Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 101 of 235
Found at i:34829500 original size:31 final size:29
Alignment explanation
Indices: 34829465--34829522 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
34829455 TCAGTTCATA
*
34829465 TTTTACATACTTCAACTTCA-CATTTATATTC
1 TTTTACA-ACTT-AA-TTCAGCATATATATTC
34829496 TTTTACAACTTAATTCAGCATATATAT
1 TTTTACAACTTAATTCAGCATATATAT
34829523 ATAATGCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 4 0.16
29 10 0.40
30 4 0.16
31 7 0.28
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTACAACTTAATTCAGCATATATATTC
Found at i:34836018 original size:42 final size:42
Alignment explanation
Indices: 34835972--34836057 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
34835962 AATGAATTTA
*
34835972 TCAGCTTCTGATTAAATTTAATCAATACGATGCTAAGGTGTT
1 TCAGCTTCTGAATAAATTTAATCAATACGATGCTAAGGTGTT
* *
34836014 TCAGCTTCTGAATAAATTTAATGAATACGATGCTAAGGTTTT
1 TCAGCTTCTGAATAAATTTAATCAATACGATGCTAAGGTGTT
34836056 TC
1 TC
34836058 TTTGATTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (42 bp):
TCAGCTTCTGAATAAATTTAATCAATACGATGCTAAGGTGTT
Found at i:34839553 original size:23 final size:23
Alignment explanation
Indices: 34839527--34839574 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
34839517 ATAGAAAGTT
34839527 AAACAAATTCACAAGTAACACTA
1 AAACAAATTCACAAGTAACACTA
34839550 AAACAAATTCACAAGTAACACTA
1 AAACAAATTCACAAGTAACACTA
34839573 AA
1 AA
34839575 TTTATTCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.21, G:0.04, T:0.17
Consensus pattern (23 bp):
AAACAAATTCACAAGTAACACTA
Found at i:34840784 original size:12 final size:12
Alignment explanation
Indices: 34840756--34840786 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34840746 GAGATGAACC
*
34840756 CTATGATGAATT
1 CTATTATGAATT
34840768 CTATTATGAATT
1 CTATTATGAATT
34840780 CTATTAT
1 CTATTAT
34840787 TTGATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (12 bp):
CTATTATGAATT
Found at i:34862504 original size:20 final size:20
Alignment explanation
Indices: 34862450--34862496 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
34862440 CCAAAGGCTG
34862450 AACAGAAGCACATAATGCTA
1 AACAGAAGCACATAATGCTA
34862470 AACAGAAGCACATAATGCTA
1 AACAGAAGCACATAATGCTA
34862490 AACAGAA
1 AACAGAA
34862497 ACCCATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (20 bp):
AACAGAAGCACATAATGCTA
Found at i:34862526 original size:21 final size:21
Alignment explanation
Indices: 34862490--34862551 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
34862480 CATAATGCTA
34862490 AACAGAAACCCATAAGGGTTG
1 AACAGAAACCCATAAGGGTTG
* * * * *
34862511 AACGGAAGCTCATAAGAGCTG
1 AACAGAAACCCATAAGGGTTG
34862532 AACAGAAACCCATAAGGGTT
1 AACAGAAACCCATAAGGGTT
34862552 AAATAGAAGC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
AACAGAAACCCATAAGGGTTG
Found at i:34862541 original size:42 final size:42
Alignment explanation
Indices: 34862490--34862603 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 42
34862480 CATAATGCTA
* * *
34862490 AACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAGCTG
1 AACAGAAACCCATAAGGGTTGAACAGAAGCTCAAAAAAGCTG
* *
34862532 AACAGAAACCCATAAGGGTTAAATAGAAGCTCAAAAAAGCTG
1 AACAGAAACCCATAAGGGTTGAACAGAAGCTCAAAAAAGCTG
* * * * *
34862574 -ATAGAAACTCATATGAGTTGAACAAAAGCT
1 AACAGAAACCCATAAGGGTTGAACAGAAGCT
34862604 AATGAGAGCT
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 23 0.38
42 37 0.62
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AACAGAAACCCATAAGGGTTGAACAGAAGCTCAAAAAAGCTG
Found at i:34862559 original size:21 final size:21
Alignment explanation
Indices: 34862488--34862559 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
34862478 CACATAATGC
34862488 TAAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * * * *
34862509 TGAACGGAAGCTCATAAGAGC
1 TAAACAGAAACCCATAAGGGT
*
34862530 TGAACAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
*
34862551 TAAATAGAA
1 TAAACAGAA
34862560 GCTCAAAAAA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:34889261 original size:67 final size:67
Alignment explanation
Indices: 34889153--34889281 Score: 199
Period size: 67 Copynumber: 1.9 Consensus size: 67
34889143 CACACTCGTT
*
34889153 TCTTAGGCCGTGTGGACATTCGATATGAGGCACACAGTCGTGTCCCAGACC-GTGTAACTCTCCC
1 TCTTAGGCCGTGAGGACATTCGATATGAGGCACACAGTCGTGTCCCAG-CCTGTGTAACTCTCCC
34889217 GAG
65 GAG
* *
34889220 TCTTAGGCCGTGAGGACATTCGATGTGAGGCATAC-GATCGTGTCCCAGCCTGTGTAACTCTC
1 TCTTAGGCCGTGAGGACATTCGATATGAGGCACACAG-TCGTGTCCCAGCCTGTGTAACTCTC
34889282 TAACTTGGGC
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
66 3 0.05
67 54 0.95
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.26
Consensus pattern (67 bp):
TCTTAGGCCGTGAGGACATTCGATATGAGGCACACAGTCGTGTCCCAGCCTGTGTAACTCTCCCG
AG
Found at i:34889415 original size:72 final size:73
Alignment explanation
Indices: 34889298--34889454 Score: 235
Period size: 72 Copynumber: 2.2 Consensus size: 73
34889288 GGGCCGAACA
* **
34889298 GCCAAGACACACGCCCGTCTGCTAGGCCGTGTGAGCATATTAATTTGTGAAATTAAGGTACAGGG
1 GCCAAGCCACACGCCCGTCTGCTAGGCCGTGTGAGCATATTAATTTGTGAAATTAAAATACAGGG
* *
34889363 GTCGCA-T
66 GTCACACG
* * *
34889370 GCCAAGCCACATGCCCGTGTGCTAGGCCGTGTGAGCATATTAATTTGTGAAATTAAAATGCAGGG
1 GCCAAGCCACACGCCCGTCTGCTAGGCCGTGTGAGCATATTAATTTGTGAAATTAAAATACAGGG
34889435 GTCACACG
66 GTCACACG
34889443 GCCAAGCCACAC
1 GCCAAGCCACAC
34889455 ACTTGTGTGC
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
72 64 0.85
73 11 0.15
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (73 bp):
GCCAAGCCACACGCCCGTCTGCTAGGCCGTGTGAGCATATTAATTTGTGAAATTAAAATACAGGG
GTCACACG
Found at i:34889974 original size:42 final size:42
Alignment explanation
Indices: 34889927--34890089 Score: 112
Period size: 42 Copynumber: 3.9 Consensus size: 42
34889917 TCAGAAGCCC
* *
34889927 AAAGGTTGAATAGAAGCACATAAGTGCTAAACAGAAACCCAT
1 AAAGGTTGAACAGAAGCACATAAGAGCTAAACAGAAACCCAT
* * * * **
34889969 AAAGGTTGAACGGAAGCTCATAAGAGCTGAACGGAAACTTAT
1 AAAGGTTGAACAGAAGCACATAAGAGCTAAACAGAAACCCAT
** * * * * * * *
34890011 ACGGGTTAAAAAGAAGCTCAAAAGAGCTTAACGGAAACTCAT
1 AAAGGTTGAACAGAAGCACATAAGAGCTAAACAGAAACCCAT
* * * * *
34890053 -ATGAGTTGAACAGAAGCTCGTGAGAGCTAAACGGAAA
1 AAAG-GTTGAACAGAAGCACATAAGAGCTAAACAGAAA
34890090 GTAAACACGA
Statistics
Matches: 96, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
41 1 0.01
42 95 0.99
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17
Consensus pattern (42 bp):
AAAGGTTGAACAGAAGCACATAAGAGCTAAACAGAAACCCAT
Found at i:34903188 original size:6 final size:6
Alignment explanation
Indices: 34903172--34903206 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
34903162 TTTATGAATT
34903172 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
34903207 GATCTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:34908670 original size:115 final size:116
Alignment explanation
Indices: 34908466--34908697 Score: 394
Period size: 115 Copynumber: 2.0 Consensus size: 116
34908456 GGACAATTAA
*
34908466 ACAAACTTGTTTATTCTTTCAAAAGCACTCACAAAAATCTCATTCCACAATAAACAAATAAATGC
1 ACAAACTTATTTATTCTTTCAAAAGCACTCACAAAAA-CTCATTCCACAATAAACAAATAAATGC
* **
34908531 TCTCAATCCCCTATACAAATCCTATGTAACTCTCTTAATATATAAGAGTTTT
65 TCTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
* *
34908583 ACAAACTTATTTATTCTTTCAAATGCACTCACAAAAA-TCATTCCACAATAAACAAATAAGTGCT
1 ACAAACTTATTTATTCTTTCAAAAGCACTCACAAAAACTCATTCCACAATAAACAAATAAATGCT
34908647 CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
66 CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
34908698 TGAGACTTCC
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
115 74 0.68
117 35 0.32
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (116 bp):
ACAAACTTATTTATTCTTTCAAAAGCACTCACAAAAACTCATTCCACAATAAACAAATAAATGCT
CTCAATCCCCTATACAAAACCTATACAACTCTCTTAATATATAAGAGTTTT
Found at i:34909223 original size:9 final size:9
Alignment explanation
Indices: 34909204--34909249 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
34909194 TTTTACGAAC
34909204 TTTTA-ATT
1 TTTTATATT
34909212 TTTTATATT
1 TTTTATATT
34909221 TTTTATA--
1 TTTTATATT
34909228 TTTTA-ATT
1 TTTTATATT
*
34909236 TTTTATAAT
1 TTTTATATT
34909245 TTTTA
1 TTTTA
34909250 AATTATTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
6 1 0.03
7 5 0.15
8 10 0.30
9 17 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATATT
Found at i:34909231 original size:24 final size:24
Alignment explanation
Indices: 34909204--34909249 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
34909194 TTTTACGAAC
*
34909204 TTTTAATTTTTTATATTTTTTATA
1 TTTTAATTTTTTATAATTTTTATA
34909228 TTTTAATTTTTTATAATTTTTA
1 TTTTAATTTTTTATAATTTTTA
34909250 AATTATTTGT
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:0.00, T:0.74
Consensus pattern (24 bp):
TTTTAATTTTTTATAATTTTTATA
Found at i:34909236 original size:15 final size:17
Alignment explanation
Indices: 34909212--34909247 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
34909202 ACTTTTAATT
34909212 TTTTATATTTTTTAT-A
1 TTTTATATTTTTTATAA
34909228 TTTTA-ATTTTTTATAA
1 TTTTATATTTTTTATAA
34909244 TTTT
1 TTTT
34909248 TAAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATATTTTTTATAA
Found at i:34920426 original size:44 final size:44
Alignment explanation
Indices: 34920304--34920428 Score: 178
Period size: 44 Copynumber: 2.8 Consensus size: 44
34920294 TTGATTTGAG
* * *
34920304 AAAAGGGAAAAACCATGATTGAAAGATATCATGACATTATACTC
1 AAAAAGGAAATACCATGATTGAAAGATATCATGGCATTATACTC
* * *
34920348 AAAAAGGAAATACAATGATTCAAAGATATCATGGCATTATATTC
1 AAAAAGGAAATACCATGATTGAAAGATATCATGGCATTATACTC
* *
34920392 AAAAAGGAAATACCATGGTTGAAAGATATTATGGCAT
