Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 199 of 250
Found at i:62025504 original size:53 final size:52
Alignment explanation
Indices: 62025323--62025577 Score: 230
Period size: 55 Copynumber: 4.8 Consensus size: 52
62025313 ATTAGGGTTT
* *
62025323 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTTAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGG-TAAG-TTCTAAGGC
* ** * * * *
62025378 AAGGAAATTATGTAAGACCATGTCAAGACATGACATTGATAAGTTACTATAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C--TAAGGC
* * * *
62025433 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTC-TAAGGC
* *
62025486 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCT-AAGGC
* * ** *
62025535 AAGGATACCACGTAAGACCATGACAAGTTATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
62025578 GTACCCGCGT
Statistics
Matches: 166, Mismatches: 30, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
49 39 0.23
51 1 0.01
52 4 0.02
53 49 0.30
54 5 0.03
55 68 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCTAAGGC
Found at i:62025529 original size:108 final size:110
Alignment explanation
Indices: 62025330--62025530 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
62025320 TTTAAGGATA
* **
62025330 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTTAGGTTTCTAAGGCAAGGAAATTATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
62025395 CCATGTCAAGACATGACATTGATAAGTTACTATAAGGTAAAGATC
66 CCATGTCAAGACATGACAATGATAAGTTACTATAAGGTAAAGATC
*
62025440 CCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTC-TAAGGCAAGGAAACCATGTAAG
* *
62025502 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGACAATGATAAGTT
62025531 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.55
109 7 0.08
110 27 0.33
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGCAATTGGTGAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATGACAATGATAAGTTACTATAAGGTAAAGATC
Found at i:62025790 original size:16 final size:16
Alignment explanation
Indices: 62025769--62025799 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62025759 ATAAATTTGA
62025769 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
62025785 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
62025800 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:62030095 original size:14 final size:15
Alignment explanation
Indices: 62030056--62030097 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
62030046 CGATGAATTT
*
62030056 ATTGAAATTACATTA
1 ATTGAAATTATATTA
*
62030071 ATTGAAATTATATTG
1 ATTGAAATTATATTA
62030086 ATTG-AATTATAT
1 ATTGAAATTATAT
62030098 AATATATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (15 bp):
ATTGAAATTATATTA
Found at i:62030580 original size:37 final size:38
Alignment explanation
Indices: 62030539--62030612 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
62030529 TACTGGGTAC
62030539 CAACTTT-CTTCG-ACTAGGCCGATGAGACACTAGGTGT
1 CAACTTTGCTTCGAACTA-GCCGATGAGACACTAGGTGT
* * *
62030576 CAACTTTGCTTCGAACTATCCGATGAGGCACTGGGTG
1 CAACTTTGCTTCGAACTAGCCGATGAGACACTAGGTG
62030613 CCAAACTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 7 0.22
38 21 0.66
39 4 0.12
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (38 bp):
CAACTTTGCTTCGAACTAGCCGATGAGACACTAGGTGT
Found at i:62034847 original size:22 final size:23
Alignment explanation
Indices: 62034821--62034866 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
62034811 CAACCAAACC
62034821 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
62034843 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
62034866 A
1 A
62034867 CGTCATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:62034872 original size:23 final size:23
Alignment explanation
Indices: 62034828--62034872 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
62034818 ACCAATTCAA
*
62034828 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
62034851 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
62034873 TACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:62038495 original size:18 final size:18
Alignment explanation
Indices: 62038474--62038516 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
62038464 GTTAATTTGA
* *
62038474 TTAATTTGGGTAATTCGG
1 TTAATTTGAGTAATTCAG
* *
62038492 TTAATTCGATTAATTCAG
1 TTAATTTGAGTAATTCAG
62038510 TTAATTT
1 TTAATTT
62038517 TATACTTATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (18 bp):
TTAATTTGAGTAATTCAG
Found at i:62038514 original size:27 final size:27
Alignment explanation
Indices: 62038457--62038515 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
62038447 TTTATACAAA
* **
62038457 TAATTCGGTTAATTTGATTAATTTGGG
1 TAATTCGGTTAATTCGATTAATTCAGG
*
62038484 TAATTCGGTTAATTCGATTAATTCAGT
1 TAATTCGGTTAATTCGATTAATTCAGG
62038511 TAATT
1 TAATT
62038516 TTATACTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (27 bp):
TAATTCGGTTAATTCGATTAATTCAGG
Found at i:62042194 original size:37 final size:37
Alignment explanation
Indices: 62042139--62042214 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
62042129 ATATTATGAG
62042139 TTTGATTGCATTTTACATCAAAGAGCAAACAATCCTT
1 TTTGATTGCATTTTACATCAAAGAGCAAACAATCCTT
*
62042176 TTTGGTTGCATTTTACATCAAAGAGCAAACAATCCTT
1 TTTGATTGCATTTTACATCAAAGAGCAAACAATCCTT
62042213 TT
1 TT
62042215 ATGTTAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTGATTGCATTTTACATCAAAGAGCAAACAATCCTT
Found at i:62042922 original size:13 final size:13
Alignment explanation
Indices: 62042906--62042956 Score: 72
Period size: 12 Copynumber: 4.1 Consensus size: 13
62042896 AATGGAAGAT
62042906 GGAAAATGGG-AAG
1 GGAAAA-GGGAAAG
62042919 GG-AAAGGGAAAG
1 GGAAAAGGGAAAG
62042931 GGAAAAGGGAAAG
1 GGAAAAGGGAAAG
62042944 GG-AAAGGGAAAG
1 GGAAAAGGGAAAG
62042956 G
1 G
62042957 AAAGGAGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.08
12 19 0.53
13 14 0.39
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (13 bp):
GGAAAAGGGAAAG
Found at i:62042927 original size:6 final size:6
Alignment explanation
Indices: 62042916--62042961 Score: 76
Period size: 6 Copynumber: 7.7 Consensus size: 6
62042906 GGAAAATGGG
62042916 AAGGGA AAGGGA AAGGGAA AAGGGA AAGGGA AAGGGA AA-GGA AAGG
1 AAGGGA AAGGGA AAGGG-A AAGGGA AAGGGA AAGGGA AAGGGA AAGG
62042962 AGAGATTGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.13
6 27 0.71
7 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:62042938 original size:19 final size:19
Alignment explanation
Indices: 62042916--62042954 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
62042906 GGAAAATGGG
62042916 AAGGGAAAGGGAAAGGGAA
1 AAGGGAAAGGGAAAGGGAA
62042935 AAGGGAAAGGGAAAGGGAA
1 AAGGGAAAGGGAAAGGGAA
62042954 A
1 A
62042955 GGAAAGGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (19 bp):
AAGGGAAAGGGAAAGGGAA
Found at i:62042944 original size:25 final size:25
Alignment explanation
Indices: 62042891--62042956 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
62042881 CAATTTTATG
* *
62042891 AGGGAAATGGAAGATGGAAAATGGGA
1 AGGGAAAGGGAA-AGGGAAAATGGGA
62042917 AGGGAAAGGGAAAGGGAAAA-GGGAA
1 AGGGAAAGGGAAAGGGAAAATGGG-A
62042942 AGGGAAAGGGAAAGG
1 AGGGAAAGGGAAAGG
62042957 AAAGGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 3 0.08
25 23 0.62
26 11 0.30
ACGTcount: A:0.48, C:0.00, G:0.47, T:0.05
Consensus pattern (25 bp):
AGGGAAAGGGAAAGGGAAAATGGGA
Found at i:62042975 original size:25 final size:23
Alignment explanation
Indices: 62042916--62042961 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
62042906 GGAAAATGGG
62042916 AAGGGAAAGGGAAAGGGAAAAGGGA
1 AAGGGAAAGGGAAA-GG-AAAGGGA
62042941 AAGGGAAAGGGAAAGGAAAGG
1 AAGGGAAAGGGAAAGGAAAGG
62042962 AGAGATTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 14 0.67
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (23 bp):
AAGGGAAAGGGAAAGGAAAGGGA
Found at i:62051048 original size:36 final size:37
Alignment explanation
Indices: 62050998--62051069 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
62050988 ATAAAGTTTC
*
62050998 GGATAACTGAGTATTGAAATTATTAT-TTCTTAGGAT
1 GGATAACTGAGTATTGAAATTAGTATATTCTTAGGAT
* *
62051034 GGATAACTTG-GTATTGTACTTAGTATATTCTTAGGA
1 GGATAAC-TGAGTATTGAAATTAGTATATTCTTAGGA
62051070 GGGCTTGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 20 0.65
37 11 0.35
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.42
Consensus pattern (37 bp):
GGATAACTGAGTATTGAAATTAGTATATTCTTAGGAT
Found at i:62060730 original size:25 final size:26
Alignment explanation
Indices: 62060697--62060759 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 26
62060687 ATGTTGAAAG
* *
62060697 ATACGTACATAATACAG-TATTTAAA
1 ATACATACATAATACAGTTATTAAAA
* *
62060722 ATACATACATCATATAGTTATTAAAA
1 ATACATACATAATACAGTTATTAAAA
* *
62060748 ATATATATATAA
1 ATACATACATAA
62060760 GATAGTACAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (26 bp):
ATACATACATAATACAGTTATTAAAA
Found at i:62061151 original size:24 final size:26
Alignment explanation
Indices: 62061122--62061184 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
62061112 ATATACGAAG
*
62061122 CAATTTAAAGTAGA-TAATATA-AA-A
1 CAATTTAAAATA-ATTAATATATAATA
62061146 CAATTTAAAATAATTAATATATAATA
1 CAATTTAAAATAATTAATATATAATA
*
62061172 TAATTTAAAATAA
1 CAATTTAAAATAA
62061185 AATAAAGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 18 0.53
25 2 0.06
26 13 0.38
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (26 bp):
CAATTTAAAATAATTAATATATAATA
Found at i:62062206 original size:16 final size:16
Alignment explanation
Indices: 62062185--62062255 Score: 106
Period size: 16 Copynumber: 4.4 Consensus size: 16
62062175 GTTTGGTTCA
*
62062185 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
62062201 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
62062217 CTGTAATGGAATAGAT
1 CTGTAATGGAATAGAG
*
62062233 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAG
62062249 CTGTAAT
1 CTGTAAT
62062256 AAGTAATTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:62062294 original size:46 final size:44
Alignment explanation
Indices: 62062237--62062330 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
62062227 ATAGATCTGT
62062237 AATGGAATAGAACTGTAATAAGTAATTCAACTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTCAACTGTTTGGTTGAATGG
***
62062283 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
62062327 AATG
1 AATG
62062331 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.51
45 3 0.07
46 19 0.42
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCAACTGTTTGGTTGAATGG
Found at i:62062523 original size:17 final size:17
Alignment explanation
Indices: 62062501--62062533 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
62062491 AATTATTATT
62062501 AAATATAATTTAATAAA
1 AAATATAATTTAATAAA
62062518 AAATATAATTTAATAA
1 AAATATAATTTAATAA
62062534 CATTCATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATAATTTAATAAA
