Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 19 of 433
Found at i:5115489 original size:27 final size:27
Alignment explanation
Indices: 5115454--5115578 Score: 135
Period size: 27 Copynumber: 4.6 Consensus size: 27
5115444 AATATATTTG
* *
5115454 ATATCATAATTTACATAACTTATATAAC
1 ATAT-ATAACTTACATAACATATATAAC
*
5115482 ATATATAACTTACATAACTTATATAAC
1 ATATATAACTTACATAACATATATAAC
* * * *
5115509 ATACATAACTTATATAGCATACATAAC
1 ATATATAACTTACATAACATATATAAC
* *
5115536 TTATATAACTTAGATAA-ATATATAAC
1 ATATATAACTTACATAACATATATAAC
* *
5115562 TTACATAACTTACATAA
1 ATATATAACTTACATAA
5115579 TACTTAAATA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.27
27 57 0.68
28 4 0.05
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATATAACTTACATAACATATATAAC
Found at i:5121276 original size:21 final size:21
Alignment explanation
Indices: 5121222--5121277 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5121212 AACTTAGAGT
* * *
5121222 AGAGGCAGCAGAGAGGGAGGC
1 AGAGGCTGCAGCGAGAGAGGC
*
5121243 AGCGGCTGCAGCGAGAGAGGC
1 AGAGGCTGCAGCGAGAGAGGC
5121264 AGAGGCATG-AGCGA
1 AGAGGC-TGCAGCGA
5121278 TGGTAGCAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.18, G:0.48, T:0.04
Consensus pattern (21 bp):
AGAGGCTGCAGCGAGAGAGGC
Found at i:5121717 original size:42 final size:43
Alignment explanation
Indices: 5121666--5121827 Score: 290
Period size: 43 Copynumber: 3.8 Consensus size: 43
5121656 TAAAAAAAGC
*
5121666 GCCGCTAAAAGCCTTGACCTTTAGCGGCGC-TTTACCACAAAT
1 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAAT
*
5121708 GCCGCTAAAAGTCTTGACCTTTAGCGGCGCTTTTCCCACAAAT
1 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAAT
*
5121751 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAAT
5121794 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTT
1 GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTT
5121828 TTCCAATAAA
Statistics
Matches: 115, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 29 0.25
43 86 0.75
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAAT
Found at i:5122130 original size:27 final size:27
Alignment explanation
Indices: 5122100--5122157 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
5122090 ATGTATATAT
*
5122100 ATTTAAGTCCATAATCTAATATTTTTC
1 ATTTAAGTCCATAATCTAACATTTTTC
* **
5122127 ATTTAAGTCTATTGTCTAACATTTTTC
1 ATTTAAGTCCATAATCTAACATTTTTC
5122154 ATTT
1 ATTT
5122158 TCTTAATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (27 bp):
ATTTAAGTCCATAATCTAACATTTTTC
Found at i:5123971 original size:21 final size:21
Alignment explanation
Indices: 5123923--5123971 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5123913 ATCTGTGAAT
*
5123923 AAATTGAATAAATTCTGAAGA
1 AAATTGCATAAATTCTGAAGA
* *
5123944 ACATTGCATCAATTCTGAAGA
1 AAATTGCATAAATTCTGAAGA
5123965 AAATTGC
1 AAATTGC
5123972 TCTTCAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (21 bp):
AAATTGCATAAATTCTGAAGA
Found at i:5125073 original size:6 final size:6
Alignment explanation
Indices: 5125062--5125089 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5125052 GGAGATTATT
5125062 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
5125090 GGACCCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:5127967 original size:15 final size:15
Alignment explanation
Indices: 5127947--5127976 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5127937 TTTTTGCATA
*
5127947 ATGATGATGGTGGTG
1 ATGATGATGATGGTG
5127962 ATGATGATGATGGTG
1 ATGATGATGATGGTG
5127977 CCATTTGCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.43, T:0.33
Consensus pattern (15 bp):
ATGATGATGATGGTG
Found at i:5130686 original size:18 final size:17
Alignment explanation
Indices: 5130635--5130686 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
5130625 GCAACCTTAT
*
5130635 TTTATTTTATTTTCTTA
1 TTTATTTTATTTTTTTA
* **
5130652 TTTATTTGAATAATTTTA
1 TTTATTT-TATTTTTTTA
5130670 TTTATCTTTATTTTTTT
1 TTTAT-TTTATTTTTTT
5130687 TTGTTCTAGT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
17 7 0.27
18 17 0.65
19 2 0.08
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTATTTTATTTTTTTA
Found at i:5133208 original size:21 final size:21
Alignment explanation
Indices: 5133182--5133222 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5133172 ATCTGCTCAA
* *
5133182 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5133203 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5133223 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5144344 original size:39 final size:39
Alignment explanation
Indices: 5144167--5144318 Score: 236
Period size: 39 Copynumber: 3.8 Consensus size: 39
5144157 AGAAAGCATG
5144167 CGGGACTTTAAGCCCGGATATAATACCAGCATAAA-G-CTT
1 CGGGAC-TT-AGCCCGGATATAATACCAGCATAAATGCCTT
5144206 GCGGGACTTTAGCCCGGATATAATACCAGCATAAATGCCTT
1 -CGGGAC-TTAGCCCGGATATAATACCAGCATAAATGCCTT
* *
5144247 CGGGACTTAGCCCGGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCATAAATGCCTT
5144286 CGGGACTTAGCCCGGATATAATACCAGCATAAA
1 CGGGACTTAGCCCGGATATAATACCAGCATAAA
5144319 GCTTTGCTGA
Statistics
Matches: 106, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
39 87 0.82
40 16 0.15
41 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAATACCAGCATAAATGCCTT
Found at i:5145103 original size:2 final size:2
Alignment explanation
Indices: 5145096--5145122 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5145086 ACACATGCAC
5145096 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5145123 ATGCATACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5146777 original size:17 final size:17
Alignment explanation
Indices: 5146755--5146788 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5146745 TGTTAGCCTA
5146755 TATATGCCAATAAATAC
1 TATATGCCAATAAATAC
5146772 TATATGCCAATAAATAC
1 TATATGCCAATAAATAC
5146789 CTTATTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
TATATGCCAATAAATAC
Found at i:5148922 original size:46 final size:46
Alignment explanation
Indices: 5148872--5149011 Score: 203
Period size: 46 Copynumber: 3.0 Consensus size: 46
5148862 GCCATAGTGC
* *
5148872 CTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTAT
1 CTTTCAACTATGGTCTTACTCA-TTTCATATCAGGTTGCCATGGTAT
**
5148918 CTTTCAACTATGGTCTTGTTCATTTCATATCAGGTTGCCATGGTAT
1 CTTTCAACTATGGTCTTACTCATTTCATATCAGGTTGCCATGGTAT
*
5148964 CTTTCAAAC-ATGGTCTTACACATTTCATATCAGGTTGCCATGGTAT
1 CTTTC-AACTATGGTCTTACTCATTTCATATCAGGTTGCCATGGTAT
5149010 CT
1 CT
5149012 CGCCATGGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 4 0.05
46 78 0.92
47 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (46 bp):
CTTTCAACTATGGTCTTACTCATTTCATATCAGGTTGCCATGGTAT
Found at i:5149018 original size:13 final size:13
Alignment explanation
Indices: 5149000--5149024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5148990 ATATCAGGTT
5149000 GCCATGGTATCTC
1 GCCATGGTATCTC
5149013 GCCATGGTATCT
1 GCCATGGTATCT
5149025 TTCAACCATG
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:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (13 bp):
GCCATGGTATCTC
Found at i:5149205 original size:42 final size:42
Alignment explanation
Indices: 5149146--5149225 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
5149136 TATTGTCGGG
*
5149146 ATTACCAGTCCAGGCTAAATTCAGACCCTAATTCGGATCTGA
1 ATTACCAGTCCAGGCTAAATTCAGACCATAATTCGGATCTGA
*
5149188 ATTACCAGTCCAGGCTAAATTCAGACTATAATTCGGAT
1 ATTACCAGTCCAGGCTAAATTCAGACCATAATTCGGAT
5149226 TACCCATCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (42 bp):
ATTACCAGTCCAGGCTAAATTCAGACCATAATTCGGATCTGA
Found at i:5151183 original size:3 final size:3
Alignment explanation
Indices: 5151169--5151217 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
5151159 TTTTATACTA
*
5151169 AAT AATT AAT AAT AA- AAT AAT AAT GA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5151212 AA- AAT A
1 AAT AAT A
5151218 TCTCATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 29 0.74
4 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:5151191 original size:11 final size:11
Alignment explanation
Indices: 5151175--5151213 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
5151165 ACTAAATAAT
5151175 TAATAATAAAA
1 TAATAATAAAA
*
5151186 TAATAATGAAA
1 TAATAATAAAA
5151197 TAATAATAAAA
1 TAATAATAAAA
5151208 TAATAA
1 TAATAA
5151214 AATATCTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:5151200 original size:19 final size:19
Alignment explanation
Indices: 5151176--5151217 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5151166 CTAAATAATT
*
5151176 AATAATAAAATAATAATGA
1 AATAATAAAATAATAATAA
5151195 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
5151214 AATA
1 AATA
5151218 TCTCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:5151240 original size:20 final size:21
Alignment explanation
Indices: 5151187--5151262 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 21
5151177 ATAATAAAAT
* *
5151187 AATAATGAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
5151206 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
5151227 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
5151248 TAATCATAAAATATC
1 -AATAATAAAATATC
5151263 ATCAACATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 11 0.24
20 12 0.27
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:5152899 original size:44 final size:45
Alignment explanation
Indices: 5152809--5152937 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5152799 GACAGAACGA
*