1 AAAAAGGAAATACCATGATTGAAAGATATCATGGCAT
34920429 CCCTGAAACA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (44 bp):
AAAAAGGAAATACCATGATTGAAAGATATCATGGCATTATACTC
Found at i:34926852 original size:39 final size:39
Alignment explanation
Indices: 34926798--34926875 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
34926788 TAGCTTGGCG
34926798 ACTCCACTAGGGACAAATAAGAGGGTCAAGCCACGATTT
1 ACTCCACTAGGGACAAATAAGAGGGTCAAGCCACGATTT
*
34926837 ACTCCACTGGGGACAAATAAGAGGGTCAAGCCACGATTT
1 ACTCCACTAGGGACAAATAAGAGGGTCAAGCCACGATTT
34926876 GATTAATTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (39 bp):
ACTCCACTAGGGACAAATAAGAGGGTCAAGCCACGATTT
Found at i:34933325 original size:80 final size:80
Alignment explanation
Indices: 34933208--34933358 Score: 268
Period size: 80 Copynumber: 1.9 Consensus size: 80
34933198 TCATATTGAG
34933208 CAAATATTCTTTTATTCTTTCCATTTCATTCATAATCATACTATAA-AGATAATTATTCTTAGAT
1 CAAATATTCTTTTATTCTTTCCATTTCATTCATAATCATACTATAAGA-ATAATTATTCTTAGAT
34933272 TCTTTTAACTTTCTTT
65 TCTTTTAACTTTCTTT
* *
34933288 CAAATATTCTTTTATTCTTTCCATTTTATTCATAATCATACTATACGAATAATTATTCTTAGATT
1 CAAATATTCTTTTATTCTTTCCATTTCATTCATAATCATACTATAAGAATAATTATTCTTAGATT
34933353 CTTTTA
66 CTTTTA
34933359 TTCTTTGGAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
80 67 0.99
81 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (80 bp):
CAAATATTCTTTTATTCTTTCCATTTCATTCATAATCATACTATAAGAATAATTATTCTTAGATT
CTTTTAACTTTCTTT
Found at i:34934525 original size:19 final size:21
Alignment explanation
Indices: 34934481--34934527 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
34934471 ATTGAGTGGT
34934481 TAATTAGACTTTAATTAAGTA
1 TAATTAGACTTTAATTAAGTA
*
34934502 AAATTAG-C-TTAATTAAG-A
1 TAATTAGACTTTAATTAAGTA
34934520 GTAATTAG
1 -TAATTAG
34934528 TGGAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 1 0.04
21 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATTAGACTTTAATTAAGTA
Found at i:34934742 original size:60 final size:60
Alignment explanation
Indices: 34934649--34934769 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
34934639 GATAAAAATC
*
34934649 TTAGATTTTTTTTCATGAATGTATTATTTAATAAGACTATATATTTATTTTATTATATTG
1 TTAGATTTTTTTTCATGAATGTATTATTTAATAAGACTATATATTTATTTTATTACATTG
34934709 TTAGATTTTTTTTCATGAATGTATTATTTAATAAGACTATATATTTATTTTATTACATTG
1 TTAGATTTTTTTTCATGAATGTATTATTTAATAAGACTATATATTTATTTTATTACATTG
34934769 T
1 T
34934770 AATTTATATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (60 bp):
TTAGATTTTTTTTCATGAATGTATTATTTAATAAGACTATATATTTATTTTATTACATTG
Found at i:34934920 original size:5 final size:5
Alignment explanation
Indices: 34934896--34934951 Score: 58
Period size: 5 Copynumber: 10.6 Consensus size: 5
34934886 AAGAAATTGT
* * *
34934896 TATTA TATGA TATTA TTATTA TATTA TAGTA TATTT TATTATA TATTA
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TA-T-TA TATTA
34934944 TATTA TAT
1 TATTA TAT
34934952 AAATAAGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 32 0.76
6 7 0.17
7 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:34936067 original size:15 final size:15
Alignment explanation
Indices: 34936047--34936103 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
34936037 CAATGAATTT
34936047 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
34936062 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
34936077 ATTGAATTTATATTG
1 ATTGAATTTATATTG
*
34936092 ATTTAA-TTATAT
1 ATTGAATTTATAT
34936104 AATATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:34936198 original size:22 final size:21
Alignment explanation
Indices: 34936162--34936202 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
34936152 TGAAATATAT
34936162 ATTGATTGAAAATATGAGAAA
1 ATTGATTGAAAATATGAGAAA
*
34936183 ATTGATATGAATATATGAGA
1 ATTGAT-TGAAAATATGAGA
34936203 TTGTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTGATTGAAAATATGAGAAA
Found at i:34936514 original size:23 final size:22
Alignment explanation
Indices: 34936488--34936583 Score: 117
Period size: 21 Copynumber: 4.5 Consensus size: 22
34936478 AAGCACTTTA
*
34936488 TGTGTCATATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
34936511 TGTGTCGTATT-AGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
34936532 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
* * **
34936553 TGTGTCGT-TTTAGGCACTTTA
1 TGTGTCGTATTCAGGCACCTCG
34936574 TGTGTCGTAT
1 TGTGTCGTAT
34936584 ACTGATCAGG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
20 1 0.02
21 53 0.82
22 3 0.05
23 8 0.12
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.38
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:34936549 original size:42 final size:42
Alignment explanation
Indices: 34936499--34936583 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
34936489 GTGTCATATT
*
34936499 TCAGGCACCTCGTGTGTCGTATTAGGCACCTCGTGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTATTAGGCACCTCATGTGTCGTA
* * *
34936541 TCAGGCACCTCGTGTGTCGTTTTAGGCACTTTATGTGTCGTA
1 TCAGGCACCTCGTGTGTCGTATTAGGCACCTCATGTGTCGTA
34936583 T
1 T
34936584 ACTGATCAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.35
Consensus pattern (42 bp):
TCAGGCACCTCGTGTGTCGTATTAGGCACCTCATGTGTCGTA
Found at i:34936577 original size:21 final size:21
Alignment explanation
Indices: 34936501--34936583 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
34936491 GTCATATTTC
34936501 AGGCACCTCGTGTGTCGTATT
1 AGGCACCTCGTGTGTCGTATT
*
34936522 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATT
*
34936543 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCGTGTGTCGTATT
* **
34936564 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCGTGTGTCGTAT
34936584 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATT
Found at i:34940508 original size:65 final size:65
Alignment explanation
Indices: 34940404--34940599 Score: 302
Period size: 65 Copynumber: 3.0 Consensus size: 65
34940394 ATCTTACCCA
**
34940404 TATTGAATTTGCTATCTTTGATTAATTTATTCGTTTCGAGCTACACTCTCAATAAATTTCCTTCT
1 TATTGAATTTGCTATCTTTGATTAATTTATTCGTTTCGAGCTATGCTCTCAATAAATTTCCTTCT
* * * *
34940469 TATTGTATTTTCTATATTTGATTAATTTATTCGTTTCGAGCTATGCTCTCAATTAATTTCCTTCT
1 TATTGAATTTGCTATCTTTGATTAATTTATTCGTTTCGAGCTATGCTCTCAATAAATTTCCTTCT
* * * *
34940534 TATTGCATTTGCTATCTTTGATTAATTTATTCATTTCGAGCTATGCTCCCAATCAATTTCCTTCT
1 TATTGAATTTGCTATCTTTGATTAATTTATTCGTTTCGAGCTATGCTCTCAATAAATTTCCTTCT
34940599 T
1 T
34940600 GTCCACTATA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 119 1.00
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.50
Consensus pattern (65 bp):
TATTGAATTTGCTATCTTTGATTAATTTATTCGTTTCGAGCTATGCTCTCAATAAATTTCCTTCT
Found at i:34941232 original size:45 final size:44
Alignment explanation
Indices: 34941120--34941237 Score: 155
Period size: 44 Copynumber: 2.7 Consensus size: 44
34941110 CTACCATAGA
*
34941120 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCTAT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATAT
* * ** *
34941164 TAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATAGT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATA-T
* *
34941209 GGATCTTATTTCCCTGAAGTTGCAGTGGA
1 GAATCTTATCTCCCTGAAGTTGCAGTGGA
34941238 ATAGATTACA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 37 0.59
45 26 0.41
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGATAT
Found at i:34941383 original size:44 final size:43
Alignment explanation
Indices: 34941302--34941478 Score: 153
Period size: 44 Copynumber: 4.1 Consensus size: 43
34941292 AGTTATTATG
* * * *
34941302 ACAATTCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTT
1 ACAAATCTTATATCC-TAAAGTTGCAGTGGAGCAGATTGAAGTT
* * * **
34941346 ACAAATCTCATATCTCTGAAGTTGCAGAGGAGCAGATT--A-CC
1 ACAAATCTTATATC-CTAAAGTTGCAGTGGAGCAGATTGAAGTT
* * * *
34941387 ACAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGAGTGAAGAT
1 ACAAATCTTATAT-CCTAAAGTTGCAGTGGAGCAGATTGAAGTT
* * *
34941431 AGCAAATCTTATTTCCTAAAGTTGCAGTGGAACAGATTAAAGTT
1 A-CAAATCTTATATCCTAAAGTTGCAGTGGAGCAGATTGAAGTT
34941475 ACAA
1 ACAA
34941479 GTCACAAATT
Statistics
Matches: 106, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
41 30 0.28
42 2 0.02
43 4 0.04
44 58 0.55
45 12 0.11
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (43 bp):
ACAAATCTTATATCCTAAAGTTGCAGTGGAGCAGATTGAAGTT
Found at i:34941453 original size:85 final size:85
Alignment explanation
Indices: 34941302--34941469 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
34941292 AGTTATTATG
* * * * * * * *
34941302 ACAATTCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTGAAGTTACAAATCTCATATCTCTGAAG
1 ACAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGAGTGAAGATACAAATCTCATATCTCTAAAG
*
34941367 TTGCAGAGGAGCAGATTACC
66 TTGCAGAGGAACAGATTACC
* *
34941387 ACAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGAGTGAAGATAGCAAATCTTATTTC-CTAAA
1 ACAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGAGTGAAGATA-CAAATCTCATATCTCTAAA
*
34941451 GTTGCAGTGGAACAGATTA
65 GTTGCAGAGGAACAGATTA
34941470 AAGTTACAAG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
85 59 0.84
86 11 0.16
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (85 bp):
ACAAATCTTATCTCCCTAAAGTGGCAGTGGAGCAGAGTGAAGATACAAATCTCATATCTCTAAAG
TTGCAGAGGAACAGATTACC
Found at i:34941650 original size:44 final size:43
Alignment explanation
Indices: 34941548--34941651 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 43
34941538 CCTTATCTCC
* *
34941548 TTGAAGTTGCAGTGGAGCTGGTTAAAAACAACAAATCTTAACT
1 TTGAAGTTGCAGTGGAGCAGATTAAAAACAACAAATCTTAACT
* * * * *
34941591 TCATGAAGATACAGTGGAGCAGATT-AAAGCAACAATTCCTATACCT
