Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 101 of 206
Found at i:29612942 original size:43 final size:41
Alignment explanation
Indices: 29612845--29612960 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
29612835 TAACCGTTAC
*
29612845 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTT-TAATCAAGGAT
*
29612887 ACGG-GGAATCAGCACATAGCAACC-CCTTTCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTT-A-A-TCAAGGAT
29612929 ACGGTGGAATCAGCACTTAGCAACCACCTTTA
1 ACGGTGGAATCAGCACTTAGCAACCACCTTTA
29612961 TATTCAATGA
Statistics
Matches: 66, Mismatches: 3, Indels: 9
0.85 0.04 0.12
Matches are distributed among these distances:
39 1 0.02
40 5 0.08
41 20 0.30
42 15 0.23
43 20 0.30
44 5 0.08
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (41 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTTAATCAAGGAT
Found at i:29613074 original size:51 final size:49
Alignment explanation
Indices: 29612990--29613165 Score: 187
Period size: 51 Copynumber: 3.5 Consensus size: 49
29612980 ACATAGAGCA
* * *
29612990 TGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACGA-C-CTATCCGGTACACGTAGTAGCC
* * * *
29613041 TGCATATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCC
1 TGCACATAGTACTACACACGTGA-CG-ACCTATCCGGTACACGTAGTAGCC
29613092 TGCACATAGTACTACACA--T-ACGACCTATCATTCTGGTACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACGACCTATC---C-GGTACACGTAGTAGCC
*
29613142 TACACATAGTACTACACACGTGAC
1 TGCACATAGTACTACACACGTGAC
29613166 CATCACTTTC
Statistics
Matches: 104, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
46 6 0.06
47 2 0.02
48 1 0.01
49 2 0.02
50 31 0.30
51 57 0.55
52 2 0.02
53 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (49 bp):
TGCACATAGTACTACACACGTGACGACCTATCCGGTACACGTAGTAGCC
Found at i:29613156 original size:101 final size:101
Alignment explanation
Indices: 29612981--29613164 Score: 273
Period size: 101 Copynumber: 1.8 Consensus size: 101
29612971 TGCGGATTCA
** * *
29612981 CATAGAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCAT
1 CATAGAGCATGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGCCTACAC
29613046 ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
29613082 CATAGTAGCCTGCACATAGTACTACACATACGACCTATCA-T-TCTGGTACACGTAGTAGCCTAC
1 CATAG-AGCATGCACATAGTACTACACATACGACC-ATCACTATCCGATACACGTAGTAGCCTAC
29613145 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
29613165 CCATCACTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
101 43 0.58
102 27 0.36
103 4 0.05
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGAGCATGCACATAGTACTACACATACGACCATCACTATCCGATACACGTAGTAGCCTACAC
ATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:29615065 original size:11 final size:10
Alignment explanation
Indices: 29615029--29615075 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
29615019 GCTTATTACA
*
29615029 TAAAAAAATA
1 TAAAAAAATT
29615039 TATAAAAAATT
1 TA-AAAAAATT
29615050 T--AAAAATT
1 TAAAAAAATT
29615058 TAAAAAAATT
1 TAAAAAAATT
*
29615068 CAAAAAAA
1 TAAAAAAA
29615076 ATTGAGGGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 8 0.25
10 16 0.50
11 8 0.25
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:29615297 original size:26 final size:26
Alignment explanation
Indices: 29615268--29615321 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
29615258 TAACTCAAAC
*
29615268 AATTTTA-TTTGATTCAACTCGAATCG
1 AATTTTATTTTG-CTCAACTCGAATCG
*
29615294 AATTTTATTTTGCTCAACTCGATTCG
1 AATTTTATTTTGCTCAACTCGAATCG
29615320 AA
1 AA
29615322 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (26 bp):
AATTTTATTTTGCTCAACTCGAATCG
Found at i:29616620 original size:18 final size:18
Alignment explanation
Indices: 29616580--29616623 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29616570 TGGGCCAGGC
29616580 CATGTGGG-CCACACGAG
1 CATGTGGGCCCACACGAG
** *
29616597 TGTGTGGGCCCACACGGG
1 CATGTGGGCCCACACGAG
29616615 CATGTGGGC
1 CATGTGGGC
29616624 ATGTGTGACC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
CATGTGGGCCCACACGAG
Found at i:29617195 original size:18 final size:17
Alignment explanation
Indices: 29617153--29617196 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
29617143 TGTCGTTTGT
29617153 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
29617170 TTTGCAAATCGTTATTCAA
1 TTT-CAAAACATTATTC-A
29617189 TTTCAAAA
1 TTTCAAAA
29617197 TGTCAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:29623586 original size:5 final size:5
Alignment explanation
Indices: 29623576--29623600 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29623566 AAAACTCATA
29623576 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
29623601 CAATATAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:29628929 original size:28 final size:29
Alignment explanation
Indices: 29628892--29628964 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
29628882 TTTGCATATT
*
29628892 ATTCTATTTATTTTAAAA-T-TGATAAATTA
1 ATTCT-TTTATGTTAAAACTAT-ATAAATTA
29628921 ATTCTTTTATGTTAAAACTATATAAATTA
1 ATTCTTTTATGTTAAAACTATATAAATTA
*
29628950 A-TC-TTTCTGTTAAAA
1 ATTCTTTTATGTTAAAA
29628965 AAATTATTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
27 11 0.28
28 13 0.32
29 15 0.38
30 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTCTTTTATGTTAAAACTATATAAATTA
Found at i:29629615 original size:11 final size:11
Alignment explanation
Indices: 29629583--29629616 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
29629573 GTGTGCATAT
* *
29629583 ATAATAATTTT
1 ATAATTATTTA
29629594 ATAATTATTTA
1 ATAATTATTTA
29629605 ATAATTATTTA
1 ATAATTATTTA
29629616 A
1 A
29629617 AAAACTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAATTATTTA
Found at i:29629723 original size:21 final size:20
Alignment explanation
Indices: 29629692--29629735 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
29629682 ATGGATGTTG
**
29629692 TTTTTAATATTTTTTTATAA
1 TTTTTAATATTTTTAAATAA
29629712 TTTTTAATTATTTTTAAATAA
1 TTTTTAA-TATTTTTAAATAA
29629733 TTT
1 TTT
29629736 GTTATACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTAATATTTTTAAATAA
Found at i:29629735 original size:11 final size:10
Alignment explanation
Indices: 29629692--29629735 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
29629682 ATGGATGTTG
*
29629692 TTTTTAATAT
1 TTTTTAATAA
*
29629702 TTTTTTATAA
1 TTTTTAATAA
*
29629712 TTTTTAATTA
1 TTTTTAATAA
29629722 TTTTTAAATAA
1 TTTTT-AATAA
29629733 TTT
1 TTT
29629736 GTTATACTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:29639844 original size:23 final size:23
Alignment explanation
Indices: 29639815--29639866 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
29639805 AAAAAAAATG
29639815 TTTTTCTT-TTGTT-TTCTTGCTAT
1 TTTTTCTTATT-TTCTTCTTG-TAT
*
29639838 TTTTTCTTATTTTCTTCTTGTTT
1 TTTTTCTTATTTTCTTCTTGTAT
29639861 TTTTTC
1 TTTTTC
29639867 ACTATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (23 bp):
TTTTTCTTATTTTCTTCTTGTAT
Found at i:29639872 original size:24 final size:24
Alignment explanation
Indices: 29639828--29639874 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
29639818 TTCTTTTGTT
*
29639828 TTCTTGCTATTTTTTCTTATTTTC
1 TTCTTGCTATTTTTTCCTATTTTC
*
29639852 TTCTTG-TTTTTTTTCACTATTTT
1 TTCTTGCTATTTTTTC-CTATTTT
29639875 GATACCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (24 bp):
TTCTTGCTATTTTTTCCTATTTTC
Found at i:29648065 original size:28 final size:27
Alignment explanation
Indices: 29648021--29648088 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
29648011 AAATCCATTA
* *
29648021 ATATATACTATAT-AATAAAACCATGC
1 ATATATATTATATAAATAAAACCATCC
*
29648047 ATATATATTATATAAAATAAAGCCATCC
1 ATATATATTATAT-AAATAAAACCATCC
*
29648075 ATATATATAATATA
1 ATATATATTATATA
29648089 TGCATAACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 12 0.33
27 1 0.03
28 23 0.64
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (27 bp):
ATATATATTATATAAATAAAACCATCC
Found at i:29648298 original size:2 final size:2
Alignment explanation
Indices: 29648291--29648330 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
29648281 CCATTTACGC
* *
29648291 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AC GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29648331 CACACACCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:29649591 original size:3 final size:3
Alignment explanation
Indices: 29649583--29649617 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
29649573 AAATTAGTCT
29649583 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29649618 TTACTAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29651179 original size:28 final size:27
Alignment explanation
Indices: 29651130--29651187 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
29651120 CAAATTCCTA
*
29651130 TTTAAAAAAGCTTTAATTTTTTAATTATT
1 TTTAAAAAAGCTTTAATATTTT-ATT-TT
*
29651159 TTTAAAAAAGTTTTAA-ATTTTATTTT
1 TTTAAAAAAGCTTTAATATTTTATTTT
29651185 TTT
1 TTT
29651188 GAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 3 0.11
28 4 0.15
29 15 0.56
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTAAAAAAGCTTTAATATTTTATTTT
Found at i:29656945 original size:126 final size:127
Alignment explanation
Indices: 29656677--29656967 Score: 476
Period size: 126 Copynumber: 2.3 Consensus size: 127
29656667 CCAAACATGC
* * *
29656677 GCTATTGTAACAAAATCGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
* * *
29656742 ACATAAAGGGTTTTTTTACACTATTTGCTCAGAAACGTCTACTTAAAATTATTTTTTCAGGA
66 ACATAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
* * *
29656804 GCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGACAATGCATCCT
1 GCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
* *
29656869 GCTTAAAGCG-TTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
66 ACATAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
29656930 GCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTT
1 GCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTT
29656968 CCCTTAAAAA
Statistics
Matches: 150, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
126 84 0.56
127 66 0.44
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (127 bp):
