Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 29 of 131
Found at i:9480818 original size:16 final size:16
Alignment explanation
Indices: 9480797--9480835 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
9480787 ATTTTGTTAC
*
9480797 AACAATTATTACAATT
1 AACAATTAATACAATT
9480813 AACAATTAATACAATT
1 AACAATTAATACAATT
*
9480829 AATAATT
1 AACAATT
9480836 TGATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
AACAATTAATACAATT
Found at i:9480926 original size:16 final size:16
Alignment explanation
Indices: 9480905--9480946 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
9480895 AATAATTTGA
*
9480905 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
9480921 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
9480937 TAGTTTTAAT
1 TAATTTTAAT
9480947 TTTATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:9483738 original size:25 final size:25
Alignment explanation
Indices: 9483686--9483760 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
9483676 TTCATATTTA
*
9483686 GGAATGCTCATGTGAG-CATATAAGCG
1 GGAA-GCTCATGTGAGCCATGTAA-CG
*
9483712 GGTAA-CTC-TTTCGAGCCATGTAACG
1 GG-AAGCTCATGT-GAGCCATGTAACG
9483737 GGAAGCTCATGTGAGCCATGTAAC
1 GGAAGCTCATGTGAGCCATGTAAC
9483761 AAGAAACTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 4 0.10
25 25 0.61
26 10 0.24
27 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (25 bp):
GGAAGCTCATGTGAGCCATGTAACG
Found at i:9483776 original size:25 final size:25
Alignment explanation
Indices: 9483724--9483777 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
9483714 TAACTCTTTC
** * *
9483724 GAGCCATGTAACGGGAAGCTCATGT
1 GAGCCATGTAACAAGAAACTCATCT
*
9483749 GAGCCATGTAACAAGAAACTCCTCT
1 GAGCCATGTAACAAGAAACTCATCT
9483774 GAGC
1 GAGC
9483778 TGTATAATGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATGTAACAAGAAACTCATCT
Found at i:9483890 original size:25 final size:25
Alignment explanation
Indices: 9483862--9483923 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
9483852 ATTAATTAGG
* *
9483862 AAGCTCATAAGAGCCAGTT-ATCGAA
1 AAGCTCATAAGAGCCAATTAAT-AAA
***
9483887 AAGCTCCGGAGAGCCAATTAATAAA
1 AAGCTCATAAGAGCCAATTAATAAA
9483912 AAGCTCATAAGA
1 AAGCTCATAAGA
9483924 TCCACAAATG
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.18
Consensus pattern (25 bp):
AAGCTCATAAGAGCCAATTAATAAA
Found at i:9489870 original size:23 final size:23
Alignment explanation
Indices: 9489840--9489885 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9489830 CTTTCTTATT
9489840 GTAGTAATTTTCGAGG-TATTACA
1 GTAGTAATTTTCG-GGATATTACA
9489863 GTAGTAATTTTCGGGATATTACA
1 GTAGTAATTTTCGGGATATTACA
9489886 CTTTAAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (23 bp):
GTAGTAATTTTCGGGATATTACA
Found at i:9492694 original size:25 final size:26
Alignment explanation
Indices: 9492637--9492706 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
9492627 TTCATATTCA
*
9492637 GGAATGCTCATGTGAG-CATATAAATG
1 GGAA-GCTCATGTGAGCCATATAAACG
* * *
9492663 GGTAGCTCTTTTGAGCCATAT-AACG
1 GGAAGCTCATGTGAGCCATATAAACG
9492688 GGAAGCTCATGTGAGCCAT
1 GGAAGCTCATGTGAGCCAT
9492707 GTAATGAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 28 0.78
26 8 0.22
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (26 bp):
GGAAGCTCATGTGAGCCATATAAACG
Found at i:9492816 original size:25 final size:24
Alignment explanation
Indices: 9492749--9492864 Score: 83
Period size: 24 Copynumber: 4.8 Consensus size: 24
9492739 GAAACTCATA
*
9492749 AGAGCCATAATCAGGAAGTTCAAG
1 AGAGCCATAATCAGGAAGCTCAAG
* ** *
9492773 CGAGCCA-ATATCAAAAAGCTCCAG
1 AGAGCCATA-ATCAGGAAGCTCAAG
9492797 AGAGCCATTAATCAGGAAGCTCATA-
1 AGAGCCA-TAATCAGGAAGCTCA-AG
* * * *
9492822 AGAGCCACAAACGGGAACCTCAAG
1 AGAGCCATAATCAGGAAGCTCAAG
* *
9492846 AGAGTCATTAATCGGGAAG
1 AGAGCCA-TAATCAGGAAG
9492865 GTCACAAGAA
Statistics
Matches: 69, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
23 2 0.03
24 40 0.58
25 25 0.36
26 2 0.03
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.15
Consensus pattern (24 bp):
AGAGCCATAATCAGGAAGCTCAAG
Found at i:9495206 original size:10 final size:10
Alignment explanation
Indices: 9495178--9495207 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
9495168 TAATTTTAGG
9495178 TTTAGTTTTC
1 TTTAGTTTTC
9495188 TTTAGGTTTTC
1 TTTA-GTTTTC
9495199 TTTAGTTTT
1 TTTAGTTTT
9495208 TCTCTGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:9498060 original size:3 final size:3
Alignment explanation
Indices: 9498052--9498080 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9498042 ATGGAATTGT
9498052 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9498081 TATTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9503756 original size:16 final size:17
Alignment explanation
Indices: 9503719--9503756 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
9503709 AATTTAATAC
9503719 TTTTATCTCTTAAACTAA
1 TTTTATCTCTTAAAC-AA
*
9503737 TTTTATCTCTTTAA-AA
1 TTTTATCTCTTAAACAA
9503753 TTTT
1 TTTT
9503757 CTTAATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATCTCTTAAACAA
Found at i:9504223 original size:69 final size:69
Alignment explanation
Indices: 9504147--9504275 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
9504137 ACCTTTTTCT
*
9504147 TTCTTTTATTTTCAATTCCAAATCGTTAACTTTGATTTTGTAACATTTTGATATAACAACATTTA
1 TTCTTTTATTTTCAATTCCAAATCATTAACTTTGATTTTGTAACATTTTGATATAACAACATTTA
9504212 AGAA
66 AGAA
* *
9504216 TTCTTTTATTTTCGATTCCAAATCATTAACTTTGATTTTGTAATATTTTGATATAACAAC
1 TTCTTTTATTTTCAATTCCAAATCATTAACTTTGATTTTGTAACATTTTGATATAACAAC
9504276 TGTTAGAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (69 bp):
TTCTTTTATTTTCAATTCCAAATCATTAACTTTGATTTTGTAACATTTTGATATAACAACATTTA
AGAA
Found at i:9510811 original size:13 final size:13
Alignment explanation
Indices: 9510793--9510824 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
9510783 GAAAGTTCTT
9510793 TGCAGATTCAATA
1 TGCAGATTCAATA
9510806 TGCAGATTCAATA
1 TGCAGATTCAATA
9510819 TGCAGA
1 TGCAGA
9510825 ATGTTAAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (13 bp):
TGCAGATTCAATA
Found at i:9511660 original size:29 final size:29
Alignment explanation
Indices: 9511618--9511698 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
9511608 AGAGGTGGAG
9511618 AACTTGTTCATTGAGAGTTCGTGATGAAA
1 AACTTGTTCATTGAGAGTTCGTGATGAAA
**
9511647 AACTTGTTCATTGAGAGTTCACGATGAAA
1 AACTTGTTCATTGAGAGTTCGTGATGAAA
* *
9511676 AACTTGTTTATTGAGAATTCGTG
1 AACTTGTTCATTGAGAGTTCGTG
9511699 TCAAGGTGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (29 bp):
AACTTGTTCATTGAGAGTTCGTGATGAAA
Found at i:9514215 original size:33 final size:33
Alignment explanation
Indices: 9514178--9514243 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
9514168 TGGTAAGTAT
9514178 ATCAAATACTTAGTAAGTCCATATGAAATTTAA
1 ATCAAATACTTAGTAAGTCCATATGAAATTTAA
9514211 ATCAAATACTTAGTAAGTCCATATGAAATTTAA
1 ATCAAATACTTAGTAAGTCCATATGAAATTTAA
9514244 CTTAATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (33 bp):
ATCAAATACTTAGTAAGTCCATATGAAATTTAA
Found at i:9515678 original size:18 final size:18
Alignment explanation
Indices: 9515657--9515698 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
9515647 AAAAACATAA
9515657 AAATTACAAAAAAGAACT
1 AAATTACAAAAAAGAACT
9515675 AAATTACAAAAAAGAACT
1 AAATTACAAAAAAGAACT
9515693 AAATTA
1 AAATTA
9515699 TACTTACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATTACAAAAAAGAACT
Found at i:9516730 original size:37 final size:37
Alignment explanation
Indices: 9516689--9516762 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
9516679 TTTACTTTTG
*
9516689 GGGTGAAAATAAAAATTCTCTCTTCTTTTAATAGAAA
1 GGGTGAAAATAAAAATTCTCTCTTATTTTAATAGAAA
9516726 GGGTGAAAATAAAAATTCTCTCTTATTTTAATAGAAA
1 GGGTGAAAATAAAAATTCTCTCTTATTTTAATAGAAA
9516763 TCGGTAGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (37 bp):
GGGTGAAAATAAAAATTCTCTCTTATTTTAATAGAAA
Found at i:9520220 original size:31 final size:29
Alignment explanation
Indices: 9520151--9520224 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
9520141 ACAAAATAAT
**
9520151 AACATAAGTGACTAAAACGTAACTTTTCA
1 AACATAAGTGACTAAAACGTAACTTGGCA
*
9520180 AACATAAGTGACTAAAATGTAACTTGAGGCA
1 AACATAAGTGACTAAAACGTAACTT--GGCA
*
9520211 AACAAAAGTGACTA
1 AACATAAGTGACTA
9520225 TTTTTGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACTTGGCA
Found at i:9522575 original size:90 final size:90
Alignment explanation
Indices: 9522450--9522639 Score: 371
Period size: 90 Copynumber: 2.1 Consensus size: 90
9522440 GGCAAGGTGC
9522450 AGCAGCAACTACTTTAGAGAAAATATCTCGAACTTGGAACAATATTGAGAAAGTATAACAACATT
1 AGCAGCAACTACTTTAGAGAAAATATCTCGAACTTGGAACAATATTGAGAAAGTATAACAACATT
*
9522515 CAAATCAGCTCGTATCAAGATTTAA
66 CAAATCAGCTCGTATCAAGATTCAA
9522540 AGCAGCAACTACTTTAGAGAAAATATCTCGAACTTGGAACAATATTGAGAAAGTATAACAACATT
1 AGCAGCAACTACTTTAGAGAAAATATCTCGAACTTGGAACAATATTGAGAAAGTATAACAACATT
9522605 CAAATCAGCTCGTATCAAGATTCAA
66 CAAATCAGCTCGTATCAAGATTCAA
9522630 AGCAGCAACT