Found at i:62063060 original size:18 final size:18
Alignment explanation
Indices: 62063037--62063071 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62063027 ACGTGGTAGT
*
62063037 CCAACTAGATTTTAAGTG
1 CCAACTAGATCTTAAGTG
62063055 CCAACTAGATCTTAAGT
1 CCAACTAGATCTTAAGT
62063072 ATATCTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (18 bp):
CCAACTAGATCTTAAGTG
Found at i:62063130 original size:40 final size:40
Alignment explanation
Indices: 62063079--62063323 Score: 384
Period size: 40 Copynumber: 6.1 Consensus size: 40
62063069 AGTATATCTG
* * *
62063079 TTAATACATACTTTATCAGGGTAAATTATACAATTTTCTG
1 TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
62063119 TTAATACATACTTT-TCCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTTAT-CCGGGTAAATTATACAGTTTTCTA
* *
62063159 TTAATACATACTTTATCCGGATAAATTATACAGTTTTCTG
1 TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
*
62063199 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
*
62063239 TTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTA
1 TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
* * *
62063279 TTAATATATACTTCATCCGGATAAATTATACAGTTTTCTA
1 TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
62063319 TTAAT
1 TTAAT
62063324 GTGCTTGTGA
Statistics
Matches: 191, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 189 0.99
41 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (40 bp):
TTAATACATACTTTATCCGGGTAAATTATACAGTTTTCTA
Found at i:62063290 original size:120 final size:120
Alignment explanation
Indices: 62063075--62063323 Score: 426
Period size: 120 Copynumber: 2.1 Consensus size: 120
62063065 CTTAAGTATA
* * *
62063075 TCTGTTAATACATACTTTATCAGGGTAAATTATACAATTTTCTGTTAATACATACTTTTCCCGGG
1 TCTGTTAATACATACTTTACCAGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
*
62063140 TAAATTATACAGTTTTCTATTAATACATACTTTATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
* *
62063195 TCTGTTAATACATACTTTACCCGGGTAAATTATACAGTTTTCTATTAATACATACTTTACCCGGG
1 TCTGTTAATACATACTTTACCAGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
*
62063260 TAAATTATACAGTTTTCTATTAATATATACTTCATCCGGATAAATTATACAGTTT
66 TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
*
62063315 TCTATTAAT
1 TCTGTTAAT
62063324 GTGCTTGTGA
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 121 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (120 bp):
TCTGTTAATACATACTTTACCAGGGTAAATTATACAATTTTCTATTAATACATACTTTACCCGGG
TAAATTATACAGTTTTCTATTAATACATACTTCATCCGGATAAATTATACAGTTT
Found at i:62067169 original size:21 final size:22
Alignment explanation
Indices: 62067136--62067178 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
62067126 TTTTAACTTG
62067136 AGAAATCAATTTTTG-ATATAAA
1 AGAAATC-ATTTTTGCATATAAA
62067158 AGAAAT-ATTTTTGCATATAAA
1 AGAAATCATTTTTGCATATAAA
62067179 TTTCTAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 7 0.35
22 6 0.30
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (22 bp):
AGAAATCATTTTTGCATATAAA
Found at i:62075362 original size:3 final size:3
Alignment explanation
Indices: 62075354--62075381 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
62075344 CCCGCATCCT
62075354 CAC CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC C
62075382 GCCATTGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:62084630 original size:11 final size:11
Alignment explanation
Indices: 62084616--62084660 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
62084606 AGATAAATAT
62084616 TATTTTATTAA
1 TATTTTATTAA
*
62084627 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
62084640 TATTTTATTAT
1 TATTTTATTAA
62084651 TATTTTATTA
1 TATTTTATTA
62084661 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:62086841 original size:46 final size:46
Alignment explanation
Indices: 62086789--62087098 Score: 469
Period size: 46 Copynumber: 6.7 Consensus size: 46
62086779 AGTGTGCTCT
* *
62086789 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCACGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
62086835 CTGATATTAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
62086881 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
62086927 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
62086973 CTGATATGAGATGTGTAAGACTATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** *
62087019 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
62087065 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGA
62087099 CACTATGACA
Statistics
Matches: 245, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 1 0.00
46 244 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:62093627 original size:27 final size:26
Alignment explanation
Indices: 62093564--62093627 Score: 60
Period size: 28 Copynumber: 2.3 Consensus size: 26
62093554 TCATAACTTA
*
62093564 TTTATAAAAAAATTACTTTCTAAAGT
1 TTTATAAAAAAATTACTTTATAAAGT
62093590 TATGGTA-AAAAAAATTA-TTTATAAGAAGT
1 T-T--TATAAAAAAATTACTTTAT-A-AAGT
62093619 TTTATAAAA
1 TTTATAAAA
62093628 TGCTTGGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
26 3 0.10
27 9 0.29
28 12 0.39
29 7 0.23
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (26 bp):
TTTATAAAAAAATTACTTTATAAAGT
Found at i:62097988 original size:23 final size:23
Alignment explanation
Indices: 62097961--62098008 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
62097951 TTTCTGATTA
*
62097961 ATGGCTC-TCTGGAACTTTCCGAT
1 ATGGCTCGT-TGGAACTTCCCGAT
*
62097984 ATGGCTCGTTTGAACTTCCCGAT
1 ATGGCTCGTTGGAACTTCCCGAT
62098007 AT
1 AT
62098009 ATATGGCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (23 bp):
ATGGCTCGTTGGAACTTCCCGAT
Found at i:62098051 original size:25 final size:25
Alignment explanation
Indices: 62097948--62098051 Score: 65
Period size: 25 Copynumber: 4.2 Consensus size: 25
62097938 GTTCTTTGTG
* *
62097948 AGCTTTCTGATTAATGGCTCTCTGGA
1 AGCTTCCTGATTAATGGCTCT-TCGA
*
62097974 A-CTTTCC-GA-T-ATGGCTCGTTTGA
1 AGC-TTCCTGATTAATGGCTC-TTCGA
* * * *
62097997 A-CTTCCCGATATATATGGCTATCCGG
1 AGCTTCCTGAT-TA-ATGGCTCTTCGA
62098023 AGCTTCCTGATTAATGGCTCTTCGA
1 AGCTTCCTGATTAATGGCTCTTCGA
62098048 AGCT
1 AGCT
62098052 ACTCGTTATT
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
22 4 0.07
23 14 0.23
24 2 0.03
25 17 0.28
26 9 0.15
27 14 0.23
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
AGCTTCCTGATTAATGGCTCTTCGA
Found at i:62098149 original size:25 final size:25
Alignment explanation
Indices: 62098086--62098165 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
62098076 TCCTAATTAT
* *
62098086 GGCTCCTATAAGCTTCCCGTTATATA
1 GGCTCATAT-AGCTTCCCGTTACATA
* * *
62098112 GCCTGAAATAGCTTCCCGTTACA-A
1 GGCTCATATAGCTTCCCGTTACATA
* *
62098136 GGCTCATATGAGCTTCTCGTTATAT-
1 GGCTCATAT-AGCTTCCCGTTACATA
62098161 GGCTC
1 GGCTC
62098166 GAAAGAGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
24 7 0.17
25 30 0.71
26 5 0.12
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (25 bp):
GGCTCATATAGCTTCCCGTTACATA
Found at i:62099674 original size:19 final size:18
Alignment explanation
Indices: 62099650--62099703 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
62099640 CTTCCAAGAT
62099650 CCACACGGCCTGGCCATTC
1 CCACACGG-CTGGCCATTC
*
62099669 CCACACAGGTTGGCCATTC
1 CCACAC-GGCTGGCCATTC
62099688 CCACACGGGCTGGCCA
1 CCACAC-GGCTGGCCA
62099704 CACATTCATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 29 0.94
20 2 0.06
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.15
Consensus pattern (18 bp):
CCACACGGCTGGCCATTC
Found at i:62105981 original size:20 final size:21
Alignment explanation
Indices: 62105943--62105982 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62105933 GATATTATAT
62105943 TTTTATAATTGAATAGAAAAG
1 TTTTATAATTGAATAGAAAAG
*
62105964 TTTTATAATT-ATTAGAAAA
1 TTTTATAATTGAATAGAAAA
62105983 CCGTAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTATAATTGAATAGAAAAG
Found at i:62110492 original size:18 final size:18
Alignment explanation
Indices: 62110469--62110523 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
62110459 CGAATAAAAC
*
62110469 TTGAGAAAATTGAGAGAG
1 TTGAGAGAATTGAGAGAG
62110487 TTGAGAGAATT-A-AGAG
1 TTGAGAGAATTGAGAGAG
62110503 TTTAGAGAGAATTGAGAGAG
1 -TT-GAGAGAATTGAGAGAG
62110523 T
1 T
62110524 AAAATTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 19 0.59
19 2 0.06
20 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (18 bp):
TTGAGAGAATTGAGAGAG
Found at i:62110502 original size:9 final size:9
Alignment explanation
Indices: 62110469--62110521 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
62110459 CGAATAAAAC
*
62110469 TTGAGAAAA
1 TTGAGAGAA
*
62110478 TTGAGAGAG
1 TTGAGAGAA
62110487 TTGAGAGAA
1 TTGAGAGAA
* *
62110496 TTAAGAG-T
1 TTGAGAGAA
62110504 TTAGAGAGAA
1 TT-GAGAGAA
62110514 TTGAGAGA
1 TTGAGAGA
62110522 GTAAAATTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 2 0.06
9 31 0.89
10 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:62111436 original size:21 final size:21
Alignment explanation
Indices: 62111412--62111453 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
62111402 AGGACTAAAG
62111412 TAAACAAAAAAGTTTAAATAC
1 TAAACAAAAAAGTTTAAATAC
62111433 TAAACAAAAAAGTTTAAATAC
1 TAAACAAAAAAGTTTAAATAC
62111454 CAAAATAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (21 bp):
TAAACAAAAAAGTTTAAATAC
Found at i:62111753 original size:25 final size:25
Alignment explanation
Indices: 62111725--62111773 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
62111715 TATTATTTTT
62111725 AATTTAATAT-TTAATAATTTTATAC
1 AATTTAATATATTAA-AATTTTATAC
* *
62111750 AATTTTATTTATTAAAATTTTATA
1 AATTTAATATATTAAAATTTTATA
62111774 TATAGTCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
AATTTAATATATTAAAATTTTATAC
Found at i:62113018 original size:18 final size:18
Alignment explanation
Indices: 62112995--62113029 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62112985 TTTTTTATAT
62112995 TTTTAGCATTTCTTTTAA
1 TTTTAGCATTTCTTTTAA
* *
62113013 TTTTAGGATTTTTTTTA
1 TTTTAGCATTTCTTTTA
62113030 TTTCAAAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTTAGCATTTCTTTTAA
Found at i:62114682 original size:18 final size:18
Alignment explanation
Indices: 62114655--62114706 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
62114645 AAAAATTAAT
62114655 TTAAATTTAATATGCACAA
1 TTAAA-TTAATATGCACAA
*
62114674 TTAAATTAATATGTACAA
1 TTAAATTAATATGCACAA
**
62114692 TTATTTTAATATGCA
1 TTAAATTAATATGCA
62114707 TGTTATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 24 0.83
19 5 0.17
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (18 bp):
TTAAATTAATATGCACAA
Found at i:62114895 original size:26 final size:25
Alignment explanation
Indices: 62114865--62114914 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
62114855 ACATTGTTTC
* *
62114865 TAAATTTAAAATTTTTAAATCTATT
1 TAAAATTAAAATTTTTAAATATATT
62114890 TAAAATTAAAATTTTTAAATATATT
