Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_pilon, whole genome shotgun sequence
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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1928605 original size:22 final size:21
Alignment explanation
Indices: 1928562--1928606 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1928552 TTTTTAGTAA
** *
1928562 TTTAATTTAATTTTTTAGTAT
1 TTTAATTTAATTTTAAAATAT
1928583 TTTATATTTAATTTTAAAATAT
1 TTTA-ATTTAATTTTAAAATAT
1928605 TT
1 TT
1928607 AAATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAATTTAATTTTAAAATAT
Found at i:1932413 original size:17 final size:17
Alignment explanation
Indices: 1932391--1932429 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1932381 TCTCTTAAAA
1932391 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
* *
1932408 ATTTTAATTTTTTATAT
1 ATTTTAAATTATTATAT
1932425 ATTTT
1 ATTTT
1932430 CTATTAATGA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:1935239 original size:20 final size:20
Alignment explanation
Indices: 1935214--1935251 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1935204 GCTGCCTTTG
1935214 CCATTAAAATCCAGGAGACT
1 CCATTAAAATCCAGGAGACT
*
1935234 CCATTAAAATTCAGGAGA
1 CCATTAAAATCCAGGAGA
1935252 AGGGGTATAC
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:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (20 bp):
CCATTAAAATCCAGGAGACT
Found at i:1941852 original size:2 final size:2
Alignment explanation
Indices: 1941845--1941870 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1941835 CTATAATTTA
1941845 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
1941871 TTAATTATAA
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):
AT
Found at i:1944246 original size:17 final size:16
Alignment explanation
Indices: 1944218--1944251 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1944208 GTTGATTTTA
*
1944218 TTTATTTTATTTCAAT
1 TTTATTTTATTTAAAT
1944234 TTTATTCTTATTTAAAT
1 TTTATT-TTATTTAAAT
1944251 T
1 T
1944252 AGCTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTTATTTAAAT
Found at i:1944461 original size:14 final size:14
Alignment explanation
Indices: 1944444--1944476 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1944434 TATTTCTTTC
*
1944444 CAGGTCCGAGCATT
1 CAGGTCCAAGCATT
1944458 CAGGTCCAAGCATT
1 CAGGTCCAAGCATT
1944472 CAGGT
1 CAGGT
1944477 AATTTATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (14 bp):
CAGGTCCAAGCATT
Found at i:1944747 original size:29 final size:29
Alignment explanation
Indices: 1944706--1944801 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
1944696 CTAGGATTAT
1944706 ATTTTTACACTTAGGT-CTCTAGAATTTAG
1 ATTTTTACACTTAGGTCCT-TAGAATTTAG
*
1944735 ATTTTTACACTTAGGTCCTTAGACTTTAG
1 ATTTTTACACTTAGGTCCTTAGAATTTAG
* * * * *
1944764 ATCTTTCACAATTTA-GTCCATAGACTTTAT
1 AT-TTTTAC-ACTTAGGTCCTTAGAATTTAG
1944794 ATTTTTAC
1 ATTTTTAC
1944802 CATATTAGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
29 32 0.55
30 22 0.38
31 4 0.07
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (29 bp):
ATTTTTACACTTAGGTCCTTAGAATTTAG
Found at i:1948209 original size:57 final size:57
Alignment explanation
Indices: 1948039--1948646 Score: 907
Period size: 57 Copynumber: 10.7 Consensus size: 57
1948029 TCGAATACAA
* ** * **
1948039 AAATTCATACACTTAGTATGAATTTCTTATCATTTTAGCACATGAAGTGCCCTATCTGG
1 AAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT-G
* * * *
1948098 AAATTCATACACTTAATATGATTTCCTTATCATTTTAACGTATGAAA--CCCTATCTG
1 AAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAACGCCCTATCTG
* *
1948154 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* * * *
1948211 AAATGCATACACTTAGTATGATTTCTTAACATTTTAGCATACAAAATG-CCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
1948267 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
1948324 AAATTCATACGCTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
1948381 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
** ***
1948438 AAATTTGTACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACTTACTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
* ** *
1948495 AAATCCATACACTTAGTATGATTTCTTAACATTTTAGTATACGAAACGCCCTATCTA
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
*
1948552 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTG
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
1948609 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGC
1 AAATTCATACACTTAGTATGATTTCTTAACATTTTAGC
1948647 AGTGTATGAA
Statistics
Matches: 503, Mismatches: 42, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
55 19 0.04
56 76 0.15
57 367 0.73
58 4 0.01
59 37 0.07
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
AAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTG
Found at i:1948713 original size:84 final size:83
Alignment explanation
Indices: 1948567--1948728 Score: 299
Period size: 84 Copynumber: 1.9 Consensus size: 83
1948557 CATACACTTA
1948567 GTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATT
1 GTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATT
1948632 TCTTAACATTTTAGCAGT
66 TCTTAACATTTTAGCAGT
1948650 GTATGAATTTCTTAACATTTTAGCGTACGAAACT-CCCTATCTGAAATTCATACACTTAGTATGA
1 GTATG-ATTTCTTAACATTTTAGCGTACGAAA-TGCCCTATCTGAAATTCATACACTTAGTATGA
1948714 TTTCTTAACATTTTA
64 TTTCTTAACATTTTA
1948729 ACGTACGAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
83 5 0.06
84 71 0.92
85 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (83 bp):
GTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATT
TCTTAACATTTTAGCAGT
Found at i:1948739 original size:57 final size:57
Alignment explanation
Indices: 1948650--1948891 Score: 396
Period size: 57 Copynumber: 4.2 Consensus size: 57
1948640 TTTTAGCAGT
* * *
1948650 GTATGAATTTCTTAACATTTTAGCGTACGAAACTCCCTATCTGAAATTCATACACTTA
1 GTATG-ATTTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
1948708 GTATGATTTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
1 GTATGATTTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
*
1948765 GTATGATTT-TGTAACATTTTAATGTACGAAACGCCCTATCTAAAATTCATACACTTA
1 GTATGATTTCT-TAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
* * *
1948822 GTATGATTTCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTA
1 GTATGATTTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
1948879 GTATGATTTCTTA
1 GTATGATTTCTTA
1948892 TATTTTGCAC
Statistics
Matches: 174, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
56 1 0.01
57 167 0.96
58 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
GTATGATTTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTA
Found at i:1948769 original size:141 final size:140
Alignment explanation
Indices: 1948510--1948785 Score: 464
Period size: 141 Copynumber: 2.0 Consensus size: 140
1948500 CATACACTTA
*
1948510 GTATGATTTCTTAACATTTTAGTATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATT
1 GTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATT
* * *
1948575 TCTTAACATTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCT-TAAC
66 TCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTT-TGTAAC
1948639 ATTTTAGCAGT
130 ATTTTAGCAGT
* * *
1948650 GTATGAATTTCTTAACATTTTAGCGTACGAAACTCCCTATCTGAAATTCATACACTTAGTATGAT
1 GTATG-ATTTCTTAACATTTTAGCATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGAT
1948715 TTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTTGTAAC
65 TTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTTGTAAC
1948780 ATTTTA
130 ATTTTA
1948786 ATGTACGAAA
Statistics
Matches: 127, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
140 6 0.05
141 121 0.95
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (140 bp):
GTATGATTTCTTAACATTTTAGCATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATT
TCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTTGTAACA
TTTTAGCAGT
Found at i:1948803 original size:198 final size:197
Alignment explanation
Indices: 1948453--1948844 Score: 669
Period size: 198 Copynumber: 2.0 Consensus size: 197
1948443 TGTACACTTA
*
1948453 GTATGATTTCTTAACATTTTAGCGTACGAAACTTACTATCTGAAATCCATACACTTAGTATGATT
1 GTATGATTTCTTAACATTTTAGCGTACGAAACTCACTATCTGAAATCCATACACTTAGTATGATT
**
1948518 TCTTAACATTTTAGTATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACA
66 TCTTAACATTTTAACATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACA
* * *
1948583 TTTTAGCGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCA
131 TTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCA
1948648 GT
196 GT
* *
1948650 GTATGAATTTCTTAACATTTTAGCGTACGAAACTCCCTATCTGAAATTCATACACTTAGTATGAT
1 GTATG-ATTTCTTAACATTTTAGCGTACGAAACTCACTATCTGAAATCCATACACTTAGTATGAT
*
1948715 TTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTT-TGTAA
65 TTCTTAACATTTTAACATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCT-TAA
*
1948779 CATTTTAATGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAG
129 CATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAG
1948844 C
194 C
1948845 GTACGAAATG
Statistics
Matches: 183, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
197 6 0.03
198 177 0.97
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (197 bp):
GTATGATTTCTTAACATTTTAGCGTACGAAACTCACTATCTGAAATCCATACACTTAGTATGATT
TCTTAACATTTTAACATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACA
TTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCA
GT
Found at i:1948852 original size:255 final size:254
Alignment explanation
Indices: 1948396--1948891 Score: 868
Period size: 255 Copynumber: 1.9 Consensus size: 254
1948386 CATACACTTA
**
1948396 GTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTTGTACACTTAGTATGATT
1 GTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTCATACACTTAGTATGATT
* ** *
1948461 TCTTAACATTTTAGCGTACGAAACTTACTATCTGAAATCCATACACTTAGTATGATTTCTTAACA
66 TCTTAACATTTTAACGTACGAAACGCACTATCTAAAATCCATACACTTAGTATGATTTCTTAACA
*
1948526 TTTTAGTATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCG
131 TTTTAATATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCG
1948591 TACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCAGT
196 TACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCAGT
*
1948650 GTATGAATTTCTTAACATTTTAGCGTACGAAACTCCCTATCTGAAATTCATACACTTAGTATGAT
1 GTATG-ATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTCATACACTTAGTATGAT
* *
1948715 TTCTTAACATTTTAACGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTT-TGTAA
65 TTCTTAACATTTTAACGTACGAAACGCACTATCTAAAATCCATACACTTAGTATGATTTCT-TAA
*
1948779 CATTTTAATGTACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAG
129 CATTTTAATATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAG
1948844 CGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTA
194 CGTACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTA
1948892 TATTTTGCAC
Statistics
Matches: 229, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
254 6 0.03
255 223 0.97
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (254 bp):
GTATGATTTCTTAACATTTTAGCGTACGAAACACCCTATCTGAAATTCATACACTTAGTATGATT
TCTTAACATTTTAACGTACGAAACGCACTATCTAAAATCCATACACTTAGTATGATTTCTTAACA
TTTTAATATACGAAACGCCCTATCTAAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCG
TACGAAATGCCCTATCTGAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCAGT
Found at i:1952475 original size:28 final size:28
Alignment explanation
Indices: 1952435--1952496 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1952425 CCAAAAAAAC
*
1952435 CAACCTGAAACACAT-TACCTCCTCAAAT
1 CAACCTGAAACAC-TCTACCTCCACAAAT
*
1952463 CAACCTGAAACACTCTACCTCCACAAGT
1 CAACCTGAAACACTCTACCTCCACAAAT
1952491 CAACCT
1 CAACCT
1952497 AAGTCTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 1 0.03
28 30 0.97
ACGTcount: A:0.37, C:0.39, G:0.05, T:0.19
Consensus pattern (28 bp):
CAACCTGAAACACTCTACCTCCACAAAT
Found at i:1953914 original size:59 final size:58
Alignment explanation
Indices: 1953844--1954242 Score: 285
Period size: 59 Copynumber: 6.7 Consensus size: 58
1953834 TAACGTGACT
* * * * *
1953844 TTTTTAAGAAACTAAGTCTGATTTTTAGAGGTTTCTCGACATGGTATTTTTAAATGAG
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTCAAATGAA
* * * *
1953902 TTTTCAAAGAAACTAAGTCTGATTTTTAAAGGTTTCTTGAAGATTAACATGGT-GTTTCAAAAGA
1 TTTT-AAAGAAACTAAGTCTGATTTTCAGAGGTTTCTT---G----ACATGGTATTTTCAAATGA
1953966 A
58 A
* * * *
1953967 TTTTTAAAAGAAAC-AAGTTTGATTTTCAGAGGTTTCTTGACATGATGTTCTT-AAATGAGC
1 -TTTT-AAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATT-TTCAAATGA-A
* * * * *
1954027 TTTTAAAGAAGCGAAGTTTGACTTTT-AGAAGTTT-TTGA-TTGAGATGAGGTTTTCAAATGAA
1 TTTTAAAGAAACTAAGTCTGA-TTTTCAGAGGTTTCTTGACATG-G-T-A--TTTTCAAATGAA
* * * *
1954088 TTTTCAAAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTCTTCAAATGAA
1 TTTT-AAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTCAAATGAA
* * * * * *
1954147 TTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTT--TATGAT-TTCTTCAAACGAG
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATT-TTCAAATGAA
* *
1954203 TTTTTAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGAC
1 TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGAC
1954243 GATTACTCAA
Statistics
Matches: 273, Mismatches: 41, Indels: 54
0.74 0.11 0.15
Matches are distributed among these distances:
55 1 0.00
56 46 0.17
57 2 0.01
58 51 0.19
59 71 0.26
60 6 0.02
61 10 0.04
62 32 0.12
63 4 0.01
64 2 0.01
65 29 0.11
66 19 0.07
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (58 bp):
TTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGGTATTTTCAAATGAA
Found at i:1954123 original size:121 final size:122
Alignment explanation
Indices: 1953849--1954164 Score: 358
Period size: 124 Copynumber: 2.6 Consensus size: 122
1953839 TGACTTTTTT
* * * * * *
1953849 AAGAAACTAAGTCTGATTTTTAGAGGTTTCTCGACATGGTATTTTTAAATGAGTTTTCAAAGAAA
1 AAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTTCTTAAATGAGTTTT-AAAGAAA
* *
1953914 CTAAGTCTGATTTTTAAAGGTTTCTTGAAGATTAACATGGTGTTTCAAAAGAATTTTTAA
65 CGAAGTCTGACTTTTAAAGGTTTCTT--AGATTAACATGGTGTTTCAAAAGAATTTTTAA
* *
1953974 AAGAAA-CAAGTTTGATTTTCAGAGGTTTCTTGACATGATGTTCTTAAATGAGCTTTTAAAGAAG
1 AAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTTCTTAAATGAG-TTTTAAAGAAA
* * * * *
1954038 CGAAGTTTGACTTTTAGAA-GTTT-TT-GATTGAGATGAG-GTTTTCAAATGAA-TTTTCA
65 CGAAGTCTGACTTTTA-AAGGTTTCTTAGATTAACATG-GTG-TTTCAAAAGAATTTTTAA
*
1954094 AAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATG-TCTTCAAATGAATTTTAAAGAAA
1 AAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTTCTT-AAATGAGTTTTAAAGAAA
*
1954158 CTAAGTC
65 CGAAGTC
1954165 CGATTTTCAG
Statistics
Matches: 165, Mismatches: 20, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
120 39 0.24
121 50 0.30
123 2 0.01
124 62 0.38
125 12 0.07
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.38
Consensus pattern (122 bp):
AAGAAACCAAGTCTGATTTTCAGAGGTTTCTTGACATGATGTTCTTAAATGAGTTTTAAAGAAAC
GAAGTCTGACTTTTAAAGGTTTCTTAGATTAACATGGTGTTTCAAAAGAATTTTTAA
Found at i:1954170 original size:58 final size:58
Alignment explanation
Indices: 1953948--1954242 Score: 278
Period size: 56 Copynumber: 5.0 Consensus size: 58
1953938 TTGAAGATTA
* * *
1953948 ACATGGTGT-TTCAAAAGAATTTTTAAAAGAAAC-AAGTTTGATTTTCAGAGGTTTCTTG
1 ACATGATGTCTTCAAATGAA-TTTT-AAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTG
* * * * * *
1954006 ACATGATGTTCTT-AAATGAGCTTTTAAAGAAGCGAAGTTTGACTTTT-AGAAGTTTTTGATTG
1 ACATGATG-TCTTCAAATGA-ATTTTAAAGAAACTAAGTCTGA-TTTTCAG-AG-GTTT-CTTG
* * * *
1954068 AGATGAGGTTTTCAAATGAATTTTCAAAGAAACCAAGTCTGATTTTCAGAGGTTTCTTG
1 ACATGATGTCTTCAAATGAATTTT-AAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTG
* *
1954127 ACATGATGTCTTCAAATGAATTTTAAAGAAACTAAGTCCGATTTTCAGAAGTTTCTT-
1 ACATGATGTCTTCAAATGAATTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTG
* * * * * *
1954184 -TATGATTTCTTCAAACGAGTTTTTAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTG
1 ACATGATGTCTTCAAATGAATTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTG
1954241 AC
1 AC
1954243 GATTACTCAA
Statistics
Matches: 194, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
56 48 0.25
58 44 0.23
59 44 0.23
60 11 0.06
61 16 0.08
62 31 0.16
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (58 bp):
ACATGATGTCTTCAAATGAATTTTAAAGAAACTAAGTCTGATTTTCAGAGGTTTCTTG
Found at i:1955040 original size:20 final size:20
Alignment explanation
Indices: 1954978--1955041 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1954968 CTGAGGAAGG
* **
1954978 GTTCGTAATGAGATTAACTT
1 GTTCATAATGAGAAGAACTT
***
1954998 G-TC-TAATGAGGAAGAAAAA
1 GTTCATAATGA-GAAGAACTT
1955017 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1955037 GTTCA
1 GTTCA
1955042 GAACTCGGCG
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 6 0.18
19 7 0.21
20 14 0.42
21 6 0.18
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1955271 original size:116 final size:116
Alignment explanation
Indices: 1955062--1955573 Score: 459
Period size: 116 Copynumber: 4.4 Consensus size: 116
1955052 CATCCATCAC
** * * **
1955062 ATCAACATTTCAGAAGAAGGGTTCATAATGGGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCAT
1 ATCAACATTTCTTAAAAAGGGTTAATAATGAAAAGAACTCATCCAAAGAGGAAGAAAAAGTTCAT
* ** * *
1955127 AATGAGAAGAACTTGTTCGAAAATCGACACATCCATCACACAATGAGATAT
66 AATGAGAAGAACTTGTTCGAAACTCGACACATCTGTCACACAAAGAGATAG
* ** * *
1955178 ATTAACA-TT-TTAGAAAGAGGGTTCGT-A-GCAATAAGAACTCATCCAACGAGGAATG-AGAAG
1 ATCAACATTTCTTA-AAA-AGGGTTAATAATG-AA-AAGAACTCATCCAAAGAGGAA-GAAAAAG
* * *
1955238 TTCATAATGAGAAGAACTTGTTCGAAACCCGACACATCTGTCACACAAGGAGATGG
61 TTCATAATGAGAAGAACTTGTTCGAAACTCGACACATCTGTCACACAAAGAGATAG
* * * * *
1955294 ATCAATATTTCTTAATAAGGGTTAATAATGAAAAGAACTCACCCAATGAGGAAGAATAAGTTCAT
1 ATCAACATTTCTTAAAAAGGGTTAATAATGAAAAGAACTCATCCAAAGAGGAAGAAAAAGTTCAT
*
1955359 AATGAGAAGAACTTGTTCGGAACTCGACACATCTGTCACACAAAGAGAT-G
66 AATGAGAAGAACTTGTTCGAAACTCGACACATCTGTCACACAAAGAGATAG
* * * * * * **
1955409 AATAAACATCTC-TAAAGAAGGGTTATTAATGAGAAA-AACTCACCCAATA-ATGAATAATGAGT
1 -ATCAACATTTCTTAAA-AAGGGTTAATAATGA-AAAGAACTCATCCAA-AGAGGAAGAAAAAGT
* * *
1955471 TCATAATGAGAAGAACTTGTTCGGAACTTGACACATC-ATCACACAAAGAGATAG
62 TCATAATGAGAAGAACTTGTTCGAAACTCGACACATCTGTCACACAAAGAGATAG
* * ** * ** * * *
1955525 ACCGACATTTCGGAAGAATAGTTCATAATGAGAAGAACTCATCCGAAGA
1 ATCAACATTTCTTAAAAAGGGTTAATAATGAAAAGAACTCATCCAAAGA
1955574 AGGGTTCGTA
Statistics
Matches: 327, Mismatches: 51, Indels: 37
0.79 0.12 0.09
Matches are distributed among these distances:
114 5 0.02
115 52 0.16
116 255 0.78
117 11 0.03
118 4 0.01
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (116 bp):
ATCAACATTTCTTAAAAAGGGTTAATAATGAAAAGAACTCATCCAAAGAGGAAGAAAAAGTTCAT
AATGAGAAGAACTTGTTCGAAACTCGACACATCTGTCACACAAAGAGATAG
Found at i:1955484 original size:232 final size:231
Alignment explanation
Indices: 1955078--1955522 Score: 547
Period size: 232 Copynumber: 1.9 Consensus size: 231
1955068 ATTTCAGAAG
* ** *
1955078 AAGGGTTCATAATGGGAAGAACTCATCCAAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGT
1 AAGGGTTAATAATGAAAAGAACTCACCCAAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGT
* * * * *
1955143 TCGAAAATCGACACATCCATCACACAATGAGATATATTAACATTTTAGAAAGAGGGTTCGTAGCA
66 TCGAAAATCGACACATCCATCACACAAAGAGATATATAAACATTCTAGAAAGAGGGTTAGTAACA
* * * * *
1955208 ATAAGAACTCATCCAACGAGGAATGAGAAGTTCATAATGAGAAGAACTTGTTCGAAACCCGACAC
131 AGAAAAACTCACCCAACAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCGAAACCCGACAC
* *
1955273 ATCTGTCACACAAGGAGATGGATCAATATTTCTTAAT
196 ATC-ATCACACAAAGAGATGGATCAATATTTCTTAAT
* *
1955310 AAGGGTTAATAATGAAAAGAACTCACCCAATGAGGAAGAATAAGTTCATAATGAGAAGAACTTGT
1 AAGGGTTAATAATGAAAAGAACTCACCCAAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGT
* * ** *
1955375 TCGGAACTCGACACATCTGTCACACAAAGAGATGA-ATAAACATCTCT--AAAGAAGGGTTATTA
66 TCGAAAATCGACACATCCATCACACAAAGAGAT-ATATAAACAT-TCTAGAAAG-AGGGTTAGTA
** * * * **
1955437 ATGAGAAAAACTCACCCAATAATGAATAATG-AGTTCATAATGAGAAGAACTTGTTCGGAACTTG
128 ACAAGAAAAACTCACCCAACAAGGAATAA-GAAGTTCATAATGAGAAGAACTTGTTCGAAACCCG
1955501 ACACATCATCACACAAAGAGAT
192 ACACATCATCACACAAAGAGAT
1955523 AGACCGACAT
Statistics
Matches: 179, Mismatches: 30, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
231 17 0.09
232 158 0.88
233 4 0.02
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.22
Consensus pattern (231 bp):
AAGGGTTAATAATGAAAAGAACTCACCCAAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTTGT
TCGAAAATCGACACATCCATCACACAAAGAGATATATAAACATTCTAGAAAGAGGGTTAGTAACA
AGAAAAACTCACCCAACAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTCGAAACCCGACAC
ATCATCACACAAAGAGATGGATCAATATTTCTTAAT
Found at i:1957821 original size:29 final size:29
Alignment explanation
Indices: 1957770--1957835 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
1957760 CTAGGATTAT
* * *
1957770 ATTTTTACACTTAGGTCTCTAGACTTTAG
1 ATTTTTACACTAAGGCCTCTAGACTTTAA
1957799 ATTTTTACACTAAGGCC-CTTAGACTTTAA
1 ATTTTTACACTAAGGCCTC-TAGACTTTAA
1957828 ATCTTTTA
1 AT-TTTTA
1957836 TAGTTTAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (29 bp):
ATTTTTACACTAAGGCCTCTAGACTTTAA
Found at i:1962921 original size:31 final size:31
Alignment explanation
Indices: 1962886--1962944 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1962876 CGTTTAATAT
*
1962886 CTAAACTATCAGTTTTGATTCGTTTTAGTAC
1 CTAAACTATCAGCTTTGATTCGTTTTAGTAC
*
1962917 CTAAACTATCAGCTTTGGTTCGTTTTAG
1 CTAAACTATCAGCTTTGATTCGTTTTAG
1962945 AAAATTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (31 bp):
CTAAACTATCAGCTTTGATTCGTTTTAGTAC
Found at i:1968717 original size:11 final size:11
Alignment explanation
Indices: 1968701--1968726 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1968691 TTAAGGTAAT
1968701 TTTATTAGTCA
1 TTTATTAGTCA
1968712 TTTATTAGTCA
1 TTTATTAGTCA
1968723 TTTA
1 TTTA
1968727 GTCATTGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (11 bp):
TTTATTAGTCA
Found at i:1969538 original size:42 final size:42
Alignment explanation
Indices: 1969478--1969619 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 42
1969468 GAATAGTGAT
* * ** *
1969478 AAAATTATT-TCGCCACAAATCATGAATTAAAACTAGTGACA
1 AAAATAATTATCGTCACAAATCACCAATTAAGACTAGTGACA
* * *
1969519 AAAATAATTATCGTCACAAATAACCAATTAAGACTAGTTACC
1 AAAATAATTATCGTCACAAATCACCAATTAAGACTAGTGACA
* * * *
1969561 ATAACAATTATCGTCACAAATCACCAACTAAGACTAGTGA-T
1 AAAATAATTATCGTCACAAATCACCAATTAAGACTAGTGACA
*
1969602 AAAAT-GTTATCGTCACAA
1 AAAATAATTATCGTCACAA
1969620 TTATTAATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
40 12 0.14
41 11 0.13
42 60 0.72
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (42 bp):
AAAATAATTATCGTCACAAATCACCAATTAAGACTAGTGACA
Found at i:1970069 original size:16 final size:18
Alignment explanation
Indices: 1970033--1970071 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1970023 AATAAAATTT
1970033 TAAAATAAACAATACTAA
1 TAAAATAAACAATACTAA
*
1970051 TAAAATAAA-AA-ATTAA
1 TAAAATAAACAATACTAA
1970067 TAAAA
1 TAAAA
1970072 AATTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAATAAACAATACTAA
Found at i:1970073 original size:18 final size:18
Alignment explanation
Indices: 1970033--1970074 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1970023 AATAAAATTT
* *
1970033 TAAAATAAACAATACTAA
1 TAAAATAAAAAATAATAA
1970051 TAAAATAAAAAATTAATAA
1 TAAAATAAAAAA-TAATAA
1970070 -AAAAT
1 TAAAAT
1970075 TAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
TAAAATAAAAAATAATAA
Found at i:1970517 original size:31 final size:30
Alignment explanation
Indices: 1970436--1970522 Score: 77
Period size: 31 Copynumber: 2.9 Consensus size: 30
1970426 ATTATGATTT
* *
1970436 TTATTTTAAATTAGTCATT-AATTTTTTAA
1 TTATTTTAAATTAATCATTAAATTTTATAA
* * * * *
1970465 ATATTTTAATTTCATCCTTAAATTATTATGA
1 TTATTTTAAATTAATCATTAAATT-TTATAA
*
1970496 TTATTTTAAATTAATCTTTAAACTTTT
1 TTATTTTAAATTAATCATTAAA-TTTT
1970523 GAATATTTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
29 14 0.32
30 4 0.09
31 24 0.55
32 2 0.05
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (30 bp):
TTATTTTAAATTAATCATTAAATTTTATAA
Found at i:1970548 original size:60 final size:60
Alignment explanation
Indices: 1970436--1970550 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
1970426 ATTATGATTT
* ** * **
1970436 TTATTTTAAATTAGTCATTAATTTTTTAAATATTTTAATTTCATCCTTAAATTATTATGA
1 TTATTTTAAATTAATCATTAAACTTTTAAATATTTCAATTTCATCCCCAAATTATTATGA
* * * *
1970496 TTATTTTAAATTAATCTTTAAACTTTTGAATATTTCATTTTTATCCCCAAATTAT
1 TTATTTTAAATTAATCATTAAACTTTTAAATATTTCAATTTCATCCCCAAATTAT
1970551 GAGCTTCACT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.54
Consensus pattern (60 bp):
TTATTTTAAATTAATCATTAAACTTTTAAATATTTCAATTTCATCCCCAAATTATTATGA
Found at i:1971105 original size:58 final size:58
Alignment explanation
Indices: 1971023--1971133 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
1971013 AATAAGAGTC
* * *
1971023 ATAGTTTGAGGATGGAATTTGAATGTAAAAAAGTTTAAAGACTAATTTAAAATGAGAG
1 ATAGTTTGAGGATGAAATTAGAATGTAAAAAAGTTTAAAGACTAATATAAAATGAGAG
* ** **
1971081 ATAGTTTTAGGATGAAATTAGAATGTTTAAAAGTTTAGGGACTAATATAAAAT
1 ATAGTTTGAGGATGAAATTAGAATGTAAAAAAGTTTAAAGACTAATATAAAAT
1971134 AAAGGTCATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 45 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (58 bp):
ATAGTTTGAGGATGAAATTAGAATGTAAAAAAGTTTAAAGACTAATATAAAATGAGAG
Found at i:1971598 original size:77 final size:78
Alignment explanation
Indices: 1971451--1971601 Score: 214
Period size: 80 Copynumber: 1.9 Consensus size: 78
1971441 GTAGAAAAAT
* * *
1971451 AACATTTTAGGTAGCGTCCAATATTAACATTTTCGGTAGAAAAAAATAATATTTTAGGTAGTGCT
1 AACATTTTAGGTAGCGCCCAATATTAACATTTTCGGTAG--AAAAATAATATTTTAAGTAGCGCT
1971516 TTACTGAAAATGTTA
64 TTACTGAAAATGTTA
* ** *
1971531 AACATTTTAGGTAGTGCCCAATATTATTATTTTCGGTAG-AAAATAATGTTTTAAGTAGCGCTTT
1 AACATTTTAGGTAGCGCCCAATATTAACATTTTCGGTAGAAAAATAATATTTTAAGTAGCGCTTT
1971595 ACTGAAA
66 ACTGAAA
1971602 TATTAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
77 29 0.45
80 35 0.55
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (78 bp):
AACATTTTAGGTAGCGCCCAATATTAACATTTTCGGTAGAAAAATAATATTTTAAGTAGCGCTTT
ACTGAAAATGTTA
Found at i:1973605 original size:103 final size:104
Alignment explanation
Indices: 1973384--1973606 Score: 256
Period size: 103 Copynumber: 2.2 Consensus size: 104
1973374 TATTTATTCG
* * * * * * *
1973384 ACACAATTATCAAT-ATAATTGTGATGAATTTATTTGACATTAAAAGTATATTTTGTGATCATCA
1 ACACTATTATCAATAAAAATTGTGATAAATTTATTTAACACTAAAAGTATATTTTGTGACCACCA
* * * * **
1973448 ATATTGTCCTGCTAAGTATTTTTTAGTGACTAAATGTTTG
66 ATATTGT-CTACTAAATACTTTTTAGTGACCAAATGTTCA
1973488 ACACTATTATCAATAAAAATTGTGATAAATTTATTTAACACTAAAAGTATA-TTTGT-ACCACCA
1 ACACTATTATCAATAAAAATTGTGATAAATTTATTTAACACTAAAAGTATATTTTGTGACCACCA
*
1973551 ATGTTGT-TACAATAAATACTTTTTAGTGACCAAATGTTCA
66 ATATTGTCTAC--TAAATACTTTTTAGTGACCAAATGTTCA
*
1973591 ATACTATTATCAATAA
1 ACACTATTATCAATAA
1973607 CTCTGTCACT
Statistics
Matches: 101, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
101 2 0.02
103 49 0.49
104 18 0.18
105 32 0.32
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (104 bp):
ACACTATTATCAATAAAAATTGTGATAAATTTATTTAACACTAAAAGTATATTTTGTGACCACCA
ATATTGTCTACTAAATACTTTTTAGTGACCAAATGTTCA
Found at i:1974250 original size:24 final size:25
Alignment explanation
Indices: 1974223--1974284 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 25
1974213 TTGTTGGAAT
1974223 TATAATTTTATTTATT-TTAATATA
1 TATAATTTTATTTATTATTAATATA
*
1974247 TATAA---TATTTATTATTATTATA
1 TATAATTTTATTTATTATTAATATA
*
1974269 -ATAATTTTTTTTATTA
1 TATAATTTTATTTATTA
1974285 ACCTAAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 12 0.38
22 7 0.22
24 13 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TATAATTTTATTTATTATTAATATA
Found at i:1974270 original size:18 final size:18
Alignment explanation
Indices: 1974237--1974284 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1974227 ATTTTATTTA
*
1974237 TTTTAATATATATAAT-AT
1 TTTTATTAT-TATAATAAT
1974255 TTATTATTATTATAATAAT
1 TT-TTATTATTATAATAAT
*
1974274 TTTTTTTATTA
1 TTTTATTATTA
1974285 ACCTAAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTATTATAATAAT
Found at i:1974282 original size:21 final size:22
Alignment explanation
Indices: 1974223--1974285 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
1974213 TTGTTGGAAT
*
1974223 TATAATTTTATTTATTTTAATATA
1 TATAATTTT-TTT-TATTAATATA
* * *
1974247 TATAATATTTATTATTATTATA
1 TATAATTTTTTTTATTAATATA
1974269 -ATAATTTTTTTTATTAA
1 TATAATTTTTTTTATTAA
1974286 CCTAAGGTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 14 0.44
22 8 0.25
23 2 0.06
24 8 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATAATTTTTTTTATTAATATA
Found at i:1974906 original size:19 final size:19
Alignment explanation
Indices: 1974878--1974916 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1974868 AAAGGTTAAG
1974878 ATAATATTATTAGTCACAT
1 ATAATATTATTAGTCACAT
*
1974897 ATAATTTTATTAGTCACAT
1 ATAATATTATTAGTCACAT
1974916 A
1 A
1974917 GTCATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (19 bp):
ATAATATTATTAGTCACAT
Found at i:1975079 original size:17 final size:17
Alignment explanation
