Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 96 of 135
Found at i:29844866 original size:79 final size:79
Alignment explanation
Indices: 29844718--29844869 Score: 187
Period size: 79 Copynumber: 1.9 Consensus size: 79
29844708 AAAAGATTGG
* * * ** * *
29844718 ATTGTTTCAATTTGCCACATGGTCGGGGTAAAAGATCAAATGGTCTTCAATTTGCCATATGGTTG
1 ATTGATTCAATCTGCCACATGGTCGGGGTAAAAAATCAAATGGTCTTCAAGCTGCCATATAGTTA
29844783 GGGTAAAATACTAT
66 GGGTAAAATACTAT
* *** * *
29844797 ATTGATTCAATCTGCCCCATGGTCGGGGTAAAAAATTGGATGGTCTTCAAGCTGCCCTCTAGTTA
1 ATTGATTCAATCTGCCACATGGTCGGGGTAAAAAATCAAATGGTCTTCAAGCTGCCATATAGTTA
29844862 GGGTAAAA
66 GGGTAAAA
29844870 GATTGGATGG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 60 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (79 bp):
ATTGATTCAATCTGCCACATGGTCGGGGTAAAAAATCAAATGGTCTTCAAGCTGCCATATAGTTA
GGGTAAAATACTAT
Found at i:29845065 original size:50 final size:50
Alignment explanation
Indices: 29845000--29845109 Score: 184
Period size: 50 Copynumber: 2.2 Consensus size: 50
29844990 AGATTCGTCC
*
29845000 TTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
1 TTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
* * *
29845050 TTGCGGCTTCAATCTGCCCCTCTACGGCTTTAGGTGTATGGGATTTGCCA
1 TTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
29845100 TTGCGGCTTC
1 TTGCGGCTTC
29845110 GATTCATTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (50 bp):
TTGCGGCTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
Found at i:29845122 original size:50 final size:49
Alignment explanation
Indices: 29845000--29845131 Score: 167
Period size: 50 Copynumber: 2.6 Consensus size: 49
29844990 AGATTCGTCC
*
29845000 TTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
1 TTGCGGCTTCAATCT-CCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
* * *
29845050 TTGCGGCTTCAATCTGCCCCTCTACGGCTTTAGGTGTATGGGATTTGCCA
1 TTGCGGCTTCAATCT-CCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
* *
29845100 TTGCGGCTTCGAT-TCATTCCTCTACAGCTTTA
1 TTGCGGCTTCAATCTC--CCCTCTACAGCTTTA
29845132 AGGCTATAAG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 71 0.97
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (49 bp):
TTGCGGCTTCAATCTCCCCTCTACAGCTTTAGGTGAATGAGATTTGCCA
Found at i:29866608 original size:30 final size:30
Alignment explanation
Indices: 29866574--29866816 Score: 186
Period size: 30 Copynumber: 8.1 Consensus size: 30
29866564 CATTAAAATC
* *
29866574 GGGTCAAATTTGAATTTTTGGAAACTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
*** * *
29866604 GGGTCAAATCAAAATTTTTAGAAAATTT-A
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* * * * *
29866633 GAGGTCAAATTTAAAGTTTTAGAAATTTTAT
1 G-GGTCAAATTTGAATTTTTGGAAAGTTTAA
*
29866664 GGGTCAAATTTGAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* ** *
29866694 GGGTCAAAATCAAATTTTTGGAAAGTTTAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* * * *
29866724 GGGTAAAATTTGAATTATTGAAAAGTTCAA
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* * * *
29866754 -GGTCAAATTTGAATTTATGGAAAATTGAG
1 GGGTCAAATTTGAATTTTTGGAAAGTTTAA
* ** *
29866783 GGGTTAAAACATG-ATTTTTAGAAAGTTTAA
1 GGG-TCAAATTTGAATTTTTGGAAAGTTTAA
29866813 GGGT
1 GGGT
29866817 TAAAACATGA
Statistics
Matches: 167, Mismatches: 42, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
29 25 0.15
30 135 0.81
31 7 0.04
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
GGGTCAAATTTGAATTTTTGGAAAGTTTAA
Found at i:29866709 original size:90 final size:89
Alignment explanation
Indices: 29866574--29866811 Score: 259
Period size: 90 Copynumber: 2.7 Consensus size: 89
29866564 CATTAAAATC
* * *
29866574 GGGTCAAATTTGAATTTTTGGAAACTTCAAGGGTC-AAATCAAAATTTTTAGAAAATTTAGAGGT
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAAATC-AAATTTTTAGAAAGTTTAGAGGT
* * *
29866638 CAAATTTAAAGTT-TT-AGAAATTTTA
65 AAAATTTAAA-TTATTGA-AAAGTTCA
* * * *
29866663 TGGGTCAAATTTGAATTTTTGGAAAGTTTAGGGGTCAAAATCAAATTTTTGGAAAGTTTAGGGGT
1 -GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAAATCAAATTTTTAGAAAGTTTAGAGGT
*
29866728 AAAATTTGAATTATTGAAAAGTTCA
65 AAAATTTAAATTATTGAAAAGTTCA
* * * * *
29866753 AGGTCAAATTTGAATTTATGGAAAATTGAGGGGTTAAAA-CATGATTTTTAGAAAGTTTA
1 GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAAATCA-AATTTTTAGAAAGTTTA
29866812 AGGGTTAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
88 2 0.02
89 51 0.40
90 68 0.54
91 6 0.05
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (89 bp):
GGGTCAAATTTGAATTTTTGGAAAATTCAGGGGTCAAAATCAAATTTTTAGAAAGTTTAGAGGTA
AAATTTAAATTATTGAAAAGTTCA
Found at i:29866819 original size:30 final size:31
Alignment explanation
Indices: 29866778--29866845 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
29866768 TTATGGAAAA
* *
29866778 TTGAGGGGTTAAAACATGATTTTTAGAAAGT
1 TTGAAGGGTTAAAACATGATTTTCAGAAAGT
*
29866809 TT-AAGGGTTAAAACATGATTTTCAGATAGT
1 TTGAAGGGTTAAAACATGATTTTCAGAAAGT
29866839 TTGAAGG
1 TTGAAGG
29866846 TCAAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.35
Consensus pattern (31 bp):
TTGAAGGGTTAAAACATGATTTTCAGAAAGT
Found at i:29867876 original size:9 final size:10
Alignment explanation
Indices: 29867862--29867898 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
29867852 TTTAGTATCT
29867862 ATAAAATA-A
1 ATAAAATATA
29867871 ATAAAATAATA
1 ATAAAAT-ATA
29867882 ATAAAA-ATA
1 ATAAAATATA
29867891 ATAAAATA
1 ATAAAATA
29867899 AAAATTGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 16 0.64
10 2 0.08
11 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAAATATA
Found at i:29871058 original size:88 final size:88
Alignment explanation
Indices: 29870909--29871084 Score: 280
Period size: 88 Copynumber: 2.0 Consensus size: 88
29870899 CTGAGGCTTG
* *
29870909 ACATCTTGCTCTTATCCATGCGACCTAATGCTACGAGGACAAGGATGATGCCAACGTTATTGCGA
1 ACATCCTGCTCTTATCCATGCGACCTAATGCCACGAGGACAAGGATGATGCCAACGTTATTGCGA
*
29870974 GTACATTCTTTATTTTTATAGTA
66 GTACATTCTTTATTTTTACAGTA
* * * * *
29870997 ACATCCTGGTCTTATCTATGCGACCTGATGCCGCGAGGACAAGGATGATGCCAACGTTATTGTGA
1 ACATCCTGCTCTTATCCATGCGACCTAATGCCACGAGGACAAGGATGATGCCAACGTTATTGCGA
29871062 GTACATTCTTTATTTTTACAGTA
66 GTACATTCTTTATTTTTACAGTA
29871085 CCCTACTTTG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (88 bp):
ACATCCTGCTCTTATCCATGCGACCTAATGCCACGAGGACAAGGATGATGCCAACGTTATTGCGA
GTACATTCTTTATTTTTACAGTA
Found at i:29889073 original size:27 final size:29
Alignment explanation
Indices: 29889020--29889089 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
29889010 TTAATTCTTT
* **
29889020 AAAAAAAGGAAATAAAAGGTTTTAATTT-A
1 AAAAAAAAG-AATAAAAGGTTAAAATTTGA
29889049 AAAAAAAAGAATAAAAGG-TAAAATTTGA
1 AAAAAAAAGAATAAAAGGTTAAAATTTGA
*
29889077 AAAAGAAA-AATAA
1 AAAAAAAAGAATAA
29889090 TACAAGGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 11 0.31
28 17 0.47
29 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (29 bp):
AAAAAAAAGAATAAAAGGTTAAAATTTGA
Found at i:29889157 original size:2 final size:2
Alignment explanation
Indices: 29889152--29889176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29889142 TTAAAAAAAG
29889152 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 A
29889177 CGAGGGTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29891793 original size:25 final size:25
Alignment explanation
Indices: 29891763--29891814 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
29891753 ATTGAAAAAG
* *
29891763 TTAATTTATTTTATAA-AATGTTTAA
1 TTAATTTAATTAATAATAA-GTTTAA
29891788 TTAATTTAATTAATAATAAGTTTAA
1 TTAATTTAATTAATAATAAGTTTAA
29891813 TT
1 TT
29891815 TTTTTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
TTAATTTAATTAATAATAAGTTTAA
Found at i:29893428 original size:31 final size:30
Alignment explanation
Indices: 29893392--29893459 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
29893382 AAACTCAACA
*
29893392 ATTCAATTA-TCTAAATAAAAACTTTCGAAT
1 ATTCAATTACT-TAAATAAAAACTTCCGAAT
*
29893422 AGTTCAATTACTTGAATAAAAACTTCCGAAT
1 A-TTCAATTACTTAAATAAAAACTTCCGAAT
29893453 ATTCAAT
1 ATTCAAT
29893460 GATCATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.21
31 26 0.76
32 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (30 bp):
ATTCAATTACTTAAATAAAAACTTCCGAAT
Found at i:29894039 original size:29 final size:31
Alignment explanation
Indices: 29893981--29894044 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
29893971 ATACTTCATA
* *
29893981 AAAATTCAAAAGAATCAATAAAAATA-TTTT
1 AAAATTCAAAAAAATCAATAAAAAAATTTTT
29894011 AAAATT-AAAAAAATC-ATAAAAAAACTTTTT
1 AAAATTCAAAAAAATCAATAAAAAAA-TTTTT
29894041 AAAA
1 AAAA
29894045 ATTTATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 8 0.27
30 14 0.47
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAATTCAAAAAAATCAATAAAAAAATTTTT
Found at i:29894208 original size:24 final size:25
Alignment explanation
Indices: 29894167--29894217 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
29894157 ATTAAATTTT
* *
29894167 AAAAGATTAAGGTC-AAAATGATAA
1 AAAAAATTAAGATCAAAAATGATAA
* *
29894191 AAAAAATTAAGATTAAAAATGGTAA
1 AAAAAATTAAGATCAAAAATGATAA
29894216 AA
1 AA
29894218 TAAGTAAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.14, T:0.22
Consensus pattern (25 bp):
AAAAAATTAAGATCAAAAATGATAA
Found at i:29901741 original size:30 final size:30
Alignment explanation
Indices: 29901705--29901945 Score: 156
Period size: 30 Copynumber: 8.1 Consensus size: 30
29901695 CTCAGAAGGT
*
29901705 CCTCGAA-TTTCTTAAAAATTATATTTTAAC
1 CCTCGAACTTTC-TAAAAATCATATTTTAAC
*
29901735 CCTCGAACTTTCTAAAAATCATATTTTGAC
1 CCTCGAACTTTCTAAAAATCATATTTTAAC
* * *
29901765 ACC-CGAACTTTCCAAAAATCACATTTTGAC
1 -CCTCGAACTTTCTAAAAATCATATTTTAAC
* * * *
29901795 CCT-AAACTTTCCAAAAATCACA-TTTGAC
1 CCTCGAACTTTCTAAAAATCATATTTTAAC
* * *
29901823 CCTCGAAGTTCCTAAAAATCACATTTTAAC
1 CCTCGAACTTTCTAAAAATCATATTTTAAC
* * *
29901853 TCC-CAAACCTTTCT-AAAATCACATTTTAAA
1 -CCTCGAA-CTTTCTAAAAATCATATTTTAAC
** * *
29901883 CCTAAAACTTTTCT-AAAATCACATTTTAGC
1 CCTCGAAC-TTTCTAAAAATCATATTTTAAC
* * * *
29901913 CCCCTAAACTTT-TCCAAAATCATATTTTCAC
1 CCTC-GAACTTTCT-AAAAATCATATTTTAAC
29901944 CC
1 CC
29901946 CTAAACTTCT
Statistics