1 T--TGAAGTTGCAGTGGAGCAGATTAAAAACAACAAAT-CT-TAACT
34941637 TTGAAGTTGCAGTGG
1 TTGAAGTTGCAGTGG
34941652 GTTGGAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
43 1 0.02
44 22 0.46
45 20 0.42
46 5 0.10
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (43 bp):
TTGAAGTTGCAGTGGAGCAGATTAAAAACAACAAATCTTAACT
Found at i:34946039 original size:20 final size:22
Alignment explanation
Indices: 34946014--34946056 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
34946004 GTAAAATATT
34946014 AAAAAATAAAT-A-TTTTTAAA
1 AAAAAATAAATAATTTTTTAAA
*
34946034 AAAAAATACATAATTTTTTAAA
1 AAAAAATAAATAATTTTTTAAA
34946056 A
1 A
34946057 TTACTTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 9 0.45
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAAATAAATAATTTTTTAAA
Found at i:34951887 original size:17 final size:19
Alignment explanation
Indices: 34951867--34951901 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
34951857 GATGAAGAAC
34951867 TGAAGAA-GAAA-AAGGAA
1 TGAAGAACGAAAGAAGGAA
34951884 TGAAGAACGAAAGAAGGA
1 TGAAGAACGAAAGAAGGA
34951902 GAAGGAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.60, C:0.03, G:0.31, T:0.06
Consensus pattern (19 bp):
TGAAGAACGAAAGAAGGAA
Found at i:34953016 original size:22 final size:24
Alignment explanation
Indices: 34952960--34953016 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
34952950 ACCCAAATTC
* *
34952960 AGTTTAAGTATTTGAAAACATTTT
1 AGTTTAAATATTTGAAAACATTAT
34952984 AGTTTAAATATTTG-AAACA-TAT
1 AGTTTAAATATTTGAAAACATTAT
* *
34953006 ATTTTATATAT
1 AGTTTAAATAT
34953017 ATTAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.38
23 5 0.17
24 13 0.45
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (24 bp):
AGTTTAAATATTTGAAAACATTAT
Found at i:34955003 original size:66 final size:66
Alignment explanation
Indices: 34954897--34955027 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
34954887 CAAAACTTAG
34954897 TAAGAATGGATGATAATACACTGAAGTTTGATAAGAAACAATGCTTTAATTATATATACCAGTTA
1 TAAGAATGGATGATAATACACTGAAGTTTGATAAGAAACAATGCTTTAATTATATATACCAGTTA
34954962 C
66 C
*
34954963 TAAGAATGGATGATAATACACTGAAGTTTGATAAGAAACAATGTTTTAATTATATATACCAGTTA
1 TAAGAATGGATGATAATACACTGAAGTTTGATAAGAAACAATGCTTTAATTATATATACCAGTTA
34955028 GGTTTCTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (66 bp):
TAAGAATGGATGATAATACACTGAAGTTTGATAAGAAACAATGCTTTAATTATATATACCAGTTA
C
Found at i:34958212 original size:25 final size:25
Alignment explanation
Indices: 34958149--34958213 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
34958139 CATGTATCAG
* *
34958149 GAAGCTCAAAAGAGCCAAATATAGG
1 GAAGCTCATAAGAGCCAAATATAGA
** * *
34958174 GAAGCTTGTGAGAGCCAAATATTGA
1 GAAGCTCATAAGAGCCAAATATAGA
*
34958199 GATGCTCATAAGAGC
1 GAAGCTCATAAGAGC
34958214 TAAAAAACAG
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCAAATATAGA
Found at i:34961859 original size:20 final size:18
Alignment explanation
Indices: 34961828--34961864 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
34961818 TAATTAAAGT
34961828 TTAATTAAGTTAATTAGC
1 TTAATTAAGTTAATTAGC
34961846 TTAATTTAAGGTTAATTAG
1 TTAA-TTAA-GTTAATTAG
34961865 GTATAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.46
Consensus pattern (18 bp):
TTAATTAAGTTAATTAGC
Found at i:34962138 original size:19 final size:19
Alignment explanation
Indices: 34962110--34962148 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34962100 TGATATATAG
*
34962110 ATACATATGTACT-AATAAT
1 ATACACATGTA-TAAATAAT
34962129 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
34962148 A
1 A
34962149 AATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 17 0.94
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:34965184 original size:15 final size:15
Alignment explanation
Indices: 34965166--34965195 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34965156 TCATGTTCTG
34965166 TTCTTTCTATTCTTT
1 TTCTTTCTATTCTTT
*
34965181 TTCTTTCTTTTCTTT
1 TTCTTTCTATTCTTT
34965196 CTTTATTTAA
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:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTCTATTCTTT
Found at i:34965268 original size:19 final size:19
Alignment explanation
Indices: 34965244--34965282 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34965234 AATACTTATT
*
34965244 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
34965263 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
34965282 T
1 T
34965283 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:34965329 original size:16 final size:16
Alignment explanation
Indices: 34965305--34965346 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
34965295 ATACACTTGT
34965305 CTTTTTATTTATTATA
1 CTTTTTATTTATTATA
*
34965321 CTTTATA-TTATTATA
1 CTTTTTATTTATTATA
34965336 -TTTTTATTTAT
1 CTTTTTATTTAT
34965347 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTTTTATTTATTATA
Found at i:34965907 original size:15 final size:15
Alignment explanation
Indices: 34965889--34965918 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34965879 TCATGTTCTG
34965889 TTCTTTCTATTCTTT
1 TTCTTTCTATTCTTT
*
34965904 TTCTTTCTTTTCTTT
1 TTCTTTCTATTCTTT
34965919 CTTTATTTAA
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:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTCTATTCTTT
Found at i:34965991 original size:19 final size:19
Alignment explanation
Indices: 34965967--34966005 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34965957 AATACTTATT
*
34965967 TATTATTTA-TACATGTGTA
1 TATTA-TTAGTACATATGTA
34965986 TATTATTAGTACATATGTA
1 TATTATTAGTACATATGTA
34966005 T
1 T
34966006 CCATATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.51
Consensus pattern (19 bp):
TATTATTAGTACATATGTA
Found at i:34966026 original size:723 final size:723
Alignment explanation
Indices: 34964640--34966089 Score: 2900
Period size: 723 Copynumber: 2.0 Consensus size: 723
34964630 CCCGTTAGCT
34964640 ACAAAATTAATACAATTTATAATCATTAATACAGTAAAATTTTCACATTGAATGTTTTAATTTTT
1 ACAAAATTAATACAATTTATAATCATTAATACAGTAAAATTTTCACATTGAATGTTTTAATTTTT
34964705 ATTCAACTTTTGTCTAAATTTCAATTTAGTCCCAAACCGAGACTAACTTTTATTCTTCACATTTA
66 ATTCAACTTTTGTCTAAATTTCAATTTAGTCCCAAACCGAGACTAACTTTTATTCTTCACATTTA
34964770 ACTCAATATTTTCATTCAATTTTCACTTTAAACTAATTTCAACTCTCTAATTTCAGCATAAAACC
131 ACTCAATATTTTCATTCAATTTTCACTTTAAACTAATTTCAACTCTCTAATTTCAGCATAAAACC
34964835 AAAATTTTGAAATTCTTTAATTTAGTCCCTACTATTCAAAACTTATGATTTACTTTACAATTTAA
196 AAAATTTTGAAATTCTTTAATTTAGTCCCTACTATTCAAAACTTATGATTTACTTTACAATTTAA
34964900 TCCTTATTTCACTTCTAACTTGAAATTCTATCAATTTAACCCCTAATTCATCATTTTATTCAACA
261 TCCTTATTTCACTTCTAACTTGAAATTCTATCAATTTAACCCCTAATTCATCATTTTATTCAACA
34964965 TGAATAATATCTAGAAATCTAATAACCTTCAAAATATCAACTTAATTTCATTAAAACTTTGTTTT
326 TGAATAATATCTAGAAATCTAATAACCTTCAAAATATCAACTTAATTTCATTAAAACTTTGTTTT
34965030 AAAACTTCTAAAATATCAAAATTAAGTAAAAATGGCTTGATTAACTTACCAATTTAAACTTCAAG
391 AAAACTTCTAAAATATCAAAATTAAGTAAAAATGGCTTGATTAACTTACCAATTTAAACTTCAAG
34965095 CTCCAAATACCTAGTTTTCCCTTTTTCTTTTCTTTCTCTATTCTTTCTCCCCATTTTCGTTTCAT
456 CTCCAAATACCTAGTTTTCCCTTTTTCTTTTCTTTCTCTATTCTTTCTCCCCATTTTCGTTTCAT
34965160 GTTCTGTTCTTTCTATTCTTTTTCTTTCTTTTCTTTCTTTATTTAACTATTATAATATTATATTA
521 GTTCTGTTCTTTCTATTCTTTTTCTTTCTTTTCTTTCTTTATTTAACTATTATAATATTATATTA
34965225 TTACTAAATAATACTTATTTATTATTTATACATGTGTATATTATTAGTACATATGTATCCATATA
586 TTACTAAATAATACTTATTTATTATTTATACATGTGTATATTATTAGTACATATGTATCCATATA
34965290 TCACCATACACTTGTCTTTTTATTTATTATACTTTATATTATTATATTTTTATTTATAATTATTA
651 TCACCATACACTTGTCTTTTTATTTATTATACTTTATATTATTATATTTTTATTTATAATTATTA
34965355 TTTCTTAA
716 TTTCTTAA
34965363 ACAAAATTAATACAATTTATAATCATTAATACAGTAAAATTTTCACATTGAATGTTTTAATTTTT
1 ACAAAATTAATACAATTTATAATCATTAATACAGTAAAATTTTCACATTGAATGTTTTAATTTTT
34965428 ATTCAACTTTTGTCTAAATTTCAATTTAGTCCCAAACCGAGACTAACTTTTATTCTTCACATTTA
66 ATTCAACTTTTGTCTAAATTTCAATTTAGTCCCAAACCGAGACTAACTTTTATTCTTCACATTTA
34965493 ACTCAATATTTTCATTCAATTTTCACTTTAAACTAATTTCAACTCTCTAATTTCAGCATAAAACC
131 ACTCAATATTTTCATTCAATTTTCACTTTAAACTAATTTCAACTCTCTAATTTCAGCATAAAACC
34965558 AAAATTTTGAAATTCTTTAATTTAGTCCCTACTATTCAAAACTTATGATTTACTTTACAATTTAA
196 AAAATTTTGAAATTCTTTAATTTAGTCCCTACTATTCAAAACTTATGATTTACTTTACAATTTAA
34965623 TCCTTATTTCACTTCTAACTTGAAATTCTATCAATTTAACCCCTAATTCATCATTTTATTCAACA
261 TCCTTATTTCACTTCTAACTTGAAATTCTATCAATTTAACCCCTAATTCATCATTTTATTCAACA
34965688 TGAATAATATCTAGAAATCTAATAACCTTCAAAATATCAACTTAATTTCATTAAAACTTTGTTTT
326 TGAATAATATCTAGAAATCTAATAACCTTCAAAATATCAACTTAATTTCATTAAAACTTTGTTTT
34965753 AAAACTTCTAAAATATCAAAATTAAGTAAAAATGGCTTGATTAACTTACCAATTTAAACTTCAAG
391 AAAACTTCTAAAATATCAAAATTAAGTAAAAATGGCTTGATTAACTTACCAATTTAAACTTCAAG
34965818 CTCCAAATACCTAGTTTTCCCTTTTTCTTTTCTTTCTCTATTCTTTCTCCCCATTTTCGTTTCAT
456 CTCCAAATACCTAGTTTTCCCTTTTTCTTTTCTTTCTCTATTCTTTCTCCCCATTTTCGTTTCAT
34965883 GTTCTGTTCTTTCTATTCTTTTTCTTTCTTTTCTTTCTTTATTTAACTATTATAATATTATATTA
521 GTTCTGTTCTTTCTATTCTTTTTCTTTCTTTTCTTTCTTTATTTAACTATTATAATATTATATTA
34965948 TTACTAAATAATACTTATTTATTATTTATACATGTGTATATTATTAGTACATATGTATCCATATA
586 TTACTAAATAATACTTATTTATTATTTATACATGTGTATATTATTAGTACATATGTATCCATATA
34966013 TCACCATACACTTGTCTTTTTATTTATTATACTTTATATTATTATATTTTTATTTATAATTATTA
651 TCACCATACACTTGTCTTTTTATTTATTATACTTTATATTATTATATTTTTATTTATAATTATTA
34966078 TTTCTTAA
716 TTTCTTAA
34966086 ACAA
1 ACAA
34966090 TAAGCAAATA
Statistics
Matches: 727, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
723 727 1.00
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (723 bp):
ACAAAATTAATACAATTTATAATCATTAATACAGTAAAATTTTCACATTGAATGTTTTAATTTTT
ATTCAACTTTTGTCTAAATTTCAATTTAGTCCCAAACCGAGACTAACTTTTATTCTTCACATTTA
ACTCAATATTTTCATTCAATTTTCACTTTAAACTAATTTCAACTCTCTAATTTCAGCATAAAACC
