Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 25 of 147
Found at i:5289752 original size:19 final size:19
Alignment explanation
Indices: 5289715--5289772 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 19
5289705 AAAATTTTAA
*
5289715 ATTATATTAT-TTTTATATT
1 ATTATATTATATTATA-ATT
*
5289734 ATT-T-TCATATTAT-ATT
1 ATTATATTATATTATAATT
*
5289750 ATTATATTATATTTTAATT
1 ATTATATTATATTATAATT
5289769 ATTA
1 ATTA
5289773 AATGTATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.19
17 4 0.13
18 11 0.35
19 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTATATTATATTATAATT
Found at i:5289769 original size:16 final size:16
Alignment explanation
Indices: 5289708--5289770 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
5289698 TTTTATTAAA
5289708 ATTTTAAATTATATTAT
1 ATTTT-AATTATATTAT
*
5289725 -TTTTATATTATTTTCAT
1 ATTTTA-ATTATATT-AT
*
5289742 ATTATATTATTATATTAT
1 ATT-T-TAATTATATTAT
5289760 ATTTTAATTAT
1 ATTTTAATTAT
5289771 TAAATGTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.03
16 17 0.46
17 3 0.08
18 7 0.19
19 8 0.22
20 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTAATTATATTAT
Found at i:5290099 original size:22 final size:22
Alignment explanation
Indices: 5290048--5290100 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
5290038 AAATATAAAA
* *
5290048 TATAAA-ATTTTTTATTATATT
1 TATAAATAATTTTTATTAAATT
*
5290069 TATATATAATTTTTATTAAAATT
1 TATAAATAATTTTTATT-AAATT
5290092 T-TAAATAAT
1 TATAAATAAT
5290101 ATAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 16 0.62
23 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATAAATAATTTTTATTAAATT
Found at i:5292267 original size:53 final size:51
Alignment explanation
Indices: 5292169--5292267 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 51
5292159 ATAATTAGCA
* **
5292169 AATAAATTTTTATTAAATAATATAAATTATTGTTATAGATTAATTAAAATT
1 AATAAATTTTTATTAAATAATATAAATTATTGTTATAAAAAAATTAAAATT
*
5292220 AATATATTTTTATTAAA-AATATATTAATATATAT-TTATAAAAAAATTA
1 AATAAATTTTTATTAAATAATATA--AAT-TAT-TGTTATAAAAAAATTA
5292268 CCTATACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
50 6 0.15
51 16 0.40
52 3 0.08
53 14 0.35
54 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (51 bp):
AATAAATTTTTATTAAATAATATAAATTATTGTTATAAAAAAATTAAAATT
Found at i:5292415 original size:17 final size:18
Alignment explanation
Indices: 5292389--5292422 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5292379 ATATTCACTG
5292389 AATATAAATACAAAAATA
1 AATATAAATACAAAAATA
*
5292407 AATAT-AATATAAAAAT
1 AATATAAATACAAAAAT
5292423 TTAAAGATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAATACAAAAATA
Found at i:5295263 original size:14 final size:14
Alignment explanation
Indices: 5295244--5295270 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5295234 AATATTATAT
5295244 AAAAAAATAAAAAC
1 AAAAAAATAAAAAC
5295258 AAAAAAATAAAAA
1 AAAAAAATAAAAA
5295271 TTTTTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.04, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAAATAAAAAC
Found at i:5296096 original size:15 final size:15
Alignment explanation
Indices: 5296076--5296109 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5296066 TAATAAGTAT
*
5296076 TTAATTTTGGTTTTC
1 TTAATTTTGATTTTC
*
5296091 TTAATTTTGATTTTT
1 TTAATTTTGATTTTC
5296106 TTAA
1 TTAA
5296110 AATAACAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (15 bp):
TTAATTTTGATTTTC
Found at i:5297177 original size:38 final size:35
Alignment explanation
Indices: 5297126--5297218 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 35
5297116 GTATGTAGTG
*
5297126 CATGCA-TCTTATCTCATGTACATCATAATAAGATAATA
1 CATGCATTC-TATCTCATGCACATC--AAT-AGATAATA
* *
5297164 CATGCATTCTATCTCATCCACATCAATAGATAGTA
1 CATGCATTCTATCTCATGCACATCAATAGATAATA
*
5297199 CATGCATTCTATTTCATGCA
1 CATGCATTCTATCTCATGCA
5297219 ATGCATCCTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
35 25 0.51
36 3 0.06
38 19 0.39
39 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (35 bp):
CATGCATTCTATCTCATGCACATCAATAGATAATA
Found at i:5297887 original size:24 final size:24
Alignment explanation
Indices: 5297859--5297904 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5297849 AATAAATTTT
5297859 TTGATAATTACCAATGGATTTTCG
1 TTGATAATTACCAATGGATTTTCG
*
5297883 TTGATAATTATCAATGGATTTT
1 TTGATAATTACCAATGGATTTT
5297905 AAGCATTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (24 bp):
TTGATAATTACCAATGGATTTTCG
Found at i:5300326 original size:41 final size:41
Alignment explanation
Indices: 5300269--5300352 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
5300259 AGGGGTCTAG
5300269 TGGGGCTCAAGTCGGCTGAGATAAAAAATATTTTAAAATTA
1 TGGGGCTCAAGTCGGCTGAGATAAAAAATATTTTAAAATTA
5300310 TGGGGCTCAAGTCGGCTGAGATAAAAAATATTTTAAAATTA
1 TGGGGCTCAAGTCGGCTGAGATAAAAAATATTTTAAAATTA
5300351 TG
1 TG
5300353 TGTTCTAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (41 bp):
TGGGGCTCAAGTCGGCTGAGATAAAAAATATTTTAAAATTA
Found at i:5300730 original size:30 final size:30
Alignment explanation
Indices: 5300664--5300768 Score: 142
Period size: 29 Copynumber: 3.5 Consensus size: 30
5300654 TTTTCACATT
*
5300664 TAAATAAGTTTTTAATTTTTAATTTATATC
1 TAAATAAATTTTTAATTTTTAATTTATATC
5300694 -AAATAAATTTTTAATTTTTAATTTATATC
1 TAAATAAATTTTTAATTTTTAATTTATATC
* * *
5300723 TAAATAAATCTTTAAAATTTTAATTTGTATC
1 TAAATAAAT-TTTTAATTTTTAATTTATATC
*
5300754 TAAAT-AATCTTTAAT
1 TAAATAAATTTTTAAT
5300769 AAAATTATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 32 0.48
30 11 0.17
31 23 0.35
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (30 bp):
TAAATAAATTTTTAATTTTTAATTTATATC
Found at i:5300747 original size:31 final size:31
Alignment explanation
Indices: 5300680--5300767 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
5300670 AGTTTTTAAT
* *
5300680 TTTTAATTTATATC-AAATAAAT-TTTTAAT
1 TTTTAATTTATATCTAAATAAATCTTTAAAA
5300709 TTTTAATTTATATCTAAATAAATCTTTAAAA
1 TTTTAATTTATATCTAAATAAATCTTTAAAA
*
5300740 TTTTAATTTGTATCTAAAT-AATCTTTAA
1 TTTTAATTTATATCTAAATAAATCTTTAA
5300768 TAAAATTATT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
29 14 0.26
30 17 0.31
31 23 0.43
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (31 bp):
TTTTAATTTATATCTAAATAAATCTTTAAAA
Found at i:5300774 original size:27 final size:28
Alignment explanation
Indices: 5300683--5300767 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 28
5300673 TTTTAATTTT
* **
5300683 TAATTTATATC-AAATAAATTTTTAATTTT
1 TAATTTATATCTAAATAAATCTTTAA--AA
5300712 TAATTTATATCTAAATAAATCTTTAAAA
1 TAATTTATATCTAAATAAATCTTTAAAA
*
5300740 TTTTAATTTGTATCTAAAT-AATCTTTAA
1 ---TAATTTATATCTAAATAAATCTTTAA
5300768 TAAAATTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 11 0.23
30 22 0.46
31 15 0.31
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (28 bp):
TAATTTATATCTAAATAAATCTTTAAAA
Found at i:5301182 original size:29 final size:29
Alignment explanation
Indices: 5301129--5301222 Score: 100
Period size: 29 Copynumber: 3.1 Consensus size: 29
5301119 ATCAATTATC
* *
5301129 TTAAATTATAATAAAATATTTAATATAATAT
1 TTAAATT-TAA-AAATTTTTTAATATAATAT
5301160 TTAAATTTAAAAATTTTTTAATATAATAT
1 TTAAATTTAAAAATTTTTTAATATAATAT
*
5301189 TTAAA-TTAGAAATATATTATTTAATATGATAT
1 TTAAATTTA-AAA-AT-TT-TTTAATATAATAT
5301221 TT
1 TT
5301223 TAAAAAATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
28 3 0.05
29 25 0.45
30 5 0.09
31 9 0.16
32 14 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TTAAATTTAAAAATTTTTTAATATAATAT
Found at i:5301221 original size:32 final size:30
Alignment explanation
Indices: 5301145--5301222 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 30
5301135 TATAATAAAA
5301145 TATTTAATATAATATTTAAATTTAAAAATT
1 TATTTAATATAATATTTAAATTTAAAAATT
5301175 T-TTTAATATAATATTTAAA-TTAGAAATATAT
1 TATTTAATATAATATTTAAATTTA-AAA-AT-T
*
5301206 TATTTAATATGATATTT
1 TATTTAATATAATATTT
5301223 TAAAAAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 3 0.07
29 21 0.49
30 3 0.07
31 2 0.05
32 14 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TATTTAATATAATATTTAAATTTAAAAATT
Found at i:5301285 original size:17 final size:18
Alignment explanation
Indices: 5301263--5301300 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
5301253 CTACCTAATC
5301263 ATATTAA-AAATAAAATT
1 ATATTAATAAATAAAATT
* *
5301280 ATATTAATTAATAAATTT
1 ATATTAATAAATAAAATT
5301298 ATA
1 ATA
5301301 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTAATAAATAAAATT
Found at i:5305122 original size:20 final size:21
Alignment explanation
Indices: 5305097--5305142 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5305087 CACGAAATTA
5305097 ATAAAATATTA-TTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
*
5305117 ATAAAATATTATTTTTTTAAT
1 ATAAAATATTATTTTTTAAAT
5305138 ATAAA
1 ATAAA
5305143 TATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:5305143 original size:20 final size:19
Alignment explanation
Indices: 5305094--5305145 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
5305084 TAACACGAAA
5305094 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
*
5305112 TAAATATAAAATATTATTTTT
1 TTAATAT-AAATATTA-TTTT
5305133 TTAATATAAATAT
1 TTAATATAAATAT
5305146 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 5 0.17
