Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 119 of 126
Found at i:35633222 original size:29 final size:29
Alignment explanation
Indices: 35633167--35633230 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
35633157 GAATTTTGGA
*
35633167 AAGTTTGGGGGTAAAACGGTAATTTTTAG
1 AAGTTTCGGGGTAAAACGGTAATTTTTAG
* *
35633196 AAGTTTCGGGGTCAAAA-TGTAATTTTTTG
1 AAGTTTCGGGGT-AAAACGGTAATTTTTAG
35633225 AAGTTT
1 AAGTTT
35633231 TAGGATCACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.39
Consensus pattern (29 bp):
AAGTTTCGGGGTAAAACGGTAATTTTTAG
Found at i:35633249 original size:30 final size:29
Alignment explanation
Indices: 35633186--35633252 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
35633176 GGTAAAACGG
* * *
35633186 TAATTTTTAGAAGTTTCGGGGTCAAAATG
1 TAATTTTTAGAAGTTTCAGGATCAAAATA
* *
35633215 TAATTTTTTGAAGTTTTAGGATCACAAATA
1 TAATTTTTAGAAGTTTCAGGATCA-AAATA
35633245 TAATTTTT
1 TAATTTTT
35633253 GAACAGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 20 0.62
30 12 0.38
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (29 bp):
TAATTTTTAGAAGTTTCAGGATCAAAATA
Found at i:35634348 original size:12 final size:12
Alignment explanation
Indices: 35634254--35634350 Score: 50
Period size: 12 Copynumber: 7.2 Consensus size: 12
35634244 TTTTTAATTT
*
35634254 TATTATTATAAA
1 TATTATTATTAA
*
35634266 TATTATTATTAT
1 TATTATTATTAA
35634278 TATTAATTACTATAAA
1 TATT-ATTA-T-T-AA
* *
35634294 TATCAATAATTAA
1 TAT-TATTATTAA
*
35634307 TATTATTAGTGATA
1 TATTATTA-TTA-A
35634321 TATTAGGTGGTATTAA
1 TATTA--T--TATTAA
35634337 TATTATTATTAA
1 TATTATTATTAA
35634349 TA
1 TA
35634351 AAATAAAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
12 25 0.38
13 11 0.17
14 9 0.14
15 2 0.03
16 14 0.22
17 2 0.03
18 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:35635149 original size:17 final size:18
Alignment explanation
Indices: 35635127--35635167 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
35635117 TTTCAAATAT
*
35635127 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
35635144 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
35635162 TTTAAA
1 TTTAAA
35635168 CCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:35640561 original size:17 final size:17
Alignment explanation
Indices: 35640536--35640574 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
35640526 CCAACTTTTA
*
35640536 ATTTAAAATTT-AAATTC
1 ATTTTAAATTTGAAA-TC
35640553 ATTTTAAATTTGAAATC
1 ATTTTAAATTTGAAATC
35640570 ATTTT
1 ATTTT
35640575 GGGTTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTTAAATTTGAAATC
Found at i:35640581 original size:24 final size:24
Alignment explanation
Indices: 35640554--35640599 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
35640544 TTTAAATTCA
35640554 TTTTAAATTTGAAATCATTTTGGG
1 TTTTAAATTTGAAATCATTTTGGG
* *
35640578 TTTTAAATTTGAATTTATTTTG
1 TTTTAAATTTGAAATCATTTTG
35640600 AATTGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (24 bp):
TTTTAAATTTGAAATCATTTTGGG
Found at i:35641673 original size:17 final size:17
Alignment explanation
Indices: 35641651--35641683 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35641641 TGTAAACTTT
*
35641651 CAGATCTGGTTTTGAAC
1 CAGATCTGGGTTTGAAC
35641668 CAGATCTGGGTTTGAA
1 CAGATCTGGGTTTGAA
35641684 TAAAAAAAAG
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:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (17 bp):
CAGATCTGGGTTTGAAC
Found at i:35642563 original size:30 final size:30
Alignment explanation
Indices: 35642529--35642652 Score: 105
Period size: 30 Copynumber: 4.2 Consensus size: 30
35642519 AAACTATCCA
* *
35642529 AAAATGGTATTTTAACCTCAAAACTTTTTG
1 AAAATGATATTTTAACCTCAAAACTTTTAG
* * *
35642559 AAAATTACATTTTAACCCTC-AAAC-TTTACC
1 AAAATGATATTTTAA-CCTCAAAACTTTTA-G
* *
35642589 AAAATTATATTTTAACCCCAAAACTTTTAG
1 AAAATGATATTTTAACCTCAAAACTTTTAG
*
35642619 -AAATGGTATTTTAAACCT-AAAACTTTCTA-
1 AAAATGATATTTT-AACCTCAAAACTTT-TAG
35642648 AAAAT
1 AAAAT
35642653 TGCATTTTGA
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
29 24 0.32
30 44 0.58
31 8 0.11
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATGATATTTTAACCTCAAAACTTTTAG
Found at i:35642660 original size:59 final size:59
Alignment explanation
Indices: 35642527--35642666 Score: 147
Period size: 59 Copynumber: 2.4 Consensus size: 59
35642517 CTAAACTATC
* * * * * *
35642527 CAAAAATGGTATTTTAACCTCAAAACTTTTTGAAAATTACATTTTAACCCTCAAACTTT
1 CAAAAATTGTATTTTAACCCCAAAACTTTTAGAAAATGACATTTTAAACCTAAAACTTT
* * **
35642586 ACCAAAATTATATTTTAACCCCAAAACTTTTAG-AAATGGTATTTTAAACCTAAAACTTT
1 -CAAAAATTGTATTTTAACCCCAAAACTTTTAGAAAATGACATTTTAAACCTAAAACTTT
* *
35642645 CTAAAAATTGCATTTTGACCCC
1 C-AAAAATTGTATTTTAACCCC
35642667 CAAGTTTTTT
Statistics
Matches: 65, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
58 1 0.02
59 37 0.57
60 27 0.42
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (59 bp):
CAAAAATTGTATTTTAACCCCAAAACTTTTAGAAAATGACATTTTAAACCTAAAACTTT
Found at i:35642764 original size:58 final size:57
Alignment explanation
Indices: 35642697--35642958 Score: 314
Period size: 58 Copynumber: 4.5 Consensus size: 57
35642687 TTTGCCCTCG
*
35642697 ATTTCACCAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCTCG
1 ATTTCACCAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACC-CA
* * *
35642755 ATTTTACCAAAAATTACTATTTTACCCTCGAACTTTCTGAAATTCCATTTTTAACCCTA
1 ATTTCACC-AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCC-A
* * * *
35642814 ATTTCACTAAAATTACCATTTTACCC-CTAAGCTTTCTAAAATTTCATTTTTACCCCTA
1 ATTTCACCAAAATTACCATTTTACCCTCGAA-CTTTCTAAAATTCCATTTTTAACCC-A
* * * *
35642872 ATTTCACCAAAATTATCATTTTACCC-CTGAACTTTCCAAAA-TCTCGTTTTTGACCCA
1 ATTTCACCAAAATTACCATTTTACCCTC-GAACTTTCTAAAATTC-CATTTTTAACCCA
*
35642929 ATTTCGACCAAAATTACCATTTTGCCCTCG
1 ATTTC-ACCAAAATTACCATTTTACCCTCG
35642959 GGTATCCAAA
Statistics
Matches: 176, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
57 10 0.06
58 112 0.64
59 54 0.31
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.39
Consensus pattern (57 bp):
ATTTCACCAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCA
Found at i:35642778 original size:30 final size:29
Alignment explanation
Indices: 35642678--35642839 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
35642668 AAGTTTTTTG
* *
35642678 AAATT-CCATTTTGCCCTCGATTTCACCA
1 AAATTACCATTTTACCCTCGATTTTACCA
* *
35642706 AAATTACCATTTTACCCTCGAACTTT-CTA
1 AAATTACCATTTTACCCTCG-ATTTTACCA
*
35642735 AAATT-CCATTTTTAACCTCGATTTTACCAA
1 AAATTACCA-TTTTACCCTCGATTTTACC-A
* * **
35642765 AAATTACTATTTTACCCTCGAACTTT-CTG
1 AAATTACCATTTTACCCTCG-ATTTTACCA
* * *
35642794 AAATT-CCATTTTTAACCCT-AATTTCACTA
1 AAATTACCA-TTTT-ACCCTCGATTTTACCA
35642823 AAATTACCATTTTACCC
1 AAATTACCATTTTACCC
35642840 CTAAGCTTTC
Statistics
Matches: 106, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
28 21 0.20
29 51 0.48
30 28 0.26
31 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATTACCATTTTACCCTCGATTTTACCA
Found at i:35642893 original size:30 final size:30
Alignment explanation
Indices: 35642800--35642951 Score: 117
Period size: 29 Copynumber: 5.2 Consensus size: 30
35642790 TCTGAAATTC
* * *
35642800 CATTTTTAACCCTAATTTCACTAAAATTAC
1 CATTTTTACCCCTAATTTCACCAAAATTAT
*
35642830 CA-TTTTACCCCTAAGCTTT--CTAAAATT-T
1 CATTTTTACCCCTAA--TTTCACCAAAATTAT
35642858 CATTTTTACCCCTAATTTCACCAAAATTAT
1 CATTTTTACCCCTAATTTCACCAAAATTAT
*
35642888 CA-TTTTACCCCTGAACTTT--CCAAAA-TCT
1 CATTTTTACCCCT-AA-TTTCACCAAAATTAT
* *
35642916 CGTTTTTGA-CCC-AATTTCGACCAAAATTAC
1 CATTTTT-ACCCCTAATTTC-ACCAAAATTAT
35642946 CATTTT
1 CATTTT
35642952 GCCCTCGGGT
Statistics
Matches: 100, Mismatches: 8, Indels: 28
0.74 0.06 0.21
Matches are distributed among these distances:
26 3 0.03
27 5 0.05
28 5 0.05
29 67 0.67
30 14 0.14
31 6 0.06
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.39
Consensus pattern (30 bp):
CATTTTTACCCCTAATTTCACCAAAATTAT
Found at i:35642910 original size:29 final size:28
Alignment explanation
Indices: 35642703--35642913 Score: 125
Period size: 29 Copynumber: 7.2 Consensus size: 28
35642693 CTCGATTTCA
35642703 CCAAAATTACCATTTTACCCTCGAACTTT
1 CCAAAATTACCATTTTACCCT-GAACTTT
* * *
35642732 CTAAAATT-CCATTTTTAACCTCG-ATTTT
1 CCAAAATTACCA-TTTTACCCT-GAACTTT
*
35642760 ACCAAAAATTACTATTTTACCCTCGAACTTT
1 -CC-AAAATTACCATTTTACCCT-GAACTTT
**
35642791 CTGAAATT-CCATTTTTAACCCT-AA-TTT
1 CCAAAATTACCA-TTTT-ACCCTGAACTTT
35642818 CACTAAAATTACCATTTTACCCCT-AAGCTTT
1 C-C-AAAATTACCATTTTA-CCCTGAA-CTTT
* *
35642849 CTAAAATT-TCATTTTTACCCCT-AA-TTT
1 CCAAAATTACCA-TTTTA-CCCTGAACTTT
*
35642876 CACCAAAATTATCATTTTACCCCTGAACTTT
1 --CCAAAATTACCATTTTA-CCCTGAACTTT
35642907 CCAAAAT
1 CCAAAAT
35642914 CTCGTTTTTG
Statistics
Matches: 148, Mismatches: 15, Indels: 38
0.74 0.07 0.19
Matches are distributed among these distances:
27 7 0.05
28 14 0.09
29 84 0.57
30 30 0.20
31 13 0.09
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCTGAACTTT
Found at i:35644743 original size:16 final size:16
Alignment explanation
Indices: 35644722--35644753 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35644712 TTTTAAGAAG
35644722 CACTTTTGAGACAAAA
1 CACTTTTGAGACAAAA
*
35644738 CACTTTTGAGATAAAA
1 CACTTTTGAGACAAAA
35644754 AATTGCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
