Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007967.1 Hibiscus syriacus cultivar Beakdansim tig00110402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2476418
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1284736 original size:2 final size:2
Alignment explanation
Indices: 1284724--1284772 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1284714 TAAATTAAAA
* * *
1284724 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1284764 AT AT AT AT A
1 AT AT AT AT A
1284773 CCAGTCCCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1288418 original size:14 final size:15
Alignment explanation
Indices: 1288389--1288421 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1288379 TTTTTATTAA
*
1288389 TATAATATTTTAATT
1 TATAATATTATAATT
1288404 TATAAT-TTATAATT
1 TATAATATTATAATT
1288418 TATA
1 TATA
1288422 GTAGTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATAATATTATAATT
Found at i:1290338 original size:298 final size:299
Alignment explanation
Indices: 1289783--1290383 Score: 1143
Period size: 298 Copynumber: 2.0 Consensus size: 299
1289773 TATTGGGATC
1289783 ATGGATGATATAATAAATCGGATTCATAAAATAATTTCTTTTGTCTGTAGGTTTATTTTAATAAA
1 ATGGATGATATAATAAATCGGATTCATAAAATAATTTCTTTTGTCTGTAGGTTTATTTTAATAAA
1289848 ATCCGAACCAACAAATTTGTCAGCGTTATTATATTTAAAAATACCTAATAATTATTTTTTTGAAG
66 ATCCGAACCAACAAATTTGTCAGCGTTATTATATTTAAAAATACCTAATAATTATTTTTTTGAAG
1289913 ACAACTCTTAAACCAGATTAGTTAGAAAAATAACCCTCAAAATGTCACCTAGGATAACCTTGCGC
131 ACAACTCTTAAACCAGATTAGTTAGAAAAATAACCCTCAAAATGTCACCTAGGATAACCTTGCGC
1289978 TTTGCAAAAAAACAGATCAGATTTTGCATTTTACGAAAGCGAGTTTCATGCATTTATTATTATTA
196 TTTGCAAAAAAACAGATCAGATTTTGCATTTTACGAAAGCGAGTTTCATGCA-TTATTATTATTA
1290043 -TTTTAATATTAAAC-ACTTTATTTAAAAAAGTTGATGAT
260 TTTTTAATATTAAACAACTTTATTTAAAAAAGTTGATGAT
1290081 ATGGATGATATAATAAATCGGATTCATAAAATAATTTCTTTTGTCTGTAGGTTTATTTTAATAAA
1 ATGGATGATATAATAAATCGGATTCATAAAATAATTTCTTTTGTCTGTAGGTTTATTTTAATAAA
1290146 ATCCGAACCAACAAATTTGTCAGCGTTATTATATTTAAAAATACCTAATAATTATTTTTTTGAAG
66 ATCCGAACCAACAAATTTGTCAGCGTTATTATATTTAAAAATACCTAATAATTATTTTTTTGAAG
1290211 AACAACTCTTAAACCAGATTAGTTAGAAAAATAACCCTCAAAATGTCACCTAGGATAACCTTGCG
131 -ACAACTCTTAAACCAGATTAGTTAGAAAAATAACCCTCAAAATGTCACCTAGGATAACCTTGCG
1290276 CTTTGCAAAAAAACAAGATCAGATTTTGCATTTTACGAAAAGCGAGTTTCATGCATTTATTATTA
195 CTTTGCAAAAAAAC-AGATCAGATTTTGCATTTTACG-AAAGCGAGTTTCATGCA-TTATTATTA
1290341 TTATTTTTAATATTAAACAACTTTATTTAAAAAAGTTGATGAT
257 TTATTTTTAATATTAAACAACTTTATTTAAAAAAGTTGATGAT
1290384 CTTACCTCCT
Statistics
Matches: 298, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
298 130 0.44
299 78 0.26
300 22 0.07
301 30 0.10
302 14 0.05
303 24 0.08
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.37
Consensus pattern (299 bp):
ATGGATGATATAATAAATCGGATTCATAAAATAATTTCTTTTGTCTGTAGGTTTATTTTAATAAA
ATCCGAACCAACAAATTTGTCAGCGTTATTATATTTAAAAATACCTAATAATTATTTTTTTGAAG
ACAACTCTTAAACCAGATTAGTTAGAAAAATAACCCTCAAAATGTCACCTAGGATAACCTTGCGC
TTTGCAAAAAAACAGATCAGATTTTGCATTTTACGAAAGCGAGTTTCATGCATTATTATTATTAT
TTTTAATATTAAACAACTTTATTTAAAAAAGTTGATGAT
Found at i:1298160 original size:21 final size:20
Alignment explanation
Indices: 1298136--1298228 Score: 132
Period size: 21 Copynumber: 4.5 Consensus size: 20
1298126 TCGTACCAAG
1298136 GACGAGAAGAGCATTCATCAA
1 GACGAGAAG-GCATTCATCAA
*
1298157 GACGAGAATGTCATTCATCAA
1 GACGAGAA-GGCATTCATCAA
*
1298178 GACGAGAATGCCATTCATCAA
1 GACGAGAA-GGCATTCATCAA
1298199 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGG-CATTCATCAA
1298220 GACGAGAAG
1 GACGAGAAG
1298229 ACCACATCGC
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (20 bp):
GACGAGAAGGCATTCATCAA
Found at i:1298183 original size:42 final size:42
Alignment explanation
Indices: 1298136--1298232 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
1298126 TCGTACCAAG
* * *
1298136 GACGAGAAGAGCATTCATCAAGACGAGAATGTCATTCATCAA
1 GACGAGAAGACCATTCATCAAGACGAGAAGGCCATTCATCAA
1298178 GACGAGAATG-CCATTCATCAAGACGAGAAGGCCATTCATCAA
1 GACGAGAA-GACCATTCATCAAGACGAGAAGGCCATTCATCAA
1298220 GACGAGAAGACCA
1 GACGAGAAGACCA
1298233 CATCGCATGG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.02
42 48 0.96
43 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.23, T:0.15
Consensus pattern (42 bp):
GACGAGAAGACCATTCATCAAGACGAGAAGGCCATTCATCAA
Found at i:1304373 original size:9 final size:9
Alignment explanation
Indices: 1304359--1304439 Score: 102
Period size: 9 Copynumber: 9.6 Consensus size: 9
1304349 CTTGAAGATG
1304359 AAAAATGAA
1 AAAAATGAA
1304368 AAAAATG--
1 AAAAATGAA
1304375 AAAAAT--A
1 AAAAATGAA
1304382 AAAAAT-AA
1 AAAAATGAA
1304390 AAAAATG-A
1 AAAAATGAA
1304398 AAAAATGAA
1 AAAAATGAA
1304407 AAAAATGAAA
1 AAAAATG-AA
1304417 AAAAATGAA
1 AAAAATGAA
*
1304426 AAAAACGAA
1 AAAAATGAA
1304435 AAAAA
1 AAAAA
1304440 ACAAAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
7 12 0.18
8 15 0.23
9 30 0.45
10 9 0.14
ACGTcount: A:0.80, C:0.01, G:0.09, T:0.10
Consensus pattern (9 bp):
AAAAATGAA
Found at i:1304378 original size:8 final size:8
Alignment explanation
Indices: 1304359--1304429 Score: 83
Period size: 8 Copynumber: 8.6 Consensus size: 8
1304349 CTTGAAGATG
1304359 AAAAATGAA
1 AAAAATG-A
1304368 AAAAATG-
1 AAAAATGA
1304375 AAAAAT-A
1 AAAAATGA
*
1304382 AAAAATAA
1 AAAAATGA
1304390 AAAAATGA
1 AAAAATGA
1304398 AAAAATGAA
1 AAAAATG-A
1304407 AAAAATGAAA
1 AAAAATG--A
1304417 AAAAATGA
1 AAAAATGA
1304425 AAAAA
1 AAAAA
1304430 ACGAAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
7 12 0.21
8 21 0.37
9 15 0.26
10 9 0.16
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.11
Consensus pattern (8 bp):
AAAAATGA
Found at i:1304379 original size:10 final size:10
Alignment explanation
Indices: 1304359--1304449 Score: 86
Period size: 9 Copynumber: 9.5 Consensus size: 10
1304349 CTTGAAGATG
1304359 AAAAATG-AA
1 AAAAATGAAA
1304368 AAAAATGAAA
1 AAAAATGAAA
**
1304378 AATAAAAAATAA
1 AA-AAATGA-AA
1304390 AAAAATG--A
1 AAAAATGAAA
1304398 AAAAATG-AA
1 AAAAATGAAA
1304407 AAAAATGAAA
1 AAAAATGAAA
1304417 AAAAATG-AA
1 AAAAATGAAA
*
1304426 AAAAACGAAA
1 AAAAATGAAA
*
1304436 AAAAA-CAAA
1 AAAAATGAAA
1304445 AAAAA
1 AAAAA
1304450 AATAAAGGGG
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
8 8 0.11
9 31 0.44
10 20 0.29
11 7 0.10
12 4 0.06
ACGTcount: A:0.81, C:0.02, G:0.08, T:0.09
Consensus pattern (10 bp):
AAAAATGAAA
Found at i:1304410 original size:19 final size:19
Alignment explanation
Indices: 1304359--1304440 Score: 98
Period size: 19 Copynumber: 4.3 Consensus size: 19
1304349 CTTGAAGATG
1304359 AAAAATGAAAAAAATGAAAAATA
1 AAAAATGAAAAAAATG---AA-A
1304382 AAAAAT-AAAAAAATG--A
1 AAAAATGAAAAAAATGAAA
1304398 AAAAATGAAAAAAATGAAA
1 AAAAATGAAAAAAATGAAA
*
1304417 AAAAATGAAAAAAACGAAA
1 AAAAATGAAAAAAATGAAA
1304436 AAAAA
1 AAAAA
1304441 CAAAAAAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
16 7 0.13
17 9 0.16
19 24 0.44
22 9 0.16
23 6 0.11
ACGTcount: A:0.80, C:0.01, G:0.09, T:0.10
Consensus pattern (19 bp):
AAAAATGAAAAAAATGAAA
Found at i:1304428 original size:7 final size:7
Alignment explanation
Indices: 1304356--1304409 Score: 54
Period size: 7 Copynumber: 7.1 Consensus size: 7
1304346 TTGCTTGAAG
1304356 ATGAAAA
1 ATGAAAA
1304363 ATGAAAAAA
1 ATG--AAAA
1304372 ATGAAAA
1 ATGAAAA
*
1304379 ATAAAAA
1 ATGAAAA
*
1304386 ATAAAAAA
1 AT-GAAAA
1304394 ATGAAAAA
1 ATG-AAAA
1304402 ATGAAAA
1 ATGAAAA
1304409 A
1 A
1304410 AATGAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 20 0.49
8 14 0.34
9 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (7 bp):
ATGAAAA
Found at i:1304446 original size:19 final size:19
Alignment explanation
Indices: 1304405--1304449 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1304395 TGAAAAAATG
* **
1304405 AAAAAAATGAAAAAAAATG
1 AAAAAAACGAAAAAAAACA
1304424 AAAAAAACGAAAAAAAACA
1 AAAAAAACGAAAAAAAACA
1304443 AAAAAAA
1 AAAAAAA
1304450 AATAAAGGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.84, C:0.04, G:0.07, T:0.04
Consensus pattern (19 bp):
AAAAAAACGAAAAAAAACA
Found at i:1305972 original size:53 final size:53
Alignment explanation
Indices: 1305682--1306338 Score: 975
Period size: 53 Copynumber: 12.5 Consensus size: 53
1305672 AGCACAGAAG
1305682 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGA-T
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATT
*
1305733 A-TGTTCGAGTTCTACTCCCTG-A-AAATAG-G-GTGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1305781 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-G-CCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1305833 ATTGTTCGAGTTCTTACT-CCTGAAGAAA-AGAGAGCGGACCCGTAGG-A-ATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1305883 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAATAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1305937 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1305990 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCTGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
1306044 AGTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1306097 ATTGTTCGAGTTCTTTCTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
1306151 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * * * *
1306204 ATTATTCGAGTTCTACTCCCTGAAGGAAGAGAGAGCAGACCCGTAGGAAGATG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* **
1306257 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGAGCGAGCCCGTAGGAAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCG-GA-CCCGTAGGAAGATT
*
1306311 AATGTTCGAGTTCTACTCCCTGAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
1306339 GAGGAAGTGA
Statistics
Matches: 561, Mismatches: 28, Indels: 31
0.90 0.05 0.05
Matches are distributed among these distances:
47 23 0.04
48 2 0.00
49 12 0.02
50 57 0.10
51 24 0.04
52 69 0.12
53 217 0.39
54 157 0.28
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:1306026 original size:107 final size:107
Alignment explanation
Indices: 1305682--1306338 Score: 1008
Period size: 107 Copynumber: 6.3 Consensus size: 107
1305672 AGCACAGAAG
1305682 ATTGTTCGAGTTC-TACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGA-TA-TGTTCGAG
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAA-AGAGAGCGGACCCGTAGGAAGATTATTGTTCGAG
*
1305742 TTCTACTCCCTG-A-AAATAG-G-GTGGACCCGTAGGAAGATT
65 TTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
1305781 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-G-CCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1305844 TCTTACT-CCTGAAGAAA-AGAGAGCGGACCCGTAGG-A-ATT
66 TC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
*
1305883 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAATAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1305948 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1305990 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCTGTAGGAAGATTAGTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1306055 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1306097 ATTGTTCGAGTTCTTTCTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTTGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