1 AGCAGCAACT
9522640 GCAGGGTGAG
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 99 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (90 bp):
AGCAGCAACTACTTTAGAGAAAATATCTCGAACTTGGAACAATATTGAGAAAGTATAACAACATT
CAAATCAGCTCGTATCAAGATTCAA
Found at i:9526005 original size:21 final size:21
Alignment explanation
Indices: 9525946--9526085 Score: 153
Period size: 21 Copynumber: 6.9 Consensus size: 21
9525936 GTACATCATT
9525946 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
9525965 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
9525984 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * * *
9526005 AACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTG
9526026 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * * * *
9526047 AACAGAAACTTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTG
* *
9526068 AATAGAAGCTCATAAGAG
1 AACAGAAGCTCGTAAGAG
9526086 TTAAACATAA
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 31 0.31
20 2 0.02
21 68 0.67
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:9526037 original size:42 final size:41
Alignment explanation
Indices: 9525946--9526085 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 41
9525936 GTACATCATT
* * * *
9525946 AACAGAAGCTCG-AA-AGCTGAACAGAAGCTCGAA-AGCTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCTAAGAGTTA
9525984 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTC-TAAGAGTTA
* *
9526026 AACAGAAGCTCGTAAGAGCTGAACAGAAACTTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAAC-TCTAAGAGTTA
* *
9526068 AATAGAAGCTCATAAGAG
1 AACAGAAGCTCGTAAGAG
9526086 TTAAACATAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
38 12 0.13
39 2 0.02
40 15 0.17
41 2 0.02
42 57 0.64
43 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (41 bp):
AACAGAAGCTCGTAAGAGCTGAACAGAAACTCTAAGAGTTA
Found at i:9526053 original size:63 final size:61
Alignment explanation
Indices: 9525965--9526092 Score: 175
Period size: 63 Copynumber: 2.1 Consensus size: 61
9525955 TCGAAAGCTG
* *
9525965 AACAGAAGCTCGAAAGCTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTA
1 AACAGAAGCTCGAAAGCTGAACAGAAACTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
* * * * *
9526026 AACAGAAGCTCGTAAGAGCTGAACAGAAACTTGTATGAGTTAAATAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCG-AA-AGCTGAACAGAAACTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
9526089 AACA
1 AACA
9526093 TAAAGTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 12 0.21
62 2 0.03
63 44 0.76
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.18
Consensus pattern (61 bp):
AACAGAAGCTCGAAAGCTGAACAGAAACTCGTAAGAGCTAAACAGAAACTCATAAGAGTTA
Found at i:9527622 original size:20 final size:20
Alignment explanation
Indices: 9527593--9527630 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9527583 GATCATTAGA
*
9527593 TTAATTAAAATAAGGTTTGT
1 TTAATCAAAATAAGGTTTGT
9527613 TTAATCAAAATAAGGTTT
1 TTAATCAAAATAAGGTTT
9527631 ATTAAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (20 bp):
TTAATCAAAATAAGGTTTGT
Found at i:9531205 original size:50 final size:50
Alignment explanation
Indices: 9531130--9531231 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
9531120 TACCCGCTTC
*
9531130 CGATTTCAGCTTTGTATCCTTCTCCGACTCGACGGTGTCAGATCTCCGGA
1 CGATTTCAGCTTTGCATCCTTCTCCGACTCGACGGTGTCAGATCTCCGGA
9531180 CGATTTCAGCTTTGCATCCTTCTCCGACTCGACGGTGTCAGATCTCCGGA
1 CGATTTCAGCTTTGCATCCTTCTCCGACTCGACGGTGTCAGATCTCCGGA
9531230 CG
1 CG
9531232 GCTTGAATCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.16, C:0.31, G:0.23, T:0.30
Consensus pattern (50 bp):
CGATTTCAGCTTTGCATCCTTCTCCGACTCGACGGTGTCAGATCTCCGGA
Found at i:9532828 original size:21 final size:22
Alignment explanation
Indices: 9532804--9532852 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
9532794 CCCATTGCTT
* *
9532804 GTGGCTGTACAA-TTGTTTGCA
1 GTGGCTATACAATTTATTTGCA
*
9532825 GTGGCTATATAATTTATTTGCA
1 GTGGCTATACAATTTATTTGCA
9532847 GTGGCT
1 GTGGCT
9532853 CCATCTGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (22 bp):
GTGGCTATACAATTTATTTGCA
Found at i:9538575 original size:39 final size:40
Alignment explanation
Indices: 9538526--9538634 Score: 121
Period size: 44 Copynumber: 2.6 Consensus size: 40
9538516 AGTTTTTTCC
9538526 ATTATGCTATTACACCTCTATTCCATTCAACCAAACACAAG
1 ATTA-GCTATTACACCTCTATTCCATTCAACCAAACACAAG
* **
9538567 ATTA-CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTAG
1 ATTAGCTATTACACCTCTATT-C----CATTCAACCAAACACAAG
*
9538611 ATTAGCTATTACACCTCTAATCCA
1 ATTAGCTATTACACCTCTATTCCA
9538635 ATACACCTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
39 15 0.26
40 3 0.05
41 4 0.07
44 21 0.37
45 14 0.25
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (40 bp):
ATTAGCTATTACACCTCTATTCCATTCAACCAAACACAAG
Found at i:9538613 original size:44 final size:45
Alignment explanation
Indices: 9538549--9538639 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
9538539 ACCTCTATTC
* * *
9538549 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
**
9538593 CATTCAACCAAACAGTAGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
9538638 CA
1 CA
9538640 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.38, C:0.29, G:0.05, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:9538641 original size:16 final size:16
Alignment explanation
Indices: 9538620--9538671 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
9538610 GATTAGCTAT
9538620 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
9538636 TACACCTCTAATCCAG
1 TACACCTCTAATCCAA
9538652 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
9538668 TACA
1 TACA
9538672 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:9541314 original size:73 final size:73
Alignment explanation
Indices: 9541195--9541343 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
9541185 ACTAATCTGT
9541195 CTCCATAGAGAAGACCATCTGGGGATCATATATCTTTAGCGAATGCCAAAGTCGTCGCACTGTCC
1 CTCCATAGAGAAGACCATCTGGGGATCATATATCTTTAGCGAATGCCAAAGTCGTCGCACTGTCC
9541260 GTGGATTC
66 GTGGATTC
9541268 CTCCATAGAGAAGACCATCTGGGGATCATATATCTTTAGCGAATGCCAAAGTCGTCGCACTGTCC
1 CTCCATAGAGAAGACCATCTGGGGATCATATATCTTTAGCGAATGCCAAAGTCGTCGCACTGTCC
9541333 GTGGATTC
66 GTGGATTC
9541341 CTC
1 CTC
9541344 GATTTATTTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (73 bp):
CTCCATAGAGAAGACCATCTGGGGATCATATATCTTTAGCGAATGCCAAAGTCGTCGCACTGTCC
GTGGATTC
Found at i:9542739 original size:12 final size:12
Alignment explanation
Indices: 9542694--9542744 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
9542684 GTGATATTTA
*
9542694 AAATTTTAATAT
1 AAATATTAATAT
*
9542706 AATTATT-ATATT
1 AAATATTAATA-T
*
9542718 TAATATTTAATAT
1 AAATA-TTAATAT
9542731 AAATATTAATAT
1 AAATATTAATAT
9542743 AA
1 AA
9542745 TTTTATAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.10
12 18 0.58
13 7 0.23
14 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATATTAATAT
Found at i:9542742 original size:26 final size:26
Alignment explanation
Indices: 9542687--9542738 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
9542677 ATTATTAGTG
*
9542687 ATATTTAAAATTTTAATATAATTATT
1 ATATTTAAAATTTTAATATAAATATT
*
9542713 ATATTTAATA-TTTAATATAAATATT
1 ATATTTAAAATTTTAATATAAATATT
9542738 A
1 A
9542739 ATATAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTTAAAATTTTAATATAAATATT
Found at i:9542753 original size:25 final size:25
Alignment explanation
Indices: 9542698--9542749 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
9542688 TATTTAAAAT
* *
9542698 TTTAATATAATTATTATATTTAATA
1 TTTAATATAAATATTATATATAATA
9542723 TTTAATATAAATATTA-ATATAAT-
1 TTTAATATAAATATTATATATAATA
9542746 TTTA
1 TTTA
9542750 TAATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 6 0.24
25 15 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAATATAAATATTATATATAATA
Found at i:9545923 original size:14 final size:14
Alignment explanation
Indices: 9545901--9545930 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9545891 TTCTGGAAGA
9545901 TTTTAAAAGTTATG
1 TTTTAAAAGTTATG
*
9545915 TTTTGAAAGTTATG
1 TTTTAAAAGTTATG
9545929 TT
1 TT
9545931 GAGAAATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTTTAAAAGTTATG
Found at i:9553481 original size:24 final size:27
Alignment explanation
Indices: 9553449--9553498 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
9553439 ATGATTATCG
9553449 TATTAATGTTATTTA-AAT-TGAATGT
1 TATTAATGTTATTTATAATGTGAATGT
9553474 TATT-ATGTTATTTATAATGTGAATG
1 TATTAATGTTATTTATAATGTGAATG
9553499 GATCGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.43
25 7 0.30
26 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (27 bp):
TATTAATGTTATTTATAATGTGAATGT
Found at i:9553507 original size:26 final size:24
Alignment explanation
Indices: 9553454--9553507 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
9553444 TATCGTATTA
* *
9553454 ATGTTATTTAAATTGAATGTTATT
1 ATGTTATTTAAATTGAATGTGATG
9553478 ATGTTATTTATAATGTGAATG-GATCG
