Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011834.1 Kokia drynarioides strain JFW-HI SEQ_126830, 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: 294964
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Warning! 520 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:9536 original size:38 final size:38
Alignment explanation
Indices: 9487--9562 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
9477 ACATTTCACC
9487 TTTTCAATTGTTTTGAAGATGGTGATGAGGTAAAAACT
1 TTTTCAATTGTTTTGAAGATGGTGATGAGGTAAAAACT
9525 TTTTCAATTGTTTTGAAGATGGTGATGAGGTAAAAACT
1 TTTTCAATTGTTTTGAAGATGGTGATGAGGTAAAAACT
9563 ATGGCTGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (38 bp):
TTTTCAATTGTTTTGAAGATGGTGATGAGGTAAAAACT
Found at i:12786 original size:20 final size:20
Alignment explanation
Indices: 12763--12852 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
12753 AAATTCATAT
12763 AAATTTTGATAAATCGTTAG
1 AAATTTTGATAAATCGTTAG
*
12783 AAATATTGATAAAATC-TTAG
1 AAATTTTGAT-AAATCGTTAG
* * *
12803 ATATTTTCATAAAT-GTTTAT
1 AAATTTTGATAAATCG-TTAG
* * *
12823 AAATATTGATAAATTGTTAA
1 AAATTTTGATAAATCGTTAG
12843 AAATTTTGAT
1 AAATTTTGAT
12853 CGATCAAGTA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 46 0.82
21 6 0.11
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (20 bp):
AAATTTTGATAAATCGTTAG
Found at i:12803 original size:60 final size:60
Alignment explanation
Indices: 12739--12852 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
12729 TAGCAAATTA
** * *
12739 TTAGATATTTTGGTAAAT-TCATATAAATTTTGATAAATCGTTAGAAATATTGATAAAATC
1 TTAGATATTTTCATAAATGT-ATATAAATATTGATAAATCGTTAAAAATATTGATAAAATC
* * *
12799 TTAGATATTTTCATAAATGTTTATAAATATTGATAAATTGTTAAAAATTTTGAT
1 TTAGATATTTTCATAAATGTATATAAATATTGATAAATCGTTAAAAATATTGAT
12853 CGATCAAGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 45 0.98
61 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.45
Consensus pattern (60 bp):
TTAGATATTTTCATAAATGTATATAAATATTGATAAATCGTTAAAAATATTGATAAAATC
Found at i:12807 original size:80 final size:80
Alignment explanation
Indices: 12653--12809 Score: 174
Period size: 80 Copynumber: 2.0 Consensus size: 80
12643 GAATTGTGGT
* * * * *
12653 AAATTGTTAAATATTTTCATAAATTTATATAAATATTAGTAAATCATTAGCAATATTAGTGAAGT
1 AAATTATTAAATATTTTCATAAATTCATATAAATATTAGTAAATCATTAGAAATATTAGTAAAAT
*
12718 GTTACATATTTTAGC
66 CTTACATATTTTAGC
* ** * *
12733 AAATTATTAGATATTTTGGTAAATTCATATAAAT-TTTGATAAATCGTTAGAAATATT-GATAAA
1 AAATTATTAAATATTTTCATAAATTCATATAAATATTAG-TAAATCATTAGAAATATTAG-TAAA
*
12796 ATCTTAGATATTTT
64 ATCTTACATATTTT
12810 CATAAATGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
79 4 0.06
80 59 0.94
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (80 bp):
AAATTATTAAATATTTTCATAAATTCATATAAATATTAGTAAATCATTAGAAATATTAGTAAAAT
CTTACATATTTTAGC
Found at i:12849 original size:40 final size:40
Alignment explanation
Indices: 12763--12849 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
12753 AAATTCATAT
* *
12763 AAATTTTGATAAATCGTTAGAAATATTGATAAAATCTTAG
1 AAATTTTCATAAATCGTTAGAAATATTGATAAAATCTTAA
* * * *
12803 ATATTTTCATAAAT-GTTTATAAATATTGATAAATTGTTAA
1 AAATTTTCATAAATCG-TTAGAAATATTGATAAAATCTTAA
12843 AAATTTT
1 AAATTTT
12850 GATCGATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.03
40 38 0.97
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (40 bp):
AAATTTTCATAAATCGTTAGAAATATTGATAAAATCTTAA
Found at i:12911 original size:20 final size:20
Alignment explanation
Indices: 12886--12923 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12876 AAATGATATC
*
12886 CTTAGAAATTTTGATAAAGA
1 CTTAGAAAATTTGATAAAGA
*
12906 CTTAGAAAATTTGTTAAA
1 CTTAGAAAATTTGATAAA
12924 TTTTAAGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (20 bp):
CTTAGAAAATTTGATAAAGA
Found at i:13090 original size:19 final size:19
Alignment explanation
Indices: 13053--13103 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
13043 AAAAATGTTA
13053 GTAAATTCTTA-AATTTTG
1 GTAAATTCTTAGAATTTTG
13071 GTAAATT-TTAGAAGTTTTG
1 GTAAATTCTTAGAA-TTTTG
*
13090 GTAAATTGTTAGAA
1 GTAAATTCTTAGAA
13104 ATAATAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.10
18 9 0.30
19 12 0.40
20 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (19 bp):
GTAAATTCTTAGAATTTTG
Found at i:21756 original size:30 final size:31
Alignment explanation
Indices: 21722--21786 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
21712 AACAGCCCAG
21722 TGACTTAAAT-AAAAATTTTAAATAGTTCAA
1 TGACTTAAATGAAAAATTTTAAATAGTTCAA
* * *
21752 TGACTTAAATGAAAAGTTTTGAATAGTTTAA
1 TGACTTAAATGAAAAATTTTAAATAGTTCAA
21783 TGAC
1 TGAC
21787 CAAATTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (31 bp):
TGACTTAAATGAAAAATTTTAAATAGTTCAA
Found at i:24957 original size:25 final size:25
Alignment explanation
Indices: 24920--24975 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
24910 AATATATCAA
* *
24920 ATAT-TAACTTATAAAATTTTATAT
1 ATATATAAATTATAAAATTATATAT
* **
24944 TTATATAAATTATATGATTATATAT
1 ATATATAAATTATAAAATTATATAT
24969 ATATATA
1 ATATATA
24976 TGTGTGTGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATATAAATTATAAAATTATATAT
Found at i:26665 original size:14 final size:15
Alignment explanation
Indices: 26639--26671 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
26629 CGAAAGCACC
26639 TTAAAATTTAAAAAA
1 TTAAAATTTAAAAAA
*
26654 TTAAAA-TTAAAATA
1 TTAAAATTTAAAAAA
26668 TTAA
1 TTAA
26672 TTTCAACTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAATTTAAAAAA
Found at i:31666 original size:20 final size:19
Alignment explanation
Indices: 31641--31688 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
31631 ATATTATTTT
* *
31641 ATTAATTCATTAAACACTTA
1 ATTAATTAAATAAACA-TTA
31661 ATTAATTAAATAAACATTA
1 ATTAATTAAATAAACATTA
31680 ATTAATTAA
1 ATTAATTAA
31689 TCTTAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTAATTAAATAAACATTA
Found at i:32465 original size:45 final size:46
Alignment explanation
Indices: 32418--32514 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
32408 TTTTTTCTAC
* *
32418 TTTATTTTTAGTTTTTACTTTAAAAGTTA-TGCA-ATAACATTTTACT
1 TTTATTTTTAATTTTTA-TTTAAAA-TTATTGCACATAAAATTTTACT
* *
32464 TTTTTTTTTAATTTTTATTTTAAATTATTGCACATAAAATTTTACAT
1 TTTATTTTTAATTTTTATTTAAAATTATTGCACATAAAATTTTAC-T
32511 TTTA
1 TTTA
32515 ATGGTTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 3 0.07
45 10 0.23
46 26 0.60
47 4 0.09
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (46 bp):
TTTATTTTTAATTTTTATTTAAAATTATTGCACATAAAATTTTACT
Found at i:44889 original size:59 final size:59
Alignment explanation
Indices: 44821--45147 Score: 404
Period size: 59 Copynumber: 5.5 Consensus size: 59
44811 TTCGGACATC
* * * *
44821 CGGGAGTAAAATAGTAATCTTTGGATGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
* * * * * * * *
44880 CGGGGGTAAAATGGTAATTTTTAGAAATTTTGGGGTTAAAAATGTGATTTGTGGGAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
* * * * *
44939 CGGGGGTAAAATGATAATTTTTGCAAGGTTC-AGGGTCAAAATTGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGA-GGTCAAAAATGAGATTTTTGGAAGTT
* * *
44998 CAGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTC-AAAAATGAGATTTTTGGAAGTT
* *
45058 CGGGGGTAAAATGGTAATTTTTAGAAGTTTCGGGGTCAAAAATGAGATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
* *
45117 CGAGGGTAAAATGATAATTTTTGGACAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGA-AGTTT
45148 AGGGACCTTC
Statistics
Matches: 228, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
59 168 0.74
60 60 0.26
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.34
Consensus pattern (59 bp):
CGGGGGTAAAATGGTAATTTTTGGAAGTTTCGAGGTCAAAAATGAGATTTTTGGAAGTT
Found at i:44989 original size:30 final size:27
Alignment explanation
Indices: 44859--45129 Score: 148
Period size: 29 Copynumber: 9.2 Consensus size: 27
44849 TTCGAGGTCA
* *
44859 AAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAATGGGATTTTTGGAAGTTC-AGGGT
* * * **
44887 AAAATGGTAATTTTTAGAAATTTTGGGGTT
1 AAAATGG-GATTTTT-GGAAGTTCAGGG-T
* * * *
44917 AAAAATGTGATTTGTGGGAGTTCGGGGGT
1 -AAAATGGGATTTTTGGAAGTTC-AGGGT
** *
44946 AAAATGATAATTTTTGCAAGGTTCAGGGT
1 AAAATG-GGATTTTTGGAA-GTTCAGGGT
44975 CAAAATTGGGATTTTTGGAAGTTCAGGGGT
1 -AAAA-TGGGATTTTTGGAAGTTCA-GGGT
*
45005 AAAATGGTAATTTTTGGAAGGTTC-GAGGT
1 AAAATGG-GATTTTTGGAA-GTTCAG-GGT
*
45034 CAAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 ---AAAATGGGATTTTTGGAAGTTC-AGGGT
* * *
45065 AAAATGGTAATTTTTAGAAGTTTCGGGGT
1 AAAATGG-GATTTTTGGAAG-TTCAGGGT
*
45094 CAAAAATGAGATTTTTGGAAGTTCGAGGGT
1 --AAAATGGGATTTTTGGAAGTTC-AGGGT
45124 AAAATG
1 AAAATG
45130 ATAATTTTTG
Statistics
Matches: 192, Mismatches: 28, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
28 29 0.15
29 67 0.35
30 61 0.32
31 27 0.14
32 8 0.04
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (27 bp):
AAAATGGGATTTTTGGAAGTTCAGGGT
Found at i:45151 original size:29 final size:28
Alignment explanation
Indices: 44942--45151 Score: 120
Period size: 29 Copynumber: 7.1 Consensus size: 28
44932 GGGAGTTCGG
* *
44942 GGGTAAAATGATAATTTTTGCAAGGTTCA
1 GGGTAAAATGATAATTTTTGGAA-GTTTA
** *
44971 GGGTCAAAATTG-GGATTTTTGGAAGTTCA
1 GGGT-AAAA-TGATAATTTTTGGAAGTTTA
* * *
45000 GGGGTAAAATGGTAATTTTTGGAAGGTTC
1 -GGGTAAAATGATAATTTTTGGAAGTTTA
** **
45029 GAGGTCAAAAAATG-GGATTTTTGGAAGTTCGG
1 G-GGT---AAAATGATAATTTTTGGAAGTT-TA
* * *
45061 GGGTAAAATGGTAATTTTTAGAAGTTTCG
1 GGGTAAAATGATAATTTTTGGAAGTTT-A
* *
45090 GGGTCAAAAATGA-GATTTTTGGAAGTTCGA
1 GGGT--AAAATGATAATTTTTGGAAGTT-TA
45120 GGGTAAAATGATAATTTTTGGACAGTTTA
1 GGGTAAAATGATAATTTTTGGA-AGTTTA
45149 GGG
1 GGG
45152 ACCTTCGGGG
Statistics
Matches: 141, Mismatches: 24, Indels: 32
0.72 0.12 0.16
Matches are distributed among these distances:
28 16 0.11
29 58 0.41
30 37 0.26
31 23 0.16
32 7 0.05
ACGTcount: A:0.31, C:0.05, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGATAATTTTTGGAAGTTTA
Found at i:46238 original size:15 final size:15
Alignment explanation
Indices: 46197--46239 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
46187 TATTATTAAA
*
46197 TATTATTATTGATGT
1 TATTATTATTGTTGT
*
46212 CATTATTATTGTTGT
1 TATTATTATTGTTGT
*
46227 TATTAATATTGTT
1 TATTATTATTGTT
46240 AATGATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (15 bp):
TATTATTATTGTTGT
Found at i:46916 original size:5 final size:5
Alignment explanation
Indices: 46906--46963 Score: 53
Period size: 6 Copynumber: 10.6 Consensus size: 5
46896 TTTAATTTTG
* *
46906 AAATT AAATT AAATTT AAATTT AAGATT AATTT AAAATT AAATTT AAAAT
1 AAATT AAATT AAA-TT AAA-TT AA-ATT AAATT -AAATT AAA-TT AAATT
46956 AAATT AAA
1 AAATT AAA
46964 AAGGGCCCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 21 0.47
6 23 0.51
7 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:46923 original size:6 final size:6
Alignment explanation
Indices: 46896--46953 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
46886 TTTTGGACTT
*