1306162 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
66 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * * * *
1306204 ATTATTCGAGTTC-TACTCCCTGAAGGAAGAGAGAGCAGACCCGTAGGAAGATGATTGTTCGAGT
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* **
1306268 TCTACTCCCTGAAGAAA-AGAGAGAGCGAGCCCGTAGGAAGAAG
66 TCTACTCCCTGAAGAAATAGAGAGCG-GA-CCCGTAGGAAGATT
*
1306311 AATGTTCGAGTTC-TACTCCCTGAAGAAA
1 ATTGTTCGAGTTCTTACTCCCTGAAGAAA
1306339 GAGGAAGTGA
Statistics
Matches: 516, Mismatches: 24, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
99 27 0.05
100 19 0.04
101 17 0.03
102 45 0.09
103 10 0.02
104 49 0.09
105 25 0.05
106 65 0.13
107 259 0.50
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (107 bp):
ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:1306093 original size:160 final size:160
Alignment explanation
Indices: 1305682--1306338 Score: 979
Period size: 160 Copynumber: 4.2 Consensus size: 160
1305672 AGCACAGAAG
1305682 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCGGACCCGTAGGAAGA-TA-TGTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
1305743 TCTACTCCCTG-A-AAATAG-G-GTGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
1305804 AAGAAATAGAGAGC-G-CCCGTAGGAAGATT
130 AAGAAATAGAGAGCGGACCCGTAGGAAGATT
1305833 ATTGTTCGAGTTCTTACT-CCTGAAG-AAAAGAGAGCGGACCCGTAGG-A-ATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* *
1305894 TCTTACTCCCTGAAGAAAAATAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCT
65 TC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCT
1305958 GAAGAAATAGAGAGCGGACCCGTAGGAAGATT
129 GAAGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
1305990 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCTGTAGGAAGATTAGTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
*
1306055 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTTCTCCCTG
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
*
1306120 AAGAAAAAGAGAGCGGACCCGTAGGAAGATT
130 AAGAAATAGAGAGCGGACCCGTAGGAAGATT
* * *
1306151 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* * * *
1306216 CTACTCCCTGAAGGAAGAGAGAGCAGACCCGTAGGAAGATGATTGTTCGAGTTC-TACTCCCTGA
66 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
* **
1306280 AGAAA-AGAGAGAGCGAGCCCGTAGGAAGAAG
131 AGAAATAGAGAGCG-GA-CCCGTAGGAAGATT
*
1306311 AATGTTCGAGTTCTACTCCCTGAAGAAA
1 ATTGTTCGAGTTCTACTCCCTGAAGAAA
1306339 GAGGAAGTGA
Statistics
Matches: 463, Mismatches: 24, Indels: 29
0.90 0.05 0.06
Matches are distributed among these distances:
149 3 0.01
150 7 0.02
151 44 0.10
152 13 0.03
153 1 0.00
154 4 0.01
155 24 0.05
156 32 0.07
157 32 0.07
158 14 0.03
159 36 0.08
160 188 0.41
161 65 0.14
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (160 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
AGAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:1312696 original size:38 final size:38
Alignment explanation
Indices: 1312645--1312722 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1312635 TTACTCATTT
1312645 AACAAAGCAATTCACCTAGTTAAGGTTTTGCTGATAGA
1 AACAAAGCAATTCACCTAGTTAAGGTTTTGCTGATAGA
1312683 AACAAAGCAATTCACCTAGTTAAGGTTTTGCTGATAGA
1 AACAAAGCAATTCACCTAGTTAAGGTTTTGCTGATAGA
1312721 AA
1 AA
1312723 TATTTGAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (38 bp):
AACAAAGCAATTCACCTAGTTAAGGTTTTGCTGATAGA
Found at i:1318736 original size:18 final size:19
Alignment explanation
Indices: 1318700--1318741 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
1318690 TGATAGAATA
*
1318700 TTTTATTTATTATTTAAAT
1 TTTTATTTATTATTAAAAT
1318719 TTTTATTTATT-TTAAAAT
1 TTTTATTTATTATTAAAAT
1318737 TTTTA
1 TTTTA
1318742 ATATTAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTTATTATTAAAAT
Found at i:1318941 original size:25 final size:25
Alignment explanation
Indices: 1318906--1318968 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1318896 TCTAAAACCA
*
1318906 AAAACCAAAAAGAACATT-GTTTTTCG
1 AAAA-CAAAAAGAA-ATTAGTATTTCG
* *
1318932 AAAACAAAAAGGATTTAGTATTTCG
1 AAAACAAAAAGAAATTAGTATTTCG
*
1318957 AAAACAGAAAGA
1 AAAACAAAAAGA
1318969 GAATACCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.22
Consensus pattern (25 bp):
AAAACAAAAAGAAATTAGTATTTCG
Found at i:1320746 original size:18 final size:18
Alignment explanation
Indices: 1320712--1320745 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1320702 AAGTAAGAAA
1320712 ATTAAAAAAACATAAAAC
1 ATTAAAAAAACATAAAAC
*
1320730 ATTATAAAAA-ATAAAA
1 ATTAAAAAAACATAAAA
1320746 AATAAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (18 bp):
ATTAAAAAAACATAAAAC
Found at i:1322568 original size:3 final size:3
Alignment explanation
Indices: 1322554--1322608 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1322544 TAAATATTGT
1322554 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1322601 TAA TAA TA
1 TAA TAA TA
1322609 GTTAATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1329175 original size:22 final size:22
Alignment explanation
Indices: 1329115--1329175 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
1329105 GAATCGATAC
*
1329115 CCCCCTTGAAGGGAAACTGATT
1 CCCCCTTGAAGGGGAACTGATT
*
1329137 CCCCATTTGAAGGGGAACTGATT
1 CCCC-CTTGAAGGGGAACTGATT
*
1329160 CCCCCTTGTAGGGGAA
1 CCCCCTTGAAGGGGAA
1329176 TCGATACCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACTGATT
Found at i:1329185 original size:22 final size:22
Alignment explanation
Indices: 1329103--1329191 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
1329093 TTAGTGCAGA
*
1329103 GGGAATC-GATACCCCCCTTGAA
1 GGGAATCTGATA-CCCCCTTGAG
* * *
1329125 GGGAAACTGATTCCCCATTTGAAG
1 GGGAATCTGATACCCC-CTTG-AG
*
1329149 GGGAA-CTGATTCCCCCTTGTAG
1 GGGAATCTGATACCCCCTTG-AG
1329171 GGGAATC-GATACCCCC-TGAG
1 GGGAATCTGATACCCCCTTGAG
1329191 G
1 G
1329192 TTCTGGTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
20 3 0.05
21 2 0.04
22 28 0.50
23 17 0.30
24 6 0.11
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
GGGAATCTGATACCCCCTTGAG
Found at i:1335959 original size:21 final size:20
Alignment explanation
Indices: 1335917--1335959 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1335907 AATTTTTAAT
* *
1335917 TATATTTTAAAAAAAATTAA
1 TATAATTTAAAAAAAATAAA
*
1335937 TATAATTTAAATATAAATAAA
1 TATAATTTAAA-AAAAATAAA
1335958 TA
1 TA
1335960 AAAAATGAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TATAATTTAAAAAAAATAAA
Found at i:1342406 original size:60 final size:60
Alignment explanation
Indices: 1342294--1342408 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1342284 ATATTTGGAT
* * *
1342294 GACCATTTTGTAACTTTTGATAGCCGAGGGACTCAACAAAGCAACACTCTATAGTTAGAG
1 GACCATTTTGTAACTTGTAATAGCCGAGGGACTCAACAAAGCAACACCCTATAGTTAGAG
* * * * * *
1342354 GACCATTTTGTAACTTGTAATAGTCTAGGGACTTAATAAAGTAATACCCTATAGT
1 GACCATTTTGTAACTTGTAATAGCCGAGGGACTCAACAAAGCAACACCCTATAGT
1342409 CGGGAGACCA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (60 bp):
GACCATTTTGTAACTTGTAATAGCCGAGGGACTCAACAAAGCAACACCCTATAGTTAGAG
Found at i:1343269 original size:31 final size:31
Alignment explanation
Indices: 1343234--1343330 Score: 115
Period size: 31 Copynumber: 3.1 Consensus size: 31
1343224 TTTTAATTAT
* * * *
1343234 ATTTTTATCAATCAATTATGATTAAGTTAAC
1 ATTTTAATCACTCAATTATGAATAAGTTTAC
* *
1343265 ATTTTAATCACTCGATTACGAATAAGTTTAC
1 ATTTTAATCACTCAATTATGAATAAGTTTAC
*
1343296 ATTTTGATCACT-AGATTATGAATAAGTTTAC
1 ATTTTAATCACTCA-ATTATGAATAAGTTTAC
1343327 ATTT
1 ATTT
1343331 GACCATTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.43
Consensus pattern (31 bp):
ATTTTAATCACTCAATTATGAATAAGTTTAC
Found at i:1344048 original size:30 final size:30
Alignment explanation
Indices: 1344012--1344162 Score: 302
Period size: 30 Copynumber: 5.0 Consensus size: 30
1344002 AAACTAACAC
1344012 AAGCAATTAATAAACAGATTATGGATGATT
1 AAGCAATTAATAAACAGATTATGGATGATT
1344042 AAGCAATTAATAAACAGATTATGGATGATT
1 AAGCAATTAATAAACAGATTATGGATGATT
1344072 AAGCAATTAATAAACAGATTATGGATGATT
1 AAGCAATTAATAAACAGATTATGGATGATT
1344102 AAGCAATTAATAAACAGATTATGGATGATT
1 AAGCAATTAATAAACAGATTATGGATGATT
1344132 AAGCAATTAATAAACAGATTATGGATGATT
1 AAGCAATTAATAAACAGATTATGGATGATT
1344162 A
1 A
1344163 TTTATATGTA
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 121 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (30 bp):
AAGCAATTAATAAACAGATTATGGATGATT
Found at i:1346494 original size:14 final size:13
Alignment explanation
Indices: 1346459--1346500 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1346449 ATTCGATTCA
* *
1346459 TATTTATTTTACT
1 TATTTATTTAAAT
1346472 TATTTATTTAAAT
1 TATTTATTTAAAT
1346485 TATATTATTTAAAT
1 TAT-TTATTTAAAT
1346499 TA
1 TA
1346501 CAAAATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATTTAAAT
Found at i:1349459 original size:21 final size:21
Alignment explanation
Indices: 1349433--1349472 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1349423 GATGGGGAAA
1349433 GAAAATTGTGATAACTTATGG
1 GAAAATTGTGATAACTTATGG
1349454 GAAAATTGTGATAACTTAT
1 GAAAATTGTGATAACTTAT
1349473 ATACCATTTC
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:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (21 bp):
GAAAATTGTGATAACTTATGG
Found at i:1376081 original size:28 final size:28
Alignment explanation
Indices: 1376049--1376172 Score: 230
Period size: 28 Copynumber: 4.4 Consensus size: 28
1376039 GGGTTGATGT
*
1376049 CAATATGATAATTATACTTCAATTTTCA
1 CAATATGATCATTATACTTCAATTTTCA
*
1376077 CAATATGATCATTATACTTCAATTTTAA
1 CAATATGATCATTATACTTCAATTTTCA
1376105 CAATATGATCATTATACTTCAATTTTCA
1 CAATATGATCATTATACTTCAATTTTCA
1376133 CAATATGATCATTATACTTCAATTTTCA
1 CAATATGATCATTATACTTCAATTTTCA
1376161 CAATATGATCAT
1 CAATATGATCAT
1376173 ATAACTATTT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 93 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (28 bp):
CAATATGATCATTATACTTCAATTTTCA
Found at i:1378069 original size:16 final size:17
Alignment explanation
Indices: 1378043--1378079 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1378033 CACAATAAAT
1378043 ATATAAAATTAAAAAAA
1 ATATAAAATTAAAAAAA
*
1378060 ATAT-AAATTATAAAAA
1 ATATAAAATTAAAAAAA
1378076 ATAT
1 ATAT
1378080 CACTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAAAATTAAAAAAA
Found at i:1385525 original size:31 final size:31
Alignment explanation
Indices: 1385455--1385529 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
1385445 GTTTTAAAAG
* * *
1385455 TAACAAATTAGTCATTAATGTTATCGAATTG
1 TAACAAATTGGTCATTAACGTTATCGAATTC
1385486 TAA-AAATTGGTC-TATAACGTTATC-AATTTC
1 TAACAAATTGGTCAT-TAACGTTATCGAA-TTC
1385516 TAACAAATTGGTCA
1 TAACAAATTGGTCA
1385530 CTTGATGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 3 0.08
