Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009603.1 Hibiscus syriacus cultivar Beakdansim tig00116983_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1462390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:622786 original size:42 final size:43
Alignment explanation
Indices: 622738--622857 Score: 122
Period size: 43 Copynumber: 2.8 Consensus size: 43
622728 TACATAAATT
622738 AAAAATATTTAATTAGTATATGT-TT-TGATAGTTA-TATAGT-TA
1 AAAAATATTTAATTAGT-T-TGTATTGTGATAGTTATTATA-TATA
* * *
622780 AAAAATAATTAATTAGTTTGTATTGTTATAGTTATTTTATATA
1 AAAAATATTTAATTAGTTTGTATTGTGATAGTTATTATATATA
* * *
622823 AAAATTATTTAATTAGTTTGTGTTAGTTATAGTTA
1 AAAAATATTTAATTAGTTTGTATT-GTGATAGTTA
622858 AGTTATATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
42 25 0.37
43 26 0.39
44 10 0.15
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (43 bp):
AAAAATATTTAATTAGTTTGTATTGTGATAGTTATTATATATA
Found at i:622838 original size:43 final size:40
Alignment explanation
Indices: 622736--622857 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 40
622726 TATACATAAA
*
622736 TTAAAAATATTTAATTAGTATATGTTT-TGATAGTTATATAG
1 TTAAAAATATTTAATTAGT-T-TGTTTGTTATAGTTATATAG
* *
622777 TTAAAAAATAATTAATTAGTTTGTATTGTTATAGTTATTTTA-
1 TT-AAAAATATTTAATTAGTTTGT-TTGTTATAGTTA-TATAG
622819 TATAAAAATTATTTAATTAGTTTGTGTTAGTTATAGTTA
1 T-TAAAAA-TATTTAATTAGTTTGT-TT-GTTATAGTTA
622858 AGTTATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
40 3 0.04
41 5 0.07
42 30 0.43
43 21 0.30
44 10 0.14
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (40 bp):
TTAAAAATATTTAATTAGTTTGTTTGTTATAGTTATATAG
Found at i:624719 original size:26 final size:24
Alignment explanation
Indices: 624661--624719 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
624651 CTAATAAACC
*
624661 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
624685 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
624713 TAATAAT
1 TAATAAT
624720 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:625521 original size:46 final size:43
Alignment explanation
Indices: 625438--625529 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 43
625428 GACACTAACA
*
625438 AATTAATTAATATTTTTATATTTAATAACTTAAACTAAGAACT
1 AATTAACTAATATTTTTATATTTAATAACTTAAACTAAGAACT
*
625481 AATTAACTAAT-TTTTTATATATAATATATAACTTAAACTAATAACT
1 AATTAACTAATATTTTTATAT-T--TA-ATAACTTAAACTAAGAACT
625527 AAT
1 AAT
625530 ATAATATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
42 9 0.21
43 11 0.26
45 2 0.05
46 21 0.49
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (43 bp):
AATTAACTAATATTTTTATATTTAATAACTTAAACTAAGAACT
Found at i:625559 original size:21 final size:21
Alignment explanation
Indices: 625535--625578 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
625525 CTAATATAAT
*
625535 ATAACTTAAACTTACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
625556 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
625577 AT
1 AT
625579 TACTAGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:625922 original size:13 final size:13
Alignment explanation
Indices: 625904--625950 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
625894 ATGAGCTATG
625904 ATGCAACGCATGC
1 ATGCAACGCATGC
625917 ATGCAA-GCTATGAGC
1 ATGCAACGC-AT--GC
625932 TATGCAACGCATGC
1 -ATGCAACGCATGC
625946 ATGCA
1 ATGCA
625951 GGACCTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 2 0.07
13 13 0.45
14 2 0.07
15 2 0.07
16 8 0.28
17 2 0.07
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (13 bp):
ATGCAACGCATGC
Found at i:625946 original size:29 final size:31
Alignment explanation
Indices: 625890--625950 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
625880 GGAATCTCTG
625890 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGC-ATGATGCAACGCATGCATGCA
625922 AGCTATGAGC-T-ATGCAACGCATGCATGCA
1 AGCTATGAGCATGATGCAACGCATGCATGCA
625951 GGACCTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 18 0.62
30 1 0.03
32 10 0.34
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (31 bp):
AGCTATGAGCATGATGCAACGCATGCATGCA
Found at i:626079 original size:52 final size:51
Alignment explanation
Indices: 626021--626158 Score: 223
Period size: 49 Copynumber: 2.8 Consensus size: 51
626011 ATGCACAGTT
626021 CCACGTCCAATGCACCATCCCCTCCCCCCATGCATTCCCACCCCATGCATTC
1 CCACGTCCAATGCACCATCCCCT-CCCCCATGCATTCCCACCCCATGCATTC
626073 CCACGTCCAATGCACCATCCCCTCCCCCATGCATT-CC-CCCCATGCATTC
1 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTC
*
626122 CCACGTCCCATG---CATCCCCTCCCCCATGCATTCCCAC
1 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCAC
626159 ATCCCATGTT
Statistics
Matches: 83, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
46 20 0.24
47 2 0.02
48 1 0.01
49 23 0.28
50 2 0.02
51 12 0.14
52 23 0.28
ACGTcount: A:0.18, C:0.54, G:0.08, T:0.20
Consensus pattern (51 bp):
CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTC
Found at i:626114 original size:13 final size:13
Alignment explanation
Indices: 626096--626123 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
626086 ACCATCCCCT
626096 CCCCCATGCATTC
1 CCCCCATGCATTC
626109 CCCCCATGCATTC
1 CCCCCATGCATTC
626122 CC
1 CC
626124 ACGTCCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.57, G:0.07, T:0.21
Consensus pattern (13 bp):
CCCCCATGCATTC
Found at i:626147 original size:16 final size:16
Alignment explanation
Indices: 626088--626217 Score: 99
Period size: 16 Copynumber: 8.2 Consensus size: 16
626078 TCCAATGCAC
626088 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
*
626104 CAT--TC-CCCCCATG
1 CATCCCCTCCCCCATG
* * *
626117 CATTCCCACGTCCCATG
1 CATCCCCTC-CCCCATG
626134 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* * *
626150 CATTCCCACATCCCATG
1 CATCCCCTC-CCCCATG
*
626167 TTGAT-CCCTCCCCCATG
1 --CATCCCCTCCCCCATG
* *
626184 CATTCCC-ACCCCATG
1 CATCCCCTCCCCCATG
626199 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
626215 CAT
1 CAT
626218 TCCCACGTCC
Statistics
Matches: 89, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
13 11 0.12
14 1 0.01
15 16 0.18
16 30 0.34
17 25 0.28
18 4 0.04
19 2 0.02
ACGTcount: A:0.16, C:0.54, G:0.08, T:0.22
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:626155 original size:46 final size:47
Alignment explanation
Indices: 626021--626156 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 47
626011 ATGCACAGTT
626021 CCACGTCCAATGCACCATCCCCTCCCCCCATGCATTCCCACCCCATGCATTC
1 CCACGTCCAATG--CCATCCCCT-CCCCCATGCATT-CC-CCCCATGCATTC
626073 CCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCCCCATGCATTC
1 CCACGTCCAATG--CCATCCCCTCCCCCATGCATTCCCCCCATGCATTC
*
626122 CCACGTCCCATG-CATCCCCTCCCCCATGCATTCCC
1 CCACGTCCAATGCCATCCCCTCCCCCATGCATTCCC
626157 ACATCCCATG
Statistics
Matches: 83, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
46 23 0.28
49 23 0.28
50 2 0.02
51 12 0.14
52 23 0.28
ACGTcount: A:0.18, C:0.54, G:0.08, T:0.20
Consensus pattern (47 bp):
CCACGTCCAATGCCATCCCCTCCCCCATGCATTCCCCCCATGCATTC
Found at i:626196 original size:82 final size:81
Alignment explanation
Indices: 626047--626223 Score: 207
Period size: 82 Copynumber: 2.2 Consensus size: 81
626037 ATCCCCTCCC
* *
626047 CCCATGCATTCCCACCCCATGCATTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCC
1 CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCC
626112 CCATGCATTCCCACGT
66 CCATGCATTCCCACGT
* * ***
626128 CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG-TTGAT-CCCTCCCCCATGCATTCCC
1 CCCATGCATCCCC-ACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATT-CC
* * *
626191 ACCCCATGCATCCCCTC-C
64 -CCCCATGCATTCCCACGT
*
626209 CCCATGCATTCCCAC
1 CCCATGCATCCCCAC
626224 GTCCATGTTG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
80 17 0.21
81 28 0.35
82 36 0.44
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (81 bp):
CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCC
CCATGCATTCCCACGT
Found at i:626204 original size:65 final size:65
Alignment explanation
Indices: 626109--626235 Score: 220
Period size: 65 Copynumber: 1.9 Consensus size: 65
626099 CCATGCATTC
626109 CCCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCC
1 CCCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACAT-CCATGTTGATCC
626174 CT
64 CT
*
626176 CCCCCATGCATTCCCAC-CCCATGCATCCCCTCCCCCATGCATTCCCACGTCCATGTTGAT
1 CCCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCATGTTGAT
626236 TGCATGGCAT
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
64 10 0.17
65 32 0.54
67 17 0.29
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (65 bp):
CCCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCATGTTGATCCCT
Found at i:626247 original size:44 final size:45
Alignment explanation
Indices: 626198--626286 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 45
626188 CCCACCCCAT
626198 GCATCCCCTCCCCCATGCATTCCCACGT-CCATGTTGATTGCATG
1 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
626242 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
1 GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
626287 TCCCATGTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 28 0.64
45 16 0.36
ACGTcount: A:0.16, C:0.42, G:0.16, T:0.27
Consensus pattern (45 bp):
GCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGATTGCATG
Found at i:626311 original size:17 final size:18
Alignment explanation
Indices: 626268--626321 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
626258 GCATTCCCAC
626268 GTCCCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
626286 GTCCCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
626304 GT-CCATGTTGATTGCAT
1 GTCCCATGTTGATTGCAT
626321 G
1 G
626322 GCCCTATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (18 bp):
GTCCCATGTTGATTGCAT
Found at i:626378 original size:29 final size:29
Alignment explanation
Indices: 626336--626424 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