1 TAAAATTAAAATTTTTAAATATATT
62114915 ATATGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAATTAAAATTTTTAAATATATT
Found at i:62122028 original size:31 final size:33
Alignment explanation
Indices: 62121973--62122036 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
62121963 TATTTAAAAA
62121973 TTAATAATATATTTTTATAATTAAATATT-AATT
1 TTAATAATATATTTTTATAATTAAA-ATTGAATT
**
62122006 TTAA-AATAT-TTTTTATTTTTAAAATTGAATT
1 TTAATAATATATTTTTATAATTAAAATTGAATT
62122037 CGAGTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 3 0.11
31 16 0.57
32 5 0.18
33 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (33 bp):
TTAATAATATATTTTTATAATTAAAATTGAATT
Found at i:62124696 original size:24 final size:28
Alignment explanation
Indices: 62124646--62124701 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
62124636 CTAGCCTCTC
*
62124646 CCCACTTGCCTCAGTGCCGCAACCACCCT
1 CCCACTTGCCTCA-TGCCGCAACCACCAT
62124675 CCCACTTGCCTC-TG-C-CAA-CACCAT
1 CCCACTTGCCTCATGCCGCAACCACCAT
62124699 CCC
1 CCC
62124702 CTGGCGCCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 8 0.31
25 3 0.12
26 1 0.04
27 2 0.08
29 12 0.46
ACGTcount: A:0.18, C:0.54, G:0.11, T:0.18
Consensus pattern (28 bp):
CCCACTTGCCTCATGCCGCAACCACCAT
Found at i:62125162 original size:15 final size:14
Alignment explanation
Indices: 62125137--62125181 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
62125127 GCCGGTAGCC
62125137 CCCCTCTCTCCTTT
1 CCCCTCTCTCCTTT
62125151 CCCCTCTCCTCCTTT
1 CCCCTCT-CTCCTTT
* *
62125166 CTCTTCCTCTCCTTT
1 CCCCT-CTCTCCTTT
62125181 C
1 C
62125182 TTCTCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 7 0.26
15 18 0.67
16 2 0.07
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (14 bp):
CCCCTCTCTCCTTT
Found at i:62129113 original size:17 final size:17
Alignment explanation
Indices: 62129091--62129151 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 17
62129081 ACAATAATAT
62129091 AAAATA-ATGATATGTAC
1 AAAATATAT-ATATGTAC
62129108 AAAATATATATATGTAC
1 AAAATATATATATGTAC
*
62129125 ATAATATAGT-TA--TA-
1 AAAATATA-TATATGTAC
62129139 AAAATATATATAT
1 AAAATATATATAT
62129152 TAAATTCGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 2 0.05
17 23 0.61
18 3 0.08
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (17 bp):
AAAATATATATATGTAC
Found at i:62129944 original size:15 final size:16
Alignment explanation
Indices: 62129908--62129950 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
62129898 TTTTTTGTTG
62129908 TTTTTTTTTGCTGGAA
1 TTTTTTTTTGCTGGAA
**
62129924 AATTTTTTTGCT-GAA
1 TTTTTTTTTGCTGGAA
62129939 TTTTTTTTTGCT
1 TTTTTTTTTGCT
62129951 CTTTTTTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.65
Consensus pattern (16 bp):
TTTTTTTTTGCTGGAA
Found at i:62130206 original size:30 final size:30
Alignment explanation
Indices: 62130179--62130289 Score: 136
Period size: 30 Copynumber: 3.7 Consensus size: 30
62130169 TTTAGAAAAA
* *
62130179 TTTA-GGGTTAAAATGTAATTTAAAGAAAG
1 TTTAGGGGTCAAAATGAAATTTAAAGAAAG
* *
62130208 TTTAGGGGTCTAAGTGAAATTTAAAGAAAG
1 TTTAGGGGTCAAAATGAAATTTAAAGAAAG
* *
62130238 TTTAAGGGTCAAAATAAAATTT-AAGAAAAG
1 TTTAGGGGTCAAAATGAAATTTAAAG-AAAG
*
62130268 TTTAGGGGTCAAAATGCAATTT
1 TTTAGGGGTCAAAATGAAATTT
62130290 TTATTTTTTG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 7 0.10
30 62 0.90
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.32
Consensus pattern (30 bp):
TTTAGGGGTCAAAATGAAATTTAAAGAAAG
Found at i:62130314 original size:24 final size:24
Alignment explanation
Indices: 62130286--62130331 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
62130276 TCAAAATGCA
62130286 ATTTTTATTTTTTGAAAATTTTTT
1 ATTTTTATTTTTTGAAAATTTTTT
*
62130310 ATTTTTATTTTTTTAAAATTTT
1 ATTTTTATTTTTTGAAAATTTT
62130332 GAAAATTAAA
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:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTATTTTTTGAAAATTTTTT
Found at i:62130689 original size:75 final size:77
Alignment explanation
Indices: 62130519--62130803 Score: 223
Period size: 80 Copynumber: 3.7 Consensus size: 77
62130509 GACCCTAAGT
* *
62130519 TCAACTCACCTCTCG-AATTATGAGTTGA--TCTTTTGAAAAAGTA-AAAAATTGAAAATACCTC
1 TCAACTCACCTCTCGCAA-TATGAGTTGACTTTTTTTG--AAAG-ACAGAAATTGAAAATACCTC
*
62130580 AGCATGTGACCTGAGGC
62 A-CATATGACCTGAGGC
* *
62130597 TTAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAGAAATTGAAAATATCTCA-AT
1 TCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTGAAAGACAGAAATTGAAAATACCTCACAT
* *
62130660 ATGTCTTGAGGC
66 ATGACCTGAGGC
** * * * *
62130672 TCAACTCATTTCTCGCAATATGAGTTGACTTTTTTTAAAAAAAAAGCAGGAATTGAAATTACCTC
1 TCAACTCACCTCTCGCAATATGAGTTGACTTTTTTT---GAAAGA-CAGAAATTGAAAATACCTC
* * *
62130737 AGC--GTGTCCCGAGGC
62 A-CATATGACCTGAGGC
* * * *
62130752 TCAACTCACCTCTCGTAATATGAATTGA---TTTTTGAAAAACATAAATTGAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTGAAAGACAGAAATTGAAAA
62130804 ACGGAAATCG
Statistics
Matches: 171, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
73 10 0.06
74 5 0.03
75 36 0.21
76 8 0.05
77 26 0.15
78 24 0.14
79 12 0.07
80 50 0.29
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (77 bp):
TCAACTCACCTCTCGCAATATGAGTTGACTTTTTTTGAAAGACAGAAATTGAAAATACCTCACAT
ATGACCTGAGGC
Found at i:62130766 original size:80 final size:79
Alignment explanation
Indices: 62130519--62131033 Score: 365
Period size: 89 Copynumber: 6.3 Consensus size: 79
62130509 GACCCTAAGT
* * **
62130519 TCAACTCACCTCTCG-AATTATGAGTTGATCTTTTGAAAAA-GTAA-A-AAATTGAAAATACCTC
1 TCAACTCACCTCTCGCAA-TATGAGTTGATTTTTTTAAAAACAAAACAGAAATTGAAAATACCTC
*
62130580 AGCATGTGACCTGAGGC
65 AGC--GTGTCCTGAGGC
* * * *
62130597 TTAACTCACCTCTCGCAATATGAGTTGATTTTTTT---GA-AAGACAGAAATTGAAAATATCTCA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAACAGAAATTGAAAATACCTCA
*** *
62130658 ATATGTCTTGAGGC
66 GCGTGTCCTGAGGC
** * *
62130672 TCAACTCATTTCTCGCAATATGAGTTGACTTTTTTTAAAAA-AAAAGCAGGAATTGAAATTACCT
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTAAAAACAAAA-CAGAAATTGAAAATACCT
*
62130736 CAGCGTGTCCCGAGGC
64 CAGCGTGTCCTGAGGC
* * * * *
62130752 TCAACTCACCTCTCGTAATATGAATTGA-TTTTTGAAAAACATAAATTGAAAAACGGAAATCGAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAAC---------AAAACAGAAATTGAA
* * *
62130816 AATACATCAACATGTCCTGAGGC
57 AATACCTCAGCGTGTCCTGAGGC
* *
62130839 TCAATTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGGAA-AAAACAGAAATTG
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTT------T-TA-A---AAACAAAACAGAAATTG
62130903 AAAATACCTCAGCGTGTCCTGAGGC
55 AAAATACCTCAGCGTGTCCTGAGGC
* *
62130928 TCAACTCACCTCTCGCAATATGAGTTGA---TTTAAAAACAGTCATTAAGAACAGAAATTAAAAA
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAA-A--C---AA-AACAGAAATTGAAAA
62130990 TACCTCAGCGTGTCCTGAGGC
59 TACCTCAGCGTGTCCTGAGGC
*
62131011 TCAACTCACCTCTTGCAATATGA
1 TCAACTCACCTCTCGCAATATGA
62131034 AATCACCTCT
Statistics
Matches: 345, Mismatches: 54, Indels: 71
0.73 0.11 0.15
Matches are distributed among these distances:
75 37 0.11
76 9 0.03
77 16 0.05
78 40 0.12
79 7 0.02
80 51 0.15
82 2 0.01
83 57 0.17
86 2 0.01
87 51 0.15
88 8 0.02
89 60 0.17
94 1 0.00
95 1 0.00
96 1 0.00
99 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (79 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAAAACAGAAATTGAAAATACCTCA
GCGTGTCCTGAGGC
Found at i:62130929 original size:89 final size:87
Alignment explanation
Indices: 62130712--62131033 Score: 420
Period size: 87 Copynumber: 3.7 Consensus size: 87
62130702 TTTTTTAAAA
* * * * *
62130712 AAAAAGCAGGAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAAT
1 AAAAA-CAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
62130777 TGATTTTTGAAAAACATAAATTG
65 TGATTTTTGAAAAACATAAATTG
* * * * * *
62130800 AAAAACGGAAATCGAAAATACATCAACATGTCCTGAGGCTCAATTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
62130865 GATTTTTGAAAAATATAGATTGG
66 GATTTTTGAAAAACATAAATT-G
62130888 AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 -AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
62130953 TGA--TTT-AAAAACAGT-CATT-
65 TGATTTTTGAAAAACA-TAAATTG
* * *
62130972 AAGAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
62131034 AATCACCTCT
Statistics
Matches: 207, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
83 59 0.29
86 9 0.04
87 72 0.35
88 6 0.03
89 61 0.29
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAACATAAATTG
Found at i:62131041 original size:20 final size:20
Alignment explanation
Indices: 62131016--62131054 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
62131006 GAGGCTCAAC
*
62131016 TCACCTCTTGCAATATGAAA
1 TCACCTCTCGCAATATGAAA
62131036 TCACCTCTCGCAATATGAA
1 TCACCTCTCGCAATATGAA
62131055 TTGATTTTTG
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:0.33, C:0.28, G:0.10, T:0.28
Consensus pattern (20 bp):
TCACCTCTCGCAATATGAAA
Found at i:62131082 original size:176 final size:175
Alignment explanation
Indices: 62130711--62131045 Score: 417
Period size: 176 Copynumber: 1.9 Consensus size: 175
62130701 TTTTTTTAAA
* * *
62130711 AAAAAAGCAGGAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGAA
1 AAAAAA-CAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAA
* *
62130776 TTGATTTTTGAAAAACATAAATTGAAAAACGGAAATCGAAAATACATCAACATGTCCTGAGGCTC
65 TTGA-TTTTGAAAAACATAAATTGAAAAACAGAAATCAAAAATACATCAACATGTCCTGAGGCTC
* ** * * * *
62130841 AATTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGG
129 AACTCACCTCTCGCAATATGAAATCACTCTCGAAAAATATAGATTGG
* *
62130888 AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAAT
* * * * * *
62130953 TGA-TTT-AAAAACAGT-CATT-AAGAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCA
66 TGATTTTGAAAAACA-TAAATTGAAAAACAGAAATCAAAAATACATCAACATGTCCTGAGGCTCA
*
62131014 ACTCACCTCTTGCAATATGAAATCACCTCTCG
130 ACTCACCTCTCGCAATATGAAATCA-CTCTCG
62131046 CAATATGAAT
Statistics
Matches: 135, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
172 55 0.41
173 13 0.10
174 4 0.03
176 57 0.42
177 6 0.04
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (175 bp):
AAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAAT
TGATTTTGAAAAACATAAATTGAAAAACAGAAATCAAAAATACATCAACATGTCCTGAGGCTCAA
CTCACCTCTCGCAATATGAAATCACTCTCGAAAAATATAGATTGG
Found at i:62131088 original size:14 final size:14
Alignment explanation
Indices: 62131066--62131095 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62131056 TGATTTTTGC
*
62131066 AAAATATAAATTGA
1 AAAACATAAATTGA
62131080 AAAACATAAATTGA
1 AAAACATAAATTGA
62131094 AA
1 AA
62131096 TTACCTCAGC
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:0.03, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAACATAAATTGA
Found at i:62143288 original size:22 final size:20
Alignment explanation
Indices: 62143237--62143290 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
62143227 ATATATTTGG
62143237 TAATA-ATA-ATATAAAATAA
1 TAATATATACATA-AAAATAA
*
62143256 TAATATGTACATAAAAATACA
