Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 18 of 199
Found at i:5445846 original size:23 final size:23
Alignment explanation
Indices: 5445816--5445870 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
5445806 AGCTTTGCCG
* *
5445816 ATCAGGCACTATATGTGTTGTAT
1 ATCAGGCACTATATGTGTCGCAT
*
5445839 ATCAGGCACTTTATGTGTCGCAT
1 ATCAGGCACTATATGTGTCGCAT
*
5445862 TTCAGGCAC
1 ATCAGGCAC
5445871 CTCGTGTGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (23 bp):
ATCAGGCACTATATGTGTCGCAT
Found at i:5445878 original size:23 final size:21
Alignment explanation
Indices: 5445852--5445912 Score: 95
Period size: 21 Copynumber: 2.8 Consensus size: 21
5445842 AGGCACTTTA
5445852 TGTGTCGCATTTCAGGCACCTCG
1 TGTGTCG--TTTCAGGCACCTCG
*
5445875 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTTTCAGGCACCTCG
5445896 TGTGTCGTTTCAGGCAC
1 TGTGTCGTTTCAGGCAC
5445913 TTATGTATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 29 0.81
23 7 0.19
ACGTcount: A:0.13, C:0.28, G:0.28, T:0.31
Consensus pattern (21 bp):
TGTGTCGTTTCAGGCACCTCG
Found at i:5448447 original size:13 final size:13
Alignment explanation
Indices: 5448429--5448453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5448419 AAATTCAATG
5448429 TCAATTTCATATA
1 TCAATTTCATATA
5448442 TCAATTTCATAT
1 TCAATTTCATAT
5448454 CCAAACATAT
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:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:5449016 original size:2 final size:2
Alignment explanation
Indices: 5449009--5449035 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5448999 TAGTAATTCC
5449009 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 T
5449036 TCATCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5449647 original size:22 final size:22
Alignment explanation
Indices: 5449633--5449735 Score: 75
Period size: 23 Copynumber: 4.4 Consensus size: 22
5449623 GTAGGCTCTG
5449633 ACGAGCTGAATAGTAAGCTCAT
1 ACGAGCTGAATAGTAAGCTCAT
5449655 ACGAGCTGAA-ACGGTAAGCTCCA-
1 ACGAGCTGAATA--GTAAGCT-CAT
* * * *
5449678 ATGAGCTGAAAACAGTAGGCTCTT
1 ACGAGCTG--AATAGTAAGCTCAT
5449702 ACGAGCTGATATATCGGTAAGCTCAT
1 ACGAGCTGA-ATA---GTAAGCTCAT
5449728 ACGAGCTG
1 ACGAGCTG
5449736 TGGTGAGTCC
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
21 1 0.02
22 11 0.17
23 17 0.27
24 15 0.24
25 2 0.03
26 17 0.27
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (22 bp):
ACGAGCTGAATAGTAAGCTCAT
Found at i:5453648 original size:45 final size:45
Alignment explanation
Indices: 5453584--5453673 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
5453574 ACAACATACA
* *
5453584 TGGTGGCTTCGTCTACAACCTACATGACAGCTTATCTGTGAATAT
1 TGGTGACTTCGTCTACAACCTACATGACAACTTATCTGTGAATAT
* *
5453629 TGGTGACTTCGTCTACAACCTACATGGCAACTTGTCTGTGAATAT
1 TGGTGACTTCGTCTACAACCTACATGACAACTTATCTGTGAATAT
5453674 CGGTAGTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
TGGTGACTTCGTCTACAACCTACATGACAACTTATCTGTGAATAT
Found at i:5461588 original size:12 final size:12
Alignment explanation
Indices: 5461571--5461602 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
5461561 TTAAAAATAA
5461571 AAATAATTTATT
1 AAATAATTTATT
5461583 AAATAATTTATT
1 AAATAATTTATT
5461595 AAGATAAT
1 AA-ATAAT
5461603 AAATTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
AAATAATTTATT
Found at i:5461781 original size:22 final size:22
Alignment explanation
Indices: 5461756--5461798 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5461746 TAATTTAAGT
5461756 TAAT-TTTTATATAAAAATAAAC
1 TAATATTTTATA-AAAAATAAAC
*
5461778 TAATATTTTTTAAAAAATAAA
1 TAATATTTTATAAAAAATAAA
5461799 TTTCGCGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATATTTTATAAAAAATAAAC
Found at i:5465226 original size:62 final size:62
Alignment explanation
Indices: 5465155--5465272 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
5465145 AGTATTATTT
*
5465155 ATATATGTCAAATTCTGCTGTTTGTCATTGCACTATGTGTCCTTATACTCTAATTTAGTTTA
1 ATATATGTCAAATTCTGCTGTTTGTCATTGCACTATGTGTACTTATACTCTAATTTAGTTTA
*
5465217 ATATATGTCAAATTCTGCTGTTTGTCATTTCACTATGTGTACTTATACTCTAATTT
1 ATATATGTCAAATTCTGCTGTTTGTCATTGCACTATGTGTACTTATACTCTAATTT
5465273 GGTTATTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (62 bp):
ATATATGTCAAATTCTGCTGTTTGTCATTGCACTATGTGTACTTATACTCTAATTTAGTTTA
Found at i:5467614 original size:2 final size:2
Alignment explanation
Indices: 5467601--5467637 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5467591 CAAGACAGAA
*
5467601 AT AT AT AA 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 A
5467638 CAGGGAAAAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5469066 original size:17 final size:18
Alignment explanation
Indices: 5469040--5469073 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5469030 ATTAAGTTTA
*
5469040 TATAAGATATTA-ATTAT
1 TATAAAATATTATATTAT
5469057 TATAAAATATTATATTA
1 TATAAAATATTATATTA
5469074 AATCATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATAAAATATTATATTAT
Found at i:5471080 original size:5 final size:5
Alignment explanation
Indices: 5471062--5471107 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
5471052 AATAAATAAG
5471062 TATTA TATTA -ATTA TA-T- TATTA TATTA TATTA TATATA TATGTA TA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TAT-TA TA
5471108 ACTTAAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 19 0.53
6 9 0.25
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:5481935 original size:3 final size:3
Alignment explanation
Indices: 5481927--5481952 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5481917 TGCAAAATTG
5481927 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
5481953 TTATTTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5484952 original size:66 final size:66
Alignment explanation
Indices: 5484826--5484956 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
5484816 TCTGAAGCAA
* * ** *
5484826 TAGCTGGAGTTCGTCATATTTTTTTGTTGCCTCTGCTTCTCTCGCTGCTGCCTTCGCTTTAAGTT
1 TAGCTGGAGTTCATCATATTTTTTTGTAGCCTCTGCTTCTCTCAATGCTGCCTTCACTTTAAGTT
5484891 G
66 G
* *
5484892 TAGCTGGAGTTCATTATATTTTCTTTG-AGCTTCTGCTTCTCTCAATGCTGCC-TCTACTTTAAG
1 TAGCTGGAGTTCATCATATTTT-TTTGTAGCCTCTGCTTCTCTCAATGCTGCCTTC-ACTTTAAG
5484955 TT
64 TT
5484957 AAGCAATTTG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 2 0.04
66 50 0.89
67 4 0.07
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (66 bp):
TAGCTGGAGTTCATCATATTTTTTTGTAGCCTCTGCTTCTCTCAATGCTGCCTTCACTTTAAGTT
G
Found at i:5491314 original size:26 final size:26
Alignment explanation
Indices: 5491284--5491333 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5491274 CATGTATGTG
*
5491284 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
5491310 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
5491334 TAAATGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Found at i:5491361 original size:24 final size:24
Alignment explanation
Indices: 5491297--5491361 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
5491287 ATATGTATGA
* *
5491297 ATTATAAAATGGAAAAATGTATATGT
1 ATTATAAAAT--ATAAATGTAAATGT
*
5491323 ATTATAAAATGTAAATGTAAATGT
1 ATTATAAAATATAAATGTAAATGT
*
5491347 A-TATATATATATAAA
1 ATTATA-AAATATAAA
5491362 ACTAAGAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
23 4 0.12
24 19 0.58
26 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAAATGTAAATGT
Found at i:5491483 original size:3 final size:3
Alignment explanation
Indices: 5491475--5491548 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
5491465 ATGTATAAGT
*
5491475 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
5491523 ATA ATA ATA ATA ATA ATA ATA CTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
5491549 TGAATTCAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5491605 original size:30 final size:27
Alignment explanation
Indices: 5491551--5491606 Score: 67
Period size: 30 Copynumber: 2.0 Consensus size: 27
5491541 ATACTAATTG
* *
5491551 AATTCAACAAATTAAGGGCTAATTTGA
1 AATTCAACAAATTAAGAGCAAATTTGA
5491578 AATTCAAACAAAATTTAAGAGCAAATTTG
1 AATTC-AAC-AAA-TTAAGAGCAAATTTG
5491607 GAAGAAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 3 0.12
29 3 0.12
30 13 0.54
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.29
Consensus pattern (27 bp):
AATTCAACAAATTAAGAGCAAATTTGA
Found at i:5492789 original size:23 final size:22
Alignment explanation
Indices: 5492725--5492789 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
5492715 TAAACTACGG
5492725 TTACTTAAGTGTTCTAAATAGAT
1 TTACTTAAGTG-TCTAAATAGAT
* * *
5492748 TTAATTCA-TGTTTATAATATGA-
1 TTACTTAAGTGTCTA-AATA-GAT
5492770 TTACTTAAGTGATCTAAATA
1 TTACTTAAGTG-TCTAAATA
5492790 AATATAAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 14 0.44
24 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (22 bp):
TTACTTAAGTGTCTAAATAGAT
Found at i:5495855 original size:70 final size:70
Alignment explanation
Indices: 5495767--5495897 Score: 217
Period size: 70 Copynumber: 1.9 Consensus size: 70
