Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 116 of 208
Found at i:35257459 original size:51 final size:51
Alignment explanation
Indices: 35257403--35257515 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
35257393 TTCCAAAATT
35257403 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
* *
35257454 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTGAATTTC
1 CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
*
35257505 CCCTCAATTTC
1 CTCTCAATTTC
35257516 ATTTTTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.28, C:0.29, G:0.01, T:0.42
Consensus pattern (51 bp):
CTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTC
Found at i:35257543 original size:10 final size:10
Alignment explanation
Indices: 35257530--35257581 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
35257520 TTGAAAATAA
*
35257530 TTTTAAATTC
1 TTTTAAATTT
*
35257540 TTTTATATTT
1 TTTTAAATTT
**
35257550 TTTTAAAATAA
1 TTTT-AAATTT
35257561 TTTTAAATTT
1 TTTTAAATTT
*
35257571 TTTTATATTT
1 TTTTAAATTT
35257581 T
1 T
35257582 CATCAATGGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
10 26 0.79
11 7 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:35257558 original size:31 final size:31
Alignment explanation
Indices: 35257517--35257581 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
35257507 CTCAATTTCA
35257517 TTTTTGAAAATAATTTTAAATTCTTTTATAT
1 TTTTTGAAAATAATTTTAAATTCTTTTATAT
* *
35257548 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTGAAAATAATTTTAAATTCTTTTATAT
35257579 TTT
1 TTT
35257582 CATCAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTTGAAAATAATTTTAAATTCTTTTATAT
Found at i:35259358 original size:18 final size:18
Alignment explanation
Indices: 35259332--35259366 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35259322 AGGTGTGTTT
* *
35259332 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
35259350 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
35259367 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:35260241 original size:35 final size:35
Alignment explanation
Indices: 35260174--35260242 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
35260164 NNNNNACTGG
* *
35260174 TACTAACAATTAATAAGTAATAATATTGATAATTT
1 TACTAACAATTAATAAATAATAATATTAATAATTT
* *
35260209 TACTAACAATTAATACAATTATCA-ATTAATAATT
1 TACTAACAATTAATA-AATAATAATATTAATAATT
35260243 GAATAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (35 bp):
TACTAACAATTAATAAATAATAATATTAATAATTT
Found at i:35263584 original size:122 final size:123
Alignment explanation
Indices: 35263252--35263598 Score: 545
Period size: 123 Copynumber: 2.8 Consensus size: 123
35263242 CCCAAACTTG
** * *
35263252 CTACTGTAGCAAAATCGCACCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
* * *
35263317 TAGACGCGATTTTTTACTATTTGCTAAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
* * *
35263375 CTATTGTAGCAAAATCGCGTACACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
* *
35263440 TAGAGGCGGTTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
* *
35263498 CTACTGTAGCAAAATCGCGTCCGCGAGGGTGCGATTT-ACAATTTCTTCTCAAATAGCATCCTAG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
35263562 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACGTCAA
35263599 CTCGAAATAA
Statistics
Matches: 206, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
122 59 0.29
123 147 0.71
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (123 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTAG
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGAC
Found at i:35266556 original size:52 final size:52
Alignment explanation
Indices: 35266478--35266581 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
35266468 TTGTCTTTAA
35266478 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
1 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
*
35266530 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCGATTCCCATTCAAGT
1 TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
35266582 ATTTAAGCTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (52 bp):
TTAGCCACATTGCAAATGTCTTTATTGTCAGTCACCCAATTCCCATTCAAGT
Found at i:35267167 original size:22 final size:22
Alignment explanation
Indices: 35267142--35267186 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
35267132 TGCTTCCACC
35267142 ACTCCTATTCTTAACCCAAGTG
1 ACTCCTATTCTTAACCCAAGTG
35267164 ACTCCTATTCTTAACCCAAGTG
1 ACTCCTATTCTTAACCCAAGTG
35267186 A
1 A
35267187 ACCACCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (22 bp):
ACTCCTATTCTTAACCCAAGTG
Found at i:35270871 original size:20 final size:20
Alignment explanation
Indices: 35270822--35270871 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
35270812 ACAATTTAAA
*
35270822 ATATGAAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
* *
35270842 GTATATAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
*
35270862 ATGTAAAAAT
1 ATATAAAAAT
35270872 AACTTTTCCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
ATATAAAAATTTATTAATAT
Found at i:35270982 original size:19 final size:19
Alignment explanation
Indices: 35270958--35270996 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35270948 AAATATTTTC
*
35270958 AGTAAATTATTTTCCAGAA
1 AGTAAATCATTTTCCAGAA
*
35270977 AGTAAATCATTTTCTAGAA
1 AGTAAATCATTTTCCAGAA
35270996 A
1 A
35270997 TTATTTTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (19 bp):
AGTAAATCATTTTCCAGAA
Found at i:35270998 original size:33 final size:31
Alignment explanation
Indices: 35270948--35271009 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 31
35270938 AAACACTAGA
35270948 AAATATTTTCAGTAAATTATTTTCCAGAAAGT
1 AAATATTTTCAGTAAATTATTTTCC-GAAAGT
35270980 AAATCATTTTCTAG-AAATTATTTTCCGAAA
1 AAAT-ATTTTC-AGTAAATTATTTTCCGAAA
35271010 AATATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 8 0.29
33 18 0.64
34 2 0.07
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (31 bp):
AAATATTTTCAGTAAATTATTTTCCGAAAGT
Found at i:35272559 original size:19 final size:19
Alignment explanation
Indices: 35272521--35272559 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35272511 AAATACTTTA
*
35272521 AAAATATTTTTTTATTTTT
1 AAAATATTTTTTTATGTTT
*
35272540 AAAATATTTTTTTGTGTTT
1 AAAATATTTTTTTATGTTT
35272559 A
1 A
35272560 TTAAAAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
AAAATATTTTTTTATGTTT
Found at i:35273741 original size:17 final size:19
Alignment explanation
Indices: 35273704--35273741 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
35273694 ATTTTTCATC
*
35273704 AATAAGTGTCTTTCTAAAT
1 AATAAGTGTCTTTCAAAAT
35273723 AATAA-TGTCTTT-AAAAT
1 AATAAGTGTCTTTCAAAAT
35273740 AA
1 AA
35273742 ACACATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
AATAAGTGTCTTTCAAAAT
Found at i:35276081 original size:50 final size:50
Alignment explanation
Indices: 35275968--35276257 Score: 309
Period size: 50 Copynumber: 5.7 Consensus size: 50
35275958 ATTTGGGTAA
*
35275968 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* * *
35276024 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
35276074 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
35276124 AGAGGTCCCCAAT-T-AGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGT-CCC-ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
35276174 AGAACTCCCATGTAAGGCCATATCTGGGATATGGAATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* **
35276223 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
35276258 TTTAGCATGT
Statistics
Matches: 203, Mismatches: 26, Indels: 17
0.83 0.11 0.07
Matches are distributed among these distances:
48 3 0.01
49 36 0.18
50 114 0.56
51 4 0.02
52 2 0.01
53 3 0.01
55 1 0.00
56 40 0.20
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:35282610 original size:11 final size:11
Alignment explanation
Indices: 35282596--35282621 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35282586 CCCCTTGCCA
35282596 CCTTAATCCAG
1 CCTTAATCCAG
35282607 CCTTAATCCAG
1 CCTTAATCCAG
35282618 CCTT
1 CCTT
35282622 GAAAGCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (11 bp):
CCTTAATCCAG
Found at i:35291654 original size:18 final size:18
Alignment explanation
Indices: 35291602--35291654 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 18
35291592 AATTTTACCC
35291602 TCTCCAGGAGGTCATTAA
1 TCTCCAGGAGGTCATTAA
***
35291620 TCTCC--TCCGTCATTAA
1 TCTCCAGGAGGTCATTAA
*
35291636 TCTCCAGGAGGTCACTAA
1 TCTCCAGGAGGTCATTAA
35291654 T
1 T
35291655 TTCCTTTGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 4
0.70 0.19 0.11
Matches are distributed among these distances:
16 13 0.50
18 13 0.50
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (18 bp):
TCTCCAGGAGGTCATTAA
Found at i:35292280 original size:15 final size:15
Alignment explanation
Indices: 35292260--35292292 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
35292250 CCCAACAGGT
35292260 AAAAAAAG-AAAAGTA
1 AAAAAAAGTAAAAG-A
35292275 AAAAAAAGTAAAAGA
1 AAAAAAAGTAAAAGA
35292290 AAA
1 AAA
35292293 CATCGAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAAAGTAAAAGA
Found at i:35292283 original size:10 final size:11
Alignment explanation
Indices: 35292263--35292292 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
35292253 AACAGGTAAA
35292263 AAAAGAAAAGT
1 AAAAGAAAAGT
35292274 AAAA-AAAAGT
1 AAAAGAAAAGT
35292284 AAAAGAAAA
1 AAAAGAAAA
35292293 CATCGAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAAGAAAAGT
Found at i:35293581 original size:17 final size:17
Alignment explanation
Indices: 35293559--35293591 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35293549 AAACAACATA
*
35293559 ACTCTTGACCTTTCATG
1 ACTCTTAACCTTTCATG
35293576 ACTCTTAACCTTTCAT
1 ACTCTTAACCTTTCAT
