Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 47 of 62
Found at i:10837715 original size:6 final size:6
Alignment explanation
Indices: 10837704--10837730 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10837694 CCAACACTTT
10837704 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
10837731 CACTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:10839605 original size:60 final size:60
Alignment explanation
Indices: 10839497--10839610 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
10839487 TGAGTGACCA
* * *
10839497 TTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTTTATAGTCAGGTGATCG
1 TTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGCCAGGTGATCG
* * *
10839557 TTTTATAACTTTTAATAGTC-ATATGATTCAACAAAGCAATA-TCCTATAGCCAGG
1 TTTTATAACTTTTAATAGTCGAGA-GACTCAACAAAGCAACACT-CTATAGCCAGG
10839611 GGACCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGAGAGACTCAACAAAGCAACACTCTATAGCCAGGTGATCG
Found at i:10841605 original size:60 final size:60
Alignment explanation
Indices: 10841490--10841835 Score: 318
Period size: 60 Copynumber: 5.8 Consensus size: 60
10841480 TTGTTGTTTT
* * * * * * *
10841490 CTCATT-TAAATTGGTGCTTAGACTTTTTGAATATTCCAATTTTATTCTCAAACTATGAATC
1 CTCATTCTAAATTGATCCTTAAAC-TTTTGAACATTCCAATTTCATCCCCAAACTATGAA-C
* * *
10841551 C-CATTCT-AGTTTATCCCTTAAACTTTTGAACATTCCAGTTTCATCCCCAAACTATGAAC
1 CTCATTCTAAATTGAT-CCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAAC
* * **
10841610 CTCGTTTTAAATTGATCCACAAACTTTTGAATC-TTCCAATTTCAT-CCC---CTATGAAC
1 CTCATTCTAAATTGATCCTTAAACTTTTGAA-CATTCCAATTTCATCCCCAAACTATGAAC
* * * * *
10841666 CTCTTTTTAAATTGATCCTTAAACTTTTGAATATTCCAATTTCATCCTCAAACTATGAAT
1 CTCATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAAC
* * * *
10841726 CTCATTCTATATT-AGTCATTAAACTTTTAAACATTCTAATTTCATCCCCAAACTATGAAC
1 CTCATTCTAAATTGA-TCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAAC
* ** *
10841786 CTCAATT-TAAATTGGTCCCCAAACTTTTGAA-TTTCCAATTTCATCCCCAA
1 CTC-ATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATCCCCAA
10841836 TTTCATCCAA
Statistics
Matches: 232, Mismatches: 40, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
56 48 0.21
57 2 0.01
59 23 0.10
60 142 0.61
61 17 0.07
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (60 bp):
CTCATTCTAAATTGATCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAAC
Found at i:10841694 original size:116 final size:117
Alignment explanation
Indices: 10841566--10841835 Score: 307
Period size: 116 Copynumber: 2.3 Consensus size: 117
10841556 CTAGTTTATC
* * *
10841566 CCTTAAACTTTTGAACATTCCAGTTTCATCCCCAAACTATGAACCTCGTTTTAAATT-GATCCA-
1 CCTTAAACTTTTGAA-ATTCCAATTTCATCCCCAAACTATGAACCTCATTCTAAATTAG-T-CAT
* **
10841629 CAAACTTTTGAATC-TTCCAATTTCAT-CCC-CTATGAACCTCTTTTTAAATTGAT
63 CAAACTTTT-AAACATTCCAATTTCATCCCCACTATGAACCTCAATTTAAATTGAT
* * * *
10841682 CCTTAAACTTTTGAATATTCCAATTTCATCCTCAAACTATGAATCTCATTCTATATTAGTCATTA
1 CCTTAAACTTTTGAA-ATTCCAATTTCATCCCCAAACTATGAACCTCATTCTAAATTAGTCATCA
* *
10841747 AACTTTTAAACATTCTAATTTCATCCCCAAACTATGAACCTCAATTTAAATTGGT
65 AACTTTTAAACATTCCAATTTCATCCCC--ACTATGAACCTCAATTTAAATTGAT
** *
10841802 CCCCAAACTTTTGAATTTCCAATTTCATCCCCAA
1 CCTTAAACTTTTGAAATTCCAATTTCATCCCCAA
10841836 TTTCATCCAA
Statistics
Matches: 130, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
115 5 0.04
116 70 0.54
117 4 0.03
119 17 0.13
120 34 0.26
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (117 bp):
CCTTAAACTTTTGAAATTCCAATTTCATCCCCAAACTATGAACCTCATTCTAAATTAGTCATCAA
ACTTTTAAACATTCCAATTTCATCCCCACTATGAACCTCAATTTAAATTGAT
Found at i:10841811 original size:176 final size:176
Alignment explanation
Indices: 10841494--10841833 Score: 506
Period size: 176 Copynumber: 1.9 Consensus size: 176
10841484 TGTTTTCTCA
* * * * *
10841494 TTTAAATTGGTGCTTAGACTTTTTGAATATTCCAATTTTATTCTCAAACTATGAATCCCATTCTA
1 TTTAAATTGATCCTTAAACTTTTTGAATATTCCAATTTCATCCTCAAACTATGAATCCCATTCTA
* * * **
10841559 GTTTATCCCTTAAACTTTTGAACATTCCAGTTTCATCCCCAAACTATGAACCTCGTTTTAAATTG
66 GTTTATCCATTAAACTTTTAAACATTCCAATTTCATCCCCAAACTATGAACCTCAATTTAAATTG
10841624 ATCCACAAACTTTTGAATCTTCCAATTTCATCCCCTATGAACCTCTT
131 ATCCACAAACTTTTGAAT-TTCCAATTTCATCCCCTATGAACCTCTT
*
10841671 TTTAAATTGATCCTTAAAC-TTTTGAATATTCCAATTTCATCCTCAAACTATGAATCTCATTCTA
1 TTTAAATTGATCCTTAAACTTTTTGAATATTCCAATTTCATCCTCAAACTATGAATCCCATTCTA
*
10841735 -TATTAGT-CATTAAACTTTTAAACATTCTAATTTCATCCCCAAACTATGAACCTCAATTTAAAT
66 GT-TTA-TCCATTAAACTTTTAAACATTCCAATTTCATCCCCAAACTATGAACCTCAATTTAAAT
* *
10841798 TGGTCCCCAAACTTTTGAATTTCCAATTTCATCCCC
129 TGATCCACAAACTTTTGAATTTCCAATTTCATCCCC
10841834 AATTTCATCC
Statistics
Matches: 147, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
175 17 0.12
176 113 0.77
177 17 0.12
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (176 bp):
TTTAAATTGATCCTTAAACTTTTTGAATATTCCAATTTCATCCTCAAACTATGAATCCCATTCTA
GTTTATCCATTAAACTTTTAAACATTCCAATTTCATCCCCAAACTATGAACCTCAATTTAAATTG
ATCCACAAACTTTTGAATTTCCAATTTCATCCCCTATGAACCTCTT
Found at i:10842041 original size:60 final size:59
Alignment explanation
Indices: 10841963--10842145 Score: 210
Period size: 60 Copynumber: 3.1 Consensus size: 59
10841953 ATGCATATAT
*
10841963 TTTG-GGATGAAATTGAAATGTTCAAAAAGTTTGGGACTAATTTATAATGATGGTCATAG
1 TTTGAGGATGAAATTGAAATGTTC-AAAAGTTTGGGACTAATTTAAAATGATGGTCATAG
* * * * *
10842022 TTTGAGGATGGAATTGAAATGTTCAAAAGTTTGAGGCCTAATATAGAATGAT-ATCCATAG
1 TTTGAGGATGAAATTGAAATGTTCAAAAGTTTG-GGACTAATTTAAAATGATGGT-CATAG
* * * *
10842082 TTTAAGGATGAAATTGGAATGTTTAAAAGTTTAGGGACTAATTTAAAATGA-GAGGCATAG
1 TTTGAGGATGAAATTGAAATGTTCAAAAGTTT-GGGACTAATTTAAAATGATG-GTCATAG
10842142 TTTG
1 TTTG
10842146 GGGACATATG
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
59 14 0.14
60 88 0.85
61 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (59 bp):
TTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGACTAATTTAAAATGATGGTCATAG
Found at i:10843425 original size:28 final size:28
Alignment explanation
Indices: 10843363--10843425 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
10843353 AAAGAAAATC
* * *
10843363 AGAAAAGAAATTGAAGCACTCCAAAAGA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
10843391 A-AGAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
10843419 AGAAAAG
1 AGAAAAG
10843426 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 27 0.93
29 1 0.03
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.08
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:10844680 original size:24 final size:21
Alignment explanation
Indices: 10844646--10844688 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
10844636 TGCACAAGAT
*
10844646 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
10844668 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
10844689 AGAATTAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:10859077 original size:31 final size:31
Alignment explanation
Indices: 10859039--10859143 Score: 138
Period size: 31 Copynumber: 3.4 Consensus size: 31
10859029 TATAATATGG
10859039 TCTCTCGATTATATGATATTATTTTATTGAA
1 TCTCTCGATTATATGATATTATTTTATTGAA
*
10859070 TCTCTCGATTATAGGATATTATTTTATTGAA
1 TCTCTCGATTATATGATATTATTTTATTGAA
* * * * * *
10859101 TCCCCCAATTATATGACACTATTTTATTGAG
1 TCTCTCGATTATATGATATTATTTTATTGAA
*
10859132 TCTCACGATTAT
1 TCTCTCGATTAT
10859144 TAAAAGTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (31 bp):
TCTCTCGATTATATGATATTATTTTATTGAA
Found at i:10859564 original size:59 final size:59
Alignment explanation
Indices: 10859499--10859618 Score: 161
Period size: 59 Copynumber: 2.0 Consensus size: 59
10859489 TAGTCGAATA
* * * *
10859499 ACTATTTTGCAACTTTTAAAAGTT-GGGGACTCAACAAAATAGTATCCTTTAGTTGAGGG
1 ACTATTTTGCAACTTTTAAAAGTTAAGGGACTCAACAAAACAGTACCCTATAGTTG-GGG
* * *
10859558 ACTATTTTGTAACTTTTAATAGTTAAGGGACTCAACAAAGCAGTACCCTATAGTTGGGG
1 ACTATTTTGCAACTTTTAAAAGTTAAGGGACTCAACAAAACAGTACCCTATAGTTGGGG
10859617 AC
1 AC
10859619 CATATGTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
59 27 0.51
60 26 0.49
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (59 bp):
ACTATTTTGCAACTTTTAAAAGTTAAGGGACTCAACAAAACAGTACCCTATAGTTGGGG
Found at i:10859918 original size:16 final size:17
Alignment explanation
Indices: 10859897--10859930 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
10859887 TATTAATTGA
10859897 TAAATAA-ATAAAATAT
1 TAAATAATATAAAATAT
10859913 TAAATAATTATAAAATAT
1 TAAATAA-TATAAAATAT
10859931 AATCATCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAATAATATAAAATAT
Found at i:10869336 original size:20 final size:20
Alignment explanation
Indices: 10869313--10869408 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 20
10869303 GAGGGATTAT