GCTACTGTAGCAAAAGCGCGTCCACATGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCATCCT
ACATAAAGCGTTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAGGA
Found at i:29657199 original size:14 final size:14
Alignment explanation
Indices: 29657170--29657204 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29657160 CCAAAACTCT
*
29657170 AACCCT-AACCTTA
1 AACCCTAAACCTAA
29657183 AACCCTAAACCTAA
1 AACCCTAAACCTAA
29657197 AACCCTAA
1 AACCCTAA
29657205 CTGTAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
AACCCTAAACCTAA
Found at i:29660153 original size:183 final size:183
Alignment explanation
Indices: 29659838--29660192 Score: 557
Period size: 183 Copynumber: 1.9 Consensus size: 183
29659828 TCAACCATGG
* * ** * *
29659838 GCACTTTTCTCCGTACAGTCTGTCTGAACCTCTGTGAAGTCAATTGTTATTAATATTCATTTTCG
1 GCACTTTTCTCCGTACAGTCTGTCCGAACCTCCGCAAAGTCAATTATCATTAATATTCATTTTCG
* * *
29659903 ATTTAGTTTGCCCAAACCTTTGCAAATCCTCCTTGTTAATTTGAACACATAAGTGTTCTCCCGCA
66 ATATAGTTTGCCCAAACCTCTACAAATCCTCCTTGTTAATTTGAACACATAAGTGTTCTCCCGCA
*
29659968 AGGCCGGGTTTATTTGCCAATATTGATTTGCATTCACATGCCAATATTGATTT
131 AGGCCGGGTTCATTTGCCAATATTGATTTGCATTCACATGCCAATATTGATTT
* * * * *
29660021 GCACTTTTCTCTGTATAGTTTGTCCGAACCTCCGCAAAGTTAATTATCATTAATATTCATTTTTG
1 GCACTTTTCTCCGTACAGTCTGTCCGAACCTCCGCAAAGTCAATTATCATTAATATTCATTTTCG
* *
29660086 ATATAGTTTGCCCAAACCTCTACAAATCCTCCTTGTTAATTTGAACACATAAGTTTTCTCTCGCA
66 ATATAGTTTGCCCAAACCTCTACAAATCCTCCTTGTTAATTTGAACACATAAGTGTTCTCCCGCA
29660151 AGGCCGGGTTCATTTGCCAATATTGATTTGCATTCACATGCC
131 AGGCCGGGTTCATTTGCCAATATTGATTTGCATTCACATGCC
29660193 TTACTAGAGG
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 155 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (183 bp):
GCACTTTTCTCCGTACAGTCTGTCCGAACCTCCGCAAAGTCAATTATCATTAATATTCATTTTCG
ATATAGTTTGCCCAAACCTCTACAAATCCTCCTTGTTAATTTGAACACATAAGTGTTCTCCCGCA
AGGCCGGGTTCATTTGCCAATATTGATTTGCATTCACATGCCAATATTGATTT
Found at i:29660888 original size:98 final size:98
Alignment explanation
Indices: 29660719--29660915 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
29660709 ATACAATAAA
*
29660719 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
29660784 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
* * *
29660817 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
* **
29660882 CCTTTAGAATCTCAAACTTGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
29660915 A
1 A
29660916 TGATTTTAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAACCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
Found at i:29661246 original size:13 final size:12
Alignment explanation
Indices: 29661224--29661268 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
29661214 CATTAATGAC
*
29661224 ATAAAAAAATAA
1 ATAAACAAATAA
29661236 TATAAACAAATAA
1 -ATAAACAAATAA
29661249 ATAAACGAAATAA
1 ATAAAC-AAATAA
29661262 A-AAACAA
1 ATAAACAA
29661269 TAATCCATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 2 0.07
12 10 0.33
13 18 0.60
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (12 bp):
ATAAACAAATAA
Found at i:29661655 original size:16 final size:15
Alignment explanation
Indices: 29661633--29661671 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29661623 AGATTATTTA
29661633 AAAAAAAAGCTACATAT
1 AAAAAAAA-CTACAT-T
*
29661650 AAAAAAAATTACATT
1 AAAAAAAACTACATT
29661665 AAAAAAA
1 AAAAAAA
29661672 TATGCATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.38
16 5 0.24
17 8 0.38
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAAAAAACTACATT
Found at i:29661764 original size:28 final size:26
Alignment explanation
Indices: 29661716--29661771 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
29661706 ATATATATTT
*
29661716 AAAAAAATTAAATATGAAAAATAATAA
1 AAAAAAATTAAATAAGAAAAATAA-AA
29661743 AAAAATAATTAAATAA-AGAAAATAAAA
1 AAAAA-AATTAAATAAGA-AAAATAAAA
29661770 AA
1 AA
29661772 TGGACTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAAAAATTAAATAAGAAAAATAAAA
Found at i:29661766 original size:25 final size:26
Alignment explanation
Indices: 29661716--29661771 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
29661706 ATATATATTT
29661716 AAAAAAATTAAATATGAAAAATAATAA
1 AAAAAAATTAAATA-GAAAAATAATAA
*
29661743 AAAAATAATTAAATA-AAGAA-AATAA
1 AAAAA-AATTAAATAGAAAAATAATAA
29661768 AAAA
1 AAAA
29661772 TGGACTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 9 0.33
26 4 0.15
27 5 0.19
28 9 0.33
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (26 bp):
AAAAAAATTAAATAGAAAAATAATAA
Found at i:29664181 original size:17 final size:17
Alignment explanation
Indices: 29664161--29664193 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29664151 TATTTGTATG
*
29664161 GAATATTTCTTTGAATA
1 GAATATTTCTTCGAATA
29664178 GAATATTTCTTCGAAT
1 GAATATTTCTTCGAAT
29664194 CTCCACGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (17 bp):
GAATATTTCTTCGAATA
Found at i:29671090 original size:16 final size:16
Alignment explanation
Indices: 29671069--29671101 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29671059 ATATATCACA
*
29671069 TTTGCATATATAAAGC
1 TTTGCACATATAAAGC
29671085 TTTGCACATATAAAGC
1 TTTGCACATATAAAGC
29671101 T
1 T
29671102 AAAGCAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (16 bp):
TTTGCACATATAAAGC
Found at i:29674549 original size:16 final size:16
Alignment explanation
Indices: 29674528--29674562 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
29674518 TTACACAGGC
29674528 ACAGACACAGGCTAGG
1 ACAGACACAGGCTAGG
29674544 ACAGACACAGGCTAGG
1 ACAGACACAGGCTAGG
29674560 ACA
1 ACA
29674563 TGGCCGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.29, T:0.06
Consensus pattern (16 bp):
ACAGACACAGGCTAGG
Found at i:29680253 original size:23 final size:21
Alignment explanation
Indices: 29680227--29680269 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
29680217 CGTGTTCATT
*
29680227 TGTTTTCAAATGAATCATACATG
1 TGTTATCAAATG--TCATACATG
*
29680250 TGTTATGAAATGTCATACAT
1 TGTTATCAAATGTCATACAT
29680270 ACATACGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
23 10 0.56
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
TGTTATCAAATGTCATACATG
Found at i:29682132 original size:136 final size:136
Alignment explanation
Indices: 29681893--29682146 Score: 320
Period size: 135 Copynumber: 1.9 Consensus size: 136
29681883 GGTTACCCTA
* * * *
29681893 TTTCAAGTGCTGGTCTTGAATGTCCTATCGAAGGCTGAGTTTCGGCATGTGTTGCGGATACTTGA
1 TTTCAAGTGCTGGTCTTGAATGTCCTATCCAAGGCTGAGGTTCGGCATGTGTTACGGATACTCGA
* **
29681958 CAGCTTGTGTGAGTAACACTGTGTAGCTACTTTCTGACCGAAAAATTGTGTGAACAGACTAGGTT
66 CAGCTTGTGTGAGCAACACTAAGTAGCTACTTTCTGACCGAAAAATTGTGTGAACAGACTAGGTT
29682023 ACTATG
131 ACTATG
* *
29682029 TTTCAGGTGCTGGTCTTGAATGTCCTA-CCATGGCTGAGGTTC-G-ATAGTAGTTACGGATACTC
1 TTTCAAGTGCTGGTCTTGAATGTCCTATCCAAGGCTGAGGTTCGGCAT-GT-GTTACGGATACTC
* * *
29682091 GATAGCTTGTGTGAGCAACA-TCAAGTAGCTTACATTT-TGACCGACAACTTGTGTGA
64 GACAGCTTGTGTGAGCAACACT-AAGTAGC-TAC-TTTCTGACCGAAAAATTGTGTGA
29682147 GCAAGCCCAT
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
133 2 0.02
134 4 0.04
135 46 0.46
136 46 0.46
137 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (136 bp):
TTTCAAGTGCTGGTCTTGAATGTCCTATCCAAGGCTGAGGTTCGGCATGTGTTACGGATACTCGA
CAGCTTGTGTGAGCAACACTAAGTAGCTACTTTCTGACCGAAAAATTGTGTGAACAGACTAGGTT
ACTATG
Found at i:29687494 original size:29 final size:28
Alignment explanation
Indices: 29687421--29687495 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 28
29687411 ATAAGGAATG
* *
29687421 AAATT-TAATTTT-CGAGATTTGGGACA
1 AAATTGTAATTTTGCAAAATTTGGGACA
* * *
29687447 AAAATGTAAATATGCCAAAATTTGGAGACA
1 AAATTGTAATTTTG-CAAAATTTGG-GACA
29687477 AAATTGTAATTTTGCAAAA
1 AAATTGTAATTTTGCAAAA
29687496 AGTTGAGTCG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
26 4 0.11
27 5 0.14
29 13 0.35
30 15 0.41
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (28 bp):
AAATTGTAATTTTGCAAAATTTGGGACA
Found at i:29687999 original size:85 final size:85
Alignment explanation
Indices: 29687894--29688176 Score: 397
Period size: 85 Copynumber: 3.3 Consensus size: 85
29687884 TTATTGACTC
* * * * * * *
29687894 TAAAGGTGGTTGCTAAGTGCTGATCCCACTGTATTTTTTATTGTGAAAGGGGTTGCTATGTGTTG
1 TAAAGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
29687959 ATTCCCCGTATCACTGAATA
66 ATTCCCCGTATCACTGAATA
29687979 TAAAGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
1 TAAAGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
* * *
29688044 ATTCCCTGAATCACTAAATA
66 ATTCCCCGTATCACTGAATA
* * * * *
29688064 TAAAGGTGGTTTCTAACTACTGATTCCACCGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
1 TAAAGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
*
29688129 ATTCCCCGTATCACTGAATT
66 ATTCCCCGTATCACTGAATA
* *
29688149 TATA-GTAGTTGCTAAGTGCTGAATCCAC
1 TAAAGGTAGTTGCTAAGTGCTGATTCCAC
29688177 CGAGTAACGA
Statistics
Matches: 173, Mismatches: 25, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
84 19 0.11
85 154 0.89
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (85 bp):
TAAAGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTG
ATTCCCCGTATCACTGAATA
Found at i:29688003 original size:42 final size:42
Alignment explanation
Indices: 29687859--29688179 Score: 170
Period size: 42 Copynumber: 7.6 Consensus size: 42
29687849 TTCCCCGAGG
* * * * * * *
29687859 GGTTGCTAAGTGCTAATACCCTGAATTATTGACTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATAAAGGT
* *** * * *
29687901 GGTTGCTAAGTGCTGA-TCCCACTGTATTTTTTATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCC-C-GAATCACTGAATAT-AAAGGT
* * *
29687944 GGTTGCTATGTGTTGATTCCCCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATAAAGGT
* * * * *
29687986 AGTTGCTAAGTGCTGATTCCACTGAATC-TTTAAGTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGAA-TAT-AAAGGT
* * *
29688029 GGTTGCTATGTGCTGATTCCCTGAATCACTAAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATAAAGGT
* * * * * *
29688071 GGTTTCTAACTACTGATTCCACCGAATC-TTTAAGTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGAA-TAT-AAAGGT
* * * *
29688114 GGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTATA-GT
