Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 15 of 143
Found at i:4627663 original size:22 final size:23
Alignment explanation
Indices: 4627615--4627663 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
4627605 TTTTTCTAGT
4627615 TTTTTATCTGTCTTGATGGCAT-
1 TTTTTATCTGTCTTGATGGCATC
*
4627637 TTTTTTTCTGTCTTG-TGGCATGC
1 TTTTTATCTGTCTTGATGGCAT-C
4627660 TTTT
1 TTTT
4627664 GTCTTATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 14 0.58
23 4 0.17
ACGTcount: A:0.08, C:0.14, G:0.18, T:0.59
Consensus pattern (23 bp):
TTTTTATCTGTCTTGATGGCATC
Found at i:4632273 original size:16 final size:16
Alignment explanation
Indices: 4632252--4632286 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4632242 ATCAAACTTG
*
4632252 AATAATGCAAACCTAA
1 AATAATGCAAACCCAA
*
4632268 AATAATTCAAACCCAA
1 AATAATGCAAACCCAA
4632284 AAT
1 AAT
4632287 TACTTGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (16 bp):
AATAATGCAAACCCAA
Found at i:4645500 original size:16 final size:16
Alignment explanation
Indices: 4645450--4645510 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
4645440 ACAGCACGCC
* * *
4645450 CTATTTAATTTCAGCT
1 CTATTTCATTACAGAT
* *
4645466 CTATTACATTATA-ACT
1 CTATTTCATTACAGA-T
4645482 CTATTTCATTACAGAT
1 CTATTTCATTACAGAT
4645498 CTATTTCATTACA
1 CTATTTCATTACA
4645511 AAGAACCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (16 bp):
CTATTTCATTACAGAT
Found at i:4646079 original size:17 final size:17
Alignment explanation
Indices: 4646054--4646087 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4646044 TTAATTATAA
*
4646054 TTAACTTTTTATTTTTT
1 TTAACTTTTCATTTTTT
*
4646071 TTAATTTTTCATTTTTT
1 TTAACTTTTCATTTTTT
4646088 GTTGAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTAACTTTTCATTTTTT
Found at i:4652185 original size:220 final size:220
Alignment explanation
Indices: 4651789--4652226 Score: 786
Period size: 220 Copynumber: 2.0 Consensus size: 220
4651779 TCAATAAAAC
4651789 TCATTTCCAATCATAACTCCAAAGGTATAAACTGTAACTCAAGTCAAAGGCAGCCCCTAGGAGCA
1 TCATTTCCAATCATAACTCCAAAGGTATAAACTGTAACTCAAGTCAAAGGCAGCCCCTAGGAGCA
* *
4651854 TATTGCAGTAATGCTCTTGGAGGTAAACATGATGCAAATAAGCTGACTGAATAAAAAGTTTAGGC
66 TATTGCAGTAATGCTCTTGAAGGTAAACATGATGCAAATAAGCTGACTGAATAAAAAGTTTAGAC
*
4651919 ACTCAATTAAACGAACAGCTTTCGTTCTAAGGTTCCTCCAATTCATTTACCATGTCACGTTGAGG
131 ACTCAATAAAACGAACAGCTTTCGTTCTAAGGTTCCTCCAATTCATTTACCATGTCACGTTGAGG
4651984 AATTCCTTCTGTGATACAAACAAGG
196 AATTCCTTCTGTGATACAAACAAGG
* *
4652009 TCATTTTCAATCATAACTCCAAAGGTATAAACTGTAACTCGAGTCAAAGGCAGCCCCTAGGAGCA
1 TCATTTCCAATCATAACTCCAAAGGTATAAACTGTAACTCAAGTCAAAGGCAGCCCCTAGGAGCA
*
4652074 TATTGCAGTAATGCTCTTGAAGGTACACATGATGCAAATAAGCTGACTGAATAAAAAGTTTAGAC
66 TATTGCAGTAATGCTCTTGAAGGTAAACATGATGCAAATAAGCTGACTGAATAAAAAGTTTAGAC
* * * *
4652139 ACTCAATAAAATGATCAGCTTTCGTTCTAAGGTTCCTCCGATTCATTTACCATGTCATGTTGAGG
131 ACTCAATAAAACGAACAGCTTTCGTTCTAAGGTTCCTCCAATTCATTTACCATGTCACGTTGAGG
4652204 AATTCCTTCTGTGATACAAACAA
196 AATTCCTTCTGTGATACAAACAA
4652227 CAAGGTCCAG
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
220 208 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (220 bp):
TCATTTCCAATCATAACTCCAAAGGTATAAACTGTAACTCAAGTCAAAGGCAGCCCCTAGGAGCA
TATTGCAGTAATGCTCTTGAAGGTAAACATGATGCAAATAAGCTGACTGAATAAAAAGTTTAGAC
ACTCAATAAAACGAACAGCTTTCGTTCTAAGGTTCCTCCAATTCATTTACCATGTCACGTTGAGG
AATTCCTTCTGTGATACAAACAAGG
Found at i:4654553 original size:29 final size:28
Alignment explanation
Indices: 4654519--4654612 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
4654509 AAAATTTGTT
4654519 TTTAAAAATATAAACATATATAAAAATTA
1 TTTAAAAATATAAA-ATATATAAAAATTA
*
4654548 TTTAAAAATAGTAGAAAGT-TGTAAAAATT-
1 TTTAAAAATA-TA-AAA-TATATAAAAATTA
* * * *
4654577 CTTAAAAATATAAAAAATGTTAAAAAATA
1 TTTAAAAATATAAAATAT-ATAAAAATTA
4654606 TTTAAAA
1 TTTAAAA
4654613 TTGTAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.08
28 9 0.17
29 25 0.47
30 12 0.23
31 3 0.06
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
TTTAAAAATATAAAATATATAAAAATTA
Found at i:4655521 original size:19 final size:20
Alignment explanation
Indices: 4655499--4655536 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
4655489 AGAAAGTTGT
*
4655499 AAAATTTCTTAAAA-ATATA
1 AAAAATTCTTAAAAGATATA
*
4655518 AAAAATTGTTAAAAGATAT
1 AAAAATTCTTAAAAGATAT
4655537 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAAATTCTTAAAAGATATA
Found at i:4661856 original size:15 final size:13
Alignment explanation
Indices: 4661845--4661884 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 13
4661835 TTTTTTATAT
4661845 TATTTTAATTTAA
1 TATTTTAATTTAA
4661858 TATTTAATAATTTAA
1 TATTT--TAATTTAA
*
4661873 TATTTTTATTTA
1 TATTTTAATTTA
4661885 TTGAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 11 0.46
15 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTAATTTAA
Found at i:4665409 original size:19 final size:18
Alignment explanation
Indices: 4665358--4665409 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
4665348 TATTCAGTAG
*
4665358 TTTTATA-TATTATCAAT
1 TTTTATATTATTATTAAT
* *
4665375 TTTTATATAACATATTATAT
1 TTTTATATTA-TTATTA-AT
4665395 TTTTATATTATTATT
1 TTTTATATTATTATT
4665410 TTGAGGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 7 0.26
18 1 0.04
19 8 0.30
20 11 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATTATTATTAAT
Found at i:4665659 original size:15 final size:15
Alignment explanation
Indices: 4665617--4665659 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4665607 TGTGTGTATT
*
4665617 TTTAAATTATCTTTA
1 TTTAAATTATTTTTA
* *
4665632 ATT-AATTAATTTTA
1 TTTAAATTATTTTTA
4665646 TTTAAATTATTTTT
1 TTTAAATTATTTTT
4665660 TTGACGAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAAATTATTTTTA
Found at i:4668290 original size:18 final size:18
Alignment explanation
Indices: 4668237--4668300 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
4668227 ACCTTTAAAA
* * *
4668237 ATTGGCTAACACATCAAG
1 ATTGGCGAACTCAACAAG
* ***
4668255 ATCGGCGAACTTGCCAAG
1 ATTGGCGAACTCAACAAG
4668273 ATTGGCGAACTCAACAAG
1 ATTGGCGAACTCAACAAG
*
4668291 ATTGGTGAAC
1 ATTGGCGAAC
4668301 CCTCTAGGAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (18 bp):
ATTGGCGAACTCAACAAG
Found at i:4668546 original size:16 final size:16
Alignment explanation
Indices: 4668525--4668569 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
4668515 TTTCTAAAAG
4668525 ATTTAATATTTATTAT
1 ATTTAATATTTATTAT
*
4668541 -TATTAATA--TAATAT
1 AT-TTAATATTTATTAT
4668555 ATTTAATATTTATTA
1 ATTTAATATTTATTA
4668570 GTATAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTAATATTTATTAT
Found at i:4668574 original size:24 final size:23
Alignment explanation
Indices: 4668530--4668575 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
4668520 AAAAGATTTA
*
4668530 ATATTTATTATTATTAATATAAT
1 ATATTTAATATTATTAATATAAT
*
4668553 ATATTTAATATTTATTAGTATAA
1 ATATTTAATA-TTATTAATATAA
4668576 AACCTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATTTAATATTATTAATATAAT
Found at i:4682910 original size:24 final size:23
Alignment explanation
Indices: 4682860--4682918 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 23
4682850 TTATTTTGAC
**
4682860 TTTTTAAAA-TTTATAATTATAT
1 TTTTTAAAATTTTATAAAAATAT
*
4682882 ATTTTAAAATTTTATAAAAAATAT
1 TTTTTAAAATTTTAT-AAAAATAT
4682906 TTTTTAAAATTTT
1 TTTTTAAAATTTT
4682919 TTATATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 8 0.26
23 5 0.16
24 18 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTAAAATTTTATAAAAATAT
Found at i:4683415 original size:10 final size:9
Alignment explanation
Indices: 4683400--4683438 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4683390 AAAATACAAC
4683400 ATTTTTTATA
1 ATTTTTT-TA
*
4683410 ATTTTTTCA
1 ATTTTTTTA
4683419 ATTTTTTTA
1 ATTTTTTTA
*
4683428 ATATTTTTA
1 ATTTTTTTA
4683437 AT
1 AT
4683439 AATATTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:4689988 original size:28 final size:28
Alignment explanation
Indices: 4689948--4690004 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
4689938 TAACAGTCCC
4689948 ATATGCGCATCCATCTACCACGTGTAGT
1 ATATGCGCATCCATCTACCACGTGTAGT
4689976 ATATGCGCATCCATCTACCACGTGTAGT
1 ATATGCGCATCCATCTACCACGTGTAGT
4690004 A
1 A
4690005 CTGGTAAACC
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:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (28 bp):
ATATGCGCATCCATCTACCACGTGTAGT
Found at i:4690309 original size:27 final size:29
Alignment explanation
Indices: 4690270--4690334 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 29
4690260 CAAAATATTG
*
4690270 TTTTTAAAAGGCC-TAATTTTTTTTTA-AA
1 TTTTT-AAAGGCCAAAATTTTTTTTTACAA
4690298 TTTTTAAAGGCCAAAATTTTTTTTTATCAA
1 TTTTTAAAGGCCAAAATTTTTTTTTA-CAA
4690328 TTTTTAA
1 TTTTTAA
4690335 GGGATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 7 0.21
28 17 0.52
30 9 0.27
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (29 bp):
TTTTTAAAGGCCAAAATTTTTTTTTACAA
Found at i:4693228 original size:24 final size:24
Alignment explanation
Indices: 4693199--4693253 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
4693189 TTTAGCCAAC
*
4693199 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCTAAAATGATTAGCTCTT
*
4693223 ATGAGCCTAAAATGATTAGCTCTT
1 ACGAGCCTAAAATGATTAGCTCTT
4693247 ACGAGCC
1 ACGAGCC
4693254 CAGACAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (24 bp):
ACGAGCCTAAAATGATTAGCTCTT
Found at i:4698284 original size:12 final size:13
Alignment explanation
Indices: 4698246--4698297 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
4698236 CATCGAAAAA
4698246 AAAATTAAATA-T
1 AAAATTAAATATT
*
4698258 CAAATTAAATATT
1 AAAATTAAATATT
*
4698271 AAAATTATAT-TT
1 AAAATTAAATATT
*
4698283 AAATACTAAATATT
1 AAA-ATTAAATATT
4698297 A
1 A
4698298 TATTAATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 15 0.47
13 14 0.44
14 3 0.09
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATTAAATATT
Found at i:4698303 original size:19 final size:19
Alignment explanation
Indices: 4698251--4698303 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
4698241 AAAAAAAAAT
* * *
4698251 TAAATATCAAATTAAATAT
1 TAAATATTATATTAAATAC
4698270 TAAA-ATTATATTTAAATAC
1 TAAATATTATA-TTAAATAC
4698289 TAAATATTATATTAA
1 TAAATATTATATTAA
4698304 TCATTTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.14
19 19 0.66
20 6 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAATATTATATTAAATAC
Found at i:4699908 original size:11 final size:11
Alignment explanation
Indices: 4699894--4699978 Score: 57
Period size: 11 Copynumber: 7.6 Consensus size: 11
4699884 ATATCCAAAC
*
4699894 AATAACAACAA
1 AATAATAACAA
4699905 AATAATAACAA
1 AATAATAACAA
* *
4699916 TATAATAA-TA
1 AATAATAACAA
*
4699926 AATAAAAACAA
1 AATAATAACAA
* *
4699937 AACAATGAA-AT
1 AATAAT-AACAA
*
4699948 AATAATAATAA
1 AATAATAACAA
*
4699959 TAATAATAATAA
1 -AATAATAACAA
4699971 TAATAATA