46896 TTTAAT TTTGAAA -TTAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
*
46942 ATTAAA TTTAAA
1 TTTAAA TTTAAA
46954 ATAAATTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 1 0.02
5 11 0.25
6 29 0.66
7 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:46923 original size:23 final size:22
Alignment explanation
Indices: 46896--46963 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
46886 TTTTGGACTT
*
46896 TTTAATTTTGAAATTAAATTAAA
1 TTTAAATTT-AAATTAAATTAAA
*
46919 TTTAAATTTAAGATTAATTTAAA
1 TTTAAATTTAA-ATTAAATTAAA
* *
46942 ATTAAATTTAAAATAAATTAAA
1 TTTAAATTTAAATTAAATTAAA
46964 AAGGGCCCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.28
23 28 0.72
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (22 bp):
TTTAAATTTAAATTAAATTAAA
Found at i:46925 original size:11 final size:11
Alignment explanation
Indices: 46906--46960 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
46896 TTTAATTTTG
46906 AAATTAAA-TT
1 AAATTAAATTT
46916 AAATTTAAATTT
1 AAA-TTAAATTT
46928 AAGATT-AATTT
1 AA-ATTAAATTT
46939 AAAATTAAATTT
1 -AAATTAAATTT
*
46951 AAAATAAATT
1 AAATTAAATT
46961 AAAAAGGGCC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 3 0.08
11 22 0.56
12 13 0.33
13 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:46952 original size:17 final size:17
Alignment explanation
Indices: 46896--46952 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
46886 TTTTGGACTT
*
46896 TTTAATTTTGAAATTAAA
1 TTTAA-TTTAAAATTAAA
* *
46914 TTAAATTTAAATTTAAGA
1 TTTAATTTAAAATTAA-A
46932 -TTAATTTAAAATTAAA
1 TTTAATTTAAAATTAAA
46948 TTTAA
1 TTTAA
46953 AATAAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.03
17 26 0.81
18 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
TTTAATTTAAAATTAAA
Found at i:47829 original size:204 final size:203
Alignment explanation
Indices: 47191--47840 Score: 951
Period size: 204 Copynumber: 3.2 Consensus size: 203
47181 TTACCGATTT
* * * *
47191 GGTCTTCTTCTTAGTATCTCATCAGGAAGATGATCACGTCGCTGTTTGTTTCAATTCGCTCCTCT
1 GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCT
* * * * * *
47256 GTATCTCGTCAGGAAGATGATTTTGGTTAACTTCTCAGTATCTCATCAGGAAGTGAACATTTTAT
66 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGT-AACCTTTTAT
* *
47321 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCCGGGGTTGGAAGATTTCACTCGTTTTGAG
130 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTCACTCGTTTTGAG
*
47386 TCTCGTTTG
195 CCTCGTTTG
* *
47395 GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATTGCTGTTTGTTTCAATTCACTCCTCT
1 GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCT
*
47460 GTACCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCAGGAAGTTAACCTTTTAT
66 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG-TAACCTTTTAT
* * *
47525 TGC-T-----T-C-T-T-AGTGTCTCATCAAGAAGCTGGGGTTTGAAGATTTTACTTGTTTTGAG
130 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTCACTCGTTTTGAG
47580 CCTCGTTTG
195 CCTCGTTTG
* * ** *
47589 GGTCTTCTTCTCAATGTTTCATCAGGAGGATGATCACATCGCCATTTGTTTCAATTCGTTCCTCT
1 GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCT
*
47654 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACCTTTTAT
66 GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAG-TAACCTTTTAT
*
47719 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTCGCTCGTTTTGAG
130 TGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTCACTCGTTTTGAG
47784 CCTCGTTTG
195 CCTCGTTTG
* *
47793 GATCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACATCGCTGTTTG
1 GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATCGCTGTTTG
47841 GATAATCGTA
Statistics
Matches: 396, Mismatches: 39, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
194 173 0.44
195 2 0.01
196 1 0.00
197 1 0.00
198 1 0.00
200 1 0.00
201 1 0.00
202 1 0.00
203 2 0.01
204 212 0.54
205 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (203 bp):
GGTCTTCTTCTCAATGTCTCATCAGGAAGATGATCACATCGCTGTTTGTTTCAATTCGCTCCTCT
GTACCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGTAACCTTTTATT
GCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAGATTTCACTCGTTTTGAGC
CTCGTTTG
Found at i:59497 original size:59 final size:59
Alignment explanation
Indices: 59434--59688 Score: 291
Period size: 59 Copynumber: 4.3 Consensus size: 59
59424 ACATCCGGGA
* * * * * * *
59434 GTAAAATAGTAATCTTTGGATGTTTCGGGGACAAAAATGAGATTTTTGGAAGTTCAGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
* * ** * * *
59493 GTAAAATGGTAATTTTTAGAA-ATTTTAGGTTAAAAAT-AGGATTTTTGGGAGTTT-GATG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGA-GATTTTTGGAAGTTTAG-GG
*
59551 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
* * * *
59610 GTAAAATGATAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
*
59669 GTAAAATGGTAATTTATGGA
1 GTAAAATGGTAATTTTTGGA
59689 TATTTTAGGG
Statistics
Matches: 164, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
57 2 0.01
58 44 0.27
59 117 0.71
60 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTTAGGG
Found at i:59507 original size:29 final size:29
Alignment explanation
Indices: 59475--59688 Score: 147
Period size: 29 Copynumber: 7.3 Consensus size: 29
59465 CAAAAATGAG
59475 ATTTTTGGAAGTTCAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCAGGGGTAAAATGGTA
* * * *
59504 ATTTTTAGAAATTTTA-GGTTAAAAATAGG--
1 ATTTTT-GGAAGTTCAGGGGT-AAAAT-GGTA
* * *
59533 ATTTTTGGGAGTT-TGATGGTAAAATGGTA
1 ATTTTTGGAAGTTCAG-GGGTAAAATGGTA
* *
59562 ATTTTTGGAAGGTTC-GAGGTCAAAAATGG-G
1 ATTTTTGGAA-GTTCAGGGGT--AAAATGGTA
* *
59592 ATTTTTGGAAGTTTAGGGGTAAAATGATA
1 ATTTTTGGAAGTTCAGGGGTAAAATGGTA
* *
59621 ATTTTTAGAAGGTTC-GGGGTCAAAAATGG-G
1 ATTTTTGGAA-GTTCAGGGGT--AAAATGGTA
*
59651 ATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCAGGGGTAAAATGGTA
*
59680 ATTTATGGA
1 ATTTTTGGA
59689 TATTTTAGGG
Statistics
Matches: 142, Mismatches: 25, Indels: 36
0.70 0.12 0.18
Matches are distributed among these distances:
27 2 0.01
28 22 0.15
29 57 0.40
30 46 0.32
31 15 0.11
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (29 bp):
ATTTTTGGAAGTTCAGGGGTAAAATGGTA
Found at i:59523 original size:117 final size:118
Alignment explanation
Indices: 59372--59630 Score: 283
Period size: 117 Copynumber: 2.2 Consensus size: 118
59362 AAAACATTTG
* * *
59372 GGGGTAAAAATGGTAATTTTGAG-AGTTTCGAGGTTGAAAAT-GGAGTCTTAGGACATCCG-GGA
1 GGGGT-AAAATGGTAATTTTTAGAAATTTCGAGGTTAAAAATAGGAGTCTTAGGA-ATCCGAGG-
* * *
59434 GTAAAATAGTAATCTTTGGATGTTTCGGGGACAAAAATGAGATTTTTGGAAGTTCA
63 GTAAAATAGTAATCTTTGGAAGGTTCGAGGACAAAAATGAGATTTTTGGAAGTTCA
* * * * * ** *
59490 GGGGTAAAATGGTAATTTTTAGAAATTT-TAGGTTAAAAATAGGATTTTTGGGAGTTTGATGGTA
1 GGGGTAAAATGGTAATTTTTAGAAATTTCGAGGTTAAAAATAGGAGTCTTAGGAATCCGAGGGTA
* * * * *
59554 AAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTA
66 AAATAGTAATCTTTGGAAGGTTCGAGGACAAAAATGAGATTTTTGGAAGTTCA
*
59607 GGGGTAAAATGATAATTTTTAGAA
1 GGGGTAAAATGGTAATTTTTAGAA
59631 GGTTCGGGGT
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
117 99 0.84
118 19 0.16
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (118 bp):
GGGGTAAAATGGTAATTTTTAGAAATTTCGAGGTTAAAAATAGGAGTCTTAGGAATCCGAGGGTA
AAATAGTAATCTTTGGAAGGTTCGAGGACAAAAATGAGATTTTTGGAAGTTCA
Found at i:59670 original size:30 final size:29
Alignment explanation
Indices: 59448--59674 Score: 158
Period size: 30 Copynumber: 7.7 Consensus size: 29
59438 AATAGTAATC
* * * *
59448 TTTGGATGTTTCGGGGACAAAAATGAGATT
1 TTTGGAAGTTTAGGGG-TAAAAATGGGATT
* *
59478 TTTGGAAGTTCAGGGGT-AAAATGGTAATT
1 TTTGGAAGTTTAGGGGTAAAAATGG-GATT
* * * *
59507 TTTAGAAATTTTA-GGTTAAAAATAGGATT
1 TTT-GGAAGTTTAGGGGTAAAAATGGGATT
* * *
59536 TTTGGGAGTTT-GATGGT-AAAATGGTAATT
1 TTTGGAAGTTTAG-GGGTAAAAATGG-GATT
* * *
59565 TTTGGAAGGTTCGAGGTCAAAAATGGGATT
1 TTTGGAAGTTTAGGGGT-AAAAATGGGATT
**
59595 TTTGGAAGTTTAGGGGT-AAAATGATAATT
1 TTTGGAAGTTTAGGGGTAAAAATG-GGATT
* * *
59624 TTTAGAAGGTTCGGGGTCAAAAATGGGATT
1 TTTGGAAGTTTAGGGGT-AAAAATGGGATT
59654 TTTGGAAGTTTAGGGGTAAAA
1 TTTGGAAGTTTAGGGGTAAAA
59675 TGGTAATTTA
Statistics
Matches: 149, Mismatches: 36, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
28 23 0.15
29 53 0.36
30 60 0.40
31 13 0.09
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
TTTGGAAGTTTAGGGGTAAAAATGGGATT
Found at i:60814 original size:15 final size:15
Alignment explanation
Indices: 60774--60815 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
60764 ATTATTAAAT
*
60774 ATTATTATTGATGTC
1 ATTATTATTGTTGTC
60789 ATTATTATTGTTGTC
1 ATTATTATTGTTGTC
*
60804 ATTAATATTGTT
1 ATTATTATTGTT
60816 AGATATTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (15 bp):
ATTATTATTGTTGTC
Found at i:61500 original size:5 final size:5
Alignment explanation
Indices: 61490--61558 Score: 57
Period size: 6 Copynumber: 12.6 Consensus size: 5
61480 TTTAATTTTG
* *
61490 AAATT AAATT AAATTT AAACTT AAGATT AATTT AAAATT AAATTT AAATC
1 AAATT AAATT AAA-TT AAA-TT AA-ATT AAATT -AAATT AAA-TT AAATT
*
61540 AAATTT AAAAT AAATT AAA
1 AAA-TT AAATT AAATT AAA
61559 AAGGGCCAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
5 25 0.48
6 26 0.50
7 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (5 bp):
AAATT
Found at i:61513 original size:17 final size:17
Alignment explanation
Indices: 61490--61559 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
61480 TTTAATTTTG
61490 AAATTAAATTAAATTTA
1 AAATTAAATTAAATTTA
*
61507 AACTTAAGATT-AATTTA
1 AAATTAA-ATTAAATTTA
*
61524 AAATTAAATTTAAA-TCA
1 AAATTAAA-TTAAATTTA
* *
61541 AATTTAAAATAAA-TTA
1 AAATTAAATTAAATTTA
61557 AAA
1 AAA
61560 AGGGCCAGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
16 9 0.21
17 29 0.67
18 5 0.12
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (17 bp):
AAATTAAATTAAATTTA
Found at i:61518 original size:23 final size:22
Alignment explanation
Indices: 61490--61558 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 22
61480 TTTAATTTTG
*
61490 AAATTAAATTAAATTTAAACTT
1 AAATTAAATTAAAATTAAACTT
* *
61512 AAGATTAATTTAAAATTAAATTT
1 AA-ATTAAATTAAAATTAAACTT
*
61535 AAATCAAATTTAAAA-TAAA-TT
1 AAATTAAA-TTAAAATTAAACTT
61556 AAA
1 AAA
61559 AAGGGCCAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.12
22 10 0.25
23 25 0.62
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
AAATTAAATTAAAATTAAACTT
Found at i:61524 original size:11 final size:12
Alignment explanation
Indices: 61490--61559 Score: 69
Period size: 11 Copynumber: 6.2 Consensus size: 12
61480 TTTAATTTTG
61490 AAATTAAA-TTA
1 AAATTAAATTTA
* *
61501 AATTTAAACTTA
1 AAATTAAATTTA
*
61513 AGATT-AATTTA
1 AAATTAAATTTA
61524 AAATTAAATTT-
1 AAATTAAATTTA
*
61535 AAATCAAATTTA
1 AAATTAAATTTA
61547 AAA-TAAA-TTA
1 AAATTAAATTTA
61557 AAA
1 AAA
61560 AGGGCCAGTC
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
10 6 0.12
11 29 0.59
12 14 0.29
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (12 bp):
AAATTAAATTTA
Found at i:61881 original size:27 final size:25
Alignment explanation
Indices: 61840--61917 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 25