10869313 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
10869333 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
* * * *
10869351 TAGTGGTTCTTCGGAACAAC
1 CAGTGGTCCTTCGGGACAAA
*
10869371 CAGTGGTCCTTCGAGAC--A
1 CAGTGGTCCTTCGGGACAAA
* *
10869389 TATTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
10869409 TATTCAGTGC
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
18 29 0.48
20 31 0.52
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:10869357 original size:18 final size:18
Alignment explanation
Indices: 10869313--10869406 Score: 98
Period size: 18 Copynumber: 5.0 Consensus size: 18
10869303 GAGGGATTAT
10869313 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGAC--A
10869333 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* * *
10869351 TAGTGGTTCTTCGGAACAA
1 CAGTGGTCCTTCGGGAC-A
*
10869370 CCAGTGGTCCTTCGAGACA
1 -CAGTGGTCCTTCGGGACA
* *
10869389 TATTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
10869407 AATATTCAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
18 30 0.48
19 2 0.03
20 30 0.48
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:10869375 original size:38 final size:38
Alignment explanation
Indices: 10869314--10869408 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 38
10869304 AGGGATTATC
*
10869314 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGAGACAT
* * *
10869352 AGTGGTTCTTCGGAACAACCAGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGAGACAT
*
10869390 ATTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
10869409 TATTCAGTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGAGACAT
Found at i:10872874 original size:24 final size:20
Alignment explanation
Indices: 10872842--10872897 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
10872832 GCATGGGCAG
10872842 TGCATCGATGCATATGTTAAAGAA
1 TGCATCGATGCA-ATG-T--AGAA
*
10872866 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCAATGTAGAA
10872886 TGCATCGATGCA
1 TGCATCGATGCA
10872898 CTTCAAGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCAATGTAGAA
Found at i:10872887 original size:20 final size:20
Alignment explanation
Indices: 10872862--10872899 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10872852 CATATGTTAA
10872862 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
10872882 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
10872900 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:10873796 original size:20 final size:20
Alignment explanation
Indices: 10873771--10873905 Score: 134
Period size: 20 Copynumber: 7.0 Consensus size: 20
10873761 AAGGATTATT
*
10873771 AGTGGTCCTTCAGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
* *
10873791 AATGGTCCTTTGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
10873811 AGTGGTCCTTCGGGACAAAC
1 AGTGGTCCTTCGGGACAAAC
* *
10873831 AGTTGTCCTTCGGGAC--AT
1 AGTGGTCCTTCGGGACAAAC
* * ** *
10873849 AGTGGTTCTTTGTAACAACC
1 AGTGGTCCTTCGGGACAAAC
* *
10873869 AGTGGTCCTTCAGGAC--AT
1 AGTGGTCCTTCGGGACAAAC
10873887 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
10873906 TATTCAGTGC
Statistics
Matches: 89, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
18 27 0.30
20 62 0.70
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (20 bp):
AGTGGTCCTTCGGGACAAAC
Found at i:10873892 original size:18 final size:18
Alignment explanation
Indices: 10873869--10873903 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10873859 TGTAACAACC
10873869 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
10873887 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCAGGACA
10873904 AATATTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:10890503 original size:12 final size:12
Alignment explanation
Indices: 10890486--10890515 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
10890476 ACCTGAAAAT
10890486 AGTGAGTAACAG
1 AGTGAGTAACAG
10890498 AGTGAGTAACAG
1 AGTGAGTAACAG
10890510 AGTGAG
1 AGTGAG
10890516 CTTTGGGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.37, T:0.17
Consensus pattern (12 bp):
AGTGAGTAACAG
Found at i:10892216 original size:28 final size:27
Alignment explanation
Indices: 10892184--10892244 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
10892174 AATTCCATAG
* *
10892184 TTTAGAAGTATTTTAGGTCATTTTACAC
1 TTTAGAAGCATTTT-GGTCATTTTAAAC
**
10892212 TTTAGGGGCATTTTGGTCATTTTAAAC
1 TTTAGAAGCATTTTGGTCATTTTAAAC
10892239 TTTAGA
1 TTTAGA
10892245 GGTCTTTCTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (27 bp):
TTTAGAAGCATTTTGGTCATTTTAAAC
Found at i:10893431 original size:18 final size:18
Alignment explanation
Indices: 10893385--10893432 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
10893375 GGTCAACGGC
* *
10893385 TTGGCTCGGCTCAGCAGC
1 TTGGCTCGGCTCAACAGA
* * *
10893403 TCGACTTGGCTCAACAGA
1 TTGGCTCGGCTCAACAGA
10893421 TTGGCTCGGCTC
1 TTGGCTCGGCTC
10893433 GGCTCGGCTC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.31, G:0.29, T:0.25
Consensus pattern (18 bp):
TTGGCTCGGCTCAACAGA
Found at i:10893433 original size:5 final size:5
Alignment explanation
Indices: 10893423--10893447 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
10893413 TCAACAGATT
10893423 GGCTC GGCTC GGCTC GGCTC GGCTC
1 GGCTC GGCTC GGCTC GGCTC GGCTC
10893448 AGACCGGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (5 bp):
GGCTC
Found at i:10897747 original size:19 final size:19
Alignment explanation
Indices: 10897720--10897771 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
10897710 GAATGCCATC
*
10897720 AGTGTATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
10897739 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
10897758 AGTGCATCGATGCA
1 AGTGCATCGATGCA
10897772 CCCCCCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:10900599 original size:17 final size:17
Alignment explanation
Indices: 10900557--10900600 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
10900547 CATAGGTACC
* *
10900557 AAATGTTAAAAGTTACT
1 AAATGTTACAAGCTACT
10900574 AAATGTTACAAGCTACT
1 AAATGTTACAAGCTACT
10900591 AAATGTTACA
1 AAATGTTACA
10900601 GAGGTCTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (17 bp):
AAATGTTACAAGCTACT
Found at i:10900787 original size:27 final size:27
Alignment explanation
Indices: 10900701--10900777 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
10900691 ACTTCGGTAG
*
10900701 GATGCATAGTATTCCACCTTTCAGGGT
1 GATGCATAGTATTCCATCTTTCAGGGT
* * *
10900728 GATGCATAATAATT-CATCATTCGGGGT
1 GATGCATAGT-ATTCCATCTTTCAGGGT
10900755 GATGCATAGTATTCCATCTTTCA
1 GATGCATAGTATTCCATCTTTCA
10900778 AGATGTTGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 3 0.07
27 35 0.85
28 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
GATGCATAGTATTCCATCTTTCAGGGT
Found at i:10900966 original size:16 final size:16
Alignment explanation
Indices: 10900945--10900975 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10900935 TAGGCAGATC
10900945 TTAGGCAGTCATGTTT
1 TTAGGCAGTCATGTTT
10900961 TTAGGCAGTCATGTT
1 TTAGGCAGTCATGTT
10900976 GCCTAAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (16 bp):
TTAGGCAGTCATGTTT
Found at i:10902662 original size:27 final size:28
Alignment explanation
Indices: 10902610--10902662 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
10902600 TTTTAATAAA
* *
10902610 AGAGTAATTAAAATTAATTTTGAAATTT
1 AGAGTAATTAAAATTAATTATAAAATTT
*
10902638 AGAG-AATTAAATTTAATTATAAAAT
1 AGAGTAATTAAAATTAATTATAAAAT
10902663 ATAGCACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (28 bp):
AGAGTAATTAAAATTAATTATAAAATTT
Found at i:10907014 original size:24 final size:24
Alignment explanation
Indices: 10906960--10907054 Score: 113
Period size: 24 Copynumber: 4.0 Consensus size: 24
10906950 ATTTTCGACT
*
10906960 TGAATTCTGTTTTGA-TACATGA-C
1 TGAATTCTGTTTTGATTTC-TGATC
10906983 TTGAATTCTGTTTTGATTTCTGATC
1 -TGAATTCTGTTTTGATTTCTGATC
* * *
10907008 TGGATTCTGTTCTGATATCTGATC
1 TGAATTCTGTTTTGATTTCTGATC
*
10907032 TGAATTCTATTTTGATTTCTGAT
1 TGAATTCTGTTTTGATTTCTGAT
10907055 ATCTCCATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
24 58 0.95
25 3 0.05
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATC
Found at i:10907024 original size:48 final size:48
Alignment explanation
Indices: 10906963--10907054 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
10906953 TTCGACTTGA
* *
10906963 ATTCTGTTTTGATA-CATGA-CTTGAATTCTGTTTTGATTTCTGATCTGG
1 ATTCTGTTCTGATATC-TGATC-TGAATTCTATTTTGATTTCTGATCTGG
10907011 ATTCTGTTCTGATATCTGATCTGAATTCTATTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGATCTGAATTCTATTTTGATTTCTGAT
10907055 ATCTCCATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGATCTGAATTCTATTTTGATTTCTGATCTGG