30 22 0.59
31 12 0.32
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (31 bp):
TAACAAATTGGTCATTAACGTTATCGAATTC
Found at i:1388652 original size:33 final size:33
Alignment explanation
Indices: 1388614--1388682 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
1388604 AATATAACAT
* *
1388614 TAATTCATTGTCTAATGCTGATTTTAATATTAA
1 TAATTCATTGTCTAATGATAATTTTAATATTAA
1388647 TAATTCATTGTCTAATGATAATTTTAATATTAA
1 TAATTCATTGTCTAATGATAATTTTAATATTAA
1388680 TAA
1 TAA
1388683 AATGGTTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (33 bp):
TAATTCATTGTCTAATGATAATTTTAATATTAA
Found at i:1389294 original size:23 final size:23
Alignment explanation
Indices: 1389242--1389295 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1389232 CATATTCATC
* *
1389242 AACACGTTCGTGAACATATAAAA
1 AACATGTTCGCGAACATATAAAA
* *
1389265 AATATGTTCGCGAACAT-TAAACG
1 AACATGTTCGCGAACATATAAA-A
1389288 AACATGTT
1 AACATGTT
1389296 TGTGAACAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.26
Consensus pattern (23 bp):
AACATGTTCGCGAACATATAAAA
Found at i:1389724 original size:15 final size:15
Alignment explanation
Indices: 1389701--1389757 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 15
1389691 ATTTTGATAG
* *
1389701 AAAACTAAAACGTTA
1 AAAATTAAAACATTA
*
1389716 AAAATTAAAATATTA
1 AAAATTAAAACATTA
* *
1389731 AAAAGTTAAAATACTA
1 AAAA-TTAAAACATTA
1389747 AAAAGTTAAAA
1 AAAA-TTAAAA
1389758 TTAAAATGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 16 0.43
16 21 0.57
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAATTAAAACATTA
Found at i:1389725 original size:7 final size:7
Alignment explanation
Indices: 1389713--1389763 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 7
1389703 AACTAAAACG
1389713 TTAAAAA
1 TTAAAAA
1389720 TTAAAATA
1 TTAAAA-A
1389728 TTAAAAA
1 TTAAAAA
1389735 GTTAAAATA
1 -TTAAAA-A
*
1389744 CTAAAAA
1 TTAAAAA
1389751 GTT-AAAA
1 -TTAAAAA
1389758 TTAAAA
1 TTAAAA
1389764 TGATGATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 2 0.05
7 15 0.41
8 19 0.51
9 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:1389739 original size:16 final size:16
Alignment explanation
Indices: 1389713--1389758 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
1389703 AACTAAAACG
1389713 TTAAAAA-TTAAAATA
1 TTAAAAAGTTAAAATA
1389728 TTAAAAAGTTAAAATA
1 TTAAAAAGTTAAAATA
*
1389744 CTAAAAAGTTAAAAT
1 TTAAAAAGTTAAAAT
1389759 TAAAATGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 7 0.24
16 22 0.76
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (16 bp):
TTAAAAAGTTAAAATA
Found at i:1393015 original size:21 final size:21
Alignment explanation
Indices: 1392989--1393035 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
1392979 GATTCGAAAC
1392989 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
1393010 GCGAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
1393031 GCGAA
1 GCGAA
1393036 TATGTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:1393075 original size:21 final size:21
Alignment explanation
Indices: 1393049--1393139 Score: 105
Period size: 21 Copynumber: 4.3 Consensus size: 21
1393039 GTAAATTGCA
* *
1393049 TTGCGATAGTCGAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
1393070 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
1393091 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
*
1393112 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1393133 TTGCGAT
1 TTGCGAT
1393140 TTATTACAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.14
21 42 0.71
23 9 0.15
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1393096 original size:42 final size:40
Alignment explanation
Indices: 1393049--1393167 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 40
1393039 GTAAATTGCA
* *
1393049 TTGCGATAGTCGAAGTTCACGTTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CGTTGCGATAGTCCAAGTTCGCG
* *
1393091 TTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGA--TAGTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* *
1393133 TTGCGATTTATTACAAATTCGTTGCGATAGTCCAA
1 TTGCGA--TAGTCCAAATTCGTTGCGATAGTCCAA
1393168 AATCGCAACG
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 61 0.88
44 8 0.12
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (40 bp):
TTGCGATAGTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:1393155 original size:21 final size:20
Alignment explanation
Indices: 1393089--1393160 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
1393079 TCCAAGTTCG
1393089 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATT-CAAATT
* *
1393110 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTC-AAATT
1393129 CGCGTTGCGATTTATTACAAATT
1 --CGTTGCGATTTATT-CAAATT
1393152 CGTTGCGAT
1 CGTTGCGAT
1393161 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 1 0.02
19 7 0.17
21 25 0.61
23 7 0.17
24 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTATTCAAATT
Found at i:1396426 original size:15 final size:15
Alignment explanation
Indices: 1396408--1396477 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
1396398 TATTTTATTT
1396408 TTAATTATTTATTAA
1 TTAATTATTTATTAA
* *
1396423 TTAAATATATATTAA
1 TTAATTATTTATTAA
*
1396438 TTATTTATTTGATTTTAA
1 TTAATTATTT-A--TTAA
1396456 CTTTAATTATTT-TT-A
1 --TTAATTATTTATTAA
1396471 TTAATTA
1 TTAATTA
1396478 AATATCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 7 0.16
15 21 0.48
16 3 0.07
18 4 0.09
20 9 0.20
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (15 bp):
TTAATTATTTATTAA
Found at i:1397006 original size:15 final size:15
Alignment explanation
Indices: 1396972--1397007 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1396962 TATTTTAATT
1396972 TATAAT-TTAAAAAA
1 TATAATATTAAAAAA
1396986 TA-AATATTAAAAAA
1 TATAATATTAAAAAA
1397000 TATAATAT
1 TATAATAT
1397008 CATTTATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 12 0.60
15 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAATATTAAAAAA
Found at i:1397768 original size:28 final size:28
Alignment explanation
Indices: 1397728--1397784 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1397718 TACCGCCTCT
1397728 ACATGAACCAAACGTGTTAAATACATGG
1 ACATGAACCAAACGTGTTAAATACATGG
1397756 ACATGAACCAAACGTGTTAAATACATGG
1 ACATGAACCAAACGTGTTAAATACATGG
1397784 A
1 A
1397785 AATTGCAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.21
Consensus pattern (28 bp):
ACATGAACCAAACGTGTTAAATACATGG
Found at i:1399503 original size:19 final size:20
Alignment explanation
Indices: 1399481--1399522 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
1399471 TCCCGCTTCT
1399481 TCCCCTCTT-TCCTCCACC-C
1 TCCCCTCTTCT-CTCCACCTC
*
1399500 TCCCTTCTTCTCTCCACCTC
1 TCCCCTCTTCTCTCCACCTC
1399520 TCC
1 TCC
1399523 ATCTCCGACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.05, C:0.60, G:0.00, T:0.36
Consensus pattern (20 bp):
TCCCCTCTTCTCTCCACCTC
Found at i:1406582 original size:46 final size:46
Alignment explanation
Indices: 1406512--1406787 Score: 471
Period size: 46 Copynumber: 6.0 Consensus size: 46
1406502 AAACTGAATT
* * *
1406512 CATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAATGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1406558 CATAACTAAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1406604 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1406650 CAGAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
*
1406696 CAGAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
1406742 CATAATTAAAATGCATGAAAGGATGCATTAAGGCATTAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1406788 ATTAAGGCAT
Statistics
Matches: 219, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 219 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:1406802 original size:158 final size:158
Alignment explanation
Indices: 1406616--1406945 Score: 597
Period size: 158 Copynumber: 2.1 Consensus size: 158
1406606 TAACTAAAAT
1406616 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAA
1406681 GGCATGAAAGGATGCCAGAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGCCAGAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
1406746 ATTAAAATGCATGAAAGGATGCATTAAG
131 ATTAAAATACATGAAAGGATGCATTAAG
* *
1406774 GCATTAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAA
* * *
1406839 GGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAATGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGCCAGAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
1406904 ATTAAAATACATGAAATGATGCATTAAG
131 ATTAAAATACATGAAAGGATGCATTAAG
1406932 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1406946 CATAATTAAA
Statistics
Matches: 164, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 164 1.00
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (158 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAA
GGCATGAAAGGATGCCAGAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
ATTAAAATACATGAAAGGATGCATTAAG
Found at i:1406826 original size:92 final size:89
Alignment explanation
Indices: 1406564--1407102 Score: 350
Period size: 92 Copynumber: 5.9 Consensus size: 89
1406554 ATGCCATAAC
* *
1406564 TAAAATGCATGAAAGGATG-CATT-AAGACATGAAAGGATGCCATAACTAAAATGCATGAAAGGA
1 TAAAATGCATGAAAGGATGCCATTAAAGGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGA
* *
1406627 TG-CAT--T--AAGGCATGAAAGGATGCCAGAAC
60 TGCCATAATAAAATGCATGAAAGGATG-C---AT
* * *
1406656 TAAAATGTATGAAAGGATG-CATT-AAGGCATGAAAGGATGCCAGAACTAAAATGCATGAAAGGA
1 TAAAATGCATGAAAGGATGCCATTAAAGGCATGAAAGGATG-C---A-T-TAAGGCATGAAAGGA
*
1406719 TG-CAT--T--AAGGCATGAAAGGATGCCATAAT
60 TGCCATAATAAAATGCATGAAAGGATG-C---AT
*
1406748 TAAAATGCATGAAAGGATG-CATT-AAGGCATTAAAGGATGCATTAAGGCATGAAAGGATGCCAT
1 TAAAATGCATGAAAGGATGCCATTAAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT
*
1406811 AACTAAAATGTATGAAAGGATGCAT
66 AA-TAAAATGCATGAAAGGATGCAT
* * * *
1406836 T--AAGGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAATGCATGAAAGGATG
1 TAAAATGCATGAAAGGATGCCAT---T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1406899 CCATAATTAAAATACATGAAATGATGCAT
62 CCATAA-TAAAATGCATGAAAGGATGCAT
* * * *
1406928 T--AAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGTATGCATTAAGGCATGAAAGGATG
1 TAAAATGCATGAAAGGATGCC---ATT-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1406991 CCATAATTAAAATGCATTAACA-GATGCAT
62 CCATAA-TAAAATGCATGAA-AGGATGCAT
* * *
1407020 TAAGA--CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTGAGGCATGAAAGGATG
1 TAAAATGCATGAAAGGATGCCAT---T-AAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1407083 CCATGATAAAAATGTATGAA
62 CCATAAT-AAAATGCATGAA
1407103 CAGATGTATT
Statistics
Matches: 388, Mismatches: 33, Indels: 52
0.82 0.07 0.11
Matches are distributed among these distances:
86 30 0.08
87 7 0.02
88 4 0.01
89 2 0.01
90 2 0.01
91 3 0.01
92 334 0.86
93 1 0.00
94 1 0.00
95 3 0.01