61830 ACTTTATATA
*
61840 TTTTT-TAATCTGGTATCTAAATTT
1 TTTTTCTAATTTGGTATCTAAATTT
*
61864 TTTTTACTCAATTTGGTACTCAAACATTT
1 TTTTT-CT-AATTTGGTA-TCTAA-ATTT
61893 TTTTTCTAATTTGGTA-CTTAAATTT
1 TTTTTCTAATTTGGTATC-TAAATTT
61918 GACACTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
24 5 0.11
25 5 0.11
26 3 0.07
27 17 0.38
28 6 0.13
29 9 0.20
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.55
Consensus pattern (25 bp):
TTTTTCTAATTTGGTATCTAAATTT
Found at i:65174 original size:49 final size:49
Alignment explanation
Indices: 65100--65193 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
65090 AAGTATAAGA
*
65100 TAATAGAGTTATTTTGCGTAATTATCTAATAATTAAAG-GTCAGATAAAG
1 TAATAGAGTTATTTTACGTAATTATCTAATAATT-AAGTGTCAGATAAAG
* *
65149 TAATGGAGTTATTTTACGTAGTTATCTAATAATTAAGTGTCAGAT
1 TAATAGAGTTATTTTACGTAATTATCTAATAATTAAGTGTCAGAT
65194 TATCTAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 3 0.07
49 38 0.93
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.39
Consensus pattern (49 bp):
TAATAGAGTTATTTTACGTAATTATCTAATAATTAAGTGTCAGATAAAG
Found at i:65215 original size:23 final size:23
Alignment explanation
Indices: 65170--65216 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
65160 TTTTACGTAG
****
65170 TTATCTAATAATTAAGTGTCAGA
1 TTATCTAATAATTAAACACCAGA
65193 TTATCTAATAATTAAACACCAGA
1 TTATCTAATAATTAAACACCAGA
65216 T
1 T
65217 AAGGTAATGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (23 bp):
TTATCTAATAATTAAACACCAGA
Found at i:65927 original size:22 final size:23
Alignment explanation
Indices: 65879--65927 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
65869 TGAAAATAAA
65879 ATTA-GTTTTCTAAATTAATTTT
1 ATTATGTTTTCTAAATTAATTTT
*
65901 TTTATGTTTT-TAAATTTAA-TTT
1 ATTATGTTTTCTAAA-TTAATTTT
65923 ATTAT
1 ATTAT
65928 TCTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTATGTTTTCTAAATTAATTTT
Found at i:66299 original size:27 final size:25
Alignment explanation
Indices: 66249--66300 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
66239 TTGTTAAAGC
**
66249 TTTTTATATTTAATATATTAATTAT
1 TTTTTATATTTAATATAAAAATTAT
66274 TTTTTATATTTCATATATAAAAATTAT
1 TTTTTATATTT-A-ATATAAAAATTAT
66301 ATTAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 1 0.04
27 11 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTTATATTTAATATAAAAATTAT
Found at i:72898 original size:28 final size:28
Alignment explanation
Indices: 72808--72898 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 28
72798 TTCAAAATTT
*
72808 TACATAAAATCTAAAAAAATGAAAG-AAG
1 TACATAAAATCTAAAAAAAT-AATGAAAG
* * * * *
72836 TACAAAAAATTTAAAAAAAAAAATTAAATTT
1 TACATAAAATCT-AAAAAAATAATGAAA--G
72867 TACATAAAATCTAAAAAAATAATGAAAG
1 TACATAAAATCTAAAAAAATAATGAAAG
72895 TACA
1 TACA
72899 AATTTTTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 16 0.33
29 9 0.19
30 13 0.27
31 10 0.21
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (28 bp):
TACATAAAATCTAAAAAAATAATGAAAG
Found at i:73295 original size:21 final size:21
Alignment explanation
Indices: 73269--73311 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73259 TCATATTATT
*
73269 TTTTAATTTTTAAAAAAATTA
1 TTTTAATGTTTAAAAAAATTA
* *
73290 TTTTAATGTTTAATAAATTTA
1 TTTTAATGTTTAAAAAAATTA
73311 T
1 T
73312 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAATGTTTAAAAAAATTA
Found at i:74692 original size:2 final size:2
Alignment explanation
Indices: 74685--74709 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74675 CGATATTAAA
74685 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
74710 ATTTGAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80613 original size:30 final size:30
Alignment explanation
Indices: 80570--80947 Score: 286
Period size: 29 Copynumber: 12.8 Consensus size: 30
80560 CTCTGCTTTA
* * * *
80570 TTCTAAAAGTATATTTTGACCCCCAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* * *
80600 TTTTAAAATTATA-TTTAACCCATAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* *
80629 ATCCAAAATTACATTTTAACCCCTAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* *
80659 CTCATAAAATCACATTTTAACCCCTAAACTT
1 TTC-TAAAATTACATTTTAACCCCTAAACTT
* * * *
80690 TTCAAAAATTAGATTTTAACACTTAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
** * * *
80720 CACCAAAATTACATTTTGACCTCT-AACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* * * * *
80749 CTCCAAAATTACATCTTAATCCTTAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* *
80779 TTCCAAATTTACATTTTAA-CCCTAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* * *
80808 CTT-TAAAATCACATTTTAATCCC-AAAC-C
1 -TTCTAAAATTACATTTTAACCCCTAAACTT
* * *
80836 TTCTCAAAATCACATGTTGA-CCCTAAACTT
1 TTCT-AAAATTACATTTTAACCCCTAAACTT
* * * * *
80866 CTCCAAAATCACATTTTGAGCCC-AAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* * *
80895 TCCTAAAATTACATTTTTACCCTTAAACTT
1 TTCTAAAATTACATTTTAACCCCTAAACTT
* *
80925 TTCCAAAATTACATTTTGACCCC
1 TTCTAAAATTACATTTTAACCCC
80948 ATATTCTCCG
Statistics
Matches: 279, Mismatches: 58, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
27 2 0.01
28 4 0.01
29 124 0.44
30 122 0.44
31 27 0.10
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
TTCTAAAATTACATTTTAACCCCTAAACTT
Found at i:80651 original size:59 final size:59
Alignment explanation
Indices: 80582--80947 Score: 292
Period size: 59 Copynumber: 6.2 Consensus size: 59
80572 CTAAAAGTAT
* *** * *
80582 ATTTTGACCCCCAAACTTTTTTAAAATTATA-TTTAACCCATAAACTTATCCAAAATTAC
1 ATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCC-TAAACTTCTCCAAAATTAC
* ** * * * *
80641 ATTTTAACCCCTAAACTTCTCATAAAATCACATTTTAACCCCTAAACTTTTCAAAAATTAG
1 ATTTTAACCCCCAAACTT-TCCCAAAATTACATTTTAA-CCCTAAACTTCTCCAAAATTAC
* ** *
80702 ATTTTAACACTTAAAC-TTCACCAAAATTACATTTTGACCTCT-AACTTCTCCAAAATTAC
1 ATTTTAACCCCCAAACTTTC-CCAAAATTACATTTTAACC-CTAAACTTCTCCAAAATTAC
* * ** * * ** *
80761 ATCTTAATCCTTAAACTTTTCCAAATTTACATTTTAACCCTAAACTTCTTTAAAATCAC
1 ATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCCTAAACTTCTCCAAAATTAC
* * * * * * *
80820 ATTTTAA-TCCCAAACCTTCTCAAAATCACATGTTGACCCTAAACTTCTCCAAAATCAC
1 ATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCCTAAACTTCTCCAAAATTAC
* * * * *
80878 ATTTTGA-GCCCAAACTTTCCTAAAATTACATTTTTACCCTTAAACTTTTCCAAAATTAC
1 ATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCC-TAAACTTCTCCAAAATTAC
*
80937 ATTTTGACCCC
1 ATTTTAACCCC
80948 ATATTCTCCG
Statistics
Matches: 247, Mismatches: 51, Indels: 17
0.78 0.16 0.05
Matches are distributed among these distances:
58 72 0.29
59 108 0.44
60 29 0.12
61 35 0.14
62 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
ATTTTAACCCCCAAACTTTCCCAAAATTACATTTTAACCCTAAACTTCTCCAAAATTAC
Found at i:86774 original size:79 final size:79
Alignment explanation
Indices: 86643--86884 Score: 475
Period size: 79 Copynumber: 3.1 Consensus size: 79
86633 AACTCAAACC
*
86643 ATTCTCCACATTCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
1 ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
86708 AGGCATTATAGCCT
66 AGGCATTATAGCCT
86722 ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
1 ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
86787 AGGCATTATAGCCT
66 AGGCATTATAGCCT
86801 ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
1 ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
86866 AGGCATTATAGCCT
66 AGGCATTATAGCCT
86880 ATTCT
1 ATTCT
86885 TCTCCCCAAC
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 162 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (79 bp):
ATTCTCCACATCCATCAATTGAAACCTCATAGATGGTTTCCACATTGTACAAACTTTGTTCCATA
AGGCATTATAGCCT
Found at i:87544 original size:36 final size:37
Alignment explanation
Indices: 87499--87574 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 37
87489 TCTTCCATTA
* * *
87499 TCTTCAAGGTTTTTGCTATTGCTTCTTTCTCTTTCTC
1 TCTTCAAGGTTTTTGCTAATGCTTCTCTCTCTCTCTC
87536 TCTT-AAGGTTTTTGCTAATGCTTCTCTCTCTCTCTC
1 TCTTCAAGGTTTTTGCTAATGCTTCTCTCTCTCTCTC
87572 TCT
1 TCT
87575 CTCTCTCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
36 32 0.89
37 4 0.11
ACGTcount: A:0.09, C:0.26, G:0.11, T:0.54
Consensus pattern (37 bp):
TCTTCAAGGTTTTTGCTAATGCTTCTCTCTCTCTCTC
Found at i:87565 original size:2 final size:2
Alignment explanation
Indices: 87558--87596 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
87548 TGCTAATGCT
87558 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
87597 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:87632 original size:2 final size:2
Alignment explanation
Indices: 87625--87649 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87615 NNNNNNNNNN
87625 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
87650 CTATCTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:88662 original size:18 final size:18
Alignment explanation
Indices: 88639--88673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
88629 TGTATTTTTG
*
88639 AAAATCATTTTTAGCTTA
1 AAAATCACTTTTAGCTTA
*
88657 AAAATCACTTTTGGCTT
1 AAAATCACTTTTAGCTT
88674 TGAAGTTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (18 bp):
AAAATCACTTTTAGCTTA
Found at i:89683 original size:441 final size:435
Alignment explanation
Indices: 88223--89742 Score: 1252
Period size: 442 Copynumber: 3.4 Consensus size: 435
88213 TGAAAAGAAG
* ***
88223 TTTTGACTTTAAAGCTATGCTAAACAAGCATCATTTGCTTAAAAAAAACTT-CTTCTTAAAAA-C
1 TTTTGACTTTAAAGCTGTGCTAAACAAGCATCATTTGCTT-AAAAATTTTTACTTC-TAAAAAGC
* * * *
88286 ACTTTTGCTCAAAATGGAAAAAC-AAAAATTTTTAGCTTTTTTTAGCCAAATGCACTTTTGGCTC
64 A-TTTTGCTC-AAATGAAAAAACTAAAAA-TTTTAGCCTTTTTTAGCCAAAAGCACTTTTGGCAC
* * * * *
88350 AAAATTTACTTTTTCATCCTCCATTTTCCTTCTCCCAAAACACACGATATAC-ACATTTTTTTTT
126 -TAATTTACTTTTTCATCCTCAATTTT-CTTCTCTCAAAACACACGATATACTTCA--ATTTTTT
* * *
88414 TCATTTTCCCTTTCAAAGTTGGTTCTTTGGTTTTCCTTGGCTTTTATTTTCTTTAATTCTTCCAT
187 T-ATTTTCTCTTTCAAAG-TGGTTCTTTGGTTCTCC-T--CTTTTATTTT-TTTTATTCTTCCAT
* * * * * * *
88479 TTACTTCAATGTTTTTATT--TCTATCTCTC-TC--TCTCTCTACTCCCCTAATCACAACTTCTC
246 TTTCTTCAAGGTTTTTATTGCTCTCTCTCTCTTCTTTCTTTCTACTTCCTTAATCACATCTTCTC
* *
88539 ATTTAAACTCTCCATTTAATTTTTTCAGTTTTT-CCAATTTTAGGTTGAGCTATTTTTGGTTGTT
311 ATTT-AACTCTCCATTTAATTTTTTC-GTTTTTCCCAA-TTTAAGTTAAGCTATTTTTGGTTGTT
* * * * * *
88603 GGTTTTTGTGTTAGACTTTGTGTAATTGTATTTTTGAAAATCATTTTTAGCTT-AAAAATCAC-
373 GCTTTTTGTGTTAGTCTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAAT-ACT
* * * * * * *
88665 TTTTGGCTTTGAAGTTGTGCTAAACAAGCATAATTTGCTTAAAAATTTTTTACTTTTGAAAAGTA
1 TTTTGACTTTAAAGCTGTGCTAAACAAGCATCATTTGCTTAAAAA-TTTTTACTTCTAAAAAGCA
** * * * * * *
88730 TTTTTG-TCGGAGGAAAAAGCTAAAAATTTAAGCCTTTTTT-GTCAAAAGTAATTTTGGCTACTA
65 -TTTTGCTCAAATGAAAAAACTAAAAATTTTAGCCTTTTTTAGCCAAAAGCACTTTTGGC-ACTA
* * *
88793 ATTTA-TTTTTTATCCTCAATTTTTCTACT-TCCAAACTACACGATATACTTCCAATTTCTTTTT
128 ATTTACTTTTTCATCCTCAA-TTTTCTTCTCTCAAAAC-ACACGATATACTT-CAA-TT-TTTTT
** * * **
88856 CATTTTCTCCCTCAAA---G--C-TT-GTTCTCCTCTTTTGTTTTTTTTTAGTTTTTTTATTTTC