626326 TATTACACAC
626336 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
626365 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
626394 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
626423 AG
1 AG
626425 ACCACTGTAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:628671 original size:2 final size:2
Alignment explanation
Indices: 628664--628694 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
628654 TAAAAAGAGT
628664 TA TA TA 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 TA TA TA T
628695 TAATATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:628991 original size:50 final size:49
Alignment explanation
Indices: 628923--629082 Score: 212
Period size: 50 Copynumber: 3.2 Consensus size: 49
628913 TTTGAGCTCT
*
628923 TTCCATTTTAGGTGAATTGTGCATTTAGTATATAAACAATCAGTCTTCA
1 TTCCATTTTAGGTGAATTGTGCATTTAGTATCTAAACAATCAGTCTTCA
**
628972 TTCCATTTTAAGGTGAATTGCACATTTAGTATCTAAACAATCAGTCTTCA
1 TTCCATTTT-AGGTGAATTGTGCATTTAGTATCTAAACAATCAGTCTTCA
* * * ** *
629022 TTCCATTTTAGGATAAATTATGTATTTAGTATCTAAATTATCAGTTTTCA
1 TTCCATTTTAGG-TGAATTGTGCATTTAGTATCTAAACAATCAGTCTTCA
*
629072 TTTCATTTTAG
1 TTCCATTTTAG
629083 TACTTAAACT
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
49 12 0.12
50 85 0.88
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.44
Consensus pattern (49 bp):
TTCCATTTTAGGTGAATTGTGCATTTAGTATCTAAACAATCAGTCTTCA
Found at i:630633 original size:2 final size:2
Alignment explanation
Indices: 630626--630661 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
630616 TTAAGGACTG
*
630626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
630662 TTAAGTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:631742 original size:21 final size:21
Alignment explanation
Indices: 631718--631771 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
631708 CTCGGAGGGA
631718 ACCGATTCCCCCCCAGGGGGT
1 ACCGATTCCCCCCCAGGGGGT
631739 ACCGATTCCCCCCCAGGGGGT
1 ACCGATTCCCCCCCAGGGGGT
631760 ACCGATTCCCCC
1 ACCGATTCCCCC
631772 TTGTATAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.15, C:0.46, G:0.24, T:0.15
Consensus pattern (21 bp):
ACCGATTCCCCCCCAGGGGGT
Found at i:637934 original size:24 final size:24
Alignment explanation
Indices: 637888--637936 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
637878 AGAATTTTCC
*
637888 AAAAAAAATTAAATTTTTGAAATT
1 AAAAAAAATTAAATTTTTCAAATT
*
637912 AAAAAAAATGTTAA-TTTTCAAATT
1 AAAAAAAAT-TAAATTTTTCAAATT
637936 A
1 A
637937 TTGTGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAAAAAAATTAAATTTTTCAAATT
Found at i:649022 original size:3 final size:3
Alignment explanation
Indices: 649005--649054 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
648995 CGCCAAAAAG
649005 ATT ATT AATT A-T ATT ATT A-T ATTT ATT ATT AATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT A-TT ATT ATT -ATT ATT ATT ATT ATT
649051 ATT A
1 ATT A
649055 ATTTATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.10
3 30 0.71
4 8 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:649063 original size:19 final size:19
Alignment explanation
Indices: 649005--649057 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
648995 CGCCAAAAAG
649005 ATTATTAATTATATTATTA-T
1 ATTATT-ATTA-ATTATTATT
649025 ATTTATTATTAATTATTATT
1 A-TTATTATTAATTATTATT
649045 ATTATTATTAATT
1 ATTATTATTAATT
649058 TATATTTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 19 0.61
20 7 0.23
21 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATTAATTATTATT
Found at i:652297 original size:32 final size:32
Alignment explanation
Indices: 652260--652336 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
652250 TACATGTTTG
* * * *
652260 AACTAATTTCTTTCCTTTTGTTTGTTTACATT
1 AACTAATTTCTTTCATTTTGTTTATGTACACT
652292 AACTAATTTCTTTCATTTTGTTTATGTACACT
1 AACTAATTTCTTTCATTTTGTTTATGTACACT
*
652324 AACTTATTTCTTT
1 AACTAATTTCTTT
652337 TGATTGTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.05, T:0.57
Consensus pattern (32 bp):
AACTAATTTCTTTCATTTTGTTTATGTACACT
Found at i:652890 original size:15 final size:14
Alignment explanation
Indices: 652861--652917 Score: 73
Period size: 15 Copynumber: 4.1 Consensus size: 14
652851 GATCAACATT
652861 TTTGCATTTGCATC
1 TTTGCATTTGCATC
*
652875 TTTGCATTTTGAATC
1 TTTGCA-TTTGCATC
652890 --TGCATTTGCATC
1 TTTGCATTTGCATC
652902 TTTGCAATTTGCATC
1 TTTGC-ATTTGCATC
652917 T
1 T
652918 GCATTTCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
12 7 0.19
13 4 0.11
14 9 0.24
15 17 0.46
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (14 bp):
TTTGCATTTGCATC
Found at i:652893 original size:21 final size:21
Alignment explanation
Indices: 652860--652917 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
652850 GGATCAACAT
*
652860 TTTTGCATTTGCATCTTTGCA
1 TTTTGAATTTGCATCTTTGCA
*
652881 TTTTGAATCTGCA--TTTGCA
1 TTTTGAATTTGCATCTTTGCA
652900 TCTTTGCAATTTGCATCT
1 T-TTTG-AATTTGCATCT
652918 GCATTTCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 7 0.23
20 4 0.13
21 18 0.60
23 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTTGAATTTGCATCTTTGCA
Found at i:652938 original size:27 final size:27
Alignment explanation
Indices: 652863--652923 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
652853 TCAACATTTT
*
652863 TGCATTTGCATCTTTGCATTTTGAATC
1 TGCATTTGCATCTTTGCAATTTGAATC
*
652890 TGCATTTGCATCTTTGCAATTTGCATC
1 TGCATTTGCATCTTTGCAATTTGAATC
652917 TGCATTT
1 TGCATTT
652924 CATTTTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.48
Consensus pattern (27 bp):
TGCATTTGCATCTTTGCAATTTGAATC
Found at i:655258 original size:32 final size:32
Alignment explanation
Indices: 655216--655303 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 32
655206 ATGAATAATG
*
655216 GGGGCATCTTTGAAGATTCAACATC-ATATGTT
1 GGGGCATCTTTGAAGATTCAACATCGA-ATATT
*
655248 GGGGCTTCTTT-AGAGATT-AGACATCGAATATT
1 GGGGCATCTTTGA-AGATTCA-ACATCGAATATT
* *
655280 GGTGCATCTTTGGAGATTCAACAT
1 GGGGCATCTTTGAAGATTCAACAT
655304 TATGATGTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
31 2 0.04
32 42 0.91
33 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (32 bp):
GGGGCATCTTTGAAGATTCAACATCGAATATT
Found at i:655773 original size:124 final size:124
Alignment explanation
Indices: 655547--655866 Score: 498
Period size: 124 Copynumber: 2.6 Consensus size: 124
655537 TAAAGATAGC
* * * *
655547 CAAGAGTTATCATAGTATGAGCAATATCATCCCCGACCAGATCTTCTCATCACGTAGGAGCCGTG
1 CAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTG
* *
655612 TCAAACCTGGATAACCAAGATTCATCATAGTATGAGCAGTGTTATCACCCTTATATGG-
66 TCAACCCTGGATAACCAAGATTCATCATAGTATGAGCAGTGTTATCACCCTTAGATGGT
* *
655670 CTAAGACTTATCATAGTATGAGCAGTGTCATCCCTGACCAGATCTCCTCATCACGTAGGAGCCTT
1 C-AAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGT
655735 GTCAACCCTGGATAACCAAGATTCATCATAGTATGAGCAGTGTTATCACCCTTAGATGGT
65 GTCAACCCTGGATAACCAAGATTCATCATAGTATGAGCAGTGTTATCACCCTTAGATGGT
* * * * * *
655795 CAAGACTTATTATATTATGAGCAGTGTTATCCCCAACCAGATATCCTCATCACGTAAGAGCCGTG
1 CAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTG
655860 TCAACCC
66 TCAACCC
655867 AGATAATCAG
Statistics
Matches: 179, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
123 1 0.01
124 177 0.99
125 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (124 bp):
CAAGACTTATCATAGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTG
TCAACCCTGGATAACCAAGATTCATCATAGTATGAGCAGTGTTATCACCCTTAGATGGT
Found at i:656031 original size:129 final size:128
Alignment explanation
Indices: 655838--656158 Score: 401
Period size: 129 Copynumber: 2.5 Consensus size: 128
655828 CAACCAGATA
* *
655838 TCCTCATCACGTAAGAGCCGTGTCAACCCAGATAATCAGCCATCCTCATCACGTAGGAATCGTGT
1 TCCTCATCACGTAAGAGCCGTGTCAACCCAGATAATCAGCCATCCTCATCACGTAGAAACCGTGT
* * *
655903 TATCA-CTTTTAGATGGCTATAACTCTTCATCACATATGAGCCATGTCATCACCCGACCTCATC
66 TATCAGC-TTTAGATGGCCAGAACTCTTCATCACATATAAGCCATGTCATCACCCGACCTCATC
* * ** * * *
655966 TCCTCATCACGTAGGATCCGTGTCAACCTTTGATAATTAGTCGTCCTCATCACGTAGAAACCGTG
1 TCCTCATCACGTAAGAGCCGTGTCAACC-CAGATAATCAGCCATCCTCATCACGTAGAAACCGTG
* * *
656031 TTATCAGCTTTAGATGGCCAGAACTCTTCATCGCGTATAAGCCATGTCATCACCCGACCTGATC
65 TTATCAGCTTTAGATGGCCAGAACTCTTCATCACATATAAGCCATGTCATCACCCGACCTCATC
* * * * * * *
656095 TCCTCATTATGTAAGAGTCGTGTCAACCCTCAGATAACCAGCTATCCTCATCATGTAGGAACCG
1 TCCTCATCACGTAAGAGCCGTGTCAA-CC-CAGATAATCAGCCATCCTCATCACGTAGAAACCG
656159 AGAATTGTTC
Statistics
Matches: 161, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
128 26 0.16
129 106 0.66
130 29 0.18
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (128 bp):
TCCTCATCACGTAAGAGCCGTGTCAACCCAGATAATCAGCCATCCTCATCACGTAGAAACCGTGT
TATCAGCTTTAGATGGCCAGAACTCTTCATCACATATAAGCCATGTCATCACCCGACCTCATC
Found at i:663281 original size:21 final size:22
Alignment explanation
Indices: 663241--663290 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
663231 TTTTCCAGAA
*
663241 TGCTACAGGGGTATCGATACCC
1 TGCTACAGGGGTACCGATACCC
* *
663263 TGCTACA-GTGTACCGATACCT
1 TGCTACAGGGGTACCGATACCC
663284 TGCTACA
1 TGCTACA
663291 ATAATTTCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCTACAGGGGTACCGATACCC
Found at i:663863 original size:31 final size:31
Alignment explanation
Indices: 663824--663915 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
663814 CCCGAAGGAC
* * *
663824 CAGTCCATA-GATCCATAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
* *
663855 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCAGAAGAACATAGGTAAA
* *
663886 CAGTCCATATGTCCTGAAGAACATATGTAA
1 CAGTCCATATGTCCAGAAGAACATAGGTAA
663916 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 51 0.98
32 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (31 bp):
CAGTCCATATGTCCAGAAGAACATAGGTAAA
Found at i:668937 original size:14 final size:15
Alignment explanation