1 ATGTTATTTA-AAT-TGAATGTGAT-G
9553504 ATGT
1 ATGT
9553508 ATAAACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 10 0.40
25 5 0.20
26 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (24 bp):
ATGTTATTTAAATTGAATGTGATG
Found at i:9555119 original size:4 final size:4
Alignment explanation
Indices: 9555110--9555141 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
9555100 TTTAGAGATG
*
9555110 GTAT GTAT GTAT GTAT GTAT GCAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
9555142 ATATAAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:9559716 original size:23 final size:24
Alignment explanation
Indices: 9559689--9559738 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
9559679 TGATTTAGAG
9559689 GAAAACTATTTTA-ATATAAA-TTA
1 GAAAACTATTTTAGAT-TAAATTTA
*
9559712 GAAAATTATTTTAGATTAAATTTA
1 GAAAACTATTTTAGATTAAATTTA
9559736 GAA
1 GAA
9559739 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (24 bp):
GAAAACTATTTTAGATTAAATTTA
Found at i:9565998 original size:20 final size:19
Alignment explanation
Indices: 9565949--9566000 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
9565939 AATTTCAAAA
* *
9565949 AAAAAATCAAAATAATTGT
1 AAAAATTCAAAATAATTAT
* *
9565968 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATAATTAT
9565987 AAAAATTTCAAAAT
1 AAAAA-TTCAAAAT
9566001 TTATATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTAT
Found at i:9566020 original size:16 final size:17
Alignment explanation
Indices: 9565996--9566040 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
9565986 TAAAAATTTC
9565996 AAAATT-TATATTTTAAA
1 AAAATTATATA-TTTAAA
9566013 AAAATTATAATAATTTAAA
1 AAAATTAT-AT-ATTTAAA
9566032 AAAATTATA
1 AAAATTATA
9566041 AATAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 16 0.64
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTATATATTTAAA
Found at i:9566033 original size:20 final size:20
Alignment explanation
Indices: 9566007--9566046 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
9565997 AAATTTATAT
9566007 TTTAAAAAAATTAT-AATAA
1 TTTAAAAAAATTATAAATAA
9566026 TTTAAAAAAATTATAAATAA
1 TTTAAAAAAATTATAAATAA
9566046 T
1 T
9566047 ATATAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAAAATTATAAATAA
Found at i:9567111 original size:23 final size:22
Alignment explanation
Indices: 9567079--9567121 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
9567069 TTGTTTGGTT
*
9567079 ATTATCATTTTTATATTATTATA
1 ATTATAATTTTTAT-TTATTATA
9567102 ATTATAATTTTTATTTATTA
1 ATTATAATTTTTATTTATTA
9567122 ATATTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTATAATTTTTATTTATTATA
Found at i:9568422 original size:25 final size:23
Alignment explanation
Indices: 9568387--9568437 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
9568377 TGATTGGTTG
*
9568387 AATATTTTATTATTATTTCATTAT
1 AATATTTTATTAATATTTCATT-T
*
9568411 AATATATTTATTAATATTTTATTT
1 AATAT-TTTATTAATATTTCATTT
9568435 AAT
1 AAT
9568438 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
AATATTTTATTAATATTTCATTT
Found at i:9576576 original size:23 final size:23
Alignment explanation
Indices: 9576546--9576594 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
9576536 ATTAATTATT
9576546 ATTTTTAGATAACTAATGAATTA
1 ATTTTTAGATAACTAATGAATTA
9576569 ATTTTTAGATAACTAATGAATTA
1 ATTTTTAGATAACTAATGAATTA
9576592 ATT
1 ATT
9576595 ATTAAATCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (23 bp):
ATTTTTAGATAACTAATGAATTA
Found at i:9579521 original size:62 final size:62
Alignment explanation
Indices: 9579435--9579559 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
9579425 CCTTAGCACA
* * *
9579435 TCCAGAAGGAAAAATCGAGGACGTATTGGTACATGTAGGTAAGTTTATCCTTCCTGCTGACT
1 TCCAAAAGGAAAAATCGAGAACGTATTGGTACATGTAGATAAGTTTATCCTTCCTGCTGACT
* *
9579497 TCCAAAAGGATAAATCGAGAACGTATTGGTACATGTAGATAAGTTTATCTTTCCTGCTGACT
1 TCCAAAAGGAAAAATCGAGAACGTATTGGTACATGTAGATAAGTTTATCCTTCCTGCTGACT
9579559 T
1 T
9579560 TATAATTCTA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (62 bp):
TCCAAAAGGAAAAATCGAGAACGTATTGGTACATGTAGATAAGTTTATCCTTCCTGCTGACT
Found at i:9584769 original size:12 final size:10
Alignment explanation
Indices: 9584739--9584781 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
9584729 AATATGAACA
*
9584739 TAATAAATTT
1 TAATTAATTT
9584749 TAATTAATTT
1 TAATTAATTT
9584759 TATAGTTAATTT
1 TA-A-TTAATTT
*
9584771 TGATTAATTT
1 TAATTAATTT
9584781 T
1 T
9584782 GACTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (10 bp):
TAATTAATTT
Found at i:9590158 original size:44 final size:44
Alignment explanation
Indices: 9590110--9590568 Score: 293
Period size: 44 Copynumber: 10.6 Consensus size: 44
9590100 ATTTTGATCC
* * *
9590110 GCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
* * * * *
9590154 GCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGCGATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
* * ** * * *
9590195 GCTCTACTACAACTTCAGAAAGATAAGATTTGTGGTT-TT-AATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTG-GTTTCTTCTATCT
* * * *
9590239 GCTCCACTGCAACTTTAGGGAGATAGGATTGTTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
* * * * * *
9590283 GCTCCACTGCAACTTCAAGGCGATAAGACTGG---ATGCGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
* * * * * *
9590324 GCTCTACTGCAACTTCAGAGAGATAAGTTCTGTGGTT-TT-AATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTTTCTTCTATCT
* * * *
9590368 GCTCCACAGCAACTTCAGGGAGATAGGACTGGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
* * * * * * *
9590412 GCTCCATTGCAACTTCCA-GGAGATAAGACTAG---ATGCGATTT
1 GCTCCACTGCAACTT-CAGGGAGATAAGATTGGTTTCTTCTATCT
* * * *
9590453 GCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATT-TT-AATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTG-GTTTCTTCTATCT
* * *
9590497 GCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
*
9590541 GCTCCACTACAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
9590569 CTGAATGTGA
Statistics
Matches: 308, Mismatches: 84, Indels: 46
0.70 0.19 0.11
Matches are distributed among these distances:
40 2 0.01
41 82 0.27
42 13 0.04
43 17 0.06
44 189 0.61
45 5 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCT
Found at i:9590239 original size:129 final size:129
Alignment explanation
Indices: 9590061--9590586 Score: 768
Period size: 129 Copynumber: 4.1 Consensus size: 129
9590051 AGTCTGATAT
* *** * * *
9590061 GATCTGCTCTACTGCAACTTCAGAGAGATGAGATCCATCATTTTGATCCGCTCCACTGTAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTC
9590126 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC
* * * * *
9590190 GATTTGCTCTACTACAACTTCAGAAAGATAAGATTTGTGGTTTTAATCCGCTCCACTGCAACTTT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTC
* * *
9590255 AGGGAGATAGGATTGTTTTCTTCTGTCTGCTCCACTGCAACTTCAAGGCGATAAGACTGGATGC
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC
* *
9590319 GATCTGCTCTACTGCAACTTCAGAGAGATAAG-TTCTGTGGTTTTAATCCGCTCCACAGCAACTT
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATT-TGTGATTTTAATCCGCTCCACTGCAACTT
* * *
9590383 CAGGGAGATAGGACTGGTTTCTTCTGTCTGCTCCATTGCAACTTCCA-GGAGATAAGACTAGATG
65 CAGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTT-CAGGGAGATAAGACTGGATG
9590447 C
129 C
* * *
9590448 GATTTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCTGCTCCACTGTAACTTC
1 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTC
* * * * *
9590513 AGGGAGATAGGATTGGTTTCTTCTATTTGCTCCACTACAACTTCAGGGAGATAAGACTGAATGT
66 AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC
9590577 GATCTGCTCT
1 GATCTGCTCT
9590587 TTTTTACCTA
Statistics
Matches: 354, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
128 4 0.01
129 346 0.98
130 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (129 bp):
GATCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTC
AGGGAGATAGGATTGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGC
Found at i:9590582 original size:85 final size:85
Alignment explanation
Indices: 9590151--9590585 Score: 217
Period size: 85 Copynumber: 5.1 Consensus size: 85
9590141 GTTTCTTCTG
* * * * * *
9590151 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGG---ATGCGATTTGCTCTACTACAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCTGCTCCACTACAACTTCAG
** * ** * *
9590213 AAAGATAAGATTTGTGGTTTTAA
66 GGAGATAAGA---CTGAATGTGA
* * * * * * *
9590236 TCCGCTCCACTGCAACTTTAGGGAGATAGGATTGTTTTCTTCTGTCTGCTCCACTGCAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCTGCTCCACTACAACTTCAG
* * *
9590301 GGCGATAAGACTGGATGCGA
66 GGAGATAAGACTGAATGTGA
* * * * * *
9590321 TCTGCTCTACTGCAACTTCAGAGAGATAAGTTCTGTGGTT-TT-AATCCGCTCCAC-AGCAACTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-GTTTCTTCTATCTGCTCCACTA-CAACTT
* ** *
9590383 CAGGGAGATAGGACTGGTTTCTTCTG-
63 CAGGGAGATAAGACT-G---AATGTGA
* * * * * * * * *
9590409 TCTGCTCCATTGCAACTTCCA-GGAGATAAGACTAG---ATGCGATTTGCTCTACTGCAACTTCA
1 TCTGCTCCACTGCAACTT-CAGGGAGATAAGATTGGTTTCTTCTATCTGCTCCACTACAACTTCA
* * * * *
