Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 291 of 325
Found at i:89436006 original size:17 final size:19
Alignment explanation
Indices: 89435908--89435998 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
89435898 AATCATATCT
89435908 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89435927 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
89435945 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
89435962 TCTAAGATTGCATGTCATA
1 TCTAAGATTGCATATCATA
89435981 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
89435999 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 35 0.52
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:89436154 original size:21 final size:20
Alignment explanation
Indices: 89436117--89436155 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
89436107 TTGGACTTCG
**
89436117 TTTTTTTTTGGGTTTATTAT
1 TTTTTTTTTGGACTTATTAT
89436137 TTTTGTTTTTGGACTTATT
1 TTTT-TTTTTGGACTTATT
89436156 TCTGGGCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTGGACTTATTAT
Found at i:89436403 original size:45 final size:45
Alignment explanation
Indices: 89436348--89436621 Score: 277
Period size: 45 Copynumber: 6.1 Consensus size: 45
89436338 GGAAGGCGAT
* * * * *
89436348 ATCTGCTATCTTTGATCTGCTCTCCGTCTAATATAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
*
89436393 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
89436438 ATCTGTT-TCTTCAATCTACTCCCCGTCTAATACAGAGATACCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * *
89436482 ATCTGTTATCTCCGATTTACTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * * *
89436527 ATCTGTCATCTTAGATCTG--CCTCGATGTAA-ACAAATAAAGGTCAG
1 ATCTGTTATCTTCGATCTGCTCCCCG-TCTAATAC--AGAGATGCCAA
*
89436572 ATCTGCTATATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
89436619 ATC
1 ATC
89436622 ATCTTGGATC
Statistics
Matches: 187, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
43 6 0.03
44 44 0.24
45 106 0.57
46 1 0.01
47 20 0.11
48 4 0.02
49 6 0.03
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:89436483 original size:89 final size:89
Alignment explanation
Indices: 89436362--89436532 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 89
89436352 GCTATCTTTG
* * * * * *
89436362 ATCTGCTCTCCGTCTAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
89436427 AGAGACGCCAAATCTGTTTCTTCA
66 AGAGACGCCAAATCTGTTTCTTCA
* *
89436451 ATCTACTCCCCGTCTAATACAGAGATACCAAATCTGTTATCTCCGATTTACTCCCCGTCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
*
89436516 AGAGATGCCAAATCTGT
66 AGAGACGCCAAATCTGT
89436533 CATCTTAGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.30
Consensus pattern (89 bp):
ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTATCTCCGATCTACTCCCCGTCTAATAC
AGAGACGCCAAATCTGTTTCTTCA
Found at i:89436693 original size:78 final size:78
Alignment explanation
Indices: 89436564--89437088 Score: 811
Period size: 78 Copynumber: 6.7 Consensus size: 78
89436554 TAAACAAATA
* *
89436564 AAGGTCAGATCTGCTATATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
89436629 ATCTGCTTCAATG
66 ATCTGCTTCAATG
* * *
89436642 AAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATTATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
89436706 GATCTGCTTCAATG
65 GATCTGCTTCAATG
* * *
89436720 AAGGTTAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGATATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
89436785 ATCTGCTTCAATA
66 ATCTGCTTCAATG
*
89436798 AAGATCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
89436863 ATCTGCTTTAATG
66 ATCTGCTTCAATG
* * * *
89436876 AAGGTCAGATCTACTGTGTCTTTGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
89436941 -TCTGCATCAATG
66 ATCTGCTTCAATG
*
89436953 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
89437018 ATCTGCTTCAATA
66 ATCTGCTTCAATG
* * * * **
89437031 AAGGTTAGATCTGCTATGTCTTCGATCTGTTCTCCGTCGAATATGGAGATGCCAAATC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
89437089 TGTTTCTTCG
Statistics
Matches: 409, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
77 73 0.18
78 334 0.82
79 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:89437058 original size:233 final size:234
Alignment explanation
Indices: 89436560--89437088 Score: 873
Period size: 233 Copynumber: 2.3 Consensus size: 234
89436550 GATGTAAACA
* *
89436560 AATAAAGGTCAGATCTGCTATATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 AATAAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
**
89436625 TTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTTGATCTGCTCCCCGTCTAATACAGAG
66 TTGGATCTGCTTCAATGAAGGTCCAATCTACTATGTCTTTGATCTGCTCCCCGTCTAATACAGAG
* * *
89436690 ATGCCAAATTATCTTGGATCTGCTTCAATGAAGGTTAGATCTGCTGTGTCTTCGATCTGCTCCCC
131 ATGCCAAATCATCTTGGATCTGCATCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCC
*
89436755 GTCTAATACAGATATGCCAAATCATCTTGGATCTGCTTC
196 GTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
*
89436794 AATAAAGATCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
1 AATAAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
* * *
89436859 TTGGATCTGCTTTAATGAAGGT-CAGATCTACTGTGTCTTTGATCTGCTCCCTGTCTAATACAGA
66 TTGGATCTGCTTCAATGAAGGTCCA-ATCTACTATGTCTTTGATCTGCTCCCCGTCTAATACAGA
89436923 GATGCCAAATCATCTTGG-TCTGCATCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCC
130 GATGCCAAATCATCTTGGATCTGCATCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCC
89436987 CGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
195 CGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
* * * * **
89437027 AATAAAGGTTAGATCTGCTATGTCTTCGATCTGTTCTCCGTCGAATATGGAGATGCCAAATC
1 AATAAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
89437089 TGTTTCTTCG
Statistics
Matches: 275, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
233 140 0.51
234 135 0.49
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (234 bp):
AATAAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
TTGGATCTGCTTCAATGAAGGTCCAATCTACTATGTCTTTGATCTGCTCCCCGTCTAATACAGAG
ATGCCAAATCATCTTGGATCTGCATCAATGAAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCC
GTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTC
Found at i:89437372 original size:40 final size:40
Alignment explanation
Indices: 89437313--89437390 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
89437303 CAAATATGTT
* * *
89437313 TCTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCA
1 TCTTCGATCTACTCCCTGACAATACAGAGATGCCAAATCA
89437353 TCTTCGATCTACTCCCTGACAATACAGAGATGCCAAAT
1 TCTTCGATCTACTCCCTGACAATACAGAGATGCCAAAT
89437391 TTGCTATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (40 bp):
TCTTCGATCTACTCCCTGACAATACAGAGATGCCAAATCA
Found at i:89437499 original size:217 final size:219
Alignment explanation
Indices: 89437031--89437580 Score: 786
Period size: 217 Copynumber: 2.5 Consensus size: 219
89437021 TGCTTCAATA
* *
89437031 AAGGTTAGATCTGCTATGTCTTCGATCTGTTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
* ** * * *
89437096 TCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGTTTCAGCGTAAACATGT
66 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGACTCACCGCAAACATGA
* * * *
89437161 GAAAGCCAAATCTGCTATATCTTCAATCTGCTCCTTTTCAATGCAAGGATGCCAAATCATCTTGG
131 GAAAGCCAAATCTGC-ATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTAG
*
89437226 ATCTACTTCGATGTGAAGACATCCG
195 ATCTACTTCGATGTGAAAACATCCG
*
89437251 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATATGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
* *
89437316 TCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTCGATCT-ACTC-CCTGACAATACA
66 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGACTCACC-G-CAA-ACA
* * **
89437379 -GAG-ATGCCAAATTTGC-TATCTTTGATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTT
128 TGAGAAAGCCAAATCTGCATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTT
**
89437441 AGATCTACTTCGATGTGAAAATGTCCG
193 AGATCTACTTCGATGTGAAAACATCCG
89437468 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
* * ** *
89437533 TCGATTTGTTCTCTGATAATACAGAGAAGTTAAATCATCTTGGATCTG
66 TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTG
89437581 CTTCAGCGTA
Statistics
Matches: 297, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
217 169 0.57
218 1 0.00
219 14 0.05
220 110 0.37
221 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.34
Consensus pattern (219 bp):
AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
TCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGACTCACCGCAAACATGA
GAAAGCCAAATCTGCATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTAGA
TCTACTTCGATGTGAAAACATCCG
Found at i:89446163 original size:22 final size:21
Alignment explanation
Indices: 89446128--89446221 Score: 65
Period size: 17 Copynumber: 4.7 Consensus size: 21
89446118 AAAAGGTATC
* *
89446128 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
89446149 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
89446172 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
89446191 T--ATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
89446208 TGCATATCATATCT
1 TACAAATCATATCT
89446222 AAGATTGCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
17 17 0.27
19 17 0.27
21 4 0.06
22 15 0.24
23 10 0.16
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:89446171 original size:23 final size:22
Alignment explanation
Indices: 89446128--89446185 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
89446118 AAAAGGTATC
* *
89446128 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
89446149 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
89446172 TGCATATCATATCT
1 TACAAATCATATCT