1 -AATAATA
4699979 TAGCGAAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
10 9 0.15
11 29 0.49
12 21 0.36
ACGTcount: A:0.69, C:0.06, G:0.01, T:0.24
Consensus pattern (11 bp):
AATAATAACAA
Found at i:4699911 original size:3 final size:3
Alignment explanation
Indices: 4699905--4699978 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
4699895 ATAACAACAA
* * * * *
4699905 AAT AAT AAC AAT -AT AAT AAT AAAT AAA AAC AA- AAC AAT GA- AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT
4699948 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
4699979 TAGCGAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 5 0.08
3 52 0.87
4 3 0.05
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:4699917 original size:9 final size:9
Alignment explanation
Indices: 4699891--4699976 Score: 50
Period size: 9 Copynumber: 9.2 Consensus size: 9
4699881 ATAATATCCA
*
4699891 AACAATAAC
1 AACAATAAT
4699900 AACAAAATAAT
1 AAC--AATAAT
4699911 AACAAT-AT
1 AACAATAAT
*
4699919 AATAATAAAT
1 AACAAT-AAT
* *
4699929 AAAAACAA-
1 AACAATAAT
4699937 AACAATGAAAT
1 AACAAT--AAT
*
4699948 AATAATAAT
1 AACAATAAT
*
4699957 AATAATAAT
1 AACAATAAT
*
4699966 AATAATAAT
1 AACAATAAT
4699975 AA
1 AA
4699977 TATAGCGAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
8 11 0.17
9 31 0.49
10 8 0.13
11 13 0.21
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.22
Consensus pattern (9 bp):
AACAATAAT
Found at i:4722082 original size:35 final size:35
Alignment explanation
Indices: 4722036--4722107 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4722026 AATTTTATGG
4722036 GTGAACGGTCTTTAACCATCAAACCAATCAAGTGA
1 GTGAACGGTCTTTAACCATCAAACCAATCAAGTGA
4722071 GTGAACGGTCTTTAACCATCAAACCAATCAAGTGA
1 GTGAACGGTCTTTAACCATCAAACCAATCAAGTGA
4722106 GT
1 GT
4722108 TTGAATTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (35 bp):
GTGAACGGTCTTTAACCATCAAACCAATCAAGTGA
Found at i:4731276 original size:21 final size:21
Alignment explanation
Indices: 4731250--4731289 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4731240 CAAATCGACC
* *
4731250 ACCCCCACGTCTACCACCACG
1 ACCCCCACGGCCACCACCACG
4731271 ACCCCCACGGCCACCACCA
1 ACCCCCACGGCCACCACCA
4731290 TCTCTTCCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.60, G:0.10, T:0.05
Consensus pattern (21 bp):
ACCCCCACGGCCACCACCACG
Found at i:4736198 original size:418 final size:421
Alignment explanation
Indices: 4735249--4736295 Score: 1192
Period size: 418 Copynumber: 2.5 Consensus size: 421
4735239 CATGAACATA
* * * *
4735249 ATACTTACTTCATCGGAGGATGAATCTTCCTCACTACTAGACTCTGAACTACTATCAGCTTTCAC
1 ATACTCACTTCGTCAGAGGATGAATCTTCCTCACTACTAGACTCAGAACTACTATCAGCTTTCAC
* * * *
4735314 TGTCTTAGCAGCTGGTATAGAGCCACTTTTAGCAACTACAGGTTTTTTCTTCTGAGCAGGAGCTT
66 TGTCTTAGCAGCCGGAATAGAGCCACTTTTAGCAACTACAGGTTTTTTATTCTGAGAAGGAGCTT
* *
4735379 CCTAGAATAAAACAAACAATTGAACATTAACAATCATGCAAAAGAATATTCCCAACCATGCTAAT
131 CCT-GAATAAAACAAACAATTGAACATTAACAATCATACAAAAGAATAGTCCCAACCATGCTAAT
* * * * *
4735444 ATTATAAGCATGAGTATAATACTCACTTCGTCGGAGGATGAATCCTCCTCGCTACTAGACTCAGA
195 ATTATAAGCAAGAGCATAATACTCACTTCATCAGAGGATGAATCCTCCTCACTACTAGA--CAGA
*** *
4735509 ACTACTATCAGCTTTCACAGTCTTAGCAACTGGAACAGAGTCACTTTTAGTGACTACAGATTTTT
258 ACTACTATCAGCTTTCACAGTCTTAGCAACTGGAACAGAGTCACTTTTACCAACTACAGAGTTTT
* * * * *
4735574 TATTCTGTGCAGGAGCTTCCTGGGATAAGACAATAAAATTGAACATCAACAATGATGCAAAGGAA
323 TATTCTGAGCAGGAGCTTCCTGGAATAAAACAATAAAATTGAACATCAACAATCATGCAAAAGAA
* *
4735639 TACTCCCAACCATACTAAAAATAAAAGTATGAAT
388 TACTACCAACCATACTAAAAATAAAAGCATGAAT
* *
4735673 ATTACTCACTTCGTCAGAGGATGAGTCTTCCTCACTACTAGACTCAGAACTACTATCAGCTTTAA
1 A-TACTCACTTCGTCAGAGGATGAATCTTCCTCACTACTAGACTCAGAACTACTATCAGCTTTCA
* * * * *
4735738 CAGTCTTAGCAGCCGGAATAGAGCCAGTTTTTGCAGCTACAGGTTTTTTATTCTGAGTAGGAGCT
65 CTGTCTTAGCAGCCGGAATAGAGCCACTTTTAGCAACTACAGGTTTTTTATTCTGAGAAGGAGCT
* * **
4735803 TCCTG-A-AAAA-AAAC-CTTGAACATTAACAATTATACAAAAGAAT-GT-CCAATTATGCTAAT
130 TCCTGAATAAAACAAACAATTGAACATTAACAATCATACAAAAGAATAGTCCCAACCATGCTAA-
* * * * *
4735862 GTTTTAACTAAGCAAGAGCATAATGCTTACTTCATCAGAGGATGAATCTTCCTCACTACTTGA-A
194 -TATT-A-TAAGCAAGAGCATAATACTCACTTCATCAGAGGATGAATCCTCCTCACTACTAGACA
* * * * * *
4735926 GAACTGCTATCAGCTTTCACTGTCTTGGCAGCTGGAACAGAG-CCCTCTTTACCAACTACAGGGT
256 GAACTACTATCAGCTTTCACAGTCTTAGCAACTGGAACAGAGTCACT-TTTACCAACTACAGAGT
*
4735990 TTTTCTTCTGAGCAGGAGCTTCCT-GAATAAAACAA-AAAATTGAACATCAA-ATATCATAG-AA
320 TTTTATTCTGAGCAGGAGCTTCCTGGAATAAAACAATAAAATTGAACATCAACA-ATCAT-GCAA
* * * * *
4736051 AAGAATA-TAACCAGCCATGCT-ATATTACAAGCATGAGGAT
383 AAGAATACT-ACCAACCATACTAAAAATAAAAGCATGA--AT
* *
4736091 GATACTCACTTCGTCAGAGGATGAATCTTCCTCACTGCTAGACTCAGAACTACTATCACCTTTCA
1 -ATACTCACTTCGTCAGAGGATGAATCTTCCTCACTACTAGACTCAGAACTACTATCAGCTTTCA
* * * *
4736156 CTGTCTT-GACAGCCAGAACAGGGCCACTTTTAGAAACTACAGGTTTTTTATTCTGAGAAGGAGC
65 CTGTCTTAG-CAGCCGGAATAGAGCCACTTTTAGCAACTACAGGTTTTTTATTCTGAGAAGGAGC
* * **
4736220 TTCCTGGAATATTAAA-AAAAATTATTTGAATATTAACAATCATAC-AAAGAATACGTCCTGACC
129 TTCCT-GAATA--AAACAAACA--A-TTGAACATTAACAATCATACAAAAGAATA-GTCCCAACC
4736283 ATGCTAATATTAT
187 ATGCTAATATTAT
4736296 GATGCACCTA
Statistics
Matches: 523, Mismatches: 75, Indels: 49
0.81 0.12 0.08
Matches are distributed among these distances:
416 13 0.02
417 37 0.07
418 143 0.27
419 76 0.15
420 30 0.06
421 6 0.01
422 50 0.10
423 7 0.01
424 2 0.00
425 119 0.23
426 8 0.02
427 21 0.04
428 2 0.00
429 9 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (421 bp):
ATACTCACTTCGTCAGAGGATGAATCTTCCTCACTACTAGACTCAGAACTACTATCAGCTTTCAC
TGTCTTAGCAGCCGGAATAGAGCCACTTTTAGCAACTACAGGTTTTTTATTCTGAGAAGGAGCTT
CCTGAATAAAACAAACAATTGAACATTAACAATCATACAAAAGAATAGTCCCAACCATGCTAATA
TTATAAGCAAGAGCATAATACTCACTTCATCAGAGGATGAATCCTCCTCACTACTAGACAGAACT
ACTATCAGCTTTCACAGTCTTAGCAACTGGAACAGAGTCACTTTTACCAACTACAGAGTTTTTAT
TCTGAGCAGGAGCTTCCTGGAATAAAACAATAAAATTGAACATCAACAATCATGCAAAAGAATAC
TACCAACCATACTAAAAATAAAAGCATGAAT
Found at i:4739768 original size:22 final size:22
Alignment explanation
Indices: 4739740--4739847 Score: 85
Period size: 22 Copynumber: 4.9 Consensus size: 22
4739730 TTGTACGGGT
*
4739740 TTAGCACTTTAGTGATCTCTAC
1 TTAGCACTTTAGTGCTCTCTAC
** *
4739762 TTAGCACTTCGGTGCTCTTTGA-
1 TTAGCACTTTAGTGCTCTCT-AC
* *
4739784 TCAGCA-TTTCGATGCTCTCTAC
1 TTAGCACTTTAG-TGCTCTCTAC
* **
4739806 TTAGCACTTCAGTGCTCTCTGT
1 TTAGCACTTTAGTGCTCTCTAC
* *
4739828 TTAGCACTATAGTGTTCTCT
1 TTAGCACTTTAGTGCTCTCT
4739848 TGTGTGGTGT
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
21 4 0.06
22 58 0.88
23 4 0.06
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.41
Consensus pattern (22 bp):
TTAGCACTTTAGTGCTCTCTAC
Found at i:4739847 original size:44 final size:44
Alignment explanation
Indices: 4739738--4739847 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
4739728 GCTTGTACGG
* *
4739738 GTTTAGCACTTTAGTGATCTCTACTTAGCACTTCGGTGCTCTTT
1 GTTTAGCACTTTAGTGATCTCTACTTAGCACTTCAGTGCTCTCT
* * * *
4739782 GATCAGCA-TTTCGATGCTCTCTACTTAGCACTTCAGTGCTCTCT
1 GTTTAGCACTTTAG-TGATCTCTACTTAGCACTTCAGTGCTCTCT
* *
4739826 GTTTAGCACTATAGTGTTCTCT
1 GTTTAGCACTTTAGTGATCTCT
4739848 TGTGTGGTGT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 4 0.08
44 46 0.87
45 3 0.06
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (44 bp):
GTTTAGCACTTTAGTGATCTCTACTTAGCACTTCAGTGCTCTCT
Found at i:4741905 original size:17 final size:18
Alignment explanation
Indices: 4741883--4741923 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
4741873 TCAATGGCCA
4741883 CCACCGGTC-ACCATGCT
1 CCACCGGTCGACCATGCT
4741900 CCACC-GTCGACCATGCT
1 CCACCGGTCGACCATGCT
4741917 -CACCGGT
1 CCACCGGT
4741924 AGTCATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (18 bp):
CCACCGGTCGACCATGCT
Found at i:4750881 original size:29 final size:30
Alignment explanation
Indices: 4750800--4750881 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 30
4750790 TCATTAGGGT
* ** *
4750800 TTATCAAGCACTATGTGTCAATGATTACAT
1 TTATCAAGCACTTTGTGTCGGTGATTACAA
* * *
4750830 TTATCAAGTACTTTGTATTGGTG-TTACAA
1 TTATCAAGCACTTTGTGTCGGTGATTACAA
*
4750859 TTATCAAGCACTTTGTGCCGGTG
1 TTATCAAGCACTTTGTGTCGGTG
4750882 CTATATTTAT
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (30 bp):
TTATCAAGCACTTTGTGTCGGTGATTACAA
Found at i:4753598 original size:97 final size:97
Alignment explanation
Indices: 4753432--4753691 Score: 367
Period size: 97 Copynumber: 2.7 Consensus size: 97
4753422 ATCGATATCA
* *
4753432 CAACACATTTAATTCAACAGAAAACGACTAACTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
1 CAACACATTTAAATCAACAGAAAACGACTAATTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
* * * *
4753497 CCATTAAGTTCGCGAATAATTATTAAGGCTTT
66 CCATTAAGTACGCGAAGAACTATTAAGGCATT
* * *
4753529 CAACACAGTTAAAGCAACAGAAATCGACTAATTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
1 CAACACATTTAAATCAACAGAAAACGACTAATTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
*
4753594 CCATTATGTACGCGAAGAACTATTAAGGCATT
66 CCATTAAGTACGCGAAGAACTATTAAGGCATT
* * * * * * *
4753626 CAACGCATTTAAATAAACAGAAACCGACTAATTTTTCTCGAATCTATTTCAAATTTAGGGTTTAG
1 CAACACATTTAAATCAACAGAAAACGACTAATTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
4753691 C
66 C
4753692 AATCAGGTAT
Statistics
Matches: 144, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 144 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (97 bp):
CAACACATTTAAATCAACAGAAAACGACTAATTTTTCTCGAATGTGTTTCAAATTCAGGATTTAG
CCATTAAGTACGCGAAGAACTATTAAGGCATT
Found at i:4756211 original size:59 final size:59
Alignment explanation
Indices: 4756096--4756211 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
4756086 TCCAAGATTG
* * * *
4756096 CATCCCTAACAAAGTGATAATCCACTTCAATTGCAATATGCAATGCAAATTGACTATTA
1 CATCCCGAACAAAGTAATAATCCACTTCAATTGCAATATGCAACGCAAATTAACTATTA
* *
4756155 CATCCCGAACAAAGTAATTATCCATTTCAATTGCAATATGCAACG-AAGATTAACTAT
1 CATCCCGAACAAAGTAATAATCCACTTCAATTGCAATATGCAACGCAA-ATTAACTAT
4756212 GGCCTCGAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 2 0.04
59 48 0.96
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (59 bp):
CATCCCGAACAAAGTAATAATCCACTTCAATTGCAATATGCAACGCAAATTAACTATTA
Found at i:4760444 original size:21 final size:21
Alignment explanation
Indices: 4760420--4760460 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4760410 AACCTTTAAA
*
4760420 ACAATCAAATTATTATGTAAG
1 ACAATCAAATTATCATGTAAG
4760441 ACAATCAAATTATCATGTAA
1 ACAATCAAATTATCATGTAA
4760461 TAAATCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (21 bp):
ACAATCAAATTATCATGTAAG
Found at i:4769447 original size:24 final size:24
Alignment explanation
Indices: 4769415--4769463 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
4769405 TAAAGCTGGG
4769415 AGCTACATTTGGCTATGTTTTTCA
1 AGCTACATTTGGCTATGTTTTTCA
4769439 AGCTACATTTGGCTATGTTTTTCA
1 AGCTACATTTGGCTATGTTTTTCA
4769463 A
1 A
4769464 TAGGAATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (24 bp):