Indices: 668918--668963 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
668908 TTCATCTCCA
668918 TCTTCTCT-TCATTT
1 TCTTCTCTCTCATTT
*
668932 TCTTCTTTCTCATTT
1 TCTTCTCTCTCATTT
*
668947 TCTCTTTCTCTCATTT
1 TCT-TCTCTCTCATTT
668963 T
1 T
668964 TCTCTCTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 7 0.26
15 9 0.33
16 11 0.41
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (15 bp):
TCTTCTCTCTCATTT
Found at i:668946 original size:15 final size:14
Alignment explanation
Indices: 668926--668956 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
668916 CATCTTCTCT
668926 TCATTTTCTTCTTTC
1 TCATTTTC-TCTTTC
668941 TCATTTTCTCTTTC
1 TCATTTTCTCTTTC
668955 TC
1 TC
668957 TCATTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (14 bp):
TCATTTTCTCTTTC
Found at i:669710 original size:32 final size:32
Alignment explanation
Indices: 669623--669733 Score: 107
Period size: 32 Copynumber: 3.5 Consensus size: 32
669613 TATCAGCTTC
* ** *
669623 GCATTCA-TTAATGCATAGTGGAGTCAATATT
1 GCATTCAGATAATGCATAGTATAGTCAGTATT
* **
669654 GTATTCAGATAATGCATAACATAGTCAGTATT
1 GCATTCAGATAATGCATAGTATAGTCAGTATT
* * * *
669686 GCATTTAGATAATGCATAGTATAGTTAGTGTA
1 GCATTCAGATAATGCATAGTATAGTCAGTATT
*
669718 ACATTCAGATAATGCA
1 GCATTCAGATAATGCA
669734 CAGGAGTGTG
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 6 0.10
32 57 0.90
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
GCATTCAGATAATGCATAGTATAGTCAGTATT
Found at i:675880 original size:21 final size:21
Alignment explanation
Indices: 675856--675972 Score: 216
Period size: 21 Copynumber: 5.6 Consensus size: 21
675846 ATTAAGGTAT
*
675856 GAGTATAGATACTAGTTGAAT
1 GAGTATAGATACTAGTTGAAC
675877 GAGTATAGATACTAGTTGAAC
1 GAGTATAGATACTAGTTGAAC
675898 GAGTATAGATACTAGTTGAAC
1 GAGTATAGATACTAGTTGAAC
675919 GAGTATAGATACTAGTTGAAC
1 GAGTATAGATACTAGTTGAAC
675940 GAGTATAGATACTAGTTGAAC
1 GAGTATAGATACTAGTTGAAC
*
675961 GAGTATCGATAC
1 GAGTATAGATAC
675973 CATAAGACAT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 94 1.00
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (21 bp):
GAGTATAGATACTAGTTGAAC
Found at i:677619 original size:31 final size:31
Alignment explanation
Indices: 677577--677641 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
677567 AAGAGTCAAG
677577 GGTTACATATGTCCTTCAGGACATATGGACA
1 GGTTACATATGTCCTTCAGGACATATGGACA
*
677608 GGTTACCTATGTCCTTCAGGACATATGGACA
1 GGTTACATATGTCCTTCAGGACATATGGACA
677639 GGT
1 GGT
677642 CATTCGGGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (31 bp):
GGTTACATATGTCCTTCAGGACATATGGACA
Found at i:683438 original size:21 final size:19
Alignment explanation
Indices: 683410--683455 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
683400 TCATTGAATC
683410 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
683430 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
683449 ACTTAGT
1 A-TTAGT
683456 AATTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:694935 original size:31 final size:31
Alignment explanation
Indices: 694892--695031 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
694882 CGAGGGTTAC
*
694892 TCGGAACATATGGACAGGTTACCTATGTCAT
1 TCGGGACATATGGACAGGTTACCTATGTCAT
694923 TCGGGACATATGGACAGGTTACCTATGTCAT
1 TCGGGACATATGGACAGGTTACCTATGTCAT
* *
694954 TCAGGATATATGGACAGGTTACCTATGTCAT
1 TCGGGACATATGGACAGGTTACCTATGTCAT
* *
694985 TCGGGACATATGGACATGTTACCTATGTCCT
1 TCGGGACATATGGACAGGTTACCTATGTCAT
*
695016 TCGGGATATATGGACA
1 TCGGGACATATGGACA
695032 AGTCCTTCGG
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (31 bp):
TCGGGACATATGGACAGGTTACCTATGTCAT
Found at i:695061 original size:19 final size:19
Alignment explanation
Indices: 695037--695074 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
695027 GGACAAGTCC
*
695037 TTCGGGACATATATGACAT
1 TTCGGGACATAGATGACAT
695056 TTCGGGACATAGATGACAT
1 TTCGGGACATAGATGACAT
695075 CATTCAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (19 bp):
TTCGGGACATAGATGACAT
Found at i:701169 original size:21 final size:21
Alignment explanation
Indices: 701118--701166 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
701108 AGTTTAATAA
701118 TTTTAAATTCATAATTAAATT
1 TTTTAAATTCATAATTAAATT
* *
701139 TAATTAAATTCA-ACTTAAATT
1 T-TTTAAATTCATAATTAAATT
701160 TTTTAAA
1 TTTTAAA
701167 ATTAAATCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 10 0.42
22 9 0.38
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAATTCATAATTAAATT
Found at i:704215 original size:26 final size:27
Alignment explanation
Indices: 704184--704234 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
704174 TTAAATTCAT
704184 AATATTTTGTATA-T-ATTAACTTAAAA
1 AATATTTT-TATATTCATTAACTTAAAA
704210 AATATTTTTATATTCATTAACTTAA
1 AATATTTTTATATTCATTAACTTAA
704235 TTTAAAGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 9 0.39
27 10 0.43
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (27 bp):
AATATTTTTATATTCATTAACTTAAAA
Found at i:704240 original size:32 final size:30
Alignment explanation
Indices: 704199--704257 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
704189 TTTGTATATA
704199 TTAACTTAAAAAATATTTTTATATTCATTAAC
1 TTAACTT-AAAAATA-TTTTATATTCATTAAC
* * *
704231 TTAATTTAAAGATATTTTATTTTCATT
1 TTAACTTAAAAATATTTTATATTCATT
704258 TAAACATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.50
31 6 0.25
32 6 0.25
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (30 bp):
TTAACTTAAAAATATTTTATATTCATTAAC
Found at i:704273 original size:20 final size:21
Alignment explanation
Indices: 704234--704281 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
704224 CATTAACTTA
* *
704234 ATTTAAAGATATTTTATTTTC
1 ATTTAAACATATTATATTTTC
704255 ATTTAAACATA-TATATTTT-
1 ATTTAAACATATTATATTTTC
704274 ATGTTAAA
1 AT-TTAAA
704282 ATTTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTTAAACATATTATATTTTC
Found at i:709938 original size:17 final size:18
Alignment explanation
Indices: 709895--709935 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
709885 AAATTATATT
709895 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
709912 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
709930 ATTAAA
1 AGTAAA
709936 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:721290 original size:13 final size:13
Alignment explanation
Indices: 721272--721305 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
721262 ACATAGTTGA
721272 GCAGTCTTCATAT
1 GCAGTCTTCATAT
*
721285 GCAGTCATCATAT
1 GCAGTCTTCATAT
721298 GCACGTCT
1 GCA-GTCT
721306 ATAATGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (13 bp):
GCAGTCTTCATAT
Found at i:730484 original size:17 final size:18
Alignment explanation
Indices: 730459--730496 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
730449 TTTGTCGCGG
730459 CGACTTTTTTCGAAGTGA
1 CGACTTTTTTCGAAGTGA
730477 CGAC-TTTTTCGAAGTGA
1 CGACTTTTTTCGAAGTGA
730494 CGA
1 CGA
730497 AAATCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (18 bp):
CGACTTTTTTCGAAGTGA
Found at i:730535 original size:16 final size:16
Alignment explanation
Indices: 730502--730535 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
730492 GACGAAAATC
730502 AAAATAAATTTAGAAA
1 AAAATAAATTTAGAAA
730518 AAAATCAAATTTAGAAA
1 AAAAT-AAATTTAGAAA
730535 A
1 A
730536 GATTTGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATAAATTTAGAAA
Found at i:732544 original size:12 final size:12
Alignment explanation
Indices: 732529--732554 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
732519 TTTAATCGAA
732529 TTTTCTTGATTT
1 TTTTCTTGATTT
732541 TTTTCTTGATTT
1 TTTTCTTGATTT
732553 TT
1 TT
732555 GCATGCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTTTCTTGATTT
Found at i:733338 original size:22 final size:22
Alignment explanation
Indices: 733313--733385 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
733303 TGCTAATTAC
* *
733313 TTAACAT-CTAATGTAATATGAA
1 TTAACATGC-AATGCAACATGAA
*
733335 TTAATATGCAATGCAACATGAA
1 TTAACATGCAATGCAACATGAA
733357 TTAATAACATGCAATG-ACACATGAA
1 -T--TAACATGCAATGCA-ACATGAA
733382 TTAA
1 TTAA
733386 TAACATGCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 20 0.48
23 2 0.05
24 2 0.05
25 18 0.43
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (22 bp):
TTAACATGCAATGCAACATGAA
Found at i:733378 original size:25 final size:26
Alignment explanation
Indices: 733340--733398 Score: 104
Period size: 25 Copynumber: 2.3 Consensus size: 26
733330 ATGAATTAAT
733340 ATGCAATG-CAACATGAATTAATAAC
1 ATGCAATGACAACATGAATTAATAAC
733365 ATGCAATGAC-ACATGAATTAATAAC
1 ATGCAATGACAACATGAATTAATAAC
733390 ATGCAATGA
1 ATGCAATGA
733399 ATTACTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (26 bp):
ATGCAATGACAACATGAATTAATAAC
Found at i:733400 original size:18 final size:18
Alignment explanation
Indices: 733377--733414 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
733367 GCAATGACAC
733377 ATGAATTAATAACATGCA
1 ATGAATTAATAACATGCA
*
733395 ATGAATTACTAACATGCA
1 ATGAATTAATAACATGCA
733413 AT
1 AT
733415 TATTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (18 bp):
ATGAATTAATAACATGCA
Found at i:742164 original size:25 final size:25
Alignment explanation
Indices: 742098--742183 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
742088 GCTGATTACT
*
742098 TAACAT-CTAATGTAATATGAATTAA
1 TAACATGC-AATGAAATATGAATTAA
** *
742123 T---ATGCAATTCAACATGAATTAA
1 TAACATGCAATGAAATATGAATTAA
742145 TAACATGCAATGAAATATGAATTAA
1 TAACATGCAATGAAATATGAATTAA
*
742170 TAACATACAATGAA
1 TAACATGCAATGAA
742184 TTACTAAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
22 17 0.34
23 1 0.02
25 32 0.64
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.30
Consensus pattern (25 bp):
TAACATGCAATGAAATATGAATTAA
Found at i:742660 original size:3 final size:3
Alignment explanation
Indices: 742652--742720 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
742642 CAAATAATGG
*