Found at i:10907219 original size:2 final size:2
Alignment explanation
Indices: 10907212--10907250 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10907202 GGATGGGGTG
10907212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10907251 GTTTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10911011 original size:21 final size:22
Alignment explanation
Indices: 10910957--10911011 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
10910947 TTTGCGACAC
*
10910957 ATATTTGGTCCTT-AGCATATG
1 ATATATGGTCCTTAAGCATATG
* * *
10910978 -TATATGATTCTTAAGGA-ATG
1 ATATATGGTCCTTAAGCATATG
10910998 ATATATGGTCCTTA
1 ATATATGGTCCTTA
10911012 TGGACATTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (22 bp):
ATATATGGTCCTTAAGCATATG
Found at i:10911089 original size:23 final size:23
Alignment explanation
Indices: 10911026--10911078 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
10911016 CATTATTATA
10911026 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
10911049 CGGCACTCCGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
10911072 TGGCACT
1 TGGCACT
10911079 TCAGTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:10914739 original size:12 final size:12
Alignment explanation
Indices: 10914700--10914793 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
10914690 GATTTCCAAC
10914700 TTGAATTCTGTT
1 TTGAATTCTGTT
* **
10914712 TTG-ATGCATGAC
1 TTGAATTC-TGTT
10914724 TTGAATTCTGTT
1 TTGAATTCTGTT
* *
10914736 TTGATTTCTGAT
1 TTGAATTCTGTT
* *
10914748 CTGGATTCTGTT
1 TTGAATTCTGTT
* *
10914760 ATG-ATATCTGAT
1 TTGAAT-TCTGTT
*
10914772 CTGAATTCTGTT
1 TTGAATTCTGTT
*
10914784 TTGATTTCTG
1 TTGAATTCTG
10914794 ATAACTTCGT
Statistics
Matches: 60, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
11 5 0.08
12 50 0.83
13 5 0.08
ACGTcount: A:0.18, C:0.12, G:0.19, T:0.51
Consensus pattern (12 bp):
TTGAATTCTGTT
Found at i:10914755 original size:24 final size:24
Alignment explanation
Indices: 10914701--10914795 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
10914691 ATTTCCAACT
*
10914701 TGAATTCTGTTTTGA-TGCATGA-C
1 TGAATTCTGTTTTGATTTC-TGATC
10914724 TTGAATTCTGTTTTGATTTCTGATC
1 -TGAATTCTGTTTTGATTTCTGATC
* * *
10914749 TGGATTCTGTTATGATATCTGATC
1 TGAATTCTGTTTTGATTTCTGATC
10914773 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTTTGATTTCTGAT
10914796 AACTTCGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 59 0.95
25 3 0.05
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTTTGATTTCTGATC
Found at i:10914959 original size:2 final size:2
Alignment explanation
Indices: 10914952--10914986 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10914942 TGATGGGGTG
10914952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10914987 GTTTTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10916217 original size:2 final size:2
Alignment explanation
Indices: 10916210--10916239 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10916200 TTTTGAATCG
*
10916210 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
10916240 AGCCCTAGAA
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10918180 original size:13 final size:13
Alignment explanation
Indices: 10918162--10918187 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10918152 TTTGTTAATA
10918162 GATGAAGGGACCT
1 GATGAAGGGACCT
10918175 GATGAAGGGACCT
1 GATGAAGGGACCT
10918188 AATGTAAGAC
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:0.38, T:0.15
Consensus pattern (13 bp):
GATGAAGGGACCT
Found at i:10931024 original size:20 final size:20
Alignment explanation
Indices: 10930999--10931038 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
10930989 AGCAACAGAA
*
10930999 TAAAACTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
10931019 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
10931039 AACTAACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:10935667 original size:21 final size:20
Alignment explanation
Indices: 10935618--10935709 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 20
10935608 AGCAACAGAA
* *
10935618 TAAAACTGGTTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
10935638 TAAAACTGATCCTATCTAA-
1 TAAAACTGATCCTATCTAAT
10935657 T--AACT-A----A-CTGAAT
1 TAAAACTGATCCTATCT-AAT
* * *
10935670 AAAAACTTATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
10935690 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
10935710 AACTAACAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
11 2 0.04
12 3 0.05
15 4 0.07
16 2 0.04
17 4 0.07
19 1 0.02
20 38 0.68
21 2 0.04
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:10935683 original size:52 final size:52
Alignment explanation
Indices: 10935611--10935725 Score: 196
Period size: 52 Copynumber: 2.2 Consensus size: 52
10935601 TAAAATTAGC
**
10935611 AACAGAAT-AAAACTGGTTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAGAATAAAAACTTATTCTATCTAATTAAAACTGATCCTATCTAATAACT
*
10935662 AACTGAATAAAAACTTATTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAGAATAAAAACTTATTCTATCTAATTAAAACTGATCCTATCTAATAACT
10935714 AACAGAATAAAA
1 AACAGAATAAAA
10935726 TATCTAGTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 7 0.12
52 52 0.88
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (52 bp):
AACAGAATAAAAACTTATTCTATCTAATTAAAACTGATCCTATCTAATAACT
Found at i:10941279 original size:36 final size:36
Alignment explanation
Indices: 10941232--10941309 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
10941222 GGTACAATTC
10941232 TAACTAGTTGCACATATGAAGGTTGCAGCTCGGAAG
1 TAACTAGTTGCACATATGAAGGTTGCAGCTCGGAAG
*
10941268 TAACTAGTTGCACATATGAAGGTTGTAGCTCGGAAG
1 TAACTAGTTGCACATATGAAGGTTGCAGCTCGGAAG
*
10941304 TGACTA
1 TAACTA
10941310 CCAATAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (36 bp):
TAACTAGTTGCACATATGAAGGTTGCAGCTCGGAAG
Found at i:10943270 original size:31 final size:31
Alignment explanation
Indices: 10943234--10943373 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
10943224 AAACTACCCG
* *
10943234 TTTAGTATTTAAATTATCAGTTTTGGTCCGA-
1 TTTAGTACTTAAATTATTAGTTTTGGTCC-AT
* * * **
10943265 TTTAGTACTTAAACTATTAATTTTGATCGGT
1 TTTAGTACTTAAATTATTAGTTTTGGTCCAT
* * *
10943296 TTTAATAATTAAAATATTAGTTTTGGTCCAT
1 TTTAGTACTTAAATTATTAGTTTTGGTCCAT
* * *
10943327 TTTAGTACCTAAATTATGAGTTTTGGTTCAT
1 TTTAGTACTTAAATTATTAGTTTTGGTCCAT
*
10943358 TTTAGTATCTAAAATT
1 TTTAGTA-CTTAAATT
10943374 TTAATATTTT
Statistics
Matches: 85, Mismatches: 22, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
31 79 0.93
32 6 0.07
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTAGTACTTAAATTATTAGTTTTGGTCCAT
Found at i:10949250 original size:2 final size:2
Alignment explanation
Indices: 10949243--10949267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10949233 TTTTAAGAAT
10949243 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10949268 TTATTTATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10951690 original size:13 final size:14
Alignment explanation
Indices: 10951672--10951727 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
10951662 GTAACAAAAT
10951672 AAAATAAAATAA-A
1 AAAATAAAATAATA
10951685 AAAATAAAA-AAGTA
1 AAAATAAAATAA-TA
10951699 AAAATAAAATAGATA
1 AAAATAAAATA-ATA
10951714 AATAATAATAATAA
1 AA-AATAA-AATAA
10951728 AAGATTCAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.05
13 9 0.24
14 10 0.27
15 5 0.14
16 7 0.19
17 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AAAATAAAATAATA
Found at i:10951703 original size:22 final size:22
Alignment explanation
Indices: 10951672--10951729 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
10951662 GTAACAAAAT
10951672 AAAAT-AAAATAAAA-AAATAA
1 AAAATAAAAATAAAATAAATAA
*
10951692 AAAAGTAAAAATAAAATAGATAA
1 AAAA-TAAAAATAAAATAAATAA
* *
10951715 ATAATAATAATAAAA
1 AAAATAAAAATAAAA
10951730 GATTCAGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 19 0.59
23 8 0.25
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (22 bp):
AAAATAAAAATAAAATAAATAA
Found at i:10951723 original size:19 final size:19
Alignment explanation
Indices: 10951667--10951724 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
10951657 GGCCTGTAAC
*
10951667 AAAATAAAATAA--AATAAA
1 AAAATAAAA-AAGTAATAAT
*
10951685 AAAATAAAAAAGTAAAAAT
1 AAAATAAAAAAGTAATAAT
*
10951704 AAAATAGATAAA-TAATAAT
1 AAAATA-AAAAAGTAATAAT
10951723 AA
1 AA
10951725 TAAAAGATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 9 0.27
19 18 0.55
20 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAATAAAAAAGTAATAAT
Found at i:10951728 original size:13 final size:13
Alignment explanation
Indices: 10951673--10951728 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