35293592 ATAATATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.30, G:0.06, T:0.42
Consensus pattern (17 bp):
ACTCTTAACCTTTCATG
Found at i:35297906 original size:17 final size:17
Alignment explanation
Indices: 35297884--35297916 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35297874 AAACAACATA
35297884 ACTCTTGACATTTCATG
1 ACTCTTGACATTTCATG
*
35297901 ACTCTTGACCTTTCAT
1 ACTCTTGACATTTCAT
35297917 ATAACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.27, G:0.09, T:0.42
Consensus pattern (17 bp):
ACTCTTGACATTTCATG
Found at i:35306219 original size:17 final size:17
Alignment explanation
Indices: 35306197--35306234 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
35306187 AATTATGTTA
35306197 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAGAGT
35306214 TATGAAAGGTCAAGAGT
1 TATGAAAGGTCAAGAGT
35306231 TATG
1 TATG
35306235 TTGTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.26
Consensus pattern (17 bp):
TATGAAAGGTCAAGAGT
Found at i:35308150 original size:29 final size:28
Alignment explanation
Indices: 35308118--35308178 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
35308108 CAAAGCCGTT
35308118 TTTTTTCAAAATTTACCAAAATGGGCCGA
1 TTTTTTCAAAATTTACCAAAATGGGCC-A
* *** *
35308147 TTTTTTGATTGTTTACCGAAATGGGCCA
1 TTTTTTCAAAATTTACCAAAATGGGCCA
35308175 TTTT
1 TTTT
35308179 CTAGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCAAAATGGGCCA
Found at i:35308499 original size:22 final size:22
Alignment explanation
Indices: 35308471--35308518 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
35308461 TCTAATCCTT
35308471 TCAATTTCCTTCCAAAATTCAC
1 TCAATTTCCTTCCAAAATTCAC
*
35308493 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCAC
35308515 TCAA
1 TCAA
35308519 ACCCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCAC
Found at i:35308550 original size:22 final size:22
Alignment explanation
Indices: 35308525--35308605 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 22
35308515 TCAAACCCAT
35308525 ATTTAATTTCAATTTCCTCTCA
1 ATTTAATTTCAATTTCCTCTCA
** * *
35308547 ATTTCCTTCCAAAATTCTCTCAATTCA
1 ATTTAATTTC-AATTTC-CTC---TCA
*
35308574 TATTTAATTTCAATTTCCCCTCA
1 -ATTTAATTTCAATTTCCTCTCA
*
35308597 ATTTCATTT
1 ATTTAATTT
35308606 TTTAAAATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
22 15 0.35
23 8 0.19
24 3 0.07
26 2 0.05
27 8 0.19
28 7 0.16
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTAATTTCAATTTCCTCTCA
Found at i:35308597 original size:50 final size:51
Alignment explanation
Indices: 35308492--35308601 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 51
35308482 CCAAAATTCA
*
35308492 CTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCT
1 CTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCC
**
35308543 CTCAATTTCCTTCCAAAATTCTCTC-AATTCATATTTAATTTCAATTTCCC
1 CTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCC
35308593 CTCAATTTC
1 CTCAATTTC
35308602 ATTTTTTAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 31 0.55
51 25 0.45
ACGTcount: A:0.28, C:0.29, G:0.00, T:0.43
Consensus pattern (51 bp):
CTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATTTCCC
Found at i:35308628 original size:10 final size:10
Alignment explanation
Indices: 35308602--35308660 Score: 75
Period size: 10 Copynumber: 5.8 Consensus size: 10
35308592 CCTCAATTTC
35308602 ATTTTTTAAA
1 ATTTTTTAAA
35308612 ATATTTTTAAA
1 AT-TTTTTAAA
35308623 A-TTTTTAAA
1 ATTTTTTAAA
35308632 ATTTTTTAAA
1 ATTTTTTAAA
*
35308642 ATAATTTTAAA
1 AT-TTTTTAAA
*
35308653 TTTTTTTA
1 ATTTTTTA
35308661 TATTTTCATC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
9 9 0.21
10 17 0.40
11 17 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:35308653 original size:20 final size:19
Alignment explanation
Indices: 35308604--35308660 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 19
35308594 TCAATTTCAT
35308604 TTTTTAAAATATTTTTAAAA
1 TTTTTAAAAT-TTTTTAAAA
35308624 TTTTTAAAATTTTTTAAAA
1 TTTTTAAAATTTTTTAAAA
*
35308643 TAATTTTAAATTTTTTTA
1 T--TTTTAAAATTTTTTA
35308661 TATTTTCATC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 10 0.29
20 10 0.29
21 14 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAAAATTTTTTAAAA
Found at i:35308666 original size:30 final size:30
Alignment explanation
Indices: 35308602--35308658 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
35308592 CCTCAATTTC
*
35308602 ATTTTTTAAAATATTTTTAAAATTTTTAAA
1 ATTTTTTAAAATAATTTTAAAATTTTTAAA
*
35308632 ATTTTTTAAAATAATTTTAAATTTTTT
1 ATTTTTTAAAATAATTTTAAAATTTTT
35308659 TATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
ATTTTTTAAAATAATTTTAAAATTTTTAAA
Found at i:35309757 original size:7 final size:7
Alignment explanation
Indices: 35309745--35309769 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35309735 AGTCGATTGA
35309745 TATTTAG
1 TATTTAG
35309752 TATTTAG
1 TATTTAG
35309759 TATTTAG
1 TATTTAG
35309766 TATT
1 TATT
35309770 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:35310447 original size:18 final size:18
Alignment explanation
Indices: 35310421--35310455 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35310411 AGGTGTGTTT
* *
35310421 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
35310439 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
35310456 TCCTTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:35310898 original size:25 final size:26
Alignment explanation
Indices: 35310870--35310928 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
35310860 TTATCTGATG
35310870 TAATAAAATAAAAGTT-TATTTAATA
1 TAATAAAATAAAAGTTCTATTTAATA
* * *
35310895 TAATAAAATAGAAGTTCTATTTGATG
1 TAATAAAATAAAAGTTCTATTTAATA
35310921 TAATAAAA
1 TAATAAAA
35310929 ACCCTAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
TAATAAAATAAAAGTTCTATTTAATA
Found at i:35310965 original size:19 final size:18
Alignment explanation
Indices: 35310924--35310972 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
35310914 TTTGATGTAA
* *
35310924 TAAAAACCCTAATTTGAT
1 TAAAAACCCTAACTTAAT
35310942 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
35310960 TAAAAACTCTAAC
1 TAAAAACCCTAAC
35310973 CCTAACCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:35310991 original size:29 final size:29
Alignment explanation
Indices: 35310949--35311171 Score: 258
Period size: 29 Copynumber: 8.2 Consensus size: 29
35310939 GATTAAAAAC
*
35310949 CCTAACTTAATTAAAAACTCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
*
35310978 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *
35311007 CCTAATTTAATTAAAAACCCTAA-CTTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
* *****
35311035 -TTAA---AAACCCTAACCCTAA--C---
1 CCTAACTTAATTAAAAACCCTAACCCTAA
35311055 --T--CTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
35311080 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
35311109 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
35311138 CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAA
35311167 CCTAA
1 CCTAA
35311172 TTTTACATAA
Statistics
Matches: 167, Mismatches: 15, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
22 1 0.01
24 10 0.06
27 4 0.02
28 4 0.02
29 137 0.82
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (29 bp):
CCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:35311021 original size:58 final size:58
Alignment explanation
Indices: 35310949--35311171 Score: 321
Period size: 58 Copynumber: 4.1 Consensus size: 58
35310939 GATTAAAAAC
* *
35310949 CCTAACTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
*
35311007 CCTAATTTAATT--AAA----AA--C---CCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
35311054 -CT--CTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
35311109 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
1 CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
35311167 CCTAA
1 CCTAA
35311172 TTTTACATAA
Statistics
Matches: 148, Mismatches: 3, Indels: 28
0.83 0.02 0.16
Matches are distributed among these distances:
44 6 0.04
46 5 0.03
47 28 0.19
50 3 0.02
52 3 0.02
55 29 0.20
56 5 0.03
58 69 0.47
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (58 bp):
CCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAA
Found at i:35311034 original size:18 final size:18
Alignment explanation
Indices: 35311007--35311048 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
35310997 CTAACCCTAA
*
35311007 CCTAATTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
35311025 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
35311043 CCTAAC
1 CCTAAC
35311049 CCTAACTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:35311074 original size:102 final size:100
Alignment explanation
Indices: 35310946--35311132 Score: 329
Period size: 102 Copynumber: 1.9 Consensus size: 100
35310936 TTTGATTAAA
* *
35310946 AACCCTAACTTAATTAAAAACTCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTA
1 AACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTA
*
35311011 ATTTAATTAAAAACCCTAACTTAATTAAAAACCCT
66 ACTTAATTAAAAACCCTAACTTAATTAAAAACCCT
35311046 AACCCTAACTCTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACC
1 AACCCTAA--CTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACC
35311111 TAACTTAATTAAAAACCCTAAC
64 TAACTTAATTAAAAACCCTAAC
35311133 CCTAACCTAA
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
100 8 0.10
102 74 0.90
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.26
Consensus pattern (100 bp):
AACCCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTA
ACTTAATTAAAAACCCTAACTTAATTAAAAACCCT
Found at i:35311230 original size:55 final size:54
Alignment explanation
Indices: 35311169--35311415 Score: 305
Period size: 55 Copynumber: 4.3 Consensus size: 54
35311159 AACCCTAACC
*