Matches: 177, Mismatches: 22, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
28 9 0.05
29 39 0.22
30 98 0.55
31 31 0.18
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (30 bp):
CCTCGAACTTTCTAAAAATCATATTTTAAC
Found at i:29901803 original size:29 final size:29
Alignment explanation
Indices: 29901740--29902038 Score: 200
Period size: 29 Copynumber: 10.1 Consensus size: 29
29901730 TTAACCCTCG
* * **
29901740 AACTTTCTAAAAATCATATTTTGACACCCG
1 AACTTTCCAAAAATCACATTTTGAC-CCTA
29901770 AACTTTCCAAAAATCACATTTTGACCCTA
1 AACTTTCCAAAAATCACATTTTGACCCTA
*
29901799 AACTTTCCAAAAATCACA-TTTGACCCTCG
1 AACTTTCCAAAAATCACATTTTGACCCT-A
* * *
29901828 AA-GTTCCTAAAAATCACATTTTAACTCCCA
1 AACTTTCC-AAAAATCACATTTTGAC-CCTA
* * *
29901858 AACCTTT-CTAAAATCACATTTTAAACCTAA
1 AA-CTTTCCAAAAATCACATTTTGACCCT-A
* * *
29901888 AACTTTTCTAAAATCACATTTTAGCCCCCTA
1 AACTTTCCAAAAATCACATTTT-G-ACCCTA
* *
29901919 AACTTTTCC-AAAATCATATTTTCACCCCTA
1 AAC-TTTCCAAAAATCACATTTTGA-CCCTA
* *
29901949 AACTTCTCC-AAAAT-ACCTTTTGACCCCA
1 AACTT-TCCAAAAATCACATTTTGACCCTA
* *
29901977 AAATTTCTC-AAAATTACATTTT-ACCCCTA
1 AACTTTC-CAAAAATCACATTTTGA-CCCTA
* * * * *
29902006 AACTTTTCTAAAATTACATTTTAACCTTA
1 AACTTTCCAAAAATCACATTTTGACCCTA
29902035 AACT
1 AACT
29902039 CTCTGAAACT
Statistics
Matches: 221, Mismatches: 30, Indels: 37
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.01
28 29 0.13
29 82 0.37
30 80 0.36
31 19 0.09
32 9 0.04
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAAATCACATTTTGACCCTA
Found at i:29901871 original size:88 final size:89
Alignment explanation
Indices: 29901733--29901908 Score: 230
Period size: 88 Copynumber: 2.0 Consensus size: 89
29901723 TTATATTTTA
* * * * * *
29901733 ACCCTCGAACTTTCTAAAAATCATATTTTGACACCCGAACTTTCCAAAAATCACATTTTGACCCT
1 ACCCTCGAACTTCCTAAAAATCACATTTTAACACCCAAACTTTCCAAAAATCACATTTTAAACCT
29901798 -AAACTTTCCAAAAATCACATTTG
66 AAAACTTTCCAAAAATCACATTTG
* * *
29901821 ACCCTCGAAGTTCCTAAAAATCACATTTTAACTCCCAAACCTTT-CTAAAATCACATTTTAAACC
1 ACCCTCGAACTTCCTAAAAATCACATTTTAACACCCAAA-CTTTCCAAAAATCACATTTTAAACC
* *
29901885 TAAAACTTTTCTAAAATCACATTT
65 TAAAACTTTCCAAAAATCACATTT
29901909 TAGCCCCCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
88 51 0.68
89 24 0.32
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.32
Consensus pattern (89 bp):
ACCCTCGAACTTCCTAAAAATCACATTTTAACACCCAAACTTTCCAAAAATCACATTTTAAACCT
AAAACTTTCCAAAAATCACATTTG
Found at i:29911498 original size:6 final size:6
Alignment explanation
Indices: 29911487--29911570 Score: 73
Period size: 6 Copynumber: 13.3 Consensus size: 6
29911477 ACTCGAAAAG
*
29911487 AAGAAA AAGAAAA AAGAAA AGACAAAA AAGCAAA AAGAAGA AAGAAGA
1 AAGAAA AAG-AAA AAGAAA A-A-GAAA AAG-AAA AAGAA-A AAGAA-A
* *
29911535 AA-AAA AAGAAA GAGAAA GAGAAA AAG-AA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
29911571 AATGAAGAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
5 8 0.12
6 31 0.46
7 24 0.36
8 4 0.06
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:29911502 original size:7 final size:7
Alignment explanation
Indices: 29911481--29911584 Score: 68
Period size: 7 Copynumber: 14.1 Consensus size: 7
29911471 GATTTCACTC
29911481 GAAAAGAA
1 GAAAA-AA
29911489 G-AAAAA
1 GAAAAAA
29911495 GAAAAAA
1 GAAAAAA
*
29911502 GAAAAGA
1 GAAAAAA
*
29911509 CAAAAAA
1 GAAAAAA
*
29911516 GCAAAAA
1 GAAAAAA
*
29911523 GAAGAAA
1 GAAAAAA
29911530 GAAGAAAA
1 GAA-AAAA
*
29911538 AAAAGAAA
1 GAAA-AAA
*
29911546 G-AGAAA
1 GAAAAAA
29911552 GAGAAAAA
1 GA-AAAAA
29911560 GAAAAGAA
1 GAAAA-AA
*
29911568 AAAAATGAA
1 GAAAA--AA
29911577 GAAAAAA
1 GAAAAAA
29911584 G
1 G
29911585 GTGAGGTCGA
Statistics
Matches: 75, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
6 7 0.09
7 40 0.53
8 21 0.28
9 7 0.09
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.01
Consensus pattern (7 bp):
GAAAAAA
Found at i:29911528 original size:31 final size:29
Alignment explanation
Indices: 29911482--29911572 Score: 100
Period size: 31 Copynumber: 3.1 Consensus size: 29
29911472 ATTTCACTCG
29911482 AAAAGAAGAAA-AAGAAAAAAGAAAAGACAA
1 AAAAGAA-AAAGAAGAAAAAAGAAAAGA-AA
*
29911512 AAAAGCAAAAAGAAGAAAGAAGAAAA-AAA
1 AAAAG-AAAAAGAAGAAAAAAGAAAAGAAA
*
29911541 AGAAAGAGAAAG-AG-AAAAAGAAAAGAAA
1 A-AAAGAAAAAGAAGAAAAAAGAAAAGAAA
29911569 AAAA
1 AAAA
29911573 TGAAGAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
27 12 0.22
28 6 0.11
29 8 0.15
30 13 0.24
31 15 0.28
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAAGAAGAAAAAAGAAAAGAAA
Found at i:29911560 original size:44 final size:42
Alignment explanation
Indices: 29911482--29911583 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 42
29911472 ATTTCACTCG
29911482 AAAAGAAGAAAAAGAAAAAAGAAAAGACAAAAAAGCAAAA-AGAA
1 AAAAGAAGAAAAA-AAAAAAGAAAAGACAAAAAAG-AAAAGA-AA
* *
29911526 GAAAGAAGAAAAAAAAGAAAGAGAAAGA-GAAAAAGAAAAGAAA
1 AAAAGAAGAAAAAAAA-AAAGA-AAAGACAAAAAAGAAAAGAAA
29911569 AAAATGAAGAAAAAA
1 AAAA-GAAGAAAAAA
29911584 GGTGAGGTCG
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
43 12 0.24
44 34 0.67
45 5 0.10
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.01
Consensus pattern (42 bp):
AAAAGAAGAAAAAAAAAAAGAAAAGACAAAAAAGAAAAGAAA
Found at i:29912719 original size:99 final size:99
Alignment explanation
Indices: 29912540--29912789 Score: 295
Period size: 99 Copynumber: 2.5 Consensus size: 99
29912530 ACATGATGGG
* * * * *
29912540 AAAGGTTGAGGCTGCGACGGCGAACCCGGTGCCTTAAAAGATGTGATGGGAAGAATTAAGGCTGC
1 AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATAGGAAGAATTAAGGCTGC
* **
29912605 AACGGCGAATTCGATACCATGAAGATATGAAGGA
66 AACGGCGAATCCGATACCATGAAGATACAAAGGA
* * * * *
29912639 AAAGGTTGAGGCCACAACGGTGAACCCGGTACCTTAGAAGATGTGATTGGAAGGATTGAA-GTTG
1 AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATAGGAAGAATT-AAGGCTG
* * * *
29912703 TAACGGTGAATCCGATACCATGAAGATGCAAAGGG
65 CAACGGCGAATCCGATACCATGAAGATACAAAGGA
** * *
29912738 AAAGGTTGAGGCCGCAACTACGGACCCGGTACCCTAGAAGATGTGATAGGAA
1 AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATAGGAA
29912790 AGGTTGAGGC
Statistics
Matches: 127, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
99 125 0.98
100 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (99 bp):
AAAGGTTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGATGTGATAGGAAGAATTAAGGCTGC
AACGGCGAATCCGATACCATGAAGATACAAAGGA
Found at i:29913226 original size:39 final size:39
Alignment explanation
Indices: 29913178--29913576 Score: 255
Period size: 39 Copynumber: 10.3 Consensus size: 39
29913168 TAACCATTCG
* * *
29913178 ATCTTTTACCTCGAGCTTGATGCAGATCACAATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * * * * * *
29913217 ATCTCTTACCCCGATCATGGGGCAAATCACAGTCATCCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * *
29913256 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * * ** ** * *
29913295 ATCTCTTACCCTGAGCTTGGGGTAGATTGCAGCCATCCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * * *
29913334 ATCTCTTACCCTGAGCCT-AGAGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAG-GCAGATCACAATCAGCCA
* * * * * * *
29913373 ATCTCTTATCCCGAGCTTGGGGCAAATTACAACCATCCG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * * * *
29913412 ATCTTTTACCCCGAGCCT-AGGGCAAATCACTATCAGTCA
1 ATCTCTTACCCCGAGCTTGA-GGCAGATCACAATCAGCCA
* * * * * * **
29913451 ATCTTTTACCTCGAGCTTG-GGTAGATTACAACCATCTG
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
* * * *
29913489 ATCTTTTACCCCGAGTTTGAGGCAGATCACCATCAGCTA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
** * * * *
29913528 ATCTCTTACCCCGAATTTAAGGCAAATCACCATCAACCA
1 ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
29913567 ATCTCTTACC
1 ATCTCTTACC
29913577 TAAACCTAAA
Statistics
Matches: 272, Mismatches: 83, Indels: 10
0.75 0.23 0.03
Matches are distributed among these distances:
38 28 0.10
39 243 0.89
40 1 0.00
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGAGGCAGATCACAATCAGCCA
Found at i:29913273 original size:78 final size:78
Alignment explanation
Indices: 29913169--29913541 Score: 428
Period size: 78 Copynumber: 4.8 Consensus size: 78
29913159 GACAGATCGT
* * * * * *
29913169 AACCATTCGATCTTTTACCTCGAGCTTGATGCAGATCACAATCAGCCAATCTCTTACCCCGATCA
1 AACCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCT
*
29913234 TGGGGCAAATCAC
66 TGGGGCAAATTAC
** * *
29913247 AGTCATCCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCTGAGCT
1 AACCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCT
* * *
29913312 TGGGGTAGATTGC
66 TGGGGCAAATTAC
* * * * * *
29913325 AGCCATCCGATCTCTTACCCTGAGCCT-AGAGCAGATCACCATCAACCAATCTCTTATCCCGAGC
1 AACCATCCGATCTTTTACCCCGAGCTTGAG-GCAGATCACCATCAGCCAATCTCTTACCCCGAGC
29913389 TTGGGGCAAATTAC
65 TTGGGGCAAATTAC
* * * * * *
29913403 AACCATCCGATCTTTTACCCCGAGCCT-AGGGCAAATCACTATCAGTCAATCTTTTACCTCGAGC
1 AACCATCCGATCTTTTACCCCGAGCTTGA-GGCAGATCACCATCAGCCAATCTCTTACCCCGAGC
* *
29913467 TT-GGGTAGATTAC
65 TTGGGGCAAATTAC
* * *
29913480 AACCATCTGATCTTTTACCCCGAGTTTGAGGCAGATCACCATCAGCTAATCTCTTACCCCGA
1 AACCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGA
29913542 ATTTAAGGCA
Statistics
Matches: 246, Mismatches: 46, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
77 61 0.25
78 184 0.75
79 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.26
Consensus pattern (78 bp):
AACCATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCT
TGGGGCAAATTAC
Found at i:29913338 original size:117 final size:117
Alignment explanation
Indices: 29913097--29913344 Score: 257
Period size: 117 Copynumber: 2.1 Consensus size: 117
29913087 TATTGAAGAT
* * * *
29913097 TCCGATCTCTTA-CCCGTTCATAGGGCATATCATAGTCATTCGATCTTTTACCCCGAGCCTGGGA
1 TCCGATCTCTTACCCCGATCATAGGGCAAATCACAGTCATCCGATCTTTTACCCCGAGCCTGGGA
** ** * * * *
29913161 CAGATCGTAACCATTCGATCTTTTACCTCGAGCTTGATGCAGATCACAATCA
66 CAGATCACAACCAGCCAATCTCTTACCTCGAGCTTGAGGCAGATCACAACCA
* * * * *
29913213 GCCAATCTCTTACCCCGATCATGGGGCAAATCACAGTCATCCGATCTTTTACCCCGAGCTTGGGG
1 TCCGATCTCTTACCCCGATCATAGGGCAAATCACAGTCATCCGATCTTTTACCCCGAGCCTGGGA
* * * * ** *
29913278 CAGATCACCATCAGCCAATCTCTTACC-CTGAGCTTGGGGTAGATTGCAGCCA
66 CAGATCACAACCAGCCAATCTCTTACCTC-GAGCTTGAGGCAGATCACAACCA