CACTTTTGAGACAAAA
Found at i:35646436 original size:20 final size:20
Alignment explanation
Indices: 35646413--35646477 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 20
35646403 GACTAAAAGC
35646413 ATTGTTGTTTCTTTAAATCG
1 ATTGTTGTTTCTTTAAATCG
35646433 ATTGTTTGTTGT-TTTAAATCG
1 ATTG-TTGTT-TCTTTAAATCG
*
35646454 ATTCTT-TACTTCTTTAAATCG
1 ATTGTTGT--TTCTTTAAATCG
35646475 ATT
1 ATT
35646478 CAGTATTGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 7 0.18
21 30 0.77
22 1 0.03
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (20 bp):
ATTGTTGTTTCTTTAAATCG
Found at i:35646469 original size:21 final size:21
Alignment explanation
Indices: 35646421--35646518 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 21
35646411 GCATTGTTGT
* *
35646421 TTCTTTAAATCGATTGTTT-G
1 TTCTTTAAATCGATTCTTTAC
*
35646441 TTGTTTTAAATCGATTCTTTAC
1 TT-CTTTAAATCGATTCTTTAC
**
35646463 TTCTTTAAATCGATTCAGTA-
1 TTCTTTAAATCGATTCTTTAC
* * *
35646483 TTGTTTAAATCAATTCTTTTC
1 TTCTTTAAATCGATTCTTTAC
* *
35646504 -TGTTTAACTCGATTC
1 TTCTTTAAATCGATTC
35646519 AAACTCTAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
20 30 0.48
21 30 0.48
22 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.10, T:0.52
Consensus pattern (21 bp):
TTCTTTAAATCGATTCTTTAC
Found at i:35646487 original size:42 final size:41
Alignment explanation
Indices: 35646421--35646519 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
35646411 GCATTGTTGT
*** * *
35646421 TTCTTTAAATCGATTGTTTGTTGTTTTAAATCGATTCTTTAC
1 TTCTTTAAATCGATTCAGTATTG-TTTAAATCAATTCTTTAC
*
35646463 TTCTTTAAATCGATTCAGTATTGTTTAAATCAATTCTTTTC
1 TTCTTTAAATCGATTCAGTATTGTTTAAATCAATTCTTTAC
* *
35646504 -TGTTTAACTCGATTCA
1 TTCTTTAAATCGATTCA
35646520 AACTCTAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 14 0.29
41 16 0.33
42 19 0.39
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (41 bp):
TTCTTTAAATCGATTCAGTATTGTTTAAATCAATTCTTTAC
Found at i:35646491 original size:20 final size:21
Alignment explanation
Indices: 35646445--35646498 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
35646435 TGTTTGTTGT
**
35646445 TTTAAATCGATTCTTTACTTC
1 TTTAAATCGATTCAGTACTTC
*
35646466 TTTAAATCGATTCAGTA-TTG
1 TTTAAATCGATTCAGTACTTC
*
35646486 TTTAAATCAATTC
1 TTTAAATCGATTC
35646499 TTTTCTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (21 bp):
TTTAAATCGATTCAGTACTTC
Found at i:35648556 original size:14 final size:13
Alignment explanation
Indices: 35648527--35648569 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
35648517 CAAGCATTTT
35648527 GAAATCAAAAAAA
1 GAAATCAAAAAAA
*
35648540 GAAATCAATACAAA
1 GAAATCAA-AAAAA
35648554 GAAATAGCAAAAAAA
1 GAAAT--CAAAAAAA
35648569 G
1 G
35648570 GAAACAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 8 0.32
14 9 0.36
15 5 0.20
16 3 0.12
ACGTcount: A:0.70, C:0.09, G:0.12, T:0.09
Consensus pattern (13 bp):
GAAATCAAAAAAA
Found at i:35649609 original size:30 final size:30
Alignment explanation
Indices: 35649573--35649708 Score: 139
Period size: 30 Copynumber: 4.5 Consensus size: 30
35649563 TATTTTATTT
35649573 AAAAATTATATTTTGACCCCTAAACTTTCC
1 AAAAATTATATTTTGACCCCTAAACTTTCC
* *
35649603 AAAAATTATATTTTGACCCCTAAAGTTTTC
1 AAAAATTATATTTTGACCCCTAAACTTTCC
* * * * * *
35649633 TAAAATTACATTTTAACCCTTAGACTTTCT
1 AAAAATTATATTTTGACCCCTAAACTTTCC
* * * *
35649663 AGAAATTACATTTT-AACCCTCAAACTTTTC
1 AAAAATTATATTTTGACCCCT-AAACTTTCC
*
35649693 TAAAATTATATTTTGA
1 AAAAATTATATTTTGA
35649709 TCCTCAAAAT
Statistics
Matches: 84, Mismatches: 20, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
29 4 0.05
30 79 0.94
31 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAAATTATATTTTGACCCCTAAACTTTCC
Found at i:35649669 original size:60 final size:60
Alignment explanation
Indices: 35649574--35649706 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 60
35649564 ATTTTATTTA
* * * *
35649574 AAAATTATATTTTGACCCCTAAACTTTCCAAAAATTATATTTTGACCC-CTAAAGTTTTCT
1 AAAATTATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTC-AAACTTTTCT
* * * * *
35649634 AAAATTACATTTTAACCCTTAGACTTTCTAGAAATTACATTTTAACCCTCAAACTTTTCT
1 AAAATTATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTCAAACTTTTCT
35649694 AAAATTATATTTT
1 AAAATTATATTTT
35649707 GATCCTCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 61 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (60 bp):
AAAATTATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTCAAACTTTTCT
Found at i:35654886 original size:29 final size:29
Alignment explanation
Indices: 35654846--35655168 Score: 266
Period size: 29 Copynumber: 11.1 Consensus size: 29
35654836 CTGAACTCAG
* *
35654846 AAATTACATTTTGACCCCAAAACTTCTAA
1 AAATTACATTTTGACCCCGAAACTTCCAA
* *
35654875 AAATTATATTTTTGA--CCTAACAC-TCCAA
1 AAATTACA-TTTTGACCCCGAA-ACTTCCAA
** *
35654903 AAATTACATTTTTGACCCTAAAACTTCTAA
1 AAATTACA-TTTTGACCCCGAAACTTCCAA
* * * *
35654933 AAATTATATTTTTACTCCGAAACTTTCAA
1 AAATTACATTTTGACCCCGAAACTTCCAA
**
35654962 AAATTACATTTTTCCCCCG-AACTTCC-A
1 AAATTACATTTTGACCCCGAAACTTCCAA
* *
35654989 AAATT-CTATTTTTAACCTCGAAACTTCCAA
1 AAATTAC-A-TTTTGACCCCGAAACTTCCAA
* * *
35655019 AAATTTCATTTTTGTCCCC-AAACTTTCAA
1 AAATTACA-TTTTGACCCCGAAACTTCCAA
* *
35655048 AAATTCCATTTTTGACCTCGAAACTTCCAA
1 AAATTACA-TTTTGACCCCGAAACTTCCAA
**
35655078 AAATTACAGTTTT-ACCCTTAAACTTCCAA
1 AAATTACA-TTTTGACCCCGAAACTTCCAA
* *
35655107 AAATTCCATTTTCAACCCCGAAACTTCCAA
1 AAATTACATTTT-GACCCCGAAACTTCCAA
* *
35655137 AAATTACATTGTTGACCTCGAAACTTTCAA
1 AAATTACATT-TTGACCCCGAAACTTCCAA
35655167 AA
1 AA
35655169 CTACCATTCT
Statistics
Matches: 239, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.00
27 7 0.03
28 40 0.17
29 94 0.39
30 94 0.39
31 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATTACATTTTGACCCCGAAACTTCCAA
Found at i:35654890 original size:30 final size:30
Alignment explanation
Indices: 35654846--35655168 Score: 308
Period size: 30 Copynumber: 11.1 Consensus size: 30
35654836 CTGAACTCAG
* *
35654846 AAATTACA-TTTTGACCCCAAAACTTCTAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* *
35654875 AAATTATATTTTTGA--CCTAACAC-TCCAA
1 AAATTACATTTTTGACCCCGAA-ACTTCCAA
** *
35654903 AAATTACATTTTTGACCCTAAAACTTCTAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* * *
35654933 AAATTATATTTTT-ACTCCGAAACTTTCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
*
35654962 AAATTACATTTTT-CCCCCG-AACTTCC-A
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* *
35654989 AAATT-CTATTTTTAACCTCGAAACTTCCAA
1 AAATTAC-ATTTTTGACCCCGAAACTTCCAA
* * *
35655019 AAATTTCATTTTTGTCCCC-AAACTTTCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* *
35655048 AAATTCCATTTTTGACCTCGAAACTTCCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* **
35655078 AAATTACAGTTTT-ACCCTTAAACTTCCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* **
35655107 AAATTCCATTTTCAACCCCGAAACTTCCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
* * *
35655137 AAATTACATTGTTGACCTCGAAACTTTCAA
1 AAATTACATTTTTGACCCCGAAACTTCCAA
35655167 AA
1 AA
35655169 CTACCATTCT
Statistics
Matches: 239, Mismatches: 43, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.00
27 12 0.05
28 32 0.13
29 93 0.39
30 100 0.42
31 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTTGACCCCGAAACTTCCAA
Found at i:35655066 original size:59 final size:58
Alignment explanation
Indices: 35654846--35655168 Score: 320
Period size: 59 Copynumber: 5.5 Consensus size: 58
35654836 CTGAACTCAG
* *
35654846 AAATTACA-TTTTGACCCCAAAACTTCTAAAAATTATATTTTTGACCT--AACAC-TCCAA
1 AAATTACATTTTTGACCCC-AAACTTC-AAAAATTCTATTTTTAACCTCGAA-ACTTCCAA
* * *
35654903 AAATTACATTTTTGACCCTAAAACTTCTAAAAATTATATTTTT-A-CTCCGAAACTTTCAA
1 AAATTACATTTTTGACCC-CAAACTTC-AAAAATTCTATTTTTAACCT-CGAAACTTCCAA
* * *
35654962 AAATTACATTTTT-CCCCCGAACTTCCAAAATTCTATTTTTAACCTCGAAACTTCCAA
1 AAATTACATTTTTGACCCCAAACTTCAAAAATTCTATTTTTAACCTCGAAACTTCCAA
* * * *
35655019 AAATTTCATTTTTGTCCCCAAACTTTCAAAAATTCCATTTTTGACCTCGAAACTTCCAA
1 AAATTACATTTTTGACCCCAAAC-TTCAAAAATTCTATTTTTAACCTCGAAACTTCCAA
* * * * *
35655078 AAATTACAGTTTT-ACCCTTAAACTTCCAAAAATTCCATTTTCAACCCCGAAACTTCCAA
1 AAATTACATTTTTGACCC-CAAACTT-CAAAAATTCTATTTTTAACCTCGAAACTTCCAA
* *
35655137 AAATTACATTGTTGACCTCGAAACTTTCAAAA
1 AAATTACATTTTTGACC-CCAAAC-TTCAAAA
35655169 CTACCATTCT
Statistics
Matches: 227, Mismatches: 24, Indels: 27
0.82 0.09 0.10
Matches are distributed among these distances:
56 15 0.07
57 39 0.17
58 51 0.22
59 107 0.47
60 12 0.05
61 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
AAATTACATTTTTGACCCCAAACTTCAAAAATTCTATTTTTAACCTCGAAACTTCCAA
Found at i:35655666 original size:96 final size:96
Alignment explanation
Indices: 35655559--35655740 Score: 215
Period size: 96 Copynumber: 1.9 Consensus size: 96
35655549 AAAGCTTTAA
* * * * *
35655559 AATCGAAGCAATA-TTCTTTTAT-TTCGAGTTTTGAAATTTTGCGTCTTAACTTATTAGGTGCAA
1 AATCGAAGCAATATTTC-CTTATCTTCG-GTTATGAAAATTTGCGCCTTAACTTACTAGGTGCAA
** *
35655622 TTTTTCTTCAAATCAAAATAATCGAATACCCTT
64 CCTTTCTCCAAATCAAAATAATCGAATACCCTT
* * *
35655655 AATCGAGGCAATGTTTCCTTATCTTCGGTTATGAAAATTTGCGCCTTAATTTACTAGGTGCAACC
1 AATCGAAGCAATATTTCCTTATCTTCGGTTATGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
* *
35655720 TTTCTCCAAATCGAGATAATC
66 TTTCTCCAAATCAAAATAATC
35655741 AAACATCCTT