5152809 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5152855 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5152899 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5152938 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5160286 original size:44 final size:45
Alignment explanation
Indices: 5160196--5160324 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
5160186 GACAGAACGA
*
5160196 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
5160242 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
5160286 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5160325 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:5163445 original size:48 final size:48
Alignment explanation
Indices: 5163365--5163494 Score: 145
Period size: 48 Copynumber: 2.7 Consensus size: 48
5163355 CATATCGATG
* * **** **
5163365 CCATGCCCCAGACATGGTCTTACACAAAATCACATATTGATGCAAATGT
1 CCATGTCCCAGACATGGTATTACATGGGATCACATATCAATGCAAAT-T
* *
5163414 -CATGTCCTAGACATGGTATTACATGGGATCACATATCAATGCCAATT
1 CCATGTCCCAGACATGGTATTACATGGGATCACATATCAATGCAAATT
*
5163461 CCATGTCCCAGACATGGTCTTACATGGGATCACA
1 CCATGTCCCAGACATGGTATTACATGGGATCACA
5163495 CATAACTCTA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.01
48 67 0.99
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (48 bp):
CCATGTCCCAGACATGGTATTACATGGGATCACATATCAATGCAAATT
Found at i:5166271 original size:21 final size:21
Alignment explanation
Indices: 5166222--5166271 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5166212 AATGCATAGG
*
5166222 CCGTGTGG-GGGTCAACACGC
1 CCGTGTGGAGGGGCAACACGC
*
5166242 CCATGTGGAGGGGCACACAC-C
1 CCGTGTGGAGGGGCA-ACACGC
5166263 CCGTGTGGA
1 CCGTGTGGA
5166272 AAGAGGCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 14 0.56
22 4 0.16
ACGTcount: A:0.18, C:0.30, G:0.38, T:0.14
Consensus pattern (21 bp):
CCGTGTGGAGGGGCAACACGC
Found at i:5166996 original size:5 final size:6
Alignment explanation
Indices: 5166974--5167010 Score: 65
Period size: 6 Copynumber: 6.0 Consensus size: 6
5166964 CAGAAGAAGA
5166974 AAAAAT AAAAAT AGAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT
5167011 CCAAACTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5166996 original size:19 final size:18
Alignment explanation
Indices: 5166974--5167010 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
5166964 CAGAAGAAGA
5166974 AAAAATAAAAATAGAAAAT
1 AAAAATAAAAATA-AAAAT
5166993 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAT
5167011 CCAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAT
Found at i:5169227 original size:2 final size:2
Alignment explanation
Indices: 5169220--5169261 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5169210 TTCCATTGAT
5169220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5169261 T
1 T
5169262 CTTTACCTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5170377 original size:3 final size:3
Alignment explanation
Indices: 5170365--5170416 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
5170355 AATGAAAATA
5170365 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5170410 T-T TAT TA
1 TAT TAT TA
5170417 ATAATTGAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5171009 original size:7 final size:7
Alignment explanation
Indices: 5170997--5171035 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
5170987 ATATGATGTC
5170997 ATATCAT
1 ATATCAT
5171004 ATATCAT
1 ATATCAT
5171011 ATATCAT
1 ATATCAT
5171018 ATATCAT
1 ATATCAT
5171025 ATATCAT
1 ATATCAT
5171032 ATAT
1 ATAT
5171036 AATTAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATCAT
Found at i:5171437 original size:31 final size:31
Alignment explanation
Indices: 5171379--5171437 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
5171369 GCCATATATG
*
5171379 TATTAATATTTTTAGTAATAGTGATATATTA
1 TATTAATATTTTTAGTAATAGTAATATATTA
* *
5171410 TATTATTA-TTTTATGTATTAGTAATATA
1 TATTAATATTTTTA-GTAATAGTAATATA
5171438 CTAATTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.54
Consensus pattern (31 bp):
TATTAATATTTTTAGTAATAGTAATATATTA
Found at i:5171555 original size:17 final size:16
Alignment explanation
Indices: 5171517--5171570 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
5171507 AAATTTAATT
*
5171517 TTATATATTTTA-ATAC
1 TTAT-TATTTTATATAA
5171533 TTATTAATTTTATATAA
1 TTATT-ATTTTATATAA
5171550 TTATTATTCTTATATAA
1 TTATTATT-TTATATAA
5171567 TTAT
1 TTAT
5171571 AGTGCTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 1 0.03
16 13 0.38
17 20 0.59
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATTTTATATAA
Found at i:5173715 original size:8 final size:9
Alignment explanation
Indices: 5173682--5173760 Score: 85
Period size: 8 Copynumber: 8.9 Consensus size: 9
5173672 TTTTTTTAAG
5173682 TAATTTTTA
1 TAATTTTTA
5173691 TAATTTTTA
1 TAATTTTTA
* *
5173700 -CATATTTA
1 TAATTTTTA
5173708 -AATTTTTA
1 TAATTTTTA
5173716 TAATTTTTAA
1 TAATTTTT-A
5173726 GTAATTTTTAA
1 -TAATTTTT-A
5173737 TAATTTTTA
1 TAATTTTTA
5173746 T-ATTTTTA
1 TAATTTTTA
5173754 -AATTTTT
1 TAATTTTT
5173761 TTATAGTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
8 25 0.40
9 18 0.29
10 9 0.15
11 10 0.16
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5173743 original size:46 final size:45
Alignment explanation
Indices: 5173674--5173760 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
5173664 TGTAGTGCTT
5173674 TTTTTAAGTAATTTTTATAATTTTTACATATTTAAATTTTTATAA
1 TTTTTAAGTAATTTTTATAATTTTTACATATTTAAATTTTTATAA
* *
5173719 TTTTTAAGTAATTTTTAATAATTTTTATATTTTTAAATTTTT
1 TTTTTAAGTAATTTTT-ATAATTTTTACATATTTAAATTTTT
5173761 TTATAGTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 16 0.41
46 23 0.59
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (45 bp):
TTTTTAAGTAATTTTTATAATTTTTACATATTTAAATTTTTATAA
Found at i:5174523 original size:2 final size:2
Alignment explanation
Indices: 5174516--5174543 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5174506 CTATTAATAC
5174516 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
5174544 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5187014 original size:3 final size:3
Alignment explanation
Indices: 5187006--5187050 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5186996 AAAATGGAGT
5187006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5187051 AAAAACCACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5193337 original size:26 final size:26
Alignment explanation
Indices: 5193300--5193435 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5193290 TGATACAAAT
* *
5193300 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5193326 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
5193352 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5193378 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5193404 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5193430 TGATAA
1 TGATAA
5193436 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5194974 original size:26 final size:25
Alignment explanation
Indices: 5194922--5194974 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
5194912 TTTACAGTTT
5194922 TACCCCTAGTAGATAAATTACCGAAA
1 TACCCCTAG-AGATAAATTACCGAAA
*
5194948 TACCCCTAG-GATTAAATTGACCTAAA
1 TACCCCTAGAGA-TAAATT-ACCGAAA
5194974 T
1 T
5194975 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.08
25 6 0.25
26 16 0.67
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (25 bp):
TACCCCTAGAGATAAATTACCGAAA
Found at i:5199871 original size:18 final size:17
Alignment explanation
Indices: 5199848--5199881 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5199838 GTGTGCCTTT
5199848 CCCGTGTAGGCCCACACC
1 CCCGTGT-GGCCCACACC
*
5199866 CCCGTGTGGCTCACAC
1 CCCGTGTGGCCCACAC
5199882 GGCCCAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.15, C:0.47, G:0.24, T:0.15
Consensus pattern (17 bp):
CCCGTGTGGCCCACACC
Found at i:5199981 original size:17 final size:18
Alignment explanation
Indices: 5199951--5199984 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5199941 GTGTGGTTCA
5199951 TCCGTGTAGGCCCATACG
1 TCCGTGTAGGCCCATACG
5199969 TCCGTGT-GGCCCATAC
1 TCCGTGTAGGCCCATAC
5199985 AACCCAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (18 bp):
TCCGTGTAGGCCCATACG
Found at i:5203747 original size:2 final size:2
Alignment explanation
Indices: 5203740--5203769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5203730 TCGTTTTAGA
5203740 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5203770 CTTAGAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5205526 original size:19 final size:20
Alignment explanation
Indices: 5205464--5205545 Score: 98
Period size: 19 Copynumber: 4.2 Consensus size: 20
5205454 AGGTTACAAA
*
5205464 ATCATATCTTCAAGATTGCAT
1 ATCATATCAT-AAGATTGCAT
**
5205485 ATCATATCATATCATAT-CAT
1 ATCATATCATAAGAT-TGCAT
5205505 ATCATATC-TAAGATTGCAT
1 ATCATATCATAAGATTGCAT
5205524 ATCATATC-TAAGATTGCAT
1 ATCATATCATAAGATTGCAT
5205543 ATC
1 ATC
5205546 CTTAAAGATT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
18 1 0.02
19 29 0.54
20 14 0.26
21 10 0.19
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (20 bp):
ATCATATCATAAGATTGCAT
Found at i:5205531 original size:5 final size:5
Alignment explanation
Indices: 5205482--5205512 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5205472 TTCAAGATTG
5205482 CATAT CATAT CATAT CATAT CATAT CATAT C
1 CATAT CATAT CATAT CATAT CATAT CATAT C
5205513 TAAGATTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:5215163 original size:36 final size:37
Alignment explanation
Indices: 5215098--5215172 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 37