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATAAAGGT
* *
29688155 AGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
29688180 GTAACGAATA
Statistics
Matches: 213, Mismatches: 50, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
40 1 0.00
41 32 0.15
42 82 0.38
43 79 0.37
44 19 0.09
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCACTGAATATAAAGGT
Found at i:29688036 original size:43 final size:41
Alignment explanation
Indices: 29687856--29688134 Score: 193
Period size: 43 Copynumber: 6.6 Consensus size: 41
29687846 TGATTCCCCG
* * * * *
29687856 AGGGGTTGCTAAGTGCTAATACCCTGAAT-TATTGACTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCTGAATCT-TTAAGTGTAA
* * * * *
29687897 AGGTGGTTGCTAAGTGCTGATCCCACTGTATTTTTTATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CTGAATCTTTAAGTGT-AA
* * * * * * *
29687941 AGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAA-TATAA
1 AGGGGTTGCTAAGTGCTGATTCCCTGAATC-TTTAAGTGTAA
*
29687982 AGGTAGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CTGAATCTTTAAGTGT-AA
* ** * *
29688026 AGGGGTTGCTATGTGCTGATTCCCTGAATCACTAAATATAA
1 AGGGGTTGCTAAGTGCTGATTCCCTGAATCTTTAAGTGTAA
* * * *
29688067 AGGTGGTTTCTAACTACTGATTCCACCGAATCTTTAAGTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CTGAATCTTTAAGTGT-AA
*
29688111 AGGGGTTGCTATGTGCTGATTCCC
1 AGGGGTTGCTAAGTGCTGATTCCC
29688135 CGTATCACTG
Statistics
Matches: 184, Mismatches: 42, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
41 13 0.07
42 74 0.40
43 81 0.44
44 16 0.09
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCTGAATCTTTAAGTGTAA
Found at i:29688138 original size:170 final size:169
Alignment explanation
Indices: 29687856--29688176 Score: 444
Period size: 170 Copynumber: 1.9 Consensus size: 169
29687846 TGATTCCCCG
* * * * * * *
29687856 AGGGGTTGCTAAGTGCTAATACCCTGAATTATTGACTCTAAAGGTGGTTGCTAAGTGCTGATCCC
1 AGGGGTTGCTAAGTGCTAATACCCTGAATCACTAAATATAAAGGTGGTTGCTAACTACTGATCCC
* * * * * *
29687921 ACTGTATTTTTTATTGTGAAAGGGGTTGCTATGTGTTGATTCCCCGTATCACTGAATATAAAGGT
66 ACCGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAA-GT
*
29687986 AGTTGCTAAGTGCTGATTCCACTGAATCTTTAAGTGTGAA
130 AGTTGCTAAGTGCTGAATCCACTGAATCTTTAAGTGTGAA
* * * * *
29688026 AGGGGTTGCTATGTGCTGATTCCCTGAATCACTAAATATAAAGGTGGTTTCTAACTACTGATTCC
1 AGGGGTTGCTAAGTGCTAATACCCTGAATCACTAAATATAAAGGTGGTTGCTAACTACTGATCCC
* *
29688091 ACCGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATTTATAGTA
66 ACCGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGTA
29688156 GTTGCTAAGTGCTGAATCCAC
131 GTTGCTAAGTGCTGAATCCAC
29688177 CGAGTAACGA
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
169 23 0.18
170 107 0.82
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (169 bp):
AGGGGTTGCTAAGTGCTAATACCCTGAATCACTAAATATAAAGGTGGTTGCTAACTACTGATCCC
ACCGAATCTTTAAGTGTGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGTA
GTTGCTAAGTGCTGAATCCACTGAATCTTTAAGTGTGAA
Found at i:29693056 original size:30 final size:30
Alignment explanation
Indices: 29693010--29693089 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
29693000 TTCACGAGCC
*
29693010 TAGGGG-AAAATTGTAATTTTGTGAAACTT
1 TAGGGGCAAAAATGTAATTTTGTGAAACTT
29693039 TAGGGGCAAAAATGTAATTTTGTGAAACTT
1 TAGGGGCAAAAATGTAATTTTGTGAAACTT
*
29693069 TAAGGGCAAAAATGTAATTTT
1 TAGGGGCAAAAATGTAATTTT
29693090 CCAAAGTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 6 0.12
30 42 0.88
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTTTGTGAAACTT
Found at i:29693429 original size:43 final size:43
Alignment explanation
Indices: 29693315--29693474 Score: 154
Period size: 42 Copynumber: 3.8 Consensus size: 43
29693305 GGAATACATG
* *
29693315 GAATAAAAAGG-GGTTGCTAAGTGCTGATTCC-CTGA-ATTATT
1 GAATATAAAGGTGGTTGCTAAGTGCTGATTCCACT-ATATCATT
* * *
29693356 -AACTCTAAAGGTGGTTGCTATGTGCTGATTCCACTATATCTTT
1 GAA-TATAAAGGTGGTTGCTAAGTGCTGATTCCACTATATCATT
* * * * *
29693399 GATTGTGAAAGG-GGTAGCTACGTGCTGATTCC-CTGTATCATT
1 GAATAT-AAAGGTGGTTGCTAAGTGCTGATTCCACTATATCATT
29693441 GAATAT-AAGGTGGTTGCTAAGTGCTGATTCCACT
1 GAATATAAAGGTGGTTGCTAAGTGCTGATTCCACT
29693475 GAGTAATGGT
Statistics
Matches: 96, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
40 6 0.06
41 24 0.25
42 34 0.35
43 26 0.27
44 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
GAATATAAAGGTGGTTGCTAAGTGCTGATTCCACTATATCATT
Found at i:29695014 original size:21 final size:20
Alignment explanation
Indices: 29694965--29695021 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
29694955 ATTAAATGGA
29694965 AATTGCAAATGATATTATTTG
1 AATTG-AAATGATATTATTTG
29694986 AATT-AAATGA-ATTATTGTGG
1 AATTGAAATGATATTATT-T-G
*
29695006 TATTGAAATGTATATT
1 AATTGAAATG-ATATT
29695022 GGATTGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 4 0.13
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
AATTGAAATGATATTATTTG
Found at i:29695060 original size:15 final size:15
Alignment explanation
Indices: 29695040--29695080 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
29695030 AAATTGAATT
29695040 GAATCGTGAATATGA
1 GAATCGTGAATATGA
*
29695055 GAATCGTGAACATGA
1 GAATCGTGAATATGA
29695070 GAATCGTGAAT
1 GAATCGTGAAT
29695081 TAAATGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (15 bp):
GAATCGTGAATATGA
Found at i:29696856 original size:21 final size:20
Alignment explanation
Indices: 29696832--29696897 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
29696822 GGAATGTAAA
29696832 CAGGGGCACGTATGTGCAATT
1 CAGGGGCACGTATGTGCAA-T
* * * *
29696853 CAGGGGTATCG-AAGTACAAA
1 CAGGGGCA-CGTATGTGCAAT
*
29696873 CAGGGGCACATATGTGCAAAT
1 CAGGGGCACGTATGTGC-AAT
29696894 CAGG
1 CAGG
29696898 AAATAATTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 19 0.58
22 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:29703465 original size:23 final size:23
Alignment explanation
Indices: 29703439--29703487 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29703429 AATTATGTTT
* *
29703439 CATATA-CATGTATCATCCATTTC
1 CATATACCATGTAACA-ACATTTC
29703462 CATATACCATGTAACAACATTTC
1 CATATACCATGTAACAACATTTC
29703485 CAT
1 CAT
29703488 GTAATTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (23 bp):
CATATACCATGTAACAACATTTC
Found at i:29708838 original size:19 final size:20
Alignment explanation
Indices: 29708816--29708870 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
29708806 CTAAATCCTT
29708816 AAAAAACCTTAACCCTAAC-
1 AAAAAACCTTAACCCTAACA
* * *
29708835 -AAAACCCCTAAACCTAACA
1 AAAAAACCTTAACCCTAACA
29708854 AAAAAACCTTAACCCTA
1 AAAAAACCTTAACCCTA
29708871 GGAGAAAGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAAACCTTAACCCTAACA
Found at i:29708850 original size:18 final size:18
Alignment explanation
Indices: 29708801--29708856 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
29708791 TTTGCACTTT
29708801 AACCCCTAAATCCTTAA-AA
1 AACCCCTAAA-CC-TAACAA
* *
29708820 AA-CCTTAACCCTAACAA
1 AACCCCTAAACCTAACAA
29708837 AACCCCTAAACCTAACAA
1 AACCCCTAAACCTAACAA
29708855 AA
1 AA
29708857 AAACCTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 3 0.10
17 6 0.19
18 20 0.65
19 2 0.06
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (18 bp):
AACCCCTAAACCTAACAA
Found at i:29709592 original size:2 final size:2
Alignment explanation
Indices: 29709585--29709621 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29709575 CTCGTTACAA
29709585 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
29709622 TATATACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29713133 original size:13 final size:13
Alignment explanation
Indices: 29713117--29713143 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29713107 GGGGTGCTTT
29713117 TTAGAAATTTAAG
1 TTAGAAATTTAAG
29713130 TTAGAAATTTAAG
1 TTAGAAATTTAAG
29713143 T
1 T
29713144 GATTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (13 bp):
TTAGAAATTTAAG
Found at i:29713749 original size:22 final size:21
Alignment explanation
Indices: 29713724--29713767 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
29713714 AAGCATATAA
*
29713724 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
29713746 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
29713767 A
1 A
29713768 CTTATATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:29713776 original size:22 final size:22
Alignment explanation
Indices: 29713751--29713821 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
29713741 TCAATAAATG
29713751 ATTTGGTTAATACAATACTTAT
1 ATTTGGTTAATACAATACTTAT
* * **
29713773 ATTT-GATAA-GCATATGA-AAAT
1 ATTTGGTTAATACA-AT-ACTTAT
29713794 AATTTGGTTAATACAATACTTAT
1 -ATTTGGTTAATACAATACTTAT
29713817 ATTTG
1 ATTTG
29713822 ATAAGCATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 8 0.23
22 15 0.43
23 8 0.23
24 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (22 bp):
ATTTGGTTAATACAATACTTAT
Found at i:29713799 original size:44 final size:44
Alignment explanation
Indices: 29713746--29713837 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
29713736 TATATTCAAT
*
29713746 AAATGATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATAATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
29713790 AAATAATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
1 AAATAATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
29713834 AAAT
1 AAAT
29713838 GAAAGTCGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (44 bp):
AAATAATTTGGTTAATACAATACTTATATTTGATAAGCATATGA
Found at i:29722345 original size:19 final size:20
Alignment explanation
Indices: 29722317--29722363 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29722307 TTTTCGTTAT
*
29722317 TTTTTATTAAGTTAAAAAT-A
1 TTTTT-TTAAATTAAAAATAA
*
29722337 TTTTTTTAAATTTAAAATAA
1 TTTTTTTAAATTAAAAATAA
29722357 TTTTTTT
1 TTTTTTT
29722364 GTTGTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTTTAAATTAAAAATAA
Found at i:29741411 original size:9 final size:9
Alignment explanation
Indices: 29741397--29741425 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29741387 AAAAACTAAG
29741397 AAACTAAAT
1 AAACTAAAT
29741406 AAACTAAAT
1 AAACTAAAT
29741415 AAA-TAAAT
1 AAACTAAAT