35311169 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATT-TTGGACTTAA
*
35311224 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACA-AAATTTTGGACTTAA
** * *
35311279 TAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTTTGGCTTAATAAATTTAC
1 TAATTTTACATAATTTGATAATTTTA-CTAA--CCATTAACAAAATTTTGG--------ACTTA-
35311344 A
54 A
35311345 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTT-GGACTTAA
35311400 TAATTTTACATAATTT
1 TAATTTTACATAATTT
35311416 TACATAATGT
Statistics
Matches: 167, Mismatches: 11, Indels: 28
0.81 0.05 0.14
Matches are distributed among these distances:
55 92 0.55
56 11 0.07
57 8 0.05
58 6 0.04
63 13 0.08
64 2 0.01
65 8 0.05
66 27 0.16
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.44
Consensus pattern (54 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAATTTTGGACTTAA
Found at i:35311301 original size:18 final size:18
Alignment explanation
Indices: 35311278--35311312 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35311268 TTTGGACTTA
35311278 ATAATTTTACATAATTTG
1 ATAATTTTACATAATTTG
*
35311296 ATAATTTTACCTAATTT
1 ATAATTTTACATAATTT
35311313 AATTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.03, T:0.51
Consensus pattern (18 bp):
ATAATTTTACATAATTTG
Found at i:35311367 original size:56 final size:62
Alignment explanation
Indices: 35311223--35311423 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
35311213 GTTGGACTTA
* *
35311223 ATAATTTTACATAATTTGA-TAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTA
1 ATAATTTTACATAATTTGACTAA-TTTA-TAA-CATTAA-AAAAATTTTGGACTTAATAATTTTA
35311287 C
62 C
* * *
35311288 ATAA-TTT-GATAATTTTACCTAA-TT-T-A-ATTAAAAAAATTTTGG-CTTAATAAATTTAC
1 ATAATTTTACATAATTTGA-CTAATTTATAACATTAAAAAAATTTTGGACTTAATAATTTTAC
*
35311344 ATAATTTTACATAATTTGA-TAATTTTACTAACCATTAACAAAATTTTGGGACTTAATAATTTTA
1 ATAATTTTACATAATTTGACTAA-TTTA-TAA-CATTAAAAAAATTTT-GGACTTAATAATTTTA
35311408 C
62 C
35311409 ATAATTTTACATAAT
1 ATAATTTTACATAAT
35311424 GTTAGATTTG
Statistics
Matches: 114, Mismatches: 9, Indels: 26
0.77 0.06 0.17
Matches are distributed among these distances:
56 20 0.18
57 12 0.11
58 15 0.13
60 2 0.02
61 2 0.02
63 23 0.20
64 5 0.04
65 35 0.31
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (62 bp):
ATAATTTTACATAATTTGACTAATTTATAACATTAAAAAAATTTTGGACTTAATAATTTTAC
Found at i:35311414 original size:10 final size:10
Alignment explanation
Indices: 35311399--35311423 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35311389 TTGGGACTTA
35311399 ATAATTTTAC
1 ATAATTTTAC
35311409 ATAATTTTAC
1 ATAATTTTAC
35311419 ATAAT
1 ATAAT
35311424 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:35311423 original size:65 final size:65
Alignment explanation
Indices: 35311278--35311423 Score: 215
Period size: 65 Copynumber: 2.2 Consensus size: 65
35311268 TTTGGACTTA
*
35311278 ATAATTTTACATAATTTGATAATTTTACCTAATTTAATTAAAAAAATTTTGGCTTAATAAATTTA
1 ATAATTTTACATAATTTGATAATTTTACCTAA-TCAATTAAAAAAATTTTGGCTTAATAAATTTA
35311343 C
65 C
* * *
35311344 ATAATTTTACATAATTTGATAATTTTA-CTAA-CCATTAACAAAATTTTGGGACTTAATAATTTT
1 ATAATTTTACATAATTTGATAATTTTACCTAATCAATTAAAAAAATTTT-GG-CTTAATAAATTT
35311407 AC
64 AC
35311409 ATAATTTTACATAAT
1 ATAATTTTACATAAT
35311424 GTTAGATTTG
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
63 13 0.18
64 2 0.03
65 32 0.43
66 27 0.36
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (65 bp):
ATAATTTTACATAATTTGATAATTTTACCTAATCAATTAAAAAAATTTTGGCTTAATAAATTTAC
Found at i:35314730 original size:124 final size:124
Alignment explanation
Indices: 35314510--35314735 Score: 391
Period size: 124 Copynumber: 1.8 Consensus size: 124
35314500 CCCAAACTTG
*
35314510 CTACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
*
35314575 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTACATGAA
* * *
35314634 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTTAAATAACATCCTGG
1 CTACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
35314699 TAGAAGCGATTTTATACTATTTGAC-CAGAAACATCAA
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAA
35314736 CACGAAATAA
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
124 95 0.99
125 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCATCCACGAGGGCGCGATTTCACAATTTATTCTCAAATAACATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAAAAAAAATTATTTCTTACATGAA
Found at i:35329915 original size:31 final size:31
Alignment explanation
Indices: 35329877--35329937 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
35329867 TGTATGAAGG
*
35329877 TTTAAGTCTTTAGAATTGACTTAGTAACTTT
1 TTTAAGTCTTTAGAATTGACTTAGGAACTTT
35329908 TTTAAGTCTTTAGAATTGACTTAGGAACTT
1 TTTAAGTCTTTAGAATTGACTTAGGAACTT
35329938 CTTTCGATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.46
Consensus pattern (31 bp):
TTTAAGTCTTTAGAATTGACTTAGGAACTTT
Found at i:35333221 original size:38 final size:39
Alignment explanation
Indices: 35333175--35333274 Score: 121
Period size: 38 Copynumber: 2.6 Consensus size: 39
35333165 GAAATCTTTG
* * * *
35333175 TTATAATTATTGAAATTATAATTTATGATT-GAATATTA
1 TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
* *
35333213 TTATAATTATTGTAATTGTAATTTTTCATTCAAACATTA
1 TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
* *
35333252 TTATAAATATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
35333275 ATTACATTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
38 26 0.50
39 26 0.50
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (39 bp):
TTATAATTATTGTAATTATAATTTATCATTCAAACATTA
Found at i:35334899 original size:17 final size:17
Alignment explanation
Indices: 35334852--35334899 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
35334842 CTCTTGTGAG
*
35334852 AGCAATCTTATTGCCAC
1 AGCAATCCTATTGCCAC
* * *
35334869 TGCAAGCCTTTTGCCAC
1 AGCAATCCTATTGCCAC
35334886 AGCAATCCTATTGC
1 AGCAATCCTATTGC
35334900 TGTCACAAGC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (17 bp):
AGCAATCCTATTGCCAC
Found at i:35339951 original size:25 final size:25
Alignment explanation
Indices: 35339923--35339983 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
35339913 TGTACCTGAA
* * *
35339923 TATCAGGCTTTATGTCAGTGTTATT
1 TATCGGGCTTTATGCCAGTGTTATC
*
35339948 TATCGGGCTTTATGCCGGTGTTATC
1 TATCGGGCTTTATGCCAGTGTTATC
35339973 TATCGGGCTTT
1 TATCGGGCTTT
35339984 GTGATGGTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (25 bp):
TATCGGGCTTTATGCCAGTGTTATC
Found at i:35339992 original size:25 final size:25
Alignment explanation
Indices: 35339940--35340010 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
35339930 CTTTATGTCA
* *
35339940 GTGTTATTTATCGGGCTTTATGCCG
1 GTGTTATTTATCGGGCTTTGTGACG
* *
35339965 GTGTTATCTATCGGGCTTTGTGATG
1 GTGTTATTTATCGGGCTTTGTGACG
* *
35339990 GTG-AATTTATCTGGCTTTGTG
1 GTGTTATTTATCGGGCTTTGTG
35340011 CCTAGCAAGC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 15 0.38
25 24 0.62
ACGTcount: A:0.13, C:0.13, G:0.30, T:0.45
Consensus pattern (25 bp):
GTGTTATTTATCGGGCTTTGTGACG
Found at i:35340023 original size:40 final size:40
Alignment explanation
Indices: 35339979--35340066 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
35339969 TATCTATCGG
35339979 GCTTTGTGAT-GGTGAATTTATCTG-GCTTTGTGCCTAGCAA
1 GCTTTGTG-TCGGTGAATTTATC-GAGCTTTGTGCCTAGCAA
** *
35340019 GCTTTGTGTCGGTGTGTTTATCGAGCTTTGTGCCTAGCAG
1 GCTTTGTGTCGGTGAATTTATCGAGCTTTGTGCCTAGCAA
*
35340059 GCCTTGTG
1 GCTTTGTG
35340067 CTAGGTTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.12, C:0.17, G:0.31, T:0.40
Consensus pattern (40 bp):
GCTTTGTGTCGGTGAATTTATCGAGCTTTGTGCCTAGCAA
Found at i:35340282 original size:110 final size:111
Alignment explanation
Indices: 35340102--35340421 Score: 414
Period size: 110 Copynumber: 2.9 Consensus size: 111
35340092 CGGTGATCAT
* * *
35340102 TTAGTACGTGCTATGTACC-ATTGATACAGACAC-TAACGATGGCTTGAGATCCTGCATATGTTG
1 TTAGTAGGTACTATGTACCGA-TGATACAGAC-CGTAACGATGGCTTGAGATCCTACATATGTTG
* * * * *
35340165 CAGATTCTCTGCAGCTTATGTGAGCAGCATCGTGAGCCG-GGGGTTAA
64 CGGATTCTCTACAGCTTGTGTGAGCAGCATCATGAGCCGAGGGATTAA
** * *
35340212 TTAGTAGGTACTATGTACCGATGATACAGGTCGTAACGTTGGCTTGAGATCCTACATATGTTGTG
1 TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTACATATGTTGCG
* *
35340277 GATTCTCTACAACTTGTGTGAGCAGTATCATGAG-CGAGGGATTAA
66 GATTCTCTACAGCTTGTGTGAGCAGCATCATGAGCCGAGGGATTAA
* * * *
35340322 TTAGTAGGTACTATGTACTGGTGATACAGACCGTAACGATGGCTTGAGATCCTACATGTATTGCG
1 TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTACATATGTTGCG
* *
35340387 GATTCTCTATAGCTTGTGTGAGTAGCATCATGAGC
66 GATTCTCTACAGCTTGTGTGAGCAGCATCATGAGC
35340422 TGGTCAAAGT
Statistics
Matches: 180, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
109 3 0.02
110 176 0.98
111 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (111 bp):
TTAGTAGGTACTATGTACCGATGATACAGACCGTAACGATGGCTTGAGATCCTACATATGTTGCG
GATTCTCTACAGCTTGTGTGAGCAGCATCATGAGCCGAGGGATTAA
Found at i:35343263 original size:18 final size:18
Alignment explanation
Indices: 35343240--35343274 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35343230 TTAAGAATCT
*
35343240 TGGGCCTACATGCCCGTA
1 TGGGCCTACACGCCCGTA
35343258 TGGGCCTACACGCCCGT
1 TGGGCCTACACGCCCGT
35343275 GTGGCCCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.37, G:0.29, T:0.20
Consensus pattern (18 bp):
TGGGCCTACACGCCCGTA
Found at i:35349511 original size:26 final size:25
Alignment explanation
Indices: 35349464--35349537 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 25
35349454 TTTATCACCC
*
35349464 CAATTTTATCCAAGTAAAATTTTGA
1 CAATTTTACCCAAGTAAAATTTTGA
*
35349489 CAATTTTACCCACGCTAAAATTTTGA
1 CAATTTTACCCAAG-TAAAATTTTGA
* *
35349515 CGATTTTACCCTTAGTAAAATTT
1 CAATTTTACCC-AAGTAAAATTT
35349538 CGAAAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 12 0.29
26 29 0.69
27 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (25 bp):