10951663 TAACAAAATA
* *
10951673 AAATAAAATAAAA
1 AAATAAAATAGAT
* *
10951686 AAATAAAAAAGTAA
1 AAATAAAATAG-AT
10951700 AAATAAAATAGAT
1 AAATAAAATAGAT
10951713 AAATAATAATA-AT
1 AAATAA-AATAGAT
10951726 AAA
1 AAA
10951729 AGATTCAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 21 0.57
14 16 0.43
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.20
Consensus pattern (13 bp):
AAATAAAATAGAT
Found at i:10951729 original size:27 final size:25
Alignment explanation
Indices: 10951667--10951729 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
10951657 GGCCTGTAAC
10951667 AAAATAAAATAAAATAAAAAAATAA
1 AAAATAAAATAAAATAAAAAAATAA
* *
10951692 AAAAGTAAAAATAAAATAGATAAATAA
1 AAAA-T-AAAATAAAATAAAAAAATAA
10951719 TAATAATAAAA
1 -AA-AATAAAA
10951730 GATTCAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 22 0.69
28 3 0.09
29 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (25 bp):
AAAATAAAATAAAATAAAAAAATAA
Found at i:10960042 original size:19 final size:19
Alignment explanation
Indices: 10960018--10960065 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
10960008 AAGTGAAGTT
10960018 GAGTTTAAAGGCAGTAAAG
1 GAGTTTAAAGGCAGTAAAG
*
10960037 GAGTTTAAAGGCATTAAAG
1 GAGTTTAAAGGCAGTAAAG
*
10960056 GAGATTAAAG
1 GAGTTTAAAG
10960066 TGGGAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.29, T:0.23
Consensus pattern (19 bp):
GAGTTTAAAGGCAGTAAAG
Found at i:10960744 original size:23 final size:22
Alignment explanation
Indices: 10960714--10960806 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 22
10960704 GAGGGTTCTG
10960714 TGTGGTCATTCGGGACAAAATTA
1 TGTGGTCATTCGGGAC-AAATTA
* *
10960737 TGTGGTCATTTGGGACAAAACTA
1 TGTGGTCATTCGGGAC-AAATTA
*
10960760 TGTGGTCATTCGAGACAAA-TA
1 TGTGGTCATTCGGGACAAATTA
10960781 TGTGG-CACTTCGGTG-CAAATTA
1 TGTGGTCA-TTCGG-GACAAATTA
10960803 TGTG
1 TGTG
10960807 TGTTGTGGTG
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
20 2 0.03
21 15 0.24
22 10 0.16
23 35 0.56
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (22 bp):
TGTGGTCATTCGGGACAAATTA
Found at i:10960784 original size:21 final size:23
Alignment explanation
Indices: 10960714--10960793 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
10960704 GAGGGTTCTG
*
10960714 TGTGGTCATTCGGGACAAAATTA
1 TGTGGTCATTCGGGACAAAACTA
*
10960737 TGTGGTCATTTGGGACAAAACTA
1 TGTGGTCATTCGGGACAAAACTA
*
10960760 TGTGGTCATTCGAGAC-AAA-TA
1 TGTGGTCATTCGGGACAAAACTA
10960781 TGTGG-CACTTCGG
1 TGTGGTCA-TTCGG
10960794 TGCAAATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 3 0.06
23 35 0.69
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (23 bp):
TGTGGTCATTCGGGACAAAACTA
Found at i:10962874 original size:18 final size:18
Alignment explanation
Indices: 10962851--10962889 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
10962841 TTAATGAATA
10962851 AAATGCAATGCAAAAAGT
1 AAATGCAATGCAAAAAGT
*
10962869 AAATGCAATGCATAAAGT
1 AAATGCAATGCAAAAAGT
10962887 AAA
1 AAA
10962890 ATGTAGATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (18 bp):
AAATGCAATGCAAAAAGT
Found at i:10966436 original size:21 final size:21
Alignment explanation
Indices: 10966424--10966495 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
10966414 GGAGAATCGA
10966424 TACCCCCTGGGGGGGAATCTG
1 TACCCCCTGGGGGGGAATCTG
* *
10966445 TTCCCCCT-GGGGGGAATCGG
1 TACCCCCTGGGGGGGAATCTG
*
10966465 TATCCCCTGGGGGGGAATCTG
1 TACCCCCTGGGGGGGAATCTG
10966486 TACCCCCTGG
1 TACCCCCTGG
10966496 ACATTCTGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.12, C:0.31, G:0.36, T:0.21
Consensus pattern (21 bp):
TACCCCCTGGGGGGGAATCTG
Found at i:10966450 original size:20 final size:20
Alignment explanation
Indices: 10966427--10966491 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
10966417 GAATCGATAC
10966427 CCCCTGGGGGGGAATCTGTT
1 CCCCTGGGGGGGAATCTGTT
*
10966447 CCCCCT-GGGGGGAATCGGTAT
1 -CCCCTGGGGGGGAATCTGT-T
*
10966468 CCCCTGGGGGGGAATCTGTA
1 CCCCTGGGGGGGAATCTGTT
10966488 CCCC
1 CCCC
10966492 CTGGACATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
20 21 0.54
21 18 0.46
ACGTcount: A:0.12, C:0.31, G:0.37, T:0.20
Consensus pattern (20 bp):
CCCCTGGGGGGGAATCTGTT
Found at i:10966472 original size:41 final size:41
Alignment explanation
Indices: 10966412--10966495 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
10966402 TCGTTAGACA
*
10966412 GGGGAGAATCGATACCCCCTGGGGGGGAATCTGTTCCCCCT
1 GGGGAGAATCGATACCCCCTGGGGGGGAATCTGTACCCCCT
* * *
10966453 GGGGGGAATCGGTATCCCCTGGGGGGGAATCTGTACCCCCT
1 GGGGAGAATCGATACCCCCTGGGGGGGAATCTGTACCCCCT
10966494 GG
1 GG
10966496 ACATTCTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.19
Consensus pattern (41 bp):
GGGGAGAATCGATACCCCCTGGGGGGGAATCTGTACCCCCT
Found at i:10966554 original size:22 final size:22
Alignment explanation
Indices: 10966528--10966569 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10966518 AAAACCTACA
10966528 GGGGGAATCTGTACCCCCTGGG
1 GGGGGAATCTGTACCCCCTGGG
*
10966550 GGGGGAATCTGTATCCCCTG
1 GGGGGAATCTGTACCCCCTG
10966570 AACAATCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.38, T:0.21
Consensus pattern (22 bp):
GGGGGAATCTGTACCCCCTGGG
Found at i:10968035 original size:19 final size:20
Alignment explanation
Indices: 10967992--10968039 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
10967982 TCTAAATCCT
*
10967992 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
10968012 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
10968031 TTTTCAAAA
1 TTTTCAAAA
10968040 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:10969404 original size:21 final size:20
Alignment explanation
Indices: 10969367--10969463 Score: 160
Period size: 20 Copynumber: 4.8 Consensus size: 20
10969357 AAAACCTACA
10969367 GGGGGAATCTGTACCCCCAG
1 GGGGGAATCTGTACCCCCAG
10969387 GGGGGAATCTGTACCCCCAG
1 GGGGGAATCTGTACCCCCAG
10969407 GGGGGAATCTGTACCCCCTAG
1 GGGGGAATCTGTACCCCC-AG
*
10969428 GGGGGAATATGTACCCCCA-
1 GGGGGAATCTGTACCCCCAG
*
10969447 GGGGGAATCTATACCCC
1 GGGGGAATCTGTACCCC
10969464 TGGACAATCA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.21
20 39 0.53
21 19 0.26
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCAG
Found at i:10972266 original size:3 final size:3
Alignment explanation
Indices: 10972225--10972279 Score: 53
Period size: 3 Copynumber: 18.3 Consensus size: 3
10972215 CTGTAACAAA
*
10972225 AAT AAA AAT AA- AAT AA- AAT ATAT AA- AAT AGAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT -AAT AAT AAT AAT
10972270 AAT AAT AAT A
1 AAT AAT AAT A
10972280 TAACAAAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
2 6 0.14
3 30 0.68
4 7 0.16
5 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:10973389 original size:16 final size:17
Alignment explanation
Indices: 10973339--10973390 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
10973329 ATAAAAAATA
10973339 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
10973356 -AGTT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
10973371 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
10973387 AATT
1 AATT
10973391 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 13 0.45
17 3 0.10
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:10974013 original size:21 final size:21
Alignment explanation
Indices: 10973989--10974028 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
10973979 TTCCTGCTAT
10973989 TTTTTAAA-ATTATTTTTAAAA
1 TTTTTAAATATT-TTTTTAAAA
10974010 TTTTTAAATATTTTTTTAA
1 TTTTTAAATATTTTTTTAA
10974029 TTTACATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTAAATATTTTTTTAAAA
Found at i:10974025 original size:12 final size:11
Alignment explanation
Indices: 10973988--10974028 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
10973978 TTTCCTGCTA
10973988 TTTTTTAAAAT
1 TTTTTTAAAAT
10973999 TATTTTTAAAA-
1 T-TTTTTAAAAT
10974010 -TTTTTAAATAT
1 TTTTTTAAA-AT
10974021 TTTTTTAA
1 TTTTTTAA
10974029 TTTACATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 8 0.31
10 1 0.04
11 1 0.04
12 16 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:10983160 original size:24 final size:24
Alignment explanation
Indices: 10983133--10983182 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
10983123 GGTTTAGGTA
*
10983133 GGCTCCGGGTCGAGTTCTGGTTTG
1 GGCTCCGGGTCGAGTCCTGGTTTG
** *
10983157 GGCTTTGGGTCGGGTCCTGGTTTG
1 GGCTCCGGGTCGAGTCCTGGTTTG
10983181 GG
1 GG
10983183 TGTTTCGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.02, C:0.18, G:0.46, T:0.34
Consensus pattern (24 bp):
GGCTCCGGGTCGAGTCCTGGTTTG
Found at i:10983686 original size:135 final size:135
Alignment explanation
Indices: 10983445--10984087 Score: 878