29741423 AAA
1 AAA
29741426 TCTCAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACTAAAT
Found at i:29753755 original size:30 final size:30
Alignment explanation
Indices: 29753695--29753756 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
29753685 GCTTTTTAAA
* * * *
29753695 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGAACCAAAATTTT
29753725 AATATTTACAAAAAGAGGAACCAAAATTTT
1 AATATTTACAAAAAGAGGAACCAAAATTTT
29753755 AA
1 AA
29753757 AAATAATTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGAACCAAAATTTT
Found at i:29756189 original size:15 final size:15
Alignment explanation
Indices: 29756169--29756198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29756159 TGTTTATGAG
29756169 TATTGATCAAATTAT
1 TATTGATCAAATTAT
*
29756184 TATTGATCGAATTAT
1 TATTGATCAAATTAT
29756199 CAACTTACTC
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:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
TATTGATCAAATTAT
Found at i:29766635 original size:20 final size:20
Alignment explanation
Indices: 29766608--29766664 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
29766598 CAAACTAAAG
29766608 TAAGCTAAAAATGAGCTCAT
1 TAAGCTAAAAATGAGCTCAT
* * *
29766628 TGAGCTAAGAACGAGCTCAT
1 TAAGCTAAAAATGAGCTCAT
*
29766648 TAAGCTAAAATTGAGCT
1 TAAGCTAAAAATGAGCT
29766665 GAATTGAACT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (20 bp):
TAAGCTAAAAATGAGCTCAT
Found at i:29768174 original size:21 final size:21
Alignment explanation
Indices: 29768135--29768175 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29768125 TGGAAACAGG
**
29768135 AATGATCTTAATGGTAATCCA
1 AATGATCTTAATGAAAATCCA
29768156 AATGATCTTAATGAAAATCC
1 AATGATCTTAATGAAAATCC
29768176 TCTCATTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (21 bp):
AATGATCTTAATGAAAATCCA
Found at i:29775121 original size:102 final size:100
Alignment explanation
Indices: 29774943--29775283 Score: 357
Period size: 102 Copynumber: 3.4 Consensus size: 100
29774933 GTCGATGAAA
* * * *
29774943 ACGTGTGTAGTACTGTGTGGAGGCTACTACATGTATCGATAAA-TAATGGTCACATGTGTAGTAC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTAC
29775007 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTAAGC
65 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTT-AGC
* * * * * *
29775045 ATGTGTGTAGTACTTTGTGAATGCTACTACGTGTATCGGTAAACTACGGTTACATGTGTAGTACG
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTACT
* * *
29775110 AAGTGAAGGCTACAATGGGTACCGAAATGCTTTGGTC
66 AAGTGAAGGCTACTATGTGTACCGAAA-GCTTTAG-C
* * * * * *
29775147 ACGTATGTGGTACTATGTGAAGGCTACTACGTG-AGCCGTAAAACT-TGATCACGTGTGTAGTAC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGTAC
* * * * * * *
29775210 TATGTGAAGGCTACTACGTGAACTGTAAAAC-TGATC
65 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTAGC
29775246 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
29775284 AATGATAAAA
Statistics
Matches: 195, Mismatches: 38, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
99 32 0.16
100 3 0.02
101 40 0.21
102 119 0.61
103 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (100 bp):
ACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTACT
AAGTGAAGGCTACTATGTGTACCGAAAGCTTTAGC
Found at i:29775264 original size:49 final size:50
Alignment explanation
Indices: 29774943--29775278 Score: 250
Period size: 51 Copynumber: 6.7 Consensus size: 50
29774933 GTCGATGAAA
* * * * * * *
29774943 ACGTGTGTAGTACTGTGTGGAGGCTACTACATGTATCGATAAATA-ATGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATC
* * * * * * *
29774994 ACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AGAAGCTTTAAGC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATC
* * * * * * * *
29775045 ATGTGTGTAGTACTTTGTGAATGCTACTACGTGTATCGGT-AAACTACGGTT
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AACCGTAAAACT-TGATC
* * * * * * * * *
29775096 ACATGTGTAGTACGAAGTGAAGGCTACAATGGGTACCG-AAATGCTTTGGTC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAA-AC-TTGATC
* * *
29775147 ACGTATGTGGTACTATGTGAAGGCTACTACGTGAGCCGTAAAACTTGATC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATC
*
29775197 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC-TGATC
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATC
29775246 ACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 ACGTGTGTAGTACTATGTGAAGGCTACTACGTG
29775279 TATCGAATGA
Statistics
Matches: 217, Mismatches: 58, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
49 39 0.18
50 52 0.24
51 120 0.55
52 6 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (50 bp):
ACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATC
Found at i:29782647 original size:51 final size:50
Alignment explanation
Indices: 29782571--29782804 Score: 175
Period size: 51 Copynumber: 4.6 Consensus size: 50
29782561 GATGAACACG
** *
29782571 TGTGTAGTACTGTGTGGAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAAT-ATGGTCACA
* * * * * *
29782622 TGTGTACTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAG-CACA
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAA-ATATG-GTCACA
* ** * * * *
29782673 TCTGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACTACGGTTACA
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAA-TATGGTCACA
* * * * * *
29782724 TGTGTAGTACTAAGTGAAGGCTACAATGGGTACCGA-AATGCTTTGGTCACA
1 TGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAA--ATATGGTCACA
* * *
29782775 TATGTGGTACTATGTGAAGGCTACTACGTG
1 TGTGTAGTACTAAGTGAAGGCTACTACGTG
29782805 AAGGCTACTA
Statistics
Matches: 136, Mismatches: 41, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
50 3 0.02
51 131 0.96
52 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGAAGGCTACTACGTGTATCGATAAATATGGTCACA
Found at i:29782757 original size:102 final size:102
Alignment explanation
Indices: 29782573--29782804 Score: 317
Period size: 102 Copynumber: 2.3 Consensus size: 102
29782563 TGAACACGTG
* *
29782573 TGTAGTACTGTGTGGAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTACTACTAAGTG
1 TGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAACGGTCACATGTGTACTACTAAGTG
* * *
29782638 AAGGCTACTATGTGTACCGAGAA-GCTTTGAG-CACATC
66 AAGGCTACAATGGGTACCGA-AATGCTTTG-GTCACATA
* * * *
29782675 TGTAGTACTGTGTGAATGCTACTACGTGTATCGGTAAACT-ACGGTTACATGTGTAGTACTAAGT
1 TGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAACGGTCACATGTGTACTACTAAGT
29782739 GAAGGCTACAATGGGTACCGAAATGCTTTGGTCACATA
65 GAAGGCTACAATGGGTACCGAAATGCTTTGGTCACATA
* *
29782777 TGTGGTACTATGTGAAGGCTACTACGTG
1 TGTAGTACTGTGTGAAGGCTACTACGTG
29782805 AAGGCTACTA
Statistics
Matches: 115, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
101 3 0.03
102 111 0.97
103 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (102 bp):
TGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAACGGTCACATGTGTACTACTAAGTG
AAGGCTACAATGGGTACCGAAATGCTTTGGTCACATA
Found at i:29782805 original size:14 final size:14
Alignment explanation
Indices: 29782782--29782819 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
29782772 ACATATGTGG
*
29782782 TACTATGTGAAGGC
1 TACTACGTGAAGGC
29782796 TACTACGTGAAGGC
1 TACTACGTGAAGGC
29782810 TACTACGTGA
1 TACTACGTGA
29782820 GCCGTAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (14 bp):
TACTACGTGAAGGC
Found at i:29782877 original size:50 final size:49
Alignment explanation
Indices: 29782796--29782913 Score: 182
Period size: 49 Copynumber: 2.4 Consensus size: 49
29782786 ATGTGAAGGC
* * *
29782796 TACTACGTGAAGGCTACTACGTGAGCCGTAAAACTTGATCACGTGTGTAG
1 TACTATGTGAAGGCTACTACGTGAACCGTAAAAC-TGATCACATGTGTAG
*
29782846 TACTATGTGAAGGCTACTACGTGAACTGTAAAACTGATCACATGTGTAG
1 TACTATGTGAAGGCTACTACGTGAACCGTAAAACTGATCACATGTGTAG
*
29782895 TACTATATGAAGGCTACTA
1 TACTATGTGAAGGCTACTA
29782914 AGTGTATCGA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
49 32 0.51
50 31 0.49
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (49 bp):
TACTATGTGAAGGCTACTACGTGAACCGTAAAACTGATCACATGTGTAG
Found at i:29788140 original size:25 final size:25
Alignment explanation
Indices: 29788099--29788159 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
29788089 TCCTGTACAT
* * *
29788099 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACAAGCTATAAATCA
29788124 GTATGCTC-TCACAAGCTATAAATCA
1 GTATGCTCAT-ACAAGCTATAAATCA
*
29788149 GTAAGCTCATA
1 GTATGCTCATA
29788160 TGTGCTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (25 bp):
GTATGCTCATACAAGCTATAAATCA
Found at i:29790455 original size:25 final size:25
Alignment explanation
Indices: 29790417--29790464 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29790407 TAAGTTCGTG
*
29790417 TAATTAAATCATGTTTATATGTTTT
1 TAATTAAATCATGTATATATGTTTT
29790442 TAATTGAAAT-ATGTATATATGTT
1 TAATT-AAATCATGTATATATGTT
29790465 ATGAATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.52
Consensus pattern (25 bp):
TAATTAAATCATGTATATATGTTTT
Found at i:29790471 original size:25 final size:26
Alignment explanation
Indices: 29790418--29790472 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
29790408 AAGTTCGTGT
* * *
29790418 AATT-AAATCATGTTTATATGTTTTT
1 AATTGAAATCATGTATATATGTTATG
29790443 AATTGAAAT-ATGTATATATGTTATG
1 AATTGAAATCATGTATATATGTTATG
29790468 AATTG
1 AATTG
29790473 TATGGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (26 bp):
AATTGAAATCATGTATATATGTTATG
Found at i:29798696 original size:27 final size:27
Alignment explanation
Indices: 29798658--29798710 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
29798648 ATTAAATATA
29798658 AAGGGATTGCTAAGTGCTGATTCCCCC
1 AAGGGATTGCTAAGTGCTGATTCCCCC
*
29798685 AAGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGATTGCTAAGTGCTGATTCCCC
29798711 GAATCATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (27 bp):
AAGGGATTGCTAAGTGCTGATTCCCCC
Found at i:29806187 original size:21 final size:22
Alignment explanation
Indices: 29806153--29806197 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
29806143 GGACGTTGGT
29806153 ATTTAAAACATC-AAATAAGCA
1 ATTTAAAACATCAAAATAAGCA
** *
29806174 ATTTAAAAGTTCAAAATATGCA
1 ATTTAAAACATCAAAATAAGCA
29806196 AT
1 AT
29806198 AATAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (22 bp):