CAATTTTACCCAAGTAAAATTTTGA
Found at i:35351615 original size:38 final size:40
Alignment explanation
Indices: 35351540--35351627 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 40
35351530 ATAAAAGTAT
*
35351540 ATTTT-TTT-ATAATTTTTATAATTTTTAATAATGTTAAA
1 ATTTTATTTAATAATTTTTATAATTTTAAATAATGTTAAA
35351578 ATTTTATTTAATAATTTTT-TAAATTTTAAAT-AT-TTAAA
1 ATTTTATTTAATAATTTTTAT-AATTTTAAATAATGTTAAA
**
35351616 AAATTATTTAAT
1 ATTTTATTTAAT
35351628 TATTGACGTG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
38 20 0.45
39 6 0.14
40 18 0.41
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (40 bp):
ATTTTATTTAATAATTTTTATAATTTTAAATAATGTTAAA
Found at i:35351750 original size:12 final size:12
Alignment explanation
Indices: 35351707--35351744 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
35351697 AAGATAATTT
*
35351707 AATAAAAATAAA
1 AATATAAATAAA
*
35351719 AATATAAATATA
1 AATATAAATAAA
35351731 AATATAAATAAA
1 AATATAAATAAA
35351743 AA
1 AA
35351745 GCTAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATATAAATAAA
Found at i:35359137 original size:2 final size:2
Alignment explanation
Indices: 35359130--35359173 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
35359120 TTTTGTTTTA
35359130 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
35359172 AT
1 AT
35359174 TACCTTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35359608 original size:16 final size:17
Alignment explanation
Indices: 35359576--35359737 Score: 76
Period size: 17 Copynumber: 8.8 Consensus size: 17
35359566 CCCGATATAG
* *
35359576 TAAATATATTTATTTTT
1 TAAATATTTTTAATTTT
35359593 TAAAT-TTTTTAATTTT
1 TAAATATTTTTAATTTT
* *
35359609 AAAATAAATATATTTATTTTT
1 ----TAAATATTTTTAATTTT
35359630 TAAAT-TTTTTAATTTT
1 TAAATATTTTTAATTTT
*
35359646 AAAATATTTTTAAAATACTTTT
1 TAAATATTTTT---A-A-TTTT
* *
35359668 TTATTATTTTTTAATTTT
1 TAAATA-TTTTTAATTTT
*
35359686 AAAATATTTTTAAAATACTTTT
1 TAAATATTTTT---A-A-TTTT
* *
35359708 TAATTTTTTTTAATTTT
1 TAAATATTTTTAATTTT
*
35359725 AAAATATTTTTAA
1 TAAATATTTTTAA
35359738 AATACTTTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 34
0.67 0.12 0.21
Matches are distributed among these distances:
16 22 0.20
17 34 0.31
18 8 0.07
19 2 0.02
20 8 0.07
21 11 0.10
22 19 0.17
23 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAATATTTTTAATTTT
Found at i:35359618 original size:37 final size:37
Alignment explanation
Indices: 35359576--35359651 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
35359566 CCCGATATAG
35359576 TAAATATATTTATTTTTTAAATTTTTTAATTTTAAAA
1 TAAATATATTTATTTTTTAAATTTTTTAATTTTAAAA
35359613 TAAATATATTTATTTTTTAAATTTTTTAATTTTAAAA
1 TAAATATATTTATTTTTTAAATTTTTTAATTTTAAAA
35359650 TA
1 TA
35359652 TTTTTAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
TAAATATATTTATTTTTTAAATTTTTTAATTTTAAAA
Found at i:35359680 original size:40 final size:40
Alignment explanation
Indices: 35359588--35359756 Score: 224
Period size: 39 Copynumber: 4.4 Consensus size: 40
35359578 AATATATTTA
** * **
35359588 TTTTTTA-AATTTTTTAATTTTAAAATAAATAT-ATTTA-
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
35359625 TTTTTTA-AATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
*
35359664 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
* *
35359704 TTTTTAAT-TTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
35359743 TTTTTT-TAATTTTT
1 TTTTTTATAATTTTT
35359757 AAAATAAATT
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
37 29 0.25
38 4 0.03
39 47 0.40
40 38 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (40 bp):
TTTTTTATAATTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:35359685 original size:29 final size:29
Alignment explanation
Indices: 35359653--35359714 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
35359643 TTTAAAATAT
* * *
35359653 TTTTAAAATACTTTTT-TATTATTTTTTAA
1 TTTTAAAATA-TTTTTAAAATACTTTTTAA
35359682 TTTTAAAATATTTTTAAAATACTTTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTAA
35359711 TTTT
1 TTTT
35359715 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:35359709 original size:12 final size:11
Alignment explanation
Indices: 35359642--35359747 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
35359632 AATTTTTTAA
35359642 TTTTAAAATAT
1 TTTTAAAATAT
35359653 TTTTAAAATACT
1 TTTTAAAATA-T
* *
35359665 TTTT-TATTAT
1 TTTTAAAATAT
*
35359675 TTTT----TAA
1 TTTTAAAATAT
35359682 TTTTAAAATAT
1 TTTTAAAATAT
35359693 TTTTAAAATACT
1 TTTTAAAATA-T
35359705 TTTT--AAT-T
1 TTTTAAAATAT
* *
35359713 TTTT---TTAA
1 TTTTAAAATAT
35359721 TTTTAAAATAT
1 TTTTAAAATAT
35359732 TTTTAAAATACT
1 TTTTAAAATA-T
35359744 TTTT
1 TTTT
35359748 TTAATTTTTA
Statistics
Matches: 76, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.09
8 9 0.12
10 8 0.11
11 37 0.49
12 15 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:35359768 original size:21 final size:21
Alignment explanation
Indices: 35359730--35359769 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35359720 ATTTTAAAAT
**
35359730 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
35359751 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
35359770 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:35359776 original size:22 final size:20
Alignment explanation
Indices: 35359729--35359783 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
35359719 AATTTTAAAA
* *
35359729 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
35359749 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
35359772 TATTTATTAAAA
1 TATTT-TTAAAA
35359784 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:35360203 original size:19 final size:17
Alignment explanation
Indices: 35360179--35360213 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
35360169 ATTGTTTAAA
35360179 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
35360198 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
35360214 ACCATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:35362679 original size:2 final size:2
Alignment explanation
Indices: 35362672--35362700 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35362662 ATAAAACAAC
35362672 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
35362701 AAAATTACCA
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:35367532 original size:13 final size:13
Alignment explanation
Indices: 35367514--35367539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35367504 ATCAACAGGG
35367514 TTTATTTTTTTTT
1 TTTATTTTTTTTT
35367527 TTTATTTTTTTTT
1 TTTATTTTTTTTT
35367540 ATTTTGGGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTATTTTTTTTT
Found at i:35369598 original size:36 final size:39
Alignment explanation
Indices: 35369558--35369629 Score: 105
Period size: 36 Copynumber: 1.9 Consensus size: 39
35369548 ATGATTAAAC
*
35369558 AATTCAATAAAATAAATA-T-TACA-AAATGTGAAATTT
1 AATTCAATAAAATAAATAGTAGACATAAATGTGAAATTT
*
35369594 AATTCAATAATATAAATAGTAGACATAAATGTGAAA
1 AATTCAATAAAATAAATAGTAGACATAAATGTGAAA
35369630 AAAAAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 17 0.55
37 1 0.03
38 3 0.10
39 10 0.32
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (39 bp):
AATTCAATAAAATAAATAGTAGACATAAATGTGAAATTT
Found at i:35371376 original size:24 final size:24
Alignment explanation
Indices: 35371347--35371400 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
35371337 CAGAAACAAA
*
35371347 CATTAAGCAGAAATATGGTACTCG
1 CATTAACCAGAAATATGGTACTCG
35371371 CATTAACCAGAAATATGGTACTCG
1 CATTAACCAGAAATATGGTACTCG
35371395 CATTAA
1 CATTAA
35371401 TACAGATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.26
Consensus pattern (24 bp):
CATTAACCAGAAATATGGTACTCG
Found at i:35371573 original size:44 final size:44
Alignment explanation
Indices: 35371520--35371610 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
35371510 TAAGCAAAAT
35371520 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
1 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
*
35371564 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAGAAACAA
1 ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
35371608 ACA
1 ACA
35371611 AACAGAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.11
Consensus pattern (44 bp):
ACAGCCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAA
Found at i:35371617 original size:40 final size:43
Alignment explanation
Indices: 35371524--35371621 Score: 157
Period size: 44 Copynumber: 2.3 Consensus size: 43
35371514 CAAAATACAG
35371524 CCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAAACA
1 CCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAAACA
*
35371567 GCCAAACAGAAAATGAAGTTACCCAGATTAACCAGAAAC-AA-A
1 -CCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAAACA
35371609 -CAAACAGAAAATG
1 CCAAACAGAAAATG
35371622 GAAGGGAATC
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
40 13 0.25
42 1 0.02
43 2 0.04
44 37 0.70
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.11
Consensus pattern (43 bp):
CCAAACAGAAAATGAAGTTACCCAGATTAACCAAAAACAAACA
Found at i:35371792 original size:14 final size:14
Alignment explanation
Indices: 35371773--35371801 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35371763 GGAGGATTGA
35371773 AGGTGGATCGGTGG
1 AGGTGGATCGGTGG
35371787 AGGTGGATCGGTGG
1 AGGTGGATCGGTGG
35371801 A
1 A
35371802 CTGGAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.07, G:0.55, T:0.21
Consensus pattern (14 bp):
AGGTGGATCGGTGG
Found at i:35371808 original size:19 final size:19
Alignment explanation
Indices: 35371784--35371836 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
35371774 GGTGGATCGG
*
35371784 TGGAGGTGGATCGGTGGAC
1 TGGAGGAGGATCGGTGGAC
*
35371803 TGGAGGAGGATCTGTGGAC
1 TGGAGGAGGATCGGTGGAC