AGCTACATTTGGCTATGTTTTTCA
Found at i:4782437 original size:178 final size:178
Alignment explanation
Indices: 4782138--4782493 Score: 703
Period size: 178 Copynumber: 2.0 Consensus size: 178
4782128 AAAGACGAAA
*
4782138 GAAGGAGAAGGACCAAATTGAAGAAATAGGAAAGGAGAAAGCTAATGTGTGAGAAGAAATTATCT
1 GAAGGAGAAGGACCAAATTGAAGAAATAGGAAAGGAGAAAGCTAAGGTGTGAGAAGAAATTATCT
4782203 ACAAGTGAGGTAAGTACTACAAGTATTATGAGACTTAGAAACATTTAAGTTAAAGTGTTTATAAT
66 ACAAGTGAGGTAAGTACTACAAGTATTATGAGACTTAGAAACATTTAAGTTAAAGTGTTTATAAT
4782268 TTTAATATATGATTAATCATGTTAAAAATGATATGTTTAATTATAAGT
131 TTTAATATATGATTAATCATGTTAAAAATGATATGTTTAATTATAAGT
4782316 GAAGGAGAAGGACCAAATTGAAGAAATAGGAAAGGAGAAAGCTAAGGTGTGAGAAGAAATTATCT
1 GAAGGAGAAGGACCAAATTGAAGAAATAGGAAAGGAGAAAGCTAAGGTGTGAGAAGAAATTATCT
4782381 ACAAGTGAGGTAAGTACTACAAGTATTATGAGACTTAGAAACATTTAAGTTAAAGTGTTTATAAT
66 ACAAGTGAGGTAAGTACTACAAGTATTATGAGACTTAGAAACATTTAAGTTAAAGTGTTTATAAT
4782446 TTTAATATATGATTAATCATGTTAAAAATGATATGTTTAATTATAAGT
131 TTTAATATATGATTAATCATGTTAAAAATGATATGTTTAATTATAAGT
4782494 ATTGTTTATA
Statistics
Matches: 177, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 177 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.30
Consensus pattern (178 bp):
GAAGGAGAAGGACCAAATTGAAGAAATAGGAAAGGAGAAAGCTAAGGTGTGAGAAGAAATTATCT
ACAAGTGAGGTAAGTACTACAAGTATTATGAGACTTAGAAACATTTAAGTTAAAGTGTTTATAAT
TTTAATATATGATTAATCATGTTAAAAATGATATGTTTAATTATAAGT
Found at i:4782757 original size:23 final size:23
Alignment explanation
Indices: 4782731--4782872 Score: 126
Period size: 23 Copynumber: 6.1 Consensus size: 23
4782721 ATTAGCGCGT
*
4782731 TCTCTGATTAGCACAGTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
* *
4782754 TCTCCGATTAGCACTGTATGTGC
1 TCTCTGATTAGCACTGTGTGTGC
* * * *
4782777 TCTCCGTTTAGAACTTTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
* *
4782800 TCTCTGTTTAGCAC-GTCTCGTGC
1 TCTCTGATTAGCACTGTGT-GTGC
* *
4782823 TTTCTGTTATTAGCACT-TCGTTTGC
1 TCTCTG--ATTAGCACTGT-GTGTGC
*
4782848 TCTCTGATTAGCACTTTGTGTGC
1 TCTCTGATTAGCACTGTGTGTGC
4782871 TC
1 TC
4782873 AATACTTTGT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
22 2 0.02
23 76 0.79
24 1 0.01
25 16 0.17
26 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (23 bp):
TCTCTGATTAGCACTGTGTGTGC
Found at i:4782823 original size:46 final size:48
Alignment explanation
Indices: 4782747--4782872 Score: 132
Period size: 48 Copynumber: 2.7 Consensus size: 48
4782737 ATTAGCACAG
*
4782747 TGTGTGCTCTCCGATTAGCACTGTATGTGCTCTCCG-T-TTAGAACTT
1 TGTGTGCTCTCTGATTAGCACTGTATGTGCTCTCCGTTATTAGAACTT
* * * * *
4782793 TGTGTGCTCTCTGTTTAGCAC-GTCTCGTGCTTTCTGTTATTAGCACTT
1 TGTGTGCTCTCTGATTAGCACTGTAT-GTGCTCTCCGTTATTAGAACTT
* * * *
4782841 CGTTTGCTCTCTGATTAGCACTTTGTGTGCTC
1 TGTGTGCTCTCTGATTAGCACTGTATGTGCTC
4782873 AATACTTTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
45 3 0.05
46 27 0.42
47 1 0.02
48 31 0.48
49 2 0.03
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (48 bp):
TGTGTGCTCTCTGATTAGCACTGTATGTGCTCTCCGTTATTAGAACTT
Found at i:4784275 original size:16 final size:17
Alignment explanation
Indices: 4784242--4784383 Score: 54
Period size: 16 Copynumber: 7.9 Consensus size: 17
4784232 GACATGTGAC
4784242 AAAAAATTATAAAAAAT
1 AAAAAATTATAAAAAAT
* *
4784259 AAAAAA-TATTAATAAT
1 AAAAAATTATAAAAAAT
* * * *
4784275 AATATATTA-AAATATT
1 AAAAAATTATAAAAAAT
** *
4784291 AAAATTTTATTAAAAATTT
1 AAAAAATTA-TAAAAA-AT
* *
4784310 AAAACATTATAAAATCAT
1 AAAAAATTATAAAA-AAT
**
4784328 AAAATTTTTATAAAAATAGT
1 AAAA-AATTATAAAAA-A-T
*
4784348 AAAAATTTATAAAAAATCAT
1 AAAAAATTAT-AAAAA--AT
4784368 AAAAAAATTATAAAAA
1 -AAAAAATTATAAAAA
4784384 GCACCAAAAA
Statistics
Matches: 95, Mismatches: 19, Indels: 19
0.71 0.14 0.14
Matches are distributed among these distances:
16 24 0.25
17 8 0.08
18 14 0.15
19 23 0.24
20 16 0.17
21 10 0.11
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (17 bp):
AAAAAATTATAAAAAAT
Found at i:4784303 original size:19 final size:19
Alignment explanation
Indices: 4784279--4784361 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 19
4784269 AATAATAATA
4784279 TATTAAAATATTAAAATTT
1 TATTAAAATATTAAAATTT
**
4784298 TATTAAAA-ATTTAAAACAT
1 TATTAAAATA-TTAAAATTT
4784317 TA-TAAAATCA-TAAAATTTT
1 TATTAAAAT-ATTAAAA-TTT
* * *
4784336 TATAAAAATAGTAAAAATT
1 TATTAAAATATTAAAATTT
4784355 TA-TAAAA
1 TATTAAAA
4784362 AATCATAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
18 15 0.29
19 25 0.49
20 11 0.22
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (19 bp):
TATTAAAATATTAAAATTT
Found at i:4784323 original size:37 final size:38
Alignment explanation
Indices: 4784282--4784371 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 38
4784272 AATAATATAT
*
4784282 TAAAAT-ATTAAAA-TTTTATTAAAAAT-TTAAAACA-TTA
1 TAAAATCA-TAAAATTTTTA-TAAAAATAGTAAAA-ATTTA
4784319 TAAAATCATAAAATTTTTATAAAAATAGTAAAAATTTA
1 TAAAATCATAAAATTTTTATAAAAATAGTAAAAATTTA
4784357 TAAAAAATCATAAAA
1 T--AAAATCATAAAA
4784372 AAATTATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
37 19 0.41
38 15 0.33
40 12 0.26
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (38 bp):
TAAAATCATAAAATTTTTATAAAAATAGTAAAAATTTA
Found at i:4784362 original size:19 final size:20
Alignment explanation
Indices: 4784260--4784362 Score: 65
Period size: 19 Copynumber: 5.2 Consensus size: 20
4784250 ATAAAAAATA
* *
4784260 AAAAATATTAATAATAATATAT
1 AAAAATATTAA-AA-CATTTAT
* *
4784282 TAAAATATTAAAA-TTTTATT
1 AAAAATATTAAAACATTTA-T
4784302 AAAAAT-TTAAAACA-TTAT
1 AAAAATATTAAAACATTTAT
**
4784320 -AAAATCA-TAAAATTTTTAT
1 AAAAAT-ATTAAAACATTTAT
*
4784339 AAAAATAGTAAAA-ATTTAT
1 AAAAATATTAAAACATTTAT
4784358 AAAAA
1 AAAAA
4784363 ATCATAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
17 5 0.08
18 6 0.09
19 27 0.41
20 16 0.24
21 2 0.03
22 10 0.15
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (20 bp):
AAAAATATTAAAACATTTAT
Found at i:4784371 original size:19 final size:20
Alignment explanation
Indices: 4784320--4784371 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4784310 AAAACATTAT
*
4784320 AAAATCATAAAATTTTTATA
1 AAAATCATAAAATTTATATA
4784340 AAAAT-AGTAAAAATTTATA-A
1 AAAATCA-T-AAAATTTATATA
4784360 AAAATCATAAAA
1 AAAATCATAAAA
4784372 AAATTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 5 0.18
20 13 0.46
21 10 0.36
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATCATAAAATTTATATA
Found at i:4784373 original size:21 final size:21
Alignment explanation
Indices: 4784320--4784383 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
4784310 AAAACATTAT
**
4784320 AAAATCATAAAATTTTTAT-A
1 AAAATCATAAAAAATTTATAA
4784340 AAAAT-AGT-AAAAATTTATAA
1 AAAATCA-TAAAAAATTTATAA
*
4784360 AAAATCATAAAAAAATTATAA
1 AAAATCATAAAAAATTTATAA
4784381 AAA
1 AAA
4784384 GCACCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 9 0.24
20 13 0.35
21 15 0.41
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (21 bp):
AAAATCATAAAAAATTTATAA
Found at i:4784382 original size:19 final size:19
Alignment explanation
Indices: 4784310--4784382 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 19
4784300 TTAAAAATTT
*
4784310 AAAACATTATAAAATCATA
1 AAAAAATTATAAAATCATA
***
4784329 AAATTTTTATAAAA--ATA
1 AAAAAATTATAAAATCATA
*
4784346 GTAAAAATTTATAAAAAATCATA
1 --AAAAAATTAT--AAAATCATA
4784369 AAAAAATTATAAAA
1 AAAAAATTATAAAA
4784383 AGCACCAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
17 3 0.07
19 23 0.55
21 13 0.31
23 3 0.07
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAAATTATAAAATCATA
Found at i:4784589 original size:19 final size:19
Alignment explanation
Indices: 4784567--4784625 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
4784557 TGATACGATA
4784567 ATATTTTTTTATGAATTTT
1 ATATTTTTTTATGAATTTT
* * *
4784586 ATATTTATTTA-CATTTTT
1 ATATTTTTTTATGAATTTT
4784604 ATATTTTTCTTATG-ATTTT
1 ATATTTTT-TTATGAATTTT
4784623 ATA
1 ATA
4784626 AAATTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
18 12 0.38
19 20 0.62
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
ATATTTTTTTATGAATTTT
Found at i:4784616 original size:29 final size:28
Alignment explanation
Indices: 4784600--4784663 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 28
4784590 TTATTTACAT
4784600 TTTTATATTTTTCTTATGATTTTATAAAA
1 TTTTATATTTTTCTTAT-ATTTTATAAAA
*
4784629 TTTTATATTTTTCTATATATATCTTATAAAT
1 TTTTATATTTTTCT-TATAT-T-TTATAAAA
4784660 TTTT
1 TTTT
4784664 TACAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 16 0.52
30 4 0.13
31 11 0.35
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (28 bp):
TTTTATATTTTTCTTATATTTTATAAAA
Found at i:4784639 original size:37 final size:37
Alignment explanation
Indices: 4784567--4784640 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
4784557 TGATACGATA
**
4784567 ATATTTTTTTATGAATTTTATATTTATTTACATTTTT
1 ATATTTTTTTATGAATTTTATAAATATTTACATTTTT
*
4784604 ATATTTTTCTTATG-ATTTTATAAA-ATTTTATATTTTT
1 ATATTTTT-TTATGAATTTTATAAATA-TTTACATTTTT
4784641 CTATATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 1 0.03
37 26 0.81
38 5 0.16
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (37 bp):
ATATTTTTTTATGAATTTTATAAATATTTACATTTTT
Found at i:4784689 original size:27 final size:27
Alignment explanation
Indices: 4784659--4784711 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4784649 ATCTTATAAA
*
4784659 TTTTTTAC-AATTTTTATAAAATTTTAT
1 TTTTTTACTAATTTTAAT-AAATTTTAT
*
4784686 TTTTTTTCTAATTTTAATAAATTTTA
1 TTTTTTACTAATTTTAATAAATTTTA
4784712 AATAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTTTACTAATTTTAATAAATTTTAT
Found at i:4784715 original size:11 final size:10
Alignment explanation
Indices: 4784695--4784745 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
4784685 TTTTTTTTCT
4784695 AATTTTAATA
1 AATTTTAATA
4784705 AATTTTAAATA
1 AATTTT-AATA
*
4784716 AATTTTTAT-
1 AATTTTAATA
* *
4784725 ATTTTTATTA
1 AATTTTAATA
*
4784735 AAATTTAATA
1 AATTTTAATA
4784745 A
1 A
4784746 TTTATTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 6 0.19
10 16 0.50
11 10 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATTTTAATA
Found at i:4784731 original size:30 final size:27
Alignment explanation
Indices: 4784668--4784758 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 27
4784658 ATTTTTTACA
* **
4784668 ATTTTT-ATAAAATTTTATTTTTTTTCT
1 ATTTTTAATAAAATTTAATAATTTTT-T
* *
4784695 AATTTTAATAAATTTTAAATAAATTTTTAT
1 ATTTTTAATAAAATTT-AAT-AATTTTT-T
* *
4784725 ATTTTTATTAAAATTTAATAATTTATT
1 ATTTTTAATAAAATTTAATAATTTTTT
4784752 ATTTTTA
1 ATTTTTA
4784759 TTTTTAACCA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 13 0.25
28 14 0.27
29 5 0.10
30 19 0.37
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTTTAATAAAATTTAATAATTTTTT
Found at i:4786017 original size:2 final size:2
Alignment explanation
Indices: 4786010--4786052 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4786000 TAAGTTTGTA
