-TTG-CAATTTTTTCTTGA-AAAAGGG-GTGTCGGCCATTTGATGGTCAACA-C
*
13995401 AAAAAA-TGCAATTTTTT-TTGAAATAAGGGGTGTCGGCCATTTGATGGCCAACAC
1 AAAAAATTGCAATTTTTTCTTGAAA-AAGGGGTGTCGGCCATTTGATGGTCAACAC
13995455 AAAAAATT
1 AAAAAATT
13995463 TTTAATTTTT
Statistics
Matches: 108, Mismatches: 7, Indels: 21
0.79 0.05 0.15
Matches are distributed among these distances:
54 7 0.06
55 25 0.23
56 9 0.08
57 8 0.07
58 2 0.02
59 2 0.02
60 13 0.12
61 37 0.34
62 4 0.04
63 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (55 bp):
AAAAAATTGCAATTTTTTCTTGAAAAAGGGGTGTCGGCCATTTGATGGTCAACAC
Found at i:13995472 original size:55 final size:55
Alignment explanation
Indices: 13995305--13995474 Score: 191
Period size: 55 Copynumber: 3.0 Consensus size: 55
13995295 TTTTTCTATA
*
13995305 GAAAAAGAGGTGTCGGCCATTTGATGGTCAACACGAGAAAAATTTGAAAATTTTTTCTT
1 GAAAAAGGGGTGTCGGCCATTTGATGGTCAACAC-A-AAAAATTT-AAAATTTTTT-TT
* **
13995364 GAGAAAAGGGAGTGTCAGCCATTTGATGGTCAACACCAAAAAA--TGCAATTTTTTTT
1 GA-AAAAGGG-GTGTCGGCCATTTGATGGTCAACA-CAAAAAATTTAAAATTTTTTTT
* **
13995420 GAAATAAGGGGTGTCGGCCATTTGATGGCCAACACAAAAAATTTTTAATTTTTTT
1 GAAA-AAGGGGTGTCGGCCATTTGATGGTCAACACAAAAAATTTAAAATTTTTTT
13995475 CTCGAGAAAA
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
54 7 0.07
55 24 0.25
56 19 0.20
57 8 0.08
58 1 0.01
59 2 0.02
60 11 0.11
61 24 0.25
62 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (55 bp):
GAAAAAGGGGTGTCGGCCATTTGATGGTCAACACAAAAAATTTAAAATTTTTTTT
Found at i:13995512 original size:114 final size:115
Alignment explanation
Indices: 13995305--13995555 Score: 303
Period size: 114 Copynumber: 2.2 Consensus size: 115
13995295 TTTTTCTATA
* *
13995305 GAAAAAGAGGTGTCGGCCATTTGATGGTCAACACGAGAAAAATTTGAAAATTTTTTCTTGAGAAA
1 GAAAAAGAGGTGTCGGCCATTTGATGGCCAACACGAGAAAAATTTGAAAATTTTTTCTCGAGAAA
*** *
13995370 AGGGAGTGTCAGCCATTTGATGGTCAACACCAAAAAATGCAATTTTTTTT
66 AGGGAGTGTCAGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTT
* ** *
13995420 GAAATAAGGGGTGTCGGCCATTTGATGGCCAACAC-A-AAAAATTTTTAATTTTTTTCTCGAGAA
1 GAAA-AAGAGGTGTCGGCCATTTGATGGCCAACACGAGAAAAATTTGAAAATTTTTTCTCGAGAA
* *
13995483 AA-GGAGATGTC-GACCATGCAATGGCCAACACCTAAAAATGTAATTTTTTTT
65 AAGGGAG-TGTCAG-CCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTT
*
13995534 CGAGAAAAAGAGGTGTTGGCCA
1 ---GAAAAAGAGGTGTCGGCCA
13995556 ATTTTTTTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
113 5 0.04
114 61 0.53
115 5 0.04
116 41 0.35
117 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (115 bp):
GAAAAAGAGGTGTCGGCCATTTGATGGCCAACACGAGAAAAATTTGAAAATTTTTTCTCGAGAAA
AGGGAGTGTCAGCCATGCAATGGCCAACACCAAAAAATGCAATTTTTTTT
Found at i:13996157 original size:30 final size:30
Alignment explanation
Indices: 13996123--13996184 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
13996113 AAATAAATAA
* *
13996123 AATATA-TTATATATAAATTTTGGTTCGATT
1 AATATATTTAAATA-AAATTTTGATTCGATT
*
13996153 AATATATTTAAATAAAATTTTGATTCGTTT
1 AATATATTTAAATAAAATTTTGATTCGATT
13996183 AA
1 AA
13996185 GGATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (30 bp):
AATATATTTAAATAAAATTTTGATTCGATT
Found at i:13999442 original size:31 final size:30
Alignment explanation
Indices: 13999369--13999442 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
13999359 AAAAATTATA
*
13999369 ATTTAATCACTAAACTATTCAAACGTTTTC
1 ATTTAATCACTGAACTATTCAAACGTTTTC
* *
13999399 ATTTAAATCACTGAACTATTTAATA-GTTTTT
1 ATTT-AATCACTGAACTATTCAA-ACGTTTTC
13999430 ATTTAAGTCACTG