29913330 TCCGATCTCTTACCC
1 TCCGATCTCTTACCC
29913345 TGAGCCTAGA
Statistics
Matches: 104, Mismatches: 26, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
116 11 0.11
117 93 0.89
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (117 bp):
TCCGATCTCTTACCCCGATCATAGGGCAAATCACAGTCATCCGATCTTTTACCCCGAGCCTGGGA
CAGATCACAACCAGCCAATCTCTTACCTCGAGCTTGAGGCAGATCACAACCA
Found at i:29914224 original size:26 final size:25
Alignment explanation
Indices: 29914189--29914247 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 25
29914179 GAAAAATTTG
29914189 TTAAACAAAATAAA-AAAAACAGATT
1 TTAAACAAAA-AAATAAAAACAGATT
*
29914214 TTAAAGCAAAAAAATAAAAAGAGATAT
1 TTAAA-CAAAAAAATAAAAACAGAT-T
29914241 TTGAAAC
1 TT-AAAC
29914248 TCTTTTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 8 0.28
26 14 0.48
27 4 0.14
28 3 0.10
ACGTcount: A:0.64, C:0.07, G:0.08, T:0.20
Consensus pattern (25 bp):
TTAAACAAAAAAATAAAAACAGATT
Found at i:29928451 original size:15 final size:15
Alignment explanation
Indices: 29928428--29928457 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29928418 GAACGAGGAC
29928428 TTTCACAAAGAGAAT
1 TTTCACAAAGAGAAT
*
29928443 TTTCGCAAAGAGAAT
1 TTTCACAAAGAGAAT
29928458 CCATTTGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
TTTCACAAAGAGAAT
Found at i:29929347 original size:30 final size:30
Alignment explanation
Indices: 29929306--29929392 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 30
29929296 ATCCTAAAAT
*
29929306 TATTATTTTAGAAAATTTT-AATTTTTTATA
1 TATT-TTTTAGAAAATTTTAAATTTTTGATA
***
29929336 TATTTATTTAGAGTTTTTTAAAATTTTTGATA
1 TATTT-TTTAGAAAATTTT-AAATTTTTGATA
*
29929368 TATTTTTTA-AAAATATATAAATTTT
1 TATTTTTTAGAAAAT-TTTAAATTTT
29929393 GAAAATTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
29 1 0.02
30 23 0.51
31 6 0.13
32 15 0.33
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (30 bp):
TATTTTTTAGAAAATTTTAAATTTTTGATA
Found at i:29932641 original size:10 final size:9
Alignment explanation
Indices: 29932613--29932638 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29932603 CAATAAATAA
29932613 TTTAAAAAT
1 TTTAAAAAT
29932622 TTTAAAAAT
1 TTTAAAAAT
29932631 TTTAAAAA
1 TTTAAAAA
29932639 ATTAATGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:29935854 original size:19 final size:19
Alignment explanation
Indices: 29935826--29935867 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
29935816 AATAGAATGT
*
29935826 AAAA-ATTAAATTAAAAAC
1 AAAATATTAAAATAAAAAC
*
29935844 AAAATATTAAAATAAAAAT
1 AAAATATTAAAATAAAAAC
29935863 AAAAT
1 AAAAT
29935868 TGACTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATATTAAAATAAAAAC
Found at i:29937202 original size:16 final size:16
Alignment explanation
Indices: 29937181--29937211 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29937171 TTTAGGTTGA
*
29937181 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
29937197 GAAAATTAATTAATT
1 GAAAATTAATTAATT
29937212 TAAATTAAAT
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:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:29937224 original size:15 final size:14
Alignment explanation
Indices: 29937199--29937230 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
29937189 TTTAATTGGA
29937199 AAATTAATTAATTT
1 AAATTAATTAATTT
29937213 AAATTAAATTAATTT
1 AAATT-AATTAATTT
29937228 AAA
1 AAA
29937231 ATGTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTAATTAATTT
Found at i:29939353 original size:40 final size:39
Alignment explanation
Indices: 29939299--29939381 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 39
29939289 TAATCGAACG
* * *
29939299 GAAATTTTTGGTTAATTCGGTCGATTAACCGAATTAACT
1 GAAATTTTTAGTTAATTCGATCGATTAACCGAATTAACC
*
29939338 GAAATTTTTTAGTTAATTCGATCGATTAACTGAATTAACC
1 GAAA-TTTTTAGTTAATTCGATCGATTAACCGAATTAACC
29939378 GAAA
1 GAAA
29939382 ATTATATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 4 0.10
40 35 0.90
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (39 bp):
GAAATTTTTAGTTAATTCGATCGATTAACCGAATTAACC
Found at i:29939431 original size:9 final size:9
Alignment explanation
Indices: 29939419--29939460 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
29939409 AAATTATCCA
*
29939419 AATTAATCG
1 AATTAACCG
29939428 AATT-ACCTG
1 AATTAACC-G
*
29939437 AATTACCCG
1 AATTAACCG
29939446 AATTAACCG
1 AATTAACCG
29939455 AATTAA
1 AATTAA
29939461 AGTATTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.86
10 2 0.07
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:29942269 original size:194 final size:195
Alignment explanation
Indices: 29941929--29942288 Score: 515
Period size: 194 Copynumber: 1.9 Consensus size: 195
29941919 ACTGATGCGA
* **
29941929 TGGCTGAGATACCACATATATTGCAAGTCCTCGACAGCTCGTGTGAGCAGCATTGTGAGTCGAGA
1 TGGCCGAGATACCACATATATTGCAAGTCCTCGACAGCTCGTGTGAGCAGCATCATGAGTCGAGA
* *
29941994 AATGAGAAATGAATCCAACAATGGATTACAAGCCCTACGATGGCTGGGATTTATGCATAAGTGCA
66 AAAGAGAAATGAATCCAACAATGGATTACAAGCCCTACGATGGCTGGGAATTATGCATAAGTGCA
** * *
29942059 TATTCTTGATAGCTCGTGTGAGCAGCATTGTTAGGGAATAATTATATGCGTGGATACCGTATCGT
131 TATTCTCAACAGCTCGTGTGAGCAGCATCGTTAGGGAATAATTATATGCGTGGATACCGTATCGT
* * * *
29942124 TGGCCGAGGTACCACATATGTTGCGAGTCCTCGACAGCTCGTGTGAGTAGCATCATGAGTCGA-A
1 TGGCCGAGATACCACATATATTGCAAGTCCTCGACAGCTCGTGTGAGCAGCATCATGAGTCGAGA
* * * * * *
29942188 AAAGAGATATGAATCCTAGAATGGATTACAGGCCCTACGATGGTTGGGAATTATGCATAGGTGCA
66 AAAGAGAAATGAATCCAACAATGGATTACAAGCCCTACGATGGCTGGGAATTATGCATAAGTGCA
* * *
29942253 TGTTCTCAACAGCTCGTGTGAGTAGTATCGTTAGGG
131 TATTCTCAACAGCTCGTGTGAGCAGCATCGTTAGGG
29942289 GACAGTTTAT
Statistics
Matches: 143, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
194 87 0.61
195 56 0.39
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (195 bp):
TGGCCGAGATACCACATATATTGCAAGTCCTCGACAGCTCGTGTGAGCAGCATCATGAGTCGAGA
AAAGAGAAATGAATCCAACAATGGATTACAAGCCCTACGATGGCTGGGAATTATGCATAAGTGCA
TATTCTCAACAGCTCGTGTGAGCAGCATCGTTAGGGAATAATTATATGCGTGGATACCGTATCGT
Found at i:29946663 original size:22 final size:22
Alignment explanation
Indices: 29946638--29946692 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
29946628 GATTGGGATT
*
29946638 TTTTAGTTTTAGTCTTTTAAAC
1 TTTTAGTTTTAGCCTTTTAAAC
* *
29946660 TTTTAGTTTTAGCCTTTTAGAT
1 TTTTAGTTTTAGCCTTTTAAAC
*
29946682 TTTTATTTTTA
1 TTTTAGTTTTA
29946693 TTTATTAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTAGTTTTAGCCTTTTAAAC
Found at i:29946801 original size:15 final size:15
Alignment explanation
Indices: 29946781--29946810 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29946771 GGTAGTGGGC
29946781 TAATATTATATATTA
1 TAATATTATATATTA
*
29946796 TAATATTATTTATTA
1 TAATATTATATATTA
29946811 ATTCGATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:29953617 original size:12 final size:13
Alignment explanation
Indices: 29953575--29953617 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
29953565 CCTTGGTCTT
29953575 CTTCTTCTTTGGGC
1 CTTCTTCTTT-GGC
29953589 GC-TCTTCTTTGGC
1 -CTTCTTCTTTGGC
29953602 CTTCTTCTTT-GC
1 CTTCTTCTTTGGC
29953614 CTTC
1 CTTC
29953618 CGTTTGCGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 7 0.26
13 11 0.41
14 8 0.30
15 1 0.04
ACGTcount: A:0.00, C:0.33, G:0.16, T:0.51
Consensus pattern (13 bp):
CTTCTTCTTTGGC
Found at i:29953928 original size:21 final size:22
Alignment explanation
Indices: 29953889--29953934 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
29953879 AAGGAAATAG
*
29953889 TTTCTTCTTCTTCCTTTTCTTC
1 TTTCTTCTTCTTCCTTTTCTCC
29953911 TTTC-TCTTCTT-CTCTTTCTCC
1 TTTCTTCTTCTTCCT-TTTCTCC
29953932 TTT
1 TTT
29953935 ATCTCGTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCTTCTTCTTCCTTTTCTCC
Found at i:29968626 original size:9 final size:9
Alignment explanation
Indices: 29968612--29968643 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
29968602 TTTTAACCAT
29968612 AAATCCTTA
1 AAATCCTTA
29968621 AAATCCTTA
1 AAATCCTTA
*
29968630 AAATCCCTA
1 AAATCCTTA
29968639 AAATC
1 AAATC
29968644 TTATTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATCCTTA
Found at i:29968933 original size:36 final size:36
Alignment explanation
Indices: 29968886--29968954 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
29968876 TTGTTAACCA
29968886 TAAATCCCTAAAATCTCAATTATGTTA-TTATTTTTT
1 TAAATCCCTAAAATCTCAATTAT-TTATTTATTTTTT
* *
29968922 TAAATCCCTAAAATCTTATTTATTTATTTATTT
1 TAAATCCCTAAAATCTCAATTATTTATTTATTT
29968955 CATTTGTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 3 0.10
36 27 0.90
ACGTcount: A:0.33, C:0.13, G:0.01, T:0.52
Consensus pattern (36 bp):
TAAATCCCTAAAATCTCAATTATTTATTTATTTTTT
Found at i:29972605 original size:36 final size:36
Alignment explanation
Indices: 29972558--29972630 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
29972548 TGGAAGAGAA
29972558 TGATTCATCGCTATTCAAGACTCAAGTAATATGTTT
1 TGATTCATCGCTATTCAAGACTCAAGTAATATGTTT
29972594 TGATTCATCGCTATTCAAGACTCAAGTAATATGTTT
1 TGATTCATCGCTATTCAAGACTCAAGTAATATGTTT
29972630 T
1 T
29972631 TACTTATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (36 bp):
TGATTCATCGCTATTCAAGACTCAAGTAATATGTTT
Found at i:29974874 original size:22 final size:23
Alignment explanation
Indices: 29974834--29974885 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
29974824 TTAACAAGCA
*
29974834 GAGAAACACAGTTATGGAGAATG
1 GAGAAACACAGATATGGAGAATG
29974857 GAGAAACACA-ATATGGAGAATG
1 GAGAAACACAGATATGGAGAATG
29974879 GAGAAAC
1 GAGAAAC
29974886 CTCAGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.48, C:0.10, G:0.29, T:0.13
Consensus pattern (23 bp):
GAGAAACACAGATATGGAGAATG
Found at i:29978156 original size:16 final size:17
Alignment explanation
Indices: 29978121--29978160 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
29978111 TGATTTCGAG
*
29978121 AAAGAAGCAGGGGAATT
1 AAAGAAGCAGGGGAAGT
*
29978138 AAAGAAGCA-TGGAAGT
1 AAAGAAGCAGGGGAAGT
29978154 AAAGAAG
1 AAAGAAG
29978161 GGTTGGTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.53, C:0.05, G:0.33, T:0.10
Consensus pattern (17 bp):
AAAGAAGCAGGGGAAGT
Found at i:29989567 original size:27 final size:28