Period size: 135 Copynumber: 4.8 Consensus size: 135
10983435 CAAGCTGCGG
* ** * * * * * * *
10983445 GTTCTTCTCATCATGAACTCTTTATTGGAAATGTTGATCTCTCGAGTG-TGCGTCGTTGATTCGA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
* * * * *
10983509 AATGCGGTGAATCGAGAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTT-TGCCCTCTATT
66 AATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCT-CCCTCTATC
*
10983573 AGATGA
130 GGATGA
**
10983579 GTTCTTCTCATTATGAACTCTCTTTTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
* * * *
10983644 AATACCATGAATCGAGCAAAGATTGAACAAGTTCTTCTCATTACAAACTTCTTCTCCCTCTATCG
66 AATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCG
10983709 GATGA
131 GATGA
* * **
10983714 GTTCTTCTCATTATGAGCTCTCCATTAGAAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCAA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
*
10983779 AATGTCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCG
66 AATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCG
*
10983844 GACGA
131 GATGA
* * *
10983849 GTTCTTCTCATTATGAACTCT-CACTTGGAAATATTAATCCCTCAAGTGAAGCATCGCTGATTCG
1 GTTCTTCTCATTATGAACTCTCCA-TTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCA
* * * * *
10983913 AAATACCGTGAATCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAGCTTATTCTCCCTCTATC
65 AAATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATC
10983978 GGATGA
130 GGATGA
* *
10983984 GTTCTTCTTATTATGAACTCTCCATTGGAAATGTTGATCCCTCAAGTGAGGCATCGCTGATTCAA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
* * *
10984049 AATGTCGTCAATCAAGCAAAGGTTGAACAAGTTCTTCTC
66 AATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTC
10984088 CCTCTATCGG
Statistics
Matches: 451, Mismatches: 54, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
134 44 0.10
135 404 0.90
136 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (135 bp):
GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCATCGCTGATTCAA
AATGCCGTGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTACGAACTTCTTCTCCCTCTATCG
GATGA
Found at i:10985189 original size:14 final size:14
Alignment explanation
Indices: 10985170--10985197 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10985160 CCTCCTTTAC
10985170 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
10985184 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
10985198 CTTAGGCGTA
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:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:10998183 original size:12 final size:13
Alignment explanation
Indices: 10998152--10998185 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10998142 TTGGTGCCTG
10998152 CTTGGGTTTAAAT
1 CTTGGGTTTAAAT
*
10998165 CTGGGGTTTAAAT
1 CTTGGGTTTAAAT
10998178 -TTGGGTTT
1 CTTGGGTTT
10998186 TGTTTAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (13 bp):
CTTGGGTTTAAAT
Found at i:10998598 original size:20 final size:20
Alignment explanation
Indices: 10998573--10998641 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
10998563 ATATATTATT
* *
10998573 TTTTCGAGTTGCTCGTGAGC
1 TTTTCGAGTTACTCGCGAGC
10998593 TTTTCGAGTTACTCGCGAGC
1 TTTTCGAGTTACTCGCGAGC
10998613 TTTTCGAGTTACTCGCGAGC
1 TTTTCGAGTTACTCGCGAGC
10998633 TTTTCGAGT
1 TTTTCGAGT
10998642 CGAGTATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.13, C:0.22, G:0.26, T:0.39
Consensus pattern (20 bp):
TTTTCGAGTTACTCGCGAGC
Found at i:11001256 original size:11 final size:11
Alignment explanation
Indices: 11001180--11001263 Score: 62
Period size: 11 Copynumber: 7.2 Consensus size: 11
11001170 ATATATATAT
11001180 AATAATAATAA
1 AATAATAATAA
*
11001191 AAT-ATAGTAA
1 AATAATAATAA
*
11001201 AAAAATAAATGAA
1 AATAAT-AAT-AA
*
11001214 AATAATTTATATA
1 AATAA-TAATA-A
* *
11001227 TATATATACATAT
1 AATA-ATA-ATAA
11001240 AATAATAATAA
1 AATAATAATAA
11001251 AATAATAATAA
1 AATAATAATAA
11001262 AA
1 AA
11001264 ATGAATAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
10 8 0.14
11 21 0.38
12 6 0.11
13 16 0.29
14 5 0.09
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:11001685 original size:21 final size:21
Alignment explanation
Indices: 11001661--11001724 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
11001651 GTAGAACTCT
11001661 ATCCTATTTTTAGGAGTTTGA
1 ATCCTATTTTTAGGAGTTTGA
** **
11001682 ATCCTA---GCAAAAGTTT--
1 ATCCTATTTTTAGGAGTTTGA
11001698 ATCCTATTTTTAGGAGTTTGA
1 ATCCTATTTTTAGGAGTTTGA
11001719 ATCCTA
1 ATCCTA
11001725 GTAGGACGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 6 0.20
18 6 0.20
19 6 0.20
21 12 0.40
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (21 bp):
ATCCTATTTTTAGGAGTTTGA
Found at i:11002073 original size:164 final size:165
Alignment explanation
Indices: 11001802--11002132 Score: 655
Period size: 164 Copynumber: 2.0 Consensus size: 165
11001792 AGATTAAAAG
11001802 ACACACTTTTCGTTCAGTGGAGTTGAAAATTAACTCTGATGTTTCAATAACTCCCTGTCGAATTG
1 ACACACTTTTCGTTCAGTGGAGTTGAAAATTAACTCTGATGTTTCAATAACTCCCTGTCGAATTG
11001867 AGTTACGGACGACTCCTCCATCGTGAAGTCGAGTTCATCTTGAAATGATATGAAATTGAAGCCGT
66 AGTTACGGACGACTCCTCCATCGTGAAGTCGAGTTCATCTTGAAATGATATGAAATTGAAGCCGT
11001932 AATTCGGAATTTAAATCAGCACGT-GCTTCCCGTT
131 AATTCGGAATTTAAATCAGCACGTGGCTTCCCGTT
11001966 ACACACTTTTCGTTCAGTGGAGTTGAAAATTAACTCTGATGTTTCAATAACTCCCTGTCGAATTG
1 ACACACTTTTCGTTCAGTGGAGTTGAAAATTAACTCTGATGTTTCAATAACTCCCTGTCGAATTG
11002031 AGTTACGGACGACTCCTCCATCGTGAAGTCGAGTTCATCTTGAAATGATATGAAATTGAAGCCGT
66 AGTTACGGACGACTCCTCCATCGTGAAGTCGAGTTCATCTTGAAATGATATGAAATTGAAGCCGT
11002096 AATTCGGAATTTAAATCAGCACGTGGCTTCCCGTT
131 AATTCGGAATTTAAATCAGCACGTGGCTTCCCGTT
11002131 AC
1 AC
11002133 CCTTCGGTCT
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 154 0.93
165 12 0.07
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (165 bp):
ACACACTTTTCGTTCAGTGGAGTTGAAAATTAACTCTGATGTTTCAATAACTCCCTGTCGAATTG
AGTTACGGACGACTCCTCCATCGTGAAGTCGAGTTCATCTTGAAATGATATGAAATTGAAGCCGT
AATTCGGAATTTAAATCAGCACGTGGCTTCCCGTT
Found at i:11002739 original size:105 final size:105
Alignment explanation
Indices: 11002435--11003275 Score: 1363
Period size: 105 Copynumber: 8.0 Consensus size: 105
11002425 GCATTGTTCC
* * ** *
11002435 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * *
11002499 ACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11002541 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
11002601 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
11002641 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11002706 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
11002746 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11002811 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
11002851 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11002916 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
11002956 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
11003021 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11003061 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
11003126 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
11003166 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * * *
11003231 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
11003272 GAGT
1 GAGT
11003276 GTCATGATAT
Statistics
Matches: 701, Mismatches: 26, Indels: 16
0.94 0.03 0.02
Matches are distributed among these distances:
99 1 0.00
100 83 0.12
101 1 0.00
102 7 0.01
104 5 0.01
105 517 0.74
106 87 0.12
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:11003535 original size:36 final size:36
Alignment explanation
Indices: 11003479--11003549 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
11003469 TGGAGAGAAA
* *
11003479 CTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAG
1 CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAG
*
11003515 CTGTCTCAAGCGAGATAAAATTCATTTCAAGGGAA
1 CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAA
11003550 ATGTTTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (36 bp):
CTGTCTCAAGCGAGACAAAATTCATTTCAAGGGAAG
Found at i:11003620 original size:39 final size:39
Alignment explanation
Indices: 11003566--11003745 Score: 116
Period size: 39 Copynumber: 4.9 Consensus size: 39
11003556 TCAATGTTTA
*
11003566 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * * ***
11003605 TGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAAATC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * *
11003644 -ATTTCAAGGGAAA-TGTTTCAA---TG-------TTTA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
*
11003671 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * *
11003710 TGTTTCGAGGGAAACTATCTC-AGGAGAGAAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGG-GAGACAAAATT