20 14 0.48
21 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:5307560 original size:57 final size:57
Alignment explanation
Indices: 5307447--5307558 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 57
5307437 AAAAATTTGA
* * *
5307447 AAAAAAATATTTTTGAAGGAAAGTTTAATGTATCAATTTCCTTTGAACATAAAAATT
1 AAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAATT
* *
5307504 AAAAAAATATTTTTTGAGGGAAAGTTGAAAGTATCAATTT-TTCTTGAAAATAAAA
1 AAAAAAATA-TTTTTGAAGGAAAGTTGAAAGTATCAATTTCCT-TTGAAAATAAAA
5307559 TTTTTTTAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 10 0.21
58 38 0.79
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.36
Consensus pattern (57 bp):
AAAAAAATATTTTTGAAGGAAAGTTGAAAGTATCAATTTCCTTTGAAAATAAAAATT
Found at i:5318896 original size:73 final size:73
Alignment explanation
Indices: 5318665--5318930 Score: 275
Period size: 73 Copynumber: 3.6 Consensus size: 73
5318655 AGTCATTCAT
* * * * * * *
5318665 TTCAA-ACTTCGATTCAATCCAAGTCATTCTATTTGTGGATTTTGACATATGCTAGATCATTCTT
1 TTCAAGACTTCGGTTCAATCCAGGTCATTCTATTTTTAGATTTTGACATATGCCAAATCTTTCTT
5318729 TGGCTTAG
66 TGGCTTAG
* ** * * * * *
5318737 TTCAAGATTTTTGTTCAATCTAGGTCATTTTATTTTTTAAATTTTAACATATGCCAAATCTTTTT
1 TTCAAGACTTCGGTTCAATCCAGGTCATTCTA-TTTTTAGATTTTGACATATGCCAAATCTTTCT
5318802 TTGGCTTAG
65 TTGGCTTAG
* * * *
5318811 TTTAAGATTTCGGTTCAATCTAGGTCATTCTATTTTTAGATTTCGACATATGCCAAATCTTTCTT
1 TTCAAGACTTCGGTTCAATCCAGGTCATTCTATTTTTAGATTTTGACATATGCCAAATCTTTCTT
**
5318876 CAGCTTAG
66 TGGCTTAG
* * * *
5318884 TCCAAGACTTCGGTTTC-ATCCAGATCATTTTATTTTTGGATTTTGAC
1 TTCAAGACTTCGG-TTCAATCCAGGTCATTCTATTTTTAGATTTTGAC
5318931 TTTTATTAAA
Statistics
Matches: 158, Mismatches: 33, Indels: 5
0.81 0.17 0.03
Matches are distributed among these distances:
72 5 0.03
73 89 0.56
74 64 0.41
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (73 bp):
TTCAAGACTTCGGTTCAATCCAGGTCATTCTATTTTTAGATTTTGACATATGCCAAATCTTTCTT
TGGCTTAG
Found at i:5319132 original size:85 final size:86
Alignment explanation
Indices: 5318947--5319137 Score: 251
Period size: 85 Copynumber: 2.2 Consensus size: 86
5318937 TAAATCTTTC
* * * *
5318947 TCAGTCTAAGTTATTCATTTTAGGCTTCGGTTTAATTCAGGTCATTCTATTTTTGGATTTCGGCC
1 TCAGTCCAAGTTATTCATTTTAGACTTCGATTCAATTCAGGTCATTCTATTTTTGGATTTCGGCC
* *
5319012 TATGCCGAATCCTTCTTCAGC
66 TATGCCGAATCCTTATTCAGA
* ** *
5319033 TCAGTCCAAGTTATTCATTTTAGACTTCGATTCAATTTAGGTCATT-TATTTTTTTATTTTGGCC
1 TCAGTCCAAGTTATTCATTTTAGACTTCGATTCAATTCAGGTCATTCTATTTTTGGATTTCGGCC
*
5319097 TATGCC-AGATCCTTATTCGGA
66 TATGCCGA-ATCCTTATTCAGA
*
5319118 TCAGTCCAAATTATTCATTT
1 TCAGTCCAAGTTATTCATTT
5319138 AAGCTTTGGT
Statistics
Matches: 92, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
84 1 0.01
85 50 0.54
86 41 0.45
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (86 bp):
TCAGTCCAAGTTATTCATTTTAGACTTCGATTCAATTCAGGTCATTCTATTTTTGGATTTCGGCC
TATGCCGAATCCTTATTCAGA
Found at i:5319214 original size:80 final size:79
Alignment explanation
Indices: 5319120--5319292 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 79
5319110 TATTCGGATC
* * * *
5319120 AGTCCAAATTATTCATTT-AAGCTTTGGTTTAGTCCGGGTCTTTCAGTTTTGAGATTTCAATTTT
1 AGTCCAAATTATTCATTTCAAGCTTCGATTCAGTCCAGGTCTTTCAGTTTTG-GATTTCAATTTT
* *
5319184 TGGTTAAATTCTTCTT
65 T-GTTAAATCCATCTT
* * ** **
5319200 AGTCCAAGTTATTCATTTCAGGCTTCGATTCAGTCCAGGTCTTTTTGTTTTGGATTTTGATTTTT
1 AGTCCAAATTATTCATTTCAAGCTTCGATTCAGTCCAGGTCTTTCAGTTTTGGATTTCAATTTTT
5319265 GTTAAATCCATCTT
66 GTTAAATCCATCTT
* *
5319279 AGTTCAGATTATTC
1 AGTCCAAATTATTC
5319293 GTTTTAGACT
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
79 23 0.30
80 28 0.36
81 26 0.34
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (79 bp):
AGTCCAAATTATTCATTTCAAGCTTCGATTCAGTCCAGGTCTTTCAGTTTTGGATTTCAATTTTT
GTTAAATCCATCTT
Found at i:5319316 original size:79 final size:81
Alignment explanation
Indices: 5319120--5319324 Score: 186
Period size: 79 Copynumber: 2.6 Consensus size: 81
5319110 TATTCGGATC
* * * * * * * **
5319120 AGTCCAAATTATTCATTTAAG-CTTTGGTTTAGTCCGGGTCTTTCAGTTTTGAGATTTCAATTTT
1 AGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCTTTTTGTTTTGAGATTTCAATTTT
* *
5319184 TGGTTAAATTCTTCTT
66 TGGTTAAATCCATCTT
* * **
5319200 AGTCCAAGTTATTCATTTCAGGCTTCGATTCAGTCCAGGTCTTTTTGTTTTG-GATTTTGATTTT
1 AGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCTTTTTGTTTTGAGATTTCAATTTT
5319264 T-GTTAAATCCATCTT
66 TGGTTAAATCCATCTT
* * * *
5319279 AGTTC-AGATTATTCGTTTTAGACTTC-AGTTCAATCCAGGTCATTTT
1 AGTCCAAG-TTATTCATTTCAGACTTCGA-TTCAATCCAGGTCTTTTT
5319325 ATCTTCGAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
78 3 0.03
79 47 0.45
80 30 0.29
81 24 0.23
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (81 bp):
AGTCCAAGTTATTCATTTCAGACTTCGATTCAATCCAGGTCTTTTTGTTTTGAGATTTCAATTTT
TGGTTAAATCCATCTT
Found at i:5319388 original size:86 final size:85
Alignment explanation
Indices: 5319276--5319434 Score: 196
Period size: 86 Copynumber: 1.9 Consensus size: 85
5319266 TTAAATCCAT
* * * * *
5319276 CTTAGTTCAGATTATTCGTTTTAGACTTC-AGTTCAATCCAGGTCATTTTATCTTCGAATTTTGG
1 CTTAGTTCAGATTATTCATTTCAGACTACGA-TTCAATCCAGGTCATTTTATATT-GAATTTTGA
5319340 CTTATGTCAAATCTTTCTTCAG
64 CTTATGTCAAATCTTTCTTCAG
* ***
5319362 CTTAGTTCA-AGTTATTCATTTCAGACTACGATTCAGTTTGGGTCATTTTATATTGAATTTTGAC
1 CTTAGTTCAGA-TTATTCATTTCAGACTACGATTCAATCCAGGTCATTTTATATTGAATTTTGAC
5319426 TTATGTCAA
65 TTATGTCAA
5319435 GTCCATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
85 19 0.31
86 42 0.68
87 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.45
Consensus pattern (85 bp):
CTTAGTTCAGATTATTCATTTCAGACTACGATTCAATCCAGGTCATTTTATATTGAATTTTGACT
TATGTCAAATCTTTCTTCAG
Found at i:5320157 original size:11 final size:12
Alignment explanation
Indices: 5320136--5320167 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5320126 AAAAATTACC
5320136 TAGAGAGAGAAA
1 TAGAGAGAGAAA
5320148 TAGA-AGAGAAA
1 TAGAGAGAGAAA
5320159 -AGAGAGAGA
1 TAGAGAGAGA
5320168 GGGTGTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 12 0.63
12 4 0.21
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.06
Consensus pattern (12 bp):
TAGAGAGAGAAA
Found at i:5320467 original size:14 final size:15
Alignment explanation
Indices: 5320443--5320478 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5320433 TTCCTTTAGT
5320443 TTTATTATTTATTTA
1 TTTATTATTTATTTA
5320458 TTTA-TATTTATTTA
1 TTTATTATTTATTTA
*
5320472 TTGATTA
1 TTTATTA
5320479 AATTGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:5320807 original size:59 final size:58
Alignment explanation
Indices: 5320538--5321070 Score: 447
Period size: 60 Copynumber: 8.9 Consensus size: 58
5320528 TCTCTTTAAG
5320538 ATAAAATTTTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTGAAA
1 ATAAAA-TTTTC-AAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTT-TTGAAA
* * * *
5320599 ATAAAAAAAAATTT---AAAAATATTTTTAAGAAAAAGTTGAAATTATCAATTTTTCTTGAAA
1 AT----AAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTT-TTGAAA
* *
5320659 ATAAAATTTTCAAAGGAAAAACATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAA
1 ATAAAATTTTC-AA--AAAAATA-TTTTTGAGGAAAAGTTGAAAATATCAATTTTT-TTGAAA
*
5320722 ATAAAATTTTCAAAAAAAAGTATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTTAAAAA
1 ATAAAATTTTC-AAAAAAA-TATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTT-GAAA
* *** ** * **
5320783 ATAAAGTTTTCAAAAAGGGATTTTTGAAAAAAAGTT-AAAAGTGTCAACTTTCCTTGAAA
1 ATAAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAA-TATCAA-TTTTTTTGAAA
* * * * * *
5320842 ATAAAATTTTCAAAAAAGTGA-TTTTGAGAAAAAATTGAAAGTATTAATTTTCTTCGAAA
1 ATAAAATTTTCAAAAAAAT-ATTTTTGAGGAAAAGTTGAAAATATCAATTTT-TTTGAAA
* * **
5320901 ATAAAGA-TTTCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATCTTCCTTGAAA
1 ATAAA-ATTTTCAA-AAAAATATTTTTGAGGAAAAGTTGAAAATATCAAT-TTTTTTGAAA
* * * *
5320961 ATAAAATTTT-TAAAAAACATTTTTGAGGAAAAGTT-AGAAGT-TCTAATTTTCCTTGAAA
1 ATAAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGA-AAATATC-AATTTT-TTTGAAA
* * *
5321019 ATAAAATTCTT-AAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCGATTTT
1 ATAAAATT-TTCAA-AAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTT
5321071 CCTTGAATAA
Statistics
Matches: 393, Mismatches: 49, Indels: 61
0.78 0.10 0.12
Matches are distributed among these distances:
56 7 0.02
57 5 0.01
58 50 0.13
59 78 0.20
60 133 0.34
61 56 0.14
62 7 0.02
63 50 0.13
64 3 0.01
65 4 0.01
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (58 bp):
ATAAAATTTTCAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTTGAAA
Found at i:5320985 original size:118 final size:116
Alignment explanation
Indices: 5320546--5321077 Score: 536
Period size: 118 Copynumber: 4.4 Consensus size: 116
5320536 AGATAAAATT
* * * * **
5320546 TTTCAAAAAAAATATTTTTGAGGAAAAGTTGAAAATATCAATTTTTCTTGAAAATAAAAAAAAAT
1 TTTCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT---AAAATTT
* *
5320611 TT-AAAAATATTTTTAAGAAAAAGTTGAAATTATCAATTTTTCTTGAAAATAAAA
63 TTAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTGAAAATAAAA
* * *
5320665 TTTTCAAAGGAAAAACATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATT
1 -TTTC-AA-GAAAAATA-TTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATT
* * * * * *
5320730 TTCAAAAAAAAGTATTTTTGAGGAAAAGTTGAAAATATCAATTTTTTTAAAAAATAAAGT
62 TT--TAAAAAA-TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTT-GAAAATAAA-A
*** * * * * *
5320790 TTTCAA-AAAGGGATTTTTGAA-AAAAAGTTAAAAGTGTCAACTTTCCTTGAAAATAAAATTTTC
1 TTTCAAGAAAAATATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTT
* *
5320853 AAAAAAGTGA-TTTTGAGAAAAAATTGAAAGTATTAATTTTCTTCGAAAATAAAGA
65 AAAAAA-T-ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTT-GAAAATAAA-A
*
5320908 TTTCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATCTTCCTTGAAAATAAAATTTTTA
1 TTTCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTA
* *
5320973 AAAAACATTTTTGAGGAAAAGTT-AGAAGT-TCTAATTTTCCTTGAAAATAAAA
66 AAAAATATTTTTGAGAAAAAGTTGA-AAGTATC-AATTTT-CTTGAAAATAAAA
* *
5321025 TTCTTAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCGATTTTCCTTGAA
1 TT-TCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAA
5321078 TAAAAGCATG
Statistics
Matches: 348, Mismatches: 46, Indels: 38
0.81 0.11 0.09
Matches are distributed among these distances:
117 6 0.02
118 132 0.38
119 55 0.16
120 51 0.15
121 7 0.02
122 6 0.02
123 53 0.15
124 38 0.11
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (116 bp):
TTTCAAGAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAATTTTTA
AAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTGAAAATAAAA
Found at i:5322490 original size:505 final size:504
Alignment explanation
Indices: 5321596--5322530 Score: 1627
Period size: 505 Copynumber: 1.9 Consensus size: 504
5321586 ATAAGTCTAT
* * * *
5321596 GAATCTAGACATTATGACACAATACATTATCATTATTGACCAAGGCTACACTTTACCATAGTTTT
1 GAATCTAAACATTATGACACAACACATGATCATTATTGACCAAGGCTACACTTTACCATACTTTT
5321661 ATCACCTTCAATGGATTATGCTGCAGGAAATTCCTGATCTGCCAACTTTTTGGGTTAGGAGGACA
66 ATCACCTTCAATGGATTATGCTGCAGGAAATTCCTGATCTGCCAACTTTTTGGGTTAGGAGGACA
*
5321726 GCTTGTTTATTAGATAGGGCAAGCCATCTACTGCTCAAAATCTGCAATATTGGCCCAATGGATCT
131 GCTTGTTTATTAGATAGCGCAAGCCATCTACTGCTCAAAATCTGCAATATTGGCCCAATGGATCT
* * * *
5321791 TCTTGGATTCCTGTATCTATGGTTGAAAATCCTACACATGCTATTCCAGCAACAATAGTCGAAGA
196 CCTTGGATTCCTGTATCTACGGTTGAAAATCCTACACATGCTACTCCAGCAACAATAGTCAAAGA
*
5321856 AACAAAACATTAATTTTTTTACACGAAAGTCTTAGAAGCATTTGGATTAAAATGTCAGATCTTTT
261 AACAAAACATTAATTTTTTTACACGAAAGTCTTACAAGCATTTGGATTAAAATGTCAGATCTTTT
* *
5321921 GAATGTAATTTCTTAAAATTAGTTATACGAAGCAAATGAATTAATTTTTGAATTTAACAAACTGT
326 GAATGTAATTTCTTAAAATTAGTTATACGAAGCAAATAAAATAATTTTTGAATTTAACAAACTGT
5321986 TAATTTAACTAAATAGATATTACTGGAGAACAAAAAATATTTACGTGATCAATTGTATCTAAATA
391 TAATTTAACTAAATAGATATTACTGGAGAACAAAAAATATTTACGTGATCAATTGTATCTAAATA
5322051 AAAAAAATTAATAATAATTTTTTAAGTCAATATCTTATGATAAATTCAC
456 AAAAAAATTAATAATAATTTTTTAAGTCAATATCTTATGATAAATTCAC
* * *
5322100 GAATCTAAATATTATGACACAGCACATGATCATTATTGACCAAGGCTACACTTTTACCCTACTTT
1 GAATCTAAACATTATGACACAACACATGATCATTATTGACCAAGGCTACAC-TTTACCATACTTT
*
5322165 TATCACCTTCAATGGATTATTCTGCAGGAAATTCCTGATCTGCCAACTTTTTGGGTTAGGAGGAC
65 TATCACCTTCAATGGATTATGCTGCAGGAAATTCCTGATCTGCCAACTTTTTGGGTTAGGAGGAC
* *
5322230 AGCTTGTTTATTAGATAGCTCAAGCCTTCTACTGCTCAAAATCTGCAATATTGGCCCAATGGATC
130 AGCTTGTTTATTAGATAGCGCAAGCCATCTACTGCTCAAAATCTGCAATATTGGCCCAATGGATC
5322295 TCCTTGGATTCCTGTATCTACGGTTGAAAATCCTACACATGCTACTCCAGCAACAATAGTCAAAG
195 TCCTTGGATTCCTGTATCTACGGTTGAAAATCCTACACATGCTACTCCAGCAACAATAGTCAAAG
* * *
5322360 AAACAAAACATTAATTTTTTTACATGTAAGTCTTACAAGTATTTGGATTAAAATGTCAGATCTTT
260 AAACAAAACATTAATTTTTTTACACGAAAGTCTTACAAGCATTTGGATTAAAATGTCAGATCTTT
* * * *
5322425 TGGATGTAATTTTTTAAAATTAGTTATACGAATCAATTAAAATAATTTTTGAATTTAACAAACTG
325 TGAATGTAATTTCTTAAAATTAGTTATACGAAGCAAATAAAATAATTTTTGAATTTAACAAACTG
*
5322490 TTAATTTAACTAAATAGATATTACTGGAGAACAAAAGATAT
390 TTAATTTAACTAAATAGATATTACTGGAGAACAAAAAATAT
5322531 GTTGTGGAGA
Statistics
Matches: 404, Mismatches: 26, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
504 46 0.11
505 358 0.89
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (504 bp):
GAATCTAAACATTATGACACAACACATGATCATTATTGACCAAGGCTACACTTTACCATACTTTT
ATCACCTTCAATGGATTATGCTGCAGGAAATTCCTGATCTGCCAACTTTTTGGGTTAGGAGGACA
GCTTGTTTATTAGATAGCGCAAGCCATCTACTGCTCAAAATCTGCAATATTGGCCCAATGGATCT
CCTTGGATTCCTGTATCTACGGTTGAAAATCCTACACATGCTACTCCAGCAACAATAGTCAAAGA
AACAAAACATTAATTTTTTTACACGAAAGTCTTACAAGCATTTGGATTAAAATGTCAGATCTTTT
GAATGTAATTTCTTAAAATTAGTTATACGAAGCAAATAAAATAATTTTTGAATTTAACAAACTGT
TAATTTAACTAAATAGATATTACTGGAGAACAAAAAATATTTACGTGATCAATTGTATCTAAATA
AAAAAAATTAATAATAATTTTTTAAGTCAATATCTTATGATAAATTCAC
Found at i:5322958 original size:7 final size:7
Alignment explanation
Indices: 5322946--5322971 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5322936 TTAGAATTTG
5322946 AATTTTA
1 AATTTTA
5322953 AATTTTA
1 AATTTTA
5322960 AATTTTA
1 AATTTTA
5322967 AATTT
1 AATTT
5322972 ATTTAATGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:5324548 original size:61 final size:60
Alignment explanation
Indices: 5324469--5324614 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 60
5324459 CTTCAATAAT
* * *
5324469 AAAAAAAT-AAAAGAGATTATTCAAGGTATTTTTTGTCAGAAACACCTTAAAGAATCTCTA
1 AAAAAAATCAAAAGAGATTATTCAAGGTATTTTTAGCCA-AAACACCTTAAAGAATCTCCA
** * * * * ** * *
5324529 AAAAAAATTGAAGGAGATTATTAAATGTGTTTTTAGCCAAAAGGCCTTGAATAATCTCCA
1 AAAAAAATCAAAAGAGATTATTCAAGGTATTTTTAGCCAAAACACCTTAAAGAATCTCCA
5324589 AAAAAAATCAAAAGAGATTATTCAAG
1 AAAAAAATCAAAAGAGATTATTCAAG
5324615 TCATTTCTAG
Statistics
Matches: 68, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
60 45 0.66
61 23 0.34
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (60 bp):
AAAAAAATCAAAAGAGATTATTCAAGGTATTTTTAGCCAAAACACCTTAAAGAATCTCCA
Found at i:5324895 original size:187 final size:193
Alignment explanation
Indices: 5324574--5324944 Score: 427
Period size: 188 Copynumber: 2.0 Consensus size: 193
5324564 GCCAAAAGGC
* * * *
5324574 CTTGAATAATCTCCAAAAAAAATCAAAAGAGATTATTCAAGTCATTTCTAGCAAGAAACGCCTTG
1 CTTGAATAATCTCAAAAAAAAATCAAAAGAGATTATTCAAGGCATTTCTAGCAAGAAACACCATG
* * * * * *
5324639 AATAACTCAATTCAATTTTTTGTAAGGGAATATTGAAGGCATTTTTTGATAAAAAAATATTTTGA
66 AATAACCCAATTAAATTTTTTGTAAGGGAATATTCAAGGCATTTTTTGAGAAAAAAACATCTTGA
*
5324704 ATAATC-TCAAAAAA-AT-GGAAGAGATTATTAAAGGCA-TTTTTTACAAAAAAAAAAAAAAA
131 ATAATCTTCAAAAAACATAGAAAGAGATTATTAAAGGCATTTTTTTACAAAAAAAAAAAAAAA
* * *
5324763 CTTGAATAATC-CAAAAAAAAAT-GAAGGAGATTATTCAAGGCATTT-TAGGCTAA-AAGCACCA
1 CTTGAATAATCTCAAAAAAAAATCAAAAGAGATTATTCAAGGCATTTCTA-GC-AAGAAACACCA
* * * ** **
5324824 TGAATAGCCCCATTTAAATTTTTTGTAAGGGATTATTCAAGTTATTTTTTG-GCCAAAAACATCT
64 TGAATA-ACCCAATTAAATTTTTTGTAAGGGAATATTCAAGGCATTTTTTGAGAAAAAAACATCT
* * * *
5324888 TGAATAATCTTCAAAAAACATAGAAAGGGATTATTCAAGGTATTTTTTTACCAAAAA
128 TGAATAATCTTCAAAAAACATAGAAAGAGATTATTAAAGGCATTTTTTTACAAAAAA
5324945 CGTTTTGAAT
Statistics
Matches: 150, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
186 2 0.01
187 50 0.33
188 56 0.37
189 13 0.09
190 16 0.11
191 13 0.09
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (193 bp):
CTTGAATAATCTCAAAAAAAAATCAAAAGAGATTATTCAAGGCATTTCTAGCAAGAAACACCATG
AATAACCCAATTAAATTTTTTGTAAGGGAATATTCAAGGCATTTTTTGAGAAAAAAACATCTTGA
ATAATCTTCAAAAAACATAGAAAGAGATTATTAAAGGCATTTTTTTACAAAAAAAAAAAAAAA
Found at i:5324942 original size:62 final size:61
Alignment explanation
Indices: 5324850--5325116 Score: 258
Period size: 62 Copynumber: 4.4 Consensus size: 61
5324840 AATTTTTTGT
* * * * *
5324850 AAGGGATTATTCAAGTTATTTTTTGGCCAAAAACATCTTGAATAATCTTCAAAAAACATAGA
1 AAGGGATTATTCAAGGTATTTTTTGACCAAAAACACCTTCAATAATC-TCAAAAAAAATAGA
* *** *
5324912 AAGGGATTATTCAAGGTATTTTTTTACCAAAAACGTTTTGAATAATCTTCAAAAAAAATTA-A
1 AAGGGATTATTCAAGGTATTTTTTGACCAAAAACACCTTCAATAATC-TCAAAAAAAA-TAGA
* * * * *
5324974 AAAGGATTATTAAATGT-GTTTTTGACCAAAAATACCTTCAATAATC-CAAAAAAAAT-GA
1 AAGGGATTATTCAAGGTATTTTTTGACCAAAAACACCTTCAATAATCTCAAAAAAAATAGA
* * ** * *
5325032 AATGAGATTATTGAAGGTA-TTTTTGGTCAAAAACACCTTCAATAATCTCAAAGAAAATGGA
1 AA-GGGATTATTCAAGGTATTTTTTGACCAAAAACACCTTCAATAATCTCAAAAAAAATAGA
5325093 ACA-GGATTATTCAAGGTATTTTTT
1 A-AGGGATTATTCAAGGTATTTTTT
5325117 ATTAGAAATA
Statistics
Matches: 171, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
58 4 0.02
59 45 0.26
60 22 0.13
61 30 0.18
62 68 0.40
63 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (61 bp):
AAGGGATTATTCAAGGTATTTTTTGACCAAAAACACCTTCAATAATCTCAAAAAAAATAGA
Found at i:5325220 original size:60 final size:58
Alignment explanation
Indices: 5325154--5325283 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 58
5325144 CAATTTTTGT
* ** *
5325154 AAGGGATTATTCAAGATTTTTCTAGTTAAAAACGCC-TGAATAATCTTCAAAAAAAATTA
1 AAGGGATTATTAAAGACGTTT-TAGCTAAAAACGCCTTGAATAATC-TCAAAAAAAATTA
* * * *
5325213 GAAGGGATTATTAAAGGCGTTTTGGCTAGAAATGCCTTGAATAATCTCAAAAAAAATTA
1 -AAGGGATTATTAAAGACGTTTTAGCTAAAAACGCCTTGAATAATCTCAAAAAAAATTA
5325272 AAGGGGATTATT
1 AA-GGGATTATT
5325284 GAAGTTATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.03
59 32 0.53
60 26 0.43
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.31
Consensus pattern (58 bp):
AAGGGATTATTAAAGACGTTTTAGCTAAAAACGCCTTGAATAATCTCAAAAAAAATTA
Found at i:5325301 original size:30 final size:30
Alignment explanation
Indices: 5325267--5325326 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5325257 TCTCAAAAAA