96 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (89 bp):
TAAAATGCATGAAAGGATGCCATTAAAGGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCAT
AATAAAATGCATGAAAGGATGCAT
Found at i:1406872 original size:138 final size:135
Alignment explanation
Indices: 1406728--1407102 Score: 449
Period size: 138 Copynumber: 2.7 Consensus size: 135
1406718 ATGCATTAAG
* *
1406728 GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG-CATT-AAGGCATTAAAGGATGCATT
1 GCATGAAAGGATG-C---ATTAAAATGCATGAAAGGATGCCATTAAATGCATGAAAGGATGCATT
1406791 AAGGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
62 AAGGCATGAAAGGATGCCATAA-TAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
1406856 TAACTAAAAT
126 TAACTAAAAT
* * *
1406866 GTATGAAAGGATGCATT--AATGCATGAAAGGATGCCATAATTAAAATACATGAAATGATGCATT
1 GCATGAAAGGATGCATTAAAATGCATGAAAGGATGCC---ATT-AAATGCATGAAAGGATGCATT
* *
1406929 AAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGTATGCATTAAGGCATGAAAGGATGCCA
62 AAGGCATGAAAGGATGCCATAA-TAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCA
*
1406994 TAATTAAAAT
126 TAACTAAAAT
* *
1407004 GCATTAACA-GATGCATTAAGA--CATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCAT
1 GCATGAA-AGGATGCATTAAAATGCATGAAAGGATGCCAT---T-AAATGCATGAAAGGATGCAT
* *
1407066 TGAGGCATGAAAGGATGCCATGATAAAAATGTATGAA
61 TAAGGCATGAAAGGATGCCATAAT-AAAATGTATGAA
1407103 CAGATGTATT
Statistics
Matches: 207, Mismatches: 17, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
132 16 0.08
133 1 0.00
134 3 0.01
135 2 0.01
136 3 0.01
137 2 0.01
138 178 0.86
139 1 0.00
140 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (135 bp):
GCATGAAAGGATGCATTAAAATGCATGAAAGGATGCCATTAAATGCATGAAAGGATGCATTAAGG
CATGAAAGGATGCCATAATAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
AAAAT
Found at i:1406874 original size:204 final size:204
Alignment explanation
Indices: 1406570--1406991 Score: 745
Period size: 204 Copynumber: 2.1 Consensus size: 204
1406560 TAACTAAAAT
1406570 GCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
1406635 GGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGA
66 GGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGA
* *
1406700 ACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGA
131 ACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGGA
1406765 TGCATTAAG
196 TGCATTAAG
* * *
1406774 GCATTAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
* * *
1406839 GGCATGAAAGGATGCCATAACTAAAATGTATGAAAGGATGCATTAATGCATGAAAGGATGCCATA
66 GGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGA
* * *
1406904 ATTAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGTA
131 ACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGGA
1406969 TGCATTAAG
196 TGCATTAAG
1406978 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1406992 CATAATTAAA
Statistics
Matches: 206, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
204 206 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (204 bp):
GCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAA
GGCATGAAAGGATGCCAGAACTAAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATGCCAGA
ACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGAATGAAAGGA
TGCATTAAG
Found at i:1407141 original size:46 final size:46
Alignment explanation
Indices: 1406774--1407141 Score: 490
Period size: 46 Copynumber: 8.0 Consensus size: 46
1406764 ATGCATTAAG
* *
1406774 GCATTAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* *
1406820 GTATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* *
1406866 GTATGAAAGGATGCATTAATGCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* *
1406912 ACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* *
1406958 GAATGAAAGTATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * *
1407004 GCATTAACA-GATGCATTAAGACATGAAAGGATGCCATAACTAAAAT
1 GCATGAA-AGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * *
1407050 GCATGAAAGGATGCATTGAGGCATGAAAGGATGCCATGATAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
* * ** * *
1407096 GTATGAACA-GATGTATTAATACATGAAAAGA-GACCCTAATTAAAAT
1 GCATGAA-AGGATGCATTAAGGCATGAAAGGATG-CCATAATTAAAAT
1407142 TAATGAATAA
Statistics
Matches: 286, Mismatches: 32, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
45 2 0.01
46 282 0.99
47 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (46 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAT
Found at i:1408128 original size:8 final size:7
Alignment explanation
Indices: 1408100--1408126 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1408090 AAACCTGTCA
1408100 AAAAAAT
1 AAAAAAT
1408107 AAAAAAT
1 AAAAAAT
1408114 AAAAAAT
1 AAAAAAT
1408121 AAAAAA
1 AAAAAA
1408127 ATGAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1411412 original size:2 final size:2
Alignment explanation
Indices: 1411405--1411441 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1411395 ATTTTAAAAC
1411405 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 A
1411442 AAACATGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1411638 original size:24 final size:24
Alignment explanation
Indices: 1411611--1411681 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
1411601 AAACGGAGAT
* *
1411611 ATCATAAATCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAA
* * *
1411635 ATCAGATATCAGAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAA
*
1411659 ATCAGAAATCAGAACATAATTCA
1 ATCAGAAATCAGAACAGAATTCA
1411682 GGTAATGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAA
Found at i:1413290 original size:2 final size:2
Alignment explanation
Indices: 1413283--1413314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1413273 TAGACCAATC
1413283 AT 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 AT
1413315 CCATGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1415990 original size:17 final size:18
Alignment explanation
Indices: 1415957--1416012 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
1415947 ACTTGGAGAC
1415957 GAAG-AAGAGAAGAAAAT
1 GAAGAAAGAGAAGAAAAT
1415974 G-AGAAAGAGGAAG-AAAT
1 GAAGAAAGA-GAAGAAAAT
* *
1415991 GAAGAAA-ATAAGAAGAT
1 GAAGAAAGAGAAGAAAAT
1416008 GAAGA
1 GAAGA
1416013 GAAACAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 5 0.15
17 19 0.58
18 9 0.27
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (18 bp):
GAAGAAAGAGAAGAAAAT
Found at i:1415994 original size:26 final size:25
Alignment explanation
Indices: 1415957--1416012 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1415947 ACTTGGAGAC
*
1415957 GAAGAAGAGAAGAAAATGAGAAAGAG
1 GAAGAAGAGAAGAAAATAAG-AAGAG
*
1415983 GAAGAA-ATGAAGAAAATAAGAAGAT
1 GAAGAAGA-GAAGAAAATAAGAAGAG
1416008 GAAGA
1 GAAGA
1416013 GAAACAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.07
Consensus pattern (25 bp):
GAAGAAGAGAAGAAAATAAGAAGAG
Found at i:1418824 original size:17 final size:17
Alignment explanation
Indices: 1418802--1418844 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
1418792 ACTGAGCCTG
1418802 GAATTTTAAGATAGGAT
1 GAATTTTAAGATAGGAT
1418819 GAATTTTAAGATAGGAT
1 GAATTTTAAGATAGGAT
1418836 GAATTTTAA
1 GAATTTTAA
1418845 TAGAAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
GAATTTTAAGATAGGAT
Found at i:1423881 original size:2 final size:2
Alignment explanation
Indices: 1423874--1423899 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1423864 CAGATAATTC
1423874 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
1423900 TTCAGTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1430433 original size:2 final size:2
Alignment explanation
Indices: 1430426--1430516 Score: 51
Period size: 2 Copynumber: 51.0 Consensus size: 2
1430416 GAAAATATTT
* * *
1430426 TA TA TA TA -A T- TA -A TA TA AA AA TA TA TA -A AA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1430463 TA TA TA -A T- TA -A TA TA -A AA AA TA TA -A AA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1430499 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1430517 ATCGGGGCGG
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
1 11 0.15
2 62 0.85
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1430512 original size:35 final size:35
Alignment explanation
Indices: 1430417--1430502 Score: 156
Period size: 35 Copynumber: 2.5 Consensus size: 35
1430407 TCCGAACCAG
*
1430417 AAAATATTTTATATATAATTAATATAAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAATATAT
1430452 AAAATATTATATATATAATTAATATAAAAA-ATAT
1 AAAATATTATATATATAATTAATATAAAAATATAT
1430486 AAAATATTATATATATA
1 AAAATATTATATATATA
1430503 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 21 0.42
35 29 0.58
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAATATTATATATATAATTAATATAAAAATATAT
Found at i:1432350 original size:31 final size:31
Alignment explanation
Indices: 1432315--1432375 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1432305 GGTATGATTT
*
1432315 TGAAAAAAAAATGAAAGTTTAGGTACTAAAA
1 TGAAAAAAAAATGAAAGTTTAGATACTAAAA
* * *
1432346 TGAAATAAAACTGATAGTTTAGATACTAAA
1 TGAAAAAAAAATGAAAGTTTAGATACTAAA
1432376 CATGTAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (31 bp):
TGAAAAAAAAATGAAAGTTTAGATACTAAAA
Found at i:1436909 original size:82 final size:80
Alignment explanation
Indices: 1436755--1436909 Score: 177
Period size: 82 Copynumber: 1.9 Consensus size: 80
1436745 GTAAAAAAAT
* * * * **
1436755 TACCTAAAATATTATTATTTCTACCGGAAATGTTATTATTGGACGCTTTACCGGATTTGTTAACA
1 TACCTAAAACATTATTATTTCTACCGGAAATGTTAATATTGGACACTTTACCGAAAATGTTAACA
* *
1436820 TATTTAATAAAGCGC
66 AAATTAATAAAGCGC
* * *
1436835 TACCTAAAACATTATTATTTTTCTATCGGAAATGTTAATATTGGGCATTTTACCGAAAATGTTAA
1 TACCTAAAACATTATTA--TTTCTACCGGAAATGTTAATATTGGACACTTTACCGAAAATGTTAA
1436900 -AAACATTAAT
64 CAAA-ATTAAT
1436910 GTTTTAGGTA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
80 16 0.26
81 2 0.03
82 43 0.70
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (80 bp):
TACCTAAAACATTATTATTTCTACCGGAAATGTTAATATTGGACACTTTACCGAAAATGTTAACA
AAATTAATAAAGCGC
Found at i:1438409 original size:26 final size:22
Alignment explanation
Indices: 1438358--1438414 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 22
1438348 GAAAAAAAAA
*
1438358 AATCTTTAACTTAACTCGATTG
1 AATCTTAAACTTAACTCGATTG
1438380 AATCGTTAAACTTAAACTCGAACTTG
1 AATC-TTAAACTT-AACTCG-A-TTG
1438406 AATCTTAAA
1 AATCTTAAA
1438415 TACATGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 6 0.20
25 6 0.20
26 7 0.23
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
AATCTTAAACTTAACTCGATTG
Found at i:1443184 original size:20 final size:22
Alignment explanation
Indices: 1443159--1443212 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1443149 AGAATAATTA
1443159 TATCTTTGTGACATG-T-TCTC
1 TATCTTTGTGACATGTTATCTC
* *
1443179 TATCTTTATGGCATGTTTATCTC
1 TATCTTTGTGACATG-TTATCTC
1443202 TATCTTTGTGA
1 TATCTTTGTGA