5215088 TTATATATTT
*
5215098 AATTTAAATTAATAAATCATTATAATATATGTAAAAAC
1 AATTTAAAATAATAAAT-ATTATAATATATGTAAAAAC
5215136 AATTTAAAAT-ATAAAT-TTATTAATATATGTAAAAAC
1 AATTTAAAATAATAAATATTA-TAATATATGTAAAAAC
5215172 A
1 A
5215173 GCTTTTCCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
35 3 0.09
36 17 0.49
37 6 0.17
38 9 0.26
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (37 bp):
AATTTAAAATAATAAATATTATAATATATGTAAAAAC
Found at i:5215422 original size:3 final size:3
Alignment explanation
Indices: 5215414--5215442 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5215404 AGGTCAATTG
5215414 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5215443 CAACAACTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5224147 original size:30 final size:30
Alignment explanation
Indices: 5224113--5224171 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
5224103 ATTCAAAGAG
5224113 ATTGCTTGCAAGTCAAGCTAAACAAAATAT
1 ATTGCTTGCAAGTCAAGCTAAACAAAATAT
*
5224143 ATTGCTTGCAAGTCAAGTTAAACAAAATA
1 ATTGCTTGCAAGTCAAGCTAAACAAAATA
5224172 CATTTTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (30 bp):
ATTGCTTGCAAGTCAAGCTAAACAAAATAT
Found at i:5224274 original size:37 final size:37
Alignment explanation
Indices: 5224195--5224275 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
5224185 AAAGATTTAG
* *
5224195 TATTTATTAGTATAATATATTTAACATTTATATTTGA
1 TATTTATTAGTATAAAATATTTAACATTTATATTTCA
* ** *
5224232 CATTTATTAGTATAAAAATATTTATTATTTCT-TTTCA
1 TATTTATTAGTAT-AAAATATTTAACATTTATATTTCA
5224269 TATTTAT
1 TATTTAT
5224276 GAGTTTTTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.56
Consensus pattern (37 bp):
TATTTATTAGTATAAAATATTTAACATTTATATTTCA
Found at i:5231172 original size:14 final size:14
Alignment explanation
Indices: 5231132--5231161 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5231122 TTAATATATA
5231132 TTAAGGTTTTGGGT
1 TTAAGGTTTTGGGT
5231146 TTAAGGTTTTGGGT
1 TTAAGGTTTTGGGT
5231160 TT
1 TT
5231162 GAGTCTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.53
Consensus pattern (14 bp):
TTAAGGTTTTGGGT
Found at i:5231265 original size:22 final size:24
Alignment explanation
Indices: 5231239--5231283 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5231229 GTTATCTTTA
5231239 TTATTTTA-TTTT-ATTTTTGGTT
1 TTATTTTATTTTTAATTTTTGGTT
5231261 TTATTTTATTTTTAATTTTTGGT
1 TTATTTTATTTTTAATTTTTGGT
5231284 CTGGGACGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.76
Consensus pattern (24 bp):
TTATTTTATTTTTAATTTTTGGTT
Found at i:5231279 original size:17 final size:17
Alignment explanation
Indices: 5231241--5231279 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5231231 TATCTTTATT
*
5231241 ATTTTATTTTATTTTTG
1 ATTTTATTTTATTTTTA
*
5231258 GTTTTATTTTATTTTTA
1 ATTTTATTTTATTTTTA
5231275 ATTTT
1 ATTTT
5231280 TGGTCTGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (17 bp):
ATTTTATTTTATTTTTA
Found at i:5232961 original size:721 final size:726
Alignment explanation
Indices: 5231689--5233138 Score: 2552
Period size: 721 Copynumber: 2.0 Consensus size: 726
5231679 CATTGCCATA
*
5231689 TGGCCGATTTGGGGACTTTATCGTTTCTCACACCGTCGTGCCTATCAGGCACATAGGCGTTTGAG
1 TGGCCGATTTGGGGACTTTATCGTTTCTCACACCGTCGTGCCTATCAGGCACACAGGCGTTTGAG
5231754 TTTAGGGATTAAAGTTAAGTGATTTGATGTTACACGGTCGTGTGGATAATTTTGGGGATTTACGG
66 TTTAGGGATTAAAGTTAAGTGATTTGATGTTACACGGTCGTGTGGATAATTTTGGGGATTTACGG
*
5231819 TTTCCACACAGGCATGTGTTTTAGACACACGACCTTGTCTGGTGGGCACATAGGCGTATGAGACC
131 TTTCCACACAGGCATGTGTTTTAGACACACGACCTTGTCTGGTGGGCACACAGGCGTATGAGACC
5231884 CTCTCACAGCCGTGTCAGCCCTGTACTTAAATTTAGTGCAAATGGACAGATAGTTACACAGCCTG
196 CTCTCACAGCCGTGTCAGCCCTGTACTTAAATTTAGTGCAAATGGACAGATAGTTACACAGCCTG
* *
5231949 TCCCCACGGCCATGTCCTTGGTCCACATGGGCATGTGCCTTAATCACACAATCGTGTGCCTCTCT
261 TCCCCACGACCATGTCCCTGGTCCACATGGGCATGTGCCTTAATCACACAATCGTGTGCCTCTCT
*
5232014 TCACACGGGCATGTGCTTCTGTCACACAGCCATGTGCCCCTTTTTACACGGGCTTTTGACCTTCC
326 TCACACGGGCATGTGCTTCTGTCACACAGCCATGTGCCCCTTTTTACACGAGCTTTTGACCTTCC
* *
5232079 CTACGGCCTAGGCATTTCCACCCGGCCAGAGCACATGGGCATGTGGTCCTAAGGCACTTATATTG
391 CTACAGCCTAGGCATTTCCACCCGGCCAGAGCACACGGGCATGTGGTCCTAAGGCACTTATATTG
5232144 GTTCCAAGTGCGTCTTTGATCTGAAAATGTATTTGTGTGTGCTCCGACCCTTAGCTAAGTTTAGT
456 GTTCCAAGTGCGTCTTTGATCTGAAAATGTATTTGTGTGTGCTCCGACCCTTAGCTAAGTTTAGT
*
5232209 AAGGGTGTTCATGACTCGATATCTGTGATGATTGTGTGTGATAGG-TGAGTTTGAATCTGGTCTG
521 AAGGGTGTTCATGACTCGATATCTGTGATGATTGTGTGTGAT-GGATGAGTTTGAATCTAGTCTG
* *
5232273 TGGAGTGTGTTGTTTATCTGTTCCGTCTGACTGACTGTGTAAATGTCTCTGTTCTATGAGCTTGA
585 TGGAGTGTGTTGTTTATCTATTACGTCTGACTGACTGTGTAAATGTCTCTGTTCTATGAGCTTGA
* * *
5232338 ATGCA-T-T-CA-TGCA-AAAGTATTTTGGGTTGGGTTGTGAAGAGAAGGAAGACTGTATCTGTT
650 ATGCATTATGCATTGCATAAAGTATTTTGGGTTGGGTTGTGAAGAGAAGAAAAACTGTATCTATT
5232398 CTGATCTAGCAG
715 CTGATCTAGCAG
*
5232410 TGGCCGATTTGGGGATTTTATCGTTTCTCACACCGTCGTGCCTATCAGGCACACAGGCGTTTGAG
1 TGGCCGATTTGGGGACTTTATCGTTTCTCACACCGTCGTGCCTATCAGGCACACAGGCGTTTGAG
* * * *
5232475 TTTAGGGATTAAGGTTGAGTGATTTGATGTTACACGGTCGTGTGGCTAATTTTGGGGATTTGCGG
66 TTTAGGGATTAAAGTTAAGTGATTTGATGTTACACGGTCGTGTGGATAATTTTGGGGATTTACGG
* *
5232540 TTTCCACACAGGCGTGTGTTTTAGACACACGACCTTGTCTGGTGGGCACACAGGCGTGTGAGACC
131 TTTCCACACAGGCATGTGTTTTAGACACACGACCTTGTCTGGTGGGCACACAGGCGTATGAGACC
* *
5232605 CTCTCACGGCCGTGTCAGCCCTGTACTTAAATTTAGTGCAAATGGATAGATAGTTACACAGCCTG
196 CTCTCACAGCCGTGTCAGCCCTGTACTTAAATTTAGTGCAAATGGACAGATAGTTACACAGCCTG
*
5232670 TCCCCACGACCATGTCCCTGGTCCACATGGGCATGTGCCTTAATCACACGATCGTGTGCCTCTCT
261 TCCCCACGACCATGTCCCTGGTCCACATGGGCATGTGCCTTAATCACACAATCGTGTGCCTCTCT
* * *
5232735 TCACATGGGCGTGTGCTTCTGTCACACGGCCATGTGCCCCTTTTTACACGAGCTTTTGACCTTCC
326 TCACACGGGCATGTGCTTCTGTCACACAGCCATGTGCCCCTTTTTACACGAGCTTTTGACCTTCC
5232800 CTACAGCCTAGGCATTTCCACCCGGCCAGAGCACACGGGCATGTGGTCCTAAGGCACTTATATTG
391 CTACAGCCTAGGCATTTCCACCCGGCCAGAGCACACGGGCATGTGGTCCTAAGGCACTTATATTG
5232865 GTTCCAAGTGCGTCTTTGATCTGAAAATGTATTTGTGTGTGCTCCGACCCTTAGCTAAGTTTAGT
456 GTTCCAAGTGCGTCTTTGATCTGAAAATGTATTTGTGTGTGCTCCGACCCTTAGCTAAGTTTAGT
* *
5232930 AAGGGTGTTCATGATTTGATATCTGTGATGATTGTGTGTGATGGATGAGTTTGAATCTAGTCTGT
521 AAGGGTGTTCATGACTCGATATCTGTGATGATTGTGTGTGATGGATGAGTTTGAATCTAGTCTGT
* *
5232995 GGAGTGTGTTGTTTATCTATTACGTCTGACTGATTGTGTAAATGTCTCTGTTCTGTGAGCTTGAA
586 GGAGTGTGTTGTTTATCTATTACGTCTGACTGACTGTGTAAATGTCTCTGTTCTATGAGCTTGAA
5233060 TGCATTCATGCATTTGCATAAAGTATTTTGGGTTGGGTTGTGAAGAGAAGAAAAACTGTATCTAT
651 TGCATT-ATGCA-TTGCATAAAGTATTTTGGGTTGGGTTGTGAAGAGAAGAAAAACTGTATCTAT
*
5233125 TCTGATCTGGCAG
714 TCTGATCTAGCAG
5233138 T
1 T
5233139 TTAACTGCAA
Statistics
Matches: 690, Mismatches: 31, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
720 2 0.00
721 624 0.90
722 1 0.00
724 1 0.00
725 2 0.00
727 4 0.01
728 56 0.08
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (726 bp):
TGGCCGATTTGGGGACTTTATCGTTTCTCACACCGTCGTGCCTATCAGGCACACAGGCGTTTGAG
TTTAGGGATTAAAGTTAAGTGATTTGATGTTACACGGTCGTGTGGATAATTTTGGGGATTTACGG
TTTCCACACAGGCATGTGTTTTAGACACACGACCTTGTCTGGTGGGCACACAGGCGTATGAGACC
CTCTCACAGCCGTGTCAGCCCTGTACTTAAATTTAGTGCAAATGGACAGATAGTTACACAGCCTG
TCCCCACGACCATGTCCCTGGTCCACATGGGCATGTGCCTTAATCACACAATCGTGTGCCTCTCT
TCACACGGGCATGTGCTTCTGTCACACAGCCATGTGCCCCTTTTTACACGAGCTTTTGACCTTCC
CTACAGCCTAGGCATTTCCACCCGGCCAGAGCACACGGGCATGTGGTCCTAAGGCACTTATATTG
GTTCCAAGTGCGTCTTTGATCTGAAAATGTATTTGTGTGTGCTCCGACCCTTAGCTAAGTTTAGT
AAGGGTGTTCATGACTCGATATCTGTGATGATTGTGTGTGATGGATGAGTTTGAATCTAGTCTGT
GGAGTGTGTTGTTTATCTATTACGTCTGACTGACTGTGTAAATGTCTCTGTTCTATGAGCTTGAA
TGCATTATGCATTGCATAAAGTATTTTGGGTTGGGTTGTGAAGAGAAGAAAAACTGTATCTATTC
TGATCTAGCAG
Found at i:5240253 original size:2 final size:2
Alignment explanation
Indices: 5240246--5240274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5240236 ACATTAATTA
5240246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5240275 AGAAATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5240481 original size:3 final size:3
Alignment explanation
Indices: 5240456--5240499 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
5240446 AAACAAATAC
* *
5240456 AAT AAT ATAT AAA AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5240500 TAGTAACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:5240850 original size:7 final size:7
Alignment explanation
Indices: 5240834--5240940 Score: 50
Period size: 7 Copynumber: 15.7 Consensus size: 7
5240824 AATAAATGAA
*
5240834 ATAATTT
1 ATAATAT
5240841 ATAATAT
1 ATAATAT
5240848 ATAATAT
1 ATAATAT
*
5240855 A-AAAAT
1 ATAATAT
* *
5240861 GTAAGTTT
1 ATAA-TAT
*
5240869 TTAA-A-
1 ATAATAT
*
5240874 ATAATGT
1 ATAATAT
5240881 ATAATAT
1 ATAATAT
*
5240888 A-AATAA
1 ATAATAT
5240894 ATAAATAT
1 AT-AATAT
5240902 ATAAGATAT
1 AT-A-ATAT
5240911 ATAAGT-T
1 ATAA-TAT
5240918 A-AA-AT
1 ATAATAT
5240923 ATAATAT
1 ATAATAT
5240930 ATAATA-
1 ATAATAT
5240936 ATAAT
1 ATAAT
5240941 TTACAAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
5 5 0.06
6 18 0.23
7 34 0.44
8 14 0.18
9 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:5240904 original size:21 final size:21
Alignment explanation
Indices: 5240872--5240936 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
5240862 TAAGTTTTTA
*
5240872 AAAT-AATGTATAATATAAAT
1 AAATAAATATATAATATAAAT
* *
5240892 AAATAAATATATAAGATATAT
1 AAATAAATATATAATATAAAT
*
5240913 AAGTTAAA-ATATAATATATAAT
1 AA-ATAAATATATAATATA-AAT
5240935 AA
1 AA
5240937 TAATTTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 4 0.11
21 24 0.67
22 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAATATATAATATAAAT
Found at i:5240905 original size:28 final size:29
Alignment explanation
Indices: 5240874--5240934 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
5240864 AGTTTTTAAA
5240874 ATAATGTATAATATAA-AT-AAATA-AATAT
1 ATAATG-AT-ATATAAGATAAAATATAATAT
*
5240902 ATAA-GATATATAAGTTAAAATATAATAT
1 ATAATGATATATAAGATAAAATATAATAT
5240930 ATAAT
1 ATAAT
5240935 AATAATTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 6 0.21
26 3 0.11
27 6 0.21
28 13 0.46
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
ATAATGATATATAAGATAAAATATAATAT
Found at i:5240975 original size:12 final size:13
Alignment explanation
Indices: 5240956--5240986 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
5240946 AATTTTGAAA
5240956 ATATAAATAATAT
1 ATATAAATAATAT
5240969 A-ATAAATAATAT
1 ATATAAATAATAT
5240981 ATATAA
1 ATATAA
5240987 TAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:5240984 original size:16 final size:15
Alignment explanation
Indices: 5240961--5240991 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5240951 TGAAAATATA
5240961 AATAATATAATAAAT
1 AATAATATAATAAAT
5240976 AATATATATAATAAAT
1 AATA-ATATAATAAAT
5240992 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:5241347 original size:17 final size:18
Alignment explanation
Indices: 5241294--5241391 Score: 137
Period size: 18 Copynumber: 5.5 Consensus size: 18
5241284 AATCATATCT
*
5241294 TCTAAGATTGTATATCATA
1 TCTAAGATTG-CTATCATA
*
5241313 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
5241331 TCTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
*
5241348 TCTAAGATTGCAATCATA
1 TCTAAGATTGCTATCATA
*
5241366 TTTAAGATTG-TATCATA
1 TCTAAGATTGCTATCATA
5241383 TCTAAGATT
1 TCTAAGATT
5241392 ACATATCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
17 30 0.42
18 31 0.44
19 10 0.14
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (18 bp):
TCTAAGATTGCTATCATA
Found at i:5241352 original size:35 final size:35
Alignment explanation
Indices: 5241294--5241400 Score: 169
Period size: 35 Copynumber: 3.0 Consensus size: 35
5241284 AATCATATCT
5241294 TCTAAGATTGTATATCATATCTAAGATTGCAATCATA
1 TCTAAGATTG--TATCATATCTAAGATTGCAATCATA
5241331 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
1 TCTAAGATTGTATCATATCTAAGATTGCAATCATA
* *
5241366 TTTAAGATTGTATCATATCTAAGATTACATATCAT
1 TCTAAGATTGTATCATATCTAAGATTGCA-ATCAT
5241401 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 52 0.78
36 5 0.07
37 10 0.15
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (35 bp):
TCTAAGATTGTATCATATCTAAGATTGCAATCATA
Found at i:5244344 original size:11 final size:11
Alignment explanation
Indices: 5244328--5244370 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5244318 ATTAGATCTC
5244328 TACTTCTTTTA
1 TACTTCTTTTA
**
5244339 TACTTCTTATGCC
1 TACTTCTT-T-TA
5244352 TACTTCTTTTA
1 TACTTCTTTTA
5244363 TACTTCTT
1 TACTTCTT
5244371 ATGCCTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 16 0.62
12 2 0.08
13 8 0.31
ACGTcount: A:0.16, C:0.23, G:0.02, T:0.58
Consensus pattern (11 bp):
TACTTCTTTTA
Found at i:5244354 original size:24 final size:24
Alignment explanation
Indices: 5244327--5244377 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5244317 AATTAGATCT
5244327 CTACTTCTTTTATACTTCTTATGC
1 CTACTTCTTTTATACTTCTTATGC
5244351 CTACTTCTTTTATACTTCTTATGC
1 CTACTTCTTTTATACTTCTTATGC
5244375 CTA
1 CTA
5244378 TAAATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (24 bp):
CTACTTCTTTTATACTTCTTATGC
Found at i:5247905 original size:17 final size:18
Alignment explanation
Indices: 5247892--5248049 Score: 93
Period size: 17 Copynumber: 8.8 Consensus size: 18
5247882 TAATCTTCAA
5247892 TGATATGCAATCTTAGATG
1 TGATATGCAATCTTAGA-G
5247911 TGATATGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
* *
5247928 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
*
5247947 TGAT-TGCAACCTTAGA-
1 TGATATGCAATCTTAGAG
* *
5247963 T-ATGATACAATCTTAGATA
1 TGAT-ATGCAATCTTAGA-G
5247982 TGAT-TGCAATCTTAGA-
1 TGATATGCAATCTTAGAG
*
5247998 T-ATGATACAATCTTAGA-
1 TGAT-ATGCAATCTTAGAG
*
5248015 T-ATGACTGCAATCTTAGATA
1 TGAT-A-TGCAATCTTAGA-G
*
5248035 TGATATACAATCTTA
1 TGATATGCAATCTTA
5248050 AAAGATATGA
Statistics
Matches: 115, Mismatches: 9, Indels: 30
0.75 0.06 0.19
Matches are distributed among these distances:
15 4 0.03
16 4 0.03
17 39 0.34
18 32 0.28
19 28 0.24
20 6 0.05
21 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (18 bp):
TGATATGCAATCTTAGAG
Found at i:5247962 original size:35 final size:35
Alignment explanation
Indices: 5247899--5248049 Score: 248
Period size: 35 Copynumber: 4.2 Consensus size: 35
5247889 CAATGATATG
*
5247899 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
*
5247935 CAATCTTAGATATGATTGCAACCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
5247970 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
5248005 CAATCTTAGATATGACTGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATTGCAATCTTAGATATG--ATA
5248042 CAATCTTA
1 CAATCTTA
5248050 AAAGATATGA
Statistics
Matches: 109, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
35 83 0.76
36 15 0.14
37 11 0.10
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:5248374 original size:12 final size:11
Alignment explanation
Indices: 5248359--5248392 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
5248349 TATTTTTAAT
5248359 TTATTATATATA
1 TTATT-TATATA
5248371 TTATTTATTATA
1 TTATTTA-TATA
5248383 TTATTTATAT
1 TTATTTATAT
5248393 TTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTATATA
Found at i:5248384 original size:21 final size:21
Alignment explanation
Indices: 5248360--5248468 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
5248350 ATTTTTAATT
5248360 TATTATATATATTATTTATTA
1 TATTATATATATTATTTATTA
* *
5248381 TATTATTTATATT-TTCA--A
1 TATTATATATATTATTTATTA
* * *
5248399 AATT-TGTAAATTA-TTATTA
1 TATTATATATATTATTTATTA
* *
5248418 TA-TATTATATTTTAACTTATATA
1 TATTA-TATATATT-ATTTAT-TA
*
5248441 TCTTATATAT-TTATTTATTTA
1 TATTATATATATTATTTA-TTA
5248462 TATTATA
1 TATTATA
5248469 CATTATTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 20
0.66 0.13 0.20
Matches are distributed among these distances:
17 8 0.12
18 5 0.08
19 2 0.03
20 8 0.12
21 25 0.38
22 7 0.11
23 8 0.12
24 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TATTATATATATTATTTATTA
Found at i:5248390 original size:16 final size:16
Alignment explanation
Indices: 5248357--5248387 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5248347 CTTATTTTTA
5248357 ATTTATTATATATATT
1 ATTTATTATATATATT
5248373 ATTTATTATAT-TATT
1 ATTTATTATATATATT
5248388 TATATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTATATATATT
Found at i:5248425 original size:7 final size:7
Alignment explanation
Indices: 5248408--5248555 Score: 57
Period size: 7 Copynumber: 21.4 Consensus size: 7
5248398 AAATTTGTAA
5248408 ATTAT-T
1 ATTATAT
5248414 ATTATAT
1 ATTATAT
5248421 ATTATAT
1 ATTATAT
5248428 -TT-TA-
1 ATTATAT
5248432 ACTTATAT
1 A-TTATAT
5248440 ATCTTATAT
1 A--TTATAT
*
5248449 ATTTATTT
1 A-TTATAT
5248457 ATT-TAT
1 ATTATAT
*
5248463 ATTATAC
1 ATTATAT
5248470 ATTAT-T
1 ATTATAT
* *
5248476 -TTAAAA
1 ATTATAT
*
5248482 ACTTACAT
1 A-TTATAT
5248490 -TT-TAT
1 ATTATAT
5248495 ATTATAT
1 ATTATAT
*
5248502 ATTATAA
1 ATTATAT
*
5248509 ATTATTT
1 ATTATAT
5248516 CATT-TATT
1 -ATTATA-T
5248524 ATTAT-T
1 ATTATAT
*
5248530 TTTATAT
1 ATTATAT
5248537 ATATCATAT
1 AT-T-ATAT
*
5248546 ATTATCT
1 ATTATAT
5248553 ATT
1 ATT
5248556 TTAAAATTCA
Statistics
Matches: 107, Mismatches: 17, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
5 7 0.07
6 23 0.21
7 45 0.42
8 18 0.17
9 14 0.13
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.58
Consensus pattern (7 bp):
ATTATAT
Found at i:5250228 original size:20 final size:20
Alignment explanation
Indices: 5250203--5250246 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5250193 AATCCATTTG
5250203 TAAACAATAGCTCATCCATA
1 TAAACAATAGCTCATCCATA
* **
5250223 TAAACAGTATTTCATCCATA
1 TAAACAATAGCTCATCCATA
5250243 TAAA
1 TAAA
5250247 TAGTATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAACAATAGCTCATCCATA
Found at i:5250251 original size:20 final size:20
Alignment explanation
Indices: 5250214--5250254 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5250204 AAACAATAGC
5250214 TCATCCATATAAACAGTATT
1 TCATCCATATAAACAGTATT
*
5250234 TCATCCATATAAATAGTATT
1 TCATCCATATAAACAGTATT
5250254 T
1 T
5250255 ATGCCCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (20 bp):
TCATCCATATAAACAGTATT
Found at i:5252369 original size:93 final size:93
Alignment explanation
Indices: 5252260--5252430 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
5252250 GCCCATAAGT
* ** * * *
5252260 GAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
5252325 TGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
5252353 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
5252418 CGAGTTCGGATGC
66 CGAGCTCGGATGC
5252431 TCAACCATCC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:5252425 original size:46 final size:46
Alignment explanation
Indices: 5252252--5252421 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 46
5252242 TGTAACCCGC
* ** * *
5252252 CCATAAGTGAACTCAGACTCAACTCAATGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCAT
* * * *
5252298 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTC-GA--AC-A-TTCGCAT
* * *
5252348 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCAT
5252391 CCATAAGTGAACTCAGACTCAACTCAACGAG
1 CCATAAGTGAACTCAGACTCAACTCAACGAG