742652 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
742700 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
742721 ACATACATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:744497 original size:67 final size:66
Alignment explanation
Indices: 744420--744679 Score: 313
Period size: 66 Copynumber: 3.9 Consensus size: 66
744410 GAAAGAAATT
* * * * ** *
744420 TGTTTCAAGAGAAACTATCTGAGGTGAGATAAAATTTTGTTTTGAGTGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTT
*
744485 TT
65 TA
* * * * * * * *
744487 TGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAATTTGTTTCGAGAGAAATAATCTTAAAAGTTG
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
744552 A
66 A
* * *
744553 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAATAATCTCATAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
744618 A
66 A
* *
744619 TGTTTCAAGAGAAATTGTCTCAAGCGAGATAAATCTTTGTTTCAAGAGAAACAATCTCAAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAA-ATTTGTTTCAAGAGAAACAATCTCAAA
744680 TAAGACAGAC
Statistics
Matches: 164, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
66 113 0.69
67 51 0.31
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
A
Found at i:744508 original size:30 final size:30
Alignment explanation
Indices: 744474--744641 Score: 75
Period size: 30 Copynumber: 5.2 Consensus size: 30
744464 AGTGAAACAA
744474 TCTCAAAGGTTTTTGTTTCAAGAGAAATTG
1 TCTCAAAGGTTTTTGTTTCAAGAGAAATTG
** * **
744504 TCTCAAGCAAGATGAAATTTGTTTCGAGAGAAATAA
1 TCTC-A--AAG--G-TTTTTGTTTCAAGAGAAATTG
* * ** *
744540 TCTTAAAAGTTGATGTTTCAAGAGAAACTG
1 TCTCAAAGGTTTTTGTTTCAAGAGAAATTG
*** **
744570 TCTCAAGCGAGACAAAATTTGTTTCAAGAGAAATAA
1 TCTCAA---AG---GTTTTTGTTTCAAGAGAAATTG
* *
744606 TCTCATAGGTTTATGTTTCAAGAGAAATTG
1 TCTCAAAGGTTTTTGTTTCAAGAGAAATTG
744636 TCTCAA
1 TCTCAA
744642 GCGAGATAAA
Statistics
Matches: 93, Mismatches: 33, Indels: 24
0.62 0.22 0.16
Matches are distributed among these distances:
30 43 0.46
31 2 0.02
33 8 0.09
35 2 0.02
36 38 0.41
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (30 bp):
TCTCAAAGGTTTTTGTTTCAAGAGAAATTG
Found at i:744534 original size:36 final size:36
Alignment explanation
Indices: 744485--744669 Score: 121
Period size: 36 Copynumber: 5.4 Consensus size: 36
744475 CTCAAAGGTT
744485 TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
* ** * *
744521 TTTGTTTCGAGAGAAATAATCTTAA--AAGTTG--A
1 TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
* * **
744553 --TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
**
744587 TTTGTTTCAAGAGAAATAATCTCATAG---G-T----
1 TTTGTTTCAAGAGAAATTGTCTCA-AGCAAGATGAAA
*
744616 TTATGTTTCAAGAGAAATTGTCTCAAGCGAGAT-AAA
1 TT-TGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
744652 TCTTTGTTTCAAGAGAAA
1 --TTTGTTTCAAGAGAAA
744670 CAATCTCAAA
Statistics
Matches: 112, Mismatches: 20, Indels: 33
0.68 0.12 0.20
Matches are distributed among these distances:
29 4 0.04
30 38 0.34
32 4 0.04
33 1 0.01
34 7 0.06
36 40 0.36
37 16 0.14
38 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA
Found at i:744624 original size:132 final size:133
Alignment explanation
Indices: 744420--744675 Score: 354
Period size: 132 Copynumber: 1.9 Consensus size: 133
744410 GAAAGAAATT
* * * * ** *
744420 TGTTTCAAGAGAAACTATCTGAGGTGAGATAAAATTTTGTTTTGAGTGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGAGAAACAATCTCAAAGGTT
* * *
744485 TTTGTTTCAAGAGAAATTGTCTCAAGCAAGATGAAA-TTTGTTTCGAGAGAAATAATCTTAAAAG
66 TATGTTTCAAGAGAAATTGTCTCAAGCAAGAT-AAACTTTGTTTCAAGAGAAACAATCTTAAAAG
744549 TTGA
130 TTGA
* * *
744553 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAATAATCTCATAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGAGAAACAATCTCAAAGGTT
*
744617 TATGTTTCAAGAGAAATTGTCTCAAGCGAGATAAATCTTTGTTTCAAGAGAAACAATCT
66 TATGTTTCAAGAGAAATTGTCTCAAGCAAGATAAA-CTTTGTTTCAAGAGAAACAATCT
744676 CAAATAAGAC
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
131 3 0.03
132 55 0.51
133 49 0.46
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (133 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTTGTTTCAAGAGAAACAATCTCAAAGGTT
TATGTTTCAAGAGAAATTGTCTCAAGCAAGATAAACTTTGTTTCAAGAGAAACAATCTTAAAAGT
TGA
Found at i:746798 original size:10 final size:10
Alignment explanation
Indices: 746783--746839 Score: 55
Period size: 10 Copynumber: 5.4 Consensus size: 10
746773 CATTTCAGTT
746783 TTCTTTTTTC
1 TTCTTTTTTC
746793 TTCTTTTCTTTC
1 TTC-TTT-TTTC
746805 TTTCTCTTTTT-
1 -TTCT-TTTTTC
746816 TTCTTTTTTC
1 TTCTTTTTTC
746826 TTCTTATTTT-
1 TTCTT-TTTTC
746836 TTCT
1 TTCT
746840 GGTGTAATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.12
10 16 0.39
11 7 0.17
12 8 0.20
13 5 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:746801 original size:15 final size:15
Alignment explanation
Indices: 746781--746830 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
746771 TTCATTTCAG
746781 TTTTCTTTTTTCTTC
1 TTTTCTTTTTTCTTC
*
746796 TTTTCTTTCTTTCTCTTT
1 TTTTC-TT-TTT-TCTTC
746814 TTTTCTTTTTTCTTC
1 TTTTCTTTTTTCTTC
746829 TT
1 TT
746831 ATTTTTTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 11 0.37
16 5 0.17
17 5 0.17
18 9 0.30
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTCTTC
Found at i:746817 original size:18 final size:18
Alignment explanation
Indices: 746781--746836 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
746771 TTCATTTCAG
746781 TTTTCTTTTTTCTTC---
1 TTTTCTTTTTTCTTCTTT
746796 TTTTCTTTCTTTC-TCTTT
1 TTTTCTTT-TTTCTTCTTT
746814 TTTTCTTTTTTCTTCTTAT
1 TTTTCTTTTTTCTTCTT-T
746833 TTTT
1 TTTT
746837 TCTGGTGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 10 0.29
16 4 0.11
17 4 0.11
18 12 0.34
19 5 0.14
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTCTTCTTT
Found at i:752785 original size:35 final size:36
Alignment explanation
Indices: 752715--752789 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
752705 CCAAAATAAC
752715 CCCTAAATTAGTGACCATTATAGAAAATACGACGAA
1 CCCTAAATTAGTGACCATTATAGAAAATACGACGAA
752751 CCCTAAATTAGTGACCATTATAG-AAATACGACGAA
1 CCCTAAATTAGTGACCATTATAGAAAATACGACGAA
752786 CCCT
1 CCCT
752790 CAGGGACCTG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 16 0.41
36 23 0.59
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (36 bp):
CCCTAAATTAGTGACCATTATAGAAAATACGACGAA
Found at i:754090 original size:24 final size:24
Alignment explanation
Indices: 754035--754090 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
754025 CCTGTGGAAT
* * *
754035 CTGTCATACTCGGGACTCCTGTGC
1 CTGTCATACTCAGGACTCCGGTAC
** *
754059 CTCCCATATTCAGGACTCCGGTAC
1 CTGTCATACTCAGGACTCCGGTAC
754083 CTGTCATA
1 CTGTCATA
754091 AGCAGGACCA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.34, G:0.20, T:0.29
Consensus pattern (24 bp):
CTGTCATACTCAGGACTCCGGTAC
Found at i:755789 original size:26 final size:25
Alignment explanation
Indices: 755741--755789 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
755731 ATTTATATAC
* *
755741 TTTTTAATAAAATTTATATATAATT
1 TTTTTAATAAAATTTAAAGATAATT
*
755766 TTTTTTATAAAATTTAAAAGATAA
1 TTTTTAATAAAATTT-AAAGATAA
755790 ATGGGTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTTAATAAAATTTAAAGATAATT
Found at i:755837 original size:21 final size:21
Alignment explanation
Indices: 755813--755852 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
755803 CAGAGTAAAT
755813 ATATGTATTATTTTA-ATTATA
1 ATAT-TATTATTTTACATTATA
*
755834 ATATTATTTTTTTACATTA
1 ATATTATTATTTTACATTA
755853 ATTATCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
ATATTATTATTTTACATTATA
Found at i:761837 original size:92 final size:93
Alignment explanation
Indices: 761671--761858 Score: 360
Period size: 92 Copynumber: 2.0 Consensus size: 93
761661 AATATTATCA
761671 AGTCCACGAATAGCATCTTCAGCATCACGTTATTCCTCAAAATAAATGAAGGCAAATCCTGCAAT
1 AGTCCACGAATAGCATCTTCAGCATCACGTTATTCCTCAAAATAAATGAAGGCAAATCCTGCAAT
*
761736 TTGAACTCAAATTAGTTGCACAAGTGAT
66 ATGAACTCAAATTAGTTGCACAAGTGAT
761764 AGTCCACG-ATAGCATCTTCAGCATCACGTTATTCCTCAAAATAAATGAAGGCAAATCCTGCAAT
1 AGTCCACGAATAGCATCTTCAGCATCACGTTATTCCTCAAAATAAATGAAGGCAAATCCTGCAAT
761828 ATGAACTCAAATTAGTTGCACAAGTGAT
66 ATGAACTCAAATTAGTTGCACAAGTGAT
761856 AGT
1 AGT
761859 TTTCGTAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 86 0.91
93 8 0.09
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (93 bp):
AGTCCACGAATAGCATCTTCAGCATCACGTTATTCCTCAAAATAAATGAAGGCAAATCCTGCAAT
ATGAACTCAAATTAGTTGCACAAGTGAT
Found at i:765202 original size:26 final size:26
Alignment explanation
Indices: 765166--765232 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
765156 ATGTTGTATG
765166 ATAAAATTTTATAGTAAATAGATTAT
1 ATAAAATTTTATAGTAAATAGATTAT
*
765192 ATAAAATTTTATAGTAAATAGATTGT
1 ATAAAATTTTATAGTAAATAGATTAT
765218 ATAAAATTTTATAGT
1 ATAAAATTTTATAGT
765233 TTCATAGTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (26 bp):
ATAAAATTTTATAGTAAATAGATTAT
Found at i:773929 original size:18 final size:18
Alignment explanation
Indices: 773906--773978 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
773896 AGGGATAATC
773906 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
773924 AGTGGTTCTTCGGAATAAT
1 AGTGGTCCTTCGGGA-CAT
773943 AAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
773962 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
773979 AATATTCAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 4 0.09
20 13 0.28
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:773951 original size:38 final size:38
Alignment explanation
Indices: 773900--773974 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
773890 GAGTCGAGGG
* *
773900 ATAATCAGTGGTCCTTCGGGACATAGTGGTTCTTCGGA
1 ATAATAAGTGGTCCTTCGGGACATAGTGGTCCTTCGGA
773938 ATAATAAGTGGTCCTTCGGGACATAGTGGTCCTTCGG
1 ATAATAAGTGGTCCTTCGGGACATAGTGGTCCTTCGG
773975 GACAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (38 bp):
ATAATAAGTGGTCCTTCGGGACATAGTGGTCCTTCGGA