AAAATTTTGAAATTCTTTAATTTAGTCCCTACTATTCAAAACTTATGATTTACTTTACAATTTAA
TCCTTATTTCACTTCTAACTTGAAATTCTATCAATTTAACCCCTAATTCATCATTTTATTCAACA
TGAATAATATCTAGAAATCTAATAACCTTCAAAATATCAACTTAATTTCATTAAAACTTTGTTTT
AAAACTTCTAAAATATCAAAATTAAGTAAAAATGGCTTGATTAACTTACCAATTTAAACTTCAAG
CTCCAAATACCTAGTTTTCCCTTTTTCTTTTCTTTCTCTATTCTTTCTCCCCATTTTCGTTTCAT
GTTCTGTTCTTTCTATTCTTTTTCTTTCTTTTCTTTCTTTATTTAACTATTATAATATTATATTA
TTACTAAATAATACTTATTTATTATTTATACATGTGTATATTATTAGTACATATGTATCCATATA
TCACCATACACTTGTCTTTTTATTTATTATACTTTATATTATTATATTTTTATTTATAATTATTA
TTTCTTAA
Found at i:34966052 original size:16 final size:16
Alignment explanation
Indices: 34966028--34966069 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
34966018 ATACACTTGT
34966028 CTTTTTATTTATTATA
1 CTTTTTATTTATTATA
*
34966044 CTTTATA-TTATTATA
1 CTTTTTATTTATTATA
34966059 -TTTTTATTTAT
1 CTTTTTATTTAT
34966070 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 12 0.52
16 6 0.26
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
CTTTTTATTTATTATA
Found at i:34966563 original size:27 final size:27
Alignment explanation
Indices: 34966533--34966612 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 27
34966523 CTTTTATCTA
*
34966533 ATAGATTGCCACAAAAACTTCCATTTC
1 ATAGATTGCCACAAAGACTTCCATTTC
*
34966560 ATAGATTGCCATAAAGACTTCCATTTC
1 ATAGATTGCCACAAAGACTTCCATTTC
* ** *
34966587 ATAAATTATCACAAAGGCTTCCATTT
1 ATAGATTGCCACAAAGACTTCCATTT
34966613 TCTAGCGTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.33
Consensus pattern (27 bp):
ATAGATTGCCACAAAGACTTCCATTTC
Found at i:34970555 original size:22 final size:22
Alignment explanation
Indices: 34970527--34970570 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34970517 TTCACAGGCA
*
34970527 AAAAATTGCTCCATTGGAATAG
1 AAAAATTCCTCCATTGGAATAG
34970549 AAAAATTCCTCCATTGGAATAG
1 AAAAATTCCTCCATTGGAATAG
34970571 TCATTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (22 bp):
AAAAATTCCTCCATTGGAATAG
Found at i:34988543 original size:42 final size:42
Alignment explanation
Indices: 34988496--34988583 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
34988486 GAAGCCTAAA
* * * *
34988496 GGTTGAACAGAAGCTCATGAGAGCTAAATAGAAACCCATAAG
1 GGTTGAACAGAAACTCATAAGAGCTAAAAAAAAACCCATAAG
** * *
34988538 GGTTGAATGGAAACTCGTAAGATCTAAAAAAAAACCCATAAG
1 GGTTGAACAGAAACTCATAAGAGCTAAAAAAAAACCCATAAG
34988580 GGTT
1 GGTT
34988584 ACTAGAACTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.43, C:0.15, G:0.23, T:0.19
Consensus pattern (42 bp):
GGTTGAACAGAAACTCATAAGAGCTAAAAAAAAACCCATAAG
Found at i:34989847 original size:29 final size:29
Alignment explanation
Indices: 34989733--34989861 Score: 118
Period size: 29 Copynumber: 4.4 Consensus size: 29
34989723 TGGTCGAAAT
* * * *
34989733 CATCCCTTTTCATATTCGACGGTCATCAC
1 CATCCCTTTTCATATTCAATGATCGTCAC
**
34989762 CATCCCTTTTCATATTCAAT-ATTCGAAAC
1 CATCCCTTTTCATATTCAATGA-TCGTCAC
* * * *
34989791 TATCCCTTTTCATATTCAATGGTTGTCAG
1 CATCCCTTTTCATATTCAATGATCGTCAC
*
34989820 CATCCCTTTTCATAATT-GATGATCGTCAC
1 CATCCCTTTTCAT-ATTCAATGATCGTCAC
*
34989849 CATCCCGTTTCAT
1 CATCCCTTTTCAT
34989862 GGTCGATAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
29 76 0.96
30 3 0.04
ACGTcount: A:0.23, C:0.29, G:0.09, T:0.39
Consensus pattern (29 bp):
CATCCCTTTTCATATTCAATGATCGTCAC
Found at i:34989947 original size:13 final size:13
Alignment explanation
Indices: 34989931--34989955 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34989921 AACATGATAG
34989931 AATTTAAAACACA
1 AATTTAAAACACA
34989944 AATTTAAAACAC
1 AATTTAAAACAC
34989956 TATTCAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (13 bp):
AATTTAAAACACA
Found at i:34993314 original size:16 final size:16
Alignment explanation
Indices: 34993295--34993333 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
34993285 AATTTTTCCC
*
34993295 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
34993311 TTTTTCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
34993327 TCTTTCC
1 TTTTTCC
34993334 CCTGCTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:34993393 original size:16 final size:17
Alignment explanation
Indices: 34993362--34993407 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
34993352 TCATCCTTTC
*
34993362 TTTCTTTTTCTATTCTT
1 TTTCTTTTTATATTCTT
34993379 TTTCTTTTTAT-TTCTT
1 TTTCTTTTTATATTCTT
* *
34993395 TTACTTTATATAT
1 TTTCTTTTTATAT
34993408 ATATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTCTTTTTATATTCTT
Found at i:34993396 original size:10 final size:10
Alignment explanation
Indices: 34993358--34993395 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
34993348 CGTTTCATCC
34993358 TTTCTTTCTT
1 TTTCTTTCTT
34993368 TTTCTATTCTT
1 TTTCT-TTCTT
34993379 TTTCTTT-TT
1 TTTCTTTCTT
34993388 ATTTCTTT
1 -TTTCTTT
34993396 TACTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:34996957 original size:21 final size:20
Alignment explanation
Indices: 34996931--34996970 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
34996921 TTATTTTTAT
34996931 TTATATATAAGAAACATAAAA
1 TTATAT-TAAGAAACATAAAA
* *
34996952 TTATATTTAGAAATATAAA
1 TTATATTAAGAAACATAAA
34996971 CAACTCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (20 bp):
TTATATTAAGAAACATAAAA
Found at i:34997433 original size:15 final size:15
Alignment explanation
Indices: 34997413--34997443 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34997403 AAAACATTTT
34997413 ATATTGTTGATCTAG
1 ATATTGTTGATCTAG
34997428 ATATTGTTGATCTAG
1 ATATTGTTGATCTAG
34997443 A
1 A
34997444 AAAAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
ATATTGTTGATCTAG
Found at i:35006255 original size:20 final size:20
Alignment explanation
Indices: 35006194--35006244 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
35006184 CTGCTTTCAC
*
35006194 TTGCTGACAAATCAAACATT
1 TTGCTAACAAATCAAACATT
35006214 TTGCTAACAAATCAAACATT
1 TTGCTAACAAATCAAACATT
35006234 TTGCT-ACAAAT
1 TTGCTAACAAAT
35006245 TCACAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (20 bp):
TTGCTAACAAATCAAACATT
Found at i:35011075 original size:21 final size:21
Alignment explanation
Indices: 35010995--35011103 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 21
35010985 GCCCGAAGGC
* * *
35010995 TGAACAGAAGCTCATGAGAGC
1 TGAACAGAAACTCATAAGAGT
* * * *
35011016 TAAAAAGAAACCCATAAGGGT
1 TGAACAGAAACTCATAAGAGT
** *
35011037 TGAACAGATGCTCTTAAGAGT
1 TGAACAGAAACTCATAAGAGT
* *
35011058 TGAACAAAAACTCATAAGGGT
1 TGAACAGAAACTCATAAGAGT
* * * *
35011079 TAAACAGAAGCTCAAAAGAGC
1 TGAACAGAAACTCATAAGAGT
35011100 TGAA
1 TGAA
35011104 TGGAAACATA
Statistics
Matches: 62, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (21 bp):
TGAACAGAAACTCATAAGAGT
Found at i:35011098 original size:42 final size:43
Alignment explanation
Indices: 35010997--35011103 Score: 128
Period size: 42 Copynumber: 2.5 Consensus size: 43
35010987 CCGAAGGCTG
* *
35010997 AACAGAAGCTCATGAGAGCT-AAAAAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTGAAAAAGAAACCCATAAGGGTTA
* * * * *
35011039 AACAGATGCTCTTAAGAGTTGAACAA-AAACTCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTGAAAAAGAAACCCATAAGGGTTA
*
35011081 AACAGAAGCTCAAAAGAGCTGAA
1 AACAGAAGCTCATAAGAGCTGAA
35011104 TGGAAACATA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 49 0.92
43 4 0.08
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (43 bp):
AACAGAAGCTCATAAGAGCTGAAAAAGAAACCCATAAGGGTTA
Found at i:35012744 original size:16 final size:16
Alignment explanation
Indices: 35012723--35012758 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
35012713 CTAAAAGACT
35012723 ATGGAAAGGAAATTTA
1 ATGGAAAGGAAATTTA
35012739 ATGG-AAGGAAATTTA
1 ATGGAAAGGAAATTTA
35012754 ATGGA
1 ATGGA
35012759 CTTAAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.25
Consensus pattern (16 bp):
ATGGAAAGGAAATTTA
Found at i:35021107 original size:46 final size:46
Alignment explanation
Indices: 35021023--35021241 Score: 171
Period size: 46 Copynumber: 4.7 Consensus size: 46
35021013 TATGGGAGCC
* *
35021023 AGTGTAAGACCGTGTCTGGGACATGGCATCGGCATTGAGACGAGAGGT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTTGAGACGA-AGGT
* * **
35021071 AGGGTAAGACATGTTTGGGACAT-GCATCGGCCTTGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCTTGAGACG-AAGGT
* * *
35021117 AGTGTAAGACATGTCTAGGACAT-GCGTCGG-CTATGAGATGATA-GT
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCCT-TGAGACGA-AGGT
* * * *
35021162 CAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGAGA-TATGAGC
1 -AGTGTAAGA-CATGTCTGGGACATGGCATCGGCCTTGAGACGAAG-GT
* * *
35021209 AGTGTAAGACAATGTGTGGGATATGACATCGGC
1 AGTGTAAGAC-ATGTCTGGGACATGGCATCGGC
35021242 ACCTTACCCA
Statistics
Matches: 138, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
45 4 0.03
46 86 0.62
47 34 0.25
48 14 0.10
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGGCCTTGAGACGAAGGT
Found at i:35021184 original size:93 final size:93
Alignment explanation
Indices: 35021019--35021242 Score: 224
Period size: 93 Copynumber: 2.4 Consensus size: 93
35021009 ATATTATGGG
* *
35021019 AGCCAGTGTAAGACCGTGTCTGGGACATGGCATCGGCATTGAGACGAGAGGTAGGGTAAGACATG
1 AGCCAGTGTAAGA-CATGTCTAGGACATGGCATCGGCATTGAGACGAGAGGTAGGGTAAGACATG
* * *
35021084 TTTGGGACAT-GCATCGGCCTTGAGACGTA
65 TCTGGGACATGGCATC-GACTTGAGACATA
* * * *
35021113 AGCCAGTGTAAGACATGTCTAGGACAT-GCGTCGGC-TATGAGATGATA-GTCAGTGTAAGACCA
1 AGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCAT-TGAGACGAGAGGT-AGGGTAAGA-CA
* *
35021175 TGTCTGGGACATGGCATCGACTTGAGATATG
63 TGTCTGGGACATGGCATCGACTTGAGACATA
* * * *
35021206 AG-CAGTGTAAGACAATGTGTGGGATATGACATCGGCA
1 AGCCAGTGTAAGAC-ATGTCTAGGACATGGCATCGGCA
35021243 CCTTACCCAC