4786010 AT AT AT AT AT 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 AT AT AT AT AT
4786052 A
1 A
4786053 AATTCAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4787444 original size:35 final size:35
Alignment explanation
Indices: 4787413--4787489 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
4787403 ATATCAACCT
*
4787413 TTATA-CA-AGTCAGAAAATTTTAATTTCATCAAA
1 TTATATCATAGTCACAAAATTTTAATTTCATCAAA
* *
4787446 TTATATCATTGTCACAAAGTTTTAATTTCATCAAA
1 TTATATCATAGTCACAAAATTTTAATTTCATCAAA
4787481 TTATATCAT
1 TTATATCAT
4787490 TAAATTCTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
33 5 0.13
34 2 0.05
35 32 0.82
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (35 bp):
TTATATCATAGTCACAAAATTTTAATTTCATCAAA
Found at i:4787490 original size:35 final size:35
Alignment explanation
Indices: 4787421--4787490 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
4787411 CTTTATACAA
*
4787421 GTCAGAAAATTTTAATTTCATCAAATTATATCATT
1 GTCACAAAATTTTAATTTCATCAAATTATATCATT
*
4787456 GTCACAAAGTTTTAATTTCATCAAATTATATCATT
1 GTCACAAAATTTTAATTTCATCAAATTATATCATT
4787491 AAATTCTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (35 bp):
GTCACAAAATTTTAATTTCATCAAATTATATCATT
Found at i:4792033 original size:21 final size:22
Alignment explanation
Indices: 4791994--4792040 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
4791984 ATTTTTAGAC
4791994 TATTGAAAAAAGATAATATTTT
1 TATTGAAAAAAGATAATATTTT
* *
4792016 TATTG-AAAAGGATTATATTTT
1 TATTGAAAAAAGATAATATTTT
4792037 TATT
1 TATT
4792041 TTATATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
TATTGAAAAAAGATAATATTTT
Found at i:4798298 original size:11 final size:12
Alignment explanation
Indices: 4798272--4798300 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4798262 TTGAAATGTT
4798272 ACAAATTTTGTA
1 ACAAATTTTGTA
4798284 ACAAATTTT-TA
1 ACAAATTTTGTA
4798295 ACAAAT
1 ACAAAT
4798301 AATTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.38
Consensus pattern (12 bp):
ACAAATTTTGTA
Found at i:4800985 original size:15 final size:15
Alignment explanation
Indices: 4800949--4800990 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
4800939 ATAATAAAAA
4800949 TATAATTTTATTATT
1 TATAATTTTATTATT
4800964 TAAATAATTTATATT-TT
1 T--ATAATTT-TATTATT
4800981 TATAATTTTA
1 TATAATTTTA
4800991 AAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
17 10 0.42
18 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATAATTTTATTATT
Found at i:4801005 original size:84 final size:82
Alignment explanation
Indices: 4800917--4801086 Score: 184
Period size: 84 Copynumber: 2.0 Consensus size: 82
4800907 TAAAAATCGT
* * *
4800917 AATTAAA-TTATATATTTTTATGATA-ATAAAAATATAATTTTATTATTTAAATAATTTATATTT
1 AATTAAATTTATATA-TTTTA--AAAGATAAAAATATAATTTTATTA-TT-AATAATTTAAAATT
* *
4800980 TTAT-AATTTTAAAAAAAATTA
61 TTATAAACTATAAAAAAAATTA
* * *
4801001 AATTAAATTTTTATCATTTTAAAAGATAAAAATGTAATTTTATTATTATTAATTTAAAATTTTAT
1 AATTAAATTTATAT-ATTTTAAAAGATAAAAATATAATTTTATTATTAATAATTTAAAATTTTAT
*
4801066 AAACTATAAAAAAATTTA
65 AAACTATAAAAAAAATTA
4801084 AAT
1 AAT
4801087 ATTTCATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
82 15 0.21
83 21 0.29
84 26 0.36
85 10 0.14
86 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (82 bp):
AATTAAATTTATATATTTTAAAAGATAAAAATATAATTTTATTATTAATAATTTAAAATTTTATA
AACTATAAAAAAAATTA
Found at i:4803649 original size:20 final size:20
Alignment explanation
Indices: 4803624--4803661 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4803614 TAATCCCATA
*
4803624 ATTTTAACTTTTAAATATAT
1 ATTTTAAATTTTAAATATAT
*
4803644 ATTTTAAATTTTCAATAT
1 ATTTTAAATTTTAAATAT
4803662 TAACTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATTTTAAATTTTAAATATAT
Found at i:4805671 original size:19 final size:19
Alignment explanation
Indices: 4805647--4805692 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4805637 TACAGAAACT
* *
4805647 TACTAACTGTCTCAACTAA
1 TACTAACTGCCTCAACAAA
*
4805666 TACTAACTGCCTTAACAAA
1 TACTAACTGCCTCAACAAA
4805685 TACTAACT
1 TACTAACT
4805693 ATCTAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.30
Consensus pattern (19 bp):
TACTAACTGCCTCAACAAA
Found at i:4809264 original size:21 final size:21
Alignment explanation
Indices: 4809225--4809264 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4809215 CTCTTGAAGC
*
4809225 ACCTCTTGCTCCCCTAAAATA
1 ACCTCTTGCTCCCCGAAAATA
* *
4809246 ACCTCTTGTTCCTCGAAAA
1 ACCTCTTGCTCCCCGAAAA
4809265 CCACCTCTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.35, G:0.07, T:0.30
Consensus pattern (21 bp):
ACCTCTTGCTCCCCGAAAATA
Found at i:4810250 original size:19 final size:19
Alignment explanation
Indices: 4810226--4810271 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
4810216 TACAGAAACT
* *
4810226 TACTAACTGTCTCAACTAA
1 TACTAACTGCCTCAACAAA
*
4810245 TACTAACTGCCTTAACAAA
1 TACTAACTGCCTCAACAAA
4810264 TACTAACT
1 TACTAACT
4810272 ACCTAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.30
Consensus pattern (19 bp):
TACTAACTGCCTCAACAAA
Found at i:4810323 original size:16 final size:15
Alignment explanation
Indices: 4810298--4810327 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4810288 TTAACAGAGT
4810298 GATCAAAATGAAAGC
1 GATCAAAATGAAAGC
4810313 GATCTAAAATGAAAG
1 GATC-AAAATGAAAG
4810328 TGTAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.17
Consensus pattern (15 bp):
GATCAAAATGAAAGC
Found at i:4811028 original size:127 final size:127
Alignment explanation
Indices: 4810802--4811060 Score: 509
Period size: 127 Copynumber: 2.0 Consensus size: 127
4810792 GTCCAAGCTT
*
4810802 TATCAGAATACTTTTTCAAACACCATTTTATCCTAACCAAGGATATTATATTCCATACCCAGTTC
1 TATCAGAATACTTTTTCAAACACCATTTTATCCTAACAAAGGATATTATATTCCATACCCAGTTC
4810867 AAACTCAAACATATACACCACAGGTAAACTACTTACCTTGGTCCCAAGATCCCAACACTGCA
66 AAACTCAAACATATACACCACAGGTAAACTACTTACCTTGGTCCCAAGATCCCAACACTGCA
4810929 TATCAGAATACTTTTTCAAACACCATTTTATCCTAACAAAGGATATTATATTCCATACCCAGTTC
1 TATCAGAATACTTTTTCAAACACCATTTTATCCTAACAAAGGATATTATATTCCATACCCAGTTC
4810994 AAACTCAAACATATACACCACAGGTAAACTACTTACCTTGGTCCCAAGATCCCAACACTGCA
66 AAACTCAAACATATACACCACAGGTAAACTACTTACCTTGGTCCCAAGATCCCAACACTGCA
4811056 TATCA
1 TATCA
4811061 AACCAATTAT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 131 1.00
ACGTcount: A:0.37, C:0.28, G:0.08, T:0.28
Consensus pattern (127 bp):
TATCAGAATACTTTTTCAAACACCATTTTATCCTAACAAAGGATATTATATTCCATACCCAGTTC
AAACTCAAACATATACACCACAGGTAAACTACTTACCTTGGTCCCAAGATCCCAACACTGCA
Found at i:4811115 original size:16 final size:15
Alignment explanation
Indices: 4811094--4811123 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4811084 AAAATGCAGA
4811094 AAAATTTGTGTGAAAG
1 AAAATTTGT-TGAAAG
4811110 AAAATTTGTTGAAA
1 AAAATTTGTTGAAA
4811124 ACACAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAATTTGTTGAAAG
Found at i:4815667 original size:34 final size:31
Alignment explanation
Indices: 4815598--4815669 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
4815588 AGCCACACCC
* **
4815598 TCATTTTATATATTTTTTAAATTATTTAATG
1 TCATTTTATATATTTTTTAAATTATTAAACA
*
4815629 TCATTTTAATATATATTTTTATATTATTAACACA
1 TCATTTT-ATATAT-TTTTTAAATTATTAA-ACA
4815663 TCATTTT
1 TCATTTT
4815670 GTTAATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 7 0.21
32 6 0.18
33 13 0.38
34 8 0.24
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.58
Consensus pattern (31 bp):
TCATTTTATATATTTTTTAAATTATTAAACA
Found at i:4818790 original size:84 final size:84
Alignment explanation
Indices: 4818605--4818790 Score: 246
Period size: 84 Copynumber: 2.2 Consensus size: 84
4818595 TCCAGCTCTG
** * * * * **
4818605 GAAACTTCTCCCTCACCAGCCGAAACCCCGGAATTGGCTCCGGAAACTTCTCCTTCTTTCCCACC
1 GAAACTTCTCCCTTGCCAGCCGAAACCCCAGAATTGGCTCCAGAAACCTCGCCTTCGCTCCCACC
*
4818670 ATCAGTGTATCCAGCTCCC
66 ATCAGTGTATCCAGCCCCC
* *
4818689 GAAACTTCTCCCATGCCAGCGGAAACCCCAGAATTGGCTCCAGAAACCTCGCCTTCGCTCCCACC
1 GAAACTTCTCCCTTGCCAGCCGAAACCCCAGAATTGGCTCCAGAAACCTCGCCTTCGCTCCCACC
**
4818754 ATCAGTGTATCTGGCCCCC
66 ATCAGTGTATCCAGCCCCC
*
4818773 GAAACTTCTCCTTTGCCA
1 GAAACTTCTCCCTTGCCA
4818791 ACAGAAACTC
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 87 1.00
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.23
Consensus pattern (84 bp):
GAAACTTCTCCCTTGCCAGCCGAAACCCCAGAATTGGCTCCAGAAACCTCGCCTTCGCTCCCACC
ATCAGTGTATCCAGCCCCC
Found at i:4823881 original size:15 final size:13
Alignment explanation
Indices: 4823845--4823875 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4823835 AAATTTAAAC
4823845 TTTTTAATAAGTG
1 TTTTTAATAAGTG
*
4823858 TTTTTAATACGTG
1 TTTTTAATAAGTG
4823871 TTTTT
1 TTTTT
4823876 TGAATAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.13, T:0.61
Consensus pattern (13 bp):
TTTTTAATAAGTG
Found at i:4824177 original size:18 final size:18
Alignment explanation
Indices: 4824142--4824183 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
4824132 CAAAATTTAT
* *
4824142 ATTTTAAAAAATTCTAAAA
1 ATTTAAAAAAAATCT-AAA
4824161 ATTTAAAAAAAAT-TAAA
1 ATTTAAAAAAAATCTAAA
4824178 ATTTAA
1 ATTTAA
4824184 TATTTTGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTTAAAAAAAATCTAAA
Found at i:4832247 original size:16 final size:15
Alignment explanation
Indices: 4832211--4832247 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
4832201 TGATCTGGGG
4832211 AAAAATTAAAAGAAA
1 AAAAATTAAAAGAAA
4832226 ACAAAATTAAAAGAAA
1 A-AAAATTAAAAGAAA
4832242 TAAAAA
1 -AAAAA
4832248 ATAGAGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 18 0.90
17 1 0.05
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAAATTAAAAGAAA
Found at i:4833111 original size:27 final size:28
Alignment explanation
Indices: 4833044--4833111 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
4833034 GATAAACATG
4833044 AATTAAATACAAG-TTTAAATATAAATAA
1 AATTAAAT-CAAGTTTTAAATATAAATAA
*
4833072 TATCCT-AAT-AAGTTTTAAA-ATAAATAA
1 AAT--TAAATCAAGTTTTAAATATAAATAA
4833099 AATTAAATCAAGT
1 AATTAAATCAAGT
4833112 CTTTTTGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
25 1 0.03
26 3 0.09
27 17 0.52
28 8 0.24
29 3 0.09
30 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (28 bp):
AATTAAATCAAGTTTTAAATATAAATAA
Found at i:4851173 original size:20 final size:19
Alignment explanation
Indices: 4851149--4851213 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 19
4851139 TTATTTTGAC
4851149 TTTTTAAAATTTAAAATTAT
1 TTTTTAAAATTTAAAATT-T
*
4851169 ATTTTTAAAATGTTATAA-TT
1 -TTTTTAAAAT-TTAAAATTT
4851189 TTTTTAAACATTTTAAAATTCT
1 TTTTTAAA-A-TTTAAAATT-T
4851211 TTT
1 TTT
4851214 ACACATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 8 0.22
20 7 0.19
21 13 0.35
22 9 0.24
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTAAAATTTAAAATTT
Found at i:4851214 original size:20 final size:20
Alignment explanation
Indices: 4851171--4851220 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4851161 AAAATTATAT