ATTTAAAACATCAAAATAAGCA
Found at i:29808788 original size:27 final size:27
Alignment explanation
Indices: 29808612--29808778 Score: 221
Period size: 27 Copynumber: 6.3 Consensus size: 27
29808602 AGAGGTCAAT
* *
29808612 AAATGACCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCTCATAGGGTA
* *
29808639 AAATGACCGAAATACTCT-ATAGGAT-
1 AAATGACCGAAATACCCTCATAGGGTA
*
29808664 AAATGATCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
* * *
29808691 AAATGATCGAAATACCCCCATATGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
**
29808718 AAATGACCGAAATACCCTCATAGAATA
1 AAATGACCGAAATACCCTCATAGGGTA
*
29808745 AAATGACCAAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCTCATAGGGTA
29808772 AAATGAC
1 AAATGAC
29808779 TGTTATACCC
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
25 16 0.13
26 13 0.11
27 94 0.76
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCATAGGGTA
Found at i:29808789 original size:81 final size:79
Alignment explanation
Indices: 29808612--29808777 Score: 253
Period size: 79 Copynumber: 2.1 Consensus size: 79
29808602 AGAGGTCAAT
* * * * *
29808612 AAATGACCGAAATACCCCCATAGGATAAAATGACCGAAATACTCTATAGGATAAATGATCGAAAT
1 AAATGATCGAAATACCCCCATAGGATAAAATGACCGAAATACCCTATAGAATAAATGACCAAAAT
29808677 ACCCTCATAGGGTA
66 ACCCTCATAGGGTA
29808691 AAATGATCGAAATACCCCCATATGG-TAAAATGACCGAAATACCCTCATAGAATAAAATGACCAA
1 AAATGATCGAAATACCCCCATA-GGATAAAATGACCGAAATACCCT-ATAGAAT-AAATGACCAA
29808755 AATACCCTCATAGGGTA
63 AATACCCTCATAGGGTA
29808772 AAATGA
1 AAATGA
29808778 CTGTTATACC
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
79 40 0.51
80 8 0.10
81 31 0.39
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (79 bp):
AAATGATCGAAATACCCCCATAGGATAAAATGACCGAAATACCCTATAGAATAAATGACCAAAAT
ACCCTCATAGGGTA
Found at i:29808972 original size:26 final size:26
Alignment explanation
Indices: 29808942--29809048 Score: 160
Period size: 26 Copynumber: 4.1 Consensus size: 26
29808932 TGGAGGAAGT
* **
29808942 ATACTATTACTGGTAGCTTTGCTGTG
1 ATACTATTACTGGCAGCTTTGCTACG
29808968 ATACTATTACTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTACG
* * *
29808994 GTACTGTTATTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTACG
29809020 ATACTATTACTGGCAGCTTTGCTACG
1 ATACTATTACTGGCAGCTTTGCTACG
29809046 ATA
1 ATA
29809049 TTGGTGTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTACG
Found at i:29809177 original size:28 final size:28
Alignment explanation
Indices: 29809145--29809211 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
29809135 TATTGCACTG
* ** *
29809145 CACTGATATTGTATTGGGCTAAGGCCCA
1 CACTGATACTGTATCAGGCGAAGGCCCA
*
29809173 CACTGTTACTGTATCAGGCGAAGGCCCA
1 CACTGATACTGTATCAGGCGAAGGCCCA
29809201 CACTG-TACTGT
1 CACTGATACTGT
29809212 TACTGAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (28 bp):
CACTGATACTGTATCAGGCGAAGGCCCA
Found at i:29813985 original size:43 final size:43
Alignment explanation
Indices: 29813912--29814042 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 43
29813902 ACACATATAT
* * * * * *
29813912 CATATACAATGTC-ATATCCCATATATGGTCTTACATGTTATCA
1 CATAT-CAATGCCAATATCCCAGACAGGGTCTTACACGTAATCA
* * * * **
29813955 CATATCGATGCCACTGTCCTAGACAGGGTCTTACACGTAATTT
1 CATATCAATGCCAATATCCCAGACAGGGTCTTACACGTAATCA
* *
29813998 CATATCAATGCCAATATCCCAGACATGGTCTTACACGAAATCA
1 CATATCAATGCCAATATCCCAGACAGGGTCTTACACGTAATCA
29814041 CA
1 CA
29814043 CTCGAGAGTC
Statistics
Matches: 67, Mismatches: 20, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
42 5 0.07
43 62 0.93
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (43 bp):
CATATCAATGCCAATATCCCAGACAGGGTCTTACACGTAATCA
Found at i:29821764 original size:43 final size:43
Alignment explanation
Indices: 29821717--29821821 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
29821707 TCCCAAATAT
* * *
29821717 GGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGACAA
1 GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAA
* *
29821760 GGTCTTACACGTAATCGCATATCGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAA
*
29821803 GGTCTTACACGAAATCACA
1 GGTCTTACACGTAATCACA
29821822 CCTCGAGAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAA
Found at i:29827002 original size:39 final size:39
Alignment explanation
Indices: 29826954--29827091 Score: 141
Period size: 39 Copynumber: 3.5 Consensus size: 39
29826944 CATATTCACT
* * *
29826954 TTTAAGCATATATCACATTACACATATAATAACATAACA
1 TTTAAGCATATATCAAAATACTCATATAATAACATAACA
* * **
29826993 TTTATGCATATATAAAAATACTCATATAATCGCATAACA
1 TTTAAGCATATATCAAAATACTCATATAATAACATAACA
* * * * *
29827032 TTCAAGCATATATCATAATACTCATATAATCACAGAATA
1 TTTAAGCATATATCAAAATACTCATATAATAACATAACA
* * *
29827071 TTCAACCATATATCATAATAC
1 TTTAAGCATATATCAAAATAC
29827092 ACACAATCAT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCAAAATACTCATATAATAACATAACA
Found at i:29829355 original size:15 final size:14
Alignment explanation
Indices: 29829334--29829369 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
29829324 ATAATCCTTA
*
29829334 ATAATTATCTTAAT
1 ATAATTATCCTAAT
29829348 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
29829363 ATAATTA
1 ATAATTA
29829370 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:29833230 original size:39 final size:39
Alignment explanation
Indices: 29833147--29833285 Score: 147
Period size: 39 Copynumber: 3.6 Consensus size: 39
29833137 ATTCACTTTT
* * * *
29833147 AAGCTTATATCACATTACACATATAATCAC-ATACATTT
1 AAGCATATATCACAATACACATATAATCACAAAACATTC
* * * *
29833185 ACGCATATACCACAATACTCATACAATCACAAAACATTC
1 AAGCATATATCACAATACACATATAATCACAAAACATTC
* * *
29833224 AAGCATATATCATAGTACTCATATAATCACATAAA-ATTC
1 AAGCATATATCACAATACACATATAATCACA-AAACATTC
*
29833263 AAGCATATATCATAATACACATA
1 AAGCATATATCACAATACACATA
29833286 ATCATATTTA
Statistics
Matches: 84, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
38 24 0.29
39 57 0.68
40 3 0.04
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (39 bp):
AAGCATATATCACAATACACATATAATCACAAAACATTC
Found at i:29840028 original size:20 final size:20
Alignment explanation
Indices: 29840000--29840052 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
29839990 AAGACTATGA
*
29840000 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
29840020 ACCATTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
*
29840040 TCCATTCCATTTA
1 ACCATTCCATTTA
29840053 TTTAGCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:29854165 original size:6 final size:6
Alignment explanation
Indices: 29854154--29854187 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29854144 AGGTTTCTCA
* *
29854154 AAATGG AAATGG AAATGG AAATGA AAATGA AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
29854188 AAGAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.18
Consensus pattern (6 bp):
AAATGG
Found at i:29857047 original size:50 final size:50
Alignment explanation
Indices: 29856993--29857948 Score: 592
Period size: 50 Copynumber: 19.1 Consensus size: 50
29856983 TTGTACCTTC
* * * *
29856993 AATCTTTTTAACTGCGATGTCAGGGAAGCAAGATTTGCCGTTGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* ** ** * * * *
29857043 AATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCTGTTGTAGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * * * * *
29857093 AATCTTGTTGACTGCAATGTCGGGGAAGCAAGATTCACCGATATGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* *** * * * * *
29857143 AATCTGTTCCGCTGC-ATCGCCTGGGAAGTAAGATTCGTTGTTGTAGCTTT
1 AATCTTTTTAACTGCAAT-GTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * * * *
29857193 AATATTTTTTACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* *** * * * * *
29857243 AATCTGTTCCGCTG-TATGGCCTGAGG-AGTAAGATTCGCTGTTGTAGCTTT
1 AATCTTTTTAACTGCAAT-GTC-GGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * * *
29857293 AATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCACCGATGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * * * *
29857343 AATCTGTTCT-GCTGC-ATCGACTGGGG-AGTAAGATTCGCTGTTGTAGCTTT
1 AATCT-TTTTAACTGCAAT-GTC-GGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * * * * *
29857393 AATCTTTTTAATTGCAATGTTGGGGAAGAAAGATTCACCGATGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
*** * * *
29857443 AAT-TTGTTCCGCTGC-ATCGCCTGGGG-AGTAAGATTCGCTGTTGTAGCTTT
1 AATCTT-TTTAACTGCAAT-GTC-GGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * *
29857493 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
** *** ** * *
29857543 AATCTGCTCCGCTGC-ATCACCTGGGG-AGTAAGATTTGCTGTTGTGGCTTT
1 AATCTTTTTAACTGCAAT-GTC-GGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * *
29857593 AATCTTTTTAACTGCAATGT-GGGGAAAGCAAGATTCACCGTTGTAGCTTT
1 AATCTTTTTAACTGCAATGTCGGGG-AAGCAAGATTCGCTGTTGTGGCTTT
** ** * * * * * *
29857643 AATCTGCTCCACTGTACTGGCTGGGAGAGTAAGATTCG-TCGTTGTGACTTT
1 AATCTTTTTAACTGCAATGTCGGGGA-AGCAAGATTCGCT-GTTGTGGCTTT
* * *
29857694 AATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCACTGATT-TAGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTG-TTGTGGCTTT
* ** ** * * ** * *
29857744 AATCTGTTCCACTGCACCGCCTGGGAAGTTAGATTCGTTGTTGTAGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* *
29857794 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTC-ATCGATGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCT-GTTGTGGCTTT
* ** **** * * * * *
29857844 AATCTGTTCCACTGCACCACCAGGGAAGTAAGATTCGTTGTTATAGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
* * *
29857894 AATCTTTTTAATTGTAATGTCGGGGAAGCATGATTCGCTGTTGTGGCTTT
1 AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
29857944 AATCT
1 AATCT
29857949 GTTCCACTAC
Statistics
Matches: 655, Mismatches: 220, Indels: 62
0.70 0.23 0.07
Matches are distributed among these distances:
48 4 0.01
49 29 0.04
50 550 0.84
51 72 0.11
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (50 bp):
AATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTGGCTTT
Found at i:29857141 original size:100 final size:100
Alignment explanation
Indices: 29856968--29857978 Score: 1355
Period size: 100 Copynumber: 10.1 Consensus size: 100
29856958 AACTTTTGGA