5325267 AATTAAAGGGGATTATTGAAGTTATTTTTG
1 AATTAAAGGGGATTATTGAAGTTATTTTTG
*
5325297 AATTAAAGGGGATTATTGAAGTTGTTTTTG
1 AATTAAAGGGGATTATTGAAGTTATTTTTG
5325327 GCCAAAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (30 bp):
AATTAAAGGGGATTATTGAAGTTATTTTTG
Found at i:5326341 original size:15 final size:15
Alignment explanation
Indices: 5326318--5326348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5326308 AATCAATATT
5326318 AAAAGAAAAATTTTA
1 AAAAGAAAAATTTTA
*
5326333 AAAATAAAAATTTTA
1 AAAAGAAAAATTTTA
5326348 A
1 A
5326349 TTTAACGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAGAAAAATTTTA
Found at i:5328079 original size:23 final size:22
Alignment explanation
Indices: 5328048--5328090 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5328038 ACAATCGAAG
* *
5328048 ATAGGATTCTTGATAAATTCGA
1 ATAGGATTCTTAAGAAATTCGA
5328070 ATAGTGATTCTTAAGAAATTC
1 ATAG-GATTCTTAAGAAATTC
5328091 TTAGGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
ATAGGATTCTTAAGAAATTCGA
Found at i:5329071 original size:67 final size:67
Alignment explanation
Indices: 5328993--5329139 Score: 242
Period size: 67 Copynumber: 2.2 Consensus size: 67
5328983 ATTAGAATCA
* *
5328993 AATATATTTGCCTCTAAAAATGCATT-TCAAAGACAAATTTATTGCCTCCATAGCTCTTTTAAAA
1 AATATATTTGCCTCTAAAAATGCATTAT-AAAGACAAATTGATTGCCTACATAGCTCTTTTAAAA
5329057 ACT
65 ACT
* *
5329060 AATATATTTGCCTCTAAAAATGGATTATAAAGACAAATTGATTGTCTACATAGCTCTTTTAAAAA
1 AATATATTTGCCTCTAAAAATGCATTATAAAGACAAATTGATTGCCTACATAGCTCTTTTAAAAA
5329125 CT
66 CT
5329127 AATATATTTGCCT
1 AATATATTTGCCT
5329140 ATAATTCGGT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 74 0.99
68 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (67 bp):
AATATATTTGCCTCTAAAAATGCATTATAAAGACAAATTGATTGCCTACATAGCTCTTTTAAAAA
CT
Found at i:5329073 original size:33 final size:33
Alignment explanation
Indices: 5329034--5329139 Score: 81
Period size: 33 Copynumber: 3.2 Consensus size: 33
5329024 GACAAATTTA
5329034 TTGCCTCCATAGCTCTTTTAAAAACTAATATAT
1 TTGCCTCCATAGCTCTTTTAAAAACTAATATAT
* * ** * * * *
5329067 TTGCCTCTAAAAATGGATTATAAAGACAAAT-TGA-
1 TTGCCTCCATAGCT--CTTTTAAAAACTAATAT-AT
* *
5329101 TTGTCTACATAGCTCTTTTAAAAACTAATATAT
1 TTGCCTCCATAGCTCTTTTAAAAACTAATATAT
5329134 TTGCCT
1 TTGCCT
5329140 ATAATTCGGT
Statistics
Matches: 49, Mismatches: 19, Indels: 10
0.63 0.24 0.13
Matches are distributed among these distances:
32 12 0.24
33 16 0.33
34 9 0.18
35 12 0.24
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (33 bp):
TTGCCTCCATAGCTCTTTTAAAAACTAATATAT
Found at i:5329597 original size:19 final size:19
Alignment explanation
Indices: 5329548--5329604 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
5329538 GGAGGGGAAT
* *
5329548 GAAAAGAAAGGAAAATAAA
1 GAAAAGTAATGAAAATAAA
*
5329567 GAAAAGTAATGAGAATAAA
1 GAAAAGTAATGAAAATAAA
* * *
5329586 GGAGAGTTATGAAAATAAA
1 GAAAAGTAATGAAAATAAA
5329605 AAATTCTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAAAGTAATGAAAATAAA
Found at i:5332612 original size:41 final size:41
Alignment explanation
Indices: 5332565--5332647 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
5332555 ACTTAAAAAG
* *
5332565 TATACAAATGGT-TTTTAGATTTTAAGTAGATAAAAATATCT
1 TATACAAA-GGTCTTTTAGACTTAAAGTAGATAAAAATATCT
* * *
5332606 TATACAAAGTTCTTTTAGACTTAAAGTATATGAAAATATCT
1 TATACAAAGGTCTTTTAGACTTAAAGTAGATAAAAATATCT
5332647 T
1 T
5332648 TAGTATGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 2 0.06
41 34 0.94
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (41 bp):
TATACAAAGGTCTTTTAGACTTAAAGTAGATAAAAATATCT
Found at i:5333538 original size:27 final size:26
Alignment explanation
Indices: 5333507--5333557 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
5333497 ATCAATTAAA
* *
5333507 ATTAATATATTTTTATTGAAAAAATAT
1 ATTAATATATATTTA-TAAAAAAATAT
5333534 ATTAATATATATTTATAAAAAAAT
1 ATTAATATATATTTATAAAAAAAT
5333558 TACCTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTAATATATATTTATAAAAAAATAT
Found at i:5334341 original size:17 final size:18
Alignment explanation
Indices: 5334308--5334340 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5334298 ATAAACTTGT
5334308 CTATTAAGAATCTTTTTC
1 CTATTAAGAATCTTTTTC
5334326 CTATT-AGAAT-TTTTT
1 CTATTAAGAATCTTTTT
5334341 TTTTGCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (18 bp):
CTATTAAGAATCTTTTTC
Found at i:5334364 original size:52 final size:52
Alignment explanation
Indices: 5334300--5334403 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 52
5334290 ATAAATATAT
* * * *
5334300 AAACTTGTCTATTAAGAA-TCTTTTTCCTATTAGAATTTTTTTTTTGCAAGTC
1 AAACTTGCCTATTAAGAATTCATTTT-CTATTAGAATTCTTTTTCTGCAAGTC
* * *
5334352 AAACTTGCCTATTAATAATTCATTTTCTCTTAGAATTCTTTTTCTGTAAGTC
1 AAACTTGCCTATTAAGAATTCATTTTCTATTAGAATTCTTTTTCTGCAAGTC
5334404 TTTTTATCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 38 0.86
53 6 0.14
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATTCATTTTCTATTAGAATTCTTTTTCTGCAAGTC
Found at i:5342856 original size:42 final size:43
Alignment explanation
Indices: 5342791--5342921 Score: 134
Period size: 42 Copynumber: 3.1 Consensus size: 43
5342781 GAGGCTTCAC
* *
5342791 AAAATATAGAAGGCT-CTTCTAAATAG-AGACTCAACAAC-TTTA
1 AAAATATAAAAGGCTCCTTCTAAATAGAAG-CAC-ACAACTTTTA
5342833 AAAATATAAAAGGCTCCTT-TAAATAGAAGCACACAACTTTTA
1 AAAATATAAAAGGCTCCTTCTAAATAGAAGCACACAACTTTTA
* *
5342875 AAAATA-AAGAAGGCTCATTCTAACA-A-AGGCACACAAC-TTTA
1 AAAATATAA-AAGGCTCCTTCTAA-ATAGAAGCACACAACTTTTA
5342916 AAAATA
1 AAAATA
5342922 AAGGCTCCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
41 17 0.22
42 52 0.66
43 9 0.11
44 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.24
Consensus pattern (43 bp):
AAAATATAAAAGGCTCCTTCTAAATAGAAGCACACAACTTTTA
Found at i:5343713 original size:50 final size:50
Alignment explanation
Indices: 5343621--5343715 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
5343611 GCAATCACAA
* * * * *
5343621 ATTTCTTCCATTACAAGGTATTTAAAGGAAAATAACAGGAATGGATTAGG
1 ATTTCTACCATTACAAGGTATTCAAAAGAAAAGAACAAGAATGGATTAGG
* *
5343671 ATTTCTACCATTGCAAGGTATTCAAAAGAAAAGAATAAGAATGGA
1 ATTTCTACCATTACAAGGTATTCAAAAGAAAAGAACAAGAATGGA
5343716 ATGGGAATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (50 bp):
ATTTCTACCATTACAAGGTATTCAAAAGAAAAGAACAAGAATGGATTAGG
Found at i:5356133 original size:58 final size:58
Alignment explanation
Indices: 5356043--5356165 Score: 192
Period size: 58 Copynumber: 2.1 Consensus size: 58
5356033 TAAAAGAACC
* *
5356043 TTAAACATGGGAATATATCTCTATATCAAGCAAGTTGTGTACTTTGTAGCTTCGAAAA
1 TTAAATATGGGAATATATCTCAATATCAAGCAAGTTGTGTACTTTGTAGCTTCGAAAA
* * * *
5356101 TTAAATATGGGAATATATCTCAATGTTAAGCAAGTTGTGTACTTTGTAGTTTTGAAAA
1 TTAAATATGGGAATATATCTCAATATCAAGCAAGTTGTGTACTTTGTAGCTTCGAAAA
5356159 TTAAATA
1 TTAAATA
5356166 AAAGAACCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (58 bp):
TTAAATATGGGAATATATCTCAATATCAAGCAAGTTGTGTACTTTGTAGCTTCGAAAA
Found at i:5356222 original size:2 final size:2
Alignment explanation
Indices: 5356217--5356241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5356207 TCCAAAAGAA
5356217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5356242 CTTTTTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5363345 original size:24 final size:24
Alignment explanation
Indices: 5363318--5363365 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5363308 TGGTCCTGCT
5363318 TATGACAGGCACAA-GAGTCCTGAG
1 TATGACAGGCA-AAGGAGTCCTGAG
**
5363342 TATGGGAGGCAAAGGAGTCCTGAG
1 TATGACAGGCAAAGGAGTCCTGAG
5363366 CATGGCAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.31, C:0.17, G:0.35, T:0.17
Consensus pattern (24 bp):
TATGACAGGCAAAGGAGTCCTGAG
Found at i:5363370 original size:24 final size:24
Alignment explanation
Indices: 5363324--5363370 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
5363314 TGCTTATGAC
*
5363324 AGGCACAAGAGTCCTGAGTATGGG
1 AGGCACAAGAGTCCTGAGCATGGG
5363348 AGGCA-AAGGAGTCCTGAGCATGG
1 AGGCACAA-GAGTCCTGAGCATGG
5363371 CAGATATCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.30, C:0.17, G:0.38, T:0.15
Consensus pattern (24 bp):
AGGCACAAGAGTCCTGAGCATGGG
Found at i:5364908 original size:16 final size:15
Alignment explanation
Indices: 5364884--5364913 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5364874 TTAACAATTC
5364884 ATTTATTTATATTGT
1 ATTTATTTATATTGT
5364899 ATTTATTTTATATTG
1 ATTTA-TTTATATTG
5364914 AATAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
ATTTATTTATATTGT
Found at i:5366155 original size:23 final size:24
Alignment explanation
Indices: 5366122--5366167 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
5366112 AGCCAAATGA
5366122 AGTTTCTTGTTTCTTCTCTGGGGC
1 AGTTTCTTGTTTCTTCTCTGGGGC
*
5366146 AGTTT-TTGTTTCTTTTCTGGGG
1 AGTTTCTTGTTTCTTCTCTGGGG
5366168 TCTCTCGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.04, C:0.15, G:0.26, T:0.54
Consensus pattern (24 bp):
AGTTTCTTGTTTCTTCTCTGGGGC
Found at i:5366645 original size:20 final size:20
Alignment explanation
Indices: 5366620--5366659 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5366610 TGATTTTAAC
*
5366620 ATTAAA-CATATAAAATGTTT
1 ATTAAATCA-ATAAAAAGTTT
5366640 ATTAAATCAATAAAAAGTTT
1 ATTAAATCAATAAAAAGTTT