* * *
4851171 TTTTAAA-ATGTTATAATTT
1 TTTTAAACATTTTAAAATTC
4851190 TTTTAAACATTTTAAAATTC
1 TTTTAAACATTTTAAAATTC
*
4851210 TTTTACACATT
1 TTTTAAACATT
4851221 ATATATGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAAACATTTTAAAATTC
Found at i:4855431 original size:17 final size:18
Alignment explanation
Indices: 4855406--4855450 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
4855396 AATTTTTTAA
*
4855406 AATTATAAAAAAATATA-
1 AATTTTAAAAAAATATAC
* *
4855423 ATTTTTAAAAAATTATAC
1 AATTTTAAAAAAATATAC
4855441 AATTTTAAAA
1 AATTTTAAAA
4855451 TATTATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTTAAAAAAATATAC
Found at i:4855444 original size:19 final size:20
Alignment explanation
Indices: 4855422--4855485 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 20
4855412 AAAAAAATAT
*
4855422 AATTTTTAAAAAATTA-TAC
1 AATTTTTAAAAAATTATTAA
*
4855441 AA-TTTTAAAATATTATTAA
1 AATTTTTAAAAAATTATTAA
* *
4855460 AATTTATAAAAATTTTAATTAA
1 AATTTTTAAAAA-ATT-ATTAA
4855482 AATT
1 AATT
4855486 CAAAAAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 12 0.33
19 6 0.17
20 7 0.19
21 2 0.06
22 9 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTTAAAAAATTATTAA
Found at i:4855446 original size:18 final size:17
Alignment explanation
Indices: 4855405--4855473 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
4855395 AAATTTTTTA
* *
4855405 AAATTATAAAAAAATAT
1 AAATTTTAAAAAATTAT
*
4855422 AATTTTTAAAAAATTAT
1 AAATTTTAAAAAATTAT
*
4855439 ACAATTTTAAAATATTATT
1 A-AATTTTAAAAAATTA-T
*
4855458 AAAATTTATAAAAATT
1 AAATTTTA-AAAAATT
4855474 TTAATTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
17 15 0.36
18 19 0.45
19 8 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTTTAAAAAATTAT
Found at i:4855477 original size:18 final size:18
Alignment explanation
Indices: 4855400--4855477 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
4855390 GATTTAAATT
4855400 TTTTAAAA-TTATAAAAA
1 TTTTAAAATTTATAAAAA
** * *
4855417 -AATATAATTTTTAAAAAA
1 TTTTAAAATTTAT-AAAAA
* *
4855435 TTATACAATTT-TAAAATA
1 TTTTAAAATTTATAAAA-A
4855453 TTATTAAAATTTATAAAAA
1 TT-TTAAAATTTATAAAAA
4855472 TTTTAA
1 TTTTAA
4855478 TTAAAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
16 4 0.09
17 7 0.15
18 13 0.28
19 18 0.38
20 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAATTTATAAAAA
Found at i:4855494 original size:21 final size:21
Alignment explanation
Indices: 4855447--4855494 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4855437 ATACAATTTT
* *
4855447 AAAATATTATTAAAATTTATA
1 AAAATTTTATTAAAATTCATA
4855468 AAAATTTTAATTAAAATTCA-A
1 AAAATTTT-ATTAAAATTCATA
4855489 AAAATT
1 AAAATT
4855495 CAAAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTTTATTAAAATTCATA
Found at i:4856993 original size:29 final size:28
Alignment explanation
Indices: 4856962--4857343 Score: 122
Period size: 29 Copynumber: 13.1 Consensus size: 28
4856952 TCGAGGGGCA
*
4856962 AAAATGTAATTTTGGGAAATTTGGGGTT
1 AAAATGTAATTTTGGGAAATTCGGGGTT
** * * * *
4856990 AAAAATGGGATTTT-AGAAGGTTTGGGGGT
1 -AAAATGTAATTTTGGGAA-ATTCGGGGTT
* *
4857019 AAAATGGTAATTTTTAGTGAAATT-GAGGTT
1 AAAAT-GTAA-TTTT-GGGAAATTCGGGGTT
*** * * *
4857049 AAAAATGGGGTTTT-GAAAAGTTTGGGGGT
1 -AAAATGTAATTTTGGGAAA-TTCGGGGTT
*
4857078 AAAATAGTAATTTTGGTGAAA-TCGGGGTCA
1 AAAAT-GTAATTTTGG-GAAATTCGGGGT-T
* *
4857108 AAAATGGAATTTT-GGAAGATTCAAGGG-T
1 AAAATGTAATTTTGGGAA-ATTC-GGGGTT
* * *
4857136 AAAACGATAATTTTGGTGAAA-TCGAGGTCA
1 AAAATG-TAATTTTGG-GAAATTCGGGGT-T
* * *
4857166 AAAATG-GATTTTTGGAAGATTCGGGGGT
1 AAAATGTAATTTTGGGAA-ATTCGGGGTT
* *
4857194 AAAATGGTAATTTTGGTGAAA-TCGAGGTCA
1 AAAAT-GTAATTTTGG-GAAATTCGGGGT-T
* * * *
4857224 AAAATGGAATTTT-GAAAGATTTGGGGGT
1 AAAATGTAATTTTGGGAA-ATTCGGGGTT
*
4857252 AAAATGGTAATTTTGGGCAAAATT-GAGGTT
1 AAAAT-GTAATTTTGGG--AAATTCGGGGTT
* * *
4857282 AAAATGGAA-TTTAGGAAAGTTCGGGGGT
1 AAAATGTAATTTTGGGAAA-TTCGGGGTT
* *
4857310 AAAATGGTAATTTTTGGTAAAATCGGGGTT
1 AAAAT-GTAA-TTTTGGGAAATTCGGGGTT
4857340 AAAA
1 AAAA
4857344 ATGGAAATTT
Statistics
Matches: 253, Mismatches: 63, Indels: 73
0.65 0.16 0.19
Matches are distributed among these distances:
26 3 0.01
27 13 0.05
28 57 0.23
29 91 0.36
30 58 0.23
31 26 0.10
32 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGTAATTTTGGGAAATTCGGGGTT
Found at i:4857136 original size:58 final size:58
Alignment explanation
Indices: 4856962--4857362 Score: 411
Period size: 58 Copynumber: 6.9 Consensus size: 58
4856952 TCGAGGGGCA
* * * * * * *
4856962 AAAAT-GTAATTTTGG-GAAATTTGGGGTTAAAAATGGGATTTTAGAAGGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAA-TCGAGGTCAAAAATGGAATTTTGGAAGATTCGGGGGT
* * * ** * *
4857019 AAAATGGTAATTTTTAGTGAAATTGAGGTTAAAAATGGGGTTTT-GAAAAGTTTGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGA-TTCGGGGGT
* * **
4857078 AAAATAGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGATTCAAGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGATTCGGGGGT
* * *
4857136 AAAACGATAATTTTGGTGAAATCGAGGTCAAAAATGGATTTTTGGAAGATTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGATTCGGGGGT
* *
4857194 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGAAAGATTTGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGATTCGGGGGT
* * *
4857252 AAAATGGTAATTTTGG-GCAAAATTGAGGT-TAAAATGGAATTTAGGAA-AGTTCGGGGGT
1 AAAATGGTAATTTTGGTG--AAATCGAGGTCAAAAATGGAATTTTGGAAGA-TTCGGGGGT
* * * * *
4857310 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAAATTT-GAAGTTTCG
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGATTCG
4857363 AGGTCAAAAT
Statistics
Matches: 292, Mismatches: 40, Indels: 23
0.82 0.11 0.06
Matches are distributed among these distances:
57 7 0.02
58 208 0.71
59 73 0.25
60 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAGATTCGGGGGT
Found at i:4857206 original size:116 final size:115
Alignment explanation
Indices: 4856962--4857354 Score: 461
Period size: 116 Copynumber: 3.4 Consensus size: 115
4856952 TCGAGGGGCA
* * * * *
4856962 AAAAT-GTAATTTTGG-GAAATTTGGGGTTAAAAATGGGATTTTAGAAGGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTGGTGAAA-TCGGGGTCAAAAATGGAATTTTGGAAGATTTGGGGGTAAAATG
* ** * *
4857025 GTAATTTTTAGTGAAATTGAGGTTAAAAATGGGGTTTTGAAAAGTTTGGGGGT
65 GTAA-TTTTGGTGAAATTGAGG-TAAAAATGGAATTTTGGAAAGTTCGGGGGT
* *** * *
4857078 AAAATAGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGATTCAAGGGTAAAACGA
1 AAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGATTTGGGGGTAAAATGG
* *
4857143 TAATTTTGGTGAAATCGAGGTCAAAAATGGATTTTTGG-AAGATTCGGGGGT
66 TAATTTTGGTGAAATTGAGGT-AAAAATGGAATTTTGGAAAG-TTCGGGGGT
* *
4857194 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGAAAGATTTGGGGGTAAAATGG
1 AAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGATTTGGGGGTAAAATGG
* *
4857259 TAATTTTGG-GCAAAATTGAGGTTAAAATGGAATTTAGGAAAGTTCGGGGGT
66 TAATTTTGGTG--AAATTGAGGTAAAAATGGAATTTTGGAAAGTTCGGGGGT
* * *
4857310 AAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAAATTTG
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTCAAAAATGGAATTTTG
4857355 AAGTTTCGAG
Statistics
Matches: 237, Mismatches: 32, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
115 5 0.02
116 139 0.59
117 89 0.38
118 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.32
Consensus pattern (115 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGATTTGGGGGTAAAATGG
TAATTTTGGTGAAATTGAGGTAAAAATGGAATTTTGGAAAGTTCGGGGGT
Found at i:4857354 original size:29 final size:27
Alignment explanation
Indices: 4857072--4857354 Score: 129
Period size: 29 Copynumber: 9.7 Consensus size: 27
4857062 TGAAAAGTTT
* * *
4857072 GGGGGTAAAATAGTAATTTTGGTGAAATC
1 GGGGTTAAAAT-GGAATTTTGG-AAAATC
* *
4857101 GGGGTCAAAAATGGAATTTTGGAAGATTC
1 GGGGT-TAAAATGGAATTTTGGAA-AATC
* * * *
4857130 AAGGG-TAAAACGATAATTTTGGTGAAATC
1 -GGGGTTAAAATG-GAATTTTGG-AAAATC
* * * *
4857159 GAGGTCAAAAATGGATTTTTGGAAGATTC
1 GGGGT-TAAAATGGAATTTTGGAA-AATC
* *
4857188 GGGGGTAAAATGGTAATTTTGGTGAAATC
1 GGGGTTAAAATGG-AATTTTGG-AAAATC
* * *
4857217 GAGGTCAAAAATGGAATTTT-GAAAGATTT
1 GGGGT-TAAAATGGAATTTTGGAAA-A-TC
* *
4857246 GGGGGTAAAATGGTAATTTTGGGCAAAATT
1 GGGGTTAAAATGG-AATTTT-GG-AAAATC
* * *
4857276 GAGGTTAAAATGGAATTTAGGAAAGTTC
1 GGGGTTAAAATGGAATTTTGGAAA-ATC
*
4857304 GGGGGTAAAATGGTAATTTTTGGTAAAATC
1 GGGGTTAAAATGG-AA-TTTTGG-AAAATC
*
4857334 GGGGTTAAAAATGGAAATTTG
1 GGGGTT-AAAATGGAATTTTG
4857355 AAGTTTCGAG
Statistics
Matches: 188, Mismatches: 44, Indels: 44
0.68 0.16 0.16
Matches are distributed among these distances:
27 5 0.03
28 39 0.21
29 80 0.43
30 49 0.26
31 12 0.06
32 3 0.02
ACGTcount: A:0.36, C:0.04, G:0.30, T:0.30
Consensus pattern (27 bp):
GGGGTTAAAATGGAATTTTGGAAAATC
Found at i:4859035 original size:38 final size:38
Alignment explanation
Indices: 4858920--4859038 Score: 102
Period size: 38 Copynumber: 3.1 Consensus size: 38
4858910 GATTGGAGTA
* * *
4858920 AGATTGATTGATGGTGATCTGCCCCAACCTGGGGTAA-
1 AGATTGATTAATGATGATCTGCCCCAACTTGGGGTAAG
* ** *
4858957 AG---GATCAAATGATTGTAATCTGCCCCTGGCTCGGGGTAAG
1 AGATTGAT-TAATGA-TG--ATCTGCCCC-AACTTGGGGTAAG
4858997 AGATTGATTAATGATGATCTGCCCCAACTTGGGGTAAG
1 AGATTGATTAATGATGATCTGCCCCAACTTGGGGTAAG
4859035 AGAT
1 AGAT
4859039 CAAATGGCTC
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
34 3 0.05
35 3 0.05
36 2 0.03
37 2 0.03
38 23 0.37
39 17 0.27
40 2 0.03
41 2 0.03
42 5 0.08
43 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (38 bp):
AGATTGATTAATGATGATCTGCCCCAACTTGGGGTAAG
Found at i:4859054 original size:77 final size:77
Alignment explanation
Indices: 4858920--4859076 Score: 199
Period size: 77 Copynumber: 2.0 Consensus size: 77
4858910 GATTGGAGTA
* * * ** *
4858920 AGATTGATTGATGGTGATCTGCCCCAACCTGGGGTAAAGGATCAAATGATTGTAATCTGCCCCTG
1 AGATTGATTAATGATGATCTGCCCCAACCTGGGGTAAAGGATCAAATGACTCCAATCTGCCCCTC
*
4858985 GCTCGGGGTAAG
66 GCTCGGGGCAAG
* * *
4858997 AGATTGATTAATGATGATCTGCCCCAACTTGGGGT-AAGAGATCAAATGGCTCCAATCTGTCCCT
1 AGATTGATTAATGATGATCTGCCCCAACCTGGGGTAAAG-GATCAAATGACTCCAATCTGCCCCT
*
4859061 CGTTCGGGGCAAG
65 CGCTCGGGGCAAG
4859074 AGA
1 AGA
4859077 CCAGAATCTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 3 0.04
77 65 0.96
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (77 bp):
AGATTGATTAATGATGATCTGCCCCAACCTGGGGTAAAGGATCAAATGACTCCAATCTGCCCCTC
GCTCGGGGCAAG
Found at i:4865939 original size:29 final size:29
Alignment explanation
Indices: 4865907--4866055 Score: 73
Period size: 29 Copynumber: 5.1 Consensus size: 29
4865897 AAAAATAGGG
4865907 TTTTGGAAAGTTTGAGGGTAAAATAGTAA
1 TTTTGGAAAGTTTGAGGGTAAAATAGTAA
* *
4865936 TTTTGGTGAAA--TCG-GGGTCAAAA-ATGGAA
1 TTTT-G-GAAAGTTTGAGGGT-AAAATA-GTAA
* * *
4865965 TTTT-GAAAGATTCGGGGGTAAAATTGTAA
1 TTTTGGAAAG-TTTGAGGGTAAAATAGTAA
* *
4865994 TTTTGGGCAAA-ATT-AGGGTTAAAAT-GGAA
1 TTTT-GG-AAAGTTTGAGGG-TAAAATAGTAA
* *
4866023 TTTAGGAAAGTTT-AGGGGTAAAATGGTAA
1 TTTTGGAAAGTTTGA-GGGTAAAATAGTAA
4866052 TTTT
1 TTTT
4866056 TGGTGAAATC