1 ATTTAA-TCACTG
13999443 GATTGTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
30 6 0.16
31 31 0.82
32 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (30 bp):
ATTTAATCACTGAACTATTCAAACGTTTTC
Found at i:14010533 original size:32 final size:32
Alignment explanation
Indices: 14010496--14010598 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 32
14010486 AATTAATTTT
*
14010496 ATTAAAATATCAATTTAAAGGAATAAATTTAA
1 ATTAAAATATCAATTTAAAGGAAAAAATTTAA
14010528 ATTAAAAATAGAATTCAA-TTAAAGGAAAACATATTTAA
1 ATT-AAAAT---A-TCAATTTAAAGGAAAA-A-ATTTAA
*
14010566 A-GAATAA-ATCAATTTAAA-GAAAAAATTTAA
1 ATTAA-AATATCAATTTAAAGGAAAAAATTTAA
14010596 ATT
1 ATT
14010599 TTAAAAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 21
0.71 0.04 0.26
Matches are distributed among these distances:
30 7 0.12
31 1 0.02
32 12 0.21
33 11 0.19
36 13 0.22
37 7 0.12
38 7 0.12
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (32 bp):
ATTAAAATATCAATTTAAAGGAAAAAATTTAA
Found at i:14010566 original size:33 final size:30
Alignment explanation
Indices: 14010529--14010596 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
14010519 TAAATTTAAA
14010529 TTAAA-AATAGAATTCAA-TTAAAGGAAAACATAT
1 TTAAAGAATA-AA-TCAATTTAAA-GAAAA-A-AT
14010562 TTAAAGAATAAATCAATTTAAAGAAAAAAT
1 TTAAAGAATAAATCAATTTAAAGAAAAAAT
14010592 TTAAA
1 TTAAA
14010597 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
30 7 0.21
31 1 0.03
32 9 0.27
33 12 0.36
34 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.28
Consensus pattern (30 bp):
TTAAAGAATAAATCAATTTAAAGAAAAAAT
Found at i:14010582 original size:17 final size:17
Alignment explanation
Indices: 14010504--14010591 Score: 67
Period size: 17 Copynumber: 5.1 Consensus size: 17
14010494 TTATTAAAAT
14010504 ATCAATTTAAAGGAATAA
1 ATCAATTTAAA-GAATAA
* *
14010522 ATTTAAATTAAA-AATAGA
1 A-TCAATTTAAAGAATA-A
*
14010540 ATTCAA-TTAAAGGA-AA
1 A-TCAATTTAAAGAATAA
14010556 A-CATATTTAAAGAATAA
1 ATCA-ATTTAAAGAATAA
*
14010573 ATCAATTTAAAGAAAAA
1 ATCAATTTAAAGAATAA
14010590 AT
1 AT
14010592 TTAAATTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 9 0.16
17 27 0.47
18 10 0.18
19 8 0.14
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (17 bp):
ATCAATTTAAAGAATAA
Found at i:14010637 original size:71 final size:71
Alignment explanation
Indices: 14010504--14010678 Score: 191
Period size: 71 Copynumber: 2.5 Consensus size: 71
14010494 TTATTAAAAT
*
14010504 ATCAATTTAAAGGAATAAATTTAAA--TT-AAAAATAGAATTCAATTAAAGGAAAACATATTTAA
1 ATCAATTTAAAGGAATAAATTTAAATTTTAAAAAATAGAATTCAATTAAAGGAAAACATAATTAA
14010566 AGAATAA
66 AGAAT-A
* *
14010573 ATCAATTTAAA-GAAAAAATTTAAATTTTAAAAAATAGAATTTAATTGAAA-GAAGAA-ATAATT
1 ATCAATTTAAAGGAATAAATTTAAATTTTAAAAAATAGAATTCAATT-AAAGGAA-AACATAATT
*
14010635 AAAGGATA
64 AAAGAATA
* ** * *
14010643 ATTATATTTAAATTAATAGATTTTAATTTTAAAAAA
1 ATCA-ATTTAAAGGAATAAATTTAAATTTTAAAAAA
14010679 AAAAAGAGAA
Statistics
Matches: 90, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
68 12 0.13
69 11 0.12
70 6 0.07
71 37 0.41
72 24 0.27
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (71 bp):
ATCAATTTAAAGGAATAAATTTAAATTTTAAAAAATAGAATTCAATTAAAGGAAAACATAATTAA
AGAATA
Found at i:14020945 original size:9 final size:10
Alignment explanation
Indices: 14020918--14020950 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
14020908 ATTTCTCAAC
14020918 ATTTGAAAAA
1 ATTTGAAAAA
14020928 ATTTGAAAAA
1 ATTTGAAAAA
*
14020938 ATTTAAAAAA