5366660 TTGCCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTAAATCAATAAAAAGTTT
Found at i:5369765 original size:15 final size:15
Alignment explanation
Indices: 5369747--5369794 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
5369737 TTTACTGAAA
5369747 ATTTGTTTTTTTATT
1 ATTTGTTTTTTTATT
5369762 ATTTGTTTTTTTATT
1 ATTTGTTTTTTTATT
* *
5369777 TTTTATTTTTTTATT
1 ATTTGTTTTTTTATT
5369792 ATT
1 ATT
5369795 GTTCAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (15 bp):
ATTTGTTTTTTTATT
Found at i:5370954 original size:21 final size:20
Alignment explanation
Indices: 5370923--5370973 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5370913 ATATATATTT
5370923 ATATATTTATATTTAAAAAATA
1 ATAT-TTTATATTT-AAAAATA
5370945 ATATTTTATATTTAAAAATA
1 ATATTTTATATTTAAAAATA
5370965 ATATTTTAT
1 ATATTTTAT
5370974 TAATTTCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 16 0.55
21 9 0.31
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTTATATTTAAAAATA
Found at i:5371327 original size:18 final size:18
Alignment explanation
Indices: 5371300--5371342 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5371290 ATTTTTCTAT
*
5371300 TCTCTTTCTCTCTCTA-AC
1 TCTCTCTCTCT-TCTAGAC
*
5371318 TCTCTCTCTCTTTTAGAC
1 TCTCTCTCTCTTCTAGAC
5371336 TCTCTCT
1 TCTCTCT
5371343 TTTTCTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.09, C:0.37, G:0.02, T:0.51
Consensus pattern (18 bp):
TCTCTCTCTCTTCTAGAC
Found at i:5372410 original size:51 final size:50
Alignment explanation
Indices: 5372354--5372512 Score: 205
Period size: 49 Copynumber: 3.2 Consensus size: 50
5372344 TCATTTTGGT
* * * *
5372354 AGAGGCTCAACAACTTTAAAAATTTTTATTTTGAAAAAAACTTCTCTAAGC
1 AGAGGCTCAACGACTTTAAAAATTTTCATCTTG-AAAAAGCTTCTCTAAGC
* * *
5372405 AGAGGCTCAACGACTTTAAAAA-TCTCATCTTGAAAAAGTTTCTCTCAGC
1 AGAGGCTCAACGACTTTAAAAATTTTCATCTTGAAAAAGCTTCTCTAAGC
* *
5372454 AGAAGTTCAACGACTTT-AAAATTTTCATCTTGAAAAAGCTTCTCTAAGC
1 AGAGGCTCAACGACTTTAAAAATTTTCATCTTGAAAAAGCTTCTCTAAGC
*
5372503 AGAGACTCAA
1 AGAGGCTCAA
5372513 TAAAAATAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
48 4 0.04
49 60 0.65
50 7 0.08
51 21 0.23
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (50 bp):
AGAGGCTCAACGACTTTAAAAATTTTCATCTTGAAAAAGCTTCTCTAAGC
Found at i:5372918 original size:99 final size:99
Alignment explanation
Indices: 5372726--5373081 Score: 412
Period size: 99 Copynumber: 3.6 Consensus size: 99
5372716 CCATAAAAAA
* * * *
5372726 ATCACCATCGAGAAAATGCAATTGAAGCTTTAACACTCGGATATCACCATTGAGAAGATATG--A
1 ATCACCATCGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCATCGAGAA-A-ATGCAA
*
5372789 ATGACTTC-GACTATCACCATCAAAGGAAACTCGAAT
64 ATGACTTCGGA-TATCATCATCAAAGGAAACTCGAAT
* *
5372825 ATCACCATCGAGAAAATACAATTCAAGCTTTAATATTTGGATATCACCATCGAGAAAATGCAAAT
1 ATCACCATCGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCATCGAGAAAATGCAAAT
* * * *
5372890 GACTTCGGATATCGTCATCGAAGAAAACTCTAAT
66 GACTTCGGATATCATCATCAAAGGAAACTCGAAT
** * * ** ** *
5372924 ATCATTATCGAGAAAATACAATTCGAGTTTTAATACTCAAATATCACCATTAAGAATATGCAAAT
1 ATCACCATCGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCATCGAGAAAATGCAAAT
* * * *
5372989 AACTTCGGATATTATCACCAAAGGAAACTTGAAT
66 GACTTCGGATATCATCATCAAAGGAAACTCGAAT
* * * *
5373023 ATCATCATCAAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCACCGAAAAAAT
1 ATCACCATCGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCATCGAGAAAAT
5373082 AAAAGTGCAA
Statistics
Matches: 213, Mismatches: 41, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
97 3 0.01
98 1 0.00
99 207 0.97
100 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (99 bp):
ATCACCATCGAGAAAATACAATTCAAGCTTTAATACTCGGATATCACCATCGAGAAAATGCAAAT
GACTTCGGATATCATCATCAAAGGAAACTCGAAT
Found at i:5373488 original size:35 final size:35
Alignment explanation
Indices: 5373407--5373530 Score: 151
Period size: 35 Copynumber: 3.5 Consensus size: 35
5373397 CACCATTATG
* * *
5373407 ATGCAAATTTCTTCTCTTAAAATGATGATGCAAATGAA
1 ATGCAAATGTCTTTTCTTAAAATGATG-T--ACATGAA
* *
5373445 ATGTAAATGTCTTTTCTTAAAATGATGCT-CATGAG
1 ATGCAAATGTCTTTTCTTAAAATGATG-TACATGAA
*
5373480 ATGCAAATGTCTTTTCTTAAAAAGATGTACATGAA
1 ATGCAAATGTCTTTTCTTAAAATGATGTACATGAA
5373515 ATGCAAATGTCTTTTC
1 ATGCAAATGTCTTTTC
5373531 CAATAATACT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.01
35 50 0.66
38 25 0.33
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (35 bp):
ATGCAAATGTCTTTTCTTAAAATGATGTACATGAA
Found at i:5373794 original size:22 final size:23
Alignment explanation
Indices: 5373751--5373796 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
5373741 TCGCTGCTTA
*
5373751 TTCTTCATCAATTTCTACTTTTT
1 TTCTTCATCAATTTCGACTTTTT
*
5373774 TTCTTCA-CAATTTGGA-TTTTT
1 TTCTTCATCAATTTCGACTTTTT
5373795 TT
1 TT
5373797 ACTTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.17, C:0.17, G:0.04, T:0.61
Consensus pattern (23 bp):
TTCTTCATCAATTTCGACTTTTT
Found at i:5382099 original size:28 final size:28
Alignment explanation
Indices: 5382060--5382113 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
5382050 TAATTTTAAA
*
5382060 ATATTAATTTAATAAA-AATATTATATTC
1 ATATTAATTTAAAAAATAAT-TTATATTC
5382088 ATATATAA-TTAAAAAATAATTTATAT
1 ATAT-TAATTTAAAAAATAATTTATAT
5382114 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATTAATTTAAAAAATAATTTATATTC
Found at i:5382116 original size:16 final size:17
Alignment explanation
Indices: 5382097--5382133 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
5382087 CATATATAAT
5382097 TAAAAAATAAT-TTATA
1 TAAAAAATAATATTATA
*
5382113 TAAAAAATAATATTTTA
1 TAAAAAATAATATTATA
5382130 TAAA
1 TAAA
5382134 TATGATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATAATATTATA
Found at i:5383747 original size:2 final size:2
Alignment explanation
Indices: 5383740--5383778 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5383730 TCGTCGGTAT
*
5383740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5383779 AGTGGACACC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5386008 original size:37 final size:39
Alignment explanation
Indices: 5385946--5386018 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 39
5385936 TATTTTATTT
*
5385946 TATTTTTTTTATTTGTCTATTTATTAATATATATATATA
1 TATTTTTTTTATTTGTCTATCTATTAATATATATATATA
* *
5385985 TATTTTTTTT-TTT-TTTATCTATTAATATTTATAT
1 TATTTTTTTTATTTGTCTATCTATTAATATATATAT
5386019 TACTTATCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 18 0.58
38 3 0.10
39 10 0.32
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.68
Consensus pattern (39 bp):
TATTTTTTTTATTTGTCTATCTATTAATATATATATATA
Found at i:5386060 original size:17 final size:17
Alignment explanation
Indices: 5386040--5386110 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
5386030 TTTTATTTTT
5386040 TATTATTATTATTTATC
1 TATTATTATTATTTATC
*
5386057 TATT-TCTTTTATTTATC
1 TATTAT-TATTATTTATC
* *
5386074 TAATTATTTTTTTTGTTATC
1 T-ATTA-TTATTAT-TTATC
*
5386094 TATTAATA-TATTTATC
1 TATTATTATTATTTATC
5386110 T
1 T
5386111 TTTTATTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
16 7 0.16
17 17 0.39
18 4 0.09
19 9 0.20
20 7 0.16
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTTATC
Found at i:5386060 original size:24 final size:25
Alignment explanation
Indices: 5386033--5386114 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 25
5386023 TATCTGCTTT
5386033 TATTTTTTATTATTAT-TATTTATC
1 TATTTTTTATTATTATATATTTATC
* * * *
5386057 TATTTCTT-TTATTTATCTAATTATT
1 TATTTTTTATTA-TTATATATTTATC
*
5386082 TTTTTTGTTATCTATTAATATATTTATC
1 TATTTT-TTAT-TATT-ATATATTTATC
5386110 T-TTTT
1 TATTTT
5386115 ATTTTGATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.07
24 11 0.25
25 10 0.23
26 2 0.05
27 7 0.16
28 11 0.25
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (25 bp):
TATTTTTTATTATTATATATTTATC
Found at i:5386086 original size:20 final size:21
Alignment explanation
Indices: 5386057--5386095 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5386047 ATTATTTATC
5386057 TATTTCTTTTAT-TTATCTAAT
1 TATTTCTTTT-TGTTATCTAAT
5386078 TATTT-TTTTTGTTATCTA
1 TATTTCTTTTTGTTATCTA
5386096 TTAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 11 0.65
21 5 0.29
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (21 bp):
TATTTCTTTTTGTTATCTAAT
Found at i:5386221 original size:13 final size:13
Alignment explanation
Indices: 5386203--5386229 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5386193 GACAGAGTTG
5386203 AGATTGAATTCAA
1 AGATTGAATTCAA
5386216 AGATTGAATTCAA
1 AGATTGAATTCAA
5386229 A
1 A
5386230 TCCCAGAAAG
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:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (13 bp):
AGATTGAATTCAA
Found at i:5387072 original size:6 final size:5
Alignment explanation
Indices: 5387049--5387096 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
5387039 GTTTAGTACT
5387049 TTTTA TTTTA TTTTA TTTTCA TTTT- TTTTAA TTTTA --TTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT-A TTTTA TTTTA TTTTA TTTT
5387097 CTTTAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 3 0.08
4 4 0.11
5 22 0.58
6 9 0.24
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:5387195 original size:58 final size:57
Alignment explanation