Indices: 1975059--1975100 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1975049 CCTTTTGAAA
1975059 AACTAATTTATCTTAAC
1 AACTAATTTATCTTAAC
*
1975076 AACTAGTTTATCTTAAC
1 AACTAATTTATCTTAAC
1975093 AAC-AATTT
1 AACTAATTT
1975101 TAATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (17 bp):
AACTAATTTATCTTAAC
Found at i:1986734 original size:36 final size:35
Alignment explanation
Indices: 1986687--1986757 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
1986677 TGGAAACCAA
*
1986687 CTTTGAAAAATGTTTTTCAAAGTTTGTTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1986723 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
1986758 GGTAGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAAGTTT
Found at i:1989571 original size:21 final size:21
Alignment explanation
Indices: 1989547--1989611 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 21
1989537 AATTTTGAAA
1989547 AAATGTTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
* **
1989568 AAA--TATTTC----TTTGAA
1 AAATGTTTTTCAAAGTTTGGT
1989583 AAATGTTTTTCAAAGTTTGGT
1 AAATGTTTTTCAAAGTTTGGT
*
1989604 AGATGTTT
1 AAATGTTT
1989612 GTTGAAAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 12
0.62 0.14 0.24
Matches are distributed among these distances:
15 7 0.23
17 5 0.16
19 5 0.16
21 14 0.45
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
AAATGTTTTTCAAAGTTTGGT
Found at i:1992777 original size:2 final size:2
Alignment explanation
Indices: 1992733--1992757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1992723 TTCATTGACA
1992733 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 T
1992758 GACTTCCTTT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1996616 original size:29 final size:28
Alignment explanation
Indices: 1996566--1996644 Score: 79
Period size: 29 Copynumber: 2.8 Consensus size: 28
1996556 TATCTAAGTG
1996566 TTTAAAATATTTTTGTCAAAAATAAATA
1 TTTAAAATATTTTTGTCAAAAATAAATA
* *
1996594 TTTAAATATATTTTT-TGATAAAATAAGTA
1 TTTAAA-ATATTTTTGTCA-AAAATAAATA
* * *
1996623 CTTAAAGTATTTTGTATCAAAA
1 TTTAAAATATTTT-TGTCAAAA
1996645 TATGTACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 14 0.33
29 26 0.62
30 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (28 bp):
TTTAAAATATTTTTGTCAAAAATAAATA
Found at i:1996634 original size:28 final size:27
Alignment explanation
Indices: 1996567--1996661 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 27
1996557 ATCTAAGTGT
* *
1996567 TTAAAATATTTTTGTCA-AAAATAAATAT
1 TTAAAATATTTTT-T-ATAAAATAAGTAC
1996595 TTAAATATATTTTTTGATAAAATAAGTAC
1 TTAAA-ATATTTTTT-ATAAAATAAGTAC
* * *
1996624 TTAAAGTATTTTGTATCAAAATATGTAC
1 TTAAAATATTTTTTAT-AAAATAAGTAC
* *
1996652 CTAAAGTATT
1 TTAAAATATT
1996662 CAATACTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
27 2 0.04
28 33 0.58
29 22 0.39
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (27 bp):
TTAAAATATTTTTTATAAAATAAGTAC
Found at i:1996932 original size:18 final size:19
Alignment explanation
Indices: 1996900--1996937 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1996890 TCAAATCAAA
* *
1996900 AAAATTATTTTTTTA-AAT
1 AAAATTAATTATTTATAAT
1996918 AAAATTAATTATTTATAAT
1 AAAATTAATTATTTATAAT
1996937 A
1 A
1996938 TCTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATTAATTATTTATAAT
Found at i:1997184 original size:2 final size:2
Alignment explanation
Indices: 1997177--1997206 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1997167 CCAACCGGAA
*
1997177 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1997207 TATTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2001135 original size:3 final size:3
Alignment explanation
Indices: 2001098--2001122 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2001088 AATATGGTTT
2001098 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
2001123 ATCATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:2004773 original size:14 final size:14
Alignment explanation
Indices: 2004754--2004784 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2004744 TGAGATCCAA
2004754 CGGGTAGAGATAGG
1 CGGGTAGAGATAGG
2004768 CGGGTAGAGATAGG
1 CGGGTAGAGATAGG
2004782 CGG
1 CGG
2004785 TACTGAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.52, T:0.13
Consensus pattern (14 bp):
CGGGTAGAGATAGG
Found at i:2008451 original size:22 final size:21
Alignment explanation
Indices: 2008410--2008453 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
2008400 AATAAATTAC
*
2008410 TTTTAAAATATATTTTTATAA
1 TTTTAAAATATATTTATATAA
*
2008431 TTTTAAACATGTATTTATATAA
1 TTTTAAA-ATATATTTATATAA
2008453 T
1 T
2008454 ATATAAGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTTAAAATATATTTATATAA
Found at i:2009462 original size:19 final size:17
Alignment explanation
Indices: 2009438--2009494 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 17
2009428 AAAGGCATGC
2009438 AAAATAAATAAATATATTA
1 AAAATAAATAAATATA--A
*
2009457 AAAATAAATAAATGTAA
1 AAAATAAATAAATATAA
2009474 AAAATAAA-AGAA-ATAA
1 AAAATAAATA-AATATAA
2009490 AAAAT
1 AAAAT
2009495 GACTAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 9 0.26
17 11 0.31
19 15 0.43
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAAATAAATATAA
Found at i:2010612 original size:30 final size:31
Alignment explanation
Indices: 2010555--2010613 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
2010545 GATTTAGTTA
* * * *
2010555 GTGATCAAATTATAAGATTTTGTAAAGTTTG
1 GTGACCAAAGTATAAGACTTTGAAAAGTTTG
2010586 GTGACCAAAGTATAA-ACTTTGAAAAGTT
1 GTGACCAAAGTATAAGACTTTGAAAAGTT
2010614 CATATAATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (31 bp):
GTGACCAAAGTATAAGACTTTGAAAAGTTTG
Found at i:2011415 original size:30 final size:31
Alignment explanation
Indices: 2011372--2011441 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
2011362 ACAAGCCTTA
* * * * *
2011372 GAAAAATTTGGGGACCATTTTG-TAATTTTT
1 GAAAAGTTGGGGGACCAATTCGATAATTTTG
*
2011402 GAAAAGTTGGGGGACCAATTCGATGATTTTG
1 GAAAAGTTGGGGGACCAATTCGATAATTTTG
2011433 GAAAAGTTG
1 GAAAAGTTG
2011442 TGAATGATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 18 0.55
31 15 0.45
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.34
Consensus pattern (31 bp):
GAAAAGTTGGGGGACCAATTCGATAATTTTG
Found at i:2012258 original size:45 final size:46
Alignment explanation
Indices: 2012166--2012269 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 46
2012156 ACATACCATA
* * * *
2012166 CATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTGATG
1 CATCGATGCACTCAGGCTTTTATGAAAACATCAAATGCACTTCATG
*
2012212 CATCGATGCACTCAGTCTATTT-TG-AAACATCAAATGCACTTCATG
1 CATCGATGCACTCAGGCT-TTTATGAAAACATCAAATGCACTTCATG
2012257 CATCGATGCACTC
1 CATCGATGCACTC
2012270 TTAGTGCACC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 31 0.60
46 18 0.35
47 3 0.06
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (46 bp):
CATCGATGCACTCAGGCTTTTATGAAAACATCAAATGCACTTCATG
Found at i:2017279 original size:44 final size:44
Alignment explanation
Indices: 2017194--2017290 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
2017184 TTGGGCATAA
*
2017194 TGCATCGATACACTGAACAGTGCATCGATGCATCCCTTTGAATG
1 TGCATCGATACACTGAACAGTGCACCGATGCATCCCTTTGAATG
*
2017238 TGCATCGATACATCATGAAGA-TGCACCGATGCA-CTCC-TTGAATG
1 TGCATCGATACA-C-TGAACAGTGCACCGATGCATC-CCTTTGAATG
2017282 TGCATCGAT
1 TGCATCGAT
2017291 GCACAAGGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
44 29 0.60
45 14 0.29
46 5 0.10
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (44 bp):
TGCATCGATACACTGAACAGTGCACCGATGCATCCCTTTGAATG
Found at i:2017294 original size:23 final size:22
Alignment explanation
Indices: 2017213--2017293 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
2017203 ACACTGAACA
2017213 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
* *
2017237 GTGCATCGATACAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
*
2017257 GATGCACCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
2017281 GTGCATCGATGCA
1 GTGCATCGATGCA
2017294 CAAGGTCATG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.30
22 2 0.04
23 16 0.34
24 14 0.30
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:2018871 original size:44 final size:45
Alignment explanation
Indices: 2018753--2018876 Score: 169
Period size: 47 Copynumber: 2.7 Consensus size: 45
2018743 TAAAATCCCT
*
2018753 TACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
1 TACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
* * *
2018798 TACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATACT
1 TACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
* *
2018845 TGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 TACCATTTATTCCATAAGCTCGTAAGCTTATTT
2018877 GTATTTCAAC
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 24 0.34
45 8 0.11
46 2 0.03
47 37 0.52
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.36
Consensus pattern (45 bp):
TACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACA
Found at i:2019026 original size:59 final size:59
Alignment explanation
Indices: 2018934--2019062 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
2018924 CGTAGTGCTA
* * **
2018934 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
2018993 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
2019052 TCCCGAATATG
1 TCCCGAATATG
2019063 CAGCCTGCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:2026097 original size:44 final size:45
Alignment explanation
Indices: 2025977--2026102 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
2025967 TATAAAATCC
*
2025977 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2026022 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
2026069 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