Statistics
Matches: 107, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
91 3 0.03
92 34 0.32
93 46 0.43
94 24 0.22
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.23
Consensus pattern (93 bp):
AGCCAGTGTAAGACATGTCTAGGACATGGCATCGGCATTGAGACGAGAGGTAGGGTAAGACATGT
CTGGGACATGGCATCGACTTGAGACATA
Found at i:35022567 original size:132 final size:130
Alignment explanation
Indices: 35022032--35022681 Score: 493
Period size: 132 Copynumber: 4.9 Consensus size: 130
35022022 AGAAAATACA
* * * ** * * *
35022032 AGTGAAATTCTGAAGAGATATTCGATTATTTTGACCAAACGGGAAATTGCTACCTAGCACGATAG
1 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGATAG
* * * * * * * *** *
35022097 GGTACTATTCCCCGAACTGCCAAACATCGAACA-CTTCTTTCATTTTAAAGGGCTTTTAAAA-AA
66 GGCACGATT-CTCGAATTGCCAAACATCGAACATC-GCCTTCGTTTTAAA-AATTTTTAAAAGAC
35022160 AGTG
128 A-TG
* *** ** * * * * * * *
35022164 AATGAAATTCCCAAGGGACCTTCGATTGTTTAGACCAAATGAAAAAAGTGCAACCCAAAACGATA
1 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAA-CAAGAAATTGCAACCCAACACGATA
* * * *
35022229 GGGCACGATTCTCAAATCGCCAAACATCGAACAT--CCTTTGTTTTGAAAAGTTTTTAATAA-AC
65 GGGCACGATTCTCGAATTGCCAAACATCGAACATCGCCTTCGTTTT-AAAAATTTTTAA-AAGAC
35022291 ATG
128 ATG
*** * * * * ** *
35022294 AGTGAAAACCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAAATCACAACCCAGCACGATAG
1 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGATAG
* * * * * * *
35022359 GGCATGATTCTCGAATTGTCAAACGTCGAATATTGCCTTCGTTTTAAATGATTTTTAGAAGACAT
66 GGCACGATTCTCGAATTGCCAAACATCGAACATCGCCTTCGTTTTAAA-AATTTTTAAAAGACAT
35022424 G
130 G
* * * * * *
35022425 AGTGAAATTTTGAAGGGATATTTGATTATTTTAAGCAACCAAGAGATTGCAACCCAGCACGTTAG
1 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGATAG
* * * *
35022490 GGCACGATTCTGGGAATTGCCAAATATCGCACATCGCCTTCGTTTTAAAAATTTTTTAAAAGGCA
66 GGCACGATTCT-CGAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAAA-TTTTTAAAAGACA
35022555 TG
129 TG
* * *
35022557 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGAAAACACGAAATTGCAACCCAACACGTTAG
1 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGATAG
* * * * * *
35022622 GGCACTATTCCGCGAATTGTCAAATATCGAATC-TCGTCTTCGTTTTAAAGGATTTTTAAA
66 GGCACGATT-CTCGAATTGCCAAACATCGAA-CATCGCCTTCGTTTTAAA-AATTTTTAAA
35022682 CGAATACTTA
Statistics
Matches: 409, Mismatches: 96, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
129 45 0.11
130 50 0.12
131 89 0.22
132 198 0.48
133 27 0.07
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (130 bp):
AGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGATAG
GGCACGATTCTCGAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAAATTTTTAAAAGACATG
Found at i:35026027 original size:132 final size:132
Alignment explanation
Indices: 35025786--35026036 Score: 364
Period size: 132 Copynumber: 1.9 Consensus size: 132
35025776 ATTTGCAATC
* * *
35025786 TTCAGCCTACTCCGCTGCAACTTTAGGGAGCTAGGTTGGTGGTGTAAATCTGCTTCACTGCAACT
1 TTCAGCCTACTCCACTACAACTTTAGAGAGCTAGGTTGGTGGTGTAAATCTGCTTCACTGCAACT
* * **
35025851 TCAGGAAGACTAGATTCATCGTCTTTGATCTGTTACACTACAACTTTC-GGGAAAAAAGATCTAA
66 TCAGGAAGACAAGATTCAACGTCTTCAATCTGTTACACTACAAC-TTCAGGGAAAAAAGATCTAA
35025915 AAT
130 AAT
*
35025918 TTCAGCCTACTCCACTACAACTTTAGAGAGCTGGGTTGGTGGCT-TAAATCTGCTTCACTGCAAC
1 TTCAGCCTACTCCACTACAACTTTAGAGAGCTAGGTTGGTGG-TGTAAATCTGCTTCACTGCAAC
* *
35025982 TTCAGGAAGCCAAGATTCAACGTCTTCAATCTGCTT-CACTGCAACTTCAGGGAAA
65 TTCAGGAAGACAAGATTCAACGTCTTCAATCTG-TTACACTACAACTTCAGGGAAA
35026037 CAGGATTTGT
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
131 3 0.03
132 100 0.94
133 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
TTCAGCCTACTCCACTACAACTTTAGAGAGCTAGGTTGGTGGTGTAAATCTGCTTCACTGCAACT
TCAGGAAGACAAGATTCAACGTCTTCAATCTGTTACACTACAACTTCAGGGAAAAAAGATCTAAA
AT
Found at i:35038159 original size:132 final size:131
Alignment explanation
Indices: 35037642--35038283 Score: 434
Period size: 132 Copynumber: 4.9 Consensus size: 131
35037632 AAAATACGAG
** * * * * * *
35037642 TGAAATTCCGAAGAGATATTCGATTATTTTGACCAAACGAGAAATTGCTACCCAGCACGATAGGG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGG
* * * * * * * * * ** * **
35037707 TACTATTCCCCGAACTGCCAAACATCGAA-CACTTCTTTCGTTTTAAAGGGCTTTTAAAAAATGT
66 CACGATTCCGCAAATTGCCAAATATCGAATCTC-GCCTTCGTTTTAAA-GATTTTTAAAAGACAT
35037771 GAA
129 GAA
*** * * * * * ** *
35037774 TGAAATTCCCAAGGGATCTTCGATT-GTTTAGGCCAAATGAAAAAAGCGCAACCCAACACGATAG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAG-CAAACG-AGAAATTGCAACCCAACACGTTAG
* * * *
35037838 GGCACGATT-CTCAAATCGCCAAACATCGAA-CAT--CCTTTGTTTTGAAA-AGTTTTTAATAA-
64 GGCACGATTCCGCAAATTGCCAAATATCGAATC-TCGCCTTCGTTTT-AAAGA-TTTTTAA-AAG
*
35037897 ACATGAG
125 ACATGAA
*** * * * * **
35037904 TGAAAACCTAAAGGAATATTCGATTGTTTTGAGCAAACGAGAAA-T-C-A--CAAC-CCATAGGG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGG
* * * *** * * *
35037963 CATGATTCC-CGAATTGTCAAACGCCGAATATTGCCTTCGTTTTAAATGATTTTTAGAAGACATG
66 CACGATTCCGCAAATTGCCAAATATCGAATCTCGCCTTCGTTTTAAA-GATTTTTAAAAGACATG
35038027 AA
130 AA
* * * *
35038029 TGCAATTTTGAAGGGATATTTGATTATTTTAAGCAAACGAGAGATTGCAACCCAGCACGTTAGGG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGG
* *
35038094 CACGATTCCGCAAATTGCCAAATATCGCA-CATCGCCTTCGTTTTAAAGAATTTTTAAAAGGCAT
66 CACGATTCCGCAAATTGCCAAATATCGAATC-TCGCCTTCGTTTTAAAG-ATTTTTAAAAGACAT
*
35038158 GAG
129 GAA
* * *
35038161 TGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGCAGCCCAACACGTTAGGG
1 TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGG
* * * *
35038226 CACTATTCCGCGAATTGTCAAATATCGAATCTCGTCTTCGTTTTAAAGGATTTTTAAA
66 CACGATTCCGCAAATTGCCAAATATCGAATCTCGCCTTCGTTTTAAA-GATTTTTAAA
35038284 TGAATACTTA
Statistics
Matches: 398, Mismatches: 87, Indels: 50
0.74 0.16 0.09
Matches are distributed among these distances:
123 28 0.07
124 10 0.03
125 55 0.14
126 3 0.01
127 2 0.01
128 1 0.00
129 4 0.01
130 45 0.11
131 27 0.07
132 195 0.49
133 28 0.07
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (131 bp):
TGAAATTTTGAAGGGATATTCGATTATTTTAAGCAAACGAGAAATTGCAACCCAACACGTTAGGG
CACGATTCCGCAAATTGCCAAATATCGAATCTCGCCTTCGTTTTAAAGATTTTTAAAAGACATGA
A
Found at i:35039210 original size:12 final size:12
Alignment explanation
Indices: 35039193--35039218 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35039183 AGCGTATTAG
35039193 TATATATGTATA
1 TATATATGTATA
35039205 TATATATGTATA
1 TATATATGTATA
35039217 TA
1 TA
35039219 AATTCAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATATGTATA
Found at i:35052003 original size:22 final size:22
Alignment explanation
Indices: 35051955--35052004 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
35051945 TCCAAGTTTG
* **
35051955 ATATTTTTTAAATATAGTATTT
1 ATATTTTTTAAATATAATACAT
* *
35051977 GTATTTTTTCAATATAATACAT
1 ATATTTTTTAAATATAATACAT
35051999 ATATTT
1 ATATTT
35052005 GATAAATGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (22 bp):
ATATTTTTTAAATATAATACAT
Found at i:35059528 original size:44 final size:44
Alignment explanation
Indices: 35059447--35059536 Score: 101
Period size: 44 Copynumber: 2.0 Consensus size: 44
35059437 AACTGATGTA
* *
35059447 AAGTAGCAGTATGACACACATGGTGCCTCATCGACTCATA-GTCG
1 AAGTAACAGTATGACACACATAGTGCCTCATCGACTCA-AGGTCG
** * **
35059491 AAGTAACAGTATGACACTTATAGTGCCTTATTTACTCAAGGTCG
1 AAGTAACAGTATGACACACATAGTGCCTCATCGACTCAAGGTCG
35059535 AA
1 AA
35059537 ATATCCTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 1 0.03
44 37 0.97
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
AAGTAACAGTATGACACACATAGTGCCTCATCGACTCAAGGTCG
Found at i:35060728 original size:22 final size:22
Alignment explanation
Indices: 35060691--35060737 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
35060681 TCTGTTTCTT
*
35060691 TTTTATGCTTTATTTTGTTT-G
1 TTTTATGCTTTATTTTATTTAG
35060712 TTTTAT-CTTTTATTTTTATTTAG
1 TTTTATGC-TTTA-TTTTATTTAG
35060735 TTT
1 TTT
35060738 ATTATATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.05
21 10 0.45
22 7 0.32
23 4 0.18
ACGTcount: A:0.13, C:0.04, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTATGCTTTATTTTATTTAG
Found at i:35060935 original size:18 final size:19
Alignment explanation
Indices: 35060912--35060961 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
35060902 CAATTAAATA
35060912 ATAATAATAAATAT-TATT
1 ATAATAATAAATATCTATT
35060930 ATAATAATAAATATCTATT
1 ATAATAATAAATATCTATT
*
35060949 -TAATAACAAATAT
1 ATAATAATAAATAT
35060962 AAATATTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATAATAAATATCTATT
Found at i:35060954 original size:42 final size:43
Alignment explanation
Indices: 35060888--35060969 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
35060878 TTCGCTGATC
*
35060888 TAATAATATAATATCAATTAAATAA-TAATAATAAATATTATTA
1 TAATAATATAATATCAATTAAATAACAAAT-ATAAATATTATTA
* *
35060931 TAATAATA-AATATCTATTTAATAACAAATATAAATATTA
1 TAATAATATAATATCAATTAAATAACAAATATAAATATTA
35060970 CAAATGTACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 24 0.69
43 11 0.31
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (43 bp):
TAATAATATAATATCAATTAAATAACAAATATAAATATTATTA
Found at i:35061099 original size:33 final size:32
Alignment explanation
Indices: 35061047--35061118 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 32
35061037 TATTTATCAT
35061047 ATAAAA-ATCTTTTACTAATTA-ATAATAAATA
1 ATAAAATATCTTTTACTAATTATAT-ATAAATA
*
35061078 ATAAAATATCTTTTTATTAATTATATATAAATA
1 ATAAAATATC-TTTTACTAATTATATATAAATA
35061111 ATACAAAT
1 ATA-AAAT
35061119 GTACTCATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 6 0.17
32 3 0.08
33 21 0.58
34 6 0.17
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (32 bp):
ATAAAATATCTTTTACTAATTATATATAAATA