11003746 AATTTCAAGG
Statistics
Matches: 103, Mismatches: 25, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
27 1 0.01
28 11 0.11
29 7 0.07
32 1 0.01
34 1 0.01
37 6 0.06
38 14 0.14
39 62 0.60
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
Found at i:11003784 original size:105 final size:104
Alignment explanation
Indices: 11003450--11003768 Score: 493
Period size: 105 Copynumber: 3.1 Consensus size: 104
11003440 TTCGTTAAAT
* ** *
11003450 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * * * *
11003512 AAGCTGTCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAGGAGAGAAAAAATTCATTTCAAGGGAAA
11003551 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
11003616 AAACTATCTCAAGAGAGAGAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTC-AG-GAGAGAAAAAATTCATTTCAAGGGAAA
11003657 TG-TTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
11003721 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAGGAGAGAAAAAATTCATTTCAAGGGAAA
11003760 TGTTTTCAA
1 TGTTTTCAA
11003769 GAGAAAATGT
Statistics
Matches: 200, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
101 46 0.23
103 30 0.15
104 25 0.12
105 73 0.37
106 26 0.13
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAGGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:11003988 original size:72 final size:75
Alignment explanation
Indices: 11003839--11004009 Score: 208
Period size: 72 Copynumber: 2.3 Consensus size: 75
11003829 TAAAATCTTC
* ** **
11003839 TTAAAAAAAACAGCCTTGAGTGAAATGAAATGCCTTATTTCGAGTGAAAATGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAATGAAAT-CCTTATTTCGAGTGAAAACAGTCTCAAGCGAGA
*
11003904 CAAATCTTGTT
65 CAAATCATGTT
* *
11003915 TTAAGAAAAACAATCTTGAGTGAAATG-AAT-CTTCTTTCGAGT-AAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTATTTCGAGTGAAAACAGTCTCAAGCGAGAC
11003977 AAAGT-ATGTT
66 AAA-TCATGTT
11003987 TTAAGAAAAACAAAT-TTGAGTGA
1 TTAAGAAAAAC-AATCTTGAGTGA
11004010 GATAATCATT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
72 43 0.51
73 15 0.18
75 3 0.04
76 24 0.28
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTGAAATGAAATCCTTATTTCGAGTGAAAACAGTCTCAAGCGAGAC
AAATCATGTT
Found at i:11005629 original size:183 final size:182
Alignment explanation
Indices: 11005156--11005689 Score: 939
Period size: 180 Copynumber: 2.9 Consensus size: 182
11005146 ATCACGTTTA
*
11005156 ACTGAAGGGTTCATCTCATCACAAAGTATTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGT-TTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** **
11005221 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGATAGGGCTTTCGAGT
65 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
*
11005285 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAACTTTAGAGGGACAAATC
129 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
11005339 ACTGAA-GGTTCATCTCATCACAAAG-TTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
1 ACTGAAGGGTTCATCTCATCACAAAGTTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
11005402 CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
66 CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
*
11005467 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGATAAATC
131 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
11005519 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGT-TTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
11005584 GTCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
65 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
11005649 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
11005690 CGGATTTAAT
Statistics
Matches: 338, Mismatches: 9, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
180 151 0.45
181 20 0.06
182 19 0.06
183 148 0.44
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (182 bp):
ACTGAAGGGTTCATCTCATCACAAAGTTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATTG
CCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTTT
CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:11009810 original size:21 final size:22
Alignment explanation
Indices: 11009766--11009816 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
11009756 AGGGAAAAAA
*
11009766 TAAAATAA-ATAAAATAAATAAG
1 TAAAATAAGA-AAAAAAAATAAG
*
11009788 TAAGATAAGAAAAAAAAAT-AG
1 TAAAATAAGAAAAAAAAATAAG
11009809 TAAAATAA
1 TAAAATAA
11009817 TAATTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 9 0.36
22 15 0.60
23 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.20
Consensus pattern (22 bp):
TAAAATAAGAAAAAAAAATAAG
Found at i:11009953 original size:18 final size:17
Alignment explanation
Indices: 11009930--11009968 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11009920 ATATATACAT
* *
11009930 ATAATAATAATACACTGA
1 ATAATAAAAATA-AATGA
11009948 ATAATAAAAATAAATGA
1 ATAATAAAAATAAATGA
11009965 ATAA
1 ATAA
11009969 ATATCCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAAAAATAAATGA
Found at i:11010620 original size:13 final size:14
Alignment explanation
Indices: 11010604--11010637 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
11010594 AGCACCTAAA
11010604 TTTTTATA-AATAC
1 TTTTTATATAATAC
*
11010617 TTTTTATATAATAT
1 TTTTTATATAATAC
11010631 TTTTTAT
1 TTTTTAT
11010638 TTACATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTATATAATAC
Found at i:11011917 original size:32 final size:34
Alignment explanation
Indices: 11011848--11011917 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
11011838 TCGATTCTAG
* *
11011848 TTTATGACATTCGAGTAAAGTCAAGTTGTTATAT
1 TTTATGAAATTCGAGTAAAATCAAGTTGTTATAT
11011882 TTTATGAAATTCGAGTAAAATCAAG-T-TTATAT
1 TTTATGAAATTCGAGTAAAATCAAGTTGTTATAT
11011914 TTTA
1 TTTA
11011918 GTCGATTCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 10 0.29
33 1 0.03
34 23 0.68
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (34 bp):
TTTATGAAATTCGAGTAAAATCAAGTTGTTATAT
Found at i:11012384 original size:24 final size:24
Alignment explanation
Indices: 11012352--11012398 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11012342 CTACTTTCAT
11012352 ATAAATTATAATAATTT-ATTTTAA
1 ATAAATTAT-ATAATTTAATTTTAA
*
11012376 ATAAATTATATCATTTAATTTTA
1 ATAAATTATATAATTTAATTTTA
11012399 TTACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAAATTATATAATTTAATTTTAA
Found at i:11012714 original size:2 final size:2
Alignment explanation
Indices: 11012707--11012785 Score: 135
Period size: 2 Copynumber: 40.5 Consensus size: 2
11012697 GTTTAAACTA
*
11012707 AT AT AT AT AT AT AT AT AT AG 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
11012749 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11012786 ATCAACACAA
Statistics
Matches: 73, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11021501 original size:18 final size:18
Alignment explanation
Indices: 11021478--11021512 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11021468 GACGGTCAAT
11021478 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
* *
11021496 GGTCAATGGGTTGGGTC
1 GGTCAACGGGTCGGGTC
11021513 AGAACCGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.17, G:0.49, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:11027645 original size:20 final size:20
Alignment explanation
Indices: 11027600--11027638 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11027590 TACTGACGAT
* *
11027600 GAATAATATCGGTACTGAAC
1 GAATAATACCGGTACTAAAC
11027620 GAATAATACCGGTACTAAA
1 GAATAATACCGGTACTAAA
11027639 TGCATAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (20 bp):
GAATAATACCGGTACTAAAC
Found at i:11027765 original size:4 final size:4
Alignment explanation
Indices: 11027756--11027790 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
11027746 AAGATACTAG
11027756 CATT CATT CATT CATT CATT CATT CATT CATT CAT
1 CATT CATT CATT CATT CATT CATT CATT CATT CAT
11027791 ACAAGGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
CATT
Found at i:11031312 original size:55 final size:55
Alignment explanation
Indices: 11031243--11031352 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
11031233 TAATTGGAAC
11031243 ATTTTGTCAATTTTCATGAAAATCCTAAACTCCCCCTAACTAATTGCATAGTATG
1 ATTTTGTCAATTTTCATGAAAATCCTAAACTCCCCCTAACTAATTGCATAGTATG
11031298 ATTTTGTCAATTTTCATGAAAATCCTAAACTCCCCCTAACTAATTGCATAGTATG
1 ATTTTGTCAATTTTCATGAAAATCCTAAACTCCCCCTAACTAATTGCATAGTATG
11031353 CATTAAAGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (55 bp):
ATTTTGTCAATTTTCATGAAAATCCTAAACTCCCCCTAACTAATTGCATAGTATG
Found at i:11035578 original size:19 final size:20
Alignment explanation
Indices: 11035535--11035582 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
11035525 TCTAAATCCT
*
11035535 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