1443213 TACGTTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.48
22 1 0.04
23 13 0.48
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.52
Consensus pattern (22 bp):
TATCTTTGTGACATGTTATCTC
Found at i:1443219 original size:23 final size:23
Alignment explanation
Indices: 1443175--1443219 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1443165 TGTGACATGT
* *
1443175 TCTCTATCTTTATGGCATGTTTA
1 TCTCTATCTTTATGACACGTTTA
* *
1443198 TCTCTATCTTTGTGATACGTTT
1 TCTCTATCTTTATGACACGTTT
1443220 TTCTGCATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.18, G:0.13, T:0.53
Consensus pattern (23 bp):
TCTCTATCTTTATGACACGTTTA
Found at i:1444075 original size:14 final size:14
Alignment explanation
Indices: 1444056--1444135 Score: 151
Period size: 14 Copynumber: 5.7 Consensus size: 14
1444046 TACTTTAAAT
1444056 GTGAATTATAGAAA
1 GTGAATTATAGAAA
1444070 GTGAATTATAGAAA
1 GTGAATTATAGAAA
1444084 GTGAATTATAGAAA
1 GTGAATTATAGAAA
1444098 GTGAATTATAGAAA
1 GTGAATTATAGAAA
*
1444112 GGGAATTATAGAAA
1 GTGAATTATAGAAA
1444126 GTGAATTATA
1 GTGAATTATA
1444136 TTTTTAGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 64 1.00
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.29
Consensus pattern (14 bp):
GTGAATTATAGAAA
Found at i:1446525 original size:24 final size:23
Alignment explanation
Indices: 1446447--1446532 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
1446437 ACATATTATA
* *
1446447 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1446470 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1446493 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
*
1446517 TGGCACTTCGATGCAA
1 TGGCACTTCGGTGCAA
1446533 ATTTATACGA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.02
23 32 0.63
24 17 0.33
25 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1446533 original size:24 final size:23
Alignment explanation
Indices: 1446461--1446535 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
1446451 ACTACGGTGT
1446461 AATTCTACGTGGCACTTCGGTGC-
1 AATTCTACGTGGCACTTC-GTGCA
* * *
1446484 ATTTCTACGCGGTC-CTTCGGGACA
1 AATTCTACGTGG-CACTTCGTG-CA
1446508 AATTCTACGTGGCACTTCGATGCA
1 AATTCTACGTGGCACTTCG-TGCA
1446532 AATT
1 AATT
1446536 TATACGAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 2 0.05
23 16 0.39
24 22 0.54
25 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (23 bp):
AATTCTACGTGGCACTTCGTGCA
Found at i:1450720 original size:21 final size:22
Alignment explanation
Indices: 1450696--1450737 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1450686 TTCCATAATC
*
1450696 AAATCCTAAAAA-ATTAAGCAA
1 AAATCCTAAAAACACTAAGCAA
*
1450717 AAATGCTAAAAACACTAAGCA
1 AAATCCTAAAAACACTAAGCA
1450738 TTTTGGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (22 bp):
AAATCCTAAAAACACTAAGCAA
Found at i:1450882 original size:11 final size:11
Alignment explanation
Indices: 1450866--1450904 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1450856 TTGGTCAAAG
1450866 TCAACGGCCGA
1 TCAACGGCCGA
*
1450877 TCAACGGCCAAA
1 TCAACGGCC-GA
1450889 GTCAACGGCCGA
1 -TCAACGGCCGA
1450901 TCAA
1 TCAA
1450905 TGGTCAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 13 0.54
12 2 0.08
13 9 0.38
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.10
Consensus pattern (11 bp):
TCAACGGCCGA
Found at i:1450895 original size:13 final size:13
Alignment explanation
Indices: 1450861--1450898 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1450851 ACTATTTGGT
1450861 CAAAGTCAACGGC
1 CAAAGTCAACGGC
*
1450874 C-GA-TCAACGGC
1 CAAAGTCAACGGC
1450885 CAAAGTCAACGGC
1 CAAAGTCAACGGC
1450898 C
1 C
1450899 GATCAATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.34, C:0.34, G:0.24, T:0.08
Consensus pattern (13 bp):
CAAAGTCAACGGC
Found at i:1471085 original size:31 final size:31
Alignment explanation
Indices: 1471045--1471143 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
1471035 CCAACCTAAG
* *
1471045 GGAAAGCCTTGGGGCCTTAGAGCCTACTCAA
1 GGAATGCCTTGGGGCCTCAGAGCCTACTCAA
* *
1471076 GGAATGCCTTAGGACCTCAGAGCCTA-TCCAA
1 GGAATGCCTTGGGGCCTCAGAGCCTACT-CAA
* * *
1471107 GGAA-GCACCTTGGGGACTGAGAGCCTACCCAA
1 GGAATG--CCTTGGGGCCTCAGAGCCTACTCAA
*
1471139 TGAAT
1 GGAAT
1471144 CACACTGGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
30 2 0.04
31 29 0.55
32 22 0.42
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.18
Consensus pattern (31 bp):
GGAATGCCTTGGGGCCTCAGAGCCTACTCAA
Found at i:1471132 original size:32 final size:32
Alignment explanation
Indices: 1471094--1471204 Score: 102
Period size: 32 Copynumber: 3.5 Consensus size: 32
1471084 TTAGGACCTC
*
1471094 AGAGCCTATCCAAGGAAGCAC-CTTGGGGACTG
1 AGAGCCTACCCAAGGAAGCACAC-TGGGGACTG
* * *
1471126 AGAGCCTACCCAATGAATCACACTGGGGCCTG
1 AGAGCCTACCCAAGGAAGCACACTGGGGACTG
* * * *
1471158 AGAACCTACCCAAGGGAA-CATCAC-GAGGCCTA
1 AGAGCCTACCCAA-GGAAGCA-CACTGGGGACTG
1471190 AGAGCCTACCCAAGG
1 AGAGCCTACCCAAGG
1471205 GTCACCTTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.03
32 58 0.87
33 7 0.10
ACGTcount: A:0.32, C:0.30, G:0.26, T:0.13
Consensus pattern (32 bp):
AGAGCCTACCCAAGGAAGCACACTGGGGACTG
Found at i:1487745 original size:19 final size:19
Alignment explanation
Indices: 1487717--1487765 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1487707 AAGTGACTAA
*
1487717 ATTAACAAGTGTAATCAAT
1 ATTAAGAAGTGTAATCAAT
1487736 ATTAAGAAGTGTAATCAAT
1 ATTAAGAAGTGTAATCAAT
1487755 ATTAAGAAGTG
1 ATTAAGAAGTG
1487766 ATTATTCGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (19 bp):
ATTAAGAAGTGTAATCAAT
Found at i:1490368 original size:2 final size:2
Alignment explanation
Indices: 1490361--1490395 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1490351 AAATAAAATC
1490361 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
1490396 AAAGTTGGGA
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:1493481 original size:154 final size:158
Alignment explanation
Indices: 1493302--1493608 Score: 586
Period size: 157 Copynumber: 2.0 Consensus size: 158
1493292 ATGGTGTGTG
1493302 AAGCTAAGCTCACCCCGTTCCCACCATGCTGTTGTAA-CCTAACGTCAACGACACGCCA-CGGCT
1 AAGCTAAGCTCACCCCGTTCCCACCATGCTGTTGTAACCCTAACGTCAACGACACGCCACCGGCT
1493365 GCCGTCTGATGACTGTAGGAAGAGATGTCCAAAT-CATGGCACCATAAGTCGAGAAATCATGTTG
66 GCCGTCTGATGACTGTAGGAAGAGATGTCCAAATCCATGGCACCATAAGTCGAGAAATCATGTTG
1493429 TTGTTGATGATGATGATGCAAACGGTGA
131 TTGTTGATGATGATGATGCAAACGGTGA
1493457 AAGCTAAGCTCA-CCCGTTCCCACCATGCTGTTGTAACCCTAACGTCAACGACACGCCACCGGCT
1 AAGCTAAGCTCACCCCGTTCCCACCATGCTGTTGTAACCCTAACGTCAACGACACGCCACCGGCT
1493521 GCCGTCTGATGACTGTAGGAAGAGATGTCCAAATCCATGGCACCATAAGTCGAGAAATCATGTTG
66 GCCGTCTGATGACTGTAGGAAGAGATGTCCAAATCCATGGCACCATAAGTCGAGAAATCATGTTG
1493586 TTGTTGATGATGATGATGCAAAC
131 TTGTTGATGATGATGATGCAAAC
1493609 CGTGCTGGTT
Statistics
Matches: 149, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
154 24 0.16
155 33 0.22
156 39 0.26
157 53 0.36
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (158 bp):
AAGCTAAGCTCACCCCGTTCCCACCATGCTGTTGTAACCCTAACGTCAACGACACGCCACCGGCT
GCCGTCTGATGACTGTAGGAAGAGATGTCCAAATCCATGGCACCATAAGTCGAGAAATCATGTTG
TTGTTGATGATGATGATGCAAACGGTGA
Found at i:1493974 original size:15 final size:15
Alignment explanation
Indices: 1493954--1493985 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1493944 GGCCTGATGC
1493954 TTCTTGAGAGACCTG
1 TTCTTGAGAGACCTG
1493969 TTCTTGAGAGACCTG
1 TTCTTGAGAGACCTG
1493984 TT
1 TT
1493986 TGGCGGCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (15 bp):
TTCTTGAGAGACCTG
Found at i:1495237 original size:29 final size:29
Alignment explanation
Indices: 1495194--1495276 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1495184 CTCACCTAAC
1495194 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1495224 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1495253 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1495277 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1500000 original size:29 final size:29
Alignment explanation
Indices: 1499957--1500039 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1499947 CTCACCTAAC
1499957 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1499987 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1500016 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1500040 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1501634 original size:31 final size:31
Alignment explanation
Indices: 1501592--1501655 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1501582 TTTTATTATT
1501592 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG
1 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG
*
1501623 TCGGGTTGGGTGAAATCTTGTTTTGGTCGGG
1 TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG
1501654 TC
1 TC
1501656 AGGTGGACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.09, C:0.12, G:0.41, T:0.38
Consensus pattern (31 bp):
TCGGGTCGGGTGAAATCTTGTTTTGGTCGGG
Found at i:1505724 original size:19 final size:20
Alignment explanation
Indices: 1505692--1505732 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
1505682 TTAAAATTTC
1505692 ATTTTGCTTTTCAAAATCAA
1 ATTTTGCTTTTCAAAATCAA
1505712 ATTTTGC-TTTCAAAATCAA
1 ATTTTGCTTTTCAAAATCAA
1505731 AT
1 AT
1505733 CATTTTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTTGCTTTTCAAAATCAA
Found at i:1509862 original size:4 final size:4
Alignment explanation
Indices: 1509853--1509898 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
1509843 AGGTACCTCC
1509853 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1509899 AATGGTGAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1521512 original size:17 final size:17
Alignment explanation
Indices: 1521472--1521512 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
1521462 TGATAAATCA
*
1521472 GGTCGGGTCAATTTTCG
1 GGTCGAGTCAATTTTCG
*
1521489 GGT-GAGTCAATTTTTG
1 GGTCGAGTCAATTTTCG
1521505 GGTCGAGT
1 GGTCGAGT
1521513 GATTATCGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.15, C:0.12, G:0.37, T:0.37
Consensus pattern (17 bp):
GGTCGAGTCAATTTTCG
Found at i:1521906 original size:32 final size:32
Alignment explanation
Indices: 1521870--1521946 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
1521860 AATTTGGTTT
*
1521870 GGGTTACTTTTGGATAGAGTTAAACTCAGTTC
1 GGGTTACTTTCGGATAGAGTTAAACTCAGTTC
* * * * *
1521902 GGGTTACTTTCGGTTTGAGTTATATTCTGTTC
1 GGGTTACTTTCGGATAGAGTTAAACTCAGTTC
*
1521934 GGGTTGCTTTCGG
1 GGGTTACTTTCGG
1521947 CTCGGGCTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.43
Consensus pattern (32 bp):
GGGTTACTTTCGGATAGAGTTAAACTCAGTTC
Found at i:1524499 original size:21 final size:21
Alignment explanation
Indices: 1524473--1524528 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1524463 AACATGACAG
1524473 ATAGACTGTCACGTCAGTATC
1 ATAGACTGTCACGTCAGTATC
1524494 ATAGACTGTCACGTCAGTATC
1 ATAGACTGTCACGTCAGTATC
* *
1524515 ATGGACTGCCACGT