2026103 GTATGCTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:2026303 original size:59 final size:60
Alignment explanation
Indices: 2026211--2026340 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 60
2026201 CGTAGTGCTA
* * **
2026211 TCCCGAATATGACACATAAGATCGTGTCCACCATCTGTA-CTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGATCGTGCCCACCATATACACCTAGGTATCCTTAAGTACAG
* * ** *
2026270 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACCTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGATCGTGCCCACCATATACACCTAGGTATCCTTAAGTACAG
2026330 TCCCGAATATG
1 TCCCGAATATG
2026341 CAGCCTGCTG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 34 0.56
60 27 0.44
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (60 bp):
TCCCGAATATGACACATAAGATCGTGCCCACCATATACACCTAGGTATCCTTAAGTACAG
Found at i:2030004 original size:17 final size:17
Alignment explanation
Indices: 2029982--2030016 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2029972 AAAAGGGGGA
2029982 GAAGTGTTAGAGTAAGG
1 GAAGTGTTAGAGTAAGG
2029999 GAAGTGTTAGAGTAAGG
1 GAAGTGTTAGAGTAAGG
2030016 G
1 G
2030017 GGAGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.43, T:0.23
Consensus pattern (17 bp):
GAAGTGTTAGAGTAAGG
Found at i:2030019 original size:19 final size:19
Alignment explanation
Indices: 2029977--2030019 Score: 63
Period size: 17 Copynumber: 2.3 Consensus size: 19
2029967 TAACAAAAAG
2029977 GGGGAGAAGTGTTAGAGTAA
1 GGGG-GAAGTGTTAGAGTAA
2029997 --GGGAAGTGTTAGAGTAA
1 GGGGGAAGTGTTAGAGTAA
2030014 GGGGGA
1 GGGGGA
2030020 GTAATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 15 0.71
18 2 0.10
19 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.19
Consensus pattern (19 bp):
GGGGGAAGTGTTAGAGTAA
Found at i:2030470 original size:65 final size:61
Alignment explanation
Indices: 2030401--2030554 Score: 167
Period size: 57 Copynumber: 2.5 Consensus size: 61
2030391 GAATAAATTG
*
2030401 AACATCGAATGCATTTTATGCATCAATGCACATACCAAGCATCGATGCACTCAGGGT-TTTATGA
1 AACATCGAATGCATTTTATGCATCAATGCAC-T--CAAGCATCGATGCACTCAGGCTATTT-TG-
2030465 A
61 A
* * *
2030466 AACATCAAATGCATTTGATGCA-CAA-G---TCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTTATGCATCAATGCACTCAAGCATCGATGCACTCAGGCTATTTTGA
* *
2030522 AACATCGAATGCACTTTATGCATCGATGCACTC
1 AACATCGAATGCATTTTATGCATCAATGCACTC
2030555 TTAGTGCACC
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
56 20 0.27
57 24 0.32
58 4 0.05
59 1 0.01
61 2 0.03
63 1 0.01
64 3 0.04
65 20 0.27
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (61 bp):
AACATCGAATGCATTTTATGCATCAATGCACTCAAGCATCGATGCACTCAGGCTATTTTGA
Found at i:2030547 original size:18 final size:19
Alignment explanation
Indices: 2030524--2030572 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
2030514 TATTTTGAAA
2030524 CATCGAATGCACT-TTA-TG
1 CATCG-ATGCACTCTTAGTG
2030542 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTTAGTG
*
2030561 CACCGATGCACT
1 CATCGATGCACT
2030573 AAGGGTCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.25
18 8 0.29
19 13 0.46
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
CATCGATGCACTCTTAGTG
Found at i:2032181 original size:22 final size:22
Alignment explanation
Indices: 2032151--2032214 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
2032141 AGTCGAGGGT
*
2032151 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCAGGACATA
*
2032173 TACAGAGGTCCTTCAGGACATA
1 TACATAGGTCCTTCAGGACATA
* *
2032195 TACATAGGTCTTTCTGGACA
1 TACATAGGTCCTTCAGGACA
2032215 AATTTTACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCAGGACATA
Found at i:2035528 original size:30 final size:31
Alignment explanation
Indices: 2035471--2035528 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
2035461 GATTTAGTTA
* * * *
2035471 GTGATCAAATTATAAGATTTTGTAAAGTTTG
1 GTGACCAAAGTATAAGACTTTGAAAAGTTTG
2035502 GTGACCAAAGTATAA-ACTTTGAAAAGT
1 GTGACCAAAGTATAAGACTTTGAAAAGT
2035529 CCATGGACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 10 0.43
31 13 0.57
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (31 bp):
GTGACCAAAGTATAAGACTTTGAAAAGTTTG
Found at i:2037644 original size:22 final size:23
Alignment explanation
Indices: 2037614--2037656 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2037604 AGTCAAGGGT
*
2037614 TACATAGGTCCTTC-GGGATATA
1 TACAAAGGTCCTTCAGGGATATA
2037636 TACAAAGGTCCTTCAGGGATA
1 TACAAAGGTCCTTCAGGGATA
2037657 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (23 bp):
TACAAAGGTCCTTCAGGGATATA
Found at i:2040556 original size:2 final size:2
Alignment explanation
Indices: 2040549--2040579 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2040539 ATATCTGTAA
2040549 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2040580 AGAATGAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2045075 original size:4 final size:4
Alignment explanation
Indices: 2045066--2045109 Score: 56
Period size: 4 Copynumber: 11.0 Consensus size: 4
2045056 AAGACATGCA
2045066 AAAT AAAT AAAT ATAAT ATAAT -AA- AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT A-AAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
2045110 GTAAAAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 4 0.11
4 25 0.68
5 8 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:2045114 original size:18 final size:20
Alignment explanation
Indices: 2045070--2045108 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2045060 CATGCAAAAT
2045070 AAATAAATATAATATAATAA
1 AAATAAATATAATATAATAA
2045090 AAATAAATA-AATA-AATAA
1 AAATAAATATAATATAATAA
2045108 A
1 A
2045109 TGTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAATATAATATAATAA
Found at i:2046790 original size:8 final size:8
Alignment explanation
Indices: 2046772--2046800 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2046762 TCATGTATTC
2046772 TTGCA-TT
1 TTGCATTT
2046779 TTGCATTT
1 TTGCATTT
2046787 TTGCATTT
1 TTGCATTT
2046795 TTGCAT
1 TTGCAT
2046801 CTTCATCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (8 bp):
TTGCATTT
Found at i:2047975 original size:17 final size:17
Alignment explanation
Indices: 2047953--2048041 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 17
2047943 AATCAAGAAC
*
2047953 AAAAAAGAAAAGAAGCA
1 AAAAAAGAAAAGAAACA
*
2047970 AAAAAAGAAAAAAAAACA
1 AAAAAAG-AAAAGAAACA
*
2047988 AAGAAAA-AAGAGAAACA
1 AA-AAAAGAAAAGAAACA
*
2048005 AAAAAGAGAAACA-AAAGA
1 AAAAA-AGAAA-AGAAACA
2048023 AAAAAAG-AAAG-AACA
1 AAAAAAGAAAAGAAACA
2048038 AAAA
1 AAAA
2048042 TTAAAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 8 0.14
16 5 0.08
17 20 0.34
18 21 0.36
19 5 0.08
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAACA
Found at i:2047977 original size:12 final size:12
Alignment explanation
Indices: 2047960--2048020 Score: 63
Period size: 13 Copynumber: 5.1 Consensus size: 12
2047950 AACAAAAAAG
*
2047960 AAAAGAAGCAAA
1 AAAAGAAACAAA
2047972 AAAAG-AA-AAA
1 AAAAGAAACAAA
* *
2047982 AAAACAAAGAAA
1 AAAAGAAACAAA
2047994 AAAGAGAAACAAA
1 AAA-AGAAACAAA
2048007 AAAGAGAAACAAA
1 AAA-AGAAACAAA
2048020 A
1 A
2048021 GAAAAAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 7 0.17
11 3 0.07
12 11 0.26
13 21 0.50
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAGAAACAAA
Found at i:2047980 original size:22 final size:21
Alignment explanation
Indices: 2047954--2048050 Score: 81
Period size: 22 Copynumber: 4.4 Consensus size: 21
2047944 ATCAAGAACA
2047954 AAAAAGAAAAGAAGCAAAAAAAG
1 AAAAA-AAAAGAAG-AAAAAAAG
*
2047977 AAAAAAAAACAAAGAAAAAAGAG
1 AAAAAAAAA-GAAGAAAAAA-AG
2048000 AAACAAAAAAG-AGAAACAAAAG
1 AAA-AAAAAAGAAGAAA-AAAAG
* *
2048022 AAAAAAAGA-AAGAACAAAAAT
1 AAAAAAAAAGAAGAA-AAAAAG
*
2048043 TAAAAAAA
1 AAAAAAAA
2048051 GGGACAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
21 19 0.31
22 21 0.34
23 16 0.26
24 6 0.10
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAAGAAAAAAAG
Found at i:2047994 original size:13 final size:12
Alignment explanation
Indices: 2047953--2048041 Score: 58
Period size: 12 Copynumber: 7.6 Consensus size: 12
2047943 AATCAAGAAC
*
2047953 AAAAAAGAAAAG
1 AAAAAAAAAAAG
**
2047965 AAGCAAAAAAAG
1 AAAAAAAAAAAG
*
2047977 AAAAAAAAACA-
1 AAAAAAAAAAAG
* *
2047988 AAGAAAAAAGAG
1 AAAAAAAAAAAG
*
2048000 -AAACAAAAAAG
1 AAAAAAAAAAAG
* *
2048011 -AGAAACAAAAG
1 AAAAAAAAAAAG
*
2048022 AAAAAAAGAAAG
1 AAAAAAAAAAAG
2048034 AACAAAAA
1 AA-AAAAA
2048042 TTAAAAAAAG
Statistics
Matches: 57, Mismatches: 17, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
11 25 0.44
12 27 0.47
13 5 0.09
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:2048033 original size:12 final size:12
Alignment explanation
Indices: 2047960--2048041 Score: 54
Period size: 11 Copynumber: 7.3 Consensus size: 12
2047950 AACAAAAAAG
2047960 AAAAG-AAGCAAA
1 AAAAGAAAG-AAA
2047972 AAAAG-AA-AAA
1 AAAAGAAAGAAA
*
2047982 AAAACAAAG-AA
1 AAAAGAAAGAAA
2047993 AAAAG--AGAAA
1 AAAAGAAAGAAA
* *
2048003 CAAA-AAAGAGA
1 AAAAGAAAGAAA
*
2048014 AACA-AAAGAAA
1 AAAAGAAAGAAA
2048025 AAAAGAAAGAACA
1 AAAAGAAAGAA-A
2048038 AAAA
1 AAAA
2048042 TTAAAAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
9 2 0.04
10 12 0.22
11 23 0.42
12 13 0.24
13 5 0.09
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:2048051 original size:30 final size:30
Alignment explanation
Indices: 2047953--2048032 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 30
2047943 AATCAAGAAC
*
2047953 AAAAAAGAAAAGAAGCA-AAA-AAAGAAA-AAA
1 AAAAAAGAAAA-AAG-AGAAACAAA-AAAGAGA
2047983 AAACAAAGAAAAAAGAGAAACAAAAAAGAGA
1 AAA-AAAGAAAAAAGAGAAACAAAAAAGAGA
2048014 AACAAAAGAAAAAA-AGAAA
1 AA-AAAAGAAAAAAGAGAAA
2048033 GAACAAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
29 1 0.02
30 17 0.39
31 25 0.57
32 1 0.02