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
96 64 0.90
97 7 0.10
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (96 bp):
AATCGAAGCAATATTTCCTTATCTTCGGTTATGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
TTTCTCCAAATCAAAATAATCGAATACCCTT
Found at i:35663888 original size:24 final size:24
Alignment explanation
Indices: 35663861--35663907 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
35663851 GACTAATCAA
* *
35663861 AGTTTGATTGAGACAAATAAACAG
1 AGTTTGATTAAAACAAATAAACAG
35663885 AGTTTGATTAAAACAAATAAACA
1 AGTTTGATTAAAACAAATAAACA
35663908 TAATTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.15, T:0.26
Consensus pattern (24 bp):
AGTTTGATTAAAACAAATAAACAG
Found at i:35666811 original size:20 final size:20
Alignment explanation
Indices: 35666786--35666823 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35666776 GGTTTTTCGA
*
35666786 AAAAAGTCAACGGTCAACCC
1 AAAAAGTCAACGATCAACCC
35666806 AAAAAGTCAACGATCAAC
1 AAAAAGTCAACGATCAAC
35666824 TGTCAATGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAAAGTCAACGATCAACCC
Found at i:35666829 original size:7 final size:7
Alignment explanation
Indices: 35666811--35666884 Score: 67
Period size: 7 Copynumber: 10.6 Consensus size: 7
35666801 AACCCAAAAA
35666811 GTCAACG
1 GTCAACG
* *
35666818 ATCAACT
1 GTCAACG
*
35666825 GTCAATG
1 GTCAACG
*
35666832 GTCAACA
1 GTCAACG
*
35666839 GCCAACG
1 GTCAACG
*
35666846 GTCAATG
1 GTCAACG
*
35666853 TTCAACG
1 GTCAACG
*
35666860 GTCAATG
1 GTCAACG
*
35666867 TTCAACG
1 GTCAACG
35666874 GTCAACG
1 GTCAACG
35666881 GTCA
1 GTCA
35666885 GGTCAAATTG
Statistics
Matches: 49, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (7 bp):
GTCAACG
Found at i:35668083 original size:29 final size:28
Alignment explanation
Indices: 35668037--35668319 Score: 196
Period size: 30 Copynumber: 9.6 Consensus size: 28
35668027 CCCTATTTCA
*
35668037 TTTAAAAATCATATTTTTACCCTAAAACTT
1 TTTAAAAATCACA-TTTTACCCT-AAACTT
*
35668067 TTTTAAAATCACATTTTGACCCTAAAACTT
1 TTTAAAAATCACATTTT-ACCCT-AAACTT
* * * *
35668097 TCCT-AAAATTACATTTTCCCCTGAACTT
1 T-TTAAAAATCACATTTTACCCTAAACTT
** *
35668125 TTCCAAAATCAAATTTTAACCCTCAAACTT
1 TTTAAAAATCACATTTT-ACCCT-AAACTT
* *
35668155 TTTTAAAA-CTACATTTAACCCCTAAAC-T
1 TTTAAAAATC-ACATTTTA-CCCTAAACTT
* * *
35668183 TCTCAAAATCACATTTTAACCTTAAA-TT
1 TTTAAAAATCACATTTT-ACCCTAAACTT
*
35668211 TTTCCAAAATCACATTTTAACCCCTAAACTT
1 TTT-AAAAATCACATTTT-A-CCCTAAACTT
* * *
35668242 TTCAAAAATTACATTTTAACCTCTGAACTT
1 TTTAAAAATCACATTTT-ACC-CTAAACTT
* * *
35668272 TTGAAAAATTACATTTTAACCTTAAACTT
1 TTTAAAAATCACATTTT-ACCCTAAACTT
35668301 TTTAAAATATCACATTTTA
1 TTTAAAA-ATCACATTTTA
35668320 ACCCCAAATT
Statistics
Matches: 207, Mismatches: 31, Indels: 31
0.77 0.12 0.12
Matches are distributed among these distances:
28 39 0.19
29 51 0.25
30 112 0.54
31 5 0.02
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (28 bp):
TTTAAAAATCACATTTTACCCTAAACTT
Found at i:35668133 original size:58 final size:58
Alignment explanation
Indices: 35668051--35668323 Score: 228
Period size: 58 Copynumber: 4.6 Consensus size: 58
35668041 AAAATCATAT
* ** *
35668051 TTTTACCCTAAAACTTTTTTAAAATCACATTTTGACCCTAAAACTTTCCTAAAATTACA
1 TTTTCCCCT-AAACTTTTCCAAAATCACATTTTAACCCTAAAACTTTCCTAAAATTACA
* * * ** *
35668110 TTTTCCCCTGAACTTTTCCAAAATCAAATTTTAACCCTCAAACTTTTTTAAAACTACA
1 TTTTCCCCTAAACTTTTCCAAAATCACATTTTAACCCTAAAACTTTCCTAAAATTACA
* * * ** *
35668168 TTTAACCCCTAAACTTCT-CAAAATCACATTTTAACCTTAAATTTTTCC-AAAATCACA
1 TTT-TCCCCTAAACTTTTCCAAAATCACATTTTAACCCTAAAACTTTCCTAAAATTACA
* * * ***
35668225 TTTTAACCCCTAAACTTTTCAAAAATTACATTTTAACCTCT-GAACTTTTGAAAAATTACA
1 TTTT--CCCCTAAACTTTTCCAAAATCACATTTTAACC-CTAAAACTTTCCTAAAATTACA
* * **
35668285 TTTTAACCTTAAACTTTTTAAAATATCACATTTTAACCC
1 TTTT-CCCCTAAACTTTTCCAAA-ATCACATTTTAACCC
35668324 CAAATTCACC
Statistics
Matches: 170, Mismatches: 37, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
57 10 0.06
58 78 0.46
59 56 0.33
60 26 0.15
ACGTcount: A:0.37, C:0.23, G:0.01, T:0.38
Consensus pattern (58 bp):
TTTTCCCCTAAACTTTTCCAAAATCACATTTTAACCCTAAAACTTTCCTAAAATTACA
Found at i:35672629 original size:30 final size:30
Alignment explanation
Indices: 35672595--35672754 Score: 188
Period size: 30 Copynumber: 5.4 Consensus size: 30
35672585 ATTTTATTTA
* *
35672595 AAAATCACTTTTTTACCCTCAAACTTTTCC
1 AAAATTACATTTTTACCCTCAAACTTTTCC
35672625 AAAATTACATTTTTACCC-CGAAAC-TTTCTC
1 AAAATTACATTTTTACCCTC-AAACTTTTC-C
*
35672655 AAAATTACA-TTTT-CCCTCAAAATTTTCC
1 AAAATTACATTTTTACCCTCAAACTTTTCC
*
35672683 AAAATTACATTTTAACCCT-AAACTTTTCC
1 AAAATTACATTTTTACCCTCAAACTTTTCC
* * *
35672712 AAAATCACATTTTGACCC-CTAAACTTTTCA
1 AAAATTACATTTTTACCCTC-AAACTTTTCC
35672742 AAAATTACATTTT
1 AAAATTACATTTT
35672755 AACCTTAAAT
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
28 16 0.14
29 42 0.37
30 55 0.49
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTTACCCTCAAACTTTTCC
Found at i:35672707 original size:87 final size:88
Alignment explanation
Indices: 35672595--35672793 Score: 244
Period size: 87 Copynumber: 2.3 Consensus size: 88
35672585 ATTTTATTTA
* * * * *
35672595 AAAATCACTTTTTTACCCTCAAACTTTTCCAAAATTACATTTTTACCCCGAAACTTTCTC-AAAA
1 AAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTGACCCCGAAACTTT-TCAAAAA
*
35672659 TTACATTTT-CCCTCAAAATTTTCC
65 TTACATTTTAACCT-AAAATTTTCC
*
35672683 AAAATTACATTTTAACCCT-AAACTTTTCCAAAATCACATTTTGACCCCTAAACTTTTCAAAAAT
1 AAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTGACCCCGAAACTTTTCAAAAAT
* **
35672747 TACATTTTAACCTTAAATTTTTT
66 TACATTTTAACCTAAAATTTTCC
35672770 AAAATATCACATTTTAACCC-CAAA
1 AAAAT-T-ACATTTTAACCCTCAAA
35672794 TTCTTTGAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
86 2 0.02
87 59 0.61
88 20 0.21
89 15 0.16
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (88 bp):
AAAATTACATTTTAACCCTCAAACTTTTCCAAAATCACATTTTGACCCCGAAACTTTTCAAAAAT
TACATTTTAACCTAAAATTTTCC
Found at i:35672763 original size:29 final size:29
Alignment explanation
Indices: 35672605--35672790 Score: 184
Period size: 30 Copynumber: 6.3 Consensus size: 29
35672595 AAAATCACTT
35672605 TTTTA-CCCTCAAACTTTTCCAAAATTACA
1 TTTTACCCCT-AAACTTTTCCAAAATTACA
*
35672634 TTTTTACCCCGAAAC-TTTCTCAAAATTACA
1 -TTTTACCCCTAAACTTTTC-CAAAATTACA
*
35672664 TTTT--CCCTCAAAATTTTCCAAAATTACA
1 TTTTACCCCT-AAACTTTTCCAAAATTACA
* *
35672692 TTTTAACCCTAAACTTTTCCAAAATCACA
1 TTTTACCCCTAAACTTTTCCAAAATTACA
*
35672721 TTTTGACCCCTAAACTTTTCAAAAATTACA
1 TTTT-ACCCCTAAACTTTTCCAAAATTACA
* * **
35672751 TTTTAACCTTAAA-TTTTTTAAAATATCACA
1 TTTTACCCCTAAACTTTTCCAAAAT-T-ACA
35672781 TTTTAACCCC
1 TTTT-ACCCC
35672791 AAATTCTTTG
Statistics
Matches: 132, Mismatches: 14, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.02
28 26 0.20
29 41 0.31
30 56 0.42
31 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (29 bp):
TTTTACCCCTAAACTTTTCCAAAATTACA
Found at i:35675496 original size:3 final size:3
Alignment explanation
Indices: 35675488--35675530 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35675478 TTGAACAAAG
35675488 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35675531 CTTTTAGGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35693608 original size:35 final size:33
Alignment explanation
Indices: 35693564--35693639 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 33
35693554 GGTCCAAAAA
* *
35693564 TTAT-TATTTTAGCTGTTTTTAATTTTAAATTTTT
1 TTATATATTTTAGAT-TTTTAAATTTT-AATTTTT
35693598 TTATATATTTTTAGATTTTTAAATTTTAATTTTT
1 TTATATA-TTTTAGATTTTTAAATTTTAATTTTT
*
35693632 TTAAATAT
1 TTATATAT
35693640 AAAATTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 1 0.03
34 17 0.46
35 12 0.32
36 7 0.19
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (33 bp):
TTATATATTTTAGATTTTTAAATTTTAATTTTT
Found at i:35696838 original size:28 final size:28
Alignment explanation
Indices: 35696803--35696865 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
35696793 AAACGGGACT
* *
35696803 TTTTGGATGTCCGAGGGTAAAATGGTAA
1 TTTTGGATGTCCGAGGGCAAAATGATAA
* ** *
35696831 TTTTGGATTTTTGGGGGCAAAATGATAA
1 TTTTGGATGTCCGAGGGCAAAATGATAA
35696859 TTTTGGA
1 TTTTGGA
35696866 AAATTTCGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38
Consensus pattern (28 bp):
TTTTGGATGTCCGAGGGCAAAATGATAA
Found at i:35696883 original size:144 final size:145
Alignment explanation
Indices: 35696735--35697040 Score: 332
Period size: 144 Copynumber: 2.1 Consensus size: 145
35696725 AATTAGGGTT
* * * * ** *
35696735 AAAATGATATTTTAGACACTTAAGAGTAAAATAGTAA-TTTTCGAAAGAATCGGGATC-AAAACG
1 AAAATGAAATTTTAGACAATCAAGAGTAAAATAGTAATTTTTAGAAA-AATCGAAATCAAAAACA
* ** * * * * *
35696798 GGACTTTTTGGATGTCCGAGGGTAAAATGGTAATTTTG-GATTTTTGGGGGC-AAAATGATAATT
65 GGA-TTTTTAGACATCCAAGAGTAAAATGGTAATTTCGAGAATTTTAGGGGCAAAAATGA-AATT
35696861 TTGGAAAATTTCGAGTTA
128 TTGGAAAATTTCGAGTTA
* * *
35696879 AAAATGAAATTTTAGACAATCAAGGGTAAAATGGTAATTTTTAGAAAAATCGAAATCAAAAATAG
1 AAAATGAAATTTTAGACAATCAAGAGTAAAATAGTAATTTTTAGAAAAATCGAAATCAAAAACAG
* *
35696944 GATTTTTAGACATCCAAGAGTAAAATGGTAATTTCGAGAATTTTAGGGTCAAAAATGAAATTTTT
66 GATTTTTAGACATCCAAGAGTAAAATGGTAATTTCGAGAATTTTAGGGGCAAAAATGAAATTTTG
* * *
35697009 GAAAATTTGGGGTCA
131 GAAAATTTCGAGTTA
*
35697024 AAAATAGAATTTTTAGA
1 AAAAT-GAAATTTTAGA
35697041 AGCTCGGAGG