11035555 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
11035574 TTTTCAAAA
1 TTTTCAAAA
11035583 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:11036487 original size:34 final size:32
Alignment explanation
Indices: 11036434--11036503 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
11036424 CCTTACAAAC
*
11036434 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
11036466 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
11036500 TCCC
1 TCCC
11036504 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:11037153 original size:29 final size:31
Alignment explanation
Indices: 11037115--11037174 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
11037105 AAATTTTGAA
* *
11037115 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATACAATTCAAGTCCAAAAACCATTTTG
11037144 TAAATACAATTCAAGTCCAAAAACCATTTTG
1 TAAATACAATTCAAGTCCAAAAACCATTTTG
11037175 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 10 0.37
31 7 0.26
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATACAATTCAAGTCCAAAAACCATTTTG
Found at i:11038941 original size:75 final size:75
Alignment explanation
Indices: 11038790--11038995 Score: 279
Period size: 75 Copynumber: 2.7 Consensus size: 75
11038780 CAAAGCCAAA
* * * **
11038790 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
11038855 TTGGCTCCGAG
65 TTGGCTCCGAG
*
11038866 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
11038931 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
11038941 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCC
11038996 ATGTTCAACG
Statistics
Matches: 116, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 84 0.72
76 32 0.28
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:11046799 original size:9 final size:8
Alignment explanation
Indices: 11046777--11046827 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
11046767 TGTTTCAACA
11046777 TTTTGGAT
1 TTTTGGAT
11046785 ATTTTGGAT
1 -TTTTGGAT
11046794 TGTTT-GAT
1 T-TTTGGAT
11046802 TTTGTGGAT
1 TTT-TGGAT
*
11046811 TGTTGGA-
1 TTTTGGAT
11046818 TTTTGGAT
1 TTTTGGAT
11046826 TT
1 TT
11046828 ATGAATAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:11046811 original size:17 final size:17
Alignment explanation
Indices: 11046779--11046822 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
11046769 TTTCAACATT
11046779 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
11046796 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
11046813 TTGGATTTTG
1 TTGGATTTTG
11046823 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:11047123 original size:21 final size:21
Alignment explanation
Indices: 11047097--11047139 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11047087 TGAAGAAGTG
*
11047097 TTAAAGTAAGGCGGAGTAATT
1 TTAAAGTAAGGAGGAGTAATT
11047118 TTAAAGTAAGGAGGAGTAATT
1 TTAAAGTAAGGAGGAGTAATT
11047139 T
1 T
11047140 CAAAACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (21 bp):
TTAAAGTAAGGAGGAGTAATT
Found at i:11047558 original size:74 final size:74
Alignment explanation
Indices: 11047431--11047634 Score: 248
Period size: 74 Copynumber: 2.8 Consensus size: 74
11047421 CAAAGCCAAA
* * * * **
11047431 AATTCCAGATTACTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTGAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
11047496 TGGCTCCGAG
65 TGGCTCCGAG
* *
11047506 ATTTCCAGAATGCTCGGAGGGAATCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* * *
11047571 TGTTTCGAG
66 GGCTCCGAG
* ** * *
11047580 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCCAGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCT
11047635 TGTTCAACGG
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
73 24 0.22
74 63 0.57
75 24 0.22
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:11053211 original size:21 final size:21
Alignment explanation
Indices: 11053185--11053228 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11053175 CATAACATAT
*
11053185 ATTGCTTCGTTAAATGA-ATCC
1 ATTGCTTCATTAAAT-ACATCC
11053206 ATTGCTTCATTAAATACATCC
1 ATTGCTTCATTAAATACATCC
11053227 AT
1 AT
11053229 GTTGCATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (21 bp):
ATTGCTTCATTAAATACATCC
Found at i:11060208 original size:23 final size:24
Alignment explanation
Indices: 11060154--11060253 Score: 150
Period size: 23 Copynumber: 4.2 Consensus size: 24
11060144 TTTAGGCCAA
11060154 GTATCAGATCAGAATCCAGGTCAT
1 GTATCAGATCAGAATCCAGGTCAT
* *
11060178 GTATCAGATCAAAATCCATGTCA-
1 GTATCAGATCAGAATCCAGGTCAT
*
11060201 GTATCAGATCAGAATCCATGT-AT
1 GTATCAGATCAGAATCCAGGTCAT
*
11060224 GTATCAGATCAGAATCCAGGTCAG
1 GTATCAGATCAGAATCCAGGTCAT
11060248 GTATCA
1 GTATCA
11060254 TAACAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
22 1 0.01
23 40 0.58
24 28 0.41
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (24 bp):
GTATCAGATCAGAATCCAGGTCAT
Found at i:11060252 original size:47 final size:47
Alignment explanation
Indices: 11060153--11060253 Score: 159
Period size: 47 Copynumber: 2.1 Consensus size: 47
11060143 ATTTAGGCCA
*
11060153 AGTATCAGATCAGAATCCAGGTCATGTATCAGATCAAAATCCATGTC
1 AGTATCAGATCAGAATCCAGGTCATGTATCAGATCAAAATCCAGGTC
* *
11060200 AGTATCAGATCAGAATCCATGT-ATGTATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTCATGTATCAGATCAAAATCCAGGTC
11060246 AGGTATCA
1 A-GTATCA
11060254 TAACAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
46 23 0.46
47 27 0.54
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (47 bp):
AGTATCAGATCAGAATCCAGGTCATGTATCAGATCAAAATCCAGGTC
Found at i:11066791 original size:20 final size:20
Alignment explanation
Indices: 11066754--11066792 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11066744 CTCAAAATCA
* *
11066754 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
11066774 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
11066793 CCTTTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:11074405 original size:18 final size:17
Alignment explanation
Indices: 11074362--11074405 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11074352 AGAAAATTGC
*
11074362 TAAAGAAAACTAATAAAA
1 TAAA-AAAACTAAAAAAA
*
11074380 TAACAAAATCTAAAAAAA
1 TAA-AAAAACTAAAAAAA
11074398 TAAAAAAA
1 TAAAAAAA
11074406 ATATAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.18
18 17 0.77
19 1 0.05
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
TAAAAAAACTAAAAAAA
Found at i:11076849 original size:23 final size:23
Alignment explanation
Indices: 11076823--11076866 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
11076813 ACGGGGTAAT
*
11076823 TATGTGGTACTTCAGTGCAAACC
1 TATGTGGCACTTCAGTGCAAACC
11076846 TATGTGGCACTTCAGTGCAAA
1 TATGTGGCACTTCAGTGCAAA
11076867 TTACGAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (23 bp):
TATGTGGCACTTCAGTGCAAACC
Found at i:11082446 original size:19 final size:20
Alignment explanation
Indices: 11082422--11082462 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
11082412 GCAAAGGTAA
11082422 GTTTCTATAATT-TTT-GTTG
1 GTTTCTA-AATTATTTGGTTG
11082441 GTTTCTAAATTATTTGGTTG
1 GTTTCTAAATTATTTGGTTG
11082461 GT
1 GT
11082463 ATTGATAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 10 0.50
20 6 0.30
ACGTcount: A:0.17, C:0.05, G:0.20, T:0.59
Consensus pattern (20 bp):
GTTTCTAAATTATTTGGTTG
Found at i:11083707 original size:23 final size:23
Alignment explanation
Indices: 11083649--11083709 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
11083639 TCTGGATAAT
* * *
11083649 TATGTGGGACTTCAGTTCAAACC
1 TATGTGGCACTTCGGTGCAAACC
11083672 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTCGGTGCAAACC
11083695 TATGTGGTC-CTTCGG
1 TATGTGG-CACTTCGG
11083710 GATAATTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.26, T:0.31
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAACC
Found at i:11086433 original size:21 final size:21
Alignment explanation
Indices: 11086379--11086427 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
11086369 GATGATATAA
*
11086379 TGGATTTAAGAAGATTTTTGG
1 TGGATTTAAGAAGATTTTGGG
11086400 TGGATTTAAGAAGATTTTGGG
1 TGGATTTAAGAAGATTTTGGG
*
11086421 TTGATTT
1 TGGATTT
11086428 TCGAAGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (21 bp):
TGGATTTAAGAAGATTTTGGG
Found at i:11087248 original size:21 final size:21
Alignment explanation
Indices: 11087219--11087334 Score: 110
Period size: 21 Copynumber: 5.4 Consensus size: 21
11087209 GTCGAGGGTC
* * *
11087219 TTATATGGTCATTCAGGATAA
1 TTATGTGGTCATTCGGGACAA
11087240 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
*
11087261 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
* *
11087282 ATATGTGG-AACTTCGGTG-CAAA
1 TTATGTGGTCA-TTCGG-GAC-AA