5252422 TTCGGATGCT
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 58 0.58
47 24 0.24
48 2 0.02
49 2 0.02
50 2 0.02
51 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGAACATTCGCAT
Found at i:5252446 original size:46 final size:45
Alignment explanation
Indices: 5252353--5252438 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
5252343 TACATCTCAC
* *
5252353 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGT
1 GAACTCAGACTCAACTCAACGAGTTCG-ACATGCGCAACCATAAGT
* *
5252399 GAACTCAGACTCAACTCAACGAGTTCG-GATGCTCAACCAT
1 GAACTCAGACTCAACTCAACGAGTTCGACATGCGCAACCAT
5252439 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
46 27 0.75
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (45 bp):
GAACTCAGACTCAACTCAACGAGTTCGACATGCGCAACCATAAGT
Found at i:5255795 original size:46 final size:45
Alignment explanation
Indices: 5255728--5255886 Score: 159
Period size: 46 Copynumber: 3.5 Consensus size: 45
5255718 ATCGATACCG
* * *
5255728 TGTCCCAGAC-TGGTTTTACACTGACACATGTAACCGTGCTGACGCA
1 TGTCCCAGACAT-GTCTTACACTGACACATCTAA-CGTGCCGACGCA
5255774 TGTCCCAGACATGTCTTACACT-AGCACATCT--CGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTGA-CACATCTAACGT-GCCGACGCA
* * *
5255818 TGTCCCAGACATGTCTGACACTGGCTATCATCTCAA-G-GCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAC-A-CATCT-AACGTGCCGACGCA
5255864 TGTCCCAGACATGTCTTACACTG
1 TGTCCCAGACATGTCTTACACTG
5255887 GCTCTCATAC
Statistics
Matches: 97, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
43 3 0.03
44 30 0.31
45 2 0.02
46 60 0.62
47 1 0.01
48 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGACACATCTAACGTGCCGACGCA
Found at i:5255887 original size:46 final size:46
Alignment explanation
Indices: 5255771--5255982 Score: 216
Period size: 46 Copynumber: 4.6 Consensus size: 46
5255761 CCGTGCTGAC
* * *
5255771 GCATGTCCCAGACATGTCTTACACTAGC-A-CATCTCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTC-AAGGCCGAT
*
5255815 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCAAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCAAGGCCGAT
* ** *
5255861 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCAT-CTCAAGGCCGAT
* * * ** * *
5255907 ACATGTCCTAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCAAGGCCGAT
*
5255953 GCCATGTCCCATACATGGTCTTACACTGGC
1 G-CATGTCCCAGACAT-GTCTTACACTGGC
5255983 ACACAAATCT
Statistics
Matches: 139, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
44 26 0.19
45 4 0.03
46 83 0.60
47 14 0.10
48 12 0.09
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTGGCTATCATCTCAAGGCCGAT
Found at i:5255944 original size:92 final size:91
Alignment explanation
Indices: 5255771--5255987 Score: 249
Period size: 92 Copynumber: 2.4 Consensus size: 91
5255761 CCGTGCTGAC
* *
5255771 GCATGTCCCAGACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACACATGTCCCAGACATGTCTG
* *
5255835 ACACTGGCTATCATCTCAAGGCCGAT
66 ACACTAGCCATCATCTCAAGGCCGAT
* * * * *
5255861 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGATACATGTCCTAGACATGTC
1 GCATGTCCCAGACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACACATGTCCCAGACATGTC
* * * *
5255925 TTACACTAGCCCTCGTCTCAATGCCGAT
64 TGACACTAGCCATCATCTCAAGGCCGAT
*
5255953 GCCATGTCCCATACATGGTCTTACACTGGCACACA
1 G-CATGTCCCAGACAT-GTCTTACACTGGC-CACA
5255988 AATCTCATGT
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
90 26 0.25
92 49 0.46
93 15 0.14
94 16 0.15
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.26
Consensus pattern (91 bp):
GCATGTCCCAGACATGTCTTACACTGGCCACATCTCGTAGCCGACACATGTCCCAGACATGTCTG
ACACTAGCCATCATCTCAAGGCCGAT
Found at i:5261790 original size:30 final size:30
Alignment explanation
Indices: 5261756--5261816 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5261746 TCCTTAACTC
5261756 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
5261786 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
5261816 A
1 A
5261817 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:5266522 original size:2 final size:2
Alignment explanation
Indices: 5266515--5266571 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5266505 CATGTCATAG
5266515 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5266557 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
5266572 CATCATGTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5266674 original size:2 final size:2
Alignment explanation
Indices: 5266667--5266706 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5266657 GTAACAAGTC
5266667 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
5266707 TTATTGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5266881 original size:9 final size:9
Alignment explanation
Indices: 5266869--5266893 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5266859 ACATAGCTTA
5266869 CATTTTATT
1 CATTTTATT
5266878 CATTTTATT
1 CATTTTATT
5266887 CATTTTA
1 CATTTTA
5266894 GTCCCTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (9 bp):
CATTTTATT
Found at i:5270259 original size:17 final size:17
Alignment explanation
Indices: 5270211--5270259 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 17
5270201 TAAAATTTTA
5270211 AAATTCAAAATATATAA--
1 AAATT-AAAATATA-AACT
5270228 AAATTAAAA-AT-AACT
1 AAATTAAAATATAAACT
5270243 AAATTAAAATATAAACT
1 AAATTAAAATATAAACT
5270260 TACATTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.07
15 11 0.39
16 6 0.21
17 9 0.32
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTAAAATATAAACT
Found at i:5273691 original size:19 final size:19
Alignment explanation
Indices: 5273667--5273719 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5273657 TATTATATTG
*
5273667 ATATTTTATTATGTGTCAT
1 ATATTTTATTATATGTCAT
* *
5273686 ATATTTTTACTATATGTTAT
1 ATA-TTTTATTATATGTCAT
*
5273706 TTATTTTATTATAT
1 ATATTTTATTATAT
5273720 TTTATCTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (19 bp):
ATATTTTATTATATGTCAT
Found at i:5273706 original size:55 final size:54
Alignment explanation
Indices: 5273616--5273720 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 54
5273606 TTTTATAAAT
*
5273616 TTTTATTATATGTTATTTTTTTAAATATATATTATTTATTCTATTATATTGATA
1 TTTTATTATATGTTATATTTTTAAATATATATTATTTATTCTATTATATTGATA
* * * *
5273670 TTTTATTATGTGTCATATATTTTT-ACTATATGTTATTTATTTTATTATATT
1 TTTTATTATATGT--TATATTTTTAAATATATATTATTTATTCTATTATATT
5273721 TTATCTATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
54 12 0.27
55 24 0.55
56 8 0.18
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (54 bp):
TTTTATTATATGTTATATTTTTAAATATATATTATTTATTCTATTATATTGATA
Found at i:5273724 original size:19 final size:19
Alignment explanation
Indices: 5273616--5273724 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 19
5273606 TTTTATAAAT
5273616 TTTTATTATATGTTATTT-
1 TTTTATTATATGTTATTTA
* *
5273634 TTTTAAATATATATTATTTA
1 TTTT-ATTATATGTTATTTA
* *
5273654 TTCTATTATAT-TGA--TA
1 TTTTATTATATGTTATTTA
* * *
5273670 TTTTATTATGTGTCATATA
1 TTTTATTATATGTTATTTA
*
5273689 TTTTTACTATATGTTATTTA
1 -TTTTATTATATGTTATTTA
*
5273709 TTTTATTATATTTTAT
1 TTTTATTATATGTTAT
5273725 CTATCATATA
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
16 11 0.15
17 2 0.03
18 6 0.08
19 34 0.48
20 18 0.25
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTATTATATGTTATTTA
Found at i:5275092 original size:26 final size:26
Alignment explanation
Indices: 5275059--5275168 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
5275049 TGATACAAAT
5275059 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* * * *
5275085 TGACAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5275111 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
5275137 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5275163 TGATAA
1 TGATAA
5275169 GAAATTCATG
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5277223 original size:136 final size:137
Alignment explanation
Indices: 5276954--5277239 Score: 511
Period size: 136 Copynumber: 2.1 Consensus size: 137
5276944 GAGTAGTCTC
*
5276954 CCCAAATGGGCTTGCATCTGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
5277019 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5277084 ACTGTTA
131 ACTGTTA
*
5277091 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5277155 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5277220 ACTGTTA
131 ACTGTTA
**
5277227 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5277240 AGGCCCAATG
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
136 124 0.87
137 19 0.13
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5279253 original size:26 final size:25
Alignment explanation
Indices: 5279218--5279267 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5279208 ATATATATCA
*
5279218 TAAAATAGCACATAAAAGAAATAAT
1 TAAAATAGCACATAAAAAAAATAAT
*
5279243 TAAACATAGCATATAAAAAAAATAA
1 TAAA-ATAGCACATAAAAAAAATAA
5279268 AACTATGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.20
Consensus pattern (25 bp):
TAAAATAGCACATAAAAAAAATAAT
Found at i:5279781 original size:22 final size:21
Alignment explanation
Indices: 5279746--5279821 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 21
5279736 AAAGGATATC
* *
5279746 TACAAATTAAATCTCCAAGAT
1 TACAAATCATATCTCCAAGAT
*
5279767 TACAAAATCATATCTTCAAGAT
1 TAC-AAATCATATCTCCAAGAT
* *
5279789 TGCATATCATATCT--AAGAT
1 TACAAATCATATCTCCAAGAT
* *
5279808 TGCATATCATATCT
1 TACAAATCATATCT
5279822 AAGATTGTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 19 0.39
21 13 0.27
22 17 0.35
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (21 bp):