1 TAATATATACATAAAAATA-A
62143277 TATATATATACATA
1 TA-ATATATACATA
62143291 TAATAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 6 0.21
22 10 0.34
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (20 bp):
TAATATATACATAAAAATAA
Found at i:62143300 original size:21 final size:21
Alignment explanation
Indices: 62143245--62143302 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
62143235 GGTAATAATA
* *
62143245 ATATAAAATAATA-ATATGTAC
1 ATATAATA-AATATATATATAC
* *
62143266 ATAAAAATACATATATATATAC
1 AT-ATAATAAATATATATATAC
62143288 ATATAATAAATATAT
1 ATATAATAAATATAT
62143303 GTAATAATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
ATATAATAAATATATATATAC
Found at i:62143409 original size:17 final size:19
Alignment explanation
Indices: 62143387--62143430 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
62143377 ACAATAATAT
62143387 AAAATA-AT-GATATGTAC
1 AAAATATATAGATATGTAC
*
62143404 AAAATATATATATATGTAC
1 AAAATATATAGATATGTAC
*
62143423 ATAATATA
1 AAAATATA
62143431 GTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (19 bp):
AAAATATATAGATATGTAC
Found at i:62144251 original size:17 final size:16
Alignment explanation
Indices: 62144207--62144247 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
62144197 TTTTTTGTTG
62144207 TTTTTTTTTGCTAGAA
1 TTTTTTTTTGCTAGAA
62144223 TTTTTTTTTGCT-GAAA
1 TTTTTTTTTGCTAG-AA
62144239 TTTTTTTTT
1 TTTTTTTTT
62144248 TGCTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (16 bp):
TTTTTTTTTGCTAGAA
Found at i:62144506 original size:29 final size:29
Alignment explanation
Indices: 62144474--62144588 Score: 117
Period size: 29 Copynumber: 3.9 Consensus size: 29
62144464 GTAATTTTTA
*
62144474 GAAAATTTAGGGTTAAAATGCAATTTAAG
1 GAAAATTTAGGGTTAAAATGAAATTTAAG
* * *
62144503 GAAAGTTTAGGGTCT-AAGTGAAATTTAAA
1 GAAAATTTAGGGT-TAAAATGAAATTTAAG
*
62144532 GAAAGTTTAAGGGTTAAAATGAAATTT-AG
1 GAAAATTT-AGGGTTAAAATGAAATTTAAG
* *
62144561 GAAAAGTTTAGGGGTCAAAATGCAATTT
1 GAAAA-TTTA-GGGTTAAAATGAAATTT
62144589 TTATTTTTTG
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
29 38 0.53
30 34 0.47
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (29 bp):
GAAAATTTAGGGTTAAAATGAAATTTAAG
Found at i:62144555 original size:30 final size:29
Alignment explanation
Indices: 62144473--62144588 Score: 119
Period size: 30 Copynumber: 3.9 Consensus size: 29
62144463 TGTAATTTTT
* *
62144473 AGAAAATTTAGGGTTAAAATGCAATTTAA
1 AGAAAGTTTAGGGTTAAAATGAAATTTAA
* *
62144502 GGAAAGTTTAGGGTCT-AAGTGAAATTTAA
1 AGAAAGTTTAGGGT-TAAAATGAAATTTAA
62144531 AGAAAGTTTAAGGGTTAAAATGAAATTT-A
1 AGAAAGTTT-AGGGTTAAAATGAAATTTAA
* * *
62144560 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AG-AAAGTTTA-GGGTTAAAATGAAATTT
62144589 TTATTTTTTG
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
29 35 0.48
30 38 0.52
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (29 bp):
AGAAAGTTTAGGGTTAAAATGAAATTTAA
Found at i:62144613 original size:24 final size:24
Alignment explanation
Indices: 62144585--62144630 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
62144575 TCAAAATGCA
62144585 ATTTTTATTTTTTGAAAATTTTTT
1 ATTTTTATTTTTTGAAAATTTTTT
*
62144609 ATTTTTATTTTTTTAAAATTTT
1 ATTTTTATTTTTTGAAAATTTT
62144631 GAAAATTAAA
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:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTATTTTTTGAAAATTTTTT
Found at i:62145450 original size:19 final size:19
Alignment explanation
Indices: 62145428--62145484 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
62145418 ATTCCTAATA
*
62145428 TATATTGTATATGTTTATT
1 TATATTGTATATATTTATT
*
62145447 TATATTATGTATATATATATT
1 TATA-T-TGTATATATTTATT
62145468 TAGTA-TGTATATATTTA
1 TA-TATTGTATATATTTA
62145485 GTATTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 15 0.47
20 1 0.03
21 14 0.44
22 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (19 bp):
TATATTGTATATATTTATT
Found at i:62145483 original size:15 final size:15
Alignment explanation
Indices: 62145455--62145488 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
62145445 TTTATATTAT
62145455 GTATATATATATTTA
1 GTATATATATATTTA
*
62145470 GTATGTATATATTTA
1 GTATATATATATTTA
62145485 GTAT
1 GTAT
62145489 TATTATGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
GTATATATATATTTA
Found at i:62145495 original size:21 final size:19
Alignment explanation
Indices: 62145433--62145504 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 19
62145423 TAATATATAT
*
62145433 TGTATATGTTTATTTATATTA
1 TGTATATATTTA-TT-TATTA
* *
62145454 TGTATATATATATTTAGTA
1 TGTATATATTTATTTATTA
62145473 TGTATATATTTAGTATTATTA
1 TGTATATATTTA-T-TTATTA
*
62145494 TGTCTATATTT
1 TGTATATATTT
62145505 TTCATTCCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 15 0.35
20 3 0.07
21 25 0.58
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (19 bp):
TGTATATATTTATTTATTA
Found at i:62145819 original size:14 final size:15
Alignment explanation
Indices: 62145800--62145828 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62145790 GTTATAAATA
62145800 GTTATT-TTTTTAAT
1 GTTATTATTTTTAAT
62145814 GTTATTATTTTTAAT
1 GTTATTATTTTTAAT
62145829 ATGTATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
GTTATTATTTTTAAT
Found at i:62153156 original size:17 final size:17
Alignment explanation
Indices: 62153134--62153168 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
62153124 AACATTCAAG
62153134 TTAATGATATAATTTTA
1 TTAATGATATAATTTTA
62153151 TTAATGATATAATTTTA
1 TTAATGATATAATTTTA
62153168 T
1 T
62153169 CTTTATTTTT
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:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAATGATATAATTTTA
Found at i:62155321 original size:26 final size:25
Alignment explanation
Indices: 62155263--62155323 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
62155253 CCATTAGAAT
*
62155263 AAAAAAATAGAAATTAAAAAACCAA
1 AAAAAAACAGAAATTAAAAAACCAA
62155288 AAATAAAACAGAAA-TAAAAACACACAA
1 AAA-AAAACAGAAATTAAAAA-AC-CAA
62155315 ATAAAAAAC
1 A-AAAAAAC
62155324 CCAAAATCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 9 0.29
26 11 0.35
27 9 0.29
28 2 0.06
ACGTcount: A:0.75, C:0.11, G:0.03, T:0.10
Consensus pattern (25 bp):
AAAAAAACAGAAATTAAAAAACCAA
Found at i:62158661 original size:17 final size:16
Alignment explanation
Indices: 62158618--62158660 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
62158608 GAGAAAAAAG
62158618 AGCAAAAAAAATTTCC
1 AGCAAAAAAAATTTCC
62158634 AGCAAAAAAAATTTCC
1 AGCAAAAAAAATTTCC
62158650 AGCAAAAAAAA
1 AGCAAAAAAAA
62158661 ACAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (16 bp):
AGCAAAAAAAATTTCC
Found at i:62159226 original size:15 final size:16
Alignment explanation
Indices: 62159193--62159226 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
62159183 TTTTATTTGT
62159193 AATTGGTCTAAACAAA
1 AATTGGTCTAAACAAA
*
62159209 AATTGGTCTTAA-AAA
1 AATTGGTCTAAACAAA
62159224 AAT
1 AAT
62159227 AATAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (16 bp):
AATTGGTCTAAACAAA
Found at i:62159238 original size:11 final size:10
Alignment explanation
Indices: 62159220--62159253 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
62159210 ATTGGTCTTA
62159220 AAAAAATAAT
1 AAAAAATAAT
62159230 AATAAAATAAT
1 AA-AAAATAAT
*
62159241 AAAAAATATT
1 AAAAAATAAT
62159251 AAA
1 AAA
62159254 TTTTAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:62159490 original size:17 final size:17
Alignment explanation
Indices: 62159431--62159492 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
62159421 TTCGAATTTA
*
62159431 ATATATATATTTT-T-T
1 ATATATATATTTTGTAC
* *
62159446 ATA-ACTATATTATATAC
1 ATATA-TATATTTTGTAC
62159463 ATATATATATTTTGTAC
1 ATATATATATTTTGTAC
62159480 ATATCAT-TATTTT
1 ATAT-ATATATTTT
62159493 ATATTATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 1 0.03
15 10 0.26
16 1 0.03
17 23 0.61
18 3 0.08
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (17 bp):
ATATATATATTTTGTAC
Found at i:62159633 original size:3 final size:3
Alignment explanation
Indices: 62159625--62159653 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
62159615 TTTATGTACA
62159625 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
62159654 CCAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:62169271 original size:72 final size:73
Alignment explanation
Indices: 62169154--62169907 Score: 879
Period size: 72 Copynumber: 10.1 Consensus size: 73
62169144 TGATGCTTTT
* *
62169154 ATTTCTG-TTTCAAAAATTCAACTCATATTGCAAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
62169218 TAATTTCA
66 TATTTTCA
* * *
62169226 ATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATAAGTTGAGCCTCAAGACACATTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
62169290 TATTTTCA
66 TATTTTCA
* **
62169298 ATATCTGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
1 ATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAG
62169363 GTATTTTCA
65 GTATTTTCA
*
62169372 ATTTCTGTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
1 ATTTCTGTT---TTCA--------AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
* * *
62169437 ACACATTAAAGTATTTTCA
55 ACACGTTGAGGTATTTTCA
* * * * *
62169456 ATTTCTGTTTTC-AAAATTCAATTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGTTAAAG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
62169520 TATTTTCA
66 TATTTTCA
* *
62169528 ATTTCTGTTTTC-AAAATTCAACTGATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
*
62169592 TAATTTCA
66 TATTTTCA
* * *
62169600 ATTTCTGTTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
1 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
62169664 TATTTTCA
66 TATTTTCA
* * *
62169672 ATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACATGC
1 ATTTCTG-TTTTC----AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
62169737 TGAGGTATTTTCA
61 TGAGGTATTTTCA
* * ** * *
62169750 ATTTTTATCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
1 ATTTCTGT-TTTC---AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
*
62169815 GAGGTAATTTCA
62 GAGGTATTTTCA
* * * *** * *
62169827 ATTTTTGTTGTCAAAAAAATCAACTCGTATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCG
1 ATTTCTGTTTTC-AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG--ACACGTTG
62169892 AGGTATTTTCA
63 AGGTATTTTCA
62169903 ATTTC
1 ATTTC
62169908 CATTTTTTAA
Statistics
Matches: 609, Mismatches: 50, Indels: 42
0.87 0.07 0.06
Matches are distributed among these distances:
72 266 0.44
73 16 0.03
74 102 0.17
76 26 0.04
77 66 0.11
78 67 0.11
81 2 0.00
84 64 0.11
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (73 bp):
ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
TATTTTCA
Found at i:62169436 original size:84 final size:85
Alignment explanation
Indices: 62169306--62169464 Score: 266
Period size: 84 Copynumber: 1.9 Consensus size: 85
62169296 CAATATCTGC