Statistics
Matches: 133, Mismatches: 24, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
144 68 0.51
145 48 0.36
146 17 0.13
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (145 bp):
AAAATGAAATTTTAGACAATCAAGAGTAAAATAGTAATTTTTAGAAAAATCGAAATCAAAAACAG
GATTTTTAGACATCCAAGAGTAAAATGGTAATTTCGAGAATTTTAGGGGCAAAAATGAAATTTTG
GAAAATTTCGAGTTA
Found at i:35697094 original size:59 final size:56
Alignment explanation
Indices: 35697020--35697131 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 56
35697010 AAAATTTGGG
*
35697020 GTCAAAAATAGAATTTTTAGAAGCTCGGAGGTAAAAACGTAATTTTTGGAAGTTTTTAA
1 GTCAAAAATAGAATTTATAGAAGCTCGGAGGT-AAAACGTAA-TTTTGGAA-TTTTTAA
* * * *
35697079 GTCAAAAAT-GAAATTTATAGAAGTTTGGGGGTAAAATGTAATTTTGGAATTTT
1 GTCAAAAATAG-AATTTATAGAAGCTCGGAGGTAAAACGTAATTTTGGAATTTT
35697132 AGGGGTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.09
57 8 0.17
58 9 0.19
59 26 0.55
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (56 bp):
GTCAAAAATAGAATTTATAGAAGCTCGGAGGTAAAACGTAATTTTGGAATTTTTAA
Found at i:35697136 original size:28 final size:27
Alignment explanation
Indices: 35696965--35697166 Score: 84
Period size: 29 Copynumber: 6.9 Consensus size: 27
35696955 ATCCAAGAGT
* * *
35696965 AAAATGGTAATTTCGAGAATTTTAGGGTCA
1 AAAAT-GTAATTTTG-GAAGTTTGGGGT-A
* * *
35696995 AAAATGAAATTTTTGAAAATTTGGGGTCA
1 AAAATGTAA-TTTTGGAAGTTTGGGGT-A
* * *
35697024 AAAATAG-AATTTTTAGAAGCTCGGAGGTA
1 AAAAT-GTAA-TTTTGGAAGTTTGG-GGTA
* ***
35697053 AAAACGTAATTTTTGGAAGTTTTTAAGTCA
1 AAAATGTAA-TTTTGGAAG-TTTGGGGT-A
* *
35697083 AAAATGAAATTTATAGAAGTTTGGGGGT-
1 AAAATGTAATTT-TGGAAGTTT-GGGGTA
*
35697111 AAAATGTAATTTTGGAATTTTAGGGGTCA
1 AAAATGTAATTTTGGAAGTTT-GGGGT-A
*
35697140 AAAATATAATTTTGGAGAAGTTTGGGG
1 AAAATGTAATTTT-G-GAAGTTTGGGG
35697167 GCCAACATAC
Statistics
Matches: 131, Mismatches: 29, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
27 12 0.09
28 12 0.09
29 67 0.51
30 34 0.26
31 6 0.05
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (27 bp):
AAAATGTAATTTTGGAAGTTTGGGGTA
Found at i:35697164 original size:58 final size:57
Alignment explanation
Indices: 35696989--35697167 Score: 161
Period size: 58 Copynumber: 3.1 Consensus size: 57
35696979 GAGAATTTTA
* * * * *
35696989 GGGTCAAAAATGAAATTTTTGAAAATTT-GGGGTCAAAAATAGAATTTTTAGAAGCTCGG
1 GGGT-AAAAATGTAATTTTTGGAATTTTAGGGGTCAAAAATA-AA-TTTTAGAAGTTTGG
* * *
35697048 AGGTAAAAACGTAATTTTTGGAAGTTTTTA--AGTCAAAAATGAAATTTATAGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGGAA--TTTTAGGGGTCAAAAAT-AAATTT-TAGAAGTTTGG
35697107 GGGT-AAAATGTAA-TTTTGGAATTTTAGGGGTCAAAAATATAATTTTGGAGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGGAATTTTAGGGGTCAAAAATA-AATTTT--AGAAGTTTGG
35697165 GGG
1 GGG
35697168 CCAACATACA
Statistics
Matches: 99, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
55 5 0.05
56 2 0.02
57 22 0.22
58 40 0.40
59 26 0.26
60 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (57 bp):
GGGTAAAAATGTAATTTTTGGAATTTTAGGGGTCAAAAATAAATTTTAGAAGTTTGG
Found at i:35698283 original size:3 final size:3
Alignment explanation
Indices: 35698275--35698325 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
35698265 AGATTAATAT
* * *
35698275 TTA TTA TTA TTA TTA TTA -TA TTAA TTA CTA CTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
35698320 TTA TTA
1 TTA TTA
35698326 AAATATCTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:35698291 original size:30 final size:31
Alignment explanation
Indices: 35698251--35698337 Score: 79
Period size: 33 Copynumber: 2.7 Consensus size: 31
35698241 ACGAATTTAT
*
35698251 TTATTTTTATTAAAAGATTAATA-T-TTATTA
1 TTATTATTATTAAAA-ATTAATACTATTATTA
* *
35698281 TTATTATTATTATATTAATTACTACTATTATTA
1 TTATTATTATTA-A-AAATTAATACTATTATTA
*
35698314 TTAATATTATTAAAATATCTAATA
1 TTATTATTATTAAAA-AT-TAATA
35698338 ATTAGTAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
30 11 0.24
31 8 0.18
32 5 0.11
33 21 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (31 bp):
TTATTATTATTAAAAATTAATACTATTATTA
Found at i:35698326 original size:9 final size:9
Alignment explanation
Indices: 35698267--35698326 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
35698257 TTATTAAAAG
35698267 ATTAATATTT
1 ATTAATA-TT
*
35698277 ATTATTATT
1 ATTAATATT
*
35698286 ATTATTA-T
1 ATTAATATT
*
35698294 ATTAATTACT
1 ATTAA-TATT
* *
35698304 ACTATTATT
1 ATTAATATT
35698313 ATTAATATT
1 ATTAATATT
35698322 ATTAA
1 ATTAA
35698327 AATATCTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
8 5 0.12
9 26 0.63
10 10 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTAATATT
Found at i:35699108 original size:17 final size:17
Alignment explanation
Indices: 35699086--35699193 Score: 155
Period size: 17 Copynumber: 6.3 Consensus size: 17
35699076 GAACATTTTA
* *
35699086 TTAAATTTATAATAATT
1 TTAAATTTAAAATAAAT
35699103 TTAAATTTGAAAATAAAT
1 TTAAATTT-AAAATAAAT
* *
35699121 TTAAACTTAAATTAAAT
1 TTAAATTTAAAATAAAT
35699138 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
35699155 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
35699172 TT-AATCTTAAAATAAAT
1 TTAAAT-TTAAAATAAAT
35699189 TTAAA
1 TTAAA
35699194 ATGGGTTTGG
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
16 3 0.04
17 63 0.77
18 16 0.20
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:35699130 original size:6 final size:6
Alignment explanation
Indices: 35699102--35699193 Score: 79
Period size: 6 Copynumber: 16.0 Consensus size: 6
35699092 TTATAATAAT
* *
35699102 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
35699149 -ATAAA TTTAAA TTTAAA -ATAAA TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
35699194 ATGGGTTTGG
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
5 23 0.33
6 41 0.59
7 5 0.07
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:35699141 original size:11 final size:11
Alignment explanation
Indices: 35699103--35699193 Score: 78
Period size: 11 Copynumber: 8.0 Consensus size: 11
35699093 TATAATAATT
35699103 TTAAATTTGAAA
1 TTAAATTT-AAA
*
35699115 ATAAATTTAAA
1 TTAAATTTAAA
35699126 CTTAAA-TTAAA
1 -TTAAATTTAAA
35699137 TTTAAATTTAAA
1 -TTAAATTTAAA
*
35699149 ATAAATTTAAA
1 TTAAATTTAAA
*
35699160 TTTAAA-ATAAA
1 -TTAAATTTAAA
*
35699171 TTTAATCTTAAA
1 TTAAAT-TTAAA
*
35699183 ATAAATTTAAA
1 TTAAATTTAAA
35699194 ATGGGTTTGG
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
10 4 0.06
11 32 0.50
12 28 0.44
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:35699145 original size:23 final size:23
Alignment explanation
Indices: 35699117--35699195 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
35699107 ATTTGAAAAT
*
35699117 AAATTTAAACTTAAA-TTAAATTT
1 AAATTTAAA-ATAAATTTAAATTT
35699140 AAATTTAAAATAAATTTAAATTT
1 AAATTTAAAATAAATTTAAATTT
* * * *
35699163 AAA-ATAAATTTAATCTTAAA-AT
1 AAATTTAAAATAAAT-TTAAATTT
35699185 AAATTTAAAAT
1 AAATTTAAAAT
35699196 GGGTTTGGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 16 0.35
23 30 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTTAAAATAAATTTAAATTT
Found at i:35699272 original size:17 final size:17
Alignment explanation
Indices: 35699233--35699289 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
35699223 AGACTTCAAG
*
35699233 AATATATTTTATTATTT-
1 AATATATATTATT-TTTA
*
35699250 ATTATATATTATTTTTA
1 AATATATATTATTTTTA
*
35699267 AATATAAATTTATGTTTTA
1 AATATATA-TTAT-TTTTA
35699286 AATA
1 AATA
35699290 CGTGATTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.09
17 17 0.52
18 4 0.12
19 9 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
AATATATATTATTTTTA
Found at i:35702792 original size:18 final size:18
Alignment explanation
Indices: 35702769--35702805 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
35702759 GATAAAATAC
*
35702769 TTTATATATTATGTTATT
1 TTTATATATTATGTAATT
35702787 TTTATATATTATGTAATT
1 TTTATATATTATGTAATT
35702805 T
1 T
35702806 AGAACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATATATTATGTAATT
Found at i:35719382 original size:13 final size:13
Alignment explanation
Indices: 35719337--35719382 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
35719327 AATTTGAACT
*
35719337 TTATTTTATTA-A
1 TTATTTTAATATA
*
35719349 TTATTTTTAA-ATT
1 TTA-TTTTAATATA
35719362 TTATTTTAATATA
1 TTATTTTAATATA
35719375 TTATTTTA
1 TTATTTTA
35719383 TTTTTACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTTTAATATA
Found at i:35726025 original size:2 final size:2
Alignment explanation
Indices: 35726020--35726098 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
35726010 ATATATGTAT
35726020 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35726062 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
35726099 CCTGCTTTAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35747153 original size:6 final size:6
Alignment explanation
Indices: 35747128--35747166 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
35747118 ACAATTCATA
* * *
35747128 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
35747167 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:35747840 original size:21 final size:22
Alignment explanation
Indices: 35747805--35747846 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
35747795 TAAATTTCAG
*
35747805 TTTCTAATAATTTTTCTAAGTT
1 TTTCTAATAATTTTTCAAAGTT