5495757 TGCTAACGCT
* *
5495767 ACTATTGATTTACCTTTTGTTGCATTTATGAGAAAAACGCCACTAATGCCTTACCTTTTGCAAAA
1 ACTATTGATTTACCTTTTGTTACATTTATGAGAAAAAAGCCACTAATGCCTTACCTTTTGCAAAA
5495832 ATACC
66 ATACC
* * *
5495837 ACTATTGCTTTACCTTTTGTTACGTTTATGAGAAAAAAGTCACTAATGCCTTACCTTTTGC
1 ACTATTGATTTACCTTTTGTTACATTTATGAGAAAAAAGCCACTAATGCCTTACCTTTTGC
5495898 GGCGTTTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 56 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (70 bp):
ACTATTGATTTACCTTTTGTTACATTTATGAGAAAAAAGCCACTAATGCCTTACCTTTTGCAAAA
ATACC
Found at i:5502077 original size:67 final size:67
Alignment explanation
Indices: 5501999--5502136 Score: 258
Period size: 67 Copynumber: 2.1 Consensus size: 67
5501989 AAAATAAAAA
*
5501999 TAAAAAAAACAGCACATAGAAACCAAAAAGAAAATTCAATCAAAACACAGAATCCTACATTAACC
1 TAAAAAAAACAGCACATAGAAACCAAAAAGAAAATTCAATCAAAACACAAAATCCTACATTAACC
5502064 CT
66 CT
*
5502066 TAAAAAAAACAGCACATAGAAACCAAAAAGAATATTCAATCAAAACACAAAATCCTACATTAACC
1 TAAAAAAAACAGCACATAGAAACCAAAAAGAAAATTCAATCAAAACACAAAATCCTACATTAACC
5502131 CT
66 CT
5502133 TAAA
1 TAAA
5502137 GAACATCACA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (67 bp):
TAAAAAAAACAGCACATAGAAACCAAAAAGAAAATTCAATCAAAACACAAAATCCTACATTAACC
CT
Found at i:5510223 original size:9 final size:9
Alignment explanation
Indices: 5510209--5510254 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
5510199 TATAGTTTGA
5510209 TATTCGAAT
1 TATTCGAAT
5510218 TATTCGAAT
1 TATTCGAAT
5510227 TATTCGAAT
1 TATTCGAAT
*
5510236 TATTCGAGT
1 TATTCGAAT
5510245 TATTCGAAT
1 TATTCGAAT
5510254 T
1 T
5510255 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5511819 original size:63 final size:60
Alignment explanation
Indices: 5511751--5511868 Score: 164
Period size: 63 Copynumber: 1.9 Consensus size: 60
5511741 TTAATAGTGT
* *
5511751 TAATATTAAATTTAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATATATATA
1 TAATATTAAATTTAATATAATATTTATC-T-T-GATAAATATTATATTAATTTAATATATATA
* * *
5511814 TAATATTAGATTTAATATGATATTTATCTTGATAAGTATTATATTAATTTAATAT
1 TAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATAT
5511869 TAAAGTGATT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 23 0.46
61 1 0.02
62 1 0.02
63 25 0.50
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (60 bp):
TAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATATATATA
Found at i:5515393 original size:53 final size:53
Alignment explanation
Indices: 5515313--5515464 Score: 207
Period size: 53 Copynumber: 2.9 Consensus size: 53
5515303 GTATTTTTCA
* * *
5515313 ATTTGTAAGATACAATGTTGTTGGTCTTGAACAAAA-CTATTTAATTATGTTTT
1 ATTTGTAAGATACAATGTTGTCGGTCTTAAACAAAATC-ATTTAATTATGTATT
* * * *
5515366 ATTTGTAAGATAGAATGATGTCAGTCTTAAATAAAATCATTTAATTATGTATT
1 ATTTGTAAGATACAATGTTGTCGGTCTTAAACAAAATCATTTAATTATGTATT
* *
5515419 ATTTGTAAGACACAATGTTGTCGGTCTTAAACAAAATCGTTTAATT
1 ATTTGTAAGATACAATGTTGTCGGTCTTAAACAAAATCATTTAATT
5515465 TTTTTTAGTA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 84 0.99
54 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (53 bp):
ATTTGTAAGATACAATGTTGTCGGTCTTAAACAAAATCATTTAATTATGTATT
Found at i:5519983 original size:17 final size:18
Alignment explanation
Indices: 5519961--5519998 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5519951 TTCTTCCATT
5519961 AAAAAAA-GAAAAAAGAA
1 AAAAAAAGGAAAAAAGAA
*
5519978 AAAAAAAGGAAAAAGGAA
1 AAAAAAAGGAAAAAAGAA
5519996 AAA
1 AAA
5519999 GGGAACTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAGGAAAAAAGAA
Found at i:5525041 original size:19 final size:20
Alignment explanation
Indices: 5525005--5525043 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5524995 AAATTTCATA
5525005 ACACAATACATCGAAAATCT
1 ACACAATACATCGAAAATCT
*
5525025 ACACAATA-ATGGAAAATCT
1 ACACAATACATCGAAAATCT
5525044 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.21, G:0.08, T:0.21
Consensus pattern (20 bp):
ACACAATACATCGAAAATCT
Found at i:5525093 original size:29 final size:30
Alignment explanation
Indices: 5525058--5525136 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
5525048 AAATTATAAT
*
5525058 GTGCAATTGTATACATGAACTTTAATT-TG
1 GTGCAATTGTATACATGAACTCTAATTGTG
* * *
5525087 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTGTATACATG-AACTCTAATTGTG
* * *
5525118 GTTCAAATGTATACTTGAA
1 GTGCAATTGTATACATGAA
5525137 ACTTGAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
29 14 0.36
30 11 0.28
31 14 0.36
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.37
Consensus pattern (30 bp):
GTGCAATTGTATACATGAACTCTAATTGTG
Found at i:5531240 original size:16 final size:17
Alignment explanation
Indices: 5531219--5531250 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5531209 GGCAACAATG
5531219 ATTTTTTTTTT-AACTA
1 ATTTTTTTTTTCAACTA
5531235 ATTTTTTTTTTCAACT
1 ATTTTTTTTTTCAACT
5531251 TCAAGTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTTTTTTTCAACTA
Found at i:5535333 original size:41 final size:38
Alignment explanation
Indices: 5535277--5535511 Score: 218
Period size: 41 Copynumber: 5.8 Consensus size: 38
5535267 ACCTTTTGGG
* * *
5535277 GCTTTAGTGGCGTTTTCTCAAAAGTGCCGCTAATGCTCTA
1 GCTTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGCTC-A
* *
5535317 GCTTTTAGCGGCGTTTTTAATAAAGCGTCGCTAATGCACAGA
1 GC-TTTAGCGGCGTTTTTAA-AAAGCGCCGCTAATGCTC--A
* *
5535359 GCTTTAGCGGCGTTTTTAGGAATGCGCCGCTAATGCTCA
1 GCTTTAGCGGCGTTTTTA-AAAAGCGCCGCTAATGCTCA
* *
5535398 GACCTTTAGTGGTGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 G--CTTTAGCGGCGTTTTT-AAAAAGCGCCGCTAATGCTCA
* *
5535439 GACCTTTAGCGGAGTTTTCGAAAAAGCGCCGCTAATGCTCA
1 G--CTTTAGCGGCGTTTT-TAAAAAGCGCCGCTAATGCTCA
*
5535480 GGGCTTTAGCGGCGCTTTTCAAAAAGCGCCGC
1 --GCTTTAGCGGCG-TTTTTAAAAAGCGCCGC
5535512 AAAAACATTT
Statistics
Matches: 165, Mismatches: 19, Indels: 21
0.80 0.09 0.10
Matches are distributed among these distances:
39 2 0.01
40 4 0.02
41 150 0.91
42 8 0.05
43 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (38 bp):
GCTTTAGCGGCGTTTTTAAAAAGCGCCGCTAATGCTCA
Found at i:5535415 original size:82 final size:81
Alignment explanation
Indices: 5535296--5535511 Score: 247
Period size: 82 Copynumber: 2.6 Consensus size: 81
5535286 GCGTTTTCTC
* * * *
5535296 AAAAGTGCCGCTAATGCTCTAGCTTTTAGCGGCGTTTTT-AATAAAGCGTCGCTAATGCACAGAG
1 AAAAGCGCCGCTAATGCTC-AGCCTTTAGCGGCGTTTTTGAA-AAAGCGCCGCTAATGCACAGAC
*
5535360 CTTTAGCGGCGTTTTTAG-
64 CTTTAGCGGAG-TTTTAGA
* * * * *
5535378 GAATGCGCCGCTAATGCTCAGACCTTTAGTGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
1 AAAAGCGCCGCTAATGCTCAG-CCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCACAGACC
*
5535443 TTTAGCGGAGTTTTCGA
65 TTTAGCGGAGTTTTAGA
* * *
5535460 AAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGCTTTTCAAAAAGCGCCGC
1 AAAAGCGCCGCTAATGCTCA-GCCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
5535512 AAAAACATTT
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
81 7 0.06
82 102 0.91
83 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (81 bp):
AAAAGCGCCGCTAATGCTCAGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCACAGACCT
TTAGCGGAGTTTTAGA
Found at i:5535509 original size:123 final size:123
Alignment explanation
Indices: 5535278--5535511 Score: 296
Period size: 123 Copynumber: 1.9 Consensus size: 123
5535268 CCTTTTGGGG
* * * * *
5535278 CTTTAGTGGCGTTTTCTCAAAAGTGCCGCTAATGCTCTAGCTTTTAGCGGCGTTTTTAATAAAGC
1 CTTTAGTGGCGTTTTCTAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGAGTTTTGAATAAAGC
* * * *
5535343 GTCGCTAATGCACAGAGCTTTAGCGGCGTTTTTAGGAATGCGCCGCTAATGCTCAGAC
66 GCCGCTAATGCACAGAGCTTTAGCGGCGTTTTCAGAAAAGCGCCGCTAATGCTCAGAC
*
5535401 CTTTAGTGGTGTTTT-TGAAAAAGCGCCGCTAATGCTC-AGACCTTTAGCGGAGTTTTCGAA-AA
1 CTTTAGTGGCGTTTTCT-AAAAAGCGCCGCTAATGCTCTAG-CCTTTAGCGGAGTTTT-GAATAA
* *
5535463 AGCGCCGCTAATGCTCAGGGCTTTAGCGGCGCTTTTCA-AAAAGCGCCGC
63 AGCGCCGCTAATGCACAGAGCTTTAGCGGCG-TTTTCAGAAAAGCGCCGC
5535512 AAAAACATTT
Statistics
Matches: 95, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
122 3 0.03
123 85 0.89
124 7 0.07
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (123 bp):
CTTTAGTGGCGTTTTCTAAAAAGCGCCGCTAATGCTCTAGCCTTTAGCGGAGTTTTGAATAAAGC
GCCGCTAATGCACAGAGCTTTAGCGGCGTTTTCAGAAAAGCGCCGCTAATGCTCAGAC
Found at i:5536240 original size:15 final size:15
Alignment explanation
Indices: 5536217--5536247 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5536207 AAGTTAAAAG
*
5536217 TTAGTGATTTAGGGT
1 TTAGAGATTTAGGGT
5536232 TTAGAGATTTAGGGT
1 TTAGAGATTTAGGGT
5536247 T
1 T
5536248 GGGTTAGAGT
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:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (15 bp):
TTAGAGATTTAGGGT
Found at i:5536636 original size:17 final size:17
Alignment explanation
Indices: 5536616--5536650 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5536606 CAATTTTATT
5536616 ATAGTTTAAATTATTAA
1 ATAGTTTAAATTATTAA
5536633 ATAGTTTAAATTATTAA
1 ATAGTTTAAATTATTAA
5536650 A
1 A
5536651 ATATACTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