9590470 GAGAGATAAGATTTGTGATTTTAA
65 GGGAGATAAGA---CTGAATGTGA
* * *
9590494 TCTGCTCCACTGTAACTTCAGGGAGATAGGATTGGTTTCTTCTATTTGCTCCACTACAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCTGCTCCACTACAACTTCAG
9590559 GGAGATAAGACTGAATGTGA
66 GGAGATAAGACTGAATGTGA
9590579 TCTGCTC
1 TCTGCTC
9590586 TTTTTTACCT
Statistics
Matches: 255, Mismatches: 73, Indels: 44
0.69 0.20 0.12
Matches are distributed among these distances:
84 6 0.02
85 153 0.60
86 6 0.02
87 4 0.02
88 82 0.32
89 4 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (85 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTATCTGCTCCACTACAACTTCAG
GGAGATAAGACTGAATGTGA
Found at i:9591014 original size:218 final size:217
Alignment explanation
Indices: 9590683--9591192 Score: 770
Period size: 218 Copynumber: 2.3 Consensus size: 217
9590673 ATTTTCAACA
** * * *
9590683 TACTCCACTGCCGC-TCAGGGAGATAAGACCTGCCATCTTTAGTCTGCCCCACTGCAACTTTAGG
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCCATCTTCAGTCTGCCCCACTGCAACTTAAGG
* * * *
9590747 AGGATAAGACCTGTTTACTCAGTCTACTCCACTGCAACCTCAGGGAGATAAGACCTAATGCGATC
66 -GGATAAGACCTGCTTACTCAGTCTACTCCACTACAACCTCAAGGAGATAAGACCTAATGCAATC
* *
9590812 TACTCTATTGCAACTTCAGAGAGATAAGATCAATTATTTTAATCTACTCCACTGCAACTTCAGGG
130 TACTCTACTGCAACTTCAGAGAGATAAGATCAATTATTTTAATCCACTCCACTGCAACTTCAGGG
9590877 AGATAGGATTATTGGCTTTAATC
195 AGATAGGATTATTGGCTTTAATC
* ** *
9590900 TACTCCACTGCAACTTTAGGGAGATAAGATCTGCCATCTTCAGTCTGTTCCACTGTAACTTCAAG
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCCATCTTCAGTCTGCCCCACTGCAACTT-AAG
*
9590965 GGGATAAGACCTGCTTACTCAGTCTGCTCCACTACAACCTCAAGGAGATAAGACCTAATGCAATC
65 GGGATAAGACCTGCTTACTCAGTCTACTCCACTACAACCTCAAGGAGATAAGACCTAATGCAATC
* * * *
9591030 TACTCTGCTGCAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGCATCTTCAGGG
130 TACTCTACTGCAACTTCAGAGAGATAAGATCAATTATTTTAATCCACTCCACTGCAACTTCAGGG
9591095 AGATAGGATTATTGGCTTTAATC
195 AGATAGGATTATTGGCTTTAATC
* * * *
9591118 TACTCCACTGTAACTTCAGGGATATACGATCTGCCATCTTCAGTCTGCCCCACTGCAACTTTAGG
1 TACTCCACTGCAACTTCAGGGAGATAAGATCTGCCATCTTCAGTCTGCCCCACTGCAAC-TTAAG
9591183 GGGATAAGAC
65 GGGATAAGAC
9591193 TTTGTGATTT
Statistics
Matches: 262, Mismatches: 28, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
217 12 0.05
218 245 0.94
219 5 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (217 bp):
TACTCCACTGCAACTTCAGGGAGATAAGATCTGCCATCTTCAGTCTGCCCCACTGCAACTTAAGG
GGATAAGACCTGCTTACTCAGTCTACTCCACTACAACCTCAAGGAGATAAGACCTAATGCAATCT
ACTCTACTGCAACTTCAGAGAGATAAGATCAATTATTTTAATCCACTCCACTGCAACTTCAGGGA
GATAGGATTATTGGCTTTAATC
Found at i:9591137 original size:44 final size:43
Alignment explanation
Indices: 9590769--9591139 Score: 215
Period size: 44 Copynumber: 8.6 Consensus size: 43
9590759 GTTTACTCAG
* * * *
9590769 TCTACTCCACTGCAACCTCAGGGAGATAAGACCTAATGC---GA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGA-TTATTGCTTTAA
* * * * **
9590810 TCTACTCTATTGCAACTTCAGAGAGATAAGATCAATTATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TATTGCTTTAA
*
9590854 TCTACTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTATT-GCTTTAA
* * *
9590898 TCTACTCCACTGCAACTTTAGGGAGATAAGATCTGCCA-T-CTTCAG
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-T---ATTGCTTTAA
** * ** *
9590943 TCTGTTCCACTGTAACTTCAAGGG-GATAAGA--CCTGCTTACTCAG
1 TCTACTCCACTGCAACTTC-AGGGAGATAAGATTATTGCTT--T-AA
* * * * * *
9590987 TCTGCTCCACTACAACCTCAAGGAGATAAGACCTAATGC---AA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGA-TTATTGCTTTAA
** * **
9591028 TCTACTCTGCTGCAACTTCAGAGAGATAAGATCTATTATTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGAT-TATTGCTTTAA
** * *
9591072 TCCGCTCCACTGCATCTTCAGGGAGATAGGATTATTGGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGATTATT-GCTTTAA
*
9591116 TCTACTCCACTGTAACTTCAGGGA
1 TCTACTCCACTGCAACTTCAGGGA
9591140 TATACGATCT
Statistics
Matches: 247, Mismatches: 59, Indels: 45
0.70 0.17 0.13
Matches are distributed among these distances:
40 1 0.00
41 60 0.24
43 10 0.04
44 140 0.57
45 27 0.11
46 4 0.02
47 4 0.02
48 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
TCTACTCCACTGCAACTTCAGGGAGATAAGATTATTGCTTTAA
Found at i:9592542 original size:53 final size:53
Alignment explanation
Indices: 9592463--9592609 Score: 242
Period size: 53 Copynumber: 2.8 Consensus size: 53
9592453 ATTATTATTA
* * *
9592463 TTTTA-GACTCAAAGCGCCCTTTGCGGGTCTTCACTTTGGTCTCTCCTTTTTT
1 TTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTCTCCCTTTTT
9592515 TTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTCTCCCTTTTT
1 TTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTCTCCCTTTTT
* *
9592568 TTTTAGGAATCAAAGTGCCCTTTGCAGGTTTTCACTTTGGTC
1 TTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTC
9592610 CATTCTTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 5 0.06
53 84 0.94
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (53 bp):
TTTTAGGAATCAAAGCGCCCTTTGCGGGTTTTCACTTTGGTCTCTCCCTTTTT
Found at i:9597490 original size:22 final size:22
Alignment explanation
Indices: 9597464--9597508 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9597454 AGCAAGCGTT
9597464 AAAAA-GAAAATCGAAAAAGAAA
1 AAAAATGAAAA-CGAAAAAGAAA
* *
9597486 AAAAATGCAAAGGAAAAAGAAA
1 AAAAATGAAAACGAAAAAGAAA
9597508 A
1 A
9597509 TCAAATCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAATGAAAACGAAAAAGAAA
Found at i:9600645 original size:15 final size:15
Alignment explanation
Indices: 9600625--9600654 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9600615 GTGTGTTACA
9600625 TCATTCTCCTAATAT
1 TCATTCTCCTAATAT
9600640 TCATTCTCCTAATAT
1 TCATTCTCCTAATAT
9600655 GATCCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATTCTCCTAATAT
Found at i:9601982 original size:11 final size:11
Alignment explanation
Indices: 9601966--9601990 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9601956 GCTAAGCGTG
9601966 TAACCGATATA
1 TAACCGATATA
9601977 TAACCGATATA
1 TAACCGATATA
9601988 TAA
1 TAA
9601991 TCCCTTATTT
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (11 bp):
TAACCGATATA
Found at i:9618107 original size:3 final size:3
Alignment explanation
Indices: 9618101--9618130 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9618091 GATGATGATA
9618101 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
9618131 AAACAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:9618657 original size:13 final size:13
Alignment explanation
Indices: 9618638--9618671 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
9618628 ATCACTTGTG
*
9618638 AAGCACTTTTTCA
1 AAGCACTTTTTAA
*
9618651 TAGCACTTTTTAA
1 AAGCACTTTTTAA
9618664 AAGCACTT
1 AAGCACTT
9618672 CTCAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (13 bp):
AAGCACTTTTTAA
Found at i:9618925 original size:16 final size:16
Alignment explanation
Indices: 9618904--9618937 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
9618894 TTTAAATAAA
9618904 AATTTTATAGTTTTTT
1 AATTTTATAGTTTTTT
*
9618920 AATTTTATTGTTTTTT
1 AATTTTATAGTTTTTT
9618936 AA
1 AA
9618938 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
AATTTTATAGTTTTTT
Found at i:9628125 original size:25 final size:24
Alignment explanation
Indices: 9628097--9628150 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 24
9628087 TGGTTTTAAA
*
9628097 TCTTTCCTTGGTTTTTTTTTCTT-TT
1 TCTTTCCTT--TTTATTTTTCTTCTT
9628122 TCTTT-CTTTTTATTTTTCTTCTT
1 TCTTTCCTTTTTATTTTTCTTCTT
9628145 TCTTTC
1 TCTTTC
9628151 GGTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.42
23 7 0.27
24 3 0.12
25 5 0.19
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.76
Consensus pattern (24 bp):
TCTTTCCTTTTTATTTTTCTTCTT
Found at i:9628137 original size:16 final size:15
Alignment explanation
Indices: 9628112--9628145 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
9628102 CCTTGGTTTT
*
9628112 TTTTTCTTTTTCTTTC
1 TTTTTATTTTTC-TTC
9628128 TTTTTATTTTTCTTC
1 TTTTTATTTTTCTTC
9628143 TTT
1 TTT
9628146 CTTTCGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTATTTTTCTTC
Found at i:9631109 original size:6 final size:6
Alignment explanation
Indices: 9631100--9631124 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9631090 TATTTGGGCT
9631100 TGGGTA TGGGTA TGGGTA TGGGTA T
1 TGGGTA TGGGTA TGGGTA TGGGTA T
9631125 AAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.36
Consensus pattern (6 bp):
TGGGTA
Found at i:9635897 original size:19 final size:18
Alignment explanation
Indices: 9635843--9635911 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
9635833 AAAAAAATTC
9635843 TAATTTTTAATAA-ATCTTA
1 TAATTTTT-ATAATAT-TTA
*
9635862 T-ATTTTTATTAAAATTTAA
1 TAATTTTTA-TAATATTT-A
*
9635881 TAATTTTTCTAATATTTA
1 TAATTTTTATAATATTTA
*
9635899 TTATTTTTATAAT
1 TAATTTTTATAAT
9635912 TTTTTTTCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 1 0.02
18 23 0.55
19 12 0.29
20 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATTTTTATAATATTTA
Found at i:9636337 original size:14 final size:15
Alignment explanation