Found at i:779101 original size:26 final size:27
Alignment explanation
Indices: 779072--779135 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 27
779062 TTCACACCTA
779072 AATTAAG-TGATGTCATTGCTTACATC
1 AATTAAGTTGATGTCATTGCTTACATC
*
779098 AATTTAGTTTTGATGTCATTGCTTACATC
1 AATTAAG--TTGATGTCATTGCTTACATC
*
779127 AATTTAGTT
1 AATTAAGTT
779136 AGGTGCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.18
27 2 0.06
29 26 0.76
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (27 bp):
AATTAAGTTGATGTCATTGCTTACATC
Found at i:779112 original size:29 final size:29
Alignment explanation
Indices: 779079--779135 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
779069 CTAAATTAAG
779079 TGATGTCATTGCTTACATCAATTTAGTTT
1 TGATGTCATTGCTTACATCAATTTAGTTT
779108 TGATGTCATTGCTTACATCAATTTAGTT
1 TGATGTCATTGCTTACATCAATTTAGTT
779136 AGGTGCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCAATTTAGTTT
Found at i:783634 original size:29 final size:29
Alignment explanation
Indices: 783601--783658 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
783591 CCTAAATTAA
783601 TTGATGTCATTGCTTACATCAATTTAGTT
1 TTGATGTCATTGCTTACATCAATTTAGTT
*
783630 TTGATGTCATTGCTTATATCAATTTAGTT
1 TTGATGTCATTGCTTACATCAATTTAGTT
783659 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTT
Found at i:790376 original size:12 final size:12
Alignment explanation
Indices: 790357--790388 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
790347 CACCCATCTC
790357 CCGTATACCTTT
1 CCGTATACCTTT
*
790369 CTGTATACCTTT
1 CCGTATACCTTT
790381 CCGTATAC
1 CCGTATAC
790389 GAGATTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (12 bp):
CCGTATACCTTT
Found at i:791678 original size:26 final size:26
Alignment explanation
Indices: 791649--791911 Score: 241
Period size: 26 Copynumber: 11.0 Consensus size: 26
791639 CGTTAAATTT
791649 CATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
791675 CATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
791701 CATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
*
791727 C--CTTA---AT-GCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
* * *
791747 CATTTTATTTATGGCATTCGTTCCTG
1 CATTTTATTTATGGCATCCTTTCATG
* *
791773 C--CTTA---AT-GAATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
*
791793 CATTTTATTTATGGCATCCTTTTATG
1 CATTTTATTTATGGCATCCTTTCATG
* *
791819 C--CTTA---AT-GCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
791839 CATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
* *
791865 C--CTTA---AT-GCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
* *
791885 CATTTTATTTATGACATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATG
791911 C
1 C
791912 CTTAATGCAT
Statistics
Matches: 191, Mismatches: 22, Indels: 48
0.73 0.08 0.18
Matches are distributed among these distances:
20 49 0.26
21 8 0.04
22 12 0.06
24 12 0.06
25 8 0.04
26 102 0.53
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (26 bp):
CATTTTATTTATGGCATCCTTTCATG
Found at i:791744 original size:46 final size:46
Alignment explanation
Indices: 791649--791931 Score: 404
Period size: 46 Copynumber: 6.0 Consensus size: 46
791639 CGTTAAATTT
* *
791649 CATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGC--CTTA---AT-GCATCATTTCATG
*
791701 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * * * *
791747 CATTTTATTTATGGCATTCGTTCCTGCCTTAATGAATCCTTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
*
791793 CATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
791839 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
* * *
791885 CATTTTATTTATGACATCATTTCATGCCTTAATGCATTATTTCATG
1 CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
791931 C
1 C
791932 CTTAATGCAT
Statistics
Matches: 216, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
46 184 0.85
47 2 0.01
50 3 0.01
52 27 0.12
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (46 bp):
CATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATG
Found at i:791928 original size:138 final size:141
Alignment explanation
Indices: 791649--791989 Score: 423
Period size: 138 Copynumber: 2.4 Consensus size: 141
791639 CGTTAAATTT
* *
791649 CATTTTATTTATGGCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCATTTTATTTATG
1 CATTTTATTTATGGCATCCTTTCATGCA-CTTA--TATGGCATCATTTCATGCATTTTATTTATG
* * *
791714 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTATTTATGGCATTCGTTCCTGCCTTAA
63 GCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGACATTCGTTCATGCCTTAA
*
791779 TGAATCCTTTCATG
128 TGAATCATTTCATG
*
791793 CATTTTATTTATGGCATCCTTTTATGC-CTTA-AT-GCATCATTTCATGCATTTTATTTATGGCA
1 CATTTTATTTATGGCATCCTTTCATGCACTTATATGGCATCATTTCATGCATTTTATTTATGGCA
*
791855 TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGACA-TCATTTCATGCCTTAATG
66 TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGACATTC-GTTCATGCCTTAATG
* *
791919 CATTATTTCATG
130 AATCATTTCATG
* * * *
791931 C--CTTA---AT-GCATCCTTTCATGAATTTTATTTATGGCATCCTTTCATGCATTTTATTTATG
1 CATTTTATTTATGGCATCCTTTCATGCA-CTTA--TATGGCATCATTTCATGCATTTTATTTATG
791990 TATTCGGTTT
Statistics
Matches: 175, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
132 12 0.07
133 2 0.01
134 3 0.02
136 3 0.02
137 4 0.02
138 120 0.69
139 2 0.01
142 3 0.02
144 26 0.15
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (141 bp):
CATTTTATTTATGGCATCCTTTCATGCACTTATATGGCATCATTTCATGCATTTTATTTATGGCA
TCCTTTCATGCCTTAATGCATCATTTCATGCATTTTATTTATGACATTCGTTCATGCCTTAATGA
ATCATTTCATG
Found at i:791967 original size:26 final size:26
Alignment explanation
Indices: 791938--791989 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
791928 ATGCCTTAAT
791938 GCATCCTTTCATGAATTTTATTTATG
1 GCATCCTTTCATGAATTTTATTTATG
*
791964 GCATCCTTTCATGCATTTTATTTATG
1 GCATCCTTTCATGAATTTTATTTATG
791990 TATTCGGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (26 bp):
GCATCCTTTCATGAATTTTATTTATG
Found at i:791968 original size:92 final size:89
Alignment explanation
Indices: 791688--791989 Score: 358
Period size: 92 Copynumber: 3.3 Consensus size: 89
791678 TTTATTTATG
*
791688 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTT
* * *
791753 ATTTATGGCATTCGTTCCTGCCTTAAT
65 A--TATGGCATCCTTTCATGCCTTAAT
* *
791780 GAATCCTTTCATGCATTTTATTTATGGCATCCTTTTATGCCTTAATGCATCATTTCATGCATTTT
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCA-TTT
791845 ATTTATGGCATCCTTTCATGCCTTAAT
65 A--TATGGCATCCTTTCATGCCTTAAT
* * * * *
791872 GCATCATTTCATGCATTTTATTTATGACATCATTTCATGCCTTAATGCATTATTTCATGC-CTTA
1 GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
**
791936 -AT-GCATCCTTTCATGAATTTTATTTAT
66 TATGGCATCCTTTCATG--CCTTA---AT
791963 GGCATCCTTTCATGCATTTTATTTATG
1 -GCATCCTTTCATGCATTTTATTTATG
791990 TATTCGGTTT
Statistics
Matches: 188, Mismatches: 16, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
86 13 0.07
87 2 0.01
88 3 0.02
90 3 0.02
91 2 0.01
92 165 0.88
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.47
Consensus pattern (89 bp):
GCATCCTTTCATGCATTTTATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTA
TATGGCATCCTTTCATGCCTTAAT
Found at i:792556 original size:95 final size:95
Alignment explanation
Indices: 792417--792616 Score: 303
Period size: 95 Copynumber: 2.1 Consensus size: 95
792407 ACTCTCGTAC
* * * *
792417 CGATACTTCTATACTATGGTACTGATACCCATTTTCGGTATCGATACAAATTTTAGATTCGATGT
1 CGATACTACCATACTATGGTACCGATACCCATTTCCGGTATCGATACAAATTTTAGATTCGATGT
* * *
792482 TTCCTGGTATCGATATCCTTACCATGGTAT
66 TGCCTGGTATCGACACCCTTACCATGGTAT
* *
792512 CGATGCTACCATACTATGGTACCGATACCCCA-TTCCGGTATCGATACCAATTTTAGATTCGATG
1 CGATACTACCATACTATGGTACCGATA-CCCATTTCCGGTATCGATACAAATTTTAGATTCGATG
792576 TTGCCTGGTATCGACACCCTTACCATGGTAT
65 TTGCCTGGTATCGACACCCTTACCATGGTAT
792607 CGATACTACC
1 CGATACTACC
792617 TTGTCAGTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 90 0.96
96 4 0.04
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (95 bp):
CGATACTACCATACTATGGTACCGATACCCATTTCCGGTATCGATACAAATTTTAGATTCGATGT
TGCCTGGTATCGACACCCTTACCATGGTAT
Found at i:794754 original size:33 final size:33
Alignment explanation
Indices: 794712--794778 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
794702 CCTAGTACAG
* *
794712 ATGGTGGACACGACCTTATGTGTTATACGAATT
1 ATGGTGGACACGAACTTATGTGTCATACGAATT
794745 ATGGTGGACACGAACTTATGTGTCATACGAATT
1 ATGGTGGACACGAACTTATGTGTCATACGAATT
794778 A
1 A
794779 GCACTATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (33 bp):
ATGGTGGACACGAACTTATGTGTCATACGAATT
Found at i:794774 original size:17 final size:17
Alignment explanation
Indices: 794721--794775 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
794711 GATGGTGGAC
* *
794721 ACGACCTTATGTGTTAT
1 ACGAACTTATGTGTCAT
* *
794738 ACGAA-TTATG-GTGGAC
1 ACGAACTTATGTGT-CAT
794754 ACGAACTTATGTGTCAT
1 ACGAACTTATGTGTCAT
794771 ACGAA
1 ACGAA
794776 TTAGCACTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.07
16 11 0.37
17 15 0.50
18 2 0.07
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (17 bp):
ACGAACTTATGTGTCAT
Found at i:794863 original size:20 final size:20
Alignment explanation
Indices: 794838--794878 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
794828 TACATTGGGC
*
794838 TATTGTCTATGGTTTATGGT
1 TATTGTCTATGGTATATGGT
794858 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
794878 T
1 T
794879 TTGGAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.05, G:0.24, T:0.54
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:795406 original size:30 final size:30
Alignment explanation
Indices: 795318--795408 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 30
795308 TTCGGAAGTT
*
795318 ACTGTAGTAGTTACTGTAGCGTATCGATAC
1 ACTGTAGTAGTTACTGTAGCGTATCGATGC
*
795348 ACTGTAGTAGTTATTGTAGCGTATCGATGC
1 ACTGTAGTAGTTACTGTAGCGTATCGATGC
* *
795378 ACTGTAGCAATTACTGTAGCGTATCGATGC
1 ACTGTAGTAGTTACTGTAGCGTATCGATGC