Indices: 5387115--5387383 Score: 366
Period size: 58 Copynumber: 4.7 Consensus size: 57
5387105 AAAATTCAAA
*
5387115 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTC
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTC
* *
5387172 TAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTC
1 -AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTC
* * *
5387230 CAAAAATATTTTTGAG-AAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAGTTTTC
1 AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTC
* *
5387286 AAAAAATGAATTTTTGAGAAAAAGTTGAAAGTATCAATTTTC-CTCAAAATTAAAG-TTTC
1 AAAAAAT--ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAA-T-AAGTTTTC
* *
5387345 TAAAAAATA-TTTTGGGAAAAAATTGAAAGTATCAATTTT
1 -AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTT
5387384 TCCTGCACAA
Statistics
Matches: 191, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
56 43 0.23
57 42 0.22
58 69 0.36
59 27 0.14
60 10 0.05
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTC
Found at i:5387219 original size:28 final size:28
Alignment explanation
Indices: 5387132--5387220 Score: 67
Period size: 28 Copynumber: 3.1 Consensus size: 28
5387122 ATTTTTGAGG
5387132 AAAAGTTGAAAGTATCAATTTTCTTTGAA
1 AAAAGTTGAAAGTATCAATTTTCTTTG-A
* ** **
5387161 AATAAGTTTTCTAAAAAAT--ATTTT-TAAGA
1 AA-AAG--TT-GAAAGTATCAATTTTCTTTGA
5387190 AAAAGTTGAAAGTATCAATTTTCTTTGA
1 AAAAGTTGAAAGTATCAATTTTCTTTGA
5387218 AAA
1 AAA
5387221 TAAGCTTTCC
Statistics
Matches: 43, Mismatches: 10, Indels: 15
0.63 0.15 0.22
Matches are distributed among these distances:
25 5 0.12
26 2 0.05
27 5 0.12
28 9 0.21
29 5 0.12
30 5 0.12
31 5 0.12
32 2 0.05
33 5 0.12
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (28 bp):
AAAAGTTGAAAGTATCAATTTTCTTTGA
Found at i:5387312 original size:115 final size:114
Alignment explanation
Indices: 5387116--5387384 Score: 375
Period size: 115 Copynumber: 2.3 Consensus size: 114
5387106 AAATTCAAAA
* *
5387116 AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGTTTTCTAAAAAATA
1 AAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAGTTTTCTAAAAAATA
* *
5387181 TTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAA-T-AAGCTTTCC
65 TTTTTAAGAAAAAGTTGAAAGTATCAATTTTC-CTCAAAATTAAAG-TTTCC
5387231 AAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAGTTTTC-AAAAAATGA
1 AAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAGTTTTCTAAAAAAT--
* *
5387295 ATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCT
64 ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCC
* *
5387346 AAAAA-ATATTTTGGGAAAAAATTGAAAGTATCAATTTTT
1 AAAAATAT-TTTTGAG-AAAAGTTGAAAGTATCAATTTTT
5387385 CCTGCACAAA
Statistics
Matches: 140, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
113 7 0.05
114 46 0.33
115 62 0.44
116 25 0.18
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (114 bp):
AAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTTTTTAAAAATAAGTTTTCTAAAAAATAT
TTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAATTAAAGTTTCC
Found at i:5388122 original size:22 final size:22
Alignment explanation
Indices: 5388097--5388150 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
5388087 GCTACTCGGG
5388097 TTCGATTCGAAGAAAACTCGAA
1 TTCGATTCGAAGAAAACTCGAA
5388119 TTCGATTCGAAGAAAACTCGAA
1 TTCGATTCGAAGAAAACTCGAA
5388141 TTCGATTCGA
1 TTCGATTCGA
5388151 TTATTATCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (22 bp):
TTCGATTCGAAGAAAACTCGAA
Found at i:5388315 original size:6 final size:6
Alignment explanation
Indices: 5388298--5388328 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5388288 AATAAAATAT
*
5388298 TTCGAG TCCGAG TTCGAG TTCGAG TTCGAG T
1 TTCGAG TTCGAG TTCGAG TTCGAG TTCGAG T
5388329 ATAAATAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (6 bp):
TTCGAG
Found at i:5389553 original size:15 final size:15
Alignment explanation
Indices: 5389533--5389563 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5389523 CGTTTACACT
5389533 TCAAATATAAATAAA
1 TCAAATATAAATAAA
*
5389548 TCAAATATGAATAAA
1 TCAAATATAAATAAA
5389563 T
1 T
5389564 TTTATTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
TCAAATATAAATAAA
Found at i:5390062 original size:15 final size:15
Alignment explanation
Indices: 5390037--5390069 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
5390027 AAATACTTTC
5390037 AAAATTGAAAAACAAA
1 AAAATTGAAAAA-AAA
5390053 AAAATT-AAAAAAAA
1 AAAATTGAAAAAAAA
5390067 AAA
1 AAA
5390070 TTCTCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAATTGAAAAAAAA
Found at i:5394116 original size:14 final size:14
Alignment explanation
Indices: 5394072--5394120 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
5394062 ACAAATAGTC
5394072 ATAACTATTTAAAT
1 ATAACTATTTAAAT
* * **
5394086 ATAAATATATAGTT
1 ATAACTATTTAAAT
5394100 ATAACTATTTAAAT
1 ATAACTATTTAAAT
5394114 ATAACTA
1 ATAACTA
5394121 GATGATTGTT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (14 bp):
ATAACTATTTAAAT
Found at i:5403199 original size:17 final size:18
Alignment explanation
Indices: 5403172--5403212 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
5403162 ATTTATTTAA
**
5403172 TTAAATAATTTTAATTTT
1 TTAAATAATTTTAAAATT
5403190 TTAAAT-ATTTTAAAATT
1 TTAAATAATTTTAAAATT
5403207 TTAAAT
1 TTAAAT
5403213 TTAGTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAAATAATTTTAAAATT
Found at i:5403202 original size:9 final size:9
Alignment explanation
Indices: 5403172--5403212 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
5403162 ATTTATTTAA
5403172 TTAAATAATT
1 TTAAAT-ATT
*
5403182 TT-AATTTT
1 TTAAATATT
5403190 TTAAATATT
1 TTAAATATT
5403199 TTAAA-ATT
1 TTAAATATT
5403207 TTAAAT
1 TTAAAT
5403213 TTAGTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 12 0.44
9 13 0.48
10 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAAATATT
Found at i:5407824 original size:19 final size:18
Alignment explanation
Indices: 5407787--5407825 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5407777 AAATTGAAGA
* *
5407787 TAATTTTTTTTAATTTAT
1 TAATATTTTTTAATATAT
5407805 TAATATTTTTTATATATAT
1 TAATATTTTTTA-ATATAT
5407824 TA
1 TA
5407826 TAAGTGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATTTTTTAATATAT
Found at i:5408213 original size:23 final size:22
Alignment explanation
Indices: 5408187--5408232 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5408177 ATATAATTAT
5408187 TTTTAAAAATTAATATTTAATAA
1 TTTTAAAAATTAATATTT-ATAA
**
5408210 TTTTAAATTTTAATATTTATAA
1 TTTTAAAAATTAATATTTATAA
5408232 T
1 T
5408233 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTAAAAATTAATATTTATAA
Found at i:5408232 original size:9 final size:8
Alignment explanation
Indices: 5408196--5408237 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
5408186 TTTTTAAAAA
5408196 TTAATA-T
1 TTAATATT
5408203 TTAATAATT
1 TTAAT-ATT
5408212 TTAA-ATT
1 TTAATATT
5408219 TTAATATT
1 TTAATATT
5408227 TATAATATT
1 T-TAATATT
5408236 TT
1 TT
5408238 TTTATTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 12 0.39
8 6 0.19
9 13 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAATATT
Found at i:5409805 original size:36 final size:36
Alignment explanation
Indices: 5409764--5409834 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
5409754 CATTTTGTAT
* *
5409764 AGTCAT-TTTTTTTGTTTAAATAAATTTTATTTAAAC
1 AGTCATATTTTTCTGTTCAAATAAA-TTTATTTAAAC
* *
5409800 AGTCATATTTTTCTGTTCAGATATATTTATTTAAA
1 AGTCATATTTTTCTGTTCAAATAAATTTATTTAAA
5409835 ATTAATAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 16 0.53
37 14 0.47
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (36 bp):
AGTCATATTTTTCTGTTCAAATAAATTTATTTAAAC
Found at i:5409872 original size:23 final size:21
Alignment explanation
Indices: 5409834--5409877 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
5409824 ATTTATTTAA
*
5409834 AATTAATAATATTTTAAAATT
1 AATTAATAATAATTTAAAATT
5409855 AATTAATTAATTAATTTAAAATT
1 AATTAA-TAA-TAATTTAAAATT
5409878 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTAATAATAATTTAAAATT
Found at i:5410382 original size:2 final size:2
Alignment explanation
Indices: 5410375--5410415 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5410365 ATTACTACTA
5410375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5410416 CAATATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5411397 original size:12 final size:11
Alignment explanation
Indices: 5411382--5411430 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
5411372 TATATAAATG
5411382 TATATTTTATTA
1 TATATTTTA-TA
5411394 TATATTTTA-A
1 TATATTTTATA
*
5411404 T-T-TTTTATT
1 TATATTTTATA
5411413 TATATATTTATA
1 TATAT-TTTATA
5411425 TATATT
1 TATATT
5411431 GATAAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 5 0.16
9 2 0.06
10 3 0.10
11 2 0.06
12 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTTATA
Found at i:5411461 original size:13 final size:13
Alignment explanation
Indices: 5411443--5411476 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5411433 TAAAATTATC
*
5411443 ATTTAATATTTTA
1 ATTTAATATATTA
*
5411456 ATTTAAGATATTA
1 ATTTAATATATTA
5411469 ATTTAATA
1 ATTTAATA
5411477 AAAATATTAT
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:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATTTAATATATTA
Found at i:5411485 original size:17 final size:20
Alignment explanation
Indices: 5411463--5411512 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
5411453 TTAATTTAAG
5411463 ATATTA-ATTTA-A-TAAAA
1 ATATTATATTTATATTAAAA
5411480 ATATTATATTTATATTAAAA
1 ATATTATATTTATATTAAAA
* *
5411500 ATAATATTTTTAT
1 ATATTATATTTAT
5411513 GAATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 6 0.21
18 5 0.18
19 1 0.04
20 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATATTTATATTAAAA
Found at i:5411505 original size:23 final size:22
Alignment explanation
Indices: 5411463--5411507 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5411453 TTAATTTAAG
5411463 ATATTAATTTAATAAAAATATT
1 ATATTAATTTAATAAAAATATT
*
5411485 ATATTTATATTAA-AAATAATATT
1 ATATTAAT-TTAATAAA-AATATT
5411508 TTTATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTAATTTAATAAAAATATT
Found at i:5412069 original size:2 final size:2
Alignment explanation
Indices: 5412062--5412092 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5412052 AATCAAATAA
5412062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5412093 AACAAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5412541 original size:20 final size:20
Alignment explanation
Indices: 5412516--5412567 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
5412506 ATATTACAAT
5412516 TTTATGATTAAATT-TGATAA
1 TTTATGATTAAATTAT-ATAA
*
5412536 TTTATGTATTTATATTATATAA
1 TTTATG-A-TTAAATTATATAA
5412558 TTTAT-ATTAA
1 TTTATGATTAA
5412568 CTATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 1 0.04
22 15 0.56
23 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTATGATTAAATTATATAA
Found at i:5414046 original size:42 final size:40
Alignment explanation
Indices: 5413974--5414051 Score: 95
Period size: 42 Copynumber: 1.9 Consensus size: 40
5413964 ATATTTGTAT
* *
5413974 ATTAATAAAATTATTATTTAATATCTTAATTTAAAATATTA
1 ATTAATAAAAATATTATTTAATATCATAA-TTAAAATATTA
*
5414015 ATTAACTAAAAATATTATATTTATAT-ATAATTAAAAT
1 ATTAA-TAAAAATATTAT-TTAATATCATAATTAAAAT
5414052 GTAATTTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 12 0.38
42 14 0.44
43 6 0.19
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (40 bp):
ATTAATAAAAATATTATTTAATATCATAATTAAAATATTA
Found at i:5419722 original size:13 final size:13
Alignment explanation
Indices: 5419704--5419729 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5419694 TGTAATGTTG
5419704 AAATAATATATTA
1 AAATAATATATTA
5419717 AAATAATATATTA
1 AAATAATATATTA
5419730 TTTTACATTA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATAATATATTA
Found at i:5419843 original size:18 final size:18
Alignment explanation
Indices: 5419798--5419836 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
5419788 TTTCATAATT
*
5419798 TTAATTTTAA-TTTTTAA
1 TTAACTTTAATTTTTTAA
5419815 TTAACTTTAATTTTTTATA
1 TTAACTTTAATTTTTTA-A
5419834 TTA
1 TTA
5419837 TCTTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTAACTTTAATTTTTTAA
Found at i:5421732 original size:26 final size:26
Alignment explanation
Indices: 5421676--5421727 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5421666 TTGTGATTTG
* *
5421676 AATTTAAATAATTAATCAAAATATTA
1 AATTTAAATAATTAATAAAAAAATTA
*
5421702 AATTTAAATAATTTATTAAAAAAATT
1 AATTTAAATAA-TTAATAAAAAAATT
5421728 TATTTGATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTTAAATAATTAATAAAAAAATTA
Found at i:5424125 original size:126 final size:124
Alignment explanation
Indices: 5423994--5424597 Score: 479
Period size: 126 Copynumber: 4.8 Consensus size: 124
5423984 TTTTATAATG
* * * * * *
5423994 CAGTAATTAATAATTGTAAATTTTTACAAACAATCAATTATTACATTGTTTTATTTTATAACATA
1 CAGTAATTGATAATTCTAAATTTTT-CAAATAATCAATTATTGCATTGCTTTGTTTTATAACATA
* * *
5424059 GTAATTAATTATTATAATTGTTTTAAAACAATCAATTACTGCATTTATAGGCCTTGAAATA
65 GTAA-TAATAATTATAATTGTTTTAAAACAATCAATTAATGCATTTATAGGCTTTGAAATA
* * * * *
5424120 AAGTAATTGATAATTCTAATATTGTTGAAATGATCAATTACTGCATTGCTTTGTTTTATAATGCA
1 CAGTAATTGATAATTCTAA-ATTTTTCAAATAATCAATTATTGCATTGCTTTGTTTTATAA--C-
* * * * *
5424185 ATAGTAA-AACAA-TGTAATTGTTTAAAAACAATCAATTATTGCATTTATAAGCTTTG-AATCA
62 ATAGTAATAATAATTATAATTGTTTTAAAACAATCAATTAATGCATTTATAGGCTTTGAAAT-A
* * ** * *
5424246 CAGTAATTGATAATTCTAATTTTTTCAAATGAGT-TTTTATTGCGTTACTTTGTTTTATAACATA
1 CAGTAATTGATAATTCTAAATTTTTCAAAT-AATCAATTATTGCATTGCTTTGTTTTATAACATA
* * * *
5424310 GTAATAAAATAAATTTTAATTGTTTTAAAACAATCAATTAATGCGTTTATAGG-TTTTATAATG
65 GTAAT--AAT-AATTATAATTGTTTTAAAACAATCAATTAATGCATTTATAGGCTTTGA-AATA
* * * *
5424373 CAGTAATTGATAATT-TTAATTTTTCAAATAACCAAATAGATGCATTGCTTTGTTTTATAACATA
1 CAGTAATTGATAATTCTAAATTTTTCAAATAATCAATTA-TTGCATTGCTTTGTTTTATAACATA
* * * * *** * * * * *
5424437 GTAATGATCA-TATAGTTG-TTTCAAGTTATTAATTACTACATTTATAAGCTTTGAAATG
65 GTAATAATAATTATAATTGTTTTAAAACAATCAATTAATGCATTTATAGGCTTTGAAATA
** * * * ** ***
5424495 CAGTAATTGATAATTCTAGTTTTTTTCAAGTTATCAAATCA-TGGGTTGCTTTGTTTTATAATGC
1 CAGTAATTGATAATTCTA-AATTTTTCAAATAATC-AATTATTGCATTGCTTTGTTTTATAACAT
* * *
5424559 AGTAATTTATCATTATAATTTTTTTAAAACAATCAATTA
64 AGTAA-TAATAATTATAATTGTTTTAAAACAATCAATTA
5424598 TTGCGTTACT
Statistics
Matches: 374, Mismatches: 82, Indels: 44
0.75 0.16 0.09
Matches are distributed among these distances:
122 47 0.13
123 35 0.09
124 17 0.05
125 46 0.12
126 134 0.36
127 84 0.22
128 4 0.01
129 7 0.02
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (124 bp):
CAGTAATTGATAATTCTAAATTTTTCAAATAATCAATTATTGCATTGCTTTGTTTTATAACATAG
TAATAATAATTATAATTGTTTTAAAACAATCAATTAATGCATTTATAGGCTTTGAAATA
Found at i:5428365 original size:15 final size:15
Alignment explanation
Indices: 5428347--5428377 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5428337 TTTTATTTAT
5428347 TGATTTTTTAAAAAA
1 TGATTTTTTAAAAAA
5428362 TGATTTTTTAAAAAA
1 TGATTTTTTAAAAAA
5428377 T
1 T
5428378 ATGTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TGATTTTTTAAAAAA
Found at i:5430081 original size:3 final size:3
Alignment explanation
Indices: 5430073--5430103 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5430063 AGTACAATCA
5430073 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
5430104 GGGCATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:5431264 original size:2 final size:2
Alignment explanation
Indices: 5431257--5431287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5431247 GTCCAAAACA
5431257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5431288 CATTTCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5441179 original size:23 final size:23
Alignment explanation
Indices: 5441138--5441184 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5441128 TATGATTTAA
** *
5441138 ATTTTAAATTTATTAAATATTAT
1 ATTTTAAATAAATTAAATAATAT
*
5441161 ATTTTAAATAAATTTAATAATAT
1 ATTTTAAATAAATTAAATAATAT
5441184 A
1 A
5441185 AAATATAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAAATAAATTAAATAATAT
Found at i:5441912 original size:17 final size:16
Alignment explanation
Indices: 5441891--5441927 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5441881 AATAAAGAAA
5441891 AAAAAGAAATAATTAAAC
1 AAAAA-AAATAATT-AAC
5441909 AAAAAAAATAATTAAC
1 AAAAAAAATAATTAAC
5441925 AAA
1 AAA
5441928 TTATAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.32
17 8 0.42
18 5 0.26
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (16 bp):
AAAAAAAATAATTAAC
Found at i:5443440 original size:11 final size:11
Alignment explanation
Indices: 5443409--5443452 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
5443399 ATAATTATGT
5443409 AATATATATT-
1 AATATATATTA
5443419 AA-AT-T-TTA
1 AATATATATTA
5443427 AATATATATTA
1 AATATATATTA
*
5443438 AATACATATTA
1 AATATATATTA
5443449 AATA
1 AATA
5443453 GTATTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
7 2 0.07
8 3 0.10
9 4 0.14
10 3 0.10
11 17 0.59
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
AATATATATTA
Found at i:5443491 original size:27 final size:28
Alignment explanation
Indices: 5443461--5443513 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
5443451 TAGTATTTTA
* *
5443461 TTTTTTATTTTTTTAATATG-TAAGTAT
1 TTTTTTATATTATTAATATGCTAAGTAT
*
5443488 TTTTTTATATTATTGATATGCTAAGT
1 TTTTTTATATTATTAATATGCTAAGT
5443514 TTATTAAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.62
Consensus pattern (28 bp):
TTTTTTATATTATTAATATGCTAAGTAT
Found at i:5443615 original size:29 final size:29
Alignment explanation
Indices: 5443583--5443645 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
5443573 CACATATTCA
*
5443583 TATTAATCGTATCTATTCATGTATATCTG
1 TATTAATCGTATCTATTCATATATATCTG
* * * *
5443612 TATTAGTTGTATTTATTCGTATATATCTG
1 TATTAATCGTATCTATTCATATATATCTG
5443641 TATTA
1 TATTA
5443646 TTTATATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (29 bp):
TATTAATCGTATCTATTCATATATATCTG
Found at i:5445130 original size:16 final size:16
Alignment explanation
Indices: 5445092--5445138 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
5445082 ATAAAAAAAG
* *
5445092 TTATTATATTATCTCTA
1 TTATTATAATAT-TTTA
5445109 TT-TTATAATATTTTA
1 TTATTATAATATTTTA
5445124 TTATTATATATATTT
1 TTATTATA-ATATTT
5445139 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 8 0.31