ATAGTTTAAATTATTAA
Found at i:5536716 original size:14 final size:14
Alignment explanation
Indices: 5536699--5536736 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
5536689 ATAAAAATCC
5536699 AGTTTATAAAAAAT
1 AGTTTATAAAAAAT
5536713 AG-TTATAAAAAAT
1 AGTTTATAAAAAAT
*
5536726 ATTTTATAAAA
1 AGTTTATAAAA
5536737 TCACATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
AGTTTATAAAAAAT
Found at i:5540950 original size:15 final size:15
Alignment explanation
Indices: 5540922--5540962 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5540912 GAATTTAAAA
*
5540922 TAATTTTGAAATAATT
1 TAATTTT-AAATAATC
5540938 TAATTTTAAATAATC
1 TAATTTTAAATAATC
*
5540953 TAAATTTAAA
1 TAATTTTAAA
5540963 ATGATTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TAATTTTAAATAATC
Found at i:5546985 original size:27 final size:26
Alignment explanation
Indices: 5546947--5547064 Score: 98
Period size: 27 Copynumber: 4.4 Consensus size: 26
5546937 TGCGATACGT
*
5546947 GGTAAAATGATCGAATTACCCCTGAAG
1 GGTAAAATGACCGAA-TACCCCTGAAG
* *
5546974 GGTAAAATGATCGAGATACCCTCT-TAG
1 GGTAAAATGACCGA-ATACCC-CTGAAG
* *
5547001 GGTAAAATAACCAAAATACCCCTGTAA-
1 GGTAAAATGACC-GAATACCCCTG-AAG
* *
5547028 GGTAAAATGACCGTAATGCCCCTAAAG
1 GGTAAAATGACCG-AATACCCCTGAAG
5547055 GGT-AAATGAC
1 GGTAAAATGAC
5547065 TATTTTGCCC
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
26 11 0.15
27 59 0.79
28 5 0.07
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.21
Consensus pattern (26 bp):
GGTAAAATGACCGAATACCCCTGAAG
Found at i:5547135 original size:24 final size:24
Alignment explanation
Indices: 5547082--5547137 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
5547072 CCCTTCGAGG
*
5547082 TTAAATGATTGATTTGTCCGTGAT
1 TTAAATGATTGATTTATCCGTGAT
** *
5547106 GAAAATGATTGATTTATCTGTGAT
1 TTAAATGATTGATTTATCCGTGAT
5547130 TTAAATGA
1 TTAAATGA
5547138 CTGCTTTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (24 bp):
TTAAATGATTGATTTATCCGTGAT
Found at i:5547380 original size:32 final size:32
Alignment explanation
Indices: 5547339--5547446 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
5547329 TATTGCGATA
*
5547339 CTACTGATGGCTGTGTGCCGGTCATATCACTG
1 CTACTGATGGCTGTGTGCCGATCATATCACTG
* * *
5547371 CTACTGATGGCTTTGAT-TCGATCATATTA-TCG
1 CTACTGATGGCTGTG-TGCCGATCATATCACT-G
* *
5547403 TTACTGATGGTTGTGTGCCGATCATATCACTG
1 CTACTGATGGCTGTGTGCCGATCATATCACTG
5547435 CTACTGATGGCT
1 CTACTGATGGCT
5547447 TTGGGCTAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
31 2 0.03
32 57 0.93
33 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (32 bp):
CTACTGATGGCTGTGTGCCGATCATATCACTG
Found at i:5547459 original size:32 final size:32
Alignment explanation
Indices: 5547339--5547461 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 32
5547329 TATTGCGATA
* * * *
5547339 CTACTGATGGCTGTGTGCCGGTCATATCACTG
1 CTACTGATGGCTTTGGGCTGATCATATCACTG
** *
5547371 CTACTGATGGCTTT-GATTCGATCATATTA-TCG
1 CTACTGATGGCTTTGGGCT-GATCATATCACT-G
* * *
5547403 TTACTGATGG-TTGTGTGCCGATCATATCACTG
1 CTACTGATGGCTT-TGGGCTGATCATATCACTG
*
5547435 CTACTGATGGCTTTGGGCTAATCATAT
1 CTACTGATGGCTTTGGGCTGATCATAT
5547462 TGCTGTATTT
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
31 3 0.04
32 62 0.91
33 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (32 bp):
CTACTGATGGCTTTGGGCTGATCATATCACTG
Found at i:5547459 original size:64 final size:64
Alignment explanation
Indices: 5547340--5547462 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
5547330 ATTGCGATAC
* * *
5547340 TACTGATGGCTGTGTGCCGGTCATATCACTGCTACTGATGGCTTTGATTCGATCATATTATCGT
1 TACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGACTCAATCATATTATCGT
* *
5547404 TACTGATGGTTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGGGCT-AATCATATT
1 TACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCTTT-GACTCAATCATATT
5547463 GCTGTATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
64 51 0.96
65 2 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (64 bp):
TACTGATGGCTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGACTCAATCATATTATCGT
Found at i:5547500 original size:22 final size:21
Alignment explanation
Indices: 5547469--5547534 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
5547459 TATTGCTGTA
5547469 TTTATGGCTTGTAGCCATTCTG
1 TTTATGGCTT-TAGCCATTCTG
* *
5547491 TTTATAGCTTATAGCTATTCTG
1 TTTATGGCTT-TAGCCATTCTG
* *
5547513 CTTACGGCTCTTAGCCATTCTG
1 TTTATGGCT-TTAGCCATTCTG
5547535 ATTACTAGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (21 bp):
TTTATGGCTTTAGCCATTCTG
Found at i:5550519 original size:24 final size:24
Alignment explanation
Indices: 5550466--5550552 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
5550456 CCCCTCGAGG
*
5550466 TTAAATGATTGATTTGTCCATGAT
1 TTAAATGACTGATTTGTCCATGAT
** **
5550490 GAAAATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCCATGAT
* *
5550514 TTAAATGACT-ATTTTTCCTATGAA
1 TTAAATGACTGATTTGTCC-ATGAT
**
5550538 TTGTATGACTGATTT
1 TTAAATGACTGATTT
5550553 TGAGCATGAC
Statistics
Matches: 48, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
23 6 0.12
24 38 0.79
25 4 0.08
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCCATGAT
Found at i:5550765 original size:32 final size:32
Alignment explanation
Indices: 5550724--5550844 Score: 149
Period size: 32 Copynumber: 3.8 Consensus size: 32
5550714 GCTGCGATAC
5550724 TACTGATGGCTGTGTGCCGATCATATCACTGT
1 TACTGATGGCTGTGTGCCGATCATATCACTGT
* *
5550756 TACTGATGGCTTTGAT-CCGATCATATTA-TCGT
1 TACTGATGGCTGTG-TGCCGATCATATCACT-GT
*
5550788 TACTGATGGCTGTGTGCCGATCATATCACT-C
1 TACTGATGGCTGTGTGCCGATCATATCACTGT
* * *
5550819 TACTGATGGCTTTGGGCCAATCATAT
1 TACTGATGGCTGTGTGCCGATCATAT
5550845 TGCTATATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
31 25 0.32
32 50 0.65
33 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTGTGTGCCGATCATATCACTGT
Found at i:5550899 original size:22 final size:22
Alignment explanation
Indices: 5550850--5550899 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
5550840 CATATTGCTA
* * *
5550850 TATTTATGGCTTGTAGCCATTC
1 TATTTATAGCTTATAGCCATCC
* *
5550872 TGTTTATAGCTTATAGCTATCC
1 TATTTATAGCTTATAGCCATCC
5550894 TATTTA
1 TATTTA
5550900 CGGCTCTTAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (22 bp):
TATTTATAGCTTATAGCCATCC
Found at i:5555533 original size:25 final size:25
Alignment explanation
Indices: 5555490--5555544 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5555480 TCAATATAGT
* *
5555490 CTATCTATAATAGTCTCAGTATATA
1 CTATCTATAACAGTCTCAGGATATA
* *
5555515 CTATCTATAGCAGTTTCAGGATATA
1 CTATCTATAACAGTCTCAGGATATA
5555540 CTATC
1 CTATC
5555545 AATGATAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (25 bp):
CTATCTATAACAGTCTCAGGATATA
Found at i:5555554 original size:25 final size:24
Alignment explanation
Indices: 5555490--5555555 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
5555480 TCAATATAGT
* *
5555490 CTATCTATAATAGTCTCAGTATATA
1 CTATCTAT-ATAGTTTCAGGATATA
*
5555515 CTATCTATAGCAGTTTCAGGATATA
1 CTATCTATA-TAGTTTCAGGATATA
*
5555540 CTATCAATGATAGTTT
1 CTATCTAT-ATAGTTT
5555556 TAGTTTCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (24 bp):
CTATCTATATAGTTTCAGGATATA
Found at i:5555916 original size:18 final size:16
Alignment explanation
Indices: 5555874--5555916 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
5555864 TGTCGTTCGT
5555874 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
5555891 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
5555910 TTTCAAA
1 TTTCAAA
5555917 AAGTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:5557308 original size:16 final size:17
Alignment explanation
Indices: 5557296--5557328 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
5557286 ACTTTCCCTC
5557296 AAACTT-TTATTCCCCA
1 AAACTTATTATTCCCCA
5557312 AAACTTATTATTTCCCC
1 AAACTTATTA-TTCCCC
5557329 CCTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (17 bp):
AAACTTATTATTCCCCA
Found at i:5561217 original size:53 final size:53
Alignment explanation
Indices: 5561144--5561244 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
5561134 TACGTTCTAA
*
5561144 CCGTAAGGTTTTTAATTGTTGGGTTAGAATGAGTTTATGTGATAATGTTCTTT
1 CCGTAAGATTTTTAATTGTTGGGTTAGAATGAGTTTATGTGATAATGTTCTTT
5561197 CCGTAAGATTTTTAATTGTTGGGTTAGAATGAGTTTATGTGATAATGT
1 CCGTAAGATTTTTAATTGTTGGGTTAGAATGAGTTTATGTGATAATGT
5561245 GGTGAATGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.46
Consensus pattern (53 bp):
CCGTAAGATTTTTAATTGTTGGGTTAGAATGAGTTTATGTGATAATGTTCTTT
Found at i:5562536 original size:21 final size:21
Alignment explanation
Indices: 5562512--5562554 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
5562502 GAAATGATTT
5562512 AAACAAGAAT-TTTGAAATGAC
1 AAACAA-AATATTTGAAATGAC
5562533 AAACAAAATAATTTGAAATGAC
1 AAACAAAAT-ATTTGAAATGAC
5562555 TTAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 6 0.30
22 11 0.55
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (21 bp):