89446186 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:89446208 original size:36 final size:37
Alignment explanation
Indices: 89446156--89446236 Score: 132
Period size: 36 Copynumber: 2.2 Consensus size: 37
89446146 GATTACAAAA
89446156 TCATATC-T-TCTAAGATTGCATATCATATCTAAGAT
1 TCATATCATATCTAAGATTGCATATCATATCTAAGAT
89446191 T-ATATCATATCTAAGATTGCATATCATATCTAAGAT
1 TCATATCATATCTAAGATTGCATATCATATCTAAGAT
89446227 TGCATATCAT
1 T-CATATCAT
89446237 TGAAGATTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
34 5 0.12
35 2 0.05
36 28 0.67
38 7 0.17
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (37 bp):
TCATATCATATCTAAGATTGCATATCATATCTAAGAT
Found at i:89446243 original size:36 final size:36
Alignment explanation
Indices: 89446167--89446244 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
89446157 CATATCTTCT
*
89446167 AAGATTGCATATCATATCTAAGATTATATCATATCT
1 AAGATTGCATATCATATCTAAGATTATATCATATCG
89446203 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTGCATATCATATCTAAGATT--ATATCATATCG
89446239 AAGATT
1 AAGATT
89446245 ATATTTCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 31 0.79
37 1 0.03
38 7 0.18
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (36 bp):
AAGATTGCATATCATATCTAAGATTATATCATATCG
Found at i:89446244 original size:17 final size:19
Alignment explanation
Indices: 89446164--89446236 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
89446154 AATCATATCT
89446164 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89446183 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
89446200 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89446219 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
89446237 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.33
19 35 0.67
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:89446393 original size:21 final size:20
Alignment explanation
Indices: 89446355--89446394 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89446345 TTGGACTTCG
**
89446355 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
89446375 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
89446395 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:89451309 original size:5 final size:5
Alignment explanation
Indices: 89451295--89451336 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
89451285 GGTTGTTGTG
*
89451295 AAAA- AAAAT AAAAT AAAAT AAAAT AAAGAA AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AA
89451337 CACACAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:89455760 original size:5 final size:5
Alignment explanation
Indices: 89455750--89455787 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
89455740 ATTTGTGAAA
89455750 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AA
89455788 CACACAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:89455770 original size:15 final size:16
Alignment explanation
Indices: 89455750--89455787 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
89455740 ATTTGTGAAA
89455750 AAAATAAAAT-AAAAT
1 AAAATAAAATAAAAAT
89455765 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
89455781 AAAATAA
1 AAAATAA
89455788 CACACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:89456707 original size:26 final size:26
Alignment explanation
Indices: 89456678--89456733 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
89456668 TGGTACAAAT
89456678 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89456704 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89456730 TGAT
1 TGAT
89456734 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89471328 original size:36 final size:36
Alignment explanation
Indices: 89471288--89471360 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
89471278 TAATTGACTT
89471288 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
1 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
89471324 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
1 GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
89471360 G
1 G
89471361 CCCTATCTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.25
Consensus pattern (36 bp):
GGTCCAAATTTTCTGTACCTAAAACCAACCAAACTC
Found at i:89473639 original size:26 final size:26
Alignment explanation
Indices: 89473610--89473717 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
89473600 TGGTACAAAT
89473610 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
89473636 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89473662 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
89473688 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
89473714 TGAT
1 TGAT
89473718 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:89484067 original size:22 final size:22
Alignment explanation
Indices: 89484039--89484082 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
89484029 TTATGGGGTT
89484039 AGACTTTCAATATCACAATCTG
1 AGACTTTCAATATCACAATCTG
89484061 AGACTTTCAATATCACAATCTG
1 AGACTTTCAATATCACAATCTG
89484083 TGCAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (22 bp):
AGACTTTCAATATCACAATCTG
Found at i:89485179 original size:28 final size:28
Alignment explanation
Indices: 89485147--89485206 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
89485137 TAACCTACAT
*
89485147 CTCTCATTGGTGGTAGCTCTACTGATGA
1 CTCTCATTGGCGGTAGCTCTACTGATGA
89485175 CTCTCATTGGCGGTAGCTCTACTGATGA
1 CTCTCATTGGCGGTAGCTCTACTGATGA
89485203 CTCT
1 CTCT
89485207 ACAAGCCTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (28 bp):
CTCTCATTGGCGGTAGCTCTACTGATGA
Found at i:89488543 original size:2 final size:2
Alignment explanation
Indices: 89488536--89488566 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
89488526 ATAAGTTTTG
89488536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89488567 AAAGATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89512666 original size:26 final size:26
Alignment explanation
Indices: 89512633--89512689 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
89512623 TCATTTTAGG
89512633 TAAGCCAAAATAAAAAGTTTACAATT
1 TAAGCCAAAATAAAAAGTTTACAATT
89512659 TAAGCCAAAATAAAAAGTTTACAATT
1 TAAGCCAAAATAAAAAGTTTACAATT
89512685 TAAGC
1 TAAGC
89512690 ATTCGCGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (26 bp):
TAAGCCAAAATAAAAAGTTTACAATT
Found at i:89526481 original size:48 final size:48
Alignment explanation
Indices: 89526410--89526586 Score: 300
Period size: 48 Copynumber: 3.7 Consensus size: 48
89526400 CAAGACAAAT
*
89526410 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
89526458 ATATATATATGTGGTGAAGCCGAATGGCTAATGTGAAATATATATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
89526506 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
89526554 ATATGTATATGTGGTAAAGCCGAATGGCTAGTG
1 ATATATATATGTGGTAAAGCCGAATGGCTAGTG
89526587 GTACATATTT
Statistics
Matches: 121, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 121 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATATATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:89526612 original size:79 final size:79
Alignment explanation
Indices: 89526512--89526662 Score: 284
Period size: 79 Copynumber: 1.9 Consensus size: 79
89526502 TGAGATATGT
89526512 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
89526577 ATGGCTAGTGGTAC
66 ATGGCTAGTGGTAC
* *
89526591 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
89526656 ATGGCTA
66 ATGGCTA
89526663 ATGTGAAATA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 70 1.00
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.30
Consensus pattern (79 bp):
ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAGTGGTAC
Found at i:89526662 original size:48 final size:48
Alignment explanation
Indices: 89526591--89526789 Score: 272
Period size: 48 Copynumber: 3.9 Consensus size: 48
89526581 CTAGTGGTAC
89526591 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGT
1 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGT
89526639 ATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAAATATGTATGAGATATGT
1 ATATTTGGTAAAGCCGAATGGCT-A---G-----TGT--GAAATATGTATGAGATATGT
*
89526698 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGT
1 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGT
* *
89526746 ATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAGGAGAT
1 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGAT
89526790 GTGTGTATAT
Statistics
Matches: 136, Mismatches: 4, Indels: 22
0.84 0.02 0.14
Matches are distributed among these distances:
48 84 0.62
49 1 0.01
50 3 0.02
52 1 0.01
55 1 0.01
57 3 0.02
58 1 0.01
59 42 0.31
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGT
Found at i:89526685 original size:59 final size:59
Alignment explanation
Indices: 89526619--89526786 Score: 250
Period size: 59 Copynumber: 3.0 Consensus size: 59
89526609 TGGCTAGTGT
89526619 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
1 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
*
89526678 GAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCT-A---G-----TGT--
1 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
89526726 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
1 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
89526785 GA
1 GA
89526787 GATGTGTGTA
Statistics
Matches: 96, Mismatches: 2, Indels: 22
0.80 0.02 0.18
Matches are distributed among these distances:
48 42 0.44
49 1 0.01
50 3 0.03
52 1 0.01
55 1 0.01
57 3 0.03
58 1 0.01
59 44 0.46
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (59 bp):
GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
Found at i:89526699 original size:11 final size:11
Alignment explanation