795408 A
1 A
795409 TAATATTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (30 bp):
ACTGTAGTAGTTACTGTAGCGTATCGATGC
Found at i:796749 original size:15 final size:16
Alignment explanation
Indices: 796718--796750 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
796708 TGCAAAGTAT
796718 ATTATTGTTGATGTTG
1 ATTATTGTTGATGTTG
*
796734 ATTATTG-TGATTTTG
1 ATTATTGTTGATGTTG
796749 AT
1 AT
796751 GAAATTACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.58
Consensus pattern (16 bp):
ATTATTGTTGATGTTG
Found at i:802665 original size:5 final size:5
Alignment explanation
Indices: 802651--802680 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
802641 ATAACTGAAG
*
802651 ATAAA GTAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
802681 CATTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:810000 original size:20 final size:20
Alignment explanation
Indices: 809971--810009 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
809961 TTTCCACCAC
*
809971 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
809991 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
810010 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:810358 original size:22 final size:22
Alignment explanation
Indices: 810318--810361 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
810308 TTATATTTTA
* **
810318 TTAAAATATATTATTTAATTAT
1 TTAAAATATAATAAATAATTAT
810340 TTAAAATATAATAAATAATTAT
1 TTAAAATATAATAAATAATTAT
810362 AAATATATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATATAATAAATAATTAT
Found at i:821515 original size:288 final size:287
Alignment explanation
Indices: 820962--821547 Score: 1104
Period size: 288 Copynumber: 2.0 Consensus size: 287
820952 TCAACAGCAC
820962 ATTGAACTCTTTTGTGCAAAGGTCAATGTGCAGTCATTCTCAGGGGAGAAGGAAAAAGTGGGGAG
1 ATTGAACT-TTTTGTGCAAAGGTCAATGTGCAGTCATTCTCAGGGGAGAAGGAAAAAGTGGGGAG
821027 AATGTTAAGTATAGCTAAGGTGCACCTGCTGTGATGGTGTGCTTGGGTGGTTGTAACTGTGTTAG
65 AATGTTAAGTATAGCTAAGGTGCACCTGCTGTGATGGTGTGCTTGGGTGGTTGTAACTGTGTTAG
821092 TCTTAGCTGACTGTTAAGATTGTTAGTTTTTTATTCATTACGGTTAGCAGTTAGTACCAGTTAGC
130 TCTTAGCTGACTGTTAAGATTGTTAGTTTTTTATTCATTACGGTTAGCAGTTAGTACCAGTTAGC
821157 TTGAGTTTGTGCGTGTATATAACAGCTTGTAACTTCAGTAAAGTACACTGAATATTCTTATGATA
195 TTGAGTTTGTGCGTGTATATAACAGCTTGTAACTTCAGTAAAGTACACTGAATATTCTTATGA-A
821222 TTTTACAAAGTCTATAGTTTCTCAACAAG
259 TTTTACAAAGTCTATAGTTTCTCAACAAG
821251 ATTGAACTTTTTGTGCAAAGGTCAATGTGCAGTCATTTCTCAGGGGAGAAGGAAAAAGTGGGGAG
1 ATTGAACTTTTTGTGCAAAGGTCAATGTGCAGTCA-TTCTCAGGGGAGAAGGAAAAAGTGGGGAG
821316 AATGTTAAGTATAGCTAAGGTGCACCTGCTGTGATGGTGTGCTTGGGTGGTTGTAACT-TGTTAG
65 AATGTTAAGTATAGCTAAGGTGCACCTGCTGTGATGGTGTGCTTGGGTGGTTGTAACTGTGTTAG
821380 TCTTAGCTGACTGTTAAGATTGTTAGTTTTTTATTCATTACGGTTAGCAGTTAGTACCAGTTAGC
130 TCTTAGCTGACTGTTAAGATTGTTAGTTTTTTATTCATTACGGTTAGCAGTTAGTACCAGTTAGC
*
821445 TTGAGTTTGTGCGTGTATATAACAGCTTGTAAACTTCAGTAATGTACACTTGAATATTCTTATG-
195 TTGAGTTTGTGCGTGTATATAACAGCTTGT-AACTTCAGTAAAGTACAC-TGAATATTCTTATGA
821509 ATTTTACAAAGTCTATAGTTTCTCAACAAG
258 ATTTTACAAAGTCTATAGTTTCTCAACAAG
821539 ATTGAACTT
1 ATTGAACTT
821548 GAATGCCCCA
Statistics
Matches: 293, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
288 167 0.57
289 112 0.38
290 14 0.05
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (287 bp):
ATTGAACTTTTTGTGCAAAGGTCAATGTGCAGTCATTCTCAGGGGAGAAGGAAAAAGTGGGGAGA
ATGTTAAGTATAGCTAAGGTGCACCTGCTGTGATGGTGTGCTTGGGTGGTTGTAACTGTGTTAGT
CTTAGCTGACTGTTAAGATTGTTAGTTTTTTATTCATTACGGTTAGCAGTTAGTACCAGTTAGCT
TGAGTTTGTGCGTGTATATAACAGCTTGTAACTTCAGTAAAGTACACTGAATATTCTTATGAATT
TTACAAAGTCTATAGTTTCTCAACAAG
Found at i:821662 original size:21 final size:21
Alignment explanation
Indices: 821636--821678 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
821626 TTACACTTAC
821636 ATGAAAATTACACCAACTAAG
1 ATGAAAATTACACCAACTAAG
821657 ATGAAAATTACACCAACTAAG
1 ATGAAAATTACACCAACTAAG
821678 A
1 A
821679 AGATTTTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (21 bp):
ATGAAAATTACACCAACTAAG
Found at i:830078 original size:48 final size:47
Alignment explanation
Indices: 830008--830103 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 47
829998 ACTCAGCATT
830008 ATACGAGGATTGTGATCTTGAATTGTTTGTTGGTGATGTGATATATA
1 ATACGAGGATTGTGATCTTGAATTGTTTGTTGGTGATGTGATATATA
830055 ATACGATGGATTGTGATCTTGAATTGTTTGTTGGTGATGTGATATATA
1 ATACGA-GGATTGTGATCTTGAATTGTTTGTTGGTGATGTGATATATA
830103 A
1 A
830104 ACACACTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 6 0.12
48 42 0.88
ACGTcount: A:0.26, C:0.04, G:0.27, T:0.43
Consensus pattern (47 bp):
ATACGAGGATTGTGATCTTGAATTGTTTGTTGGTGATGTGATATATA
Found at i:831265 original size:2 final size:2
Alignment explanation
Indices: 831243--831349 Score: 88
Period size: 2 Copynumber: 56.5 Consensus size: 2
831233 ATATTTTATG
*
831243 TA TA GTA TA TT TA TA TA -A TA TA T- TA TA TA TA CTA TA -A TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * *
831284 TT TA TT TA T- TA TA T- TA TA T- TA TA GTA TA TT TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
831323 TA -A TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
831350 TGTGAGCACC
Statistics
Matches: 85, Mismatches: 8, Indels: 24
0.73 0.07 0.21
Matches are distributed among these distances:
1 9 0.11
2 70 0.82
3 6 0.07
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:831298 original size:5 final size:5
Alignment explanation
Indices: 831231--831350 Score: 99
Period size: 5 Copynumber: 24.4 Consensus size: 5
831221 GTCTGATCTT
* * * *
831231 TTATA TTTTA TGTATA GTATA TT-TA -TATA ATATA TTATA -TATA CTATA
1 TTATA TTATA T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * *
831279 ATATA TT-TA TT-TA TTATA TTATA TTATA GTATA TTTATA TTATA TAATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA
831328 -TATA TATATA TATATA TTATA TT
1 TTATA T-TATA T-TATA TTATA TT
831351 GTGAGCACCA
Statistics
Matches: 96, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
3 1 0.01
4 19 0.20
5 58 0.60
6 18 0.19
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (5 bp):
TTATA
Found at i:831324 original size:60 final size:62
Alignment explanation
Indices: 831231--831350 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 62
831221 GTCTGATCTT
* *
831231 TTATATTTTATGTATAGTATATTTATATAATATATTATATATACTATA-ATATATT-TATTTA
1 TTATATTATATGTATAGTATATTTATATAATATAATATATATA-TATATATATATTATATTTA
*
831292 TTATATTATAT-TATAGTATATTTATATTATATAATATATATATATATATATATTATATT
1 TTATATTATATGTATAGTATATTTATATAATATAATATATATATATATATATATTATATT
831351 GTGAGCACCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
59 4 0.07
60 36 0.67
61 14 0.26
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (62 bp):
TTATATTATATGTATAGTATATTTATATAATATAATATATATATATATATATATTATATTTA
Found at i:833232 original size:17 final size:17
Alignment explanation
Indices: 833212--833277 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
833202 TATATTTAGG
833212 TTTATTTTATTTTATTT
1 TTTATTTTATTTTATTT
*
833229 TTTATTTTATGTTATTT
1 TTTATTTTATTTTATTT
* * *
833246 TTTCTTTTTTCTTTCTTT
1 TTTATTTTAT-TTTATTT
*
833264 CTTATGTTTATTTT
1 TTTAT-TTTATTTT
833278 TTAATTAAGT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
17 24 0.62
18 11 0.28
19 4 0.10
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTATTTTATTTTATTT
Found at i:835682 original size:2 final size:2
Alignment explanation
Indices: 835663--835771 Score: 81
Period size: 2 Copynumber: 57.0 Consensus size: 2
835653 CGGTGTCGAC
*
835663 AT AT AT -T AT AT -T AT -T AT AT AT AGT AT AT TT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
835702 AGT AT AT AT AT AT -T AT AT AT AT AT TT AT TT TT AT AT AT A- AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
835743 AT TT AT AT -T AT AGT GT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
835772 TTATTTGTTT
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
1 8 0.09
2 73 0.85
3 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (2 bp):
AT
Found at i:835700 original size:18 final size:18
Alignment explanation
Indices: 835679--835771 Score: 106
Period size: 18 Copynumber: 5.3 Consensus size: 18
835669 TATATTATTA
835679 TATATAGTATATTTATAT
1 TATATAGTATATTTATAT
*
835697 TATATAGTATATATATAT
1 TATATAGTATATTTATAT
*
835715 TATATA-TATATTTATTTT
1 TATATAGTATATTTA-TAT
835733 TATATA-TAATATTTATAT
1 TATATAGT-ATATTTATAT
835751 TATAGT-GTATA--TATAT
1 TATA-TAGTATATTTATAT
835767 TATAT
1 TATAT
835772 TTATTTGTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
15 1 0.01
16 9 0.13
17 7 0.10
18 41 0.61
19 9 0.13
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATATAGTATATTTATAT
Found at i:835787 original size:54 final size:55
Alignment explanation
Indices: 835663--835783 Score: 162
Period size: 52 Copynumber: 2.3 Consensus size: 55
835653 CGGTGTCGAC
*
835663 ATATATTATATTATTATATATAGTATATTTATATTATATAGTATATATATATTATAT
1 ATATATT-TATTTTTATATATAG-ATATTTATATTATATAGTATATATATATTATAT
*
835720 ATATATTTATTTTTATATATA-ATATTTATA-T-TATAGTGTATATATATTATAT
1 ATATATTTATTTTTATATATAGATATTTATATTATATAGTATATATATATTATAT
*
835772 -T-TATTTGTTTTT
1 ATATATTTATTTTT
835784 TTTTGTTTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
50 10 0.16
51 1 0.02
52 20 0.33
53 1 0.02
54 9 0.15
56 13 0.21
57 7 0.11
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (55 bp):
ATATATTTATTTTTATATATAGATATTTATATTATATAGTATATATATATTATAT
Found at i:836316 original size:27 final size:25
Alignment explanation
Indices: 836267--836318 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
836257 CAAAGCCACA
* *
836267 AACCGAAAGCAAAATTAATCAAAGC
1 AACCGAAAGCAAAAATAAACAAAGC
836292 AACCGAAAGCAAAAAAATAAACAAAGC
1 AACCGAAAGC--AAAAATAAACAAAGC
836319 TTGGGGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 10 0.43
27 13 0.57
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.08
Consensus pattern (25 bp):
AACCGAAAGCAAAAATAAACAAAGC