188 -ATTTTCTCTTTCAAAGTGGTTCTTTGGTTCTCCTCTTTT-ATTTTTTTTA-TTCTTCCATTTTC
* * *
88914 TTCAAGGTTTTTATGGCTCTCTCTCCCTCTCTCTCTTTCTTTTTAC-TCTTCTAATCACATCTTC
250 TTCAAGGTTTTTATTG--CTCTCT--CTCTCT-TCTTTCTTTCTACTTCCT-TAATCACATCTTC
* * * *
88978 TCATTTAACTAC-CCATTTAATTTTTTTCCTTTTTTTCTC-ATTTCAGATTAAGTTATTTTTGGT
309 TCATTTAACT-CTCCATTTAA-TTTTTT-C-GTTTTTCCCAATTTAAG-TTAAGCTATTTTTGGT
* * * * * * *
89041 TTTTGCTTTTTGTGTTA-TGCTTTGGGTAGTTATGCTTTTAAAAAACACTTTTAGCTAAAAAAAA
369 TGTTGCTTTTTGTGTTAGT-CTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAAT
89105 ACAT
433 AC-T
* * * * * * ** * * * *
89109 ATTTGATTTTAAAGTTGTACTAAATAAACA-CTATTTATTTGAAATTTTTTACTTTTGAAAAGCA
1 TTTTGACTTTAAAGCTGTGCTAAACAAGCATC-ATTTGCTTAAAAATTTTTACTTCTAAAAAGCA
** * * * * *
89173 CTTTTGCTCAAATGAAAAAGTTACAAATTTTAG-CTTTTTTGAACTAAAAGCACTTTTGGTTATT
65 -TTTTGCTCAAATGAAAAAACTAAAAATTTTAGCCTTTTTT-AGCCAAAAGCACTTTTGG-CACT
* **
89237 AATTTACTTTTTCATCCTCCATTATTCTTCTCTCAAAACACATTATATACTTCAATTTTTTT-TT
127 AATTTACTTTTTCATCCTCAATT-TTCTTCTCTCAAAACACACGATATACTTCAATTTTTTTATT
*
89301 TTCTCTTTCAAAGGTGGTTCTTTGGTTCTCCTCCTCTTTATTTTTTTTATTCTTCCATTTTCTTT
191 TTCTCTTTCAAA-GTGGTTCTTTGGTTCTCCT-CT-TTTATTTTTTTTATTCTTCCATTTTCTTC
* * * *
89366 AAGGTTTTTGTTGCTCTCTCTCTCTTCGTTTCTTTCTACTTCCTTAATCTCATCTTTTAATTTCA
253 AAGGTTTTTATTGCTCTCTCTCTCTTC-TTTCTTTCTACTTCCTTAATCACATCTTCTCATTT-A
*
89431 ACTCTCCATTTAATTTTTTCGTTTTTCCCCAATTTAAGTTAAACTATTTTTGGTTGTTGCTTTTT
316 ACTCTCCATTTAATTTTTTCGTTTTT-CCCAATTTAAGTTAAGCTATTTTTGGTTGTTGCTTTTT
* * * *
89496 GTATTAGTTTTTGTCTAGTTGTGTTTTTGAAAAACACTTTTAACTTAAAAAATACT
380 GTGTTAGTCTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAATACT
* * * * *
89552 TTTTGGCTTTAAAGCTGTGTTAAACAAGTATCATTTGCTTGAAAATTTTGACTTCTAAAAAGCA-
1 TTTTGACTTTAAAGCTGTGCTAAACAAGCATCATTTGCTTAAAAATTTTTACTTCTAAAAAGCAT
* *
89616 TTTGCTCAAATGAAAAAACTAAAAATTTTAG-TTTTTTTGAGCCAAAAGCACTTTTAGCAGCTAA
66 TTTGCTCAAATGAAAAAACTAAAAATTTTAGCCTTTTTT-AGCCAAAAGCACTTTTGGCA-CTAA
* * * *
89680 TTTATTTTTTTCATCTTCAATTGTTCTTCTC-CTAATACACCCGATATACTTCCAATTTCTTTT
129 TTTA-CTTTTTCATCCTCAATT-TTCTTCTCTC-AAAACACACGATATACTT-CAATTT-TTTT
89743 TCTTTTTCTT
Statistics
Matches: 848, Mismatches: 166, Indels: 126
0.74 0.15 0.11
Matches are distributed among these distances:
430 9 0.01
431 26 0.03
432 1 0.00
433 6 0.01
434 2 0.00
435 5 0.01
437 6 0.01
438 5 0.01
439 29 0.03
440 40 0.05
441 151 0.18
442 152 0.18
443 109 0.13
444 131 0.15
445 72 0.08
446 44 0.05
447 13 0.02
448 2 0.00
449 31 0.04
450 11 0.01
451 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.48
Consensus pattern (435 bp):
TTTTGACTTTAAAGCTGTGCTAAACAAGCATCATTTGCTTAAAAATTTTTACTTCTAAAAAGCAT
TTTGCTCAAATGAAAAAACTAAAAATTTTAGCCTTTTTTAGCCAAAAGCACTTTTGGCACTAATT
TACTTTTTCATCCTCAATTTTCTTCTCTCAAAACACACGATATACTTCAATTTTTTTATTTTCTC
TTTCAAAGTGGTTCTTTGGTTCTCCTCTTTTATTTTTTTTATTCTTCCATTTTCTTCAAGGTTTT
TATTGCTCTCTCTCTCTTCTTTCTTTCTACTTCCTTAATCACATCTTCTCATTTAACTCTCCATT
TAATTTTTTCGTTTTTCCCAATTTAAGTTAAGCTATTTTTGGTTGTTGCTTTTTGTGTTAGTCTT
TGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAATACT
Found at i:89745 original size:441 final size:434
Alignment explanation
Indices: 88223--90109 Score: 1247
Period size: 442 Copynumber: 4.2 Consensus size: 434
88213 TGAAAAGAAG
* * * * *** *
88223 TTTTGACTTTAAAGCTATGCTAAACAAGCATCATTTGCTTAAAAAAAACTT-CTTCTT-AAAAAC
1 TTTTGGCTTTAAAGTTGTGCTAAACAAGCATCATTTGCTT-GAAAATTTTTACTT-TTGAAAAGC
* * *
88286 ACTTTTGCTCAAAATGGAAAAA-C-AAAAATTTTTAGCTTTTTTTAGCCAAATGCACTTTTGGCT
64 A-TTTTGCTC-AAAT-GAAAAAGCTAAAAA-TTTTAGCTTTTTTGAGCCAAAAGCACTTTTGGCA
* * * * ****
88349 CAAAATTTACTTTTTCATCCTCCATT-TTCCTTCTCCCAAAACACACGATATACACATTTTTTTT
125 C-TAATTTATTTTTTCATCCTCAATTATT-CTTCT-CCTAAACACACGATAT--AC--TTCCAAT
* * * * *
88413 TTCATTTTCCCTTTCAAAGTTGGTTCTTTGGTTTTCCTTGGCTTTTATTTTCTTTAATTCTTCCA
183 TTCTTTTTCTCTTTCAAAGCTGGTTCTTTGGTTCTCC-T--CTTTTATTTT-TTTTATTCTTCCA
* * * * * * *
88478 TTTACTTCAATGTTTTTATT--TCTATCTCTC-TC--TCTCTCTACTCCCCTAATCACAACTTCT
244 TTTTCTTCAAGGTTTTTATTGCTCTCTCTCTCTTCTTTCTTTCTACTTCCTTAATCACATCTTCT
* *
88538 CATTTAAACTCTCCATTTAATTTTTTCAGTTTTT-CCAATTTTAGGTTGAGCTATTTTTGGTTGT
309 CATTT-AACTCTCCATTTAATTTTTTC-GTTTTTCCCAA-TTTAAGTTAAGCTATTTTTGGTTGT
* * * * * *
88602 TGGTTTTTGTGTTAGACTTTGTGTAATTGTATTTTTGAAAATCATTTTTAGCTT-AAAAATCAC-
371 TGCTTTTTGTGTTAGTCTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAAT-ACT
* * * *
88665 TTTTGGCTTTGAAGTTGTGCTAAACAAGCATAATTTGCTTAAAAATTTTTTACTTTTGAAAAGTA
1 TTTTGGCTTTAAAGTTGTGCTAAACAAGCATCATTTGCTTGAAAA-TTTTTACTTTTGAAAAGCA
** * * * * *
88730 TTTTTG-TCGGAGGAAAAAGCTAAAAATTTAAGCCTTTTTT--GTCAAAAGTAATTTTGGCTACT
65 -TTTTGCTCAAATGAAAAAGCTAAAAATTTTAG-CTTTTTTGAGCCAAAAGCACTTTTGGC-ACT
* *
88792 AATTTATTTTTT-ATCCTCAATTTTTCTACTTCC-AAACTACACGATATACTTCCAATTTCTTTT
127 AATTTATTTTTTCATCCTCAATTATTCTTC-TCCTAAAC-ACACGATATACTTCCAATTTCTTTT
*** **** * * **
88855 TCAT-TTTC-TCCCTCAAAGC-TT-GTTCTCCTCTTTTGTTTTTTTTTAGTTTTTTTATTTTCTT
190 TC-TCTTTCAAAGCT-GGTTCTTTGGTTCTCCTCTTTT-ATTTTTTTTA-TTCTTCCATTTTCTT
* * *
88916 CAAGGTTTTTATGGCTCTCTCTCCCTCTCTCTCTTTCTTTTTAC-TCTTCTAATCACATCTTCTC
251 CAAGGTTTTTATTG--CTCTCT--CTCTCT-TCTTTCTTTCTACTTCCT-TAATCACATCTTCTC
* * * * *
88980 ATTTAACTAC-CCATTTAATTTTTTTCCTTTTTTTCTC-ATTTCAGATTAAGTTATTTTTGGTTT
310 ATTTAACT-CTCCATTTAA-TTTTTT-C-GTTTTTCCCAATTTAAG-TTAAGCTATTTTTGGTTG
* * * * * *
89043 TTGCTTTTTGTGTTA-TGCTTTGGGTAGTTATGCTTTTAAAAAACACTTTTAGCTAAAAAAAAAC
370 TTGCTTTTTGTGTTAGT-CTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAATAC
89107 AT
434 -T
* ** * * * ** *
89109 ATTTGATTTTAAAGTTGTACTAAATAAACA-CTATTTATTTGAAATTTTTTACTTTTGAAAAGCA
1 TTTTGGCTTTAAAGTTGTGCTAAACAAGCATC-ATTTGCTTGAAAATTTTTACTTTTGAAAAGCA
* * * * * *
89173 CTTTTGCTCAAATGAAAAAGTTACAAATTTTAGCTTTTTTGAACTAAAAGCACTTTTGGTTATTA
65 -TTTTGCTCAAATGAAAAAGCTAAAAATTTTAGCTTTTTTGAGCCAAAAGCACTTTTGG-CACTA
* * * ** *
89238 ATTTACTTTTTCATCCTCCATTATTCTTCTCTCAAAACACATTATATACTT-CAATTTTTTTTTT
128 ATTTATTTTTTCATCCTCAATTATTCTTCTC-CTAAACACACGATATACTTCCAA--TTTCTTTT
* *
89302 TCTCTTTCAAAGGTGGTTCTTTGGTTCTCCTCCTCTTTATTTTTTTTATTCTTCCATTTTCTTTA
190 TCTCTTTCAAAGCTGGTTCTTTGGTTCTCCT-CT-TTTATTTTTTTTATTCTTCCATTTTCTTCA
* * * *
89367 AGGTTTTTGTTGCTCTCTCTCTCTTCGTTTCTTTCTACTTCCTTAATCTCATCTTTTAATTTCAA
253 AGGTTTTTATTGCTCTCTCTCTCTTC-TTTCTTTCTACTTCCTTAATCACATCTTCTCATTT-AA
*
89432 CTCTCCATTTAATTTTTTCGTTTTTCCCCAATTTAAGTTAAACTATTTTTGGTTGTTGCTTTTTG
316 CTCTCCATTTAATTTTTTCGTTTTT-CCCAATTTAAGTTAAGCTATTTTTGGTTGTTGCTTTTTG
* * * *
89497 TATTAGTTTTTGTCTAGTTGTGTTTTTGAAAAACACTTTTAACTTAAAAAATACT
380 TGTTAGTCTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAATACT
* * * * * *
89552 TTTTGGCTTTAAAGCTGTGTTAAACAAGTATCATTTGCTTGAAAATTTTGACTTCTAAAAAGCA-
1 TTTTGGCTTTAAAGTTGTGCTAAACAAGCATCATTTGCTTGAAAATTTTTACTTTTGAAAAGCAT
* * *
89616 TTTGCTCAAATGAAAAAACTAAAAATTTTAGTTTTTTTGAGCCAAAAGCACTTTTAGCAGCTAAT
66 TTTGCTCAAATGAAAAAGCTAAAAATTTTAGCTTTTTTGAGCCAAAAGCACTTTTGGCA-CTAAT
* * *
89681 TTATTTTTTTCATCTTCAATTGTTCTTCTCCTAATACACCCGATATACTTCCAATTTCTTTTTCT
130 TTA-TTTTTTCATCCTCAATTATTCTTCTCCTAA-ACACACGATATACTTCCAATTTCTTTTTC-
***** ** * * *
89746 TTTTCTTTTTTTTTTTCTTTTTCAAAATTGGTTCTCCTTCTCTTTTATTTTCTTTGATTCTTTCA
192 ---TC---TTTCAAAGCTGGTTC---TTTGGTTCT-C--CTCTTTTATTTT-TTTTATTCTTCCA
* * * * * * * * * *
89811 TTTTTTTTCGAGGTTTTTTTTGCTGCTAT-TGTAGC-TCTCTCTCTCTAGTCCCCTAATC-CTAT
244 -TTTTCTTCAAGGTTTTTATTGCT-CTCTCTCT--CTTCTTTCTTTCTACTTCCTTAATCAC-AT
* * * * * * *
89873 ATTCTCATTTTAACTC-CACATTTAATTTTTT-TTATTTTCCCCCATTTCAGGATAAACTCTTTT
304 CTTCTCA-TTTAACTCTC-CATTTAATTTTTTCGT-TTTT-CCCAATTT-AAGTTAAGCTATTTT
* * * ** * * *
89936 TGGTTATTGTTTTTTGTGTTAAGT-TTTGTTTAACTGTGCTTTTGAAGAGCACTTTTAGCTT-AA
364 TGGTTGTTGCTTTTTGTGTT-AGTCTTTGTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAA
* *
89999 AAACACA
428 AAATACT
* * * * * ** **
90006 TTTT-GCTTTAAAATTGTGCCAAACAAGTACCATTTGCTTGAAAAATTAGACTTTTGAAAAATAT
1 TTTTGGCTTTAAAGTTGTGCTAAACAAGCATCATTTGCTTGAAAATTTTTACTTTTGAAAAGCAT
90070 TTTGCTCAAATGAAAAAGCTAAAAATTTTAAGCCTTTTTT
66 TTTGCTCAAATGAAAAAGCTAAAAATTTT-AG-CTTTTTT
90110 TTTATTCTTC
Statistics
Matches: 1124, Mismatches: 232, Indels: 164
0.74 0.15 0.11
Matches are distributed among these distances:
430 9 0.01
431 26 0.02
432 1 0.00
433 6 0.01
434 3 0.00
435 20 0.02
437 7 0.01
438 4 0.00
439 25 0.02
440 48 0.04
441 118 0.10
442 154 0.14
443 105 0.09
444 125 0.11
445 78 0.07
446 42 0.04
447 24 0.02
448 10 0.01
449 31 0.03
450 11 0.01
451 11 0.01
452 9 0.01
453 64 0.06
454 114 0.10
455 69 0.06
456 10 0.01
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (434 bp):
TTTTGGCTTTAAAGTTGTGCTAAACAAGCATCATTTGCTTGAAAATTTTTACTTTTGAAAAGCAT
TTTGCTCAAATGAAAAAGCTAAAAATTTTAGCTTTTTTGAGCCAAAAGCACTTTTGGCACTAATT
TATTTTTTCATCCTCAATTATTCTTCTCCTAAACACACGATATACTTCCAATTTCTTTTTCTCTT
TCAAAGCTGGTTCTTTGGTTCTCCTCTTTTATTTTTTTTATTCTTCCATTTTCTTCAAGGTTTTT
ATTGCTCTCTCTCTCTTCTTTCTTTCTACTTCCTTAATCACATCTTCTCATTTAACTCTCCATTT
AATTTTTTCGTTTTTCCCAATTTAAGTTAAGCTATTTTTGGTTGTTGCTTTTTGTGTTAGTCTTT
GTGTAGTTGTGTTTTTGAAAAACACTTTTAGCTTAAAAAATACT
Found at i:89746 original size:6 final size:6
Alignment explanation
Indices: 89735--89768 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
89725 ATACTTCCAA
*
89735 TTTCTT TTTCTT TTTCTT TTTTTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
89769 AAAATTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:90313 original size:18 final size:18
Alignment explanation
Indices: 90282--90316 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90272 TAACTGTGCT
*
90282 TTTAAAAAGCACTTTTAG
1 TTTAAAAAACACTTTTAG
*
90300 TTTAAAAAATACTTTTA
1 TTTAAAAAACACTTTTA
90317 ACTTTAAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTAAAAAACACTTTTAG
Found at i:90322 original size:19 final size:18
Alignment explanation
Indices: 90282--90324 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
90272 TAACTGTGCT
* *
90282 TTTAAAAAGCACTTTTAG
1 TTTAAAAAACACTTTTAC
*
90300 TTTAAAAAATACTTTTAAC
1 TTTAAAAAACACTTTT-AC
90319 TTTAAA
1 TTTAAA
90325 GTTATGCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (18 bp):
TTTAAAAAACACTTTTAC
Found at i:90780 original size:17 final size:18
Alignment explanation
Indices: 90754--90792 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
90744 TGTGTTTTTA
90754 AAAAACACTTTTAGC-TT
1 AAAAACACTTTTAGCTTT
* *
90771 AAAAAGACTTTTGGCTTT
1 AAAAACACTTTTAGCTTT
90789 AAAA
1 AAAA
90793 TTGTGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAAACACTTTTAGCTTT
Found at i:91064 original size:2 final size:2
Alignment explanation
Indices: 91057--91085 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
91047 TTTTTATGGA
91057 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
91086 TTACTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:91124 original size:456 final size:464
Alignment explanation
Indices: 90475--91337 Score: 1058
Period size: 456 Copynumber: 1.9 Consensus size: 464
90465 TTATTCTTCT
* * * * *
90475 AAAACATACGATATACTTCCAATTTCTTTTTCATTTTCTCTTTCAAAGTTGGTTTTTTGGTTCTC