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (30 bp):
AAAAAAGAAAAAAGAGAAACAAAAAAGAGA
Found at i:2049896 original size:212 final size:212
Alignment explanation
Indices: 2049618--2050567 Score: 1314
Period size: 211 Copynumber: 4.5 Consensus size: 212
2049608 ATATCTTGCC
* * * * *
2049618 ACTCGAGATAACACAAGTTCAACTTCACGACAAAGGGACGGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2049683 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* *
2049748 TCACGACGAAGGAACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAAAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
2049813 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
* *
2049830 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2049895 AATTTTAGAGACAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
2049960 TCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
2050025 ACAGCGAAGGATATTGG
196 ACAGCGAAGGATATTGG
* * *
2050042 ACTCAAGACAACACAAGTTCAACTTCACAACGAA-GGAACGACTGGTTGTCAAC-AACAA-TCTC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACT-TC
* * ** *
2050104 CTAATTTCAGAGCCAGTTTCAACTTCGTAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
2050169 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
129 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
*
2050234 TCACAGCGAAGGTTATTGG
194 TCACAGCGAAGGATATTGG
* * * *
2050253 ACTCCAGACAACGCAAGTTCAACTTCACGAC-ATAGGG-CCGCTGGTTGTAAATAAATAACTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGA-AGGGACCGCTGGTTGTCAACAAACAACTTCC
* * * * **
2050316 CAATTTCAGAGCCAATTTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCCCAA
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAA
* * * * *
2050380 CTTCACGATGAAGGGGCAGCTGATTGTCAAT-AA-AATTT--C-A-TTCAGAGTCAATTTCAACT
129 CTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACT
2050439 TCACAGCGAAGGATATTGG
194 TCACAGCGAAGGATATTGG
* * * * *
2050458 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * *
2050523 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2050568 GAAACAATGC
Statistics
Matches: 658, Mismatches: 69, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
205 69 0.10
206 59 0.09
207 2 0.00
209 5 0.01
210 16 0.02
211 265 0.40
212 242 0.37
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (212 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
TCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGG
Found at i:2050569 original size:106 final size:106
Alignment explanation
Indices: 2049631--2050567 Score: 1277
Period size: 106 Copynumber: 8.9 Consensus size: 106
2049621 CGAGATAACA
* * * * *
2049631 CAAGTTCAACTTCACGACAAAGGGACGGTTGGTTGTCAACAAACAACTTCCCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2049696 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
2049737 CAAGTTCAACTTCACGACGAAGGAACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
2049802 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
2049843 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAGACA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
2049908 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
2049949 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2050014 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
2050055 CAAGTTCAACTTCACAACGAA-GGAACGACTGGTTGTCAAC-AACAATCTCCTAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
* ** *
2050118 AGTTTCAACTTCGTAACGAAGGATATTGGACTCCAGACAACG
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
2050160 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2050225 ATTTCAACTTCACAGCGAAGGTTATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
2050266 CAAGTTCAACTTCACGAC-ATAGGG-CCGCTGGTTGTAAATAAATAACTTCCCAATTTCAGAGCC
1 CAAGTTCAACTTCACGACGA-AGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCC
* * * *
2050329 AATTTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACA
65 AATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
** * * * * * *
2050371 CAAGCCCAACTTCACGATGAAGGGGCAGCTGATTGTCAA-TAA-AATTT--C-A-TTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
2050430 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * ** *
2050471 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
2050536 ATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 ATTTCAACTTCACAG-CGAAGGATATTGGACTC
2050568 GAAACAATGC
Statistics
Matches: 739, Mismatches: 77, Indels: 30
0.87 0.09 0.04
Matches are distributed among these distances:
100 76 0.10
101 4 0.01
102 6 0.01
104 7 0.01
105 183 0.25
106 463 0.63
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:2051324 original size:37 final size:37
Alignment explanation
Indices: 2051266--2051362 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
2051256 CCTTTTCGTC
*
2051266 CTACTAGAATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
2051303 TTTCTAGGATTCAAACTCCTAAAAATAGGATTGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
2051340 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
2051363 GATAAGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2051934 original size:19 final size:19
Alignment explanation
Indices: 2051901--2051959 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
2051891 CATTTGGTTA
*
2051901 TTTTTTAATACTATATTTA-
1 TTTTTTTATA-TATATTTAC
*
2051920 TTATTTTTATATATATATAC
1 TT-TTTTTATATATATTTAC
*
2051940 TTTTTTTAAATAT-TTTAC
1 TTTTTTTATATATATTTAC
2051958 TT
1 TT
2051960 ATAAGCGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.18
19 19 0.56
20 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTTATATATATTTAC
Found at i:2052156 original size:18 final size:19
Alignment explanation
Indices: 2052130--2052165 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2052120 TGGTTTTGTT
*
2052130 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
2052148 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
2052166 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:2052293 original size:15 final size:16
Alignment explanation
Indices: 2052275--2052308 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2052265 TTTTTACTTA
*
2052275 TTTTTA-TTCTTCATT
1 TTTTTATTTATTCATT
2052290 TTTTTATTTATTCATT
1 TTTTTATTTATTCATT
2052306 TTT
1 TTT
2052309 CCCTCTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTATTTATTCATT
Found at i:2053916 original size:2 final size:2
Alignment explanation
Indices: 2053904--2053946 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2053894 TGAATATTAA
2053904 AT AT A- 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
2053945 AT
1 AT
2053947 GTCGTTAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2054914 original size:3 final size:3
Alignment explanation
Indices: 2054906--2054936 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2054896 ACTATATAAA
2054906 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2054937 TTAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2056924 original size:12 final size:12
Alignment explanation
Indices: 2056893--2056985 Score: 69
Period size: 12 Copynumber: 7.8 Consensus size: 12
2056883 AATCAACATT
*
2056893 TCCAGGCATCCC
1 TCCAGGCATACC
* * *
2056905 ACCTGGCATGCC
1 TCCAGGCATACC
2056917 TCCAGGCATACC
1 TCCAGGCATACC
* *
2056929 TGCAGGCATTCC
1 TCCAGGCATACC
* *
2056941 TCCAGGAAAACC
1 TCCAGGCATACC
* *
2056953 TCCGGGCATCCC
1 TCCAGGCATACC
* * *
2056965 ACCAGGAAAACC
1 TCCAGGCATACC
2056977 TCCAGGCAT
1 TCCAGGCAT
2056986 CCCACCCGGG
Statistics
Matches: 57, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
12 57 1.00
ACGTcount: A:0.25, C:0.40, G:0.20, T:0.15
Consensus pattern (12 bp):
TCCAGGCATACC
Found at i:2056953 original size:24 final size:24
Alignment explanation
Indices: 2056909--2057018 Score: 103
Period size: 24 Copynumber: 4.6 Consensus size: 24
2056899 CATCCCACCT
* * * *
2056909 GGCATGCCTCCAGGCATACCTGCA
1 GGCATCCCTCCAGGAAAACCTCCA
* *
2056933 GGCATTCCTCCAGGAAAACCTCCG
1 GGCATCCCTCCAGGAAAACCTCCA
*
2056957 GGCATCCCACCAGGAAAACCTCCA
1 GGCATCCCTCCAGGAAAACCTCCA
* * * * *
2056981 GGCATCCCACCCGGGAACCCACCA
1 GGCATCCCTCCAGGAAAACCTCCA
*
2057005 GGCATGCCTCCAGG
1 GGCATCCCTCCAGG
2057019 TTTTCTACTG
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.25, C:0.41, G:0.23, T:0.12
Consensus pattern (24 bp):
GGCATCCCTCCAGGAAAACCTCCA
Found at i:2058998 original size:7 final size:7
Alignment explanation
Indices: 2058988--2059016 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2058978 AGATTGAGAG
2058988 TTGAAAA
1 TTGAAAA
2058995 TTGAAAA
1 TTGAAAA
2059002 TTGAAAA
1 TTGAAAA
2059009 TTGAAAA
1 TTGAAAA
2059016 T
1 T
2059017 ACCTTTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (7 bp):
TTGAAAA
Found at i:2060105 original size:40 final size:40
Alignment explanation
Indices: 2060061--2060137 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
2060051 ATTTTAAATG
* * *
2060061 ACCTAAATGATTAAACCTAAAAATATATGCTCTAATATTA
1 ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATATTA
2060101 ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATA
1 ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATA
2060138 GAAAGGTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (40 bp):
ACCTAAATAATTAAACCTAAAAATATAGGCCCTAATATTA
Found at i:2061993 original size:222 final size:212
Alignment explanation
Indices: 2061562--2062003 Score: 611
Period size: 222 Copynumber: 2.0 Consensus size: 212
2061552 CGGGTCGAGT
* * *
2061562 TCGGGTTTAGGGTGAAAAATACCCGACTCGAAAATATATATAATTTTACCTTATATATTTAGGAA
1 TCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTACCTTATATATTTAGGAA
* *
2061627 TAATTACAATAATACCCCTCTATATATAACTTTTGTCAATTAAGTCACTGTTTTTATTGAATAAA
66 TAATTACAATAATACCCCTATATATATAAATTTTGTCAATTAAGTCACTGTTTTTATTGAATAAA
* *