Alignment explanation
Indices: 29989536--29989596 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 28
29989526 TTAAGAGTAT
* *
29989536 TTTAAAATTTTTGAAAAGTTAATTAAAA
1 TTTAAAACTTTTGAAAAGTTAATAAAAA
* *
29989564 -TT-AAACTTTTGGAAAGTTACTAAAAA
1 TTTAAAACTTTTGAAAAGTTAATAAAAA
29989590 TTTAAAA
1 TTTAAAA
29989597 AAAAATTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
26 20 0.74
27 4 0.15
28 3 0.11
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (28 bp):
TTTAAAACTTTTGAAAAGTTAATAAAAA
Found at i:29989948 original size:20 final size:19
Alignment explanation
Indices: 29989918--29989984 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
29989908 ATACAAAAAT
29989918 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTTCAA
* *
29989937 ATATTTAAAAT-ATTTTTAA
1 A-ATTCAAAATAATTTTCAA
*
29989956 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TCAA
29989975 AATTACAAAA
1 AATT-CAAAA
29989985 CTTATATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 12 0.29
19 16 0.39
20 13 0.32
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTCAAAATAATTTTCAA
Found at i:29989966 original size:18 final size:18
Alignment explanation
Indices: 29989918--29989975 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
29989908 ATACAAAAAT
*
29989918 AATTCAAAATAATTTTCAA
1 AATTCAAAAT-ATTTTTAA
*
29989937 ATATTTAAAATATTTTTAA
1 A-ATTCAAAATATTTTTAA
*
29989956 AATTCAAAATATTTATAA
1 AATTCAAAATATTTTTAA
29989974 AA
1 AA
29989976 ATTACAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.50
19 9 0.26
20 8 0.24
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTCAAAATATTTTTAA
Found at i:29990037 original size:38 final size:40
Alignment explanation
Indices: 29989972--29990062 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 40
29989962 AAATATTTAT
* *
29989972 AAAAATTAC-AAAACTTATATTTAAAAAAAAAAAAAATTA
1 AAAAATTTCTAAAAATTATATTTAAAAAAAAAAAAAATTA
** **
29990011 AAAAATTTCTAAAAATTATA-TT-AAAAATTAAAATTTTA
1 AAAAATTTCTAAAAATTATATTTAAAAAAAAAAAAAATTA
29990049 AAAAATTTCTAAAA
1 AAAAATTTCTAAAA
29990063 TAATAATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 26 0.58
39 10 0.22
40 9 0.20
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (40 bp):
AAAAATTTCTAAAAATTATATTTAAAAAAAAAAAAAATTA
Found at i:29991273 original size:5 final size:5
Alignment explanation
Indices: 29991263--29991288 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29991253 AATTTGAATG
29991263 AAATC AAATC AAATC AAATC AAATC A
1 AAATC AAATC AAATC AAATC AAATC A
29991289 TTTAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATC
Found at i:29992513 original size:17 final size:17
Alignment explanation
Indices: 29992491--29992533 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29992481 TTAACGATAT
* *
29992491 TGTGTCGATGATTCATA
1 TGTGTCGACGATGCATA
29992508 TGTGTCGACGATGCATA
1 TGTGTCGACGATGCATA
*
29992525 TGTCTCGAC
1 TGTGTCGAC
29992534 TTACCATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (17 bp):
TGTGTCGACGATGCATA
Found at i:29995231 original size:13 final size:13
Alignment explanation
Indices: 29995213--29995237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29995203 TGGGAGCTCC
29995213 TCTTTGCTTTTCT
1 TCTTTGCTTTTCT
29995226 TCTTTGCTTTTC
1 TCTTTGCTTTTC
29995238 GTTTGCGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (13 bp):
TCTTTGCTTTTCT
Found at i:30003325 original size:20 final size:20
Alignment explanation
Indices: 30003300--30003340 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30003290 AAAATTGTCA
30003300 GTGCAAAAGCAATATAAAAT
1 GTGCAAAAGCAATATAAAAT
** *
30003320 GTGCAACTGTAATATAAAAT
1 GTGCAAAAGCAATATAAAAT
30003340 G
1 G
30003341 AATTGATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (20 bp):
GTGCAAAAGCAATATAAAAT
Found at i:30004677 original size:15 final size:16
Alignment explanation
Indices: 30004657--30004689 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30004647 AATACGTATG
30004657 AAAATTTT-ACAAAGA
1 AAAATTTTGACAAAGA
*
30004672 AAAATTTTGAGAAAGA
1 AAAATTTTGACAAAGA
30004688 AA
1 AA
30004690 GAAAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAATTTTGACAAAGA
Found at i:30010347 original size:77 final size:76
Alignment explanation
Indices: 30010252--30010529 Score: 335
Period size: 81 Copynumber: 3.6 Consensus size: 76
30010242 CAAAATCAAA
* **
30010252 TCTGTTGAACGGCAGGAATAAATCCTGAAACAAAATTATTTAATTAATTCTTAATTGGAAACAAA
1 TCTGTTGAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAA-AAA
30010317 AATAGAATAAAT
65 AATAGAATAAAT
* * * *
30010329 TCTATTGAACGACAGGAATAAATCCTAAAATAGAATTATTTAATTAAATT-TTGTTTGGAAATAA
1 TCTGTTGAACGACAGGAATAAATCCTGAAACAAAATTATTTAATT-AATTCTTGTTTGG----AA
*
30010393 AAAAAGAAAGAATAAAT
61 AAAAA-ATAGAATAAAT
* * *
30010410 TCTGTTGAACGGCAAGAATAAATCCTGAAACAAAATTATTTAATTAATTCTTGTTTTG-AAAAAA
1 TCTGTTGAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAAAAAA
*
30010474 ATCGAATAAAT
66 ATAGAATAAAT
* * * *
30010485 TTTGTTGAACGACAGGAATAAATCCCGAAACAGAATTATTCAATT
1 TCTGTTGAACGACAGGAATAAATCCTGAAACAAAATTATTTAATT
30010530 TTAATTTTTA
Statistics
Matches: 171, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
75 48 0.28
76 6 0.04
77 46 0.27
78 4 0.02
80 8 0.05
81 59 0.35
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (76 bp):
TCTGTTGAACGACAGGAATAAATCCTGAAACAAAATTATTTAATTAATTCTTGTTTGGAAAAAAA
ATAGAATAAAT
Found at i:30017629 original size:10 final size:11
Alignment explanation
Indices: 30017604--30017633 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
30017594 ATTCACCAAA
30017604 AAAAATATTTT
1 AAAAATATTTT
30017615 AAAAATATTTT
1 AAAAATATTTT
30017626 AAAAATAT
1 AAAAATAT
30017634 AATTATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:30018792 original size:23 final size:22
Alignment explanation
Indices: 30018762--30018813 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
30018752 TTTGAAATAG
*
30018762 TTATAAAT-GAAAAAATTATTATA
1 TTATAAATCCAAAAAA--ATTATA
*
30018785 TTATAAATCCTAAAAAATTATA
1 TTATAAATCCAAAAAAATTATA
30018807 TTATAAA
1 TTATAAA
30018814 AATAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 13 0.50
23 8 0.31
24 5 0.19
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TTATAAATCCAAAAAAATTATA
Found at i:30026267 original size:41 final size:41
Alignment explanation
Indices: 30026160--30026379 Score: 192
Period size: 41 Copynumber: 5.3 Consensus size: 41
30026150 TTATTCTACA
* * *
30026160 CCGAGTCATAAGTCTTCCTTTCAA-ATAATCTTATGCTC-TA
1 CCGAGTCATGAGTCTTCCTTT-AACATAATCTCATGCTCTTT
* * * *
30026200 CCGAGACATAAGTTTTCCTTTAAACATAATCTCACGCTCTTT
1 CCGAGTCATGAGTCTTCCTTT-AACATAATCTCATGCTCTTT
* * *
30026242 CTGAGTCATGAGTCTTCCTTTAACATAGTCTCATGCTCCTT
1 CCGAGTCATGAGTCTTCCTTTAACATAATCTCATGCTCTTT
* ** * *
30026283 CTGAGAGATGTGTCTTCCTTTAACATAGTCTCATGCTCTTT
1 CCGAGTCATGAGTCTTCCTTTAACATAATCTCATGCTCTTT
* * * * * *
30026324 CCGGGTCACGAGTATTCCATTTATACATAATCTCACGCTCATC
1 CCGAGTCATGAGTCTTCC-TTTA-ACATAATCTCATGCTCTTT
*
30026367 CCGAGACATGAGT
1 CCGAGTCATGAGT
30026380 TTTCTATTTA
Statistics
Matches: 145, Mismatches: 31, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
40 21 0.14
41 77 0.53
42 22 0.15
43 25 0.17
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (41 bp):
CCGAGTCATGAGTCTTCCTTTAACATAATCTCATGCTCTTT
Found at i:30026278 original size:82 final size:81
Alignment explanation
Indices: 30026160--30026383 Score: 234
Period size: 82 Copynumber: 2.7 Consensus size: 81
30026150 TTATTCTACA
* * *
30026160 CCGAGTCATAAGTCTTCCTTTCAA-ATAATCTTATGCTCTACCGAGACATAAGTTTTCCTTTAAA
1 CCGAGTCATGAGTCTTCCTTT-AACATAATCTCATGCTCTACCGAGACATGAGTTTTCCTTT-AA
30026224 CATAATCTCACGCTCTTT
64 CATAATCTCACGCTCTTT
* * * * * * *
30026242 CTGAGTCATGAGTCTTCCTTTAACATAGTCTCATGCTCCTTCTGAGAGATGTGTCTTCCTTTAAC
1 CCGAGTCATGAGTCTTCCTTTAACATAATCTCATGCT-CTACCGAGACATGAGTTTTCCTTTAAC
* *
30026307 ATAGTCTCATGCTCTTT
65 ATAATCTCACGCTCTTT
* * * * *
30026324 CCGGGTCACGAGTATTCCATTTATACATAATCTCACGCTCATCCCGAGACATGAGTTTTC
1 CCGAGTCATGAGTCTTCC-TTTA-ACATAATCTCATGCTC-TACCGAGACATGAGTTTTC
30026384 TATTTATACA
Statistics
Matches: 114, Mismatches: 23, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
81 2 0.02
82 62 0.54
83 23 0.20
84 27 0.24
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (81 bp):
CCGAGTCATGAGTCTTCCTTTAACATAATCTCATGCTCTACCGAGACATGAGTTTTCCTTTAACA
TAATCTCACGCTCTTT
Found at i:30026281 original size:21 final size:21
Alignment explanation
Indices: 30026257--30026320 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
30026247 TCATGAGTCT
30026257 TCCTTTAACATAGTCTCATGC
1 TCCTTTAACATAGTCTCATGC
* *
30026278 TCCTTCTGAGAGAT-GTGTC-T--
1 TCCTT-T-A-ACATAGTCTCATGC
30026298 TCCTTTAACATAGTCTCATGC
1 TCCTTTAACATAGTCTCATGC
30026319 TC
1 TC
30026321 TTTCCGGGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 3 0.09
18 5 0.16
19 2 0.06
20 5 0.16
21 7 0.22
22 2 0.06
23 5 0.16
24 3 0.09
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (21 bp):
TCCTTTAACATAGTCTCATGC
Found at i:30032068 original size:122 final size:122
Alignment explanation
Indices: 30031847--30032090 Score: 452
Period size: 122 Copynumber: 2.0 Consensus size: 122
30031837 ACAACTGTTG
*
30031847 GAGGAGGCAGAGGCATAACGGGAGGTACTGGTGGTACTGCAGGTCTTACGACAGGCTGTGCCACA
1 GAGGAGGCAGAGGCATAACGGGAGGTACTGGTGGTACTACAGGTCTTACGACAGGCTGTGCCACA
*
30031912 GGAGGTGAAGGTTGCAATGTCATCGAATTGTTCTTCATGAACTTTGAAAACCACTAC
66 GGAGGTGAAGGTTGCAATGTCATCGAATTATTCTTCATGAACTTTGAAAACCACTAC
*
30031969 GAGGAGGCGGAGGCATAACGGGAGGTACTGGTGGTACTACAGGTCTTACGACAGGCTGTGCCACA
1 GAGGAGGCAGAGGCATAACGGGAGGTACTGGTGGTACTACAGGTCTTACGACAGGCTGTGCCACA
*
30032034 GGAGGTGAAGGTTGCAATGTCATTGAATTATTCTTCATGAACTTTGAAAACCACTAC
66 GGAGGTGAAGGTTGCAATGTCATCGAATTATTCTTCATGAACTTTGAAAACCACTAC
30032091 CTCATTAACC
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
122 118 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.23
Consensus pattern (122 bp):
GAGGAGGCAGAGGCATAACGGGAGGTACTGGTGGTACTACAGGTCTTACGACAGGCTGTGCCACA
GGAGGTGAAGGTTGCAATGTCATCGAATTATTCTTCATGAACTTTGAAAACCACTAC
Found at i:30032684 original size:21 final size:21
Alignment explanation
Indices: 30032660--30032713 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