1 AAAACATACGATATACTTCCAATTTATTTTTCATTTTCTCTATCAAAGTTGGTTCTCTAGTTCTC
* * * * *
90540 CTTCTCTTTTTTTTTTTCTTTAATTCTTCCATTTTCTTCAAGGTTTTTGTTGCTCTCTCTCTCTC
66 C-TCTCTTTTTTATTTTCTTTAATTCTTCCATTTCCTTCAAGGTTTTTATGGATCTCTCTCTCTC
*
90605 TCTCCCTCCCTCTTTCTTTATCTTTCTACTCCCTTAATCACATTTTCTCATTGTAACTTTTCATT
130 TCT-CCT-CCTC-TTCTCTATCTTTCTACTCCCTTAATCACATTTTCTCATTGTAACTTTTCATT
* *
90670 TAAGTTTTTTCATT-TTTTT-CC-ATTTTAGGTTAAGCTATTTTTTATT-TTGATTTTTGTGTTA
192 TAA-TTTTTT-ATTGTTTTTCCCTATTTTAGGTTAAACTATTTTTGATTGTTGATTTTTGTGTTA
** * * *
90731 GATTTTATGTAGATGTGTTTTTAAAAAACACTTTTAGCTT-AAAAAGACTTTTGGCTTTAAAATT
255 GATTTTATGTAGATGTAATTTTAAAAAACACTTTTAG-TTAAAAAACACTTTTGACTTTAAAACT
** * * * * *
90795 GTGTTAAACAATCAT-TATTTACTTGAAATTTTTTACTTCTGAAAAGCATGTTTGCTCATATAGA
319 GTCCTAAACAAACGTAT-TTTACTTGAAAATTTTGACTTCTAAAAAGCATGTTTGCT-ATA-A-A
90859 AAAGCTAAAAATTTTAAATTTTTTTTTTAACCAAAAGCACTTTTGACTATTAATTTATTTTTTTA
380 AAAGCTAAAAATTTTAAATTTTTTTTTTAACCAAAAGCACTTTTGACTATTAATTTATTTTTTTA
90924 TCTTCAATTTTTCTTCTCCC
445 TCTTCAATTTTTCTTCTCCC
* *
90944 AAAACATA-G-TATACTTTCAATTTATTTTTCATTTTTTCTATCAAAGTTGGTTCTCTAGTTCT-
1 AAAACATACGATATACTTCCAATTTATTTTTCATTTTCTCTATCAAAGTTGGTTCTCTAGTTCTC
* * *
91006 C-CTC-TTTTTATTTTCTTTAATTTTTTCATTTCCTTTTAAGGTTTTTATGGATCTCTCTCTCTC
66 CTCTCTTTTTTATTTTCTTTAATTCTTCCATTTCC-TTCAAGGTTTTTATGGATCTCTCTCTCTC
* *
91069 TCT-CT-CTC-TCTCTCTC-TT-TACTCCCTTAATCACATCTTT-TCATTTTAACTTTTCATTTA
130 TCTCCTCCTCTTCTCTATCTTTCTACTCCCTTAATCACAT-TTTCTCATTGTAACTTTTCATTTA
* * * * *
91128 ATTTTTTTTTGTTTTTCCCTATTTTAGGTTAAATTATTTTTGGTTGTTGCTTTTTGTGTTAGGTT
194 ATTTTTTATTGTTTTTCCCTATTTTAGGTTAAACTATTTTTGATTGTTGATTTTTGTGTTAGATT
* * * *
91193 TTATGTAGTTGTAATTTTGAAAAACATTTTTAGTTAAAAAAACACTTTTGACTTTAAACCTGTCC
259 TTATGTAGATGTAATTTTAAAAAACACTTTTAGTT-AAAAAACACTTTTGACTTTAAAACTGTCC
* * * * *
91258 TAAATAAACGTATTTTGCTTGAAAATTTTGACTTTTAAAAATCATTTTTGCTATAAAAAAGCTAA
323 TAAACAAACGTATTTTACTTGAAAATTTTGACTTCTAAAAAGCATGTTTGCTATAAAAAAGCTAA
*
91323 AAATTTTAACTTTTT
388 AAATTTTAAATTTTT
91338 GCTTTTAGCT
Statistics
Matches: 338, Mismatches: 47, Indels: 31
0.81 0.11 0.07
Matches are distributed among these distances:
454 2 0.01
455 11 0.03
456 62 0.18
457 29 0.09
458 54 0.16
459 62 0.18
460 4 0.01
462 2 0.01
463 25 0.07
464 31 0.09
466 1 0.00
467 46 0.14
468 1 0.00
469 8 0.02
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (464 bp):
AAAACATACGATATACTTCCAATTTATTTTTCATTTTCTCTATCAAAGTTGGTTCTCTAGTTCTC
CTCTCTTTTTTATTTTCTTTAATTCTTCCATTTCCTTCAAGGTTTTTATGGATCTCTCTCTCTCT
CTCCTCCTCTTCTCTATCTTTCTACTCCCTTAATCACATTTTCTCATTGTAACTTTTCATTTAAT
TTTTTATTGTTTTTCCCTATTTTAGGTTAAACTATTTTTGATTGTTGATTTTTGTGTTAGATTTT
ATGTAGATGTAATTTTAAAAAACACTTTTAGTTAAAAAACACTTTTGACTTTAAAACTGTCCTAA
ACAAACGTATTTTACTTGAAAATTTTGACTTCTAAAAAGCATGTTTGCTATAAAAAAGCTAAAAA
TTTTAAATTTTTTTTTTAACCAAAAGCACTTTTGACTATTAATTTATTTTTTTATCTTCAATTTT
TCTTCTCCC
Found at i:92060 original size:18 final size:19
Alignment explanation
Indices: 92037--92080 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
92027 TAATTGTGCT
* *
92037 TTTAAAAAGCACTTTT-AG
1 TTTAAAAAACACTTTTGAC
92055 TTTAAAAAACACTTTTGAC
1 TTTAAAAAACACTTTTGAC
92074 TTTAAAA
1 TTTAAAA
92081 TTGTACTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (19 bp):
TTTAAAAAACACTTTTGAC
Found at i:92517 original size:17 final size:18
Alignment explanation
Indices: 92486--92519 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
92476 AGTTGTAATT
92486 TTGAAAAATACTTTTGAC
1 TTGAAAAATACTTTTGAC
*
92504 TTGAAAACTA-TTTTGA
1 TTGAAAAATACTTTTGA
92520 ACAAACACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (18 bp):
TTGAAAAATACTTTTGAC
Found at i:97335 original size:29 final size:28
Alignment explanation
Indices: 97291--97345 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
97281 AACTTTAAAA
97291 TATTTAATTAAATTATCAAAATATTATT
1 TATTTAATTAAATTATCAAAATATTATT
*
97319 TATTCTAATTAAGTTATCAAAATATTA
1 TATT-TAATTAAATTATCAAAATATTA
97346 GTGTAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TATTTAATTAAATTATCAAAATATTATT
Found at i:97948 original size:18 final size:17
Alignment explanation
Indices: 97925--97959 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
97915 AATAAATATT
97925 TAATTAAATAATTTTAAA
1 TAATTAAA-AATTTTAAA
*
97943 TAATTAAAATTTTTAAA
1 TAATTAAAAATTTTAAA
97960 CACTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTAAAAATTTTAAA
Found at i:105814 original size:84 final size:84
Alignment explanation
Indices: 105661--105827 Score: 282
Period size: 84 Copynumber: 2.0 Consensus size: 84
105651 GGAGCTTTCA
* * *
105661 TTCCGCGTTTTACTATGTTTTTTTTTGGATTAATTTCATCATATCTCCTTAAGCTATGACCCAAA
1 TTCCGCGTTTTACTATATATTTTTTTGGATTAATTTCATCATATCTCCTTAAACTATGACCCAAA
105726 TTTTAGATTGATCCCAAAC
66 TTTTAGATTGATCCCAAAC
*
105745 TTCCGCTTTTTACTATATATTTTTTTGGATTAATTTCATCA-ATCTCCTTAAACTATGACCCAAA
1 TTCCGCGTTTTACTATATATTTTTTTGGATTAATTTCATCATATCTCCTTAAACTATGACCCAAA
105809 TTTTTAGATTGATCCCAAA
66 -TTTTAGATTGATCCCAAA
105828 TTTCAGTATT
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 22 0.28
84 56 0.72
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (84 bp):
TTCCGCGTTTTACTATATATTTTTTTGGATTAATTTCATCATATCTCCTTAAACTATGACCCAAA
TTTTAGATTGATCCCAAAC
Found at i:110755 original size:78 final size:79
Alignment explanation
Indices: 110625--110782 Score: 273
Period size: 78 Copynumber: 2.0 Consensus size: 79
110615 TTCCTTAGTG
*
110625 TCTTAACCCAGAGCATCTCCGGGTCAACAACAAGTTTATAGCCCAACTTCAATAGGAATAAGAAA
1 TCTTAACCCAGAGCACCTCCGGGTCAACAACAAGTTTATAGCCCAACTTCAATAGGAATAAGAAA
*
110690 TTTTGATCCTGTAA
66 TTCTGATCCTGTAA
*
110704 TCTTAACCCAGAGCACCTCC-GTTCAACAACAAGTTTATAGCCCAACTTCAATAGGAATAAGAAA
1 TCTTAACCCAGAGCACCTCCGGGTCAACAACAAGTTTATAGCCCAACTTCAATAGGAATAAGAAA
*
110768 TTCTGATCTTGTAA
66 TTCTGATCCTGTAA
110782 T
1 T
110783 TTCCTGACGC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
78 56 0.75
79 19 0.25
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (79 bp):
TCTTAACCCAGAGCACCTCCGGGTCAACAACAAGTTTATAGCCCAACTTCAATAGGAATAAGAAA
TTCTGATCCTGTAA
Found at i:111414 original size:267 final size:267
Alignment explanation
Indices: 110939--111474 Score: 1054
Period size: 267 Copynumber: 2.0 Consensus size: 267
110929 GTCGTAGTCA
110939 TAAAATAATTTGGAATGGAAAGAAGCACAGATTTCACAAGCGTTAATCTACCCGCAAAGGATAAA
1 TAAAATAATTTGGAATGGAAAGAAGCACAGATTTCACAAGCGTTAATCTACCCGCAAAGGATAAA
111004 TTCCGGCTCTCTCATCCACTTAAACGATCTCGGACCTTATCAACAATAAAAGAAAAGGTGCTCCT
66 TTCCGGCTCTCTCATCCACTTAAACGATCTCGGACCTTATCAACAATAAAAGAAAAGGTGCTCCT
*
111069 GCTCACCCTTTGATGAAATACAGGCATGTCAAGATACTCACCCAAATAAGTTACTTGATGAAACC
131 GCTCACCCTTTGATGAAATAAAGGCATGTCAAGATACTCACCCAAATAAGTTACTTGATGAAACC
111134 CAAGTGTAGCACAGATTTCCTCTCTAACATTATCTCCGACATTATGGGAGAATAAGACTTGTATC
196 CAAGTGTAGCACAGATTTCCTCTCTAACATTATCTCCGACATTATGGGAGAATAAGACTTGTATC
111199 TTTCGAT
261 TTTCGAT
111206 TAAAATAATTTGGAATGGAAAGAAGCACAGATTTCACAAGCGTTAATCTACCCGCAAAGGATAAA
1 TAAAATAATTTGGAATGGAAAGAAGCACAGATTTCACAAGCGTTAATCTACCCGCAAAGGATAAA
111271 TTCCGGCTCTCTCATCCACTTAAACGATCTCGGACCTTATCAACAATAAAAGAAAAGGTGCTCCT
66 TTCCGGCTCTCTCATCCACTTAAACGATCTCGGACCTTATCAACAATAAAAGAAAAGGTGCTCCT
*
111336 GCTCACCCTTTGATGAAATAAAGGTATGTCAAGATACTCACCCAAATAAGTTACTTGATGAAACC
131 GCTCACCCTTTGATGAAATAAAGGCATGTCAAGATACTCACCCAAATAAGTTACTTGATGAAACC
111401 CAAGTGTAGCACAGATTTCCTCTCTAACATTATCTCCGACATTATGGGAGAATAAGACTTGTATC
196 CAAGTGTAGCACAGATTTCCTCTCTAACATTATCTCCGACATTATGGGAGAATAAGACTTGTATC
111466 TTTCGAT
261 TTTCGAT
111473 TA
1 TA
111475 TTCACTTTAT
Statistics
Matches: 267, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 267 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (267 bp):
TAAAATAATTTGGAATGGAAAGAAGCACAGATTTCACAAGCGTTAATCTACCCGCAAAGGATAAA
TTCCGGCTCTCTCATCCACTTAAACGATCTCGGACCTTATCAACAATAAAAGAAAAGGTGCTCCT
GCTCACCCTTTGATGAAATAAAGGCATGTCAAGATACTCACCCAAATAAGTTACTTGATGAAACC
CAAGTGTAGCACAGATTTCCTCTCTAACATTATCTCCGACATTATGGGAGAATAAGACTTGTATC
TTTCGAT
Found at i:114644 original size:23 final size:23
Alignment explanation
Indices: 114617--114660 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
114607 TTATTTAAAC
114617 AAATACTCATATTTATATAATTA
1 AAATACTCATATTTATATAATTA
* *
114640 AAATATTCATATTTTTATAAT
1 AAATACTCATATTTATATAAT
114661 AGGTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATACTCATATTTATATAATTA
Found at i:124301 original size:31 final size:31
Alignment explanation
Indices: 124234--124301 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
124224 TTCAATAAAT
**
124234 TTTTTTGAATAATTCAATAGTTTAAATGAAA
1 TTTTTTGAATAATTCAATAGACTAAATGAAA
* * *
124265 ATTTTTGAATAATTCAGT-GACTAAATTGTAA
1 TTTTTTGAATAATTCAATAGACTAAA-TGAAA
124296 TTTTTT
1 TTTTTT
124302 TAATTAAGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (31 bp):
TTTTTTGAATAATTCAATAGACTAAATGAAA
Found at i:125521 original size:21 final size:22
Alignment explanation
Indices: 125486--125536 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
125476 ATAACTTTAA
125486 AATTTTTATAAATTTTGTCT-AT
1 AATTTTTATAAATTTT-TCTAAT
* *
125508 AATTTTTAT-GATTTTTTTAAT
1 AATTTTTATAAATTTTTCTAAT
125529 AATTTTTA
1 AATTTTTA
125537 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.58
22 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (22 bp):
AATTTTTATAAATTTTTCTAAT
Found at i:125523 original size:22 final size:21
Alignment explanation
Indices: 125481--125536 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
125471 AAATTATAAC
125481 TTTAA-AATTTTTATAAATTT
1 TTTAATAATTTTTATAAATTT
* *
125501 TGTCT-ATAATTTTTATGATTTT
1 T-T-TAATAATTTTTATAAATTT
125523 TTTAATAATTTTTA
1 TTTAATAATTTTTA
125537 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 13 0.43
22 15 0.50
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTAATAATTTTTATAAATTT
Found at i:131276 original size:60 final size:60
Alignment explanation
Indices: 131126--131284 Score: 209
Period size: 59 Copynumber: 2.7 Consensus size: 60
131116 TTTGGTACCG
* * * *
131126 GAACTTGACATTTTTT--TAATTTGGTACCTAA-ATTTTCTTTTGACTCAATTTGATACAT
1 GAACTTGACATTTTTTCCTAATTTGGTACCTAAGCTTTT-TTTGGACCCAATTTGACACAT
* *
131184 GAACTTGACA-TTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGGCACTT
1 GAACTTGACATTTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGACACAT
* *
131243 GAACTTGGCATTTTTTCCTAATTTAGTACCTAAGCTTTTTTT
1 GAACTTGACATTTTTTCCTAATTTGGTACCTAAGCTTTTTTT
131285 TAAGATTCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
57 5 0.06
58 10 0.11
59 40 0.45
60 34 0.38
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.47
Consensus pattern (60 bp):
GAACTTGACATTTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGACACAT
Found at i:131569 original size:30 final size:30
Alignment explanation
Indices: 131535--131638 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
131525 AAAAGAAAGT
131535 GTCAAGTTTAGGTACTAAATTAGGAAAAAA
1 GTCAAGTTTAGGTACTAAATTAGGAAAAAA
*
131565 GTCAAGTTTAAGTA-TCAAATT-GGACCAAAAA
1 GTCAAGTTTAGGTACT-AAATTAGGA--AAAAA