2061692 AATAATTTTTTACTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTTGGTTCGGGTG
131 AATAATTTTTTACTATTTCGGGTC-GG-CGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTG
2061757 AAACTTTATTTTGGTCGGG
194 AAACTTTATTTTGGTCGGG
*
2061776 TCGGGTTTAGGGTGAAAAATACCTGACCCAACCCAAAAAATATATAATTTTACCTTATATATTTA
1 TCGGGTTTAGGGTGAAAAATACCCGA--C--CCCAAAAAATATATAATTTTACCTTATATATTTA
* *
2061841 GGAATAATTACAATAATACCCCTTTATATATATATATATATATATATTCCAATTAAGTTACTGTT
62 GGAATAATTACAATAATACCCC--TATATATATA-A-AT-T-T-T-GT-CAATTAAGTCACTGTT
*
2061906 TTTATTGAATAAAAATAATTTTTTATTATTTCGGGTC-G-GG-TTTCTAATTCATATATTCGGGT
118 TTTATTGAATAAAAATAATTTTTTACTATTTCGGGTCGGCGGATTTCTAATTCATATATTCGGGT
*
2061968 CGGGTCGGGTGAAACTTTGTTTTGGTCGGG
183 CGGGTCGGGTGAAACTTTATTTTGGTCGGG
*
2061998 TTGGGT
1 TCGGGT
2062004 CTCGGATGAA
Statistics
Matches: 202, Mismatches: 13, Indels: 18
0.87 0.06 0.08
Matches are distributed among these distances:
214 25 0.12
216 1 0.00
218 53 0.26
220 9 0.04
221 1 0.00
222 55 0.27
223 3 0.01
224 1 0.00
225 2 0.01
226 1 0.00
227 51 0.25
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.40
Consensus pattern (212 bp):
TCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAATTTTACCTTATATATTTAGGAA
TAATTACAATAATACCCCTATATATATAAATTTTGTCAATTAAGTCACTGTTTTTATTGAATAAA
AATAATTTTTTACTATTTCGGGTCGGCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAA
ACTTTATTTTGGTCGGG
Found at i:2062418 original size:18 final size:17
Alignment explanation
Indices: 2062375--2062421 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
2062365 TATGGAATTG
*
2062375 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
* *
2062392 GATTTCAATTCCTTCATA
1 GATTCCAATTCC-TCACA
2062410 GATTCCAATTCC
1 GATTCCAATTCC
2062422 CTCAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:2063620 original size:20 final size:20
Alignment explanation
Indices: 2063595--2063709 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
2063585 AATTTGGAAA
2063595 ATCGCAACGCGATACTAACT
1 ATCGCAACGCGATACTAACT
* **
2063615 ATCGCAACGCGATAATAAAAA
1 ATCGCAACGCGATACT-AACT
*
2063636 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTAACT
*
2063656 TTCGCAACGCGATACTTAA-T
1 ATCGCAACGCGATAC-TAACT
* * *
2063676 TTCGCAACGCAATACTGACT
1 ATCGCAACGCGATACTAACT
* *
2063696 TTCGCAACGAGATA
1 ATCGCAACGCGATA
2063710 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 58 0.73
21 19 0.24
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:2063692 original size:40 final size:41
Alignment explanation
Indices: 2063592--2063729 Score: 170
Period size: 41 Copynumber: 3.4 Consensus size: 41
2063582 GCGAATTTGG
* *
2063592 AAAATCGCAACGCGATACTAACTATCGCAACGCGATAATAA
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
2063633 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACT-T
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
** * * *
2063673 AATTTCGCAACGCAATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
* *
2063714 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
2063730 TTTCAAAGCA
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 34 0.42
41 47 0.58
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAA
Found at i:2063923 original size:22 final size:22
Alignment explanation
Indices: 2063896--2063939 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2063886 CACTCTCTCA
2063896 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2063918 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2063940 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2064251 original size:20 final size:20
Alignment explanation
Indices: 2064202--2064260 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2064192 TTTATTCTCT
* **
2064202 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
2064222 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
2064242 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
2064261 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:2066191 original size:19 final size:20
Alignment explanation
Indices: 2066137--2066203 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
2066127 TAGTTTACTT
* *
2066137 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
2066157 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
2066177 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
2066196 TCGCAACG
1 TCGCAACG
2066204 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:2066211 original size:14 final size:14
Alignment explanation
Indices: 2066192--2066250 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2066182 ATGCGAAATG
2066192 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2066206 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2066225 AAAATCGCAACGAC
1 AAAATCGCAACGAC
2066239 AAAATCGCAACG
1 AAAATCGCAACG
2066251 TGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2066218 original size:33 final size:33
Alignment explanation
Indices: 2066176--2066267 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
2066166 GGAAATGGCT
2066176 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2066209 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* * *
2066242 ATCGCAACGTGAAATGAAAATGGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
2066268 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2066230 original size:19 final size:19
Alignment explanation
Indices: 2066176--2066272 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
2066166 GGAAATGGCT
2066176 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2066195 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2066209 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2066228 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
* *
2066242 ATCGCAACGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2066261 ATGGCAATGCGA
1 ATCGCAATGCGA
2066273 TTTGTGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 4 0.07
18 2 0.03
19 29 0.48
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2066344 original size:20 final size:20
Alignment explanation
Indices: 2066319--2066384 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
2066309 TTATTTCGCA
2066319 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
*
2066339 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGCG
* *
2066359 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
2066379 TTGCGA
1 TTGCGA
2066385 AAGTAAGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:2066395 original size:20 final size:20
Alignment explanation
Indices: 2066358--2066410 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2066348 CCATTTCCGT
* * *
2066358 GTTGCGATAGTCATTTTCGC
1 GTTGCGAAAGTAAGTTTCGC
*
2066378 GTTGCGAAAGTAAGTTTCGT
1 GTTGCGAAAGTAAGTTTCGC
2066398 GTTGCGAAAGTAA
1 GTTGCGAAAGTAA
2066411 ACTATTCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (20 bp):
GTTGCGAAAGTAAGTTTCGC
Found at i:2066399 original size:40 final size:40
Alignment explanation
Indices: 2066319--2066404 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
2066309 TTATTTCGCA
* *
2066319 TTGCGATAGCCATTTCCGCGTTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGCAATTTCCGTG
* * *
2066359 TTGCGATAGTCATTTTCGCGTTGCGAAAGTAAGTTT-CGTG
1 TTGCGATAGCCATTTCCGCGTTGCGAAAGCAA-TTTCCGTG
2066399 TTGCGA
1 TTGCGA
2066405 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 37 0.93
41 3 0.08
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (40 bp):
TTGCGATAGCCATTTCCGCGTTGCGAAAGCAATTTCCGTG
Found at i:2066786 original size:21 final size:20
Alignment explanation
Indices: 2066760--2066828 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
2066750 CTGTCATCCC
2066760 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
2066781 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
2066802 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
2066822 TCAAGAG
1 TCAAGAG
2066829 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:2066840 original size:41 final size:42
Alignment explanation
Indices: 2066750--2066840 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
2066740 CCCGACTCAC
* *
2066750 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
2066792 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
2066833 CTGTCATC
1 CTGTCATC
2066841 GTTGAAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:2068286 original size:14 final size:14
Alignment explanation
Indices: 2068252--2068290 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2068242 TTGATTGTTT
2068252 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
2068266 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
2068280 TGTTGATTTGT
1 AATTGATTTGT
2068291 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:2068538 original size:20 final size:20
Alignment explanation
Indices: 2068513--2068584 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 20
2068503 TCGCATTGCG
*
2068513 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
2068533 ATTTTCGTGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* **
2068553 ATTTACGCGTTGCGATAATC
1 ATTTTCGCGTTGCGATAGCC
2068573 ATTTTCGCGTTG
1 ATTTTCGCGTTG
2068585 TGATTTCCCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2068827 original size:20 final size:20
Alignment explanation
Indices: 2068811--2068887 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
2068801 ATTGCGATTT
*
2068811 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
2068831 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
2068851 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
2068871 TCAGTATCGCATTGCGA
1 TCAGAATCGCGTTGCGA
2068888 TTTTCCAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:2068921 original size:20 final size:21
Alignment explanation