Found at i:35067039 original size:21 final size:21
Alignment explanation
Indices: 35066980--35067044 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
35066970 CAGAAGCAGT
*
35066980 ATACGACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCT-A
** *
35067002 AT-CGACACACGTGGTGCCTA
1 ATACGACACATATAGTGCCTA
*
35067022 ATACAACACATATAGTGCCTA
1 ATACGACACATATAGTGCCTA
35067043 AT
1 AT
35067045 CAGCAAAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
20 3 0.09
21 29 0.85
22 2 0.06
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (21 bp):
ATACGACACATATAGTGCCTA
Found at i:35076682 original size:52 final size:52
Alignment explanation
Indices: 35076621--35076724 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
35076611 CTGATAAGTT
* * *
35076621 AGCTTCACAATGTGTGCAAGATAAGTTTTGTAATTTTCTATGTAATTAGTGG
1 AGCTTCACAATGTGTGCAAGATAAATTATGTAATTTTCAATGTAATTAGTGG
35076673 AGCTTCACAATGTGTGCAAGATAAATTATGTAATTTTCAATGTAATTAGTGG
1 AGCTTCACAATGTGTGCAAGATAAATTATGTAATTTTCAATGTAATTAGTGG
35076725 GAGTAGTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (52 bp):
AGCTTCACAATGTGTGCAAGATAAATTATGTAATTTTCAATGTAATTAGTGG
Found at i:35077439 original size:48 final size:48
Alignment explanation
Indices: 35077368--35077463 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
35077358 ATGGGAGAAG
*
35077368 GGGTTTCAATTTGGTTACTACCTATTTCTATGTGGGTCAAACTCAATA
1 GGGTTTCAATTTGGTTACTACCTATTTCTATATGGGTCAAACTCAATA
35077416 GGGTTTCAATTTGGTTACTACCTATTTCTATATGGGTCAAACTCAATA
1 GGGTTTCAATTTGGTTACTACCTATTTCTATATGGGTCAAACTCAATA
35077464 CAAATGGTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (48 bp):
GGGTTTCAATTTGGTTACTACCTATTTCTATATGGGTCAAACTCAATA
Found at i:35078040 original size:3 final size:3
Alignment explanation
Indices: 35078032--35078064 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
35078022 AACCAAAGCC
35078032 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
35078065 ATGACAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:35079846 original size:3 final size:3
Alignment explanation
Indices: 35079840--35079874 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
35079830 TTATAGCCAT
*
35079840 TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35079875 GGCATATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:35082486 original size:131 final size:131
Alignment explanation
Indices: 35082202--35082706 Score: 337
Period size: 131 Copynumber: 3.8 Consensus size: 131
35082192 TAGAAAATAC
* * * * * *
35082202 GAGTGAAATTCCGAAGGGATCTTCGATTGTTTTGAACAAATGAAAAAGCGCAACCCAGCACGATA
1 GAGTGAAATTCTGAAGGGATATTCTATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
* *
35082267 GGGCACGATTCTCAAATTTCCAAACATCGAACATCGCCTTCGTTTTGAAAGGTTTTTAATAAACA
66 GGGCACGATTCTCAAATTTCCAAACACCGAACATCGCCTTCGTTTTGAAAGGTCTTTAATAAACA
35082332 T
131 T
** * * *
35082333 GAGTGAAAACCTAAAGGAATATTCTATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATA
1 GAGTGAAATTCTGAAGGGATATTCTATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
* * * ** *
35082398 GGGCATGATTC-CTGAATTGT-CAAACCCCGAGTATTGCCTTCGTTTT-AAAGGATCTTTAA-AA
66 GGGCACGATTCTC-AAATT-TCCAAACACCGAACATCGCCTTCGTTTTGAAAGG-TCTTTAATAA
*
35082459 GATAT
128 -ACAT
* * * * * *
35082464 GAGTGAAATTTTGAAGGGATATT-TGATTATTTT-AAGCAGACGAGAAATTGCAACCTAGCACGT
1 GAGTGAAATTCTGAAGGGATATTCT-ATTGTTTTGAA-CAAACGAGAAATCGCAACCCAGCACGA
* * * * * ** * * * *
35082527 TAGGGTACGATTTCGCGAATTGCCAAATATAGCATATCGCCTTCG-TTT-AAGGGATTTTTAA-A
64 TAGGGCACGA-TTCTCAAATTTCCAAACACCGAACATCGCCTTCGTTTTGAAAGG-TCTTTAATA
*
35082589 GGACAT
127 -AACAT
* * * ** * ** ** * * *
35082595 AAGTAAAATTCTAAAGGGACCTTCGATTACTTTGAGTAAACGAGAAATTGCAACCCAACACGTTA
1 GAGTGAAATTCTGAAGGGATATTCTATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
* ** * *
35082660 GGGCACGATTC-CACGAATTACCAAGGATCGAATATCGCCTTCGTTTT
66 GGGCACGATTCTCA--AATTTCCAAACACCGAACATCGCCTTCGTTTT
35082707 AAGGAATTCC
Statistics
Matches: 294, Mismatches: 65, Indels: 29
0.76 0.17 0.07
Matches are distributed among these distances:
129 1 0.00
130 14 0.05
131 250 0.85
132 28 0.10
133 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (131 bp):
GAGTGAAATTCTGAAGGGATATTCTATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
GGGCACGATTCTCAAATTTCCAAACACCGAACATCGCCTTCGTTTTGAAAGGTCTTTAATAAACA
T
Found at i:35088848 original size:26 final size:26
Alignment explanation
Indices: 35088812--35088999 Score: 340
Period size: 26 Copynumber: 7.2 Consensus size: 26
35088802 CATGAAATTC
35088812 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
35088838 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
35088864 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
35088890 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
35088916 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
35088942 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
35088968 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
35088994 TTATCA
1 TTATCA
35089000 ATTTGTATCA
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 158 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:35092575 original size:20 final size:20
Alignment explanation
Indices: 35092550--35092596 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
35092540 AGGATGACAT
35092550 AAATCTACTGAATTAGAGTC
1 AAATCTACTGAATTAGAGTC
35092570 AAATCTACTGAATTAGAGTC
1 AAATCTACTGAATTAGAGTC
35092590 AAATCTA
1 AAATCTA
35092597 ATAAGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (20 bp):
AAATCTACTGAATTAGAGTC
Found at i:35096546 original size:32 final size:32
Alignment explanation
Indices: 35096508--35096568 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
35096498 TTATTATTCT
35096508 TATACTTATATT-TTTTATATTTTAATTTTTTA
1 TATACTTATATTATTTT-TATTTTAATTTTTTA
* * *
35096540 TATACTTTTGTTATTTTTATTTTTATTTT
1 TATACTTATATTATTTTTATTTTAATTTT
35096569 GCTATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 21 0.84
33 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (32 bp):
TATACTTATATTATTTTTATTTTAATTTTTTA
Found at i:35096568 original size:5 final size:6
Alignment explanation
Indices: 35096550--35096583 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
35096540 TATACTTTTG
35096550 TTATTT TTATTT TTATTT TGCTATTT TTATTT TT
1 TTATTT TTATTT TTATTT T--TATTT TTATTT TT
35096584 TTCTTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:35096568 original size:20 final size:20
Alignment explanation
Indices: 35096545--35096583 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
35096535 TTTTATATAC
*
35096545 TTTTGTTATTTTTATTTTTA
1 TTTTGCTATTTTTATTTTTA
35096565 TTTTGCTATTTTTATTTTT
1 TTTTGCTATTTTTATTTTT
35096584 TTCTTCTTTT
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:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTGCTATTTTTATTTTTA
Found at i:35096610 original size:17 final size:17
Alignment explanation
Indices: 35096551--35096610 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
35096541 ATACTTTTGT
*
35096551 TATTTTTATTTTTATTTTG
1 TATTTTTA-TTTT-TTTCG
*
35096570 CTATTTTTATTTTTTTCT
1 -TATTTTTATTTTTTTCG
*
35096588 TCTTTTT-TTTTCTTTCG
1 TATTTTTATTTT-TTTCG
35096605 TATTTT
1 TATTTT
35096611 ATTATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.12
17 15 0.44
18 3 0.09
19 4 0.12
20 8 0.24
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.78
Consensus pattern (17 bp):
TATTTTTATTTTTTTCG
Found at i:35096698 original size:20 final size:21
Alignment explanation
Indices: 35096673--35096716 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
35096663 TTTATTATTG
*
35096673 TTTTTTATTTTTATTTTT-AT
1 TTTTTTATCTTTATTTTTAAT
*
35096693 TTTTTTATCTTTCTTTTTAAT
1 TTTTTTATCTTTATTTTTAAT
35096714 TTT
1 TTT
35096717 GTTTTAGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTATCTTTATTTTTAAT
Found at i:35117356 original size:17 final size:19
Alignment explanation
Indices: 35117334--35117368 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35117324 CTAAAATAGT
35117334 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
35117351 AACAAAAGTTATACAATA
1 AACAAAAGTTATACAATA
35117369 TCCAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:35126785 original size:21 final size:20
Alignment explanation
Indices: 35126761--35126803 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
35126751 AGCTGAACGT
35126761 AAACCCAT-TAGGGTTAAACTG
1 AAACCCATATA-GGTT-AACTG
*
35126782 AAACTCATATAGGTTAACTG
1 AAACCCATATAGGTTAACTG
35126802 AA
1 AA
35126804 GCTCATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (20 bp):
AAACCCATATAGGTTAACTG
Found at i:35129457 original size:18 final size:18
Alignment explanation
Indices: 35129417--35129472 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
35129407 AAATTACAAA
*
35129417 AAAAATCAAAATAATTT-T
1 AAAATTCAAAAT-ATTTAT
35129435 CAAAATTCAAAATATTTAT
1 -AAAATTCAAAATATTTAT
*
35129454 AAAATATCCAAA-ATTTAT
1 AAAAT-TCAAAATATTTAT
35129472 A
1 A
35129473 CTTTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTCAAAATATTTAT
Found at i:35130222 original size:20 final size:22
Alignment explanation
Indices: 35130197--35130245 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
35130187 TTAAAAAATC
35130197 TTAAAAATAAATA-TAAAT-TA
1 TTAAAAATAAATATTAAATATA
*
35130217 TTAAAAA-ATATATTAAATATA
1 TTAAAAATAAATATTAAATATA
35130238 TTAAAAAT
1 TTAAAAAT
35130246 TATGTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAAATAAATATTAAATATA
Found at i:35130223 original size:21 final size:21
Alignment explanation
Indices: 35130199--35130244 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35130189 AAAAAATCTT
35130199 AAAAATAAATATAAAT-TATTA
1 AAAAATAAAT-TAAATATATTA
*