30032650 CCTATGATAG
30032660 TTCTACCGATACAAGT-ATAAC
1 TTCTACCGATACAAGTCAT-AC
* *
30032681 TTCTATCGATACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
30032702 TTCTACCGATAC
1 TTCTACCGATAC
30032714 TAGAAACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:30032808 original size:24 final size:24
Alignment explanation
Indices: 30032781--30032828 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
30032771 CAGACTACTA
*
30032781 ATACTTCTATGAACAGAACTACCG
1 ATACTTCTATAAACAGAACTACCG
*
30032805 ATACTTCTATAAATAGAACTACCG
1 ATACTTCTATAAACAGAACTACCG
30032829 TTACAACTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (24 bp):
ATACTTCTATAAACAGAACTACCG
Found at i:30033393 original size:41 final size:40
Alignment explanation
Indices: 30033348--30033436 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
30033338 TTAACATTAT
**
30033348 AGTCATAAAACTTCCTTTTTGAACAATCTTATGCTAC-ACCG
1 AGTCATAAAACTTCC-TTTCAAACAATCTTATGCT-CTACCG
**
30033389 AGTCATAAGTCTTCCTTTCAAACAATCTTATGCTCTACCG
1 AGTCATAAAACTTCCTTTCAAACAATCTTATGCTCTACCG
*
30033429 AGACATAA
1 AGTCATAA
30033437 GTCTTCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 1 0.02
40 28 0.67
41 13 0.31
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (40 bp):
AGTCATAAAACTTCCTTTCAAACAATCTTATGCTCTACCG
Found at i:30033429 original size:40 final size:39
Alignment explanation
Indices: 30033369--30033451 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 39
30033359 TTCCTTTTTG
*
30033369 AACAATCTTATGCTACACCGAGTCATAAGTCTTCCTTTCA
1 AACAATCTTATGCTACACCGAGACATAAGTCTT-CTTTCA
*
30033409 AACAATCTTATGCT-CTACCGAGACATAAGTCTTCTTTTA
1 AACAATCTTATGCTAC-ACCGAGACATAAGTCTTCTTTCA
30033448 AACA
1 AACA
30033452 TAATCTCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
39 10 0.25
40 30 0.75
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (39 bp):
AACAATCTTATGCTACACCGAGACATAAGTCTTCTTTCA
Found at i:30035983 original size:23 final size:23
Alignment explanation
Indices: 30035956--30036175 Score: 278
Period size: 23 Copynumber: 9.6 Consensus size: 23
30035946 GTTTTAATGA
* *
30035956 ATTTAAGCTTAAATATTAATTTG
1 ATTTATGCTTAAATATTAATATG
*
30035979 ATTTATGCTTAAGTATTAATATG
1 ATTTATGCTTAAATATTAATATG
* *
30036002 ATTTGTTCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATATG
* * *
30036025 ATTTGTGCTCAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
*
30036048 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
30036071 ATTTATGCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATATG
** * * *
30036094 GCTTGTGCTCAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
*
30036117 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
* *
30036140 ATTTGTGCTTAAACATTAATATG
1 ATTTATGCTTAAATATTAATATG
*
30036163 ATTTGTGCTTAAA
1 ATTTATGCTTAAA
30036176 GAATTAAGAT
Statistics
Matches: 173, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 173 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATATG
Found at i:30036050 original size:69 final size:69
Alignment explanation
Indices: 30035966--30036171 Score: 340
Period size: 69 Copynumber: 3.0 Consensus size: 69
30035956 ATTTAAGCTT
* * * *
30035966 AAATATTAATTTGATTTATGCTTAAGTATTAATATGATTTGTTCTTAAATATTAATATGATTTGT
1 AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGT
30036031 GCTC
66 GCTC
* **
30036035 AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATATGGCTTGT
1 AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGT
30036100 GCTC
66 GCTC
*
30036104 AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAACATTAATATGATTTGT
1 AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGT
30036169 GCT
66 GCT
30036172 TAAAGAATTA
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 126 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (69 bp):
AAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTGTGCTTAAATATTAATATGATTTGT
GCTC
Found at i:30036321 original size:36 final size:36
Alignment explanation
Indices: 30036281--30036367 Score: 156
Period size: 36 Copynumber: 2.4 Consensus size: 36
30036271 CTTCATGCCA
30036281 TTCATGCCATGTGACAGAAAATATGTGGGTATGTTC
1 TTCATGCCATGTGACAGAAAATATGTGGGTATGTTC
* *
30036317 TTCATGCCATGTGACAGAGAATATGTGTGTATGTTC
1 TTCATGCCATGTGACAGAAAATATGTGGGTATGTTC
30036353 TTCATGCCATGTGAC
1 TTCATGCCATGTGAC
30036368 TGATTATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (36 bp):
TTCATGCCATGTGACAGAAAATATGTGGGTATGTTC
Found at i:30037660 original size:58 final size:58
Alignment explanation
Indices: 30037587--30037894 Score: 377
Period size: 58 Copynumber: 5.3 Consensus size: 58
30037577 ACTCGGGGGC
* * * * * * *
30037587 AAAACGGTAATTTTGGTTGAAATTA-GGTCAAAATGGGGATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGGTAAAATCAGGGTAAAAAT-GGAATTTTGGAAAGTTTGAGGGT
* * *
30037645 AAAATGGTAATTTTGGGTAAAATCGATGTTAAAAATGGAATTTT-GAAAATTTGAGGGT
1 AAAATGGTAATTTTGGGTAAAATC-AGGGTAAAAATGGAATTTTGGAAAGTTTGAGGGT
* * * * *
30037703 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGGTAAAATCAGGG-TAAAAATGGAATTTTGGAAAGTTTGAGGGT
* *
30037762 AAAATGGTAATTTTGGGTAAAATCAGGGTTAAAATGGAATTTTGGAAAGTTTAAGGGGT
1 AAAATGGTAATTTTGGGTAAAATCAGGGTAAAAATGGAATTTTGGAAAGTTTGA-GGGT
* * * *
30037821 AAAGTGGTAATTTTGGGTAAAATTAGGGCAAAAATGGAATTTTGGAAAGTTTTAGGGT
1 AAAATGGTAATTTTGGGTAAAATCAGGGTAAAAATGGAATTTTGGAAAGTTTGAGGGT
30037879 AAAATGGTAATTTTGG
1 AAAATGGTAATTTTGG
30037895 AAAGTTTTGG
Statistics
Matches: 215, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
57 2 0.01
58 108 0.50
59 98 0.46
60 7 0.03
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGTAAAATCAGGGTAAAAATGGAATTTTGGAAAGTTTGAGGGT
Found at i:30037770 original size:59 final size:59
Alignment explanation
Indices: 30037616--30037894 Score: 368
Period size: 59 Copynumber: 4.7 Consensus size: 59
30037606 AAATTAGGTC
* *
30037616 AAAATGGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATC-GATGTTA
1 AAAAT-GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATCAG-GGTTA
* * * *
30037676 AAAATGGAATTTT-GAAAATTTGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATCAGGGTTA
* *
30037734 AAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGGTAAAATCAGGGTT-
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATCAGGGTTA
** * * *
30037792 AAAATGGAATTTTGGAAAGTTTAAGGGGTAAAGTGGTAATTTTGGGTAAAATTAGGG-CA
1 AAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTGGGTAAAATCAGGGTTA
**
30037851 AAAATGGAATTTTGGAAAGTTTTAGGGTAAAATGGTAATTTTGG
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGG
30037895 AAAGTTTTGG
Statistics
Matches: 194, Mismatches: 21, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
58 89 0.46
59 100 0.52
60 5 0.03
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGGGTAAAATCAGGGTTA
Found at i:30037937 original size:30 final size:30
Alignment explanation
Indices: 30037858--30038071 Score: 204
Period size: 30 Copynumber: 7.2 Consensus size: 30
30037848 GCAAAAATGG
* *
30037858 AATTTTGG-AAAGTTTTAGGGT-AAAATGGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAAT-AT
*
30037887 AATTTTGG-AAAGTTTTGGGGTCAAAATTT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* *
30037916 AATTTTGGAAAAGTTTGGGGGTCAAAATGT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
** * * *
30037946 AATTTTCAAAAATTTTTGGGGTTAAAATAC
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * *
30037976 AATTTTAGAAAAGTTTAGGGCTCAAAATAT
1 AATTTTGGAAAAGTTTTGGGGTCAAAATAT
* * *
30038006 AATTTT-TAAGAAGTTTTGAGGTTAAAATAT
1 AATTTTGGAA-AAGTTTTGGGGTCAAAATAT
* *
30038036 AATTTTGGAAAAGTTTAGGAGTCAAAATGA-
1 AATTTTGGAAAAGTTTTGGGGTCAAAAT-AT
30038066 AATTTT
1 AATTTT
30038072 TGAACAGTCC
Statistics
Matches: 152, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
29 31 0.20
30 118 0.78
31 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTTGGGGTCAAAATAT
Found at i:30037937 original size:117 final size:117
Alignment explanation
Indices: 30037581--30037951 Score: 414
Period size: 117 Copynumber: 3.2 Consensus size: 117
30037571 TTGGATACTC
* * * *
30037581 GGGGGCAAAACGGTAATTTTGGTTGAAATTAGGTC-AAAATGGGGATTTTGGAAAGTTCGAGGGT
1 GGGGGTAAAATGGTAATTTTGGGTGAAATTAGGGCAAAAAT-GGGATTTTGGAAAGTTCGAGGGT
* *
30037645 AAAATGGTAATTTTGGGTAAAATCGATGTTAAAAATGGAATTTT-GAAAA-TTT
65 AAAATGGTAATTTTGGGTAAAATCG-GGGTAAAAATGGAATTTTGGAAAAGTTT
* * * * *
30037697 GAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGT
1 GGGGGTAAAATGGTAATTTTGGGTGAAATTAGGG-CAAAAATGGGATTTTGGAAAGTTCGAGGGT
* *
30037762 AAAATGGTAATTTTGGGTAAAATCAGGGTTAAAATGGAATTTTGG-AAAGTTT
65 AAAATGGTAATTTTGGGTAAAATCGGGGTAAAAATGGAATTTTGGAAAAGTTT
* * * * **
30037814 AAGGGGTAAAGTGGTAATTTTGGGTAAAATTAGGGCAAAAATGGAATTTTGGAAAGTTTTAGGGT
1 -GGGGGTAAAATGGTAATTTTGGGTGAAATTAGGGCAAAAATGGGATTTTGGAAAGTTCGAGGGT
* * * **
30037879 AAAATGGTAATTTT-GG-AAAGTTTTGGGGTCAAAATTTAATTTTGGAAAAGTTT
65 AAAATGGTAATTTTGGGTAAA--ATCGGGGTAAAAATGGAATTTTGGAAAAGTTT
30037932 GGGGGTCAAAAT-GTAATTTT
1 GGGGGT-AAAATGGTAATTTT
30037952 CAAAAATTTT
Statistics
Matches: 214, Mismatches: 32, Indels: 17
0.81 0.12 0.06
Matches are distributed among these distances:
115 3 0.01
116 47 0.22
117 120 0.56
118 44 0.21
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (117 bp):
GGGGGTAAAATGGTAATTTTGGGTGAAATTAGGGCAAAAATGGGATTTTGGAAAGTTCGAGGGTA
AAATGGTAATTTTGGGTAAAATCGGGGTAAAAATGGAATTTTGGAAAAGTTT
Found at i:30037973 original size:60 final size:59
Alignment explanation
Indices: 30037858--30038071 Score: 245
Period size: 60 Copynumber: 3.6 Consensus size: 59
30037848 GCAAAAATGG
** * *
30037858 AATTTTGG-AAAGTTTTA-GGGT-AAAATGGTAATTTTGGAAAGTTTTGGGGTCAAAATTT
1 AATTTTGGAAAAG-TTTAGGGGTCAAAAT-GTAATTTTAAAAAGTTTTGGGGTTAAAATAT
* * *
30037916 AATTTTGGAAAAGTTTGGGGGTCAAAATGTAATTTTCAAAAATTTTTGGGGTTAAAATAC
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT-AAAAAGTTTTGGGGTTAAAATAT
* * * * *
30037976 AATTTTAGAAAAGTTTAGGGCTCAAAATATAATTTTTAAGAAGTTTTGAGGTTAAAATAT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAA-TTTTAAAAAGTTTTGGGGTTAAAATAT
* *
30038036 AATTTTGGAAAAGTTTAGGAGTCAAAATGAAATTTT
1 AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTT
30038072 TGAACAGTCC