Indices: 9636312--9636342 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9636302 TTTAATATAT
9636312 AAAAATTATAAAGAA
1 AAAAATTATAAAGAA
9636327 AAAAATT-TAAAGAA
1 AAAAATTATAAAGAA
9636341 AA
1 AA
9636343 TGCATAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAAATTATAAAGAA
Found at i:9637409 original size:29 final size:31
Alignment explanation
Indices: 9637334--9637410 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
9637324 TTAACGGCTC
* *
9637334 AGTGACTAAAATGTTACATCATGATAACATA
1 AGTGACTAAAATGTAACATCATCATAACATA
* * * *
9637365 AGTGAGTACAACGTAACAT-TTCA-AACATA
1 AGTGACTAAAATGTAACATCATCATAACATA
9637394 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
9637411 CTAAACCAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 20 0.54
30 2 0.05
31 15 0.41
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.26
Consensus pattern (31 bp):
AGTGACTAAAATGTAACATCATCATAACATA
Found at i:9641375 original size:3 final size:3
Alignment explanation
Indices: 9641367--9641393 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9641357 CTCGAAATGT
9641367 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
9641394 ACAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:9644744 original size:4 final size:4
Alignment explanation
Indices: 9644730--9644777 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
9644720 GAATAGAAGG
9644730 AGAA A-AA AGAA AGAA ATGAGA AGAA AGAA AGAA A-AA A-AA A-AA AGAA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA AGAA AGAA
9644776 AG
1 AG
9644778 GGAAGGTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.30
4 22 0.55
5 4 0.10
6 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:9644756 original size:18 final size:18
Alignment explanation
Indices: 9644729--9644777 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
9644719 GGAATAGAAG
9644729 GAGAAAAAAGAAAGAAAT
1 GAGAAAAAAGAAAGAAAT
*
9644747 GAGAAGAAAGAAAGAAA-
1 GAGAAAAAAGAAAGAAAT
* *
9644764 AAAAAAAAAGAAAG
1 GAGAAAAAAGAAAG
9644778 GGAAGGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
GAGAAAAAAGAAAGAAAT
Found at i:9644843 original size:27 final size:29
Alignment explanation
Indices: 9644799--9644859 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
9644789 ATATTTGTAA
*
9644799 TTTTTTTAAAATTTGAAGGGATTA-ATAT
1 TTTTTTTAAAATTAGAAGGGATTATATAT
* *
9644827 TTTTTTTTAAA-TAGAAGGGATTATTTAT
1 TTTTTTTAAAATTAGAAGGGATTATATAT
9644855 TTTTT
1 TTTTT
9644860 ATGTTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (29 bp):
TTTTTTTAAAATTAGAAGGGATTATATAT
Found at i:9644982 original size:4 final size:4
Alignment explanation
Indices: 9644968--9645015 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
9644958 GAATAGAAGG
9644968 AGAA A-AA AGAA AGAA ATGAGA AGAA AGAA AGAA A-AA A-AA A-AA AGAA
1 AGAA AGAA AGAA AGAA A-GA-A AGAA AGAA AGAA AGAA AGAA AGAA AGAA
9645014 AG
1 AG
9645016 GGAAGGTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.30
4 22 0.55
5 4 0.10
6 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:9644994 original size:18 final size:18
Alignment explanation
Indices: 9644967--9645015 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
9644957 GGAATAGAAG
9644967 GAGAAAAAAGAAAGAAAT
1 GAGAAAAAAGAAAGAAAT
*
9644985 GAGAAGAAAGAAAGAAA-
1 GAGAAAAAAGAAAGAAAT
* *
9645002 AAAAAAAAAGAAAG
1 GAGAAAAAAGAAAG
9645016 GGAAGGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
GAGAAAAAAGAAAGAAAT
Found at i:9645081 original size:27 final size:29
Alignment explanation
Indices: 9645037--9645097 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
9645027 ATATTTGTAA
*
9645037 TTTTTTTAAAATTTGAAGGGATTA-ATAT
1 TTTTTTTAAAATTAGAAGGGATTATATAT
* *
9645065 TTTTTTTTAAA-TAGAAGGGATTATTTAT
1 TTTTTTTAAAATTAGAAGGGATTATATAT
9645093 TTTTT
1 TTTTT
9645098 ATGTTGTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (29 bp):
TTTTTTTAAAATTAGAAGGGATTATATAT
Found at i:9645133 original size:238 final size:239
Alignment explanation
Indices: 9644715--9645192 Score: 949
Period size: 238 Copynumber: 2.0 Consensus size: 239
9644705 CTTTGAGAAG
9644715 ATCCGGAATAGAAGGAGAAAAAAGAAAGAAATGAGAAGAAAGAAAGAAAAAAAAAAAAGAAAGGG
1 ATCCGGAATAGAAGGAGAAAAAAGAAAGAAATGAGAAGAAAGAAAGAAAAAAAAAAAAGAAAGGG
9644780 AAGGTATGTATATTTGTAATTTTTTTAAAATTTGAAGGGATTAATATTTTTTTTTAAATAGAAGG
66 AAGGTATGTATATTTGTAATTTTTTTAAAATTTGAAGGGATTAATATTTTTTTTTAAATAGAAGG
9644845 GATTATTTATTTTTTATGTTGTTTTTAATTTATTTTAAAGTTTTTTGGTTAATTATTATTATAAA
131 GATTATTTATTTTTTATGTTGTTTTTAATTTATTTTAAAGTTTTTTGGTTAATTATTATTATAAA
9644910 TTGTTTGTGTTTAGTTTAGTGTTTATTGTGA-TTTAAATTTTTT
196 TTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAAATTTTTT
9644953 ATCCGGAATAGAAGGAGAAAAAAGAAAGAAATGAGAAGAAAGAAAGAAAAAAAAAAAAGAAAGGG
1 ATCCGGAATAGAAGGAGAAAAAAGAAAGAAATGAGAAGAAAGAAAGAAAAAAAAAAAAGAAAGGG
9645018 AAGGTATGTATATTTGTAATTTTTTTAAAATTTGAAGGGATTAATATTTTTTTTTAAATAGAAGG
66 AAGGTATGTATATTTGTAATTTTTTTAAAATTTGAAGGGATTAATATTTTTTTTTAAATAGAAGG
9645083 GATTATTTATTTTTTATGTTGTTTTTAATTTATTTTAAAGTTTTTTGGTTAATTATTATTATAAA
131 GATTATTTATTTTTTATGTTGTTTTTAATTTATTTTAAAGTTTTTTGGTTAATTATTATTATAAA
9645148 TTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAAATTTTTT
196 TTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAAATTTTTT
9645192 A
1 A
9645193 ATTTTTTTAA
Statistics
Matches: 239, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
238 226 0.95
239 13 0.05
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (239 bp):
ATCCGGAATAGAAGGAGAAAAAAGAAAGAAATGAGAAGAAAGAAAGAAAAAAAAAAAAGAAAGGG
AAGGTATGTATATTTGTAATTTTTTTAAAATTTGAAGGGATTAATATTTTTTTTTAAATAGAAGG
GATTATTTATTTTTTATGTTGTTTTTAATTTATTTTAAAGTTTTTTGGTTAATTATTATTATAAA
TTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAAATTTTTT
Found at i:9645365 original size:104 final size:100
Alignment explanation
Indices: 9645141--9645608 Score: 522
Period size: 104 Copynumber: 4.5 Consensus size: 100
9645131 TTAATTATTA
** ** * *
9645141 TTATAAATTGTTTGTGTTTAGTTTAGTGTTTATTGTGATTTTAAATTTTTTAATTTTTTTAAAAT
1 TTATAAATTGTTTGTGTTTAGTTTA--GTTTATTGTGATTTTTTATAATGTAATTTTTTAAAAAT
* *
9645206 CATTTTAAAGTTATTTTGTTAGTAATTTATGTTTAGG
64 TATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * *
9645243 TTATATATTGTCTGTGTTTAGCTTAGTTTATTGTGATTTTTTATGAATGTAAATTTTTTAAAAAA
1 TTATAAATTGTTTGTGTTTAGTTTAGTTTATTGTGATTTTTTAT-AATGT-AATTTTTT--AAAA
*
9645308 AGTTATTTTAAAGTTATTTT-TTAATAATTTATGATTAGG
62 A-TTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
9645347 TGT-TAAATTGTTTGTGTTTAGTTTAG-----TGTGATTTTTTATTAATGTAATTTTTTTTGTTT
1 T-TATAAATTGTTTGTGTTTAGTTTAGTTTATTGTGATTTTTTA-TAATGTAA-------T-TTT
9645406 TTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
56 TTAAAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* *
9645451 TTATAAATTGTTTGTGTTTAGTTTAGTATTTATTGTGATTTTTTATGAATATAATTTTTTTAAAA
1 TTATAAATTGTTTGTGTTTAGTTTAG--TTTATTGTGATTTTTTAT-AATGTAATTTTTTAAAAA
9645516 TTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
63 TTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
* * *
9645554 TTATAAATT-ATT-TGTTTAGTTTAATGTGTATTGTGATTTGTTATAATGTAATTTT
1 TTATAAATTGTTTGTGTTTAGTTT-A-GTTTATTGTGATTTTTTATAATGTAATTTT
9645609 ATTTGTTTTT
Statistics
Matches: 317, Mismatches: 22, Indels: 56
0.80 0.06 0.14
Matches are distributed among these distances:
98 2 0.01
99 17 0.05
100 28 0.09
101 28 0.09
102 33 0.10
103 76 0.24
104 90 0.28
105 19 0.06
106 5 0.02
110 1 0.00
111 18 0.06
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (100 bp):
TTATAAATTGTTTGTGTTTAGTTTAGTTTATTGTGATTTTTTATAATGTAATTTTTTAAAAATTA
TTTTAAAGTTATTTTGTTAGTAATTTATGATTAGG
Found at i:9645649 original size:20 final size:22
Alignment explanation
Indices: 9645609--9645652 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
9645599 ATGTAATTTT
9645609 ATTTGTTTTTGATTTATTTGAA
1 ATTTGTTTTTGATTTATTTGAA
9645631 ATTT-TTTTTGATTTA-TTGAA
1 ATTTGTTTTTGATTTATTTGAA
9645651 AT
1 AT
9645653 GTTGATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (22 bp):
ATTTGTTTTTGATTTATTTGAA
Found at i:9645661 original size:20 final size:21
Alignment explanation
Indices: 9645617--9645661 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
9645607 TTATTTGTTT
* **
9645617 TTGATTTATTTGAAATTTTTT
1 TTGATTTATTTGAAATGTTGA
9645638 TTGATTTA-TTGAAATGTTGA
1 TTGATTTATTTGAAATGTTGA
9645658 TTGA
1 TTGA
9645662 ATTTGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
TTGATTTATTTGAAATGTTGA
Found at i:9647824 original size:48 final size:48
Alignment explanation
Indices: 9647754--9647876 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
9647744 AACACAGAAT
*
9647754 AACTTTGTAATTT-AATTGAGATTCATTGCAACATTAAAACT-TGGAACA
1 AACTTTGTAATTTAAATT-AGATTCATTGCAACATTAAAA-TGCGGAACA
* *
9647802 AAGTTTGTAATTTAAATTAGATTAATTGCAACATTAAAATGCGGAACA
1 AACTTTGTAATTTAAATTAGATTCATTGCAACATTAAAATGCGGAACA
* *
9647850 AACTTTGTAATATAAATTAGATACATT
1 AACTTTGTAATTTAAATTAGATTCATT
9647877 AGAGTACATT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 1 0.02
48 61 0.92
49 4 0.06