35371822 TGGAGGAGGATCGGT
1 TGGAGGAGGATCGGT
35371837 ATTTTGGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.19, C:0.09, G:0.51, T:0.21
Consensus pattern (19 bp):
TGGAGGAGGATCGGTGGAC
Found at i:35372198 original size:20 final size:20
Alignment explanation
Indices: 35372173--35372222 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
35372163 TCACCTCTAG
35372173 TTTAGGGGGAAGTAAAACTT
1 TTTAGGGGGAAGTAAAACTT
*
35372193 TTTA-GGGGAAGTAAAAGTT
1 TTTAGGGGGAAGTAAAACTT
*
35372212 TTGAGGGGGAA
1 TTTAGGGGGAA
35372223 AAAAAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.28
Consensus pattern (20 bp):
TTTAGGGGGAAGTAAAACTT
Found at i:35380308 original size:38 final size:39
Alignment explanation
Indices: 35380252--35380342 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 39
35380242 AAAAAAAACT
* *
35380252 TAATAAAAGACACATATTAATGATGTTCAAATTATGACA
1 TAATTAAAGACTCATATTAATGATGTTCAAATTATGACA
*
35380291 TAATTAAA-ACTCATATTAATGTTGTTCAAATTATGACA
1 TAATTAAAGACTCATATTAATGATGTTCAAATTATGACA
35380329 TAATTAAAGACTCA
1 TAATTAAAGACTCA
35380343 AACTATAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
38 36 0.75
39 12 0.25
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (39 bp):
TAATTAAAGACTCATATTAATGATGTTCAAATTATGACA
Found at i:35386904 original size:38 final size:39
Alignment explanation
Indices: 35386862--35386940 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 39
35386852 ATAAAAGGTA
35386862 CATATTAATGATGTTCAAATTATGAAATAATTAAA-ACT
1 CATATTAATGATGTTCAAATTATGAAATAATTAAAGACT
* *
35386900 CATATTAATGTTGTTCAAATTATGACATAATTAAAGACT
1 CATATTAATGATGTTCAAATTATGAAATAATTAAAGACT
35386939 CA
1 CA
35386941 AACTATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 33 0.87
39 5 0.13
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (39 bp):
CATATTAATGATGTTCAAATTATGAAATAATTAAAGACT
Found at i:35387439 original size:16 final size:17
Alignment explanation
Indices: 35387413--35387448 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
35387403 TTATAATTGG
*
35387413 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTAATTA
35387430 ATTG-GAAAATTAATTA
1 ATTGAGAAAATTAATTA
35387446 ATT
1 ATT
35387449 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGAGAAAATTAATTA
Found at i:35401092 original size:21 final size:20
Alignment explanation
Indices: 35401054--35401116 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
35401044 ATTCAATTTC
35401054 TCAATCC-AAT-ATA-CATT
1 TCAATCCAAATAATATCATT
35401071 TCAATACCACAATAAT-TCATT
1 TCAAT-CCA-AATAATATCATT
*
35401092 T-AATTCAAATAATATCATT
1 TCAATCCAAATAATATCATT
35401111 TGCAAT
1 T-CAAT
35401117 TTCCATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 8 0.22
20 6 0.16
21 10 0.27
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TCAATCCAAATAATATCATT
Found at i:35402538 original size:23 final size:22
Alignment explanation
Indices: 35402495--35402538 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
35402485 TTCTAAGTTG
35402495 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
35402518 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
35402539 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:35402648 original size:45 final size:45
Alignment explanation
Indices: 35402584--35402676 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
35402574 ACAGATACTT
* *
35402584 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
* *
35402629 GGTGGAATCAGCACATAGCAAGCACCTTACTAATCAATGATGTTC
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
35402674 GGT
1 GGT
35402677 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCC
Found at i:35404036 original size:21 final size:21
Alignment explanation
Indices: 35404010--35404051 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
35404000 ACAAAGGCAA
35404010 CCACAACGAGACCGTTCACCT
1 CCACAACGAGACCGTTCACCT
*
35404031 CCACAACGAGGCCGTTCACCT
1 CCACAACGAGACCGTTCACCT
35404052 TGTGTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.14
Consensus pattern (21 bp):
CCACAACGAGACCGTTCACCT
Found at i:35404822 original size:21 final size:22
Alignment explanation
Indices: 35404784--35404828 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
35404774 ATTACGAATA
*
35404784 TTAATTTATAATATAATTAATT
1 TTAATTTATAATACAATTAATT
* *
35404806 TTAATTT-TAATCCAATTTATT
1 TTAATTTATAATACAATTAATT
35404827 TT
1 TT
35404829 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTATAATACAATTAATT
Found at i:35411476 original size:43 final size:43
Alignment explanation
Indices: 35411389--35411551 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
35411379 GATTCGTACA
* * * * *
35411389 ATGCCAACGTCCCAGACATGGTCCTACATG-TAATCACAAATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACGAAAAT-ACAAATCG
* *
35411432 ATGCCA-CTGTCCCAGACAG-GGTCTTACCCGAAAATACAAGTCG
1 ATGCCATC-GTCCCAGAC-GTGGTCTTACACGAAAATACAAATCG
* * *
35411475 ATGCCATCATCCCAGATGTGGTCTTACACGAAAATACAACTCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACGAAAATACAAATCG
* *
35411518 ATGCCATCGTTCCAGACGTGGTCTTACATGAAAA
1 ATGCCATCGTCCCAGACGTGGTCTTACACGAAAA
35411552 CACTTATCAG
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 95 0.94
44 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCATCGTCCCAGACGTGGTCTTACACGAAAATACAAATCG
Found at i:35434675 original size:58 final size:58
Alignment explanation
Indices: 35434595--35434719 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 58
35434585 TTTTAATAAG
* *
35434595 ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAACCATATT-TTAACATA
1 ATTATTATTAAAAATAATTTAAT-AAAATAATAAATAATTTAACAAAATTCTTAACATA
* * * *
35434653 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAAATTCTTAATATA
1 ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
35434711 ATTATTATT
1 ATTATTATT
35434720 TTATGAATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 22 0.37
58 38 0.63
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (58 bp):
ATTATTATTAAAAATAATTTAATAAAATAATAAATAATTTAACAAAATTCTTAACATA
Found at i:35435006 original size:16 final size:16
Alignment explanation
Indices: 35434981--35435011 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35434971 CATATGTTAT
*
35434981 AAAATTTTACAACATC
1 AAAATGTTACAACATC
35434997 AAAATGTTACAACAT
1 AAAATGTTACAACAT
35435012 TGTAATGACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATGTTACAACATC
Found at i:35445951 original size:9 final size:9
Alignment explanation
Indices: 35445939--35445978 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
35445929 TTTTTTTTTA
35445939 ATTTTATAT
1 ATTTTATAT
35445948 ATTTTATAT
1 ATTTTATAT
35445957 ATTTTTATAAT
1 A-TTTTAT-AT
*
35445968 TTTTTATAT
1 ATTTTATAT
35445977 AT
1 AT
35445979 ATTAATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 13 0.48
10 12 0.44
11 2 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTATAT
Found at i:35445962 original size:10 final size:10
Alignment explanation
Indices: 35445940--35445978 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
35445930 TTTTTTTTAA
35445940 TTTTATATA-
1 TTTTATATAT
35445949 TTTTATATAT
1 TTTTATATAT
35445959 TTTTATA-ATT
1 TTTTATATA-T
35445969 TTTTATATAT
1 TTTTATATAT
35445979 ATTAATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 10 0.37
10 16 0.59
11 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:35445971 original size:35 final size:34
Alignment explanation
Indices: 35445932--35446017 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 34
35445922 AAATGAGTTT
*
35445932 TTTTTTAATTT-TATATATTTTATATATTTTTATAA
1 TTTTTTAATTTATATA-ATTGTATATATTTTTAT-A
* *
35445967 TTTTTT-ATATATATTAATTGTATTTATTTTTATA
1 TTTTTTAATTTATA-TAATTGTATATATTTTTATA
35446001 TTTTTATAAATTTATAT
1 TTTTT-T-AATTTATAT
35446018 TTGATGCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
34 9 0.21
35 24 0.57
36 3 0.07
37 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (34 bp):
TTTTTTAATTTATATAATTGTATATATTTTTATA
Found at i:35446005 original size:9 final size:9
Alignment explanation
Indices: 35445932--35446005 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
35445922 AAATGAGTTT
35445932 TTTTTTA-A
1 TTTTTTATA
*
35445940 TTTTATATA
1 TTTTTTATA
*
35445949 TTTTATATA
1 TTTTTTATA
35445958 -TTTTTATAA
1 TTTTTTAT-A
35445967 TTTTTTATA
1 TTTTTTATA
* *
35445976 TATATTA-A
1 TTTTTTATA
*
35445984 TTGTATT-TA
1 TT-TTTTATA
35445993 -TTTTTATA
1 TTTTTTATA
35446001 TTTTT
1 TTTTT
35446006 ATAAATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
7 3 0.06
8 17 0.32
9 26 0.49
10 7 0.13
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTTTATA
Found at i:35452082 original size:15 final size:15
Alignment explanation
Indices: 35452062--35452092 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35452052 TATGAATGTC
35452062 ACAATAACAAATACA
1 ACAATAACAAATACA
*
35452077 ACAATAATAAATACA
1 ACAATAACAAATACA
35452092 A
1 A
35452093 TAATGGCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
ACAATAACAAATACA
Found at i:35452264 original size:20 final size:19
Alignment explanation
Indices: 35452221--35452266 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
35452211 ATGAAAACAC
*
35452221 AAATAAATAAACAAATAAA
1 AAATAAACAAACAAATAAA
35452240 AAATAAACAAA-AAATATAA
1 AAATAAACAAACAAATA-AA
35452259 AGAATAAA
1 A-AATAAA
35452267 AGTTACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAACAAACAAATAAA
Found at i:35454543 original size:44 final size:44
Alignment explanation
Indices: 35454477--35456353 Score: 1806
Period size: 44 Copynumber: 42.5 Consensus size: 44
35454467 TGCCTCACTA
* *
35454477 CCAATATAAGAAGACATGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35454521 CTAATACATGAATACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** *
35454566 CCAGTATGGGAAGACAATATCTGC-ATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * *
35454609 CCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35454653 CCAATACATGAAGACAAGATATGTTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * *
35454698 CCAGTATGGGAAGACAAGATCTACTATCTTCGATCTACTTCGCG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * *
35454742 CCCAATACATGAGGACAGGATCTGCTATCTTCGATCTACTTCACG
1 -CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* *
35454787 CCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * *
35454831 CCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * * * *
35454876 CCAGTATGGGAAGAAAAGATCTTC-ATCTTCGATCCACTTC-CTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* * *
35454919 CCAATATAGGAAGACAGGATCTTCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35454963 CCAATACATGAAGACAAGATCTACTTTCTTCGATATACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** *
35455008 CCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
*
35455052 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35455096 CTAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * * *
35455141 CCAGTATGGGAAGACAAGATCTGC-ATCTTCAATCCACTTC-CTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* * *
35455184 CCAATATA-GAAAGACAGGATCTTCTATTTTCGATCTACTTCACG
1 CCAATATATG-AAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * *
35455228 CCAATACATGAAGAAAAGATCTGCTTTCTTCGATCTACTTCACCG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CG
** * * * *
35455273 CCAATATGGGAAGATAAGATCTGC-ATATTCGATCCACTTCACTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* * * * *
35455317 CCAATATAGGAAGATAGGATCTTCTATCTTCGATCTACTCCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* *
35455361 CCAATATATGAAGACAAGATCTACTATCTTCGATCTACTTCATG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * *
35455405 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * *
35455450 CCAGTATGGGAAAACAAGATCTACTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * *
35455494 CTAATACATGAAGACAAGATCTGCTATCTTCGACCTACTTCACA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * * *
35455538 CTAA-ACATGAAGATAAGATATGCTTTCTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * * * *
35455582 CCAGTATGGGAAGACAAGATCTGC-GTCTTTGATCCACTTC-CTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* * *
35455625 CCAATATAGGAAGACAAGATCTGCTTTCTACGATCTACTTCACCG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CG
** * *
35455670 CCAATATGGGAAGACAAGATCTGCTTTCTACGATCTACTTCACCG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CG
** * * *
35455715 CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* *
35455759 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* *
35455803 CCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * *
35455847 CCAATACATGAAGAAAAGATCTTC-ATCTTCGATCCACTTC-CTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* * *
35455890 CCAATATAGGAAGACAGGATCTTCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35455934 CCAATACATGAAGACAAGATCTACTTTCTTCGATATACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** *
35455979 CCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
*
35456023 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * ***
35456067 CCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGTTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * *
35456112 CCAGTATCGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* *
35456155 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * * *
35456199 CCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCGCCA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACG
* ** * * * *
35456244 CCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCCATTTCGCTA
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-G
* *
35456288 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
1 CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
*
35456332 CCAATTTATGAAGACAAGATCT
1 CCAATATATGAAGACAAGATCT
35456354 TCTGTTTTTT
Statistics
Matches: 1508, Mismatches: 287, Indels: 76
0.81 0.15 0.04
Matches are distributed among these distances:
42 5 0.00
43 174 0.12
44 906 0.60
45 422 0.28
46 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (44 bp):
CCAATATATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
Found at i:35455061 original size:265 final size:265
Alignment explanation
Indices: 35454477--35456353 Score: 1897
Period size: 265 Copynumber: 7.1 Consensus size: 265
35454467 TGCCTCACTA
* * * * *
35454477 CCAATATAAGAAGACATGATCTGCTATCTTCGATCTACTTCACGCTAATACATGAATACAAGATC
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
* * * *
35454542 TGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGC-ATCTTCGATCTACTTC
66 TGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
* * * * * * * *
35454606 -ACGCCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCA-CGCCAATACATGAAGACA
129 GCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACA
* * * * * *** *
35454669 AGATATGT-TTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTCGATC
194 AGATCT-TCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTATCTTCGATC
*
35454733 TACTTCGCG
257 TACTTCACG
* *
35454742 CCCAATACATGAGGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
1 -CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
* * * * * *
35454807 TTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTC
65 CTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
* ** * * * * *
35454872 GCCACCAGTATGGGAAGAAAAGATCTTC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACA
129 GCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACA
* * * *
35454935 GGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATATA
194 AGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTA
* *
35455000 CTTCGCCA
259 CTTC-ACG
* *** *
35455008 CCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATC
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
* * * *
35455073 TGCTATCTTCGATCTACTT-CACGCTAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTC
66 TGCTATCTTCGATCTACTTCCAC-C-AATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
* ** * * * * *
35455137 GCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCAATCCACTTC-CTACCAATATAGAAAGACA
129 GCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACA
* * * *
35455200 GGATCTTCTATTTTCGATCTACTTCACGCCAATACATGAAGAAAAGATCTGCTTTCTTCGATCTA
194 AGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTA
35455265 CTTCACCG
259 CTTCA-CG
*** * * * * * * * *
35455273 CCAATATGGGAAGATAAGATCTGC-ATATTCGATCCACTTCACTACCAATATAGGAAGATAGGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
* * *
35455337 CTTCTATCTTCGATCTAC-TCCACGCCAATATATGAAGACAAGATCTACTATCTTCGATCTACTT
65 CTGCTATCTTCGATCTACTTCCA--CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT
*** * * * * *
35455401 C-ATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAAAC
128 CGCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGAC
* * *
35455465 AAGATCTACTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTATCTTCGACCT
193 AAGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCT
*
35455530 ACTTCACA
258 ACTTCACG
* * * * * * * ***
35455538 CTAA-ACATGAAGATAAGATATGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGAT
* * * * *
35455602 CTGC-GTCTTTGATCCACTTCCTACCAATATAGGAAGACAAGATCTGCTTTCTACGATCTACTTC
65 CTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTC
* * ** * * *
35455666 ACCGCCAATATGGGAAGACAAGATCTGCTTTCTACGATCTACTTCACCGCCAATATGGGAAGACA
129 GCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACA
* * * * * * *
35455731 AGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCT
194 AGATCTTCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTCGATCT
35455795 ACTTCACG
258 ACTTCACG
* *
35455803 CCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAAAAGATC
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
* * * *
35455868 TTC-ATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTTCTATCTTCGATCTACTTC-
66 TGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCG
* * * * * * * *
35455931 ACGCCAATACATGAAGACAAGATCTACTTTCTTCGATATACTTCGCCACCAGTATGGGAAGACAA
130 CCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACAA
* *
35455996 GATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTAC
195 GATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTAC
35456061 TTCACG
260 TTCACG
* * * *** * *
35456067 CCAATACATGAAGACAAGATCTGTTTTCTTCAATCTACTTCGTTACCAGTATC-GGAAGACAAGA
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAAGA
* *
35456131 TCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTT
64 TCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTT
* * * * * * * *
35456195 C-ACGCCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGAC
128 CGCCACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGAC
* * * * * * * *
35456259 AAGATCTGC-ATCTTCGATCCATTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATC
193 AAGATCTTCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTATCTTCGATC
35456323 TACTTCACG
257 TACTTCACG
**
35456332 CCAATTTATGAAGACAAGATCT
1 CCAATACATGAAGACAAGATCT
35456354 TCTGTTTTTT
Statistics
Matches: 1382, Mismatches: 203, Indels: 53
0.84 0.12 0.03
Matches are distributed among these distances:
263 2 0.00
264 270 0.20
265 837 0.61
266 253 0.18
267 20 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (265 bp):
CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATC
TGCTATCTTCGATCTACTTCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCGC
CACCAATACAGGAAGACAAGATCTGCTTTCTTCGATCTACTTCACCACCAATATAGGAAGACAAG
ATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACT
TCACG
Found at i:35455346 original size:309 final size:309
Alignment explanation
Indices: 35454477--35456353 Score: 1940