35130220 AAAAATATATTAAATATATTA
1 AAAAATAAATTAAATATATTA
35130241 AAAA
1 AAAA
35130245 TTATGTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATAAATTAAATATATTA
Found at i:35138707 original size:15 final size:15
Alignment explanation
Indices: 35138687--35138720 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35138677 ATTGAAAATT
35138687 AAATATAGAGTTAAA
1 AAATATAGAGTTAAA
**
35138702 AAATATAGTTTTAAA
1 AAATATAGAGTTAAA
35138717 AAAT
1 AAAT
35138721 TTAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (15 bp):
AAATATAGAGTTAAA
Found at i:35138858 original size:3 final size:3
Alignment explanation
Indices: 35138850--35138878 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35138840 AGATTAAGAG
35138850 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35138879 GTTTTCTATT
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):
ATT
Found at i:35140311 original size:48 final size:46
Alignment explanation
Indices: 35140210--35140317 Score: 130
Period size: 48 Copynumber: 2.3 Consensus size: 46
35140200 TCACTTGTGT
* * * *
35140210 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCATATTATGT
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGACATATGACGA
35140256 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATC-GACAT-TGAGACGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGACATAT--GACGA
35140304 GAGCTAGTGTAAGA
1 GAGCTAGTGTAAGA
35140318 GCTAGTGTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
46 15 0.28
47 18 0.33
48 21 0.39
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.24
Consensus pattern (46 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGACATATGACGA
Found at i:35140320 original size:12 final size:12
Alignment explanation
Indices: 35140303--35140329 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35140293 CATTGAGACG
35140303 AGAGCTAGTGTA
1 AGAGCTAGTGTA
35140315 AGAGCTAGTGTA
1 AGAGCTAGTGTA
35140327 AGA
1 AGA
35140330 CATGTCTGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
AGAGCTAGTGTA
Found at i:35140441 original size:46 final size:45
Alignment explanation
Indices: 35140321--35140443 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 45
35140311 TGTAAGAGCT
**
35140321 AGTGTAAGACATGTCTGGGACATGCATTAGCTTCGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGATGT-AGCC
*
35140367 AGTGTAAGACATGTCTGGGACATGCATCGGCTGT-GAGATGT-GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCT-TCGAGATGTAGCC
*
35140411 AGTGTAAAACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
35140444 ACCCTACCCC
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
44 10 0.14
45 14 0.20
46 45 0.64
47 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGATGTAGCC
Found at i:35146545 original size:21 final size:20
Alignment explanation
Indices: 35146508--35146546 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
35146498 CCCATGTTGC
*
35146508 CCCATTTTCTCTATTTTTGG
1 CCCATTTTCGCTATTTTTGG
*
35146528 CCCATTTCTCGCTCTTTTT
1 CCCATTT-TCGCTATTTTT
35146547 ACTCTCCTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.54
Consensus pattern (20 bp):
CCCATTTTCGCTATTTTTGG
Found at i:35148831 original size:42 final size:42
Alignment explanation
Indices: 35148783--35148867 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
35148773 ATTTTTATTA
*
35148783 CTTAATTTATTATATTTAGTCCGACAAGATTTTTGTTTAAAT
1 CTTAATTTATTATAGTTAGTCCGACAAGATTTTTGTTTAAAT
* *
35148825 CTTAATTTATTATAGTTAGTTCGATAAGATTTTTGTTTAAAT
1 CTTAATTTATTATAGTTAGTCCGACAAGATTTTTGTTTAAAT
35148867 C
1 C
35148868 GTCGAACTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.51
Consensus pattern (42 bp):
CTTAATTTATTATAGTTAGTCCGACAAGATTTTTGTTTAAAT
Found at i:35167718 original size:32 final size:32
Alignment explanation
Indices: 35167614--35167720 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 32
35167604 GGTGTACATT
* **
35167614 CCTTTCCAAGTGGTACACACAAAGTATACATTT
1 CCTTTTCAA-TGGTACACACAAAGTATACATAA
* *
35167647 CCTTTTCATATGGTATACACAAAGTATACCTAA
1 CCTTTTCA-ATGGTACACACAAAGTATACATAA
* * *
35167680 CATTTTCAACT-GTACACACAAGGTGTACATAA
1 CCTTTTCAA-TGGTACACACAAAGTATACATAA
35167712 CCTTTTCAA
1 CCTTTTCAA
35167721 ATTGTACCAT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
32 26 0.43
33 34 0.56
34 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (32 bp):
CCTTTTCAATGGTACACACAAAGTATACATAA
Found at i:35169140 original size:22 final size:22
Alignment explanation
Indices: 35169109--35169150 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35169099 ACTATCATTT
35169109 TCTAAATAAAATAATAATAATA
1 TCTAAATAAAATAATAATAATA
* *
35169131 TCTAAGTAAAATATTAATAA
1 TCTAAATAAAATAATAATAA
35169151 AATAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (22 bp):
TCTAAATAAAATAATAATAATA
Found at i:35170676 original size:43 final size:43
Alignment explanation
Indices: 35170615--35170834 Score: 293
Period size: 43 Copynumber: 5.1 Consensus size: 43
35170605 ATGTGATTTC
* *
35170615 GATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCGTT
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATT
* * *
35170658 GATATGTGATTACGTGTAAGACCACGTCTGGGACATTGACATC
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATT
* * *
35170701 GATATGTGATTACATGTAAGACCACGTCTAGGATGTTGGCATT
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATT
* * *
35170744 GATACGTGATTACGTGTAAGACC-CTGTCTGGAACAG-TGGCATC
1 GATATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATT
*
35170787 GATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATT
35170830 G-TATG
1 GATATG
35170835 ATATGTGTGA
Statistics
Matches: 152, Mismatches: 21, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
42 6 0.04
43 144 0.95
44 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.30
Consensus pattern (43 bp):
GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATT
Found at i:35170758 original size:86 final size:86
Alignment explanation
Indices: 35170613--35170830 Score: 339
Period size: 86 Copynumber: 2.5 Consensus size: 86
35170603 ATATGTGATT
* * * *
35170613 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCGTTGATATGTGATTACGTGTAAG
1 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATTGATACGTGATTACGTGTAAG
* *
35170678 ACCAC-GTCTGGGACATTGACA
66 ACC-CTGTCTGGAACAGTGACA
* *
35170699 TCGATATGTGATTACATGTAAGACCACGTCTAGGATGTTGGCATTGATACGTGATTACGTGTAAG
1 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATTGATACGTGATTACGTGTAAG
*
35170764 ACCCTGTCTGGAACAGTGGCA
66 ACCCTGTCTGGAACAGTGACA
35170785 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATTG
1 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATTG
35170831 TATGATATGT
Statistics
Matches: 120, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
85 1 0.01
86 119 0.99
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (86 bp):
TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCATTGATACGTGATTACGTGTAAG
ACCCTGTCTGGAACAGTGACA
Found at i:35172016 original size:10 final size:10
Alignment explanation
Indices: 35172003--35172041 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
35171993 ATATGTGAAT
35172003 ATATCATGGC
1 ATATCATGGC
35172013 ATATCATGTGC
1 ATATCATG-GC
*
35172024 ATATCATGGT
1 ATATCATGGC
35172034 ATATCATG
1 ATATCATG
35172042 TACAAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (10 bp):
ATATCATGGC
Found at i:35172029 original size:21 final size:21
Alignment explanation
Indices: 35172003--35172042 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35171993 ATATGTGAAT
35172003 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
*
35172024 ATATCATGGTATATCATGT
1 ATATCATGGCATATCATGT
35172043 ACAAAAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:35172108 original size:25 final size:25
Alignment explanation
Indices: 35172080--35172130 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
35172070 ATAACATAAC
* * *
35172080 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCAAAAAGGTCATTTTCA
35172105 CCTAGGGGCAAAAAGGTCATTTTCA
1 CCTAGGGGCAAAAAGGTCATTTTCA
35172130 C
1 C
35172131 ATTATAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (25 bp):
CCTAGGGGCAAAAAGGTCATTTTCA
Found at i:35179744 original size:24 final size:25
Alignment explanation
Indices: 35179717--35179768 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
35179707 GCCTAGCCTC
*
35179717 TTTTAAT-AACTC-GGGCAAAGCCCT
1 TTTTAATAAAC-CGGGGCAAAACCCT
*
35179741 TTTTAGTAAACCGGGGCAAAACCCT
1 TTTTAATAAACCGGGGCAAAACCCT
35179766 TTT
1 TTT
35179769 AGCACTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACCGGGGCAAAACCCT
Found at i:35179828 original size:10 final size:10
Alignment explanation
Indices: 35179815--35179853 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
35179805 ATATGTGAAT
35179815 ATATCATGGC
1 ATATCATGGC
35179825 ATATCATGTGC
1 ATATCATG-GC
35179836 ATATCATGGC
1 ATATCATGGC
35179846 ATATCATG
1 ATATCATG
35179854 TACAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:35179841 original size:21 final size:21
Alignment explanation
Indices: 35179815--35179854 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35179805 ATATGTGAAT
35179815 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
35179836 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
35179855 ACAAAAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:35179939 original size:24 final size:25
Alignment explanation
Indices: 35179894--35179943 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
35179884 ATAACATAAC
* *
35179894 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCATAAAGGTCATTTTCA
35179919 CCTAGGGGCA-AAAGGTCATTTTCA
1 CCTAGGGGCATAAAGGTCATTTTCA
35179943 C
1 C