*
35747827 TTTCT-ATGATTTTTCAAAGT
1 TTTCTAATAATTTTTCAAAGT
35747847 CAGAACAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (22 bp):
TTTCTAATAATTTTTCAAAGTT
Found at i:35755276 original size:1 final size:1
Alignment explanation
Indices: 35755270--35755295 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35755260 TAGCGAAAGC
35755270 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
35755296 AAGAAATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35759800 original size:2 final size:2
Alignment explanation
Indices: 35759793--35759838 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35759783 AATTAAAGGC
35759793 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
35759835 AT AT
1 AT AT
35759839 GTTATGGGAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35761950 original size:23 final size:22
Alignment explanation
Indices: 35761910--35761952 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35761900 CTAAAATAAT
* *
35761910 AATAAAATTATATTTTTATTAC
1 AATAAAAATATATATTTATTAC
35761932 AATAAAAATATATAATTTATT
1 AATAAAAATATAT-ATTTATT
35761953 TTAGGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
AATAAAAATATATATTTATTAC
Found at i:35766266 original size:13 final size:13
Alignment explanation
Indices: 35766248--35766273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35766238 GTGGCGTTCC
35766248 TTAGTTACTCTAA
1 TTAGTTACTCTAA
35766261 TTAGTTACTCTAA
1 TTAGTTACTCTAA
35766274 ATAATAGAAA
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:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTAGTTACTCTAA
Found at i:35771811 original size:18 final size:18
Alignment explanation
Indices: 35771788--35771826 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
35771778 TGCAAGGCGT
*
35771788 AAAGGGAGTTTGGTCGCG
1 AAAGGGAATTTGGTCGCG
*
35771806 AAAGGGAATTTGGTCGTG
1 AAAGGGAATTTGGTCGCG
35771824 AAA
1 AAA
35771827 TGGTGTTCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.38, T:0.23
Consensus pattern (18 bp):
AAAGGGAATTTGGTCGCG
Found at i:35773823 original size:3 final size:3
Alignment explanation
Indices: 35773815--35773844 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35773805 TTTGTTCTTC
35773815 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35773845 TCTTTGTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35776084 original size:15 final size:15
Alignment explanation
Indices: 35776052--35776083 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
35776042 TGGTCTGATC
35776052 ATATTAATTTTTTTT
1 ATATTAATTTTTTTT
35776067 ATATT-A-TTTTTTT
1 ATATTAATTTTTTTT
35776080 ATAT
1 ATAT
35776084 AAAAATGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.65
14 1 0.06
15 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATATTAATTTTTTTT
Found at i:35778494 original size:2 final size:2
Alignment explanation
Indices: 35778489--35778513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35778479 TTTTTTTTTT
35778489 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
35778514 TTTTACTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:35781073 original size:23 final size:23
Alignment explanation
Indices: 35781047--35781094 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
35781037 CTATGATAAA
* *
35781047 GAATTTAAATGAAGTAATGAATC
1 GAATTTAAATAAAATAATGAATC
35781070 GAATTTAAATAAAATAATGAATC
1 GAATTTAAATAAAATAATGAATC
35781093 GA
1 GA
35781095 TTACAAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.29
Consensus pattern (23 bp):
GAATTTAAATAAAATAATGAATC
Found at i:35788308 original size:20 final size:20
Alignment explanation
Indices: 35788283--35788323 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35788273 AGATTATACA
35788283 ATATGATAATGTTTACACCG
1 ATATGATAATGTTTACACCG
35788303 ATATGATAATGTTTACACCG
1 ATATGATAATGTTTACACCG
35788323 A
1 A
35788324 AGCTGATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
ATATGATAATGTTTACACCG
Found at i:35798960 original size:7 final size:6
Alignment explanation
Indices: 35798930--35798959 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
35798920 TATTAATCCT
35798930 TTTATC TTTATC TTTATC TTTATTC TTTAT
1 TTTATC TTTATC TTTATC TTTA-TC TTTAT
35798960 TGGCCAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATC
Found at i:35799396 original size:56 final size:56
Alignment explanation
Indices: 35799224--35799401 Score: 189
Period size: 57 Copynumber: 3.1 Consensus size: 56
35799214 AAGTTTGTCC
* * ** *
35799224 AATTTGGTACCTTAAGC-TGACAATTTTTTTCTAATTTGGTACATAAGTTTTTTTTATTT
1 AATTTGGTACCTCAA-CTTGAC-A-TTTTTTCTAATTTGATAC-TAAGTTTTTTTGGTCT
* * * * *
35799283 AATTTGGCACCTCAACTTGATACTTTTTCTAATTTGATGTCTAAGTTTTTTGGGTCT
1 AATTTGGTACCTCAACTTGACATTTTTTCTAATTTGAT-ACTAAGTTTTTTTGGTCT
*
35799340 AATTTGGTACCTCAACTTGACATTTTTTCATAATTTGATACCAA-TTTTTTTGGTCT
1 AATTTGGTACCTCAACTTGACATTTTTTC-TAATTTGATACTAAGTTTTTTTGGTCT
35799396 AATTTG
1 AATTTG
35799402 ACACCTAAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
56 17 0.17
57 55 0.55
58 12 0.12
59 16 0.16
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.49
Consensus pattern (56 bp):
AATTTGGTACCTCAACTTGACATTTTTTCTAATTTGATACTAAGTTTTTTTGGTCT
Found at i:35808568 original size:59 final size:59
Alignment explanation
Indices: 35808505--35808861 Score: 504
Period size: 59 Copynumber: 6.1 Consensus size: 59
35808495 AGACCCTCGA
* * *
35808505 GGGTAAAATGATAATTTTTGGTGAAATCAGGATTAAAAATGGAATTTTGGAAAGTTCAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
** * *
35808564 GGGTAAAATGGTAA-TTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGAGACTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
35808622 GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAGACTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
35808681 GGGTAAAATGGCAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * *
35808740 GGGTAAAATAGTAATTTTTGGTGAAATCGGGGCTAAAAATGGAATTTTGGAGAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
35808799 GGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATAGAATTTTGGAAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTAG
35808858 GGGT
1 GGGT
35808862 CTATAAATAA
Statistics
Matches: 274, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
58 54 0.20
59 219 0.80
60 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:35808777 original size:30 final size:30
Alignment explanation
Indices: 35808517--35808846 Score: 148
Period size: 29 Copynumber: 11.2 Consensus size: 30
35808507 GTAAAATGAT
* *
35808517 AATTTTTGGTGAAATCAGGATTAAAA-ATGG
1 AATTTTTGGTGAAATCGGGGTTAAAATA-GG
35808547 AA-TTTT-G-GAAAGTTCAGGGG-TAAAAT-GG
1 AATTTTTGGTGAAA--TC-GGGGTTAAAATAGG
*
35808575 TAA-TTTTGGTGAAATTGGGGTTAAAA-ATGG
1 -AATTTTTGGTGAAATCGGGGTTAAAATA-GG
* ** *
35808605 AA-TTTTGGAGACTTTAGGGG-TAAAAT-GG
1 AATTTTTGGTGA-AATCGGGGTTAAAATAGG
35808633 TAATTTTTGGTGAAATCGGGGTTAAAA-ATGG
1 -AATTTTTGGTGAAATCGGGGTTAAAATA-GG
* ** *
35808664 AA-TTTTGGAGACTTTAGGGG-TAAAAT-GG
1 AATTTTTGGTGA-AATCGGGGTTAAAATAGG
*
35808692 CAATTTTTGGTGAAATCGAGGTTAAAA-ATGG
1 -AATTTTTGGTGAAATCGGGGTTAAAATA-GG
* * *
35808723 AA-TTTT-G-GAAAGTTTGGGGGTAAAATAGT
1 AATTTTTGGTGAAA--TCGGGGTTAAAATAGG
*
35808752 AATTTTTGGTGAAATCGGGGCTAAAA-ATGG
1 AATTTTTGGTGAAATCGGGGTTAAAATA-GG
* ** * *
35808782 AA-TTTTGGAGAGTTTGGGGGTAAAAT-GG
1 AATTTTTGGTGAAATCGGGGTTAAAATAGG
*
35808810 TAATTTTTGGTGAAATCGAGGTTAAAAATA-G
1 -AATTTTTGGTGAAATCGGGGTT-AAAATAGG
35808841 AATTTT
1 AATTTT
35808847 GGAAAGTTTG
Statistics
Matches: 226, Mismatches: 38, Indels: 72
0.67 0.11 0.21
Matches are distributed among these distances:
27 8 0.04
28 14 0.06
29 101 0.45
30 84 0.37
31 15 0.07
32 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (30 bp):
AATTTTTGGTGAAATCGGGGTTAAAATAGG
Found at i:35810602 original size:6 final size:6
Alignment explanation
Indices: 35810593--35810685 Score: 61
Period size: 6 Copynumber: 16.0 Consensus size: 6
35810583 ATTTTTAATG
* * * *
35810593 TTTAAA TTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTTAAGA --TAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA
* * * *
35810641 TTTAAA TTTAAA --TAAA TTTAAA -ATCAA TTTAAC TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
35810686 CAAGAAGTCC
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
4 5 0.07
5 6 0.09
6 52 0.76
7 5 0.07
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:35810622 original size:12 final size:12
Alignment explanation
Indices: 35810578--35810632 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
35810568 CTTTATGGAC
35810578 TTTTAATTTTTAA
1 TTTTAA-TTTTAA
*
35810591 TGTTTAAATTTAGTA
1 T-TTTAATTTTA--A
35810606 TTTTAATTTTAA
1 TTTTAATTTTAA
*
35810618 TTTTAATTTAAA
1 TTTTAATTTTAA
35810630 TTT
1 TTT
35810633 AAGATAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 15 0.42
13 5 0.14
14 14 0.39
15 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:35810633 original size:11 final size:11
Alignment explanation
Indices: 35810607--35810672 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
35810597 AATTTAGTAT
*
35810607 TTTAATTTTAAT
1 TTTAA-TTTAAA
35810619 TTTAATTTAAA
1 TTTAATTTAAA
**
35810630 TTTAAGATAAA
1 TTTAATTTAAA
35810641 TTTAAATTTAAA
1 TTT-AATTTAAA
*
35810653 -TAAATTTAAA
1 TTTAATTTAAA
* *
35810663 ATCAATTTAA
1 TTTAATTTAA