Statistics
Matches: 92, Mismatches: 12, Indels: 32
0.68 0.09 0.24
Matches are distributed among these distances:
26 4 0.04
27 3 0.03
28 16 0.17
29 49 0.53
30 12 0.13
31 5 0.05
32 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAGTTTGAGGGTAAAATAGTAA
Found at i:4865986 original size:117 final size:117
Alignment explanation
Indices: 4865839--4866088 Score: 321
Period size: 117 Copynumber: 2.1 Consensus size: 117
4865829 ATTTGGAGTT
* * * * **
4865839 AAAAATGGGATTTAG-AAGGTTCGGGGGTAAAATGGTAATTTTTAGTGAAATT-GAGGTTAAAAA
1 AAAAATGGAATTTTGAAAGATTCGGGGGTAAAATGGTAATTTTGAGCAAAATTAG-GGTT-AAAA
* *
4865902 TAGG-GTTTTGGAAAGTTT-GAGGGTAAAATAGTAA-TTTTGGTGAAATCGGGGTC
64 T-GGAATTTAGGAAAGTTTAG-GGGTAAAATAGTAATTTTTGGTGAAATCGGGGTC
* *
4865955 AAAAATGGAATTTTGAAAGATTCGGGGGTAAAATTGTAATTTTGGGCAAAATTAGGGTTAAAATG
1 AAAAATGGAATTTTGAAAGATTCGGGGGTAAAATGGTAATTTTGAGCAAAATTAGGGTTAAAATG
* *
4866020 GAATTTAGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT
66 GAATTTAGGAAAGTTTAGGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTC
4866072 AAAAATGGAATTTTGAA
1 AAAAATGGAATTTTGAA
4866089 GTTTTGGGGT
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
115 2 0.02
116 43 0.37
117 71 0.61
118 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.32
Consensus pattern (117 bp):
AAAAATGGAATTTTGAAAGATTCGGGGGTAAAATGGTAATTTTGAGCAAAATTAGGGTTAAAATG
GAATTTAGGAAAGTTTAGGGGTAAAATAGTAATTTTTGGTGAAATCGGGGTC
Found at i:4866086 original size:29 final size:28
Alignment explanation
Indices: 4865934--4866086 Score: 91
Period size: 29 Copynumber: 5.2 Consensus size: 28
4865924 GTAAAATAGT
*
4865934 AATTTTGGTGAAATCGGGGTCAAAAATGG
1 AATTTTGG-GAAATCGGGGTTAAAAATGG
* * * *
4865963 AATTTT-GAAAGATTCGGGGGTAAAATTGT
1 AATTTTGGGAA-A-TCGGGGTTAAAAATGG
**
4865992 AATTTTGGGCAAAATTAGGGTT-AAAATGG
1 AATTTTGGG--AAATCGGGGTTAAAAATGG
* *
4866021 AA-TTTAGGAAAGTTTAGGGG-T-AAAATGG
1 AATTTTGGGAAA---TCGGGGTTAAAAATGG
4866049 TAATTTTTGGTGAAATCGGGGTTAAAAATGG
1 -AA-TTTTGG-GAAATCGGGGTTAAAAATGG
4866080 AATTTTG
1 AATTTTG
4866087 AAGTTTTGGG
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
26 3 0.03
27 2 0.02
28 15 0.16
29 47 0.50
30 9 0.10
31 12 0.13
32 6 0.06
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (28 bp):
AATTTTGGGAAATCGGGGTTAAAAATGG
Found at i:4866104 original size:58 final size:58
Alignment explanation
Indices: 4865836--4866115 Score: 282
Period size: 58 Copynumber: 4.8 Consensus size: 58
4865826 AAAATTTGGA
* * * * * * *
4865836 GTTAAAAATGGGATTTAGAAGGTTCGGGGGTAAAATGGTAATTTTTAGTGAAATTGAG
1 GTTAAAAATGGAATTTTGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
* * *
4865894 GTTAAAAATAGG-GTTTTGGAAAGTTTGAGGGTAAAATAGTAA-TTTTGGTGAAATCGGG
1 GTTAAAAAT-GGAATTTT-GAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
* * * * ** **
4865952 GTCAAAAATGGAATTTTGAAAGATTCGGGGGTAAAATTGTAATTTTGGGCAAAATTAGG
1 GTTAAAAATGGAATTTTGAAAG-TTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
* *
4866011 GTT-AAAATGGAATTTAGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
1 GTTAAAAATGGAATTT-TGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
* *
4866069 GTTAAAAATGGAATTTTG-AAGTTTTGGGGTCAAAAT-ATAATTTTTGG
1 GTTAAAAATGGAATTTTGAAAGTTTGGGGGT-AAAATGGTAATTTTTGG
4866116 ACAATTCAGG
Statistics
Matches: 182, Mismatches: 32, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
57 28 0.15
58 102 0.56
59 52 0.29
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (58 bp):
GTTAAAAATGGAATTTTGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGG
Found at i:4867984 original size:17 final size:17
Alignment explanation
Indices: 4867943--4867982 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
4867933 TTCTAAATGT
4867943 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
4867960 GTTTAAATTTAAAA-AA
1 ATTTAAATTTAAAACAA
4867976 ATTTAAA
1 ATTTAAA
4867983 ATCAATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:4867998 original size:27 final size:27
Alignment explanation
Indices: 4867947--4867998 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4867937 AAATGTATTT
* *
4867947 AAATTTAAAACAAGTTTAAATTTAAAA
1 AAATTTAAAACAAGTTCAAACTTAAAA
4867974 AAATTTAAAATCAA-TTCAAACTTAA
1 AAATTTAAAA-CAAGTTCAAACTTAA
4867999 TTTAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATTTAAAACAAGTTCAAACTTAAAA
Found at i:4869103 original size:16 final size:16
Alignment explanation
Indices: 4869082--4869114 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4869072 TATAAAAAAT
4869082 AAAAAATATTTTTTTA
1 AAAAAATATTTTTTTA
4869098 AAAAAATATTTTTTTA
1 AAAAAATATTTTTTTA
4869114 A
1 A
4869115 TTTTATTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAAAAATATTTTTTTA
Found at i:4869924 original size:18 final size:16
Alignment explanation
Indices: 4869885--4869924 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4869875 AATTTTAATC
4869885 ATTTTAGATCACTTTT
1 ATTTTAGATCACTTTT
*
4869901 AATTTAGATCACCATTTT
1 ATTTTAGATCA-C-TTTT
4869919 ATTTTA
1 ATTTTA
4869925 ATAAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTAGATCACTTTT
Found at i:4871429 original size:57 final size:58
Alignment explanation
Indices: 4871335--4871724 Score: 238
Period size: 57 Copynumber: 6.8 Consensus size: 58
4871325 TAGGATAACC
* * *
4871335 TTATGACTC-ATTAAGATATCCAA-ATAGACAGCTTGAATAACCTTAATTTGGATAG-TA
1 TTATGACTCAATTAA-ACAT-CAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* * * * *
4871392 TTTTGACTCAGTTAAACATCAATATAAACAGTTTGAATAACCTTATTTTGGACTGCTA
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* * *** * * * * *
4871450 -TATGACTCAATTTATCATCAATACGGACAGTTTGATTAACCTTGATTCGGACAAC-A
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* * * * * * **
4871506 TTTTAAGTCACTTAAGCATTAATATAAACAGCTTGAATAACCTTCTTTTGGACAGCT-
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* *** * * * * * *
4871563 TTATGACTCAATTTAACATCAATACGGACAACTTGATTAATCTTGATTAGGACAAC-A
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* * * * * * * **
4871620 TTTTAACTCACTTAAGCATTAATATAAACAGCTTAAATAACCTTATTTTTAACAGCT-
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
* * * *** *
4871677 TTATTACTGAATTTAACATCAATACGGACAGCTTGATTAACCTTAATT
1 TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATT
4871725 CAGACAACAT
Statistics
Matches: 240, Mismatches: 86, Indels: 14
0.71 0.25 0.04
Matches are distributed among these distances:
56 4 0.02
57 230 0.96
58 6 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (58 bp):
TTATGACTCAATTAAACATCAATATAAACAGCTTGAATAACCTTAATTTGGACAGCTA
Found at i:4871546 original size:114 final size:114
Alignment explanation
Indices: 4871361--4871739 Score: 515
Period size: 114 Copynumber: 3.3 Consensus size: 114
4871351 TATCCAAATA
* * * * ** * * * * *
4871361 GACAGCTTGAATAACCTTAATTTGGATAGTATTTTGACTCAGTTAAACATCAATATAAACAGTTT
1 GACAGCTTGATTAACCTTGATTCGGACAACATTTTAACTCACTTAAGCATTAATATAAACAGCTT
* * *
4871426 GAATAACCTTATTTTGGACTGCTATATGACTCAATTTATCATCAATACG
66 GAATAACCTTATTTTGGACAGCTTTATGACTCAATTTAACATCAATACG
* *
4871475 GACAGTTTGATTAACCTTGATTCGGACAACATTTTAAGTCACTTAAGCATTAATATAAACAGCTT
1 GACAGCTTGATTAACCTTGATTCGGACAACATTTTAACTCACTTAAGCATTAATATAAACAGCTT
*
4871540 GAATAACCTTCTTTTGGACAGCTTTATGACTCAATTTAACATCAATACG
66 GAATAACCTTATTTTGGACAGCTTTATGACTCAATTTAACATCAATACG
* * *
4871589 GACAACTTGATTAATCTTGATTAGGACAACATTTTAACTCACTTAAGCATTAATATAAACAGCTT
1 GACAGCTTGATTAACCTTGATTCGGACAACATTTTAACTCACTTAAGCATTAATATAAACAGCTT
* ** * *
4871654 AAATAACCTTATTTTTAACAGCTTTATTACTGAATTTAACATCAATACG
66 GAATAACCTTATTTTGGACAGCTTTATGACTCAATTTAACATCAATACG
* *
4871703 GACAGCTTGATTAACCTTAATTCAGACAACATTTTAA
1 GACAGCTTGATTAACCTTGATTCGGACAACATTTTAA
4871740 TCCGAATTTT
Statistics
Matches: 232, Mismatches: 33, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 232 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (114 bp):
GACAGCTTGATTAACCTTGATTCGGACAACATTTTAACTCACTTAAGCATTAATATAAACAGCTT
GAATAACCTTATTTTGGACAGCTTTATGACTCAATTTAACATCAATACG
Found at i:4874198 original size:329 final size:329
Alignment explanation
Indices: 4873446--4874426 Score: 1532
Period size: 329 Copynumber: 3.0 Consensus size: 329
4873436 TCAAAACGAG
* * * *
4873446 AAAATATGGGGACCAATTGTATAATTTAACCTAGAATATTTTGTTTAAAATGATGATTTAATGTG
1 AAAATATGGGGACCAATTGTATAATTTAACCTAAAATTTTTTGTTTGAAATGATGATTTAACGTG
* *
4873511 CCACGTCAGCTTATCGTTACACCGTTAACGACAATTAACGGCTCAGTGGCTAAAATGTTACAATA
66 TCACGTCAGCTTATCATTACACCGTTAACGACAATTAACGGCTCAGTGGCTAAAATGTTACAATA
* *
4873576 CGATAACGTAAGTGACTAAAACGGAACATTTCAAACATAAGTGACTAAAATATAACCCAAGACAA
131 CGATAACGTAAGTGACTAAAACGTAACATTTCAAACATAAGTGACTAAAATATAACCCGAGACAA
* *
4873641 ACAAAAATGACTATTTTGATGGTTTACTCATTA-TTTAATAAATTTGATTTTTTAAATTATTACA
196 ACAAAAGTGACTATTTTGATAGTTTACTCATTATTTTAATAAATTTGATTTTTTAAATTATTACA
* * * ***
4873705 TATTCTGAACCGATGTAAATCTTCATAAGATGTGCTCATCATACTTTTAACAACAAATCATAAAA
261 TATTCTGAACCGATGTAAATATTCATAGGATGTGTTTGCCATACTTTTAACAACAAATCATAAAA
4873770 CAAA
326 CAAA
* * * *
4873774 AAAATATGGGGATCAATTCTATAATTTAACCTAAAAATTTTTGTTTGAAATGATGTTTTAACGTG
1 AAAATATGGGGACCAATTGTATAATTTAACCTAAAATTTTTTGTTTGAAATGATGATTTAACGTG
* * *
4873839 TCACGTCAGCTTATCATTACACCATTAACGACAATTAACAGCTCGGTGGCTAAAATGTTACAATA
66 TCACGTCAGCTTATCATTACACCGTTAACGACAATTAACGGCTCAGTGGCTAAAATGTTACAATA
** *
4873904 CGATAACGTAAGTGACTAAAATATAATATTTCAAACATAAGTGACTAAAATATAACCCGAGACAA
131 CGATAACGTAAGTGACTAAAACGTAACATTTCAAACATAAGTGACTAAAATATAACCCGAGACAA
4873969 ACAAAAGTGACTATTTTGATAGTTTACTCATTATTTTAATAAATTTGATTTTTTAAATTATTACA
196 ACAAAAGTGACTATTTTGATAGTTTACTCATTATTTTAATAAATTTGATTTTTTAAATTATTACA
* **
4874034 TATTTTGAACCGATGTAAATATTCATAGGATGTGTTTGCCATGTTTTTAACAACAAATCATAAAA
261 TATTCTGAACCGATGTAAATATTCATAGGATGTGTTTGCCATACTTTTAACAACAAATCATAAAA
4874099 CAAA
326 CAAA
* * * *
4874103 AAAATATGAGGACCAATTGTATAACTTAACCTAAAATTTTTTATTTGAAATGATAATTTAACGTG
1 AAAATATGGGGACCAATTGTATAATTTAACCTAAAATTTTTTGTTTGAAATGATGATTTAACGTG
* * * * *
4874168 TCATGTCAGCTTATCATTATACCGTTAACGATAATTAATGGCTCAGTGGCTAAAATGTTACAACA
66 TCACGTCAGCTTATCATTACACCGTTAACGACAATTAACGGCTCAGTGGCTAAAATGTTACAATA
* * * *
4874233 TGATAACGTAAGTGACTAAAACGTAACATTTCAAACGTAAGTGACTAAAATATAATCCGAGAAAA
131 CGATAACGTAAGTGACTAAAACGTAACATTTCAAACATAAGTGACTAAAATATAACCCGAGACAA
* * * *
4874298 ATAAAAGTGACTATTTTAATAGTTTACTCATTATTTAAATAAATTCGATTTTTTAAATTATTACA
196 ACAAAAGTGACTATTTTGATAGTTTACTCATTATTTTAATAAATTTGATTTTTTAAATTATTACA
*
4874363 TATTCTAAACCGATGTAAATATTCATAGGATGTGTTTGCCATACTTTTAACAACAAATCATAAA
261 TATTCTGAACCGATGTAAATATTCATAGGATGTGTTTGCCATACTTTTAACAACAAATCATAAA
4874427 TTTGAAAGGT
Statistics
Matches: 592, Mismatches: 60, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
328 208 0.35
329 384 0.65
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (329 bp):
AAAATATGGGGACCAATTGTATAATTTAACCTAAAATTTTTTGTTTGAAATGATGATTTAACGTG
TCACGTCAGCTTATCATTACACCGTTAACGACAATTAACGGCTCAGTGGCTAAAATGTTACAATA
CGATAACGTAAGTGACTAAAACGTAACATTTCAAACATAAGTGACTAAAATATAACCCGAGACAA