AAACAAAATATTTGAAATGAC
Found at i:5568092 original size:20 final size:22
Alignment explanation
Indices: 5568057--5568097 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
5568047 CAAATTTTAA
5568057 ATTTATAAATAAATATGTATAT
1 ATTTATAAATAAATATGTATAT
5568079 ATTT-TAAA-AAATATGTATA
1 ATTTATAAATAAATATGTATA
5568098 CTTGAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTTATAAATAAATATGTATAT
Found at i:5568999 original size:2 final size:2
Alignment explanation
Indices: 5568992--5569018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5568982 CTAATTCTAA
5568992 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 A
5569019 ATCAACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5569670 original size:24 final size:24
Alignment explanation
Indices: 5569628--5569673 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5569618 CCTGCTTTGC
* *
5569628 CCACATTGCCTACTGTACCAAGGG
1 CCACATTGCCCACTCTACCAAGGG
*
5569652 CCACATTGCCCCCTCTACCAAG
1 CCACATTGCCCACTCTACCAAG
5569674 CATGCCTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (24 bp):
CCACATTGCCCACTCTACCAAGGG
Found at i:5570623 original size:27 final size:27
Alignment explanation
Indices: 5570584--5570638 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
5570574 ATACTTATAC
5570584 TATATTTAAATTAAATAATATATGAAAA
1 TATATTTAAATTAAATAATA-ATGAAAA
* *
5570612 TATA-TTATATTAAATCATAATGAAAA
1 TATATTTAAATTAAATAATAATGAAAA
5570638 T
1 T
5570639 CATTACATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 13 0.52
28 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (27 bp):
TATATTTAAATTAAATAATAATGAAAA
Found at i:5580813 original size:7 final size:7
Alignment explanation
Indices: 5580803--5580835 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5580793 AAAATATAAA
5580803 AAACCTT
1 AAACCTT
5580810 AAACCTT
1 AAACCTT
5580817 AAACCTT
1 AAACCTT
*
5580824 AAACCAT
1 AAACCTT
5580831 AAACC
1 AAACC
5580836 CCTAAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCTT
Found at i:5581454 original size:40 final size:39
Alignment explanation
Indices: 5581398--5581476 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 39
5581388 TAAATATTTT
*
5581398 ATTTTTTTAATTTTTTAATTTTAAAATACTTTTAAAATA
1 ATTTTTTAAATTTTTTAATTTTAAAATACTTTTAAAATA
*
5581437 ATTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAATA
1 ATTTTTTAAA-TTTTTTAATTTTAAAATACTTTTAAAATA
5581477 CTTTGTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
39 9 0.24
40 28 0.76
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (39 bp):
ATTTTTTAAATTTTTTAATTTTAAAATACTTTTAAAATA
Found at i:5581464 original size:17 final size:17
Alignment explanation
Indices: 5581409--5581472 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
5581399 TTTTTTTAAT
5581409 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
* *
5581426 CTTTTAAAATAATTTTTTAAATT
1 -TTTT----TAA-TTTTAAAATA
5581449 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
5581466 TTTTTAA
1 TTTTTAA
5581473 AATACTTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 15 0.41
18 7 0.19
22 7 0.19
23 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:5581470 original size:11 final size:11
Alignment explanation
Indices: 5581416--5581476 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
5581406 AATTTTTTAA
*
5581416 TTTTAAAATAC
1 TTTTAAAATAT
5581427 TTTTAAAATAAT
1 TTTTAAAAT-AT
*
5581439 TTTTTAAAT-T
1 TTTTAAAATAT
*
5581449 TTTT----TAA
1 TTTTAAAATAT
5581456 TTTTAAAATAT
1 TTTTAAAATAT
5581467 TTTTAAAATA
1 TTTTAAAATA
5581477 CTTTGTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
6 1 0.03
7 4 0.10
10 5 0.12
11 21 0.52
12 9 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:5584955 original size:16 final size:16
Alignment explanation
Indices: 5584897--5584948 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5584887 TTTCTTCAAC
*
5584897 TTAAATTTAAATTGAT
1 TTAAATTTAAAATGAT
* * **
5584913 TTGAATTCAAAACAAT
1 TTAAATTTAAAATGAT
5584929 TTAAATTTAAAATGAT
1 TTAAATTTAAAATGAT
5584945 TTAA
1 TTAA
5584949 TTCTAAATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATGAT
Found at i:5584966 original size:31 final size:32
Alignment explanation
Indices: 5584899--5584976 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
5584889 TCTTCAACTT
* ***
5584899 AAATTTAAATTGATTTGAATTCAAAACAATTT
1 AAATTTAAAATGATTTGAATTCAAAACAACCA
* *
5584931 AAATTTAAAATGATTT-AATTCTAAATAACCA
1 AAATTTAAAATGATTTGAATTCAAAACAACCA
5584962 AAATTTAAAATGATT
1 AAATTTAAAATGATT
5584977 AGAGCTCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 25 0.62
32 15 0.38
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.38
Consensus pattern (32 bp):
AAATTTAAAATGATTTGAATTCAAAACAACCA
Found at i:5585926 original size:24 final size:24
Alignment explanation
Indices: 5585884--5585929 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5585874 CCTGCTTTGC
* *
5585884 CCACATTGCCTACTGTACCAAGGG
1 CCACATTGCCCACTCTACCAAGGG
*
5585908 CCACATTGCCCCCTCTACCAAG
1 CCACATTGCCCACTCTACCAAG
5585930 CATGCCTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.20
Consensus pattern (24 bp):
CCACATTGCCCACTCTACCAAGGG
Found at i:5590040 original size:9 final size:9
Alignment explanation
Indices: 5590026--5590092 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
5590016 GTAGTGATTC
*
5590026 AATTTGGTT
1 AATTCGGTT
*
5590035 AATTTGGTT
1 AATTCGGTT
*
5590044 AATTCGGGT
1 AATTCGGTT
5590053 AATTCGGTT
1 AATTCGGTT
*
5590062 AATTCTGTT
1 AATTCGGTT
5590071 AATTCGGTT
1 AATTCGGTT
5590080 AATTCGGTT
1 AATTCGGTT
5590089 AATT
1 AATT
5590093 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (9 bp):
AATTCGGTT
Found at i:5590261 original size:12 final size:12
Alignment explanation
Indices: 5590244--5590268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5590234 TGTTATTTCG
5590244 GGTCGGTTAACC
1 GGTCGGTTAACC
5590256 GGTCGGTTAACC
1 GGTCGGTTAACC
5590268 G
1 G
5590269 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:5591438 original size:14 final size:14
Alignment explanation
Indices: 5591403--5591447 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
5591393 AAAAATCCTG
*
5591403 AACCTTGAA-CTCA
1 AACCTTGAACCTTA
*
5591416 AACCATGAACCTTA
1 AACCTTGAACCTTA
*
5591430 AACCTTGAACCCTA
1 AACCTTGAACCTTA
5591444 AACC
1 AACC
5591448 CTAAAGTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.40, C:0.33, G:0.07, T:0.20
Consensus pattern (14 bp):
AACCTTGAACCTTA
Found at i:5591900 original size:14 final size:14
Alignment explanation
Indices: 5591864--5591902 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5591854 CTAAATCTAG
*
5591864 AATCTCAAACCCTA
1 AATCTTAAACCCTA
* *
5591878 AACCATAAACCCTA
1 AATCTTAAACCCTA
5591892 AATCTTAAACC
1 AATCTTAAACC
5591903 ATATACCCTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
AATCTTAAACCCTA
Found at i:5591973 original size:27 final size:28
Alignment explanation
Indices: 5591943--5592029 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 28
5591933 CCCTAAACAA
5591943 CATAACAATAAA-CCATAAAT-TAGAACC
1 CATAACAATAAATCC-TAAATCTAGAACC
*
5591970 CATAACACTAAATCCTAAATCTAGAA--
1 CATAACAATAAATCCTAAATCTAGAACC
* * * *
5591996 CTTGAACCATAAACCCTAAA-CTCGAACC
1 CAT-AACAATAAATCCTAAATCTAGAACC
5592024 CATAAC
1 CATAAC
5592030 CCTAAATCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
26 7 0.15
27 32 0.67
28 9 0.19
ACGTcount: A:0.48, C:0.28, G:0.05, T:0.20
Consensus pattern (28 bp):
CATAACAATAAATCCTAAATCTAGAACC
Found at i:5592525 original size:14 final size:14
Alignment explanation
Indices: 5592494--5592522 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5592484 TTAGACTAAT
5592494 AACCATAAATCCCA
1 AACCATAAATCCCA
5592508 AACCATAAA-CCCA
1 AACCATAAATCCCA
5592521 AA
1 AA
5592523 ACCTAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.55, C:0.34, G:0.00, T:0.10
Consensus pattern (14 bp):
AACCATAAATCCCA
Found at i:5592822 original size:14 final size:15
Alignment explanation
Indices: 5592777--5592829 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5592767 ACCCTAAATC
*
5592777 TAAAACATAAAACCTA
1 TAAACCATAAAA-CTA
*
5592793 -AAACCCT-AAACT-
1 TAAACCATAAAACTA
5592805 TAAA-CATAAAACTA
1 TAAACCATAAAACTA
5592819 TAAACCATAAA
1 TAAACCATAAA
5592830 TTTAGAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
12 2 0.07
13 10 0.33
14 7 0.23
15 11 0.37
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAACCATAAAACTA
Found at i:5592823 original size:27 final size:28
Alignment explanation
Indices: 5592766--5592830 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
5592756 TAAAATCTCG
5592766 AACCCTAAATCTAAAACATAAAACCTAA
1 AACCCTAAATCTAAAACATAAAACCTAA
*
5592794 AACCCTAAA-CTTAAACATAAAA-CTATA
1 AACCCTAAATCTAAAACATAAAACCTA-A
*
5592821 AACCATAAAT
1 AACCCTAAAT
5592831 TTAGAATCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 21 0.64
28 9 0.27
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (28 bp):
AACCCTAAATCTAAAACATAAAACCTAA
Found at i:5592939 original size:14 final size:14