TACAAATCATATCTCCAAGAT
Found at i:5279808 original size:19 final size:19
Alignment explanation
Indices: 5279773--5279870 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
5279763 AGATTACAAA
5279773 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
5279794 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
5279813 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
5279830 ATCATATCTAATATTGCAT
1 ATCATATCTAAGATTGCAT
5279849 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
5279868 ATC
1 ATC
5279871 CTTAAAGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 16 0.22
19 48 0.66
20 1 0.01
21 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:5279837 original size:36 final size:37
Alignment explanation
Indices: 5279773--5279870 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 37
5279763 AGATTACAAA
5279773 ATCATATCTTCAAGATTGCATATCATATCTAAGATTGCAT
1 ATCATATC-T-AAGATTG-ATATCATATCTAAGATTGCAT
*
5279813 ATCATATCTAAGATTG-TATCATATCTAATATTGCAT
1 ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
5279849 ATCATATCTAAGATTGCATATC
1 ATCATATCTAAGATTG-ATATC
5279871 CTTAAAGATT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
36 35 0.64
38 11 0.20
39 1 0.02
40 8 0.15
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (37 bp):
ATCATATCTAAGATTGATATCATATCTAAGATTGCAT
Found at i:5280010 original size:7 final size:7
Alignment explanation
Indices: 5279993--5280028 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
5279983 TTGAACTTTG
5279993 TTTTA-T
1 TTTTATT
5279999 TTTTATT
1 TTTTATT
5280006 TTTTATT
1 TTTTATT
5280013 TTTTATT
1 TTTTATT
5280020 TTTTATT
1 TTTTATT
5280027 TT
1 TT
5280029 AGTTTAAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:5281236 original size:57 final size:55
Alignment explanation
Indices: 5280994--5281514 Score: 356
Period size: 54 Copynumber: 9.6 Consensus size: 55
5280984 AAAAAAGGAT
* ** * *
5280994 TTTTTTTTGTGCTGGCCTGTCAATTCCCGGCACCAGTAATTTT-AAAAAAATCAAT
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGT-ATTTTAAAAAAAATTAAA
* ***
5281049 TTTTTTTGGTGGTGGCCTGTCAATGGCCGGCACCAGAATACAATTTTTTTTAAAAA--AAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAG--T---A-TTTTAAAAAAAATTAAA
** * * * *
5281108 -----TTGGTATTGGCTTGTCAATAGTCGGCACCAGTAATTTAAAAAAAAATTAAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGT-ATTTTAAAAAAAATTAAA
* * *
5281159 TTTTTTTTGTGCTGGTCTGTCAATGACCGGCACCAGTATTTTAAAAAAAAATTCAAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTTT-AAAAAAAATT-AAA
* * *
5281216 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGT-ATTTTAAAAAAAATTAAA
* * *
5281272 TTTTTTTGGTGCTGGCCTATCAATGGCTGACACCAGTA--TT-AAAAAAA-T-AA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTTTAAAAAAAATTAAA
* *
5281322 TTTTTTT-GTGCTGGTCTGTCAATGGCCGGCACCAGAATACGAGTTTT--CAAAAA--AAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAG--T---A-TTTTAAAAAAAATTAAA
** * * *
5281378 ----TTTGGTGCTGGCCTGTCAATGGCCAACATCA--ATATTAAAAAAAATTTGAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTTTAAAAAAAA-TTAAA
** * *
5281428 TTTTTTTTATGCTGGCCTATCAATGGCCGACACCAGTA--TTAAAAAAAATTCAAA
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTTTAAAAAAAATT-AAA
* *
5281482 TTTTTTTGGAGCTGGCCTGTTAATGGCCGGCAC
1 TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCAC
5281515 TAAATTTGAG
Statistics
Matches: 367, Mismatches: 61, Indels: 77
0.73 0.12 0.15
Matches are distributed among these distances:
45 3 0.01
46 1 0.00
47 5 0.01
49 32 0.09
50 13 0.04
51 5 0.01
52 11 0.03
53 26 0.07
54 92 0.25
55 37 0.10
56 77 0.21
57 48 0.13
58 4 0.01
59 4 0.01
60 4 0.01
61 5 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (55 bp):
TTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCAGTATTTTAAAAAAAATTAAA
Found at i:5281264 original size:113 final size:105
Alignment explanation
Indices: 5281115--5281352 Score: 296
Period size: 113 Copynumber: 2.2 Consensus size: 105
5281105 AAATTGGTAT
* * * * * * * *
5281115 TGGCTTGTCAATAGTCGGCACCAGTAATTTAAAAAAAAATTAAATTTTTTTTGTGCTGGTCTGTC
1 TGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAATTTTTTTGGTGCTGGCCTATC
*
5281180 AATGACCGGCACCAGTATTTTAAAAAAAAATTCAAATTTTTTTGGTGC
66 AATGACCGACACCAGTA--TT--AAAAAAA-T--AATTTTTTT-GTGC
5281228 TGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAATTTTTTTGGTGCTGGCCTATC
1 TGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAATTTTTTTGGTGCTGGCCTATC
* *
5281293 AATGGCTGACACCAGTATTAAAAAAATAATTTTTTTGTGC
66 AATGACCGACACCAGTATTAAAAAAATAATTTTTTTGTGC
*
5281333 TGGTCTGTCAATGGCCGGCA
1 TGGCCTGTCAATGGCCGGCA
5281353 CCAGAATACG
Statistics
Matches: 113, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
105 23 0.20
106 9 0.08
108 1 0.01
109 7 0.06
111 2 0.02
113 71 0.63
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (105 bp):
TGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAATTTTTTTGGTGCTGGCCTATC
AATGACCGACACCAGTATTAAAAAAATAATTTTTTTGTGC
Found at i:5281452 original size:156 final size:162
Alignment explanation
Indices: 5281220--5281514 Score: 440
Period size: 156 Copynumber: 1.9 Consensus size: 162
5281210 TTCAAATTTT
** *
5281220 TTTGGTGCTGGCCTGTCAATGGCCGGCAACAATAATTTAAAAAAAAATTAAATTTTTTTGGTGCT
1 TTTGGTGCTGGCCTGTCAATGGCCAACAACAATAATTTAAAAAAAAATTAAATTTTTTTGATGCT
* * *
5281285 GGCCTATCAATGGCTGACACCAGTATT-AAAAAAA-T-AATTTTTTT-GTGCTGGTCTGTCAATG
66 GGCCTATCAATGGCCGACACCAGTATTAAAAAAAATTAAATTTTTTTGGAGCTGGCCTGTCAATG
5281346 GCCGGCACCAGAATACGAGTTTTCAAAAAAAA
131 GCCGGCACCAGAATACGAGTTTTCAAAAAAAA
* * * *
5281378 TTTGGTGCTGGCCTGTCAATGGCCAACATCAAT-A-TTAAAAAAAATTTGAATTTTTTTTATGCT
1 TTTGGTGCTGGCCTGTCAATGGCCAACAACAATAATTTAAAAAAAAATTAAATTTTTTTGATGCT
*
5281441 GGCCTATCAATGGCCGACACCAGTATTAAAAAAAATTCAAATTTTTTTGGAGCTGGCCTGTTAAT
66 GGCCTATCAATGGCCGACACCAGTATTAAAAAAAATT-AAATTTTTTTGGAGCTGGCCTGTCAAT
5281506 GGCCGGCAC
130 GGCCGGCAC
5281515 TAAATTTGAG
Statistics
Matches: 121, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
156 51 0.42
157 8 0.07
158 31 0.26
160 9 0.07
161 22 0.18
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (162 bp):
TTTGGTGCTGGCCTGTCAATGGCCAACAACAATAATTTAAAAAAAAATTAAATTTTTTTGATGCT
GGCCTATCAATGGCCGACACCAGTATTAAAAAAAATTAAATTTTTTTGGAGCTGGCCTGTCAATG
GCCGGCACCAGAATACGAGTTTTCAAAAAAAA
Found at i:5284973 original size:131 final size:131
Alignment explanation
Indices: 5284803--5285058 Score: 419
Period size: 131 Copynumber: 2.0 Consensus size: 131
5284793 AGTTTAGAAA
* * *
5284803 ACATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCAC
1 ACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACAC
*
5284868 GATAGGGC-CTGATTCCCCGAATTGCCAAACGTCGAACACTT-CCTTCGTTTTAAAGAATTTCTA
66 GATAGGGCAC-GATTCCCCGAATTGCCAAACATCGAACA-TTGCCTTCGTTTTAAAGAATTTCTA
5284931 AGG
129 AGG
*
5284934 ACATGAGTGAAATT-TCAAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAATCCAACA
1 ACATGAGTGAAATTCT-AAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACA
5284998 CGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGAATTT
65 CGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGAATTT
5285059 TTAAATGAAT
Statistics
Matches: 117, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
130 3 0.03
131 113 0.97
132 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (131 bp):
ACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACAC
GATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGAATTTCTAAG
G
Found at i:5286676 original size:130 final size:130
Alignment explanation
Indices: 5286496--5286982 Score: 363
Period size: 130 Copynumber: 3.7 Consensus size: 130
5286486 TTGCCCTCAT
* *
5286496 TTTAAAGGATTTTTAAAAGAGCCGAGTGAAATTTTGAAGGGATATTTGATTACTTTAAAC-AATC
1 TTTAAGGGA-TTTTAAAAGAGCCGAGCGAAATTTTGAAGGGATATTTGATTACTTTAAACAAAT-
* ** * * * * *
5286560 GAGAAATTGCTATTCAACACGTTAGGGCGCGATCCCACGAAATGCCAAATACCACATATCGCCTT
64 GAGAAATTGCAACCCAACACGTTAAGGCACGATCCCACGAAATGCCAAACACCAAATATCACCTT
5286625 CG
129 CG
* * * * *
5286627 TTTTAGGGATTTTAAAAGA-CACGAGCGAAATTTT-AATGTGATATTTGATTATTTTGAGCAAAT
1 TTTAAGGGATTTTAAAAGAGC-CGAGCGAAATTTTGAA-GGGATATTTGATTACTTTAAACAAAT
* * * * * * *
5286690 GCGAAATTGCAACCCAACACGTTAAGGCACGATTCCGCGAATTGCCAAACATCAAATCTCATCTT
64 GAGAAATTGCAACCCAACACGTTAAGGCACGATCCCACGAAATGCCAAACACCAAATATCACCTT
5286755 CG
129 CG
*** *** * * * * * * * *
5286757 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAAGGAAATTCGATTATTTTGAGCAAATGC
1 TTTAAGGGATTTTAAAAGAGCCGAGCGAAATTTTGAAGGGATATTTGATTACTTTAAACAAATGA
* * * * * * *
5286822 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGC-AAATTGCCGAACATCAAATCTCATCTTC
66 GAAATTGCAACCCAACACGTTAAGGCACGATCCCACGAAA-TGCCAAACACCAAATATCACCTTC
5286886 G
130 G
*** *** ** * * * *
5286887 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCAAAGGGAAATTCGATTA-TCTTGAGCAAATG
1 TTTAAGGGATTTTAAAAGAGCCGAGCGAAATTTTGAAGGGATATTTGATTACT-TTAAACAAATG
* * *
5286951 CGAAATTTCAACCCAACACGTTAGGGCACGAT
65 AGAAATTGCAACCCAACACGTTAAGGCACGAT
5286983 TCCGCAAATT
Statistics
Matches: 310, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
129 6 0.02
130 292 0.94
131 12 0.04
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (130 bp):
TTTAAGGGATTTTAAAAGAGCCGAGCGAAATTTTGAAGGGATATTTGATTACTTTAAACAAATGA
GAAATTGCAACCCAACACGTTAAGGCACGATCCCACGAAATGCCAAACACCAAATATCACCTTCG
Found at i:5286983 original size:130 final size:130
Alignment explanation
Indices: 5286622--5287019 Score: 609
Period size: 130 Copynumber: 3.1 Consensus size: 130
5286612 CACATATCGC
* * * *** * * * * *
5286622 CTTCGTTTTAGGGATTTTAAAAGACACGAGCGAAATTTTAATGTGATATTTGATTATTTTGAGCA