Indices: 89526666--89526699 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
89526656 ATGGCTAATG
89526666 TGAAATATGTA
1 TGAAATATGTA
*
89526677 GGAAATATGTA
1 TGAAATATGTA
*
89526688 TGAGATATGTA
1 TGAAATATGTA
89526699 T
1 T
89526700 ATGTGGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (11 bp):
TGAAATATGTA
Found at i:89526732 original size:107 final size:107
Alignment explanation
Indices: 89526591--89526786 Score: 383
Period size: 107 Copynumber: 1.8 Consensus size: 107
89526581 CTAGTGGTAC
*
89526591 ATATTTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
89526656 ATGGCTAATGTGAAATATGTAGGAAATATGTATGAGATATGT
66 ATGGCTAATGTGAAATATGTAGGAAATATGTATGAGATATGT
89526698 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
89526763 ATGGCTAATGTGAAATATGTAGGA
66 ATGGCTAATGTGAAATATGTAGGA
89526787 GATGTGTGTA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 88 1.00
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (107 bp):
ATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTAGGAAATATGTATGAGATATGT
Found at i:89526735 original size:175 final size:169
Alignment explanation
Indices: 89526421--89526769 Score: 455
Period size: 186 Copynumber: 1.9 Consensus size: 169
89526411 TATATATGTG
*
89526421 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATATATATGTGGTGAAGCCGAATGGC
1 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGC
89526486 TAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAT
66 TAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG-GTG----ATGTA-
89526551 GAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGGTACATATT
125 GAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGGTACATATT
* *
89526596 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGC
1 TGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGC
89526661 TAATGTGAAATATGTAGGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGT
66 TAATGTG-AA-A--T-----ATA--TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAG-GT
*
89526726 GAAATATGTATGAGATATGTATATTTGGTAAAGCCGAATGGCTA
119 G----ATGTA-GAGATATGTATATGTGGTAAAGCCGAATGGCTA
89526770 ATGTGAAATA
Statistics
Matches: 159, Mismatches: 4, Indels: 11
0.91 0.02 0.06
Matches are distributed among these distances:
175 69 0.43
176 2 0.01
177 1 0.01
179 1 0.01
184 3 0.02
186 83 0.52
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (169 bp):
TGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATATATATGTGGTAAAGCCGAATGGC
TAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAGGTGATGTAGAGATA
TGTATATGTGGTAAAGCCGAATGGCTAGTGGTACATATT
Found at i:89527025 original size:37 final size:37
Alignment explanation
Indices: 89526930--89527031 Score: 179
Period size: 36 Copynumber: 2.8 Consensus size: 37
89526920 GGAAATATAT
89526930 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
89526967 TCC-GGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
89527003 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
89527032 GGACTATTCA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 35 0.56
37 27 0.44
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:89530438 original size:16 final size:18
Alignment explanation
Indices: 89530417--89530454 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
89530407 TAATTTTATA
89530417 TTTATAAA-TTT-AAATT
1 TTTATAAATTTTAAAATT
89530433 TTTATAAATTTTAAAATT
1 TTTATAAATTTTAAAATT
89530451 TTTA
1 TTTA
89530455 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 3 0.15
18 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATAAATTTTAAAATT
Found at i:89530456 original size:16 final size:16
Alignment explanation
Indices: 89530416--89530471 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
89530406 ATAATTTTAT
*
89530416 ATTTATAAA-TTTAAA
1 ATTTTTAAATTTTAAA
*
89530431 TTTTTATAAATTTTAAA
1 ATTTT-TAAATTTTAAA
***
89530448 ATTTTTAAATAAAAAA
1 ATTTTTAAATTTTAAA
89530464 ATTTTTAA
1 ATTTTTAA
89530472 TTTAAGGAGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 3 0.09
16 20 0.61
17 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTAAATTTTAAA
Found at i:89530982 original size:17 final size:17
Alignment explanation
Indices: 89530935--89530982 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
89530925 GTATTTTCAA
*
89530935 TAAAAATATAAAAAATTT
1 TAAAAAT-TAAAAAATCT
89530953 TGAAAAA-TAAAAAATCT
1 T-AAAAATTAAAAAATCT
89530970 TAAAAATTTAAAA
1 TAAAAA-TTAAAA
89530983 TAAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 6 0.23
19 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAAAATTAAAAAATCT
Found at i:89544589 original size:12 final size:12
Alignment explanation
Indices: 89544572--89544597 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
89544562 ACTTTGCTTC
89544572 TTTCTTCTTTTT
1 TTTCTTCTTTTT
89544584 TTTCTTCTTTTT
1 TTTCTTCTTTTT
89544596 TT
1 TT
89544598 AATTTTAAAA
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:89545103 original size:15 final size:15
Alignment explanation
Indices: 89545083--89545112 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89545073 TAGCAAAAGG
89545083 GTATTTACAACAATC
1 GTATTTACAACAATC
*
89545098 GTATTTACACCAATC
1 GTATTTACAACAATC
89545113 ATATATTTGA
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:0.23, G:0.07, T:0.33
Consensus pattern (15 bp):
GTATTTACAACAATC
Found at i:89555061 original size:17 final size:18
Alignment explanation
Indices: 89555034--89555067 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
89555024 TTCTCCATCT
89555034 TGAAGTATTTTTTGAAAA
1 TGAAGTATTTTTTGAAAA
89555052 TGAA-TATTTTTTGAAA
1 TGAAGTATTTTTTGAAA
89555068 TGTTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (18 bp):
TGAAGTATTTTTTGAAAA
Found at i:89562373 original size:90 final size:88
Alignment explanation
Indices: 89562271--89562475 Score: 306
Period size: 90 Copynumber: 2.3 Consensus size: 88
89562261 AATCTTTATT
* * *
89562271 TTTTTGCACTCAATTGGGTACTTGAATTTTCAAAATGCAT-AAAAAAGACTCTCAAACTTTTTCA
1 TTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAACCCTCAAACTTTTTCA
*
89562335 AAAAAAGCAATTAAGCCCCTACTTTG
66 AAAAAAACAATTAAG-CCCT--TTTG
*
89562361 TTTTTGCACTCAATTGGGTACTT-AACTTTCAAAATGCATAAAAAAAAACCCTTAAACTTTTTCA
1 TTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAACCCTCAAACTTTTTCA
*
89562425 AAAAAAACAATTAAGCCCTTTTT
66 AAAAAAACAATTAAGCCCTTTTG
*
89562448 TTTTTGCACTCAATTGGGTATTTGAACT
1 TTTTTGCACTCAATTGGGTACTTGAACT
89562476 GTGAAATACA
Statistics
Matches: 106, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
87 25 0.24
88 4 0.04
89 19 0.18
90 58 0.55
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (88 bp):
TTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAAAACCCTCAAACTTTTTCA
AAAAAAACAATTAAGCCCTTTTG
Found at i:89562610 original size:10 final size:10
Alignment explanation
Indices: 89562595--89562729 Score: 52
Period size: 10 Copynumber: 13.6 Consensus size: 10
89562585 TGACATGTGA
89562595 AAAAAATTAT
1 AAAAAATTAT
89562605 AAAAAATAAATAT
1 AAAAAAT---TAT
89562618 CAATAAAATTTAT
1 -AA-AAAA-TTAT
89562631 AAAAAA-TAT
1 AAAAAATTAT
* ***
89562640 TAACTTTTAAT
1 AAAAAATT-AT
89562651 AAAAAA-TAT
1 AAAAAATTAT
*
89562660 AAAATATTAT
1 AAAAAATTAT
89562670 --AAAATTAT
1 AAAAAATTAT
89562678 --AAAATTAT
1 AAAAAATTAT
*
89562686 -AAAAATCAT
1 AAAAAATTAT
*
89562695 AAAAAATTGT
1 AAAAAATTAT
*** *
89562705 AAACCTTTGT
1 AAAAAATTAT
89562715 -AAAAATTAT
1 AAAAAATTAT
89562724 AAAAAA
1 AAAAAA
89562730 ATTTATTAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 24
0.68 0.15 0.18
Matches are distributed among these distances:
8 15 0.16
9 24 0.26
10 31 0.33
11 8 0.09
12 2 0.02
13 6 0.06
14 2 0.02
15 4 0.04
16 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:89562690 original size:17 final size:16
Alignment explanation
Indices: 89562649--89562698 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
89562639 TTAACTTTTA
*
89562649 ATAAAAAATATAAAAT
1 ATAAAAATTATAAAAT
89562665 ATTATAAAATTATAAAATT
1 A-TA-AAAATTATAAAA-T
*
89562684 ATAAAAATCATAAAA
1 ATAAAAATTATAAAA
89562699 AATTGTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 13 0.45
19 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATTATAAAAT
Found at i:89562696 original size:9 final size:9
Alignment explanation
Indices: 89562596--89562728 Score: 67
Period size: 9 Copynumber: 14.6 Consensus size: 9
89562586 GACATGTGAA
89562596 AAAAATTAT
1 AAAAATTAT
89562605 AAAAA--AT
1 AAAAATTAT
* *
89562612 AAATATCAAT
1 AAAAAT-TAT
*
89562622 AAAATTTAT
1 AAAAATTAT
*
89562631 AAAAAATATT
1 AAAAATTA-T
***
89562641 AACTTTTAAT
1 AAAAATT-AT
*
89562651 AAAAAATAT
1 AAAAATTAT
89562660 AAAATATTAT
1 AAAA-ATTAT
89562670 -AAAATTAT
1 AAAAATTAT
89562678 -AAAATTAT
1 AAAAATTAT
*
89562686 AAAAATCAT
1 AAAAATTAT
*
89562695 AAAAAATTGT
1 -AAAAATTAT
** *
89562705 AAACCTTTGT
1 AAA-AATTAT
89562715 AAAAATTAT
1 AAAAATTAT
89562724 AAAAA
1 AAAAA
89562729 AATTTATTAA
Statistics
Matches: 92, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
7 6 0.07
8 13 0.14
9 40 0.43
10 32 0.35
11 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:89562698 original size:8 final size:8
Alignment explanation
Indices: 89562665--89562689 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
89562655 AATATAAAAT
89562665 ATTATAAA
1 ATTATAAA
89562673 ATTATAAA
1 ATTATAAA
89562681 ATTATAAA
1 ATTATAAA
89562689 A
1 A
89562690 ATCATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTATAAA
Found at i:89562938 original size:10 final size:10
Alignment explanation
Indices: 89562919--89563083 Score: 55
Period size: 10 Copynumber: 17.2 Consensus size: 10
89562909 TTTTAGTACG
89562919 ATAA-TTTTT
1 ATAATTTTTT
89562928 ATAATTTTTT
1 ATAATTTTTT
* *
89562938 ACAA-ATTTT
1 ATAATTTTTT
89562947 AT-ATTTCTTT