1 ATTTGAAAAA
14020948 ATT
1 ATT
14020951 ATTTATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (10 bp):
ATTTGAAAAA
Found at i:14021077 original size:30 final size:30
Alignment explanation
Indices: 14021024--14021083 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
14021014 TAATATTAAC
** *
14021024 AATAAAATAATAATTATACAATATTCAAAT
1 AATAAAATAATAACAATACAATATTAAAAT
* *
14021054 AATAAAATAATAGCAATATAATATTAAAAT
1 AATAAAATAATAACAATACAATATTAAAAT
14021084 GACAGCAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (30 bp):
AATAAAATAATAACAATACAATATTAAAAT
Found at i:14026249 original size:3 final size:3
Alignment explanation
Indices: 14026241--14026272 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
14026231 GGCGGCAATC
*
14026241 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
14026273 CTTCCTAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:14037636 original size:3 final size:3
Alignment explanation
Indices: 14037624--14037657 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
14037614 ATTGAGGAGT
14037624 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
14037658 TAAGAAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:14038041 original size:27 final size:27
Alignment explanation
Indices: 14038000--14038067 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
14037990 ATATTTGGAG
* *
14038000 ATATT-TTTCATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
14038026 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
14038053 ATATTTATTATTATT
1 ATA-TTATT-TTATT
14038068 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.14
27 19 0.54
28 6 0.17
29 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:14038057 original size:13 final size:11
Alignment explanation
Indices: 14038030--14038072 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
14038020 AGTTAAATAT
14038030 TATTTTATTAA
1 TATTTTATTAA
14038041 TATTTTACTTAA
1 TATTTTA-TTAA
*
14038053 -ATATTTATTAT
1 TAT-TTTATTAA
14038064 TATTTTATT
1 TATTTTATT
14038073 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:14039631 original size:31 final size:33
Alignment explanation
Indices: 14039569--14039632 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
14039559 TAAACCCGTC
*
14039569 TATATTATTTTTAATTTTTTTAAAATATTTATAT
1 TATATTATTTTTAA-TTATTTAAAATATTTATAT
14039603 TATATTA-TTTTAA-TATTTAATAAT-TTTATA
1 TATATTATTTTTAATTATTTAA-AATATTTATA
14039633 CATTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 12 0.43
32 3 0.11
33 6 0.21
34 7 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TATATTATTTTTAATTATTTAAAATATTTATAT
Found at i:14041066 original size:21 final size:21
Alignment explanation
Indices: 14041032--14041083 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
14041022 AAAAATGTAT
*
14041032 AAAATTAT-TAAA-ATTTAAA
1 AAAATAATATAAATATTTAAA
14041051 ATAATATAATATAAATATTTAAA
1 A-AA-ATAATATAAATATTTAAA
14041074 AAAATAATAT
1 AAAATAATAT
14041084 GGGCGGGCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 11 0.39
22 6 0.21
23 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATAATATAAATATTTAAA
Found at i:14041074 original size:23 final size:20
Alignment explanation
Indices: 14041040--14041083 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 20
14041030 ATAAAATTAT
14041040 TAAAATTTAAAATAATATAATA
1 TAAAATTTAAAA-AA-ATAATA
14041062 TAAATATTTAAAAAAATAATA
1 TAAA-ATTTAAAAAAATAATA
14041083 T
1 T