** * * *
62169306 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAAAGTATTTTC
62169371 AATTTCTGTTCAATTTATGT
66 AATTTCTGTTCAATTTATGT
62169391 TTTTC-AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAAAGTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAAAGTATTTTC
62169455 AATTTCTGTT
66 AATTTCTGTT
62169465 TTCAAAATTC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 64 0.93
85 5 0.07
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (85 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTAAAGTATTTTC
AATTTCTGTTCAATTTATGT
Found at i:62170039 original size:77 final size:79
Alignment explanation
Indices: 62169909--62170944 Score: 272
Period size: 81 Copynumber: 12.7 Consensus size: 79
62169899 TTCAATTTCC
* * *
62169909 ATTTTTTAATTTCTGCCTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTT-G
1 ATTTTTCAATTTCTGCCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCA
* * *
62169973 GCTCACGCGCTGAGCT
64 GATCACACACTGAGCT
*
62169989 A-TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAG-CTTCAGA
1 ATTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCAGA
* *
62170052 TTACACACTGAGGT
66 TCACACACTGAGCT
* *** * * *
62170066 ATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGCC-TCGG
1 A-TTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCAG
* ** *
62170130 GTCACA-TGTCGAGGT
65 ATCACACACT-GAGCT
* ** * *
62170145 ATTTTCAAAATCTATTTTCAATTTCTGTTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGT
1 ATTTT-----TC-AATTTC--TGCCT-TTCA-AAAAAA--TCAACTCATATTGCGAGAGGTGAGT
* * * *
62170210 TGAGCCTT-GGCTCACACGCTGAGGT
54 TGAGCCTTCAGATCACACACTGAGCT
* * *
62170235 A-TTTTCAATTTATG--TTCGTC--AAAAATCAACTAATATTGTC-AGAGGTGAGTTGAGTC-TC
1 ATTTTTCAATTTCTGCCTT--TCAAAAAAATCAACTCATATTG-CGAGAGGTGAGTTGAGCCTTC
* ** * *
62170293 GGGCCACATACCGAGGTCTTTT
63 AGATCACACACTGA-G-C---T
* *** *
62170315 CAAATTCTGTTTTTAATTTCTATTTTTCAAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTT
1 ---A---T-TTTTCAATTTCTGCCTTTCAAAAAA----ATCAACTCATATTGCGAGAGGTGAGTT
* * * *
62170380 GAGCCTT-GGCTCACACGCTGAGGT
55 GAGCCTTCAGATCACACACTGAGCT
* *
62170404 A-TTTTCAATTTCTG--TTCGTC--AAAAATCAACTCATATTGCGAGAGATGAGTTGAGTC-TC-
1 ATTTTTCAATTTCTGCCTT--TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCA
* *
62170462 GAGC-CACATGCCGAAGTCT
64 GATCACACA--CTG-AG-CT
* *** * *
62170481 -TTTCAAATTCTATTT-TTAATTTCTATTTTTCAAAAA--AACTCAACTCATATTGTGAGAGGTG
1 ATTT----TTCAATTTCTGCCTTTC-A-----AAAAAATCAA--C---TCATATTGCGAGAGGTG
* * * *
62170542 AGTTGAGCC-TCAGGTCACACGCCGAGGT
51 AGTTGAGCCTTCAGATCACACACTGAGCT
** * * * * *
62170570 ATTTTTCAATTTCTGTTTTTTTTAAAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGC-TC
1 ATTTTTCAATTTCTG---CCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTC
* * * * *
62170634 GGGTCACGCACCGAGGT
63 AGATCACACACTGAGCT
* *** * *
62170651 ATTTTTTAATTTCTATTTTTCAAAAAAATCAGCTCATATTAG-GAGAGGTGAGTTGAGCC-TCAA
1 ATTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCCTTCAG
* *
62170714 ATCACGCACTGAGGT
65 ATCACACACTGAGCT
** * *
62170729 A-TTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAACC-TC
1 ATTTTTCAATTTCTGCCTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTC
* * * * *
62170792 GGGTCACACGCCGAGGT
63 AGATCACACACTGAGCT
** * *
62170809 ATTTTTCAATTGT-TGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCC-T
1 ATTTTTCAATT-TCTGCCTTTC---AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
* * *
62170872 CAGGTCACACGCTGAGGT
62 CAGATCACACACTGAGCT
* * *** *
62170890 A-TTTTCAATTTTTTTGGCTTTTTTAAAAATTAACTCATAATT-CGAGAGGTGAGTT
1 ATTTTTCAA--TTTCTGCCTTTCAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTT
62170945 AAACTTCGGG
Statistics
Matches: 740, Mismatches: 123, Indels: 187
0.70 0.12 0.18
Matches are distributed among these distances:
73 3 0.00
74 4 0.01
75 67 0.09
76 7 0.01
77 71 0.10
78 59 0.08
79 112 0.15
80 65 0.09
81 145 0.20
82 10 0.01
83 7 0.01
84 12 0.02
86 15 0.02
87 5 0.01
88 23 0.03
89 6 0.01
90 55 0.07
91 30 0.04
92 2 0.00
93 4 0.01
94 37 0.05
95 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (79 bp):
ATTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTCAGA
TCACACACTGAGCT
Found at i:62170075 original size:79 final size:78
Alignment explanation
Indices: 62169909--62170124 Score: 249
Period size: 79 Copynumber: 2.8 Consensus size: 78
62169899 TTCAATTTCC
* *
62169909 ATTTTTT-AATTTCTGCCTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTG
1 ATTTTTTCAATTTCTGCCTTTC--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTA
* * *
62169973 GCTCACGCGCTGAGCT
63 GATCACACACTGAGCT
*
62169989 A--TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCTTCAGA
1 ATTTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTT-AGA
* *
62170052 TTACACACTGAGGT
65 TCACACACTGAGCT
* *** * *
62170066 ATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATGTGAGTTGAGC
1 ATTTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
62170125 CTCGGGTCAC
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
76 3 0.03
77 46 0.39
78 4 0.03
79 63 0.54
80 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (78 bp):
ATTTTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTAGAT
CACACACTGAGCT
Found at i:62170192 original size:169 final size:165
Alignment explanation
Indices: 62169987--62170900 Score: 802
Period size: 169 Copynumber: 5.5 Consensus size: 165
62169977 ACGCGCTGAG
*
62169987 CTATTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCTTCAGA
1 CTATTTTCAATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGA
* * * *
62170052 TTACACACTGAGGTATTTTTTCAATTTATATTTTTCAAAAAAATCAACTCACATTGCGAGATG-T
64 TCACACGCTGAGGTA--TTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGA-GAT
* *
62170116 GAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAAT
126 GAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATT
* *
62170156 CTATTTTCAATTTCTGTTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTT-GG
1 CTATTTTCAATTTCTGTT--TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTCAG
* ** * *
62170220 CTCACACGCTGAGGTATTTTCAATTTATGTTCGTC--AAAAATCAACTAATATTGTC-AGAGGTG
63 ATCACACGCTGAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTG-CGAGAGATG
* * * *
62170282 AGTTGAGTCTCGGGCCACATACCGAGGTCTTTTCAAATT
127 AGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATT
* * * *
62170321 CTGTTTTTAATTTCTATTTTTCAAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
1 CTATTTTCAATTTC--TGTTTC----AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CT
* * * **
62170386 T-GGCTCACACGCTGAGGTATTTTCAATTTCTGTTCGTC--AAAAATCAACTCATATTGCGAGAG
59 TCAGATCACACGCTGAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAG
* * * * *
62170448 ATGAGTTGAGTCTCGAGCCACATGCCGAAGTCTTTTCAAATT
124 ATGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATT
* * * *
62170490 CTATTTTTAATTTCTATTTTTCAAAAAAACTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAG
1 CTATTTTCAATTTC--TGTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
* * * * * *
62170555 GTCACACGCCGAGGTATTTTTCAATTTCTGTTTTTTTTAAAAAAAATTAACTCATATTACGAGAG
63 ATCACACGCTGAGGTA-TTTTCAATTTATG---TTTTTCAAAAAAATCAACTCATATTGCGAGAG
* ***
62170620 ATGAGTTGAGGCTCGGGTCACGCACCGAGGTA-TTT----TT
124 ATGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCAAATT
* * * * *
62170657 -TAATTTC--TAT-T-TTTCAAAAAAATCAGCTCATATTAG-GAGAGGTGAGTTGAGCCTCAAAT
1 CTATTTTCAATTTCTGTTTCAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCTTCAGAT
* * *
62170716 CACGCACTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATG
65 CACACGCTGAGGTATTTTCAATTTATGTTTTTC---AAAAAAATCAACTCATATTGCGAGAGATG
* *
62170781 AGTTGAACCTCGGGTCACACGCCGAGGTATTTTTC-AATT
127 AGTTGAGCCTCGGGTCACATGCCGAGGTA-TTTTCAAATT
* * *** * * * *
62170820 GT-TGTT---TTTC---AAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAGGTC
1 CTATTTTCAATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
62170878 ACACGCTGAGGTATTTTCAATTT
66 ACACGCTGAGGTATTTTCAATTT
62170901 TTTTGGCTTT
Statistics
Matches: 639, Mismatches: 74, Indels: 72
0.81 0.09 0.09
Matches are distributed among these distances:
155 5 0.01
158 65 0.10
159 43 0.07
160 16 0.03
161 61 0.10
162 2 0.00
163 4 0.01
164 4 0.01
165 77 0.12
166 50 0.08
167 36 0.06
168 1 0.00
169 220 0.34
170 6 0.01
171 3 0.00
172 46 0.07
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (165 bp):
CTATTTTCAATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAGATC
ACACGCTGAGGTATTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGATGAGTT
GAGCCTCGGGTCACATGCCGAGGTATTTTCAAATT
Found at i:62170207 original size:246 final size:243
Alignment explanation
Indices: 62169666--62170245 Score: 697
Period size: 246 Copynumber: 2.4 Consensus size: 243
62169656 TGCTGAGGTA
* ** **
62169666 TTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCC-T--C
1 TTTTCAATTTCTG--CTTC-AAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGC
** * * * *
62169728 AAGACATGCTGAGGTATTTTCAATTTTTATCTTTCAAAAAAAAATCAACTCATATTGCGAGAGGT
63 -TCACACGCTGAGGTATTTTCAATTTCTACCTTTC-AAAAAAAATCAACTCATATTACGAGAGGT
* **
62169793 GAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCGTATT
126 GAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCACATT
**
62169858 GCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAATTTCCAT
191 GCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATCCAT
* * *
62169911 TTTTTAATTTCTGCCTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
1 TTTTCAATTTCTG-C-TTCAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCT
* * *
62169976 CACGCGCTGAGCTATTTTCAATTTCTGCCTTTC-AAAAAAATCAACTCATATTACGAGAGGTGAG
64 CACACGCTGAGGTATTTTCAATTTCTACCTTTCAAAAAAAATCAACTCATATTACGAGAGGTGAG
* * * *
62170040 TTGAGCTTCAGATTACACACTGAGGTATTTTTTCAATTTATAT-TTTTCAAAAAAATCAACTCAC
129 TTGAGCCTCAG--GACACACTGAGGTA--ATTTCAATTT-T-TGTTGTCAAAAAAATCAACTCAC
* * * * *
62170104 ATTGCGAGATGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATCTA-
188 ATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATCCAT
*
62170159 TTTTCAATTTCTG-TTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTC
1 TTTTCAATTTCTGCTTCA-AAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTC
62170223 ACACGCTGAGGTATTTTCAATTT
65 ACACGCTGAGGTATTTTCAATTT
62170246 ATGTTCGTCA
Statistics
Matches: 288, Mismatches: 36, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
244 76 0.26
245 20 0.07
246 102 0.35
247 1 0.00
248 21 0.07
249 67 0.23
250 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (243 bp):
TTTTCAATTTCTGCTTCAAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCTCA
CACGCTGAGGTATTTTCAATTTCTACCTTTCAAAAAAAATCAACTCATATTACGAGAGGTGAGTT
GAGCCTCAGGACACACTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCACATTGCGAG
AGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATCCAT
Found at i:62170259 original size:246 final size:239
Alignment explanation
Indices: 62169664--62170288 Score: 694
Period size: 244 Copynumber: 2.6 Consensus size: 239