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (48 bp):
AACTTTGTAATTTAAATTAGATTCATTGCAACATTAAAATGCGGAACA
Found at i:9649809 original size:24 final size:25
Alignment explanation
Indices: 9649780--9649832 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
9649770 TAGTTTATAT
9649780 ATATAC-GTTTACATTTTATAATAC
1 ATATACAGTTTACATTTTATAATAC
* * *
9649804 ATATACATTTTTCCATTTTATAATTC
1 ATATACA-GTTTACATTTTATAATAC
9649830 ATA
1 ATA
9649833 CATATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
26 18 0.75
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (25 bp):
ATATACAGTTTACATTTTATAATAC
Found at i:9649839 original size:26 final size:26
Alignment explanation
Indices: 9649791--9649840 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9649781 TATACGTTTA
*
9649791 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
9649817 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
9649841 CACATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:9651682 original size:15 final size:15
Alignment explanation
Indices: 9651662--9651715 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
9651652 CACCTTAGCC
9651662 TTTCCATTTTTACTT
1 TTTCCATTTTTACTT
9651677 TTTCCATTTTT-CATT
1 TTTCCATTTTTAC-TT
*
9651692 TTT-CATTTTCA-TT
1 TTTCCATTTTTACTT
*
9651705 TTTTCATTTTT
1 TTTCCATTTTT
9651716 TTCACATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.15
14 13 0.38
15 16 0.47
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCCATTTTTACTT
Found at i:9651707 original size:7 final size:7
Alignment explanation
Indices: 9651666--9651715 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
9651656 TTAGCCTTTC
9651666 CATTTTT
1 CATTTTT
9651673 -ACTTTTT
1 CA-TTTTT
9651680 CCATTTTT
1 -CATTTTT
9651688 CATTTTT
1 CATTTTT
9651695 CA-TTTT
1 CATTTTT
9651701 CATTTTTT
1 CA-TTTTT
9651709 CATTTTT
1 CATTTTT
9651716 TTCACATCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 7 0.18
7 19 0.50
8 11 0.29
9 1 0.03
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:9652262 original size:10 final size:10
Alignment explanation
Indices: 9652204--9652277 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 10
9652194 CTGGTGGAGG
9652204 TTTTTTGTTT
1 TTTTTTGTTT
*
9652214 CTTTTTGTTT
1 TTTTTTGTTT
*
9652224 TTGTTTTTTTGT
1 TT-TTTTGTT-T
*
9652236 TCTTCTTTTTTCCT
1 T-TT-TTTGTT--T
9652250 TTTTTTGTTTT
1 TTTTTTG-TTT
9652261 TTTTTTGTTT
1 TTTTTTGTTT
9652271 TTTTTTG
1 TTTTTTG
9652278 CATTGAATCT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 20 0.38
11 14 0.26
12 6 0.11
13 11 0.21
14 2 0.04
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:9655366 original size:18 final size:19
Alignment explanation
Indices: 9655334--9655371 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
9655324 ATAAAATGGA
* *
9655334 AAAATGTATATGTAT-TAT
1 AAAATGTAAACGTATATAT
9655352 AAAATGTAAACGTATATAT
1 AAAATGTAAACGTATATAT
9655371 A
1 A
9655372 TAAACTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (19 bp):
AAAATGTAAACGTATATAT
Found at i:9655370 original size:26 final size:26
Alignment explanation
Indices: 9655308--9655357 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
9655298 TATGTATGTG
*
9655308 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
9655334 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
9655358 TAAACGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Found at i:9655517 original size:3 final size:3
Alignment explanation
Indices: 9655509--9655542 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9655499 ATGTATAAGT
9655509 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9655543 CAAAAATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:9659708 original size:11 final size:11
Alignment explanation
Indices: 9659692--9659732 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
9659682 AGTTGCTAAC
*
9659692 AAAATAACTTT
1 AAAATAACTTA
*
9659703 AAAATAAATTA
1 AAAATAACTTA
*
9659714 AAAATAACATA
1 AAAATAACTTA
9659725 AAAATAAC
1 AAAATAAC
9659733 AATAAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAATAACTTA
Found at i:9659733 original size:11 final size:11
Alignment explanation
Indices: 9659692--9659738 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
9659682 AGTTGCTAAC
* *
9659692 AAAATAACTTT
1 AAAATAACATA
9659703 AAAATAA-ATTA
1 AAAATAACA-TA
9659714 AAAATAACATA
1 AAAATAACATA
9659725 AAAATAACAATA
1 AAAATAAC-ATA
9659737 AA
1 AA
9659739 CAAACTACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAACATA
Found at i:9660873 original size:16 final size:16
Alignment explanation
Indices: 9660853--9660907 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
9660843 TTGGTTCGCT
*
9660853 GTAATAGAATAGAGGT
1 GTAATAGAATAGAGGC
* *
9660869 GTAATGGAATAGATGC
1 GTAATAGAATAGAGGC
* *
9660885 GTAATGGAATAAAGGC
1 GTAATAGAATAGAGGC
9660901 GTAATAG
1 GTAATAG
9660908 GTAATTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.42, C:0.04, G:0.31, T:0.24
Consensus pattern (16 bp):
GTAATAGAATAGAGGC
Found at i:9660973 original size:44 final size:46
Alignment explanation
Indices: 9660887--9660979 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
9660877 ATAGATGCGT
*
9660887 AATGGAATAAAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
*
9660933 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
9660977 AAT
1 AAT
9660980 AGAGATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 24 0.53
45 3 0.07
46 18 0.40
ACGTcount: A:0.29, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGGAATAAAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:9660975 original size:39 final size:44
Alignment explanation
Indices: 9660887--9660983 Score: 123
Period size: 46 Copynumber: 2.3 Consensus size: 44
9660877 ATAGATGCGT
* *
9660887 AATGGAATAAAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
9660933 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
9660972 AATGGAATAGAG
1 AATGGAATAGAG
9660984 ATATAATAGC
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
39 13 0.27
40 1 0.02
43 1 0.02
44 13 0.27
45 3 0.06
46 18 0.37
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:9661598 original size:39 final size:39
Alignment explanation
Indices: 9661471--9661604 Score: 128
Period size: 40 Copynumber: 3.4 Consensus size: 39
9661461 GTTTAGACAA
* **
9661471 AAAACGCCACTAAAAATCAAGCATTAGCGGCACTTTTAGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCA-TTTTTTG
** * ** * *
9661511 AAAACGCCGCTAAAGGTCGATTATTAGCGGCGTTTTTTA
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCATTTTTTG
9661550 AAAATCGCCGCTAAAAAT-AAGCATTAGCGGCATTTATTTG
1 AAAA-CGCCGCTAAAAATCAAGCATTAGCGGCATTT-TTTG
*
9661590 AAAGCGCCGC-AAAAA
1 AAAACGCCGCTAAAAA
9661605 GCCTAAGCCA
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 5 0.07
39 27 0.36
40 42 0.57
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCATTTTTTG
Found at i:9671557 original size:66 final size:66
Alignment explanation
Indices: 9671451--9671620 Score: 225
Period size: 66 Copynumber: 2.6 Consensus size: 66
9671441 AGCAAATTAC
* * * *
9671451 ACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAG
*
9671515 CT
65 CA
*
9671517 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGC
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGC
9671582 A
66 A
* * * * *
9671583 ACAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGG
9671621 CGGCAGCGAG
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 88 0.96
67 4 0.04
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.13
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGC
A
Found at i:9671616 original size:21 final size:21
Alignment explanation
Indices: 9671592--9671703 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
9671582 AACAGCTTAG
*
9671592 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
*
9671613 AGCAGAGGCGGCAGCGAGAGA
1 AGCAGAGGCGGCAGCAAGAGA
* * * * *
9671634 AGTACAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
*** * *
9671655 AGCAGAGGCTAAAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
* * *
9671676 AGCAGAGGCTGCAGCGAGGGA
1 AGCAGAGGCGGCAGCAAGAGA
9671697 AGCAGAG
1 AGCAGAG
9671704 CAGCGTCAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 79 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (21 bp):
AGCAGAGGCGGCAGCAAGAGA
Found at i:9671661 original size:42 final size:42
Alignment explanation
Indices: 9671602--9671703 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
9671592 AGCAGATGCG
* * ** *
9671602 GCAGCAAGAGAAGCAGAGGCGGCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
* * *
9671644 GCAGCGAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
9671686 GCAGCGAGGGAAGCAGAG
1 GCAGCGAGGGAAGCAGAG
9671704 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.34, C:0.18, G:0.44, T:0.04
Consensus pattern (42 bp):
GCAGCGAGGGAAGCAGAGGCGAAAGCGAGAGAAGCACAGGCT
Found at i:9672072 original size:43 final size:43
Alignment explanation
Indices: 9672006--9672319 Score: 217