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
58 11 0.08
59 20 0.15
60 96 0.73
61 4 0.03
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (59 bp):
AATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTAAAAAGTTTTGGGGTTAAAATAT
Found at i:30039267 original size:12 final size:11
Alignment explanation
Indices: 30039252--30039310 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
30039242 AATACTATCA
30039252 TTATTACTATAT
1 TTATTA-TATAT
*
30039264 TTATTAT-GA-
1 TTATTATATAT
30039273 TTATTAT-TA-
1 TTATTATATAT
*
30039282 TTAATATATAT
1 TTATTATATAT
30039293 TTATTACTATAT
1 TTATTA-TATAT
30039305 TTATTA
1 TTATTA
30039311 GATACATGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 14 0.35
10 3 0.08
11 6 0.15
12 17 0.43
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (11 bp):
TTATTATATAT
Found at i:30039936 original size:17 final size:17
Alignment explanation
Indices: 30039914--30039971 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
30039904 TGGACATTTG
30039914 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
*
30039931 AATTTAAATTTTAAA-A
1 AATTTAAATTTAAAATA
* *
30039947 CATTT-AATCTTAAGATA
1 AATTTAAAT-TTAAAATA
30039964 AATTTAAA
1 AATTTAAA
30039972 ATGGGTTTGG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 3 0.09
16 9 0.27
17 19 0.58
18 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:30046035 original size:21 final size:21
Alignment explanation
Indices: 30046011--30046065 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
30046001 TGAGATAGTA
*
30046011 CTACCGATACAAGTGA-GACTT
1 CTACCGATACAAGTCATG-CTT
* *
30046032 CTACCGAAACATGTCATGCTT
1 CTACCGATACAAGTCATGCTT
30046053 -TACCGATACAAGT
1 CTACCGATACAAGT
30046066 ATACAAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 11 0.39
21 16 0.57
22 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTCATGCTT
Found at i:30046762 original size:24 final size:24
Alignment explanation
Indices: 30046726--30046776 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
30046716 CCAAACAACA
30046726 TTAGCTTTCACGAGCCCA-ATATGG
1 TTAGCTTTCACGAGCCCAGA-ATGG
30046750 TTAGCTCTT-ACGAGCCCAGAATGG
1 TTAGCT-TTCACGAGCCCAGAATGG
30046774 TTA
1 TTA
30046777 ACTAGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (24 bp):
TTAGCTTTCACGAGCCCAGAATGG
Found at i:30047133 original size:21 final size:21
Alignment explanation
Indices: 30047104--30047156 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
30047094 CTTGTGCTGC
*
30047104 TCTACCGATACAAGT-ATG-A
1 TCTATCGATACAAGTCATGCA
30047123 TTTCTATCGATACAAGTCATGCA
1 --TCTATCGATACAAGTCATGCA
30047146 TCTATCGATAC
1 TCTATCGATAC
30047157 CAAAAACTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 25 0.86
22 3 0.10
23 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (21 bp):
TCTATCGATACAAGTCATGCA
Found at i:30054282 original size:21 final size:20
Alignment explanation
Indices: 30054236--30054285 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
30054226 TTGTGCTAGG
*
30054236 TCTACCGATATAAGTATGAT
1 TCTACCGATACAAGTATGAT
30054256 TCCTACCGATACAAGTCATGCA-
1 T-CTACCGATACAAGT-ATG-AT
30054278 TCTACCGA
1 TCTACCGA
30054286 ACCAAAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 4 0.15
23 1 0.04
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAT
Found at i:30068045 original size:79 final size:78
Alignment explanation
Indices: 30067901--30068118 Score: 242
Period size: 79 Copynumber: 2.8 Consensus size: 78
30067891 TTTAAATTGA
* * * * * *
30067901 AAATTAATTAAATAATTTTGTTTCGGGA-TTTATACCTGTCATTCAACAGAATTTATTCGATTTT
1 AAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT-TCGTTCAACAGAATTTATTCGAGTTT
*
30067965 CTGTTTCCAAATAG
65 CTGTTTCCAAACAG
*
30067979 AAATTACTTAAACAATTCTGTTTCAGGATTTTATTCCTATCGTTCAACAGAATTTAATT-GAGTT
1 AAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT-TCGTTCAACAGAATTT-ATTCGAGTT
*
30068043 TCTGTTTTCAAACAG
64 TCTGTTTCCAAACAG
* * * * * * *
30068058 AAATCAATTGAACAATTCTGTTTCAAGCTTCTATTCCTTCCGTTCAATAGAATTGATTCGA
1 AAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCTT-CGTTCAACAGAATTTATTCGA
30068119 TATCTATTGT
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
78 28 0.24
79 87 0.74
80 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (78 bp):
AAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCTTCGTTCAACAGAATTTATTCGAGTTTC
TGTTTCCAAACAG
Found at i:30068620 original size:18 final size:19
Alignment explanation
Indices: 30068577--30068624 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
30068567 TTATAAATGG
*
30068577 CTTAAATTATGACAAAAGC
1 CTTAAATTGTGACAAAAGC
*
30068596 CTTAAATTGTGACAGAAG-
1 CTTAAATTGTGACAAAAGC
*
30068614 TTTAAATTGTG
1 CTTAAATTGTG
30068625 GTTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (19 bp):
CTTAAATTGTGACAAAAGC
Found at i:30068640 original size:31 final size:31
Alignment explanation
Indices: 30068597--30068719 Score: 147
Period size: 31 Copynumber: 3.9 Consensus size: 31
30068587 GACAAAAGCC
* *
30068597 TTAAATTGTGACAGAAGTTTAAATTGTGGTT
1 TTAAATTGTGACAAAAGCTTAAATTGTGGTT
* * *
30068628 TTAAATTATGACAAAAGCCTTATATTGTGGCT
1 TTAAATTGTGACAAAAG-CTTAAATTGTGGTT
** * *
30068660 TTAAATTGTGACAAAAAATTAAATTGTCGTA
1 TTAAATTGTGACAAAAGCTTAAATTGTGGTT
*
30068691 TTAAATTGTGAAAAAAGCTTAAATTGTGG
1 TTAAATTGTGACAAAAGCTTAAATTGTGG
30068720 CATCAAAGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
31 49 0.65
32 26 0.35
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (31 bp):
TTAAATTGTGACAAAAGCTTAAATTGTGGTT
Found at i:30068670 original size:63 final size:62
Alignment explanation
Indices: 30068597--30068720 Score: 167
Period size: 63 Copynumber: 2.0 Consensus size: 62
30068587 GACAAAAGCC
* ** * * * *
30068597 TTAAATTGTGACAGAAGTTTAAATTGTGGTTTTAAATTATGACAAAAGCCTTATATTGTGGCT
1 TTAAATTGTGACAAAAAATTAAATTGTCGTATTAAATTATGAAAAAAG-CTTAAATTGTGGCT
*
30068660 TTAAATTGTGACAAAAAATTAAATTGTCGTATTAAATTGTGAAAAAAGCTTAAATTGTGGC
1 TTAAATTGTGACAAAAAATTAAATTGTCGTATTAAATTATGAAAAAAGCTTAAATTGTGGC
30068721 ATCAAAGATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
62 12 0.23
63 41 0.77
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (62 bp):
TTAAATTGTGACAAAAAATTAAATTGTCGTATTAAATTATGAAAAAAGCTTAAATTGTGGCT
Found at i:30073964 original size:19 final size:18
Alignment explanation
Indices: 30073928--30073969 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
30073918 TCACTATGAA
*
30073928 TTCTTCTTCTTTTTCTCT
1 TTCTCCTTCTTTTTCTCT
30073946 TTCTCCTTCTTTCTTCTCT
1 TTCTCCTTCTTT-TTCTCT
30073965 TTCTC
1 TTCTC
30073970 AGCACTTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTCCTTCTTTTTCTCT
Found at i:30073967 original size:9 final size:10
Alignment explanation
Indices: 30073928--30073968 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
30073918 TCACTATGAA
30073928 TTCTTCTTCT
1 TTCTTCTTCT
30073938 TT-TTC-TCT
1 TTCTTCTTCT
*
30073946 TTCTCCTTCT
1 TTCTTCTTCT
30073956 TTCTTC-TCT
1 TTCTTCTTCT
30073965 TTCT
1 TTCT
30073969 CAGCACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 5 0.19
9 12 0.44
10 10 0.37
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:30081026 original size:18 final size:17
Alignment explanation
Indices: 30081002--30081046 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
30080992 AAAAGAATTG
30081002 AGAAAAATAAAACAGATT
1 AGAAAAATAAAACAG-TT
*
30081020 A-ATAAAAAAAAACAGTT
1 AGA-AAAATAAAACAGTT
30081037 AGAAAAATAA
1 AGAAAAATAA
30081047 TAATAATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (17 bp):
AGAAAAATAAAACAGTT
Found at i:30081258 original size:163 final size:165
Alignment explanation
Indices: 30080986--30081317 Score: 542
Period size: 163 Copynumber: 2.0 Consensus size: 165
30080976 TAGACATAAA
*
30080986 ACACCTAAAAGAATTGAGAAAAATAAAACAGATTAATAAAAAAAAACAGTTAGAAAAATAATAAT
1 ACACCTAAAAGAATTGAGAAAAATAAAACAGATTAATAAAAAAAAACAGTCAGAAAAATAATAAT
** *
30081051 AATTGCAACTACAAAAATAAACATCAAACAAACACCATCCTCGGCAATGGCGGCAAAACTTGATC
66 AATTGCAACTACAAAAATAAACATCAAACAAACACCATCCTCGGCAACAGCGCCAAAACTTGATC
30081116 ACGCTATAAACGTCACAGCAATAATGTGCAAGCGG
131 ACGCTATAAACGTCACAGCAATAATGTGCAAGCGG
* * * *
30081151 ACACCTAAAGGAATTGAGAAAAATAAAATAGATT-AT-AAAAATAATAGTCAGAAAAATAATAAT
1 ACACCTAAAAGAATTGAGAAAAATAAAACAGATTAATAAAAAAAAACAGTCAGAAAAATAATAAT
*
30081214 AATTGCAACTACAAAAATAAATATCAAACAAACACCATCCTCGGCAACAGCGCCAAAACTTGATC
66 AATTGCAACTACAAAAATAAACATCAAACAAACACCATCCTCGGCAACAGCGCCAAAACTTGATC
* * *
30081279 GCGCTATAAATGTCACAGCAATAATGTGCAAGTGG
131 ACGCTATAAACGTCACAGCAATAATGTGCAAGCGG
30081314 ACAC
1 ACAC
30081318 TGTCGATGCA
Statistics
Matches: 155, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
163 121 0.78
164 2 0.01
165 32 0.21
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (165 bp):
ACACCTAAAAGAATTGAGAAAAATAAAACAGATTAATAAAAAAAAACAGTCAGAAAAATAATAAT
AATTGCAACTACAAAAATAAACATCAAACAAACACCATCCTCGGCAACAGCGCCAAAACTTGATC
ACGCTATAAACGTCACAGCAATAATGTGCAAGCGG
Found at i:30085550 original size:12 final size:12
Alignment explanation
Indices: 30085533--30085557 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30085523 CTGCAATAAA
30085533 TATAATAATTTT
1 TATAATAATTTT
30085545 TATAATAATTTT
1 TATAATAATTTT
30085557 T
1 T
30085558 TTTGGACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATAATAATTTT
Found at i:30088538 original size:42 final size:42
Alignment explanation
Indices: 30088479--30088558 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
30088469 CGAGTCTAAA
*
30088479 TCACCACATTTACATAATTATGTCTCTTGTGCAATTTCTAGG
1 TCACCACATTTACATAATTATGTCTCTTGTCCAATTTCTAGG
*
30088521 TCACCACATTTATATAATTATGTCTCTTGTCCAATTTC
1 TCACCACATTTACATAATTATGTCTCTTGTCCAATTTC
30088559 GTATTACCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (42 bp):
TCACCACATTTACATAATTATGTCTCTTGTCCAATTTCTAGG
Found at i:30090650 original size:14 final size:14
Alignment explanation
Indices: 30090631--30090662 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
30090621 TTGGCATGCC
30090631 ATAGGGTCATCGGT
1 ATAGGGTCATCGGT
30090645 ATAGGGTCATCGGT
1 ATAGGGTCATCGGT
30090659 ATAG
1 ATAG
30090663 TGGTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.34, T:0.28