* *
131596 ---AAGTTTAGGTACCAAATTAAGAAAAAA
1 GTCAAGTTTAGGTACTAAATTAGGAAAAAA
*
131623 TGTCAAGTTCAGGTAC
1 -GTCAAGTTTAGGTAC
131639 CATATGTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
27 5 0.08
28 15 0.25
29 6 0.10
30 18 0.30
31 16 0.27
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (30 bp):
GTCAAGTTTAGGTACTAAATTAGGAAAAAA
Found at i:131584 original size:89 final size:90
Alignment explanation
Indices: 131453--131638 Score: 261
Period size: 89 Copynumber: 2.1 Consensus size: 90
131443 ATTAAAAAAA
131453 TAGGTACAAAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCCAAAAAAA-TTTAAGT
1 TAGGTACAAAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTGGA-CCAAAAAAAGTTTAAGT
* ** *
131517 ACGAGCTTAA-AAGAAAGTGTCAAGTT
65 ACCAAATTAAGAA-AAAATGTCAAGTT
* * *
131543 TAGGTACTAAATTAGGAAAAA-AGTCAAGTTTAAGTATCAAATTGGACCAAAAAAAGTTTAGGTA
1 TAGGTACAAAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCAAAAAAAGTTTAAGTA
131607 CCAAATTAAGAAAAAATGTCAAGTT
66 CCAAATTAAGAAAAAATGTCAAGTT
*
131632 CAGGTAC
1 TAGGTAC
131639 CATATGTTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
88 9 0.10
89 55 0.64
90 22 0.26
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (90 bp):
TAGGTACAAAATTAGGAAAAAGAGTCAAGTTCAAGTATCAAATTGGACCAAAAAAAGTTTAAGTA
CCAAATTAAGAAAAAATGTCAAGTT
Found at i:131611 original size:28 final size:28
Alignment explanation
Indices: 131537--131640 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 28
131527 AAGAAAGTGT
*
131537 CAAGTTTAGGTACTAAATTAGGAAAAAA
1 CAAGTTTAGGTACCAAATTAGGAAAAAA
* *
131565 GTCAAGTTTAAGTATCAAATT-GGACCAAAAA
1 --CAAGTTTAGGTACCAAATTAGGA--AAAAA
*
131596 -AAGTTTAGGTACCAAATTAAGAAAAAA
1 CAAGTTTAGGTACCAAATTAGGAAAAAA
*
131623 TGTCAAGTTCAGGTACCA
1 ---CAAGTTTAGGTACCA
131641 TATGTTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
27 5 0.08
28 16 0.27
29 5 0.08
30 16 0.27
31 18 0.30
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (28 bp):
CAAGTTTAGGTACCAAATTAGGAAAAAA
Found at i:132190 original size:11 final size:10
Alignment explanation
Indices: 132142--132189 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
132132 CTGCTGATGT
132142 TATTTTTTAA
1 TATTTTTTAA
*
132152 TTTTTTTTAA
1 TATTTTTTAA
*
132162 TA-TTTATAA
1 TATTTTTTAA
132171 TA-TTTTTATA
1 TATTTTTTA-A
132181 TATTTTTTA
1 TATTTTTTA
132190 TTTATTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
9 13 0.41
10 13 0.41
11 6 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTTTTTAA
Found at i:134861 original size:18 final size:18
Alignment explanation
Indices: 134838--134874 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
134828 ACAATTTATA
134838 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
134856 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
134874 T
1 T
134875 TCATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:135774 original size:8 final size:8
Alignment explanation
Indices: 135761--135786 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
135751 ATATTTATTT
135761 TACAAATA
1 TACAAATA
135769 TACAAATA
1 TACAAATA
135777 TACAAATA
1 TACAAATA
135785 TA
1 TA
135787 ATTTTTACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (8 bp):
TACAAATA
Found at i:142626 original size:17 final size:18
Alignment explanation
Indices: 142592--142627 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
142582 TGAATTTCTA
142592 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
142610 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
142627 T
1 T
142628 AAGTCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:142869 original size:25 final size:25
Alignment explanation
Indices: 142835--142884 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
142825 TCCTTAATTC
142835 ACTATTTTGTTCAACATGAACTATG
1 ACTATTTTGTTCAACATGAACTATG
142860 ACTATTTTGTTCAACATGAACTATG
1 ACTATTTTGTTCAACATGAACTATG
142885 TTCAAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (25 bp):
ACTATTTTGTTCAACATGAACTATG
Found at i:146838 original size:16 final size:17
Alignment explanation
Indices: 146805--146842 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
146795 AATACGCTCT
146805 TTCT-TTTGTTCTCCTA
1 TTCTCTTTGTTCTCCTA
*
146821 TTCTCTTTGTTCT-TTA
1 TTCTCTTTGTTCTCCTA
146837 TTCTCT
1 TTCTCT
146843 ATCATTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.05, C:0.24, G:0.05, T:0.66
Consensus pattern (17 bp):
TTCTCTTTGTTCTCCTA
Found at i:147164 original size:13 final size:13
Alignment explanation
Indices: 147146--147175 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
147136 AATTAGCATA
*
147146 TAAAATAGAAATT
1 TAAAATAAAAATT
147159 TAAAATAAAAATT
1 TAAAATAAAAATT
147172 TAAA
1 TAAA
147176 TTTCGTGCAA
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:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
TAAAATAAAAATT
Found at i:147200 original size:60 final size:60
Alignment explanation
Indices: 147116--147232 Score: 216
Period size: 60 Copynumber: 1.9 Consensus size: 60
147106 ATACTAAATT
* *
147116 TTTCTTGCAACATTATCACTAATTAGCATATAAAATAGAAATTTAAAATAAAAATTTAAA
1 TTTCGTGCAACATTATCACTAATTAGAATATAAAATAGAAATTTAAAATAAAAATTTAAA
147176 TTTCGTGCAACATTATCACTAATTAGAATATAAAATAGAAATTTAAAATAAAAATTT
1 TTTCGTGCAACATTATCACTAATTAGAATATAAAATAGAAATTTAAAATAAAAATTT
147233 GAAAACATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (60 bp):
TTTCGTGCAACATTATCACTAATTAGAATATAAAATAGAAATTTAAAATAAAAATTTAAA
Found at i:150977 original size:13 final size:13
Alignment explanation
Indices: 150961--150985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
150951 TTCACCACAC
150961 TTTTTAAAAGCAT
1 TTTTTAAAAGCAT
150974 TTTTTAAAAGCA
1 TTTTTAAAAGCA
150986 ATACTAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTTAAAAGCAT
Found at i:157061 original size:43 final size:43
Alignment explanation
Indices: 157002--157104 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
156992 CAACCAAGTT
** *
157002 ATAAGTTCTTCCATTTACAAATAATCCTATGCTCTTGCTGAGAC
1 ATAAG-TCTTCCATTTACAAATAATCCTATGCTCTACCCGAGAC
* * * *
157046 ATAGGTCTTCTATTTATAAATAATCTTATGCTCTACCCGAGAC
1 ATAAGTCTTCCATTTACAAATAATCCTATGCTCTACCCGAGAC
157089 ATAAGTCTTCCATTTA
1 ATAAGTCTTCCATTTA
157105 ATAATCACCA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 46 0.92
44 4 0.08
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (43 bp):
ATAAGTCTTCCATTTACAAATAATCCTATGCTCTACCCGAGAC
Found at i:173766 original size:15 final size:15
Alignment explanation
Indices: 173746--173776 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
173736 AAAAGAAAGG
173746 ATAATAGAAAAAATA
1 ATAATAGAAAAAATA
*
173761 ATAATAGATAAAATA
1 ATAATAGAAAAAATA
173776 A
1 A
173777 AGAAAACAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
ATAATAGAAAAAATA
Found at i:174589 original size:30 final size:30
Alignment explanation
Indices: 174555--174719 Score: 185
Period size: 30 Copynumber: 5.5 Consensus size: 30
174545 CTATTTTTGT
*
174555 TAAAAATTATATTTTAACCCTTAAACTTTC
1 TAAAAATTACATTTTAACCCTTAAACTTTC
* *
174585 TAAAAATTATATTTTGACCCTTAAACTCTTC
1 TAAAAATTACATTTTAACCCTTAAACT-TTC
* *
174616 -CAAAATTACATTTTAACCCTTAAA-TTTT
1 TAAAAATTACATTTTAACCCTTAAACTTTC
* *
174644 TACAAAATTACATTTTGATCCTTAAACTTTTC
1 TA-AAAATTACATTTTAACCCTTAAAC-TTTC
* *
174676 T-AAAATTACATGTTAACCCCTAAACTTTTC
1 TAAAAATTACATTTTAACCCTTAAAC-TTTC
174706 T-AAAATTACATTTT
1 TAAAAATTACATTTT
174720 GCCCCAAAAT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.02
29 1 0.01
30 106 0.91
31 3 0.03
32 4 0.03
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAAAATTACATTTTAACCCTTAAACTTTC
Found at i:174651 original size:60 final size:60
Alignment explanation
Indices: 174557--174720 Score: 215
Period size: 60 Copynumber: 2.7 Consensus size: 60
174547 ATTTTTGTTA
* * *
174557 AAAATTATATTTTAACCCTTAAACTTTCTA-AAAATTATATTTTGACCCTTAAACTCTTCC
1 AAAATTACATTTTAACCCTTAAA-TTTTTACAAAATTACATTTTGACCCTTAAACTCTTCC
* * *
174617 AAAATTACATTTTAACCCTTAAATTTTTACAAAATTACATTTTGATCCTTAAACTTTTCT
1 AAAATTACATTTTAACCCTTAAATTTTTACAAAATTACATTTTGACCCTTAAACTCTTCC
* * *
174677 AAAATTACATGTTAACCCCTAAACTTTT-CTAAAATTACATTTTG
1 AAAATTACATTTTAACCCTTAAATTTTTAC-AAAATTACATTTTG
174721 CCCCAAAATT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
59 6 0.06
60 87 0.94
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.42
Consensus pattern (60 bp):
AAAATTACATTTTAACCCTTAAATTTTTACAAAATTACATTTTGACCCTTAAACTCTTCC
Found at i:174833 original size:13 final size:15
Alignment explanation
Indices: 174803--174835 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
174793 TTTTTTTTTT
174803 TTTTTGTATTCGATG
1 TTTTTGTATTCGATG
174818 TTTTTG-ATTC-ATG
1 TTTTTGTATTCGATG
174831 TTTTT
1 TTTTT
174836 TCGTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.12, C:0.06, G:0.15, T:0.67
Consensus pattern (15 bp):
TTTTTGTATTCGATG
Found at i:174836 original size:14 final size:16
Alignment explanation
Indices: 174802--174842 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
174792 ATTTTTTTTT
174802 TTTTTTGTATTCGATG
1 TTTTTTGTATTCGATG
174818 -TTTTTG-ATTC-ATG
1 TTTTTTGTATTCGATG
174831 TTTTTTCGTATT
1 TTTTTT-GTATT
174843 TTGTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.14
14 9 0.41
15 7 0.32
16 3 0.14
ACGTcount: A:0.12, C:0.07, G:0.15, T:0.66
Consensus pattern (16 bp):
TTTTTTGTATTCGATG
Found at i:182957 original size:44 final size:44
Alignment explanation
Indices: 182868--182955 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
182858 TAGTGTCGAG
* * *
182868 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
182912 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
182956 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:184467 original size:6 final size:6
Alignment explanation
Indices: 184456--184500 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
184446 TGATCAAAAT
* * *
184456 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
184501 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:189690 original size:48 final size:47
Alignment explanation
Indices: 189619--189785 Score: 158
Period size: 48 Copynumber: 3.7 Consensus size: 47
189609 TTCAAACCCT
189619 ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGATC
1 ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAA-CAATAAAACGATC
**
189667 ATCTTCCTGATGAGATACAGAGAAGT--G---AAC--TAATCCG--C
1 ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAACAATAAAACGATC
* * * *
189705 --CTTCTTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGATC
1 ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAA-CAATAAAACGATC
* * *
189751 ACCTTCCTGATGAGATACAGAGAAGTAGATCAAAC
1 ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAC
189786 CAAAGAAGCG
Statistics
Matches: 98, Mismatches: 9, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
36 23 0.23
38 1 0.01
40 5 0.05
41 2 0.02
42 2 0.02
43 2 0.02
44 4 0.04
46 2 0.02
47 1 0.01
48 56 0.57
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (47 bp):