Alignment explanation
Indices: 5592890--5592940 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5592880 TCAAACATCT
*
5592890 AACCATAAACACTTA
1 AACCATAAACA-ATA
* *
5592905 AACCCTAAAC-CTA
1 AACCATAAACAATA
*
5592918 AACAATAAACAATA
1 AACCATAAACAATA
5592932 AACCATAAA
1 AACCATAAA
5592941 ACCTCAATCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 10 0.34
14 10 0.34
15 9 0.31
ACGTcount: A:0.59, C:0.25, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCATAAACAATA
Found at i:5592985 original size:7 final size:7
Alignment explanation
Indices: 5592890--5592996 Score: 60
Period size: 7 Copynumber: 15.3 Consensus size: 7
5592880 TCAAACATCT
5592890 AACCATA
1 AACCATA
*
5592897 AACACTTA
1 AAC-CATA
*
5592905 AACCCTA
1 AACCATA
5592912 AACC-TA
1 AACCATA
*
5592918 AACAATA
1 AACCATA
*
5592925 AACAATA
1 AACCATA
5592932 AACCATAA
1 AACCAT-A
5592940 AACC-TCA
1 AACCAT-A
*
5592947 ATCACAT-
1 AAC-CATA
* *
5592954 AACCGTC
1 AACCATA
*
5592961 AACCCTA
1 AACCATA
5592968 AACC-TA
1 AACCATA
5592974 AACCATA
1 AACCATA
*
5592981 AACCATT
1 AACCATA
*
5592988 AACCTTA
1 AACCATA
5592995 AA
1 AA
5592997 TCTAGAATCA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
6 13 0.16
7 54 0.68
8 12 0.15
9 1 0.01
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (7 bp):
AACCATA
Found at i:5593160 original size:13 final size:15
Alignment explanation
Indices: 5593139--5593176 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5593129 TATAAAATCT
5593139 AAACTTTAAA-CCTA
1 AAACTTTAAACCCTA
5593153 AAAC-TTAAACCCTA
1 AAACTTTAAACCCTA
*
5593167 AACCTTTAAA
1 AAACTTTAAA
5593177 TTATAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 5 0.24
14 11 0.52
15 5 0.24
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACTTTAAACCCTA
Found at i:5593269 original size:14 final size:14
Alignment explanation
Indices: 5593252--5593294 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5593242 TTAAAGCCAT
*
5593252 AACCCTAAATATTA
1 AACCCTAAATACTA
* *
5593266 AACCATAAACACTA
1 AACCCTAAATACTA
*
5593280 AACCCTAAATCCTA
1 AACCCTAAATACTA
5593294 A
1 A
5593295 GCCCAAACCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
AACCCTAAATACTA
Found at i:5593424 original size:21 final size:20
Alignment explanation
Indices: 5593377--5593427 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
5593367 CATAACCACA
* *
5593377 AAACCTT-AACTTTAAACTC
1 AAACCTTAAACCTTAAACCC
*
5593396 AAATCTTAAACCTTAAATCCC
1 AAACCTTAAACCTTAAA-CCC
5593417 AAACCTTAAAC
1 AAACCTTAAAC
5593428 TTTAGGATCC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 6 0.23
20 8 0.31
21 12 0.46
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (20 bp):
AAACCTTAAACCTTAAACCC
Found at i:5597393 original size:49 final size:50
Alignment explanation
Indices: 5597299--5597395 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 50
5597289 GAATGATCCC
* *
5597299 ACCTCTCAAAATATCTTTTTACCATTAGGGGTGTTTCTCGTAGTGCGAAG
1 ACCTCTCAAAATATCTTTTTACCATCAGGGGTGTTTCTCGCAGTGCGAAG
*
5597349 ACCTCTCAAAATCTC-TTTTACCATCAGGGGTGTTT-TCCGCAGTGCGA
1 ACCTCTCAAAATATCTTTTTACCATCAGGGGTGTTTCT-CGCAGTGCGA
5597396 TGTGCAGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 1 0.02
49 28 0.65
50 14 0.33
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
ACCTCTCAAAATATCTTTTTACCATCAGGGGTGTTTCTCGCAGTGCGAAG
Found at i:5605305 original size:4 final size:4
Alignment explanation
Indices: 5605296--5605329 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
5605286 CCCTTTTCTT
5605296 TTTA TTTA TTTA -TTA TTTA TTTA TTTA TCTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TT
5605330 CTTACTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 21 0.75
5 4 0.14
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:5605316 original size:15 final size:15
Alignment explanation
Indices: 5605296--5605410 Score: 57
Period size: 15 Copynumber: 7.7 Consensus size: 15
5605286 CCCTTTTCTT
5605296 TTTATTTATTTATTA
1 TTTATTTATTTATTA
5605311 TTTATTTATTTATCT-
1 TTTATTTATTTAT-TA
* *
5605326 TATT-CTTACTTTTAGTA
1 T-TTATTTA--TTTATTA
* *
5605343 TTTATTCATTTACTA
1 TTTATTTATTTATTA
5605358 -TTATTT-TATTATTA
1 TTTATTTAT-TTATTA
5605372 TTACTATTT-TTTATT-
1 TT--TATTTATTTATTA
*
5605387 TTTA-TTATTTTTTA
1 TTTATTTATTTATTA
5605401 GTTT-TTTATT
1 -TTTATTTATT
5605411 ACTTAGCATT
Statistics
Matches: 78, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
12 2 0.03
13 8 0.10
14 10 0.13
15 34 0.44
16 11 0.14
17 13 0.17
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:5605411 original size:18 final size:16
Alignment explanation
Indices: 5605294--5605410 Score: 76
Period size: 16 Copynumber: 7.1 Consensus size: 16
5605284 TGCCCTTTTC
5605294 TTTTTATTTATTTATTAT
1 TTTTTA-TT-TTTATTAT
* *
5605312 TTATTTATTTATCTTA-
1 TT-TTTATTTTTATTAT
* * *
5605328 TTCTTACTTTTAGTAT
1 TTTTTATTTTTATTAT
* *
5605344 TTATTCATTTACTATTAT
1 TT-TTTATTT-TTATTAT
* *
5605362 TTTATTATTATTACTAT
1 TTT-TTATTTTTATTAT
5605379 TTTTTATTTTTATTAT
1 TTTTTATTTTTATTAT
*
5605395 TTTTTAGTTTT-TTAT
1 TTTTTATTTTTATTAT
5605410 T
1 T
5605411 ACTTAGCATT
Statistics
Matches: 75, Mismatches: 19, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
15 13 0.17
16 25 0.33
17 18 0.24
18 15 0.20
19 4 0.05
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTATTTTTATTAT
Found at i:5613974 original size:20 final size:20
Alignment explanation
Indices: 5613949--5613987 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5613939 TAAATTTCAA
*
5613949 ATATAAATTAGTCATTAATT
1 ATATAAATTACTCATTAATT
5613969 ATATAAATTACTCATTAAT
1 ATATAAATTACTCATTAAT
5613988 AAGCTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATAAATTACTCATTAATT
Found at i:5614285 original size:24 final size:24
Alignment explanation
Indices: 5614253--5614301 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
5614243 CGTTTCAATT
5614253 AAATTTTTAGCATAATAGTAAATA
1 AAATTTTTAGCATAATAGTAAATA
5614277 AAATTTTTAGCATAATAGTAAATA
1 AAATTTTTAGCATAATAGTAAATA
5614301 A
1 A
5614302 TTAAGAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (24 bp):
AAATTTTTAGCATAATAGTAAATA
Found at i:5615526 original size:159 final size:159
Alignment explanation
Indices: 5615237--5615856 Score: 992
Period size: 159 Copynumber: 3.9 Consensus size: 159
5615227 AACGAGAACG
* * *
5615237 TGGTGGAGAAAAGAAAGGAATAGAAGGAATTACAGTTGGGATTATGGGGACTGAGGGAATGCTTG
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
* *
5615302 GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGAAAGTGGAGGAAGTGCCCCA
66 GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
*
5615367 GGGTTTGGGAGATTAGGGAAAGATGGCAA
131 GGCTTTGGGAGATTAGGGAAAGATGGCAA
*
5615396 TGGTGGAGAAGAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACT-ACGGGAATGCTT
1 TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGA-GGGAATGCTT
5615460 GGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCC
65 GGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCC
*
5615525 AGGATTTGGGAGATTAGGGAAAGATGGCAA
130 AGGCTTTGGGAGATTAGGGAAAGATGGCAA
* * *
5615555 TGGTGGA-AAAGAGAAAGGAATCGAGGGAATTGCAGTTGGGAATGTGGGGATTGAGGGAATGCTT
1 TGGTGGAGAAA-AGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTT
* * *
5615619 GGCAGAGGGGGCAGTGTGGCCTTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGTAGTGCCCC
65 GGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCC
*
5615684 AGGCTTTGGGAGATTAGGGAAAGATGGAAA
130 AGGCTTTGGGAGATTAGGGAAAGATGGCAA
* * * *
5615714 TGATGGAGAAAATAAATTAGCAATAGAGGGAATTGCAGTTGGGATTCTGGGGACTGAGGGAATGC
1 TGGTGGAGAAAA-GAA--AGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGC
*
5615779 TTGGCAGAGGGGGCAGTGTGGCCTTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCC
63 TTGGCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCC
*
5615844 CCAAGCTTTGGGA
128 CCAGGCTTTGGGA
5615857 ATGAGGGTAT
Statistics
Matches: 428, Mismatches: 26, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
158 3 0.01
159 302 0.71
160 6 0.01
162 117 0.27
ACGTcount: A:0.28, C:0.11, G:0.40, T:0.21
Consensus pattern (159 bp):
TGGTGGAGAAAAGAAAGGAATAGAGGGAATTGCAGTTGGGATTGTGGGGACTGAGGGAATGCTTG
GCAGAGGGGGCAGTGTGGCCCTTGGTCCACTTGGAAATATGGTAGGAAGTGGAGGAAGCGCCCCA
GGCTTTGGGAGATTAGGGAAAGATGGCAA
Found at i:5617327 original size:15 final size:15
Alignment explanation
Indices: 5617309--5617337 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5617299 CCCTCTTTCT
5617309 TTTTTTTTTCTTATA
1 TTTTTTTTTCTTATA
5617324 TTTTTTTTTCTTAT
1 TTTTTTTTTCTTAT
5617338 CTGTTTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTTTCTTATA
Found at i:5617511 original size:17 final size:17
Alignment explanation
Indices: 5617479--5617512 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5617469 ATTTCCCCTT
* *
5617479 AATCCCAATCCTACAAA
1 AATCCCAATACAACAAA
5617496 AATCCCAATACAACAAA
1 AATCCCAATACAACAAA
5617513 CCTCAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
AATCCCAATACAACAAA
Found at i:5618530 original size:10 final size:11
Alignment explanation