35810673 CTCTAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 8 0.18
11 26 0.58
12 11 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:35810664 original size:17 final size:17
Alignment explanation
Indices: 35810622--35810662 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
35810612 TTTTAATTTT
35810622 AATTTAAATTTAAGATA
1 AATTTAAATTTAAGATA
35810639 AATTTAAATTTAA-ATA
1 AATTTAAATTTAAGATA
35810655 AATTTAAA
1 AATTTAAA
35810663 ATCAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAGATA
Found at i:35810679 original size:27 final size:27
Alignment explanation
Indices: 35810626--35810680 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
35810616 AATTTTAATT
* *
35810626 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
* *
35810653 TAAATTTAAAATCAATTTAACTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
35810680 T
1 T
35810681 TTAAACAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:35819619 original size:58 final size:62
Alignment explanation
Indices: 35819549--35819707 Score: 200
Period size: 69 Copynumber: 2.5 Consensus size: 62
35819539 TTTTTTTTTT
*
35819549 GGCACTGATTTGCAACCAGGTGGCTGAACTTC-TTG-T-C-CTTTGGTGGCTTAACCTGCTA
1 GGCACTGCTTTGCAACCAGGTGGCTGAACTTCTTTGATGCTCTTTGGTGGCTTAACCTGCTA
*
35819607 GGCACTGCTTTGCAGCCAGGTGGCTGAACTTCTTGTCCTTTGATGGCTCTTTGGTGGCTTAACCT
1 GGCACTGCTTTGCAACCAGGTGGCTGAA---C-T-T-CTTTGAT-GCTCTTTGGTGGCTTAACCT
35819672 GCTA
59 GCTA
*
35819676 GGCACTGCTTTGCAACCAGGTGGCTAAACTTC
1 GGCACTGCTTTGCAACCAGGTGGCTGAACTTC
35819708 AATGAAAGAA
Statistics
Matches: 86, Mismatches: 4, Indels: 17
0.80 0.04 0.16
Matches are distributed among these distances:
58 26 0.30
61 1 0.01
62 1 0.01
63 2 0.02
64 2 0.02
65 4 0.05
66 2 0.02
68 1 0.01
69 47 0.55
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.32
Consensus pattern (62 bp):
GGCACTGCTTTGCAACCAGGTGGCTGAACTTCTTTGATGCTCTTTGGTGGCTTAACCTGCTA
Found at i:35820307 original size:16 final size:17
Alignment explanation
Indices: 35820281--35820312 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
35820271 ATTATTTTAT
35820281 AAAACTTTTAAATTTTC
1 AAAACTTTTAAATTTTC
35820298 AAAA-TTTTAAATTTT
1 AAAACTTTTAAATTTT
35820313 TATATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAACTTTTAAATTTTC
Found at i:35831763 original size:56 final size:56
Alignment explanation
Indices: 35831701--35831812 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
35831691 TACTGTATAA
35831701 ACATATATCATTTTAAATTCTAATCACATTTTGAATTTAAAATATTTCAATTTTTT
1 ACATATATCATTTTAAATTCTAATCACATTTTGAATTTAAAATATTTCAATTTTTT
35831757 ACATATATCATTTTAAATTCTAATCACATTTTGAATTTAAAATATTTCAATTTTTT
1 ACATATATCATTTTAAATTCTAATCACATTTTGAATTTAAAATATTTCAATTTTTT
35831813 TTATTCGAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (56 bp):
ACATATATCATTTTAAATTCTAATCACATTTTGAATTTAAAATATTTCAATTTTTT
Found at i:35846108 original size:19 final size:21
Alignment explanation
Indices: 35846080--35846120 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
35846070 CATTTAACAG
*
35846080 TAATATAAAT-TTA-ATTATT
1 TAATACAAATGTTATATTATT
35846099 TAATACAAATGTTATATTATT
1 TAATACAAATGTTATATTATT
35846120 T
1 T
35846121 TTATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATACAAATGTTATATTATT
Found at i:35847536 original size:4 final size:4
Alignment explanation
Indices: 35847529--35847555 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35847519 ACACGCATGC
35847529 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
35847556 GCAGCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:35847722 original size:170 final size:172
Alignment explanation
Indices: 35847438--35847775 Score: 482
Period size: 170 Copynumber: 2.0 Consensus size: 172
35847428 AAGCCTGCAG
** * * * **
35847438 ATTTATAAACACATCAACCATATGGAATATATCACAGTCCAACATGACAAGTTCTTGATGGCATC
1 ATTTATAAACACATCAACCATATACAACATAT-ACAGTCCAAAATGACAAATTCTTGACAGCATC
* * ** * *
35847503 TCCGAATACAATACACACACGCATGCACATACATACATACATACATACATACAGCAGCTTTTAAA
65 TCAGAATACAATACACACACACACACACACACACACATACATACATACATACAGCAGCTTTTAAA
35847568 GAGAAAG-AAATACCTTTATAAGACCTGCCAAGCAATGCACAC
130 GAGAAAGAAAATACCTTTATAAGACCTGCCAAGCAATGCACAC
* *
35847610 ATTTATAAACACATCAACCATATACAACATAT-CAGTTCAAAATGAGAAATTCTTGACAGCATCT
1 ATTTATAAACACATCAACCATATACAACATATACAGTCCAAAATGACAAATTCTTGACAGCATCT
* * * *
35847674 CAGCATACAATATACACACACACACACACACACACATACATACATACATACAGCCGTTTTTAAAG
66 CAGAATACAATACACACACACACACACACACACACATACATACATACATACAGCAGCTTTTAAAG
35847739 AGAAAGAAAATACCTTTATAAGACCTGCCAAGCAATG
131 AGAAAGAAAATACCTTTATAAGACCTGCCAAGCAATG
35847776 GACATCTATT
Statistics
Matches: 146, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
170 87 0.60
171 30 0.21
172 29 0.20
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (172 bp):
ATTTATAAACACATCAACCATATACAACATATACAGTCCAAAATGACAAATTCTTGACAGCATCT
CAGAATACAATACACACACACACACACACACACACATACATACATACATACAGCAGCTTTTAAAG
AGAAAGAAAATACCTTTATAAGACCTGCCAAGCAATGCACAC
Found at i:35849699 original size:19 final size:19
Alignment explanation
Indices: 35849674--35849717 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
35849664 GAATTTTATA
* *
35849674 AATTTTTTATTTTTTGAAAT
1 AATTTTATAATTTTT-AAAT
35849694 AATTTTATAATTTTTAAAT
1 AATTTTATAATTTTTAAAT
*
35849713 TATTT
1 AATTT
35849718 ATTGATGTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTTTATAATTTTTAAAT
Found at i:35849718 original size:18 final size:18
Alignment explanation
Indices: 35849665--35849719 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 18
35849655 TAGTTTTTTG
35849665 AATTTTATAAATT-TTT-T
1 AATTTT-TAAATTATTTAT
* *
35849682 ATTTTTTGAAATAATTTTAT
1 AATTTTT-AAATTA-TTTAT
35849702 AATTTTTAAATTATTTAT
1 AATTTTTAAATTATTTAT
35849720 TGATGTGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 1 0.03
17 9 0.30
18 5 0.17
19 8 0.27
20 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATTTTTAAATTATTTAT
Found at i:35851235 original size:29 final size:30
Alignment explanation
Indices: 35851181--35851244 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
35851171 ATGTCAAAAT
35851181 TATACATGAATTATGATTTAATGTGTAATTG
1 TATACATGAATTATGATTT-ATGTGTAATTG
* *
35851212 TATACATGAATTTTGATTT-TGTGTAATTT
1 TATACATGAATTATGATTTATGTGTAATTG
35851241 TATA
1 TATA
35851245 TATAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 13 0.42
31 18 0.58
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (30 bp):
TATACATGAATTATGATTTATGTGTAATTG
Found at i:35851261 original size:29 final size:29
Alignment explanation
Indices: 35851202--35851261 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
35851192 TATGATTTAA
* *
35851202 TGTGTAATTGTATACATGAATTTTGATTT
1 TGTGTAATTGTATACATAAATTTTGAATT
* *
35851231 TGTGTAATTTTATATATAAAATTTT-AATT
1 TGTGTAATTGTATACAT-AAATTTTGAATT
35851260 TG
1 TG
35851262 ATTCAATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATAAATTTTGAATT
Found at i:35852296 original size:17 final size:17
Alignment explanation
Indices: 35852274--35852312 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
35852264 CTCCACCTTG
* *
35852274 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
35852291 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
35852308 ACAAG
1 ACAAG
35852313 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:35859784 original size:43 final size:42
Alignment explanation
Indices: 35859727--35860003 Score: 123
Period size: 43 Copynumber: 6.4 Consensus size: 42
35859717 AAAGATATTG
* *
35859727 GCACATATAGTGCATCATC-GAGCAATCCGAAGCAATTATACTG
1 GCACATA-AGTGCATCATCGGA-CAAACCGAAGCAATTATACTA
* *
35859770 GCATACATAA-TGCATCATCGGATAAACCGAAGCAATTTTACTA
1 GC--ACATAAGTGCATCATCGGACAAACCGAAGCAATTATACTA
* *** * * *
35859813 GCACATAAGTGCATCATCAGATTTACCTAATCAAATATACTA
1 GCACATAAGTGCATCATCGGACAAACCGAAGCAATTATACTA
* * * * ** * * * *
35859855 ACACACAAGGTGCA-CTATCGAATAAATAGAAACAATTTTATTG
1 GCACATAA-GTGCATC-ATCGGACAAACCGAAGCAATTATACTA
* * *
35859898 GCACATAAGTGCATCATCGGA-AGTACCGAAGTAAATATAATACTG
1 GCACATAAGTGCATCATCGGACA-AACCGAAG-CAAT-T-ATACTA
** * ** * *
35859943 GCACACGAGATGCATCATCGGATAAACTAAAGTAATCATACT-
1 GCACATAAG-TGCATCATCGGACAAACCGAAGCAATTATACTA
*
35859985 GACACATAAATGCATCATC
1 G-CACATAAGTGCATCATC
35860004 AAATAGATCA
Statistics
Matches: 175, Mismatches: 45, Indels: 29
0.70 0.18 0.12
Matches are distributed among these distances:
41 7 0.04
42 57 0.33
43 70 0.40
44 4 0.02
45 19 0.11
46 17 0.10
47 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (42 bp):
GCACATAAGTGCATCATCGGACAAACCGAAGCAATTATACTA
Found at i:35859852 original size:85 final size:85
Alignment explanation
Indices: 35859727--35860004 Score: 212
Period size: 85 Copynumber: 3.2 Consensus size: 85
35859717 AAAGATATTG
* *
35859727 GCACATATAGTGCATCATCGAGCAA-T-CCGAAG-CAAT-TATACTGGCATACATAATGCATCAT
1 GCACATA-AGTGCATCATC-AG-AAGTACCGAAGTAAATATATACTGGCACACA-AATGCATCAT
*
35859788 CGGATAAACCGAAGCAATTTTACT
62 CGGATAAACAGAAGCAATTTTACT
** * * ** *
35859812 AGCACATAAGTGCATCATCAGATTTACCTAA-TCAA-ATATACTAACACACAAGGTGCA-CTATC
1 -GCACATAAGTGCATCATCAGAAGTACCGAAGTAAATATATACTGGCACACAA-ATGCATC-ATC
* * * *
35859874 GAATAAATAGAAACAATTTTATT
63 GGATAAACAGAAGCAATTTTACT
* *
35859897 GGCACATAAGTGCATCATCGGAAGTACCGAAGTAAATATAATACTGGCACACGAGATGCATCATC
1 -GCACATAAGTGCATCATCAGAAGTACCGAAGTAAATAT-ATACTGGCACAC-AAATGCATCATC