ATCTTCCTGATGAGATACAGAGAAGTGGGTCAAACAATAAAACGATC
Found at i:189767 original size:84 final size:84
Alignment explanation
Indices: 189621--189776 Score: 258
Period size: 84 Copynumber: 1.9 Consensus size: 84
189611 CAAACCCTAT
* *
189621 CTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCACCTTCCTGATGAGATACA
189686 GAGAAGTGAACTAATCCGC
66 GAGAAGTGAACTAATCCGC
* * * *
189705 CTTCTTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGATCACCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCACCTTCCTGATGAGATACA
189770 GAGAAGT
66 GAGAAGT
189777 AGATCAAACC
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (84 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAACGATCACCTTCCTGATGAGATACA
GAGAAGTGAACTAATCCGC
Found at i:189794 original size:48 final size:48
Alignment explanation
Indices: 189704--189796 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
189694 AACTAATCCG
* * * *
189704 CCTTCTTGATGAGATACAGAGAAGTGGATCAAATCAATGAAGCGATCA
1 CCTTCCTGATGAGATACAGAGAAGTAGATCAAACCAAAGAAGCGATCA
189752 CCTTCCTGATGAGATACAGAGAAGTAGATCAAACCAAAGAAGCGA
1 CCTTCCTGATGAGATACAGAGAAGTAGATCAAACCAAAGAAGCGA
189797 AGCTCAATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (48 bp):
CCTTCCTGATGAGATACAGAGAAGTAGATCAAACCAAAGAAGCGATCA
Found at i:189981 original size:85 final size:85
Alignment explanation
Indices: 189828--189992 Score: 240
Period size: 85 Copynumber: 1.9 Consensus size: 85
189818 CAAACCCTAT
* * * *
189828 CTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGATCATCTTCCTAATGAGATATA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCACCTTCCTAATGAGATACA
*
189893 GAGAAGTGGACCAAATCCGC
66 GAGAAGTAGACCAAATCCGC
* * * * *
189913 CTTCTTGATGAGATATAGAGAAGTGGATCAAATCAATGAAGCGATCACCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCACCTTCCTAATGAGATACA
189978 GAGAAGTAGACCAAA
66 GAGAAGTAGACCAAA
189993 CCAAAGAAGC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGATCACCTTCCTAATGAGATACA
GAGAAGTAGACCAAATCCGC
Found at i:190010 original size:208 final size:208
Alignment explanation
Indices: 189546--190313 Score: 1214
Period size: 208 Copynumber: 3.7 Consensus size: 208
189536 AAAAGGTCAT
* * * *
189546 CTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAATCTCAATACGAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCGAAGCTCAATACAAATGAGACTT
* * *
189611 CAAACCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAACGATCATCTTCCTG
66 CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGACCATCTTCCTG
* *
189676 ATGAGATACAGAGAAGT-GAACTAATCCGCCTTCTTGATGAGATACAGAGAAGTGGATCAAATCA
131 ATGAGATACAGAGAAGTGGACCAAATCCGCCTTCTTGATGAGATACAGAGAAGTGGATCAAATCA
189740 ATGAAGCGATCAC
196 ATGAAGCGATCAC
* *
189753 CTTCCTGATGAGATACAGAGAAGTAGATCAAACCAAAGAAGCGAAGCTCAATACGAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCGAAGCTCAATACAAATGAGACTT
* * * *
189818 CAAACCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGTGATCATCTTCCTA
66 CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGACCATCTTCCTG
* *
189883 ATGAGATATAGAGAAGTGGACCAAATCCGCCTTCTTGATGAGATATAGAGAAGTGGATCAAATCA
131 ATGAGATACAGAGAAGTGGACCAAATCCGCCTTCTTGATGAGATACAGAGAAGTGGATCAAATCA
189948 ATGAAGCGATCAC
196 ATGAAGCGATCAC
*
189961 CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCAAAGCTCAATACAAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCGAAGCTCAATACAAATGAGACTT
* * *
190026 CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAATGACCATTTTCTTG
66 CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGACCATCTTCCTG
* *
190091 ATGAGATACAGAGAAGTGGACCAAATCTGCCTTCTTGATGAGATACAGAGAAGTGGATTAAATCA
131 ATGAGATACAGAGAAGTGGACCAAATCCGCCTTCTTGATGAGATACAGAGAAGTGGATCAAATCA
* *
190156 ATGAAGCGGTCAT
196 ATGAAGCGATCAC
* * ** *
190169 CTTCTTGATGAGATATAGAGAAGTAGACCAAATTAACGAAGCGAAGCTCAATACAAATGAGACTT
1 CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCGAAGCTCAATACAAATGAGACTT
* * * *
190234 CAAACCCCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGTGACCATCTTCCTG
66 CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGACCATCTTCCTG
*
190299 ATGAGGTACAGAGAA
131 ATGAGATACAGAGAA
190314 ATGAGTCAAA
Statistics
Matches: 519, Mismatches: 41, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
207 139 0.27
208 380 0.73
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.22
Consensus pattern (208 bp):
CTTCCTGATGAGATACAGAGAAGTAGACCAAACCAAAGAAGCGAAGCTCAATACAAATGAGACTT
CAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGACCATCTTCCTG
ATGAGATACAGAGAAGTGGACCAAATCCGCCTTCTTGATGAGATACAGAGAAGTGGATCAAATCA
ATGAAGCGATCAC
Found at i:190311 original size:48 final size:48
Alignment explanation
Indices: 190240--190361 Score: 226
Period size: 48 Copynumber: 2.5 Consensus size: 48
190230 ACTTCAAACC
* *
190240 CCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGTGA
1 CCATCTTCCTGATGAGGTACAGAGAAATGAGTCAAAGCAATAAAGTGA
190288 CCATCTTCCTGATGAGGTACAGAGAAATGAGTCAAAGCAATAAAGTGA
1 CCATCTTCCTGATGAGGTACAGAGAAATGAGTCAAAGCAATAAAGTGA
190336 CCATCTTCCTGATGAGGTACAGAGAA
1 CCATCTTCCTGATGAGGTACAGAGAA
190362 GTGGACCAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (48 bp):
CCATCTTCCTGATGAGGTACAGAGAAATGAGTCAAAGCAATAAAGTGA
Found at i:190324 original size:256 final size:256
Alignment explanation
Indices: 190032--190628 Score: 822
Period size: 256 Copynumber: 2.3 Consensus size: 256
190022 ACTTCAAACC
* * * *
190032 CCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGAAATAAAATGACCATTTTCTTGATGAGA
1 CCATCTTCCTGATGAGATACAGAGAAATGAGTCAAAGAAATAAAATGACCATCTTCCTGATGAGA
*
190097 TACAGAGAAGTGGACCAAA-TCTGCCTTCTTGATGAGATACAGAGAAGTGGATTAAATCAATGAA
66 TACAGAGAAGTGGACCAAATTC-GCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAA
** * * * * *
190161 GCGGTCATCTTCTTGATGAGATATAGAGAAGTAGACCAAATTAACGAAGCGAAGCTCAATACA-A
130 GCGACCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAGCTCAATA-AGA
*
190225 ATGAGACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGTGA
194 ATGAGACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGA
* * * *
190288 CCATCTTCCTGATGAGGTACAGAGAAATGAGTCAAAGCAATAAAGTGACCATCTTCCTGATGAGG
1 CCATCTTCCTGATGAGATACAGAGAAATGAGTCAAAGAAATAAAATGACCATCTTCCTGATGAGA
* *
190353 TACAGAGAAGTGGACCAAATTCGGCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAT
66 TACAGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAG
* *
190418 CGACCATCTTCCTAATGAGATACAAAGAAGTAGATCAAATCAACGAAGCGAAGCTTAATAAGAAT
131 CGACCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAGCTCAATAAGAAT
* * *
190483 GAGAGTTCAAACCTCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGG
196 GAGACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGA
* * * * ** * **
190544 TCATCTTCCTGATGAGATACAGAGAAGTG-GACCGAATCAATGAAATGGTCATCTTCCTGATGAG
1 CCATCTTCCTGATGAGATACAGAGAAATGAG-TCAAAGAAATAAAATGACCATCTTCCTGATGAG
* * *
190608 ATATAAAGAAGTAGACCAAAT
65 ATACAGAGAAGTGGACCAAAT
190629 CAATGAAGTG
Statistics
Matches: 300, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
255 2 0.01
256 296 0.99
257 2 0.01
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (256 bp):
CCATCTTCCTGATGAGATACAGAGAAATGAGTCAAAGAAATAAAATGACCATCTTCCTGATGAGA
TACAGAGAAGTGGACCAAATTCGCCTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAAG
CGACCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAGCTCAATAAGAAT
GAGACTTCAAACCCCATCTTCTTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGA
Found at i:190396 original size:85 final size:85
Alignment explanation
Indices: 190292--190457 Score: 210
Period size: 85 Copynumber: 2.0 Consensus size: 85
190282 AAGTGACCAT
* * *
190292 CTTCCTGATGAGGTACAGAGAAAT-GAGTCAAAGCAATAAAGT-GACCATCTTCCTGATGAGGTA
1 CTTCCTGATGAGATACAGAGAAATGGA-TCAAAGCAATAAA-TCGACCATCTTCCTAATGAGATA
* *
190355 CAGAGAAGTGGACCAAATTCGG
64 CAAAGAAGTAGACCAAATTCGG
* * * *
190377 CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAATCGACCATCTTCCTAATGAGATACA
1 CTTCCTGATGAGATACAGAGAAATGGATCAAAGCAATAAATCGACCATCTTCCTAATGAGATACA
*
190442 AAGAAGTAGATCAAAT
66 AAGAAGTAGACCAAAT
190458 CAACGAAGCG
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 1 0.01
85 66 0.96
86 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAATGGATCAAAGCAATAAATCGACCATCTTCCTAATGAGATACA
AAGAAGTAGACCAAATTCGG
Found at i:190567 original size:48 final size:48
Alignment explanation
Indices: 190496--190635 Score: 149
Period size: 48 Copynumber: 2.9 Consensus size: 48
190486 AGTTCAAACC
* *
190496 TCATCTTCTTGATGAGATACAGAGAAAT-GAGTCAAAGCAAT-AAAGCGG
1 TCATCTTCCTGATGAGATACAGAGAAATGGA-CCAAAGCAATGAAA-CGG
* * * *
190544 TCATCTTCCTGATGAGATACAGAGAAGTGGACCGAATCAATGAAATGG
1 TCATCTTCCTGATGAGATACAGAGAAATGGACCAAAGCAATGAAACGG
* * * * *
190592 TCATCTTCCTGATGAGATATAAAGAAGTAGACCAAATCAATGAA
1 TCATCTTCCTGATGAGATACAGAGAAATGGACCAAAGCAATGAA
190636 GTGAAGTTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
48 75 0.94
49 5 0.06
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (48 bp):
TCATCTTCCTGATGAGATACAGAGAAATGGACCAAAGCAATGAAACGG
Found at i:190666 original size:171 final size:172
Alignment explanation
Indices: 190377--190750 Score: 493
Period size: 171 Copynumber: 2.2 Consensus size: 172
190367 CCAAATTCGG
**
190377 CTTCCTGATGAGATACAGAGAAGTGGATTAAATCAATGAATCGACCATCTTCCTAATGAGATACA
1 CTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAATCGACCATCTTCCTAATGAGATACA
* * * ** *
190442 AAGAAGTAGATCAAATCAACGAAGCGAAGCTTAATAAGAATGAGAGTTCAAACCTC-ATCTTCTT
66 AAGAAGTAGACCAAATCAACGAAGCGAAGCTTAATAACAATGAAACCTCAAACCCCTATCTTCTT
*
190506 GATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGGTCAT
131 GATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGATCAT
* ** * *
190548 CTTCCTGATGAGATACAGAGAAGTGGACCGAATCAATGAAAT-GGTCATCTTCCTGATGAGATAT
1 CTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATG-AATCGACCATCTTCCTAATGAGATAC
* * ** *
190612 AAAGAAGTAGACCAAATCAATGAAGTGAAG-TTCAATGCCAGTGAAACCTCAAACCCCTATCTTC
65 AAAGAAGTAGACCAAATCAACGAAGCGAAGCTT-AATAACAATGAAACCTCAAACCCCTATCTTC
* * * *
190676 TTGATGAGATATAGAGAAGTGGGTCGAAGCAATAAAGCGATCAT
129 TTGATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGATCAT
*
190720 CTTCCTGATGAGATACAGAGAAGTAGACCAA
1 CTTCCTGATGAGATACAGAGAAGTGGACCAA
190751 GAGATGAAGC
Statistics
Matches: 175, Mismatches: 25, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
170 2 0.01
171 96 0.55
172 77 0.44
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (172 bp):
CTTCCTGATGAGATACAGAGAAGTGGACCAAATCAATGAATCGACCATCTTCCTAATGAGATACA
AAGAAGTAGACCAAATCAACGAAGCGAAGCTTAATAACAATGAAACCTCAAACCCCTATCTTCTT
GATGAGATACAGAGAAATGAGTCAAAGCAATAAAGCGATCAT
Found at i:191826 original size:30 final size:29
Alignment explanation
Indices: 191784--191924 Score: 124
Period size: 30 Copynumber: 4.8 Consensus size: 29
191774 TCCTATTTTA
*
191784 TTAAAAAATACATTTTAACCCCTAAACTT
1 TTAAAAATTACATTTTAACCCCTAAACTT
** *
191813 TCTAAAAATTACA-TTTAACATCTAAGCTCT
1 T-TAAAAATTACATTTTAACCCCTAAACT-T
** * * *
191843 TCCAAAATTATATTTTGACCCTTAAACTT