62169654 CATGCTGAGG
* **
62169664 TATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCC-T-
1 TATTTTCAATTTCTG--TTTC-AAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG
** * *
62169727 -CAAGACATGCTGAGGTATTTTCAATTTT-TATCTTTCAAAAAAAAATCAACTCATATTGCGAGA
63 GC-TCACACGCTGAGGTATTTTCAATTTTGT-TC--TC--AAAAAAATCAACTCATATTACGAGA
* **
62169790 GGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCGT
122 GGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCAC
**
62169855 ATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAATTTC
187 ATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATC
* * *
62169908 CATTTTTTAATTTCTGCCTTTCAAAAAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTTG
1 TA-TTTTCAATTTCTG--TTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTG
* *
62169973 GCTCACGCGCTGAGCTATTTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTACGAGAGGT
63 GCTCACACGCTGAGGTATTTTCAATTT-TG--TTCTCAAAAAAATCAACTCATATTACGAGAGGT
* * * *
62170037 GAGTTGAGCTTCAGATTACACACTGAGGTATTTTTTCAATTTATAT-TTTTCAAAAAAATCAACT
125 GAGTTGAGCCTCAG--GACACACTGAGGTA--ATTTCAATTT-T-TGTTGTCAAAAAAATCAACT
* * * *
62170101 CACATTGCGAGATGTGAGTTGAGCCTCGGGTCACATGTCGAGGTATTTTCAAAATC
184 CACATTGCGAGAGGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATC
* *
62170157 TATTTTCAATTTCTG-TTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGC
1 TATTTTCAATTTCTGTTTCA-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC
* *
62170221 TCACACGCTGAGGTATTTTCAATTTATGTTCGTC--AAAAATCAACTAATATTGTC-AGAGGTGA
65 TCACACGCTGAGGTATTTTCAATTT-TGTTC-TCAAAAAAATCAACTCATATT-ACGAGAGGTGA
62170283 GTTGAG
127 GTTGAG
62170289 TCTCGGGCCA
Statistics
Matches: 326, Mismatches: 37, Indels: 36
0.82 0.09 0.09
Matches are distributed among these distances:
244 109 0.33
245 22 0.07
246 102 0.31
247 2 0.01
248 21 0.06
249 68 0.21
250 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (239 bp):
TATTTTCAATTTCTGTTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT
CACACGCTGAGGTATTTTCAATTTTGTTCTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTG
AGCCTCAGGACACACTGAGGTAATTTCAATTTTTGTTGTCAAAAAAATCAACTCACATTGCGAGA
GGCGAGTTGAGCCTCAGGTCACACGTCGAGGTATTTTCAAAATC
Found at i:62170309 original size:75 final size:76
Alignment explanation
Indices: 62170157--62170317 Score: 193
Period size: 75 Copynumber: 2.1 Consensus size: 76
62170147 TTTCAAAATC
* * *
62170157 TATTTTCAATTTCTGTTCATCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTTGGCT
1 TATTTTCAATTTATGTTCATC-AAAAAATCAACTAATATTGCAAGAGGTGAGTTGAGCCTGGGCT
* *
62170222 CACACGCTGAGG
65 CACACACCGAGG
* *
62170234 TATTTTCAATTTATGTTCGTC-AAAAATCAACTAATATTGTC-AGAGGTGAGTTGAGTCTCGGGC
1 TATTTTCAATTTATGTTCATCAAAAAATCAACTAATATTG-CAAGAGGTGAGTTGAGCCT-GGGC
*
62170297 -CACATACCGAGG
64 TCACACACCGAGG
*
62170309 TCTTTTCAA
1 TATTTTCAA
62170318 ATTCTGTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 50 0.68
76 4 0.05
77 19 0.26
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (76 bp):
TATTTTCAATTTATGTTCATCAAAAAATCAACTAATATTGCAAGAGGTGAGTTGAGCCTGGGCTC
ACACACCGAGG
Found at i:62170484 original size:75 final size:75
Alignment explanation
Indices: 62170349--62170491 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 75
62170339 TTTCAAAAAA
* * * * * *
62170349 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACACGCCGAAGTATTTTCAAAT
62170414 TCTGTTCGTC
66 TCTGTTCGTC
* * *
62170424 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGTCTCGAGC-CACATGCCGAAGTCTTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCG-GCTCACACGCCGAAGTATTTTCAAA
62170488 TTCT
65 TTCT
62170492 ATTTTTAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 56 0.97
76 2 0.03
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (75 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGGCTCACACGCCGAAGTATTTTCAAAT
TCTGTTCGTC
Found at i:62170566 original size:91 final size:91
Alignment explanation
Indices: 62170424--62170589 Score: 219
Period size: 91 Copynumber: 1.8 Consensus size: 91
62170414 TCTGTTCGTC
* *
62170424 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGTCTCGAGCCACATGCCGAAGT-CTTTTCAAA
1 AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGAGCCACACGCCGAAGTACTTTTCAAA
62170488 TTCTATTTTTAATTTCTATTTTTCAA
66 TTCTATTTTTAATTTCTATTTTTCAA
* * * * *
62170514 AAAAACTCAACTCATATTGTGAGAGGTGAGTTGAGCCTC-AGGTCACACGCCGAGGTATTTTTCA
1 AAAAA-TCAACTCATATTGCGAGAGATGAGTTGAGCCTCGA-GCCACACGCCGAAGTACTTTTCA
* *
62170578 ATTTCTGTTTTT
64 AATTCTATTTTT
62170590 TTTAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
90 6 0.09
91 42 0.66
92 16 0.25
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (91 bp):
AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCGAGCCACACGCCGAAGTACTTTTCAAA
TTCTATTTTTAATTTCTATTTTTCAA
Found at i:62170598 original size:81 final size:81
Alignment explanation
Indices: 62170491--62170900 Score: 453
Period size: 81 Copynumber: 5.2 Consensus size: 81
62170481 TTTCAAATTC
* * * *
62170491 TATTTTT-AATTTC--TATTTTTCAAAAAAACTCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
1 TATTTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
62170553 AGGTCACACGCCGAGG
66 AGGTCACACGCCGAGG
* * * * *
62170569 TATTTTTCAATTTCTGTTTTTTTTAAAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGCTC
1 TATTTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
* * *
62170634 GGGTCACGCACCGAGG
66 AGGTCACACGCCGAGG
* * * *
62170650 TATTTTTTAATTTC--TATTTTT-CAAAAAAATCAGCTCATATTAG-GAGAGGTGAGTTGAGCCT
1 TATTTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTGAGCCT
** * * *
62170711 CAAATCACGCACTGAGG
65 CAGGTCACACGCCGAGG
** * *
62170728 TA-TTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAACCTC
1 TATTTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
*
62170792 GGGTCACACGCCGAGG
66 AGGTCACACGCCGAGG
** * *
62170808 TATTTTTCAATTGT-TGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCT
1 TATTTTTCAATT-TCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
62170872 CAGGTCACACGCTGAGG
65 CAGGTCACACGCCGAGG
62170889 TA-TTTTCAATTT
1 TATTTTTCAATTT
62170901 TTTTGGCTTT
Statistics
Matches: 279, Mismatches: 43, Indels: 19
0.82 0.13 0.06
Matches are distributed among these distances:
77 10 0.04
78 55 0.20
79 18 0.06
80 56 0.20
81 139 0.50
82 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (81 bp):
TATTTTTCAATTTCTGTTTTTTTAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
AGGTCACACGCCGAGG
Found at i:62170793 original size:158 final size:158
Alignment explanation
Indices: 62170493--62170900 Score: 577
Period size: 158 Copynumber: 2.6 Consensus size: 158
62170483 TCAAATTCTA
62170493 TTTTTAATTTCTATTTTTCAAAAAAACTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTC
1 TTTTTAATTTCTATTTTTCAAAAAAA-TCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTC
* *** *
62170558 ACACGCCGAGGTATTTTTCAATTTCTGTTTTTTTTAAAAAAAATTAACTCATATTACGAGAGATG
65 ACACGCTGAGGTA-TTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTACGAGAGATG
** *
62170623 AGTTGAGGCTCGGGTCACGCACCGAGGTAT
129 AGTTGAACCTCGGGTCACACACCGAGGTAT
* **
62170653 TTTTTAATTTCTATTTTTCAAAAAAATCAGCTCATATTAG-GAGAGGTGAGTTGAGCCTCAAATC
1 TTTTTAATTTCTATTTTTCAAAAAAATCAACTCATATT-GTGAGAGGTGAGTTGAGCCTCAGGTC
* * *
62170717 ACGCACTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGA
65 ACACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTACGAGAGATGA
*
62170782 GTTGAACCTCGGGTCACACGCCGAGGTAT
130 GTTGAACCTCGGGTCACACACCGAGGTAT
* * *
62170811 TTTTCAATTGT-TGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAG
1 TTTTTAATT-TCTATTTTTC---AAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAG
62170875 GTCACACGCTGAGGTATTTTCAATTT
62 GTCACACGCTGAGGTATTTTCAATTT
62170901 TTTTGGCTTT
Statistics
Matches: 219, Mismatches: 23, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
158 87 0.40
159 44 0.20
160 28 0.13
161 60 0.27
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (158 bp):
TTTTTAATTTCTATTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCA
CACGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTACGAGAGATGAG
TTGAACCTCGGGTCACACACCGAGGTAT
Found at i:62170918 original size:81 final size:79
Alignment explanation
Indices: 62170506--62170988 Score: 375
Period size: 81 Copynumber: 6.1 Consensus size: 79
62170496 TTAATTTCTA
* * *
62170506 TTTTTCAAAAAAACTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTA
1 TTTTT-AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTA
62170571 TTTTTCAATTTCTGTTT-
65 -TTTTCAATTT-T-TTTG
* * * * * * * *
62170588 TTTTTAAAAAAAATTAACTCATATTACGAGAGATGAGTTGAGGCTCGGGTCACGCACCGAGGTAT
1 TTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTA-
* * *
62170653 TTTTTAA--TTTCTA
65 TTTTCAATTTTTTTG
* * * ** * * *
62170666 TTTTTCAAAAAAATCAGCTCATATTAG-GAGAGGTGAGTTGAGCCTCAAATCACGCACTGAGGTA
1 TTTTTAAAAAAAATCAACTCATATT-GCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTA
*
62170730 TTTTCAA--TTTCTG
65 TTTTCAATTTTTTTG
* *
62170743 TTTTTCAAAAAAAAAATCAACTCATATTGCGAGAGATGAGTTGAA-CCTCGGGTCACACGCCGAG
1 TTTTT---AAAAAAAATCAACTCATATTGCGAGAGGTGAGTT-AAGCCTCAGGTCACACGCCGAG
*
62170807 GTATTTTTCAA--TTGTTG
62 GTA-TTTTCAATTTTTTTG
* *
62170824 TTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTAAGCCTCAGGTCACACGCTGAGG
1 TTTTT---AAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGG
62170889 TATTTTCAATTTTTTTGG
63 TATTTTCAATTTTTTT-G
* * * * *
62170907 CTTTTT--TAAAAATTAACTCATAATT-CGAGAGGTGAGTTAAACTTCGGGT-AGCATC-CCGAG
1 -TTTTTAAAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTAAGCCTCAGGTCA-CA-CGCCGAG
* *
62170967 CTATTTTCAA-TTTCTTG
62 GTATTTTCAATTTTTTTG
62170984 TTTTT
1 TTTTT
62170989 CAATAAAGAA
Statistics
Matches: 336, Mismatches: 49, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
76 5 0.01
77 19 0.06
78 60 0.18
79 50 0.15
80 58 0.17
81 129 0.38
82 9 0.03
83 1 0.00
84 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (79 bp):
TTTTTAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCAGGTCACACGCCGAGGTAT
TTTCAATTTTTTTG
Found at i:62171494 original size:16 final size:16
Alignment explanation
Indices: 62171473--62171516 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
62171463 GAGAAAAAAG
62171473 AGCAAAAAAAAATTCC
1 AGCAAAAAAAAATTCC
*
62171489 AGCAAAAAAAATTTCC
1 AGCAAAAAAAAATTCC
62171505 AGCAAAAAAAAA
1 AGCAAAAAAAAA
62171517 CTAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.66, C:0.16, G:0.07, T:0.11
Consensus pattern (16 bp):
AGCAAAAAAAAATTCC
Found at i:62172087 original size:15 final size:16
Alignment explanation
Indices: 62172054--62172087 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
62172044 TTTTATTTGT
62172054 AATTGGTCTAAACAAA
1 AATTGGTCTAAACAAA
*
62172070 AATTGGTCTTAA-AAA
1 AATTGGTCTAAACAAA
62172085 AAT
1 AAT
62172088 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (16 bp):
AATTGGTCTAAACAAA
Found at i:62179822 original size:25 final size:25