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATAATATTTTA
Found at i:5445640 original size:14 final size:15
Alignment explanation
Indices: 5445633--5445668 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 15
5445623 TATTTTTATT
5445633 AAAATATTTGTATAA
1 AAAATATTTGTATAA
5445648 AAAATA-TT-TA-AA
1 AAAATATTTGTATAA
5445660 AAAATATTT
1 AAAATATTT
5445669 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.40
13 4 0.20
14 2 0.10
15 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATATTTGTATAA
Found at i:5446742 original size:12 final size:12
Alignment explanation
Indices: 5446725--5446768 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
5446715 GTTCCCCTTT
5446725 TTATATTTTATA
1 TTATATTTTATA
*
5446737 TTATATTATATA
1 TTATATTTTATA
5446749 -T-TA-TTTATA
1 TTATATTTTATA
5446758 TTATATTTTAT
1 TTATATTTTAT
5446769 GATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.19
10 3 0.11
11 3 0.11
12 16 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:5454371 original size:21 final size:21
Alignment explanation
Indices: 5454312--5454371 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
5454302 ATTAAATAAA
* *
5454312 ATAT-TAATAATTTATATATTT
1 ATATGTAATAATTTA-AAAATT
* **
5454333 ATATTGTATTAACATAAAAATT
1 ATA-TGTAATAATTTAAAAATT
5454355 ATATGTAATAATTTAAA
1 ATATGTAATAATTTAAA
5454372 TTAATATAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
21 14 0.48
22 8 0.28
23 7 0.24
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (21 bp):
ATATGTAATAATTTAAAAATT
Found at i:5454426 original size:21 final size:22
Alignment explanation
Indices: 5454400--5454442 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5454390 ATATTTTTTA
5454400 TTTTATT-AAATTATAAATAAT
1 TTTTATTAAAATTATAAATAAT
*
5454421 TTTTATTAAAATTTTAAATAAT
1 TTTTATTAAAATTATAAATAAT
5454443 ATTATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATTAAAATTATAAATAAT
Found at i:5454447 original size:21 final size:21
Alignment explanation
Indices: 5454402--5454448 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
5454392 ATTTTTTATT
*
5454402 TTATTAAATTATAAATAATTT
1 TTATTAAATTATAAATAATTA
*
5454423 TTATTAAAATTTTAAATAA-TA
1 TTATT-AAATTATAAATAATTA
5454444 TTATT
1 TTATT
5454449 TTATATCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTAAATTATAAATAATTA
Found at i:5459839 original size:23 final size:24
Alignment explanation
Indices: 5459796--5459844 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
5459786 ATTTTTAATA
5459796 AAAATATATTAATTCTAATTAATTT
1 AAAATATATTAATTCTAATT-ATTT
5459821 AAAATA-A-TAATT-TATATTATTT
1 AAAATATATTAATTCTA-ATTATTT
5459843 AA
1 AA
5459845 TAAAAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 8 0.35
23 8 0.35
24 1 0.04
25 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATATATTAATTCTAATTATTT
Found at i:5461774 original size:132 final size:132
Alignment explanation
Indices: 5461537--5461801 Score: 485
Period size: 132 Copynumber: 2.0 Consensus size: 132
5461527 TTCAATTGTG
* *
5461537 CAGTTATCAAAAGACAAGCAAAGCACTGAAGAGGATTTAAAAAATATGAAGAGTACTTTACCCTT
1 CAGTTATCAAAAGACAAGCAAAACACTGAAGAGGATTTAAAAAATATGAAGAGTACTATACCCTT
5461602 ATTAGTCAAAGAAGAAGTTATGCAGTCGCCCATTATTCCTGATAACGAATCGTATATTGCAAAGA
66 ATTAGTCAAAGAAGAAGTTATGCAGTCGCCCATTATTCCTGATAACGAATCGTATATTGCAAAGA
5461667 GC
131 GC
* *
5461669 CAGTTATCAAAAGACAAGCAAAATACTGGAGAGGATTTAAAAAATATGAAGAGTACTATACCCTT
1 CAGTTATCAAAAGACAAGCAAAACACTGAAGAGGATTTAAAAAATATGAAGAGTACTATACCCTT
*
5461734 ATTAGTCAAAGAAGAAGTTATGCAGTCGCCCGTTATTCCTGATAACGAATCGTATATTGCAAAGA
66 ATTAGTCAAAGAAGAAGTTATGCAGTCGCCCATTATTCCTGATAACGAATCGTATATTGCAAAGA
5461799 GC
131 GC
5461801 C
1 C
5461802 CATCTTTTGG
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (132 bp):
CAGTTATCAAAAGACAAGCAAAACACTGAAGAGGATTTAAAAAATATGAAGAGTACTATACCCTT
ATTAGTCAAAGAAGAAGTTATGCAGTCGCCCATTATTCCTGATAACGAATCGTATATTGCAAAGA
GC
Found at i:5464765 original size:14 final size:14
Alignment explanation
Indices: 5464736--5464765 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5464726 AAAAAAATGA
*
5464736 AAAAACCAAAATCC
1 AAAAACCAAAAGCC
5464750 AAAAACCAAAAGCC
1 AAAAACCAAAAGCC
5464764 AA
1 AA
5464766 TATGAAACCA
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:0.67, C:0.27, G:0.03, T:0.03
Consensus pattern (14 bp):
AAAAACCAAAAGCC
Found at i:5466572 original size:2 final size:2
Alignment explanation
Indices: 5466560--5466596 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5466550 AGTATCCCTC
*
5466560 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5466597 GAGAAGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5469831 original size:18 final size:20
Alignment explanation
Indices: 5469808--5469846 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5469798 AAAAAAATTG
5469808 AAAATTA-AA-AATCGATTT
1 AAAATTATAATAATCGATTT
*
5469826 AAAATTATAATAATTGATTT
1 AAAATTATAATAATCGATTT
5469846 A
1 A
5469847 GTTTGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAATTATAATAATCGATTT
Found at i:5473694 original size:286 final size:285
Alignment explanation
Indices: 5473176--5473743 Score: 969
Period size: 286 Copynumber: 2.0 Consensus size: 285
5473166 TTCCATTGAA
*
5473176 ATGCTTAGTTTGTGTTCTTGAACTTTTCAAATTCAACTTTACTCCATTACCTTTTTCTAGAATGA
1 ATGCTTAGTTTGTGTTCTTGAACTTTTCAAATTCAACTTTACTCCATTACCTTTTTCTAGAATAA
* * * *
5473241 ACAATTCATTTTAGAAAATGGCATACAATGGCACAAACGTCTTTGTTCATTGTGATTGTAGAATT
66 ACAATTCATTTTAGAAAATGGCATACAATGGAACAAACATCTTTGTTCATTGCGATTATAGAATT
* *
5473306 AATATTCAACCTTTTGGATTTTCACAAACTTACATTTATTCAACCAAACTCTAAGCTTATTAGAA
131 AATATTCAACCTTTTGGATATTCACAAACTTACATTTATCCAACCAAACTCTAAGCTTATTAGAA
5473371 GATGCATACTTCATGCAAGTAATACATTTTCCAAATCTTTTAATTATGACATGTGTGGCATCTTG
196 GATGCATACTTCATGCAAGTAATACATTTTCCAAATCTTTTAATTATGACATGTGTGGCATCTTG
* *
5473436 CCATTCCATACCTCATATGTTAATT
261 CCATTCCATAACTCATACGTTAATT
* * *
5473461 ATGCTTAGTTTTTGTTCTTGAACTTTTCAAGTTCAACTTTACTCCCATTACCTTTTTTTAGAATA
1 ATGCTTAGTTTGTGTTCTTGAACTTTTCAAATTCAACTTTACT-CCATTACCTTTTTCTAGAATA
5473526 AACAATTCATTTTAGAAAATGGCATACAATGGAACAAACATCTTTGTTCATTGCGATTATAGAAT
65 AACAATTCATTTTAGAAAATGGCATACAATGGAACAAACATCTTTGTTCATTGCGATTATAGAAT
5473591 TAATATTCAACCTTTTGGATATTCACAAACTTACATTTATCCAA-CAAAGCT-TCAAGCTTATTA
130 TAATATTCAACCTTTTGGATATTCACAAACTTACATTTATCCAACCAAA-CTCT-AAGCTTATTA
* *
5473654 GAAGATGCATAGTTCATGCAAGTAATACATTTTTCAAATCTTTTAATTATGACATGTGTGGCATC
193 GAAGATGCATACTTCATGCAAGTAATACATTTTCCAAATCTTTTAATTATGACATGTGTGGCATC
5473719 TTGCCATTCCATAACTCATACGTTA
258 TTGCCATTCCATAACTCATACGTTA
5473744 TCATGTCAAT
Statistics
Matches: 266, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
285 46 0.17
286 220 0.83
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (285 bp):
ATGCTTAGTTTGTGTTCTTGAACTTTTCAAATTCAACTTTACTCCATTACCTTTTTCTAGAATAA
ACAATTCATTTTAGAAAATGGCATACAATGGAACAAACATCTTTGTTCATTGCGATTATAGAATT
AATATTCAACCTTTTGGATATTCACAAACTTACATTTATCCAACCAAACTCTAAGCTTATTAGAA
GATGCATACTTCATGCAAGTAATACATTTTCCAAATCTTTTAATTATGACATGTGTGGCATCTTG
CCATTCCATAACTCATACGTTAATT
Found at i:5474804 original size:23 final size:23
Alignment explanation
Indices: 5474766--5474809 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5474756 TCATAATAGC
*
5474766 CAATATCATATATATGGTTTTAT
1 CAATATCATATATATGATTTTAT
* *
5474789 CAATATCATCTCTATGATTTT
1 CAATATCATATATATGATTTT
5474810 GATAGATTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (23 bp):
CAATATCATATATATGATTTTAT
Found at i:5475935 original size:18 final size:18
Alignment explanation
Indices: 5475914--5475978 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
5475904 ACAATTATGT
*
5475914 AAATATACAATATCATGC
1 AAATATAAAATATCATGC
*
5475932 AAATATATTAATCATCATGC
1 AAATATA-AAAT-ATCATGC
*
5475952 AATAATATAAAATACCATGC
1 -A-AATATAAAATATCATGC
5475972 AAATATA
1 AAATATA
5475979 TTAATAACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 13 0.32
19 4 0.10
20 13 0.32
21 4 0.10
22 6 0.15
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (18 bp):
AAATATAAAATATCATGC
Found at i:5475948 original size:20 final size:20
Alignment explanation
Indices: 5475925--5476009 Score: 77
Period size: 20 Copynumber: 4.1 Consensus size: 20
5475915 AATATACAAT
5475925 ATCATGCAAATATATTAATC
1 ATCATGCAAATATATTAATC
*
5475945 ATCATGC-AATAATATAAAAT-
1 ATCATGCAAAT-ATAT-TAATC
*
5475965 ACCATGCAAATATATTAATAACC
1 ATCATGCAAATATATTAAT---C
5475988 ATTCATGCAAATATA-TAATC
1 A-TCATGCAAATATATTAATC
5476008 AT
1 AT
5476010 GAAATTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
19 7 0.13
20 23 0.43
21 6 0.11
23 5 0.09
24 12 0.23
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.32
Consensus pattern (20 bp):
ATCATGCAAATATATTAATC
Found at i:5476274 original size:20 final size:20
Alignment explanation
Indices: 5476251--5476317 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
5476241 AATTATGCAA
5476251 ATAAACATGCAATTAAATAT
1 ATAAACATGCAATTAAATAT
* *
5476271 ATAATCATGCAAATAAAAATAT
1 ATAAACATGC-AAT-TAAATAT
5476293 ATAAACCATGCAATTAAATAT
1 ATAAA-CATGCAATTAAATAT
5476314 ATAA
1 ATAA
5476318 TATGCAACTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.22
21 13 0.32
22 13 0.32
23 5 0.12
ACGTcount: A:0.57, C:0.10, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAACATGCAATTAAATAT
Done.