Indices: 5618505--5618530 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5618495 ATTTCAAAGG
5618505 AAAAAATAAAT
1 AAAAAATAAAT
5618516 AAAAAATAAAT
1 AAAAAATAAAT
5618527 AAAA
1 AAAA
5618531 GGTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:5621091 original size:10 final size:10
Alignment explanation
Indices: 5621076--5621104 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5621066 CTCAATTCTA
5621076 AAAGATAAAT
1 AAAGATAAAT
5621086 AAAGATAAAT
1 AAAGATAAAT
5621096 AAAGATAAA
1 AAAGATAAA
5621105 AGCTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5622967 original size:19 final size:19
Alignment explanation
Indices: 5622943--5622989 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
5622933 TAGAAGAAAG
5622943 GGTGTTTGGCTATAAGGTA
1 GGTGTTTGGCTATAAGGTA
*
5622962 GGTGTTTGGCTATAGGGTA
1 GGTGTTTGGCTATAAGGTA
5622981 GGTGTTTGG
1 GGTGTTTGG
5622990 ATGCATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.43, T:0.38
Consensus pattern (19 bp):
GGTGTTTGGCTATAAGGTA
Found at i:5623165 original size:20 final size:19
Alignment explanation
Indices: 5623140--5623180 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
5623130 TTAATATCCA
*
5623140 AATAAAATAAAGTAATAAAT
1 AATAAAATAAAATAA-AAAT
5623160 AATAAAATAAAATAAAAAT
1 AATAAAATAAAATAAAAAT
5623179 AA
1 AA
5623181 AGAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (19 bp):
AATAAAATAAAATAAAAAT
Found at i:5623181 original size:16 final size:16
Alignment explanation
Indices: 5623139--5623194 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 16
5623129 ATTAATATCC
5623139 AAATAAAATAAAGTAATAA
1 AAATAAAAT-AA--AATAA
5623158 ATAATAAAATAAAATAA
1 A-AATAAAATAAAATAA
5623175 AAATAAAGA-AAAATAA
1 AAATAAA-ATAAAATAA
5623191 AAAT
1 AAAT
5623195 TAGGTTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 17 0.49
17 7 0.20
19 3 0.09
20 8 0.23
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:5623186 original size:20 final size:21
Alignment explanation
Indices: 5623143--5623192 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
5623133 ATATCCAAAT
* *
5623143 AAAATAAAGTAATAAATAA-T
1 AAAATAAAATAATAAATAAGA
5623163 AAAATAAAATAA-AAATAAAGA
1 AAAATAAAATAATAAAT-AAGA
5623184 AAAATAAAA
1 AAAATAAAA
5623193 ATTAGGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
21 9 0.35
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAATAAAATAATAAATAAGA
Found at i:5624625 original size:34 final size:33
Alignment explanation
Indices: 5624575--5624653 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 33
5624565 TTGTTTCTTT
* *
5624575 TTGGAAATTAAGAGTTTGCCGTTGTATTTGCTG
1 TTGGAAATCAAGAGTTTGCCGTTGTATCTGCTG
* ***
5624608 TTGGGAAATCAATAGTTTTTTGTTGTATCTGCTG
1 TT-GGAAATCAAGAGTTTGCCGTTGTATCTGCTG
5624642 TTGGAAATCAAG
1 TTGGAAATCAAG
5624654 CACATTAGCT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 11 0.29
34 27 0.71
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (33 bp):
TTGGAAATCAAGAGTTTGCCGTTGTATCTGCTG
Found at i:5627008 original size:12 final size:12
Alignment explanation
Indices: 5626991--5627021 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5626981 AAATTAAATA
5626991 TTAATAATAATC
1 TTAATAATAATC
5627003 TTAATAATAATC
1 TTAATAATAATC
*
5627015 CTAATAA
1 TTAATAA
5627022 AATTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAATAATAATC
Found at i:5627434 original size:11 final size:12
Alignment explanation
Indices: 5627409--5627438 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5627399 GTGAGAAGAA
5627409 TAATGATGAATT
1 TAATGATGAATT
5627421 TAATGATG-ATT
1 TAATGATGAATT
5627432 TAATGAT
1 TAATGAT
5627439 TTTTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (12 bp):
TAATGATGAATT
Found at i:5628606 original size:25 final size:25
Alignment explanation
Indices: 5628578--5628635 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
5628568 TAACTTATTT
* *
5628578 TATTTTATTCTT-AATTTATTTTTAG
1 TATTTTATT-TTCAATTAATTTTAAG
*
5628603 TATTTTTATTTTCTATTAATTTTAAG
1 TA-TTTTATTTTCAATTAATTTTAAG
5628629 TATTTTA
1 TATTTTA
5628636 CCATTAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (25 bp):
TATTTTATTTTCAATTAATTTTAAG
Found at i:5629135 original size:10 final size:9
Alignment explanation
Indices: 5629095--5629258 Score: 59
Period size: 9 Copynumber: 17.4 Consensus size: 9
5629085 TATGTGACAG
*
5629095 AAAAATGAT
1 AAAAATTAT
*
5629104 AAAAA-AAT
1 AAAAATTAT
*
5629112 AAAAATCAAT
1 AAAAAT-TAT
*
5629122 AAAAGTTAT
1 AAAAATTAT
5629131 AAAAATTAT
1 AAAAATTAT
*
5629140 AAAAATTGT
1 AAAAATTAT
* *
5629149 -TAAATTTT
1 AAAAATTAT
5629157 AATAAAATTAT
1 -A-AAAATTAT
5629168 AAAAA-TACT
1 AAAAATTA-T
* *
5629177 TAAAATTAGAA
1 AAAAATT--AT
5629188 AAAAATTAT
1 AAAAATTAT
*
5629197 AAAACTCGTA-
1 AAAAAT--TAT
*
5629207 AAAAATATAA
1 AAAAAT-TAT
* *
5629217 AAAAACTGT
1 AAAAATTAT
*
5629226 AAAATTTTAT
1 AAAA-ATTAT
5629236 AAAAAGTGTA-
1 AAAAA-T-TAT
5629246 AAAAATTAT
1 AAAAATTAT
5629255 AAAA
1 AAAA
5629259 CATATAGAAA
Statistics
Matches: 116, Mismatches: 23, Indels: 32
0.68 0.13 0.19
Matches are distributed among these distances:
8 17 0.15
9 50 0.43
10 32 0.28
11 16 0.14
12 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:5629152 original size:19 final size:19
Alignment explanation
Indices: 5629130--5629258 Score: 59
Period size: 19 Copynumber: 6.7 Consensus size: 19
5629120 ATAAAAGTTA
5629130 TAAAAATTATAAAAATTGT
1 TAAAAATTATAAAAATTGT
** *
5629149 TAAATTTTA-ATAAAATT-A
1 TAAAAATTATA-AAAATTGT
* *
5629167 TAAAAA-TACTTAAAATTAGA
1 TAAAAATTA-TAAAAATT-GT
* * *
5629187 AAAAAATTATAAAACTCGT
1 TAAAAATTATAAAAATTGT
* * *
5629206 AAAAAATATAAAAAAACTG-
1 TAAAAAT-TATAAAAATTGT
* *
5629225 TAAAATTTTATAAAAAGTGT
1 TAAAA-ATTATAAAAATTGT
*
5629245 AAAAAATTATAAAA
1 TAAAAATTATAAAA
5629259 CATATAGAAA
Statistics
Matches: 80, Mismatches: 21, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
17 2 0.03
18 11 0.14
19 42 0.52
20 23 0.29
21 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAAATTGT
Found at i:5629162 original size:29 final size:29
Alignment explanation
Indices: 5629129--5629200 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
5629119 AATAAAAGTT
** *
5629129 ATAAAAATTATAAAAATTGTTAAATTTTA-
1 ATAAAAATTATAAAAATACTTAAA-ATTAG
5629158 AT-AAAATTATAAAAATACTTAAAATTAG
1 ATAAAAATTATAAAAATACTTAAAATTAG
*
5629186 AAAAAAATTATAAAA
1 ATAAAAATTATAAAA
5629201 CTCGTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.08
28 20 0.54
29 14 0.38
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (29 bp):
ATAAAAATTATAAAAATACTTAAAATTAG
Found at i:5629163 original size:28 final size:29
Alignment explanation
Indices: 5629131--5629200 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
5629121 TAAAAGTTAT
** **
5629131 AAAAATTATAAAAATTGTT-AAATTTTAA
1 AAAAATTATAAAAATACTTAAAATTAGAA
*
5629159 TAAAATTATAAAAATACTTAAAATTAGAA
1 AAAAATTATAAAAATACTTAAAATTAGAA
5629188 AAAAATTATAAAA
1 AAAAATTATAAAA
5629201 CTCGTAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 16 0.46
29 19 0.54
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAAATTATAAAAATACTTAAAATTAGAA
Found at i:5629208 original size:28 final size:28
Alignment explanation
Indices: 5629131--5629209 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
5629121 TAAAAGTTAT
* * **
5629131 AAAAATTATAAAAATTGTTAAATTTTAA
1 AAAAATTATAAAAATCGTAAAATTAGAA
* *
5629159 TAAAATTATAAAAATACTTAAAATTAGAA
1 AAAAATTATAAAAAT-CGTAAAATTAGAA
*
5629188 AAAAATTATAAAACTCGTAAAA
1 AAAAATTATAAAAATCGTAAAA
5629210 AATATAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 20 0.49
29 21 0.51
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (28 bp):
AAAAATTATAAAAATCGTAAAATTAGAA
Found at i:5629210 original size:29 final size:29
Alignment explanation
Indices: 5629160--5629279 Score: 77
Period size: 29 Copynumber: 4.1 Consensus size: 29
5629150 AAATTTTAAT
* *
5629160 AAAATTATAAAAATACTTAAAATTAGAAA
1 AAAATTATAAAAATACTAAAAAATAGAAA
* *
5629189 AAAATTATAAAACT-CGTAAAAAATATAAA
1 AAAATTATAAAAATAC-TAAAAAATAGAAA
* * * * *
5629218 AAAACTGTAAAATTTTA-TAAAAAGT-GTAA
1 AAAATTATAAAA--ATACTAAAAAATAGAAA
*
5629247 AAAATTATAAAACATA-TAGAAATATAGAAA
1 AAAATTATAAAA-ATACTA-AAAAATAGAAA
5629277 AAA
1 AAA
5629280 GAATTTATAA
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
28 5 0.07
29 49 0.72
30 13 0.19
31 1 0.01
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (29 bp):
AAAATTATAAAAATACTAAAAAATAGAAA
Found at i:5629617 original size:30 final size:31
Alignment explanation
Indices: 5629550--5629617 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 31
5629540 TTTGTTATGA
*
5629550 TTTTTA-TAAAATTTTATAATTTTTAATAAT
1 TTTTTATTAAAATTTAATAATTTTTAATAAT
5629580 TTTTTATTAAAATTTAATAATTTTT-ATAAT
1 TTTTTATTAAAATTTAATAATTTTTAATAAT
5629610 TTTTTATT
1 TTTTTATT
5629618 TTTTATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 19 0.53
31 17 0.47
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTTATTAAAATTTAATAATTTTTAATAAT
Found at i:5629628 original size:10 final size:10
Alignment explanation
Indices: 5629532--5629631 Score: 75