1 TTAAAAATTACATTTTAACCCCTAAACTT
191872 TTACAAAATTACATTTTAACGCCC-AAACTT
1 TTA-AAAATTACATTTTAAC-CCCTAAACTT
* *
191902 TTCCAAAATTACATTTTTACCCC
1 TT-AAAAATTACATTTTAACCCC
191925 GAACAAAAAC
Statistics
Matches: 87, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
29 26 0.30
30 59 0.68
31 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAAAATTACATTTTAACCCCTAAACTT
Found at i:191869 original size:59 final size:60
Alignment explanation
Indices: 191787--191924 Score: 163
Period size: 59 Copynumber: 2.3 Consensus size: 60
191777 TATTTTATTA
* * * *
191787 AAAAATACATTTTAACCCCTAAACTTTCTA-AAAATTACA-TTTAACATCTAAGCTCTTCC
1 AAAATTACATTTTAACCCCTAAACTTT-TACAAAATTACATTTTAACACCCAAACTCTTCC
* * * * *
191846 AAAATTATATTTTGACCCTTAAACTTTTACAAAATTACATTTTAACGCCCAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTACAAAATTACATTTTAACACCCAAACTCTTCC
*
191906 AAAATTACATTTTTACCCC
1 AAAATTACATTTTAACCCC
191925 GAACAAAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
58 2 0.03
59 32 0.49
60 31 0.48
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTTACAAAATTACATTTTAACACCCAAACTCTTCC
Found at i:194397 original size:17 final size:16
Alignment explanation
Indices: 194358--194399 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
194348 TTGAAAATTC
194358 ACCAAAAATTTTTTTA
1 ACCAAAAATTTTTTTA
**
194374 AAAAAAATATTTTTTTA
1 ACCAAAA-ATTTTTTTA
194391 ACCAAAAAT
1 ACCAAAAAT
194400 AGAATAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
ACCAAAAATTTTTTTA
Found at i:199898 original size:20 final size:21
Alignment explanation
Indices: 199873--199912 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
199863 CTAAATTTTA
199873 AAATTT-AAAAAATAAAAATT
1 AAATTTCAAAAAATAAAAATT
199893 AAATTTCAAAAAATAAAAAT
1 AAATTTCAAAAAATAAAAAT
199913 ACAGAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATTTCAAAAAATAAAAATT
Found at i:200965 original size:21 final size:20
Alignment explanation
Indices: 200928--200968 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
200918 TCTAGAGTTT
* *
200928 CCATTAATTTTTTATAATTG
1 CCATGAATTTTTCATAATTG
200948 CCATGAATATTTTCATAATTG
1 CCATGAAT-TTTTCATAATTG
200969 GATTGGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (20 bp):
CCATGAATTTTTCATAATTG
Found at i:201187 original size:6 final size:6
Alignment explanation
Indices: 201178--201211 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
201168 ATATATTTTC
*
201178 TTATTT TTATTT TTATTTT TTATTA TTATTT TTA
1 TTATTT TTATTT TTA-TTT TTATTT TTATTT TTA
201212 AATTAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:201199 original size:13 final size:13
Alignment explanation
Indices: 201181--201210 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
201171 TATTTTCTTA
*
201181 TTTTTATTTTTAT
1 TTTTTATTATTAT
201194 TTTTTATTATTAT
1 TTTTTATTATTAT
201207 TTTT
1 TTTT
201211 AAATTAAACC
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATTATTAT
Found at i:201206 original size:19 final size:20
Alignment explanation
Indices: 201171--201211 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
201161 TGAATATATA
*
201171 TATTTTCTTATTTTTATTTT
1 TATTTTCTTATTATTATTTT
201191 TATTTT-TTATTATTATTTT
1 TATTTTCTTATTATTATTTT
201210 TA
1 TA
201212 AATTAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TATTTTCTTATTATTATTTT
Found at i:203637 original size:32 final size:32
Alignment explanation
Indices: 203598--203668 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
203588 TTTTTAAAAG
* *
203598 TTGATTAATACAAA-TGTTTGAAGAAATTAGGA
1 TTGATTAATACAAACCG-TTGAAGAAATTAAGA
203630 TTGATTAATACAAACCGTTGAAGAAATTAAGA
1 TTGATTAATACAAACCGTTGAAGAAATTAAGA
203662 TTGATTA
1 TTGATTA
203669 GAAATTTAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 35 0.97
33 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (32 bp):
TTGATTAATACAAACCGTTGAAGAAATTAAGA
Found at i:205112 original size:17 final size:17
Alignment explanation
Indices: 205080--205113 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
205070 TCTGCCAAAG
*
205080 GGGTTCGCCAGGTATAA
1 GGGTTCGCCAAGTATAA
*
205097 GGGTTCGCCAATTATAA
1 GGGTTCGCCAAGTATAA
205114 AGTTGGTGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (17 bp):
GGGTTCGCCAAGTATAA
Found at i:206003 original size:91 final size:91
Alignment explanation
Indices: 205893--206077 Score: 307
Period size: 91 Copynumber: 2.0 Consensus size: 91
205883 ACTTAGACCT
* *
205893 ATTTGTTCTTAGTTTTATTTTGTTTTTCTTATTTTATGGGTTTCTAAACTTACCTTTCTGGTCGA
1 ATTTGTTCTTACTTTTATTTTGTTTTTCTTATTTTATGGGTTTCTAAACTTACCTTTATGGTCGA
*
205958 AGGTTAATTGAAGTTTGATTTAATAA
66 AGGTTAATTGAAATTTGATTTAATAA
* * *
205984 ATTTGTTTTTACTTTTATTTTGTTTTTCTTATTTTATGTGTTTCTAGACTTACCTTTATGGTCGA
1 ATTTGTTCTTACTTTTATTTTGTTTTTCTTATTTTATGGGTTTCTAAACTTACCTTTATGGTCGA
*
206049 AGGTTGATTGAAATTTGATTTAATAA
66 AGGTTAATTGAAATTTGATTTAATAA
206075 ATT
1 ATT
206078 CGTGAGACTT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.22, C:0.08, G:0.15, T:0.55
Consensus pattern (91 bp):
ATTTGTTCTTACTTTTATTTTGTTTTTCTTATTTTATGGGTTTCTAAACTTACCTTTATGGTCGA
AGGTTAATTGAAATTTGATTTAATAA
Found at i:210779 original size:28 final size:28
Alignment explanation
Indices: 210739--210819 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
210729 GTTGAAACAC
210739 CTTATTCTAATCAAAATAAAATAAATGA
1 CTTATTCTAATCAAAATAAAATAAATGA
210767 CTTATTCTAATCAAAATAAAATAAATGA
1 CTTATTCTAATCAAAATAAAATAAATGA
* *
210795 CATATTCTAATGAAAATAAAATAAA
1 CTTATTCTAATCAAAATAAAATAAA
210820 AAAAGTGTAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.31
Consensus pattern (28 bp):
CTTATTCTAATCAAAATAAAATAAATGA
Found at i:217930 original size:15 final size:16
Alignment explanation
Indices: 217905--217934 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
217895 CAATAGCCCC
217905 TCAAGTTTAATTTTTT
1 TCAAGTTTAATTTTTT
217921 TCAA-TTTAATTTTT
1 TCAAGTTTAATTTTT
217935 AGTAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (16 bp):
TCAAGTTTAATTTTTT
Found at i:226208 original size:17 final size:17
Alignment explanation
Indices: 226166--226226 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 17
226156 TACAATAACA
*
226166 AATGGAAATGCAATGAC
1 AATGAAAATGCAATGAC
* *
226183 AATGCAAATGCAGTGAC
1 AATGAAAATGCAATGAC
* * *
226200 AATTAAAATGTAATAAC
1 AATGAAAATGCAATGAC
*
226217 AATGAGAATG
1 AATGAAAATG
226227 TGATAACAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (17 bp):
AATGAAAATGCAATGAC
Found at i:235259 original size:26 final size:26
Alignment explanation
Indices: 235187--235263 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 26
235177 TTCTGGGTGC
* * *
235187 AATTCTGGACTTGCTCATACAACGAT
1 AATTCTGGACATGCTCATGCAGCGAT
* * * ** *
235213 AATTCTGCACAAGTTTTTGCAGTGAT
1 AATTCTGGACATGCTCATGCAGCGAT
235239 AATTCTGGACATGCTCATGCAGCGA
1 AATTCTGGACATGCTCATGCAGCGA
235264 CATTAGTAGT
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (26 bp):
AATTCTGGACATGCTCATGCAGCGAT
Found at i:239430 original size:30 final size:29
Alignment explanation
Indices: 239366--239430 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
239356 TTTTTTTTAA
* *
239366 ATTTTTAAAAATTAAAAAAATATAAAACT
1 ATTTTTAAAAATTAAAAAAATACAAAAAT
239395 ATTTTTAAAAATTAAAAATAA-ACAAACAAT
1 ATTTTTAAAAATTAAAAA-AATACAAA-AAT
239425 ATTTTT
1 ATTTTT
239431 TATATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAAAAATACAAAAAT
Found at i:244790 original size:11 final size:11
Alignment explanation
Indices: 244774--244798 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
244764 CGTGTGATGT
244774 GGAAAAGTGAG
1 GGAAAAGTGAG
244785 GGAAAAGTGAG
1 GGAAAAGTGAG
244796 GGA
1 GGA
244799 GATTTTTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.48, T:0.08
Consensus pattern (11 bp):
GGAAAAGTGAG
Found at i:251289 original size:18 final size:18
Alignment explanation
Indices: 251251--251292 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
251241 CCAAATTAAT
251251 CAATCC-AAAACCAATAA
1 CAATCCAAAAACCAATAA
251268 -AATCCAAAAATCCAA-AA
1 CAATCCAAAAA-CCAATAA
251285 CAATCCAA
1 CAATCCAA
251293 CTTAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 11 0.50
ACGTcount: A:0.60, C:0.29, G:0.00, T:0.12
Consensus pattern (18 bp):
CAATCCAAAAACCAATAA
Found at i:253026 original size:30 final size:30
Alignment explanation
Indices: 252992--253049 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
252982 TTGTTTAATG
252992 TGTAATTTGTATATA-AAAATTTTGATTTTT
1 TGTAATTT-TATATATAAAATTTTGATTTTT
*
253022 TGTAATTTTATATATGAAATTTTGATTT
1 TGTAATTTTATATATAAAATTTTGATTT
253050 AATCTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (30 bp):
TGTAATTTTATATATAAAATTTTGATTTTT
Found at i:253058 original size:30 final size:29
Alignment explanation
Indices: 252994--253066 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
252984 GTTTAATGTG
** *
252994 TAATTTGTATATAAAAATTTTGATTTTTTG
1 TAATTT-TATATAAAAATTTTGATTTAATC
*
253024 TAATTTTATATATGAAATTTTGATTTAATC
1 TAATTTTATATA-AAAATTTTGATTTAATC
253054 TAATTTT-TATAAA
1 TAATTTTATATAAA
253067 TTATTAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.03
29 10 0.27
30 26 0.70
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (29 bp):
TAATTTTATATAAAAATTTTGATTTAATC
Found at i:253671 original size:12 final size:13
Alignment explanation
Indices: 253653--253682 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
253643 CAACTAAAGC
253653 ATTTTATTTTTAT
1 ATTTTATTTTTAT
253666 -TTTTATTTTTAT
1 ATTTTATTTTTAT
253678 ATTTT
1 ATTTT
253683 TATGTGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
ATTTTATTTTTAT
Found at i:253732 original size:14 final size:14
Alignment explanation
Indices: 253702--253743 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
253692 CTTTAATAAT
253702 TATATTTGTTATATA
1 TATATTT-TTATATA
253717 TATATTTTT-T-TA
1 TATATTTTTATATA
*
253729 TATATTTTTGTATA
1 TATATTTTTATATA
253743 T
1 T
253744 TTATAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.44
13 2 0.08
14 5 0.20
15 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TATATTTTTATATA
Found at i:254005 original size:20 final size:21
Alignment explanation
Indices: 253980--254022 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
253970 ATTAATTCTA
253980 TTTTATTTTTAAACACAT-AT
1 TTTTATTTTTAAACACATGAT
*
254000 TTTTATTTTTAAATACATGAT
1 TTTTATTTTTAAACACATGAT
254021 TT
1 TT
254023 CCACACGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTTTTAAACACATGAT
Found at i:254471 original size:17 final size:17
Alignment explanation
Indices: 254451--254516 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
254441 TTCATTTTGG
254451 GTTTAAATTTAATTTAA
1 GTTTAAATTTAATTTAA
**
254468 GTTTAAACTTTTCTTTTAAA
1 GTTTAAA--TTTAATTT-AA
*
254488 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
254505 GATTAAATTTAA
1 GTTTAAATTTAA
254517 ATTGAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
17 20 0.50
18 5 0.12
19 6 0.15
20 9 0.22
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Done.