* **
35859962 GGATAAACTA-AAGTAATCATACT
63 GGATAAAC-AGAAGCAATTTTACT
*
35859985 GACACATAAATGCATCATCA
1 G-CACATAAGTGCATCATCA
35860005 AATAGATCAA
Statistics
Matches: 149, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
83 1 0.01
84 5 0.03
85 80 0.54
86 10 0.07
87 3 0.02
88 47 0.32
89 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (85 bp):
GCACATAAGTGCATCATCAGAAGTACCGAAGTAAATATATACTGGCACACAAATGCATCATCGGA
TAAACAGAAGCAATTTTACT
Found at i:35865562 original size:2 final size:2
Alignment explanation
Indices: 35865555--35865581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35865545 GATTACTCAA
35865555 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
35865582 TTTTTTCTTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35866436 original size:15 final size:15
Alignment explanation
Indices: 35866418--35866469 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
35866408 AGAGGAAGAG
*
35866418 GAGGAAGTGGAAGTT
1 GAGGAAGTGGAAGTA
* * *
35866433 GAGGAAGAGGTAGAA
1 GAGGAAGTGGAAGTA
35866448 GAGGAAGTGGAAGTA
1 GAGGAAGTGGAAGTA
35866463 GAGGAAG
1 GAGGAAG
35866470 ACGAGGACGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.48, T:0.12
Consensus pattern (15 bp):
GAGGAAGTGGAAGTA
Found at i:35866441 original size:24 final size:24
Alignment explanation
Indices: 35866409--35866455 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
35866399 TGAAGAAATA
*
35866409 GAGGAAGAGG-AGGAAGTGGAAGTT
1 GAGGAAGAGGTA-GAAGAGGAAGTT
35866433 GAGGAAGAGGTAGAAGAGGAAGT
1 GAGGAAGAGGTAGAAGAGGAAGT
35866456 GGAAGTAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.11
Consensus pattern (24 bp):
GAGGAAGAGGTAGAAGAGGAAGTT
Found at i:35866442 original size:30 final size:30
Alignment explanation
Indices: 35866408--35866470 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
35866398 ATGAAGAAAT
* *
35866408 AGAGGAAGAGGAGGAAGTGGAAGTTGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
*
35866438 AGAGGTAGAAGAGGAAGTGGAAGTAGAGGA
1 AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
35866468 AGA
1 AGA
35866471 CGAGGACGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.48, T:0.10
Consensus pattern (30 bp):
AGAGGAAGAAGAGGAAGTGGAAGTAGAGGA
Found at i:35869892 original size:14 final size:14
Alignment explanation
Indices: 35869873--35869902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35869863 GAATAAATCT
35869873 TTAATTAAATAAAA
1 TTAATTAAATAAAA
*
35869887 TTAATTAATTAAAA
1 TTAATTAAATAAAA
35869901 TT
1 TT
35869903 TTTAAACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAATTAAATAAAA
Found at i:35872107 original size:21 final size:21
Alignment explanation
Indices: 35872083--35872127 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35872073 TTCTGTCACC
35872083 TTTACAAGCTCTTCTTCGGGT
1 TTTACAAGCTCTTCTTCGGGT
* * *
35872104 TTTACGATCTCTTTTTCGGGT
1 TTTACAAGCTCTTCTTCGGGT
35872125 TTT
1 TTT
35872128 GATGAAGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.20, G:0.18, T:0.51
Consensus pattern (21 bp):
TTTACAAGCTCTTCTTCGGGT
Found at i:35879119 original size:16 final size:16
Alignment explanation
Indices: 35879098--35879153 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
35879088 ATACATAGTA
35879098 TATATTATAAAATATT
1 TATATTATAAAATATT
**
35879114 TATATTAATTTTAAT-TT
1 TATATT-A-TAAAATATT
35879131 TA-ATTATAAAATATT
1 TATATTATAAAATATT
35879146 TATTATTA
1 TA-TATTA
35879154 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 4 0.13
15 5 0.16
16 9 0.29
17 9 0.29
18 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATATTATAAAATATT
Found at i:35879770 original size:9 final size:9
Alignment explanation
Indices: 35879756--35879786 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35879746 ATATATATTA
35879756 AATTCAGTT
1 AATTCAGTT
35879765 AATTCAGTT
1 AATTCAGTT
*
35879774 AATTCGGTT
1 AATTCAGTT
35879783 AATT
1 AATT
35879787 TTTTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (9 bp):
AATTCAGTT
Found at i:35881409 original size:59 final size:59
Alignment explanation
Indices: 35881291--35881409 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 59
35881281 AAAGGTGTTC
* * * * *
35881291 ACCATCCCAAGTGTCACTTAGGTTCGAGTCGCTCTAATCGTATTTGTTGTTCGGGCTTT
1 ACCATCCCAAGTGTCACTTAGATTCGAGTCGCACTAATCGTATTTATTGTTCAGACTTT
* *
35881350 ACCATCTCAAGTGTGACTT-GAATTCGAGTCGCACTAATCGTATTTATTGTTCAGACTTT
1 ACCATCCCAAGTGTCACTTAG-ATTCGAGTCGCACTAATCGTATTTATTGTTCAGACTTT
35881409 A
1 A
35881410 TCCTGTTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
58 1 0.02
59 51 0.98
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (59 bp):
ACCATCCCAAGTGTCACTTAGATTCGAGTCGCACTAATCGTATTTATTGTTCAGACTTT
Found at i:35884829 original size:59 final size:59
Alignment explanation
Indices: 35884738--35884877 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 59
35884728 TTAGACTCGC
* * * * * *
35884738 GGGGTGAAATGGTAATTTTCGATGAAATCGGGGTCAAAAA-GAGAATTTTGGAAAATT-T
1 GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTCAAAAATG-GAATTTTGGAAAGTTCA
* * * *
35884796 GAGGGTAAAATAGTAATTTTTGGTTAAACCGGGGTTAAAAATGGAATTTTGGGAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGGTGAAACCGGGGTCAAAAATGGAATTTTGGAAAGTTCA
35884856 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
35884878 ACCATCTAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 1 0.01
59 65 0.96
60 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.31
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAACCGGGGTCAAAAATGGAATTTTGGAAAGTTCA
Found at i:35885203 original size:33 final size:34
Alignment explanation
Indices: 35885152--35885217 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
35885142 TTACCGGGCA
*
35885152 AAATTGTAAAT-AATTAAAAAATGCAGAAAGGACT
1 AAATTGTAAATAAATAAAAAAATGC-GAAAGGACT
35885186 AAATTG-AAATAAATAAAAAAATGCGAAAGGAC
1 AAATTGTAAATAAATAAAAAAATGCGAAAGGAC
35885218 CAAACGCACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.59, C:0.06, G:0.15, T:0.20
Consensus pattern (34 bp):
AAATTGTAAATAAATAAAAAAATGCGAAAGGACT
Found at i:35885281 original size:16 final size:15
Alignment explanation
Indices: 35885260--35885289 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
35885250 GCGGATCCCA
35885260 GATCGGGTTCGGGTCG
1 GATCGGG-TCGGGTCG
35885276 GATCGGGTCGGGTC
1 GATCGGGTCGGGTC
35885290 TGTGGGTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.20, G:0.50, T:0.23
Consensus pattern (15 bp):
GATCGGGTCGGGTCG
Found at i:35886664 original size:14 final size:14
Alignment explanation
Indices: 35886645--35886671 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35886635 TTAAATTTAA
35886645 AGTAAATTTAAATG
1 AGTAAATTTAAATG
35886659 AGTAAATTTAAAT
1 AGTAAATTTAAAT
35886672 TTAAAACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:35889886 original size:21 final size:22
Alignment explanation
Indices: 35889848--35889895 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
35889838 TTGTTTTATC
*
35889848 ATTATTTTGTTATCA-TTTACT
1 ATTATGTTGTTATCATTTTACT
*
35889869 ATTATGTTGTTA-CTATTTTATT
1 ATTATGTTGTTATC-ATTTTACT
35889891 ATTAT
1 ATTAT
35889896 TATTTGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (22 bp):
ATTATGTTGTTATCATTTTACT
Found at i:35891818 original size:31 final size:31
Alignment explanation
Indices: 35891778--35891865 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
35891768 ATATTGTCAT
*
35891778 TAAACTATTCAGAAGTTTTCATTTAAATTAC
1 TAAACTATTCAGAAGTTTTCATTTAAATCAC
* * *
35891809 TGAATTATTC-GAATGTTTTCATTTAAATCAG
1 TAAACTATTCAGAA-GTTTTCATTTAAATCAC
* *
35891840 TAAACTATTCAAAAGTTTTTATTTAA
1 TAAACTATTCAGAAGTTTTCATTTAA
35891866 GTTATTGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 3 0.06
31 42 0.89
32 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (31 bp):
TAAACTATTCAGAAGTTTTCATTTAAATCAC
Found at i:35896162 original size:24 final size:25
Alignment explanation
Indices: 35896135--35896194 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 25
35896125 TTATAAGAAA
35896135 TTATATTC-GTTTGAATTCAAAATG
1 TTATATTCTGTTTGAATTCAAAATG
35896159 TTATATTTCGTTAGTTTGAATTCAAAATG
1 TTATA-TTC--T-GTTTGAATTCAAAATG
35896188 TTATATT
1 TTATATT
35896195 TTATTAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.16
25 3 0.10
28 2 0.06
29 21 0.68
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.50
Consensus pattern (25 bp):
TTATATTCTGTTTGAATTCAAAATG
Found at i:35896185 original size:29 final size:29
Alignment explanation
Indices: 35896143--35896204 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
35896133 AATTATATTC
*
35896143 GTTTGAATTCAAAATGTTATATTTCGTTA
1 GTTTGAATTCAAAATGTTATATTTCATTA
*
35896172 GTTTGAATTCAAAATGTTATATTTTATTA
1 GTTTGAATTCAAAATGTTATATTTCATTA
35896201 GTTT
1 GTTT
35896205 TTAAAGTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.52
Consensus pattern (29 bp):
GTTTGAATTCAAAATGTTATATTTCATTA
Found at i:35898018 original size:21 final size:23
Alignment explanation
Indices: 35897992--35898043 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
35897982 TAACTACGGA
35897992 ATTAAATACACA-ATA-TATTTT
1 ATTAAATACACACATATTATTTT
35898013 ATTAAA-ACACATCCATATTATTTT
1 ATTAAATACACA--CATATTATTTT
35898037 ATTAAAT
1 ATTAAAT
35898044 TTAACTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.19
21 6 0.23