** * * * * **
29856968 AAGTAAGATTCGCCATTGTACCTTCAATCTTTTTAACTGCGATGTCAGGGAAGCAAGATTTGCCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
*
29857033 TTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* *
29857068 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTGTTGACTGCAATGTCGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * *
29857133 ATATGGCTTTAATCTGTTCCGCTGCATCGCCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * *
29857168 AAGTAAGATTCGTTGTTGTAGCTTTAATATTTTTTACTGCAATGTCGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * **
29857233 ATGTGGCTTTAATCTGTTCCGCTGTATGGCCTGAGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTG-GG
*
29857269 -AGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTTGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
** * *
29857333 ATGTGGCTTTAATCTGTTCTGCTGCATCGACTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * * *
29857368 GAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAATTGCAATGTTGGGGAAGAAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * *
29857433 ATGTGGCTTTAATTTGTTCCGCTGCATCGCCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
*
29857468 GAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* * * *
29857533 ATGTGGCTTTAATCTGCTCCGCTGCATCACCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * *
29857568 GAGTAAGATTTGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGT-GGGGAAAGCAAGATTCACC
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGG-AAGCAAGATTCACC
* * * * * *
29857632 GTTGTAGCTTTAATCTGCTCCACTGTACTGGCTGGG
65 GATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
*
29857668 AGAGTAAGATTCG-TCGTTGT-GACTTTAATCTTTTTAACTGCAATGTAGGGGAAGCAAGATTCA
1 A-AGTAAGATTCGCT-GTTGTAG-CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCA
* * *
29857731 CTGATTTAGCTTTAATCTGTTCCACTGCACCGCCTGGG
63 CCGATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * *
29857769 AAGTTAGATTCGTTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCATCG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* *
29857834 ATGTGGCTTTAATCTGTTCCACTGCACCACCAGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
* * * * * * *
29857869 AAGTAAGATTCGTTGTTATAGCTTTAATCTTTTTAATTGTAATGTCGGGGAAGCATGATTCGCTG
1 AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
* *
29857934 TTGTGGCTTTAATCTGTTCCACTACACCGCCTGGG
66 ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
29857969 AGAGTAAGAT
1 A-AGTAAGAT
29857979 CTGTAATTCT
Statistics
Matches: 822, Mismatches: 79, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
99 6 0.01
100 717 0.87
101 95 0.12
102 4 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (100 bp):
AAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCG
ATGTGGCTTTAATCTGTTCCACTGCACCGCCTGGG
Found at i:29858135 original size:44 final size:44
Alignment explanation
Indices: 29858087--29858198 Score: 145
Period size: 44 Copynumber: 2.5 Consensus size: 44
29858077 ATCCGCTCTA
*
29858087 CTGTAATCTCAGGGAAATAGGATTACTAGCTTCAATCTGCTCCG
1 CTGTAATCTCAGGGAAATAAGATTACTAGCTTCAATCTGCTCCG
* * * *
29858131 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAAATAAGATTACTAGCTTCAATCTGCTCCG
* *
29858175 TTGTAA-CATCAGGGAGATAAGATT
1 CTGTAATC-TCAGGGAAATAAGATT
29858199 CACCATTTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.02
44 60 0.98
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
CTGTAATCTCAGGGAAATAAGATTACTAGCTTCAATCTGCTCCG
Found at i:29858501 original size:129 final size:129
Alignment explanation
Indices: 29858271--29858526 Score: 458
Period size: 129 Copynumber: 2.0 Consensus size: 129
29858261 AATCTTCAAT
*
29858271 CTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCATACACTTGAAGAT
1 CTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCATACACTTGAAGAT
*
29858336 AAGATTTGCAGTCTTTGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAAC
66 AAGATTTGCAGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAAC
* * *
29858400 CTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACTCTTGAAGAT
1 CTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCATACACTTGAAGAT
*
29858465 AAGATTTGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTA
66 AAGATTTGCAGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTA
29858527 GATCTTTTCT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 121 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (129 bp):
CTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCATACACTTGAAGAT
AAGATTTGCAGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGTAATTTCCTAAC
Found at i:29860656 original size:16 final size:15
Alignment explanation
Indices: 29860637--29860678 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
29860627 TTTTTTGTCA
29860637 TTTTTTATTTTGATT
1 TTTTTTATTTTGATT
* *
29860652 TTTTTTCATCTAGATT
1 TTTTTT-ATTTTGATT
29860668 TTTTTTATTTT
1 TTTTTTATTTT
29860679 TTCTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTTTTATTTTGATT
Found at i:29865365 original size:3 final size:3
Alignment explanation
Indices: 29865351--29865390 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
29865341 CAAATAAAAC
*
29865351 TAA TAA TGA TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
29865391 CATTGATGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29865490 original size:5 final size:5
Alignment explanation
Indices: 29865475--29865507 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
29865465 GGCAAATTTG
29865475 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
29865508 GAGAACCGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:29880046 original size:22 final size:24
Alignment explanation
Indices: 29880021--29880075 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
29880011 ATAAGAAGAG
29880021 AAATATTTTAAAAATTACAA-AA-A
1 AAATATTTTAAAAATTA-AAGAATA
* * *
29880044 AATTCTTTTAAAATTTAAAGAATA
1 AAATATTTTAAAAATTAAAGAATA
29880068 AAATATTT
1 AAATATTT
29880076 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 16 0.64
24 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATTTTAAAAATTAAAGAATA
Found at i:29884110 original size:13 final size:13
Alignment explanation
Indices: 29884094--29884119 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29884084 ATGACTTTTA
29884094 AATGATAATAAGT
1 AATGATAATAAGT
29884107 AATGATAATAAGT
1 AATGATAATAAGT
29884120 TACGATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
AATGATAATAAGT
Found at i:29890390 original size:32 final size:32
Alignment explanation
Indices: 29890339--29890512 Score: 192
Period size: 32 Copynumber: 5.5 Consensus size: 32
29890329 GAATGGCTAC
* ** *
29890339 AAGCCATAAGT-ACAGTAATATGATTAGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
**
29890370 AAGCCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* **
29890402 CAA-CCATCAGTAACAATAATATGA-CTGGTGCA
1 -AAGCCATCAGTAACAGTAATATGATC-GGCACA
*
29890434 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
**
29890466 AAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
29890498 AAGCTATCAGTAACA
1 AAGCCATCAGTAACA
29890513 TCGTAGCAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
31 13 0.11
32 103 0.87
33 3 0.03
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:29890509 original size:96 final size:95
Alignment explanation
Indices: 29890339--29890512 Score: 251
Period size: 96 Copynumber: 1.8 Consensus size: 95
29890329 GAATGGCTAC
* * *
29890339 AAGCCATAAGTACAGTAATATGATTAGCATAAAGCCATCAGTAGTAGTAATATGATCGGCACACA
1 AAGCCATAAGTACAGTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACA
29890404 ACCATCAGTAACAATAATATGACTGGTGCA
66 ACCATCAGTAACAATAATATGACTGGTGCA
* * * *
29890434 AAGCCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAATGGTAATATGATCGGCACA-
1 AAGCCATAAGT-ACAGTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACAC
*
29890498 AAGCTATCAGTAACA
65 AA-CCATCAGTAACA
29890513 TCGTAGCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
95 12 0.17
96 57 0.83
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (95 bp):
AAGCCATAAGTACAGTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACA
ACCATCAGTAACAATAATATGACTGGTGCA
Found at i:29891068 original size:27 final size:27
Alignment explanation
Indices: 29890734--29891055 Score: 326
Period size: 27 Copynumber: 11.9 Consensus size: 27
29890724 GGGCAAAATA
*
29890734 GTCA-TTTACCCTCTAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* *
29890760 ATCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
*
29890787 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* * * *
29890814 GTCTTTTTA-CCTCATGGGGGTATTATG
1 GTCATTTTACCCT-ATAGGGGCATTACG
* * *
29890841 ATTATTTTACCCTAT-GAGGGTATTACG
1 GTCATTTTACCCTATAG-GGGCATTACG
*
29890868 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
*
29890895 ATCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTATAGGGGCATTACG
* * * *
29890922 GGCATTTTAACCTAAAGGGGCATTACA
1 GTCATTTTACCCTATAGGGGCATTACG
* * * *
29890949 GTCTTTTTACCCTACAGAGGCATTACA
1 GTCATTTTACCCTATAGGGGCATTACG
* * *
29890976 GTCTTTTTACCCAAACAGGGGCATTACG
1 GTCATTTTACCC-TATAGGGGCATTACG
* * * * *
29891004 GTAATTTTATCCTATAAGGGCCTTACA
1 GTCATTTTACCCTATAGGGGCATTACG
*
29891031 ATCATTTTACCCTATAGGGGCATTA
1 GTCATTTTACCCTATAGGGGCATTA
29891056 TGGTTATTAT
Statistics
Matches: 245, Mismatches: 45, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
26 7 0.03
27 213 0.87
28 25 0.10
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGCATTACG
Found at i:29902010 original size:20 final size:20
Alignment explanation
Indices: 29901985--29902057 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
29901975 GAACCCTTCC
*
29901985 ATTTACTTACTTTCCATTAT
1 ATTTACTTACTTTCCATTGT
*
29902005 ATTTACTTACTTTTCATTGT
1 ATTTACTTACTTTCCATTGT
*
29902025 ATTTACTTACTTTCCATTGC
1 ATTTACTTACTTTCCATTGT
*
29902045 ATTTAATTACTTT
1 ATTTACTTACTTT
29902058 AGCTTAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTACTTACTTTCCATTGT
Found at i:29923140 original size:79 final size:79
Alignment explanation
Indices: 29923009--29923167 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
29922999 AAAATATGAT
29923009 TCTAAAAAATCCAGTCATAAACTCATTTTAAAATTGGTTAAGGTGATATCCCATGGAATTTGATT