1 ATAGACTGTCACGT
1524529 TAGTGCCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (21 bp):
ATAGACTGTCACGTCAGTATC
Found at i:1525430 original size:87 final size:88
Alignment explanation
Indices: 1525330--1525494 Score: 203
Period size: 88 Copynumber: 1.9 Consensus size: 88
1525320 TTTAATTTAG
** * * *
1525330 TTTTTTATTTTTATAATTGAT-GTCCATAA-TTTTGT-AATCATACTTTTTATCTTTATAATTGA
1 TTTTTTACATTTATAATTGATAAT-CATAAGTTTT-TCAATCATACTTTGTACCTTTATAATTGA
*
1525392 AGC-CCTTATTTTTTTTCAAACCCGT
64 A-CTCCTGATTTTTTTTCAAACCCGT
* *
1525417 TTTTTTACATTTATAATTGATAATCTTAAGTTTTTCAATCCTACTTTGTACCTTTATAATTGAAC
1 TTTTTTACATTTATAATTGATAATCATAAGTTTTTCAATCATACTTTGTACCTTTATAATTGAAC
1525482 TCCTGATTTTTTT
66 TCCTGATTTTTTT
1525495 CAATCTCACT
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
87 25 0.38
88 41 0.62
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (88 bp):
TTTTTTACATTTATAATTGATAATCATAAGTTTTTCAATCATACTTTGTACCTTTATAATTGAAC
TCCTGATTTTTTTTCAAACCCGT
Found at i:1525494 original size:43 final size:43
Alignment explanation
Indices: 1525447--1525704 Score: 146
Period size: 44 Copynumber: 6.0 Consensus size: 43
1525437 TAATCTTAAG
* *
1525447 TTTTTCAATC-CTACTTTGTACCTTTATAATTGAA-CTCCTGATT
1 TTTTTCAATCTC-ACTTTGTACCTTTAT-ATTGAAGCCCCTAATT
*
1525490 TTTTTCAATCTCACTTTTTACCTTTATATTGAAGCCCCTAA-T
1 TTTTTCAATCTCACTTTGTACCTTTATATTGAAGCCCCTAATT
* * * *
1525532 TTTTTCTATCTC-CTTTTTA-CTTCTATAATTTAGGCCCCTAA--
1 TTTTTCAATCTCACTTTGTACCTT-TAT-ATTGAAGCCCCTAATT
* * * *
1525573 -TTTTCAATCTC-GTTTATTACCTTTAAAATTGAGGCCCCTAATT
1 TTTTTCAATCTCACTTT-GTACCTTT-ATATTGAAGCCCCTAATT
* * * * * * *
1525616 TTTTTTAATCTAAC-TTGATACCTATATAATTGAGGTCTCTATTT
1 TTTTTCAATCTCACTTTG-TACCTTTAT-ATTGAAGCCCCTAATT
*
1525660 TTTTTCAATCAT-ACCTTTG-A-CTGTTATAGTTTAAGCCCCTAATT
1 TTTTTCAATC-TCA-CTTTGTACCT-TTATA-TTGAAGCCCCTAATT
1525704 T
1 T
1525705 AATCATTTTT
Statistics
Matches: 171, Mismatches: 26, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
40 16 0.09
41 27 0.16
42 34 0.20
43 33 0.19
44 56 0.33
45 2 0.01
46 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (43 bp):
TTTTTCAATCTCACTTTGTACCTTTATATTGAAGCCCCTAATT
Found at i:1525522 original size:42 final size:43
Alignment explanation
Indices: 1525339--1525648 Score: 192
Period size: 42 Copynumber: 7.3 Consensus size: 43
1525329 GTTTTTTATT
* * * * *
1525339 TTTATAATTGATGTCCATAATTTTGT-AATCAT-ACTTTTTATC
1 TTTATAATTGAAGCCCCTAATTTTTTCAATC-TCACTTTTTACC
* * * * ** *
1525381 TTTATAATTGAAGCCCTTATTTTTTTTCAAACCCGTTTTTTTACA
1 TTTATAATTGAAGCCCCTA-ATTTTTTCAATCTC-ACTTTTTACC
** * * *
1525426 TTTATAATTGATA-ATCTTAAGTTTTTCAATC-CTACTTTGTACC
1 TTTATAATTGA-AGCCCCTAATTTTTTCAATCTC-ACTTTTTACC
* *
1525469 TTTATAATTGAA-CTCCTGATTTTTTTCAATCTCACTTTTTACC
1 TTTATAATTGAAGCCCCT-AATTTTTTCAATCTCACTTTTTACC
*
1525512 TTTAT-ATTGAAGCCCCTAATTTTTTCTATCTC-CTTTTTA-C
1 TTTATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTTTACC
* * *
1525552 TTCTATAATTTAGGCCCCTAA--TTTTCAATCTC-GTTTATTACC
1 TT-TATAATTGAAGCCCCTAATTTTTTCAATCTCACTTT-TTACC
* * * * **
1525594 TTTAAAATTGAGGCCCCTAATTTTTTTTAATCTAACTTGATACC
1 TTTATAATTGAAGCCCCTAA-TTTTTTCAATCTCACTTTTTACC
*
1525638 TATATAATTGA
1 TTTATAATTGA
1525649 GGTCTCTATT
Statistics
Matches: 210, Mismatches: 42, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
40 16 0.08
41 29 0.14
42 54 0.26
43 52 0.25
44 35 0.17
45 23 0.11
46 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (43 bp):
TTTATAATTGAAGCCCCTAATTTTTTCAATCTCACTTTTTACC
Found at i:1526478 original size:6 final size:6
Alignment explanation
Indices: 1526469--1526494 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1526459 GTTATCAACA
1526469 TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TC
1526495 GTGCATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:1537043 original size:34 final size:34
Alignment explanation
Indices: 1536967--1537246 Score: 236
Period size: 34 Copynumber: 8.3 Consensus size: 34
1536957 GATTTTTTTA
* ** *
1536967 ATATACGTTTTCAAAA-TCCTTTAAAAACCATAT
1 ATATATGTTTTCAAAACTATTTTAAAAACTATAT
* * *
1537000 ATTACATGTTTTCAAAACCATTTTGAAAA-TATATT
1 A-TATATGTTTTCAAAACTATTTTAAAAACTATA-T
*
1537035 ATATATGTTTTC-AAACCATTTT-AAAACTATAT
1 ATATATGTTTTCAAAACTATTTTAAAAACTATAT
* * *
1537067 ATTATACGTTTT-TAAACTATTTAAAAAACTATAT
1 A-TATATGTTTTCAAAACTATTTTAAAAACTATAT
* **
1537101 ATACACATTTTCAAAACTATTTTAAAAACTATAT
1 ATATATGTTTTCAAAACTATTTTAAAAACTATAT
** * *
1537135 ATTATACATTTTCCAAACTATTTTGAAAA-TATAT
1 A-TATATGTTTTCAAAACTATTTTAAAAACTATAT
* *
1537169 ACTATATGTTATCAAAACCATTTT-AAAACTATAT
1 A-TATATGTTTTCAAAACTATTTTAAAAACTATAT
* *
1537203 -TATACGTTTTTTTAAAACTATTTTAAAAACTATAT
1 ATATA--TGTTTTCAAAACTATTTTAAAAACTATAT
1537238 -TATATGTTT
1 ATATATGTTT
1537247 CTTAAAAATA
Statistics
Matches: 205, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
32 10 0.05
33 48 0.23
34 100 0.49
35 47 0.23
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (34 bp):
ATATATGTTTTCAAAACTATTTTAAAAACTATAT
Found at i:1537167 original size:135 final size:136
Alignment explanation
Indices: 1536986--1537237 Score: 368
Period size: 135 Copynumber: 1.9 Consensus size: 136
1536976 TTCAAAATCC
** *
1536986 TTTAAAAACCATATATTACATGTTTTCAAAACCATTTTGAAAATATATTA-TATATGTTTTC-AA
1 TTTAAAAACCATATATTACACATTTTCAAAACCATTTTGAAAATATA-TACTATATGTTATCAAA
1537049 ACCATTTTAAAACTATATATTATACG-TTTTT-AAACTATTTAAAAAACTATATATACACATTTT
65 ACCATTTTAAAAC--TATATTATACGTTTTTTAAAACTATTTAAAAAACTATATATACACATTTT
1537112 CAAAACTAT
128 CAAAACTAT
* * * *
1537121 TTTAAAAACTATATATTATACATTTTCCAAACTATTTTGAAAATATATACTATATGTTATCAAAA
1 TTTAAAAACCATATATTACACATTTTCAAAACCATTTTGAAAATATATACTATATGTTATCAAAA
*
1537186 CCATTTTAAAACTATATTATACGTTTTTTTAAAACTATTTTAAAAACTATAT
66 CCATTTTAAAACTATATTATACG-TTTTTTAAAACTATTTAAAAAACTATAT
1537238 TATATGTTTC
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
134 13 0.12
135 51 0.49
136 20 0.19
137 20 0.19
ACGTcount: A:0.43, C:0.12, G:0.03, T:0.42
Consensus pattern (136 bp):
TTTAAAAACCATATATTACACATTTTCAAAACCATTTTGAAAATATATACTATATGTTATCAAAA
CCATTTTAAAACTATATTATACGTTTTTTAAAACTATTTAAAAAACTATATATACACATTTTCAA
AACTAT
Found at i:1537168 original size:68 final size:67
Alignment explanation
Indices: 1536967--1537246 Score: 284
Period size: 68 Copynumber: 4.1 Consensus size: 67
1536957 GATTTTTTTA
* * * * * *
1536967 ATATACGTTTTCAAAATCC-TTTAAAAACCATATATTACATGTTTTCAAAACCATTTTGAAAATA
1 ATATATGTTTTCAAAA-CCATTTTAAAACTATATATTATACGTTTTCAAAACTATTTTGAAAATA
1537031 TATT
65 TA-T
* **
1537035 ATATATGTTTTC-AAACCATTTTAAAACTATATATTATACGTTTT-TAAACTATTTAAAAAACTA
1 ATATATGTTTTCAAAACCATTTTAAAACTATATATTATACGTTTTCAAAACTATTTTGAAAA-TA
1537098 TAT
65 TAT
* ** * * *
1537101 ATACACATTTTCAAAACTATTTTAAAAACTATATATTATACATTTTCCAAACTATTTTGAAAATA
1 ATATATGTTTTCAAAACCATTTT-AAAACTATATATTATACGTTTTCAAAACTATTTTGAAAATA
1537166 TAT
65 TAT
* * *
1537169 ACTATATGTTATCAAAACCATTTTAAAAC--TATATTATACGTTTTTTTAAAACTATTTTAAAAA
1 A-TATATGTTTTCAAAACCATTTTAAAACTATATATTATACG--TTTTCAAAACTATTTTGAAAA
1537232 CTATAT
63 -TATAT
1537238 -TATATGTTT
1 ATATATGTTT
1537247 CTTAAAAATA
Statistics
Matches: 176, Mismatches: 27, Indels: 19
0.79 0.12 0.09
Matches are distributed among these distances:
66 34 0.19
67 46 0.26
68 61 0.35
69 35 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (67 bp):
ATATATGTTTTCAAAACCATTTTAAAACTATATATTATACGTTTTCAAAACTATTTTGAAAATAT
AT
Found at i:1537226 original size:103 final size:103
Alignment explanation
Indices: 1536968--1537237 Score: 268
Period size: 103 Copynumber: 2.6 Consensus size: 103
1536958 ATTTTTTTAA
* ** * *
1536968 TATACGTTTTCAAAATCC-TTT-AAAAACCATATATTACATGTTTTCAAAACCATTTT-GAAA--
1 TATACG-TTTCAAAA-CCATTTAAAAAACTATATA-TACACATTTTCAAAACTATTTTAAAAACT
* * *
1537028 ATATATTATATATGTTTTCAAACCATTTTAAAACTATATAT
63 ATATATTATACATGTTTCCAAACCATTTTAAAACTATATAC
** *
1537069 TATACGTTTTTAAACTATTTAAAAAACTATATATACACATTTTCAAAACTATTTTAAAAACTATA
1 TATACGTTTCAAAACCATTTAAAAAACTATATATACACATTTTCAAAACTATTTTAAAAACTATA
*
1537134 TATTATACAT-TTTCCAAACTATTTTGAAAA-TATATAC
66 TATTATACATGTTTCCAAACCATTTT-AAAACTATATAC
* * *** *
1537171 TATATGTTATCAAAACCATTT-TAAAACTATATTATACGTTTTTTTAAAACTATTTTAAAAACTA
1 TATACGTT-TCAAAACCATTTAAAAAACTATA-TATACACATTTTCAAAACTATTTTAAAAACTA
1537235 TAT
64 TAT
1537238 TATATGTTTC
Statistics
Matches: 140, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
99 1 0.01
100 28 0.20
101 20 0.14
102 35 0.25
103 56 0.40
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (103 bp):
TATACGTTTCAAAACCATTTAAAAAACTATATATACACATTTTCAAAACTATTTTAAAAACTATA
TATTATACATGTTTCCAAACCATTTTAAAACTATATAC
Found at i:1547269 original size:3 final size:3
Alignment explanation
Indices: 1547261--1547307 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
1547251 TTAGTGAGGC
*
1547261 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
1547306 AT
1 AT
1547308 GCCATAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 1 0.03
3 38 0.95
4 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1547731 original size:2 final size:2
Alignment explanation
Indices: 1547724--1547757 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1547714 TTCACGTAAT
1547724 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1547758 CATTTCTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1554141 original size:3 final size:3
Alignment explanation
Indices: 1554133--1554206 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
1554123 TTAGTGTGGC
1554133 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
1554178 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1554207 GAGATAAAGT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 64 0.93
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1556412 original size:11 final size:11
Alignment explanation
Indices: 1556396--1556427 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1556386 AAAGAAATAA
1556396 AAGAAAACAAC
1 AAGAAAACAAC
1556407 AAGAAAACAAC
1 AAGAAAACAAC
1556418 AAGAAAACAA
1 AAGAAAACAA
1556428 ATTAGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.16, G:0.09, T:0.00
Consensus pattern (11 bp):
AAGAAAACAAC
Found at i:1557684 original size:24 final size:24
Alignment explanation
Indices: 1557656--1557727 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
1557646 AATAAAAAAT
1557656 AATAAAAATAAAAGA-ATATTGAAA
1 AATAAAAATAAAA-ATATATTGAAA
* *
1557680 GATAAATAA-AAAAATATATTTAAA
1 AATAAA-AATAAAAATATATTGAAA
*
1557704 AATAATAATAAAAATA-A-TGAAA
1 AATAAAAATAAAAATATATTGAAA
1557726 AA
1 AA
1557728 CATGTTAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
22 6 0.15
23 4 0.10
24 28 0.70
25 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (24 bp):
AATAAAAATAAAAATATATTGAAA
Found at i:1557727 original size:23 final size:23
Alignment explanation
Indices: 1557662--1557727 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 23
1557652 AAATAATAAA
* *
1557662 AATAAAAGAATAT-TG-AAAGAT