Indices: 2068877--2068928 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2068867 AAAGTCAGTA
*
2068877 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
2068898 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
2068918 TCGCATTGCGA
1 TCGCATTGCGA
2068929 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:2069031 original size:20 final size:20
Alignment explanation
Indices: 2068939--2069035 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
2068929 ATTGGGAAAA
* *
2068939 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATTCTGACTT
*
2068959 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
2068979 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
2068999 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
2069019 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
2069036 ATATTGCAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:2069050 original size:20 final size:20
Alignment explanation
Indices: 2068957--2069050 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 20
2068947 CGATACTTAC
* *
2068957 TTTCGCAACGC-GATACTGAC
1 TTTCGCAAC-CAGATTCTGAA
*
2068977 TTTCGCAACGC-GATTCTGAC
1 TTTCGCAAC-CAGATTCTGAA
*
2068997 TTTCGCAACGC-GATTCTGAC
1 TTTCGCAAC-CAGATTCTGAA
*
2069017 TTTCGCAACGAGATTCTGAA
1 TTTCGCAACCAGATTCTGAA
2069037 TATT-GCAACCAGAT
1 T-TTCGCAACCAGAT
2069051 AATACAGAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 66 0.97
21 2 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (20 bp):
TTTCGCAACCAGATTCTGAA
Found at i:2069808 original size:24 final size:24
Alignment explanation
Indices: 2069781--2069834 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2069771 GTATTCGAAA
*
2069781 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
2069805 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
2069829 TTTGAT
1 TTTGAT
2069835 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:2070026 original size:12 final size:12
Alignment explanation
Indices: 2070009--2070033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2069999 ATATAATCCT
2070009 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2070021 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2070033 G
1 G
2070034 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2072383 original size:19 final size:19
Alignment explanation
Indices: 2072361--2072419 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
2072351 GGAAATTACT
2072361 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2072380 ATCGTAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
2072394 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2072413 ATCGCAA
1 ATCGCAA
2072420 CGAGAGAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 17 0.55
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2072403 original size:33 final size:33
Alignment explanation
Indices: 2072361--2072487 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
2072351 GGAAATTACT
* *
2072361 ATCGCAATGCGAAATGAAAATCGTAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2072394 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
2072427 ATCGCAACGTGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2072460 ATCGCAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2072488 CGAATTTAGT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2072529 original size:19 final size:19
Alignment explanation
Indices: 2072487--2072530 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2072477 AAATCACAAC
*
2072487 GCGAATTTAGTTCCGCGTT
1 GCGATTTTAGTTCCGCGTT
*
2072506 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTCCGCGTT
2072525 GCGATT
1 GCGATT
2072531 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.18, G:0.27, T:0.41
Consensus pattern (19 bp):
GCGATTTTAGTTCCGCGTT
Found at i:2074543 original size:91 final size:90
Alignment explanation
Indices: 2074373--2074557 Score: 266
Period size: 91 Copynumber: 2.0 Consensus size: 90
2074363 ATTTCAAACT
* *
2074373 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACATTATTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAAACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAAT--A-AGTTTAGC
2074438 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
2074466 TTCAACCAAAAAACAAAACAAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT-AGTTTAGC
1 TTCAACCAAAAAACAAAAC--AAAGACAAATACTAACTTCACAGTATTAA-AGAATAAGTTTAGC
*
2074529 AGTATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
2074557 T
1 T
2074558 AAGCAATCTA
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
91 36 0.42
93 18 0.21
95 30 0.35
96 1 0.01
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (90 bp):
TTCAACCAAAAAACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATAAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:2076276 original size:33 final size:33
Alignment explanation
Indices: 2076224--2076319 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
2076214 AGATAATGAA
2076224 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
*
2076258 AATTGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
2076291 AATCGCAACGCGAAATGAAAATCGCAACG
1 AATCGCAACGCGAAATGACTATCGCAACG
2076320 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:2076315 original size:19 final size:19
Alignment explanation
Indices: 2076196--2076341 Score: 123
Period size: 19 Copynumber: 8.1 Consensus size: 19
2076186 TCTTTTGGTT
*
2076196 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
2076215 GATAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2076235 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
2076253 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
**
2076269 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2076286 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2076302 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2076321 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2076340 GA
1 GA
2076342 TTTTGGTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 43 0.42
20 28 0.27
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2076391 original size:33 final size:33
Alignment explanation
Indices: 2076337--2076408 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
2076327 AAAATCGCAA
**
2076337 TGCGATTTTGGTTTCACGTTGCAATTATCTCGT
1 TGCGATTTTCATTTCACGTTGCAATTATCTCGT
* *
2076370 TGCGATTTTCATTTCGA-GTTGCGATTCTCTCGT
1 TGCGATTTTCATTTC-ACGTTGCAATTATCTCGT
2076403 TGCGAT
1 TGCGAT
2076409 AGTTATTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 33 0.97
34 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCAATTATCTCGT
Found at i:2076417 original size:33 final size:34
Alignment explanation
Indices: 2076354--2076429 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
2076344 TTGGTTTCAC
* *
2076354 GTTGCAATTATCTCGTTGCGATTTTCATTT-CGA
1 GTTGCGATTATCTCGTTGCGATGTTCATTTCCGA
* *
2076387 GTTGCGATTCTCTCGTTGCGATAGTT-ATTTCCGC
1 GTTGCGATTATCTCGTTGCGAT-GTTCATTTCCGA
2076421 GTTGCGATT
1 GTTGCGATT
2076430 TTCATTCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 24 0.65
34 13 0.35
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (34 bp):
GTTGCGATTATCTCGTTGCGATGTTCATTTCCGA
Found at i:2077002 original size:20 final size:20
Alignment explanation
Indices: 2076961--2077072 Score: 118
Period size: 20 Copynumber: 5.5 Consensus size: 20
2076951 GCTATGTAAA
* *
2076961 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
* *
2076981 TCACATTGCAATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
2077001 TCGCATTGCGATTTTCGTAAT
1 TCGCATTGCGATTTACGT-AT
* *
2077022 TCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTAT
*
2077042 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
*
2077062 TCGTATTGCGA
1 TCGCATTGCGA
2077073 ATTATGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 3 0.04
20 54 0.72
21 18 0.24
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:2077037 original size:41 final size:40
Alignment explanation
Indices: 2076959--2077072 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 40
2076949 ACGCTATGTA
* * * *
2076959 AATCGCATTGCGATAGTAAG-ATTCACATTGCAATTTACGT
1 AATCGCATTGCGAT-TTACGTATTCGCATTGCGATTTACGT
* * *
2076999 ATTCGCATTGCGATTTTCGTAATTCGCATTGCGATTTACTT
1 AATCGCATTGCGATTTACGT-ATTCGCATTGCGATTTACGT
* *
2077040 AATCGCGTTGCGATTTACGTATTCGTATTGCGA
1 AATCGCATTGCGATTTACGTATTCGCATTGCGA
2077073 ATTATGAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
39 2 0.03
40 25 0.41
41 34 0.56
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (40 bp):
AATCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:2079875 original size:4 final size:4
Alignment explanation
Indices: 2079859--2079893 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
2079849 TCATTTGTAA
2079859 TCAT TCAAT TCAT TCAT TCAT TCAT TCAT TCAT TC
1 TCAT TC-AT TCAT TCAT TCAT TCAT TCAT TCAT TC
2079894 TCGCTCTCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TCAT
Found at i:2085180 original size:39 final size:39
Alignment explanation
Indices: 2085137--2085273 Score: 177
Period size: 39 Copynumber: 3.5 Consensus size: 39
2085127 ACATGATGGA
* *
2085137 GCATCGAGAGCTGCAAGCCCGGGTGATGAGCATCCTGCT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
*
2085176 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGTT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
* * * *
2085215 ACATCGAGAGTTGCAAGTCCGGATGATGAGCATTCTACT
1 GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
* *
2085254 GCGTCAAGAG-TGGCAAGTCC
1 GCATCGAGAGCT-GCAAGTCC
2085274 TGCTTTGGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 1 0.01
39 85 0.99
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (39 bp):
GCATCGAGAGCTGCAAGTCCGGATGATGAGCATCCTGCT
Done.