1 ATAATTT-TTT
*
89562957 A-CATTTTTT
1 ATAATTTTTT
89562966 ATAATTTTCTT
1 ATAATTTT-TT
* *
89562977 ATGA--CTTT
1 ATAATTTTTT
**
89562985 ATAAAATTTT
1 ATAATTTTTT
89562995 ATAATTTTTT
1 ATAATTTTTT
* *
89563005 CT-ATATTTCT
1 ATAAT-TTTTT
*
89563015 AT-A-TATTT
1 ATAATTTTTT
*
89563023 ATAATTCTTT
1 ATAATTTTTT
**
89563033 ACGA-TTTTT
1 ATAATTTTTT
**
89563042 ATAACATTTT
1 ATAATTTTTT
**
89563052 ATAATTTTAA
1 ATAATTTTTT
89563062 AT-ATTTTTT
1 ATAATTTTTT
*
89563071 AAATATTTTTT
1 ATA-ATTTTTT
89563082 AT
1 AT
89563084 TAAAATTTAA
Statistics
Matches: 111, Mismatches: 31, Indels: 26
0.66 0.18 0.15
Matches are distributed among these distances:
8 11 0.10
9 30 0.27
10 57 0.51
11 13 0.12
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:89562948 original size:19 final size:19
Alignment explanation
Indices: 89562924--89562973 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
89562914 GTACGATAAT
89562924 TTTTATAATTTTTTACAAA
1 TTTTATAATTTTTTACAAA
**
89562943 TTTTAT-ATTTCTTTACATT
1 TTTTATAATTT-TTTACAAA
89562962 TTTTATAATTTT
1 TTTTATAATTTT
89562974 CTTATGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.15
19 19 0.70
20 4 0.15
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAA
Found at i:89563070 original size:11 final size:11
Alignment explanation
Indices: 89563056--89563082 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
89563046 CATTTTATAA
89563056 TTTTAAATATT
1 TTTTAAATATT
89563067 TTTTAAATATT
1 TTTTAAATATT
89563078 TTTTA
1 TTTTA
89563083 TTAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTAAATATT
Found at i:89565257 original size:23 final size:23
Alignment explanation
Indices: 89565231--89565274 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
89565221 GTAAATAGTA
89565231 AAAATA-AATAAAGTATAACAAGC
1 AAAATATAAT-AAGTATAACAAGC
*
89565254 AAAATATAGTAAGTATAACAA
1 AAAATATAATAAGTATAACAA
89565275 TCTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAATATAATAAGTATAACAAGC
Found at i:89567134 original size:133 final size:133
Alignment explanation
Indices: 89566908--89567392 Score: 774
Period size: 133 Copynumber: 3.6 Consensus size: 133
89566898 GATCTGCTGT
* *
89566908 AATTTGATCTGCTTTACTCCTGCTCAGTAAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCC
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTA--TTTAGCCTGCTCCACTCC
*
89566973 TGCTTAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGA-TT
64 TGCTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTT
*
89567037 CACCAA
129 -GCCAA
* * * * * * *
89567043 AATTTGATCTGCTCCGCTCCTGCTCTGCGAAGATAAGATCTAGTATATAGCCTGCTCCACTTCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
* *
89567108 CTCAGTGAAGATAAGGCTGGTAGCTGAAATCTGCTCCATTGCCGATACATAGAGATAAGACTTGC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
89567173 CAA
131 CAA
* * *
89567176 AATTTGATCTGCTTCACTTCTGTTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTTCACTCCTG
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
89567241 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
66 CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
89567306 CAA
131 CAA
* *
89567309 AATTTGATCTGCTTCACTTCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTA
1 AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
89567374 CTCAGTGAAGATAAGGCTG
66 CTCAGTGAAGATAAGGCTG
89567393 ATGATATCTG
Statistics
Matches: 321, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
133 281 0.88
134 2 0.01
135 38 0.12
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (133 bp):
AATTTGATCTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATTTAGCCTGCTCCACTCCTG
CTCAGTGAAGATAAGGCTGGTGGCTGAAATCTGCTCCATTGCCGATACATGGAGATAAGACTTGC
CAA
Found at i:89575140 original size:21 final size:21
Alignment explanation
Indices: 89575110--89575153 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
89575100 CTAGCTCATT
*
89575110 ATGTTGTTCT-GTGACTCCAGC
1 ATGTTGTTCTAG-AACTCCAGC
*
89575131 ATGTTTTTCTAGAACTCCAGC
1 ATGTTGTTCTAGAACTCCAGC
89575152 AT
1 AT
89575154 TTGATCCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (21 bp):
ATGTTGTTCTAGAACTCCAGC
Found at i:89579492 original size:16 final size:15
Alignment explanation
Indices: 89579467--89579514 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
89579457 CTATTTTAAG
89579467 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
89579482 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
89579499 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
89579514 T
1 T
89579515 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:89580426 original size:19 final size:18
Alignment explanation
Indices: 89580402--89580447 Score: 83
Period size: 19 Copynumber: 2.5 Consensus size: 18
89580392 TATTTCGTTA
89580402 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATC-T
89580421 TTTATTTTTATTTCATCT
1 TTTATTTTTATTTCATCT
89580439 TTTATTTTT
1 TTTATTTTT
89580448 TACTTTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTTTATTTCATCT
Found at i:89586795 original size:22 final size:22
Alignment explanation
Indices: 89586770--89586816 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
89586760 TCTACACCCC
89586770 ACCTCGTGCCGCGCCACCGTCG
1 ACCTCGTGCCGCGCCACCGTCG
*
89586792 ACCTCGTTCCGCGCCACCGTCG
1 ACCTCGTGCCGCGCCACCGTCG
89586814 ACC
1 ACC
89586817 ACACGTCCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.11, C:0.51, G:0.23, T:0.15
Consensus pattern (22 bp):
ACCTCGTGCCGCGCCACCGTCG
Found at i:89589891 original size:16 final size:15
Alignment explanation
Indices: 89589866--89589913 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
89589856 CTATTTTAAG
89589866 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
89589881 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
89589898 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
89589913 T
1 T
89589914 ATTAATTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:89590847 original size:19 final size:19
Alignment explanation
Indices: 89590800--89590839 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
89590790 TATTTTGTTA
89590800 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
89590819 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
89590838 TT
1 TT
89590840 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:89591312 original size:2 final size:2
Alignment explanation
Indices: 89591305--89591340 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
89591295 ACCTTTAATA
* *
89591305 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89591341 TTAAGATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:89594069 original size:5 final size:5
Alignment explanation
Indices: 89594061--89594085 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
89594051 ATTCAATCAA
89594061 TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT
89594086 CTTCAATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:89597646 original size:67 final size:67
Alignment explanation
Indices: 89597529--89597666 Score: 186
Period size: 67 Copynumber: 2.1 Consensus size: 67
89597519 AGTTATTTGA
* ** * * * * * *
89597529 GTTAGCTGAGTTAAGCTTGCAACTCCGCAACAGCTCGCGGACTTATGCTCCCAGCTGATGATTAA
1 GTTAGATGAGTTAAGCTCACAACTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAA
89597594 AG
66 AG
*
89597596 GTTAGATGAGTTAAGCTCACATCTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAA
1 GTTAGATGAGTTAAGCTCACAACTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAA
89597661 AG
66 AG
89597663 GTTA
1 GTTA
89597667 TCTAAGTAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (67 bp):
GTTAGATGAGTTAAGCTCACAACTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAA
AG
Found at i:89597679 original size:67 final size:67
Alignment explanation
Indices: 89597551--89597681 Score: 172
Period size: 67 Copynumber: 2.0 Consensus size: 67
89597541 AAGCTTGCAA
* * * * * * * *
89597551 CTCCGCAACAGCTCGCGGACTTATGCTCCCAGCTGATGATTAAAGGTTAGATGAGTTAAGCTCAC
1 CTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGTTAGATAAGTAAAGCTCAC
89597616 AT
66 AT
**
89597618 CTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGTTATCTAAGTAAAGCTCA
1 CTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGTTAGATAAGTAAAGCTCA
89597682 GAACCTTCAG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (67 bp):
CTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGTTAGATAAGTAAAGCTCAC
AT
Found at i:89597783 original size:104 final size:104
Alignment explanation
Indices: 89597602--89598118 Score: 659
Period size: 104 Copynumber: 5.0 Consensus size: 104
89597592 AAAGGTTAGA
* * * *** * *
89597602 TGAGTTAAGCTCACATCTCCGAAACAGCTCACAGACCTACGCTCCCAACTGATGATTAAAGGTTA
1 TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGCTCCTAGCTGATGATTAAAGGTTA
* * * *
89597667 TCTAAGTAAAGCTCAG-AACCTTCAGTTATTTGAGTTAAC
66 GCTGAGTTAAGCTC-GCAACCTCCAGTTATTTGAGTTAAC
* *
89597706 TGAGTTAAGCTCGCAACTCCAAAATAGCTCGTGGACTTACGCTCCTAGCTGATGATTAAAGGTTA
1 TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGCTCCTAGCTGATGATTAAAGGTTA
* *
89597771 GCTGAGTTAAGCTCGCAAACTCCAGTTATTTGAGTTAGC
66 GCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTAAC
* *
89597810 TAAGTTAAGCTCGCAACTCCAAAATAGCTCGTGGACCTACGCTTCC-AGCTGATGATTAAAGGTT
1 TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGC-TCCTAGCTGATGATTAAAGGTT
*
89597874 AGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTACC
65 AGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTAAC
* * * * *
89597914 TAAGTTAAGCTCGCAACTTCGAAATAGCTCGTGAACCTACGCT-CTCAGCTAATAATTAAAGGTT
1 TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGCTCCT-AGCTGATGATTAAAGGTT
*
89597978 AGCTGAGTTAAGCTCAG-AACCTCTAGTTATTTGAGTTAAC