* *
11087304 CCTATATGGTCATTCGGGACAA
1 -TTATGTGGTCATTCGGGACAA
11087326 TTATGTGGT
1 TTATGTGGT
11087335 ACTTTGGTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
21 58 0.75
22 6 0.08
23 12 0.16
24 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:11094038 original size:21 final size:21
Alignment explanation
Indices: 11093980--11094032 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
11093970 GGGACTTATA
* *
11093980 TGGTCCTTCGGGATAATTATG
1 TGGTCCTTCGGGACAAATATG
11094001 TGGTCCTTCGGGACAAATATG
1 TGGTCCTTCGGGACAAATATG
11094022 TGG-CACTTCGG
1 TGGTC-CTTCGG
11094033 TGCAAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (21 bp):
TGGTCCTTCGGGACAAATATG
Found at i:11097018 original size:39 final size:39
Alignment explanation
Indices: 11096949--11097024 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
11096939 TTCTCAAATT
* * *
11096949 ATTTCATCATAATATTTTATATTCTCAATTTCTTAAACC
1 ATTTCATCATAATATTCTAAATTATCAATTTCTTAAACC
* *
11096988 ATTTCA-CTATAATATTCTAAATTATTAATTTTTTAAA
1 ATTTCATC-ATAATATTCTAAATTATCAATTTCTTAAA
11097025 TTATTACACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (39 bp):
ATTTCATCATAATATTCTAAATTATCAATTTCTTAAACC
Found at i:11097669 original size:16 final size:13
Alignment explanation
Indices: 11097632--11097661 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11097622 AATATTATTA
*
11097632 TATTTTTATATAT
1 TATTCTTATATAT
11097645 TATTCTTATATAT
1 TATTCTTATATAT
11097658 TATT
1 TATT
11097662 TCAATTATGA
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:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTCTTATATAT
Found at i:11099431 original size:17 final size:17
Alignment explanation
Indices: 11099409--11099444 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
11099399 AACTCAATTT
11099409 GAATTTGAAATTTTTTC
1 GAATTTGAAATTTTTTC
11099426 GAATTTGAAATTTTTTC
1 GAATTTGAAATTTTTTC
11099443 GA
1 GA
11099445 GTCGAGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (17 bp):
GAATTTGAAATTTTTTC
Found at i:11099566 original size:16 final size:16
Alignment explanation
Indices: 11099541--11099573 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11099531 ATATATGATT
11099541 TTAAAAGAAA-AAAAA
1 TTAAAAGAAATAAAAA
11099556 TTAATAAGAAATAAAAA
1 TTAA-AAGAAATAAAAA
11099573 T
1 T
11099574 ATCCATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (16 bp):
TTAAAAGAAATAAAAA
Found at i:11100447 original size:23 final size:24
Alignment explanation
Indices: 11100421--11100473 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
11100411 TGTCCTTGGT
*
11100421 TTGTTTCTTCT-TCTCTGAACATC
1 TTGTTTCTTCTGACTCTGAACATC
* *
11100444 TTGTTT-TTCTGAGTTTGAACATC
1 TTGTTTCTTCTGACTCTGAACATC
11100467 TTGTTTC
1 TTGTTTC
11100474 GAAAGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.13, C:0.19, G:0.13, T:0.55
Consensus pattern (24 bp):
TTGTTTCTTCTGACTCTGAACATC
Found at i:11104831 original size:22 final size:22
Alignment explanation
Indices: 11104803--11104851 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
11104793 GTCTTTTTCT
11104803 GCTTTCGAATACAAAAATAATA
1 GCTTTCGAATACAAAAATAATA
** *
11104825 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATACAAAAATAATA
11104847 GCTTT
1 GCTTT
11104852 TCAAAACATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATACAAAAATAATA
Found at i:11107548 original size:11 final size:11
Alignment explanation
Indices: 11107532--11107561 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
11107522 TCTAGGCAAT
*
11107532 GCTAGAACTGC
1 GCTAGAACTAC
11107543 GCTAGAACTAC
1 GCTAGAACTAC
11107554 GCTAGAAC
1 GCTAGAAC
11107562 ATTGATTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (11 bp):
GCTAGAACTAC
Found at i:11108867 original size:28 final size:26
Alignment explanation
Indices: 11108835--11108911 Score: 104
Period size: 24 Copynumber: 3.0 Consensus size: 26
11108825 CATAGGATGC
11108835 ATGAAGTGTTGTTTTTAAGAGACAAATA
1 ATGAAGTGTTG-TTTTAAGAGACAAA-A
*
11108863 ATGAAGTGTTGTTTT-A-AGACACAA
1 ATGAAGTGTTGTTTTAAGAGACAAAA
*
11108887 ATGAAGTATTGTTTTAAGAGACAAA
1 ATGAAGTGTTGTTTTAAGAGACAAA
11108912 CTTATTATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.34
25 7 0.16
26 7 0.16
27 4 0.09
28 11 0.25
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (26 bp):
ATGAAGTGTTGTTTTAAGAGACAAAA
Found at i:11109082 original size:18 final size:18
Alignment explanation
Indices: 11109059--11109093 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11109049 TAGCAAATAA
*
11109059 ATGTGAACTTAAATTATT
1 ATGTGAAATTAAATTATT
11109077 ATGTGAAATTAAATTAT
1 ATGTGAAATTAAATTAT
11109094 GCGTGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATGTGAAATTAAATTATT
Found at i:11115180 original size:44 final size:44
Alignment explanation
Indices: 11115044--11115311 Score: 308
Period size: 44 Copynumber: 6.2 Consensus size: 44
11115034 TTTAACAAAG
* * *
11115044 GCCGCTATATATCA-ACCTTTAGCGGCATTTCTATTCTAAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
**
11115087 GCCGCTATATACCAGACCTTT-GCGGTGTTTGTATACTAAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
* * * ** *
11115130 GACGCTATATATCAGATCTTTAGCGGCATTTGTATTTTAAAAAT
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
* * *
11115174 GTCGCTATATACCAGACCTTTAGCGGCATTTATATACTGAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
** * * * *
11115218 ATCGCTATATACCAAACCTTTAGCGGCGTTTGTATCCTAAAAAT
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
* * *
11115262 GCCTCTATATACCAGACCTTTAGCGGCGTTTGTAT-CCAAAAAC
1 GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
11115305 GCCGCTA
1 GCCGCTA
11115312 AATCTCAAAA
Statistics
Matches: 188, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
43 61 0.32
44 127 0.68
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (44 bp):
GCCGCTATATACCAGACCTTTAGCGGCATTTGTATACTAAAAAC
Found at i:11115410 original size:43 final size:45
Alignment explanation
Indices: 11115301--11115439 Score: 112
Period size: 42 Copynumber: 3.2 Consensus size: 45
11115291 TTGTATCCAA
* * ** **
11115301 AAACGCCGCTAAATCTCAAAACCTATTGCAACG-T-TTT-AAAAC
1 AAACGCCGCTAAATATCAGAACCTATTGCGGCGTTGTTTGTTAAC
* *
11115343 AAACGCCACTAAATATCAGAACCTATTG-TG-G-TGTTTGTTCAAC
1 AAACGCCGCTAAATATCAGAACCTATTGCGGCGTTGTTTGTT-AAC
* * *
11115386 AAACGCCGCTATATATC-GTTACCTATTGCGGCGTTTTTTGTTAAC
1 AAACGCCGCTAAATATCAG-AACCTATTGCGGCGTTGTTTGTTAAC
11115431 AAACGCCGC
1 AAACGCCGC
11115440 GAATTTTAGC
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.03
41 3 0.04
42 26 0.33
43 26 0.33
44 1 0.01
45 13 0.17
46 7 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (45 bp):
AAACGCCGCTAAATATCAGAACCTATTGCGGCGTTGTTTGTTAAC
Found at i:11126096 original size:18 final size:18
Alignment explanation
Indices: 11126073--11126153 Score: 117
Period size: 18 Copynumber: 4.5 Consensus size: 18
11126063 TTTGTCCAAT
* *
11126073 AGGACCACTATATCTCGA
1 AGGACCACTATGTCCCGA
*
11126091 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
* *
11126109 AGTACCACTATGTCCCAA
1 AGGACCACTATGTCCCGA
11126127 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
11126145 AGGACCACT
1 AGGACCACT
11126154 GATAATCCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:11130651 original size:18 final size:18
Alignment explanation
Indices: 11130622--11130692 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
11130612 GCGTAGAATT
*
11130622 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
11130640 TGCCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
11130658 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
11130676 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
11130693 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.35, G:0.23, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:11130663 original size:36 final size:36
Alignment explanation
Indices: 11130622--11130693 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
11130612 GCGTAGAATT
*
11130622 TGTCCCGTAGGACCACTATGCCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTATGCCCCGAAGGACCACTG
* *
11130658 TGTCCCGAAGGACCACTATGTCCCGAATGACCACTG
1 TGTCCCGAAGGACCACTATGCCCCGAAGGACCACTG
11130694 ATAATCCCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (36 bp):
TGTCCCGAAGGACCACTATGCCCCGAAGGACCACTG
Found at i:11133856 original size:20 final size:20
Alignment explanation
Indices: 11133801--11133858 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
11133791 AGCGAGAGTT
*
11133801 CATAGGTCATTCAGGACATA
1 CATAGGTCATTCGGGACATA
*
11133821 CATAGGTCATTCGGGATATA
1 CATAGGTCATTCGGGACATA
*
11133841 CATAGGTCATTTGGGACA
1 CATAGGTCATTCGGGACA
11133859 AATTTCACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
CATAGGTCATTCGGGACATA
Done.