14041084 GGGCGGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATTTAAAAAAATAATA
Found at i:14046859 original size:93 final size:92
Alignment explanation
Indices: 14046693--14046885 Score: 359
Period size: 93 Copynumber: 2.1 Consensus size: 92
14046683 TTTACAGGTA
*
14046693 TAAAATCCTACAGAATGTTAGTTAAAGTATATACCCTTAGCACCTCTATTTAGTAATTTTCGATA
1 TAAAATTCTACAGAATGTTAGTTAAAGTATATACCCTTAGCACCTCTATTTAGTAATTTTCGATA
14046758 AAAATCATATCCTTTAACAAAGCATTC
66 AAAATCATATCCTTTAACAAAGCATTC
14046785 TATAAATTCTACAGAATGTTAGTTAAAGTATATACCCTTAGCACCTCTATTTAGTAATTTTCGAT
1 TA-AAATTCTACAGAATGTTAGTTAAAGTATATACCCTTAGCACCTCTATTTAGTAATTTTCGAT
*
14046850 AAAAATCATATCCTTTAACAAAGCGTTC
65 AAAAATCATATCCTTTAACAAAGCATTC
14046878 TAAAATTC
1 TAAAATTC
14046886 ATATAGCATT
Statistics
Matches: 98, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
92 8 0.08
93 90 0.92
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (92 bp):
TAAAATTCTACAGAATGTTAGTTAAAGTATATACCCTTAGCACCTCTATTTAGTAATTTTCGATA
AAAATCATATCCTTTAACAAAGCATTC
Found at i:14059945 original size:29 final size:29
Alignment explanation
Indices: 14059878--14059948 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 29
14059868 ATTAATTTTA
*
14059878 AAATTTATTACTAAAATAAATTATACTATT
1 AAATTTATTACAAAAATAAATTATACT-TT
14059908 AAAGTTTTATTA-AAATAATAAATTATA-TTT
1 AAA--TTTATTACAAA-AATAAATTATACTTT
14059938 ATAATTTATTA
1 A-AATTTATTA
14059949 TATGATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
29 7 0.19
30 6 0.17
31 5 0.14
32 18 0.50
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (29 bp):
AAATTTATTACAAAAATAAATTATACTTT
Found at i:14072691 original size:15 final size:16
Alignment explanation
Indices: 14072671--14072703 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
14072661 ATTTTAATTT
14072671 AATTATAAAAAT-ATA
1 AATTATAAAAATAATA
*
14072686 AATTATTAAAATAATA
1 AATTATAAAAATAATA
14072702 AA
1 AA
14072704 ATTACATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTATAAAAATAATA
Found at i:14072738 original size:24 final size:24
Alignment explanation
Indices: 14072651--14072740 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 24
14072641 AAGCCCCAAC
*
14072651 AAAATATAAAATTTTAATTTAATTATA
1 AAAATATACAA-TTTAA-TT-ATTATA
**
14072678 AAAATATA-AA-TT-ATTAAAATA
1 AAAATATACAATTTAATTATTATA
*
14072699 ATAAA-ATTACATTTTAATTATTATA
1 A-AAATA-TACAATTTAATTATTATA
14072724 AAAATATACAATTTAAT
1 AAAATATACAATTTAAT
14072741 CCCAAGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
21 6 0.12
22 7 0.14
23 2 0.04
24 17 0.33
25 9 0.18
26 2 0.04
27 8 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AAAATATACAATTTAATTATTATA
Found at i:14073651 original size:13 final size:13
Alignment explanation
Indices: 14073633--14073662 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
14073623 TATTTGATAG
*
14073633 TACAAATTATAAT
1 TACAAATGATAAT
14073646 TACAAATGATAAT
1 TACAAATGATAAT
14073659 TACA
1 TACA
14073663 CGATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (13 bp):
TACAAATGATAAT
Found at i:14080693 original size:2 final size:2
Alignment explanation
Indices: 14080686--14080718 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
14080676 TCATAACAAA
14080686 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
14080719 AATAATTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:14083852 original size:30 final size:29
Alignment explanation
Indices: 14083816--14083892 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