65 AGCTGAGTTAAGCTC-GCAACCTCCAGTTATTTGAGTTAAC
* * * * *
89598018 TGAGTTAAGCTCGCAACTTCGAAATAGCTCATGGACCTATGCTCCCAAG-TAATGATTAAAGGTT
1 TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGCT-CCTAGCTGATGATTAAAGGTT
* *
89598082 AGCTGAGTTAAGCTCGTAACCTCCAATTA-TTGAGTTA
65 AGCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTA
89598119 GCTAATTTAA
Statistics
Matches: 370, Mismatches: 35, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
102 1 0.00
103 11 0.03
104 351 0.95
105 6 0.02
106 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (104 bp):
TGAGTTAAGCTCGCAACTCCGAAATAGCTCGTGGACCTACGCTCCTAGCTGATGATTAAAGGTTA
GCTGAGTTAAGCTCGCAACCTCCAGTTATTTGAGTTAAC
Found at i:89601032 original size:2 final size:2
Alignment explanation
Indices: 89601025--89601065 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
89601015 ACATGCGTAA
89601025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89601066 ATCATATTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89601309 original size:212 final size:209
Alignment explanation
Indices: 89601051--89601486 Score: 773
Period size: 212 Copynumber: 2.1 Consensus size: 209
89601041 ATATATATAT
*
89601051 ATATATATATATATAATCATATTAGTGAATTTGCTAATACATACTTCATCCAGGTAAAGTATGCA
1 ATATATATATATATAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCA
*
89601116 TTATTAAAATTAAATTAAAATATTAAATAGGAAATAAAATTATAAAACAATATGTTATTTGGAAA
66 TTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAA
89601181 ATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAATATTTAAATTTTTGTTTTTGTA
131 ATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAATATTTAAA--TTT-TTTTTGTA
* **
89601246 ATGTGATACATGCGTGT
193 ATGTGATACATGCATAA
*
89601263 GTATATATATATATAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCA
1 ATATATATATATATAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCA
*
89601328 TTGTTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAA
66 TTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAA
*
89601393 ATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAGTATTTAAATTTTTTTTGTAATG
131 ATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAATATTTAAATTTTTTTTGTAATG
89601458 TGATACATGCATAA
196 TGATACATGCATAA
89601472 ATATATATATATATA
1 ATATATATATATATA
89601487 TATATATATA
Statistics
Matches: 215, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
209 36 0.17
210 3 0.01
212 176 0.82
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (209 bp):
ATATATATATATATAATCATATTAGTGAATCTGCTAATACATACTTCATCCAGGTAAAGTATGCA
TTATTAAAATTAAATTAAAATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAA
ATAACTATTATTGTAATGAGATACATGTTTTATTAGGTATAAATATTTAAATTTTTTTTGTAATG
TGATACATGCATAA
Found at i:89601479 original size:2 final size:2
Alignment explanation
Indices: 89601472--89601506 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
89601462 ACATGCATAA
89601472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
89601507 ATCATATTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89605199 original size:22 final size:21
Alignment explanation
Indices: 89605153--89605230 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 21
89605143 TTATTATTGG
89605153 TTTTATAAAA-TTTAAA-ATGTA
1 TTTT-TAAAATTTTAAATAT-TA
89605174 TATTTTAAATATTTTATAATATTA
1 T-TTTTAAA-ATTTTA-AATATTA
89605198 TTTTTAAAATTTTAAATA-TA
1 TTTTTAAAATTTTAAATATTA
89605218 CTTTTATAAAATT
1 -TTTT-TAAAATT
89605231 ATTTTTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.04
21 13 0.26
22 17 0.34
23 11 0.22
24 5 0.10
25 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (21 bp):
TTTTTAAAATTTTAAATATTA
Found at i:89605253 original size:20 final size:22
Alignment explanation
Indices: 89605221--89605277 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
89605211 AAATATACTT
89605221 TTATAAA-ATTATTTTTTTAA-A
1 TTATAAATA-TATTTTTTTAATA
89605242 TT-TAAATATATTATTTTTTAATA
1 TTATAAATATA-T-TTTTTTAATA
89605265 TTATAAA-ATATTT
1 TTATAAATATATTT
89605278 AAAATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
20 6 0.19
21 6 0.19
22 9 0.29
23 6 0.19
24 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAAATATATTTTTTTAATA
Found at i:89605258 original size:23 final size:23
Alignment explanation
Indices: 89605221--89605276 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
89605211 AAATATACTT
89605221 TTAT-AAA-ATTATTTTTTTAA-A
1 TTATAAAATATTA-TTTTTTAATA
89605242 TT-TAAATATATTATTTTTTAATA
1 TTATAAA-ATATTATTTTTTAATA
89605265 TTATAAAATATT
1 TTATAAAATATT
89605277 TAAAATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 9 0.30
23 12 0.40
24 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATAAAATATTATTTTTTAATA
Found at i:89605268 original size:36 final size:36
Alignment explanation
Indices: 89605182--89605268 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 36
89605172 TATATTTTAA
89605182 ATATTTTATAATATTA-TTTTTAAAATTTTAAATAT
1 ATATTTTATAATATTATTTTTTAAAATTTTAAATAT
* * *
89605217 A-CTTTTATAAAATTATTTTTTTAAA-TTTAAATAT
1 ATATTTTATAATATTATTTTTTAAAATTTTAAATAT
*
89605251 ATTATTTTTTAATATTAT
1 A-TATTTTATAATATTAT
89605269 AAAATATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 22 0.51
35 9 0.21
36 12 0.28
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (36 bp):
ATATTTTATAATATTATTTTTTAAAATTTTAAATAT
Found at i:89605303 original size:33 final size:33
Alignment explanation
Indices: 89605241--89605303 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
89605231 ATTTTTTTAA
* *
89605241 ATTTAAATATATTATTTTTTAATATTATAAAAT
1 ATTTAAATATATTATTTTTAAAGATTATAAAAT
89605274 ATTTAAAATATATTATTTTTAAAGA-TATAA
1 ATTT-AAATATATTATTTTTAAAGATTATAA
89605304 CATTTCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (33 bp):
ATTTAAATATATTATTTTTAAAGATTATAAAAT
Found at i:89605369 original size:20 final size:19
Alignment explanation
Indices: 89605344--89605390 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
89605334 TTTTTAATGC
89605344 ATATTTTAAAAATTTTAAAT
1 ATATTTT-AAAATTTTAAAT
* *
89605364 ATATTTTTAATTTTTAAAT
1 ATATTTTAAAATTTTAAAT
89605383 ATAATTTT
1 AT-ATTTT
89605391 TTAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTAAAATTTTAAAT
Found at i:89605401 original size:12 final size:14
Alignment explanation
Indices: 89605374--89605406 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
89605364 ATATTTTTAA
89605374 TTTTTAAATATAAT
1 TTTTTAAATATAAT
89605388 TTTTTAAAT-T-AT
1 TTTTTAAATATAAT
89605400 TTTTTAA
1 TTTTTAA
89605407 GAATTGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 1 0.05
14 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTAAATATAAT
Found at i:89605434 original size:12 final size:12
Alignment explanation
Indices: 89605373--89605442 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 12
89605363 TATATTTTTA
*
89605373 ATTTTTAAATATA
1 ATTTTTAAA-ATT
*
89605386 ATTTTTTAAATT
1 ATTTTTAAAATT
89605398 ATTTTTTAAGAATTGT
1 A-TTTTTAA-AA-T-T
89605414 GATTTTTTAAAATT
1 -A-TTTTTAAAATT
*
89605428 ATTTTTAAAAAT
1 ATTTTTAAAATT
89605440 ATT
1 ATT
89605443 CAAATGATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
12 16 0.33
13 15 0.31
14 3 0.06
15 2 0.04
16 3 0.06
17 9 0.19
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:89605598 original size:13 final size:13
Alignment explanation
Indices: 89605555--89605602 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 13
89605545 GTTAAAAAAG
89605555 ATTAAAAATATAT
1 ATTAAAAATATAT
89605568 ATTAGAAAATTTATATAT
1 ATT--AAAA---ATATAT
89605586 ATTAAAAATATAT
1 ATTAAAAATATAT
89605599 ATTA
1 ATTA
89605603 TAACTGTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 13 0.43
15 4 0.13
16 4 0.13
18 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATTAAAAATATAT
Found at i:89605599 original size:15 final size:16
Alignment explanation
Indices: 89605558--89605600 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
89605548 AAAAAAGATT
89605558 AAAA-ATATATATTAG
1 AAAATATATATATTAG
89605573 AAAATTTATATATATTA-
1 AAAA--TATATATATTAG
89605590 AAAATATATAT
1 AAAATATATAT
89605601 TATAACTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 11 0.44
17 4 0.16
18 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATATATATATTAG
Found at i:89605604 original size:18 final size:18
Alignment explanation
Indices: 89605562--89605600 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
89605552 AAGATTAAAA
*
89605562 ATATATATTAGAAAATTT
1 ATATATATTAGAAAATAT
89605580 ATATATATTA-AAAATAT
1 ATATATATTAGAAAATAT
89605597 ATAT
1 ATAT
89605601 TATAACTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATATTAGAAAATAT
Found at i:89605842 original size:17 final size:16
Alignment explanation
Indices: 89605798--89605842 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
89605788 TTTTGTATTT
*
89605798 TTATATTTTATAGTTA
1 TTATATTTAATAGTTA
*
89605814 TTATAATATAATAGTTAA
1 TTAT-ATTTAATAGTT-A
89605832 TTATATTTAAT
1 TTATATTTAAT
89605843 TTATGTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
TTATATTTAATAGTTA
Found at i:89607802 original size:24 final size:24
Alignment explanation
Indices: 89607773--89607828 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
89607763 TTAAGTGTAG
89607773 ACAATTTGTGCTGGTCGAGGCACA
1 ACAATTTGTGCTGGTCGAGGCACA
89607797 ACAATTTGTGCTGGTCGAGGCACA
1 ACAATTTGTGCTGGTCGAGGCACA
89607821 ACAATTTG
1 ACAATTTG
89607829 CTGATGTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (24 bp):
ACAATTTGTGCTGGTCGAGGCACA
Found at i:89611590 original size:22 final size:23
Alignment explanation
Indices: 89611565--89611642 Score: 92
Period size: 22 Copynumber: 3.5 Consensus size: 23
89611555 TAAAAATCAT
89611565 AATTTTTAAAAAT-TATATTTAA
1 AATTTTTAAAAATATATATTTAA
*
89611587 AA--TTAAAAATATATATATTTAA