Period size: 43 Copynumber: 7.3 Consensus size: 43
9671996 ATCTGCCAAA
* * ** *
9672006 TTTAGTGGCGTTTTTGGTCAAAGCGCCACTAAAGATAAGGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATAAGGGTC
* * *
9672049 TTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATAAGGGTC
** * *
9672092 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATAAGGGTC
* * * * *
9672135 TATT-GCGGCGTTTGAAGG-GAAAGCGCCGCTAAAGATTAGGTTT
1 T-TTAGCGGCGTTTG-TGGAAAAAGCGCCGCTAAAGATAAGGGTC
* * ** *
9672178 TTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAA-GGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAT-AAGGGTC
* * * * **** *
9672221 TATT-GCGGCATTTGAGAAAAAAACGCCGCTAAAGACCCTGATC
1 T-TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATAAGGGTC
* * **
9672264 TTTAGCGGCGCTTCTCCCAAAAA-CGCCGCTAAAGATTAA-GGTC
1 TTTAGCGGCGTTTGT-GGAAAAAGCGCCGCTAAAGA-TAAGGGTC
9672307 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
9672320 CCACTAAAGC
Statistics
Matches: 215, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
42 6 0.03
43 197 0.92
44 12 0.06
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATAAGGGTC
Found at i:9672158 original size:86 final size:87
Alignment explanation
Indices: 9672006--9672255 Score: 285
Period size: 86 Copynumber: 2.9 Consensus size: 87
9671996 ATCTGCCAAA
* * * * *
9672006 TTTAGTGGCGTTTTTGGTCAAAGCGCCACTAAAGATAAGGGTCT-TTAGCGGCGTTTG-TGGAAA
1 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTGAAGGAAA
9672069 AAGCGCCACTAAAGATCATGG-TC
65 AAGCGCCACTAAAGATCA-GGTTC
* ** *
9672092 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAAGG-GAA
1 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAAGGAAAA
* * *
9672156 AGCGCCGCTAAAGATTAGGTTT
66 AGCGCCACTAAAGATCAGGTTC
* * * *
9672178 TTTCGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAAGGTCTATTGCGGCATTTG-AGAAAAA
1 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAAGGAAAA
* *
9672242 AACGCCGCTAAAGA
66 AGCGCCACTAAAGA
9672256 CCCTGATCTT
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
85 4 0.03
86 131 0.94
87 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (87 bp):
TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCTATTGCGGCGTTTGAAGGAAAA
AGCGCCACTAAAGATCAGGTTC
Found at i:9672350 original size:42 final size:41
Alignment explanation
Indices: 9672239--9672361 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
9672229 CATTTGAGAA
**** *
9672239 AAAAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTCTCCC
1 AAAAACGCCGCTAAAGATTAAGGTCTTTAGCGGCG-TT-TCCC
9672282 AAAAACGCCGCTAAAGATTAAGGTCTTTAGCGGCGTTTCCAC
1 AAAAACGCCGCTAAAGATTAAGGTCTTTAGCGGCGTTTCC-C
* * * * *
9672324 TAAAGCGCCGCTAAAGGTCTTA-GTCTTCAGCGGCGTTT
1 AAAAACGCCGCTAAAGAT-TAAGGTCTTTAGCGGCGTTT
9672362 GTGCTAGAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.04
42 33 0.49
43 32 0.47
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGATTAAGGTCTTTAGCGGCGTTTCCC
Found at i:9672525 original size:22 final size:22
Alignment explanation
Indices: 9672498--9672540 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9672488 CTGCGGAGAT
*
9672498 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
9672520 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
9672541 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:9673062 original size:10 final size:10
Alignment explanation
Indices: 9673030--9673072 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
9673020 GCTGTTTGAG
9673030 CATCCATGAA
1 CATCCATGAA
*
9673040 CATCTCTTG--
1 CATC-CATGAA
9673049 CATCCATGAA
1 CATCCATGAA
9673059 CATCCATGAA
1 CATCCATGAA
9673069 CATC
1 CATC
9673073 TCTTGCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 3 0.11
9 4 0.14
10 18 0.64
11 3 0.11
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.26
Consensus pattern (10 bp):
CATCCATGAA
Found at i:9675258 original size:32 final size:32
Alignment explanation
Indices: 9675222--9675285 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
9675212 TATATAATAC
*
9675222 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
** ** *
9675254 TATAATTTATAATATACTTTATTATTATTAAA
1 TATAAAATATAATATAAATAATTATTATTAAA
9675286 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATATAAATAATTATTATTAAA
Found at i:9695480 original size:55 final size:55
Alignment explanation
Indices: 9695396--9695508 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
9695386 TAGATGTGCT
*
9695396 ACATAACAATCAATGTAAACATATAAACAATCGATTCAAAAGAAGTAATATTCCA
1 ACATAACAATCAATGTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCA
* * *
9695451 ACATAATAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCA
1 ACATAACAATCAATGTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCA
9695506 ACA
1 ACA
9695509 ATTAAGAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (55 bp):
ACATAACAATCAATGTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCCA
Found at i:9698192 original size:17 final size:16
Alignment explanation
Indices: 9698166--9698218 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
9698156 TTCTATAATC
9698166 CATTTCCATTTTCATAT
1 CATTT-CATTTTCATAT
* *
9698183 CATTCTCATTTTAATTT
1 CATT-TCATTTTCATAT
* *
9698200 CATTTCATATTCAAAT
1 CATTTCATTTTCATAT
9698216 CAT
1 CAT
9698219 AAATCGCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 11 0.38
17 17 0.59
18 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (16 bp):
CATTTCATTTTCATAT
Found at i:9699017 original size:25 final size:25
Alignment explanation
Indices: 9698983--9699035 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
9698973 ATGAAAAAAG
9698983 TCTGGTCATCTATCATCTTTTCTTT
1 TCTGGTCATCTATCATCTTTTCTTT
9699008 TCTGGTCATCTATCATCTTTTCTTT
1 TCTGGTCATCTATCATCTTTTCTTT
9699033 TCT
1 TCT
9699036 TTATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.11, C:0.25, G:0.08, T:0.57
Consensus pattern (25 bp):
TCTGGTCATCTATCATCTTTTCTTT
Found at i:9699344 original size:73 final size:75
Alignment explanation
Indices: 9699213--9699351 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 75
9699203 TATAAAAATA
* ** *
9699213 TTGGAGGGGCCTACTTCTATTTTTAGGAGGGCTATAATATATATACAAAGGGGGAAATTGCAAAA
1 TTGGAGGGGCCTACTTATATTTTTAGGAGGGCTATAATATATATACAAAGGACGAAATTGAAAAA
9699278 ATCTTAAACC
66 ATCTTAAACC
* * *
9699288 TTGGA-GGGCCTACTTAT-TTTTTAGGAGGGCTATAGTATATTTACAAAGGACTAAATTGAAAAA
1 TTGGAGGGGCCTACTTATATTTTTAGGAGGGCTATAATATATATACAAAGGACGAAATTGAAAAA
9699351 A
66 A
9699352 ATTAAACTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 41 0.72
74 11 0.19
75 5 0.09
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (75 bp):
TTGGAGGGGCCTACTTATATTTTTAGGAGGGCTATAATATATATACAAAGGACGAAATTGAAAAA
ATCTTAAACC
Found at i:9699818 original size:21 final size:21
Alignment explanation
Indices: 9699778--9699819 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9699768 AATACCTGGT
*
9699778 AAAAGGTATCGATAATTTTTG
1 AAAAGGTATCGATAACTTTTG
* *
9699799 AAAAGGTATTGATACCTTTTG
1 AAAAGGTATCGATAACTTTTG
9699820 TAATTGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCGATAACTTTTG
Found at i:9705517 original size:37 final size:38
Alignment explanation
Indices: 9705463--9705534 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
9705453 ACTTAATCAC
*
9705463 TTTAATATTAAATTAATA-AAATACTATTAAGATAAGTA
1 TTTAATATTAAATTAATATAAA-ACTATTAAAATAAGTA
* *
9705501 TTTAAT-TTAATTTAATATTAAACTATTAAAATAA
1 TTTAATATTAAATTAATATAAAACTATTAAAATAA
9705535 TAATATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 22 0.73
38 8 0.27
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (38 bp):
TTTAATATTAAATTAATATAAAACTATTAAAATAAGTA
Found at i:9705983 original size:19 final size:19
Alignment explanation
Indices: 9705950--9705989 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
9705940 AAAATATTAT
*
9705950 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
9705969 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
9705988 AT
1 AT
9705990 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:9707167 original size:15 final size:15
Alignment explanation
Indices: 9707147--9707176 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9707137 CTATGCATGC
*
9707147 AAAATATAAAAGACA
1 AAAATACAAAAGACA
9707162 AAAATACAAAAGACA
1 AAAATACAAAAGACA
9707177 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Found at i:9713727 original size:153 final size:153
Alignment explanation
Indices: 9713449--9713753 Score: 583
Period size: 153 Copynumber: 2.0 Consensus size: 153
9713439 TTCTAGATCG
**
9713449 AGATACGAGAGCTTTTGTTGCCAATCGTGAAAAAGAGAAAGCTACTGAATAATTGTTCACAAGCA
1 AGATACGAGAGCTTCCGTTGCCAATCGTGAAAAAGAGAAAGCTACTGAATAATTGTTCACAAGCA
*
9713514 TAATTCCGGTAAGTTCGTGGACTCGAACTTAATTTTTCTAATTACTATTTAATTAATTAATGCTA
66 TAATTCCAGTAAGTTCGTGGACTCGAACTTAATTTTTCTAATTACTATTTAATTAATTAATGCTA
9713579 AATTAGCTATTGATATAAAATGA
131 AATTAGCTATTGATATAAAATGA
9713602 AGATACGAGAGCTTCCGTTGCCAATCGTGAAAAAGAGAAAGCTACTGAATAATTGTTCACAAGCA
1 AGATACGAGAGCTTCCGTTGCCAATCGTGAAAAAGAGAAAGCTACTGAATAATTGTTCACAAGCA