Alignment explanation
Indices: 62179788--62179841 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
62179778 CATAAACATA
62179788 TCATACAAAGCAATAATTACCAAAT
1 TCATACAAAGCAATAATTACCAAAT
*
62179813 TCATACAAAGCAATGATTACCAAAT
1 TCATACAAAGCAATAATTACCAAAT
62179838 TCAT
1 TCAT
62179842 TCATTCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (25 bp):
TCATACAAAGCAATAATTACCAAAT
Found at i:62183264 original size:70 final size:72
Alignment explanation
Indices: 62183150--62183300 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
62183140 GGGGAATCAT
* *
62183150 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
62183214 GATATCG
66 GATATCG
***
62183221 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
62183285 GATATCG
66 GATATCG
62183292 CACTTAGCA
1 CACTTAGCA
62183301 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:62183404 original size:104 final size:103
Alignment explanation
Indices: 62183220--62183442 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
62183210 AATGGATATC
62183220 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
62183285 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
62183323 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
62183388 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
62183427 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
62183443 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:62183804 original size:29 final size:29
Alignment explanation
Indices: 62183771--62183834 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
62183761 TAATCCACCA
62183771 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
62183800 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
62183830 CCCAA
1 CCCAA
62183835 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:62183808 original size:30 final size:30
Alignment explanation
Indices: 62183778--62183834 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
62183768 CCACCCAACT
62183778 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
62183807 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
62183835 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:62187684 original size:180 final size:179
Alignment explanation
Indices: 62187365--62188105 Score: 909
Period size: 180 Copynumber: 4.2 Consensus size: 179
62187355 CATTGGTAAA
* * * * * ***
62187365 AAATTGAAGATCTTATTTCCCTGAAGTTGCAGTGGAGTAGATCTTTGGAGATGGTGAATCTTATC
1 AAATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGGTGAATCTTATC
** * * *
62187430 TCCATGTATCGATAATGGAGCAGATTTTACCACC--AAGCCTTACCTCTCTAAGGTAGCAAGAGA
66 TCCATGTATCGGCAATGGAGCAGA-TTTA-AACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGA
* *
62187493 GTAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
129 GCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* *
62187544 AGAATTAAAGATTTTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCT-AATCTTA
1 A-AATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGG-TGAATCTTA
62187608 TCTCCATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGA
64 TCTCCATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGA
* *
62187673 GCAAGTTGAAGATTGAGTCTTATCTTTCC-GAGGTAGCAAGAAAGCAGACTG
129 GCAAGTTGAAGAATGAGTCTTATC-TTCCTGAGGTAGCAAGGAAGCAGACTG
* * * *
62187724 AAGATTGAAGGTTTTATCTCCCT-AA---ACAGTAGTGGAGCAAATC--GA-AGACGGTGAATCT
1 AA-ATTGAAGATTTTATCTCCCTGAAGTTACA--A-TGGAGCAGATCTTCACAGATGGTGAATCT
* * * *
62187782 TATCTCCGTGTATCGGCAATGGAGCAGATTT-TACCACTAA-CCTCATCTCTCTGAGGTAGCAAG
62 TATCTCCATGTATCGGCAATGGAGCAGATTTAAACC-TTAAGCCTTATCTCTCTGAGGTAGCAAG
* *
62187845 AGAGCAAGTTGAAGAATGAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACCG
126 AGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
* * **
62187899 AAGATTGAAGATTCTATCTCCCTGAAGTTGCAGGGGAGCAGATCTTCACAGATGGCT-AATCTTA
1 AA-ATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGG-TGAATCTTA
* * * *
62187963 TCTCTATGTATCGGTAATGGAGCAGATTTAAGCCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGA
64 TCTCCATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGA
* *
62188028 GCAGGTTGAAGAATGAGTCTCATCTTCCTGAGGTAGCAAGGAAGCAGACTG
129 GCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
62188079 AGAATTGAAGATTTTATCTCCCT-AAGT
1 A-AATTGAAGATTTTATCTCCCTGAAGT
62188106 AGTAGCGGAG
Statistics
Matches: 485, Mismatches: 54, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
174 3 0.01
175 93 0.19
176 57 0.12
177 1 0.00
178 5 0.01
179 64 0.13
180 256 0.53
181 6 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (179 bp):
AAATTGAAGATTTTATCTCCCTGAAGTTACAATGGAGCAGATCTTCACAGATGGTGAATCTTATC
TCCATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGAGC
AAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTG
Found at i:62187706 original size:43 final size:43
Alignment explanation
Indices: 62187648--62187731 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
62187638 AACCTTAAGC
* * *
62187648 CTTATCTCTCTGAGGTAGCAAGAGAGCA-AGTTGAAGATTGAGT
1 CTTATCTCTCCGAGGTAGCAAGAAAGCAGA-CTGAAGATTGAGT
*
62187691 CTTATCTTTCCGAGGTAGCAAGAAAGCAGACTGAAGATTGA
1 CTTATCTCTCCGAGGTAGCAAGAAAGCAGACTGAAGATTGA
62187732 AGGTTTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (43 bp):
CTTATCTCTCCGAGGTAGCAAGAAAGCAGACTGAAGATTGAGT
Found at i:62188075 original size:355 final size:356
Alignment explanation
Indices: 62187417--62188122 Score: 1096
Period size: 355 Copynumber: 2.0 Consensus size: 356
62187407 CTTTGGAGAT
* *
62187417 GGTGAATCTTATCTCCATGTATCGATAATGGAGCAGATTTTACCACCAAGCCTTACCTCTCTAAG
1 GGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
* * *
62187482 GTAGCAAGAGAGTAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAGA
66 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
*
62187547 ATTAAAGATTTTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
131 ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
*
62187612 CATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAGGTAGCAAGAGAGCAA
196 CATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAA
* * *
62187677 GTTGAAGATTGAGTCTTATCTTTCCGAGGTAGCAAGAAAGCAGACTGA-AGATTGAAGGTTTTAT
261 GTTGAAGAATGAGTCTCATCTTTCCGAGGTAGCAAGAAAGCAGACTGAGA-ATTGAAGATTTTAT
*
62187741 CTCCCTAAACAGTAGTGGAGCAAATCGAAGAC
325 CTCCCTAAACAGTAGCGGAGCAAATCGAAGAC
* * * * *
62187773 GGTGAATCTTATCTCCGTGTATCGGCAATGGAGCAGATTTTACCACTAA-CCTCATCTCTCTGAG
1 GGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
*
62187837 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACCGA-A
66 GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
* * **
62187901 GATTGAAGATTCTATCTCCCTGAAGTTGCAGGGGAGCAGATCTTCACAGATGGCTAATCTTATCT
131 -ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCT
* * *
62187966 CTATGTATCGGTAATGGAGCAGATTTAAGCCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGAGCA
195 CCATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGAGCA
* *
62188031 GGTTGAAGAATGAGTCTCATC-TTCCTGAGGTAGCAAGGAAGCAGACTGAGAATTGAAGATTTTA
260 AGTTGAAGAATGAGTCTCATCTTTCC-GAGGTAGCAAGAAAGCAGACTGAGAATTGAAGATTTTA
** *
62188095 TCTCCCTAAGTAGTAGCGGAGCAGATCG
324 TCTCCCTAAACAGTAGCGGAGCAAATCG
62188123 GGGATAACAA
Statistics
Matches: 318, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
354 5 0.02
355 267 0.84
356 46 0.14
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (356 bp):
GGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTACCACCAAGCCTCACCTCTCTAAG
GTAGCAAGAGAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACCGAGA
ATTAAAGATTCTATCTCCCTGAAGTTACAACGGAGCAGATCTTCACAGATGGCTAATCTTATCTC
CATGTATCGGCAATGGAGCAGATTTAAACCTTAAGCCTTATCTCTCTGAAGTAGCAAGAGAGCAA
GTTGAAGAATGAGTCTCATCTTTCCGAGGTAGCAAGAAAGCAGACTGAGAATTGAAGATTTTATC
TCCCTAAACAGTAGCGGAGCAAATCGAAGAC
Found at i:62189220 original size:26 final size:24
Alignment explanation
Indices: 62189189--62189238 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
62189179 TAAATAAAAA
*
62189189 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
62189215 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
62189239 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:62189258 original size:21 final size:21
Alignment explanation
Indices: 62189209--62189267 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
62189199 ATAATAAATC
*
62189209 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
62189229 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
62189251 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
62189268 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:62191898 original size:25 final size:26
Alignment explanation
Indices: 62191856--62191910 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
62191846 ATTTTGGGTT
*
62191856 TTTTATTTGTGTGTTTTT-ATTTCTG
1 TTTTATTTGTGTGTTTTTAATTTCTA
*
62191881 TTTTATTTTTG-GTTTTTTAATTTCTA
1 TTTTATTTGTGTG-TTTTTAATTTCTA
62191907 TTTT
1 TTTT
62191911 TTATTCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.11, C:0.04, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTATTTGTGTGTTTTTAATTTCTA
Found at i:62192996 original size:25 final size:26
Alignment explanation
Indices: 62192954--62193008 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
62192944 ATTTTGGGTT
*
62192954 TTTTATTTGTGTGTTTTT-ATTTCTG
1 TTTTATTTGTGTGTTTTTAATTTCTA
*
62192979 TTTTATTTTTG-GTTTTTTAATTTCTA
1 TTTTATTTGTGTG-TTTTTAATTTCTA
62193005 TTTT
1 TTTT
62193009 TTATTCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.11, C:0.04, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTATTTGTGTGTTTTTAATTTCTA
Found at i:62207541 original size:23 final size:22
Alignment explanation
Indices: 62207489--62207542 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
62207479 ACACAACCGT
62207489 GAATTTTTTGGACTTTTTAACA
1 GAATTTTTTGGACTTTTTAACA
* * *
62207511 GAAATTTTTGTACCTTTTTTACTA
1 GAATTTTTTGGA-CTTTTTAAC-A
62207535 -AATTTTTT
1 GAATTTTTT
62207543 CAAAGTTGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.38
23 15 0.58
24 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (22 bp):
GAATTTTTTGGACTTTTTAACA
Found at i:62214532 original size:21 final size:21
Alignment explanation
Indices: 62214506--62214546 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62214496 AGACGAGCAA
* *
62214506 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
62214527 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
62214547 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:62221089 original size:121 final size:122
Alignment explanation
Indices: 62220963--62221218 Score: 333
Period size: 122 Copynumber: 2.1 Consensus size: 122
62220953 TACCTAACTG
* *
62220963 AATTTTAATACGACATTCTAATAACCTTAT-AATATTAAATAAATAATATTTACTAATTCACTGG
1 AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
** * *
62221027 TC-AGAATTGTGGTCC-CAAAACCACTTTTTCTGACA-TCATTGAAAAT-GAGTTATTACA
66 TCTA-AATTGTGG-CCACAAAACCACGATTTCCGACACT-ACTGAAAATAG-GTTATTACA