1 AATTTTTAAAA-ATATATATTTAA
*
89611609 AATTTTT-AAAATATACATTTAA
1 AATTTTTAAAAATATATATTTAA
89611631 AATTTTATAAAA
1 AATTTT-TAAAA
89611643 CAAATAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 6 0.13
21 2 0.04
22 30 0.64
23 4 0.09
24 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTTTAAAAATATATATTTAA
Found at i:89611729 original size:20 final size:20
Alignment explanation
Indices: 89611690--89611806 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 20
89611680 ATATATTTTA
*
89611690 AATATTTTATAATATTAAAAAT
1 AATA-TTTAAAAT-TTAAAAAT
*
89611712 AATATTTAAAATTTAAAAAA
1 AATATTTAAAATTTAAAAAT
89611732 AATATTT-AAATTT-AAAAT
1 AATATTTAAAATTTAAAAAT
* *
89611750 AATA-AT-AATTTTAAAAA-
1 AATATTTAAAATTTAAAAAT
89611767 ATATATTTAAAATTTTAAAAAAAT
1 A-ATATTTAAAA-TTT--AAAAAT
89611791 AATATTATAAACATTT
1 AATATT-TAAA-ATTT
89611807 CAAATATACA
Statistics
Matches: 78, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
17 7 0.09
18 15 0.19
19 7 0.09
20 16 0.21
21 10 0.13
22 4 0.05
23 10 0.13
24 8 0.10
25 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTTAAAATTTAAAAAT
Found at i:89611773 original size:36 final size:38
Alignment explanation
Indices: 89611723--89611794 Score: 112
Period size: 36 Copynumber: 1.9 Consensus size: 38
89611713 ATATTTAAAA
*
89611723 TTTAAAAAAAATATTT-AAA-TTTAAAATAATAATAAT
1 TTTAAAAAAAATATTTAAAATTTTAAAAAAATAATAAT
*
89611759 TTTAAAAAATATATTTAAAATTTTAAAAAAATAATA
1 TTTAAAAAAAATATTTAAAATTTTAAAAAAATAATA
89611795 TTATAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 15 0.47
37 3 0.09
38 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (38 bp):
TTTAAAAAAAATATTTAAAATTTTAAAAAAATAATAAT
Found at i:89611790 original size:22 final size:23
Alignment explanation
Indices: 89611751--89611806 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 23
89611741 ATTTAAAATA
89611751 ATAATAATTTTAAAAAAT-ATATT
1 ATAA-AATTTTAAAAAATAATATT
89611774 -TAAAATTTTAAAAAAATAATATT
1 ATAAAATTTT-AAAAAATAATATT
89611797 ATAAACATTT
1 ATAAA-ATTT
89611807 CAAATATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.21
22 10 0.34
23 5 0.17
24 4 0.14
25 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAAATTTTAAAAAATAATATT
Found at i:89611903 original size:24 final size:23
Alignment explanation
Indices: 89611882--89611942 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
89611872 AAATAAAGCA
89611882 CAAATAAAT-AAAACTTAAAAAG
1 CAAATAAATAAAAACTTAAAAAG
* *
89611904 TAAATAAATAAAAAACTTAAAAAA
1 CAAATAAAT-AAAAACTTAAAAAG
*
89611928 CAAAAAAATGAAAAA
1 CAAATAAAT-AAAAA
89611943 TGACAAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 8 0.25
24 24 0.75
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.16
Consensus pattern (23 bp):
CAAATAAATAAAAACTTAAAAAG
Found at i:89611908 original size:22 final size:23
Alignment explanation
Indices: 89611883--89611926 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
89611873 AATAAAGCAC
89611883 AAATAAAT-AAAACTTAAAAAGT
1 AAATAAATAAAAACTTAAAAAGT
89611905 AAATAAATAAAAAACTTAAAAA
1 AAATAAAT-AAAAACTTAAAAA
89611927 ACAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAATAAAAACTTAAAAAGT
Found at i:89612568 original size:16 final size:20
Alignment explanation
Indices: 89612534--89612578 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 20
89612524 TTAAGTCTAA
89612534 ATTAATAAAATCTATAAA-T
1 ATTAATAAAATCTATAAATT
89612553 ATTAA-AAAA-CTA-AAATT
1 ATTAATAAAATCTATAAATT
*
89612570 ATTATTAAA
1 ATTAATAAA
89612579 CAAATAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 7 0.30
19 5 0.22
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAATAAAATCTATAAATT
Found at i:89624028 original size:56 final size:57
Alignment explanation
Indices: 89623958--89624080 Score: 212
Period size: 56 Copynumber: 2.2 Consensus size: 57
89623948 ATAATGTGAA
*
89623958 AATGTTAAAGGTTAATTTTTTGAAATTAATACTAAATTGACATAATGTATAATGTTT
1 AATGCTAAAGGTTAATTTTTTGAAATTAATACTAAATTGACATAATGTATAATGTTT
* *
89624015 AGTGC-AAAGGTTAATTTTTTGGAATTAATACTAAATTGACATAATGTATAATGTTT
1 AATGCTAAAGGTTAATTTTTTGAAATTAATACTAAATTGACATAATGTATAATGTTT
89624071 AATGCTAAAG
1 AATGCTAAAG
89624081 TTGTTATTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
56 54 0.89
57 7 0.11
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.41
Consensus pattern (57 bp):
AATGCTAAAGGTTAATTTTTTGAAATTAATACTAAATTGACATAATGTATAATGTTT
Found at i:89624837 original size:2 final size:2
Alignment explanation
Indices: 89624830--89624854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89624820 TTTCAACATA
89624830 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
89624855 ATGAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:89632056 original size:24 final size:23
Alignment explanation
Indices: 89632023--89632067 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
89632013 TAATAAATAA
89632023 TATATATTTTCAAGTTTTTAAAGT
1 TATATATTTTCAA-TTTTTAAAGT
* *
89632047 TATATTTTTTGAATTTTTAAA
1 TATATATTTTCAATTTTTAAA
89632068 ATTTGGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (23 bp):
TATATATTTTCAATTTTTAAAGT
Found at i:89632284 original size:31 final size:31
Alignment explanation
Indices: 89632248--89632315 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
89632238 GTGAAGCAAT
* * *
89632248 TAAAATTGATAACTTATTTAATAG-GAGTGAC
1 TAAAATTGACAACTTATCTAA-AGAGAATGAC
89632279 TAAAATTGACAACTTATCTAAAGAGAATGAC
1 TAAAATTGACAACTTATCTAAAGAGAATGAC
89632310 TAAAAT
1 TAAAAT
89632316 AACAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (31 bp):
TAAAATTGACAACTTATCTAAAGAGAATGAC
Found at i:89639015 original size:35 final size:35
Alignment explanation
Indices: 89638976--89639067 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
89638966 CATGGAAAAG
*
89638976 TGTGAAACGTAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTAAGT
* * * *
89639011 TGTGAAACGTAGGTGTGATATCATCCATACTAAGT
1 TGTGAAACGTAGGTATGGTATTAACCATACTAAGT
*
89639046 TGTGAAATGTAGGTATGGTATT
1 TGTGAAACGTAGGTATGGTATT
89639068 TCAAGGAGGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (35 bp):
TGTGAAACGTAGGTATGGTATTAACCATACTAAGT
Found at i:89644489 original size:23 final size:23
Alignment explanation
Indices: 89644463--89644511 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
89644453 TAAATTAATA
89644463 AAATGTATAAATATTAAAGAGCT
1 AAATGTATAAATATTAAAGAGCT
*
89644486 AAATGTATAAATATTAAAGGGCT
1 AAATGTATAAATATTAAAGAGCT
89644509 AAA
1 AAA
89644512 CTTATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (23 bp):
AAATGTATAAATATTAAAGAGCT
Found at i:89652497 original size:26 final size:27
Alignment explanation
Indices: 89652468--89652527 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
89652458 TTTACTCCAC
*
89652468 TAAAATTTTTGACAATTTTATCC-CGG
1 TAAAATTTTTGACAATTTTACCCTCGG
**
89652494 TAAAA-TTTTGATGATTTTACCCTCGG
1 TAAAATTTTTGACAATTTTACCCTCGG
89652520 TAAAATTT
1 TAAAATTT
89652528 CGAGAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 14 0.48
26 13 0.45
27 2 0.07
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (27 bp):
TAAAATTTTTGACAATTTTACCCTCGG
Found at i:89652510 original size:25 final size:26
Alignment explanation
Indices: 89652468--89652527 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
89652458 TTTACTCCAC
*
89652468 TAAAATTTTTGACAATTTTATCC-CGG
1 TAAAA-TTTTGACAATTTTACCCTCGG
**
89652494 TAAAATTTTGATGATTTTACCCTCGG
1 TAAAATTTTGACAATTTTACCCTCGG
89652520 TAAAATTT
1 TAAAATTT
89652528 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACCCTCGG
Found at i:89665500 original size:15 final size:16
Alignment explanation
Indices: 89665475--89665504 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
89665465 TTAAATCAAT
89665475 TTATAAATTATATTAA
1 TTATAAATTATATTAA
89665491 TTAT-AATTATATTA
1 TTATAAATTATATTA
89665505 TGAAATAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAAATTATATTAA
Found at i:89668889 original size:27 final size:28
Alignment explanation
Indices: 89668851--89668991 Score: 168
Period size: 27 Copynumber: 5.2 Consensus size: 28
89668841 CAGCATGGCT
* *
89668851 ACCAGA-ACAGATA-ATGTGACAGAGTC
1 ACCAGATACAGATATATGTGGCAGAGCC
89668877 ACCAGATACAGATA-ATCGTGGCAGAGCC
1 ACCAGATACAGATATAT-GTGGCAGAGCC
89668905 ACCAGA-ACAGATATATGTGGCAGAGCC
1 ACCAGATACAGATATATGTGGCAGAGCC
*
89668932 ACCAGAT-CAGATATTTGTGGCAGAGCC
1 ACCAGATACAGATATATGTGGCAGAGCC
* * *
89668959 ACTAGAT-CAGATATTTGTGGCATAGCC
1 ACCAGATACAGATATATGTGGCAGAGCC
*
89668986 ATCAGA
1 ACCAGA
89668992 ACGCTTCCTC
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.06
27 81 0.78
28 17 0.16
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (28 bp):
ACCAGATACAGATATATGTGGCAGAGCC
Found at i:89669120 original size:26 final size:26
Alignment explanation
Indices: 89669094--89669168 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
89669084 CAAAATTAAC
*
89669094 CCTA-GGGTATAACGGTAATTTTGAA
1 CCTAGGGGTATAACAGTAATTTTGAA
*
89669119 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATAACAGTAATTTT-GA-A
* * *
89669147 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAACAGTAATTT
89669169 AGCTACTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.10
26 17 0.40
27 1 0.02
28 20 0.48
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTATAACAGTAATTTTGAA
Found at i:89670631 original size:26 final size:26
Alignment explanation
Indices: 89670602--89670737 Score: 218
Period size: 26 Copynumber: 5.2 Consensus size: 26
89670592 CATGAAATTC
*
89670602 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
89670628 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
*
89670654 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
89670680 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
* *