14083806 TACTAAACAT
14083816 AAATTAAATACAAATAAATAATAT-CTTTA
1 AAATTAAATACAAATAAA-AATATACTTTA
*
14083845 AATATTAAAT-CATAATAAAAATATATTTTA
1 AA-ATTAAATACA-AATAAAAATATACTTTA
*
14083875 AAATAAAATA-AAATAAAA
1 AAATTAAATACAAATAAAA
14083893 TCAAGTCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 7 0.17
29 16 0.38
30 19 0.45
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTAAATACAAATAAAAATATACTTTA
Found at i:14083883 original size:29 final size:31
Alignment explanation
Indices: 14083831--14083892 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 31
14083821 AAATACAAAT
* *
14083831 AAATAATATCTTTAAATATTAAATCATAATAA
1 AAATAATATCTTTAAATATAAAAT-AAAATAA
14083863 AAAT-ATAT-TTTAAA-ATAAAATAAAATAA
1 AAATAATATCTTTAAATATAAAATAAAATAA
14083891 AA
1 AA
14083893 TCAAGTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 8 0.29
29 6 0.21
30 6 0.21
31 4 0.14
32 4 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATAATATCTTTAAATATAAAATAAAATAA
Found at i:14085875 original size:27 final size:28
Alignment explanation
Indices: 14085832--14085898 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
14085822 AAACATCATT
*
14085832 AAAA-ATAATAGAAAATACAAATT-TA-A
1 AAAATATAATATAAAATA-AAATTATATA
*
14085858 AAAATATAATATATAATAAAATTATATA
1 AAAATATAATATAAAATAAAATTATATA
*
14085886 AATAATTTAATAT
1 AA-AATATAATAT
14085899 TTATAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.26
27 13 0.38
28 3 0.09
29 9 0.26
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAATATAATATAAAATAAAATTATATA
Found at i:14086034 original size:14 final size:14
Alignment explanation
Indices: 14086017--14086044 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14086007 AAATTAAATT
14086017 TTAAAAATAAATAA
1 TTAAAAATAAATAA
14086031 TTAAAAATAAATAA
1 TTAAAAATAAATAA
14086045 AACACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAAATAAATAA
Found at i:14089905 original size:13 final size:14
Alignment explanation
Indices: 14089883--14089912 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
14089873 TTAGATAGTT
14089883 AAAAGCAAAAAAAA
1 AAAAGCAAAAAAAA
14089897 AAAAG-AAAAAAAA
1 AAAAGCAAAAAAAA
14089910 AAA
1 AAA
14089913 GGTTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAGCAAAAAAAA
Found at i:14089906 original size:14 final size:14
Alignment explanation
Indices: 14089883--14089912 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
14089873 TTAGATAGTT
*
14089883 AAAAGCAAAAAAAA
1 AAAAGAAAAAAAAA
14089897 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
14089911 AA
1 AA
14089913 GGTTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:14105518 original size:3 final size:3
Alignment explanation
Indices: 14105504--14105535 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
14105494 CTCTTGTTGC
*
14105504 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
14105536 AACTTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:14113355 original size:15 final size:15
Alignment explanation
Indices: 14113330--14113370 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
14113320 ATATTTTATT
14113330 AATAAAT-ATAT-TA
1 AATAAATCATATATA
14113343 AATGAAATCATATATA
1 AAT-AAATCATATATA
14113359 AATAAATTCATA
1 AATAAA-TCATA
14113371 ACTCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 4 0.17
15 7 0.29
16 10 0.42
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (15 bp):
AATAAATCATATATA
Done.