1 AATAAAAAAATATATGAAAAAAT
**
1557683 AAATAAAAAAATATATTTAAAAAT
1 -AATAAAAAAATATATGAAAAAAT
1557707 AATAATAAAAATA-ATGAAAAA
1 AATAA-AAAAATATATGAAAAA
1557728 CATGTTAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 12 0.33
23 12 0.33
24 12 0.33
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (23 bp):
AATAAAAAAATATATGAAAAAAT
Found at i:1559025 original size:35 final size:34
Alignment explanation
Indices: 1558975--1559299 Score: 270
Period size: 35 Copynumber: 9.3 Consensus size: 34
1558965 TTTTTTTAAA
* *
1558975 TATAAGTTTTCAAAATCCTTTAAAAAACTATATAT
1 TATACGTTTTCAAAATCATTT-AAAAACTATATAT
*
1559010 TACTA-GTTTTCAAAATCATTTCGAAAACTATAT-T
1 TA-TACGTTTTCAAAATCATTT-AAAAACTATATAT
* * * *
1559044 ATATATGTTTTCAAAACCGTTTTAAAACTATATAT
1 -TATACGTTTTCAAAATCATTTAAAAACTATATAT
* * *
1559079 TATACATTTTTTTC-AACT-ATTTAAAAAACTATATAC
1 TATAC---GTTTTCAAAATCATTT-AAAAACTATATAT
* * *
1559115 TATATGTTTTCAAAACCATTTTAAAACTATATAT
1 TATACGTTTTCAAAATCATTTAAAAACTATATAT
*
1559149 TATACGTTTTTAAAA-CTATTTTAAAAACTATATAT
1 TATACGTTTTCAAAATC-A-TTTAAAAACTATATAT
* *
1559184 TATACGTTTTCCAAA-CTATTTTGAAAAACTATATAC
1 TATACGTTTTCAAAATC-A-TTT-AAAAACTATATAT
*
1559220 TATATGTTTTCAAAATCATTTTAAAAA-TATATAT
1 TATACGTTTTCAAAATCA-TTTAAAAACTATATAT
*
1559254 TATACGTTTTTTTAAAA-CTATTTTAAAAACTATATAT
1 TATACG--TTTTCAAAATC-A-TTTAAAAACTATATAT
1559291 TATACGTTT
1 TATACGTTT
1559300 CTTACAAATA
Statistics
Matches: 242, Mismatches: 30, Indels: 36
0.79 0.10 0.12
Matches are distributed among these distances:
33 6 0.02
34 55 0.23
35 95 0.39
36 67 0.28
37 19 0.08
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (34 bp):
TATACGTTTTCAAAATCATTTAAAAACTATATAT
Found at i:1559107 original size:36 final size:36
Alignment explanation
Indices: 1559038--1559330 Score: 239
Period size: 35 Copynumber: 8.2 Consensus size: 36
1559028 TTTCGAAAAC
* * **
1559038 TATATTATATATGTTTTCAAAACCGTTTT-AAAACTA
1 TATATTATACATTTTTTC-AAACTATTTTAAAAACTA
*
1559074 TATATTATACATTTTTTTC-AACTATTTAAAAAACTA
1 TATATTATACA-TTTTTTCAAACTATTTTAAAAACTA
* * *
1559110 TATACTAT--ATGTTTTCAAAACCATTTT-AAAACTA
1 TATATTATACATTTTTTC-AAACTATTTTAAAAACTA
* *
1559144 TATATTATAC-GTTTTTAAAACTATTTTAAAAACTA
1 TATATTATACATTTTTTCAAACTATTTTAAAAACTA
* *
1559179 TATATTATAC-GTTTTCCAAACTATTTTGAAAAACTA
1 TATATTATACATTTTTTCAAACTATTTT-AAAAACTA
* * *
1559215 TATACTAT--ATGTTTTCAAAATCATTTTAAAAA-TA
1 TATATTATACATTTTTTCAAACT-ATTTTAAAAACTA
* *
1559249 TATATTATACGTTTTTTTAAAACTATTTTAAAAACTA
1 TATATTATAC-ATTTTTTCAAACTATTTTAAAAACTA
* *
1559286 TATATTATACGTTTCTTACAAA-TAAGTTTTCAAAAACTA
1 TATATTATACATTT-TTTCAAACT-A-TTTT-AAAAACTA
*
1559325 CATATT
1 TATATT
1559331 TATATATACT
Statistics
Matches: 209, Mismatches: 30, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
33 6 0.03
34 33 0.16
35 62 0.30
36 58 0.28
37 33 0.16
38 4 0.02
39 13 0.06
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
TATATTATACATTTTTTCAAACTATTTTAAAAACTA
Found at i:1559110 original size:105 final size:105
Alignment explanation
Indices: 1558993--1559299 Score: 381
Period size: 105 Copynumber: 2.9 Consensus size: 105
1558983 TTCAAAATCC
* * *
1558993 TTTAAAAAACTATATATTACTA-GTTTTCAAAATCATTTCGAAAACTATATTATATATGTTTTCA
1 TTTAAAAAACTATATACTA-TATGTTTTCAAAATCATTT-AAAAACTATATTATATATGTTTTTA
** * *
1559057 AAACCGTTTT-AAAACTATATATTATACATTTTTTTC-AACTA-
64 AAACTATTTTAAAAACTATATATTATAC--GTTTTCCAAACTAT
* * *
1559098 TTTAAAAAACTATATACTATATGTTTTCAAAACCATTTTAAAACTATA-TATTATACGTTTTTAA
1 TTTAAAAAACTATATACTATATGTTTTCAAAATCATTTAAAAACTATATTA-TATATGTTTTTAA
1559162 AACTATTTTAAAAACTATATATTATACGTTTTCCAAACTAT
65 AACTATTTTAAAAACTATATATTATACGTTTTCCAAACTAT
* * ** *
1559203 TTTGAAAAACTATATACTATATGTTTTCAAAATCATTTTAAAAATATATATTATACGTTTTTTTA
1 TTTAAAAAACTATATACTATATGTTTTCAAAATCA-TTTAAAAA-CTATATTATATATGTTTTTA
1559268 AAACTATTTTAAAAACTATATATTATACGTTT
64 AAACTATTTTAAAAACTATATATTATACGTTT
1559300 CTTACAAATA
Statistics
Matches: 177, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
103 7 0.04
104 34 0.19
105 83 0.47
106 7 0.04
107 44 0.25
108 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (105 bp):
TTTAAAAAACTATATACTATATGTTTTCAAAATCATTTAAAAACTATATTATATATGTTTTTAAA
ACTATTTTAAAAACTATATATTATACGTTTTCCAAACTAT
Found at i:1560127 original size:17 final size:17
Alignment explanation
Indices: 1560092--1560123 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1560082 TAAATTACAA
1560092 AAAAAATCTAAATTCCT
1 AAAAAATCTAAATTCCT
1560109 AAAAAATCT-AATTCC
1 AAAAAATCTAAATTCC
1560124 CTAACACGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAAATCTAAATTCCT
Found at i:1560613 original size:17 final size:19
Alignment explanation
Indices: 1560591--1560625 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1560581 TATTTTTTAA
1560591 ATTTGG-ATTAA-AATTTG
1 ATTTGGTATTAATAATTTG
1560608 ATTTGGTATTAATAATTT
1 ATTTGGTATTAATAATTT
1560626 AATGAGTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTGGTATTAATAATTTG
Found at i:1563030 original size:90 final size:92
Alignment explanation
Indices: 1562887--1563052 Score: 230
Period size: 90 Copynumber: 1.8 Consensus size: 92
1562877 TACGGCTTAA
* * * *
1562887 TACACTTTTAAGTGTCTAAATTATATGTCAAATTGACTTTTTGTGTCTAAAGAATTT-TTAT-TA
1 TACACTTTTAAGTGCCTAAACTATATCTCAAATTGACTTTTTGTGACTAAAGAATTTATTATATA
1562950 AAAATAGGTGTTTATCGTTCTCTCTGT
66 AAAATAGGTGTTTATCGTTCTCTCTGT
* * * *
1562977 TACACTTTTAGGTGCCTAGACTATATCTCAAATTGA-TTTTTAGTGACTCAAGAATTTATTTTAT
1 TACACTTTTAAGTGCCTAAACTATATCTCAAATTGACTTTTT-GTGACTAAAGAATTTATTATAT
1563041 AAAAATAGGTGT
65 AAAAATAGGTGT
1563053 CTAACGTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
89 5 0.08
90 44 0.68
91 3 0.05
92 13 0.20
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (92 bp):
TACACTTTTAAGTGCCTAAACTATATCTCAAATTGACTTTTTGTGACTAAAGAATTTATTATATA
AAAATAGGTGTTTATCGTTCTCTCTGT
Found at i:1563078 original size:92 final size:90
Alignment explanation
Indices: 1562888--1563081 Score: 221
Period size: 90 Copynumber: 2.1 Consensus size: 90
1562878 ACGGCTTAAT
* * * * *
1562888 ACACTTTTAAGTGTCTAAATTATATGTCAAATTGACTTTTTGTGTCTAAAGAATTTTTATTAAAA
1 ACACTTTTAGGTGCCTAAACTATATCTCAAATTGACTTTTTGTGACTAAAGAATTTTTATTAAAA
* * * *
1562953 ATAGGTGTTTATCGTTCTCTCTGTT
66 ATAGGTGTCTAACGTTCTCACTGTC
* * *
1562978 ACACTTTTAGGTGCCTAGACTATATCTCAAATTGA-TTTTTAGTGACTCAAGAATTTATTTTATA
1 ACACTTTTAGGTGCCTAAACTATATCTCAAATTGACTTTTT-GTGACTAAAGAATTT-TTAT-TA
*
1563042 AAAATAGGTGTCTAACGTTTTCAAC-GTC
63 AAAATAGGTGTCTAACGTTCTC-ACTGTC
1563070 ACACTTTTAGGT
1 ACACTTTTAGGT
1563082 ATCTGAATCA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
89 5 0.06
90 43 0.49
91 3 0.03
92 35 0.40
93 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.43
Consensus pattern (90 bp):
ACACTTTTAGGTGCCTAAACTATATCTCAAATTGACTTTTTGTGACTAAAGAATTTTTATTAAAA
ATAGGTGTCTAACGTTCTCACTGTC
Found at i:1568282 original size:22 final size:22
Alignment explanation
Indices: 1568256--1568300 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1568246 AACATGAAGT
1568256 TATAATTACAAAATTTGTTCTA
1 TATAATTACAAAATTTGTTCTA
1568278 TATAATTACAAAATTTGTTCTA
1 TATAATTACAAAATTTGTTCTA
1568300 T
1 T
1568301 GTAAGAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (22 bp):
TATAATTACAAAATTTGTTCTA
Found at i:1572567 original size:15 final size:15
Alignment explanation
Indices: 1572549--1572622 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
1572539 GTGAAATTCT
1572549 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
1572564 AATTATTTATATAAA
1 AATTATTTAAATAAA
**
1572579 AATTCA--TCGAT-AA
1 AATT-ATTTAAATAAA
*
1572592 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
1572606 AATTATTTATATAAA
1 AATTATTTAAATAAA
1572621 AA
1 AA
1572623 ATCATCGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.13
14 6 0.13
15 31 0.67
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:1572601 original size:42 final size:42
Alignment explanation
Indices: 1572548--1572639 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
1572538 TGTGAAATTC
*
1572548 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
1572589 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
1572631 TAATATATT
1 TAATATATT
1572640 ATTTTATTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAAATCATCGA
Found at i:1572637 original size:21 final size:21
Alignment explanation
Indices: 1572571--1572638 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1572561 AAAAATTATT
*
1572571 TATATAAAAATTCATCGATAA
1 TATATAAAAAATCATCGATAA
* * *
1572592 TATATTTAAATAAA-AAT-TAT-T
1 TATA--TAAA-AAATCATCGATAA
1572613 TATATAAAAAATCATCGATAA
1 TATATAAAAAATCATCGATAA
1572634 TATAT
1 TATAT
1572639 TATTTTATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
18 3 0.09
19 6 0.18
20 2 0.06
21 13 0.38
22 2 0.06
23 6 0.18
24 2 0.06
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAAAAATCATCGATAA
Found at i:1577227 original size:23 final size:23
Alignment explanation
Indices: 1577183--1577227 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1577173 AACATATTAG
* **
1577183 GTAGTGCTTATATAATGTAATAA
1 GTAGCGCTTATATAATAAAATAA
*
1577206 GTAGCGCTTATCTAATAAAATA
1 GTAGCGCTTATATAATAAAATA
1577228 TGCATTTAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAA
Found at i:1577297 original size:87 final size:86
Alignment explanation
Indices: 1577139--1577303 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 86
1577129 CGGTTATATT
* *
1577139 ATATCATTTAACCAGAAATATTATCAAATATAATAACATATTAGGTAGTGCTTATATAATGTAAT
1 ATATCATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGAGCTTATATAATGTAAT
1577204 AAGTAGCGCTTATCTAATAAA
66 AAGTAGCGCTTATCTAATAAA
* * *
1577225 ATATGCATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGAGTTTATATAATGTGA
1 ATAT-CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGAGCTTATATAATGTAA
*
1577290 TAGGTAGCGCTTAT
65 TAAGTAGCGCTTAT
1577304 ATTAACCTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 4 0.06
87 68 0.94
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (86 bp):
ATATCATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGAGCTTATATAATGTAAT
AAGTAGCGCTTATCTAATAAA
Found at i:1577692 original size:199 final size:198
Alignment explanation
Indices: 1577322--1578020 Score: 840
Period size: 199 Copynumber: 3.5 Consensus size: 198
1577312 ATTTTATAGG
* * * * * *
1577322 AAACCGATATATTTATACCAGTAACATTGTAAATTTACTTATTACATTACAATTATCGGTTTCGA
1 AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * * *
1577387 TATTTTTTGGATCGATACAATTT--GAAATGTATCGATACTTTATGCGTGCACCTCGTTGGGCAT
66 T-GTTTTTGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCAT
* * * * * *
1577450 TCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAATGTCGATACATCAT-TTAGATATATTTT
129 TCATTCTGGACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTT-GACATATTTT
1577514 CTCATA
193 CTCATA
* * * * * *
1577520 AAACCGGTATATTTCTATCGGGTACATTGTAAATTTACCTATCACATTGTAATTATCGGTTTCGA