89670706 TTATCATGTAACATTTACCGAACCTA
1 TTATCATGAAACATTTACCTAACCTA
89670732 TTATCA
1 TTATCA
89670738 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:89674669 original size:27 final size:28
Alignment explanation
Indices: 89674632--89674771 Score: 184
Period size: 27 Copynumber: 5.2 Consensus size: 28
89674622 AGCATGGCTG
* *
89674632 CCAGA-ACAGATA-ATGTGACAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
89674658 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
89674686 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
*
89674713 CCAGAT-CAGATATTTGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
89674740 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
89674767 CCAGA
1 CCAGA
89674772 ACGCTTCTCC
Statistics
Matches: 106, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
26 5 0.05
27 84 0.79
28 17 0.16
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:89674891 original size:24 final size:25
Alignment explanation
Indices: 89674864--89674917 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
89674854 TTTCAGTCAA
*
89674864 AATTAAC-CCTAGGGGTATAACGGT
1 AATTAACACCTAGGGGTATAACAGT
**
89674888 AATTTTGCACCTAGGGGTATAACAGT
1 AA-TTAACACCTAGGGGTATAACAGT
89674914 AATT
1 AATT
89674918 TTCCATACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.08
25 5 0.20
26 18 0.72
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (25 bp):
AATTAACACCTAGGGGTATAACAGT
Found at i:89676415 original size:26 final size:26
Alignment explanation
Indices: 89676386--89676521 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
89676376 CATGAAATTC
* *
89676386 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* *
89676412 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
89676438 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
89676464 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
89676490 TTGTCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
89676516 TTATCA
1 TTATCA
89676522 ATTTGTATCA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:89679083 original size:41 final size:41
Alignment explanation
Indices: 89678976--89679093 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
89678966 AATACTCGAT
* * * *
89678976 ATCTCGCACACTAAGTACCGTACATAGCTGAAGCTATCTCA
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCA
* * *
89679017 A-ATCACACACTAAGTGCTATATATAGCCGAAGCTATCTCA
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCA
*
89679057 ATCTCGCACCCTAAGTGCCATATATAGCCGAAGCTAT
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTAT
89679094 GTTGAATAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (41 bp):
ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCA
Found at i:89679119 original size:19 final size:19
Alignment explanation
Indices: 89679080--89679119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
89679070 AGTGCCATAT
*
89679080 ATAGCCGAAGCTATGTTGA
1 ATAGCCGAAGCTATGTCGA
* *
89679099 ATAGTCGAAGCTTTGTCGA
1 ATAGCCGAAGCTATGTCGA
89679118 AT
1 AT
89679120 CACACACTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (19 bp):
ATAGCCGAAGCTATGTCGA
Found at i:89680823 original size:11 final size:11
Alignment explanation
Indices: 89680807--89680831 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
89680797 AATCCAATAG
89680807 TTATTTTTCTT
1 TTATTTTTCTT
89680818 TTATTTTTCTT
1 TTATTTTTCTT
89680829 TTA
1 TTA
89680832 AGTTTAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTCTT
Found at i:89690422 original size:11 final size:9
Alignment explanation
Indices: 89690371--89690428 Score: 70
Period size: 9 Copynumber: 6.7 Consensus size: 9
89690361 AATTAAAAAG
89690371 TTGAGAGAA
1 TTGAGAGAA
89690380 TTGAGAGAA
1 TTGAGAGAA
89690389 -T-AGATGAA
1 TTGAGA-GAA
89690397 TTGAGAGAA
1 TTGAGAGAA
89690406 TTGAGAGAA
1 TTGAGAGAA
89690415 TT-AGGAGAA
1 TTGA-GAGAA
89690424 -TGAGA
1 TTGAGA
89690429 TTTGAATGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
7 3 0.07
8 8 0.18
9 30 0.68
10 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:89690867 original size:2 final size:2
Alignment explanation
Indices: 89690860--89690889 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
89690850 AGTTTGGCTG
89690860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89690890 TCAAATAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:89693924 original size:21 final size:20
Alignment explanation
Indices: 89693902--89693941 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
89693892 ATATATTCTA
89693902 AAAATT-ATTAAATTTTAAAT
1 AAAATTAATT-AATTTTAAAT
89693922 AAAATTAAATTAATTTTAAA
1 AAAATT-AATTAATTTTAAA
89693942 ATCATGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 9 0.50
22 3 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTAATTAATTTTAAAT
Found at i:89694656 original size:30 final size:31
Alignment explanation
Indices: 89694615--89694672 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
89694605 GCCCAAAATT
*
89694615 TTTTTTACCAACTTTGAAGGACCTAAAAAGA
1 TTTTTTACCAACTTTGAAGAACCTAAAAAGA
*
89694646 TTTTTT-CCAACTTTTAAGAACCTAAAA
1 TTTTTTACCAACTTTGAAGAACCTAAAA
89694673 TCCCATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (31 bp):
TTTTTTACCAACTTTGAAGAACCTAAAAAGA
Found at i:89695513 original size:24 final size:24
Alignment explanation
Indices: 89695498--89695549 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
89695488 AATTAGTGTC
*
89695498 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
89695522 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
89695546 AAAT
1 AAAT
89695550 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:89695675 original size:29 final size:29
Alignment explanation
Indices: 89695629--89695716 Score: 149
Period size: 29 Copynumber: 3.0 Consensus size: 29
89695619 TCTACATTGA
*
89695629 CACGAATTCTCAACGAACAAGTTCTCCAC
1 CACGAACTCTCAACGAACAAGTTCTCCAC
*
89695658 CACGAACTCTCAATGAACAAGTTCTCCAC
1 CACGAACTCTCAACGAACAAGTTCTCCAC
*
89695687 CACGAACTCTCAACAAACAAGTTCTCCAC
1 CACGAACTCTCAACGAACAAGTTCTCCAC
89695716 C
1 C
89695717 TCTTTCACGA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.35, C:0.36, G:0.09, T:0.19
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTCTCCAC
Found at i:89698655 original size:30 final size:28
Alignment explanation
Indices: 89698621--89698676 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
89698611 TGGTTATAAA
89698621 AAAAATCAATAGATTCGATTATGAAATGAG
1 AAAAATCAATAGATT--ATTATGAAATGAG
* *
89698651 AAAAATGAATATATTATTATGAAATG
1 AAAAATCAATAGATTATTATGAAATG
89698677 TCAAATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
30 13 0.54
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (28 bp):
AAAAATCAATAGATTATTATGAAATGAG
Found at i:89700494 original size:47 final size:47
Alignment explanation
Indices: 89700440--89700529 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
89700430 ATTTGTTCAC
* *
89700440 TCCATTCAGAGAAGTTTAACATATTAAATAATGTAACAGTTGATCAT
1 TCCATTCAGAGAAGTATAACACATTAAATAATGTAACAGTTGATCAT
89700487 TCCATTCAGAGAAGTATAACACATTAAATAATGTAACAGTTGA
1 TCCATTCAGAGAAGTATAACACATTAAATAATGTAACAGTTGA
89700530 AGCTTGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (47 bp):
TCCATTCAGAGAAGTATAACACATTAAATAATGTAACAGTTGATCAT
Found at i:89703766 original size:12 final size:12
Alignment explanation
Indices: 89703749--89703776 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
89703739 AAGAACACAC
89703749 CAGAATTCATAG
1 CAGAATTCATAG
89703761 CAGAATTCATAG
1 CAGAATTCATAG
89703773 CAGA
1 CAGA
89703777 TGACAGTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (12 bp):
CAGAATTCATAG
Found at i:89703820 original size:16 final size:15
Alignment explanation
Indices: 89703795--89703824 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
89703785 GGAAAATAGG
89703795 ATTTTTTTTATTTTT
1 ATTTTTTTTATTTTT
89703810 ATTTTTATTTATTTT
1 ATTTTT-TTTATTTT
89703825 GTAAATCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
ATTTTTTTTATTTTT
Found at i:89705391 original size:32 final size:32
Alignment explanation
Indices: 89705355--89705419 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
89705345 TGTATGCGTT
89705355 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
89705387 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
89705419 T
1 T
89705420 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:89706929 original size:26 final size:26
Alignment explanation
Indices: 89706900--89706952 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
89706890 TTTACAGTTT
89706900 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
89706926 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
89706952 T
1 T
89706953 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:89709398 original size:131 final size:132
Alignment explanation
Indices: 89709138--89709476 Score: 467
Period size: 131 Copynumber: 2.6 Consensus size: 132
89709128 TCCAATGAAA
* * * * *
89709138 AAATCGAAACCCAGCACAATAGAGCACGATTCCTCGAATTTCTAAACATCGAACATTGCCTT-AT
1 AAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTGCCTTCGT
** ** * *
89709202 TTT--AG-AA-TTTAGGGAACATGAGTGAAATTTTAAAGGGATATTCGATTATTTTGAACAAATA
66 TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACA
89709263 GG
131 GG
* *
89709265 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGT
1 AAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTGCCTTCGT
*
89709330 TTTAAAGAAATTTTAAAG-ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACG
66 TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACA
89709394 GG
131 GG
* * *
89709396 AAATCGTAACCCAGCACGATAGGGCACGACTCC-CGAATTGCCAAACATCGAGCATTGCCTTCGT
1 AAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTGCCTTCGT
*
89709460 TTTAAAGAATTTTTAAA
66 TTTAAAGAAATTTTAAA
89709477 TGAATAATTA
Statistics
Matches: 188, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
127 56 0.30
128 4 0.02
130 47 0.25
131 76 0.40
132 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (132 bp):
AAATCGAAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTGCCTTCGT
TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACA
GG
Found at i:89710533 original size:2 final size:2
Alignment explanation
Indices: 89710526--89710555 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89710516 ATGTATTAAC
*
89710526 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89710556 TTAAACAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:89712777 original size:132 final size:133
Alignment explanation
Indices: 89712360--89713066 Score: 1094
Period size: 133 Copynumber: 5.3 Consensus size: 133
89712350 AGGTTCAACT
* * * * ** * *
89712360 TCTTTGATCTGTTCCACTACAACTTCAGGGAGACGGGATCTGCAATCTTCAGCCTACTCTACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* *
89712425 AACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACTAGATTCG
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
89712490 CCG
131 CCG
* * *
89712493 TCTTCGATCTCCTCCACTGTAACTTTAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* * * *
89712558 AACTTTAGGGAGTTAGGATGGTGGCTTAAATCTGTTTCATTGCAACTTTAGGAAGATTAGATTCG
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
*
89712623 CTG
131 CCG
*
89712626 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATTTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* * * *
89712691 AACTTTA-AGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAATTTCAGGAAGACTAGATTCG
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
89712755 CCG
131 CCG
89712758 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* * *
89712823 AACTTTA-GGAGCTAGGATGGTGGCTTAAATTTGTTTCACTGCAACTTCAAGAAGACTAGATTTG
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
89712887 CCG
131 CCG
* * *
89712890 TCTTCGATCTGTTCCACAGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
* *
89712955 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTACAACTTCAGGAAGACTAGATTCA
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
89713020 CCG
131 CCG
* * *
89713023 TATTCGATCTACTCCACTGCAACTTCAAGGAAACAAGATCTACA
1 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACA
89713067 GAATCGGTTT
Statistics
Matches: 521, Mismatches: 52, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
132 244 0.47
133 277 0.53
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (133 bp):
TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCACTAC
AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAGGAAGACTAGATTCG
CCG
Found at i:89712785 original size:45 final size:44
Alignment explanation
Indices: 89712454--89713062 Score: 133
Period size: 45 Copynumber: 13.8 Consensus size: 44
89712444 GGTGGCTTAA
* *
89712454 ATCTGCTTCACTGCAACTTCAGGAAGACTAGATTCGCCGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACTAGA-TCGCTGTCTTCG
* * * * * **
89712499 ATCTCCTCCACTGTAACTTTAGGGAA-ACAAGATCTACAATCTTC-
1 ATCTGCTCCACTGCAACTTCA-GGAAGACTAGATC-GCTGTCTTCG
* * * * * * * * **
89712543 AGCCTACTCCACTACAACTTTAGGGAG-TTAGGAT-GGTGGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACTA-GATCGCTGTCTTCG
* * * * *
89712587 ATCTGTTTCATTGCAACTTTAGGAAGATTAGATTCGCTGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACTAGA-TCGCTGTCTTCG
* * ** *
89712632 ATCTGCTCCACTGCAACTTCAGGGAA-ACAAGATCTACAATTTTC-
1 ATCTGCTCCACTGCAACTTCA-GGAAGACTAGATC-GCTGTCTTCG
* * * * * * * **
89712676 AGCCTACTCCACTACAACTTTAAG-AG-CTAGGAT-GGTGGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACTA-GATCGCTGTCTTCG
* * * *
89712719 ATCTGCTTCACTACAATTTCAGGAAGACTAGATTCGCCGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACTAGA-TCGCTGTCTTCG
* * **
89712764 ATCTGCTCCACTGCAACTTCAGGGAA-ACAAGATCTACAATCTTC-
1 ATCTGCTCCACTGCAACTTCA-GGAAGACTAGATC-GCTGTCTTCG
* * * * * * **
89712808 AGCCTACTCCACTACAACTTTAGG-AG-CTAGGAT-GGTGGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACTA-GATCGCTGTCTTCG
* * * * * *
89712851 ATTTGTTTCACTGCAACTTCAAGAAGACTAGATTTGCCGTCTTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACTAGA-TCGCTGTCTTCG
* * * **
89712896 ATCTGTTCCACAGCAACTTCAGGGAA-AC-AGGATCTACAATCTTC-
1 ATCTGCTCCACTGCAACTTCA-GGAAGACTA-GATC-GCTGTCTTCG
* * * * * * * **
89712940 AGCCTACTCCACTACAACTTTAGGGAG-CTAGGAT-GGTGGCTTAA
1 A-TCTGCTCCACTGCAACTTCAGGAAGACTA-GATCGCTGTCTTCG
* * * * * *
89712984 ATCTGTTTCACTACAACTTCAGGAAGACTAGATTCACCGTATTCG
1 ATCTGCTCCACTGCAACTTCAGGAAGACTAGA-TCGCTGTCTTCG
* *
89713029 ATCTACTCCACTGCAACTTCAAGGAA-ACAAGATC
1 ATCTGCTCCACTGCAACTTC-AGGAAGACTAGATC
89713063 TACAGAATCG
Statistics
Matches: 388, Mismatches: 136, Indels: 81
0.64 0.22 0.13
Matches are distributed among these distances:
42 35 0.09
43 63 0.16
44 49 0.13
45 221 0.57
46 20 0.05
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGAAGACTAGATCGCTGTCTTCG
Found at i:89712970 original size:265 final size:266
Alignment explanation
Indices: 89712360--89713066 Score: 1123
Period size: 265 Copynumber: 2.7 Consensus size: 266
89712350 AGGTTCAACT
* * * * *
89712360 TCTTTGATCTGTTCCACTA-CAACTTCAGGGAGACGGGATCTGCAATCTTCAGCCTACTCTACTA
1 TCTTCGATCTGTTCCAC-AGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTA
* *
89712424 CAACTTTAGGGAGATAGGATGGTGGCTTAAATCTGCTTCACTGCAACTTCAGGAAGACTAGATTC
65 CAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAACTTCAGGAAGACTAGATTC
* * *
89712489 GCCGTCTTCGATCTCCTCCACTGTAACTTTAGGGAAACAAGATCTACAATCTTCAGCCTACTCCA
130 GCCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCA
* * * * *
89712554 CTACAACTTTAGGGAGTTAGGATGGTGGCTTAAATCTGTTTCATTGCAACTTTAGGAAGATTAGA
195 CTACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAAGAAGACTAGA
*
89712619 TTCGCTG
260 TTCGCCG
* * * *
89712626 TCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATTTTCAGCCTACTCCACTAC
1 TCTTCGATCTGTTCCACAGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTAC
* *
89712691 AACTTTA-AGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAATTTCAGGAAGACTAGATTCG
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAACTTCAGGAAGACTAGATTCG
*
89712755 CCGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCAC
131 CCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCAC
*
89712820 TACAACTTTA-GGAGCTAGGATGGTGGCTTAAATTTGTTTCACTGCAACTTCAAGAAGACTAGAT
196 TACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAAGAAGACTAGAT
*
89712884 TTGCCG
261 TCGCCG
89712890 TCTTCGATCTGTTCCACAGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTAC
1 TCTTCGATCTGTTCCACAGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTAC
* *
89712955 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTACAACTTCAGGAAGACTAGATTCA
66 AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAACTTCAGGAAGACTAGATTCG
* *
89713020 CCGTATTCGATCTACTCCACTGCAACTTCAAGGAAACAAGATCTACA
131 CCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTACA
89713067 GAATCGGTTT
Statistics
Matches: 404, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
264 120 0.30
265 222 0.55
266 62 0.15
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (266 bp):
TCTTCGATCTGTTCCACAGCAACTTCAGGGAAACAGGATCTACAATCTTCAGCCTACTCCACTAC
AACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGCTTCACTACAACTTCAGGAAGACTAGATTCG
CCGTCTTCGATCTACTCCACTGCAACTTCAGGGAAACAAGATCTACAATCTTCAGCCTACTCCAC
TACAACTTTAGGGAGCTAGGATGGTGGCTTAAATCTGTTTCACTGCAACTTCAAGAAGACTAGAT
TCGCCG
Found at i:89718685 original size:131 final size:132
Alignment explanation
Indices: 89718425--89718763 Score: 460
Period size: 131 Copynumber: 2.6 Consensus size: 132
89718415 TCCAATGAAA
* * * * * *
89718425 AAATCGAAACCCAGCACAATAGAGCACGATTCCTCGAATTTCTAAACATCGAACATTACCTT-AT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGT
** ** *
89718489 TTT--AG-AA-TTTAGGGAACATGAGTGAAATTTTAAAGGGATATTCGATTATTTTGAACAAATA
66 TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGGATATTCGATTATTTTGAACAAACA
89718550 GG
131 GG
*
89718552 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAGACATCGAACATTACCTTCGT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGT
89718617 TTTAAAGAAATTTTAAAG-ACATGAGTGAAATTCCAAA-GGACTATTCGATTATTTTGAACAAAC
66 TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGGA-TATTCGATTATTTTGAACAAAC
*
89718680 GGG
130 AGG
* * *
89718683 AAATCGCAACACAGCACGATAGGGCACGATTCC-CGAATTGCCAAACATCGAGCATTGCCTTCGT
1 AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGT
*
89718747 TTTAAAGAATTTTTAAA
66 TTTAAAGAAATTTTAAA
89718764 TGAATAATTA
Statistics
Matches: 188, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
127 56 0.30
128 4 0.02
130 49 0.26
131 74 0.39
132 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (132 bp):
AAATCGCAACCCAGCACGATAGGGCACGATTCCTCGAATTGCCAAACATCGAACATTACCTTCGT
TTTAAAGAAATTTTAAAGAACATGAGTGAAATTCCAAAGGGATATTCGATTATTTTGAACAAACA
GG
Found at i:89719822 original size:2 final size:2
Alignment explanation
Indices: 89719815--89719844 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89719805 ATGTATTAAC
*
89719815 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89719845 TTAAACAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:89722841 original size:15 final size:15
Alignment explanation
Indices: 89722823--89722852 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
89722813 AAATTTTAAT
*
89722823 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
89722838 TTTTTATAATTTATA
1 TTTTTATAATTTATA
89722853 AAGGATTAAA
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:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Done.