ACAAAAGTGACTATTTTGATAGTTTACTCATTATTTTAATAAATTTGATTTTTTAAATTATTACA
TATTCTGAACCGATGTAAATATTCATAGGATGTGTTTGCCATACTTTTAACAACAAATCATAAAA
CAAA
Found at i:4884693 original size:20 final size:19
Alignment explanation
Indices: 4884647--4884694 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
4884637 ATTTATTTTA
*
4884647 TTTATTTTAT-TAAAATTC
1 TTTATTTAATATAAAATTC
4884665 -TTA-TTAATATAAAATTC
1 TTTATTTAATATAAAATTC
4884682 TTTTATTTAATAT
1 -TTTATTTAATAT
4884695 TTTATTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 11 0.44
19 3 0.12
20 7 0.28
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTATTTAATATAAAATTC
Found at i:4891923 original size:129 final size:125
Alignment explanation
Indices: 4891678--4891923 Score: 359
Period size: 129 Copynumber: 1.9 Consensus size: 125
4891668 GGATTGCGTT
*
4891678 CCTAGACGACAAGTAGATAATTAATCGATGAAATCACGCGCGATGTGGATCGAACCACCAAGAGT
1 CCTAGACGACAAGTAGATAATTAATCGATGAAATCACGCGCGATGTGAATCGAACCACCAAGAGT
** *
4891743 ACCCTTTTCAAGAAGACATGGTATCACTTGGGCTAGTTATGCCTTGGTTGGTGGAGCTTA
66 ACCCTTTTCAAGAAGACATGGTATCACTTGAACTAGTTATGCCTTGATTGGTGGAGCTTA
* * *
4891803 CCTAGAGGACAAGTAGATAATTAATCGATGAAATCACGTGTGATGTGAATCGAATCATCAACCAA
1 CCTAGACGACAAGTAGATAATTAATCGATGAAATCACGCGCGATGTGAATCGAA-C--C-ACCAA
* *
4891868 GCA-TAGCCTTTTCAAGGAGACATGGTATCACTTGAACTAGTTATGCCTTGATTGGT
62 G-AGTACCCTTTTCAAGAAGACATGGTATCACTTGAACTAGTTATGCCTTGATTGGT
4891924 AGTTCGATTC
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
125 50 0.47
126 1 0.01
128 1 0.01
129 54 0.50
130 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (125 bp):
CCTAGACGACAAGTAGATAATTAATCGATGAAATCACGCGCGATGTGAATCGAACCACCAAGAGT
ACCCTTTTCAAGAAGACATGGTATCACTTGAACTAGTTATGCCTTGATTGGTGGAGCTTA
Found at i:4893463 original size:16 final size:15
Alignment explanation
Indices: 4893438--4893471 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
4893428 GGTCGACGTC
*
4893438 TATGTATTTTTTTAA
1 TATGTATTTTATTAA
4893453 TATGATATTTTATTAA
1 TATG-TATTTTATTAA
4893469 TAT
1 TAT
4893472 ACGAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TATGTATTTTATTAA
Found at i:4893864 original size:62 final size:62
Alignment explanation
Indices: 4893558--4893919 Score: 352
Period size: 62 Copynumber: 6.0 Consensus size: 62
4893548 AATCAAACCT
* **
4893558 TTTTTGTCAGAT-AAAAAATTT--AA-TTTTTTGGTGTTGGTCATGCAATGGCCGACACCCTA
1 TTTTTG-CAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCC
* * * * * *
4893617 TTTTTGCAGATAAAAAAATTTCAACTTTTTTTTGTGTTGGCCATATC-ATGGTCGACATCTCC
1 TTTTTGCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCAT-GCAATGGTCGACACCCCC
* * * *
4893679 TTTTTACAAATAAAAAAATTTCAAAGTTTTTTGGTGTTAGTCATGCAATGGTCGACACCCCC
1 TTTTTGCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCC
* * *
4893741 TTTTTGCAGATAAAAAAATTTCAAAATTTTTTGATGTTGGCCATGCAATGGTCGACA-CCCC
1 TTTTTGCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCC
* ** *
4893802 TTTTTTCAGATAAAAAAATTTCAAATTTTTTTTATATTGGTCATGTC-ATGG-CTGACACCCCC
1 TTTTTGCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATG-CAATGGTC-GACACCCCC
*** * * * *
4893864 TTTTTATTTGGT-AAAAAA-TT-AAA-TTTTTTGGTGTTGGCCATGTAATGGCCGACACC
1 TTTTT-GCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGTCGACACC
4893920 AACTTCCCCT
Statistics
Matches: 253, Mismatches: 38, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
58 5 0.02
59 40 0.16
60 5 0.02
61 56 0.22
62 143 0.57
63 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.39
Consensus pattern (62 bp):
TTTTTGCAGATAAAAAAATTTCAAATTTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCC
Found at i:4894769 original size:30 final size:29
Alignment explanation
Indices: 4894723--4894828 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 29
4894713 TAAATTTAAA
* *
4894723 AAAATAAAAATAAAAATATACAAGAAATTAG
1 AAAAT-AAAATTAAAATA-AAAAGAAATTAG
* *
4894754 AAAATAAAATTAAAATACATAGGAAATTAG
1 AAAATAAAATTAAAATA-AAAAGAAATTAG
* *
4894784 AAATTAAATTTAAAATAAAAACGAAATTA-
1 AAAATAAAATTAAAATAAAAA-GAAATTAG
*
4894813 AAAATTAAATTTAAAA
1 AAAA-TAAAATTAAAA
4894829 AGTAAACGGA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
29 5 0.08
30 54 0.84
31 5 0.08
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (29 bp):
AAAATAAAATTAAAATAAAAAGAAATTAG
Found at i:4894836 original size:30 final size:30
Alignment explanation
Indices: 4894746--4894828 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
4894736 AAATATACAA
* * * *
4894746 GAAATTAGAAAA-TAAAATTAAAATACATAG
1 GAAATTA-AAAATTAAATTTAAAATAAAAAC
*
4894776 GAAATTAGAAATTAAATTTAAAATAAAAAC
1 GAAATTAAAAATTAAATTTAAAATAAAAAC
4894806 GAAATTAAAAATTAAATTTAAAA
1 GAAATTAAAAATTAAATTTAAAA
4894829 AGTAAACGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 3 0.07
30 43 0.93
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (30 bp):
GAAATTAAAAATTAAATTTAAAATAAAAAC
Found at i:4896637 original size:84 final size:84
Alignment explanation
Indices: 4896481--4897291 Score: 1159
Period size: 84 Copynumber: 9.6 Consensus size: 84
4896471 TAAATTTAAA
* *
4896481 ATTTGATAAAAATTATAATATAATAATAA-TTTTTATTTAAATATTTAAAATTAGTAAATAATGC
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* * *
4896545 ATTATCAAATCAATATATT
66 ATTGTCAAATCAACACATT
* * *
4896564 ATTTGACAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAAAAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
4896629 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
4896648 ATTTGATAAAAATTGTAATAAAATAATTAA-TTTTTATTTAAATATTTAAAATTAGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAA-TAATTTTTTATTTAAATATTTAAAATTAGTAAATAATG
*
4896712 TATTATCAAATCAACACATT
65 TATTGTCAAATCAACACATT
*
4896732 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTTAAATTTAGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAATATTTAAAATTAGTAAATAATG
*
4896797 TATTATCAAATCAACACATT
65 TATTGTCAAATCAACACATT
* * *
4896817 ATTTGATAAAAATTATAATATAATAATAATATTTTTTATTTAAATA-TGAAAATTTGATAAATAA
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATATTTAAAATTAG-TAAATAA
4896881 TGTATTGTCAAATCAACACATT
63 TGTATTGTCAAATCAACACATT
*
4896903 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* * *
4896968 ATTCTGAAATCAATACATT
66 ATTGTCAAATCAACACATT
* * *
4896987 ATTTGATAAAAATTGTAATA-AATAATAATTTTTTATTCAAATA-TGAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
*
4897050 TATTGTTAAATCAACACATT
65 TATTGTCAAATCAACACATT
* *
4897070 ATTTGATAAAAATTATAATATAATAATAA-TTTTTATTTAAATATTTAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
* *
4897134 ATTCTCAAATTAACACATT
66 ATTGTCAAATCAACACATT
* * * *
4897153 ATTTGATAAAAATTGTAATATAATAATAATTTGTAATTTAAATA-TAAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATG
* *
4897217 TATTGTCAAATGAACACAAT
65 TATTGTCAAATCAACACATT
* * *
4897237 ATTTGATATAAATTGCAATATAATAATAATCATTTTTATTTAAATAATTTTAAAT
1 ATTTGATAAAAATTGTAATATAATAATAAT--TTTTTATTTAAAT-ATTTAAAAT
4897292 GTAATTTAAA
Statistics
Matches: 654, Mismatches: 57, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
82 7 0.01
83 171 0.26
84 291 0.44
85 97 0.15
86 81 0.12
87 2 0.00
88 5 0.01
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGT
ATTGTCAAATCAACACATT
Found at i:4897080 original size:167 final size:168
Alignment explanation
Indices: 4896481--4897291 Score: 1211
Period size: 167 Copynumber: 4.8 Consensus size: 168
4896471 TAAATTTAAA
* * *
4896481 ATTTGATAAAAATTATAATATAATAATAA-TTTTTATTTAAATATTTAAAATTAG-TAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATA-TGAAAATTTGATAAATAATG
* * * * *
4896544 CATTATCAAATCAATATATTATTTGACAAAAATTGTAATATAATAATAATTTTTTATTTAAATAT
65 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAT
* * * *
4896609 TTAAAATTAGTAAAAAATATATTGTCAAATCAACACATT
130 TTAAATTTAGTAAATAATGTATTCTCAAATCAACACATT
* * *
4896648 ATTTGATAAAAATTGTAATAAAATAATTAA-TTTTTATTTAAATATTTAAAATTAG-TAAATAAT
1 ATTTGATAAAAATTGTAATATAATAA-TAATTTTTTATTTAAATA-TGAAAATTTGATAAATAAT
*
4896711 GTATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAAT
64 GTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAAT
*
4896776 ATTTAAATTTAGTAAATAATGTATTATCAAATCAACACATT
128 ATTTAAATTTAGTAAATAATGTATTCTCAAATCAACACATT
*
4896817 ATTTGATAAAAATTATAATATAATAATAATATTTTTTATTTAAATATGAAAATTTGATAAATAAT
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATATGAAAATTTGATAAATAAT
4896882 GTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATA
64 GTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATA
* *
4896947 TTTAAATTTAGTAAATAATGTATTCTGAAATCAATACATT
129 TTTAAATTTAGTAAATAATGTATTCTCAAATCAACACATT
*
4896987 ATTTGATAAAAATTGTAATA-AATAATAATTTTTTATTCAAATATGAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGT
* *
4897051 ATTGTTAAATCAACACATTATTTGATAAAAATTATAATATAATAATAA-TTTTTATTTAAATATT
66 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
*
4897115 TAAATTTAGTAAATAATGTATTCTCAAATTAACACATT
131 TAAATTTAGTAAATAATGTATTCTCAAATCAACACATT
* * *
4897153 ATTTGATAAAAATTGTAATATAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGT
* * * *
4897218 ATTGTCAAATGAACACAATATTTGATATAAATTGCAATATAATAATAATCATTTTTATTTAAATA
66 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAAT--TTTTTATTTAAAT-
4897283 ATTTTAAAT
128 A-TTTAAAT
4897292 GTAATTTAAA
Statistics
Matches: 597, Mismatches: 35, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
166 71 0.12
167 188 0.31
168 84 0.14
169 82 0.14
170 93 0.16
171 72 0.12
172 7 0.01
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (168 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGT
ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
TAAATTTAGTAAATAATGTATTCTCAAATCAACACATT
Found at i:4897431 original size:16 final size:16
Alignment explanation
Indices: 4897395--4897429 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4897385 ATCAATTTTC
*
4897395 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
4897411 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
4897428 AA
1 AA
4897430 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:4897442 original size:28 final size:27
Alignment explanation
Indices: 4897388--4897450 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
4897378 CATGTTCATC
**
4897388 AATTTTCAAATTAATTTCAACTTAAATT
1 AATTTTCAAATTAATTTCAACACAAA-T
**
4897416 AATTTTCAAATTAATTTTTACACAAAT
1 AATTTTCAAATTAATTTCAACACAAAT
*
4897443 ATTTTTCA
1 AATTTTCA
4897451 TGTATACTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTTCAAATTAATTTCAACACAAAT
Found at i:4901317 original size:62 final size:61
Alignment explanation
Indices: 4901110--4901564 Score: 398
Period size: 62 Copynumber: 7.5 Consensus size: 61
4901100 GGTGTCGTGG
* * * ** *
4901110 CGGCCATTACATAGCCAACACCAAAAAAAATTT--AA-TTTTTTA-CCAAATAAAAAAGGATGT
1 CGGCCATTGCATGGCCAACACC-AAAAAATTTTGAAATTTTTTTATCTGAA-AAAAGAGG-TGT
* * * *
4901170 CGGCCATGGCATGGCCAACA-CAAAAAAATTTG-AA-TTTTTTATCTGACAAAAAGGGGGTAT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAA-GAGGTGT