Found at i:837070 original size:40 final size:39
Alignment explanation
Indices: 837012--837088 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
837002 CTTTCTTTTT
* * *
837012 TTTTTTTTTTTTTTTTTTAAAAATTAACATTTTCTTCACC
1 TTTTTATTTATTTCTTTTAAAAATTAA-ATTTTCTTCACC
*
837052 TTTTTATTTATTTCTTTTAAAATTTAAATTTTCTTCA
1 TTTTTATTTATTTCTTTTAAAAATTAAATTTTCTTCA
837089 TTTTATTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 10 0.30
40 23 0.70
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (39 bp):
TTTTTATTTATTTCTTTTAAAAATTAAATTTTCTTCACC
Found at i:838318 original size:21 final size:19
Alignment explanation
Indices: 838280--838325 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
838270 AATTAATCCT
838280 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
838300 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
838321 A-TAAT
1 ACTAAT
838326 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:840925 original size:270 final size:269
Alignment explanation
Indices: 840430--840974 Score: 1027
Period size: 270 Copynumber: 2.0 Consensus size: 269
840420 TTTAATAATT
*
840430 CTGGCCTAGGCAATAAAATTTTGCATTCATTATTGGGCATCCCTAATTCATTCCTAACAATAATC
1 CTGGCCTAGGCAATAAAATTTTGCATTCATCATTGGGCATCCCTAATTCATTCCTAACAATAATC
840495 CTAACCTGCTTATGTCATGACAACCAATTTCAACCAATTAACATCAATTACTATTTAACAAAGTA
66 CTAACCTGCTTATGTCATGACAACCAATTTCAACCAATTAACATCAATTACTATTTAACAAAGTA
840560 TGGTAGAATGGACAAAACATCCCCCAAACTTTAGGGATGCATTATCCTCAATGCATGAAACTACA
131 TGGTAGAATGGACAAAACATCCCCCAAACTTTAGGGATGCATTATCCTCAATGCATGAAACTACA
*
840625 CTAAATGGTTATATGCAAATGCAAAAAAAAAAAATTACAAAAACTTATTATGTGGTGTGGCTTGA
196 CTAAATGGTTATATGCAAATGCAAAAAATAAAAATTACAAAAACTTATTATGTGGTGTGGCTTGA
840690 CTGGACGCC
261 CTGGACGCC
840699 CTGGCCTAGGCAATAAAATTTTGCATTCATCATTGGGCATCCCTAATTCATTCCTAACAATAATC
1 CTGGCCTAGGCAATAAAATTTTGCATTCATCATTGGGCATCCCTAATTCATTCCTAACAATAATC
840764 CTAACCTGCTTATGTCATGACAACCAAATTTCAACCAATTAACATCAATTACTATTTAACAAAGT
66 CTAACCTGCTTATGTCATGACAACC-AATTTCAACCAATTAACATCAATTACTATTTAACAAAGT
840829 ATGGTAGAATGGACAAAACATCCCCCAAACTTTAGGGATGCATTATCCTCAATGCATGAAAACTA
130 ATGGTAGAATGGACAAAACATCCCCCAAACTTTAGGGATGCATTATCCTCAATGCATG-AAACTA
840894 CACTAAATGTGTTATATGCAAATGCAAAAAAAATAAAAATTACAAAAACTTATTATGTGGTGTGG
194 CACTAAATG-GTTATATGCAAATGC--AAAAAATAAAAATTACAAAAACTTATTATGTGGTGTGG
840959 CTTGACTGGACGCC
256 CTTGACTGGACGCC
840973 CT
1 CT
840975 CGTGCGGCAT
Statistics
Matches: 269, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
269 89 0.33
270 97 0.36
271 15 0.06
272 15 0.06
274 53 0.20
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (269 bp):
CTGGCCTAGGCAATAAAATTTTGCATTCATCATTGGGCATCCCTAATTCATTCCTAACAATAATC
CTAACCTGCTTATGTCATGACAACCAATTTCAACCAATTAACATCAATTACTATTTAACAAAGTA
TGGTAGAATGGACAAAACATCCCCCAAACTTTAGGGATGCATTATCCTCAATGCATGAAACTACA
CTAAATGGTTATATGCAAATGCAAAAAATAAAAATTACAAAAACTTATTATGTGGTGTGGCTTGA
CTGGACGCC
Found at i:843089 original size:450 final size:448
Alignment explanation
Indices: 842190--843089 Score: 1591
Period size: 450 Copynumber: 2.0 Consensus size: 448
842180 TCAGATTTTA
842190 ATTGTCTAGGCAACTAATATTTGCTCAATTAAGAAAAGAAAACTCTTGGGCATCATGTGCCAACA
1 ATTGTCTAGGCAACTAATATTTGCTCAATTAAGAAAAGAAAACTCTTGGGCATCATGTGCCAACA
*
842255 ATGCCGGTTGCCATGAATGACTGGGGATCCTTTGTACTCCTTGAGTCTTGACCCGTTCACTTTAA
66 ATGCCGGTTGCCACGAATGACTGGGGATCCTTTGTACTCCTTGAGTCTTGACCCGTTCACTTTAA
842320 ATGGGAACCATCGTTTTGGTTCTGAATTTCAATTGCTCCATTGTCATGGACTTGGTGTACATTAA
131 ATGGGAACCATCGTTTTGGTTCTGAATTTCAATTGCTCCATTGTCA--GACTTGGTGTACATTAA
842385 TGGTCACTATCGTGATTTAGCTTGTCTGGGAATAACTTAAGGCGTGAATTGTAGAGCAATACTTG
194 TGGTCACTATCGTGATTTAGCTTGTCTGGGAATAACTTAAGGCGTGAATTGTAGAGCAATACTTG
842450 TTGTCCAAAATAAAATTGCCTCGGCAATATTTGTCTATCATGCATCGTTTTGTTTTCTCCTTGTA
259 TTGTCCAAAATAAAATTGCCTCGGCAATATTTGTCTATCATGCATCGTTTTGTTTTCTCCTTGTA
842515 AAGGCGGGCATTCTCGTATGCATGTGCTCTAAATTCATCCATCTCATTCATTTCCTATAGTCTTC
324 AAGGCGGGCATTCTCGTATGCATGTGCTCTAAATTCATCCATCTCATTCATTTCCTATAGTCTTC
842580 TTTCTCCAGCAAGCTGAGCATCTATGTTTATCTTTTTGATGGCCCAATAAGCTTTGTGTT
389 TTTCTCCAGCAAGCTGAGCATCTATGTTTATCTTTTTGATGGCCCAATAAGCTTTGTGTT
842640 ATTGTCTAGGCAACTAATATTTGCTCAATTAAGAAAAGAAAACTCTTGGGCATCATGTGCCAACA
1 ATTGTCTAGGCAACTAATATTTGCTCAATTAAGAAAAGAAAACTCTTGGGCATCATGTGCCAACA
*
842705 ATGCCGGTTTGTCACGAA-GACTGGGGATCCTTTGTACTCCTTGAGTCTTGACCCGTTCACTTTA
66 ATGCCGG-TTGCCACGAATGACTGGGGATCCTTTGTACTCCTTGAGTCTTGACCCGTTCACTTTA
842769 AA-GATGGAACCATCGTTTTGGTTCTGAATTTCAATTGCTCCATTGTCA-ACTTGGTGTACGATT
130 AATG--GGAACCATCGTTTTGGTTCTGAATTTCAATTGCTCCATTGTCAGACTTGGTGTAC-ATT
842832 AATGGTCCTGACTATCGTGATTTTAGCTTGTCTGGGAATAACTTAAGGCGTGAATTGTAGAGCAA
192 AATGGT-C--ACTATCGTGA-TTTAGCTTGTCTGGGAATAACTTAAGGCGTGAATTGTAGAGCAA
*
842897 TACTTGTTGTCCAGAATAAAATTGCCTCGGCAATATTTGTCTATCATGCCATCG-TTTG-TTTCT
253 TACTTGTTGTCCAAAATAAAATTGCCTCGGCAATATTTGTCTATCATG-CATCGTTTTGTTTTCT
842960 CCTTGTAAAGGCGGGCATTCTCGTATGCATGTGCTCTAAATTCATCCATCTCATTCATTTTCCTA
317 CCTTGTAAAGGCGGGCATTCTCGTATGCATGTGCTCTAAATTCATCCATCTCATTCA-TTTCCTA
* *
843025 TAGTCTTCTTTCTCTAGCAAGTTGAGCA-CTATGTTTATCTTTTTGATGGCCC-ATAAGC-TTGT
381 TAGTCTTCTTTCTCCAGCAAGCTGAGCATCTATGTTTATCTTTTTGATGGCCCAATAAGCTTTGT
843087 GTT
446 GTT
843090 CGAGTTCAAC
Statistics
Matches: 435, Mismatches: 5, Indels: 20
0.95 0.01 0.04
Matches are distributed among these distances:
448 11 0.03
449 10 0.02
450 128 0.29
451 57 0.13
452 96 0.22
453 128 0.29
454 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (448 bp):
ATTGTCTAGGCAACTAATATTTGCTCAATTAAGAAAAGAAAACTCTTGGGCATCATGTGCCAACA
ATGCCGGTTGCCACGAATGACTGGGGATCCTTTGTACTCCTTGAGTCTTGACCCGTTCACTTTAA
ATGGGAACCATCGTTTTGGTTCTGAATTTCAATTGCTCCATTGTCAGACTTGGTGTACATTAATG
GTCACTATCGTGATTTAGCTTGTCTGGGAATAACTTAAGGCGTGAATTGTAGAGCAATACTTGTT
GTCCAAAATAAAATTGCCTCGGCAATATTTGTCTATCATGCATCGTTTTGTTTTCTCCTTGTAAA
GGCGGGCATTCTCGTATGCATGTGCTCTAAATTCATCCATCTCATTCATTTCCTATAGTCTTCTT
TCTCCAGCAAGCTGAGCATCTATGTTTATCTTTTTGATGGCCCAATAAGCTTTGTGTT
Found at i:843899 original size:53 final size:53
Alignment explanation
Indices: 843819--843926 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
843809 GGTCTTCGCA
843819 CTGCTTGAATAGAAATGGGTCATCCCAGTAGTAATGTCGCACATCATGTCCAC
1 CTGCTTGAATAGAAATGGGTCATCCCAGTAGTAATGTCGCACATCATGTCCAC
843872 CTGCTTGAATAGAAATGGGTCATCCCAGTAGTAATGTCGCACATCATGTCCAC
1 CTGCTTGAATAGAAATGGGTCATCCCAGTAGTAATGTCGCACATCATGTCCAC
843925 CT
1 CT
843927 TTTCGTTTGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (53 bp):
CTGCTTGAATAGAAATGGGTCATCCCAGTAGTAATGTCGCACATCATGTCCAC
Found at i:848591 original size:21 final size:19
Alignment explanation
Indices: 848553--848598 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
848543 AATTAATCCT
848553 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
848573 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
848594 A-TAAT
1 ACTAAT
848599 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:852049 original size:56 final size:54
Alignment explanation
Indices: 851946--852055 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 54
851936 CAGCAAAGGG
851946 GAAAGCCAGAGATATGGTCATTCGACTTCTTAGAGCAAGTACAGAAAGTGGCAA
1 GAAAGCCAGAGATATGGTCATTCGACTTCTTAGAGCAAGTACAGAAAGTGGCAA
852000 GAAAGCCAGAGATATGGTCATTCGAGACTTCTTAGAGCAAGTACAGAAAGTGGCAA
1 GAAAGCCAGAGATATGGTCATTC--GACTTCTTAGAGCAAGTACAGAAAGTGGCAA
852056 ATCACTTGCA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 23 0.43
56 31 0.57
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.20
Consensus pattern (54 bp):
GAAAGCCAGAGATATGGTCATTCGACTTCTTAGAGCAAGTACAGAAAGTGGCAA
Found at i:856301 original size:23 final size:22
Alignment explanation
Indices: 856275--856355 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
856265 CACCACAGCT
* *
856275 CGTATAAATGCACCGAAGTGCTG
1 CGTAGAAATGCACCGAAGTGC-A
*
856298 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTG-CA
**
856321 CGTAGAGTTGCACCGAAGTGCA
1 CGTAGAAATGCACCGAAGTGCA
856343 CGTAGAAATGCAC
1 CGTAGAAATGCAC
856356 TGTAGTTCAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 13 0.27
23 35 0.71
24 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCA
Found at i:858575 original size:43 final size:46
Alignment explanation
Indices: 858451--858575 Score: 150
Period size: 47 Copynumber: 2.8 Consensus size: 46
858441 TATAAAATCT
*
858451 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
858496 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTTCCAATA-A
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
858542 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
858576 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 22 0.31
45 12 0.17
46 7 0.10
47 29 0.41
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.39
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:858733 original size:27 final size:27
Alignment explanation
Indices: 858698--858750 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
858688 GCTAAAACTG
858698 CACTAAGCTTACGCCATAGTGCTAATT
1 CACTAAGCTTACGCCATAGTGCTAATT
858725 CACTAAGCTTACGCCATAGTGCTAAT
1 CACTAAGCTTACGCCATAGTGCTAAT
858751 CGGACAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (27 bp):
CACTAAGCTTACGCCATAGTGCTAATT
Found at i:864493 original size:188 final size:187
Alignment explanation
Indices: 864191--864568 Score: 642
Period size: 188 Copynumber: 2.0 Consensus size: 187
864181 ACTTTTAGCG
864191 GAAATCATATTACCGCTACTCAATTTCTCTTCTCAAATCTCAATGATTAAATAATTAATGCTTAG
1 GAAATCATATTACCGCTACTCAATTTCTCTTCTCAAATCTCAATGATTAAATAATTAATGCTTAG
864256 CTTAATATTTCTCACTTATTAAGCTTACTTGGAGAACCTCAGAATCATCACTAGATTCAAAAATC
66 CTTAATATTTCTCACTTATTAAGCTTACTTGGAGAACCTCAGAATCATCACTAGATTCAAAAATC
864321 TCCTCTGAATCCTTATCCGATTCGAC-TTTCTTG-AAGTCA-TCAAAC-TTTTAATC
131 TCCTCTGAATCCTTATCCGATTCGACTTTTCTTGTAAGTCATTCAAACTTTTTAATC
864374 GAAATCAT-TTACCGCTTACTCAATTTCTCTTACTCAAATCCTCAATGATTTAAATAATTTAATG
1 GAAATCATATTACCGC-TACTCAATTTCTCTT-CTCAAAT-CTCAATGA-TTAAATAA-TTAATG