1 TCTAAAAAATCCAGTCATAAACTCATTTTAAAATTGGTTAAGGTGATATCCCATGGAATTTGATT
29923074 TTCATGATCTGTTG
66 TTCATGATCTGTTG
* *
29923088 TCTAAAAAATCCAGTCATAAACTCATTTTGAAATTTGTTAAGGTGATATCCCATGGAATTTGATT
1 TCTAAAAAATCCAGTCATAAACTCATTTTAAAATTGGTTAAGGTGATATCCCATGGAATTTGATT
29923153 TTCATGATCTGTTG
66 TTCATGATCTGTTG
29923167 T
1 T
29923168 GTGTGGATAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (79 bp):
TCTAAAAAATCCAGTCATAAACTCATTTTAAAATTGGTTAAGGTGATATCCCATGGAATTTGATT
TTCATGATCTGTTG
Found at i:29923337 original size:42 final size:42
Alignment explanation
Indices: 29923265--29923469 Score: 268
Period size: 42 Copynumber: 4.9 Consensus size: 42
29923255 GGAAAACATT
* *
29923265 CATTACATTTAG-AGACCCAGGTGTGAAGGTCCATTTACTTTG
1 CATTGCATTTAGAAG-CCCAGGTGTGGAGGTCCATTTACTTTG
* * *
29923307 CATTGCATTTAGAATCCTAGGTATGGAGGTCCATTTACTTTG
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * *
29923349 CATTCCATTTGGAATCCCAGGTGTGGAGGTCCATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
* * * *
29923391 CATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTT
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
*
29923433 CATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA
1 CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTA
29923470 TTTTTTCATT
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 143 0.99
43 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
CATTGCATTTAGAAGCCCAGGTGTGGAGGTCCATTTACTTTG
Found at i:29923518 original size:84 final size:84
Alignment explanation
Indices: 29923270--29923526 Score: 256
Period size: 84 Copynumber: 3.0 Consensus size: 84
29923260 ACATTCATTA
* * * * *
29923270 CATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAATCCTAGGTATGGAG
1 CATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTG-ATTTAGAAGCCTAGGTGTGGAG
* * *
29923335 GTCCATTTAC-TTTGCAT-TC
65 GTCTAATTACATTT-CATCTG
* ** *
29923354 CATTTGGAATCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGTGTGGAG
1 CATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTG-ATTTAGAAGCCTAGGTGTGGAG
* *
29923419 GTCTATTTACTTTTCAT-TG
65 GTCTAATTACATTTCATCTG
* *
29923438 CATTTAGAGGCCCAGGTGTGGAGGTCCATTTATTTTTTCATTG-TTTATGAAAGCAC-ATGTGT-
1 CATTTAGAGGCCCAGGTGTGGAGGTCCATTTA-CTTTTCATTGATTTA-G-AAGC-CTAGGTGTG
*
29923500 GAGGTGTAATTACATTTCATCTG
62 GAGGTCTAATTACATTTCATCTG
29923523 CATT
1 CATT
29923527 CTCATTTCAA
Statistics
Matches: 148, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
83 4 0.03
84 117 0.79
85 26 0.18
86 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (84 bp):
CATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGATTTAGAAGCCTAGGTGTGGAGG
TCTAATTACATTTCATCTG
Found at i:29923518 original size:126 final size:126
Alignment explanation
Indices: 29923263--29923526 Score: 289
Period size: 126 Copynumber: 2.1 Consensus size: 126
29923253 AAGGAAAACA
* * *
29923263 TTCATTACATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAATCCTAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * * *
29923328 TATGGAGGTCCATTTACTTTGCATTCCATTTGGAATCCCAGGTGTGGAGGTCCATTTACTT
66 TATGGAGGTCCATTTACTTTGCATTCCATTTGAAAGCACAGGTGTGGAGGTCCAATTACAT
* * * * * *
29923389 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCTATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
* * * ** * **
29923454 TGTGGAGGTCCATTTATTTTTTCATT-GTTTATGAAAGCACATGTGT-GAGGTGTAATTACAT
66 TATGGAGGTCCATTTA-CTTTGCATTCCATT-TGAAAGCACAGGTGTGGAGGTCCAATTACAT
29923515 TTCATCTGCATT
1 TTCAT-TGCATT
29923527 CTCATTTCAA
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
126 89 0.79
127 24 0.21
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (126 bp):
TTCATTGCATTTAGAGACCCAGGTGTGAAGGTCCATTTACTTTGCATTGCATTTAGAAGCCCAGG
TATGGAGGTCCATTTACTTTGCATTCCATTTGAAAGCACAGGTGTGGAGGTCCAATTACAT
Found at i:29925483 original size:20 final size:19
Alignment explanation
Indices: 29925437--29925488 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29925427 TACTAGCCCC
29925437 CGTACTCTTATGTAGGCAA
1 CGTACTCTTATGTAGGCAA
* **
29925456 CTTACTCTTATGTAGGCCTT
1 CGTACTCTTATGTAGG-CAA
29925476 CGTACTCTTATGT
1 CGTACTCTTATGT
29925489 TAGTAAGTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (19 bp):
CGTACTCTTATGTAGGCAA
Found at i:29926101 original size:12 final size:12
Alignment explanation
Indices: 29926084--29926113 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29926074 CCTCACATCC
29926084 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
29926096 CCGTGTGCTAGG
1 CCGTGTGCCAGG
29926108 CCGTGT
1 CCGTGT
29926114 AACTACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:29938320 original size:23 final size:22
Alignment explanation
Indices: 29938288--29938330 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
29938278 TAATATCTCA
*
29938288 ACATTTCATACCATTCAATAAG
1 ACATTTCATACCATGCAATAAG
*
29938310 ACATTCTCATATCATGCAATA
1 ACATT-TCATACCATGCAATA
29938331 TAATTATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (22 bp):
ACATTTCATACCATGCAATAAG
Found at i:29944626 original size:27 final size:27
Alignment explanation
Indices: 29944547--29944919 Score: 326
Period size: 27 Copynumber: 14.0 Consensus size: 27
29944537 CACCGAGACC
*
29944547 CCGAAATACCCCCATAAGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
** *
29944574 AAGAAATA--CCCGTAGGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* *
29944599 CCGAAATATCCCCATAGGGTAAATTGA
1 CCGAAATACCCCCATAGGGTAAAATGA
** *
29944626 CTAAAATACCCCCATAAGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * *
29944653 CCAAAATACCCCCATATGGTAAAATAA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * *
29944680 TCGAAATACCCCCATACGATAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * * * *
29944707 CAGCAATACCCTCATAGTGTGAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* *
29944734 CCAAAATACCCCCATAGGGTAAAATAA
1 CCGAAATACCCCCATAGGGTAAAATGA
* **
29944761 TCGAAATACCCCCGCAGGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* ** * *
29944788 TCGAAATACCCTGATAAGATAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* *
29944815 CCAAAATACCTCCATAGGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * *
29944842 CCAAAATACCCTCGTAGGGTAAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * *
29944869 CTGAAATA-CCTC-T--GGTAGAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
* * * *
29944892 ACAAAATACCCCGATAGGGTCAAATGA
1 CCGAAATACCCCCATAGGGTAAAATGA
29944919 C
1 C
29944920 TGTTATACCC
Statistics
Matches: 272, Mismatches: 68, Indels: 12
0.77 0.19 0.03
Matches are distributed among these distances:
23 14 0.05
24 2 0.01
25 23 0.08
26 4 0.01
27 229 0.84
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.18
Consensus pattern (27 bp):
CCGAAATACCCCCATAGGGTAAAATGA
Found at i:29944732 original size:81 final size:81
Alignment explanation
Indices: 29944549--29944916 Score: 378
Period size: 81 Copynumber: 4.6 Consensus size: 81
29944539 CCGAGACCCC
* * * * * *
29944549 GAAATACCCCCATAAGGTAAAATGA-AAGAAATA--CCCGTAGGGTAAAATGACCGAAATATCCC
1 GAAATACCCTCATAAGGTAAAATGACCA-AAATACCCCCATAGGGTAAAATAATCGAAATACCCC
*
29944611 CATAGGGTAAATTGACTA
65 CATAGGGTAAAATGAC-A
* *
29944629 -AAATACCCCCATAAGGTAAAATGACCAAAATACCCCCATATGGTAAAATAATCGAAATACCCCC
1 GAAATACCCTCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCCC
* *
29944693 ATACGATAAAATGACA
66 ATAGGGTAAAATGACA
* *
29944709 GCAATACCCTCAT-AGTGTGAAATGACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCC
1 GAAATACCCTCATAAG-GTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCC
**
29944773 CGCAGGGTAAAATGATC-
65 CATAGGGTAAAATGA-CA
* * * * * * *
29944790 GAAATACCCTGATAAGATAAAATGACCAAAATACCTCCATAGGGTAAAATGACCAAAATACCCTC
1 GAAATACCCTCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCCC
* *
29944855 GTAGGGTAAAATGACT
66 ATAGGGTAAAATGACA
* * * *
29944871 GAAATA-CCTC-T--GGTAGAATGAACAAAATACCCCGATAGGGTCAAAT
1 GAAATACCCTCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAAT
29944917 GACTGTTATA
Statistics
Matches: 246, Mismatches: 34, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
77 29 0.12
79 30 0.12
80 8 0.03
81 176 0.72
82 3 0.01
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (81 bp):
GAAATACCCTCATAAGGTAAAATGACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCCC
ATAGGGTAAAATGACA
Found at i:29945309 original size:28 final size:28
Alignment explanation
Indices: 29945272--29945390 Score: 177
Period size: 28 Copynumber: 4.3 Consensus size: 28
29945262 CACTGTACTG
29945272 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
29945300 GTTACTGTATTGGGCTAAGTCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
29945328 GTTACTGTATTGGGCTAAGGCCGATACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
29945356 ATTACTGTATTGGGATAAGACCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
29945384 G-TACTGT
1 GTTACTGT
29945391 TACTGAATAG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 6 0.07
28 75 0.93
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:29947677 original size:23 final size:23
Alignment explanation
Indices: 29947645--29947756 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
29947635 CTTTTTGAAC
* *
29947645 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
29947668 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * * *
29947691 CCTTTCCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
29947714 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
29947737 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
29947757 CCCAAAACCG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:29947721 original size:46 final size:46
Alignment explanation
Indices: 29947645--29947756 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
29947635 CTTTTTGAAC
* *
29947645 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* * *
29947691 CCTTTCCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
29947737 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
29947757 CCCAAAACCG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:29949003 original size:50 final size:49
Alignment explanation