Consensus pattern (14 bp):
ATAGGGTCATCGGT
Found at i:30090746 original size:49 final size:49
Alignment explanation
Indices: 30090693--30090882 Score: 166
Period size: 49 Copynumber: 3.9 Consensus size: 49
30090683 CAACCCACCT
*
30090693 AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGGCCATTC
1 AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGGCCACTC
* * * * * *
30090742 AGGATGGTACAATATTCAAATTGTGAAAGTCATCGTTGTC-GAGCCACCC
1 AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAG-GCCACTC
* * * * * *
30090791 GGGATGGTAGAATATGTAGATAGTGAAAATCATCATTGTCGGGCCACTC
1 AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGGCCACTC
* *** ** ** *
30090840 AGAATAAAAGAATATTAAAATTTTAAAAGTCATCGTTGTCAGG
1 AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGG
30090883 TAACCTGGGA
Statistics
Matches: 109, Mismatches: 30, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
48 1 0.01
49 107 0.98
50 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (49 bp):
AGGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGGCCACTC
Found at i:30090854 original size:98 final size:98
Alignment explanation
Indices: 30090694--30090879 Score: 246
Period size: 98 Copynumber: 1.9 Consensus size: 98
30090684 AACCCACCTA
* * * *** *
30090694 GGATGGTAGAATATGCAAATAGTAAAAATCATCGTTGTCAGGCCATTCAGGATGGTACAATATTC
1 GGATGGTAGAATATGCAAATAGTAAAAATCATCATTGTCAGGCCACTCAGAATAAAACAATATTA
*
30090759 AAATTGTGAAAGTCATCGTTGTCGAGCCACCCG
66 AAATTGTAAAAGTCATCGTTGTCGAGCCACCCG
* * * * *
30090792 GGATGGTAGAATATGTAGATAGTGAAAATCATCATTGTCGGGCCACTCAGAATAAAAGAATATTA
1 GGATGGTAGAATATGCAAATAGTAAAAATCATCATTGTCAGGCCACTCAGAATAAAACAATATTA
*
30090857 AAATTTTAAAAGTCATCGTTGTC
66 AAATTGTAAAAGTCATCGTTGTC
30090880 AGGTAACCTG
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
98 74 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (98 bp):
GGATGGTAGAATATGCAAATAGTAAAAATCATCATTGTCAGGCCACTCAGAATAAAACAATATTA
AAATTGTAAAAGTCATCGTTGTCGAGCCACCCG
Found at i:30091219 original size:37 final size:37
Alignment explanation
Indices: 30091178--30091251 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
30091168 TTATTCTGTG
*
30091178 TTAGAAACTAAAGGCAGTATATAATAAATATAAATTT
1 TTAGAAACTAAAGACAGTATATAATAAATATAAATTT
30091215 TTAGAAACTAAAGACAGTATATAATAAATATAAATTT
1 TTAGAAACTAAAGACAGTATATAATAAATATAAATTT
30091252 AAAAACAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.32
Consensus pattern (37 bp):
TTAGAAACTAAAGACAGTATATAATAAATATAAATTT
Found at i:30098778 original size:20 final size:19
Alignment explanation
Indices: 30098749--30098812 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
30098739 AGAAGAAGAA
*
30098749 AAATCATTTTATTTATTTTT
1 AAAT-ATTTTATATATTTTT
30098769 AAATACTTTTATAT-TTTTT
1 AAATA-TTTTATATATTTTT
* *
30098788 AAA-ATATTTATGTATTTAT
1 AAATAT-TTTATATATTTTT
30098807 AAATAT
1 AAATAT
30098813 ATTTGAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.19
19 16 0.43
20 13 0.35
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (19 bp):
AAATATTTTATATATTTTT
Found at i:30098814 original size:20 final size:20
Alignment explanation
Indices: 30098756--30098816 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
30098746 GAAAAATCAT
*
30098756 TTTATTTATTTTTAAATACT-
1 TTTATATATTTTTAAATA-TA
30098776 TTTATAT-TTTTTAAA-ATA
1 TTTATATATTTTTAAATATA
* *
30098794 TTTATGTATTTATAAATATA
1 TTTATATATTTTTAAATATA
30098814 TTT
1 TTT
30098817 GAAATTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 7 0.20
19 15 0.43
20 12 0.34
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTATATATTTTTAAATATA
Found at i:30099457 original size:30 final size:31
Alignment explanation
Indices: 30099423--30099482 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
30099413 AAATGAACAC
* *
30099423 TGAACTGTTCAAAAG-TTTTATTTAAGTCAT
1 TGAACTATTCAAAAGATCTTATTTAAGTCAT
*
30099453 TGAACTATTCGAAAGATCTTATTTAAGTCA
1 TGAACTATTCAAAAGATCTTATTTAAGTCA
30099483 CTAGGTTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (31 bp):
TGAACTATTCAAAAGATCTTATTTAAGTCAT
Found at i:30103394 original size:17 final size:18
Alignment explanation
Indices: 30103372--30103407 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
30103362 TCATAACAAT
30103372 TATGAAGATTTTGG-ATA
1 TATGAAGATTTTGGCATA
30103389 TATGAAGATTTTGGCATA
1 TATGAAGATTTTGGCATA
30103407 T
1 T
30103408 TCCTTGAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (18 bp):
TATGAAGATTTTGGCATA
Found at i:30104204 original size:13 final size:13
Alignment explanation
Indices: 30104186--30104215 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30104176 TAAATTTAAA
30104186 TAAATTAAAAATT
1 TAAATTAAAAATT
*
30104199 TAAATTCAAAATT
1 TAAATTAAAAATT
30104212 TAAA
1 TAAA
30104216 ACATAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATTAAAAATT
Found at i:30104578 original size:31 final size:31
Alignment explanation
Indices: 30104540--30104601 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
30104530 AAGAGGATAG
30104540 GAAATGATATTTGATGCTTTGTCCAGCTCTT
1 GAAATGATATTTGATGCTTTGTCCAGCTCTT
30104571 GAAATGATATTTGATGCTTTGTCCAGCTCTT
1 GAAATGATATTTGATGCTTTGTCCAGCTCTT
30104602 ACTTCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (31 bp):
GAAATGATATTTGATGCTTTGTCCAGCTCTT
Found at i:30104680 original size:76 final size:76
Alignment explanation
Indices: 30104596--30105506 Score: 1364
Period size: 76 Copynumber: 12.0 Consensus size: 76
30104586 GCTTTGTCCA
* * * *
30104596 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCTAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
30104661 GAAATGAGGTT
66 GAAATGATGTT
* * * * *
30104672 GCTCTTACTTTAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGAATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
30104737 GAAATGATGTT
66 GAAATGATGTT
* * *
30104748 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
30104813 GAAATGATGTT
66 GAAATGATGTT
*
30104824 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
30104889 GAAATGACGTT
66 GAAATGATGTT
*
30104900 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTTAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* * *
30104965 GAGACGATCTT
66 GAAATGATGTT
* * * **
30104976 GCTCTGACTTCAATTTTAGAGATAAAGACTTGATATTGAACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
30105041 GAAATGACGTT
66 GAAATGATGTT
*
30105052 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
30105116 GAAAAGATCTT
66 GAAATGATGTT
*
30105127 GGTCTTACTTCAATTTCAGAGATAAAGA-TGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATA
1 GCTCTTACTTCAATTTCAGAGATAAAGACT-TGTTATCCAACTCTACTTCAATTTCAAGAGGATA
* *
30105190 GGAAAAGATCTT
65 GGAAATGATGTT
* *
30105202 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTTCTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
*
30105267 GAAATGACGTT
66 GAAATGATGTT
*
30105278 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
30105342 GAAAAGATCTT
66 GAAATGATGTT
* *
30105353 GGTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
30105417 GAAAAGATCTT
66 GAAATGATGTT
* * *
30105428 ACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTTAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
* *
30105493 GGAATGATCTT
66 GAAATGATGTT
30105504 GCT
1 GCT
30105507 ACGGTCTGAT
Statistics
Matches: 774, Mismatches: 57, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
75 283 0.37
76 491 0.63
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (76 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAG
GAAATGATGTT
Found at i:30105253 original size:226 final size:226
Alignment explanation
Indices: 30104596--30105499 Score: 1425
Period size: 226 Copynumber: 4.0 Consensus size: 226
30104586 GCTTTGTCCA
* * * *
30104596 GCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCTAGCTTTACTTCAATTTCAAGAGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCAAGAGGATAG
* ** * * *
30104661 GAAATGAGGTTGCTCTTACTTTAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTT
65 GAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCA-CTCTACTTCAATTT
* * * * *
30104726 CAAGAGAATAGGAAATGATGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGCTT
129 CAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTC
*
30104791 TACTTCAATTTCAAGAGGATAGGAAATGATGTT
194 TACTTCAATTTCAAGAGGATAGGAAATGACGTT
* *
30104824 GCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAG
*
30104889 GAAATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATT
65 GAAAAGATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATT
* * * * * **
30104953 TTAAGAGGATAGGAGACGATCTTGCTCTGACTTCAATTTTAGAGATAAAGACTTGATATTGAACT
128 TCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACT
30105018 CTACTTCAATTTCAAGAGGATAGGAAATGACGTT
193 CTACTTCAATTTCAAGAGGATAGGAAATGACGTT
30105052 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGG
*
30105117 AAAAGATCTTGGTCTTACTTCAATTTCAGAGATAAAGA-TGTGTTATCCACTCTACTTCAATTTC
66 AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACT-TGTTATCCACTCTACTTCAATTTC
30105181 AAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCT
130 AAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCT
*
30105246 TCTTCAATTTCAAGAGGATAGGAAATGACGTT
195 ACTTCAATTTCAAGAGGATAGGAAATGACGTT
30105278 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGG
1 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGG
* *
30105343 AAAAGATCTTGGTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
66 AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCA
* * *
30105408 AGAGGATAGGAAAAGATCTTACTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTA
131 AGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTA
* *
30105473 CTTTAATTTCAAGAGGATAGGGAATGA
196 CTTCAATTTCAAGAGGATAGGAAATGA
30105500 TCTTGCTACG
Statistics
Matches: 631, Mismatches: 39, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
226 320 0.51
227 68 0.11
228 241 0.38
229 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (226 bp):
GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGATAGG
AAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCA
AGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTA
CTTCAATTTCAAGAGGATAGGAAATGACGTT