Period size: 10 Copynumber: 10.4 Consensus size: 10
5629522 TTTTGATGCA
*
5629532 TTTTAGAATT
1 TTTTATAATT
* *
5629542 TGTTATGA-T
1 TTTTATAATT
**
5629551 TTTTATAAAA
1 TTTTATAATT
5629561 TTTTATAATT
1 TTTTATAATT
*
5629571 TTTAATAATT
1 TTTTATAATT
**
5629581 TTTTATTAAAA
1 TTTTA-TAATT
*
5629592 TTTAATAA-T
1 TTTTATAATT
5629601 TTTTATAA-T
1 TTTTATAATT
5629610 TTTT-T-ATT
1 TTTTATAATT
5629618 TTTTATAATT
1 TTTTATAATT
5629628 TTTT
1 TTTT
5629632 TTCCACATGT
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
7 1 0.01
8 6 0.09
9 20 0.29
10 36 0.51
11 7 0.10
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5630344 original size:22 final size:22
Alignment explanation
Indices: 5630314--5630356 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5630304 ACAGCAGAAC
* *
5630314 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
5630336 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
5630357 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:5630548 original size:41 final size:41
Alignment explanation
Indices: 5630447--5630655 Score: 235
Period size: 43 Copynumber: 5.0 Consensus size: 41
5630437 CGCTTACATA
* * *
5630447 AAAAAACGCCGCTAAAGATCATGCTCTTTAGCAGTGCTTAG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
5630488 AATAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 -A-AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
*
5630531 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
* * * *
5630573 AAGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATT
1 AA-AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTA-G
* *
5630616 CAAAAACGCCACTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 AAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
5630656 TTTCACAAAC
Statistics
Matches: 149, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
41 37 0.25
42 44 0.30
43 68 0.46
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:5630580 original size:84 final size:86
Alignment explanation
Indices: 5630433--5630654 Score: 249
Period size: 84 Copynumber: 2.6 Consensus size: 86
5630423 GCTAACTTTT
* * * *
5630433 GCGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGCTCTTTAGCAGTGC-TTAGAATAAAAAC
1 GCGGCGCTT--ATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTAGAATAAAAAC
* *
5630497 GCCGCT-AAAGATCATGTTCTTTA
64 GCCGCTAAAAG-TAATGTTCTATA
* *
5630520 GCGGCGCTTA-GAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGAA-GAAAACGC
1 GCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTAGAATAAAAACGC
*
5630583 CTCTAAAAGTAATGTTCTATA
66 CGCTAAAAGTAATGTTCTATA
** *
5630604 GCGGCGCTTATTCAAAAACGCCACTAAA-AGT-AGTGTTCTTTAGCGGCGCTT
1 GCGGCGCTTATGAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTT
5630655 ATTTCACAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
84 66 0.56
85 43 0.36
87 9 0.08
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (86 bp):
GCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTAGAATAAAAACGC
CGCTAAAAGTAATGTTCTATA
Found at i:5631090 original size:12 final size:12
Alignment explanation
Indices: 5631073--5631112 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5631063 TTTTGAACCT
*
5631073 CTGCTTCTATTG
1 CTGCTTCTATCG
*
5631085 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
5631097 CTGCTTCTCTCG
1 CTGCTTCTATCG
5631109 CTGC
1 CTGC
5631113 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:5631123 original size:21 final size:21
Alignment explanation
Indices: 5631097--5631165 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
5631087 GCTTCTCTCG
*
5631097 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
5631118 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
5631139 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
5631160 CTGCTT
1 CTGCTT
5631166 TAAGTTGCTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.01, C:0.43, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:5633579 original size:23 final size:22
Alignment explanation
Indices: 5633545--5633593 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
5633535 CACAATATTA
*
5633545 ATATATATATAT-GTTTCATAAT
1 ATATATATATATCGTTGCAT-AT
5633567 ATATAATATATATCGTTGCATAT
1 ATAT-ATATATATCGTTGCATAT
5633590 ATAT
1 ATAT
5633594 CTTTTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 14 0.58
24 6 0.25
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (22 bp):
ATATATATATATCGTTGCATAT
Found at i:5636531 original size:5 final size:5
Alignment explanation
Indices: 5636454--5636515 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
5636444 AATATGAAAA
5636454 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
5636504 ATAAT ATAAT AT
1 ATAAT ATAAT AT
5636516 TATTCATAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:5650132 original size:20 final size:20
Alignment explanation
Indices: 5650103--5650144 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5650093 CACGTATCCT
*
5650103 AATTTTATTTGATTCTAATC
1 AATTTGATTTGATTCTAATC
*
5650123 AATTTGATTTGATTTTAATC
1 AATTTGATTTGATTCTAATC
5650143 AA
1 AA
5650145 ATGGATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (20 bp):
AATTTGATTTGATTCTAATC
Found at i:5650151 original size:20 final size:20
Alignment explanation
Indices: 5650109--5650152 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5650099 TCCTAATTTT
* *
5650109 ATTTGATTCTAATCAATTTG
1 ATTTGATTCTAATCAAATGG
*
5650129 ATTTGATTTTAATCAAATGG
1 ATTTGATTCTAATCAAATGG
5650149 ATTT
1 ATTT
5650153 AATTGCTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (20 bp):
ATTTGATTCTAATCAAATGG
Found at i:5650932 original size:87 final size:87
Alignment explanation
Indices: 5650821--5651439 Score: 702
Period size: 87 Copynumber: 7.2 Consensus size: 87
5650811 GCCGTTCATA
* * * * * *
5650821 TTTTATTTTGTTTCCCAACAAG-TATTAAAATTAAATAAAACTCTATTTCAGGATTTGTTCCC-C
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAA-TCTATTTCGGGTTTTATTCCCGC
5650884 CGTTCAACAGATTTTATTCCATTT
65 CGTTCAACAGATTTTATTCCA-TT
* * * * *
5650908 TTTTCTTTTGTTTCCAAATGAG-TATTAAAATAAAATAAAATCTATTTCAGGG-TTTATTCCCGT
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTC-GGGTTTTATTCCCGC
* *
5650971 CGTTCAATAGATTTTATTCCATC
65 CGTTCAACAGATTTTATTCCATT
* * * *
5650994 TTTTATTTTGTTTCCAAACAAG-TACTAAAATTAAATAAAATCTATTTTGGGTTTTATTCCCGCC
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCC
*
5651058 GTTCAACAGATTTTTTTCCATT
66 GTTCAACAGATTTTATTCCATT
* *
5651080 TTTTATTTTGTTGT-CAAACGAGAAATTAAAATTAAATAAAATC-AGTTTTGGGTTTTATTCTCG
1 TTTTATTTTGTT-TCCAAACGAGAAATTAAAATTAAATAAAATCTA-TTTCGGGTTTTATTCCCG
* * *
5651143 CCATTAAACAGACTTTATTCCATT
64 CCGTTCAACAGATTTTATTCCATT
* * * * * *
5651167 TTTTATTTTGTTGCCAAAAGAGAAATTAAAATTAAATAAAATATGTTTCGGGTTTTATTCTCGCT
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCC
*
5651232 GTTCAATAGATTTTATTCCATT
66 GTTCAACAGATTTTATTCCATT
* * *
5651254 TTTTATTTT-TTGCCAAACGAGAAATTAAAATTAAATAAAATTTGTTTCGGGTTTTATTCCCGCC
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCC
*
5651318 GTTCAACTGATTTTATTCCATTT
66 GTTCAACAGATTTTATTCCA-TT
* * * *
5651341 TTTTATTTT-TTTCTAAACGAGAAATTAAAATTAAATAAAATCTA-TTCTGGGATCTAATCCCGC
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTC-GGGTTTTATTCCCGC
* * * * *
5651404 TGTTTAATAGAATTTATTCGA-T
65 CGTTCAACAGATTTTATTCCATT
*
5651426 TTTAATTTTGTTTC
1 TTTTATTTTGTTTC
5651440 TAAATTAGAA
Statistics
Matches: 463, Mismatches: 58, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
85 12 0.03
86 185 0.40
87 266 0.57
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (87 bp):
TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGTTTTATTCCCGCC
GTTCAACAGATTTTATTCCATT
Found at i:5651407 original size:173 final size:174
Alignment explanation
Indices: 5650821--5651437 Score: 705
Period size: 173 Copynumber: 3.6 Consensus size: 174
5650811 GCCGTTCATA
* * * * *
5650821 TTTTATTTTGTTTCCCAACAAG-TATTAAAATTAAATAAAACTCTATTTCAGGATTTGTTCCC-C
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAA-TCTATTTCGGGATTTATTCCCGC
* * * * *
5650884 CGTTCAACAGATTTTATTCCATTTTTTTCTTTTGTTTCCAAATGAG-TATTAAAATAAAATAAAA
65 CGTTCAACAGATTTTATTCCA-TTTTTTATTTTGTTGCCAAACGAGAAATTAAAATTAAATAAAA
* * *
5650948 TCTATTTCAGGG-TTTATTCCCGTCGTTCAA-TAGATTTTATTCCATC
129 TCTGTTTC-GGGTTTTATTCCCGCCGTTCAACT-GATTTTATTCCATT
* * * * *
5650994 TTTTATTTTGTTTCCAAACAAG-TACTAAAATTAAATAAAATCTATTTTGGGTTTTATTCCCGCC
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCC
* *
5651058 GTTCAACAGATTTTTTTCCATTTTTTATTTTGTTGTCAAACGAGAAATTAAAATTAAATAAAATC
66 GTTCAACAGATTTTATTCCATTTTTTATTTTGTTGCCAAACGAGAAATTAAAATTAAATAAAATC
* * * * * * *
5651123 AGTTTTGGGTTTTATTCTCGCCATTAAACAGACTTTATTCCATT
131 TGTTTCGGGTTTTATTCCCGCCGTTCAACTGATTTTATTCCATT
* * * * * * *
5651167 TTTTATTTTGTTGCCAAAAGAGAAATTAAAATTAAATAAAATATGTTTCGGGTTTTATTCTCGCT
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCC
* *
5651232 GTTCAATAGATTTTATTCCATTTTTTATTTT-TTGCCAAACGAGAAATTAAAATTAAATAAAATT
66 GTTCAACAGATTTTATTCCATTTTTTATTTTGTTGCCAAACGAGAAATTAAAATTAAATAAAATC