1 CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTCAAAGGGAAATTCGATTATTTTGAGCA
* * *
5286687 AATGCGAAATTGCAACCCAACACGTTAAGGCACGATTCCGCGAATTGCCAAACATCAAATCTCAT
66 AATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCAAATTGCCGAACATCAAATCTCAT
5286752 CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAA-GGAAATTCGATTATTTTGAGC
1 CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTC-AAAGGGAAATTCGATTATTTTGAGC
5286816 AAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCAAATTGCCGAACATCAAATCTCA
65 AAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCAAATTGCCGAACATCAAATCTCA
5286881 T
130 T
*
5286882 CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTCAAAGGGAAATTCGATTATCTTGAGCA
1 CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTCAAAGGGAAATTCGATTATTTTGAGCA
* * * *
5286947 AATGCGAAATTTCAACCCAACACGTTAGGGCACGATTCCGCAAATTGTCGAACATCAAATTTCGT
66 AATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCAAATTGCCGAACATCAAATCTCAT
5287012 CTTCGTTT
1 CTTCGTTT
5287020 TGAAGAATTT
Statistics
Matches: 247, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
129 3 0.01
130 242 0.98
131 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (130 bp):
CTTCGTTTAAGGGATTTTAAAAGATATGAATAAAATTTCAAAGGGAAATTCGATTATTTTGAGCA
AATGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCAAATTGCCGAACATCAAATCTCAT
Found at i:5287590 original size:17 final size:18
Alignment explanation
Indices: 5287556--5287603 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 18
5287546 AAAATTTAAC
5287556 AAAATATATGATAGTACAAA
1 AAAATATATG--AGTACAAA
5287576 AAAATATATGA-TACAAA
1 AAAATATATGAGTACAAA
5287593 AAAATATATGA
1 AAAATATATGA
5287604 CAAAAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.61
18 1 0.04
20 10 0.36
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAATATATGAGTACAAA
Found at i:5290144 original size:43 final size:43
Alignment explanation
Indices: 5290091--5290280 Score: 114
Period size: 43 Copynumber: 4.3 Consensus size: 43
5290081 CAGCCTACTC
* * *
5290091 CACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTT
1 CACTGCAACTTTAGGGAGCTAGATTAGTAACTTAAATCTGCTT
* * * * ** **
5290134 CACTGCAACTTCAGGAAGTCAAGATTCGTCGTCTTCGATCTGC-T
1 CACTGCAACTTTAGGGAG-CTAGATTAGT-AACTTAAATCTGCTT
* * * * * * * * *
5290178 CTACTGCAACTTCAGGGAAACGAGATCTA-AAATTTCAACCTACTC
1 C-ACTGCAACTTTAGGG-AGCTAGAT-TAGTAACTTAAATCTGCTT
* *
5290223 CACTACAACTTTAGGGAGCTAGGTTAGTAACTTAAATCTGCTT
1 CACTGCAACTTTAGGGAGCTAGATTAGTAACTTAAATCTGCTT
*
5290266 CGCTGCAACTTTAGG
1 CACTGCAACTTTAGG
5290281 AAGTTAAGAT
Statistics
Matches: 106, Mismatches: 34, Indels: 14
0.69 0.22 0.09
Matches are distributed among these distances:
42 2 0.02
43 43 0.41
44 29 0.27
45 30 0.28
46 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
CACTGCAACTTTAGGGAGCTAGATTAGTAACTTAAATCTGCTT
Found at i:5290272 original size:132 final size:132
Alignment explanation
Indices: 5289952--5290594 Score: 880
Period size: 132 Copynumber: 4.9 Consensus size: 132
5289942 AATCGTCAGA
** * **
5289952 CTACTCCACTACAACTTTAGGGAGCTAGG-GCGAT-AATCTAAATCTGCTTCATTGCAACATT-A
1 CTACTCCACTACAACTTTAGGGAGCTAGGTTAG-TGACT-TAAATCTGCTTCGCTGCAAC-TTCA
* * * * * * * * * * * *
5290014 AGAAGCCTAGATTCATCGTCTTTGATCTGTTCCACTGCAA-TCCCAGGGAAACAAAATCTATATT
63 GGAAGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACT-TCAGGGAAACGAGATCTAAAAT
*
5290078 TCTCAGC
127 T-TCAAC
*
5290085 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCACTGCAACTTCAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
* *
5290150 AGTCAAGATTCGTCGTCTTCGATCTGCTCTACTGCAACTTCAGGGAAACGAGATCTAAAATTTCA
66 AGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTCA
5290215 AC
131 AC
* *
5290217 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTAACTTAAATCTGCTTCGCTGCAACTTTAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
* * ** *
5290282 AGTTAAGATTCGTTGTCTTTGATCTATTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTTA
66 AGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTCA
5290347 AC
131 AC
* *
5290349 CTACTCCGCTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGTAACTTCAGGA
1 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
* *
5290414 AGTCAAGATTCATTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTTA
66 AGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTCA
5290479 AC
131 AC
* * * *
5290481 CTACTCTACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTAGCTGCGACTTCAGAA
1 CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
*
5290546 AGTTAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAAC
66 AGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAAC
5290595 AGGATCTGTA
Statistics
Matches: 462, Mismatches: 44, Indels: 9
0.90 0.09 0.02
Matches are distributed among these distances:
132 357 0.77
133 101 0.22
134 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (132 bp):
CTACTCCACTACAACTTTAGGGAGCTAGGTTAGTGACTTAAATCTGCTTCGCTGCAACTTCAGGA
AGTCAAGATTCGTTGTCTTCGATCTGCTCCACTGCAACTTCAGGGAAACGAGATCTAAAATTTCA
AC
Found at i:5302626 original size:130 final size:130
Alignment explanation
Indices: 5302492--5302949 Score: 628
Period size: 130 Copynumber: 3.5 Consensus size: 130
5302482 AAACAATCGA
* * * ** * * * * * * **
5302492 GAAATTGCTACTCAACACGTTAGGGCGCGACCCCACAAAATGCCAAATACCACATATCGCCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAACATCAAATCTCATCTTCG
* * * ** ** * * *
5302557 TTTTAGGGATTTTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATAC
66 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
* * *
5302622 GAAATTGCAACCCAACACGTTAAGGCACGATTTCGCGAATTGCCAAACATCAAATCTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAACATCAAATCTCATCTTCG
5302687 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
66 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
*
5302752 GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCGAACATCAAATCTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAACATCAAATCTCATCTTCG
*
5302817 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATCTTGAGCAAATGC
66 TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
* * * *
5302882 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCGAACATCAAATTTCGTCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAACATCAAATCTCATCTTCG
5302947 TTT
66 TTT
5302950 TGAAGAATTT
Statistics
Matches: 294, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 294 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (130 bp):
GAAATTGCAACCCAACACGTTAGGGCACGATTCCACGAATTGCCAAACATCAAATCTCATCTTCG
TTTAAGGGATTTTAAAAGATATGAATAAAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
Found at i:5303536 original size:17 final size:18
Alignment explanation
Indices: 5303502--5303549 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 18
5303492 AAAAGTTAAC
5303502 AAAATATATGATAGTACAAA
1 AAAATATATG--AGTACAAA
5303522 AAAATATATGA-TACAAA
1 AAAATATATGAGTACAAA
5303539 AAAATATATGA
1 AAAATATATGA
5303550 CAAAAACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.61
18 1 0.04
20 10 0.36
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAATATATGAGTACAAA
Found at i:5307451 original size:22 final size:23
Alignment explanation
Indices: 5307416--5307465 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
5307406 TAAATAAAAT
**
5307416 AAAATTAGATAAATTGTATGAGAA
1 AAAATTAGATAAATTACATG-GAA
5307440 AAAATT-GA-AAATTACATGGAA
1 AAAATTAGATAAATTACATGGAA
5307461 AAAAT
1 AAAAT
5307466 GATAATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 8 0.33
23 2 0.08
24 6 0.25
ACGTcount: A:0.58, C:0.02, G:0.14, T:0.26
Consensus pattern (23 bp):
AAAATTAGATAAATTACATGGAA
Found at i:5307488 original size:27 final size:26
Alignment explanation
Indices: 5307458--5307670 Score: 81
Period size: 27 Copynumber: 8.3 Consensus size: 26
5307448 AAATTACATG
5307458 GAAAAAATGATAATTTAAATGAAATGA
1 GAAAAAA-GATAATTTAAATGAAATGA
* * *
5307485 GAAAAAAAATAAATTGAAATGAAACG-
1 GAAAAAAGAT-AATTTAAATGAAATGA
* *
5307511 G--TACA-A-AATTTAAATGAAAATTGA
1 GAAAAAAGATAATTTAAATG-AAA-TGA
*
5307535 -AAGAAAGATAAATTTAAATGAAATGA
1 GAAAAAAGAT-AATTTAAATGAAATGA
*** * *
5307561 GGAAAAATTTTAATTGAAATGAAATAA
1 -GAAAAAAGATAATTTAAATGAAATGA
* *
5307588 GAAAAAA-ATGAAATTAAAT---TTGA
1 GAAAAAAGAT-AATTTAAATGAAATGA
* *
5307611 -AAGAAAGATAAATTTAAATGAAATGG
1 GAAAAAAGAT-AATTTAAATGAAATGA
****
5307637 GAGAAACTTTTAATTTAAAT-AAGATGA
1 GA-AAAAAGATAATTTAAATGAA-ATGA
5307664 GAAAAAA
1 GAAAAAA
5307671 ATTAAATGGA
Statistics
Matches: 133, Mismatches: 34, Indels: 39
0.65 0.17 0.19
Matches are distributed among these distances:
21 9 0.07
22 8 0.06
23 14 0.11
24 2 0.02
25 3 0.02
26 27 0.20
27 52 0.39
28 18 0.14
ACGTcount: A:0.59, C:0.01, G:0.15, T:0.25
Consensus pattern (26 bp):
GAAAAAAGATAATTTAAATGAAATGA
Found at i:5307553 original size:22 final size:23
Alignment explanation
Indices: 5307528--5307584 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
5307518 ATTTAAATGA
*
5307528 AAATTGAAA-GAAAGATAAATTT
1 AAATTGAAATGAAAGAAAAATTT
*
5307550 AAA-TGAAATG-AGGAAAAATTT
1 AAATTGAAATGAAAGAAAAATTT
*
5307571 TAATTGAAATGAAA
1 AAATTGAAATGAAA
5307585 TAAGAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 16 0.57
22 11 0.39
23 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (23 bp):
AAATTGAAATGAAAGAAAAATTT
Found at i:5307555 original size:76 final size:76
Alignment explanation
Indices: 5307469--5307635 Score: 219
Period size: 76 Copynumber: 2.2 Consensus size: 76
5307459 AAAAAATGAT
** * * *
5307469 AATTTAAATGAAATGAGAAAAAAAATAAATTGAAATGAAA-CGGTACAAAATTTAAATGAAAATT