Period size: 309 Copynumber: 6.1 Consensus size: 309
35454467 TGCCTCACTA
* * * * * * * * *
35454477 CCAATATAAGAAGACATGATCTGCTATCTTCGATCTACTTC-ACGCTAATACATGAATACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * * * *
35454541 CTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGC-ATCTTCGATCTACTT
66 CTGCTATCTTCGATCTACTTCG-CACCAATAT-AGAAGACAAGATCTTCTATCTTCGATCTACTT
* * * * *
35454605 CACGCCAATACATGAAGACAAGATCTACTTTTTTCGATCTACTTCACGCCAATACATGAAGACAA
129 CACACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACAA
* * * * *
35454670 GATATGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTACTATCTTCGATCTA
194 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * * * *
35454735 CTTCGCGCCCAATACATGAGGACAGGATCTGCTATCTTCGATCTACTTCACG
259 CTTCACG-CCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * *
35454787 CCAATACATGAAGACAAGATTTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * * * * *
35454851 CTACTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGAAAAGATCTTC-ATCTTCGATCCACTT
66 CTGCTATCTTCGATCTACTTCG-CACCAATAT-AGAAGACAAGATCTTCTATCTTCGATCTACTT
* * * * *
35454915 C-CTACCAATATAGGAAGACAGGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACA
129 CAC-ACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACA
* * * * *
35454979 AGATCTACTTTCTTCGATATACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCT
193 AGATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* *
35455044 ACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
258 ACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * * *
35455096 CTAATACATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * * *
35455161 CTGC-ATCTTCAATCCACTTC-CTACCAATATAGAAAGACAGGATCTTCTATTTTCGATCTACTT
66 CTGCTATCTTCGATCTACTTCGC-ACCAATATAG-AAGACAAGATCTTCTATCTTCGATCTACTT
* * * ** *
35455224 CACGCCAATACATGAAGAAAAGATCTGCTTTCTTCGATCTACTTCACCGCCAATATGGGAAGATA
129 CACACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATACAGGAAGACA
* * * * * * * *
35455289 AGATCTGC-ATATTCGATCCACTTCACTACCAATATAGGAAGATAGGATCTTCTATCTTCGATCT
193 AGATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * *
35455353 ACTCCACGCCAATATATGAAGACAAGATCTACTATCTTCGATCTACTTCATG
258 ACTTCACGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * *
35455405 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAAACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * * * * * *
35455470 CTACTATCTTCGATCTACTTCACGCTAATACATGAAGACAAGATCTGCTATCTTCGACCTACTTC
66 CTGCTATCTTCGATCTACTTCGCACCAATATA-GAAGACAAGATCTTCTATCTTCGATCTACTTC
* * * * * * * **
35455535 ACACTAA-ACATGAAGATAAGATATGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAA
130 ACACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAGGAAGACAA
* * * * * *
35455599 GATCTGC-GTCTTTGATCCACTTC-CTACCAATATAGGAAGACAAGATCTGCTTTCTACGATCTA
194 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTA
* * *
35455662 CTTCACCGCCAATATGGGAAGACAAGATCTGCTTTCTACGATCTACTTCACCG
259 CTTCA-CGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CG
*** * * *
35455715 CCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAGGAAGACAGGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * *
35455779 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT-TTGCTATCTTCGATCTACTT
66 CTGCTATCTTCGATCTACTTCGCACCAATATA-GAAGACAAGATCTT-CTATCTTCGATCTACTT
* * * * * *
35455843 CACGCCAATACATGAAGAAAAGATCTTC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACA
129 CACACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATACAGGAAGACA
* * * * * * * * * *
35455906 GGATCTTCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTACTTTCTTCGATAT
193 AGATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * * *
35455970 ACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACG
258 ACTTC-ACGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
* * * *
35456023 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGAT
1 CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
* * * * * * * *
35456087 CTGTTTTCTTCAATCTACTTCGTTACCAGTATCGGAAGACAAGATCTGC-ATCTTCGATCCACTT
66 CTGCTATCTTCGATCTACTTCG-CACCAATAT-AGAAGACAAGATCTTCTATCTTCGATCTACTT
* * * *
35456151 C-CTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACA
129 CAC-ACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACA
* * * * *
35456215 AGATCTACTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-ATCTTCGATCC
193 AGATCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * *
35456279 ATTTCGCTACCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACG
258 ACTTCAC-GCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
**
35456332 CCAATTTATGAAGACAAGATCT
1 CCAATACATGAAGACAAGATCT
35456354 TCTGTTTTTT
Statistics
Matches: 1334, Mismatches: 206, Indels: 55
0.84 0.13 0.03
Matches are distributed among these distances:
307 4 0.00
308 173 0.13
309 763 0.57
310 392 0.29
311 2 0.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.29
Consensus pattern (309 bp):
CCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGAT
CTGCTATCTTCGATCTACTTCGCACCAATATAGAAGACAAGATCTTCTATCTTCGATCTACTTCA
CACCAATACATGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAGGAAGACAAGA
TCTGCTTTCTTCGATCTACTTCGCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACT
TCACGCCAATATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
Found at i:35457263 original size:25 final size:26
Alignment explanation
Indices: 35457225--35457273 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
35457215 TGTCTTGAAA
35457225 AAGAAAAAGATATT-CAAGAACAATG
1 AAGAAAAAGATATTACAAGAACAATG
35457250 AAGAATAAAG-TATTACAAGAACAA
1 AAGAA-AAAGATATTACAAGAACAA
35457274 ACAAATTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.61, C:0.08, G:0.14, T:0.16
Consensus pattern (26 bp):
AAGAAAAAGATATTACAAGAACAATG
Found at i:35471089 original size:15 final size:15
Alignment explanation
Indices: 35471069--35471099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35471059 TATGAATGTC
35471069 ACAATAACAAATACA
1 ACAATAACAAATACA
*
35471084 ACAATAATAAATACA
1 ACAATAACAAATACA
35471099 A
1 A
35471100 TAATGGCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (15 bp):
ACAATAACAAATACA
Found at i:35471272 original size:20 final size:19
Alignment explanation
Indices: 35471229--35471274 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
35471219 ATGAAAACAC
*
35471229 AAATAAATAAACAAATAAA
1 AAATAAACAAACAAATAAA
35471248 AAATAAACAAA-AAATATAA
1 AAATAAACAAACAAATA-AA
35471267 AGAATAAA
1 A-AATAAA
35471275 AGGTACATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (19 bp):
AAATAAACAAACAAATAAA
Found at i:35483397 original size:25 final size:24
Alignment explanation
Indices: 35483359--35483431 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
35483349 GTCATGAAGG
* *
35483359 TTACCGATTCCAGCTCTTATGAGC
1 TTACCGATACCAGCTCGTATGAGC
35483383 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATAC-CAGCTCGTATGAGC
* *
35483408 TTACCGTTTACCA-CTCATATGAGC
1 TTACCG-ATACCAGCTCGTATGAGC
35483432 ATACATGTAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.44
25 21 0.49
26 3 0.07
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (24 bp):
TTACCGATACCAGCTCGTATGAGC
Found at i:35484597 original size:12 final size:12
Alignment explanation
Indices: 35484580--35484610 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35484570 CTCTAGTTTT
35484580 CACACGGCCTAG
1 CACACGGCCTAG
*
35484592 CACACGGCCTGG
1 CACACGGCCTAG
35484604 CACACGG
1 CACACGG
35484611 GCGTGTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.42, G:0.29, T:0.06
Consensus pattern (12 bp):
CACACGGCCTAG
Found at i:35494637 original size:27 final size:26
Alignment explanation
Indices: 35494607--35494671 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 26
35494597 CATAATCATT
35494607 TAATCTCATTAAGCATATAAC-ACATAA
1 TAAT-TCATTAAG-ATATAACAACATAA
35494634 TAA-TCATTTAAGATATAACTAACATAA
1 TAATTCA-TTAAGATATAAC-AACATAA
*
35494661 TTATTCATTAA
1 TAATTCATTAA
35494672 CATTTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
25 10 0.30
26 5 0.15
27 15 0.45
28 3 0.09
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (26 bp):
TAATTCATTAAGATATAACAACATAA
Found at i:35494640 original size:25 final size:26
Alignment explanation
Indices: 35494612--35494671 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
35494602 TCATTTAATC
35494612 TCATTAAGCATATAAC-ACATAA-TAA
1 TCATTAAG-ATATAACAACATAATTAA
*
35494637 TCATTTAAGATATAACTAACATAATTAT
1 TCA-TTAAGATATAAC-AACATAATTAA
35494665 TCATTAA
1 TCATTAA
35494672 CATTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 10 0.33
26 5 0.17
27 10 0.33
28 5 0.17
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (26 bp):
TCATTAAGATATAACAACATAATTAA
Found at i:35505829 original size:154 final size:155
Alignment explanation
Indices: 35505547--35505857 Score: 556
Period size: 154 Copynumber: 2.0 Consensus size: 155
35505537 TCGCCTGGCT
35505547 TTTTGAATTTTTGTTCAAATAGTTTAGTCTTTTTTTTGTAGATGATGTGGCATTTCATACCAACA
1 TTTTGAATTTTTGTTCAAATAGTTTAGTCTTTTTTTTGTAGATGATGTGGCATTTCATACCAACA
*
35505612 TTTGAATTTTTTAAATATATAAAATTTTAATAAATCTAAAAAAATTCAAATTTATATAAATTAAA
66 TTTGAATTTTTTAAATATATAAAATTTTAATAAATCTAAAAAAATTCAAATATATATAAATTAAA
*
35505677 AGTTTCTAAAAAGCTATAAAAAAATA
131 AGTTTCTAAAAAGCCAT-AAAAAATA
35505703 TTTTGAATTTTTGTTCAAATAG-TT-GTC-TTTTTTTGTAGATGATGTGGCATTTCATACCAACA
1 TTTTGAATTTTTGTTCAAATAGTTTAGTCTTTTTTTTGTAGATGATGTGGCATTTCATACCAACA
*
35505765 TTTGAATTTTTTTAAATATATAAAATTTTAATAAGTCTAAAAAAATTCAAATATATATAAATTAA
66 TTTGAA-TTTTTTAAATATATAAAATTTTAATAAATCTAAAAAAATTCAAATATATATAAATTAA
35505830 AAGTTTCTAAAAAGCCATAAAAAATA
130 AAGTTTCTAAAAAGCCATAAAAAATA
35505856 TT
1 TT
35505858 AACAATTAAA
Statistics
Matches: 151, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