Found at i:30116912 original size:6 final size:6
Alignment explanation
Indices: 30116901--30116997 Score: 85
Period size: 6 Copynumber: 16.2 Consensus size: 6
30116891 TCATAATTTG
* *
30116901 ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATAGTTGA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
* * *
30116950 A-ATAA ATTTAA ATTTAA A--TAA ATTAAAA ATTTAA ATTCAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATT-TAA ATTTAA
30116997 A
1 A
30116998 ACATAAAAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.11
6 46 0.63
7 10 0.14
8 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:30116924 original size:11 final size:11
Alignment explanation
Indices: 30116910--30116961 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
30116900 GATTTAAATT
30116910 TAAATTTAAAA
1 TAAATTTAAAA
30116921 TAAATTT-AAA
1 TAAATTTAAAA
* * **
30116931 T-AGTTGAATT
1 TAAATTTAAAA
30116941 TAAATTTAAAA
1 TAAATTTAAAA
30116952 TAAATTTAAA
1 TAAATTTAAA
30116962 TTTAAATAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 22 0.71
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:30116924 original size:17 final size:17
Alignment explanation
Indices: 30116904--30116984 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
30116894 TAATTTGATT
30116904 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
**
30116921 TAAATTTAAA--T-AGT
1 TAAATTTAAATTTAAAA
*
30116935 TGAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
30116952 TAAATTTAAATTT-AAA
1 TAAATTTAAATTTAAAA
*
30116968 TAAATTAAAAATTTAAA
1 TAAATT-TAAATTTAAA
30116985 TTCAAAATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 10 0.19
17 29 0.56
18 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:30116986 original size:13 final size:13
Alignment explanation
Indices: 30116968--30116997 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
30116958 TAAATTTAAA
30116968 TAAATTAAAAATT
1 TAAATTAAAAATT
*
30116981 TAAATTCAAAATT
1 TAAATTAAAAATT
30116994 TAAA
1 TAAA
30116998 ACATAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATTAAAAATT
Found at i:30119970 original size:14 final size:14
Alignment explanation
Indices: 30119951--30119977 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30119941 ATCCTAAAAT
30119951 TCATAAGTGTTTTG
1 TCATAAGTGTTTTG
30119965 TCATAAGTGTTTT
1 TCATAAGTGTTTT
30119978 TATACGACAT
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:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (14 bp):
TCATAAGTGTTTTG
Found at i:30123830 original size:28 final size:28
Alignment explanation
Indices: 30123774--30123927 Score: 139
Period size: 28 Copynumber: 5.4 Consensus size: 28
30123764 TTTTTCATAA
*
30123774 TTCGCCACAAAGACTTTTTCATTTAAGAGG
1 TTCGCCACAAAGAC--TTTCCTTTAAGAGG
*
30123804 TTCGCCACAAAGGCTTTCCTTTAAGAGG
1 TTCGCCACAAAGACTTTCCTTTAAGAGG
** * * *
30123832 TTCGCCACAAAGTTTTTCCCTTCATAGG
1 TTCGCCACAAAGACTTTCCTTTAAGAGG
* * * * *
30123860 TTCAACAAAAAAGCCTTT-CTTTCAAAAGG
1 TTC-GCCACAAAGACTTTCCTTT-AAGAGG
*
30123889 TTCGCCACAAAGACTTTCCTTTTAGAGG
1 TTCGCCACAAAGACTTTCCTTTAAGAGG
*
30123917 TTCGCGACAAA
1 TTCGCCACAAA
30123928 AGCTTTCTTT
Statistics
Matches: 99, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
28 66 0.67
29 20 0.20
30 13 0.13
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (28 bp):
TTCGCCACAAAGACTTTCCTTTAAGAGG
Found at i:30123929 original size:57 final size:54
Alignment explanation
Indices: 30123774--30123937 Score: 157
Period size: 57 Copynumber: 2.9 Consensus size: 54
30123764 TTTTTCATAA
* * *
30123774 TTCGCCACAAAGACTTTTTCATTTAAGAGGTTCGCCACAAAGGCTTTCCTTTAAGAGG
1 TTCGCCACAAAGAC--TTTCCTTTAAGAGGTTCG-CACAAAAGCTTT-CTTTAAAAGG
** * * * * *
30123832 TTCGCCACAAAGTTTTTCCCTTCATAGGTTCAACAAAAAAGCCTTTCTTTCAAAAGG
1 TTCGCCACAAAGACTTTCCTTTAAGAGGTTC-GCACAAAAG-CTTTCTTT-AAAAGG
*
30123889 TTCGCCACAAAGACTTTCCTTTTAGAGGTTCGCGACAAAAGCTTTCTTT
1 TTCGCCACAAAGACTTTCCTTTAAGAGGTTCGC-ACAAAAGCTTTCTTT
30123938 TCCTAACATG
Statistics
Matches: 85, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
56 32 0.38
57 41 0.48
58 12 0.14
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (54 bp):
TTCGCCACAAAGACTTTCCTTTAAGAGGTTCGCACAAAAGCTTTCTTTAAAAGG
Found at i:30127320 original size:20 final size:20
Alignment explanation
Indices: 30127291--30127345 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
30127281 ACTTTATTTG
30127291 CATTACTGGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCCA
* * *
30127311 CATTATTGGTAGCTTGTCTA
1 CATTACTGGTGGCTTGTCCA
*
30127331 CATTACTAGTGGCTT
1 CATTACTGGTGGCTT
30127346 ACAAATTGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
CATTACTGGTGGCTTGTCCA
Found at i:30131455 original size:14 final size:15
Alignment explanation
Indices: 30131438--30131472 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
30131428 TTAATTATTT
30131438 ATTATT-TAAAAAGA
1 ATTATTATAAAAAGA
30131452 ATTACTTATAAAAAGA
1 ATTA-TTATAAAAAGA
30131468 ATTAT
1 ATTAT
30131473 CATGGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 3 0.16
16 12 0.63
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (15 bp):
ATTATTATAAAAAGA
Found at i:30131922 original size:3 final size:3
Alignment explanation
Indices: 30131914--30131954 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
30131904 GTCTCTTACA
*
30131914 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
30131955 CGGGATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:30132824 original size:30 final size:31
Alignment explanation
Indices: 30132742--30132824 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
30132732 GTTGGATCTG
*
30132742 AATTTTTAAATTTA-AAAAATA-GAAAAATTA
1 AATTTTTAAATATATAAAAATATG-AAAATTA
* **
30132772 AATTTTTAGA-A-ATAAATGTATGAAAATTA
1 AATTTTTAAATATATAAAAATATGAAAATTA
30132801 AA-TTTTAAATATATAAAAATATGA
1 AATTTTTAAATATATAAAAATATGA
30132825 TGTTTTATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.17
29 15 0.36
30 20 0.48
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (31 bp):
AATTTTTAAATATATAAAAATATGAAAATTA
Found at i:30133366 original size:12 final size:12
Alignment explanation
Indices: 30133346--30133378 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
30133336 TATTTATTTA
30133346 AATATTTAAATAT
1 AATA-TTAAATAT
30133359 AATATTAAATAT
1 AATATTAAATAT
30133371 AATATTAA
1 AATATTAA
30133379 TTAATTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTAAATAT
Found at i:30134149 original size:14 final size:15
Alignment explanation
Indices: 30134130--30134161 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
30134120 TAGGTGAATT
30134130 ATAAGAATAAA-ATC
1 ATAAGAATAAATATC
30134144 ATAAGAATAAATATC
1 ATAAGAATAAATATC
30134159 ATA
1 ATA
30134162 TTTTAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (15 bp):
ATAAGAATAAATATC
Found at i:30142376 original size:14 final size:14
Alignment explanation
Indices: 30142357--30142384 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30142347 TAATTATTTG
30142357 ATTATTGTATAAGA
1 ATTATTGTATAAGA
30142371 ATTATTGTATAAGA
1 ATTATTGTATAAGA
30142385 GATTTTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
ATTATTGTATAAGA
Found at i:30162747 original size:21 final size:22
Alignment explanation
Indices: 30162721--30162761 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
30162711 TCGCTCTTAC
30162721 TTTCTC-ACAAGTTTATTTTCT
1 TTTCTCTACAAGTTTATTTTCT
*
30162742 TTTCTCTACAAGTTTCTTTT
1 TTTCTCTACAAGTTTATTTT
30162762 AACCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTCTCTACAAGTTTATTTTCT
Found at i:30165118 original size:19 final size:19
Alignment explanation
Indices: 30165081--30165119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30165071 GAACAATTTA
*
30165081 TTCTTTTTCTTTTTCTTTC
1 TTCTTTTTCTATTTCTTTC
30165100 TTCTTTTTCTCATTT-TTTC
1 TTCTTTTTCT-ATTTCTTTC
30165119 T
1 T
30165120 AAGTGATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTTCTATTTCTTTC
Found at i:30166191 original size:18 final size:18
Alignment explanation
Indices: 30166152--30166191 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30166142 CTCGACAGGT
* * *
30166152 TCTTCTTTTTCTTTCTCT
1 TCTTCTTTCTCTTCCTCG
30166170 TCTTCTTTCTCTTCCTCG
1 TCTTCTTTCTCTTCCTCG
30166188 TCTT
1 TCTT
30166192 GATCCTTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (18 bp):
TCTTCTTTCTCTTCCTCG
Found at i:30182042 original size:13 final size:13
Alignment explanation
Indices: 30182024--30182049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30182014 TTTTATTTAA
30182024 CCTTATAGAATTT
1 CCTTATAGAATTT
30182037 CCTTATAGAATTT
1 CCTTATAGAATTT
30182050 AGAACTGCTG
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):
CCTTATAGAATTT
Found at i:30188028 original size:39 final size:39
Alignment explanation
Indices: 30187985--30188129 Score: 123
Period size: 39 Copynumber: 3.7 Consensus size: 39
30187975 ACTGGCAGTG
*
30187985 ACACTATAAACA-T-TACGATGCAATACTGAACTGACGATA
1 ACACTATAAACACTGTA--ATGCAATACTGAACTAACGATA
* *
30188024 ACACTATAAATACTGTAATGCAATACTGAACTAACGGTA
1 ACACTATAAACACTGTAATGCAATACTGAACTAACGATA
* * * * * * * *
30188063 TCACTATAAATACTGTAACGTAATATTGAACCAATGGTA
1 ACACTATAAACACTGTAATGCAATACTGAACTAACGATA
* * * *
30188102 ACACTGTAAATACCGTATTGCAATACTG
1 ACACTATAAACACTGTAATGCAATACTG
30188130 GACCGATGGT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
39 85 0.97
40 1 0.01
41 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (39 bp):
ACACTATAAACACTGTAATGCAATACTGAACTAACGATA
Found at i:30188139 original size:39 final size:39
Alignment explanation
Indices: 30188002--30188129 Score: 139
Period size: 39 Copynumber: 3.3 Consensus size: 39
30187992 AAACATTACG
** * *
30188002 ATGCAATACTGAACTGACGATAACACTATAAATACTGTA
1 ATGCAATACTGAACCAACGGTAACACTATAAATACCGTA
* * *
30188041 ATGCAATACTGAACTAACGGTATCACTATAAATACTGTA
1 ATGCAATACTGAACCAACGGTAACACTATAAATACCGTA
* * * * *
30188080 ACGTAATATTGAACCAATGGTAACACTGTAAATACCGTA
1 ATGCAATACTGAACCAACGGTAACACTATAAATACCGTA
*
30188119 TTGCAATACTG
1 ATGCAATACTG
30188130 GACCGATGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (39 bp):
ATGCAATACTGAACCAACGGTAACACTATAAATACCGTA
Done.