9713667 TAATTCCAGTAAGTTCGTGGACTCGAACTTAATTTTTCTAATTACTATTTAATTAATTAATGCTA
66 TAATTCCAGTAAGTTCGTGGACTCGAACTTAATTTTTCTAATTACTATTTAATTAATTAATGCTA
9713732 AATTAGCTATTGATATAAAATG
131 AATTAGCTATTGATATAAAATG
9713754 TATGTATATT
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (153 bp):
AGATACGAGAGCTTCCGTTGCCAATCGTGAAAAAGAGAAAGCTACTGAATAATTGTTCACAAGCA
TAATTCCAGTAAGTTCGTGGACTCGAACTTAATTTTTCTAATTACTATTTAATTAATTAATGCTA
AATTAGCTATTGATATAAAATGA
Found at i:9714032 original size:75 final size:73
Alignment explanation
Indices: 9713935--9714114 Score: 209
Period size: 75 Copynumber: 2.4 Consensus size: 73
9713925 CATACAACTA
* * * *
9713935 TCGGTTTATCCGATTAACGCTGGGCGCAAACACCGTTG-TTTCATCCAACTAGAGCTAGACTCAC
1 TCGGTATATCCGACTAGCGCTGGGCGCAAACACCGTCGATTT-ATCCAACTAGAGCTAGACTCAC
*
9713999 TTTTATTATCG
65 TTTCA--ATCG
* ** * *
9714010 TTGGTATATCCGACTAGCGCTGGGCGCAAACATTGTCGATTTATCCAACTAGAGCTGGGCTCACT
1 TCGGTATATCCGACTAGCGCTGGGCGCAAACACCGTCGATTTATCCAACTAGAGCTAGACTCACT
*
9714075 TTCAATTG
66 TTCAATCG
* *
9714083 TCGGTATATTCAACTAGCGCTGGGCGCAAACA
1 TCGGTATATCCGACTAGCGCTGGGCGCAAACA
9714115 TTGTTGGTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
73 32 0.36
75 55 0.61
76 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (73 bp):
TCGGTATATCCGACTAGCGCTGGGCGCAAACACCGTCGATTTATCCAACTAGAGCTAGACTCACT
TTCAATCG
Found at i:9714067 original size:35 final size:35
Alignment explanation
Indices: 9714016--9714127 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 35
9714006 ATCGTTGGTA
* *
9714016 TATCCGACTAGCGCTGGGCGCAAACATTGTCGATT
1 TATCCAACTAGCGCTGGGCGCAAACATTGTCGGTT
* * ** *
9714051 TATCCAACTAGAGCTGGGCTCACTTTCAATTGTCGGTA
1 TATCCAACTAGCGCTGGGCGCA--AAC-ATTGTCGGTT
* *
9714089 TATTCAACTAGCGCTGGGCGCAAACATTGTTGGTT
1 TATCCAACTAGCGCTGGGCGCAAACATTGTCGGTT
9714124 TATC
1 TATC
9714128 AGGGCTCACT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
35 30 0.51
36 1 0.02
37 1 0.02
38 27 0.46
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (35 bp):
TATCCAACTAGCGCTGGGCGCAAACATTGTCGGTT
Found at i:9714116 original size:73 final size:73
Alignment explanation
Indices: 9713952--9714127 Score: 219
Period size: 73 Copynumber: 2.4 Consensus size: 73
9713942 ATCCGATTAA
** * *
9713952 CGCTGGGCGCAAACACCGTTGTTTCATCCAACTAGAGCTAGACTCACTTTTATTATCGTTGGTAT
1 CGCTGGGCGCAAACATTGTTGTTT-ATCCAACTAGAGCTAGACTCACTTTCA-TATCGTCGGTAT
*
9714017 ATCCGACTAG
64 ATCCAACTAG
* * * *
9714027 CGCTGGGCGCAAACATTGTCGATTTATCCAACTAGAGCTGGGCTCACTTTCA-ATTGTCGGTATA
1 CGCTGGGCGCAAACATTGTTG-TTTATCCAACTAGAGCTAGACTCACTTTCATATCGTCGGTATA
*
9714091 TTCAACTAG
65 TCCAACTAG
9714100 CGCTGGGCGCAAACATTGTTGGTTTATC
1 CGCTGGGCGCAAACATTGTT-GTTTATC
9714128 AGGGCTCACT
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
73 42 0.48
74 1 0.01
75 42 0.48
76 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (73 bp):
CGCTGGGCGCAAACATTGTTGTTTATCCAACTAGAGCTAGACTCACTTTCATATCGTCGGTATAT
CCAACTAG
Found at i:9715904 original size:25 final size:25
Alignment explanation
Indices: 9715872--9715922 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
9715862 ATGTTTTTCC
9715872 CCACTTACTTTCTTTCTCTCGCATT
1 CCACTTACTTTCTTTCTCTCGCATT
9715897 CCACTTACTTTCTTTCTCTCGCATT
1 CCACTTACTTTCTTTCTCTCGCATT
9715922 C
1 C
9715923 TTTCTCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.37, G:0.04, T:0.47
Consensus pattern (25 bp):
CCACTTACTTTCTTTCTCTCGCATT
Found at i:9718701 original size:37 final size:37
Alignment explanation
Indices: 9718647--9718721 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
9718637 CACATTTCAT
*
9718647 AACTCAATATCACATTCACTTCCATTATCTATTAATC
1 AACTCAATATCACATTCACTTCAATTATCTATTAATC
*
9718684 AACTCAATATCATATTCACTTCAATTATCTATTAATC
1 AACTCAATATCACATTCACTTCAATTATCTATTAATC
9718721 A
1 A
9718722 TTCATTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.37, C:0.24, G:0.00, T:0.39
Consensus pattern (37 bp):
AACTCAATATCACATTCACTTCAATTATCTATTAATC
Found at i:9721715 original size:69 final size:69
Alignment explanation
Indices: 9721629--9721767 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
9721619 AAAACACTTT
* *
9721629 GGGACTAATAGAAATCATTTGAAAAGTTAAAGAAGAATTTGCAAAAATTTTTACTACAGGGTTCA
1 GGGACTAATAGAAATCATTTGAAAAGTTAAAGAAGAATTTGCAAAAAATTTTACTACAGGATTCA
9721694 CACG
66 CACG
9721698 GGGACTAATAGAAATCATTTGAAAAGTTAAAGAAGAATTTGCAAAAAATTTTACTACAGGATTCA
1 GGGACTAATAGAAATCATTTGAAAAGTTAAAGAAGAATTTGCAAAAAATTTTACTACAGGATTCA
9721763 CACG
66 CACG
9721767 G
1 G
9721768 TCGTGTGGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.27
Consensus pattern (69 bp):
GGGACTAATAGAAATCATTTGAAAAGTTAAAGAAGAATTTGCAAAAAATTTTACTACAGGATTCA
CACG
Found at i:9723037 original size:35 final size:35
Alignment explanation
Indices: 9722998--9723093 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 35
9722988 AACTCTGGTT
9722998 GGATAAACCAATGATATTTGCGCCCAGCGCTAGTC
1 GGATAAACCAATGATATTTGCGCCCAGCGCTAGTC
** * * * *
9723033 GGATAAACTGACGATATAAATAGTGAGCCCAGCTCTAGTT
1 GGATAAACCAATGATAT---T--TGCGCCCAGCGCTAGTC
9723073 GGATAAACCAATGATATTTGC
1 GGATAAACCAATGATATTTGC
9723094 ACCTAGTGCT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
35 16 0.35
37 1 0.02
38 1 0.02
40 28 0.61
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (35 bp):
GGATAAACCAATGATATTTGCGCCCAGCGCTAGTC
Found at i:9723078 original size:75 final size:75
Alignment explanation
Indices: 9722941--9723185 Score: 243
Period size: 75 Copynumber: 3.3 Consensus size: 75
9722931 TTGACGGAAG
* * * * * *
9722941 TTGCGCCCAGTGCTAGTCAGATATACCAACGA-AT-AATCAATGAGCCCAACTCTGGTTGGATAA
1 TTGCGCCCAGCGCTAGTCGGATATACTAACGATATAAAT-AGTGAGCCCAGCTCTAGTTGGATAA
9723004 ACCAATGATAT
65 ACCAATGATAT
* *
9723015 TTGCGCCCAGCGCTAGTCGGATAAACTGACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAA
1 TTGCGCCCAGCGCTAGTCGGATATACTAACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAA
9723080 CCAATGATAT
66 CCAATGATAT
* * * * *
9723090 TTGCACCTAGTGCTAG-CTGAGTATA-TCAACGAT-TATAATTGTGAGCCCAGCTCTAGTTGGAT
1 TTGCGCCCAGCGCTAGTCGGA-TATACT-AACGATATA-AATAGTGAGCCCAGCTCTAGTTGGAT
* **
9723152 GAA-CAGCGATGA-
63 AAACCAATGAT-AT
*
9723164 TTGCGCCCAACGCTAGTCGGAT
1 TTGCGCCCAGCGCTAGTCGGAT
9723186 GAACCGACAA
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
74 51 0.36
75 87 0.62
76 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (75 bp):
TTGCGCCCAGCGCTAGTCGGATATACTAACGATATAAATAGTGAGCCCAGCTCTAGTTGGATAAA
CCAATGATAT
Found at i:9723089 original size:40 final size:35
Alignment explanation
Indices: 9722981--9723092 Score: 107
Period size: 35 Copynumber: 3.1 Consensus size: 35
9722971 GAATAATCAA
* *
9722981 TGAGCCCAACTCTGGTTGGATAAACCAATGATATT
1 TGAGCCCAGCTCTAGTTGGATAAACCAATGATATT
* * * ** *
9723016 TGCGCCCAGCGCTAGTCGGATAAACTGACGATATAAAT
1 TGAGCCCAGCTCTAGTTGGATAAACCAATGATAT---T
9723054 AGTGAGCCCAGCTCTAGTTGGATAAACCAATGATATT
1 --TGAGCCCAGCTCTAGTTGGATAAACCAATGATATT
9723091 TG
1 TG
9723093 CACCTAGTGC
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
35 28 0.48
37 1 0.02
38 1 0.02
40 28 0.48
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (35 bp):
TGAGCCCAGCTCTAGTTGGATAAACCAATGATATT
Found at i:9723273 original size:20 final size:21
Alignment explanation
Indices: 9723228--9723273 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
9723218 CTATAAAATG
*
9723228 ACATTTCATAATCTCCATATC
1 ACATTTCATAATCTCAATATC
*
9723249 GCATTTCATAA-CTCAATATC
1 ACATTTCATAATCTCAATATC
9723269 ACATT
1 ACATT
9723274 CACTTCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (21 bp):
ACATTTCATAATCTCAATATC
Found at i:9723299 original size:37 final size:37
Alignment explanation
Indices: 9723258--9723332 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
9723248 CGCATTTCAT
9723258 AACTCAATATCACATTCACTTCAATTATCTATTAATC
1 AACTCAATATCACATTCACTTCAATTATCTATTAATC
*
9723295 AACTCAATATCATATTCACTTCAATTATCTATTAATC
1 AACTCAATATCACATTCACTTCAATTATCTATTAATC
9723332 A
1 A
9723333 TTCATTAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (37 bp):
AACTCAATATCACATTCACTTCAATTATCTATTAATC
Found at i:9723327 original size:17 final size:17
Alignment explanation
Indices: 9723271--9723327 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
9723261 TCAATATCAC
9723271 ATTCACTTCAATTATCT
1 ATTCACTTCAATTATCT
9723288 ATTAATCAAC-TCAA-TATCAT
1 A-T--TC-ACTTCAATTATC-T
9723308 ATTCACTTCAATTATCT
1 ATTCACTTCAATTATCT
9723325 ATT
1 ATT
9723328 AATCATTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
16 2 0.06
17 11 0.33
18 5 0.15
19 5 0.15
20 8 0.24
21 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTCACTTCAATTATCT
Found at i:9730885 original size:24 final size:24
Alignment explanation
Indices: 9730841--9730886 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
9730831 GGCACCACCA
* *
9730841 TTTTTTTAAATATTTTTTTTTATT
1 TTTTTTTAAATATTATATTTTATT
9730865 TTTTTTTAAA-ATTAATATTTTA
1 TTTTTTTAAATATT-ATATTTTA
9730887 ATAATGGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTTTTAAATATTATATTTTATT
Done.