5651296 TGTTTCGGGTTTTATTCCCGCCGTTCAACTGATTTTATTCCATTT
131 TGTTTCGGGTTTTATTCCCGCCGTTCAACTGATTTTATTCCA-TT
* * *
5651341 TTTTATTTT-TTTCTAAACGAGAAATTAAAATTAAATAAAATCTA-TTCTGGGATCTAATCCCGC
1 TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTC-GGGATTTATTCCCGC
* * * * * *
5651404 TGTTTAATAGAATTTATTCGA-TTTTAATTTTGTT
65 CGTTCAACAGATTTTATTCCATTTTTTATTTTGTT
5651438 TCTAAATTAG
Statistics
Matches: 379, Mismatches: 57, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
172 52 0.14
173 252 0.66
174 75 0.20
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (174 bp):
TTTTATTTTGTTTCCAAACGAGAAATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCC
GTTCAACAGATTTTATTCCATTTTTTATTTTGTTGCCAAACGAGAAATTAAAATTAAATAAAATC
TGTTTCGGGTTTTATTCCCGCCGTTCAACTGATTTTATTCCATT
Found at i:5657752 original size:113 final size:113
Alignment explanation
Indices: 5657432--5657763 Score: 331
Period size: 113 Copynumber: 3.0 Consensus size: 113
5657422 GATTCACAAC
* * * *
5657432 AAGCGCCGCAAAAAA-ATAAGGCCAACGACGCCGTTTACTAAGTTTTTGGGCCATTAGCGG-G-T
1 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGCT
* * ** *
5657494 TTTTATAAAAACGCTGCTAATGCTCGGGGGA-CTTTGCGGCGATTTCTAAA
66 TTTT-TAAAAGCGCCGCTAATGCTC--ATGATCTTTGCGGCGTTTTCTAAA
* * * ** *
5657544 AAGCGCCGCAAAAAACCTAA-TGCGAACGACGTCGTTTTC-GAGTTTTTGTCCCTTTTGCGGCGC
1 AAGCGCCGCAAAAAACCTAAGGGC-AACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGC
* *
5657607 TTTTTTAAAAGCGCCGGTAATGCTCAT-ATCTTTCGCGGCGTTTTCTGAGA
65 TTTTTTAAAAGCGCCGCTAATGCTCATGATCTTT-GCGGCGTTTTCT-AAA
**
5657657 AA-CGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTTTGTTTTTGGGCCTTTAGCGGCGCT
1 AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGCT
* * * *
5657721 TTCTTAAAAGCGCCGCTAATGAT-TTGTTCTTTAGCGGCGTTTT
66 TTTTTAAAAGCGCCGCTAATGCTCATGATCTTT-GCGGCGTTTT
5657764 TTTGGAAGCG
Statistics
Matches: 180, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
110 1 0.01
111 4 0.02
112 75 0.42
113 95 0.53
114 5 0.03
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (113 bp):
AAGCGCCGCAAAAAACCTAAGGGCAACGACGCCGTTTTCTAAGTTTTTGGGCCTTTAGCGGCGCT
TTTTTAAAAGCGCCGCTAATGCTCATGATCTTTGCGGCGTTTTCTAAA
Found at i:5658159 original size:18 final size:21
Alignment explanation
Indices: 5658113--5658161 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
5658103 TAGTTCGACT
5658113 AAATTAATATATAAATCAAAC
1 AAATTAATATATAAATCAAAC
* *
5658134 AAAGTAATATA-AAA-C-ACC
1 AAATTAATATATAAATCAAAC
5658152 AAATTAATAT
1 AAATTAATAT
5658162 CGTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAATATATAAATCAAAC
Found at i:5658753 original size:14 final size:13
Alignment explanation
Indices: 5658736--5658775 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
5658726 TTGGGGGTAA
5658736 GGGTTTGTGGTTTG
1 GGGTTTG-GGTTTG
5658750 GGGTTTGGGGTTTG
1 GGGTTT-GGGTTTG
*
5658764 GGATTTGGGTTT
1 GGGTTTGGGTTT
5658776 TTAAGTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
14 17 0.71
15 1 0.04
ACGTcount: A:0.03, C:0.00, G:0.50, T:0.47
Consensus pattern (13 bp):
GGGTTTGGGTTTG
Found at i:5658760 original size:21 final size:21
Alignment explanation
Indices: 5658710--5658772 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
5658700 TGGTTTTTGA
*
5658710 GTTTGGGGTTTAGT-TTTTGGG
1 GTTTGGGGTTT-GTGGTTTGGG
* **
5658731 GGTAAGGGTTTGTGGTTTGGG
1 GTTTGGGGTTTGTGGTTTGGG
5658752 GTTTGGGGTTTG-GGATTTGGG
1 GTTTGGGGTTTGTGG-TTTGGG
5658773 TTTTTAAGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.06, C:0.00, G:0.49, T:0.44
Consensus pattern (21 bp):
GTTTGGGGTTTGTGGTTTGGG
Found at i:5659859 original size:232 final size:229
Alignment explanation
Indices: 5659454--5660005 Score: 813
Period size: 231 Copynumber: 2.4 Consensus size: 229
5659444 NNNNNNNNNN
* * * *
5659454 AAAGATTACACGAGTTTGCATTAAACGACTGCGTTTGACCTTATATTTAGTGTCAC-TATATATA
1 AAAGATTACAGGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
* * * *
5659518 AACGCTGCAAAATCGAAATGGTGTTACGAAAAACGGCGCCGTTTTTTATTACATTTAGTGGCGTT
66 AACGCCGCAAAATCGAAATGGTGTTACAAAAAACGGCACCATTTTTTATTACATTTAGTGGCGTT
* * *** *
5659583 TTAGAGAAAATGCCGCAAGTATGTTTTCTTTGTTACGTAAACGGCGTCGTTTTCCTTTGTTATTA
131 TTAGAGAAAACGCCGCAAGTATATTTTCTTTGTTACGTAAACGGCGTCGTTTT-CAAGGATATTA
* * * *
5659648 GTGGCGTTATACCCGAAATGCCTCAAATAAATTTT
195 GTGGCGTTACACCCAAAACGCCGCAAATAAATTTT
*
5659683 AAAGATTATAGGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
1 AAAGATTACAGGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
*
5659748 AACGCCGCAAACTCGAAAATGGTGTTACAAAAAACGGCACCATTTTCTTATTACATTTAGTGGCG
66 AACGCCGCAAAATCG-AAATGGTGTTACAAAAAACGGCACCATTTT-TTATTACATTTAGTGGCG
*
5659813 TTTTAGATAAAACGCCGCAAGTATATTTTCTTTGTTACAG-AAACGGCGTCGTTTTCAAGGATAT
129 TTTTAGAGAAAACGCCGCAAGTATATTTTCTTTGTTAC-GTAAACGGCGTCGTTTTCAAGGATAT
* *
5659877 TTGTGGCGTTACACCCAAAACGCCGCAAATATATTTT
193 TAGTGGCGTTACACCCAAAACGCCGCAAATAAATTTT
*
5659914 AAAGATTACAGGAGTTTG-GTTTAAACGACTGCGTTTGACCTTATATTTGGTGGCGCTTATATAT
1 AAAGATTACAGGAGTTTGCG-TTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATAT
*
5659978 AAACGCCTCAAAATCGAAATGGTGTTAC
65 AAACGCCGCAAAATCGAAATGGTGTTAC
5660006 GGAAAACGAC
Statistics
Matches: 291, Mismatches: 27, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
229 51 0.18
230 34 0.12
231 137 0.47
232 68 0.23
233 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (229 bp):
AAAGATTACAGGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
AACGCCGCAAAATCGAAATGGTGTTACAAAAAACGGCACCATTTTTTATTACATTTAGTGGCGTT
TTAGAGAAAACGCCGCAAGTATATTTTCTTTGTTACGTAAACGGCGTCGTTTTCAAGGATATTAG
TGGCGTTACACCCAAAACGCCGCAAATAAATTTT
Found at i:5660131 original size:231 final size:228
Alignment explanation
Indices: 5659454--5660114 Score: 778
Period size: 231 Copynumber: 2.9 Consensus size: 228
5659444 NNNNNNNNNN
* * * *
5659454 AAAGATTACACGAGTTTGCATTAAACGACTGCGTTTGACCTTATATTTAGTGTCAC-TATATATA
1 AAAGATTACAGGAGTTTG-GTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
*
5659518 AACG-CTGCAAAATCGAAATGGTGTTACGAAAAACGGCGCCGTTTTTTATTACATTTAGTGGCGT
65 AACGCCT-CAAAATCGAAATGGTGTTACGAAAAACGGCGCCGTTTCTTATTACATTTAGTGGCGT
* * * * * *
5659582 TTTAGAGAAAATGCCGCAAGTATGTTTTCTTTGTTACGTAAACGGCGTCGTTTTCCTTTGTTATT
129 TTTA-ATAAAACGCCGCAAGTATGATTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATT
* * *
5659647 AGTGGCGTTATACCCGAAATGCCTCAAATAAATTTT
193 AGTGGCGTTATACCCAAAACGCCGCAAATAAATTTT
*
5659683 AAAGATTATAGGAGTTTGCGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
1 AAAGATTACAGGAGTTTG-GTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
* * * * *
5659748 AACGCCGCAAACTCGAAAATGGTGTTACAAAAAACGGCACCATTTTCTTATTACATTTAGTGGCG
65 AACGCCTCAAAATCG-AAATGGTGTTACGAAAAACGGCGCC-GTTTCTTATTACATTTAGTGGCG
** *
5659813 TTTTAGATAAAACGCCGCAAGTAT-ATTTTCTTTGTTACA-GAAACGGCGTCGTTTT-CAAGGAT
128 TTTTA-ATAAAACGCCGCAAGTATGA-TTTCTTTGTTA-AGGAAACGGCGTCGTTTTCCATTGTT
* * *
5659875 ATTTGTGGCGTTACACCCAAAACGCCGCAAATATATTTT
190 ATTAGTGGCGTTATACCCAAAACGCCGCAAATAAATTTT
*
5659914 AAAGATTACAGGAGTTTGGTTTAAACGACTGCGTTTGACCTTATATTTGGTGGCGCTTATATATA
1 AAAGATTACAGGAGTTTGG-TTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATA
* * ***
5659979 AACGCCTCAAAATCGAAATGGTGTTACGGAAAACGACGCCGTTTCCTTAGTTGGTTTTAGTGGCG
65 AACGCCTCAAAATCGAAATGGTGTTACGAAAAACGGCGCCGTTT-CTTA-TTACATTTAGTGGCG
* * * * *** *
5660044 CTTTT-ATTAAACGCCGCAAATTTGCATTAC-AACTTAAGGAAACTGCGTCGTTTTCCATTGTTA
128 -TTTTAATAAAACGCCGCAAGTATG-ATTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTA
*
5660107 GTAGTGGC
191 TTAGTGGC
5660115 ACTTTGCTTA
Statistics
Matches: 367, Mismatches: 51, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
229 55 0.15
230 78 0.21
231 160 0.44
232 74 0.20
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (228 bp):
AAAGATTACAGGAGTTTGGTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCTTATATATAA
ACGCCTCAAAATCGAAATGGTGTTACGAAAAACGGCGCCGTTTCTTATTACATTTAGTGGCGTTT
TAATAAAACGCCGCAAGTATGATTTCTTTGTTAAGGAAACGGCGTCGTTTTCCATTGTTATTAGT
GGCGTTATACCCAAAACGCCGCAAATAAATTTT
Found at i:5660412 original size:19 final size:19
Alignment explanation
Indices: 5660390--5660433 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5660380 GAGACATCTC
*
5660390 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* * *
5660409 CCCCTAATTCCTAATAGTT
1 CCCCAAATCCCTAAAAGTT
5660428 CCCCAA
1 CCCCAA
5660434 CGTAGTCCAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.32, C:0.39, G:0.02, T:0.27
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:5665402 original size:21 final size:21
Alignment explanation
Indices: 5665376--5665443 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
5665366 CTACAACTTA
* *
5665376 AAGCAGAGGCGGAAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
5665397 AAGCAGCA-GCTGCAGCGAGGG
1 AAGCAG-AGGCTGCAGCGAGGG
*
5665418 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
5665439 AAGCA
1 AAGCA
5665444 AAGCAGAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.44, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Done.