* * *
62221084 AATTTTGATATGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCATTGG
1 AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
** *
62221149 TCTAAATTGTGGCCACAAAATTACGATTTCCGACACTACTGAAAATAGGTTGTTACA
66 TCTAAATTGTGGCCACAAAACCACGATTTCCGACACTACTGAAAATAGGTTATTACA
62221206 AATTTTAATACGA
1 AATTTTAATACGA
62221219 AATTGTAGTC
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
121 29 0.25
122 84 0.72
123 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (122 bp):
AATTTTAATACGACACTCTAATAACCTTATAAATATTAAATAAATAATATTTACTAACTCACTGG
TCTAAATTGTGGCCACAAAACCACGATTTCCGACACTACTGAAAATAGGTTATTACA
Found at i:62224070 original size:15 final size:15
Alignment explanation
Indices: 62224052--62224081 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62224042 AAAATAAGGT
62224052 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
*
62224067 TTTTTATAATATTTA
1 TTTTTAAAATATTTA
62224082 AAATCTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:62229867 original size:36 final size:36
Alignment explanation
Indices: 62229820--62229892 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
62229810 AATTAATTAG
62229820 TGAGTATTGTTACAATTGAATTTGCCACATTTATTC
1 TGAGTATTGTTACAATTGAATTTGCCACATTTATTC
*
62229856 TGAGTATTGTTACAATTGAATTTGCCACGTTTATTC
1 TGAGTATTGTTACAATTGAATTTGCCACATTTATTC
62229892 T
1 T
62229893 TTCTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (36 bp):
TGAGTATTGTTACAATTGAATTTGCCACATTTATTC
Found at i:62230505 original size:68 final size:68
Alignment explanation
Indices: 62230391--62230533 Score: 268
Period size: 68 Copynumber: 2.1 Consensus size: 68
62230381 CACTCACTTG
*
62230391 TGGTAGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
1 TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
62230456 GGA
66 GGA
*
62230459 TGGTGGAAACATCTGAGAAGGCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
1 TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
62230524 GGA
66 GGA
62230527 TGGTGGA
1 TGGTGGA
62230534 CTAAGCTTGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 73 1.00
ACGTcount: A:0.28, C:0.12, G:0.32, T:0.28
Consensus pattern (68 bp):
TGGTGGAAACATCTGAGAAGCCAAGTAAGCTTGAGTGTCCCAAGTTTGATGGTAGTGATTTTCGA
GGA
Found at i:62231349 original size:20 final size:18
Alignment explanation
Indices: 62231320--62231364 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
62231310 AACGAAAAGC
62231320 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
62231338 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
62231357 AGGGAAAA
1 AGGGAAAA
62231365 TTGAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:62233883 original size:23 final size:23
Alignment explanation
Indices: 62233801--62233887 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
62233791 CCTGATCAGT
*
62233801 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
62233823 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
62233843 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
62233866 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
62233888 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:62234284 original size:15 final size:15
Alignment explanation
Indices: 62234259--62234316 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
62234249 TCATATATAT
62234259 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
62234275 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
62234290 AATAATTTCAATCAA
1 TATAAATTCAATCAA
62234305 TATAAATTCAAT
1 TATAAATTCAAT
62234317 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:62234576 original size:22 final size:23
Alignment explanation
Indices: 62234551--62234601 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
62234541 CAATTTTCCC
62234551 TTTTCTCCCCT-TCTTTCTTTCT
1 TTTTCTCCCCTCTCTTTCTTTCT
*
62234573 TTTTCTCCCCTGCTCTTTGTTTCT
1 TTTTCTCCCCT-CTCTTTCTTTCT
*
62234597 ATTTC
1 TTTTC
62234602 CTTTCATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.44
24 14 0.56
ACGTcount: A:0.02, C:0.33, G:0.04, T:0.61
Consensus pattern (23 bp):
TTTTCTCCCCTCTCTTTCTTTCT
Found at i:62234636 original size:5 final size:5
Alignment explanation
Indices: 62234623--62234654 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
62234613 TTCTTTAGTT
62234623 TATATA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA T
62234655 TAAAACGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:62234690 original size:8 final size:8
Alignment explanation
Indices: 62234677--62234705 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
62234667 TATCTTTATT
62234677 ATATAATA
1 ATATAATA
62234685 ATATAATA
1 ATATAATA
62234693 ATATAATA
1 ATATAATA
62234701 ATATA
1 ATATA
62234706 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:62239065 original size:23 final size:23
Alignment explanation
Indices: 62239035--62239080 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
62239025 AGGAAAGAAA
62239035 GATAAAGAATCATCATCTTTTTC
1 GATAAAGAATCATCATCTTTTTC
*
62239058 GATAAAGAATCATCATTTTTTTC
1 GATAAAGAATCATCATCTTTTTC
62239081 CCATGCACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (23 bp):
GATAAAGAATCATCATCTTTTTC
Found at i:62241209 original size:46 final size:46
Alignment explanation
Indices: 62241157--62241613 Score: 585
Period size: 46 Copynumber: 10.0 Consensus size: 46
62241147 GCTTTCTGAA
* **
62241157 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGGC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** *
62241203 ATGAAATGAATAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
62241249 ATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACACGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
62241295 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
62241341 ATAAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
62241387 ATGAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*
62241433 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGA-
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
** * ** * ** * *
62241478 CGGGAATGAATAAGACCATGGTTGAAAGATAACATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** * * *
62241524 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGAAACCTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
62241570 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
62241614 TCGAAGATAA
Statistics
Matches: 362, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 36 0.10
46 326 0.90
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:62247295 original size:95 final size:96
Alignment explanation
Indices: 62247132--62247324 Score: 379
Period size: 95 Copynumber: 2.0 Consensus size: 96
62247122 TAATTTAATT
62247132 CTCTAAGGAACTTACACTGGCTGTATTGTATCATAGTCAACGGTTTGATAATATCTGTATTTGGG
1 CTCTAAGGAACTTACACTGGCTGTATTGTATCATAGTCAACGGTTTGATAATATCTGTATTTGGG
62247197 TGTGG-CATGCGTACATGACTATTTGTAAGA
66 TGTGGACATGCGTACATGACTATTTGTAAGA
62247227 CTCTAAGGAACTTACACTGGCTGTATTGTATCATAGTCAACGGTTTGATAATATCTGTATTTGGG
1 CTCTAAGGAACTTACACTGGCTGTATTGTATCATAGTCAACGGTTTGATAATATCTGTATTTGGG
62247292 TGTGGACATGCGTACATGACTATTTGTAAGA
66 TGTGGACATGCGTACATGACTATTTGTAAGA
62247323 CT
1 CT
62247325 GGCCAATCTT
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 70 0.72
96 27 0.28
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (96 bp):
CTCTAAGGAACTTACACTGGCTGTATTGTATCATAGTCAACGGTTTGATAATATCTGTATTTGGG
TGTGGACATGCGTACATGACTATTTGTAAGA
Found at i:62249842 original size:13 final size:13
Alignment explanation
Indices: 62249807--62249843 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
62249797 TGTAATACAT
* *
62249807 AAAATATATAATA
1 AAAAAATATCATA
62249820 AAAAAATATCATA
1 AAAAAATATCATA
62249833 AAAAAATATCA
1 AAAAAATATCA
62249844 ATTTGACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATATCATA
Found at i:62250487 original size:125 final size:125
Alignment explanation
Indices: 62250265--62250518 Score: 508
Period size: 125 Copynumber: 2.0 Consensus size: 125
62250255 GTGGCATAAC
62250265 AATTGCCTCCTTTAGAATCGAAGGGAAAGTTATAAAGTGACTAGCTCTGTACCCATTGAAAACTT
1 AATTGCCTCCTTTAGAATCGAAGGGAAAGTTATAAAGTGACTAGCTCTGTACCCATTGAAAACTT
62250330 AGAACCTAAATGGGCTTAGGCGAGGAGTTTTTTGTATTTTCGTTTTTGCTTGTATTTTGT
66 AGAACCTAAATGGGCTTAGGCGAGGAGTTTTTTGTATTTTCGTTTTTGCTTGTATTTTGT
62250390 AATTGCCTCCTTTAGAATCGAAGGGAAAGTTATAAAGTGACTAGCTCTGTACCCATTGAAAACTT
1 AATTGCCTCCTTTAGAATCGAAGGGAAAGTTATAAAGTGACTAGCTCTGTACCCATTGAAAACTT
62250455 AGAACCTAAATGGGCTTAGGCGAGGAGTTTTTTGTATTTTCGTTTTTGCTTGTATTTTGT
66 AGAACCTAAATGGGCTTAGGCGAGGAGTTTTTTGTATTTTCGTTTTTGCTTGTATTTTGT
62250515 AATT
1 AATT
62250519 TTTAGATTTA
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 129 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (125 bp):
AATTGCCTCCTTTAGAATCGAAGGGAAAGTTATAAAGTGACTAGCTCTGTACCCATTGAAAACTT
AGAACCTAAATGGGCTTAGGCGAGGAGTTTTTTGTATTTTCGTTTTTGCTTGTATTTTGT
Found at i:62253176 original size:37 final size:37
Alignment explanation
Indices: 62253133--62253252 Score: 199
Period size: 37 Copynumber: 3.3 Consensus size: 37
62253123 TATACATGTT
62253133 AGTGATAAGTGGCTACACTTATCTGATCAAGAGACAA
1 AGTGATAAGTGGCTACACTTATCTGATCAAGAGACAA
*
62253170 AGTGATAAGTGGCTACACTTATCTGATCAAGAAACAA
1 AGTGATAAGTGGCTACACTTATCTGATCAAGAGACAA
* *
62253207 AGTGATAGGTGGCTACACTTATCTGATC-AGGGAC-A
1 AGTGATAAGTGGCTACACTTATCTGATCAAGAGACAA
62253242 AGTGATAAGTG
1 AGTGATAAGTG
62253253 ATCATACGTA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.14
36 4 0.05
37 63 0.81
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
AGTGATAAGTGGCTACACTTATCTGATCAAGAGACAA
Found at i:62270245 original size:12 final size:12
Alignment explanation
Indices: 62270228--62270261 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
62270218 CGGCCCACCC
62270228 ATATTAATTTTT
1 ATATTAATTTTT
*
62270240 ATATTATTTTTT
1 ATATTAATTTTT
62270252 ATA-TAATTTT
1 ATATTAATTTT
62270262 AAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:62270423 original size:30 final size:30
Alignment explanation
Indices: 62270387--62270448 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
62270377 CTTAACAAGA
62270387 AAATGTCTATAAAATAATAACAAAATTAAC
1 AAATGTCTATAAAATAATAACAAAATTAAC
*
62270417 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGTCTATAAAATAATAACAAAATTAAC
62270447 AA
1 AA
62270449 TAAATAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGTCTATAAAATAATAACAAAATTAAC
Found at i:62271243 original size:18 final size:17
Alignment explanation
Indices: 62271203--62271258 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
62271193 AATTAAACTC
62271203 AATTCAAATAATTAATTT
1 AATT-AAATAATTAATTT
62271221 AATTATAA-AATTAATTT
1 AATTA-AATAATTAATTT
*
62271238 ATATTAAATAAATAATTT
1 A-ATTAAATAATTAATTT
62271256 AAT
1 AAT
62271259 AAAAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 15 0.44
18 19 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTAAATAATTAATTT
Done.