23 3 0.12
24 12 0.46
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTAAATACACACATATTATTTT
Found at i:35899227 original size:16 final size:16
Alignment explanation
Indices: 35899205--35899262 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
35899195 TTTCTTTTTA
35899205 ATTTTCGATTTGACTT
1 ATTTTCGATTTGACTT
* *
35899221 GTTTTCGAATTTTATCATT
1 ATTTTCG-ATTTGA-C-TT
35899240 AATTTTCGATTTGACTT
1 -ATTTTCGATTTGACTT
35899257 ATTTTC
1 ATTTTC
35899263 AAATTTTGTC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 12 0.35
17 7 0.21
18 2 0.06
19 7 0.21
20 6 0.18
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (16 bp):
ATTTTCGATTTGACTT
Found at i:35907129 original size:30 final size:29
Alignment explanation
Indices: 35907095--35907246 Score: 182
Period size: 30 Copynumber: 5.1 Consensus size: 29
35907085 TACATTAAAA
*
35907095 GGGTTAAATTTTAATTTTTGAAAACTTTAG
1 GGGTTAAATTTGAATTTTTGAAAACTTT-G
35907125 GGGTTAAATTTGAATTTTTGAAAACTTTG
1 GGGTTAAATTTGAATTTTTGAAAACTTTG
*
35907154 GGGATTAAATTTGAATTTTT-AGAAATTTTAG
1 GGG-TTAAATTTGAATTTTTGA-AAACTTT-G
* * *
35907185 GGGTGAAATTTCAATTTTTAGAAAA-TATG
1 GGGTTAAATTTGAATTTTT-GAAAACTTTG
*
35907214 GGGTTTAAATTTGAATTTTTAAAAACTTTG
1 GGG-TTAAATTTGAATTTTTGAAAACTTTG
35907244 GGG
1 GGG
35907247 GTATAAAATG
Statistics
Matches: 106, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
29 13 0.12
30 85 0.80
31 7 0.07
32 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (29 bp):
GGGTTAAATTTGAATTTTTGAAAACTTTG
Found at i:35907592 original size:21 final size:22
Alignment explanation
Indices: 35907543--35907592 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
35907533 ATTATTTCCA
*
35907543 TTTAAAAAAACCATTCTTTCTG
1 TTTAAAAAAACCATTCTTTATG
* * *
35907565 ATAAAAAAAACCATT-TTTATT
1 TTTAAAAAAACCATTCTTTATG
35907586 TTTAAAA
1 TTTAAAA
35907593 TTCCCTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTAAAAAAACCATTCTTTATG
Found at i:35912320 original size:18 final size:17
Alignment explanation
Indices: 35912263--35912322 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
35912253 TTTTAGACTT
*
35912263 TTTTTTTAATTTTATATA
1 TTTTTTAAATTTTA-ATA
*
35912281 TTCTTTAGAAATTTTAATA
1 TT-TTT-TAAATTTTAATA
*
35912300 TTTTTTAAATTTTTATGA
1 TTTTTTAAATTTTAAT-A
35912318 TTTTT
1 TTTTT
35912323 AAAAAATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.26
18 11 0.31
19 8 0.23
20 7 0.20
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTTAAATTTTAATA
Found at i:35912322 original size:19 final size:18
Alignment explanation
Indices: 35912262--35912322 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 18
35912252 ATTTTAGACT
*
35912262 TTTTTTTTAATTTTATATA
1 TTTTTTTAAATTTT-TATA
** *
35912281 TTCTTTAGAAATTTTAATA
1 TT-TTTTTAAATTTTTATA
35912300 -TTTTTTAAATTTTTATGA
1 TTTTTTTAAATTTTTAT-A
35912318 TTTTT
1 TTTTT
35912323 AAAAAATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.38
18 2 0.06
19 9 0.28
20 9 0.28
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTTTTTAAATTTTTATA
Found at i:35913622 original size:23 final size:25
Alignment explanation
Indices: 35913595--35913642 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
35913585 GAAAAATACA
35913595 AAAAATATATATAA-TATT-TAAAT
1 AAAAATATATATAACTATTCTAAAT
* *
35913618 AAAAATCTCTATAACTATTCTAAAT
1 AAAAATATATATAACTATTCTAAAT
35913643 TTTTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAATATATATAACTATTCTAAAT
Found at i:35915153 original size:32 final size:32
Alignment explanation
Indices: 35915112--35915185 Score: 148
Period size: 32 Copynumber: 2.3 Consensus size: 32
35915102 TCCCCTACAT
35915112 GTGAACTCCTTGGGTATAAGCAATCTGAGACC
1 GTGAACTCCTTGGGTATAAGCAATCTGAGACC
35915144 GTGAACTCCTTGGGTATAAGCAATCTGAGACC
1 GTGAACTCCTTGGGTATAAGCAATCTGAGACC
35915176 GTGAACTCCT
1 GTGAACTCCT
35915186 CTTGGCTCGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (32 bp):
GTGAACTCCTTGGGTATAAGCAATCTGAGACC
Found at i:35917247 original size:18 final size:19
Alignment explanation
Indices: 35917208--35917255 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
35917198 ATTGTTTGGA
*
35917208 TATTGTATAATTTTTATTT
1 TATTGTATAATTTTTATAT
35917227 TATTGT-TAA-TTTTACTAT
1 TATTGTATAATTTTTA-TAT
*
35917245 TATTTTATAAT
1 TATTGTATAAT
35917256 CATTTGCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (19 bp):
TATTGTATAATTTTTATAT
Found at i:35921405 original size:2 final size:2
Alignment explanation
Indices: 35921398--35921423 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35921388 ACCAAATTCT
35921398 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
35921424 CAACCACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35922020 original size:2 final size:2
Alignment explanation
Indices: 35922013--35922057 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
35922003 AGTAAAGAAT
35922013 AC AC AC AC AC AC 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 AC AC AC AC AC AC
35922055 AC A
1 AC A
35922058 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:35922534 original size:29 final size:31
Alignment explanation
Indices: 35922485--35922557 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
35922475 ATTTAAAATT
*
35922485 AATAATGATAAAATTACATTTTAA-CTTC-AAA
1 AATAATGA-AAATTTACA-TTTAATCTTCTAAA
35922516 AATAATGAAAATTTA-ATTTAATCTTCTAAA
1 AATAATGAAAATTTACATTTAATCTTCTAAA
* *
35922546 AATTATAAAAAT
1 AATAATGAAAAT
35922558 ATAAACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 5 0.14
30 19 0.51
31 8 0.22
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (31 bp):
AATAATGAAAATTTACATTTAATCTTCTAAA
Found at i:35923021 original size:81 final size:81
Alignment explanation
Indices: 35922929--35923084 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
35922919 TTGTATCATA
* * * * *
35922929 AAAATATAATTTCATCATT-TTAATAGTTTATATTTTTAT-AATTTTTAAAAAA-TTAAA-TCAA
1 AAAATATAATTTCACCATTATT-A-A-TTTAAAATTTTATGAA-TTATAAAAAATTTAAATTAAA
*
35922990 TTTTTATCATTTTAAGAACT
62 ATTTTATCATTTTAAGAACT
*
35923010 AAAATGTAATTTCACCATTATTAATTTAAAATTTTATGAATTATAAAAAATTTAAATTAAAATTT
1 AAAATATAATTTCACCATTATTAATTTAAAATTTTATGAATTATAAAAAATTTAAATTAAAATTT
35923075 TATCATTTTA
66 TATCATTTTA
35923085 GGGGTTAATG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
79 20 0.31
80 8 0.12
81 34 0.53
82 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (81 bp):
AAAATATAATTTCACCATTATTAATTTAAAATTTTATGAATTATAAAAAATTTAAATTAAAATTT
TATCATTTTAAGAACT
Found at i:35931524 original size:30 final size:30
Alignment explanation
Indices: 35931437--35931568 Score: 162
Period size: 29 Copynumber: 4.5 Consensus size: 30
35931427 TTGGGAGTCA
* * *
35931437 AAAATACAATTTTGGAAAAGTTC-AGGGTT
1 AAAATATAATTTTTGAAAAGTTCGAGGGTC
* *
35931466 AAAATGTAATTTTGGAAAAGTTCG-GGGTC
1 AAAATATAATTTTTGAAAAGTTCGAGGGTC
* * *
35931495 AAAATGTGATTTTTGAGAAGTTCGAGGGTC
1 AAAATATAATTTTTGAAAAGTTCGAGGGTC
*
35931525 AAAATATAATTTTTGTAAA-TTCGAGGGTC
1 AAAATATAATTTTTGAAAAGTTCGAGGGTC
35931554 AAAATATAATTTTTG
1 AAAATATAATTTTTG
35931569 TGAAGTTCAG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
29 71 0.78
30 20 0.22
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAAGTTCGAGGGTC
Found at i:35931583 original size:59 final size:59
Alignment explanation
Indices: 35931412--35931583 Score: 170
Period size: 59 Copynumber: 2.9 Consensus size: 59
35931402 GCCAAAATGG
** * * * * * *
35931412 TAATTTTGGATGAGTTTGGGAGTCAAAAATACAATTTTGGAAAAGTTCA-GGGTTAAAATG
1 TAATTTTGGAAAAGTTCGGG-GTC-AAAATATAATTTTTGAGAAGTTCAGGGGTCAAAATA
* *
35931472 TAATTTTGGAAAAGTTCGGGGTCAAAATGTGATTTTTGAGAAGTTC-GAGGGTCAAAATA
1 TAATTTTGGAAAAGTTCGGGGTCAAAATATAATTTTTGAGAAGTTCAG-GGGTCAAAATA
* * *
35931531 TAATTTTTGTAAA-TTCGAGGGTCAAAATATAATTTTTGTGAAGTTCAGGGGTC
1 TAATTTTGGAAAAGTTCG-GGGTCAAAATATAATTTTTGAGAAGTTCAGGGGTC
35931584 TTTTAAATTA
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
58 22 0.24
59 53 0.57
60 18 0.19
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (59 bp):
TAATTTTGGAAAAGTTCGGGGTCAAAATATAATTTTTGAGAAGTTCAGGGGTCAAAATA
Found at i:35932090 original size:18 final size:17
Alignment explanation
Indices: 35932069--35932103 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35932059 AAAGTCCAGT
35932069 CGCCATCCACTGTCCGTC
1 CGCCATCCACTG-CCGTC
*
35932087 CGCCATCGACTGCCGTC
1 CGCCATCCACTGCCGTC
35932104 GGTCGCCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.49, G:0.20, T:0.20
Consensus pattern (17 bp):
CGCCATCCACTGCCGTC
Found at i:35932642 original size:5 final size:5
Alignment explanation
Indices: 35932632--35932662 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
35932622 TAAGTAAATA
35932632 TATAT TATAT TATAT TATAT TATA- TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TA
35932663 AAAACGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:35933955 original size:27 final size:26
Alignment explanation
Indices: 35933913--35933965 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
35933903 GTAGAATATA
35933913 TTTTTTTAATTGATTAA-ATAAATTAT
1 TTTTTTTAATTGATTAATAT-AATTAT
35933939 TTTTTTTGAATAT-ATTAATATAATTAT
1 TTTTTTT-AAT-TGATTAATATAATTAT
35933966 ATGATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.29
27 14 0.58
28 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (26 bp):
TTTTTTTAATTGATTAATATAATTAT
Done.