1 AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
1577585 TGTTTTTGCGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CGTTTGGTATT
66 TGTTTTTG-GATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATT
* * * * *
1577649 TATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTCGATACTTTATGCTGACCTATTTTC
130 CATTCTGGACAAAA-GTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACATATTTTC
1577714 TCATA
194 TCATA
* *
1577719 AAACTGATATATTTATACCGGTTACATTGTAAATTTACTTATTACATTATAATTATCGGTTTCGA
1 AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
1577784 T-TTTATTGGGATCGATACTTTTAATAAATGTATCAACACTTTATGCGTGCACCTCGTTTGAGCA
66 TGTTT-TT-GGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTG-GCA
* * * ** *
1577848 TTCATTCTAGACATTAAGTATCGATACAAATTGCACAAGTGTCGATACATTATGTTGACATGTTT
128 TTCATTCTGGACA-AAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACATATTT
* *
1577913 TGTAAT-
192 TCTCATA
* * *
1577919 TAACTGATATA-TTATATCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGA
1 AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*
1577983 TGTTTTTTGGGTCGATAC-TTTAGA-AAATGTATCGACAC
66 TG-TTTTTGGATCGATACTTTTA-ATAAATGTATCGACAC
1578021 ATATTTAGGT
Statistics
Matches: 431, Mismatches: 57, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
197 9 0.02
198 105 0.24
199 235 0.55
200 20 0.05
201 60 0.14
202 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAACTGATATATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTC
ATTCTGGACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACATATTTTCTC
ATA
Found at i:1586998 original size:23 final size:24
Alignment explanation
Indices: 1586972--1587035 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
1586962 TAGCTCATAT
*
1586972 AATTACACC-TAAGTGCCACGTAG
1 AATTGCACCGTAAGTGCCACGTAG
* *
1586995 AATTGCACCGGAA-TGTCACGTAG
1 AATTGCACCGTAAGTGCCACGTAG
1587018 AATTGCACCGT-AGTGCCA
1 AATTGCACCGTAAGTGCCA
1587036 TATAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.91
24 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (24 bp):
AATTGCACCGTAAGTGCCACGTAG
Found at i:1587740 original size:45 final size:44
Alignment explanation
Indices: 1587646--1587748 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
1587636 GCACTACACC
* *
1587646 ATGCATCGATGCATAAATCTTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCATAAATCTTATTCGATGTTTCTATTTAAT-GGA
* *
1587691 ATGCATCGATGCATAAAT-TCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCATAAATCT-TATTCGATG-TTTCTATTT-AATGGA
1587736 ATGCATCGATGCA
1 ATGCATCGATGCA
1587749 CTGCATGTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
44 1 0.02
45 40 0.78
46 7 0.14
47 3 0.06
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (44 bp):
ATGCATCGATGCATAAATCTTATTCGATGTTTCTATTTAATGGA
Found at i:1589297 original size:19 final size:19
Alignment explanation
Indices: 1589252--1589300 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1589242 TTACATTCAC
*
1589252 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
** *
1589271 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1589290 ATACAAAATTA
1 ATACAAAATTA
1589301 ACCCTATATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1591362 original size:200 final size:198
Alignment explanation
Indices: 1590906--1591837 Score: 967
Period size: 179 Copynumber: 4.8 Consensus size: 198
1590896 TTATTTAAAT
* * * * *
1590906 AGTATCGACACAAATT-TAAAAGTGTCGATACATTATGTTGGCCTATTCTCTCATAAAACTGATA
1 AGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* *
1590970 TATTTATACCTGTTACATTATAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTTGG
66 TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
** * * * *
1591035 GATCGATACAATTTCAAATGTATCGACACTTTGTTCCTGCACCCTGTTTGGCATTCATTATGGAC
131 GATCGATACTTTTTAAAATGTATCGACACTTTATGCATGCACCCT-TTTGGCATTCATTATGGAC
1591100 AAAA
195 AAAA
* * * ** *
1591104 TGTATTGACACAAA-TCTAAAATGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGGT
1 AGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGT
* * * *
1591168 AAATTTATACCCGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTG
65 ATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* *
1591233 GGATCGATACTTTTTAAAACTGTATCGACACTTTATGCGTGCAACCCTTTTGGCATTCATTTTGG
130 GGATCGATACTTTTTAAAA-TGTATCGACACTTTATGCATGC-ACCCTTTTGGCATTCATTATGG
1591298 ACAAAA
193 ACAAAA
* * * * * *
1591304 AGGATCAACACAAATTCCACAAGTGTCAATACATTATGTAAACCTATTCTCTCATAAAATCGGTA
1 AGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * * * *
1591369 TAGTTATAACGGTTAC------AATTTACCTATTAC---AT-A-TATGGGTTTCGATGTTTCTAG
66 TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
* * * * *
1591423 GATTGATACTTTTTATAAATGTATCGACACTTTATGCATTCACCATTTTGGGCAATCATTCTGGA
131 GATCGATACTTTTTA-AAATGTATCGACACTTTATGCATGCACCCTTTT-GGCATTCATTATGGA
1591488 CAAAA
194 CAAAA
* * *
1591493 AGTATCGACACAAAATT-CAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGT
1 AGTATCGACAC-AAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGT
* * * * * *
1591557 ATATTTATACTGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTG
65 ATATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* * * *
1591622 GGATCGACAC--TTT---ATG--T-G--------TGCA--C-CACGTTTGGCATTCATTTTGGAC
130 GGATCGATACTTTTTAAAATGTATCGACACTTTATGCATGCACCCTTTTGGCATTCATTATGGAC
1591668 AAAA
195 AAAA
* * * * * *
1591672 AGTATCGACACAAATTCCACAAGTGTCGATACATTATGTATATCTATTTTCTCAAAAAAACGGTA
1 AGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * * * * *
1591737 TATGTATACCGATTACATTGTAAATTTACCTATTATATTATAATTTTCGGTTTTGATGTTTTTGG
66 TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
1591802 GATCGATACTTTTTAAACATGTATCGACACTTTATG
131 GATCGATACTTTTTAAA-ATGTATCGACACTTTATG
1591838 GGAAACTTTA
Statistics
Matches: 609, Mismatches: 88, Indels: 76
0.79 0.11 0.10
Matches are distributed among these distances:
178 5 0.01
179 131 0.22
180 4 0.01
181 4 0.01
183 4 0.01
185 3 0.00
187 1 0.00
188 8 0.01
189 131 0.22
190 9 0.01
191 3 0.00
192 1 0.00
194 17 0.03
195 13 0.02
196 2 0.00
197 1 0.00
198 22 0.04
199 114 0.19
200 126 0.21
201 10 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (198 bp):
AGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
TATTTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
GATCGATACTTTTTAAAATGTATCGACACTTTATGCATGCACCCTTTTGGCATTCATTATGGACA
AAA
Found at i:1591540 original size:189 final size:190
Alignment explanation
Indices: 1590906--1591837 Score: 780
Period size: 189 Copynumber: 4.8 Consensus size: 190
1590896 TTATTTAAAT
* * * * *
1590906 AGTATCGACACAAATTTAAAAGTGTCGATACATTATGTTGGCCTATTCTCTCATAAAACTGATAT
1 AGTATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
*
1590971 ATTTATACCTGTTACATTATAAATTTACCTATTACGTTATAATTATCGGTTTCGATGTTTTTGGG
66 ATTTATACCCGTTAC----T-AATTTACCTATTAC--TATAATTATCGGTTTCGATGTTTTTGGG
** * * * *
1591036 ATCGATACAATTTCAAATGTATCGACACTTTGTTCCTGCACCCTGTTTGGCATTCATTATGGACA
124 ATCGATACTTTTTAAAATGTATCGACACTTTATGCATGCACCCT-TTTGGCATTCATTATGGACA
1591101 AAA
188 AAA
* * ** *
1591104 TGTATTGACACAAA-TCTAAAATGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACCGGT
1 AGTATCGACACAAATTC-AAAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGT
* *
1591168 AAATTTATACCCGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTG
64 ATATTTATACCCGTTAC----T-AATTTACCTATTAC--TATAATTATCGGTTTCGATGTTTTTG
* *
1591233 GGATCGATACTTTTTAAAACTGTATCGACACTTTATGCGTGCAACCCTTTTGGCATTCATTTTGG
122 GGATCGATACTTTTTAAAA-TGTATCGACACTTTATGCATGC-ACCCTTTTGGCATTCATTATGG
1591298 ACAAAA
185 ACAAAA
* * * * * *
1591304 AGGATCAACACAAATTCCACAAGTGTCAATACATTATGTAAACCTATTCTCTCATAAAATCGGTA
1 AGTATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * * * * * *
1591369 TAGTTATAACGGTTAC-AATTTACCTATTAC-AT-A-TATGGGTTTCGATGTTTCTAGGATTGAT
65 TATTTATACCCGTTACTAATTTACCTATTACTATAATTATCGGTTTCGATGTTTTTGGGATCGAT
* * * *
1591430 ACTTTTTATAAATGTATCGACACTTTATGCATTCACCATTTTGGGCAATCATTCTGGACAAAA
130 ACTTTTTA-AAATGTATCGACACTTTATGCATGCACCCTTTT-GGCATTCATTATGGACAAAA
* * *
1591493 AGTATCGACACAAAATTCAAAAGTGTCGACACATTATGTAGACCTATTTTCACATAAAACCGGTA
1 AGTATCGACAC-AAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
** * * * *
1591558 TATTTATACTGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCAATGTTTTTGG
65 TATTTATACCCG-----TTACTAATTTACCTATTAC--TATAATTATCGGTTTCGATGTTTTTGG
* * * *
1591623 GATCGACAC--TTT---ATG--T-G--------TGCA--C-CACGTTTGGCATTCATTTTGGACA
123 GATCGATACTTTTTAAAATGTATCGACACTTTATGCATGCACCCTTTTGGCATTCATTATGGACA
1591669 AAA
188 AAA
* * * * * *
1591672 AGTATCGACACAAATTCCACAAGTGTCGATACATTATGTATATCTATTTTCTCAAAAAAACGGTA
1 AGTATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTA
* * * *
1591737 TATGTATA-CCGATTACATTGTAAATTTACCTATTATATTATAATTTTCGGTTTTGATGTTTTTG
65 TATTTATACCCG-TTAC----T-AATTTACCTA-T-TACTATAATTATCGGTTTCGATGTTTTTG
1591801 GGATCGATACTTTTTAAACATGTATCGACACTTTATG
122 GGATCGATACTTTTTAAA-ATGTATCGACACTTTATG
1591838 GGAAACTTTA
Statistics
Matches: 604, Mismatches: 85, Indels: 92
0.77 0.11 0.12
Matches are distributed among these distances:
174 5 0.01
178 6 0.01
179 117 0.19
180 5 0.01
181 6 0.01
183 4 0.01
185 3 0.00
187 1 0.00
188 8 0.01
189 128 0.21
190 9 0.01
191 3 0.00
192 1 0.00
194 21 0.03
195 13 0.02
196 2 0.00
197 1 0.00
198 21 0.03
199 114 0.19
200 126 0.21
201 9 0.01
202 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (190 bp):
AGTATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
ATTTATACCCGTTACTAATTTACCTATTACTATAATTATCGGTTTCGATGTTTTTGGGATCGATA
CTTTTTAAAATGTATCGACACTTTATGCATGCACCCTTTTGGCATTCATTATGGACAAAA
Found at i:1594524 original size:6 final size:6
Alignment explanation
Indices: 1594516--1594555 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
1594506 ATCATCATAA
* *
1594516 TCATCA TCATCT TCATCT TCATCG TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1594556 TGACCTCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.20, C:0.33, G:0.03, T:0.45
Consensus pattern (6 bp):
TCATCT
Found at i:1594531 original size:12 final size:12
Alignment explanation
Indices: 1594506--1594555 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1594496 ACTTGTTTGG
**
1594506 ATCATCATAATC
1 ATCATCATCTTC
1594518 ATCATCATCTTC
1 ATCATCATCTTC
* *
1594530 ATCTTCATCGTC
1 ATCATCATCTTC
*
1594542 ATCTTCATCTTC
1 ATCATCATCTTC
1594554 AT
1 AT
1594556 TGACCTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.42
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:1594537 original size:18 final size:18
Alignment explanation
Indices: 1594516--1594555 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1594506 ATCATCATAA
1594516 TCATCATCATCTTCATCT
1 TCATCATCATCTTCATCT
*
1594534 TCATCGTCATCTTCATCT
1 TCATCATCATCTTCATCT
1594552 TCAT
1 TCAT
1594556 TGACCTCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.33, G:0.03, T:0.45
Consensus pattern (18 bp):
TCATCATCATCTTCATCT
Done.