153 51 0.34
154 76 0.50
155 2 0.01
156 22 0.15
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (155 bp):
TTTTGAATTTTTGTTCAAATAGTTTAGTCTTTTTTTTGTAGATGATGTGGCATTTCATACCAACA
TTTGAATTTTTTAAATATATAAAATTTTAATAAATCTAAAAAAATTCAAATATATATAAATTAAA
AGTTTCTAAAAAGCCATAAAAAATA
Found at i:35506043 original size:34 final size:34
Alignment explanation
Indices: 35505999--35506084 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
35505989 AAAAATTGAA
*
35505999 AATTTTGAATTAATCCAAATTAAATGTTAGAATT
1 AATTCTGAATTAATCCAAATTAAATGTTAGAATT
35506033 AATTCTGAATTAATCCAAATTAAATGTTAGAATT
1 AATTCTGAATTAATCCAAATTAAATGTTAGAATT
35506067 AATTCTGAATT-ATCCAAA
1 AATTCTGAATTAATCCAAA
35506085 GTCCTGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 7 0.14
34 44 0.86
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.38
Consensus pattern (34 bp):
AATTCTGAATTAATCCAAATTAAATGTTAGAATT
Found at i:35506683 original size:3 final size:3
Alignment explanation
Indices: 35506667--35506725 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
35506657 AATATTGTAT
* *
35506667 TTA TTA TCTC TTA TTA TT- TTA TTA TTA TTA TTA TTA TT- TTGA ATA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
*
35506712 TT- TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA
35506726 AGTATTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:35506697 original size:17 final size:18
Alignment explanation
Indices: 35506666--35506701 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
35506656 CAATATTGTA
*
35506666 TTTATTATCTCTTATTAT
1 TTTATTATCTATTATTAT
35506684 TTTATTAT-TATTATTAT
1 TTTATTATCTATTATTAT
35506701 T
1 T
35506702 ATTTTGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTATCTATTATTAT
Found at i:35506702 original size:20 final size:21
Alignment explanation
Indices: 35506667--35506724 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
35506657 AATATTGTAT
*
35506667 TTATTATCTCTTATTATTTT-A
1 TTATTAT-TATTATTATTTTGA
35506688 TTATTATTATTATTATTTTGA
1 TTATTATTATTATTATTTTGA
* *
35506709 ATATT-TTATAATTATT
1 TTATTATTATTATTATT
35506725 AAGTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATTATTATTATTATTTTGA
Found at i:35510999 original size:14 final size:14
Alignment explanation
Indices: 35510979--35511016 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
35510969 AAAAAGTAGG
35510979 CCATTTTCAGGAAA
1 CCATTTTCAGGAAA
*
35510993 TCATTTTTC-GGAAA
1 CCA-TTTTCAGGAAA
35511007 CCATTTTCAG
1 CCATTTTCAG
35511017 TCAAACAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (14 bp):
CCATTTTCAGGAAA
Found at i:35512169 original size:18 final size:17
Alignment explanation
Indices: 35512136--35512174 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35512126 TTTTATAAAT
35512136 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
35512154 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
35512171 TGTG
1 TGTG
35512175 GAAAGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:35512413 original size:23 final size:23
Alignment explanation
Indices: 35512386--35512507 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
35512376 AGTGTTATTG
*
35512386 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
* * * *
35512409 TTCAGTGGTAGCTACAGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
35512432 ATCAATGGTAGCTTCAGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
35512455 ATCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
35512478 ATCAATGGTAGCTTCGGCTACAT
1 ATCAATGGTAGCTTCGGCTACAT
*
35512501 ACCAATG
1 ATCAATG
35512508 TGGCACTTAT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (23 bp):
ATCAATGGTAGCTTCGGCTACAT
Found at i:35519623 original size:18 final size:17
Alignment explanation
Indices: 35519590--35519628 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35519580 TTTTATAAAT
35519590 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
35519608 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
35519625 TGTG
1 TGTG
35519629 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:35525289 original size:8 final size:8
Alignment explanation
Indices: 35525221--35525288 Score: 109
Period size: 8 Copynumber: 8.5 Consensus size: 8
35525211 GACTATCTAC
35525221 CTATGTAT
1 CTATGTAT
35525229 CTATGTAT
1 CTATGTAT
35525237 CTATGTAT
1 CTATGTAT
35525245 CTATGTAT
1 CTATGTAT
35525253 CTATGTAT
1 CTATGTAT
35525261 CTATGTAT
1 CTATGTAT
*
35525269 CTATCTAT
1 CTATGTAT
* *
35525277 GTATCTAT
1 CTATGTAT
35525285 CTAT
1 CTAT
35525289 CAATATAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 57 1.00
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (8 bp):
CTATGTAT
Found at i:35525301 original size:3 final size:3
Alignment explanation
Indices: 35525293--35525328 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
35525283 ATCTATCAAT
35525293 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35525329 TTATTATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35525333 original size:3 final size:3
Alignment explanation
Indices: 35525327--35525386 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
35525317 ATAATAATAA
*
35525327 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35525375 TAT TAT TAT TAT
1 TAT TAT TAT TAT
35525387 AACTTATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:35527606 original size:20 final size:19
Alignment explanation
Indices: 35527595--35527676 Score: 64
Period size: 18 Copynumber: 4.4 Consensus size: 19
35527585 AATAATTTTC
35527595 AAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
35527614 AAAAATTTCCAAAT-TTTCAT
1 AAAAATTT-AAAATATTT-AT
** *
35527634 -AATTTTTAAAA-ATATAT
1 AAAAATTTAAAATATTTAT
* *
35527651 AAAAATTTAAAAT-TCTAA
1 AAAAATTTAAAATATTTAT
35527669 AAAAATTT
1 AAAAATTT
35527677 TAAAGAATAT
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
17 2 0.04
18 25 0.51
19 16 0.33
20 6 0.12
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:35527661 original size:18 final size:18
Alignment explanation
Indices: 35527638--35527696 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
35527628 TTTCATAATT
35527638 TTTAAAAATATATAAAAA
1 TTTAAAAATATATAAAAA
* * *
35527656 TTTAAAATTCTAAAAAAA
1 TTTAAAAATATATAAAAA
*
35527674 TTTTAAAGAATATATAAAGA
1 -TTTAAA-AATATATAAAAA
35527694 TTT
1 TTT
35527697 TTTAAAATTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 15 0.47
19 9 0.28
20 8 0.25
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (18 bp):
TTTAAAAATATATAAAAA
Found at i:35528064 original size:21 final size:20
Alignment explanation
Indices: 35528027--35528083 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
35528017 AATAAACACC
** *
35528027 AAAAAAAGT-TTAGAAAATT
1 AAAAAAAGTATTTTAAAAAT
*
35528046 AAAAAAAGTCTTTTAAAAAT
1 AAAAAAAGTATTTTAAAAAT
35528066 AAAAAAAGTATTTTAAAA
1 AAAAAAAGTATTTTAAAA
35528084 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
AAAAAAAGTATTTTAAAAAT
Found at i:35533218 original size:19 final size:19
Alignment explanation
Indices: 35533194--35533230 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35533184 ATTATTTCCA
35533194 CTTAAATTTTAGAAAAATC
1 CTTAAATTTTAGAAAAATC
*
35533213 CTTAAATTTTAGTAAAAT
1 CTTAAATTTTAGAAAAAT
35533231 TTGAAAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
CTTAAATTTTAGAAAAATC
Found at i:35541290 original size:29 final size:27
Alignment explanation
Indices: 35541249--35541311 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 27
35541239 AAGAAGAAGT
* *
35541249 ATAAACATGTTGGGCCATTTAAGTAAAA
1 ATAAAAATATTGGGCCATTT-AGTAAAA
*
35541277 AGTAAAAATATTGGGCCATTTATTAAAA
1 A-TAAAAATATTGGGCCATTTAGTAAAA
35541305 ATAAAAA
1 ATAAAAA
35541312 AGGAGGACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 6 0.19
28 8 0.26
29 17 0.55
ACGTcount: A:0.49, C:0.08, G:0.14, T:0.29
Consensus pattern (27 bp):
ATAAAAATATTGGGCCATTTAGTAAAA
Found at i:35541312 original size:28 final size:29
Alignment explanation
Indices: 35541258--35541311 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
35541248 TATAAACATG
35541258 TTGGGCCATTTAAGTAAAAAGTAAAAATA
1 TTGGGCCATTTAAGTAAAAAGTAAAAATA
*
35541287 TTGGGCCATTT-ATTAAAAA-TAAAAA
1 TTGGGCCATTTAAGTAAAAAGTAAAAA
35541312 AGGAGGACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.25
28 7 0.29
29 11 0.46
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (29 bp):
TTGGGCCATTTAAGTAAAAAGTAAAAATA
Found at i:35545383 original size:15 final size:12
Alignment explanation
Indices: 35545346--35545376 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35545336 AAAAAAATTT
*
35545346 ATACTCAAAATA
1 ATACACAAAATA
35545358 ATACACAAAATA
1 ATACACAAAATA
35545370 ATACACA
1 ATACACA
35545377 CTAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ATACACAAAATA
Found at i:35545554 original size:18 final size:17
Alignment explanation
Indices: 35545524--35545557 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
35545514 GTTTATTTTC
35545524 GTAAATAAAAATAATAA
1 GTAAATAAAAATAATAA
*
35545541 GTAACATAATAATAATA
1 GTAA-ATAAAAATAATA
35545558 CAAGTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
GTAAATAAAAATAATAA
Found at i:35545631 original size:3 final size:3
Alignment explanation
Indices: 35545623--35545657 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35545613 TCTTAATACT
35545623 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
35545658 TAATAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:35545742 original size:19 final size:21
Alignment explanation
Indices: 35545718--35545756 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35545708 ACTAAAACAA
*
35545718 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
35545737 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
35545757 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Done.