1 AATTTAAATGAAATGAGAAAAAAAATAAATTGAAATGAAATAAG-AAAAAAATGAAATGAAAATT
5307533 GAAAGAAAGATA
65 GAAAGAAAGATA
* ** * * *
5307545 AATTTAAATGAAATGAGGAAAAATTTTAATTGAAATGAAATAAGAAAAAAATGAAATTAAATTTG
1 AATTTAAATGAAATGAGAAAAAAAATAAATTGAAATGAAATAAGAAAAAAATGAAATGAAAATTG
5307610 AAAGAAAGATA
66 AAAGAAAGATA
5307621 AATTTAAATGAAATG
1 AATTTAAATGAAATG
5307636 GGAGAAACTT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
76 78 0.99
77 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.14, T:0.25
Consensus pattern (76 bp):
AATTTAAATGAAATGAGAAAAAAAATAAATTGAAATGAAATAAGAAAAAAATGAAATGAAAATTG
AAAGAAAGATA
Found at i:5307568 original size:49 final size:49
Alignment explanation
Indices: 5307469--5307579 Score: 120
Period size: 49 Copynumber: 2.3 Consensus size: 49
5307459 AAAAAATGAT
*
5307469 AATTTAAATG-AAATGAGAAAAAAAATAAATTGAAATGAAACGGTACAA
1 AATTTAAATGAAAATGAGAAAAAAAATAAATTGAAATGAAACGGGACAA
* * * *
5307517 AATTTAAATGAAAATTGA-AAGAAAGATAAATTTAAATGAAATGAGGA-AA
1 AATTTAAATGAAAA-TGAGAAAAAAAATAAATTGAAATGAAACG-GGACAA
*
5307566 AATTTTAATTGAAA
1 AA-TTTAAATGAAA
5307580 TGAAATAAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
48 10 0.19
49 28 0.53
50 15 0.28
ACGTcount: A:0.59, C:0.02, G:0.14, T:0.25
Consensus pattern (49 bp):
AATTTAAATGAAAATGAGAAAAAAAATAAATTGAAATGAAACGGGACAA
Found at i:5307633 original size:17 final size:17
Alignment explanation
Indices: 5307593--5307633 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5307583 AATAAGAAAA
*
5307593 AAATGAAATTAAATTTG
1 AAATGAAAATAAATTTG
5307610 AAA-GAAAGATAAATTT-
1 AAATGAAA-ATAAATTTG
5307626 AAATGAAA
1 AAATGAAA
5307634 TGGGAGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (17 bp):
AAATGAAAATAAATTTG
Found at i:5307648 original size:76 final size:76
Alignment explanation
Indices: 5307522--5307678 Score: 228
Period size: 76 Copynumber: 2.1 Consensus size: 76
5307512 TACAAAATTT
5307522 AAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAAAAATTTTAATTGAAATGAA-AT
1 AAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAAAAATTTTAATTGAAAT-AAGAT
5307586 AAGAAAAAAATG
65 AAGAAAAAAATG
* * * *
5307598 AAATTAAATTTGAAAGAAAGATAAATTTAAATGAAATG-GGAGAAACTTTTAATTTAAATAAGAT
1 AAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGA-AAAATTTTAATTGAAATAAGAT
* *
5307662 GAGAAAAAAATT
65 AAGAAAAAAATG
5307674 AAATG
1 AAATG
5307679 GAAAGATAGA
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 5 0.07
76 67 0.93
ACGTcount: A:0.58, C:0.01, G:0.15, T:0.26
Consensus pattern (76 bp):
AAATGAAAATTGAAAGAAAGATAAATTTAAATGAAATGAGGAAAAATTTTAATTGAAATAAGATA
AGAAAAAAATG
Found at i:5307766 original size:20 final size:20
Alignment explanation
Indices: 5307743--5307873 Score: 78
Period size: 21 Copynumber: 6.5 Consensus size: 20
5307733 ATTGAAAATT
*
5307743 TAAATGAAATGAGGAAAAAA
1 TAAATGAAATGAGAAAAAAA
*
5307763 T-AA--AAAT-AAAAATAAAA
1 TAAATGAAATGAGAAA-AAAA
*
5307780 TAAATGAATTGAGAAAAAAA
1 TAAATGAAATGAGAAAAAAA
*
5307800 TAAATTTAAATTGA-AAAAAAA
1 TAAA-TGAAA-TGAGAAAAAAA
*
5307821 TTTAAATGAAATGA-AATAAAA
1 --TAAATGAAATGAGAAAAAAA
5307842 TGAAGATGAAATGA-AAATGAAAA
1 T-AA-ATGAAATGAGAAA--AAAA
*
5307865 GAAATGAAA
1 TAAATGAAA
5307874 AAAAAAAAGA
Statistics
Matches: 88, Mismatches: 10, Indels: 25
0.72 0.08 0.20
Matches are distributed among these distances:
16 3 0.03
17 9 0.10
18 2 0.02
19 3 0.03
20 14 0.16
21 40 0.45
22 9 0.10
23 8 0.09
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (20 bp):
TAAATGAAATGAGAAAAAAA
Found at i:5307821 original size:17 final size:17
Alignment explanation
Indices: 5307795--5307831 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5307785 GAATTGAGAA
5307795 AAAAATAAATTTAAATTG
1 AAAAATAAATTTAAA-TG
5307813 AAAAA-AAATTTAAATG
1 AAAAATAAATTTAAATG
5307829 AAA
1 AAA
5307832 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 9 0.47
18 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AAAAATAAATTTAAATG
Found at i:5307834 original size:5 final size:5
Alignment explanation
Indices: 5307824--5307873 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
5307814 AAAAAAATTT
* *
5307824 AAATG AAATG AAATA AAATG AAGATG AAATG AAAATG AAAAG AAATG AAA
1 AAATG AAATG AAATG AAATG AA-ATG AAATG -AAATG AAATG AAATG AAA
5307874 AAAAAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (5 bp):
AAATG
Found at i:5307837 original size:16 final size:16
Alignment explanation
Indices: 5307818--5307874 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
5307808 AATTGAAAAA
*
5307818 AAATTTAAATGAAATG
1 AAATTAAAATGAAATG
5307834 AAA-TAAAATGAAGATG
1 AAATTAAAATGAA-ATG
* *
5307850 AAATGAAAATGAAAAG
1 AAATTAAAATGAAATG
*
5307866 AAATGAAAA
1 AAATTAAAA
5307875 AAAAAAAGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 8 0.22
16 20 0.56
17 8 0.22
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (16 bp):
AAATTAAAATGAAATG
Found at i:5308198 original size:19 final size:20
Alignment explanation
Indices: 5308174--5308257 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 20
5308164 ACCACTTCTA
*
5308174 ATTAATTTGAAAAAAA-AAT
1 ATTAATATGAAAAAAATAAT
5308193 ATTAATATGAAAAAAATAAT
1 ATTAATATGAAAAAAATAAT
*
5308213 ATGAAAAAATATGAAAAAAATAAT
1 AT----TAATATGAAAAAAATAAT
* * *
5308237 ATGAA-AAGAAAATAATAAT
1 ATTAATATGAAAAAAATAAT
5308256 AT
1 AT
5308258 GAAATGAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
19 29 0.53
20 7 0.13
24 19 0.35
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
ATTAATATGAAAAAAATAAT
Found at i:5308207 original size:17 final size:15
Alignment explanation
Indices: 5308185--5308253 Score: 62
Period size: 16 Copynumber: 4.9 Consensus size: 15
5308175 TTAATTTGAA
5308185 AAAAAAATATTAATATG
1 AAAAAAA-A-TAATATG
5308202 -AAAAAAATAATATG
1 AAAAAAAATAATATG
5308216 ----AAAA-AATATG
1 AAAAAAAATAATATG
5308226 -AAAAAAATAATATG
1 AAAAAAAATAATATG
5308240 AAAAGAAAATAATA
1 AAAA-AAAATAATA
5308254 ATATGAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
10 6 0.13
11 4 0.09
13 4 0.09
14 13 0.28
15 4 0.09
16 15 0.33
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (15 bp):
AAAAAAAATAATATG
Found at i:5308224 original size:24 final size:24
Alignment explanation
Indices: 5308196--5308243 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
5308186 AAAAAATATT
5308196 AATATGAAAAAAATAATATGAAAA
1 AATATGAAAAAAATAATATGAAAA
5308220 AATATGAAAAAAATAATATGAAAA
1 AATATGAAAAAAATAATATGAAAA
5308244 GAAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (24 bp):
AATATGAAAAAAATAATATGAAAA
Found at i:5308231 original size:43 final size:43
Alignment explanation
Indices: 5308180--5308295 Score: 130
Period size: 43 Copynumber: 2.7 Consensus size: 43
5308170 TCTAATTAAT
* *
5308180 TTGAAAAAAA-AATATTAATATGAAAAAAATAATATGAAA-AAA
1 TTGAAAAAAATAATATGAA-AAGAAAAAAATAATATGAAATAAA
* *
5308222 TATGAAAAAAATAATATGAAAAGAAAATAATAATATGAAATGAA
1 T-TGAAAAAAATAATATGAAAAGAAAAAAATAATATGAAATAAA
* *
5308266 TTGAAAAAAATACT-TGAAATGAAATAAAAT
1 TTGAAAAAAATAATATGAAAAGAAA-AAAAT
5308296 TAAATTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 10 0.16
43 43 0.68
44 10 0.16
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.24
Consensus pattern (43 bp):
TTGAAAAAAATAATATGAAAAGAAAAAAATAATATGAAATAAA
Found at i:5308261 original size:14 final size:14
Alignment explanation
Indices: 5308195--5308253 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
5308185 AAAAAAATAT
5308195 TAATATGAAAAAAA
1 TAATATGAAAAAAA
5308209 TAATATG---AAAA
1 TAATATGAAAAAAA
5308220 -AATATGAAAAAAA
1 TAATATGAAAAAAA
5308233 TAATATGAAAAGAAAA
1 TAATATG-AAA-AAAA
5308249 TAATA
1 TAATA
5308254 ATATGAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.15
11 4 0.10
13 4 0.10
14 13 0.33
15 3 0.08
16 9 0.23
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (14 bp):
TAATATGAAAAAAA
Found at i:5308264 original size:24 final size:23
Alignment explanation
Indices: 5308201--5308289 Score: 64
Period size: 24 Copynumber: 4.0 Consensus size: 23
5308191 ATATTAATAT
5308201 GAAAAAAATAATATGAAA--AAATA
1 GAAAAAAATAAT-TGAAATGAAA-A
5308224 TGAAAAAAATAA-T---ATGAAAA
1 -GAAAAAAATAATTGAAATGAAAA
* **
5308244 GAAAATAATAATATGAAATGAATT
1 GAAAAAAATAAT-TGAAATGAAAA
*
5308268 GAAAAAAATACTTGAAATGAAA
1 GAAAAAAATAATTGAAATGAAA
5308290 TAAAATTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
19 11 0.21
20 1 0.02
21 4 0.08
22 1 0.02
23 9 0.17
24 26 0.50
ACGTcount: A:0.66, C:0.01, G:0.11, T:0.21
Consensus pattern (23 bp):
GAAAAAAATAATTGAAATGAAAA
Found at i:5311723 original size:17 final size:17
Alignment explanation
Indices: 5311701--5311734 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5311691 GATATGATAC
5311701 TAAAAT-TATTAAAAAAA
1 TAAAATATA-TAAAAAAA
5311718 TAAAATATATAAAAAAA
1 TAAAATATATAAAAAAA
5311735 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATATATAAAAAAA
Found at i:5311734 original size:18 final size:17
Alignment explanation
Indices: 5311701--5311734 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5311691 GATATGATAC
*
5311701 TAAAATTATTAAAAAAA
1 TAAAATTATAAAAAAAA
5311718 TAAAATATATAAAAAAA
1 TAAAAT-TATAAAAAAA
5311735 CAGGGAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAATTATAAAAAAAA
Found at i:5312031 original size:23 final size:22
Alignment explanation
Indices: 5311988--5312045 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
5311978 AAAAGGTATC
* *
5311988 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5312009 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
5312032 TGCATATCATATCT
1 TACAAATCATATCT
5312046 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Done.