35179944 ATTATAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (25 bp):
CCTAGGGGCATAAAGGTCATTTTCA
Found at i:35182317 original size:33 final size:33
Alignment explanation
Indices: 35182275--35182341 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
35182265 TATATAAGTA
35182275 TACATATATGTGAATCTTGTTTGATATGCTTTG
1 TACATATATGTGAATCTTGTTTGATATGCTTTG
35182308 TACATATATGTGAATCTTGTTTGATATGCTTTG
1 TACATATATGTGAATCTTGTTTGATATGCTTTG
35182341 T
1 T
35182342 TAAGGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (33 bp):
TACATATATGTGAATCTTGTTTGATATGCTTTG
Found at i:35185060 original size:6 final size:6
Alignment explanation
Indices: 35185049--35185083 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
35185039 AGGTTTCCAA
*
35185049 AAATGG AAATGG AAAATGA AAATGG AAATGG AAAT
1 AAATGG AAATGG -AAATGG AAATGG AAATGG AAAT
35185084 TTACAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:35185066 original size:13 final size:13
Alignment explanation
Indices: 35185048--35185083 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
35185038 TAGGTTTCCA
35185048 AAAATGGAAATGG
1 AAAATGGAAATGG
*
35185061 AAAATGAAAATGG
1 AAAATGGAAATGG
35185074 -AAATGGAAAT
1 AAAATGGAAAT
35185084 TTACAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (13 bp):
AAAATGGAAATGG
Found at i:35187178 original size:30 final size:30
Alignment explanation
Indices: 35187078--35187180 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 30
35187068 GTTATTTATA
* **
35187078 TATAATATATATGGGTTTTGGTGTTATA--
1 TATAATATATTTGGGTCATGGTGTTATATG
* **
35187106 TATAATATATGTACGTGCATGGGTGTTATATG
1 TATAATATATTTGGGT-CAT-GGTGTTATATG
*
35187138 AATAATATATTTGGGTCATGGTGTTATATG
1 TATAATATATTTGGGTCATGGTGTTATATG
35187168 TATAATATATTTG
1 TATAATATATTTG
35187181 CGTGGGTCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 13 0.21
29 1 0.02
30 32 0.52
31 3 0.05
32 12 0.20
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (30 bp):
TATAATATATTTGGGTCATGGTGTTATATG
Found at i:35189705 original size:17 final size:18
Alignment explanation
Indices: 35189672--35189705 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35189662 ATGTGACATG
*
35189672 CCCGTGTGGGCCTACACC
1 CCCGTGTGGGCCCACACC
35189690 CCCGTGT-GGCCCACAC
1 CCCGTGTGGGCCCACAC
35189706 GACCCAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.47, G:0.26, T:0.15
Consensus pattern (18 bp):
CCCGTGTGGGCCCACACC
Found at i:35197322 original size:6 final size:6
Alignment explanation
Indices: 35197295--35197332 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
35197285 GATATGAAAC
* *
35197295 AAATAA ATATAA AAA-AA GAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAA
35197333 ATTTACCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:35198911 original size:26 final size:25
Alignment explanation
Indices: 35198868--35198922 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
35198858 TATGCTACAT
*
35198868 TTTTACATATTATCTTATGTA-TATA
1 TTTTACATATTATATTATGTACT-TA
*
35198893 TTTTATATATATATATTATGTACTTA
1 TTTTACATAT-TATATTATGTACTTA
35198919 TTTT
1 TTTT
35198923 TAGTGTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 16 0.62
27 1 0.04
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTACATATTATATTATGTACTTA
Found at i:35212361 original size:47 final size:47
Alignment explanation
Indices: 35212287--35212651 Score: 255
Period size: 48 Copynumber: 7.7 Consensus size: 47
35212277 AAGGTATAAT
* * *
35212287 GTTGATGCCATGTCTCGGACATAGTCTTACACTGGCTCATC-TATCAA
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATATCAA
* * * * *
35212334 GTTGATGTCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAG
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-ATATC-AA
** * * *
35212383 GCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATC-C
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--CATATCAA
* * * * * * *
35212431 GTGCTGATGTCATATCCCAGACATGGTCTAATACTGACACCTC-TAT-AC
1 GT--TGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATATCAA
* * *
35212479 GTTCCGATGCCATGTCCCAGACATGGTCTTACACTGACACATCTTAT--A
1 GTT--GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATATCAA
* * * *
35212527 GTTGATG-CATGTCCCAGACAT-GTTTTACACTAGCTCTCGTCTCAA
1 GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAA
** ***
35212572 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTG
1 -GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-ATCAA
35212621 GTTGATG-CATGTCCCAGACAT-GTCTTACACT
1 GTTGATGCCATGTCCCAGACATGGTCTTACACT
35212652 AGCACACAAA
Statistics
Matches: 249, Mismatches: 50, Indels: 39
0.74 0.15 0.12
Matches are distributed among these distances:
43 4 0.02
44 11 0.04
45 15 0.06
46 22 0.09
47 61 0.24
48 65 0.26
49 38 0.15
50 30 0.12
51 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GTTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAA
Found at i:35212467 original size:99 final size:97
Alignment explanation
Indices: 35212336--35212513 Score: 241
Period size: 99 Copynumber: 1.8 Consensus size: 97
35212326 TCTATCAAGT
* *
35212336 TGATGTCATGTCCCAGACATGGTCTTACACTGACTA-TCGAAATCGAGGCCGACGCCATGTCCCA
1 TGATGTCATATCCCAGACATGGTCTAACACTGAC-ACTCGAAA-CG-GGCCGACGCCATGTCCCA
35212400 GACATGGTCTTACACTAGCTCTCACATATCCGTGC
63 GACATGGTCTTACACTAGCTCTCACATATCCGTGC
* * * ** *
35212435 TGATGTCATATCCCAGACATGGTCTAATACTGACACCTCTATACGTTCCGATGCCATGTCCCAGA
1 TGATGTCATATCCCAGACATGGTCTAACACTGACA-CTCGAAACGGGCCGACGCCATGTCCCAGA
35212500 CATGGTCTTACACT
65 CATGGTCTTACACT
35212514 GACACATCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
98 32 0.46
99 33 0.48
100 4 0.06
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (97 bp):
TGATGTCATATCCCAGACATGGTCTAACACTGACACTCGAAACGGGCCGACGCCATGTCCCAGAC
ATGGTCTTACACTAGCTCTCACATATCCGTGC
Found at i:35212605 original size:92 final size:93
Alignment explanation
Indices: 35212290--35212654 Score: 282
Period size: 92 Copynumber: 3.8 Consensus size: 93
35212280 GTATAATGTT
* * * * *
35212290 GATGCCATGTCTCGGACATAGTCTTACACTG--GCTCATCTATCAAGTTGATGTCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACTCATATAT--AGTTGATG-CATGTCCCAGA
* ** * *
35212353 CATGGTCTTACACT-GACTATCGAAATCGAGGCC
63 CAT-GTCTTACACTAG-CTCTCG-TCTCAATGCC
* * * * *
35212386 GACGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCACATATCCGTGCTGATGTCATATCCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGA-CACTCATATAT-AGT--TGATG-CATGTCCCA
* * * *
35212450 GACATGGTCTAATACT-GACAC-C-TCT-ATACGTTCC
61 GACAT-GTCTTACACTAG-CTCTCGTCTCA-A--TGCC
35212484 GATGCCATGTCCCAGACATGGTCTTACACTGACACATC-T-TATAGTTGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACAC-TCATATATAGTTGATGCATGTCCCAGACA
*
35212547 TGTTTTACACTAGCTCTCGTCTCAATGCC
65 TGTCTTACACTAGCTCTCGTCTCAATGCC
* * * *
35212576 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTTGATGCATGTCCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTGACACTCAT-ATATAGTTGATGCATGTCCCAGACA
35212641 TGTCTTACACTAGC
65 TGTCTTACACTAGC
35212655 ACACAAATGA
Statistics
Matches: 218, Mismatches: 34, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
91 2 0.01
92 46 0.21
93 15 0.07
94 44 0.20
95 1 0.00
96 30 0.14
97 5 0.02
98 41 0.19
99 34 0.16
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (93 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACACTCATATATAGTTGATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCGTCTCAATGCC
Found at i:35212611 original size:48 final size:47
Alignment explanation
Indices: 35212290--35212651 Score: 224
Period size: 47 Copynumber: 7.6 Consensus size: 47
35212280 GTATAATGTT
* * * **
35212290 GATGCCATGTCTCGGACATAGTCTTACACTGGCTCATCTATCAA-GTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATCAATGCC
* * * * * *
35212337 GATGTCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--TATCAATGCC
* * ** *
35212386 GACGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--C-TATCAATGCC
* * * * * * * *
35212436 GATGTCATATCCCAGACATGGTCTAATACTGACACCTCTAT-ACGTTCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCTATCA-ATGCC
* * **
35212484 GATGCCATGTCCCAGACATGGTCTTACACTGACACATCT-T--ATAGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCTATCAAT-GCC
* * *
35212530 GATG-CATGTCCCAGACAT-GTTTTACACTAGCTCTCGTCTCAATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-TATCAATGCC
**
35212576 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC-AT-AATGTGGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATCAA--T-GCC
35212624 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
35212652 AGCACACAAA
Statistics
Matches: 246, Mismatches: 51, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
43 2 0.01
44 12 0.05
45 18 0.07
46 22 0.09
47 62 0.25
48 62 0.25
49 33 0.13
50 32 0.13
51 3 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCTATCAATGCC
Found at i:35215425 original size:46 final size:46
Alignment explanation
Indices: 35215373--35215636 Score: 368
Period size: 46 Copynumber: 5.7 Consensus size: 46
35215363 AGTGTGCTCT
* * *
35215373 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
35215419 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
35215465 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
35215511 GTGACATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
35215557 GTGACATGAAATGAATAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
35215603 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGA
1 CTGACATG-AAATGAGTAAGACCATGGTTGAAAGA
35215637 CACTATGGAT
Statistics
Matches: 207, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 206 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (46 bp):
CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Done.