864438 CTTAGCTTAAATATTTCTCACTTATTTAAGCTTACTTGGAG-ACCTCAGAATCATCACTAGATTC
61 CTTAGCTT-AATATTTCTCACTTA-TTAAGCTTACTTGGAGAACCTCAGAATCATCACTAGATTC
864502 AAAAATCTCCTCTGAATCCTTATCCGATTCGACTTTTCTTGTAAGTCATTTCAAACTTTTTAATC
124 AAAAATCTCCTCTGAATCCTTATCCGATTCGACTTTTCTTGTAAGTCA-TTCAAACTTTTTAATC
864567 GA
1 GA
864569 TTCTTCCACA
Statistics
Matches: 183, Mismatches: 0, Indels: 14
0.93 0.00 0.07
Matches are distributed among these distances:
182 7 0.04
183 23 0.13
184 7 0.04
185 8 0.04
186 8 0.04
187 14 0.08
188 71 0.39
189 23 0.13
190 6 0.03
192 6 0.03
193 10 0.05
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (187 bp):
GAAATCATATTACCGCTACTCAATTTCTCTTCTCAAATCTCAATGATTAAATAATTAATGCTTAG
CTTAATATTTCTCACTTATTAAGCTTACTTGGAGAACCTCAGAATCATCACTAGATTCAAAAATC
TCCTCTGAATCCTTATCCGATTCGACTTTTCTTGTAAGTCATTCAAACTTTTTAATC
Found at i:865674 original size:47 final size:45
Alignment explanation
Indices: 865602--865727 Score: 139
Period size: 47 Copynumber: 2.8 Consensus size: 45
865592 TATAAAATCT
865602 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
865647 CTTACCATTTAAAT-TCTATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATCTC-ATAAGCTCGTAAGCTTATTTTACCAAAATA
* ** * * *
865694 TTTGTCA-TTATTTCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATCTCATAAGCTCGTAAGCTTATTT
865728 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
44 20 0.29
45 12 0.17
46 4 0.06
47 34 0.49
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (45 bp):
CTTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:868256 original size:18 final size:17
Alignment explanation
Indices: 868233--868278 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 17
868223 TTTTAAGGGG
868233 TGCATCGATGCACTACTT
1 TGCATCGATGCACTAC-T
868251 TGCATCGATGCACTACT
1 TGCATCGATGCACTACT
868268 TGCATTCGATG
1 TGCA-TCGATG
868279 TTTGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (17 bp):
TGCATCGATGCACTACT
Found at i:872408 original size:2 final size:2
Alignment explanation
Indices: 872381--872509 Score: 109
Period size: 2 Copynumber: 67.5 Consensus size: 2
872371 AGTTTTTATG
*
872381 TA TA GTA TA TT TA TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
872422 T- TA TA -A TA T- TA TT TA TA T- TA TA TA -A TA CTA T- TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
872459 T- TA TA GTA TA CT- TA TA T- TA TA TA GTA TA TA TA TA TA TA TA
1 TA TA TA -TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
872499 TA TA TA TA TA T
1 TA TA TA TA TA T
872510 TTGTTTGTTG
Statistics
Matches: 106, Mismatches: 5, Indels: 32
0.74 0.03 0.22
Matches are distributed among these distances:
1 11 0.10
2 86 0.81
3 9 0.08
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:872474 original size:36 final size:38
Alignment explanation
Indices: 872398--872507 Score: 127
Period size: 38 Copynumber: 2.9 Consensus size: 38
872388 TATTTATATA
* *
872398 ATATAATATATATATATATATATATTATAATATTATTT
1 ATATTATATATATATATATATATATTATAATATTACTT
* *
872436 ATATTATATA-ATACTAT-TATATGTTATAGTA-TACTT
1 ATATTATATATATA-TATATATATATTATAATATTACTT
872472 ATATTATATAGTATATATATATATATATATATATAT
1 ATATTATATA-TATATATATATATAT-TATA-ATAT
872508 ATTTGTTTGT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
36 14 0.24
37 18 0.31
38 21 0.36
39 4 0.07
40 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (38 bp):
ATATTATATATATATATATATATATTATAATATTACTT
Found at i:873039 original size:25 final size:25
Alignment explanation
Indices: 873011--873084 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 25
873001 CAAAGCCACA
* *
873011 AACCGAAAGTAAAAATAAGCAAAGC
1 AACCGAAAGCAAAAATAAACAAAGC
873036 AACCGAAAGCAAAAATAAACAAAGC
1 AACCGAAAGCAAAAATAAACAAAGC
* *
873061 AACCGAAAGCAAAAAAAAAAAAAG
1 AACCGAAAGCAAAAATAAACAAAG
873085 AAACAAAACT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.66, C:0.16, G:0.14, T:0.04
Consensus pattern (25 bp):
AACCGAAAGCAAAAATAAACAAAGC
Found at i:873045 original size:15 final size:15
Alignment explanation
Indices: 873027--873073 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
873017 AAGTAAAAAT
873027 AAGCAAAGCAACCGA
1 AAGCAAAGCAACCGA
*
873042 AAGCAAA--AA--TA
1 AAGCAAAGCAACCGA
873053 AA-CAAAGCAACCGA
1 AAGCAAAGCAACCGA
873067 AAGCAAA
1 AAGCAAA
873074 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
10 4 0.16
11 3 0.12
12 2 0.08
13 2 0.08
14 3 0.12
15 11 0.44
ACGTcount: A:0.62, C:0.21, G:0.15, T:0.02
Consensus pattern (15 bp):
AAGCAAAGCAACCGA
Found at i:877002 original size:45 final size:43
Alignment explanation
Indices: 876951--877070 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
876941 GCTAAAGTTC
876951 GCGGCGTTTGGTAACAAAAAACGCCGCAATAGGTAACGATATATA
1 GCGGCGTTT-GT-ACAAAAAACGCCGCAATAGGTAACGATATATA
* * * *** *
876996 GCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTA
1 GCGGCGTTTGTACAAAAAACGCCGCAATAGGTAACGATATATA
* * * *
877039 GCGGCGTTTTTCCAACAAACGTCGCAATAGGT
1 GCGGCGTTTGTACAAAAAACGCCGCAATAGGT
877071 GTTGAGATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 54 0.83
44 2 0.03
45 9 0.14
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (43 bp):
GCGGCGTTTGTACAAAAAACGCCGCAATAGGTAACGATATATA
Found at i:877025 original size:43 final size:43
Alignment explanation
Indices: 876969--877237 Score: 360
Period size: 43 Copynumber: 6.3 Consensus size: 43
876959 TGGTAACAAA
*** * * *
876969 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* *
877012 AAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* * * *
877055 AAACGTCGCAATAGGTGTTGAGATTTAGCAGAGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* *
877098 AAACGCCGCAATAAGTGTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
877141 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCAAC
* * *
877184 AAACGCCGTAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
*
877227 AAACACCGCAA
1 AAACGCCGCAA
877238 AAGATCTGGT
Statistics
Matches: 203, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 7 0.03
43 189 0.93
44 7 0.03
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
Found at i:877264 original size:43 final size:43
Alignment explanation
Indices: 876994--877285 Score: 295
Period size: 43 Copynumber: 6.8 Consensus size: 43
876984 TAACGATATA
* * * * * *
876994 TAGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGCTGAGATT
* * * *
877037 TAGCGGCGTTTTTCCAACAAACGTCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGCTGAGATT
* * *
877080 TAGCAGAGTTTTTCCCACAAACGCCGCAATAA-GTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAA-AAGGTGCTGAGATT
* *
877123 TAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGCTGAGATT
* * *
877166 TAGCGGCGTTTTTTCCACAAACGCCGTAATAGGT-CTTGAGATT
1 TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGC-TGAGATT
* * *
877209 TAGCGGCGTTTTTCCCACAAACACCGCAAAAGAT-CTG-GTATA
1 TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGCTGAG-ATT
* ***
877251 TAGAGGCGTTTTTTAGAACAAACGCCGCAAAAGGT
1 TAGCGGCG-TTTTTCCCACAAACGCCGCAAAAGGT
877286 CATATCTATA
Statistics
Matches: 217, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.00
42 12 0.06
43 203 0.94
44 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTCCCACAAACGCCGCAAAAGGTGCTGAGATT
Found at i:877264 original size:129 final size:130
Alignment explanation
Indices: 876990--877285 Score: 386
Period size: 129 Copynumber: 2.3 Consensus size: 130
876980 TAGGTAACGA
* * *
876990 TATATAGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGATATTTAGCGGCGTTTTTCCAAC
1 TATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
* * * *
877055 AAACGTCGCAATAGGTGTTGAGATTTAGCAGAGTTTTTCCCACAAACGCCGCAATAAGTGTTGAG
66 AAACGCCGCAATAGGTCTTGAGATTTAGCAGAGTTTTTCCCACAAACACCGCAATAAGTGCTGAG
* *
877120 -ATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCC-A
1 TATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCG-TTTTTCCAA
* * *
877183 CAAACGCCGTAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAACACCGCAA-AAGAT-CTG
65 CAAACGCCGCAATAGGTCTTGAGATTTAGCAGAGTTTTTCCCACAAACACCGCAATAAG-TGCTG
877246 -G
129 AG
* ** *
877247 TATATAGAGGCGTTTTTTAGAACAAACGCCGCAAAAGGT
1 TATATAGCGGCG-TTTTTCCAACAAACGCCGCAATAGGT
877286 CATATCTATA
Statistics
Matches: 144, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
127 1 0.01
128 14 0.10
129 122 0.85
130 7 0.05
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (130 bp):
TATATAGCGGCGTTTTTCCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCAAC
AAACGCCGCAATAGGTCTTGAGATTTAGCAGAGTTTTTCCCACAAACACCGCAATAAGTGCTGAG
Found at i:877272 original size:86 final size:86
Alignment explanation
Indices: 876969--877286 Score: 336
Period size: 86 Copynumber: 3.7 Consensus size: 86
876959 TGGTAACAAA
*** * * * * * * * *
876969 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCCAACAAACGCCGTAATAGGTGTTGAT
1 AAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAG
*
877034 ATTTAGCGGCGTTTTTCCAAC
66 ATTTAGCGGCGTTTTTCCCAC
* * * * * *
877055 AAACGTCGCAATAGGTGTTGAGATTTAGCA-GAGTTTTTCCCACAAACGCCGCAATAAGTGTTGA
1 AAACGCCGCAATAGGTGTTGAGATTTAG-AGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGA
877119 GATTTAGCGGCGTTTTTCCCAC
65 GATTTAGCGGCGTTTTTCCCAC
* * *
877141 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTTCCACAAACGCCGTAATAGGTCTTGAG
1 AAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAG
877206 ATTTAGCGGCGTTTTTCCCAC
66 ATTTAGCGGCGTTTTTCCCAC
* * * * * * *
877227 AAACACCGCAAAAGAT-CTG-GTATATAGAGGCGTTTTTTAGAACAAACGCCGCAAAAGGTC
1 AAACGCCGCAATAGGTGTTGAG-ATTTAGAGGCGTTTTTT-CAACAAACGCCGCAATAGGTC
877287 ATATCTATAG
Statistics
Matches: 197, Mismatches: 31, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
84 1 0.01
85 17 0.09
86 179 0.91
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (86 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGAGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAG
ATTTAGCGGCGTTTTTCCCAC
Done.