Indices: 29948949--29949044 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 49
29948939 TAGCTCGTAT
* *
29948949 GAGCTTACCATTACTT-AGCTC-ACATGAGCTTACCGTTATTCAGCTCGGTG
1 GAGCTTACCATTA-TTCAGCTCGA-AGGAGCTTACCGTT-TACAGCTCGGTG
* *
29948999 GAGCTTATCGTTATTCAGCTCGAAGGAGCTTACCGTTTACAGCTCG
1 GAGCTTACCATTATTCAGCTCGAAGGAGCTTACCGTTTACAGCTCG
29949045 TAAGAGCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 10 0.25
50 29 0.73
51 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (49 bp):
GAGCTTACCATTATTCAGCTCGAAGGAGCTTACCGTTTACAGCTCGGTG
Found at i:29949035 original size:25 final size:25
Alignment explanation
Indices: 29948940--29949044 Score: 99
Period size: 25 Copynumber: 4.2 Consensus size: 25
29948930 TACTAATTTT
* * *
29948940 AGCTCGTATGAGCTTACCATTACTT-
1 AGCTCGAAGGAGCTTACCGTTA-TTC
*
29948965 AGCTC-ACATGAGCTTACCGTTATTC
1 AGCTCGA-AGGAGCTTACCGTTATTC
** *
29948990 AGCTCGGTGGAGCTTATCGTTATTC
1 AGCTCGAAGGAGCTTACCGTTATTC
*
29949015 AGCTCGAAGGAGCTTACCGTT-TAC
1 AGCTCGAAGGAGCTTACCGTTATTC
29949039 AGCTCG
1 AGCTCG
29949045 TAAGAGCATA
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
24 10 0.15
25 57 0.85
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (25 bp):
AGCTCGAAGGAGCTTACCGTTATTC
Found at i:29956749 original size:23 final size:23
Alignment explanation
Indices: 29956717--29956782 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
29956707 CTTTTTGAAC
* *
29956717 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
29956740 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
29956763 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
29956783 CCCAAAACCG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:29964251 original size:25 final size:25
Alignment explanation
Indices: 29964212--29964340 Score: 113
Period size: 25 Copynumber: 5.2 Consensus size: 25
29964202 GTCATTAGGG
* *
29964212 TTACCGAT-TTTAGCTCGTATGAGC
1 TTACCGTTATTTAGCTCGTAAGAGC
* ** *
29964236 TTACCGTTACTTAGCTCACATGAGC
1 TTACCGTTATTTAGCTCGTAAGAGC
* *
29964261 TTACCATTATTTAG-T-TTAGAGGAGC
1 TTACCGTTATTTAGCTCGTA-A-GAGC
*
29964286 TTACCGTTATTTAGCTTGTAAGAGC
1 TTACCGTTATTTAGCTCGTAAGAGC
*
29964311 TTACCGTT-TATAGCTCGTAAGAGC
1 TTACCGTTATTTAGCTCGTAAGAGC
*
29964335 ATACCG
1 TTACCG
29964341 ATTTAGAGCT
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
23 1 0.01
24 27 0.31
25 54 0.63
26 2 0.02
27 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (25 bp):
TTACCGTTATTTAGCTCGTAAGAGC
Found at i:29964330 original size:24 final size:24
Alignment explanation
Indices: 29964282--29964359 Score: 93
Period size: 25 Copynumber: 3.2 Consensus size: 24
29964272 TAGTTTAGAG
* *
29964282 GAGCTTACCGTTATTTAGCTTGTAA
1 GAGCTTACCGTT-TATAGCTCGTAA
29964307 GAGCTTACCGTTTATAGCTCGTAA
1 GAGCTTACCGTTTATAGCTCGTAA
* * *
29964331 GAGCATACCGATTTAGAGCTCGTAT
1 GAGCTTACCG-TTTATAGCTCGTAA
29964356 GAGC
1 GAGC
29964360 ATACATGTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 19 0.40
25 28 0.60
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (24 bp):
GAGCTTACCGTTTATAGCTCGTAA
Found at i:29979845 original size:13 final size:13
Alignment explanation
Indices: 29979827--29979851 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29979817 CCCAATGTAG
29979827 CTCATTACTTTCA
1 CTCATTACTTTCA
29979840 CTCATTACTTTC
1 CTCATTACTTTC
29979852 CAGCTGATTC
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:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
CTCATTACTTTCA
Found at i:29980655 original size:27 final size:28
Alignment explanation
Indices: 29980591--29980660 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
29980581 TGAAACAAGA
29980591 ACATATTAAAAACATGTAATAGACTAAG
1 ACATATTAAAAACATGTAATAGACTAAG
* * * *
29980619 ACAAAGTAAAAACATGTACTAG-CTATG
1 ACATATTAAAAACATGTAATAGACTAAG
29980646 ACATATT-AAAACATG
1 ACATATTAAAAACATG
29980661 CATTAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 8 0.22
27 9 0.25
28 19 0.53
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
ACATATTAAAAACATGTAATAGACTAAG
Found at i:29982572 original size:34 final size:34
Alignment explanation
Indices: 29982534--29982628 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 34
29982524 TCTTCACACA
* * **
29982534 TTTCTTTTTCAAGCTCTCTCTCTTTTTCACTCTT
1 TTTCTTTTTCAAGCTCTCTTTCCTTTTCACTCGC
29982568 TTTC-TTTTCAAGCTCTCTTTCCTTTTCACTCGC
1 TTTCTTTTTCAAGCTCTCTTTCCTTTTCACTCGC
**
29982601 TTTCTTTTGAAAGCTCTCTTTCCTTTTC
1 TTTCTTTTTCAAGCTCTCTTTCCTTTTC
29982629 TTGCTCACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.54
34 25 0.46
ACGTcount: A:0.09, C:0.29, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTCTTTTTCAAGCTCTCTTTCCTTTTCACTCGC
Found at i:29982573 original size:16 final size:18
Alignment explanation
Indices: 29982534--29982628 Score: 92
Period size: 18 Copynumber: 5.6 Consensus size: 18
29982524 TCTTCACACA
29982534 TTTCTTTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
* *
29982552 TCTCTTTTTC-A-CTCTT
1 TTTCTTTTTCAAGCTCTC
29982568 TTTC-TTTTCAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
* *
29982585 TTTCCTTTTC-A-CTCGC
1 TTTCTTTTTCAAGCTCTC
**
29982601 TTTCTTTTGAAAGCTCTC
1 TTTCTTTTTCAAGCTCTC
*
29982619 TTTCCTTTTC
1 TTTCTTTTTC
29982629 TTGCTCACAC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
15 5 0.08
16 19 0.32
17 11 0.18
18 25 0.42
ACGTcount: A:0.09, C:0.29, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTCTTTTTCAAGCTCTC
Found at i:29982711 original size:17 final size:16
Alignment explanation
Indices: 29982673--29982711 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
29982663 TCTTTTTCGA
29982673 TTTTTTCTTTCATTTC
1 TTTTTTCTTTCATTTC
*
29982689 TCTTTTTCTTTTTATTTC
1 T-TTTTTC-TTTCATTTC
29982707 TTTTT
1 TTTTT
29982712 GACTCGTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTTTCATTTC
Found at i:29983716 original size:12 final size:12
Alignment explanation
Indices: 29983701--29983741 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29983691 TTGTTCACGA
29983701 TTTTTTTGAATT
1 TTTTTTTGAATT
**
29983713 TTTTTTCAAATT
1 TTTTTTTGAATT
*
29983725 GTTTTTTGAATT
1 TTTTTTTGAATT
29983737 TTTTT
1 TTTTT
29983742 CGTCAAATAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:29983992 original size:39 final size:39
Alignment explanation
Indices: 29983936--29984013 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
29983926 TAGGTTTGCA
*
29983936 AAGTGTTTTAAGAATAGGATAGGTGATGGTTCGACTAAG
1 AAGTGTTTTAAGAATAGGATAGGTGATGGCTCGACTAAG
* * *
29983975 AAGTGTTTTAGGGATAGGATAGGTGATGGCTCGGCTAAG
1 AAGTGTTTTAAGAATAGGATAGGTGATGGCTCGACTAAG
29984014 GATAAAAACA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.29
Consensus pattern (39 bp):
AAGTGTTTTAAGAATAGGATAGGTGATGGCTCGACTAAG
Found at i:29989681 original size:4 final size:4
Alignment explanation
Indices: 29989674--29989703 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
29989664 AATTAATCAA
*
29989674 TCAT TCAT TCAT CCAT TCAT TCAT TCAT TC
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
29989704 GCTCATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (4 bp):
TCAT
Found at i:29998972 original size:9 final size:9
Alignment explanation
Indices: 29998958--29999071 Score: 86
Period size: 9 Copynumber: 12.7 Consensus size: 9
29998948 CAAGTTTGGG
*
29998958 CATGCACTC
1 CATGCATTC
29998967 CATGCATTC
1 CATGCATTC
***
29998976 CATGCAAAA
1 CATGCATTC
*
29998985 CATGCTTTC
1 CATGCATTC
29998994 CATGCATTC
1 CATGCATTC
* ***
29999003 CATGAAAAA
1 CATGCATTC
29999012 CATGCATTC
1 CATGCATTC
29999021 CATGCATTC
1 CATGCATTC
**
29999030 CATGCAACC
1 CATGCATTC
*
29999039 CATGCATTT
1 CATGCATTC
*
29999048 CATGCGA-AC
1 CATGC-ATTC
*
29999057 CATGCATCC
1 CATGCATTC
29999066 CATGCA
1 CATGCA
29999072 ATGTGCTGCA
Statistics
Matches: 78, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
8 1 0.01
9 76 0.97
10 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.25
Consensus pattern (9 bp):
CATGCATTC
Found at i:29998996 original size:27 final size:27
Alignment explanation
Indices: 29998958--29999052 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
29998948 CAAGTTTGGG
*
29998958 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
* *
29998985 CATGCTTTCCATGCATTCCATGAAAAA
1 CATGCATTCCATGCATTCCATGCAAAA
**
29999012 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCCATGCAAAA
*
29999039 CATGCATTTCATGC
1 CATGCATTCCATGC
29999053 GAACCATGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (27 bp):
CATGCATTCCATGCATTCCATGCAAAA
Found at i:29999059 original size:27 final size:27
Alignment explanation
Indices: 29998958--29999071 Score: 104
Period size: 27 Copynumber: 4.2 Consensus size: 27
29998948 CAAGTTTGGG
* * **
29998958 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
* * * **
29998985 CATGCTTTCCATGCATTCCATGAAAAA
1 CATGCATTCCATGCATACCATGCAACC
*
29999012 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATACCATGCAACC
* *
29999039 CATGCATTTCATGCGA-ACCATGCATCC
1 CATGCATTCCATGC-ATACCATGCAACC
29999066 CATGCA
1 CATGCA
29999072 ATGTGCTGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.25
Consensus pattern (27 bp):
CATGCATTCCATGCATACCATGCAACC
Found at i:29999234 original size:41 final size:41
Alignment explanation
Indices: 29999187--29999270 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
29999177 GTTTAGACAT
* *
29999187 TTTAAATGTGTGTCTCAAATACTGCACTTTAATTATAAGTC
1 TTTAAATATGTGTCTCAAATACTACACTTTAATTATAAGTC
* *
29999228 TTTAAATATGTGTCTTAAATACTACACTTTAATTATATGTC
1 TTTAAATATGTGTCTCAAATACTACACTTTAATTATAAGTC
29999269 TT
1 TT
29999271 AGTTCTTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (41 bp):
TTTAAATATGTGTCTCAAATACTACACTTTAATTATAAGTC
Found at i:30002281 original size:27 final size:27
Alignment explanation
Indices: 30002243--30002313 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
30002233 AGTTTAGGCA
*
30002243 TGCACTCTATGCATTCCATGAAAAACC
1 TGCATTCTATGCATTCCATGAAAAACC
** * * *
30002270 TGCATTCTATGCGCTCTATGCAAAACT
1 TGCATTCTATGCATTCCATGAAAAACC
30002297 TGCATTTCT-TGCATTCC
1 TGCA-TTCTATGCATTCC
30002314 GTGCAACCCA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (27 bp):
TGCATTCTATGCATTCCATGAAAAACC
Done.