* * * * * * *
4901230 CGACCATGGAATGACTAACAACAAAAAAGTTTGAAATTTTTTTATCTGGAAAAAAGAGGTGT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCT-GAAAAAAGAGGTGT
** **
4901292 CGGCCATTGCATAACCAATGCCAAAAAATTTTGAAATTTTTTTATCT-ACAAAAAGATGGTGT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGA-GGTGT
* ** * *
4901354 CGGCCATGGCATGGCCAACATAAAAAAATTTTAAAATTTTTTTATCTGAAAAAAGGGGATGT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGAGG-TGT
* *
4901416 CGGCCATTGCATGGCCAACACTAAAAAATTTTGAAA-TTTTTTATCTGAAAAAAGGGAGTGT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGAG-GTGT
* * * * *
4901477 CGACCATTGCATGGCTAACACCCAAAAA-TTT--AA-TTTTTTATCAGATAAATAG-GAGTGT
1 CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGA-AAAAAGAG-GTGT
*
4901535 CGGCCATTGCATGGCTAACACCAAAAAATT
1 CGGCCATTGCATGGCCAACACCAAAAAATT
4901565 AAATTTTTTA
Statistics
Matches: 335, Mismatches: 45, Indels: 31
0.82 0.11 0.08
Matches are distributed among these distances:
58 55 0.16
59 16 0.05
60 45 0.13
61 70 0.21
62 131 0.39
63 16 0.05
64 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (61 bp):
CGGCCATTGCATGGCCAACACCAAAAAATTTTGAAATTTTTTTATCTGAAAAAAGAGGTGT
Found at i:4901391 original size:124 final size:123
Alignment explanation
Indices: 4901158--4901597 Score: 451
Period size: 124 Copynumber: 3.6 Consensus size: 123
4901148 TTTACCAAAT
* ** *
4901158 AAAAA-AGGATGTCGGCCATGGCATGGCCAACA-CAAAAAAATTTG-AATTTTTTATCTGACAAA
1 AAAAAGAGGATGTCGGCCATTGCATAACCAACACCAAAAAATTTTGAAATTTTTTATCTGACAAA
* * * *
4901220 AAGGGGGTATCGACCATGGAATGACTAACAACAAAAAAGTTTGAAATTTTTTTATCTGGA
66 AA-GGGGTGTCGACCATGGCATGGCTAACAACAAAAAAGTTTAAAATTTTTTTATCT-GA
**
4901280 AAAAAGAGG-TGTCGGCCATTGCATAACCAATGCCAAAAAATTTTGAAATTTTTTTATCT-ACAA
1 AAAAAGAGGATGTCGGCCATTGCATAACCAACACCAAAAAATTTTGAAA-TTTTTTATCTGACAA
* * * *
4901343 AAAGATGGTGTCGGCCATGGCATGGCCAACATA-AAAAAATTTTAAAATTTTTTTATCTGA
65 AAAG-GGGTGTCGACCATGGCATGGCTAACA-ACAAAAAAGTTTAAAATTTTTTTATCTGA
* ** *
4901403 AAAAAGGGGATGTCGGCCATTGCATGGCCAACACTAAAAAATTTTGAAATTTTTTATCTGA-AAA
1 AAAAAGAGGATGTCGGCCATTGCATAACCAACACCAAAAAATTTTGAAATTTTTTATCTGACAAA
* * * *
4901467 AAGGGAGTGTCGACCATTGCATGGCTAACACCCAAAAA-TTT--AA-TTTTTTATCAG-
66 AAGGG-GTGTCGACCATGGCATGGCTAACAACAAAAAAGTTTAAAATTTTTTTATCTGA
* * ** * *
4901521 ATAAATAGGAGTGTCGGCCATTGCATGGCTAACACCAAAAAA--TT-AAATTTTTTATCCGACAA
1 AAAAAGAGGA-TGTCGGCCATTGCATAACCAACACCAAAAAATTTTGAAATTTTTTATCTGACAA
4901583 AAAGGGGGTGTCGAC
65 AAA-GGGGTGTCGAC
4901598 TATTGCAAAT
Statistics
Matches: 272, Mismatches: 33, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
116 14 0.05
117 15 0.06
118 10 0.04
119 39 0.14
120 2 0.01
122 27 0.10
123 67 0.25
124 87 0.32
125 11 0.04
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (123 bp):
AAAAAGAGGATGTCGGCCATTGCATAACCAACACCAAAAAATTTTGAAATTTTTTATCTGACAAA
AAGGGGTGTCGACCATGGCATGGCTAACAACAAAAAAGTTTAAAATTTTTTTATCTGA
Found at i:4902150 original size:34 final size:34
Alignment explanation
Indices: 4902112--4902177 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
4902102 AACTCTTTAT
*
4902112 ATTTTTAAAAAATTAAA-AAAAATTATAAAAAATC
1 ATTTTGAAAAAATTAAATAAAAA-TATAAAAAATC
**
4902146 ATTTTGAAAATTTTAAATTAAAAATATAAAAA
1 ATTTTGAAAAAATTAAA-TAAAAATATAAAAA
4902178 TTTCAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 14 0.52
35 8 0.30
36 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (34 bp):
ATTTTGAAAAAATTAAATAAAAATATAAAAAATC
Found at i:4903750 original size:17 final size:17
Alignment explanation
Indices: 4903719--4903752 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4903709 ACAAAAAATA
**
4903719 TTTATTTTTTTAATTTT
1 TTTATTTTTAAAATTTT
4903736 TTTATTTTTAAAATTTT
1 TTTATTTTTAAAATTTT
4903753 AAAGAGTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTAAAATTTT
Found at i:4904119 original size:28 final size:31
Alignment explanation
Indices: 4904086--4904149 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
4904076 TATTACTATA
* *
4904086 TTAATAAATTA-TTAATA-TA-ATTTTTATT
1 TTAATAAATTATTTAACATTACAATTTTATT
4904114 TTAATAAATTATTTAACATTACAATTTTATT
1 TTAATAAATTATTTAACATTACAATTTTATT
4904145 TTAAT
1 TTAAT
4904150 TATACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 11 0.35
29 5 0.16
30 2 0.06
31 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
TTAATAAATTATTTAACATTACAATTTTATT
Found at i:4904373 original size:21 final size:22
Alignment explanation
Indices: 4904341--4904383 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4904331 CCCCACCCTT
4904341 AATATTGTATAA-AAAAATATG
1 AATATTGTATAATAAAAATATG
*
4904362 AATATT-TAATAATATAAATATG
1 AATATTGT-ATAATAAAAATATG
4904384 TTTAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.05
21 10 0.53
22 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
AATATTGTATAATAAAAATATG
Found at i:4904858 original size:140 final size:141
Alignment explanation
Indices: 4904594--4904904 Score: 457
Period size: 140 Copynumber: 2.2 Consensus size: 141
4904584 GTTTACATTT
* *
4904594 CAGTCACTCAATTTTGAAAATGTGACAAAACAATTATTTTTTCATGTTTTCCGTCACAAAAATCA
1 CAGTCACTCAACTTTGAAAATGTGACAAAACAATTATTTTTTCACGTTTTCCGTCACAAAAATCA
* * * *
4904659 CGGAACAGTGACATGGCAGTTGGCGGCGACGGTGGAGTGTGGAAAACGTCCAGCTGGTCGGTTAC
66 CGGAACAGTGACATGACAGTTGACGGCGACGGTGGAGTGTGGAAAACATCCAACTGGTCGGTTAC
4904724 ATTTAACACAA
131 ATTTAACACAA
* * *
4904735 CAGTCA-TCAACTTTGAAAATGTGACAAAACAATCT-TTTTTTCACGTTTTTCGTCACAGAAGTC
1 CAGTCACTCAACTTTGAAAATGTGACAAAACAAT-TATTTTTTCACGTTTTCCGTCACAAAAATC
* * *
4904798 ACGGAACAGTGACGTGACTGTTGATGGC-ATCGGTGGAGTGTGGAAAACATCCAACTGGTCGGTT
65 ACGGAACAGTGACATGACAGTTGACGGCGA-CGGTGGAGTGTGGAAAACATCCAACTGGTCGGTT
**
4904862 AGGTTTAACACAA
129 ACATTTAACACAA
4904875 CAGTCACTCAACTTTGAAAATGTGACAAAA
1 CAGTCACTCAACTTTGAAAATGTGACAAAA
4904905 TAGTCACTAA
Statistics
Matches: 153, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
139 1 0.01
140 122 0.80
141 30 0.20
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (141 bp):
CAGTCACTCAACTTTGAAAATGTGACAAAACAATTATTTTTTCACGTTTTCCGTCACAAAAATCA
CGGAACAGTGACATGACAGTTGACGGCGACGGTGGAGTGTGGAAAACATCCAACTGGTCGGTTAC
ATTTAACACAA
Found at i:4907910 original size:24 final size:26
Alignment explanation
Indices: 4907869--4907921 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4907859 TTTTTTTAAA
*
4907869 TTATATTATTTTAATATTTAAT-AATT
1 TTATATAATTTT-ATATTTAATAAATT
*
4907895 TTATATAATTTT-TATTTATTAAATT
1 TTATATAATTTTATATTTAATAAATT
4907920 TT
1 TT
4907922 TTTATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 6 0.25
26 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATATAATTTTATATTTAATAAATT
Found at i:4907912 original size:15 final size:14
Alignment explanation
Indices: 4907893--4907932 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4907883 TATTTAATAA
4907893 TTTTATATAATTTT
1 TTTTATATAATTTT
*
4907907 TATTTAT-TAAATTT
1 T-TTTATATAATTTT
4907921 TTTTATATAATT
1 TTTTATATAATT
4907933 ATCTTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.23
14 12 0.55
15 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTATATAATTTT
Found at i:4912694 original size:28 final size:30
Alignment explanation
Indices: 4912623--4912708 Score: 86
Period size: 32 Copynumber: 2.8 Consensus size: 30
4912613 AAAAAGGGCT
* *
4912623 CAAAATTTTATTTTTTTAATTTTTAAGTGGTC
1 CAAAA-TTT-TTTTTTTAACTTTTAAATGGTC
4912655 CAAAAATATTTTTTTTTAACTTTTAAAT-G-C
1 C-AAAAT-TTTTTTTTTAACTTTTAAATGGTC
**
4912685 CAAAATTTTTTTACTAACTTTTAA
1 CAAAATTTTTTTTTTAACTTTTAA
4912709 GGAGCCCCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 16 0.33
29 5 0.10
30 2 0.04
31 1 0.02
32 18 0.38
33 6 0.12
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (30 bp):
CAAAATTTTTTTTTTAACTTTTAAATGGTC
Found at i:4912816 original size:31 final size:31
Alignment explanation
Indices: 4912749--4912815 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
4912739 AAGAGCTCCA
* * *
4912749 AAAAATTTTTCTATCAACTTTTAAGAGATTT
1 AAAAATTTTTCTATCAACTTCTAAGAAACTT
* *
4912780 AAAAATTTTTTTCTCCAACTTCTAAGAAACTT
1 AAAAATTTTTCTAT-CAACTTCTAAGAAACTT
4912812 AAAA
1 AAAA
4912816 TCTCATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (31 bp):
AAAAATTTTTCTATCAACTTCTAAGAAACTT
Found at i:4914178 original size:2 final size:2
Alignment explanation
Indices: 4914171--4914202 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4914161 AAATTACAAA
4914171 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
4914203 TTTTTTTTTT
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:4917761 original size:3 final size:3
Alignment explanation
Indices: 4917753--4917784 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
4917743 CCACAATATT
*
4917753 ATG ATG ATG ATG ATG ATG ATA ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
4917785 TAAATTGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:4921257 original size:182 final size:182
Alignment explanation
Indices: 4920950--4921314 Score: 712
Period size: 182 Copynumber: 2.0 Consensus size: 182
4920940 TAATATGCAT
4920950 TATATCCAAGTCAATCTGACAATAAATGCTGAAAATGAACTTTTAGCAATCTTTTGAATTCCTAT
1 TATATCCAAGTCAATCTGACAATAAATGCTGAAAATGAACTTTTAGCAATCTTTTGAATTCCTAT
*
4921015 AAGTCTGTTCCACAAAAGATGGGATATAAAGCTTTGGAGTTGGTATTTTGCAAAGCTTTTCTTTT
66 AAGTCTGTTCCACAAAAGATGGCATATAAAGCTTTGGAGTTGGTATTTTGCAAAGCTTTTCTTTT
4921080 TTAGTGGTCCATTGCATCTTTGGCTTAGGTAGTCTCCCATTCTTAGAATCCG
131 TTAGTGGTCCATTGCATCTTTGGCTTAGGTAGTCTCCCATTCTTAGAATCCG
*
4921132 TATATCCAAGTCAATCTGACAATAAATGCTGGAAATGAACTTTTAGCAATCTTTTGAATTCCTAT
1 TATATCCAAGTCAATCTGACAATAAATGCTGAAAATGAACTTTTAGCAATCTTTTGAATTCCTAT
4921197 AAGTCTGTTCCACAAAAGATGGCATATAAAGCTTTGGAGTTGGTATTTTGCAAAGCTTTTCTTTT
66 AAGTCTGTTCCACAAAAGATGGCATATAAAGCTTTGGAGTTGGTATTTTGCAAAGCTTTTCTTTT
4921262 TTAGTGGTCCATTGCATCTTTGGCTTAGGTAGTCTCCCATTCTTAGAATCCG
131 TTAGTGGTCCATTGCATCTTTGGCTTAGGTAGTCTCCCATTCTTAGAATCCG
4921314 T
1 T
4921315 CATTGGTAAC
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 181 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (182 bp):
TATATCCAAGTCAATCTGACAATAAATGCTGAAAATGAACTTTTAGCAATCTTTTGAATTCCTAT
AAGTCTGTTCCACAAAAGATGGCATATAAAGCTTTGGAGTTGGTATTTTGCAAAGCTTTTCTTTT
TTAGTGGTCCATTGCATCTTTGGCTTAGGTAGTCTCCCATTCTTAGAATCCG
Found at i:4923280 original size:19 final size:19
Alignment explanation
Indices: 4923258--4923296 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4923248 ATTATAAACA
*
4923258 AAAAGAGTATAAAAATAAT
1 AAAAGAATATAAAAATAAT
* *
4923277 AAAATAATATCAAAATAAT
1 AAAAGAATATAAAAATAAT
4923296 A
1 A
4923297 TTTCACTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAGAATATAAAAATAAT
Found at i:4923831 original size:13 final size:13
Alignment explanation
Indices: 4923815--4923839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4923805 TTTATAAGTA
4923815 TAAAAAATAAATT
1 TAAAAAATAAATT
4923828 TAAAAAATAAAT
1 TAAAAAATAAAT
4923840 GAATAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TAAAAAATAAATT
Done.